Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008242.1 Hibiscus syriacus cultivar Beakdansim tig00110890_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: 16962412
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 22 of 73
Found at i:4911950 original size:21 final size:22
Alignment explanation
Indices: 4911909--4911954 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
4911899 TTTTGATTTG
*
4911909 TTTTAATTTAGTTCTATTTTAT
1 TTTTAATTTAGTTCCATTTTAT
*
4911931 TTTTAATTT-GTTCCCATTTAAT
1 TTTTAATTTAGTT-CCATTTTAT
4911953 TT
1 TT
4911955 AGTAATTTCA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 3 0.14
22 18 0.86
ACGTcount: A:0.22, C:0.09, G:0.04, T:0.65
Consensus pattern (22 bp):
TTTTAATTTAGTTCCATTTTAT
Found at i:4912044 original size:9 final size:8
Alignment explanation
Indices: 4911987--4912040 Score: 54
Period size: 9 Copynumber: 6.4 Consensus size: 8
4911977 TAGGTCCTTA
*
4911987 TTTTATAT
1 TTTTTTAT
4911995 TTATTTTAT
1 TT-TTTTAT
4912004 TTTTATTAT
1 TTTT-TTAT
* *
4912013 GTTTTTAC
1 TTTTTTAT
4912021 TTTTTTAT
1 TTTTTTAT
4912029 TTTATTTAT
1 TTT-TTTAT
4912038 TTT
1 TTT
4912041 ATTTGTTATT
Statistics
Matches: 38, Mismatches: 5, Indels: 5
0.79 0.10 0.10
Matches are distributed among these distances:
8 16 0.42
9 22 0.58
ACGTcount: A:0.19, C:0.02, G:0.02, T:0.78
Consensus pattern (8 bp):
TTTTTTAT
Found at i:4912049 original size:16 final size:18
Alignment explanation
Indices: 4911987--4912050 Score: 59
Period size: 17 Copynumber: 3.8 Consensus size: 18
4911977 TAGGTCCTTA
*
4911987 TTTTA-TAT-TTATTTTAT
1 TTTTATTATGTTA-TTTAC
4912004 TTTTATTATGTT-TTTAC
1 TTTTATTATGTTATTTAC
*
4912021 TTTT-TTATTTTATTTA-
1 TTTTATTATGTTATTTAC
4912037 TTTTATT-TGTTATT
1 TTTTATTATGTTATT
4912051 AATATTTTTT
Statistics
Matches: 40, Mismatches: 3, Indels: 9
0.77 0.06 0.17
Matches are distributed among these distances:
16 16 0.40
17 19 0.47
18 3 0.08
19 2 0.05
ACGTcount: A:0.19, C:0.02, G:0.03, T:0.77
Consensus pattern (18 bp):
TTTTATTATGTTATTTAC
Found at i:4915581 original size:38 final size:36
Alignment explanation
Indices: 4915516--4915805 Score: 199
Period size: 38 Copynumber: 7.5 Consensus size: 36
4915506 ATTTTTTTGA
* * *
4915516 AAAATATA-ATATATA-ATTTTTACAAAACAGATTTC
1 AAAATATATATATATATAGTTTT-GAAAACAGTTTTC
*
4915551 AAATATATATATATCATATAGTTTTGAAAACGGTTTTC
1 AAA-ATATATATAT-ATATAGTTTTGAAAACAGTTTTC
*
4915589 GAAAATATATATATCATATAGTTTTAAAAACAGTTTTC
1 -AAAATATATATAT-ATATAGTTTTGAAAACAGTTTTC
*
4915627 GAAAATATATATATTATATAGTTTTGAAAACA-TTTTGAAA
1 -AAAATATATATA-TATATAGTTTTGAAAACAGTTTT---C
* * *
4915667 AAAATATATATAATATATAGTTTTGGAAAATATTTTTA
1 AAAATATATAT-ATATATAGTTTT-GAAAACAGTTTTC
* * * *
4915705 AAATATATATATAATATATATATTTTGAAAAAATATATATTTTG
1 AAA-ATATATAT-ATATATA-GTTTTG---AAA-ACA-GTTTTC
* * * *
4915749 AAAAAATATATATTATATAGTTTTGGAAACATTTTTG
1 AAAATATATATA-TATATAGTTTTGAAAACAGTTTTC
4915786 AAAGCATATATATATATATA
1 AAA--ATATATATATATATA
4915806 TATATATTAT
Statistics
Matches: 215, Mismatches: 18, Indels: 41
0.78 0.07 0.15
Matches are distributed among these distances:
35 3 0.01
36 5 0.02
37 16 0.07
38 86 0.40
39 58 0.27
40 11 0.05
41 4 0.02
42 9 0.04
43 16 0.07
44 7 0.03
ACGTcount: A:0.47, C:0.04, G:0.08, T:0.41
Consensus pattern (36 bp):
AAAATATATATATATATAGTTTTGAAAACAGTTTTC
Found at i:4915619 original size:76 final size:73
Alignment explanation
Indices: 4915510--4915946 Score: 242
Period size: 76 Copynumber: 5.5 Consensus size: 73
4915500 GAAAATATTT
* *
4915510 TTTTGAAAAATATA-ATATATA-ATTTTTACAAAACAGATTTCAAATATATATATATCATATAGT
1 TTTTGAAAAATATATATATATATAGTTTTA-AAAACAGTTTTCAAATATATATATAT-ATATAGT
*
4915573 TTTGAAAACGG
64 TTTGAAAAC-A
4915584 TTTTCG-AAAATATATATATCATATAGTTTTAAAAACAGTTTTCGAAA-ATATATATATTATATA
1 TTTT-GAAAAATATATATAT-ATATAGTTTTAAAAACAGTTTTC-AAATATATATATA-TATATA
4915647 GTTTTGAAAACA
62 GTTTTGAAAACA
* * * *
4915659 TTTTGAAAAAAATATATATAATATATAGTTTTGGAAAATATTTTTAAAATATATATATAATATAT
1 TTTTG--AAAAATATATAT-ATATATAGTTTT-AAAAACAGTTTTCAAATATATATAT-ATATAT
* *
4915724 ATATTTTGAAAAAATATATA
61 A-GTTTTG----AA-A-ACA
** *
4915744 TTTTGAAAAA-ATATATATTATATAGTTTTGGAAACATTTTTGAAAGCATATATATATATATATA
1 TTTTGAAAAATATATATA-TATATAGTTTTAAAAACAGTTTT-----CA-A-ATATATATATATA
4915808 TATA-TTATATAGTTTTTAAAAACA
58 TATAGTT-T-T-G------AAAACA
* * *
4915832 TTTTG-AAAACATATATATAATATATAGTTTTTAAAAACA-TTTTGAAAAAATATATATAATATA
1 TTTTGAAAAATATA--TAT-ATATATAG-TTTTAAAAACAGTTTT-CAAATATATATAT-ATATA
* *
4915895 TAGTTTTTAAAAAATA
60 TAG-TTTT-GAAAACA
*
4915911 TTTTGAAAATATGTATATAATATATAGTTTTAAAAA
1 TTTTGAAAA-ATATATAT-ATATATAGTTTTAAAAA
4915947 TGCTTTTGAA
Statistics
Matches: 296, Mismatches: 24, Indels: 82
0.74 0.06 0.20
Matches are distributed among these distances:
74 13 0.04
75 9 0.03
76 39 0.13
77 34 0.11
78 34 0.11
79 28 0.09
80 3 0.01
81 14 0.05
82 17 0.06
83 7 0.02
84 10 0.03
85 19 0.06
86 5 0.02
87 15 0.05
88 21 0.07
89 1 0.00
90 17 0.06
91 10 0.03
ACGTcount: A:0.47, C:0.03, G:0.07, T:0.42
Consensus pattern (73 bp):
TTTTGAAAAATATATATATATATAGTTTTAAAAACAGTTTTCAAATATATATATATATATAGTTT
TGAAAACA
Found at i:4915714 original size:15 final size:15
Alignment explanation
Indices: 4915696--4915759 Score: 51
Period size: 15 Copynumber: 4.3 Consensus size: 15
4915686 GTTTTGGAAA
4915696 ATATTTTTAAAATAT
1 ATATTTTTAAAATAT
* *
4915711 ATA--TATAATATAT
1 ATATTTTTAAAATAT
*
4915724 ATATTTTGAAAAAATAT
1 ATATTTT--TAAAATAT
* *
4915741 ATATTTTGAAAAAAT
1 ATATTTTTAAAATAT
4915756 ATAT
1 ATAT
4915760 ATTATATAGT
Statistics
Matches: 38, Mismatches: 7, Indels: 8
0.72 0.13 0.15
Matches are distributed among these distances:
13 11 0.29
15 14 0.37
17 13 0.34
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (15 bp):
ATATTTTTAAAATAT
Found at i:4915741 original size:19 final size:18
Alignment explanation
Indices: 4915717--4915762 Score: 78
Period size: 17 Copynumber: 2.7 Consensus size: 18
4915707 ATATATATAT
4915717 AATATATATATTTTGAAA
1 AATATATATATTTTGAAA
4915735 AA-ATATATATTTTGAAA
1 AATATATATATTTTGAAA
4915752 AA-ATATATATT
1 AATATATATATT
4915763 ATATAGTTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
17 26 0.93
18 2 0.07
ACGTcount: A:0.52, C:0.00, G:0.04, T:0.43
Consensus pattern (18 bp):
AATATATATATTTTGAAA
Found at i:4915822 original size:51 final size:50
Alignment explanation
Indices: 4915754--4915857 Score: 156
Period size: 51 Copynumber: 2.1 Consensus size: 50
4915744 TTTTGAAAAA
** *
4915754 ATATATATTATATAG-TTTTGGAAACATTTTTGAAAGCATATATATATATAT
1 ATATATATTATATAGTTTTTAAAAACA-TTTTGAAAACATATATATA-ATAT
4915805 ATATATATTATATAGTTTTTAAAAACATTTTGAAAACATATATATAATAT
1 ATATATATTATATAGTTTTTAAAAACATTTTGAAAACATATATATAATAT
4915855 ATA
1 ATA
4915858 GTTTTTAAAA
Statistics
Matches: 49, Mismatches: 3, Indels: 3
0.89 0.05 0.05
Matches are distributed among these distances:
50 7 0.14
51 33 0.67
52 9 0.18
ACGTcount: A:0.45, C:0.04, G:0.07, T:0.44
Consensus pattern (50 bp):
ATATATATTATATAGTTTTTAAAAACATTTTGAAAACATATATATAATAT
Found at i:4915880 original size:51 final size:52
Alignment explanation
Indices: 4915775--4915880 Score: 119
Period size: 51 Copynumber: 2.1 Consensus size: 52
4915765 ATAGTTTTGG
* * * * *
4915775 AAACATTTTTGAAAGCATATATATATATATATATATATTATATAGTTTTTAA
1 AAACATTTTTGAAAACATATATATATATATATATATATTAAAAAATTTTGAA
*
4915827 AAACA-TTTTGAAAACATATATATA-ATATATAGT-TTTTAAAAACATTTTGAA
1 AAACATTTTTGAAAACATATATATATATATATA-TATATTAAAAA-ATTTTGAA
4915878 AAA
1 AAA
4915881 ATATATATAA
Statistics
Matches: 46, Mismatches: 6, Indels: 5
0.81 0.11 0.09
Matches are distributed among these distances:
50 13 0.28
51 28 0.61
52 5 0.11
ACGTcount: A:0.48, C:0.05, G:0.06, T:0.42
Consensus pattern (52 bp):
AAACATTTTTGAAAACATATATATATATATATATATATTAAAAAATTTTGAA
Found at i:4915969 original size:40 final size:39
Alignment explanation
Indices: 4915519--4915961 Score: 322
Period size: 39 Copynumber: 10.9 Consensus size: 39
4915509 TTTTTGAAAA
* * *
4915519 ATATAATATATAATTTTTACAAAACAGATTT-CAAATATAT
1 ATATAATATATAGTTTTTA-AAAACA-TTTTGAAAATATAT
* *
4915559 ATAT-ATCATATAG-TTTTGAAAACGGTTTTCGAAAATATAT
1 ATATAAT-ATATAGTTTTTAAAAAC-ATTTT-GAAAATATAT
*
4915599 ATAT--CATATAG-TTTTAAAAACAGTTTTCGAAAATATAT
1 ATATAATATATAGTTTTTAAAAACA-TTTT-GAAAATATAT
* *
4915637 ATAT--TATATAG-TTTTGAAAACATTTTGAAAAAAATAT
1 ATATAATATATAGTTTTTAAAAACATTTTG-AAAATATAT
** * *
4915674 ATATAATATATAGTTTTGGAAAATATTTTTAAAATATAT
1 ATATAATATATAGTTTTTAAAAACATTTTGAAAATATAT
*
4915713 ATATAATATATA-TATTTTGAAAAAATATATATTTTGAAAA-A-AT
1 ATATAATATATAGT-TTTT----AAA-A-ACATTTTGAAAATATAT
* **
4915756 ATATATTATATAG-TTTTGGAAACATTTTTGAAAGCATATATATATATAT
1 ATATAATATATAGTTTTTAAAAACA-TTTT----G---A-A-A-ATATAT
*
4915805 ATATATATTATATAGTTTTTAAAAACATTTTGAAAACATAT
1 ATATA-A-TATATAGTTTTTAAAAACATTTTGAAAATATAT
*
4915846 ATATAATATATAGTTTTTAAAAACATTTTGAAAAAATAT
1 ATATAATATATAGTTTTTAAAAACATTTTGAAAATATAT
* *
4915885 ATATAATATATAGTTTTTAAAAAATATTTTGAAAATATGT
1 ATATAATATATAGTTTTT-AAAAACATTTTGAAAATATAT
4915925 ATATAATATATAG-TTTTAAAAATGC-TTTTGAAAATAT
1 ATATAATATATAGTTTTTAAAAA--CATTTTGAAAATAT
4915962 GTTATATAGT
Statistics
Matches: 336, Mismatches: 31, Indels: 73
0.76 0.07 0.17
Matches are distributed among these distances:
36 3 0.01
37 21 0.06
38 65 0.19
39 102 0.30
40 66 0.20
41 11 0.03
42 5 0.01
43 16 0.05
44 4 0.01
45 12 0.04
46 1 0.00
47 2 0.01
48 1 0.00
49 7 0.02
51 11 0.03
52 9 0.03
ACGTcount: A:0.47, C:0.04, G:0.07, T:0.42
Consensus pattern (39 bp):
ATATAATATATAGTTTTTAAAAACATTTTGAAAATATAT
Found at i:4916030 original size:73 final size:73
Alignment explanation
Indices: 4915805--4916062 Score: 194
Period size: 73 Copynumber: 3.4 Consensus size: 73
4915795 ATATATATAT
*
4915805 ATATATATTATATAGTTTTTAAAAA-CA--TTTTGAAAACATA-TATATAATATATAGTTTTTAA
1 ATATATA-TATATAG-TTTTAAAAATAATTTTTTG-AAA-ATAGTATAT-ATATATAG-TTTTAA
4915866 AAA--CATTTTGAAAAAA
60 AAATGC-TTTTG---AAA
* *
4915882 TATATATAATATATAGTTTTTAAAA-AATATTTTGAAAATATGTATATAATATATAGTTTTAAAA
1 -ATATAT-ATATATAGTTTTAAAAATAATTTTTTGAAAATA-GTATAT-ATATATAGTTTTAAAA
4915946 ATGCTTTTGAAA
62 ATGCTTTTGAAA
* * *
4915958 ATATGT-TATATAGTTTTAAAAATAATTTTTTGAAAATA-TATAT-TGTATGGTTTTGTAAACAA
1 ATATATATATATAGTTTTAAAAATAATTTTTTGAAAATAGTATATATATATAG-TTT-TAAA-AA
*
4916020 TGTTTTTGAAA
63 TGCTTTTGAAA
* * *
4916031 ATATATAATATATAATTCTAAAAATGATTTTT
1 ATATAT-ATATATAGTTTTAAAAATAATTTTT
4916063 ATTTATTTTT
Statistics
Matches: 155, Mismatches: 12, Indels: 29
0.79 0.06 0.15
Matches are distributed among these distances:
70 5 0.03
71 3 0.02
72 9 0.06
73 32 0.21
74 14 0.09
75 26 0.17
76 3 0.02
77 12 0.08
78 25 0.16
79 25 0.16
80 1 0.01
ACGTcount: A:0.45, C:0.02, G:0.08, T:0.45
Consensus pattern (73 bp):
ATATATATATATAGTTTTAAAAATAATTTTTTGAAAATAGTATATATATATAGTTTTAAAAATGC
TTTTGAAA
Found at i:4917527 original size:39 final size:38
Alignment explanation
Indices: 4917484--4917594 Score: 95
Period size: 39 Copynumber: 2.8 Consensus size: 38
4917474 AATTTAACCT
*
4917484 TTTTATTATTTTTTATTTTATTTCATTTTATTTCTTTA
1 TTTTATTATTTTTTAATTTATTTCATTTTATTTCTTTA
* *
4917522 GTTTTATT-TTTTTT-CTTTATACTCAATTTTATTTTTCTTTA
1 -TTTTATTATTTTTTAATTTAT-TTC-ATTTTA--TTTCTTTA
*
4917563 -TTTATTAATTTTATTAATTTA-TTAATTTTATT
1 TTTTATT-ATTTT-TTAATTTATTTCATTTTATT
4917595 ATTATTATTA
Statistics
Matches: 59, Mismatches: 5, Indels: 17
0.73 0.06 0.21
Matches are distributed among these distances:
37 5 0.08
38 10 0.17
39 19 0.32
40 6 0.10
41 13 0.22
42 2 0.03
43 4 0.07
ACGTcount: A:0.22, C:0.05, G:0.01, T:0.72
Consensus pattern (38 bp):
TTTTATTATTTTTTAATTTATTTCATTTTATTTCTTTA
Found at i:4917536 original size:19 final size:18
Alignment explanation
Indices: 4917489--4917541 Score: 63
Period size: 19 Copynumber: 2.9 Consensus size: 18
4917479 AACCTTTTTA
*
4917489 TTATTTTTTAT-TTTATT
1 TTATTTTTTTTCTTTATT
* *
4917506 TCATTTTATTTCTTTAGTT
1 TTATTTTTTTTCTTTA-TT
4917525 TTATTTTTTTTCTTTAT
1 TTATTTTTTTTCTTTAT
4917542 ACTCAATTTT
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
17 8 0.28
18 5 0.17
19 16 0.55
ACGTcount: A:0.15, C:0.06, G:0.02, T:0.77
Consensus pattern (18 bp):
TTATTTTTTTTCTTTATT
Found at i:4917577 original size:9 final size:9
Alignment explanation
Indices: 4917563--4917614 Score: 65
Period size: 9 Copynumber: 6.0 Consensus size: 9
4917553 TTTTTCTTTA
4917563 TTTATTAAT
1 TTTATTAAT
4917572 TTTATTAA-
1 TTTATTAAT
4917580 TTTATTAAT
1 TTTATTAAT
4917589 TTTATT-AT
1 TTTATTAAT
4917597 TATTATT-AT
1 T-TTATTAAT
*
4917606 TATATTAAT
1 TTTATTAAT
4917615 ATTTCTTTCT
Statistics
Matches: 39, Mismatches: 1, Indels: 6
0.85 0.02 0.13
Matches are distributed among these distances:
8 15 0.38
9 24 0.62
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (9 bp):
TTTATTAAT
Found at i:4917592 original size:26 final size:26
Alignment explanation
Indices: 4917563--4917614 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 26
4917553 TTTTTCTTTA
4917563 TTTATTAATT-TTATTAATT-TATTAAT
1 TTTATT-ATTATTATT-ATTATATTAAT
4917589 TTTATTATTATTATTATTATATTAAT
1 TTTATTATTATTATTATTATATTAAT
4917615 ATTTCTTTCT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
25 6 0.25
26 18 0.75
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (26 bp):
TTTATTATTATTATTATTATATTAAT
Found at i:4917617 original size:17 final size:18
Alignment explanation
Indices: 4917564--4917617 Score: 76
Period size: 17 Copynumber: 3.1 Consensus size: 18
4917554 TTTTCTTTAT
4917564 TTATTAATTTTATTAAT-
1 TTATTAATTTTATTAATA
*
4917581 TTATTAATTTTATTATTA
1 TTATTAATTTTATTAATA
*
4917599 TTATT-ATTATATTAATA
1 TTATTAATTTTATTAATA
4917616 TT
1 TT
4917618 TCTTTCTTTT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
17 28 0.85
18 5 0.15
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (18 bp):
TTATTAATTTTATTAATA
Found at i:4921641 original size:3 final size:3
Alignment explanation
Indices: 4921633--4921661 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
4921623 ATCTGAATCT
4921633 GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
4921662 GGTACCTATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:4928318 original size:5 final size:5
Alignment explanation
Indices: 4928308--4928349 Score: 59
Period size: 5 Copynumber: 8.6 Consensus size: 5
4928298 CTCTTTTGAA
**
4928308 TTTCT TTTCT TTTCT TTTCT TTTCT GAT-T TTTCT TTTCT TTT
1 TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT TTT
4928350 GTCTTTTTCT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
4 2 0.06
5 30 0.94
ACGTcount: A:0.02, C:0.17, G:0.02, T:0.79
Consensus pattern (5 bp):
TTTCT
Found at i:4928341 original size:14 final size:15
Alignment explanation
Indices: 4928308--4928346 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 15
4928298 CTCTTTTGAA
**
4928308 TTTCTTTTCTTTTCT
1 TTTCTTTTCTGATCT
4928323 TTTCTTTTCTGAT-T
1 TTTCTTTTCTGATCT
4928337 TTTCTTTTCT
1 TTTCTTTTCT
4928347 TTTGTCTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 11 0.50
15 11 0.50
ACGTcount: A:0.03, C:0.18, G:0.03, T:0.77
Consensus pattern (15 bp):
TTTCTTTTCTGATCT
Found at i:4928356 original size:18 final size:19
Alignment explanation
Indices: 4928317--4928366 Score: 68
Period size: 19 Copynumber: 2.7 Consensus size: 19
4928307 ATTTCTTTTC
4928317 TTTTCTTTTCTTTTCTGAT
1 TTTTCTTTTCTTTTCTGAT
* *
4928336 TTTTCTTTTCTTTTGT-CT
1 TTTTCTTTTCTTTTCTGAT
4928354 TTTTC-TTTCTTTT
1 TTTTCTTTTCTTTT
4928367 TGCACTCCAA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.28
18 6 0.21
19 15 0.52
ACGTcount: A:0.02, C:0.16, G:0.04, T:0.78
Consensus pattern (19 bp):
TTTTCTTTTCTTTTCTGAT
Found at i:4928367 original size:18 final size:17
Alignment explanation
Indices: 4928317--4928368 Score: 52
Period size: 18 Copynumber: 2.9 Consensus size: 17
4928307 ATTTCTTTTC
4928317 TTTTCTTTTCTTTTCTGAT
1 TTTTC-TTTCTTTT-TGAT
*
4928336 TTTTCTTT-TCTTTTGTCT
1 TTTTCTTTCT-TTTTG-AT
4928354 TTTTCTTTCTTTTTG
1 TTTTCTTTCTTTTTG
4928369 CACTCCAATT
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
17 3 0.10
18 20 0.69
19 6 0.21
ACGTcount: A:0.02, C:0.15, G:0.06, T:0.77
Consensus pattern (17 bp):
TTTTCTTTCTTTTTGAT
Found at i:4932493 original size:91 final size:91
Alignment explanation
Indices: 4932338--4932518 Score: 299
Period size: 91 Copynumber: 2.0 Consensus size: 91
4932328 TAGTTGATGC
* *
4932338 TTGGCCGAATAGGGAGAGAACTCTTCATCTTGGCGCCTAAATGAACCATATGCAAGGCACATGGG
1 TTGGCCGAATAGGGAGAGAACTCTTCATCTTGGCGCATAAATGAACCATATGCAAGGAACATGGG
4932403 GGCTGATCACATGCAAAACACATGGA
66 GGCTGATCACATGCAAAACACATGGA
*
4932429 TTGGCCGAATAGGGAGAGAACTCTTCATCTTGGCGCATAAATGATCCATATGCAAGGAACATGGG
1 TTGGCCGAATAGGGAGAGAACTCTTCATCTTGGCGCATAAATGAACCATATGCAAGGAACATGGG
* * **
4932494 GGCTGGTCATATGCAAGGCACATGG
66 GGCTGATCACATGCAAAACACATGG
4932519 GTGTTCTAGG
Statistics
Matches: 83, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
91 83 1.00
ACGTcount: A:0.30, C:0.20, G:0.28, T:0.21
Consensus pattern (91 bp):
TTGGCCGAATAGGGAGAGAACTCTTCATCTTGGCGCATAAATGAACCATATGCAAGGAACATGGG
GGCTGATCACATGCAAAACACATGGA
Found at i:4933556 original size:19 final size:21
Alignment explanation
Indices: 4933518--4933563 Score: 69
Period size: 19 Copynumber: 2.3 Consensus size: 21
4933508 GTACCTTCCT
*
4933518 AAAATAACAAGATTTTTAATG
1 AAAATAACAAGATCTTTAATG
4933539 AAAA-AACAAGA-CTTTAATG
1 AAAATAACAAGATCTTTAATG
4933558 AAAATA
1 AAAATA
4933564 CATGCTCTTG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
19 11 0.48
20 8 0.35
21 4 0.17
ACGTcount: A:0.59, C:0.07, G:0.09, T:0.26
Consensus pattern (21 bp):
AAAATAACAAGATCTTTAATG
Found at i:4934036 original size:10 final size:10
Alignment explanation
Indices: 4934021--4934048 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
4934011 AACTACTCTC
4934021 CCAGCTACTT
1 CCAGCTACTT
4934031 CCAGCTACTT
1 CCAGCTACTT
4934041 CCAGCTAC
1 CCAGCTAC
4934049 CTCTAGTCCA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.21, C:0.43, G:0.11, T:0.25
Consensus pattern (10 bp):
CCAGCTACTT
Found at i:4946008 original size:19 final size:20
Alignment explanation
Indices: 4945968--4946020 Score: 72
Period size: 19 Copynumber: 2.6 Consensus size: 20
4945958 GAAACCCCTT
4945968 TGAAAATACATGATTTTTTTAA
1 TGAAAATACATGA--TTTTTAA
4945990 TGAAAATACATGA-TTTTAA
1 TGAAAATACATGATTTTTAA
*
4946009 TGAAGATACATG
1 TGAAAATACATG
4946021 CTATTGGCCG
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
19 17 0.57
22 13 0.43
ACGTcount: A:0.43, C:0.06, G:0.13, T:0.38
Consensus pattern (20 bp):
TGAAAATACATGATTTTTAA
Found at i:4946415 original size:20 final size:20
Alignment explanation
Indices: 4946386--4946434 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
4946376 TTGGTCTTCT
* *
4946386 CAGCTCCTTAGCTACTCTCC
1 CAGCTACTTAGCAACTCTCC
4946406 CAGCTACTTAGCAACTCTCC
1 CAGCTACTTAGCAACTCTCC
*
4946426 CAACTACTT
1 CAGCTACTT
4946435 CCAGCTACCT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.22, C:0.41, G:0.08, T:0.29
Consensus pattern (20 bp):
CAGCTACTTAGCAACTCTCC
Found at i:4946511 original size:30 final size:30
Alignment explanation
Indices: 4946484--4946566 Score: 139
Period size: 30 Copynumber: 2.8 Consensus size: 30
4946474 GATCCTCCGG
*
4946484 CTAATTTCAGCTACATGCTAGCTCCTCCAA
1 CTAAGTTCAGCTACATGCTAGCTCCTCCAA
4946514 CTAAGTTCAGCTACATGCTAGCTCCTCCAA
1 CTAAGTTCAGCTACATGCTAGCTCCTCCAA
* *
4946544 CTAAGTTCAGTTACATTCTAGCT
1 CTAAGTTCAGCTACATGCTAGCT
4946567 ATCGAAAGAT
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 50 1.00
ACGTcount: A:0.27, C:0.30, G:0.12, T:0.31
Consensus pattern (30 bp):
CTAAGTTCAGCTACATGCTAGCTCCTCCAA
Found at i:4954718 original size:23 final size:24
Alignment explanation
Indices: 4954692--4954743 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 24
4954682 AGAAAAGCCA
4954692 AAAAGAAGAAA-A-TTCAAAAA-AGG
1 AAAAGAA-AAAGATTTCAAAAATA-G
4954715 AAAAGAAAAAGATTTCAAAAATAG
1 AAAAGAAAAAGATTTCAAAAATAG
4954739 AAAAG
1 AAAAG
4954744 CAAGCCAAGG
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
22 3 0.12
23 8 0.31
24 14 0.54
25 1 0.04
ACGTcount: A:0.69, C:0.04, G:0.15, T:0.12
Consensus pattern (24 bp):
AAAAGAAAAAGATTTCAAAAATAG
Found at i:4969256 original size:17 final size:17
Alignment explanation
Indices: 4969236--4969283 Score: 69
Period size: 17 Copynumber: 2.8 Consensus size: 17
4969226 AAAGTTGGTT
4969236 CATTAATCAAACTAGTG
1 CATTAATCAAACTAGTG
* *
4969253 CATTCATTAAACTAGTG
1 CATTAATCAAACTAGTG
*
4969270 AATTAATCAAACTA
1 CATTAATCAAACTA
4969284 ACTCTTAATT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
17 26 1.00
ACGTcount: A:0.44, C:0.17, G:0.08, T:0.31
Consensus pattern (17 bp):
CATTAATCAAACTAGTG
Found at i:4973958 original size:21 final size:21
Alignment explanation
Indices: 4973934--4974011 Score: 95
Period size: 21 Copynumber: 3.6 Consensus size: 21
4973924 TTCGTAAAAG
4973934 TACTTTGTGTACTTGGAGTAA
1 TACTTTGTGTACTTGGAGTAA
*
4973955 TACTTTGTGCACTATGGAAAG-AA
1 TACTTTGTGTACT-TGG--AGTAA
* *
4973978 TACTTTGTGTACTTGTAGTAG
1 TACTTTGTGTACTTGGAGTAA
4973999 TACTTTGTGTACT
1 TACTTTGTGTACT
4974012 ATGGCACTTG
Statistics
Matches: 49, Mismatches: 4, Indels: 8
0.80 0.07 0.13
Matches are distributed among these distances:
20 2 0.04
21 26 0.53
22 5 0.10
23 14 0.29
24 2 0.04
ACGTcount: A:0.24, C:0.12, G:0.22, T:0.42
Consensus pattern (21 bp):
TACTTTGTGTACTTGGAGTAA
Found at i:4981143 original size:44 final size:44
Alignment explanation
Indices: 4981070--4981158 Score: 128
Period size: 44 Copynumber: 2.0 Consensus size: 44
4981060 TCATTTTCGT
4981070 AAGAGTACTTTGTGTTCTTGGAGTAGTACTTTGTGTACTATGGC
1 AAGAGTACTTTGTGTTCTTGGAGTAGTACTTTGTGTACTATGGC
* *
4981114 AAGAGTACTCTT-T-TTACTTGTAGTTGTACTTTGTGTACTATGGC
1 AAGAGTACT-TTGTGTT-CTTGGAGTAGTACTTTGTGTACTATGGC
4981158 A
1 A
4981159 CTTTGTGTGC
Statistics
Matches: 41, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
43 2 0.05
44 37 0.90
45 2 0.05
ACGTcount: A:0.21, C:0.12, G:0.24, T:0.43
Consensus pattern (44 bp):
AAGAGTACTTTGTGTTCTTGGAGTAGTACTTTGTGTACTATGGC
Found at i:4981152 original size:21 final size:21
Alignment explanation
Indices: 4981073--4981152 Score: 65
Period size: 21 Copynumber: 3.7 Consensus size: 21
4981063 TTTTCGTAAG
* *
4981073 AGTACTTTGTGTTCTTGGAGT
1 AGTACTTTGTGTACTTGAAGT
4981094 AGTACTTTGTGTACTATGGCAAG-
1 AGTACTTTGTGTACT-T-G-AAGT
* *
4981117 AGTACTCTT-TTTACTTGTAGT
1 AGTACT-TTGTGTACTTGAAGT
*
4981138 TGTACTTTGTGTACT
1 AGTACTTTGTGTACT
4981153 ATGGCACTTT
Statistics
Matches: 47, Mismatches: 6, Indels: 12
0.72 0.09 0.18
Matches are distributed among these distances:
20 4 0.09
21 25 0.53
22 2 0.04
23 12 0.26
24 4 0.09
ACGTcount: A:0.19, C:0.12, G:0.23, T:0.46
Consensus pattern (21 bp):
AGTACTTTGTGTACTTGAAGT
Found at i:4981709 original size:2 final size:2
Alignment explanation
Indices: 4981698--4981732 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
4981688 ATGTATTTTA
4981698 AT AT -T 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
4981733 TTGAAGAATG
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:4986577 original size:17 final size:17
Alignment explanation
Indices: 4986555--4986596 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
4986545 GTGTTTGTTG
* *
4986555 CTCGAACGGGAATTTTT
1 CTCGAACGAGAATTTCT
*
4986572 CTCGAAAGAGAATTTCT
1 CTCGAACGAGAATTTCT
4986589 CTC-AACGA
1 CTCGAACGA
4986597 AAGGGAAGGG
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
16 4 0.19
17 17 0.81
ACGTcount: A:0.31, C:0.21, G:0.19, T:0.29
Consensus pattern (17 bp):
CTCGAACGAGAATTTCT
Found at i:4988608 original size:2 final size:2
Alignment explanation
Indices: 4988601--4988630 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
4988591 GTGCACTTAA
4988601 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
4988631 TAAATACACA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4999406 original size:30 final size:30
Alignment explanation
Indices: 4999370--4999429 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
4999360 TGCTAACCTT
4999370 TTTTTCTAAGATTGATCTTAAGAGTGGTTA
1 TTTTTCTAAGATTGATCTTAAGAGTGGTTA
4999400 TTTTTCTAAGATTGATCTTAAGAGTGGTTA
1 TTTTTCTAAGATTGATCTTAAGAGTGGTTA
4999430 CCACCAAATA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.27, C:0.07, G:0.20, T:0.47
Consensus pattern (30 bp):
TTTTTCTAAGATTGATCTTAAGAGTGGTTA
Found at i:5002012 original size:17 final size:17
Alignment explanation
Indices: 5001992--5002044 Score: 63
Period size: 17 Copynumber: 3.1 Consensus size: 17
5001982 TTAATAAAGT
5001992 TAGTTCATTGATCAAAC
1 TAGTTCATTGATCAAAC
5002009 TAGTTCATTCG-TCAAAC
1 TAGTTCATT-GATCAAAC
** *
5002026 TAGCACATTAATCAAAC
1 TAGTTCATTGATCAAAC
5002043 TA
1 TA
5002045 ACTCTTAATT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
17 30 0.97
18 1 0.03
ACGTcount: A:0.38, C:0.21, G:0.09, T:0.32
Consensus pattern (17 bp):
TAGTTCATTGATCAAAC
Found at i:5009002 original size:14 final size:12
Alignment explanation
Indices: 5008972--5008996 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
5008962 ATATTATATC
5008972 ACATAATATTTA
1 ACATAATATTTA
5008984 ACATAATATTTA
1 ACATAATATTTA
5008996 A
1 A
5008997 AACATATATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.52, C:0.08, G:0.00, T:0.40
Consensus pattern (12 bp):
ACATAATATTTA
Found at i:5017355 original size:30 final size:30
Alignment explanation
Indices: 5017321--5017432 Score: 167
Period size: 30 Copynumber: 3.8 Consensus size: 30
5017311 AAGGAGAAGA
5017321 TAGACCAAGCATTCCCAATGGAAGGGTTTT
1 TAGACCAAGCATTCCCAATGGAAGGGTTTT
5017351 TAGACCAAGCATTCCC---GGAAGGGTTTT
1 TAGACCAAGCATTCCCAATGGAAGGGTTTT
*
5017378 TAGACCAAGCATTCTCAATGGAAGGGTTTT
1 TAGACCAAGCATTCCCAATGGAAGGGTTTT
* * *
5017408 TAGACTAAACATTCTCAATGGAAGG
1 TAGACCAAGCATTCCCAATGGAAGG
5017433 ATTCTTAATG
Statistics
Matches: 76, Mismatches: 3, Indels: 6
0.89 0.04 0.07
Matches are distributed among these distances:
27 26 0.34
30 50 0.66
ACGTcount: A:0.31, C:0.19, G:0.23, T:0.27
Consensus pattern (30 bp):
TAGACCAAGCATTCCCAATGGAAGGGTTTT
Found at i:5017746 original size:13 final size:12
Alignment explanation
Indices: 5017728--5017770 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 12
5017718 ATTTTTAGTT
5017728 AATAAAAAAATGA
1 AATAAAAAAAT-A
5017741 AATAAAAAAATAA
1 AATAAAAAAAT-A
5017754 TAATAAATAAAATA
1 -AATAAA-AAAATA
5017768 AAT
1 AAT
5017771 CCTTAGACAT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
13 15 0.56
14 7 0.26
15 5 0.19
ACGTcount: A:0.77, C:0.00, G:0.02, T:0.21
Consensus pattern (12 bp):
AATAAAAAAATA
Found at i:5017766 original size:23 final size:21
Alignment explanation
Indices: 5017728--5017769 Score: 57
Period size: 23 Copynumber: 1.9 Consensus size: 21
5017718 ATTTTTAGTT
*
5017728 AATAAAAAAATGAAATAAAAA
1 AATAAAAAAATAAAATAAAAA
5017749 AATAATAATAAATAAAATAAA
1 AATAA-AA-AAATAAAATAAA
5017770 TCCTTAGACA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 5 0.28
22 2 0.11
23 11 0.61
ACGTcount: A:0.79, C:0.00, G:0.02, T:0.19
Consensus pattern (21 bp):
AATAAAAAAATAAAATAAAAA
Found at i:5022102 original size:15 final size:15
Alignment explanation
Indices: 5022075--5022126 Score: 52
Period size: 15 Copynumber: 3.5 Consensus size: 15
5022065 CTTATTTTAT
5022075 TAATATATGATTAAAA
1 TAATAT-TGATTAAAA
*
5022091 TAATATTGATTAAAT
1 TAATATTGATTAAAA
* *
5022106 TAAAATT-TTTAAAA
1 TAATATTGATTAAAA
*
5022120 TTATATT
1 TAATATT
5022127 AAAAAATATT
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
14 10 0.33
15 14 0.47
16 6 0.20
ACGTcount: A:0.50, C:0.00, G:0.04, T:0.46
Consensus pattern (15 bp):
TAATATTGATTAAAA
Found at i:5022122 original size:20 final size:21
Alignment explanation
Indices: 5022099--5022153 Score: 58
Period size: 23 Copynumber: 2.6 Consensus size: 21
5022089 AATAATATTG
*
5022099 ATTAAATTAAAAT-TTTTAAA
1 ATTAAATTAAAATATTGTAAA
* *
5022119 ATTATATTAAAAAATATTGTATA
1 ATTAAATT--AAAATATTGTAAA
5022142 ATTAAATTAAAA
1 ATTAAATTAAAA
5022154 AATATACCCT
Statistics
Matches: 28, Mismatches: 4, Indels: 5
0.76 0.11 0.14
Matches are distributed among these distances:
20 7 0.25
21 4 0.14
22 5 0.18
23 12 0.43
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (21 bp):
ATTAAATTAAAATATTGTAAA
Found at i:5022368 original size:18 final size:18
Alignment explanation
Indices: 5022347--5022386 Score: 71
Period size: 18 Copynumber: 2.2 Consensus size: 18
5022337 GGTTGAAAAA
5022347 AAATGCCACATCATACAT
1 AAATGCCACATCATACAT
*
5022365 AAATGTCACATCATACAT
1 AAATGCCACATCATACAT
5022383 AAAT
1 AAAT
5022387 ATTAATAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.47, C:0.23, G:0.05, T:0.25
Consensus pattern (18 bp):
AAATGCCACATCATACAT
Found at i:5022981 original size:16 final size:16
Alignment explanation
Indices: 5022919--5022981 Score: 65
Period size: 16 Copynumber: 3.9 Consensus size: 16
5022909 TTTTAACAAC
* *
5022919 AATAAGTTAATCTAAA
1 AATAATTTAAACTAAA
*
5022935 CATTAATTTAAAC-AAA
1 -AATAATTTAAACTAAA
*
5022951 AATAATTTAATCTAAA
1 AATAATTTAAACTAAA
*
5022967 AATAATCTAAACTAA
1 AATAATTTAAACTAA
5022982 CTAATTAACT
Statistics
Matches: 38, Mismatches: 7, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
15 10 0.26
16 19 0.50
17 9 0.24
ACGTcount: A:0.57, C:0.10, G:0.02, T:0.32
Consensus pattern (16 bp):
AATAATTTAAACTAAA
Found at i:5030802 original size:61 final size:61
Alignment explanation
Indices: 5030678--5030807 Score: 170
Period size: 61 Copynumber: 2.1 Consensus size: 61
5030668 AGGACACTAG
** *
5030678 GTGCAGGTGGTGGGCACAACCTTATGTGTCATATTCAGATCATCACTAGAGTGTAAACCTA
1 GTGCAGGTGGTGGGCACAACCTTATGTGTCATATTCAGATCAGAACTAGAGCGTAAACCTA
* * ** * * *
5030739 GTGTAGGTGGTGGGCACGACCTTATGTGTCATATTTGGATTAGAACTAGAGCGTAAGCTTA
1 GTGCAGGTGGTGGGCACAACCTTATGTGTCATATTCAGATCAGAACTAGAGCGTAAACCTA
5030800 GTGCAGGT
1 GTGCAGGT
5030808 TTAGCACTAC
Statistics
Matches: 58, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
61 58 1.00
ACGTcount: A:0.25, C:0.16, G:0.29, T:0.29
Consensus pattern (61 bp):
GTGCAGGTGGTGGGCACAACCTTATGTGTCATATTCAGATCAGAACTAGAGCGTAAACCTA
Found at i:5035984 original size:134 final size:133
Alignment explanation
Indices: 5035741--5036248 Score: 610
Period size: 134 Copynumber: 3.8 Consensus size: 133
5035731 AAGAATCAAA
* * * * ** * *
5035741 CTCGATTCAATCTTCCCTGAACAATAGT-GGAATGAATAAATATTTCCAGATATGATTTTCTCTC
1 CTCGATTCAATCTTCCCTGAAGAACA-TAGGAATGAATCAACATCCCCAGATCTGATTTTCCCTC
* * * *
5035805 AAGAAGAAATATAACATATCTC-TCTCTTTCAAGATTTGATCTTCCCTAAGTAATAGTGGAACAA
65 AAGAAGAAACAGAACATATC-CATCTCTTTCAAGATTTGATCTTCCCTGAGTAACAGTGGAA-AA
5035869 GTCTGC
128 GTCTGC
* *
5035875 CTCGATTTAATCTTCCCTGAAGAACATAGGAATGAATCAACGTCCCCAGATCTGATTTTCCCTCA
1 CTCGATTCAATCTTCCCTGAAGAACATAGGAATGAATCAACATCCCCAGATCTGATTTTCCCTCA
* * * *
5035940 AGAAGAAGCAGAACATATCCATCTCTTTCAAGATTTAATATTCCCTGCGTAACAGTGGAATAAGT
66 AGAAGAAACAGAACATATCCATCTCTTTCAAGATTTGATCTTCCCTGAGTAACAGTGGAA-AAGT
5036005 CTGC
130 CTGC
** * *
5036009 CTCGATTCAATCTTCCCTGAAGAACAGGGGAATGAATCAACATCCTCAGATCCGATTTTCCCTCA
1 CTCGATTCAATCTTCCCTGAAGAACATAGGAATGAATCAACATCCCCAGATCTGATTTTCCCTCA
* * * * *
5036074 AGAAGAAACATAACATATCCCTTTCTTTCAAGATTTGATCTTTCCTGAGTAACAATGGAAAACGT
66 AGAAGAAACAGAACATATCCATCTCTTTCAAGATTTGATCTTCCCTGAGTAACAGTGGAAAA-GT
* *
5036139 TTTC
130 CTGC
**
5036143 CTCGATTCAATCTTCCCTGAAGAA-A-AGTGAAATGAATCAACATTTCCAGATCTGATTTTCCCT
1 CTCGATTCAATCTTCCCTGAAGAACATAG-G-AATGAATCAACATCCCCAGATCTGATTTTCCCT
* * * *
5036206 CAAGAAGAAGCGGAATAGATCCATCTCTTTCAAGATTTGATCT
64 CAAGAAGAAACAGAACATATCCATCTCTTTCAAGATTTGATCT
5036249 ATCACACCCT
Statistics
Matches: 321, Mismatches: 48, Indels: 10
0.85 0.13 0.03
Matches are distributed among these distances:
132 1 0.00
133 6 0.02
134 314 0.98
ACGTcount: A:0.33, C:0.22, G:0.15, T:0.31
Consensus pattern (133 bp):
CTCGATTCAATCTTCCCTGAAGAACATAGGAATGAATCAACATCCCCAGATCTGATTTTCCCTCA
AGAAGAAACAGAACATATCCATCTCTTTCAAGATTTGATCTTCCCTGAGTAACAGTGGAAAAGTC
TGC
Found at i:5036230 original size:268 final size:268
Alignment explanation
Indices: 5035741--5036243 Score: 717
Period size: 268 Copynumber: 1.9 Consensus size: 268
5035731 AAGAATCAAA
* * * * * *
5035741 CTCGATTCAATCTTCCCTGAACAATAGTGGAATGAATAAATATTTCCAGATATGATTTTCTCTCA
1 CTCGATTCAATCTTCCCTGAACAACAGGGGAATGAATAAACATCTCCAGATACGATTTTCCCTCA
* * * *
5035806 AGAAGAAATATAACATATCTCTCTCTTTCAAGATTTGATCTTCCCTAAGTAATAGTGGAACAAGT
66 AGAAGAAACATAACATATCCCTCTCTTTCAAGATTTGATCTTCCCTAAGTAACAATGGAACAAGT
* *
5035871 CTGCCTCGATTTAATCTTCCCTGAAGAACATAGGAATGAATCAACGTCCCCAGATCTGATTTTCC
131 CTGCCTCGATTCAATCTTCCCTGAAGAACATAGGAATGAATCAACATCCCCAGATCTGATTTTCC
*
5035936 CTCAAGAAGAAGCAGAACATATCCATCTCTTTCAAGATTTAATATTCCCTGCGTAACAGTGGAAT
196 CTCAAGAAGAAGCAGAACAGATCCATCTCTTTCAAGATTTAATATTCCCTGCGTAACAGTGGAAT
5036001 AAGTCTGC
261 AAGTCTGC
* * *
5036009 CTCGATTCAATCTTCCCTGAAGAACAGGGGAATGAATCAACATC-CTCAGATCCGATTTTCCCTC
1 CTCGATTCAATCTTCCCTGAACAACAGGGGAATGAATAAACATCTC-CAGATACGATTTTCCCTC
* * *
5036073 AAGAAGAAACATAACATATCCCTTTCTTTCAAGATTTGATCTTTCCTGAGTAACAATGGAA-AAC
65 AAGAAGAAACATAACATATCCCTCTCTTTCAAGATTTGATCTTCCCTAAGTAACAATGGAACAA-
* * **
5036137 GTTTTCCTCGATTCAATCTTCCCTGAAGAA-A-AGTGAAATGAATCAACATTTCCAGATCTGATT
129 GTCTGCCTCGATTCAATCTTCCCTGAAGAACATAG-G-AATGAATCAACATCCCCAGATCTGATT
* *
5036200 TTCCCTCAAGAAGAAGCGGAATAGATCCATCTCTTTCAAGATTT
192 TTCCCTCAAGAAGAAGCAGAACAGATCCATCTCTTTCAAGATTT
5036244 GATCTATCAC
Statistics
Matches: 206, Mismatches: 25, Indels: 8
0.86 0.10 0.03
Matches are distributed among these distances:
266 2 0.01
267 5 0.02
268 199 0.97
ACGTcount: A:0.33, C:0.22, G:0.15, T:0.30
Consensus pattern (268 bp):
CTCGATTCAATCTTCCCTGAACAACAGGGGAATGAATAAACATCTCCAGATACGATTTTCCCTCA
AGAAGAAACATAACATATCCCTCTCTTTCAAGATTTGATCTTCCCTAAGTAACAATGGAACAAGT
CTGCCTCGATTCAATCTTCCCTGAAGAACATAGGAATGAATCAACATCCCCAGATCTGATTTTCC
CTCAAGAAGAAGCAGAACAGATCCATCTCTTTCAAGATTTAATATTCCCTGCGTAACAGTGGAAT
AAGTCTGC
Found at i:5039069 original size:31 final size:31
Alignment explanation
Indices: 5039033--5039102 Score: 106
Period size: 31 Copynumber: 2.3 Consensus size: 31
5039023 GTCACCCTTG
*
5039033 GGTAGGCTCTGCGACCCCGAGATCTTTC-TTA
1 GGTAGGCCCTGCGACCCCGAGAT-TTTCTTTA
*
5039064 GGTAGGCCCTGCGACCCCGAGATTTTCTTTG
1 GGTAGGCCCTGCGACCCCGAGATTTTCTTTA
5039095 GGTAGGCC
1 GGTAGGCC
5039103 TCGTGGCCCT
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
30 4 0.11
31 32 0.89
ACGTcount: A:0.14, C:0.29, G:0.30, T:0.27
Consensus pattern (31 bp):
GGTAGGCCCTGCGACCCCGAGATTTTCTTTA
Found at i:5039127 original size:31 final size:32
Alignment explanation
Indices: 5039087--5039164 Score: 104
Period size: 31 Copynumber: 2.4 Consensus size: 32
5039077 ACCCCGAGAT
* *
5039087 TTTCTTTGGGTAGGCCTCGTGGCCCTAAAAA-C
1 TTTC-TTGGGTAGGCCCCGTGGCCCCAAAAATC
5039119 TTTCTTGGGTAGGCCCCGTGGCCCCAAAAATC
1 TTTCTTGGGTAGGCCCCGTGGCCCCAAAAATC
* *
5039151 TTTTTTGAGTAGGC
1 TTTCTTGGGTAGGC
5039165 TCTCAGGCTC
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
31 24 0.59
32 17 0.41
ACGTcount: A:0.18, C:0.24, G:0.26, T:0.32
Consensus pattern (32 bp):
TTTCTTGGGTAGGCCCCGTGGCCCCAAAAATC
Found at i:5040141 original size:134 final size:132
Alignment explanation
Indices: 5039896--5040313 Score: 507
Period size: 134 Copynumber: 3.1 Consensus size: 132
5039886 CCCATATCCG
* * * * *
5039896 ATTTTCCCTCAAGAAGAAGCATAACAAATCCATCTATTTCAAGATTTGATCTTCCTTGAGTAACA
1 ATTTTCCCTCAAGAAGAAACAGAACAAATCCATCTCTTTCAAGATTTGATATTCCCTGAGTAACA
*
5039961 GTGGAACAAGTCTGCCTCGATTCAATCTTCCCTGAAGAA-AAGTGGAATGAATCAACATTTCCAG
66 GTGGAACAAGTCTG-CTCGATTCAATCTTCCCTGAAGAACAA-TGGAATGAATCAACGTTTCCA-
5040025 ATCTA
128 ATCTA
* * * * * * *
5040030 ATTTTCCCTCAAGAATAAACAGAACAGATCCCTATCTTTAAAGATTTAATATCCCCTGAGTAACA
1 ATTTTCCCTCAAGAAGAAACAGAACAAATCCATCTCTTTCAAGATTTGATATTCCCTGAGTAACA
* * *
5040095 GTGGAACAAGTCTGCATGGATTCAATATTTCCTGAAGAACAATGGAATGAATCAACGTTTCCATA
66 GTGGAACAAGTCTGC-TCGATTCAATCTTCCCTGAAGAACAATGGAATGAATCAACGTTTCCA-A
*
5040160 TATA
129 TCTA
* * * *
5040164 ATTTTCCCTCAAGAAGCAACGGAACAAATCCATCTCTTTTCCAA-ATTTGATATTCCCTTAGTAG
1 ATTTTCCCTCAAGAAGAAACAGAACAAATCCATCTC-TTT-CAAGATTTGATATTCCCTGAGTAA
* *
5040228 CAGTGGAACAAGTCTGTCTCGATTCAATCTTCCCTAAAGAACAGTGGAATGAATCAACGTTTCTC
64 CAGTGGAACAAGTCTG-CTCGATTCAATCTTCCCTGAAGAACAATGGAATGAATCAACGTTTC-C
*
5040293 AATCTG
127 AATCTA
* *
5040299 ATCTTCCCTGAAGAA
1 ATTTTCCCTCAAGAA
5040314 ACAGTGGAGC
Statistics
Matches: 240, Mismatches: 38, Indels: 11
0.83 0.13 0.04
Matches are distributed among these distances:
133 1 0.00
134 141 0.59
135 93 0.39
136 5 0.02
ACGTcount: A:0.34, C:0.22, G:0.15, T:0.29
Consensus pattern (132 bp):
ATTTTCCCTCAAGAAGAAACAGAACAAATCCATCTCTTTCAAGATTTGATATTCCCTGAGTAACA
GTGGAACAAGTCTGCTCGATTCAATCTTCCCTGAAGAACAATGGAATGAATCAACGTTTCCAATC
TA
Found at i:5040533 original size:17 final size:17
Alignment explanation
Indices: 5040511--5040543 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
5040501 TTTCTACTAT
5040511 TATTTCTATTTTCATTA
1 TATTTCTATTTTCATTA
5040528 TATTTCTATTTTCATT
1 TATTTCTATTTTCATT
5040544 TTTTTATTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.21, C:0.12, G:0.00, T:0.67
Consensus pattern (17 bp):
TATTTCTATTTTCATTA
Found at i:5043011 original size:131 final size:132
Alignment explanation
Indices: 5042653--5043019 Score: 450
Period size: 131 Copynumber: 2.8 Consensus size: 132
5042643 GAATCGATAT
* * *
5042653 TGAGAATAGTAATATCTTTTCATTTCAATTGGAGTAATAAATGATTGCTTTAAGGCATGAGAGGT
1 TGAGAATAGTAATATCTCTTCATTTCGATTGGAGTAATAAATGATTGTTTTAAGGCATGAGAGGT
* * * * * * * *
5042718 CATTTATTCTCGATTGGAAATAATTCGATAATACCGTTTTCTCTTGAATTAATATTGATTTTTAA
66 CATTTATTCTCGATTGGAAATAATTAGATATTATCATTTTCACTCGAATCAATATTGAATTTTAA
5042783 GA
131 GA
* * * * * * * *
5042785 TG-GAATAGTGATATCTCTTCATTTCGATTAGAGCAATAAATGACTATTTTGAGGTATGAGAGAT
1 TGAGAATAGTAATATCTCTTCATTTCGATTGGAGTAATAAATGATTGTTTTAAGGCATGAGAGGT
* * *
5042849 CATTTATTCTCGATTGGAAATCATTAGATATTATTATTTTCACTCGAATCGATATTGAATTTTAA
66 CATTTATTCTCGATTGGAAATAATTAGATATTATCATTTTCACTCGAATCAATATTGAATTTTAA
5042914 GA
131 GA
* *
5042916 TGAG-ATAGTAATATCTCTCCATTTCGATTGGAGTAATAAATGATTGTTTTAAGGCATGAAAGGT
1 TGAGAATAGTAATATCTCTTCATTTCGATTGGAGTAATAAATGATTGTTTTAAGGCATGAGAGGT
* *** * *
5042980 CATTTGTTCTCGATCATAAATAACTAAATATTATCATTTT
66 CATTTATTCTCGATTGGAAATAATTAGATATTATCATTTT
5043020 ATCTCTTAAA
Statistics
Matches: 194, Mismatches: 40, Indels: 3
0.82 0.17 0.01
Matches are distributed among these distances:
131 191 0.98
132 3 0.02
ACGTcount: A:0.33, C:0.11, G:0.16, T:0.40
Consensus pattern (132 bp):
TGAGAATAGTAATATCTCTTCATTTCGATTGGAGTAATAAATGATTGTTTTAAGGCATGAGAGGT
CATTTATTCTCGATTGGAAATAATTAGATATTATCATTTTCACTCGAATCAATATTGAATTTTAA
GA
Found at i:5044141 original size:14 final size:14
Alignment explanation
Indices: 5044122--5044153 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
5044112 CTTATGATAT
*
5044122 TTTTATTTTTATTA
1 TTTTATTTTTATCA
5044136 TTTTATTTTTATCA
1 TTTTATTTTTATCA
5044150 TTTT
1 TTTT
5044154 GTTACGTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.19, C:0.03, G:0.00, T:0.78
Consensus pattern (14 bp):
TTTTATTTTTATCA
Found at i:5044709 original size:24 final size:24
Alignment explanation
Indices: 5044682--5044729 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
5044672 TCAATTTAAA
* *
5044682 AATAATT-TATGTAATTTATGATAT
1 AATAATTGTATCT-ATTTATCATAT
5044706 AATAATTGTATCTATTTATCATAT
1 AATAATTGTATCTATTTATCATAT
5044730 TAATCTAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 17 0.81
25 4 0.19
ACGTcount: A:0.40, C:0.04, G:0.06, T:0.50
Consensus pattern (24 bp):
AATAATTGTATCTATTTATCATAT
Found at i:5045494 original size:70 final size:70
Alignment explanation
Indices: 5045381--5045513 Score: 248
Period size: 70 Copynumber: 1.9 Consensus size: 70
5045371 AAGAGCATAG
*
5045381 AAGAGCAAAAATAGGAGAACAAAACAATCTCACATGGCTAAGAAACATAGAAGAGCATCCCAAAA
1 AAGAGCAAAAATAGGAGAACAAAACAATCACACATGGCTAAGAAACATAGAAGAGCATCCCAAAA
5045446 GTCTA
66 GTCTA
*
5045451 AAGAGTAAAAATAGGAGAACAAAACAATCACACATGGCTAAGAAACATAGAAGAGCATCCCAA
1 AAGAGCAAAAATAGGAGAACAAAACAATCACACATGGCTAAGAAACATAGAAGAGCATCCCAA
5045514 CTGACTTCAA
Statistics
Matches: 61, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
70 61 1.00
ACGTcount: A:0.53, C:0.18, G:0.17, T:0.12
Consensus pattern (70 bp):
AAGAGCAAAAATAGGAGAACAAAACAATCACACATGGCTAAGAAACATAGAAGAGCATCCCAAAA
GTCTA
Found at i:5052956 original size:17 final size:17
Alignment explanation
Indices: 5052925--5052957 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
5052915 TACTATAAAA
5052925 ATAGAAAAATGTATTAT
1 ATAGAAAAATGTATTAT
5052942 ATAGATAAAAT-TATTA
1 ATAGA-AAAATGTATTA
5052958 GAAACTAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.55, C:0.00, G:0.09, T:0.36
Consensus pattern (17 bp):
ATAGAAAAATGTATTAT
Found at i:5053679 original size:15 final size:16
Alignment explanation
Indices: 5053647--5053686 Score: 55
Period size: 16 Copynumber: 2.5 Consensus size: 16
5053637 ACTCACATTT
5053647 ATTTAAAAAAATTATA
1 ATTTAAAAAAATTATA
*
5053663 ATTTAATAAAA-TATA
1 ATTTAAAAAAATTATA
5053678 ATATTAAAA
1 AT-TTAAAA
5053687 TAAGCTCAAC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
15 6 0.29
16 15 0.71
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (16 bp):
ATTTAAAAAAATTATA
Found at i:5054689 original size:405 final size:405
Alignment explanation
Indices: 5053903--5055367 Score: 1666
Period size: 405 Copynumber: 3.6 Consensus size: 405
5053893 GGGTCTCGTT
* * * * * * *
5053903 TCAGGGAAGATCAAATATGGAAAAAGAGAGG-TGTTGTTCCGTTGTTTTTTTTAGGGAAAATCAG
1 TCAGGGAAGATCAAATATGGAAAGAGAGAGGAT-CTGTTCTGTTG-TTTCTTCAGGGAAGATCAA
* ** * * * *
5053967 ATTTGGGGATGTTGATTCATTCTACTGTTCTTTAGGGAAGATTGAATCGAGGCAGACTTATTCCA
64 ATATGGGGACATTGATTCATTCCACTATTCTTCAGGGAAGATTGAATCGAGGCAGACTTGTTCCA
** *
5054032 CTGTTACTCTGGGAAGATCAAATCTGGAAAGAGAGGGGGGATCTGTTTCGCTATTTCTTCAGGGA
129 CTACTACTCAGGGAAGATCAAATCTGGAAAGAGA--GGGGATCTGTTTCGCTATTTCTTCAGGGA
* * * * * * * * *
5054097 AGATCAAATATGCAGG-CGTTGATACGTTCCATTGTTCTTCAGGGAAAATTGAATCAAGGAAGAG
192 AAATCAGATCT-TAGGACGTTGATTCATTCCACTGTTCTTCAGGGAATATTGAATCAAGGAAGAC
* * * ** **
5054161 TTGTTCTACTACTATTCAAGGAAGATCAAATCTGGAAAGAGAGGGGACCTAATCCACTGTTTCTT
256 TTGTTCCACTACTACTCAGGGAAGATCAAATCTGGAAAGAGAGGGGATTTGTTCCACTGTTTCTT
* * * * * * *
5054226 CAGGGAAAATTAGATATGAGGACGTTGTTTAATTCCAGTGTTCTTTAGGGAAGATTGAATTGAGG
321 CAGGGAAAATCAGATATGGGGACGTTGATTCATTCCACTGTTCTTTAGGGAAGATTGAATCGAGA
*
5054291 CAGACTTGTTCTACTGCTAC
386 CAGACTTGTTCTACTACTAC
* * * * * * *
5054311 ACAGGCAAGATCAAATCTGGAAAGAAAGAGGATATGTTATGTTGTTTCTTCAGGGGAAGATCATA
1 TCAGGGAAGATCAAATATGGAAAGAGAGAGGATCTGTTCTGTTGTTTCTTCA-GGGAAGATCAAA
* * *
5054376 TATGTGGACATTGATTCATTCCACTATTCTTCAGGGAAGATTGAATTGACGCA-ACCTTGTTCCA
65 TATGGGGACATTGATTCATTCCACTATTCTTCAGGGAAGATTGAATCGAGGCAGA-CTTGTTCCA
* * ** ** *
5054440 CTACTACTCAAGGAAGATCAAATCTGGAATGAGACCGGATCTGTTTTTCTATTTCTTTAGGGAAA
129 CTACTACTCAGGGAAGATCAAATCTGGAAAGAGAGGGGATCTGTTTCGCTATTTCTTCAGGGAAA
* * * * *
5054505 ATCAGTTCTTAGGACGTTGATTCATTCCACTATT-TTTAGGGAATATTGAATCGAGGCAGACTTG
194 ATCAGATCTTAGGACGTTGATTCATTCCACTGTTCTTCAGGGAATATTGAATCAAGGAAGACTTG
* *
5054569 TTCCACTACTACTCAGGGAAGATCAAATCTGGAAAGAGAGGGGATTTGTTCCCCTGTTTATTCAG
259 TTCCACTACTACTCAGGGAAGATCAAATCTGGAAAGAGAGGGGATTTGTTCCACTGTTTCTTCAG
** * *
5054634 GGAAAATCAGATCCGGGGATGTTGATTCATTCCACTGTTCTTCAGGGAAGATTGAATCGAGACAG
324 GGAAAATCAGATATGGGGACGTTGATTCATTCCACTGTTCTTTAGGGAAGATTGAATCGAGACAG
*
5054699 ACTTGTTCCACTACTAC
389 ACTTGTTCTACTACTAC
** * * * * * * *
5054716 TCAGGGAAGATCAAATATAAAAAGTGGGGGGGATCTGTTCTGCTGCTTCTTCAAGGAAGATTAAA
1 TCAGGGAAGATCAAATATGGAAAG-AGAGAGGATCTGTTCTGTTGTTTCTTCAGGGAAGATCAAA
* * * *
5054781 TCTGGGGACATTGATTCATTCCATTGTTCTTCAGGGAAGATTGAATCGAAGCAGACTTGTTCCAC
65 TATGGGGACATTGATTCATTCCACTATTCTTCAGGGAAGATTGAATCGAGGCAGACTTGTTCCAC
* *
5054846 TACTACTCAGGGAAGATCAACTCTGGAAAGAGAGGGGATCTGTTTCGCTGTTTCTTCA-GGAAAA
130 TACTACTCAGGGAAGATCAAATCTGGAAAGAGAGGGGATCTGTTTCGCTATTTCTTCAGGGAAAA
* * * * * *
5054910 CTCAGATCATGGGACATTGATTCATTCTACTGTTCTTCAGGGAATATTGAATCAAGGTAGATTTG
195 -TCAGATCTTAGGACGTTGATTCATTCCACTGTTCTTCAGGGAATATTGAATCAAGGAAGACTTG
* * * * *
5054975 TTCCACTACTACTCAGGGAAGATCAAATATGGAAAAAGAGGAGATTTGTTCCATTGTTTCTTTAG
259 TTCCACTACTACTCAGGGAAGATCAAATCTGGAAAGAGAGGGGATTTGTTCCACTGTTTCTTCAG
* * * * * * *
5055040 GGAAGATCAGATATTGGGACGTTGATTCATTTCATTGTTCTTTAGGGAATATTTAATCAAGACAG
324 GGAAAATCAGATATGGGGACGTTGATTCATTCCACTGTTCTTTAGGGAAGATTGAATCGAGACAG
*
5055105 ACTTGTTCTACTTCTAC
389 ACTTGTTCTACTACTAC
* ** *
5055122 TCAGGGAAGATCAAATATGGAAAGAGACAGGATCTGTTCCATTGTTTCTTCAGGGAAAATCAAAT
1 TCAGGGAAGATCAAATATGGAAAGAGAGAGGATCTGTTCTGTTGTTTCTTCAGGGAAGATCAAAT
** * * *
5055187 ATGGGGATGTTGATTCATTCCACTATTCTTCAGGGAAGATTGAATCTAGGCAAACTTGTTTCACT
66 ATGGGGACATTGATTCATTCCACTATTCTTCAGGGAAGATTGAATCGAGGCAGACTTGTTCCACT
* * * * * *
5055252 GCTACTCAGGGAAGATCAAATCTGGAAAGAGAAGAGATATGTTAT-GATGTTTCTTCAGGGAAAA
131 ACTACTCAGGGAAGATCAAATCTGGAAAGAGAGGGGATCTGTT-TCGCTATTTCTTCAGGGAAAA
** ** *
5055316 TCAGATCTGGGGACGTTGATTCATTCCGTTGTCCTTCAGGGAAGT-TTGAATC
195 TCAGATCTTAGGACGTTGATTCATTCCACTGTTCTTCAGGGAA-TATTGAATC
5055368 GAGTTCGGCT
Statistics
Matches: 882, Mismatches: 164, Indels: 25
0.82 0.15 0.02
Matches are distributed among these distances:
404 6 0.01
405 492 0.56
406 251 0.28
407 7 0.01
408 125 0.14
409 1 0.00
ACGTcount: A:0.29, C:0.16, G:0.24, T:0.31
Consensus pattern (405 bp):
TCAGGGAAGATCAAATATGGAAAGAGAGAGGATCTGTTCTGTTGTTTCTTCAGGGAAGATCAAAT
ATGGGGACATTGATTCATTCCACTATTCTTCAGGGAAGATTGAATCGAGGCAGACTTGTTCCACT
ACTACTCAGGGAAGATCAAATCTGGAAAGAGAGGGGATCTGTTTCGCTATTTCTTCAGGGAAAAT
CAGATCTTAGGACGTTGATTCATTCCACTGTTCTTCAGGGAATATTGAATCAAGGAAGACTTGTT
CCACTACTACTCAGGGAAGATCAAATCTGGAAAGAGAGGGGATTTGTTCCACTGTTTCTTCAGGG
AAAATCAGATATGGGGACGTTGATTCATTCCACTGTTCTTTAGGGAAGATTGAATCGAGACAGAC
TTGTTCTACTACTAC
Found at i:5055382 original size:135 final size:135
Alignment explanation
Indices: 5053903--5055370 Score: 1450
Period size: 135 Copynumber: 10.8 Consensus size: 135
5053893 GGGTCTCGTT
* * ** * * *
5053903 TCAGGGAAGATCAAATATGGAAAAAGAGAGGTG-T-TGTTCCGTTGTTTTTTTTAGGGAAAATCA
1 TCAGGGAAGATCAAATCTGG--AAAGAGAGGGGATCTGTTATGCTG-TTTCTTCAGGGAAAATCA
* * * * *
5053966 GATTTGGGGATGTTGATTCATTCTACTGTTCTTTAGGGAAGATTGAATCGAGGCAGACTTATTCC
63 GATATGGGGACGTTGATTCATTCCACTGTTCTTCAGGGAAGATTGAATCGAGGCAGACTTGTTCC
**
5054031 ACTGTTAC
128 ACTACTAC
* * *
5054039 TCTGGGAAGATCAAATCTGGAAAGAGAGGGGGGATCTGTT-TCGCTATTTCTTCAGGGAAGATCA
1 TCAGGGAAGATCAAATCTGGAAAGAGA--GGGGATCTGTTAT-GCTGTTTCTTCAGGGAAAATCA
* * * * * * * * *
5054103 AATATGCAGG-CGTTGATACGTTCCATTGTTCTTCAGGGAAAATTGAATCAAGGAAGAGTTGTTC
63 GATATG-GGGACGTTGATTCATTCCACTGTTCTTCAGGGAAGATTGAATCGAGGCAGACTTGTTC
* *
5054167 TACTACTAT
127 CACTACTAC
* * ** *** *
5054176 TCAAGGAAGATCAAATCTGGAAAGAGAGGGGACCTAATCCACTGTTTCTTCAGGGAAAATTAGAT
1 TCAGGGAAGATCAAATCTGGAAAGAGAGGGGATCTGTTATGCTGTTTCTTCAGGGAAAATCAGAT
* * * * * * *
5054241 ATGAGGACGTTGTTTAATTCCAGTGTTCTTTAGGGAAGATTGAATTGAGGCAGACTTGTTCTACT
66 ATGGGGACGTTGATTCATTCCACTGTTCTTCAGGGAAGATTGAATCGAGGCAGACTTGTTCCACT
*
5054306 GCTAC
131 ACTAC
* * * * * * * *
5054311 ACAGGCAAGATCAAATCTGGAAAGAAAGAGGATATGTTATGTTGTTTCTTCAGGGGAAGATCATA
1 TCAGGGAAGATCAAATCTGGAAAGAGAGGGGATCTGTTATGCTGTTTCTTCA-GGGAAAATCAGA
* * * * *
5054376 TATGTGGACATTGATTCATTCCACTATTCTTCAGGGAAGATTGAATTGACGCA-ACCTTGTTCCA
65 TATGGGGACGTTGATTCATTCCACTGTTCTTCAGGGAAGATTGAATCGAGGCAGA-CTTGTTCCA
5054440 CTACTAC
129 CTACTAC
* * ** * * * * *
5054447 TCAAGGAAGATCAAATCTGGAATGAGACCGGATCTGTTTTTCTATTTCTTTAGGGAAAATCAGTT
1 TCAGGGAAGATCAAATCTGGAAAGAGAGGGGATCTGTTATGCTGTTTCTTCAGGGAAAATCAGAT
* ** * * *
5054512 CTTAGGACGTTGATTCATTCCACTATT-TTTAGGGAATATTGAATCGAGGCAGACTTGTTCCACT
66 ATGGGGACGTTGATTCATTCCACTGTTCTTCAGGGAAGATTGAATCGAGGCAGACTTGTTCCACT
5054576 ACTAC
131 ACTAC
* *** *
5054581 TCAGGGAAGATCAAATCTGGAAAGAGAGGGGATTTGTTCCCCTGTTTATTCAGGGAAAATCAGAT
1 TCAGGGAAGATCAAATCTGGAAAGAGAGGGGATCTGTTATGCTGTTTCTTCAGGGAAAATCAGAT
** * *
5054646 CCGGGGATGTTGATTCATTCCACTGTTCTTCAGGGAAGATTGAATCGAGACAGACTTGTTCCACT
66 ATGGGGACGTTGATTCATTCCACTGTTCTTCAGGGAAGATTGAATCGAGGCAGACTTGTTCCACT
5054711 ACTAC
131 ACTAC
* ** * * * * * * * *
5054716 TCAGGGAAGATCAAATATAAAAAGTGGGGGGGATCTGTTCTGCTGCTTCTTCAAGGAAGATTAAA
1 TCAGGGAAGATCAAATCTGGAAAG-AGAGGGGATCTGTTATGCTGTTTCTTCAGGGAAAATCAGA
* * * *
5054781 TCTGGGGACATTGATTCATTCCATTGTTCTTCAGGGAAGATTGAATCGAAGCAGACTTGTTCCAC
65 TATGGGGACGTTGATTCATTCCACTGTTCTTCAGGGAAGATTGAATCGAGGCAGACTTGTTCCAC
5054846 TACTAC
130 TACTAC
*
5054852 TCAGGGAAGATCAACTCTGGAAAGAGAGGGGATCTGTT-TCGCTGTTTCTTCA-GGAAAACTCAG
1 TCAGGGAAGATCAAATCTGGAAAGAGAGGGGATCTGTTAT-GCTGTTTCTTCAGGGAAAA-TCAG
* * * * * *
5054915 ATCAT-GGGACATTGATTCATTCTACTGTTCTTCAGGGAATATTGAATCAAGGTAGATTTGTTCC
64 AT-ATGGGGACGTTGATTCATTCCACTGTTCTTCAGGGAAGATTGAATCGAGGCAGACTTGTTCC
5054979 ACTACTAC
128 ACTACTAC
* * * * * *
5054987 TCAGGGAAGATCAAATATGGAAAAAGAGGAGATTTGTTCCAT--TGTTTCTTTAGGGAAGATCAG
1 TCAGGGAAGATCAAATCTGGAAAGAGAGGGGATCTGTT--ATGCTGTTTCTTCAGGGAAAATCAG
* * * * * * * * *
5055050 ATATTGGGACGTTGATTCATTTCATTGTTCTTTAGGGAATATTTAATCAAGACAGACTTGTTCTA
64 ATATGGGGACGTTGATTCATTCCACTGTTCTTCAGGGAAGATTGAATCGAGGCAGACTTGTTCCA
*
5055115 CTTCTAC
129 CTACTAC
* ** *
5055122 TCAGGGAAGATCAAATATGGAAAGAGACAGGATCTGTTCCAT--TGTTTCTTCAGGGAAAATCAA
1 TCAGGGAAGATCAAATCTGGAAAGAGAGGGGATCTGTT--ATGCTGTTTCTTCAGGGAAAATCAG
* * * * *
5055185 ATATGGGGATGTTGATTCATTCCACTATTCTTCAGGGAAGATTGAATCTAGGCAAACTTGTTTCA
64 ATATGGGGACGTTGATTCATTCCACTGTTCTTCAGGGAAGATTGAATCGAGGCAGACTTGTTCCA
*
5055250 CTGCTAC
129 CTACTAC
* * * *
5055257 TCAGGGAAGATCAAATCTGGAAAGAGAAGAGATATGTTATGATGTTTCTTCAGGGAAAATCAGAT
1 TCAGGGAAGATCAAATCTGGAAAGAGAGGGGATCTGTTATGCTGTTTCTTCAGGGAAAATCAGAT
* ** * *
5055322 CTGGGGACGTTGATTCATTCCGTTGTCCTTCAGGGAAGTTTGAATCGAG
66 ATGGGGACGTTGATTCATTCCACTGTTCTTCAGGGAAGATTGAATCGAG
5055371 TTCGGCTTGT
Statistics
Matches: 1096, Mismatches: 213, Indels: 47
0.81 0.16 0.03
Matches are distributed among these distances:
133 2 0.00
134 129 0.12
135 615 0.56
136 248 0.23
137 93 0.08
138 9 0.01
ACGTcount: A:0.29, C:0.16, G:0.24, T:0.31
Consensus pattern (135 bp):
TCAGGGAAGATCAAATCTGGAAAGAGAGGGGATCTGTTATGCTGTTTCTTCAGGGAAAATCAGAT
ATGGGGACGTTGATTCATTCCACTGTTCTTCAGGGAAGATTGAATCGAGGCAGACTTGTTCCACT
ACTAC
Found at i:5056567 original size:14 final size:13
Alignment explanation
Indices: 5056548--5056589 Score: 52
Period size: 14 Copynumber: 3.3 Consensus size: 13
5056538 TTAAACCCCC
5056548 TTTTATTTATTCTA
1 TTTTATTT-TTCTA
5056562 TTTTATTTTTCT-
1 TTTTATTTTTCTA
*
5056574 TTCT-TTTTTCTA
1 TTTTATTTTTCTA
5056586 TTTT
1 TTTT
5056590 TTCATTTCAT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
11 7 0.28
12 6 0.24
13 4 0.16
14 8 0.32
ACGTcount: A:0.12, C:0.10, G:0.00, T:0.79
Consensus pattern (13 bp):
TTTTATTTTTCTA
Found at i:5056587 original size:19 final size:19
Alignment explanation
Indices: 5056565--5056658 Score: 58
Period size: 18 Copynumber: 5.1 Consensus size: 19
5056555 TATTCTATTT
5056565 TATTTTTCTTTCTTTTTTC
1 TATTTTTCTTTCTTTTTTC
5056584 TATTTTTTCATTTCATTTCTTT-
1 TA-TTTTTC-TTTC-TTT-TTTC
* *
5056606 T-TTTAT-TTTC-ATTTTC
1 TATTTTTCTTTCTTTTTTC
* *
5056622 -ATTTTTTCCTTATTTTTTC
1 TA-TTTTTCTTTCTTTTTTC
5056641 -ATTTTTCTTT-TTTTTTC
1 TATTTTTCTTTCTTTTTTC
5056658 T
1 T
5056659 TCAGGCGAAG
Statistics
Matches: 58, Mismatches: 7, Indels: 21
0.67 0.08 0.24
Matches are distributed among these distances:
15 3 0.05
16 1 0.02
17 11 0.19
18 14 0.24
19 8 0.14
20 10 0.17
21 4 0.07
22 4 0.07
23 3 0.05
ACGTcount: A:0.10, C:0.14, G:0.00, T:0.77
Consensus pattern (19 bp):
TATTTTTCTTTCTTTTTTC
Found at i:5056607 original size:18 final size:20
Alignment explanation
Indices: 5056579--5056629 Score: 63
Period size: 19 Copynumber: 2.6 Consensus size: 20
5056569 TTTCTTTCTT
5056579 TTTTCTATTTTTTCA-TTTCA
1 TTTTCT-TTTTTTCATTTTCA
5056599 -TTTCTTTTTTT-ATTTTCA
1 TTTTCTTTTTTTCATTTTCA
*
5056617 TTTTCATTTTTTC
1 TTTTCTTTTTTTC
5056630 CTTATTTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
17 1 0.04
18 11 0.41
19 15 0.56
ACGTcount: A:0.12, C:0.14, G:0.00, T:0.75
Consensus pattern (20 bp):
TTTTCTTTTTTTCATTTTCA
Found at i:5056634 original size:23 final size:23
Alignment explanation
Indices: 5056588--5056637 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
5056578 TTTTTCTATT
**
5056588 TTTTCATTTCATTTCTTTTTTTA
1 TTTTCATTTCATTTCTTTCCTTA
5056611 TTTTCATTTTCATTT-TTTCCTTA
1 TTTTCA-TTTCATTTCTTTCCTTA
5056634 TTTT
1 TTTT
5056638 TTCATTTTTC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 16 0.67
24 8 0.33
ACGTcount: A:0.12, C:0.14, G:0.00, T:0.74
Consensus pattern (23 bp):
TTTTCATTTCATTTCTTTCCTTA
Found at i:5066489 original size:21 final size:22
Alignment explanation
Indices: 5066464--5066506 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
5066454 AAAAAAAGGG
5066464 GAAAAACAA-AACAT-TTCAAAA
1 GAAAAA-AAGAACATGTTCAAAA
5066485 GAAAAAAAGAACATGTTCAAAA
1 GAAAAAAAGAACATGTTCAAAA
5066507 AAAGGAAGAG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
20 2 0.10
21 11 0.55
22 7 0.35
ACGTcount: A:0.65, C:0.12, G:0.09, T:0.14
Consensus pattern (22 bp):
GAAAAAAAGAACATGTTCAAAA
Found at i:5067376 original size:26 final size:26
Alignment explanation
Indices: 5067328--5067377 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 26
5067318 TCTAACGTGA
* *
5067328 AAGTTTCTAGAAGGTCCATTCAGCGG
1 AAGTTTCTAGAAGATCCACTCAGCGG
* *
5067354 AAGTTTCTAGCAGATCTACTCAGC
1 AAGTTTCTAGAAGATCCACTCAGC
5067378 ATGCCTTCTG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 20 1.00
ACGTcount: A:0.28, C:0.22, G:0.22, T:0.28
Consensus pattern (26 bp):
AAGTTTCTAGAAGATCCACTCAGCGG
Found at i:5075484 original size:24 final size:25
Alignment explanation
Indices: 5075457--5075510 Score: 67
Period size: 24 Copynumber: 2.2 Consensus size: 25
5075447 AAAATCATTG
*
5075457 CTTTTGGAA-AACCAAAAGATGTGA
1 CTTTTGGAAGAACCAAAAGATATGA
* *
5075481 CTTTT-GAAGAACCAATAGGTATGA
1 CTTTTGGAAGAACCAAAAGATATGA
5075505 CTTTTG
1 CTTTTG
5075511 CTGATTCACA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
23 3 0.12
24 22 0.88
ACGTcount: A:0.35, C:0.13, G:0.20, T:0.31
Consensus pattern (25 bp):
CTTTTGGAAGAACCAAAAGATATGA
Found at i:5078557 original size:30 final size:30
Alignment explanation
Indices: 5078519--5078579 Score: 79
Period size: 32 Copynumber: 2.0 Consensus size: 30
5078509 ATTGGAGTGC
*
5078519 AAAAAAAAAGAAGAGAA-AAATCAGAAAAGAAG
1 AAAAAAAAAGAA-A-AAGAATTCA-AAAAGAAG
5078551 AAAAAAAAAGAAAAAGAATTCAAAAAGAA
1 AAAAAAAAAGAAAAAGAATTCAAAAAGAA
5078580 AGCAAAGCCA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
30 9 0.33
31 6 0.22
32 12 0.44
ACGTcount: A:0.77, C:0.03, G:0.15, T:0.05
Consensus pattern (30 bp):
AAAAAAAAAGAAAAAGAATTCAAAAAGAAG
Found at i:5078565 original size:19 final size:20
Alignment explanation
Indices: 5078519--5078568 Score: 61
Period size: 19 Copynumber: 2.6 Consensus size: 20
5078509 ATTGGAGTGC
5078519 AAAA-AAAAAGAAGAGAAAA
1 AAAAGAAAAAGAAGAGAAAA
**
5078538 ATCAG-AAAAGAAGA-AAAA
1 AAAAGAAAAAGAAGAGAAAA
5078556 AAAAGAAAAAGAA
1 AAAAGAAAAAGAA
5078569 TTCAAAAAGA
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
18 7 0.28
19 18 0.72
ACGTcount: A:0.80, C:0.02, G:0.16, T:0.02
Consensus pattern (20 bp):
AAAAGAAAAAGAAGAGAAAA
Found at i:5085635 original size:14 final size:14
Alignment explanation
Indices: 5085616--5085658 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
5085606 ATAAGATACT
* *
5085616 ATCTATTCATCATC
1 ATCTATCCATCACC
5085630 ATCTATCCATCACC
1 ATCTATCCATCACC
*
5085644 ATC-CTCCATCACC
1 ATCTATCCATCACC
5085657 AT
1 AT
5085659 TCACGCCTAT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
13 11 0.42
14 15 0.58
ACGTcount: A:0.28, C:0.40, G:0.00, T:0.33
Consensus pattern (14 bp):
ATCTATCCATCACC
Found at i:5086088 original size:6 final size:6
Alignment explanation
Indices: 5086041--5086090 Score: 57
Period size: 6 Copynumber: 8.2 Consensus size: 6
5086031 AAAAGCTACA
* *
5086041 AAAAGAG AAAAAG AAAGAAG AAAAAT AAAAAT AAAAAG -AAAAG AAAAAG
1 AAAA-AG AAAAAG AAA-AAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG
5086090 A
1 A
5086091 CTCCTACATC
Statistics
Matches: 39, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
5 5 0.13
6 24 0.62
7 10 0.26
ACGTcount: A:0.80, C:0.00, G:0.16, T:0.04
Consensus pattern (6 bp):
AAAAAG
Found at i:5086155 original size:18 final size:18
Alignment explanation
Indices: 5086112--5086159 Score: 53
Period size: 18 Copynumber: 2.7 Consensus size: 18
5086102 AATTTGGAGT
5086112 GAAAAAGAAAGAAAACAAA
1 GAAAAAGAAA-AAAACAAA
* **
5086131 -AAGAAGAAAAATTCAAA
1 GAAAAAGAAAAAAACAAA
5086148 GAAAAAGAAAAA
1 GAAAAAGAAAAA
5086160 GTGAAGAAAG
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
17 6 0.25
18 18 0.75
ACGTcount: A:0.77, C:0.04, G:0.15, T:0.04
Consensus pattern (18 bp):
GAAAAAGAAAAAAACAAA
Found at i:5097553 original size:14 final size:14
Alignment explanation
Indices: 5097534--5097576 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
5097524 ATAAGATACT
* *
5097534 ATCTATTCATCATC
1 ATCTATCCATCACC
5097548 ATCTATCCATCACC
1 ATCTATCCATCACC
*
5097562 ATC-CTCCATCACC
1 ATCTATCCATCACC
5097575 AT
1 AT
5097577 TCACGCCTAT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
13 11 0.42
14 15 0.58
ACGTcount: A:0.28, C:0.40, G:0.00, T:0.33
Consensus pattern (14 bp):
ATCTATCCATCACC
Found at i:5100171 original size:19 final size:20
Alignment explanation
Indices: 5100147--5100187 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
5100137 AGCATTTATC
*
5100147 TTCATT-AAAATTATGTATT
1 TTCATTAAAAATCATGTATT
5100166 TTCATTAAAAATCATGTATT
1 TTCATTAAAAATCATGTATT
5100186 TT
1 TT
5100188 TCAAAGGGTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
19 6 0.30
20 14 0.70
ACGTcount: A:0.37, C:0.07, G:0.05, T:0.51
Consensus pattern (20 bp):
TTCATTAAAAATCATGTATT
Found at i:5100546 original size:14 final size:13
Alignment explanation
Indices: 5100527--5100579 Score: 63
Period size: 14 Copynumber: 3.9 Consensus size: 13
5100517 ATAAGATACT
5100527 ATCTTTCCATCATC
1 ATCTTTCCATCA-C
*
5100541 ATCTTTCCATTACC
1 ATCTTTCCATCA-C
5100555 ATCTTTCCATCAC
1 ATCTTTCCATCAC
5100568 TATC-TTCCATCA
1 -ATCTTTCCATCA
5100580 ACAATCACGC
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
13 9 0.26
14 26 0.74
ACGTcount: A:0.23, C:0.36, G:0.00, T:0.42
Consensus pattern (13 bp):
ATCTTTCCATCAC
Found at i:5105477 original size:11 final size:11
Alignment explanation
Indices: 5105454--5105500 Score: 51
Period size: 11 Copynumber: 4.1 Consensus size: 11
5105444 GTTGTAGGAG
5105454 TCTTTTC-TTT
1 TCTTTTCTTTT
5105464 TCTTTTCTTTT
1 TCTTTTCTTTT
*
5105475 TCTTTTATTCTT
1 TCTTTTCTT-TT
5105487 TCTTGTTTCTTTT
1 TC-T-TTTCTTTT
5105500 T
1 T
5105501 GTTGTAGCAC
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
10 7 0.23
11 11 0.35
12 4 0.13
13 4 0.13
14 5 0.16
ACGTcount: A:0.02, C:0.17, G:0.02, T:0.79
Consensus pattern (11 bp):
TCTTTTCTTTT
Found at i:5105924 original size:35 final size:37
Alignment explanation
Indices: 5105878--5105957 Score: 119
Period size: 35 Copynumber: 2.2 Consensus size: 37
5105868 TTTGAGAATT
*
5105878 TGGTGATGATATAGGCGTGAT-ATGG-TGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGAAGATGGACTA
*
5105913 TGGTGATGATATAGGCGTGATAATGGAAGATGGATTA
1 TGGTGATGATATAGGCGTGATAATGGAAGATGGACTA
*
5105950 TGGGGATG
1 TGGTGATG
5105958 GAAATAGTAT
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
35 21 0.52
36 4 0.10
37 15 0.38
ACGTcount: A:0.28, C:0.04, G:0.39, T:0.30
Consensus pattern (37 bp):
TGGTGATGATATAGGCGTGATAATGGAAGATGGACTA
Found at i:5122634 original size:24 final size:25
Alignment explanation
Indices: 5122588--5122635 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 25
5122578 CACCATGATC
* * *
5122588 TGCATTTTCTTCAGTTTCTTCATCT
1 TGCATTGTCTTCAGGTTCCTCATCT
5122613 TGCATTGT-TTCAGGTTCCTCATC
1 TGCATTGTCTTCAGGTTCCTCATC
5122636 AAAAATAGGC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 13 0.65
25 7 0.35
ACGTcount: A:0.12, C:0.25, G:0.12, T:0.50
Consensus pattern (25 bp):
TGCATTGTCTTCAGGTTCCTCATCT
Found at i:5130663 original size:8 final size:8
Alignment explanation
Indices: 5130650--5130677 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
5130640 ATCTTTTTCT
5130650 TTTTCTTC
1 TTTTCTTC
5130658 TTTTCTTC
1 TTTTCTTC
5130666 TTTTCTTC
1 TTTTCTTC
5130674 TTTT
1 TTTT
5130678 TATCTTTTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (8 bp):
TTTTCTTC
Found at i:5130691 original size:25 final size:25
Alignment explanation
Indices: 5130646--5130694 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
5130636 TGAAATCTTT
*
5130646 TTCTTTTTCTTCTTTTCTTCTTTTC
1 TTCTTTTTCATCTTTTCTTCTTTTC
*
5130671 TTCTTTTT-ATCTTTTATTTCTTTT
1 TTCTTTTTCATCTTTT-CTTCTTTT
5130695 TGCACTCCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 6 0.29
25 15 0.71
ACGTcount: A:0.04, C:0.18, G:0.00, T:0.78
Consensus pattern (25 bp):
TTCTTTTTCATCTTTTCTTCTTTTC
Found at i:5130695 original size:17 final size:15
Alignment explanation
Indices: 5130643--5130695 Score: 61
Period size: 16 Copynumber: 3.3 Consensus size: 15
5130633 TTTTGAAATC
5130643 TTTTTCTTTTTCTTCT
1 TTTTTCTTTTT-TTCT
*
5130659 TTTCTTCTTTTCTTCT
1 TTT-TTCTTTTTTTCT
5130675 TTTTATCTTTTATTTCT
1 TTTT-TCTTTT-TTTCT
5130692 TTTT
1 TTTT
5130696 GCACTCCAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
15 1 0.03
16 16 0.50
17 15 0.47
ACGTcount: A:0.04, C:0.17, G:0.00, T:0.79
Consensus pattern (15 bp):
TTTTTCTTTTTTTCT
Found at i:5133241 original size:20 final size:19
Alignment explanation
Indices: 5133197--5133249 Score: 72
Period size: 18 Copynumber: 2.8 Consensus size: 19
5133187 TCATTCGACC
* *
5133197 AAAAGCATGTACTTTCATT
1 AAAATCATGTATTTTCATT
5133216 -AAATCATGTATTTTCATT
1 AAAATCATGTATTTTCATT
5133234 AAAAATCATGTATTTT
1 -AAAATCATGTATTTT
5133250 TCAAAGGGGT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
18 16 0.53
20 14 0.47
ACGTcount: A:0.38, C:0.11, G:0.08, T:0.43
Consensus pattern (19 bp):
AAAATCATGTATTTTCATT
Found at i:5134845 original size:30 final size:31
Alignment explanation
Indices: 5134811--5134870 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 31
5134801 CTTAGCTTTA
**
5134811 TATTATGTTTACATATGTTTTAGAT-TCATT
1 TATTATGTTTACATATCATTTAGATATCATT
5134841 TATTATGTTTACATATCATTTAGATATCAT
1 TATTATGTTTACATATCATTTAGATATCAT
5134871 GGCAGCATGT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 23 0.85
31 4 0.15
ACGTcount: A:0.30, C:0.08, G:0.08, T:0.53
Consensus pattern (31 bp):
TATTATGTTTACATATCATTTAGATATCATT
Found at i:5135818 original size:20 final size:20
Alignment explanation
Indices: 5135793--5135848 Score: 103
Period size: 20 Copynumber: 2.8 Consensus size: 20
5135783 ATCTTCATTT
*
5135793 AAATCATGTATTTTCATCAA
1 AAATCATGTATTTTCATAAA
5135813 AAATCATGTATTTTCATAAA
1 AAATCATGTATTTTCATAAA
5135833 AAATCATGTATTTTCA
1 AAATCATGTATTTTCA
5135849 AAGGGGTTTC
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.41, C:0.12, G:0.05, T:0.41
Consensus pattern (20 bp):
AAATCATGTATTTTCATAAA
Found at i:5136383 original size:2 final size:2
Alignment explanation
Indices: 5136376--5136405 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
5136366 AGTTATTTTC
5136376 AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
5136406 CCTATAGTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5138033 original size:19 final size:18
Alignment explanation
Indices: 5138009--5138047 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 18
5137999 TTGGAGTGCA
*
5138009 AAAAGAAGAGAAAAATCAG
1 AAAAGAAAAGAAAAA-CAG
5138028 AAAAGAAAAGAAAAACAG
1 AAAAGAAAAGAAAAACAG
5138046 AA
1 AA
5138048 GTTCAAAAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 5 0.26
19 14 0.74
ACGTcount: A:0.74, C:0.05, G:0.18, T:0.03
Consensus pattern (18 bp):
AAAAGAAAAGAAAAACAG
Found at i:5146595 original size:30 final size:31
Alignment explanation
Indices: 5146559--5146618 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 31
5146549 CTTAGCTTTA
**
5146559 TATTATGTTTACATATGTTTTAGAT-TCATT
1 TATTATGTTTACATATCATTTAGATATCATT
5146589 TATTATGTTTACATATCATTTAGATATCAT
1 TATTATGTTTACATATCATTTAGATATCAT
5146619 GTGATGTGAA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 23 0.85
31 4 0.15
ACGTcount: A:0.30, C:0.08, G:0.08, T:0.53
Consensus pattern (31 bp):
TATTATGTTTACATATCATTTAGATATCATT
Found at i:5149071 original size:24 final size:24
Alignment explanation
Indices: 5149044--5149099 Score: 62
Period size: 24 Copynumber: 2.3 Consensus size: 24
5149034 GAAAGCAAGA
5149044 AAAAAAATCAGAAA-AG-AAGCACTC
1 AAAAAAA--AGAAATAGAAAGCACTC
* *
5149068 AAAAAGAAGAAATTGAAAGCACTC
1 AAAAAAAAGAAATAGAAAGCACTC
5149092 AAAAAAAA
1 AAAAAAAA
5149100 AGTTGGAAGC
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
22 5 0.19
23 1 0.04
24 21 0.78
ACGTcount: A:0.66, C:0.12, G:0.12, T:0.09
Consensus pattern (24 bp):
AAAAAAAAGAAATAGAAAGCACTC
Found at i:5149112 original size:22 final size:24
Alignment explanation
Indices: 5149059--5149114 Score: 80
Period size: 22 Copynumber: 2.4 Consensus size: 24
5149049 AATCAGAAAA
5149059 GAAGCACTCAAAAAGAAGAAATTG
1 GAAGCACTCAAAAAGAAGAAATTG
* *
5149083 AAAGCACTCAAAAA-AA-AAGTTG
1 GAAGCACTCAAAAAGAAGAAATTG
5149105 GAAGCACTCA
1 GAAGCACTCA
5149115 TCAACAATTC
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
22 14 0.48
23 2 0.07
24 13 0.45
ACGTcount: A:0.54, C:0.16, G:0.18, T:0.12
Consensus pattern (24 bp):
GAAGCACTCAAAAAGAAGAAATTG
Found at i:5161537 original size:24 final size:25
Alignment explanation
Indices: 5161510--5161557 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 25
5161500 GCCTATTTTT
* * *
5161510 GACGAGGAACCTGAA-ACAATGCAA
1 GACGAAGAAACTGAAGAAAATGCAA
5161534 GACGAAGAAACTGAAGAAAATGCA
1 GACGAAGAAACTGAAGAAAATGCA
5161558 GATCATGGTG
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 13 0.65
25 7 0.35
ACGTcount: A:0.50, C:0.17, G:0.25, T:0.08
Consensus pattern (25 bp):
GACGAAGAAACTGAAGAAAATGCAA
Found at i:5164239 original size:24 final size:26
Alignment explanation
Indices: 5164197--5164255 Score: 68
Period size: 25 Copynumber: 2.3 Consensus size: 26
5164187 AAGAAAAATC
* *
5164197 AGAAAAAAAAAGTGAAGCATTC-AAA
1 AGAAAAAAAAAGTCAAGCACTCAAAA
*
5164222 AGAAAAAAAAA-TCCAGCACTCAAAA
1 AGAAAAAAAAAGTCAAGCACTCAAAA
*
5164247 AGAAGAAAA
1 AGAAAAAAA
5164256 GCAAAGAAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
24 7 0.24
25 22 0.76
ACGTcount: A:0.66, C:0.12, G:0.14, T:0.08
Consensus pattern (26 bp):
AGAAAAAAAAAGTCAAGCACTCAAAA
Found at i:5164266 original size:5 final size:5
Alignment explanation
Indices: 5164249--5164278 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
5164239 ACTCAAAAAG
*
5164249 AAGAA AAGCA AAGAA AAGAA AAGAA AAGAA
1 AAGAA AAGAA AAGAA AAGAA AAGAA AAGAA
5164279 GTTTAAGCAC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.77, C:0.03, G:0.20, T:0.00
Consensus pattern (5 bp):
AAGAA
Found at i:5168574 original size:5 final size:5
Alignment explanation
Indices: 5168557--5168586 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
5168547 ACTCAAAAAG
*
5168557 AAGAA AAGCA AAGAA AAGAA AAGAA AAGAA
1 AAGAA AAGAA AAGAA AAGAA AAGAA AAGAA
5168587 GTTTAAGCAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.77, C:0.03, G:0.20, T:0.00
Consensus pattern (5 bp):
AAGAA
Found at i:5180663 original size:18 final size:18
Alignment explanation
Indices: 5180640--5180674 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
5180630 CGGACAAAAG
5180640 CATGTACTTTCATTAAAT
1 CATGTACTTTCATTAAAT
*
5180658 CATGTATTTTCATTAAA
1 CATGTACTTTCATTAAA
5180675 AAAAATCATG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.34, C:0.14, G:0.06, T:0.46
Consensus pattern (18 bp):
CATGTACTTTCATTAAAT
Found at i:5192887 original size:18 final size:19
Alignment explanation
Indices: 5192852--5192888 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
5192842 CACGGAATGT
5192852 AAGATTACCAGTGGGAATAA
1 AAGATTACCAG-GGGAATAA
5192872 AAGATTACCA-GGGAATA
1 AAGATTACCAGGGGAATA
5192889 GGATTACTAG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
20 10 0.59
ACGTcount: A:0.46, C:0.11, G:0.24, T:0.19
Consensus pattern (19 bp):
AAGATTACCAGGGGAATAA
Found at i:5194842 original size:19 final size:21
Alignment explanation
Indices: 5194806--5194851 Score: 60
Period size: 20 Copynumber: 2.3 Consensus size: 21
5194796 CTTTTTAAAC
* *
5194806 TTTTTCTTTCTTTCTTTTG-T
1 TTTTTTTTTATTTCTTTTGAT
5194826 TTTTTTTTTATTT-TTTTGAT
1 TTTTTTTTTATTTCTTTTGAT
5194846 TTTTTT
1 TTTTTT
5194852 ACTAACCCGG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 5 0.22
20 18 0.78
ACGTcount: A:0.04, C:0.07, G:0.04, T:0.85
Consensus pattern (21 bp):
TTTTTTTTTATTTCTTTTGAT
Found at i:5202535 original size:21 final size:21
Alignment explanation
Indices: 5202499--5202544 Score: 51
Period size: 19 Copynumber: 2.2 Consensus size: 21
5202489 CCTAGCCAAG
*
5202499 ACCTCTTTGGCTCC-TTAGC-
1 ACCTCTTTAGCTCCTTTAGCT
5202518 ACCTCTCTTAGCTACCTTTAGCT
1 ACCTCT-TTAGCT-CCTTTAGCT
5202541 ACCT
1 ACCT
5202545 TCAGCTACCT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
19 6 0.27
20 5 0.23
21 2 0.09
22 5 0.23
23 4 0.18
ACGTcount: A:0.15, C:0.37, G:0.11, T:0.37
Consensus pattern (21 bp):
ACCTCTTTAGCTCCTTTAGCT
Found at i:5202540 original size:10 final size:10
Alignment explanation
Indices: 5202525--5202554 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
5202515 AGCACCTCTC
5202525 TTAGCTACCT
1 TTAGCTACCT
5202535 TTAGCTACCT
1 TTAGCTACCT
*
5202545 TCAGCTACCT
1 TTAGCTACCT
5202555 ACTTGGTCAC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.20, C:0.33, G:0.10, T:0.37
Consensus pattern (10 bp):
TTAGCTACCT
Found at i:5205225 original size:19 final size:20
Alignment explanation
Indices: 5205184--5205234 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
5205174 GAAACCCCTT
*
5205184 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTTAA
5205204 TGAAAATACATGA-TTTTAA
1 TGAAAATACATGATTTTTAA
*
5205223 TGAAGATACATG
1 TGAAAATACATG
5205235 CTCTTGGCCG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 16 0.55
20 13 0.45
ACGTcount: A:0.43, C:0.06, G:0.16, T:0.35
Consensus pattern (20 bp):
TGAAAATACATGATTTTTAA
Found at i:5209419 original size:19 final size:20
Alignment explanation
Indices: 5209378--5209428 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
5209368 GAAACCCCTT
*
5209378 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTTAA
5209398 TGAAAATACATGA-TTTTAA
1 TGAAAATACATGATTTTTAA
*
5209417 TGAAGATACATG
1 TGAAAATACATG
5209429 CTCTTGGCCG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 16 0.55
20 13 0.45
ACGTcount: A:0.43, C:0.06, G:0.16, T:0.35
Consensus pattern (20 bp):
TGAAAATACATGATTTTTAA
Found at i:5213345 original size:46 final size:46
Alignment explanation
Indices: 5213278--5213461 Score: 307
Period size: 46 Copynumber: 4.0 Consensus size: 46
5213268 TAACCCCTTT
5213278 ATTTTCTTCTTTCTATTTCTAAGCCACCATTTTCATTATTATTTGC
1 ATTTTCTTCTTTCTATTTCTAAGCCACCATTTTCATTATTATTTGC
* *
5213324 ATTTTCTTCTTTATATTTCTAAGCCACCCTTTTCATTATTATTTGC
1 ATTTTCTTCTTTCTATTTCTAAGCCACCATTTTCATTATTATTTGC
* *
5213370 ATTTTCTTCTTTCTGTTTCTAAGCCA-CATTTTTCATTATCATTTGC
1 ATTTTCTTCTTTCTATTTCTAAGCCACCA-TTTTCATTATTATTTGC
*
5213416 ATTTTCTTCTTTCTATTTCTAAGCCACCTTTTTCATTATTATTTGC
1 ATTTTCTTCTTTCTATTTCTAAGCCACCATTTTCATTATTATTTGC
5213462 TTTCCATTCC
Statistics
Matches: 127, Mismatches: 9, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
45 1 0.01
46 125 0.98
47 1 0.01
ACGTcount: A:0.18, C:0.22, G:0.05, T:0.55
Consensus pattern (46 bp):
ATTTTCTTCTTTCTATTTCTAAGCCACCATTTTCATTATTATTTGC
Found at i:5214890 original size:16 final size:16
Alignment explanation
Indices: 5214869--5214899 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
5214859 AAGTTGCTTG
5214869 TCTCCACTTACCCATA
1 TCTCCACTTACCCATA
*
5214885 TCTCCACTTAGCCAT
1 TCTCCACTTACCCAT
5214900 CACTTTGAAG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.23, C:0.42, G:0.03, T:0.32
Consensus pattern (16 bp):
TCTCCACTTACCCATA
Found at i:5216701 original size:21 final size:21
Alignment explanation
Indices: 5216651--5216693 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
5216641 TGCGGGTGAA
5216651 AAACATATTTTATCTAATTCT
1 AAACATATTTTATCTAATTCT
5216672 AAACATATTTTATCTAATTCT
1 AAACATATTTTATCTAATTCT
5216693 A
1 A
5216694 CTCCTATTGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.40, C:0.14, G:0.00, T:0.47
Consensus pattern (21 bp):
AAACATATTTTATCTAATTCT
Found at i:5218140 original size:16 final size:16
Alignment explanation
Indices: 5218119--5218149 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
5218109 AAGATACTTG
5218119 TCTCCACTTAGCCATA
1 TCTCCACTTAGCCATA
5218135 TCTCCACTTAGCCAT
1 TCTCCACTTAGCCAT
5218150 CACTTTGAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.23, C:0.39, G:0.06, T:0.32
Consensus pattern (16 bp):
TCTCCACTTAGCCATA
Found at i:5228257 original size:30 final size:30
Alignment explanation
Indices: 5228223--5228309 Score: 147
Period size: 30 Copynumber: 2.9 Consensus size: 30
5228213 CAAGTTGGAA
5228223 AGCTTGGTGGAGCATTTGGAAGACATATAC
1 AGCTTGGTGGAGCATTTGGAAGACATATAC
* *
5228253 AGCTTAGTGGAGTATTTGGAAGACATATAC
1 AGCTTGGTGGAGCATTTGGAAGACATATAC
*
5228283 AGCTTGGTGGAGCATTTGGGAGACATA
1 AGCTTGGTGGAGCATTTGGAAGACATA
5228310 AACAACTCAC
Statistics
Matches: 52, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 52 1.00
ACGTcount: A:0.30, C:0.11, G:0.31, T:0.28
Consensus pattern (30 bp):
AGCTTGGTGGAGCATTTGGAAGACATATAC
Found at i:5233390 original size:8 final size:8
Alignment explanation
Indices: 5233379--5233403 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
5233369 GAAAAAAATC
5233379 AGAAAAGA
1 AGAAAAGA
5233387 AGAAAAGA
1 AGAAAAGA
5233395 AGAAAAGA
1 AGAAAAGA
5233403 A
1 A
5233404 AAGAAAAAGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (8 bp):
AGAAAAGA
Found at i:5233402 original size:13 final size:12
Alignment explanation
Indices: 5233347--5233417 Score: 54
Period size: 13 Copynumber: 5.6 Consensus size: 12
5233337 GTGCAAAAAG
*
5233347 AAAGAAAAAGACA
1 AAAG-AAAAGAAA
*
5233360 AAAGAAGAGGAAA
1 AAAGAA-AAGAAA
**
5233373 AAA-ATCAGAAA
1 AAAGAAAAGAAA
5233384 AGAAGAAAAGAAGA
1 A-AAGAAAAGAA-A
5233398 AAAGAAAAGAAA
1 AAAGAAAAGAAA
5233410 AAGAGAAA
1 AA-AGAAA
5233418 GCAAGCCAAG
Statistics
Matches: 46, Mismatches: 7, Indels: 10
0.73 0.11 0.16
Matches are distributed among these distances:
11 5 0.11
12 8 0.17
13 31 0.67
14 2 0.04
ACGTcount: A:0.75, C:0.03, G:0.21, T:0.01
Consensus pattern (12 bp):
AAAGAAAAGAAA
Found at i:5241012 original size:16 final size:16
Alignment explanation
Indices: 5240991--5241022 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
5240981 TAGTTAGCTC
5240991 ATTTGCATTCTAACAT
1 ATTTGCATTCTAACAT
5241007 ATTTGCATTCTAACAT
1 ATTTGCATTCTAACAT
5241023 TGGTGGAAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.31, C:0.19, G:0.06, T:0.44
Consensus pattern (16 bp):
ATTTGCATTCTAACAT
Found at i:5244667 original size:24 final size:24
Alignment explanation
Indices: 5244620--5244667 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
5244610 TAGAAAAGGT
* *
5244620 TAAGAAAAGGATAAAGTAATGAAA
1 TAAGAAAAGGATAAAGAAAAGAAA
5244644 TAAGAAAA-GATGAAAGAAAAGAAA
1 TAAGAAAAGGAT-AAAGAAAAGAAA
5244668 ATGAAATAGT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 3 0.14
24 18 0.86
ACGTcount: A:0.67, C:0.00, G:0.21, T:0.12
Consensus pattern (24 bp):
TAAGAAAAGGATAAAGAAAAGAAA
Found at i:5244938 original size:22 final size:20
Alignment explanation
Indices: 5244895--5244939 Score: 54
Period size: 22 Copynumber: 2.1 Consensus size: 20
5244885 TGTAGGAGTC
* *
5244895 TTTTTCTTTTCTTTTTGTTT
1 TTTTTCTTTTCTTGTTGCTT
5244915 TTTTTCTTCTTTCTTGTTGCTT
1 TTTTTC-T-TTTCTTGTTGCTT
5244937 TTT
1 TTT
5244940 GTTGTAGCAC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 6 0.29
21 1 0.05
22 14 0.67
ACGTcount: A:0.00, C:0.13, G:0.07, T:0.80
Consensus pattern (20 bp):
TTTTTCTTTTCTTGTTGCTT
Found at i:5247114 original size:17 final size:16
Alignment explanation
Indices: 5247057--5247111 Score: 56
Period size: 17 Copynumber: 3.3 Consensus size: 16
5247047 ATTGGAGTAC
*
5247057 AAAAAGAAAGAAAAGAT
1 AAAAAG-AAGAAAAGAA
**
5247074 AAAAAGAAGAAAATTCA
1 AAAAAGAAGAAAA-GAA
*
5247091 GAAAAGAAGAAAAGAA
1 AAAAAGAAGAAAAGAA
5247107 AAAAA
1 AAAAA
5247112 AGATTTCAAA
Statistics
Matches: 30, Mismatches: 7, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
16 12 0.40
17 18 0.60
ACGTcount: A:0.76, C:0.02, G:0.16, T:0.05
Consensus pattern (16 bp):
AAAAAGAAGAAAAGAA
Found at i:5248000 original size:35 final size:37
Alignment explanation
Indices: 5247954--5248033 Score: 128
Period size: 35 Copynumber: 2.2 Consensus size: 37
5247944 TTTGAGAATT
*
5247954 TGGTGATGATATAGGCGTGAT-ATGG-TGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGAAGATGGACTA
*
5247989 TGGTGATGATATAGGCGTGATAATGGAAGATGGATTA
1 TGGTGATGATATAGGCGTGATAATGGAAGATGGACTA
5248026 TGGTGATG
1 TGGTGATG
5248034 GAAATAGTAT
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
35 21 0.51
36 4 0.10
37 16 0.39
ACGTcount: A:0.28, C:0.04, G:0.38, T:0.31
Consensus pattern (37 bp):
TGGTGATGATATAGGCGTGATAATGGAAGATGGACTA
Found at i:5249165 original size:19 final size:20
Alignment explanation
Indices: 5249124--5249174 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
5249114 GAAACCCCTT
*
5249124 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTTAA
5249144 TGAAAATACATGA-TTTTAA
1 TGAAAATACATGATTTTTAA
*
5249163 TGAAGATACATG
1 TGAAAATACATG
5249175 CTCTTGGCCG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 16 0.55
20 13 0.45
ACGTcount: A:0.43, C:0.06, G:0.16, T:0.35
Consensus pattern (20 bp):
TGAAAATACATGATTTTTAA
Found at i:5252568 original size:30 final size:29
Alignment explanation
Indices: 5252533--5252590 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
5252523 TGGCTTTGCT
*
5252533 TTCTTTT-TGAATTCTTTTTCTTTTCTTTTC
1 TTCTTTTCTG-ATT-TTTCTCTTTTCTTTTC
*
5252563 TTCTTTTCTGATTTTTCTCTTTTTTTTT
1 TTCTTTTCTGATTTTTCTCTTTTCTTTT
5252591 TGCACTCCAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 13 0.52
30 10 0.40
31 2 0.08
ACGTcount: A:0.05, C:0.16, G:0.03, T:0.76
Consensus pattern (29 bp):
TTCTTTTCTGATTTTTCTCTTTTCTTTTC
Found at i:5253351 original size:19 final size:20
Alignment explanation
Indices: 5253310--5253360 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
5253300 GAAACCCCTT
*
5253310 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTTAA
5253330 TGAAAATACATGA-TTTTAA
1 TGAAAATACATGATTTTTAA
*
5253349 TGAAGATACATG
1 TGAAAATACATG
5253361 CTCTTGGCCG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 16 0.55
20 13 0.45
ACGTcount: A:0.43, C:0.06, G:0.16, T:0.35
Consensus pattern (20 bp):
TGAAAATACATGATTTTTAA
Found at i:5265338 original size:19 final size:21
Alignment explanation
Indices: 5265314--5265365 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
5265304 CGGCCAAGAG
*
5265314 CATGTATCTTCA-TTAAAA-T
1 CATGTATTTTCATTTAAAAGT
5265333 CATGTATTTTCATTTAAAAGT
1 CATGTATTTTCATTTAAAAGT
5265354 CATGTATTTTCA
1 CATGTATTTTCA
5265366 AAGGGGTTTC
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 11 0.37
20 6 0.20
21 13 0.43
ACGTcount: A:0.33, C:0.13, G:0.08, T:0.46
Consensus pattern (21 bp):
CATGTATTTTCATTTAAAAGT
Found at i:5266101 original size:16 final size:17
Alignment explanation
Indices: 5266073--5266104 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
5266063 AAATTGGAGT
5266073 ACAAAAAGAAAGAAAAG
1 ACAAAAAGAAAGAAAAG
5266090 ACAAAAAG-AAGAAAA
1 ACAAAAAGAAAGAAAA
5266105 TTCAGAAAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.78, C:0.06, G:0.16, T:0.00
Consensus pattern (17 bp):
ACAAAAAGAAAGAAAAG
Found at i:5266122 original size:23 final size:24
Alignment explanation
Indices: 5266083--5266144 Score: 67
Period size: 23 Copynumber: 2.5 Consensus size: 24
5266073 ACAAAAAGAA
5266083 AGAAAAGACAAAAAGAAGAAA-A-TTC
1 AGAAAAG--AAAAAGAA-AAAGATTTC
5266108 AGAAAAGAAAAAGAAAAAGATTTC
1 AGAAAAGAAAAAGAAAAAGATTTC
5266132 A-AAAAGAGAAAAG
1 AGAAAAGA-AAAAG
5266145 CAAGCCAAGG
Statistics
Matches: 34, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
22 3 0.09
23 15 0.44
24 9 0.26
25 7 0.21
ACGTcount: A:0.69, C:0.05, G:0.18, T:0.08
Consensus pattern (24 bp):
AGAAAAGAAAAAGAAAAAGATTTC
Found at i:5269464 original size:19 final size:21
Alignment explanation
Indices: 5269440--5269491 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
5269430 CGGCCAAGAG
*
5269440 CATGTATATTCA-TTAAAA-T
1 CATGTATTTTCATTTAAAAGT
5269459 CATGTATTTTCATTTAAAAGT
1 CATGTATTTTCATTTAAAAGT
5269480 CATGTATTTTCA
1 CATGTATTTTCA
5269492 AAGGGGTTTC
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 11 0.37
20 6 0.20
21 13 0.43
ACGTcount: A:0.35, C:0.12, G:0.08, T:0.46
Consensus pattern (21 bp):
CATGTATTTTCATTTAAAAGT
Found at i:5272728 original size:6 final size:6
Alignment explanation
Indices: 5272688--5272730 Score: 52
Period size: 6 Copynumber: 7.2 Consensus size: 6
5272678 CTGCAACAAA
* *
5272688 AAAAAG CAAAAG AAAGAAG AAAAAC AAAAAG -AAAAG AAAAAG A
1 AAAAAG AAAAAG AAA-AAG AAAAAG AAAAAG AAAAAG AAAAAG A
5272731 CCCCTAAAAC
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
5 5 0.16
6 20 0.65
7 6 0.19
ACGTcount: A:0.79, C:0.05, G:0.16, T:0.00
Consensus pattern (6 bp):
AAAAAG
Done.