Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D07
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: 58101237
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1550000 characters in sequence are not A, C, G, or T
File 28 of 199
Found at i:9130962 original size:101 final size:100
Alignment explanation
Indices: 9130761--9131019 Score: 317
Period size: 101 Copynumber: 2.7 Consensus size: 100
9130751 ATATTTAGTG
* *
9130761 TTTATAGTTTGGATTAGAATTTTGTATGAATATTCTAATTTTTTTGTATGAATATTGTAATTTTT
1 TTTATAGTTTGGATTAG-ATTTTGTATGAATATTGTAATTTTTTTGTATGAATATTGTAATTTTG
*
9130826 TATGAATATTGTAATTATTTTATAATTAAATTTGTA
65 TATGAATATTGTAATTATTTTATAATGAAATTTGTA
*
9130862 TTTATAGTTTTGGATTAGTATTTTGTATGAATATTGTAA-TTTTTTGTATGACTATTGTAATTTT
1 TTTATAG-TTTGGATTAG-ATTTTGTATGAATATTGTAATTTTTTTGTATGAATATTGTAATTTT
* *
9130926 GTATGAATATTGTAATT-TTTTTTGTATG-AATATTGTA
64 GTATGAATATTGTAATTATTTTAT-AATGAAAT-TTGTA
* *
9130963 ---ATA--TT--A-TA-ATTTTATATGAATATTGCAATTTTTTTGTATGAATATTGTAATTTTGT
1 TTTATAGTTTGGATTAGATTTTGTATGAATATTGTAATTTTTTTGTATGAATATTGTAATTTTGT
9131019 A
66 A
9131020 ATTTTGTATG
Statistics
Matches: 144, Mismatches: 10, Indels: 18
0.84 0.06 0.10
Matches are distributed among these distances:
90 18 0.12
91 27 0.19
92 2 0.01
93 1 0.01
95 2 0.01
98 3 0.02
100 8 0.06
101 54 0.38
102 29 0.20
ACGTcount: A:0.30, C:0.01, G:0.13, T:0.56
Consensus pattern (100 bp):
TTTATAGTTTGGATTAGATTTTGTATGAATATTGTAATTTTTTTGTATGAATATTGTAATTTTGT
ATGAATATTGTAATTATTTTATAATGAAATTTGTA
Found at i:9130983 original size:27 final size:26
Alignment explanation
Indices: 9130914--9131040 Score: 151
Period size: 27 Copynumber: 5.0 Consensus size: 26
9130904 TTTGTATGAC
9130914 TATTGTAATTTTGTATGAATATTGTAA
1 TATT-TAATTTTGTATGAATATTGTAA
9130941 T-TTT--TTTTGTATGAATATTGTAA
1 TATTTAATTTTGTATGAATATTGTAA
* *
9130964 TATTATAATTTTATATGAATATTG-CA
1 TATT-TAATTTTGTATGAATATTGTAA
9130990 -ATTT--TTTTGTATGAATATTGTAA
1 TATTTAATTTTGTATGAATATTGTAA
*
9131013 TTTTGTAATTTTGTATGAATATTGTAA
1 TATT-TAATTTTGTATGAATATTGTAA
9131040 T
1 T
9131041 GTCGGGATAT
Statistics
Matches: 86, Mismatches: 5, Indels: 18
0.79 0.05 0.17
Matches are distributed among these distances:
22 15 0.17
23 21 0.24
24 5 0.06
25 6 0.07
26 3 0.03
27 36 0.42
ACGTcount: A:0.31, C:0.01, G:0.13, T:0.55
Consensus pattern (26 bp):
TATTTAATTTTGTATGAATATTGTAA
Found at i:9131022 original size:49 final size:50
Alignment explanation
Indices: 9130914--9131036 Score: 203
Period size: 49 Copynumber: 2.5 Consensus size: 50
9130904 TTTGTATGAC
*
9130914 TATTGTAATTTTGTATGAATATTGTAATTTTTTTTGTATGAATATTGTAA
1 TATTGTAATTTTGTATGAATATTGCAATTTTTTTTGTATGAATATTGTAA
* *
9130964 TATTATAATTTTATATGAATATTGCAA-TTTTTTTGTATGAATATTGTAA
1 TATTGTAATTTTGTATGAATATTGCAATTTTTTTTGTATGAATATTGTAA
*
9131013 TTTTGTAATTTTGTATGAATATTG
1 TATTGTAATTTTGTATGAATATTG
9131037 TAATGTCGGG
Statistics
Matches: 67, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
49 43 0.64
50 24 0.36
ACGTcount: A:0.31, C:0.01, G:0.13, T:0.55
Consensus pattern (50 bp):
TATTGTAATTTTGTATGAATATTGCAATTTTTTTTGTATGAATATTGTAA
Found at i:9131040 original size:19 final size:19
Alignment explanation
Indices: 9130778--9131019 Score: 146
Period size: 19 Copynumber: 12.5 Consensus size: 19
9130768 TTTGGATTAG
*
9130778 AATTTTGTATGAATATTCT
1 AATTTTGTATGAATATTGT
9130797 AATTTTTTTGTATGAATATTGT
1 AA---TTTTGTATGAATATTGT
*
9130819 AATTTTTTATGAATATTGT
1 AATTTTGTATGAATATTGT
*
9130838 AATTATTTTAT-AATTAAATTTGT
1 AATT-TTGTATGAA-T--A-TTGT
* * *
9130861 -ATTTATAGTTTTGGAT-TAGT
1 AATTT-T-G-TATGAATATTGT
9130881 -ATTTTGTATGAATATTGT
1 AATTTTGTATGAATATTGT
*
9130899 AATTTTTTGTATGACTATTGT
1 AA--TTTTGTATGAATATTGT
9130920 AATTTTGTATGAATATTGT
1 AATTTTGTATGAATATTGT
* *
9130939 AATTTTTTTTG--TA-TG-
1 AATTTTGTATGAATATTGT
* *
9130954 AATATTG--T-AATATTAT
1 AATTTTGTATGAATATTGT
* *
9130970 AATTTTATATGAATATTGC
1 AATTTTGTATGAATATTGT
9130989 AATTTTTTTGTATGAATATTGT
1 AA---TTTTGTATGAATATTGT
9131011 AATTTTGTA
1 AATTTTGTA
9131020 ATTTTGTATG
Statistics
Matches: 175, Mismatches: 22, Indels: 52
0.70 0.09 0.21
Matches are distributed among these distances:
13 1 0.01
14 2 0.01
15 6 0.03
16 7 0.04
17 7 0.04
18 5 0.03
19 66 0.38
20 14 0.08
21 19 0.11
22 40 0.23
23 4 0.02
24 3 0.02
25 1 0.01
ACGTcount: A:0.31, C:0.01, G:0.12, T:0.56
Consensus pattern (19 bp):
AATTTTGTATGAATATTGT
Found at i:9131147 original size:60 final size:60
Alignment explanation
Indices: 9131081--9131202 Score: 156
Period size: 60 Copynumber: 2.0 Consensus size: 60
9131071 TGTATGAATA
* * * * * *
9131081 TTGTAATTATTTTATAA-GTAATTTGTTAGTAATTTAGGATTATGTTATAAATTTTTGTGT
1 TTGTAATTA-TTTAAAATGTAATTTATTAGTAATTTAAGATTAAGCTATAAATTGTTGTGT
* *
9131141 TTGTAATTATTTAAAATTTAATTTATTAGTAATTTAAGATTAAGCTATAAGTTGTTGTGT
1 TTGTAATTATTTAAAATGTAATTTATTAGTAATTTAAGATTAAGCTATAAATTGTTGTGT
9131201 TT
1 TT
9131203 AGTTTAGTAT
Statistics
Matches: 53, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
59 6 0.11
60 47 0.89
ACGTcount: A:0.32, C:0.01, G:0.14, T:0.53
Consensus pattern (60 bp):
TTGTAATTATTTAAAATGTAATTTATTAGTAATTTAAGATTAAGCTATAAATTGTTGTGT
Found at i:9131288 original size:37 final size:37
Alignment explanation
Indices: 9131242--9131317 Score: 152
Period size: 37 Copynumber: 2.1 Consensus size: 37
9131232 AAGTTTATAA
9131242 AAAAAATTAAAAATCATTTTATTAAAAGTTTAATTAT
1 AAAAAATTAAAAATCATTTTATTAAAAGTTTAATTAT
9131279 AAAAAATTAAAAATCATTTTATTAAAAGTTTAATTAT
1 AAAAAATTAAAAATCATTTTATTAAAAGTTTAATTAT
9131316 AA
1 AA
9131318 CTGACTTTTT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 39 1.00
ACGTcount: A:0.55, C:0.03, G:0.03, T:0.39
Consensus pattern (37 bp):
AAAAAATTAAAAATCATTTTATTAAAAGTTTAATTAT
Found at i:9135120 original size:22 final size:23
Alignment explanation
Indices: 9135092--9135134 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
9135082 AAATACCTTA
*
9135092 TTTTTTTCTTCT-TTTCCTTCCT
1 TTTTTTTCTTCTGCTTCCTTCCT
9135114 TTTTTTTCTTCTGCTTCCTTC
1 TTTTTTTCTTCTGCTTCCTTC
9135135 TTATTTCTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 12 0.63
23 7 0.37
ACGTcount: A:0.00, C:0.28, G:0.02, T:0.70
Consensus pattern (23 bp):
TTTTTTTCTTCTGCTTCCTTCCT
Found at i:9135122 original size:19 final size:19
Alignment explanation
Indices: 9135093--9135145 Score: 61
Period size: 20 Copynumber: 2.7 Consensus size: 19
9135083 AATACCTTAT
*
9135093 TTTTTTCTTCTTTTCCTTCC
1 TTTTTT-TTCTTCTCCTTCC
*
9135113 TTTTTTTTCTTCTGCTTCC
1 TTTTTTTTCTTCTCCTTCC
*
9135132 TTCTTATTTCTTCT
1 TT-TTTTTTCTTCT
9135146 GTTTCTCTAG
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
19 13 0.45
20 16 0.55
ACGTcount: A:0.02, C:0.26, G:0.02, T:0.70
Consensus pattern (19 bp):
TTTTTTTTCTTCTCCTTCC
Found at i:9135145 original size:23 final size:23
Alignment explanation
Indices: 9135087--9135145 Score: 68
Period size: 22 Copynumber: 2.6 Consensus size: 23
9135077 AACCAAAATA
*
9135087 CCTTATTTTTTTCTTCTTTTCCTT
1 CCTTA-TTTTTTCTTCTCTTCCTT
9135111 CCTT-TTTTTTCTTCTGCTTCCTT
1 CCTTATTTTTTCTTCT-CTTCCTT
*
9135134 -CTTATTTCTTCT
1 CCTTATTTTTTCT
9135146 GTTTCTCTAG
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
22 14 0.45
23 13 0.42
24 4 0.13
ACGTcount: A:0.03, C:0.27, G:0.02, T:0.68
Consensus pattern (23 bp):
CCTTATTTTTTCTTCTCTTCCTT
Found at i:9139780 original size:7 final size:7
Alignment explanation
Indices: 9139764--9139793 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
9139754 ATTTTATTTC
9139764 ATTT-TT
1 ATTTCTT
9139770 ATTTCTT
1 ATTTCTT
9139777 ATTTCTT
1 ATTTCTT
9139784 ATTTCTT
1 ATTTCTT
9139791 ATT
1 ATT
9139794 GTATTTATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 4 0.17
7 19 0.83
ACGTcount: A:0.17, C:0.10, G:0.00, T:0.73
Consensus pattern (7 bp):
ATTTCTT
Found at i:9139787 original size:14 final size:13
Alignment explanation
Indices: 9139755--9139793 Score: 55
Period size: 14 Copynumber: 3.1 Consensus size: 13
9139745 CTTGTCTTTA
9139755 TTTTATTTC--AT
1 TTTTATTTCTTAT
9139766 TTTTATTTCTTAT
1 TTTTATTTCTTAT
9139779 TTCTTATTTCTTAT
1 TT-TTATTTCTTAT
9139793 T
1 T
9139794 GTATTTATTT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
11 9 0.36
13 4 0.16
14 12 0.48
ACGTcount: A:0.15, C:0.10, G:0.00, T:0.74
Consensus pattern (13 bp):
TTTTATTTCTTAT
Found at i:9141585 original size:6 final size:6
Alignment explanation
Indices: 9141574--9141608 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
9141564 AGTTTATTTG
* *
9141574 TTTTAT TTTTAT TTTTAT GTTTAT TGTTAT TTTTA
1 TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTA
9141609 GTTGTTTTTA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.17, C:0.00, G:0.06, T:0.77
Consensus pattern (6 bp):
TTTTAT
Found at i:9141598 original size:18 final size:17
Alignment explanation
Indices: 9141575--9141620 Score: 58
Period size: 18 Copynumber: 2.7 Consensus size: 17
9141565 GTTTATTTGT
9141575 TTTATTTTTATTTTTATG
1 TTTATTTTTATTTTTA-G
*
9141593 TTTATTGTTATTTTTAG
1 TTTATTTTTATTTTTAG
*
9141610 -TTGTTTTTATT
1 TTTATTTTTATT
9141621 GTCACTTTCT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
16 9 0.36
17 1 0.04
18 15 0.60
ACGTcount: A:0.15, C:0.00, G:0.09, T:0.76
Consensus pattern (17 bp):
TTTATTTTTATTTTTAG
Found at i:9147603 original size:12 final size:12
Alignment explanation
Indices: 9147586--9147613 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
9147576 CGGGGCAACT
9147586 TGGTCTGCTTCA
1 TGGTCTGCTTCA
9147598 TGGTCTGCTTCA
1 TGGTCTGCTTCA
9147610 TGGT
1 TGGT
9147614 TTGCATGTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.07, C:0.21, G:0.29, T:0.43
Consensus pattern (12 bp):
TGGTCTGCTTCA
Found at i:9160803 original size:20 final size:21
Alignment explanation
Indices: 9160778--9160823 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
9160768 GGGTAAAAGG
9160778 GGAAAAT-CTAAGTTTTTATA
1 GGAAAATACTAAGTTTTTATA
* **
9160798 GGAAAATATTGGGTTTTTATA
1 GGAAAATACTAAGTTTTTATA
9160819 GGAAA
1 GGAAA
9160824 TGTTGGCTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
20 7 0.32
21 15 0.68
ACGTcount: A:0.39, C:0.02, G:0.22, T:0.37
Consensus pattern (21 bp):
GGAAAATACTAAGTTTTTATA
Found at i:9160824 original size:20 final size:21
Alignment explanation
Indices: 9160789--9160836 Score: 71
Period size: 20 Copynumber: 2.3 Consensus size: 21
9160779 GAAAATCTAA
9160789 GTTTTTATAGGAAAATATTGG
1 GTTTTTATAGGAAAATATTGG
*
9160810 GTTTTTATAGG-AAATGTTGG
1 GTTTTTATAGGAAAATATTGG
*
9160830 CTTTTTA
1 GTTTTTA
9160837 CAGGGATAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
20 14 0.56
21 11 0.44
ACGTcount: A:0.27, C:0.02, G:0.23, T:0.48
Consensus pattern (21 bp):
GTTTTTATAGGAAAATATTGG
Found at i:9165337 original size:3 final size:3
Alignment explanation
Indices: 9165316--9165361 Score: 56
Period size: 3 Copynumber: 15.3 Consensus size: 3
9165306 ATTTTTATAA
* * * *
9165316 TAT TAT TAC TAT TAC TAT TAT TAT TAT CAT TAT TAT TAT CAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
9165362 TTTTAAAACT
Statistics
Matches: 35, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.33, C:0.09, G:0.00, T:0.59
Consensus pattern (3 bp):
TAT
Found at i:9166714 original size:25 final size:25
Alignment explanation
Indices: 9166669--9166716 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
9166659 CTTTTAGATT
* *
9166669 TTTTTATTTTTTAAATTTAATATAA
1 TTTTTATTTATTAAATATAATATAA
9166694 TTTTTATATTATTAAA-ATAATAT
1 TTTTTAT-TTATTAAATATAATAT
9166717 GGAATATTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
25 13 0.65
26 7 0.35
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (25 bp):
TTTTTATTTATTAAATATAATATAA
Found at i:9167528 original size:3 final size:3
Alignment explanation
Indices: 9167508--9167547 Score: 53
Period size: 3 Copynumber: 13.0 Consensus size: 3
9167498 TCCACCTCTA
* *
9167508 CTT CTT GCTT CCT CTT CTT CTT CTT CTT CTT CTT TTT CTT
1 CTT CTT -CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
9167548 TTTTCTTTTT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
3 29 0.91
4 3 0.09
ACGTcount: A:0.00, C:0.33, G:0.03, T:0.65
Consensus pattern (3 bp):
CTT
Found at i:9175771 original size:13 final size:13
Alignment explanation
Indices: 9175755--9175784 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
9175745 TCAACCTATG
9175755 TGCCTAACCAATA
1 TGCCTAACCAATA
9175768 TGCCTAACCAATA
1 TGCCTAACCAATA
9175781 TGCC
1 TGCC
9175785 CTCATTGGCA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.33, C:0.33, G:0.10, T:0.23
Consensus pattern (13 bp):
TGCCTAACCAATA
Found at i:9177745 original size:25 final size:25
Alignment explanation
Indices: 9177709--9177764 Score: 76
Period size: 25 Copynumber: 2.2 Consensus size: 25
9177699 GAAGGTCTTC
* *
9177709 CGAGCTATATAACAGAAAGCTCATG
1 CGAGCTAAATAACAGAAAGATCATG
* *
9177734 TGAGCTAAATAACAGGAAGATCATG
1 CGAGCTAAATAACAGAAAGATCATG
9177759 CGAGCT
1 CGAGCT
9177765 GTATATCGGG
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.39, C:0.18, G:0.23, T:0.20
Consensus pattern (25 bp):
CGAGCTAAATAACAGAAAGATCATG
Found at i:9177763 original size:50 final size:49
Alignment explanation
Indices: 9177709--9177814 Score: 115
Period size: 50 Copynumber: 2.1 Consensus size: 49
9177699 GAAGGTCTTC
**
9177709 CGAGCTATATAACAGAAAGCTCATGTGAGCT-AAATAACAGGAAGATCATG
1 CGAGCTATATAACAGAAAGCTCATAAGAGCTGAAAT--CAGGAAGATCATG
* * * * * *
9177759 CGAGCTGTATATCGGGAAGCTCATAAGAGCTGAAATCGGGAAGCTCATG
1 CGAGCTATATAACAGAAAGCTCATAAGAGCTGAAATCAGGAAGATCATG
9177808 CGAGCTA
1 CGAGCTA
9177815 AATATTGGGA
Statistics
Matches: 46, Mismatches: 9, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
49 17 0.37
50 25 0.54
51 4 0.09
ACGTcount: A:0.36, C:0.18, G:0.26, T:0.20
Consensus pattern (49 bp):
CGAGCTATATAACAGAAAGCTCATAAGAGCTGAAATCAGGAAGATCATG
Found at i:9177776 original size:25 final size:24
Alignment explanation
Indices: 9177725--9177829 Score: 95
Period size: 25 Copynumber: 4.2 Consensus size: 24
9177715 ATATAACAGA
* *
9177725 AAGCTCATGTGAGCT-AAATAACAGG
1 AAGCTCATGCGAGCTGAAAT--CGGG
* *
9177750 AAGATCATGCGAGCTGTATATCGGG
1 AAGCTCATGCGAGCTG-AAATCGGG
**
9177775 AAGCTCATAAGAGCTGAAATCGGG
1 AAGCTCATGCGAGCTGAAATCGGG
* *
9177799 AAGCTCATGCGAGCTAAATATTGGG
1 AAGCTCATGCGAGCTGAA-ATCGGG
9177824 AAGCTC
1 AAGCTC
9177830 TTAAAAGCTA
Statistics
Matches: 65, Mismatches: 12, Indels: 6
0.78 0.14 0.07
Matches are distributed among these distances:
24 22 0.34
25 40 0.62
27 3 0.05
ACGTcount: A:0.34, C:0.17, G:0.28, T:0.21
Consensus pattern (24 bp):
AAGCTCATGCGAGCTGAAATCGGG
Found at i:9177801 original size:24 final size:24
Alignment explanation
Indices: 9177760--9177838 Score: 77
Period size: 24 Copynumber: 3.2 Consensus size: 24
9177750 AAGATCATGC
*
9177760 GAGCTGTATATCGGGAAGCTCATAA
1 GAGCTG-AAATCGGGAAGCTCATAA
**
9177785 GAGCTGAAATCGGGAAGCTCATGC
1 GAGCTGAAATCGGGAAGCTCATAA
* * *
9177809 GAGCTAAATATTGGGAAGCTCTTAA
1 GAGCTGAA-ATCGGGAAGCTCATAA
*
9177834 AAGCT
1 GAGCT
9177839 ATGGTGTGTT
Statistics
Matches: 44, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
24 22 0.50
25 22 0.50
ACGTcount: A:0.33, C:0.16, G:0.28, T:0.23
Consensus pattern (24 bp):
GAGCTGAAATCGGGAAGCTCATAA
Found at i:9179000 original size:13 final size:13
Alignment explanation
Indices: 9178982--9179156 Score: 77
Period size: 13 Copynumber: 13.2 Consensus size: 13
9178972 TATTTATATC
9178982 CATATAAACATTT
1 CATATAAACATTT
9178995 CATATAAACATTT
1 CATATAAACATTT
9179008 CATAT-AACTATTT
1 CATATAAAC-ATTT
** *
9179021 CCATATAGCCGA-AT
1 -CATATAAAC-ATTT
9179035 CATATAAACATTT
1 CATATAAACATTT
***
9179048 CATATATTTATTT
1 CATATAAACATTT
* * *
9179061 CCATACAATCAATT
1 -CATATAAACATTT
* * *
9179075 CACATAACCATTC
1 CATATAAACATTT
*
9179088 CATAT-ATCTATTT
1 CATATAAAC-ATTT
*
9179101 CCATATAATCATTT
1 -CATATAAACATTT
* * **
9179115 CGTATATATGTTT
1 CATATAAACATTT
* *
9179128 CCATATAATCAATT
1 -CATATAAACATTT
*
9179142 CATATAACCATTT
1 CATATAAACATTT
9179155 CA
1 CA
9179157 AATATTCATT
Statistics
Matches: 118, Mismatches: 35, Indels: 18
0.69 0.20 0.11
Matches are distributed among these distances:
12 6 0.05
13 76 0.64
14 31 0.26
15 5 0.04
ACGTcount: A:0.38, C:0.20, G:0.02, T:0.39
Consensus pattern (13 bp):
CATATAAACATTT
Found at i:9179026 original size:40 final size:40
Alignment explanation
Indices: 9178971--9179120 Score: 158
Period size: 40 Copynumber: 3.8 Consensus size: 40
9178961 CACTTTTTAC
* * *
9178971 ATATTTATATCCATATAAACATTTCATATAAACATTTCAT
1 ATATCTATTTCCATATAATCATTTCATATAAACATTTCAT
* ** *
9179011 ATAACTATTTCCATATAGCCGA-ATCATATAAACATTTCAT
1 ATATCTATTTCCATATAATC-ATTTCATATAAACATTTCAT
* * * * * *
9179051 ATATTTATTTCCATACAATCAATTCACATAACCATTCCAT
1 ATATCTATTTCCATATAATCATTTCATATAAACATTTCAT
*
9179091 ATATCTATTTCCATATAATCATTTCGTATA
1 ATATCTATTTCCATATAATCATTTCATATA
9179121 TATGTTTCCA
Statistics
Matches: 88, Mismatches: 20, Indels: 4
0.79 0.18 0.04
Matches are distributed among these distances:
39 1 0.01
40 86 0.98
41 1 0.01
ACGTcount: A:0.39, C:0.19, G:0.02, T:0.40
Consensus pattern (40 bp):
ATATCTATTTCCATATAATCATTTCATATAAACATTTCAT
Found at i:9179104 original size:14 final size:14
Alignment explanation
Indices: 9179085--9179134 Score: 50
Period size: 14 Copynumber: 3.6 Consensus size: 14
9179075 CACATAACCA
9179085 TTCCATATATCTAT
1 TTCCATATATCTAT
9179099 TTCCATATAATC-AT
1 TTCCATAT-ATCTAT
* * *
9179113 TT-CGTATATATGT
1 TTCCATATATCTAT
9179126 TTCCATATA
1 TTCCATATA
9179135 ATCAATTCAT
Statistics
Matches: 29, Mismatches: 4, Indels: 6
0.74 0.10 0.15
Matches are distributed among these distances:
12 2 0.07
13 7 0.24
14 17 0.59
15 3 0.10
ACGTcount: A:0.30, C:0.18, G:0.04, T:0.48
Consensus pattern (14 bp):
TTCCATATATCTAT
Found at i:9179155 original size:27 final size:27
Alignment explanation
Indices: 9178982--9179155 Score: 81
Period size: 27 Copynumber: 6.5 Consensus size: 27
9178972 TATTTATATC
* * *
9178982 CATATAAACATTT-CATATAAACATTT
1 CATATAACCATTTCCATATAATCAATT
* **
9179008 CATATAACTATTTCCATATAGCCGAA-T
1 CATATAACCATTTCCATATAATC-AATT
* * * *
9179035 CATATAAACATTT-CATATATTTATTT
1 CATATAACCATTTCCATATAATCAATT
* * * * *
9179061 CCATACAATCAATT-CACATAA-CCATT
1 -CATATAACCATTTCCATATAATCAATT
* * *
9179087 CCATATATCTATTTCCATATAATCATTT
1 -CATATAACCATTTCCATATAATCAATT
* **
9179115 CGTATATA-TGTTTCCATATAATCAATT
1 CATATA-ACCATTTCCATATAATCAATT
9179142 CATATAACCATTTC
1 CATATAACCATTTC
9179156 AAATATTCAT
Statistics
Matches: 106, Mismatches: 34, Indels: 15
0.68 0.22 0.10
Matches are distributed among these distances:
25 1 0.01
26 30 0.28
27 71 0.67
28 4 0.04
ACGTcount: A:0.38, C:0.20, G:0.02, T:0.40
Consensus pattern (27 bp):
CATATAACCATTTCCATATAATCAATT
Found at i:9179328 original size:13 final size:13
Alignment explanation
Indices: 9179312--9179458 Score: 82
Period size: 13 Copynumber: 11.1 Consensus size: 13
9179302 TATAGCCAAA
*
9179312 TCATATAAACATT
1 TCATATAATCATT
* *
9179325 TCATATATTTATT
1 TCATATAATCATT
* *
9179338 TCCATACAATCAAT
1 T-CATATAATCATT
*
9179352 TCATATAACCATT
1 TCATATAATCATT
*
9179365 CCATAT-ATCTATT
1 TCATATAATC-ATT
*
9179378 TCCATATAATCAAT
1 T-CATATAATCATT
*
9179392 TCATATAACCATT
1 TCATATAATCATT
* * *
9179405 TCGTGTATAT-GTT
1 TCATATA-ATCATT
* *
9179418 TCCATATAATAAAT
1 T-CATATAATCATT
*
9179432 TCATATAACCATT
1 TCATATAATCATT
* *
9179445 TCAAATATTCATT
1 TCATATAATCATT
9179458 T
1 T
9179459 TTCCACCCAA
Statistics
Matches: 97, Mismatches: 30, Indels: 14
0.69 0.21 0.10
Matches are distributed among these distances:
12 2 0.02
13 68 0.70
14 24 0.25
15 3 0.03
ACGTcount: A:0.37, C:0.18, G:0.02, T:0.42
Consensus pattern (13 bp):
TCATATAATCATT
Found at i:9179338 original size:40 final size:40
Alignment explanation
Indices: 9179294--9179458 Score: 188
Period size: 40 Copynumber: 4.1 Consensus size: 40
9179284 CCCATATAGC
** *
9179294 TATTTCCATATAGCCAAATCATATAAACATTTCATATATT
1 TATTTCCATATAATCAAATCATATAACCATTTCATATATT
* * * *
9179334 TATTTCCATACAATCAATTCATATAACCATTCCATATATC
1 TATTTCCATATAATCAAATCATATAACCATTTCATATATT
* * * *
9179374 TATTTCCATATAATCAATTCATATAACCATTTCGTGTATA
1 TATTTCCATATAATCAAATCATATAACCATTTCATATATT
* *
9179414 TGTTTCCATATAAT-AAATTCATATAACCATTTCAAATATT
1 TATTTCCATATAATCAAA-TCATATAACCATTTCATATATT
*
9179454 CATTT
1 TATTT
9179459 TTCCACCCAA
Statistics
Matches: 104, Mismatches: 20, Indels: 2
0.83 0.16 0.02
Matches are distributed among these distances:
39 2 0.02
40 102 0.98
ACGTcount: A:0.38, C:0.19, G:0.02, T:0.41
Consensus pattern (40 bp):
TATTTCCATATAATCAAATCATATAACCATTTCATATATT
Found at i:9179405 original size:27 final size:28
Alignment explanation
Indices: 9179285--9179406 Score: 74
Period size: 27 Copynumber: 4.5 Consensus size: 28
9179275 TAAACTATTC
* * ** *
9179285 CCATATAGCTATTTCCATATAGCCAAAT
1 CCATATAACCATTTCCATATAATCAATT
* * * *
9179313 -CATATAAACATTT-CATATATTTATTT
1 CCATATAACCATTTCCATATAATCAATT
* * * *
9179339 CCATACAATCAATT-CATATAA-CCATT
1 CCATATAACCATTTCCATATAATCAATT
* *
9179365 CCATATATCTATTTCCATATAATCAATT
1 CCATATAACCATTTCCATATAATCAATT
9179393 -CATATAACCATTTC
1 CCATATAACCATTTC
9179407 GTGTATATGT
Statistics
Matches: 68, Mismatches: 23, Indels: 7
0.69 0.23 0.07
Matches are distributed among these distances:
26 19 0.28
27 45 0.66
28 4 0.06
ACGTcount: A:0.38, C:0.22, G:0.02, T:0.39
Consensus pattern (28 bp):
CCATATAACCATTTCCATATAATCAATT
Found at i:9179420 original size:80 final size:80
Alignment explanation
Indices: 9179285--9179444 Score: 221
Period size: 80 Copynumber: 2.0 Consensus size: 80
9179275 TAAACTATTC
* * *
9179285 CCATATAGCTATTTCCATATAGCCAAATCATATAAACATTTCATATATTTATTTCCATACAATCA
1 CCATATAGCTATTTCCATATAACCAAATCATATAAACATTTCATATATATATTTCCATACAATAA
9179350 ATTCATATAACCATT
66 ATTCATATAACCATT
* * * * * * * *
9179365 CCATATATCTATTTCCATATAATCAATTCATATAACCATTTCGTGTATATGTTTCCATATAATAA
1 CCATATAGCTATTTCCATATAACCAAATCATATAAACATTTCATATATATATTTCCATACAATAA
9179430 ATTCATATAACCATT
66 ATTCATATAACCATT
9179445 TCAAATATTC
Statistics
Matches: 69, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
80 69 1.00
ACGTcount: A:0.38, C:0.20, G:0.03, T:0.39
Consensus pattern (80 bp):
CCATATAGCTATTTCCATATAACCAAATCATATAAACATTTCATATATATATTTCCATACAATAA
ATTCATATAACCATT
Found at i:9181900 original size:12 final size:13
Alignment explanation
Indices: 9181878--9181909 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
9181868 AGCTCAAATG
9181878 GAGATGAAATGAA
1 GAGATGAAATGAA
9181891 GAGA-GAAATGAA
1 GAGATGAAATGAA
9181903 GA-ATGAA
1 GAGATGAA
9181910 TGGGATAATG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 1 0.06
12 13 0.72
13 4 0.22
ACGTcount: A:0.56, C:0.00, G:0.31, T:0.12
Consensus pattern (13 bp):
GAGATGAAATGAA
Found at i:9184368 original size:18 final size:18
Alignment explanation
Indices: 9184315--9184373 Score: 55
Period size: 20 Copynumber: 3.1 Consensus size: 18
9184305 AATAAATTAA
*
9184315 TTATATCATTCTTATAATTT
1 TTATA-CATT-TTAAAATTT
* *
9184335 TTACAAATATTATAAAATTT
1 TTATACAT-TT-TAAAATTT
9184355 TTATACATTTTAAAATTT
1 TTATACATTTTAAAATTT
9184373 T
1 T
9184374 ACCATTTTTA
Statistics
Matches: 32, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
18 9 0.28
19 5 0.16
20 18 0.56
ACGTcount: A:0.39, C:0.07, G:0.00, T:0.54
Consensus pattern (18 bp):
TTATACATTTTAAAATTT
Found at i:9186086 original size:19 final size:18
Alignment explanation
Indices: 9186055--9186097 Score: 68
Period size: 19 Copynumber: 2.3 Consensus size: 18
9186045 TTTTTTTGAG
9186055 AAAAAAATCGAATACAAA
1 AAAAAAATCGAATACAAA
*
9186073 AAAAAAGATTGAATACAAA
1 AAAAAA-ATCGAATACAAA
9186092 AAAAAA
1 AAAAAA
9186098 TCAAAGATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 6 0.26
19 17 0.74
ACGTcount: A:0.74, C:0.07, G:0.07, T:0.12
Consensus pattern (18 bp):
AAAAAAATCGAATACAAA
Found at i:9187261 original size:13 final size:12
Alignment explanation
Indices: 9187238--9187270 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
9187228 TTTGATGTTA
9187238 TTTATTATTTAT
1 TTTATTATTTAT
9187250 TTTATATATTTA-
1 TTTAT-TATTTAT
9187262 TTTATTATT
1 TTTATTATT
9187271 CTTTCACTTC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
11 4 0.20
12 10 0.50
13 6 0.30
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (12 bp):
TTTATTATTTAT
Found at i:9203025 original size:18 final size:18
Alignment explanation
Indices: 9203002--9203036 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
9202992 CCCAGCCGTC
9203002 TTCTCATTTCTTTCTCAT
1 TTCTCATTTCTTTCTCAT
9203020 TTCTCATTTCTTTCTCA
1 TTCTCATTTCTTTCTCA
9203037 CGTCTGAAAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.11, C:0.29, G:0.00, T:0.60
Consensus pattern (18 bp):
TTCTCATTTCTTTCTCAT
Found at i:9206507 original size:59 final size:58
Alignment explanation
Indices: 9206327--9206610 Score: 150
Period size: 59 Copynumber: 4.7 Consensus size: 58
9206317 ATGATAAATT
* ** * *
9206327 ATATATTTTTATTAACTTATATTTAATAATAATTATGTTAAATTATATTTTATAGTATT
1 ATATATTTTAATTAAAATATATTTAATATTAATTAT-TTAAATTATATTTTATAGTATC
* * * * * * * *
9206386 ATATATTATGATTTTAGAA-A-A-TTCATATAAGAATATTTAATATTAAGAATTTTATTA-AATC
1 ATATATT-TTA-ATTAAAATATATTTAATATTA-ATTATTTAA-ATT-A-TATTTTA-TAGTATC
9206447 ATATATTTTAATTAAAATATATTTAATATTAATTATTTCAAATTATATTTTATAGTATC
1 ATATATTTTAATTAAAATATATTTAATATTAATTATTT-AAATTATATTTTATAGTATC
* * ** * * * *
9206506 ATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAGAATT-T-TATTATA-AAT
1 ATATATT-TTAATT-A--AAA-T-ATAT-TTAATATTAATTATTTA-AATTATATTTTATAGTAT
*
9206568 T
58 C
*
9206569 ATATATTTTAATTAAAATATATTTAATAATAATTATGTTAAA
1 ATATATTTTAATTAAAATATATTTAATATTAATTAT-TTAAA
9206611 ATATGATTAA
Statistics
Matches: 167, Mismatches: 37, Indels: 45
0.67 0.15 0.18
Matches are distributed among these distances:
56 12 0.07
57 6 0.04
58 13 0.08
59 39 0.23
60 11 0.07
61 30 0.18
62 15 0.09
63 12 0.07
64 7 0.04
65 6 0.04
66 16 0.10
ACGTcount: A:0.44, C:0.02, G:0.05, T:0.49
Consensus pattern (58 bp):
ATATATTTTAATTAAAATATATTTAATATTAATTATTTAAATTATATTTTATAGTATC
Found at i:9206534 original size:120 final size:122
Alignment explanation
Indices: 9206320--9206610 Score: 462
Period size: 120 Copynumber: 2.4 Consensus size: 122
9206310 TATTATGATG
* **
9206320 ATAAATTATATATTTTTATTAACTTATATTTAATAATAATTATGTTAAATTATATTTTATAGTAT
1 ATAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTAAATTATATTTTATAGTAT
* * *
9206385 TATATATTATGATTTTAGAAAATTCATATAAGAATATTTAATATTAAGAATTTTA-T
66 CATATATTATGATTTGAGAAAATTCATATAAGAATATTGAATATTAAGAATTTTATT
* *
9206441 -TAAATCATATATTTTAATTAAAATATATTTAATATTAATTAT-TTCAAATTATATTTTATAGTA
1 ATAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTT-AAATTATATTTTATAGTA
* *
9206504 TCATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAGAATTTTATT
65 TCATATATTATGATTTGAGAAAATTCATATAAGAATATTGAATATTAAGAATTTTATT
9206562 ATAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTAAA
1 ATAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTAAA
9206611 ATATGATTAA
Statistics
Matches: 154, Mismatches: 12, Indels: 7
0.89 0.07 0.04
Matches are distributed among these distances:
119 2 0.01
120 106 0.69
121 1 0.01
122 43 0.28
123 2 0.01
ACGTcount: A:0.44, C:0.02, G:0.05, T:0.49
Consensus pattern (122 bp):
ATAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTAAATTATATTTTATAGTAT
CATATATTATGATTTGAGAAAATTCATATAAGAATATTGAATATTAAGAATTTTATT
Found at i:9206589 original size:18 final size:19
Alignment explanation
Indices: 9206554--9206590 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
9206544 ATTATTAAGA
9206554 ATTTTATTATAAATTATAT
1 ATTTTATTATAAATTATAT
9206573 ATTTTAATTA-AAA-TATAT
1 ATTTT-ATTATAAATTATAT
9206591 TTAATAATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
18 5 0.29
19 8 0.47
20 4 0.24
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (19 bp):
ATTTTATTATAAATTATAT
Found at i:9206847 original size:16 final size:16
Alignment explanation
Indices: 9206826--9206861 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
9206816 GATTAGCTAT
*
9206826 TACACCTCTAATTCAA
1 TACACCTCTAATCCAA
9206842 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
9206858 TACA
1 TACA
9206862 GCGAACCAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.39, C:0.33, G:0.00, T:0.28
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:9209555 original size:21 final size:24
Alignment explanation
Indices: 9209526--9209582 Score: 68
Period size: 21 Copynumber: 2.5 Consensus size: 24
9209516 TAATATATAC
9209526 ATATACATATTTTCATA-ATTTAT
1 ATATACATATTTTCATACATTTAT
* *
9209549 -T-TACATA-TATCATACTTTTAT
1 ATATACATATTTTCATACATTTAT
9209570 ATATACATATTTT
1 ATATACATATTTT
9209583 GTAAATACAT
Statistics
Matches: 27, Mismatches: 3, Indels: 7
0.73 0.08 0.19
Matches are distributed among these distances:
20 6 0.22
21 11 0.41
22 2 0.07
23 6 0.22
24 2 0.07
ACGTcount: A:0.37, C:0.11, G:0.00, T:0.53
Consensus pattern (24 bp):
ATATACATATTTTCATACATTTAT
Found at i:9209573 original size:15 final size:15
Alignment explanation
Indices: 9209553--9209594 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
9209543 ATTTATTTAC
9209553 ATATAT-CATACTTTT
1 ATATATACATA-TTTT
9209568 ATATATACATATTTT
1 ATATATACATATTTT
* *
9209583 GTAAATACATAT
1 ATATATACATAT
9209595 ACATATATAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
15 20 0.83
16 4 0.17
ACGTcount: A:0.40, C:0.10, G:0.02, T:0.48
Consensus pattern (15 bp):
ATATATACATATTTT
Found at i:9209573 original size:17 final size:15
Alignment explanation
Indices: 9209523--9209582 Score: 54
Period size: 17 Copynumber: 4.1 Consensus size: 15
9209513 TTTTAATATA
9209523 TACATATACATATTT
1 TACATATACATATTT
**
9209538 T-CATA-ATTTA-TT
1 TACATATACATATTT
9209550 TACATATATCATACTTT
1 TACATATA-CATA-TTT
*
9209567 TATATATACATATTT
1 TACATATACATATTT
9209582 T
1 T
9209583 GTAAATACAT
Statistics
Matches: 35, Mismatches: 5, Indels: 10
0.70 0.10 0.20
Matches are distributed among these distances:
12 3 0.09
13 7 0.20
14 5 0.14
15 7 0.20
16 4 0.11
17 9 0.26
ACGTcount: A:0.37, C:0.12, G:0.00, T:0.52
Consensus pattern (15 bp):
TACATATACATATTT
Found at i:9213844 original size:6 final size:6
Alignment explanation
Indices: 9213833--9213869 Score: 58
Period size: 6 Copynumber: 6.2 Consensus size: 6
9213823 ATCAGAGGAG
9213833 TATTTT TATTTT TATTTTT TATTTT TATTTT T-TTTT T
1 TATTTT TATTTT TA-TTTT TATTTT TATTTT TATTTT T
9213870 GTTGAAAAGA
Statistics
Matches: 30, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
5 5 0.17
6 19 0.63
7 6 0.20
ACGTcount: A:0.14, C:0.00, G:0.00, T:0.86
Consensus pattern (6 bp):
TATTTT
Found at i:9213853 original size:13 final size:13
Alignment explanation
Indices: 9213835--9213869 Score: 63
Period size: 13 Copynumber: 2.8 Consensus size: 13
9213825 CAGAGGAGTA
9213835 TTTTTATTTTTAT
1 TTTTTATTTTTAT
9213848 TTTTTATTTTTAT
1 TTTTTATTTTTAT
9213861 TTTTT-TTTT
1 TTTTTATTTT
9213870 GTTGAAAAGA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
12 4 0.18
13 18 0.82
ACGTcount: A:0.11, C:0.00, G:0.00, T:0.89
Consensus pattern (13 bp):
TTTTTATTTTTAT
Found at i:9213857 original size:19 final size:18
Alignment explanation
Indices: 9213833--9213869 Score: 65
Period size: 19 Copynumber: 2.0 Consensus size: 18
9213823 ATCAGAGGAG
9213833 TATTTTTATTTTTATTTTT
1 TATTTTTATTTTT-TTTTT
9213852 TATTTTTATTTTTTTTTT
1 TATTTTTATTTTTTTTTT
9213870 GTTGAAAAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 5 0.28
19 13 0.72
ACGTcount: A:0.14, C:0.00, G:0.00, T:0.86
Consensus pattern (18 bp):
TATTTTTATTTTTTTTTT
Found at i:9214326 original size:7 final size:6
Alignment explanation
Indices: 9214310--9214360 Score: 50
Period size: 6 Copynumber: 8.2 Consensus size: 6
9214300 GTTTTCCTGC
* *
9214310 AAAAAT AAAAAT GAAAAT -AAAAT AAAATAGT AAAAAT AAATAAT AATAAT
1 AAAAAT AAAAAT AAAAAT AAAAAT AAAA-A-T AAAAAT AAA-AAT AAAAAT
9214360 A
1 A
9214361 GGAATTTTTT
Statistics
Matches: 39, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
5 5 0.13
6 22 0.56
7 7 0.18
8 5 0.13
ACGTcount: A:0.75, C:0.00, G:0.04, T:0.22
Consensus pattern (6 bp):
AAAAAT
Found at i:9219753 original size:45 final size:44
Alignment explanation
Indices: 9219703--9219806 Score: 120
Period size: 44 Copynumber: 2.3 Consensus size: 44
9219693 TAACATTTTC
* ** * *
9219703 TATTTTTGAAATTTTGATCTATTATTTTAAATTTT-TAGAATTTA
1 TATTTTTGAAATTTTAAAAT-TTATTATAAATTTTCTAGAATGTA
* *
9219747 TAATTTTTAAAAATTTAAAATTTATTATAAATTTTCTAGAATGTA
1 T-ATTTTTGAAATTTTAAAATTTATTATAAATTTTCTAGAATGTA
9219792 TATTTTTGAAATTTT
1 TATTTTTGAAATTTT
9219807 CTAGAATTTA
Statistics
Matches: 49, Mismatches: 9, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
44 26 0.53
45 23 0.47
ACGTcount: A:0.37, C:0.02, G:0.06, T:0.56
Consensus pattern (44 bp):
TATTTTTGAAATTTTAAAATTTATTATAAATTTTCTAGAATGTA
Found at i:9219761 original size:17 final size:16
Alignment explanation
Indices: 9219728--9219780 Score: 54
Period size: 17 Copynumber: 3.2 Consensus size: 16
9219718 GATCTATTAT
*
9219728 TTTAAATTTTT-AGAA
1 TTTAAATTTTTAAAAA
9219743 TTTATAATTTTTAAAAA
1 TTTA-AATTTTTAAAAA
*
9219760 TTTAAAATTTATTATAAA
1 TTT-AAATTT-TTAAAAA
9219778 TTT
1 TTT
9219781 TCTAGAATGT
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
15 4 0.12
16 7 0.22
17 11 0.34
18 10 0.31
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (16 bp):
TTTAAATTTTTAAAAA
Found at i:9226383 original size:47 final size:47
Alignment explanation
Indices: 9226286--9226384 Score: 146
Period size: 47 Copynumber: 2.1 Consensus size: 47
9226276 CCTATAACTG
*
9226286 TTTGTTGGGGAGACCTTGGATACACTCGGCCTTCATCACTGCATCGAAA
1 TTTGTTGGGGAGACCTTGGATACA--CAGCCTTCATCACTGCATCGAAA
*
9226335 TTTGTTGGGGAGACCTTGGATATCA-AGCCTTCATCACTTCATCGAAA
1 TTTGTTGGGGAGACCTTGGATA-CACAGCCTTCATCACTGCATCGAAA
9226382 TTT
1 TTT
9226385 AAAGTTAGTG
Statistics
Matches: 47, Mismatches: 2, Indels: 4
0.89 0.04 0.08
Matches are distributed among these distances:
47 23 0.49
49 22 0.47
50 2 0.04
ACGTcount: A:0.23, C:0.22, G:0.22, T:0.32
Consensus pattern (47 bp):
TTTGTTGGGGAGACCTTGGATACACAGCCTTCATCACTGCATCGAAA
Found at i:9231994 original size:45 final size:45
Alignment explanation
Indices: 9231929--9232412 Score: 538
Period size: 45 Copynumber: 10.8 Consensus size: 45
9231919 AACAGATTGG
* * * * * *
9231929 TGAAAATAGCAAATCCTATCTTCCTGAGGTTGCAGTGGAGTGGAT
1 TGAAGATAGCAAGTCTTATCTCCCTGAAGTTGCAGTGGAGTGGAC
* **
9231974 TGAAGATAGCAAGTCTTATCTCCCTGAAGTTGCAGCGGAGCAGAC
1 TGAAGATAGCAAGTCTTATCTCCCTGAAGTTGCAGTGGAGTGGAC
* * * * *
9232019 TGAAGATAGCAAATCCTATCTCCTTGAAGTTACAGTGGAGTGGAT
1 TGAAGATAGCAAGTCTTATCTCCCTGAAGTTGCAGTGGAGTGGAC
* * * **
9232064 TGAAGATAACAAGTTTTATCTCCCTGAAGTTGCAGCGGAGCAGAC
1 TGAAGATAGCAAGTCTTATCTCCCTGAAGTTGCAGTGGAGTGGAC
* * *
9232109 TGAAGATAGCAAATCCTATCTCCCTGAAGTTGCAGTGGAGTGGAT
1 TGAAGATAGCAAGTCTTATCTCCCTGAAGTTGCAGTGGAGTGGAC
** ** **
9232154 TGAAGATAGCAAGTCTTATCTCCCTGAAGTTATAGCAGAGCAGAC
1 TGAAGATAGCAAGTCTTATCTCCCTGAAGTTGCAGTGGAGTGGAC
* * * *
9232199 TGAAGATAGCAAATCCTATCTCCCTAAAGTTGCAGTGGAGTGGAT
1 TGAAGATAGCAAGTCTTATCTCCCTGAAGTTGCAGTGGAGTGGAC
* * ** **
9232244 TGAAGATAGCAAGTCTTATCTTCCTGAAGTTACAGCAGAGCAGAC
1 TGAAGATAGCAAGTCTTATCTCCCTGAAGTTGCAGTGGAGTGGAC
* *
9232289 TGAAGATAGCAAGTCTTATCTCCTTGAAGTTGCAGTGGAGCAGG-C
1 TGAAGATAGCAAGTCTTATCTCCCTGAAGTTGCAGTGGAG-TGGAC
* * * *
9232334 TGAAGATAGCAAATCCTATCTCCCTGAGGTTGCAGTGGAGTGGAT
1 TGAAGATAGCAAGTCTTATCTCCCTGAAGTTGCAGTGGAGTGGAC
* *
9232379 TGAAGATAGAAAGTCTTATCTCTCTGAAGTTGCA
1 TGAAGATAGCAAGTCTTATCTCCCTGAAGTTGCA
9232413 AAGAGCATAT
Statistics
Matches: 355, Mismatches: 82, Indels: 4
0.80 0.19 0.01
Matches are distributed among these distances:
44 2 0.01
45 352 0.99
46 1 0.00
ACGTcount: A:0.30, C:0.18, G:0.25, T:0.26
Consensus pattern (45 bp):
TGAAGATAGCAAGTCTTATCTCCCTGAAGTTGCAGTGGAGTGGAC
Found at i:9232087 original size:90 final size:90
Alignment explanation
Indices: 9231929--9232412 Score: 670
Period size: 90 Copynumber: 5.4 Consensus size: 90
9231919 AACAGATTGG
* *
9231929 TGAAAATAGCAAATCCTATCTTCC-TGAGGTTGCAGTGGAGTGGATTGAAGATAGCAAGTCTTAT
1 TGAAGATAGCAAATCCTATC-TCCTTGAAGTTGCAGTGGAGTGGATTGAAGATAGCAAGTCTTAT
9231993 CTCCCTGAAGTTGCAGCGGAGCAGAC
65 CTCCCTGAAGTTGCAGCGGAGCAGAC
* * *
9232019 TGAAGATAGCAAATCCTATCTCCTTGAAGTTACAGTGGAGTGGATTGAAGATAACAAGTTTTATC
1 TGAAGATAGCAAATCCTATCTCCTTGAAGTTGCAGTGGAGTGGATTGAAGATAGCAAGTCTTATC
9232084 TCCCTGAAGTTGCAGCGGAGCAGAC
66 TCCCTGAAGTTGCAGCGGAGCAGAC
*
9232109 TGAAGATAGCAAATCCTATCTCCCTGAAGTTGCAGTGGAGTGGATTGAAGATAGCAAGTCTTATC
1 TGAAGATAGCAAATCCTATCTCCTTGAAGTTGCAGTGGAGTGGATTGAAGATAGCAAGTCTTATC
** *
9232174 TCCCTGAAGTTATAGCAGAGCAGAC
66 TCCCTGAAGTTGCAGCGGAGCAGAC
* *
9232199 TGAAGATAGCAAATCCTATCTCCCTAAAGTTGCAGTGGAGTGGATTGAAGATAGCAAGTCTTATC
1 TGAAGATAGCAAATCCTATCTCCTTGAAGTTGCAGTGGAGTGGATTGAAGATAGCAAGTCTTATC
* * *
9232264 TTCCTGAAGTTACAGCAGAGCAGAC
66 TCCCTGAAGTTGCAGCGGAGCAGAC
* * * * * *
9232289 TGAAGATAGCAAGTCTTATCTCCTTGAAGTTGCAGTGGAGCAGG-CTGAAGATAGCAAATCCTAT
1 TGAAGATAGCAAATCCTATCTCCTTGAAGTTGCAGTGGAG-TGGATTGAAGATAGCAAGTCTTAT
* * ** *
9232353 CTCCCTGAGGTTGCAGTGGAGTGGAT
65 CTCCCTGAAGTTGCAGCGGAGCAGAC
*
9232379 TGAAGATAG-AAAGTCTTATCT-CTCTGAAGTTGCA
1 TGAAGATAGCAAA-TCCTATCTCCT-TGAAGTTGCA
9232413 AAGAGCATAT
Statistics
Matches: 358, Mismatches: 32, Indels: 8
0.90 0.08 0.02
Matches are distributed among these distances:
89 7 0.02
90 349 0.97
91 2 0.01
ACGTcount: A:0.30, C:0.18, G:0.25, T:0.26
Consensus pattern (90 bp):
TGAAGATAGCAAATCCTATCTCCTTGAAGTTGCAGTGGAGTGGATTGAAGATAGCAAGTCTTATC
TCCCTGAAGTTGCAGCGGAGCAGAC
Found at i:9232203 original size:135 final size:135
Alignment explanation
Indices: 9231929--9232412 Score: 637
Period size: 135 Copynumber: 3.6 Consensus size: 135
9231919 AACAGATTGG
* * * *
9231929 TGAAAATAGCAAATCCTATCTTCCTGAGGTTGCAGTGGAGTGGATTGAAGATAGCAAGTCTTATC
1 TGAAGATAGCAAATCCTATCTCCCTGAAGTTGCAGTGGAGTGGATTGAAGATAGCAAATCTTATC
* *
9231994 TCCCTGAAGTTGCAGCGGAGCAGACTGAAGATAGCAAATCCTATCTCCTTGAAGTTACAGTGGAG
66 TCCCTGAAGTTGCAGCGGAGCAGACTGAAGATAGCAAGTCTTATCTCCTTGAAGTTACAGTGGAG
** *
9232059 TGGAT
131 CAGAC
* * ** * ** * *
9232064 TGAAGATAACAAGTTTTATCTCCCTGAAGTTGCAGCGGAGCAGACTGAAGATAGCAAATCCTATC
1 TGAAGATAGCAAATCCTATCTCCCTGAAGTTGCAGTGGAGTGGATTGAAGATAGCAAATCTTATC
* ** * * * **
9232129 TCCCTGAAGTTGCAGTGGAGTGGATTGAAGATAGCAAGTCTTATCTCCCTGAAGTTATAGCAGAG
66 TCCCTGAAGTTGCAGCGGAGCAGACTGAAGATAGCAAGTCTTATCTCCTTGAAGTTACAGTGGAG
9232194 CAGAC
131 CAGAC
* *
9232199 TGAAGATAGCAAATCCTATCTCCCTAAAGTTGCAGTGGAGTGGATTGAAGATAGCAAGTCTTATC
1 TGAAGATAGCAAATCCTATCTCCCTGAAGTTGCAGTGGAGTGGATTGAAGATAGCAAATCTTATC
* * * *
9232264 TTCCTGAAGTTACAGCAGAGCAGACTGAAGATAGCAAGTCTTATCTCCTTGAAGTTGCAGTGGAG
66 TCCCTGAAGTTGCAGCGGAGCAGACTGAAGATAGCAAGTCTTATCTCCTTGAAGTTACAGTGGAG
*
9232329 CAGGC
131 CAGAC
*
9232334 TGAAGATAGCAAATCCTATCTCCCTGAGGTTGCAGTGGAGTGGATTGAAGATAG-AAAGTCTTAT
1 TGAAGATAGCAAATCCTATCTCCCTGAAGTTGCAGTGGAGTGGATTGAAGATAGCAAA-TCTTAT
*
9232398 CTCTCTGAAGTTGCA
65 CTCCCTGAAGTTGCA
9232413 AAGAGCATAT
Statistics
Matches: 292, Mismatches: 56, Indels: 2
0.83 0.16 0.01
Matches are distributed among these distances:
134 2 0.01
135 290 0.99
ACGTcount: A:0.30, C:0.18, G:0.25, T:0.26
Consensus pattern (135 bp):
TGAAGATAGCAAATCCTATCTCCCTGAAGTTGCAGTGGAGTGGATTGAAGATAGCAAATCTTATC
TCCCTGAAGTTGCAGCGGAGCAGACTGAAGATAGCAAGTCTTATCTCCTTGAAGTTACAGTGGAG
CAGAC
Found at i:9232492 original size:44 final size:44
Alignment explanation
Indices: 9232436--9232543 Score: 171
Period size: 44 Copynumber: 2.5 Consensus size: 44
9232426 ATTTAGTCAT
*
9232436 ATTTCCCTGAAGTTGCAATGGAGCAGACTAAATAAACGAATCTG
1 ATTTCCCTGAAGTTGCAATGGAGCAGACTAAATAAACCAATCTG
* * *
9232480 ATTTCTCTGAAGTTGCAGTGGAGCAGACTGAATAAACCAATCTG
1 ATTTCCCTGAAGTTGCAATGGAGCAGACTAAATAAACCAATCTG
*
9232524 ATTTCCCTGAAGTGGCAATG
1 ATTTCCCTGAAGTTGCAATG
9232544 AAATAAATTG
Statistics
Matches: 57, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
44 57 1.00
ACGTcount: A:0.32, C:0.19, G:0.22, T:0.27
Consensus pattern (44 bp):
ATTTCCCTGAAGTTGCAATGGAGCAGACTAAATAAACCAATCTG
Found at i:9234405 original size:27 final size:27
Alignment explanation
Indices: 9234366--9234431 Score: 82
Period size: 27 Copynumber: 2.4 Consensus size: 27
9234356 ACGTATTTTA
9234366 ATATATACATATA-CATA-TTTTCATAAT
1 ATATATACATATATCATACTTTT-AT-AT
* *
9234393 TTATTTACATATATCATACTTTTATAT
1 ATATATACATATATCATACTTTTATAT
9234420 ATATATACATAT
1 ATATATACATAT
9234432 TTTGTAAATA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
27 23 0.70
28 6 0.18
29 4 0.12
ACGTcount: A:0.41, C:0.11, G:0.00, T:0.48
Consensus pattern (27 bp):
ATATATACATATATCATACTTTTATAT
Found at i:9234416 original size:21 final size:19
Alignment explanation
Indices: 9234387--9234452 Score: 60
Period size: 21 Copynumber: 3.3 Consensus size: 19
9234377 TACATATTTT
* *
9234387 CATAATTTATTTACATATA
1 CATATTTTATATACATATA
*
9234406 TCATACTTTTATATATATATA
1 -CATA-TTTTATATACATATA
*
9234427 CATATTTTGTAAATACATATA
1 CATA-TTT-TATATACATATA
9234448 CATAT
1 CATAT
9234453 ATAATTCATA
Statistics
Matches: 38, Mismatches: 6, Indels: 4
0.79 0.12 0.08
Matches are distributed among these distances:
20 12 0.32
21 26 0.68
ACGTcount: A:0.41, C:0.11, G:0.02, T:0.47
Consensus pattern (19 bp):
CATATTTTATATACATATA
Found at i:9236348 original size:63 final size:62
Alignment explanation
Indices: 9236241--9236424 Score: 190
Period size: 63 Copynumber: 2.9 Consensus size: 62
9236231 TTTTTTGTTC
* * * * * * *
9236241 CAACCCAA-TTTATTTGATACAAGCATCACAGTACGCACACTCATTCCTCGCATCAACACCTT
1 CAACACAAGTTTATTTTACACAAGCACCACAGCACGCACAATCATTCCT-GCATCAACACATT
* * * * * *
9236303 CAGCTCCAGTTTATTTTACACAAGCACCATAGCACACACAATCATTCACTGCATTAACACATT
1 CAACACAAGTTTATTTTACACAAGCACCACAGCACGCACAATCATTC-CTGCATCAACACATT
* * *
9236366 CAACACAAGTTTATTTTACACAAGCACCACAACACGCGCAATCATTCCATGTATCAACA
1 CAACACAAGTTTATTTTACACAAGCACCACAGCACGCACAATCATTCC-TGCATCAACA
9236425 TCTTCTCCAA
Statistics
Matches: 98, Mismatches: 21, Indels: 5
0.79 0.17 0.04
Matches are distributed among these distances:
62 6 0.06
63 90 0.92
64 2 0.02
ACGTcount: A:0.35, C:0.32, G:0.08, T:0.25
Consensus pattern (62 bp):
CAACACAAGTTTATTTTACACAAGCACCACAGCACGCACAATCATTCCTGCATCAACACATT
Found at i:9245749 original size:8 final size:8
Alignment explanation
Indices: 9245736--9245762 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
9245726 TATAGATTTT
9245736 TTTTAGAA
1 TTTTAGAA
9245744 TTTTAGAA
1 TTTTAGAA
9245752 TTTTAGAA
1 TTTTAGAA
9245760 TTT
1 TTT
9245763 ATATATTTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.33, C:0.00, G:0.11, T:0.56
Consensus pattern (8 bp):
TTTTAGAA
Found at i:9245953 original size:26 final size:26
Alignment explanation
Indices: 9245923--9245974 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
9245913 AATATTAAGA
* *
9245923 TAAATATTATTTATCTTAATGATAAT
1 TAAATAATATTTATATTAATGATAAT
*
9245949 TAAATAATATTTATATTTATGATAAT
1 TAAATAATATTTATATTAATGATAAT
9245975 ACTATTTATA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.44, C:0.02, G:0.04, T:0.50
Consensus pattern (26 bp):
TAAATAATATTTATATTAATGATAAT
Found at i:9245994 original size:21 final size:21
Alignment explanation
Indices: 9245951--9245995 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
9245941 ATGATAATTA
** *
9245951 AATAATATTTATATTTATGAT
1 AATAATATTTATACGTATAAT
*
9245972 AATACTATTTATACGTATAAT
1 AATAATATTTATACGTATAAT
9245993 AAT
1 AAT
9245996 TTTATATATT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.44, C:0.04, G:0.04, T:0.47
Consensus pattern (21 bp):
AATAATATTTATACGTATAAT
Found at i:9247593 original size:10 final size:10
Alignment explanation
Indices: 9247578--9247708 Score: 64
Period size: 9 Copynumber: 13.6 Consensus size: 10
9247568 GTCACATATG
9247578 ATAAAAAATT
1 ATAAAAAATT
9247588 AT-AAAAA--
1 ATAAAAAATT
*
9247595 ATAAAAAATC
1 ATAAAAAATT
**
9247605 A-ATAAAAGCT
1 ATA-AAAAATT
9247615 AT-AAAAATT
1 ATAAAAAATT
* *
9247624 AT-TAAACTT
1 ATAAAAAATT
9247633 -TAAAAAA-T
1 ATAAAAAATT
*
9247641 ATTAAAAATT
1 ATAAAAAATT
* *
9247651 AGAAAAAAAT
1 ATAAAAAATT
9247661 ATATAAAAATT
1 ATA-AAAAATT
*
9247672 GTAAAAAAATT
1 AT-AAAAAATT
* *
9247683 GT-AAAAATC
1 ATAAAAAATT
9247692 ATAAAAAATTT
1 ATAAAAAA-TT
9247703 ATAAAA
1 ATAAAA
9247709 TGCATCAAAA
Statistics
Matches: 90, Mismatches: 19, Indels: 23
0.68 0.14 0.17
Matches are distributed among these distances:
7 2 0.02
8 7 0.08
9 34 0.38
10 23 0.26
11 23 0.26
12 1 0.01
ACGTcount: A:0.66, C:0.03, G:0.03, T:0.27
Consensus pattern (10 bp):
ATAAAAAATT
Found at i:9247611 original size:17 final size:17
Alignment explanation
Indices: 9247578--9247611 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
9247568 GTCACATATG
*
9247578 ATAAAAAATTATAAAAA
1 ATAAAAAATAATAAAAA
9247595 ATAAAAAATCAATAAAA
1 ATAAAAAAT-AATAAAA
9247612 GCTATAAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.76, C:0.03, G:0.00, T:0.21
Consensus pattern (17 bp):
ATAAAAAATAATAAAAA
Found at i:9247657 original size:20 final size:21
Alignment explanation
Indices: 9247634--9247708 Score: 77
Period size: 20 Copynumber: 3.7 Consensus size: 21
9247624 ATTAAACTTT
9247634 AAAAAATAT-TAAAAATTAG-A
1 AAAAAATATATAAAAATT-GTA
9247654 AAAAAATATATAAAAATTGTA
1 AAAAAATATATAAAAATTGTA
* **
9247675 AAAAAAT-TGTAAAAATCAT-
1 AAAAAATATATAAAAATTGTA
*
9247694 AAAAAATTTATAAAA
1 AAAAAATATATAAAA
9247709 TGCATCAAAA
Statistics
Matches: 48, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
19 7 0.15
20 25 0.52
21 16 0.33
ACGTcount: A:0.68, C:0.01, G:0.04, T:0.27
Consensus pattern (21 bp):
AAAAAATATATAAAAATTGTA
Found at i:9247683 original size:11 final size:11
Alignment explanation
Indices: 9247644--9247689 Score: 51
Period size: 11 Copynumber: 4.3 Consensus size: 11
9247634 AAAAAATATT
9247644 AAAAATTAG-AA
1 AAAAATT-GTAA
* *
9247655 AAAAA-TATAT
1 AAAAATTGTAA
9247665 AAAAATTGTAA
1 AAAAATTGTAA
9247676 AAAAATTGTAA
1 AAAAATTGTAA
9247687 AAA
1 AAA
9247690 TCATAAAAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
10 7 0.24
11 22 0.76
ACGTcount: A:0.70, C:0.00, G:0.07, T:0.24
Consensus pattern (11 bp):
AAAAATTGTAA
Found at i:9247718 original size:20 final size:19
Alignment explanation
Indices: 9247675--9247719 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 19
9247665 AAAAATTGTA
9247675 AAAAAATTGTAAAAATCAT
1 AAAAAATTGTAAAAATCAT
9247694 AAAAAATT-TATAAAATGCAT
1 AAAAAATTGTA-AAAAT-CAT
*
9247714 CAAAAA
1 AAAAAA
9247720 GACCCTTTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
18 2 0.09
19 13 0.57
20 8 0.35
ACGTcount: A:0.64, C:0.07, G:0.04, T:0.24
Consensus pattern (19 bp):
AAAAAATTGTAAAAATCAT
Found at i:9247844 original size:15 final size:16
Alignment explanation
Indices: 9247824--9247854 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
9247814 ACATGTGGCA
9247824 AAAAAT-CATAAAAAT
1 AAAAATCCATAAAAAT
9247839 AAAAATCCATAAAAAT
1 AAAAATCCATAAAAAT
9247855 TATAGAAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.40
16 9 0.60
ACGTcount: A:0.71, C:0.10, G:0.00, T:0.19
Consensus pattern (16 bp):
AAAAATCCATAAAAAT
Found at i:9252612 original size:37 final size:35
Alignment explanation
Indices: 9252519--9252612 Score: 91
Period size: 37 Copynumber: 2.5 Consensus size: 35
9252509 GTCTCCAAAT
* * *
9252519 TCACATTTCAGTTCAATTTCACTTTTTCACTTTCAA
1 TCACAATTCAATTCAA-TTCACTTTTCCACTTTCAA
*
9252555 TCACAATTCAATTCAAAATTCACTTTTCCATTTTTCAA
1 TCACAATTCAATTC--AATTCACTTTTCCA-CTTTCAA
9252593 GTCA-ATATTCAATTCAATTC
1 -TCACA-ATTCAATTCAATTC
9252613 CACACATATA
Statistics
Matches: 49, Mismatches: 4, Indels: 9
0.79 0.06 0.15
Matches are distributed among these distances:
36 12 0.24
37 16 0.33
38 9 0.18
39 12 0.24
ACGTcount: A:0.31, C:0.23, G:0.02, T:0.44
Consensus pattern (35 bp):
TCACAATTCAATTCAATTCACTTTTCCACTTTCAA
Found at i:9253680 original size:22 final size:22
Alignment explanation
Indices: 9253650--9253692 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
9253640 ACACCAAAAC
*
9253650 AGGCTTTTAGCGGCGCTTTTTT
1 AGGCCTTTAGCGGCGCTTTTTT
9253672 AGGCCTTTAGCGGCGCTTTTT
1 AGGCCTTTAGCGGCGCTTTTT
9253693 AGCGCCGTAG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.09, C:0.21, G:0.28, T:0.42
Consensus pattern (22 bp):
AGGCCTTTAGCGGCGCTTTTTT
Found at i:9253927 original size:43 final size:43
Alignment explanation
Indices: 9253880--9254108 Score: 207
Period size: 43 Copynumber: 5.3 Consensus size: 43
9253870 CTTCTCTCTC
* * *
9253880 AAACGCCGCTAAAGATCCTTATCTTTAGCGGCGCTTCT-CCCAA
1 AAACGCCACTAAAGACCCTTATCTTTAGCGGCGCTT-TGACCAA
* ** **
9253923 AAACGCAACTAAAGA---TTAGGGTCTTTAGCGGCGCTTTCCCCTC
1 AAACGCCACTAAAGACCCTTA---TCTTTAGCGGCGCTTTGACCAA
* *
9253966 AAACGCCGC-AATAGACCCTGATCTTTAGCGGCGCTTTGACCAA
1 AAACGCCACTAA-AGACCCTTATCTTTAGCGGCGCTTTGACCAA
** * * ** *
9254009 AAACGCCACTAAAGACTATGATCTTTAGTGGCGCTTTTTCCAC
1 AAACGCCACTAAAGACCCTTATCTTTAGCGGCGCTTTGACCAA
* *
9254052 AAACGCCGCTAAAGCCCCTTATCTTTAGCGGCGCTTTGACCAA
1 AAACGCCACTAAAGACCCTTATCTTTAGCGGCGCTTTGACCAA
9254095 AAACGCCACTAAAG
1 AAACGCCACTAAAG
9254109 GCCAACACCT
Statistics
Matches: 149, Mismatches: 28, Indels: 18
0.76 0.14 0.09
Matches are distributed among these distances:
40 3 0.02
42 3 0.02
43 139 0.93
44 2 0.01
46 2 0.01
ACGTcount: A:0.28, C:0.30, G:0.18, T:0.24
Consensus pattern (43 bp):
AAACGCCACTAAAGACCCTTATCTTTAGCGGCGCTTTGACCAA
Found at i:9253967 original size:86 final size:86
Alignment explanation
Indices: 9253840--9254108 Score: 337
Period size: 86 Copynumber: 3.1 Consensus size: 86
9253830 TCCACTAAAG
* * * * * *
9253840 CGCCGCTAAAGACAAGGGTCTTTAACGGTGC-TTCTCTCTCAAACGCCGCTAAAGATCCTTATCT
1 CGCCACTAAAGACTAGGGTCTTTAGCGGCGCTTTC-CCCTCAAACGCCGCTAAAGACCCTTATCT
*
9253904 TTAGCGGCGCTTCT-CCCAAAAA
65 TTAGCGGCGCTT-TGACCAAAAA
* * *
9253926 CGCAACTAAAGATTAGGGTCTTTAGCGGCGCTTTCCCCTCAAACGCCGC-AATAGACCCTGATCT
1 CGCCACTAAAGACTAGGGTCTTTAGCGGCGCTTTCCCCTCAAACGCCGCTAA-AGACCCTTATCT
9253990 TTAGCGGCGCTTTGACCAAAAA
65 TTAGCGGCGCTTTGACCAAAAA
* * * ** * *
9254012 CGCCACTAAAGACTATGATCTTTAGTGGCGCTTTTTCCACAAACGCCGCTAAAGCCCCTTATCTT
1 CGCCACTAAAGACTAGGGTCTTTAGCGGCGCTTTCCCCTCAAACGCCGCTAAAGACCCTTATCTT
9254077 TAGCGGCGCTTTGACCAAAAA
66 TAGCGGCGCTTTGACCAAAAA
9254098 CGCCACTAAAG
1 CGCCACTAAAG
9254109 GCCAACACCT
Statistics
Matches: 159, Mismatches: 20, Indels: 8
0.85 0.11 0.04
Matches are distributed among these distances:
85 3 0.02
86 151 0.95
87 5 0.03
ACGTcount: A:0.27, C:0.30, G:0.19, T:0.25
Consensus pattern (86 bp):
CGCCACTAAAGACTAGGGTCTTTAGCGGCGCTTTCCCCTCAAACGCCGCTAAAGACCCTTATCTT
TAGCGGCGCTTTGACCAAAAA
Found at i:9254471 original size:21 final size:21
Alignment explanation
Indices: 9254445--9254536 Score: 103
Period size: 21 Copynumber: 4.4 Consensus size: 21
9254435 TTTGACGCTG
9254445 CTCTGCTTCCCTCGCTGCAGC
1 CTCTGCTTCCCTCGCTGCAGC
9254466 CTCTGCTTCCCTCGCTGCAGC
1 CTCTGCTTCCCTCGCTGCAGC
* * * * *
9254487 CTATACTTCTCTTGCTGCCGC
1 CTCTGCTTCCCTCGCTGCAGC
* * *
9254508 CTCTGCTTCTCTTGCTGCCGC
1 CTCTGCTTCCCTCGCTGCAGC
*
9254529 ATCTGCTT
1 CTCTGCTT
9254537 TAAGCTGCTG
Statistics
Matches: 63, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 63 1.00
ACGTcount: A:0.05, C:0.42, G:0.17, T:0.35
Consensus pattern (21 bp):
CTCTGCTTCCCTCGCTGCAGC
Found at i:9254591 original size:66 final size:66
Alignment explanation
Indices: 9254507--9254653 Score: 190
Period size: 66 Copynumber: 2.2 Consensus size: 66
9254497 CTTGCTGCCG
* * *
9254507 CCTCTGCTTCTCTTGCTGCCGCATCTGCTTTAAGCTGCT-GCTGGAGTTCTTCATA-CTTTCGTT
1 CCTCAGCTTCTCTCGCTGCCGCATCTGCTTTAAGCTG-TAGCTAGAGTTCTTCATATCTTT-GTT
9254570 GAA
64 GAA
* * * * *
9254573 CCTCAGCTTCTCTCGCTGCTGGATCTGCTTTCAGTTGTAGCTAGAGTTCTTCATATCTTTTTTGA
1 CCTCAGCTTCTCTCGCTGCCGCATCTGCTTTAAGCTGTAGCTAGAGTTCTTCATATCTTTGTTGA
9254638 A
66 A
9254639 CCTCAGCTTCTCTCG
1 CCTCAGCTTCTCTCG
9254654 ATGTTGCCTC
Statistics
Matches: 71, Mismatches: 8, Indels: 4
0.86 0.10 0.05
Matches are distributed among these distances:
65 1 0.01
66 66 0.93
67 4 0.06
ACGTcount: A:0.13, C:0.29, G:0.18, T:0.40
Consensus pattern (66 bp):
CCTCAGCTTCTCTCGCTGCCGCATCTGCTTTAAGCTGTAGCTAGAGTTCTTCATATCTTTGTTGA
A
Found at i:9254669 original size:66 final size:66
Alignment explanation
Indices: 9254507--9254676 Score: 182
Period size: 66 Copynumber: 2.6 Consensus size: 66
9254497 CTTGCTGCCG
* * * * * * *
9254507 CCTCTGCTTCTCTTGCTGCCGCATCTGCTTTAAGCTGCT-GCTGGAGTTCTTCATACTTTCGTTG
1 CCTCAGCTTCTCTCGATGCTGCATCCGCTTTAAGTTG-TAGCTAGAGTTCTTCATACTTTCGTTG
9254571 AA
65 AA
* * * * *
9254573 CCTCAGCTTCTCTCGCTGCTGGATCTGCTTTCAGTTGTAGCTAGAGTTCTTCATATCTTT-TTTG
1 CCTCAGCTTCTCTCGATGCTGCATCCGCTTTAAGTTGTAGCTAGAGTTCTTCATA-CTTTCGTTG
9254637 AA
65 AA
* *
9254639 CCTCAGCTTCTCTCGATGTTGCCTCCGCTTTAAGTTGT
1 CCTCAGCTTCTCTCGATGCTGCATCCGCTTTAAGTTGT
9254677 GTAATTTGCT
Statistics
Matches: 88, Mismatches: 14, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
65 1 0.01
66 83 0.94
67 4 0.05
ACGTcount: A:0.13, C:0.28, G:0.19, T:0.41
Consensus pattern (66 bp):
CCTCAGCTTCTCTCGATGCTGCATCCGCTTTAAGTTGTAGCTAGAGTTCTTCATACTTTCGTTGA
A
Found at i:9260126 original size:16 final size:16
Alignment explanation
Indices: 9260105--9260221 Score: 67
Period size: 16 Copynumber: 7.8 Consensus size: 16
9260095 ACTAAGCTAC
9260105 GTAAGTTATGTATTAT
1 GTAAGTTATGTATTAT
*
9260121 GTAAGTTATTTATTAT
1 GTAAGTTATGTATTAT
9260137 G-AA---A---ATTAT
1 GTAAGTTATGTATTAT
*
9260146 GTAAGTTGTGTATTA-
1 GTAAGTTATGTATTAT
* *
9260161 GTCAAATTATG--CTAT
1 GT-AAGTTATGTATTAT
9260176 GTAAGTTATGTATGTCAT
1 GTAAGTTATGTAT-T-AT
* *
9260194 ATAAGTTATGTAAGT-T
1 GTAAGTTATGT-ATTAT
9260210 GTAAGTTATGTA
1 GTAAGTTATGTA
9260222 AGTTATTTAT
Statistics
Matches: 77, Mismatches: 10, Indels: 29
0.66 0.09 0.25
Matches are distributed among these distances:
9 6 0.08
10 2 0.03
12 1 0.01
14 9 0.12
15 7 0.09
16 37 0.48
17 1 0.01
18 13 0.17
19 1 0.01
ACGTcount: A:0.33, C:0.03, G:0.19, T:0.45
Consensus pattern (16 bp):
GTAAGTTATGTATTAT
Found at i:9260167 original size:25 final size:25
Alignment explanation
Indices: 9260116--9260188 Score: 74
Period size: 25 Copynumber: 2.7 Consensus size: 25
9260106 TAAGTTATGT
*
9260116 ATTATGTAAGTTATTTATTATGAAA
1 ATTATGTAAGTTATGTATTATGAAA
* *
9260141 ATTATGTAAGTTGTGTATTAGTCAAA
1 ATTATGTAAGTTATGTATTA-TGAAA
9260167 TTATGCTATGTAAGTTATGTAT
1 --AT--TATGTAAGTTATGTAT
9260189 GTCATATAAG
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
25 18 0.46
26 4 0.10
28 2 0.05
30 15 0.38
ACGTcount: A:0.34, C:0.03, G:0.16, T:0.47
Consensus pattern (25 bp):
ATTATGTAAGTTATGTATTATGAAA
Found at i:9260185 original size:9 final size:9
Alignment explanation
Indices: 9260173--9260888 Score: 83
Period size: 9 Copynumber: 81.7 Consensus size: 9
9260163 CAAATTATGC
9260173 TATGTAAGT
1 TATGTAAGT
*
9260182 TATGTATGT
1 TATGTAAGT
* *
9260191 CATATAAGT
1 TATGTAAGT
9260200 TATGTAAG-
1 TATGTAAGT
9260208 T-TGTAAGT
1 TATGTAAGT
9260216 TATGTAAGT
1 TATGTAAGT
*
9260225 TAT-TTA-T
1 TATGTAAGT
* *
9260232 TATGAAAAT
1 TATGTAAGT
*
9260241 TAAGTAAGT
1 TATGTAAGT
*
9260250 TATGTAATT
1 TATGTAAGT
*
9260259 TACG-AA-T
1 TATGTAAGT
* **
9260266 AAT-TAAAA
1 TATGTAAGT
*
9260274 AATTGTAAGT
1 TA-TGTAAGT
*
9260284 TATGTAATT
1 TATGTAAGT
*
9260293 TACG-AA-T
1 TATGTAAGT
* **
9260300 AAT-TAAAA
1 TATGTAAGT
*
9260308 AATTGTAAGT
1 TA-TGTAAGT
9260318 TATGTAAG-
1 TATGTAAGT
9260326 T-TGTAAGT
1 TATGTAAGT
9260334 TATGTAAG-
1 TATGTAAGT
*
9260342 T-TGTAAAT
1 TATGTAAGT
9260350 TATGT-A-T
1 TATGTAAGT
*
9260357 AATGTTAA-T
1 TATG-TAAGT
**
9260366 TAACTAAGT
1 TATGTAAGT
*
9260375 TATGTAATT
1 TATGTAAGT
*
9260384 TATGTATAATAT
1 TATG--TAA-GT
9260396 TAAT-TAA-T
1 T-ATGTAAGT
9260404 TAAT-TAAGT
1 T-ATGTAAGT
*
9260413 TATGTAATT
1 TATGTAAGT
9260422 TATGT-A--
1 TATGTAAGT
*
9260428 TAT-TAACT
1 TATGTAAGT
*
9260436 AAT-TAAGT
1 TATGTAAGT
*
9260444 TATGTAATT
1 TATGTAAGT
9260453 TATG-AA-T
1 TATGTAAGT
* **
9260460 AAT-TAAAAA
1 TATGT-AAGT
*
9260469 AATGTAAGT
1 TATGTAAGT
9260478 TATGTAAG-
1 TATGTAAGT
9260486 T-TGTAAG-
1 TATGTAAGT
9260493 T-TGTAAGT
1 TATGTAAGT
*
9260501 TATGTATA-A
1 TATGTA-AGT
9260510 TAT-TAA-T
1 TATGTAAGT
**
9260517 TAACTAAGT
1 TATGTAAGT
*
9260526 TATGTAATT
1 TATGTAAGT
*
9260535 TATGTATCATAT
1 TATGTA--A-GT
9260547 TAATGTAAGT
1 T-ATGTAAGT
**
9260557 TATGTAACA
1 TATGTAAGT
*
9260566 TATGTATA-A
1 TATGTA-AGT
9260575 TAT-TAA-T
1 TATGTAAGT
**
9260582 TAACTAAGT
1 TATGTAAGT
*
9260591 TATGTAATT
1 TATGTAAGT
*
9260600 TATGTATCATAT
1 TATGTA--A-GT
9260612 TAATGTAAGT
1 T-ATGTAAGT
*
9260622 TATGTAACT
1 TATGTAAGT
9260631 TATGT-A--
1 TATGTAAGT
9260637 TAT-TAA-T
1 TATGTAAGT
9260644 TAAT-TAAGT
1 T-ATGTAAGT
*
9260653 TATGTAATT
1 TATGTAAGT
*
9260662 TATGTATAATAT
1 TATG--TAA-GT
9260674 TAAT-TAA-T
1 T-ATGTAAGT
9260682 TAAT-TAAGT
1 T-ATGTAAGT
*
9260691 TATGTAATT
1 TATGTAAGT
*
9260700 TATGTATAATAT
1 TATG--TAA-GT
9260712 TAATGTAAGT
1 T-ATGTAAGT
*
9260722 TATGTATA-A
1 TATGTA-AGT
9260731 TAT-TAA-T
1 TATGTAAGT
**
9260738 TAACTAAGT
1 TATGTAAGT
*
9260747 TATGTAATT
1 TATGTAAGT
*
9260756 TATGTATCATAT
1 TATGTA--A-GT
9260768 TAATGTAAGT
1 T-ATGTAAGT
**
9260778 TATGTAACA
1 TATGTAAGT
*
9260787 TATGTATA-A
1 TATGTA-AGT
9260796 TAT-TAA-T
1 TATGTAAGT
**
9260803 TAACTAAGT
1 TATGTAAGT
*
9260812 TATGTAATT
1 TATGTAAGT
*
9260821 TATGTATCATAT
1 TATGTA--A-GT
9260833 TAATGTAAGT
1 T-ATGTAAGT
*
9260843 TATGTAACT
1 TATGTAAGT
9260852 TATGT-A--
1 TATGTAAGT
9260858 TAT-TAA-T
1 TATGTAAGT
9260865 TAAT-TAAGT
1 T-ATGTAAGT
*
9260874 TATGTAATT
1 TATGTAAGT
9260883 TATGTA
1 TATGTA
9260889 TAATATTAAT
Statistics
Matches: 534, Mismatches: 90, Indels: 166
0.68 0.11 0.21
Matches are distributed among these distances:
5 3 0.01
6 12 0.02
7 63 0.12
8 93 0.17
9 273 0.51
10 29 0.05
11 20 0.04
12 14 0.03
13 27 0.05
ACGTcount: A:0.40, C:0.02, G:0.12, T:0.45
Consensus pattern (9 bp):
TATGTAAGT
Found at i:9260282 original size:34 final size:34
Alignment explanation
Indices: 9260244--9260324 Score: 162
Period size: 34 Copynumber: 2.4 Consensus size: 34
9260234 TGAAAATTAA
9260244 GTAAGTTATGTAATTTACGAATAATTAAAAAATT
1 GTAAGTTATGTAATTTACGAATAATTAAAAAATT
9260278 GTAAGTTATGTAATTTACGAATAATTAAAAAATT
1 GTAAGTTATGTAATTTACGAATAATTAAAAAATT
9260312 GTAAGTTATGTAA
1 GTAAGTTATGTAA
9260325 GTTGTAAGTT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 47 1.00
ACGTcount: A:0.46, C:0.02, G:0.14, T:0.38
Consensus pattern (34 bp):
GTAAGTTATGTAATTTACGAATAATTAAAAAATT
Found at i:9260331 original size:16 final size:16
Alignment explanation
Indices: 9260310--9260355 Score: 83
Period size: 16 Copynumber: 2.9 Consensus size: 16
9260300 AATTAAAAAA
9260310 TTGTAAGTTATGTAAG
1 TTGTAAGTTATGTAAG
9260326 TTGTAAGTTATGTAAG
1 TTGTAAGTTATGTAAG
*
9260342 TTGTAAATTATGTA
1 TTGTAAGTTATGTA
9260356 TAATGTTAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
16 29 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.46
Consensus pattern (16 bp):
TTGTAAGTTATGTAAG
Found at i:9260559 original size:22 final size:22
Alignment explanation
Indices: 9260527--9260737 Score: 107
Period size: 22 Copynumber: 10.1 Consensus size: 22
9260517 TAACTAAGTT
9260527 ATGTAATTTATGTATCATATTA
1 ATGTAATTTATGTATCATATTA
* *
9260549 ATGTAAGTTATGTAACATATGT-
1 ATGTAATTTATGTATCATAT-TA
*
9260571 A--TAATATTAAT-TAAC-TAAGTT-
1 ATGTAAT-TT-ATGTATCAT-A-TTA
9260592 ATGTAATTTATGTATCATATTA
1 ATGTAATTTATGTATCATATTA
* * *
9260614 ATGTAAGTTATGTAACTTATGTA
1 ATGTAATTTATGTATCATAT-TA
* *
9260637 TAT-TAATTAAT-TA--A-GTT-
1 -ATGTAATTTATGTATCATATTA
*
9260654 ATGTAATTTATGTATAATATTA
1 ATGTAATTTATGTATCATATTA
* *
9260676 AT-TAATTAAT-TA--A-GTT-
1 ATGTAATTTATGTATCATATTA
*
9260692 ATGTAATTTATGTATAATATTA
1 ATGTAATTTATGTATCATATTA
* *
9260714 ATGTAAGTTATGTATAATATTA
1 ATGTAATTTATGTATCATATTA
9260736 AT
1 AT
9260738 TAACTAAGTT
Statistics
Matches: 147, Mismatches: 18, Indels: 48
0.69 0.08 0.23
Matches are distributed among these distances:
16 4 0.03
17 16 0.11
18 6 0.04
19 1 0.01
20 8 0.05
21 24 0.16
22 72 0.49
23 14 0.10
24 2 0.01
ACGTcount: A:0.40, C:0.02, G:0.10, T:0.47
Consensus pattern (22 bp):
ATGTAATTTATGTATCATATTA
Found at i:9260563 original size:65 final size:64
Alignment explanation
Indices: 9260494--9261076 Score: 470
Period size: 65 Copynumber: 9.2 Consensus size: 64
9260484 AGTTGTAAGT
* *
9260494 TGTAAGTTATGTATAATATTAATTAACTAAGTTATGTAATTTATGTATCATATTAATGTAAGTTA
1 TGTAAGTTATGTATAATATTAATTAAGTAAGTTATGTAATTTATGTATAATATTAAT-TAAGTTA
** * *
9260559 TGTAACATATGTATAATATTAATTAACTAAGTTATGTAATTTATGTATCATATTAATGTAAGTTA
1 TGTAAGTTATGTATAATATTAATTAAGTAAGTTATGTAATTTATGTATAATATTAAT-TAAGTTA
* *
9260624 TGTAACTTATG--T-ATATTAATTAATTAAGTTATGTAATTTATGTATAATATTAATTAA-TTAA
1 TGTAAGTTATGTATAATATTAATTAAGTAAGTTATGTAATTTATGTATAATATTAATTAAGTT-A
* * * * *
9260685 T-TAAGTTATGTAATTTATGTATAATATTAATGTAAGTTATGT-A--TA-ATATTA-ATTAACTA
1 TGTAAGTTATGT-A--TA-ATATTA-ATTAA-GTAAGTTATGTAATTTATGTATAATATTAATTA
9260744 AGTTA
60 AGTTA
* * **
9260749 TGTAATTTATGTATCATATTAA-T--GTAAGTTATGTAACATATGTATAATATTAATTAACTAAG
1 TGTAAGTTATGTATAATATTAATTAAGTAAGTTATGTAATTTATGTATAATATTAA-T---TAAG
9260811 TTA
62 TTA
* * * *
9260814 TGTAATTTATGTATCATATTAA-T--GTAAGTTATGTAACTTATGTATATTAATTAATTAAGTTA
1 TGTAAGTTATGTATAATATTAATTAAGTAAGTTATGTAATTTATGTATAAT-ATTAATTAAGTTA
* * *
9260876 TGTAATTTATGTATAATATTAA-T--GTAAGTTATGT-A--TA---ATAACATAAAATTAAGTTA
1 TGTAAGTTATGTATAATATTAATTAAGTAAGTTATGTAATTTATGTATAATAT-TAATTAAGTTA
* * *
9260932 TGTAATTTATGTATAATATTAATTAATTAATTAAGTTATGTAATTTATG--TAAT-TTATGTATA
1 TGTAAGTTATGTAT-A-A-T-ATTAATTAAGTAAGTTATGTAATTTATGTATAATATTA-AT-TA
*
9260994 ATATTAA
60 A-GTT-A
* *
9261001 TGTAAGTTATGTATAATCTTAATTAATTAAGTTATGTAATTTATGTATAATATTAATTAA-TTAA
1 TGTAAGTTATGTATAATATTAATTAAGTAAGTTATGTAATTTATGTATAATATTAATTAAGTT-A
9261065 T-TAAGTTATGTA
1 TGTAAGTTATGTA
9261077 ATTTATGTAT
Statistics
Matches: 443, Mismatches: 33, Indels: 86
0.79 0.06 0.15
Matches are distributed among these distances:
55 2 0.00
56 38 0.09
57 2 0.00
58 1 0.00
59 6 0.01
60 20 0.05
61 16 0.04
62 81 0.18
63 22 0.05
64 17 0.04
65 171 0.39
66 15 0.03
67 16 0.04
68 12 0.03
69 24 0.05
ACGTcount: A:0.40, C:0.02, G:0.10, T:0.47
Consensus pattern (64 bp):
TGTAAGTTATGTATAATATTAATTAAGTAAGTTATGTAATTTATGTATAATATTAATTAAGTTA
Found at i:9260746 original size:25 final size:22
Alignment explanation
Indices: 9260699--9260752 Score: 72
Period size: 22 Copynumber: 2.3 Consensus size: 22
9260689 GTTATGTAAT
*
9260699 TTATGTATAATATTAATGTAAG
1 TTATGTATAATATTAATCTAAG
9260721 TTATGTATAATATTAATTAACTAAG
1 TTATGTATAATATTAA-T--CTAAG
9260746 TTATGTA
1 TTATGTA
9260753 ATTTATGTAT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
22 16 0.57
23 1 0.04
25 11 0.39
ACGTcount: A:0.41, C:0.02, G:0.11, T:0.46
Consensus pattern (22 bp):
TTATGTATAATATTAATCTAAG
Found at i:9260758 original size:56 final size:56
Alignment explanation
Indices: 9260676--9261057 Score: 446
Period size: 56 Copynumber: 6.7 Consensus size: 56
9260666 TATAATATTA
9260676 ATTAATTAATTAAGTTATGTAATTTATGTATAATATTAATGTAAGTTATGTATAAT
1 ATTAATTAATTAAGTTATGTAATTTATGTATAATATTAATGTAAGTTATGTATAAT
* *
9260732 ATTAATTAACTAAGTTATGTAATTTATGTATCATATTAATGTAAGTTATGTAACATATGTATAAT
1 ATTAATTAATTAAGTTATGTAATTTATGTATAATATTAATGT-A---A-GT----TATGTATAAT
* *
9260797 ATTAATTAACTAAGTTATGTAATTTATGTATCATATTAATGTAAGTTATGTAACTTATGTAT
1 ATTAATTAATTAAGTTATGTAATTTATGTATAATATTAATGTAAGTTATGT-A--TA---AT
9260859 ATTAATTAATTAAGTTATGTAATTTATGTATAATATTAATGTAAGTTATGTATAAT
1 ATTAATTAATTAAGTTATGTAATTTATGTATAATATTAATGTAAGTTATGTATAAT
*
9260915 A--ACATAAAATTAAGTTATGTAATTTATGTATAATATTAAT-TAA-TTA---AT--T
1 ATTA-AT-TAATTAAGTTATGTAATTTATGTATAATATTAATGTAAGTTATGTATAAT
* *
9260964 A--AGTT-ATGTAATTTATGTAATTTATGTATAATATTAATGTAAGTTATGTATAAT
1 ATTAATTAAT-TAAGTTATGTAATTTATGTATAATATTAATGTAAGTTATGTATAAT
*
9261018 CTTAATTAATTAAGTTATGTAATTTATGTATAATATTAAT
1 ATTAATTAATTAAGTTATGTAATTTATGTATAATATTAAT
9261058 TAATTAATTA
Statistics
Matches: 287, Mismatches: 11, Indels: 56
0.81 0.03 0.16
Matches are distributed among these distances:
46 2 0.01
47 29 0.10
48 4 0.01
49 6 0.02
51 2 0.01
52 2 0.01
54 5 0.02
55 5 0.02
56 113 0.39
57 4 0.01
59 4 0.01
60 3 0.01
61 4 0.01
62 51 0.18
64 1 0.00
65 52 0.18
ACGTcount: A:0.41, C:0.02, G:0.10, T:0.47
Consensus pattern (56 bp):
ATTAATTAATTAAGTTATGTAATTTATGTATAATATTAATGTAAGTTATGTATAAT
Found at i:9260762 original size:221 final size:216
Alignment explanation
Indices: 9260335--9261192 Score: 976
Period size: 221 Copynumber: 3.9 Consensus size: 216
9260325 GTTGTAAGTT
* *
9260335 ATGTAAG-T-TGTAA-ATTATGTATAATGTTAATTAACTAAGTTATGTAATTTATGTATAATATT
1 ATGTAAGTTATGTAACA-TATGTATAATATTAATTAACTAAGTTATGTAATTTATGTAT-ACATT
* * *
9260397 AATTAATTAATTAAGTTATGTAATTTATGTATATTAACTAATTAAGTTATGTAATTTATGAATAA
64 AATTAATT-AGTAAGTTATGTAACTTATGTATATTAATTAATTAAGTTATGTAATTTATGAATAA
*
9260462 TTAAAAAAATGTAAGTTATGTAAGTTGT-AAGT-TGTAAGTTATGTATAATATTAATTAACTAAG
128 TTAAAAAAATGTAAGTTATGTAAGTTGTAAATTATGTAAGTTATGTATAATATTAATTAACTAAG
9260525 TTATGTAATTTATGTATCATATTA
193 TTATGTAATTTATGTATCATATTA
9260549 ATGTAAGTTATGTAACATATGTATAATATTAATTAACTAAGTTATGTAATTTATGTAT-CA-T-A
1 ATGTAAGTTATGTAACATATGTATAATATTAATTAACTAAGTTATGTAATTTATGTATACATTAA
*
9260611 TTAA-T-GTAAGTTATGTAACTTATGTATATTAATTAATTAAGTTATGTAATTTATGTATAATAT
66 TTAATTAGTAAGTTATGTAACTTATGTATATTAATTAATTAAGTTATGTAATTTATGAAT-A-AT
* *
9260674 TAATTAATTAAT-TAAGTTATGTAATTTATGTATAATATTAATGTAAGTTATGTATAATATTAAT
129 TAA--AA-AAATGTAAGTTATGTAA-GT-TG--TAA-ATT-ATGTAAGTTATGTATAATATTAAT
9260738 TAACTAAGTTATGTAATTTATGTATCATATTA
185 TAACTAAGTTATGTAATTTATGTATCATATTA
9260770 ATGTAAGTTATGTAACATATGTATAATATTAATTAACTAAGTTATGTAATTTATGTAT-CA-T-A
1 ATGTAAGTTATGTAACATATGTATAATATTAATTAACTAAGTTATGTAATTTATGTATACATTAA
*
9260832 TTAA-T-GTAAGTTATGTAACTTATGTATATTAATTAATTAAGTTATGTAATTTATGTATAA-T-
66 TTAATTAGTAAGTTATGTAACTTATGTATATTAATTAATTAAGTTATGTAATTTATGAATAATTA
** * * * *
9260893 -ATTAATGTAAGTTATGTATAATAACATAAAATTAAGTTATGTAATTTATGTATAATATTAATTA
131 AAAAAATGTAAGTTATGTA-AGT----T----GTAAATTATGTAAGTTATGTAT-A-A-T-ATTA
*
9260957 ATTAATTAAGTTATGTAATTTATGTA--AT-TT-
183 ATTAACTAAGTTATGTAATTTATGTATCATATTA
* ** * * *
9260987 ATGTATAATATTAATGTAAGTTATGTATAATCTTAATTAATTAAGTTATGTAATTTATGTATAAT
1 ATG--TAA-GTT-ATGTAACATATGTATAATATTAATTAACTAAGTTATGTAATTTATGTAT-AC
* * * *
9261052 ATTAATTAATTAATTAAGTTATGTAATTTATGTATAAT-ATTAATGTATGTTATGTAATTTATGA
61 ATTAATTAATT-AGTAAGTTATGTAACTTATGTATATTAATTAAT-TAAGTTATGTAATTTATGA
*
9261116 ATAATTAAAAAAATGTAAGTTATGTAAGTTGTAAGTTA--TAAGTTATGTATAATATTAATTAAC
124 ATAATTAAAAAAATGTAAGTTATGTAAGTTGTAAATTATGTAAGTTATGTATAATATTAATTAAC
9261179 TAAGTTATGTAATT
189 TAAGTTATGTAATT
9261193 AGAGATGGGT
Statistics
Matches: 568, Mismatches: 32, Indels: 86
0.83 0.05 0.13
Matches are distributed among these distances:
209 49 0.09
210 1 0.00
211 6 0.01
212 5 0.01
213 19 0.03
214 25 0.04
215 4 0.01
216 68 0.12
217 22 0.04
218 8 0.01
219 13 0.02
220 15 0.03
221 249 0.44
222 7 0.01
223 1 0.00
224 1 0.00
225 5 0.01
226 2 0.00
227 6 0.01
228 43 0.08
229 1 0.00
230 2 0.00
231 16 0.03
ACGTcount: A:0.41, C:0.02, G:0.11, T:0.46
Consensus pattern (216 bp):
ATGTAAGTTATGTAACATATGTATAATATTAATTAACTAAGTTATGTAATTTATGTATACATTAA
TTAATTAGTAAGTTATGTAACTTATGTATATTAATTAATTAAGTTATGTAATTTATGAATAATTA
AAAAAATGTAAGTTATGTAAGTTGTAAATTATGTAAGTTATGTATAATATTAATTAACTAAGTTA
TGTAATTTATGTATCATATTA
Found at i:9260780 original size:22 final size:22
Alignment explanation
Indices: 9260748--9261023 Score: 82
Period size: 22 Copynumber: 13.1 Consensus size: 22
9260738 TAACTAAGTT
*
9260748 ATGTAATTTATGTATCATATTA
1 ATGTAAGTTATGTATCATATTA
*
9260770 ATGTAAGTTATGTAACATATGT-
1 ATGTAAGTTATGTATCATAT-TA
* *
9260792 A--TAATATTAAT-TAAC-TAAGTT-
1 ATGTAA-GTT-ATGTATCAT-A-TTA
*
9260813 ATGTAATTTATGTATCATATTA
1 ATGTAAGTTATGTATCATATTA
* *
9260835 ATGTAAGTTATGTAACTTATGTA
1 ATGTAAGTTATGTATCATAT-TA
*
9260858 TAT-TAA-TTAAT-TA--A-GTT-
1 -ATGTAAGTT-ATGTATCATATTA
* *
9260875 ATGTAATTTATGTATAATATTA
1 ATGTAAGTTATGTATCATATTA
* *
9260897 ATGTAAGTTATGTATAATAACATAAA
1 ATGTAAGTTATGTATCAT---AT-TA
9260923 AT-TAAGTTATGTA--AT-TT-
1 ATGTAAGTTATGTATCATATTA
* *
9260940 ATGTATA-ATAT-TAATTA-ATTA
1 ATGTA-AGTTATGT-ATCATATTA
9260961 AT-TAAGTTATGTA--AT-TT-
1 ATGTAAGTTATGTATCATATTA
* *
9260978 ATGTAATTTATGTATAATATTA
1 ATGTAAGTTATGTATCATATTA
* *
9261000 ATGTAAGTTATGTATAATCTTA
1 ATGTAAGTTATGTATCATATTA
9261022 AT
1 AT
9261024 TAATTAAGTT
Statistics
Matches: 196, Mismatches: 19, Indels: 78
0.67 0.06 0.27
Matches are distributed among these distances:
16 2 0.01
17 10 0.05
18 24 0.12
19 4 0.02
20 16 0.08
21 20 0.10
22 88 0.45
23 14 0.07
24 2 0.01
25 13 0.07
26 3 0.02
ACGTcount: A:0.40, C:0.03, G:0.11, T:0.47
Consensus pattern (22 bp):
ATGTAAGTTATGTATCATATTA
Found at i:9260943 original size:9 final size:9
Alignment explanation
Indices: 9260929--9261114 Score: 73
Period size: 9 Copynumber: 19.6 Consensus size: 9
9260919 TAAAATTAAG
9260929 TTATGTAAT
1 TTATGTAAT
9260938 TTATGTATAAT
1 TTATG--TAAT
9260949 ATTAAT-TAAT
1 -TT-ATGTAAT
* *
9260959 TAAT-TAAG
1 TTATGTAAT
9260967 TTATGTAAT
1 TTATGTAAT
9260976 TTATGTAAT
1 TTATGTAAT
9260985 TTATGTATAAT
1 TTATG--TAAT
*
9260996 ATTAATGTAAG
1 -TT-ATGTAAT
9261007 TTATGT-A-
1 TTATGTAAT
* *
9261014 TAATCTTAAT
1 TTAT-GTAAT
* *
9261024 TAAT-TAAG
1 TTATGTAAT
9261032 TTATGTAAT
1 TTATGTAAT
9261041 TTATGTATAAT
1 TTATG--TAAT
9261052 ATTAAT-TAAT
1 -TT-ATGTAAT
* *
9261062 TAAT-TAAG
1 TTATGTAAT
9261070 TTATGTAAT
1 TTATGTAAT
9261079 TTATGTATAAT
1 TTATG--TAAT
9261090 ATTAATGT-AT
1 -TT-ATGTAAT
9261100 GTTATGTAAT
1 -TTATGTAAT
9261110 TTATG
1 TTATG
9261115 AATAATTAAA
Statistics
Matches: 139, Mismatches: 15, Indels: 46
0.69 0.08 0.23
Matches are distributed among these distances:
7 3 0.02
8 24 0.17
9 54 0.39
10 20 0.14
11 20 0.14
12 8 0.06
13 10 0.07
ACGTcount: A:0.39, C:0.01, G:0.10, T:0.51
Consensus pattern (9 bp):
TTATGTAAT
Found at i:9261114 original size:103 final size:100
Alignment explanation
Indices: 9260873--9261085 Score: 363
Period size: 103 Copynumber: 2.1 Consensus size: 100
9260863 ATTAATTAAG
*
9260873 TTATGTAATTTATGTATAATATTAATGTAAGTTATGTATAATAACATAAAATTAAGTTATGTAAT
1 TTATGTAATTTATG-ATAATATTAATGTAAGTTATGTATAAT--CTTAAAATTAAGTTATGTAAT
9260938 TTATGTATAATATTAATTAATTAATTAAGTTATGTAAT
63 TTATGTATAATATTAATTAATTAATTAAGTTATGTAAT
9260976 TTATGTAATTTATGTATAATATTAATGTAAGTTATGTATAATCTTAATTAATTAAGTTATGTAAT
1 TTATGTAATTTATG-ATAATATTAATGTAAGTTATGTATAATCTTAA--AATTAAGTTATGTAAT
9261041 TTATGTATAATATTAATTAATTAATTAAGTTATGTAAT
63 TTATGTATAATATTAATTAATTAATTAAGTTATGTAAT
9261079 TTATGTA
1 TTATGTA
9261086 TAATATTAAT
Statistics
Matches: 107, Mismatches: 1, Indels: 4
0.96 0.01 0.04
Matches are distributed among these distances:
101 4 0.04
103 103 0.96
ACGTcount: A:0.41, C:0.01, G:0.10, T:0.48
Consensus pattern (100 bp):
TTATGTAATTTATGATAATATTAATGTAAGTTATGTATAATCTTAAAATTAAGTTATGTAATTTA
TGTATAATATTAATTAATTAATTAAGTTATGTAAT
Found at i:9261120 original size:103 final size:101
Alignment explanation
Indices: 9260873--9261142 Score: 359
Period size: 103 Copynumber: 2.6 Consensus size: 101
9260863 ATTAATTAAG
*
9260873 TTATGTAATTTATGTATAATATTAATGTAAGTTATGTATAA-TAACATAAAATTAAGTTATGTAA
1 TTATGTAATTTATG-ATAATATTAATGTAAGTTATGAATAATTAA-A-AAAATTAAGTTATGTAA
9260937 TTTATGTATAATATTAATTAATTAATTAAGTTATGTAAT
63 TTTATGTATAATATTAATTAATTAATTAAGTTATGTAAT
* * **
9260976 TTATGTAATTTATGTATAATATTAATGTAAGTTATGTATAATCTTAATTAATTAAGTTATGTAAT
1 TTATGTAATTTATG-ATAATATTAATGTAAGTTATGAATAAT-TAAAAAAATTAAGTTATGTAAT
9261041 TTATGTATAATATTAATTAATTAATTAAGTTATGTAAT
64 TTATGTATAATATTAATTAATTAATTAAGTTATGTAAT
* *
9261079 TTATGTATAATATTAATG-T-ATGTT-ATGTAATTTATGAATAATTAAAAAAATGTAAGTTATGT
1 TTATG--TAAT-TT-ATGATAATATTAATGTAAGTTATGAATAATTAAAAAAAT-TAAGTTATGT
9261141 AA
61 AA
9261143 GTTGTAAGTT
Statistics
Matches: 151, Mismatches: 9, Indels: 14
0.87 0.05 0.08
Matches are distributed among these distances:
102 6 0.04
103 128 0.85
104 5 0.03
105 7 0.05
106 2 0.01
107 3 0.02
ACGTcount: A:0.42, C:0.01, G:0.10, T:0.47
Consensus pattern (101 bp):
TTATGTAATTTATGATAATATTAATGTAAGTTATGAATAATTAAAAAAATTAAGTTATGTAATTT
ATGTATAATATTAATTAATTAATTAAGTTATGTAAT
Found at i:9266141 original size:41 final size:41
Alignment explanation
Indices: 9266014--9266333 Score: 269
Period size: 41 Copynumber: 7.8 Consensus size: 41
9266004 TTTTGTTACT
** * * *
9266014 ATTAGCGGCGCTTC-GGTAAAAACGCCGCTAAAGGT-CAATAC
1 ATTAGCGGCGC-TCAGACAAAAACGCCGCTAAAGATCCGA-GC
* * * * * * *
9266055 ATTAGCGACGCTTAGATACAAACGCCGCTGAAGA-CAAGAGA
1 ATTAGCGGCGCTCAGACAAAAACGCCGCTAAAGATC-CGAGC
* ** * *
9266096 ATTAGTGGCGCTCAGTTAAAAACACCGCTAAAGATCCGAGT
1 ATTAGCGGCGCTCAGACAAAAACGCCGCTAAAGATCCGAGC
* * * *
9266137 ATTAGCGGCGCT-TGTATAACAACGCCGCTAAAGATCCAAGC
1 ATTAGCGGCGCTCAG-ACAAAAACGCCGCTAAAGATCCGAGC
9266178 ATTAGCGGCGCAT-AGACAAAAACGCCGCTAAAGATCCGAGC
1 ATTAGCGGCGC-TCAGACAAAAACGCCGCTAAAGATCCGAGC
* * *
9266219 ATTAGCGGCGC-CTACACGAAAACTCCGCTAAAGA-CTCGAGC
1 ATTAGCGGCGCTC-AGACAAAAACGCCGCTAAAGATC-CGAGC
*
9266260 ATTAGCGGCG-TCTAGACAAAAACGCCGCTAAAGATCTGAGC
1 ATTAGCGGCGCTC-AGACAAAAACGCCGCTAAAGATCCGAGC
* *
9266301 ATTAGCGGCGCTTACACAAAAACGCCGCTAAAG
1 ATTAGCGGCGCTCAGACAAAAACGCCGCTAAAG
9266334 GTTTAAAAAA
Statistics
Matches: 228, Mismatches: 39, Indels: 24
0.78 0.13 0.08
Matches are distributed among these distances:
40 3 0.01
41 219 0.96
42 6 0.03
ACGTcount: A:0.34, C:0.26, G:0.23, T:0.17
Consensus pattern (41 bp):
ATTAGCGGCGCTCAGACAAAAACGCCGCTAAAGATCCGAGC
Found at i:9266161 original size:82 final size:82
Alignment explanation
Indices: 9266014--9266333 Score: 303
Period size: 82 Copynumber: 3.9 Consensus size: 82
9266004 TTTTGTTACT
** * * * * * *
9266014 ATTAGCGGCGCTTC-GGTAAAAACGCCGCTAAAGGT-CAATACATTAGCGACGCTTAGA-TACAA
1 ATTAGCGGCGC-TCAGACAAAAACGCCGCTAAAGATCCGA-GCATTAGCGGCGCTTACACGA-AA
* *
9266076 ACGCCGCTGAAGACAAGAGA
63 ACGCCGCTAAAGACAAGAGC
* ** * * ** *
9266096 ATTAGTGGCGCTCAGTTAAAAACACCGCTAAAGATCCGAGTATTAGCGGCGCTTGTA-TAACAAC
1 ATTAGCGGCGCTCAGACAAAAACGCCGCTAAAGATCCGAGCATTAGCGGCGCTTACACGAA-AAC
*
9266160 GCCGCTAAAGATCCA-AGC
65 GCCGCTAAAGA-CAAGAGC
*
9266178 ATTAGCGGCGCAT-AGACAAAAACGCCGCTAAAGATCCGAGCATTAGCGGCGCCTACACGAAAAC
1 ATTAGCGGCGC-TCAGACAAAAACGCCGCTAAAGATCCGAGCATTAGCGGCGCTTACACGAAAAC
* **
9266242 TCCGCTAAAGACTCGAGC
65 GCCGCTAAAGACAAGAGC
* *
9266260 ATTAGCGGCG-TCTAGACAAAAACGCCGCTAAAGATCTGAGCATTAGCGGCGCTTACACAAAAAC
1 ATTAGCGGCGCTC-AGACAAAAACGCCGCTAAAGATCCGAGCATTAGCGGCGCTTACACGAAAAC
9266324 GCCGCTAAAG
65 GCCGCTAAAG
9266334 GTTTAAAAAA
Statistics
Matches: 200, Mismatches: 29, Indels: 18
0.81 0.12 0.07
Matches are distributed among these distances:
80 1 0.00
81 4 0.02
82 188 0.94
83 7 0.04
ACGTcount: A:0.34, C:0.26, G:0.23, T:0.17
Consensus pattern (82 bp):
ATTAGCGGCGCTCAGACAAAAACGCCGCTAAAGATCCGAGCATTAGCGGCGCTTACACGAAAACG
CCGCTAAAGACAAGAGC
Found at i:9266241 original size:123 final size:119
Alignment explanation
Indices: 9266013--9266333 Score: 335
Period size: 123 Copynumber: 2.6 Consensus size: 119
9266003 TTTTTGTTAC
* * * * *
9266013 TATTAGCGGCGCTTCGGTAAAAACGCCGCTAAAGGT-CAATACATTAGCGACGCTTAGATACAAA
1 TATTAGCGGCGCTT--GTAAAAACGCCGCTAAAGATCCAA-GCATTAGCGGCGCTTAGACAAAAA
* *
9266077 CGCCGCTGAAGACAAGAGAATTAGTGGCGCTCAGTTAAAAACACCGCTAAAGA-TCCGAG
63 CGCCGCTAAAGACAAGAGAATTAGCGGCGCTCAG-T-AAAACACCGCTAAAGACT-CGAG
*
9266136 TATTAGCGGCGCTTGTATAACAACGCCGCTAAAGATCCAAGCATTAGCGGCGCATAGACAAAAAC
1 TATTAGCGGCGCTTGTA-AA-AACGCCGCTAAAGATCCAAGCATTAGCGGCGCTTAGACAAAAAC
* * *
9266201 GCCGCTAAAGATC-CGAGCATTAGCGGCGCCTACACG-AAAACTCCGCTAAAGACTCGAG
64 GCCGCTAAAGA-CAAGAGAATTAGCGGCG-CT-CA-GTAAAACACCGCTAAAGACTCGAG
* * * ** *
9266259 CATTAGCGGCGTCTAGACAAAAACGCCGCTAAAGATCTGAGCATTAGCGGCGCTTACACAAAAAC
1 TATTAGCGGCG-CTTG-TAAAAACGCCGCTAAAGATCCAAGCATTAGCGGCGCTTAGACAAAAAC
9266324 GCCGCTAAAG
64 GCCGCTAAAG
9266334 GTTTAAAAAA
Statistics
Matches: 170, Mismatches: 18, Indels: 20
0.82 0.09 0.10
Matches are distributed among these distances:
121 3 0.02
122 2 0.01
123 149 0.88
124 12 0.07
125 3 0.02
126 1 0.01
ACGTcount: A:0.34, C:0.26, G:0.23, T:0.17
Consensus pattern (119 bp):
TATTAGCGGCGCTTGTAAAAACGCCGCTAAAGATCCAAGCATTAGCGGCGCTTAGACAAAAACGC
CGCTAAAGACAAGAGAATTAGCGGCGCTCAGTAAAACACCGCTAAAGACTCGAG
Found at i:9266768 original size:15 final size:14
Alignment explanation
Indices: 9266741--9266771 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
9266731 AACTTATTTC
9266741 ATAATAATAATATA
1 ATAATAATAATATA
9266755 ATAATAATTAATATA
1 ATAATAA-TAATATA
9266770 AT
1 AT
9266772 TTATTATTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.44
15 9 0.56
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (14 bp):
ATAATAATAATATA
Found at i:9269228 original size:15 final size:16
Alignment explanation
Indices: 9269210--9269247 Score: 51
Period size: 18 Copynumber: 2.3 Consensus size: 16
9269200 AAAGTATGTC
9269210 GAAC-TCTATTATGAG
1 GAACATCTATTATGAG
9269225 GAACAGTTCTATTATGAG
1 GAACA--TCTATTATGAG
9269243 GAACA
1 GAACA
9269248 GTTGCTCCTA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
15 4 0.20
18 16 0.80
ACGTcount: A:0.37, C:0.13, G:0.21, T:0.29
Consensus pattern (16 bp):
GAACATCTATTATGAG
Found at i:9269237 original size:18 final size:18
Alignment explanation
Indices: 9269214--9269250 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
9269204 TATGTCGAAC
9269214 TCTATTATGAGGAACAGT
1 TCTATTATGAGGAACAGT
9269232 TCTATTATGAGGAACAGT
1 TCTATTATGAGGAACAGT
9269250 T
1 T
9269251 GCTCCTATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.32, C:0.11, G:0.22, T:0.35
Consensus pattern (18 bp):
TCTATTATGAGGAACAGT
Found at i:9279453 original size:24 final size:25
Alignment explanation
Indices: 9279415--9279462 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 25
9279405 TTTTTACTTT
* *
9279415 TGAAAAAATTATTAATAATTTTAGA
1 TGAAAAAAATATTAAGAATTTTAGA
9279440 TGAAAAAAAT-TTAAGAATTTTAG
1 TGAAAAAAATATTAAGAATTTTAG
9279463 TTTATTGGTA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 12 0.57
25 9 0.43
ACGTcount: A:0.52, C:0.00, G:0.10, T:0.38
Consensus pattern (25 bp):
TGAAAAAAATATTAAGAATTTTAGA
Found at i:9279587 original size:15 final size:15
Alignment explanation
Indices: 9279569--9279602 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
9279559 TTGTATATAT
*
9279569 AAAATTTATTTATTA
1 AAAAGTTATTTATTA
*
9279584 AAAAGTTATTTTTTA
1 AAAAGTTATTTATTA
9279599 AAAA
1 AAAA
9279603 AATTGACATC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (15 bp):
AAAAGTTATTTATTA
Found at i:9285346 original size:23 final size:22
Alignment explanation
Indices: 9285312--9285356 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 22
9285302 TATTATATTA
* **
9285312 TTTTTAATAAATATTAAATTTT
1 TTTTTAAGAAATACAAAATTTT
9285334 TTTTTAAAGAAATACAAAATTTT
1 TTTTT-AAGAAATACAAAATTTT
9285357 AGTTTTATGT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 5 0.26
23 14 0.74
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.51
Consensus pattern (22 bp):
TTTTTAAGAAATACAAAATTTT
Found at i:9286290 original size:29 final size:29
Alignment explanation
Indices: 9286248--9286303 Score: 85
Period size: 29 Copynumber: 1.9 Consensus size: 29
9286238 GTCTTAAAGG
* * *
9286248 GGTGGAGGAGATGTGTTAGGCGACACTCA
1 GGTGGACGAGATGTGTCAAGCGACACTCA
9286277 GGTGGACGAGATGTGTCAAGCGACACT
1 GGTGGACGAGATGTGTCAAGCGACACT
9286304 GGGCCCTATT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.25, C:0.16, G:0.39, T:0.20
Consensus pattern (29 bp):
GGTGGACGAGATGTGTCAAGCGACACTCA
Found at i:9291284 original size:125 final size:125
Alignment explanation
Indices: 9291057--9291288 Score: 358
Period size: 125 Copynumber: 1.9 Consensus size: 125
9291047 AAGCTTAATC
* * *
9291057 TATTGTTGCCTCCTATAAACCCTAAACCACAAAACATAACAAAGATATTAGTTATAACACCACAA
1 TATTGCTGCCTCCTATAAACCCTAAACCACAAAACATAACAAAGATATCACTTATAACACCACAA
* * *
9291122 AATAATCTTAAACCCTAAACAAATAAATGATAGTTAAAAAAAGTTTACCAAACTCAAATA
66 AATAACCCTAAACCCTAAACAAATAAATGATAATTAAAAAAAGTTTACCAAACTCAAATA
* * *
9291182 TATTGCTGCCTCCTCTAAACCCTAAGCCACAAAATATAACAAA-ACTATCACTTATAACACCACA
1 TATTGCTGCCTCCTATAAACCCTAAACCACAAAACATAACAAAGA-TATCACTTATAACACCACA
*
9291246 AAATAACCCTAAATCCTAAACAAATAAATGATAATTAAAAAAA
65 AAATAACCCTAAACCCTAAACAAATAAATGATAATTAAAAAAA
9291289 TTACCTTTGA
Statistics
Matches: 96, Mismatches: 10, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
124 1 0.01
125 95 0.99
ACGTcount: A:0.50, C:0.22, G:0.05, T:0.24
Consensus pattern (125 bp):
TATTGCTGCCTCCTATAAACCCTAAACCACAAAACATAACAAAGATATCACTTATAACACCACAA
AATAACCCTAAACCCTAAACAAATAAATGATAATTAAAAAAAGTTTACCAAACTCAAATA
Found at i:9292074 original size:25 final size:24
Alignment explanation
Indices: 9292034--9292086 Score: 63
Period size: 25 Copynumber: 2.2 Consensus size: 24
9292024 ATAAATAATA
9292034 AAAAGAGTAAAAAAATAGAAAAGC
1 AAAAGAGTAAAAAAATAGAAAAGC
* *
9292058 AAAAGAG-AACAAGAAATAGGAAAGT
1 AAAAGAGTAA-AA-AAATAGAAAAGC
9292083 AAAA
1 AAAA
9292087 ATGAACGAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
23 2 0.08
24 9 0.36
25 14 0.56
ACGTcount: A:0.70, C:0.04, G:0.19, T:0.08
Consensus pattern (24 bp):
AAAAGAGTAAAAAAATAGAAAAGC
Found at i:9292256 original size:19 final size:19
Alignment explanation
Indices: 9292232--9292272 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
9292222 CATAATGATA
*
9292232 TATATAA-TATATATTTTAT
1 TATATAATTACATA-TTTAT
9292251 TATATAATTACATATTTAT
1 TATATAATTACATATTTAT
9292270 TAT
1 TAT
9292273 TTTATTTATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 15 0.75
20 5 0.25
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.56
Consensus pattern (19 bp):
TATATAATTACATATTTAT
Found at i:9304978 original size:20 final size:20
Alignment explanation
Indices: 9304953--9304992 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
9304943 CGTAAAATGA
*
9304953 TTTCTGGAAAATGTTTTACT
1 TTTCTGGAAAATGATTTACT
*
9304973 TTTCTGTAAAATGATTTACT
1 TTTCTGGAAAATGATTTACT
9304993 GGAAAATATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.28, C:0.10, G:0.12, T:0.50
Consensus pattern (20 bp):
TTTCTGGAAAATGATTTACT
Found at i:9304982 original size:34 final size:35
Alignment explanation
Indices: 9304938--9305004 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
9304928 CAATAAAATA
*
9304938 TTTTCCGTAAAATGATTT-CTGGAAAATGTTTTAC
1 TTTTCCGTAAAATGATTTACTGGAAAATATTTTAC
*
9304972 TTTTCTGTAAAATGATTTACTGGAAAATATTTT
1 TTTTCCGTAAAATGATTTACTGGAAAATATTTT
9305005 CTGGTGTTTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 17 0.57
35 13 0.43
ACGTcount: A:0.31, C:0.09, G:0.13, T:0.46
Consensus pattern (35 bp):
TTTTCCGTAAAATGATTTACTGGAAAATATTTTAC
Found at i:9305008 original size:14 final size:15
Alignment explanation
Indices: 9304932--9305008 Score: 52
Period size: 14 Copynumber: 5.0 Consensus size: 15
9304922 GATTGCCAAT
* *
9304932 AAAAT-ATTTTCCGT
1 AAAATGATTTTCTGG
9304946 AAAATGA-TTTCTGG
1 AAAATGATTTTCTGG
*
9304960 AAAATGTTTTACTTTTCTGT
1 AAAATG----A-TTTTCTGG
*
9304980 AAAATGATTTACTGG
1 AAAATGATTTTCTGG
9304995 AAAAT-ATTTTCTGG
1 AAAATGATTTTCTGG
9305009 TGTTTGATTG
Statistics
Matches: 50, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
14 24 0.48
15 12 0.24
16 1 0.02
18 1 0.02
20 12 0.24
ACGTcount: A:0.34, C:0.09, G:0.14, T:0.43
Consensus pattern (15 bp):
AAAATGATTTTCTGG
Found at i:9319819 original size:6 final size:6
Alignment explanation
Indices: 9319808--9319865 Score: 107
Period size: 6 Copynumber: 9.7 Consensus size: 6
9319798 AAAGGACATA
9319808 TATATC TATATC TATATC TATATC TATATC TATATC TATATC TATATC
1 TATATC TATATC TATATC TATATC TATATC TATATC TATATC TATATC
*
9319856 TATATA TATA
1 TATATC TATA
9319866 AATTCTTATT
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
6 51 1.00
ACGTcount: A:0.36, C:0.14, G:0.00, T:0.50
Consensus pattern (6 bp):
TATATC
Found at i:9334167 original size:15 final size:15
Alignment explanation
Indices: 9334144--9334186 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
9334134 AGCGATTTGC
*
9334144 AAAAGAAGAGAAAAT
1 AAAAGAAGAGAAAAG
* *
9334159 AAAATAAGATAAAAG
1 AAAAGAAGAGAAAAG
9334174 AAAACGAAGAGAA
1 AAAA-GAAGAGAA
9334187 CTGTTCAAAA
Statistics
Matches: 22, Mismatches: 5, Indels: 1
0.79 0.18 0.04
Matches are distributed among these distances:
15 16 0.73
16 6 0.27
ACGTcount: A:0.72, C:0.02, G:0.19, T:0.07
Consensus pattern (15 bp):
AAAAGAAGAGAAAAG
Found at i:9335109 original size:88 final size:86
Alignment explanation
Indices: 9334972--9335191 Score: 223
Period size: 88 Copynumber: 2.5 Consensus size: 86
9334962 CCACTTCCTA
* * * * * *
9334972 CCAATATAGGAAGACAGGACCTACTATCTTCGATCTACTT-C-ACGTCAATACATGAAGACAAGA
1 CCAATACAGGAAGACAAGATCTGC-ATCTTCGATCCACTTCCTAC--CAATACAAGAAGACAAGA
*
9335035 TCTGCTTTCTTCGATTTACTTC-G
63 TCTGCTTTCTTCGATCTACTTCAG
** * * *
9335058 CCACCAGTATGGGAAGACAAGATCTGCA-CATTTGATCCACTTCCTACCAATATAAGAAGACATG
1 CCA--A-TACAGGAAGACAAGATCTGCATC-TTCGATCCACTTCCTACCAATACAAGAAGACAAG
9335122 ATCTGCTTTCTTCGATCTACTTCATG
62 ATCTGCTTTCTTCGATCTACTTCA-G
*
9335148 CCAATACATGAAGACAAGATCTGCATCTTCGATCCACTTCCTAC
1 CCAATACAGGAAGACAAGATCTGCATCTTCGATCCACTTCCTAC
9335192 TAAAAAAAAG
Statistics
Matches: 111, Mismatches: 14, Indels: 17
0.78 0.10 0.12
Matches are distributed among these distances:
86 3 0.03
87 35 0.32
88 50 0.45
89 17 0.15
90 6 0.05
ACGTcount: A:0.30, C:0.26, G:0.15, T:0.29
Consensus pattern (86 bp):
CCAATACAGGAAGACAAGATCTGCATCTTCGATCCACTTCCTACCAATACAAGAAGACAAGATCT
GCTTTCTTCGATCTACTTCAG
Found at i:9335161 original size:44 final size:44
Alignment explanation
Indices: 9334956--9335187 Score: 186
Period size: 44 Copynumber: 5.3 Consensus size: 44
9334946 GGATCTATTT
* * * * *
9334956 TTCGATCCACTTCCTACCAATATAGGAAGACAGGACCTACTATC
1 TTCGATCCACTTCATGCCAATATAGGAAGACAAGATCTGCTATC
* * * * * *
9335000 TTCGATCTACTTCACGTCAATACATGAAGACAAGATCTGCTTTC
1 TTCGATCCACTTCATGCCAATATAGGAAGACAAGATCTGCTATC
** *
9335044 TTCGATTTACTTC--GCCACCAGTATGGGAAGACAAGATCTGC-A-C
1 TTCGATCCACTTCATGCCA--A-TATAGGAAGACAAGATCTGCTATC
* * * * * *
9335087 ATTTGATCCACTTCCTACCAATATAAGAAGACATGATCTGCTTTC
1 -TTCGATCCACTTCATGCCAATATAGGAAGACAAGATCTGCTATC
* * *
9335132 TTCGATCTACTTCATGCCAATACATGAAGACAAGATCTGC-ATC
1 TTCGATCCACTTCATGCCAATATAGGAAGACAAGATCTGCTATC
9335175 TTCGATCCACTTC
1 TTCGATCCACTTC
9335188 CTACTAAAAA
Statistics
Matches: 146, Mismatches: 34, Indels: 17
0.74 0.17 0.09
Matches are distributed among these distances:
42 3 0.02
43 32 0.22
44 90 0.62
45 18 0.12
46 3 0.02
ACGTcount: A:0.30, C:0.27, G:0.14, T:0.29
Consensus pattern (44 bp):
TTCGATCCACTTCATGCCAATATAGGAAGACAAGATCTGCTATC
Found at i:9335456 original size:109 final size:106
Alignment explanation
Indices: 9335202--9335517 Score: 389
Period size: 110 Copynumber: 3.0 Consensus size: 106
9335192 TAAAAAAAAG
* *
9335202 AATTTTTTTAAAATTTTTTCGTATATTTATATCTGA-TCTGACACGAAAAAAAAGAATTTTTTTT
1 AATTTTTTT-TAATTTTTTCGTATATTTATATCTAATTCTGACACGAAAAAAAAGAATTTTTTTT
*
9335266 TAATTTGTACTGGGTGCCGGCCATTGACAGGCCAGCACCCAA
65 TAAATTGTACTGGGTGCCGGCCATTGACAGGCCAGCACCCAA
* * *
9335308 ATTTTTTTTTAATTTTTTTGTATATTTATATCTAATTCTGACACGAAAGAAAAGTAAATTTTTTT
1 AATTTTTTTTAATTTTTTCGTATATTTATATCTAATTCTGACACGAAAAAAAAG--AA-TTTTTT
*
9335373 TTTAAAATTGTACTGGGTGTCGGCCATTGACAGGCCAGCACCCAA
63 TTT-AAATTGTACTGGGTGCCGGCCATTGACAGGCCAGCACCCAA
* * * *
9335418 AATTTTTTTT-ATTTTTTCGTATATTTATATATTATTCTG--A-TAAAAAAAGGAATTTTTTTTT
1 AATTTTTTTTAATTTTTTCGTATATTTATATCTAATTCTGACACGAAAAAAAAGAATTTTTTTTT
* * * *
9335479 --ACTGT--TGAGTGCCGGCCATTGACAGGCCAGTACCAAA
66 AAATTGTACTGGGTGCCGGCCATTGACAGGCCAGCACCCAA
9335516 AA
1 AA
9335518 ATAATTTTTT
Statistics
Matches: 186, Mismatches: 19, Indels: 18
0.83 0.09 0.08
Matches are distributed among these distances:
98 30 0.16
100 4 0.02
103 9 0.05
104 2 0.01
105 23 0.12
106 32 0.17
107 1 0.01
108 2 0.01
109 35 0.19
110 48 0.26
ACGTcount: A:0.31, C:0.14, G:0.15, T:0.41
Consensus pattern (106 bp):
AATTTTTTTTAATTTTTTCGTATATTTATATCTAATTCTGACACGAAAAAAAAGAATTTTTTTTT
AAATTGTACTGGGTGCCGGCCATTGACAGGCCAGCACCCAA
Found at i:9342317 original size:28 final size:29
Alignment explanation
Indices: 9342247--9342321 Score: 79
Period size: 29 Copynumber: 2.7 Consensus size: 29
9342237 TAAAATATTA
*
9342247 TTTT-CTAA-TTTTTAATGGGCCTAAATTTT
1 TTTTACTAACTTTTTAA-GGGCCCAAA-TTT
9342276 TTTTA-TCAAC-TTTTAAGGGCCCAAA-TT
1 TTTTACT-AACTTTTTAAGGGCCCAAATTT
9342303 TTTTACTAACTTTTTAAGG
1 TTTTACTAACTTTTTAAGG
9342322 AACCTAAAGT
Statistics
Matches: 40, Mismatches: 1, Indels: 11
0.77 0.02 0.21
Matches are distributed among these distances:
27 10 0.25
28 9 0.22
29 13 0.32
30 8 0.20
ACGTcount: A:0.27, C:0.13, G:0.11, T:0.49
Consensus pattern (29 bp):
TTTTACTAACTTTTTAAGGGCCCAAATTT
Found at i:9357256 original size:7 final size:7
Alignment explanation
Indices: 9357244--9357310 Score: 53
Period size: 7 Copynumber: 8.7 Consensus size: 7
9357234 AACTTAAGTT
9357244 TATTTAA
1 TATTTAA
9357251 TATTTAA
1 TATTTAA
*
9357258 TGATTTTA
1 T-ATTTAA
*
9357266 TATTTAT
1 TATTTAA
9357273 TATTTATTA
1 TATTTA--A
*
9357282 TAATTTTA
1 T-ATTTAA
9357290 TATTTAA
1 TATTTAA
9357297 TCATTTTAA
1 T-A-TTTAA
9357306 TATTT
1 TATTT
9357311 GCTTATAGAG
Statistics
Matches: 48, Mismatches: 6, Indels: 12
0.73 0.09 0.18
Matches are distributed among these distances:
7 27 0.56
8 10 0.21
9 7 0.15
10 4 0.08
ACGTcount: A:0.34, C:0.01, G:0.01, T:0.63
Consensus pattern (7 bp):
TATTTAA
Found at i:9357292 original size:24 final size:22
Alignment explanation
Indices: 9357244--9357307 Score: 74
Period size: 24 Copynumber: 2.7 Consensus size: 22
9357234 AACTTAAGTT
*
9357244 TATTTAATATTTAATGATTTTA
1 TATTTAATATTTAATAATTTTA
*
9357266 TATTTATTATTTATTATAATTTTA
1 TATTTAATATTTA--ATAATTTTA
9357290 TATTTAATCATTTTAATA
1 TATTTAAT-A-TTTAATA
9357308 TTTGCTTATA
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
22 12 0.34
24 18 0.51
25 1 0.03
26 4 0.11
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.61
Consensus pattern (22 bp):
TATTTAATATTTAATAATTTTA
Found at i:9363285 original size:22 final size:20
Alignment explanation
Indices: 9363249--9363307 Score: 57
Period size: 21 Copynumber: 2.8 Consensus size: 20
9363239 GGCCCAGCCC
9363249 ATTT-TTTTAATAAATACCAAAA
1 ATTTATTTTAA-AAATA--AAAA
9363271 ATTTATTTTAAAAATTAAAAA
1 ATTTATTTTAAAAA-TAAAAA
**
9363292 AAGTATTTTAAAAATA
1 ATTTATTTTAAAAATA
9363308 TTTTAAAATT
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
20 2 0.06
21 16 0.48
22 7 0.21
23 8 0.24
ACGTcount: A:0.54, C:0.03, G:0.02, T:0.41
Consensus pattern (20 bp):
ATTTATTTTAAAAATAAAAA
Found at i:9363309 original size:11 final size:11
Alignment explanation
Indices: 9363289--9363356 Score: 54
Period size: 11 Copynumber: 6.4 Consensus size: 11
9363279 TAAAAATTAA
9363289 AAAAAGTATTTT
1 AAAAA-TATTTT
9363301 AAAAATATTTT
1 AAAAATATTTT
*
9363312 --AAA-A-TTA
1 AAAAATATTTT
* **
9363319 AAAAATAATAA
1 AAAAATATTTT
9363330 AAAAAGTATTTT
1 AAAAA-TATTTT
9363342 AAAAATATTTT
1 AAAAATATTTT
9363353 AAAA
1 AAAA
9363357 TTAAAAAAAT
Statistics
Matches: 46, Mismatches: 5, Indels: 11
0.74 0.08 0.18
Matches are distributed among these distances:
7 2 0.04
8 1 0.02
9 6 0.13
10 1 0.02
11 23 0.50
12 13 0.28
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (11 bp):
AAAAATATTTT
Found at i:9363338 original size:41 final size:40
Alignment explanation
Indices: 9363280--9363374 Score: 163
Period size: 41 Copynumber: 2.4 Consensus size: 40
9363270 AATTTATTTT
*
9363280 AAAAATTAAAAAAAGTATTTTAAAAATATTTTAAAATTAA
1 AAAAAATAAAAAAAGTATTTTAAAAATATTTTAAAATTAA
9363320 AAAATAATAAAAAAAGTATTTTAAAAATATTTTAAAATTAA
1 AAAA-AATAAAAAAAGTATTTTAAAAATATTTTAAAATTAA
*
9363361 AAAAATTAAAAAAA
1 AAAAAATAAAAAAA
9363375 TAAATATATT
Statistics
Matches: 52, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
40 13 0.25
41 39 0.75
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (40 bp):
AAAAAATAAAAAAAGTATTTTAAAAATATTTTAAAATTAA
Found at i:9365698 original size:3 final size:3
Alignment explanation
Indices: 9365690--9365741 Score: 52
Period size: 3 Copynumber: 17.3 Consensus size: 3
9365680 GTAGTTTTTG
* * *
9365690 TTA TTA TTA TTA TTA CTA TTA TCA TTA TTA -TA TTA TATA GTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA
*
9365735 TAA TTA T
1 TTA TTA T
9365742 ACTTACATAT
Statistics
Matches: 39, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
2 2 0.05
3 35 0.90
4 2 0.05
ACGTcount: A:0.37, C:0.04, G:0.02, T:0.58
Consensus pattern (3 bp):
TTA
Found at i:9365733 original size:24 final size:24
Alignment explanation
Indices: 9365690--9365741 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
9365680 GTAGTTTTTG
*
9365690 TTATTATTATTATTACTATTATCA
1 TTATTATTATTATTACTATTATAA
*
9365714 TTATTA-TATTATATAGTATTATAA
1 TTATTATTATTAT-TACTATTATAA
9365738 TTAT
1 TTAT
9365742 ACTTACATAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 6 0.24
24 19 0.76
ACGTcount: A:0.37, C:0.04, G:0.02, T:0.58
Consensus pattern (24 bp):
TTATTATTATTATTACTATTATAA
Found at i:9367819 original size:19 final size:19
Alignment explanation
Indices: 9367779--9367820 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
9367769 GTCTCTTTTC
* *
9367779 GCATTCATTTCATGCATTT
1 GCATTCATTACATGCATAT
9367798 GCATTACATTACAT-CATAT
1 GCATT-CATTACATGCATAT
9367817 GCAT
1 GCAT
9367821 CAAAGATTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 13 0.65
20 7 0.35
ACGTcount: A:0.29, C:0.21, G:0.10, T:0.40
Consensus pattern (19 bp):
GCATTCATTACATGCATAT
Found at i:9370671 original size:7 final size:7
Alignment explanation
Indices: 9370649--9370711 Score: 74
Period size: 7 Copynumber: 8.7 Consensus size: 7
9370639 TGAGTCATTA
9370649 AAAAATG
1 AAAAATG
*
9370656 ATGAAATG
1 A-AAAATG
9370664 AAAAATG
1 AAAAATG
9370671 AAAAAGTG
1 AAAAA-TG
*
9370679 -AAAAGG
1 AAAAATG
9370685 AAAAATG
1 AAAAATG
9370692 AAAAATG
1 AAAAATG
9370699 AAAAATGG
1 AAAAAT-G
9370707 AAAAA
1 AAAAA
9370712 GTAAAATAGA
Statistics
Matches: 48, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
6 1 0.02
7 33 0.69
8 14 0.29
ACGTcount: A:0.68, C:0.00, G:0.19, T:0.13
Consensus pattern (7 bp):
AAAAATG
Found at i:9370717 original size:28 final size:28
Alignment explanation
Indices: 9370659--9370718 Score: 86
Period size: 28 Copynumber: 2.1 Consensus size: 28
9370649 AAAAATGATG
*
9370659 AAATGAAAAATGAAAAAGTGAAAAGGAA
1 AAATGAAAAATGAAAAAGTGAAAAAGAA
*
9370687 AAATGAAAAATGAAAAA-TGGAAAAAGTA
1 AAATGAAAAATGAAAAAGT-GAAAAAGAA
9370715 AAAT
1 AAAT
9370719 AGAGAGGCTA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
27 1 0.03
28 28 0.97
ACGTcount: A:0.68, C:0.00, G:0.18, T:0.13
Consensus pattern (28 bp):
AAATGAAAAATGAAAAAGTGAAAAAGAA
Done.