Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009639.1 Hibiscus syriacus cultivar Beakdansim tig00117048_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 15077257
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 11 of 62
Found at i:2532536 original size:24 final size:25
Alignment explanation
Indices: 2532479--2532544 Score: 116
Period size: 26 Copynumber: 2.6 Consensus size: 25
2532469 AAAATATTTT
2532479 AGTTCATATTACTCGTGTAGTACATG
1 AGTTCATATTACTCGTGTAGTACA-G
2532505 AGTTCATATTACTCGTGTAGTAC-G
1 AGTTCATATTACTCGTGTAGTACAG
2532529 AGTTCATATTACTCGT
1 AGTTCATATTACTCGT
2532545 CTATATCATG
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
24 17 0.43
26 23 0.57
ACGTcount: A:0.26, C:0.17, G:0.18, T:0.39
Consensus pattern (25 bp):
AGTTCATATTACTCGTGTAGTACAG
Found at i:2533604 original size:21 final size:20
Alignment explanation
Indices: 2533589--2533627 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
2533579 TGTAACATTC
*
2533589 GTAATTACTCTTGTAACTGGT
1 GTAATTACACTTGTAACT-GT
2533610 GTAATTACACTTGTAACT
1 GTAATTACACTTGTAACT
2533628 AGTTAAATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.28, C:0.15, G:0.15, T:0.41
Consensus pattern (20 bp):
GTAATTACACTTGTAACTGT
Found at i:2534278 original size:2 final size:2
Alignment explanation
Indices: 2534271--2534307 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
2534261 GATGTGCAAG
2534271 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2534308 CACACACACA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2539228 original size:45 final size:45
Alignment explanation
Indices: 2539162--2539248 Score: 147
Period size: 45 Copynumber: 1.9 Consensus size: 45
2539152 AAAGAGCCAA
*
2539162 AAGCTTAGAAAGTTTTAAGAGAGTTGAGAGATGTTTGAGTGATAT
1 AAGCTTAGAAAGCTTTAAGAGAGTTGAGAGATGTTTGAGTGATAT
* *
2539207 AAGCTTAGAAAGCTTTGAGAGAGTTGATAGATGTTTGAGTGA
1 AAGCTTAGAAAGCTTTAAGAGAGTTGAGAGATGTTTGAGTGA
2539249 ATTGGTGAGT
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 39 1.00
ACGTcount: A:0.34, C:0.03, G:0.30, T:0.32
Consensus pattern (45 bp):
AAGCTTAGAAAGCTTTAAGAGAGTTGAGAGATGTTTGAGTGATAT
Found at i:2539959 original size:34 final size:34
Alignment explanation
Indices: 2539916--2539981 Score: 123
Period size: 34 Copynumber: 1.9 Consensus size: 34
2539906 TGAAATGCTC
*
2539916 ACTATTTTTAAATTTGTGTCATTATGACTATTAG
1 ACTATTTTTAAATTTGTGTCAATATGACTATTAG
2539950 ACTATTTTTAAATTTGTGTCAATATGACTATT
1 ACTATTTTTAAATTTGTGTCAATATGACTATT
2539982 TAAAAGATTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 31 1.00
ACGTcount: A:0.30, C:0.09, G:0.11, T:0.50
Consensus pattern (34 bp):
ACTATTTTTAAATTTGTGTCAATATGACTATTAG
Found at i:2542579 original size:60 final size:62
Alignment explanation
Indices: 2542515--2542632 Score: 195
Period size: 62 Copynumber: 1.9 Consensus size: 62
2542505 AAAATCCGTC
*
2542515 GGAATGTTATATATAAA-AAA-TACTATATTTTATATTTCCGACGAATATATCTTTTCCTTT
1 GGAATGTTATATATAAATAAACTACTATATTTTATATTTCCGACGAACATATCTTTTCCTTT
* *
2542575 GGAATGTTCTATATAAATAAACTACTATATTTTATATTTCCGATGAACATATCTTTTC
1 GGAATGTTATATATAAATAAACTACTATATTTTATATTTCCGACGAACATATCTTTTC
2542633 ATTCGGGATA
Statistics
Matches: 53, Mismatches: 3, Indels: 2
0.91 0.05 0.03
Matches are distributed among these distances:
60 16 0.30
61 3 0.06
62 34 0.64
ACGTcount: A:0.35, C:0.13, G:0.08, T:0.44
Consensus pattern (62 bp):
GGAATGTTATATATAAATAAACTACTATATTTTATATTTCCGACGAACATATCTTTTCCTTT
Found at i:2542810 original size:33 final size:33
Alignment explanation
Indices: 2542764--2542841 Score: 93
Period size: 33 Copynumber: 2.3 Consensus size: 33
2542754 TTATACCAGA
*
2542764 AAATATTTCATTCCCTCAAAAAAATTATGAATCC
1 AAAT-TTTTATTCCCTCAAAAAAATTATGAATCC
* * *
2542798 AAATTTTTATTCCCTCCATAATATTATGAATCC
1 AAATTTTTATTCCCTCAAAAAAATTATGAATCC
**
2542831 AACCTTTTATT
1 AAATTTTTATT
2542842 TAATTAATTA
Statistics
Matches: 38, Mismatches: 6, Indels: 1
0.84 0.13 0.02
Matches are distributed among these distances:
33 34 0.89
34 4 0.11
ACGTcount: A:0.37, C:0.21, G:0.03, T:0.40
Consensus pattern (33 bp):
AAATTTTTATTCCCTCAAAAAAATTATGAATCC
Found at i:2543627 original size:122 final size:123
Alignment explanation
Indices: 2543499--2543736 Score: 347
Period size: 122 Copynumber: 1.9 Consensus size: 123
2543489 ACCTCAAAAA
* *
2543499 TTTGTGACGGAACATGTAGACTAATCACAAATTTGTGATAGG-ATAGGTGGATCTGTCAGAAATT
1 TTTGTGACGGAACATGTAGACCAATCACAAATTAGTGAT-GGAATAGGTGGATCTGTCAGAAATT
2543563 TGTGACGAGTACACAAATTCCT-TCACAAATTTAAAATAC-TTTCTAAAAAATGATTTTT
65 TGTGACGAGTACACAAATT-CTGTCACAAATTTAAAATACTTTTCTAAAAAATGATTTTT
* * *
2543621 TTTGTGACGGAACATGTGGACCCATCACAAATTAGTGATGGAATAGGTGGGTCTGTCAGAAATTT
1 TTTGTGACGGAACATGTAGACCAATCACAAATTAGTGATGGAATAGGTGGATCTGTCAGAAATTT
* * * *
2543686 GTGACGATTCCACAAATTCTGTCCCAAATTTAAAATGCTTTTTCTAAAAAA
66 GTGACGAGTACACAAATTCTGTCACAAATTTAAAATAC-TTTTCTAAAAAA
2543737 AATTATCATA
Statistics
Matches: 103, Mismatches: 9, Indels: 6
0.87 0.08 0.05
Matches are distributed among these distances:
121 4 0.04
122 88 0.85
124 11 0.11
ACGTcount: A:0.34, C:0.15, G:0.18, T:0.32
Consensus pattern (123 bp):
TTTGTGACGGAACATGTAGACCAATCACAAATTAGTGATGGAATAGGTGGATCTGTCAGAAATTT
GTGACGAGTACACAAATTCTGTCACAAATTTAAAATACTTTTCTAAAAAATGATTTTT
Found at i:2544359 original size:31 final size:31
Alignment explanation
Indices: 2544324--2544390 Score: 93
Period size: 30 Copynumber: 2.2 Consensus size: 31
2544314 AAAAAAACTG
2544324 AATTTTGTGA-GGAACACGGGGACCCGTCACA
1 AATTTTGTGACGGAACACGGGGA-CCGTCACA
* *
2544355 AA-TTTGTGACGGAACATGTGGACCGTCACA
1 AATTTTGTGACGGAACACGGGGACCGTCACA
2544385 AATTTT
1 AATTTT
2544391 ACCCTCCATT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
30 17 0.53
31 15 0.47
ACGTcount: A:0.30, C:0.19, G:0.25, T:0.25
Consensus pattern (31 bp):
AATTTTGTGACGGAACACGGGGACCGTCACA
Found at i:2550385 original size:199 final size:197
Alignment explanation
Indices: 2550042--2550413 Score: 595
Period size: 199 Copynumber: 1.9 Consensus size: 197
2550032 AATAAGTATA
*
2550042 TTATAAATGCATATAAATCAAAAAAAATAAAGGATAAAAGCATAAAAATGGTAATTGTTTATAGG
1 TTATAAATGCATATAAATCAAAAAAAATAAAGGATAAAAGCATAAAAATGGTAATTGTTTACAGG
* *
2550107 TGGTGATAATATTTTTTATTTCTGATGGAATGATTATTTCGTCACAAATTGAATTGATAAATTTT
66 TGGTGATAATATTTTTTATTTCCGATGGAATGATTATTTCATCACAAATTGAATTGATAAATTTT
* *
2550172 TATTATAGTGAACAAAATTTCCGACAGAATCATTGTTCTATCATAAATTAAATTGATATTTTTGT
131 TATTAAAGTGAACAAAATTTCCGACAGAATCATTGTTCCATCATAAATTAAATTGATATTTTTGT
2550237 TT
196 TT
* * *
2550239 TTATAAATGCATATAAAT-AAAAAAAAGTAAAGGATACAAGCATATAAATGTTAATTGTTTACAG
1 TTATAAATGCATATAAATCAAAAAAAA-TAAAGGATAAAAGCATAAAAATGGTAATTGTTTACAG
*
2550303 GTGGTGATAATATATTTTTTATTTCCGATGGAACT-ATTATTTCATCACAAATTGAATTGATATA
65 GTGGTGAT-A-ATATTTTTTATTTCCGATGGAA-TGATTATTTCATCACAAATTGAATTGATAAA
* *
2550367 TTTTTATTAAAGTGAACAAAATTTCCGACGGAATCATTTTTCCATCA
127 TTTTTATTAAAGTGAACAAAATTTCCGACAGAATCATTGTTCCATCA
2550414 ATCACCATCT
Statistics
Matches: 160, Mismatches: 11, Indels: 6
0.90 0.06 0.03
Matches are distributed among these distances:
196 8 0.05
197 59 0.37
198 1 0.01
199 91 0.57
200 1 0.01
ACGTcount: A:0.40, C:0.09, G:0.13, T:0.38
Consensus pattern (197 bp):
TTATAAATGCATATAAATCAAAAAAAATAAAGGATAAAAGCATAAAAATGGTAATTGTTTACAGG
TGGTGATAATATTTTTTATTTCCGATGGAATGATTATTTCATCACAAATTGAATTGATAAATTTT
TATTAAAGTGAACAAAATTTCCGACAGAATCATTGTTCCATCATAAATTAAATTGATATTTTTGT
TT
Found at i:2553985 original size:158 final size:158
Alignment explanation
Indices: 2553693--2554012 Score: 633
Period size: 158 Copynumber: 2.0 Consensus size: 158
2553683 TCACGTGGTA
2553693 TATC-TCATAAACATATAATTTCCTTACCTTTATCACATGTCTCATAAACTTTTCATGCATGTTC
1 TATCATCATAAACATATAATTTCCTTACCTTTATCACATGTCTCATAAACTTTTCATGCATGTTC
2553757 ATTTCAAACATATCACATAATGCATATGGTATGAATTCATATCATGTTTTATCATATGGAACGAA
66 ATTTCAAACATATCACATAATGCATATGGTATGAATTCATATCATGTTTTATCATATGGAACGAA
2553822 TCATGTGTAAAGATATTAAATCTAGACT
131 TCATGTGTAAAGATATTAAATCTAGACT
2553850 TATCATCATAAACATATAATTTCCTTACCTTTATCACATGTCTCATAAACTTTTCATGCATGTTC
1 TATCATCATAAACATATAATTTCCTTACCTTTATCACATGTCTCATAAACTTTTCATGCATGTTC
2553915 ATTTCAAACATATCACATAATGCATATGGTATGAATTCATATCATGTTTTATCATATGGAACGAA
66 ATTTCAAACATATCACATAATGCATATGGTATGAATTCATATCATGTTTTATCATATGGAACGAA
2553980 TCATGTGTAAAGATATTAAATCTAGACT
131 TCATGTGTAAAGATATTAAATCTAGACT
2554008 TATCA
1 TATCA
2554013 CAAGTCTAAA
Statistics
Matches: 162, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
157 4 0.02
158 158 0.98
ACGTcount: A:0.35, C:0.17, G:0.09, T:0.38
Consensus pattern (158 bp):
TATCATCATAAACATATAATTTCCTTACCTTTATCACATGTCTCATAAACTTTTCATGCATGTTC
ATTTCAAACATATCACATAATGCATATGGTATGAATTCATATCATGTTTTATCATATGGAACGAA
TCATGTGTAAAGATATTAAATCTAGACT
Found at i:2554876 original size:7 final size:7
Alignment explanation
Indices: 2554842--2554876 Score: 52
Period size: 7 Copynumber: 5.0 Consensus size: 7
2554832 CACGGTGGAG
*
2554842 AAGAAGG
1 AAGAAGA
*
2554849 AAGAAGG
1 AAGAAGA
2554856 AAGAAGA
1 AAGAAGA
2554863 AAGAAGA
1 AAGAAGA
2554870 AAGAAGA
1 AAGAAGA
2554877 GTTATCTGGA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 27 1.00
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (7 bp):
AAGAAGA
Found at i:2558831 original size:6 final size:6
Alignment explanation
Indices: 2558820--2558856 Score: 65
Period size: 6 Copynumber: 6.2 Consensus size: 6
2558810 TTTCTCTGTT
*
2558820 TCTATA TCTATA TTTATA TCTATA TCTATA TCTATA T
1 TCTATA TCTATA TCTATA TCTATA TCTATA TCTATA T
2558857 ATTATATATC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.32, C:0.14, G:0.00, T:0.54
Consensus pattern (6 bp):
TCTATA
Found at i:2558839 original size:12 final size:12
Alignment explanation
Indices: 2558822--2558863 Score: 66
Period size: 12 Copynumber: 3.4 Consensus size: 12
2558812 TCTCTGTTTC
2558822 TATATCTATATT
1 TATATCTATATT
*
2558834 TATATCTATATC
1 TATATCTATATT
2558846 TATATCTATATAT
1 TATATCTATAT-T
2558859 TATAT
1 TATAT
2558864 ATCGATATAC
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
12 22 0.81
13 5 0.19
ACGTcount: A:0.36, C:0.10, G:0.00, T:0.55
Consensus pattern (12 bp):
TATATCTATATT
Found at i:2560019 original size:36 final size:35
Alignment explanation
Indices: 2559936--2560030 Score: 93
Period size: 35 Copynumber: 2.7 Consensus size: 35
2559926 CTTGATCCTT
* ***
2559936 GTTTTGATGGAACGAGAAGCTTCCCAAATCTTCCA
1 GTTTTGATGGAACGAGAAGGTTCCCAAATAGGCCA
* *
2559971 GTTTTAAGGGAACGAGAAGGTTCCCGAAA-AGGCCA
1 GTTTTGATGGAACGAGAAGGTTCCC-AAATAGGCCA
* *
2560006 GGTTTTGATGGAACAAGAATGTTCC
1 -GTTTTGATGGAACGAGAAGGTTCC
2560031 ATGTACAAAG
Statistics
Matches: 48, Mismatches: 10, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
35 25 0.52
36 23 0.48
ACGTcount: A:0.31, C:0.18, G:0.26, T:0.25
Consensus pattern (35 bp):
GTTTTGATGGAACGAGAAGGTTCCCAAATAGGCCA
Found at i:2560934 original size:9 final size:10
Alignment explanation
Indices: 2560918--2560954 Score: 56
Period size: 10 Copynumber: 3.7 Consensus size: 10
2560908 TTCTAAAATT
*
2560918 CCAAAAAACC
1 CCAAAAATCC
*
2560928 CCTAAAATCC
1 CCAAAAATCC
2560938 CCAAAAATCC
1 CCAAAAATCC
2560948 CCAAAAA
1 CCAAAAA
2560955 CTAGAAACAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
10 24 1.00
ACGTcount: A:0.54, C:0.38, G:0.00, T:0.08
Consensus pattern (10 bp):
CCAAAAATCC
Found at i:2571290 original size:6 final size:5
Alignment explanation
Indices: 2571242--2571278 Score: 51
Period size: 5 Copynumber: 7.6 Consensus size: 5
2571232 TGGGGAAAAA
2571242 TTTA- TTTAT TTCT-T TTTAT TTTAT TTTAT TTTAT TTT
1 TTTAT TTTAT TT-TAT TTTAT TTTAT TTTAT TTTAT TTT
2571279 GGTTTTAATT
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
4 5 0.17
5 24 0.80
6 1 0.03
ACGTcount: A:0.16, C:0.03, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTAT
Found at i:2576337 original size:26 final size:26
Alignment explanation
Indices: 2576301--2576352 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
2576291 GCGTGCATTA
2576301 ATCACAGATAAATCGCAGAGAATCTT
1 ATCACAGATAAATCGCAGAGAATCTT
*
2576327 ATCACGGATAAATCGCAGAGAATCTT
1 ATCACAGATAAATCGCAGAGAATCTT
2576353 GTGATAGTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.40, C:0.19, G:0.17, T:0.23
Consensus pattern (26 bp):
ATCACAGATAAATCGCAGAGAATCTT
Found at i:2577771 original size:26 final size:27
Alignment explanation
Indices: 2577726--2577790 Score: 82
Period size: 25 Copynumber: 2.4 Consensus size: 27
2577716 CAATAAATTC
2577726 ATAAAAAAGAGAAAATAAAAAGATA-AAG
1 ATAAAAAAGA-AAAATAAAAAGA-AGAAG
*
2577754 ATAAAAAAGAAAGA-AAAAAGAAGAAG
1 ATAAAAAAGAAAAATAAAAAGAAGAAG
2577780 A-AAAAAAGAAA
1 ATAAAAAAGAAA
2577791 TAAAGAATAA
Statistics
Matches: 35, Mismatches: 1, Indels: 5
0.85 0.02 0.12
Matches are distributed among these distances:
25 11 0.31
26 11 0.31
27 3 0.09
28 10 0.29
ACGTcount: A:0.78, C:0.00, G:0.15, T:0.06
Consensus pattern (27 bp):
ATAAAAAAGAAAAATAAAAAGAAGAAG
Found at i:2577775 original size:7 final size:7
Alignment explanation
Indices: 2577728--2577858 Score: 78
Period size: 7 Copynumber: 18.7 Consensus size: 7
2577718 ATAAATTCAT
2577728 AAAAAAG
1 AAAAAAG
*
2577735 AGAAAA-
1 AAAAAAG
*
2577741 TAAAAAG
1 AAAAAAG
*
2577748 -ATAAAG
1 AAAAAAG
*
2577754 ATAAAA-
1 AAAAAAG
*
2577760 AAGAAAG
1 AAAAAAG
2577767 AAAAAAG
1 AAAAAAG
*
2577774 -AAGAAG
1 AAAAAAG
2577780 AAAAAAAG
1 -AAAAAAG
2577788 AAATAAAG
1 AAA-AAAG
2577796 AATAAAA-
1 AA-AAAAG
2577803 ATAGAAAA-
1 A-A-AAAAG
*
2577811 AAAATAG
1 AAAAAAG
2577818 -AAAAAG
1 AAAAAAG
2577824 AAAAATAG
1 AAAAA-AG
*
2577832 GAAAAAG
1 AAAAAAG
2577839 AAAAAAG
1 AAAAAAG
2577846 AAAAAAAG
1 -AAAAAAG
2577854 AAAAA
1 AAAAA
2577859 GTGAGAAAAT
Statistics
Matches: 96, Mismatches: 16, Indels: 24
0.71 0.12 0.18
Matches are distributed among these distances:
6 26 0.27
7 36 0.38
8 33 0.34
9 1 0.01
ACGTcount: A:0.79, C:0.00, G:0.15, T:0.06
Consensus pattern (7 bp):
AAAAAAG
Found at i:2577790 original size:8 final size:8
Alignment explanation
Indices: 2577728--2577858 Score: 83
Period size: 8 Copynumber: 15.6 Consensus size: 8
2577718 ATAAATTCAT
2577728 AAAAAAGAG
1 AAAAAA-AG
2577737 AAAATAAA-
1 AAAA-AAAG
*
2577745 AAGATAAAG
1 AA-AAAAAG
2577754 ATAAAAAAG
1 A-AAAAAAG
2577763 AAAGAAAA-
1 AAA-AAAAG
*
2577771 AAGAAGAAG
1 AA-AAAAAG
2577780 AAAAAAAG
1 AAAAAAAG
*
2577788 AAATAAAG
1 AAAAAAAG
2577796 AATAAAAATAG
1 -A-AAAAA-AG
2577807 AAAAAAA-
1 AAAAAAAG
2577814 ATAGAAAAAG
1 A-A-AAAAAG
*
2577824 AAAAATAG
1 AAAAAAAG
*
2577832 -GAAAAAG
1 AAAAAAAG
2577839 -AAAAAAG
1 AAAAAAAG
2577846 AAAAAAAG
1 AAAAAAAG
2577854 AAAAA
1 AAAAA
2577859 GTGAGAAAAT
Statistics
Matches: 98, Mismatches: 10, Indels: 29
0.72 0.07 0.21
Matches are distributed among these distances:
7 12 0.12
8 43 0.44
9 32 0.33
10 9 0.09
11 2 0.02
ACGTcount: A:0.79, C:0.00, G:0.15, T:0.06
Consensus pattern (8 bp):
AAAAAAAG
Found at i:2577802 original size:19 final size:18
Alignment explanation
Indices: 2577769--2577851 Score: 69
Period size: 19 Copynumber: 4.3 Consensus size: 18
2577759 AAAGAAAGAA
*
2577769 AAAAGAAGAAGAAAAAAAG
1 AAAA-AAGAATAAAAAAAG
*
2577788 AAATAAAGAATAAAAATAG
1 AAA-AAAGAATAAAAAAAG
*
2577807 AAAAAA-AATAGAAAAAG
1 AAAAAAGAATAAAAAAAG
*
2577824 AAAAATAGGAAAAAGAAAAAAG
1 AAAAA-A-G-AATA-AAAAAAG
2577846 AAAAAA
1 AAAAAA
2577852 AGAAAAAGTG
Statistics
Matches: 52, Mismatches: 6, Indels: 10
0.76 0.09 0.15
Matches are distributed among these distances:
17 14 0.27
18 4 0.08
19 18 0.35
20 1 0.02
21 4 0.08
22 11 0.21
ACGTcount: A:0.80, C:0.00, G:0.14, T:0.06
Consensus pattern (18 bp):
AAAAAAGAATAAAAAAAG
Found at i:2577842 original size:28 final size:27
Alignment explanation
Indices: 2577729--2577850 Score: 80
Period size: 25 Copynumber: 4.7 Consensus size: 27
2577719 TAAATTCATA
*
2577729 AAAAAGAGAAA-ATAAAAAGATAAAGATA-
1 AAAAAGA-AAATAGAAAAAGA-AAA-ATAG
* * * *
2577757 AAAAAG-AAAGA-AAAAAGAAGAAGAA
1 AAAAAGAAAATAGAAAAAGAAAAATAG
* *
2577782 AAAAAG-AAATA-AAGAATAAAAATAG
1 AAAAAGAAAATAGAAAAAGAAAAATAG
2577807 -AAAA-AAAATAGAAAAAGAAAAATAGG
1 AAAAAGAAAATAGAAAAAGAAAAATA-G
*
2577833 AAAAAGAAAAAAGAAAAA
1 AAAAAGAAAATAGAAAAA
2577851 AAGAAAAAGT
Statistics
Matches: 76, Mismatches: 11, Indels: 14
0.75 0.11 0.14
Matches are distributed among these distances:
24 11 0.14
25 32 0.42
26 11 0.14
27 5 0.07
28 17 0.22
ACGTcount: A:0.79, C:0.00, G:0.15, T:0.07
Consensus pattern (27 bp):
AAAAAGAAAATAGAAAAAGAAAAATAG
Found at i:2577850 original size:13 final size:13
Alignment explanation
Indices: 2577728--2577850 Score: 83
Period size: 13 Copynumber: 8.9 Consensus size: 13
2577718 ATAAATTCAT
2577728 AAAAAAGAGAAAA-
1 AAAAAAGA-AAAAG
* *
2577741 TAAAAAGATAAAG
1 AAAAAAGAAAAAG
*
2577754 ATAAAAA-AGAAAG
1 A-AAAAAGAAAAAG
*
2577767 AAAAAAGAAGAAG
1 AAAAAAGAAAAAG
2577780 AAAAAAAGAAATAAAG
1 -AAAAAAG-AA-AAAG
2577796 AATAAAA-ATAGAAA-
1 AA-AAAAGA-A-AAAG
2577810 AAAAATAGAAAAAG
1 AAAAA-AGAAAAAG
2577824 AAAAATAGGAAAAAG
1 AAAAA-A-GAAAAAG
2577839 AAAAAAGAAAAA
1 AAAAAAGAAAAA
2577851 AAGAAAAAGT
Statistics
Matches: 90, Mismatches: 8, Indels: 24
0.74 0.07 0.20
Matches are distributed among these distances:
12 8 0.09
13 29 0.32
14 25 0.28
15 21 0.23
16 7 0.08
ACGTcount: A:0.79, C:0.00, G:0.15, T:0.07
Consensus pattern (13 bp):
AAAAAAGAAAAAG
Found at i:2577859 original size:14 final size:14
Alignment explanation
Indices: 2577728--2577858 Score: 92
Period size: 15 Copynumber: 9.3 Consensus size: 14
2577718 ATAAATTCAT
*
2577728 AAAAAAGAGAAA-A
1 AAAAAAGAAAAAGA
* *
2577741 TAAAAAGATAAAGA
1 AAAAAAGAAAAAGA
2577755 TAAAAAAG--AAAG-
1 -AAAAAAGAAAAAGA
*
2577767 AAAAAAGAAGAAGA
1 AAAAAAGAAAAAGA
2577781 AAAAAAGAAATAAAGA
1 AAAAAAG-AA-AAAGA
* *
2577797 ATAAAAATAGAAA-A
1 A-AAAAAGAAAAAGA
*
2577811 AAAATAGAAAAAGA
1 AAAAAAGAAAAAGA
*
2577825 AAAATAGGAAAAAGA
1 AAAA-AAGAAAAAGA
*
2577840 AAAAAGAAAAAAAGA
1 AAAAA-AGAAAAAGA
2577855 AAAA
1 AAAA
2577859 GTGAGAAAAT
Statistics
Matches: 93, Mismatches: 14, Indels: 20
0.73 0.11 0.16
Matches are distributed among these distances:
11 7 0.08
13 25 0.27
14 16 0.17
15 34 0.37
16 6 0.06
17 5 0.05
ACGTcount: A:0.79, C:0.00, G:0.15, T:0.06
Consensus pattern (14 bp):
AAAAAAGAAAAAGA
Found at i:2579072 original size:50 final size:50
Alignment explanation
Indices: 2579012--2579110 Score: 171
Period size: 50 Copynumber: 2.0 Consensus size: 50
2579002 CATCCAGGAA
* *
2579012 TACAAAATCATTGAATTGAAGAAACATTTATTTTCAGTGAAACATAAAGG
1 TACAAAATCATTGAATTGAACAAACATTTATTTTCAATGAAACATAAAGG
*
2579062 TACAAGATCATTGAATTGAACAAACATTTATTTTCAATGAAACATAAAG
1 TACAAAATCATTGAATTGAACAAACATTTATTTTCAATGAAACATAAAG
2579111 ATGTGAAGAA
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
50 46 1.00
ACGTcount: A:0.46, C:0.11, G:0.12, T:0.30
Consensus pattern (50 bp):
TACAAAATCATTGAATTGAACAAACATTTATTTTCAATGAAACATAAAGG
Found at i:2579923 original size:38 final size:38
Alignment explanation
Indices: 2579840--2580293 Score: 462
Period size: 38 Copynumber: 11.6 Consensus size: 38
2579830 AACTTGGCTC
* * *
2579840 CCTCGTGAAGAGGAGTCAATCTTTCAATGTCATTCTTGACTC
1 CCTCGTGAAGAGAAGTCAATC-TT---TGTTATTCTTGACTT
* * * *
2579882 CCTCGTGAATAAAAGTCAATCTTTGTTGTTCTTGACTC
1 CCTCGTGAAGAGAAGTCAATCTTTGTTATTCTTGACTT
* * *
2579920 CCTCGCGAAGAGGAGTCAATTCTTTGTTATTCTTAACTT
1 CCTCGTGAAGAGAAGTCAA-TCTTTGTTATTCTTGACTT
* * *
2579959 TCTCGCGAAGAGGAA-TCAATCTTTCAATGTAATTCTTGACTT
1 CCTCGTGAAGA-GAAGTCAATC-TT---TGTTATTCTTGACTT
*
2580001 CCTCGTGAAGAGAAGTCAATCTTTTTTATTCTTGACTT
1 CCTCGTGAAGAGAAGTCAATCTTTGTTATTCTTGACTT
* * *
2580039 CCTTGTGAAGAGAAGTTAATCTTTGTTATTCTTGAATT
1 CCTCGTGAAGAGAAGTCAATCTTTGTTATTCTTGACTT
* *
2580077 CCTCTTGAAGAGAAGTCAATCTATGTTATT-TTGACTT
1 CCTCGTGAAGAGAAGTCAATCTTTGTTATTCTTGACTT
* * * *
2580114 CCTCATTAAGATAAGTCGATCTTTGTTATTCTTGACTT
1 CCTCGTGAAGAGAAGTCAATCTTTGTTATTCTTGACTT
* * *
2580152 CCTTGTGAAGAGAAGTTAATCTTTTTTATTCTTGACTT
1 CCTCGTGAAGAGAAGTCAATCTTTGTTATTCTTGACTT
* *
2580190 CCTCGTGAAGAGAAGTCAATATTTGTTATTCTTGACTC
1 CCTCGTGAAGAGAAGTCAATCTTTGTTATTCTTGACTT
* * *
2580228 CCTTGCGAAGAGGAGTCAATCTTTCAGTGTTATTCTTGACTT
1 CCTCGTGAAGAGAAGTCAATC-TT---TGTTATTCTTGACTT
* * *
2580270 TCTCGTAAAAAGAAGTCAATCTTT
1 CCTCGTGAAGAGAAGTCAATCTTT
2580294 CAGTATTGTC
Statistics
Matches: 343, Mismatches: 57, Indels: 28
0.80 0.13 0.07
Matches are distributed among these distances:
37 31 0.09
38 192 0.56
39 34 0.10
40 2 0.01
41 9 0.03
42 75 0.22
ACGTcount: A:0.25, C:0.18, G:0.17, T:0.40
Consensus pattern (38 bp):
CCTCGTGAAGAGAAGTCAATCTTTGTTATTCTTGACTT
Found at i:2580143 original size:113 final size:114
Alignment explanation
Indices: 2579840--2580293 Score: 437
Period size: 113 Copynumber: 3.9 Consensus size: 114
2579830 AACTTGGCTC
* * * * * *
2579840 CCTCGTGAAGAGGAGTCAATCTTTCAATGTCATTCTTGACTCCCTCGTGAATAAAAGTCAATCTT
1 CCTCGTGAAGAGAAGTCAATC--T--ATGTTATTCTTGACTTCCTCATGAAGAGAAGTCAATCTT
* * * * * *
2579905 TGTTGTTCTTGACTCCCTCGCGAAGAGGAGTCAATTCTTTGTTATTCTT-AACTT
62 TGTTATTCTTGACTTCCTTGTGAAGAGAAGTTAA-TCTTTGTTATTCTTGAA-TT
* * * *
2579959 TCTCGCGAAGAGGAA-TCAATCTTTCAATGTAATTCTTGACTTCCTCGTGAAGAGAAGTCAATCT
1 CCTCGTGAAGA-GAAGTCAATC--T--ATGTTATTCTTGACTTCCTCATGAAGAGAAGTCAATCT
*
2580023 TTTTTATTCTTGACTTCCTTGTGAAGAGAAGTTAATCTTTGTTATTCTTGAATT
61 TTGTTATTCTTGACTTCCTTGTGAAGAGAAGTTAATCTTTGTTATTCTTGAATT
* * * *
2580077 CCTCTTGAAGAGAAGTCAATCTATGTTATT-TTGACTTCCTCATTAAGATAAGTCGATCTTTGTT
1 CCTCGTGAAGAGAAGTCAATCTATGTTATTCTTGACTTCCTCATGAAGAGAAGTCAATCTTTGTT
* *
2580141 ATTCTTGACTTCCTTGTGAAGAGAAGTTAATCTTTTTTATTCTTGACTT
66 ATTCTTGACTTCCTTGTGAAGAGAAGTTAATCTTTGTTATTCTTGAATT
* * * *** *
2580190 CCTCGTGAAGAGAAGTCAATATTTGTTATTCTTGACTCCCTTGCGAAGAGGAGTCAATCTTTCAG
1 CCTCGTGAAGAGAAGTCAATCTATGTTATTCTTGACTTCCTCATGAAGAGAAGTCAATC-TT---
* * * * *
2580255 TGTTATTCTTGACTTTCTCGTAAAAAGAAGTCAATCTTT
62 TGTTATTCTTGACTTCCTTGTGAAGAGAAGTTAATCTTT
2580294 CAGTATTGTC
Statistics
Matches: 286, Mismatches: 41, Indels: 17
0.83 0.12 0.05
Matches are distributed among these distances:
113 103 0.36
114 27 0.09
115 2 0.01
116 1 0.00
117 3 0.01
118 64 0.22
119 84 0.29
120 2 0.01
ACGTcount: A:0.25, C:0.18, G:0.17, T:0.40
Consensus pattern (114 bp):
CCTCGTGAAGAGAAGTCAATCTATGTTATTCTTGACTTCCTCATGAAGAGAAGTCAATCTTTGTT
ATTCTTGACTTCCTTGTGAAGAGAAGTTAATCTTTGTTATTCTTGAATT
Found at i:2580318 original size:45 final size:45
Alignment explanation
Indices: 2580241--2580437 Score: 244
Period size: 45 Copynumber: 4.4 Consensus size: 45
2580231 TGCGAAGAGG
*
2580241 AGTCAATCTTTCAG---TGTTATTCTTGACTTTCTCGTAAAAAGA
1 AGTCAATCTTTCAGTATTGTCATTCTTGACTTTCTCGTAAAAAGA
* *
2580283 AGTCAATCTTTCAGTATTGTCATTCTTGACTTTCTCAGGAAGAAG-
1 AGTCAATCTTTCAGTATTGTCATTCTTGACTTTCTC-GTAAAAAGA
* * * *
2580328 AGTCAATATTTCAATATTGTCATTCTTGACTTTCTCGTGAAGAGA
1 AGTCAATCTTTCAGTATTGTCATTCTTGACTTTCTCGTAAAAAGA
* *
2580373 AGTCAATCTTTCAGTATTGTCATTCTTGACTTT-TC-TACGAAGATA
1 AGTCAATCTTTCAGTATTGTCATTCTTGACTTTCTCGTA--AAAAGA
2580418 AGTCAATCTTTCAGTATTGT
1 AGTCAATCTTTCAGTATTGT
2580438 AAGTCAAACT
Statistics
Matches: 135, Mismatches: 13, Indels: 11
0.85 0.08 0.07
Matches are distributed among these distances:
42 14 0.10
43 1 0.01
44 6 0.04
45 108 0.80
46 6 0.04
ACGTcount: A:0.27, C:0.17, G:0.15, T:0.41
Consensus pattern (45 bp):
AGTCAATCTTTCAGTATTGTCATTCTTGACTTTCTCGTAAAAAGA
Found at i:2580374 original size:90 final size:90
Alignment explanation
Indices: 2580259--2580437 Score: 281
Period size: 90 Copynumber: 2.0 Consensus size: 90
2580249 TTTCAGTGTT
*
2580259 ATTCTTGACTTTCTCGTAAAAAGAAGTCAATCTTTCAGTATTGTCATTCTTGAC-TTTCTCAGGA
1 ATTCTTGACTTTCTCGTAAAAAGAAGTCAATCTTTCAGTATTGTCATTCTTGACTTTTCT-ACGA
2580323 AGA-AGAGTCAATATTTCAATATTGTC
65 AGATA-AGTCAATATTTCAATATTGTC
* *
2580349 ATTCTTGACTTTCTCGTGAAGAGAAGTCAATCTTTCAGTATTGTCATTCTTGACTTTTCTACGAA
1 ATTCTTGACTTTCTCGTAAAAAGAAGTCAATCTTTCAGTATTGTCATTCTTGACTTTTCTACGAA
* *
2580414 GATAAGTCAATCTTTCAGTATTGT
66 GATAAGTCAATATTTCAATATTGT
2580438 AAGTCAAACT
Statistics
Matches: 82, Mismatches: 5, Indels: 4
0.90 0.05 0.04
Matches are distributed among these distances:
90 76 0.93
91 6 0.07
ACGTcount: A:0.28, C:0.17, G:0.15, T:0.40
Consensus pattern (90 bp):
ATTCTTGACTTTCTCGTAAAAAGAAGTCAATCTTTCAGTATTGTCATTCTTGACTTTTCTACGAA
GATAAGTCAATATTTCAATATTGTC
Found at i:2580440 original size:21 final size:21
Alignment explanation
Indices: 2580416--2580456 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
2580406 TCTACGAAGA
* *
2580416 TAAGTCAATCTTTCAGTATTG
1 TAAGTCAAACTCTCAGTATTG
2580437 TAAGTCAAACTCTCAGTATT
1 TAAGTCAAACTCTCAGTATT
2580457 TTCATTCTTG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.32, C:0.17, G:0.12, T:0.39
Consensus pattern (21 bp):
TAAGTCAAACTCTCAGTATTG
Found at i:2580481 original size:66 final size:65
Alignment explanation
Indices: 2580372--2580503 Score: 176
Period size: 66 Copynumber: 2.0 Consensus size: 65
2580362 TCGTGAAGAG
* * *
2580372 AAGTCAATCTTTCAGTATTGTCATTCTTGACTTTTCTACGAAGATAAGTCAATCTTTCAGTATTG
1 AAGTCAAACTCTCAGTATTGTCATTCTTGACTTTTCTA-GAAGAGAAGTCAATCTTTCAGTATTG
2580437 T
65 T
* * *
2580438 AAGTCAAACTCTCAGTATTTTCATTCTTGACTTTCTCGT-GAAGAGGAGTCAATCTTTCAGTGTT
1 AAGTCAAACTCTCAGTATTGTCATTCTTGACTTT-TC-TAGAAGAGAAGTCAATCTTTCAGTATT
2580502 GT
64 GT
2580504 CTTCATTGAC
Statistics
Matches: 58, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
66 55 0.95
67 2 0.03
68 1 0.02
ACGTcount: A:0.26, C:0.17, G:0.16, T:0.41
Consensus pattern (65 bp):
AAGTCAAACTCTCAGTATTGTCATTCTTGACTTTTCTAGAAGAGAAGTCAATCTTTCAGTATTGT
Found at i:2580498 original size:45 final size:45
Alignment explanation
Indices: 2580439--2580636 Score: 222
Period size: 45 Copynumber: 4.4 Consensus size: 45
2580429 CAGTATTGTA
* * *
2580439 AGTCAAACTCTCAGTATTTTCATTCTTGACTTTCTCGTGAAGAGG
1 AGTCAATCTTTCAGTATTTTCCTTCTTGACTTTCTCGTGAAGAGG
* *
2580484 AGTCAATCTTTCAGTGTTGT-CTTCATTGACTTTCTCGTGAAGAGG
1 AGTCAATCTTTCAGTATTTTCCTTC-TTGACTTTCTCGTGAAGAGG
* * * * * *
2580529 AATCAATTTTTCAGT-GTTACCTTCCTTGACTTTCTTGTGAAGATG
1 AGTCAATCTTTCAGTATTTTCCTT-CTTGACTTTCTCGTGAAGAGG
* * *
2580574 AGTCAATCTTTTAGTGTTGTCCTTCTTGACTTTCTCGTGAAGAGG
1 AGTCAATCTTTCAGTATTTTCCTTCTTGACTTTCTCGTGAAGAGG
*
2580619 AGTCAATTTTTCAG-ATTT
1 AGTCAATCTTTCAGTATTT
2580637 GGTCTTCCTG
Statistics
Matches: 125, Mismatches: 24, Indels: 9
0.79 0.15 0.06
Matches are distributed among these distances:
44 6 0.05
45 113 0.90
46 6 0.05
ACGTcount: A:0.22, C:0.18, G:0.19, T:0.42
Consensus pattern (45 bp):
AGTCAATCTTTCAGTATTTTCCTTCTTGACTTTCTCGTGAAGAGG
Found at i:2580526 original size:111 final size:110
Alignment explanation
Indices: 2580342--2580543 Score: 293
Period size: 111 Copynumber: 1.8 Consensus size: 110
2580332 AATATTTCAA
2580342 TATTGTCATTCTTGACTTTCTCGTGAAGAGAAGTCAATCTTTCAGTATTGTCATTCTTGACTTTT
1 TATTGTCATTCTTGACTTTCTCGTGAAGAGAAGTCAATCTTTCAGTATTGTCATTCTTGACTTTT
*
2580407 CTACGAAGA-TAAGTCAATCTTTCAGTATTGTAAGTCAAACTCTCAG
66 CTA-GAAGAGGAA-TCAATCTTTCAGTATTGTAAGTCAAACTCTCAG
* * *
2580453 TATTTTCATTCTTGACTTTCTCGTGAAGAGGAGTCAATCTTTCAGTGTTGTC-TTCATTGACTTT
1 TATTGTCATTCTTGACTTTCTCGTGAAGAGAAGTCAATCTTTCAGTATTGTCATTC-TTGACTTT
*
2580517 CTCGT-GAAGAGGAATCAATTTTTCAGT
65 -TC-TAGAAGAGGAATCAATCTTTCAGT
2580544 GTTACCTTCC
Statistics
Matches: 82, Mismatches: 5, Indels: 8
0.86 0.05 0.08
Matches are distributed among these distances:
110 3 0.04
111 74 0.90
112 4 0.05
113 1 0.01
ACGTcount: A:0.25, C:0.17, G:0.17, T:0.41
Consensus pattern (110 bp):
TATTGTCATTCTTGACTTTCTCGTGAAGAGAAGTCAATCTTTCAGTATTGTCATTCTTGACTTTT
CTAGAAGAGGAATCAATCTTTCAGTATTGTAAGTCAAACTCTCAG
Found at i:2580571 original size:156 final size:156
Alignment explanation
Indices: 2580282--2580593 Score: 400
Period size: 156 Copynumber: 2.0 Consensus size: 156
2580272 TCGTAAAAAG
* *
2580282 AAGTCAATCTTTCAGTATTGTCATTCTTGACTTTCTCAGGAAGAAGAGTCAATATTTCAATATTG
1 AAGTCAAACTCTCAGTATTGTCATTCTTGACTTTCTCAGGAAGAAGAGTCAATATTTCAATATTG
*
2580347 TCATTCTTGACTTTCTCGTGAAGAGAAGTCAATCTTTCAGTATTGTCATTCTTGACTTTTCTACG
66 TCATTCTTGACTTTCTCGTGAAGAGAAGTCAATCTTTCAGTATTGACATTCTTGACTTTTCTACG
2580412 AAGATAAGTCAATCTTTCAGTATTGT
131 AAGATAAGTCAATCTTTCAGTATTGT
* * * * *
2580438 AAGTCAAACTCTCAGTATTTTCATTCTTGACTTTCTC-GTGAAGAGGAGTCAATCTTTCAGTGTT
1 AAGTCAAACTCTCAGTATTGTCATTCTTGACTTTCTCAG-GAAGAAGAGTCAATATTTCAATATT
* * *
2580502 GTC-TTCATTGACTTTCTCGTGAAGAGGAA-TCAATTTTTCAGTGTT-ACCTTCCTTGAC-TTTC
65 GTCATTC-TTGACTTTCTCGTGAAGA-GAAGTCAATCTTTCAGTATTGACATT-CTTGACTTTTC
** * * *
2580563 TTGTGAAGATGAGTCAATCTTTTAGTGTTGT
127 -TACGAAGATAAGTCAATCTTTCAGTATTGT
2580594 CCTTCTTGAC
Statistics
Matches: 135, Mismatches: 16, Indels: 10
0.84 0.10 0.06
Matches are distributed among these distances:
155 11 0.08
156 121 0.90
157 3 0.02
ACGTcount: A:0.25, C:0.17, G:0.17, T:0.41
Consensus pattern (156 bp):
AAGTCAAACTCTCAGTATTGTCATTCTTGACTTTCTCAGGAAGAAGAGTCAATATTTCAATATTG
TCATTCTTGACTTTCTCGTGAAGAGAAGTCAATCTTTCAGTATTGACATTCTTGACTTTTCTACG
AAGATAAGTCAATCTTTCAGTATTGT
Found at i:2580603 original size:90 final size:90
Alignment explanation
Indices: 2580463--2580632 Score: 288
Period size: 90 Copynumber: 1.9 Consensus size: 90
2580453 TATTTTCATT
2580463 CTTGACTTTCTCGTGAAGAGGAGTCAATCTTTCAGTGTTGTCTTCATTGACTTTCTCGTGAAGAG
1 CTTGACTTTCTCGTGAAGAGGAGTCAATCTTTCAGTGTTGTCTTCATTGACTTTCTCGTGAAGAG
2580528 GAATCAATTTTTCAGTGTTACCTTC
66 GAATCAATTTTTCAGTGTTACCTTC
* * *
2580553 CTTGACTTTCTTGTGAAGATGAGTCAATCTTTTAGTGTTGTCCTTC-TTGACTTTCTCGTGAAGA
1 CTTGACTTTCTCGTGAAGAGGAGTCAATCTTTCAGTGTTGT-CTTCATTGACTTTCTCGTGAAGA
*
2580617 GGAGTCAATTTTTCAG
65 GGAATCAATTTTTCAG
2580633 ATTTGGTCTT
Statistics
Matches: 75, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
90 71 0.95
91 4 0.05
ACGTcount: A:0.21, C:0.18, G:0.21, T:0.41
Consensus pattern (90 bp):
CTTGACTTTCTCGTGAAGAGGAGTCAATCTTTCAGTGTTGTCTTCATTGACTTTCTCGTGAAGAG
GAATCAATTTTTCAGTGTTACCTTC
Found at i:2580625 original size:201 final size:200
Alignment explanation
Indices: 2580259--2580632 Score: 488
Period size: 201 Copynumber: 1.9 Consensus size: 200
2580249 TTTCAGTGTT
2580259 ATTCTTGACTTTCTCGTAAAAAGAAGTCAATCTTTCAGTATTGTCATTCTTGACTTTCTCAGGAA
1 ATTCTTGACTTTCTCGTAAAAAGAAGTCAATCTTTCAGTATTGTCATTCTTGACTTTCTCAGGAA
* *
2580324 GAAGAGTCAATATTTCAATATTGTCATTCTTGACTTTCTCGTGAAGAGAAGTCAATCTTTCAGTA
66 GAAGAATCAATATTTCAATATTGACATTCTTGACTTTCTCGTGAAGAGAAGTCAATCTTTCAGTA
*
2580389 TTGTCATTCTTGACTTTTCTACGAAGATAAGTCAATCTTTCAGTATTGTAAGTCAAACTCTCAGT
131 TTGTCATTCTTGACTTTTCTA-GAAGAGAAGTCAATCTTTCAGTATTGTAAGTCAAACTCTCAGT
2580454 ATTTTC
195 ATTTTC
* * * *
2580460 ATTCTTGACTTTCTCGTGAAGAGGAGTCAATCTTTCAGTGTTGTC-TTCATTGACTTTCTC-GTG
1 ATTCTTGACTTTCTCGTAAAAAGAAGTCAATCTTTCAGTATTGTCATTC-TTGACTTTCTCAG-G
* * * * * * *
2580523 AAGAGGAATCAATTTTTCAGTGTT-ACCTTCCTTGACTTTCTTGTGAAGATG-AGTCAATCTTTT
64 AAGAAGAATCAATATTTCAATATTGACATT-CTTGACTTTCTCGTGAAGA-GAAGTCAATCTTTC
* * * *
2580586 AGTGTTGTCCTTCTTGACTTTCTCGT-GAAGAGGAGTCAATTTTTCAG
127 AGTATTGTCATTCTTGACTTT-TC-TAGAAGAGAAGTCAATCTTTCAG
2580633 ATTTGGTCTT
Statistics
Matches: 149, Mismatches: 18, Indels: 12
0.83 0.10 0.07
Matches are distributed among these distances:
200 7 0.05
201 138 0.93
202 3 0.02
203 1 0.01
ACGTcount: A:0.25, C:0.17, G:0.17, T:0.41
Consensus pattern (200 bp):
ATTCTTGACTTTCTCGTAAAAAGAAGTCAATCTTTCAGTATTGTCATTCTTGACTTTCTCAGGAA
GAAGAATCAATATTTCAATATTGACATTCTTGACTTTCTCGTGAAGAGAAGTCAATCTTTCAGTA
TTGTCATTCTTGACTTTTCTAGAAGAGAAGTCAATCTTTCAGTATTGTAAGTCAAACTCTCAGTA
TTTTC
Found at i:2581044 original size:133 final size:132
Alignment explanation
Indices: 2580627--2581133 Score: 490
Period size: 134 Copynumber: 3.8 Consensus size: 132
2580617 GGAGTCAATT
* ** * *
2580627 TTTCAGATTTGGTCTTCCTGAAGAATAGCGAAGCAAATCA-AGTTCGATTCAATCTTCCCTAAAG
1 TTTCAGATTTGGTCTTCCTAAAGAGCAGCGAAGCAAAT-AGAGTTCGATTCAATCTTCCTTGAAG
* * * * * *
2580691 AGTAGGAAAGTGAATCAAAGTTTTCTCGAGTTTGATTTCCCTTAAAGAGTAGTGGCGCAGATTCT
65 AGCAGG-AAGTGAATCAAAGTTTT-TCGAGTCTGATCTCCCCTAAAGAGTAGTGGAGCAAATTCT
2580756 TCTTC
128 TCTTC
* * * * *
2580761 TTTTAGATTTGGTCTTTCTAAAGAGCTGCGAAGCAAAT-GAAGTTCAATTCAATCTT-CTCGAAA
1 TTTCAGATTTGGTCTTCCTAAAGAGCAGCGAAGCAAATAG-AGTTCGATTCAATCTTCCTTG-AA
** * * * * *
2580824 GAGCAACAAAGTGAATCAAAATATTCTCGAGTCTGATCTCCCCTAAAGAGTATTAGATCAAATTC
64 GAGC-AGGAAGTGAATCAAAGT-TTTTCGAGTCTGATCTCCCCTAAAGAGTAGTGGAGCAAATTC
2580889 TTCTTC
127 TTCTTC
* * ** * *
2580895 TTTCAGATTCGGTCTTCCTGAAGAGCAATGAAGCAAATAGA-TTCTTATTCAATCTTCCTTGGAG
1 TTTCAGATTTGGTCTTCCTAAAGAGCAGCGAAGCAAATAGAGTTC-GATTCAATCTTCCTTGAAG
* *
2580959 AGCAGTGAAGTGGATCAAAGTTTTTCGAGTCTGATCTCCCCTAAAGAGTAGTGGAGCATATTCTT
65 AGCAG-GAAGTGAATCAAAGTTTTTCGAGTCTGATCTCCCCTAAAGAGTAGTGGAGCAAATTCTT
2581024 CTTC
129 CTTC
* * * * *
2581028 TTTCATATTTGGTCTTCCTAAAGAGCAGTGAAGCAAATCGA-CTCTGATTCAATCTTCCCTGAAG
1 TTTCAGATTTGGTCTTCCTAAAGAGCAGCGAAGCAAATAGAGTTC-GATTCAATCTTCCTTGAAG
* * *
2581092 AACAATGGAA-TGAATCAACA-TTTCTCGA-TCTGATCTACCCTA
65 AGC-A-GGAAGTGAATCAA-AGTTTTTCGAGTCTGATCTCCCCTA
2581134 CAAAAACAGT
Statistics
Matches: 306, Mismatches: 55, Indels: 26
0.79 0.14 0.07
Matches are distributed among these distances:
132 13 0.04
133 119 0.39
134 166 0.54
135 8 0.03
ACGTcount: A:0.30, C:0.19, G:0.18, T:0.32
Consensus pattern (132 bp):
TTTCAGATTTGGTCTTCCTAAAGAGCAGCGAAGCAAATAGAGTTCGATTCAATCTTCCTTGAAGA
GCAGGAAGTGAATCAAAGTTTTTCGAGTCTGATCTCCCCTAAAGAGTAGTGGAGCAAATTCTTCT
TC
Found at i:2581108 original size:267 final size:266
Alignment explanation
Indices: 2580627--2581133 Score: 616
Period size: 267 Copynumber: 1.9 Consensus size: 266
2580617 GGAGTCAATT
* * *
2580627 TTTCAGATTTGGTCTTCCTGAAGAATAGCGAAGCAAATCAAGTTCGATTCAATCTTCCCTAAAGA
1 TTTCAGATTCGGTCTTCCTGAAGAACAACGAAGCAAATCAAGTTCGATTCAATCTTCCCTAAAGA
* * * * *
2580692 GTAGGAAAGTGAATCAAAGTTTTCTCGAGTTTGATTTCCCTTAAAGAGTAGTGGCGCAGATTCTT
66 GCAGGAAAGTGAATCAAAGTTTTCTCGAGTCTGATCTCCCCTAAAGAGTAGTGGAGCAGATTCTT
* * * * *
2580757 CTTCTTTTAGATTTGGTCTTTCTAAAGAGCTGCGAAGCAAATGAAGTTCAATTCAATCTTCTCGA
131 CTTCTTTCAGATTTGGTCTTCCTAAAGAGCAGCGAAGCAAATGAACTTCAATTCAATCTTCCCGA
* *
2580822 AAGAGCAACAAAGTGAATCAAAATATTCTCGAGTCTGATCTCCCCTAAAGAGTATTAGATCAAAT
196 AAGAACAACAAAGTGAATCAAAAT-TTCTCGA-TCTGATCTACCCTAAAGAGTATTAGATCAAAT
2580887 TCTTCTTC
259 TCTTCTTC
* * * * **
2580895 TTTCAGATTCGGTCTTCCTGAAGAGCAATGAAGCAAAT--AGATTCTTATTCAATCTTCCTTGGA
1 TTTCAGATTCGGTCTTCCTGAAGAACAACGAAGCAAATCAAG-TTC-GATTCAATCTTCCCTAAA
* *
2580958 GAGCAGTG-AAGTGGATCAAAGTTTT-TCGAGTCTGATCTCCCCTAAAGAGTAGTGGAGCATATT
64 GAGCAG-GAAAGTGAATCAAAGTTTTCTCGAGTCTGATCTCCCCTAAAGAGTAGTGGAGCAGATT
* * *
2581021 CTTCTTCTTTCATATTTGGTCTTCCTAAAGAGCAGTGAAGCAAATCG-AC-TCTGATTCAATCTT
128 CTTCTTCTTTCAGATTTGGTCTTCCTAAAGAGCAGCGAAGCAAAT-GAACTTC-AATTCAATCTT
** *
2581084 CCCTG-AAGAACAATGGAA-TGAATCAACATTTCTCGATCTGATCTACCCTA
191 CCC-GAAAGAACAA-CAAAGTGAATCAAAATTTCTCGATCTGATCTACCCTA
2581134 CAAAAACAGT
Statistics
Matches: 203, Mismatches: 29, Indels: 17
0.82 0.12 0.07
Matches are distributed among these distances:
265 13 0.06
266 11 0.05
267 106 0.52
268 72 0.35
269 1 0.00
ACGTcount: A:0.30, C:0.19, G:0.18, T:0.32
Consensus pattern (266 bp):
TTTCAGATTCGGTCTTCCTGAAGAACAACGAAGCAAATCAAGTTCGATTCAATCTTCCCTAAAGA
GCAGGAAAGTGAATCAAAGTTTTCTCGAGTCTGATCTCCCCTAAAGAGTAGTGGAGCAGATTCTT
CTTCTTTCAGATTTGGTCTTCCTAAAGAGCAGCGAAGCAAATGAACTTCAATTCAATCTTCCCGA
AAGAACAACAAAGTGAATCAAAATTTCTCGATCTGATCTACCCTAAAGAGTATTAGATCAAATTC
TTCTTC
Found at i:2581301 original size:3 final size:3
Alignment explanation
Indices: 2581288--2581339 Score: 74
Period size: 3 Copynumber: 18.0 Consensus size: 3
2581278 GGGCCTATCT
2581288 TTA TT- TTA TTA TTA -TA TTA TTA TT- TTA TTA TTA TTTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA
2581331 TTA TTA TTA
1 TTA TTA TTA
2581340 ACGTTTATTT
Statistics
Matches: 45, Mismatches: 0, Indels: 8
0.85 0.00 0.15
Matches are distributed among these distances:
2 6 0.13
3 36 0.80
4 3 0.07
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:2581312 original size:19 final size:18
Alignment explanation
Indices: 2581288--2581339 Score: 86
Period size: 19 Copynumber: 2.8 Consensus size: 18
2581278 GGGCCTATCT
2581288 TTATTTTATTATTATATTA
1 TTATTTTATTATTAT-TTA
2581307 TTATTTTATTATTATTTA
1 TTATTTTATTATTATTTA
2581325 TTATTATTATTATTA
1 TTATT-TTATTATTA
2581340 ACGTTTATTT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
18 8 0.25
19 24 0.75
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (18 bp):
TTATTTTATTATTATTTA
Found at i:2581315 original size:16 final size:18
Alignment explanation
Indices: 2581287--2581337 Score: 72
Period size: 16 Copynumber: 2.9 Consensus size: 18
2581277 CGGGCCTATC
2581287 TTTATT-TTATTATTATA
1 TTTATTATTATTATTATA
2581304 -TTATTATT-TTATTATTA
1 TTTATTATTATTATTA-TA
2581321 TTTATTATTATTATTAT
1 TTTATTATTATTATTAT
2581338 TAACGTTTAT
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
16 11 0.37
17 4 0.13
18 9 0.30
19 6 0.20
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (18 bp):
TTTATTATTATTATTATA
Found at i:2582722 original size:85 final size:85
Alignment explanation
Indices: 2582534--2582703 Score: 263
Period size: 85 Copynumber: 2.0 Consensus size: 85
2582524 ATTTTTATTT
* * *
2582534 CTCAGCAATAACTTTTTGGTTTATTTTTTTACAGGTCCCTCTACTTTATGCGTATTTTTTCCTTT
1 CTCAGCAATAAC-TTTTGGTTTATTTTCTTACAGGTCCCTCTACTTTATGCATATTTTTTCCATT
2582599 CGGTCACTAATCCTCTGTTTA
65 CGGTCACTAATCCTCTGTTTA
* *
2582620 CTCAGCAATAACTTTTTGGTTTA-TTTCTTATAGGTCCCTCTACTTTATGCATGTTTTTT-CATT
1 CTCAGCAATAAC-TTTTGGTTTATTTTCTTACAGGTCCCTCTACTTTATGCATATTTTTTCCATT
2582683 CGGTCACTAATCCTCTGTTTA
65 CGGTCACTAATCCTCTGTTTA
2582704 TTTTATTTCT
Statistics
Matches: 79, Mismatches: 5, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
84 24 0.30
85 32 0.41
86 23 0.29
ACGTcount: A:0.18, C:0.22, G:0.12, T:0.48
Consensus pattern (85 bp):
CTCAGCAATAACTTTTGGTTTATTTTCTTACAGGTCCCTCTACTTTATGCATATTTTTTCCATTC
GGTCACTAATCCTCTGTTTA
Found at i:2586666 original size:32 final size:32
Alignment explanation
Indices: 2586625--2586686 Score: 115
Period size: 32 Copynumber: 1.9 Consensus size: 32
2586615 CATCTATTTT
2586625 CATTGTTCAACTCTTTGACAACACGAAAAATC
1 CATTGTTCAACTCTTTGACAACACGAAAAATC
*
2586657 CATTGTTCAACTCTTTGACAACATGAAAAA
1 CATTGTTCAACTCTTTGACAACACGAAAAA
2586687 ACAAAAAGCT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.39, C:0.23, G:0.10, T:0.29
Consensus pattern (32 bp):
CATTGTTCAACTCTTTGACAACACGAAAAATC
Found at i:2588510 original size:2 final size:2
Alignment explanation
Indices: 2588503--2588540 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
2588493 AGTACATGTA
2588503 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2588541 GATAGTCTTA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2591267 original size:2 final size:2
Alignment explanation
Indices: 2591260--2591287 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2591250 ATATGAAAGA
2591260 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2591288 TATGCTTAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2594126 original size:60 final size:57
Alignment explanation
Indices: 2593989--2594128 Score: 147
Period size: 57 Copynumber: 2.4 Consensus size: 57
2593979 AACTTTATAA
* * **
2593989 GAAATAAATTCAACAATTTCTTTCCTTTTCAAAATAGAATCATGTTAGATTCACAGG
1 GAAATAAATTCAACAATTTATTTCCTTTTCAAAATAGAATCACGCAAGATTCACAGG
* *** *
2594046 AAAATAAATTCAATGGTTTATTTCCTTTTTAAAATTAGAATCAACGCAAGATTCTA-AGG
1 GAAATAAATTCAACAATTTATTTCCTTTTCAAAA-TAGAATC-ACGCAAGATTC-ACAGG
*
2594105 TGAAATAAATTTAACAATTTATTT
1 -GAAATAAATTCAACAATTTATTT
2594129 ATCTTTTCTA
Statistics
Matches: 65, Mismatches: 14, Indels: 5
0.77 0.17 0.06
Matches are distributed among these distances:
57 28 0.43
58 7 0.11
59 11 0.17
60 19 0.29
ACGTcount: A:0.41, C:0.12, G:0.10, T:0.37
Consensus pattern (57 bp):
GAAATAAATTCAACAATTTATTTCCTTTTCAAAATAGAATCACGCAAGATTCACAGG
Found at i:2600148 original size:2 final size:2
Alignment explanation
Indices: 2600143--2600191 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
2600133 AATGAAGTAA
2600143 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2600185 AT AT AT A
1 AT AT AT A
2600192 AGCAGGATAT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2600591 original size:15 final size:16
Alignment explanation
Indices: 2600573--2600612 Score: 57
Period size: 15 Copynumber: 2.6 Consensus size: 16
2600563 AATAAAAGAA
*
2600573 ATTAAAATTATTAA-T
1 ATTAAAATTATAAAGT
2600588 ATTAAAA-TATAAAGT
1 ATTAAAATTATAAAGT
2600603 ATTAAAATTA
1 ATTAAAATTA
2600613 AAGATACTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
14 5 0.23
15 15 0.68
16 2 0.09
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (16 bp):
ATTAAAATTATAAAGT
Found at i:2602004 original size:20 final size:20
Alignment explanation
Indices: 2601981--2602039 Score: 59
Period size: 20 Copynumber: 3.0 Consensus size: 20
2601971 GAACAAGTTA
2601981 TTCTCATTATGAACTTCTTC
1 TTCTCATTATGAACTTCTTC
* * **
2602001 TTCTTCTTTA-GGACTAGTTC
1 TTC-TCATTATGAACTTCTTC
2602021 TTCTCATTATGAAC-TCTTC
1 TTCTCATTATGAACTTCTTC
2602040 CACTGGGAAT
Statistics
Matches: 29, Mismatches: 8, Indels: 5
0.69 0.19 0.12
Matches are distributed among these distances:
19 8 0.28
20 16 0.55
21 5 0.17
ACGTcount: A:0.19, C:0.24, G:0.08, T:0.49
Consensus pattern (20 bp):
TTCTCATTATGAACTTCTTC
Found at i:2602555 original size:238 final size:234
Alignment explanation
Indices: 2602239--2602891 Score: 755
Period size: 235 Copynumber: 2.8 Consensus size: 234
2602229 CGTTATGAAC
* * * *
2602239 TTCTTCCTCTTCAGATAAGTTCTTCTCATTATGAACTTTATCTGGAAATGTTGGTGATGATCTAT
1 TTCTT-CTTTTCAGATGAGTTCTTCTCATTATGAACTCT-TCTGGAAATGTTGATGATGATCTAT
* * *
2602304 CTCCTTCTGTGATAGAGTCAAGCAAAAGATTGAACCAGTTCTTCTCATTATGAACTTCTTCTTCC
64 CTCCTTCTGTGATAGAATCAAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCC
*
2602369 TCTTCAGATGAGTTCTTCTCATTATGAACTTCTTCTGGAAATGTTGATCTTCAAAAGAGGGGTTG
129 TCTTCAGATGAGTTCTTCTCATTATGAACTTCTTCTGGAAATGTTGATC--C-AAAGA-GGGATG
** * * * ** *
2602434 TTAATTC-AGCTTCATATG-TGATGAA-TTAAGGT-AAGATGGAA-CAAA
190 --AATTCGAG--AAAAAGGTTAAACAAGTTAAGCTCAAGAT-GAATCAAA
* * *
2602479 TTCTTCTTTTCAGATGAGTTCTTCTCATTATAAACTCTTCTGGAAATGTTGATGCTGATATATCT
1 TTCTTCTTTTCAGATGAGTTCTTCTCATTATGAACTCTTCTGGAAATGTTGATGATGATCTATCT
* *
2602544 CCTTCTGTGATAGAATCAAGCAAAAGGTTGAACAAGTTCTTCTAATTATGAATTTCTTCTTCCTC
66 CCTTCTGTGATAGAATCAAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTC
* ** *
2602609 TTCAGATGAGTTCTTCTCATTATGAACTT-TCTCTGGAAAAGTTGATCCATCGAGTGATGAATTC
131 TTCAGATGAGTTCTTCTCATTATGAACTTCT-TCTGGAAATGTTGATCCAAAGAGGGATGAATTC
*** ** **
2602673 GAGAAAAAGGTTAAACAAGTTCTTCTCATTATGAACTTCTTA
195 GAGAAAAAGGTTAAACAAGTTAAGCTCAAGATGAA--TCAAA
*** * *
2602715 TTCTT-TTTTCAGATGAGTTCTTCTCATTATGAACTCTTCCAAAAATGTTAATGTTGATCTATCT
1 TTCTTCTTTTCAGATGAGTTCTTCTCATTATGAACTCTTCTGGAAATGTTGATGATGATCTATCT
* *
2602779 CCTTCTGCGATAGAATCGAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTC
66 CCTTCTGTGATAGAATCAAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTC
* *
2602844 TTCAGATGAGTTCTTCTCATTACGAAC-TCTTTTGGAAATGTTGATCCA
131 TTCAGATGAGTTCTTCTCATTATGAACTTCTTCTGGAAATGTTGATCCA
2602892 TCGAGTGATG
Statistics
Matches: 358, Mismatches: 46, Indels: 24
0.84 0.11 0.06
Matches are distributed among these distances:
231 3 0.01
232 9 0.03
233 8 0.02
234 24 0.07
235 143 0.40
236 8 0.02
237 1 0.00
238 128 0.36
239 29 0.08
240 5 0.01
ACGTcount: A:0.27, C:0.18, G:0.16, T:0.39
Consensus pattern (234 bp):
TTCTTCTTTTCAGATGAGTTCTTCTCATTATGAACTCTTCTGGAAATGTTGATGATGATCTATCT
CCTTCTGTGATAGAATCAAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTC
TTCAGATGAGTTCTTCTCATTATGAACTTCTTCTGGAAATGTTGATCCAAAGAGGGATGAATTCG
AGAAAAAGGTTAAACAAGTTAAGCTCAAGATGAATCAAA
Found at i:2602631 original size:122 final size:121
Alignment explanation
Indices: 2602479--2602888 Score: 484
Period size: 122 Copynumber: 3.4 Consensus size: 121
2602469 ATGGAACAAA
* *
2602479 TTCTT-CTTTTCAGATGAGTTCTTCTCATTATAAACTCTTCTGGAAATGTTGATGCTGATATATC
1 TTCTTCCTCTTCAGATGAGTTCTTCTCATTATGAACTCTTCTGGAAATGTTGATGCTGAT-TATC
* * *
2602543 TCCTTCTGTGATAGAATCAAGCAAAAGGTTGAACAAGTTCTTCTAATTATGAATTTC
65 TCCTTCTGTGATAGAATCGAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTC
* * *
2602600 TTCTTCCTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGTTGAT-C----CA--
1 TTCTTCCTCTTCAGATGAGTTCTTCTCATTATGAACTCT-TCTGGAAATGTTGATGCTGATTATC
** * *
2602658 T-C--GAGTGAT-GAATTCGAGAAAAAGGTTAAACAAGTTCTTCTCATTATGAACTTC
65 TCCTTCTGTGATAGAA-TCGAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTC
* * * *** * *
2602712 TTATTCTTTTTTCAGATGAGTTCTTCTCATTATGAACTCTTCCAAAAATGTTAATGTTGATCTAT
1 TTCTTC-CTCTTCAGATGAGTTCTTCTCATTATGAACTCTTCTGGAAATGTTGATGCTGAT-TAT
*
2602777 CTCCTTCTGCGATAGAATCGAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTC
64 CTCCTTCTGTGATAGAATCGAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTC
* *
2602835 TTCTTCCTCTTCAGATGAGTTCTTCTCATTACGAACTCTTTTGGAAATGTTGAT
1 TTCTTCCTCTTCAGATGAGTTCTTCTCATTATGAACTCTTCTGGAAATGTTGAT
2602889 CCATCGAGTG
Statistics
Matches: 236, Mismatches: 37, Indels: 31
0.78 0.12 0.10
Matches are distributed among these distances:
111 3 0.01
112 56 0.24
113 30 0.13
114 1 0.00
115 1 0.00
117 1 0.00
118 1 0.00
120 1 0.00
121 6 0.03
122 71 0.30
123 62 0.26
124 3 0.01
ACGTcount: A:0.27, C:0.18, G:0.15, T:0.40
Consensus pattern (121 bp):
TTCTTCCTCTTCAGATGAGTTCTTCTCATTATGAACTCTTCTGGAAATGTTGATGCTGATTATCT
CCTTCTGTGATAGAATCGAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTC
Found at i:2602967 original size:36 final size:35
Alignment explanation
Indices: 2602927--2603124 Score: 139
Period size: 36 Copynumber: 5.5 Consensus size: 35
2602917 AGTGAAACTG
*
2602927 TCTCAAGCGAGACAAATCTTGTTTTAAGAAAAACAA
1 TCTCAAGTGAGACAAAT-TTGTTTTAAGAAAAACAA
* ** ** **
2602963 TCTCAAGTGAGATAAATTGTTGTTTCGAGTGAAACTG
1 TCTCAAGTGAGACAAA-T-TTGTTTTAAGAAAAACAA
* *
2603000 TCTCAAGTGAGCCAAATTATGTTTTAAGAAAAAAAA
1 TCTCAAGTGAGACAAATT-TGTTTTAAGAAAAACAA
* ** * **
2603036 TCTCAAGTGAGATAAATTTTTGTTTCGAGTAAAACTG
1 TCTCAAGTGAGACAAA--TTTGTTTTAAGAAAAACAA
* *
2603073 TCTCAA--GAGACGCAGTTTGTTTTAAGAAAAACAA
1 TCTCAAGTGAGAC-AAATTTGTTTTAAGAAAAACAA
* *
2603107 TATCAAGTGAGATAAATT
1 TCTCAAGTGAGACAAATT
2603125 ACTATTTGAA
Statistics
Matches: 117, Mismatches: 38, Indels: 15
0.69 0.22 0.09
Matches are distributed among these distances:
34 19 0.16
35 8 0.07
36 44 0.38
37 44 0.38
38 2 0.02
ACGTcount: A:0.39, C:0.12, G:0.18, T:0.31
Consensus pattern (35 bp):
TCTCAAGTGAGACAAATTTGTTTTAAGAAAAACAA
Found at i:2603004 original size:37 final size:36
Alignment explanation
Indices: 2602903--2603079 Score: 147
Period size: 37 Copynumber: 4.8 Consensus size: 36
2602893 CGAGTGATGG
* * *
2602903 AAATTTCTGTTTCTAGTGAAACTGTCTCAAGCGAGAC
1 AAATTT-TGTTTCAAGTAAAACTGTCTCAAGTGAGAC
* * * ** *
2602940 AAATCTTGTTTTAAGAAAAACAATCTCAAGTGAGAT
1 AAATTTTGTTTCAAGTAAAACTGTCTCAAGTGAGAC
* * *
2602976 AAATTGTTGTTTCGAGTGAAACTGTCTCAAGTGAGCC
1 AAATT-TTGTTTCAAGTAAAACTGTCTCAAGTGAGAC
* * * *** *
2603013 AAATTATGTTTTAAGAAAAAAAATCTCAAGTGAGAT
1 AAATTTTGTTTCAAGTAAAACTGTCTCAAGTGAGAC
*
2603049 AAATTTTTGTTTCGAGTAAAACTGTCTCAAG
1 AAA-TTTTGTTTCAAGTAAAACTGTCTCAAG
2603080 AGACGCAGTT
Statistics
Matches: 103, Mismatches: 35, Indels: 4
0.73 0.25 0.03
Matches are distributed among these distances:
36 50 0.49
37 53 0.51
ACGTcount: A:0.37, C:0.13, G:0.18, T:0.33
Consensus pattern (36 bp):
AAATTTTGTTTCAAGTAAAACTGTCTCAAGTGAGAC
Found at i:2603016 original size:73 final size:72
Alignment explanation
Indices: 2602910--2603124 Score: 308
Period size: 73 Copynumber: 3.0 Consensus size: 72
2602900 TGGAAATTTC
* * *
2602910 TGTTTCTAGTGAAACTGTCTCAAGCGAGACAAATCTTGTTTTAAGAAAAACAATCTCAAGTGAGA
1 TGTTTCGAGTGAAACTGTCTCAAGAGAGCCAAAT-TTGTTTTAAGAAAAACAATCTCAAGTGAGA
2602975 TAAATTGT
65 TAAATTGT
* *
2602983 TGTTTCGAGTGAAACTGTCTCAAGTGAGCCAAATTATGTTTTAAGAAAAAAAATCTCAAGTGAGA
1 TGTTTCGAGTGAAACTGTCTCAAGAGAGCCAAATT-TGTTTTAAGAAAAACAATCTCAAGTGAGA
*
2603048 TAAATTTT
65 TAAATTGT
* * *
2603056 TGTTTCGAGTAAAACTGTCTCAAGAGA-CGC-AGTTTGTTTTAAGAAAAACAATATCAAGTGAGA
1 TGTTTCGAGTGAAACTGTCTCAAGAGAGC-CAAATTTGTTTTAAGAAAAACAATCTCAAGTGAGA
2603119 TAAATT
65 TAAATT
2603125 ACTATTTGAA
Statistics
Matches: 130, Mismatches: 10, Indels: 6
0.89 0.07 0.04
Matches are distributed among these distances:
71 33 0.25
72 5 0.04
73 92 0.71
ACGTcount: A:0.38, C:0.12, G:0.18, T:0.32
Consensus pattern (72 bp):
TGTTTCGAGTGAAACTGTCTCAAGAGAGCCAAATTTGTTTTAAGAAAAACAATCTCAAGTGAGAT
AAATTGT
Found at i:2604253 original size:54 final size:54
Alignment explanation
Indices: 2604171--2604308 Score: 186
Period size: 54 Copynumber: 2.6 Consensus size: 54
2604161 TCACTGGTTT
* * * *
2604171 GTAAAACATGTGACAATACATTCATCCTTTCTCGTGGCTTCTGCCCAGATTTTC
1 GTAAAGCATTTGACAACACATTCATCCTTTCTCGTGGCTTCTGCCCAGATGTTC
* * * *
2604225 GTAAAGCTTTTGATAACACATTCATCCTTTCTTGTGGCTTCTGGCCAGATGTTC
1 GTAAAGCATTTGACAACACATTCATCCTTTCTCGTGGCTTCTGCCCAGATGTTC
* *
2604279 GTAAAGCATTTGACAACACGTTCATTCTTT
1 GTAAAGCATTTGACAACACATTCATCCTTT
2604309 TCTGTGGTAT
Statistics
Matches: 72, Mismatches: 12, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
54 72 1.00
ACGTcount: A:0.24, C:0.23, G:0.16, T:0.37
Consensus pattern (54 bp):
GTAAAGCATTTGACAACACATTCATCCTTTCTCGTGGCTTCTGCCCAGATGTTC
Found at i:2609987 original size:27 final size:26
Alignment explanation
Indices: 2609950--2610005 Score: 76
Period size: 27 Copynumber: 2.1 Consensus size: 26
2609940 ATGTAAATGC
**
2609950 AAAAATGAAAATGTAAATACAAACGT
1 AAAAATGAAAATACAAATACAAACGT
*
2609976 AAAAATGCAAAATACAAATACAAATGT
1 AAAAATG-AAAATACAAATACAAACGT
2610003 AAA
1 AAA
2610006 TATGTTAATG
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
26 7 0.27
27 19 0.73
ACGTcount: A:0.64, C:0.09, G:0.09, T:0.18
Consensus pattern (26 bp):
AAAAATGAAAATACAAATACAAACGT
Found at i:2610231 original size:43 final size:44
Alignment explanation
Indices: 2610167--2610253 Score: 113
Period size: 43 Copynumber: 2.0 Consensus size: 44
2610157 CCGTGCATCA
* * * *
2610167 AACAAAACTTTTACATGTAGGGGACAGCTTTCAGTCCTAACTTC
1 AACAAAACATTTACATATAGGGGACAACTTTCACTCCTAACTTC
* *
2610211 AACAAAA-ATTTACATATAGGGGATAACTTTCCCTCCTAACTTC
1 AACAAAACATTTACATATAGGGGACAACTTTCACTCCTAACTTC
2610254 TCTAAAGCCA
Statistics
Matches: 37, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
43 30 0.81
44 7 0.19
ACGTcount: A:0.34, C:0.23, G:0.13, T:0.30
Consensus pattern (44 bp):
AACAAAACATTTACATATAGGGGACAACTTTCACTCCTAACTTC
Found at i:2611234 original size:23 final size:23
Alignment explanation
Indices: 2611186--2611231 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
2611176 ATTTAATATC
2611186 TAAAAATAAAATAAAAACATTAA
1 TAAAAATAAAATAAAAACATTAA
*
2611209 TAAAAA-AAATATAATAAATATTA
1 TAAAAATAAA-ATAA-AAACATTA
2611232 TAAGTAATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 3 0.15
23 10 0.50
24 7 0.35
ACGTcount: A:0.72, C:0.02, G:0.00, T:0.26
Consensus pattern (23 bp):
TAAAAATAAAATAAAAACATTAA
Found at i:2611766 original size:2 final size:2
Alignment explanation
Indices: 2611761--2611785 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2611751 AATTAAATAA
2611761 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
2611786 AGGTTTTGTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2612240 original size:11 final size:11
Alignment explanation
Indices: 2612224--2612257 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
2612214 GACTAAGATG
2612224 AAAATAATAAT
1 AAAATAATAAT
2612235 AAAATAATAATT
1 AAAATAATAA-T
*
2612247 AAAGTAATAAT
1 AAAATAATAAT
2612258 TTAAACATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
11 11 0.52
12 10 0.48
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.29
Consensus pattern (11 bp):
AAAATAATAAT
Found at i:2612254 original size:12 final size:12
Alignment explanation
Indices: 2612224--2612258 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
2612214 GACTAAGATG
2612224 AAAATAATAA-T
1 AAAATAATAATT
2612235 AAAATAATAATT
1 AAAATAATAATT
*
2612247 AAAGTAATAATT
1 AAAATAATAATT
2612259 TAAACATATA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
11 10 0.45
12 12 0.55
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.31
Consensus pattern (12 bp):
AAAATAATAATT
Found at i:2612333 original size:15 final size:15
Alignment explanation
Indices: 2612315--2612372 Score: 57
Period size: 15 Copynumber: 3.9 Consensus size: 15
2612305 AATAATGACC
*
2612315 AAAATAAAAGAAATT
1 AAAATAAAAGATATT
*
2612330 AAAATTAATA-ATATT
1 AAAA-TAAAAGATATT
2612345 AAAATATAAAG-TATT
1 AAAATA-AAAGATATT
*
2612360 AAAATTAAAGATA
1 AAAATAAAAGATA
2612373 CTAATTTGAA
Statistics
Matches: 35, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
14 6 0.17
15 25 0.71
16 4 0.11
ACGTcount: A:0.66, C:0.00, G:0.05, T:0.29
Consensus pattern (15 bp):
AAAATAAAAGATATT
Found at i:2612784 original size:30 final size:30
Alignment explanation
Indices: 2612745--2612830 Score: 84
Period size: 30 Copynumber: 2.9 Consensus size: 30
2612735 TGGCTGGCAA
* * * *
2612745 TGAACCGGCTGAAAACCAGTAGAACC-TGT
1 TGAATCGGCTGAAAACCAGTAAAACCGGGG
* *
2612774 TAGAATCGGCTGAAAATCGGTAAAACCGGGG
1 T-GAATCGGCTGAAAACCAGTAAAACCGGGG
* *
2612805 TGAATCGGCTGAAAACCGGCAAAACC
1 TGAATCGGCTGAAAACCAGTAAAACC
2612831 AGTTTGAACC
Statistics
Matches: 47, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
29 1 0.02
30 44 0.94
31 2 0.04
ACGTcount: A:0.36, C:0.22, G:0.27, T:0.15
Consensus pattern (30 bp):
TGAATCGGCTGAAAACCAGTAAAACCGGGG
Found at i:2613631 original size:21 final size:21
Alignment explanation
Indices: 2613605--2613658 Score: 99
Period size: 21 Copynumber: 2.6 Consensus size: 21
2613595 TAAATAAAAT
*
2613605 CCGGTTCAACCACAGTTGAAC
1 CCGGTTGAACCACAGTTGAAC
2613626 CCGGTTGAACCACAGTTGAAC
1 CCGGTTGAACCACAGTTGAAC
2613647 CCGGTTGAACCA
1 CCGGTTGAACCA
2613659 GTGAACTAGT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.28, C:0.31, G:0.22, T:0.19
Consensus pattern (21 bp):
CCGGTTGAACCACAGTTGAAC
Found at i:2613634 original size:10 final size:10
Alignment explanation
Indices: 2613605--2613657 Score: 61
Period size: 10 Copynumber: 5.1 Consensus size: 10
2613595 TAAATAAAAT
*
2613605 CCGGTTCAAC
1 CCGGTTGAAC
*
2613615 CACAGTTGAAC
1 C-CGGTTGAAC
2613626 CCGGTTGAAC
1 CCGGTTGAAC
*
2613636 CACAGTTGAAC
1 C-CGGTTGAAC
2613647 CCGGTTGAAC
1 CCGGTTGAAC
2613657 C
1 C
2613658 AGTGAACTAG
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
10 19 0.53
11 17 0.47
ACGTcount: A:0.26, C:0.32, G:0.23, T:0.19
Consensus pattern (10 bp):
CCGGTTGAAC
Found at i:2613643 original size:11 final size:11
Alignment explanation
Indices: 2613612--2613658 Score: 62
Period size: 10 Copynumber: 4.5 Consensus size: 11
2613602 AATCCGGTTC
2613612 AACCACAGTTG
1 AACCACAGTTG
*
2613623 AACC-CGGTTG
1 AACCACAGTTG
2613633 AACCACAGTTG
1 AACCACAGTTG
*
2613644 AACC-CGGTTG
1 AACCACAGTTG
2613654 AACCA
1 AACCA
2613659 GTGAACTAGT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
10 18 0.58
11 13 0.42
ACGTcount: A:0.32, C:0.30, G:0.21, T:0.17
Consensus pattern (11 bp):
AACCACAGTTG
Found at i:2614631 original size:12 final size:12
Alignment explanation
Indices: 2614614--2614652 Score: 69
Period size: 12 Copynumber: 3.2 Consensus size: 12
2614604 AAAATATATT
*
2614614 TAATAATTATTA
1 TAATAATTATAA
2614626 TAATAATTATAA
1 TAATAATTATAA
2614638 TAATAATTATAA
1 TAATAATTATAA
2614650 TAA
1 TAA
2614653 AATAAATATA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 26 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (12 bp):
TAATAATTATAA
Found at i:2617110 original size:23 final size:23
Alignment explanation
Indices: 2617080--2617125 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
2617070 TGCTTTGAAG
2617080 TTACACTTTTGTGATTGTAAATT
1 TTACACTTTTGTGATTGTAAATT
2617103 TTACACTTTTGTGATTGTAAATT
1 TTACACTTTTGTGATTGTAAATT
2617126 AACATACTCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.26, C:0.09, G:0.13, T:0.52
Consensus pattern (23 bp):
TTACACTTTTGTGATTGTAAATT
Found at i:2618161 original size:25 final size:24
Alignment explanation
Indices: 2618116--2618182 Score: 64
Period size: 25 Copynumber: 2.7 Consensus size: 24
2618106 ATTTTTTTCT
*
2618116 AAAAAATCAAACACTTA-TTTAATTTA
1 AAAAAAT-AAA-A-TTATTTTAAATTA
2618142 AAAAAATGAAAATTATTTTAAATTA
1 AAAAAAT-AAAATTATTTTAAATTA
* *
2618167 TAAATATAAAATTATT
1 AAAAAATAAAATTATT
2618183 CAAAATTTCA
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
24 12 0.33
25 14 0.39
26 10 0.28
ACGTcount: A:0.57, C:0.04, G:0.01, T:0.37
Consensus pattern (24 bp):
AAAAAATAAAATTATTTTAAATTA
Found at i:2618219 original size:31 final size:31
Alignment explanation
Indices: 2618156--2618219 Score: 83
Period size: 31 Copynumber: 2.1 Consensus size: 31
2618146 AATGAAAATT
* * * * *
2618156 ATTTTAAATTATAAATATAAAATTATTCAAA
1 ATTTCAAAATATAAATATAAAAATACTAAAA
2618187 ATTTCAAAATATAAATATAAAAATACTAAAA
1 ATTTCAAAATATAAATATAAAAATACTAAAA
2618218 AT
1 AT
2618220 AAAAAAAAAT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.59, C:0.05, G:0.00, T:0.36
Consensus pattern (31 bp):
ATTTCAAAATATAAATATAAAAATACTAAAA
Found at i:2618221 original size:15 final size:14
Alignment explanation
Indices: 2618192--2618268 Score: 50
Period size: 15 Copynumber: 5.2 Consensus size: 14
2618182 TCAAAATTTC
*
2618192 AAAATATAAATATA
1 AAAATAAAAATATA
2618206 AAAATACTAAAA-ATA
1 AAAATA--AAAATATA
*
2618221 AAAA-AAAATTATTA
1 AAAATAAAAATA-TA
2618235 AAAATAATAAATATA
1 AAAATAA-AAATATA
* *
2618250 CATATTAAAAATAATA
1 -AAAATAAAAAT-ATA
2618266 AAA
1 AAA
2618269 TTATTATAAA
Statistics
Matches: 49, Mismatches: 6, Indels: 15
0.70 0.09 0.21
Matches are distributed among these distances:
12 3 0.06
13 1 0.02
14 13 0.27
15 17 0.35
16 15 0.31
ACGTcount: A:0.71, C:0.03, G:0.00, T:0.26
Consensus pattern (14 bp):
AAAATAAAAATATA
Found at i:2618920 original size:16 final size:15
Alignment explanation
Indices: 2618880--2618927 Score: 55
Period size: 16 Copynumber: 3.2 Consensus size: 15
2618870 AAGTTTTATT
*
2618880 TTTTATATTT-AATT
1 TTTTATATTTAAATA
2618894 TTTTAATATTTAAATAA
1 TTTT-ATATTTAAAT-A
2618911 TTTTATATTTAAA-A
1 TTTTATATTTAAATA
2618925 TTT
1 TTT
2618928 GAAATAACTT
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
14 8 0.27
15 6 0.20
16 12 0.40
17 4 0.13
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (15 bp):
TTTTATATTTAAATA
Found at i:2619516 original size:21 final size:21
Alignment explanation
Indices: 2619490--2619534 Score: 90
Period size: 21 Copynumber: 2.1 Consensus size: 21
2619480 GTGACCTACC
2619490 ACGTCAATATCATAACAGTCA
1 ACGTCAATATCATAACAGTCA
2619511 ACGTCAATATCATAACAGTCA
1 ACGTCAATATCATAACAGTCA
2619532 ACG
1 ACG
2619535 ATGAAAAATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.42, C:0.24, G:0.11, T:0.22
Consensus pattern (21 bp):
ACGTCAATATCATAACAGTCA
Found at i:2620070 original size:48 final size:48
Alignment explanation
Indices: 2619999--2620094 Score: 192
Period size: 48 Copynumber: 2.0 Consensus size: 48
2619989 AAAGGGAGAA
2619999 GTTGACATTAAGGGTGACATGGATAAGTAACTCTCTTTAACTTCATAC
1 GTTGACATTAAGGGTGACATGGATAAGTAACTCTCTTTAACTTCATAC
2620047 GTTGACATTAAGGGTGACATGGATAAGTAACTCTCTTTAACTTCATAC
1 GTTGACATTAAGGGTGACATGGATAAGTAACTCTCTTTAACTTCATAC
2620095 CTCTCTCTCA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 48 1.00
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.33
Consensus pattern (48 bp):
GTTGACATTAAGGGTGACATGGATAAGTAACTCTCTTTAACTTCATAC
Found at i:2624505 original size:17 final size:20
Alignment explanation
Indices: 2624466--2624506 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
2624456 AATTTTAAAT
2624466 ATTTATAATATTATTTATTTA
1 ATTTATAATATTATTTA-TTA
2624487 ATTTA-AATATT-TTTA-TA
1 ATTTATAATATTATTTATTA
2624504 ATT
1 ATT
2624507 ATATTATATA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
17 5 0.25
19 4 0.20
20 6 0.30
21 5 0.25
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (20 bp):
ATTTATAATATTATTTATTA
Found at i:2624507 original size:29 final size:31
Alignment explanation
Indices: 2624454--2624513 Score: 81
Period size: 29 Copynumber: 2.0 Consensus size: 31
2624444 GAATTAGAAA
2624454 TTAATTTTAAATATTTATAATATTAT-TTAT
1 TTAATTTTAAATATTTATAATATTATATTAT
*
2624484 TTAA-TTTAAATATTT-TTATAATTATATTAT
1 TTAATTTTAAATATTTATAAT-ATTATATTAT
2624514 ATATATATAT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
28 3 0.11
29 16 0.59
30 8 0.30
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (31 bp):
TTAATTTTAAATATTTATAATATTATATTAT
Found at i:2624530 original size:27 final size:28
Alignment explanation
Indices: 2624500--2624558 Score: 70
Period size: 29 Copynumber: 2.1 Consensus size: 28
2624490 TAAATATTTT
*
2624500 TATAAT-TATATT-ATATATATATATTCA
1 TATAATCTATATTAATATACATATATT-A
2624527 TAT-ATCTATATTCAATATACATATATTA
1 TATAATCTATATT-AATATACATATATTA
2624555 TATA
1 TATA
2624559 GAGTTGATAT
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
26 2 0.07
27 9 0.33
28 4 0.15
29 12 0.44
ACGTcount: A:0.44, C:0.07, G:0.00, T:0.49
Consensus pattern (28 bp):
TATAATCTATATTAATATACATATATTA
Found at i:2624898 original size:31 final size:31
Alignment explanation
Indices: 2624862--2624927 Score: 96
Period size: 31 Copynumber: 2.1 Consensus size: 31
2624852 AAACTTCATA
*
2624862 TTTGGTCACTTATTTATTCTAGCATTTATCT
1 TTTGGTCACTCATTTATTCTAGCATTTATCT
* * *
2624893 TTTGGTTACTCATTTATTCTTGCATTTATGT
1 TTTGGTCACTCATTTATTCTAGCATTTATCT
2624924 TTTG
1 TTTG
2624928 CCACTAAATT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.17, C:0.14, G:0.12, T:0.58
Consensus pattern (31 bp):
TTTGGTCACTCATTTATTCTAGCATTTATCT
Found at i:2627698 original size:32 final size:32
Alignment explanation
Indices: 2627655--2627718 Score: 119
Period size: 32 Copynumber: 2.0 Consensus size: 32
2627645 GATGAGACAT
*
2627655 TTATGGTCAGGTTTAACTTGTCATAGGGTGGA
1 TTATGGCCAGGTTTAACTTGTCATAGGGTGGA
2627687 TTATGGCCAGGTTTAACTTGTCATAGGGTGGA
1 TTATGGCCAGGTTTAACTTGTCATAGGGTGGA
2627719 GGTTATGGTG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.22, C:0.11, G:0.31, T:0.36
Consensus pattern (32 bp):
TTATGGCCAGGTTTAACTTGTCATAGGGTGGA
Found at i:2628974 original size:23 final size:23
Alignment explanation
Indices: 2628943--2629020 Score: 138
Period size: 23 Copynumber: 3.4 Consensus size: 23
2628933 TATAACTAAC
*
2628943 ATAAAAAGAACACAACTATTATA
1 ATAATAAGAACACAACTATTATA
2628966 ATAATAAGAACACAACTATTATA
1 ATAATAAGAACACAACTATTATA
*
2628989 ATAATAAGAACACAACTATTACA
1 ATAATAAGAACACAACTATTATA
2629012 ATAATAAGA
1 ATAATAAGA
2629021 GGGAGGAAGA
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 53 1.00
ACGTcount: A:0.59, C:0.13, G:0.05, T:0.23
Consensus pattern (23 bp):
ATAATAAGAACACAACTATTATA
Found at i:2629407 original size:20 final size:20
Alignment explanation
Indices: 2629382--2629454 Score: 146
Period size: 20 Copynumber: 3.6 Consensus size: 20
2629372 AGCTTTGACC
2629382 AGTTTCGAAACTTCTACAAG
1 AGTTTCGAAACTTCTACAAG
2629402 AGTTTCGAAACTTCTACAAG
1 AGTTTCGAAACTTCTACAAG
2629422 AGTTTCGAAACTTCTACAAG
1 AGTTTCGAAACTTCTACAAG
2629442 AGTTTCGAAACTT
1 AGTTTCGAAACTT
2629455 TTCAAGACAA
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 53 1.00
ACGTcount: A:0.34, C:0.19, G:0.15, T:0.32
Consensus pattern (20 bp):
AGTTTCGAAACTTCTACAAG
Found at i:2632364 original size:20 final size:19
Alignment explanation
Indices: 2632297--2632355 Score: 73
Period size: 20 Copynumber: 2.9 Consensus size: 19
2632287 TACTAGTAGG
**
2632297 TTGGTATCCATTTCGAATGAA
1 TTGGTATCCATACCGAA-G-A
2632318 TTGGTATCCATACCGAAGA
1 TTGGTATCCATACCGAAGA
2632337 TTGGGTATCCATACCGAAG
1 TT-GGTATCCATACCGAAG
2632356 GCTTGGTATT
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
19 3 0.09
20 17 0.49
21 15 0.43
ACGTcount: A:0.29, C:0.19, G:0.22, T:0.31
Consensus pattern (19 bp):
TTGGTATCCATACCGAAGA
Found at i:2664481 original size:20 final size:19
Alignment explanation
Indices: 2664422--2664475 Score: 90
Period size: 19 Copynumber: 2.8 Consensus size: 19
2664412 GGATCACATA
*
2664422 TTTTCTATATATTTTAGAT
1 TTTTCTATGTATTTTAGAT
2664441 TTTTCTATGTATTTTAGAT
1 TTTTCTATGTATTTTAGAT
2664460 TTTTCCTATGTATTTT
1 TTTT-CTATGTATTTT
2664476 CTATTTAAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
19 22 0.67
20 11 0.33
ACGTcount: A:0.20, C:0.07, G:0.07, T:0.65
Consensus pattern (19 bp):
TTTTCTATGTATTTTAGAT
Found at i:2666787 original size:14 final size:13
Alignment explanation
Indices: 2666709--2666792 Score: 50
Period size: 13 Copynumber: 6.1 Consensus size: 13
2666699 TTGATAGATT
2666709 ATAAAATAAA-AA
1 ATAAAATAAATAA
*
2666721 ATAAAAATGAAAAAAGA
1 AT-AAAAT--AAATA-A
2666738 ATAAAA-AATATTAA
1 ATAAAATAA-A-TAA
2666752 TATAATAAT-AAT-A
1 -ATAA-AATAAATAA
2666765 ATAAAATAAATAA
1 ATAAAATAAATAA
2666778 ATAAAGATAAATAA
1 ATAAA-ATAAATAA
2666792 A
1 A
2666793 ATTGAGTGAA
Statistics
Matches: 58, Mismatches: 1, Indels: 24
0.70 0.01 0.29
Matches are distributed among these distances:
11 3 0.05
12 9 0.16
13 14 0.24
14 12 0.21
15 9 0.16
16 8 0.14
17 3 0.05
ACGTcount: A:0.74, C:0.00, G:0.04, T:0.23
Consensus pattern (13 bp):
ATAAAATAAATAA
Found at i:2666897 original size:18 final size:19
Alignment explanation
Indices: 2666865--2666907 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 19
2666855 AATAAAAAAT
**
2666865 AAAAATAAAAAATTATTAA
1 AAAAATAAAAAATTAACAA
*
2666884 AAAAAT-AAATATTAACAA
1 AAAAATAAAAAATTAACAA
2666902 AAAAAT
1 AAAAAT
2666908 CGAAACATAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
18 15 0.71
19 6 0.29
ACGTcount: A:0.74, C:0.02, G:0.00, T:0.23
Consensus pattern (19 bp):
AAAAATAAAAAATTAACAA
Found at i:2673834 original size:29 final size:30
Alignment explanation
Indices: 2673801--2673869 Score: 122
Period size: 29 Copynumber: 2.3 Consensus size: 30
2673791 GATTTGAAAG
*
2673801 AGAATTAGGCTTGTAACCTTGG-AAAAAAA
1 AGAATTAGGCTTGTAACCCTGGAAAAAAAA
2673830 AGAATTAGGCTTGTAACCCTGGAAAAAAAA
1 AGAATTAGGCTTGTAACCCTGGAAAAAAAA
2673860 AGAATTAGGC
1 AGAATTAGGC
2673870 CTAATTGCGT
Statistics
Matches: 38, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
29 21 0.55
30 17 0.45
ACGTcount: A:0.45, C:0.12, G:0.22, T:0.22
Consensus pattern (30 bp):
AGAATTAGGCTTGTAACCCTGGAAAAAAAA
Found at i:2674961 original size:20 final size:20
Alignment explanation
Indices: 2674936--2674977 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
2674926 AAACTCAAAT
*
2674936 TGATATAGACTACCAAGAGA
1 TGATATAAACTACCAAGAGA
*
2674956 TGATATAAAGTACCAAGAGA
1 TGATATAAACTACCAAGAGA
2674976 TG
1 TG
2674978 GTACCAAGGG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.45, C:0.12, G:0.21, T:0.21
Consensus pattern (20 bp):
TGATATAAACTACCAAGAGA
Found at i:2677941 original size:20 final size:22
Alignment explanation
Indices: 2677890--2677945 Score: 66
Period size: 20 Copynumber: 2.6 Consensus size: 22
2677880 GCATGGGTAG
2677890 TGCATCGATGCACATGTTAAAGAA
1 TGCATCGATGCAC-TGTT-AAGAA
2677914 TG--TCGATGCACTG-T-AGAA
1 TGCATCGATGCACTGTTAAGAA
2677932 TGCATCGATGCACT
1 TGCATCGATGCACT
2677946 TCAAGGGGAA
Statistics
Matches: 30, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
18 6 0.20
20 11 0.37
21 2 0.07
22 9 0.30
24 2 0.07
ACGTcount: A:0.30, C:0.20, G:0.23, T:0.27
Consensus pattern (22 bp):
TGCATCGATGCACTGTTAAGAA
Found at i:2681858 original size:20 final size:22
Alignment explanation
Indices: 2681813--2681870 Score: 84
Period size: 20 Copynumber: 2.6 Consensus size: 22
2681803 GCATGGGTAG
2681813 TGCATCGATGCACATGTTAAAGAA
1 TGCATCGATGCAC-TGTT-AAGAA
2681837 TGCATCGATGCACTG-T-AGAA
1 TGCATCGATGCACTGTTAAGAA
2681857 TGCATCGATGCACT
1 TGCATCGATGCACT
2681871 TCAAGGGGAA
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
20 18 0.53
22 1 0.03
23 2 0.06
24 13 0.38
ACGTcount: A:0.31, C:0.21, G:0.22, T:0.26
Consensus pattern (22 bp):
TGCATCGATGCACTGTTAAGAA
Found at i:2684031 original size:16 final size:16
Alignment explanation
Indices: 2684010--2684040 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
2684000 CTTAATACAA
2684010 TGAGGAAATCATGAAT
1 TGAGGAAATCATGAAT
2684026 TGAGGAAATCATGAA
1 TGAGGAAATCATGAA
2684041 CCTTATAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.45, C:0.06, G:0.26, T:0.23
Consensus pattern (16 bp):
TGAGGAAATCATGAAT
Found at i:2685923 original size:10 final size:11
Alignment explanation
Indices: 2685902--2685927 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
2685892 ATTTGAGGGA
2685902 TTTTTCGTTTT
1 TTTTTCGTTTT
2685913 TTTTTCGTTTT
1 TTTTTCGTTTT
2685924 TTTT
1 TTTT
2685928 AAGTTGCAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.00, C:0.08, G:0.08, T:0.85
Consensus pattern (11 bp):
TTTTTCGTTTT
Found at i:2699133 original size:12 final size:11
Alignment explanation
Indices: 2699110--2699157 Score: 53
Period size: 12 Copynumber: 4.2 Consensus size: 11
2699100 TTTAAAAATG
2699110 TTTAATTTATTA
1 TTTAA-TTATTA
2699122 CTTTAATTATTA
1 -TTTAATTATTA
2699134 TTTAAATTATTA
1 TTT-AATTATTA
*
2699146 TTTTATT-TTA
1 TTTAATTATTA
2699156 TT
1 TT
2699158 CATATAAATG
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
10 5 0.15
11 6 0.18
12 17 0.52
13 5 0.15
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (11 bp):
TTTAATTATTA
Found at i:2699138 original size:24 final size:22
Alignment explanation
Indices: 2699110--2699157 Score: 60
Period size: 24 Copynumber: 2.1 Consensus size: 22
2699100 TTTAAAAATG
*
2699110 TTTAATTTATTACTTTAATTATTA
1 TTTAAATTATTA-TTTAATT-TTA
*
2699134 TTTAAATTATTATTTTATTTTA
1 TTTAAATTATTATTTAATTTTA
2699156 TT
1 TT
2699158 CATATAAATG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 5 0.23
23 6 0.27
24 11 0.50
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (22 bp):
TTTAAATTATTATTTAATTTTA
Found at i:2699338 original size:16 final size:14
Alignment explanation
Indices: 2699311--2699385 Score: 53
Period size: 15 Copynumber: 4.9 Consensus size: 14
2699301 TACTTATTTT
*
2699311 ATTTTTTTATATCAA
1 ATTTTTTAATAT-AA
2699326 ATTATTTTAATATAA
1 ATT-TTTTAATATAA
2699341 ATTTTTTAGGA-ATAA
1 ATTTTTTA--ATATAA
*
2699356 TTATTCTTATTAATATAT
1 --ATT-TT-TTAATATAA
2699374 ATTTTTTAATAT
1 ATTTTTTAATAT
2699386 TAAGAAAATG
Statistics
Matches: 50, Mismatches: 2, Indels: 17
0.72 0.03 0.25
Matches are distributed among these distances:
14 12 0.24
15 14 0.28
16 12 0.24
17 4 0.08
18 5 0.10
19 3 0.06
ACGTcount: A:0.37, C:0.03, G:0.03, T:0.57
Consensus pattern (14 bp):
ATTTTTTAATATAA
Found at i:2706465 original size:20 final size:18
Alignment explanation
Indices: 2706432--2706470 Score: 51
Period size: 20 Copynumber: 2.1 Consensus size: 18
2706422 ATGAGCAAAG
2706432 AGATGAAGAGAAGAGTGA
1 AGATGAAGAGAAGAGTGA
*
2706450 AGATAGAAGAGCAAGATTGA
1 AGAT-GAAGAG-AAGAGTGA
2706470 A
1 A
2706471 AGAAAAGAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 4 0.22
19 6 0.33
20 8 0.44
ACGTcount: A:0.51, C:0.03, G:0.33, T:0.13
Consensus pattern (18 bp):
AGATGAAGAGAAGAGTGA
Found at i:2711615 original size:123 final size:123
Alignment explanation
Indices: 2711356--2711857 Score: 778
Period size: 123 Copynumber: 4.1 Consensus size: 123
2711346 CACTTGATAG
2711356 ATCAACATTTCCAGAAGAAGTTCGTAATAAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATA
1 ATCAACATTTCCAGAAGAAGTTCGTAATAAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATA
* *
2711421 A-CTGAAGAACTTATTCAACCTTTTGCTTGACTCTATCGCAGAAAGATATAGAGCAGA
66 ATCTGAAGAACTTATTCAACCTTTTGCTTGACTCTATCGCAGAAGGAGATAGAGCAGA
*
2711478 ATCAACATTTCCAGAAGAAGTTCGTAATAAGAATAACTCATCTGAAGAGGAAGAAGAAGTTCATA
1 ATCAACATTTCCAGAAGAAGTTCGTAATAAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATA
*
2711543 ATCTGAAGAACTTATTCAACCTTTTGCTTGACTCTATCGCAGAAGGAGATAGAGCAGC
66 ATCTGAAGAACTTATTCAACCTTTTGCTTGACTCTATCGCAGAAGGAGATAGAGCAGA
* * * *
2711601 ATCAACGTTTCCAGAAGAAGTTTGCAATAAGAAGAACTCATCTAAAGAGGAAGAAGAAGTTCATA
1 ATCAACATTTCCAGAAGAAGTTCGTAATAAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATA
* * *
2711666 ATCTGAAGAACTTATTCAACCTTATGCTTGACTCTATCGCAGAAGGAGACAGAGTAGA
66 ATCTGAAGAACTTATTCAACCTTTTGCTTGACTCTATCGCAGAAGGAGATAGAGCAGA
* * * *
2711724 ATCAACGTTTCCAGAAGGAGTTTGTAATAAGAAGAACTCATTTGAAGAGGAAGAAGAAGTTCATA
1 ATCAACATTTCCAGAAGAAGTTCGTAATAAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATA
* * * * * *
2711789 ATCTGAAGAACTTGTTCAACC-TTAGCTTAATTC-ATCGCATAAGGAGATAGATCA-A
66 ATCTGAAGAACTTATTCAACCTTTTGCTTGACTCTATCGCAGAAGGAGATAGAGCAGA
2711844 CATCAACATTTCCA
1 -ATCAACATTTCCA
2711858 TCTTAATCAA
Statistics
Matches: 351, Mismatches: 27, Indels: 5
0.92 0.07 0.01
Matches are distributed among these distances:
120 1 0.00
121 29 0.08
122 73 0.21
123 248 0.71
ACGTcount: A:0.39, C:0.17, G:0.19, T:0.25
Consensus pattern (123 bp):
ATCAACATTTCCAGAAGAAGTTCGTAATAAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATA
ATCTGAAGAACTTATTCAACCTTTTGCTTGACTCTATCGCAGAAGGAGATAGAGCAGA
Found at i:2712003 original size:16 final size:16
Alignment explanation
Indices: 2711984--2712026 Score: 61
Period size: 16 Copynumber: 2.6 Consensus size: 16
2711974 CATTTTTTCA
2711984 TTTATTATTATTTTAT
1 TTTATTATTATTTTAT
2712000 TTTATTTATT-TTTTAT
1 TTTA-TTATTATTTTAT
2712016 TATTATTATTA
1 T-TTATTATTA
2712027 ATAAATAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
16 16 0.67
17 8 0.33
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (16 bp):
TTTATTATTATTTTAT
Found at i:2713351 original size:12 final size:13
Alignment explanation
Indices: 2713328--2713361 Score: 52
Period size: 12 Copynumber: 2.7 Consensus size: 13
2713318 ATTTCAAATG
2713328 TTTAATTTATTAA
1 TTTAATTTATTAA
2713341 TTTAA-TTATTAA
1 TTTAATTTATTAA
*
2713353 TTTATTTTA
1 TTTAATTTA
2713362 GTCATATAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
12 11 0.58
13 8 0.42
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (13 bp):
TTTAATTTATTAA
Found at i:2713546 original size:15 final size:15
Alignment explanation
Indices: 2713515--2713552 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
2713505 TACTTATTTT
*
2713515 ATTTTTTTATATCAA
1 ATTTTTTAATATCAA
2713530 ATTATTTTAATAT-AA
1 ATT-TTTTAATATCAA
2713545 ATTTTTTA
1 ATTTTTTA
2713553 GGAATAATTA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
14 5 0.24
15 8 0.38
16 8 0.38
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.61
Consensus pattern (15 bp):
ATTTTTTAATATCAA
Found at i:2715657 original size:16 final size:17
Alignment explanation
Indices: 2715626--2715658 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
2715616 CTCTAAATAA
*
2715626 TTTTAATATAGTTTTAT
1 TTTTAATATAGATTTAT
2715643 TTTTAATATA-ATTTAT
1 TTTTAATATAGATTTAT
2715659 ATATTATTGT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (17 bp):
TTTTAATATAGATTTAT
Found at i:2717643 original size:17 final size:19
Alignment explanation
Indices: 2717607--2717660 Score: 58
Period size: 19 Copynumber: 2.9 Consensus size: 19
2717597 TTTTAATAAT
* *
2717607 ATAATATACTATTTTTATTA
1 ATAATATA-TAATATTATTA
2717627 A-AAT-TATAATATTATTA
1 ATAATATATAATATTATTA
*
2717644 ATAATATGTAATATTAT
1 ATAATATATAATATTAT
2717661 AATTTTATTT
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
17 10 0.34
18 5 0.17
19 13 0.45
20 1 0.03
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.50
Consensus pattern (19 bp):
ATAATATATAATATTATTA
Found at i:2717787 original size:17 final size:17
Alignment explanation
Indices: 2717765--2717827 Score: 54
Period size: 17 Copynumber: 3.4 Consensus size: 17
2717755 TCTTAAAATA
2717765 TAATAATATTTTTATTT
1 TAATAATATTTTTATTT
2717782 TAATAATATAATTATTAAAATTT
1 TAATAATAT--TT-TT---ATTT
* *
2717805 TAATGATATTATTATTT
1 TAATAATATTTTTATTT
2717822 TAATAA
1 TAATAA
2717828 GTAATTAATA
Statistics
Matches: 37, Mismatches: 3, Indels: 12
0.71 0.06 0.23
Matches are distributed among these distances:
17 18 0.49
19 2 0.05
20 4 0.11
21 1 0.03
23 12 0.32
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (17 bp):
TAATAATATTTTTATTT
Found at i:2717823 original size:40 final size:39
Alignment explanation
Indices: 2717742--2717856 Score: 121
Period size: 39 Copynumber: 3.0 Consensus size: 39
2717732 TTATTGAATA
* * *
2717742 TTTAA-AATATACTTCTTAAAATATAATAATATTTTTAT
1 TTTAATAATATAATTATTAAAATATAATAATATTATTAT
* *
2717780 TTTAATAATATAATTATTAAAATTTTAATGATATTATTAT
1 TTTAATAATATAATTATTAAAA-TATAATAATATTATTAT
* * *
2717820 TTTAATAA-GTAATTAATATAAT-TAATAATA-TATTAT
1 TTTAATAATATAATTATTAAAATATAATAATATTATTAT
2717856 T
1 T
2717857 CTTATTTTAA
Statistics
Matches: 66, Mismatches: 9, Indels: 6
0.81 0.11 0.07
Matches are distributed among these distances:
36 7 0.11
37 7 0.11
38 6 0.09
39 24 0.36
40 22 0.33
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.50
Consensus pattern (39 bp):
TTTAATAATATAATTATTAAAATATAATAATATTATTAT
Found at i:2717854 original size:20 final size:20
Alignment explanation
Indices: 2717743--2717856 Score: 71
Period size: 20 Copynumber: 5.8 Consensus size: 20
2717733 TATTGAATAT
* *
2717743 TTAA-AATATACTTCTTAAAA
1 TTAATAATATA-TTATTATAA
*
2717763 TATAATAATAT-TT-TTAT-T
1 T-TAATAATATATTATTATAA
*
2717781 TTAATAATATAATTATTAAAA
1 TTAATAATAT-ATTATTATAA
* *
2717802 TT-TTAATGATATTATTAT-T
1 TTAATAAT-ATATTATTATAA
*
2717821 TTAATAAGTA-ATTAATATAA
1 TTAATAA-TATATTATTATAA
2717841 TTAATAATATATTATT
1 TTAATAATATATTATT
2717857 CTTATTTTAA
Statistics
Matches: 72, Mismatches: 11, Indels: 22
0.69 0.10 0.21
Matches are distributed among these distances:
17 9 0.12
18 1 0.01
19 16 0.22
20 33 0.46
21 8 0.11
22 5 0.07
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.50
Consensus pattern (20 bp):
TTAATAATATATTATTATAA
Found at i:2717988 original size:20 final size:23
Alignment explanation
Indices: 2717969--2718017 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
2717959 TTCTAATATT
2717969 TTCA-AAATAATATTATTATTTA
1 TTCATAAATAATATTATTATTTA
*
2717991 TTGATAAATAATATTATTTATTGTA
1 TTCATAAATAATATTA-TTATT-TA
2718016 TT
1 TT
2718018 TGATGTTTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
22 3 0.13
23 11 0.48
24 5 0.22
25 4 0.17
ACGTcount: A:0.41, C:0.02, G:0.04, T:0.53
Consensus pattern (23 bp):
TTCATAAATAATATTATTATTTA
Found at i:2720747 original size:21 final size:21
Alignment explanation
Indices: 2720711--2720763 Score: 65
Period size: 21 Copynumber: 2.5 Consensus size: 21
2720701 TGTATGAACA
2720711 GTATCGATATCCTA--TGGATGAG
1 GTATCGATA-CCTATGTGGA-G-G
2720733 GTATCGATACCTATGTGGAGG
1 GTATCGATACCTATGTGGAGG
2720754 GTATCGATAC
1 GTATCGATAC
2720764 AAGGGGAACT
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
21 15 0.52
22 10 0.34
23 4 0.14
ACGTcount: A:0.26, C:0.15, G:0.28, T:0.30
Consensus pattern (21 bp):
GTATCGATACCTATGTGGAGG
Found at i:2723493 original size:3 final size:3
Alignment explanation
Indices: 2723485--2723520 Score: 63
Period size: 3 Copynumber: 12.0 Consensus size: 3
2723475 TGTTTTAAAT
*
2723485 CTC CTC CTC CTC CTC CCC CTC CTC CTC CTC CTC CTC
1 CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC
2723521 ATCATCATCA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.00, C:0.69, G:0.00, T:0.31
Consensus pattern (3 bp):
CTC
Found at i:2723525 original size:3 final size:3
Alignment explanation
Indices: 2723519--2723585 Score: 134
Period size: 3 Copynumber: 22.3 Consensus size: 3
2723509 CTCCTCCTCC
2723519 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA
2723567 TCA TCA TCA TCA TCA TCA T
1 TCA TCA TCA TCA TCA TCA T
2723586 GCATTATAAG
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 64 1.00
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.34
Consensus pattern (3 bp):
TCA
Found at i:2725337 original size:31 final size:31
Alignment explanation
Indices: 2725302--2725362 Score: 122
Period size: 31 Copynumber: 2.0 Consensus size: 31
2725292 GCATCTGATC
2725302 TTTCTTTTCTTTTTTCAGAATAGTGGATCTG
1 TTTCTTTTCTTTTTTCAGAATAGTGGATCTG
2725333 TTTCTTTTCTTTTTTCAGAATAGTGGATCT
1 TTTCTTTTCTTTTTTCAGAATAGTGGATCT
2725363 CGGATGTTCT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.16, C:0.13, G:0.15, T:0.56
Consensus pattern (31 bp):
TTTCTTTTCTTTTTTCAGAATAGTGGATCTG
Found at i:2730633 original size:12 final size:12
Alignment explanation
Indices: 2730613--2730646 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
2730603 TTCGTGTGAT
2730613 TTTTCGTTATAAA
1 TTTT-GTTATAAA
2730626 TTTTGTTATAAA
1 TTTTGTTATAAA
*
2730638 TTTTTTTAT
1 TTTTGTTAT
2730647 TATACTTATT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
12 16 0.80
13 4 0.20
ACGTcount: A:0.26, C:0.03, G:0.06, T:0.65
Consensus pattern (12 bp):
TTTTGTTATAAA
Found at i:2734044 original size:35 final size:35
Alignment explanation
Indices: 2733968--2734045 Score: 90
Period size: 35 Copynumber: 2.2 Consensus size: 35
2733958 TTAAATACAA
2733968 AAAACTTACAATAAGAATTAAATGGTAAATGATAAC
1 AAAA-TTACAATAAGAATTAAATGGTAAATGATAAC
*
2734004 CAAATTACAATAACTGATATTAAATGGT-AAT-A-AAC
1 AAAATTACAATAA--GA-ATTAAATGGTAAATGATAAC
2734039 AAAATTA
1 AAAATTA
2734046 ATTGAAATAC
Statistics
Matches: 37, Mismatches: 2, Indels: 7
0.80 0.04 0.15
Matches are distributed among these distances:
35 18 0.49
36 4 0.11
37 5 0.14
38 10 0.27
ACGTcount: A:0.55, C:0.09, G:0.09, T:0.27
Consensus pattern (35 bp):
AAAATTACAATAAGAATTAAATGGTAAATGATAAC
Found at i:2734665 original size:18 final size:18
Alignment explanation
Indices: 2734642--2734677 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
2734632 AAGGCGGCGA
* *
2734642 CATCATATATGGTTGCGG
1 CATCATAAATGGCTGCGG
2734660 CATCATAAATGGCTGCGG
1 CATCATAAATGGCTGCGG
2734678 TGGCTGCTGT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.25, C:0.19, G:0.28, T:0.28
Consensus pattern (18 bp):
CATCATAAATGGCTGCGG
Found at i:2736381 original size:17 final size:18
Alignment explanation
Indices: 2736361--2736401 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
2736351 AAATTATATT
2736361 AGTAAAAT-ATTAAATAA
1 AGTAAAATGATTAAATAA
*
2736378 AGTAAAATGCTTAAATAA
1 AGTAAAATGATTAAATAA
*
2736396 ATTAAA
1 AGTAAA
2736402 TACATAATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 8 0.38
18 13 0.62
ACGTcount: A:0.61, C:0.02, G:0.07, T:0.29
Consensus pattern (18 bp):
AGTAAAATGATTAAATAA
Found at i:2744547 original size:12 final size:12
Alignment explanation
Indices: 2744530--2744555 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
2744520 ATAAGAATTA
2744530 AATAAAATAAAT
1 AATAAAATAAAT
2744542 AATAAAATAAAT
1 AATAAAATAAAT
2744554 AA
1 AA
2744556 ATAATTTAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (12 bp):
AATAAAATAAAT
Found at i:2744547 original size:16 final size:16
Alignment explanation
Indices: 2744529--2744560 Score: 55
Period size: 16 Copynumber: 1.9 Consensus size: 16
2744519 GATAAGAATT
2744529 AAATAAAATAAATAATA
1 AAAT-AAATAAATAATA
2744546 AAATAAATAAATAAT
1 AAATAAATAAATAAT
2744561 TTAAAGAGAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (16 bp):
AAATAAATAAATAATA
Found at i:2744978 original size:23 final size:23
Alignment explanation
Indices: 2744952--2745002 Score: 93
Period size: 23 Copynumber: 2.2 Consensus size: 23
2744942 AGCCTTCGCT
*
2744952 TTAGTCTTTGGCTTGAAAGAAAA
1 TTAGCCTTTGGCTTGAAAGAAAA
2744975 TTAGCCTTTGGCTTGAAAGAAAA
1 TTAGCCTTTGGCTTGAAAGAAAA
2744998 TTAGC
1 TTAGC
2745003 TAAGCATGAC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.33, C:0.12, G:0.22, T:0.33
Consensus pattern (23 bp):
TTAGCCTTTGGCTTGAAAGAAAA
Found at i:2745314 original size:43 final size:42
Alignment explanation
Indices: 2745212--2745341 Score: 104
Period size: 43 Copynumber: 3.0 Consensus size: 42
2745202 AATAATGACT
*
2745212 TAAATCCTAATTAAAATACTAAAACCTATTTAAACTAAAATACC
1 TAAATCCTAATTAAAATAC-AAAAACTATTTAAAC-AAAATACC
***
2745256 TAAA-AAGAATATAAAATA-AAAATACTATTTAAA-AATAATATCC
1 TAAATCCTAAT-TAAAATACAAAA-ACTATTTAAACAA-AATA-CC
* * *
2745299 TAAATCCTAATTAAAACATTAAAACCTATTTAAACTAAAATAC
1 TAAATCCTAATTAAAATA-CAAAAACTATTTAAAC-AAAATAC
2745342 AAAGATAAAA
Statistics
Matches: 68, Mismatches: 9, Indels: 18
0.72 0.09 0.19
Matches are distributed among these distances:
41 2 0.03
42 8 0.12
43 24 0.35
44 24 0.35
45 8 0.12
46 2 0.03
ACGTcount: A:0.56, C:0.14, G:0.01, T:0.29
Consensus pattern (42 bp):
TAAATCCTAATTAAAATACAAAAACTATTTAAACAAAATACC
Found at i:2752058 original size:14 final size:14
Alignment explanation
Indices: 2752041--2752081 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
2752031 GCAAACTTTT
*
2752041 TTTTATTCTATTTA
1 TTTTATTTTATTTA
*
2752055 TTTTATTTTAATTA
1 TTTTATTTTATTTA
*
2752069 ATTTATTTTATTT
1 TTTTATTTTATTT
2752082 TTCTCTAAAC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.24, C:0.02, G:0.00, T:0.73
Consensus pattern (14 bp):
TTTTATTTTATTTA
Found at i:2752275 original size:16 final size:15
Alignment explanation
Indices: 2752245--2752274 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
2752235 TCGAACAATG
2752245 CAGTGCAGAAAAAAA
1 CAGTGCAGAAAAAAA
2752260 CAGTGCAGAAAAAAA
1 CAGTGCAGAAAAAAA
2752275 AAACAGTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.60, C:0.13, G:0.20, T:0.07
Consensus pattern (15 bp):
CAGTGCAGAAAAAAA
Done.