Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008242.1 Hibiscus syriacus cultivar Beakdansim tig00110890_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 16962412
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 23 of 73
Found at i:5272800 original size:22 final size:22
Alignment explanation
Indices: 5272752--5272800 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 22
5272742 AATTTGTAGT
5272752 GCAAAAGAAAGAAAAAGAAGAA
1 GCAAAAGAAAGAAAAAGAAGAA
* *
5272774 TCAAAAGCAAAGAAAAAG-TGAA
1 GCAAAAG-AAAGAAAAAGAAGAA
5272796 GCAAA
1 GCAAA
5272801 GTTGCAAAGT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
22 13 0.57
23 10 0.43
ACGTcount: A:0.67, C:0.08, G:0.20, T:0.04
Consensus pattern (22 bp):
GCAAAAGAAAGAAAAAGAAGAA
Found at i:5279236 original size:22 final size:22
Alignment explanation
Indices: 5279196--5279237 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
5279186 ATCAAAAGGG
*
5279196 TTCATAATAATATCTTCATACA
1 TTCATAATAATATCATCATACA
5279218 TTCATAAT-ATCATCATCATA
1 TTCATAATAAT-ATCATCATA
5279238 ACTATAAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 2 0.11
22 16 0.89
ACGTcount: A:0.40, C:0.19, G:0.00, T:0.40
Consensus pattern (22 bp):
TTCATAATAATATCATCATACA
Found at i:5288361 original size:22 final size:22
Alignment explanation
Indices: 5288321--5288362 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
5288311 ATCAAAAGGG
*
5288321 TTCATAATAATATCTTCATACA
1 TTCATAATAATATCATCATACA
5288343 TTCATAAT-ATCATCATCATA
1 TTCATAATAAT-ATCATCATA
5288363 ACTATAAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 2 0.11
22 16 0.89
ACGTcount: A:0.40, C:0.19, G:0.00, T:0.40
Consensus pattern (22 bp):
TTCATAATAATATCATCATACA
Found at i:5288918 original size:17 final size:18
Alignment explanation
Indices: 5288896--5288929 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
5288886 AGATACAACA
*
5288896 TCATCACCATC-TCCATT
1 TCATCAACATCATCCATT
5288913 TCATCAACATCATCCAT
1 TCATCAACATCATCCAT
5288930 CAAGACCATC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.29, C:0.38, G:0.00, T:0.32
Consensus pattern (18 bp):
TCATCAACATCATCCATT
Found at i:5289260 original size:30 final size:30
Alignment explanation
Indices: 5289168--5289261 Score: 138
Period size: 30 Copynumber: 3.1 Consensus size: 30
5289158 CAAGTTGGAA
5289168 AGCTTGGTGGAGCATTTGGAAGACATATAC
1 AGCTTGGTGGAGCATTTGGAAGACATATAC
*
5289198 AACTTAGG-GGAGCATTTGGAAGACATATAC
1 AGCTT-GGTGGAGCATTTGGAAGACATATAC
*
5289228 AGCTTGGTGGAGCATTTAGG-AGACATAAAC
1 AGCTTGGTGGAGCATTT-GGAAGACATATAC
5289258 AGCT
1 AGCT
5289262 CACAAACAGC
Statistics
Matches: 58, Mismatches: 3, Indels: 6
0.87 0.04 0.09
Matches are distributed among these distances:
29 2 0.03
30 52 0.90
31 4 0.07
ACGTcount: A:0.33, C:0.14, G:0.29, T:0.24
Consensus pattern (30 bp):
AGCTTGGTGGAGCATTTGGAAGACATATAC
Found at i:5289270 original size:11 final size:11
Alignment explanation
Indices: 5289254--5289278 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
5289244 TAGGAGACAT
5289254 AAACAGCTCAC
1 AAACAGCTCAC
5289265 AAACAGCTCAC
1 AAACAGCTCAC
5289276 AAA
1 AAA
5289279 GAACATGGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.52, C:0.32, G:0.08, T:0.08
Consensus pattern (11 bp):
AAACAGCTCAC
Found at i:5299706 original size:25 final size:26
Alignment explanation
Indices: 5299675--5299733 Score: 72
Period size: 23 Copynumber: 2.4 Consensus size: 26
5299665 AAAATCCAGC
5299675 AAAGAAAAAGCACTC-AAAA-GAAGA
1 AAAGAAAAAGCACTCAAAAATGAAGA
*
5299699 AATTG--AAAGCACTCAAAAATGAAGA
1 AA-AGAAAAAGCACTCAAAAATGAAGA
5299724 AAAGAAAAAG
1 AAAGAAAAAG
5299734 AAAGAAAGTT
Statistics
Matches: 28, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
23 9 0.32
24 7 0.25
25 8 0.29
26 4 0.14
ACGTcount: A:0.64, C:0.10, G:0.17, T:0.08
Consensus pattern (26 bp):
AAAGAAAAAGCACTCAAAAATGAAGA
Found at i:5314456 original size:90 final size:89
Alignment explanation
Indices: 5314298--5314474 Score: 300
Period size: 90 Copynumber: 2.0 Consensus size: 89
5314288 CCTAACACAC
* *
5314298 CCTTTTATAGCCAAGTTACCCTAATCATATTAGGGTTTTATTATTTCAAATTAATTAAATCTATA
1 CCTTTTATAGCCAAGTTACCCTAATCATATTAGGATTTTATTATTTCAAATTAATTAAATATATA
* *
5314363 TTTAATTAATTGGAATTTAATAAT
66 TTTAATTAATTGAAATTAAATAAT
*
5314387 CCTTTTATATCCAAGTTACCCTAATCATATTAGGAATTTTATTATTTCAAATTAATTAAATATAT
1 CCTTTTATAGCCAAGTTACCCTAATCATATTAGG-ATTTTATTATTTCAAATTAATTAAATATAT
5314452 ATTTAATTAATTGAAATTAAATA
65 ATTTAATTAATTGAAATTAAATA
5314475 TTCAGGATTA
Statistics
Matches: 82, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
89 33 0.40
90 49 0.60
ACGTcount: A:0.38, C:0.11, G:0.06, T:0.45
Consensus pattern (89 bp):
CCTTTTATAGCCAAGTTACCCTAATCATATTAGGATTTTATTATTTCAAATTAATTAAATATATA
TTTAATTAATTGAAATTAAATAAT
Found at i:5314506 original size:22 final size:21
Alignment explanation
Indices: 5314444--5314506 Score: 54
Period size: 22 Copynumber: 2.8 Consensus size: 21
5314434 CAAATTAATT
*
5314444 AAATATATATTTAATTAATTGA
1 AAATATATATTTAATT-ATTAA
* * *
5314466 AATTAAATATTCAGGATTATTAA
1 AAATATATATTTA--ATTATTAA
5314489 AACATATATATTTAATTA
1 AA-ATATATATTTAATTA
5314507 ACTCTAGATA
Statistics
Matches: 31, Mismatches: 7, Indels: 6
0.70 0.16 0.14
Matches are distributed among these distances:
22 14 0.45
23 6 0.19
24 11 0.35
ACGTcount: A:0.49, C:0.03, G:0.05, T:0.43
Consensus pattern (21 bp):
AAATATATATTTAATTATTAA
Found at i:5318332 original size:19 final size:21
Alignment explanation
Indices: 5318308--5318359 Score: 72
Period size: 21 Copynumber: 2.6 Consensus size: 21
5318298 CGGCCAAGAG
*
5318308 CATGTATCTTCA-TT-AAAAT
1 CATGTATTTTCATTTAAAAAT
5318327 CATGTATTTTCATTTAAAAAT
1 CATGTATTTTCATTTAAAAAT
*
5318348 CTTGTATTTTCA
1 CATGTATTTTCA
5318360 AAGGGGTTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 11 0.38
20 2 0.07
21 16 0.55
ACGTcount: A:0.33, C:0.13, G:0.06, T:0.48
Consensus pattern (21 bp):
CATGTATTTTCATTTAAAAAT
Found at i:5319135 original size:18 final size:17
Alignment explanation
Indices: 5319086--5319135 Score: 55
Period size: 18 Copynumber: 2.8 Consensus size: 17
5319076 AATTGGAGTG
5319086 CAAAAAGAAAGAAAAAGA
1 CAAAAAGAAA-AAAAAGA
**
5319104 CAAAAAGAAGAAAAAATT
1 CAAAAAGAA-AAAAAAGA
5319122 CAGAAAAGAAAAAA
1 CA-AAAAGAAAAAA
5319136 GAAATTTCAA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
18 20 0.71
19 8 0.29
ACGTcount: A:0.76, C:0.06, G:0.14, T:0.04
Consensus pattern (17 bp):
CAAAAAGAAAAAAAAGA
Found at i:5327323 original size:35 final size:35
Alignment explanation
Indices: 5327282--5327397 Score: 196
Period size: 35 Copynumber: 3.3 Consensus size: 35
5327272 TGGTAAGGGA
*
5327282 ATGGTGATGATATAGGCATGAAATGGTGATAGAAG
1 ATGGTGATGATATAGGCATGAAATGGTGATGGAAG
*
5327317 ATGGTGATGATATAGGCATGCAATGGTGATGGAAG
1 ATGGTGATGATATAGGCATGAAATGGTGATGGAAG
*
5327352 ATGGTGATGATATAGGCGTGAAAATGGTGATGGAAG
1 ATGGTGATGATATAGGCATG-AAATGGTGATGGAAG
5327388 ATGGTGATGA
1 ATGGTGATGA
5327398 AAATAGTATC
Statistics
Matches: 76, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
35 52 0.68
36 24 0.32
ACGTcount: A:0.34, C:0.03, G:0.37, T:0.26
Consensus pattern (35 bp):
ATGGTGATGATATAGGCATGAAATGGTGATGGAAG
Found at i:5327357 original size:13 final size:13
Alignment explanation
Indices: 5327339--5327396 Score: 52
Period size: 13 Copynumber: 4.7 Consensus size: 13
5327329 TAGGCATGCA
5327339 ATGGTGATGGAAG
1 ATGGTGATGGAAG
*
5327352 ATGGTGAT-G-AT
1 ATGGTGATGGAAG
* *
5327363 ATAGGCG-T-GAAA
1 AT-GGTGATGGAAG
5327375 ATGGTGATGGAAG
1 ATGGTGATGGAAG
5327388 ATGGTGATG
1 ATGGTGATG
5327397 AAAATAGTAT
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
11 8 0.22
12 8 0.22
13 20 0.56
ACGTcount: A:0.31, C:0.02, G:0.41, T:0.26
Consensus pattern (13 bp):
ATGGTGATGGAAG
Found at i:5327776 original size:19 final size:20
Alignment explanation
Indices: 5327734--5327784 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
5327724 GAAACCCCTT
*
5327734 TGAAAATACATGATTTTTAA
1 TGAAAATACATGATTTTAAA
*
5327754 TGAAAATACATTA-TTTAAA
1 TGAAAATACATGATTTTAAA
*
5327773 TGAAGATACATG
1 TGAAAATACATG
5327785 CTCTTGGCCG
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
19 15 0.56
20 12 0.44
ACGTcount: A:0.47, C:0.06, G:0.12, T:0.35
Consensus pattern (20 bp):
TGAAAATACATGATTTTAAA
Found at i:5331362 original size:21 final size:23
Alignment explanation
Indices: 5331329--5331370 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
5331319 ATATGCTTGA
5331329 ATATCAATCAATG-ATGCAAACC
1 ATATCAATCAATGAATGCAAACC
*
5331351 ATAT-AATGAATGAATGCAAA
1 ATATCAATCAATGAATGCAAA
5331371 TGTTATGATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.50, C:0.14, G:0.12, T:0.24
Consensus pattern (23 bp):
ATATCAATCAATGAATGCAAACC
Found at i:5335689 original size:23 final size:24
Alignment explanation
Indices: 5335650--5335711 Score: 67
Period size: 23 Copynumber: 2.5 Consensus size: 24
5335640 AAAAAAAGGA
5335650 AGAAAAGACAAAAAGAAGAAA-A-TTC
1 AGAAAAG--AAAAAGAA-AAAGATTTC
5335675 AGAAAAGAAAAAGAAAAAGATTTC
1 AGAAAAGAAAAAGAAAAAGATTTC
5335699 A-AAAAGAGAAAAG
1 AGAAAAGA-AAAAG
5335712 CAAGCCAAGG
Statistics
Matches: 34, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
22 3 0.09
23 15 0.44
24 9 0.26
25 7 0.21
ACGTcount: A:0.69, C:0.05, G:0.18, T:0.08
Consensus pattern (24 bp):
AGAAAAGAAAAAGAAAAAGATTTC
Found at i:5345319 original size:19 final size:20
Alignment explanation
Indices: 5345276--5345329 Score: 83
Period size: 19 Copynumber: 2.7 Consensus size: 20
5345266 GAAACCCCTT
5345276 TGAAAATACATGATTTTTAAA
1 TGAAAATACATGA-TTTTAAA
5345297 TGAAAATACATGATTTT-AA
1 TGAAAATACATGATTTTAAA
*
5345316 TGAAGATACATGAT
1 TGAAAATACATGAT
5345330 CTTGGCCAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 15 0.47
20 4 0.12
21 13 0.41
ACGTcount: A:0.46, C:0.06, G:0.13, T:0.35
Consensus pattern (20 bp):
TGAAAATACATGATTTTAAA
Found at i:5349895 original size:9 final size:8
Alignment explanation
Indices: 5349880--5349920 Score: 55
Period size: 9 Copynumber: 4.9 Consensus size: 8
5349870 ATTGGAGTAC
5349880 AAAAAGAA
1 AAAAAGAA
*
5349888 AGAAAAGAC
1 A-AAAAGAA
5349897 AAAAAGAA
1 AAAAAGAA
5349905 GAAAAAGAA
1 -AAAAAGAA
5349914 AAAAAGA
1 AAAAAGA
5349921 TTTCAAAAAG
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
8 14 0.48
9 15 0.52
ACGTcount: A:0.80, C:0.02, G:0.17, T:0.00
Consensus pattern (8 bp):
AAAAAGAA
Found at i:5349900 original size:17 final size:18
Alignment explanation
Indices: 5349878--5349920 Score: 63
Period size: 17 Copynumber: 2.5 Consensus size: 18
5349868 AAATTGGAGT
5349878 ACAAAAAGAAAG-AAAAG
1 ACAAAAAGAAAGAAAAAG
5349895 ACAAAAAG-AAGAAAAAG
1 ACAAAAAGAAAGAAAAAG
*
5349912 AAAAAAAGA
1 ACAAAAAGA
5349921 TTTCAAAAAG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
16 3 0.13
17 20 0.87
ACGTcount: A:0.79, C:0.05, G:0.16, T:0.00
Consensus pattern (18 bp):
ACAAAAAGAAAGAAAAAG
Found at i:5354841 original size:19 final size:21
Alignment explanation
Indices: 5354798--5354849 Score: 81
Period size: 19 Copynumber: 2.6 Consensus size: 21
5354788 GAAACCCCTT
5354798 TGAAAATACATGATTTTTAAA
1 TGAAAATACATGATTTTTAAA
5354819 TGAAAATACATGA-TTTT-AA
1 TGAAAATACATGATTTTTAAA
*
5354838 TGAAGATACATG
1 TGAAAATACATG
5354850 CTCTTGGCCG
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 13 0.43
20 4 0.13
21 13 0.43
ACGTcount: A:0.46, C:0.06, G:0.13, T:0.35
Consensus pattern (21 bp):
TGAAAATACATGATTTTTAAA
Found at i:5361891 original size:16 final size:16
Alignment explanation
Indices: 5361860--5361906 Score: 51
Period size: 16 Copynumber: 2.8 Consensus size: 16
5361850 TGGTAATGAA
5361860 ATAAGAAAAGATGAAA-G
1 ATAA-AAAA-ATGAAATG
*
5361877 AATAAAGAAATGAAATG
1 -ATAAAAAAATGAAATG
5361894 ATAAAAAAATGAA
1 ATAAAAAAATGAA
5361907 GATAACTTAG
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
16 18 0.69
17 4 0.15
18 4 0.15
ACGTcount: A:0.68, C:0.00, G:0.17, T:0.15
Consensus pattern (16 bp):
ATAAAAAAATGAAATG
Found at i:5363142 original size:19 final size:20
Alignment explanation
Indices: 5363101--5363151 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
5363091 GAAACCCCTT
*
5363101 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTTAA
*
5363121 TGAAAATACATTA-TTTTAA
1 TGAAAATACATGATTTTTAA
*
5363140 TGAAGATACATG
1 TGAAAATACATG
5363152 CTCTTGGCCG
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
19 15 0.56
20 12 0.44
ACGTcount: A:0.43, C:0.06, G:0.14, T:0.37
Consensus pattern (20 bp):
TGAAAATACATGATTTTTAA
Found at i:5368542 original size:33 final size:33
Alignment explanation
Indices: 5368505--5368573 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
5368495 GTTGATGAAT
*
5368505 GAAGGATGAT-TTAATGGTGATGAAATGGTAATG
1 GAAGGATGATGTTAATGGCG-TGAAATGGTAATG
* * *
5368538 GAAGGATGATGTTATTGGCGTGATATGGTGATG
1 GAAGGATGATGTTAATGGCGTGAAATGGTAATG
5368571 GAA
1 GAA
5368574 TATGGTGATG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
33 24 0.77
34 7 0.23
ACGTcount: A:0.32, C:0.01, G:0.36, T:0.30
Consensus pattern (33 bp):
GAAGGATGATGTTAATGGCGTGAAATGGTAATG
Found at i:5368578 original size:13 final size:12
Alignment explanation
Indices: 5368560--5368657 Score: 55
Period size: 13 Copynumber: 8.1 Consensus size: 12
5368550 TATTGGCGTG
5368560 ATATGGTGATGGA
1 ATATGGTGAT-GA
5368573 ATATGGTGATG-
1 ATATGGTGATGA
*
5368584 ATATAGGCG-TG-
1 ATAT-GGTGATGA
5368595 ATAATGGTGATGGA
1 AT-ATGGTGAT-GA
*
5368609 CTATGGTGATGA
1 ATATGGTGATGA
5368621 TATATGCGTGAT--
1 -ATATG-GTGATGA
*
5368633 A-ATGGAGATGGA
1 ATATGGTGAT-GA
*
5368645 TTATGGTGATGA
1 ATATGGTGATGA
5368657 A
1 A
5368658 AATAGTATCT
Statistics
Matches: 66, Mismatches: 8, Indels: 23
0.68 0.08 0.24
Matches are distributed among these distances:
9 4 0.06
10 3 0.05
11 12 0.18
12 11 0.17
13 30 0.45
14 6 0.09
ACGTcount: A:0.31, C:0.03, G:0.35, T:0.32
Consensus pattern (12 bp):
ATATGGTGATGA
Found at i:5368614 original size:36 final size:36
Alignment explanation
Indices: 5368544--5368656 Score: 165
Period size: 36 Copynumber: 3.2 Consensus size: 36
5368534 AATGGAAGGA
* *
5368544 TGATGTTATTGGCGTGAT-ATGGTGATGGAATATGG
1 TGATGATATAGGCGTGATAATGGTGATGGAATATGG
*
5368579 TGATGATATAGGCGTGATAATGGTGATGGACTATGG
1 TGATGATATAGGCGTGATAATGGTGATGGAATATGG
* * *
5368615 TGATGATATATGCGTGATAATGGAGATGGATTATGG
1 TGATGATATAGGCGTGATAATGGTGATGGAATATGG
5368651 TGATGA
1 TGATGA
5368657 AAATAGTATC
Statistics
Matches: 71, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
35 16 0.23
36 55 0.77
ACGTcount: A:0.27, C:0.04, G:0.35, T:0.34
Consensus pattern (36 bp):
TGATGATATAGGCGTGATAATGGTGATGGAATATGG
Found at i:5373070 original size:20 final size:22
Alignment explanation
Indices: 5373041--5373080 Score: 57
Period size: 20 Copynumber: 1.9 Consensus size: 22
5373031 GGGAGAGCTT
5373041 TGGACCAAA-GT-GCTGAAAAG
1 TGGACCAAAGGTAGCTGAAAAG
*
5373061 TGGACTAAAGGTAGCTGAAA
1 TGGACCAAAGGTAGCTGAAA
5373081 GTAGCTGGGA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 8 0.47
21 2 0.12
22 7 0.41
ACGTcount: A:0.40, C:0.12, G:0.30, T:0.17
Consensus pattern (22 bp):
TGGACCAAAGGTAGCTGAAAAG
Found at i:5376775 original size:20 final size:22
Alignment explanation
Indices: 5376746--5376785 Score: 57
Period size: 20 Copynumber: 1.9 Consensus size: 22
5376736 GGGAGAGCTT
5376746 TGGACCAAA-GT-GCTGAAAAG
1 TGGACCAAAGGTAGCTGAAAAG
*
5376766 TGGACTAAAGGTAGCTGAAA
1 TGGACCAAAGGTAGCTGAAA
5376786 GTAGCTGGGA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 8 0.47
21 2 0.12
22 7 0.41
ACGTcount: A:0.40, C:0.12, G:0.30, T:0.17
Consensus pattern (22 bp):
TGGACCAAAGGTAGCTGAAAAG
Found at i:5378640 original size:33 final size:33
Alignment explanation
Indices: 5378572--5378711 Score: 88
Period size: 36 Copynumber: 4.1 Consensus size: 33
5378562 GTTGATGAAT
* * * *
5378572 GAAGGATGAT-TTAATGGTGATGAAATGGTAATG
1 GAAGGATGATGTTATTGGCG-TGATATGGTGATG
*
5378605 GAAGGATGATGTTATTGGCGTGATATGGTGTTG
1 GAAGGATGATGTTATTGGCGTGATATGGTGATG
* *
5378638 GAATATGG-TGATGATATAGGCGTGATAATGGTGATG
1 G-A-A-GGATGATGTTATTGGCGTGAT-ATGGTGATG
* * *
5378674 GACTATGG-TGATGATATAGGCGTGATAATGGAGATG
1 GA--A-GGATGATGTTATTGGCGTGAT-ATGGTGATG
5378710 GA
1 GA
5378712 TTATGGTGAT
Statistics
Matches: 92, Mismatches: 9, Indels: 9
0.84 0.08 0.08
Matches are distributed among these distances:
33 21 0.23
34 8 0.09
35 18 0.20
36 45 0.49
ACGTcount: A:0.30, C:0.03, G:0.36, T:0.31
Consensus pattern (33 bp):
GAAGGATGATGTTATTGGCGTGATATGGTGATG
Found at i:5378681 original size:36 final size:36
Alignment explanation
Indices: 5378611--5378723 Score: 165
Period size: 36 Copynumber: 3.2 Consensus size: 36
5378601 AATGGAAGGA
* * *
5378611 TGATGTTATTGGCGTGAT-ATGGTGTTGGAATATGG
1 TGATGATATAGGCGTGATAATGGTGATGGAATATGG
*
5378646 TGATGATATAGGCGTGATAATGGTGATGGACTATGG
1 TGATGATATAGGCGTGATAATGGTGATGGAATATGG
* *
5378682 TGATGATATAGGCGTGATAATGGAGATGGATTATGG
1 TGATGATATAGGCGTGATAATGGTGATGGAATATGG
5378718 TGATGA
1 TGATGA
5378724 AAATAGTATC
Statistics
Matches: 71, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
35 16 0.23
36 55 0.77
ACGTcount: A:0.27, C:0.04, G:0.36, T:0.34
Consensus pattern (36 bp):
TGATGATATAGGCGTGATAATGGTGATGGAATATGG
Found at i:5380447 original size:16 final size:16
Alignment explanation
Indices: 5380416--5380462 Score: 51
Period size: 16 Copynumber: 2.8 Consensus size: 16
5380406 TGGTAATGAA
5380416 ATAAGAAAAGATGAAA-G
1 ATAA-AAAA-ATGAAATG
*
5380433 AATAAAGAAATGAAATG
1 -ATAAAAAAATGAAATG
5380450 ATAAAAAAATGAA
1 ATAAAAAAATGAA
5380463 GATAACTTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
16 18 0.69
17 4 0.15
18 4 0.15
ACGTcount: A:0.68, C:0.00, G:0.17, T:0.15
Consensus pattern (16 bp):
ATAAAAAAATGAAATG
Found at i:5382775 original size:29 final size:29
Alignment explanation
Indices: 5382743--5382799 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
5382733 GGAGTGCAAA
5382743 AAAAAAAAAGAGAAAA-A-TCAGAAAAGAAG
1 AAAAAAAAAGA-AAAAGATTCA-AAAAGAAG
*
5382772 AAAAGAAAAGAAAAAGATTCAAAAAGAA
1 AAAAAAAAAGAAAAAGATTCAAAAAGAA
5382800 AGCAAAGCCA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
28 4 0.16
29 18 0.72
30 3 0.12
ACGTcount: A:0.75, C:0.04, G:0.16, T:0.05
Consensus pattern (29 bp):
AAAAAAAAAGAAAAAGATTCAAAAAGAAG
Found at i:5387313 original size:35 final size:37
Alignment explanation
Indices: 5387262--5387341 Score: 110
Period size: 35 Copynumber: 2.2 Consensus size: 37
5387252 TTTGAGAATT
* *
5387262 TGGTAATGATATAGGCGTGAT-ATGG-TGATGAACTA
1 TGGTGATGATATAGGCGTGATAATGGAAGATGAACTA
*
5387297 TGGTGATGATATAGGCGTGATAATGGAAGATGAATTA
1 TGGTGATGATATAGGCGTGATAATGGAAGATGAACTA
*
5387334 TGGGGATG
1 TGGTGATG
5387342 GAAATAGTAT
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
35 20 0.51
36 4 0.10
37 15 0.38
ACGTcount: A:0.31, C:0.04, G:0.35, T:0.30
Consensus pattern (37 bp):
TGGTGATGATATAGGCGTGATAATGGAAGATGAACTA
Found at i:5396812 original size:17 final size:20
Alignment explanation
Indices: 5396767--5396814 Score: 75
Period size: 20 Copynumber: 2.5 Consensus size: 20
5396757 CCCAAGAGTT
5396767 TGAAATACATGACTTTTAAA
1 TGAAATACATGACTTTTAAA
5396787 TGAAATACATGA-TTTT-AA
1 TGAAATACATGACTTTTAAA
5396805 TG-AATACATG
1 TGAAATACATG
5396815 CTCTTGGCCG
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
17 8 0.29
18 4 0.14
19 4 0.14
20 12 0.43
ACGTcount: A:0.44, C:0.08, G:0.12, T:0.35
Consensus pattern (20 bp):
TGAAATACATGACTTTTAAA
Found at i:5399829 original size:12 final size:12
Alignment explanation
Indices: 5399812--5399866 Score: 76
Period size: 12 Copynumber: 4.7 Consensus size: 12
5399802 CTATTTTTTT
*
5399812 CAAAAAAAAAAA
1 CAAAAAAAAAAG
5399824 CAAAAAAAAAAG
1 CAAAAAAAAAAG
*
5399836 C-AAAAAAAAGG
1 CAAAAAAAAAAG
*
5399847 CACAAAAAAAAG
1 CAAAAAAAAAAG
5399859 CAAAAAAA
1 CAAAAAAA
5399867 GCCAAAATTT
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
11 10 0.27
12 27 0.73
ACGTcount: A:0.82, C:0.11, G:0.07, T:0.00
Consensus pattern (12 bp):
CAAAAAAAAAAG
Found at i:5399843 original size:23 final size:23
Alignment explanation
Indices: 5399814--5399866 Score: 79
Period size: 23 Copynumber: 2.3 Consensus size: 23
5399804 ATTTTTTTCA
5399814 AAAAAAAAAACAAAAAAAAAAGC
1 AAAAAAAAAACAAAAAAAAAAGC
** *
5399837 AAAAAAAAGGCACAAAAAAAAGC
1 AAAAAAAAAACAAAAAAAAAAGC
5399860 AAAAAAA
1 AAAAAAA
5399867 GCCAAAATTT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.83, C:0.09, G:0.08, T:0.00
Consensus pattern (23 bp):
AAAAAAAAAACAAAAAAAAAAGC
Found at i:5407094 original size:27 final size:28
Alignment explanation
Indices: 5407033--5407094 Score: 74
Period size: 27 Copynumber: 2.2 Consensus size: 28
5407023 AAAGAAAATC
* *
5407033 AGAAAAGAAATTGAAGCACTCCAAAAGA
1 AGAAAAGAAATTCAAGCACTCAAAAAGA
*
5407061 A-ATAAAGAAA-TCCAGCACTCAAAAAGA
1 AGA-AAAGAAATTCAAGCACTCAAAAAGA
5407088 AGAAAAG
1 AGAAAAG
5407095 TAAAGAAAAG
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
27 20 0.69
28 9 0.31
ACGTcount: A:0.60, C:0.15, G:0.16, T:0.10
Consensus pattern (28 bp):
AGAAAAGAAATTCAAGCACTCAAAAAGA
Found at i:5408297 original size:24 final size:24
Alignment explanation
Indices: 5408257--5408307 Score: 59
Period size: 24 Copynumber: 2.1 Consensus size: 24
5408247 TCACTTCAAG
* *
5408257 TTGAAGATTCAAGAAACATGTCTT
1 TTGAAGATTCAAGAAACACGACTT
*
5408281 TTGAAGAATT-AATAAACACGACTT
1 TTGAAG-ATTCAAGAAACACGACTT
5408305 TTG
1 TTG
5408308 GTGATCCACA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
24 20 0.87
25 3 0.13
ACGTcount: A:0.39, C:0.12, G:0.16, T:0.33
Consensus pattern (24 bp):
TTGAAGATTCAAGAAACACGACTT
Found at i:5415333 original size:10 final size:10
Alignment explanation
Indices: 5415318--5415374 Score: 62
Period size: 10 Copynumber: 5.5 Consensus size: 10
5415308 TATTTTTTTC
5415318 AAAAAAAACA
1 AAAAAAAACA
*
5415328 AAAAAAAGGCA
1 AAAAAAA-ACA
5415339 AAAAAACAA-A
1 AAAAAA-AACA
5415349 AAAACAAAACA
1 AAAA-AAAACA
*
5415360 AAACAAAACA
1 AAAAAAAACA
5415370 AAAAA
1 AAAAA
5415375 GCCAAAATTT
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
10 24 0.62
11 14 0.36
12 1 0.03
ACGTcount: A:0.84, C:0.12, G:0.04, T:0.00
Consensus pattern (10 bp):
AAAAAAAACA
Found at i:5415349 original size:5 final size:5
Alignment explanation
Indices: 5415317--5415372 Score: 53
Period size: 5 Copynumber: 11.0 Consensus size: 5
5415307 CTATTTTTTT
* *
5415317 CAAAA -AAAA CAAAA -AAAA GGCAAAA AAACAA AAAAA CAAAA CAAAA
1 CAAAA CAAAA CAAAA CAAAA --CAAAA CAA-AA CAAAA CAAAA CAAAA
5415363 CAAAA CAAAA
1 CAAAA CAAAA
5415373 AAGCCAAAAT
Statistics
Matches: 44, Mismatches: 2, Indels: 10
0.79 0.04 0.18
Matches are distributed among these distances:
4 8 0.18
5 27 0.61
6 5 0.11
7 4 0.09
ACGTcount: A:0.82, C:0.14, G:0.04, T:0.00
Consensus pattern (5 bp):
CAAAA
Found at i:5419813 original size:50 final size:50
Alignment explanation
Indices: 5419708--5419814 Score: 119
Period size: 50 Copynumber: 2.1 Consensus size: 50
5419698 TCACACTCCA
* * * * *
5419708 ATTTTCCTTTTCATCGCGACTAGGAGGGTTGGTTAGAGCCATATTATCGT
1 ATTTTCCTTTTCATCGCGACTAGGAGGGCTCGATAGAGACATATCATCGT
* *
5419758 GTTTTCCTTTTCATTGCGACTAGGAGGGCTCGATAG-GACATTATCCATCG-
1 ATTTTCCTTTTCATCGCGACTAGGAGGGCTCGATAGAGACA-TAT-CATCGT
5419808 ATTTTCC
1 ATTTTCC
5419815 ACATCCATCC
Statistics
Matches: 47, Mismatches: 8, Indels: 4
0.80 0.14 0.07
Matches are distributed among these distances:
49 3 0.06
50 40 0.85
51 4 0.09
ACGTcount: A:0.20, C:0.21, G:0.22, T:0.37
Consensus pattern (50 bp):
ATTTTCCTTTTCATCGCGACTAGGAGGGCTCGATAGAGACATATCATCGT
Found at i:5420238 original size:19 final size:20
Alignment explanation
Indices: 5420200--5420242 Score: 61
Period size: 19 Copynumber: 2.2 Consensus size: 20
5420190 GAAACCCCTT
*
5420200 TGAAAACACATGATTTTTAA
1 TGAAAACACATGAATTTTAA
*
5420220 TGAAAATACAT-AATTTTAA
1 TGAAAACACATGAATTTTAA
5420239 TGAA
1 TGAA
5420243 GATAAATGCT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 11 0.52
20 10 0.48
ACGTcount: A:0.49, C:0.07, G:0.09, T:0.35
Consensus pattern (20 bp):
TGAAAACACATGAATTTTAA
Found at i:5425212 original size:25 final size:22
Alignment explanation
Indices: 5425188--5425234 Score: 78
Period size: 23 Copynumber: 2.1 Consensus size: 22
5425178 TTTGCTTTTC
5425188 TTCTT-TTTTGAGTGCTTTCAAT
1 TTCTTCTTTTGAGTGCTTTC-AT
5425210 TTCTTCTTTTGAGTGCTTTCAT
1 TTCTTCTTTTGAGTGCTTTCAT
5425232 TTC
1 TTC
5425235 ATTTTCTGAT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
22 10 0.42
23 14 0.58
ACGTcount: A:0.11, C:0.17, G:0.13, T:0.60
Consensus pattern (22 bp):
TTCTTCTTTTGAGTGCTTTCAT
Found at i:5429442 original size:23 final size:24
Alignment explanation
Indices: 5429397--5429453 Score: 82
Period size: 23 Copynumber: 2.4 Consensus size: 24
5429387 GCTTCAACTT
*
5429397 CTTTCTTTTCTTCCTTTTTGAGTG
1 CTTTCATTTCTTCCTTTTTGAGTG
5429421 CTTTCAATTTCTT-C-TTTTGAGTG
1 CTTTC-ATTTCTTCCTTTTTGAGTG
5429444 CTTTCATTTC
1 CTTTCATTTC
5429454 ATTTTCTGAT
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
22 5 0.16
23 14 0.45
24 6 0.19
25 6 0.19
ACGTcount: A:0.09, C:0.21, G:0.11, T:0.60
Consensus pattern (24 bp):
CTTTCATTTCTTCCTTTTTGAGTG
Found at i:5434450 original size:23 final size:23
Alignment explanation
Indices: 5434402--5434452 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
5434392 AAATTTTGGC
* **
5434402 TTTTTTTGGCTCTTTTTTTGTTT
1 TTTTTTTGCCTCTTTTTTTGCCT
*
5434425 TTTTTTTGCCTTTTTTTTTGCCT
1 TTTTTTTGCCTCTTTTTTTGCCT
5434448 TTTTT
1 TTTTT
5434453 ATTGTTTTTT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.00, C:0.12, G:0.10, T:0.78
Consensus pattern (23 bp):
TTTTTTTGCCTCTTTTTTTGCCT
Found at i:5434462 original size:12 final size:11
Alignment explanation
Indices: 5434402--5434462 Score: 61
Period size: 12 Copynumber: 5.5 Consensus size: 11
5434392 AAATTTTGGC
*
5434402 TTTTTTTGGCT
1 TTTTTTTTGCT
* *
5434413 CTTTTTTTGTT
1 TTTTTTTTGCT
5434424 TTTTTTTTGCCT
1 TTTTTTTTG-CT
5434436 TTTTTTTTGCCT
1 TTTTTTTTG-CT
*
5434448 TTTTTATTG-T
1 TTTTTTTTGCT
5434458 TTTTT
1 TTTTT
5434463 GTTTTTTTGT
Statistics
Matches: 43, Mismatches: 6, Indels: 3
0.83 0.12 0.06
Matches are distributed among these distances:
10 6 0.14
11 16 0.37
12 21 0.49
ACGTcount: A:0.02, C:0.10, G:0.10, T:0.79
Consensus pattern (11 bp):
TTTTTTTTGCT
Found at i:5434472 original size:15 final size:16
Alignment explanation
Indices: 5434448--5434477 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
5434438 TTTTTTGCCT
5434448 TTTTTATTGTTTTTTG
1 TTTTTATTGTTTTTTG
5434464 TTTTT-TTGTTTTTT
1 TTTTTATTGTTTTTT
5434478 TGAAAAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.03, C:0.00, G:0.10, T:0.87
Consensus pattern (16 bp):
TTTTTATTGTTTTTTG
Found at i:5442726 original size:16 final size:16
Alignment explanation
Indices: 5442693--5442741 Score: 53
Period size: 16 Copynumber: 2.9 Consensus size: 16
5442683 TAAGGTAATG
5442693 GAATAAGAATAGATGAAA
1 GAATAAGAA-A-ATGAAA
5442711 GAATAAGAAAATGAAA
1 GAATAAGAAAATGAAA
* * *
5442727 TAGTAAGAAAGTGAA
1 GAATAAGAAAATGAA
5442742 GATAACTTAC
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
16 18 0.64
17 1 0.04
18 9 0.32
ACGTcount: A:0.61, C:0.00, G:0.22, T:0.16
Consensus pattern (16 bp):
GAATAAGAAAATGAAA
Found at i:5443127 original size:78 final size:78
Alignment explanation
Indices: 5443033--5443188 Score: 303
Period size: 78 Copynumber: 2.0 Consensus size: 78
5443023 AATTACTGCT
5443033 TGATGTAAGGCTAACCAGGCTTCTTCAATAATGGAGAAGTTGGCAACCTTGTTGTTTCCCGATCT
1 TGATGTAAGGCTAACCAGGCTTCTTCAATAATGGAGAAGTTGGCAACCTTGTTGTTTCCCGATCT
*
5443098 AGGAGAGACACCA
66 AGGAAAGACACCA
5443111 TGATGTAAGGCTAACCAGGCTTCTTCAATAATGGAGAAGTTGGCAACCTTGTTGTTTCCCGATCT
1 TGATGTAAGGCTAACCAGGCTTCTTCAATAATGGAGAAGTTGGCAACCTTGTTGTTTCCCGATCT
5443176 AGGAAAGACACCA
66 AGGAAAGACACCA
5443189 AAATGCTACA
Statistics
Matches: 77, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
78 77 1.00
ACGTcount: A:0.29, C:0.21, G:0.24, T:0.27
Consensus pattern (78 bp):
TGATGTAAGGCTAACCAGGCTTCTTCAATAATGGAGAAGTTGGCAACCTTGTTGTTTCCCGATCT
AGGAAAGACACCA
Found at i:5448421 original size:6 final size:6
Alignment explanation
Indices: 5448410--5448453 Score: 54
Period size: 6 Copynumber: 7.2 Consensus size: 6
5448400 GATGCAGGAG
*
5448410 TCTTTT TC-TTT TCTTTT TGTTTT TCTTCTT TCTTTT TCTCTTT T
1 TCTTTT TCTTTT TCTTTT TCTTTT TCTT-TT TCTTTT TCT-TTT T
5448454 TGTTGCTTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
5 5 0.15
6 18 0.55
7 10 0.30
ACGTcount: A:0.00, C:0.18, G:0.02, T:0.80
Consensus pattern (6 bp):
TCTTTT
Found at i:5448433 original size:12 final size:12
Alignment explanation
Indices: 5448410--5448453 Score: 54
Period size: 13 Copynumber: 3.6 Consensus size: 12
5448400 GATGCAGGAG
5448410 TCTTTTTC-TTT
1 TCTTTTTCTTTT
*
5448421 TCTTTTTGTTTT
1 TCTTTTTCTTTT
5448433 TCTTCTTTCTTTT
1 TCTT-TTTCTTTT
5448446 TCTCTTTT
1 TCT-TTTT
5448454 TGTTGCTTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
11 7 0.25
12 7 0.25
13 13 0.46
14 1 0.04
ACGTcount: A:0.00, C:0.18, G:0.02, T:0.80
Consensus pattern (12 bp):
TCTTTTTCTTTT
Found at i:5450890 original size:177 final size:179
Alignment explanation
Indices: 5450594--5450949 Score: 698
Period size: 177 Copynumber: 2.0 Consensus size: 179
5450584 AGGACTTAAG
5450594 AAAGAGAAAAATCTCACTTCAATTAAAATAAAAGGTCTGATTACAAATGAAATATAATGGCCTAT
1 AAAGAGAAAAATCTCACTTCAATTAAAATAAAAGGTCTGATTACAAATGAAATATAATGGCCTAT
5450659 TTATAGTTTTTGAAGGGACTTGGATGAATAGGTACATGTTGGTTCGGCCAGCCCTTGTACCTTCC
66 TTATAGTTTTTGAAGGGACTTGGATGAATAGGTACATGTTGGTTCGGCCAGCCCTTGTACCTTCC
5450724 TAAAATGACATGA-TTTTAATG-AAAAACAAGACTTTAATGAAAATACA
131 TAAAATGACATGATTTTTAATGAAAAAACAAGACTTTAATGAAAATACA
5450771 AAAGAGAAAAATCTCACTTCAATTAAAATAAAAGGTCTGATTACAAATGAAATATAATGGCCTAT
1 AAAGAGAAAAATCTCACTTCAATTAAAATAAAAGGTCTGATTACAAATGAAATATAATGGCCTAT
5450836 TTATAGTTTTTGAAGGGACTTGGATGAATAGGTACATGTTGGTTCGGCCAGCCCTTGTACCTTCC
66 TTATAGTTTTTGAAGGGACTTGGATGAATAGGTACATGTTGGTTCGGCCAGCCCTTGTACCTTCC
5450901 TAAAATGACATGATTTTTAATGAAAAAACAAGACTTTAATGAAAATACA
131 TAAAATGACATGATTTTTAATGAAAAAACAAGACTTTAATGAAAATACA
5450950 TGCTTTTGGC
Statistics
Matches: 177, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
177 143 0.81
178 8 0.05
179 26 0.15
ACGTcount: A:0.40, C:0.13, G:0.17, T:0.30
Consensus pattern (179 bp):
AAAGAGAAAAATCTCACTTCAATTAAAATAAAAGGTCTGATTACAAATGAAATATAATGGCCTAT
TTATAGTTTTTGAAGGGACTTGGATGAATAGGTACATGTTGGTTCGGCCAGCCCTTGTACCTTCC
TAAAATGACATGATTTTTAATGAAAAAACAAGACTTTAATGAAAATACA
Found at i:5454170 original size:10 final size:10
Alignment explanation
Indices: 5454155--5454180 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
5454145 TTCAACTTTC
5454155 TTTCTTTCCT
1 TTTCTTTCCT
5454165 TTTCTTTCCT
1 TTTCTTTCCT
5454175 TTTCTT
1 TTTCTT
5454181 CTTTTTGAGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (10 bp):
TTTCTTTCCT
Found at i:5454935 original size:19 final size:20
Alignment explanation
Indices: 5454894--5454944 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
5454884 GAAACCCCTT
*
5454894 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTTAA
5454914 TGAAAATACATGA-TTTTAA
1 TGAAAATACATGATTTTTAA
*
5454933 TGAAGATACATG
1 TGAAAATACATG
5454945 CTCTTGGCCG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 16 0.55
20 13 0.45
ACGTcount: A:0.43, C:0.06, G:0.16, T:0.35
Consensus pattern (20 bp):
TGAAAATACATGATTTTTAA
Found at i:5457884 original size:30 final size:29
Alignment explanation
Indices: 5457827--5457884 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
5457817 TTGGAGTGCA
*
5457827 AAAAAAAAAGAGAAAAATCAGAAAAGAAG
1 AAAAAAAAAGAAAAAAATCAGAAAAGAAG
*
5457856 AAAAGAAAAGAAAAAGAATTCA-AAAAGAA
1 AAAAAAAAAGAAAAA-AA-TCAGAAAAGAA
5457885 AGCAAAGCCA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 13 0.52
30 9 0.36
31 3 0.12
ACGTcount: A:0.76, C:0.03, G:0.16, T:0.05
Consensus pattern (29 bp):
AAAAAAAAAGAAAAAAATCAGAAAAGAAG
Found at i:5465678 original size:19 final size:18
Alignment explanation
Indices: 5465656--5465711 Score: 59
Period size: 19 Copynumber: 3.3 Consensus size: 18
5465646 AAATTTTGGC
5465656 TTTTTTGGCTCTTTTTTTG
1 TTTTTTGGC-CTTTTTTTG
*
5465675 TTTTTTTGCC---TTTT-
1 TTTTTTGGCCTTTTTTTG
5465689 TTTTTT-GCCTTTTTTTG
1 TTTTTTGGCCTTTTTTTG
5465706 TTTTTT
1 TTTTTT
5465712 TTTGAAAAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 10
0.74 0.02 0.23
Matches are distributed among these distances:
13 3 0.09
14 6 0.19
15 4 0.12
16 4 0.12
17 6 0.19
18 1 0.03
19 8 0.25
ACGTcount: A:0.00, C:0.11, G:0.11, T:0.79
Consensus pattern (18 bp):
TTTTTTGGCCTTTTTTTG
Found at i:5465679 original size:20 final size:18
Alignment explanation
Indices: 5465656--5465712 Score: 61
Period size: 13 Copynumber: 3.4 Consensus size: 18
5465646 AAATTTTGGC
*
5465656 TTTTTTGGCTCTTTTTTTG
1 TTTTTTTGC-CTTTTTTTG
5465675 TTTTTTTGCC----TTT-
1 TTTTTTTGCCTTTTTTTG
5465688 TTTTTTTGCCTTTTTTTG
1 TTTTTTTGCCTTTTTTTG
5465706 TTTTTTT
1 TTTTTTT
5465713 TTGAAAAAAC
Statistics
Matches: 32, Mismatches: 1, Indels: 11
0.73 0.02 0.25
Matches are distributed among these distances:
13 10 0.31
14 3 0.09
17 3 0.09
18 8 0.25
19 8 0.25
ACGTcount: A:0.00, C:0.11, G:0.11, T:0.79
Consensus pattern (18 bp):
TTTTTTTGCCTTTTTTTG
Found at i:5465691 original size:21 final size:20
Alignment explanation
Indices: 5465667--5465714 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 20
5465657 TTTTTGGCTC
5465667 TTTTTTTG-TTTTTTTGCCTTT
1 TTTTTTTGCTTTTTTTG--TTT
5465688 TTTTTTTGCCTTTTTTTGTTT
1 TTTTTTTG-CTTTTTTTGTTT
5465709 TTTTTT
1 TTTTTT
5465715 GAAAAAACAA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
21 17 0.68
23 8 0.32
ACGTcount: A:0.00, C:0.08, G:0.08, T:0.83
Consensus pattern (20 bp):
TTTTTTTGCTTTTTTTGTTT
Found at i:5474132 original size:19 final size:20
Alignment explanation
Indices: 5474091--5474141 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
5474081 GAAACCCCTT
*
5474091 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTTAA
5474111 TGAAAATACATGA-TTTTAA
1 TGAAAATACATGATTTTTAA
*
5474130 TGAAGATACATG
1 TGAAAATACATG
5474142 CTCTTGGCCG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 16 0.55
20 13 0.45
ACGTcount: A:0.43, C:0.06, G:0.16, T:0.35
Consensus pattern (20 bp):
TGAAAATACATGATTTTTAA
Found at i:5481466 original size:8 final size:8
Alignment explanation
Indices: 5481455--5481511 Score: 64
Period size: 8 Copynumber: 6.9 Consensus size: 8
5481445 CTTTTTGAAA
5481455 TCTTTTTT
1 TCTTTTTT
5481463 TC--TTTT
1 TCTTTTTT
5481469 TCTTTTTT
1 TCTTTTTT
5481477 TCTTTTTT
1 TCTTTTTT
5481485 TCTTCTTTTT
1 TC-T-TTTTT
5481495 GTCTTTTCTT
1 -TCTTTT-TT
5481505 TCTTTTT
1 TCTTTTT
5481512 GTACTCCAAT
Statistics
Matches: 43, Mismatches: 0, Indels: 12
0.78 0.00 0.22
Matches are distributed among these distances:
6 6 0.14
8 17 0.40
9 10 0.23
10 8 0.19
11 2 0.05
ACGTcount: A:0.00, C:0.16, G:0.02, T:0.82
Consensus pattern (8 bp):
TCTTTTTT
Found at i:5481482 original size:19 final size:20
Alignment explanation
Indices: 5481460--5481508 Score: 75
Period size: 19 Copynumber: 2.5 Consensus size: 20
5481450 TGAAATCTTT
*
5481460 TTTTCTTT-TTCTTTTTTTC
1 TTTTCTTTCTTCTTTTTGTC
5481479 TTTT-TTTCTTCTTTTTGTC
1 TTTTCTTTCTTCTTTTTGTC
5481498 TTTTCTTTCTT
1 TTTTCTTTCTT
5481509 TTTGTACTCC
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
18 3 0.11
19 18 0.67
20 6 0.22
ACGTcount: A:0.00, C:0.16, G:0.02, T:0.82
Consensus pattern (20 bp):
TTTTCTTTCTTCTTTTTGTC
Found at i:5481484 original size:16 final size:16
Alignment explanation
Indices: 5481455--5481511 Score: 64
Period size: 14 Copynumber: 3.4 Consensus size: 16
5481445 CTTTTTGAAA
5481455 TCTTTTTTTC--TTTT
1 TCTTTTTTTCTTTTTT
5481469 TCTTTTTTTCTTTTTT
1 TCTTTTTTTCTTTTTT
5481485 TCTTCTTTTTGTCTTTTCTT
1 TC-T-TTTTT-TCTTTT-TT
5481505 TCTTTTT
1 TCTTTTT
5481512 GTACTCCAAT
Statistics
Matches: 37, Mismatches: 0, Indels: 8
0.82 0.00 0.18
Matches are distributed among these distances:
14 10 0.27
16 6 0.16
17 1 0.03
18 9 0.24
19 7 0.19
20 4 0.11
ACGTcount: A:0.00, C:0.16, G:0.02, T:0.82
Consensus pattern (16 bp):
TCTTTTTTTCTTTTTT
Found at i:5481485 original size:17 final size:17
Alignment explanation
Indices: 5481457--5481511 Score: 62
Period size: 19 Copynumber: 3.2 Consensus size: 17
5481447 TTTTGAAATC
5481457 TTTTTTTC--TTTTTC-
1 TTTTTTTCTTTTTTTCT
5481471 TTTTTTTCTTTTTTTCT
1 TTTTTTTCTTTTTTTCT
5481488 TCTTTTTGTCTTTTCTTTCT
1 T-TTTTT-TCTTTT-TTTCT
5481508 TTTT
1 TTTT
5481512 GTACTCCAAT
Statistics
Matches: 35, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
14 8 0.23
16 6 0.17
17 1 0.03
18 5 0.14
19 9 0.26
20 6 0.17
ACGTcount: A:0.00, C:0.15, G:0.02, T:0.84
Consensus pattern (17 bp):
TTTTTTTCTTTTTTTCT
Found at i:5494737 original size:30 final size:29
Alignment explanation
Indices: 5494702--5494759 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
5494692 TGGCTTTGCT
*
5494702 TTCTTTT-TGAATTCTTTTTCTTTTCTTTTC
1 TTCTTTTCTG-ATT-TTTCTCTTTTCTTTTC
*
5494732 TTCTTTTCTGATTTTTCTCTTTTTTTTT
1 TTCTTTTCTGATTTTTCTCTTTTCTTTT
5494760 TTTTGCACTC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 13 0.52
30 10 0.40
31 2 0.08
ACGTcount: A:0.05, C:0.16, G:0.03, T:0.76
Consensus pattern (29 bp):
TTCTTTTCTGATTTTTCTCTTTTCTTTTC
Found at i:5495140 original size:20 final size:21
Alignment explanation
Indices: 5495103--5495141 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
5495093 GATGGTCTTG
*
5495103 ATGAAGGATGTTGATGATGAA
1 ATGAAGGATGGTGATGATGAA
*
5495124 ATGAA-GATGGTGGTGATG
1 ATGAAGGATGGTGATGATG
5495142 TTGTATCTCA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 11 0.69
21 5 0.31
ACGTcount: A:0.33, C:0.00, G:0.38, T:0.28
Consensus pattern (21 bp):
ATGAAGGATGGTGATGATGAA
Found at i:5501749 original size:23 final size:23
Alignment explanation
Indices: 5501719--5501771 Score: 65
Period size: 23 Copynumber: 2.3 Consensus size: 23
5501709 ATTGGAGTAA
5501719 AAAAAGAAGAAA-A-TTCAGAAAAG
1 AAAAAGAA-AAAGATTTCA-AAAAG
5501742 AAAAAGAAAAAGATTTCAAAAAG
1 AAAAAGAAAAAGATTTCAAAAAG
5501765 AGAAAAG
1 A-AAAAG
5501772 CAAGCCAAGG
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
22 3 0.11
23 15 0.56
24 9 0.33
ACGTcount: A:0.70, C:0.04, G:0.17, T:0.09
Consensus pattern (23 bp):
AAAAAGAAAAAGATTTCAAAAAG
Found at i:5507941 original size:20 final size:21
Alignment explanation
Indices: 5507904--5507942 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
5507894 GATGGTCTTG
*
5507904 ATGAAGGATGTTGATGATGAA
1 ATGAAGGATGGTGATGATGAA
*
5507925 ATGAA-GATGGTGGTGATG
1 ATGAAGGATGGTGATGATG
5507943 TTGTATCTCA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 11 0.69
21 5 0.31
ACGTcount: A:0.33, C:0.00, G:0.38, T:0.28
Consensus pattern (21 bp):
ATGAAGGATGGTGATGATGAA
Found at i:5515549 original size:16 final size:16
Alignment explanation
Indices: 5515524--5515564 Score: 75
Period size: 16 Copynumber: 2.6 Consensus size: 16
5515514 TTGGATTCAA
5515524 TTTC-ACTCCTCTCAT
1 TTTCAACTCCTCTCAT
5515539 TTTCAACTCCTCTCAT
1 TTTCAACTCCTCTCAT
5515555 TTTCAACTCC
1 TTTCAACTCC
5515565 AACGTCTTCT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
15 4 0.16
16 21 0.84
ACGTcount: A:0.17, C:0.39, G:0.00, T:0.44
Consensus pattern (16 bp):
TTTCAACTCCTCTCAT
Found at i:5517387 original size:19 final size:21
Alignment explanation
Indices: 5517344--5517395 Score: 81
Period size: 19 Copynumber: 2.6 Consensus size: 21
5517334 GAAACCCCTT
*
5517344 TGAAAATACATGACTTTTAAA
1 TGAAGATACATGACTTTTAAA
5517365 TGAAGATACATGA-TTTT-AA
1 TGAAGATACATGACTTTTAAA
5517384 TGAAGATACATG
1 TGAAGATACATG
5517396 CTCTTGGCCG
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 14 0.47
20 4 0.13
21 12 0.40
ACGTcount: A:0.44, C:0.08, G:0.15, T:0.33
Consensus pattern (21 bp):
TGAAGATACATGACTTTTAAA
Found at i:5519742 original size:19 final size:20
Alignment explanation
Indices: 5519704--5519744 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
5519694 GAAACCCCTT
*
5519704 TGAAAACACATGATTTTTAA
1 TGAAAACACATGAATTTTAA
*
5519724 TGAAAATACAT-AATTTTAA
1 TGAAAACACATGAATTTTAA
5519743 TG
1 TG
5519745 TAGATAAATG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 9 0.47
20 10 0.53
ACGTcount: A:0.46, C:0.07, G:0.10, T:0.37
Consensus pattern (20 bp):
TGAAAACACATGAATTTTAA
Found at i:5524493 original size:12 final size:11
Alignment explanation
Indices: 5524476--5524501 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
5524466 TCAAAAAAAC
5524476 AAAAAAAGGCA
1 AAAAAAAGGCA
5524487 AAAAAAAGGCA
1 AAAAAAAGGCA
5524498 AAAA
1 AAAA
5524502 CAAAAAGTCA
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:0.77, C:0.08, G:0.15, T:0.00
Consensus pattern (11 bp):
AAAAAAAGGCA
Found at i:5528231 original size:40 final size:43
Alignment explanation
Indices: 5528137--5528231 Score: 117
Period size: 40 Copynumber: 2.2 Consensus size: 43
5528127 TAGGATCAGA
*
5528137 TTTATTA-TTTATTAGGAATTAAGTTGAGTTAAAACAATATTTTTAG
1 TTTATTATTTTATTAGGAATTAA--TGAGTTAAAAC-A-ATGTTTAG
5528183 TTTATTATTTTATTAGGAATT-A-GAGTTAAAAC-ATGTTTAG
1 TTTATTATTTTATTAGGAATTAATGAGTTAAAACAATGTTTAG
5528223 TTTATTATT
1 TTTATTATT
5528232 ATTTTATTCT
Statistics
Matches: 47, Mismatches: 1, Indels: 8
0.84 0.02 0.14
Matches are distributed among these distances:
40 16 0.34
43 10 0.21
46 8 0.17
47 13 0.28
ACGTcount: A:0.35, C:0.02, G:0.13, T:0.51
Consensus pattern (43 bp):
TTTATTATTTTATTAGGAATTAATGAGTTAAAACAATGTTTAG
Found at i:5529526 original size:43 final size:47
Alignment explanation
Indices: 5529424--5529528 Score: 121
Period size: 50 Copynumber: 2.3 Consensus size: 47
5529414 AGAATTATAT
5529424 TTATTATTTTATTAGGAATTAAGGTTGAGTTAAAACATTAATTTTAGTTA
1 TTATTATTTTATTAGGAATTAA-G--GAGTTAAAACATTAATTTTAGTTA
* *
5529474 TTATTATTTTATTAGGAATT-A-GAGTTAAGACA-T-A-TTTAGTTTG
1 TTATTATTTTATTAGGAATTAAGGAGTTAAAACATTAATTTTAG-TTA
5529517 TTATTATTTTAT
1 TTATTATTTTAT
5529529 ACCTTAGTTA
Statistics
Matches: 52, Mismatches: 2, Indels: 9
0.83 0.03 0.14
Matches are distributed among these distances:
42 5 0.10
43 15 0.29
44 1 0.02
45 10 0.19
49 1 0.02
50 20 0.38
ACGTcount: A:0.33, C:0.02, G:0.13, T:0.51
Consensus pattern (47 bp):
TTATTATTTTATTAGGAATTAAGGAGTTAAAACATTAATTTTAGTTA
Found at i:5532643 original size:11 final size:11
Alignment explanation
Indices: 5532574--5532662 Score: 74
Period size: 11 Copynumber: 7.5 Consensus size: 11
5532564 ACAATCTGTC
5532574 CATCACCATTAT
1 CATCACCA-TAT
*
5532586 CA-CGCCTATAT
1 CATCACC-ATAT
5532597 CATCACCATAGT
1 CATCACCATA-T
5532609 CCATCACCATTAT
1 -CATCACCA-TAT
*
5532622 CA-CGCCTATAT
1 CATCACC-ATAT
5532633 CATCACCATATT
1 CATCACCATA-T
5532645 CCATCACCATAT
1 -CATCACCATAT
5532657 CATCAC
1 CATCAC
5532663 GCCTATATTA
Statistics
Matches: 64, Mismatches: 4, Indels: 19
0.74 0.05 0.22
Matches are distributed among these distances:
11 28 0.44
12 15 0.23
13 19 0.30
14 2 0.03
ACGTcount: A:0.31, C:0.37, G:0.03, T:0.28
Consensus pattern (11 bp):
CATCACCATAT
Found at i:5532676 original size:38 final size:36
Alignment explanation
Indices: 5532571--5532678 Score: 180
Period size: 36 Copynumber: 2.9 Consensus size: 36
5532561 GATACAATCT
5532571 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
5532607 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
* *
5532643 TTCCATCACCATATCATCACGCCTATATTATCACCA
1 GTCCATCACCAT-T-ATCACGCCTATATCATCACCA
5532679 ACTTATAAAT
Statistics
Matches: 68, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
36 47 0.69
37 1 0.01
38 20 0.29
ACGTcount: A:0.31, C:0.36, G:0.05, T:0.29
Consensus pattern (36 bp):
GTCCATCACCATTATCACGCCTATATCATCACCATA
Found at i:5533157 original size:14 final size:15
Alignment explanation
Indices: 5533123--5533169 Score: 51
Period size: 14 Copynumber: 3.1 Consensus size: 15
5533113 AATTTGGGGT
5533123 GCAAAAGAAAGAAAA
1 GCAAAAGAAAGAAAA
*
5533138 GAAAAAG-AAGAAAA
1 GCAAAAGAAAGAAAA
*
5533152 TCAAAAGCAAAAGAAAA
1 GCAAAAG--AAAGAAAA
5533169 G
1 G
5533170 TGAAGCAAGT
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
14 12 0.48
15 6 0.24
17 7 0.28
ACGTcount: A:0.72, C:0.06, G:0.19, T:0.02
Consensus pattern (15 bp):
GCAAAAGAAAGAAAA
Found at i:5538400 original size:21 final size:21
Alignment explanation
Indices: 5538374--5538415 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
5538364 TCACTTTTCA
5538374 TGAATTAATGCAACTATCTAT
1 TGAATTAATGCAACTATCTAT
5538395 TGAATTAATGCAACTATCTAT
1 TGAATTAATGCAACTATCTAT
5538416 GGAAAGGGGC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.38, C:0.14, G:0.10, T:0.38
Consensus pattern (21 bp):
TGAATTAATGCAACTATCTAT
Found at i:5548067 original size:13 final size:11
Alignment explanation
Indices: 5548026--5548110 Score: 66
Period size: 11 Copynumber: 7.2 Consensus size: 11
5548016 ACAATCTGTC
5548026 CATCACCATTAT
1 CATCACCA-TAT
*
5548038 CA-CGCCTATAT
1 CATCACC-ATAT
5548049 CATCACCATAGT
1 CATCACCATA-T
5548061 CCATCACCATTAT
1 -CATCACCA-TAT
*
5548074 CA-CGCCTATAT
1 CATCACC-ATAT
5548085 CATCACCATATT
1 CATCACCATA-T
5548097 CCATCACCATAT
1 -CATCACCATAT
5548109 CA
1 CA
5548111 CGCCTATATT
Statistics
Matches: 60, Mismatches: 4, Indels: 19
0.72 0.05 0.23
Matches are distributed among these distances:
11 24 0.40
12 15 0.25
13 19 0.32
14 2 0.03
ACGTcount: A:0.32, C:0.36, G:0.04, T:0.28
Consensus pattern (11 bp):
CATCACCATAT
Found at i:5548070 original size:36 final size:36
Alignment explanation
Indices: 5548023--5548127 Score: 185
Period size: 36 Copynumber: 2.9 Consensus size: 36
5548013 GATACAATCT
5548023 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
5548059 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
* *
5548095 TTCCATCACCA-TATCACGCCTATATTATCACCA
1 GTCCATCACCATTATCACGCCTATATCATCACCA
5548128 ACTTATGAAT
Statistics
Matches: 67, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
35 21 0.31
36 46 0.69
ACGTcount: A:0.30, C:0.36, G:0.05, T:0.29
Consensus pattern (36 bp):
GTCCATCACCATTATCACGCCTATATCATCACCATA
Found at i:5551575 original size:21 final size:19
Alignment explanation
Indices: 5551531--5551580 Score: 73
Period size: 19 Copynumber: 2.5 Consensus size: 19
5551521 CGGCCAAGAG
*
5551531 CATGTATCTTCATTAAAAT
1 CATGTATTTTCATTAAAAT
5551550 CATGTATTTTCATTTAAAAGT
1 CATGTATTTTCA-TTAAAA-T
5551571 CATGTATTTT
1 CATGTATTTT
5551581 AAAAGGGGTT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
19 11 0.39
20 6 0.21
21 11 0.39
ACGTcount: A:0.32, C:0.12, G:0.08, T:0.48
Consensus pattern (19 bp):
CATGTATTTTCATTAAAAT
Found at i:5552312 original size:16 final size:16
Alignment explanation
Indices: 5552282--5552312 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
5552272 ATTGGAGTGC
*
5552282 AAAAAGAAAGAAAAAG
1 AAAAAGAAAAAAAAAG
5552298 AAAAAGAAAAAAAAA
1 AAAAAGAAAAAAAAA
5552313 TCAGAATAGA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (16 bp):
AAAAAGAAAAAAAAAG
Found at i:5554652 original size:17 final size:17
Alignment explanation
Indices: 5554630--5554663 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
5554620 ACCTATAGTT
*
5554630 CACATCTTTATAATATA
1 CACATCATTATAATATA
*
5554647 CACATCATTATATTATA
1 CACATCATTATAATATA
5554664 TGCATTATAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.41, C:0.18, G:0.00, T:0.41
Consensus pattern (17 bp):
CACATCATTATAATATA
Found at i:5555490 original size:19 final size:21
Alignment explanation
Indices: 5555466--5555512 Score: 71
Period size: 19 Copynumber: 2.3 Consensus size: 21
5555456 CGGCCAAGAG
5555466 CATGTATCTTCA-TTAAAA-T
1 CATGTATCTTCATTTAAAAGT
*
5555485 CATGTATTTTCATTTAAAAGT
1 CATGTATCTTCATTTAAAAGT
5555506 CATGTAT
1 CATGTAT
5555513 TATAAAAGGG
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
19 11 0.44
20 6 0.24
21 8 0.32
ACGTcount: A:0.34, C:0.13, G:0.09, T:0.45
Consensus pattern (21 bp):
CATGTATCTTCATTTAAAAGT
Found at i:5556674 original size:36 final size:35
Alignment explanation
Indices: 5556583--5556691 Score: 148
Period size: 35 Copynumber: 3.1 Consensus size: 35
5556573 GGTGGTTATT
* * *
5556583 TAGGCGTGAAATGGTGATAGAAGATGGTAATGATA
1 TAGGCGTGAAATGGTGATGGAAGATGGTGATGTTA
* *
5556618 TAGGCGTGCAATGGTAATGGAAGATGGTGATGTTA
1 TAGGCGTGAAATGGTGATGGAAGATGGTGATGTTA
*
5556653 TAGGCGTGAAAATGGCGATGGAAGATGGTGATGTT-
1 TAGGCGTG-AAATGGTGATGGAAGATGGTGATGTTA
5556688 TAGG
1 TAGG
5556692 TAGTATCTTA
Statistics
Matches: 65, Mismatches: 8, Indels: 2
0.87 0.11 0.03
Matches are distributed among these distances:
35 42 0.65
36 23 0.35
ACGTcount: A:0.31, C:0.05, G:0.38, T:0.27
Consensus pattern (35 bp):
TAGGCGTGAAATGGTGATGGAAGATGGTGATGTTA
Found at i:5561056 original size:14 final size:14
Alignment explanation
Indices: 5561037--5561063 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
5561027 TTATTGAATG
5561037 ATTGAAGGATGATA
1 ATTGAAGGATGATA
5561051 ATTGAAGGATGAT
1 ATTGAAGGATGAT
5561064 TGAATGATGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.41, C:0.00, G:0.30, T:0.30
Consensus pattern (14 bp):
ATTGAAGGATGATA
Found at i:5561192 original size:36 final size:35
Alignment explanation
Indices: 5561101--5561209 Score: 157
Period size: 35 Copynumber: 3.1 Consensus size: 35
5561091 GGTGGTTATT
* * *
5561101 TAGGCGTGAAATGGTGATAGAAGATGGTAATGATA
1 TAGGCGTGAAATGGTGATGGAAGATGGTGATGTTA
* *
5561136 TAGGCGTGCAATGGTAATGGAAGATGGTGATGTTA
1 TAGGCGTGAAATGGTGATGGAAGATGGTGATGTTA
5561171 TAGGCGTGAAAATGGTGATGGAAGATGGTGATGTT-
1 TAGGCGTG-AAATGGTGATGGAAGATGGTGATGTTA
5561206 TAGG
1 TAGG
5561210 TAGTATGAAA
Statistics
Matches: 66, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
35 42 0.64
36 24 0.36
ACGTcount: A:0.31, C:0.04, G:0.38, T:0.28
Consensus pattern (35 bp):
TAGGCGTGAAATGGTGATGGAAGATGGTGATGTTA
Found at i:5570922 original size:22 final size:23
Alignment explanation
Indices: 5570880--5570923 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
5570870 TGATGTTGCT
* *
5570880 GGAAGTATGCATTTAATGATGAA
1 GGAAGGATGCATTCAATGATGAA
5570903 GGAAGGATGC-TTCAATGATGA
1 GGAAGGATGCATTCAATGATGA
5570924 TGAAAATGGT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 10 0.53
23 9 0.47
ACGTcount: A:0.36, C:0.07, G:0.30, T:0.27
Consensus pattern (23 bp):
GGAAGGATGCATTCAATGATGAA
Found at i:5576637 original size:14 final size:14
Alignment explanation
Indices: 5576618--5576657 Score: 71
Period size: 14 Copynumber: 2.9 Consensus size: 14
5576608 GCCAATAGGT
5576618 ACCTTTCCTAAAGA
1 ACCTTTCCTAAAGA
5576632 ACCTTTCCTAAAGA
1 ACCTTTCCTAAAGA
*
5576646 ACCTTTCTTAAA
1 ACCTTTCCTAAA
5576658 AGACACCTCC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 25 1.00
ACGTcount: A:0.35, C:0.28, G:0.05, T:0.33
Consensus pattern (14 bp):
ACCTTTCCTAAAGA
Found at i:5579027 original size:19 final size:19
Alignment explanation
Indices: 5579003--5579039 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
5578993 TACTTGATTT
5579003 TTTTAATGAAAATACATGA
1 TTTTAATGAAAATACATGA
*
5579022 TTTTAATGAAGATACATG
1 TTTTAATGAAAATACATG
5579040 CTCTTGTCCG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.43, C:0.05, G:0.14, T:0.38
Consensus pattern (19 bp):
TTTTAATGAAAATACATGA
Found at i:5579950 original size:19 final size:21
Alignment explanation
Indices: 5579907--5579958 Score: 81
Period size: 19 Copynumber: 2.6 Consensus size: 21
5579897 GAAACCCCTT
5579907 TGAAAATACATGACTTTTAAA
1 TGAAAATACATGACTTTTAAA
5579928 TGAAAATACATGA-TTTT-AA
1 TGAAAATACATGACTTTTAAA
*
5579947 TGAAGATACATG
1 TGAAAATACATG
5579959 CTCTTGGCCG
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 13 0.43
20 4 0.13
21 13 0.43
ACGTcount: A:0.46, C:0.08, G:0.13, T:0.33
Consensus pattern (21 bp):
TGAAAATACATGACTTTTAAA
Found at i:5581828 original size:24 final size:24
Alignment explanation
Indices: 5581778--5581827 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
5581768 AACACAACCC
* *
5581778 TTGGCACTTCAAATGACATTTCTT
1 TTGGAACTTCAAATGACATATCTT
*
5581802 TTGGAACTTCAAATGGCATCATCTT
1 TTGGAACTTCAAATGACAT-ATCTT
5581827 T
1 T
5581828 GAAACATCAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
24 17 0.77
25 5 0.23
ACGTcount: A:0.26, C:0.20, G:0.14, T:0.40
Consensus pattern (24 bp):
TTGGAACTTCAAATGACATATCTT
Found at i:5583104 original size:18 final size:17
Alignment explanation
Indices: 5583083--5583162 Score: 62
Period size: 18 Copynumber: 4.6 Consensus size: 17
5583073 CCTTGGCTTG
5583083 CTTTCTTTTTGAATTTTT
1 CTTTCTTTTTG-ATTTTT
5583101 CTTT-TTCTTT--TCTTTT
1 CTTTCTT-TTTGAT-TTTT
5583117 C-TTCTTTTCTGATTTTT
1 CTTTCTTTT-TGATTTTT
*
5583134 CTCTTC-TTTTGTCTTTTT
1 CT-TTCTTTTTG-ATTTTT
5583152 CTTTCTTTTTG
1 CTTTCTTTTTG
5583163 CACTCCAATT
Statistics
Matches: 51, Mismatches: 1, Indels: 20
0.71 0.01 0.28
Matches are distributed among these distances:
15 5 0.10
16 8 0.16
17 12 0.24
18 23 0.45
19 3 0.06
ACGTcount: A:0.04, C:0.17, G:0.05, T:0.74
Consensus pattern (17 bp):
CTTTCTTTTTGATTTTT
Found at i:5583121 original size:13 final size:12
Alignment explanation
Indices: 5583097--5583155 Score: 57
Period size: 13 Copynumber: 4.7 Consensus size: 12
5583087 CTTTTTGAAT
5583097 TTTTC-TTTTTC
1 TTTTCTTTTTTC
5583108 TTTTCTTTTCTTC
1 TTTTCTTTT-TTC
5583121 TTTTCTGATTTTTC
1 TTTTCT--TTTTTC
* *
5583135 TCTTCTTTTGTC
1 TTTTCTTTTTTC
5583147 TTTTTCTTT
1 -TTTTCTTT
5583156 CTTTTTGCAC
Statistics
Matches: 40, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
11 5 0.12
12 8 0.20
13 16 0.40
14 8 0.20
15 3 0.08
ACGTcount: A:0.02, C:0.19, G:0.03, T:0.76
Consensus pattern (12 bp):
TTTTCTTTTTTC
Found at i:5583121 original size:19 final size:19
Alignment explanation
Indices: 5583099--5583155 Score: 55
Period size: 19 Copynumber: 2.9 Consensus size: 19
5583089 TTTTGAATTT
5583099 TTCTTTTTCTTTTCTTTTC
1 TTCTTTTTCTTTTCTTTTC
*
5583118 TTC-TTTTCTGATTT-TTCTC
1 TTCTTTTTCT--TTTCTTTTC
5583137 TTCTTTTGTCTTTTTCTTT
1 TTCTTTT-TC-TTTTCTTT
5583156 CTTTTTGCAC
Statistics
Matches: 30, Mismatches: 2, Indels: 10
0.71 0.05 0.24
Matches are distributed among these distances:
18 6 0.20
19 10 0.33
20 9 0.30
21 4 0.13
22 1 0.03
ACGTcount: A:0.02, C:0.19, G:0.04, T:0.75
Consensus pattern (19 bp):
TTCTTTTTCTTTTCTTTTC
Found at i:5583906 original size:19 final size:21
Alignment explanation
Indices: 5583863--5583906 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
5583853 GAAACCCCTT
5583863 TGAAAATACATGACTTTTAAA
1 TGAAAATACATGACTTTTAAA
5583884 TGAAAATACATGA-TTTT-AA
1 TGAAAATACATGACTTTTAAA
5583903 TGAA
1 TGAA
5583907 GATATAGGCT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
19 6 0.26
20 4 0.17
21 13 0.57
ACGTcount: A:0.48, C:0.07, G:0.11, T:0.34
Consensus pattern (21 bp):
TGAAAATACATGACTTTTAAA
Found at i:5588421 original size:19 final size:20
Alignment explanation
Indices: 5588397--5588447 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
5588387 CGGCCAAGAG
* *
5588397 CATGTATCTTCAT-TAAAAT
1 CATGTATTTTCATCAAAAAT
5588416 CATGTATTTTCATCAAAAAT
1 CATGTATTTTCATCAAAAAT
5588436 CATGTATTTTCA
1 CATGTATTTTCA
5588448 AAGGGGTTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 12 0.41
20 17 0.59
ACGTcount: A:0.35, C:0.16, G:0.06, T:0.43
Consensus pattern (20 bp):
CATGTATTTTCATCAAAAAT
Found at i:5592602 original size:19 final size:20
Alignment explanation
Indices: 5592578--5592628 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
5592568 CGGCCAAGAG
* *
5592578 CATGTATCTTCAT-TAAAAT
1 CATGTATTTTCATCAAAAAT
5592597 CATGTATTTTCATCAAAAAT
1 CATGTATTTTCATCAAAAAT
5592617 CATGTATTTTCA
1 CATGTATTTTCA
5592629 AAGGGGTTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 12 0.41
20 17 0.59
ACGTcount: A:0.35, C:0.16, G:0.06, T:0.43
Consensus pattern (20 bp):
CATGTATTTTCATCAAAAAT
Found at i:5602417 original size:30 final size:29
Alignment explanation
Indices: 5602382--5602439 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
5602372 TGGCTTTGCT
*
5602382 TTCTTTT-TGAATTCTTTTTCTTTTCTTTTC
1 TTCTTTTCTG-ATT-TTTCTCTTTTCTTTTC
*
5602412 TTCTTTTCTGATTTTTCTCTTTTTTTTT
1 TTCTTTTCTGATTTTTCTCTTTTCTTTT
5602440 TGCACTCCAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 13 0.52
30 10 0.40
31 2 0.08
ACGTcount: A:0.05, C:0.16, G:0.03, T:0.76
Consensus pattern (29 bp):
TTCTTTTCTGATTTTTCTCTTTTCTTTTC
Found at i:5605681 original size:12 final size:12
Alignment explanation
Indices: 5605664--5605695 Score: 64
Period size: 12 Copynumber: 2.7 Consensus size: 12
5605654 TTTCACTACA
5605664 AAAACTTGTCCT
1 AAAACTTGTCCT
5605676 AAAACTTGTCCT
1 AAAACTTGTCCT
5605688 AAAACTTG
1 AAAACTTG
5605696 AGTTTAATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.38, C:0.22, G:0.09, T:0.31
Consensus pattern (12 bp):
AAAACTTGTCCT
Found at i:5608492 original size:19 final size:21
Alignment explanation
Indices: 5608468--5608519 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
5608458 TGGCCAAGAG
*
5608468 CATGTATCTTCA-TTAAAA-T
1 CATGTATTTTCATTTAAAAGT
5608487 CATGTATTTTCATTTAAAAGT
1 CATGTATTTTCATTTAAAAGT
5608508 CATGTATTTTCA
1 CATGTATTTTCA
5608520 AAGGGGTTTC
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 11 0.37
20 6 0.20
21 13 0.43
ACGTcount: A:0.33, C:0.13, G:0.08, T:0.46
Consensus pattern (21 bp):
CATGTATTTTCATTTAAAAGT
Found at i:5611198 original size:17 final size:16
Alignment explanation
Indices: 5611167--5611201 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
5611157 AACAAAAAGC
5611167 AACAAAAAAAAAAGAA
1 AACAAAAAAAAAAGAA
*
5611183 AACAAAAGAGAAAAGAA
1 AACAAAA-AAAAAAGAA
5611200 AA
1 AA
5611202 GACTCCTACA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 7 0.41
17 10 0.59
ACGTcount: A:0.83, C:0.06, G:0.11, T:0.00
Consensus pattern (16 bp):
AACAAAAAAAAAAGAA
Found at i:5616603 original size:19 final size:21
Alignment explanation
Indices: 5616560--5616611 Score: 72
Period size: 19 Copynumber: 2.6 Consensus size: 21
5616550 GAAACCCCTT
5616560 TGAAAATACATGACTATTAAA
1 TGAAAATACATGACTATTAAA
*
5616581 TGAAAATACATGA-T-TTTAA
1 TGAAAATACATGACTATTAAA
*
5616600 TGAAGATACATG
1 TGAAAATACATG
5616612 CTCTTGGCCG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 15 0.52
20 1 0.03
21 13 0.45
ACGTcount: A:0.48, C:0.08, G:0.13, T:0.31
Consensus pattern (21 bp):
TGAAAATACATGACTATTAAA
Found at i:5618058 original size:16 final size:16
Alignment explanation
Indices: 5618033--5618071 Score: 69
Period size: 16 Copynumber: 2.4 Consensus size: 16
5618023 TAATAAATAA
*
5618033 ACGAATATAAACGAAC
1 ACGAACATAAACGAAC
5618049 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
5618065 ACGAACA
1 ACGAACA
5618072 CGAACATAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.56, C:0.23, G:0.13, T:0.08
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:5618062 original size:10 final size:10
Alignment explanation
Indices: 5618029--5618109 Score: 52
Period size: 10 Copynumber: 8.7 Consensus size: 10
5618019 CATTTAATAA
*
5618029 ATAAACGAAT
1 ATAAACGAAC
5618039 ATAAACGAAC
1 ATAAACGAAC
5618049 ----ACGAAC
1 ATAAACGAAC
5618055 ATAAACGAAC
1 ATAAACGAAC
*
5618065 ACGAACACGAAC
1 A-TAA-ACGAAC
*
5618077 ATAAATG---
1 ATAAACGAAC
*
5618084 A-AAATGAAC
1 ATAAACGAAC
5618093 ATAAACGAAC
1 ATAAACGAAC
5618103 ATAAACG
1 ATAAACG
5618110 TTGGAGACCC
Statistics
Matches: 56, Mismatches: 5, Indels: 20
0.69 0.06 0.25
Matches are distributed among these distances:
6 11 0.20
7 1 0.02
9 1 0.02
10 32 0.57
11 4 0.07
12 7 0.12
ACGTcount: A:0.58, C:0.19, G:0.12, T:0.11
Consensus pattern (10 bp):
ATAAACGAAC
Found at i:5618092 original size:22 final size:22
Alignment explanation
Indices: 5618041--5618093 Score: 79
Period size: 22 Copynumber: 2.4 Consensus size: 22
5618031 AAACGAATAT
5618041 AAACGAACACGAACATAAACGA
1 AAACGAACACGAACATAAACGA
* *
5618063 ACACGAACACGAACATAAATGA
1 AAACGAACACGAACATAAACGA
*
5618085 AAATGAACA
1 AAACGAACA
5618094 TAAACGAACA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.58, C:0.21, G:0.13, T:0.08
Consensus pattern (22 bp):
AAACGAACACGAACATAAACGA
Found at i:5619212 original size:10 final size:10
Alignment explanation
Indices: 5619197--5619244 Score: 51
Period size: 10 Copynumber: 4.4 Consensus size: 10
5619187 ATAAATGAAT
*
5619197 GAACATAAGC
1 GAACATAACC
5619207 GAACATAACCGAAC
1 GAACATAA-C---C
5619221 GAACATAACC
1 GAACATAACC
5619231 GAACATAACC
1 GAACATAACC
5619241 GAAC
1 GAAC
5619245 GTTCACGAAC
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
10 23 0.70
13 1 0.03
14 9 0.27
ACGTcount: A:0.50, C:0.27, G:0.15, T:0.08
Consensus pattern (10 bp):
GAACATAACC
Found at i:5619223 original size:14 final size:14
Alignment explanation
Indices: 5619206--5619234 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
5619196 TGAACATAAG
5619206 CGAACATAACCGAA
1 CGAACATAACCGAA
5619220 CGAACATAACCGAA
1 CGAACATAACCGAA
5619234 C
1 C
5619235 ATAACCGAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.48, C:0.31, G:0.14, T:0.07
Consensus pattern (14 bp):
CGAACATAACCGAA
Found at i:5619224 original size:24 final size:24
Alignment explanation
Indices: 5619197--5619245 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
5619187 ATAAATGAAT
*
5619197 GAACATAAGCGAACATAACCGAAC
1 GAACATAACCGAACATAACCGAAC
5619221 GAACATAACCGAACATAACCGAAC
1 GAACATAACCGAACATAACCGAAC
5619245 G
1 G
5619246 TTCACGAACG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.49, C:0.27, G:0.16, T:0.08
Consensus pattern (24 bp):
GAACATAACCGAACATAACCGAAC
Found at i:5621108 original size:20 final size:21
Alignment explanation
Indices: 5621069--5621108 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
5621059 GAAACCCCTT
5621069 TGAAAATACATGACTTTTAAA
1 TGAAAATACATGACTTTTAAA
5621090 TGAAAATACATGA-TTTTAA
1 TGAAAATACATGACTTTTAA
5621109 TCAAGATACA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 6 0.32
21 13 0.68
ACGTcount: A:0.47, C:0.07, G:0.10, T:0.35
Consensus pattern (21 bp):
TGAAAATACATGACTTTTAAA
Found at i:5621119 original size:19 final size:21
Alignment explanation
Indices: 5621071--5621120 Score: 68
Period size: 19 Copynumber: 2.5 Consensus size: 21
5621061 AACCCCTTTG
*
5621071 AAAATACATGACTTTTAAATG
1 AAAATACATGACTTTTAAATC
5621092 AAAATACATGA-TTTT-AATC
1 AAAATACATGACTTTTAAATC
*
5621111 AAGATACATG
1 AAAATACATG
5621121 CTCTTGGCCG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
19 12 0.44
20 4 0.15
21 11 0.41
ACGTcount: A:0.48, C:0.10, G:0.10, T:0.32
Consensus pattern (21 bp):
AAAATACATGACTTTTAAATC
Found at i:5622188 original size:24 final size:23
Alignment explanation
Indices: 5622161--5622223 Score: 63
Period size: 24 Copynumber: 2.7 Consensus size: 23
5622151 AGAAAAATGT
*
5622161 CTTTTGAAGAACCAATAGTCATGA
1 CTTTTGAAGAACCAA-AGACATGA
** * *
5622185 CTTTTGGTGATCCACAAGACATGT
1 CTTTTGAAGAACCA-AAGACATGA
5622209 CTTTTGAAGAACCAA
1 CTTTTGAAGAACCAA
5622224 CAATTATGTC
Statistics
Matches: 30, Mismatches: 8, Indels: 3
0.73 0.20 0.07
Matches are distributed among these distances:
23 1 0.03
24 28 0.93
25 1 0.03
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.30
Consensus pattern (23 bp):
CTTTTGAAGAACCAAAGACATGA
Found at i:5630502 original size:18 final size:18
Alignment explanation
Indices: 5630463--5630514 Score: 54
Period size: 18 Copynumber: 2.8 Consensus size: 18
5630453 CTTCTTTATC
5630463 TTTTCTTCTTTTTTGAATTT
1 TTTTCTTC-TTTTTG-ATTT
5630483 TTTTCTTCTTTTTG-TCTT
1 TTTTCTTCTTTTTGAT-TT
5630501 TTCTT-TTCTTTTTG
1 TT-TTCTTCTTTTTG
5630515 CACTCCAATT
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
17 1 0.03
18 13 0.43
19 8 0.27
20 8 0.27
ACGTcount: A:0.04, C:0.13, G:0.06, T:0.77
Consensus pattern (18 bp):
TTTTCTTCTTTTTGATTT
Found at i:5631006 original size:220 final size:222
Alignment explanation
Indices: 5630615--5631027 Score: 622
Period size: 220 Copynumber: 1.9 Consensus size: 222
5630605 AATTACCGCT
* *
5630615 TGATGTAAGGCTGATCTACACGATTTGATGGAAGAGAGTATATAGCCTTATTGTGTCCCGATCTA
1 TGATGTAAGGCTGATCTACACGATTTGATGGAAGAGAGTAGATAGCCTTATTGTGTCCCAATCTA
* * *
5630680 GGATTGACAAGTACTGATGTCCTTGAATTTATAAGCTTGGGATGCACAAAATAAGAAATGAAATA
66 GGATTGACAAGTACTGATGTCCTTGAATTAATAAGCTTGGGATGAAAAAAATAAGAAATGAAATA
*
5630745 TGATTAATGATGGACTTAATCAAAGGAATAATAACATAAGTAATGAAATGAAAGAATAAGAATGA
131 TGATTAATAATGGACTTAATCAAAGGAATAATAACATAAGTAATGAAATGAAAGAATAAGAATGA
5630810 AATGAAATAAAGAAAGGATAGAGATGG
196 AATGAAATAAAGAAAGGATAGAGATGG
*
5630837 TGATGTAAGGC-GAATCTACAC-ATTTTGATGG-A-AGAGTAGATAGCGTTATTGTGTCCCAATC
1 TGATGTAAGGCTG-ATCTACACGA-TTTGATGGAAGAGAGTAGATAGCCTTATTGTGTCCCAATC
*
5630898 TAGGATTGACAAGTACTGATGTCCTTGAATTAATAAGCTTGGGCTGTAAAAATAATAAGAAA-GA
64 TAGGATTGACAAGTACTGATGTCCTTGAATTAATAAGCTTGGGATG-AAAAA-AATAAGAAATGA
** * * * *
5630962 AATATGATTAATAATGGGTTTAA-GAAATGAATAATAATATAAGTAATGGAATGAAAGAATAAGA
127 AATATGATTAATAATGGACTTAATCAAAGGAATAATAACATAAGTAATGAAATGAAAGAATAAGA
5631026 AT
192 AT
5631028 AGAGATGGCT
Statistics
Matches: 173, Mismatches: 14, Indels: 10
0.88 0.07 0.05
Matches are distributed among these distances:
220 109 0.63
221 28 0.16
222 36 0.21
ACGTcount: A:0.42, C:0.08, G:0.22, T:0.28
Consensus pattern (222 bp):
TGATGTAAGGCTGATCTACACGATTTGATGGAAGAGAGTAGATAGCCTTATTGTGTCCCAATCTA
GGATTGACAAGTACTGATGTCCTTGAATTAATAAGCTTGGGATGAAAAAAATAAGAAATGAAATA
TGATTAATAATGGACTTAATCAAAGGAATAATAACATAAGTAATGAAATGAAAGAATAAGAATGA
AATGAAATAAAGAAAGGATAGAGATGG
Found at i:5631104 original size:20 final size:21
Alignment explanation
Indices: 5631067--5631105 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
5631057 GATGGTCTTG
*
5631067 ATGAAGGATGTTGATGATGGA
1 ATGAAGGATGGTGATGATGGA
*
5631088 ATGAA-GATGGTGGTGATG
1 ATGAAGGATGGTGATGATG
5631106 TTGTATCTCA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 11 0.69
21 5 0.31
ACGTcount: A:0.31, C:0.00, G:0.41, T:0.28
Consensus pattern (21 bp):
ATGAAGGATGGTGATGATGGA
Found at i:5635296 original size:40 final size:40
Alignment explanation
Indices: 5635241--5635320 Score: 160
Period size: 40 Copynumber: 2.0 Consensus size: 40
5635231 CTAGCATGCA
5635241 TAGGAACAACATCGCACATAACCTCGTCCTTGTACTTACC
1 TAGGAACAACATCGCACATAACCTCGTCCTTGTACTTACC
5635281 TAGGAACAACATCGCACATAACCTCGTCCTTGTACTTACC
1 TAGGAACAACATCGCACATAACCTCGTCCTTGTACTTACC
5635321 AATTGAAAAA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.30, C:0.33, G:0.12, T:0.25
Consensus pattern (40 bp):
TAGGAACAACATCGCACATAACCTCGTCCTTGTACTTACC
Found at i:5637630 original size:20 final size:21
Alignment explanation
Indices: 5637593--5637631 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
5637583 GATGGTCTTG
*
5637593 ATGAAGGATGTTGATGATGGA
1 ATGAAGGATGGTGATGATGGA
*
5637614 ATGAA-GATGGTGGTGATG
1 ATGAAGGATGGTGATGATG
5637632 TTGTATCTCA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 11 0.69
21 5 0.31
ACGTcount: A:0.31, C:0.00, G:0.41, T:0.28
Consensus pattern (21 bp):
ATGAAGGATGGTGATGATGGA
Found at i:5640156 original size:24 final size:23
Alignment explanation
Indices: 5640129--5640191 Score: 63
Period size: 24 Copynumber: 2.7 Consensus size: 23
5640119 AGAAAAATGT
*
5640129 CTTTTGAAGAACCAATAGTCATGA
1 CTTTTGAAGAACCAA-AGACATGA
** * *
5640153 CTTTTGGTGATCCACAAGACATGT
1 CTTTTGAAGAACCA-AAGACATGA
5640177 CTTTTGAAGAACCAA
1 CTTTTGAAGAACCAA
5640192 CAATTATGTC
Statistics
Matches: 30, Mismatches: 8, Indels: 3
0.73 0.20 0.07
Matches are distributed among these distances:
23 1 0.03
24 28 0.93
25 1 0.03
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.30
Consensus pattern (23 bp):
CTTTTGAAGAACCAAAGACATGA
Found at i:5641537 original size:30 final size:31
Alignment explanation
Indices: 5641485--5641544 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 31
5641475 CTTAGCTTTA
**
5641485 TATTATGTTTACATATGTTTTAGAT-TCATT
1 TATTATGTTTACATATCATTTAGATATCATT
* *
5641515 TATTATGTTTGCATTTCATTTAGATATCAT
1 TATTATGTTTACATATCATTTAGATATCAT
5641545 GGCAGCATGT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 21 0.84
31 4 0.16
ACGTcount: A:0.27, C:0.08, G:0.10, T:0.55
Consensus pattern (31 bp):
TATTATGTTTACATATCATTTAGATATCATT
Found at i:5644499 original size:13 final size:12
Alignment explanation
Indices: 5644477--5644506 Score: 51
Period size: 13 Copynumber: 2.4 Consensus size: 12
5644467 ACTAAACACC
5644477 TTTCACATACCT
1 TTTCACATACCT
5644489 TTTCTACATACCT
1 TTTC-ACATACCT
5644502 TTTCA
1 TTTCA
5644507 TCTTTGGCCA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
12 5 0.29
13 12 0.71
ACGTcount: A:0.23, C:0.30, G:0.00, T:0.47
Consensus pattern (12 bp):
TTTCACATACCT
Found at i:5650047 original size:13 final size:12
Alignment explanation
Indices: 5650025--5650054 Score: 51
Period size: 13 Copynumber: 2.4 Consensus size: 12
5650015 ACTAAACACC
5650025 TTTCACATACCT
1 TTTCACATACCT
5650037 TTTCTACATACCT
1 TTTC-ACATACCT
5650050 TTTCA
1 TTTCA
5650055 TCTTTGGCCA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
12 5 0.29
13 12 0.71
ACGTcount: A:0.23, C:0.30, G:0.00, T:0.47
Consensus pattern (12 bp):
TTTCACATACCT
Found at i:5655585 original size:13 final size:12
Alignment explanation
Indices: 5655563--5655592 Score: 51
Period size: 13 Copynumber: 2.4 Consensus size: 12
5655553 ACTAAACACC
5655563 TTTCACATACCT
1 TTTCACATACCT
5655575 TTTCTACATACCT
1 TTTC-ACATACCT
5655588 TTTCA
1 TTTCA
5655593 TCTTTGGCCA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
12 5 0.29
13 12 0.71
ACGTcount: A:0.23, C:0.30, G:0.00, T:0.47
Consensus pattern (12 bp):
TTTCACATACCT
Done.