Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr02 ID=Chr02-JGI_221_v2.0
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: 62769430
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1067035 characters in sequence are not A, C, G, or T
File 127 of 206
Found at i:38265644 original size:13 final size:13
Alignment explanation
Indices: 38265612--38265723 Score: 51
Period size: 13 Copynumber: 8.5 Consensus size: 13
38265602 ATCAAATGAG
38265612 AGAAAAA-GAAAA
1 AGAAAAATGAAAA
38265624 GAGCAAAAAT-ACAAA
1 -AG-AAAAATGA-AAA
38265639 AGAAAAA-GAAAA
1 AGAAAAATGAAAA
* *
38265651 ATGAAAAA-CAGAA
1 A-GAAAAATGAAAA
* *
38265664 AGAAAATTCAAAA
1 AGAAAAATGAAAA
38265677 A-AAGAGAATG--AA
1 AGAA-A-AATGAAAA
38265689 A-AAAAATGAGAAA
1 AGAAAAATGA-AAA
38265702 AGCAAAAGATGAAAA
1 AG-AAAA-ATGAAAA
38265717 AGAAAAA
1 AGAAAAA
38265724 GTGATTGAAA
Statistics
Matches: 79, Mismatches: 6, Indels: 28
0.70 0.05 0.25
Matches are distributed among these distances:
10 4 0.05
11 1 0.01
12 16 0.20
13 28 0.35
14 14 0.18
15 12 0.15
16 4 0.05
ACGTcount: A:0.73, C:0.04, G:0.16, T:0.06
Consensus pattern (13 bp):
AGAAAAATGAAAA
Found at i:38265650 original size:5 final size:6
Alignment explanation
Indices: 38265612--38265669 Score: 53
Period size: 6 Copynumber: 9.0 Consensus size: 6
38265602 ATCAAATGAG
* * *
38265612 AGAAAA AGAAAA GAGCAAAA ATACAAA AGAAAA AGAAAA ATGAAAA ACAGAA
1 AGAAAA AGAAAA -AG-AAAA AGA-AAA AGAAAA AGAAAA A-GAAAA AGAAAA
38265664 AGAAAA
1 AGAAAA
38265670 TTCAAAAAAA
Statistics
Matches: 42, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
6 24 0.57
7 14 0.33
8 4 0.10
ACGTcount: A:0.76, C:0.05, G:0.16, T:0.03
Consensus pattern (6 bp):
AGAAAA
Found at i:38266989 original size:21 final size:21
Alignment explanation
Indices: 38266963--38267025 Score: 90
Period size: 21 Copynumber: 3.0 Consensus size: 21
38266953 TTGGTATTTG
38266963 GGAATTGGTACGAAATGGTAT
1 GGAATTGGTACGAAATGGTAT
*
38266984 GGAATTGGTATGAAATGGTAT
1 GGAATTGGTACGAAATGGTAT
* *
38267005 GGTATTTGGTACGAATTGGTA
1 GG-AATTGGTACGAAATGGTA
38267026 ATGGTTCAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
21 22 0.59
22 15 0.41
ACGTcount: A:0.30, C:0.03, G:0.33, T:0.33
Consensus pattern (21 bp):
GGAATTGGTACGAAATGGTAT
Found at i:38268216 original size:30 final size:30
Alignment explanation
Indices: 38268158--38268216 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
38268148 TTGAAAAGGT
* *
38268158 TTGAGCTGAAGTTGAGCTAATTCGAGCTCA
1 TTGAGCTGAAATGGAGCTAATTCGAGCTCA
*
38268188 TTGAGCTGAAATGGAAGTTAATTC-AGCTC
1 TTGAGCTGAAATGG-AGCTAATTCGAGCTC
38268217 GTATTAAAGT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 17 0.68
31 8 0.32
ACGTcount: A:0.29, C:0.15, G:0.25, T:0.31
Consensus pattern (30 bp):
TTGAGCTGAAATGGAGCTAATTCGAGCTCA
Found at i:38271183 original size:10 final size:10
Alignment explanation
Indices: 38271168--38271229 Score: 52
Period size: 10 Copynumber: 5.9 Consensus size: 10
38271158 TTTGAACCAT
*
38271168 TACCAATTCG
1 TACCAATTCA
*
38271178 TACCAAATACCA
1 TACC-AAT-TCA
*
38271190 TACCATTTCA
1 TACCAATTCA
38271200 TACCAATTCCA
1 TACCAATT-CA
* *
38271211 TACCATTTCG
1 TACCAATTCA
38271221 TACCAATTC
1 TACCAATTC
38271230 CCAAATACCA
Statistics
Matches: 41, Mismatches: 8, Indels: 6
0.75 0.15 0.11
Matches are distributed among these distances:
10 22 0.54
11 14 0.34
12 5 0.12
ACGTcount: A:0.34, C:0.32, G:0.03, T:0.31
Consensus pattern (10 bp):
TACCAATTCA
Found at i:38271213 original size:21 final size:21
Alignment explanation
Indices: 38271168--38271230 Score: 90
Period size: 21 Copynumber: 3.0 Consensus size: 21
38271158 TTTGAACCAT
* *
38271168 TACCAATTCGTACCAAATACCA
1 TACCATTTCGTACC-AATTCCA
*
38271190 TACCATTTCATACCAATTCCA
1 TACCATTTCGTACCAATTCCA
38271211 TACCATTTCGTACCAATTCC
1 TACCATTTCGTACCAATTCC
38271231 CAAATACCAA
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
21 25 0.68
22 12 0.32
ACGTcount: A:0.33, C:0.33, G:0.03, T:0.30
Consensus pattern (21 bp):
TACCATTTCGTACCAATTCCA
Found at i:38298594 original size:14 final size:14
Alignment explanation
Indices: 38298566--38298607 Score: 57
Period size: 14 Copynumber: 2.9 Consensus size: 14
38298556 ATTTCTTTCC
*
38298566 TTTTCTTTTCACTCT
1 TTTTCTTTT-TCTCT
*
38298581 TTTTGTTTTTCTCT
1 TTTTCTTTTTCTCT
38298595 TTTTCTTTTTCTC
1 TTTTCTTTTTCTC
38298608 GCTCAATAGA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
14 16 0.67
15 8 0.33
ACGTcount: A:0.02, C:0.21, G:0.02, T:0.74
Consensus pattern (14 bp):
TTTTCTTTTTCTCT
Found at i:38299975 original size:15 final size:16
Alignment explanation
Indices: 38299955--38299984 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
38299945 TCAGGACGGT
38299955 CTCGATTTC-TTGGAC
1 CTCGATTTCGTTGGAC
38299970 CTCGATTTCGTTGGA
1 CTCGATTTCGTTGGA
38299985 ACCGTTGTGG
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:0.13, C:0.23, G:0.23, T:0.40
Consensus pattern (16 bp):
CTCGATTTCGTTGGAC
Found at i:38300695 original size:12 final size:12
Alignment explanation
Indices: 38300675--38300715 Score: 55
Period size: 12 Copynumber: 3.3 Consensus size: 12
38300665 TATATATATA
*
38300675 TTTTCGAATTTT
1 TTTTTGAATTTT
38300687 TTTTTGAATTTT
1 TTTTTGAATTTT
*
38300699 TTTTTCAAATTTT
1 TTTTT-GAATTTT
38300712 TTTT
1 TTTT
38300716 ACAATCTCGT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
12 16 0.62
13 10 0.38
ACGTcount: A:0.17, C:0.05, G:0.05, T:0.73
Consensus pattern (12 bp):
TTTTTGAATTTT
Found at i:38300699 original size:13 final size:13
Alignment explanation
Indices: 38300675--38300715 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 13
38300665 TATATATATA
*
38300675 TTTTCGAATTTTT
1 TTTTCAAATTTTT
*
38300688 TTTT-GAATTTTT
1 TTTTCAAATTTTT
38300700 TTTTCAAATTTTT
1 TTTTCAAATTTTT
38300713 TTT
1 TTT
38300716 ACAATCTCGT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
12 12 0.46
13 14 0.54
ACGTcount: A:0.17, C:0.05, G:0.05, T:0.73
Consensus pattern (13 bp):
TTTTCAAATTTTT
Found at i:38306042 original size:16 final size:17
Alignment explanation
Indices: 38306010--38306042 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
38306000 TAATTTTTGG
38306010 GTCAAAAAAATTCAAGA
1 GTCAAAAAAATTCAAGA
*
38306027 GTCAAGAAAA-TCAAGA
1 GTCAAAAAAATTCAAGA
38306043 TTCCATATCT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.58, C:0.12, G:0.15, T:0.15
Consensus pattern (17 bp):
GTCAAAAAAATTCAAGA
Found at i:38316551 original size:20 final size:20
Alignment explanation
Indices: 38316526--38316572 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
38316516 AGCTCATTTC
*
38316526 CAGCTCACTT-GAGCTCAAGT
1 CAGCTCA-TTCGAGATCAAGT
*
38316546 CAGCTCATTCGAGATCAATT
1 CAGCTCATTCGAGATCAAGT
38316566 CAGCTCA
1 CAGCTCA
38316573 ATTTTAACCC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 2 0.08
20 22 0.92
ACGTcount: A:0.28, C:0.30, G:0.17, T:0.26
Consensus pattern (20 bp):
CAGCTCATTCGAGATCAAGT
Found at i:38316575 original size:10 final size:10
Alignment explanation
Indices: 38316516--38316575 Score: 50
Period size: 10 Copynumber: 5.9 Consensus size: 10
38316506 AGCTCTGTTT
*
38316516 AGCTCATTTCC
1 AGCTCAATT-C
* *
38316527 AGCTCACTTG
1 AGCTCAATTC
*
38316537 AGCTCAAGTC
1 AGCTCAATTC
38316547 AGCTC-ATTC
1 AGCTCAATTC
*
38316556 GAGATCAATTC
1 -AGCTCAATTC
38316567 AGCTCAATT
1 AGCTCAATT
38316576 TTAACCCAAT
Statistics
Matches: 39, Mismatches: 8, Indels: 5
0.75 0.15 0.10
Matches are distributed among these distances:
9 3 0.08
10 24 0.62
11 12 0.31
ACGTcount: A:0.27, C:0.28, G:0.15, T:0.30
Consensus pattern (10 bp):
AGCTCAATTC
Found at i:38320860 original size:23 final size:23
Alignment explanation
Indices: 38320828--38320939 Score: 125
Period size: 23 Copynumber: 4.9 Consensus size: 23
38320818 CTTTTTGAAC
* *
38320828 CATTAACATTTCGTACCAAATCG
1 CATTACCATTTCGTACCAAATCA
* *
38320851 TATTACCATTTCGAACCAAATCA
1 CATTACCATTTCGTACCAAATCA
* * *
38320874 CCTTACCAATTCGTACCAAATCG
1 CATTACCATTTCGTACCAAATCA
* * *
38320897 TATTACCATTTTGAACCAAATCA
1 CATTACCATTTCGTACCAAATCA
*
38320920 CATTACCATTTCGTAACAAA
1 CATTACCATTTCGTACCAAA
38320940 CCCAAAACCG
Statistics
Matches: 70, Mismatches: 19, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
23 70 1.00
ACGTcount: A:0.37, C:0.27, G:0.06, T:0.30
Consensus pattern (23 bp):
CATTACCATTTCGTACCAAATCA
Found at i:38320904 original size:46 final size:46
Alignment explanation
Indices: 38320828--38320939 Score: 170
Period size: 46 Copynumber: 2.4 Consensus size: 46
38320818 CTTTTTGAAC
* *
38320828 CATTAACATTTCGTACCAAATCGTATTACCATTTCGAACCAAATCA
1 CATTACCAATTCGTACCAAATCGTATTACCATTTCGAACCAAATCA
* *
38320874 CCTTACCAATTCGTACCAAATCGTATTACCATTTTGAACCAAATCA
1 CATTACCAATTCGTACCAAATCGTATTACCATTTCGAACCAAATCA
* *
38320920 CATTACCATTTCGTAACAAA
1 CATTACCAATTCGTACCAAA
38320940 CCCAAAACCG
Statistics
Matches: 59, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
46 59 1.00
ACGTcount: A:0.37, C:0.27, G:0.06, T:0.30
Consensus pattern (46 bp):
CATTACCAATTCGTACCAAATCGTATTACCATTTCGAACCAAATCA
Found at i:38326072 original size:8 final size:9
Alignment explanation
Indices: 38326059--38326096 Score: 53
Period size: 8 Copynumber: 4.3 Consensus size: 9
38326049 TAACTAAGTA
38326059 AAAT-AAAT
1 AAATAAAAT
38326067 AAAT-AAAT
1 AAATAAAAT
38326075 AAATAAAAT
1 AAATAAAAT
38326084 AAAATAAAAT
1 -AAATAAAAT
38326094 AAA
1 AAA
38326097 CTTTACAACT
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
8 12 0.43
9 7 0.25
10 9 0.32
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (9 bp):
AAATAAAAT
Found at i:38326083 original size:5 final size:5
Alignment explanation
Indices: 38326057--38326096 Score: 52
Period size: 5 Copynumber: 8.8 Consensus size: 5
38326047 ATTAACTAAG
38326057 TAAAA T-AAA T-AAA T-AAA T-AAA TAAAA TAAAA TAAAA TAAA
1 TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA TAAA
38326097 CTTTACAACT
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
4 16 0.47
5 18 0.53
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.23
Consensus pattern (5 bp):
TAAAA
Found at i:38329797 original size:18 final size:19
Alignment explanation
Indices: 38329752--38329800 Score: 57
Period size: 18 Copynumber: 2.6 Consensus size: 19
38329742 GAATATTTAC
*
38329752 ATAAAAATTAAACTAAGTAA
1 ATAAAAA-TAAACTAAATAA
38329772 A-AATAAATAAA-TAAATAA
1 ATAA-AAATAAACTAAATAA
38329790 ATAAAAATAAA
1 ATAAAAATAAA
38329801 ACTTTACAAC
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
18 14 0.54
19 8 0.31
20 4 0.15
ACGTcount: A:0.73, C:0.02, G:0.02, T:0.22
Consensus pattern (19 bp):
ATAAAAATAAACTAAATAA
Found at i:38334120 original size:14 final size:14
Alignment explanation
Indices: 38334092--38334126 Score: 54
Period size: 14 Copynumber: 2.5 Consensus size: 14
38334082 TTTTCTTTTC
38334092 TTTTTTAACTCAAA
1 TTTTTTAACTCAAA
38334106 TTATTTTAA-TCAAA
1 TT-TTTTAACTCAAA
38334120 TTTTTTA
1 TTTTTTA
38334127 TATTTTTCAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
13 5 0.25
14 9 0.45
15 6 0.30
ACGTcount: A:0.34, C:0.09, G:0.00, T:0.57
Consensus pattern (14 bp):
TTTTTTAACTCAAA
Found at i:38337428 original size:41 final size:40
Alignment explanation
Indices: 38337383--38337513 Score: 208
Period size: 41 Copynumber: 3.2 Consensus size: 40
38337373 AATTCGGCCA
*
38337383 AACATGTAGTAGTAGCATTAAATTCGTCCAGGCATATTTAT
1 AACATGTAGT-GCAGCATTAAATTCGTCCAGGCATATTTAT
*
38337424 AACATGTAGTGACAGCATTAAATTCATCCAGGCATATTTAT
1 AACATGTAGTG-CAGCATTAAATTCGTCCAGGCATATTTAT
*
38337465 AACATGTAGTGGCAGCATTAAATTCGTCCAGACATATTTAT
1 AACATGTAGT-GCAGCATTAAATTCGTCCAGGCATATTTAT
38337506 AACATGTA
1 AACATGTA
38337514 TGAAAATAGG
Statistics
Matches: 84, Mismatches: 4, Indels: 4
0.91 0.04 0.04
Matches are distributed among these distances:
40 1 0.01
41 82 0.98
42 1 0.01
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (40 bp):
AACATGTAGTGCAGCATTAAATTCGTCCAGGCATATTTAT
Found at i:38337729 original size:20 final size:20
Alignment explanation
Indices: 38337691--38337741 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
38337681 AGCTAATAAC
* *
38337691 GAGCTC-AATGTGCTGACTT
1 GAGCTCGAATGAGCTAACTT
38337710 GAGCTCGAATGAGCTAACTT
1 GAGCTCGAATGAGCTAACTT
38337730 GAGCTCGAATGA
1 GAGCTCGAATGA
38337742 ACCAAAAATG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 6 0.21
20 23 0.79
ACGTcount: A:0.27, C:0.20, G:0.27, T:0.25
Consensus pattern (20 bp):
GAGCTCGAATGAGCTAACTT
Found at i:38339849 original size:39 final size:33
Alignment explanation
Indices: 38339807--38339874 Score: 136
Period size: 33 Copynumber: 2.1 Consensus size: 33
38339797 TTGAGGCCAA
38339807 ACCTAAACCTGTGCTCGAGAGATAGTTGTCCAT
1 ACCTAAACCTGTGCTCGAGAGATAGTTGTCCAT
38339840 ACCTAAACCTGTGCTCGAGAGATAGTTGTCCAT
1 ACCTAAACCTGTGCTCGAGAGATAGTTGTCCAT
38339873 AC
1 AC
38339875 ACTGATAAGG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.28, C:0.25, G:0.21, T:0.26
Consensus pattern (33 bp):
ACCTAAACCTGTGCTCGAGAGATAGTTGTCCAT
Found at i:38340228 original size:27 final size:27
Alignment explanation
Indices: 38340187--38340462 Score: 351
Period size: 27 Copynumber: 10.2 Consensus size: 27
38340177 ACTTGATGGC
* * *
38340187 TAAAATTATCAAAATACCCTCAAAAGG
1 TAAAATTACCGAAATACCCTCAAAGGG
*
38340214 TAAAATTACTGAAATACCCTCGAAA-GG
1 TAAAATTACCGAAATACCCTC-AAAGGG
* * **
38340241 TAAAAGTACCAAAATACCCTTGAAGGG
1 TAAAATTACCGAAATACCCTCAAAGGG
*
38340268 TAAAATTACCGAAATACCCTCGAAGGG
1 TAAAATTACCGAAATACCCTCAAAGGG
*
38340295 TAAAATTATCGAAATACCCTCAAAGGG
1 TAAAATTACCGAAATACCCTCAAAGGG
* *
38340322 TAAAATTACTGATATACCCTCAAAGGG
1 TAAAATTACCGAAATACCCTCAAAGGG
38340349 TAAAATTACCGAAATACCCAT-AAAGGG
1 TAAAATTACCGAAATACCC-TCAAAGGG
* * *
38340376 TAAAATTACCAAAATACACTCGAAGGG
1 TAAAATTACCGAAATACCCTCAAAGGG
38340403 TAAAATTACCGAAATACCCTCAAAGGG
1 TAAAATTACCGAAATACCCTCAAAGGG
* *
38340430 TAAAATTACCAAAATACCC-CTGAAGGG
1 TAAAATTACCGAAATACCCTC-AAAGGG
38340457 TAAAAT
1 TAAAAT
38340463 AACTGTTATA
Statistics
Matches: 218, Mismatches: 26, Indels: 10
0.86 0.10 0.04
Matches are distributed among these distances:
26 4 0.02
27 210 0.96
28 4 0.02
ACGTcount: A:0.46, C:0.19, G:0.14, T:0.21
Consensus pattern (27 bp):
TAAAATTACCGAAATACCCTCAAAGGG
Found at i:38344588 original size:25 final size:25
Alignment explanation
Indices: 38344546--38344596 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 25
38344536 TTGGGTTGTG
*
38344546 TGCTGACGCATGAAGGTAAGGTGAT
1 TGCTGACGCAGGAAGGTAAGGTGAT
* *
38344571 TGCTGATGCAGGAGGGTAAGGTGAT
1 TGCTGACGCAGGAAGGTAAGGTGAT
38344596 T
1 T
38344597 CCTTATGCGT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.25, C:0.10, G:0.39, T:0.25
Consensus pattern (25 bp):
TGCTGACGCAGGAAGGTAAGGTGAT
Found at i:38347636 original size:197 final size:197
Alignment explanation
Indices: 38347301--38347659 Score: 619
Period size: 197 Copynumber: 1.8 Consensus size: 197
38347291 TATTTGCAAT
38347301 GTACTTACTTAATTTTAACTAGCTCTGATACCAAATGATGCAATCCCGTATTCAATGGTTGAATC
1 GTACTTACTTAATTTTAACTAGCTCTGATACCAAATGATGCAATCCCGTATTCAATGGTTGAATC
* *
38347366 GAGTCACTTGTGTTTCCGATGGTAAAATTCAGTAGTAAAGGTTTCATTTAACAAAAGGCTAATTT
66 GAGTCACTTGTGTTCCCGATGGTAAAATTAAGTAGTAAAGGTTTCATTTAACAAAAGGCTAATTT
*
38347431 CAGAGAAAGATAGGATTAACAAAGAAAACGTATTTTTAAAGTTCAACCCTGGGAGTGATAAATAA
131 CAGAGAAAGATAGGAATAACAAAGAAAACGTATTTTTAAAGTTCAACCCTGGGAGTGATAAATAA
38347496 TA
196 TA
* * * *
38347498 GTACTTACTTAATTTTAACTAGCTCTGATACCAAATGATGCGATCTCGTATTCGATGGTTGGATC
1 GTACTTACTTAATTTTAACTAGCTCTGATACCAAATGATGCAATCCCGTATTCAATGGTTGAATC
* * *
38347563 GAGTCGCTTGTGTTCCCGATGGTAAAATTAAGTAGTAAGGGTTTCGTTTAACAAAAGGCTAATTT
66 GAGTCACTTGTGTTCCCGATGGTAAAATTAAGTAGTAAAGGTTTCATTTAACAAAAGGCTAATTT
*
38347628 CGGAGAAAGATAGGAATAACAAAGAAAACGTA
131 CAGAGAAAGATAGGAATAACAAAGAAAACGTA
38347660 AAGTTGATAA
Statistics
Matches: 151, Mismatches: 11, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
197 151 1.00
ACGTcount: A:0.35, C:0.14, G:0.20, T:0.31
Consensus pattern (197 bp):
GTACTTACTTAATTTTAACTAGCTCTGATACCAAATGATGCAATCCCGTATTCAATGGTTGAATC
GAGTCACTTGTGTTCCCGATGGTAAAATTAAGTAGTAAAGGTTTCATTTAACAAAAGGCTAATTT
CAGAGAAAGATAGGAATAACAAAGAAAACGTATTTTTAAAGTTCAACCCTGGGAGTGATAAATAA
TA
Found at i:38349125 original size:24 final size:23
Alignment explanation
Indices: 38349071--38349126 Score: 58
Period size: 24 Copynumber: 2.4 Consensus size: 23
38349061 GATTAATTAA
**
38349071 GAAATGGTATTTGGTTTTGGTAC
1 GAAATGGTATTTGGAATTGGTAC
***
38349094 GTTTTGGTATTTGGGAATTGGTAC
1 GAAATGGTATTT-GGAATTGGTAC
38349118 GAAATGGTA
1 GAAATGGTA
38349127 ATGGTTCAAA
Statistics
Matches: 24, Mismatches: 8, Indels: 1
0.73 0.24 0.03
Matches are distributed among these distances:
23 9 0.38
24 15 0.62
ACGTcount: A:0.23, C:0.04, G:0.32, T:0.41
Consensus pattern (23 bp):
GAAATGGTATTTGGAATTGGTAC
Found at i:38350120 original size:20 final size:19
Alignment explanation
Indices: 38350095--38350141 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 19
38350085 TTTGGTTCAT
*
38350095 TTGAGCTCAAGTTAGCTCA
1 TTGAGCTCAAGTCAGCTCA
*
38350114 TTCGAGCTCAAGTCAGCACA
1 TT-GAGCTCAAGTCAGCTCA
38350134 TTGAGCTC
1 TTGAGCTC
38350142 GTTATTAGCT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 8 0.32
20 17 0.68
ACGTcount: A:0.26, C:0.26, G:0.21, T:0.28
Consensus pattern (19 bp):
TTGAGCTCAAGTCAGCTCA
Found at i:38351314 original size:20 final size:20
Alignment explanation
Indices: 38351277--38351314 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
38351267 AGCTCGTTTC
*
38351277 CAGCTCACTTGAGCTCAAGT
1 CAGCTCACTTGAGATCAAGT
38351297 CAGCTCA-TTCGAGATCAA
1 CAGCTCACTT-GAGATCAA
38351315 TTCAACTCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 2 0.12
20 14 0.88
ACGTcount: A:0.29, C:0.29, G:0.18, T:0.24
Consensus pattern (20 bp):
CAGCTCACTTGAGATCAAGT
Found at i:38352877 original size:11 final size:11
Alignment explanation
Indices: 38352863--38352925 Score: 54
Period size: 11 Copynumber: 5.3 Consensus size: 11
38352853 AAAAAAATTT
38352863 GAAAAAAAAAA
1 GAAAAAAAAAA
38352874 GAAAAAAAGAAGTGA
1 GAAAAAAA-AA---A
*
38352889 GCAAAAAAAAA
1 GAAAAAAAAAA
*
38352900 GAGTAAAAAAAA
1 GA-AAAAAAAAA
*
38352912 GAAGAAAAAAA
1 GAAAAAAAAAA
38352923 GAA
1 GAA
38352926 GTGAAAAGTC
Statistics
Matches: 42, Mismatches: 5, Indels: 10
0.74 0.09 0.18
Matches are distributed among these distances:
11 20 0.48
12 12 0.29
14 2 0.05
15 8 0.19
ACGTcount: A:0.78, C:0.02, G:0.17, T:0.03
Consensus pattern (11 bp):
GAAAAAAAAAA
Found at i:38352931 original size:13 final size:13
Alignment explanation
Indices: 38352862--38352932 Score: 51
Period size: 11 Copynumber: 5.5 Consensus size: 13
38352852 AAAAAAAATT
38352862 TGAAAAAAA-AA-
1 TGAAAAAAAGAAG
*
38352873 AGAAAAAAAGAAG
1 TGAAAAAAAGAAG
*
38352886 TGAGCAAAAAAAAAGAG
1 T--G-AAAAAAAGA-AG
*
38352903 TAAAAAAAAGAA-
1 TGAAAAAAAGAAG
38352915 -GAAAAAAAGAAG
1 TGAAAAAAAGAAG
38352927 TGAAAA
1 TGAAAA
38352933 GTCTTGCGAG
Statistics
Matches: 46, Mismatches: 6, Indels: 14
0.70 0.09 0.21
Matches are distributed among these distances:
11 18 0.39
12 2 0.04
13 6 0.13
14 8 0.17
15 1 0.02
16 8 0.17
17 3 0.07
ACGTcount: A:0.75, C:0.01, G:0.18, T:0.06
Consensus pattern (13 bp):
TGAAAAAAAGAAG
Found at i:38353994 original size:15 final size:15
Alignment explanation
Indices: 38353969--38354015 Score: 60
Period size: 15 Copynumber: 3.1 Consensus size: 15
38353959 AGAAAAGAAT
38353969 AAAGAAAATGAAAATG
1 AAAG-AAATGAAAATG
*
38353985 AAAGAAATGAAAAAG
1 AAAGAAATGAAAATG
38354000 AAA-AATATGAAAATG
1 AAAGAA-ATGAAAATG
38354015 A
1 A
38354016 GATTTCAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
14 2 0.07
15 22 0.79
16 4 0.14
ACGTcount: A:0.70, C:0.00, G:0.17, T:0.13
Consensus pattern (15 bp):
AAAGAAATGAAAATG
Found at i:38354062 original size:12 final size:12
Alignment explanation
Indices: 38354045--38354084 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
38354035 AGTGAAAAGC
38354045 AAAAAGAGATTG
1 AAAAAGAGATTG
*
38354057 AAAAAGAAATTG
1 AAAAAGAGATTG
* *
38354069 AAAGAGAGCTTG
1 AAAAAGAGATTG
38354081 AAAA
1 AAAA
38354085 GAAATCGAGT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.60, C:0.03, G:0.23, T:0.15
Consensus pattern (12 bp):
AAAAAGAGATTG
Found at i:38357094 original size:20 final size:20
Alignment explanation
Indices: 38357057--38357094 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
38357047 AGCTCGTTTC
*
38357057 CAGCTCACTTGAGCTCAAGT
1 CAGCTCACTTGAGATCAAGT
38357077 CAGCTCA-TTCGAGATCAA
1 CAGCTCACTT-GAGATCAA
38357095 TTCAACTCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 2 0.12
20 14 0.88
ACGTcount: A:0.29, C:0.29, G:0.18, T:0.24
Consensus pattern (20 bp):
CAGCTCACTTGAGATCAAGT
Found at i:38366888 original size:20 final size:19
Alignment explanation
Indices: 38366865--38366929 Score: 51
Period size: 20 Copynumber: 3.3 Consensus size: 19
38366855 AAGCTCAAAC
38366865 GAGCTAAAGTAAGCTAAATT
1 GAGCTAAAGT-AGCTAAATT
38366885 GAGCTCAAACG-AGCTAAATT
1 GAGCT-AAA-GTAGCTAAATT
* * * *
38366905 AAGCTCATGTGAGCTAAATC
1 GAGCTAAAGT-AGCTAAATT
38366925 GAGCT
1 GAGCT
38366930 GGGAAAAACT
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 30 0.83
21 3 0.08
22 1 0.03
ACGTcount: A:0.38, C:0.17, G:0.22, T:0.23
Consensus pattern (19 bp):
GAGCTAAAGTAGCTAAATT
Found at i:38367829 original size:30 final size:30
Alignment explanation
Indices: 38367771--38367829 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
38367761 TTGAAAATGT
* *
38367771 TTGAGCTGAAGTTGAGCTAATTCGAGCTCA
1 TTGAGCTGAAATGGAGCTAATTCGAGCTCA
*
38367801 TTGAGCTGAAATGGAAGTTAATTC-AGCTC
1 TTGAGCTGAAATGG-AGCTAATTCGAGCTC
38367830 GTATTAAAGT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 17 0.68
31 8 0.32
ACGTcount: A:0.29, C:0.15, G:0.25, T:0.31
Consensus pattern (30 bp):
TTGAGCTGAAATGGAGCTAATTCGAGCTCA
Found at i:38376913 original size:20 final size:20
Alignment explanation
Indices: 38376890--38376936 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
38376880 GGGTTGAGGT
38376890 TGAGCTGAATTCAACTCGAA
1 TGAGCTGAATTCAACTCGAA
* * * *
38376910 TGAGCTGACTTGAGCTCGAG
1 TGAGCTGAATTCAACTCGAA
38376930 TGAGCTG
1 TGAGCTG
38376937 GAAACGAGCT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.26, C:0.19, G:0.30, T:0.26
Consensus pattern (20 bp):
TGAGCTGAATTCAACTCGAA
Found at i:38377835 original size:14 final size:14
Alignment explanation
Indices: 38377816--38377849 Score: 68
Period size: 14 Copynumber: 2.4 Consensus size: 14
38377806 TGCTGATTTC
38377816 TTTTTTTCACAAAT
1 TTTTTTTCACAAAT
38377830 TTTTTTTCACAAAT
1 TTTTTTTCACAAAT
38377844 TTTTTT
1 TTTTTT
38377850 ATATTTCATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.24, C:0.12, G:0.00, T:0.65
Consensus pattern (14 bp):
TTTTTTTCACAAAT
Found at i:38386175 original size:14 final size:14
Alignment explanation
Indices: 38386147--38386188 Score: 57
Period size: 14 Copynumber: 2.9 Consensus size: 14
38386137 GTTTCTTTCC
*
38386147 TTTTCTTTTCACTCT
1 TTTTCTTTT-TCTCT
*
38386162 TTTTGTTTTTCTCT
1 TTTTCTTTTTCTCT
38386176 TTTTCTTTTTCTC
1 TTTTCTTTTTCTC
38386189 GCTCAATAGA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
14 16 0.67
15 8 0.33
ACGTcount: A:0.02, C:0.21, G:0.02, T:0.74
Consensus pattern (14 bp):
TTTTCTTTTTCTCT
Found at i:38388278 original size:14 final size:13
Alignment explanation
Indices: 38388258--38388293 Score: 63
Period size: 13 Copynumber: 2.8 Consensus size: 13
38388248 TAATATATAT
38388258 ATTTTTTTTTCAA
1 ATTTTTTTTTCAA
*
38388271 ATTTTTTTTTCGA
1 ATTTTTTTTTCAA
38388284 ATTTTTTTTT
1 ATTTTTTTTT
38388294 ACAATATCGT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.17, C:0.06, G:0.03, T:0.75
Consensus pattern (13 bp):
ATTTTTTTTTCAA
Found at i:38391099 original size:34 final size:34
Alignment explanation
Indices: 38391060--38391140 Score: 105
Period size: 33 Copynumber: 2.4 Consensus size: 34
38391050 TGTTTGAGCA
* * *
38391060 CTCTCTTCTTCTTCACTC-ATTTCTTGTTGAAGCT
1 CTCTCTTCTTTTTCACTCAATTTCTT-TTCAAACT
38391094 CTCTC-TCTTTTTCACTCAATTTCTTTTCAAACT
1 CTCTCTTCTTTTTCACTCAATTTCTTTTCAAACT
38391127 CTCT-TTCTTTTTCA
1 CTCTCTTCTTTTTCA
38391141 ATCTCTTTTT
Statistics
Matches: 42, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
33 30 0.71
34 12 0.29
ACGTcount: A:0.14, C:0.30, G:0.04, T:0.53
Consensus pattern (34 bp):
CTCTCTTCTTTTTCACTCAATTTCTTTTCAAACT
Found at i:38391140 original size:18 final size:18
Alignment explanation
Indices: 38391092--38391156 Score: 55
Period size: 18 Copynumber: 3.7 Consensus size: 18
38391082 CTTGTTGAAG
*
38391092 CTCTCTCTCTTTTTC--A
1 CTCTCTTTCTTTTTCAAA
**
38391108 CTCAATTTC-TTTTCAAA
1 CTCTCTTTCTTTTTCAAA
*
38391125 CTCTCTTTCTTTTTCAAT
1 CTCTCTTTCTTTTTCAAA
*
38391143 CTCTTTTTGCTTTT
1 CTCTCTTT-CTTTT
38391157 CACTCTCTTT
Statistics
Matches: 38, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
15 5 0.13
16 6 0.16
17 8 0.21
18 14 0.37
19 5 0.13
ACGTcount: A:0.12, C:0.28, G:0.02, T:0.58
Consensus pattern (18 bp):
CTCTCTTTCTTTTTCAAA
Found at i:38391147 original size:16 final size:16
Alignment explanation
Indices: 38391093--38391148 Score: 51
Period size: 16 Copynumber: 3.4 Consensus size: 16
38391083 TTGTTGAAGC
* *
38391093 TCTCTCTCTTTTTCAC
1 TCTCTTTCTTTTTCAA
**
38391109 TCAATTTC-TTTTCAAA
1 TCTCTTTCTTTTTC-AA
38391125 CTCTCTTTCTTTTTCAA
1 -TCTCTTTCTTTTTCAA
38391142 TCTCTTT
1 TCTCTTT
38391149 TTGCTTTTCA
Statistics
Matches: 31, Mismatches: 6, Indels: 6
0.72 0.14 0.14
Matches are distributed among these distances:
15 5 0.16
16 13 0.42
17 8 0.26
18 5 0.16
ACGTcount: A:0.14, C:0.29, G:0.00, T:0.57
Consensus pattern (16 bp):
TCTCTTTCTTTTTCAA
Found at i:38391157 original size:18 final size:17
Alignment explanation
Indices: 38391113--38391167 Score: 65
Period size: 18 Copynumber: 3.1 Consensus size: 17
38391103 TTTCACTCAA
* *
38391113 TTTCTTTTCAAACTCTC
1 TTTCTTTTCAATCTCTT
38391130 TTTCTTTTTCAATCTCTT
1 TTTC-TTTTCAATCTCTT
*
38391148 TTTGCTTTTCACTCTCTT
1 TTT-CTTTTCAATCTCTT
38391166 TT
1 TT
38391168 GTTTTTGAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
17 4 0.12
18 28 0.85
19 1 0.03
ACGTcount: A:0.11, C:0.25, G:0.02, T:0.62
Consensus pattern (17 bp):
TTTCTTTTCAATCTCTT
Found at i:38391220 original size:15 final size:15
Alignment explanation
Indices: 38391180--38391226 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
38391170 TTTTGAAATC
* *
38391180 TCATTTTCATATATT
1 TCATTTTCATTTCTT
*
38391195 TCTTTTTCATTTCTT
1 TCATTTTCATTTCTT
38391210 TCATTTTCATTTTCTT
1 TCATTTTCA-TTTCTT
38391226 T
1 T
38391227 ATTCTTTTCT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
15 20 0.74
16 7 0.26
ACGTcount: A:0.15, C:0.17, G:0.00, T:0.68
Consensus pattern (15 bp):
TCATTTTCATTTCTT
Found at i:38406429 original size:17 final size:17
Alignment explanation
Indices: 38406396--38406441 Score: 51
Period size: 17 Copynumber: 2.7 Consensus size: 17
38406386 CTCACAAGAC
38406396 TTTTCACTTC--TTCTTT
1 TTTTCACTTCAATT-TTT
*
38406412 TTTTATACTTCAATTTTT
1 TTTT-CACTTCAATTTTT
38406430 TTTTCACTTCAA
1 TTTTCACTTCAA
38406442 ATACAATTGA
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
16 4 0.16
17 12 0.48
18 7 0.28
19 2 0.08
ACGTcount: A:0.17, C:0.20, G:0.00, T:0.63
Consensus pattern (17 bp):
TTTTCACTTCAATTTTT
Found at i:38406511 original size:11 final size:11
Alignment explanation
Indices: 38406495--38406598 Score: 67
Period size: 11 Copynumber: 9.7 Consensus size: 11
38406485 CCTCTTCTCT
38406495 TTTTTTTTCAA
1 TTTTTTTTCAA
38406506 TTTTTTTTCAA
1 TTTTTTTTCAA
38406517 -TTTTTTTC--
1 TTTTTTTTCAA
* * *
38406525 TTTCTCTCTC-T
1 TTT-TTTTTCAA
*
38406536 TTTTTTTGCTCGA
1 TTTTTTT--TCAA
*
38406549 TTTTTTTTCAC
1 TTTTTTTTCAA
*
38406560 TTTTTTTTGAA
1 TTTTTTTTCAA
*
38406571 TTTTTTTTCGA
1 TTTTTTTTCAA
*
38406582 TTTTCTTTC--
1 TTTTTTTTCAA
38406591 TTTTTTTT
1 TTTTTTTT
38406599 AATCCAATAC
Statistics
Matches: 74, Mismatches: 13, Indels: 14
0.73 0.13 0.14
Matches are distributed among these distances:
9 9 0.12
10 14 0.19
11 42 0.57
12 2 0.03
13 7 0.09
ACGTcount: A:0.09, C:0.13, G:0.04, T:0.74
Consensus pattern (11 bp):
TTTTTTTTCAA
Found at i:38406575 original size:33 final size:31
Alignment explanation
Indices: 38406538--38406598 Score: 77
Period size: 33 Copynumber: 1.9 Consensus size: 31
38406528 CTCTCTCTTT
*
38406538 TTTTTGCTCGATTTTTTTTCACTTTTTTTTGAA
1 TTTTTGCTCGATTTTCTTT--CTTTTTTTTGAA
**
38406571 TTTTTTTTCGATTTTCTTTCTTTTTTTT
1 TTTTTGCTCGATTTTCTTTCTTTTTTTT
38406599 AATCCAATAC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
31 9 0.36
33 16 0.64
ACGTcount: A:0.08, C:0.11, G:0.07, T:0.74
Consensus pattern (31 bp):
TTTTTGCTCGATTTTCTTTCTTTTTTTTGAA
Found at i:38411125 original size:13 final size:12
Alignment explanation
Indices: 38411107--38411150 Score: 79
Period size: 12 Copynumber: 3.6 Consensus size: 12
38411097 ACTAGATTGT
38411107 AAAAAAATTTGA
1 AAAAAAATTTGA
38411119 AAAAAAATTTGA
1 AAAAAAATTTGA
38411131 AAAAAAATTTCGA
1 AAAAAAATTT-GA
38411144 AAAAAAA
1 AAAAAAA
38411151 AGTTTGTATT
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
12 22 0.71
13 9 0.29
ACGTcount: A:0.70, C:0.02, G:0.07, T:0.20
Consensus pattern (12 bp):
AAAAAAATTTGA
Found at i:38411235 original size:29 final size:29
Alignment explanation
Indices: 38411193--38411259 Score: 84
Period size: 30 Copynumber: 2.3 Consensus size: 29
38411183 TTTAGTATTG
* *
38411193 AAAAAAAA-TAAAAAAAATTCGGAATT-AA
1 AAAAAAAAGAAAAAAAAATT-GAAATTGAA
38411221 AAAAAAGAAGAAAAAAAAATTGAAATTGAA
1 AAAAAA-AAGAAAAAAAAATTGAAATTGAA
38411251 AAAAAAAAG
1 AAAAAAAAG
38411260 TGATTGAAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
28 6 0.18
29 10 0.29
30 18 0.53
ACGTcount: A:0.75, C:0.01, G:0.10, T:0.13
Consensus pattern (29 bp):
AAAAAAAAGAAAAAAAAATTGAAATTGAA
Found at i:38411265 original size:17 final size:18
Alignment explanation
Indices: 38411231--38411268 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
38411221 AAAAAAGAAG
*
38411231 AAAAAAAAATTGAAATTGA
1 AAAAAAAAAGTG-AATTGA
38411250 AAAAAAAAAGTG-ATTGA
1 AAAAAAAAAGTGAATTGA
38411267 AA
1 AA
38411269 TTCATTTTGA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 7 0.39
19 11 0.61
ACGTcount: A:0.68, C:0.00, G:0.13, T:0.18
Consensus pattern (18 bp):
AAAAAAAAAGTGAATTGA
Found at i:38415057 original size:21 final size:22
Alignment explanation
Indices: 38415031--38415072 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
38415021 TGTAGTTTCG
*
38415031 AAAAAAAAATTGAAAA-AAAAT
1 AAAAAAAAATCGAAAAGAAAAT
38415052 AAAAAAAAATCGAAAAGAAAA
1 AAAAAAAAATCGAAAAGAAAA
38415073 AAATTTGAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 15 0.79
22 4 0.21
ACGTcount: A:0.81, C:0.02, G:0.07, T:0.10
Consensus pattern (22 bp):
AAAAAAAAATCGAAAAGAAAAT
Found at i:38426189 original size:12 final size:12
Alignment explanation
Indices: 38426172--38426198 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
38426162 TCATTTCAAT
38426172 TTGATACTCACC
1 TTGATACTCACC
38426184 TTGATACTCACC
1 TTGATACTCACC
38426196 TTG
1 TTG
38426199 GCTTGACGAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.22, C:0.30, G:0.11, T:0.37
Consensus pattern (12 bp):
TTGATACTCACC
Found at i:38435211 original size:15 final size:14
Alignment explanation
Indices: 38435183--38435217 Score: 52
Period size: 15 Copynumber: 2.4 Consensus size: 14
38435173 CCGTATGCAA
38435183 TTTTTTTTCAATTT
1 TTTTTTTTCAATTT
*
38435197 TTTTCTTTTCGATTT
1 TTTT-TTTTCAATTT
38435212 TTTTTT
1 TTTTTT
38435218 ATTTTTTTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
14 6 0.32
15 13 0.68
ACGTcount: A:0.09, C:0.09, G:0.03, T:0.80
Consensus pattern (14 bp):
TTTTTTTTCAATTT
Found at i:38435228 original size:21 final size:23
Alignment explanation
Indices: 38435197--38435240 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
38435187 TTTTCAATTT
38435197 TTTTCTTTTCG-ATTTTTTTTTA
1 TTTTCTTTTCGAATTTTTTTTTA
38435219 TTTT-TTTTCGAAATTTTTTTTT
1 TTTTCTTTTCG-AATTTTTTTTT
38435241 GAAACTACAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
21 6 0.30
22 4 0.20
23 10 0.50
ACGTcount: A:0.11, C:0.07, G:0.05, T:0.77
Consensus pattern (23 bp):
TTTTCTTTTCGAATTTTTTTTTA
Found at i:38449506 original size:16 final size:15
Alignment explanation
Indices: 38449481--38449516 Score: 63
Period size: 16 Copynumber: 2.3 Consensus size: 15
38449471 CCGTATGCAA
38449481 TTTTTTTTCAATTTT
1 TTTTTTTTCAATTTT
38449496 TTTTCTTTTCAATTTT
1 TTTT-TTTTCAATTTT
38449512 TTTTT
1 TTTTT
38449517 GATTTTTTTC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
15 5 0.25
16 15 0.75
ACGTcount: A:0.11, C:0.08, G:0.00, T:0.81
Consensus pattern (15 bp):
TTTTTTTTCAATTTT
Found at i:38457233 original size:19 final size:18
Alignment explanation
Indices: 38457209--38457247 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
38457199 TTTGCCTTAG
38457209 TTTTCTTGTAATAGAACCT
1 TTTTCTTGTAAT-GAACCT
* *
38457228 TTTTCTTTTAGTGAACCT
1 TTTTCTTGTAATGAACCT
38457246 TT
1 TT
38457248 GGAACACCTC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 8 0.44
19 10 0.56
ACGTcount: A:0.21, C:0.15, G:0.10, T:0.54
Consensus pattern (18 bp):
TTTTCTTGTAATGAACCT
Found at i:38458715 original size:52 final size:52
Alignment explanation
Indices: 38458654--38458754 Score: 166
Period size: 52 Copynumber: 1.9 Consensus size: 52
38458644 CATGCACATA
* * * *
38458654 TTTGAGCTTCAACCGCGCTAGAAATGAGGTCTTAAGCTGCTGTCTATTATTG
1 TTTGAGCTTCAACCGAGCTAGAAATGAGATCTTAAGCTACTGTCCATTATTG
38458706 TTTGAGCTTCAACCGAGCTAGAAATGAGATCTTAAGCTACTGTCCATTA
1 TTTGAGCTTCAACCGAGCTAGAAATGAGATCTTAAGCTACTGTCCATTA
38458755 CGTTTCCCCC
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
52 45 1.00
ACGTcount: A:0.27, C:0.20, G:0.21, T:0.33
Consensus pattern (52 bp):
TTTGAGCTTCAACCGAGCTAGAAATGAGATCTTAAGCTACTGTCCATTATTG
Found at i:38459973 original size:30 final size:30
Alignment explanation
Indices: 38459937--38459997 Score: 122
Period size: 30 Copynumber: 2.0 Consensus size: 30
38459927 AAAGAACAAG
38459937 TTAGCCACATTAACAGCATCATCAGTCTAA
1 TTAGCCACATTAACAGCATCATCAGTCTAA
38459967 TTAGCCACATTAACAGCATCATCAGTCTAA
1 TTAGCCACATTAACAGCATCATCAGTCTAA
38459997 T
1 T
38459998 GGCATGAAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.36, C:0.26, G:0.10, T:0.28
Consensus pattern (30 bp):
TTAGCCACATTAACAGCATCATCAGTCTAA
Found at i:38464659 original size:26 final size:26
Alignment explanation
Indices: 38464622--38464681 Score: 111
Period size: 26 Copynumber: 2.3 Consensus size: 26
38464612 GTGAAGTTGC
*
38464622 TTGAATACGTCAAGGAACTTCTTGAA
1 TTGAATATGTCAAGGAACTTCTTGAA
38464648 TTGAATATGTCAAGGAACTTCTTGAA
1 TTGAATATGTCAAGGAACTTCTTGAA
38464674 TTGAATAT
1 TTGAATAT
38464682 CATGCTTCTA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 33 1.00
ACGTcount: A:0.35, C:0.12, G:0.18, T:0.35
Consensus pattern (26 bp):
TTGAATATGTCAAGGAACTTCTTGAA
Found at i:38466396 original size:14 final size:15
Alignment explanation
Indices: 38466376--38466417 Score: 59
Period size: 14 Copynumber: 2.8 Consensus size: 15
38466366 AGTTGTAAAG
38466376 TTTTATTTTTATTTA
1 TTTTATTTTTATTTA
*
38466391 -TTTATTTTTACTTA
1 TTTTATTTTTATTTA
38466405 TTTTAATTTTTAT
1 TTTT-ATTTTTAT
38466418 GTAAATATTC
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
14 13 0.57
15 3 0.13
16 7 0.30
ACGTcount: A:0.21, C:0.02, G:0.00, T:0.76
Consensus pattern (15 bp):
TTTTATTTTTATTTA
Found at i:38472082 original size:53 final size:50
Alignment explanation
Indices: 38471960--38472082 Score: 122
Period size: 50 Copynumber: 2.4 Consensus size: 50
38471950 GTGTTCTGCA
* * *
38471960 TTTAATAAAGTCATGTATTATGTTACTCTCATGTTAGTTAAGATTGCATC
1 TTTAATAAAGTCATGCATTATATAACTCTCATGTTAGTTAAGATTGCATC
* * * * * *
38472010 ATAAATTATGTCATGCATTATATAACTC-CTATGTTAGTTAAAGTTTGCATTTT
1 TTTAATAAAGTCATGCATTATATAACTCTC-ATGTTAGTT-AAGATTGCA--TC
38472063 TTTAATAAAGTCATGCATTA
1 TTTAATAAAGTCATGCATTA
38472083 CGTAATTCAT
Statistics
Matches: 56, Mismatches: 13, Indels: 5
0.76 0.18 0.07
Matches are distributed among these distances:
49 1 0.02
50 30 0.54
51 8 0.14
53 17 0.30
ACGTcount: A:0.33, C:0.11, G:0.12, T:0.44
Consensus pattern (50 bp):
TTTAATAAAGTCATGCATTATATAACTCTCATGTTAGTTAAGATTGCATC
Found at i:38475509 original size:82 final size:82
Alignment explanation
Indices: 38475356--38475518 Score: 231
Period size: 82 Copynumber: 2.0 Consensus size: 82
38475346 TTGTGTCTGC
* * *
38475356 AGGTCATTGAATTCGGCTACTTAATGGCTAAGGAGACATGCATTTAAGGTGCTGTTAACATGCAA
1 AGGTCATTGAATTCGGCTACTTAATGGCAAAGGAGACATGCATTTAAGGAGATGTTAACATGCAA
38475421 GGAACGGCATTTAAAGA
66 GGAACGGCATTTAAAGA
**
38475438 AGGTCATTGAAATTCGGCTACTTAATGGCAAAGGA-ATCATGCA-TTAAGGAGATGTTCCCATGC
1 AGGTCATTG-AATTCGGCTACTTAATGGCAAAGGAGA-CATGCATTTAAGGAGATGTTAACATGC
* *
38475501 ATGGAACGGTATTTAAAG
64 AAGGAACGGCATTTAAAG
38475519 GGAAGTAAAA
Statistics
Matches: 72, Mismatches: 7, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
82 42 0.58
83 30 0.42
ACGTcount: A:0.33, C:0.15, G:0.25, T:0.27
Consensus pattern (82 bp):
AGGTCATTGAATTCGGCTACTTAATGGCAAAGGAGACATGCATTTAAGGAGATGTTAACATGCAA
GGAACGGCATTTAAAGA
Found at i:38475590 original size:32 final size:32
Alignment explanation
Indices: 38475554--38475640 Score: 156
Period size: 32 Copynumber: 2.7 Consensus size: 32
38475544 GGTGTTCCCA
* *
38475554 TGCATGGACGGCATTAATTAGTTGCTGGAGCT
1 TGCATGCATGGCATTAATTAGTTGCTGGAGCT
38475586 TGCATGCATGGCATTAATTAGTTGCTGGAGCT
1 TGCATGCATGGCATTAATTAGTTGCTGGAGCT
38475618 TGCATGCATGGCATTAATTAGTT
1 TGCATGCATGGCATTAATTAGTT
38475641 AATTTTTCGT
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
32 53 1.00
ACGTcount: A:0.23, C:0.15, G:0.28, T:0.34
Consensus pattern (32 bp):
TGCATGCATGGCATTAATTAGTTGCTGGAGCT
Found at i:38484336 original size:62 final size:62
Alignment explanation
Indices: 38484209--38484336 Score: 166
Period size: 62 Copynumber: 2.1 Consensus size: 62
38484199 AGACGCAAGC
* * * * * * *
38484209 GTGTTTCTAGGTCGTGTAACTCACTGTTTGTGGTTTCAGACCACACGGCCAAGGACACGAGT
1 GTGTGTCTAGGCCGTGTAACTAACTGTTTGTGGTATAAAACCACACGGCCAAGGACACGAAT
* * *
38484271 GTGTGTCTAGGCCGTGTAACTAACTGTTTGTGGTATAAAACCACACGGCTAGGGATACGAAT
1 GTGTGTCTAGGCCGTGTAACTAACTGTTTGTGGTATAAAACCACACGGCCAAGGACACGAAT
38484333 GTGT
1 GTGT
38484337 ACCCAGGCCA
Statistics
Matches: 56, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
62 56 1.00
ACGTcount: A:0.23, C:0.20, G:0.28, T:0.29
Consensus pattern (62 bp):
GTGTGTCTAGGCCGTGTAACTAACTGTTTGTGGTATAAAACCACACGGCCAAGGACACGAAT
Found at i:38489714 original size:20 final size:20
Alignment explanation
Indices: 38489689--38489735 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
38489679 AGCTCGTTTC
*
38489689 CAGCTCACTT-GAGCTCAAGT
1 CAGCTCA-TTCGAGATCAAGT
*
38489709 CAGCTCATTCGAGATCAATT
1 CAGCTCATTCGAGATCAAGT
38489729 CAGCTCA
1 CAGCTCA
38489736 ATTTTAACCC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 2 0.08
20 22 0.92
ACGTcount: A:0.28, C:0.30, G:0.17, T:0.26
Consensus pattern (20 bp):
CAGCTCATTCGAGATCAAGT
Found at i:38491380 original size:25 final size:24
Alignment explanation
Indices: 38491329--38491380 Score: 68
Period size: 25 Copynumber: 2.1 Consensus size: 24
38491319 AAAACTCTTC
* *
38491329 TAAAAGAATCTCAAGAGAAATTCT
1 TAAAAAAATCTCAAGAGAAATTAT
*
38491353 TAAAAAAATCTCAAAGAGAATTTAT
1 TAAAAAAATCTC-AAGAGAAATTAT
38491378 TAA
1 TAA
38491381 CTCAAAAGAG
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
24 11 0.46
25 13 0.54
ACGTcount: A:0.54, C:0.10, G:0.10, T:0.27
Consensus pattern (24 bp):
TAAAAAAATCTCAAGAGAAATTAT
Found at i:38492612 original size:32 final size:30
Alignment explanation
Indices: 38492552--38492631 Score: 79
Period size: 32 Copynumber: 2.6 Consensus size: 30
38492542 GCGTTTGAAG
** *
38492552 TGTCTTTGGTGTGAACACTTGGATTTGGAC
1 TGTCTTTGGTGTGAACACCAGGAATTGGAC
38492582 TGTCGTTTGGGTGTGAACACCAGGAATTGGAC
1 TGTC-TTT-GGTGTGAACACCAGGAATTGGAC
* * *
38492614 GGTCCATTAGTGTGAACA
1 TGT-CTTTGGTGTGAACA
38492632 AAAGTAGCTG
Statistics
Matches: 41, Mismatches: 6, Indels: 5
0.79 0.12 0.10
Matches are distributed among these distances:
30 4 0.10
31 12 0.29
32 24 0.59
33 1 0.02
ACGTcount: A:0.21, C:0.15, G:0.31, T:0.33
Consensus pattern (30 bp):
TGTCTTTGGTGTGAACACCAGGAATTGGAC
Found at i:38496631 original size:32 final size:32
Alignment explanation
Indices: 38496595--38496674 Score: 135
Period size: 32 Copynumber: 2.5 Consensus size: 32
38496585 TTCACTTCCT
*
38496595 AGTGTTCACACCCAAAGGACCGTCTAAGTCCA
1 AGTGTTCACACCCAAAGGACCGTCCAAGTCCA
*
38496627 AGTGTTCACACCCAAAAGACCGTCCAAGTCCA
1 AGTGTTCACACCCAAAGGACCGTCCAAGTCCA
38496659 AGTGTTCACA-CCAAAG
1 AGTGTTCACACCCAAAG
38496675 ACTCTTCAAA
Statistics
Matches: 45, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
31 5 0.11
32 40 0.89
ACGTcount: A:0.34, C:0.31, G:0.17, T:0.17
Consensus pattern (32 bp):
AGTGTTCACACCCAAAGGACCGTCCAAGTCCA
Found at i:38503960 original size:21 final size:21
Alignment explanation
Indices: 38503930--38503969 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
38503920 GTTAGTTTCT
38503930 TTCTTCGAGTTGG-TCTAATCA
1 TTCTTCGAG-TGGCTCTAATCA
*
38503951 TTCTTGGAGTGGCTCTAAT
1 TTCTTCGAGTGGCTCTAAT
38503970 TGTTGTTGTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 3 0.18
21 14 0.82
ACGTcount: A:0.17, C:0.17, G:0.23, T:0.42
Consensus pattern (21 bp):
TTCTTCGAGTGGCTCTAATCA
Found at i:38507589 original size:39 final size:38
Alignment explanation
Indices: 38507521--38507658 Score: 120
Period size: 39 Copynumber: 3.6 Consensus size: 38
38507511 TGGTCTAAAC
* *
38507521 TAAAGACATGTATTAAAGATGTCTAAACTAAGACATATT
1 TAAA-ACATATATTAAAGATGTCTAAACTAAGACATAAT
* *
38507560 TAAAACATATATTTAAGATGTCCTAAACTATGACATAAT
1 TAAAACATATATTAAAGATGT-CTAAACTAAGACATAAT
* * * *
38507599 TAAAA-ATCCTTATTAAAGATGT-TCAGATTATGACATAAT
1 TAAAACAT--ATATTAAAGATGTCT-AAACTAAGACATAAT
*
38507638 TAAAAC-TCATATTAATGATGT
1 TAAAACAT-ATATTAAAGATGT
38507659 TCAAATTATG
Statistics
Matches: 84, Mismatches: 10, Indels: 11
0.80 0.10 0.10
Matches are distributed among these distances:
38 30 0.36
39 43 0.51
40 11 0.13
ACGTcount: A:0.45, C:0.11, G:0.10, T:0.34
Consensus pattern (38 bp):
TAAAACATATATTAAAGATGTCTAAACTAAGACATAAT
Found at i:38507618 original size:78 final size:77
Alignment explanation
Indices: 38507531--38507679 Score: 178
Period size: 78 Copynumber: 1.9 Consensus size: 77
38507521 TAAAGACATG
*
38507531 TATTAAAGATG-TCTAAACTAAGACATATTTAAAACAT-ATATTTAA-GATGTCCTAAACTATGA
1 TATTAAAGATGTTC-AAACTAAGACATAATTAAAAC-TCATA-TTAATGATGTCC-AAACTATGA
*
38507593 CATAATTAAAAATCCT
62 CATAAGTAAAAATCCT
* * * * *
38507609 TATTAAAGATGTTCAGATTATGACATAATTAAAACTCATATTAATGATGTTCAAATTATGACATA
1 TATTAAAGATGTTCAAACTAAGACATAATTAAAACTCATATTAATGATGTCCAAACTATGACATA
38507674 AGTAAA
66 AGTAAA
38507680 GACTTAAACT
Statistics
Matches: 61, Mismatches: 7, Indels: 7
0.81 0.09 0.09
Matches are distributed among these distances:
77 22 0.36
78 37 0.61
79 2 0.03
ACGTcount: A:0.46, C:0.11, G:0.09, T:0.34
Consensus pattern (77 bp):
TATTAAAGATGTTCAAACTAAGACATAATTAAAACTCATATTAATGATGTCCAAACTATGACATA
AGTAAAAATCCT
Found at i:38507660 original size:38 final size:39
Alignment explanation
Indices: 38507531--38507679 Score: 144
Period size: 38 Copynumber: 3.8 Consensus size: 39
38507521 TAAAGACATG
* * *
38507531 TATTAAAGATG-TCTAAACTAAGACATATTTAAAACAT--A
1 TATTAAAGATGTTC-AAATTATGACATAATTAAAA-ATCCA
* * * *
38507569 TATTTAAGATGTCCTAAACTATGACATAATTAAAAATCCT
1 TATTAAAGATGTTC-AAATTATGACATAATTAAAAATCCA
* *
38507609 TATTAAAGATGTTCAGATTATGACATAATTAAAACT-CA
1 TATTAAAGATGTTCAAATTATGACATAATTAAAAATCCA
* *
38507647 TATTAATGATGTTCAAATTATGACATAAGTAAA
1 TATTAAAGATGTTCAAATTATGACATAATTAAA
38507680 GACTTAAACT
Statistics
Matches: 94, Mismatches: 14, Indels: 6
0.82 0.12 0.05
Matches are distributed among these distances:
38 43 0.46
39 39 0.41
40 12 0.13
ACGTcount: A:0.46, C:0.11, G:0.09, T:0.34
Consensus pattern (39 bp):
TATTAAAGATGTTCAAATTATGACATAATTAAAAATCCA
Found at i:38527114 original size:38 final size:38
Alignment explanation
Indices: 38527014--38527121 Score: 105
Period size: 38 Copynumber: 2.9 Consensus size: 38
38527004 TTGAGTAAAA
** * **
38527014 AAATTTGGTATTTTGTTAAATATTTT-GTTATACATTAG
1 AAATTTGGTATCAT-TTACATATTTTGGTTATTTATTAG
* *
38527052 AGATTTGGTATCATTTACAGATTTTGGTTATTTATTAG
1 AAATTTGGTATCATTTACATATTTTGGTTATTTATTAG
*
38527090 AAATTTTGGTATCATTT-GATATTTTGG-TATTT
1 AAA-TTTGGTATCATTTACATATTTTGGTTATTT
38527122 GGTATTTGGT
Statistics
Matches: 58, Mismatches: 10, Indels: 5
0.79 0.14 0.07
Matches are distributed among these distances:
37 14 0.24
38 31 0.53
39 13 0.22
ACGTcount: A:0.28, C:0.04, G:0.16, T:0.53
Consensus pattern (38 bp):
AAATTTGGTATCATTTACATATTTTGGTTATTTATTAG
Found at i:38527115 original size:18 final size:18
Alignment explanation
Indices: 38527035--38527119 Score: 73
Period size: 18 Copynumber: 4.6 Consensus size: 18
38527025 TTTGTTAAAT
*
38527035 ATTTTGTTATACATTAGAG
1 ATTTTGGTAT-CATTAGAG
*
38527054 A-TTTGGTATCATTTACAG
1 ATTTTGGTATCA-TTAGAG
* *
38527072 ATTTTGGTTATTTATTAGAA
1 ATTTTGG-TA-TCATTAGAG
* *
38527092 ATTTTGGTATCATTTGAT
1 ATTTTGGTATCATTAGAG
38527110 ATTTTGGTAT
1 ATTTTGGTAT
38527120 TTGGTATTTG
Statistics
Matches: 54, Mismatches: 8, Indels: 9
0.76 0.11 0.13
Matches are distributed among these distances:
17 2 0.04
18 29 0.54
19 8 0.15
20 13 0.24
21 2 0.04
ACGTcount: A:0.27, C:0.05, G:0.16, T:0.52
Consensus pattern (18 bp):
ATTTTGGTATCATTAGAG
Found at i:38530012 original size:25 final size:24
Alignment explanation
Indices: 38529983--38530041 Score: 75
Period size: 24 Copynumber: 2.4 Consensus size: 24
38529973 TCAATTAGAA
*
38529983 TAAAATATTAATAATTCAAT-AAAT
1 TAAAAT-TTAATAATTAAATAAAAT
*
38530007 TGAAAATTAAATAATTAAATAAAAT
1 T-AAAATTTAATAATTAAATAAAAT
38530032 TAAAATTTAA
1 TAAAATTTAA
38530042 GAGGAAAATT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
24 20 0.67
25 10 0.33
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.36
Consensus pattern (24 bp):
TAAAATTTAATAATTAAATAAAAT
Found at i:38538039 original size:27 final size:27
Alignment explanation
Indices: 38538001--38538057 Score: 96
Period size: 27 Copynumber: 2.1 Consensus size: 27
38537991 AAGTATGTTA
38538001 TAATTAGGACAGCATCAATGCAGGTTT
1 TAATTAGGACAGCATCAATGCAGGTTT
* *
38538028 TAATTCGGACAGCATCAATGCATGTTT
1 TAATTAGGACAGCATCAATGCAGGTTT
38538055 TAA
1 TAA
38538058 GTCAGACCTA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.33, C:0.16, G:0.19, T:0.32
Consensus pattern (27 bp):
TAATTAGGACAGCATCAATGCAGGTTT
Found at i:38540844 original size:20 final size:20
Alignment explanation
Indices: 38540821--38541014 Score: 106
Period size: 20 Copynumber: 9.7 Consensus size: 20
38540811 GTAAATTATA
* *
38540821 CCCTGTTTGTACTTCGGTAC
1 CCCTGATTGCACTTCGGTAC
* * *
38540841 CCCTAATTACACTTAC-GTGC
1 CCCTGATTGCACTT-CGGTAC
* * * **
38540861 CCTTGTTTGTACTTCGCAAC
1 CCCTGATTGCACTTCGGTAC
* *
38540881 CCCTGATTACACTTAC-GTGC
1 CCCTGATTGCACTT-CGGTAC
* *
38540901 CCCTGTTTGTACTTCGGTAC
1 CCCTGATTGCACTTCGGTAC
* * *
38540921 CCCTAATTACACTTAC-GTGC
1 CCCTGATTGCACTT-CGGTAC
* *
38540941 CCCTGTTTGTACTTCGGTAC
1 CCCTGATTGCACTTCGGTAC
** *
38540961 CCCTGATTGCACTTAAGTGC
1 CCCTGATTGCACTTCGGTAC
* * **
38540981 CCTTGCTTGTTCTTCGGTAC
1 CCCTGATTGCACTTCGGTAC
38541001 CCCTGATTGCACTT
1 CCCTGATTGCACTT
38541015 GCGTGCCCCT
Statistics
Matches: 118, Mismatches: 50, Indels: 12
0.66 0.28 0.07
Matches are distributed among these distances:
19 3 0.03
20 112 0.95
21 3 0.03
ACGTcount: A:0.15, C:0.32, G:0.16, T:0.36
Consensus pattern (20 bp):
CCCTGATTGCACTTCGGTAC
Found at i:38541039 original size:40 final size:40
Alignment explanation
Indices: 38540821--38541028 Score: 308
Period size: 40 Copynumber: 5.2 Consensus size: 40
38540811 GTAAATTATA
*
38540821 CCCTGTTTGTACTTCGGTACCCCTAATTACACTTACGTGC
1 CCCTGTTTGTACTTCGGTACCCCTGATTACACTTACGTGC
* **
38540861 CCTTGTTTGTACTTCGCAACCCCTGATTACACTTACGTGC
1 CCCTGTTTGTACTTCGGTACCCCTGATTACACTTACGTGC
*
38540901 CCCTGTTTGTACTTCGGTACCCCTAATTACACTTACGTGC
1 CCCTGTTTGTACTTCGGTACCCCTGATTACACTTACGTGC
* *
38540941 CCCTGTTTGTACTTCGGTACCCCTGATTGCACTTAAGTGC
1 CCCTGTTTGTACTTCGGTACCCCTGATTACACTTACGTGC
* * * * *
38540981 CCTTGCTTGTTCTTCGGTACCCCTGATTGCACTTGCGTGC
1 CCCTGTTTGTACTTCGGTACCCCTGATTACACTTACGTGC
38541021 CCCTGTTT
1 CCCTGTTT
38541029 ACATTTCGGT
Statistics
Matches: 150, Mismatches: 18, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
40 150 1.00
ACGTcount: A:0.14, C:0.32, G:0.17, T:0.36
Consensus pattern (40 bp):
CCCTGTTTGTACTTCGGTACCCCTGATTACACTTACGTGC
Found at i:38542726 original size:55 final size:54
Alignment explanation
Indices: 38542557--38542731 Score: 133
Period size: 55 Copynumber: 3.2 Consensus size: 54
38542547 AGCCAAGCCA
*
38542557 CAAGCCCGTGTGCCAAGTCGTGTAACACTCGAAATGGCCTTACACACCTGTGTGC
1 CAAG-CCGTGTGCCAAGCCGTGTAACACTCGAAATGGCCTTACACACCTGTGTGC
* * * * * * ** * * ** *
38542612 CAAGCCGTG-ACTCATGCTTGTGTTACTCTTTGAGTTGG-GTCACACAGCC-AAG-CC
1 CAAGCCGTGTGC-CAAGC-CGTGTAACAC-TCGAAATGGCCTTACACA-CCTGTGTGC
38542666 ACAAGCCCGTGTGCCAAGCCGTGTAACACTCGAAATGGCCTTACACACCTGTGTGC
1 -CAAG-CCGTGTGCCAAGCCGTGTAACACTCGAAATGGCCTTACACACCTGTGTGC
38542722 CAAGCCGTGT
1 CAAGCCGTGT
38542732 CTAGACCATG
Statistics
Matches: 83, Mismatches: 27, Indels: 21
0.63 0.21 0.16
Matches are distributed among these distances:
53 1 0.01
54 23 0.28
55 40 0.48
56 18 0.22
57 1 0.01
ACGTcount: A:0.23, C:0.30, G:0.24, T:0.23
Consensus pattern (54 bp):
CAAGCCGTGTGCCAAGCCGTGTAACACTCGAAATGGCCTTACACACCTGTGTGC
Found at i:38546210 original size:127 final size:127
Alignment explanation
Indices: 38545991--38546233 Score: 450
Period size: 127 Copynumber: 1.9 Consensus size: 127
38545981 AAAAAACACA
* *
38545991 GAAAAATTAGCTAAGTTAAAATTGAACAGAAAAAATTTAACCAAAATGCAAAATTAACAAATTCA
1 GAAAAATTAGCTAAGTGAAAATTGAACAGAAAAAATTTAACCAAAATGAAAAATTAACAAATTCA
38546056 CAAATAATGACTTTTAAAACAGTCCCCGACAACGGCACCAAAAACTTGGAACAACAAACATT
66 CAAATAATGACTTTTAAAACAGTCCCCGACAACGGCACCAAAAACTTGGAACAACAAACATT
*
38546118 GAAAAATTAGCTAAGTGAAAATTGAACAGAAAAAATTTAAGCAAAATGAAAAATTAACAAATTCA
1 GAAAAATTAGCTAAGTGAAAATTGAACAGAAAAAATTTAACCAAAATGAAAAATTAACAAATTCA
*
38546183 CAAATAATGACTTTTAAAACAGTCCCCGACAACGGCGCCAAAAACTTGGAA
66 CAAATAATGACTTTTAAAACAGTCCCCGACAACGGCACCAAAAACTTGGAA
38546234 TGACAGAAAT
Statistics
Matches: 112, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
127 112 1.00
ACGTcount: A:0.51, C:0.17, G:0.12, T:0.20
Consensus pattern (127 bp):
GAAAAATTAGCTAAGTGAAAATTGAACAGAAAAAATTTAACCAAAATGAAAAATTAACAAATTCA
CAAATAATGACTTTTAAAACAGTCCCCGACAACGGCACCAAAAACTTGGAACAACAAACATT
Found at i:38548770 original size:23 final size:22
Alignment explanation
Indices: 38548727--38548770 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 22
38548717 TTCTAAGTCG
38548727 ATATTCAATTCAATTCCACACCT
1 ATATTCAATTCAATT-CACACCT
38548750 ATATTCATTATTCAATT-ACAC
1 ATATTCA--ATTCAATTCACAC
38548771 TTAGTCAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
23 11 0.58
25 8 0.42
ACGTcount: A:0.36, C:0.25, G:0.00, T:0.39
Consensus pattern (22 bp):
ATATTCAATTCAATTCACACCT
Found at i:38548866 original size:45 final size:45
Alignment explanation
Indices: 38548815--38548908 Score: 143
Period size: 45 Copynumber: 2.1 Consensus size: 45
38548805 AACAGATACT
* * * *
38548815 CGGTGGATTCAGCACATAGCAACCACTTTATTAATTAATGATGTC
1 CGGTGGAATCAGCACATAGCAACCACCTTACTAATCAATGATGTC
*
38548860 CGGTGGAATCAGCACATAGTAACCACCTTACTAATCAATGATGTC
1 CGGTGGAATCAGCACATAGCAACCACCTTACTAATCAATGATGTC
38548905 CGGT
1 CGGT
38548909 TCACATAGTA
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
45 44 1.00
ACGTcount: A:0.31, C:0.22, G:0.19, T:0.28
Consensus pattern (45 bp):
CGGTGGAATCAGCACATAGCAACCACCTTACTAATCAATGATGTC
Found at i:38548977 original size:51 final size:50
Alignment explanation
Indices: 38548903--38549096 Score: 237
Period size: 51 Copynumber: 3.8 Consensus size: 50
38548893 ATCAATGATG
* *
38548903 TCCGGTTCACATAGTAGCCTGCACATAGTACTACACATGTGACCATTACCA
1 TCCGGTACACGTAGTAGCCTGCACATAGTACTACACATGTGACCA-TACCA
* * * * *
38548954 TCCGATACACGTACTAGCCTGCACATAGTACTACACATGTGATCGAAACTA
1 TCCGGTACACGTAGTAGCCTGCACATAGTACTACACATGTGA-CCATACCA
* * * *
38549005 TCCGGTACGCATAGTAGCCTGCACATAGTACTACACATGCGACC-TATCA
1 TCCGGTACACGTAGTAGCCTGCACATAGTACTACACATGTGACCATACCA
* *
38549054 TTCTGGTACACGTAGTAGCCTGCACATAGTACTACACACGTGA
1 -TCCGGTACACGTAGTAGCCTGCACATAGTACTACACATGTGA
38549097 TCATCACTTT
Statistics
Matches: 120, Mismatches: 21, Indels: 5
0.82 0.14 0.03
Matches are distributed among these distances:
49 2 0.02
50 38 0.32
51 78 0.65
52 2 0.02
ACGTcount: A:0.30, C:0.28, G:0.18, T:0.24
Consensus pattern (50 bp):
TCCGGTACACGTAGTAGCCTGCACATAGTACTACACATGTGACCATACCA
Found at i:38549120 original size:101 final size:99
Alignment explanation
Indices: 38548911--38549098 Score: 270
Period size: 101 Copynumber: 1.9 Consensus size: 99
38548901 TGTCCGGTTC
*
38548911 ACATAGTAGCCTGCACATAGTACTACACATGTGACCATTACCATCCGATACACGTACTAGCCTGC
1 ACATAGTAGCCTGCACATAGTACTACACATGCGACCA-TACCATCCGATACACGTACTAGCCTGC
* *
38548976 ACATAGTACTACACATGTGATCGAAACTATCCGGT
65 ACATAGTACTACACACGTGATCGAAACTAACCGGT
* * * *
38549011 ACGCATAGTAGCCTGCACATAGTACTACACATGCGACC-TATCATTCTGGTACACGTAGTAGCCT
1 A--CATAGTAGCCTGCACATAGTACTACACATGCGACCATACCA-TCCGATACACGTACTAGCCT
38549075 GCACATAGTACTACACACGTGATC
63 GCACATAGTACTACACACGTGATC
38549099 ATCACTTTAA
Statistics
Matches: 79, Mismatches: 6, Indels: 5
0.88 0.07 0.06
Matches are distributed among these distances:
100 5 0.06
101 40 0.51
102 34 0.43
ACGTcount: A:0.31, C:0.28, G:0.17, T:0.24
Consensus pattern (99 bp):
ACATAGTAGCCTGCACATAGTACTACACATGCGACCATACCATCCGATACACGTACTAGCCTGCA
CATAGTACTACACACGTGATCGAAACTAACCGGT
Found at i:38549361 original size:30 final size:30
Alignment explanation
Indices: 38549327--38549385 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 30
38549317 CAAAAATCAC
* *
38549327 ACTTTGGCAAAATTACCTTTTTGCCCCTAA
1 ACTTTGACAAAATTACCATTTTGCCCCTAA
* *
38549357 ACTTTTACAAAATTACGATTTTGCCCCTA
1 ACTTTGACAAAATTACCATTTTGCCCCTA
38549386 GGCTCGTAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.29, C:0.25, G:0.08, T:0.37
Consensus pattern (30 bp):
ACTTTGACAAAATTACCATTTTGCCCCTAA
Found at i:38557220 original size:11 final size:11
Alignment explanation
Indices: 38557204--38557228 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
38557194 ATTAACCTTT
38557204 AAAATTCATTA
1 AAAATTCATTA
38557215 AAAATTCATTA
1 AAAATTCATTA
38557226 AAA
1 AAA
38557229 CCTATCTATG
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:0.60, C:0.08, G:0.00, T:0.32
Consensus pattern (11 bp):
AAAATTCATTA
Found at i:38559605 original size:42 final size:41
Alignment explanation
Indices: 38559474--38559744 Score: 242
Period size: 41 Copynumber: 6.5 Consensus size: 41
38559464 TACTCGGTGA
* * *
38559474 AATCAGCACTTAGCAACCACCTTAT--ATTCAGTGATACGGGG
1 AATCAGCACTTAGCAACC-CCTTTTCGA-TAAGTGATTCGGGG
* * * * * *
38559515 ATTCAACACATAGCAACCCCTTTCACAATCAAG-GATACGGTGG
1 AATCAGCACTTAGCAACCCCTTT-TCGAT-AAGTGATTCGG-GG
* * * * *
38559558 AATCAGCACTTAGCAACCACTTTTAGAATAAATAATTCAGGG
1 AATCAGCACTTAGCAACCCCTTTTCG-ATAAGTGATTCGGGG
*
38559600 AATCAGCACTTAGCAACCCCTTTTCGATCAGTGATTCGGGG
1 AATCAGCACTTAGCAACCCCTTTTCGATAAGTGATTCGGGG
**
38559641 AATTTGCACTTAGCAACCCCTTTTCGATAAGTGATTCGGGG
1 AATCAGCACTTAGCAACCCCTTTTCGATAAGTGATTCGGGG
* * * * *
38559682 AATCTGCAATTAGCAACCCCTTTTTGATCAGTGATTCGGAG
1 AATCAGCACTTAGCAACCCCTTTTCGATAAGTGATTCGGGG
** *
38559723 AATTTGCACTTAACAACCCCTT
1 AATCAGCACTTAGCAACCCCTT
38559745 ACATTCAATG
Statistics
Matches: 189, Mismatches: 34, Indels: 14
0.80 0.14 0.06
Matches are distributed among these distances:
40 4 0.02
41 119 0.63
42 36 0.19
43 30 0.16
ACGTcount: A:0.31, C:0.24, G:0.18, T:0.27
Consensus pattern (41 bp):
AATCAGCACTTAGCAACCCCTTTTCGATAAGTGATTCGGGG
Found at i:38559640 original size:126 final size:124
Alignment explanation
Indices: 38559474--38559705 Score: 283
Period size: 126 Copynumber: 1.9 Consensus size: 124
38559464 TACTCGGTGA
38559474 AATCAGCACTTAGCAACCACCTTATATTCAGTGATACGGGG-ATTCAACACATAGCAACCCCTTT
1 AATCAGCACTTAGCAACCACCTTATATTCAGTGATACGGGGAATT-AACACATAGCAACCCCTTT
*
38559538 CACAATCAAG-GATACGGTGGAATCAGCACTTAGCAACCACTTTTAGAATAAATAATTCAGGG
65 -ACAAT-AAGTGATACGG-GGAATCAGCAATTAGCAACCACTTTTAGAATAAATAATTCAGGG
* * ** *
38559600 AATCAGCACTTAGCAACC-CCTTTTCGA-TCAGTGATTCGGGGAATTTGCACTTAGCAACCCCTT
1 AATCAGCACTTAGCAACCACCTTAT--ATTCAGTGATACGGGGAATTAACACATAGCAACCCCTT
* * * * *
38559663 TTCGATAAGTGATTCGGGGAATCTGCAATTAGCAACCCCTTTT
64 TACAATAAGTGATACGGGGAATCAGCAATTAGCAACCACTTTT
38559706 TGATCAGTGA
Statistics
Matches: 91, Mismatches: 11, Indels: 10
0.81 0.10 0.09
Matches are distributed among these distances:
124 26 0.29
125 14 0.15
126 47 0.52
127 4 0.04
ACGTcount: A:0.31, C:0.25, G:0.18, T:0.27
Consensus pattern (124 bp):
AATCAGCACTTAGCAACCACCTTATATTCAGTGATACGGGGAATTAACACATAGCAACCCCTTTA
CAATAAGTGATACGGGGAATCAGCAATTAGCAACCACTTTTAGAATAAATAATTCAGGG
Found at i:38559711 original size:82 final size:83
Alignment explanation
Indices: 38559563--38559744 Score: 267
Period size: 82 Copynumber: 2.2 Consensus size: 83
38559553 GGTGGAATCA
* *
38559563 GCACTTAGCAACCACTTTTAGAATAAATAATTCAGGGAATCAGCACTTAGCAACCCCTTTTCGAT
1 GCACTTAGCAACCCCTTTTAGAATAAATAATTCAGGGAATCAGCAATTAGCAACCCCTTTTCGAT
*
38559628 CAGTGATTCGGGGAATTT
66 CAGTGATTCGGAGAATTT
* * * * * *
38559646 GCACTTAGCAACCCCTTTTCG-ATAAGTGATTCGGGGAATCTGCAATTAGCAACCCCTTTTTGAT
1 GCACTTAGCAACCCCTTTTAGAATAAATAATTCAGGGAATCAGCAATTAGCAACCCCTTTTCGAT
38559710 CAGTGATTCGGAGAATTT
66 CAGTGATTCGGAGAATTT
*
38559728 GCACTTAACAACCCCTT
1 GCACTTAGCAACCCCTT
38559745 ACATTCAATG
Statistics
Matches: 89, Mismatches: 10, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
82 70 0.79
83 19 0.21
ACGTcount: A:0.29, C:0.24, G:0.18, T:0.30
Consensus pattern (83 bp):
GCACTTAGCAACCCCTTTTAGAATAAATAATTCAGGGAATCAGCAATTAGCAACCCCTTTTCGAT
CAGTGATTCGGAGAATTT
Found at i:38562636 original size:4 final size:4
Alignment explanation
Indices: 38562624--38562658 Score: 63
Period size: 4 Copynumber: 9.0 Consensus size: 4
38562614 TAAAATTAGT
38562624 TAAA T-AA TAAA TAAA TAAA TAAA TAAA TAAA TAAA
1 TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA
38562659 AAGGATAGAT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 3 0.10
4 27 0.90
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (4 bp):
TAAA
Found at i:38563056 original size:31 final size:31
Alignment explanation
Indices: 38562963--38563058 Score: 174
Period size: 31 Copynumber: 3.1 Consensus size: 31
38562953 GGCAAATTAC
*
38562963 AAGAGTAATTGAATCCTAATAAAACTCTTTC
1 AAGAGTAATTGAATCCTAATAAAACTCTTTA
38562994 AAGAGTAATTGAATCCTAATAAAAACTCTTTA
1 AAGAGTAATTGAATCCTAAT-AAAACTCTTTA
38563026 AAGAGTAATTGAATCCTAATAAAACTCTTTA
1 AAGAGTAATTGAATCCTAATAAAACTCTTTA
38563057 AA
1 AA
38563059 ATTATCTAAG
Statistics
Matches: 63, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
31 33 0.52
32 30 0.48
ACGTcount: A:0.46, C:0.14, G:0.09, T:0.31
Consensus pattern (31 bp):
AAGAGTAATTGAATCCTAATAAAACTCTTTA
Found at i:38568614 original size:30 final size:29
Alignment explanation
Indices: 38568600--38568675 Score: 84
Period size: 28 Copynumber: 2.6 Consensus size: 29
38568590 CTTTTTTGCT
* *
38568600 TTTTGCTTTTTTTTTTTGCGC-TTTTTAC
1 TTTTTCTTTTTTTTTTTGCGCTTTTTTGC
*
38568628 TCTTTCTTTTTTTTTTTGCGCTTTTTTTTGC
1 TTTTTCTTTTTTTTTTTGCGC--TTTTTTGC
38568659 TTTTT-TTTTGTTTTTTT
1 TTTTTCTTTT-TTTTTTT
38568676 AAAGAATAAG
Statistics
Matches: 40, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
28 19 0.47
30 4 0.10
31 17 0.43
ACGTcount: A:0.01, C:0.12, G:0.09, T:0.78
Consensus pattern (29 bp):
TTTTTCTTTTTTTTTTTGCGCTTTTTTGC
Found at i:38568624 original size:28 final size:28
Alignment explanation
Indices: 38568578--38568667 Score: 116
Period size: 28 Copynumber: 3.2 Consensus size: 28
38568568 GGTAGGCAAC
38568578 TTTTTTTTTGCGCTTTTTTGCTTTTTGCTT
1 TTTTTTTTTGCGC-TTTTT-CTTTTTGCTT
*
38568608 TTTTTTTTTGCGCTTTTTACTCTTT-CTT
1 TTTTTTTTTGCGCTTTTT-CTTTTTGCTT
38568636 TTTTTTTTTGCGC--TTT-TTTTTGCTT
1 TTTTTTTTTGCGCTTTTTCTTTTTGCTT
38568661 TTTTTTT
1 TTTTTTT
38568668 GTTTTTTTAA
Statistics
Matches: 56, Mismatches: 3, Indels: 7
0.85 0.05 0.11
Matches are distributed among these distances:
24 4 0.07
25 10 0.18
26 3 0.05
28 16 0.29
29 10 0.18
30 13 0.23
ACGTcount: A:0.01, C:0.13, G:0.10, T:0.76
Consensus pattern (28 bp):
TTTTTTTTTGCGCTTTTTCTTTTTGCTT
Found at i:38568903 original size:4 final size:4
Alignment explanation
Indices: 38568891--38568921 Score: 55
Period size: 4 Copynumber: 8.0 Consensus size: 4
38568881 TAAAATTAGT
38568891 TAAA T-AA TAAA TAAA TAAA TAAA TAAA TAAA
1 TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA
38568922 AAGGATAGAT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 3 0.12
4 23 0.88
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (4 bp):
TAAA
Found at i:38569319 original size:31 final size:31
Alignment explanation
Indices: 38569226--38569321 Score: 165
Period size: 31 Copynumber: 3.1 Consensus size: 31
38569216 GGCAAATTAC
*
38569226 AAGAGTAATTGAATCCTAATAAAACTCTTTC
1 AAGAGTAATTGAATCCTAATAAAACTCTTTA
38569257 AAGAGTAATTGAATCCTAATAAAAACTCTTTA
1 AAGAGTAATTGAATCCTAAT-AAAACTCTTTA
*
38569289 AAGAGTAATTAAATCCTAATAAAACTCTTTA
1 AAGAGTAATTGAATCCTAATAAAACTCTTTA
38569320 AA
1 AA
38569322 ATTATCTAAG
Statistics
Matches: 62, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
31 33 0.53
32 29 0.47
ACGTcount: A:0.47, C:0.14, G:0.08, T:0.31
Consensus pattern (31 bp):
AAGAGTAATTGAATCCTAATAAAACTCTTTA
Found at i:38570053 original size:20 final size:19
Alignment explanation
Indices: 38570014--38570054 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
38570004 CACTATACCC
*
38570014 TTTTTTTACTAGACTCTTT
1 TTTTTTTACTAGAATCTTT
*
38570033 TTTTCTTTACTAGAATGTTT
1 TTTT-TTTACTAGAATCTTT
38570053 TT
1 TT
38570055 CCCACAGGGT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 4 0.21
20 15 0.79
ACGTcount: A:0.17, C:0.12, G:0.07, T:0.63
Consensus pattern (19 bp):
TTTTTTTACTAGAATCTTT
Found at i:38588809 original size:1 final size:1
Alignment explanation
Indices: 38588803--38588828 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
38588793 TTCTAGCTTC
38588803 TTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTT
38588829 GCTCCCAATC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:38591306 original size:13 final size:13
Alignment explanation
Indices: 38591288--38591316 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
38591278 TGTCAACTTA
38591288 GAATACTAATTAT
1 GAATACTAATTAT
38591301 GAATACTAATTAT
1 GAATACTAATTAT
38591314 GAA
1 GAA
38591317 CTTCATTTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.48, C:0.07, G:0.10, T:0.34
Consensus pattern (13 bp):
GAATACTAATTAT
Found at i:38594020 original size:10 final size:10
Alignment explanation
Indices: 38594001--38594083 Score: 51
Period size: 10 Copynumber: 9.1 Consensus size: 10
38593991 GGTTTAGAAT
38594001 ATTA-TAAAA
1 ATTATTAAAA
38594010 ATTATTAAAA
1 ATTATTAAAA
*
38594020 ATT-GTAAATA
1 ATTATTAAA-A
38594030 ATTA-T-AAA
1 ATTATTAAAA
38594038 ATTATTTAAAA
1 ATTA-TTAAAA
**
38594049 A--GGTAAAA
1 ATTATTAAAA
38594057 A-TATT-AAA
1 ATTATTAAAA
38594065 A--ATTAAAA
1 ATTATTAAAA
38594073 ATTATTAAAA
1 ATTATTAAAA
38594083 A
1 A
38594084 ATTGTCAAAA
Statistics
Matches: 59, Mismatches: 5, Indels: 19
0.71 0.06 0.23
Matches are distributed among these distances:
7 3 0.05
8 19 0.32
9 11 0.19
10 22 0.37
11 4 0.07
ACGTcount: A:0.61, C:0.00, G:0.04, T:0.35
Consensus pattern (10 bp):
ATTATTAAAA
Found at i:38594062 original size:29 final size:29
Alignment explanation
Indices: 38593998--38594069 Score: 87
Period size: 28 Copynumber: 2.5 Consensus size: 29
38593988 GATGGTTTAG
*
38593998 AATATTATAAAAATTATTAAAAATTGTAAA
1 AATATTAT-AAAATTATTAAAAATGGTAAA
*
38594028 TA-ATTATAAAATTATTTAAAAA-GGTAAA
1 AATATTATAAAATTA-TTAAAAATGGTAAA
38594056 AATATTA-AAAATTA
1 AATATTATAAAATTA
38594070 AAAATTATTA
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
28 20 0.54
29 16 0.43
30 1 0.03
ACGTcount: A:0.60, C:0.00, G:0.04, T:0.36
Consensus pattern (29 bp):
AATATTATAAAATTATTAAAAATGGTAAA
Found at i:38594065 original size:17 final size:17
Alignment explanation
Indices: 38594035--38594083 Score: 64
Period size: 17 Copynumber: 2.8 Consensus size: 17
38594025 AAATAATTAT
38594035 AAAATTATTTAAAAAGGTA
1 AAAATTA-TTAAAAA-GTA
*
38594054 AAAA-TATTAAAAATTA
1 AAAATTATTAAAAAGTA
38594070 AAAATTATTAAAAA
1 AAAATTATTAAAAA
38594084 ATTGTCAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
16 6 0.21
17 16 0.57
18 2 0.07
19 4 0.14
ACGTcount: A:0.65, C:0.00, G:0.04, T:0.31
Consensus pattern (17 bp):
AAAATTATTAAAAAGTA
Found at i:38594084 original size:18 final size:18
Alignment explanation
Indices: 38594013--38594086 Score: 73
Period size: 18 Copynumber: 4.2 Consensus size: 18
38594003 TATAAAAATT
* *
38594013 ATTAAAAATT-GTAAATA
1 ATTAAAAATTATTAAAAA
38594030 ATTATAAAATTATTTAAAAA
1 ATTA-AAAATTA-TTAAAAA
**
38594050 GGTAAAAA-TATT-AAAA
1 ATTAAAAATTATTAAAAA
38594066 ATTAAAAATTATTAAAAA
1 ATTAAAAATTATTAAAAA
38594084 ATT
1 ATT
38594087 GTCAAAATAG
Statistics
Matches: 46, Mismatches: 6, Indels: 9
0.75 0.10 0.15
Matches are distributed among these distances:
16 10 0.22
17 10 0.22
18 15 0.33
19 4 0.09
20 7 0.15
ACGTcount: A:0.61, C:0.00, G:0.04, T:0.35
Consensus pattern (18 bp):
ATTAAAAATTATTAAAAA
Found at i:38594459 original size:19 final size:19
Alignment explanation
Indices: 38594437--38594479 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 19
38594427 ATTTTCATCT
*
38594437 TTTTACAATTTTTTAATAA
1 TTTTACAATTTTTAAATAA
* *
38594456 TTTTATAATTTTTAAATAT
1 TTTTACAATTTTTAAATAA
38594475 TTTTA
1 TTTTA
38594480 GAACTCTTAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (19 bp):
TTTTACAATTTTTAAATAA
Found at i:38594468 original size:9 final size:9
Alignment explanation
Indices: 38594436--38594540 Score: 54
Period size: 9 Copynumber: 11.6 Consensus size: 9
38594426 TATTTTCATC
*
38594436 TTTTTACAA
1 TTTTTATAA
38594445 TTTTT-TAA
1 TTTTTATAA
38594453 TAATTTTATAA
1 T--TTTTATAA
*
38594464 TTTTTAAATA
1 TTTTTATA-A
*
38594474 TTTTTAGAA
1 TTTTTATAA
* * *
38594483 CTCTTAT-T
1 TTTTTATAA
*
38594491 TTTTTATGA
1 TTTTTATAA
38594500 TTTTTATAA
1 TTTTTATAA
* *
38594509 ATTTTA-ATT
1 TTTTTATA-A
*
38594518 TTTTTAGAA
1 TTTTTATAA
*
38594527 TTATTATAA
1 TTTTTATAA
38594536 TTTTT
1 TTTTT
38594541 TACCATTTTT
Statistics
Matches: 71, Mismatches: 18, Indels: 14
0.69 0.17 0.14
Matches are distributed among these distances:
8 9 0.13
9 45 0.63
10 13 0.18
11 4 0.06
ACGTcount: A:0.31, C:0.03, G:0.03, T:0.63
Consensus pattern (9 bp):
TTTTTATAA
Found at i:38594502 original size:26 final size:27
Alignment explanation
Indices: 38594473--38594523 Score: 68
Period size: 26 Copynumber: 1.9 Consensus size: 27
38594463 ATTTTTAAAT
*
38594473 ATTTTTAGAACTCTT-ATTTTTTTATG
1 ATTTTTAGAAATCTTAATTTTTTTATG
* *
38594499 ATTTTTATAAATTTTAATTTTTTTA
1 ATTTTTAGAAATCTTAATTTTTTTA
38594524 GAATTATTAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
26 12 0.57
27 9 0.43
ACGTcount: A:0.27, C:0.04, G:0.04, T:0.65
Consensus pattern (27 bp):
ATTTTTAGAAATCTTAATTTTTTTATG
Found at i:38594518 original size:27 final size:27
Alignment explanation
Indices: 38594488--38594540 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
38594478 TAGAACTCTT
*
38594488 ATTTTTTTATG-ATTTTTATAAATTTTA
1 ATTTTTTTA-GAATTATTATAAATTTTA
*
38594515 ATTTTTTTAGAATTATTATAATTTTT
1 ATTTTTTTAGAATTATTATAAATTTT
38594541 TACCATTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
26 1 0.04
27 22 0.96
ACGTcount: A:0.30, C:0.00, G:0.04, T:0.66
Consensus pattern (27 bp):
ATTTTTTTAGAATTATTATAAATTTTA
Found at i:38594595 original size:34 final size:36
Alignment explanation
Indices: 38594527--38594597 Score: 101
Period size: 35 Copynumber: 2.0 Consensus size: 36
38594517 TTTTTTAGAA
* *
38594527 TTATTATAATTTTTTACCATTTTTAATATTTAATGTT
1 TTATTAT-ATTTTTTACCATTTATAATATATAATGTT
38594564 TTATTAT-TTTTTTACCATTTAT-ATATATAATGTT
1 TTATTATATTTTTTACCATTTATAATATATAATGTT
38594598 CTGAACCACA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
34 11 0.34
35 14 0.44
37 7 0.22
ACGTcount: A:0.30, C:0.06, G:0.03, T:0.62
Consensus pattern (36 bp):
TTATTATATTTTTTACCATTTATAATATATAATGTT
Found at i:38596271 original size:21 final size:22
Alignment explanation
Indices: 38596247--38596297 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 22
38596237 TGAACAGTTA
38596247 ATAGAAATGCA-A-ACAACTGCT
1 ATAGAAAT-CATATACAACTGCT
*
38596268 ATAGAAATCATATAGAACTGCT
1 ATAGAAATCATATACAACTGCT
*
38596290 ATGGAAAT
1 ATAGAAAT
38596298 AAGTGATCTG
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
20 2 0.08
21 9 0.35
22 15 0.58
ACGTcount: A:0.47, C:0.14, G:0.16, T:0.24
Consensus pattern (22 bp):
ATAGAAATCATATACAACTGCT
Found at i:38600687 original size:2 final size:2
Alignment explanation
Indices: 38600682--38600714 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
38600672 ATATATATAC
38600682 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
38600715 TGGGTAAAAG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:38610511 original size:24 final size:24
Alignment explanation
Indices: 38610484--38610534 Score: 84
Period size: 24 Copynumber: 2.1 Consensus size: 24
38610474 GGATAAAAGT
38610484 GGATATTGAGAGTATGAGAGGAAG
1 GGATATTGAGAGTATGAGAGGAAG
* *
38610508 GGATTTTGAGAGTATGAGCGGAAG
1 GGATATTGAGAGTATGAGAGGAAG
38610532 GGA
1 GGA
38610535 AGATAGACTG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.33, C:0.02, G:0.43, T:0.22
Consensus pattern (24 bp):
GGATATTGAGAGTATGAGAGGAAG
Found at i:38614483 original size:19 final size:19
Alignment explanation
Indices: 38614459--38614497 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
38614449 GGGTGGGAAT
38614459 TTGGAAGACCAAAATTCTA
1 TTGGAAGACCAAAATTCTA
38614478 TTGGAAGACCAAAATTCTA
1 TTGGAAGACCAAAATTCTA
38614497 T
1 T
38614498 ATTTTCATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.28
Consensus pattern (19 bp):
TTGGAAGACCAAAATTCTA
Found at i:38627515 original size:18 final size:18
Alignment explanation
Indices: 38627492--38627528 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
38627482 TTTAAAAATA
38627492 CAACCTAAAATCATTCCC
1 CAACCTAAAATCATTCCC
38627510 CAACCTAAAATCATTCCC
1 CAACCTAAAATCATTCCC
38627528 C
1 C
38627529 CTTACAGATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.38, C:0.41, G:0.00, T:0.22
Consensus pattern (18 bp):
CAACCTAAAATCATTCCC
Found at i:38628945 original size:13 final size:13
Alignment explanation
Indices: 38628904--38628937 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
38628894 GCAAATTAGA
*
38628904 AAAAGAAAGAAAAA
1 AAAAGAAAG-AAAG
38628918 AAAAGAAAGAAAG
1 AAAAGAAAGAAAG
38628931 AAAAGAA
1 AAAAGAA
38628938 GAAGAGAATG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 10 0.53
14 9 0.47
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (13 bp):
AAAAGAAAGAAAG
Found at i:38630091 original size:42 final size:44
Alignment explanation
Indices: 38630036--38630123 Score: 117
Period size: 42 Copynumber: 2.0 Consensus size: 44
38630026 TATGTGATTG
*
38630036 ATATTGAAATGGCCAAGATGAGAAATG-AATATGAGATGAT-AA
1 ATATTGAAATGGCCAAGATGAGAAATGCAATATGAAATGATGAA
* * * *
38630078 ATATTGAATTGGCCAATATTAGAAATGCGATATGAAATGATGAA
1 ATATTGAAATGGCCAAGATGAGAAATGCAATATGAAATGATGAA
38630122 AT
1 AT
38630124 GAGATGTGAA
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
42 24 0.62
43 11 0.28
44 4 0.10
ACGTcount: A:0.45, C:0.06, G:0.22, T:0.27
Consensus pattern (44 bp):
ATATTGAAATGGCCAAGATGAGAAATGCAATATGAAATGATGAA
Found at i:38634862 original size:22 final size:24
Alignment explanation
Indices: 38634812--38634862 Score: 70
Period size: 25 Copynumber: 2.2 Consensus size: 24
38634802 TGAGAGAAGT
*
38634812 AAAAAAATAATATTTTTAAATAATT
1 AAAAAAATAATATTTTT-AATAATG
38634837 AAAAAAATAATATTTTT-A-AATG
1 AAAAAAATAATATTTTTAATAATG
38634859 AAAA
1 AAAA
38634863 TATTGAAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
22 7 0.28
23 1 0.04
25 17 0.68
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (24 bp):
AAAAAAATAATATTTTTAATAATG
Found at i:38639679 original size:12 final size:12
Alignment explanation
Indices: 38639662--38639693 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
38639652 CTTGTGTTTG
38639662 ATGTTTAGTTGA
1 ATGTTTAGTTGA
38639674 ATGTTTAGTTGA
1 ATGTTTAGTTGA
*
38639686 ATGCTTAG
1 ATGTTTAG
38639694 ATGTTGAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.25, C:0.03, G:0.25, T:0.47
Consensus pattern (12 bp):
ATGTTTAGTTGA
Found at i:38641878 original size:22 final size:24
Alignment explanation
Indices: 38641829--38641879 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 24
38641819 TAAATTGCAA
*
38641829 ACTTTGAATCAACTAGGAAAAAACAC
1 ACTTTCAATCAACTAGG--AAAACAC
38641855 ACTTTCAATCAACTAGGAAAACAC
1 ACTTTCAATCAACTAGGAAAACAC
38641879 A
1 A
38641880 AAACAGGGTC
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
24 8 0.33
26 16 0.67
ACGTcount: A:0.49, C:0.22, G:0.10, T:0.20
Consensus pattern (24 bp):
ACTTTCAATCAACTAGGAAAACAC
Found at i:38644318 original size:50 final size:50
Alignment explanation
Indices: 38644190--38644325 Score: 161
Period size: 49 Copynumber: 2.7 Consensus size: 50
38644180 GGGAATGAGA
* * **
38644190 TCCCATGTAAGACCATGTCTGGGACATGGCATTA-GCACTGAGATGAGAGG
1 TCCCATGTAAGACCATGTCTGGGACATGACA-TAGGCACCGAGATGAGAAC
*
38644240 TCCC-CGTAAGACCATGTCTGGGACATGACATAGGCACCG-GTATGAGAAC
1 TCCCATGTAAGACCATGTCTGGGACATGACATAGGCACCGAG-ATGAGAAC
* * *
38644289 TCCCATGTAAGACCATATCTGGGATATGACATTGGCA
1 TCCCATGTAAGACCATGTCTGGGACATGACATAGGCA
38644326 GTACATAAAA
Statistics
Matches: 74, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
48 3 0.04
49 39 0.53
50 32 0.43
ACGTcount: A:0.29, C:0.23, G:0.26, T:0.22
Consensus pattern (50 bp):
TCCCATGTAAGACCATGTCTGGGACATGACATAGGCACCGAGATGAGAAC
Found at i:38644591 original size:12 final size:12
Alignment explanation
Indices: 38644574--38644612 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
38644564 ATGAGTTATT
38644574 TAAGTAAGCAAG
1 TAAGTAAGCAAG
*
38644586 TAAGTAAACAAG
1 TAAGTAAGCAAG
* *
38644598 TAAGTGAGTAAG
1 TAAGTAAGCAAG
38644610 TAA
1 TAA
38644613 AGAAGCGAGT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.51, C:0.05, G:0.23, T:0.21
Consensus pattern (12 bp):
TAAGTAAGCAAG
Found at i:38651256 original size:50 final size:50
Alignment explanation
Indices: 38651177--38651285 Score: 130
Period size: 50 Copynumber: 2.2 Consensus size: 50
38651167 ACAGATAAAT
* * * * **
38651177 TGCCACTGATAACACTTTGTGCACAAACCACCACTGGTATGTAGGTATAC
1 TGCCACTTATAACACTTTATGCACAAACCACCACTGATATGCAAATATAC
* *
38651227 TGCCACTTATAACACTTTATAG-ACCAACCATCACTGATATGCAAATATAC
1 TGCCACTTATAACACTTTAT-GCACAAACCACCACTGATATGCAAATATAC
38651277 TGCCACTTA
1 TGCCACTTA
38651286 CTTCCACCTT
Statistics
Matches: 50, Mismatches: 8, Indels: 2
0.83 0.13 0.03
Matches are distributed among these distances:
50 49 0.98
51 1 0.02
ACGTcount: A:0.33, C:0.27, G:0.13, T:0.28
Consensus pattern (50 bp):
TGCCACTTATAACACTTTATGCACAAACCACCACTGATATGCAAATATAC
Done.