Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr9
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: 38630433
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 2298367 characters in sequence are not A, C, G, or T
File 54 of 97
Found at i:21690354 original size:26 final size:24
Alignment explanation
Indices: 21690324--21690389 Score: 78
Period size: 26 Copynumber: 2.7 Consensus size: 24
21690314 TTTTTTTTCA
*
21690324 ACATGGTGTGTAACAACTTTTTGT
1 ACATGGCGTGTAACAACTTTTTGT
* **
21690348 AACCATGGCGTGTAATATGTTTTTGT
1 -A-CATGGCGTGTAACAACTTTTTGT
21690374 ACATGGCGTGTAACAA
1 ACATGGCGTGTAACAA
21690390 TAGTATTTTT
Statistics
Matches: 34, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
24 13 0.38
25 2 0.06
26 19 0.56
ACGTcount: A:0.27, C:0.14, G:0.23, T:0.36
Consensus pattern (24 bp):
ACATGGCGTGTAACAACTTTTTGT
Found at i:21690504 original size:45 final size:45
Alignment explanation
Indices: 21690454--21690577 Score: 131
Period size: 45 Copynumber: 2.8 Consensus size: 45
21690444 TATGTACATA
* *
21690454 ACGTGTAACATGTTTCTGTAAATGGCGTGTAATAACCTAACCATG
1 ACGTGTAACATGTTTTTGTAAATGGCGTGTAACAACCTAACCATG
* * * * * * * *
21690499 TCGTGTCACATGTTTTTGCATATGACGTGCAACAACTTAATCATG
1 ACGTGTAACATGTTTTTGTAAATGGCGTGTAACAACCTAACCATG
* * *
21690544 ACGTGTAACATATTTTTGTACATAGCGTGTAACA
1 ACGTGTAACATGTTTTTGTAAATGGCGTGTAACA
21690578 TCATAGCGTG
Statistics
Matches: 61, Mismatches: 18, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
45 61 1.00
ACGTcount: A:0.30, C:0.18, G:0.19, T:0.34
Consensus pattern (45 bp):
ACGTGTAACATGTTTTTGTAAATGGCGTGTAACAACCTAACCATG
Found at i:21690846 original size:22 final size:21
Alignment explanation
Indices: 21690815--21690890 Score: 62
Period size: 22 Copynumber: 3.3 Consensus size: 21
21690805 TTTATTTAAT
21690815 TTTATCTTTTAAGTATTAATAA
1 TTTAT-TTTTAAGTATTAATAA
* *
21690837 TTTATATTTTTTAAAATATTAATAG
1 -TT-TA-TTTTT-AAGTATTAATAA
* *
21690862 TTGATTATTTAAGTATTAATAT
1 TTTATT-TTTAAGTATTAATAA
21690884 TTTATTT
1 TTTATTT
21690891 GTAATTTAAT
Statistics
Matches: 43, Mismatches: 6, Indels: 10
0.73 0.10 0.17
Matches are distributed among these distances:
21 1 0.02
22 17 0.40
23 6 0.14
24 8 0.19
25 11 0.26
ACGTcount: A:0.36, C:0.01, G:0.05, T:0.58
Consensus pattern (21 bp):
TTTATTTTTAAGTATTAATAA
Found at i:21691079 original size:48 final size:51
Alignment explanation
Indices: 21690988--21691088 Score: 140
Period size: 48 Copynumber: 2.0 Consensus size: 51
21690978 AATTTATAAT
21690988 TGATTGAAAATATTAATAATTGGTAATTTAATTTATAATTT-AAATATTATTA
1 TGATTGAAAATATTAATAATT-GTAATTTAATTTATAATTTAAAATATT-TTA
21691040 TGATT-AAAATATTAATAATT-TAA-TTAATTT-TAAATTTAAAATATTTTA
1 TGATTGAAAATATTAATAATTGTAATTTAATTTAT-AATTTAAAATATTTTA
21691088 T
1 T
21691089 AATATATAAT
Statistics
Matches: 47, Mismatches: 0, Indels: 8
0.85 0.00 0.15
Matches are distributed among these distances:
47 1 0.02
48 16 0.34
49 10 0.21
51 15 0.32
52 5 0.11
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.50
Consensus pattern (51 bp):
TGATTGAAAATATTAATAATTGTAATTTAATTTATAATTTAAAATATTTTA
Found at i:21691215 original size:15 final size:15
Alignment explanation
Indices: 21691176--21691216 Score: 57
Period size: 15 Copynumber: 2.7 Consensus size: 15
21691166 TAAATTTCAC
*
21691176 TTAATAATTTAAAAA
1 TTAATATTTTAAAAA
21691191 TTAATATTTTAAAATA
1 TTAATATTTTAAAA-A
21691207 TTAAT-TTTTA
1 TTAATATTTTA
21691217 TTTCTAATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
15 18 0.75
16 6 0.25
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (15 bp):
TTAATATTTTAAAAA
Found at i:21691284 original size:28 final size:28
Alignment explanation
Indices: 21691237--21691291 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 28
21691227 AAAAATATGG
* *
21691237 AAATATTAATATTTTTAATTTGAATTTA
1 AAATATTAATATTTTAAATTTAAATTTA
21691265 AAATATTAAT-TTTATAAATTTAAATTT
1 AAATATTAATATTT-TAAATTTAAATTT
21691292 GTAATTTTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 3 0.12
28 21 0.88
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (28 bp):
AAATATTAATATTTTAAATTTAAATTTA
Found at i:21693989 original size:2 final size:2
Alignment explanation
Indices: 21693982--21694006 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
21693972 GTACGTAAAT
21693982 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
21694007 TGATTTCAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:21721951 original size:21 final size:22
Alignment explanation
Indices: 21721922--21721962 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
21721912 AAACCTGAGA
*
21721922 GTTTCTCGCTGCAGCGAGATTC
1 GTTTCTCGCTACAGCGAGATTC
*
21721944 GTTT-TCGCTACAGTGAGAT
1 GTTTCTCGCTACAGCGAGAT
21721963 GCTACAGTGA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.17, C:0.22, G:0.27, T:0.34
Consensus pattern (22 bp):
GTTTCTCGCTACAGCGAGATTC
Found at i:21723780 original size:27 final size:28
Alignment explanation
Indices: 21723731--21723783 Score: 83
Period size: 28 Copynumber: 1.9 Consensus size: 28
21723721 GAGAAGTGCT
21723731 GGGGCAAAAAATTTACCGATTTGCCCTC
1 GGGGCAAAAAATTTACCGATTTGCCCTC
21723759 GGGGCAAAAAA-TTA-CGATTTTGCCC
1 GGGGCAAAAAATTTACCGA-TTTGCCC
21723784 CAATACTCCG
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
26 3 0.12
27 10 0.42
28 11 0.46
ACGTcount: A:0.30, C:0.23, G:0.23, T:0.25
Consensus pattern (28 bp):
GGGGCAAAAAATTTACCGATTTGCCCTC
Found at i:21724548 original size:2 final size:2
Alignment explanation
Indices: 21724541--21724569 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
21724531 ACAGCACCAA
21724541 CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
21724570 CCTTGCACCA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:21725028 original size:25 final size:22
Alignment explanation
Indices: 21725004--21725056 Score: 61
Period size: 23 Copynumber: 2.3 Consensus size: 22
21724994 ATTTTCTCTC
21725004 CTTTTTTCCTTTCCTTTCCTTTCT
1 CTTTTTT-CTTT-CTTTCCTTTCT
* *
21725028 CTTTTCTTCTTTTTTTCCTTTTT
1 CTTTT-TTCTTTCTTTCCTTTCT
21725051 CTTTTT
1 CTTTTT
21725057 CCCCTTTGGA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
22 1 0.04
23 14 0.54
24 9 0.35
25 2 0.08
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (22 bp):
CTTTTTTCTTTCTTTCCTTTCT
Found at i:21730770 original size:20 final size:20
Alignment explanation
Indices: 21730733--21730770 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
21730723 AACCCTCGTT
*
21730733 GCTCGCCCATCTTTGAGCTG
1 GCTCGCCCATCTTCGAGCTG
21730753 GCTCGCCCA-CTCTCGAGC
1 GCTCGCCCATCT-TCGAGC
21730771 CTCAAGCCTC
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:0.11, C:0.42, G:0.24, T:0.24
Consensus pattern (20 bp):
GCTCGCCCATCTTCGAGCTG
Found at i:21730888 original size:2 final size:2
Alignment explanation
Indices: 21730881--21730923 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
21730871 AATGCACAAC
21730881 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
21730923 A
1 A
21730924 NCATAACAGC
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:21737785 original size:19 final size:19
Alignment explanation
Indices: 21737763--21737802 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
21737753 CTCACCCAGC
* *
21737763 TCATGTGCATCCCCCCACA
1 TCATGTACATACCCCCACA
*
21737782 TCATGTACATATCCCCACA
1 TCATGTACATACCCCCACA
21737801 TC
1 TC
21737803 GTGCACACGG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.25, C:0.42, G:0.07, T:0.25
Consensus pattern (19 bp):
TCATGTACATACCCCCACA
Found at i:21749733 original size:23 final size:23
Alignment explanation
Indices: 21749703--21749762 Score: 84
Period size: 23 Copynumber: 2.6 Consensus size: 23
21749693 TATACGTATA
* * *
21749703 CCCATCATTATCATGCACATCAT
1 CCCATCATCATCATACACACCAT
21749726 CCCATCATCATCATACACACCAT
1 CCCATCATCATCATACACACCAT
*
21749749 CACATCATCATCAT
1 CCCATCATCATCAT
21749763 CCCCAGCTCA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.33, C:0.38, G:0.02, T:0.27
Consensus pattern (23 bp):
CCCATCATCATCATACACACCAT
Found at i:21749846 original size:43 final size:43
Alignment explanation
Indices: 21749772--21749890 Score: 123
Period size: 43 Copynumber: 2.8 Consensus size: 43
21749762 TCCCCAGCTC
* * * * * *
21749772 ATGCGCACTCCCTATTCGCACATGGCTGGGTCATAGC-CGGGTT
1 ATGCGCACTCCCTACTCGTACATAGCCGGGTCAT-CCTCGAGTT
* * *
21749815 ATGCACACTCCCTACTCGTACATAACCGGGTCATCCTCGATTT
1 ATGCGCACTCCCTACTCGTACATAGCCGGGTCATCCTCGAGTT
* *
21749858 ATGTGCACTCCCTACTCGTACATAGCCGAGTCA
1 ATGCGCACTCCCTACTCGTACATAGCCGGGTCA
21749891 ATATAATTAC
Statistics
Matches: 62, Mismatches: 13, Indels: 2
0.81 0.17 0.03
Matches are distributed among these distances:
42 1 0.02
43 61 0.98
ACGTcount: A:0.21, C:0.33, G:0.20, T:0.26
Consensus pattern (43 bp):
ATGCGCACTCCCTACTCGTACATAGCCGGGTCATCCTCGAGTT
Found at i:21750699 original size:19 final size:19
Alignment explanation
Indices: 21750675--21750713 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
21750665 AGAAGAAGAC
21750675 AAGCTGCTGAAAATTCAAG
1 AAGCTGCTGAAAATTCAAG
* *
21750694 AAGCTGTTGGAAATTCAAG
1 AAGCTGCTGAAAATTCAAG
21750713 A
1 A
21750714 TATTTATAGG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.41, C:0.13, G:0.23, T:0.23
Consensus pattern (19 bp):
AAGCTGCTGAAAATTCAAG
Found at i:21754526 original size:35 final size:35
Alignment explanation
Indices: 21754464--21754543 Score: 81
Period size: 35 Copynumber: 2.3 Consensus size: 35
21754454 ATGTGGGCGA
**
21754464 GAGTGCATGTGATGATATTGAAATGTGCGA-GCAAG
1 GAGTGCACATGATGATATTGAAATGTGC-ATGCAAG
*** * *
21754499 GAGTGCACATGATGATATTGCCTTGTGCATGTAGG
1 GAGTGCACATGATGATATTGAAATGTGCATGCAAG
21754534 GAGTGCACAT
1 GAGTGCACAT
21754544 TGGCTGAGTG
Statistics
Matches: 37, Mismatches: 7, Indels: 2
0.80 0.15 0.04
Matches are distributed among these distances:
34 1 0.03
35 36 0.97
ACGTcount: A:0.28, C:0.12, G:0.33, T:0.28
Consensus pattern (35 bp):
GAGTGCACATGATGATATTGAAATGTGCATGCAAG
Found at i:21758083 original size:2 final size:2
Alignment explanation
Indices: 21758076--21758117 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
21758066 GATACACAAC
21758076 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
21758118 CAGCATCTTA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:21764230 original size:20 final size:21
Alignment explanation
Indices: 21764182--21764223 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
21764172 TTAGTAGGTA
* *
21764182 TATATATGAATATATGTTTTG
1 TATAGATGAATATATGTTGTG
21764203 TATAGATGAATA-ATGTTGTG
1 TATAGATGAATATATGTTGTG
21764223 T
1 T
21764224 GATGATGTTG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 8 0.42
21 11 0.58
ACGTcount: A:0.33, C:0.00, G:0.19, T:0.48
Consensus pattern (21 bp):
TATAGATGAATATATGTTGTG
Found at i:21764277 original size:37 final size:37
Alignment explanation
Indices: 21764235--21764307 Score: 128
Period size: 37 Copynumber: 2.0 Consensus size: 37
21764225 ATGATGTTGA
21764235 AGTGTGCGAGTAGGGAGTGCACACATGACGATGATAG
1 AGTGTGCGAGTAGGGAGTGCACACATGACGATGATAG
* *
21764272 AGTGTGCGGGTAGGGAGTGCACACATGATGATGATA
1 AGTGTGCGAGTAGGGAGTGCACACATGACGATGATA
21764308 TTGCATTGAG
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 34 1.00
ACGTcount: A:0.29, C:0.12, G:0.38, T:0.21
Consensus pattern (37 bp):
AGTGTGCGAGTAGGGAGTGCACACATGACGATGATAG
Found at i:21772302 original size:13 final size:13
Alignment explanation
Indices: 21772281--21772317 Score: 51
Period size: 12 Copynumber: 3.0 Consensus size: 13
21772271 GTACCACATA
*
21772281 TTTTATTCTTTTC
1 TTTTTTTCTTTTC
21772294 TTTTTTTC-TTTC
1 TTTTTTTCTTTTC
21772306 TTTTTTT-TTTTC
1 TTTTTTTCTTTTC
21772318 AACCCCTAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
12 15 0.68
13 7 0.32
ACGTcount: A:0.03, C:0.14, G:0.00, T:0.84
Consensus pattern (13 bp):
TTTTTTTCTTTTC
Found at i:21772308 original size:17 final size:16
Alignment explanation
Indices: 21772286--21772317 Score: 55
Period size: 16 Copynumber: 1.9 Consensus size: 16
21772276 ACATATTTTA
21772286 TTCTTTTCTTTTTTTCT
1 TTCTTTT-TTTTTTTCT
21772303 TTCTTTTTTTTTTTC
1 TTCTTTTTTTTTTTC
21772318 AACCCCTAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (16 bp):
TTCTTTTTTTTTTTCT
Found at i:21781402 original size:113 final size:112
Alignment explanation
Indices: 21781203--21781431 Score: 449
Period size: 113 Copynumber: 2.0 Consensus size: 112
21781193 TCCCTATGTG
21781203 ATTTGAAATTAAAACAGACTCATTAGTTCAGGCTCTAATCTAGCTACATACGGCCTATAGGTATA
1 ATTTGAAATTAAAACAGACTCATTAGTTCAGGCTCTAATCTAGCTACATACGGCCTATAGGTATA
21781268 TCCTTATCCTATACGCAAATCAATTAATTTGATCATATGCTATCCTA
66 TCCTTATCCTATACGCAAATCAATTAATTTGATCATATGCTATCCTA
21781315 ANTTTGAAATTAAAACAGACTCATTAGTTCAGGCTCTAATCTAGCTACATACGGCCTATAGGTAT
1 A-TTTGAAATTAAAACAGACTCATTAGTTCAGGCTCTAATCTAGCTACATACGGCCTATAGGTAT
21781380 ATCCTTATCCTATACGCAAATCAATTAATTTGATCATATGCTATCCTA
65 ATCCTTATCCTATACGCAAATCAATTAATTTGATCATATGCTATCCTA
21781428 ATTT
1 ATTT
21781432 TAGTCTACTC
Statistics
Matches: 116, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
112 4 0.03
113 112 0.97
ACGTcount: A:0.34, C:0.20, G:0.11, T:0.34
Consensus pattern (112 bp):
ATTTGAAATTAAAACAGACTCATTAGTTCAGGCTCTAATCTAGCTACATACGGCCTATAGGTATA
TCCTTATCCTATACGCAAATCAATTAATTTGATCATATGCTATCCTA
Found at i:21783960 original size:43 final size:43
Alignment explanation
Indices: 21783878--21783994 Score: 119
Period size: 43 Copynumber: 2.7 Consensus size: 43
21783868 CCATAATCCC
* * * ** **
21783878 CCAACTCATGCGCACTCCCTACTTGCACGTGGCTAGGTCATCA
1 CCAACTTATGCACACTCCCTACTTGCACATAACCGGGTCATCA
* *
21783921 CCAAGTTATG-AGCACTCCTTACTTGCACATAACCGGGTCATCA
1 CCAACTTATGCA-CACTCCCTACTTGCACATAACCGGGTCATCA
* *
21783964 TCGACTTATGCACACTCCCTACTTGCACATA
1 CCAACTTATGCACACTCCCTACTTGCACATA
21783995 GCTGAGTCAA
Statistics
Matches: 59, Mismatches: 13, Indels: 4
0.78 0.17 0.05
Matches are distributed among these distances:
43 58 0.98
44 1 0.02
ACGTcount: A:0.25, C:0.34, G:0.15, T:0.26
Consensus pattern (43 bp):
CCAACTTATGCACACTCCCTACTTGCACATAACCGGGTCATCA
Found at i:21786325 original size:43 final size:43
Alignment explanation
Indices: 21786272--21786407 Score: 150
Period size: 43 Copynumber: 3.2 Consensus size: 43
21786262 AGCTGGCTAA
** * *
21786272 TCATCATCGGCTTATGCGCACTCCCTACTTGCCCATAGTTGGG
1 TCATCATCGGCTTATGCGCACTCCCTACTCACACATAGTCGGG
*
21786315 TCATCATCGGCTTATGCGCACTCTCTACTCACACATAGTCGGG
1 TCATCATCGGCTTATGCGCACTCCCTACTCACACATAGTCGGG
** * * *
21786358 TCATCATCATCTCATGTGCACTCCC-ACATCATACATAG-CTGGG
1 TCATCATCGGCTTATGCGCACTCCCTAC-TCACACATAGTC-GGG
21786401 TCATCAT
1 TCATCAT
21786408 TATCACACAA
Statistics
Matches: 80, Mismatches: 11, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
42 3 0.04
43 77 0.96
ACGTcount: A:0.21, C:0.32, G:0.17, T:0.29
Consensus pattern (43 bp):
TCATCATCGGCTTATGCGCACTCCCTACTCACACATAGTCGGG
Found at i:21793590 original size:43 final size:43
Alignment explanation
Indices: 21793500--21793635 Score: 150
Period size: 43 Copynumber: 3.2 Consensus size: 43
21793490 AGCCGGCTCA
* * **
21793500 TCATCATCGGCTTATGCGAACTCCCTACTCGCACATAGCCT-AA
1 TCATCATCAGCTTATGCGCACTCCCTACTCGCACATAG-CTGGG
** *
21793543 TCATCATCTCCTTATGCGCACTCCCTACTTGCACATAGCTGGG
1 TCATCATCAGCTTATGCGCACTCCCTACTCGCACATAGCTGGG
* * *
21793586 TCATCATCAGCTCATGTGCACTCCC-ACATCACACATAGCTGGG
1 TCATCATCAGCTTATGCGCACTCCCTAC-TCGCACATAGCTGGG
21793629 TCATCAT
1 TCATCAT
21793636 TATCACACAA
Statistics
Matches: 79, Mismatches: 12, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
42 4 0.05
43 75 0.95
ACGTcount: A:0.24, C:0.35, G:0.15, T:0.27
Consensus pattern (43 bp):
TCATCATCAGCTTATGCGCACTCCCTACTCGCACATAGCTGGG
Found at i:21804235 original size:29 final size:29
Alignment explanation
Indices: 21804198--21804257 Score: 111
Period size: 29 Copynumber: 2.1 Consensus size: 29
21804188 AAGTTGTAGA
21804198 GATAGTCCCAAGAAGTAAGGGGACTAAAG
1 GATAGTCCCAAGAAGTAAGGGGACTAAAG
*
21804227 GATAGTCCCAAGAGGTAAGGGGACTAAAG
1 GATAGTCCCAAGAAGTAAGGGGACTAAAG
21804256 GA
1 GA
21804258 ATGGCAAAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.40, C:0.13, G:0.33, T:0.13
Consensus pattern (29 bp):
GATAGTCCCAAGAAGTAAGGGGACTAAAG
Found at i:21806012 original size:36 final size:36
Alignment explanation
Indices: 21805919--21806030 Score: 145
Period size: 36 Copynumber: 3.1 Consensus size: 36
21805909 TAGTCAGAGT
* * * *
21805919 CATCGTGTGCA-CCATCACATCACGTACAACTAATAC
1 CATCGTGTGCACCCAT-ACATCGCGCACAGCTAATGC
*
21805955 CATCGTGTGCACCCCTACATCGCGCACAGCTAATGC
1 CATCGTGTGCACCCATACATCGCGCACAGCTAATGC
* *
21805991 CATCGTGTGCACCCATACATCGCACATAGCTAATGC
1 CATCGTGTGCACCCATACATCGCGCACAGCTAATGC
21806027 CATC
1 CATC
21806031 ATTCATACTC
Statistics
Matches: 67, Mismatches: 8, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
36 64 0.96
37 3 0.04
ACGTcount: A:0.28, C:0.36, G:0.15, T:0.21
Consensus pattern (36 bp):
CATCGTGTGCACCCATACATCGCGCACAGCTAATGC
Found at i:21807005 original size:67 final size:65
Alignment explanation
Indices: 21806878--21807009 Score: 230
Period size: 67 Copynumber: 2.0 Consensus size: 65
21806868 TAATTAAATA
21806878 TTTACCTCAAGAAACGTGAAGTGAAAGCCTTCATTGAGAAGAAAAGTTCATTTAATGTCACTCAT
1 TTTACCTCAAGAAACGTGAAGTGAAAGCCTTCATTGAGAAGAAAAGTTCATTTAATGTCACTCAT
21806943 NTTTACCTCAAGAAACGTGAAGTGAAAGCCCTTCATTGAGAAGAAAAGTTCATTT-ATAGTCACT
1 -TTTACCTCAAGAAACGTGAAGTGAAAG-CCTTCATTGAGAAGAAAAGTTCATTTAAT-GTCACT
21807007 CAT
63 CAT
21807010 ACCTCTGAAA
Statistics
Matches: 64, Mismatches: 0, Indels: 3
0.96 0.00 0.04
Matches are distributed among these distances:
66 29 0.45
67 35 0.55
ACGTcount: A:0.36, C:0.17, G:0.17, T:0.29
Consensus pattern (65 bp):
TTTACCTCAAGAAACGTGAAGTGAAAGCCTTCATTGAGAAGAAAAGTTCATTTAATGTCACTCAT
Found at i:21808208 original size:21 final size:21
Alignment explanation
Indices: 21808184--21808223 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
21808174 TGTGGCTGAA
*
21808184 ATTGATGATATTTCATGATAT
1 ATTGATGATATTTAATGATAT
* *
21808205 ATTGGTGGTATTTAATGAT
1 ATTGATGATATTTAATGAT
21808224 TGGTGAGGCT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.30, C:0.03, G:0.20, T:0.47
Consensus pattern (21 bp):
ATTGATGATATTTAATGATAT
Found at i:21809804 original size:19 final size:18
Alignment explanation
Indices: 21809770--21809805 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
21809760 GAAATTAGAA
*
21809770 TATTTTATTGAATAGTTT
1 TATTTTATTAAATAGTTT
21809788 TATTTTATTCAAATAGTT
1 TATTTTATT-AAATAGTT
21809806 GCAATATTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 9 0.56
19 7 0.44
ACGTcount: A:0.31, C:0.03, G:0.08, T:0.58
Consensus pattern (18 bp):
TATTTTATTAAATAGTTT
Found at i:21817903 original size:171 final size:170
Alignment explanation
Indices: 21817345--21818605 Score: 1348
Period size: 171 Copynumber: 7.4 Consensus size: 170
21817335 AGGTCGTGAC
* *
21817345 AGAAGAAAAGTTCATTTATAGTCAGTTATGCCTTCAAAAGCCTTATTACTCGCTTTAAATGGTTT
1 AGAAGAAAAGTT-ATTTATAGTCACTCATGCCTTCAAAAGCCTTATTACTCGCTTTAAATGGTTT
* * * * * *
21817410 TATAATCTCATAATT-ATTTTAGGTTGAATTGTTTTACCTTTTTGGTTAAAACAGATTATAATTT
65 TATAATCTCATAATTGATTTTAAGTTGAATTTTTTTACATTTTTGGTTAAAACATATCATAATTG
* * * *
21817474 AATATTTACCTCAAGAAACGTGAAGTGAAAGCTATTCATTG
130 AATATTTACCTCAAGAAACATGAAGCGAAAACCATTCATTG
* * * * * *
21817515 AGCAGAAAAATTCATTTATAGTCACTCATACCTTCACAAGCCTTATTACACACTTTAAATGGTTT
1 AGAAGAAAAGTT-ATTTATAGTCACTCATGCCTTCAAAAGCCTTATTACTCGCTTTAAATGGTTT
* * * * * * *
21817580 TATAAGCTTATAATTGATTTTAAGTTGATTTTTTTTTACATTTTTGGTCAACACAGATTATAATT
65 TATAATCTCATAATTGATTTTAAGTTGA-ATTTTTTTACATTTTTGGTTAAAACATATCATAATT
* * * * *
21817645 GAATGTTTCCCCCACA-AAATATGAAGC-AAAAGCCATCCATTG
129 GAATATTTACCTCA-AGAAACATGAAGCGAAAA-CCATTCATTG
* * * * * * *
21817687 ACAAGAAAAGTCCATTTATAGTCACCCATGCATTCGAAAGCCTTATTACTCACTTTAAAT-ATTT
1 AGAAGAAAAGT-TATTTATAGTCACTCATGCCTTCAAAAGCCTTATTACTCGCTTTAAATGGTTT
* * * * * *
21817751 TTTAAATCTCATAATTGATTTTACGATGAATTTTTTTACGTTTTTGGTTAAAAGATATCACAATT
65 TAT-AATCTCATAATTGATTTTAAGTTGAATTTTTTTACATTTTTGGTTAAAACATATCATAATT
* *
21817816 GAATATTTTCCTTC-GGAAACATGAAGCGAAAACCATTCATTG
129 GAATATTTACC-TCAAGAAACATGAAGCGAAAACCATTCATTG
* * * * *
21817858 AGAACAAAACTATATTTACAGTCACTCATGCCTTCAAAAGCCTTATTACTTGCATTAAATGGTTT
1 AGAAGAAAAGT-TATTTATAGTCACTCATGCCTTCAAAAGCCTTATTACTCGCTTTAAATGGTTT
* * *
21817923 TATAATCTCATAATTGATTTTAAGTTGATTTTTTTTACATTTTTGGTTATAACA-ATTTATAATT
65 TATAATCTCATAATTGATTTTAAGTTGAATTTTTTTACATTTTTGGTTAAAACATA-TCATAATT
* *
21817987 GAATGTTTACCTCAAGAAA-AGTGAAGC-AAAAGCCATCCATTG
129 GAATATTTACCTCAAGAAACA-TGAAGCGAAAA-CCATTCATTG
* * * * *
21818029 GGAAGAAAAGTTCATTTATAGTCACTCATGCCTTCAAAAGGCTTGTTACTCACTTTAACTGGTTT
1 AGAAGAAAAGTT-ATTTATAGTCACTCATGCCTTCAAAAGCCTTATTACTCGCTTTAAATGGTTT
* *
21818094 TATAATCTCATAATTGATTTTATGTTGAATTTTTTTACCTTTTTGGTTAAAACATATCATAATTG
65 TATAATCTCATAATTGATTTTAAGTTGAATTTTTTTACATTTTTGGTTAAAACATATCATAATTG
* * *
21818159 AATATTTGCCTCAAGAAACATAAAGCGAAAGCCA-TCTATTG
130 AATATTTACCTCAAGAAACATGAAGCGAAAACCATTC-ATTG
* * * * *
21818200 -GTAAGAAAAGTCCATTTATAGTGACTCATGACATCAAAAGCTTTATTACTCGCTTTAAATGGTT
1 AG-AAGAAAAGT-TATTTATAGTCACTCATGCCTTCAAAAGCCTTATTACTCGCTTTAAATGGTT
*
21818264 TTATAATCTCATAATTGATTTTAAGTT-AATTTTTTTTACATTTTTGGTTAAAACA-ATTTATAA
64 TTATAATCTCATAATTGATTTTAAGTTGAA-TTTTTTTACATTTTTGGTTAAAACATA-TCATAA
* * * * ** *
21818327 TTGAATGTCTACCTTAGGAAATGTGAAGC-AAAAGCCATCCATTG
127 TTGAATATTTACCTCAAGAAACATGAAGCGAAAA-CCATTCATTG
*
21818371 AGAAGAAAAGTTCATTTATAG-CACTCATGCCTTCAAAAGGCTTATTACTCGCTTTAAATGGTTT
1 AGAAGAAAAGTT-ATTTATAGTCACTCATGCCTTCAAAAGCCTTATTACTCGCTTTAAATGGTTT
* * * * * **
21818435 TATAATCTCATAATTGATTTTAAGTTGAATTCTTTGACCTTTTCGATTAAAACGGATCATAATTG
65 TATAATCTCATAATTGATTTTAAGTTGAATTTTTTTACATTTTTGGTTAAAACATATCATAATTG
* * *
21818500 AATATTTGCCTCAAGAAACGTGAAGCGAAAGCC-TTACATT-
130 AATATTTACCTCAAGAAACATGAAGCGAAAACCATT-CATTG
* * * * * *
21818540 AGTAAGAAAAGTCAATTTATAGTCATTCATGCCATCAAAAGCTTTGTTACTTGCTTTAAATGGTT
1 AG-AAGAAAAGT-TATTTATAGTCACTCATGCCTTCAAAAGCCTTATTACTCGCTTTAAATGGTT
21818605 T
64 T
21818606 GATGGGATCT
Statistics
Matches: 905, Mismatches: 152, Indels: 67
0.81 0.14 0.06
Matches are distributed among these distances:
169 3 0.00
170 221 0.24
171 536 0.59
172 144 0.16
173 1 0.00
ACGTcount: A:0.34, C:0.15, G:0.13, T:0.38
Consensus pattern (170 bp):
AGAAGAAAAGTTATTTATAGTCACTCATGCCTTCAAAAGCCTTATTACTCGCTTTAAATGGTTTT
ATAATCTCATAATTGATTTTAAGTTGAATTTTTTTACATTTTTGGTTAAAACATATCATAATTGA
ATATTTACCTCAAGAAACATGAAGCGAAAACCATTCATTG
Found at i:21818014 original size:342 final size:342
Alignment explanation
Indices: 21817345--21818605 Score: 1634
Period size: 342 Copynumber: 3.7 Consensus size: 342
21817335 AGGTCGTGAC
* * *
21817345 AGAAGAAAAGTTCATTTATAGTCAGTTATGCCTTCAAAAGCCTTATTACTCGCTTTAAATGGTTT
1 AGAAGAAAAGTTCATTTATAGTCACTCATGCCTTCAAAAGCCTTATTACTCACTTTAAATGGTTT
* * * *
21817410 TATAATCTCATAATT-ATTTTAGGTTGAATTGTTTTACCTTTTTGGTTAAAACAGATTATAATTT
66 TATAATCTCATAATTGATTTTAAGTTGAATTTTTTTACCTTTTTGGTTAAAACAGATCATAATTG
* * * * * *
21817474 AATATTTACCTCAAGAAACGTGAAGTGAAAGCTATTCATTGAG-CAGAAAAAT-TCATTTATAGT
131 AATATTTGCCTCAAGAAACATGAAGCGAAAGCCATTCATTGAGTAAGAAAAGTAT-ATTTATAGT
* * * * * * *
21817537 CACTCATACCTTCACAAGCCTTATTACACACTTTAAATGGTTTTATAAGCTTATAATTGATTTTA
195 CACTCATGCCATCAAAAGCCTTATTACTCGCTTTAAATGGTTTTATAATCTCATAATTGATTTTA
* * *
21817602 AGTTGATTTTTTTTTACATTTTTGGTCAACACAGA-TTATAATTGAATGTTTCCCCCACA-AAAT
260 AGTTGA-TTTTTTTTACATTTTTGGTTAA-ACA-ATTTATAATTGAATGTTTACCTCA-AGAAA-
21817665 A-TGAAGCAAAAGCCATCCATTG
320 AGTGAAGCAAAAGCCATCCATTG
* * * * * *
21817687 ACAAGAAAAGTCCATTTATAGTCACCCATGCATTCGAAAGCCTTATTACTCACTTTAAAT-ATTT
1 AGAAGAAAAGTTCATTTATAGTCACTCATGCCTTCAAAAGCCTTATTACTCACTTTAAATGGTTT
* * * * * * *
21817751 TTTAAATCTCATAATTGATTTTACGATGAATTTTTTTACGTTTTTGGTTAAAAGATATCACAATT
66 TAT-AATCTCATAATTGATTTTAAGTTGAATTTTTTTACCTTTTTGGTTAAAACAGATCATAATT
* * * * * *
21817816 GAATATTTTCCTTC-GGAAACATGAAGCGAAAACCATTCATTGAG-AACAAAACTATATTTACAG
130 GAATATTTGCC-TCAAGAAACATGAAGCGAAAGCCATTCATTGAGTAAGAAAAGTATATTTATAG
* * *
21817879 TCACTCATGCCTTCAAAAGCCTTATTACTTGCATTAAATGGTTTTATAATCTCATAATTGATTTT
194 TCACTCATGCCATCAAAAGCCTTATTACTCGCTTTAAATGGTTTTATAATCTCATAATTGATTTT
21817944 AAGTTGATTTTTTTTACATTTTTGGTTATAACAATTTATAATTGAATGTTTACCTCAAGAAAAGT
259 AAGTTGATTTTTTTTACATTTTTGGTTA-AACAATTTATAATTGAATGTTTACCTCAAGAAAAGT
21818009 GAAGCAAAAGCCATCCATTG
323 GAAGCAAAAGCCATCCATTG
* * * *
21818029 GGAAGAAAAGTTCATTTATAGTCACTCATGCCTTCAAAAGGCTTGTTACTCACTTTAACTGGTTT
1 AGAAGAAAAGTTCATTTATAGTCACTCATGCCTTCAAAAGCCTTATTACTCACTTTAAATGGTTT
* *
21818094 TATAATCTCATAATTGATTTTATGTTGAATTTTTTTACCTTTTTGGTTAAAACATATCATAATTG
66 TATAATCTCATAATTGATTTTAAGTTGAATTTTTTTACCTTTTTGGTTAAAACAGATCATAATTG
* **
21818159 AATATTTGCCTCAAGAAACATAAAGCGAAAGCCA-TCTATTG-GTAAGAAAAGTCCATTTATAGT
131 AATATTTGCCTCAAGAAACATGAAGCGAAAGCCATTC-ATTGAGTAAGAAAAGTATATTTATAGT
* * *
21818222 GACTCATGACATCAAAAGCTTTATTACTCGCTTTAAATGGTTTTATAATCTCATAATTGATTTTA
195 CACTCATGCCATCAAAAGCCTTATTACTCGCTTTAAATGGTTTTATAATCTCATAATTGATTTTA
* * * * *
21818287 AGTTAATTTTTTTTACATTTTTGGTTAAAACAATTTATAATTGAATGTCTACCTTAGGAAATGTG
260 AGTTGATTTTTTTTACATTTTTGGTT-AAACAATTTATAATTGAATGTTTACCTCAAGAAAAGTG
21818352 AAGCAAAAGCCATCCATTG
324 AAGCAAAAGCCATCCATTG
* *
21818371 AGAAGAAAAGTTCATTTATAG-CACTCATGCCTTCAAAAGGCTTATTACTCGCTTTAAATGGTTT
1 AGAAGAAAAGTTCATTTATAGTCACTCATGCCTTCAAAAGCCTTATTACTCACTTTAAATGGTTT
* * * * *
21818435 TATAATCTCATAATTGATTTTAAGTTGAATTCTTTGACCTTTTCGATTAAAACGGATCATAATTG
66 TATAATCTCATAATTGATTTTAAGTTGAATTTTTTTACCTTTTTGGTTAAAACAGATCATAATTG
*
21818500 AATATTTGCCTCAAGAAACGTGAAGCGAAAGCC-TTACATT-AGTAAGAAAAGTCA-ATTTATAG
131 AATATTTGCCTCAAGAAACATGAAGCGAAAGCCATT-CATTGAGTAAGAAAAGT-ATATTTATAG
* * * *
21818562 TCATTCATGCCATCAAAAGCTTTGTTACTTGCTTTAAATGGTTT
194 TCACTCATGCCATCAAAAGCCTTATTACTCGCTTTAAATGGTTT
21818606 GATGGGATCT
Statistics
Matches: 807, Mismatches: 95, Indels: 35
0.86 0.10 0.04
Matches are distributed among these distances:
341 204 0.25
342 442 0.55
343 158 0.20
344 3 0.00
ACGTcount: A:0.34, C:0.15, G:0.13, T:0.38
Consensus pattern (342 bp):
AGAAGAAAAGTTCATTTATAGTCACTCATGCCTTCAAAAGCCTTATTACTCACTTTAAATGGTTT
TATAATCTCATAATTGATTTTAAGTTGAATTTTTTTACCTTTTTGGTTAAAACAGATCATAATTG
AATATTTGCCTCAAGAAACATGAAGCGAAAGCCATTCATTGAGTAAGAAAAGTATATTTATAGTC
ACTCATGCCATCAAAAGCCTTATTACTCGCTTTAAATGGTTTTATAATCTCATAATTGATTTTAA
GTTGATTTTTTTTACATTTTTGGTTAAACAATTTATAATTGAATGTTTACCTCAAGAAAAGTGAA
GCAAAAGCCATCCATTG
Found at i:21818372 original size:513 final size:513
Alignment explanation
Indices: 21817345--21818605 Score: 1574
Period size: 513 Copynumber: 2.5 Consensus size: 513
21817335 AGGTCGTGAC
* * * *
21817345 AGAAGAAAAGTTCATTTATAGTCAGTTATGCCTTCAAAAGCCTTATTACTCGCTTTAAATGGTTT
1 AGAACAAAACTTCATTTATAGTCACTCATGCCTTCAAAAGCCTTATTACTCGCTTTAAATGGTTT
* * *
21817410 TATAATCTCATAATT-ATTTTAGGTTGAATTGTTTTACCTTTTTGGTTAAAACAGATTATAATTT
66 TATAATCTCATAATTGATTTTAAGTTGAATTCTTTTACCTTTTTGGTTAAAACA-ATTATAATTG
* * * * * *
21817474 AATATTTACCTCAAGAAACGTGAAGTGAAAGCTATTCATTGAGCAGAAAAATTCATTTATAGTCA
130 AATATTTACCTCAAGAAACGTGAAGCGAAAGCCATACATTGGGAAGAAAAGTTCATTTATAGTCA
* * * * * *
21817539 CTCATACCTTCACAAGCCTTATTACACACTTTAAATGGTTTTATAAGCTTATAATTGATTTTAAG
195 CTCATGCCTTCAAAAGGCTTGTTACTCACTTTAAATGGTTTTATAAGCTCATAATTGATTTTAAG
* * * * * *
21817604 TTGATTTTTTTTTACATTTTTGGTCAACACAGATTATAATTGAATGTTTCCCCCACAAAATATGA
260 TTGATATTTTTTTACATTTTTGGTCAAAACAGATCATAATTGAATATTTCCCCCACAAAACATAA
*
21817669 AGCAAAAGCCATCCATTGACAAGAAAAGTCCATTTATAGTCACCCATGCATTCGAAAGCCTTATT
325 AGCAAAAGCCATCCATTGACAAGAAAAGTCCATTTATAGTCACCCATGCATTCAAAAGCCTTATT
* * *
21817734 ACTCACTTTAAATATTTTTTAAATCTCATAATTGATTTTACGATGAATTTTTTTACGTTTTTGGT
390 ACTCACTTTAAATATTTTATAAATCTCATAATTGATTTTAAGATGAATTTTTTTACATTTTTGGT
* * * * *
21817799 TAAAAGATATCACAATTGAATATTTTCCTTCGGAAACATGAAGCGAAAACCATTCATTG
455 TAAAAAATATCACAATTGAATATCTACCTTAGGAAACATGAAGCGAAAACCATCCATTG
* * *
21817858 AGAACAAAACTAT-ATTTACAGTCACTCATGCCTTCAAAAGCCTTATTACTTGCATTAAATGGTT
1 AGAACAAAACT-TCATTTATAGTCACTCATGCCTTCAAAAGCCTTATTACTCGCTTTAAATGGTT
* * * *
21817922 TTATAATCTCATAATTGATTTTAAGTTGATTTTTTTTACATTTTTGGTTATAACAATTTATAATT
65 TTATAATCTCATAATTGATTTTAAGTTGAATTCTTTTACCTTTTTGGTTAAAACAA-TTATAATT
* * * *
21817987 GAATGTTTACCTCAAGAAAAGTGAAGCAAAAGCCATCCATTGGGAAGAAAAGTTCATTTATAGTC
129 GAATATTTACCTCAAGAAACGTGAAGCGAAAGCCATACATTGGGAAGAAAAGTTCATTTATAGTC
* * *
21818052 ACTCATGCCTTCAAAAGGCTTGTTACTCACTTTAACTGGTTTTATAATCTCATAATTGATTTTAT
194 ACTCATGCCTTCAAAAGGCTTGTTACTCACTTTAAATGGTTTTATAAGCTCATAATTGATTTTAA
* * * * *
21818117 GTTGA-ATTTTTTTACCTTTTTGGTTAAAACATATCATAATTGAATATTTGCCTCA-AGAAACAT
259 GTTGATATTTTTTTACATTTTTGGTCAAAACAGATCATAATTGAATATTTCCCCCACA-AAACAT
* * ** * * *
21818180 AAAGCGAAAGCCATCTATTGGTAAGAAAAGTCCATTTATAGTGACTCATGACA-TCAAAAGCTTT
323 AAAGCAAAAGCCATCCATTGACAAGAAAAGTCCATTTATAGTCACCCATG-CATTCAAAAGCCTT
* * *
21818244 ATTACTCGCTTTAAATGGTTTTAT-AATCTCATAATTGATTTTAAG-TTAATTTTTTTTACATTT
387 ATTACTCACTTTAAAT-ATTTTATAAATCTCATAATTGATTTTAAGATGAA-TTTTTTTACATTT
* * * **
21818307 TTGGTTAAAACAAT-TTATAATTGAATGTCTACCTTAGGAAATGTGAAGC-AAAAGCCATCCATT
450 TTGGTTAAAA-AATATCACAATTGAATATCTACCTTAGGAAACATGAAGCGAAAA-CCATCCATT
21818370 G
513 G
* * *
21818371 AGAAGAAAAGTTCATTTATAG-CACTCATGCCTTCAAAAGGCTTATTACTCGCTTTAAATGGTTT
1 AGAACAAAACTTCATTTATAGTCACTCATGCCTTCAAAAGCCTTATTACTCGCTTTAAATGGTTT
* * * * *
21818435 TATAATCTCATAATTGATTTTAAGTTGAATTCTTTGACCTTTTCGATTAAAACGGATCATAATTG
66 TATAATCTCATAATTGATTTTAAGTTGAATTCTTTTACCTTTTTGGTTAAAAC-AATTATAATTG
* * * *
21818500 AATATTTGCCTCAAGAAACGTGAAGCGAAAGCCTTACATTAGTAAGAAAAG-TCAATTTATAGTC
130 AATATTTACCTCAAGAAACGTGAAGCGAAAGCCATACATTGGGAAGAAAAGTTC-ATTTATAGTC
* * **
21818564 ATTCATGCCATCAAAA-GCTTTGTTACTTGCTTTAAATGGTTT
194 ACTCATGCCTTCAAAAGGC-TTGTTACTCACTTTAAATGGTTT
21818606 GATGGGATCT
Statistics
Matches: 641, Mismatches: 94, Indels: 27
0.84 0.12 0.04
Matches are distributed among these distances:
511 4 0.01
512 190 0.30
513 280 0.44
514 167 0.26
ACGTcount: A:0.34, C:0.15, G:0.13, T:0.38
Consensus pattern (513 bp):
AGAACAAAACTTCATTTATAGTCACTCATGCCTTCAAAAGCCTTATTACTCGCTTTAAATGGTTT
TATAATCTCATAATTGATTTTAAGTTGAATTCTTTTACCTTTTTGGTTAAAACAATTATAATTGA
ATATTTACCTCAAGAAACGTGAAGCGAAAGCCATACATTGGGAAGAAAAGTTCATTTATAGTCAC
TCATGCCTTCAAAAGGCTTGTTACTCACTTTAAATGGTTTTATAAGCTCATAATTGATTTTAAGT
TGATATTTTTTTACATTTTTGGTCAAAACAGATCATAATTGAATATTTCCCCCACAAAACATAAA
GCAAAAGCCATCCATTGACAAGAAAAGTCCATTTATAGTCACCCATGCATTCAAAAGCCTTATTA
CTCACTTTAAATATTTTATAAATCTCATAATTGATTTTAAGATGAATTTTTTTACATTTTTGGTT
AAAAAATATCACAATTGAATATCTACCTTAGGAAACATGAAGCGAAAACCATCCATTG
Found at i:21819161 original size:2 final size:2
Alignment explanation
Indices: 21819154--21819179 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
21819144 CAATGGTATT
21819154 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
21819180 GTTCAACTGC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:21824013 original size:2 final size:2
Alignment explanation
Indices: 21824006--21824046 Score: 55
Period size: 2 Copynumber: 20.0 Consensus size: 2
21823996 NNNNNNNNNN
* *
21824006 AT AT AT AT AT AT AT AT AT AT AT AT CT AA AT AT AT AT GAT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT
21824047 GTATTGATAG
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
2 32 0.94
3 2 0.06
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.46
Consensus pattern (2 bp):
AT
Found at i:21824294 original size:2 final size:2
Alignment explanation
Indices: 21824287--21824317 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
21824277 GGTGGTTATG
*
21824287 TA TA TA TA TA TA TA TA TA TA TA TG TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
21824318 TTATTTATGC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (2 bp):
TA
Found at i:21828240 original size:67 final size:68
Alignment explanation
Indices: 21828132--21828267 Score: 211
Period size: 67 Copynumber: 2.0 Consensus size: 68
21828122 AAGCTTTTAC
* * ** *
21828132 AATGGCTTGTCATAGGCTCAGCCATTACCTTTAACAATGGTTTTTCACGAGATCAACCAAAA-TC
1 AATGGCTTGTCAAAGGCTCAACCACAACCTTTAACAATGGTTTTTCACAAGATCAACCAAAACTC
21828196 AAA
66 AAA
*
21828199 AATGGCTTTTCAAAGGCTCAACCACAACCTTTAACAATGGTTTTTCACAAGATCAACCAAAACTC
1 AATGGCTTGTCAAAGGCTCAACCACAACCTTTAACAATGGTTTTTCACAAGATCAACCAAAACTC
21828264 AAA
66 AAA
21828267 A
1 A
21828268 CTAACTTTTC
Statistics
Matches: 62, Mismatches: 6, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
67 56 0.90
68 6 0.10
ACGTcount: A:0.38, C:0.24, G:0.12, T:0.26
Consensus pattern (68 bp):
AATGGCTTGTCAAAGGCTCAACCACAACCTTTAACAATGGTTTTTCACAAGATCAACCAAAACTC
AAA
Found at i:21828244 original size:35 final size:34
Alignment explanation
Indices: 21828125--21828259 Score: 89
Period size: 35 Copynumber: 4.0 Consensus size: 34
21828115 TTCTACCAAG
* * * * *
21828125 CTTTTACAATGGCTTGTCATAGGCTCAGCCATTAC
1 CTTTAACAATGGCTTTTCAAAGGCTCAACCA-AAC
* * *
21828160 CTTTAACAATGGTTTTTC-ACGAGATCAACCAAA-
1 CTTTAACAATGGCTTTTCAAAG-GCTCAACCAAAC
* * *
21828193 -ATCAAAAATGGCTTTTCAAAGGCTCAACCACAAC
1 CTTTAACAATGGCTTTTCAAAGGCTCAACCA-AAC
* *
21828227 CTTTAACAATGGTTTTTCACAA-GATCAACCAAA
1 CTTTAACAATGGCTTTTCA-AAGGCTCAACCAAA
21828260 ACTCAAAACT
Statistics
Matches: 75, Mismatches: 19, Indels: 13
0.70 0.18 0.12
Matches are distributed among these distances:
32 21 0.28
33 4 0.05
34 4 0.05
35 44 0.59
36 2 0.03
ACGTcount: A:0.35, C:0.24, G:0.13, T:0.29
Consensus pattern (34 bp):
CTTTAACAATGGCTTTTCAAAGGCTCAACCAAAC
Found at i:21830312 original size:26 final size:27
Alignment explanation
Indices: 21830275--21830344 Score: 76
Period size: 26 Copynumber: 2.7 Consensus size: 27
21830265 CATTATTAAG
*
21830275 CATTTTGAGCAAGT-ATTT-TCCAAAT
1 CATTTTAAGCAAGTCATTTATCCAAAT
*
21830300 CAATTTTAAGCAA-TCATTTATCCAAGT
1 C-ATTTTAAGCAAGTCATTTATCCAAAT
21830327 CATTTTGAAGCAAG-CATT
1 CATTTT-AAGCAAGTCATT
21830345 ACAAGATGTA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
25 2 0.05
26 19 0.50
27 17 0.45
ACGTcount: A:0.34, C:0.17, G:0.11, T:0.37
Consensus pattern (27 bp):
CATTTTAAGCAAGTCATTTATCCAAAT
Found at i:21840464 original size:35 final size:35
Alignment explanation
Indices: 21840425--21840503 Score: 149
Period size: 35 Copynumber: 2.3 Consensus size: 35
21840415 GAGTGCGTGT
21840425 GATGATATTGAAATGTTCGTGTAGGGAGTGCACAA
1 GATGATATTGAAATGTTCGTGTAGGGAGTGCACAA
*
21840460 GATGATATTGAAATGTTCGTGTAGGGAGTGCACAT
1 GATGATATTGAAATGTTCGTGTAGGGAGTGCACAA
21840495 GATGATATT
1 GATGATATT
21840504 TCCTTGTGCA
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
35 43 1.00
ACGTcount: A:0.30, C:0.08, G:0.30, T:0.32
Consensus pattern (35 bp):
GATGATATTGAAATGTTCGTGTAGGGAGTGCACAA
Found at i:21843392 original size:19 final size:19
Alignment explanation
Indices: 21843365--21843401 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
21843355 TTAAATTTTC
21843365 AACTAGCCGAGGGTTTCTT
1 AACTAGCCGAGGGTTTCTT
*
21843384 AACTGGCCGAGGGTTTCT
1 AACTAGCCGAGGGTTTCT
21843402 CACCAAACTT
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:0.19, C:0.22, G:0.30, T:0.30
Consensus pattern (19 bp):
AACTAGCCGAGGGTTTCTT
Found at i:21844037 original size:42 final size:42
Alignment explanation
Indices: 21843950--21844075 Score: 146
Period size: 42 Copynumber: 3.0 Consensus size: 42
21843940 TCTCCCATCG
* * * *
21843950 TCATCAGCTCATGTGCACTCCCCACT-AGCACATGGCTGGGTCA
1 TCATCAGCTTATGTGCACT-CCTACTCA-CACATAGCCGGGTCA
*
21843993 TCATCTGCTTATGTGCACTCCTACTCACACATAGCCGGGTCA
1 TCATCAGCTTATGTGCACTCCTACTCACACATAGCCGGGTCA
* * * *
21844035 TCATCGGCTTATGTACACTCTTACTCGCACATAGCCGGGTC
1 TCATCAGCTTATGTGCACTCCTACTCACACATAGCCGGGTC
21844076 CACATCAACA
Statistics
Matches: 73, Mismatches: 9, Indels: 3
0.86 0.11 0.04
Matches are distributed among these distances:
42 55 0.75
43 18 0.25
ACGTcount: A:0.21, C:0.33, G:0.19, T:0.27
Consensus pattern (42 bp):
TCATCAGCTTATGTGCACTCCTACTCACACATAGCCGGGTCA
Found at i:21849164 original size:44 final size:44
Alignment explanation
Indices: 21849104--21849198 Score: 154
Period size: 44 Copynumber: 2.2 Consensus size: 44
21849094 TGTGTAAATC
21849104 ATTTTGTGGCAGCTATGGTGACCATGGGTGTGAGGAAATTATAA
1 ATTTTGTGGCAGCTATGGTGACCATGGGTGTGAGGAAATTATAA
* * *
21849148 ATTTTGTGGCAGCTATGGTGACCATTGGTGTGAGGTAATTATGA
1 ATTTTGTGGCAGCTATGGTGACCATGGGTGTGAGGAAATTATAA
*
21849192 CTTTTGT
1 ATTTTGT
21849199 TGGGTGAAAT
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
44 47 1.00
ACGTcount: A:0.23, C:0.09, G:0.31, T:0.37
Consensus pattern (44 bp):
ATTTTGTGGCAGCTATGGTGACCATGGGTGTGAGGAAATTATAA
Found at i:21850237 original size:35 final size:35
Alignment explanation
Indices: 21850195--21850309 Score: 142
Period size: 35 Copynumber: 3.3 Consensus size: 35
21850185 TGATGTAGGC
** *
21850195 GGGAGTGCATGTGATGCTATTCAAATGTGCGTGTA
1 GGGAGTGCACATGATGATATTCAAATGTGCGTGTA
* * *
21850230 GGGAGTGCACATGATGATATTAAAATGTTCATGTA
1 GGGAGTGCACATGATGATATTCAAATGTGCGTGTA
**
21850265 GGGAGTGCACATGATGATATTTC-TTTGTGCGTGTA
1 GGGAGTGCACATGATGATA-TTCAAATGTGCGTGTA
21850300 GGGAGTGCAC
1 GGGAGTGCAC
21850310 GTGAGCTAAG
Statistics
Matches: 68, Mismatches: 11, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
35 66 0.97
36 2 0.03
ACGTcount: A:0.25, C:0.11, G:0.32, T:0.31
Consensus pattern (35 bp):
GGGAGTGCACATGATGATATTCAAATGTGCGTGTA
Found at i:21857416 original size:24 final size:23
Alignment explanation
Indices: 21857383--21857434 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 23
21857373 AGGTATTTTT
*
21857383 ATTTATTTT-ATTAGTTTAATTTA
1 ATTTATTTTAAAT-GTTTAATTTA
*
21857406 ATTTATGTTTAAATGTTTATTTTA
1 ATTTAT-TTTAAATGTTTAATTTA
21857430 ATTTA
1 ATTTA
21857435 ATAATGTTAG
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
23 6 0.24
24 17 0.68
25 2 0.08
ACGTcount: A:0.31, C:0.00, G:0.06, T:0.63
Consensus pattern (23 bp):
ATTTATTTTAAATGTTTAATTTA
Found at i:21857938 original size:32 final size:33
Alignment explanation
Indices: 21857902--21858047 Score: 120
Period size: 35 Copynumber: 4.4 Consensus size: 33
21857892 TTTATCGAGA
21857902 TCAACCAAAACC-CAAAGTGGTTTTTCAAAGGC
1 TCAACCAAAACCTCAAAGTGGTTTTTCAAAGGC
* * * **
21857934 TCAACCACAACCTTTTACAA-TGGCTTTTCACGGGC
1 TCAACCAAAACC--TCA-AAGTGGTTTTTCAAAGGC
*
21857969 TCAACCAAAACC-CAAAGTTGTTTTTCAAAGGC
1 TCAACCAAAACCTCAAAGTGGTTTTTCAAAGGC
* * * *
21858001 TCAACCACAACCTACAACAATGGTTTTTC-ACGAGA
1 TCAACCAAAACCT-CAA-AGTGGTTTTTCAAAG-GC
21858036 TCAACCAAAACC
1 TCAACCAAAACC
21858048 AAACAACTAA
Statistics
Matches: 88, Mismatches: 17, Indels: 15
0.73 0.14 0.12
Matches are distributed among these distances:
31 2 0.02
32 34 0.39
34 5 0.06
35 45 0.51
36 2 0.02
ACGTcount: A:0.36, C:0.29, G:0.12, T:0.23
Consensus pattern (33 bp):
TCAACCAAAACCTCAAAGTGGTTTTTCAAAGGC
Found at i:21857948 original size:67 final size:66
Alignment explanation
Indices: 21857875--21858047 Score: 249
Period size: 67 Copynumber: 2.6 Consensus size: 66
21857865 GCTTAGCCAA
21857875 AACCTTTCACAATGGTTTTTATCGAGATCAACCAAAACCCAAAGTGGTTTTTCAAAGGCTCAACC
1 AACCTTTCACAATGGTTTTTA-CGAGATCAACCAAAACCCAAAGTGGTTTTTCAAAGGCTCAACC
21857940 AC
65 AC
* * * * *
21857942 AACCTTTTACAATGGCTTTTCACGGGCTCAACCAAAACCCAAAGTTGTTTTTCAAAGGCTCAACC
1 AACCTTTCACAATGG-TTTTTACGAGATCAACCAAAACCCAAAGTGGTTTTTCAAAGGCTCAACC
21858007 AC
65 AC
*
21858009 AACC-TACAACAATGGTTTTTCACGAGATCAACCAAAACC
1 AACCTTTC-ACAATGGTTTTT-ACGAGATCAACCAAAACC
21858048 AAACAACTAA
Statistics
Matches: 93, Mismatches: 10, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
66 5 0.05
67 83 0.89
68 5 0.05
ACGTcount: A:0.35, C:0.27, G:0.13, T:0.25
Consensus pattern (66 bp):
AACCTTTCACAATGGTTTTTACGAGATCAACCAAAACCCAAAGTGGTTTTTCAAAGGCTCAACCA
C
Found at i:21858027 original size:35 final size:34
Alignment explanation
Indices: 21857902--21858030 Score: 122
Period size: 32 Copynumber: 3.9 Consensus size: 34
21857892 TTTATCGAGA
* *
21857902 TCAACCAAAACC-CAA-AGTGGTTTTTCAAAGGC
1 TCAACCACAACCTCAACAATGGTTTTTCAAAGGC
** * **
21857934 TCAACCACAACCTTTTACAATGGCTTTTCACGGGC
1 TCAACCACAACC-TCAACAATGGTTTTTCAAAGGC
* * *
21857969 TCAACCAAAACC-CAA-AGTTGTTTTTCAAAGGC
1 TCAACCACAACCTCAACAATGGTTTTTCAAAGGC
21858001 TCAACCACAACCTACAACAATGGTTTTTCA
1 TCAACCACAACCT-CAACAATGGTTTTTCA
21858031 CGAGATCAAC
Statistics
Matches: 73, Mismatches: 18, Indels: 9
0.73 0.18 0.09
Matches are distributed among these distances:
32 34 0.47
33 1 0.01
34 4 0.05
35 34 0.47
ACGTcount: A:0.34, C:0.28, G:0.12, T:0.26
Consensus pattern (34 bp):
TCAACCACAACCTCAACAATGGTTTTTCAAAGGC
Found at i:21858040 original size:35 final size:33
Alignment explanation
Indices: 21857883--21858053 Score: 118
Period size: 35 Copynumber: 5.1 Consensus size: 33
21857873 AAAACCTTTC
*
21857883 ACAATGGTTTTT-ATCGAGATCAACCAAAACCCA
1 ACAATGGTTTTTCA-CGAGCTCAACCAAAACCCA
* * * **
21857916 A-AGTGGTTTTTCA-AAGGCTCAACCACAACCTTTT
1 ACAATGGTTTTTCACGA-GCTCAACCAAAACC--CA
* *
21857950 ACAATGGCTTTTCACGGGCTCAACCAAAACCCA
1 ACAATGGTTTTTCACGAGCTCAACCAAAACCCA
* * * *
21857983 A-AGTTGTTTTTCA-AAGGCTCAACCACAACCTACA
1 ACAATGGTTTTTCACGA-GCTCAACCAAAACC--CA
* *
21858017 ACAATGGTTTTTCACGAGATCAACCAAAACCAA
1 ACAATGGTTTTTCACGAGCTCAACCAAAACCCA
21858050 ACAA
1 ACAA
21858054 CTAACTTTTC
Statistics
Matches: 102, Mismatches: 25, Indels: 22
0.68 0.17 0.15
Matches are distributed among these distances:
31 1 0.01
32 43 0.42
33 8 0.08
34 4 0.04
35 45 0.44
36 1 0.01
ACGTcount: A:0.37, C:0.26, G:0.13, T:0.24
Consensus pattern (33 bp):
ACAATGGTTTTTCACGAGCTCAACCAAAACCCA
Found at i:21861561 original size:20 final size:21
Alignment explanation
Indices: 21861516--21861561 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 21
21861506 AAATGTCTAA
*
21861516 AATAATTATTTGAAATGAAAT
1 AATAATTATTTGAAATAAAAT
* *
21861537 TATAATTGTTTG-AATAAAAT
1 AATAATTATTTGAAATAAAAT
21861557 AATAA
1 AATAA
21861562 CATTCAATGA
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
20 11 0.52
21 10 0.48
ACGTcount: A:0.52, C:0.00, G:0.09, T:0.39
Consensus pattern (21 bp):
AATAATTATTTGAAATAAAAT
Found at i:21862526 original size:13 final size:13
Alignment explanation
Indices: 21862508--21862533 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
21862498 TTCCAGAAAA
21862508 TTTATAAAATCAT
1 TTTATAAAATCAT
21862521 TTTATAAAATCAT
1 TTTATAAAATCAT
21862534 AATTTCTCCT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.08, G:0.00, T:0.46
Consensus pattern (13 bp):
TTTATAAAATCAT
Found at i:21863711 original size:27 final size:27
Alignment explanation
Indices: 21863660--21863711 Score: 70
Period size: 28 Copynumber: 1.9 Consensus size: 27
21863650 ATGTCCTGGT
*
21863660 GGTGGAAAATTACAATTTTGCCCCTAG
1 GGTGGAAAATTACAATTTTGACCCTAG
*
21863687 GGTGGCAAAATTACCATTTT-ACCCT
1 GGTGG-AAAATTACAATTTTGACCCT
21863712 TATACTTCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
27 9 0.41
28 13 0.59
ACGTcount: A:0.29, C:0.21, G:0.19, T:0.31
Consensus pattern (27 bp):
GGTGGAAAATTACAATTTTGACCCTAG
Found at i:21868290 original size:66 final size:67
Alignment explanation
Indices: 21868178--21868352 Score: 216
Period size: 66 Copynumber: 2.6 Consensus size: 67
21868168 GCTTAGCCAA
* *
21868178 AACCTTTCACAATGGTTTTTATCGGGATCAACCAAAACCCAAAGTGGTTTTTCAAAGGCTCAACC
1 AACCTTTCACAATGGCTTTCATCGGGATCAACCAAAACCCAAAGTGGTTTTTCAAAGGCTCAACC
21868243 AC
66 AC
*
21868245 AACCTTTCACAATGGCCTTTCA-CGGGCTC-ACCAAAA-CCATAAGTGGTTTTTCAAAGGCTCAA
1 AACCTTTCACAATGG-CTTTCATCGGGATCAACCAAAACCCA-AAGTGGTTTTTCAAAGGCTCAA
21868307 CCAC
64 CCAC
* ** *
21868311 AACC-TACAACAATAGTTTTTCA-CAGGATCAACCAAAACCCAA
1 AACCTTTC-ACAAT-GGCTTTCATCGGGATCAACCAAAACCCAA
21868353 CAACTAACTT
Statistics
Matches: 94, Mismatches: 8, Indels: 12
0.82 0.07 0.11
Matches are distributed among these distances:
65 5 0.05
66 52 0.55
67 30 0.32
68 7 0.07
ACGTcount: A:0.35, C:0.28, G:0.13, T:0.24
Consensus pattern (67 bp):
AACCTTTCACAATGGCTTTCATCGGGATCAACCAAAACCCAAAGTGGTTTTTCAAAGGCTCAACC
AC
Found at i:21869859 original size:54 final size:54
Alignment explanation
Indices: 21869795--21869986 Score: 294
Period size: 54 Copynumber: 3.6 Consensus size: 54
21869785 CATCTCGCCT
* ** *
21869795 AGCTCATGTGCATCCCTCCACATCGTGCACATAGCCGGACACCTCGTCTCACCC
1 AGCTCATGTGCATCCCCCCACATCGTGCACATAGCCGGAGTCATCGTCTCACCC
*
21869849 AGCTCATGTGCATCCCCCCACATCGTGCACATAGCTGGAGTCATCGTCTCACCC
1 AGCTCATGTGCATCCCCCCACATCGTGCACATAGCCGGAGTCATCGTCTCACCC
* * * *
21869903 AGCACATGTGTATCCCCCCACATCGTGCACATAGCCAGAGTCATCGTTTCACCC
1 AGCTCATGTGCATCCCCCCACATCGTGCACATAGCCGGAGTCATCGTCTCACCC
*
21869957 AGGTCATGTGCATCCCCCCACATCGTGCAC
1 AGCTCATGTGCATCCCCCCACATCGTGCAC
21869987 GAGCAATATC
Statistics
Matches: 125, Mismatches: 13, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
54 125 1.00
ACGTcount: A:0.21, C:0.40, G:0.18, T:0.21
Consensus pattern (54 bp):
AGCTCATGTGCATCCCCCCACATCGTGCACATAGCCGGAGTCATCGTCTCACCC
Found at i:21876856 original size:2 final size:2
Alignment explanation
Indices: 21876841--21876883 Score: 68
Period size: 2 Copynumber: 21.0 Consensus size: 2
21876831 CAAACATCTC
*
21876841 TA TA TA GTA AA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
21876884 AAAGCATACA
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
2 36 0.95
3 2 0.05
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (2 bp):
TA
Found at i:21876971 original size:54 final size:53
Alignment explanation
Indices: 21876900--21877116 Score: 256
Period size: 54 Copynumber: 4.0 Consensus size: 53
21876890 TACACCACCA
* * * *
21876900 TCTCGCCCAGCTTATATGCATCCCCCCACATCATGCACATAGTCAGACA-CCTCG
1 TCTCACCCAGCTCATATGCATCCCCCCACATCATGCACATAG-CCGA-AGCATCG
* * * *
21876954 TCTCACCCAACTCATATGCATCCCCCCACAACGTGCACATAGCCGAAGTCATCA
1 TCTCACCCAGCTCATATGCATCCCCCCACATCATGCACATAGCCGAAG-CATCG
* *
21877008 TCTCACCCAGCTCATGTGCATCCCCCCACATCATGCATATAGCCGAAGTCATCG
1 TCTCACCCAGCTCATATGCATCCCCCCACATCATGCACATAGCCGAAG-CATCG
* * * *
21877062 TCTCACCCAGCTCATGTGCATCCCCCCAAATCGTGCACATAGCCGGAGTCATCG
1 TCTCACCCAGCTCATATGCATCCCCCCACATCATGCACATAGCCGAAG-CATCG
21877116 T
1 T
21877117 GTGCATCCCC
Statistics
Matches: 143, Mismatches: 18, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
52 1 0.01
53 3 0.02
54 139 0.97
ACGTcount: A:0.25, C:0.40, G:0.14, T:0.21
Consensus pattern (53 bp):
TCTCACCCAGCTCATATGCATCCCCCCACATCATGCACATAGCCGAAGCATCG
Found at i:21877087 original size:108 final size:108
Alignment explanation
Indices: 21876898--21877114 Score: 305
Period size: 108 Copynumber: 2.0 Consensus size: 108
21876888 CATACACCAC
* * *
21876898 CATCTCGCCCAGCTTATATGCATCCCCCCACATCATGCACATAGTCAGACACCTCGTCTCACCCA
1 CATCTCACCCAGCTCATATGCATCCCCCCACATCATGCACATAGTCAGACACATCGTCTCACCCA
21876963 ACTCATATGCATCCCCCCACAA-CGTGCACATAGCCGAAGTCAT
66 ACTCATATGCATCCCCCCA-AATCGTGCACATAGCCGAAGTCAT
* * *
21877006 CATCTCACCCAGCTCATGTGCATCCCCCCACATCATGCATATAG-CCGA-AGTCATCGTCTCACC
1 CATCTCACCCAGCTCATATGCATCCCCCCACATCATGCACATAGTCAGACA--CATCGTCTCACC
* * *
21877069 CAGCTCATGTGCATCCCCCCAAATCGTGCACATAGCCGGAGTCAT
64 CAACTCATATGCATCCCCCCAAATCGTGCACATAGCCGAAGTCAT
21877114 C
1 C
21877115 GTGTGCATCC
Statistics
Matches: 97, Mismatches: 9, Indels: 6
0.87 0.08 0.05
Matches are distributed among these distances:
106 1 0.01
107 5 0.05
108 91 0.94
ACGTcount: A:0.25, C:0.40, G:0.14, T:0.21
Consensus pattern (108 bp):
CATCTCACCCAGCTCATATGCATCCCCCCACATCATGCACATAGTCAGACACATCGTCTCACCCA
ACTCATATGCATCCCCCCAAATCGTGCACATAGCCGAAGTCAT
Found at i:21880643 original size:30 final size:31
Alignment explanation
Indices: 21880609--21880671 Score: 92
Period size: 31 Copynumber: 2.1 Consensus size: 31
21880599 CACATGACGG
*
21880609 TGCCGGTGGTG-TGTGGTGTGGGAATGCACA
1 TGCCGGTGATGATGTGGTGTGGGAATGCACA
* *
21880639 TGCCGGTGATGATGTGGTGTGGGAGTGTACA
1 TGCCGGTGATGATGTGGTGTGGGAATGCACA
21880670 TG
1 TG
21880672 ATGATATTGC
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
30 10 0.34
31 19 0.66
ACGTcount: A:0.14, C:0.11, G:0.46, T:0.29
Consensus pattern (31 bp):
TGCCGGTGATGATGTGGTGTGGGAATGCACA
Found at i:21889384 original size:22 final size:22
Alignment explanation
Indices: 21889356--21889397 Score: 84
Period size: 22 Copynumber: 1.9 Consensus size: 22
21889346 AATTCTTTTG
21889356 TTGAGTCCCCTTTTAGGCTCAA
1 TTGAGTCCCCTTTTAGGCTCAA
21889378 TTGAGTCCCCTTTTAGGCTC
1 TTGAGTCCCCTTTTAGGCTC
21889398 TAACATTTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.14, C:0.29, G:0.19, T:0.38
Consensus pattern (22 bp):
TTGAGTCCCCTTTTAGGCTCAA
Found at i:21891456 original size:28 final size:29
Alignment explanation
Indices: 21891384--21891474 Score: 89
Period size: 29 Copynumber: 3.2 Consensus size: 29
21891374 CATAACATTT
* *
21891384 AGTGATCAAT-GTCCAACCCATATAACTCA
1 AGTGATCAATAAT-CAATCCATATAACTCA
* ** *
21891413 AGTAATCAATTTTCAATTCATATAACT-A
1 AGTGATCAATAATCAATCCATATAACTCA
21891441 AGTGATCAATAATCAATCCATGA-AACTCA
1 AGTGATCAATAATCAATCCAT-ATAACTCA
21891470 AGTGA
1 AGTGA
21891475 CCATTATTTC
Statistics
Matches: 51, Mismatches: 8, Indels: 6
0.78 0.12 0.09
Matches are distributed among these distances:
28 22 0.43
29 28 0.55
30 1 0.02
ACGTcount: A:0.42, C:0.20, G:0.10, T:0.29
Consensus pattern (29 bp):
AGTGATCAATAATCAATCCATATAACTCA
Found at i:21891842 original size:22 final size:22
Alignment explanation
Indices: 21891812--21891854 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
21891802 TGTGCATTGG
21891812 CACAACATGTGGAATGTTATCT
1 CACAACATGTGGAATGTTATCT
*
21891834 CACACCATGTGGAATGTTATC
1 CACAACATGTGGAATGTTATC
21891855 ATCATCATAC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.30, C:0.21, G:0.19, T:0.30
Consensus pattern (22 bp):
CACAACATGTGGAATGTTATCT
Found at i:21891891 original size:64 final size:64
Alignment explanation
Indices: 21891819--21891972 Score: 182
Period size: 64 Copynumber: 2.4 Consensus size: 64
21891809 TGGCACAACA
* ** *** * * *
21891819 TGTGGAATGTTATCTCACACCATGTGGAATGTTATCATCATCATACTTGGCGCACTTCACCATG
1 TGTGGAATGTTACCTCACACCATGTGGAATGGCATCATCATCATACTACACACAATTCACCACG
* * * * *
21891883 TGTGGAATGTTACCTCACACCCTGGGGAGTGGCATCATCATCATGCTACATACAATTCACCACG
1 TGTGGAATGTTACCTCACACCATGTGGAATGGCATCATCATCATACTACACACAATTCACCACG
21891947 TGTGGAATGTTACCTCACACCATGTG
1 TGTGGAATGTTACCTCACACCATGTG
21891973 AAAGCTCTAA
Statistics
Matches: 74, Mismatches: 16, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
64 74 1.00
ACGTcount: A:0.25, C:0.25, G:0.20, T:0.29
Consensus pattern (64 bp):
TGTGGAATGTTACCTCACACCATGTGGAATGGCATCATCATCATACTACACACAATTCACCACG
Found at i:21898421 original size:19 final size:19
Alignment explanation
Indices: 21898394--21898434 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
21898384 GCTCAAATTA
21898394 TCAACTGGCCAAGGGTTTC
1 TCAACTGGCCAAGGGTTTC
* **
21898413 TCAATTGGCTGAGGGTTTC
1 TCAACTGGCCAAGGGTTTC
21898432 TCA
1 TCA
21898435 CTAAAACCCC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.20, C:0.22, G:0.27, T:0.32
Consensus pattern (19 bp):
TCAACTGGCCAAGGGTTTC
Found at i:21898781 original size:2 final size:2
Alignment explanation
Indices: 21898774--21898800 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
21898764 TTTCTATTGC
21898774 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
21898801 CATACATAAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:21900674 original size:10 final size:10
Alignment explanation
Indices: 21900659--21900689 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
21900649 TTTTTCTCAA
*
21900659 CCCTTTGTTT
1 CCCTTTCTTT
21900669 CCCTTTCTTT
1 CCCTTTCTTT
21900679 CCCTTTCTTT
1 CCCTTTCTTT
21900689 C
1 C
21900690 TCTAGAAACC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.00, C:0.39, G:0.03, T:0.58
Consensus pattern (10 bp):
CCCTTTCTTT
Found at i:21903115 original size:20 final size:20
Alignment explanation
Indices: 21903064--21903115 Score: 86
Period size: 20 Copynumber: 2.6 Consensus size: 20
21903054 CTCCTCCACC
21903064 TTCATGCTCCCAACGCCATT
1 TTCATGCTCCCAACGCCATT
* *
21903084 TTCATCCACCCAACGCCATT
1 TTCATGCTCCCAACGCCATT
21903104 TTCATGCTCCCA
1 TTCATGCTCCCA
21903116 TGTCATTTCA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.21, C:0.42, G:0.08, T:0.29
Consensus pattern (20 bp):
TTCATGCTCCCAACGCCATT
Found at i:21903856 original size:35 final size:35
Alignment explanation
Indices: 21903775--21903882 Score: 135
Period size: 35 Copynumber: 3.1 Consensus size: 35
21903765 GGAGTGCGTG
*** **
21903775 TGATGATATTGAAATGTGCGTGTAGGGAACGCACA
1 TGATGATATTGCCTTGTGCGTGTAGGGAGTGCACA
*
21903810 TGATGATATTGCTTTGTGCGTGTAGGGAGTGCACA
1 TGATGATATTGCCTTGTGCGTGTAGGGAGTGCACA
* * *
21903845 TGATTATATTGCCTTGTGCATGTAAGGAGTGCACA
1 TGATGATATTGCCTTGTGCGTGTAGGGAGTGCACA
21903880 TGA
1 TGA
21903883 GTTGAGTAAG
Statistics
Matches: 64, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
35 64 1.00
ACGTcount: A:0.26, C:0.12, G:0.31, T:0.31
Consensus pattern (35 bp):
TGATGATATTGCCTTGTGCGTGTAGGGAGTGCACA
Found at i:21947022 original size:2 final size:2
Alignment explanation
Indices: 21947015--21947044 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
21947005 TCTATGTATG
21947015 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
21947045 CAATACNNNN
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:21947136 original size:42 final size:42
Alignment explanation
Indices: 21947085--21947165 Score: 117
Period size: 42 Copynumber: 1.9 Consensus size: 42
21947075 ACATGGTTGG
* * **
21947085 GTCATCATCGGCTTATGGGCACTTTTACTCGCACATAGCCAA
1 GTCAGCATCGGCTTATGCGCACTCCTACTCGCACATAGCCAA
*
21947127 GTCAGCATCGGCTTATGCGCTCTCCTACTCGCACATAGC
1 GTCAGCATCGGCTTATGCGCACTCCTACTCGCACATAGC
21947166 TAGGTCATTA
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
42 34 1.00
ACGTcount: A:0.21, C:0.32, G:0.20, T:0.27
Consensus pattern (42 bp):
GTCAGCATCGGCTTATGCGCACTCCTACTCGCACATAGCCAA
Found at i:21952292 original size:16 final size:16
Alignment explanation
Indices: 21952266--21952310 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 16
21952256 TTTGACAATA
21952266 AATAAAATATTATATT
1 AATAAAATATTATATT
* *
21952282 -TTAATAATATTTTATT
1 AATAA-AATATTATATT
21952298 AATAAAATATTAT
1 AATAAAATATTAT
21952311 TTTATTCCAA
Statistics
Matches: 23, Mismatches: 4, Indels: 4
0.74 0.13 0.13
Matches are distributed among these distances:
15 3 0.13
16 17 0.74
17 3 0.13
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (16 bp):
AATAAAATATTATATT
Found at i:21959246 original size:21 final size:22
Alignment explanation
Indices: 21959221--21959261 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
21959211 CCTAGTTGGA
*
21959221 AAAATTCAAGGGAA-AAGTGTG
1 AAAATTCAAGGAAACAAGTGTG
21959242 AAAATTCAAGGAAACAAGTG
1 AAAATTCAAGGAAACAAGTG
21959262 AAAAAAAGGT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.51, C:0.07, G:0.24, T:0.17
Consensus pattern (22 bp):
AAAATTCAAGGAAACAAGTGTG
Found at i:21959262 original size:20 final size:21
Alignment explanation
Indices: 21959221--21959265 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 21
21959211 CCTAGTTGGA
*
21959221 AAAATTCAAGGGAAAAGTGTG
1 AAAATTCAAGGGAAAAGAGTG
21959242 AAAATTCAA-GGAAACA-AGTG
1 AAAATTCAAGGGAAA-AGAGTG
21959262 AAAA
1 AAAA
21959266 AAAGGTAAGA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
20 12 0.55
21 10 0.45
ACGTcount: A:0.56, C:0.07, G:0.22, T:0.16
Consensus pattern (21 bp):
AAAATTCAAGGGAAAAGAGTG
Found at i:21959266 original size:21 final size:20
Alignment explanation
Indices: 21959219--21959266 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 20
21959209 ACCCTAGTTG
*
21959219 GAAAAATTCAAGGGAAAAGT
1 GAAAAATTCAAGGAAAAAGT
*
21959239 GTGAAAATTCAAGGAAACAAGT
1 G-AAAAATTCAAGGAAA-AAGT
21959261 GAAAAA
1 GAAAAA
21959267 AAGGTAAGAT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
20 1 0.04
21 17 0.74
22 5 0.22
ACGTcount: A:0.56, C:0.06, G:0.23, T:0.15
Consensus pattern (20 bp):
GAAAAATTCAAGGAAAAAGT
Found at i:21961709 original size:28 final size:27
Alignment explanation
Indices: 21961676--21961729 Score: 81
Period size: 28 Copynumber: 2.0 Consensus size: 27
21961666 ATTTGGAGTA
*
21961676 TAAGGGTAAAATGGTAATTTTGCCACCC
1 TAAGGGCAAAATGGTAATTTT-CCACCC
*
21961704 TAAGGGCAAAATTGTAATTTTCCACC
1 TAAGGGCAAAATGGTAATTTTCCACC
21961730 ACTAGAACAT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
27 5 0.21
28 19 0.79
ACGTcount: A:0.33, C:0.19, G:0.19, T:0.30
Consensus pattern (27 bp):
TAAGGGCAAAATGGTAATTTTCCACCC
Found at i:21965106 original size:12 final size:12
Alignment explanation
Indices: 21965068--21965106 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
21965058 TGTTCAACAC
21965068 TTCCTTCTTTTT
1 TTCCTTCTTTTT
* *
21965080 CTCCTTCTTTCT
1 TTCCTTCTTTTT
*
21965092 TTCCTTTTTTTT
1 TTCCTTCTTTTT
21965104 TTC
1 TTC
21965107 AATTTCACAC
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
TTCCTTCTTTTT
Found at i:21965700 original size:74 final size:74
Alignment explanation
Indices: 21965563--21965702 Score: 201
Period size: 74 Copynumber: 1.9 Consensus size: 74
21965553 AATTTCGAAG
* * *
21965563 CAAAGAAGACTTAATCGACCAAAAAGTATAGTTAGCCAACTAAAAGCTCATTGCTAGAGAATTTA
1 CAAAGAAGACTTAATCGACCAAAAAGTATAGTTAGCCAACTAAAAGCACACTGCTAGAAAATTTA
21965628 ATTACAAGA
66 ATTACAAGA
* * * *
21965637 CAAAGAAGACTTAATCGACTAAGAAGTATGGTTAGTCAACTAAAAGCACACTGTCT-GAAAATTT
1 CAAAGAAGACTTAATCGACCAAAAAGTATAGTTAGCCAACTAAAAGCACACTG-CTAGAAAATTT
21965701 AA
65 AA
21965703 ATATGAATTA
Statistics
Matches: 58, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
74 56 0.97
75 2 0.03
ACGTcount: A:0.45, C:0.16, G:0.16, T:0.24
Consensus pattern (74 bp):
CAAAGAAGACTTAATCGACCAAAAAGTATAGTTAGCCAACTAAAAGCACACTGCTAGAAAATTTA
ATTACAAGA
Found at i:21969888 original size:74 final size:75
Alignment explanation
Indices: 21969742--21969893 Score: 173
Period size: 74 Copynumber: 2.0 Consensus size: 75
21969732 AGTAAAGCAG
** * * ** *
21969742 ATTACAAAACAGAGAAGACTTAATGGACTAAAAAGTATTGTTAACCAGCTACGAGCTCACTGCTA
1 ATTACAAAACAGAGAAGACTTAATCAACTAAAAAGTATGGTTAACCAACTAAAAGCACACTGCTA
*
21969807 GAGAATTT-A
66 GAAAATTTGA
* * **
21969816 ATTACAAGACAGAGAAGACTTAATCAACTAAGAAGTATGGTTAGTCAACTAAAAGCACACTGTCT
1 ATTACAAAACAGAGAAGACTTAATCAACTAAAAAGTATGGTTAACCAACTAAAAGCACACTG-CT
21969881 A-AAAATTTGA
65 AGAAAATTTGA
21969891 ATT
1 ATT
21969894 TGAATGATTG
Statistics
Matches: 64, Mismatches: 12, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
74 57 0.89
75 7 0.11
ACGTcount: A:0.43, C:0.15, G:0.16, T:0.25
Consensus pattern (75 bp):
ATTACAAAACAGAGAAGACTTAATCAACTAAAAAGTATGGTTAACCAACTAAAAGCACACTGCTA
GAAAATTTGA
Found at i:21972194 original size:21 final size:20
Alignment explanation
Indices: 21972170--21972218 Score: 53
Period size: 21 Copynumber: 2.4 Consensus size: 20
21972160 AAGATTTTGA
21972170 AATGATGTTGCTTTGACTCTG
1 AATGATGTTG-TTTGACTCTG
* *
21972191 AATGAGAGTTGTTTGACTTTG
1 AATGA-TGTTGTTTGACTCTG
*
21972212 TATGATG
1 AATGATG
21972219 CTATCATTCT
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
20 1 0.04
21 18 0.78
22 4 0.17
ACGTcount: A:0.22, C:0.08, G:0.27, T:0.43
Consensus pattern (20 bp):
AATGATGTTGTTTGACTCTG
Found at i:21979028 original size:37 final size:37
Alignment explanation
Indices: 21978987--21979105 Score: 184
Period size: 37 Copynumber: 3.2 Consensus size: 37
21978977 TAATGTTGTG
*
21978987 TGATGATGTTAAAGTGTGCGAGTAGGGAGTGCACACC
1 TGATGATGTTAAAGTGTGCGAGTAGGGAGTGCACACA
* * * *
21979024 TGATGATGATAGAGTTTGCGAGTAAGGAGTGCACACA
1 TGATGATGTTAAAGTGTGCGAGTAGGGAGTGCACACA
*
21979061 TGATGATGTTGAAGTGTGCGAGTAGGGAGTGCACACA
1 TGATGATGTTAAAGTGTGCGAGTAGGGAGTGCACACA
21979098 TGATGATG
1 TGATGATG
21979106 ATATTGCATT
Statistics
Matches: 72, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 72 1.00
ACGTcount: A:0.29, C:0.11, G:0.35, T:0.25
Consensus pattern (37 bp):
TGATGATGTTAAAGTGTGCGAGTAGGGAGTGCACACA
Found at i:21982721 original size:58 final size:57
Alignment explanation
Indices: 21982631--21982750 Score: 168
Period size: 58 Copynumber: 2.1 Consensus size: 57
21982621 AGGGTTTCAT
* * * *
21982631 CTTTGCATACATGGCATTTATTAAATCACATAAAATAAATCTATCATATGTATACTA
1 CTTTGCATACATAGCATTTATTAAATCACATAAAATAAATCTATCACATGCAAACTA
* **
21982688 CTTTGCATTGCATAGCATTTATTAAATTGCATAAAATAAATCTATCACATGCAAACTA
1 CTTTGCA-TACATAGCATTTATTAAATCACATAAAATAAATCTATCACATGCAAACTA
21982746 CTTTG
1 CTTTG
21982751 GATGATTATG
Statistics
Matches: 55, Mismatches: 7, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
57 7 0.13
58 48 0.87
ACGTcount: A:0.38, C:0.17, G:0.08, T:0.37
Consensus pattern (57 bp):
CTTTGCATACATAGCATTTATTAAATCACATAAAATAAATCTATCACATGCAAACTA
Found at i:21984461 original size:37 final size:37
Alignment explanation
Indices: 21984414--21984525 Score: 199
Period size: 37 Copynumber: 3.0 Consensus size: 37
21984404 ATGCATTCAC
21984414 CATCATGTGTGCACTCCCTACTCGCACACTTCAACAT
1 CATCATGTGTGCACTCCCTACTCGCACACTTCAACAT
21984451 CATCATGTGTGCACTCCCTACTCGCACAC-TCAAACAT
1 CATCATGTGTGCACTCCCTACTCGCACACTTC-AACAT
*
21984488 CATCATGTGTGCATTCCCTACTCGCACACTTCAACAT
1 CATCATGTGTGCACTCCCTACTCGCACACTTCAACAT
21984525 C
1 C
21984526 CTCACACAAC
Statistics
Matches: 72, Mismatches: 1, Indels: 4
0.94 0.01 0.05
Matches are distributed among these distances:
36 2 0.03
37 68 0.94
38 2 0.03
ACGTcount: A:0.25, C:0.38, G:0.11, T:0.27
Consensus pattern (37 bp):
CATCATGTGTGCACTCCCTACTCGCACACTTCAACAT
Found at i:21984896 original size:70 final size:69
Alignment explanation
Indices: 21984783--21984921 Score: 260
Period size: 70 Copynumber: 2.0 Consensus size: 69
21984773 TGTTAATTCT
*
21984783 TTTGCTTGACTCTAACCTTAACTAATACTCCAAATGGACATGTGAGGCCTTGTTGGAACCTATAC
1 TTTGCTTGACTCTAACCTCAACTAATACTCCAAATGGACATGTGAGGCCTTGTTGGAACCTATAC
21984848 ACAC
66 ACAC
21984852 NTTTGCTTGACTCTAACCTCAACTAATACTCCAAATGGACATGTGAGGCCTTGTTGGAACCTATA
1 -TTTGCTTGACTCTAACCTCAACTAATACTCCAAATGGACATGTGAGGCCTTGTTGGAACCTATA
21984917 CACAC
65 CACAC
21984922 ACAACATCAC
Statistics
Matches: 68, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
70 68 1.00
ACGTcount: A:0.29, C:0.25, G:0.16, T:0.29
Consensus pattern (69 bp):
TTTGCTTGACTCTAACCTCAACTAATACTCCAAATGGACATGTGAGGCCTTGTTGGAACCTATAC
ACAC
Found at i:21987070 original size:180 final size:178
Alignment explanation
Indices: 21986705--21987178 Score: 496
Period size: 180 Copynumber: 2.6 Consensus size: 178
21986695 GTGTATCTTT
* *
21986705 AGGAATTTAATTCGAATAAAATTTGTCCTGATAGATAACTCATGAAAATATTCCAGAATAAATTT
1 AGGAATTTAATTCCAATAAAATTT-TCCTGATAGATAACTCATGGAAATATTCCAGAATAAATTT
* * ** * *
21986770 TCAGGATTGTAGGAGGTG-ATTTGGCCACTC-AAAAAATTCAAAAATCGTGACCTTTATCTGCAG
65 TCAGGATTTTAGGAGGTGTTTTTGG-CTGTCAAAAAAATTC-AAAACCGTGACCTTTATCTGCAA
* * * * *
21986833 GAGGCAGAATTGGTTTTTGAGTACTTTTGAAATTCTTTGTGACTAAAACTT
128 GAGGCAGAATTAGTTTGTGAGTACTTTTGAAACTATTTGTGACTAAAACTC
*
21986884 AGGAATTTAATTCCTAATAAAATTTATCCTGATAGATAACTCATGGAAATATTTCAGAATAAATT
1 AGGAATTTAATTCC-AATAAAATTT-TCCTGATAGATAACTCATGGAAATATTCCAGAATAAATT
21986949 TTCAGGATTTTAGGAGGTGTTTTTGGCTGTCAAAAAAATTCAAAACCGTGACCTTTATCTG-AAG
64 TTCAGGATTTTAGGAGGTGTTTTTGGCTGTCAAAAAAATTCAAAACCGTGACCTTTATCTGCAAG
* ** *
21987013 AGGCAG-TTTCAGTTATGT-CTTACTTTTGAAGCTATTTGGTCG-CATAAAA-TC
129 AGGCAGAATT-AGTT-TGTGAGTACTTTTGAAACTATTT-GT-GAC-TAAAACTC
* * * * * * *
21987064 AGGAATTTAATTTCCAATTAAATTTTCCTTGATATAAAACTTATGGAACA-ATTCCATAGTAACT
1 AGGAATTTAA-TTCCAATAAAATTTTCC-TGATAGATAACTCATGGAA-ATATTCCAGAATAAAT
* *** * *
21987128 TTTCAGGATATTAGGAAACGTTTGTAGCTGTCAAAAAAATTCAAAACCGTG
63 TTTCAGGATTTTAGGAGGTGTTTTTGGCTGTCAAAAAAATTCAAAACCGTG
21987179 GCTTGCTGCT
Statistics
Matches: 251, Mismatches: 33, Indels: 21
0.82 0.11 0.07
Matches are distributed among these distances:
178 2 0.01
179 41 0.16
180 183 0.73
181 25 0.10
ACGTcount: A:0.35, C:0.13, G:0.17, T:0.35
Consensus pattern (178 bp):
AGGAATTTAATTCCAATAAAATTTTCCTGATAGATAACTCATGGAAATATTCCAGAATAAATTTT
CAGGATTTTAGGAGGTGTTTTTGGCTGTCAAAAAAATTCAAAACCGTGACCTTTATCTGCAAGAG
GCAGAATTAGTTTGTGAGTACTTTTGAAACTATTTGTGACTAAAACTC
Found at i:21988779 original size:20 final size:19
Alignment explanation
Indices: 21988754--21988801 Score: 53
Period size: 20 Copynumber: 2.4 Consensus size: 19
21988744 TTGGCAATGG
21988754 AATTAATTAATGACTTC-ATC
1 AATTAATTAA--ACTTCAATC
*
21988774 AATTAATATAAATTTCAATC
1 AATTAAT-TAAACTTCAATC
21988794 AATTAATT
1 AATTAATT
21988802 TATAATCAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
19 5 0.20
20 17 0.68
21 3 0.12
ACGTcount: A:0.46, C:0.10, G:0.02, T:0.42
Consensus pattern (19 bp):
AATTAATTAAACTTCAATC
Found at i:21990403 original size:2 final size:2
Alignment explanation
Indices: 21990396--21990422 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
21990386 CGAAGGCAAT
21990396 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
21990423 TATTTTAGTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:21993100 original size:43 final size:43
Alignment explanation
Indices: 21992983--21993101 Score: 114
Period size: 43 Copynumber: 2.8 Consensus size: 43
21992973 TCATCATCCT
* * ** *
21992983 CACCAGCTCATGCGCACTCCCTACTCGCACATGGCTGGGTCAG
1 CACCGGCTTATGCGCACTCCCTACTCGCACATAACCGGGTCAG
* * * * *
21993026 CACCGGGTTATGTGTACTCCCTACTCACACATAACCGGGTCAT
1 CACCGGCTTATGCGCACTCCCTACTCGCACATAACCGGGTCAG
* *
21993069 C-CTTGGCTTATGCGCACTCCCTACTTGCACATA
1 CAC-CGGCTTATGCGCACTCCCTACTCGCACATA
21993102 GCGGAGTCAA
Statistics
Matches: 59, Mismatches: 16, Indels: 2
0.77 0.21 0.03
Matches are distributed among these distances:
42 1 0.02
43 58 0.98
ACGTcount: A:0.20, C:0.36, G:0.19, T:0.24
Consensus pattern (43 bp):
CACCGGCTTATGCGCACTCCCTACTCGCACATAACCGGGTCAG
Found at i:21995781 original size:15 final size:15
Alignment explanation
Indices: 21995761--21995791 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
21995751 TAGGATTTTC
21995761 ACACATAGACACTTT
1 ACACATAGACACTTT
21995776 ACACATAGACACTTT
1 ACACATAGACACTTT
21995791 A
1 A
21995792 TTATATTCAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.42, C:0.26, G:0.06, T:0.26
Consensus pattern (15 bp):
ACACATAGACACTTT
Found at i:21998734 original size:35 final size:32
Alignment explanation
Indices: 21998695--21998804 Score: 107
Period size: 35 Copynumber: 3.2 Consensus size: 32
21998685 ACCCAAAGTA
21998695 GTTTTTCAAAGGCTCAACCAATACCTTTCACAATG
1 GTTTTTCAAAGGCTCAACCAA-ACC--TCACAATG
**
21998730 GTTTTTCACGGGCTCAACCAAAACC-CA-AAGTG
1 GTTTTTCAAAGGCTCAACC-AAACCTCACAA-TG
*
21998762 GCTTTTCAAAGGCTCAACCACAACCTACAACAATG
1 GTTTTTCAAAGGCTCAACCA-AACCT-C-ACAATG
21998797 GTTTTTCA
1 GTTTTTCA
21998805 CGGGATCAAC
Statistics
Matches: 62, Mismatches: 6, Indels: 14
0.76 0.07 0.17
Matches are distributed among these distances:
31 3 0.05
32 24 0.39
34 1 0.02
35 30 0.48
36 4 0.06
ACGTcount: A:0.32, C:0.27, G:0.14, T:0.27
Consensus pattern (32 bp):
GTTTTTCAAAGGCTCAACCAAACCTCACAATG
Found at i:21998758 original size:67 final size:66
Alignment explanation
Indices: 21998648--21998814 Score: 239
Period size: 67 Copynumber: 2.5 Consensus size: 66
21998638 AGCTTAGCCA
* *
21998648 AAACCTTTCACAATGGTTTTT-ACCGGGATCAACTAAAACCCAAAGTAGTTTTTCAAAGGCTCAA
1 AAACCTTTCACAATGGTTTTTCA-CGGGATCAACCAAAACCCAAAGTAGCTTTTCAAAGGCTCAA
21998712 CC
65 CC
* *
21998714 AATACCTTTCACAATGGTTTTTCACGGGCTCAACCAAAACCCAAAGTGGCTTTTCAAAGGCTCAA
1 AA-ACCTTTCACAATGGTTTTTCACGGGATCAACCAAAACCCAAAGTAGCTTTTCAAAGGCTCAA
21998779 CC
65 CC
*
21998781 ACAACC-TACAACAATGGTTTTTCACGGGATCAAC
1 A-AACCTTTC-ACAATGGTTTTTCACGGGATCAAC
21998815 TGAAACCCCA
Statistics
Matches: 91, Mismatches: 6, Indels: 7
0.88 0.06 0.07
Matches are distributed among these distances:
66 4 0.04
67 85 0.93
68 2 0.02
ACGTcount: A:0.34, C:0.26, G:0.14, T:0.26
Consensus pattern (66 bp):
AAACCTTTCACAATGGTTTTTCACGGGATCAACCAAAACCCAAAGTAGCTTTTCAAAGGCTCAAC
C
Found at i:21998814 original size:35 final size:33
Alignment explanation
Indices: 21998657--21998814 Score: 117
Period size: 32 Copynumber: 4.7 Consensus size: 33
21998647 AAAACCTTTC
* *
21998657 ACAATGGTTTTT-ACCGGGATCAACTAAAACCCA
1 ACAATGGTTTTTCA-CGGGCTCAACCAAAACCCA
* * ** *
21998690 A-AGTAGTTTTTCAAAGGCTCAACCAATACCTTTC-
1 ACAATGGTTTTTCACGGGCTCAACCAAAACC---CA
21998724 ACAATGGTTTTTCACGGGCTCAACCAAAACCCA
1 ACAATGGTTTTTCACGGGCTCAACCAAAACCCA
* * ** *
21998757 A-AGTGGCTTTTCAAAGGCTCAACCACAACCTACA
1 ACAATGGTTTTTCACGGGCTCAACCAAAACC--CA
*
21998791 ACAATGGTTTTTCACGGGATCAAC
1 ACAATGGTTTTTCACGGGCTCAAC
21998815 TGAAACCCCA
Statistics
Matches: 94, Mismatches: 22, Indels: 16
0.71 0.17 0.12
Matches are distributed among these distances:
32 45 0.48
33 3 0.03
34 4 0.04
35 42 0.45
ACGTcount: A:0.34, C:0.26, G:0.15, T:0.25
Consensus pattern (33 bp):
ACAATGGTTTTTCACGGGCTCAACCAAAACCCA
Found at i:22005435 original size:80 final size:79
Alignment explanation
Indices: 22005300--22005516 Score: 267
Period size: 80 Copynumber: 2.7 Consensus size: 79
22005290 CATTATACTC
* * * * * **
22005300 AGCCCATAGTGTATATGACTATCCCAACACATATATCTCATGGCATGCT-TTTCATAATCTTGTA
1 AGCCCATAGTGTACATGA-TATCTCAACACATACATCTCATGGCAT-ATATGTCATAATCTCATA
* *
22005364 AGT-CATTCACATGCTT
64 A-TCCATCCACACGCTT
22005380 AGCCCATAGTGTACATGATATGCTCAACACATACATCTCATGGCATATATGTCATAATCTCATAA
1 AGCCCATAGTGTACATGATAT-CTCAACACATACATCTCATGGCATATATGTCATAATCTCATAA
22005445 TCCATCCACACGCTT
65 TCCATCCACACGCTT
* * *
22005460 AGCCCATAGTGTACATGACACTCTCAACACATACATCTCATGCCATACATGTCATAA
1 AGCCCATAGTGTACATGATA-TCTCAACACATACATCTCATGGCATATATGTCATAA
22005517 CCCCGTAAAT
Statistics
Matches: 121, Mismatches: 12, Indels: 8
0.86 0.09 0.06
Matches are distributed among these distances:
79 5 0.04
80 115 0.95
81 1 0.01
ACGTcount: A:0.32, C:0.27, G:0.12, T:0.30
Consensus pattern (79 bp):
AGCCCATAGTGTACATGATATCTCAACACATACATCTCATGGCATATATGTCATAATCTCATAAT
CCATCCACACGCTT
Found at i:22008757 original size:2 final size:2
Alignment explanation
Indices: 22008750--22008795 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
22008740 ATGTATGTAA
22008750 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
22008792 AT AT
1 AT AT
22008796 CAATCATCAT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:22008927 original size:42 final size:41
Alignment explanation
Indices: 22008868--22008979 Score: 136
Period size: 42 Copynumber: 2.7 Consensus size: 41
22008858 CAGCTCATAT
* *
22008868 GCACTCCCACTAGCACATGGCTGGGTCAGCATCGGCTTATGC
1 GCACTCCCACTA-CACATAGCTGGGTCAGCATCGGCTTACGC
*
22008910 GCACTCCCACTCACACATTG-TAGGGTCAGCATCGGCTTACGC
1 GCACTCCCACT-ACACATAGCT-GGGTCAGCATCGGCTTACGC
* *
22008952 GCACTCCTACTTGCACATAGCTGGGTCA
1 GCACTCCCAC-TACACATAGCTGGGTCA
22008980 ATATCATTAC
Statistics
Matches: 61, Mismatches: 5, Indels: 8
0.82 0.07 0.11
Matches are distributed among these distances:
41 1 0.02
42 57 0.93
43 3 0.05
ACGTcount: A:0.21, C:0.34, G:0.23, T:0.22
Consensus pattern (41 bp):
GCACTCCCACTACACATAGCTGGGTCAGCATCGGCTTACGC
Found at i:22013705 original size:15 final size:16
Alignment explanation
Indices: 22013679--22013708 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
22013669 TTTTTAATTT
22013679 TTAAAAATTAAAATCA
1 TTAAAAATTAAAATCA
22013695 TTAAAAA-TAAAATC
1 TTAAAAATTAAAATC
22013709 CACATAACAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.63, C:0.07, G:0.00, T:0.30
Consensus pattern (16 bp):
TTAAAAATTAAAATCA
Found at i:22013866 original size:14 final size:14
Alignment explanation
Indices: 22013847--22013903 Score: 57
Period size: 14 Copynumber: 4.1 Consensus size: 14
22013837 AATATAATTG
22013847 ATAAAAATAAATAA
1 ATAAAAATAAATAA
22013861 ATAAAAAT-AAT-A
1 ATAAAAATAAATAA
22013873 ATAACAATATAAATAGA
1 ATAA-AA-ATAAATA-A
*
22013890 A-AAAATTAAATAA
1 ATAAAAATAAATAA
22013903 A
1 A
22013904 AACTTTATCT
Statistics
Matches: 37, Mismatches: 1, Indels: 11
0.76 0.02 0.22
Matches are distributed among these distances:
12 5 0.14
13 7 0.19
14 16 0.43
15 5 0.14
16 2 0.05
17 2 0.05
ACGTcount: A:0.74, C:0.02, G:0.02, T:0.23
Consensus pattern (14 bp):
ATAAAAATAAATAA
Found at i:22014218 original size:36 final size:36
Alignment explanation
Indices: 22014137--22014253 Score: 139
Period size: 36 Copynumber: 3.3 Consensus size: 36
22014127 CGTCCCTCTN
* *
22014137 TTTTTTTTTTAAATATGATAAGAT-TAACTGACTG-
1 TTTTTTTTTTAAATATGATAAGATAAAACTGATTGA
* * * * *
22014171 CTTTTCTTTTAAACATGCTAAGATAAAATTGATTGA
1 TTTTTTTTTTAAATATGATAAGATAAAACTGATTGA
*
22014207 TTTTTTTTTTAAATATGATAAGGTAAAACTGATTGA
1 TTTTTTTTTTAAATATGATAAGATAAAACTGATTGA
*
22014243 TTTTCTTTTTA
1 TTTTTTTTTTA
22014254 GATGTTATAA
Statistics
Matches: 67, Mismatches: 14, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
34 20 0.30
35 7 0.10
36 40 0.60
ACGTcount: A:0.32, C:0.07, G:0.11, T:0.50
Consensus pattern (36 bp):
TTTTTTTTTTAAATATGATAAGATAAAACTGATTGA
Found at i:22025620 original size:17 final size:17
Alignment explanation
Indices: 22025600--22025633 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
22025590 TCCTCTTTTT
22025600 CTCGTTCCACCACATGG
1 CTCGTTCCACCACATGG
22025617 CTCGTTCCACCACATGG
1 CTCGTTCCACCACATGG
22025634 ACAACTTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.18, C:0.41, G:0.18, T:0.24
Consensus pattern (17 bp):
CTCGTTCCACCACATGG
Found at i:22031102 original size:18 final size:18
Alignment explanation
Indices: 22031059--22031102 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
22031049 TATCATTATC
*
22031059 ATCATCATATTTTCCACT
1 ATCATCATATTTTCCAAT
*
22031077 GTCATCATATTTTCCAAT
1 ATCATCATATTTTCCAAT
*
22031095 ATCCTCAT
1 ATCATCAT
22031103 CAGTATCAGA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.27, C:0.27, G:0.02, T:0.43
Consensus pattern (18 bp):
ATCATCATATTTTCCAAT
Found at i:22036178 original size:6 final size:6
Alignment explanation
Indices: 22036167--22036198 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
22036157 AGAGCAGCGT
22036167 GTTGGA GTTGGA GTTGGA GTTGGA GTTGGA GT
1 GTTGGA GTTGGA GTTGGA GTTGGA GTTGGA GT
22036199 GAGAGGGAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.16, C:0.00, G:0.50, T:0.34
Consensus pattern (6 bp):
GTTGGA
Found at i:22039748 original size:14 final size:14
Alignment explanation
Indices: 22039726--22039763 Score: 67
Period size: 14 Copynumber: 2.7 Consensus size: 14
22039716 ACTAGTATGA
*
22039726 TAACATGGCAATGC
1 TAACGTGGCAATGC
22039740 TAACGTGGCAATGC
1 TAACGTGGCAATGC
22039754 TAACGTGGCA
1 TAACGTGGCA
22039764 CTGACAAACT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.32, C:0.21, G:0.26, T:0.21
Consensus pattern (14 bp):
TAACGTGGCAATGC
Found at i:22040011 original size:15 final size:15
Alignment explanation
Indices: 22039993--22040022 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
22039983 ATGGTGTTAA
*
22039993 AATATATGTATATAT
1 AATATATATATATAT
22040008 AATATATATATATAT
1 AATATATATATATAT
22040023 TTTTTACTTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (15 bp):
AATATATATATATAT
Found at i:22041247 original size:32 final size:31
Alignment explanation
Indices: 22041211--22041270 Score: 77
Period size: 32 Copynumber: 1.9 Consensus size: 31
22041201 ATTGCCATAA
*
22041211 CATCATA-ATAGTGCCACGTGGCATTGTCACAT
1 CATCATATA-AGTGCCACATGGCA-TGTCACAT
*
22041243 CATCATGTAAGTGCCACATGGCATGTCA
1 CATCATATAAGTGCCACATGGCATGTCA
22041271 TGTCATCAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
31 5 0.20
32 19 0.76
33 1 0.04
ACGTcount: A:0.28, C:0.25, G:0.20, T:0.27
Consensus pattern (31 bp):
CATCATATAAGTGCCACATGGCATGTCACAT
Found at i:22041494 original size:35 final size:35
Alignment explanation
Indices: 22041455--22041522 Score: 100
Period size: 35 Copynumber: 1.9 Consensus size: 35
22041445 GTATTTTGAC
* *
22041455 CAAATTTAAATTTAAATAATCAAAAACAAATATCT
1 CAAATATAAACTTAAATAATCAAAAACAAATATCT
* *
22041490 CAAATATCAACTTAAATAATTAAAAACAAATAT
1 CAAATATAAACTTAAATAATCAAAAACAAATAT
22041523 TCATACAACA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
35 29 1.00
ACGTcount: A:0.59, C:0.12, G:0.00, T:0.29
Consensus pattern (35 bp):
CAAATATAAACTTAAATAATCAAAAACAAATATCT
Found at i:22041698 original size:15 final size:17
Alignment explanation
Indices: 22041680--22041712 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 17
22041670 ATTATAAACA
22041680 ATAATTT-TATAA-GTT
1 ATAATTTCTATAACGTT
22041695 ATAATTTCTATAACGTT
1 ATAATTTCTATAACGTT
22041712 A
1 A
22041713 ACACAAAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.44
16 5 0.31
17 4 0.25
ACGTcount: A:0.39, C:0.06, G:0.06, T:0.48
Consensus pattern (17 bp):
ATAATTTCTATAACGTT
Found at i:22046815 original size:17 final size:17
Alignment explanation
Indices: 22046795--22046827 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
22046785 TTCTTGATAA
22046795 AATAA-AACTCCTTATTG
1 AATAATAACT-CTTATTG
22046812 AATAATAACTCTTATT
1 AATAATAACTCTTATT
22046828 TATTATTATT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.42, C:0.15, G:0.03, T:0.39
Consensus pattern (17 bp):
AATAATAACTCTTATTG
Found at i:22047023 original size:28 final size:27
Alignment explanation
Indices: 22046992--22047138 Score: 161
Period size: 28 Copynumber: 5.1 Consensus size: 27
22046982 TTAAGACAAA
*
22046992 AAATATTTTATCTTGTCTAAATTGAGAC
1 AAATATTTT-TCTTGTCTAAATTAAGAC
*
22047020 AAATATGTTTTCTTGACTAAATTAAGAC
1 AAATAT-TTTTCTTGTCTAAATTAAGAC
*
22047048 AAAAAATATTTTTCTTGTCTTAAATTAAGGC
1 ---AAATATTTTTCTTGTC-TAAATTAAGAC
22047079 AAACATATTTTT-TTGTCTAAATTAAGACC
1 -AA-ATATTTTTCTTGTCTAAATTAAGA-C
*
22047108 AAACATGTTTTCTTGTCTAAATTAAGAC
1 AAATAT-TTTTCTTGTCTAAATTAAGAC
22047136 AAA
1 AAA
22047139 CATGTCCAAG
Statistics
Matches: 104, Mismatches: 6, Indels: 18
0.81 0.05 0.14
Matches are distributed among these distances:
27 3 0.03
28 41 0.39
29 27 0.26
30 17 0.16
31 16 0.15
ACGTcount: A:0.39, C:0.12, G:0.10, T:0.40
Consensus pattern (27 bp):
AAATATTTTTCTTGTCTAAATTAAGAC
Found at i:22047044 original size:59 final size:58
Alignment explanation
Indices: 22046980--22047143 Score: 222
Period size: 59 Copynumber: 2.8 Consensus size: 58
22046970 TCTTGTTTGT
* *
22046980 AATTAAGACAAAAAATATTTTATCTTGTCTAAATTGAGACAAATATGTTTTCTTGACTA
1 AATTAAGACAAAAAATATTTT-TCTTGTCTAAATTAAGACAAACATGTTTTCTTGACTA
* * * *
22047039 AATTAAGACAAAAAATATTTTTCTTGTCTTAAATTAAGGCAAACATATTTTTTTGTCTA
1 AATTAAGACAAAAAATATTTTTCTTGTC-TAAATTAAGACAAACATGTTTTCTTGACTA
* * *
22047098 AATTAAGACCAAACAT-GTTTTCTTGTCTAAATTAAGACAAACATGT
1 AATTAAGACAAAAAATATTTTTCTTGTCTAAATTAAGACAAACATGT
22047144 CCAAGCTGCC
Statistics
Matches: 93, Mismatches: 11, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
57 17 0.18
58 17 0.18
59 59 0.63
ACGTcount: A:0.40, C:0.12, G:0.10, T:0.38
Consensus pattern (58 bp):
AATTAAGACAAAAAATATTTTTCTTGTCTAAATTAAGACAAACATGTTTTCTTGACTA
Found at i:22047110 original size:29 final size:29
Alignment explanation
Indices: 22046980--22047141 Score: 159
Period size: 29 Copynumber: 5.6 Consensus size: 29
22046970 TCTTGTTTGT
* *
22046980 AATTAAGACAAAAAATATTTTATCTTGTCTA
1 AATTAAGACCAAACATATTTT-T-TTGTCTA
* * * * *
22047011 AATTGAGA-CAAATATGTTTTCTTGACTA
1 AATTAAGACCAAACATATTTTTTTGTCTA
* *
22047039 AATTAAGACAAAAAATATTTTTCTTGTCTTA
1 AATTAAGACCAAACATATTTTT-TTGTC-TA
*
22047070 AATTAAG-GCAAACATATTTTTTTGTCTA
1 AATTAAGACCAAACATATTTTTTTGTCTA
* *
22047098 AATTAAGACCAAACATGTTTTCTTGTCTA
1 AATTAAGACCAAACATATTTTTTTGTCTA
22047127 AATTAAGA-CAAACAT
1 AATTAAGACCAAACAT
22047142 GTCCAAGCTG
Statistics
Matches: 109, Mismatches: 18, Indels: 11
0.79 0.13 0.08
Matches are distributed among these distances:
28 29 0.27
29 40 0.37
30 24 0.22
31 16 0.15
ACGTcount: A:0.41, C:0.12, G:0.09, T:0.38
Consensus pattern (29 bp):
AATTAAGACCAAACATATTTTTTTGTCTA
Found at i:22047139 original size:28 final size:28
Alignment explanation
Indices: 22047002--22047143 Score: 176
Period size: 29 Copynumber: 4.9 Consensus size: 28
22046992 AAATATTTTA
* *
22047002 TCTTGTCTAAATTGAGACAAATATGTTT
1 TCTTGTCTAAATTAAGACAAACATGTTT
* * *
22047030 TCTTGACTAAATTAAGACAAAAAATATTTT
1 TCTTGTCTAAATTAAGAC-AAACAT-GTTT
* *
22047060 TCTTGTCTTAAATTAAGGCAAACATATTT
1 TCTTGTC-TAAATTAAGACAAACATGTTT
*
22047089 TTTTGTCTAAATTAAGACCAAACATGTTT
1 TCTTGTCTAAATTAAGA-CAAACATGTTT
22047118 TCTTGTCTAAATTAAGACAAACATGT
1 TCTTGTCTAAATTAAGACAAACATGT
22047144 CCAAGCTGCC
Statistics
Matches: 98, Mismatches: 12, Indels: 8
0.83 0.10 0.07
Matches are distributed among these distances:
28 34 0.35
29 40 0.41
30 14 0.14
31 10 0.10
ACGTcount: A:0.37, C:0.13, G:0.11, T:0.39
Consensus pattern (28 bp):
TCTTGTCTAAATTAAGACAAACATGTTT
Found at i:22048993 original size:22 final size:21
Alignment explanation
Indices: 22048968--22049008 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
22048958 AATTTATAAA
22048968 TAAAAAATAATATATAAAAAAT
1 TAAAAAATAATAT-TAAAAAAT
**
22048990 TAAAATTTAATATTAAAAA
1 TAAAAAATAATATTAAAAA
22049009 TTACTGTTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 6 0.35
22 11 0.65
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (21 bp):
TAAAAAATAATATTAAAAAAT
Found at i:22052101 original size:86 final size:86
Alignment explanation
Indices: 22051954--22052121 Score: 250
Period size: 86 Copynumber: 2.0 Consensus size: 86
22051944 ATGAAAAACA
* *
22051954 TCAAACCAGCAGCTACAAAATAATGCCCCTCAAATAGAGAGTATTTGTGACACCACATATTTGTA
1 TCAAACCAGCAGCGACAAAATAATGCCCCTCAAATACAGAGTATTTGTGACACCACATATTTGTA
*
22052019 ATACTTTCATTATGTATAACT
66 ATAATTTCATTATGTATAACT
** *
22052040 TCAAACCAGTGGCGACAAAATAATGCTCCC-CAAATACAGTGTATTTGTGACACC-CACTATTTG
1 TCAAACCAGCAGCGACAAAATAATGC-CCCTCAAATACAGAGTATTTGTGACACCACA-TATTTG
22052103 TAATAATTTCATTATGTAT
64 TAATAATTTCATTATGTAT
22052122 CTGGACACTT
Statistics
Matches: 74, Mismatches: 6, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
85 2 0.03
86 69 0.93
87 3 0.04
ACGTcount: A:0.36, C:0.21, G:0.12, T:0.31
Consensus pattern (86 bp):
TCAAACCAGCAGCGACAAAATAATGCCCCTCAAATACAGAGTATTTGTGACACCACATATTTGTA
ATAATTTCATTATGTATAACT
Found at i:22063767 original size:23 final size:23
Alignment explanation
Indices: 22063739--22063784 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
22063729 TTAATAGTAA
22063739 GAATTAATTCAATTCTTTGTGAG
1 GAATTAATTCAATTCTTTGTGAG
22063762 GAATTAATTCAATTCTTTGTGAG
1 GAATTAATTCAATTCTTTGTGAG
22063785 ATTGACACTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.30, C:0.09, G:0.17, T:0.43
Consensus pattern (23 bp):
GAATTAATTCAATTCTTTGTGAG
Found at i:22065236 original size:114 final size:114
Alignment explanation
Indices: 22065028--22065256 Score: 264
Period size: 114 Copynumber: 2.0 Consensus size: 114
22065018 TGGGCATTTA
*** * *
22065028 AGGGTTCACACTGTTTTCAACCAGTAAGGTACCTTTTGTGAGACAAAATAGTTAGGCCAAGAGAC
1 AGGGTTCACACTACCTTCAACCAGTAAGGTACCTTTTGTGAGACAAAACAGTAAGGCCAAGAGAC
* *
22065093 CAAAGTGGACAATACCACGTAAGGATTGGTGTGGACTGTGACAGTTGGT
66 CAAAGTGGACAATACCACATAAGGATTGGTGTAGACTGTGACAGTTGGT
* * * *
22065142 AGGGTTCACACTACCTTCAACCTA-TAATGTACTTTTTGTGGGACAAAACAGTAAGTCCAATG-G
1 AGGGTTCACACTACCTTCAACC-AGTAAGGTACCTTTTGTGAGACAAAACAGTAAGGCCAA-GAG
*** ** * *
22065205 ACCAAAGTGGACAATACTTTATGGGGGTTGGTGTAGATTGTGACAGTTGGT
64 ACCAAAGTGGACAATACCACATAAGGATTGGTGTAGACTGTGACAGTTGGT
22065256 A
1 A
22065257 TCAACACAGA
Statistics
Matches: 95, Mismatches: 18, Indels: 4
0.81 0.15 0.03
Matches are distributed among these distances:
114 93 0.98
115 2 0.02
ACGTcount: A:0.30, C:0.16, G:0.26, T:0.28
Consensus pattern (114 bp):
AGGGTTCACACTACCTTCAACCAGTAAGGTACCTTTTGTGAGACAAAACAGTAAGGCCAAGAGAC
CAAAGTGGACAATACCACATAAGGATTGGTGTAGACTGTGACAGTTGGT
Found at i:22065457 original size:33 final size:34
Alignment explanation
Indices: 22065389--22065460 Score: 101
Period size: 34 Copynumber: 2.1 Consensus size: 34
22065379 TCTCAATGGT
* *
22065389 TAGAGTCATAAATCCAATACCAAAGAGAAATTCC
1 TAGAGCCATAAATCCAATACCAAAGAGAAACTCC
* *
22065423 TAGAGCCATAAATCCAATATCGAA-AGAAACTCC
1 TAGAGCCATAAATCCAATACCAAAGAGAAACTCC
22065456 TAGAG
1 TAGAG
22065461 GGGAGTTAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
33 13 0.38
34 21 0.62
ACGTcount: A:0.46, C:0.21, G:0.14, T:0.19
Consensus pattern (34 bp):
TAGAGCCATAAATCCAATACCAAAGAGAAACTCC
Found at i:22067849 original size:17 final size:18
Alignment explanation
Indices: 22067827--22067862 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
22067817 TGTTATAATC
22067827 AAAATT-ATAATAATTTT
1 AAAATTAATAATAATTTT
*
22067844 AAAATTAATAATATTTTT
1 AAAATTAATAATAATTTT
22067862 A
1 A
22067863 TAACTCAAGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 6 0.35
18 11 0.65
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (18 bp):
AAAATTAATAATAATTTT
Found at i:22072667 original size:103 final size:104
Alignment explanation
Indices: 22072484--22072690 Score: 327
Period size: 103 Copynumber: 2.0 Consensus size: 104
22072474 TTTAGGGAAA
22072484 GAGAGAGAGAGAGAGGGTTTTGTCCATACCAAAGTGGGGTGTATTACAAATAGCACCGACGGGGG
1 GAGAGAGAGAGAGAGGGTTTTGTCCATACCAAAGTGGGGTGTATTACAAATAGCACCGACGGGGG
22072549 CTCTTATTTTTCTCCTTCTCTTCCTATTGTCCACCCGTCTC
66 CTCTTATTTTTCTCCTTCTCTTCC-ATTGT-CACCCGTCTC
22072590 NGAGAGAGAGAGAGAGGGTTTTGTCCAT-CCAAA-TGGGGTG-ATT-CAAATAGCACC-ACGGGG
1 -GAGAGAGAGAGAGAGGGTTTTGTCCATACCAAAGTGGGGTGTATTACAAATAGCACCGAC-GGG
22072650 GGCTC-TATTTTTTCTCCTTCTCTTCCATTGTCACCCGTCTC
64 GGCTCTTA-TTTTTCTCCTTCTCTTCCATTGTCACCCGTCTC
22072691 TCACCTAAAC
Statistics
Matches: 98, Mismatches: 0, Indels: 10
0.91 0.00 0.09
Matches are distributed among these distances:
101 10 0.10
102 9 0.09
103 37 0.38
104 3 0.03
105 7 0.07
106 5 0.05
107 27 0.28
ACGTcount: A:0.21, C:0.24, G:0.25, T:0.30
Consensus pattern (104 bp):
GAGAGAGAGAGAGAGGGTTTTGTCCATACCAAAGTGGGGTGTATTACAAATAGCACCGACGGGGG
CTCTTATTTTTCTCCTTCTCTTCCATTGTCACCCGTCTC
Found at i:22075212 original size:20 final size:20
Alignment explanation
Indices: 22075189--22075227 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
22075179 GGCGAAAAGG
*
22075189 TTTTAATCAATTAACACAAA
1 TTTTAATCAATTAAAACAAA
22075209 TTTTAATCAATTAAAACAA
1 TTTTAATCAATTAAAACAA
22075228 CATTGGAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.51, C:0.13, G:0.00, T:0.36
Consensus pattern (20 bp):
TTTTAATCAATTAAAACAAA
Found at i:22075249 original size:71 final size:71
Alignment explanation
Indices: 22075138--22075295 Score: 167
Period size: 71 Copynumber: 2.2 Consensus size: 71
22075128 TTAACTTATG
** * **
22075138 GTTTAATCAATTAAAGTAACATTGGAAGGAACTTTAAGACAGGCGAAA-AGGTTTTAATCAATTA
1 GTTTAATCAATTAAAACAACATTGGAAGGAACATTAAGACAAAC-AAAGAGGTTTTAATCAATTA
22075202 ACACAAA
65 ACACAAA
* * * * *
22075209 TTTTAATCAATTAAAACAACATTGGAA-TACACATTGAGACAAACAAAGAGTTTTTAATCGATTA
1 GTTTAATCAATTAAAACAACATTGGAAGGA-ACATTAAGACAAACAAAGAGGTTTTAATCAATTA
* *
22075273 ATACAAG
65 ACACAAA
*
22075280 GCTTAATCAATTAAAA
1 GTTTAATCAATTAAAA
22075296 TGGTACTGGA
Statistics
Matches: 71, Mismatches: 14, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
70 4 0.06
71 67 0.94
ACGTcount: A:0.46, C:0.12, G:0.13, T:0.28
Consensus pattern (71 bp):
GTTTAATCAATTAAAACAACATTGGAAGGAACATTAAGACAAACAAAGAGGTTTTAATCAATTAA
CACAAA
Done.