Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr12
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: 101062743
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 4026412 characters in sequence are not A, C, G, or T
File 135 of 297
Found at i:46294702 original size:66 final size:66
Alignment explanation
Indices: 46294596--46294719 Score: 203
Period size: 66 Copynumber: 1.9 Consensus size: 66
46294586 ACAGAAATTG
* * *
46294596 AAAATACCTCAGCGTGCCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGATGA
1 AAAATACCTCAACGTGACCTGAGGCCCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGATGA
46294661 T
66 T
* *
46294662 AAAATACCTCAATGTGACTTGAGGCCCAACTCACCTCTCGCAATATGAGTTGATTTTT
1 AAAATACCTCAACGTGACCTGAGGCCCAACTCACCTCTCGCAATATGAGTTGATTTTT
46294720 GAAACATAAA
Statistics
Matches: 53, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
66 53 1.00
ACGTcount: A:0.27, C:0.24, G:0.17, T:0.31
Consensus pattern (66 bp):
AAAATACCTCAACGTGACCTGAGGCCCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGATGA
T
Found at i:46295017 original size:71 final size:72
Alignment explanation
Indices: 46294898--46295126 Score: 286
Period size: 71 Copynumber: 3.2 Consensus size: 72
46294888 ATAAATTGAG
*
46294898 CAGAAATTGAAAATACCTCAACAG-GTCTTGAGGCTCAACTCACCTCTCGTAATATGAGTTGATT
1 CAGAAATTGAAAATACCTCAA-AGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATT
*
46294962 TTTTG-AT
65 TTTTGAAA
* * * * *
46294969 GATAAATTGAAAATACCTCAATGTGACTTGAGGTTCAACTCACCTCTCGCAATATGAGTTGATTT
1 CAGAAATTGAAAATACCTCAAAGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TT
46295034 TTTTGAAAAA
65 TTTTG--AAA
** * *
46295044 CAGAAATTGAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATAAGTTGA-TT
1 CAGAAATTGAAAATACCTCAAAGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTT
46295108 TTTGAAA
66 TTTGAAA
*
46295115 CATAAATT-AAAA
1 CAGAAATTGAAAA
46295127 CACAAAAATT
Statistics
Matches: 137, Mismatches: 16, Indels: 11
0.84 0.10 0.07
Matches are distributed among these distances:
70 5 0.04
71 64 0.47
72 7 0.05
73 6 0.04
75 55 0.40
ACGTcount: A:0.34, C:0.19, G:0.16, T:0.31
Consensus pattern (72 bp):
CAGAAATTGAAAATACCTCAAAGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTT
TTTGAAA
Found at i:46295088 original size:75 final size:72
Alignment explanation
Indices: 46294893--46295110 Score: 287
Period size: 75 Copynumber: 3.0 Consensus size: 72
46294883 AAAACATAAA
* *
46294893 TTGAGCAGAAATTGAAAATACCTCAACAG-GTCTTGAGGCTCAACTCACCTCTCGTAATATGAGT
1 TTGAACAGAAATTGAAAATACCTCAAC-GTGTCTTGAGGCTCAACTCACCTCTCGCAATATGAGT
46294957 TGA-TTTT
65 TGATTTTT
** * * * *
46294964 TTGATGATAAATTGAAAATACCTCAATGTGACTTGAGGTTCAACTCACCTCTCGCAATATGAGTT
1 TTGAACAGAAATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGAGTT
46295029 GATTTTT
66 GATTTTT
* * *
46295036 TTGAAAAACAGAAATTGAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATAA
1 TTG---AACAGAAATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGA
46295101 GTTGATTTTT
63 GTTGATTTTT
46295111 GAAACATAAA
Statistics
Matches: 126, Mismatches: 16, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
70 1 0.01
71 58 0.46
72 7 0.06
75 60 0.48
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32
Consensus pattern (72 bp):
TTGAACAGAAATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGAGTT
GATTTTT
Found at i:46295195 original size:85 final size:86
Alignment explanation
Indices: 46295039--46295290 Score: 266
Period size: 85 Copynumber: 2.9 Consensus size: 86
46295029 GATTTTTTTG
* * *
46295039 AAAAACAGAAATTGAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATAT-AAGT
1 AAAAACAGAAATTGAAAATACCTCAGCGTGACCCGAAGCTCAACTCACCTCT-GCAATATGAA-T
*
46295103 TGA--TTTTTGAAACAT-AAATT
64 TGATTTTTTTGAAAAATAAAATT
* * * *
46295123 AAAACACAAAAATTGACAATACCTCAGCGCGCCCCGAAGCTCAACTCACCTCT-CAATATGAATT
1 AAAA-ACAGAAATTGAAAATACCTCAGCGTGACCCGAAGCTCAACTCACCTCTGCAATATGAATT
* *
46295187 AATTTTTTTAAAAAATAGAAATT
65 GATTTTTTTGAAAAATA-AAATT
* *
46295210 -AAAACAGAAATTAAAAATACCTCAGCGTGTGAGCC-AAGACTCAACTCACCTCTTGCAATATGA
1 AAAAACAGAAATTGAAAATACCTCAGC--GTGACCCGAAG-CTCAACTCACCTC-TGCAATATGA
*
46295273 GTTGATTTTTTTGAAAAA
62 ATTGATTTTTTTGAAAAA
46295291 CAGAAATTGA
Statistics
Matches: 139, Mismatches: 18, Indels: 17
0.80 0.10 0.10
Matches are distributed among these distances:
83 9 0.06
84 6 0.04
85 72 0.52
86 6 0.04
87 22 0.16
88 1 0.01
89 23 0.17
ACGTcount: A:0.40, C:0.21, G:0.13, T:0.27
Consensus pattern (86 bp):
AAAAACAGAAATTGAAAATACCTCAGCGTGACCCGAAGCTCAACTCACCTCTGCAATATGAATTG
ATTTTTTTGAAAAATAAAATT
Found at i:46299247 original size:48 final size:48
Alignment explanation
Indices: 46299191--46299284 Score: 120
Period size: 48 Copynumber: 2.0 Consensus size: 48
46299181 AGGGAATTCT
* *
46299191 GTTGAATCCTTTATTGTTGCG-AGTT-GAGCTAACTTAGGCGTTTTTACG
1 GTTGAATCCATTATTGGTG-GAAGTTAG-GCTAACTTAGGCGTTTTTACG
* *
46299239 GTTGAATCCATTATTGGTGGAAGTTAGGCTGACTTAGGTGTTTTTA
1 GTTGAATCCATTATTGGTGGAAGTTAGGCTAACTTAGGCGTTTTTA
46299285 AGCCAAGAAA
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
47 1 0.03
48 38 0.95
49 1 0.03
ACGTcount: A:0.20, C:0.12, G:0.27, T:0.41
Consensus pattern (48 bp):
GTTGAATCCATTATTGGTGGAAGTTAGGCTAACTTAGGCGTTTTTACG
Found at i:46301381 original size:15 final size:15
Alignment explanation
Indices: 46301351--46301394 Score: 79
Period size: 15 Copynumber: 2.9 Consensus size: 15
46301341 TGGCCTGTCA
46301351 CATTAAGTATTTTACT
1 CATTAAGTA-TTTACT
46301367 CATTAAGTATTTACT
1 CATTAAGTATTTACT
46301382 CATTAAGTATTTA
1 CATTAAGTATTTA
46301395 AAACACATGT
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
15 19 0.68
16 9 0.32
ACGTcount: A:0.34, C:0.11, G:0.07, T:0.48
Consensus pattern (15 bp):
CATTAAGTATTTACT
Found at i:46301518 original size:39 final size:39
Alignment explanation
Indices: 46301475--46301553 Score: 140
Period size: 39 Copynumber: 2.0 Consensus size: 39
46301465 ACATAGGCAA
* *
46301475 TATGGATGAAATGAAAGATGCAATGCGTGGATAAAAATT
1 TATGGATGAAATGAAAAATGCAATGCATGGATAAAAATT
46301514 TATGGATGAAATGAAAAATGCAATGCATGGATAAAAATT
1 TATGGATGAAATGAAAAATGCAATGCATGGATAAAAATT
46301553 T
1 T
46301554 TGTATGATAA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 38 1.00
ACGTcount: A:0.46, C:0.05, G:0.23, T:0.27
Consensus pattern (39 bp):
TATGGATGAAATGAAAAATGCAATGCATGGATAAAAATT
Found at i:46308462 original size:19 final size:19
Alignment explanation
Indices: 46308438--46308477 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
46308428 AAAAAAAAAC
46308438 TTAAAACCTAGTAATGAAA
1 TTAAAACCTAGTAATGAAA
46308457 TTAAAACCTAGTAATGAAA
1 TTAAAACCTAGTAATGAAA
46308476 TT
1 TT
46308478 TAGAAAACAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.50, C:0.10, G:0.10, T:0.30
Consensus pattern (19 bp):
TTAAAACCTAGTAATGAAA
Found at i:46311420 original size:192 final size:192
Alignment explanation
Indices: 46311093--46311477 Score: 707
Period size: 192 Copynumber: 2.0 Consensus size: 192
46311083 CGAACAGGTG
*
46311093 GCAAACCCGGTAACTCTTCAGGAAAAACATCCGGGTATTCACAAACCACCGGCACAGATTCGGGT
1 GCAAACCCGGTAACTCTTCAGGAAAAACATCCGGGTATTCACAAACCACCGACACAGATTCGGGT
* * *
46311158 TTCTTTTCTAATTCTTTGTCATCAAGTACATACGCAAGGTATGCTTCGCACCCTTTTCTTACATA
66 TTCTTTTCTAACTCCTTGTCATCAAGTACATACGCAAGGTATGCTTCGCACCCTTTCCTTACATA
46311223 TTTCTGGGCCAACATTGCTGATATTACAGCTGGCAACCCCCTGAAGTCCGTAGACTCAACTC
131 TTTCTGGGCCAACATTGCTGATATTACAGCTGGCAACCCCCTGAAGTCCGTAGACTCAACTC
* *
46311285 GCAAACCCGGTAACTCTTCAGGAAAAACATCCGGGTATTCACAGACCACCGACACCGATTCGGGT
1 GCAAACCCGGTAACTCTTCAGGAAAAACATCCGGGTATTCACAAACCACCGACACAGATTCGGGT
*
46311350 TTCTTTTCTAACTCCTTGTCATCAAGTACATACGCGAGGTATGCTTCGCACCCTTTCCTTACATA
66 TTCTTTTCTAACTCCTTGTCATCAAGTACATACGCAAGGTATGCTTCGCACCCTTTCCTTACATA
46311415 TTTCTGGGCCAACATTGCTGATATTACAGCTGGCAACCCCCTGAAGTCCGTAGACTCAACTC
131 TTTCTGGGCCAACATTGCTGATATTACAGCTGGCAACCCCCTGAAGTCCGTAGACTCAACTC
46311477 G
1 G
46311478 GATTATCTCG
Statistics
Matches: 186, Mismatches: 7, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
192 186 1.00
ACGTcount: A:0.26, C:0.29, G:0.18, T:0.27
Consensus pattern (192 bp):
GCAAACCCGGTAACTCTTCAGGAAAAACATCCGGGTATTCACAAACCACCGACACAGATTCGGGT
TTCTTTTCTAACTCCTTGTCATCAAGTACATACGCAAGGTATGCTTCGCACCCTTTCCTTACATA
TTTCTGGGCCAACATTGCTGATATTACAGCTGGCAACCCCCTGAAGTCCGTAGACTCAACTC
Found at i:46314857 original size:28 final size:28
Alignment explanation
Indices: 46314794--46314944 Score: 223
Period size: 28 Copynumber: 5.4 Consensus size: 28
46314784 ATATTAAGTC
*
46314794 CGCACACTCAGTGCTATATAATC-AACT
1 CGCACACTTAGTGCTATATAATCAAACT
46314821 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
*
46314849 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
*
46314877 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
* * * *
46314905 CGCACACTTAGTGCTGTACAATTTAAACC
1 CGCACACTTAGTGCTATATAA-TCAAACT
46314934 CGCACACTTAG
1 CGCACACTTAG
46314945 CGCCAATCTC
Statistics
Matches: 115, Mismatches: 7, Indels: 2
0.93 0.06 0.02
Matches are distributed among these distances:
27 22 0.19
28 77 0.67
29 16 0.14
ACGTcount: A:0.34, C:0.28, G:0.12, T:0.26
Consensus pattern (28 bp):
CGCACACTTAGTGCTATATAATCAAACT
Found at i:46321069 original size:40 final size:40
Alignment explanation
Indices: 46321032--46321227 Score: 254
Period size: 40 Copynumber: 4.9 Consensus size: 40
46321022 GGATATAGCT
* *
46321032 ACTCGCTCAAATGCCTTCGGGACATAGCCCGGTTATAGTA
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGTTATAGTA
* *
46321072 ACTCGCACCAATGCCTTCGGGACTTAGCCCGGATT-TGGTA
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGG-TTATAGTA
* * *
46321112 ACTCCCAAAAATGCCTTCGGGACTTAGCCCGG-AATTAGTA
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGTTA-TAGTA
* * *
46321152 ACTCGCACAAATGCCATCGGGACTTAGCCCGAATT-TGGTA
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCG-GTTATAGTA
46321192 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGTTAT
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGTTAT
46321228 CATCTGAACA
Statistics
Matches: 133, Mismatches: 17, Indels: 12
0.82 0.10 0.07
Matches are distributed among these distances:
39 2 0.02
40 129 0.97
41 2 0.02
ACGTcount: A:0.25, C:0.29, G:0.22, T:0.24
Consensus pattern (40 bp):
ACTCGCACAAATGCCTTCGGGACTTAGCCCGGTTATAGTA
Found at i:46321153 original size:80 final size:80
Alignment explanation
Indices: 46321040--46321223 Score: 289
Period size: 80 Copynumber: 2.3 Consensus size: 80
46321030 CTACTCGCTC
* * * * *
46321040 AAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCACCAATGCCTTCGGGACTTAGCCCGGA
1 AAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATGCCATCGGGACTTAGCCCGAA
46321105 TTTGGTAACTCCCAA
66 TTTGGTAACTCCCAA
46321120 AAATGCCTTCGGGACTTAGCCCGGA-ATTAGTAACTCGCACAAATGCCATCGGGACTTAGCCCGA
1 AAATGCCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCACAAATGCCATCGGGACTTAGCCCGA
* *
46321184 ATTTGGTAACTCGCAC
65 ATTTGGTAACTCCCAA
46321200 AAATGCCTTCGGGACTTAGCCCGG
1 AAATGCCTTCGGGACTTAGCCCGG
46321224 TTATCATCTG
Statistics
Matches: 96, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
79 1 0.01
80 95 0.99
ACGTcount: A:0.26, C:0.28, G:0.23, T:0.23
Consensus pattern (80 bp):
AAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATGCCATCGGGACTTAGCCCGAA
TTTGGTAACTCCCAA
Found at i:46321893 original size:38 final size:38
Alignment explanation
Indices: 46321842--46321934 Score: 168
Period size: 38 Copynumber: 2.4 Consensus size: 38
46321832 TGCTTACCTA
46321842 TGGCCGAACATACACATCAACTTACGTACTCATTCATG
1 TGGCCGAACATACACATCAACTTACGTACTCATTCATG
*
46321880 TGGCCGAACATACACATCAACTTATGTACTCATTCATG
1 TGGCCGAACATACACATCAACTTACGTACTCATTCATG
*
46321918 TGGCCAAACATACACAT
1 TGGCCGAACATACACAT
46321935 ATATACACTA
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
38 53 1.00
ACGTcount: A:0.33, C:0.28, G:0.13, T:0.26
Consensus pattern (38 bp):
TGGCCGAACATACACATCAACTTACGTACTCATTCATG
Found at i:46332747 original size:21 final size:21
Alignment explanation
Indices: 46332723--46332763 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
46332713 GAGGTTTCAA
46332723 AAATAAAAAAAGAAAAAAAAC
1 AAATAAAAAAAGAAAAAAAAC
* **
46332744 AAATAGAAAATTAAAAAAAA
1 AAATAAAAAAAGAAAAAAAA
46332764 ACAGAGAGGC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.83, C:0.02, G:0.05, T:0.10
Consensus pattern (21 bp):
AAATAAAAAAAGAAAAAAAAC
Found at i:46332751 original size:15 final size:14
Alignment explanation
Indices: 46332721--46332762 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 14
46332711 TTGAGGTTTC
46332721 AAAAATAAAAAAAG
1 AAAAATAAAAAAAG
46332735 AAAAA-AAACAAATAG
1 AAAAATAAA-AAA-AG
*
46332750 AAAATTAAAAAAA
1 AAAAATAAAAAAA
46332763 AACAGAGAGG
Statistics
Matches: 24, Mismatches: 1, Indels: 6
0.77 0.03 0.19
Matches are distributed among these distances:
13 3 0.12
14 9 0.38
15 9 0.38
16 3 0.12
ACGTcount: A:0.83, C:0.02, G:0.05, T:0.10
Consensus pattern (14 bp):
AAAAATAAAAAAAG
Found at i:46334026 original size:202 final size:203
Alignment explanation
Indices: 46333661--46334172 Score: 758
Period size: 202 Copynumber: 2.5 Consensus size: 203
46333651 GCAGATCTGG
* * *
46333661 CTGAAGCAAGATCGAAGATGGTTTGGCATCCTTGTGTTTACAAGGAGCAAATCGAAGACATAGCT
1 CTGAAGC-AGATCCAAGATGGTTTAGCATCCTTGTGCTTACAAGGAGCAAATCGAAGACATAGCT
* * *
46333726 GATTTGGTTTTCGCGTGCTTACACTGAAGTAAATCTAAGATGATTTGGCATCTCTGTATTGTTAG
65 GATTTGGTTTTCGCGTG--T-CACTGAAGCAAATCTAAGATGATTTGGCATCTCTATATTGTCAG
* * * * *
46333791 AGAACGAATCGAAGTTTGGCATCTCCATATTCGACGGAGGGCAGACACATAGCAGATCCAACCTT
127 AGAACAAATCGAAGTATGGCATCTCCATATTCGACGGAGAGCAGACACATAGAAGATCCAACATT
* * *
46333856 CAAATGTTTATA
192 CAAACGATTAGA
46333868 CTGAAGCAGATCCAAGATGGTTTAGCATCCTTGTGCTTACAAGGAGCAAATCGAAGACATAGCTG
1 CTGAAGCAGATCCAAGATGGTTTAGCATCCTTGTGCTTACAAGGAGCAAATCGAAGACATAGCTG
46333933 ATTTGGTTTTCGCGTG-CACTGAAGCAAATCTAAGATGATTTGGCATCTCTATATTGTCAGAGAA
66 ATTTGGTTTTCGCGTGTCACTGAAGCAAATCTAAGATGATTTGGCATCTCTATATTGTCAGAGAA
*
46333997 CAAATCGAAGTATGGCATCTCCATATTCGACGGAGAGCAGACACATAGAAGATCTAACATTCAAA
131 CAAATCGAAGTATGGCATCTCCATATTCGACGGAGAGCAGACACATAGAAGATCCAACATTCAAA
46334062 CGATTAGA
196 CGATTAGA
* *
46334070 CTGAAGCAGATCCAAGATGATTTAGCATCCTTGTGCTTACAAGGAGTAAATCGAAGACATAG-TA
1 CTGAAGCAGATCCAAGATGGTTTAGCATCCTTGTGCTTACAAGGAGCAAATCGAAGACATAGCT-
* * *
46334134 GATTTGGCTTTCACGTGTTTACGCTGAAGCAAATCTAAG
65 GATTTGGTTTTCGCGTG--T-CACTGAAGCAAATCTAAG
46334173 CATCTCTGTA
Statistics
Matches: 280, Mismatches: 20, Indels: 11
0.90 0.06 0.04
Matches are distributed among these distances:
201 1 0.00
202 184 0.66
206 88 0.31
207 7 0.03
ACGTcount: A:0.32, C:0.18, G:0.22, T:0.28
Consensus pattern (203 bp):
CTGAAGCAGATCCAAGATGGTTTAGCATCCTTGTGCTTACAAGGAGCAAATCGAAGACATAGCTG
ATTTGGTTTTCGCGTGTCACTGAAGCAAATCTAAGATGATTTGGCATCTCTATATTGTCAGAGAA
CAAATCGAAGTATGGCATCTCCATATTCGACGGAGAGCAGACACATAGAAGATCCAACATTCAAA
CGATTAGA
Found at i:46334587 original size:20 final size:21
Alignment explanation
Indices: 46334557--46334595 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
46334547 ACCCAGCAAA
*
46334557 CCCAGACTTAAACTAGACCAG
1 CCCAGACTTAAACCAGACCAG
46334578 CCCA-ACTTAAACCAGACC
1 CCCAGACTTAAACCAGACC
46334596 CAAACAGACC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.38, C:0.38, G:0.10, T:0.13
Consensus pattern (21 bp):
CCCAGACTTAAACCAGACCAG
Found at i:46335788 original size:24 final size:25
Alignment explanation
Indices: 46335734--46335785 Score: 70
Period size: 26 Copynumber: 2.1 Consensus size: 25
46335724 TGTTATTTTT
46335734 TTATT-TTAAAAAACTATACATATA
1 TTATTATTAAAAAACTATACATATA
**
46335758 TTATTATTAAAAATACTATTTATATA
1 TTATTATTAAAAA-ACTATACATATA
46335784 TT
1 TT
46335786 TATATAAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 5 0.21
25 7 0.29
26 12 0.50
ACGTcount: A:0.46, C:0.06, G:0.00, T:0.48
Consensus pattern (25 bp):
TTATTATTAAAAAACTATACATATA
Found at i:46335817 original size:14 final size:14
Alignment explanation
Indices: 46335798--46335844 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 14
46335788 TATAAAATTT
46335798 TTATTTATCATATA
1 TTATTTATCATATA
*
46335812 TTATTT-TCCTATA
1 TTATTTATCATATA
* *
46335825 TATATTTATTATATT
1 T-TATTTATCATATA
46335840 TTATT
1 TTATT
46335845 ATATAACGTT
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
13 7 0.26
14 15 0.56
15 5 0.19
ACGTcount: A:0.30, C:0.06, G:0.00, T:0.64
Consensus pattern (14 bp):
TTATTTATCATATA
Found at i:46335867 original size:11 final size:11
Alignment explanation
Indices: 46335823--46335898 Score: 55
Period size: 11 Copynumber: 6.5 Consensus size: 11
46335813 TATTTTCCTA
*
46335823 TATATATTTAT
1 TATATTTTTAT
46335834 TATA-TTTTAT
1 TATATTTTTAT
*
46335844 TATATAACGTTTAT
1 TATAT---TTTTAT
46335858 TATATTTTTAT
1 TATATTTTTAT
*
46335869 TATATATTACTTGT
1 TATAT-TT--TTAT
*
46335883 TATTTTTTTAT
1 TATATTTTTAT
46335894 TATAT
1 TATAT
46335899 GTTATGTATA
Statistics
Matches: 51, Mismatches: 7, Indels: 14
0.71 0.10 0.19
Matches are distributed among these distances:
10 9 0.18
11 21 0.41
12 2 0.04
13 2 0.04
14 17 0.33
ACGTcount: A:0.30, C:0.03, G:0.03, T:0.64
Consensus pattern (11 bp):
TATATTTTTAT
Found at i:46335885 original size:25 final size:24
Alignment explanation
Indices: 46335830--46335898 Score: 79
Period size: 25 Copynumber: 2.8 Consensus size: 24
46335820 CTATATATAT
46335830 TTATTATA-TTTTATTATATAACG
1 TTATTATATTTTTATTATATAACG
46335853 TTTATTATATTTTTATTATATATTAC-
1 -TTATTATATTTTTATTATATA--ACG
* *
46335879 TTGTTATTTTTTTATTATAT
1 TTATTATATTTTTATTATAT
46335899 GTTATGTATA
Statistics
Matches: 40, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
24 8 0.20
25 30 0.75
27 2 0.05
ACGTcount: A:0.29, C:0.03, G:0.03, T:0.65
Consensus pattern (24 bp):
TTATTATATTTTTATTATATAACG
Found at i:46335946 original size:28 final size:29
Alignment explanation
Indices: 46335914--46335970 Score: 80
Period size: 28 Copynumber: 2.0 Consensus size: 29
46335904 GTATATCGTG
*
46335914 TATTATCCATTACATTATTTAT-GTTTTA
1 TATTATCCATTACAATATTTATAGTTTTA
* *
46335942 TATTATTCATTATAATATTTATAGTTTTA
1 TATTATCCATTACAATATTTATAGTTTTA
46335971 AAATTCGTAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
28 19 0.76
29 6 0.24
ACGTcount: A:0.32, C:0.07, G:0.04, T:0.58
Consensus pattern (29 bp):
TATTATCCATTACAATATTTATAGTTTTA
Found at i:46343614 original size:27 final size:27
Alignment explanation
Indices: 46343566--46343618 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
46343556 CCCGATATGA
* *
46343566 AAAATTACCAAAGTGCCTCTAGTTTGC
1 AAAATTACCAAAGTACCCCTAGTTTGC
46343593 AAAATTACCGAAA-TACCCCTAGTTTG
1 AAAATTACC-AAAGTACCCCTAGTTTG
46343619 TAAGATGATC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 20 0.87
28 3 0.13
ACGTcount: A:0.36, C:0.23, G:0.13, T:0.28
Consensus pattern (27 bp):
AAAATTACCAAAGTACCCCTAGTTTGC
Found at i:46346230 original size:28 final size:29
Alignment explanation
Indices: 46346176--46346254 Score: 88
Period size: 28 Copynumber: 2.8 Consensus size: 29
46346166 GCGTGAATAC
** *
46346176 AAGGTGATTTGGGCCTAGCGGGCCATAT-
1 AAGGTGATTTGGGCCTAATGGGACATATG
46346204 AAGGTGATTTGGGCCTAATGGGACATATG
1 AAGGTGATTTGGGCCTAATGGGACATATG
** * *
46346233 AATATGAATTGGGCTTAATGGG
1 AAGGTGATTTGGGCCTAATGGG
46346255 CTGAATGAAT
Statistics
Matches: 43, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
28 25 0.58
29 18 0.42
ACGTcount: A:0.27, C:0.11, G:0.34, T:0.28
Consensus pattern (29 bp):
AAGGTGATTTGGGCCTAATGGGACATATG
Found at i:46346251 original size:29 final size:28
Alignment explanation
Indices: 46346212--46346318 Score: 94
Period size: 29 Copynumber: 3.7 Consensus size: 28
46346202 ATAAGGTGAT
*
46346212 TTGGGCCTAATGGGACATATGAATATGAA
1 TTGGGCCTAATGGG-CATATGAATATAAA
*
46346241 TTGGGCTTAATGGGC-TGAATGAATATAAA
1 TTGGGCCTAATGGGCAT--ATGAATATAAA
* * *
46346270 TTGGGCCTGATGGGCCATATGAAT-GAGA
1 TTGGGCCTAATGGG-CATATGAATATAAA
46346298 TTGGGCC-AAGTGGGTCATATG
1 TTGGGCCTAA-TGGG-CATATG
46346319 CATGTATGTA
Statistics
Matches: 65, Mismatches: 8, Indels: 11
0.77 0.10 0.13
Matches are distributed among these distances:
27 2 0.03
28 20 0.31
29 41 0.63
30 1 0.02
31 1 0.02
ACGTcount: A:0.29, C:0.11, G:0.32, T:0.28
Consensus pattern (28 bp):
TTGGGCCTAATGGGCATATGAATATAAA
Found at i:46348766 original size:33 final size:33
Alignment explanation
Indices: 46348726--46348792 Score: 116
Period size: 33 Copynumber: 2.0 Consensus size: 33
46348716 GAAGCTTTGA
* *
46348726 AAGTATGTTGCAAAGGCGTGGTGTTTTGAAAGC
1 AAGTATGTTGCAAAGGCATGATGTTTTGAAAGC
46348759 AAGTATGTTGCAAAGGCATGATGTTTTGAAAGC
1 AAGTATGTTGCAAAGGCATGATGTTTTGAAAGC
46348792 A
1 A
46348793 TTTAATCTTA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.31, C:0.09, G:0.30, T:0.30
Consensus pattern (33 bp):
AAGTATGTTGCAAAGGCATGATGTTTTGAAAGC
Found at i:46349161 original size:34 final size:34
Alignment explanation
Indices: 46349123--46349199 Score: 86
Period size: 34 Copynumber: 2.3 Consensus size: 34
46349113 AGTAACAGTC
* *
46349123 CAGTAACAGT-TAGGACCTTAGCCCGA-TACAGTAT
1 CAGTAACAGTGT-GGACCTTAACCC-ATTACAGTAA
* *
46349157 CAGTAGCAGTGTGGGCCTTAACCCATTACAGTAA
1 CAGTAACAGTGTGGACCTTAACCCATTACAGTAA
46349191 CAGTAACAG
1 CAGTAACAG
46349200 AAATGCATTC
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
33 1 0.03
34 34 0.94
35 1 0.03
ACGTcount: A:0.32, C:0.23, G:0.22, T:0.22
Consensus pattern (34 bp):
CAGTAACAGTGTGGACCTTAACCCATTACAGTAA
Found at i:46365191 original size:34 final size:34
Alignment explanation
Indices: 46365148--46365231 Score: 91
Period size: 34 Copynumber: 2.5 Consensus size: 34
46365138 CAAATCAGTA
**
46365148 ACAGT-TCAGTAACAGT-TAGGATCTTAGCTTAAT
1 ACAGTATCAGTAACAGTCTAGGAT-TTAGCCCAAT
* * *
46365181 ACAGTATCAGTAGCAGTCTGGGCTTTAGCCCAAT
1 ACAGTATCAGTAACAGTCTAGGATTTAGCCCAAT
*
46365215 ACAGTAACAGTAACAGT
1 ACAGTATCAGTAACAGT
46365232 AATTCAATCA
Statistics
Matches: 42, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
33 5 0.12
34 33 0.79
35 4 0.10
ACGTcount: A:0.33, C:0.19, G:0.20, T:0.27
Consensus pattern (34 bp):
ACAGTATCAGTAACAGTCTAGGATTTAGCCCAAT
Found at i:46379766 original size:28 final size:31
Alignment explanation
Indices: 46379735--46379819 Score: 92
Period size: 31 Copynumber: 2.9 Consensus size: 31
46379725 CGAATTTTTC
* * *
46379735 ATAAAGGCTTAA-TTTTTCAAAA-T-TTCAA
1 ATAAAGGCTAAACATTTTCAAAACTAATCAA
46379763 ATAATA-GCTAAACATTTTCAAAACTAATCAA
1 ATAA-AGGCTAAACATTTTCAAAACTAATCAA
46379794 ATAAAGGCTAAACATTTT-AAAA-TAAT
1 ATAAAGGCTAAACATTTTCAAAACTAAT
46379820 TAATATAATT
Statistics
Matches: 49, Mismatches: 3, Indels: 9
0.80 0.05 0.15
Matches are distributed among these distances:
28 9 0.18
29 14 0.29
30 6 0.12
31 20 0.41
ACGTcount: A:0.49, C:0.12, G:0.06, T:0.33
Consensus pattern (31 bp):
ATAAAGGCTAAACATTTTCAAAACTAATCAA
Found at i:46379797 original size:31 final size:30
Alignment explanation
Indices: 46379759--46379828 Score: 90
Period size: 31 Copynumber: 2.3 Consensus size: 30
46379749 TTTCAAAATT
46379759 TCAAATAATA-GCTAAACATTTTCAAAACTAA
1 TCAAATAATAGGCTAAACATTTT-AAAA-TAA
46379790 TCAAATAA-AGGCTAAACATTTTAAAATAA
1 TCAAATAATAGGCTAAACATTTTAAAATAA
*
46379819 TTAATATAAT
1 TCAA-ATAAT
46379829 TATCAAATAA
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
29 6 0.17
30 9 0.26
31 20 0.57
ACGTcount: A:0.53, C:0.11, G:0.04, T:0.31
Consensus pattern (30 bp):
TCAAATAATAGGCTAAACATTTTAAAATAA
Found at i:46384120 original size:42 final size:43
Alignment explanation
Indices: 46383980--46384178 Score: 165
Period size: 43 Copynumber: 4.7 Consensus size: 43
46383970 ATTGAGATCC
* * *
46383980 CGTATAAGACCATATCTAGGATATGGCATCAGCATGTG-G-TTT
1 CGTATAAGACCATATCTGGGATATGGCATCAG-ATATGAGACTT
* * * * * * *
46384022 CGTATAAGACCATGTCTGAGACATGGCTTCAAAAATGAAACTT
1 CGTATAAGACCATATCTGGGATATGGCATCAGATATGAGACTT
*
46384065 CGTATAAGACCATATCTGGGATATGGCATC-GATATGAGACAT
1 CGTATAAGACCATATCTGGGATATGGCATCAGATATGAGACTT
* * * * * *
46384107 CGTGTAAGACCATAACTGGGTTATCAGCATC-GATATGTGA-TCC
1 CGTATAAGACCATATCTGGGATAT-GGCATCAGATATGAGACT-T
* *
46384150 CATGTAAGACCATATCTGGGATATGGCAT
1 CGTATAAGACCATATCTGGGATATGGCAT
46384179 TGAGATCTTA
Statistics
Matches: 124, Mismatches: 29, Indels: 8
0.77 0.18 0.05
Matches are distributed among these distances:
41 3 0.02
42 59 0.48
43 62 0.50
ACGTcount: A:0.32, C:0.18, G:0.23, T:0.28
Consensus pattern (43 bp):
CGTATAAGACCATATCTGGGATATGGCATCAGATATGAGACTT
Found at i:46384671 original size:317 final size:315
Alignment explanation
Indices: 46384091--46385038 Score: 1591
Period size: 317 Copynumber: 3.0 Consensus size: 315
46384081 TGGGATATGG
** *
46384091 CATCGATATGAGACATCGTGTAAGACCATAACTGGGTTATCAGCATCGATATGTGATCCCATGTA
1 CATCGATATGAGACATCGTGTAAGACCATAGTTGGGTTATCGGCATCGATATGTGATCCCATGTA
* * *
46384156 AGACCATATCTGGGATATGGCATTGAGATCTTACTATGTGTATTAGATTTCCCGAGTATCCTTTG
66 AGACCATATTTGGGATATGGCATTGACATCTTACTATGTGTATTAGATTTCCCGAGTATCCTTTA
*
46384221 GTATTCCAAGAGGTTCAACGGGTAATCCAAAGATTATGGCAAAGAAATGACAAGGTATGATCATG
131 GTATTCCAAGAGGTTCAACGGGTAATCCAAAGATTATGTCAAAGAAATGACAAGGTATGATCATG
* *
46384286 TTGGAAAGGTACAGGTATGTCCACAAAGCTCATAAATATTGAGATTATGAATTGATGAGACCTCG
196 TTGGAAAGGTACA-GTATGTACAC-AAGCTCATAAATATTGAGATTATGAATCGATGAGACCTCG
** *
46384351 GTAAGAAGTGAATGAATGTATCATGATCATGAGTTTTATAATACATTATGTAAATGA
259 GTAAGAAGTGAATGAATGTATCATGATCATGAGTTTTATTGTACACTATGTAAATGA
* *
46384408 CATCAATATGAGACATCGTGTAAGACCATAGTTGGGCTATCGGCATCGATATGTGATCCCATGTA
1 CATCGATATGAGACATCGTGTAAGACCATAGTTGGGTTATCGGCATCGATATGTGATCCCATGTA
*
46384473 AGACCATATTTGGGATATGGCCTTGACATCTTACTATGTGTATTAGATTTCCCGAGTATCCTTTA
66 AGACCATATTTGGGATATGGCATTGACATCTTACTATGTGTATTAGATTTCCCGAGTATCCTTTA
*
46384538 GTATTCCAAGAGGTTCAACGGGTAATCCAAAGATTATGTCAAAGAAATGAAAAGGTATGATCATG
131 GTATTCCAAGAGGTTCAACGGGTAATCCAAAGATTATGTCAAAGAAATGACAAGGTATGATCATG
* *
46384603 TTGGAAAGGTACATGTATGTACACAACGCTCATAAATATTGAGATTATGAATCGATAAGTCCTCG
196 TTGGAAAGGTACA-GTATGTACACAA-GCTCATAAATATTGAGATTATGAATCGATGAGACCTCG
46384668 GTAAGAAGTGAATGAATGTATCATGATCATGAGTTTTATTGTACACTATGTAAATGA
259 GTAAGAAGTGAATGAATGTATCATGATCATGAGTTTTATTGTACACTATGTAAATGA
*
46384725 CATCGATATGAGACATCGTGTAAGACCATAGTTGGGTTATCGGCATTGATATGTGATCCCATGTA
1 CATCGATATGAGACATCGTGTAAGACCATAGTTGGGTTATCGGCATCGATATGTGATCCCATGTA
* *
46384790 AGACCATATTTGGGATATGACATTGACATCTTATTATGTGTATTAGATTTCCC-AGGTATCCTTT
66 AGACCATATTTGGGATATGGCATTGACATCTTACTATGTGTATTAGATTTCCCGA-GTATCCTTT
*
46384854 AGTATTCCAAGAGGTTCAACGGGTAATCCAAAGATTATGTAAAAGAAATGACAAGGTATGATCAT
130 AGTATTCCAAGAGGTTCAACGGGTAATCCAAAGATTATGTCAAAGAAATGACAAGGTATGATCAT
* *
46384919 GTTGGAAGGGTACAG---GTACA-AAGCTCATAAATATTGAGATTATGAATCGATGAGACCTTGG
195 GTTGGAAAGGTACAGTATGTACACAAGCTCATAAATATTGAGATTATGAATCGATGAGACCTCGG
*
46384980 CAAGAAGTGAATGAATGTATCATGATCATGAGTTTTATTGTACACTATGTAAATGA
260 TAAGAAGTGAATGAATGTATCATGATCATGAGTTTTATTGTACACTATGTAAATGA
46385036 CAT
1 CAT
46385039 GATTTAAGAT
Statistics
Matches: 597, Mismatches: 32, Indels: 10
0.93 0.05 0.02
Matches are distributed among these distances:
311 94 0.16
312 2 0.00
313 5 0.01
316 4 0.01
317 492 0.82
ACGTcount: A:0.33, C:0.14, G:0.22, T:0.31
Consensus pattern (315 bp):
CATCGATATGAGACATCGTGTAAGACCATAGTTGGGTTATCGGCATCGATATGTGATCCCATGTA
AGACCATATTTGGGATATGGCATTGACATCTTACTATGTGTATTAGATTTCCCGAGTATCCTTTA
GTATTCCAAGAGGTTCAACGGGTAATCCAAAGATTATGTCAAAGAAATGACAAGGTATGATCATG
TTGGAAAGGTACAGTATGTACACAAGCTCATAAATATTGAGATTATGAATCGATGAGACCTCGGT
AAGAAGTGAATGAATGTATCATGATCATGAGTTTTATTGTACACTATGTAAATGA
Found at i:46385988 original size:20 final size:20
Alignment explanation
Indices: 46385963--46386012 Score: 82
Period size: 20 Copynumber: 2.5 Consensus size: 20
46385953 CGGGCTGAGG
*
46385963 ACACGGGTGTGTCCCAAGCC
1 ACACGGGCGTGTCCCAAGCC
*
46385983 ACACGGGCGTGTCCGAAGCC
1 ACACGGGCGTGTCCCAAGCC
46386003 ACACGGGCGT
1 ACACGGGCGT
46386013 ATGTGACCAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.20, C:0.34, G:0.34, T:0.12
Consensus pattern (20 bp):
ACACGGGCGTGTCCCAAGCC
Found at i:46386351 original size:17 final size:17
Alignment explanation
Indices: 46386329--46386362 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
46386319 AACTAACATT
*
46386329 AAAATGCAATTACAATA
1 AAAATGCAATGACAATA
46386346 AAAATGCAATGACAATA
1 AAAATGCAATGACAATA
46386363 TGCACTAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.59, C:0.12, G:0.09, T:0.21
Consensus pattern (17 bp):
AAAATGCAATGACAATA
Found at i:46390255 original size:79 final size:81
Alignment explanation
Indices: 46390153--46390336 Score: 222
Period size: 79 Copynumber: 2.3 Consensus size: 81
46390143 GCTCCTCGTT
* *
46390153 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAAT-TCGCACAAATGCCTTCGGGA-CTTAACC
1 CAAATGCCTTCGGGACTTAGCCCGGAAT-TAGT-ATCTCGCACAAATGCCTTC-GGATCTTAACC
*
46390215 CGGAT-TTAGTAAC-TCGCA
63 CGGATATT-GTAACTTAGCA
**
46390233 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCACAAATGCCTTCGGATCTTAGTCCGG
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCACAAATGCCTTCGGATCTTAACCCGG
*
46390297 ATATTGTCACTTAGCA
66 ATATTGTAACTTAGCA
46390313 C-AA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
46390337 CAGCATTCAA
Statistics
Matches: 92, Mismatches: 6, Indels: 13
0.83 0.05 0.12
Matches are distributed among these distances:
78 14 0.15
79 56 0.61
80 22 0.24
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.26
Consensus pattern (81 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCACAAATGCCTTCGGATCTTAACCCGG
ATATTGTAACTTAGCA
Found at i:46390270 original size:39 final size:41
Alignment explanation
Indices: 46390153--46390336 Score: 199
Period size: 40 Copynumber: 4.6 Consensus size: 41
46390143 GCTCCTCGTT
* *
46390153 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAAT-TCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAAT-TAGTAATCTCGCA
* *
46390193 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAA-CTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTAATCTCGCA
46390233 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGT-ATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTAATCTCGCA
* * *
46390272 CAAATGCCTTC-GGATCTTAGTCCGGATATT-GTCA-CTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGA-ATTAGTAATC-TCGCA
46390313 C-AA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
46390337 CAGCATTCAA
Statistics
Matches: 128, Mismatches: 7, Indels: 19
0.83 0.05 0.12
Matches are distributed among these distances:
38 3 0.02
39 48 0.38
40 66 0.52
41 11 0.09
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.26
Consensus pattern (41 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATTAGTAATCTCGCA
Found at i:46391478 original size:20 final size:21
Alignment explanation
Indices: 46391431--46391478 Score: 57
Period size: 20 Copynumber: 2.4 Consensus size: 21
46391421 AAATTGTCAG
*
46391431 CATAATAATAAAAATCATTCC
1 CATAAAAATAAAAATCATTCC
46391452 CAT-AAAATAAGAAATCA-T-C
1 CATAAAAATAA-AAATCATTCC
46391471 CATAAAAA
1 CATAAAAA
46391479 CCTCTAAAGA
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
19 4 0.17
20 11 0.46
21 9 0.38
ACGTcount: A:0.58, C:0.17, G:0.02, T:0.23
Consensus pattern (21 bp):
CATAAAAATAAAAATCATTCC
Found at i:46395049 original size:40 final size:40
Alignment explanation
Indices: 46394999--46395268 Score: 354
Period size: 40 Copynumber: 6.8 Consensus size: 40
46394989 GATATAGCTC
* *
46394999 CTCGCTCAAATGCCTTCGGGACATAGCCCGG-TTATAGTAA
1 CTCGCACAAATGCCTTCGGGACTTAGCCCGGATT-TAGTAA
* *
46395039 TTCGCACAAATGCCTTCGGGACTTAACCCGGATTTAGTAA
1 CTCGCACAAATGCCTTCGGGACTTAGCCCGGATTTAGTAA
*
46395079 CTCGCACAAATGCCTTCGGGACTTAACCCGGATTTAGTAA
1 CTCGCACAAATGCCTTCGGGACTTAGCCCGGATTTAGTAA
* *
46395119 CTCGAACAAATGCCTTCGGGACTTAACCCGGATTTAGTAA
1 CTCGCACAAATGCCTTCGGGACTTAGCCCGGATTTAGTAA
* *
46395159 CTCGCACAAATGCCTTCGGG-CTTAGCCCGGAATTAGTAT
1 CTCGCACAAATGCCTTCGGGACTTAGCCCGGATTTAGTAA
* *
46395198 CTCGCACAAATGCCTTC-GGATCTTAGTCCGGATATT-GTCA
1 CTCGCACAAATGCCTTCGGGA-CTTAGCCCGGAT-TTAGTAA
*
46395238 CTTAGCAC-AA-GCCTTCGGGACTTAGCCCGGA
1 C-TCGCACAAATGCCTTCGGGACTTAGCCCGGA
46395269 CAGCATTCAA
Statistics
Matches: 208, Mismatches: 16, Indels: 13
0.88 0.07 0.05
Matches are distributed among these distances:
38 2 0.01
39 49 0.24
40 148 0.71
41 9 0.04
ACGTcount: A:0.26, C:0.27, G:0.21, T:0.26
Consensus pattern (40 bp):
CTCGCACAAATGCCTTCGGGACTTAGCCCGGATTTAGTAA
Found at i:46396365 original size:14 final size:14
Alignment explanation
Indices: 46396346--46396372 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
46396336 AGGATGAGCA
46396346 TTTTTTTTTCTTTG
1 TTTTTTTTTCTTTG
46396360 TTTTTTTTTCTTT
1 TTTTTTTTTCTTT
46396373 CTAGTTTCGG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.00, C:0.07, G:0.04, T:0.89
Consensus pattern (14 bp):
TTTTTTTTTCTTTG
Found at i:46396964 original size:20 final size:21
Alignment explanation
Indices: 46396917--46396964 Score: 57
Period size: 20 Copynumber: 2.4 Consensus size: 21
46396907 AAATTGTCAG
*
46396917 CATAATAATAAAAATCATTCC
1 CATAAAAATAAAAATCATTCC
46396938 CAT-AAAATAAGAAATCA-T-C
1 CATAAAAATAA-AAATCATTCC
46396957 CATAAAAA
1 CATAAAAA
46396965 CCTCTAAAGA
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
19 4 0.17
20 11 0.46
21 9 0.38
ACGTcount: A:0.58, C:0.17, G:0.02, T:0.23
Consensus pattern (21 bp):
CATAAAAATAAAAATCATTCC
Found at i:46402495 original size:42 final size:41
Alignment explanation
Indices: 46402448--46402531 Score: 141
Period size: 42 Copynumber: 2.0 Consensus size: 41
46402438 ACTGCTACTG
* *
46402448 AGATCTCTTTCGATGTCCTACAATTGATTAGCACAGTTCTT
1 AGATCTCTTCCGATGTCCTACAATCGATTAGCACAGTTCTT
46402489 NAGATCTCTTCCGATGTCCTACAATCGATTAGCACAGTTCTT
1 -AGATCTCTTCCGATGTCCTACAATCGATTAGCACAGTTCTT
46402531 A
1 A
46402532 TTTACAAACC
Statistics
Matches: 40, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
41 1 0.03
42 39 0.98
ACGTcount: A:0.25, C:0.24, G:0.14, T:0.36
Consensus pattern (41 bp):
AGATCTCTTCCGATGTCCTACAATCGATTAGCACAGTTCTT
Found at i:46406726 original size:30 final size:30
Alignment explanation
Indices: 46406685--46406745 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
46406675 CATGGAAGCT
* *
46406685 CTTCTGAAAAAAGATCCCAGAATTCCCTAA
1 CTTCCGAAAAAACATCCCAGAATTCCCTAA
**
46406715 CTTCCGAAAAAACATCCTGGAATTCCCTAA
1 CTTCCGAAAAAACATCCCAGAATTCCCTAA
46406745 C
1 C
46406746 AGTTCTGATG
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.38, C:0.30, G:0.10, T:0.23
Consensus pattern (30 bp):
CTTCCGAAAAAACATCCCAGAATTCCCTAA
Found at i:46410727 original size:39 final size:40
Alignment explanation
Indices: 46410576--46410745 Score: 191
Period size: 40 Copynumber: 4.3 Consensus size: 40
46410566 GGACTAAGAT
* * * * *
46410576 CCGAAGGCATTTGTGCGAGATAC-AAATTCTGGGTTAAGCC
1 CCGAAGGCATTCGTGCGAGTTACTAAA-TCCGGGTTATGTC
* * * * *
46410616 CCGAAGGCCTTTGTCCGAGATACTAAATCCGGGTTAAGTC
1 CCGAAGGCATTCGTGCGAGTTACTAAATCCGGGTTATGTC
*
46410656 CCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTATGTC
1 CCGAAGGCATTCGTGCGAGTTACTAAATCCGGGTTATGTC
* * *
46410696 CCGAAGGCATT-GTGTGAGTTACTAAAACCGGGCTATGTC
1 CCGAAGGCATTCGTGCGAGTTACTAAATCCGGGTTATGTC
46410735 CCGAAGGCATT
1 CCGAAGGCATT
46410746 TGAACGAGGA
Statistics
Matches: 115, Mismatches: 14, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
39 35 0.30
40 77 0.67
41 3 0.03
ACGTcount: A:0.25, C:0.22, G:0.27, T:0.26
Consensus pattern (40 bp):
CCGAAGGCATTCGTGCGAGTTACTAAATCCGGGTTATGTC
Found at i:46416939 original size:40 final size:40
Alignment explanation
Indices: 46416879--46417027 Score: 226
Period size: 40 Copynumber: 3.7 Consensus size: 40
46416869 TGAGCATTGG
46416879 AATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTT
1 AATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTT
* * *
46416919 AATATGTCCGGGCTATGACCCGAAGGCAATTATGCGAGAT
1 AATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTT
* *
46416959 GATATATCCGGGCTAAGACCCGAAGGCAATTATGCAAGTT
1 AATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTT
* * *
46416999 GATATGTCCGGGTTAAGACCCGAAGGCAA
1 AATATATCCGGGCTAAGACCCGAAGGCAA
46417028 ATGTGTTTGC
Statistics
Matches: 99, Mismatches: 10, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
40 99 1.00
ACGTcount: A:0.32, C:0.20, G:0.27, T:0.21
Consensus pattern (40 bp):
AATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTT
Found at i:46417019 original size:80 final size:80
Alignment explanation
Indices: 46416880--46417027 Score: 260
Period size: 80 Copynumber: 1.9 Consensus size: 80
46416870 GAGCATTGGA
* *
46416880 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTAATATGTCCGGGCTATGACCCGAAGG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCAAGTTAATATGTCCGGGCTAAGACCCGAAGG
46416945 CAATTATGCGAGATG
66 CAATTATGCGAGATG
* *
46416960 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCAAGTTGATATGTCCGGGTTAAGACCCGAAGG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCAAGTTAATATGTCCGGGCTAAGACCCGAAGG
46417025 CAA
66 CAA
46417028 ATGTGTTTGC
Statistics
Matches: 64, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
80 64 1.00
ACGTcount: A:0.31, C:0.20, G:0.27, T:0.22
Consensus pattern (80 bp):
ATATATCCGGGCTAAGACCCGAAGGCAATTATGCAAGTTAATATGTCCGGGCTAAGACCCGAAGG
CAATTATGCGAGATG
Found at i:46421398 original size:17 final size:16
Alignment explanation
Indices: 46421365--46421424 Score: 50
Period size: 16 Copynumber: 3.7 Consensus size: 16
46421355 AGGAGAAAGT
*
46421365 GAAAAAAAAAACCAAA
1 GAAAAAAAAAACAAAA
*
46421381 GAAAAAAGAAACAAAAA
1 GAAAAAAAAAAC-AAAA
* *
46421398 GAAGAAAAATA-AAAA
1 GAAAAAAAAAACAAAA
*
46421413 TAAAAATAAAAA
1 GAAAAA-AAAAA
46421425 TAAATAAATA
Statistics
Matches: 34, Mismatches: 8, Indels: 4
0.74 0.17 0.09
Matches are distributed among these distances:
15 8 0.24
16 15 0.44
17 11 0.32
ACGTcount: A:0.82, C:0.05, G:0.08, T:0.05
Consensus pattern (16 bp):
GAAAAAAAAAACAAAA
Found at i:46421425 original size:6 final size:6
Alignment explanation
Indices: 46421402--46421428 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
46421392 CAAAAAGAAG
46421402 AAAAAT AAAAAT AAAAAT AAAAAT AAA
1 AAAAAT AAAAAT AAAAAT AAAAAT AAA
46421429 TAAATAAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (6 bp):
AAAAAT
Found at i:46424202 original size:30 final size:31
Alignment explanation
Indices: 46424118--46424205 Score: 92
Period size: 30 Copynumber: 2.9 Consensus size: 31
46424108 TCCATCACTA
*
46424118 AAAATTATTTAAAAGATAGGTGATCAAATTG
1 AAAATTATTTAAAAGATAGGTGACCAAATTG
* * * **
46424149 TAAATT-TTTCAAAGTTAAATGACCTAAA-T-
1 AAAATTATTTAAAAGATAGGTGACC-AAATTG
46424178 AAAATTATTTAAAAGATAGGTGACCAAA
1 AAAATTATTTAAAAGATAGGTGACCAAA
46424206 AGTTTAATTT
Statistics
Matches: 44, Mismatches: 11, Indels: 6
0.72 0.18 0.10
Matches are distributed among these distances:
29 8 0.18
30 28 0.64
31 8 0.18
ACGTcount: A:0.49, C:0.07, G:0.12, T:0.32
Consensus pattern (31 bp):
AAAATTATTTAAAAGATAGGTGACCAAATTG
Found at i:46437367 original size:7 final size:7
Alignment explanation
Indices: 46437355--46437396 Score: 52
Period size: 7 Copynumber: 6.3 Consensus size: 7
46437345 TTCATATAAA
46437355 ATCATAT
1 ATCATAT
46437362 ATCATAT
1 ATCATAT
46437369 ATC-TAT
1 ATCATAT
46437375 ATC-TAT
1 ATCATAT
*
46437381 ATAATAT
1 ATCATAT
*
46437388 ATCTTAT
1 ATCATAT
46437395 AT
1 AT
46437397 GGTGCAACTC
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
6 11 0.35
7 20 0.65
ACGTcount: A:0.40, C:0.12, G:0.00, T:0.48
Consensus pattern (7 bp):
ATCATAT
Found at i:46437381 original size:19 final size:20
Alignment explanation
Indices: 46437359--46437396 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
46437349 TATAAAATCA
*
46437359 TATATCATATATC-TATATC
1 TATATAATATATCTTATATC
46437378 TATATAATATATCTTATAT
1 TATATAATATATCTTATAT
46437397 GGTGCAACTC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.39, C:0.11, G:0.00, T:0.50
Consensus pattern (20 bp):
TATATAATATATCTTATATC
Found at i:46437997 original size:15 final size:16
Alignment explanation
Indices: 46437979--46438016 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
46437969 TTAAATAAAA
*
46437979 TATAATTCA-TTAATT
1 TATAATTAATTTAATT
46437994 TATAATTAATTTAATT
1 TATAATTAATTTAATT
*
46438010 TAAAATT
1 TATAATT
46438017 TTTAAATTGC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
15 8 0.40
16 12 0.60
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.53
Consensus pattern (16 bp):
TATAATTAATTTAATT
Found at i:46438708 original size:100 final size:100
Alignment explanation
Indices: 46438533--46438718 Score: 309
Period size: 100 Copynumber: 1.9 Consensus size: 100
46438523 ACCGTTGGAA
*
46438533 TTGGGGACCCTTCCATATTTACGTTTACAACATTCTAGACATTTCCCGTATCGTTTACAAAATTT
1 TTGGGGACCCTTCCATATTTACGTTTACAACATTCTAGACATTTCCCATATCGTTTACAAAATTT
*
46438598 TACTTTTCTATTATAAAACAAAATAGCTTTCGTGT
66 TACTTCTCTATTATAAAACAAAATAGCTTTCGTGT
* * * *
46438633 TTGGGTACCCTTTCATATTTGCGTTTACAACATTCTAGATATTTCCCATATCGTTTACAAAATTT
1 TTGGGGACCCTTCCATATTTACGTTTACAACATTCTAGACATTTCCCATATCGTTTACAAAATTT
*
46438698 TCCTTCTCTATTATAAAACAA
66 TACTTCTCTATTATAAAACAA
46438719 GTTTTTTTTT
Statistics
Matches: 79, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
100 79 1.00
ACGTcount: A:0.29, C:0.20, G:0.10, T:0.41
Consensus pattern (100 bp):
TTGGGGACCCTTCCATATTTACGTTTACAACATTCTAGACATTTCCCATATCGTTTACAAAATTT
TACTTCTCTATTATAAAACAAAATAGCTTTCGTGT
Found at i:46455419 original size:46 final size:46
Alignment explanation
Indices: 46455368--46456221 Score: 1665
Period size: 46 Copynumber: 18.6 Consensus size: 46
46455358 CGAGGGCTAG
46455368 TGTAAGACATGTCTGGGACATGCATCAGCCTCGGGACGTAAGCCAA
1 TGTAAGACATGTCTGGGACATGCATCAGCCTCGGGACGTAAGCCAA
* * *
46455414 TGTAAGACATGTCTGGGACATGCATC-GGCTACGAGATGTAAGCCAA
1 TGTAAGACATGTCTGGGACATGCATCAGCCT-CGGGACGTAAGCCAA
46455460 TGTAAGACATGTCTGGGACATGCATCAGCCTCGGGACGTAAGCCAA
1 TGTAAGACATGTCTGGGACATGCATCAGCCTCGGGACGTAAGCCAA
46455506 TGTAAGACATGTCTGGGACATGCATCAGCCTCGGGACGTAAGCCAA
1 TGTAAGACATGTCTGGGACATGCATCAGCCTCGGGACGTAAGCCAA
46455552 TGTAAGACATGTCTGGGACATGCATCAGCCTCGGGACGTAAGCCAA
1 TGTAAGACATGTCTGGGACATGCATCAGCCTCGGGACGTAAGCCAA
46455598 TGTAAGACATGTCTGGGACATGCATCAGCCTCGGGACGTAAGCCAA
1 TGTAAGACATGTCTGGGACATGCATCAGCCTCGGGACGTAAGCCAA
46455644 TGTAAGACATGTCTGGGACATGCATCAGCCTCGGGACGTAAGCCAA
1 TGTAAGACATGTCTGGGACATGCATCAGCCTCGGGACGTAAGCCAA
46455690 TGTAAGACATGTCTGGGACATGCATCAGCCTCGGGACGTAAGCCAA
1 TGTAAGACATGTCTGGGACATGCATCAGCCTCGGGACGTAAGCCAA
46455736 TGTAAGACATGTCTGGGACATGCATCAGCCTCGGGACGTAAGCCAA
1 TGTAAGACATGTCTGGGACATGCATCAGCCTCGGGACGTAAGCCAA
46455782 TGTAAGACATGTCTGGGACATGCATCAGCCTCGGGACGTAAGCCAA
1 TGTAAGACATGTCTGGGACATGCATCAGCCTCGGGACGTAAGCCAA
46455828 TGTAAGACATGTCTGGGACATGCATCAGCCTCGGGACGTAAGCCAA
1 TGTAAGACATGTCTGGGACATGCATCAGCCTCGGGACGTAAGCCAA
46455874 TGTAAGACATGTCTGGGACATGCATCAGCCTCGGGACGTAAGCCAA
1 TGTAAGACATGTCTGGGACATGCATCAGCCTCGGGACGTAAGCCAA
46455920 TGTAAGACATGTCTGGGACATGCATCAGCCTCGGGACGTAAGCCAA
1 TGTAAGACATGTCTGGGACATGCATCAGCCTCGGGACGTAAGCCAA
46455966 TGTAAGACATGTCTGGGACATGCATCAGCCTCGGGACGTAAGCCAA
1 TGTAAGACATGTCTGGGACATGCATCAGCCTCGGGACGTAAGCCAA
46456012 TGTAAGACATGTCTGGGACATGCATCAGCCTCGGGACGTAAGCCAA
1 TGTAAGACATGTCTGGGACATGCATCAGCCTCGGGACGTAAGCCAA
46456058 TGTAAGACATGTCTGGGACATGCATCAGCCTCGGGACGTAAGCCAA
1 TGTAAGACATGTCTGGGACATGCATCAGCCTCGGGACGTAAGCCAA
46456104 TGTAAGACATGTCTGGGACATGCATCAGCCTCGGGACGTAAGCCAA
1 TGTAAGACATGTCTGGGACATGCATCAGCCTCGGGACGTAAGCCAA
46456150 TGTAAGACATGTCTGGGACATGCATCAGCCTCGGGACGTAAGCCAA
1 TGTAAGACATGTCTGGGACATGCATCAGCCTCGGGACGTAAGCCAA
46456196 TGTAAGACATGTCTGGGACATGCATC
1 TGTAAGACATGTCTGGGACATGCATC
46456222 GGCTACGAGA
Statistics
Matches: 800, Mismatches: 6, Indels: 4
0.99 0.01 0.00
Matches are distributed among these distances:
45 3 0.00
46 794 0.99
47 3 0.00
ACGTcount: A:0.28, C:0.24, G:0.28, T:0.20
Consensus pattern (46 bp):
TGTAAGACATGTCTGGGACATGCATCAGCCTCGGGACGTAAGCCAA
Found at i:46459848 original size:27 final size:27
Alignment explanation
Indices: 46459818--46459875 Score: 62
Period size: 27 Copynumber: 2.1 Consensus size: 27
46459808 CTCAAAAGCC
46459818 TTTCATTAAAAGTTCACCACAAAGGAA
1 TTTCATTAAAAGTTCACCACAAAGGAA
* * * * * *
46459845 TTTCCTTCAGAGTTCGCTACAAAGGCA
1 TTTCATTAAAAGTTCACCACAAAGGAA
46459872 TTTC
1 TTTC
46459876 TTTCAGAGTT
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.33, C:0.22, G:0.14, T:0.31
Consensus pattern (27 bp):
TTTCATTAAAAGTTCACCACAAAGGAA
Found at i:46459880 original size:27 final size:27
Alignment explanation
Indices: 46459836--46459934 Score: 117
Period size: 27 Copynumber: 3.7 Consensus size: 27
46459826 AAAGTTCACC
* * *
46459836 ACAAAGGAATTTCCTTCAGAGTTCGCT
1 ACAAAGGCATTTCTTTCAGAGTTAGCT
* *
46459863 ACAAAGGCATTTCTTTCAGAGTTTGCC
1 ACAAAGGCATTTCTTTCAGAGTTAGCT
* * * *
46459890 ACAAAGACATGTCTTTTAGAGTTATCT
1 ACAAAGGCATTTCTTTCAGAGTTAGCT
46459917 ACAAAGGCATTTCTTTCA
1 ACAAAGGCATTTCTTTCA
46459935 TGACGTGTTT
Statistics
Matches: 59, Mismatches: 13, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
27 59 1.00
ACGTcount: A:0.30, C:0.20, G:0.16, T:0.33
Consensus pattern (27 bp):
ACAAAGGCATTTCTTTCAGAGTTAGCT
Found at i:46461045 original size:43 final size:43
Alignment explanation
Indices: 46460966--46461067 Score: 105
Period size: 43 Copynumber: 2.3 Consensus size: 43
46460956 ACAAACGCTA
* * *
46460966 TAAATGATCTTGTTCTTTAGCAGCGTTTGTAATAAAAGCACCGC
1 TAAA-GATCATGTTCTTTAGCAGCGTTTATAATAAAAGCACCAC
* * ** *
46461010 TAAAGATCATGTTTTTTAGCGGCGTTTATTGTAAAAGCACTAC
1 TAAAGATCATGTTCTTTAGCAGCGTTTATAATAAAAGCACCAC
* *
46461053 TAAAGACCAGGTTCT
1 TAAAGATCATGTTCT
46461068 ATAGTGGCGC
Statistics
Matches: 47, Mismatches: 11, Indels: 1
0.80 0.19 0.02
Matches are distributed among these distances:
43 43 0.91
44 4 0.09
ACGTcount: A:0.30, C:0.17, G:0.19, T:0.34
Consensus pattern (43 bp):
TAAAGATCATGTTCTTTAGCAGCGTTTATAATAAAAGCACCAC
Found at i:46471086 original size:20 final size:20
Alignment explanation
Indices: 46471043--46471088 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
46471033 ACTGTTTTAT
*
46471043 TATGGG-CCAACTGTATTAA
1 TATGGGCCCAACTGTATCAA
* *
46471062 AATGGGCCCAACTGTGTCAA
1 TATGGGCCCAACTGTATCAA
46471082 TATGGGC
1 TATGGGC
46471089 AAGGCCTAAT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
19 5 0.23
20 17 0.77
ACGTcount: A:0.28, C:0.20, G:0.26, T:0.26
Consensus pattern (20 bp):
TATGGGCCCAACTGTATCAA
Found at i:46471180 original size:60 final size:60
Alignment explanation
Indices: 46471081--46471215 Score: 168
Period size: 60 Copynumber: 2.2 Consensus size: 60
46471071 AACTGTGTCA
* *
46471081 ATATGGGCAAGGCCTAATATATCTCGACTTGTAATAGGGCTACGGCCCAGATTGATACTG
1 ATATGGGCTAGGCCTAATATATCTCGACTTGTAATAGGGCTACGGCCCAGATTAATACTG
* * *
46471141 ATATGGGCTAGGCCTAGTATA-CTCTGTTAC-TGTAA-AGGGCTATGGCCCAGATTAATATTG
1 ATATGGGCTAGGCCTAATATATCTC-G--ACTTGTAATAGGGCTACGGCCCAGATTAATACTG
46471201 ATATGGGCTAAGGCC
1 ATATGGGCT-AGGCC
46471216 CAGTTAACAC
Statistics
Matches: 66, Mismatches: 5, Indels: 7
0.85 0.06 0.09
Matches are distributed among these distances:
59 3 0.05
60 51 0.77
61 10 0.15
62 2 0.03
ACGTcount: A:0.27, C:0.19, G:0.26, T:0.28
Consensus pattern (60 bp):
ATATGGGCTAGGCCTAATATATCTCGACTTGTAATAGGGCTACGGCCCAGATTAATACTG
Found at i:46476849 original size:40 final size:40
Alignment explanation
Indices: 46476790--46477087 Score: 392
Period size: 40 Copynumber: 7.5 Consensus size: 40
46476780 CGGATGATAA
* *
46476790 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTA-ATT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATA-T
* *
46476830 CTGGGCTAAGTCCCAAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
*
46476870 CCGGGCTAGGTCCCGAAGGCATTTGTGCGAGTTACTATCA-
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAT-AT
* *
46476910 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTA-ATT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATA-T
* *
46476950 CTGGGCTAAGTCCCAAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
*
46476990 CCGGGCTAGGTCCCGAAGGCATTTGTGCGAGTTACTATCA-
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAT-AT
*
46477030 CCGGGCTAAGTCCCGAAGGCATTTGAGCGAG-TAGCTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATAT
* *
46477070 CC-GGCTAAATCTCGAAGG
1 CCGGGCTAAGTCCCGAAGG
46477088 TACTTGGTTT
Statistics
Matches: 229, Mismatches: 21, Indels: 17
0.86 0.08 0.06
Matches are distributed among these distances:
38 1 0.00
39 17 0.07
40 207 0.90
41 4 0.02
ACGTcount: A:0.23, C:0.23, G:0.28, T:0.26
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
Found at i:46477002 original size:120 final size:120
Alignment explanation
Indices: 46476789--46477054 Score: 532
Period size: 120 Copynumber: 2.2 Consensus size: 120
46476779 TCGGATGATA
46476789 ACCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTAATTCTGGGCTAAGTCCCAAAGGCATTT
1 ACCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTAATTCTGGGCTAAGTCCCAAAGGCATTT
46476854 GTGCGAGTTACTATATCCGGGCTAGGTCCCGAAGGCATTTGTGCGAGTTACTATC
66 GTGCGAGTTACTATATCCGGGCTAGGTCCCGAAGGCATTTGTGCGAGTTACTATC
46476909 ACCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTAATTCTGGGCTAAGTCCCAAAGGCATTT
1 ACCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTAATTCTGGGCTAAGTCCCAAAGGCATTT
46476974 GTGCGAGTTACTATATCCGGGCTAGGTCCCGAAGGCATTTGTGCGAGTTACTATC
66 GTGCGAGTTACTATATCCGGGCTAGGTCCCGAAGGCATTTGTGCGAGTTACTATC
46477029 ACCGGGCTAAGTCCCGAAGGCATTTG
1 ACCGGGCTAAGTCCCGAAGGCATTTG
46477055 AGCGAGTAGC
Statistics
Matches: 146, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
120 146 1.00
ACGTcount: A:0.23, C:0.23, G:0.28, T:0.27
Consensus pattern (120 bp):
ACCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTAATTCTGGGCTAAGTCCCAAAGGCATTT
GTGCGAGTTACTATATCCGGGCTAGGTCCCGAAGGCATTTGTGCGAGTTACTATC
Found at i:46485257 original size:40 final size:39
Alignment explanation
Indices: 46485199--46485375 Score: 221
Period size: 40 Copynumber: 4.5 Consensus size: 39
46485189 GGATGATAAC
* * *
46485199 CGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTAATTT
1 CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT-ATAT
*
46485239 CGGGCTAAGTCCCAAAGGCATTTGTGCGAGTTACTATAT
1 CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* *
46485278 CTGGGCTAGGTCCCGAAGGCATTTGTGCGAGTTACTATAAC
1 C-GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAT-AT
*
46485319 CGGGCTAAGTCCCGAAGGCATTTGAGCGAG-TAGCTATAT
1 CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATAT
* * *
46485358 CCGGCTAAATCCCAAAGG
1 CGGGCTAAGTCCCGAAGG
46485376 TACTTGGTTT
Statistics
Matches: 121, Mismatches: 13, Indels: 7
0.86 0.09 0.05
Matches are distributed among these distances:
39 22 0.18
40 97 0.80
41 2 0.02
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (39 bp):
CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
Found at i:46486791 original size:25 final size:25
Alignment explanation
Indices: 46486758--46486811 Score: 101
Period size: 25 Copynumber: 2.2 Consensus size: 25
46486748 AGCAATGAGA
46486758 ACCC-TTTTACAAACCTTCGATAAT
1 ACCCATTTTACAAACCTTCGATAAT
46486782 ACCCATTTTACAAACCTTCGATAAT
1 ACCCATTTTACAAACCTTCGATAAT
46486807 ACCCA
1 ACCCA
46486812 GCCAGTCCCA
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
24 4 0.14
25 25 0.86
ACGTcount: A:0.35, C:0.31, G:0.04, T:0.30
Consensus pattern (25 bp):
ACCCATTTTACAAACCTTCGATAAT
Found at i:46494327 original size:17 final size:18
Alignment explanation
Indices: 46494305--46494347 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
46494295 AATTTCGGCG
46494305 TGTGGGCC-ACACA-GGCA
1 TGTGGGCCTACA-AGGGCA
*
46494322 TGTGGGCCTACAAGGGTA
1 TGTGGGCCTACAAGGGCA
46494340 TGTGGGCC
1 TGTGGGCC
46494348 CAAATTTCTA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
17 9 0.39
18 14 0.61
ACGTcount: A:0.19, C:0.23, G:0.40, T:0.19
Consensus pattern (18 bp):
TGTGGGCCTACAAGGGCA
Found at i:46495023 original size:126 final size:126
Alignment explanation
Indices: 46494798--46495052 Score: 393
Period size: 126 Copynumber: 2.0 Consensus size: 126
46494788 CTGTATTTAT
**
46494798 ATCTATTTCTGACTGTGTATACGATTCTGTATGATTGCATGCTTAATTATATTGGCTTACACACT
1 ATCTATTTCCAACTGTGTATACGATTCTGTATGATTGCATGCTTAATTATATTGGCTTACACACT
* *
46494863 GAGTTTACGTAAAATCACATCTGTTTGTCTGTATTGTCAAGTAATCCACAGTCTTAGGCAG
66 GAGTTTACATAAAATCACATCTGTTTCTCTGTATTGTCAAGTAATCCACAGTCTTAGGCAG
* * * * * *
46494924 ATCTATTTCCAACTGTGTCTATGATTTTGTATGATTGCATGCTTAATTCTGTTGGGTTACACACT
1 ATCTATTTCCAACTGTGTATACGATTCTGTATGATTGCATGCTTAATTATATTGGCTTACACACT
* * *
46494989 GAGTTTACATAAACTCACATCTGTTTCTCTGTATTGTCAGGTAATCCACAGTCTTAGGCGG
66 GAGTTTACATAAAATCACATCTGTTTCTCTGTATTGTCAAGTAATCCACAGTCTTAGGCAG
46495050 ATC
1 ATC
46495053 GGTGTAGTAG
Statistics
Matches: 116, Mismatches: 13, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
126 116 1.00
ACGTcount: A:0.25, C:0.18, G:0.18, T:0.39
Consensus pattern (126 bp):
ATCTATTTCCAACTGTGTATACGATTCTGTATGATTGCATGCTTAATTATATTGGCTTACACACT
GAGTTTACATAAAATCACATCTGTTTCTCTGTATTGTCAAGTAATCCACAGTCTTAGGCAG
Found at i:46499248 original size:31 final size:31
Alignment explanation
Indices: 46499202--46499288 Score: 140
Period size: 32 Copynumber: 2.8 Consensus size: 31
46499192 TCAATCTCAG
*
46499202 CATAT-ACTGGGCCGAAGCCTTTACATTATT
1 CATATCACTAGGCCGAAGCCTTTACATTATT
*
46499232 CATATCACTAGGCCGAAGCCTTTTTCATTATT
1 CATATCACTAGGCCGAAGCC-TTTACATTATT
46499264 CATATCACTAGGCCGAAGCCTTTAC
1 CATATCACTAGGCCGAAGCCTTTAC
46499289 TGTATACGGT
Statistics
Matches: 52, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
30 5 0.10
31 17 0.33
32 30 0.58
ACGTcount: A:0.26, C:0.26, G:0.15, T:0.32
Consensus pattern (31 bp):
CATATCACTAGGCCGAAGCCTTTACATTATT
Found at i:46499534 original size:25 final size:24
Alignment explanation
Indices: 46499482--46499601 Score: 143
Period size: 25 Copynumber: 4.9 Consensus size: 24
46499472 TTTATCATAT
** *
46499482 AACTGGGGCCTAGCCTCTTTTAAT-
1 AACTGGGGCAAAGCC-CTTTTGATA
46499506 AACTGGGGCTAAAGCCCTTTTGATA
1 AACTGGGGC-AAAGCCCTTTTGATA
46499531 AACTGGGGCAAAGCCCTTTTTGATA
1 AACTGGGGCAAAGCCC-TTTTGATA
* *
46499556 AACTGGGGCAAAGCCCTTTCCGGTA
1 AACTGGGGCAAAGCCCTTT-TGATA
*
46499581 AACTGGGGCATAGCCCTTTTG
1 AACTGGGGCAAAGCCCTTTTG
46499602 CACTTCTGCC
Statistics
Matches: 85, Mismatches: 7, Indels: 8
0.85 0.07 0.08
Matches are distributed among these distances:
24 27 0.32
25 58 0.68
ACGTcount: A:0.24, C:0.23, G:0.25, T:0.28
Consensus pattern (24 bp):
AACTGGGGCAAAGCCCTTTTGATA
Found at i:46499679 original size:11 final size:11
Alignment explanation
Indices: 46499648--46499695 Score: 57
Period size: 11 Copynumber: 4.6 Consensus size: 11
46499638 TTATGGATAC
46499648 ATCATGTGCAT
1 ATCATGTGCAT
*
46499659 ATCA--TACAT
1 ATCATGTGCAT
46499668 ATCATGTGCAT
1 ATCATGTGCAT
*
46499679 ATCATGT-CAA
1 ATCATGTGCAT
46499689 ATCATGT
1 ATCATGT
46499696 ATATCAAAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
9 8 0.25
10 9 0.28
11 15 0.47
ACGTcount: A:0.33, C:0.19, G:0.12, T:0.35
Consensus pattern (11 bp):
ATCATGTGCAT
Found at i:46499760 original size:25 final size:25
Alignment explanation
Indices: 46499732--46499780 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
46499722 ATAATTAAAC
* * *
46499732 CCTAGGGGTATAATGGTCATTTTTA
1 CCTAGGGGCAAAATAGTCATTTTTA
46499757 CCTAGGGGCAAAATAGTCATTTTT
1 CCTAGGGGCAAAATAGTCATTTTT
46499781 CATATTATAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.27, C:0.14, G:0.22, T:0.37
Consensus pattern (25 bp):
CCTAGGGGCAAAATAGTCATTTTTA
Found at i:46504562 original size:39 final size:39
Alignment explanation
Indices: 46504398--46504580 Score: 170
Period size: 40 Copynumber: 4.6 Consensus size: 39
46504388 TTGAATGCTG
* * * * * * *
46504398 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGAATATA
1 TCCGGGTTATGTCCCGAAGGCATTGTGC-GAGTTACTAAA
* * * *
46504438 TCCGGATTAAGAT-CCGAAGGCCTTTGTGCGAGATACTAAA
1 TCCGGGTTATG-TCCCGAAGG-CATTGTGCGAGTTACTAAA
* **
46504478 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAAA
1 TCCGGGTTATGTCCCGAAGGCATT-GTGCGAGTTACTAAA
*
46504518 TCCGGGTTATGTCCCGAAGGCATTGTGTGAGTTACTAAA
1 TCCGGGTTATGTCCCGAAGGCATTGTGCGAGTTACTAAA
* *
46504557 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGTTATGTCCCGAAGGCATT
46504581 TGAACGAGGA
Statistics
Matches: 121, Mismatches: 18, Indels: 9
0.82 0.12 0.06
Matches are distributed among these distances:
39 38 0.31
40 74 0.61
41 9 0.07
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.27
Consensus pattern (39 bp):
TCCGGGTTATGTCCCGAAGGCATTGTGCGAGTTACTAAA
Found at i:46504600 original size:79 final size:80
Alignment explanation
Indices: 46504434--46504615 Score: 190
Period size: 79 Copynumber: 2.3 Consensus size: 80
46504424 GCTAAGTGAA
* * * *
46504434 TATATCCGGATTAAGAT-CCGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGTCCCGAAGG
1 TATATCCGGGTTAAG-TCCCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGG
** ** *
46504498 CATTCGTGCGAGTTGT
65 CATTCGAACGAGGAGC
* * * * *
46504514 TAAATCCGGGTTATGTCCCGAAGG-CATTGTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGGC
1 TATATCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGC
*
46504578 ATTTGAACGAGGAGC
66 ATTCGAACGAGGAGC
*
46504593 TATATCC-GGTTAAATCCCGAAGG
1 TATATCCGGGTTAAGTCCCGAAGG
46504616 TACGTGATTT
Statistics
Matches: 83, Mismatches: 18, Indels: 4
0.79 0.17 0.04
Matches are distributed among these distances:
78 14 0.17
79 50 0.60
80 19 0.23
ACGTcount: A:0.26, C:0.20, G:0.27, T:0.26
Consensus pattern (80 bp):
TATATCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGC
ATTCGAACGAGGAGC
Found at i:46510522 original size:24 final size:24
Alignment explanation
Indices: 46510490--46510598 Score: 139
Period size: 25 Copynumber: 4.4 Consensus size: 24
46510480 CTGGAGGCCT
*
46510490 AGCCTCTTTTAAT-AACTGGGGCCAA
1 AGCC-CTTTTGATAAACTGGGG-CAA
46510515 AGCCCTTTTGATAAACTGGGGCAA
1 AGCCCTTTTGATAAACTGGGGCAA
46510539 AGCCCTTTTTGATAAACTGGGGCAA
1 AGCCC-TTTTGATAAACTGGGGCAA
* * *
46510564 AGCCCTTTCCGATAAACTAGGGCAT
1 AGCCCTTT-TGATAAACTGGGGCAA
46510589 AGCCCTTTTG
1 AGCCCTTTTG
46510599 CACTTCTTCG
Statistics
Matches: 76, Mismatches: 5, Indels: 7
0.86 0.06 0.08
Matches are distributed among these distances:
24 19 0.25
25 57 0.75
ACGTcount: A:0.27, C:0.24, G:0.22, T:0.28
Consensus pattern (24 bp):
AGCCCTTTTGATAAACTGGGGCAA
Found at i:46510679 original size:19 final size:20
Alignment explanation
Indices: 46510644--46510686 Score: 61
Period size: 19 Copynumber: 2.2 Consensus size: 20
46510634 TTATGGATAC
*
46510644 ATCATGTGCATATCATGCAT
1 ATCATGTGCAAATCATGCAT
*
46510664 ATCATGT-CAAATCATGTAT
1 ATCATGTGCAAATCATGCAT
46510683 ATCA
1 ATCA
46510687 AAATCTCATG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 14 0.67
20 7 0.33
ACGTcount: A:0.35, C:0.19, G:0.12, T:0.35
Consensus pattern (20 bp):
ATCATGTGCAAATCATGCAT
Found at i:46518069 original size:46 final size:45
Alignment explanation
Indices: 46517925--46518132 Score: 177
Period size: 46 Copynumber: 4.5 Consensus size: 45
46517915 ATTTTGTGCT
* * *
46517925 AGTGTAAGACATGTCTGGGACATGCATCGGCCAC-ATTATGAAAGCC
1 AGTGTAAGACATGTCTAGGACATGCATCGGCCTCGA-GATG-AAGCC
* * * * *
46517971 TGTGTAAGACTGTGTCTAGGACATGGCATCGGCATTGAGATGAGAGCT
1 AGTGTAAGAC-ATGTCTAGGACAT-GCATCGGCCTCGAGATGA-AGCC
* * * *
46518019 AGTGTAAGACATGTTTGGGACACGCATCGGCCTCGCGATGTAAGCC
1 AGTGTAAGACATGTCTAGGACATGCATCGGCCTCGAGATG-AAGCC
* ** * *
46518065 AGTGTAAGACATATCTAGGACATGCATCGGCAACGAGATG-TGTC
1 AGTGTAAGACATGTCTAGGACATGCATCGGCCTCGAGATGAAGCC
*
46518109 AGTGTAAGACCATCTCTAGGACAT
1 AGTGTAAGA-CATGTCTAGGACAT
46518133 ATCATCAGCA
Statistics
Matches: 129, Mismatches: 27, Indels: 13
0.76 0.16 0.08
Matches are distributed among these distances:
44 11 0.09
45 13 0.10
46 59 0.46
47 22 0.17
48 23 0.18
49 1 0.01
ACGTcount: A:0.28, C:0.20, G:0.28, T:0.24
Consensus pattern (45 bp):
AGTGTAAGACATGTCTAGGACATGCATCGGCCTCGAGATGAAGCC
Found at i:46518273 original size:49 final size:50
Alignment explanation
Indices: 46518154--46518282 Score: 172
Period size: 49 Copynumber: 2.6 Consensus size: 50
46518144 GTATAGAGGT
* *
46518154 GTTAGTGTAAGATCATGTCTGGGACATGGCGTCGGCACAGATATGTGAGA
1 GTTAGTGTAAGACCATGTCTGGGACATGGCGTCGCCACAGATATGTGAGA
* * * * *
46518204 GCTAGTGTAAGACCATGTCTGGGACGTGGCGTCAGCCTCA-AT-TTTGATA
1 GTTAGTGTAAGACCATGTCTGGGACATGGCGTC-GCCACAGATATGTGAGA
46518253 GTTAGTGTAAGACCATGTCTGGGACATGGC
1 GTTAGTGTAAGACCATGTCTGGGACATGGC
46518283 ATCGGCATCA
Statistics
Matches: 69, Mismatches: 9, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
49 33 0.48
50 32 0.46
51 4 0.06
ACGTcount: A:0.24, C:0.17, G:0.32, T:0.27
Consensus pattern (50 bp):
GTTAGTGTAAGACCATGTCTGGGACATGGCGTCGCCACAGATATGTGAGA
Found at i:46522738 original size:8 final size:8
Alignment explanation
Indices: 46522720--46522757 Score: 51
Period size: 8 Copynumber: 4.8 Consensus size: 8
46522710 TTTAAGAAAT
46522720 TAATAATTA
1 TAATAA-TA
46522729 TAATAATA
1 TAATAATA
*
46522737 TAATAGT-
1 TAATAATA
46522744 TAATAATA
1 TAATAATA
46522752 TAATAA
1 TAATAA
46522758 AAGAAATAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
7 6 0.23
8 14 0.54
9 6 0.23
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (8 bp):
TAATAATA
Found at i:46522765 original size:24 final size:24
Alignment explanation
Indices: 46522719--46522765 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
46522709 ATTTAAGAAA
* *
46522719 TTAATAATTATAATAATATAATAG
1 TTAATAATTATAATAAAAAAATAG
46522743 TTAATAA-TATAATAAAAGAAATA
1 TTAATAATTATAATAAAA-AAATA
46522766 AAAAAAGAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 9 0.45
24 11 0.55
ACGTcount: A:0.60, C:0.00, G:0.04, T:0.36
Consensus pattern (24 bp):
TTAATAATTATAATAAAAAAATAG
Found at i:46522778 original size:20 final size:20
Alignment explanation
Indices: 46522757--46522798 Score: 70
Period size: 19 Copynumber: 2.2 Consensus size: 20
46522747 TAATATAATA
46522757 AAAGAAATAAAA-AAAGAAT
1 AAAGAAATAAAATAAAGAAT
46522776 AAAGAAATAAAATAAAGAA-
1 AAAGAAATAAAATAAAGAAT
46522795 AAAG
1 AAAG
46522799 GAAAGAAAGA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
19 16 0.73
20 6 0.27
ACGTcount: A:0.79, C:0.00, G:0.12, T:0.10
Consensus pattern (20 bp):
AAAGAAATAAAATAAAGAAT
Found at i:46522805 original size:11 final size:10
Alignment explanation
Indices: 46522756--46522867 Score: 50
Period size: 11 Copynumber: 10.4 Consensus size: 10
46522746 ATAATATAAT
*
46522756 AAAAGAAA-T
1 AAAAGAAAGA
46522765 AAAA-AAAGA
1 AAAAGAAAGA
*
46522774 ATAAAGAAA-T
1 A-AAAGAAAGA
*
46522784 AAAATAAAGA
1 AAAAGAAAGA
46522794 AAAAGGAAAGA
1 AAAA-GAAAGA
*
46522805 AAGAAGAACGA
1 AA-AAGAAAGA
*
46522816 AACAGAACAGGGAA
1 AAAAGAA-A--G-A
46522830 AGAAAGAAAGA
1 A-AAAGAAAGA
*
46522841 AAAAGGGAAATA
1 AAAA--GAAAGA
46522853 AAAAGAAAGGA
1 AAAAGAAA-GA
46522864 AAAA
1 AAAA
46522868 TAGGGTTTTA
Statistics
Matches: 78, Mismatches: 11, Indels: 26
0.68 0.10 0.23
Matches are distributed among these distances:
8 3 0.04
9 11 0.14
10 19 0.24
11 24 0.31
12 12 0.15
13 1 0.01
14 3 0.04
15 5 0.06
ACGTcount: A:0.72, C:0.03, G:0.21, T:0.04
Consensus pattern (10 bp):
AAAAGAAAGA
Found at i:46529395 original size:27 final size:27
Alignment explanation
Indices: 46529365--46529542 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
46529355 ATATTGAGTC
* * * *
46529365 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
46529392 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
46529419 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
46529447 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
46529474 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
46529501 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
46529528 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
46529543 GTACAATTTA
Statistics
Matches: 130, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 24 0.18
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:46529504 original size:82 final size:81
Alignment explanation
Indices: 46529386--46529541 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
46529376 TGCTATATAA
* *
46529386 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
46529451 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
46529468 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
46529532 CACTTAGTGC
65 CACTTAGTGC
46529542 TGTACAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 16 0.24
82 51 0.76
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:46537458 original size:27 final size:27
Alignment explanation
Indices: 46537428--46537605 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
46537418 ATATTGAGTC
* * * *
46537428 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
46537455 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
46537482 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
46537510 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
46537537 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
46537564 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
46537591 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
46537606 GTACAATTTA
Statistics
Matches: 130, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 24 0.18
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:46537567 original size:82 final size:81
Alignment explanation
Indices: 46537449--46537604 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
46537439 TGCTATATAA
* *
46537449 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
46537514 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
46537531 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
46537595 CACTTAGTGC
65 CACTTAGTGC
46537605 TGTACAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 16 0.24
82 51 0.76
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:46540011 original size:18 final size:18
Alignment explanation
Indices: 46539988--46540047 Score: 79
Period size: 18 Copynumber: 3.4 Consensus size: 18
46539978 ATATTTTTAA
46539988 TCATTCAAATAATCAAAT
1 TCATTCAAATAATCAAAT
* * *
46540006 TCATTCAATTTAT-TAA-
1 TCATTCAAATAATCAAAT
46540022 TCATTCAAATAATCAAAT
1 TCATTCAAATAATCAAAT
46540040 TCATTCAA
1 TCATTCAA
46540048 TTTACTCATT
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
16 11 0.32
17 4 0.12
18 19 0.56
ACGTcount: A:0.45, C:0.17, G:0.00, T:0.38
Consensus pattern (18 bp):
TCATTCAAATAATCAAAT
Found at i:46540027 original size:34 final size:34
Alignment explanation
Indices: 46539980--46540051 Score: 137
Period size: 34 Copynumber: 2.1 Consensus size: 34
46539970 TCCTTCTCAT
46539980 ATTT-TTAATCATTCAAATAATCAAATTCATTCA
1 ATTTATTAATCATTCAAATAATCAAATTCATTCA
46540013 ATTTATTAATCATTCAAATAATCAAATTCATTCA
1 ATTTATTAATCATTCAAATAATCAAATTCATTCA
46540047 ATTTA
1 ATTTA
46540052 CTCATTTCAT
Statistics
Matches: 38, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
33 4 0.11
34 34 0.89
ACGTcount: A:0.43, C:0.14, G:0.00, T:0.43
Consensus pattern (34 bp):
ATTTATTAATCATTCAAATAATCAAATTCATTCA
Found at i:46540263 original size:13 final size:14
Alignment explanation
Indices: 46540240--46540269 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
46540230 GAATATAAAC
46540240 ATCAGCATCTCCAA
1 ATCAGCATCTCCAA
46540254 ATCA-CATCTCCAA
1 ATCAGCATCTCCAA
46540267 ATC
1 ATC
46540270 CCTTCTCAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 12 0.75
14 4 0.25
ACGTcount: A:0.37, C:0.37, G:0.03, T:0.23
Consensus pattern (14 bp):
ATCAGCATCTCCAA
Found at i:46540276 original size:13 final size:13
Alignment explanation
Indices: 46540245--46540283 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
46540235 TAAACATCAG
*
46540245 CATCTCCAAATCA
1 CATCTCCAAATCC
46540258 CATCTCCAAATCC
1 CATCTCCAAATCC
* *
46540271 CTTCTCAAAATCC
1 CATCTCCAAATCC
46540284 TATGGCATGC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.33, C:0.41, G:0.00, T:0.26
Consensus pattern (13 bp):
CATCTCCAAATCC
Found at i:46540427 original size:16 final size:17
Alignment explanation
Indices: 46540388--46540433 Score: 51
Period size: 16 Copynumber: 2.8 Consensus size: 17
46540378 ATCAGTTTCA
*
46540388 ATTCCATTTCAATATAC
1 ATTCCAATTCAATATAC
*
46540405 AAT-CAATTCAATATAC
1 ATTCCAATTCAATATAC
46540421 -TTCCAATCTCAAT
1 ATTCCAAT-TCAAT
46540434 CCACATGTAA
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
15 1 0.04
16 16 0.67
17 7 0.29
ACGTcount: A:0.39, C:0.24, G:0.00, T:0.37
Consensus pattern (17 bp):
ATTCCAATTCAATATAC
Found at i:46543007 original size:39 final size:39
Alignment explanation
Indices: 46542953--46543036 Score: 150
Period size: 39 Copynumber: 2.2 Consensus size: 39
46542943 TAATGGAGAA
* *
46542953 TTATATCCGGGCCAAGTCCCGAAGGCATTCGTGCTGGTG
1 TTATATCCAGGCCAAGTCCCGAAGGCATTCGTGCTGATG
46542992 TTATATCCAGGCCAAGTCCCGAAGGCATTCGTGCTGATG
1 TTATATCCAGGCCAAGTCCCGAAGGCATTCGTGCTGATG
46543031 TTATAT
1 TTATAT
46543037 ACGGGCTAAA
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
39 43 1.00
ACGTcount: A:0.21, C:0.24, G:0.26, T:0.29
Consensus pattern (39 bp):
TTATATCCAGGCCAAGTCCCGAAGGCATTCGTGCTGATG
Found at i:46545196 original size:17 final size:17
Alignment explanation
Indices: 46545176--46545209 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
46545166 ATTCACTAAT
46545176 ATAAT-ATCAATTAAATA
1 ATAATAATCAA-TAAATA
46545193 ATAATAATCAATAAATA
1 ATAATAATCAATAAATA
46545210 TCTTTTACTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.62, C:0.06, G:0.00, T:0.32
Consensus pattern (17 bp):
ATAATAATCAATAAATA
Found at i:46549163 original size:48 final size:47
Alignment explanation
Indices: 46549057--46549232 Score: 171
Period size: 48 Copynumber: 3.7 Consensus size: 47
46549047 GATATAAGCC
* * *
46549057 AGTGCAAGA-CATGTCTGGGACAT-GCATCGGCTACG--AGATGTGTC
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGC-ACGATAGAGGTGTT
*
46549101 AGTGTAAGACCATGTTTGGGACATGGCATCGGCACGTATAGAGGTGTT
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCACG-ATAGAGGTGTT
* * * ** *
46549149 AGTGTAAGATCATGTCTAGGACATGGCATCGGCACGGATATGTGAAAGCT
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCAC-GATA-GAG-GTGTT
* *
46549199 AGTGTAAGACCATGTTTGGGACATGGCATTGGCA
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCA
46549233 TCATACCCTA
Statistics
Matches: 109, Mismatches: 15, Indels: 10
0.81 0.11 0.07
Matches are distributed among these distances:
44 8 0.07
45 16 0.15
46 8 0.07
48 42 0.39
49 3 0.03
50 32 0.29
ACGTcount: A:0.27, C:0.16, G:0.32, T:0.25
Consensus pattern (47 bp):
AGTGTAAGACCATGTCTGGGACATGGCATCGGCACGATAGAGGTGTT
Found at i:46550366 original size:20 final size:21
Alignment explanation
Indices: 46550327--46550366 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
46550317 GTTATAATGA
*
46550327 CCACACGGGCATGTTGCCCTT
1 CCACACGGGCATGATGCCCTT
*
46550348 CCACACGGGTAT-ATGCCCT
1 CCACACGGGCATGATGCCCT
46550367 GTTTCAAGGG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.17, C:0.38, G:0.23, T:0.23
Consensus pattern (21 bp):
CCACACGGGCATGATGCCCTT
Found at i:46550930 original size:20 final size:19
Alignment explanation
Indices: 46550890--46550933 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
46550880 ATTTAAAAAG
*
46550890 ATATTTAATTATTAATATA
1 ATATTTAACTATTAATATA
46550909 ATATTATAACTATT-ATAGTA
1 ATATT-TAACTATTAATA-TA
46550929 ATATT
1 ATATT
46550934 GTCCGAATAG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
19 8 0.36
20 14 0.64
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.50
Consensus pattern (19 bp):
ATATTTAACTATTAATATA
Found at i:46560267 original size:3 final size:3
Alignment explanation
Indices: 46560259--46560481 Score: 310
Period size: 3 Copynumber: 74.3 Consensus size: 3
46560249 AGTCATATAT
*
46560259 TTA TTA TTA TGT- TTA TTA TTA TT- TTGA GTA TTA TTA TT- TCTA TTA
1 TTA TTA TTA T-TA TTA TTA TTA TTA TT-A TTA TTA TTA TTA T-TA TTA
* * * * * * *
46560304 TTG CTA TTA CTA TTG TTT TTA TT- TGTA TTA TTA CTA TCA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA TTA TTA
46560349 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
46560397 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
46560445 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
46560482 ATTTGTTATA
Statistics
Matches: 197, Mismatches: 15, Indels: 16
0.86 0.07 0.07
Matches are distributed among these distances:
2 5 0.03
3 188 0.95
4 4 0.02
ACGTcount: A:0.30, C:0.02, G:0.03, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:46560615 original size:28 final size:29
Alignment explanation
Indices: 46560584--46560640 Score: 73
Period size: 28 Copynumber: 2.0 Consensus size: 29
46560574 TATTTACTTA
*
46560584 TCATTTTATATATAAA-TTCT-TTTTATTT
1 TCATTTT-TATACAAATTTCTATTTTATTT
*
46560612 TCATTTTTTTACAAATTTCTATTTTATTT
1 TCATTTTTATACAAATTTCTATTTTATTT
46560641 GTTTATTTCA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
27 6 0.24
28 11 0.44
29 8 0.32
ACGTcount: A:0.26, C:0.09, G:0.00, T:0.65
Consensus pattern (29 bp):
TCATTTTTATACAAATTTCTATTTTATTT
Found at i:46568057 original size:20 final size:20
Alignment explanation
Indices: 46568029--46568070 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
46568019 ATTTTATGTC
*
46568029 TTATTCTGAGCAAATATTCT
1 TTATCCTGAGCAAATATTCT
46568049 TTATCCTGAGCAAATATTCT
1 TTATCCTGAGCAAATATTCT
46568069 TT
1 TT
46568071 TCTTGCATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.29, C:0.17, G:0.10, T:0.45
Consensus pattern (20 bp):
TTATCCTGAGCAAATATTCT
Found at i:46573137 original size:175 final size:176
Alignment explanation
Indices: 46572727--46573176 Score: 616
Period size: 177 Copynumber: 2.6 Consensus size: 176
46572717 GAAGTTACAT
* * * * *
46572727 ATCTTATCTCCCTAAGCAATAGTGGAGCAGATTGAAGACGGTGAATCTTATCTCCATATAGCAGC
1 ATCTTATCTCCCTAAGCAGTAGTGGAGTAGATCGAAGACGGTGAATCTTATCTCCATGTAGCGGC
* * * * * *
46572792 AATGGAGCAGATTTAAGCCACCAACTTTATCTTCTTGAGGTTGCAGTGGAGCAGGCTCAAGATAC
66 AATGGAGCAGATTTAAGCCACCAGCCTTATCTCCCTGAGGTTGCAATGAAGCAGGCTCAAGATAC
* * * *
46572857 AAGTCTTATCTCCCTGAAGTAGTAGTAGAGCGTACTGAAAGTTGTAG
131 AAGTCTTA-CTCCCTGAAGTAGCAGTAGAGAGTACTGAAAATTGCAG
* ** * *
46572904 ATTTTATCTCCCTAAATAGTAGTGGAGTAGATCGACGATGGTGAATCTTATCTCCATGTAGCGGC
1 ATCTTATCTCCCTAAGCAGTAGTGGAGTAGATCGAAGACGGTGAATCTTATCTCCATGTAGCGGC
*
46572969 AATGGAGCAGATTTAAGCCACCAGCCTTATCTCCCTGAGGTTGCAATGAAGCAGGCTCAGGATAC
66 AATGGAGCAGATTTAAGCCACCAGCCTTATCTCCCTGAGGTTGCAATGAAGCAGGCTCAAGATAC
*
46573034 AAGTCTTA-TCCCTGAAGTTGCAGTAGAGTAG-ACTGAAAATTGCAG
131 AAGTCTTACTCCCTGAAGTAGCAGTAGAG-AGTACTGAAAATTGCAG
* * **
46573079 ATCTTATCTCCCTAAGCCGTAGTGGAGTAGATCGAAGAGGGCAAATCTTATCTCCATGTAGCGGC
1 ATCTTATCTCCCTAAGCAGTAGTGGAGTAGATCGAAGACGGTGAATCTTATCTCCATGTAGCGGC
* *
46573144 AATGGAGCAGATTTAAGCCACAAGTCTTATCTC
66 AATGGAGCAGATTTAAGCCACCAGCCTTATCTC
46573177 TCTAAAAGTT
Statistics
Matches: 240, Mismatches: 32, Indels: 4
0.87 0.12 0.01
Matches are distributed among these distances:
175 118 0.49
176 1 0.00
177 121 0.50
ACGTcount: A:0.29, C:0.20, G:0.23, T:0.27
Consensus pattern (176 bp):
ATCTTATCTCCCTAAGCAGTAGTGGAGTAGATCGAAGACGGTGAATCTTATCTCCATGTAGCGGC
AATGGAGCAGATTTAAGCCACCAGCCTTATCTCCCTGAGGTTGCAATGAAGCAGGCTCAAGATAC
AAGTCTTACTCCCTGAAGTAGCAGTAGAGAGTACTGAAAATTGCAG
Found at i:46584231 original size:3 final size:3
Alignment explanation
Indices: 46584223--46584489 Score: 323
Period size: 3 Copynumber: 89.3 Consensus size: 3
46584213 AGTCATATAT
*
46584223 TTA TTA TTA TGT- TTA TTA TTA TT- TTGA GTA TTA TTA TT- TCTA TTA
1 TTA TTA TTA T-TA TTA TTA TTA TTA TT-A TTA TTA TTA TTA T-TA TTA
* * * * * * *
46584268 TTG CTA TTA CTA TTG TTT TTA TT- TGTA TTA TTA CTA TCA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA TTA TTA
46584313 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
46584361 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
46584409 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTG TTA -TA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * *
46584456 TTTG TTA TTA TT- TTT TTGA -TA CTA TTA TTA TTA T
1 -TTA TTA TTA TTA TTA TT-A TTA TTA TTA TTA TTA T
46584490 CATACTATTA
Statistics
Matches: 230, Mismatches: 21, Indels: 26
0.83 0.08 0.09
Matches are distributed among these distances:
2 10 0.04
3 215 0.93
4 5 0.02
ACGTcount: A:0.29, C:0.02, G:0.03, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:46584579 original size:28 final size:29
Alignment explanation
Indices: 46584548--46584604 Score: 73
Period size: 28 Copynumber: 2.0 Consensus size: 29
46584538 TATTTACTTA
*
46584548 TCATTTTATATATAAA-TTCT-TTTTATTT
1 TCATTTT-TATACAAATTTCTATTTTATTT
*
46584576 TCATTTTTTTACAAATTTCTATTTTATTT
1 TCATTTTTATACAAATTTCTATTTTATTT
46584605 GTTTATTTCA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
27 6 0.24
28 11 0.44
29 8 0.32
ACGTcount: A:0.26, C:0.09, G:0.00, T:0.65
Consensus pattern (29 bp):
TCATTTTTATACAAATTTCTATTTTATTT
Found at i:46589399 original size:12 final size:12
Alignment explanation
Indices: 46589382--46589406 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
46589372 TTGGGTTAGT
46589382 GTTTTGGGCTAA
1 GTTTTGGGCTAA
46589394 GTTTTGGGCTAA
1 GTTTTGGGCTAA
46589406 G
1 G
46589407 GGTTTTGGGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.08, G:0.36, T:0.40
Consensus pattern (12 bp):
GTTTTGGGCTAA
Found at i:46589944 original size:42 final size:44
Alignment explanation
Indices: 46589837--46589956 Score: 138
Period size: 42 Copynumber: 2.8 Consensus size: 44
46589827 TATTTGATTT
* * *
46589837 TCAACCTGTTACCCTACTGCTTAGGGGGTTAAGGCTTGTCATCA
1 TCAACCTGTTACCCTACTGCTTAGGGGTTTAAGGCTTGTAAACA
** * * *
46589881 TTGATCTGTTTCCCTACTGCTTAGGGGTTT-A-GATCTGTAAAC-
1 TCAACCTGTTACCCTACTGCTTAGGGGTTTAAGGCT-TGTAAACA
46589923 TCAACCTGTTACCCTACTGCTTAGGGGTTTAAGG
1 TCAACCTGTTACCCTACTGCTTAGGGGTTTAAGG
46589957 TTTAAAAATT
Statistics
Matches: 61, Mismatches: 12, Indels: 6
0.77 0.15 0.08
Matches are distributed among these distances:
42 28 0.46
43 7 0.11
44 26 0.43
ACGTcount: A:0.20, C:0.23, G:0.23, T:0.35
Consensus pattern (44 bp):
TCAACCTGTTACCCTACTGCTTAGGGGTTTAAGGCTTGTAAACA
Found at i:46590403 original size:43 final size:43
Alignment explanation
Indices: 46590317--46590411 Score: 111
Period size: 43 Copynumber: 2.2 Consensus size: 43
46590307 TTGTACATTT
* *
46590317 AGTCTGCTCCACTACGACTTCAAGGAGATGAGACTTGTAACTTC
1 AGTCTGCTCCACTA-GACTTCAAGGAGATAAGACTAGTAACTTC
* * *
46590361 AGTCTGCTCCACT-GTACTTCAGGGAGATAAGGCTAGTGACTTC
1 AGTCTGCTCCACTAG-ACTTCAAGGAGATAAGACTAGTAACTTC
*
46590404 AATCTGCT
1 AGTCTGCT
46590412 TCGCTGAGGC
Statistics
Matches: 44, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
42 1 0.02
43 30 0.68
44 13 0.30
ACGTcount: A:0.25, C:0.24, G:0.22, T:0.28
Consensus pattern (43 bp):
AGTCTGCTCCACTAGACTTCAAGGAGATAAGACTAGTAACTTC
Found at i:46592310 original size:46 final size:46
Alignment explanation
Indices: 46592260--46592431 Score: 308
Period size: 46 Copynumber: 3.7 Consensus size: 46
46592250 TGGTTGAGCA
46592260 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
*
46592306 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
*
46592352 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* *
46592398 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTA
46592432 GGGGCGGGTT
Statistics
Matches: 121, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
46 121 1.00
ACGTcount: A:0.22, C:0.22, G:0.27, T:0.30
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:46595422 original size:30 final size:29
Alignment explanation
Indices: 46595377--46595454 Score: 79
Period size: 30 Copynumber: 2.6 Consensus size: 29
46595367 CATAGTATCG
* *
46595377 TATCTTAGG-TTTCTTTATCCTGGATCTCTT
1 TATCTT-GGATTTCTTTATCCAGG-TCTCTC
*
46595407 TAT-TCTGGATTTCTTTATTCCAGGTTTCTC
1 TATCT-TGGATTTCTTTA-TCCAGGTCTCTC
46595437 TATCTTGGATTTCTTTAT
1 TATCTTGGATTTCTTTAT
46595455 TCAGTTTTCT
Statistics
Matches: 41, Mismatches: 3, Indels: 9
0.77 0.06 0.17
Matches are distributed among these distances:
29 4 0.10
30 31 0.76
31 6 0.15
ACGTcount: A:0.14, C:0.18, G:0.13, T:0.55
Consensus pattern (29 bp):
TATCTTGGATTTCTTTATCCAGGTCTCTC
Found at i:46595425 original size:15 final size:15
Alignment explanation
Indices: 46595386--46595456 Score: 74
Period size: 15 Copynumber: 4.7 Consensus size: 15
46595376 GTATCTTAGG
*
46595386 TTTCTTTATCCTGGA
1 TTTCTTTATTCTGGA
*
46595401 TCTCTTTATTCTGGA
1 TTTCTTTATTCTGGA
*
46595416 TTTCTTTATTCCAGG-
1 TTTCTTTATT-CTGGA
*
46595431 TTTCTCTA-TCTTGGA
1 TTTCTTTATTC-TGGA
46595446 TTTCTTTATTC
1 TTTCTTTATTC
46595457 AGTTTTCTTG
Statistics
Matches: 45, Mismatches: 7, Indels: 7
0.76 0.12 0.12
Matches are distributed among these distances:
13 1 0.02
14 3 0.07
15 36 0.80
16 5 0.11
ACGTcount: A:0.13, C:0.20, G:0.11, T:0.56
Consensus pattern (15 bp):
TTTCTTTATTCTGGA
Found at i:46597959 original size:56 final size:56
Alignment explanation
Indices: 46597868--46597977 Score: 211
Period size: 56 Copynumber: 2.0 Consensus size: 56
46597858 AACAAGCCAT
*
46597868 CTCGGGAATCGGGACGGGTCGAAGGTTCGATCACACTATCCAAAGGACTTTCATCG
1 CTCGAGAATCGGGACGGGTCGAAGGTTCGATCACACTATCCAAAGGACTTTCATCG
46597924 CTCGAGAATCGGGACGGGTCGAAGGTTCGATCACACTATCCAAAGGACTTTCAT
1 CTCGAGAATCGGGACGGGTCGAAGGTTCGATCACACTATCCAAAGGACTTTCAT
46597978 TTGGGTAAAT
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
56 53 1.00
ACGTcount: A:0.26, C:0.25, G:0.27, T:0.22
Consensus pattern (56 bp):
CTCGAGAATCGGGACGGGTCGAAGGTTCGATCACACTATCCAAAGGACTTTCATCG
Found at i:46612940 original size:10 final size:10
Alignment explanation
Indices: 46612925--46612984 Score: 79
Period size: 10 Copynumber: 6.0 Consensus size: 10
46612915 TAATTCTAGG
46612925 ATTTAT-TTT
1 ATTTATCTTT
46612934 CATTTATCTTT
1 -ATTTATCTTT
46612945 ATTTATCTTT
1 ATTTATCTTT
*
46612955 AATTATCTTT
1 ATTTATCTTT
46612965 ATTTAT-TTGT
1 ATTTATCTT-T
46612975 ATTTATCTTT
1 ATTTATCTTT
46612985 TAGAATTTCA
Statistics
Matches: 45, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
9 2 0.04
10 38 0.84
11 5 0.11
ACGTcount: A:0.22, C:0.08, G:0.02, T:0.68
Consensus pattern (10 bp):
ATTTATCTTT
Found at i:46613732 original size:17 final size:18
Alignment explanation
Indices: 46613701--46613734 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
46613691 TTTTCCTCAT
46613701 TTTAATTTCTGCAATTTA
1 TTTAATTTCTGCAATTTA
46613719 TTTAATTT-TGCAATTT
1 TTTAATTTCTGCAATTT
46613735 CAATTCACTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.26, C:0.09, G:0.06, T:0.59
Consensus pattern (18 bp):
TTTAATTTCTGCAATTTA
Found at i:46619351 original size:5 final size:5
Alignment explanation
Indices: 46619343--46619404 Score: 51
Period size: 5 Copynumber: 12.4 Consensus size: 5
46619333 GCAATCCAAT
46619343 TTTTA -TTT- TTTTA TTTTA TTATTA TTATTA TTATTTA TTTTA TTTTA
1 TTTTA TTTTA TTTTA TTTTA TT-TTA TT-TTA -T-TTTA TTTTA TTTTA
*
46619390 --TTA TATTA TTTTA TT
1 TTTTA TTTTA TTTTA TT
46619405 ATTTACTAAT
Statistics
Matches: 49, Mismatches: 1, Indels: 14
0.77 0.02 0.22
Matches are distributed among these distances:
3 3 0.06
4 6 0.12
5 25 0.51
6 10 0.20
7 4 0.08
8 1 0.02
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (5 bp):
TTTTA
Found at i:46619355 original size:8 final size:8
Alignment explanation
Indices: 46619345--46619408 Score: 67
Period size: 8 Copynumber: 7.8 Consensus size: 8
46619335 AATCCAATTT
*
46619345 TTATTTTT
1 TTATTTTA
46619353 TTATTTTA
1 TTATTTTA
46619361 TTATTATTA
1 TTATT-TTA
*
46619370 TTATTAT-
1 TTATTTTA
46619377 TTATTTTA
1 TTATTTTA
*
46619385 TTTTATTATA
1 --TTATTTTA
46619395 TTATTTTA
1 TTATTTTA
46619403 TTATTT
1 TTATTT
46619409 ACTAATTCAT
Statistics
Matches: 47, Mismatches: 5, Indels: 8
0.78 0.08 0.13
Matches are distributed among these distances:
7 6 0.13
8 26 0.55
9 8 0.17
10 7 0.15
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (8 bp):
TTATTTTA
Found at i:46619361 original size:13 final size:13
Alignment explanation
Indices: 46619343--46619408 Score: 87
Period size: 13 Copynumber: 4.8 Consensus size: 13
46619333 GCAATCCAAT
*
46619343 TTTTATTTTTTTA
1 TTTTATTATTTTA
46619356 TTTTATTATTATTA
1 TTTTATTATT-TTA
46619370 TTATTATTTATTTTA
1 TT-TTA-TTATTTTA
*
46619385 TTTTATTATATTA
1 TTTTATTATTTTA
46619398 TTTTATTATTT
1 TTTTATTATTT
46619409 ACTAATTCAT
Statistics
Matches: 47, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
13 26 0.55
14 8 0.17
15 8 0.17
16 5 0.11
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (13 bp):
TTTTATTATTTTA
Found at i:46619364 original size:3 final size:3
Alignment explanation
Indices: 46619353--46619407 Score: 66
Period size: 3 Copynumber: 19.7 Consensus size: 3
46619343 TTTTATTTTT
46619353 TTA TT- TTA TTA TTA TTA TTA TTA TTTA TT- TTA TT- TTA TTA -TA
1 TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA
46619395 TTA TT- TTA TTA TT
1 TTA TTA TTA TTA TT
46619408 TACTAATTCA
Statistics
Matches: 46, Mismatches: 0, Indels: 12
0.79 0.00 0.21
Matches are distributed among these distances:
2 10 0.22
3 33 0.72
4 3 0.07
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (3 bp):
TTA
Found at i:46622766 original size:10 final size:10
Alignment explanation
Indices: 46622751--46622810 Score: 79
Period size: 10 Copynumber: 6.0 Consensus size: 10
46622741 TAATTCTAGG
46622751 ATTTAT-TTT
1 ATTTATCTTT
46622760 CATTTATCTTT
1 -ATTTATCTTT
46622771 ATTTATCTTT
1 ATTTATCTTT
*
46622781 AATTATCTTT
1 ATTTATCTTT
46622791 ATTTAT-TTGT
1 ATTTATCTT-T
46622801 ATTTATCTTT
1 ATTTATCTTT
46622811 TAGAATTTCA
Statistics
Matches: 45, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
9 2 0.04
10 38 0.84
11 5 0.11
ACGTcount: A:0.22, C:0.08, G:0.02, T:0.68
Consensus pattern (10 bp):
ATTTATCTTT
Found at i:46622918 original size:71 final size:73
Alignment explanation
Indices: 46622836--46622977 Score: 243
Period size: 71 Copynumber: 2.0 Consensus size: 73
46622826 AATAGACTAG
* * *
46622836 GTTTTCTAGTACTATAAATAGGGGATGGAGTGGCACATATTTGACATC-TT-TTTTTCCTTTTAA
1 GTTTTCTAGTACTATAAATAAGGGATGGAGTGGCACATATTTGACATCTTTCTTTTTCCTGTAAA
46622899 CACTCCCA
66 CACTCCCA
46622907 GTTTTCTAGTACTATAAATAAGGGATGGAGTGGCACATATTTGACATCTTTCTTTTTCCTGTAAA
1 GTTTTCTAGTACTATAAATAAGGGATGGAGTGGCACATATTTGACATCTTTCTTTTTCCTGTAAA
46622972 CACTCC
66 CACTCC
46622978 TTCTCCCAAA
Statistics
Matches: 66, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
71 47 0.71
72 2 0.03
73 17 0.26
ACGTcount: A:0.26, C:0.18, G:0.17, T:0.39
Consensus pattern (73 bp):
GTTTTCTAGTACTATAAATAAGGGATGGAGTGGCACATATTTGACATCTTTCTTTTTCCTGTAAA
CACTCCCA
Found at i:46623630 original size:17 final size:18
Alignment explanation
Indices: 46623597--46623631 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
46623587 ATTTTTCCTC
46623597 ATTTAATTTCTGCAATTT
1 ATTTAATTTCTGCAATTT
46623615 ATTTAATTTC-GCAATTT
1 ATTTAATTTCTGCAATTT
46623632 CAATTCACTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 7 0.41
18 10 0.59
ACGTcount: A:0.29, C:0.11, G:0.06, T:0.54
Consensus pattern (18 bp):
ATTTAATTTCTGCAATTT
Found at i:46646962 original size:19 final size:21
Alignment explanation
Indices: 46646923--46646968 Score: 62
Period size: 19 Copynumber: 2.3 Consensus size: 21
46646913 ATCTCTTCAT
46646923 ATAA-ATATCATATATCATAC
1 ATAATATATCATATATCATAC
*
46646943 ATTATATATC-TATATC-TAC
1 ATAATATATCATATATCATAC
46646962 ATAATAT
1 ATAATAT
46646969 GTATTATAAG
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
19 9 0.39
20 9 0.39
21 5 0.22
ACGTcount: A:0.46, C:0.13, G:0.00, T:0.41
Consensus pattern (21 bp):
ATAATATATCATATATCATAC
Found at i:46647674 original size:3 final size:3
Alignment explanation
Indices: 46647668--46647701 Score: 50
Period size: 3 Copynumber: 11.3 Consensus size: 3
46647658 TAATAATGTG
* *
46647668 AAT AAT AAT AAT AAT GAT GAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
46647702 CTTTGAGAAG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.62, C:0.00, G:0.06, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:46647679 original size:18 final size:18
Alignment explanation
Indices: 46647653--46647700 Score: 71
Period size: 18 Copynumber: 2.7 Consensus size: 18
46647643 CTACTAGAAA
*
46647653 AATATTAATAATG-TGAAT
1 AATAATAATAATGATG-AT
46647671 AATAATAATAATGATGAT
1 AATAATAATAATGATGAT
46647689 AATAATAATAAT
1 AATAATAATAAT
46647701 ACTTTGAGAA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
18 26 0.93
19 2 0.07
ACGTcount: A:0.56, C:0.00, G:0.08, T:0.35
Consensus pattern (18 bp):
AATAATAATAATGATGAT
Found at i:46647919 original size:40 final size:40
Alignment explanation
Indices: 46647875--46647955 Score: 162
Period size: 40 Copynumber: 2.0 Consensus size: 40
46647865 CACCCCAAAA
46647875 TATATATGGTTAGAAGTAATAATTTATCAAGAAAAGAGTC
1 TATATATGGTTAGAAGTAATAATTTATCAAGAAAAGAGTC
46647915 TATATATGGTTAGAAGTAATAATTTATCAAGAAAAGAGTC
1 TATATATGGTTAGAAGTAATAATTTATCAAGAAAAGAGTC
46647955 T
1 T
46647956 TAGTCTTGAT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 41 1.00
ACGTcount: A:0.44, C:0.05, G:0.17, T:0.33
Consensus pattern (40 bp):
TATATATGGTTAGAAGTAATAATTTATCAAGAAAAGAGTC
Found at i:46648595 original size:30 final size:30
Alignment explanation
Indices: 46648559--46648622 Score: 128
Period size: 30 Copynumber: 2.1 Consensus size: 30
46648549 TGAACTCATA
46648559 CATAGTTGGCAAATGCCTTCTTCGAACATT
1 CATAGTTGGCAAATGCCTTCTTCGAACATT
46648589 CATAGTTGGCAAATGCCTTCTTCGAACATT
1 CATAGTTGGCAAATGCCTTCTTCGAACATT
46648619 CATA
1 CATA
46648623 ATTTAACCTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 34 1.00
ACGTcount: A:0.28, C:0.23, G:0.16, T:0.33
Consensus pattern (30 bp):
CATAGTTGGCAAATGCCTTCTTCGAACATT
Found at i:46648905 original size:27 final size:27
Alignment explanation
Indices: 46648842--46648984 Score: 150
Period size: 27 Copynumber: 5.3 Consensus size: 27
46648832 CTCAATGGCC
46648842 TTTCATTT-AGAGTTCGCCACAAAGGTAA
1 TTTC-TTTCAGAGTTCGCCACAAAGG-AA
*
46648870 -TTCTCTT-AGAACTT-GCCACAAAGGAA
1 TTTCT-TTCAG-AGTTCGCCACAAAGGAA
* * *
46648896 TTTCTTTTAGAGTTCGCTACAAAGGCA
1 TTTCTTTCAGAGTTCGCCACAAAGGAA
* *
46648923 TTTCTTTCAGAGTTTGCCACAAAGGCA
1 TTTCTTTCAGAGTTCGCCACAAAGGAA
* *
46648950 TGTCCTTCAGAGTTCGCCACAAAGGAA
1 TTTCTTTCAGAGTTCGCCACAAAGGAA
46648977 TTTCTTTC
1 TTTCTTTC
46648985 CTGACGTGTT
Statistics
Matches: 97, Mismatches: 13, Indels: 11
0.80 0.11 0.09
Matches are distributed among these distances:
26 8 0.08
27 86 0.89
28 3 0.03
ACGTcount: A:0.28, C:0.22, G:0.17, T:0.33
Consensus pattern (27 bp):
TTTCTTTCAGAGTTCGCCACAAAGGAA
Done.