Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr1
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: 106989029
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 3754247 characters in sequence are not A, C, G, or T
File 130 of 322
Found at i:42487125 original size:22 final size:22
Alignment explanation
Indices: 42487100--42487150 Score: 68
Period size: 22 Copynumber: 2.3 Consensus size: 22
42487090 GAGTTAATAT
*
42487100 TTTAAGGTTTAT-GGATTATGGG
1 TTTAAGGATTATGGGATTAT-GG
*
42487122 TTTAAGGATTATGGGTTTATGG
1 TTTAAGGATTATGGGATTATGG
42487144 TTTAAGG
1 TTTAAGG
42487151 GTTGGGTTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
22 20 0.77
23 6 0.23
ACGTcount: A:0.24, C:0.00, G:0.31, T:0.45
Consensus pattern (22 bp):
TTTAAGGATTATGGGATTATGG
Found at i:42487983 original size:15 final size:15
Alignment explanation
Indices: 42487963--42488022 Score: 61
Period size: 15 Copynumber: 4.1 Consensus size: 15
42487953 GGCCATTACA
42487963 GATTATGGGTTTAGG
1 GATTATGGGTTTAGG
*
42487978 GATTATAGGTTTAGG
1 GATTATGGGTTTAGG
* *
42487993 GTTTAAGGG-TTATGG
1 GATTATGGGTTTA-GG
*
42488008 G-TTAGGGGTTTAGG
1 GATTATGGGTTTAGG
42488022 G
1 G
42488023 GTTAAAGGGA
Statistics
Matches: 38, Mismatches: 5, Indels: 5
0.79 0.10 0.10
Matches are distributed among these distances:
14 12 0.32
15 26 0.68
ACGTcount: A:0.20, C:0.00, G:0.42, T:0.38
Consensus pattern (15 bp):
GATTATGGGTTTAGG
Found at i:42488024 original size:22 final size:22
Alignment explanation
Indices: 42487969--42488031 Score: 74
Period size: 22 Copynumber: 2.9 Consensus size: 22
42487959 TACAGATTAT
* *
42487969 GGGTTTAGGGATTATAGGTTTA
1 GGGTTTAGGGGTTATAGGGTTA
*
42487991 GGGTTTAAGGGTTAT-GGGTTA
1 GGGTTTAGGGGTTATAGGGTTA
*
42488012 GGGGTTTAGGGGTTAAAGGG
1 -GGGTTTAGGGGTTATAGGG
42488032 ATAAGCGTGA
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
21 5 0.15
22 26 0.76
23 3 0.09
ACGTcount: A:0.21, C:0.00, G:0.44, T:0.35
Consensus pattern (22 bp):
GGGTTTAGGGGTTATAGGGTTA
Found at i:42488108 original size:15 final size:14
Alignment explanation
Indices: 42488088--42488124 Score: 56
Period size: 15 Copynumber: 2.6 Consensus size: 14
42488078 AATATTTTAA
42488088 GGTTTATGAATTAT
1 GGTTTATGAATTAT
*
42488102 GGGTTTATGGATTAT
1 -GGTTTATGAATTAT
42488117 GGTTTATG
1 GGTTTATG
42488125 GTTTAAGGGT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
14 8 0.38
15 13 0.62
ACGTcount: A:0.22, C:0.00, G:0.30, T:0.49
Consensus pattern (14 bp):
GGTTTATGAATTAT
Found at i:42488111 original size:8 final size:7
Alignment explanation
Indices: 42488059--42488129 Score: 61
Period size: 7 Copynumber: 9.9 Consensus size: 7
42488049 AGGGGATAAG
42488059 GGTTTAT
1 GGTTTAT
42488066 GGTTTAT
1 GGTTTAT
*
42488073 GAGTTAAT
1 G-GTTTAT
** *
42488081 ATTTTAA
1 GGTTTAT
42488088 GGTTTAT
1 GGTTTAT
**
42488095 GAATTAT
1 GGTTTAT
42488102 GGGTTTAT
1 -GGTTTAT
*
42488110 GGATTAT
1 GGTTTAT
42488117 GGTTTAT
1 GGTTTAT
42488124 GGTTTA
1 GGTTTA
42488130 AGGGTTGGGG
Statistics
Matches: 48, Mismatches: 14, Indels: 4
0.73 0.21 0.06
Matches are distributed among these distances:
7 38 0.79
8 10 0.21
ACGTcount: A:0.24, C:0.00, G:0.25, T:0.51
Consensus pattern (7 bp):
GGTTTAT
Found at i:42488141 original size:14 final size:15
Alignment explanation
Indices: 42488124--42488172 Score: 57
Period size: 14 Copynumber: 3.4 Consensus size: 15
42488114 TATGGTTTAT
42488124 GGTTTAAGGGTT-GG
1 GGTTTAAGGGTTAGG
* *
42488138 GGTTTAAAGTTTAGG
1 GGTTTAAGGGTTAGG
*
42488153 GG-TTAAGGGTTATG
1 GGTTTAAGGGTTAGG
42488167 GGTTTA
1 GGTTTA
42488173 TAGGTTAAAA
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
14 21 0.75
15 7 0.25
ACGTcount: A:0.20, C:0.00, G:0.41, T:0.39
Consensus pattern (15 bp):
GGTTTAAGGGTTAGG
Found at i:42488379 original size:16 final size:16
Alignment explanation
Indices: 42488360--42488413 Score: 57
Period size: 16 Copynumber: 3.8 Consensus size: 16
42488350 CTATTAAATA
42488360 ATTTCAAATTTTCAAG
1 ATTTCAAATTTTCAAG
*
42488376 ATTTAAAATTTTC-A-
1 ATTTCAAATTTTCAAG
42488390 A--T--AATTTTCAAG
1 ATTTCAAATTTTCAAG
42488402 ATTTCAAATTTT
1 ATTTCAAATTTT
42488414 ATCTAATTCT
Statistics
Matches: 31, Mismatches: 1, Indels: 12
0.70 0.02 0.27
Matches are distributed among these distances:
10 7 0.23
11 1 0.03
12 2 0.06
14 2 0.06
15 1 0.03
16 18 0.58
ACGTcount: A:0.39, C:0.09, G:0.04, T:0.48
Consensus pattern (16 bp):
ATTTCAAATTTTCAAG
Found at i:42488560 original size:15 final size:16
Alignment explanation
Indices: 42488529--42488561 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
42488519 AACTGATTGT
42488529 TTTTTAATTTATATTA
1 TTTTTAATTTATATTA
42488545 TTTTTAATTTAT-TTA
1 TTTTTAATTTATATTA
42488560 TT
1 TT
42488562 AAATAATTTC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.29
16 12 0.71
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (16 bp):
TTTTTAATTTATATTA
Found at i:42488742 original size:115 final size:113
Alignment explanation
Indices: 42488618--42488828 Score: 273
Period size: 115 Copynumber: 1.8 Consensus size: 113
42488608 CGCCGCAAAA
* * * *
42488618 GGTAAAAACGCCGCAAAAGATCATTATGTTTTAAA-CTAAACGGC-GTCGTTTTATCGGATTTGT
1 GGTAAAAACGCCACAAAAGATCATTATG-TTTAAATCAAAACGGCAAT-GTTTTATCGG-TTTAT
* *
42488681 TAGTGGCATTTTTTGTAAAGCGCCGCAATAGGTTAGGATTTAGCAGTGCTAG
63 TAGTGGCA-TTTTGGTAAAACGCCGCAATAGGTTAGGATTTAGCAGTGCTAG
* * * * *
42488733 GGTATAAACGCCACAAAAGATTATTTTGTTTAAATCAAAACGTCAATGTTTTATTGGTTTATTAG
1 GGTAAAAACGCCACAAAAGATCATTATGTTTAAATCAAAACGGCAATGTTTTATCGGTTTATTAG
42488798 TGGCATTTTGGTAAAACGCCGCAATAGGTTA
66 TGGCATTTTGGTAAAACGCCGCAATAGGTTA
42488829 CCCTTTTAGC
Statistics
Matches: 83, Mismatches: 11, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
113 24 0.29
114 18 0.22
115 40 0.48
116 1 0.01
ACGTcount: A:0.31, C:0.14, G:0.22, T:0.34
Consensus pattern (113 bp):
GGTAAAAACGCCACAAAAGATCATTATGTTTAAATCAAAACGGCAATGTTTTATCGGTTTATTAG
TGGCATTTTGGTAAAACGCCGCAATAGGTTAGGATTTAGCAGTGCTAG
Found at i:42488858 original size:114 final size:115
Alignment explanation
Indices: 42488620--42488863 Score: 271
Period size: 114 Copynumber: 2.1 Consensus size: 115
42488610 CCGCAAAAGG
* * *
42488620 TAAAAACGCCGCAAAAGATCATTATGTTTTAAACTAAACGGCGTCGTTTTATCGGATTTGTTAGT
1 TAAAAACGCCGCAAAAGATCATTATGTTTTAAACAAAACGGCATCGTTTTATCGGATTTATTAGT
* * ** * *
42488685 GGCATTTTTTGTAAAGCGCCGCAATAGGTTAGGATTTAGCAGTGCTAGGG
66 GGCATTTTTGGTAAAACGCCGCAATAGGTTACCATTTAGCAGCGCTAGGA
* * * * * *
42488735 TATAAACGCCACAAAAGATTATTTTG-TTTAAATCAAAACGTCAAT-GTTTTATTGG-TTTATTA
1 TAAAAACGCCGCAAAAGATCATTATGTTTTAAA-CAAAACGGC-ATCGTTTTATCGGATTTATTA
* * *
42488797 GTGGCA-TTTTGGTAAAACGCCGCAATAGGTTACCCTTTTAGCGGCGCTATGA
64 GTGGCATTTTTGGTAAAACGCCGCAATAGGTTA-CCATTTAGCAGCGCTAGGA
42488849 TAAAAACGCCGCAAA
1 TAAAAACGCCGCAAA
42488864 GGTTAAATTA
Statistics
Matches: 106, Mismatches: 20, Indels: 7
0.80 0.15 0.05
Matches are distributed among these distances:
113 24 0.23
114 43 0.41
115 38 0.36
116 1 0.01
ACGTcount: A:0.31, C:0.16, G:0.21, T:0.32
Consensus pattern (115 bp):
TAAAAACGCCGCAAAAGATCATTATGTTTTAAACAAAACGGCATCGTTTTATCGGATTTATTAGT
GGCATTTTTGGTAAAACGCCGCAATAGGTTACCATTTAGCAGCGCTAGGA
Found at i:42491050 original size:24 final size:24
Alignment explanation
Indices: 42491020--42491072 Score: 97
Period size: 24 Copynumber: 2.2 Consensus size: 24
42491010 CTATGTTATG
42491020 ATATTTGTAACTAAAATTAATATT
1 ATATTTGTAACTAAAATTAATATT
*
42491044 ATATTTGTATCTAAAATTAATATT
1 ATATTTGTAACTAAAATTAATATT
42491068 ATATT
1 ATATT
42491073 ATAAAACACT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.43, C:0.04, G:0.04, T:0.49
Consensus pattern (24 bp):
ATATTTGTAACTAAAATTAATATT
Found at i:42494448 original size:13 final size:14
Alignment explanation
Indices: 42494432--42494460 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
42494422 TTTTAAATAT
42494432 TTATAAT-GTTTAA
1 TTATAATGGTTTAA
42494445 TTATAATGGTTTAA
1 TTATAATGGTTTAA
42494459 TT
1 TT
42494461 CGTCATTAGT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.47
14 8 0.53
ACGTcount: A:0.34, C:0.00, G:0.10, T:0.55
Consensus pattern (14 bp):
TTATAATGGTTTAA
Found at i:42494863 original size:21 final size:21
Alignment explanation
Indices: 42494837--42494881 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
42494827 ACTTAGAGTG
*
42494837 GAGGCAATAGCGAGGGAAGCA
1 GAGGCAATAACGAGGGAAGCA
*
42494858 GAGGCAGTAACGAGGGAAGCA
1 GAGGCAATAACGAGGGAAGCA
42494879 GAG
1 GAG
42494882 CAGAGCAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.38, C:0.13, G:0.44, T:0.04
Consensus pattern (21 bp):
GAGGCAATAACGAGGGAAGCA
Found at i:42495214 original size:43 final size:43
Alignment explanation
Indices: 42495149--42495311 Score: 191
Period size: 43 Copynumber: 3.8 Consensus size: 43
42495139 AATACGAGTA
* * * *
42495149 AAAAGCGCCGTTAAAGGACATGTTCTTTAGCGACGTTTGTGCT
1 AAAAGCGCCGCTAAAGGTCATGTTCTTTAGCGGCGTTTGTGAT
* * * * *
42495192 GAAAGCGCCGTTAAAGGTCATGTCCTTTAGAGGCGTTTGTGGT
1 AAAAGCGCCGCTAAAGGTCATGTTCTTTAGCGGCGTTTGTGAT
** *
42495235 AAAAGTACCACTAAAGGTCATGTTCTTTAGCGGCGTTTGTGAT
1 AAAAGCGCCGCTAAAGGTCATGTTCTTTAGCGGCGTTTGTGAT
* * *
42495278 AAAAGCGCAGCTAAAAGTCATATTCTTTAGCGGC
1 AAAAGCGCCGCTAAAGGTCATGTTCTTTAGCGGC
42495312 TGTAGTGGGC
Statistics
Matches: 100, Mismatches: 20, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
43 100 1.00
ACGTcount: A:0.27, C:0.18, G:0.26, T:0.29
Consensus pattern (43 bp):
AAAAGCGCCGCTAAAGGTCATGTTCTTTAGCGGCGTTTGTGAT
Found at i:42496712 original size:18 final size:19
Alignment explanation
Indices: 42496689--42496731 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 19
42496679 AAATGTTTTT
42496689 TATACATTAT-TATATATA
1 TATACATTATATATATATA
*
42496707 TATACA-TATATATCTATA
1 TATACATTATATATATATA
*
42496725 TGTACAT
1 TATACAT
42496732 ATGTTCTTTG
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
17 3 0.14
18 18 0.86
ACGTcount: A:0.42, C:0.09, G:0.02, T:0.47
Consensus pattern (19 bp):
TATACATTATATATATATA
Found at i:42498362 original size:132 final size:130
Alignment explanation
Indices: 42498097--42498735 Score: 402
Period size: 132 Copynumber: 4.8 Consensus size: 130
42498087 AATTATTAAG
* *
42498097 AATTCTTCAAAACGAAGGCGATATTCGATTCTTGGCAATTCGTGGAATTGTGCCCTAACGTGTTG
1 AATTCTTTAAAACGAAGGCGATATTCGATT-TTGGCAATTCG-GGAATCGTGCCCTAACGTGTTG
** * * * * *
42498162 GGTTGCAATTTCTCGTTTGCT-AAAAGTAATCGAAGGTCCCTTTAGAATTTCACCCATGTCTCTT
64 GGTTGCAATTTCTCGTTTGCTCAAAA-TAATCGAATATCCCTTCAAAATTCCACCCAGGTCTCTC
42498226 AAA
128 AAA
* * * * *
42498229 AATTCTTTAAAGCGAAGACGAGATTTGATATTTGGCAATTCGCGGAATCGTGCCCTAACATGTTG
1 AATTCTTTAAAACGAAGGCGATATTCGAT-TTTGGCAATTCG-GGAATCGTGCCCTAACGTGTTG
* *
42498294 GGTTGCAATTTCTCGTTTGCTCAAAATAATCAAATATCCCTTCAAAATTCCACTCAGGTCT-TCC
64 GGTTGCAATTTCTCGTTTGCTCAAAATAATCGAATATCCCTTCAAAATTCCACCCAGGTCTCT-C
42498358 AAA
128 AAA
** * * * * * * * *
42498361 AACCCTCTAAAACGAAGGCAATACTCGGTGTTTGACAATTCGGGAATCATGCCCTATCGTGCTGG
1 AATTCTTTAAAACGAAGGCGATATTCGAT-TTTGGCAATTCGGGAATCGTGCCCTAACGTGTTGG
** * * * * *** * * * * * *
42498426 GTTGTGATTTCTCGTTTGGTCAAAACAATCGAATATTCCTTTAGGTTTTCACTCATGTTTTTTTT
65 GTTGCAATTTCTCGTTTGCTCAAAATAATCGAATATCCCTTCAAAATTCCACCCA-G-GTCTCTC
42498491 AAGA
128 AA-A
* * * * * * * *
42498495 AA-ACATTTCAAAACGAAGGTGATGTTCAATGTTTGGCAATTTGAGAATCGTGCCCTATCGTGCT
1 AATTC-TTT-AAAACGAAGGCGATATTCGAT-TTTGGCAATTCGGGAATCGTGCCCTAACGTGTT
** * * * * * * ** * * ** * *
42498559 GGGTTGCTCTTTTTCATTTGTTCGAAACAATCGAAGATCCCTTCGGAATTTCACTCACTTTTTTC
63 GGGTTGCAATTTCTCGTTTGCTCAAAATAATCGAATATCCCTTCAAAATTCCACCCAGGTCTCTC
*
42498624 TAGA
128 -AAA
* * ** * * * *
42498628 AACTCTTTAAAACGAAAGAAATGTTCGATGTTTGGTAATTCGGGGAATAGTGCCCTATCGTGTTG
1 AATTCTTTAAAACGAAGGCGATATTCGAT-TTTGGCAATTC-GGGAATCGTGCCCTAACGTGTTG
* * * * *
42498693 GGTTGCAATCTCCCGTTTGTTCAAAATAATTGAATATCTCTTC
64 GGTTGCAATTTCTCGTTTGCTCAAAATAATCGAATATCCCTTC
42498736 GGAATTTCAC
Statistics
Matches: 399, Mismatches: 96, Indels: 23
0.77 0.19 0.04
Matches are distributed among these distances:
131 64 0.16
132 164 0.41
133 74 0.19
134 8 0.02
135 89 0.22
ACGTcount: A:0.27, C:0.19, G:0.19, T:0.35
Consensus pattern (130 bp):
AATTCTTTAAAACGAAGGCGATATTCGATTTTGGCAATTCGGGAATCGTGCCCTAACGTGTTGGG
TTGCAATTTCTCGTTTGCTCAAAATAATCGAATATCCCTTCAAAATTCCACCCAGGTCTCTCAAA
Found at i:42498549 original size:135 final size:132
Alignment explanation
Indices: 42498259--42498747 Score: 355
Period size: 135 Copynumber: 3.7 Consensus size: 132
42498249 AGATTTGATA
* * * * * *
42498259 TTTGGCAATTCGCGGAATCGTGCCCTAACATGTTGGGTTGCAATTTCTCGTTTGCTCAAAATAAT
1 TTTGGCAATTCG-GGAATCGTGCCCTATCGTGCTGGGTTG-TATTTCTCGTTTGTTCAAAACAAT
* * * ** * * * * * * **
42498324 CAAATA-TCCCTTCA-AAATTCCACTCA-GGTCTTCCAAAAAC-CCTCTAAAACGAAGGCAATAC
64 CGAATATTCCCTT-AGGAATTTCACTCACTTTTTTCTAGAAACTCTTC-AAAACGAAAGAAATGT
**
42498385 TCGGTG
127 TCAATG
* * *
42498391 TTTGACAATTCGGGAATCATGCCCTATCGTGCTGGGTTGTGATTTCTCGTTTGGTCAAAACAATC
1 TTTGGCAATTCGGGAATCGTGCCCTATCGTGCTGGGTTGT-ATTTCTCGTTTGTTCAAAACAATC
* * * * * **
42498456 GAATATTCCTTTAGG-TTTTCACTCATGTTTTTTTTAAGAAAACAT-TTCAAAACGAAGGTGATG
65 GAATATTCCCTTAGGAATTTCACTCA-CTTTTTTCT-AG-AAAC-TCTTCAAAACGAAAGAAATG
42498519 TTCAATG
126 TTCAATG
* * * * * *
42498526 TTTGGCAATTTGAGAATCGTGCCCTATCGTGCTGGGTTGCTCTTTTTCATTTGTTCGAAACAATC
1 TTTGGCAATTCGGGAATCGTGCCCTATCGTGCTGGGTTG-TATTTCTCGTTTGTTCAAAACAATC
* * * *
42498591 GAAGA-TCCCTTCGGAATTTCACTCACTTTTTTCTAGAAACTCTTTAAAACGAAAGAAATGTTCG
65 GAATATTCCCTTAGGAATTTCACTCACTTTTTTCTAGAAACTCTTCAAAACGAAAGAAATGTTCA
42498655 ATG
130 ATG
* * * * * * *
42498658 TTTGGTAATTCGGGGAATAGTGCCCTATCGTGTTGGGTTGCAATCTCCCGTTTGTTCAAAATAAT
1 TTTGGCAATTC-GGGAATCGTGCCCTATCGTGCTGGGTTG-TATTTCTCGTTTGTTCAAAACAAT
* * *
42498723 TGAATA-TCTCTTCGGAATTTCACTC
64 CGAATATTCCCTTAGGAATTTCACTC
42498748 GTGTTTTCTA
Statistics
Matches: 282, Mismatches: 62, Indels: 25
0.76 0.17 0.07
Matches are distributed among these distances:
131 59 0.21
132 49 0.17
133 69 0.24
134 15 0.05
135 87 0.31
136 3 0.01
ACGTcount: A:0.26, C:0.20, G:0.19, T:0.35
Consensus pattern (132 bp):
TTTGGCAATTCGGGAATCGTGCCCTATCGTGCTGGGTTGTATTTCTCGTTTGTTCAAAACAATCG
AATATTCCCTTAGGAATTTCACTCACTTTTTTCTAGAAACTCTTCAAAACGAAAGAAATGTTCAA
TG
Found at i:42499321 original size:43 final size:43
Alignment explanation
Indices: 42499268--42499357 Score: 144
Period size: 43 Copynumber: 2.1 Consensus size: 43
42499258 ACAGCGGCAT
*
42499268 TTTTGCCACAAACGCCGATAAAAAACATGACCTTTAGCGGCGC
1 TTTTGCCACAAACGCCGATAAAAAACATGACCTTTAGCAGCGC
* * *
42499311 TTTTGCCACAAACGTCGCTAAAGAACATGACCTTTAGCAGCGC
1 TTTTGCCACAAACGCCGATAAAAAACATGACCTTTAGCAGCGC
42499354 TTTT
1 TTTT
42499358 TACAAATAAA
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
43 43 1.00
ACGTcount: A:0.30, C:0.27, G:0.18, T:0.26
Consensus pattern (43 bp):
TTTTGCCACAAACGCCGATAAAAAACATGACCTTTAGCAGCGC
Found at i:42499465 original size:13 final size:13
Alignment explanation
Indices: 42499449--42499473 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
42499439 TTAGTGGCGC
42499449 TTAAAAGTGCCGT
1 TTAAAAGTGCCGT
42499462 TTAAAAGTGCCG
1 TTAAAAGTGCCG
42499474 CTATAGGCCT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.24, T:0.28
Consensus pattern (13 bp):
TTAAAAGTGCCGT
Found at i:42501029 original size:179 final size:179
Alignment explanation
Indices: 42500729--42501088 Score: 684
Period size: 179 Copynumber: 2.0 Consensus size: 179
42500719 GTGGTGGTGA
42500729 ATATGTTGAACCATTTGATGAATACTGTGCACAAAATGGTATTATTCATGAAGTGACACCACCAT
1 ATATGTTGAACCATTTGATGAATACTGTGCACAAAATGGTATTATTCATGAAGTGACACCACCAT
42500794 ACTCTCCTCAATCAAATGGAGTATCTGAACAAAAAATCAGACTCTGAAGGAAATGATGAACGCCT
66 ACTCTCCTCAATCAAATGGAGTATCTGAACAAAAAATCAGACTCTGAAGGAAATGATGAACGCCT
*
42500859 TGCTACAAAGCTATGGGTTATAACAGGAAATGTAGGGGGAAACTTCTCT
131 TGCTACAAAGCTATGGGTTATAACAGGAAATGTAGGAGGAAACTTCTCT
* *
42500908 ATATGTTGAACCATTTGGTGAATACTGTGCACAAAATGGTATTATTCATGAAGTGACACCACTAT
1 ATATGTTGAACCATTTGATGAATACTGTGCACAAAATGGTATTATTCATGAAGTGACACCACCAT
*
42500973 ACTCTCCTCAATCAAATGGAGTATCTGAACGAAAAATCAGACTCTGAAGGAAATGATGAACGCCT
66 ACTCTCCTCAATCAAATGGAGTATCTGAACAAAAAATCAGACTCTGAAGGAAATGATGAACGCCT
42501038 TGCTACAAAGCTATGGGTTATAACAGGAAATGTAGGAGGAAACTTCTCT
131 TGCTACAAAGCTATGGGTTATAACAGGAAATGTAGGAGGAAACTTCTCT
42501087 AT
1 AT
42501089 CAACTAATTA
Statistics
Matches: 177, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
179 177 1.00
ACGTcount: A:0.36, C:0.17, G:0.20, T:0.27
Consensus pattern (179 bp):
ATATGTTGAACCATTTGATGAATACTGTGCACAAAATGGTATTATTCATGAAGTGACACCACCAT
ACTCTCCTCAATCAAATGGAGTATCTGAACAAAAAATCAGACTCTGAAGGAAATGATGAACGCCT
TGCTACAAAGCTATGGGTTATAACAGGAAATGTAGGAGGAAACTTCTCT
Found at i:42503045 original size:19 final size:19
Alignment explanation
Indices: 42502999--42503050 Score: 52
Period size: 19 Copynumber: 2.7 Consensus size: 19
42502989 TTCGTTTGCC
* *
42502999 CTTTCTTTTTCATTATTTT
1 CTTTATTTTTTATTATTTT
*
42503018 ATTTATTTTTTATTATTATT
1 CTTTATTTTTTATTATT-TT
*
42503038 CTTT-TTTTATATT
1 CTTTATTTTTTATT
42503051 CTCTGTTATT
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
19 22 0.81
20 5 0.19
ACGTcount: A:0.17, C:0.08, G:0.00, T:0.75
Consensus pattern (19 bp):
CTTTATTTTTTATTATTTT
Found at i:42503383 original size:3 final size:3
Alignment explanation
Indices: 42503377--42503409 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
42503367 TTCTTTTCCA
42503377 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
42503410 CATTCATTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:42507933 original size:22 final size:23
Alignment explanation
Indices: 42507899--42507946 Score: 64
Period size: 22 Copynumber: 2.1 Consensus size: 23
42507889 TTAAATGTAA
42507899 TATTCTAATTCAATAAATATTATT
1 TATTCTAATTCAATAAAT-TTATT
*
42507923 TATT-TAA-TCAATAAATTTTTT
1 TATTCTAATTCAATAAATTTATT
42507944 TAT
1 TAT
42507947 GAGTATTATA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
21 7 0.30
22 9 0.39
23 3 0.13
24 4 0.17
ACGTcount: A:0.40, C:0.06, G:0.00, T:0.54
Consensus pattern (23 bp):
TATTCTAATTCAATAAATTTATT
Found at i:42509945 original size:31 final size:30
Alignment explanation
Indices: 42509898--42509972 Score: 78
Period size: 31 Copynumber: 2.5 Consensus size: 30
42509888 AATTTTTAAA
* * * *
42509898 TTAATAATAATAAAATTACACTTTAATTTT
1 TTAAAAATGATAAAATTACAATTTAATCTT
**
42509928 TATAAAAATGATAAAATTTTAATTTAATCTT
1 T-TAAAAATGATAAAATTACAATTTAATCTT
*
42509959 TTAAAAATTATAAA
1 TTAAAAATGATAAA
42509973 GATATAAATA
Statistics
Matches: 37, Mismatches: 7, Indels: 2
0.80 0.15 0.04
Matches are distributed among these distances:
30 13 0.35
31 24 0.65
ACGTcount: A:0.51, C:0.04, G:0.01, T:0.44
Consensus pattern (30 bp):
TTAAAAATGATAAAATTACAATTTAATCTT
Found at i:42510994 original size:18 final size:18
Alignment explanation
Indices: 42510971--42511014 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
42510961 TACCTTTTTC
**
42510971 TCTCTCAAATCTTTCTAT
1 TCTCTCAAATCTTTAAAT
*
42510989 TCTCTCAACTCTTTAAAT
1 TCTCTCAAATCTTTAAAT
42511007 TCTCTCAA
1 TCTCTCAA
42511015 TTTTCTCAAG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.25, C:0.30, G:0.00, T:0.45
Consensus pattern (18 bp):
TCTCTCAAATCTTTAAAT
Found at i:42516187 original size:109 final size:107
Alignment explanation
Indices: 42515984--42516304 Score: 391
Period size: 108 Copynumber: 3.0 Consensus size: 107
42515974 TCCATTGCTA
* * * * *
42515984 ATGTTGAATTGCCCAAAACCCTAAATC--ATTTTTTCTAACAGTGAAGACGATGAAGAAAGGGAA
1 ATGTTGAATTGCCCAAAACCCTAAATCTTTTTTTTTCTAACAGTAAAGAAGAT-AAAAAAAGGAA
* * *
42516047 AAAAAT-AGGAAAATCAAATCTCCTTGATGAGAAATTAAATAG
65 AAAAATCAAGAAAATCAAATCTCCCTGATGAGAAATTGAATAG
*
42516089 ATGTTGAATTACCCAAAACCCTAAATCTTTTTTTTTCTAACAGTAAAGAAGATAAAAAAAAAGGA
1 ATGTTGAATTGCCCAAAACCCTAAATCTTTTTTTTTCTAACAGTAAAGAAGAT--AAAAAAAGGA
*
42516154 AAAAAATCAAGAAAATCAAATCTCCCTAATGAGAAATTGAATAG
64 AAAAAATCAAGAAAATCAAATCTCCCTGATGAGAAATTGAATAG
** * * * *
42516198 ATGTTGAATTGCTTAAAACCCTAAATCCTTTTTTTTCCTAACAACG-AAA-ATGATGAAGAAAGG
1 ATGTTGAATTGCCCAAAACCCTAAAT-CTTTTTTTTTCTAAC-A-GTAAAGAAGATAAAAAAAGG
* *
42516261 AAAAAAATCAAGAAAATCAAATCTTCCTGATGAGTAATTGAATA
63 AAAAAAATCAAGAAAATCAAATCTCCCTGATGAGAAATTGAATA
42516305 ACCCAAAATC
Statistics
Matches: 188, Mismatches: 21, Indels: 11
0.85 0.10 0.05
Matches are distributed among these distances:
105 26 0.14
107 21 0.11
108 63 0.34
109 55 0.29
110 18 0.10
111 4 0.02
112 1 0.01
ACGTcount: A:0.46, C:0.14, G:0.14, T:0.26
Consensus pattern (107 bp):
ATGTTGAATTGCCCAAAACCCTAAATCTTTTTTTTTCTAACAGTAAAGAAGATAAAAAAAGGAAA
AAAATCAAGAAAATCAAATCTCCCTGATGAGAAATTGAATAG
Found at i:42516300 original size:108 final size:105
Alignment explanation
Indices: 42515984--42516304 Score: 380
Period size: 109 Copynumber: 3.0 Consensus size: 105
42515974 TCCATTGCTA
* * * *
42515984 ATGTTGAATTGCCCAAAACCCTAAATC-ATTTTTTCTAACAGTGAAGACGATGAAGAAAGGGAAA
1 ATGTTGAATTGCCCAAAACCCTAAATCTTTTTTTTCTAACA-AGAAAAAGATGAAGAAA-GGAAA
* *
42516048 AAAAT-AGGAAAATCAAATC-TCCTTGATGAGAAATTAAATAG
64 AAAATCAAGAAAATCAAATCTTCC-TGATGAGAAATTGAATAG
* * *
42516089 ATGTTGAATTACCCAAAACCCTAAATCTTTTTTTTTCTAAC-AGTAAAGAAGATAAAAAAAAAGG
1 ATGTTGAATTGCCCAAAACCCTAAATC-TTTTTTTTCTAACAAG-AAA-AAGAT--GAAGAAAGG
* *
42516153 AAAAAAATCAAGAAAATCAAATCTCCCTAATGAGAAATTGAATAG
61 AAAAAAATCAAGAAAATCAAATCTTCCTGATGAGAAATTGAATAG
** *
42516198 ATGTTGAATTGCTTAAAACCCTAAATCCTTTTTTTTCCTAACAACGAAAATGATGAAGAAAGGAA
1 ATGTTGAATTGCCCAAAACCCTAAAT-CTTTTTTTT-CTAACAA-GAAAAAGATGAAGAAAGGAA
*
42516263 AAAAATCAAGAAAATCAAATCTTCCTGATGAGTAATTGAATA
63 AAAAATCAAGAAAATCAAATCTTCCTGATGAGAAATTGAATA
42516305 ACCCAAAATC
Statistics
Matches: 184, Mismatches: 20, Indels: 21
0.82 0.09 0.09
Matches are distributed among these distances:
105 27 0.15
106 2 0.01
107 15 0.08
108 58 0.32
109 65 0.35
110 12 0.07
111 4 0.02
112 1 0.01
ACGTcount: A:0.46, C:0.14, G:0.14, T:0.26
Consensus pattern (105 bp):
ATGTTGAATTGCCCAAAACCCTAAATCTTTTTTTTCTAACAAGAAAAAGATGAAGAAAGGAAAAA
AATCAAGAAAATCAAATCTTCCTGATGAGAAATTGAATAG
Found at i:42517131 original size:14 final size:14
Alignment explanation
Indices: 42517112--42517140 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
42517102 TTGAAGAGTT
42517112 AACGAAATTCTCTC
1 AACGAAATTCTCTC
42517126 AACGAAATTCTCTC
1 AACGAAATTCTCTC
42517140 A
1 A
42517141 TTGGCATTGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.38, C:0.28, G:0.07, T:0.28
Consensus pattern (14 bp):
AACGAAATTCTCTC
Found at i:42520350 original size:9 final size:9
Alignment explanation
Indices: 42520330--42520362 Score: 50
Period size: 9 Copynumber: 3.7 Consensus size: 9
42520320 ATATTATATG
42520330 TTATTATTAA
1 TTATT-TTAA
42520340 TTATTTTAA
1 TTATTTTAA
42520349 TTATTTT-A
1 TTATTTTAA
42520357 TTATTT
1 TTATTT
42520363 ATTATATGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
8 7 0.30
9 11 0.48
10 5 0.22
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (9 bp):
TTATTTTAA
Found at i:42526508 original size:99 final size:99
Alignment explanation
Indices: 42526337--42526526 Score: 362
Period size: 99 Copynumber: 1.9 Consensus size: 99
42526327 AATTTATATG
42526337 ATTAAGATTTGAGTTTGGAGTTAAAATTAATTGAAACAAAGAATTAACTAAAAGCTTACAAATTT
1 ATTAAGATTTGAGTTTGGAGTTAAAATTAATTGAAACAAAGAATTAACTAAAAGCTTACAAATTT
42526402 TATTGAAATTTAAATTCCATATATTAGCTGAAGT
66 TATTGAAATTTAAATTCCATATATTAGCTGAAGT
*
42526436 ATTAAGATTTGAGTTTGGAGTTAAAATTAATTGAAACAAAGAATTAACTAAAAGTTTACAAATTT
1 ATTAAGATTTGAGTTTGGAGTTAAAATTAATTGAAACAAAGAATTAACTAAAAGCTTACAAATTT
*
42526501 TATTGAAATTTAAATTTCATATATTA
66 TATTGAAATTTAAATTCCATATATTA
42526527 ACTTAGTTAT
Statistics
Matches: 89, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
99 89 1.00
ACGTcount: A:0.44, C:0.06, G:0.12, T:0.38
Consensus pattern (99 bp):
ATTAAGATTTGAGTTTGGAGTTAAAATTAATTGAAACAAAGAATTAACTAAAAGCTTACAAATTT
TATTGAAATTTAAATTCCATATATTAGCTGAAGT
Found at i:42527099 original size:20 final size:21
Alignment explanation
Indices: 42527063--42527104 Score: 68
Period size: 20 Copynumber: 2.0 Consensus size: 21
42527053 TATTCATTTA
*
42527063 TTAATCCAAAGGAAAATACTT
1 TTAACCCAAAGGAAAATACTT
42527084 TTAACCCAAA-GAAAATACTT
1 TTAACCCAAAGGAAAATACTT
42527104 T
1 T
42527105 GAAAAAGTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 11 0.55
21 9 0.45
ACGTcount: A:0.48, C:0.17, G:0.07, T:0.29
Consensus pattern (21 bp):
TTAACCCAAAGGAAAATACTT
Found at i:42537026 original size:23 final size:24
Alignment explanation
Indices: 42536966--42537026 Score: 65
Period size: 23 Copynumber: 2.6 Consensus size: 24
42536956 CTATTTCATG
42536966 TTTAATTATA-TTAGGATAATTATT
1 TTTAATTATATTTAGGAT-ATTATT
* *
42536990 TATATTTA-ATTTTAGGAT-TTATT
1 TTTAATTATA-TTTAGGATATTATT
42537013 TTTAATTATATTTA
1 TTTAATTATATTTA
42537027 TTTATTTGTA
Statistics
Matches: 30, Mismatches: 4, Indels: 7
0.73 0.10 0.17
Matches are distributed among these distances:
23 16 0.53
24 7 0.23
25 7 0.23
ACGTcount: A:0.34, C:0.00, G:0.07, T:0.59
Consensus pattern (24 bp):
TTTAATTATATTTAGGATATTATT
Found at i:42537739 original size:18 final size:18
Alignment explanation
Indices: 42537716--42537752 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
42537706 TGGAATCTCG
42537716 CCACATAAGAAACTCTTT
1 CCACATAAGAAACTCTTT
42537734 CCACATAAGAAACTCTTT
1 CCACATAAGAAACTCTTT
42537752 C
1 C
42537753 TTTTCCCAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.38, C:0.30, G:0.05, T:0.27
Consensus pattern (18 bp):
CCACATAAGAAACTCTTT
Found at i:42540883 original size:16 final size:18
Alignment explanation
Indices: 42540862--42540952 Score: 77
Period size: 16 Copynumber: 5.2 Consensus size: 18
42540852 AGGCAACCTA
*
42540862 ATTTTTAT-TT-TTCTTT
1 ATTTTTATCTTATTATTT
42540878 ATTTTTATCTTATTATTT
1 ATTTTTATCTTATTATTT
42540896 A--TTTATCTTATTATTT
1 ATTTTTATCTTATTATTT
*
42540912 ATTTAT-TCATTACTTTATTT
1 ATTTTTATC-TTA--TTATTT
*
42540932 -TATTTTATTTTATTATTT
1 AT-TTTTATCTTATTATTT
42540950 ATT
1 ATT
42540953 ACTTTATTTT
Statistics
Matches: 61, Mismatches: 4, Indels: 18
0.73 0.05 0.22
Matches are distributed among these distances:
16 24 0.39
17 4 0.07
18 18 0.30
19 2 0.03
20 12 0.20
21 1 0.02
ACGTcount: A:0.22, C:0.05, G:0.00, T:0.73
Consensus pattern (18 bp):
ATTTTTATCTTATTATTT
Found at i:42540896 original size:12 final size:11
Alignment explanation
Indices: 42540865--42540961 Score: 62
Period size: 12 Copynumber: 8.6 Consensus size: 11
42540855 CAACCTAATT
*
42540865 TTTATTT-TTC
1 TTTATTTATTA
42540875 TTTATTT-TTA
1 TTTATTTATTA
42540885 TCTTA-TTATTTA
1 T-TTATTTA-TTA
42540897 TTTATCTTATTA
1 TTTAT-TTATTA
42540909 TTTATTTATTCA
1 TTTATTTATT-A
42540921 -TTACTTTA-T-
1 TTTA-TTTATTA
*
42540930 TTTATTTTATTT
1 TTTA-TTTATTA
42540942 TATTATTTATTA
1 T-TTATTTATTA
42540954 CTTTATTT
1 -TTTATTT
42540962 TGTTTGGGTG
Statistics
Matches: 72, Mismatches: 3, Indels: 22
0.74 0.03 0.23
Matches are distributed among these distances:
10 19 0.26
11 16 0.22
12 30 0.42
13 7 0.10
ACGTcount: A:0.22, C:0.06, G:0.00, T:0.72
Consensus pattern (11 bp):
TTTATTTATTA
Found at i:42540899 original size:4 final size:4
Alignment explanation
Indices: 42540881--42540961 Score: 55
Period size: 4 Copynumber: 19.8 Consensus size: 4
42540871 TTTCTTTATT
*
42540881 TTTA TCTTA -TTA TTTA TTTA TCTTA -TTA TTTA TTTA TTCA -TTA CTTTA
1 TTTA T-TTA TTTA TTTA TTTA T-TTA TTTA TTTA TTTA TTTA TTTA -TTTA
42540929 TTTTA TTTTA TTT- TATTA TTTA -TTA CTTTA TTT
1 -TTTA -TTTA TTTA T-TTA TTTA TTTA -TTTA TTT
42540962 TGTTTGGGTG
Statistics
Matches: 64, Mismatches: 3, Indels: 20
0.74 0.03 0.23
Matches are distributed among these distances:
3 12 0.19
4 30 0.47
5 22 0.34
ACGTcount: A:0.23, C:0.06, G:0.00, T:0.70
Consensus pattern (4 bp):
TTTA
Found at i:42540929 original size:20 final size:16
Alignment explanation
Indices: 42540881--42540961 Score: 82
Period size: 16 Copynumber: 5.2 Consensus size: 16
42540871 TTTCTTTATT
42540881 TTTATCTTATTATTTA
1 TTTATCTTATTATTTA
42540897 TTTATCTTATTATTTA
1 TTTATCTTATTATTTA
*
42540913 TTTAT-TCATTACTTTA
1 TTTATCTTATTA-TTTA
*
42540929 TTT-TATT-TTATTT-
1 TTTATCTTATTATTTA
42540942 TATTAT-TTATTACTTTA
1 T-TTATCTTATTA-TTTA
42540959 TTT
1 TTT
42540962 TGTTTGGGTG
Statistics
Matches: 56, Mismatches: 2, Indels: 14
0.78 0.03 0.19
Matches are distributed among these distances:
13 1 0.02
14 7 0.12
15 13 0.23
16 34 0.61
17 1 0.02
ACGTcount: A:0.23, C:0.06, G:0.00, T:0.70
Consensus pattern (16 bp):
TTTATCTTATTATTTA
Found at i:42542253 original size:96 final size:97
Alignment explanation
Indices: 42542088--42542266 Score: 263
Period size: 96 Copynumber: 1.9 Consensus size: 97
42542078 AAGAATGTGA
* * ** *
42542088 TGGGCTGAGTAACCAGGGTGAGGTGCTTGGCTGTCATCTCTCTTCGCGTTAAAAGGTTTGATATG
1 TGGGCTGAGTAACCAGGGTGAGGTACTTGGCTGTCATCTCTCTTCGCGTCAAAAGGTTCAATATA
42542153 TTCTTAAG-AAAAATAAAAATTAGGAGCATAT
66 TTCTTAAGCAAAAATAAAAATTAGGAGCATAT
* *
42542184 TGGGCTGAGTAACCCA-GGTGGGGTACTTGGTTGTCATCTCTCTTCGCGTCAAAAGGTTCAATAT
1 TGGGCTGAGTAA-CCAGGGTGAGGTACTTGGCTGTCATCTCTCTTCGCGTCAAAAGGTTCAATAT
*
42542248 ATTCTTAAGCAATAATAAA
65 ATTCTTAAGCAAAAATAAA
42542267 TTAATTAATT
Statistics
Matches: 73, Mismatches: 8, Indels: 3
0.87 0.10 0.04
Matches are distributed among these distances:
96 62 0.85
97 11 0.15
ACGTcount: A:0.28, C:0.16, G:0.25, T:0.31
Consensus pattern (97 bp):
TGGGCTGAGTAACCAGGGTGAGGTACTTGGCTGTCATCTCTCTTCGCGTCAAAAGGTTCAATATA
TTCTTAAGCAAAAATAAAAATTAGGAGCATAT
Found at i:42542907 original size:20 final size:20
Alignment explanation
Indices: 42542884--42542921 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
42542874 TTATTTAGAG
*
42542884 TTATTTTTAATTATCTTTAT
1 TTATTTGTAATTATCTTTAT
*
42542904 TTATTTGTATTTATCTTT
1 TTATTTGTAATTATCTTT
42542922 TAGAATTTAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.21, C:0.05, G:0.03, T:0.71
Consensus pattern (20 bp):
TTATTTGTAATTATCTTTAT
Found at i:42549916 original size:286 final size:284
Alignment explanation
Indices: 42549387--42549916 Score: 679
Period size: 286 Copynumber: 1.9 Consensus size: 284
42549377 ATCTAACCAA
* * * * *
42549387 CCAAAGTTTCCATTATTCTATCCTAAAACAATTAAAAAAAATTATAATGGTCACCTCAAAACATA
1 CCAAACTTTCCATTATTCCATCCTAAAACAATTAAAAAAAATTATAACGATCACCCCAAAACATA
* * *
42549452 CTTTAGGTCTTCTGGTTGAAAACCAAATACCCTAATTGTTAGGGTTCCCCCCCTTAAAACCATAA
66 CTTTAGGTATTCTGGTTGAAAACCAAATACCCTAATTGCTAGGGTTCCCCCCCTTAAAACCACAA
* * * * *
42549517 ATGACTTCAAAAGCCACCAAAGTTATTTATTGTCGAACTGCTATCTCTACCATGAGCTTTCGATG
131 ATGACTTCAAAAACCACCAAAGGTATCTATTGTCGAACTGCTATCGCTACCATGAGCTTTCGATA
* * * * *
42549582 CCGCCTCAGTTGACGTCATTGTCGTCAAGTTCTCTCGTTGCCATAGTCAAAGCGACCGACCACCA
196 CCACCTCAATTGACATCATTATCATCAAGTTCTCTCGTTGCCATAGTCAAAGCGACCGACCACCA
42549647 AACATAAAATTAAATGAATCTAAG
261 AACATAAAATTAAATGAATCTAAG
* * * *
42549671 CCAAACTTTCCATTTTTCCATCCTAAAATAATTAGAAAATAAAATTATAACGATTACCCCAAAGC
1 CCAAACTTTCCATTATTCCATCCTAAAACAATT--AAAA-AAAATTATAACGATCACCCCAAAAC
* **
42549736 ATACTTTAGGTATTCTGGTTGAAAGA-CAAATACCCTGATTGCTAGGGTTTTCCCCC-TAAAACC
63 ATACTTTAGGTATTCTGGTTGAAA-ACCAAATACCCTAATTGCTAGGGTTCCCCCCCTTAAAACC
* * * * *
42549799 ACAAATGACTTGAAAAACGACTAAAGGTATCTATTGTCGAACTGTTATCGCTACCATGGGCTTTC
127 ACAAATGACTTCAAAAACCACCAAAGGTATCTATTGTCGAACTGCTATCGCTACCATGAGCTTTC
* * ** *
42549864 GCTATCACCTCAATTGACATTGTTATCATCAA-TTCATCTCGTTGCGATAGTCA
192 GATACCACCTCAATTGACATCATTATCATCAAGTTC-TCTCGTTGCCATAGTCA
42549917 GGTTGCAATC
Statistics
Matches: 206, Mismatches: 35, Indels: 8
0.83 0.14 0.03
Matches are distributed among these distances:
284 29 0.14
285 3 0.01
286 104 0.50
287 69 0.33
288 1 0.00
ACGTcount: A:0.33, C:0.23, G:0.13, T:0.30
Consensus pattern (284 bp):
CCAAACTTTCCATTATTCCATCCTAAAACAATTAAAAAAAATTATAACGATCACCCCAAAACATA
CTTTAGGTATTCTGGTTGAAAACCAAATACCCTAATTGCTAGGGTTCCCCCCCTTAAAACCACAA
ATGACTTCAAAAACCACCAAAGGTATCTATTGTCGAACTGCTATCGCTACCATGAGCTTTCGATA
CCACCTCAATTGACATCATTATCATCAAGTTCTCTCGTTGCCATAGTCAAAGCGACCGACCACCA
AACATAAAATTAAATGAATCTAAG
Found at i:42563388 original size:27 final size:27
Alignment explanation
Indices: 42563346--42563478 Score: 115
Period size: 27 Copynumber: 4.9 Consensus size: 27
42563336 CTACTATCCT
* *
42563346 GGTGGACTATCTCATGTTTAGTGTCTC
1 GGTGGACTATCACATGTTTAATGTCTC
*
42563373 GGTGGACTATCACATGTTTATTGTCTC
1 GGTGGACTATCACATGTTTAATGTCTC
* * * * * * *
42563400 AGTGGACTATCCCTTATTTATTATCTT
1 GGTGGACTATCACATGTTTAATGTCTC
* *
42563427 GGCGGACCATCACATGTTTAATGTC-C
1 GGTGGACTATCACATGTTTAATGTCTC
* * *
42563453 TGGCGCACTATCCCATGTTTAATGTC
1 -GGTGGACTATCACATGTTTAATGTC
42563479 CTGGCAGTCT
Statistics
Matches: 85, Mismatches: 20, Indels: 2
0.79 0.19 0.02
Matches are distributed among these distances:
27 85 1.00
ACGTcount: A:0.20, C:0.22, G:0.20, T:0.38
Consensus pattern (27 bp):
GGTGGACTATCACATGTTTAATGTCTC
Found at i:42564206 original size:87 final size:85
Alignment explanation
Indices: 42564060--42564233 Score: 215
Period size: 87 Copynumber: 2.0 Consensus size: 85
42564050 CCGCCAAATC
* *
42564060 TTACTCCATCTATCCCATCAATAATTTCTCTTCGTACTCCATTGTTACAAACATACAATACATGT
1 TTACTCCATCTATCCCATCAATAATTTCCCTTCGTACTCCACTGTTACAAACATACAATACATGT
*
42564125 ATTTCCTAGATATATATTATCA
66 ATTT-AT-GATATATATTATCA
* * * * ** *
42564147 TTACTCCATTTATTCCATCAAT-ATGTTCCCTTTGTACTTCACTGTTGTAAACATGCAATACATG
1 TTACTCCATCTATCCCATCAATAAT-TTCCCTTCGTACTCCACTGTTACAAACATACAATACATG
*
42564211 TATTTATTATATATATTATCA
65 TATTTATGATATATATTATCA
42564232 TT
1 TT
42564234 GAGTATACTA
Statistics
Matches: 75, Mismatches: 11, Indels: 4
0.83 0.12 0.04
Matches are distributed among these distances:
85 15 0.20
86 3 0.04
87 57 0.76
ACGTcount: A:0.30, C:0.21, G:0.06, T:0.43
Consensus pattern (85 bp):
TTACTCCATCTATCCCATCAATAATTTCCCTTCGTACTCCACTGTTACAAACATACAATACATGT
ATTTATGATATATATTATCA
Found at i:42573096 original size:22 final size:22
Alignment explanation
Indices: 42573065--42573114 Score: 82
Period size: 22 Copynumber: 2.3 Consensus size: 22
42573055 TTAATTACCT
42573065 GTAAGACGTTAAATCTAATAGA
1 GTAAGACGTTAAATCTAATAGA
* *
42573087 GTAAGGCGTTAAGTCTAATAGA
1 GTAAGACGTTAAATCTAATAGA
42573109 GTAAGA
1 GTAAGA
42573115 ATATTTTGTC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.42, C:0.08, G:0.24, T:0.26
Consensus pattern (22 bp):
GTAAGACGTTAAATCTAATAGA
Found at i:42574691 original size:14 final size:16
Alignment explanation
Indices: 42574668--42574699 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
42574658 AATTGGTTTT
42574668 AAGTTGTTTA-AATTA
1 AAGTTGTTTAGAATTA
42574683 AAGTT-TTTAGAATTA
1 AAGTTGTTTAGAATTA
42574698 AA
1 AA
42574700 TCAATAGTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 4 0.25
15 12 0.75
ACGTcount: A:0.44, C:0.00, G:0.12, T:0.44
Consensus pattern (16 bp):
AAGTTGTTTAGAATTA
Found at i:42575783 original size:14 final size:14
Alignment explanation
Indices: 42575764--42575804 Score: 52
Period size: 12 Copynumber: 3.1 Consensus size: 14
42575754 CCGACCTATC
42575764 TATATTAATTTTTT
1 TATATTAATTTTTT
*
42575778 TATATT-A-TTTAT
1 TATATTAATTTTTT
42575790 TATA-TAATTTTTT
1 TATATTAATTTTTT
42575803 TA
1 TA
42575805 AAAAATATAG
Statistics
Matches: 23, Mismatches: 2, Indels: 5
0.77 0.07 0.17
Matches are distributed among these distances:
11 1 0.04
12 9 0.39
13 7 0.30
14 6 0.26
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (14 bp):
TATATTAATTTTTT
Found at i:42575857 original size:30 final size:30
Alignment explanation
Indices: 42575822--42575971 Score: 300
Period size: 30 Copynumber: 5.0 Consensus size: 30
42575812 TAGTACATAA
42575822 AAAATACTAAAACCATTAAAATAAATGTTT
1 AAAATACTAAAACCATTAAAATAAATGTTT
42575852 AAAATACTAAAACCATTAAAATAAATGTTT
1 AAAATACTAAAACCATTAAAATAAATGTTT
42575882 AAAATACTAAAACCATTAAAATAAATGTTT
1 AAAATACTAAAACCATTAAAATAAATGTTT
42575912 AAAATACTAAAACCATTAAAATAAATGTTT
1 AAAATACTAAAACCATTAAAATAAATGTTT
42575942 AAAATACTAAAACCATTAAAATAAATGTTT
1 AAAATACTAAAACCATTAAAATAAATGTTT
42575972 TCCAATAAAT
Statistics
Matches: 120, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 120 1.00
ACGTcount: A:0.57, C:0.10, G:0.03, T:0.30
Consensus pattern (30 bp):
AAAATACTAAAACCATTAAAATAAATGTTT
Found at i:42577028 original size:8 final size:8
Alignment explanation
Indices: 42577015--42577041 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
42577005 AGTGCTGAAG
42577015 AATAAACA
1 AATAAACA
42577023 AATAAACA
1 AATAAACA
42577031 AATAAACA
1 AATAAACA
42577039 AAT
1 AAT
42577042 TCAAAGTGTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.74, C:0.11, G:0.00, T:0.15
Consensus pattern (8 bp):
AATAAACA
Found at i:42577685 original size:15 final size:15
Alignment explanation
Indices: 42577651--42577685 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
42577641 TCAGTTTTTT
*
42577651 ATATATTTTTTAAAT
1 ATATATTTTTTAAAA
*
42577666 TTATATTTTTTAAAA
1 ATATATTTTTTAAAA
42577681 ATATA
1 ATATA
42577686 ATTTATTCAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (15 bp):
ATATATTTTTTAAAA
Found at i:42578647 original size:2 final size:2
Alignment explanation
Indices: 42578640--42578679 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
42578630 CAATGCCTCG
42578640 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
42578680 AAGTCAACTT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:42588040 original size:44 final size:44
Alignment explanation
Indices: 42587990--42588683 Score: 359
Period size: 44 Copynumber: 15.5 Consensus size: 44
42587980 AATTTCATCT
* *
42587990 TATCTCCCTGAAGTTACAGTGGAGCAAATTAAAGCCACAAATCC
1 TATCTCCCTGAAGTTGCAGTGGAGCAAATTAAAGCTACAAATCC
* * *
42588034 TATCTCCCTGAAGTTGCAGTGGAGCAGA-TAGAAGATAGCAAATCT
1 TATCTCCCTGAAGTTGCAGTGGAGCAAATTA-AAGCTA-CAAATCC
* * *
42588079 TATCTCTCTGAAGTTGCAGTAGAG-AAGATTAAAGCTATAAA-CC
1 TATCTCCCTGAAGTTGCAGTGGAGCAA-ATTAAAGCTACAAATCC
* ** * * * *
42588122 TTATCTCCCTGAAGTTGCAGTGGGGCAGGTTGAAGTTACAAGTCT
1 -TATCTCCCTGAAGTTGCAGTGGAGCAAATTAAAGCTACAAATCC
* * * *
42588167 TATCTCCCTGAAGTTGCAGTGGAGCAAACTGAAA-ATAGCGAATCT
1 TATCTCCCTGAAGTTGCAGTGGAGCAAA-TTAAAGCTA-CAAATCC
* * * * * * * **
42588212 TATTTCCCTAAAGTTGCAGTGGAGCAGATTGAAGTTATAGATTT
1 TATCTCCCTGAAGTTGCAGTGGAGCAAATTAAAGCTACAAATCC
* * * * ** * *
42588256 TATCTCCCTAAAGTTACAGTGGAGTAGATCGAAGATAGCAAATCT
1 TATCTCCCTGAAGTTGCAGTGGAGCAAATTAAAGCTA-CAAATCC
* * * * * *
42588301 TATCTCTCTAAAGTTGCAGTAGAGCAGATTAAAGCTA-TAACCC
1 TATCTCCCTGAAGTTGCAGTGGAGCAAATTAAAGCTACAAATCC
* * ** ** **
42588344 TTATTTCCCTGAAGTTGCAGTGGAGTAGGTTAAAAATAAACAAATTT
1 -TATCTCCCTGAAGTTGCAGTGGAGCAAATTAAAGCT--ACAAATCC
* * *
42588391 TATCTCCCTGAAGTTGCTA-TGGAACAGATTGAAGATAAGCTACAAATCT
1 TATCTCCCTGAAGTTGC-AGTGGAGCAAATT----A-AAGCTACAAATCC
* * * *
42588440 TATCTCCTTGAAGTTGTAGTGGAGCAGATTAAAGCTGCAAA-CC
1 TATCTCCCTGAAGTTGCAGTGGAGCAAATTAAAGCTACAAATCC
* ** ** **
42588483 TTATCTCCCTGATA-TTGCAGTGGAGTAGGTTAAAAATAGCAAATAT
1 -TATCTCCCTGA-AGTTGCAGTGGAGCAAATTAAAGCTA-CAAATCC
*** ** * * *
42588529 TATCTTTTTGAAGTTGCAGCAGAGCAGATTAAAGCTACACA-CTT
1 TATCTCCCTGAAGTTGCAGTGGAGCAAATTAAAGCTACAAATC-C
* * *
42588573 TATCTCCCTGAGGTTGCAGTGGAGCAGATTGAAGAC-ACAAAT-C
1 TATCTCCCTGAAGTTGCAGTGGAGCAAATTAAAG-CTACAAATCC
* * * * * *
42588616 TCATCTCCTTGAAGTTACAGCGGAGCATATTGAAGCTACAAGA-CT
1 T-ATCTCCCTGAAGTTGCAGTGGAGCAAATTAAAGCTACAA-ATCC
*
42588661 TATCTCTCTGAAGTTGCAGTGGA
1 TATCTCCCTGAAGTTGCAGTGGA
42588684 ATGGATCGAA
Statistics
Matches: 496, Mismatches: 120, Indels: 68
0.73 0.18 0.10
Matches are distributed among these distances:
43 9 0.02
44 280 0.56
45 140 0.28
46 27 0.05
47 3 0.01
48 1 0.00
49 32 0.06
50 1 0.00
51 3 0.01
ACGTcount: A:0.32, C:0.18, G:0.21, T:0.29
Consensus pattern (44 bp):
TATCTCCCTGAAGTTGCAGTGGAGCAAATTAAAGCTACAAATCC
Found at i:42588137 original size:89 final size:88
Alignment explanation
Indices: 42587986--42588721 Score: 559
Period size: 89 Copynumber: 8.2 Consensus size: 88
42587976 ATAAAATTTC
* *
42587986 ATCTTATCTCCCTGAAGTTACAGTGGAGCAA-ATTAAAGCCACAAATCC-TATCTCCCTGAAGTT
1 ATCTTATCTCCCTGAAGTTGCAGTGGAG-AAGATTAAAGCTACAAA-CCTTATCTCCCTGAAGTT
*
42588049 GCAGTGGAGCAGATAGAAGATAGCAA
64 GCAGTGGAGCAGATTGAAGATA-CAA
* * *
42588075 ATCTTATCTCTCTGAAGTTGCAGTAGAGAAGATTAAAGCTATAAACCTTATCTCCCTGAAGTTGC
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGAAGATTAAAGCTACAAACCTTATCTCCCTGAAGTTGC
* * *
42588140 AGTGGGGCAGGTTGAAGTTACAA
66 AGTGGAGCAGATTGAAGATACAA
* * * * * * *
42588163 GTCTTATCTCCCTGAAGTTGCAGTGGAGCAA-ACTGAAA-ATAGCGAATCTTATTTCCCTAAAGT
1 ATCTTATCTCCCTGAAGTTGCAGTGGAG-AAGA-TTAAAGCTA-CAAACCTTATCTCCCTGAAGT
* * *
42588226 TGCAGTGGAGCAGATTGAAGTTATAG
63 TGCAGTGGAGCAGATTGAAGATACAA
* * * * ** * * * *
42588252 ATTTTATCTCCCTAAAGTTACAGTGGAGTAGATCGAAGATAGCAAATCTTATCTCTCTAAAGTTG
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGAAGATTAAAGCTA-CAAACCTTATCTCCCTGAAGTTG
* * * *
42588317 CAGTAGAGCAGATTAAAGCTATAA
65 CAGTGGAGCAGATTGAAGATACAA
** * * * ** **
42588341 CCCTTATTTCCCTGAAGTTGCAGTGGAGTAGGTTAAAAATAAACAAATTTTATCTCCCTGAAGTT
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGAAGATTAAAGCT--ACAAACCTTATCTCCCTGAAGTT
*
42588406 GCTA-TGGAACAGATTGAAGATAAGCTACAA
64 GC-AGTGGAGCAGATTGAAG---A--TACAA
* * * *
42588436 ATCTTATCTCCTTGAAGTTGTAGTGGAGCAGATTAAAGCTGCAAACCTTATCTCCCTGATA-TTG
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGAAGATTAAAGCTACAAACCTTATCTCCCTGA-AGTTG
* * * *
42588500 CAGTGGAGTAGGTTAAAAATAGCAA
65 CAGTGGAGCAGATTGAAGATA-CAA
* *** ** * * * *
42588525 ATATTATCTTTTTGAAGTTGCAGCAGAGCAGATTAAAGCTACACACTTTATCTCCCTGAGGTTGC
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGAAGATTAAAGCTACAAACCTTATCTCCCTGAAGTTGC
*
42588590 AGTGGAGCAGATTGAAGACACAA
66 AGTGGAGCAGATTGAAGATACAA
* * * * * * * *
42588613 ATCTCATCTCCTTGAAGTTACAGCGGAGCATATTGAAGCTACAAGA-CTTATCTCTCTGAAGTTG
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGAAGATTAAAGCTACAA-ACCTTATCTCCCTGAAGTTG
*** * * *
42588677 CAGTGGAATGGATCGAAGCTATAA
65 CAGTGGAGCAGATTGAAGATACAA
* *
42588701 GTCTTATCTCTCTGAAGTTGC
1 ATCTTATCTCCCTGAAGTTGC
42588722 GGAAGAGTGG
Statistics
Matches: 516, Mismatches: 111, Indels: 41
0.77 0.17 0.06
Matches are distributed among these distances:
88 127 0.25
89 286 0.55
90 34 0.07
91 2 0.00
92 1 0.00
93 30 0.06
94 1 0.00
95 35 0.07
ACGTcount: A:0.32, C:0.18, G:0.21, T:0.29
Consensus pattern (88 bp):
ATCTTATCTCCCTGAAGTTGCAGTGGAGAAGATTAAAGCTACAAACCTTATCTCCCTGAAGTTGC
AGTGGAGCAGATTGAAGATACAA
Found at i:42588226 original size:133 final size:133
Alignment explanation
Indices: 42587988--42588326 Score: 392
Period size: 133 Copynumber: 2.5 Consensus size: 133
42587978 AAAATTTCAT
* * ** *
42587988 CTTATCTCCCTGAAGTTACAGTGGAGCAAATTAAAGCCACAAATCCTATCTCCCTGAAGTTGCAG
1 CTTATCTCCCTGAAGTTACAGTGGAGCAGATTGAAGATACAAATCTTATCTCCCTGAAGTTGCAG
* * * *
42588053 TGGAGCAGATAGAAGATAGCAAATCTTATCTCTCTGAAGTTGCAGTAGAGAAGATTAAAGCTATA
66 TGGAGCAAATAGAAAATAGCAAATCTTATCTCCCTAAAGTTGCAGTAGAGAAGATTAAAGCTATA
42588118 AAC
131 AAC
* * * * *
42588121 CTTATCTCCCTGAAGTTGCAGTGGGGCAGGTTGAAGTTACAAGTCTTATCTCCCTGAAGTTGCAG
1 CTTATCTCCCTGAAGTTACAGTGGAGCAGATTGAAGATACAAATCTTATCTCCCTGAAGTTGCAG
* * * * * *
42588186 TGGAGCAAACT-GAAAATAGCGAATCTTATTTCCCTAAAGTTGCAGTGGAGCAGATTGAAGTTAT
66 TGGAGCAAA-TAGAAAATAGCAAATCTTATCTCCCTAAAGTTGCAGTAGAGAAGATTAAAGCTAT
* *
42588250 AGAT
130 AAAC
* * * * * *
42588254 TTTATCTCCCTAAAGTTACAGTGGAGTAGATCGAAGATAGCAAATCTTATCTCTCTAAAGTTGCA
1 CTTATCTCCCTGAAGTTACAGTGGAGCAGATTGAAGATA-CAAATCTTATCTCCCTGAAGTTGCA
*
42588319 GTAGAGCA
65 GTGGAGCA
42588327 GATTAAAGCT
Statistics
Matches: 171, Mismatches: 33, Indels: 3
0.83 0.16 0.01
Matches are distributed among these distances:
133 141 0.82
134 30 0.18
ACGTcount: A:0.32, C:0.18, G:0.22, T:0.28
Consensus pattern (133 bp):
CTTATCTCCCTGAAGTTACAGTGGAGCAGATTGAAGATACAAATCTTATCTCCCTGAAGTTGCAG
TGGAGCAAATAGAAAATAGCAAATCTTATCTCCCTAAAGTTGCAGTAGAGAAGATTAAAGCTATA
AAC
Found at i:42588733 original size:44 final size:44
Alignment explanation
Indices: 42588647--42588744 Score: 124
Period size: 44 Copynumber: 2.2 Consensus size: 44
42588637 GGAGCATATT
**
42588647 GAAGCTACAAGACTTATCTCTCTGAAGTTGCAGTGGAATGGATC
1 GAAGCTACAAGACTTATCTCTCTGAAGTTGCAGAAGAATGGATC
* * * *
42588691 GAAGCTATAAGTCTTATCTCTCTGAAGTTGCGGAAGAGTGGATC
1 GAAGCTACAAGACTTATCTCTCTGAAGTTGCAGAAGAATGGATC
* *
42588735 AAAGCGACAA
1 GAAGCTACAA
42588745 TTCCTATACC
Statistics
Matches: 45, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
44 45 1.00
ACGTcount: A:0.32, C:0.17, G:0.26, T:0.26
Consensus pattern (44 bp):
GAAGCTACAAGACTTATCTCTCTGAAGTTGCAGAAGAATGGATC
Found at i:42590001 original size:94 final size:94
Alignment explanation
Indices: 42589835--42590811 Score: 981
Period size: 94 Copynumber: 10.4 Consensus size: 94
42589825 CAGTGAAACC
* * * *
42589835 ACAAACCCTATACCCCTGAAGTTGCAGTGGGTC-AGATTGAAGT-TACCGTAGCGAATCTTATTT
1 ACAAATCCTATACCCCTGAAGTTGCAGTGGGTCGA-ATTGAA-TCTACCATAGCAAATCTTATCT
* * *
42589898 CCCTAAAGTTGTAGTGGAGCAGATTAAAGCT
64 CCCTGAAGTTGTAGTGGAGTAGATTGAAGCT
* * * * *
42589929 ACAAATCCTATACCCCTGAAGTTGAAATGGGTCGAATTAAATCCACCATAGTAAATCTTATCTCC
1 ACAAATCCTATACCCCTGAAGTTGCAGTGGGTCGAATTGAATCTACCATAGCAAATCTTATCTCC
*
42589994 CTGAAGTTGTAGTGGAGCAGATTGAAGCT
66 CTGAAGTTGTAGTGGAGTAGATTGAAGCT
* ** * * * * * *
42590023 ACAGATTTTATA-CCCTAAAGTTGCAATGGGTC-AGATTTAAACTACCATAGCGAATCTTATCTA
1 ACAAATCCTATACCCCTGAAGTTGCAGTGGGTCGA-ATTGAATCTACCATAGCAAATCTTATCTC
* *
42590086 CCTGAAGTTGCAGTGTAGTAGA-TGAAGCT
65 CCTGAAGTTGTAGTGGAGTAGATTGAAGCT
* * *
42590115 AAAAATCCTATACCCCTGAAGTTGTAGTGGGTCGAATTGAATC-ACCATAGCATATCTTATCTCC
1 ACAAATCCTATACCCCTGAAGTTGCAGTGGGTCGAATTGAATCTACCATAGCAAATCTTATCTCC
* * * *
42590179 CTAAAGTTATTGTGGAGCAGA-TGAAGCT
66 CTGAAGTTGTAGTGGAGTAGATTGAAGCT
* **
42590207 GCAAATCCTATACCCCTGAAGTTGCAGTGGGTC-AGATTGAATCTACCATAGTGAATCTTATCTC
1 ACAAATCCTATACCCCTGAAGTTGCAGTGGGTCGA-ATTGAATCTACCATAGCAAATCTTATCTC
* * * * * * * *
42590271 TCTAAAATTATGGTGGAGAAGATTAAAGTT
65 CCTGAAGTTGTAGTGGAGTAGATTGAAGCT
* * * * *
42590301 ACAAATCCTATACCCCTGAAGTTGCAGCGGATCGAATTGAAGCTATCATAGCAAATATTATCTCC
1 ACAAATCCTATACCCCTGAAGTTGCAGTGGGTCGAATTGAATCTACCATAGCAAATCTTATCTCC
* * * *
42590366 CTGAAGTTGCAATAGAGTA-AGGTGAAGCT
66 CTGAAGTTGTAGTGGAGTAGA-TTGAAGCT
* * * * *
42590395 ACAAATCCTATACCCTTGAAGTTGTAGTGGGTCGGATTGAATCTACCATAGCGAATCTTATCTCT
1 ACAAATCCTATACCCCTGAAGTTGCAGTGGGTCGAATTGAATCTACCATAGCAAATCTTATCTCC
* * *
42590460 CTGAAGTTGCAGTGGAGGAGATTTAAGCT
66 CTGAAGTTGTAGTGGAGTAGATTGAAGCT
* * * ** * * *
42590489 ATAAATCCTATACCCCTAAAGCTT-CGGCAGGTC-AGATTGAATTTAGCATAGCAAATCTTGTCT
1 ACAAATCCTATACCCCTGAAG-TTGCAGTGGGTCGA-ATTGAATCTACCATAGCAAATCTTATCT
* * *
42590552 CCCTAAAGTTGTAGTAGAGTAGATTTAAGCT
64 CCCTGAAGTTGTAGTGGAGTAGATTGAAGCT
* * *
42590583 GCAAATCCTATACCCATGAAGTTGCAGTGGGTCGAATTGAATCTACCATAGCAAACCTTATCTCC
1 ACAAATCCTATACCCCTGAAGTTGCAGTGGGTCGAATTGAATCTACCATAGCAAATCTTATCTCC
* **
42590648 CTGAAGTTATAGTAAAGTAGATTGAAGCT
66 CTGAAGTTGTAGTGGAGTAGATTGAAGCT
* * * * * *
42590677 ACAAATCCTATATCCTTGAAGTTACAGTGGGT-TAGATTGAATCTACCATAGAAAATATTATCTC
1 ACAAATCCTATACCCCTGAAGTTGCAGTGGGTCGA-ATTGAATCTACCATAGCAAATCTTATCTC
* * * *
42590741 CCTAAAGTTGCAATGGAGTA-AGGTGAAGCT
65 CCTGAAGTTGTAGTGGAGTAGA-TTGAAGCT
* * *
42590771 ACAAATCTTATACCCCAGAAGTTGTAGTGGGTCGAATTGAA
1 ACAAATCCTATACCCCTGAAGTTGCAGTGGGTCGAATTGAA
42590812 ACGACAAAAA
Statistics
Matches: 721, Mismatches: 144, Indels: 36
0.80 0.16 0.04
Matches are distributed among these distances:
91 1 0.00
92 94 0.13
93 124 0.17
94 495 0.69
95 7 0.01
ACGTcount: A:0.32, C:0.19, G:0.20, T:0.29
Consensus pattern (94 bp):
ACAAATCCTATACCCCTGAAGTTGCAGTGGGTCGAATTGAATCTACCATAGCAAATCTTATCTCC
CTGAAGTTGTAGTGGAGTAGATTGAAGCT
Found at i:42592345 original size:4 final size:4
Alignment explanation
Indices: 42592336--42592384 Score: 66
Period size: 4 Copynumber: 12.2 Consensus size: 4
42592326 AATCTAACCC
42592336 TTTA TTTA TTGT- TTTA TTTA TTTA TTTA TTTA TTGT- TTTA TTTA TTTA
1 TTTA TTTA TT-TA TTTA TTTA TTTA TTTA TTTA TT-TA TTTA TTTA TTTA
42592384 T
1 T
42592385 ACCTTAAAAT
Statistics
Matches: 41, Mismatches: 0, Indels: 8
0.84 0.00 0.16
Matches are distributed among these distances:
3 2 0.05
4 37 0.90
5 2 0.05
ACGTcount: A:0.20, C:0.00, G:0.04, T:0.76
Consensus pattern (4 bp):
TTTA
Found at i:42592353 original size:12 final size:12
Alignment explanation
Indices: 42592336--42592381 Score: 76
Period size: 12 Copynumber: 3.8 Consensus size: 12
42592326 AATCTAACCC
42592336 TTTATTTATTGT
1 TTTATTTATTGT
42592348 TTTATTTATT-T
1 TTTATTTATTGT
42592359 ATTTATTTATTGT
1 -TTTATTTATTGT
42592372 TTTATTTATT
1 TTTATTTATT
42592382 TATACCTTAA
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
11 1 0.03
12 30 0.94
13 1 0.03
ACGTcount: A:0.20, C:0.00, G:0.04, T:0.76
Consensus pattern (12 bp):
TTTATTTATTGT
Found at i:42592363 original size:24 final size:24
Alignment explanation
Indices: 42592336--42592384 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
42592326 AATCTAACCC
42592336 TTTATTTATTGTTTTATTTATTTA
1 TTTATTTATTGTTTTATTTATTTA
42592360 TTTATTTATTGTTTTATTTATTTA
1 TTTATTTATTGTTTTATTTATTTA
42592384 T
1 T
42592385 ACCTTAAAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.20, C:0.00, G:0.04, T:0.76
Consensus pattern (24 bp):
TTTATTTATTGTTTTATTTATTTA
Found at i:42598753 original size:30 final size:29
Alignment explanation
Indices: 42598717--42598773 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 29
42598707 AGAAAATGCA
*
42598717 GTTTTTTTAATTATTTAAAGGATTAGGCTG
1 GTTTTTTGAA-TATTTAAAGGATTAGGCTG
**
42598747 GTTTTTTGAATATTTGTAGGATTAGGC
1 GTTTTTTGAATATTTAAAGGATTAGGC
42598774 CAATTTTTTA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 15 0.62
30 9 0.38
ACGTcount: A:0.25, C:0.04, G:0.23, T:0.49
Consensus pattern (29 bp):
GTTTTTTGAATATTTAAAGGATTAGGCTG
Found at i:42605210 original size:34 final size:35
Alignment explanation
Indices: 42605096--42605259 Score: 145
Period size: 35 Copynumber: 4.7 Consensus size: 35
42605086 TCCATGGCAA
** * * * *
42605096 AGTTGTGAAATATATGTGTGGTATCATCCATACTA
1 AGTTGTGAAACGTAGGTATGGTATTATCCATACTG
* * *
42605131 AGTTGTGAAACATAGGTATGGTATTAACCATAATG
1 AGTTGTGAAACGTAGGTATGGTATTATCCATACTG
42605166 AGTTGTGAAACGTAGGTATGGTATTATCC-TACTG
1 AGTTGTGAAACGTAGGTATGGTATTATCCATACTG
** * **
42605200 AGTTAAGAAACGTAGATATGACATT-TCCCATAGC-G
1 AGTTGTGAAACGTAGGTATGGTATTAT-CCATA-CTG
* *
42605235 AGTTGTAAAATGTAGGTATGGTATT
1 AGTTGTGAAACGTAGGTATGGTATT
42605260 TCAATGAGGA
Statistics
Matches: 104, Mismatches: 22, Indels: 6
0.79 0.17 0.05
Matches are distributed among these distances:
33 1 0.01
34 26 0.25
35 76 0.73
36 1 0.01
ACGTcount: A:0.33, C:0.10, G:0.23, T:0.34
Consensus pattern (35 bp):
AGTTGTGAAACGTAGGTATGGTATTATCCATACTG
Found at i:42615337 original size:55 final size:55
Alignment explanation
Indices: 42615276--42615381 Score: 169
Period size: 55 Copynumber: 1.9 Consensus size: 55
42615266 TTAGTTATCC
* *
42615276 AAACATCAAATCAATGCAGTAAAAAAG-AATATTCTCTCAATATCTCATCTCGCTA
1 AAACATCAAATCAACGCA-TAAAAAAGAAATATTCTCTCAATATCCCATCTCGCTA
*
42615331 AAACATCAAATCAACGCATTAAAAAGAAATATTCTCTCAATATCCCATCTC
1 AAACATCAAATCAACGCATAAAAAAGAAATATTCTCTCAATATCCCATCTC
42615382 ACCACGGCTT
Statistics
Matches: 47, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
54 7 0.15
55 40 0.85
ACGTcount: A:0.44, C:0.24, G:0.06, T:0.26
Consensus pattern (55 bp):
AAACATCAAATCAACGCATAAAAAAGAAATATTCTCTCAATATCCCATCTCGCTA
Found at i:42615948 original size:19 final size:19
Alignment explanation
Indices: 42615924--42615976 Score: 99
Period size: 18 Copynumber: 2.8 Consensus size: 19
42615914 TTTAATTAAA
42615924 TTTTAAAAATTAAAATTAT
1 TTTTAAAAATTAAAATTAT
42615943 TTTT-AAAATTAAAATTAT
1 TTTTAAAAATTAAAATTAT
42615961 TTTTAAAAATTAAAAT
1 TTTTAAAAATTAAAAT
42615977 CAATAAAATT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
18 18 0.55
19 15 0.45
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (19 bp):
TTTTAAAAATTAAAATTAT
Found at i:42621241 original size:45 final size:44
Alignment explanation
Indices: 42621190--42621279 Score: 171
Period size: 45 Copynumber: 2.0 Consensus size: 44
42621180 TTAAAGGGAA
42621190 GAAAAATAATATTGAGACAAATTTTATATCCAAAAATGATGAAAT
1 GAAAAATAATATTGAGACAAATTTTATATCCAAAAA-GATGAAAT
42621235 GAAAAATAATATTGAGACAAATTTTATATCCAAAAAGATGAAAT
1 GAAAAATAATATTGAGACAAATTTTATATCCAAAAAGATGAAAT
42621279 G
1 G
42621280 GAGGCAAAAG
Statistics
Matches: 45, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
44 9 0.20
45 36 0.80
ACGTcount: A:0.53, C:0.07, G:0.12, T:0.28
Consensus pattern (44 bp):
GAAAAATAATATTGAGACAAATTTTATATCCAAAAAGATGAAAT
Found at i:42632930 original size:27 final size:27
Alignment explanation
Indices: 42632900--42632961 Score: 88
Period size: 27 Copynumber: 2.3 Consensus size: 27
42632890 TTGTGCAAAA
* **
42632900 ATAAAGTAAAAAATGAAGTTGTAAGAT
1 ATAAAGCAAAAAATGAAGTCATAAGAT
*
42632927 ATAAAGCAAAAACTGAAGTCATAAGAT
1 ATAAAGCAAAAAATGAAGTCATAAGAT
42632954 ATAAAGCA
1 ATAAAGCA
42632962 CGACTTGTAG
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.56, C:0.06, G:0.16, T:0.21
Consensus pattern (27 bp):
ATAAAGCAAAAAATGAAGTCATAAGAT
Found at i:42633845 original size:25 final size:25
Alignment explanation
Indices: 42633816--42633873 Score: 116
Period size: 25 Copynumber: 2.3 Consensus size: 25
42633806 CCAAATACCT
42633816 ATTTAACATCATGTATAATCCATTC
1 ATTTAACATCATGTATAATCCATTC
42633841 ATTTAACATCATGTATAATCCATTC
1 ATTTAACATCATGTATAATCCATTC
42633866 ATTTAACA
1 ATTTAACA
42633874 ACTACATATC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 33 1.00
ACGTcount: A:0.38, C:0.19, G:0.03, T:0.40
Consensus pattern (25 bp):
ATTTAACATCATGTATAATCCATTC
Found at i:42646751 original size:14 final size:15
Alignment explanation
Indices: 42646732--42646761 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
42646722 ATATTTAACT
42646732 TGTTCTTAATT-TTG
1 TGTTCTTAATTCTTG
42646746 TGTTCTTAATTCTTG
1 TGTTCTTAATTCTTG
42646761 T
1 T
42646762 TTTGATAACC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 11 0.73
15 4 0.27
ACGTcount: A:0.13, C:0.10, G:0.13, T:0.63
Consensus pattern (15 bp):
TGTTCTTAATTCTTG
Found at i:42649837 original size:27 final size:27
Alignment explanation
Indices: 42649806--42649983 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
42649796 TAAATTGTAC
42649806 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** *
42649833 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
42649859 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
*
42649887 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* *
42649915 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
42649942 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
42649969 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
42649984 GACTCAATAT
Statistics
Matches: 129, Mismatches: 19, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 23 0.18
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:42649920 original size:82 final size:81
Alignment explanation
Indices: 42649807--42649962 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
42649797 AAATTGTACA
* *
42649807 GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTG
1 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTA-GCACTAAGTG
42649871 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
** *
42649888 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTG
1 GCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTG
*
42649953 TGCGAGTTGA
65 TGCGAATTGA
42649963 TTATATAGCA
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 15 0.22
82 51 0.76
83 1 0.01
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.29
Consensus pattern (81 bp):
GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:42649974 original size:82 final size:81
Alignment explanation
Indices: 42649803--42649983 Score: 229
Period size: 82 Copynumber: 2.2 Consensus size: 81
42649793 GATTAAATTG
* *
42649803 TACAGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
42649868 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * ** *
42649884 TGCGGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TAGCACT
1 TACAGCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACT
* **
42649948 AAGTGTGCGAGTTGATTA
64 AAGTGTGCGAATTGACCA
* *
42649966 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
42649984 GACTCAATAT
Statistics
Matches: 84, Mismatches: 14, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
81 18 0.21
82 66 0.79
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
GTGTGCGAATTGACCA
Found at i:42657375 original size:185 final size:185
Alignment explanation
Indices: 42657063--42657421 Score: 621
Period size: 185 Copynumber: 1.9 Consensus size: 185
42657053 TCATTCACCA
* * *
42657063 CTCATTACTTGCTTCAAAGAGCTCAACCTGGAGCTCACTATTTTGTAACGCAGTCTCGAGTTCTT
1 CTCATTACCTGCTTCAAAGAGCTCAACCCGGAGCTCACTATTTTGTAACGCAATCTCGAGTTCTT
42657128 CGACCTTCCTTTTCAGCTCTTTAATCTCATCCAAGCTCGCCTTCAGCTCCATTGCAGAGTTACGG
66 CGACCTTCCTTTTCAGCTCTTTAATCTCATCCAAGCTCGCCTTCAGCTCCATTGCAGAGTTACGG
*
42657193 CTACGATGCTGATGAAGCGATTTTTCTAGTTTGGCTATTCTGGCATATTACACTG
131 CTACGATGCTGATGAAGCGATTTTTCTAGTTTGACTATTCTGGCATATTACACTG
* * *
42657248 CTCATTACCTGCTTCAAGGAGCTCAACCCGGAGC-CTACTATTTTGTAACGTAATCTCGAGTTTT
1 CTCATTACCTGCTTCAAAGAGCTCAACCCGGAGCTC-ACTATTTTGTAACGCAATCTCGAGTTCT
42657312 TCGACCTTCCTTTTCAGCTCTTTAATCTCATCCAAGCTCGCCTTCAGCTCCATTGCAGAGTTACG
65 TCGACCTTCCTTTTCAGCTCTTTAATCTCATCCAAGCTCGCCTTCAGCTCCATTGCAGAGTTACG
* *
42657377 GTTATGATGCTGATGAAGCGATTTTTCTAGTTTGACTATTCTGGC
130 GCTACGATGCTGATGAAGCGATTTTTCTAGTTTGACTATTCTGGC
42657422 CTTCAACTCG
Statistics
Matches: 164, Mismatches: 9, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
184 1 0.01
185 163 0.99
ACGTcount: A:0.21, C:0.26, G:0.18, T:0.35
Consensus pattern (185 bp):
CTCATTACCTGCTTCAAAGAGCTCAACCCGGAGCTCACTATTTTGTAACGCAATCTCGAGTTCTT
CGACCTTCCTTTTCAGCTCTTTAATCTCATCCAAGCTCGCCTTCAGCTCCATTGCAGAGTTACGG
CTACGATGCTGATGAAGCGATTTTTCTAGTTTGACTATTCTGGCATATTACACTG
Found at i:42660667 original size:15 final size:17
Alignment explanation
Indices: 42660632--42660669 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
42660622 ATCAAGTAGA
42660632 CTTTTATCACTCAAGGT
1 CTTTTATCACTCAAGGT
*
42660649 CTTTTTTCACTC-A-GT
1 CTTTTATCACTCAAGGT
42660664 CTTTTA
1 CTTTTA
42660670 AATTTTTTCT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
15 7 0.37
16 1 0.05
17 11 0.58
ACGTcount: A:0.18, C:0.24, G:0.08, T:0.50
Consensus pattern (17 bp):
CTTTTATCACTCAAGGT
Found at i:42662747 original size:22 final size:22
Alignment explanation
Indices: 42662722--42662822 Score: 139
Period size: 22 Copynumber: 4.6 Consensus size: 22
42662712 TGCAGGGCTC
*
42662722 ACACGCCTGTGTAGTCCAAGGG
1 ACACGCCTGTGTGGTCCAAGGG
* *
42662744 ACACGCCTGTGTGGTCCATGAG
1 ACACGCCTGTGTGGTCCAAGGG
*
42662766 ACACGCCTGTGTGGTCCATGGG
1 ACACGCCTGTGTGGTCCAAGGG
* *
42662788 ACATGCCCGTGTGGTCCAAGGG
1 ACACGCCTGTGTGGTCCAAGGG
*
42662810 ACACGCCCGTGTG
1 ACACGCCTGTGTG
42662823 ACCCTAGAAC
Statistics
Matches: 71, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 71 1.00
ACGTcount: A:0.18, C:0.29, G:0.34, T:0.20
Consensus pattern (22 bp):
ACACGCCTGTGTGGTCCAAGGG
Found at i:42665793 original size:23 final size:22
Alignment explanation
Indices: 42665775--42665851 Score: 91
Period size: 22 Copynumber: 3.5 Consensus size: 22
42665765 TAAGCTGATG
42665775 TAGTAAGCTCTATTGAGCTGAAA
1 TAGTAAGCTCTATTGAGCTG-AA
* *
42665798 TGGTAAGCTCTATCGAGCTGAA
1 TAGTAAGCTCTATTGAGCTGAA
* * *
42665820 CAGTACGCTCTATTGAGTTGAA
1 TAGTAAGCTCTATTGAGCTGAA
*
42665842 CAGTAAGCTC
1 TAGTAAGCTC
42665852 ATACGAACTG
Statistics
Matches: 46, Mismatches: 8, Indels: 1
0.84 0.15 0.02
Matches are distributed among these distances:
22 28 0.61
23 18 0.39
ACGTcount: A:0.30, C:0.18, G:0.23, T:0.29
Consensus pattern (22 bp):
TAGTAAGCTCTATTGAGCTGAA
Found at i:42665832 original size:22 final size:22
Alignment explanation
Indices: 42665776--42665874 Score: 103
Period size: 23 Copynumber: 4.4 Consensus size: 22
42665766 AAGCTGATGT
*
42665776 AGTAAGCTCTATTGAGCTGAA-
1 AGTAAGCTCTATCGAGCTGAAC
42665797 ATGGTAAGCTCTATCGAGCTGAAC
1 A--GTAAGCTCTATCGAGCTGAAC
* * *
42665821 AGTACGCTCTATTGAGTTGAAC
1 AGTAAGCTCTATCGAGCTGAAC
*
42665843 AGTAAGCTC-ATACGAACTGAAAC
1 AGTAAGCTCTAT-CGAGCTG-AAC
42665866 AGTAAGCTC
1 AGTAAGCTC
42665875 CAATAAGCTA
Statistics
Matches: 65, Mismatches: 8, Indels: 8
0.80 0.10 0.10
Matches are distributed among these distances:
21 3 0.05
22 30 0.46
23 31 0.48
24 1 0.02
ACGTcount: A:0.33, C:0.19, G:0.22, T:0.25
Consensus pattern (22 bp):
AGTAAGCTCTATCGAGCTGAAC
Found at i:42665834 original size:45 final size:45
Alignment explanation
Indices: 42665776--42665874 Score: 123
Period size: 45 Copynumber: 2.2 Consensus size: 45
42665766 AAGCTGATGT
*
42665776 AGTAAGCTCTATTGAGCTGAA-ATGGTAAGCTC-TATCGAGCTG-AAC
1 AGTAAGCTCTATTGAGCTGAACA--GTAAGCTCATA-CGAACTGAAAC
* *
42665821 AGTACGCTCTATTGAGTTGAACAGTAAGCTCATACGAACTGAAAC
1 AGTAAGCTCTATTGAGCTGAACAGTAAGCTCATACGAACTGAAAC
42665866 AGTAAGCTC
1 AGTAAGCTC
42665875 CAATAAGCTA
Statistics
Matches: 47, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
44 14 0.30
45 32 0.68
46 1 0.02
ACGTcount: A:0.33, C:0.19, G:0.22, T:0.25
Consensus pattern (45 bp):
AGTAAGCTCTATTGAGCTGAACAGTAAGCTCATACGAACTGAAAC
Found at i:42672797 original size:24 final size:24
Alignment explanation
Indices: 42672770--42672826 Score: 60
Period size: 24 Copynumber: 2.4 Consensus size: 24
42672760 GGTGCTCAGC
**
42672770 TTTCACTTGCTGGTATGTCAGACA
1 TTTCACTACCTGGTATGTCAGACA
* *
42672794 TTTCCCTACCTGGTGTGTCAGACA
1 TTTCACTACCTGGTATGTCAGACA
* *
42672818 GTTCCCTAC
1 TTTCACTAC
42672827 AAACTCCGTT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.18, C:0.28, G:0.19, T:0.35
Consensus pattern (24 bp):
TTTCACTACCTGGTATGTCAGACA
Found at i:42677176 original size:16 final size:16
Alignment explanation
Indices: 42677155--42677187 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
42677145 GGCTAAAAGA
42677155 AAAAGAAAAGATGAGC
1 AAAAGAAAAGATGAGC
*
42677171 AAAAGAAGAGATGAGC
1 AAAAGAAAAGATGAGC
42677187 A
1 A
42677188 GAGAATTCAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.61, C:0.06, G:0.27, T:0.06
Consensus pattern (16 bp):
AAAAGAAAAGATGAGC
Found at i:42687846 original size:46 final size:46
Alignment explanation
Indices: 42687793--42688691 Score: 1597
Period size: 46 Copynumber: 19.7 Consensus size: 46
42687783 TTGAGCATCC
42687793 GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCT
1 GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCT
* * *
42687839 GAACTCGTTGGAGTTCGAG--AGA-TGTAAC-TA--G--GC--A-TCC-
1 GAACTCGTT-GAGTT-GAGTCCGAGT-TCACTTATGGATGCGAACGCCT
* * * *
42687876 GAGCTCGTTGAGTTGAGTCCGAGTTCACTAATGGATGTGAACGCCC
1 GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCT
** *
42687922 GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGGCGGGAACGCCT
1 GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCT
42687968 GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCT
1 GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCT
42688014 GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCT
1 GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCT
42688060 GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCT
1 GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCT
42688106 GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCT
1 GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCT
42688152 GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCT
1 GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCT
42688198 GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCT
1 GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCT
42688244 GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCT
1 GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCT
42688290 GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCT
1 GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCT
42688336 GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCT
1 GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCT
42688382 GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCT
1 GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCT
42688428 GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCT
1 GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCT
42688474 GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCT
1 GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCT
42688520 GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCT
1 GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCT
42688566 GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCT
1 GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCT
42688612 GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCT
1 GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCT
42688658 GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
42688692 GCGGGTTACA
Statistics
Matches: 820, Mismatches: 18, Indels: 30
0.94 0.02 0.03
Matches are distributed among these distances:
35 3 0.00
36 5 0.01
37 13 0.02
38 4 0.00
39 1 0.00
40 1 0.00
41 2 0.00
42 1 0.00
43 1 0.00
44 1 0.00
45 5 0.01
46 775 0.95
47 5 0.01
48 3 0.00
ACGTcount: A:0.22, C:0.21, G:0.29, T:0.28
Consensus pattern (46 bp):
GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCT
Found at i:42691652 original size:15 final size:15
Alignment explanation
Indices: 42691613--42691683 Score: 81
Period size: 15 Copynumber: 4.7 Consensus size: 15
42691603 GTATCTTGGG
*
42691613 TTTCTTTATCCTGGA
1 TTTCTTTATTCTGGA
*
42691628 TCTCTTTATTCTGGA
1 TTTCTTTATTCTGGA
* *
42691643 TTTCTTTATTCCGGG
1 TTTCTTTATTCTGGA
*
42691658 TTTCTCTA-TCTTGGA
1 TTTCTTTATTC-TGGA
42691673 TTTCTTTATTC
1 TTTCTTTATTC
42691684 GATTTTCTTG
Statistics
Matches: 45, Mismatches: 9, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
14 2 0.04
15 41 0.91
16 2 0.04
ACGTcount: A:0.11, C:0.20, G:0.13, T:0.56
Consensus pattern (15 bp):
TTTCTTTATTCTGGA
Found at i:42691682 original size:30 final size:31
Alignment explanation
Indices: 42691604--42691683 Score: 94
Period size: 30 Copynumber: 2.6 Consensus size: 31
42691594 CATAGTATCG
* *
42691604 TATCTTGGGTTTCTTTA-TCCTGGATCTCTT
1 TATCTTGGATTTCTTTATTCCTGGATCTCTC
* *
42691634 TAT-TCTGGATTTCTTTATTCC-GGGTTTCTC
1 TATCT-TGGATTTCTTTATTCCTGGATCTCTC
42691664 TATCTTGGATTTCTTTATTC
1 TATCTTGGATTTCTTTATTC
42691684 GATTTTCTTG
Statistics
Matches: 43, Mismatches: 4, Indels: 6
0.81 0.08 0.11
Matches are distributed among these distances:
29 1 0.02
30 38 0.88
31 4 0.09
ACGTcount: A:0.11, C:0.19, G:0.15, T:0.55
Consensus pattern (31 bp):
TATCTTGGATTTCTTTATTCCTGGATCTCTC
Found at i:42700420 original size:19 final size:20
Alignment explanation
Indices: 42700396--42700433 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
42700386 GGTACCACCA
42700396 AAACAT-ATATCA-CATCTTT
1 AAACATCAT-TCATCATCTTT
42700415 AAACATCATTCATCATCTT
1 AAACATCATTCATCATCTT
42700434 ACCACCTTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.39, C:0.24, G:0.00, T:0.37
Consensus pattern (20 bp):
AAACATCATTCATCATCTTT
Found at i:42700769 original size:47 final size:47
Alignment explanation
Indices: 42700708--42700876 Score: 220
Period size: 47 Copynumber: 3.6 Consensus size: 47
42700698 ATCCATAAGT
*
42700708 GAACTCGGTCTCAACTCAACGAGTTCGGATGCCTAGTTACATCTCAC
1 GAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACATCTCAC
* * * *
42700755 GAACTCGGACTCAACTCAACGAGTTCGGA---C-ATTTGCATCCATAAGT
1 GAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACAT-C-TCA-C
* *
42700801 GAACTCGGACTCAACTCAAGGAGTTCGGATGCCTAGTTCCATCTCAC
1 GAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACATCTCAC
42700848 GAACTCGGACTCAACTCAACGAGTTCGGA
1 GAACTCGGACTCAACTCAACGAGTTCGGA
42700877 CATTTGCATC
Statistics
Matches: 104, Mismatches: 11, Indels: 14
0.81 0.09 0.11
Matches are distributed among these distances:
43 6 0.06
44 2 0.02
45 2 0.02
46 28 0.27
47 56 0.54
48 2 0.02
49 2 0.02
50 6 0.06
ACGTcount: A:0.28, C:0.28, G:0.21, T:0.23
Consensus pattern (47 bp):
GAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACATCTCAC
Found at i:42700770 original size:93 final size:93
Alignment explanation
Indices: 42700662--42700925 Score: 438
Period size: 93 Copynumber: 2.8 Consensus size: 93
42700652 GCCCCTAAGT
* * * * ** *
42700662 GAACTCGAACTCAACTCAACGAGCTCGGGCGTTCACATCCATAAGTGAACTCGGTCTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGTTCGGACATTTGCATCCATAAGTGAACTCGGACTCAACTCAA
42700727 CGAGTTCGGATGCCTAGTTACATCTCAC
66 CGAGTTCGGATGCCTAGTTACATCTCAC
42700755 GAACTCGGACTCAACTCAACGAGTTCGGACATTTGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGTTCGGACATTTGCATCCATAAGTGAACTCGGACTCAACTCAA
* *
42700820 GGAGTTCGGATGCCTAGTTCCATCTCAC
66 CGAGTTCGGATGCCTAGTTACATCTCAC
*
42700848 GAACTCGGACTCAACTCAACGAGTTCGGACATTTGCATCCATAAGTGAACTTGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGTTCGGACATTTGCATCCATAAGTGAACTCGGACTCAACTCAA
42700913 CGAGTTCGGATGC
66 CGAGTTCGGATGC
42700926 TCAGCCATCC
Statistics
Matches: 160, Mismatches: 11, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
93 160 1.00
ACGTcount: A:0.28, C:0.28, G:0.20, T:0.23
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGTTCGGACATTTGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATCTCAC
Found at i:42700922 original size:46 final size:46
Alignment explanation
Indices: 42700657--42700922 Score: 265
Period size: 46 Copynumber: 5.7 Consensus size: 46
42700647 AACCCGCCCC
* * * * *
42700657 TAAGTGAACTCGAACTCAACTCAACGAGCTCGGGCGTTCACATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTTACATCCA
* *
42700703 TAAGTGAACTCGGTCTCAACTCAACGAGTTCGGATGCCTAGTTACAT-C-
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA---C-ATTTACATCCA
* * *
42700751 TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTTACATCCA
* * *
42700796 TAAGTGAACTCGGACTCAACTCAAGGAGTTCGGATGCCTAGTTCCAT-C-
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA---C-ATTTACATCCA
* * *
42700844 TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTTACATCCA
*
42700889 TAAGTGAACTTGGACTCAACTCAACGAGTTCGGA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
42700923 TGCTCAGCCA
Statistics
Matches: 181, Mismatches: 25, Indels: 28
0.77 0.11 0.12
Matches are distributed among these distances:
43 12 0.07
44 4 0.02
45 4 0.02
46 86 0.48
47 56 0.31
48 4 0.02
49 4 0.02
50 11 0.06
ACGTcount: A:0.29, C:0.27, G:0.20, T:0.23
Consensus pattern (46 bp):
TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTTACATCCA
Found at i:42704133 original size:46 final size:46
Alignment explanation
Indices: 42704083--42704258 Score: 194
Period size: 46 Copynumber: 3.8 Consensus size: 46
42704073 TGGTTGAGCA
* *
42704083 TCCGAACTCGTTGAGTTGAGTCTGAGTTCACTTATGGATGCAAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
* *** * * ** *
42704129 TCCGAACTCGTTGAGCTGAGTCCGAGTTCGAGAGATGTA-ACTAGGCA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-ACTTATGGATGC-AAACG
* *
42704176 TCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
42704222 -CCTGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 TCC-GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
42704259 GCGGGTTACA
Statistics
Matches: 103, Mismatches: 23, Indels: 8
0.77 0.17 0.06
Matches are distributed among these distances:
45 2 0.02
46 67 0.65
47 34 0.33
ACGTcount: A:0.22, C:0.20, G:0.28, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
Found at i:42704242 original size:93 final size:93
Alignment explanation
Indices: 42704080--42704250 Score: 281
Period size: 93 Copynumber: 1.8 Consensus size: 93
42704070 GGATGGTTGA
* *
42704080 GCATCCGAACTCGTTGAGTTGAGTCTGAGTTCACTTATGGATGCAAATGTCCGAACTCGTTGAGC
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGTCCGAACTCGTTGAGC
42704145 TGAGTCCGAGTTCGAGAGATGTAACTAG
66 TGAGTCCGAGTTCGAGAGATGTAACTAG
* *
42704173 GCATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG-CCTGAACTCGTTGAG
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGTCC-GAACTCGTTGAG
*
42704237 TTGAGTCCGAGTTC
65 CTGAGTCCGAGTTC
42704251 ACTTATGGGC
Statistics
Matches: 72, Mismatches: 5, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
92 2 0.03
93 70 0.97
ACGTcount: A:0.22, C:0.21, G:0.29, T:0.28
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGTCCGAACTCGTTGAGC
TGAGTCCGAGTTCGAGAGATGTAACTAG
Found at i:42704899 original size:21 final size:21
Alignment explanation
Indices: 42704873--42704918 Score: 92
Period size: 21 Copynumber: 2.2 Consensus size: 21
42704863 TCCATGGAAG
42704873 CCATGAAATAGGTAAAATTTA
1 CCATGAAATAGGTAAAATTTA
42704894 CCATGAAATAGGTAAAATTTA
1 CCATGAAATAGGTAAAATTTA
42704915 CCAT
1 CCAT
42704919 AAAAATAATG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.46, C:0.13, G:0.13, T:0.28
Consensus pattern (21 bp):
CCATGAAATAGGTAAAATTTA
Found at i:42717428 original size:23 final size:22
Alignment explanation
Indices: 42717393--42717436 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
42717383 TAATTATAAT
*
42717393 TTCAATATGATTTAATAATTAA
1 TTCAATATGATTTAACAATTAA
*
42717415 TTCAATATTTATTTAACAATTA
1 TTCAATA-TGATTTAACAATTA
42717437 TATTGCAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 7 0.37
23 12 0.63
ACGTcount: A:0.43, C:0.07, G:0.02, T:0.48
Consensus pattern (22 bp):
TTCAATATGATTTAACAATTAA
Found at i:42720732 original size:23 final size:23
Alignment explanation
Indices: 42720698--42720833 Score: 147
Period size: 23 Copynumber: 6.0 Consensus size: 23
42720688 GAGCTGATGG
42720698 ACAGTAAGCTCTATTGAGCTGAA
1 ACAGTAAGCTCTATTGAGCTGAA
*
42720721 AC-GATAAGCTCTATCGAGCTG-A
1 ACAG-TAAGCTCTATTGAGCTGAA
*
42720743 ACAGTAAGCTCTATTAAGCTG-A
1 ACAGTAAGCTCTATTGAGCTGAA
*
42720765 ACAGTAAGCTC-ATACGAGCTGAA
1 ACAGTAAGCTCTAT-TGAGCTGAA
* * *
42720788 ACGGTAAGCTCCAATGAGCTGAAA
1 ACAGTAAGCTCTATTGAGCTG-AA
42720812 ACAGTAAGCTCT-TATGAGCTGA
1 ACAGTAAGCTCTAT-TGAGCTGA
42720834 TATATTGGTA
Statistics
Matches: 95, Mismatches: 11, Indels: 14
0.79 0.09 0.12
Matches are distributed among these distances:
21 2 0.02
22 36 0.38
23 37 0.39
24 20 0.21
ACGTcount: A:0.35, C:0.20, G:0.22, T:0.23
Consensus pattern (23 bp):
ACAGTAAGCTCTATTGAGCTGAA
Found at i:42720752 original size:45 final size:45
Alignment explanation
Indices: 42720698--42720833 Score: 163
Period size: 45 Copynumber: 3.0 Consensus size: 45
42720688 GAGCTGATGG
42720698 ACAGTAAGCTCTATTGAGCTGAAAC-GATAAGCTCTATCGAGCTGA
1 ACAGTAAGCTCTATTGAGCTGAAACAG-TAAGCTCTATCGAGCTGA
*
42720743 ACAGTAAGCTCTATTAAGCTG-AACAGTAAGCTC-ATACGAGCTGAA
1 ACAGTAAGCTCTATTGAGCTGAAACAGTAAGCTCTAT-CGAGCTG-A
* * *
42720788 ACGGTAAGCTCCAATGAGCTGAAAACAGTAAGCTCTTAT-GAGCTGA
1 ACAGTAAGCTCTATTGAGCTG-AAACAGTAAGCTC-TATCGAGCTGA
42720834 TATATTGGTA
Statistics
Matches: 79, Mismatches: 5, Indels: 13
0.81 0.05 0.13
Matches are distributed among these distances:
43 2 0.03
44 17 0.22
45 39 0.49
46 1 0.01
47 18 0.23
49 2 0.03
ACGTcount: A:0.35, C:0.20, G:0.22, T:0.23
Consensus pattern (45 bp):
ACAGTAAGCTCTATTGAGCTGAAACAGTAAGCTCTATCGAGCTGA
Found at i:42721369 original size:14 final size:14
Alignment explanation
Indices: 42721352--42721379 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
42721342 TGTCCACTAG
42721352 TATTATCAATGGTA
1 TATTATCAATGGTA
42721366 TATTATCAATGGTA
1 TATTATCAATGGTA
42721380 CAATTAACTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.07, G:0.14, T:0.43
Consensus pattern (14 bp):
TATTATCAATGGTA
Found at i:42723476 original size:22 final size:22
Alignment explanation
Indices: 42723446--42723487 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
42723436 GGTAAGACAC
*
42723446 AGAATAGATCAG-ATACAGATGT
1 AGAACAGATCAGTAT-CAGATGT
42723468 AGAACAGATCAGTATCAGAT
1 AGAACAGATCAGTATCAGAT
42723488 ACAATTTCCT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 16 0.89
23 2 0.11
ACGTcount: A:0.45, C:0.12, G:0.21, T:0.21
Consensus pattern (22 bp):
AGAACAGATCAGTATCAGATGT
Found at i:42726096 original size:11 final size:11
Alignment explanation
Indices: 42726082--42726107 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
42726072 AAAAAATCAG
42726082 AATAAAATAAT
1 AATAAAATAAT
42726093 AATAAAATAAT
1 AATAAAATAAT
42726104 AATA
1 AATA
42726108 GTTGATAAGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (11 bp):
AATAAAATAAT
Found at i:42734159 original size:8 final size:8
Alignment explanation
Indices: 42734146--42734175 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
42734136 TGACTTGGGG
42734146 AGAAGAGA
1 AGAAGAGA
42734154 AGAAGAGA
1 AGAAGAGA
*
42734162 GGAAGAGA
1 AGAAGAGA
42734170 AGAAGA
1 AGAAGA
42734176 AATAAATTGG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.60, C:0.00, G:0.40, T:0.00
Consensus pattern (8 bp):
AGAAGAGA
Found at i:42742199 original size:48 final size:49
Alignment explanation
Indices: 42742105--42742199 Score: 129
Period size: 48 Copynumber: 2.0 Consensus size: 49
42742095 CTCCCCTATC
* *
42742105 TCTTTCCCCTATCCTCTCTTCTCACCCTTGCGTACCCCATGGCCTCATT
1 TCTTTCCCCTATCCTCTCTTCTCACCCTTGCGTACCCCACGACCTCATT
* * * *
42742154 TCTTT-CCCTCTCCTCTCTTCTCACCGTTGCGTGCCTCACGACCTCA
1 TCTTTCCCCTATCCTCTCTTCTCACCCTTGCGTACCCCACGACCTCA
42742200 CTGCCCACGC
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
48 35 0.88
49 5 0.12
ACGTcount: A:0.09, C:0.45, G:0.09, T:0.36
Consensus pattern (49 bp):
TCTTTCCCCTATCCTCTCTTCTCACCCTTGCGTACCCCACGACCTCATT
Found at i:42749623 original size:21 final size:21
Alignment explanation
Indices: 42749597--42749639 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 21
42749587 GCTGAATCTT
42749597 AATATCTATC-AGAGAAATAAC
1 AATATCTATCGA-AGAAATAAC
42749618 AATATCTATCGAAGAAATAAC
1 AATATCTATCGAAGAAATAAC
42749639 A
1 A
42749640 TGTGATGGAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 20 0.95
22 1 0.05
ACGTcount: A:0.53, C:0.14, G:0.09, T:0.23
Consensus pattern (21 bp):
AATATCTATCGAAGAAATAAC
Found at i:42751003 original size:45 final size:45
Alignment explanation
Indices: 42750934--42751023 Score: 144
Period size: 45 Copynumber: 2.0 Consensus size: 45
42750924 GCAAAGTATA
* **
42750934 TAGAGATTTTCTACTCAAAATATCTGTAACCACATTCACTCTTTC
1 TAGAAATTTTCTACTCAAAATATCTACAACCACATTCACTCTTTC
*
42750979 TAGAAATTTTCTACTCAGAATATCTACAACCACATTCACTCTTTC
1 TAGAAATTTTCTACTCAAAATATCTACAACCACATTCACTCTTTC
42751024 CGAGTGATAT
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
45 41 1.00
ACGTcount: A:0.32, C:0.26, G:0.06, T:0.37
Consensus pattern (45 bp):
TAGAAATTTTCTACTCAAAATATCTACAACCACATTCACTCTTTC
Found at i:42766315 original size:35 final size:35
Alignment explanation
Indices: 42766203--42766342 Score: 91
Period size: 35 Copynumber: 4.0 Consensus size: 35
42766193 GTATGTACAT
* * * * * *
42766203 ATGTGATGATATGTTGAACTTGTAAATTTGGCTAC
1 ATGTGATGAAATATTGAACTTGTATATTCGGCCAA
*** * * * *
42766238 ATGTGATGTGTTATTTAACTTGTATTTTCGGTCAT
1 ATGTGATGAAATATTGAACTTGTATATTCGGCCAA
* *
42766273 ATATGATGAAATATTGAACTTGTATATTCGACCAA
1 ATGTGATGAAATATTGAACTTGTATATTCGGCCAA
** ** *
42766308 ATGTGATGTTATAACGAACCTTGTGTATTCGGCCA
1 ATGTGATGAAATATTGAA-CTTGTATATTCGGCCA
42766343 TACATGTAAG
Statistics
Matches: 77, Mismatches: 27, Indels: 1
0.73 0.26 0.01
Matches are distributed among these distances:
35 63 0.82
36 14 0.18
ACGTcount: A:0.29, C:0.11, G:0.20, T:0.40
Consensus pattern (35 bp):
ATGTGATGAAATATTGAACTTGTATATTCGGCCAA
Found at i:42768921 original size:31 final size:31
Alignment explanation
Indices: 42768883--42768977 Score: 163
Period size: 31 Copynumber: 3.1 Consensus size: 31
42768873 CCTTTTCATA
**
42768883 TTTCATATTTCATAACACTGGGCCGAAGCCT
1 TTTCATATTTCATATTACTGGGCCGAAGCCT
42768914 TTTCATATTTCATATTACTGGGCCGAAGCCT
1 TTTCATATTTCATATTACTGGGCCGAAGCCT
*
42768945 TTTCATATTTCATATTACTAGGCCGAAGCCT
1 TTTCATATTTCATATTACTGGGCCGAAGCCT
42768976 TT
1 TT
42768978 ACTGTAAACG
Statistics
Matches: 61, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
31 61 1.00
ACGTcount: A:0.24, C:0.23, G:0.15, T:0.38
Consensus pattern (31 bp):
TTTCATATTTCATATTACTGGGCCGAAGCCT
Found at i:42769243 original size:47 final size:48
Alignment explanation
Indices: 42769190--42769309 Score: 190
Period size: 47 Copynumber: 2.5 Consensus size: 48
42769180 CCTAGCCTCG
*
42769190 TTAATAACTGGGGCAAAAGCCCTTTTAACAACTGGGGCATAAACCC-T
1 TTAATAACTGGGGCATAAGCCCTTTTAACAACTGGGGCATAAACCCTT
* *
42769237 TTAATAACTGGGGCATAAGCCC-TTTAATAACTGGGGCATAAGCCCTT
1 TTAATAACTGGGGCATAAGCCCTTTTAACAACTGGGGCATAAACCCTT
*
42769284 TTAATAATTGGGGCATAAGCCCTTTT
1 TTAATAACTGGGGCATAAGCCCTTTT
42769310 GCACTTCCTC
Statistics
Matches: 67, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
46 21 0.31
47 43 0.64
48 3 0.04
ACGTcount: A:0.31, C:0.21, G:0.20, T:0.28
Consensus pattern (48 bp):
TTAATAACTGGGGCATAAGCCCTTTTAACAACTGGGGCATAAACCCTT
Found at i:42769245 original size:23 final size:23
Alignment explanation
Indices: 42769190--42769308 Score: 184
Period size: 23 Copynumber: 5.1 Consensus size: 23
42769180 CCTAGCCTCG
*
42769190 TTAATAACTGGGGCAAAAGCCCTT
1 TTAATAACTGGGGCATAAGCCC-T
* *
42769214 TTAACAACTGGGGCATAAACCCT
1 TTAATAACTGGGGCATAAGCCCT
42769237 TTAATAACTGGGGCATAAGCCCT
1 TTAATAACTGGGGCATAAGCCCT
42769260 TTAATAACTGGGGCATAAGCCCTT
1 TTAATAACTGGGGCATAAGCCC-T
*
42769284 TTAATAATTGGGGCATAAGCCCT
1 TTAATAACTGGGGCATAAGCCCT
42769307 TT
1 TT
42769309 TGCACTTCCT
Statistics
Matches: 88, Mismatches: 6, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
23 47 0.53
24 41 0.47
ACGTcount: A:0.31, C:0.21, G:0.20, T:0.28
Consensus pattern (23 bp):
TTAATAACTGGGGCATAAGCCCT
Found at i:42769309 original size:24 final size:24
Alignment explanation
Indices: 42769190--42769309 Score: 190
Period size: 24 Copynumber: 5.1 Consensus size: 24
42769180 CCTAGCCTCG
*
42769190 TTAATAACTGGGGCAAAAGCCCTT
1 TTAATAACTGGGGCATAAGCCCTT
* *
42769214 TTAACAACTGGGGCATAAACCC-T
1 TTAATAACTGGGGCATAAGCCCTT
42769237 TTAATAACTGGGGCATAAGCCC-T
1 TTAATAACTGGGGCATAAGCCCTT
42769260 TTAATAACTGGGGCATAAGCCCTT
1 TTAATAACTGGGGCATAAGCCCTT
*
42769284 TTAATAATTGGGGCATAAGCCCTT
1 TTAATAACTGGGGCATAAGCCCTT
42769308 TT
1 TT
42769310 GCACTTCCTC
Statistics
Matches: 89, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
23 44 0.49
24 45 0.51
ACGTcount: A:0.31, C:0.21, G:0.20, T:0.28
Consensus pattern (24 bp):
TTAATAACTGGGGCATAAGCCCTT
Found at i:42769385 original size:20 final size:20
Alignment explanation
Indices: 42769360--42769398 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
42769350 TATGAATACA
42769360 TCATGTGCATATCATACATG
1 TCATGTGCATATCATACATG
42769380 TCATGTGCATATCATACAT
1 TCATGTGCATATCATACAT
42769399 ACCATGTTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.31, C:0.21, G:0.13, T:0.36
Consensus pattern (20 bp):
TCATGTGCATATCATACATG
Found at i:42769404 original size:20 final size:20
Alignment explanation
Indices: 42769361--42769405 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
42769351 ATGAATACAT
**
42769361 CATGTGCATATCATACATGT
1 CATGTGCATATCATACATAC
42769381 CATGTGCATATCATACATAC
1 CATGTGCATATCATACATAC
42769401 CATGT
1 CATGT
42769406 TTATCAAGAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.31, C:0.22, G:0.13, T:0.33
Consensus pattern (20 bp):
CATGTGCATATCATACATAC
Found at i:42769474 original size:25 final size:25
Alignment explanation
Indices: 42769442--42769489 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
42769432 ATATATAAAC
* * *
42769442 CCTAGGGGTATAATGGTCATTTTTA
1 CCTAGGGGCAAAACGGTCATTTTTA
42769467 CCTAGGGGCAAAACGGTCATTTT
1 CCTAGGGGCAAAACGGTCATTTT
42769490 CATATTATAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.25, C:0.17, G:0.25, T:0.33
Consensus pattern (25 bp):
CCTAGGGGCAAAACGGTCATTTTTA
Found at i:42781316 original size:48 final size:48
Alignment explanation
Indices: 42781244--42781414 Score: 171
Period size: 48 Copynumber: 3.6 Consensus size: 48
42781234 TCTCATATCG
* * * *
42781244 ATGCCATGTCTCAGACATGATCTTACAAGAAATCACATGTCGGTGCCA
1 ATGCCATGTCCCAGACATGGTCTTACAAGAAATCACATATCGATGCCA
* * * **
42781292 ATGCCATATCCCAGATATGGTCTTACATGGGATCACATATCGATGCCA
1 ATGCCATGTCCCAGACATGGTCTTACAAGAAATCACATATCGATGCCA
* * * ** ** *
42781340 ACGCCATGTCCCAGGCATGGTCTTACATGGGATCACATATTAATGCAA
1 ATGCCATGTCCCAGACATGGTCTTACAAGAAATCACATATCGATGCCA
* *
42781388 ATGCCATGTCCTAAACATGGTCTTACA
1 ATGCCATGTCCCAGACATGGTCTTACA
42781415 TGGGATCTGT
Statistics
Matches: 103, Mismatches: 20, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
48 103 1.00
ACGTcount: A:0.30, C:0.25, G:0.19, T:0.26
Consensus pattern (48 bp):
ATGCCATGTCCCAGACATGGTCTTACAAGAAATCACATATCGATGCCA
Found at i:42785200 original size:32 final size:31
Alignment explanation
Indices: 42785164--42785224 Score: 77
Period size: 32 Copynumber: 1.9 Consensus size: 31
42785154 CCAACCCATG
* *
42785164 CATATAATGAGTATATCATGTGCATCTCATAA
1 CATATAATGAGCATATCATGT-CATATCATAA
* *
42785196 CATATCATGTGCATATCATGTCATATCAT
1 CATATAATGAGCATATCATGTCATATCAT
42785225 GTATAACAAT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
31 7 0.28
32 18 0.72
ACGTcount: A:0.34, C:0.18, G:0.11, T:0.36
Consensus pattern (31 bp):
CATATAATGAGCATATCATGTCATATCATAA
Found at i:42785201 original size:21 final size:21
Alignment explanation
Indices: 42785176--42785226 Score: 75
Period size: 21 Copynumber: 2.4 Consensus size: 21
42785166 TATAATGAGT
*
42785176 ATATCATGTGCATCTCATAAC
1 ATATCATGTGCATATCATAAC
**
42785197 ATATCATGTGCATATCATGTC
1 ATATCATGTGCATATCATAAC
42785218 ATATCATGT
1 ATATCATGT
42785227 ATAACAATAT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.31, C:0.20, G:0.12, T:0.37
Consensus pattern (21 bp):
ATATCATGTGCATATCATAAC
Found at i:42785220 original size:10 final size:11
Alignment explanation
Indices: 42785162--42785226 Score: 62
Period size: 11 Copynumber: 6.1 Consensus size: 11
42785152 ACCCAACCCA
*
42785162 TGCATATAATG
1 TGCATATCATG
* *
42785173 AGTATATCATG
1 TGCATATCATG
*
42785184 TGCATCTCAT-
1 TGCATATCATG
**
42785194 AACATATCATG
1 TGCATATCATG
42785205 TGCATATCATG
1 TGCATATCATG
42785216 T-CATATCATG
1 TGCATATCATG
42785226 T
1 T
42785227 ATAACAATAT
Statistics
Matches: 42, Mismatches: 11, Indels: 3
0.75 0.20 0.05
Matches are distributed among these distances:
10 17 0.40
11 25 0.60
ACGTcount: A:0.32, C:0.17, G:0.14, T:0.37
Consensus pattern (11 bp):
TGCATATCATG
Found at i:42790660 original size:28 final size:28
Alignment explanation
Indices: 42790599--42790774 Score: 230
Period size: 28 Copynumber: 6.3 Consensus size: 28
42790589 AATAAGTCCA
* *
42790599 CACACTCAGTGCTATATAATC-AACTCG
1 CACACTTAGTGCTACATAATCAAACTCG
*
42790626 CACACTTAGTGCTATATAATCAAACTCG
1 CACACTTAGTGCTACATAATCAAACTCG
*
42790654 CACACTTAGTGCTACATAATCAAGCTCG
1 CACACTTAGTGCTACATAATCAAACTCG
*
42790682 CACACTTAGTGCTACATAGTCAAACTCG
1 CACACTTAGTGCTACATAATCAAACTCG
* *
42790710 CACACTTAGTGCTACATAGTC-AATTCG
1 CACACTTAGTGCTACATAATCAAACTCG
* * * *
42790737 CACACTTAGTGCTGCACAATTTAAACCCG
1 CACACTTAGTGCTACATAA-TCAAACTCG
42790766 CACACTTAG
1 CACACTTAG
42790775 CGCCAATCTC
Statistics
Matches: 134, Mismatches: 12, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
27 41 0.31
28 80 0.60
29 13 0.10
ACGTcount: A:0.32, C:0.28, G:0.13, T:0.26
Consensus pattern (28 bp):
CACACTTAGTGCTACATAATCAAACTCG
Found at i:42793604 original size:92 final size:92
Alignment explanation
Indices: 42793447--42793630 Score: 368
Period size: 92 Copynumber: 2.0 Consensus size: 92
42793437 TCCAGAAACC
42793447 ATTCTGGCCCTGTCCCACTAAAATCTGATTATCTCTTAAAATACTGCCCATATGATCTTTTCGTT
1 ATTCTGGCCCTGTCCCACTAAAATCTGATTATCTCTTAAAATACTGCCCATATGATCTTTTCGTT
42793512 ACTTCCTCATGAAAGCAGACTCATCGA
66 ACTTCCTCATGAAAGCAGACTCATCGA
42793539 ATTCTGGCCCTGTCCCACTAAAATCTGATTATCTCTTAAAATACTGCCCATATGATCTTTTCGTT
1 ATTCTGGCCCTGTCCCACTAAAATCTGATTATCTCTTAAAATACTGCCCATATGATCTTTTCGTT
42793604 ACTTCCTCATGAAAGCAGACTCATCGA
66 ACTTCCTCATGAAAGCAGACTCATCGA
42793631 GCTTCGATTA
Statistics
Matches: 92, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
92 92 1.00
ACGTcount: A:0.27, C:0.27, G:0.12, T:0.34
Consensus pattern (92 bp):
ATTCTGGCCCTGTCCCACTAAAATCTGATTATCTCTTAAAATACTGCCCATATGATCTTTTCGTT
ACTTCCTCATGAAAGCAGACTCATCGA
Found at i:42794043 original size:76 final size:76
Alignment explanation
Indices: 42793916--42794066 Score: 275
Period size: 76 Copynumber: 2.0 Consensus size: 76
42793906 GATGACTTCG
* *
42793916 ATGACGGCCCGACCCCGCAATAATAGATGAGTCCAAGCAACCTATAATGGGTGACAAGGAAACAT
1 ATGACGGCCCGACCCCGCAAAAATAGATGAATCCAAGCAACCTATAATGGGTGACAAGGAAACAT
42793981 CGAGTGAGTTA
66 CGAGTGAGTTA
*
42793992 ATGACGGCCCGACCCCGCAAAAATAGATGAATCCAAGCAACCTATAGTGGGTGACAAGGAAACAT
1 ATGACGGCCCGACCCCGCAAAAATAGATGAATCCAAGCAACCTATAATGGGTGACAAGGAAACAT
42794057 CGAGTGAGTT
66 CGAGTGAGTT
42794067 TATAACTCAG
Statistics
Matches: 72, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
76 72 1.00
ACGTcount: A:0.36, C:0.23, G:0.25, T:0.17
Consensus pattern (76 bp):
ATGACGGCCCGACCCCGCAAAAATAGATGAATCCAAGCAACCTATAATGGGTGACAAGGAAACAT
CGAGTGAGTTA
Found at i:42794541 original size:27 final size:27
Alignment explanation
Indices: 42794511--42794688 Score: 160
Period size: 27 Copynumber: 6.6 Consensus size: 27
42794501 ATATTGAGCC
* *
42794511 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAATCAACT
* * *
42794538 CGCACACTTAGTGCCACGTAATCAAAT
1 CGCACACTTAGTGCTACATAATCAACT
*
42794565 CGCACACTTAGTGCTACATAGTCAGACT
1 CGCACACTTAGTGCTACATAATCA-ACT
* ** ** *
42794593 CGCACTCTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAATCAACT
* **
42794620 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAATCAACT
* * *
42794647 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAATCAACT
*
42794674 CGCACCCTTAGTGCT
1 CGCACACTTAGTGCT
42794689 GTACAATTTA
Statistics
Matches: 124, Mismatches: 24, Indels: 6
0.81 0.16 0.04
Matches are distributed among these distances:
27 101 0.81
28 23 0.19
ACGTcount: A:0.28, C:0.29, G:0.16, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAATCAACT
Found at i:42794650 original size:82 final size:81
Alignment explanation
Indices: 42794532--42794687 Score: 215
Period size: 82 Copynumber: 1.9 Consensus size: 81
42794522 TGCTATATAA
* * *
42794532 TCAACTCGCACACTTAGTGCCACGTAATCAAATCGCACACTTAGTGCTACATAGTCAGACTCGCA
1 TCAACTCGCACACTTAGTGCCACATAATCAAATCGCACACTTAGTGCAACATAGTCA-AATCGCA
*
42794597 CTCTTAGTGCCGCATGG
65 CCCTTAGTGCCGCATGG
* * **
42794614 TCAATTCGCACACTTAGTG-CATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCCA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
42794678 CCCTTAGTGC
65 CCCTTAGTGC
42794688 TGTACAATTT
Statistics
Matches: 65, Mismatches: 8, Indels: 3
0.86 0.11 0.04
Matches are distributed among these distances:
81 17 0.26
82 48 0.74
ACGTcount: A:0.28, C:0.29, G:0.16, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCCACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
CCTTAGTGCCGCATGG
Found at i:42800648 original size:25 final size:23
Alignment explanation
Indices: 42800591--42800650 Score: 102
Period size: 23 Copynumber: 2.6 Consensus size: 23
42800581 AATGAAAAGG
*
42800591 GCACTATGTGTGCGAATGGGGCA
1 GCACTATGTGTGCGAATGCGGCA
42800614 GCACTATGTGTGCGAATGCGGCA
1 GCACTATGTGTGCGAATGCGGCA
*
42800637 GCACAATGTGTGCG
1 GCACTATGTGTGCG
42800651 TATGAAAAAG
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.22, C:0.20, G:0.37, T:0.22
Consensus pattern (23 bp):
GCACTATGTGTGCGAATGCGGCA
Found at i:42801372 original size:19 final size:19
Alignment explanation
Indices: 42801348--42801390 Score: 86
Period size: 19 Copynumber: 2.3 Consensus size: 19
42801338 AAGGTTAGTA
42801348 TTATGGTTTGAATGTTGGT
1 TTATGGTTTGAATGTTGGT
42801367 TTATGGTTTGAATGTTGGT
1 TTATGGTTTGAATGTTGGT
42801386 TTATG
1 TTATG
42801391 ATTTTTATAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.16, C:0.00, G:0.30, T:0.53
Consensus pattern (19 bp):
TTATGGTTTGAATGTTGGT
Found at i:42801887 original size:47 final size:47
Alignment explanation
Indices: 42801830--42801944 Score: 221
Period size: 47 Copynumber: 2.4 Consensus size: 47
42801820 TATACCAGTT
42801830 ATGGTCTTACATGGGATCACATATTGATCCCATGCCATGTCCCAGAC
1 ATGGTCTTACATGGGATCACATATTGATCCCATGCCATGTCCCAGAC
*
42801877 ATGGTCTTACATGGGATCACATATTGATGCCATGCCATGTCCCAGAC
1 ATGGTCTTACATGGGATCACATATTGATCCCATGCCATGTCCCAGAC
42801924 ATGGTCTTACATGGGATCACA
1 ATGGTCTTACATGGGATCACA
42801945 ATGCCATAGC
Statistics
Matches: 67, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
47 67 1.00
ACGTcount: A:0.26, C:0.25, G:0.21, T:0.28
Consensus pattern (47 bp):
ATGGTCTTACATGGGATCACATATTGATCCCATGCCATGTCCCAGAC
Found at i:42801990 original size:37 final size:37
Alignment explanation
Indices: 42801908--42802011 Score: 104
Period size: 37 Copynumber: 2.8 Consensus size: 37
42801898 TATTGATGCC
**
42801908 ATGCCAT-GTCCCAGAC-ATGGTCTTACATGGGATCACA
1 ATGCCATAG-CCCA-ACTATGGTCTTACATGTCATCACA
* *
42801945 ATGCCATAGCCCAACTATGGTCTTACATGTCATTACG
1 ATGCCATAGCCCAACTATGGTCTTACATGTCATCACA
* * * *
42801982 ATGTCATAGCCCAGCTATAGACTTACATGT
1 ATGCCATAGCCCAACTATGGTCTTACATGT
42802012 ACTCAAATGT
Statistics
Matches: 57, Mismatches: 8, Indels: 4
0.83 0.12 0.06
Matches are distributed among these distances:
36 2 0.04
37 54 0.95
38 1 0.02
ACGTcount: A:0.28, C:0.26, G:0.18, T:0.28
Consensus pattern (37 bp):
ATGCCATAGCCCAACTATGGTCTTACATGTCATCACA
Found at i:42808565 original size:15 final size:15
Alignment explanation
Indices: 42808545--42808574 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
42808535 TAGAGTATTT
42808545 TAGTACAGTCTACTA
1 TAGTACAGTCTACTA
42808560 TAGTACAGTCTACTA
1 TAGTACAGTCTACTA
42808575 CCTATAGTAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.33, C:0.20, G:0.13, T:0.33
Consensus pattern (15 bp):
TAGTACAGTCTACTA
Found at i:42810371 original size:27 final size:27
Alignment explanation
Indices: 42810341--42810518 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
42810331 ATATTGAGCC
* * * *
42810341 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
42810368 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
42810395 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
42810423 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
42810450 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
42810477 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
42810504 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
42810519 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:42810480 original size:82 final size:81
Alignment explanation
Indices: 42810362--42810517 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
42810352 TGCTATATAA
* *
42810362 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
42810427 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
42810444 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
42810508 CACTTAGTGC
65 CACTTAGTGC
42810518 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
Done.