Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr13 ID=Chr13-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 58321163
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 747533 characters in sequence are not A, C, G, or T
File 184 of 199
Found at i:53640878 original size:18 final size:17
Alignment explanation
Indices: 53640855--53640890 Score: 63
Period size: 18 Copynumber: 2.1 Consensus size: 17
53640845 ACATCCACCA
53640855 ATAATTATATCAGTCGTT
1 ATAATTATATCAGT-GTT
53640873 ATAATTATATCAGTGTT
1 ATAATTATATCAGTGTT
53640890 A
1 A
53640891 GTTTTTAACT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 4 0.22
18 14 0.78
ACGTcount: A:0.36, C:0.08, G:0.11, T:0.44
Consensus pattern (17 bp):
ATAATTATATCAGTGTT
Found at i:53644732 original size:45 final size:45
Alignment explanation
Indices: 53644667--53644793 Score: 209
Period size: 45 Copynumber: 2.8 Consensus size: 45
53644657 CTCTCACCCT
* *
53644667 CACCCTCACCCTCAACTGGTTCATCATCAGCACCCCCACCCCCAC
1 CACCCCCACCCACAACTGGTTCATCATCAGCACCCCCACCCCCAC
* *
53644712 CACCGCCACCCACTACTGGTTCATCATCAGCACCCCCACCCCCAC
1 CACCCCCACCCACAACTGGTTCATCATCAGCACCCCCACCCCCAC
*
53644757 CACCCCCACTCACAACTGGTTCATCATCAGCACCCCC
1 CACCCCCACCCACAACTGGTTCATCATCAGCACCCCC
53644794 GCCACCCCCT
Statistics
Matches: 75, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
45 75 1.00
ACGTcount: A:0.23, C:0.54, G:0.08, T:0.15
Consensus pattern (45 bp):
CACCCCCACCCACAACTGGTTCATCATCAGCACCCCCACCCCCAC
Found at i:53654340 original size:16 final size:16
Alignment explanation
Indices: 53654319--53654365 Score: 62
Period size: 15 Copynumber: 3.1 Consensus size: 16
53654309 TTTACTAGGG
53654319 TAATTTTATATTTTTA
1 TAATTTTATATTTTTA
53654335 TAATTTTATA-TTTTA
1 TAATTTTATATTTTTA
* *
53654350 AAATTTCA-ATTTTTA
1 TAATTTTATATTTTTA
53654365 T
1 T
53654366 GTGATTAAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
14 1 0.04
15 16 0.59
16 10 0.37
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (16 bp):
TAATTTTATATTTTTA
Found at i:53656066 original size:6 final size:6
Alignment explanation
Indices: 53656043--53656093 Score: 66
Period size: 6 Copynumber: 8.5 Consensus size: 6
53656033 AACCATTACT
* * * *
53656043 TGATGA TGATGC TCATGG TGATGG TGATGG TGACGG TGATGG TGATGG
1 TGATGG TGATGG TGATGG TGATGG TGATGG TGATGG TGATGG TGATGG
53656091 TGA
1 TGA
53656094 AGAACAGATA
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
6 39 1.00
ACGTcount: A:0.20, C:0.06, G:0.43, T:0.31
Consensus pattern (6 bp):
TGATGG
Found at i:53657499 original size:2 final size:2
Alignment explanation
Indices: 53657492--53657517 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
53657482 ATCTCTATTG
53657492 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
53657518 TAATTACAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:53667164 original size:42 final size:42
Alignment explanation
Indices: 53667091--53667219 Score: 129
Period size: 43 Copynumber: 3.0 Consensus size: 42
53667081 TATAGGATTT
*
53667091 TCGATATATGTTATCGTGTAAGACCAC-GTCTGGGACGTTGGCA
1 TCGATATGTGTTA-CGTGTAAGACC-CTGTCTGGGACGTTGGCA
* *
53667134 TCGACT-TGTGTTACGTGTAATACCCTGTCTGGGACAG-TGACA
1 TCGA-TATGTGTTACGTGTAAGACCCTGTCTGGGAC-GTTGGCA
* * * *
53667176 TCGATATGTGATTACATGTAAGACCATGCCAGGGACGTTGGCA
1 TCGATATGTG-TTACGTGTAAGACCCTGTCTGGGACGTTGGCA
53667219 T
1 T
53667220 TGTACGAGCT
Statistics
Matches: 71, Mismatches: 9, Indels: 12
0.77 0.10 0.13
Matches are distributed among these distances:
41 2 0.03
42 32 0.45
43 36 0.51
44 1 0.01
ACGTcount: A:0.24, C:0.19, G:0.27, T:0.29
Consensus pattern (42 bp):
TCGATATGTGTTACGTGTAAGACCCTGTCTGGGACGTTGGCA
Found at i:53671266 original size:2 final size:2
Alignment explanation
Indices: 53671253--53671287 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
53671243 ATGGCACATG
*
53671253 TA TA TT TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
53671288 TTGAATAATC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (2 bp):
TA
Found at i:53682046 original size:3 final size:3
Alignment explanation
Indices: 53681990--53682030 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
53681980 TGACATGCAG
53681990 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
53682031 TAATGATGAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:53682170 original size:3 final size:3
Alignment explanation
Indices: 53682162--53682199 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
53682152 TCATTGGCCC
53682162 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
53682200 AACACAAGAC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (3 bp):
TCT
Found at i:53684089 original size:21 final size:21
Alignment explanation
Indices: 53684063--53684114 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 21
53684053 ATATGTTTCT
* *
53684063 AATCTCACCGCTACAGTATCC
1 AATCTCACCGCTACAATAACC
** *
53684084 AATCTCACTACTACAATAACT
1 AATCTCACCGCTACAATAACC
53684105 AATCTCACCG
1 AATCTCACCG
53684115 TCACCGCTGT
Statistics
Matches: 24, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.35, C:0.35, G:0.06, T:0.25
Consensus pattern (21 bp):
AATCTCACCGCTACAATAACC
Found at i:53686572 original size:21 final size:21
Alignment explanation
Indices: 53686548--53686590 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
53686538 AGAAAAAAGG
*
53686548 TATACATATAAAATAATAAAA
1 TATACAAATAAAATAATAAAA
*
53686569 TATATAAATAAAATAATAAAA
1 TATACAAATAAAATAATAAAA
53686590 T
1 T
53686591 GATTCAAAAG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.30
Consensus pattern (21 bp):
TATACAAATAAAATAATAAAA
Found at i:53686863 original size:2 final size:2
Alignment explanation
Indices: 53686856--53686886 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
53686846 TAAGCGTTAA
53686856 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
53686887 AAATGCATAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:53689198 original size:17 final size:17
Alignment explanation
Indices: 53689176--53689238 Score: 63
Period size: 17 Copynumber: 3.5 Consensus size: 17
53689166 ATTAAATCAC
53689176 TACATAATTAAAAACAT
1 TACATAATTAAAAACAT
** * *
53689193 TACATAAGTCTTTGAATCAC
1 TACATAA---TTAAAAACAT
53689213 TACATAATTAAAAACAT
1 TACATAATTAAAAACAT
53689230 TACATAATT
1 TACATAATT
53689239 CTTGAAATTA
Statistics
Matches: 35, Mismatches: 8, Indels: 6
0.71 0.16 0.12
Matches are distributed among these distances:
17 22 0.63
20 13 0.37
ACGTcount: A:0.49, C:0.14, G:0.03, T:0.33
Consensus pattern (17 bp):
TACATAATTAAAAACAT
Found at i:53689212 original size:37 final size:37
Alignment explanation
Indices: 53689170--53689241 Score: 135
Period size: 37 Copynumber: 1.9 Consensus size: 37
53689160 AACCGAATTA
53689170 AATCACTACATAATTAAAAACATTACATAAGTCTTTG
1 AATCACTACATAATTAAAAACATTACATAAGTCTTTG
*
53689207 AATCACTACATAATTAAAAACATTACATAATTCTT
1 AATCACTACATAATTAAAAACATTACATAAGTCTT
53689242 GAAATTAACA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 34 1.00
ACGTcount: A:0.47, C:0.17, G:0.03, T:0.33
Consensus pattern (37 bp):
AATCACTACATAATTAAAAACATTACATAAGTCTTTG
Found at i:53689255 original size:37 final size:37
Alignment explanation
Indices: 53689174--53689258 Score: 120
Period size: 37 Copynumber: 2.3 Consensus size: 37
53689164 GAATTAAATC
*
53689174 ACTACATAATTAAAAACATTACATAAGTCTTTGAATC
1 ACTACATAATTAAAAACATTACATAAGTCTTTGAATA
*
53689211 ACTACATAATTAAAAACATTACATAATTC-TTGAAATTA
1 ACTACATAATTAAAAACATTACATAAGTCTTTG-AA-TA
53689249 AC-ACATAATT
1 ACTACATAATT
53689259 GAAATGTAAG
Statistics
Matches: 44, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
36 3 0.07
37 38 0.86
38 3 0.07
ACGTcount: A:0.48, C:0.15, G:0.04, T:0.33
Consensus pattern (37 bp):
ACTACATAATTAAAAACATTACATAAGTCTTTGAATA
Found at i:53689415 original size:38 final size:38
Alignment explanation
Indices: 53689371--53689447 Score: 136
Period size: 38 Copynumber: 2.0 Consensus size: 38
53689361 TACTTAGAGT
*
53689371 TAGACTTTAGTTTTATTTTTATTGGGTTGGTAATTGGG
1 TAGACTTTAGTTTTAGTTTTATTGGGTTGGTAATTGGG
*
53689409 TAGACTTTAGTTTTAGTTTTATTGGGTTTGTAATTGGG
1 TAGACTTTAGTTTTAGTTTTATTGGGTTGGTAATTGGG
53689447 T
1 T
53689448 TGGGTTGGAT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.18, C:0.03, G:0.26, T:0.53
Consensus pattern (38 bp):
TAGACTTTAGTTTTAGTTTTATTGGGTTGGTAATTGGG
Found at i:53690750 original size:68 final size:70
Alignment explanation
Indices: 53690676--53690804 Score: 183
Period size: 68 Copynumber: 1.9 Consensus size: 70
53690666 CAGGTTAGGC
* *
53690676 TTTAGGGTTTAGATTAATTAGTGTGTTTTAATTT-T-TATGAAATAAGGTTTAAGGG-TTAGGGA
1 TTTAGGGTTTAGATTAATTAATATGTTTTAATTTATATATGAAATAAGGTTT-AGGGATTAGGGA
53690738 TTCGGG
65 TTCGGG
* * *
53690744 TTTAGGGTTTTGATTAATTAATATTTTTTAATTTATATATTAAATAAGGTTTAGGGATTAG
1 TTTAGGGTTTAGATTAATTAATATGTTTTAATTTATATATGAAATAAGGTTTAGGGATTAG
53690805 TAGTTAGGGG
Statistics
Matches: 53, Mismatches: 5, Indels: 4
0.85 0.08 0.06
Matches are distributed among these distances:
68 30 0.57
69 5 0.09
70 18 0.34
ACGTcount: A:0.29, C:0.01, G:0.22, T:0.47
Consensus pattern (70 bp):
TTTAGGGTTTAGATTAATTAATATGTTTTAATTTATATATGAAATAAGGTTTAGGGATTAGGGAT
TCGGG
Found at i:53691389 original size:2 final size:2
Alignment explanation
Indices: 53691382--53691411 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
53691372 TATCATTTTA
*
53691382 AT AT AT AT AT AT AT AT AT AT AA AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
53691412 GAAAATGGGT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:53692074 original size:74 final size:74
Alignment explanation
Indices: 53691941--53692079 Score: 169
Period size: 74 Copynumber: 1.9 Consensus size: 74
53691931 TTGCAGCAGC
* *
53691941 ATTAGTGGCGCTTATACAGAAACGCCGCAAAGTCCTGTAACTAGGAAGTGGAACGGCGCCGTTTT
1 ATTAGTGGCGCTTATACAGAAACGCCGCAAAGT-CTGTAACTAGGAAATGAAACGGCGCCGTTTT
53692006 GTTCTTCTCT
65 GTTCTTCTCT
* *
53692016 ATTAGTGGCGCTTTATA-A-AAACGCCGCAAAGT-TGT-ATTAGGAGTTAATGAAACTGCGCCGT
1 ATTAGTGGCGC-TTATACAGAAACGCCGCAAAGTCTGTAACTAGGA---AATGAAACGGCGCCGT
53692077 TTT
62 TTT
53692080 ACATTGCTAT
Statistics
Matches: 56, Mismatches: 4, Indels: 9
0.81 0.06 0.13
Matches are distributed among these distances:
71 6 0.11
72 3 0.05
74 30 0.54
75 12 0.21
76 5 0.09
ACGTcount: A:0.27, C:0.19, G:0.24, T:0.29
Consensus pattern (74 bp):
ATTAGTGGCGCTTATACAGAAACGCCGCAAAGTCTGTAACTAGGAAATGAAACGGCGCCGTTTTG
TTCTTCTCT
Found at i:53692281 original size:147 final size:147
Alignment explanation
Indices: 53692110--53692558 Score: 343
Period size: 147 Copynumber: 3.1 Consensus size: 147
53692100 TTCCATGAAT
** * * * * * * ** *
53692110 CGCCGCAAAAATGTAATTATATTTATTGAAATGTTGTCGTTTTGTCTATGGTATTAGTGGC-GTT
1 CGCCGCAAAAATGTTCTAACATTTATTGAAACGCTGCCATTTTGTAAATGGTATTAGTGGCATTT
* * * *
53692174 TTTCTGGAAACGCCACAAGCTTGA-GTTAGCTGTTGGGGAAACGACTTCG-TTTGAACTTATAGT
66 TTTC-GAAAACGCCACAAGCTTGAGGTAAG-TGTTGAGGAAACGACTGCGTTTTG-ACTTATAGT
53692237 TAGTGGCACTTTACTTAAAA
128 TAGTGGCACTTTACTTAAAA
* * ** *
53692257 TGCCGCAAAATTGTTCTAACATTTACAGAAACGCTGCCATTTTGTAAATGTTATTAGTGGCATTT
1 CGCCGCAAAAATGTTCTAACATTTATTGAAACGCTGCCATTTTGTAAATGGTATTAGTGGCATTT
* * ** * * *
53692322 TTTCGAAAATGCCGCGGGTTTGAGGTAAGTGTTGATGAAGCGACTGCGTTTTGACTTATAGTTAG
66 TTTCGAAAACGCCACAAGCTTGAGGTAAGTGTTGAGGAAACGACTGCGTTTTGACTTATAGTTAG
* *
53692387 TGGCGCTTTGCTTAAAA
131 TGGCACTTTACTTAAAA
* * ** * * * ** * *
53692404 CGCCGCAAAAATGTTTTAACATTGATTGATGCGATGCCGTTTGGTTGTAT--TTTTAGTGGCGTT
1 CGCCGCAAAAATGTTCTAACATTTATTGAAACGCTGCCATTTTG-TAAATGGTATTAGTGGCATT
* * * * * ** * *
53692467 TATTCAAAAACGCCACAGGTTTGAGCTATTTCTTGATGAAACGACTGCGTTTTGACTTATAGTTA
65 TTTTCGAAAACGCCACAAGCTTGAGGTAAGTGTTGAGGAAACGACTGCGTTTTGACTTATAGTTA
* *
53692532 GTGGCGCTTATA-TTCAAA
130 GTGGCACTT-TACTTAAAA
*
53692550 TGCCGCAAA
1 CGCCGCAAA
53692559 TGGTTAAATT
Statistics
Matches: 240, Mismatches: 57, Indels: 11
0.78 0.19 0.04
Matches are distributed among these distances:
146 88 0.37
147 135 0.56
148 17 0.07
ACGTcount: A:0.26, C:0.15, G:0.23, T:0.36
Consensus pattern (147 bp):
CGCCGCAAAAATGTTCTAACATTTATTGAAACGCTGCCATTTTGTAAATGGTATTAGTGGCATTT
TTTCGAAAACGCCACAAGCTTGAGGTAAGTGTTGAGGAAACGACTGCGTTTTGACTTATAGTTAG
TGGCACTTTACTTAAAA
Found at i:53692522 original size:146 final size:147
Alignment explanation
Indices: 53692211--53692558 Score: 380
Period size: 146 Copynumber: 2.4 Consensus size: 147
53692201 AGCTGTTGGG
* * * *
53692211 GAAACGACTTCG-TTTGAACTTATAGTTAGTGGCACTTTACTTAAAATGCCGCAAAATTGTTCTA
1 GAAACGACTGCGTTTTG-ACTTATAGTTAGTGGCGCTTTACTTAAAACGCCGCAAAAATGTTCTA
* * * * * * * *
53692275 ACATTTACAGAAACGCTGCCATTTTGTAAATGTTATTAGTGGCATTTTTTCGAAAATGCCGCGGG
65 ACATTGACAGAAACGATGCCATTTGGTAAATGTTATTAGTGGCATTTATTCAAAAACGCCACAGG
* *
53692340 TTTGAGGTAAGTGTTGAT
130 TTTGAGCTAAGTCTTGAT
* * *
53692358 GAAGCGACTGCGTTTTGACTTATAGTTAGTGGCGCTTTGCTTAAAACGCCGCAAAAATGTTTTAA
1 GAAACGACTGCGTTTTGACTTATAGTTAGTGGCGCTTTACTTAAAACGCCGCAAAAATGTTCTAA
** ** * ** *
53692423 CATTGATTGATGCGATGCCGTTTGGTTGTAT-TT-TTAGTGGCGTTTATTCAAAAACGCCACAGG
66 CATTGACAGAAACGATGCCATTTGG-TAAATGTTATTAGTGGCATTTATTCAAAAACGCCACAGG
**
53692486 TTTGAGCTATTTCTTGAT
130 TTTGAGCTAAGTCTTGAT
* *
53692504 GAAACGACTGCGTTTTGACTTATAGTTAGTGGCGCTTATA-TTCAAATGCCGCAAA
1 GAAACGACTGCGTTTTGACTTATAGTTAGTGGCGCTT-TACTTAAAACGCCGCAAA
53692559 TGGTTAAATT
Statistics
Matches: 167, Mismatches: 31, Indels: 7
0.81 0.15 0.03
Matches are distributed among these distances:
146 87 0.52
147 73 0.44
148 7 0.04
ACGTcount: A:0.27, C:0.16, G:0.22, T:0.35
Consensus pattern (147 bp):
GAAACGACTGCGTTTTGACTTATAGTTAGTGGCGCTTTACTTAAAACGCCGCAAAAATGTTCTAA
CATTGACAGAAACGATGCCATTTGGTAAATGTTATTAGTGGCATTTATTCAAAAACGCCACAGGT
TTGAGCTAAGTCTTGAT
Found at i:53693237 original size:21 final size:21
Alignment explanation
Indices: 53693213--53693253 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
53693203 TTTGGAACTG
53693213 GTAGACTGTTGTTTGCCTTTA
1 GTAGACTGTTGTTTGCCTTTA
53693234 GTAGACTGTTGTTTGCCTTT
1 GTAGACTGTTGTTTGCCTTT
53693254 GCATTTGTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.12, C:0.15, G:0.24, T:0.49
Consensus pattern (21 bp):
GTAGACTGTTGTTTGCCTTTA
Found at i:53694768 original size:13 final size:13
Alignment explanation
Indices: 53694752--53694904 Score: 103
Period size: 13 Copynumber: 11.5 Consensus size: 13
53694742 TTACTAAAAT
*
53694752 TTACTTTAATATA
1 TTACTTAAATATA
*
53694765 TTACTTGAATATA
1 TTACTTAAATATA
*
53694778 TTACTTAAATAAA
1 TTACTTAAATATA
*
53694791 TTACTTACTAAAAT-
1 TTACTTA--AATATA
** *
53694805 TTGGTTAAATTTTA
1 TTACTTAAA-TATA
* *
53694819 GTACTTAAATATG
1 TTACTTAAATATA
*
53694832 TTACTTAAATACA
1 TTACTTAAATATA
*
53694845 TTACTTACTAAAAT-
1 TTACTTA--AATATA
** *
53694859 TTGTTTAAATTTA
1 TTACTTAAATATA
*
53694872 TTACTTAAATATG
1 TTACTTAAATATA
*
53694885 TTACTTAAATACA
1 TTACTTAAATATA
53694898 TTACTTA
1 TTACTTA
53694905 CTAAAATTTA
Statistics
Matches: 104, Mismatches: 29, Indels: 14
0.71 0.20 0.10
Matches are distributed among these distances:
12 5 0.05
13 77 0.74
14 16 0.15
15 6 0.06
ACGTcount: A:0.40, C:0.09, G:0.05, T:0.46
Consensus pattern (13 bp):
TTACTTAAATATA
Found at i:53694804 original size:53 final size:53
Alignment explanation
Indices: 53694742--53694914 Score: 249
Period size: 53 Copynumber: 3.2 Consensus size: 53
53694732 AACATATTTT
* * * * *
53694742 TTACTAAAATTTACTTTAATATATTACTTGAATATATTACTTAAATAAATTAC
1 TTACTAAAATTTAGTTTAATTTATTACTTAAATATGTTACTTAAATACATTAC
* * *
53694795 TTACTAAAATTTGGTTAAATTTTAGTACTTAAATATGTTACTTAAATACATTAC
1 TTACTAAAATTTAGTTTAA-TTTATTACTTAAATATGTTACTTAAATACATTAC
53694849 TTACTAAAATTT-GTTTAAATTTATTACTTAAATATGTTACTTAAATACATTAC
1 TTACTAAAATTTAGTTT-AATTTATTACTTAAATATGTTACTTAAATACATTAC
53694902 TTACTAAAATTTA
1 TTACTAAAATTTA
53694915 AGTATATATT
Statistics
Matches: 107, Mismatches: 10, Indels: 5
0.88 0.08 0.04
Matches are distributed among these distances:
53 64 0.60
54 43 0.40
ACGTcount: A:0.41, C:0.09, G:0.04, T:0.46
Consensus pattern (53 bp):
TTACTAAAATTTAGTTTAATTTATTACTTAAATATGTTACTTAAATACATTAC
Found at i:53695247 original size:28 final size:28
Alignment explanation
Indices: 53695207--53695338 Score: 95
Period size: 28 Copynumber: 4.5 Consensus size: 28
53695197 NNNNNNNNNN
*
53695207 ACATAACTTACATGTTAACTTACATAAT
1 ACATAACTTACATATTAACTTACATAAT
*
53695235 ACATTACTTACATATTAACTTACATAAGTT
1 ACATAACTTACATATTAACTTACATAA--T
* * * *
53695265 ATCTACAAGCTTATATATAAACTTGCATAACTT
1 A-C-ATAA-CTTACATATTAACTTACATAA--T
* **
53695298 ACATAA-TAACATAACAACTTACATAAT
1 ACATAACTTACATATTAACTTACATAAT
* *
53695325 ACATAGCATACATA
1 ACATAACTTACATA
53695339 ACTTACATAA
Statistics
Matches: 81, Mismatches: 17, Indels: 12
0.74 0.15 0.11
Matches are distributed among these distances:
27 6 0.07
28 30 0.37
29 15 0.19
30 2 0.02
31 4 0.05
32 3 0.04
33 21 0.26
ACGTcount: A:0.45, C:0.18, G:0.04, T:0.33
Consensus pattern (28 bp):
ACATAACTTACATATTAACTTACATAAT
Found at i:53695302 original size:9 final size:9
Alignment explanation
Indices: 53695284--53695543 Score: 183
Period size: 9 Copynumber: 29.8 Consensus size: 9
53695274 CTTATATATA
*
53695284 AACTTGCAT
1 AACTTACAT
53695293 AACTTACAT
1 AACTTACAT
*
53695302 AA-TAACAT
1 AACTTACAT
53695310 AACAACTTACAT
1 ---AACTTACAT
53695322 AA--TACAT
1 AACTTACAT
* *
53695329 AGCATACAT
1 AACTTACAT
53695338 AACTTACAT
1 AACTTACAT
53695347 AACTTACAT
1 AACTTACAT
53695356 AA--TACA-
1 AACTTACAT
53695362 AACCTTACAT
1 AA-CTTACAT
*
53695372 AACTTAAAT
1 AACTTACAT
* *
53695381 ATCTTACAC
1 AACTTACAT
53695390 AACTTACAT
1 AACTTACAT
**
53695399 AACCAACAT
1 AACTTACAT
*
53695408 AATACATA-AT
1 -A-ACTTACAT
53695418 AACTTAC--
1 AACTTACAT
53695425 AACTTACAT
1 AACTTACAT
*
53695434 AACATACA-
1 AACTTACAT
**
53695442 ATACTTTGAT
1 A-ACTTACAT
53695452 AACTTACAT
1 AACTTACAT
53695461 AACTTACAT
1 AACTTACAT
53695470 AA--TACAT
1 AACTTACAT
53695477 AACTTACAT
1 AACTTACAT
* *
53695486 AGCTTACTT
1 AACTTACAT
53695495 AA--TACAT
1 AACTTACAT
53695502 AACTTACAT
1 AACTTACAT
53695511 AACTT--AT
1 AACTTACAT
*
53695518 ACACGTACAT
1 A-ACTTACAT
53695528 AACTTACAT
1 AACTTACAT
*
53695537 AATTTAC
1 AACTTAC
53695544 TTAATACATA
Statistics
Matches: 197, Mismatches: 30, Indels: 48
0.72 0.11 0.17
Matches are distributed among these distances:
6 2 0.01
7 33 0.17
8 13 0.07
9 130 0.66
10 9 0.05
11 5 0.03
12 5 0.03
ACGTcount: A:0.46, C:0.21, G:0.02, T:0.31
Consensus pattern (9 bp):
AACTTACAT
Found at i:53695353 original size:34 final size:34
Alignment explanation
Indices: 53695313--53695516 Score: 161
Period size: 34 Copynumber: 5.9 Consensus size: 34
53695303 ATAACATAAC
*
53695313 AACTTACATAATACATAGCATACATAACTTACAT
1 AACTTACATAATACATAACATACATAACTTACAT
* *
53695347 AACTTACATAATACA-AACCTTACATAACTTAAAT
1 AACTTACATAATACATAA-CATACATAACTTACAT
* * *
53695381 ATCTTACACAACTTACATAACCA-ACATAATACATA-AT
1 AACTTACATAA--TACATAA-CATACAT-A-ACTTACAT
* **
53695418 AACTTACA-ACTTACATAACATACA-ATACTTTGAT
1 AACTTACATA-ATACATAACATACATA-ACTTACAT
53695452 AACTTACATAACTTACAT-A-ATACATAACTTACAT
1 AACTTACATAA--TACATAACATACATAACTTACAT
* * *
53695486 AGCTTACTTAATACATAACTTACATAACTTA
1 AACTTACATAATACATAACATACATAACTTA
53695517 TACACGTACA
Statistics
Matches: 138, Mismatches: 17, Indels: 30
0.75 0.09 0.16
Matches are distributed among these distances:
32 5 0.04
33 7 0.05
34 81 0.59
35 13 0.09
36 14 0.10
37 14 0.10
38 4 0.03
ACGTcount: A:0.47, C:0.21, G:0.01, T:0.31
Consensus pattern (34 bp):
AACTTACATAATACATAACATACATAACTTACAT
Found at i:53695414 original size:43 final size:45
Alignment explanation
Indices: 53695318--53695416 Score: 107
Period size: 43 Copynumber: 2.3 Consensus size: 45
53695308 ATAACAACTT
* * *
53695318 ACATAATACATAGCATACATAACTTACATAACTTACATAATACAA
1 ACATAATACATAACATAAATAACTTACACAACTTACATAATACAA
* * * *
53695363 ACCT--TACATAACTTAAATATCTTACACAACTTACAT-A-ACCA
1 ACATAATACATAACATAAATAACTTACACAACTTACATAATACAA
53695404 ACATAATACATAA
1 ACATAATACATAA
53695417 TAACTTACAA
Statistics
Matches: 44, Mismatches: 8, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
41 6 0.14
42 1 0.02
43 34 0.77
45 3 0.07
ACGTcount: A:0.49, C:0.22, G:0.01, T:0.27
Consensus pattern (45 bp):
ACATAATACATAACATAAATAACTTACACAACTTACATAATACAA
Found at i:53695484 original size:25 final size:26
Alignment explanation
Indices: 53695313--53695538 Score: 154
Period size: 25 Copynumber: 8.8 Consensus size: 26
53695303 ATAACATAAC
*
53695313 AACTTACATAA--TACATAGCATACAT
1 AACTTACATAACTTACATAAC-TACAT
53695338 AACTTACATAACTTACATAA-TACA-
1 AACTTACATAACTTACATAACTACAT
* * *
53695362 AACCTTACATAACTTAAATATCTTACAC
1 AA-CTTACATAACTTACATAAC-TACAT
**
53695390 AACTTACATAACCAACATAA-TACATAAT
1 AACTTACATAACTTACATAACTAC---AT
53695418 AACTTAC--AACTTACATAACATACA-
1 AACTTACATAACTTACATAAC-TACAT
**
53695442 ATACTTTGATAACTTACATAACTTACAT
1 A-ACTTACATAACTTACATAAC-TACAT
* *
53695470 AA--TACATAACTTACATAGCTTACTT
1 AACTTACATAACTTACATAAC-TACAT
*
53695495 AA--TACATAACTTACATAACT-TAT
1 AACTTACATAACTTACATAACTACAT
*
53695518 ACACGTACATAACTTACATAA
1 A-ACTTACATAACTTACATAA
53695539 TTTACTTAAT
Statistics
Matches: 163, Mismatches: 20, Indels: 35
0.75 0.09 0.16
Matches are distributed among these distances:
23 2 0.01
24 5 0.03
25 76 0.47
26 25 0.15
27 41 0.25
28 14 0.09
ACGTcount: A:0.46, C:0.21, G:0.02, T:0.31
Consensus pattern (26 bp):
AACTTACATAACTTACATAACTACAT
Found at i:53701465 original size:43 final size:42
Alignment explanation
Indices: 53701406--53701556 Score: 149
Period size: 43 Copynumber: 3.5 Consensus size: 42
53701396 GTTTTTTCAA
** * * *
53701406 AAAAGCGTTGCTAAAGGTCATGGTATTTTGCGGCGTTTGTGG
1 AAAAGCGCCGCTAAAGGTCATGGTCTTTAGCGACGTTTGTGG
* * * * *
53701448 AAAAAACGCCGCTAAAGGTCACGGTCTTTAGCGTCGTCTTTTAG
1 -AAAAGCGCCGCTAAAGGTCATGGTCTTTAGCGACGT-TTGTGG
* * *
53701492 AAAAGCGCCGTTAAAGGTCATGGTCTTTAGTGACATTTGTGGG
1 AAAAGCGCCGCTAAAGGTCATGGTCTTTAGCGACGTTTGT-GG
*
53701535 AAAAGCGCCGCTAAAAGTCATG
1 AAAAGCGCCGCTAAAGGTCATG
53701557 ACCTTTGGCA
Statistics
Matches: 87, Mismatches: 19, Indels: 4
0.79 0.17 0.04
Matches are distributed among these distances:
42 3 0.03
43 80 0.92
44 4 0.05
ACGTcount: A:0.27, C:0.17, G:0.28, T:0.28
Consensus pattern (42 bp):
AAAAGCGCCGCTAAAGGTCATGGTCTTTAGCGACGTTTGTGG
Found at i:53701739 original size:23 final size:23
Alignment explanation
Indices: 53701711--53701756 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
53701701 TTCCAAAGAG
53701711 TTAACCAAGGACCACTCAACACA
1 TTAACCAAGGACCACTCAACACA
53701734 TTAACCAAGGACCACTCAACACA
1 TTAACCAAGGACCACTCAACACA
53701757 CTGTTGCAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.43, C:0.35, G:0.09, T:0.13
Consensus pattern (23 bp):
TTAACCAAGGACCACTCAACACA
Found at i:53702525 original size:22 final size:22
Alignment explanation
Indices: 53702500--53702551 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 22
53702490 TAATAACAAG
* *
53702500 AAAATAGTAGT-AATATAATAGC
1 AAAATAGTAGTGAA-ACAACAGC
*
53702522 AAAATAGCAGTGAAACAACAGC
1 AAAATAGTAGTGAAACAACAGC
53702544 AAAATAGT
1 AAAATAGT
53702552 TTATTTGGGT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
22 23 0.92
23 2 0.08
ACGTcount: A:0.56, C:0.10, G:0.15, T:0.19
Consensus pattern (22 bp):
AAAATAGTAGTGAAACAACAGC
Found at i:53704122 original size:23 final size:22
Alignment explanation
Indices: 53704090--53704160 Score: 72
Period size: 24 Copynumber: 3.1 Consensus size: 22
53704080 ATTCTTTTTC
*
53704090 TTTTTGTATATTTGATTCTCTA
1 TTTTTCTATATTTGATTCTCTA
*
53704112 TTTTTCATATATGTT-ATTCTCTT
1 TTTTTC-TATAT-TTGATTCTCTA
*
53704135 TATTTTCTCATATTTGATTATCTA
1 T-TTTTCT-ATATTTGATTCTCTA
53704159 TT
1 TT
53704161 GTTATATTTT
Statistics
Matches: 40, Mismatches: 4, Indels: 9
0.75 0.08 0.17
Matches are distributed among these distances:
22 5 0.12
23 17 0.43
24 18 0.45
ACGTcount: A:0.20, C:0.11, G:0.06, T:0.63
Consensus pattern (22 bp):
TTTTTCTATATTTGATTCTCTA
Found at i:53715042 original size:22 final size:22
Alignment explanation
Indices: 53715014--53715058 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
53715004 GATCCTTAAC
53715014 TTTGAAAGTAATTTAATGAAAT
1 TTTGAAAGTAATTTAATGAAAT
53715036 TTTGAAAGTAATTTAATGAAAT
1 TTTGAAAGTAATTTAATGAAAT
53715058 T
1 T
53715059 CAAGCTTAGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.44, C:0.00, G:0.13, T:0.42
Consensus pattern (22 bp):
TTTGAAAGTAATTTAATGAAAT
Found at i:53715291 original size:26 final size:28
Alignment explanation
Indices: 53715226--53715297 Score: 85
Period size: 28 Copynumber: 2.6 Consensus size: 28
53715216 ATAAGAAAAT
* *
53715226 TTATTATTAAGAATTTTATGAAATTATATA
1 TTATTATT-A-AATTATATGAAATAATATA
*
53715256 TTATTATTAAATTATATGTAATAATA-A
1 TTATTATTAAATTATATGAAATAATATA
53715283 TTATT-TTAAATTATA
1 TTATTATTAAATTATA
53715298 CAAATTTATG
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
26 10 0.26
27 6 0.15
28 14 0.36
29 1 0.03
30 8 0.21
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.51
Consensus pattern (28 bp):
TTATTATTAAATTATATGAAATAATATA
Found at i:53715453 original size:16 final size:16
Alignment explanation
Indices: 53715432--53715477 Score: 83
Period size: 16 Copynumber: 2.9 Consensus size: 16
53715422 TTAATTTGCT
53715432 ATTACGCCTCTATTCC
1 ATTACGCCTCTATTCC
*
53715448 ATTACGCCTCTAATCC
1 ATTACGCCTCTATTCC
53715464 ATTACGCCTCTATT
1 ATTACGCCTCTATT
53715478 TCAATATAGC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 28 1.00
ACGTcount: A:0.22, C:0.35, G:0.07, T:0.37
Consensus pattern (16 bp):
ATTACGCCTCTATTCC
Found at i:53719074 original size:16 final size:17
Alignment explanation
Indices: 53719055--53719088 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
53719045 TGGAGGAAAG
*
53719055 AAAATG-AAACTTTTGA
1 AAAATGCAAAATTTTGA
53719071 AAAATGCAAAATTTTGA
1 AAAATGCAAAATTTTGA
53719088 A
1 A
53719089 CTAGTTTACA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.53, C:0.06, G:0.12, T:0.29
Consensus pattern (17 bp):
AAAATGCAAAATTTTGA
Found at i:53720909 original size:14 final size:14
Alignment explanation
Indices: 53720890--53720929 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
53720880 TTGATTGTCA
53720890 GTAAAATGTTTTCC
1 GTAAAATGTTTTCC
* *
53720904 GTAAAATGATTTCT
1 GTAAAATGTTTTCC
*
53720918 GGAAAATGTTTT
1 GTAAAATGTTTT
53720930 ACTTTTCTGT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.33, C:0.07, G:0.17, T:0.42
Consensus pattern (14 bp):
GTAAAATGTTTTCC
Found at i:53720938 original size:20 final size:20
Alignment explanation
Indices: 53720913--53720952 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
53720903 CGTAAAATGA
*
53720913 TTTCTGGAAAATGTTTTACT
1 TTTCTGGAAAATGATTTACT
*
53720933 TTTCTGTAAAATGATTTACT
1 TTTCTGGAAAATGATTTACT
53720953 AGAAAATATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.28, C:0.10, G:0.12, T:0.50
Consensus pattern (20 bp):
TTTCTGGAAAATGATTTACT
Found at i:53720942 original size:34 final size:35
Alignment explanation
Indices: 53720898--53720964 Score: 100
Period size: 34 Copynumber: 1.9 Consensus size: 35
53720888 CAGTAAAATG
* *
53720898 TTTTCCGTAAAATGATTT-CTGGAAAATGTTTTAC
1 TTTTCCGTAAAATGATTTACTAGAAAATATTTTAC
*
53720932 TTTTCTGTAAAATGATTTACTAGAAAATATTTT
1 TTTTCCGTAAAATGATTTACTAGAAAATATTTT
53720965 CTACTGTTTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 17 0.59
35 12 0.41
ACGTcount: A:0.33, C:0.09, G:0.12, T:0.46
Consensus pattern (35 bp):
TTTTCCGTAAAATGATTTACTAGAAAATATTTTAC
Found at i:53721659 original size:16 final size:16
Alignment explanation
Indices: 53721638--53721693 Score: 69
Period size: 16 Copynumber: 3.5 Consensus size: 16
53721628 TTTGGTTCGC
53721638 TGTAATAGAATAAATG
1 TGTAATAGAATAAATG
*
53721654 TGTAATAGAATATA-G
1 TGTAATAGAATAAATG
*
53721669 CTATAATAGAATAAATG
1 -TGTAATAGAATAAATG
*
53721686 CGTAATAG
1 TGTAATAG
53721694 TAATTCAATT
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
15 1 0.03
16 31 0.94
17 1 0.03
ACGTcount: A:0.48, C:0.04, G:0.18, T:0.30
Consensus pattern (16 bp):
TGTAATAGAATAAATG
Found at i:53722037 original size:13 final size:12
Alignment explanation
Indices: 53722013--53722053 Score: 55
Period size: 13 Copynumber: 3.2 Consensus size: 12
53722003 TATAATACTA
53722013 TAAAATATAATT
1 TAAAATATAATT
53722025 TAAAATAATAATT
1 TAAAAT-ATAATT
*
53722038 ATTAAATATAATT
1 -TAAAATATAATT
53722051 TAA
1 TAA
53722054 TAAAAAATAT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
12 8 0.32
13 12 0.48
14 5 0.20
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (12 bp):
TAAAATATAATT
Found at i:53722040 original size:120 final size:119
Alignment explanation
Indices: 53721903--53722142 Score: 428
Period size: 120 Copynumber: 2.0 Consensus size: 119
53721893 TTAATCATAT
* *
53721903 TTTAACATAATTATTATTAAATATAATTTAAT-AAAAATATATAATTTAATAAAATTCTTAATAT
1 TTTAAAATAATAATTATTAAATATAATTTAATAAAAAATATATAATTTAATAAAATTCTTAATA-
53721967 TAAATATTCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAATATAA
65 TAAATATTCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAA-ATAA
53722023 TTTAAAATAATAATTATTAAATATAATTTAATAAAAAATATATAATTTAATAAAATTCTTAATAT
1 TTTAAAATAATAATTATTAAATATAATTTAATAAAAAATATATAATTTAATAAAATTCTTAATAT
*
53722088 AATTATTCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAAATAA
66 AAATATTCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAAATAA
53722142 T
1 T
53722143 ATATAATCTA
Statistics
Matches: 116, Mismatches: 3, Indels: 3
0.95 0.02 0.02
Matches are distributed among these distances:
119 5 0.04
120 80 0.69
121 31 0.27
ACGTcount: A:0.53, C:0.05, G:0.01, T:0.42
Consensus pattern (119 bp):
TTTAAAATAATAATTATTAAATATAATTTAATAAAAAATATATAATTTAATAAAATTCTTAATAT
AAATATTCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAAATAA
Found at i:53722086 original size:24 final size:23
Alignment explanation
Indices: 53722017--53722088 Score: 64
Period size: 19 Copynumber: 3.1 Consensus size: 23
53722007 ATACTATAAA
53722017 ATATAATTTAAAATAATAATTATTAA-
1 ATATAATTT--AATAA-AATT-TTAAT
53722043 ATATAATTTAATAAAA----AAT
1 ATATAATTTAATAAAATTTTAAT
53722062 ATATAATTTAATAAAATTCTTAAT
1 ATATAATTTAATAAAATT-TTAAT
53722086 ATA
1 ATA
53722089 ATTATTCTTA
Statistics
Matches: 40, Mismatches: 0, Indels: 14
0.74 0.00 0.26
Matches are distributed among these distances:
18 2 0.05
19 16 0.40
23 2 0.05
24 11 0.28
26 9 0.22
ACGTcount: A:0.57, C:0.01, G:0.00, T:0.42
Consensus pattern (23 bp):
ATATAATTTAATAAAATTTTAAT
Found at i:53727203 original size:63 final size:62
Alignment explanation
Indices: 53727076--53727203 Score: 159
Period size: 63 Copynumber: 2.0 Consensus size: 62
53727066 ACAAGCATTC
* * * * *
53727076 TGATCGGTAGTGATCTTGCATGTGTTGCGGACTATCGCAGCTCTTTGTGAGTGTCCTGTTATA
1 TGATCGGTAGTGATCCTGCATATATTGCGGACTAACGCAACTCTTTGTGAGTGTCCTG-TATA
* *
53727139 TGATCGGTTGTGATCCTGCATATATTGCGGACATAAACGCAACTTTTTGTGAGTGTCCTG-ATA
1 TGATCGGTAGTGATCCTGCATATATTGCGGAC-T-AACGCAACTCTTTGTGAGTGTCCTGTATA
53727202 TG
1 TG
53727204 GCTCGCTTGA
Statistics
Matches: 56, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
63 33 0.59
64 1 0.02
65 22 0.39
ACGTcount: A:0.20, C:0.17, G:0.27, T:0.37
Consensus pattern (62 bp):
TGATCGGTAGTGATCCTGCATATATTGCGGACTAACGCAACTCTTTGTGAGTGTCCTGTATA
Found at i:53727271 original size:26 final size:26
Alignment explanation
Indices: 53727237--53727301 Score: 87
Period size: 26 Copynumber: 2.5 Consensus size: 26
53727227 TGGCTATTTG
*
53727237 GAGC-TCCTGATTAAAGGCTCTTCGT
1 GAGCTTCCTGATTAAAAGCTCTTCGT
* *
53727262 GAGCTTCCTGATTAAAAGTTCTTTGT
1 GAGCTTCCTGATTAAAAGCTCTTCGT
*
53727288 GAACTTCCTGATTA
1 GAGCTTCCTGATTA
53727302 TGGCTCCTAT
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
25 4 0.11
26 31 0.89
ACGTcount: A:0.23, C:0.20, G:0.20, T:0.37
Consensus pattern (26 bp):
GAGCTTCCTGATTAAAAGCTCTTCGT
Found at i:53729023 original size:26 final size:26
Alignment explanation
Indices: 53728994--53729172 Score: 101
Period size: 26 Copynumber: 7.2 Consensus size: 26
53728984 TCCTCTCTCA
53728994 AGCCATATAACAGGAAGCTCACAAAG
1 AGCCATATAACAGGAAGCTCACAAAG
*
53729020 AGCCAT-TAATCGGGAAGCTCACAAAG
1 AGCCATATAA-CAGGAAGCTCACAAAG
* ***
53729046 AGCC-TAT--CAGGAAGCTTA-TTCG
1 AGCCATATAACAGGAAGCTCACAAAG
* * * *
53729068 GGCTATATAACAGGAAGCTCA-TAAT
1 AGCCATATAACAGGAAGCTCACAAAG
* *
53729093 AGCCATA-ATCAGGAAGTTCACAAAG
1 AGCCATATAACAGGAAGCTCACAAAG
* * * *
53729118 A-ACTTTTAATCAGGAAGCTCACGAAG
1 AGCCATATAA-CAGGAAGCTCACAAAG
* *
53729144 AGCC-TTTAATCAGG-AGCTC-CAAAT
1 AGCCATATAA-CAGGAAGCTCACAAAG
53729168 AGCCA
1 AGCCA
53729173 CATATTGGGA
Statistics
Matches: 116, Mismatches: 27, Indels: 21
0.71 0.16 0.13
Matches are distributed among these distances:
22 3 0.03
23 12 0.10
24 20 0.17
25 29 0.25
26 51 0.44
27 1 0.01
ACGTcount: A:0.39, C:0.22, G:0.20, T:0.20
Consensus pattern (26 bp):
AGCCATATAACAGGAAGCTCACAAAG
Found at i:53729698 original size:45 final size:45
Alignment explanation
Indices: 53729630--53729718 Score: 142
Period size: 45 Copynumber: 2.0 Consensus size: 45
53729620 CTACTAATCC
* **
53729630 GACATTTTCTCTTTTCCTCGTTCTAACTCTGAATTTGGTCTATCT
1 GACATTTTCTCTTTTCCTAGTTCTAACTCCAAATTTGGTCTATCT
*
53729675 GACATTTTCTTTTTTCCTAGTTCTAACTCCAAATTTGGTCTATC
1 GACATTTTCTCTTTTCCTAGTTCTAACTCCAAATTTGGTCTATC
53729719 CGAGTCTATA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
45 40 1.00
ACGTcount: A:0.18, C:0.24, G:0.10, T:0.48
Consensus pattern (45 bp):
GACATTTTCTCTTTTCCTAGTTCTAACTCCAAATTTGGTCTATCT
Found at i:53739386 original size:15 final size:16
Alignment explanation
Indices: 53739361--53739390 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
53739351 ACATAACCTT
53739361 TTGCGATTAACCTTTC
1 TTGCGATTAACCTTTC
53739377 TTGC-ATTAACCTTT
1 TTGCGATTAACCTTT
53739391 AAGTCATTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.20, C:0.23, G:0.10, T:0.47
Consensus pattern (16 bp):
TTGCGATTAACCTTTC
Found at i:53750253 original size:27 final size:27
Alignment explanation
Indices: 53750223--53750278 Score: 103
Period size: 27 Copynumber: 2.1 Consensus size: 27
53750213 TGAGATGTAG
*
53750223 TTGTTAAGAAGTATAACTAAGCATGCT
1 TTGTTAAGAAGTATAACTAAACATGCT
53750250 TTGTTAAGAAGTATAACTAAACATGCT
1 TTGTTAAGAAGTATAACTAAACATGCT
53750277 TT
1 TT
53750279 CATGTGCCCT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.38, C:0.11, G:0.16, T:0.36
Consensus pattern (27 bp):
TTGTTAAGAAGTATAACTAAACATGCT
Found at i:53754378 original size:3 final size:3
Alignment explanation
Indices: 53754370--53754401 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
53754360 CAAGCTAGTT
53754370 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
53754402 GATAGTTTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:53754930 original size:13 final size:13
Alignment explanation
Indices: 53754912--53754939 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
53754902 AATTTAGAAG
53754912 ATTACATAATCAA
1 ATTACATAATCAA
53754925 ATTACATAATCAA
1 ATTACATAATCAA
53754938 AT
1 AT
53754940 CAAATCCAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.54, C:0.14, G:0.00, T:0.32
Consensus pattern (13 bp):
ATTACATAATCAA
Found at i:53755265 original size:59 final size:55
Alignment explanation
Indices: 53755190--53755298 Score: 130
Period size: 59 Copynumber: 1.9 Consensus size: 55
53755180 GCCCGTGACA
*
53755190 ATTACATAATATAGATTTTAGTTATTCAA-ATGGATATGTTGTTATATATATATATATAT
1 ATTACATAATATAGATTTTAG-TA-TCAATA-AGA-ATGTTGTTATATAT-TATATATAT
* * *
53755249 ATTATATATTATAGATTTTCGTATCAATAAGAATGTTGTTATATATTATA
1 ATTACATAATATAGATTTTAGTATCAATAAGAATGTTGTTATATATTATA
53755299 GTTTTTGATA
Statistics
Matches: 45, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
55 4 0.09
56 14 0.31
57 6 0.13
58 3 0.07
59 18 0.40
ACGTcount: A:0.39, C:0.04, G:0.10, T:0.48
Consensus pattern (55 bp):
ATTACATAATATAGATTTTAGTATCAATAAGAATGTTGTTATATATTATATATAT
Found at i:53755386 original size:18 final size:19
Alignment explanation
Indices: 53755363--53755399 Score: 58
Period size: 18 Copynumber: 1.9 Consensus size: 19
53755353 ATTTGATTAA
53755363 AAATACTTT-TAATTTTTG
1 AAATACTTTCTAATTTTTG
53755381 AAATACTTTGCTAATTTTT
1 AAATACTTT-CTAATTTTT
53755400 ATTTTTCATT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 9 0.53
20 8 0.47
ACGTcount: A:0.32, C:0.08, G:0.05, T:0.54
Consensus pattern (19 bp):
AAATACTTTCTAATTTTTG
Found at i:53755714 original size:26 final size:27
Alignment explanation
Indices: 53755685--53755741 Score: 98
Period size: 26 Copynumber: 2.1 Consensus size: 27
53755675 TTTTAACGGG
53755685 TATCAAAATCTATAATATATAACAAC-
1 TATCAAAATCTATAATATATAACAACA
*
53755711 TATCAAAATCTATAATATATAATAACA
1 TATCAAAATCTATAATATATAACAACA
53755738 TATC
1 TATC
53755742 TATTTATATA
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
26 25 0.86
27 4 0.14
ACGTcount: A:0.53, C:0.14, G:0.00, T:0.33
Consensus pattern (27 bp):
TATCAAAATCTATAATATATAACAACA
Found at i:53755818 original size:12 final size:11
Alignment explanation
Indices: 53755785--53755853 Score: 67
Period size: 11 Copynumber: 6.6 Consensus size: 11
53755775 ATTTTTATAT
53755785 TTTTTAAATAA
1 TTTTTAAATAA
*
53755796 ATTTT-AA-AA
1 TTTTTAAATAA
53755805 TTTTCTAAATAA
1 TTTT-TAAATAA
* *
53755817 TTTTTTACTAA
1 TTTTTAAATAA
53755828 TTTTT--ATAA
1 TTTTTAAATAA
53755837 -TTTTAAATAA
1 TTTTTAAATAA
53755847 TTTTTAA
1 TTTTTAA
53755854 TGATTTTTTA
Statistics
Matches: 47, Mismatches: 5, Indels: 12
0.73 0.08 0.19
Matches are distributed among these distances:
8 4 0.09
9 8 0.17
10 7 0.15
11 22 0.47
12 6 0.13
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.57
Consensus pattern (11 bp):
TTTTTAAATAA
Found at i:53755833 original size:32 final size:31
Alignment explanation
Indices: 53755783--53755851 Score: 86
Period size: 30 Copynumber: 2.2 Consensus size: 31
53755773 ATATTTTTAT
53755783 ATTTTTTAAATAAATTTTAAAATTTTCTAAATA
1 ATTTTTTAAATAAATTTTAAAA-TTT-TAAATA
* * *
53755816 ATTTTTT-ACTAATTTTTATAATTTTAAATA
1 ATTTTTTAAATAAATTTTAAAATTTTAAATA
53755846 ATTTTT
1 ATTTTT
53755852 AATGATTTTT
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
30 12 0.36
31 3 0.09
32 11 0.33
33 7 0.21
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (31 bp):
ATTTTTTAAATAAATTTTAAAATTTTAAATA
Found at i:53755859 original size:10 final size:10
Alignment explanation
Indices: 53755775--53755861 Score: 72
Period size: 10 Copynumber: 8.6 Consensus size: 10
53755765 TTCTTTGTAT
53755775 ATTTTT-ATA
1 ATTTTTAATA
*
53755784 TTTTTTAAATA
1 ATTTTT-AATA
*
53755795 AATTTTAA-A
1 ATTTTTAATA
53755804 ATTTTCTAAATA
1 ATTTT-T-AATA
*
53755816 ATTTTTTACTA
1 A-TTTTTAATA
53755827 ATTTTT-ATA
1 ATTTTTAATA
*
53755836 ATTTTAAATA
1 ATTTTTAATA
*
53755846 ATTTTTAATG
1 ATTTTTAATA
53755856 ATTTTT
1 ATTTTT
53755862 TAACCGTGAA
Statistics
Matches: 62, Mismatches: 9, Indels: 13
0.74 0.11 0.15
Matches are distributed among these distances:
9 17 0.27
10 25 0.40
11 13 0.21
12 3 0.05
13 4 0.06
ACGTcount: A:0.37, C:0.02, G:0.01, T:0.60
Consensus pattern (10 bp):
ATTTTTAATA
Found at i:53759238 original size:20 final size:20
Alignment explanation
Indices: 53759204--53759245 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
53759194 AACTATTTAA
** *
53759204 ATAATATTATTTGAATAGTT
1 ATAATATTAAATGAATAATT
53759224 ATAATATTAAATGAATAATT
1 ATAATATTAAATGAATAATT
53759244 AT
1 AT
53759246 GTGTTTATTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.48, C:0.00, G:0.07, T:0.45
Consensus pattern (20 bp):
ATAATATTAAATGAATAATT
Found at i:53761420 original size:5 final size:5
Alignment explanation
Indices: 53761408--53761436 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
53761398 AAAAGTTAAG
53761408 TATA- TATAT TATAT TATAT TATAT TATAT
1 TATAT TATAT TATAT TATAT TATAT TATAT
53761437 AATAAAGAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
4 4 0.17
5 20 0.83
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (5 bp):
TATAT
Found at i:53762501 original size:22 final size:22
Alignment explanation
Indices: 53762453--53762514 Score: 63
Period size: 22 Copynumber: 2.8 Consensus size: 22
53762443 NNNNNNNNNN
* * *
53762453 AGCACGTCAGTGCTCTCCGTTT
1 AGCACATCAGTGCTCTCTGTAT
*
53762475 GGCACAT-ATGTGCTCTCTGTAT
1 AGCACATCA-GTGCTCTCTGTAT
*
53762497 AGCACTTCAGTGCTCTCT
1 AGCACATCAGTGCTCTCT
53762515 ATTCATTAGT
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
21 1 0.03
22 30 0.94
23 1 0.03
ACGTcount: A:0.16, C:0.29, G:0.21, T:0.34
Consensus pattern (22 bp):
AGCACATCAGTGCTCTCTGTAT
Found at i:53762642 original size:31 final size:31
Alignment explanation
Indices: 53762607--53762665 Score: 109
Period size: 31 Copynumber: 1.9 Consensus size: 31
53762597 AAGAATATGA
*
53762607 GATAGTGAATTGAAAATAGAATGTGAAAAAC
1 GATAGTGAATTGAAAATAGAATATGAAAAAC
53762638 GATAGTGAATTGAAAATAGAATATGAAA
1 GATAGTGAATTGAAAATAGAATATGAAA
53762666 TATGTTGTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.53, C:0.02, G:0.22, T:0.24
Consensus pattern (31 bp):
GATAGTGAATTGAAAATAGAATATGAAAAAC
Found at i:53766663 original size:20 final size:19
Alignment explanation
Indices: 53766621--53766675 Score: 58
Period size: 20 Copynumber: 2.8 Consensus size: 19
53766611 AAAAAAGTAA
**
53766621 TTTTATAATTTTTATGGGTT
1 TTTTATAATTTTTAT-GGAC
53766641 TTTTATAATTTTTGA-GGAC
1 TTTTATAATTTTT-ATGGAC
53766660 TTTTATATATTTTTAT
1 TTTTATA-ATTTTTAT
53766676 TTTTAAAATG
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
19 10 0.33
20 19 0.63
21 1 0.03
ACGTcount: A:0.24, C:0.02, G:0.11, T:0.64
Consensus pattern (19 bp):
TTTTATAATTTTTATGGAC
Found at i:53766787 original size:26 final size:27
Alignment explanation
Indices: 53766758--53766814 Score: 89
Period size: 26 Copynumber: 2.1 Consensus size: 27
53766748 TTTTAACGGG
*
53766758 TATCAAAATTTATAATATATAACAAC-
1 TATCAAAATCTATAATATATAACAACA
*
53766784 TATCAAAATCTATAATATATAATAACA
1 TATCAAAATCTATAATATATAACAACA
53766811 TATC
1 TATC
53766815 TATTTATATA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
26 24 0.86
27 4 0.14
ACGTcount: A:0.53, C:0.12, G:0.00, T:0.35
Consensus pattern (27 bp):
TATCAAAATCTATAATATATAACAACA
Found at i:53766889 original size:11 final size:10
Alignment explanation
Indices: 53766858--53766948 Score: 57
Period size: 10 Copynumber: 9.4 Consensus size: 10
53766848 GTTTTTATAT
53766858 TTTTAAATAA
1 TTTTAAATAA
53766868 TTTTAAA-AA
1 TTTTAAATAA
53766877 TTTCTAAATAA
1 TTT-TAAATAA
* *
53766888 TTTTTTACTAA
1 -TTTTAAATAA
*
53766899 TTTT-TAT-A
1 TTTTAAATAA
*
53766907 TTTTTAAT--
1 TTTTAAATAA
**
53766915 TTTTTTATAA
1 TTTTAAATAA
53766925 TTTTAAATAA
1 TTTTAAATAA
* *
53766935 TTTTTAATGA
1 TTTTAAATAA
53766945 TTTT
1 TTTT
53766949 TTGACCGTGA
Statistics
Matches: 65, Mismatches: 10, Indels: 12
0.75 0.11 0.14
Matches are distributed among these distances:
8 12 0.18
9 8 0.12
10 35 0.54
11 7 0.11
12 3 0.05
ACGTcount: A:0.36, C:0.02, G:0.01, T:0.60
Consensus pattern (10 bp):
TTTTAAATAA
Found at i:53766912 original size:18 final size:19
Alignment explanation
Indices: 53766849--53766949 Score: 66
Period size: 20 Copynumber: 5.3 Consensus size: 19
53766839 TCTTTGTATG
53766849 TTTTTAT-ATTTTTAAATAA
1 TTTTTATAATTTTT-AATAA
* * *
53766868 TTTTAAAAATTTCTAAATAA
1 TTTTTATAATTT-TTAATAA
53766888 TTTTTTACTAATTTTT-AT-A
1 -TTTTTA-TAATTTTTAATAA
* *
53766907 TTTTTA-ATTTTTTTATAA
1 TTTTTATAATTTTTAATAA
* *
53766925 TTTTAAATAATTTTTAATGA
1 TTTT-TATAATTTTTAATAA
53766945 TTTTT
1 TTTTT
53766950 TGACCGTGAA
Statistics
Matches: 62, Mismatches: 12, Indels: 16
0.69 0.13 0.18
Matches are distributed among these distances:
16 6 0.10
17 2 0.03
18 11 0.18
19 7 0.11
20 24 0.39
21 7 0.11
22 5 0.08
ACGTcount: A:0.35, C:0.02, G:0.01, T:0.62
Consensus pattern (19 bp):
TTTTTATAATTTTTAATAA
Found at i:53768020 original size:391 final size:386
Alignment explanation
Indices: 53767304--53768045 Score: 1376
Period size: 391 Copynumber: 1.9 Consensus size: 386
53767294 ATTTACATTT
53767304 TAGACACCGTGGTTAACAACTATTTCCAATGGACATCGGTCTGAGCACGGAAAAGGGGCATTTTG
1 TAGACACCGTGGTTAACAACTATTTCCAATGGACATCGGTCTGAGCACGGAAAAGGGGCATTTTG
*
53767369 ACAGATGCAATGGACGACTTTCCCTATACAAAGTCCGGGTTTTGTTTCTCCGTATGAAACACAAA
66 ACAGATGCAATAGACGACTTTCCCTATACAAAGTCCGGGTTTTGTTTCTCCGTATGAAACACAAA
*
53767434 CAATTCAAAAGACTTTTCATCTTTCTCCAACAACATAAAAACACATAAATTCTACTTTGAAATTA
131 CAATTCAAAAGACTTTTCATCTTTCTCCAACAACATAAAAACACATAAATTCTACTATGAAATTA
53767499 TCATAAACAAACTGTATGACTTTCACGTTGATTTTCTAGGCAAGAGATTGATTTTCCAATGGCTT
196 TCATAAACAAACTGTATGACTTTCACGTTGATTTTCTAGGCAAGAGATTGATTTTCCAATGGCTT
*
53767564 CTAATAAACCCATCTTCTTCTTCCTCCTCTTGCTGTTTCTCTCGTTGAAGCTGCAGAGCTCAAGC
261 CTAATAAACCCATCTTCTTCTTCCTCCTCTTCCTGTTTCTCTCGTTGAAGCTGCAGAGCTCAAGC
53767629 TCACAAACATGGGTCAAAGCTGGTTACTGGACATCTATCTCTTCCCTTCCTGTTTCTGATA
326 TCACAAACATGGGTCAAAGCTGGTTACTGGACATCTATCTCTTCCCTTCCTGTTTCTGATA
*
53767690 TAGACACCGTGGTTAACAACTATTTCCAATGGACATCGGTCTGGGCACGGAAAAGGGGCATTTTG
1 TAGACACCGTGGTTAACAACTATTTCCAATGGACATCGGTCTGAGCACGGAAAAGGGGCATTTTG
53767755 ACAGATGCAATAGACGACTTTCCCTATACAAAGTCCGGGTTTTGTTTCTCCGTATGAAACACAAA
66 ACAGATGCAATAGACGACTTTCCCTATACAAAGTCCGGGTTTTGTTTCTCCGTATGAAACACAAA
* *
53767820 CAATTCAAAATTAAAGACTTTTCATCTTTCTCCAACAACATAAAAACACGTATATTCTACTATGA
131 CAATTC---A--AAAGACTTTTCATCTTTCTCCAACAACATAAAAACACATAAATTCTACTATGA
*
53767885 AATTATCATAAACAAACTGTATGACTTTCCCGTTGATTTTCTAGGCAAGAGATTGATTTTCCAAT
191 AATTATCATAAACAAACTGTATGACTTTCACGTTGATTTTCTAGGCAAGAGATTGATTTTCCAAT
53767950 GGCTTCTAATAAACCCATCTTCTTCTTCCTCCTCTTCCTGTTTCTCTCGTTGAAGCTGCAGAGCT
256 GGCTTCTAATAAACCCATCTTCTTCTTCCTCCTCTTCCTGTTTCTCTCGTTGAAGCTGCAGAGCT
53768015 CAAGCTCACAAACATGGGTCAAAGCTGGTTA
321 CAAGCTCACAAACATGGGTCAAAGCTGGTTA
53768046 ATTACTGGAC
Statistics
Matches: 344, Mismatches: 7, Indels: 5
0.97 0.02 0.01
Matches are distributed among these distances:
386 134 0.39
389 1 0.00
391 209 0.61
ACGTcount: A:0.30, C:0.23, G:0.16, T:0.31
Consensus pattern (386 bp):
TAGACACCGTGGTTAACAACTATTTCCAATGGACATCGGTCTGAGCACGGAAAAGGGGCATTTTG
ACAGATGCAATAGACGACTTTCCCTATACAAAGTCCGGGTTTTGTTTCTCCGTATGAAACACAAA
CAATTCAAAAGACTTTTCATCTTTCTCCAACAACATAAAAACACATAAATTCTACTATGAAATTA
TCATAAACAAACTGTATGACTTTCACGTTGATTTTCTAGGCAAGAGATTGATTTTCCAATGGCTT
CTAATAAACCCATCTTCTTCTTCCTCCTCTTCCTGTTTCTCTCGTTGAAGCTGCAGAGCTCAAGC
TCACAAACATGGGTCAAAGCTGGTTACTGGACATCTATCTCTTCCCTTCCTGTTTCTGATA
Found at i:53768093 original size:30 final size:30
Alignment explanation
Indices: 53768059--53768158 Score: 139
Period size: 30 Copynumber: 3.2 Consensus size: 30
53768049 ACTGGACATC
53768059 TATATTCATACCATTCGAATATTCAATATA
1 TATATTCATACCATTCGAATATTCAATATA
*
53768089 TATATTCATACCATAGTTCGAACCTATTCACTAT-
1 TATATTCATACC--A-TTCGAA--TATTCAATATA
53768123 TATATTCATACCATTCGAATATTCAATATA
1 TATATTCATACCATTCGAATATTCAATATA
53768153 TATATT
1 TATATT
53768159 TAAGCTTATA
Statistics
Matches: 62, Mismatches: 2, Indels: 12
0.82 0.03 0.16
Matches are distributed among these distances:
29 9 0.15
30 18 0.29
31 6 0.10
32 2 0.03
33 6 0.10
34 12 0.19
35 9 0.15
ACGTcount: A:0.37, C:0.18, G:0.04, T:0.41
Consensus pattern (30 bp):
TATATTCATACCATTCGAATATTCAATATA
Found at i:53768671 original size:22 final size:22
Alignment explanation
Indices: 53768642--53768930 Score: 371
Period size: 22 Copynumber: 13.1 Consensus size: 22
53768632 AGCAATTATC
* *
53768642 CAACATTTAGACAACATTTAAT
1 CAACAATTGGACAACATTTAAT
* *
53768664 TAACATTTGGACAACATTTAAT
1 CAACAATTGGACAACATTTAAT
* *
53768686 CAACAATTGGACAACAATCAAT
1 CAACAATTGGACAACATTTAAT
*
53768708 CAACAATTGGACAACATTAAAT
1 CAACAATTGGACAACATTTAAT
*
53768730 CAACATTTGGACAACATTTAAT
1 CAACAATTGGACAACATTTAAT
* * *
53768752 CAACAATTGGACAGCAATCAAT
1 CAACAATTGGACAACATTTAAT
* *
53768774 CAACATTTGGACAGCATTTAAT
1 CAACAATTGGACAACATTTAAT
* *
53768796 CAACAATTGGACAGCATTAAAT
1 CAACAATTGGACAACATTTAAT
*
53768818 CAACATTTGGACAACATTTAAT
1 CAACAATTGGACAACATTTAAT
* *
53768840 CAACAATTGGACAGCATTCAAT
1 CAACAATTGGACAACATTTAAT
* *
53768862 CAATATTTGGACAACATTTAAT
1 CAACAATTGGACAACATTTAAT
*
53768884 CAACAATTGGACAGCATTTAAT
1 CAACAATTGGACAACATTTAAT
* *
53768906 CAACAATTGGACAGCATTCAAT
1 CAACAATTGGACAACATTTAAT
53768928 CAA
1 CAA
53768931 GCCAAATTAT
Statistics
Matches: 234, Mismatches: 33, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 234 1.00
ACGTcount: A:0.43, C:0.19, G:0.11, T:0.27
Consensus pattern (22 bp):
CAACAATTGGACAACATTTAAT
Found at i:53768699 original size:44 final size:44
Alignment explanation
Indices: 53768642--53768930 Score: 416
Period size: 44 Copynumber: 6.6 Consensus size: 44
53768632 AGCAATTATC
* * * * *
53768642 CAACATTTAGACAACATTTAATTAACATTTGGACAACATTTAAT
1 CAACATTTGGACAACATTTAATCAACAATTGGACAGCATTAAAT
* * * *
53768686 CAACAATTGGACAACAATCAATCAACAATTGGACAACATTAAAT
1 CAACATTTGGACAACATTTAATCAACAATTGGACAGCATTAAAT
* *
53768730 CAACATTTGGACAACATTTAATCAACAATTGGACAGCAATCAAT
1 CAACATTTGGACAACATTTAATCAACAATTGGACAGCATTAAAT
*
53768774 CAACATTTGGACAGCATTTAATCAACAATTGGACAGCATTAAAT
1 CAACATTTGGACAACATTTAATCAACAATTGGACAGCATTAAAT
*
53768818 CAACATTTGGACAACATTTAATCAACAATTGGACAGCATTCAAT
1 CAACATTTGGACAACATTTAATCAACAATTGGACAGCATTAAAT
* *
53768862 CAATATTTGGACAACATTTAATCAACAATTGGACAGCATTTAAT
1 CAACATTTGGACAACATTTAATCAACAATTGGACAGCATTAAAT
* * *
53768906 CAACAATTGGACAGCATTCAATCAA
1 CAACATTTGGACAACATTTAATCAA
53768931 GCCAAATTAT
Statistics
Matches: 221, Mismatches: 24, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
44 221 1.00
ACGTcount: A:0.43, C:0.19, G:0.11, T:0.27
Consensus pattern (44 bp):
CAACATTTGGACAACATTTAATCAACAATTGGACAGCATTAAAT
Found at i:53769605 original size:9 final size:9
Alignment explanation
Indices: 53769591--53769654 Score: 94
Period size: 9 Copynumber: 7.2 Consensus size: 9
53769581 TTTGGTTAAA
53769591 AATTAACCG
1 AATTAACCG
*
53769600 AATTAATCG
1 AATTAACCG
*
53769609 AATTACCCG
1 AATTAACCG
53769618 AATTAACCG
1 AATTAACCG
53769627 AATT-ACCG
1 AATTAACCG
*
53769635 AATTACCCG
1 AATTAACCG
53769644 AATTAACCG
1 AATTAACCG
53769653 AA
1 AA
53769655 ATGAATCACT
Statistics
Matches: 48, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
8 8 0.17
9 40 0.83
ACGTcount: A:0.42, C:0.23, G:0.11, T:0.23
Consensus pattern (9 bp):
AATTAACCG
Found at i:53769643 original size:26 final size:27
Alignment explanation
Indices: 53769591--53769654 Score: 112
Period size: 26 Copynumber: 2.4 Consensus size: 27
53769581 TTTGGTTAAA
*
53769591 AATTAACCGAATTAATCGAATTACCCG
1 AATTAACCGAATTAACCGAATTACCCG
53769618 AATTAACCGAATT-ACCGAATTACCCG
1 AATTAACCGAATTAACCGAATTACCCG
53769644 AATTAACCGAA
1 AATTAACCGAA
53769655 ATGAATCACT
Statistics
Matches: 36, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
26 23 0.64
27 13 0.36
ACGTcount: A:0.42, C:0.23, G:0.11, T:0.23
Consensus pattern (27 bp):
AATTAACCGAATTAACCGAATTACCCG
Found at i:53769716 original size:20 final size:20
Alignment explanation
Indices: 53769693--53769736 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
53769683 TAGACTTTAG
53769693 TTTTAGTTTTAGTT-TTAGAA
1 TTTTAGTTTTAGTTATTA-AA
* *
53769713 TTTTATTTTTATTTATTAAA
1 TTTTAGTTTTAGTTATTAAA
53769733 TTTT
1 TTTT
53769737 TTGTAATTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 18 0.86
21 3 0.14
ACGTcount: A:0.25, C:0.00, G:0.07, T:0.68
Consensus pattern (20 bp):
TTTTAGTTTTAGTTATTAAA
Found at i:53772006 original size:50 final size:50
Alignment explanation
Indices: 53771892--53772034 Score: 214
Period size: 50 Copynumber: 2.8 Consensus size: 50
53771882 GATAATAACA
* * ** *
53771892 TGCCAAAGCAATGTCCCAGACATGGTCTTACATGGGATGTACTCATGTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCT-CTCATCTCGG
* *
53771943 TGCCCATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
53771993 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
53772035 TTACCCAAAT
Statistics
Matches: 83, Mismatches: 9, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
50 49 0.59
51 34 0.41
ACGTcount: A:0.22, C:0.29, G:0.24, T:0.25
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
Found at i:53779302 original size:20 final size:20
Alignment explanation
Indices: 53779273--53779312 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
53779263 ATATTTTCCA
*
53779273 GTAAATCATTTTACAGAAAT
1 GTAAAACATTTTACAGAAAT
*
53779293 GTAAAACATTTTCCAGAAAT
1 GTAAAACATTTTACAGAAAT
53779313 CATTTTACGA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.45, C:0.12, G:0.10, T:0.33
Consensus pattern (20 bp):
GTAAAACATTTTACAGAAAT
Found at i:53779317 original size:34 final size:34
Alignment explanation
Indices: 53779260--53779324 Score: 105
Period size: 35 Copynumber: 1.9 Consensus size: 34
53779250 CAAACACCAC
*
53779260 AAAATATTTTCCAGTAAATCATTTTACAGAAATGT
1 AAAACATTTTCCAGTAAATCATTTTAC-GAAATGT
53779295 AAAACATTTTCCAG-AAATCATTTTACGAAA
1 AAAACATTTTCCAGTAAATCATTTTACGAAA
53779325 AACATTTTAC
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
33 4 0.14
34 12 0.41
35 13 0.45
ACGTcount: A:0.45, C:0.14, G:0.08, T:0.34
Consensus pattern (34 bp):
AAAACATTTTCCAGTAAATCATTTTACGAAATGT
Found at i:53783097 original size:22 final size:22
Alignment explanation
Indices: 53783069--53783111 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
53783059 TTTATTGTTC
53783069 AAACATGAGAGCTTAGTACGTG
1 AAACATGAGAGCTTAGTACGTG
53783091 AAACATGAGAGCTTAGTACGT
1 AAACATGAGAGCTTAGTACGT
53783112 TAGCCAATGC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.37, C:0.14, G:0.26, T:0.23
Consensus pattern (22 bp):
AAACATGAGAGCTTAGTACGTG
Found at i:53784831 original size:2 final size:2
Alignment explanation
Indices: 53784824--53784850 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
53784814 ATATCCTTAA
53784824 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
53784851 AAGACTATGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:53788343 original size:22 final size:22
Alignment explanation
Indices: 53788281--53788352 Score: 117
Period size: 22 Copynumber: 3.3 Consensus size: 22
53788271 ATTGTTCAAA
* **
53788281 CATGAGAGCTTAGTACGTGAAA
1 CATGAGAGCTTAGTACGTTAGC
53788303 CATGAGAGCTTAGTACGTTAGC
1 CATGAGAGCTTAGTACGTTAGC
53788325 CATGAGAGCTTAGTACGTTAGC
1 CATGAGAGCTTAGTACGTTAGC
53788347 CATGAG
1 CATGAG
53788353 GGTACACAGT
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 47 1.00
ACGTcount: A:0.31, C:0.17, G:0.28, T:0.25
Consensus pattern (22 bp):
CATGAGAGCTTAGTACGTTAGC
Found at i:53789351 original size:21 final size:20
Alignment explanation
Indices: 53789309--53789349 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 20
53789299 GGCTTACTCA
53789309 TATTATTTTATTTTTAAAAAT
1 TATTATTTTATTTTT-AAAAT
53789330 TATTATTTATATATTTTAAA
1 TATTATTT-TAT-TTTTAAA
53789350 TTTAATAGTA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 8 0.44
22 6 0.33
23 4 0.22
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (20 bp):
TATTATTTTATTTTTAAAAT
Found at i:53792019 original size:40 final size:39
Alignment explanation
Indices: 53791964--53792045 Score: 146
Period size: 40 Copynumber: 2.1 Consensus size: 39
53791954 AAAAGAGTCG
53791964 GAGTAGCATAGTAGTTAAATAGTTTGTATGGTTGGAGAAT
1 GAGTAGCATAGTAGTTAAATAGTTTGTATGGTTGGAG-AT
*
53792004 GAGTAGTATAGTAGTTAAATAGTTTGTATGGTTGGAGAT
1 GAGTAGCATAGTAGTTAAATAGTTTGTATGGTTGGAGAT
53792043 GAG
1 GAG
53792046 GCAGATATCT
Statistics
Matches: 41, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
39 5 0.12
40 36 0.88
ACGTcount: A:0.32, C:0.01, G:0.32, T:0.35
Consensus pattern (39 bp):
GAGTAGCATAGTAGTTAAATAGTTTGTATGGTTGGAGAT
Found at i:53792434 original size:25 final size:25
Alignment explanation
Indices: 53792385--53792434 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
53792375 TTTATTTTGA
**
53792385 AAAAAAAAACAAAAATTAGTTGTCG
1 AAAAAAAAACAAAAATTAGGAGTCG
*
53792410 AAAAAAAAACAAAAATTGGGAGTCG
1 AAAAAAAAACAAAAATTAGGAGTCG
53792435 CCACCAACCT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.60, C:0.08, G:0.16, T:0.16
Consensus pattern (25 bp):
AAAAAAAAACAAAAATTAGGAGTCG
Found at i:53794120 original size:21 final size:21
Alignment explanation
Indices: 53794083--53794137 Score: 78
Period size: 21 Copynumber: 2.7 Consensus size: 21
53794073 AATCATATCT
53794083 TCCAAGATTGC--ATATCATA
1 TCCAAGATTGCATATATCATA
53794102 TCCAAGATTGCATATATCATA
1 TCCAAGATTGCATATATCATA
* *
53794123 GCTAAGATTGCATAT
1 TCCAAGATTGCATAT
53794138 CCTTGAAGAT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
19 11 0.34
21 21 0.66
ACGTcount: A:0.36, C:0.18, G:0.13, T:0.33
Consensus pattern (21 bp):
TCCAAGATTGCATATATCATA
Found at i:53794587 original size:20 final size:19
Alignment explanation
Indices: 53794548--53794601 Score: 56
Period size: 20 Copynumber: 2.7 Consensus size: 19
53794538 ATTAAATTTG
**
53794548 TTTAAATAAAAATATTAAA
1 TTTAAATAAAAATAAAAAA
53794567 TTTAAATTAAAAATAAAAAA
1 TTTAAA-TAAAAATAAAAAA
53794587 -TTATAATAATAAATA
1 TTTA-AATAA-AAATA
53794602 GTTAAATATT
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
19 12 0.40
20 18 0.60
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (19 bp):
TTTAAATAAAAATAAAAAA
Found at i:53794900 original size:19 final size:19
Alignment explanation
Indices: 53794874--53794915 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 19
53794864 TAAAAGAATT
* *
53794874 AATTTTTAAT-ATCTTTAC
1 AATTTTTTATAATATTTAC
53794892 AATTTTTTATAATATTTAC
1 AATTTTTTATAATATTTAC
53794911 AATTT
1 AATTT
53794916 CTTTTTACAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 9 0.43
19 12 0.57
ACGTcount: A:0.36, C:0.07, G:0.00, T:0.57
Consensus pattern (19 bp):
AATTTTTTATAATATTTAC
Found at i:53794927 original size:19 final size:19
Alignment explanation
Indices: 53794874--53794915 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 19
53794864 TAAAAGAATT
* *
53794874 AATTTTTAATATC-TTTAC
1 AATTTTTTATAACATTTAC
*
53794892 AATTTTTTATAATATTTAC
1 AATTTTTTATAACATTTAC
53794911 AATTT
1 AATTT
53794916 CTTTTTACAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
18 10 0.50
19 10 0.50
ACGTcount: A:0.36, C:0.07, G:0.00, T:0.57
Consensus pattern (19 bp):
AATTTTTTATAACATTTAC
Found at i:53795243 original size:19 final size:20
Alignment explanation
Indices: 53795208--53795253 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 20
53795198 CTTTAGATAT
53795208 TAAAT-TAAAACAAAAAAAA
1 TAAATATAAAACAAAAAAAA
*
53795227 TAAATATAAAA-ATAAAAAA
1 TAAATATAAAACAAAAAAAA
*
53795246 TAAGTATA
1 TAAATATA
53795254 CTTTAAAAGC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 19 0.79
20 5 0.21
ACGTcount: A:0.74, C:0.02, G:0.02, T:0.22
Consensus pattern (20 bp):
TAAATATAAAACAAAAAAAA
Found at i:53796165 original size:23 final size:24
Alignment explanation
Indices: 53796132--53796177 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 24
53796122 TTCAATATTT
*
53796132 AATTTGGTACTTGAGTTT-TTTTC
1 AATTTGATACTTGAGTTTGTTTTC
53796155 AATTTGATACTTGAGTTTGTTTT
1 AATTTGATACTTGAGTTTGTTTT
53796178 AACCCAAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
23 17 0.81
24 4 0.19
ACGTcount: A:0.20, C:0.07, G:0.17, T:0.57
Consensus pattern (24 bp):
AATTTGATACTTGAGTTTGTTTTC
Found at i:53803052 original size:12 final size:12
Alignment explanation
Indices: 53803032--53803081 Score: 57
Period size: 12 Copynumber: 4.1 Consensus size: 12
53803022 AATTGATGAT
53803032 ACATATATATAA
1 ACATATATATAA
*
53803044 ACATGTATAT-A
1 ACATATATATAA
*
53803055 ACATACATATATAT
1 ACAT--ATATATAA
53803069 ACATATATATAA
1 ACATATATATAA
53803081 A
1 A
53803082 TAAATCAATT
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
11 5 0.16
12 17 0.55
13 5 0.16
14 4 0.13
ACGTcount: A:0.54, C:0.10, G:0.02, T:0.34
Consensus pattern (12 bp):
ACATATATATAA
Found at i:53803236 original size:28 final size:28
Alignment explanation
Indices: 53803205--53803261 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
53803195 AAAATGTTAA
53803205 ACCGAGAAATGCCCTTAAACAGGCAAAT
1 ACCGAGAAATGCCCTTAAACAGGCAAAT
53803233 ACCGAGAAATGCCCTTAAACAGGCAAAT
1 ACCGAGAAATGCCCTTAAACAGGCAAAT
53803261 A
1 A
53803262 TAGTAAAAAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.44, C:0.25, G:0.18, T:0.14
Consensus pattern (28 bp):
ACCGAGAAATGCCCTTAAACAGGCAAAT
Found at i:53812025 original size:24 final size:24
Alignment explanation
Indices: 53811998--53812046 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
53811988 GAACTGCTCT
53811998 TGAATTTATGGACAAGACTATGTA
1 TGAATTTATGGACAAGACTATGTA
*
53812022 TGAATTTTTGGACAAGACTATGTA
1 TGAATTTATGGACAAGACTATGTA
53812046 T
1 T
53812047 CGTGCTTTGA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.35, C:0.08, G:0.20, T:0.37
Consensus pattern (24 bp):
TGAATTTATGGACAAGACTATGTA
Found at i:53816342 original size:3 final size:3
Alignment explanation
Indices: 53816334--53816362 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
53816324 ATTTTGAAAA
53816334 AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
53816363 AGGGCATCCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:53826648 original size:15 final size:15
Alignment explanation
Indices: 53826628--53826679 Score: 50
Period size: 15 Copynumber: 3.2 Consensus size: 15
53826618 ACTACAAAAC
53826628 ATTTATTATTAATAT
1 ATTTATTATTAATAT
*
53826643 ATTTATAATTGTAATAAAT
1 ATTTATTA-T-TAAT--AT
*
53826662 ATTTATTATTAAAAT
1 ATTTATTATTAATAT
53826677 ATT
1 ATT
53826680 AATATTGAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 8
0.73 0.07 0.20
Matches are distributed among these distances:
15 12 0.40
16 1 0.03
17 7 0.23
18 1 0.03
19 9 0.30
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (15 bp):
ATTTATTATTAATAT
Found at i:53826671 original size:34 final size:32
Alignment explanation
Indices: 53826628--53826691 Score: 92
Period size: 34 Copynumber: 1.9 Consensus size: 32
53826618 ACTACAAAAC
* *
53826628 ATTTATTATTAATATATTTATAATTGTAATAAAT
1 ATTTATTATTAAAATATTAAT-ATTG-AATAAAT
53826662 ATTTATTATTAAAATATTAATATTGAATAA
1 ATTTATTATTAAAATATTAATATTGAATAA
53826692 TTTCAATAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
32 5 0.18
33 4 0.14
34 19 0.68
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (32 bp):
ATTTATTATTAAAATATTAATATTGAATAAAT
Found at i:53828922 original size:17 final size:16
Alignment explanation
Indices: 53828900--53828935 Score: 54
Period size: 17 Copynumber: 2.2 Consensus size: 16
53828890 TGTTACATGA
53828900 TTTTAATATAAATATAT
1 TTTTAATATAAATAT-T
*
53828917 TTTTAATATAGATATT
1 TTTTAATATAAATATT
53828933 TTT
1 TTT
53828936 CATCCACATC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 4 0.22
17 14 0.78
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (16 bp):
TTTTAATATAAATATT
Found at i:53830110 original size:20 final size:20
Alignment explanation
Indices: 53830085--53830124 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
53830075 CGTAAAATAA
*
53830085 TTTCTGGAAAATGTTTTACT
1 TTTCTGGAAAATGATTTACT
*
53830105 TTTCTGTAAAATGATTTACT
1 TTTCTGGAAAATGATTTACT
53830125 GGAAAATATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.28, C:0.10, G:0.12, T:0.50
Consensus pattern (20 bp):
TTTCTGGAAAATGATTTACT
Found at i:53830114 original size:34 final size:35
Alignment explanation
Indices: 53830070--53830136 Score: 100
Period size: 34 Copynumber: 1.9 Consensus size: 35
53830060 TAGTAAAATG
*
53830070 TTTTCCGTAAAATAATTT-CTGGAAAATGTTTTAC
1 TTTTCCGTAAAATAATTTACTGGAAAATATTTTAC
* *
53830104 TTTTCTGTAAAATGATTTACTGGAAAATATTTT
1 TTTTCCGTAAAATAATTTACTGGAAAATATTTT
53830137 CTGGTGTTTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 16 0.55
35 13 0.45
ACGTcount: A:0.33, C:0.09, G:0.12, T:0.46
Consensus pattern (35 bp):
TTTTCCGTAAAATAATTTACTGGAAAATATTTTAC
Found at i:53832413 original size:28 final size:27
Alignment explanation
Indices: 53832360--53832413 Score: 63
Period size: 28 Copynumber: 2.0 Consensus size: 27
53832350 TTCTTAGTAA
* * *
53832360 TGAAGAAGCTGAAGATGGGAACGGAGT
1 TGAAGAAGCTGAAGAAGAGAAAGGAGT
*
53832387 TGAAGAAGGTTGAAGAAGAGAAAGGAG
1 TGAAGAA-GCTGAAGAAGAGAAAGGAG
53832414 AAAGGGAAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
27 7 0.32
28 15 0.68
ACGTcount: A:0.43, C:0.04, G:0.41, T:0.13
Consensus pattern (27 bp):
TGAAGAAGCTGAAGAAGAGAAAGGAGT
Found at i:53832683 original size:7 final size:7
Alignment explanation
Indices: 53832671--53832714 Score: 52
Period size: 7 Copynumber: 6.3 Consensus size: 7
53832661 AAAATATCAT
53832671 ATTTATA
1 ATTTATA
*
53832678 ATTTATC
1 ATTTATA
*
53832685 ATTTATC
1 ATTTATA
53832692 ATTTATA
1 ATTTATA
*
53832699 ATCTATA
1 ATTTATA
*
53832706 ATTTGTA
1 ATTTATA
53832713 AT
1 AT
53832715 ATGTATAAAA
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
7 32 1.00
ACGTcount: A:0.36, C:0.07, G:0.02, T:0.55
Consensus pattern (7 bp):
ATTTATA
Found at i:53833469 original size:2 final size:2
Alignment explanation
Indices: 53833462--53833494 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
53833452 ATTGGTCTTT
*
53833462 TA TA TA TA TA TA TA TA TA TA TA TA TA TT TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
53833495 TTGTATATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (2 bp):
TA
Found at i:53861643 original size:13 final size:13
Alignment explanation
Indices: 53861625--53861660 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
53861615 AAAGTTCAAT
53861625 AGAAACTGAAAAC
1 AGAAACTGAAAAC
*
53861638 AGAAACCGAAAAC
1 AGAAACTGAAAAC
*
53861651 AAAAACTGAA
1 AGAAACTGAA
53861661 GAAAAAGTAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.64, C:0.17, G:0.14, T:0.06
Consensus pattern (13 bp):
AGAAACTGAAAAC
Found at i:53862766 original size:31 final size:31
Alignment explanation
Indices: 53862722--53862785 Score: 85
Period size: 31 Copynumber: 2.1 Consensus size: 31
53862712 TTCTAACATA
* *
53862722 TTTAAAATTTTAAAATATATTTTTTATACTT
1 TTTAAAATTTTAAAATATAATTGTTATACTT
*
53862753 TTTATAAA-TTTAAAATTTAATTGTTATACTT
1 TTTA-AAATTTTAAAATATAATTGTTATACTT
53862784 TT
1 TT
53862786 ATTTTTAATA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
31 26 0.90
32 3 0.10
ACGTcount: A:0.38, C:0.03, G:0.02, T:0.58
Consensus pattern (31 bp):
TTTAAAATTTTAAAATATAATTGTTATACTT
Found at i:53868279 original size:19 final size:18
Alignment explanation
Indices: 53868255--53868298 Score: 61
Period size: 19 Copynumber: 2.4 Consensus size: 18
53868245 TATTATAGGA
53868255 TTAAATTTAAAATAAAATT
1 TTAAATTTAAAATAAAA-T
* *
53868274 TTAAATTTTAAATTAAAT
1 TTAAATTTAAAATAAAAT
53868292 TTAAATT
1 TTAAATT
53868299 GATAGTATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 8 0.35
19 15 0.65
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (18 bp):
TTAAATTTAAAATAAAAT
Found at i:53868865 original size:14 final size:14
Alignment explanation
Indices: 53868846--53868873 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
53868836 TACCGAGAGT
53868846 AAAAATGTGACTTC
1 AAAAATGTGACTTC
53868860 AAAAATGTGACTTC
1 AAAAATGTGACTTC
53868874 GAGCCAGTTA
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:0.43, C:0.14, G:0.14, T:0.29
Consensus pattern (14 bp):
AAAAATGTGACTTC
Found at i:53871787 original size:60 final size:59
Alignment explanation
Indices: 53871711--53871825 Score: 167
Period size: 60 Copynumber: 1.9 Consensus size: 59
53871701 TGAATAGTTA
* * * * *
53871711 GGTGATTATTTTGTAACTTTTTATAGTTTGATGATTAAAAAAGAAATTTACTAATAATTG
1 GGTGATCATTTTGTAACTTTTCATAGTTGGATGACT-AAAAAGAAATTCACTAATAATTG
*
53871771 GGTGATCATTTTGTAACTTTTCATAGTTGGGTGACTAAAAAGAAATTCACTAATA
1 GGTGATCATTTTGTAACTTTTCATAGTTGGATGACTAAAAAGAAATTCACTAATA
53871826 GTGGGGTTAC
Statistics
Matches: 49, Mismatches: 6, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
59 18 0.37
60 31 0.63
ACGTcount: A:0.36, C:0.07, G:0.17, T:0.41
Consensus pattern (59 bp):
GGTGATCATTTTGTAACTTTTCATAGTTGGATGACTAAAAAGAAATTCACTAATAATTG
Found at i:53873152 original size:23 final size:23
Alignment explanation
Indices: 53873126--53873174 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 23
53873116 CACATGACTA
* * *
53873126 TAATATCCCGAAAATTACTACTG
1 TAATACCCCAAAAATTACTACAG
53873149 TAATACCCCAAAAATTACTACAG
1 TAATACCCCAAAAATTACTACAG
53873172 TAA
1 TAA
53873175 GAAAGTAAGT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.45, C:0.22, G:0.06, T:0.27
Consensus pattern (23 bp):
TAATACCCCAAAAATTACTACAG
Found at i:53876511 original size:9 final size:9
Alignment explanation
Indices: 53876495--53876529 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
53876485 TTGATTGAGA
53876495 AATTAATTT
1 AATTAATTT
*
53876504 AGTTAATTT
1 AATTAATTT
*
53876513 AATTAATTA
1 AATTAATTT
53876522 AATTAATT
1 AATTAATT
53876530 GAATAAATTA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
9 23 1.00
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (9 bp):
AATTAATTT
Found at i:53876527 original size:18 final size:18
Alignment explanation
Indices: 53876495--53876539 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 18
53876485 TTGATTGAGA
* * *
53876495 AATTAATTTAGTTAATTT
1 AATTAATTAAATTAATTG
53876513 AATTAATTAAATTAATTG
1 AATTAATTAAATTAATTG
*
53876531 AATAAATTA
1 AATTAATTA
53876540 TATTTATTTT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.47
Consensus pattern (18 bp):
AATTAATTAAATTAATTG
Found at i:53882702 original size:183 final size:183
Alignment explanation
Indices: 53882388--53882937 Score: 893
Period size: 183 Copynumber: 3.0 Consensus size: 183
53882378 CTTTAATGGT
* * * * *
53882388 ACAAATGCCGGTAATGAGACGGTTCACGATGATGAGATCTTCGAAGGGAAAGACATAGATACTGA
1 ACAAA-GCCGGTAATGAGACAGCTCATGATGATGAGATCTTTGAAGGGAGAGACATAGATACTGA
* *
53882453 TGTTATAACAGAAGCAGATGTGGGGTTGAATAAATCTTCTACATTCGGTGAAGGTACCAAAGCTT
65 TGTTATAACAGAAGCAGATGTGGGCTTGAATAAATCTTCTACATTCGATGAAGGTACCAAAGCTT
*
53882518 GGAAGGAGTCTTCGACTGCTGAACCGGTAGAGTTAAATAAGAATTCAACAGCGG
130 GGAAGGAGTCTTCAACTGCTGAACCGGTAGAGTTAAATAAGAATTCAACAGCGG
* *
53882572 ACAAAGCCGGTAATGAGACAGCTCATGATGATGAGATCTTTGAAGGGAGAGACTTAGATGCTGAT
1 ACAAAGCCGGTAATGAGACAGCTCATGATGATGAGATCTTTGAAGGGAGAGACATAGATACTGAT
*
53882637 GTTATAACAGAAGCAGATGTGGGCTTGAATAAATCTTCTACATTCGATGAAGGTACTAAAGCTTG
66 GTTATAACAGAAGCAGATGTGGGCTTGAATAAATCTTCTACATTCGATGAAGGTACCAAAGCTTG
*
53882702 GAAGGAGTCTTCAACTGCTGAACCGGTAGAGTTAAATAAGAATTCAACAGTGG
131 GAAGGAGTCTTCAACTGCTGAACCGGTAGAGTTAAATAAGAATTCAACAGCGG
*
53882755 ACAACGCCGGTAATGAGACAGCTCATGATGATGAGATCTTTGAAGGGAGAGACATAGATACTGAT
1 ACAAAGCCGGTAATGAGACAGCTCATGATGATGAGATCTTTGAAGGGAGAGACATAGATACTGAT
* * **
53882820 ATTATAACAGAAGCAGATGTGGGCTTGAATAAATCTTCTACATTCAATGAAGGTACCAAAGCTCC
66 GTTATAACAGAAGCAGATGTGGGCTTGAATAAATCTTCTACATTCGATGAAGGTACCAAAGCTTG
* *
53882885 GAAGGAGTCTTCAACTGCTGAACTGGTACTAGAGTTAAATAAGAATTCGACAG
131 GAAGGAGTCTTCAACTGCTGAACCGG---TAGAGTTAAATAAGAATTCAACAG
53882938 TGAATAATGC
Statistics
Matches: 341, Mismatches: 22, Indels: 4
0.93 0.06 0.01
Matches are distributed among these distances:
183 313 0.92
184 5 0.01
186 23 0.07
ACGTcount: A:0.35, C:0.15, G:0.26, T:0.24
Consensus pattern (183 bp):
ACAAAGCCGGTAATGAGACAGCTCATGATGATGAGATCTTTGAAGGGAGAGACATAGATACTGAT
GTTATAACAGAAGCAGATGTGGGCTTGAATAAATCTTCTACATTCGATGAAGGTACCAAAGCTTG
GAAGGAGTCTTCAACTGCTGAACCGGTAGAGTTAAATAAGAATTCAACAGCGG
Found at i:53886539 original size:13 final size:13
Alignment explanation
Indices: 53886521--53886552 Score: 64
Period size: 13 Copynumber: 2.5 Consensus size: 13
53886511 GCTTGGACGG
53886521 GCGGTGGGTTAGT
1 GCGGTGGGTTAGT
53886534 GCGGTGGGTTAGT
1 GCGGTGGGTTAGT
53886547 GCGGTG
1 GCGGTG
53886553 CGTTTAGTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.06, C:0.09, G:0.56, T:0.28
Consensus pattern (13 bp):
GCGGTGGGTTAGT
Found at i:53888096 original size:21 final size:21
Alignment explanation
Indices: 53888070--53888122 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
53888060 AGCGGTGGCG
*
53888070 GTGAGATTAGTTACTGTAGCA
1 GTGAGATTAGATACTGTAGCA
* *
53888091 GTGAGATTGGATACTGTAGCG
1 GTGAGATTAGATACTGTAGCA
53888112 GTGAGATTAGA
1 GTGAGATTAGA
53888123 AACAATGGTG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.28, C:0.08, G:0.34, T:0.30
Consensus pattern (21 bp):
GTGAGATTAGATACTGTAGCA
Found at i:53896047 original size:42 final size:43
Alignment explanation
Indices: 53895998--53896081 Score: 143
Period size: 43 Copynumber: 2.0 Consensus size: 43
53895988 ATCCATTAAT
53895998 TAAAATGACATG-GTTTTTTTAGTATTATGTGAAAATAGTAAC
1 TAAAATGACATGCGTTTTTTTAGTATTATGTGAAAATAGTAAC
* *
53896040 TAAAATGACTTGCTTTTTTTTAGTATTATGTGAAAATAGTAA
1 TAAAATGACATGCGTTTTTTTAGTATTATGTGAAAATAGTAA
53896082 ACGACATGAT
Statistics
Matches: 39, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
42 11 0.28
43 28 0.72
ACGTcount: A:0.37, C:0.05, G:0.15, T:0.43
Consensus pattern (43 bp):
TAAAATGACATGCGTTTTTTTAGTATTATGTGAAAATAGTAAC
Found at i:53902748 original size:21 final size:22
Alignment explanation
Indices: 53902719--53902766 Score: 66
Period size: 21 Copynumber: 2.3 Consensus size: 22
53902709 ACTAATTTAA
53902719 TTAAG-TTAATC-CTTAATTAT-
1 TTAAGTTTAATCAC-TAATTATG
53902739 TTAAGTTTAATCACTAATTATG
1 TTAAGTTTAATCACTAATTATG
53902761 TTAAGT
1 TTAAGT
53902767 AAATGTCATC
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
20 5 0.20
21 13 0.52
22 7 0.28
ACGTcount: A:0.35, C:0.08, G:0.08, T:0.48
Consensus pattern (22 bp):
TTAAGTTTAATCACTAATTATG
Found at i:53906718 original size:14 final size:15
Alignment explanation
Indices: 53906681--53906724 Score: 56
Period size: 14 Copynumber: 2.9 Consensus size: 15
53906671 TATGAAATTT
53906681 TTTTAT-TTTTTAAC
1 TTTTATATTTTTAAC
53906695 TTTTAAATATTTTTAA-
1 TTTT--ATATTTTTAAC
53906711 TTTTATATTTTTAA
1 TTTTATATTTTTAA
53906725 AGTTATCTGT
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
14 14 0.52
16 6 0.22
17 7 0.26
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.68
Consensus pattern (15 bp):
TTTTATATTTTTAAC
Found at i:53909317 original size:3 final size:3
Alignment explanation
Indices: 53909309--53909367 Score: 68
Period size: 3 Copynumber: 19.7 Consensus size: 3
53909299 ATGAATTAAG
* *
53909309 TAT TAT TA- TAT TAT TAT AAT GTAT TGT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT
53909354 TAT TCA- TAT TAT TA
1 TAT T-AT TAT TAT TA
53909368 ATTAATACAA
Statistics
Matches: 48, Mismatches: 4, Indels: 8
0.80 0.07 0.13
Matches are distributed among these distances:
2 3 0.06
3 42 0.88
4 3 0.06
ACGTcount: A:0.34, C:0.02, G:0.03, T:0.61
Consensus pattern (3 bp):
TAT
Found at i:53909414 original size:16 final size:16
Alignment explanation
Indices: 53909393--53909425 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
53909383 AAATAAAGTA
*
53909393 AAAGAATAAAAGAAAC
1 AAAGAAGAAAAGAAAC
53909409 AAAGAAGAAAAGAAAC
1 AAAGAAGAAAAGAAAC
53909425 A
1 A
53909426 GAGACCATTC
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:0.76, C:0.06, G:0.15, T:0.03
Consensus pattern (16 bp):
AAAGAAGAAAAGAAAC
Found at i:53911897 original size:4 final size:4
Alignment explanation
Indices: 53911888--53911913 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
53911878 CCATAGAGAA
53911888 AAAT AAAT AAAT AAAT AAAT AAAT AA
1 AAAT AAAT AAAT AAAT AAAT AAAT AA
53911914 TAATAATAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
AAAT
Found at i:53921102 original size:41 final size:41
Alignment explanation
Indices: 53921040--53921266 Score: 373
Period size: 41 Copynumber: 5.5 Consensus size: 41
53921030 GACTTTAAGT
* *
53921040 CTAGTAGGCTAAGTGCCGGTGATCTGAACCAGGTTATAAAC
1 CTAGCAGGCTATGTGCCGGTGATCTGAACCAGGTTATAAAC
*
53921081 CTAGCAGGCTATGTGTCGGTGATCTGAACCAGGTTATAAAC
1 CTAGCAGGCTATGTGCCGGTGATCTGAACCAGGTTATAAAC
*
53921122 CTAGCAGGCTATGTGCCGGTGATCTGAACCAGGTTATGAAC
1 CTAGCAGGCTATGTGCCGGTGATCTGAACCAGGTTATAAAC
53921163 CTAGCAGGCTATGTGCCGGTGATCTGAACCAGGTTATAAAC
1 CTAGCAGGCTATGTGCCGGTGATCTGAACCAGGTTATAAAC
* * *
53921204 CTAGCAGGCTATGTGCCGGTGATCTGAATCAGGCTATAAGC
1 CTAGCAGGCTATGTGCCGGTGATCTGAACCAGGTTATAAAC
* *
53921245 CTAGCAGGCTAAGTGCGGGTGA
1 CTAGCAGGCTATGTGCCGGTGA
53921267 ATACGTTAAT
Statistics
Matches: 175, Mismatches: 11, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
41 175 1.00
ACGTcount: A:0.26, C:0.21, G:0.29, T:0.24
Consensus pattern (41 bp):
CTAGCAGGCTATGTGCCGGTGATCTGAACCAGGTTATAAAC
Found at i:53929058 original size:41 final size:41
Alignment explanation
Indices: 53928996--53929222 Score: 364
Period size: 41 Copynumber: 5.5 Consensus size: 41
53928986 GACTTTAAGT
* *
53928996 CTAGCAGGCTAAGTGCCGGTGATTTGAACCAGGTTATAAAC
1 CTAGCAGGCTATGTGCCGGTGATCTGAACCAGGTTATAAAC
* *
53929037 CTAGTAGGCTATGTACCGGTGATCTGAACCAGGTTATAAAC
1 CTAGCAGGCTATGTGCCGGTGATCTGAACCAGGTTATAAAC
53929078 CTAGCAGGCTATGTGCCGGTGATCTGAACCAGGTTATAAAC
1 CTAGCAGGCTATGTGCCGGTGATCTGAACCAGGTTATAAAC
*
53929119 CTAGCAGGCTATGTGCCGGTAATCTGAACCAGGTTATAAAC
1 CTAGCAGGCTATGTGCCGGTGATCTGAACCAGGTTATAAAC
* * *
53929160 CTAGCAGGCTATGTGCCGGTGATCTGAATCAGGCTATAAGC
1 CTAGCAGGCTATGTGCCGGTGATCTGAACCAGGTTATAAAC
* *
53929201 CTAGCAGGCTAAGTGCGGGTGA
1 CTAGCAGGCTATGTGCCGGTGA
53929223 ATACGTTAAT
Statistics
Matches: 173, Mismatches: 13, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
41 173 1.00
ACGTcount: A:0.27, C:0.21, G:0.28, T:0.24
Consensus pattern (41 bp):
CTAGCAGGCTATGTGCCGGTGATCTGAACCAGGTTATAAAC
Found at i:53947933 original size:27 final size:27
Alignment explanation
Indices: 53947903--53947995 Score: 72
Period size: 28 Copynumber: 3.5 Consensus size: 27
53947893 ATTAGTAATA
53947903 ATAAAATTATATTT-TCTTTTAATAAA-T
1 ATAAAATTATATTTAT-TTTTAA-AAATT
53947930 ATAAAAATTA-ATTTAATTTTTAAAAATT
1 AT-AAAATTATATTT-ATTTTTAAAAATT
** * *
53947958 ATAAAA--ATATAAATTATT-AAAATA
1 ATAAAATTATATTTATTTTTAAAAATT
53947982 ATAAAATTATATTT
1 ATAAAATTATATTT
53947996 TTACTATCAT
Statistics
Matches: 53, Mismatches: 6, Indels: 15
0.72 0.08 0.20
Matches are distributed among these distances:
24 11 0.21
25 6 0.11
26 6 0.11
27 13 0.25
28 16 0.30
29 1 0.02
ACGTcount: A:0.54, C:0.01, G:0.00, T:0.45
Consensus pattern (27 bp):
ATAAAATTATATTTATTTTTAAAAATT
Done.