Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D13
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: 60343961
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 596159 characters in sequence are not A, C, G, or T
File 184 of 204
Found at i:54628302 original size:20 final size:19
Alignment explanation
Indices: 54628245--54628304 Score: 59
Period size: 20 Copynumber: 2.9 Consensus size: 19
54628235 TTTGTAATTT
54628245 ATAATAATTTAAATTAATAATG
1 ATAATAATTT-AATT--TAATG
*
54628267 ATAA-AATTATATTTTAACTG
1 ATAATAATT-TAATTTAA-TG
54628287 ATAATAATTTAATTTAAT
1 ATAATAATTTAATTTAAT
54628305 TCTTTAAATT
Statistics
Matches: 33, Mismatches: 2, Indels: 9
0.75 0.05 0.20
Matches are distributed among these distances:
19 4 0.12
20 13 0.39
21 11 0.33
22 5 0.15
ACGTcount: A:0.50, C:0.02, G:0.03, T:0.45
Consensus pattern (19 bp):
ATAATAATTTAATTTAATG
Found at i:54628960 original size:15 final size:15
Alignment explanation
Indices: 54628940--54628969 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
54628930 TTAATTTATA
*
54628940 TATTTAAATTAATAT
1 TATTTAAAATAATAT
54628955 TATTTAAAATAATAT
1 TATTTAAAATAATAT
54628970 AAAAAATTTG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
TATTTAAAATAATAT
Found at i:54631017 original size:68 final size:68
Alignment explanation
Indices: 54630937--54631069 Score: 257
Period size: 68 Copynumber: 2.0 Consensus size: 68
54630927 ACTTTTCACA
*
54630937 GATCCTTATATGATCTACATATCTTATATATGAGATATGAAATCACAAAAAGATATAAGCTCACT
1 GATCCTTATATGATCTACATATATTATATATGAGATATGAAATCACAAAAAGATATAAGCTCACT
54631002 ACG
66 ACG
54631005 GATCCTTATATGATCTACATATATTATATATGAGATATGAAATCACAAAAAGATATAAGCTCACT
1 GATCCTTATATGATCTACATATATTATATATGAGATATGAAATCACAAAAAGATATAAGCTCACT
54631070 TCATGAAGAT
Statistics
Matches: 64, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
68 64 1.00
ACGTcount: A:0.42, C:0.15, G:0.11, T:0.32
Consensus pattern (68 bp):
GATCCTTATATGATCTACATATATTATATATGAGATATGAAATCACAAAAAGATATAAGCTCACT
ACG
Found at i:54636922 original size:30 final size:30
Alignment explanation
Indices: 54636888--54636946 Score: 109
Period size: 30 Copynumber: 2.0 Consensus size: 30
54636878 TATTTTATTG
54636888 TTAATTTTGTTATTATTTTAAAGGCATTTC
1 TTAATTTTGTTATTATTTTAAAGGCATTTC
*
54636918 TTAATTTTGTTATTATTTTAGAGGCATTT
1 TTAATTTTGTTATTATTTTAAAGGCATTT
54636947 ACTTGTTAAG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.25, C:0.05, G:0.12, T:0.58
Consensus pattern (30 bp):
TTAATTTTGTTATTATTTTAAAGGCATTTC
Found at i:54659485 original size:19 final size:19
Alignment explanation
Indices: 54659456--54659493 Score: 60
Period size: 20 Copynumber: 2.0 Consensus size: 19
54659446 CCGATCCAAT
54659456 TAAAAAATT-AATAAAAAA
1 TAAAAAATTAAATAAAAAA
54659474 TAAAAAATTTAAATAAAAAA
1 TAAAAAA-TTAAATAAAAAA
54659494 AACTTGGTTC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 7 0.39
19 2 0.11
20 9 0.50
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (19 bp):
TAAAAAATTAAATAAAAAA
Found at i:54664419 original size:25 final size:25
Alignment explanation
Indices: 54664391--54664504 Score: 83
Period size: 25 Copynumber: 4.6 Consensus size: 25
54664381 CTTATGAGTA
*
54664391 TCCCGATACTTGGCTCTCACGAGCT
1 TCCCGATAATTGGCTCTCACGAGCT
*
54664416 TCCC-ATTATTTGGCTCTC-CGGAGCT
1 TCCCGA-TAATTGGCTCTCAC-GAGCT
* * *
54664441 TCCCGATAATAGGCTCTTATGAGCT
1 TCCCGATAATTGGCTCTCACGAGCT
* * * *
54664466 TCTCGATTAA-AGGTTCTC-CGAACT
1 TCCCGA-TAATTGGCTCTCACGAGCT
54664490 GTCCCGATAATTGGC
1 -TCCCGATAATTGGC
54664505 ATGCAATAGC
Statistics
Matches: 69, Mismatches: 13, Indels: 14
0.72 0.14 0.15
Matches are distributed among these distances:
24 9 0.13
25 56 0.81
26 4 0.06
ACGTcount: A:0.19, C:0.29, G:0.20, T:0.32
Consensus pattern (25 bp):
TCCCGATAATTGGCTCTCACGAGCT
Found at i:54664529 original size:25 final size:25
Alignment explanation
Indices: 54664512--54664586 Score: 89
Period size: 25 Copynumber: 3.0 Consensus size: 25
54664502 GGCATGCAAT
54664512 AGCTTCCCATTACATGGCTCACATG
1 AGCTTCCCATTACATGGCTCACATG
* * * *
54664537 AGCTTCCCGTTATATGGCTCAAAAG
1 AGCTTCCCATTACATGGCTCACATG
*
54664562 AGCTTCCCGATTACAT-GCTCGCATG
1 AGCTTCCC-ATTACATGGCTCACATG
54664587 GGCATACCTG
Statistics
Matches: 40, Mismatches: 9, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
25 35 0.88
26 5 0.12
ACGTcount: A:0.24, C:0.29, G:0.19, T:0.28
Consensus pattern (25 bp):
AGCTTCCCATTACATGGCTCACATG
Found at i:54666229 original size:25 final size:25
Alignment explanation
Indices: 54666118--54666233 Score: 66
Period size: 25 Copynumber: 4.8 Consensus size: 25
54666108 GAAGCTCATA
54666118 AGAG-GCCATA-ATCGAGAAG-TTC
1 AGAGAGCCATATATCGAGAAGCTTC
* * *
54666140 AAGCGAGCCA-ATATCGGGAAGCTCC
1 -AGAGAGCCATATATCGAGAAGCTTC
* * *
54666165 GGAGAGCCAT-TAAACAAGAAGC-TC
1 AGAGAGCCATAT-ATCGAGAAGCTTC
* * *
54666189 ATAAGAACC-TATTATCGGGAAGCTTC
1 A-GAGAGCCATA-TATCGAGAAGCTTC
54666215 AGAGAGCCATATATCGAGA
1 AGAGAGCCATATATCGAGA
54666234 CGCTCATAAG
Statistics
Matches: 65, Mismatches: 18, Indels: 18
0.64 0.18 0.18
Matches are distributed among these distances:
23 4 0.06
24 22 0.34
25 33 0.51
26 6 0.09
ACGTcount: A:0.37, C:0.21, G:0.25, T:0.17
Consensus pattern (25 bp):
AGAGAGCCATATATCGAGAAGCTTC
Found at i:54689658 original size:23 final size:23
Alignment explanation
Indices: 54689614--54689658 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
54689604 TCTTATTTTG
* *
54689614 TTGATTTGTGTATAATTTATTTA
1 TTGATTTGTATATAATTGATTTA
**
54689637 TTGATTTGTATATTGTTGATTT
1 TTGATTTGTATATAATTGATTT
54689659 CAAATCTCTT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.22, C:0.00, G:0.16, T:0.62
Consensus pattern (23 bp):
TTGATTTGTATATAATTGATTTA
Found at i:54689881 original size:3 final size:3
Alignment explanation
Indices: 54689873--54689923 Score: 57
Period size: 3 Copynumber: 16.7 Consensus size: 3
54689863 ATCTTGTATC
* * *
54689873 ATT ATT ATT ATT ATT ATT ATTT ATT ATT TTT ATT TTT ATT TTT ATT
1 ATT ATT ATT ATT ATT ATT A-TT ATT ATT ATT ATT ATT ATT ATT ATT
*
54689919 TTT AT
1 ATT AT
54689924 ATTCATGTGC
Statistics
Matches: 39, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
3 36 0.92
4 3 0.08
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (3 bp):
ATT
Found at i:54690232 original size:8 final size:8
Alignment explanation
Indices: 54690206--54690243 Score: 51
Period size: 8 Copynumber: 4.8 Consensus size: 8
54690196 TTTTCAACAC
54690206 ATATGTTAT
1 ATAT-TTAT
*
54690215 A-ATATAT
1 ATATTTAT
54690222 ATATTTAT
1 ATATTTAT
54690230 ATATTTAT
1 ATATTTAT
54690238 ATATTT
1 ATATTT
54690244 TTCTTTATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
7 4 0.15
8 21 0.81
9 1 0.04
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (8 bp):
ATATTTAT
Found at i:54694783 original size:43 final size:42
Alignment explanation
Indices: 54694717--54694886 Score: 206
Period size: 43 Copynumber: 4.0 Consensus size: 42
54694707 ATAGGATTTC
54694717 CGATATGTG-TTATCGTGTAAGACCACGTCTGGGACGTTGGCAT
1 CGAT-TGTGATTA-CGTGTAAGACCACGTCTGGGACGTTGGCAT
* * *
54694760 CGACTTGTGTTTACGTGTAAGACCATGTCTGGGACATTGGCAT
1 CGA-TTGTGATTACGTGTAAGACCACGTCTGGGACGTTGGCAT
54694803 CGTATT-TGATT-CGTGTAAGACC-CTGTCTGGGACAG-TGGCAT
1 CG-ATTGTGATTACGTGTAAGACCAC-GTCTGGGAC-GTTGGCAT
*
54694844 CGATATGTGATTACATGTAAGACCACGTCTGGGACGTTGGCAT
1 CGAT-TGTGATTACGTGTAAGACCACGTCTGGGACGTTGGCAT
54694887 TGTACGAGTC
Statistics
Matches: 111, Mismatches: 6, Indels: 20
0.81 0.04 0.15
Matches are distributed among these distances:
40 2 0.02
41 29 0.26
42 10 0.09
43 64 0.58
44 6 0.05
ACGTcount: A:0.22, C:0.19, G:0.29, T:0.31
Consensus pattern (42 bp):
CGATTGTGATTACGTGTAAGACCACGTCTGGGACGTTGGCAT
Found at i:54694874 original size:84 final size:84
Alignment explanation
Indices: 54694729--54694886 Score: 232
Period size: 84 Copynumber: 1.9 Consensus size: 84
54694719 ATATGTGTTA
* * *
54694729 TCGTGTAAGACCACGTCTGGGACGTTGGCATCGACTTGTGTTTACGTGTAAGACCATGTCTGGGA
1 TCGTGTAAGACCACGTCTGGGACGTTGGCATCGACTTGTGATTACATGTAAGACCACGTCTGGGA
54694794 CATTGGCATCGTATTTGAT
66 CATTGGCATCGTATTTGAT
54694813 TCGTGTAAGACC-CTGTCTGGGACAG-TGGCATCGA-TATGTGATTACATGTAAGACCACGTCTG
1 TCGTGTAAGACCAC-GTCTGGGAC-GTTGGCATCGACT-TGTGATTACATGTAAGACCACGTCTG
*
54694875 GGACGTTGGCAT
63 GGACATTGGCAT
54694887 TGTACGAGTC
Statistics
Matches: 67, Mismatches: 4, Indels: 6
0.87 0.05 0.08
Matches are distributed among these distances:
83 2 0.03
84 64 0.96
85 1 0.01
ACGTcount: A:0.22, C:0.20, G:0.29, T:0.30
Consensus pattern (84 bp):
TCGTGTAAGACCACGTCTGGGACGTTGGCATCGACTTGTGATTACATGTAAGACCACGTCTGGGA
CATTGGCATCGTATTTGAT
Found at i:54697135 original size:24 final size:25
Alignment explanation
Indices: 54697102--54697187 Score: 70
Period size: 25 Copynumber: 3.5 Consensus size: 25
54697092 CACATGTATG
54697102 CTCCTACGAGC-G-ATAATCGGTAAA
1 CTCCTACGAGCTGAAT-ATCGGTAAA
* *
54697126 CTCCTCCGAGCTGAATATCGGTAAG
1 CTCCTACGAGCTGAATATCGGTAAA
* * * * *
54697151 CTCATACAAGCTGAGTATCGATAAG
1 CTCCTACGAGCTGAATATCGGTAAA
54697176 CT-CTCACGAGCT
1 CTCCT-ACGAGCT
54697188 ACAAATTGGT
Statistics
Matches: 50, Mismatches: 9, Indels: 5
0.78 0.14 0.08
Matches are distributed among these distances:
24 11 0.22
25 37 0.74
26 2 0.04
ACGTcount: A:0.29, C:0.27, G:0.21, T:0.23
Consensus pattern (25 bp):
CTCCTACGAGCTGAATATCGGTAAA
Found at i:54697187 original size:25 final size:25
Alignment explanation
Indices: 54697132--54697210 Score: 72
Period size: 25 Copynumber: 3.2 Consensus size: 25
54697122 TAAACTCCTC
*
54697132 CGAGCTGAATATCGGTAAGCTCATA
1 CGAGCTGAATATCGATAAGCTCATA
* *
54697157 CAAGCTGAGTATCGATAAGCTC-TCA
1 CGAGCTGAATATCGATAAGCTCAT-A
* * *
54697182 CGAGCT-ACAAATTGGTAAGCTCATA
1 CGAGCTGA-ATATCGATAAGCTCATA
54697207 CGAG
1 CGAG
54697211 TTACGGTGAG
Statistics
Matches: 43, Mismatches: 8, Indels: 6
0.75 0.14 0.11
Matches are distributed among these distances:
24 2 0.05
25 40 0.93
26 1 0.02
ACGTcount: A:0.33, C:0.22, G:0.23, T:0.23
Consensus pattern (25 bp):
CGAGCTGAATATCGATAAGCTCATA
Found at i:54698965 original size:11 final size:11
Alignment explanation
Indices: 54698951--54699002 Score: 50
Period size: 11 Copynumber: 4.6 Consensus size: 11
54698941 ATTAATCATT
54698951 TAATAATAAAA
1 TAATAATAAAA
*
54698962 TAATACTAAAAA
1 TAATAAT-AAAA
**
54698974 TTTTAATAAAA
1 TAATAATAAAA
* *
54698985 TATTAATTAAA
1 TAATAATAAAA
54698996 TAATAAT
1 TAATAAT
54699003 TATCTAATTA
Statistics
Matches: 33, Mismatches: 7, Indels: 2
0.79 0.17 0.05
Matches are distributed among these distances:
11 25 0.76
12 8 0.24
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.37
Consensus pattern (11 bp):
TAATAATAAAA
Found at i:54699001 original size:19 final size:20
Alignment explanation
Indices: 54698977--54699028 Score: 54
Period size: 19 Copynumber: 2.6 Consensus size: 20
54698967 CTAAAAATTT
54698977 TAATAAAATAT-TAATTAAA
1 TAATAAAATATCTAATTAAA
* *
54698996 TAAT-AATTATCTAATTAAT
1 TAATAAAATATCTAATTAAA
54699015 TAATTAAAAATATC
1 TAA-T-AAAATATC
54699029 ACAAACATCA
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
18 5 0.19
19 14 0.54
20 1 0.04
22 6 0.23
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.40
Consensus pattern (20 bp):
TAATAAAATATCTAATTAAA
Found at i:54702993 original size:15 final size:16
Alignment explanation
Indices: 54702968--54702998 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
54702958 TATGATAAAA
54702968 TTTTATGTTTTATTAT
1 TTTTATGTTTTATTAT
54702984 TTTTAT-TTTTATTAT
1 TTTTATGTTTTATTAT
54702999 ATATTTAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.60
16 6 0.40
ACGTcount: A:0.19, C:0.00, G:0.03, T:0.77
Consensus pattern (16 bp):
TTTTATGTTTTATTAT
Found at i:54708150 original size:18 final size:17
Alignment explanation
Indices: 54708127--54708162 Score: 63
Period size: 18 Copynumber: 2.1 Consensus size: 17
54708117 ACATCCACCA
54708127 ATAATTATATCAGTCGTT
1 ATAATTATATCAGT-GTT
54708145 ATAATTATATCAGTGTT
1 ATAATTATATCAGTGTT
54708162 A
1 A
54708163 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:54712004 original size:45 final size:45
Alignment explanation
Indices: 54711946--54712060 Score: 196
Period size: 45 Copynumber: 2.6 Consensus size: 45
54711936 CCCTCACCCT
54711946 CAACTGGTTCATCATCAGCACCCCCACCCCCACCACCGCCAAC-CA
1 CAACTGGTTCATCATCAGCACCCCCACCCCCACCACC-CCAACTCA
* *
54711991 CTACTGGTTCATCATCAGCACCCCCACCCCCACCACCCCCACTCA
1 CAACTGGTTCATCATCAGCACCCCCACCCCCACCACCCCAACTCA
54712036 CAACTGGTTCATCATCAGCACCCCC
1 CAACTGGTTCATCATCAGCACCCCC
54712061 GCCACCCCCT
Statistics
Matches: 66, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
44 4 0.06
45 62 0.94
ACGTcount: A:0.24, C:0.52, G:0.09, T:0.15
Consensus pattern (45 bp):
CAACTGGTTCATCATCAGCACCCCCACCCCCACCACCCCAACTCA
Found at i:54715139 original size:16 final size:16
Alignment explanation
Indices: 54715118--54715154 Score: 65
Period size: 16 Copynumber: 2.3 Consensus size: 16
54715108 AAGCCCTCAT
*
54715118 TTCTTCAATCATAGCC
1 TTCTTCAACCATAGCC
54715134 TTCTTCAACCATAGCC
1 TTCTTCAACCATAGCC
54715150 TTCTT
1 TTCTT
54715155 TCATCTTGGA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.22, C:0.32, G:0.05, T:0.41
Consensus pattern (16 bp):
TTCTTCAACCATAGCC
Found at i:54723313 original size:6 final size:6
Alignment explanation
Indices: 54723290--54723339 Score: 73
Period size: 6 Copynumber: 8.3 Consensus size: 6
54723280 AACCATTACT
* * *
54723290 TGATGA TGATGC TCATGG TGATGG TGATGG TGATGG TGATGG TGATGG
1 TGATGG TGATGG TGATGG TGATGG TGATGG TGATGG TGATGG TGATGG
54723338 TG
1 TG
54723340 TTGAAGATGA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
6 40 1.00
ACGTcount: A:0.18, C:0.04, G:0.44, T:0.34
Consensus pattern (6 bp):
TGATGG
Found at i:54723348 original size:18 final size:18
Alignment explanation
Indices: 54723309--54723348 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
54723299 TGCTCATGGT
**
54723309 GATGGTGATGGTGATGGT
1 GATGGTGATGGTGATGAA
*
54723327 GATGGTGATGGTGTTGAA
1 GATGGTGATGGTGATGAA
54723345 GATG
1 GATG
54723349 ATGAAGAACA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.20, C:0.00, G:0.47, T:0.33
Consensus pattern (18 bp):
GATGGTGATGGTGATGAA
Found at i:54734278 original size:42 final size:42
Alignment explanation
Indices: 54734205--54734333 Score: 129
Period size: 43 Copynumber: 3.0 Consensus size: 42
54734195 TATAGGATTT
*
54734205 TCGATATATGTTATCGTGTAAGACCAC-GTCTGGGACGTTGGCA
1 TCGATATGTGTTAT-GTGTAAGACC-CTGTCTGGGACGTTGGCA
*
54734248 TCGACT-TGTGTTATGTGTAATACCCTGTCTGGGACAG-TGGCA
1 TCGA-TATGTGTTATGTGTAAGACCCTGTCTGGGAC-GTTGGCA
** * * *
54734290 TCGATATGTGATTACATGTAAGACCATGCCAGGGACGTTGGCA
1 TCGATATGTG-TTATGTGTAAGACCCTGTCTGGGACGTTGGCA
54734333 T
1 T
54734334 TGTACGAGCT
Statistics
Matches: 72, Mismatches: 8, Indels: 12
0.78 0.09 0.13
Matches are distributed among these distances:
41 2 0.03
42 32 0.44
43 37 0.51
44 1 0.01
ACGTcount: A:0.23, C:0.19, G:0.28, T:0.30
Consensus pattern (42 bp):
TCGATATGTGTTATGTGTAAGACCCTGTCTGGGACGTTGGCA
Found at i:54742231 original size:33 final size:34
Alignment explanation
Indices: 54742184--54742252 Score: 88
Period size: 34 Copynumber: 2.1 Consensus size: 34
54742174 GTTTAAGTAT
*
54742184 ATTAAAATATATTTTATATATGA-ATTAAAAAAA
1 ATTAAAATATATTTTAGATATGATATTAAAAAAA
* *
54742217 ATTATAAATA-ATTTTAGATATTATATTATAAAAA
1 ATTA-AAATATATTTTAGATATGATATTAAAAAAA
54742251 AT
1 AT
54742253 AGATATAATT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
33 15 0.48
34 16 0.52
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (34 bp):
ATTAAAATATATTTTAGATATGATATTAAAAAAA
Found at i:54742261 original size:33 final size:33
Alignment explanation
Indices: 54742190--54742262 Score: 78
Period size: 33 Copynumber: 2.2 Consensus size: 33
54742180 GTATATTAAA
* *
54742190 ATAT-ATTTTATATATGAATTAAAAAAAATTAT
1 ATATAATTTTAGATATGAATTAAAAAAAATTAG
* * *
54742222 AAATAATTTTAGATATTATATTATAAAAAA-TAG
1 ATATAATTTTAGATATGA-ATTAAAAAAAATTAG
54742255 ATATAATT
1 ATATAATT
54742263 ATAAGGTATA
Statistics
Matches: 33, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
32 3 0.09
33 20 0.61
34 10 0.30
ACGTcount: A:0.53, C:0.00, G:0.04, T:0.42
Consensus pattern (33 bp):
ATATAATTTTAGATATGAATTAAAAAAAATTAG
Found at i:54749135 original size:3 final size:3
Alignment explanation
Indices: 54749077--54749119 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
54749067 ACATGCAGGA
54749077 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG A
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG A
54749120 TAATGATGAA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:54749259 original size:3 final size:3
Alignment explanation
Indices: 54749251--54749291 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
54749241 TCATTGGCCC
54749251 TCT 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 TCT TC
54749292 AACACAAGAC
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:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (3 bp):
TCT
Found at i:54751182 original size:21 final size:21
Alignment explanation
Indices: 54751156--54751208 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
54751146 ATCTGTTTCT
*
54751156 AATCTCACCGCTACAATATCC
1 AATCTCACCGCTACAATAACC
** *
54751177 AATCTCACTACTACAATAACT
1 AATCTCACCGCTACAATAACC
54751198 AATCTCACCGC
1 AATCTCACCGC
54751209 CACCGCTGTT
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.36, C:0.36, G:0.04, T:0.25
Consensus pattern (21 bp):
AATCTCACCGCTACAATAACC
Found at i:54753665 original size:21 final size:21
Alignment explanation
Indices: 54753641--54753683 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
54753631 AGAAAAAAGG
*
54753641 TATACATATAAAATAATAAAA
1 TATACAAATAAAATAATAAAA
*
54753662 TATATAAATAAAATAATAAAA
1 TATACAAATAAAATAATAAAA
54753683 T
1 T
54753684 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:54756192 original size:17 final size:17
Alignment explanation
Indices: 54756170--54756232 Score: 63
Period size: 17 Copynumber: 3.5 Consensus size: 17
54756160 ATTAAATCAC
54756170 TACATAATTAAAAACAT
1 TACATAATTAAAAACAT
** * *
54756187 TACATAAGTCTTTGAATCAC
1 TACATAA---TTAAAAACAT
54756207 TACATAATTAAAAACAT
1 TACATAATTAAAAACAT
54756224 TACATAATT
1 TACATAATT
54756233 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:54756206 original size:37 final size:37
Alignment explanation
Indices: 54756164--54756235 Score: 135
Period size: 37 Copynumber: 1.9 Consensus size: 37
54756154 AACCGAATTA
54756164 AATCACTACATAATTAAAAACATTACATAAGTCTTTG
1 AATCACTACATAATTAAAAACATTACATAAGTCTTTG
*
54756201 AATCACTACATAATTAAAAACATTACATAATTCTT
1 AATCACTACATAATTAAAAACATTACATAAGTCTT
54756236 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:54756249 original size:37 final size:37
Alignment explanation
Indices: 54756168--54756252 Score: 120
Period size: 37 Copynumber: 2.3 Consensus size: 37
54756158 GAATTAAATC
*
54756168 ACTACATAATTAAAAACATTACATAAGTCTTTGAATC
1 ACTACATAATTAAAAACATTACATAAGTCTTTGAATA
*
54756205 ACTACATAATTAAAAACATTACATAATTC-TTGAAATTA
1 ACTACATAATTAAAAACATTACATAAGTCTTTG-AA-TA
54756243 AC-ACATAATT
1 ACTACATAATT
54756253 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:54756408 original size:38 final size:38
Alignment explanation
Indices: 54756364--54756440 Score: 136
Period size: 38 Copynumber: 2.0 Consensus size: 38
54756354 TACTTAGAGT
*
54756364 TAGACTTTAGTTTTATTTTTATTGGGTTGGTAATTGGG
1 TAGACTTTAGTTTTAGTTTTATTGGGTTGGTAATTGGG
*
54756402 TAGACTTTAGTTTTAGTTTTATTGGGTTTGTAATTGGG
1 TAGACTTTAGTTTTAGTTTTATTGGGTTGGTAATTGGG
54756440 T
1 T
54756441 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:54757586 original size:14 final size:15
Alignment explanation
Indices: 54757558--54757590 Score: 59
Period size: 14 Copynumber: 2.3 Consensus size: 15
54757548 AACGTTTATA
54757558 GATTATGGAATTAGG
1 GATTATGGAATTAGG
54757573 GATTATGG-ATTAGG
1 GATTATGGAATTAGG
54757587 GATT
1 GATT
54757591 CTGGTTTAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 10 0.56
15 8 0.44
ACGTcount: A:0.30, C:0.00, G:0.33, T:0.36
Consensus pattern (15 bp):
GATTATGGAATTAGG
Found at i:54757746 original size:68 final size:70
Alignment explanation
Indices: 54757670--54757798 Score: 183
Period size: 68 Copynumber: 1.9 Consensus size: 70
54757660 CAGGTTAGGC
* *
54757670 TTTAGGGTTTAGATTAATTAGTGTGTTTTAATTT-T-TATGAAATAAGGTTTAAGGG-TTAGGGA
1 TTTAGGGTTTAGATTAATTAATATGTTTTAATTTATATATGAAATAAGGTTT-AGGGATTAGGGA
54757732 TTCGGG
65 TTCGGG
* * *
54757738 TTTAGGGTTTTGATTAATTAATATTTTTTAATTTATATATTAAATAAGGTTTAGGGATTAG
1 TTTAGGGTTTAGATTAATTAATATGTTTTAATTTATATATGAAATAAGGTTTAGGGATTAG
54757799 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:54759060 original size:74 final size:74
Alignment explanation
Indices: 54758927--54759065 Score: 169
Period size: 74 Copynumber: 1.9 Consensus size: 74
54758917 TTGCAGCAGC
* *
54758927 ATTAGTGGCGCTTATACAGAAACGCCGCAAAGTCCTGTAACTAGGAAGTGGAACGGCGCCGTTTT
1 ATTAGTGGCGCTTATACAGAAACGCCGCAAAGT-CTGTAACTAGGAAATGAAACGGCGCCGTTTT
54758992 GTTCTTCTCT
65 GTTCTTCTCT
* *
54759002 ATTAGTGGCGCTTTATA-A-AAACGCCGCAAAGT-TGT-ATTAGGAGTTAATGAAACTGCGCCGT
1 ATTAGTGGCGC-TTATACAGAAACGCCGCAAAGTCTGTAACTAGGA---AATGAAACGGCGCCGT
54759063 TTT
62 TTT
54759066 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:54759267 original size:147 final size:147
Alignment explanation
Indices: 54759116--54759544 Score: 330
Period size: 147 Copynumber: 2.9 Consensus size: 147
54759106 ATGTAATTAT
* * * * ** * *
54759116 ATTTATTGAAATGTTGTCGTTTTGTCTATGGTATTAGTGGC-GTTTTTCTGGAAACGCCACAAGC
1 ATTTATTGAAACGCTGCCATTTTGTAAATGGTATTAGTGGCATTTTTTC-GAAAACGCCACAAGC
* * *
54759180 TTGA-GTTAGCTGTTGGGGAAACGACTTCG-TTTGAACTTATAGTTAGTGGCACTTTACTTAAAA
65 TTGAGGTAAG-TGTTGAGGAAACGACTGCGTTTTG-ACTTATAGTTAGTGGCACTTTACTTAAAA
*
54759243 CGCCGCAAAATTGTTCAAAC
128 CGCCGCAAAAATGTTCAAAC
** * * ** *
54759263 ATTTACAGAAACGCTGCCATTTTGTAAATGTTATTAGTGGCATTTTTTCGAAAACGCCGCGGGTT
1 ATTTATTGAAACGCTGCCATTTTGTAAATGGTATTAGTGGCATTTTTTCGAAAACGCCACAAGCT
* * * *
54759328 TGAGGTAAGTGTTGATGAAGCGACTGCGTTTTGACTTATAGTTAGTGGCGCTTTGCTTAAAACGC
66 TGAGGTAAGTGTTGAGGAAACGACTGCGTTTTGACTTATAGTTAGTGGCACTTTACTTAAAACGC
**
54759393 CGCAAAAATGTTTTAAC
131 CGCAAAAATGTTCAAAC
* ** * * * ** * * * * * * *
54759410 ATTGATTGATGCGATGCCGTTTGGTTGTAT--TTTTAGTGGCGTTTATTCAAAAACGCCATAGGT
1 ATTTATTGAAACGCTGCCATTTTG-TAAATGGTATTAGTGGCATTTTTTCGAAAACGCCACAAGC
* ** * * * * * *
54759473 TTGAGCTATTTCTTGATGAAACGACTGCGTTTTGTCTTATAGTTAGTGGCGCTTATA-TTCAAAT
65 TTGAGGTAAGTGTTGAGGAAACGACTGCGTTTTGACTTATAGTTAGTGGCACTT-TACTTAAAAC
54759537 GCCGCAAA
129 GCCGCAAA
54759545 TGGTTAAATT
Statistics
Matches: 226, Mismatches: 51, Indels: 11
0.78 0.18 0.04
Matches are distributed among these distances:
146 87 0.38
147 122 0.54
148 17 0.08
ACGTcount: A:0.25, C:0.15, G:0.23, T:0.36
Consensus pattern (147 bp):
ATTTATTGAAACGCTGCCATTTTGTAAATGGTATTAGTGGCATTTTTTCGAAAACGCCACAAGCT
TGAGGTAAGTGTTGAGGAAACGACTGCGTTTTGACTTATAGTTAGTGGCACTTTACTTAAAACGC
CGCAAAAATGTTCAAAC
Found at i:54759505 original size:146 final size:147
Alignment explanation
Indices: 54759197--54759544 Score: 371
Period size: 146 Copynumber: 2.4 Consensus size: 147
54759187 AGCTGTTGGG
* * *
54759197 GAAACGACTTCG-TTTGAACTTATAGTTAGTGGCACTTTACTTAAAACGCCGCAAAATTGTTCAA
1 GAAACGACTGCGTTTTG-ACTTATAGTTAGTGGCGCTTTACTTAAAACGCCGCAAAAATGTTCAA
* * * * * * *
54759261 ACATTTACAGAAACGCTGCCATTTTGTAAATGTTATTAGTGGCATTTTTTCGAAAACGCCGCGGG
65 ACATTGACAGAAACGATGCCATTTGGTAAATGTTATTAGTGGCATTTATTCAAAAACGCCACAGG
* *
54759326 TTTGAGGTAAGTGTTGAT
130 TTTGAGCTAAGTCTTGAT
* * **
54759344 GAAGCGACTGCGTTTTGACTTATAGTTAGTGGCGCTTTGCTTAAAACGCCGCAAAAATGTTTTAA
1 GAAACGACTGCGTTTTGACTTATAGTTAGTGGCGCTTTACTTAAAACGCCGCAAAAATGTTCAAA
** ** * ** * *
54759409 CATTGATTGATGCGATGCCGTTTGGTTGTAT-TT-TTAGTGGCGTTTATTCAAAAACGCCATAGG
66 CATTGACAGAAACGATGCCATTTGG-TAAATGTTATTAGTGGCATTTATTCAAAAACGCCACAGG
**
54759472 TTTGAGCTATTTCTTGAT
130 TTTGAGCTAAGTCTTGAT
* * *
54759490 GAAACGACTGCGTTTTGTCTTATAGTTAGTGGCGCTTATA-TTCAAATGCCGCAAA
1 GAAACGACTGCGTTTTGACTTATAGTTAGTGGCGCTT-TACTTAAAACGCCGCAAA
54759545 TGGTTAAATT
Statistics
Matches: 166, Mismatches: 32, Indels: 7
0.81 0.16 0.03
Matches are distributed among these distances:
146 86 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):
GAAACGACTGCGTTTTGACTTATAGTTAGTGGCGCTTTACTTAAAACGCCGCAAAAATGTTCAAA
CATTGACAGAAACGATGCCATTTGGTAAATGTTATTAGTGGCATTTATTCAAAAACGCCACAGGT
TTGAGCTAAGTCTTGAT
Found at i:54760223 original size:21 final size:21
Alignment explanation
Indices: 54760199--54760239 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
54760189 TTTGGAACTG
54760199 GTAGACTGTTGTTTGCCTTTA
1 GTAGACTGTTGTTTGCCTTTA
54760220 GTAGACTGTTGTTTGCCTTT
1 GTAGACTGTTGTTTGCCTTT
54760240 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:54760399 original size:13 final size:13
Alignment explanation
Indices: 54760381--54760418 Score: 58
Period size: 13 Copynumber: 2.9 Consensus size: 13
54760371 TGATTTGGTT
54760381 TTAATTTATCAAA
1 TTAATTTATCAAA
* *
54760394 TTAATTTATCCAT
1 TTAATTTATCAAA
54760407 TTAATTTATCAA
1 TTAATTTATCAA
54760419 GACACCCTAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.39, C:0.11, G:0.00, T:0.50
Consensus pattern (13 bp):
TTAATTTATCAAA
Found at i:54761717 original size:13 final size:13
Alignment explanation
Indices: 54761701--54761853 Score: 103
Period size: 13 Copynumber: 11.5 Consensus size: 13
54761691 TTACTAAAAT
*
54761701 TTACTTTAATATA
1 TTACTTAAATATA
*
54761714 TTACTTGAATATA
1 TTACTTAAATATA
*
54761727 TTACTTAAATAAA
1 TTACTTAAATATA
*
54761740 TTACTTACTAAAAT-
1 TTACTTA--AATATA
** *
54761754 TTGGTTAAATTTTA
1 TTACTTAAA-TATA
* *
54761768 GTACTTAAATATG
1 TTACTTAAATATA
*
54761781 TTACTTAAATACA
1 TTACTTAAATATA
*
54761794 TTACTTACTAAAAT-
1 TTACTTA--AATATA
** *
54761808 TTGTTTAAATTTA
1 TTACTTAAATATA
*
54761821 TTACTTAAATATG
1 TTACTTAAATATA
*
54761834 TTACTTAAATACA
1 TTACTTAAATATA
54761847 TTACTTA
1 TTACTTA
54761854 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:54761753 original size:53 final size:53
Alignment explanation
Indices: 54761691--54761863 Score: 249
Period size: 53 Copynumber: 3.2 Consensus size: 53
54761681 AACATATTTT
* * * * *
54761691 TTACTAAAATTTACTTTAATATATTACTTGAATATATTACTTAAATAAATTAC
1 TTACTAAAATTTAGTTTAATTTATTACTTAAATATGTTACTTAAATACATTAC
* * *
54761744 TTACTAAAATTTGGTTAAATTTTAGTACTTAAATATGTTACTTAAATACATTAC
1 TTACTAAAATTTAGTTTAA-TTTATTACTTAAATATGTTACTTAAATACATTAC
54761798 TTACTAAAATTT-GTTTAAATTTATTACTTAAATATGTTACTTAAATACATTAC
1 TTACTAAAATTTAGTTT-AATTTATTACTTAAATATGTTACTTAAATACATTAC
54761851 TTACTAAAATTTA
1 TTACTAAAATTTA
54761864 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:54762079 original size:16 final size:16
Alignment explanation
Indices: 54762058--54762441 Score: 116
Period size: 16 Copynumber: 23.8 Consensus size: 16
54762048 CTTATATGTA
54762058 AACTTACATAATACAT
1 AACTTACATAATACAT
*
54762074 AACTTACAT-GT---T
1 AACTTACATAATACAT
54762086 AACTTACATAATACAT
1 AACTTACATAATACAT
* *
54762102 AACTTATATAAAATTTTTATAT
1 AACTTACAT--AA----TACAT
54762124 AAACTTACATAATACAT
1 -AACTTACATAATACAT
*
54762141 TACTTACAT-AT---T
1 AACTTACATAATACAT
*
54762153 AACTTACATAAGTTATCTAC
1 AACTTACATAA--TA-C-AT
*
54762173 AAGCTT--AT-ATATA-
1 AA-CTTACATAATACAT
*
54762186 AACTTGCATAACTTACAT
1 AACTTACATAA--TACAT
*
54762204 AA-TAACAT-A-ACA-
1 AACTTACATAATACAT
54762216 A-CTTACATAATACAT
1 AACTTACATAATACAT
* *
54762231 AGCATACATAACTTACAT
1 AACTTACATAA--TACAT
*
54762249 AACTTACATAATACAA
1 AACTTACATAATACAT
*
54762265 AACTTACATAACTTAAAT
1 AACTTACATAA--TACAT
* *
54762283 ATCTTACACAACTTACAT
1 AACTTACATAA--TACAT
*
54762301 AACCTACATAATACAT
1 AACTTACATAATACAT
*
54762317 AA-TAAC-T--TAC--
1 AACTTACATAATACAT
54762327 AACTTACATAACATACAT
1 AACTTACAT-A-ATACAT
* **
54762345 TACTTTGATAACTTACAT
1 AACTTACATAA--TACAT
54762363 AACTTACATAATACAT
1 AACTTACATAATACAT
* *
54762379 AACTTACATAGCTTACTT
1 AACTTACATA--ATACAT
54762397 AA--TACATAACTTACAT
1 AACTTACATAA--TACAT
* * *
54762413 AACTTATACACGTACAT
1 AACTTACATA-ATACAT
54762430 AACTTACATAAT
1 AACTTACATAAT
54762442 TTACTTAATA
Statistics
Matches: 271, Mismatches: 45, Indels: 104
0.65 0.11 0.25
Matches are distributed among these distances:
10 2 0.01
11 3 0.01
12 32 0.12
13 8 0.03
14 7 0.03
15 8 0.03
16 91 0.34
17 25 0.09
18 74 0.27
19 2 0.01
20 2 0.01
21 5 0.02
22 4 0.01
23 8 0.03
ACGTcount: A:0.46, C:0.19, G:0.02, T:0.34
Consensus pattern (16 bp):
AACTTACATAATACAT
Found at i:54762204 original size:9 final size:9
Alignment explanation
Indices: 54762186--54762445 Score: 206
Period size: 9 Copynumber: 29.8 Consensus size: 9
54762176 CTTATATATA
*
54762186 AACTTGCAT
1 AACTTACAT
54762195 AACTTACAT
1 AACTTACAT
*
54762204 AA-TAACAT
1 AACTTACAT
54762212 AACAACTTACAT
1 ---AACTTACAT
54762224 AA--TACAT
1 AACTTACAT
* *
54762231 AGCATACAT
1 AACTTACAT
54762240 AACTTACAT
1 AACTTACAT
54762249 AACTTACAT
1 AACTTACAT
*
54762258 AA--TACAA
1 AACTTACAT
54762265 AACTTACAT
1 AACTTACAT
*
54762274 AACTTAAAT
1 AACTTACAT
* *
54762283 ATCTTACAC
1 AACTTACAT
54762292 AACTTACAT
1 AACTTACAT
*
54762301 AACCTACAT
1 AACTTACAT
*
54762310 AATACATA-AT
1 -A-ACTTACAT
54762320 AACTTAC--
1 AACTTACAT
54762327 AACTTACAT
1 AACTTACAT
*
54762336 AACATACAT
1 AACTTACAT
* **
54762345 TACTTTGAT
1 AACTTACAT
54762354 AACTTACAT
1 AACTTACAT
54762363 AACTTACAT
1 AACTTACAT
54762372 AA--TACAT
1 AACTTACAT
54762379 AACTTACAT
1 AACTTACAT
* *
54762388 AGCTTACTT
1 AACTTACAT
54762397 AA--TACAT
1 AACTTACAT
54762404 AACTTACAT
1 AACTTACAT
54762413 AACTT--AT
1 AACTTACAT
*
54762420 ACACGTACAT
1 A-ACTTACAT
54762430 AACTTACAT
1 AACTTACAT
*
54762439 AATTTAC
1 AACTTAC
54762446 TTAATACATA
Statistics
Matches: 199, Mismatches: 32, Indels: 40
0.73 0.12 0.15
Matches are distributed among these distances:
7 35 0.18
8 12 0.06
9 135 0.68
10 6 0.03
11 6 0.03
12 5 0.03
ACGTcount: A:0.46, C:0.21, G:0.02, T:0.32
Consensus pattern (9 bp):
AACTTACAT
Found at i:54762246 original size:25 final size:25
Alignment explanation
Indices: 54762192--54762413 Score: 112
Period size: 25 Copynumber: 8.8 Consensus size: 25
54762182 TATAAACTTG
54762192 CATAACTTACATAA-T--A-ACATA
1 CATAACTTACATAACTACATACATA
*
54762213 -ACAACTTACATAA-TACATAGCATA
1 CATAACTTACATAACTACATA-CATA
54762237 CATAACTTACATAACTTACATA-ATA
1 CATAACTTACATAAC-TACATACATA
* * *
54762262 CAAAACTTACATAACTTAAATATCTTA
1 CATAACTTACATAAC-TACATA-CATA
*
54762289 CACAACTTACATAACCTACATA-ATA
1 CATAACTTACATAA-CTACATACATA
54762314 CATAATAACTTAC--AACTTACATAACATA
1 C---ATAACTTACATAAC-TACAT-ACATA
* ** *
54762342 CATTACTTTGATAACTTACATAACTTA
1 CATAACTTACATAAC-TACAT-ACATA
*
54762369 CATAA--TACATAACTTACATAGCTTA
1 CATAACTTACATAAC-TACATA-CATA
*
54762394 CTTAA--TACATAACTTACATA
1 CATAACTTACATAAC-TACATA
54762414 ACTTATACAC
Statistics
Matches: 165, Mismatches: 17, Indels: 34
0.76 0.08 0.16
Matches are distributed among these distances:
20 13 0.08
22 1 0.01
23 1 0.01
24 5 0.03
25 80 0.48
26 7 0.04
27 45 0.27
28 13 0.08
ACGTcount: A:0.47, C:0.21, G:0.01, T:0.31
Consensus pattern (25 bp):
CATAACTTACATAACTACATACATA
Found at i:54762255 original size:34 final size:34
Alignment explanation
Indices: 54762215--54762418 Score: 182
Period size: 34 Copynumber: 5.9 Consensus size: 34
54762205 ATAACATAAC
*
54762215 AACTTACATAATACATAGCATACATAACTTACAT
1 AACTTACATAATACATAACATACATAACTTACAT
* * *
54762249 AACTTACATAATACAAAACTTACATAACTTAAAT
1 AACTTACATAATACATAACATACATAACTTACAT
* * * *
54762283 ATCTTACACAACTTACATAACCTACATAATACATA-AT
1 AACTTACATAA--TACATAACATACAT-A-ACTTACAT
* * **
54762320 AACTTACA-ACTTACATAACATACATTACTTTGAT
1 AACTTACATA-ATACATAACATACATAACTTACAT
54762354 AACTTACATAACTTACAT-A-ATACATAACTTACAT
1 AACTTACATAA--TACATAACATACATAACTTACAT
* * *
54762388 AGCTTACTTAATACATAACTTACATAACTTA
1 AACTTACATAATACATAACATACATAACTTA
54762419 TACACGTACA
Statistics
Matches: 137, Mismatches: 22, Indels: 22
0.76 0.12 0.12
Matches are distributed among these distances:
32 5 0.04
33 4 0.03
34 81 0.59
35 15 0.11
36 18 0.13
37 10 0.07
38 4 0.03
ACGTcount: A:0.46, C:0.21, G:0.01, T:0.32
Consensus pattern (34 bp):
AACTTACATAATACATAACATACATAACTTACAT
Found at i:54762334 original size:62 final size:59
Alignment explanation
Indices: 54762235--54762380 Score: 168
Period size: 62 Copynumber: 2.4 Consensus size: 59
54762225 ATACATAGCA
*
54762235 TACATAACTTACATAACTTACATAATACAAAACTTACATAACTTAAA-TATCTTACACAACT
1 TACATAACTTACATAA--TACATAATACAAAACTTACATAACATAAATTA-CTTACACAACT
* * * ** *
54762296 TACATAACCTACATAATACATAATAACTTACAACTTACATAACATACATTACTTTGATAACT
1 TACATAACTTACATAATACATAAT-AC--AAAACTTACATAACATAAATTACTTACACAACT
54762358 TACATAACTTACATAATACATAA
1 TACATAACTTACATAATACATAA
54762381 CTTACATAGC
Statistics
Matches: 73, Mismatches: 8, Indels: 7
0.83 0.09 0.08
Matches are distributed among these distances:
59 8 0.11
60 2 0.03
61 15 0.21
62 46 0.63
63 2 0.03
ACGTcount: A:0.47, C:0.21, G:0.01, T:0.32
Consensus pattern (59 bp):
TACATAACTTACATAATACATAATACAAAACTTACATAACATAAATTACTTACACAACT
Found at i:54762418 original size:25 final size:25
Alignment explanation
Indices: 54762352--54762456 Score: 142
Period size: 25 Copynumber: 4.2 Consensus size: 25
54762342 CATTACTTTG
*
54762352 ATAACTTACATAACTTACATAATAC
1 ATAACTTACATAACTTACTTAATAC
*
54762377 ATAACTTACATAGCTTACTTAATAC
1 ATAACTTACATAACTTACTTAATAC
54762402 ATAACTTACATAACTTA--TACACGTAC
1 ATAACTTACATAACTTACTTA-A--TAC
*
54762428 ATAACTTACATAATTTACTTAATAC
1 ATAACTTACATAACTTACTTAATAC
54762453 ATAA
1 ATAA
54762457 ATATATATCA
Statistics
Matches: 71, Mismatches: 4, Indels: 10
0.84 0.05 0.12
Matches are distributed among these distances:
23 2 0.03
24 1 0.01
25 46 0.65
26 19 0.27
27 1 0.01
28 2 0.03
ACGTcount: A:0.45, C:0.19, G:0.02, T:0.34
Consensus pattern (25 bp):
ATAACTTACATAACTTACTTAATAC
Found at i:54768366 original size:43 final size:43
Alignment explanation
Indices: 54768309--54768461 Score: 164
Period size: 43 Copynumber: 3.5 Consensus size: 43
54768299 GCGTTTTTTC
* * *
54768309 AAAAAAGCGCCGCTAAAGGTCATGGTATTTTGCGGCGTTTGTGG
1 AAAAAA-CGCCGCTAAAGGTCATGGTCTTTAGCGACGTTTGTGG
* * * **
54768353 AAAAAACGCCGCTAAAGGTCACGGTCTTTAGCGTCATTT-TTT
1 AAAAAACGCCGCTAAAGGTCATGGTCTTTAGCGACGTTTGTGG
*
54768395 AGAAAAGCGCCGCTAAAGGTCATGGTCTTTAGCGACGTTTGTGG
1 A-AAAAACGCCGCTAAAGGTCATGGTCTTTAGCGACGTTTGTGG
* * * *
54768439 GAAAAGCGCCGTTAAAAGTCATG
1 AAAAAACGCCGCTAAAGGTCATG
54768462 ACCTTTGGCG
Statistics
Matches: 91, Mismatches: 16, Indels: 5
0.81 0.14 0.04
Matches are distributed among these distances:
42 2 0.02
43 82 0.90
44 7 0.08
ACGTcount: A:0.28, C:0.18, G:0.27, T:0.26
Consensus pattern (43 bp):
AAAAAACGCCGCTAAAGGTCATGGTCTTTAGCGACGTTTGTGG
Found at i:54769441 original size:22 final size:22
Alignment explanation
Indices: 54769416--54769467 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 22
54769406 TAATAACAAG
* *
54769416 AAAATAGTAGT-AATATAATAGC
1 AAAATAGTAGTGAA-ACAACAGC
*
54769438 AAAATAGCAGTGAAACAACAGC
1 AAAATAGTAGTGAAACAACAGC
54769460 AAAATAGT
1 AAAATAGT
54769468 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:54771040 original size:23 final size:22
Alignment explanation
Indices: 54771014--54771078 Score: 67
Period size: 24 Copynumber: 2.8 Consensus size: 22
54771004 TTTCTTTTTG
54771014 TATATTTGATTCTCTATTTTTCA
1 TATATTT-ATTCTCTATTTTTCA
* *
54771037 TATATGTTATTCTCTTTATTTTCT
1 TATAT-TTATTCTCTAT-TTTTCA
*
54771061 TATATTTAATTATCTATT
1 TATATTT-ATTCTCTATT
54771079 ATTATATTTT
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
23 16 0.46
24 19 0.54
ACGTcount: A:0.23, C:0.11, G:0.03, T:0.63
Consensus pattern (22 bp):
TATATTTATTCTCTATTTTTCA
Found at i:54771064 original size:24 final size:23
Alignment explanation
Indices: 54770977--54771068 Score: 80
Period size: 23 Copynumber: 3.9 Consensus size: 23
54770967 CTCTTTCATA
*
54770977 TCTTTATTTTCCTTATTTATTATTC
1 TCTTTATTTT-CTTATAT-TTATTC
* *
54771002 TTTTTCTTTT-TGTATATTTGATTC
1 TCTTTATTTTCT-TATATTT-ATTC
* *
54771026 TCTAT-TTTTCATATATGTTATTC
1 TCTTTATTTTCTTATAT-TTATTC
54771049 TCTTTATTTTCTTATATTTA
1 TCTTTATTTTCTTATATTTA
54771069 ATTATCTATT
Statistics
Matches: 54, Mismatches: 8, Indels: 12
0.73 0.11 0.16
Matches are distributed among these distances:
23 23 0.43
24 23 0.43
25 8 0.15
ACGTcount: A:0.17, C:0.12, G:0.03, T:0.67
Consensus pattern (23 bp):
TCTTTATTTTCTTATATTTATTC
Found at i:54785228 original size:38 final size:36
Alignment explanation
Indices: 54785181--54785326 Score: 100
Period size: 37 Copynumber: 4.2 Consensus size: 36
54785171 AAATATTCTT
54785181 ATATGAATTTACTAAAATCATAATATATAATACTATAAA
1 ATAT-AATTTACTAAAATCATAATATATAATACT-T-AA
54785220 ATATAA-TT--T-AAA--ATAAT-TAT--TA-TTAA
1 ATATAATTTACTAAAATCATAATATATAATACTTAA
* * * *
54785246 ATATAATTTAATAAAATTCTTAATATAATTATTCTT--
1 ATATAATTTACTAAAA-TCATAATAT-ATAATACTTAA
54785282 ATATGAATTTACTAAAATCATAATATATAATACTATAA
1 ATAT-AATTTACTAAAATCATAATATATAATACT-TAA
*
54785320 AAATAAT
1 ATATAAT
54785327 ATATAATCTA
Statistics
Matches: 84, Mismatches: 7, Indels: 34
0.67 0.06 0.27
Matches are distributed among these distances:
26 8 0.10
27 3 0.04
28 1 0.01
29 3 0.04
30 3 0.04
31 3 0.04
32 5 0.06
33 4 0.05
34 4 0.05
35 9 0.11
36 13 0.15
37 17 0.20
38 7 0.08
39 4 0.05
ACGTcount: A:0.52, C:0.05, G:0.01, T:0.41
Consensus pattern (36 bp):
ATATAATTTACTAAAATCATAATATATAATACTTAA
Found at i:54785300 original size:101 final size:101
Alignment explanation
Indices: 54785144--54785326 Score: 341
Period size: 101 Copynumber: 1.8 Consensus size: 101
54785134 TAATAAAAAT
54785144 ATATAATTTAATAAAATTCTTAATATTAAATATTCTTATATGAATTTACTAAAATCATAATATAT
1 ATATAATTTAATAAAATTCTTAATATTAAATATTCTTATATGAATTTACTAAAATCATAATATAT
54785209 AATACTATAAAATATAATTTAAAATAATTATTATTAA
66 AATACTATAAAA-ATAATTTAAAATAATTATTATTAA
*
54785246 ATATAATTTAATAAAATTCTTAATA-TAATTATTCTTATATGAATTTACTAAAATCATAATATAT
1 ATATAATTTAATAAAATTCTTAATATTAAATATTCTTATATGAATTTACTAAAATCATAATATAT
54785310 AATACTATAAAAATAAT
66 AATACTATAAAAATAAT
54785327 ATATAATCTA
Statistics
Matches: 80, Mismatches: 1, Indels: 2
0.96 0.01 0.02
Matches are distributed among these distances:
100 5 0.06
101 50 0.62
102 25 0.31
ACGTcount: A:0.51, C:0.05, G:0.01, T:0.43
Consensus pattern (101 bp):
ATATAATTTAATAAAATTCTTAATATTAAATATTCTTATATGAATTTACTAAAATCATAATATAT
AATACTATAAAAATAATTTAAAATAATTATTATTAA
Found at i:54790349 original size:63 final size:62
Alignment explanation
Indices: 54790222--54790349 Score: 141
Period size: 63 Copynumber: 2.0 Consensus size: 62
54790212 ACAAGCATTC
* * * * * * *
54790222 TGATCGGTAGTGATCTTGCATGTGTTGCGGACTATCACAGCTCTTTTTGAGTGTCTTGTTATA
1 TGATCGGTAGTGATCCTGCATATATTGCGGACTAACACAACTCTTTGTGAGTGTCCTG-TATA
* *
54790285 TGATCGGTTGTGATCCTGCATATATTGCGGACATAAACGCAACTCTTTGTGAGTGTCCTG-ATA
1 TGATCGGTAGTGATCCTGCATATATTGCGGAC-T-AACACAACTCTTTGTGAGTGTCCTGTATA
54790348 TG
1 TG
54790350 GCTCGCTTGA
Statistics
Matches: 54, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
63 33 0.61
64 1 0.02
65 20 0.37
ACGTcount: A:0.20, C:0.17, G:0.25, T:0.38
Consensus pattern (62 bp):
TGATCGGTAGTGATCCTGCATATATTGCGGACTAACACAACTCTTTGTGAGTGTCCTGTATA
Found at i:54792166 original size:26 final size:26
Alignment explanation
Indices: 54792137--54792204 Score: 90
Period size: 26 Copynumber: 2.7 Consensus size: 26
54792127 TACTCTCTCA
54792137 AGCCATATAACAGGAAGCTCACAAAG
1 AGCCATATAACAGGAAGCTCACAAAG
*
54792163 AGCCAT-TAATCGGGAAGCTCACAAAG
1 AGCCATATAA-CAGGAAGCTCACAAAG
54792189 AGCC-TAT--CAGGAAGCT
1 AGCCATATAACAGGAAGCT
54792205 TATTCGGGCT
Statistics
Matches: 38, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
23 8 0.21
25 4 0.11
26 26 0.68
ACGTcount: A:0.40, C:0.24, G:0.22, T:0.15
Consensus pattern (26 bp):
AGCCATATAACAGGAAGCTCACAAAG
Found at i:54793681 original size:24 final size:26
Alignment explanation
Indices: 54793618--54793683 Score: 70
Period size: 24 Copynumber: 2.7 Consensus size: 26
54793608 ACTTTCATAG
*
54793618 AATATAAAG-TTAAATATATATAAAC
1 AATATAAAGAATAAATATATATAAAC
*
54793643 AA-ATATAGAA-AAA-ATA-ATAATAC
1 AATATAAAGAATAAATATATATAA-AC
54793666 AATATAAAGAATAAATAT
1 AATATAAAGAATAAATAT
54793684 GATAAAAAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 9
0.73 0.07 0.20
Matches are distributed among these distances:
22 4 0.12
23 7 0.21
24 15 0.45
25 5 0.15
26 2 0.06
ACGTcount: A:0.65, C:0.03, G:0.05, T:0.27
Consensus pattern (26 bp):
AATATAAAGAATAAATATATATAAAC
Found at i:54794332 original size:12 final size:13
Alignment explanation
Indices: 54794315--54794343 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
54794305 AATCAAAACC
54794315 AAAACTG-AAAAG
1 AAAACTGAAAAAG
54794327 AAAACTGAAAAAG
1 AAAACTGAAAAAG
54794340 AAAA
1 AAAA
54794344 AAAACGGAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 7 0.44
13 9 0.56
ACGTcount: A:0.72, C:0.07, G:0.14, T:0.07
Consensus pattern (13 bp):
AAAACTGAAAAAG
Found at i:54795495 original size:87 final size:86
Alignment explanation
Indices: 54795349--54795616 Score: 344
Period size: 87 Copynumber: 3.1 Consensus size: 86
54795339 ACTTGTAATC
** * * *
54795349 TTCGATCTGCTTCACTGTCGACGCAAG-AGAGTAATATCTGCTATCTTTAACTAGCTCCACTGCA
1 TTCGATCTGCTTCACTGTTAACGCAGGAAG-GCAATATCTGCTATCTTTAACCAGCTCCACTGCA
54795413 ACCGATAGAGGCAAGGCTTTGTT
65 ACCGAT-GAGGCAAGGCTTTGTT
*
54795436 TTCGATCTGCTTCACTGTTAACGCAGGAAGGCAATATCTGCTATCTTTAACCAGCTCCACCGCAA
1 TTCGATCTGCTTCACTGTTAACGCAGGAAGGCAATATCTGCTATCTTTAACCAGCTCCACTGCAA
* *
54795501 CCGATGGAGGCAAGCCTTTATT
66 CCGAT-GAGGCAAGGCTTTGTT
* * * * * *
54795523 TTCGATCTGTTTTATTGTTAACGCAGGAAGGCAAGATTTGCT-TCTTTAACCAGCTTCACTGCAA
1 TTCGATCTGCTTCACTGTTAACGCAGGAAGGCAATATCTGCTATCTTTAACCAGCTCCACTGCAA
54795587 CCGATGAAGGCAAGG-TTTCGTT
66 CCGATG-AGGCAAGGCTTT-GTT
54795609 TTCGATCT
1 TTCGATCT
54795617 TCACTGATCT
Statistics
Matches: 160, Mismatches: 18, Indels: 7
0.86 0.10 0.04
Matches are distributed among these distances:
85 4 0.03
86 42 0.26
87 112 0.70
88 2 0.01
ACGTcount: A:0.25, C:0.24, G:0.21, T:0.31
Consensus pattern (86 bp):
TTCGATCTGCTTCACTGTTAACGCAGGAAGGCAATATCTGCTATCTTTAACCAGCTCCACTGCAA
CCGATGAGGCAAGGCTTTGTT
Found at i:54796848 original size:21 final size:21
Alignment explanation
Indices: 54796824--54796865 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
54796814 TTAGCCTCTC
*
54796824 CATTTTTACTCTTTCAT-TTTT
1 CATTTTCACT-TTTCATCTTTT
54796845 CATTTTCACTTTTCATCTTTT
1 CATTTTCACTTTTCATCTTTT
54796866 TTTTACATCT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 6 0.32
21 13 0.68
ACGTcount: A:0.14, C:0.21, G:0.00, T:0.64
Consensus pattern (21 bp):
CATTTTCACTTTTCATCTTTT
Found at i:54797226 original size:6 final size:6
Alignment explanation
Indices: 54797215--54797250 Score: 63
Period size: 6 Copynumber: 5.8 Consensus size: 6
54797205 TGGCCTCTCC
54797215 TTTTCT TTTTCT TTTTCT TTTTCT TTTTCCT TTTTC
1 TTTTCT TTTTCT TTTTCT TTTTCT TTTT-CT TTTTC
54797251 ATTCTGATTT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
6 23 0.79
7 6 0.21
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (6 bp):
TTTTCT
Found at i:54797410 original size:6 final size:6
Alignment explanation
Indices: 54797347--54797413 Score: 62
Period size: 6 Copynumber: 10.7 Consensus size: 6
54797337 TCTTTCTTCT
* * * *
54797347 TTTTGT TTTTGA TTTTGA TTTTTGA TTTTTTCA TTTTCA TTTTCA TTTTGA
1 TTTTGA TTTTGA TTTTGA -TTTTGA --TTTTGA TTTTGA TTTTGA TTTTGA
*
54797398 CTTTGA TTTTGA TTTT
1 TTTTGA TTTTGA TTTT
54797414 TCTTTTTCTT
Statistics
Matches: 54, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
6 42 0.78
7 6 0.11
8 6 0.11
ACGTcount: A:0.13, C:0.06, G:0.10, T:0.70
Consensus pattern (6 bp):
TTTTGA
Found at i:54801303 original size:15 final size:15
Alignment explanation
Indices: 54801283--54801312 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
54801273 TTTGAATGAA
54801283 TTGGAAGATAAGGCT
1 TTGGAAGATAAGGCT
54801298 TTGGAAGATAAGGCT
1 TTGGAAGATAAGGCT
54801313 CATTTGTTTT
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:0.07, G:0.33, T:0.27
Consensus pattern (15 bp):
TTGGAAGATAAGGCT
Found at i:54801524 original size:6 final size:6
Alignment explanation
Indices: 54801513--54801541 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
54801503 GAACATTGCC
54801513 TTTATT TTTATT TTTATT TTTATT TTTAT
1 TTTATT TTTATT TTTATT TTTATT TTTAT
54801542 ATATTTTTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (6 bp):
TTTATT
Found at i:54801550 original size:18 final size:18
Alignment explanation
Indices: 54801513--54801549 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
54801503 GAACATTGCC
*
54801513 TTTATTTTTATTTTTATT
1 TTTATTTTTATTATTATT
54801531 TTTATTTTTA-TA-TATT
1 TTTATTTTTATTATTATT
54801547 TTT
1 TTT
54801550 TAAAATCCTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
16 7 0.39
17 1 0.06
18 10 0.56
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (18 bp):
TTTATTTTTATTATTATT
Found at i:54802477 original size:24 final size:26
Alignment explanation
Indices: 54802414--54802479 Score: 70
Period size: 24 Copynumber: 2.7 Consensus size: 26
54802404 ACTTTCATAG
*
54802414 AATATAAAG-TTAAATATATATAAAC
1 AATATAAAGAATAAATATATATAAAC
*
54802439 AA-ATATAGAA-AAA-ATA-ATAATAC
1 AATATAAAGAATAAATATATATAA-AC
54802462 AATATAAAGAATAAATAT
1 AATATAAAGAATAAATAT
54802480 GATAAAAAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 9
0.73 0.07 0.20
Matches are distributed among these distances:
22 4 0.12
23 7 0.21
24 15 0.45
25 5 0.15
26 2 0.06
ACGTcount: A:0.65, C:0.03, G:0.05, T:0.27
Consensus pattern (26 bp):
AATATAAAGAATAAATATATATAAAC
Found at i:54807866 original size:32 final size:32
Alignment explanation
Indices: 54807812--54807879 Score: 104
Period size: 32 Copynumber: 2.1 Consensus size: 32
54807802 AATAAATACC
54807812 AAAAATTATTTTAAAAATTAAAAAAATTTATTTT
1 AAAAATTATTTTAAAAATTAAAAAAA--TATTTT
54807846 AAAAA-TATTTT-AAAATTAAAAAAATATTTT
1 AAAAATTATTTTAAAAATTAAAAAAATATTTT
54807876 AAAA
1 AAAA
54807880 TTAAATTTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
30 10 0.29
32 13 0.38
33 6 0.18
34 5 0.15
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (32 bp):
AAAAATTATTTTAAAAATTAAAAAAATATTTT
Found at i:54807870 original size:19 final size:19
Alignment explanation
Indices: 54807846--54807884 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
54807836 AATTTATTTT
54807846 AAAAATATTTTAAAATTAA
1 AAAAATATTTTAAAATTAA
54807865 AAAAATATTTTAAAATTAA
1 AAAAATATTTTAAAATTAA
54807884 A
1 A
54807885 TTTTTTTTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (19 bp):
AAAAATATTTTAAAATTAA
Found at i:54807888 original size:32 final size:33
Alignment explanation
Indices: 54807819--54807915 Score: 105
Period size: 30 Copynumber: 3.0 Consensus size: 33
54807809 ACCAAAAATT
*
54807819 ATTTTAAAAATTAAAAAAATTTATTTTAAAA--AT
1 ATTTT-AAAATTAAAAAAA-TTATTTTAAAATTAA
54807852 ATTTTAAAATTAAAAAAA-TATTTTAAAATTAA
1 ATTTTAAAATTAAAAAAATTATTTTAAAATTAA
** *
54807884 ATTTT--TTTTAAAAAAAGTATTTTAAAATTAA
1 ATTTTAAAATTAAAAAAATTATTTTAAAATTAA
54807915 A
1 A
54807916 AAAATAAAAA
Statistics
Matches: 58, Mismatches: 3, Indels: 8
0.84 0.04 0.12
Matches are distributed among these distances:
30 19 0.33
31 15 0.26
32 19 0.33
33 5 0.09
ACGTcount: A:0.56, C:0.00, G:0.01, T:0.43
Consensus pattern (33 bp):
ATTTTAAAATTAAAAAAATTATTTTAAAATTAA
Found at i:54807925 original size:9 final size:8
Alignment explanation
Indices: 54807907--54807936 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
54807897 AAAGTATTTT
*
54807907 AAAATTAA
1 AAAAATAA
54807915 AAAAATAA
1 AAAAATAA
54807923 AAAAATAA
1 AAAAATAA
54807931 AAAAAT
1 AAAAAT
54807937 TTATTATATT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (8 bp):
AAAAATAA
Found at i:54825142 original size:27 final size:27
Alignment explanation
Indices: 54825112--54825167 Score: 112
Period size: 27 Copynumber: 2.1 Consensus size: 27
54825102 TGAGATGTAG
54825112 TTGTTAAGAAGTATAACTAAACATGCT
1 TTGTTAAGAAGTATAACTAAACATGCT
54825139 TTGTTAAGAAGTATAACTAAACATGCT
1 TTGTTAAGAAGTATAACTAAACATGCT
54825166 TT
1 TT
54825168 CATGTGCCCT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.39, C:0.11, G:0.14, T:0.36
Consensus pattern (27 bp):
TTGTTAAGAAGTATAACTAAACATGCT
Found at i:54829813 original size:13 final size:13
Alignment explanation
Indices: 54829795--54829822 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
54829785 AATTTACAAG
54829795 ATTACATAATCAA
1 ATTACATAATCAA
54829808 ATTACATAATCAA
1 ATTACATAATCAA
54829821 AT
1 AT
54829823 CCAATCTAAT
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:54830249 original size:18 final size:19
Alignment explanation
Indices: 54830226--54830262 Score: 58
Period size: 18 Copynumber: 1.9 Consensus size: 19
54830216 ATTTGATTAA
54830226 AAATACTTT-TAATTTTTG
1 AAATACTTTCTAATTTTTG
54830244 AAATACTTTGCTAATTTTT
1 AAATACTTT-CTAATTTTT
54830263 ATTTTTTCAT
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:54830625 original size:27 final size:28
Alignment explanation
Indices: 54830590--54830652 Score: 76
Period size: 27 Copynumber: 2.3 Consensus size: 28
54830580 ATATAAAATC
* *
54830590 TTTTTAATTTCTTTGTATATTTT-TAT-A
1 TTTTTAATTTCTTTATA-ATTTTAAATAA
*
54830617 TTTTTAATTTGTTTATAATTTTAAATAA
1 TTTTTAATTTCTTTATAATTTTAAATAA
54830645 TTTTTAAT
1 TTTTTAAT
54830653 GATTTTTTGA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
26 5 0.16
27 17 0.55
28 9 0.29
ACGTcount: A:0.29, C:0.02, G:0.03, T:0.67
Consensus pattern (28 bp):
TTTTTAATTTCTTTATAATTTTAAATAA
Found at i:54834590 original size:20 final size:20
Alignment explanation
Indices: 54834567--54834608 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
54834557 AACTATTTAA
**
54834567 ATAATATTATTTGAATAGTT
1 ATAATATTAAATGAATAGTT
54834587 ATAATATTAAATGAATAGTT
1 ATAATATTAAATGAATAGTT
54834607 AT
1 AT
54834609 GTGTTTATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.45, C:0.00, G:0.10, T:0.45
Consensus pattern (20 bp):
ATAATATTAAATGAATAGTT
Found at i:54839452 original size:18 final size:19
Alignment explanation
Indices: 54839429--54839465 Score: 58
Period size: 18 Copynumber: 1.9 Consensus size: 19
54839419 ATTTGATTAA
54839429 AAATACTTT-TAATTTTTG
1 AAATACTTTCTAATTTTTG
54839447 AAATACTTTGCTAATTTTT
1 AAATACTTT-CTAATTTTT
54839466 ATTTTTTTTT
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:54839656 original size:21 final size:19
Alignment explanation
Indices: 54839613--54839665 Score: 63
Period size: 21 Copynumber: 2.7 Consensus size: 19
54839603 AAAAAAATAA
*
54839613 TTTTATAATTTTTATGGATTT
1 TTTTATAATTTTTATGGA--C
54839634 TTTTATAATTTTTGA-GGAC
1 TTTTATAATTTTT-ATGGAC
54839653 TTTTATAATTTTT
1 TTTTATAATTTTT
54839666 TTTTATTTTT
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
19 13 0.43
21 16 0.53
22 1 0.03
ACGTcount: A:0.25, C:0.02, G:0.09, T:0.64
Consensus pattern (19 bp):
TTTTATAATTTTTATGGAC
Found at i:54839779 original size:26 final size:27
Alignment explanation
Indices: 54839749--54839806 Score: 91
Period size: 26 Copynumber: 2.2 Consensus size: 27
54839739 TTTTTAACGG
*
54839749 GTATCAAAATTTATAATATATAACAAC
1 GTATCAAAATCTATAATATATAACAAC
*
54839776 -TATCAAAATCTATAATATATAATAAC
1 GTATCAAAATCTATAATATATAACAAC
54839802 GTATC
1 GTATC
54839807 TATTTATATA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
26 24 0.86
27 4 0.14
ACGTcount: A:0.50, C:0.12, G:0.03, T:0.34
Consensus pattern (27 bp):
GTATCAAAATCTATAATATATAACAAC
Found at i:54839927 original size:18 final size:17
Alignment explanation
Indices: 54839894--54839927 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
54839884 TTTTTACTAA
*
54839894 TTTTTATATTTTAAATT
1 TTTTTATATTTAAAATT
54839911 TTTTTATAATTTAAAAT
1 TTTTTAT-ATTTAAAAT
54839928 AATTTTTAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (17 bp):
TTTTTATATTTAAAATT
Found at i:54841470 original size:30 final size:29
Alignment explanation
Indices: 54841392--54841574 Score: 312
Period size: 29 Copynumber: 6.2 Consensus size: 29
54841382 GAATAAACAG
*
54841392 AATACAATACATATATTTTTTATTTTTAA
1 AATACACTACATATATTTTTTATTTTTAA
54841421 AATACACTACATATATTTTTTATTTTTAA
1 AATACACTACATATATTTTTTATTTTTAA
*
54841450 AATACACTACATATTTTTTTTTATTTTTAA
1 AATACACTACATA-TATTTTTTATTTTTAA
54841480 AATACACTACATATATTTTTTATTTTTAA
1 AATACACTACATATATTTTTTATTTTTAA
54841509 AATACACTACATATATTTCTTTATTTTTAA
1 AATACACTACATATATTT-TTTATTTTTAA
*
54841539 AATACATTACATATATTTTTTTATTTTTAA
1 AATACACTACATATA-TTTTTTATTTTTAA
54841569 AATACA
1 AATACA
54841575 AAAATACAAT
Statistics
Matches: 147, Mismatches: 4, Indels: 5
0.94 0.03 0.03
Matches are distributed among these distances:
29 74 0.50
30 70 0.48
31 3 0.02
ACGTcount: A:0.38, C:0.10, G:0.00, T:0.52
Consensus pattern (29 bp):
AATACACTACATATATTTTTTATTTTTAA
Found at i:54841484 original size:59 final size:59
Alignment explanation
Indices: 54841392--54841574 Score: 305
Period size: 59 Copynumber: 3.1 Consensus size: 59
54841382 GAATAAACAG
* *
54841392 AATACAATACATA-TATTTTTTATTTTTAAAATACACTACATATATTTTTTATTTTTAA
1 AATACACTACATATTTTTTTTTATTTTTAAAATACACTACATATATTTTTTATTTTTAA
54841450 AATACACTACATATTTTTTTTTATTTTTAAAATACACTACATATATTTTTTATTTTTAA
1 AATACACTACATATTTTTTTTTATTTTTAAAATACACTACATATATTTTTTATTTTTAA
* * *
54841509 AATACACTACATATATTTCTTTATTTTTAAAATACATTACATATATTTTTTTATTTTTAA
1 AATACACTACATATTTTTTTTTATTTTTAAAATACACTACATATA-TTTTTTATTTTTAA
54841569 AATACA
1 AATACA
54841575 AAAATACAAT
Statistics
Matches: 118, Mismatches: 5, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
58 12 0.10
59 86 0.73
60 20 0.17
ACGTcount: A:0.38, C:0.10, G:0.00, T:0.52
Consensus pattern (59 bp):
AATACACTACATATTTTTTTTTATTTTTAAAATACACTACATATATTTTTTATTTTTAA
Found at i:54841674 original size:43 final size:43
Alignment explanation
Indices: 54841627--54841758 Score: 162
Period size: 43 Copynumber: 3.0 Consensus size: 43
54841617 TTTCCATAGA
*
54841627 TTCCCCTCTTCTACCGTGCCCTCCTCCCATTTCCCATTCCCAT
1 TTCCCCTCTTCCACCGTGCCCTCCTCCCATTTCCCATTCCCAT
*
54841670 TTCCCCTCTTCCACCGTGCCCTCCTCCC--TGCCC-TCCTCCCAT
1 TTCCCCTCTTCCACCGTGCCCTCCTCCCATTTCCCAT--TCCCAT
* * *
54841712 TTCCCCTCTTCCATCGATTCTCCTCTTCCCATTTCCCATTCCCAT
1 TTCCCCTCTTCCACCG-TGC-CCTCCTCCCATTTCCCATTCCCAT
54841757 TT
1 TT
54841759 ACGGTTGCTT
Statistics
Matches: 76, Mismatches: 6, Indels: 12
0.81 0.06 0.13
Matches are distributed among these distances:
40 1 0.01
41 4 0.05
42 21 0.28
43 29 0.38
44 8 0.11
45 8 0.11
46 4 0.05
47 1 0.01
ACGTcount: A:0.08, C:0.52, G:0.05, T:0.36
Consensus pattern (43 bp):
TTCCCCTCTTCCACCGTGCCCTCCTCCCATTTCCCATTCCCAT
Found at i:54843269 original size:31 final size:31
Alignment explanation
Indices: 54843234--54843298 Score: 112
Period size: 31 Copynumber: 2.1 Consensus size: 31
54843224 AGCAATTAAT
* *
54843234 ACATGTAAATTGCCATGTGACATCCAAATCA
1 ACATGTAAATTGCCATGTAAAATCCAAATCA
54843265 ACATGTAAATTGCCATGTAAAATCCAAATCA
1 ACATGTAAATTGCCATGTAAAATCCAAATCA
54843296 ACA
1 ACA
54843299 AGTTAGCGTT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.43, C:0.22, G:0.11, T:0.25
Consensus pattern (31 bp):
ACATGTAAATTGCCATGTAAAATCCAAATCA
Found at i:54844464 original size:44 final size:44
Alignment explanation
Indices: 54844416--54844519 Score: 129
Period size: 44 Copynumber: 2.4 Consensus size: 44
54844406 ATTCAGACAG
* * *
54844416 CATTTAATTAACATTTAACCAACAATTGGACAGCAATCAATCAA
1 CATTTAATCAACATTTAACCAACAATTGGACAACAATAAATCAA
* * * *
54844460 CATTTGGA-CAGCATTTAATCAACAATTGGACAACATTAAATCAA
1 CATTT-AATCAACATTTAACCAACAATTGGACAACAATAAATCAA
54844504 CATTTAATCAACATTT
1 CATTTAATCAACATTT
54844520 GGACAGAATT
Statistics
Matches: 49, Mismatches: 9, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
43 1 0.02
44 47 0.96
45 1 0.02
ACGTcount: A:0.43, C:0.19, G:0.08, T:0.30
Consensus pattern (44 bp):
CATTTAATCAACATTTAACCAACAATTGGACAACAATAAATCAA
Found at i:54844466 original size:22 final size:22
Alignment explanation
Indices: 54844435--54844505 Score: 97
Period size: 22 Copynumber: 3.2 Consensus size: 22
54844425 AACATTTAAC
* *
54844435 CAACAATTGGACAGCAATCAAT
1 CAACAATTGGACAGCATTAAAT
* *
54844457 CAACATTTGGACAGCATTTAAT
1 CAACAATTGGACAGCATTAAAT
*
54844479 CAACAATTGGACAACATTAAAT
1 CAACAATTGGACAGCATTAAAT
54844501 CAACA
1 CAACA
54844506 TTTAATCAAC
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 43 1.00
ACGTcount: A:0.45, C:0.21, G:0.11, T:0.23
Consensus pattern (22 bp):
CAACAATTGGACAGCATTAAAT
Found at i:54844494 original size:33 final size:33
Alignment explanation
Indices: 54844471--54844541 Score: 99
Period size: 33 Copynumber: 2.2 Consensus size: 33
54844461 ATTTGGACAG
54844471 CATTTAATCAACAATTGGACAACATTAAATCAA
1 CATTTAATCAACAATTGGACAACATTAAATCAA
* *
54844504 CATTTAATCAACATTTGGACAGA-ATTCAATCAA
1 CATTTAATCAACAATTGGACA-ACATTAAATCAA
*
54844537 TATTT
1 CATTT
54844542 GGACAGCATT
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
33 33 0.97
34 1 0.03
ACGTcount: A:0.44, C:0.17, G:0.07, T:0.32
Consensus pattern (33 bp):
CATTTAATCAACAATTGGACAACATTAAATCAA
Found at i:54844516 original size:77 final size:77
Alignment explanation
Indices: 54844411--54844573 Score: 238
Period size: 77 Copynumber: 2.1 Consensus size: 77
54844401 CCAACATTCA
* * *
54844411 GACAGCATTTAATTAACATTTAACCAACAATTGGACAGCAA-TCAATCAACATTTGGACAGCATT
1 GACAACATTAAATCAACATTTAACCAACAATTGGACAG-AATTCAATCAACATTTGGACAGCATT
*
54844475 TAATCAACAATTG
65 AAATCAACAATTG
* * *
54844488 GACAACATTAAATCAACATTTAATCAACATTTGGACAGAATTCAATCAATATTTGGACAGCATTA
1 GACAACATTAAATCAACATTTAACCAACAATTGGACAGAATTCAATCAACATTTGGACAGCATTA
*
54844553 AATCAACATTTG
66 AATCAACAATTG
54844565 GACAACATT
1 GACAACATT
54844574 CAATTAAGCC
Statistics
Matches: 77, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
76 2 0.03
77 75 0.97
ACGTcount: A:0.42, C:0.18, G:0.11, T:0.28
Consensus pattern (77 bp):
GACAACATTAAATCAACATTTAACCAACAATTGGACAGAATTCAATCAACATTTGGACAGCATTA
AATCAACAATTG
Found at i:54844519 original size:11 final size:11
Alignment explanation
Indices: 54844471--54844519 Score: 55
Period size: 11 Copynumber: 4.5 Consensus size: 11
54844461 ATTTGGACAG
54844471 CATTTAATCAA
1 CATTTAATCAA
**
54844482 CAATTGGA-CAA
1 C-ATTTAATCAA
*
54844493 CATTAAATCAA
1 CATTTAATCAA
54844504 CATTTAATCAA
1 CATTTAATCAA
54844515 CATTT
1 CATTT
54844520 GGACAGAATT
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
10 4 0.13
11 23 0.74
12 4 0.13
ACGTcount: A:0.45, C:0.18, G:0.04, T:0.33
Consensus pattern (11 bp):
CATTTAATCAA
Found at i:54844534 original size:22 final size:22
Alignment explanation
Indices: 54844509--54844577 Score: 95
Period size: 22 Copynumber: 3.1 Consensus size: 22
54844499 ATCAACATTT
54844509 AATCAACATTTGGACAGAATTC
1 AATCAACATTTGGACAGAATTC
* * *
54844531 AATCAATATTTGGACAGCATTA
1 AATCAACATTTGGACAGAATTC
54844553 AATCAACATTTGGACA-ACATTC
1 AATCAACATTTGGACAGA-ATTC
54844575 AAT
1 AAT
54844578 TAAGCCAAAT
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
22 40 1.00
ACGTcount: A:0.42, C:0.17, G:0.12, T:0.29
Consensus pattern (22 bp):
AATCAACATTTGGACAGAATTC
Found at i:54844573 original size:55 final size:55
Alignment explanation
Indices: 54844454--54844563 Score: 175
Period size: 55 Copynumber: 2.0 Consensus size: 55
54844444 GACAGCAATC
* *
54844454 AATCAACATTTGGACAGCATTTAATCAACAATTGGACAACATTAAATCAACATTT
1 AATCAACATTTGGACAGAATTCAATCAACAATTGGACAACATTAAATCAACATTT
* * *
54844509 AATCAACATTTGGACAGAATTCAATCAATATTTGGACAGCATTAAATCAACATTT
1 AATCAACATTTGGACAGAATTCAATCAACAATTGGACAACATTAAATCAACATTT
54844564 GGACAACATT
Statistics
Matches: 50, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
55 50 1.00
ACGTcount: A:0.43, C:0.17, G:0.10, T:0.30
Consensus pattern (55 bp):
AATCAACATTTGGACAGAATTCAATCAACAATTGGACAACATTAAATCAACATTT
Found at i:54848299 original size:15 final size:15
Alignment explanation
Indices: 54848274--54848308 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
54848264 AACTCTATTT
*
54848274 TAATT-ATATTAGGA
1 TAATTAATATTAAGA
54848288 TAATTAATATTAAGA
1 TAATTAATATTAAGA
54848303 TAATTA
1 TAATTA
54848309 TTAATGGTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 5 0.26
15 14 0.74
ACGTcount: A:0.49, C:0.00, G:0.09, T:0.43
Consensus pattern (15 bp):
TAATTAATATTAAGA
Found at i:54851290 original size:10 final size:9
Alignment explanation
Indices: 54851273--54851309 Score: 56
Period size: 10 Copynumber: 3.9 Consensus size: 9
54851263 AACCTAATTT
54851273 TTATTTTTA
1 TTATTTTTA
54851282 TTCATTTTTA
1 TT-ATTTTTA
54851292 TTATTTATTA
1 TTATTT-TTA
54851302 TTATTTTT
1 TTATTTTT
54851310 CTTTACTTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
9 8 0.31
10 18 0.69
ACGTcount: A:0.22, C:0.03, G:0.00, T:0.76
Consensus pattern (9 bp):
TTATTTTTA
Found at i:54851290 original size:16 final size:17
Alignment explanation
Indices: 54851269--54851300 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
54851259 AGGCAACCTA
54851269 ATTTTTATT-TTTATTC
1 ATTTTTATTATTTATTC
54851285 ATTTTTATTATTTATT
1 ATTTTTATTATTTATT
54851301 ATTATTTTTC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.22, C:0.03, G:0.00, T:0.75
Consensus pattern (17 bp):
ATTTTTATTATTTATTC
Found at i:54851309 original size:20 final size:20
Alignment explanation
Indices: 54851272--54851328 Score: 66
Period size: 20 Copynumber: 2.9 Consensus size: 20
54851262 CAACCTAATT
54851272 TTTATTT-TTATTCATTTTT-
1 TTTATTTATTATT-ATTTTTC
*
54851291 ATTATTTATTATTATTTTTC
1 TTTATTTATTATTATTTTTC
54851311 TTTACTTTATT-TTATTTT
1 TTTA-TTTATTATTATTTT
54851329 ATGATTTATT
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
19 12 0.36
20 15 0.45
21 6 0.18
ACGTcount: A:0.19, C:0.05, G:0.00, T:0.75
Consensus pattern (20 bp):
TTTATTTATTATTATTTTTC
Found at i:54852366 original size:101 final size:101
Alignment explanation
Indices: 54852174--54852367 Score: 227
Period size: 101 Copynumber: 1.9 Consensus size: 101
54852164 TTTAAGAACA
*
54852174 TGTTGGGCTGAGTAACCGGGGTAGGGTGCTTGGGTTGTCATCTTATTTCGCGTCAAAAGGTTCGA
1 TGTTGGGCTGAGTAACCGGGGTAGGGTGCTTGGGTTGTCATCTTACTTCGCGTCAAAAGGTTCGA
* * * *
54852239 TGTGTTCTTAAGAAAAATTATAATAAATTAGGAGTC
66 TATGTCCTAAAGAAAAATAATAATAAATTAGGAGTC
* * * *
54852275 TGTTGGGTTGAGTAACTGGGGTGGGGTGCTT-GGTTGTTATCTCT-CTTCGCGTCAAAAGGTTCA
1 TGTTGGGCTGAGTAACCGGGGTAGGGTGCTTGGGTTGTCATCT-TACTTCGCGTCAAAAGGTTC-
54852338 GTATAT-TCCTAAAGTATAAAA-AAT-ATAAAT
64 G-ATATGTCCTAAAG-A-AAAATAATAATAAAT
54852368 AAATAATAAA
Statistics
Matches: 79, Mismatches: 9, Indels: 10
0.81 0.09 0.10
Matches are distributed among these distances:
100 27 0.34
101 42 0.53
102 6 0.08
103 4 0.05
ACGTcount: A:0.26, C:0.12, G:0.27, T:0.35
Consensus pattern (101 bp):
TGTTGGGCTGAGTAACCGGGGTAGGGTGCTTGGGTTGTCATCTTACTTCGCGTCAAAAGGTTCGA
TATGTCCTAAAGAAAAATAATAATAAATTAGGAGTC
Found at i:54854955 original size:15 final size:15
Alignment explanation
Indices: 54854935--54854974 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
54854925 AAATTCGCCC
54854935 TGATATGTTCGCCAG
1 TGATATGTTCGCCAG
* *
54854950 TGATATGTTTGCTAG
1 TGATATGTTCGCCAG
*
54854965 TGATGTGTTC
1 TGATATGTTC
54854975 AAGAAGAACA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.17, C:0.12, G:0.28, T:0.42
Consensus pattern (15 bp):
TGATATGTTCGCCAG
Found at i:54860639 original size:3 final size:3
Alignment explanation
Indices: 54860631--54860680 Score: 100
Period size: 3 Copynumber: 16.7 Consensus size: 3
54860621 ATCACATGTT
54860631 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
54860679 TT
1 TT
54860681 TGGATGTAAT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:54860763 original size:73 final size:73
Alignment explanation
Indices: 54860681--54860866 Score: 345
Period size: 73 Copynumber: 2.5 Consensus size: 73
54860671 TATTATTATT
*
54860681 TGGATGTAATGATGTAACTTAGTTGTATTCCAACTAAGTTTGTTAGTGGTAGTAAGTGGTGATTT
1 TGGATGTAATGATGAAACTTAGTTGTATTCCAACTAAGTTTGTTAGTGGTAGTAAGTGGTGATTT
54860746 ATTTTAAG
66 ATTTTAAG
54860754 TGGATGTAATGATGAAACTTAGTTGTATTCCAACTAAGTTTGTTAGTGGTAGTAAGTGGTGATTT
1 TGGATGTAATGATGAAACTTAGTTGTATTCCAACTAAGTTTGTTAGTGGTAGTAAGTGGTGATTT
54860819 ATTTTAAG
66 ATTTTAAG
* *
54860827 TGGATGTAATGTTGAAATTTAGTTGTATTCCAACTAAGTT
1 TGGATGTAATGATGAAACTTAGTTGTATTCCAACTAAGTT
54860867 GTCAAGTTGT
Statistics
Matches: 110, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
73 110 1.00
ACGTcount: A:0.28, C:0.06, G:0.24, T:0.42
Consensus pattern (73 bp):
TGGATGTAATGATGAAACTTAGTTGTATTCCAACTAAGTTTGTTAGTGGTAGTAAGTGGTGATTT
ATTTTAAG
Found at i:54865091 original size:3 final size:3
Alignment explanation
Indices: 54865083--54865120 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
54865073 ATCACATGTT
54865083 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
54865121 TGGATGTAAT
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:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:54865943 original size:27 final size:26
Alignment explanation
Indices: 54865882--54865932 Score: 93
Period size: 26 Copynumber: 2.0 Consensus size: 26
54865872 GAATCAGTAC
*
54865882 CGTATTAATCGGTTGAACTAAAAATT
1 CGTATTAATCGGTTCAACTAAAAATT
54865908 CGTATTAATCGGTTCAACTAAAAAT
1 CGTATTAATCGGTTCAACTAAAAAT
54865933 CGGTAATTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.39, C:0.14, G:0.14, T:0.33
Consensus pattern (26 bp):
CGTATTAATCGGTTCAACTAAAAATT
Found at i:54877313 original size:58 final size:59
Alignment explanation
Indices: 54877223--54877337 Score: 223
Period size: 58 Copynumber: 2.0 Consensus size: 59
54877213 TATGCAATAA
54877223 GATACCTTATTGTTATAATACCGAATCTGATCCTATTACATTTGAAGAAGCA-TGAATT
1 GATACCTTATTGTTATAATACCGAATCTGATCCTATTACATTTGAAGAAGCAGTGAATT
54877281 GATACCTTATTGTTATAATACCGAATCTGATCCTATTACATTTGAAGAAGCAGTGAA
1 GATACCTTATTGTTATAATACCGAATCTGATCCTATTACATTTGAAGAAGCAGTGAA
54877338 ATCTCAAGAC
Statistics
Matches: 56, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
58 52 0.93
59 4 0.07
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.35
Consensus pattern (59 bp):
GATACCTTATTGTTATAATACCGAATCTGATCCTATTACATTTGAAGAAGCAGTGAATT
Found at i:54883840 original size:26 final size:26
Alignment explanation
Indices: 54883809--54883858 Score: 91
Period size: 26 Copynumber: 1.9 Consensus size: 26
54883799 TAACTTTGAG
*
54883809 ACACTTTTTTTTCTTCTCCATTTTGC
1 ACACTTTTTTTTCATCTCCATTTTGC
54883835 ACACTTTTTTTTCATCTCCATTTT
1 ACACTTTTTTTTCATCTCCATTTT
54883859 ACAGTACGAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.14, C:0.26, G:0.02, T:0.58
Consensus pattern (26 bp):
ACACTTTTTTTTCATCTCCATTTTGC
Found at i:54887984 original size:41 final size:41
Alignment explanation
Indices: 54887929--54888033 Score: 147
Period size: 41 Copynumber: 2.5 Consensus size: 41
54887919 TTAATTTAAA
* * * *
54887929 CAGATTCACTGGCACTTAGCTTGTTAGGCTTAAAGCCTGATT
1 CAGA-TCACCGGCACTTAGCCTGCTAGACTTAAAGCCTGATT
*
54887971 CAGATCACCGGCACTTAGCCTGCTAGACTTATAGCCTGATT
1 CAGATCACCGGCACTTAGCCTGCTAGACTTAAAGCCTGATT
*
54888012 TAGATCACCGGCACTTAGCCTG
1 CAGATCACCGGCACTTAGCCTG
54888034 TAACAGCCCG
Statistics
Matches: 57, Mismatches: 6, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
41 53 0.93
42 4 0.07
ACGTcount: A:0.24, C:0.27, G:0.21, T:0.29
Consensus pattern (41 bp):
CAGATCACCGGCACTTAGCCTGCTAGACTTAAAGCCTGATT
Found at i:54890566 original size:38 final size:39
Alignment explanation
Indices: 54890512--54890594 Score: 105
Period size: 39 Copynumber: 2.2 Consensus size: 39
54890502 ATTTGCCGGC
* *
54890512 TTACTGATTAGGCAC-TTATGTGCCGACTACTATTACTG
1 TTACTGATTAGACACTTTATGTGCCGAATACTATTACTG
* * * *
54890550 TTACTGATTCGACACTTTGTGTGTCGAATACTGTTACTG
1 TTACTGATTAGACACTTTATGTGCCGAATACTATTACTG
54890589 TTACTG
1 TTACTG
54890595 TTACCGACTC
Statistics
Matches: 38, Mismatches: 6, Indels: 1
0.84 0.13 0.02
Matches are distributed among these distances:
38 13 0.34
39 25 0.66
ACGTcount: A:0.22, C:0.19, G:0.19, T:0.40
Consensus pattern (39 bp):
TTACTGATTAGACACTTTATGTGCCGAATACTATTACTG
Found at i:54890611 original size:45 final size:45
Alignment explanation
Indices: 54890539--54890723 Score: 289
Period size: 45 Copynumber: 4.1 Consensus size: 45
54890529 ATGTGCCGAC
* * * *
54890539 TACTATTACTGTTACTGATTCGACACTTTGTGTGTCGAATACTGT
1 TACTGTTACTGTTACCGACTCGGCACTTTGTGTGTCGAATACTGT
54890584 TACTGTTACTGTTACCGACTCGGCACTTTGTGTGTCGAATACTGT
1 TACTGTTACTGTTACCGACTCGGCACTTTGTGTGTCGAATACTGT
54890629 TACTGTTACTGTTACCGACTCGGCACTTTGTGTGTCGAATACTGT
1 TACTGTTACTGTTACCGACTCGGCACTTTGTGTGTCGAATACTGT
* * * * *
54890674 TACCGTTACTGTTACAGATTCAGCACTTTGTGTGTTGAATACTGT
1 TACTGTTACTGTTACCGACTCGGCACTTTGTGTGTCGAATACTGT
54890719 TACTG
1 TACTG
54890724 CTACCATTAC
Statistics
Matches: 130, Mismatches: 10, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 130 1.00
ACGTcount: A:0.20, C:0.20, G:0.21, T:0.39
Consensus pattern (45 bp):
TACTGTTACTGTTACCGACTCGGCACTTTGTGTGTCGAATACTGT
Found at i:54890627 original size:39 final size:39
Alignment explanation
Indices: 54890522--54890728 Score: 137
Period size: 45 Copynumber: 4.9 Consensus size: 39
54890512 TTACTGATTA
* * * * * *
54890522 GGCAC-TTATGTGCCGACTACTATTACTGTTACTGATTC
1 GGCACTTTGTGTGTCGAATACTGTTACTGTTACCGACTC
*
54890560 GACACTTTGTGTGTCGAATACTGTTACTGTTACTGTTACCGACTC
1 GGCACTTTGTGTGTCG-A-A----TACTGTTACTGTTACCGACTC
54890605 GGCACTTTGTGTGTCGAATACTGTTACTGTTACTGTTACCGACTC
1 GGCACTTTGTGTGTCG-A-A----TACTGTTACTGTTACCGACTC
* *
54890650 GGCACTTTGTGTGTCGAATACTGTTACCGTTACTGTTACAGATTC
1 GGCACTTTGTGTGTCGAATAC---T---GTTACTGTTACCGACTC
* * *
54890695 AGCACTTTGTGTGTTGAATACTGTTACTGCTACC
1 GGCACTTTGTGTGTCGAATACTGTTACTGTTACC
54890729 ATTACTGATT
Statistics
Matches: 142, Mismatches: 14, Indels: 25
0.78 0.08 0.14
Matches are distributed among these distances:
38 4 0.03
39 21 0.15
40 1 0.01
42 2 0.01
43 1 0.01
44 1 0.01
45 112 0.79
ACGTcount: A:0.20, C:0.22, G:0.21, T:0.38
Consensus pattern (39 bp):
GGCACTTTGTGTGTCGAATACTGTTACTGTTACCGACTC
Found at i:54891402 original size:41 final size:41
Alignment explanation
Indices: 54891345--54891438 Score: 179
Period size: 41 Copynumber: 2.3 Consensus size: 41
54891335 GGGTGTTACA
*
54891345 TAGCCTGCTAGGCTTATAGCCTGATTCAGTTCACCGGCACT
1 TAGCCTGCTAGGCTTATAGCCTAATTCAGTTCACCGGCACT
54891386 TAGCCTGCTAGGCTTATAGCCTAATTCAGTTCACCGGCACT
1 TAGCCTGCTAGGCTTATAGCCTAATTCAGTTCACCGGCACT
54891427 TAGCCTGCTAGG
1 TAGCCTGCTAGG
54891439 TTTTAAAACC
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.20, C:0.29, G:0.22, T:0.29
Consensus pattern (41 bp):
TAGCCTGCTAGGCTTATAGCCTAATTCAGTTCACCGGCACT
Found at i:54893269 original size:24 final size:23
Alignment explanation
Indices: 54893220--54893273 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 23
54893210 GTTTGTCTTT
*
54893220 TAATATATATTAACTTTATAATA
1 TAATATATATTAACTTTATAACA
*
54893243 TAATATATTGTTAACCTTTAT-ACA
1 TAATATA-TATTAA-CTTTATAACA
54893267 TAATATA
1 TAATATA
54893274 AAAACTATAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
23 7 0.26
24 14 0.52
25 6 0.22
ACGTcount: A:0.44, C:0.07, G:0.02, T:0.46
Consensus pattern (23 bp):
TAATATATATTAACTTTATAACA
Found at i:54898920 original size:40 final size:40
Alignment explanation
Indices: 54898865--54898986 Score: 219
Period size: 40 Copynumber: 3.1 Consensus size: 40
54898855 AAAAGAGTCG
54898865 GAGTAGCATAGTAGTTAAATAGTTTGTATGGTTGGAGAAT
1 GAGTAGCATAGTAGTTAAATAGTTTGTATGGTTGGAGAAT
*
54898905 GAGTAGTATAGTAGTTAAATAGTTTGTATGGTTGGAGAAT
1 GAGTAGCATAGTAGTTAAATAGTTTGTATGGTTGGAGAAT
*
54898945 GAGTAGCATAGTGGTTAAATAGTTTGTATGGTTGGAG-AT
1 GAGTAGCATAGTAGTTAAATAGTTTGTATGGTTGGAGAAT
54898984 GAG
1 GAG
54898987 GCAGATATCT
Statistics
Matches: 79, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
39 5 0.06
40 74 0.94
ACGTcount: A:0.31, C:0.02, G:0.32, T:0.35
Consensus pattern (40 bp):
GAGTAGCATAGTAGTTAAATAGTTTGTATGGTTGGAGAAT
Found at i:54899373 original size:24 final size:24
Alignment explanation
Indices: 54899326--54899373 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
54899316 TTTATTTTGA
**
54899326 AAAAAAAACAAAAATTAGTTGTCG
1 AAAAAAAACAAAAATTAGGAGTCG
*
54899350 AAAAAAAACAAAAATTGGGAGTCG
1 AAAAAAAACAAAAATTAGGAGTCG
54899374 CCACCAATCT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.58, C:0.08, G:0.17, T:0.17
Consensus pattern (24 bp):
AAAAAAAACAAAAATTAGGAGTCG
Found at i:54901042 original size:21 final size:21
Alignment explanation
Indices: 54901005--54901059 Score: 78
Period size: 21 Copynumber: 2.7 Consensus size: 21
54900995 AATCATATCT
54901005 TCCAAGATTGC--ATATCATA
1 TCCAAGATTGCATATATCATA
*
54901024 TCCAAGATTGTATATATCATA
1 TCCAAGATTGCATATATCATA
*
54901045 TCTAAGATTGCATAT
1 TCCAAGATTGCATAT
54901060 CCTTAAAGAT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
19 10 0.32
21 21 0.68
ACGTcount: A:0.36, C:0.16, G:0.11, T:0.36
Consensus pattern (21 bp):
TCCAAGATTGCATATATCATA
Found at i:54901510 original size:20 final size:19
Alignment explanation
Indices: 54901471--54901510 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
54901461 ATTAAATTTG
**
54901471 TTTAAATAAAAATATTAAA
1 TTTAAATAAAAATAGAAAA
54901490 TTTAAATTAAAAATAGAAAA
1 TTTAAA-TAAAAATAGAAAA
54901510 T
1 T
54901511 CATAATAATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 6 0.33
20 12 0.67
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (19 bp):
TTTAAATAAAAATAGAAAA
Found at i:54901822 original size:19 final size:19
Alignment explanation
Indices: 54901796--54901837 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 19
54901786 TAAAAGAATT
* *
54901796 AATTTTTAAT-ATCTTTAC
1 AATTTTTTATAATATTTAC
54901814 AATTTTTTATAATATTTAC
1 AATTTTTTATAATATTTAC
54901833 AATTT
1 AATTT
54901838 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:54901849 original size:19 final size:19
Alignment explanation
Indices: 54901796--54901837 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 19
54901786 TAAAAGAATT
* *
54901796 AATTTTTAATATC-TTTAC
1 AATTTTTTATAACATTTAC
*
54901814 AATTTTTTATAATATTTAC
1 AATTTTTTATAACATTTAC
54901833 AATTT
1 AATTT
54901838 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:54903108 original size:23 final size:24
Alignment explanation
Indices: 54903071--54903116 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 24
54903061 TTCAATATTT
*
54903071 AATTTGGTACCTGAGTTT-TTTTC
1 AATTTGATACCTGAGTTTGTTTTC
*
54903094 AATTTGATACTTGAGTTTGTTTT
1 AATTTGATACCTGAGTTTGTTTT
54903117 AACCCAAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 16 0.80
24 4 0.20
ACGTcount: A:0.20, C:0.09, G:0.17, T:0.54
Consensus pattern (24 bp):
AATTTGATACCTGAGTTTGTTTTC
Found at i:54909990 original size:12 final size:12
Alignment explanation
Indices: 54909970--54910019 Score: 57
Period size: 12 Copynumber: 4.1 Consensus size: 12
54909960 AATTGATGAT
54909970 ACATATATATAA
1 ACATATATATAA
*
54909982 ACATGTATAT-A
1 ACATATATATAA
*
54909993 ACATACATATATAT
1 ACAT--ATATATAA
54910007 ACATATATATAA
1 ACATATATATAA
54910019 A
1 A
54910020 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:54918918 original size:24 final size:24
Alignment explanation
Indices: 54918891--54918939 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
54918881 GAACTGCTCT
54918891 TGAATTTATGGACAAGACTATGTA
1 TGAATTTATGGACAAGACTATGTA
*
54918915 TGAATTTTTGGACAAGACTATGTA
1 TGAATTTATGGACAAGACTATGTA
54918939 T
1 T
54918940 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:54933335 original size:15 final size:15
Alignment explanation
Indices: 54933280--54933336 Score: 60
Period size: 15 Copynumber: 3.5 Consensus size: 15
54933270 TTTATACTAC
54933280 AAAATATTTATTATT
1 AAAATATTTATTATT
* *
54933295 AACATATTTATAATTGT
1 AAAATATTTATTA-T-T
54933312 AATAAATATTTATTATT
1 -A-AAATATTTATTATT
54933329 AAAATATT
1 AAAATATT
54933337 AATATTGAAT
Statistics
Matches: 34, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
15 18 0.53
16 2 0.06
17 2 0.06
18 2 0.06
19 10 0.29
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (15 bp):
AAAATATTTATTATT
Found at i:54933468 original size:12 final size:13
Alignment explanation
Indices: 54933435--54933471 Score: 51
Period size: 12 Copynumber: 2.9 Consensus size: 13
54933425 AAAACAATAA
54933435 ATTATATTAATTAT
1 ATTATA-TAATTAT
54933449 ATTA-ATAATT-T
1 ATTATATAATTAT
54933460 ATTATATAATTA
1 ATTATATAATTA
54933472 AATATAAACA
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
11 5 0.24
12 11 0.52
13 1 0.05
14 4 0.19
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (13 bp):
ATTATATAATTAT
Done.