Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr12 103066607
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: 103066607
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Warning! 238 characters in sequence are not A, C, G, or T
File 111 of 345
Found at i:29905388 original size:37 final size:36
Alignment explanation
Indices: 29905337--29905439 Score: 93
Period size: 37 Copynumber: 2.7 Consensus size: 36
29905327 CCAATTAACT
*
29905337 ATTTCAAAAATAATATTATTTTAATAG-ATTTAATATTTA
1 ATTT-AAAATTAATATTATTTTAATAGTATTT--TA-TTA
*
29905376 A-TTAAAATTAATATTTATGTTAATAGTATTTTATTA
1 ATTTAAAATTAATA-TTATTTTAATAGTATTTTATTA
*
29905412 ATTTAATATTAAAGTAATTATTTTAATA
1 ATTTAAAATT-AA-T-ATTATTTTAATA
29905440 TTAAATTTAA
Statistics
Matches: 54, Mismatches: 4, Indels: 12
0.77 0.06 0.17
Matches are distributed among these distances:
36 4 0.07
37 18 0.33
38 15 0.28
39 16 0.30
40 1 0.02
ACGTcount: A:0.45, C:0.01, G:0.04, T:0.50
Consensus pattern (36 bp):
ATTTAAAATTAATATTATTTTAATAGTATTTTATTA
Found at i:29905421 original size:16 final size:16
Alignment explanation
Indices: 29905353--29905421 Score: 52
Period size: 17 Copynumber: 4.2 Consensus size: 16
29905343 AAAATAATAT
*
29905353 TATTTTAATAGATTTAA
1 TATTTTATTA-ATTTAA
* *
29905370 TATTTAATTAAAATTAA
1 TATTTTATT-AATTTAA
* *
29905387 TATTTATGTTAA--TAG
1 TATTT-TATTAATTTAA
29905402 TATTTTATTAATTTAA
1 TATTTTATTAATTTAA
29905418 TATT
1 TATT
29905422 AAAGTAATTA
Statistics
Matches: 40, Mismatches: 8, Indels: 9
0.70 0.14 0.16
Matches are distributed among these distances:
14 5 0.12
15 7 0.17
16 6 0.15
17 19 0.47
18 3 0.08
ACGTcount: A:0.41, C:0.00, G:0.04, T:0.55
Consensus pattern (16 bp):
TATTTTATTAATTTAA
Found at i:29905456 original size:68 final size:70
Alignment explanation
Indices: 29905365--29905503 Score: 174
Period size: 72 Copynumber: 2.0 Consensus size: 70
29905355 TTTTAATAGA
* * * * *
29905365 TTTAATATTTAATTAAAATTAATATTTA-TGT-TAATAGTATTTTATTAATTTAATATTAAAGTA
1 TTTAATATTAAATTAAAATTAATATTTATTGTAGAAAAATATTCTATTAATTTAATATTAAAGTA
29905428 ATTAT
66 ATTAT
* *
29905433 TTTAATATTAAATTTAATTTAATATTTATCTTGTAGAAAAATATTCTATTAATTTAATATTAAAG
1 TTTAATATTAAATTAAAATTAATATTTA--TTGTAGAAAAATATTCTATTAATTTAATATTAAAG
*
29905498 TGATTA
64 TAATTA
29905504 CGTTTAATTA
Statistics
Matches: 59, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
68 25 0.42
71 3 0.05
72 31 0.53
ACGTcount: A:0.42, C:0.01, G:0.05, T:0.51
Consensus pattern (70 bp):
TTTAATATTAAATTAAAATTAATATTTATTGTAGAAAAATATTCTATTAATTTAATATTAAAGTA
ATTAT
Found at i:29906633 original size:25 final size:25
Alignment explanation
Indices: 29906605--29906656 Score: 68
Period size: 25 Copynumber: 2.1 Consensus size: 25
29906595 TTTGGCTTGA
**
29906605 CATTTACTAAGCAATATCGGATATT
1 CATTTACTAAGCAATATCAAATATT
* *
29906630 CATTTATTAGGCAATATCAAATATT
1 CATTTACTAAGCAATATCAAATATT
29906655 CA
1 CA
29906657 AATTATTCTT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.38, C:0.15, G:0.10, T:0.37
Consensus pattern (25 bp):
CATTTACTAAGCAATATCAAATATT
Found at i:29908655 original size:22 final size:22
Alignment explanation
Indices: 29908630--29908674 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
29908620 CGACTGATTT
29908630 TCAAAGTATGCGACCTTCATTC
1 TCAAAGTATGCGACCTTCATTC
29908652 TCAAAGTATGCGACCTTCATTC
1 TCAAAGTATGCGACCTTCATTC
29908674 T
1 T
29908675 TGCCATGAAC
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:0.27, C:0.27, G:0.13, T:0.33
Consensus pattern (22 bp):
TCAAAGTATGCGACCTTCATTC
Found at i:29911002 original size:23 final size:23
Alignment explanation
Indices: 29910976--29911019 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
29910966 TAAATTTTGA
*
29910976 ATTATTTAATGATAATATTTAAG
1 ATTATTCAATGATAATATTTAAG
*
29910999 ATTATTCAGTGATAATATTTA
1 ATTATTCAATGATAATATTTA
29911020 GGAAAAATCT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.41, C:0.02, G:0.09, T:0.48
Consensus pattern (23 bp):
ATTATTCAATGATAATATTTAAG
Found at i:29920660 original size:31 final size:31
Alignment explanation
Indices: 29920624--29920704 Score: 76
Period size: 31 Copynumber: 2.6 Consensus size: 31
29920614 AATGTGTATG
29920624 ATTAAATAAAAATTAAAATTTCAAGTATATA
1 ATTAAATAAAAATTAAAATTTCAAGTATATA
* * * * *
29920655 TTTAAACTATAAA-TATAATTTTACGTATATA
1 ATTAAA-TAAAAATTAAAATTTCAAGTATATA
* *
29920686 ATTATAT-CAAATTAAAATT
1 ATTAAATAAAAATTAAAATT
29920705 CATATATACT
Statistics
Matches: 39, Mismatches: 9, Indels: 5
0.74 0.17 0.09
Matches are distributed among these distances:
29 3 0.08
30 7 0.18
31 24 0.62
32 5 0.13
ACGTcount: A:0.52, C:0.05, G:0.02, T:0.41
Consensus pattern (31 bp):
ATTAAATAAAAATTAAAATTTCAAGTATATA
Found at i:29920941 original size:23 final size:23
Alignment explanation
Indices: 29920914--29920961 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
29920904 ATCTTTCTAC
29920914 ATTCTTATATTAAATCAATAAAA
1 ATTCTTATATTAAATCAATAAAA
29920937 ATTCTTATATTAAATCAATAAAA
1 ATTCTTATATTAAATCAATAAAA
29920960 AT
1 AT
29920962 CCATATATAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.52, C:0.08, G:0.00, T:0.40
Consensus pattern (23 bp):
ATTCTTATATTAAATCAATAAAA
Found at i:29920968 original size:23 final size:23
Alignment explanation
Indices: 29920919--29920969 Score: 84
Period size: 23 Copynumber: 2.2 Consensus size: 23
29920909 TCTACATTCT
* *
29920919 TATATTAAATCAATAAAAATTCT
1 TATATTAAATCAATAAAAATCCA
29920942 TATATTAAATCAATAAAAATCCA
1 TATATTAAATCAATAAAAATCCA
29920965 TATAT
1 TATAT
29920970 AATAAAACTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.53, C:0.10, G:0.00, T:0.37
Consensus pattern (23 bp):
TATATTAAATCAATAAAAATCCA
Found at i:29928871 original size:13 final size:15
Alignment explanation
Indices: 29928842--29928878 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
29928832 TTTTAATTTC
29928842 AATATTATTTATATT
1 AATATTATTTATATT
29928857 AATA-TATTT-TATT
1 AATATTATTTATATT
*
29928870 AATGTTATT
1 AATATTATT
29928879 ATTATATTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
13 7 0.35
14 9 0.45
15 4 0.20
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (15 bp):
AATATTATTTATATT
Found at i:29941095 original size:5 final size:5
Alignment explanation
Indices: 29941074--29941126 Score: 61
Period size: 5 Copynumber: 10.0 Consensus size: 5
29941064 TGTTAAAATA
* *
29941074 TATAT TAAAT TATTAT TATAT TATAG TATAT TATATT ATATAT TATAT
1 TATAT TATAT TA-TAT TATAT TATAT TATAT TATA-T -TATAT TATAT
29941122 TATAT
1 TATAT
29941127 AAATAAGTAA
Statistics
Matches: 41, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
5 31 0.76
6 6 0.15
7 4 0.10
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.57
Consensus pattern (5 bp):
TATAT
Found at i:29941105 original size:10 final size:9
Alignment explanation
Indices: 29941071--29941127 Score: 59
Period size: 8 Copynumber: 6.6 Consensus size: 9
29941061 ATGTGTTAAA
29941071 ATATATATT
1 ATATATATT
*
29941080 AAAT-TATT
1 ATATATATT
29941088 AT-TATATT
1 ATATATATT
29941096 ATAGTATATT
1 ATA-TATATT
29941106 ATAT-TA-T
1 ATATATATT
29941113 ATATTATATT
1 ATA-TATATT
29941123 ATATA
1 ATATA
29941128 AATAAGTAAA
Statistics
Matches: 40, Mismatches: 2, Indels: 12
0.74 0.04 0.22
Matches are distributed among these distances:
7 5 0.12
8 14 0.35
9 8 0.20
10 13 0.32
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (9 bp):
ATATATATT
Found at i:29941117 original size:12 final size:12
Alignment explanation
Indices: 29941072--29941127 Score: 69
Period size: 12 Copynumber: 4.5 Consensus size: 12
29941062 TGTGTTAAAA
*
29941072 TATATATTAAAT
1 TATATATTATAT
29941084 TAT-TATTATATT
1 TATATATTATA-T
29941096 ATAGTATATTATAT
1 -TA-TATATTATAT
29941110 TATATATTATAT
1 TATATATTATAT
29941122 TATATA
1 TATATA
29941128 AATAAGTAAA
Statistics
Matches: 39, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
11 6 0.15
12 20 0.51
13 4 0.10
14 2 0.05
15 7 0.18
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (12 bp):
TATATATTATAT
Found at i:29943717 original size:46 final size:44
Alignment explanation
Indices: 29943658--29943772 Score: 149
Period size: 44 Copynumber: 2.6 Consensus size: 44
29943648 ACAGGACAGA
* *
29943658 ACAGAAATGAGCCATGTAAGTCCATATTAGAAATATGGCTTTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATT--AAATATGGCATTGGAG
* *
29943704 ACAGGATTGAGCCATGTAAGTCCATATTATATATGGCATTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATTAAATATGGCATTGGAG
* **
29943748 ACAGGAATAATTCATGTAAGTCCAT
1 ACAGGAATGAGCCATGTAAGTCCAT
29943773 GTCAAAGACA
Statistics
Matches: 61, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
44 35 0.57
46 26 0.43
ACGTcount: A:0.36, C:0.14, G:0.23, T:0.28
Consensus pattern (44 bp):
ACAGGAATGAGCCATGTAAGTCCATATTAAATATGGCATTGGAG
Found at i:29943753 original size:44 final size:45
Alignment explanation
Indices: 29943658--29943791 Score: 153
Period size: 46 Copynumber: 3.0 Consensus size: 45
29943648 ACAGGACAGA
* *
29943658 ACAGAAATGAGCCATGTAAGTCCATATTAGAAATATGGCTTTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATTA-AAATATGGCATTGGAG
* *
29943704 ACAGGATTGAGCCATGTAAGTCCATATT-ATATATGGCATTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAG
* ** * * *
29943748 ACAGGAATAATTCATGTAAGTCCATGTCAAAGACATGGCATTGG
1 ACAGGAATGAGCCATGTAAGTCCATATTAAA-ATATGGCATTGG
29943792 CAGGATATTG
Statistics
Matches: 74, Mismatches: 12, Indels: 4
0.82 0.13 0.04
Matches are distributed among these distances:
44 36 0.49
45 1 0.01
46 37 0.50
ACGTcount: A:0.35, C:0.14, G:0.24, T:0.27
Consensus pattern (45 bp):
ACAGGAATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAG
Found at i:29945053 original size:18 final size:19
Alignment explanation
Indices: 29945030--29945068 Score: 62
Period size: 18 Copynumber: 2.1 Consensus size: 19
29945020 CGTTACAGAT
29945030 ATATATATTGAATA-TTGA
1 ATATATATTGAATATTTGA
*
29945048 ATATATATTGATTATTTGA
1 ATATATATTGAATATTTGA
29945067 AT
1 AT
29945069 TGAATTGAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 13 0.68
19 6 0.32
ACGTcount: A:0.41, C:0.00, G:0.10, T:0.49
Consensus pattern (19 bp):
ATATATATTGAATATTTGA
Found at i:29945585 original size:18 final size:19
Alignment explanation
Indices: 29945564--29945604 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
29945554 AATGAAATGA
29945564 GAAATTGA-AT-TGAGAATT
1 GAAATTGAGATATGAG-ATT
29945582 GAAATTGAGATATGAGATT
1 GAAATTGAGATATGAGATT
29945601 GAAA
1 GAAA
29945605 ACATGAACCA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 8 0.38
19 9 0.43
20 4 0.19
ACGTcount: A:0.46, C:0.00, G:0.24, T:0.29
Consensus pattern (19 bp):
GAAATTGAGATATGAGATT
Found at i:29947027 original size:36 final size:36
Alignment explanation
Indices: 29946980--29947051 Score: 135
Period size: 36 Copynumber: 2.0 Consensus size: 36
29946970 ATTTGTAGCC
*
29946980 GTTGAATGCGATCCCTTTCCTCTTTATGATACCTTT
1 GTTGAATGCGATCCCCTTCCTCTTTATGATACCTTT
29947016 GTTGAATGCGATCCCCTTCCTCTTTATGATACCTTT
1 GTTGAATGCGATCCCCTTCCTCTTTATGATACCTTT
29947052 TACTGTTCTT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.17, C:0.26, G:0.14, T:0.43
Consensus pattern (36 bp):
GTTGAATGCGATCCCCTTCCTCTTTATGATACCTTT
Found at i:29947748 original size:87 final size:87
Alignment explanation
Indices: 29947602--29948078 Score: 437
Period size: 87 Copynumber: 5.5 Consensus size: 87
29947592 TTGATGTTCT
* * ** *
29947602 TATTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAGGATACGCTGAGGTATTT
1 TATTTTTCAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAGGGCACGCTGAGGTAATT
*
29947667 TTAATTTCTGTTTTTCAATTTA
66 TTAATTTCTGTTTTTCAATTTC
29947689 TATTTTTCAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAGGGCACGCTGAGG-AATT
1 TATTTTTCAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAGGGCACGCTGAGGTAATT
* * * *
29947753 TTCATTTTTGCTTTTCAATCTC
66 TTAATTTCTGTTTTTCAATTTC
* * * *
29947775 TA-TTTTCAAAAATCAACTCATATTGC-A-AGGTGAGTTGAGCCT-TGGCTCACATGCTGAGG-C
1 TATTTTTCAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAGG-GCAC--GCTGAGGTA
* *
29947835 A---T--TTTCAGTTTTT--ATTTA
63 ATTTTAATTTCTGTTTTTCAATTTC
* * * *
29947853 TACTTTTCAAAAATCAACTCATATTGTGAG-AGATGAGTTGAACCTC-GGGCCACATGCCGAGGT
1 TATTTTTCAAAAATCAACTCATATTGCGAGAAG-TGAGTTGAGCCTCAGGG-CAC--GCTGAGGT
* *
29947916 -ATTTTCAAAATTCTATTTTTCAATTTC
62 AATTTT--AATTTCTGTTTTTCAATTTC
* * * *
29947943 TGTTTCTTCCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCATAAGCTGAGGT
1 TATTT-TT-CAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAGGGC--ACGCTGAGGT
* *
29948008 AATATCAATTTCTGTTTTTCAATTTC
62 AATTTTAATTTCTGTTTTTCAATTTC
** * *
29948034 TGCTTTTCAAAAATCAACTCACATTGCGAGAGGTGAGTTGAGCCT
1 TATTTTTCAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCT
29948079 TGGCTCACGT
Statistics
Matches: 322, Mismatches: 42, Indels: 50
0.78 0.10 0.12
Matches are distributed among these distances:
78 5 0.02
79 23 0.07
80 10 0.03
81 25 0.08
82 3 0.01
83 17 0.05
84 2 0.01
85 32 0.10
86 22 0.07
87 56 0.17
88 8 0.02
89 37 0.11
90 9 0.03
91 24 0.07
92 42 0.13
93 6 0.02
94 1 0.00
ACGTcount: A:0.28, C:0.17, G:0.18, T:0.37
Consensus pattern (87 bp):
TATTTTTCAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAGGGCACGCTGAGGTAATT
TTAATTTCTGTTTTTCAATTTC
Found at i:29948031 original size:14 final size:14
Alignment explanation
Indices: 29948012--29948043 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
29948002 TGAGGTAATA
*
29948012 TCAATTTCTGTTTT
1 TCAATTTCTGCTTT
29948026 TCAATTTCTGCTTT
1 TCAATTTCTGCTTT
29948040 TCAA
1 TCAA
29948044 AAATCAACTC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.19, C:0.19, G:0.06, T:0.56
Consensus pattern (14 bp):
TCAATTTCTGCTTT
Found at i:29948134 original size:163 final size:163
Alignment explanation
Indices: 29947933--29948416 Score: 661
Period size: 177 Copynumber: 2.9 Consensus size: 163
29947923 AAATTCTATT
*
29947933 TTTCAATTTCTGTTTCTTCCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCAT
1 TTTCAATTTCT-ATT-TT-CAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCAT
29947998 AAGCTGAGGTAATATCAATTTCTGTTTTTCAATTTCTGCTTTTCAAAAATCAACTCACATTGCGA
63 AAGCTGAGGTAATATCAATTTCTGTTTTTCAATTTCTGCTTTTCAAAAATCAACTCACATTGCGA
29948063 GAGGTGAGTTGAGCCTTGGCTCACGTGCTGAGCTAC
128 GAGGTGAGTTGAGCCTTGGCTCACGTGCTGAGCTAC
29948099 TTTCAATTTCTATTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCATAAG
1 TTTCAATTTCTATTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCATAAG
29948164 CT-AGGGTAATTTCAATTTCTGTTTTTCAATTTCTGTTTTTCAATTTCTGCTTTTCAAAAATCAA
66 CTGA-GGTAA--T--A----------TCAATTTCTGTTTTTCAATTTCTGCTTTTCAAAAATCAA
*
29948228 CTCACATTGTGAGAGGTGAGTTGAGCCTTGGCTCACGTGCTGAGCTAC
116 CTCACATTGCGAGAGGTGAGTTGAGCCTTGGCTCACGTGCTGAGCTAC
* * * *
29948276 TTTCAATTTCTATTTTCAAAAATCAACTTATATTGCAAGAGGTGAGTTGAGCCTCAGG--ACACG
1 TTTCAATTTCTATTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCATAAG
* * * * * *
29948339 TTGAGGTATTTTCAATTTCTGTTTTTCAATTTAT-ATATTTCAAAAATCAACTCATATTGCGAGA
66 CTGAGGTAATATCAATTTCTGTTTTTCAATTTCTGCT-TTTCAAAAATCAACTCACATTGCGAGA
29948403 GGTGAGTTGAGCCT
130 GGTGAGTTGAGCCT
29948417 CAGGGCACGC
Statistics
Matches: 288, Mismatches: 13, Indels: 39
0.85 0.04 0.11
Matches are distributed among these distances:
160 1 0.00
161 61 0.21
162 1 0.00
163 56 0.19
164 2 0.01
165 3 0.01
166 11 0.04
167 1 0.00
173 1 0.00
175 8 0.03
176 1 0.00
177 142 0.49
ACGTcount: A:0.27, C:0.18, G:0.19, T:0.37
Consensus pattern (163 bp):
TTTCAATTTCTATTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCATAAG
CTGAGGTAATATCAATTTCTGTTTTTCAATTTCTGCTTTTCAAAAATCAACTCACATTGCGAGAG
GTGAGTTGAGCCTTGGCTCACGTGCTGAGCTAC
Found at i:29948177 original size:74 final size:74
Alignment explanation
Indices: 29948024--29948188 Score: 208
Period size: 74 Copynumber: 2.2 Consensus size: 74
29948014 AATTTCTGTT
* * **
29948024 TTTCAATTTCTGCTTTTCAAAAATCAACTCACATTGCGAGAGGTGAGTTGAGCCTTGGCTCACGT
1 TTTCAATTTCT-ATTTTCAAAAATCAACTCACATTGCGAGAGGTGAGTTGAGCCTAGGCTCACAA
*
29948089 GCTGAGCTAC
65 GCTGAGCTAA
* *
29948099 TTTCAATTTCTATTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGG-TCATAA
1 TTTCAATTTCTATTTTCAAAAATCAACTCACATTGCGAGAGGTGAGTTGAGCCT-AGGCTCACAA
*
29948163 GCT-AGGGTAA
65 GCTGA-GCTAA
*
29948173 TTTCAATTTCTGTTTT
1 TTTCAATTTCTATTTT
29948189 TCAATTTCTG
Statistics
Matches: 79, Mismatches: 9, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
73 1 0.01
74 65 0.82
75 13 0.16
ACGTcount: A:0.26, C:0.19, G:0.19, T:0.36
Consensus pattern (74 bp):
TTTCAATTTCTATTTTCAAAAATCAACTCACATTGCGAGAGGTGAGTTGAGCCTAGGCTCACAAG
CTGAGCTAA
Found at i:29948192 original size:14 final size:14
Alignment explanation
Indices: 29948173--29948220 Score: 87
Period size: 14 Copynumber: 3.4 Consensus size: 14
29948163 GCTAGGGTAA
29948173 TTTCAATTTCTGTT
1 TTTCAATTTCTGTT
29948187 TTTCAATTTCTGTT
1 TTTCAATTTCTGTT
*
29948201 TTTCAATTTCTGCT
1 TTTCAATTTCTGTT
29948215 TTTCAA
1 TTTCAA
29948221 AAATCAACTC
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
14 33 1.00
ACGTcount: A:0.17, C:0.17, G:0.06, T:0.60
Consensus pattern (14 bp):
TTTCAATTTCTGTT
Found at i:29948339 original size:74 final size:72
Alignment explanation
Indices: 29948201--29948363 Score: 193
Period size: 74 Copynumber: 2.2 Consensus size: 72
29948191 AATTTCTGTT
* ** * *
29948201 TTTCAATTTCTGCTTTTCAAAAATCAACTCACATTGTGAGAGGTGAGTTGAGCCTTGGCTCACGT
1 TTTCAATTTCT-ATTTTCAAAAATCAACTCACATTGCAAGAGGTGAGTTGAGCCTAGGCACACGT
29948266 GCTGAGCTAC
65 --TGAGCTAC
* *
29948276 TTTCAATTTCTATTTTCAAAAATCAACTTATATTGCAAGAGGTGAGTTGAGCCTCAGG-ACACGT
1 TTTCAATTTCTATTTTCAAAAATCAACTCACATTGCAAGAGGTGAGTTGAGCCT-AGGCACACGT
* *
29948340 TGAGGTAT
65 TGAGCTAC
*
29948348 TTTCAATTTCTGTTTT
1 TTTCAATTTCTATTTT
29948364 TCAATTTATA
Statistics
Matches: 77, Mismatches: 10, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
72 21 0.27
74 43 0.56
75 13 0.17
ACGTcount: A:0.26, C:0.18, G:0.19, T:0.37
Consensus pattern (72 bp):
TTTCAATTTCTATTTTCAAAAATCAACTCACATTGCAAGAGGTGAGTTGAGCCTAGGCACACGTT
GAGCTAC
Found at i:29948435 original size:87 final size:86
Alignment explanation
Indices: 29948276--29948501 Score: 294
Period size: 87 Copynumber: 2.6 Consensus size: 86
29948266 GCTGAGCTAC
* * * *
29948276 TTTCAATTTCTATTTTCAAAAATCAACTTATATTGCAAGAGGTGAGTTGAGCCTCAGGACACGTT
1 TTTCAATTTATATTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCT
** *
29948341 GAGGTATTTTCAATTTCTGTT
66 GAGGTATTTTCAAAATCTGCT
*
29948362 TTTCAATTTATATATTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCACGC
1 TTTCAATTTATAT-TTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGC
29948427 TGCA-GTATTTTCAAAATCTGCT
65 TG-AGGTATTTTCAAAATCTGCT
** * * * *
29948449 TGCCAAATTA-AGTTTCAAAAACCAACTCACATTGCGAGAGGTGAGTTGAGCCT
1 TTTCAATTTATATTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCT
29948502 TGGCTCACGT
Statistics
Matches: 124, Mismatches: 14, Indels: 5
0.87 0.10 0.03
Matches are distributed among these distances:
85 39 0.31
86 13 0.10
87 71 0.57
88 1 0.01
ACGTcount: A:0.30, C:0.18, G:0.19, T:0.34
Consensus pattern (86 bp):
TTTCAATTTATATTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCT
GAGGTATTTTCAAAATCTGCT
Found at i:29949171 original size:27 final size:27
Alignment explanation
Indices: 29949136--29949190 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
29949126 AACCTAAACC
29949136 AACCAAACCCACCTAAACTAAAACCAA
1 AACCAAACCCACCTAAACTAAAACCAA
29949163 AACCAAACCCACCTAAACTAAAACCAA
1 AACCAAACCCACCTAAACTAAAACCAA
29949190 A
1 A
29949191 CCCACTGAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.56, C:0.36, G:0.00, T:0.07
Consensus pattern (27 bp):
AACCAAACCCACCTAAACTAAAACCAA
Found at i:29949201 original size:21 final size:21
Alignment explanation
Indices: 29949156--29949195 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
29949146 ACCTAAACTA
29949156 AAACCAAAACCAAACCCACCT
1 AAACCAAAACCAAACCCACCT
*
29949177 AAACTAAAACCAAACCCAC
1 AAACCAAAACCAAACCCAC
29949196 TGAAACCCTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.55, C:0.40, G:0.00, T:0.05
Consensus pattern (21 bp):
AAACCAAAACCAAACCCACCT
Found at i:29949629 original size:23 final size:21
Alignment explanation
Indices: 29949588--29949659 Score: 65
Period size: 23 Copynumber: 3.2 Consensus size: 21
29949578 ACATAAACAC
* *
29949588 TAAAAAACATTAAAAAAATACA
1 TAAAAAATA-TAAAAAAATAAA
29949610 TAAAAAGATATAAAACAAATAAA
1 TAAAAA-ATATAAAA-AAATAAA
*
29949633 TATAAAAAAATAAAAAAAATAAA
1 TA-AAAAATAT-AAAAAAATAAA
29949656 -AAAA
1 TAAAA
29949660 CTTACCTTTC
Statistics
Matches: 43, Mismatches: 3, Indels: 9
0.78 0.05 0.16
Matches are distributed among these distances:
21 3 0.07
22 12 0.28
23 20 0.47
24 8 0.19
ACGTcount: A:0.78, C:0.04, G:0.01, T:0.17
Consensus pattern (21 bp):
TAAAAAATATAAAAAAATAAA
Found at i:29949643 original size:10 final size:10
Alignment explanation
Indices: 29949588--29949659 Score: 51
Period size: 9 Copynumber: 6.8 Consensus size: 10
29949578 ACATAAACAC
29949588 TAAAAAACAT-
1 TAAAAAA-ATA
29949598 TAAAAAAATACA
1 TAAAAAAAT--A
*
29949610 TAAAAAGATA
1 TAAAAAAATA
29949620 TAAAACAAATAAA
1 TAAAA-AAAT--A
29949633 TATAAAAAA-A
1 TA-AAAAAATA
29949643 TAAAAAAA-A
1 TAAAAAAATA
29949652 TAAAAAAA
1 TAAAAAAA
29949660 CTTACCTTTC
Statistics
Matches: 53, Mismatches: 2, Indels: 15
0.76 0.03 0.21
Matches are distributed among these distances:
9 17 0.32
10 16 0.30
11 3 0.06
12 8 0.15
13 6 0.11
14 3 0.06
ACGTcount: A:0.78, C:0.04, G:0.01, T:0.17
Consensus pattern (10 bp):
TAAAAAAATA
Found at i:29949645 original size:14 final size:15
Alignment explanation
Indices: 29949617--29949646 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
29949607 ACATAAAAAG
29949617 ATATAAAACAAATAA
1 ATATAAAACAAATAA
29949632 ATATAAAA-AAATAA
1 ATATAAAACAAATAA
29949646 A
1 A
29949647 AAAAATAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.47
15 8 0.53
ACGTcount: A:0.77, C:0.03, G:0.00, T:0.20
Consensus pattern (15 bp):
ATATAAAACAAATAA
Found at i:29950252 original size:13 final size:15
Alignment explanation
Indices: 29950223--29950259 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
29950213 TTTTAATTTC
29950223 AATATTATTTATATT
1 AATATTATTTATATT
29950238 AATA-TATTT-TATT
1 AATATTATTTATATT
*
29950251 AATGTTATT
1 AATATTATT
29950260 ATTATATTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
13 7 0.35
14 9 0.45
15 4 0.20
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (15 bp):
AATATTATTTATATT
Found at i:29956217 original size:21 final size:21
Alignment explanation
Indices: 29956184--29956223 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
29956174 GACTTAAATT
*
29956184 TTTGTCAAAACTAA-CTAATA
1 TTTGTAAAAACTAATCTAATA
29956204 TTTGTAAATAACTAATCTAA
1 TTTGTAAA-AACTAATCTAA
29956224 ACTCATTTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 7 0.41
21 6 0.35
22 4 0.24
ACGTcount: A:0.45, C:0.12, G:0.05, T:0.38
Consensus pattern (21 bp):
TTTGTAAAAACTAATCTAATA
Found at i:29960500 original size:110 final size:107
Alignment explanation
Indices: 29960313--29960514 Score: 260
Period size: 110 Copynumber: 1.9 Consensus size: 107
29960303 TGAAATTTTA
* * * * *
29960313 AAAAGGATATTCGGTCATTCGGTCAAATGATAAATCGAAACCCAGCACGTAGGGCGCGATCTCTC
1 AAAAGGATATTCGGTAATTCGGTCAAACGAAAAATCAAAACCCAGCACGTAGGGCACGATCTCTC
* *
29960378 GAGTTTCTAAACACGAAATATTACCTTTAACTTTGAATATTT
66 GAATTTCCAAACACGAAATATTACCTTTAACTTTGAATATTT
* * * *
29960420 AAAAGGTTATTCGGTTAATTGGGTCAAACGAAAAAATCAAAATCCAGCACATTAGGGCACGATCT
1 AAAAGGATATTCGG-TAATTCGGTCAAACG-AAAAATCAAAACCCAGCAC-GTAGGGCACGATCT
* *
29960485 CTCGAATTTCCAAACACGGAATATTGCCTT
63 CTCGAATTTCCAAACACGAAATATTACCTT
29960515 ATTTCAAAAA
Statistics
Matches: 79, Mismatches: 13, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
107 13 0.16
108 12 0.15
109 16 0.20
110 38 0.48
ACGTcount: A:0.35, C:0.20, G:0.18, T:0.27
Consensus pattern (107 bp):
AAAAGGATATTCGGTAATTCGGTCAAACGAAAAATCAAAACCCAGCACGTAGGGCACGATCTCTC
GAATTTCCAAACACGAAATATTACCTTTAACTTTGAATATTT
Found at i:29960919 original size:3 final size:3
Alignment explanation
Indices: 29960911--29960953 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
29960901 TAAATAAATA
29960911 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
29960954 GGTAGTGTAA
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:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:29961183 original size:2 final size:2
Alignment explanation
Indices: 29961167--29961208 Score: 68
Period size: 2 Copynumber: 21.5 Consensus size: 2
29961157 AATACGAATG
*
29961167 TA TA -A TA TA TG TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
29961208 T
1 T
29961209 GAACAGGTAA
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 36 0.97
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
TA
Found at i:29961277 original size:4 final size:4
Alignment explanation
Indices: 29961268--29961292 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
29961258 TATAAACAAG
29961268 TAAA TAAA TAAA TAAA TAAA TAAA T
1 TAAA TAAA TAAA TAAA TAAA TAAA T
29961293 TAATTAAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (4 bp):
TAAA
Found at i:29963259 original size:17 final size:17
Alignment explanation
Indices: 29963239--29963273 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
29963229 CGTGTTTGGT
29963239 GATTTCGGGTTTTTGCA
1 GATTTCGGGTTTTTGCA
29963256 GATTTCGGGTTTTTGCA
1 GATTTCGGGTTTTTGCA
29963273 G
1 G
29963274 TGTTGTGGGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.11, C:0.11, G:0.31, T:0.46
Consensus pattern (17 bp):
GATTTCGGGTTTTTGCA
Found at i:29966440 original size:3 final size:3
Alignment explanation
Indices: 29966432--29966472 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
29966422 GTACGTGTGA
29966432 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
29966473 GATTTGTTTT
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:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:29970467 original size:19 final size:17
Alignment explanation
Indices: 29970443--29970487 Score: 58
Period size: 17 Copynumber: 2.6 Consensus size: 17
29970433 CTGTAATAAT
29970443 ATAATAAT-ATT-TTAA
1 ATAATAATAATTCTTAA
29970458 CATAATAATAATTCTTAA
1 -ATAATAATAATTCTTAA
29970476 ATAATAAGTAAT
1 ATAATAA-TAAT
29970488 GTATATAATT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
16 8 0.31
17 10 0.38
18 8 0.31
ACGTcount: A:0.53, C:0.04, G:0.02, T:0.40
Consensus pattern (17 bp):
ATAATAATAATTCTTAA
Found at i:29970644 original size:24 final size:24
Alignment explanation
Indices: 29970617--29970665 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
29970607 TTATTTCTTA
29970617 AATAATAAGTAAATACATATATGT
1 AATAATAAGTAAATACATATATGT
29970641 AATAATAAGTAAATACATATATGT
1 AATAATAAGTAAATACATATATGT
29970665 A
1 A
29970666 TTACAGTTGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.55, C:0.04, G:0.08, T:0.33
Consensus pattern (24 bp):
AATAATAAGTAAATACATATATGT
Found at i:29976386 original size:15 final size:15
Alignment explanation
Indices: 29976366--29976397 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
29976356 CATTTCACTA
*
29976366 TTATGTCTTTTGTAT
1 TTATGTCTTTTATAT
29976381 TTATGTCTTTTATAT
1 TTATGTCTTTTATAT
29976396 TT
1 TT
29976398 TGCATGCATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.16, C:0.06, G:0.09, T:0.69
Consensus pattern (15 bp):
TTATGTCTTTTATAT
Found at i:29976776 original size:29 final size:29
Alignment explanation
Indices: 29976743--29976801 Score: 100
Period size: 29 Copynumber: 2.0 Consensus size: 29
29976733 TTGTGAATTA
* *
29976743 ATTCACTTGTGATGTTCATGGTATGATTT
1 ATTCACATGTGACGTTCATGGTATGATTT
29976772 ATTCACATGTGACGTTCATGGTATGATTT
1 ATTCACATGTGACGTTCATGGTATGATTT
29976801 A
1 A
29976802 CCTAAATCAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.24, C:0.12, G:0.20, T:0.44
Consensus pattern (29 bp):
ATTCACATGTGACGTTCATGGTATGATTT
Found at i:29977609 original size:19 final size:19
Alignment explanation
Indices: 29977587--29977626 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
29977577 AATAATTTTG
29977587 ATCAAATAAAATT-AAATTA
1 ATCAAAT-AAATTAAAATTA
*
29977606 ATCAAATTAATTAAAATTA
1 ATCAAATAAATTAAAATTA
29977625 AT
1 AT
29977627 ATGATATTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 4 0.21
19 15 0.79
ACGTcount: A:0.60, C:0.05, G:0.00, T:0.35
Consensus pattern (19 bp):
ATCAAATAAATTAAAATTA
Found at i:29978143 original size:16 final size:16
Alignment explanation
Indices: 29978110--29978143 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
29978100 TTTTAATAAG
* *
29978110 ATATAATATTATATTA
1 ATATAATATTAAAGTA
29978126 ATATAATATTAAAGTA
1 ATATAATATTAAAGTA
29978142 AT
1 AT
29978144 TAAGTTTAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.44
Consensus pattern (16 bp):
ATATAATATTAAAGTA
Found at i:29986723 original size:18 final size:18
Alignment explanation
Indices: 29986700--29986740 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
29986690 CAAAAAATCT
29986700 AAAAAACCCT-ACAAGCCC
1 AAAAAACCCTGA-AAGCCC
*
29986718 AAAAAAGCCTGAAAGCCC
1 AAAAAACCCTGAAAGCCC
29986736 AAAAA
1 AAAAA
29986741 CCTAAACTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 20 0.95
19 1 0.05
ACGTcount: A:0.56, C:0.29, G:0.10, T:0.05
Consensus pattern (18 bp):
AAAAAACCCTGAAAGCCC
Found at i:29987448 original size:26 final size:26
Alignment explanation
Indices: 29987412--29987464 Score: 88
Period size: 26 Copynumber: 2.0 Consensus size: 26
29987402 ACCGAAAGGT
29987412 TTTCAACCCTTTTGTCGAGGCTTGAC
1 TTTCAACCCTTTTGTCGAGGCTTGAC
* *
29987438 TTTCAACCCTTTTGTTGAGGGTTGAC
1 TTTCAACCCTTTTGTCGAGGCTTGAC
29987464 T
1 T
29987465 GAGTTTCTTG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.15, C:0.23, G:0.21, T:0.42
Consensus pattern (26 bp):
TTTCAACCCTTTTGTCGAGGCTTGAC
Found at i:29988205 original size:13 final size:13
Alignment explanation
Indices: 29988189--29988213 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
29988179 TTATTTAACC
29988189 CTTTTATTTATTG
1 CTTTTATTTATTG
29988202 CTTTTATTTATT
1 CTTTTATTTATT
29988214 TATACCTAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.16, C:0.08, G:0.04, T:0.72
Consensus pattern (13 bp):
CTTTTATTTATTG
Found at i:29989592 original size:14 final size:15
Alignment explanation
Indices: 29989573--29989614 Score: 52
Period size: 14 Copynumber: 2.9 Consensus size: 15
29989563 TAATAATTAT
29989573 AAAAAT-TTTAAAGG
1 AAAAATATTTAAAGG
29989587 AAAAATATTTAAA-G
1 AAAAATATTTAAAGG
* *
29989601 AATAATATTAAAAG
1 AAAAATATTTAAAG
29989615 AATAAAAGTA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
14 18 0.75
15 6 0.25
ACGTcount: A:0.62, C:0.00, G:0.10, T:0.29
Consensus pattern (15 bp):
AAAAATATTTAAAGG
Found at i:29989615 original size:14 final size:14
Alignment explanation
Indices: 29989580--29989619 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
29989570 TATAAAAATT
* *
29989580 TTAAAGGAAAAATA
1 TTAAAAGAATAATA
*
29989594 TTTAAAGAATAATA
1 TTAAAAGAATAATA
29989608 TTAAAAGAATAA
1 TTAAAAGAATAA
29989620 AAGTAATTAA
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:0.62, C:0.00, G:0.10, T:0.28
Consensus pattern (14 bp):
TTAAAAGAATAATA
Found at i:29989848 original size:14 final size:15
Alignment explanation
Indices: 29989829--29989864 Score: 58
Period size: 14 Copynumber: 2.5 Consensus size: 15
29989819 TTGTTTCACT
29989829 GAAAATGAATTTC-G
1 GAAAATGAATTTCTG
29989843 GAAAAT-AATTTCTG
1 GAAAATGAATTTCTG
29989857 GAAAATGA
1 GAAAATGA
29989865 TTTAGTTTTC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
13 6 0.30
14 13 0.65
15 1 0.05
ACGTcount: A:0.47, C:0.06, G:0.19, T:0.28
Consensus pattern (15 bp):
GAAAATGAATTTCTG
Found at i:29990142 original size:191 final size:190
Alignment explanation
Indices: 29989921--29990308 Score: 740
Period size: 191 Copynumber: 2.0 Consensus size: 190
29989911 TGTGTAAAAT
*
29989921 ATTTTTTGTTGTTTGGTAGATTTGTTAAAAATATTTCATAAAAGTTGTTTTCAATTAAACAAACA
1 ATTTTTTGTTATTTGGTAGATTTGTTAAAAATATTTCATAAAAGTTGTTTTCAATTAAACAAACA
*
29989986 TATATTTGAGATTTTCTTATTTTTTCATTGTTTAATTGAATTTATTTTTATCTATAAGTTTATAT
66 TATATTTGAGATTTACTTATTTTTTCATTGTTTAATTGAATTTATTTTTATCTATAAGTTTATAT
29990051 TTTACATTATTTTTTGCATATATTAAAAATATTATGTTAAATTCAGATTCATTATAACGTC
131 TTTACATTA-TTTTTGCATATATTAAAAATATTATGTTAAATTCAGATTCATTATAACGTC
29990112 ATTTTTTGTTATTTGGTAGATTTGTTAAAAATATTTCATAAAAGTTGTTTTCAATTAAACAAACA
1 ATTTTTTGTTATTTGGTAGATTTGTTAAAAATATTTCATAAAAGTTGTTTTCAATTAAACAAACA
29990177 TATATTTGAGATTTACTTATTTTTTCATTGTTTAATTGAATTTATTTTTATCTATAAGTTTATAT
66 TATATTTGAGATTTACTTATTTTTTCATTGTTTAATTGAATTTATTTTTATCTATAAGTTTATAT
*
29990242 TTTACATTATTTTTGCATATATTAAAAATATTATGTTAAATTCAGATTCATTATAACGTT
131 TTTACATTATTTTTGCATATATTAAAAATATTATGTTAAATTCAGATTCATTATAACGTC
29990302 ATTTTTT
1 ATTTTTT
29990309 AATTACATGA
Statistics
Matches: 194, Mismatches: 3, Indels: 1
0.98 0.02 0.01
Matches are distributed among these distances:
190 57 0.29
191 137 0.71
ACGTcount: A:0.33, C:0.06, G:0.09, T:0.52
Consensus pattern (190 bp):
ATTTTTTGTTATTTGGTAGATTTGTTAAAAATATTTCATAAAAGTTGTTTTCAATTAAACAAACA
TATATTTGAGATTTACTTATTTTTTCATTGTTTAATTGAATTTATTTTTATCTATAAGTTTATAT
TTTACATTATTTTTGCATATATTAAAAATATTATGTTAAATTCAGATTCATTATAACGTC
Found at i:29994167 original size:26 final size:26
Alignment explanation
Indices: 29994131--29994240 Score: 184
Period size: 26 Copynumber: 4.2 Consensus size: 26
29994121 CATGAAATTC
29994131 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
29994157 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
* *
29994183 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCCA
* *
29994209 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCCA
29994235 TTATCA
1 TTATCA
29994241 ATTTGTATCA
Statistics
Matches: 82, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
26 82 1.00
ACGTcount: A:0.36, C:0.25, G:0.05, T:0.34
Consensus pattern (26 bp):
TTATCATGAAACATTTACCTAACCCA
Found at i:29998125 original size:64 final size:64
Alignment explanation
Indices: 29998052--29998262 Score: 151
Period size: 64 Copynumber: 3.2 Consensus size: 64
29998042 CTGGGCCAGA
*
29998052 GCCCTTTTCAGATTACAATAAACTGGGCCTTAGCCCCTTATTCAGATAACAGTATGGCCCATAG
1 GCCCATTTCAGATTACAATAAACTGGGCCTTAGCCCCTTATTCAGATAACAGTATGGCCCATAG
* * * *** * ** *
29998116 GCCCATTTCAAAATAC-ATGCAACATCAGTAAACATATGCAAGCCC--ATTTGGGTAACAGTGGT
1 GCCCATTTCAGATTACAAT--AA-A-CTG-GGCCTTA-GC---CCCTTATTCAGATAACA---GT
* *
29998178 ACTGGGCCAGA-
54 A-TGGCCCATAG
*
29998189 GCCCTTTTCAGATTACAATAAACTGGGCCTTAGCCCCTTATTCAGATAACAGTATGGCCCATAG
1 GCCCATTTCAGATTACAATAAACTGGGCCTTAGCCCCTTATTCAGATAACAGTATGGCCCATAG
29998253 GCCCATTTCA
1 GCCCATTTCA
29998263 AAATACATGC
Statistics
Matches: 103, Mismatches: 27, Indels: 34
0.63 0.16 0.21
Matches are distributed among these distances:
63 9 0.09
64 25 0.24
65 5 0.05
66 1 0.01
67 11 0.11
68 5 0.05
69 5 0.05
70 11 0.11
71 1 0.01
72 5 0.05
73 16 0.16
74 9 0.09
ACGTcount: A:0.30, C:0.26, G:0.18, T:0.26
Consensus pattern (64 bp):
GCCCATTTCAGATTACAATAAACTGGGCCTTAGCCCCTTATTCAGATAACAGTATGGCCCATAG
Found at i:29998264 original size:137 final size:136
Alignment explanation
Indices: 29998018--29998303 Score: 536
Period size: 137 Copynumber: 2.1 Consensus size: 136
29998008 TATTGGGCCT
**
29998018 AAGCCCATTCAGGTAACAGTGGTACTGGGCCAGAGCCCTTTTCAGATTACAATAAACTGGGCCTT
1 AAGCCCATTTGGGTAACAGTGGTACTGGGCCAGAGCCCTTTTCAGATTACAATAAACTGGGCCTT
*
29998083 AGCCCCTTATTCAGATAACAGTATGGCCCATAGGCCCATTTCAAAATACATGCAACATCAGTAAA
66 AGCCCCTTATTCAGATAACAGTATGGCCCATAGGCCCATTTCAAAATACATGCAACATCAAT-AA
29998148 CATATGC
130 CATATGC
29998155 AAGCCCATTTGGGTAACAGTGGTACTGGGCCAGAGCCCTTTTCAGATTACAATAAACTGGGCCTT
1 AAGCCCATTTGGGTAACAGTGGTACTGGGCCAGAGCCCTTTTCAGATTACAATAAACTGGGCCTT
29998220 AGCCCCTTATTCAGATAACAGTATGGCCCATAGGCCCATTTCAAAATACATGCAACATCAATAAC
66 AGCCCCTTATTCAGATAACAGTATGGCCCATAGGCCCATTTCAAAATACATGCAACATCAATAAC
29998285 ATATGC
131 ATATGC
29998291 AAGCCCATTTGGG
1 AAGCCCATTTGGG
29998304 GAGACTACTC
Statistics
Matches: 146, Mismatches: 3, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
136 22 0.15
137 124 0.85
ACGTcount: A:0.31, C:0.25, G:0.19, T:0.24
Consensus pattern (136 bp):
AAGCCCATTTGGGTAACAGTGGTACTGGGCCAGAGCCCTTTTCAGATTACAATAAACTGGGCCTT
AGCCCCTTATTCAGATAACAGTATGGCCCATAGGCCCATTTCAAAATACATGCAACATCAATAAC
ATATGC
Found at i:29998588 original size:25 final size:27
Alignment explanation
Indices: 29998551--29998603 Score: 74
Period size: 26 Copynumber: 2.0 Consensus size: 27
29998541 TCAAACATGC
29998551 ATTTAGGTCAATTTAAC-CCTAGGGGT
1 ATTTAGGTCAATTTAACTCCTAGGGGT
* *
29998577 ATTTCGGT-AATTTATCTCCTAGGGGT
1 ATTTAGGTCAATTTAACTCCTAGGGGT
29998603 A
1 A
29998604 AAATGTAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 7 0.29
26 17 0.71
ACGTcount: A:0.25, C:0.15, G:0.23, T:0.38
Consensus pattern (27 bp):
ATTTAGGTCAATTTAACTCCTAGGGGT
Found at i:30000063 original size:26 final size:26
Alignment explanation
Indices: 30000027--30000134 Score: 175
Period size: 26 Copynumber: 4.2 Consensus size: 26
30000017 CATGAAATTC
30000027 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
30000053 TTATCATGAAACATTTACCTAA-CCA
1 TTATCATGAAACATTTACCTAACCCA
*
30000078 TTATCATG-AACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCCA
* *
30000103 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCCA
30000129 TTATCA
1 TTATCA
30000135 ATTTGTATCA
Statistics
Matches: 79, Mismatches: 1, Indels: 4
0.94 0.01 0.05
Matches are distributed among these distances:
24 13 0.16
25 21 0.27
26 45 0.57
ACGTcount: A:0.37, C:0.24, G:0.05, T:0.34
Consensus pattern (26 bp):
TTATCATGAAACATTTACCTAACCCA
Found at i:30000106 original size:50 final size:52
Alignment explanation
Indices: 30000027--30000134 Score: 184
Period size: 50 Copynumber: 2.1 Consensus size: 52
30000017 CATGAAATTC
30000027 TTATCATGAAACATTTACCTAACCCATTATCATGAAACATTTACCTAACC-A
1 TTATCATGAAACATTTACCTAACCCATTATCATGAAACATTTACCTAACCTA
* *
30000078 TTATCATG-AACATTTACCTAACCTATTATCATGGAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCCATTATCATGAAACATTTACCTAACCTA
30000129 TTATCA
1 TTATCA
30000135 ATTTGTATCA
Statistics
Matches: 54, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
50 39 0.72
51 15 0.28
ACGTcount: A:0.37, C:0.24, G:0.05, T:0.34
Consensus pattern (52 bp):
TTATCATGAAACATTTACCTAACCCATTATCATGAAACATTTACCTAACCTA
Found at i:30002362 original size:40 final size:40
Alignment explanation
Indices: 30002307--30002516 Score: 305
Period size: 40 Copynumber: 5.2 Consensus size: 40
30002297 AACATTGGAA
30002307 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
30002347 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
30002387 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
* * * *
30002427 ATATATCCGGGCTAAGACCCGAAGGCCTTTGTGCAAG-TC
1 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
* * * * * *
30002466 ACCAAATCCGGGTTATGACCCGAAGGCAATCGTGCGAGTCG
1 A-TATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
*
30002507 CTATATCCGG
1 ATATATCCGG
30002517 TTAAATCCCG
Statistics
Matches: 151, Mismatches: 17, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
39 2 0.01
40 149 0.99
ACGTcount: A:0.25, C:0.24, G:0.29, T:0.22
Consensus pattern (40 bp):
ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
Found at i:30010492 original size:40 final size:40
Alignment explanation
Indices: 30010437--30010646 Score: 305
Period size: 40 Copynumber: 5.2 Consensus size: 40
30010427 AACATTGGAA
30010437 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
30010477 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
30010517 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
* * * *
30010557 ATATATCCGGGCTAAGACCCGAAGGCCTTTGTGCAAG-TC
1 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
* * * * * *
30010596 ACCAAATCCGGGTTATGACCCGAAGGCAATCGTGCGAGTCG
1 A-TATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
*
30010637 CTATATCCGG
1 ATATATCCGG
30010647 TTAAATCCCG
Statistics
Matches: 151, Mismatches: 17, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
39 2 0.01
40 149 0.99
ACGTcount: A:0.25, C:0.24, G:0.29, T:0.22
Consensus pattern (40 bp):
ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
Found at i:30015362 original size:17 final size:17
Alignment explanation
Indices: 30015340--30015372 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
30015330 CAATTTTTTT
30015340 AGTTGAAAATAGTGGGG
1 AGTTGAAAATAGTGGGG
*
30015357 AGTTGAAAATGGTGGG
1 AGTTGAAAATAGTGGG
30015373 AGGTGCAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.33, C:0.00, G:0.42, T:0.24
Consensus pattern (17 bp):
AGTTGAAAATAGTGGGG
Found at i:30019232 original size:43 final size:43
Alignment explanation
Indices: 30019158--30019315 Score: 176
Period size: 43 Copynumber: 3.7 Consensus size: 43
30019148 AAAAAAAGGT
* * * ** * *
30019158 CGCTAAAAATCATGTTCTTTAGTGGCGTTTGTAATAAAAGCGC
1 CGCTAAAGATCATGTTCTATAGCGGCGTTTGTAGGAAAAGTGA
* * *
30019201 CGCTAAATATCATGTTCTATAGCAGCATTTGTAGGAAAAGTGA
1 CGCTAAAGATCATGTTCTATAGCGGCGTTTGTAGGAAAAGTGA
*
30019244 C-CTAAAGATCAT-TTCCTATAGCGGCGTTTGTAGGAAAAGTGT
1 CGCTAAAGATCATGTT-CTATAGCGGCGTTTGTAGGAAAAGTGA
* *
30019286 TGCTAAAGATCATGTTCTATAACGGCGTTT
1 CGCTAAAGATCATGTTCTATAGCGGCGTTT
30019316 TCCCACATAA
Statistics
Matches: 97, Mismatches: 15, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
41 2 0.02
42 34 0.35
43 59 0.61
44 2 0.02
ACGTcount: A:0.30, C:0.16, G:0.22, T:0.32
Consensus pattern (43 bp):
CGCTAAAGATCATGTTCTATAGCGGCGTTTGTAGGAAAAGTGA
Found at i:30019263 original size:42 final size:43
Alignment explanation
Indices: 30019203--30019306 Score: 140
Period size: 42 Copynumber: 2.4 Consensus size: 43
30019193 AAAAGCGCCG
*
30019203 CTAAATATCATGTTCTATAGCAGCATTTGTAGGAAAAGTG-AC
1 CTAAAGATCATGTTCTATAGCAGCATTTGTAGGAAAAGTGTAC
* * **
30019245 CTAAAGATCAT-TTCCTATAGCGGCGTTTGTAGGAAAAGTGTTG
1 CTAAAGATCATGTT-CTATAGCAGCATTTGTAGGAAAAGTGTAC
30019288 CTAAAGATCATGTTCTATA
1 CTAAAGATCATGTTCTATA
30019307 ACGGCGTTTT
Statistics
Matches: 54, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
41 2 0.04
42 34 0.63
43 16 0.30
44 2 0.04
ACGTcount: A:0.33, C:0.14, G:0.20, T:0.33
Consensus pattern (43 bp):
CTAAAGATCATGTTCTATAGCAGCATTTGTAGGAAAAGTGTAC
Found at i:30019947 original size:24 final size:25
Alignment explanation
Indices: 30019905--30019951 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
30019895 ATAAAAAAAT
30019905 TATAATATTTTTATGAATATATAAG
1 TATAATATTTTTATGAATATATAAG
*
30019930 TATATTATTTTTAT-AATATATA
1 TATAATATTTTTATGAATATATA
30019952 GCGTGAACAC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
24 8 0.38
25 13 0.62
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.53
Consensus pattern (25 bp):
TATAATATTTTTATGAATATATAAG
Found at i:30026063 original size:16 final size:16
Alignment explanation
Indices: 30026042--30026075 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
30026032 TAAGAATTGG
*
30026042 ATAAAAAAATTTATAT
1 ATAAAAAAATCTATAT
*
30026058 ATAAAAAAGTCTATAT
1 ATAAAAAAATCTATAT
30026074 AT
1 AT
30026076 GAATTGTTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.59, C:0.03, G:0.03, T:0.35
Consensus pattern (16 bp):
ATAAAAAAATCTATAT
Found at i:30027520 original size:20 final size:20
Alignment explanation
Indices: 30027506--30027595 Score: 96
Period size: 19 Copynumber: 4.5 Consensus size: 20
30027496 TTTTTTGAAT
30027506 TTATTTTGAAATTTTTATAAA
1 TTATTTTGAAATTTTTA-AAA
*
30027527 -TATTTTG-AATTTTAAAAA
1 TTATTTTGAAATTTTTAAAA
30027545 TTATTTT-AAATTTTTAAAAA
1 TTATTTTGAAATTTTT-AAAA
* *
30027565 TTATTTTGAATTATTTTACAA
1 TTATTTTGAAAT-TTTTAAAA
*
30027586 TTTTTTTGAA
1 TTATTTTGAA
30027596 TTATTTTACA
Statistics
Matches: 59, Mismatches: 5, Indels: 10
0.80 0.07 0.14
Matches are distributed among these distances:
18 3 0.05
19 19 0.32
20 18 0.31
21 15 0.25
22 4 0.07
ACGTcount: A:0.38, C:0.01, G:0.04, T:0.57
Consensus pattern (20 bp):
TTATTTTGAAATTTTTAAAA
Found at i:30027537 original size:19 final size:20
Alignment explanation
Indices: 30027506--30027597 Score: 107
Period size: 20 Copynumber: 4.6 Consensus size: 20
30027496 TTTTTTGAAT
*
30027506 TTATTTTGAAATTTTTATAAA
1 TTATTTTG-AATTTTTAAAAA
30027527 -TATTTTGAA-TTTTAAAAA
1 TTATTTTGAATTTTTAAAAA
*
30027545 TTATTTTAAATTTTTAAAAA
1 TTATTTTGAATTTTTAAAAA
* *
30027565 TTATTTTGAATTATTTTACAA
1 TTATTTTGAATT-TTTAAAAA
*
30027586 TTTTTTTGAATT
1 TTATTTTGAATT
30027598 ATTTTACAAT
Statistics
Matches: 62, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
18 8 0.13
19 10 0.16
20 27 0.44
21 17 0.27
ACGTcount: A:0.37, C:0.01, G:0.04, T:0.58
Consensus pattern (20 bp):
TTATTTTGAATTTTTAAAAA
Found at i:30027576 original size:10 final size:10
Alignment explanation
Indices: 30027498--30027602 Score: 56
Period size: 10 Copynumber: 10.4 Consensus size: 10
30027488 TTATATATTT
30027498 TTTTGAATTTA
1 TTTTGAA-TTA
30027509 TTTTGAAATT-
1 TTTTG-AATTA
*
30027519 TTTAT-AAATA
1 TTT-TGAATTA
30027529 TTTTGAATT-
1 TTTTGAATTA
***
30027538 TTAAAAATTA
1 TTTTGAATTA
*
30027548 TTTTAAATT-
1 TTTTGAATTA
**
30027557 TTTAAAAATTA
1 TTT-TGAATTA
30027568 TTTTGAATTA
1 TTTTGAATTA
* *
30027578 TTTTACAATTT
1 TTTT-GAATTA
30027589 TTTTGAATTA
1 TTTTGAATTA
30027599 TTTT
1 TTTT
30027603 ACAATTTTTG
Statistics
Matches: 72, Mismatches: 14, Indels: 17
0.70 0.14 0.17
Matches are distributed among these distances:
9 13 0.18
10 38 0.53
11 19 0.26
12 2 0.03
ACGTcount: A:0.35, C:0.01, G:0.05, T:0.59
Consensus pattern (10 bp):
TTTTGAATTA
Found at i:30027592 original size:21 final size:21
Alignment explanation
Indices: 30027563--30027616 Score: 90
Period size: 21 Copynumber: 2.5 Consensus size: 21
30027553 AATTTTTAAA
*
30027563 AATTATTTTGAATTATTTTAC
1 AATTTTTTTGAATTATTTTAC
30027584 AATTTTTTTGAATTATTTTAC
1 AATTTTTTTGAATTATTTTAC
30027605 AATTTTTGTTGA
1 AATTTTT-TTGA
30027617 GAGAATCCAA
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
21 27 0.87
22 4 0.13
ACGTcount: A:0.30, C:0.04, G:0.07, T:0.59
Consensus pattern (21 bp):
AATTTTTTTGAATTATTTTAC
Found at i:30028347 original size:20 final size:19
Alignment explanation
Indices: 30028318--30028398 Score: 74
Period size: 20 Copynumber: 4.2 Consensus size: 19
30028308 ACTTTCAATA
*
30028318 AAAATTTCAAAATAATTTT
1 AAAATTTCAAAAAAATTTT
*
30028337 CAAATTTTCAAAAAAATTTT
1 -AAAATTTCAAAAAAATTTT
* * *
30028357 TAAATTTC-AGAATATTTAT
1 AAAATTTCAAAAAAATTT-T
*
30028376 AAAAATTTCAAAAAAATTCT
1 -AAAATTTCAAAAAAATTTT
30028396 AAA
1 AAA
30028399 TATATATATA
Statistics
Matches: 48, Mismatches: 10, Indels: 7
0.74 0.15 0.11
Matches are distributed among these distances:
18 7 0.15
19 10 0.21
20 25 0.52
21 6 0.12
ACGTcount: A:0.53, C:0.07, G:0.01, T:0.38
Consensus pattern (19 bp):
AAAATTTCAAAAAAATTTT
Found at i:30028362 original size:39 final size:39
Alignment explanation
Indices: 30028319--30028393 Score: 107
Period size: 39 Copynumber: 1.9 Consensus size: 39
30028309 CTTTCAATAA
* *
30028319 AAATTTCAAAATAATTT-TCAAATTTTCAAAAAAATTTTT
1 AAATTTCAAAAT-ATTTATAAAAATTTCAAAAAAATTTTT
*
30028358 AAATTTCAGAATATTTATAAAAATTTCAAAAAAATT
1 AAATTTCAAAATATTTATAAAAATTTCAAAAAAATT
30028394 CTAAATATAT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
38 4 0.12
39 28 0.88
ACGTcount: A:0.52, C:0.07, G:0.01, T:0.40
Consensus pattern (39 bp):
AAATTTCAAAATATTTATAAAAATTTCAAAAAAATTTTT
Found at i:30029897 original size:42 final size:42
Alignment explanation
Indices: 30029838--30029926 Score: 169
Period size: 42 Copynumber: 2.1 Consensus size: 42
30029828 ACACTCCGAA
*
30029838 TCAACCACCGTACTCTTTAGATCATCATCATTCTGCAAATTT
1 TCAACCAACGTACTCTTTAGATCATCATCATTCTGCAAATTT
30029880 TCAACCAACGTACTCTTTAGATCATCATCATTCTGCAAATTT
1 TCAACCAACGTACTCTTTAGATCATCATCATTCTGCAAATTT
30029922 TCAAC
1 TCAAC
30029927 TTCCTCATAA
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 46 1.00
ACGTcount: A:0.30, C:0.28, G:0.07, T:0.35
Consensus pattern (42 bp):
TCAACCAACGTACTCTTTAGATCATCATCATTCTGCAAATTT
Found at i:30035152 original size:19 final size:19
Alignment explanation
Indices: 30035123--30035164 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
30035113 CATTTATGAA
30035123 TTAAAGATTAAAT-AATTT
1 TTAAAGATTAAATAAATTT
30035141 TTAAAGGATTAAATCAAATTT
1 TTAAA-GATTAAAT-AAATTT
30035162 TTA
1 TTA
30035165 TTATTTTGAG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 5 0.24
19 8 0.38
21 8 0.38
ACGTcount: A:0.48, C:0.02, G:0.07, T:0.43
Consensus pattern (19 bp):
TTAAAGATTAAATAAATTT
Found at i:30035387 original size:312 final size:314
Alignment explanation
Indices: 30034822--30035422 Score: 845
Period size: 312 Copynumber: 1.9 Consensus size: 314
30034812 CTATGTATTT
30034822 ATAATTTTGAAAGGATTAAATCAAACTTTTATTATTTGAGGGGCTAAAATGCAACTTTACCATTA
1 ATAATTTTGAAAGGATTAAATCAAACTTTTATTATTTGAGGGGCTAAAATGCAACTTTACCATTA
* *** *
30034887 CTAATTTAAAATTTTATAACTTATAAAAGGCCTAAATGATTTTTTTTCTATTTTAGGGGTGGCTC
66 CTAATCTAAAATTTTATAACTTATAAAAGGCCTAAATGATAAATTTTCCATTTTAGGGGTGGCTC
** * * * * * * * *
30034952 GGGGCCCTTGCTTGCCCCTCTTGGCTCTGCCACTGCAAATGACATTCACCCTTCAAACTTTGCCT
131 AAGGCCCCTACCTCCCCCTCTTAGCTCTGCCACTACAAATAACATTCACCCTTCAAACATTGCCT
* * *
30035017 ACATAGCGACACTCTAGAAATGTTTTATGTAATTTTGTAGGACTTGCTTCTTTGTGGTG-TTTTT
196 ACACAACGACACTCTAGAAATGTTTTATGTAATTTTGTAGGACTTACTTCTTTGTGGTGTTTTTT
* *
30035081 -TTATAGTAATGCTTTGAGATTGTTTATTATTTCATTTATGAATTAAAGATTAA
261 CTTACAGCAATGCTTTGAGATTGTTTATTATTTCATTTATGAATTAAAGATTAA
* * * * *
30035134 ATAATTTTTAAAGGATTAAATCAAATTTTTATTATTTTGAGGGGCTAAAGTGTAATTTTACCATT
1 ATAATTTTGAAAGGATTAAATCAAACTTTTATTA-TTTGAGGGGCTAAAATGCAACTTTACCATT
**
30035199 TTTAATCTAAAATTTTATAACTTATAAAAGGCCTAAATG-TAAAATTTTCCATTTTAGAGGG-GG
65 ACTAATCTAAAATTTTATAACTTATAAAAGGCCTAAATGAT-AAATTTTCCATTTTAG-GGGTGG
*
30035262 -TCAAGGCCCCTACCTCCCCCTCTTAGCTTTGCCACTACAAATAACATTCA-CCTTGCAAACATT
128 CTCAAGGCCCCTACCTCCCCCTCTTAGCTCTGCCACTACAAATAACATTCACCCTT-CAAACATT
* * *
30035325 GCCTACACAACGACACTCTAGAGATGTTTTATGTAGTTTTGTAGGATTTACTTCTTTGTGGTGTT
192 GCCTACACAACGACACTCTAGAAATGTTTTATGTAATTTTGTAGGACTTACTTCTTTGTGGTGTT
30035390 TTTTCTTACAGCAATGCTTTGAGATTGTTTATT
257 TTTTCTTACAGCAATGCTTTGAGATTGTTTATT
30035423 CTATTTTTCT
Statistics
Matches: 252, Mismatches: 31, Indels: 10
0.86 0.11 0.03
Matches are distributed among these distances:
311 4 0.02
312 137 0.54
313 82 0.33
314 29 0.12
ACGTcount: A:0.29, C:0.16, G:0.15, T:0.40
Consensus pattern (314 bp):
ATAATTTTGAAAGGATTAAATCAAACTTTTATTATTTGAGGGGCTAAAATGCAACTTTACCATTA
CTAATCTAAAATTTTATAACTTATAAAAGGCCTAAATGATAAATTTTCCATTTTAGGGGTGGCTC
AAGGCCCCTACCTCCCCCTCTTAGCTCTGCCACTACAAATAACATTCACCCTTCAAACATTGCCT
ACACAACGACACTCTAGAAATGTTTTATGTAATTTTGTAGGACTTACTTCTTTGTGGTGTTTTTT
CTTACAGCAATGCTTTGAGATTGTTTATTATTTCATTTATGAATTAAAGATTAA
Found at i:30038589 original size:2 final size:2
Alignment explanation
Indices: 30038582--30038607 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
30038572 TTTAATGAAC
30038582 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
30038608 GAGGTTATAA
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:30043227 original size:26 final size:26
Alignment explanation
Indices: 30043192--30043249 Score: 98
Period size: 26 Copynumber: 2.2 Consensus size: 26
30043182 ATAAGAGCCA
*
30043192 TAATCAGGAAGCTCACAAAGAACTTT
1 TAATCAGGAAGCTCACAAAGAACCTT
*
30043218 TAATCAGGAAGCTCACGAAGAACCTT
1 TAATCAGGAAGCTCACAAAGAACCTT
30043244 TAATCA
1 TAATCA
30043250 AGAGCTCCGG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.41, C:0.21, G:0.16, T:0.22
Consensus pattern (26 bp):
TAATCAGGAAGCTCACAAAGAACCTT
Found at i:30043679 original size:13 final size:13
Alignment explanation
Indices: 30043661--30043693 Score: 66
Period size: 13 Copynumber: 2.5 Consensus size: 13
30043651 CATATAAAGA
30043661 TACACAATTTAGT
1 TACACAATTTAGT
30043674 TACACAATTTAGT
1 TACACAATTTAGT
30043687 TACACAA
1 TACACAA
30043694 ACTTACTTCG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.42, C:0.18, G:0.06, T:0.33
Consensus pattern (13 bp):
TACACAATTTAGT
Found at i:30047515 original size:30 final size:31
Alignment explanation
Indices: 30047480--30047537 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 31
30047470 GCATGAGATT
*
30047480 TTGATATACATGAT-TTGACATGATATGCAC
1 TTGATATACATGATATGGACATGATATGCAC
**
30047510 TTGATATGTATGATATGGACATGATATG
1 TTGATATACATGATATGGACATGATATG
30047538 TATGATATGC
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
30 12 0.50
31 12 0.50
ACGTcount: A:0.33, C:0.09, G:0.21, T:0.38
Consensus pattern (31 bp):
TTGATATACATGATATGGACATGATATGCAC
Found at i:30047524 original size:20 final size:20
Alignment explanation
Indices: 30047499--30047555 Score: 96
Period size: 20 Copynumber: 2.9 Consensus size: 20
30047489 ATGATTTGAC
*
30047499 ATGATATGCACTTGATATGT
1 ATGATATGCACATGATATGT
*
30047519 ATGATATGGACATGATATGT
1 ATGATATGCACATGATATGT
30047539 ATGATATGCACATGATA
1 ATGATATGCACATGATA
30047556 AATTCATATA
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.35, C:0.09, G:0.21, T:0.35
Consensus pattern (20 bp):
ATGATATGCACATGATATGT
Found at i:30047637 original size:25 final size:25
Alignment explanation
Indices: 30047603--30047672 Score: 131
Period size: 25 Copynumber: 2.8 Consensus size: 25
30047593 GAGGAAGTGC
30047603 AAAAGGGCTTTGCCCCAGTTTACCG
1 AAAAGGGCTTTGCCCCAGTTTACCG
*
30047628 AAAAGGGCTTTGCCCCAGTTTATCG
1 AAAAGGGCTTTGCCCCAGTTTACCG
30047653 AAAAGGGCTTTGCCCCAGTT
1 AAAAGGGCTTTGCCCCAGTT
30047673 ATTAAAAGAG
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
25 44 1.00
ACGTcount: A:0.24, C:0.26, G:0.24, T:0.26
Consensus pattern (25 bp):
AAAAGGGCTTTGCCCCAGTTTACCG
Found at i:30047685 original size:24 final size:24
Alignment explanation
Indices: 30047603--30047708 Score: 115
Period size: 25 Copynumber: 4.2 Consensus size: 24
30047593 GAGGAAGTGC
*
30047603 AAAAGGGCTTTGCCCCAGTTTACCG
1 AAAAGGGCTTTGCCCCAGTTTA-TG
30047628 AAAAGGGCTTTGCCCCAGTTTATCG
1 AAAAGGGCTTTGCCCCAGTTTAT-G
*
30047653 AAAAGGGCTTTGCCCCAG-TTATT
1 AAAAGGGCTTTGCCCCAGTTTATG
**
30047676 AAAAGAGGCTAGGCCTCCAGTTATATG
1 AAAAG-GGCTTTGCC-CCAGTT-TATG
30047703 ATAAAG
1 A-AAAG
30047709 TAGCTATGCT
Statistics
Matches: 70, Mismatches: 5, Indels: 9
0.83 0.06 0.11
Matches are distributed among these distances:
23 5 0.07
24 11 0.16
25 45 0.64
26 1 0.01
27 4 0.06
28 4 0.06
ACGTcount: A:0.29, C:0.22, G:0.24, T:0.25
Consensus pattern (24 bp):
AAAAGGGCTTTGCCCCAGTTTATG
Found at i:30047926 original size:31 final size:31
Alignment explanation
Indices: 30047891--30047967 Score: 100
Period size: 31 Copynumber: 2.5 Consensus size: 31
30047881 CATTTACAGT
* * *
30047891 AAAGGCTTCGGCCCATTGATATGAATAATAA
1 AAAGGCTTCGGCCCAATGACATGAACAATAA
* **
30047922 AAAGGCTTCGGCCCAATGGCATGAACAATGT
1 AAAGGCTTCGGCCCAATGACATGAACAATAA
30047953 AAAGGCTTCGGCCCA
1 AAAGGCTTCGGCCCA
30047968 GTATATGCTG
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 40 1.00
ACGTcount: A:0.34, C:0.22, G:0.23, T:0.21
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAATGACATGAACAATAA
Found at i:30055655 original size:19 final size:19
Alignment explanation
Indices: 30055610--30055660 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
30055600 TATGCACATG
* *
30055610 ATATGTATGCACATGATAT
1 ATATATATGCACATGATAA
*
30055629 GTATATATGCACATGATAA
1 ATATATATGCACATGATAA
30055648 ATTCATATATGCA
1 A-T-ATATATGCA
30055661 TGGGTTGGGT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
19 16 0.62
20 1 0.04
21 9 0.35
ACGTcount: A:0.39, C:0.12, G:0.14, T:0.35
Consensus pattern (19 bp):
ATATATATGCACATGATAA
Found at i:30055660 original size:21 final size:19
Alignment explanation
Indices: 30055599--30055646 Score: 68
Period size: 15 Copynumber: 2.7 Consensus size: 19
30055589 ATTTGACATG
30055599 ATATGCACATGATATG---
1 ATATGCACATGATATGTAT
30055615 -TATGCACATGATATGTAT
1 ATATGCACATGATATGTAT
30055633 ATATGCACATGATA
1 ATATGCACATGATA
30055647 AATTCATATA
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
15 15 0.54
19 13 0.46
ACGTcount: A:0.38, C:0.12, G:0.17, T:0.33
Consensus pattern (19 bp):
ATATGCACATGATATGTAT
Found at i:30055727 original size:25 final size:25
Alignment explanation
Indices: 30055693--30055762 Score: 131
Period size: 25 Copynumber: 2.8 Consensus size: 25
30055683 GAGGAAGTGC
30055693 AAAAGGGCTTTGCCCCAGTTTACCG
1 AAAAGGGCTTTGCCCCAGTTTACCG
*
30055718 AAAAGGGCTTTGCCCCAGTTTATCG
1 AAAAGGGCTTTGCCCCAGTTTACCG
30055743 AAAAGGGCTTTGCCCCAGTT
1 AAAAGGGCTTTGCCCCAGTT
30055763 ATTAAAAGAG
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
25 44 1.00
ACGTcount: A:0.24, C:0.26, G:0.24, T:0.26
Consensus pattern (25 bp):
AAAAGGGCTTTGCCCCAGTTTACCG
Found at i:30055775 original size:24 final size:24
Alignment explanation
Indices: 30055693--30055798 Score: 115
Period size: 25 Copynumber: 4.2 Consensus size: 24
30055683 GAGGAAGTGC
*
30055693 AAAAGGGCTTTGCCCCAGTTTACCG
1 AAAAGGGCTTTGCCCCAGTTTA-TG
30055718 AAAAGGGCTTTGCCCCAGTTTATCG
1 AAAAGGGCTTTGCCCCAGTTTAT-G
*
30055743 AAAAGGGCTTTGCCCCAG-TTATT
1 AAAAGGGCTTTGCCCCAGTTTATG
**
30055766 AAAAGAGGCTAGGCCTCCAGTTATATG
1 AAAAG-GGCTTTGCC-CCAGTT-TATG
30055793 ATAAAG
1 A-AAAG
30055799 TAGCTATGCT
Statistics
Matches: 70, Mismatches: 5, Indels: 9
0.83 0.06 0.11
Matches are distributed among these distances:
23 5 0.07
24 11 0.16
25 45 0.64
26 1 0.01
27 4 0.06
28 4 0.06
ACGTcount: A:0.29, C:0.22, G:0.24, T:0.25
Consensus pattern (24 bp):
AAAAGGGCTTTGCCCCAGTTTATG
Found at i:30056018 original size:31 final size:31
Alignment explanation
Indices: 30055983--30056065 Score: 114
Period size: 31 Copynumber: 2.7 Consensus size: 31
30055973 GTTTATAGTG
* * *
30055983 AAGGCTTCAGACCAGTGATATGAATAATGAA
1 AAGGCTTCGGCCCAGTGATATGAACAATGAA
* *
30056014 AAGGCTTCGGCCCAGTGACATGAACAATGTA
1 AAGGCTTCGGCCCAGTGATATGAACAATGAA
30056045 AAGGCTTCGGCCCAGT-ATATG
1 AAGGCTTCGGCCCAGTGATATG
30056066 CTGAGATTGA
Statistics
Matches: 46, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
30 4 0.09
31 42 0.91
ACGTcount: A:0.34, C:0.19, G:0.25, T:0.22
Consensus pattern (31 bp):
AAGGCTTCGGCCCAGTGATATGAACAATGAA
Found at i:30058635 original size:25 final size:25
Alignment explanation
Indices: 30058479--30058626 Score: 165
Period size: 25 Copynumber: 6.0 Consensus size: 25
30058469 TATAGTCAAA
* *
30058479 CGAGCTGTA-AACGGGAAGCTTC-TC
1 CGAGCTGAATAACGGGAAGC-TCATG
* *
30058503 CGAGCTGAATAATGGGAAGCTCATA
1 CGAGCTGAATAACGGGAAGCTCATG
*
30058528 CGAGCTAAATAACGGGAAGCTCATG
1 CGAGCTGAATAACGGGAAGCTCATG
* * *
30058553 TGAGCTGAATATCTGGAAGCTCATG
1 CGAGCTGAATAACGGGAAGCTCATG
* **
30058578 CGAGCTGAATATCAAGAAGCTCATG
1 CGAGCTGAATAACGGGAAGCTCATG
*
30058603 CGAGCTGTATAACGGGAAGCTCAT
1 CGAGCTGAATAACGGGAAGCTCAT
30058627 ATGAGCTGTG
Statistics
Matches: 105, Mismatches: 17, Indels: 3
0.84 0.14 0.02
Matches are distributed among these distances:
24 10 0.10
25 95 0.90
ACGTcount: A:0.32, C:0.20, G:0.28, T:0.21
Consensus pattern (25 bp):
CGAGCTGAATAACGGGAAGCTCATG
Found at i:30062777 original size:136 final size:136
Alignment explanation
Indices: 30062533--30062817 Score: 543
Period size: 136 Copynumber: 2.1 Consensus size: 136
30062523 GAGTAGTCTC
*
30062533 CCCAAATGGGCTTGCATATGTTATTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATACT
1 CCCAAATGGGCTTGCATATGTTACTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATACT
30062598 GTTATCTGAATAAGGGGCTAAGGCCCAGTTTATTGTAATCTGAAAAGGGCTCTGGCCCAGTACCA
66 GTTATCTGAATAAGGGGCTAAGGCCCAGTTTATTGTAATCTGAAAAGGGCTCTGGCCCAGTACCA
30062663 CTGTTA
131 CTGTTA
30062669 CCCAAATGGGCTTGCATATGTTACTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATACT
1 CCCAAATGGGCTTGCATATGTTACTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATACT
30062734 GTTATCTGAATAAGGGGCTAAGGCCCAGTTTATTGTAATCTGAAAAGGGCTCTGGCCCAGTACCA
66 GTTATCTGAATAAGGGGCTAAGGCCCAGTTTATTGTAATCTGAAAAGGGCTCTGGCCCAGTACCA
30062799 CTGTTA
131 CTGTTA
**
30062805 CCTGAATGGGCTT
1 CCCAAATGGGCTT
30062818 AGGCCCAATA
Statistics
Matches: 146, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
136 146 1.00
ACGTcount: A:0.25, C:0.19, G:0.25, T:0.31
Consensus pattern (136 bp):
CCCAAATGGGCTTGCATATGTTACTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATACT
GTTATCTGAATAAGGGGCTAAGGCCCAGTTTATTGTAATCTGAAAAGGGCTCTGGCCCAGTACCA
CTGTTA
Found at i:30066601 original size:26 final size:26
Alignment explanation
Indices: 30066565--30066674 Score: 184
Period size: 26 Copynumber: 4.2 Consensus size: 26
30066555 TGATACAAAT
30066565 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTCCA
30066591 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTCCA
* *
30066617 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTCCA
* *
30066643 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTCCA
30066669 TGATAA
1 TGATAA
30066675 GAATTTCATG
Statistics
Matches: 82, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
26 82 1.00
ACGTcount: A:0.34, C:0.05, G:0.25, T:0.36
Consensus pattern (26 bp):
TGATAATAGGTTAGGTAAATGTTCCA
Found at i:30068185 original size:26 final size:26
Alignment explanation
Indices: 30068156--30068205 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
30068146 TACAGTTTTA
30068156 CCCTAGGAGATAAATT-ACCGAAATAC
1 CCCTAGG-GATAAATTGACCGAAATAC
* *
30068182 CCCTAGGGTTAAATTGACCTAAAT
1 CCCTAGGGATAAATTGACCGAAAT
30068206 GCATGTTTGA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 7 0.33
26 14 0.67
ACGTcount: A:0.38, C:0.22, G:0.16, T:0.24
Consensus pattern (26 bp):
CCCTAGGGATAAATTGACCGAAATAC
Found at i:30072527 original size:26 final size:26
Alignment explanation
Indices: 30072491--30072600 Score: 184
Period size: 26 Copynumber: 4.2 Consensus size: 26
30072481 TGATACAAAT
30072491 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTCCA
30072517 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTCCA
* *
30072543 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTCCA
* *
30072569 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTCCA
30072595 TGATAA
1 TGATAA
30072601 GAATTTCATG
Statistics
Matches: 82, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
26 82 1.00
ACGTcount: A:0.34, C:0.05, G:0.25, T:0.36
Consensus pattern (26 bp):
TGATAATAGGTTAGGTAAATGTTCCA
Found at i:30076687 original size:18 final size:19
Alignment explanation
Indices: 30076650--30076688 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
30076640 ATTACAAAAT
*
30076650 AATTCAAAATAATTTTTAA
1 AATTCAAAATAATTTATAA
30076669 AATTCAAAAT-ATTTATAA
1 AATTCAAAATAATTTATAA
30076687 AA
1 AA
30076689 ATTCTTAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 9 0.47
19 10 0.53
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.38
Consensus pattern (19 bp):
AATTCAAAATAATTTATAA
Found at i:30079148 original size:45 final size:45
Alignment explanation
Indices: 30079084--30079286 Score: 271
Period size: 45 Copynumber: 4.5 Consensus size: 45
30079074 GTTCTATGCT
** * * * * *
30079084 GTCTTTCAAACATGGTCTTATTCGTTTGATTCGTGATGCCATAGC
1 GTCTTTCAGTCATGGTCTTACTCGATAGAATCGTGATGCCATAAC
* * *
30079129 GTCTTTTAGTTATGGTCTTACTCGATAGAATCGTGATGTCATAAC
1 GTCTTTCAGTCATGGTCTTACTCGATAGAATCGTGATGCCATAAC
* *
30079174 GTCTTTTAGTCATGGTCTTACTCGATAGAATCATGATGCCATAAC
1 GTCTTTCAGTCATGGTCTTACTCGATAGAATCGTGATGCCATAAC
* * *
30079219 GTCTCTCAATCATGGTCTTACTTGATAGAATCGTGATGCCATAAC
1 GTCTTTCAGTCATGGTCTTACTCGATAGAATCGTGATGCCATAAC
30079264 GTCTTTCAGTCATGGTCTTACTC
1 GTCTTTCAGTCATGGTCTTACTC
30079287 ATTTCTAGTA
Statistics
Matches: 137, Mismatches: 21, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
45 137 1.00
ACGTcount: A:0.23, C:0.20, G:0.19, T:0.38
Consensus pattern (45 bp):
GTCTTTCAGTCATGGTCTTACTCGATAGAATCGTGATGCCATAAC
Found at i:30079304 original size:45 final size:45
Alignment explanation
Indices: 30079168--30079306 Score: 117
Period size: 45 Copynumber: 3.1 Consensus size: 45
30079158 ATCGTGATGT
* * * *
30079168 CATAACGTCTTTTAGTCATGGTCTTACTCGA--TAGAATCATGATGC
1 CATAACGTCTTTCAGTCATGGTCTTACTC-ATTTATAGT-ATGGTGC
* * * *
30079213 CATAACGTCTCTCAATCATGGTCTTA--C-TTGATAGAATCGTGATGC
1 CATAACGTCTTTCAGTCATGGTCTTACTCATTTATAGTAT-G-G-TGC
*
30079258 CATAACGTCTTTCAGTCATGGTCTTACTCATTTCTAGTATGGTGC
1 CATAACGTCTTTCAGTCATGGTCTTACTCATTTATAGTATGGTGC
30079303 CATA
1 CATA
30079307 GTGTTTTTCA
Statistics
Matches: 73, Mismatches: 13, Indels: 16
0.72 0.13 0.16
Matches are distributed among these distances:
42 2 0.03
43 4 0.05
45 57 0.78
46 1 0.01
47 2 0.03
48 7 0.10
ACGTcount: A:0.25, C:0.22, G:0.17, T:0.36
Consensus pattern (45 bp):
CATAACGTCTTTCAGTCATGGTCTTACTCATTTATAGTATGGTGC
Found at i:30079316 original size:45 final size:45
Alignment explanation
Indices: 30079275--30079381 Score: 142
Period size: 46 Copynumber: 2.4 Consensus size: 45
30079265 TCTTTCAGTC
* * * *
30079275 ATGGTCTTACTCATTTCTAGTATGGTGCCATAGTGTTTTTCAACT
1 ATGGTCTTAATCATTTCCAGTATAGTCCCATAGTGTTTTTCAACT
* * *
30079320 ATGGTCTTATTTATTCTCCGGTATAGTCCCATAGTGTTTTTCAACT
1 ATGGTCTTAATCATT-TCCAGTATAGTCCCATAGTGTTTTTCAACT
30079366 ATGGTCTTAATCATTT
1 ATGGTCTTAATCATTT
30079382 TGCTTCAAGC
Statistics
Matches: 53, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
45 14 0.26
46 39 0.74
ACGTcount: A:0.21, C:0.18, G:0.16, T:0.46
Consensus pattern (45 bp):
ATGGTCTTAATCATTTCCAGTATAGTCCCATAGTGTTTTTCAACT
Found at i:30081652 original size:23 final size:24
Alignment explanation
Indices: 30081577--30081680 Score: 126
Period size: 23 Copynumber: 4.3 Consensus size: 24
30081567 CAACTCGTAT
30081577 GAGCTTACCGATATATTAGCTCG-TAA
1 GAGCTTACCG-T-T-TTAGCTCGATAA
* *
30081603 GTGCTTACTGTTTTCAGCTC-ATAA
1 GAGCTTACCGTTTT-AGCTCGATAA
30081627 GAGCTTACCGTTTTAGCTCGAT-A
1 GAGCTTACCGTTTTAGCTCGATAA
30081650 GAGCTTACCGTTTTAGCTCGAT-A
1 GAGCTTACCGTTTTAGCTCGATAA
30081673 GAGCTTAC
1 GAGCTTAC
30081681 TGTCCATCAG
Statistics
Matches: 71, Mismatches: 4, Indels: 9
0.85 0.05 0.11
Matches are distributed among these distances:
23 39 0.55
24 23 0.32
25 1 0.01
26 8 0.11
ACGTcount: A:0.24, C:0.21, G:0.20, T:0.35
Consensus pattern (24 bp):
GAGCTTACCGTTTTAGCTCGATAA
Found at i:30081656 original size:47 final size:49
Alignment explanation
Indices: 30081577--30081680 Score: 128
Period size: 47 Copynumber: 2.2 Consensus size: 49
30081567 CAACTCGTAT
* *
30081577 GAGCTTACCGATATATTAGCTCGTAAGTGCTTACTGTTTTCAGCTC-ATAA
1 GAGCTTACCGATATATTAGCTCGTAAGAGCTTACCGTTTT-AGCTCGAT-A
30081627 GAGCTTACCG-T-T-TTAGCTCG-ATAGAGCTTACCGTTTTAGCTCGATA
1 GAGCTTACCGATATATTAGCTCGTA-AGAGCTTACCGTTTTAGCTCGATA
30081673 GAGCTTAC
1 GAGCTTAC
30081681 TGTCCATCAG
Statistics
Matches: 50, Mismatches: 2, Indels: 8
0.83 0.03 0.13
Matches are distributed among these distances:
46 15 0.30
47 23 0.46
48 1 0.02
49 1 0.02
50 10 0.20
ACGTcount: A:0.24, C:0.21, G:0.20, T:0.35
Consensus pattern (49 bp):
GAGCTTACCGATATATTAGCTCGTAAGAGCTTACCGTTTTAGCTCGATA
Found at i:30103119 original size:16 final size:16
Alignment explanation
Indices: 30103098--30103152 Score: 92
Period size: 16 Copynumber: 3.4 Consensus size: 16
30103088 GATTAGTTCA
30103098 CTGTAATTGAATAGAG
1 CTGTAATTGAATAGAG
30103114 CTGTAATTGAATAGAG
1 CTGTAATTGAATAGAG
*
30103130 CTGTAATGGAATAGAG
1 CTGTAATTGAATAGAG
*
30103146 TTGTAAT
1 CTGTAAT
30103153 CAGTAATTCA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 37 1.00
ACGTcount: A:0.36, C:0.05, G:0.25, T:0.33
Consensus pattern (16 bp):
CTGTAATTGAATAGAG
Found at i:30112397 original size:92 final size:93
Alignment explanation
Indices: 30112248--30112460 Score: 322
Period size: 92 Copynumber: 2.3 Consensus size: 93
30112238 ATGAAATGTG
*
30112248 TAAGACCATGGTTGAAAAATACCATGGCAACCTGATATGAAATGAATAAGACCATGGTTGAAAGA
1 TAAGACCATGGTTGAAAAATACCATGGCAACCTGACATGAAATGAATAAGACCATGGTTGAAAGA
* *
30112313 TACCATGGCAACATGACGGGAAATGA-A
66 TACCATGGCAACATGACAGAAAATGAGA
* * * *
30112340 TAAGACCATGGTTGAAAGATACCATGGCAGCGTGACATGAAATGAATAAGACTATGGTTGAAAGA
1 TAAGACCATGGTTGAAAAATACCATGGCAACCTGACATGAAATGAATAAGACCATGGTTGAAAGA
30112405 TACCATGGCAACATGACAGAAAATGAGA
66 TACCATGGCAACATGACAGAAAATGAGA
* * *
30112433 -AAGACCATAGTTGAAAAACACTATGGCA
1 TAAGACCATGGTTGAAAAATACCATGGCA
30112461 TCATGTCAAA
Statistics
Matches: 109, Mismatches: 11, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
92 108 0.99
93 1 0.01
ACGTcount: A:0.43, C:0.15, G:0.23, T:0.19
Consensus pattern (93 bp):
TAAGACCATGGTTGAAAAATACCATGGCAACCTGACATGAAATGAATAAGACCATGGTTGAAAGA
TACCATGGCAACATGACAGAAAATGAGA
Found at i:30112460 original size:46 final size:46
Alignment explanation
Indices: 30112238--30112448 Score: 291
Period size: 46 Copynumber: 4.6 Consensus size: 46
30112228 GCTCTCTGAT
** * * *
30112238 ATGAAATGTGTAAGACCATGGTTGAAAAATACCATGGCAACCTGAT
1 ATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATGAC
30112284 ATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATGAC
1 ATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATGAC
** * *
30112330 GGGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAGCGTGAC
1 ATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATGAC
*
30112376 ATGAAATGAATAAGACTATGGTTGAAAGATACCATGGCAACATGAC
1 ATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATGAC
*
30112422 A-GAAAATGAGA-AAGACCATAGTTGAAA
1 ATG-AAATGA-ATAAGACCATGGTTGAAA
30112449 AACACTATGG
Statistics
Matches: 147, Mismatches: 16, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
45 1 0.01
46 145 0.99
47 1 0.01
ACGTcount: A:0.43, C:0.14, G:0.24, T:0.20
Consensus pattern (46 bp):
ATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATGAC
Found at i:30127791 original size:23 final size:23
Alignment explanation
Indices: 30127759--30127802 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
30127749 ACTATCATTT
30127759 TCTAAATAAAATAATAATAAATA
1 TCTAAATAAAATAATAATAAATA
* *
30127782 TCTAATTAAAATATTAATAAA
1 TCTAAATAAAATAATAATAAA
30127803 ATAATATTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.61, C:0.05, G:0.00, T:0.34
Consensus pattern (23 bp):
TCTAAATAAAATAATAATAAATA
Found at i:30133955 original size:27 final size:28
Alignment explanation
Indices: 30133916--30133968 Score: 65
Period size: 28 Copynumber: 1.9 Consensus size: 28
30133906 CAACAATAAT
*
30133916 TATATAAATTATT-TAAAATCTATAAAAA
1 TATATAAATTATTGAAAAAT-TATAAAAA
*
30133944 TATATATA-TATTGAAAAATTATAAA
1 TATATAAATTATTGAAAAATTATAAA
30133969 TCAACTCAAC
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
27 10 0.45
28 12 0.55
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.40
Consensus pattern (28 bp):
TATATAAATTATTGAAAAATTATAAAAA
Found at i:30142169 original size:17 final size:17
Alignment explanation
Indices: 30142149--30142222 Score: 62
Period size: 18 Copynumber: 4.3 Consensus size: 17
30142139 TGCCTGACAC
*
30142149 CTTTTTGTTTTCTTTTT
1 CTTTTTATTTTCTTTTT
*
30142166 C-TTTTATTTTCATATTT
1 CTTTTTATTTTC-TTTTT
* *
30142183 CTTTTGTTTTTTCCTTTT
1 CTTTT-TATTTTCTTTTT
*
30142201 ATTTTTATATTTCTTTTT
1 CTTTTTAT-TTTCTTTTT
30142219 -TTTT
1 CTTTT
30142223 ACTTTTTTAT
Statistics
Matches: 45, Mismatches: 8, Indels: 8
0.74 0.13 0.13
Matches are distributed among these distances:
16 9 0.20
17 12 0.27
18 18 0.40
19 6 0.13
ACGTcount: A:0.08, C:0.11, G:0.03, T:0.78
Consensus pattern (17 bp):
CTTTTTATTTTCTTTTT
Found at i:30142202 original size:30 final size:28
Alignment explanation
Indices: 30142156--30142228 Score: 101
Period size: 30 Copynumber: 2.5 Consensus size: 28
30142146 CACCTTTTTG
*
30142156 TTTTCTTTTTCTTTTATTTTCATATTTC
1 TTTTTTTTTTCTTTTATTTTCATATTTC
*
30142184 TTTTGTTTTTTCCTTTTATTTTTATATTTC
1 TTTT-TTTTTT-CTTTTATTTTCATATTTC
*
30142214 TTTTTTTTTACTTTT
1 TTTTTTTTTTCTTTT
30142229 TTATTTTGTT
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
28 9 0.22
29 10 0.25
30 21 0.52
ACGTcount: A:0.10, C:0.11, G:0.01, T:0.78
Consensus pattern (28 bp):
TTTTTTTTTTCTTTTATTTTCATATTTC
Found at i:30142321 original size:10 final size:9
Alignment explanation
Indices: 30142254--30142322 Score: 57
Period size: 10 Copynumber: 6.9 Consensus size: 9
30142244 ATAAATTGTC
30142254 TTTTTATTT
1 TTTTTATTT
30142263 TTTTTACTTT
1 TTTTTA-TTT
*
30142273 TTTGATTTTTT
1 TTT--TTATTT
30142284 TTATTTCATTT
1 TT-TTT-ATTT
*
30142295 TGTTTATTT
1 TTTTTATTT
30142304 TGTTTTATTT
1 T-TTTTATTT
30142314 TTTATTATT
1 TTT-TTATT
30142323 AACTTTAAAA
Statistics
Matches: 49, Mismatches: 4, Indels: 13
0.74 0.06 0.20
Matches are distributed among these distances:
9 13 0.27
10 24 0.49
11 9 0.18
12 3 0.06
ACGTcount: A:0.13, C:0.03, G:0.04, T:0.80
Consensus pattern (9 bp):
TTTTTATTT
Found at i:30142580 original size:20 final size:21
Alignment explanation
Indices: 30142542--30142582 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
30142532 TTGTAAATAC
30142542 AATTTCTTTAATTTCTTTTTA
1 AATTTCTTTAATTTCTTTTTA
30142563 AATTT-TTTAACTTT-TTTTTA
1 AATTTCTTTAA-TTTCTTTTTA
30142583 TTTTTGAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 11 0.58
21 8 0.42
ACGTcount: A:0.24, C:0.07, G:0.00, T:0.68
Consensus pattern (21 bp):
AATTTCTTTAATTTCTTTTTA
Found at i:30142717 original size:30 final size:30
Alignment explanation
Indices: 30142681--30142755 Score: 141
Period size: 30 Copynumber: 2.5 Consensus size: 30
30142671 TTATTAAAAT
30142681 AAGTTGCATAGCGACGTCAACTCGTAACCC
1 AAGTTGCATAGCGACGTCAACTCGTAACCC
30142711 AAGTTGCATAGCGACGTCAACTCGTAACCC
1 AAGTTGCATAGCGACGTCAACTCGTAACCC
*
30142741 AAGTTGTATAGCGAC
1 AAGTTGCATAGCGAC
30142756 ATCTTCTAAT
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
30 44 1.00
ACGTcount: A:0.31, C:0.27, G:0.21, T:0.21
Consensus pattern (30 bp):
AAGTTGCATAGCGACGTCAACTCGTAACCC
Found at i:30144401 original size:21 final size:21
Alignment explanation
Indices: 30144373--30144460 Score: 56
Period size: 21 Copynumber: 4.1 Consensus size: 21
30144363 TTAAAAAAAG
30144373 AATTT-AAAAATAATATT-TAA
1 AATTTAAAAAAT-ATATTATAA
30144393 AATTGTAAAAAATATATTATAAA
1 AATT-TAAAAAATATATTAT-AA
* * * *
30144416 ACATTTTAAATATACATTACAA
1 A-ATTTAAAAAATATATTATAA
* * *
30144438 AATTTTAAAATTA-ATAATAA
1 AATTTAAAAAATATATTATAA
30144458 AAT
1 AAT
30144461 AAATAAATAA
Statistics
Matches: 55, Mismatches: 8, Indels: 10
0.75 0.11 0.14
Matches are distributed among these distances:
20 12 0.22
21 16 0.29
22 10 0.18
23 14 0.25
24 3 0.05
ACGTcount: A:0.58, C:0.03, G:0.01, T:0.38
Consensus pattern (21 bp):
AATTTAAAAAATATATTATAA
Found at i:30144460 original size:12 final size:13
Alignment explanation
Indices: 30144443--30144476 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
30144433 TACAAAATTT
*
30144443 TAAAATTAAT-AA
1 TAAAATAAATAAA
30144455 TAAAATAAATAAA
1 TAAAATAAATAAA
30144468 TAAAATAAA
1 TAAAATAAA
30144477 ATTATGATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
12 9 0.45
13 11 0.55
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (13 bp):
TAAAATAAATAAA
Found at i:30144506 original size:25 final size:27
Alignment explanation
Indices: 30144474--30144531 Score: 84
Period size: 25 Copynumber: 2.2 Consensus size: 27
30144464 TAAATAAAAT
*
30144474 AAAATTATGATTTCTTATAT-TA-TTA
1 AAAATTATGATTTCTTAAATGTATTTA
*
30144499 AAAATTATGATTTTTTAAATGTATTTA
1 AAAATTATGATTTCTTAAATGTATTTA
30144526 AAAATT
1 AAAATT
30144532 GTATTTAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
25 18 0.62
26 2 0.07
27 9 0.31
ACGTcount: A:0.43, C:0.02, G:0.05, T:0.50
Consensus pattern (27 bp):
AAAATTATGATTTCTTAAATGTATTTA
Found at i:30144663 original size:16 final size:16
Alignment explanation
Indices: 30144640--30144678 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
30144630 AATAATAATT
30144640 AAAC-ATAAAAAAACA
1 AAACAATAAAAAAACA
*
30144655 AAACAATAAAAAAAGA
1 AAACAATAAAAAAACA
*
30144671 AAAAAATA
1 AAACAATA
30144679 TTTAATATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 4 0.19
16 17 0.81
ACGTcount: A:0.82, C:0.08, G:0.03, T:0.08
Consensus pattern (16 bp):
AAACAATAAAAAAACA
Found at i:30144712 original size:12 final size:13
Alignment explanation
Indices: 30144676--30144722 Score: 60
Period size: 12 Copynumber: 3.5 Consensus size: 13
30144666 AAAGAAAAAA
30144676 ATATTTAATATTT
1 ATATTTAATATTT
30144689 AATATTTTAATATTT
1 -ATA-TTTAATATTT
30144704 ATA-TTAATATTT
1 ATATTTAATATTT
*
30144716 AAATTTA
1 ATATTTA
30144723 TTAATAGTCA
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
12 11 0.37
13 3 0.10
14 6 0.20
15 10 0.33
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (13 bp):
ATATTTAATATTT
Found at i:30144721 original size:6 final size:7
Alignment explanation
Indices: 30144675--30144722 Score: 66
Period size: 7 Copynumber: 7.1 Consensus size: 7
30144665 AAAAGAAAAA
30144675 AATATTT
1 AATATTT
30144682 AATATTT
1 AATATTT
30144689 AATATTTT
1 AATA-TTT
30144697 AATATTT
1 AATATTT
30144704 -ATA-TT
1 AATATTT
30144709 AATATTT
1 AATATTT
30144716 AA-ATTT
1 AATATTT
30144722 A
1 A
30144723 TTAATAGTCA
Statistics
Matches: 38, Mismatches: 0, Indels: 7
0.84 0.00 0.16
Matches are distributed among these distances:
5 2 0.05
6 11 0.29
7 18 0.47
8 7 0.18
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (7 bp):
AATATTT
Found at i:30144960 original size:37 final size:37
Alignment explanation
Indices: 30144913--30145024 Score: 126
Period size: 34 Copynumber: 3.2 Consensus size: 37
30144903 TAATAATTTC
* *
30144913 AAAACTAATTTGAAAAATATATATTTAAAATTTATAA
1 AAAAATAATTTCAAAAATATATATTTAAAATTTATAA
* * *
30144950 AAAAATAATTTCACAAATATATATCT-AAA-GT-TAA
1 AAAAATAATTTCAAAAATATATATTTAAAATTTATAA
* *
30144984 AAAAATAATTTTAAAAATA-ATAATTAAAATTTA-AA
1 AAAAATAATTTCAAAAATATATATTTAAAATTTATAA
30145019 AAAAAT
1 AAAAAT
30145025 TGTAAAAATT
Statistics
Matches: 62, Mismatches: 10, Indels: 8
0.77 0.12 0.10
Matches are distributed among these distances:
33 4 0.06
34 23 0.37
35 10 0.16
36 3 0.05
37 22 0.35
ACGTcount: A:0.61, C:0.04, G:0.02, T:0.34
Consensus pattern (37 bp):
AAAAATAATTTCAAAAATATATATTTAAAATTTATAA
Found at i:30145002 original size:34 final size:33
Alignment explanation
Indices: 30144913--30145033 Score: 111
Period size: 37 Copynumber: 3.5 Consensus size: 33
30144903 TAATAATTTC
* *
30144913 AAAACTAATTTGAAAAATATATATTTAAAATTTATAA
1 AAAAATAATTTTAAAAATATATA-TTAAAA--T-TAA
* * *
30144950 AAAAATAATTTCACAAATATATATCTAAAGTTAA
1 AAAAATAATTTTAAAAATATATAT-TAAAATTAA
*
30144984 AAAAATAATTTTAAAAATA-ATAATTAAAATTTA
1 AAAAATAATTTTAAAAATATAT-ATTAAAATTAA
*
30145017 AAAAA-AATTGTAAAAAT
1 AAAAATAATTTTAAAAAT
30145034 TAATAATATA
Statistics
Matches: 73, Mismatches: 9, Indels: 9
0.80 0.10 0.10
Matches are distributed among these distances:
32 11 0.15
33 14 0.19
34 22 0.30
35 1 0.01
36 1 0.01
37 24 0.33
ACGTcount: A:0.60, C:0.03, G:0.02, T:0.34
Consensus pattern (33 bp):
AAAAATAATTTTAAAAATATATATTAAAATTAA
Found at i:30145101 original size:25 final size:23
Alignment explanation
Indices: 30145077--30145129 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 23
30145067 TAATATAAAT
30145077 TAAATAAAAAATAAAATAAGAAAA
1 TAAATAAAAAATAAAA-AAGAAAA
**
30145101 TAATATAAAACTTAAAAAAGAAAA
1 TAA-ATAAAAAATAAAAAAGAAAA
30145125 TAAAT
1 TAAAT
30145130 TAAGAAAAAG
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
23 2 0.08
24 13 0.50
25 11 0.42
ACGTcount: A:0.74, C:0.02, G:0.04, T:0.21
Consensus pattern (23 bp):
TAAATAAAAAATAAAAAAGAAAA
Found at i:30145125 original size:37 final size:34
Alignment explanation
Indices: 30145065--30145137 Score: 101
Period size: 37 Copynumber: 2.1 Consensus size: 34
30145055 TTTTAAAATT
*
30145065 AATAATATAAATTAAATAAAAAATAAAATAAGAA
1 AATAATATAAATTAAAAAAAAAATAAAATAAGAA
*
30145099 AATAATATAAAACTTAAAAAAGAAAATAAATTAAGAA
1 AATAATAT-AAA-TTAAAAAA-AAAATAAAATAAGAA
30145136 AA
1 AA
30145138 AGACAAAATT
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
34 8 0.24
35 3 0.09
36 7 0.21
37 16 0.47
ACGTcount: A:0.73, C:0.01, G:0.04, T:0.22
Consensus pattern (34 bp):
AATAATATAAATTAAAAAAAAAATAAAATAAGAA
Found at i:30145265 original size:10 final size:10
Alignment explanation
Indices: 30145252--30145300 Score: 53
Period size: 10 Copynumber: 4.8 Consensus size: 10
30145242 CAAACTTTTC
*
30145252 AAAAATTTTA
1 AAAAAATTTA
*
30145262 AAAAAAGTTA
1 AAAAAATTTA
30145272 AAAAAATTTA
1 AAAAAATTTA
*
30145282 AAAAGAAATTA
1 AAAA-AATTTA
*
30145293 AAGAAATT
1 AAAAAATT
30145301 GTATTTACAA
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
10 24 0.75
11 8 0.25
ACGTcount: A:0.67, C:0.00, G:0.06, T:0.27
Consensus pattern (10 bp):
AAAAAATTTA
Found at i:30145277 original size:21 final size:22
Alignment explanation
Indices: 30145252--30145300 Score: 66
Period size: 21 Copynumber: 2.3 Consensus size: 22
30145242 CAAACTTTTC
*
30145252 AAAAATTTTAAAAA-AAGTTAA
1 AAAAATTTTAAAAAGAAATTAA
30145273 AAAAA-TTTAAAAAGAAATTAA
1 AAAAATTTTAAAAAGAAATTAA
*
30145294 AGAAATT
1 AAAAATT
30145301 GTATTTACAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 8 0.33
21 15 0.62
22 1 0.04
ACGTcount: A:0.67, C:0.00, G:0.06, T:0.27
Consensus pattern (22 bp):
AAAAATTTTAAAAAGAAATTAA
Found at i:30145371 original size:14 final size:14
Alignment explanation
Indices: 30145352--30145378 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
30145342 AAAAATATGG
30145352 TTAATATTTAAAAA
1 TTAATATTTAAAAA
30145366 TTAATATTTAAAA
1 TTAATATTTAAAA
30145379 TTTTAAAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (14 bp):
TTAATATTTAAAAA
Done.