Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold27
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: 2789374
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 115785 characters in sequence are not A, C, G, or T
File 7 of 16
Found at i:1145656 original size:21 final size:20
Alignment explanation
Indices: 1145631--1145678 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 20
1145621 TGCTATTTCG
1145631 TCATCTAAGTCACCAT-TATCA
1 TCATCTAA-TCACCATCT-TCA
*
1145652 TCATCATCATCACCATCTTCA
1 TCATC-TAATCACCATCTTCA
1145673 TCATCT
1 TCATCT
1145679 TTGATGGTTG
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
20 1 0.04
21 20 0.83
22 3 0.12
ACGTcount: A:0.29, C:0.33, G:0.02, T:0.35
Consensus pattern (20 bp):
TCATCTAATCACCATCTTCA
Found at i:1147299 original size:33 final size:33
Alignment explanation
Indices: 1147253--1147321 Score: 79
Period size: 33 Copynumber: 2.1 Consensus size: 33
1147243 CCATTTGAAG
*
1147253 CAATGTATCGATACCAT-T-CATCATGTATCGATA
1 CAATGTATCGATACAATGTGC--CATGTATCGATA
* *
1147286 CAATGTGTTGATACAATGTGCCATGTATCGATA
1 CAATGTATCGATACAATGTGCCATGTATCGATA
1147319 CAA
1 CAA
1147322 ACAATGGTAG
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
33 29 0.94
34 1 0.03
35 1 0.03
ACGTcount: A:0.33, C:0.19, G:0.16, T:0.32
Consensus pattern (33 bp):
CAATGTATCGATACAATGTGCCATGTATCGATA
Found at i:1147398 original size:19 final size:20
Alignment explanation
Indices: 1147351--1147402 Score: 70
Period size: 19 Copynumber: 2.6 Consensus size: 20
1147341 CGCTAGTTTT
**
1147351 ATGTATCGATACAATTGTCC
1 ATGTATCGATACAATTGAAC
*
1147371 ATATATCGATACAA-TGAAC
1 ATGTATCGATACAATTGAAC
1147390 ATGTATCGATACA
1 ATGTATCGATACA
1147403 TTGTATCCAT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
19 15 0.54
20 13 0.46
ACGTcount: A:0.38, C:0.17, G:0.13, T:0.31
Consensus pattern (20 bp):
ATGTATCGATACAATTGAAC
Found at i:1150925 original size:79 final size:78
Alignment explanation
Indices: 1150809--1151165 Score: 322
Period size: 79 Copynumber: 4.5 Consensus size: 78
1150799 ATAAAAACGA
* * * * * * *
1150809 GGTTGGAGTATCCTCTCAGAAATAACGTGGTTAGAGTACCCCCAATTGTGTAAAATTAATGTTTT
1 GGTTGGAGTATCCCCTCAAAAATAAAG-GGTTGGAGTATCCCCAATTGTGAAAAATCAATGTTTT
1150874 AGAAATAAAGCCAG
65 AGAAATAAAGCCAG
* * * * * *
1150888 GGTTGGAGTATCCCTTCAAAAATAATGGGCTTGGAGTATACCCGATTTTGAAAAATCAGTGTTTT
1 GGTTGGAGTATCCCCTCAAAAATAAAGGG-TTGGAGTATCCCCAATTGTGAAAAATCAATGTTTT
* **
1150953 GGAAA-AACA-CTGG
65 AGAAATAA-AGCCAG
* * * * * ** *
1150966 GGTTGGAGTATCCCCTCAGAAATAACGGGGTTGGAGTATCCCCGATTATAAAAAATTGATATTTT
1 GGTTGGAGTATCCCCTCAAAAATAA-AGGGTTGGAGTATCCCCAATTGTGAAAAATCAATGTTTT
* *
1151031 AGAAATAAGGCCAA
65 AGAAATAAAGCCAG
* * * *
1151045 GATTGGAGTATTCCCTCAAAAATAACAGGGTTGGAGTATCCCCAATTGTGAAAAGTCGATGTTTT
1 GGTTGGAGTATCCCCTCAAAAATAA-AGGGTTGGAGTATCCCCAATTGTGAAAAATCAATGTTTT
* * * *
1151110 GAAAAAAAAAACTAG
65 -AGAAATAAAGCCAG
*
1151125 GGTTGGAGTATCCCCTCACAAATAACAGGGTTGGAGTATCC
1 GGTTGGAGTATCCCCTCAAAAATAA-AGGGTTGGAGTATCC
1151166 TCGATTATAG
Statistics
Matches: 223, Mismatches: 49, Indels: 11
0.79 0.17 0.04
Matches are distributed among these distances:
78 61 0.27
79 116 0.52
80 46 0.21
ACGTcount: A:0.34, C:0.15, G:0.23, T:0.27
Consensus pattern (78 bp):
GGTTGGAGTATCCCCTCAAAAATAAAGGGTTGGAGTATCCCCAATTGTGAAAAATCAATGTTTTA
GAAATAAAGCCAG
Found at i:1151021 original size:157 final size:158
Alignment explanation
Indices: 1150801--1151174 Score: 452
Period size: 157 Copynumber: 2.4 Consensus size: 158
1150791 TTTTGGAGAT
* * * * * * * **
1150801 AAAAACGA-GGTTGGAGTATCCTCTCAGAAATAACGTGGTTAGAGTACCCCCAATTGTGTAAAAT
1 AAAAACTAGGGTTGGAGTATCCCCTCAGAAATAACGGGGTTGGAGTATCCCCGATTATAAAAAAT
* * * *
1150865 TAATGTTTTAGAAATAAAGCCAGGGTTGGAGTA-TCCCTTCAAAAATAA-TGGGCTTGGAGTATA
66 TAATATTTTAGAAATAAAGCCAAGATTGGAGTATTCCC-TCAAAAATAACAGGG-TTGGAGTATA
* * *
1150928 CCCGATTTTGAAAAATC-AGTGTTTTG-GAA
129 CCCAATTGTGAAAAATCGA-TGTTTTGAAAA
* *
1150957 AAACACTGGGGTTGGAGTATCCCCTCAGAAATAACGGGGTTGGAGTATCCCCGATTATAAAAAAT
1 AAAAACTAGGGTTGGAGTATCCCCTCAGAAATAACGGGGTTGGAGTATCCCCGATTATAAAAAAT
* * *
1151022 TGATATTTTAGAAATAAGGCCAAGATTGGAGTATTCCCTCAAAAATAACAGGGTTGGAGTATCCC
66 TAATATTTTAGAAATAAAGCCAAGATTGGAGTATTCCCTCAAAAATAACAGGGTTGGAGTATACC
*
1151087 CAATTGTGAAAAGTCGATGTTTTGAAAAA
131 CAATTGTGAAAAATCGATGTTTTG-AAAA
* * *
1151116 AAAAACTAGGGTTGGAGTATCCCCTCACAAATAACAGGGTTGGAGTATCCTCGATTATA
1 AAAAACTAGGGTTGGAGTATCCCCTCAGAAATAACGGGGTTGGAGTATCCCCGATTATA
1151175 GAAATTTTGA
Statistics
Matches: 185, Mismatches: 27, Indels: 9
0.84 0.12 0.04
Matches are distributed among these distances:
156 5 0.03
157 116 0.63
158 8 0.04
159 56 0.30
ACGTcount: A:0.35, C:0.15, G:0.22, T:0.27
Consensus pattern (158 bp):
AAAAACTAGGGTTGGAGTATCCCCTCAGAAATAACGGGGTTGGAGTATCCCCGATTATAAAAAAT
TAATATTTTAGAAATAAAGCCAAGATTGGAGTATTCCCTCAAAAATAACAGGGTTGGAGTATACC
CAATTGTGAAAAATCGATGTTTTGAAAA
Found at i:1152103 original size:13 final size:13
Alignment explanation
Indices: 1152085--1152133 Score: 50
Period size: 13 Copynumber: 3.9 Consensus size: 13
1152075 AAGAACAAAA
1152085 GTTGC-TGGTGTAT
1 GTTGCTTGGTGT-T
*
1152098 GTTGC-T-GTGTG
1 GTTGCTTGGTGTT
*
1152109 GTTACTTGGTGTT
1 GTTGCTTGGTGTT
1152122 GTTGCTTGGTGT
1 GTTGCTTGGTGT
1152134 CGCCATTTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
11 4 0.13
12 5 0.17
13 21 0.70
ACGTcount: A:0.04, C:0.08, G:0.39, T:0.49
Consensus pattern (13 bp):
GTTGCTTGGTGTT
Found at i:1152942 original size:27 final size:27
Alignment explanation
Indices: 1152918--1152969 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
1152908 ATGGTTTTGG
*
1152918 ATTTTT-TTTTGTTTCCTTGATTTTTCA
1 ATTTTTATTTTATTT-CTTGATTTTTCA
*
1152945 ATTTTTATTTTATTTTTTGATTTTT
1 ATTTTTATTTTATTTCTTGATTTTT
1152970 AAGTTCTATA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
27 15 0.68
28 7 0.32
ACGTcount: A:0.13, C:0.06, G:0.06, T:0.75
Consensus pattern (27 bp):
ATTTTTATTTTATTTCTTGATTTTTCA
Found at i:1153741 original size:43 final size:43
Alignment explanation
Indices: 1153651--1153744 Score: 109
Period size: 43 Copynumber: 2.2 Consensus size: 43
1153641 AGAAGAGTGA
* * *
1153651 TAAAGATGCCAATATGTTGATTCAAGGCCAACGATATTAGGCT
1 TAAAGATGCCAATATGCTGATTCAAGGCCAACGACATTAGGCC
* * **
1153694 TAAAGGTGCCAATGTGCTGATTCAAGGCCAGTGACATT-GGACC
1 TAAAGATGCCAATATGCTGATTCAAGGCCAACGACATTAGG-CC
1153737 TAAAGATG
1 TAAAGATG
1153745 ACAGAGGTGC
Statistics
Matches: 42, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
42 2 0.05
43 40 0.95
ACGTcount: A:0.33, C:0.17, G:0.24, T:0.26
Consensus pattern (43 bp):
TAAAGATGCCAATATGCTGATTCAAGGCCAACGACATTAGGCC
Found at i:1153785 original size:52 final size:51
Alignment explanation
Indices: 1153695--1154104 Score: 337
Period size: 52 Copynumber: 7.9 Consensus size: 51
1153685 TATTAGGCTT
* * *
1153695 AAAGGTGCCAATGTGCTGATTCAAGGCCAGTGACATTGGACCTAAAGATGA
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGA
* * * * * * *
1153746 CAGAGGTGCCAATATGTTGATTCAAGGCCAGCAATATTGGGCTTAAAGGTGC
1 -AAAGGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGA
* * * * * * * *
1153798 GAAGAATGTCAATGTGCTAATTCATGACCAGCGACATTAGACTTAAAGATTAGA
1 AAAG-GTGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGA-T-GA
* * * * * ** *
1153852 AAA-ATACTAATGTGCTGATTCAAGGCCAGCGACATTGGGCTTAGGGATGTT
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATG-A
* * * *
1153903 AAAGATGCCAATATGCTGCTTCAAGGCCAGCGATA-TCGACTTAAAGATGA
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGA
*
1153953 AGGTGAAGGTGCCAATGA-GCTGATTCAAGGCCAGCAACATTGGACTTAAAGATG-
1 A----AAGGTGCCAAT-ATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGA
* * * * *
1154007 -AAGGTGCCAATGTACTAATTCAAGGCTAGCGACATTGGACTTAAATG-TGGT
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAA-GAT-GA
*
1154058 AAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAG
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAG
1154105 GTGCCAATCT
Statistics
Matches: 280, Mismatches: 62, Indels: 33
0.75 0.17 0.09
Matches are distributed among these distances:
49 40 0.14
50 4 0.01
51 17 0.06
52 173 0.62
53 1 0.00
54 31 0.11
55 14 0.05
ACGTcount: A:0.33, C:0.17, G:0.26, T:0.24
Consensus pattern (51 bp):
AAAGGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGA
Found at i:1154118 original size:43 final size:43
Alignment explanation
Indices: 1154057--1154182 Score: 198
Period size: 43 Copynumber: 2.9 Consensus size: 43
1154047 TTAAATGTGG
1154057 TAAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACT
1 TAAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACT
* * *
1154100 TAAAGGTGCCAATCTGCTGATTCAAGGCTAGCAATATTGGACT
1 TAAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACT
* * *
1154143 TAAAGGTGCCAATGTGCTGATTCAAGGCCAACGACATTGG
1 TAAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGG
1154183 GCCTAGAAAG
Statistics
Matches: 75, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
43 75 1.00
ACGTcount: A:0.30, C:0.19, G:0.25, T:0.25
Consensus pattern (43 bp):
TAAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACT
Found at i:1154126 original size:21 final size:21
Alignment explanation
Indices: 1154102--1154169 Score: 52
Period size: 21 Copynumber: 3.2 Consensus size: 21
1154092 ATTGGACTTA
*
1154102 AAGGTGCCAATCTGCTGATTC
1 AAGGTGCCAATATGCTGATTC
*
1154123 AAGGCTAG-CAATAT--TGGACTTA
1 AAGG-T-GCCAATATGCT-GA-TTC
*
1154145 AAGGTGCCAATGTGCTGATTC
1 AAGGTGCCAATATGCTGATTC
1154166 AAGG
1 AAGG
1154170 CCAACGACAT
Statistics
Matches: 36, Mismatches: 4, Indels: 14
0.67 0.07 0.26
Matches are distributed among these distances:
20 2 0.06
21 18 0.50
22 14 0.39
23 2 0.06
ACGTcount: A:0.29, C:0.18, G:0.26, T:0.26
Consensus pattern (21 bp):
AAGGTGCCAATATGCTGATTC
Found at i:1154232 original size:32 final size:31
Alignment explanation
Indices: 1154196--1154313 Score: 121
Period size: 32 Copynumber: 3.7 Consensus size: 31
1154186 TAGAAAGAGA
* *
1154196 TGCCACCGACTTGTCTGGGCTTTTGAAAGGGT
1 TGCCACCGACTTGTGTAGGC-TTTGAAAGGGT
** *
1154228 TGCCA-ATAGCTTGAGTAGGCTTTGAGAAGGGT
1 TGCCACCGA-CTTGTGTAGGCTTTGA-AAGGGT
* * *
1154260 TGCCACCAATTTGTGTAGGCTTTGAAGGGGT
1 TGCCACCGACTTGTGTAGGCTTTGAAAGGGT
*
1154291 TGCCACCGACTTGTGTGGGCTTT
1 TGCCACCGACTTGTGTAGGCTTT
1154314 TGAAGAAGGT
Statistics
Matches: 70, Mismatches: 13, Indels: 7
0.78 0.14 0.08
Matches are distributed among these distances:
31 31 0.44
32 38 0.54
33 1 0.01
ACGTcount: A:0.18, C:0.19, G:0.32, T:0.31
Consensus pattern (31 bp):
TGCCACCGACTTGTGTAGGCTTTGAAAGGGT
Found at i:1154975 original size:28 final size:27
Alignment explanation
Indices: 1154935--1154989 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 27
1154925 TTTTTTCTTA
1154935 CAATTCATCTTGA-CTCTACTAAGGATTG
1 CAATTCATCTTGATC-CTACT-AGGATTG
*
1154963 CAATTTATCTTGATCCTACTAGGATTG
1 CAATTCATCTTGATCCTACTAGGATTG
1154990 GGAGCCTTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
27 7 0.28
28 17 0.68
29 1 0.04
ACGTcount: A:0.27, C:0.20, G:0.15, T:0.38
Consensus pattern (27 bp):
CAATTCATCTTGATCCTACTAGGATTG
Found at i:1155930 original size:20 final size:19
Alignment explanation
Indices: 1155907--1155949 Score: 52
Period size: 19 Copynumber: 2.2 Consensus size: 19
1155897 TTTTTCCCAC
1155907 TTTTCTTT-TTTTTGTGGTTT
1 TTTTCTTTGTTTTT-T-GTTT
*
1155927 TTTTGTTTGTTTTTTGTTT
1 TTTTCTTTGTTTTTTGTTT
1155946 TTTT
1 TTTT
1155950 AAGTTTTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
19 8 0.38
20 8 0.38
21 5 0.24
ACGTcount: A:0.00, C:0.02, G:0.14, T:0.84
Consensus pattern (19 bp):
TTTTCTTTGTTTTTTGTTT
Found at i:1155939 original size:11 final size:10
Alignment explanation
Indices: 1155912--1155960 Score: 53
Period size: 11 Copynumber: 4.7 Consensus size: 10
1155902 CCCACTTTTC
1155912 TTTTTTTTGT
1 TTTTTTTTGT
*
1155922 GGTTTTTTTGT
1 -TTTTTTTTGT
1155933 TTGTTTTTTGT
1 TT-TTTTTTGT
**
1155944 TTTTTTAAGT
1 TTTTTTTTGT
1155954 TTTTTTT
1 TTTTTTT
1155961 ACAAAGGATG
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
10 13 0.41
11 19 0.59
ACGTcount: A:0.04, C:0.00, G:0.14, T:0.82
Consensus pattern (10 bp):
TTTTTTTTGT
Found at i:1165946 original size:21 final size:21
Alignment explanation
Indices: 1165922--1165968 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
1165912 TTTAATGCTG
1165922 ATTTTG-A-TGAAAAACGAAGT
1 ATTTTGAAGTGAAAAAC-AAGT
1165942 -TATTTGAAGTGAAAAACAAGT
1 AT-TTTGAAGTGAAAAACAAGT
1165963 ATTTTG
1 ATTTTG
1165969 CAAAAGATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 7
0.77 0.00 0.23
Matches are distributed among these distances:
19 1 0.04
20 4 0.17
21 9 0.39
22 9 0.39
ACGTcount: A:0.43, C:0.04, G:0.19, T:0.34
Consensus pattern (21 bp):
ATTTTGAAGTGAAAAACAAGT
Found at i:1166119 original size:68 final size:68
Alignment explanation
Indices: 1166043--1166178 Score: 272
Period size: 68 Copynumber: 2.0 Consensus size: 68
1166033 GGTGGATGTA
1166043 TCGATAGAATGAAGGAGGGTGGTTTGAACTGTTCAAATAATCACCCTGTATCGATACAGTGTATC
1 TCGATAGAATGAAGGAGGGTGGTTTGAACTGTTCAAATAATCACCCTGTATCGATACAGTGTATC
1166108 GAT
66 GAT
1166111 TCGATAGAATGAAGGAGGGTGGTTTGAACTGTTCAAATAATCACCCTGTATCGATACAGTGTATC
1 TCGATAGAATGAAGGAGGGTGGTTTGAACTGTTCAAATAATCACCCTGTATCGATACAGTGTATC
1166176 GAT
66 GAT
1166179 ATAATGTATC
Statistics
Matches: 68, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
68 68 1.00
ACGTcount: A:0.31, C:0.15, G:0.25, T:0.29
Consensus pattern (68 bp):
TCGATAGAATGAAGGAGGGTGGTTTGAACTGTTCAAATAATCACCCTGTATCGATACAGTGTATC
GAT
Found at i:1166175 original size:13 final size:13
Alignment explanation
Indices: 1166157--1166195 Score: 60
Period size: 13 Copynumber: 3.0 Consensus size: 13
1166147 ATAATCACCC
*
1166157 TGTATCGATACAG
1 TGTATCGATACAA
*
1166170 TGTATCGATATAA
1 TGTATCGATACAA
1166183 TGTATCGATACAA
1 TGTATCGATACAA
1166196 AGAAAAATGT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.36, C:0.13, G:0.18, T:0.33
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1166206 original size:20 final size:20
Alignment explanation
Indices: 1166181--1166259 Score: 77
Period size: 20 Copynumber: 3.7 Consensus size: 20
1166171 GTATCGATAT
1166181 AATGTATCGATACAAAGAAA
1 AATGTATCGATACAAAGAAA
*
1166201 AATGTATCGATACATAGAATTTCCA
1 AATGTATCGATACAAAGAA-----A
* *
1166226 GATGTATCGATACACAGAAA
1 AATGTATCGATACAAAGAAA
*
1166246 CATGTATCGATACA
1 AATGTATCGATACA
1166260 TTTTGGACAT
Statistics
Matches: 50, Mismatches: 4, Indels: 10
0.78 0.06 0.16
Matches are distributed among these distances:
20 32 0.64
25 18 0.36
ACGTcount: A:0.44, C:0.15, G:0.15, T:0.25
Consensus pattern (20 bp):
AATGTATCGATACAAAGAAA
Found at i:1168294 original size:15 final size:15
Alignment explanation
Indices: 1168274--1168304 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1168264 ATTTCGTTTG
*
1168274 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
1168289 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
1168304 G
1 G
1168305 GACATTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:1170137 original size:21 final size:21
Alignment explanation
Indices: 1170108--1170152 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
1170098 AAGTTTTCAT
*
1170108 TTTTCTTAGCTAAC-TCATTA
1 TTTTCTTAGCCAACTTCATTA
*
1170128 TTTTCATTAGCCAACTTCTTTA
1 TTTTC-TTAGCCAACTTCATTA
1170150 TTT
1 TTT
1170153 CAACTTGCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 8 0.38
22 8 0.38
ACGTcount: A:0.22, C:0.20, G:0.04, T:0.53
Consensus pattern (21 bp):
TTTTCTTAGCCAACTTCATTA
Found at i:1179652 original size:52 final size:52
Alignment explanation
Indices: 1179582--1179702 Score: 215
Period size: 52 Copynumber: 2.3 Consensus size: 52
1179572 GAAAATTTAT
*
1179582 CTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGC
* *
1179634 TTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGC
1179686 CTGCATGTATCGATACA
1 CTGCATGTATCGATACA
1179703 AAGATCAGTG
Statistics
Matches: 65, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 65 1.00
ACGTcount: A:0.29, C:0.17, G:0.18, T:0.36
Consensus pattern (52 bp):
CTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGC
Found at i:1179715 original size:52 final size:51
Alignment explanation
Indices: 1179582--1179722 Score: 203
Period size: 52 Copynumber: 2.7 Consensus size: 51
1179572 GAAAATTTAT
1179582 CTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGCAAATTTGC
* * *
1179634 TTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGCAAATTTGC
*
1179686 CTGCATGTATCGATACA-AAGATCAGTGTATCGATACA
1 CTGCATGTATCGATACATTA-AT-AGTGTATCGATACA
1179723 ATGTATCGAT
Statistics
Matches: 80, Mismatches: 7, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
51 2 0.03
52 78 0.98
ACGTcount: A:0.30, C:0.17, G:0.18, T:0.34
Consensus pattern (51 bp):
CTGCATGTATCGATACATTAATAGTGTATCGATACATCTGGGCAAATTTGC
Found at i:1179729 original size:13 final size:13
Alignment explanation
Indices: 1179711--1179735 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1179701 CAAAGATCAG
1179711 TGTATCGATACAA
1 TGTATCGATACAA
1179724 TGTATCGATACA
1 TGTATCGATACA
1179736 TTTGAGTAAT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1181393 original size:79 final size:78
Alignment explanation
Indices: 1181307--1181669 Score: 359
Period size: 79 Copynumber: 4.6 Consensus size: 78
1181297 GATAAAAACG
** * *
1181307 GGGTTGGAGTATCCTTTCAGAAATAACGGGGTTGGAGTATCCTCGATTGTGGAAAA-TCGATGTT
1 GGGTTGGAGTATCCCCTCAGAAATAACGAGGTTGGAGTATCCCCGATTGT-GAAAAGTCGATGTT
*
1181371 TTAGAAATAAAGTA
65 TTAGAAATAAACTA
*
1181385 GAGGTTGGAGTATCCCCTC-GAAAATAACGAGGTTGGAGTATCCCCGATTGTGAAAAGTC-AGCG
1 G-GGTTGGAGTATCCCCTCAG-AAATAACGAGGTTGGAGTATCCCCGATTGTGAAAAGTCGA-TG
*
1181448 TTTT-GAAA-AAACAA
63 TTTTAGAAATAAACTA
* * * * *
1181462 CCAGTTTAGAGTATCCCCTCAGAAATAAC-AGGTTGGAGTATCCCCGATTATAGAAAA-TCGAAG
1 --GGGTTGGAGTATCCCCTCAGAAATAACGAGGTTGGAGTATCCCCGATTGT-GAAAAGTCGATG
*
1181525 TTTTAGAAATAAGGC-A
63 TTTTAGAAATAA-ACTA
* * *
1181541 GGGATTGGAGTATCCCCTCTA-AAATAACGAAGTTGGAGTATCCCCGATTGTGAAAAGTTGGTGT
1 GGG-TTGGAGTATCCCCTC-AGAAATAACGAGGTTGGAGTATCCCCGATTGTGAAAAGTCGATGT
* *
1181605 TTTGAAAAAAAAAACTA
64 TTT--AGAAATAAACTA
* *
1181622 GGGTTGGAGTATCCCTTCAAAAATAAC-AGGGTTGGAGTATCCCCGATT
1 GGGTTGGAGTATCCCCTCAGAAATAACGA-GGTTGGAGTATCCCCGATT
1181670 ATAGAAATTT
Statistics
Matches: 238, Mismatches: 26, Indels: 40
0.78 0.09 0.13
Matches are distributed among these distances:
77 33 0.14
78 70 0.29
79 84 0.35
80 41 0.17
81 10 0.04
ACGTcount: A:0.33, C:0.15, G:0.25, T:0.27
Consensus pattern (78 bp):
GGGTTGGAGTATCCCCTCAGAAATAACGAGGTTGGAGTATCCCCGATTGTGAAAAGTCGATGTTT
TAGAAATAAACTA
Found at i:1181521 original size:156 final size:158
Alignment explanation
Indices: 1181307--1181676 Score: 512
Period size: 156 Copynumber: 2.3 Consensus size: 158
1181297 GATAAAAACG
* * * * * * *
1181307 GGGTTGGAGTATCCTTTCAGAAATAACGGGGTTGGAGTATCCTCGATTGTGGAAAATCGATGTTT
1 GGGTTAGAGTATCCCTTCAGAAATAAC-AGGTTGGAGTATCCCCGATTATAGAAAATCGAAGTTT
* *
1181372 TAGAAATAAAGTAGAGG-TTGGAGTATCCCCTCGAAAATAACGAGGTTGGAGTATCCCCGATTGT
65 TAGAAATAAAGCAG-GGATTGGAGTATCCCCTCGAAAATAACGAAGTTGGAGTATCCCCGATTGT
*
1181436 GAAAAGTCAGCGTTTTG-AAAAAACAACCA
129 GAAAAGTCAGCGTTTTGAAAAAAAAAACCA
* *
1181465 -GTTTAGAGTATCCCCTCAGAAATAACAGGTTGGAGTATCCCCGATTATAGAAAATCGAAGTTTT
1 GGGTTAGAGTATCCCTTCAGAAATAACAGGTTGGAGTATCCCCGATTATAGAAAATCGAAGTTTT
* *
1181529 AGAAATAAGGCAGGGATTGGAGTATCCCCTCTAAAATAACGAAGTTGGAGTATCCCCGATTGTGA
66 AGAAATAAAGCAGGGATTGGAGTATCCCCTCGAAAATAACGAAGTTGGAGTATCCCCGATTGTGA
** * *
1181594 AAAGTTGGTGTTTTGAAAAAAAAAACTA
131 AAAGTCAGCGTTTTGAAAAAAAAAACCA
* *
1181622 GGGTTGGAGTATCCCTTCAAAAATAACAGGGTTGGAGTATCCCCGATTATAGAAA
1 GGGTTAGAGTATCCCTTCAGAAATAACA-GGTTGGAGTATCCCCGATTATAGAAA
1181677 TTTTGGTATT
Statistics
Matches: 186, Mismatches: 22, Indels: 7
0.87 0.10 0.03
Matches are distributed among these distances:
155 2 0.01
156 103 0.55
157 32 0.17
158 23 0.12
159 26 0.14
ACGTcount: A:0.34, C:0.15, G:0.25, T:0.26
Consensus pattern (158 bp):
GGGTTAGAGTATCCCTTCAGAAATAACAGGTTGGAGTATCCCCGATTATAGAAAATCGAAGTTTT
AGAAATAAAGCAGGGATTGGAGTATCCCCTCGAAAATAACGAAGTTGGAGTATCCCCGATTGTGA
AAAGTCAGCGTTTTGAAAAAAAAAACCA
Found at i:1183444 original size:20 final size:20
Alignment explanation
Indices: 1183423--1183460 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
1183413 TTTCCTTGAT
*
1183423 TTTTTTTATTTTT-ATTTTA
1 TTTTTTGATTTTTAATTTTA
1183442 TTTTTTGATTTTTAATTTT
1 TTTTTTGATTTTTAATTTT
1183461 TATATCATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.16, C:0.00, G:0.03, T:0.82
Consensus pattern (20 bp):
TTTTTTGATTTTTAATTTTA
Found at i:1183504 original size:9 final size:8
Alignment explanation
Indices: 1183423--1183520 Score: 63
Period size: 8 Copynumber: 11.8 Consensus size: 8
1183413 TTTCCTTGAT
1183423 TTTTTTTA
1 TTTTTTTA
1183431 TTTTTATTTTA
1 --TTT-TTTTA
*
1183442 TTTTTTGA
1 TTTTTTTA
*
1183450 -TTTTTAA
1 TTTTTTTA
*
1183457 TTTTTATA
1 TTTTTTTA
*
1183465 TCATTTTTA
1 T-TTTTTTA
* *
1183474 TTTCTTGA
1 TTTTTTTA
* * *
1183482 ATATTTGA
1 TTTTTTTA
1183490 TTTTTTTA
1 TTTTTTTA
1183498 TTTTTTTAA
1 TTTTTTT-A
1183507 TTTTTTTA
1 TTTTTTTA
1183515 TTTTTT
1 TTTTTT
1183521 ATCAAAGATA
Statistics
Matches: 69, Mismatches: 15, Indels: 10
0.73 0.16 0.11
Matches are distributed among these distances:
7 6 0.09
8 38 0.55
9 17 0.25
10 3 0.04
11 5 0.07
ACGTcount: A:0.18, C:0.02, G:0.03, T:0.77
Consensus pattern (8 bp):
TTTTTTTA
Found at i:1187523 original size:61 final size:61
Alignment explanation
Indices: 1187339--1187830 Score: 637
Period size: 61 Copynumber: 8.1 Consensus size: 61
1187329 AACCTTTTAT
* * *
1187339 CCTTTCAATCCTTAAAGAGCAAGACGTCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCA
1 CCTTTCAGTCCTCAAAGAGCAGGACGTCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCA
** * * * *
1187400 TTTTTTAGTCCTCAAAGAGCACAGCACTTCTTTTCC-GTTAAAGCCCACACAAGTTGGTGGCA
1 CCTTTCAGTCCTCAAAGAG--CAGGACGTCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCA
* * *
1187462 CCTTTCAGTCTTTAAAGAGCAGGACGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCA
1 CCTTTCAGTCCTCAAAGAGCAGGACGTCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCA
* * * * *
1187523 CTTTTTAGTCCTCAAAGAGTAGGACATCTTTTCCTTTTAAAGCCTACACAAGTTGGTGG-A
1 CCTTTCAGTCCTCAAAGAGCAGGACGTCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCA
* *
1187583 CCTTTCAGTCCTCAAAGAGCAGGACGCCTTTTCCTTTTAAAGCCCACATAAGTTGGTGGCA
1 CCTTTCAGTCCTCAAAGAGCAGGACGTCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCA
* * * * * * *
1187644 CCTTTCAATCCTTAAAAAGTAGGATGTCTTTTCCTTTTAAAGCCCGCACGAGTTGGTGGCA
1 CCTTTCAGTCCTCAAAGAGCAGGACGTCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCA
* * * *
1187705 CCTTTCAGTCCTCAAATAGTAGAACGTCTTTTCCTTTTAAAGCTCACACAAGTTGGTGGCA
1 CCTTTCAGTCCTCAAAGAGCAGGACGTCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCA
* * * * *
1187766 CATTTCAGTCCTCAAAGAGTAAGACGCCTTTTTCTTTTAAAGCCCACACAAGTTGGTGGCA
1 CCTTTCAGTCCTCAAAGAGCAGGACGTCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCA
1187827 CCTT
1 CCTT
1187831 CTAATCCCCA
Statistics
Matches: 369, Mismatches: 58, Indels: 8
0.85 0.13 0.02
Matches are distributed among these distances:
60 65 0.18
61 253 0.69
62 39 0.11
63 12 0.03
ACGTcount: A:0.26, C:0.25, G:0.18, T:0.31
Consensus pattern (61 bp):
CCTTTCAGTCCTCAAAGAGCAGGACGTCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCA
Found at i:1187677 original size:182 final size:183
Alignment explanation
Indices: 1187339--1187830 Score: 666
Period size: 182 Copynumber: 2.7 Consensus size: 183
1187329 AACCTTTTAT
* * * * * **
1187339 CCTTTCAATCCTTAAAGAGCAAGACGTCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCATTTT
1 CCTTTCAGTCCTCAAAGAGTAGGACGTCTTTTCCTTTTAAAGCCTACACAAGTTGGTGGCACATT
* * ** *
1187404 TTAGTCCTCAAAGAGCACAGCACTTCTTTTCC-GTTAAAGCCCACACAAGTTGGTGGCACCTTTC
66 TCAGTCCTCAAAGAG--CAGGACGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTTC
* * *
1187468 AGTCTTTAAAGAGCAGGACGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCA
129 AATCCTTAAAAAGCAGGACGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCA
* * * *
1187523 CTTTTTAGTCCTCAAAGAGTAGGACATCTTTTCCTTTTAAAGCCTACACAAGTTGGTGG-ACCTT
1 CCTTTCAGTCCTCAAAGAGTAGGACGTCTTTTCCTTTTAAAGCCTACACAAGTTGGTGGCACATT
*
1187587 TCAGTCCTCAAAGAGCAGGACGCCTTTTCCTTTTAAAGCCCACATAAGTTGGTGGCACCTTTCAA
66 TCAGTCCTCAAAGAGCAGGACGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTTCAA
* * * * *
1187652 TCCTTAAAAAGTAGGATGTCTTTTCCTTTTAAAGCCCGCACGAGTTGGTGGCA
131 TCCTTAAAAAGCAGGACGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCA
* *
1187705 CCTTTCAGTCCTCAAATAGTAGAACGTCTTTTCCTTTTAAAG-CTCACACAAGTTGGTGGCACAT
1 CCTTTCAGTCCTCAAAGAGTAGGACGTCTTTTCCTTTTAAAGCCT-ACACAAGTTGGTGGCACAT
* * *
1187769 TTCAGTCCTCAAAGAGTAAGACGCCTTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTT
65 TTCAGTCCTCAAAGAGCAGGACGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCTT
1187831 CTAATCCCCA
Statistics
Matches: 271, Mismatches: 34, Indels: 7
0.87 0.11 0.02
Matches are distributed among these distances:
181 14 0.05
182 128 0.47
183 78 0.29
184 51 0.19
ACGTcount: A:0.26, C:0.25, G:0.18, T:0.31
Consensus pattern (183 bp):
CCTTTCAGTCCTCAAAGAGTAGGACGTCTTTTCCTTTTAAAGCCTACACAAGTTGGTGGCACATT
TCAGTCCTCAAAGAGCAGGACGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTTCAA
TCCTTAAAAAGCAGGACGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCA
Found at i:1188537 original size:50 final size:51
Alignment explanation
Indices: 1188457--1188593 Score: 179
Period size: 50 Copynumber: 2.7 Consensus size: 51
1188447 TTTTCATAAT
**
1188457 ATGTATCGATACATCCTTCATTGTATCGATACATTCGGAAG-TTTA-CCCAG
1 ATGTATCGATACATTTTTCATTGTATCGATACATTC-GAAGTTTTATCCCAG
* * *
1188507 ATGTTTCGATACATTTTTCATTGTATCGATACATTCTAGGTTTTATCCCAG
1 ATGTATCGATACATTTTTCATTGTATCGATACATTCGAAGTTTTATCCCAG
* * *
1188558 ATGTATCGATACATTTCTCAATCTATCGATACATTC
1 ATGTATCGATACATTTTTCATTGTATCGATACATTC
1188594 AGGCATTTTT
Statistics
Matches: 76, Mismatches: 9, Indels: 3
0.86 0.10 0.03
Matches are distributed among these distances:
49 2 0.03
50 37 0.49
51 37 0.49
ACGTcount: A:0.27, C:0.20, G:0.13, T:0.39
Consensus pattern (51 bp):
ATGTATCGATACATTTTTCATTGTATCGATACATTCGAAGTTTTATCCCAG
Found at i:1189680 original size:5 final size:5
Alignment explanation
Indices: 1189670--1189696 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
1189660 TGCATTTGTT
1189670 TTTTC TTTTC TTTTC TTTTC TTTTC TT
1 TTTTC TTTTC TTTTC TTTTC TTTTC TT
1189697 CCCATAAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTTC
Found at i:1191093 original size:80 final size:79
Alignment explanation
Indices: 1190948--1191226 Score: 350
Period size: 80 Copynumber: 3.5 Consensus size: 79
1190938 TCATTCATGT
* * * * *
1190948 TTTTATTTCTAAAACATCGA-TGTTCCACCATCGGGGATACTCCAACCTCTTATTTCTGAGGGGA
1 TTTTATTTCTAAAACATCGATTTTTTCACAATCGAGGATACTCCAACCTGTTATTTCTGAGGGGA
* *
1191012 TATTCCAACCCCGA
66 TACTCTAACCCCGA
*
1191026 TTTTATTTCTAAAACATTGATTTTTTCACAATCGAGGATACTCCAACCCTGTTATTTCTGAGGGG
1 TTTTATTTCTAAAACATCGATTTTTTCACAATCGAGGATACTCCAA-CCTGTTATTTCTGAGGGG
**
1191091 ATACTCTTGCCCCGA
65 ATACTCTAACCCCGA
* * *
1191106 TTTTATTTCCAAAGCATCGATTTTTTCACAATCGGGGATACTCCAACCTCGTTATTT-TCGAGGG
1 TTTTATTTCTAAAACATCGATTTTTTCACAATCGAGGATACTCCAACCT-GTTATTTCT-GAGGG
1191170 GATACTCTAACCCC-A
64 GATACTCTAACCCCGA
* * *
1191185 GTTTTATTTCTAAAACA-CCAATTTTTCACCATCGAGGATACT
1 -TTTTATTTCTAAAACATCGATTTTTTCACAATCGAGGATACT
1191227 TTAACCTTGA
Statistics
Matches: 174, Mismatches: 22, Indels: 9
0.85 0.11 0.04
Matches are distributed among these distances:
78 19 0.11
79 47 0.27
80 108 0.62
ACGTcount: A:0.26, C:0.24, G:0.14, T:0.35
Consensus pattern (79 bp):
TTTTATTTCTAAAACATCGATTTTTTCACAATCGAGGATACTCCAACCTGTTATTTCTGAGGGGA
TACTCTAACCCCGA
Found at i:1191546 original size:79 final size:80
Alignment explanation
Indices: 1191235--1191684 Score: 424
Period size: 81 Copynumber: 5.6 Consensus size: 80
1191225 CTTTAACCTT
** * *
1191235 GATTTTATTTCCAAAATGTCGATTTTTTCATAATCGGGGATAC-CCGAACCCCGTTATTTTTGAA
1 GATTTTATTTCCAAAACATTGATTTTTTCATAATCGGGGATACTCC-AACCCCGTTATTTTTGAG
* * *
1191299 AGGATATTCCAACCTC
65 GGGATACTCCAACCCC
** * * * *
1191315 GATTTTATTTTTAAAAAATTGATTTTTTTTATAATCGAGGATACTCCAACCCCATTATTTTTGAG
1 GATTTTATTTCCAAAACATTGA-TTTTTTCATAATCGGGGATACTCCAACCCCGTTATTTTTGAG
* * *
1191380 AGGATATTCCAACTCC
65 GGGATACTCCAACCCC
* * *** * *
1191396 GATTTTATTTCTAAAACATTAATTTTTTTCATAATCGAAAATACTCCAAGCCCGTTATTTTTGAT
1 GATTTTATTTCCAAAACATTGA-TTTTTTCATAATCGGGGATACTCCAACCCCGTTATTTTTGAG
1191461 GGGATACTCCAACCCC
65 GGGATACTCCAACCCC
* * * * *
1191477 GATTTTATTTCCAAAACATCGA-TTTTTCATAATAGGGGAAACTCCAAGCCCGTTATTTTCGAGG
1 GATTTTATTTCCAAAACATTGATTTTTTCATAATCGGGGATACTCCAACCCCGTTATTTTTGAGG
1191541 GGATACTCCAACCCC
66 GGATACTCCAACCCC
* * * * * * * *
1191556 GGTTTTATTTTCGAAACATTGA-TTTTCCACT-ATTGGAGATACTCCAACCCCGTTATTTCTAAG
1 GATTTTATTTCCAAAACATTGATTTTTTCA-TAATCGGGGATACTCCAACCCCGTTATTTTTGAG
*
1191619 GTGATACTCCAACCCC
65 GGGATACTCCAACCCC
* * * * * **
1191635 GTTTTTATCTCCAAAATATTAAATTTTTCATCAA-CGGATATACTCCAACC
1 GATTTTATTTCCAAAACATTGATTTTTTCAT-AATCGGGGATACTCCAACC
1191685 ACGTACCCTG
Statistics
Matches: 309, Mismatches: 55, Indels: 12
0.82 0.15 0.03
Matches are distributed among these distances:
79 131 0.42
80 38 0.12
81 138 0.45
82 2 0.01
ACGTcount: A:0.29, C:0.22, G:0.12, T:0.37
Consensus pattern (80 bp):
GATTTTATTTCCAAAACATTGATTTTTTCATAATCGGGGATACTCCAACCCCGTTATTTTTGAGG
GGATACTCCAACCCC
Found at i:1193178 original size:162 final size:161
Alignment explanation
Indices: 1192783--1193267 Score: 567
Period size: 159 Copynumber: 3.0 Consensus size: 161
1192773 TCCATGTTTA
* * *
1192783 TTATTTTTT-TAATCTTTTATATTCTTATGGGCATCCAT-AGGAGTACAAAAGATTTCAAAAACG
1 TTATTTTTTCTAATCTTTTATATTCTTATGGGCATCCGTAAGG-GTATAAAAGATTTCAAAAACA
* * * * * *
1192846 TTTCGTATCCTTCCGAGCTTCCATTAGGGTACGAAATGTTATTTTTGAAAGTAAATAAAATCAAA
65 TTTCGTATCCTTTCGAGCTTCCATTAGGGTACAAAATGATATTTTCGAAAATAAATAAAATAAAA
*
1192911 GTGAATTAATATTTTC-AGGATAAAGTTT-A-A-
130 CTGAATTAATATTTTCGA-GATAAA-TTTAATAT
* * *
1192941 TTATTTTTTCTAATCTTTTATATTTTTATAGGG-ATCCGTAGGGGTATAAAAGATTTCAAAAACC
1 TTATTTTTTCTAATCTTTTATATTCTTAT-GGGCATCCGTAAGGGTATAAAAGATTTCAAAAACA
* * * * *
1193005 TTTCGTATCCTTTCGGGCTTCCATTGGGGTACAAAAT-AGTATTTTCAAAAATAATTAAAATTAA
65 TTTCGTATCCTTTCGAGCTTCCATTAGGGTACAAAATGA-TATTTTCGAAAATAAATAAAATAAA
**
1193069 ACTGAATTGGTATTTTCGAGATAAATTCTAATAT
129 ACTGAATTAATATTTTCGAGATAAATT-TAATAT
*
1193103 TTATTTTTTCTAATCTTTTATATTCTTATGGGCATCCGTAATGGTATAAAAGATTTCAAAAACAT
1 TTATTTTTTCTAATCTTTTATATTCTTATGGGCATCCGTAAGGGTATAAAAGATTTCAAAAACAT
** * * * * *
1193168 TTATTATCCTTTTGATCTTCCATTAGGGTA-GAATTGATATTTTCGAAAATAAATAAAATAAAAT
66 TTCGTATCCTTTCGAGCTTCCATTAGGGTACAAAATGATATTTTCGAAAATAAATAAAATAAAAC
*
1193232 TGAATTAATACTTTT-GAGAAAAATTTTAATAT
131 TGAATTAATA-TTTTCGAGATAAA-TTTAATAT
1193264 TTAT
1 TTAT
1193268 ATTCCTATGA
Statistics
Matches: 277, Mismatches: 37, Indels: 23
0.82 0.11 0.07
Matches are distributed among these distances:
158 11 0.04
159 116 0.42
160 7 0.03
161 55 0.20
162 88 0.32
ACGTcount: A:0.35, C:0.11, G:0.13, T:0.41
Consensus pattern (161 bp):
TTATTTTTTCTAATCTTTTATATTCTTATGGGCATCCGTAAGGGTATAAAAGATTTCAAAAACAT
TTCGTATCCTTTCGAGCTTCCATTAGGGTACAAAATGATATTTTCGAAAATAAATAAAATAAAAC
TGAATTAATATTTTCGAGATAAATTTAATAT
Found at i:1197003 original size:38 final size:39
Alignment explanation
Indices: 1196919--1196999 Score: 96
Period size: 38 Copynumber: 2.1 Consensus size: 39
1196909 TATTTTAATC
* * *
1196919 ATTTTAGATATAAAAATACCCTTTAGAGGTACTTTGGTT
1 ATTTTAGGTATAAAAATACCCTTTAGAAGTACTTTGATT
*
1196958 ATTTTAGGTAT-AAAATACCCTTTA-ACAGTA-TTTTATT
1 ATTTTAGGTATAAAAATACCCTTTAGA-AGTACTTTGATT
1196995 ATTTT
1 ATTTT
1197000 TAGGCATTGA
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
37 11 0.30
38 16 0.43
39 10 0.27
ACGTcount: A:0.33, C:0.10, G:0.11, T:0.46
Consensus pattern (39 bp):
ATTTTAGGTATAAAAATACCCTTTAGAAGTACTTTGATT
Found at i:1197772 original size:13 final size:13
Alignment explanation
Indices: 1197754--1197779 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1197744 CAATTTTTTG
1197754 TGTATCGATACAT
1 TGTATCGATACAT
1197767 TGTATCGATACAT
1 TGTATCGATACAT
1197780 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1200353 original size:20 final size:20
Alignment explanation
Indices: 1200328--1200404 Score: 73
Period size: 20 Copynumber: 3.6 Consensus size: 20
1200318 ATAATCACCC
1200328 TGTATCGATACAAAGAAAAA
1 TGTATCGATACAAAGAAAAA
* *
1200348 TGTATCGATACATAGAATTTCCAGA
1 TGTATCGATACAAAGAA-----AAA
* *
1200373 TGTATCGATACACAGAAACA
1 TGTATCGATACAAAGAAAAA
1200393 TGTATCGATACA
1 TGTATCGATACA
1200405 TTTTGGACAT
Statistics
Matches: 48, Mismatches: 4, Indels: 10
0.77 0.06 0.16
Matches are distributed among these distances:
20 30 0.62
25 18 0.38
ACGTcount: A:0.43, C:0.16, G:0.16, T:0.26
Consensus pattern (20 bp):
TGTATCGATACAAAGAAAAA
Found at i:1204282 original size:21 final size:21
Alignment explanation
Indices: 1204253--1204297 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
1204243 AAGTTTTCAT
*
1204253 TTTTCTTAGCTAAC-TCATTA
1 TTTTCTTAGCCAACTTCATTA
*
1204273 TTTTCATTAGCCAACTTCTTTA
1 TTTTC-TTAGCCAACTTCATTA
1204295 TTT
1 TTT
1204298 CAACTTGCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 8 0.38
22 8 0.38
ACGTcount: A:0.22, C:0.20, G:0.04, T:0.53
Consensus pattern (21 bp):
TTTTCTTAGCCAACTTCATTA
Found at i:1206529 original size:13 final size:13
Alignment explanation
Indices: 1206511--1206536 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1206501 CAATTTTTTG
1206511 TGTATCGATACAT
1 TGTATCGATACAT
1206524 TGTATCGATACAT
1 TGTATCGATACAT
1206537 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1206984 original size:38 final size:39
Alignment explanation
Indices: 1206940--1207068 Score: 146
Period size: 37 Copynumber: 3.4 Consensus size: 39
1206930 TATCTTAGGA
*
1206940 TATTTTGGTCATTTTAGGTTAAATGGTATCC-TTT-AGAGG
1 TATTTTGGTCATTTTAGGTTAAA-AGTATCCTTTTAAGA-G
1206979 T-TTTTGGTCA-TTTAGGTTGAAAAGTATCCTTTTAAGAG
1 TATTTTGGTCATTTTAGGTT-AAAAGTATCCTTTTAAGAG
* *
1207017 TATTTTGATCATTTTAGGTTATAAGTAGT--TTTTAAGAG
1 TATTTTGGTCATTTTAGGTTAAAAGTA-TCCTTTTAAGAG
1207055 -ATTTTGGTCATTTT
1 TATTTTGGTCATTTT
1207069 TAGTCAAATA
Statistics
Matches: 80, Mismatches: 4, Indels: 14
0.82 0.04 0.14
Matches are distributed among these distances:
37 27 0.34
38 26 0.32
39 18 0.22
40 9 0.11
ACGTcount: A:0.25, C:0.06, G:0.20, T:0.49
Consensus pattern (39 bp):
TATTTTGGTCATTTTAGGTTAAAAGTATCCTTTTAAGAG
Found at i:1210643 original size:22 final size:22
Alignment explanation
Indices: 1210618--1210660 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
1210608 TACTTGTATT
1210618 TGTATAAATAAATATATATTTA
1 TGTATAAATAAATATATATTTA
* *
1210640 TGTATATATATATATATATTT
1 TGTATAAATAAATATATATTT
1210661 TTTTTTGTTC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (22 bp):
TGTATAAATAAATATATATTTA
Found at i:1213148 original size:12 final size:12
Alignment explanation
Indices: 1213131--1213158 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
1213121 AACGAGCATA
1213131 ATAATAATAATT
1 ATAATAATAATT
1213143 ATAATAATAATT
1 ATAATAATAATT
1213155 ATAA
1 ATAA
1213159 GAACAACAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (12 bp):
ATAATAATAATT
Found at i:1214741 original size:15 final size:13
Alignment explanation
Indices: 1214695--1214766 Score: 62
Period size: 14 Copynumber: 5.5 Consensus size: 13
1214685 AAATTAAAAA
1214695 AATAATATATTATT
1 AATAATATATT-TT
*
1214709 TATAAT-T-TTTT
1 AATAATATATTTT
1214720 AATAATATCATTTT
1 AATAATAT-ATTTT
1214734 AATCAATATA-TTT
1 AAT-AATATATTTT
*
1214747 ATTAATAT-TTTT
1 AATAATATATTTT
1214759 AATTAATA
1 AA-TAATA
1214767 AAGTGTAATT
Statistics
Matches: 48, Mismatches: 4, Indels: 13
0.74 0.06 0.20
Matches are distributed among these distances:
11 7 0.15
12 12 0.25
13 11 0.23
14 13 0.27
15 5 0.10
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.54
Consensus pattern (13 bp):
AATAATATATTTT
Found at i:1214752 original size:27 final size:25
Alignment explanation
Indices: 1214717--1214766 Score: 64
Period size: 25 Copynumber: 1.9 Consensus size: 25
1214707 TTTATAATTT
1214717 TTTAATAATATCATTTTAATCAATATA
1 TTTAATAATAT--TTTTAATCAATATA
* *
1214744 TTTATTAATATTTTTAATTAATA
1 TTTAATAATATTTTTAATCAATA
1214767 AAGTGTAATT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 11 0.52
27 10 0.48
ACGTcount: A:0.42, C:0.04, G:0.00, T:0.54
Consensus pattern (25 bp):
TTTAATAATATTTTTAATCAATATA
Found at i:1214763 original size:13 final size:13
Alignment explanation
Indices: 1214711--1214766 Score: 55
Period size: 12 Copynumber: 4.4 Consensus size: 13
1214701 ATATTATTTA
1214711 TAAT-TTTTTAA-
1 TAATATTTTTAAT
1214722 TAATATCATTTTAAT
1 TAATAT--TTTTAAT
* *
1214737 CAATATATTT-AT
1 TAATATTTTTAAT
1214749 TAATATTTTTAAT
1 TAATATTTTTAAT
1214762 TAATA
1 TAATA
1214767 AAGTGTAATT
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
11 4 0.11
12 11 0.31
13 10 0.28
14 6 0.17
15 5 0.14
ACGTcount: A:0.41, C:0.04, G:0.00, T:0.55
Consensus pattern (13 bp):
TAATATTTTTAAT
Found at i:1215178 original size:14 final size:14
Alignment explanation
Indices: 1215161--1215254 Score: 54
Period size: 14 Copynumber: 6.4 Consensus size: 14
1215151 TTATATTTAA
1215161 AATATTATATATTT
1 AATATTATATATTT
*
1215175 AATA-TAAAT-TTT
1 AATATTATATATTT
1215187 AATA-TATTAATAATTT
1 AATATTA-T-AT-ATTT
1215203 -ATATTATATAAATTTT
1 AATATTATAT--A-TTT
*
1215219 AATATATTTATATATT
1 AATAT-TATATAT-TT
1215235 AATATTATAT-TTAT
1 AATATTATATATT-T
1215249 AATATT
1 AATATT
1215255 TTTTATATAT
Statistics
Matches: 65, Mismatches: 4, Indels: 22
0.71 0.04 0.24
Matches are distributed among these distances:
12 9 0.14
13 5 0.08
14 16 0.25
15 11 0.17
16 16 0.25
17 4 0.06
18 4 0.06
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (14 bp):
AATATTATATATTT
Found at i:1215217 original size:32 final size:33
Alignment explanation
Indices: 1215152--1215244 Score: 116
Period size: 32 Copynumber: 2.7 Consensus size: 33
1215142 ATTTTATAAT
*
1215152 TATATTTAAAATATTATATATTTAATATAAATTTTAA
1 TATA-TTAATATATTA-ATA-TT-ATATAAATTTTAA
*
1215189 TATATTAATA-ATTTATATTATATAAATTTTAA
1 TATATTAATATATTAATATTATATAAATTTTAA
*
1215221 TATATTTATATATTAATATTATAT
1 TATATTAATATATTAATATTATAT
1215245 TTATAATATT
Statistics
Matches: 51, Mismatches: 4, Indels: 6
0.84 0.07 0.10
Matches are distributed among these distances:
32 22 0.43
33 14 0.27
34 3 0.06
35 3 0.06
36 5 0.10
37 4 0.08
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (33 bp):
TATATTAATATATTAATATTATATAAATTTTAA
Found at i:1215243 original size:38 final size:40
Alignment explanation
Indices: 1215188--1215269 Score: 109
Period size: 38 Copynumber: 2.1 Consensus size: 40
1215178 ATAAATTTTA
1215188 ATATATTAATAATTTATATTATATAA-ATTTTA-ATATATTT
1 ATATATTAATAATTTATATT-TATAATATTTTATATATA-TT
*
1215228 ATATATTAAT-A-TTATATTTATAATATTTTTTATATATT
1 ATATATTAATAATTTATATTTATAATATTTTATATATATT
1215266 ATAT
1 ATAT
1215270 TATTTTAAAA
Statistics
Matches: 39, Mismatches: 1, Indels: 6
0.85 0.02 0.13
Matches are distributed among these distances:
37 5 0.13
38 18 0.46
39 6 0.15
40 10 0.26
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (40 bp):
ATATATTAATAATTTATATTTATAATATTTTATATATATT
Found at i:1215273 original size:19 final size:19
Alignment explanation
Indices: 1215202--1215275 Score: 62
Period size: 19 Copynumber: 3.8 Consensus size: 19
1215192 ATTAATAATT
* * *
1215202 TATATTATATAAATTTTAA
1 TATATTATATTATTTTTTA
*
1215221 TATATT-TATATATTAATATTA
1 TATATTATAT-TATT--TTTTA
*
1215242 TAT-TTATAATATTTTTTA
1 TATATTATATTATTTTTTA
1215260 TATATTATATTATTTT
1 TATATTATATTATTTT
1215276 AAAATTACCA
Statistics
Matches: 43, Mismatches: 7, Indels: 10
0.72 0.12 0.17
Matches are distributed among these distances:
18 10 0.23
19 19 0.44
20 6 0.14
21 8 0.19
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (19 bp):
TATATTATATTATTTTTTA
Found at i:1215880 original size:19 final size:18
Alignment explanation
Indices: 1215844--1215882 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
1215834 CACATGTAAA
* *
1215844 TTTTTAAATTATTTAATT
1 TTTTTAAATTAATAAATT
1215862 TTTTATAAATTAATAAATT
1 TTTT-TAAATTAATAAATT
1215881 TT
1 TT
1215883 AAAATTTTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 4 0.22
19 14 0.78
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (18 bp):
TTTTTAAATTAATAAATT
Found at i:1215910 original size:26 final size:26
Alignment explanation
Indices: 1215861--1215910 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
1215851 ATTATTTAAT
* *
1215861 TTTTTATAAATTAATAAATTTTAAAA
1 TTTTAATAAATTAATAAATATTAAAA
1215887 TTTTAATAAA-TAATAATATATTAA
1 TTTTAATAAATTAATAA-ATATTAA
1215911 TTATTATTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 6 0.29
26 15 0.71
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (26 bp):
TTTTAATAAATTAATAAATATTAAAA
Found at i:1216050 original size:75 final size:75
Alignment explanation
Indices: 1215927--1216083 Score: 187
Period size: 75 Copynumber: 2.1 Consensus size: 75
1215917 TTTTTTAATT
1215927 AAAATAATATTTTTATAAAAATAAAAAATTTTAAAATAAAAAAATAAAA-A-AATTATTATAATT
1 AAAATAATATTTTTATAAAAATAAAAAATTTTAAAATAAAAAAATAAAATATAATTATTAT-ATT
1215990 TTTAATAAAATAA
65 TTT-A-AAAATAA
* * * * * *
1216003 AAAATAATATTTATT-T-AAATTTAAAAATTTTATATTAATAAATTAAAATATTAATTATTATAT
1 AAAATAATATTT-TTATAAAAATAAAAAATTTTAAAATAAAAAAATAAAATA-TAATTATTATAT
1216066 TTTTAAAAATAA
64 TTTTAAAAATAA
1216078 AAAATA
1 AAAATA
1216084 TTTTAATAAA
Statistics
Matches: 71, Mismatches: 6, Indels: 9
0.83 0.07 0.10
Matches are distributed among these distances:
75 39 0.55
76 15 0.21
77 8 0.11
78 9 0.13
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (75 bp):
AAAATAATATTTTTATAAAAATAAAAAATTTTAAAATAAAAAAATAAAATATAATTATTATATTT
TTAAAAATAA
Found at i:1216312 original size:2 final size:2
Alignment explanation
Indices: 1216307--1216338 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1216297 AAATATATGA
1216307 AT AT AT 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 AT AT AT
1216339 TTCTCTGTTC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1223937 original size:13 final size:13
Alignment explanation
Indices: 1223919--1223944 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1223909 TACACCAAGT
1223919 ATGTATCGATACA
1 ATGTATCGATACA
1223932 ATGTATCGATACA
1 ATGTATCGATACA
1223945 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1223941 original size:32 final size:33
Alignment explanation
Indices: 1223900--1223964 Score: 96
Period size: 32 Copynumber: 2.0 Consensus size: 33
1223890 GTAGCCAAAC
* **
1223900 ATGTATCGATACACCAAGTA-TGTATCGATACA
1 ATGTATCGATACACAAAAAATTGTATCGATACA
1223932 ATGTATCGATACACAAAAAATTGTATCGATACA
1 ATGTATCGATACACAAAAAATTGTATCGATACA
1223965 TTGGCTTGTA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 17 0.59
33 12 0.41
ACGTcount: A:0.42, C:0.17, G:0.14, T:0.28
Consensus pattern (33 bp):
ATGTATCGATACACAAAAAATTGTATCGATACA
Found at i:1226171 original size:22 final size:22
Alignment explanation
Indices: 1226144--1226199 Score: 64
Period size: 21 Copynumber: 2.6 Consensus size: 22
1226134 TTACAAGTTG
1226144 AAATAAAGAACTTGGCTAATG-A
1 AAATAAAGAACTTGGCTAA-GAA
* *
1226166 AAATAATGAA-TTAGCTAAGAA
1 AAATAAAGAACTTGGCTAAGAA
1226187 AAATAAA-AACTTG
1 AAATAAAGAACTTG
1226200 CATGATTCAT
Statistics
Matches: 28, Mismatches: 4, Indels: 5
0.76 0.11 0.14
Matches are distributed among these distances:
20 3 0.11
21 16 0.57
22 9 0.32
ACGTcount: A:0.55, C:0.07, G:0.14, T:0.23
Consensus pattern (22 bp):
AAATAAAGAACTTGGCTAAGAA
Found at i:1230119 original size:13 final size:13
Alignment explanation
Indices: 1230101--1230126 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1230091 ACATTTTTCT
1230101 TTGTATCGATACA
1 TTGTATCGATACA
1230114 TTGTATCGATACA
1 TTGTATCGATACA
1230127 AGGTGATTAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:1230290 original size:20 final size:20
Alignment explanation
Indices: 1230247--1230292 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 20
1230237 AAATCTTTTG
1230247 CAAAATACTTGTTTTTCACTT
1 CAAAATACTTGTTTTTCAC-T
*
1230268 CAAATTACTTCGTTTTTCA-T
1 CAAAATACTT-GTTTTTCACT
1230288 CAAAA
1 CAAAA
1230293 CCAGCATCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
20 5 0.23
21 9 0.41
22 8 0.36
ACGTcount: A:0.33, C:0.20, G:0.04, T:0.43
Consensus pattern (20 bp):
CAAAATACTTGTTTTTCACT
Found at i:1232702 original size:13 final size:13
Alignment explanation
Indices: 1232684--1232709 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1232674 TACACCAAGT
1232684 ATGTATCGATACA
1 ATGTATCGATACA
1232697 ATGTATCGATACA
1 ATGTATCGATACA
1232710 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1232706 original size:32 final size:33
Alignment explanation
Indices: 1232665--1232729 Score: 96
Period size: 32 Copynumber: 2.0 Consensus size: 33
1232655 GTAGCCAAAC
* **
1232665 ATGTATCGATACACCAAGTA-TGTATCGATACA
1 ATGTATCGATACACAAAAAATTGTATCGATACA
1232697 ATGTATCGATACACAAAAAATTGTATCGATACA
1 ATGTATCGATACACAAAAAATTGTATCGATACA
1232730 TTGGCTTGTA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 17 0.59
33 12 0.41
ACGTcount: A:0.42, C:0.17, G:0.14, T:0.28
Consensus pattern (33 bp):
ATGTATCGATACACAAAAAATTGTATCGATACA
Found at i:1234361 original size:52 final size:52
Alignment explanation
Indices: 1234160--1234341 Score: 294
Period size: 52 Copynumber: 3.5 Consensus size: 52
1234150 TCCTGAAATA
1234160 TAAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGAT-CATCTAGGG
1 TAAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCT-GGG
1234212 TAAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGG
1 TAAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGG
* ** *
1234264 TAAATTTGCCTGTATGTATCGATACATTTTGTAGTGTATCAATACATCTGGG
1 TAAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGG
* *
1234316 CAAATTTGCCTGCAAGTATCGATACA
1 TAAATTTGCCTGCATGTATCGATACA
1234342 AAGATCAGTG
Statistics
Matches: 122, Mismatches: 7, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
52 117 0.96
53 5 0.04
ACGTcount: A:0.28, C:0.17, G:0.19, T:0.36
Consensus pattern (52 bp):
TAAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGG
Found at i:1234463 original size:13 final size:13
Alignment explanation
Indices: 1234445--1234501 Score: 60
Period size: 13 Copynumber: 3.9 Consensus size: 13
1234435 TATAAACTTA
1234445 TGTATCGATACAT
1 TGTATCGATACAT
1234458 TGTATCGATACAACACTT
1 TGTATCGAT---ACA--T
1234476 ATGTATCGATACAT
1 -TGTATCGATACAT
1234490 TGTATCGATACA
1 TGTATCGATACA
1234502 ACACTTATGT
Statistics
Matches: 38, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
13 21 0.55
14 1 0.03
16 6 0.16
18 1 0.03
19 9 0.24
ACGTcount: A:0.33, C:0.18, G:0.14, T:0.35
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1234481 original size:32 final size:32
Alignment explanation
Indices: 1234422--1234520 Score: 182
Period size: 32 Copynumber: 3.1 Consensus size: 32
1234412 TTCGTAGCGG
*
1234422 TACATTGTATCGATATAA-ACTTATGTATCGA
1 TACATTGTATCGATACAACACTTATGTATCGA
1234453 TACATTGTATCGATACAACACTTATGTATCGA
1 TACATTGTATCGATACAACACTTATGTATCGA
1234485 TACATTGTATCGATACAACACTTATGTATCGA
1 TACATTGTATCGATACAACACTTATGTATCGA
1234517 TACA
1 TACA
1234521 AATCGTTGAA
Statistics
Matches: 66, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
31 17 0.26
32 49 0.74
ACGTcount: A:0.35, C:0.17, G:0.12, T:0.35
Consensus pattern (32 bp):
TACATTGTATCGATACAACACTTATGTATCGA
Found at i:1234482 original size:19 final size:19
Alignment explanation
Indices: 1234427--1234521 Score: 90
Period size: 19 Copynumber: 5.7 Consensus size: 19
1234417 AGCGGTACAT
*
1234427 TGTATCGATATAA-ACTTA
1 TGTATCGATACAACACTTA
1234445 TGTATCGAT---ACA--T-
1 TGTATCGATACAACACTTA
1234458 TGTATCGATACAACACTTA
1 TGTATCGATACAACACTTA
1234477 TGTATCGAT---ACA--T-
1 TGTATCGATACAACACTTA
1234490 TGTATCGATACAACACTTA
1 TGTATCGATACAACACTTA
1234509 TGTATCGATACAA
1 TGTATCGATACAA
1234522 ATCGTTGAAT
Statistics
Matches: 64, Mismatches: 0, Indels: 25
0.72 0.00 0.28
Matches are distributed among these distances:
13 18 0.28
14 2 0.03
15 1 0.02
16 10 0.16
18 11 0.17
19 22 0.34
ACGTcount: A:0.36, C:0.17, G:0.13, T:0.35
Consensus pattern (19 bp):
TGTATCGATACAACACTTA
Found at i:1235326 original size:166 final size:164
Alignment explanation
Indices: 1235119--1235591 Score: 576
Period size: 166 Copynumber: 2.9 Consensus size: 164
1235109 AACCAAAAGG
* * *
1235119 ATACGAAAAGTCTTGAAAATTTTTATACCTCTACAAAGGCCATAAGAATAATAAAAATCTTGAAA
1 ATACG-AAAGTCTTGAAAATTTCTATACCCCTACAAAGGCCATAAGAATAATAAAAATCTTTAAA
* * * *
1235184 AATGACTAAAATAGTGATTTTAGCACAAAAGAACTAAAATTTTCTATTTAATACCTAAACTTTTA
65 AATGACTAAAATAGTGATTTTACCTCTAAA-AACTAAAATTTTCTATTTAATCCCTAAACTTTTA
*
1235249 AAAATTTCATTTCGTAC-CTAACAAAAAATCGAGAGA
129 AAAATTTCATTTCGTACTCGAACAAAAAAT-GAGAGA
* *
1235285 ATACGAAAGTCTTGAAAATTTCTATACCCCTACCAAAGGCCATAGGAATAATAAAAGTCTTTAAA
1 ATACGAAAGTCTTGAAAATTTCTATACCCCTA-CAAAGGCCATAAGAATAATAAAAATCTTTAAA
* * * *
1235350 AATGACTAAAATAATGATTTTACCTCTAAAAAGTAATATTTGT-TATTTAATCCCTAAACTTTTG
65 AATGACTAAAATAGTGATTTTACCTCTAAAAACTAAAATTT-TCTATTTAATCCCTAAACTTTTA
* * *** * *
1235414 AAAATTTTATTTTGTACTCGATGGAAAACTGAGAGG
129 AAAATTTCATTTCGTACTCGAACAAAAAATGAGAGA
** *** *
1235450 ATACGAGAAGTCTTGAAAATTTCTATATGCCTATGGTAGGCCATAAGAATAATAGAAATCTTTAA
1 ATACGA-AAGTCTTGAAAATTTCTATACCCCTA-CAAAGGCCATAAGAATAATAAAAATCTTTAA
* *
1235515 AAATGACTAAAGT-GATGATTTTACCTCTAAAAACTAAAATTTGCTATTTAATCCCTAAAC-TTT
64 AAATGACTAAAATAG-TGATTTTACCTCTAAAAACTAAAATTTTCTATTTAATCCCTAAACTTTT
1235578 AAAAATTTTCATTT
128 AAAAA-TTTCATTT
1235592 TAGTCCCTAT
Statistics
Matches: 263, Mismatches: 37, Indels: 14
0.84 0.12 0.04
Matches are distributed among these distances:
165 86 0.33
166 177 0.67
ACGTcount: A:0.42, C:0.14, G:0.11, T:0.33
Consensus pattern (164 bp):
ATACGAAAGTCTTGAAAATTTCTATACCCCTACAAAGGCCATAAGAATAATAAAAATCTTTAAAA
ATGACTAAAATAGTGATTTTACCTCTAAAAACTAAAATTTTCTATTTAATCCCTAAACTTTTAAA
AATTTCATTTCGTACTCGAACAAAAAATGAGAGA
Found at i:1236146 original size:14 final size:14
Alignment explanation
Indices: 1236123--1236152 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
1236113 AACATGAATC
*
1236123 AACATGAATATGAT
1 AACATAAATATGAT
1236137 AACATAAATATGAT
1 AACATAAATATGAT
1236151 AA
1 AA
1236153 AACACATATT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.57, C:0.07, G:0.10, T:0.27
Consensus pattern (14 bp):
AACATAAATATGAT
Found at i:1239682 original size:13 final size:13
Alignment explanation
Indices: 1239664--1239696 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
1239654 CCGTTACAAG
1239664 CAATGTATCGATA
1 CAATGTATCGATA
1239677 CAATGTATCGATA
1 CAATGTATCGATA
*
1239690 CATTGTA
1 CAATGTA
1239697 CCATGTATCA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.33
Consensus pattern (13 bp):
CAATGTATCGATA
Found at i:1240359 original size:22 final size:21
Alignment explanation
Indices: 1240332--1240407 Score: 91
Period size: 21 Copynumber: 3.5 Consensus size: 21
1240322 AGTTTTCATT
1240332 TTTCTCTCCCTTAATTAAAGAA
1 TTTCTC-CCCTTAATTAAAGAA
*
1240354 TTTCTCCCCTCTAA-TAAAAAA
1 TTTCTCCCCT-TAATTAAAGAA
* *
1240375 TTTCTCCCCTTTAATCAAAGCA
1 TTTCTCCCC-TTAATTAAAGAA
1240397 TTTCTCCCCTT
1 TTTCTCCCCTT
1240408 TTGTCAAATC
Statistics
Matches: 47, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
21 24 0.51
22 23 0.49
ACGTcount: A:0.28, C:0.30, G:0.03, T:0.39
Consensus pattern (21 bp):
TTTCTCCCCTTAATTAAAGAA
Found at i:1240408 original size:22 final size:21
Alignment explanation
Indices: 1240332--1240408 Score: 93
Period size: 22 Copynumber: 3.6 Consensus size: 21
1240322 AGTTTTCATT
1240332 TTTCTCTCCC-TTAATTAAAGAA
1 TTTCTC-CCCTTTAA-TAAAGAA
* *
1240354 TTTCTCCCCTCTAATAAAAAA
1 TTTCTCCCCTTTAATAAAGAA
*
1240375 TTTCTCCCCTTTAATCAAAGCA
1 TTTCTCCCCTTTAAT-AAAGAA
1240397 TTTCTCCCCTTT
1 TTTCTCCCCTTT
1240409 TGTCAAATCT
Statistics
Matches: 48, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
21 23 0.48
22 25 0.52
ACGTcount: A:0.27, C:0.30, G:0.03, T:0.40
Consensus pattern (21 bp):
TTTCTCCCCTTTAATAAAGAA
Found at i:1242303 original size:13 final size:13
Alignment explanation
Indices: 1242285--1242311 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1242275 ATAGTACCCT
1242285 ATGTATCGATACA
1 ATGTATCGATACA
1242298 ATGTATCGATACA
1 ATGTATCGATACA
1242311 A
1 A
1242312 GGAATATTGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1242466 original size:30 final size:31
Alignment explanation
Indices: 1242430--1242493 Score: 87
Period size: 30 Copynumber: 2.1 Consensus size: 31
1242420 CAAAAAGCAT
* *
1242430 AATTCATTCACACAACATAA-TAAA-CATCAA
1 AATTCATTCA-ACAACAAAACAAAATCATCAA
1242460 AATTCATTCAACAACAAAACAAAATCATCAA
1 AATTCATTCAACAACAAAACAAAATCATCAA
1242491 AAT
1 AAT
1242494 CACTTTATCA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
29 8 0.27
30 13 0.43
31 9 0.30
ACGTcount: A:0.56, C:0.22, G:0.00, T:0.22
Consensus pattern (31 bp):
AATTCATTCAACAACAAAACAAAATCATCAA
Found at i:1245870 original size:52 final size:51
Alignment explanation
Indices: 1245771--1245895 Score: 139
Period size: 52 Copynumber: 2.4 Consensus size: 51
1245761 TTAAATTCTC
* * *
1245771 CACAATCGGGGATATTCCAATTCCGATTTAGGTTTTCAAAACACAATTTTCCT
1 CACAATCGGGGATACTCCAACTCCGATTTA-GTTTCCAAAACACAA-TTTCCT
* *
1245824 -ATAATCGGGGATACGTCCAACTCCGATTTTA-TTTCC-AAACACCAATTTCTT
1 CACAATCGGGGATAC-TCCAACTCCGA-TTTAGTTTCCAAAACA-CAATTTCCT
1245875 CACAATCGGGGATACTCCAAC
1 CACAATCGGGGATACTCCAAC
1245896 CCCGTTAATG
Statistics
Matches: 62, Mismatches: 6, Indels: 10
0.79 0.08 0.13
Matches are distributed among these distances:
51 16 0.26
52 32 0.52
53 10 0.16
54 4 0.06
ACGTcount: A:0.30, C:0.26, G:0.14, T:0.30
Consensus pattern (51 bp):
CACAATCGGGGATACTCCAACTCCGATTTAGTTTCCAAAACACAATTTCCT
Found at i:1261154 original size:60 final size:58
Alignment explanation
Indices: 1260669--1261444 Score: 796
Period size: 55 Copynumber: 13.4 Consensus size: 58
1260659 AATAAAGTGT
* *
1260669 ATCCTGCTCTTTGAGGACTAAAAAGTGCCACCAACTCGTGTGGGCTTT---G-AAAGGC
1 ATCCTGCTCTTTGAGGACTGAAAA-TGCCACCAACTTGTGTGGGCTTTAAAGAAAAGGC
* * *
1260724 ATCCTGTTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT---G-AAAGGT
1 ATCCTGCTCTTTGAGGACTGAAA-ATGCCACCAACTTGTGTGGGCTTTAAAGAAAAGGC
* *
1260779 GTCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTT---G-AAAGGT
1 ATCCTGCTCTTTGAGGACT-GAAAATGCCACCAACTTGTGTGGGCTTTAAAGAAAAGGC
* *
1260834 GTCCTGCTCTTTG-GAGACTGAAAAGTGCCACCAACTCGTGTGGGCTTTGAAAAGATAAA-GC
1 ATCCTGCTCTTTGAG-GACTGAAAA-TGCCACCAACTTGTGTGGGCTTT--AAAGA-AAAGGC
* *
1260895 ATCCTGCTCTTTGAGGACTAGAAAATGCCACCATCTTGTGTGGTCTTT---G-AAAGGC
1 ATCCTGCTCTTTGAGGACT-GAAAATGCCACCAACTTGTGTGGGCTTTAAAGAAAAGGC
* *
1260950 ATCCTGCTCTTTGAGGACTGGAAAATGCCACTAACTTGTGTGGGC-TT--CG-AAAGGC
1 ATCCTGCTCTTTGAGGACT-GAAAATGCCACCAACTTGTGTGGGCTTTAAAGAAAAGGC
* * * *
1261005 ATCCTACTCTTTAAGGACTGGAAAATGCTACCAACTTGTGTGGGCTTTGAAAGGAGAAGGC
1 ATCCTGCTCTTTGAGGACT-GAAAATGCCACCAACTTGTGTGGGCTTT-AAA-GAAAAGGC
* ** * *
1261066 GTCCTGCTCTTTGAGGACTGAAGGTGCCACTAACTTGTGTGGGCTTTAAAAGAAAAGGT
1 ATCCTGCTCTTTGAGGACTGAAAATGCCACCAACTTGTGTGGGCTTT-AAAGAAAAGGC
* *
1261125 GTCCTGCTCTTTGGGGACTAGAAAATGCCACCAACTTGTGTGGGCTTT---G-AAAGGC
1 ATCCTGCTCTTTGAGGACT-GAAAATGCCACCAACTTGTGTGGGCTTTAAAGAAAAGGC
*
1261180 ATCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGAGAAGGC
1 ATCCTGCTCTTTGAGGACT-GAAAATGCCACCAACTTGTGTGGGCTTT-AAA-GAAAAGGC
* ** *
1261241 GTCCTGCTCTTTGAGGACTGAAGGTGCCACTAACTTGTGTGGGCTTTAAAAGAAAAGGC
1 ATCCTGCTCTTTGAGGACTGAAAATGCCACCAACTTGTGTGGGCTTT-AAAGAAAAGGC
* * * *
1261300 GTCTTGCTCTTTGGGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGC
1 ATCCTGCTCTTTGAGGACT-GAAAATGCCACCAACTTGTGTGGGCTTT--AAAGAAAAGGC
** * *
1261361 ATCCTGCTCTTTGAGGACTGAAGGTGCCACCAACTTG-GATGGCCTTTAAAAGGAACAGGC
1 ATCCTGCTCTTTGAGGACTGAAAATGCCACCAACTTGTG-TGGGCTTT-AAA-GAAAAGGC
*
1261421 ATCCTGCTCTTTGAGGACTAAAAA
1 ATCCTGCTCTTTGAGGACTGAAAA
1261445 GCAGAAGGAG
Statistics
Matches: 623, Mismatches: 66, Indels: 59
0.83 0.09 0.08
Matches are distributed among these distances:
54 11 0.02
55 276 0.44
56 8 0.01
59 53 0.09
60 158 0.25
61 108 0.17
62 9 0.01
ACGTcount: A:0.26, C:0.20, G:0.27, T:0.27
Consensus pattern (58 bp):
ATCCTGCTCTTTGAGGACTGAAAATGCCACCAACTTGTGTGGGCTTTAAAGAAAAGGC
Found at i:1261176 original size:28 final size:28
Alignment explanation
Indices: 1261145--1261231 Score: 72
Period size: 28 Copynumber: 3.1 Consensus size: 28
1261135 TTGGGGACTA
1261145 GAAAATGCCACCAACTTGTGTGGGCTTT
1 GAAAATGCCACCAACTTGTGTGGGCTTT
* ** * * * *
1261173 G-AAA-GGCATCCTGCTCTTTGAGGAC-TG
1 GAAAATGCCA-CCAACT-TGTGTGGGCTTT
1261200 GAAAATGCCACCAACTTGTGTGGGCTTT
1 GAAAATGCCACCAACTTGTGTGGGCTTT
1261228 GAAA
1 GAAA
1261232 GGAGAAGGCG
Statistics
Matches: 40, Mismatches: 14, Indels: 10
0.62 0.22 0.16
Matches are distributed among these distances:
26 3 0.08
27 15 0.38
28 19 0.47
29 3 0.08
ACGTcount: A:0.26, C:0.21, G:0.26, T:0.26
Consensus pattern (28 bp):
GAAAATGCCACCAACTTGTGTGGGCTTT
Found at i:1261179 original size:175 final size:169
Alignment explanation
Indices: 1260669--1261439 Score: 957
Period size: 175 Copynumber: 4.5 Consensus size: 169
1260659 AATAAAGTGT
* *
1260669 ATCCTGCTCTTTGAGGACTAAAAAGTGCCACCAACTCGTGTGGGCTTT-----GA-AAGGCATCC
1 ATCCTGCTCTTTGAGGACTGAAAA-TGCCACCAACTTGTGTGGGCTTTGAAAGGAGAAGGCATCC
* *
1260728 TGTTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCTTTGA
65 TGCTCTTTGAGGACTG-AAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGCGTCCTGCTCTTTGA
*
1260793 GGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGT
129 GGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGC
* * * * *
1260834 GTCCTGCTCTTTG-GAGACTGAAAAGTGCCACCAACTCGTGTGGGCTTTGAAAAGATAAAGCATC
1 ATCCTGCTCTTTGAG-GACTGAAAA-TGCCACCAACTTGTGTGGGCTTTGAAAGGAGAAGGCATC
** * * *
1260898 CTGCTCTTTGAGGACTAGAAAATGCCACCATCTTGTGTGGTCTTTGAAAGGCATCCTGCTCTTTG
64 CTGCTCTTTGAGGACT-GAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGCGTCCTGCTCTTTG
* *
1260963 AGGACTGGAAAATGCCACTAACTTGTGTGGGCTTCGAAAGGC
128 AGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGC
* * * *
1261005 ATCCTACTCTTTAAGGACTGGAAAATGCTACCAACTTGTGTGGGCTTTGAAAGGAGAAGGCGTCC
1 ATCCTGCTCTTTGAGGACT-GAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGAGAAGGCATCC
* *
1261070 TGCTCTTTGAGGACTGAAGGTGCCACTAACTTGTGTGGGCTTTAAAAGAAAAGGTGTCCTGCTCT
65 TGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTT----G-AAAGGCGTCCTGCTCT
* *
1261135 TTGGGGACTAGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGC
125 TTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGC
*
1261180 ATCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGAGAAGGCGTCC
1 ATCCTGCTCTTTGAGGACT-GAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGAGAAGGCATCC
* *
1261245 TGCTCTTTGAGGACTGAAGGTGCCACTAACTTGTGTGGGCTTTAAAAGAAAAGGCGTCTTGCTCT
65 TGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTT----G-AAAGGCGTCCTGCTCT
*
1261310 TTGGGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGC
125 TTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTG-AAAG-----GC
** * *
1261361 ATCCTGCTCTTTGAGGACTGAAGGTGCCACCAACTTG-GATGGCCTTTAAAAGGA-ACAGGCATC
1 ATCCTGCTCTTTGAGGACTGAAAATGCCACCAACTTGTG-TGGGCTTTGAAAGGAGA-AGGCATC
1261424 CTGCTCTTTGAGGACT
64 CTGCTCTTTGAGGACT
1261440 AAAAAGCAGA
Statistics
Matches: 539, Mismatches: 44, Indels: 31
0.88 0.07 0.05
Matches are distributed among these distances:
164 1 0.00
165 44 0.08
170 25 0.05
171 165 0.31
172 7 0.01
174 1 0.00
175 218 0.40
176 4 0.01
179 2 0.00
180 51 0.09
181 21 0.04
ACGTcount: A:0.25, C:0.20, G:0.27, T:0.27
Consensus pattern (169 bp):
ATCCTGCTCTTTGAGGACTGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGAGAAGGCATCCT
GCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGCGTCCTGCTCTTTGAGG
ACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGC
Found at i:1262428 original size:1 final size:1
Alignment explanation
Indices: 1262424--1262494 Score: 52
Period size: 1 Copynumber: 71.0 Consensus size: 1
1262414 CTTTTCTCTC
* * * * * *** * *
1262424 TTTTTCTTTGTTTTGTTTTTTTGTTTTGTTTTTTTTTTTGGCTTTTTTTTTCTTTTTTTTTTTGT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1262489 TTTTTT
1 TTTTTT
1262495 GAAGAGAAGG
Statistics
Matches: 53, Mismatches: 17, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
1 53 1.00
ACGTcount: A:0.00, C:0.04, G:0.10, T:0.86
Consensus pattern (1 bp):
T
Found at i:1262494 original size:12 final size:12
Alignment explanation
Indices: 1262434--1262494 Score: 86
Period size: 12 Copynumber: 5.0 Consensus size: 12
1262424 TTTTTCTTTG
1262434 TTTTGTTTTTTT
1 TTTTGTTTTTTT
1262446 GTTTTGTTTTTTT
1 -TTTTGTTTTTTT
**
1262459 TTTTGGCTTTTT
1 TTTTGTTTTTTT
*
1262471 TTTTCTTTTTTT
1 TTTTGTTTTTTT
1262483 TTTTGTTTTTTT
1 TTTTGTTTTTTT
1262495 GAAGAGAAGG
Statistics
Matches: 42, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
12 30 0.71
13 12 0.29
ACGTcount: A:0.00, C:0.03, G:0.10, T:0.87
Consensus pattern (12 bp):
TTTTGTTTTTTT
Found at i:1263151 original size:19 final size:19
Alignment explanation
Indices: 1263127--1263194 Score: 85
Period size: 19 Copynumber: 3.9 Consensus size: 19
1263117 AATTCAACAA
1263127 TTTGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
1263146 TTTGTATCGATAC--AA--
1 TTTGTATCGATACATAAGT
1263161 --TGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
*
1263178 ATTGTATCGATACATAA
1 TTTGTATCGATACATAA
1263195 TTAGCTACTG
Statistics
Matches: 43, Mismatches: 0, Indels: 12
0.78 0.00 0.22
Matches are distributed among these distances:
13 11 0.26
15 2 0.05
17 2 0.05
19 28 0.65
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.38
Consensus pattern (19 bp):
TTTGTATCGATACATAAGT
Found at i:1263166 original size:13 final size:13
Alignment explanation
Indices: 1263148--1263172 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1263138 ACATAAGTTT
1263148 TGTATCGATACAA
1 TGTATCGATACAA
1263161 TGTATCGATACA
1 TGTATCGATACA
1263173 TAAGTATTGT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1263170 original size:32 final size:32
Alignment explanation
Indices: 1263129--1263191 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
1263119 TTCAACAATT
*
1263129 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTATTGTATCGATACAA
1263161 TGTATCGATACATAAGTATTGTATCGATACA
1 TGTATCGATACATAAGTATTGTATCGATACA
1263192 TAATTAGCTA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.37
Consensus pattern (32 bp):
TGTATCGATACATAAGTATTGTATCGATACAA
Found at i:1263252 original size:13 final size:13
Alignment explanation
Indices: 1263234--1263259 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1263224 CATTTTTCTG
1263234 TGTATCGATACAT
1 TGTATCGATACAT
1263247 TGTATCGATACAT
1 TGTATCGATACAT
1263260 GGATCTTTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1263256 original size:33 final size:33
Alignment explanation
Indices: 1263214--1263280 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
1263204 GCCAAGGAAA
***
1263214 TGTATCGATACATTTTTCTGTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
*
1263247 TGTATCGATACATGGATCTTTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
1263280 T
1 T
1263281 TGGAAATTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.25, C:0.15, G:0.16, T:0.43
Consensus pattern (33 bp):
TGTATCGATACATGGATCTGTGTATCGATACAT
Found at i:1263814 original size:17 final size:17
Alignment explanation
Indices: 1263794--1263827 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
1263784 AATCCTTTAG
1263794 CAAAAAAAAAAAAAAAC
1 CAAAAAAAAAAAAAAAC
* *
1263811 CAAAAACAAAGAAAAAC
1 CAAAAAAAAAAAAAAAC
1263828 ACTATTCCAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.82, C:0.15, G:0.03, T:0.00
Consensus pattern (17 bp):
CAAAAAAAAAAAAAAAC
Found at i:1265697 original size:51 final size:51
Alignment explanation
Indices: 1265621--1265921 Score: 195
Period size: 52 Copynumber: 5.7 Consensus size: 51
1265611 AATTCTCCAC
*
1265621 AATCGGGGATATTCCAACTCCGATTTTATTTTCAAAACACTAATTTTCTAT
1 AATCGGGGATACTCCAACTCCGATTTTATTTTCAAAACACTAATTTTCTAT
* * *
1265672 AATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAAACACCAA-TTTCTTCAC
1 AATCGGGGATACTCCAACTCCGATTTTATTTTC--AAAACACTAATTTTC-T-AT
* ** * * * *
1265726 AATCGGGGATACTCCAACCCCG-TTAATGATCGGGGATACTCCAACCCCGTTA-TTTC--T
1 AATCGGGGATACTCCAACTCCGATT--T--T-----ATTTTCAAAACAC-TAATTTTCTAT
* * * * *
1265783 GA--GGGGATACTCCAACTCCGGTTTTA-TTGCTAAAACACTAATTTTTTCAC
1 AATCGGGGATACTCCAACTCCGATTTTATTTTC-AAAACACTAATTTTCT-AT
* * * * *
1265833 AATCGGGGATACTCCAACCCCGGTTTTATTTTCAAAACGCCAATTTTCCTTT
1 AATCGGGGATACTCCAACTCCGATTTTATTTTCAAAACACTAATTTT-CTAT
*
1265885 AATCGGGGATACTCCAACTCCGATTTTATTTCCAAAA
1 AATCGGGGATACTCCAACTCCGATTTTATTTTCAAAA
1265922 AATACCAATT
Statistics
Matches: 190, Mismatches: 36, Indels: 47
0.70 0.13 0.17
Matches are distributed among these distances:
46 3 0.02
47 8 0.04
50 1 0.01
51 31 0.16
52 74 0.39
53 16 0.08
54 23 0.12
55 18 0.09
56 2 0.01
57 2 0.01
60 4 0.02
61 5 0.03
62 3 0.02
ACGTcount: A:0.29, C:0.25, G:0.14, T:0.32
Consensus pattern (51 bp):
AATCGGGGATACTCCAACTCCGATTTTATTTTCAAAACACTAATTTTCTAT
Found at i:1265797 original size:28 final size:27
Alignment explanation
Indices: 1265730--1265798 Score: 93
Period size: 27 Copynumber: 2.5 Consensus size: 27
1265720 CTTCACAATC
*
1265730 GGGGATACTCCAACCCCGTTAATGATC
1 GGGGATACTCCAACCCCGTTAATGATA
* **
1265757 GGGGATACTCCAACCCCGTTATTTCTGA
1 GGGGATACTCCAACCCCGTTAATGAT-A
1265785 GGGGATACTCCAAC
1 GGGGATACTCCAAC
1265799 TCCGGTTTTA
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
27 23 0.62
28 14 0.38
ACGTcount: A:0.25, C:0.29, G:0.23, T:0.23
Consensus pattern (27 bp):
GGGGATACTCCAACCCCGTTAATGATA
Found at i:1265808 original size:109 final size:106
Alignment explanation
Indices: 1265676--1266030 Score: 346
Period size: 109 Copynumber: 3.3 Consensus size: 106
1265666 TTCTATAATC
1265676 GGGGATACTCCAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGGGGATACTCC
1 GGGGATACTCCAACTCCGATTTTATTTCCAAAAAACACCAATTT-TTCACAATCGGGGATACTCC
*
1265741 AACCCCGTTAATGATCGGGGATACTCCAACCCCGTTATTTCTGA
65 AACCCCGTTAATCATCGGGGATACTCCAACCCCGTTA-TTC-GA
* * * *
1265785 GGGGATACTCCAACTCCGGTTTTA-TTGC-TAAAACACTAATTTTTTCACAATCGGGGATACTCC
1 GGGGATACTCCAACTCCGATTTTATTTCCAAAAAACACCAA-TTTTTCACAATCGGGGATACTCC
* ** * * * ** * *
1265848 AACCCCGGTTTTATTTTC---AAAACGCCAATTTTCCTTTAATC--
65 AACCCC-G-TTAATCATCGGGGATACTCCAA--CCCCGTTATTCGA
* *
1265889 GGGGATACTCCAACTCCGATTTTATTTCCAAAAAATACCAATTTTTCACAATCGAGGATACTCCA
1 GGGGATACTCCAACTCCGATTTTATTTCCAAAAAACACCAATTTTTCACAATCGGGGATACTCCA
* * *
1265954 ACCTCGTTATTTCATCGGGGATACTCCATCCCCGTTACTTCCGA
66 ACCCCGTTA-ATCATCGGGGATACTCCAACCCCGTTA-TT-CGA
* ** *
1265998 GGGGATACTCCAACCCCGGCTTTATTCCCAAAA
1 GGGGATACTCCAACTCCGATTTTATTTCCAAAA
1266031 TATTGATTTC
Statistics
Matches: 194, Mismatches: 37, Indels: 30
0.74 0.14 0.11
Matches are distributed among these distances:
103 2 0.01
104 27 0.14
105 35 0.18
106 16 0.08
107 44 0.23
108 12 0.06
109 58 0.30
ACGTcount: A:0.28, C:0.28, G:0.15, T:0.30
Consensus pattern (106 bp):
GGGGATACTCCAACTCCGATTTTATTTCCAAAAAACACCAATTTTTCACAATCGGGGATACTCCA
ACCCCGTTAATCATCGGGGATACTCCAACCCCGTTATTCGA
Found at i:1265840 original size:107 final size:105
Alignment explanation
Indices: 1265676--1266069 Score: 316
Period size: 107 Copynumber: 3.7 Consensus size: 105
1265666 TTCTATAATC
* * * *
1265676 GGGGATACTCCAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGGGGATACTCC
1 GGGGATACTCCAACTCCGATTTTA-TTCC-CAAAACACTAATTTTTTCACAATCGAGGATACTCC
*
1265741 AACCCCGTTAATGATCGGGGATACTCCAACCCCGTTATTTCTGA
64 AACCCCGTTAATCATCGGGGATACTCCAACCCCGTTA-TTC-GA
* * * *
1265785 GGGGATACTCCAACTCCGGTTTTATTGCTAAAACACTAATTTTTTCACAATCGGGGATACTCCAA
1 GGGGATACTCCAACTCCGATTTTATTCCCAAAACACTAATTTTTTCACAATCGAGGATACTCCAA
* ** * * * ** * *
1265850 CCCCGGTTTTATTTTC---AAAACGCCAATTTTCCTTTAATC--
66 CCCC-G-TTAATCATCGGGGATACTCCAA--CCCCGTTATTCGA
* * *
1265889 GGGGATACTCCAACTCCGATTTTATTTCCAAAA-AATACCAATTTTTCACAATCGAGGATACTCC
1 GGGGATACTCCAACTCCGATTTTATTCCCAAAACACTA--ATTTTTTCACAATCGAGGATACTCC
* * *
1265953 AACCTCGTTATTTCATCGGGGATACTCCATCCCCGTTACTTCCGA
64 AACCCCGTTA-ATCATCGGGGATACTCCAACCCCGTTA-TT-CGA
* ** * * * * * *
1265998 GGGGATACTCCAACCCCGGCTTTATTCCCAAAATATTGA-TTTCTCATAATTGAGGATACTCCAA
1 GGGGATACTCCAACTCCGATTTTATTCCCAAAACACTAATTTTTTCACAATCGAGGATACTCCAA
1266062 CCCCGTTA
66 CCCCGTTA
1266070 TTTTCGAGGG
Statistics
Matches: 226, Mismatches: 44, Indels: 32
0.75 0.15 0.11
Matches are distributed among these distances:
103 5 0.02
104 34 0.15
105 33 0.15
106 8 0.04
107 76 0.34
108 10 0.04
109 58 0.26
110 2 0.01
ACGTcount: A:0.28, C:0.27, G:0.14, T:0.30
Consensus pattern (105 bp):
GGGGATACTCCAACTCCGATTTTATTCCCAAAACACTAATTTTTTCACAATCGAGGATACTCCAA
CCCCGTTAATCATCGGGGATACTCCAACCCCGTTATTCGA
Found at i:1265850 original size:52 final size:51
Alignment explanation
Indices: 1265785--1265955 Score: 168
Period size: 52 Copynumber: 3.3 Consensus size: 51
1265775 TTATTTCTGA
* *
1265785 GGGGATACTCCAACTCCGGTTTTATTGCTAAAACACTAATTTTTTCACAATC
1 GGGGATACTCCAACTCCGATTTTATT-CTAAAACACCAATTTTTTCACAATC
* * * * *
1265837 GGGGATACTCCAACCCCGGTTTTATTTTCAAAACGCCAATTTTCCTT--TAATC
1 GGGGATACTCCAACTCCGATTTTATTCT-AAAACACCAATTTT--TTCACAATC
* *
1265889 GGGGATACTCCAACTCCGATTTTATTTCCAAAAAATACCAA-TTTTTCACAATC
1 GGGGATACTCCAACTCCGATTTTA-TT-C-TAAAACACCAATTTTTTCACAATC
*
1265942 GAGGATACTCCAAC
1 GGGGATACTCCAAC
1265956 CTCGTTATTT
Statistics
Matches: 98, Mismatches: 13, Indels: 15
0.78 0.10 0.12
Matches are distributed among these distances:
51 3 0.03
52 63 0.64
53 22 0.22
54 10 0.10
ACGTcount: A:0.30, C:0.25, G:0.13, T:0.32
Consensus pattern (51 bp):
GGGGATACTCCAACTCCGATTTTATTCTAAAACACCAATTTTTTCACAATC
Found at i:1265975 original size:28 final size:28
Alignment explanation
Indices: 1265939--1266015 Score: 91
Period size: 28 Copynumber: 2.8 Consensus size: 28
1265929 ATTTTTCACA
* * *
1265939 ATCGAGGATACTCCAACCTCGTTATTTC
1 ATCGGGGATACTCCAACCCCGTTACTTC
*
1265967 ATCGGGGATACTCCATCCCCGTTACTTC
1 ATCGGGGATACTCCAACCCCGTTACTTC
***
1265995 CGAGGGGATACTCCAACCCCG
1 ATCGGGGATACTCCAACCCCG
1266016 GCTTTATTCC
Statistics
Matches: 41, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
28 41 1.00
ACGTcount: A:0.22, C:0.34, G:0.19, T:0.25
Consensus pattern (28 bp):
ATCGGGGATACTCCAACCCCGTTACTTC
Found at i:1265989 original size:213 final size:212
Alignment explanation
Indices: 1265618--1266023 Score: 643
Period size: 213 Copynumber: 1.9 Consensus size: 212
1265608 CTAAATTCTC
* * *
1265618 CACAATCGGGGATATTCCAACTCCGATTTTATTTTCAAAACACTAATTTTCTATAATCGGGGATA
1 CACAATCGGGGATACTCCAACCCCGATTTTATTTTCAAAACACCAATTTTCTATAATCGGGGATA
*
1265683 CTCCAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGGGGATACTCCAACCCCG
66 CTCCAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGAGGATACTCCAACCCCG
* * * * *
1265748 TTAATGATCGGGGATACTCCAACCCCGTTATTTCTGAGGGGATACTCCAACTCCGGTTTTATTGC
131 TTAATCATCGGGGATACTCCAACCCCGTTACTTCCGAGGGGATACTCCAACCCCGGCTTTATTGC
1265813 TAAAACACTAATTTTTT
196 TAAAACACTAATTTTTT
* * *
1265830 CACAATCGGGGATACTCCAACCCCGGTTTTATTTTCAAAACGCCAATTTTCCTTTAATCGGGGAT
1 CACAATCGGGGATACTCCAACCCCGATTTTATTTTCAAAACACCAATTTT-CTATAATCGGGGAT
* *
1265895 ACTCCAACTCCGATTTTATTTCCAAAAAATACCAATTT-TTCACAATCGAGGATACTCCAACCTC
65 ACTCCAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGAGGATACTCCAACCCC
* *
1265959 GTTATTTCATCGGGGATACTCCATCCCCGTTACTTCCGAGGGGATACTCCAACCCCGGCTTTATT
130 GTTA-ATCATCGGGGATACTCCAACCCCGTTACTTCCGAGGGGATACTCCAACCCCGGCTTTATT
1266024 CCCAAAATAT
Statistics
Matches: 176, Mismatches: 16, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
212 73 0.41
213 103 0.59
ACGTcount: A:0.28, C:0.27, G:0.14, T:0.31
Consensus pattern (212 bp):
CACAATCGGGGATACTCCAACCCCGATTTTATTTTCAAAACACCAATTTTCTATAATCGGGGATA
CTCCAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGAGGATACTCCAACCCCG
TTAATCATCGGGGATACTCCAACCCCGTTACTTCCGAGGGGATACTCCAACCCCGGCTTTATTGC
TAAAACACTAATTTTTT
Found at i:1281510 original size:79 final size:79
Alignment explanation
Indices: 1281393--1281709 Score: 424
Period size: 79 Copynumber: 4.0 Consensus size: 79
1281383 ATATTTCCCG
* * *
1281393 ATGAGAAATTTAATATTTTGGAGATAGTAA-CGGGGTTGGAGTATCCCCTTGAAAATAACGGGGT
1 ATGAGAAA-TTAATATTTTGGAAATA-AAACCGGGGTTGGAGTATCCCCTCGAAAATAACGGGGT
1281457 TGGAGTATCCCCGATT
64 TGGAGTATCCCCGATT
* * * * *
1281473 ATGAAAAATTGATGA-TTTGGAAATAAAACTGGGGTTGGAGTATCCCCTCGGAGATAACGGGGTT
1 ATGAGAAATTAAT-ATTTTGGAAATAAAACCGGGGTTGGAGTATCCCCTCGAAAATAACGGGGTT
1281537 GGAGTATCCCCGATT
65 GGAGTATCCCCGATT
* * * *
1281552 ATGAGAAATTAATATTTTAGAAATAAAGCCGGGGTTGGAGTATCCCCTTGAAAATAACGAGGTTG
1 ATGAGAAATTAATATTTTGGAAATAAAACCGGGGTTGGAGTATCCCCTCGAAAATAACGGGGTTG
1281617 GAGTATCCCCGATT
66 GAGTATCCCCGATT
* * * *
1281631 ATGAGAAATCAATATTTTAGG-AATAAAGCCGGGGGTTAGAGTATCCCCTCAAAAATAACGGGGT
1 ATGAGAAATTAATATTTT-GGAAATAAAACC-GGGGTTGGAGTATCCCCTCGAAAATAACGGGGT
1281695 TGGAGTATCCCCGAT
64 TGGAGTATCCCCGAT
1281710 GATTAACGGG
Statistics
Matches: 209, Mismatches: 23, Indels: 10
0.86 0.10 0.04
Matches are distributed among these distances:
78 3 0.01
79 153 0.73
80 53 0.25
ACGTcount: A:0.32, C:0.14, G:0.26, T:0.27
Consensus pattern (79 bp):
ATGAGAAATTAATATTTTGGAAATAAAACCGGGGTTGGAGTATCCCCTCGAAAATAACGGGGTTG
GAGTATCCCCGATT
Found at i:1281701 original size:28 final size:27
Alignment explanation
Indices: 1281662--1281732 Score: 88
Period size: 27 Copynumber: 2.6 Consensus size: 27
1281652 AATAAAGCCG
*
1281662 GGGGTTAGAGTATCCCCTCAAAAATAAC
1 GGGGTTGGAGTATCCCC-CAAAAATAAC
* ** *
1281690 GGGGTTGGAGTATCCCCGATGATTAAC
1 GGGGTTGGAGTATCCCCCAAAAATAAC
1281717 GGGGTTGGAGTATCCC
1 GGGGTTGGAGTATCCC
1281733 TTATGAAAAA
Statistics
Matches: 38, Mismatches: 5, Indels: 1
0.86 0.11 0.02
Matches are distributed among these distances:
27 22 0.58
28 16 0.42
ACGTcount: A:0.25, C:0.20, G:0.31, T:0.24
Consensus pattern (27 bp):
GGGGTTGGAGTATCCCCCAAAAATAAC
Found at i:1284202 original size:34 final size:33
Alignment explanation
Indices: 1284164--1284230 Score: 107
Period size: 34 Copynumber: 2.0 Consensus size: 33
1284154 AACTTCCTAG
*
1284164 ATGTATCGATACAAAGAATAGATGTATCGATACA
1 ATGTATCGATACAAAGAA-AAATGTATCGATACA
*
1284198 ATGTATCGATACACAGAAAAATGTATCGATACA
1 ATGTATCGATACAAAGAAAAATGTATCGATACA
1284231 TTTCCTTGGC
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
33 14 0.45
34 17 0.55
ACGTcount: A:0.45, C:0.13, G:0.16, T:0.25
Consensus pattern (33 bp):
ATGTATCGATACAAAGAAAAATGTATCGATACA
Found at i:1284203 original size:13 final size:13
Alignment explanation
Indices: 1284185--1284210 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1284175 CAAAGAATAG
1284185 ATGTATCGATACA
1 ATGTATCGATACA
1284198 ATGTATCGATACA
1 ATGTATCGATACA
1284211 CAGAAAAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1284272 original size:13 final size:13
Alignment explanation
Indices: 1284254--1284305 Score: 50
Period size: 13 Copynumber: 3.5 Consensus size: 13
1284244 AGCTTCCTAG
1284254 CGATACATTGTAT
1 CGATACATTGTAT
1284267 CGATACAAAACTTGTGTAT
1 CGATAC---A-TT--GTAT
1284286 CGATACATTGTAT
1 CGATACATTGTAT
1284299 CGATACA
1 CGATACA
1284306 ACACTTATGT
Statistics
Matches: 33, Mismatches: 0, Indels: 12
0.73 0.00 0.27
Matches are distributed among these distances:
13 17 0.52
15 2 0.06
16 2 0.06
17 2 0.06
19 10 0.30
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.33
Consensus pattern (13 bp):
CGATACATTGTAT
Found at i:1284286 original size:19 final size:19
Alignment explanation
Indices: 1284262--1284345 Score: 99
Period size: 19 Copynumber: 4.7 Consensus size: 19
1284252 AGCGATACAT
*
1284262 TGTATCGATACAAAACTTG
1 TGTATCGATACAAAACTTA
1284281 TGTATCGATAC---A--T-
1 TGTATCGATACAAAACTTA
*
1284294 TGTATCGATACAACACTTA
1 TGTATCGATACAAAACTTA
*
1284313 TGTATCGATACAACACTTA
1 TGTATCGATACAAAACTTA
1284332 TGTATCGATACAAA
1 TGTATCGATACAAA
1284346 TCACTGAAAT
Statistics
Matches: 58, Mismatches: 1, Indels: 12
0.82 0.01 0.17
Matches are distributed among these distances:
13 11 0.19
14 1 0.02
16 2 0.03
18 1 0.02
19 43 0.74
ACGTcount: A:0.37, C:0.18, G:0.13, T:0.32
Consensus pattern (19 bp):
TGTATCGATACAAAACTTA
Found at i:1284295 original size:32 final size:32
Alignment explanation
Indices: 1284254--1284324 Score: 124
Period size: 32 Copynumber: 2.2 Consensus size: 32
1284244 AGCTTCCTAG
*
1284254 CGATACATTGTATCGATACAAAACTTGTGTAT
1 CGATACATTGTATCGATACAAAACTTATGTAT
*
1284286 CGATACATTGTATCGATACAACACTTATGTAT
1 CGATACATTGTATCGATACAAAACTTATGTAT
1284318 CGATACA
1 CGATACA
1284325 ACACTTATGT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
32 37 1.00
ACGTcount: A:0.35, C:0.18, G:0.14, T:0.32
Consensus pattern (32 bp):
CGATACATTGTATCGATACAAAACTTATGTAT
Found at i:1286718 original size:20 final size:21
Alignment explanation
Indices: 1286674--1286725 Score: 70
Period size: 20 Copynumber: 2.5 Consensus size: 21
1286664 GTTCACAATT
*
1286674 TGTATCGATACAACAAGTTAA
1 TGTATCGATACAACAAGTGAA
* *
1286695 TGTATCGATAC-ATAGGTGAA
1 TGTATCGATACAACAAGTGAA
1286715 TGTATCGATAC
1 TGTATCGATAC
1286726 TAAGACTTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 17 0.61
21 11 0.39
ACGTcount: A:0.37, C:0.13, G:0.19, T:0.31
Consensus pattern (21 bp):
TGTATCGATACAACAAGTGAA
Found at i:1290467 original size:143 final size:143
Alignment explanation
Indices: 1290184--1290466 Score: 372
Period size: 143 Copynumber: 2.0 Consensus size: 143
1290174 CTCAAAAAAG
* * * *
1290184 GTATTGATTATAATGAAATTTTCACTTTAGTTTTAAAAAGGTTTTATCTACAATTATCATATCTC
1 GTATTGATTATAATGAAATTTTCACTTCAGTTTTAAAAAAGTTTCATCTACAATTATCATAGCTC
* * * * *
1290249 TTGTAGCTCATTCTGATTGAGAGTTATATTAAATGATGTAAAAATAAGTTTTTTAAATAGAGATC
66 TTGTAGCTCATTCTAATTGAAAATTACATTAAATGATGTAAAAATAAGTTTTTTAAATAGAGATA
1290314 TTAAGAAAAAGAA
131 TTAAGAAAAAGAA
* * *
1290327 GTATTGATTATGATGAAATTTTCTCTTCAGTTTTAAAAAAGTTTCATAC-AGAATTATCATAGCT
1 GTATTGATTATAATGAAATTTTCACTTCAGTTTTAAAAAAGTTTCAT-CTACAATTATCATAGCT
* * * *
1290391 TTTGTAGCTCATTCTAATTGAAAATTACATTATATGGATGTGAAAATAAGTTTCTTT-AATAGGG
65 CTTGTAGCTCATTCTAATTGAAAATTACATTAAAT-GATGTAAAAATAAGTTT-TTTAAATAGAG
*
1290455 ATATTGAGAAAA
128 ATATTAAGAAAA
1290467 GGTATATAAA
Statistics
Matches: 120, Mismatches: 17, Indels: 5
0.85 0.12 0.04
Matches are distributed among these distances:
143 84 0.70
144 33 0.28
145 3 0.03
ACGTcount: A:0.37, C:0.08, G:0.14, T:0.40
Consensus pattern (143 bp):
GTATTGATTATAATGAAATTTTCACTTCAGTTTTAAAAAAGTTTCATCTACAATTATCATAGCTC
TTGTAGCTCATTCTAATTGAAAATTACATTAAATGATGTAAAAATAAGTTTTTTAAATAGAGATA
TTAAGAAAAAGAA
Found at i:1291672 original size:15 final size:16
Alignment explanation
Indices: 1291649--1291681 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
1291639 ATATTTTAGT
*
1291649 AATATTATTT-AGATA
1 AATACTATTTAAGATA
1291664 AATACTATTTAAGATA
1 AATACTATTTAAGATA
1291680 AA
1 AA
1291682 ACTTTAGTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 9 0.56
16 7 0.44
ACGTcount: A:0.52, C:0.03, G:0.06, T:0.39
Consensus pattern (16 bp):
AATACTATTTAAGATA
Found at i:1292232 original size:5 final size:6
Alignment explanation
Indices: 1292213--1292254 Score: 66
Period size: 6 Copynumber: 7.0 Consensus size: 6
1292203 TGGATTCATG
* *
1292213 AAAGAA AAAGAA AAAGAA AAACAA AGAGAA AAAGAA AAAGAA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA
1292255 TATTTTTTGT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
6 32 1.00
ACGTcount: A:0.81, C:0.02, G:0.17, T:0.00
Consensus pattern (6 bp):
AAAGAA
Found at i:1296595 original size:20 final size:22
Alignment explanation
Indices: 1296557--1296598 Score: 61
Period size: 20 Copynumber: 2.0 Consensus size: 22
1296547 TTATATTATA
1296557 TAATTATATTTTTAAATAAAAAG
1 TAATTATATTTTT-AATAAAAAG
1296580 TAATTAT-TTTTT-ATAAAAA
1 TAATTATATTTTTAATAAAAA
1296599 TTATTAATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 7 0.37
22 5 0.26
23 7 0.37
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (22 bp):
TAATTATATTTTTAATAAAAAG
Found at i:1296612 original size:11 final size:11
Alignment explanation
Indices: 1296596--1296663 Score: 50
Period size: 11 Copynumber: 6.0 Consensus size: 11
1296586 TTTTTTATAA
1296596 AAATTATTAAT
1 AAATTATTAAT
1296607 AAATTATTAA-
1 AAATTATTAAT
* *
1296617 ATATTTATTAGT
1 A-AATTATTAAT
*
1296629 TAATTATTATAT
1 AAATTATTA-AT
1296641 ATAA-TATGTAAT
1 A-AATTAT-TAAT
*
1296653 AAATAATTAAT
1 AAATTATTAAT
1296664 TGTTTTAAAA
Statistics
Matches: 44, Mismatches: 7, Indels: 12
0.70 0.11 0.19
Matches are distributed among these distances:
10 1 0.02
11 30 0.68
12 9 0.20
13 4 0.09
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (11 bp):
AAATTATTAAT
Found at i:1297022 original size:19 final size:19
Alignment explanation
Indices: 1296988--1297042 Score: 56
Period size: 20 Copynumber: 2.8 Consensus size: 19
1296978 AATATTATTA
* *
1296988 AAAATTATTTAAATATCGAT
1 AAAATT-TTAAAATATAGAT
* *
1297008 AAAATTTTGAAATATTATAT
1 AAAATTTTAAAATA-TAGAT
1297028 AAAATTTTAAAATAT
1 AAAATTTTAAAATAT
1297043 TATATGATAT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
19 8 0.27
20 22 0.73
ACGTcount: A:0.53, C:0.02, G:0.04, T:0.42
Consensus pattern (19 bp):
AAAATTTTAAAATATAGAT
Found at i:1297029 original size:20 final size:20
Alignment explanation
Indices: 1297006--1297047 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
1296996 TTAAATATCG
*
1297006 ATAAAATTTTGAAATATTAT
1 ATAAAATTTTAAAATATTAT
1297026 ATAAAATTTTAAAATATTAT
1 ATAAAATTTTAAAATATTAT
1297046 AT
1 AT
1297048 GATATAAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.45
Consensus pattern (20 bp):
ATAAAATTTTAAAATATTAT
Found at i:1297052 original size:25 final size:24
Alignment explanation
Indices: 1297019--1297071 Score: 79
Period size: 25 Copynumber: 2.2 Consensus size: 24
1297009 AAATTTTGAA
*
1297019 ATATTATATAAAATTTTAAAATATT
1 ATATGATATAAAATTTT-AAATATT
*
1297044 ATATGATATAAAATTTTAAATTTT
1 ATATGATATAAAATTTTAAATATT
1297068 ATAT
1 ATAT
1297072 AAAAATAATA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
24 10 0.38
25 16 0.62
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (24 bp):
ATATGATATAAAATTTTAAATATT
Found at i:1297079 original size:25 final size:25
Alignment explanation
Indices: 1297026--1297075 Score: 66
Period size: 24 Copynumber: 2.0 Consensus size: 25
1297016 GAAATATTAT
* *
1297026 ATAAAATTTTAAAATATTATATGAT
1 ATAAAATTTTAAAATATTATATAAA
*
1297051 ATAAAATTTT-AAATTTTATATAAA
1 ATAAAATTTTAAAATATTATATAAA
1297075 A
1 A
1297076 ATAATATAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
24 12 0.55
25 10 0.45
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (25 bp):
ATAAAATTTTAAAATATTATATAAA
Found at i:1297112 original size:17 final size:18
Alignment explanation
Indices: 1297077--1297119 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
1297067 TATATAAAAA
1297077 TAATATAAACTCAATTTT
1 TAATATAAACTCAATTTT
*
1297095 TAATCTAAACTC-ATTTT
1 TAATATAAACTCAATTTT
1297112 TAA-ATAAA
1 TAATATAAA
1297120 ATTTAAAATT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 4 0.17
17 8 0.35
18 11 0.48
ACGTcount: A:0.47, C:0.12, G:0.00, T:0.42
Consensus pattern (18 bp):
TAATATAAACTCAATTTT
Found at i:1297236 original size:14 final size:15
Alignment explanation
Indices: 1297217--1297253 Score: 51
Period size: 14 Copynumber: 2.5 Consensus size: 15
1297207 ATGATTTAAA
1297217 AAAATATATAAA-TT
1 AAAATATATAAATTT
1297231 AAAATAT-TAAATTT
1 AAAATATATAAATTT
1297245 AATAATATA
1 AA-AATATA
1297254 ACACTTAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
13 4 0.20
14 11 0.55
15 5 0.25
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (15 bp):
AAAATATATAAATTT
Found at i:1298029 original size:22 final size:22
Alignment explanation
Indices: 1297979--1298031 Score: 81
Period size: 22 Copynumber: 2.4 Consensus size: 22
1297969 ACATATAGTC
*
1297979 AAATATATTTATGAATAATTGA
1 AAATATGTTTATGAATAATTGA
1298001 AAATATGTTTATGAATAATT-A
1 AAATATGTTTATGAATAATTGA
1298022 AAATTATGTT
1 AAA-TATGTT
1298032 CGTGAACAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
21 4 0.14
22 25 0.86
ACGTcount: A:0.47, C:0.00, G:0.09, T:0.43
Consensus pattern (22 bp):
AAATATGTTTATGAATAATTGA
Found at i:1298037 original size:22 final size:22
Alignment explanation
Indices: 1297979--1298037 Score: 66
Period size: 22 Copynumber: 2.7 Consensus size: 22
1297969 ACATATAGTC
* *
1297979 AAATATATTTATGAATAATTGA
1 AAATATGTTCATGAATAATTGA
*
1298001 AAATATGTTTATGAATAATT-A
1 AAATATGTTCATGAATAATTGA
*
1298022 AAATTATGTTCGTGAA
1 AAA-TATGTTCATGAA
1298038 CAATAAAGAA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
21 4 0.12
22 29 0.88
ACGTcount: A:0.46, C:0.02, G:0.12, T:0.41
Consensus pattern (22 bp):
AAATATGTTCATGAATAATTGA
Found at i:1300341 original size:29 final size:29
Alignment explanation
Indices: 1300299--1300357 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
1300289 TAGAGGGGCC
1300299 ATATTCACCATTTCGAAAGCAGTTGCCTT
1 ATATTCACCATTTCGAAAGCAGTTGCCTT
1300328 ATATTCACCATTTCGAAAGCAGTTGCCTT
1 ATATTCACCATTTCGAAAGCAGTTGCCTT
1300357 A
1 A
1300358 CTTTGTGGAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.29, C:0.24, G:0.14, T:0.34
Consensus pattern (29 bp):
ATATTCACCATTTCGAAAGCAGTTGCCTT
Found at i:1302493 original size:16 final size:17
Alignment explanation
Indices: 1302468--1302502 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
1302458 AATGTCATGG
*
1302468 AAAATCAAAATAAGATA
1 AAAATCAAAATAAAATA
1302485 AAAAT-AAAATAAAATA
1 AAAATCAAAATAAAATA
1302501 AA
1 AA
1302503 GAAGGCCAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 12 0.71
17 5 0.29
ACGTcount: A:0.77, C:0.03, G:0.03, T:0.17
Consensus pattern (17 bp):
AAAATCAAAATAAAATA
Found at i:1305783 original size:50 final size:50
Alignment explanation
Indices: 1305723--1305818 Score: 133
Period size: 50 Copynumber: 1.9 Consensus size: 50
1305713 TAAATTTCTA
* *
1305723 GATTTTTCATCTC-GAGGATACTCCAACCTCGGA-TTTATTTCTAAAATATT
1 GATTTTTCATCTCGGA-GATACTCCAACC-CCGATTTTATTTCCAAAATATT
*
1305773 GATTTTTCATCTCGGAGATACTCTAACCCCGATTTTATTTCCAAAA
1 GATTTTTCATCTCGGAGATACTCCAACCCCGATTTTATTTCCAAAA
1305819 CATCAATTTT
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
49 3 0.07
50 36 0.88
51 2 0.05
ACGTcount: A:0.28, C:0.22, G:0.11, T:0.39
Consensus pattern (50 bp):
GATTTTTCATCTCGGAGATACTCCAACCCCGATTTTATTTCCAAAATATT
Found at i:1305943 original size:79 final size:79
Alignment explanation
Indices: 1305789--1306087 Score: 309
Period size: 79 Copynumber: 3.8 Consensus size: 79
1305779 TCATCTCGGA
* ** * * *
1305789 GATACTCTAACCCCGATTTTATTTCCAAAACATCAATTTT-CATAATCGGGGATACTTC-ACTCC
1 GATACTCCAACCCCGACCTTATTTCTAAAACTTCAATTTTCCATAATCGGGGATACTCCAAC-CC
*
1305852 CGTTATTTTCGAGGG
65 TGTTATTTTCGAGGG
* * * *
1305867 GATACTCTAACCCCGACCTTATTTCTAAAGCTTCAATTTTTCACAATCGGGGATACTCCAACCCT
1 GATACTCCAACCCCGACCTTATTTCTAAAACTTCAATTTTCCATAATCGGGGATACTCCAACCCT
*
1305932 GTTATTTTCGAGGA
66 GTTATTTTCGAGGG
** ** * ** ** *
1305946 GATACTCCAACCCTAATTTTATTT-TCAAAACGTC-GGTTTCCTATAATTAGGGATGCTCCAACC
1 GATACTCCAACCCCGACCTTATTTCT-AAAACTTCAATTTTCC-ATAATCGGGGATACTCCAACC
1306009 CTGTTATTTTCGAGGG
64 CTGTTATTTTCGAGGG
* * * *
1306025 GATACTCCAACCCTGGCCTTATTTCTAAAGCTTCGATTTTCCATAATCGGGGATACTCCAACC
1 GATACTCCAACCCCGACCTTATTTCTAAAACTTCAATTTTCCATAATCGGGGATACTCCAACC
1306088 TCGATTTTAT
Statistics
Matches: 180, Mismatches: 35, Indels: 11
0.80 0.15 0.05
Matches are distributed among these distances:
78 40 0.22
79 132 0.73
80 8 0.04
ACGTcount: A:0.26, C:0.26, G:0.15, T:0.33
Consensus pattern (79 bp):
GATACTCCAACCCCGACCTTATTTCTAAAACTTCAATTTTCCATAATCGGGGATACTCCAACCCT
GTTATTTTCGAGGG
Found at i:1306191 original size:130 final size:131
Alignment explanation
Indices: 1305946--1306221 Score: 353
Period size: 130 Copynumber: 2.1 Consensus size: 131
1305936 TTTTCGAGGA
* * *
1305946 GATACTCCAACC-CTAATTTTATTTTCAAAACGTCGGTTTCCTATAATTAGGGATGCTCCAACCC
1 GATACTCCAACCTC-GATTTTATTTTCAAAACGTCGATTTCCTATAATCAGGGATGCTCCAACCC
* * * * *
1306010 TGTTATTTTCGAGGGGATACTCCAACCCTGGCCTTATTTCTAAAGCTTCGATTTTCCATAATC-G
65 TGTTATTTCCAAGGGGATACTCCAACCCTGACCTTATTTCTAAAGCATCGATTTTCCATAATCAA
1306074 GG
130 GG
* * *
1306076 GATACTCCAACCTCGATTTTATTTTCAAAACGTTGATTTCCTATAGTCGGGGATGCTCCAACCCT
1 GATACTCCAACCTCGATTTTATTTTCAAAACGTCGATTTCCTATAATCAGGGATGCTCCAACCCT
* ** *
1306141 GTTATTTCCAAGGGGATACTCCAA-CGTCGATTTTATTTTTAGAA-CATCGATTTTCCATAATCA
66 GTTATTTCCAAGGGGATACTCCAACCCT-GACCTTATTTCTA-AAGCATCGATTTTCCATAATCA
1306204 AGG
129 AGG
*
1306207 GATACTCCAGCCTCG
1 GATACTCCAACCTCG
1306222 TTGTTATCCC
Statistics
Matches: 126, Mismatches: 16, Indels: 7
0.85 0.11 0.05
Matches are distributed among these distances:
129 2 0.02
130 105 0.83
131 19 0.15
ACGTcount: A:0.25, C:0.24, G:0.16, T:0.34
Consensus pattern (131 bp):
GATACTCCAACCTCGATTTTATTTTCAAAACGTCGATTTCCTATAATCAGGGATGCTCCAACCCT
GTTATTTCCAAGGGGATACTCCAACCCTGACCTTATTTCTAAAGCATCGATTTTCCATAATCAAG
G
Found at i:1317333 original size:14 final size:13
Alignment explanation
Indices: 1317314--1317368 Score: 58
Period size: 13 Copynumber: 4.2 Consensus size: 13
1317304 CCTTCTTTTT
1317314 AAAAAAAAAACAA
1 AAAAAAAAAACAA
*
1317327 GAAAAAAAAACCAA
1 -AAAAAAAAAACAA
1317341 AAAAAAAAAA-AA
1 AAAAAAAAAACAA
* * *
1317353 ACAAAATAAAGAA
1 AAAAAAAAAACAA
1317366 AAA
1 AAA
1317369 GGAGAGAAAA
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
12 10 0.29
13 13 0.37
14 12 0.34
ACGTcount: A:0.87, C:0.07, G:0.04, T:0.02
Consensus pattern (13 bp):
AAAAAAAAAACAA
Found at i:1317357 original size:16 final size:16
Alignment explanation
Indices: 1317314--1317368 Score: 60
Period size: 16 Copynumber: 3.4 Consensus size: 16
1317304 CCTTCTTTTT
*
1317314 AAAAAAAAAAC--AAG
1 AAAAAAAAAACAAAAA
*
1317328 AAAAAAAAACCAAAAA
1 AAAAAAAAAACAAAAA
1317344 AAAAAAAAAACAAAATA
1 AAAAAAAAAACAAAA-A
1317361 AAGAAAAA
1 AA-AAAAA
1317369 GGAGAGAAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
14 10 0.29
16 16 0.47
17 3 0.09
18 5 0.15
ACGTcount: A:0.87, C:0.07, G:0.04, T:0.02
Consensus pattern (16 bp):
AAAAAAAAAACAAAAA
Found at i:1318561 original size:93 final size:93
Alignment explanation
Indices: 1318383--1318662 Score: 366
Period size: 93 Copynumber: 3.0 Consensus size: 93
1318373 GACACCTTCT
* * *
1318383 CCTTTTAAAGCCCACACAAGTTGGTGGCACTTCCCAGTCCTCAAAAAGCAGGACGTTCTCTCATT
1 CCTTTTAAAGCCCACACAAGTTGGTGGCACTT-CCAGTCCTCAAAAAGCAGGACGCTCTTTCCTT
*
1318448 TCACCTTTTAGTCC-CTAAAGAGTAGGACA
65 TCACCTTTTAGTCCTC-AAAGAGCAGGACA
* ** **
1318477 CCTTTTAAAGCCCACATAAGTTGGTGGCACTTCCAGTCCTCAAAGGGCATAACGCTCTTTCCTTT
1 CCTTTTAAAGCCCACACAAGTTGGTGGCACTTCCAGTCCTCAAAAAGCAGGACGCTCTTTCCTTT
*
1318542 CACCTTTTAGTCCTCAAAGAGCAGGACG
66 CACCTTTTAGTCCTCAAAGAGCAGGACA
* * * *
1318570 CCTTTTAAAGCCCACACAAATTGGTGGCACTTCCTAATCCTCAAATAGTAGGACGCTCTCTT-CT
1 CCTTTTAAAGCCCACACAAGTTGGTGGCACTTCC-AGTCCTCAAAAAGCAGGACGCTCT-TTCCT
* *
1318634 TTTACCCTTTAGTCCTCAAAGAGCAGGAC
64 TTCACCTTTTAGTCCTCAAAGAGCAGGAC
1318663 GCATTTTTCT
Statistics
Matches: 163, Mismatches: 20, Indels: 6
0.86 0.11 0.03
Matches are distributed among these distances:
93 82 0.50
94 79 0.48
95 2 0.01
ACGTcount: A:0.26, C:0.29, G:0.17, T:0.28
Consensus pattern (93 bp):
CCTTTTAAAGCCCACACAAGTTGGTGGCACTTCCAGTCCTCAAAAAGCAGGACGCTCTTTCCTTT
CACCTTTTAGTCCTCAAAGAGCAGGACA
Done.