Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D04
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: 52479919
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
Warning! 336953 characters in sequence are not A, C, G, or T
File 48 of 173
Found at i:13132215 original size:16 final size:17
Alignment explanation
Indices: 13132174--13132216 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
13132164 TTGATTTCAG
13132174 ATTAACTATTTTAAAAAT
1 ATTAA-TATTTTAAAAAT
* *
13132192 AATAATATTTTAATAAT
1 ATTAATATTTTAAAAAT
13132209 -TTAATATT
1 ATTAATATT
13132217 AAATTTAATT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
16 7 0.32
17 11 0.50
18 4 0.18
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (17 bp):
ATTAATATTTTAAAAAT
Found at i:13132274 original size:62 final size:58
Alignment explanation
Indices: 13132197--13132325 Score: 172
Period size: 62 Copynumber: 2.2 Consensus size: 58
13132187 AAAATAATAA
* *
13132197 TATTTTAAT-AATTTAATATTAAATTTAATTTAAT-TTTAATCTTGTAGATAAATATTCTAT
1 TATTTTAATAAATTTAATATTAAATTTAATCTAATATTT-ATC-T-T-GATAAATATTATAT
13132257 TATTTTAATAAGATTTAATATTAAATTTAATCTAATATTTATCTTGATAAATATTATAT
1 TATTTTAATAA-ATTTAATATTAAATTTAATCTAATATTTATCTTGATAAATATTATAT
*
13132316 TAATTTAATA
1 TATTTTAATA
13132326 TTAAAGTGAT
Statistics
Matches: 63, Mismatches: 3, Indels: 7
0.86 0.04 0.10
Matches are distributed among these distances:
59 22 0.35
60 10 0.16
61 2 0.03
62 26 0.41
63 3 0.05
ACGTcount: A:0.42, C:0.03, G:0.03, T:0.52
Consensus pattern (58 bp):
TATTTTAATAAATTTAATATTAAATTTAATCTAATATTTATCTTGATAAATATTATAT
Found at i:13140152 original size:18 final size:18
Alignment explanation
Indices: 13140125--13140159 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
13140115 TTCATGAGGT
*
13140125 TGTGGTTGTGGTTGTGAC
1 TGTGGCTGTGGTTGTGAC
13140143 TGTGGCTGTGGTTGTGA
1 TGTGGCTGTGGTTGTGA
13140160 GGTTCTCACT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.06, C:0.06, G:0.46, T:0.43
Consensus pattern (18 bp):
TGTGGCTGTGGTTGTGAC
Found at i:13142964 original size:3 final size:3
Alignment explanation
Indices: 13142952--13142987 Score: 65
Period size: 3 Copynumber: 12.3 Consensus size: 3
13142942 TCAATTTTTT
13142952 AGA A-A AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA A
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA A
13142988 AGAATGGCAC
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.06
3 30 0.94
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:13145317 original size:18 final size:18
Alignment explanation
Indices: 13145296--13145340 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 18
13145286 AATTCTTTTC
13145296 ATTTTTTTAATTTT-AAAT
1 ATTTTTTT-ATTTTAAAAT
*
13145314 ATTTTTATATTTTAAAAT
1 ATTTTTTTATTTTAAAAT
13145332 ATATTTTTT
1 AT-TTTTTT
13145341 TAAAATCAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
17 5 0.22
18 13 0.57
19 5 0.22
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (18 bp):
ATTTTTTTATTTTAAAAT
Found at i:13145770 original size:22 final size:23
Alignment explanation
Indices: 13145745--13145790 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 23
13145735 TTTTATTTTT
13145745 AAAAAAATAAATTTTCAT-TAAA
1 AAAAAAATAAATTTTCATGTAAA
** *
13145767 AAAAGTATAAATTTTTATGTAAA
1 AAAAAAATAAATTTTCATGTAAA
13145790 A
1 A
13145791 TATGAGAAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
22 15 0.75
23 5 0.25
ACGTcount: A:0.59, C:0.02, G:0.04, T:0.35
Consensus pattern (23 bp):
AAAAAAATAAATTTTCATGTAAA
Found at i:13150374 original size:62 final size:61
Alignment explanation
Indices: 13150253--13150374 Score: 142
Period size: 62 Copynumber: 2.0 Consensus size: 61
13150243 TATATTTGTA
****
13150253 CAATCTATTTTTATATTATTTTATTTAACAAAATAAAAGTTGTTTTGAATATTTTAATAGT
1 CAATCTATTTTTATATTATTTTATTTAACAAAATAAAAGTTGTTTTGAATAAGGCAATAGT
*
13150314 CAAT-TATTTTTATATT-TTATCCTATTTAATAAAATAAAAGTTCG-TTTGAATAAGGCAATAG
1 CAATCTATTTTTATATTATT-T--TATTTAACAAAATAAAAGTT-GTTTTGAATAAGGCAATAG
13150375 AAATAATGTA
Statistics
Matches: 52, Mismatches: 5, Indels: 7
0.81 0.08 0.11
Matches are distributed among these distances:
59 2 0.04
60 13 0.25
61 4 0.08
62 32 0.62
63 1 0.02
ACGTcount: A:0.39, C:0.07, G:0.08, T:0.47
Consensus pattern (61 bp):
CAATCTATTTTTATATTATTTTATTTAACAAAATAAAAGTTGTTTTGAATAAGGCAATAGT
Found at i:13153339 original size:14 final size:15
Alignment explanation
Indices: 13153320--13153348 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
13153310 GCACTACAAG
13153320 ATTATTTT-TTTAAA
1 ATTATTTTATTTAAA
13153334 ATTATTTTATTTAAA
1 ATTATTTTATTTAAA
13153349 TATCTATATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (15 bp):
ATTATTTTATTTAAA
Found at i:13153734 original size:22 final size:22
Alignment explanation
Indices: 13153706--13153867 Score: 153
Period size: 22 Copynumber: 7.1 Consensus size: 22
13153696 CTCTCTGATA
*
13153706 TTTAGCACGTCAGTGCTCTCTG
1 TTTAGCACATCAGTGCTCTCTG
*
13153728 TTTAGCACATCTGTGCTCTCTG
1 TTTAGCACATCAGTGCTCTCTG
* *
13153750 ATATTTAGCACGTCAGTGCTCTCTA
1 ---TTTAGCACATCAGTGCTCTCTG
* **
13153775 TTTAGCAAATTTGTGCTCTCTG
1 TTTAGCACATCAGTGCTCTCTG
**
13153797 ATTATTAGCATGTCAGTGCTCTCTG
1 --T-TTAGCACATCAGTGCTCTCTG
*
13153822 TTTAGCACATCTGTGCTCTCTG
1 TTTAGCACATCAGTGCTCTCTG
* * *
13153844 TATAGCACTTTAGTGCTCTCTG
1 TTTAGCACATCAGTGCTCTCTG
13153866 TT
1 TT
13153868 CATTAGTGTA
Statistics
Matches: 112, Mismatches: 22, Indels: 12
0.77 0.15 0.08
Matches are distributed among these distances:
22 74 0.66
23 1 0.01
24 1 0.01
25 36 0.32
ACGTcount: A:0.17, C:0.23, G:0.19, T:0.41
Consensus pattern (22 bp):
TTTAGCACATCAGTGCTCTCTG
Found at i:13153764 original size:47 final size:47
Alignment explanation
Indices: 13153695--13153867 Score: 255
Period size: 47 Copynumber: 3.7 Consensus size: 47
13153685 ACTCTAGCGC
13153695 GCTCTCTGATATTTAGCACGTCAGTGCTCTCTGTTTAGCACATCTGT
1 GCTCTCTGATATTTAGCACGTCAGTGCTCTCTGTTTAGCACATCTGT
* * *
13153742 GCTCTCTGATATTTAGCACGTCAGTGCTCTCTATTTAGCAAATTTGT
1 GCTCTCTGATATTTAGCACGTCAGTGCTCTCTGTTTAGCACATCTGT
*
13153789 GCTCTCTGAT-TATTAGCATGTCAGTGCTCTCTGTTTAGCACATCTGT
1 GCTCTCTGATAT-TTAGCACGTCAGTGCTCTCTGTTTAGCACATCTGT
* *
13153836 GCTCTCTG-TA--TAGCACTTTAGTGCTCTCTGTT
1 GCTCTCTGATATTTAGCACGTCAGTGCTCTCTGTT
13153868 CATTAGTGTA
Statistics
Matches: 114, Mismatches: 10, Indels: 7
0.87 0.08 0.05
Matches are distributed among these distances:
44 19 0.17
46 2 0.02
47 93 0.82
ACGTcount: A:0.17, C:0.24, G:0.18, T:0.40
Consensus pattern (47 bp):
GCTCTCTGATATTTAGCACGTCAGTGCTCTCTGTTTAGCACATCTGT
Found at i:13162623 original size:126 final size:126
Alignment explanation
Indices: 13162399--13162787 Score: 625
Period size: 126 Copynumber: 3.1 Consensus size: 126
13162389 GCCAAGCACG
* * * *
13162399 AACTACTGTAGAAAAAGAGTGTCCATGTTGGAGCTTTTTTCAGTAATTTTACTGACAGTGCATCC
1 AACTACTGTAGAAAAAGAGCGTCCACGTAGGAGCTTTTTTCAGTAATTTTGCTGACAGTGCATCC
* * *
13162464 TGCTTGAAGCGTTTTTGATACTATTTTTTCAGAACCATCTTCTCAAAATTATTTTTTCAGG
66 TGCTTGAAGCGTTTTTGACACTATTTTTTCAGAACCGTCTTCTCAAAATTATTTTTTCAGA
* * *
13162525 AACTACTGCAGAAAAAGAGCGTCCACGTAGGAGCTTTTTTCAGTAGTTTTGTTGACAGTGCATCC
1 AACTACTGTAGAAAAAGAGCGTCCACGTAGGAGCTTTTTTCAGTAATTTTGCTGACAGTGCATCC
*
13162590 TGCTTGAAGCGTTTTTGACACTATTTTTTCAGAACCGTCTTCTCAAATTTATTTTTTCAGA
66 TGCTTGAAGCGTTTTTGACACTATTTTTTCAGAACCGTCTTCTCAAAATTATTTTTTCAGA
* *
13162651 AACTACTGTAGAAAAAGAGCGTCCACGTGGGAGCTTTTTTCAGTACTTTTGCTGACAGTGCATCC
1 AACTACTGTAGAAAAAGAGCGTCCACGTAGGAGCTTTTTTCAGTAATTTTGCTGACAGTGCATCC
* * *
13162716 TGCTTGAAACGTTTTTGTCACTATTTTTTCAGAACCGTCTTCTCAAAATTAATTTTTCAGA
66 TGCTTGAAGCGTTTTTGACACTATTTTTTCAGAACCGTCTTCTCAAAATTATTTTTTCAGA
*
13162777 AACTATTGTAG
1 AACTACTGTAG
13162788 GAGAAAAAAC
Statistics
Matches: 243, Mismatches: 20, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
126 243 1.00
ACGTcount: A:0.26, C:0.18, G:0.17, T:0.38
Consensus pattern (126 bp):
AACTACTGTAGAAAAAGAGCGTCCACGTAGGAGCTTTTTTCAGTAATTTTGCTGACAGTGCATCC
TGCTTGAAGCGTTTTTGACACTATTTTTTCAGAACCGTCTTCTCAAAATTATTTTTTCAGA
Found at i:13162929 original size:34 final size:34
Alignment explanation
Indices: 13162885--13163009 Score: 128
Period size: 34 Copynumber: 3.6 Consensus size: 34
13162875 ATTATTTTCA
* *
13162885 AAAAATCCTAAACCTTAATTTAAATAATTTTCTT
1 AAAAACCCTAAACCTTAATTTAATTAATTTTCTT
* *
13162919 AAAAACCCTAAACCCTAATTTAATTAATTTACTT
1 AAAAACCCTAAACCTTAATTTAATTAATTTTCTT
* *
13162953 AAAAACCTTAAAACC-TAAATTAATTAA-TTTCTTT
1 AAAAACCCT-AAACCTTAATTTAATTAATTTTC-TT
** *
13162987 AAAAAATTCTAAACCTTGATTTA
1 -AAAAACCCTAAACCTTAATTTA
13163010 TTTTTTAAAA
Statistics
Matches: 75, Mismatches: 12, Indels: 7
0.80 0.13 0.07
Matches are distributed among these distances:
33 3 0.04
34 56 0.75
35 16 0.21
ACGTcount: A:0.46, C:0.16, G:0.01, T:0.38
Consensus pattern (34 bp):
AAAAACCCTAAACCTTAATTTAATTAATTTTCTT
Found at i:13170899 original size:23 final size:23
Alignment explanation
Indices: 13170866--13170973 Score: 99
Period size: 23 Copynumber: 4.7 Consensus size: 23
13170856 AATTTAAAGA
*
13170866 AAACACTTCAATTTCCAACATTT
1 AAACACTTCAATTTACAACATTT
* * * **
13170889 AAACACCTCAAATTGCAACACCT
1 AAACACTTCAATTTACAACATTT
*
13170912 AAACACTTCAATTTACAAGATTT
1 AAACACTTCAATTTACAACATTT
* * * * *
13170935 GAACACCTCCATTTACAATAATT
1 AAACACTTCAATTTACAACATTT
13170958 AAACACTTCAAATTTA
1 AAACACTTC-AATTTA
13170974 TAGCCTTTAA
Statistics
Matches: 65, Mismatches: 19, Indels: 1
0.76 0.22 0.01
Matches are distributed among these distances:
23 60 0.92
24 5 0.08
ACGTcount: A:0.43, C:0.25, G:0.03, T:0.30
Consensus pattern (23 bp):
AAACACTTCAATTTACAACATTT
Found at i:13170961 original size:46 final size:46
Alignment explanation
Indices: 13170866--13170973 Score: 126
Period size: 46 Copynumber: 2.3 Consensus size: 46
13170856 AATTTAAAGA
* * *
13170866 AAACACTTCAATTTCCAACATTTAAACACCTCAAATTGCAACACCT
1 AAACACTTCAATTTACAACATTTAAACACCTCAAATTACAACAACT
* * * * * *
13170912 AAACACTTCAATTTACAAGATTTGAACACCTCCATTTACAATAATT
1 AAACACTTCAATTTACAACATTTAAACACCTCAAATTACAACAACT
13170958 AAACACTTCAAATTTA
1 AAACACTTC-AATTTA
13170974 TAGCCTTTAA
Statistics
Matches: 52, Mismatches: 9, Indels: 1
0.84 0.15 0.02
Matches are distributed among these distances:
46 46 0.88
47 6 0.12
ACGTcount: A:0.43, C:0.25, G:0.03, T:0.30
Consensus pattern (46 bp):
AAACACTTCAATTTACAACATTTAAACACCTCAAATTACAACAACT
Found at i:13172017 original size:5 final size:5
Alignment explanation
Indices: 13171996--13172065 Score: 122
Period size: 5 Copynumber: 13.6 Consensus size: 5
13171986 GTTTGGATGG
13171996 GCGGTT GCGGTT GCGGT GCGGT GCGGT GCGGT GCGGT GCGGT GCGGT GCGGT
1 GCGG-T GCGG-T GCGGT GCGGT GCGGT GCGGT GCGGT GCGGT GCGGT GCGGT
13172048 GCGGT GCGGT GCGGT GCG
1 GCGGT GCGGT GCGGT GCG
13172066 TTTAGCTTAC
Statistics
Matches: 64, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
5 54 0.84
6 10 0.16
ACGTcount: A:0.00, C:0.20, G:0.59, T:0.21
Consensus pattern (5 bp):
GCGGT
Found at i:13174433 original size:66 final size:66
Alignment explanation
Indices: 13174342--13174486 Score: 209
Period size: 66 Copynumber: 2.2 Consensus size: 66
13174332 GTCCGTGTGT
* * *
13174342 TAGGCTGTGTGAAAATTGGAGGGTATACTGACTTGTGCAACATGGCCAAGCCACACGCCCATATG
1 TAGGCCGTGTGAAAACTGGAGGGTATACTGACTTGTGCAACACGGCCAAGCCACACGCCCATATG
13174407 C
66 C
** ** *
13174408 TAGGCCGTGTGAAAACTGGAGGGTATACTGACTTGTGCCGCACGGCCAAGCCACACGCCTGTGTG
1 TAGGCCGTGTGAAAACTGGAGGGTATACTGACTTGTGCAACACGGCCAAGCCACACGCCCATATG
13174473 C
66 C
*
13174474 TAGGCCATGTGAA
1 TAGGCCGTGTGAA
13174487 GCTACTGACT
Statistics
Matches: 70, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
66 70 1.00
ACGTcount: A:0.25, C:0.24, G:0.30, T:0.21
Consensus pattern (66 bp):
TAGGCCGTGTGAAAACTGGAGGGTATACTGACTTGTGCAACACGGCCAAGCCACACGCCCATATG
C
Found at i:13175626 original size:25 final size:25
Alignment explanation
Indices: 13175563--13175652 Score: 76
Period size: 25 Copynumber: 3.6 Consensus size: 25
13175553 GTACATGTAT
*
13175563 GCTCATACGAGC-G-ATAAACGGTAA
1 GCTCATCCGAGCTGAAT-AACGGTAA
*
13175587 GCTCCTCCGAGCTGAATAACGGTAA
1 GCTCATCCGAGCTGAATAACGGTAA
* * * **
13175612 GCTCATTCGATCTGAGTATTGGTAA
1 GCTCATCCGAGCTGAATAACGGTAA
**
13175637 GCTCATAAGAGCTGAA
1 GCTCATCCGAGCTGAA
13175653 ATTAGTAACC
Statistics
Matches: 52, Mismatches: 12, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
24 10 0.19
25 40 0.77
26 2 0.04
ACGTcount: A:0.31, C:0.21, G:0.24, T:0.23
Consensus pattern (25 bp):
GCTCATCCGAGCTGAATAACGGTAA
Found at i:13177335 original size:57 final size:56
Alignment explanation
Indices: 13177139--13177347 Score: 177
Period size: 55 Copynumber: 3.8 Consensus size: 56
13177129 AAAAAAATTA
* * * * *
13177139 GGGTGCTGGGACACTGTTGGTTGGCACTCCTTTATCTGA-T---AGAAAT-TTTTTA
1 GGGTGCTGGGACACTGATGGTCGACAC-CCTTTATCTGATTAAAAAAAATATTTTTG
* *
13177191 GGGTGCTGGGACACTGATAGTCGACACCCATTTTATCAGATTTAAAAAAAA-A--TTTG
1 GGGTGCTGGGACACTGATGGTCGACACCC--TTTATCTGA-TTAAAAAAAATATTTTTG
*
13177247 GGGTGCT-GCACACTGATGGTCGACACCCCCTTTATCTGATTAAAAAAAATATTTTTG
1 GGGTGCTGGGACACTGATGGTCGACA--CCCTTTATCTGATTAAAAAAAATATTTTTG
* * * *
13177304 GGGTGTTGGGATACTGATGGTTGACATCCCTTTATTTGA-TAAAA
1 GGGTGCTGGGACACTGATGGTCGACA-CCCTTTATCTGATTAAAA
13177348 TTTTTTTTGG
Statistics
Matches: 127, Mismatches: 16, Indels: 24
0.76 0.10 0.14
Matches are distributed among these distances:
51 2 0.02
52 23 0.18
53 8 0.06
54 10 0.08
55 26 0.20
56 15 0.12
57 24 0.19
58 19 0.15
ACGTcount: A:0.27, C:0.16, G:0.23, T:0.33
Consensus pattern (56 bp):
GGGTGCTGGGACACTGATGGTCGACACCCTTTATCTGATTAAAAAAAATATTTTTG
Found at i:13177397 original size:53 final size:52
Alignment explanation
Indices: 13177334--13177436 Score: 152
Period size: 52 Copynumber: 2.0 Consensus size: 52
13177324 TTGACATCCC
* * *
13177334 TTTATTTGATAAAATTTTTTTTGGGTGCTAGGACATTAATGTCCAACACCCCT
1 TTTATCTGAT-AAATTTTTTTTGGGTGCTAAGACATTAATGGCCAACACCCCT
* *
13177387 TTTATCTGATAAATTTTTTTTGGGTGCTAAGACATTGATGGCCAGCACCC
1 TTTATCTGATAAATTTTTTTTGGGTGCTAAGACATTAATGGCCAACACCC
13177437 TAGTAGTCTA
Statistics
Matches: 45, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
52 36 0.80
53 9 0.20
ACGTcount: A:0.25, C:0.17, G:0.17, T:0.40
Consensus pattern (52 bp):
TTTATCTGATAAATTTTTTTTGGGTGCTAAGACATTAATGGCCAACACCCCT
Found at i:13184046 original size:13 final size:13
Alignment explanation
Indices: 13184030--13184054 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
13184020 TTACCTTTTA
13184030 ATTTTCTTAGTTG
1 ATTTTCTTAGTTG
13184043 ATTTTCTTAGTT
1 ATTTTCTTAGTT
13184055 AAAATCTAGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.16, C:0.08, G:0.12, T:0.64
Consensus pattern (13 bp):
ATTTTCTTAGTTG
Found at i:13192119 original size:25 final size:26
Alignment explanation
Indices: 13192076--13192129 Score: 69
Period size: 25 Copynumber: 2.1 Consensus size: 26
13192066 TTCTCCTAAA
13192076 TTTCAATTTTATATGATTATTTAAT-T
1 TTTCAATTTTATATGATTA-TTAATAT
13192102 TTTCAA-TTTAT-TGAATTATTAATAT
1 TTTCAATTTTATATG-ATTATTAATAT
13192127 TTT
1 TTT
13192130 ATGCAAATTG
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
24 7 0.27
25 13 0.50
26 6 0.23
ACGTcount: A:0.31, C:0.04, G:0.04, T:0.61
Consensus pattern (26 bp):
TTTCAATTTTATATGATTATTAATAT
Found at i:13193030 original size:3 final size:3
Alignment explanation
Indices: 13193022--13193071 Score: 91
Period size: 3 Copynumber: 16.7 Consensus size: 3
13193012 TGAGGATCGC
*
13193022 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA TAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
13193070 GA
1 GA
13193072 TCCCACAGAG
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.66, C:0.00, G:0.32, T:0.02
Consensus pattern (3 bp):
GAA
Found at i:13205051 original size:39 final size:40
Alignment explanation
Indices: 13204950--13205058 Score: 104
Period size: 38 Copynumber: 2.8 Consensus size: 40
13204940 TTACAGAGTG
* *
13204950 AAATTTTGGAAAAC--ATTTTAAAAAAAATACAAACTGAT
1 AAATTTTTGAAAACAAATTTTAAAAAAAATACAAACCGAT
* * *
13204988 AAATTTTT-AAAA-AAGGTTTT-AAAAAAATACATACCGGT
1 AAATTTTTGAAAACAA-ATTTTAAAAAAAATACAAACCGAT
*
13205026 -GATTTTTGAAAACAAATTTTAAAAAAATATACA
1 AAATTTTTGAAAACAAATTTTAAAAAAA-ATACA
13205059 CTGACAAATA
Statistics
Matches: 57, Mismatches: 7, Indels: 12
0.75 0.09 0.16
Matches are distributed among these distances:
37 10 0.18
38 30 0.53
39 12 0.21
40 5 0.09
ACGTcount: A:0.53, C:0.07, G:0.08, T:0.31
Consensus pattern (40 bp):
AAATTTTTGAAAACAAATTTTAAAAAAAATACAAACCGAT
Found at i:13212004 original size:20 final size:20
Alignment explanation
Indices: 13211948--13212054 Score: 117
Period size: 20 Copynumber: 5.3 Consensus size: 20
13211938 GATGCATAAT
*
13211948 AGAGGCACCGAAGTGCAGAC
1 AGAGGCACCGAAGTGCAAAC
* * * *
13211968 AGGGGCA-TGAATATGCAATC
1 AGAGGCACCGAA-GTGCAAAC
13211988 AGAGGCACCGAAGTGCAAAC
1 AGAGGCACCGAAGTGCAAAC
*
13212008 AGAGGCACCAAAGTGCAAAC
1 AGAGGCACCGAAGTGCAAAC
* * *
13212028 AGAGACACCGAAGAGCAAAT
1 AGAGGCACCGAAGTGCAAAC
13212048 AGAGGCA
1 AGAGGCA
13212055 TTGAAGCACA
Statistics
Matches: 70, Mismatches: 15, Indels: 4
0.79 0.17 0.04
Matches are distributed among these distances:
19 3 0.04
20 64 0.91
21 3 0.04
ACGTcount: A:0.41, C:0.21, G:0.30, T:0.07
Consensus pattern (20 bp):
AGAGGCACCGAAGTGCAAAC
Found at i:13219400 original size:51 final size:52
Alignment explanation
Indices: 13219308--13219422 Score: 135
Period size: 51 Copynumber: 2.2 Consensus size: 52
13219298 TTAGATATGG
*
13219308 TGAAAATGAAAAAATGGGAAACATTTGGAAATGATTATGGTTTTCTCCT-AAA
1 TGAAAATGAAAAAATGGGAAACATTTGGAAATGAATATGGTTTTCT-CTAAAA
* * * * * * *
13219360 TGAAAATGAATATAT-GGAATCATTTGTAAATTAATGTGGTTTTCTTTAAAA
1 TGAAAATGAAAAAATGGGAAACATTTGGAAATGAATATGGTTTTCTCTAAAA
13219411 TGAAAATGAAAA
1 TGAAAATGAAAA
13219423 TGAATTGGAA
Statistics
Matches: 53, Mismatches: 9, Indels: 3
0.82 0.14 0.05
Matches are distributed among these distances:
50 1 0.02
51 39 0.74
52 13 0.25
ACGTcount: A:0.43, C:0.05, G:0.17, T:0.34
Consensus pattern (52 bp):
TGAAAATGAAAAAATGGGAAACATTTGGAAATGAATATGGTTTTCTCTAAAA
Found at i:13223842 original size:20 final size:20
Alignment explanation
Indices: 13223814--13223851 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
13223804 TAGTTAACTT
*
13223814 TAATTTAATCATCATTAAAC
1 TAATCTAATCATCATTAAAC
13223834 TAATCTAATCATCATTAA
1 TAATCTAATCATCATTAA
13223852 GCCAAACTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.45, C:0.16, G:0.00, T:0.39
Consensus pattern (20 bp):
TAATCTAATCATCATTAAAC
Found at i:13223861 original size:20 final size:20
Alignment explanation
Indices: 13223819--13223861 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
13223809 AACTTTAATT
* *
13223819 TAATCATCATTAAACTAATC
1 TAATCATCATTAAACCAAAC
*
13223839 TAATCATCATTAAGCCAAAC
1 TAATCATCATTAAACCAAAC
13223859 TAA
1 TAA
13223862 GTGGATGATG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.47, C:0.21, G:0.02, T:0.30
Consensus pattern (20 bp):
TAATCATCATTAAACCAAAC
Found at i:13228302 original size:29 final size:28
Alignment explanation
Indices: 13228260--13228315 Score: 76
Period size: 29 Copynumber: 2.0 Consensus size: 28
13228250 ACTTTCATTT
*
13228260 ATTTCACACTTTAACCCCTCAATTTGCAC
1 ATTTCACAATTTAACCCCT-AATTTGCAC
* *
13228289 ATTTCATAATTTAATCCCTAATTTGCA
1 ATTTCACAATTTAACCCCTAATTTGCA
13228316 TTTTTATCAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
28 8 0.33
29 16 0.67
ACGTcount: A:0.30, C:0.27, G:0.04, T:0.39
Consensus pattern (28 bp):
ATTTCACAATTTAACCCCTAATTTGCAC
Found at i:13237466 original size:18 final size:19
Alignment explanation
Indices: 13237433--13237473 Score: 59
Period size: 18 Copynumber: 2.2 Consensus size: 19
13237423 ATGTCACTAA
13237433 AATAATAACAAGATTA-AC
1 AATAATAACAAGATTATAC
13237451 AATAA-AACAAGTATTATAC
1 AATAATAACAAG-ATTATAC
13237470 AATA
1 AATA
13237474 TCCAAGCAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 6 0.29
18 9 0.43
19 6 0.29
ACGTcount: A:0.61, C:0.10, G:0.05, T:0.24
Consensus pattern (19 bp):
AATAATAACAAGATTATAC
Found at i:13237560 original size:22 final size:23
Alignment explanation
Indices: 13237530--13237573 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
13237520 AGCAAATAGG
*
13237530 AAAAAAACAA-GAAAATAGCATT
1 AAAAAAACAACAAAAATAGCATT
*
13237552 AAAACAACAACAAAAATAGCAT
1 AAAAAAACAACAAAAATAGCAT
13237574 ATTTTTTGTC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 9 0.47
23 10 0.53
ACGTcount: A:0.68, C:0.14, G:0.07, T:0.11
Consensus pattern (23 bp):
AAAAAAACAACAAAAATAGCATT
Found at i:13241171 original size:28 final size:28
Alignment explanation
Indices: 13241140--13241197 Score: 116
Period size: 28 Copynumber: 2.1 Consensus size: 28
13241130 ATTTTTAGGC
13241140 TTAATTTTTATTATATATTAACTCAATA
1 TTAATTTTTATTATATATTAACTCAATA
13241168 TTAATTTTTATTATATATTAACTCAATA
1 TTAATTTTTATTATATATTAACTCAATA
13241196 TT
1 TT
13241198 GTATTTATTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.38, C:0.07, G:0.00, T:0.55
Consensus pattern (28 bp):
TTAATTTTTATTATATATTAACTCAATA
Found at i:13247483 original size:14 final size:14
Alignment explanation
Indices: 13247459--13247502 Score: 63
Period size: 14 Copynumber: 3.1 Consensus size: 14
13247449 TTGTATGAAT
*
13247459 TTTAAGATTTAGGG
1 TTTAAGATTTAGGA
13247473 TTT-AGAGTTTAGGA
1 TTTAAGA-TTTAGGA
13247487 TTTAAGATTTAGGA
1 TTTAAGATTTAGGA
13247501 TT
1 TT
13247503 GTATAGGGTT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
13 3 0.11
14 21 0.78
15 3 0.11
ACGTcount: A:0.30, C:0.00, G:0.25, T:0.45
Consensus pattern (14 bp):
TTTAAGATTTAGGA
Found at i:13247497 original size:21 final size:21
Alignment explanation
Indices: 13247459--13247498 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
13247449 TTGTATGAAT
* *
13247459 TTTAAGATTTAGGGTTTAGAG
1 TTTAAGATTTAAGATTTAGAG
*
13247480 TTTAGGATTTAAGATTTAG
1 TTTAAGATTTAAGATTTAG
13247499 GATTGTATAG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.30, C:0.00, G:0.25, T:0.45
Consensus pattern (21 bp):
TTTAAGATTTAAGATTTAGAG
Found at i:13251664 original size:13 final size:15
Alignment explanation
Indices: 13251631--13251663 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
13251621 TTTCATGTCT
13251631 TTTTTAAAATATTTA
1 TTTTTAAAATATTTA
*
13251646 TTTTTAATAT-TTTA
1 TTTTTAAAATATTTA
13251660 TTTT
1 TTTT
13251664 ATGTAATAGG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 8 0.47
15 9 0.53
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (15 bp):
TTTTTAAAATATTTA
Found at i:13252568 original size:13 final size:13
Alignment explanation
Indices: 13252550--13252574 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
13252540 CATTCTTTCT
13252550 TCCCTCTAAACGA
1 TCCCTCTAAACGA
13252563 TCCCTCTAAACG
1 TCCCTCTAAACG
13252575 CTTCCTTCCC
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:0.28, C:0.40, G:0.08, T:0.24
Consensus pattern (13 bp):
TCCCTCTAAACGA
Found at i:13253675 original size:21 final size:21
Alignment explanation
Indices: 13253634--13253676 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
13253624 AATAAAGTAG
**
13253634 ATTATATATATTTTTTATAGT
1 ATTATATATATGATTTATAGT
13253655 ATTATATATTATGATTT-TAGT
1 ATTATATA-TATGATTTATAGT
13253676 A
1 A
13253677 AATTCATATA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 13 0.68
22 6 0.32
ACGTcount: A:0.35, C:0.00, G:0.07, T:0.58
Consensus pattern (21 bp):
ATTATATATATGATTTATAGT
Found at i:13253727 original size:38 final size:36
Alignment explanation
Indices: 13253659--13253732 Score: 96
Period size: 37 Copynumber: 2.0 Consensus size: 36
13253649 TATAGTATTA
*
13253659 TATATTATGATTTTAGTAAATTCATATAATAATAAT
1 TATATTAAGATTTTAGTAAATTCATATAATAATAAT
*
13253695 TATATTAAGAATTTTATTAAATT-ATATTTAATAATAAT
1 TATATTAAG-ATTTTAGTAAATTCATA--TAATAATAAT
13253733 GTTAAAATAT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
36 11 0.33
37 12 0.36
38 10 0.30
ACGTcount: A:0.46, C:0.01, G:0.04, T:0.49
Consensus pattern (36 bp):
TATATTAAGATTTTAGTAAATTCATATAATAATAAT
Found at i:13254835 original size:15 final size:17
Alignment explanation
Indices: 13254814--13254854 Score: 59
Period size: 15 Copynumber: 2.5 Consensus size: 17
13254804 TAATCTTTTA
13254814 AAAATTATAAAAAT-AT
1 AAAATTATAAAAATAAT
*
13254830 -AAATTATTAAAATAAT
1 AAAATTATAAAAATAAT
13254846 AAAATTATA
1 AAAATTATA
13254855 TTTTTAATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
15 12 0.57
16 2 0.10
17 7 0.33
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (17 bp):
AAAATTATAAAAATAAT
Found at i:13254876 original size:22 final size:22
Alignment explanation
Indices: 13254820--13254876 Score: 55
Period size: 22 Copynumber: 2.6 Consensus size: 22
13254810 TTTAAAAATT
*
13254820 ATAA-AAATATAAATTATTAAA
1 ATAATAAATATATATTATTAAA
* *
13254841 ATAATAAA-ATTATATTTTTAAT
1 ATAATAAATA-TATATTATTAAA
*
13254863 ATCATAAATATATA
1 ATAATAAATATATA
13254877 ATTTAATTTC
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
21 5 0.17
22 23 0.79
23 1 0.03
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (22 bp):
ATAATAAATATATATTATTAAA
Found at i:13257388 original size:22 final size:22
Alignment explanation
Indices: 13257342--13257388 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
13257332 GTAATATAGA
* *
13257342 TTTAATAAATGCAGAAAAATCT
1 TTTAATAAATGAAAAAAAATCT
13257364 TTTAATAAATGAAAAGAAAAT-T
1 TTTAATAAATGAAAA-AAAATCT
13257386 TTT
1 TTT
13257389 GAACTGTTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 17 0.77
23 5 0.23
ACGTcount: A:0.51, C:0.04, G:0.09, T:0.36
Consensus pattern (22 bp):
TTTAATAAATGAAAAAAAATCT
Found at i:13260155 original size:12 final size:12
Alignment explanation
Indices: 13260138--13260171 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
13260128 ATTATATTTT
13260138 TAAAAAATTATA
1 TAAAAAATTATA
*
13260150 TAAAAAATAATA
1 TAAAAAATTATA
13260162 TAAAAAATTA
1 TAAAAAATTA
13260172 ATATGGGCAG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (12 bp):
TAAAAAATTATA
Found at i:13260167 original size:13 final size:12
Alignment explanation
Indices: 13260138--13260175 Score: 58
Period size: 12 Copynumber: 3.1 Consensus size: 12
13260128 ATTATATTTT
*
13260138 TAAAAAATTATA
1 TAAAAAATAATA
13260150 TAAAAAATAATA
1 TAAAAAATAATA
13260162 TAAAAAATTAATA
1 TAAAAAA-TAATA
13260175 T
1 T
13260176 GGGCAGACCG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
12 18 0.75
13 6 0.25
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (12 bp):
TAAAAAATAATA
Found at i:13261543 original size:22 final size:22
Alignment explanation
Indices: 13261518--13261560 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
13261508 ATGAACTTAA
13261518 TTAAA-TATAATTAACTATAAAC
1 TTAAATTATAATTAA-TATAAAC
*
13261540 TTAAATTTTAATTAATATAAA
1 TTAAATTATAATTAATATAAA
13261561 AATATAAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 11 0.58
23 8 0.42
ACGTcount: A:0.53, C:0.05, G:0.00, T:0.42
Consensus pattern (22 bp):
TTAAATTATAATTAATATAAAC
Found at i:13261572 original size:24 final size:23
Alignment explanation
Indices: 13261516--13261572 Score: 64
Period size: 23 Copynumber: 2.5 Consensus size: 23
13261506 AGATGAACTT
*
13261516 AATTAAA-TATAATTAACTATAA
1 AATTAAATTTTAATTAACTATAA
*
13261538 ACTTAAATTTTAATTAA-TATAAA
1 AATTAAATTTTAATTAACTAT-AA
13261561 AATATAAATTTT
1 AAT-TAAATTTT
13261573 TTTATATTTC
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
22 9 0.31
23 12 0.41
24 8 0.28
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.42
Consensus pattern (23 bp):
AATTAAATTTTAATTAACTATAA
Found at i:13262110 original size:22 final size:22
Alignment explanation
Indices: 13262084--13262125 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
13262074 TCACTCCCAA
* *
13262084 AATCAATCACCATTTTATTAAT
1 AATCAATAACCATTCTATTAAT
13262106 AATCAATAACCATTCTATTA
1 AATCAATAACCATTCTATTA
13262126 GATTTATCAC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.43, C:0.19, G:0.00, T:0.38
Consensus pattern (22 bp):
AATCAATAACCATTCTATTAAT
Found at i:13264754 original size:27 final size:27
Alignment explanation
Indices: 13264716--13264791 Score: 118
Period size: 27 Copynumber: 2.8 Consensus size: 27
13264706 TAGTATTGGC
13264716 GCCTATCTGGGAGGCGCCAATGGTGGT
1 GCCTATCTGGGAGGCGCCAATGGTGGT
13264743 GCCTATCTGGGAGGCGCCAATGGTGGT
1 GCCTATCTGGGAGGCGCCAATGGTGGT
* *
13264770 GTCATAT-TGAGAGGCGCCAATG
1 G-CCTATCTGGGAGGCGCCAATG
13264792 CTATGATTTT
Statistics
Matches: 46, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
27 42 0.91
28 4 0.09
ACGTcount: A:0.18, C:0.21, G:0.38, T:0.22
Consensus pattern (27 bp):
GCCTATCTGGGAGGCGCCAATGGTGGT
Found at i:13264901 original size:22 final size:23
Alignment explanation
Indices: 13264848--13264901 Score: 76
Period size: 22 Copynumber: 2.4 Consensus size: 23
13264838 TATAGAAACG
*
13264848 GAAGAAATAAGAAGGAAGGAAGCA
1 GAAGAAA-AAGAAGGAAGGAAGAA
13264872 GAAG-AAAAGAAGGAAGGAA-AA
1 GAAGAAAAAGAAGGAAGGAAGAA
13264893 GAAGAAAAA
1 GAAGAAAAA
13264902 AATTAGGTAT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
21 5 0.18
22 17 0.61
23 2 0.07
24 4 0.14
ACGTcount: A:0.65, C:0.02, G:0.31, T:0.02
Consensus pattern (23 bp):
GAAGAAAAAGAAGGAAGGAAGAA
Found at i:13269552 original size:16 final size:15
Alignment explanation
Indices: 13269521--13269562 Score: 57
Period size: 16 Copynumber: 2.7 Consensus size: 15
13269511 ACAAAATCAA
*
13269521 ATAAAATTTAATTAT
1 ATAAAAGTTAATTAT
13269536 ATAAAAGTTACATTAT
1 ATAAAAGTTA-ATTAT
*
13269552 ATAAAAATTAA
1 ATAAAAGTTAA
13269563 ATGAGTTAAC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
15 10 0.42
16 14 0.58
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.38
Consensus pattern (15 bp):
ATAAAAGTTAATTAT
Found at i:13269642 original size:38 final size:39
Alignment explanation
Indices: 13269599--13269681 Score: 150
Period size: 38 Copynumber: 2.2 Consensus size: 39
13269589 AAAAAGTCAG
13269599 TTATAATTAAACTTTTAATAAAATGATTTTTAA-TTTTT
1 TTATAATTAAACTTTTAATAAAATGATTTTTAATTTTTT
*
13269637 TTATAATTAAACTTTTAATGAAATGATTTTTAATTTTTT
1 TTATAATTAAACTTTTAATAAAATGATTTTTAATTTTTT
13269676 TTATAA
1 TTATAA
13269682 ACTTTATATG
Statistics
Matches: 43, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
38 32 0.74
39 11 0.26
ACGTcount: A:0.39, C:0.02, G:0.04, T:0.55
Consensus pattern (39 bp):
TTATAATTAAACTTTTAATAAAATGATTTTTAATTTTTT
Found at i:13269791 original size:60 final size:60
Alignment explanation
Indices: 13269715--13269836 Score: 165
Period size: 60 Copynumber: 2.0 Consensus size: 60
13269705 ATACTAAACT
* * * * * *
13269715 AAACACAACAACTTATAGCTTAATCCTAAATTACTAATAAATTAAATT-TTAAATAATTAC
1 AAACACAAAAACTTATAACATAATCCCAAATTACTAACAAATT-AATTATAAAATAATTAC
*
13269775 AAACACAAAAATTTATAACATAATCCCAAATTACTAACAAATTAATTATAAAATAATTAC
1 AAACACAAAAACTTATAACATAATCCCAAATTACTAACAAATTAATTATAAAATAATTAC
13269835 AA
1 AA
13269837 TATTCATACA
Statistics
Matches: 54, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
59 4 0.07
60 50 0.93
ACGTcount: A:0.54, C:0.15, G:0.01, T:0.30
Consensus pattern (60 bp):
AAACACAAAAACTTATAACATAATCCCAAATTACTAACAAATTAATTATAAAATAATTAC
Found at i:13269901 original size:19 final size:19
Alignment explanation
Indices: 13269877--13269955 Score: 66
Period size: 19 Copynumber: 4.6 Consensus size: 19
13269867 ATATCCCCAC
13269877 ATTACAATATTCATACAAA
1 ATTACAATATTCATACAAA
*
13269896 ATTACAATA-T--TACAAT
1 ATTACAATATTCATACAAA
*
13269912 ATT-C-ATA--CA-AAAAA
1 ATTACAATATTCATACAAA
*
13269926 ATTGCAATATTCATACAAA
1 ATTACAATATTCATACAAA
*
13269945 ATTATAATATT
1 ATTACAATATT
13269956 ACAATATTCA
Statistics
Matches: 47, Mismatches: 6, Indels: 14
0.70 0.09 0.21
Matches are distributed among these distances:
14 9 0.19
15 2 0.04
16 11 0.23
18 3 0.06
19 22 0.47
ACGTcount: A:0.52, C:0.13, G:0.01, T:0.34
Consensus pattern (19 bp):
ATTACAATATTCATACAAA
Found at i:13269913 original size:27 final size:24
Alignment explanation
Indices: 13269877--13270111 Score: 226
Period size: 22 Copynumber: 9.8 Consensus size: 24
13269867 ATATCCCCAC
13269877 ATTACAATATTCATACAAAATTACAA
1 ATTACAATATTCATACAAAA-TA-AA
13269903 TATTACAATATTCATAC-AAA-AAA
1 -ATTACAATATTCATACAAAATAAA
*
13269926 ATTGCAATATTCATACAAAATTATAA
1 ATTACAATATTCATACAAAA-TA-AA
*
13269952 TATTACAATATTCATACAAAA-CAA
1 -ATTACAATATTCATACAAAATAAA
*
13269976 A-TATAATATTCATACAAAATTATAAA
1 ATTACAATATTCATAC-AAA--ATAAA
13270002 ATTACAATATTCATAC-AAA-AAA
1 ATTACAATATTCATACAAAATAAA
*
13270024 ATTGCAATATTCATACAAAACTATAAA
1 ATTACAATATTCATAC-AAA--ATAAA
13270051 ATTACAATATTCATAC-AAA-AAA
1 ATTACAATATTCATACAAAATAAA
*
13270073 ATTATAATATTCATAC-AAAT---
1 ATTACAATATTCATACAAAATAAA
13270093 -TTACAATATTCATACAAAA
1 ATTACAATATTCATACAAAA
13270112 AATTACTAAT
Statistics
Matches: 181, Mismatches: 10, Indels: 41
0.78 0.04 0.18
Matches are distributed among these distances:
19 14 0.08
20 3 0.02
22 67 0.37
23 11 0.06
24 5 0.03
25 6 0.03
26 9 0.05
27 66 0.36
ACGTcount: A:0.54, C:0.13, G:0.01, T:0.31
Consensus pattern (24 bp):
ATTACAATATTCATACAAAATAAA
Found at i:13269934 original size:22 final size:22
Alignment explanation
Indices: 13269877--13270235 Score: 189
Period size: 22 Copynumber: 15.9 Consensus size: 22
13269867 ATATCCCCAC
13269877 ATTACAATATTCATAC---AAA
1 ATTACAATATTCATACAAAAAA
13269896 ATTACAATATTACAATATTCATACAAAAAA
1 ATTACAATATT-C-ATA--C--A-AAAA-A
*
13269926 ATTGCAATATTCATACAAAATTATAA
1 ATTACAATATTCATAC-AAA--A-AA
13269952 TATTACAATATTCATACAAAACAA
1 -ATTACAATATTCATACAAAA-AA
*
13269976 A-TATAATATTCATACAAAATTATAAA
1 ATTACAATATTCATAC--AA--A-AAA
13270002 ATTACAATATTCATACAAAAAA
1 ATTACAATATTCATACAAAAAA
*
13270024 ATTGCAATATTCATACAAAACTATAAA
1 ATTACAATATTCATAC--AA--A-AAA
13270051 ATTACAATATTCATACAAAAAA
1 ATTACAATATTCATACAAAAAA
*
13270073 ATTATAATATTCATAC---AAA
1 ATTACAATATTCATACAAAAAA
*
13270092 TTTACAATATTCATAC-AAAAA
1 ATTACAATATTCATACAAAAAA
* * *
13270113 ATTACTA-ATCCA-A-AACTATAA
1 ATTACAATATTCATACAA--AAAA
* * *
13270134 A-TACAA-ATTTAATTATAAAATA
1 ATTACAATA-TTCA-TACAAAAAA
*
13270156 ATTACAATATTCATAC---AAC
1 ATTACAATATTCATACAAAAAA
*
13270175 ATTACAAGATTCAT---AAAAA
1 ATTACAATATTCATACAAAAAA
*
13270194 ATTATAATATTCATACAAAAAA
1 ATTACAATATTCATACAAAAAA
* *
13270216 GTTAAAATATTCATACAAAA
1 ATTACAATATTCATACAAAA
13270236 TTCTAATCTA
Statistics
Matches: 268, Mismatches: 30, Indels: 81
0.71 0.08 0.21
Matches are distributed among these distances:
19 58 0.22
20 10 0.04
21 17 0.06
22 77 0.29
23 13 0.05
24 12 0.04
25 5 0.02
26 11 0.04
27 48 0.18
28 3 0.01
29 3 0.01
30 11 0.04
ACGTcount: A:0.55, C:0.13, G:0.01, T:0.31
Consensus pattern (22 bp):
ATTACAATATTCATACAAAAAA
Found at i:13269954 original size:49 final size:49
Alignment explanation
Indices: 13269881--13270102 Score: 340
Period size: 49 Copynumber: 4.5 Consensus size: 49
13269871 CCCCACATTA
*
13269881 CAATATTCATACAAAATTACAATATTACAATATTCATACAAAAAAATTG
1 CAATATTCATACAAAATTATAATATTACAATATTCATACAAAAAAATTG
13269930 CAATATTCATACAAAATTATAATATTACAATATTCATACAAAACAAATAT-
1 CAATATTCATACAAAATTATAATATTACAATATTCATACAAAA-AAAT-TG
*
13269980 -AATATTCATACAAAATTATAAAATTACAATATTCATACAAAAAAATTG
1 CAATATTCATACAAAATTATAATATTACAATATTCATACAAAAAAATTG
* * *
13270028 CAATATTCATACAAAACTATAAAATTACAATATTCATACAAAAAAATTA
1 CAATATTCATACAAAATTATAATATTACAATATTCATACAAAAAAATTG
* * *
13270077 TAATATTCATACAAATTTACAATATT
1 CAATATTCATACAAAATTATAATATT
13270103 CATACAAAAA
Statistics
Matches: 160, Mismatches: 9, Indels: 8
0.90 0.05 0.05
Matches are distributed among these distances:
47 1 0.01
48 4 0.03
49 150 0.94
50 4 0.03
51 1 0.01
ACGTcount: A:0.54, C:0.13, G:0.01, T:0.32
Consensus pattern (49 bp):
CAATATTCATACAAAATTATAATATTACAATATTCATACAAAAAAATTG
Found at i:13270102 original size:19 final size:19
Alignment explanation
Indices: 13270048--13270237 Score: 116
Period size: 19 Copynumber: 9.3 Consensus size: 19
13270038 ACAAAACTAT
13270048 AAAATTACAATATTCATAC
1 AAAATTACAATATTCATAC
*
13270067 AAAAAAATTATAATATTCATAC
1 ---AAAATTACAATATTCATAC
*
13270089 AAATTTACAATATTCATAC
1 AAAATTACAATATTCATAC
* * *
13270108 AAAAAATTACTA-ATCCAAAAC
1 --AAAATTACAATATTC-ATAC
*
13270129 TATAAA-TACAAATTTAATT-ATAA
1 -A-AAATTAC-AA--T-ATTCATAC
13270152 AATAATTACAATATTCATAC
1 AA-AATTACAATATTCATAC
* * *
13270172 AACATTACAAGATTCATAA
1 AAAATTACAATATTCATAC
*
13270191 AAAATTATAATATTCATAC
1 AAAATTACAATATTCATAC
*
13270210 AAAAAAGTTAAAATATTCATAC
1 --AAAA-TTACAATATTCATAC
13270232 AAAATT
1 AAAATT
13270238 CTAATCTAAA
Statistics
Matches: 132, Mismatches: 21, Indels: 33
0.71 0.11 0.18
Matches are distributed among these distances:
19 51 0.39
20 17 0.13
21 20 0.15
22 37 0.28
23 5 0.04
25 2 0.02
ACGTcount: A:0.55, C:0.12, G:0.01, T:0.32
Consensus pattern (19 bp):
AAAATTACAATATTCATAC
Found at i:13270139 original size:41 final size:43
Alignment explanation
Indices: 13269906--13270139 Score: 149
Period size: 49 Copynumber: 5.1 Consensus size: 43
13269896 ATTACAATAT
* * *
13269906 TACAATATTCATACAAAAAAATTGCAATATTCATACAAAATTATAATA
1 TACAATATTCATACAAAAAAATT---ATAAT-ATCCAAAACTATAA-A
*
13269954 TTACAATATTCATACAAAACAAA-TATAATATTCATACAAAATTATAAAA
1 -TACAATATTCATACAAAA-AAATTATAATA-TC---CAAAACTAT-AAA
* *
13270003 TTACAATATTCATACAAAAAAATTGCAATATTCATACAAAACTATAAAA
1 -TACAATATTCATACAAAAAAATT---ATAAT-ATCCAAAACTAT-AAA
* * *
13270052 TTACAATATTCATACAAAAAAATTATAATATTC-ATAC-A-AATT
1 -TACAATATTCATACAAAAAAATTATAATATCCAAAACTATAA-A
13270094 TACAATATTCATAC-AAAAAATTACT-A-ATCCAAAACTATAAA
1 TACAATATTCATACAAAAAAATTA-TAATATCCAAAACTATAAA
13270135 TACAA
1 TACAA
13270140 ATTTAATTAT
Statistics
Matches: 157, Mismatches: 12, Indels: 40
0.75 0.06 0.19
Matches are distributed among these distances:
39 3 0.02
40 13 0.08
41 23 0.15
42 2 0.01
43 1 0.01
44 3 0.02
45 4 0.03
46 9 0.06
48 3 0.02
49 85 0.54
50 5 0.03
52 5 0.03
53 1 0.01
ACGTcount: A:0.55, C:0.14, G:0.01, T:0.30
Consensus pattern (43 bp):
TACAATATTCATACAAAAAAATTATAATATCCAAAACTATAAA
Found at i:13270228 original size:41 final size:38
Alignment explanation
Indices: 13270148--13270242 Score: 100
Period size: 41 Copynumber: 2.4 Consensus size: 38
13270138 AAATTTAATT
* * *
13270148 ATAAAATAATTACAATATTCATACAACATTACAAGATTC
1 ATAAAA-AATTATAATATTCATACAAAATTAAAAGATTC
*
13270187 ATAAAAAATTATAATATTCATACAAAAAAGTTAAAATATTC
1 ATAAAAAATTATAATATTCATAC--AAAA-TTAAAAGATTC
* *
13270228 ATACAAAATTCTAAT
1 ATAAAAAATTATAAT
13270243 CTAAACTATA
Statistics
Matches: 47, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
38 16 0.34
39 6 0.13
40 3 0.06
41 22 0.47
ACGTcount: A:0.55, C:0.12, G:0.02, T:0.32
Consensus pattern (38 bp):
ATAAAAAATTATAATATTCATACAAAATTAAAAGATTC
Found at i:13270417 original size:3 final size:3
Alignment explanation
Indices: 13270411--13270454 Score: 56
Period size: 3 Copynumber: 15.3 Consensus size: 3
13270401 TCTTTTTTCT
* *
13270411 TTC TTC TTC TTC TTC -TC TTC TTC TTC TTG TCC TTC -TC TTC TTC T
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC T
13270455 CTTTTCTCTC
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
2 4 0.11
3 31 0.89
ACGTcount: A:0.00, C:0.34, G:0.02, T:0.64
Consensus pattern (3 bp):
TTC
Found at i:13270420 original size:17 final size:17
Alignment explanation
Indices: 13270400--13270477 Score: 63
Period size: 17 Copynumber: 4.6 Consensus size: 17
13270390 ACCTTTTTTT
13270400 TTCTTTTTTCTTTCTTC
1 TTCTTTTTTCTTTCTTC
*
13270417 TTC-TTCTTCTCTTCTTC
1 TTCTTTTTTCT-TTCTTC
* *
13270434 TTC-TTGTCCTTCTCTTC
1 TTCTTTTTTCTT-TCTTC
* *
13270451 TTCTCTTTTCTCTC-TC
1 TTCTTTTTTCTTTCTTC
*
13270467 TTTTTTTTTCT
1 TTCTTTTTTCT
13270478 CTACCGTGTG
Statistics
Matches: 49, Mismatches: 9, Indels: 7
0.75 0.14 0.11
Matches are distributed among these distances:
16 18 0.37
17 27 0.55
18 4 0.08
ACGTcount: A:0.00, C:0.29, G:0.01, T:0.69
Consensus pattern (17 bp):
TTCTTTTTTCTTTCTTC
Found at i:13270429 original size:14 final size:14
Alignment explanation
Indices: 13270407--13270461 Score: 71
Period size: 14 Copynumber: 4.1 Consensus size: 14
13270397 TTTTTCTTTT
13270407 TTCTT-TCTTCTTC
1 TTCTTCTCTTCTTC
13270420 TTCTTCTCTTCTTC
1 TTCTTCTCTTCTTC
*
13270434 TTCTTGTCCTTC-TC
1 TTCTTCT-CTTCTTC
13270448 TTCTTCTCTT-TTC
1 TTCTTCTCTTCTTC
13270461 T
1 T
13270462 CTCTCTTTTT
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
13 11 0.30
14 22 0.59
15 4 0.11
ACGTcount: A:0.00, C:0.33, G:0.02, T:0.65
Consensus pattern (14 bp):
TTCTTCTCTTCTTC
Found at i:13270475 original size:16 final size:15
Alignment explanation
Indices: 13270418--13270479 Score: 56
Period size: 14 Copynumber: 4.2 Consensus size: 15
13270408 TCTTTCTTCT
*
13270418 TCTTCTTCTCTTCT-
1 TCTTCTTCTCTTTTC
* *
13270432 TCTTCTTGTC-CTTC
1 TCTTCTTCTCTTTTC
13270446 TCTTCTTCTCTTTTC
1 TCTTCTTCTCTTTTC
* *
13270461 TCTCTCTTTTTTTTTC
1 TCT-TCTTCTCTTTTC
13270477 TCT
1 TCT
13270480 ACCGTGTGGC
Statistics
Matches: 38, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
13 1 0.03
14 18 0.47
15 6 0.16
16 13 0.34
ACGTcount: A:0.00, C:0.32, G:0.02, T:0.66
Consensus pattern (15 bp):
TCTTCTTCTCTTTTC
Found at i:13271647 original size:31 final size:30
Alignment explanation
Indices: 13271606--13271672 Score: 98
Period size: 31 Copynumber: 2.2 Consensus size: 30
13271596 AATTTTAAAT
*
13271606 TTTAAAAGTACAAGAACTAAAATTAATTAA
1 TTTAAAAGTACAAAAACTAAAATTAATTAA
*
13271636 TTTAAATAGTACAAAAATTAAAATTAATTAA
1 TTTAAA-AGTACAAAAACTAAAATTAATTAA
*
13271667 ATTAAA
1 TTTAAA
13271673 GTATATGAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
30 6 0.18
31 27 0.82
ACGTcount: A:0.58, C:0.04, G:0.04, T:0.33
Consensus pattern (30 bp):
TTTAAAAGTACAAAAACTAAAATTAATTAA
Found at i:13275609 original size:19 final size:17
Alignment explanation
Indices: 13275594--13275687 Score: 54
Period size: 17 Copynumber: 5.5 Consensus size: 17
13275584 ATTTTAATAG
13275594 TTTAATATTAAATTAAA
1 TTTAATATTAAATTAAA
13275611 TTTAATACTT--ATCTAAA
1 TTTAATA-TTAAAT-TAAA
* **
13275628 --TAGTATTTGATT-AA
1 TTTAATATTAAATTAAA
* *
13275642 TTTAATATTAAAGTGATTA
1 TTTAATATTAAA-TTA-AA
*
13275661 TCTTAATATTAAGTTAAA
1 T-TTAATATTAAATTAAA
13275679 TTTAATATT
1 TTTAATATT
13275688 TATCTTGTAG
Statistics
Matches: 58, Mismatches: 9, Indels: 20
0.67 0.10 0.23
Matches are distributed among these distances:
14 4 0.07
15 5 0.09
16 11 0.19
17 20 0.34
18 4 0.07
19 4 0.07
20 10 0.17
ACGTcount: A:0.43, C:0.03, G:0.05, T:0.49
Consensus pattern (17 bp):
TTTAATATTAAATTAAA
Found at i:13277205 original size:17 final size:16
Alignment explanation
Indices: 13277183--13277215 Score: 57
Period size: 17 Copynumber: 2.0 Consensus size: 16
13277173 CGAGTGAGAC
13277183 CATAAATATTAATTAAT
1 CATAAATATT-ATTAAT
13277200 CATAAATATTATTAAT
1 CATAAATATTATTAAT
13277216 TAATATTTAC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.52, C:0.06, G:0.00, T:0.42
Consensus pattern (16 bp):
CATAAATATTATTAAT
Found at i:13288771 original size:29 final size:29
Alignment explanation
Indices: 13288747--13288875 Score: 125
Period size: 29 Copynumber: 4.5 Consensus size: 29
13288737 AGTATCAAAA
*
13288747 ACTCTGTACCGGTGTTATATTTATCAGGT
1 ACTCTGTACCGGTGTTATATTTATCAGAT
* * * *
13288776 ACTTTGTACCAGTATTATATTTATCAGGT
1 ACTCTGTACCGGTGTTATATTTATCAGAT
* * *
13288805 ACTTTGTACCGGTGTTATA-GTATCAGAC
1 ACTCTGTACCGGTGTTATATTTATCAGAT
* * * *
13288833 ATTCTATATCGGTGTTATATTTATCAGGT
1 ACTCTGTACCGGTGTTATATTTATCAGAT
* *
13288862 GCTATGTACCGGTG
1 ACTCTGTACCGGTG
13288876 ATGGATACCA
Statistics
Matches: 79, Mismatches: 20, Indels: 2
0.78 0.20 0.02
Matches are distributed among these distances:
28 21 0.27
29 58 0.73
ACGTcount: A:0.23, C:0.16, G:0.20, T:0.41
Consensus pattern (29 bp):
ACTCTGTACCGGTGTTATATTTATCAGAT
Found at i:13289065 original size:5 final size:5
Alignment explanation
Indices: 13289057--13289086 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
13289047 TGAAATGGAA
*
13289057 ATGAG ATGAT ATGAT ATGAT ATGAT ATGAT
1 ATGAT ATGAT ATGAT ATGAT ATGAT ATGAT
13289087 GAATTATAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.40, C:0.00, G:0.23, T:0.37
Consensus pattern (5 bp):
ATGAT
Found at i:13293038 original size:36 final size:31
Alignment explanation
Indices: 13292969--13293035 Score: 125
Period size: 31 Copynumber: 2.2 Consensus size: 31
13292959 CTTTAGTATA
13292969 TTGTTAAATAAGGTAATGTAATTCATGATTT
1 TTGTTAAATAAGGTAATGTAATTCATGATTT
13293000 TTGTTAAATAAGGTAATGTAATTCATGATTT
1 TTGTTAAATAAGGTAATGTAATTCATGATTT
*
13293031 GTGTT
1 TTGTT
13293036 TTGAAGTTTG
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 35 1.00
ACGTcount: A:0.33, C:0.03, G:0.18, T:0.46
Consensus pattern (31 bp):
TTGTTAAATAAGGTAATGTAATTCATGATTT
Found at i:13295751 original size:23 final size:22
Alignment explanation
Indices: 13295708--13295765 Score: 64
Period size: 22 Copynumber: 2.6 Consensus size: 22
13295698 AAAGGATATC
* *
13295708 TACAAATTAAATC-TCTAAGAT
1 TACAAATCATATCTTCTAAGAT
13295729 TACAAAATCATATCTTCTAAGAT
1 TAC-AAATCATATCTTCTAAGAT
* *
13295752 TGCATATCATATCT
1 TACAAATCATATCT
13295766 AAGATTGCAT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
21 3 0.10
22 18 0.58
23 10 0.32
ACGTcount: A:0.41, C:0.17, G:0.05, T:0.36
Consensus pattern (22 bp):
TACAAATCATATCTTCTAAGAT
Found at i:13296687 original size:100 final size:99
Alignment explanation
Indices: 13296549--13296835 Score: 448
Period size: 100 Copynumber: 2.9 Consensus size: 99
13296539 TGCAACGCTA
* * * * *
13296549 GGGAAACAAGATTCGCTACCTTTAGCTTTAATCTGTTCCACTACACCACCAAGGAAGTAAGATTC
1 GGGAAACAAGATTCGC-ATC-GTAGCTTCAATCTGTTCCACTACACCGCCAGGGAAGTAAGATTC
*
13296614 GTCGTTGTGGCTTCAATCTATTTAACAACAATGTTG
64 GCCGTTGTGGCTTCAATCTATTTAACAACAATGTTG
13296650 GGGAAACAAGATTCGCAGTCGTAGCTTCAATCTGTTCCACTACACCGCCAGGGAAGTAAGATTCG
1 GGGAAACAAGATTCGCA-TCGTAGCTTCAATCTGTTCCACTACACCGCCAGGGAAGTAAGATTCG
**
13296715 CCGTTGTGGCTTCAATCTATTTAACTGCAATGTTG
65 CCGTTGTGGCTTCAATCTATTTAACAACAATGTTG
* *
13296750 GAGAAACAAGATTCACCATCGTAGCTTCAATCTGTTCCACTACACCGCCAGGGAAGTAAGATTCG
1 GGGAAACAAGATTC-GCATCGTAGCTTCAATCTGTTCCACTACACCGCCAGGGAAGTAAGATTCG
13296815 CCGTTGTGGCTTCAATCTATT
65 CCGTTGTGGCTTCAATCTATT
13296836 CCACTGTAAT
Statistics
Matches: 174, Mismatches: 10, Indels: 5
0.92 0.05 0.03
Matches are distributed among these distances:
100 155 0.89
101 19 0.11
ACGTcount: A:0.28, C:0.23, G:0.20, T:0.29
Consensus pattern (99 bp):
GGGAAACAAGATTCGCATCGTAGCTTCAATCTGTTCCACTACACCGCCAGGGAAGTAAGATTCGC
CGTTGTGGCTTCAATCTATTTAACAACAATGTTG
Found at i:13296838 original size:50 final size:50
Alignment explanation
Indices: 13296573--13296840 Score: 223
Period size: 50 Copynumber: 5.4 Consensus size: 50
13296563 GCTACCTTTA
* * * * *
13296573 GCTTTAATCTGTTCCACTACACCACCAAGGAAGTAAGATTCGTCGTTGTG
1 GCTTCAATCTATTCCACTACACCGCCAGGGAAGTAAGATTCGCCGTTGTG
** * ** *** ** * * *
13296623 GCTTCAATCTATTTAACAACAATGTTGGGGAAACAAGATTCGCAGTCGTA
1 GCTTCAATCTATTCCACTACACCGCCAGGGAAGTAAGATTCGCCGTTGTG
*
13296673 GCTTCAATCTGTTCCACTACACCGCCAGGGAAGTAAGATTCGCCGTTGTG
1 GCTTCAATCTATTCCACTACACCGCCAGGGAAGTAAGATTCGCCGTTGTG
** * ** ** ** * * * *
13296723 GCTTCAATCTATTTAACTGCAATG-TTGGAGAAACAAGATTCACCATCGTA
1 GCTTCAATCTATTCCACTACACCGCCAGG-GAAGTAAGATTCGCCGTTGTG
*
13296773 GCTTCAATCTGTTCCACTACACCGCCAGGGAAGTAAGATTCGCCGTTGTG
1 GCTTCAATCTATTCCACTACACCGCCAGGGAAGTAAGATTCGCCGTTGTG
13296823 GCTTCAATCTATTCCACT
1 GCTTCAATCTATTCCACT
13296841 GTAATGCCAA
Statistics
Matches: 155, Mismatches: 61, Indels: 4
0.70 0.28 0.02
Matches are distributed among these distances:
49 2 0.01
50 151 0.97
51 2 0.01
ACGTcount: A:0.27, C:0.24, G:0.20, T:0.29
Consensus pattern (50 bp):
GCTTCAATCTATTCCACTACACCGCCAGGGAAGTAAGATTCGCCGTTGTG
Found at i:13297038 original size:44 final size:44
Alignment explanation
Indices: 13296990--13297190 Score: 151
Period size: 44 Copynumber: 4.8 Consensus size: 44
13296980 TACTGCTTAA
* * *
13296990 GGAGATAAGA-TCTATAATTTTCAACCTACTCCACTGCT-ATTCAG
1 GGAGATAAGATTC-ACAATCTTCAACCTACTCCACTGCTGA-CCAG
* * *
13297034 GGAGATAGGATTCACAATCTTCAACCTATTCCATTGCTGACCAG
1 GGAGATAAGATTCACAATCTTCAACCTACTCCACTGCTGACCAG
* *
13297078 GGAGATAGGATTCAC---C-T--A--T--TCCACTACTGACCAG
1 GGAGATAAGATTCACAATCTTCAACCTACTCCACTGCTGACCAG
* * *
13297112 GAAGATAGGACTT-ACAATCTTCAACCTATTCCACTGCTGACCAG
1 GGAGATAAGA-TTCACAATCTTCAACCTACTCCACTGCTGACCAG
* *
13297156 GGAGATAGGACTT-ACAATCTTCAACCTATTCCACT
1 GGAGATAAGA-TTCACAATCTTCAACCTACTCCACT
13297191 ACTTTCCAAG
Statistics
Matches: 133, Mismatches: 11, Indels: 26
0.78 0.06 0.15
Matches are distributed among these distances:
34 24 0.18
35 2 0.02
36 1 0.01
37 1 0.01
38 2 0.02
40 2 0.02
41 1 0.01
42 1 0.01
44 96 0.72
45 3 0.02
ACGTcount: A:0.31, C:0.25, G:0.16, T:0.27
Consensus pattern (44 bp):
GGAGATAAGATTCACAATCTTCAACCTACTCCACTGCTGACCAG
Found at i:13297096 original size:34 final size:34
Alignment explanation
Indices: 13297057--13297121 Score: 103
Period size: 34 Copynumber: 1.9 Consensus size: 34
13297047 ACAATCTTCA
* * *
13297057 ACCTATTCCATTGCTGACCAGGGAGATAGGATTC
1 ACCTATTCCACTACTGACCAGGAAGATAGGATTC
13297091 ACCTATTCCACTACTGACCAGGAAGATAGGA
1 ACCTATTCCACTACTGACCAGGAAGATAGGA
13297122 CTTACAATCT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
34 28 1.00
ACGTcount: A:0.31, C:0.25, G:0.22, T:0.23
Consensus pattern (34 bp):
ACCTATTCCACTACTGACCAGGAAGATAGGATTC
Found at i:13297204 original size:44 final size:44
Alignment explanation
Indices: 13297091--13297211 Score: 181
Period size: 44 Copynumber: 2.8 Consensus size: 44
13297081 GATAGGATTC
13297091 ACCTATTCCACTACTGACC-AGGAAGATAGGACTTACAATCTTCA
1 ACCTATTCCACTACTGACCAAGG-AGATAGGACTTACAATCTTCA
* *
13297135 ACCTATTCCACTGCTGACCAGGGAGATAGGACTTACAATCTTCA
1 ACCTATTCCACTACTGACCAAGGAGATAGGACTTACAATCTTCA
** *
13297179 ACCTATTCCACTACTTTCCAAGGAGACAGGACT
1 ACCTATTCCACTACTGACCAAGGAGATAGGACT
13297212 ACTATCTCCG
Statistics
Matches: 69, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
44 67 0.97
45 2 0.03
ACGTcount: A:0.31, C:0.28, G:0.16, T:0.25
Consensus pattern (44 bp):
ACCTATTCCACTACTGACCAAGGAGATAGGACTTACAATCTTCA
Found at i:13299204 original size:13 final size:13
Alignment explanation
Indices: 13299186--13299211 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
13299176 CCCAAACCCA
13299186 ACATCAAATTGCT
1 ACATCAAATTGCT
13299199 ACATCAAATTGCT
1 ACATCAAATTGCT
13299212 TTTTAACTTT
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:0.23, G:0.08, T:0.31
Consensus pattern (13 bp):
ACATCAAATTGCT
Found at i:13299788 original size:25 final size:25
Alignment explanation
Indices: 13299735--13299800 Score: 71
Period size: 25 Copynumber: 2.6 Consensus size: 25
13299725 AAGAAAATCC
* *
13299735 AAAAGAATGAAAGAATAATTATTCG
1 AAAAGAATGAAAGAATAATTACTCA
*
13299760 AAAAGAATGAAAGAAT-ATTGGCTCA
1 AAAAGAATGAAAGAATAATT-ACTCA
13299785 AAAATGAATGCAAAGA
1 AAAA-GAATG-AAAGA
13299801 TGTATTTCAT
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
24 3 0.09
25 22 0.63
26 5 0.14
27 5 0.14
ACGTcount: A:0.56, C:0.06, G:0.18, T:0.20
Consensus pattern (25 bp):
AAAAGAATGAAAGAATAATTACTCA
Found at i:13315160 original size:20 final size:18
Alignment explanation
Indices: 13315130--13315183 Score: 63
Period size: 19 Copynumber: 2.8 Consensus size: 18
13315120 AAATTACAAA
*
13315130 AAAAATCAAAATATTTTT
1 AAAATTCAAAATATTTTT
*
13315148 CAAAATTTTAAAATAATTTTT
1 -AAAA-TTCAAAAT-ATTTTT
13315169 AAAATTCAAAATATT
1 AAAATTCAAAATATT
13315184 AATAAATATT
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
18 3 0.10
19 11 0.37
20 10 0.33
21 6 0.20
ACGTcount: A:0.54, C:0.06, G:0.00, T:0.41
Consensus pattern (18 bp):
AAAATTCAAAATATTTTT
Found at i:13317729 original size:11 final size:11
Alignment explanation
Indices: 13317715--13317790 Score: 58
Period size: 11 Copynumber: 7.4 Consensus size: 11
13317705 ATTTTTTAAA
13317715 TTTTAAAATAT
1 TTTTAAAATAT
13317726 TTTTAAAATACT
1 TTTTAAAATA-T
**
13317738 TTTT--TTTAT
1 TTTTAAAATAT
*
13317747 TTTT--TA-AT
1 TTTTAAAATAT
13317755 -TTTAAAATA-
1 TTTTAAAATAT
13317764 TTTTAAAATAT
1 TTTTAAAATAT
13317775 TTTTAAAATACT
1 TTTTAAAATA-T
13317787 TTTT
1 TTTT
13317791 TTAATTTTTA
Statistics
Matches: 54, Mismatches: 4, Indels: 13
0.76 0.06 0.18
Matches are distributed among these distances:
7 3 0.06
8 2 0.04
9 7 0.13
10 12 0.22
11 20 0.37
12 10 0.19
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.61
Consensus pattern (11 bp):
TTTTAAAATAT
Found at i:13317746 original size:49 final size:49
Alignment explanation
Indices: 13317693--13317799 Score: 171
Period size: 49 Copynumber: 2.2 Consensus size: 49
13317683 AATAAATATA
**
13317693 TTTATTTTTTACATTTTTTAA-ATTTTAAAATATTTTTAAAATACTTTTT
1 TTTATTTTTTA-ATTTTAAAATATTTTAAAATATTTTTAAAATACTTTTT
13317742 TTTATTTTTTAATTTTAAAATATTTTAAAATATTTTTAAAATACTTTTT
1 TTTATTTTTTAATTTTAAAATATTTTAAAATATTTTTAAAATACTTTTT
*
13317791 TTAATTTTT
1 TTTATTTTT
13317800 AAAATAAATT
Statistics
Matches: 54, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
48 7 0.13
49 47 0.87
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.64
Consensus pattern (49 bp):
TTTATTTTTTAATTTTAAAATATTTTAAAATATTTTTAAAATACTTTTT
Found at i:13317756 original size:39 final size:38
Alignment explanation
Indices: 13317695--13317778 Score: 125
Period size: 39 Copynumber: 2.2 Consensus size: 38
13317685 TAAATATATT
**
13317695 TATTTTTTACATTTTTTAAATTTTAAAATATTTTTAAAA
1 TATTTTTTTTATTTTTTAAATTTTAAAATA-TTTTAAAA
13317734 TACTTTTTTTTATTTTTT-AATTTTAAAATATTTTAAAA
1 TA-TTTTTTTTATTTTTTAAATTTTAAAATATTTTAAAA
13317772 TATTTTT
1 TATTTTT
13317779 AAAATACTTT
Statistics
Matches: 42, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
37 5 0.12
38 10 0.24
39 14 0.33
40 13 0.31
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (38 bp):
TATTTTTTTTATTTTTTAAATTTTAAAATATTTTAAAA
Found at i:13317797 original size:21 final size:20
Alignment explanation
Indices: 13317746--13317805 Score: 68
Period size: 21 Copynumber: 3.0 Consensus size: 20
13317736 CTTTTTTTTA
13317746 TTTTTTAA-TTTTAAAATAT
1 TTTTTTAATTTTTAAAATAT
***
13317765 TTTAAAATATTTTTAAAATACT
1 TTTTTTA-ATTTTTAAAATA-T
13317787 TTTTTTAATTTTTAAAATA
1 TTTTTTAATTTTTAAAATA
13317806 AATTTTTGGT
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
19 4 0.12
20 1 0.03
21 22 0.69
22 5 0.16
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (20 bp):
TTTTTTAATTTTTAAAATAT
Found at i:13317811 original size:21 final size:21
Alignment explanation
Indices: 13317773--13317812 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
13317763 ATTTTAAAAT
**
13317773 ATTTTTAAAATACTTTTTTTA
1 ATTTTTAAAATAAATTTTTTA
13317794 ATTTTTAAAATAAATTTTT
1 ATTTTTAAAATAAATTTTT
13317813 GGTATTTATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.60
Consensus pattern (21 bp):
ATTTTTAAAATAAATTTTTTA
Found at i:13317819 original size:22 final size:20
Alignment explanation
Indices: 13317772--13317826 Score: 56
Period size: 21 Copynumber: 2.5 Consensus size: 20
13317762 TATTTTAAAA
* *
13317772 TATTTTTAAAATACTTTTTT
1 TATTTTTAAAATAATTTTTG
13317792 TAATTTTTAAAATAAATTTTTGG
1 T-ATTTTTAAAAT-AATTTTT-G
13317815 TATTTATTAAAA
1 TATTT-TTAAAA
13317827 AATGGGCCAG
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
20 1 0.03
21 11 0.38
22 10 0.34
23 7 0.24
ACGTcount: A:0.38, C:0.02, G:0.04, T:0.56
Consensus pattern (20 bp):
TATTTTTAAAATAATTTTTG
Found at i:13319318 original size:30 final size:30
Alignment explanation
Indices: 13319284--13319595 Score: 205
Period size: 30 Copynumber: 10.4 Consensus size: 30
13319274 TCATCGACAA
*
13319284 ATGAAAAGAGATGGCTTCGGCTATCGATAT
1 ATGAAAAGGGATGGCTTCGGCTATCGATAT
** *
13319314 ATGAAAAGGGATAACTTCGGCTATCAAT-T
1 ATGAAAAGGGATGGCTTCGGCTATCGATAT
* * * *
13319343 ATGAAAAGGGATGG-TGACGACCATC-AAATT
1 ATGAAAAGGGATGGCT-TCGGCTATCGATA-T
13319373 ATGAAAAGGGATGGCTTCGGCTATCG-TAT
1 ATGAAAAGGGATGGCTTCGGCTATCGATAT
*
13319402 AATGAAAAGGGATGGCTTCGGCTATCGATCT
1 -ATGAAAAGGGATGGCTTCGGCTATCGATAT
* * *
13319433 ATGAAAAAGGATAGCTTCGGCTATCAAT-T
1 ATGAAAAGGGATGGCTTCGGCTATCGATAT
* * ** *
13319462 ATGAAAAAGGATGG-TGACAACCA-CTGA-AT
1 ATGAAAAGGGATGGCT-TCGGCTATC-GATAT
* * * *
13319491 AATGAAAAGGGATGG-TAACGACCATC-AAATT
1 -ATGAAAAGGGATGGCT-TCGGCTATCGATA-T
* *
13319522 ATGAAAAAGGATAGCTTCGGCTATCGA-ACT
1 ATGAAAAGGGATGGCTTCGGCTATCGATA-T
** * * *
13319552 ATGAAAAAGGGATAACTTCGGTTATCAATTT
1 ATG-AAAAGGGATGGCTTCGGCTATCGATAT
13319583 ATGAAAAGGGATG
1 ATGAAAAGGGATG
13319596 TGTTAACCAT
Statistics
Matches: 225, Mismatches: 39, Indels: 36
0.75 0.13 0.12
Matches are distributed among these distances:
28 4 0.02
29 40 0.18
30 150 0.67
31 31 0.14
ACGTcount: A:0.38, C:0.13, G:0.25, T:0.24
Consensus pattern (30 bp):
ATGAAAAGGGATGGCTTCGGCTATCGATAT
Found at i:13319462 original size:89 final size:89
Alignment explanation
Indices: 13319284--13319595 Score: 278
Period size: 89 Copynumber: 3.5 Consensus size: 89
13319274 TCATCGACAA
* **
13319284 ATGAAAAGAGATGGCTTCGGCTATCG-ATATATGAAAAGGGATAACTTCGGCTATCAATTATGAA
1 ATGAAAAGGGATGGCTTCGGCTATCGAATA-ATGAAAAGGGATGGCTTCGGCTATCAATTATGAA
* * * * *
13319348 AAGGGAT-GGTGACGACCATCAAATT
65 AAAGGATAGCT-TCGGCTATCAAATT
* *
13319373 ATGAAAAGGGATGGCTTCGGCTATCGTATAATGAAAAGGGATGGCTTCGGCTATCGATCTATGAA
1 ATGAAAAGGGATGGCTTCGGCTATCGAATAATGAAAAGGGATGGCTTCGGCTATCAAT-TATGAA
13319438 AAAGGATAGCTTCGGCTATC-AATT
65 AAAGGATAGCTTCGGCTATCAAATT
* * ** * * * *
13319462 ATGAAAAAGGATGG-TGACAACCA-CTGAATAATGAAAAGGGATGG-TAACGACCATCAAATTAT
1 ATGAAAAGGGATGGCT-TCGGCTATC-GAATAATGAAAAGGGATGGCT-TCGGCTATC-AATTAT
* *
13319524 GAAAAAGGATAGCTTCGGCTATCGAACT
62 GAAAAAGGATAGCTTCGGCTATCAAATT
** * *
13319552 ATGAAAAAGGGATAACTTCGGTTATC-AATTTATGAAAAGGGATG
1 ATG-AAAAGGGATGGCTTCGGCTATCGAA-TAATGAAAAGGGATG
13319596 TGTTAACCAT
Statistics
Matches: 182, Mismatches: 29, Indels: 22
0.78 0.12 0.09
Matches are distributed among these distances:
88 3 0.02
89 120 0.66
90 31 0.17
91 26 0.14
92 2 0.01
ACGTcount: A:0.38, C:0.13, G:0.25, T:0.24
Consensus pattern (89 bp):
ATGAAAAGGGATGGCTTCGGCTATCGAATAATGAAAAGGGATGGCTTCGGCTATCAATTATGAAA
AAGGATAGCTTCGGCTATCAAATT
Found at i:13319496 original size:119 final size:119
Alignment explanation
Indices: 13319283--13319595 Score: 414
Period size: 119 Copynumber: 2.6 Consensus size: 119
13319273 ATCATCGACA
* * *
13319283 AATGAAAAGAGATGGCTTCGGCTATCGATATATGAAAAGGGATAACTTCGGCTATCAATTATGAA
1 AATGAAAAGGGATGGCTTCGGCTATCGATCTATGAAAAAGGATAACTTCGGCTATCAATTATGAA
* * * * * **
13319348 AAGGGATGGTGACGACCATCAAATTATGAAAAGGGATGGCT-TCGGCTATCGTAT
66 AAGGGATGGTGACAACCATCAAATAATGAAAAGGGATGG-TAACGACCATCAAAT
*
13319402 AATGAAAAGGGATGGCTTCGGCTATCGATCTATGAAAAAGGATAGCTTCGGCTATCAATTATGAA
1 AATGAAAAGGGATGGCTTCGGCTATCGATCTATGAAAAAGGATAACTTCGGCTATCAATTATGAA
* *
13319467 AAAGGATGGTGACAACCA-CTGAATAATGAAAAGGGATGGTAACGACCATCAAAT
66 AAGGGATGGTGACAACCATC-AAATAATGAAAAGGGATGGTAACGACCATCAAAT
* * * * *
13319521 TATGAAAAAGGATAGCTTCGGCTATCGAACTATGAAAAAGGGATAACTTCGGTTATCAATTTATG
1 AATGAAAAGGGATGGCTTCGGCTATCGATCTATGAAAAA-GGATAACTTCGGCTATCAA-TTATG
13319586 AAAAGGGATG
64 AAAAGGGATG
13319596 TGTTAACCAT
Statistics
Matches: 170, Mismatches: 20, Indels: 6
0.87 0.10 0.03
Matches are distributed among these distances:
118 2 0.01
119 137 0.81
120 17 0.10
121 14 0.08
ACGTcount: A:0.38, C:0.13, G:0.25, T:0.24
Consensus pattern (119 bp):
AATGAAAAGGGATGGCTTCGGCTATCGATCTATGAAAAAGGATAACTTCGGCTATCAATTATGAA
AAGGGATGGTGACAACCATCAAATAATGAAAAGGGATGGTAACGACCATCAAAT
Found at i:13321610 original size:18 final size:19
Alignment explanation
Indices: 13321589--13321630 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
13321579 ATTAATAGAA
* *
13321589 TAAAATATAAT-TATATTT
1 TAAAATAAAATATATATTC
13321607 TAAAAATAAAATATATATTC
1 T-AAAATAAAATATATATTC
13321627 TAAA
1 TAAA
13321631 CTCAAATACT
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
18 1 0.05
19 12 0.60
20 7 0.35
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.40
Consensus pattern (19 bp):
TAAAATAAAATATATATTC
Found at i:13321625 original size:20 final size:19
Alignment explanation
Indices: 13321590--13321630 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
13321580 TTAATAGAAT
* *
13321590 AAAATATAATTATATTTTA
1 AAAATAAAATTATATTCTA
13321609 AAAATAAAATATATATTCTA
1 AAAATAAAAT-TATATTCTA
13321629 AA
1 AA
13321631 CTCAAATACT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 9 0.47
20 10 0.53
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (19 bp):
AAAATAAAATTATATTCTA
Found at i:13325147 original size:41 final size:41
Alignment explanation
Indices: 13325102--13325195 Score: 179
Period size: 41 Copynumber: 2.3 Consensus size: 41
13325092 GACTTTAAGT
*
13325102 CTAGCAAGCTAAGTGCCGGTGATCTGAATCAGGTTATAAAC
1 CTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGTTATAAAC
13325143 CTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGTTATAAAC
1 CTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGTTATAAAC
13325184 CTAGCAGGCTAA
1 CTAGCAGGCTAA
13325196 TATGTATTTG
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.31, C:0.20, G:0.26, T:0.23
Consensus pattern (41 bp):
CTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGTTATAAAC
Found at i:13326139 original size:26 final size:28
Alignment explanation
Indices: 13326092--13326143 Score: 74
Period size: 26 Copynumber: 1.9 Consensus size: 28
13326082 TACGCAGCAC
13326092 ACAAACAAGCAGCAAAACAAAGAAAAAA
1 ACAAACAAGCAGCAAAACAAAGAAAAAA
13326120 ACAAA-AAG-AGCAACAA-AAAGAAAA
1 ACAAACAAGCAGCAA-AACAAAGAAAA
13326144 TAGGACAAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
26 13 0.57
27 5 0.22
28 5 0.22
ACGTcount: A:0.73, C:0.15, G:0.12, T:0.00
Consensus pattern (28 bp):
ACAAACAAGCAGCAAAACAAAGAAAAAA
Found at i:13329972 original size:18 final size:19
Alignment explanation
Indices: 13329943--13329978 Score: 65
Period size: 18 Copynumber: 1.9 Consensus size: 19
13329933 TGATATGGCC
13329943 AAAATCACTTTTTCACTTA
1 AAAATCACTTTTTCACTTA
13329962 AAAATCA-TTTTTCACTT
1 AAAATCACTTTTTCACTT
13329979 TGGCATGTGA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 10 0.59
19 7 0.41
ACGTcount: A:0.36, C:0.19, G:0.00, T:0.44
Consensus pattern (19 bp):
AAAATCACTTTTTCACTTA
Found at i:13334613 original size:42 final size:43
Alignment explanation
Indices: 13334552--13334669 Score: 150
Period size: 42 Copynumber: 2.8 Consensus size: 43
13334542 GATTTGAGAT
*
13334552 TTACATGTAAGACCATGTCTGGGACATTGGCATCG-T-ATATAA
1 TTACATATAAGACCATGTCTGGGACATTGGCATCGATAAT-TAA
* * *
13334594 TTACGTATAAGACCTTGTCTGGGACAGTGGCATCGATAATTAA
1 TTACATATAAGACCATGTCTGGGACATTGGCATCGATAATTAA
* * *
13334637 TTACATGTAAGACCACGTCTGGGACGTTGGCAT
1 TTACATATAAGACCATGTCTGGGACATTGGCAT
13334670 TGTACAGGCT
Statistics
Matches: 64, Mismatches: 10, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
42 31 0.48
43 31 0.48
44 2 0.03
ACGTcount: A:0.29, C:0.18, G:0.24, T:0.30
Consensus pattern (43 bp):
TTACATATAAGACCATGTCTGGGACATTGGCATCGATAATTAA
Found at i:13334657 original size:43 final size:42
Alignment explanation
Indices: 13334513--13334669 Score: 167
Period size: 43 Copynumber: 3.7 Consensus size: 42
13334503 TGTGACATCG
* *
13334513 TGTAAGACCACGTCTAGGACGTTGGCCTCGAT-TTGAGATTTACA
1 TGTAAGACCACGTCTGGGACGTTGGCATCGATATT-A-A-TTACA
* * *
13334557 TGTAAGACCATGTCTGGGACATTGGCATCG-TATATAATTACG
1 TGTAAGACCACGTCTGGGACGTTGGCATCGATAT-TAATTACA
* **
13334599 TATAAGACCTTGTCTGGGACAG-TGGCATCGATAATTAATTACA
1 TGTAAGACCACGTCTGGGAC-GTTGGCATCGAT-ATTAATTACA
13334642 TGTAAGACCACGTCTGGGACGTTGGCAT
1 TGTAAGACCACGTCTGGGACGTTGGCAT
13334670 TGTACAGGCT
Statistics
Matches: 95, Mismatches: 12, Indels: 13
0.79 0.10 0.11
Matches are distributed among these distances:
42 31 0.33
43 33 0.35
44 30 0.32
45 1 0.01
ACGTcount: A:0.27, C:0.18, G:0.25, T:0.29
Consensus pattern (42 bp):
TGTAAGACCACGTCTGGGACGTTGGCATCGATATTAATTACA
Found at i:13337668 original size:41 final size:41
Alignment explanation
Indices: 13337611--13337702 Score: 141
Period size: 41 Copynumber: 2.2 Consensus size: 41
13337601 GTTGTTTAAC
*
13337611 TAGTAAGGATTAATTATT-ATGTTGTTCTCGTAATTAATTTA
1 TAGTAAGGATTAATTATTGA-GTTGTTCTCATAATTAATTTA
*
13337652 TAGTAAGGATTAATTATTGAGTTGTTTTCATAATTAATTTA
1 TAGTAAGGATTAATTATTGAGTTGTTCTCATAATTAATTTA
13337693 TAGCTAAGGA
1 TAG-TAAGGA
13337703 AAGATCGGTG
Statistics
Matches: 47, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
41 40 0.85
42 7 0.15
ACGTcount: A:0.34, C:0.04, G:0.16, T:0.46
Consensus pattern (41 bp):
TAGTAAGGATTAATTATTGAGTTGTTCTCATAATTAATTTA
Found at i:13342119 original size:23 final size:23
Alignment explanation
Indices: 13342091--13342135 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
13342081 GTTCAAAATT
*
13342091 TTAAAATAAACAATATATATGAG
1 TTAAAACAAACAATATATATGAG
*
13342114 TTAAAACAAATAATATATATGA
1 TTAAAACAAACAATATATATGA
13342136 ATGTACAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.58, C:0.04, G:0.07, T:0.31
Consensus pattern (23 bp):
TTAAAACAAACAATATATATGAG
Found at i:13342222 original size:24 final size:24
Alignment explanation
Indices: 13342184--13342483 Score: 153
Period size: 24 Copynumber: 12.8 Consensus size: 24
13342174 TGAATTGGAT
* *
13342184 AATTTACAATAAATAATATATAATA
1 AATTTAAAAT-AATAATATATGATA
* *
13342209 AATTTGAAATAATAATACAT-ATAA
1 AATTTAAAATAATAATATATGAT-A
*
13342233 AATTT-AAA-AAT--TTTGATGAT-
1 AATTTAAAATAATAATAT-ATGATA
* **
13342253 AATTCTAAAATAATCATACGTGATA
1 AATT-TAAAATAATAATATATGATA
** * *
13342278 AATCCAAAATAATAGTATATAATA
1 AATTTAAAATAATAATATATGATA
*
13342302 AATTT-AAA-AATATTA-ATGATA
1 AATTTAAAATAATAATATATGATA
* *
13342323 AATTTGAAATAGAT-ATACATGATA
1 AATTTAAAATA-ATAATATATGATA
** ** *
13342347 AATTTAAAATAATGTTA-ACAATG
1 AATTTAAAATAATAATATATGATA
13342370 AATTTAAAATAATAATAT-TGATA
1 AATTTAAAATAATAATATATGATA
* *
13342393 AA-TTACAAATAATAAAATATTATA
1 AATTTA-AAATAATAATATATGATA
* **
13342417 AATCTAAAATAATAATATACAATA
1 AATTTAAAATAATAATATATGATA
* * * * *
13342441 CACTT-AGATAATATTA-ATGATT
1 AATTTAAAATAATAATATATGATA
13342463 AATTTAATAATAATAAGTATA
1 AATTTAA-AATAATAA-TATA
13342484 AACATTCAAA
Statistics
Matches: 205, Mismatches: 48, Indels: 43
0.69 0.16 0.15
Matches are distributed among these distances:
20 5 0.02
21 13 0.06
22 26 0.13
23 59 0.29
24 85 0.41
25 16 0.08
26 1 0.00
ACGTcount: A:0.55, C:0.05, G:0.05, T:0.35
Consensus pattern (24 bp):
AATTTAAAATAATAATATATGATA
Found at i:13342288 original size:69 final size:69
Alignment explanation
Indices: 13342215--13342474 Score: 181
Period size: 69 Copynumber: 3.7 Consensus size: 69
13342205 AATAAATTTG
* * *
13342215 AAATAATAATACAT-ATAAAATTTAAAAATTTTGATGAT-AATTCTAAAATA-ATCATACGTGAT
1 AAATAATAATACATAAT-AAATTTAAAAATATTAATGATAAATT-TAAAATAGAT-ATACATGAT
13342277 AAATCCA
63 AAATCCA
* * *
13342284 AAATAATAGTATATAATAAATTTAAAAATATTAATGATAAATTTGAAATAGATATACATGATAAA
1 AAATAATAATACATAATAAATTTAAAAATATTAATGATAAATTTAAAATAGATATACATGATAAA
**
13342349 TTTA
66 TCCA
** * * * * * * *
13342353 AAATAATGTTA-ACAATGAATTTAAAATAATAATATTGATAAA-TTACAAATA-ATAAAATATTA
1 AAATAATAATACATAATAAATTT-AAA-AATATTAATGATAAATTTA-AAATAGAT-ATACATGA
*
13342415 TAAATCTA
62 TAAATCCA
* * * * * *
13342423 AAATAATAATATACAATACACTTAGATAATATTAATGATTAATTTAATAATA
1 AAATAATAATACATAATAAATTTA-AAAATATTAATGATAAATTTAA-AATA
13342475 ATAAGTATAA
Statistics
Matches: 152, Mismatches: 28, Indels: 20
0.76 0.14 0.10
Matches are distributed among these distances:
68 9 0.06
69 66 0.43
70 61 0.40
71 16 0.11
ACGTcount: A:0.55, C:0.05, G:0.05, T:0.35
Consensus pattern (69 bp):
AAATAATAATACATAATAAATTTAAAAATATTAATGATAAATTTAAAATAGATATACATGATAAA
TCCA
Found at i:13343283 original size:22 final size:21
Alignment explanation
Indices: 13343258--13343333 Score: 61
Period size: 19 Copynumber: 3.7 Consensus size: 21
13343248 TACAAATTAA
13343258 ATCTCTAAGATTACAAAATCTT
1 ATCTCTAAGATTAC-AAATCTT
* *
13343280 ATCTTCTAAGATTGCATATCTT
1 ATC-TCTAAGATTACAAATCTT
* *
13343302 A--TCTAAGATTGC--ATATT
1 ATCTCTAAGATTACAAATCTT
*
13343319 ATATCTAAGATTACA
1 ATCTCTAAGATTACA
13343334 TATCCTTTTT
Statistics
Matches: 46, Mismatches: 4, Indels: 10
0.77 0.07 0.17
Matches are distributed among these distances:
17 5 0.11
19 21 0.46
22 10 0.22
23 10 0.22
ACGTcount: A:0.37, C:0.16, G:0.08, T:0.39
Consensus pattern (21 bp):
ATCTCTAAGATTACAAATCTT
Found at i:13343291 original size:23 final size:22
Alignment explanation
Indices: 13343261--13343305 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
13343251 AAATTAAATC
13343261 TCTAAGATTACAAAATCTTATCT
1 TCTAAGATTAC-AAATCTTATCT
* *
13343284 TCTAAGATTGCATATCTTATCT
1 TCTAAGATTACAAATCTTATCT
13343306 AAGATTGCAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 10 0.50
23 10 0.50
ACGTcount: A:0.33, C:0.18, G:0.07, T:0.42
Consensus pattern (22 bp):
TCTAAGATTACAAATCTTATCT
Found at i:13343308 original size:19 final size:20
Alignment explanation
Indices: 13343284--13343337 Score: 85
Period size: 19 Copynumber: 2.8 Consensus size: 20
13343274 AATCTTATCT
13343284 TCTAAGATTGCATATCT-TA
1 TCTAAGATTGCATATCTATA
13343303 TCTAAGATTGCATAT-TATA
1 TCTAAGATTGCATATCTATA
*
13343322 TCTAAGATTACATATC
1 TCTAAGATTGCATATC
13343338 CTTTTTCAAG
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
18 1 0.03
19 31 0.97
ACGTcount: A:0.35, C:0.15, G:0.09, T:0.41
Consensus pattern (20 bp):
TCTAAGATTGCATATCTATA
Found at i:13343774 original size:41 final size:42
Alignment explanation
Indices: 13343729--13343811 Score: 102
Period size: 42 Copynumber: 2.0 Consensus size: 42
13343719 AGAAATTTAT
13343729 AAATTTTGG-GG-G-CCTAACTAA-AATTTTTAAAGAATTTTCAA
1 AAATTTTGGAGGCGTCCTAAC-AAGAA-TTTTAAA-AATTTTCAA
*
13343770 AAATTTTGGAGGCGTCCTTACAAGAATTTTAAAAATTTTCAA
1 AAATTTTGGAGGCGTCCTAACAAGAATTTTAAAAATTTTCAA
13343812 GTAAAAAGAC
Statistics
Matches: 37, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
41 9 0.24
42 11 0.30
43 10 0.27
44 7 0.19
ACGTcount: A:0.39, C:0.11, G:0.14, T:0.36
Consensus pattern (42 bp):
AAATTTTGGAGGCGTCCTAACAAGAATTTTAAAAATTTTCAA
Found at i:13346153 original size:22 final size:22
Alignment explanation
Indices: 13346125--13346168 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
13346115 CACTAAGTTG
13346125 GTAAAAGAAATTAGATTACATT
1 GTAAAAGAAATTAGATTACATT
13346147 GTAAAAGAAATTAGATTACATT
1 GTAAAAGAAATTAGATTACATT
13346169 TTATCTTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.50, C:0.05, G:0.14, T:0.32
Consensus pattern (22 bp):
GTAAAAGAAATTAGATTACATT
Found at i:13346362 original size:8 final size:9
Alignment explanation
Indices: 13346344--13346368 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
13346334 TTTTAACAAT
13346344 AAAATTAAA
1 AAAATTAAA
13346353 AAAATTAAA
1 AAAATTAAA
13346362 AAAATTA
1 AAAATTA
13346369 CTTTTTAATC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (9 bp):
AAAATTAAA
Found at i:13353459 original size:13 final size:13
Alignment explanation
Indices: 13353407--13353491 Score: 55
Period size: 13 Copynumber: 6.4 Consensus size: 13
13353397 TGAATAAATA
*
13353407 AAATGATTATATG
1 AAATGGTTATATG
* *
13353420 CATTGGTTATATAG
1 AAATGGTTATAT-G
* * *
13353434 AAGTAGATATATG
1 AAATGGTTATATG
13353447 AAATGGTTATATG
1 AAATGGTTATATG
*
13353460 -AATCAGTTATATG
1 AAAT-GGTTATATG
* *
13353473 AAAATAGATATATG
1 -AAATGGTTATATG
13353487 AAATG
1 AAATG
13353492 AAACATTGGA
Statistics
Matches: 55, Mismatches: 13, Indels: 8
0.72 0.17 0.11
Matches are distributed among these distances:
12 3 0.05
13 32 0.58
14 17 0.31
15 3 0.05
ACGTcount: A:0.44, C:0.02, G:0.19, T:0.35
Consensus pattern (13 bp):
AAATGGTTATATG
Found at i:13353469 original size:40 final size:40
Alignment explanation
Indices: 13353407--13353492 Score: 111
Period size: 40 Copynumber: 2.1 Consensus size: 40
13353397 TGAATAAATA
* ** *
13353407 AAATGATTATATGCATTGGTTATAT-AGAAGTAGATATATG
1 AAATGATTATATGAATCAGTTATATGA-AAATAGATATATG
*
13353447 AAATGGTTATATGAATCAGTTATATGAAAATAGATATATG
1 AAATGATTATATGAATCAGTTATATGAAAATAGATATATG
13353487 AAATGA
1 AAATGA
13353493 AACATTGGAT
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
40 38 0.97
41 1 0.03
ACGTcount: A:0.44, C:0.02, G:0.19, T:0.35
Consensus pattern (40 bp):
AAATGATTATATGAATCAGTTATATGAAAATAGATATATG
Found at i:13353477 original size:27 final size:26
Alignment explanation
Indices: 13353414--13353475 Score: 72
Period size: 27 Copynumber: 2.3 Consensus size: 26
13353404 ATAAAATGAT
* *
13353414 TATATGCATTGGTTATATAGAAGTAGA
1 TATATGAAATGGTTATAT-GAAGTAGA
*
13353441 TATATGAAATGGTTATATGAA-TCAGT
1 TATATGAAATGGTTATATGAAGT-AGA
13353467 TATATGAAA
1 TATATGAAA
13353476 ATAGATATAT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
25 1 0.03
26 14 0.45
27 16 0.52
ACGTcount: A:0.40, C:0.03, G:0.19, T:0.37
Consensus pattern (26 bp):
TATATGAAATGGTTATATGAAGTAGA
Found at i:13354413 original size:30 final size:30
Alignment explanation
Indices: 13354379--13354435 Score: 87
Period size: 30 Copynumber: 1.9 Consensus size: 30
13354369 GCCGCATGAT
13354379 CGTGTGTCACACACCATTGTTTGGCACGAC
1 CGTGTGTCACACACCATTGTTTGGCACGAC
* **
13354409 CGTGTGTTACACACGGTTGTTTGGCAC
1 CGTGTGTCACACACCATTGTTTGGCAC
13354436 AACCATGTAG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.18, C:0.26, G:0.26, T:0.30
Consensus pattern (30 bp):
CGTGTGTCACACACCATTGTTTGGCACGAC
Found at i:13355925 original size:23 final size:23
Alignment explanation
Indices: 13355899--13355950 Score: 68
Period size: 23 Copynumber: 2.3 Consensus size: 23
13355889 AGGCTGAAAA
* *
13355899 TGCTAAAAATCTATTTGTTACAG
1 TGCTAAAAATCTATTTGTTAAAC
* *
13355922 TGCTGAAAATGTATTTGTTAAAC
1 TGCTAAAAATCTATTTGTTAAAC
13355945 TGCTAA
1 TGCTAA
13355951 GAAGGAAGAT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.38
Consensus pattern (23 bp):
TGCTAAAAATCTATTTGTTAAAC
Found at i:13364385 original size:44 final size:44
Alignment explanation
Indices: 13364335--13364423 Score: 169
Period size: 44 Copynumber: 2.0 Consensus size: 44
13364325 ATATATCTGA
*
13364335 CAAGTTCGCTAAATCTGACATCAATATATACATGTAGAAGGTCC
1 CAAGTTCGCTAAATCTGACATCAATATATACATGTAGAAGATCC
13364379 CAAGTTCGCTAAATCTGACATCAATATATACATGTAGAAGATCC
1 CAAGTTCGCTAAATCTGACATCAATATATACATGTAGAAGATCC
13364423 C
1 C
13364424 GAAGCTTAAC
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 44 1.00
ACGTcount: A:0.37, C:0.21, G:0.15, T:0.27
Consensus pattern (44 bp):
CAAGTTCGCTAAATCTGACATCAATATATACATGTAGAAGATCC
Found at i:13368610 original size:21 final size:22
Alignment explanation
Indices: 13368581--13368627 Score: 78
Period size: 21 Copynumber: 2.2 Consensus size: 22
13368571 CAGAAGGAGT
*
13368581 GAGTAGTACTTCGCAGCAGGTG
1 GAGTAGTACTCCGCAGCAGGTG
13368603 GAGT-GTACTCCGCAGCAGGTG
1 GAGTAGTACTCCGCAGCAGGTG
13368624 GAGT
1 GAGT
13368628 TTGAGCAGAG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.21, C:0.19, G:0.38, T:0.21
Consensus pattern (22 bp):
GAGTAGTACTCCGCAGCAGGTG
Found at i:13374001 original size:29 final size:30
Alignment explanation
Indices: 13373946--13374003 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 30
13373936 ATTGCTTTAA
13373946 TATAAATATATATAATTATTATTTAACATT
1 TATAAATATATATAATTATTATTTAACATT
* *
13373976 TATAATTA-ATATAA-TATTTTTATAACAT
1 TATAAATATATATAATTATTATT-TAACAT
13374004 AATATATTTG
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
28 6 0.24
29 12 0.48
30 7 0.28
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (30 bp):
TATAAATATATATAATTATTATTTAACATT
Found at i:13376855 original size:11 final size:13
Alignment explanation
Indices: 13376835--13376866 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
13376825 AATAAATTAA
13376835 TAAAATATCAT-T
1 TAAAATATCATAT
13376847 TAAAA-ATCATAT
1 TAAAATATCATAT
13376859 TAAAATAT
1 TAAAATAT
13376867 TAATAAACTA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 5 0.28
12 11 0.61
13 2 0.11
ACGTcount: A:0.56, C:0.06, G:0.00, T:0.38
Consensus pattern (13 bp):
TAAAATATCATAT
Found at i:13402670 original size:57 final size:57
Alignment explanation
Indices: 13402600--13402715 Score: 214
Period size: 57 Copynumber: 2.0 Consensus size: 57
13402590 AACCACAAGC
*
13402600 TAAAAAGTTAGCAATATCAGCAAACCAAGGGGTATTAAGGACATGATTTACCTTTAG
1 TAAAAAGTTAGCAATATCAGCAAACCAAGGGGTATTAAGAACATGATTTACCTTTAG
*
13402657 TAAAAAGTTAGCAATATCAGCAAACCAAGGGGTATTATGAACATGATTTACCTTTAG
1 TAAAAAGTTAGCAATATCAGCAAACCAAGGGGTATTAAGAACATGATTTACCTTTAG
13402714 TA
1 TA
13402716 TGTGTTCATC
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
57 57 1.00
ACGTcount: A:0.41, C:0.14, G:0.18, T:0.28
Consensus pattern (57 bp):
TAAAAAGTTAGCAATATCAGCAAACCAAGGGGTATTAAGAACATGATTTACCTTTAG
Found at i:13418981 original size:12 final size:13
Alignment explanation
Indices: 13418964--13418995 Score: 57
Period size: 12 Copynumber: 2.5 Consensus size: 13
13418954 TAATTTATAA
13418964 AAAAAATTTAA-T
1 AAAAAATTTAATT
13418976 AAAAAATTTAATT
1 AAAAAATTTAATT
13418989 AAAAAAT
1 AAAAAAT
13418996 AATACTGACC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 11 0.58
13 8 0.42
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (13 bp):
AAAAAATTTAATT
Found at i:13420984 original size:18 final size:20
Alignment explanation
Indices: 13420945--13420987 Score: 63
Period size: 21 Copynumber: 2.2 Consensus size: 20
13420935 GTTGGGAAAA
13420945 TTATCTAATTGAAAATTTAAT
1 TTATCTAATT-AAAATTTAAT
13420966 TTATCTAATT-AAA-TTAAT
1 TTATCTAATTAAAATTTAAT
13420984 TTAT
1 TTAT
13420988 GGATAATATT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 9 0.41
19 3 0.14
21 10 0.45
ACGTcount: A:0.42, C:0.05, G:0.02, T:0.51
Consensus pattern (20 bp):
TTATCTAATTAAAATTTAAT
Found at i:13436513 original size:43 final size:43
Alignment explanation
Indices: 13436465--13436553 Score: 178
Period size: 43 Copynumber: 2.1 Consensus size: 43
13436455 AATGACTGTG
13436465 ATAAATTGCTCGTTTGAGAATGAGCAACCCATGGTCATGTTCC
1 ATAAATTGCTCGTTTGAGAATGAGCAACCCATGGTCATGTTCC
13436508 ATAAATTGCTCGTTTGAGAATGAGCAACCCATGGTCATGTTCC
1 ATAAATTGCTCGTTTGAGAATGAGCAACCCATGGTCATGTTCC
13436551 ATA
1 ATA
13436554 TTTATCAATC
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 46 1.00
ACGTcount: A:0.29, C:0.20, G:0.20, T:0.30
Consensus pattern (43 bp):
ATAAATTGCTCGTTTGAGAATGAGCAACCCATGGTCATGTTCC
Found at i:13450709 original size:27 final size:27
Alignment explanation
Indices: 13450650--13450711 Score: 67
Period size: 27 Copynumber: 2.3 Consensus size: 27
13450640 GACAAGCAAT
13450650 TTTTTTA-ATTTTACTTAATTATAAAA
1 TTTTTTATATTTTACTTAATTATAAAA
*
13450676 TTCTTTTATATTTT-CTT-GTTATTAATAA
1 TT-TTTTATATTTTACTTAATTA-TAA-AA
13450704 TTTTTTAT
1 TTTTTTAT
13450712 TTACAGTTTA
Statistics
Matches: 31, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
26 5 0.16
27 17 0.55
28 9 0.29
ACGTcount: A:0.29, C:0.05, G:0.02, T:0.65
Consensus pattern (27 bp):
TTTTTTATATTTTACTTAATTATAAAA
Found at i:13467483 original size:8 final size:8
Alignment explanation
Indices: 13467470--13467522 Score: 54
Period size: 8 Copynumber: 6.4 Consensus size: 8
13467460 CCGTAAAAAT
13467470 TAAAATAA
1 TAAAATAA
13467478 TAAAATAA
1 TAAAATAA
*
13467486 TAATAT-A
1 TAAAATAA
*
13467493 TCCATAAATAT
1 T--A-AAATAA
13467504 TAAAATAA
1 TAAAATAA
13467512 TAAAATAA
1 TAAAATAA
13467520 TAA
1 TAA
13467523 CTTACTCATC
Statistics
Matches: 37, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
7 2 0.05
8 29 0.78
9 2 0.05
10 3 0.08
11 1 0.03
ACGTcount: A:0.66, C:0.04, G:0.00, T:0.30
Consensus pattern (8 bp):
TAAAATAA
Found at i:13467490 original size:34 final size:34
Alignment explanation
Indices: 13467452--13467522 Score: 124
Period size: 34 Copynumber: 2.1 Consensus size: 34
13467442 AATACGACCT
*
13467452 TAATATATCCGTAAAAATTAAAATAATAAAATAA
1 TAATATATCCATAAAAATTAAAATAATAAAATAA
*
13467486 TAATATATCCATAAATATTAAAATAATAAAATAA
1 TAATATATCCATAAAAATTAAAATAATAAAATAA
13467520 TAA
1 TAA
13467523 CTTACTCATC
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.62, C:0.06, G:0.01, T:0.31
Consensus pattern (34 bp):
TAATATATCCATAAAAATTAAAATAATAAAATAA
Found at i:13472065 original size:22 final size:22
Alignment explanation
Indices: 13472037--13472110 Score: 71
Period size: 22 Copynumber: 3.3 Consensus size: 22
13472027 ACCATAACTG
13472037 AAAGATGCTATGACATCATGAT
1 AAAGATGCTATGACATCATGAT
* *
13472059 AAAGATGAATAAGA-A-CATAGAT
1 AAAGATG-CTATGACATCAT-GAT
**
13472081 GAAAGATGCTATGACATCACCAT
1 -AAAGATGCTATGACATCATGAT
13472104 AAAGATG
1 AAAGATG
13472111 AGTAAATGAT
Statistics
Matches: 41, Mismatches: 6, Indels: 10
0.72 0.11 0.18
Matches are distributed among these distances:
21 3 0.07
22 22 0.54
23 14 0.34
24 2 0.05
ACGTcount: A:0.47, C:0.12, G:0.19, T:0.22
Consensus pattern (22 bp):
AAAGATGCTATGACATCATGAT
Found at i:13472087 original size:45 final size:45
Alignment explanation
Indices: 13472013--13472111 Score: 137
Period size: 45 Copynumber: 2.2 Consensus size: 45
13472003 GCTATACGCC
* * * **
13472013 TAAAAATGAGTAAGACCATAACTGAAAGATGCTATGACATCATGA
1 TAAAGATGAATAAGAACATAACTGAAAGATGCTATGACATCACCA
13472058 TAAAGATGAATAAGAACATAGA-TGAAAGATGCTATGACATCACCA
1 TAAAGATGAATAAGAACATA-ACTGAAAGATGCTATGACATCACCA
13472103 TAAAGATGA
1 TAAAGATGA
13472112 GTAAATGATA
Statistics
Matches: 48, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
45 47 0.98
46 1 0.02
ACGTcount: A:0.48, C:0.12, G:0.18, T:0.21
Consensus pattern (45 bp):
TAAAGATGAATAAGAACATAACTGAAAGATGCTATGACATCACCA
Done.