Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167860.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_13, whole genome shotgun sequence
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: 22724830
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.34
Warning! 82000 characters in sequence are not A, C, G, or T
File 64 of 109
Found at i:12847110 original size:17 final size:17
Alignment explanation
Indices: 12847088--12847252 Score: 72
Period size: 17 Copynumber: 9.7 Consensus size: 17
12847078 AAAGATTCGT
12847088 AAGAATTTCAAATTTGC
1 AAGAATTTCAAATTTGC
* *
12847105 AAGAA-TTGAAGATTTGT
1 AAGAATTTCAA-ATTTGC
*
12847122 AAGAA-TTGAAGATTTGC
1 AAGAATTTCAA-ATTTGC
*** *
12847139 AAG-ATTTGGGATTTGT
1 AAGAATTTCAAATTTGC
*
12847155 AAGAATTTCATATTTG-
1 AAGAATTTCAAATTTGC
* ***
12847171 AAAAATTTTTTATTTGC
1 AAGAATTTCAAATTTGC
* *
12847188 AAGAATTTTCAGATTCGC
1 AAGAA-TTTCAAATTTGC
*
12847206 AAAAACTTTCAAATTTGATC
1 AAGAA-TTTCAAATTTG--C
* * *
12847226 AGGAA-TTCTAATTTGT
1 AAGAATTTCAAATTTGC
12847242 AAG-ATTTCAAA
1 AAGAATTTCAAA
12847253 GGTTCACAAG
Statistics
Matches: 113, Mismatches: 27, Indels: 17
0.72 0.17 0.11
Matches are distributed among these distances:
15 1 0.01
16 33 0.29
17 45 0.40
18 30 0.27
20 4 0.04
ACGTcount: A:0.38, C:0.08, G:0.16, T:0.38
Consensus pattern (17 bp):
AAGAATTTCAAATTTGC
Found at i:12847117 original size:34 final size:34
Alignment explanation
Indices: 12847079--12847170 Score: 116
Period size: 34 Copynumber: 2.7 Consensus size: 34
12847069 TCACAATTCA
*
12847079 AAGATTCGTAAGAATTTCAAATTTGCAAGAATTG
1 AAGATTTGTAAGAATTTCAAATTTGCAAGAATTG
* *
12847113 AAGATTTGTAAGAA-TTGAAGATTTGCAAGATTTG
1 AAGATTTGTAAGAATTTCAA-ATTTGCAAGAATTG
* *
12847147 -GGATTTGTAAGAATTTCATATTTG
1 AAGATTTGTAAGAATTTCAAATTTG
12847171 AAAAATTTTT
Statistics
Matches: 50, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
33 21 0.42
34 29 0.58
ACGTcount: A:0.37, C:0.05, G:0.21, T:0.37
Consensus pattern (34 bp):
AAGATTTGTAAGAATTTCAAATTTGCAAGAATTG
Found at i:12847142 original size:9 final size:8
Alignment explanation
Indices: 12847099--12847146 Score: 51
Period size: 9 Copynumber: 5.6 Consensus size: 8
12847089 AGAATTTCAA
12847099 ATTTGCAAG
1 ATTTG-AAG
*
12847108 AATTGAAG
1 ATTTGAAG
12847116 ATTTGTAAG
1 ATTTG-AAG
*
12847125 AATTGAAG
1 ATTTGAAG
12847133 ATTTGCAAG
1 ATTTG-AAG
12847142 ATTTG
1 ATTTG
12847147 GGATTTGTAA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
8 14 0.42
9 19 0.58
ACGTcount: A:0.38, C:0.04, G:0.23, T:0.35
Consensus pattern (8 bp):
ATTTGAAG
Found at i:12847301 original size:17 final size:17
Alignment explanation
Indices: 12847263--12847295 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
12847253 GGTTCACAAG
*
12847263 ATTTTTAGATTTTCAAA
1 ATTTTAAGATTTTCAAA
12847280 ATTTTAAGATTTTCAA
1 ATTTTAAGATTTTCAA
12847296 CCTTTTGGAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.36, C:0.06, G:0.06, T:0.52
Consensus pattern (17 bp):
ATTTTAAGATTTTCAAA
Found at i:12847398 original size:18 final size:17
Alignment explanation
Indices: 12847352--12847448 Score: 79
Period size: 17 Copynumber: 5.7 Consensus size: 17
12847342 TAAGATTTTT
* * *
12847352 AGATTCGCAAGAATTAA
1 AGATTTGCAAGAACTGA
*
12847369 ATATTTGCAAGAACTCGA
1 AGATTTGCAAGAACT-GA
*
12847387 AGATTTGTAAGAACTGA
1 AGATTTGCAAGAACTGA
** * *
12847404 AGATTCACAAAAACT-C
1 AGATTTGCAAGAACTGA
* *
12847420 AGATTCGCAAGAATTGA
1 AGATTTGCAAGAACTGA
12847437 AGATTTGCAAGA
1 AGATTTGCAAGA
12847449 TTTTACAATT
Statistics
Matches: 62, Mismatches: 16, Indels: 4
0.76 0.20 0.05
Matches are distributed among these distances:
16 12 0.19
17 36 0.58
18 14 0.23
ACGTcount: A:0.43, C:0.13, G:0.19, T:0.25
Consensus pattern (17 bp):
AGATTTGCAAGAACTGA
Found at i:12847476 original size:17 final size:17
Alignment explanation
Indices: 12847395--12847477 Score: 62
Period size: 17 Copynumber: 4.9 Consensus size: 17
12847385 GAAGATTTGT
*
12847395 AAGAACTGAAGATTCAC
1 AAGAATTGAAGATTCAC
* * * *
12847412 AAAAACT-CAGATTCGC
1 AAGAATTGAAGATTCAC
**
12847428 AAGAATTGAAGATTTGC
1 AAGAATTGAAGATTCAC
* *
12847445 AAGATTTTACA-ATTCAC
1 AAGAATTGA-AGATTCAC
12847462 AAGAATTGAAGATTCA
1 AAGAATTGAAGATTCA
12847478 TAAAATTTAA
Statistics
Matches: 50, Mismatches: 13, Indels: 6
0.72 0.19 0.09
Matches are distributed among these distances:
16 13 0.26
17 36 0.72
18 1 0.02
ACGTcount: A:0.45, C:0.14, G:0.16, T:0.25
Consensus pattern (17 bp):
AAGAATTGAAGATTCAC
Found at i:12848865 original size:8 final size:7
Alignment explanation
Indices: 12848863--12848913 Score: 50
Period size: 7 Copynumber: 6.9 Consensus size: 7
12848853 TTTTTTTCAT
12848863 TTTTTTA
1 TTTTTTA
*
12848870 AT-TTTA
1 TTTTTTA
12848876 TTTTTTA
1 TTTTTTA
12848883 TTTTTTCACA
1 TTTTTT---A
12848893 TTTTTTA
1 TTTTTTA
12848900 TTTTTTTA
1 -TTTTTTA
12848908 TTTTTT
1 TTTTTT
12848914 TCACTTTCAT
Statistics
Matches: 37, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
6 5 0.14
7 18 0.49
8 7 0.19
10 7 0.19
ACGTcount: A:0.16, C:0.04, G:0.00, T:0.80
Consensus pattern (7 bp):
TTTTTTA
Found at i:12848886 original size:31 final size:32
Alignment explanation
Indices: 12848844--12848913 Score: 88
Period size: 31 Copynumber: 2.2 Consensus size: 32
12848834 CTTTTATCTC
* **
12848844 ATTTTTCATTTTTTTTCATTTTTT-TAATTTT
1 ATTTTTTATTTTTTCACATTTTTTATAATTTT
**
12848875 ATTTTTTATTTTTTCACATTTTTTATTTTTTT
1 ATTTTTTATTTTTTCACATTTTTTATAATTTT
12848907 ATTTTTT
1 ATTTTTT
12848914 TCACTTTCAT
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
31 21 0.64
32 12 0.36
ACGTcount: A:0.16, C:0.06, G:0.00, T:0.79
Consensus pattern (32 bp):
ATTTTTTATTTTTTCACATTTTTTATAATTTT
Found at i:12848914 original size:8 final size:8
Alignment explanation
Indices: 12848853--12848914 Score: 58
Period size: 8 Copynumber: 7.9 Consensus size: 8
12848843 CATTTTTCAT
12848853 TTTTTTTCA
1 TTTTTTT-A
12848862 TTTTTTTA
1 TTTTTTTA
*
12848870 --ATTTTA
1 TTTTTTTA
12848876 -TTTTTTA
1 TTTTTTTA
*
12848883 TTTTTTCA
1 TTTTTTTA
*
12848891 CATTTTTTA
1 -TTTTTTTA
12848900 TTTTTTTA
1 TTTTTTTA
12848908 TTTTTTT
1 TTTTTTT
12848915 CACTTTCATT
Statistics
Matches: 44, Mismatches: 6, Indels: 7
0.77 0.11 0.12
Matches are distributed among these distances:
6 5 0.11
7 5 0.11
8 21 0.48
9 13 0.30
ACGTcount: A:0.15, C:0.05, G:0.00, T:0.81
Consensus pattern (8 bp):
TTTTTTTA
Found at i:12851713 original size:10 final size:10
Alignment explanation
Indices: 12851700--12851728 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
12851690 GATTTTTCAC
12851700 TCTTTTTTTT
1 TCTTTTTTTT
12851710 TCTTTTTTTT
1 TCTTTTTTTT
12851720 T-TTTTTTTT
1 TCTTTTTTTT
12851729 GTTTTTGCAC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 8 0.42
10 11 0.58
ACGTcount: A:0.00, C:0.07, G:0.00, T:0.93
Consensus pattern (10 bp):
TCTTTTTTTT
Found at i:12852189 original size:16 final size:17
Alignment explanation
Indices: 12852164--12852201 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
12852154 GGTTTTTTGA
*
12852164 AAAATGTCTTCC-ATAG
1 AAAATATCTTCCTATAG
*
12852180 AAAATATCTTCCTTTAG
1 AAAATATCTTCCTATAG
12852197 AAAAT
1 AAAAT
12852202 CAATTCCTCA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 11 0.58
17 8 0.42
ACGTcount: A:0.42, C:0.16, G:0.08, T:0.34
Consensus pattern (17 bp):
AAAATATCTTCCTATAG
Found at i:12853105 original size:2 final size:2
Alignment explanation
Indices: 12853100--12853125 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
12853090 TGTGTGTGTG
12853100 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
12853126 GAGAGAGAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:12853973 original size:30 final size:30
Alignment explanation
Indices: 12853929--12853987 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 30
12853919 TTTTAAAAAA
*
12853929 TTTACATAAAACATTGAAAATTGAAATAAT
1 TTTACATAAAACATTAAAAATTGAAATAAT
* * *
12853959 TTTACGTAAGACATTAAAAATTTAAATAA
1 TTTACATAAAACATTAAAAATTGAAATAA
12853988 CATTTCATAT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.53, C:0.07, G:0.07, T:0.34
Consensus pattern (30 bp):
TTTACATAAAACATTAAAAATTGAAATAAT
Found at i:12862797 original size:18 final size:18
Alignment explanation
Indices: 12862771--12862807 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
12862761 TTCCTTGGAT
*
12862771 AAAAGTTTTGAGAAGGAA
1 AAAAATTTTGAGAAGGAA
*
12862789 AAAAATTTTGAGAGGGAA
1 AAAAATTTTGAGAAGGAA
12862807 A
1 A
12862808 GATGCATGAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.51, C:0.00, G:0.27, T:0.22
Consensus pattern (18 bp):
AAAAATTTTGAGAAGGAA
Found at i:12863128 original size:18 final size:18
Alignment explanation
Indices: 12863105--12863141 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
12863095 ATTTTATATA
12863105 CTTTAAAAAATATAATTT
1 CTTTAAAAAATATAATTT
12863123 CTTTAAAAAATATAATTT
1 CTTTAAAAAATATAATTT
12863141 C
1 C
12863142 ACATATGAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.49, C:0.08, G:0.00, T:0.43
Consensus pattern (18 bp):
CTTTAAAAAATATAATTT
Found at i:12873090 original size:7 final size:7
Alignment explanation
Indices: 12873080--12873104 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
12873070 AAAAATAAAA
12873080 AATTAAT
1 AATTAAT
12873087 AATTAAT
1 AATTAAT
12873094 AATTAAT
1 AATTAAT
12873101 AATT
1 AATT
12873105 TTTTTTCATA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (7 bp):
AATTAAT
Found at i:12881622 original size:59 final size:59
Alignment explanation
Indices: 12881548--12881668 Score: 206
Period size: 59 Copynumber: 2.1 Consensus size: 59
12881538 AAAAAGAAAA
* *
12881548 ATGACATTCAAAATGAAGAGAGTACTAACTTTATTACTATTATTCATTTTGGTTTGTGT
1 ATGACATTCAAAATGAAGAGAGTACTAACTTTATTACTATTATTCATTTTGATTTGCGT
* *
12881607 ATGACATTCAAAATGAAGAGAGTGCTAACTTTATTACTATTCTTCATTTTGATTTGCGT
1 ATGACATTCAAAATGAAGAGAGTACTAACTTTATTACTATTATTCATTTTGATTTGCGT
12881666 ATG
1 ATG
12881669 TATATAGGTG
Statistics
Matches: 58, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
59 58 1.00
ACGTcount: A:0.31, C:0.12, G:0.16, T:0.41
Consensus pattern (59 bp):
ATGACATTCAAAATGAAGAGAGTACTAACTTTATTACTATTATTCATTTTGATTTGCGT
Found at i:12883669 original size:19 final size:19
Alignment explanation
Indices: 12883647--12883683 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
12883637 CAAGAATAGC
12883647 ATTGATATACACGAATAAT
1 ATTGATATACACGAATAAT
*
12883666 ATTGATATATACGAATAA
1 ATTGATATACACGAATAA
12883684 CACTGATATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.49, C:0.08, G:0.11, T:0.32
Consensus pattern (19 bp):
ATTGATATACACGAATAAT
Found at i:12883690 original size:19 final size:19
Alignment explanation
Indices: 12883649--12883692 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
12883639 AGAATAGCAT
* *
12883649 TGATATACACGAATAATAT
1 TGATATACACGAATAACAC
*
12883668 TGATATATACGAATAACAC
1 TGATATACACGAATAACAC
12883687 TGATAT
1 TGATAT
12883693 TCATGAATAG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.45, C:0.11, G:0.11, T:0.32
Consensus pattern (19 bp):
TGATATACACGAATAACAC
Found at i:12887076 original size:16 final size:16
Alignment explanation
Indices: 12887057--12887107 Score: 70
Period size: 16 Copynumber: 3.3 Consensus size: 16
12887047 AGGGCTACAC
*
12887057 GATTTTAGGGTTTTAA
1 GATTTTAGGATTTTAA
12887073 GATTTTAGGATTTTAA
1 GATTTTAGGATTTTAA
*
12887089 GA-CTTAGGATTTT-A
1 GATTTTAGGATTTTAA
12887103 GATTT
1 GATTT
12887108 CATGGTTTCA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
14 3 0.10
15 11 0.35
16 17 0.55
ACGTcount: A:0.27, C:0.02, G:0.22, T:0.49
Consensus pattern (16 bp):
GATTTTAGGATTTTAA
Found at i:12887168 original size:15 final size:15
Alignment explanation
Indices: 12887150--12887267 Score: 71
Period size: 15 Copynumber: 7.8 Consensus size: 15
12887140 AGATTTAACA
12887150 GTTTTAGGGTTTATG
1 GTTTTAGGGTTTATG
* * *
12887165 GTTTTAGGATTTTTA
1 GTTTTAGGGTTTATG
*
12887180 GTTTTAGGGTTTAAG
1 GTTTTAGGGTTTATG
* * * *
12887195 GTTTGAAGATTTAGG
1 GTTTTAGGGTTTATG
** *
12887210 GTTTTGAGTATTTAAG
1 GTTTT-AGGGTTTATG
*
12887226 GTTTT-GGGTTT-TAA
1 GTTTTAGGGTTTAT-G
12887240 GTATTTAGGGTTTA-G
1 GT-TTTAGGGTTTATG
12887255 GTTTTAAGGGTTT
1 GTTTT-AGGGTTT
12887268 GGATAAAATA
Statistics
Matches: 77, Mismatches: 20, Indels: 12
0.71 0.18 0.11
Matches are distributed among these distances:
14 9 0.12
15 50 0.65
16 18 0.23
ACGTcount: A:0.19, C:0.00, G:0.30, T:0.51
Consensus pattern (15 bp):
GTTTTAGGGTTTATG
Found at i:12887170 original size:8 final size:7
Alignment explanation
Indices: 12887150--12887260 Score: 55
Period size: 7 Copynumber: 14.9 Consensus size: 7
12887140 AGATTTAACA
12887150 GTTTTAG
1 GTTTTAG
*
12887157 GGTTTATG
1 GTTTTA-G
12887165 GTTTTAG
1 GTTTTAG
12887172 GATTTTTA-
1 G--TTTTAG
12887180 GTTTTAGG
1 GTTTTA-G
*
12887188 GTTTAAG
1 GTTTTAG
* *
12887195 GTTTGAA
1 GTTTTAG
*
12887202 GATTTAGG
1 GTTTTA-G
12887210 GTTTT-G
1 GTTTTAG
12887216 AGTATTTAAG
1 -GT-TTT-AG
*
12887226 GTTTTGG
1 GTTTTAG
*
12887233 GTTTTAA
1 GTTTTAG
12887240 GTATTTAG
1 GT-TTTAG
*
12887248 GGTTTAG
1 GTTTTAG
12887255 GTTTTA
1 GTTTTA
12887261 AGGGTTTGGA
Statistics
Matches: 78, Mismatches: 15, Indels: 22
0.68 0.13 0.19
Matches are distributed among these distances:
6 6 0.08
7 37 0.47
8 27 0.35
9 7 0.09
10 1 0.01
ACGTcount: A:0.20, C:0.00, G:0.29, T:0.51
Consensus pattern (7 bp):
GTTTTAG
Found at i:12887242 original size:23 final size:22
Alignment explanation
Indices: 12887208--12887262 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
12887198 TGAAGATTTA
* *
12887208 GGGTTTTGAGTATTTAAGGTTTT
1 GGGTTTTAAGTATTT-AGGGTTT
12887231 GGGTTTTAAGTATTTAGGGTTT
1 GGGTTTTAAGTATTTAGGGTTT
*
12887253 AGGTTTTAAG
1 GGGTTTTAAG
12887263 GGTTTGGATA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
22 15 0.52
23 14 0.48
ACGTcount: A:0.20, C:0.00, G:0.31, T:0.49
Consensus pattern (22 bp):
GGGTTTTAAGTATTTAGGGTTT
Found at i:12887344 original size:15 final size:15
Alignment explanation
Indices: 12887326--12887356 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
12887316 TGGAGTAAGC
12887326 TTTTTTTTG-TAATT
1 TTTTTTTTGATAATT
12887340 TTTTTTTTGATAATT
1 TTTTTTTTGATAATT
12887355 TT
1 TT
12887357 ATATTAATAC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.56
15 7 0.44
ACGTcount: A:0.16, C:0.00, G:0.06, T:0.77
Consensus pattern (15 bp):
TTTTTTTTGATAATT
Found at i:12887569 original size:3 final size:3
Alignment explanation
Indices: 12887561--12887616 Score: 112
Period size: 3 Copynumber: 18.7 Consensus size: 3
12887551 TAATTTAACT
12887561 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
12887609 TTA TTA TT
1 TTA TTA TT
12887617 CTCCAATATT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 53 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:12890020 original size:12 final size:12
Alignment explanation
Indices: 12890003--12890027 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
12889993 TCAAAATTTG
12890003 AAAATTTTTTTA
1 AAAATTTTTTTA
12890015 AAAATTTTTTTA
1 AAAATTTTTTTA
12890027 A
1 A
12890028 TTTGAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (12 bp):
AAAATTTTTTTA
Found at i:12890344 original size:35 final size:35
Alignment explanation
Indices: 12890305--12890382 Score: 104
Period size: 35 Copynumber: 2.2 Consensus size: 35
12890295 CGCTTGTTGA
*
12890305 AAAATAAATATAACCGA-GATTGAGCCACAAGTTAG
1 AAAATAAAGATAA-CGAGGATTGAGCCACAAGTTAG
* * *
12890340 AAAATAAGGATAACTAGGATTGAGCTACAAGTTAG
1 AAAATAAAGATAACGAGGATTGAGCCACAAGTTAG
12890375 AAAATAAA
1 AAAATAAA
12890383 AATGACCAAG
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
34 2 0.05
35 35 0.95
ACGTcount: A:0.51, C:0.10, G:0.18, T:0.21
Consensus pattern (35 bp):
AAAATAAAGATAACGAGGATTGAGCCACAAGTTAG
Found at i:12890854 original size:35 final size:35
Alignment explanation
Indices: 12890815--12891107 Score: 132
Period size: 35 Copynumber: 8.4 Consensus size: 35
12890805 AACTAAACCC
*
12890815 TAAGTCAAGAAATAAGAATGATCGGGACTGAACCA
1 TAAGTCAAGAAATAAGAATGATCGGGACTGAATCA
* * * ** * **
12890850 TAAGT--TGAAAAAAGAAATAATCGAAATTGAGCCA
1 TAAGTCAAGAAATAAG-AATGATCGGGACTGAATCA
* * * * * * *
12890884 TAAATTAAAAAATAAAAATGATCAGGACTGAGTCG
1 TAAGTCAAGAAATAAGAATGATCGGGACTGAATCA
* * *
12890919 TAAGTCAAGAAATAAGAATGATTGAGACTGAGTCA
1 TAAGTCAAGAAATAAGAATGATCGGGACTGAATCA
** *
12890954 CGAGTCGAGAAATAA-AGATGATC-GGACTGAATCA
1 TAAGTCAAGAAATAAGA-ATGATCGGGACTGAATCA
* *
12890988 TAAGTCTAGAAATAA-AGATGA-CTGTGACTGAATCA
1 TAAGTCAAGAAATAAGA-ATGATC-GGGACTGAATCA
* * * * ** *
12891023 TGAGTTAGGAAATAAAAATGATCATGA-TTAAGTCA
1 TAAGTCAAGAAATAAGAATGATCGGGACTGAA-TCA
* * * * * * *
12891058 CATGTCAAAAAATAAAAATGATCGGGATTAAATCG
1 TAAGTCAAGAAATAAGAATGATCGGGACTGAATCA
* *
12891093 TAACTCAAAAAATAA
1 TAAGTCAAGAAATAA
12891108 AAACAATCAA
Statistics
Matches: 192, Mismatches: 56, Indels: 20
0.72 0.21 0.07
Matches are distributed among these distances:
33 8 0.04
34 49 0.26
35 125 0.65
36 10 0.05
ACGTcount: A:0.48, C:0.11, G:0.19, T:0.22
Consensus pattern (35 bp):
TAAGTCAAGAAATAAGAATGATCGGGACTGAATCA
Found at i:12890981 original size:69 final size:70
Alignment explanation
Indices: 12890893--12891046 Score: 188
Period size: 69 Copynumber: 2.2 Consensus size: 70
12890883 ATAAATTAAA
* * * *
12890893 AAATAAAAATGATCAGGACTGAGTCGTAAGTCAAGAAAT-AAGAATGATTGAGACTGAGTCACGA
1 AAATAAAAATGATCAGGACTGAATCATAAGTCAAGAAATAAAG-ATGACTGAGACTGAATCACGA
12890957 GTCGA-G
65 GT-GAGG
* * * *
12890963 AAATAAAGATGATC-GGACTGAATCATAAGTCTAGAAATAAAGATGACTGTGACTGAATCATGAG
1 AAATAAAAATGATCAGGACTGAATCATAAGTCAAGAAATAAAGATGACTGAGACTGAATCACGAG
*
12891027 TTAGG
66 TGAGG
12891032 AAATAAAAATGATCA
1 AAATAAAAATGATCA
12891047 TGATTAAGTC
Statistics
Matches: 71, Mismatches: 10, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
68 1 0.01
69 54 0.76
70 16 0.23
ACGTcount: A:0.45, C:0.10, G:0.23, T:0.22
Consensus pattern (70 bp):
AAATAAAAATGATCAGGACTGAATCATAAGTCAAGAAATAAAGATGACTGAGACTGAATCACGAG
TGAGG
Found at i:12892045 original size:81 final size:81
Alignment explanation
Indices: 12891932--12892104 Score: 249
Period size: 81 Copynumber: 2.1 Consensus size: 81
12891922 TTTGAAGGTT
* * * *
12891932 TTATAAATTTTGACATCTATAAATGCTTTTTTAAAAAGAGGAATTGAAACTTTAA-ATTTTAAAA
1 TTATGAATCTTGACATCTATAAATGCTCTTTTAAAAAAAGGAATTGAAACTTTAATA-TTTAAAA
12891996 TATTCTACCTAGAGGAC
65 TATTCTACCTAGAGGAC
* **
12892013 TTATGAATCTTGAGATCTATAAATGCTCTTTTAAAAAAAGGTCTTGAAACTTTAATATTTAAAAT
1 TTATGAATCTTGACATCTATAAATGCTCTTTTAAAAAAAGGAATTGAAACTTTAATATTTAAAAT
* *
12892078 ATTCTGCCTAGAGGAT
66 ATTCTACCTAGAGGAC
12892094 TTATGAATCTT
1 TTATGAATCTT
12892105 TTTCTAAAAT
Statistics
Matches: 82, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
81 81 0.99
82 1 0.01
ACGTcount: A:0.38, C:0.10, G:0.12, T:0.39
Consensus pattern (81 bp):
TTATGAATCTTGACATCTATAAATGCTCTTTTAAAAAAAGGAATTGAAACTTTAATATTTAAAAT
ATTCTACCTAGAGGAC
Found at i:12892459 original size:28 final size:28
Alignment explanation
Indices: 12892380--12892461 Score: 94
Period size: 29 Copynumber: 2.9 Consensus size: 28
12892370 TTTATTAGGC
*
12892380 TTAAAATTTGGGTGTCAGCTAATCTGGGT
1 TTAAAATTT-GGTGTCAGCTAATTTGGGT
* * *
12892409 TTAAAATCTAGGTGCCAACTAATTTGGGT
1 TTAAAAT-TTGGTGTCAGCTAATTTGGGT
12892438 TT-AAATTTGTGTGTCAGCTAATTT
1 TTAAAATTTG-GTGTCAGCTAATTT
12892462 AACCTTAAAA
Statistics
Matches: 44, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
27 2 0.05
28 16 0.36
29 25 0.57
30 1 0.02
ACGTcount: A:0.27, C:0.11, G:0.22, T:0.40
Consensus pattern (28 bp):
TTAAAATTTGGTGTCAGCTAATTTGGGT
Found at i:12892526 original size:28 final size:28
Alignment explanation
Indices: 12892495--12892574 Score: 83
Period size: 28 Copynumber: 2.9 Consensus size: 28
12892485 GAAATAGGGT
*
12892495 TTAAATCTATATGCTAATTAAACTGGAC
1 TTAAATCTATATGCTAACTAAACTGGAC
* *
12892523 TTAAATCTGAGTA--CTAACTAAATTGGGC
1 TTAAATCT-A-TATGCTAACTAAACTGGAC
* *
12892551 TTAAATCTGTATGCTAGCTAAACT
1 TTAAATCTATATGCTAACTAAACT
12892575 AGTTTTAAAT
Statistics
Matches: 42, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
26 2 0.05
28 37 0.88
29 1 0.02
30 2 0.05
ACGTcount: A:0.36, C:0.15, G:0.14, T:0.35
Consensus pattern (28 bp):
TTAAATCTATATGCTAACTAAACTGGAC
Found at i:12902651 original size:57 final size:57
Alignment explanation
Indices: 12902527--12902793 Score: 324
Period size: 57 Copynumber: 4.7 Consensus size: 57
12902517 TTTTCTACAG
* * * * **
12902527 GAAAAATTGATACTTTCAACTTTT-CTCCAAAATATCTTTTGAAACTTTAATTTCGAA
1 GAAAAATTGATACTTTCAACTTTTCCTCAAAAACATTTTTTGAAAATTT-ATTTTTAA
* *
12902584 G-AAAATTGATACTTTTAACTTTTCCTCAAAAACCTTTTTTGAAAATTTATTTTTAA
1 GAAAAATTGATACTTTCAACTTTTCCTCAAAAACATTTTTTGAAAATTTATTTTTAA
* ** *
12902640 GAAAAATTGATACTTTCAATTTTTCCTCAAAAAC-CGTTTTAAAAATTTATTTTTAA
1 GAAAAATTGATACTTTCAACTTTTCCTCAAAAACATTTTTTGAAAATTTATTTTTAA
* * * * * *
12902696 GAAAAATTGATACTTTTAACTTTTTCTCAAAAATATTTTTAGACAGTTTATTTTTAA
1 GAAAAATTGATACTTTCAACTTTTCCTCAAAAACATTTTTTGAAAATTTATTTTTAA
* *
12902753 GAAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTT
1 GAAAAATTGATACTTTCAACTTTTCCTCAAAAACATTTTTT
12902794 TTGGATTTTA
Statistics
Matches: 180, Mismatches: 27, Indels: 6
0.85 0.13 0.03
Matches are distributed among these distances:
56 77 0.43
57 103 0.57
ACGTcount: A:0.37, C:0.13, G:0.06, T:0.44
Consensus pattern (57 bp):
GAAAAATTGATACTTTCAACTTTTCCTCAAAAACATTTTTTGAAAATTTATTTTTAA
Found at i:12902725 original size:113 final size:112
Alignment explanation
Indices: 12902527--12902785 Score: 351
Period size: 113 Copynumber: 2.3 Consensus size: 112
12902517 TTTTCTACAG
* * *
12902527 GAAAAATTGATACTTTCAACTTTT-CTCCAAAATATCTTTTGAAACTTTAATTTCGAAGAAAATT
1 GAAAAATTGATACTTTCAACTTTTCCT-CAAAA-ACCTTTTAAAAATTTAATTTCGAAGAAAATT
* *
12902591 GATACTTTTAACTTTTCCTCAAAAACCTTTTTTGAAAATTTATTTTTAA
64 GATACTTTTAACTTTTCCTCAAAAACATTTTTAGAAAATTTATTTTTAA
* **
12902640 GAAAAATTGATACTTTCAATTTTTCCTCAAAAACCGTTTTAAAAATTT-ATTTTTAAGAAAAATT
1 GAAAAATTGATACTTTCAACTTTTCCTCAAAAACC-TTTTAAAAATTTAATTTCGAAG-AAAATT
* * * *
12902704 GATACTTTTAACTTTTTCTCAAAAATATTTTTAGACAGTTTATTTTTAA
64 GATACTTTTAACTTTTCCTCAAAAACATTTTTAGAAAATTTATTTTTAA
*
12902753 GAAAAATTGATACTTTCAACTTTTCCCCAAAAA
1 GAAAAATTGATACTTTCAACTTTTCCTCAAAAA
12902786 TATTTTTTTT
Statistics
Matches: 129, Mismatches: 14, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
112 9 0.07
113 118 0.91
114 2 0.02
ACGTcount: A:0.38, C:0.14, G:0.06, T:0.42
Consensus pattern (112 bp):
GAAAAATTGATACTTTCAACTTTTCCTCAAAAACCTTTTAAAAATTTAATTTCGAAGAAAATTGA
TACTTTTAACTTTTCCTCAAAAACATTTTTAGAAAATTTATTTTTAA
Found at i:12902808 original size:113 final size:112
Alignment explanation
Indices: 12902527--12902814 Score: 328
Period size: 113 Copynumber: 2.5 Consensus size: 112
12902517 TTTTCTACAG
* * * *
12902527 GAAAAATTGATACTTTCAACTTTTCTCC-AAAATATCTTTTGAAACTTTAATTTCGAAG-AAAAT
1 GAAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTG-AA-TTTTATTT-AAAGAAAAAT
* *
12902590 TGATACTTTTAACTTTTCCTCAAAAACCTTTTTTGAAAATTTATTTTTAA
63 TGATACTTTTAACTTTTCCTCAAAAACATTTTTAGAAAATTTATTTTTAA
* * *** ** * *
12902640 GAAAAATTGATACTTTCAATTTTTCCTCAAAAACCGTTTTAAAAATTTATTTTTAAGAAAAATTG
1 GAAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTGAATTTTA-TTTAAAGAAAAATTG
* * * *
12902705 ATACTTTTAACTTTTTCTCAAAAATATTTTTAGACAGTTTATTTTTAA
65 ATACTTTTAACTTTTCCTCAAAAACATTTTTAGAAAATTTATTTTTAA
*
12902753 GAAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTTTGGATTTTATTTAAAGAAAA
1 GAAAAATTGATACTTTCAACTTTTCCCCAAAAATA--TTTTTTGAATTTTATTTAAAGAAAA
12902815 TAAAATAATA
Statistics
Matches: 142, Mismatches: 28, Indels: 9
0.79 0.16 0.05
Matches are distributed among these distances:
112 6 0.04
113 110 0.77
114 17 0.12
115 9 0.06
ACGTcount: A:0.38, C:0.12, G:0.07, T:0.44
Consensus pattern (112 bp):
GAAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTGAATTTTATTTAAAGAAAAATTGA
TACTTTTAACTTTTCCTCAAAAACATTTTTAGAAAATTTATTTTTAA
Found at i:12902819 original size:5 final size:5
Alignment explanation
Indices: 12902811--12902960 Score: 62
Period size: 5 Copynumber: 29.2 Consensus size: 5
12902801 TTATTTAAAG
* *
12902811 AAAAT AAAAT --AAT AAAAC AAAAT AAAAGT GAAAAT AAAA- AATAAA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAA-T -AAAAT AAAAT AA-AAT
* *
12902856 AAAAT AAAGA- AAAGT AAAACA AAAAT AAAAAT AAAGAT AAAGAT AAAAAT
1 AAAAT AAA-AT AAAAT AAAA-T AAAAT -AAAAT AAA-AT AAA-AT -AAAAT
* * * * **
12902906 AAAAG AATAT TAAAT AAACCT AATCT AATAAT AAAAT -AAAT -AAAT -AAAT
1 AAAAT AAAAT AAAAT AAA-AT AAAAT AA-AAT AAAAT AAAAT AAAAT AAAAT
12902955 AAAAT A
1 AAAAT A
12902961 TAAAAAAAAA
Statistics
Matches: 113, Mismatches: 17, Indels: 30
0.71 0.11 0.19
Matches are distributed among these distances:
3 3 0.03
4 14 0.12
5 59 0.52
6 30 0.27
7 7 0.06
ACGTcount: A:0.73, C:0.03, G:0.05, T:0.19
Consensus pattern (5 bp):
AAAAT
Found at i:12902856 original size:6 final size:6
Alignment explanation
Indices: 12902811--12902909 Score: 71
Period size: 6 Copynumber: 16.5 Consensus size: 6
12902801 TTATTTAAAG
* *
12902811 AAAAT- AAAATA ATAAA-A CAAAATA AAAGTG AAAATAA AAAATA AAAA-A
1 AAAATA AAAATA A-AAATA -AAAATA AAAATA AAAAT-A AAAATA AAAATA
* * * * *
12902859 ATAAAGA AAAGT- AAAACA AAAATA AAAATA AAGATA AAGATA AAAATA
1 A-AAATA AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA
12902907 AAA
1 AAA
12902910 GAATATTAAA
Statistics
Matches: 75, Mismatches: 11, Indels: 15
0.74 0.11 0.15
Matches are distributed among these distances:
5 10 0.13
6 53 0.71
7 12 0.16
ACGTcount: A:0.78, C:0.02, G:0.06, T:0.14
Consensus pattern (6 bp):
AAAATA
Found at i:12902856 original size:12 final size:12
Alignment explanation
Indices: 12902811--12902970 Score: 73
Period size: 12 Copynumber: 12.8 Consensus size: 12
12902801 TTATTTAAAG
12902811 AAAATAAAATAA
1 AAAATAAAATAA
*
12902823 TAAAACAAAAT-A
1 -AAAATAAAATAA
*
12902835 AAAGTGAAAATAA
1 AAAAT-AAAATAA
12902848 AAAATAAAA-AA
1 AAAATAAAATAA
*
12902859 ATAAAGAAAAGTAA
1 A-AAATAAAA-TAA
*
12902873 AACA-AAAAT-A
1 AAAATAAAATAA
12902883 AAAATAAAGAT-A
1 AAAATAAA-ATAA
*
12902895 AAGATAAAAATAA
1 AAAAT-AAAATAA
12902908 AAGAATATTAAATAA
1 AA-AATA--AAATAA
* **
12902923 ACCTAATCTAATAA
1 A--AAATAAAATAA
12902937 TAAAAT-AAATAA
1 -AAAATAAAATAA
12902949 ATAAATAAAATATA
1 A-AAATAAAATA-A
12902963 AAAA-AAAA
1 AAAATAAAA
12902971 ACTGGAACGA
Statistics
Matches: 115, Mismatches: 14, Indels: 37
0.69 0.08 0.22
Matches are distributed among these distances:
10 4 0.03
11 11 0.10
12 43 0.37
13 34 0.30
14 12 0.10
15 8 0.07
16 3 0.03
ACGTcount: A:0.74, C:0.03, G:0.04, T:0.18
Consensus pattern (12 bp):
AAAATAAAATAA
Found at i:12902866 original size:54 final size:53
Alignment explanation
Indices: 12902806--12902914 Score: 127
Period size: 54 Copynumber: 2.0 Consensus size: 53
12902796 GGATTTTATT
*
12902806 TAAAGAAAA-TAAAATAATAAA-ACAAAATAAA-AGTGAAA-ATAAAAAATAAAAAAA
1 TAAAGAAAAGTAAAACAA-AAATA-AAAATAAAGA-T-AAAGAT-AAAAATAAAAAAA
*
12902860 TAAAGAAAAGTAAAACAAAAATAAAAATAAAGATAAAGATAAAAATAAAAGAA
1 TAAAGAAAAGTAAAACAAAAATAAAAATAAAGATAAAGATAAAAATAAAAAAA
12902913 TA
1 TA
12902915 TTAAATAAAC
Statistics
Matches: 49, Mismatches: 2, Indels: 9
0.82 0.03 0.15
Matches are distributed among these distances:
53 17 0.35
54 23 0.47
55 9 0.18
ACGTcount: A:0.76, C:0.02, G:0.07, T:0.15
Consensus pattern (53 bp):
TAAAGAAAAGTAAAACAAAAATAAAAATAAAGATAAAGATAAAAATAAAAAAA
Found at i:12902874 original size:37 final size:35
Alignment explanation
Indices: 12902811--12902890 Score: 90
Period size: 37 Copynumber: 2.2 Consensus size: 35
12902801 TTATTTAAAG
* **
12902811 AAAATAAAATAATAAAACAAAATAAAAGTGAAAATAA
1 AAAATAAAAAAATAAAACAAAATAAAA-CAAAAAT-A
*
12902848 AAAATAAAAAAATAAAGA-AAAGTAAAACAAAAATA
1 AAAATAAAAAAATAAA-ACAAAATAAAACAAAAATA
12902883 AAAATAAA
1 AAAATAAA
12902891 GATAAAGATA
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
35 9 0.24
36 5 0.13
37 23 0.61
38 1 0.03
ACGTcount: A:0.79, C:0.03, G:0.05, T:0.14
Consensus pattern (35 bp):
AAAATAAAAAAATAAAACAAAATAAAACAAAAATA
Found at i:12902879 original size:29 final size:30
Alignment explanation
Indices: 12902807--12902914 Score: 93
Period size: 30 Copynumber: 3.6 Consensus size: 30
12902797 GATTTTATTT
* *
12902807 AAAG-AAAATAAAATAAT-AAAACA-AAATA
1 AAAGTAAAATAAAA-AATAAAAAAATAAAGA
12902835 AAAGTGAAAATAAAAAATAAAAAAATAAAGA
1 AAAGT-AAAATAAAAAATAAAAAAATAAAGA
*
12902866 AAAGTAAAA-CAAAAAT--AAAAATAAAGA
1 AAAGTAAAATAAAAAATAAAAAAATAAAGA
12902893 TAAAGATAAAAATAAAAGAATA
1 -AAAG-T-AAAATAAAA-AATA
12902915 TTAAATAAAC
Statistics
Matches: 66, Mismatches: 4, Indels: 15
0.78 0.05 0.18
Matches are distributed among these distances:
27 11 0.17
28 8 0.12
29 10 0.15
30 22 0.33
31 12 0.18
32 3 0.05
ACGTcount: A:0.77, C:0.02, G:0.07, T:0.14
Consensus pattern (30 bp):
AAAGTAAAATAAAAAATAAAAAAATAAAGA
Found at i:12902919 original size:29 final size:24
Alignment explanation
Indices: 12902847--12902914 Score: 73
Period size: 27 Copynumber: 2.6 Consensus size: 24
12902837 AGTGAAAATA
12902847 AAAAATAAAAAAATAAAGAAAAGT
1 AAAAATAAAAAAATAAAGAAAAGT
*
12902871 AAAACAAAAATAAAAATAAAGATAAAGAT
1 -AAA-AATAA-AAAAATAAAGA-AAAG-T
*
12902900 AAAAATAAAAGAATA
1 AAAAATAAAAAAATA
12902915 TTAAATAAAC
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
25 3 0.08
26 10 0.28
27 15 0.42
28 7 0.19
29 1 0.03
ACGTcount: A:0.78, C:0.01, G:0.07, T:0.13
Consensus pattern (24 bp):
AAAAATAAAAAAATAAAGAAAAGT
Found at i:12903531 original size:13 final size:13
Alignment explanation
Indices: 12903492--12903521 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
12903482 AAAATTTTTC
12903492 AAAAATTTCCAAA
1 AAAAATTTCCAAA
*
12903505 AAAAATTTGCAAA
1 AAAAATTTCCAAA
12903518 AAAA
1 AAAA
12903522 TCTTCAAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.67, C:0.10, G:0.03, T:0.20
Consensus pattern (13 bp):
AAAAATTTCCAAA
Found at i:12903836 original size:12 final size:13
Alignment explanation
Indices: 12903801--12903828 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
12903791 ATAAATCAAA
12903801 AAATAAAAATATT
1 AAATAAAAATATT
12903814 AAATAAAAATATT
1 AAATAAAAATATT
12903827 AA
1 AA
12903829 TGAAAATAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (13 bp):
AAATAAAAATATT
Found at i:12904034 original size:21 final size:21
Alignment explanation
Indices: 12903998--12904056 Score: 61
Period size: 21 Copynumber: 2.9 Consensus size: 21
12903988 ACATAAGATA
12903998 AAAATA-AAAGAA-AAAATATAT
1 AAAATACAAA-AATAAAA-ATAT
* *
12904019 AAAA-ACAATAATAAAAATGT
1 AAAATACAAAAATAAAAATAT
12904039 AAAATACAAAAATAAAAA
1 AAAATACAAAAATAAAAA
12904057 AAAAAGAAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
20 10 0.31
21 22 0.69
ACGTcount: A:0.76, C:0.03, G:0.03, T:0.17
Consensus pattern (21 bp):
AAAATACAAAAATAAAAATAT
Found at i:12904280 original size:42 final size:41
Alignment explanation
Indices: 12904217--12904426 Score: 233
Period size: 41 Copynumber: 5.1 Consensus size: 41
12904207 TTAATCAAAA
** *
12904217 CTCCTCTAAGTAGAGGCTCAACGACTTTGGAAAAATAAATAG
1 CTCCTCTAAACAGAGGCTCAACGACTTT-GAAAAATAAATTG
* * *
12904259 CTCCTCTAATCAGAGGTTCAACGACTTTTGAAAAGTAAATTG
1 CTCCTCTAAACAGAGGCTCAACGAC-TTTGAAAAATAAATTG
* * * *
12904301 CTCCTCTAAACAGAGGCACCACGACGTTGAAAAATAAATTA
1 CTCCTCTAAACAGAGGCTCAACGACTTTGAAAAATAAATTG
* * *
12904342 CTCCTCTAAACAGAGGCACTACGACTTTGAAAAGTAAATTG
1 CTCCTCTAAACAGAGGCTCAACGACTTTGAAAAATAAATTG
* * * *
12904383 CTCCTATAAACAAAGGTATC-ACGACTTTGAAAATTAAATTG
1 CTCCTCTAAACAGAGG-CTCAACGACTTTGAAAAATAAATTG
12904424 CTC
1 CTC
12904427 ACTTTGGAAA
Statistics
Matches: 145, Mismatches: 21, Indels: 5
0.85 0.12 0.03
Matches are distributed among these distances:
41 87 0.60
42 55 0.38
43 3 0.02
ACGTcount: A:0.38, C:0.21, G:0.16, T:0.26
Consensus pattern (41 bp):
CTCCTCTAAACAGAGGCTCAACGACTTTGAAAAATAAATTG
Found at i:12904430 original size:21 final size:21
Alignment explanation
Indices: 12904406--12904448 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
12904396 AGGTATCACG
12904406 ACTTTGAAAATTAAATTGCTC
1 ACTTTGAAAATTAAATTGCTC
*
12904427 ACTTTGGAAATTAAATTGCTC
1 ACTTTGAAAATTAAATTGCTC
12904448 A
1 A
12904449 TCTAAACAGA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.37, C:0.14, G:0.12, T:0.37
Consensus pattern (21 bp):
ACTTTGAAAATTAAATTGCTC
Found at i:12904468 original size:62 final size:62
Alignment explanation
Indices: 12904365--12904488 Score: 185
Period size: 62 Copynumber: 2.0 Consensus size: 62
12904355 AGGCACTACG
* * *
12904365 ACTTTGAAAAGTAAATTGCTCCTATAAACAAAGGTATCACGACTTTGAAAATTAAATTGCTC
1 ACTTTGAAAAGTAAATTGCTCATATAAACAAAGGCACCACGACTTTGAAAATTAAATTGCTC
* * * *
12904427 ACTTTGGAAATTAAATTGCTCATCTAAACAGAGGCACCACGACTTTGAAAATTAAATTGCTC
1 ACTTTGAAAAGTAAATTGCTCATATAAACAAAGGCACCACGACTTTGAAAATTAAATTGCTC
12904489 CTCTAAACAG
Statistics
Matches: 55, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
62 55 1.00
ACGTcount: A:0.39, C:0.18, G:0.14, T:0.30
Consensus pattern (62 bp):
ACTTTGAAAAGTAAATTGCTCATATAAACAAAGGCACCACGACTTTGAAAATTAAATTGCTC
Found at i:12904514 original size:103 final size:103
Alignment explanation
Indices: 12904335--12904529 Score: 309
Period size: 103 Copynumber: 1.9 Consensus size: 103
12904325 CGTTGAAAAA
* * *
12904335 TAAATTACTCCTCTAAACAGAGGCACTACGACTTTGAAAAGTAAATTGCTCCTATAAACAAAGGT
1 TAAATTACTCATCTAAACAGAGGCACCACGACTTTGAAAAGTAAATTGCTCCTATAAACAAAGGC
* *
12904400 ATCACGACTTTGAAAATTAAATTGCTCACTTTGGAAAT
66 ACCACGACTTTGAAAAGTAAATTGCTCACTTTGGAAAT
* * * *
12904438 TAAATTGCTCATCTAAACAGAGGCACCACGACTTTGAAAATTAAATTGCTCCTCTAAACAGAGGC
1 TAAATTACTCATCTAAACAGAGGCACCACGACTTTGAAAAGTAAATTGCTCCTATAAACAAAGGC
12904503 ACCACGACTTTGAAAAGTAAATTGCTC
66 ACCACGACTTTGAAAAGTAAATTGCTC
12904530 CTTGACAATC
Statistics
Matches: 83, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
103 83 1.00
ACGTcount: A:0.38, C:0.21, G:0.14, T:0.27
Consensus pattern (103 bp):
TAAATTACTCATCTAAACAGAGGCACCACGACTTTGAAAAGTAAATTGCTCCTATAAACAAAGGC
ACCACGACTTTGAAAAGTAAATTGCTCACTTTGGAAAT
Found at i:12904530 original size:41 final size:41
Alignment explanation
Indices: 12904427--12904531 Score: 183
Period size: 41 Copynumber: 2.6 Consensus size: 41
12904417 TAAATTGCTC
* *
12904427 ACTTTGGAAATTAAATTGCTCATCTAAACAGAGGCACCACG
1 ACTTTGAAAATTAAATTGCTCCTCTAAACAGAGGCACCACG
12904468 ACTTTGAAAATTAAATTGCTCCTCTAAACAGAGGCACCACG
1 ACTTTGAAAATTAAATTGCTCCTCTAAACAGAGGCACCACG
*
12904509 ACTTTGAAAAGTAAATTGCTCCT
1 ACTTTGAAAATTAAATTGCTCCT
12904532 TGACAATCAT
Statistics
Matches: 61, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 61 1.00
ACGTcount: A:0.36, C:0.22, G:0.15, T:0.27
Consensus pattern (41 bp):
ACTTTGAAAATTAAATTGCTCCTCTAAACAGAGGCACCACG
Found at i:12905542 original size:7 final size:8
Alignment explanation
Indices: 12905530--12905558 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
12905520 TCATTCACTT
12905530 TTTTTTC-
1 TTTTTTCA
12905537 TTTTTTCA
1 TTTTTTCA
12905545 TTTTTTCA
1 TTTTTTCA
12905553 TTTTTT
1 TTTTTT
12905559 TTCTTCAAGC
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
7 7 0.33
8 14 0.67
ACGTcount: A:0.07, C:0.10, G:0.00, T:0.83
Consensus pattern (8 bp):
TTTTTTCA
Found at i:12912477 original size:10 final size:10
Alignment explanation
Indices: 12912462--12912503 Score: 50
Period size: 10 Copynumber: 4.2 Consensus size: 10
12912452 ACTTTTCTAG
12912462 TTTCTTTATT
1 TTTCTTTATT
12912472 TTTCTTTATT
1 TTTCTTTATT
* *
12912482 TTTGTTCATTT
1 TTTCTTTA-TT
12912493 TTTCTTT-TT
1 TTTCTTTATT
12912502 TT
1 TT
12912504 GCACATCTTT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
9 4 0.15
10 16 0.59
11 7 0.26
ACGTcount: A:0.07, C:0.10, G:0.02, T:0.81
Consensus pattern (10 bp):
TTTCTTTATT
Found at i:12912859 original size:17 final size:17
Alignment explanation
Indices: 12912839--12912877 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
12912829 GTCCCTTCAA
* *
12912839 TTTTTTTTTTCTTTTTC
1 TTTTTTCTTTCATTTTC
12912856 TTTTTTCTTTCATTTTC
1 TTTTTTCTTTCATTTTC
12912873 TTTTT
1 TTTTT
12912878 CATTTTTGAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.03, C:0.13, G:0.00, T:0.85
Consensus pattern (17 bp):
TTTTTTCTTTCATTTTC
Found at i:12912883 original size:7 final size:6
Alignment explanation
Indices: 12912839--12912884 Score: 51
Period size: 6 Copynumber: 7.8 Consensus size: 6
12912829 GTCCCTTCAA
* *
12912839 TTTTT- TTTTTC TTTTTC TTTTT- TCTTTC ATTTTC TTTTTC ATTTTT
1 TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC -TTTTT
12912885 GATTTTGCAT
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
5 9 0.26
6 20 0.59
7 5 0.15
ACGTcount: A:0.04, C:0.13, G:0.00, T:0.83
Consensus pattern (6 bp):
TTTTTC
Found at i:12912884 original size:13 final size:13
Alignment explanation
Indices: 12912844--12912898 Score: 53
Period size: 12 Copynumber: 4.4 Consensus size: 13
12912834 TTCAATTTTT
12912844 TTTTTCTTTTTC-
1 TTTTTCTTTTTCA
*
12912856 TTTTT-TCTTTCA
1 TTTTTCTTTTTCA
12912868 -TTTTCTTTTTCA
1 TTTTTCTTTTTCA
* *
12912880 TTTTTGATTTTGCA
1 TTTTT-CTTTTTCA
12912894 TTTTT
1 TTTTT
12912899 TTATCATTTT
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
11 9 0.26
12 11 0.31
13 4 0.11
14 11 0.31
ACGTcount: A:0.07, C:0.13, G:0.04, T:0.76
Consensus pattern (13 bp):
TTTTTCTTTTTCA
Found at i:12915569 original size:15 final size:15
Alignment explanation
Indices: 12915528--12915574 Score: 53
Period size: 15 Copynumber: 3.1 Consensus size: 15
12915518 AAATTGATTT
*
12915528 TTATATATTTCAAATA
1 TTAT-TATTTAAAATA
12915544 -TATT-TTATAAAATA
1 TTATTATT-TAAAATA
12915558 TTATTATTTAAAATA
1 TTATTATTTAAAATA
12915573 TT
1 TT
12915575 TGTTAATTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 7
0.77 0.03 0.20
Matches are distributed among these distances:
13 2 0.07
14 7 0.26
15 16 0.59
16 2 0.07
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (15 bp):
TTATTATTTAAAATA
Found at i:12915715 original size:30 final size:30
Alignment explanation
Indices: 12915679--12915743 Score: 76
Period size: 30 Copynumber: 2.1 Consensus size: 30
12915669 ATAATTTTGT
* *
12915679 TAAAATTAGATATTCATTTTAAAAAATTAAA
1 TAAATTTAGATATT-AGTTTAAAAAATTAAA
** *
12915710 TAAATTTTTATATTAGTTTAAGAAATTAAA
1 TAAATTTAGATATTAGTTTAAAAAATTAAA
12915740 TAAA
1 TAAA
12915744 AATTCTATAT
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
30 18 0.62
31 11 0.38
ACGTcount: A:0.52, C:0.02, G:0.05, T:0.42
Consensus pattern (30 bp):
TAAATTTAGATATTAGTTTAAAAAATTAAA
Found at i:12915753 original size:31 final size:30
Alignment explanation
Indices: 12915696--12915753 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
12915686 AGATATTCAT
* *
12915696 TTTAAAAAATTAAATAAATTTTTATATTAG
1 TTTAAAAAATTAAATAAAATTCTATATTAG
*
12915726 TTTAAGAAATTAAATAAAAATTCTATAT
1 TTTAAAAAATTAAAT-AAAATTCTATAT
12915754 CATGTTAAAG
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
30 14 0.58
31 10 0.42
ACGTcount: A:0.52, C:0.02, G:0.03, T:0.43
Consensus pattern (30 bp):
TTTAAAAAATTAAATAAAATTCTATATTAG
Found at i:12918744 original size:26 final size:26
Alignment explanation
Indices: 12918693--12918754 Score: 81
Period size: 27 Copynumber: 2.3 Consensus size: 26
12918683 TTTGGGATAA
*
12918693 TTTTAAAGAAATTTTTCACTTAAAAAT
1 TTTTAAA-AAATTTATCACTTAAAAAT
*
12918720 TTCTTAAAAAATTTATCA-TTTAAAAT
1 TT-TTAAAAAATTTATCACTTAAAAAT
12918746 TTTTAAAAA
1 TTTTAAAAA
12918755 TCTCATCCTT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
25 7 0.22
26 9 0.28
27 11 0.34
28 5 0.16
ACGTcount: A:0.47, C:0.06, G:0.02, T:0.45
Consensus pattern (26 bp):
TTTTAAAAAATTTATCACTTAAAAAT
Found at i:12918811 original size:8 final size:8
Alignment explanation
Indices: 12918794--12918831 Score: 51
Period size: 9 Copynumber: 4.6 Consensus size: 8
12918784 TCAATCAAAA
12918794 TTTTTA-T
1 TTTTTATT
12918801 TTTTTATTT
1 TTTTTA-TT
12918810 TTTTTATT
1 TTTTTATT
12918818 TTTTTAATT
1 TTTTT-ATT
12918827 TTTTT
1 TTTTT
12918832 GATTGAAAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
7 6 0.21
8 7 0.25
9 15 0.54
ACGTcount: A:0.13, C:0.00, G:0.00, T:0.87
Consensus pattern (8 bp):
TTTTTATT
Found at i:12918814 original size:9 final size:9
Alignment explanation
Indices: 12918800--12918831 Score: 55
Period size: 9 Copynumber: 3.6 Consensus size: 9
12918790 AAAATTTTTA
12918800 TTTTTTATT
1 TTTTTTATT
12918809 TTTTTTATT
1 TTTTTTATT
*
12918818 TTTTTAATT
1 TTTTTTATT
12918827 TTTTT
1 TTTTT
12918832 GATTGAAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (9 bp):
TTTTTTATT
Found at i:12918815 original size:16 final size:18
Alignment explanation
Indices: 12918794--12918831 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
12918784 TCAATCAAAA
12918794 TTTTTA-TTTTTT-ATTT
1 TTTTTATTTTTTTAATTT
12918810 TTTTTATTTTTTTAATTT
1 TTTTTATTTTTTTAATTT
12918828 TTTT
1 TTTT
12918832 GATTGAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 6 0.30
17 6 0.30
18 8 0.40
ACGTcount: A:0.13, C:0.00, G:0.00, T:0.87
Consensus pattern (18 bp):
TTTTTATTTTTTTAATTT
Found at i:12918937 original size:24 final size:24
Alignment explanation
Indices: 12918910--12918967 Score: 57
Period size: 24 Copynumber: 2.4 Consensus size: 24
12918900 TTTTTTAAAA
12918910 AAAAATTTCACCTA-GGAAATTTAT
1 AAAAATTTCA-CTATGGAAATTTAT
* * *
12918934 AAAAGTTT-ACTATTTGAAATTTCT
1 AAAAATTTCACTA-TGGAAATTTAT
12918958 AAAAATTTCA
1 AAAAATTTCA
12918968 TTATTGGATA
Statistics
Matches: 27, Mismatches: 4, Indels: 5
0.75 0.11 0.14
Matches are distributed among these distances:
22 3 0.11
23 1 0.04
24 22 0.81
25 1 0.04
ACGTcount: A:0.45, C:0.10, G:0.07, T:0.38
Consensus pattern (24 bp):
AAAAATTTCACTATGGAAATTTAT
Found at i:12919377 original size:21 final size:20
Alignment explanation
Indices: 12919348--12919386 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
12919338 TTTCCTTAGA
12919348 TTTCACTTTCTTTCTCTCTCT
1 TTTCACTTTCTTT-TCTCTCT
*
12919369 TTTCCCTTTCTTTTCTCT
1 TTTCACTTTCTTTTCTCT
12919387 TCCTCTCTCT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.03, C:0.33, G:0.00, T:0.64
Consensus pattern (20 bp):
TTTCACTTTCTTTTCTCTCT
Found at i:12920859 original size:11 final size:11
Alignment explanation
Indices: 12920845--12920874 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
12920835 TTCAAAATTT
12920845 TATATATTTTA
1 TATATATTTTA
12920856 TATATATTTTA
1 TATATATTTTA
*
12920867 TAAATATT
1 TATATATT
12920875 AAATTTAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (11 bp):
TATATATTTTA
Found at i:12921000 original size:20 final size:19
Alignment explanation
Indices: 12920955--12921020 Score: 62
Period size: 18 Copynumber: 3.4 Consensus size: 19
12920945 GAAAATAGTT
*
12920955 TTTTAAAAATTAAAATT-A
1 TTTTAAAAATTCAAATTCA
** *
12920973 AGTTAAAAATTCAAATTCTT
1 TTTTAAAAATTCAAATTC-A
*
12920993 TTTTAAAAAATTCAATTTCA
1 TTTT-AAAAATTCAAATTCA
12921013 TTTTAAAA
1 TTTTAAAA
12921021 CAAAAAATTT
Statistics
Matches: 37, Mismatches: 8, Indels: 5
0.74 0.16 0.10
Matches are distributed among these distances:
18 14 0.38
19 4 0.11
20 6 0.16
21 13 0.35
ACGTcount: A:0.48, C:0.06, G:0.02, T:0.44
Consensus pattern (19 bp):
TTTTAAAAATTCAAATTCA
Found at i:12921003 original size:21 final size:20
Alignment explanation
Indices: 12920977--12921020 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 20
12920967 AAATTAAGTT
*
12920977 AAAAATTCAAATTCTTTTTTA
1 AAAAATTCAAATTC-ATTTTA
*
12920998 AAAAATTCAATTTCATTTTA
1 AAAAATTCAAATTCATTTTA
12921018 AAA
1 AAA
12921021 CAAAAAATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 8 0.38
21 13 0.62
ACGTcount: A:0.48, C:0.09, G:0.00, T:0.43
Consensus pattern (20 bp):
AAAAATTCAAATTCATTTTA
Found at i:12921386 original size:19 final size:19
Alignment explanation
Indices: 12921349--12921389 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
12921339 AATAATTTTG
* **
12921349 TTAAAATTACATATCATTT
1 TTAAAATTAAATAAAATTT
12921368 TTAAAATTAAATAAAATTT
1 TTAAAATTAAATAAAATTT
12921387 TTA
1 TTA
12921390 TATCAGTTTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (19 bp):
TTAAAATTAAATAAAATTT
Found at i:12921423 original size:31 final size:31
Alignment explanation
Indices: 12921370--12921433 Score: 78
Period size: 31 Copynumber: 2.1 Consensus size: 31
12921360 TATCATTTTT
* *
12921370 AAAATTAAATAAAATTTTTATATCA-GTTTAA
1 AAAATTAAATAAAATCTCTATATCATG-TTAA
12921401 AAAATTAAATAAGAA-CTCTATATCATGTTAA
1 AAAATTAAATAA-AATCTCTATATCATGTTAA
12921432 AA
1 AA
12921434 TATATGTAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
31 26 0.90
32 3 0.10
ACGTcount: A:0.53, C:0.06, G:0.05, T:0.36
Consensus pattern (31 bp):
AAAATTAAATAAAATCTCTATATCATGTTAA
Found at i:12921569 original size:14 final size:14
Alignment explanation
Indices: 12921552--12921582 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
12921542 ATTTTTTCTT
12921552 TTTTATAAAACATA
1 TTTTATAAAACATA
*
12921566 TTTTATAAAATATA
1 TTTTATAAAACATA
12921580 TTT
1 TTT
12921583 AAAAAGAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (14 bp):
TTTTATAAAACATA
Found at i:12925433 original size:5 final size:5
Alignment explanation
Indices: 12925423--12925447 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
12925413 CAAAAATTAG
12925423 AAAAT AAAAT AAAAT AAAAT AAAAT
1 AAAAT AAAAT AAAAT AAAAT AAAAT
12925448 TTTTTATAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
AAAAT
Found at i:12927482 original size:9 final size:9
Alignment explanation
Indices: 12927468--12927507 Score: 53
Period size: 9 Copynumber: 4.3 Consensus size: 9
12927458 TTCTTTATCA
12927468 TTTTTTTAT
1 TTTTTTTAT
12927477 TTTTTTTCAT
1 TTTTTTT-AT
*
12927487 TTCTTTTAT
1 TTTTTTTAT
*
12927496 TTTTTTCAT
1 TTTTTTTAT
12927505 TTT
1 TTT
12927508 AAAATTTCTT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
9 19 0.70
10 8 0.30
ACGTcount: A:0.10, C:0.07, G:0.00, T:0.82
Consensus pattern (9 bp):
TTTTTTTAT
Found at i:12927493 original size:11 final size:10
Alignment explanation
Indices: 12927468--12927507 Score: 50
Period size: 10 Copynumber: 4.3 Consensus size: 10
12927458 TTCTTTATCA
12927468 TTTTTTT-AT
1 TTTTTTTCAT
12927477 TTTTTTTCAT
1 TTTTTTTCAT
*
12927487 TTCTTTT-A-
1 TTTTTTTCAT
12927495 TTTTTTTCAT
1 TTTTTTTCAT
12927505 TTT
1 TTT
12927508 AAAATTTCTT
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
8 6 0.23
9 9 0.35
10 11 0.42
ACGTcount: A:0.10, C:0.07, G:0.00, T:0.82
Consensus pattern (10 bp):
TTTTTTTCAT
Found at i:12927495 original size:19 final size:17
Alignment explanation
Indices: 12927465--12927507 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 17
12927455 TTCTTCTTTA
12927465 TCATTTTTTTATTTTTTT
1 TCATTTTTTTA-TTTTTT
12927483 TCATTTCTTTTATTTTTT
1 TCATTT-TTTTATTTTTT
12927501 TCATTTT
1 TCATTTT
12927508 AAAATTTCTT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
17 1 0.04
18 18 0.75
19 5 0.21
ACGTcount: A:0.12, C:0.09, G:0.00, T:0.79
Consensus pattern (17 bp):
TCATTTTTTTATTTTTT
Found at i:12928225 original size:36 final size:35
Alignment explanation
Indices: 12928185--12928253 Score: 120
Period size: 36 Copynumber: 1.9 Consensus size: 35
12928175 TCAATATATA
*
12928185 TTATTTATTAATTTATTATATAATAATAATAATTGT
1 TTATTTATTAAGTTATTATATAATAATAA-AATTGT
12928221 TTATTTATTAAGTTATTATATAATAATAAAATT
1 TTATTTATTAAGTTATTATATAATAATAAAATT
12928254 TATTATATTA
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
35 4 0.12
36 28 0.88
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (35 bp):
TTATTTATTAAGTTATTATATAATAATAAAATTGT
Found at i:12928249 original size:33 final size:35
Alignment explanation
Indices: 12928185--12928266 Score: 98
Period size: 33 Copynumber: 2.4 Consensus size: 35
12928175 TCAATATATA
* **
12928185 TTATTTATTAATTTATTATATAATAATAATAATTGT
1 TTATTTATTAAGTTATTATATAATAATAATAA-AAT
12928221 TTATTTATTAAGTTA-T-TAT-ATAATAATAAAAT
1 TTATTTATTAAGTTATTATATAATAATAATAAAAT
12928253 TTATTATATTAAGT
1 TTATT-TATTAAGT
12928267 CAATAAATAA
Statistics
Matches: 42, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
32 6 0.14
33 18 0.43
34 3 0.07
35 1 0.02
36 14 0.33
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.54
Consensus pattern (35 bp):
TTATTTATTAAGTTATTATATAATAATAATAAAAT
Found at i:12928277 original size:33 final size:33
Alignment explanation
Indices: 12928206--12928277 Score: 83
Period size: 33 Copynumber: 2.2 Consensus size: 33
12928196 TTTATTATAT
** * *
12928206 AATAATAATAATTGTTTATTTATTAAGTTATTA
1 AATAATAATAATAATTTATTTATTAAGTCAATA
*
12928239 TATAATAATAA-AATTTATTATATTAAGTCAATA
1 AATAATAATAATAATTTATT-TATTAAGTCAATA
12928272 AATAAT
1 AATAAT
12928278 TTCAAAATTT
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
32 6 0.19
33 26 0.81
ACGTcount: A:0.49, C:0.01, G:0.04, T:0.46
Consensus pattern (33 bp):
AATAATAATAATAATTTATTTATTAAGTCAATA
Found at i:12932459 original size:11 final size:11
Alignment explanation
Indices: 12932443--12932467 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
12932433 ATATATCTTC
12932443 TAATAGTTTGA
1 TAATAGTTTGA
12932454 TAATAGTTTGA
1 TAATAGTTTGA
12932465 TAA
1 TAA
12932468 GATTAAAACT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.40, C:0.00, G:0.16, T:0.44
Consensus pattern (11 bp):
TAATAGTTTGA
Found at i:12933076 original size:19 final size:21
Alignment explanation
Indices: 12933041--12933091 Score: 54
Period size: 20 Copynumber: 2.5 Consensus size: 21
12933031 AAATAGTTTT
12933041 TAAAACCCT-AATGCAG-TAAC
1 TAAAA-CCTAAATGCAGTTAAC
*
12933061 TAAAACCTAAAT-CAGTTTAC
1 TAAAACCTAAATGCAGTTAAC
12933081 TAAAACACTAA
1 TAAAAC-CTAA
12933092 GCTAAACTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
19 6 0.22
20 17 0.63
21 4 0.15
ACGTcount: A:0.49, C:0.22, G:0.06, T:0.24
Consensus pattern (21 bp):
TAAAACCTAAATGCAGTTAAC
Found at i:12933242 original size:17 final size:18
Alignment explanation
Indices: 12933216--12933249 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
12933206 AAAAATTAAC
*
12933216 TGCAATAAAATATTAAAG
1 TGCAATAAAATAGTAAAG
12933234 TGCAA-AAAATAGTAAA
1 TGCAATAAAATAGTAAA
12933250 TTAAAGCCTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.59, C:0.06, G:0.12, T:0.24
Consensus pattern (18 bp):
TGCAATAAAATAGTAAAG
Found at i:12933533 original size:20 final size:20
Alignment explanation
Indices: 12933496--12933534 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
12933486 GTAAACTGTT
**
12933496 TAAAGAAAACTGTAAAGAAA
1 TAAAGAAAACCCTAAAGAAA
*
12933516 TAAAGAAAACCCTGAAGAA
1 TAAAGAAAACCCTAAAGAA
12933535 CACTTAAAGA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.62, C:0.10, G:0.15, T:0.13
Consensus pattern (20 bp):
TAAAGAAAACCCTAAAGAAA
Found at i:12934162 original size:22 final size:22
Alignment explanation
Indices: 12934113--12934180 Score: 73
Period size: 22 Copynumber: 3.1 Consensus size: 22
12934103 CAAGGTCCTA
* **
12934113 AATTTGAAATCCAAAAATTCGT
1 AATTTGAAATTCAAAAATTCAC
* *
12934135 ACTTTGAAATTCAAATATTCAC
1 AATTTGAAATTCAAAAATTCAC
* *
12934157 AATTTGAAACTAAAAAATTCAC
1 AATTTGAAATTCAAAAATTCAC
12934179 AA
1 AA
12934181 AAACTTTGAA
Statistics
Matches: 37, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
22 37 1.00
ACGTcount: A:0.49, C:0.15, G:0.06, T:0.31
Consensus pattern (22 bp):
AATTTGAAATTCAAAAATTCAC
Found at i:12934463 original size:58 final size:55
Alignment explanation
Indices: 12934381--12934490 Score: 125
Period size: 58 Copynumber: 1.9 Consensus size: 55
12934371 GATTAGCGAA
* *
12934381 AATTTAAAGATTTGCAAGAATTCAAATATTCTCA-AAAT-AAATTTCAAAGTTTTAC
1 AATTTAAAGATTTGAAAGAATTCAAA-ATT-TCACAAATGAAATTCCAAAGTTTTAC
* *
12934436 AATTGTAAAGATTTGTAAATAATTTCAAAATTTTACAAATGAAATTCCAAAGTTT
1 AATT-TAAAGATTTG-AAAGAA-TTCAAAATTTCACAAATGAAATTCCAAAGTTT
12934491 CACTTTCAAA
Statistics
Matches: 46, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
55 4 0.09
56 12 0.26
57 11 0.24
58 19 0.41
ACGTcount: A:0.45, C:0.09, G:0.08, T:0.37
Consensus pattern (55 bp):
AATTTAAAGATTTGAAAGAATTCAAAATTTCACAAATGAAATTCCAAAGTTTTAC
Found at i:12934612 original size:91 final size:91
Alignment explanation
Indices: 12934499--12934667 Score: 245
Period size: 91 Copynumber: 1.9 Consensus size: 91
12934489 TTCACTTTCA
* *
12934499 AAAAATTTTTAGAAATTCACATCTAAAATTTC-AAGATTGACATTCAAGAAATTTTA-AAGATTC
1 AAAAATTTTTAGAAATTCACATCTAAAA-TTCAAAGATTCACATTCAAG-AATATTAGAA-ATTC
*
12934562 ACATCCAAATTTTCAAATATTCGCATTTG
63 ACATCCAAAATTTCAAATATTCGCATTTG
* *
12934591 AAAAA-TTTTAGAAATTTACATCTAAAATTCAAAGATTCATATTCAAGAATATTAGAAATTCACA
1 AAAAATTTTTAGAAATTCACATCTAAAATTCAAAGATTCACATTCAAGAATATTAGAAATTCACA
12934655 TCCAAAATTTCAA
66 TCCAAAATTTCAA
12934668 GATTCAGATC
Statistics
Matches: 70, Mismatches: 5, Indels: 6
0.86 0.06 0.07
Matches are distributed among these distances:
90 28 0.40
91 37 0.53
92 5 0.07
ACGTcount: A:0.46, C:0.14, G:0.07, T:0.34
Consensus pattern (91 bp):
AAAAATTTTTAGAAATTCACATCTAAAATTCAAAGATTCACATTCAAGAATATTAGAAATTCACA
TCCAAAATTTCAAATATTCGCATTTG
Found at i:12934684 original size:20 final size:21
Alignment explanation
Indices: 12934513--12934687 Score: 77
Period size: 21 Copynumber: 8.0 Consensus size: 21
12934503 ATTTTTAGAA
*
12934513 ATTCACATCTAAAATTTCAAG
1 ATTCACATCCAAAATTTCAAG
* * *
12934534 ATTGACATTCAAGAAATTTTAAAG
1 ATTCACA-TCCA-AAA-TTTCAAG
* *
12934558 ATTCACATCCAAATTTTCAAAT
1 ATTCACATCCAAAATTTC-AAG
* ** * *
12934580 ATTCGCATTTGAAAAATTTTAGAA
1 ATTCACA--TCCAAAATTTCA-AG
* *
12934604 ATTTACATCTAAAA-TTCAAAG
1 ATTCACATCCAAAATTTC-AAG
* * *
12934625 ATTCATATTCAAGAATATT-AGAA
1 ATTCACATCCAA-AAT-TTCA-AG
12934648 ATTCACATCCAAAATTTCAAG
1 ATTCACATCCAAAATTTCAAG
*
12934669 ATTCAGATCC-AAATTTCAA
1 ATTCACATCCAAAATTTCAA
12934688 AAATTCGCAT
Statistics
Matches: 112, Mismatches: 29, Indels: 27
0.67 0.17 0.16
Matches are distributed among these distances:
20 9 0.08
21 32 0.29
22 26 0.23
23 18 0.16
24 27 0.24
ACGTcount: A:0.44, C:0.15, G:0.07, T:0.34
Consensus pattern (21 bp):
ATTCACATCCAAAATTTCAAG
Found at i:12934894 original size:21 final size:22
Alignment explanation
Indices: 12934863--12934915 Score: 63
Period size: 21 Copynumber: 2.4 Consensus size: 22
12934853 TTACATTCGA
12934863 AAAATTTTAAAAATTCACACTT
1 AAAATTTTAAAAATTCACACTT
* * *
12934885 AAAA-TTTAAAGATTCTCATTT
1 AAAATTTTAAAAATTCACACTT
12934906 AAAAATTTTA
1 -AAAATTTTA
12934916 GAGACTCAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
21 14 0.54
22 8 0.31
23 4 0.15
ACGTcount: A:0.49, C:0.09, G:0.02, T:0.40
Consensus pattern (22 bp):
AAAATTTTAAAAATTCACACTT
Found at i:12934910 original size:44 final size:44
Alignment explanation
Indices: 12934477--12934915 Score: 173
Period size: 44 Copynumber: 9.7 Consensus size: 44
12934467 TTTACAAATG
* * * *
12934477 AAATTCCAAAGTTTCACTTTCAAAAAATTTTTAGAAATTCACATCTA
1 AAATT-CAAAGATTCACATTCGAAAAA-TTTTAAAAATTCACAT-TA
* * *
12934524 AAATTTC-AAGATTGACATTC-AAGAAATTTTAAAGATTCACATCCA
1 AAA-TTCAAAGATTCACATTCGAA-AAATTTTAAAAATTCACAT-TA
* * * * * *
12934569 AATTTTCAAATATTCGCATTTGAAAAATTTTAGAAATTTACATCTA
1 AA-ATTCAAAGATTCACATTCGAAAAATTTTAAAAATTCACAT-TA
* * * * *
12934615 AAATTCAAAGATTCATATTC-AAGAATATTAGAAATTCACATCCA
1 AAATTCAAAGATTCACATTCGAAAAATTTTAAAAATTCACAT-TA
* * * *
12934659 AAATTTC-AAGATTCAGA-TC--CAAATTTCAAAAATTCGCATTTCAA
1 AAA-TTCAAAGATTCACATTCGAAAAATTTTAAAAATTCACA-TT--A
* * * * ** ** * *
12934703 AAATTTTAGAGATTCACATTTGAAATTCAAATACACATAGGTTTACATCCA
1 AAA-TTCAAAGATTCACATTCGAAA---AATTTTA-A-AAATTCACAT-TA
* * * *
12934754 AAATTTAACA-ACTAACATT--AAAAATTTTATAAATTCACATTGA
1 AAATTCAA-AGATTCACATTCGAAAAATTTTAAAAATTCACATT-A
* * * * *
12934797 AAATTCAAACATTCACATTCGAGAAATTTTAAAGATTCAAATCA
1 AAATTCAAAGATTCACATTCGAAAAATTTTAAAAATTCACATTA
*
12934841 AAATTCAGAGACTT-ACATTCGAAAAATTTTAAAAATTCACACTTA
1 AAATTCAAAGA-TTCACATTCGAAAAATTTTAAAAATTCACA-TTA
* * *
12934886 AAATTTAAAGATTCTCATT-TAAAAATTTTA
1 AAATTCAAAGATTCACATTCGAAAAATTTTA
12934916 GAGACTCAAA
Statistics
Matches: 292, Mismatches: 73, Indels: 57
0.69 0.17 0.14
Matches are distributed among these distances:
42 14 0.05
43 25 0.09
44 85 0.29
45 85 0.29
46 43 0.15
47 6 0.02
48 6 0.02
50 11 0.04
51 10 0.03
52 2 0.01
53 5 0.02
ACGTcount: A:0.45, C:0.15, G:0.06, T:0.34
Consensus pattern (44 bp):
AAATTCAAAGATTCACATTCGAAAAATTTTAAAAATTCACATTA
Found at i:12934955 original size:89 final size:88
Alignment explanation
Indices: 12934768--12934960 Score: 196
Period size: 89 Copynumber: 2.2 Consensus size: 88
12934758 TTAACAACTA
* *
12934768 ACATT-AAAAATTTTATAAATTCACATTGAAAATTCAAACATTCACATTCGAGAAATTTTAAAGA
1 ACATTCAAAAATTTTAAAAATTCACATTGAAAATTCAAACATTCACATTCGAAAAATTTTAAAGA
* * * *
12934832 TTCAAATCAAAATTCAGAGACTT
66 CTCAAATAAAAAATCAAAGACTT
* * * * *
12934855 ACATTCGAAAAATTTTAAAAATTCACACTT-AAAATTTAAAGATTCTCATT-TAAAAATTTTAGA
1 ACATTC-AAAAATTTTAAAAATTCACA-TTGAAAATTCAAACATTCACATTCGAAAAATTTTAAA
*
12934918 GACTCAAATAAAAAAAATCAAATA-TT
64 GACTCAAAT--AAAAAATCAAAGACTT
*
12934944 CACATTCAAAAAATTTA
1 -ACATTCAAAAATTTTA
12934961 GAGATTATGT
Statistics
Matches: 87, Mismatches: 13, Indels: 10
0.79 0.12 0.09
Matches are distributed among these distances:
87 5 0.06
88 18 0.21
89 47 0.54
90 17 0.20
ACGTcount: A:0.50, C:0.13, G:0.05, T:0.32
Consensus pattern (88 bp):
ACATTCAAAAATTTTAAAAATTCACATTGAAAATTCAAACATTCACATTCGAAAAATTTTAAAGA
CTCAAATAAAAAATCAAAGACTT
Found at i:12935609 original size:25 final size:27
Alignment explanation
Indices: 12935564--12935628 Score: 64
Period size: 26 Copynumber: 2.5 Consensus size: 27
12935554 ATGCTCATCA
* * *
12935564 AATGATGCAACTG-CATGATTC-TAAC
1 AATGATGCAAATGTAATGATTCAAAAC
12935589 AATGATGCAAATGTAAT-ATTCAAAAC
1 AATGATGCAAATGTAATGATTCAAAAC
* *
12935615 CATGATTCAAATGT
1 AATGATGCAAATGT
12935629 TCACTAAACG
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
25 16 0.48
26 17 0.52
ACGTcount: A:0.42, C:0.15, G:0.14, T:0.29
Consensus pattern (27 bp):
AATGATGCAAATGTAATGATTCAAAAC
Found at i:12936769 original size:18 final size:17
Alignment explanation
Indices: 12936742--12936777 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
12936732 TTTTTTTTAC
12936742 TTTTTTTTCTTATTTCT
1 TTTTTTTTCTTATTTCT
*
12936759 TTTTCTTTTCTTTTTTCT
1 TTTT-TTTTCTTATTTCT
12936777 T
1 T
12936778 ATATGTTTCC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 4 0.24
18 13 0.76
ACGTcount: A:0.03, C:0.14, G:0.00, T:0.83
Consensus pattern (17 bp):
TTTTTTTTCTTATTTCT
Found at i:12938852 original size:8 final size:8
Alignment explanation
Indices: 12938839--12938913 Score: 50
Period size: 8 Copynumber: 9.5 Consensus size: 8
12938829 GTCTATTTTC
12938839 TTTTTTAT
1 TTTTTTAT
12938847 TTTTTTAT
1 TTTTTTAT
*
12938855 TTTTGTA-
1 TTTTTTAT
*
12938862 --TTTTAC
1 TTTTTTAT
*
12938868 ATTTTTAT
1 TTTTTTAT
12938876 TTTTATTAT
1 TTTT-TTAT
12938885 TGTTTTTAT
1 T-TTTTTAT
*
12938894 ATATTTT-T
1 -TTTTTTAT
*
12938902 TCTTTTAT
1 TTTTTTAT
12938910 TTTT
1 TTTT
12938914 ATCTTATGTA
Statistics
Matches: 53, Mismatches: 7, Indels: 14
0.72 0.09 0.19
Matches are distributed among these distances:
5 4 0.08
7 5 0.09
8 27 0.51
9 13 0.25
10 4 0.08
ACGTcount: A:0.16, C:0.03, G:0.03, T:0.79
Consensus pattern (8 bp):
TTTTTTAT
Found at i:12938863 original size:16 final size:15
Alignment explanation
Indices: 12938839--12938941 Score: 50
Period size: 15 Copynumber: 6.7 Consensus size: 15
12938829 GTCTATTTTC
12938839 TTTTTTATTTTTTTAT
1 TTTTTTA-TTTTTTAT
* **
12938855 TTTTGTATTTTACAT
1 TTTTTTATTTTTTAT
*
12938870 TTTTATT-TTTATTAT
1 TTTT-TTATTTTTTAT
12938885 TGTTTTTATATATTTT-T
1 T-TTTTTAT-T-TTTTAT
*
12938902 TCTTTTA-TTTTTAT
1 TTTTTTATTTTTTAT
* * *
12938916 CTTATGTATTTATTAT
1 -TTTTTTATTTTTTAT
*
12938932 TTATTTATTT
1 TTTTTTATTT
12938942 ATTACTACTA
Statistics
Matches: 65, Mismatches: 14, Indels: 17
0.68 0.15 0.18
Matches are distributed among these distances:
13 4 0.06
14 2 0.03
15 31 0.48
16 22 0.34
17 3 0.05
18 3 0.05
ACGTcount: A:0.18, C:0.03, G:0.03, T:0.76
Consensus pattern (15 bp):
TTTTTTATTTTTTAT
Found at i:12938872 original size:28 final size:26
Alignment explanation
Indices: 12938841--12938913 Score: 83
Period size: 27 Copynumber: 2.7 Consensus size: 26
12938831 CTATTTTCTT
12938841 TTTTATTTTTTTATTTTTGTATTTTACA
1 TTTT-TTTTTTTATTTTTGT-TTTTACA
* * *
12938869 TTTTTATTTTTATTATTGTTTTTATA
1 TTTTTTTTTTTATTTTTGTTTTTACA
12938895 TATTTTTTCTTTTATTTTT
1 T-TTTTTT-TTTTATTTTT
12938914 ATCTTATGTA
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
26 7 0.18
27 18 0.47
28 13 0.34
ACGTcount: A:0.16, C:0.03, G:0.03, T:0.78
Consensus pattern (26 bp):
TTTTTTTTTTTATTTTTGTTTTTACA
Found at i:12938943 original size:34 final size:34
Alignment explanation
Indices: 12938871--12938944 Score: 82
Period size: 34 Copynumber: 2.2 Consensus size: 34
12938861 ATTTTACATT
* *
12938871 TTTATTTTTATTATTGTTTTTATATATTTTTTCT
1 TTTATTTTTATTATTGTATTTATATATTTTTTCA
12938905 TTTATTTTTATCT-TATGTATTTAT-TATTTATTT-A
1 TTTATTTTTAT-TAT-TGTATTTATATATTT-TTTCA
12938939 TTTATT
1 TTTATT
12938945 ACTACTATTT
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
34 23 0.66
35 12 0.34
ACGTcount: A:0.20, C:0.03, G:0.03, T:0.74
Consensus pattern (34 bp):
TTTATTTTTATTATTGTATTTATATATTTTTTCA
Found at i:12939061 original size:12 final size:12
Alignment explanation
Indices: 12939023--12939062 Score: 50
Period size: 11 Copynumber: 3.5 Consensus size: 12
12939013 TTATATGTCA
12939023 TAATTTATCTGT
1 TAATTTATCTGT
12939035 T-ATTTAAT-T-T
1 TAATTT-ATCTGT
12939045 TAATTTATCTGT
1 TAATTTATCTGT
12939057 TAATTT
1 TAATTT
12939063 TTTGATTTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 8
0.75 0.00 0.25
Matches are distributed among these distances:
10 4 0.17
11 10 0.42
12 10 0.42
ACGTcount: A:0.28, C:0.05, G:0.05, T:0.62
Consensus pattern (12 bp):
TAATTTATCTGT
Found at i:12939070 original size:20 final size:21
Alignment explanation
Indices: 12939023--12939075 Score: 72
Period size: 22 Copynumber: 2.5 Consensus size: 21
12939013 TTATATGTCA
*
12939023 TAATTTATCTGTTATTTAATTT
1 TAATTTATCTGTTAATT-ATTT
12939045 TAATTTATCTGTTAATT-TTT
1 TAATTTATCTGTTAATTATTT
*
12939065 TGATTTATCTG
1 TAATTTATCTG
12939076 ATTTATTTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
20 13 0.45
22 16 0.55
ACGTcount: A:0.25, C:0.06, G:0.08, T:0.62
Consensus pattern (21 bp):
TAATTTATCTGTTAATTATTT
Found at i:12939084 original size:20 final size:20
Alignment explanation
Indices: 12939023--12939084 Score: 63
Period size: 20 Copynumber: 3.0 Consensus size: 20
12939013 TTATATGTCA
*
12939023 TAATTTATCTGTTATTTAATTT
1 TAATTTATCTG--ATTTATTTT
*
12939045 TAATTTATCTG-TTAATTTTT
1 TAATTTATCTGATTTA-TTTT
*
12939065 TGATTTATCTGATTTATTTT
1 TAATTTATCTGATTTATTTT
12939085 CATTAATATT
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
19 3 0.09
20 17 0.50
21 3 0.09
22 11 0.32
ACGTcount: A:0.24, C:0.05, G:0.06, T:0.65
Consensus pattern (20 bp):
TAATTTATCTGATTTATTTT
Found at i:12940008 original size:17 final size:17
Alignment explanation
Indices: 12939988--12940026 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
12939978 TTTAATATTC
12939988 TTTTATTTTTATCTTTA
1 TTTTATTTTTATCTTTA
* *
12940005 TTTTATTTTTATTTTTG
1 TTTTATTTTTATCTTTA
12940022 TTTTA
1 TTTTA
12940027 CTTGTCTTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.15, C:0.03, G:0.03, T:0.79
Consensus pattern (17 bp):
TTTTATTTTTATCTTTA
Found at i:12940067 original size:30 final size:30
Alignment explanation
Indices: 12939994--12940080 Score: 92
Period size: 30 Copynumber: 3.0 Consensus size: 30
12939984 ATTCTTTTAT
* *
12939994 TTTTATCTTTATTTTA--TTTTTATTTT-TG
1 TTTTAT-TTTGTTTTATTTTTTTATTTTCTC
*
12940022 TTTTA-CTTGTCTTTATTTTTTTATTTTCTC
1 TTTTATTTTGT-TTTATTTTTTTATTTTCTC
*
12940052 TTTTATTTTGTTTTATTATTTTATTTTCT
1 TTTTATTTTGTTTTATTTTTTTATTTTCT
12940081 TTAAATAAAA
Statistics
Matches: 49, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
26 3 0.06
27 4 0.08
28 5 0.10
29 10 0.20
30 23 0.47
31 4 0.08
ACGTcount: A:0.13, C:0.07, G:0.03, T:0.77
Consensus pattern (30 bp):
TTTTATTTTGTTTTATTTTTTTATTTTCTC
Found at i:12940083 original size:17 final size:17
Alignment explanation
Indices: 12940002--12940083 Score: 50
Period size: 17 Copynumber: 5.0 Consensus size: 17
12939992 ATTTTTATCT
*
12940002 TTATTTTATTTT-TATTT
1 TTATTTTATTTTCT-TTA
* *
12940019 TTGTTTTACTTGTCTTTA
1 TTATTTTA-TTTTCTTTA
*
12940037 TTTTTTTATTTTCTCTT-
1 TTATTTTATTTTCT-TTA
*
12940054 TTA--TT-TTGT-TTTA
1 TTATTTTATTTTCTTTA
12940067 TTATTTTATTTTCTTTA
1 TTATTTTATTTTCTTTA
12940084 AATAAAATCC
Statistics
Matches: 49, Mismatches: 8, Indels: 16
0.67 0.11 0.22
Matches are distributed among these distances:
12 2 0.04
13 4 0.08
14 3 0.06
15 4 0.08
16 3 0.06
17 18 0.37
18 14 0.29
19 1 0.02
ACGTcount: A:0.13, C:0.06, G:0.04, T:0.77
Consensus pattern (17 bp):
TTATTTTATTTTCTTTA
Found at i:12940166 original size:58 final size:57
Alignment explanation
Indices: 12940097--12940306 Score: 266
Period size: 58 Copynumber: 3.7 Consensus size: 57
12940087 AAAATCCAAA
12940097 AAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTAGAAATTAAGGTTTTC
1 AAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTAGAAATTAA-GTTTTC
* * * *
12940155 AAAAAATATTTTTGGGAAAAAATTGAAAGTATCAATTTTCCTTA-AAAATAAATTTTC
1 AAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCC-TAGAAATTAAGTTTTC
** * *
12940212 AAAAAAGGTTTTTGAGGG-AAAGTTGAAAGTATCAATTTTTCTCGAAATTAAAGTTTTC
1 AAAAAATATTTTTG-GGGAAAAGTTGAAAGTATCAATTTTCCTAGAAATT-AAGTTTTC
* *
12940270 AAAAGATA-TTTT-GAGAAAAGTTGAAAGTATCAATTTT
1 AAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTT
12940307 TCCTGCACAA
Statistics
Matches: 131, Mismatches: 16, Indels: 12
0.82 0.10 0.08
Matches are distributed among these distances:
55 2 0.02
56 22 0.17
57 46 0.35
58 59 0.45
59 2 0.02
ACGTcount: A:0.42, C:0.06, G:0.15, T:0.36
Consensus pattern (57 bp):
AAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTAGAAATTAAGTTTTC
Found at i:12940216 original size:115 final size:113
Alignment explanation
Indices: 12940097--12940306 Score: 314
Period size: 115 Copynumber: 1.8 Consensus size: 113
12940087 AAAATCCAAA
* *
12940097 AAAAAATATTTTTG-GGGAAAAGTTGAAAGTATCAATTTTCCTAGAAATTAAGGTTTTCAAAAAA
1 AAAAAAGATTTTTGAGGG-AAAGTTGAAAGTATCAATTTTCCTAGAAATTAAAGTTTTCAAAAAA
*
12940161 TATTTTTGGGAAAAAATTGAAAGTATCAATTTTCCTTAAAAATAAATTTTC
65 TA-TTTTGAG-AAAAATTGAAAGTATCAATTTTCCTTAAAAATAAATTTTC
* * * *
12940212 AAAAAAGGTTTTTGAGGGAAAGTTGAAAGTATCAATTTTTCTCGAAATTAAAGTTTTCAAAAGAT
1 AAAAAAGATTTTTGAGGGAAAGTTGAAAGTATCAATTTTCCTAGAAATTAAAGTTTTCAAAAAAT
*
12940277 ATTTTGAGAAAAGTTGAAAGTATCAATTTT
66 ATTTTGAGAAAAATTGAAAGTATCAATTTT
12940307 TCCTGCACAA
Statistics
Matches: 86, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
113 21 0.24
114 6 0.07
115 56 0.65
116 3 0.03
ACGTcount: A:0.42, C:0.06, G:0.15, T:0.36
Consensus pattern (113 bp):
AAAAAAGATTTTTGAGGGAAAGTTGAAAGTATCAATTTTCCTAGAAATTAAAGTTTTCAAAAAAT
ATTTTGAGAAAAATTGAAAGTATCAATTTTCCTTAAAAATAAATTTTC
Found at i:12940411 original size:24 final size:24
Alignment explanation
Indices: 12940379--12940424 Score: 92
Period size: 24 Copynumber: 1.9 Consensus size: 24
12940369 CGACGGAGCC
12940379 TCTGCAAGTGAAATAGTAGTTTCT
1 TCTGCAAGTGAAATAGTAGTTTCT
12940403 TCTGCAAGTGAAATAGTAGTTT
1 TCTGCAAGTGAAATAGTAGTTT
12940425 TCTTGCATAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.30, C:0.11, G:0.22, T:0.37
Consensus pattern (24 bp):
TCTGCAAGTGAAATAGTAGTTTCT
Found at i:12941484 original size:96 final size:98
Alignment explanation
Indices: 12941305--12941519 Score: 296
Period size: 96 Copynumber: 2.2 Consensus size: 98
12941295 TATATAATCA
* **
12941305 AATAGTTTGGTAGGATTAA-AACTAAAAATTTTATTTTAAAAGATAATTAAATATTCCAATAATT
1 AATAGTTTGGTAAGATTAATTTCTAAAAATTTTATTTTAAAAGATAATTAAATATTCCAATAATT
*
12941369 TGGTAAATTTTAATTTTAAGATTTAAATC-TTCT
66 TGGTAAATCTTAATTTTAAGATTTAAATCATT-T
* * *
12941402 AATAGTTTGGTAAGATTAATTTC-AAAAATTTTTTTTTAAAA-ATCATTAAATTTTCCAATAATT
1 AATAGTTTGGTAAGATTAATTTCTAAAAATTTTATTTTAAAAGATAATTAAATATTCCAATAATT
12941465 TGGTAAGA-CTTAATTTTAAGATTTAAATCATTT
66 TGGTAA-ATCTTAATTTTAAGATTTAAATCATTT
* *
12941498 AATAATTGGGTAAGATTAATTT
1 AATAGTTTGGTAAGATTAATTT
12941520 TTTAAAAAAC
Statistics
Matches: 106, Mismatches: 9, Indels: 7
0.87 0.07 0.06
Matches are distributed among these distances:
96 67 0.63
97 38 0.36
98 1 0.01
ACGTcount: A:0.41, C:0.05, G:0.10, T:0.44
Consensus pattern (98 bp):
AATAGTTTGGTAAGATTAATTTCTAAAAATTTTATTTTAAAAGATAATTAAATATTCCAATAATT
TGGTAAATCTTAATTTTAAGATTTAAATCATTT
Found at i:12943932 original size:19 final size:18
Alignment explanation
Indices: 12943916--12943951 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
12943906 GGTTGTTTCA
12943916 TTTTTTTTT-CAAGGTTT
1 TTTTTTTTTGCAAGGTTT
12943933 TTTTTTTTTGCAA-GTTT
1 TTTTTTTTTGCAAGGTTT
12943950 TT
1 TT
12943952 CCTTTTTAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 15 0.83
18 3 0.17
ACGTcount: A:0.11, C:0.06, G:0.11, T:0.72
Consensus pattern (18 bp):
TTTTTTTTTGCAAGGTTT
Found at i:12944247 original size:3 final size:3
Alignment explanation
Indices: 12944241--12944337 Score: 50
Period size: 3 Copynumber: 32.3 Consensus size: 3
12944231 AAGAAAAATA
* * * * * * *
12944241 AAT AAT AAT AAT AAT AAT AAT AAC AAT AAG AAC AAC AAC AAT AAC AAC
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* * * * * * * * *
12944289 AAC AAT AAC AAC AAC AAC AAC AAC AAC AAC AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
12944337 A
1 A
12944338 GGGTATTTAT
Statistics
Matches: 85, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
3 85 1.00
ACGTcount: A:0.67, C:0.15, G:0.01, T:0.16
Consensus pattern (3 bp):
AAT
Found at i:12944250 original size:6 final size:6
Alignment explanation
Indices: 12944241--12944337 Score: 59
Period size: 6 Copynumber: 15.7 Consensus size: 6
12944231 AAGAAAAATA
* * * * *
12944241 AATAAT AATAAT AATAAT AATAAC AATAAGAAC AACAAC AATAAC AACAAC
1 AATAAC AATAAC AATAAC AATAAC AAT---AAC AATAAC AATAAC AATAAC
* * * * * * *
12944292 AATAAC AACAAC AACAAC AACAAC AACAAT AATAAT AATAAT AATA
1 AATAAC AATAAC AATAAC AATAAC AATAAC AATAAC AATAAC AATA
12944338 GGGTATTTAT
Statistics
Matches: 80, Mismatches: 8, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
6 75 0.94
9 5 0.06
ACGTcount: A:0.67, C:0.15, G:0.01, T:0.16
Consensus pattern (6 bp):
AATAAC
Found at i:12944255 original size:9 final size:9
Alignment explanation
Indices: 12944256--12944323 Score: 73
Period size: 9 Copynumber: 7.6 Consensus size: 9
12944246 TAATAATAAT
*
12944256 AATAATAAC
1 AATAACAAC
*
12944265 AATAAGAAC
1 AATAACAAC
* *
12944274 AACAACAAT
1 AATAACAAC
*
12944283 AACAACAAC
1 AATAACAAC
12944292 AATAACAAC
1 AATAACAAC
*
12944301 AACAACAAC
1 AATAACAAC
*
12944310 AACAACAAC
1 AATAACAAC
12944319 AATAA
1 AATAA
12944324 TAATAATAAT
Statistics
Matches: 51, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
9 51 1.00
ACGTcount: A:0.68, C:0.22, G:0.01, T:0.09
Consensus pattern (9 bp):
AATAACAAC
Found at i:12944636 original size:50 final size:51
Alignment explanation
Indices: 12944582--12944706 Score: 128
Period size: 52 Copynumber: 2.5 Consensus size: 51
12944572 AAAGCTCATT
*
12944582 TAAGCAGAGACTCAATGA-TTTT-AAAAATTTCATCTTAAAAAAACCTCCTC
1 TAAGCAGAGACTCAATGACTTTTAAAAAAATTCATCTT-AAAAAACCTCCTC
* * ** * **
12944632 TAAGCAAAGACTTAACAACTTTTAAAAAAAATTCATCTTGAAAAATTTCCTC
1 TAAGCAGAGACTCAATGACTTTT-AAAAAAATTCATCTTAAAAAACCTCCTC
* *
12944684 TAAGAAGAGGCTCAATGACTTTT
1 TAAGCAGAGACTCAATGACTTTT
12944707 TGACAATTTA
Statistics
Matches: 58, Mismatches: 14, Indels: 4
0.76 0.18 0.05
Matches are distributed among these distances:
50 14 0.24
51 4 0.07
52 27 0.47
53 13 0.22
ACGTcount: A:0.42, C:0.18, G:0.10, T:0.30
Consensus pattern (51 bp):
TAAGCAGAGACTCAATGACTTTTAAAAAAATTCATCTTAAAAAACCTCCTC
Found at i:12944862 original size:49 final size:49
Alignment explanation
Indices: 12944771--12945059 Score: 204
Period size: 49 Copynumber: 5.8 Consensus size: 49
12944761 TATCTATGTG
* * ** * *
12944771 GAGGCTAAACAACTTTTAAAAATTTCAT-GTGCAAAAGTTCCTCTAAGCA
1 GAGGCTAAACAAC-TTTAAAATTTTCATCTTAAAAAAGCTCCTCTAAACA
* * * *
12944820 TATGCTCAATAACTTTAAAATTTTCATCTTAAAAAAGCTCCTCTAAACA
1 GAGGCTAAACAACTTTAAAATTTTCATCTTAAAAAAGCTCCTCTAAACA
* * * *
12944869 GAGGCTAAACCACTTTAAAAATTTCATCTCAAAAAAGCTCCTCTAAATA
1 GAGGCTAAACAACTTTAAAATTTTCATCTTAAAAAAGCTCCTCTAAACA
* * * * * **
12944918 GAGGCTTAACCACTTTAAAAAAATTCTTCATTTTGAAAAAGGCTCTTCT-AAGT
1 GAGGCTAAACAACTTT---AAAATT-TTCATCTT-AAAAAAGCTCCTCTAAACA
* * * * *
12944971 GAAGGCTAAATAACTTTAAAATTTTCATTTTGAAAAAGCTTCTCTAAATA
1 G-AGGCTAAACAACTTTAAAATTTTCATCTTAAAAAAGCTCCTCTAAACA
* * * * * **
12945021 GAGGCTCAACCATTTTAAAAATTTCTTCTTGGAAAAGCT
1 GAGGCTAAACAACTTTAAAATTTTCATCTTAAAAAAGCT
12945060 TATCTAATTA
Statistics
Matches: 189, Mismatches: 43, Indels: 16
0.76 0.17 0.06
Matches are distributed among these distances:
48 13 0.07
49 121 0.64
50 11 0.06
51 6 0.03
52 5 0.03
53 9 0.05
54 24 0.13
ACGTcount: A:0.39, C:0.18, G:0.11, T:0.32
Consensus pattern (49 bp):
GAGGCTAAACAACTTTAAAATTTTCATCTTAAAAAAGCTCCTCTAAACA
Found at i:12944977 original size:54 final size:54
Alignment explanation
Indices: 12944836--12945167 Score: 188
Period size: 49 Copynumber: 6.5 Consensus size: 54
12944826 CAATAACTTT
* ** **
12944836 AAAATT-TTCATCTT-AAAAAAGCTCCTCTAAACAGAGGCTAAACCACTTT--A
1 AAAATTCTTCATCTTGAAAAAGGCTTATCTAATGAGAGGCTAAACCACTTTAAA
* * ** *
12944886 AAAA-T-TTCATC-TCAAAAAAGCTCCTCTAAAT-AGAGGCTTAACCACTTTAAA
1 AAAATTCTTCATCTTGAAAAAGGCTTATCT-AATGAGAGGCTAAACCACTTTAAA
* **
12944937 AAAATTCTTCATTTTGAAAAAGGCTCT-TCTAAGTGA-AGGCTAAATAACTTT---
1 AAAATTCTTCATCTTGAAAAAGGCT-TATCTAA-TGAGAGGCTAAACCACTTTAAA
* * * *
12944988 AAAATT-TTCATTTTGAAAAA-GCTTCTCTAAAT-AGAGGCTCAACCA-TTT-TA
1 AAAATTCTTCATCTTGAAAAAGGCTTATCT-AATGAGAGGCTAAACCACTTTAAA
* * * * * *
12945038 AAAA-T-TTCTTCTTGGAAAA-GCTTATCTAATTACAGGCTCAACAAC-TTAAA
1 AAAATTCTTCATCTTGAAAAAGGCTTATCTAATGAGAGGCTAAACCACTTTAAA
** * * *
12945088 AAAAAACTCTCATCATGAAAAAGGCTCAT-TTATGCAGAGGCTAAACCACTTTAAA
1 AAAATTCT-TCATCTTGAAAAAGGCTTATCTAATG-AGAGGCTAAACCACTTTAAA
*
12945143 AAAATTCTTTATCTTGAAAAAGGCT
1 AAAATTCTTCATCTTGAAAAAGGCT
12945168 ATTTTAAGCA
Statistics
Matches: 225, Mismatches: 33, Indels: 44
0.75 0.11 0.15
Matches are distributed among these distances:
48 9 0.04
49 84 0.37
50 31 0.14
51 11 0.05
52 2 0.01
53 20 0.09
54 56 0.25
55 12 0.05
ACGTcount: A:0.41, C:0.18, G:0.11, T:0.31
Consensus pattern (54 bp):
AAAATTCTTCATCTTGAAAAAGGCTTATCTAATGAGAGGCTAAACCACTTTAAA
Found at i:12945060 original size:49 final size:49
Alignment explanation
Indices: 12944831--12945090 Score: 211
Period size: 49 Copynumber: 5.2 Consensus size: 49
12944821 ATGCTCAATA
* * * * *
12944831 ACTTTAAAATTTTCATCTTAAAAAAGCTCCTCTAAACAGAGGCTAAACC
1 ACTTTAAAAATTTCTTCTTGAAAAAGCTTCTCTAAATAGAGGCTAAACC
* ** * *
12944880 ACTTTAAAAATTTCATCTCAAAAAAGCTCCTCTAAATAGAGGCTTAACC
1 ACTTTAAAAATTTCTTCTTGAAAAAGCTTCTCTAAATAGAGGCTAAACC
* * **
12944929 ACTTTAAAAAAATTCTTCATTTTGAAAAAGGC-TCTTCTAAGT-GAAGGCTAAATA
1 ACTTT-AAAAATTTCTTC---TTGAAAAA-GCTTC-TCTAAATAG-AGGCTAAACC
* *
12944983 ACTTTAAAATTTTCATT-TTGAAAAAGCTTCTCTAAATAGAGGCTCAACC
1 ACTTTAAAAATTTC-TTCTTGAAAAAGCTTCTCTAAATAGAGGCTAAACC
* * * * * * *
12945032 ATTTTAAAAATTTCTTCTTGGAAAAGCTTATCTAATTACAGGCTCAACA
1 ACTTTAAAAATTTCTTCTTGAAAAAGCTTCTCTAAATAGAGGCTAAACC
*
12945081 ACTTAAAAAA
1 ACTTTAAAAA
12945091 AAACTCTCAT
Statistics
Matches: 172, Mismatches: 28, Indels: 22
0.77 0.13 0.10
Matches are distributed among these distances:
48 2 0.01
49 112 0.65
50 21 0.12
53 15 0.09
54 22 0.13
ACGTcount: A:0.40, C:0.18, G:0.10, T:0.32
Consensus pattern (49 bp):
ACTTTAAAAATTTCTTCTTGAAAAAGCTTCTCTAAATAGAGGCTAAACC
Found at i:12945132 original size:152 final size:152
Alignment explanation
Indices: 12944827--12945114 Score: 380
Period size: 152 Copynumber: 1.9 Consensus size: 152
12944817 GCATATGCTC
12944827 AATAACTTTAAAATTTTCATCTTAAAAAAGCTCCTCTAAACAGAGGCTAAACCACTTTAAAAATT
1 AATAACTTTAAAATTTTCATCTTAAAAAAGCTCCTCTAAACAGAGGCTAAACCACTTTAAAAATT
* * * * * * **
12944892 TCATCTCAAAAAAGCTCCTCTAAATAGAGGCTTAACCACTTTAAAAAAATTCTTCATTTTGAAAA
66 TCATCTCAAAAAAGCTCATCTAAATACAGGCTCAACAACTTAAAAAAAACTCTTCATCATGAAAA
12944957 AGGCTCTTCTAAGTGAAGGCTA
131 AGGCTCTTCTAAGTGAAGGCTA
* * * * * *
12944979 AATAACTTTAAAATTTTCATTTTGAAAAAGCTTCTCTAAATAGAGGCTCAACCATTTTAAAAATT
1 AATAACTTTAAAATTTTCATCTTAAAAAAGCTCCTCTAAACAGAGGCTAAACCACTTTAAAAATT
* *** * *
12945044 TCTTCTTGGAAAAGCTTATCTAATTACAGGCTCAACAACTTAAAAAAAAACTC-TCATCATGAAA
66 TCATCTCAAAAAAGCTCATCTAAATACAGGCTCAACAACTT-AAAAAAAACTCTTCATCATGAAA
12945108 AAGGCTC
130 AAGGCTC
12945115 ATTTATGCAG
Statistics
Matches: 115, Mismatches: 20, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
152 106 0.92
153 9 0.08
ACGTcount: A:0.41, C:0.18, G:0.10, T:0.31
Consensus pattern (152 bp):
AATAACTTTAAAATTTTCATCTTAAAAAAGCTCCTCTAAACAGAGGCTAAACCACTTTAAAAATT
TCATCTCAAAAAAGCTCATCTAAATACAGGCTCAACAACTTAAAAAAAACTCTTCATCATGAAAA
AGGCTCTTCTAAGTGAAGGCTA
Found at i:12946048 original size:10 final size:10
Alignment explanation
Indices: 12946029--12946064 Score: 54
Period size: 10 Copynumber: 3.5 Consensus size: 10
12946019 TTTATCTCCC
*
12946029 TTTTTCCTTT
1 TTTTTTCTTT
12946039 TTTTTTCTTT
1 TTTTTTCTTT
12946049 TTTTCTTCTTT
1 TTTT-TTCTTT
12946060 TTTTT
1 TTTTT
12946065 CAAGCAAAAC
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
10 14 0.58
11 10 0.42
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (10 bp):
TTTTTTCTTT
Found at i:12948862 original size:66 final size:66
Alignment explanation
Indices: 12948791--12948925 Score: 270
Period size: 66 Copynumber: 2.0 Consensus size: 66
12948781 AAGCATACCA
12948791 ATTGTTATCATAAAACAAATCAAGCAAAATTGTATTGTAAGATTTCTTCTCATTTTCAAAATAAG
1 ATTGTTATCATAAAACAAATCAAGCAAAATTGTATTGTAAGATTTCTTCTCATTTTCAAAATAAG
12948856 G
66 G
12948857 ATTGTTATCATAAAACAAATCAAGCAAAATTGTATTGTAAGATTTCTTCTCATTTTCAAAATAAG
1 ATTGTTATCATAAAACAAATCAAGCAAAATTGTATTGTAAGATTTCTTCTCATTTTCAAAATAAG
12948922 G
66 G
12948923 ATT
1 ATT
12948926 AATCAATTTA
Statistics
Matches: 69, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
66 69 1.00
ACGTcount: A:0.41, C:0.12, G:0.10, T:0.37
Consensus pattern (66 bp):
ATTGTTATCATAAAACAAATCAAGCAAAATTGTATTGTAAGATTTCTTCTCATTTTCAAAATAAG
G
Found at i:12968396 original size:42 final size:42
Alignment explanation
Indices: 12968280--12968486 Score: 118
Period size: 42 Copynumber: 5.0 Consensus size: 42
12968270 CGGATGTCAT
* * *
12968280 CTTTATTTTTTAAAAAGTTATGTGCCTTTGTGTTGAAAAAGC
1 CTTTACTTTTTAAAAAGTTATGTGCTTTTGTGTTGAAAGAGC
* * * * ** *
12968322 CTTT-GTTTTT--TAAGTTTTGTTCTTTCATGTTGAAGGAGC
1 CTTTACTTTTTAAAAAGTTATGTGCTTTTGTGTTGAAAGAGC
* * *
12968361 CTTTACTTTTTAAAAAGTTGTGTGCTTTTGTGTTGAATGACC
1 CTTTACTTTTTAAAAAGTTATGTGCTTTTGTGTTGAAAGAGC
** *** * * * ** * *
12968403 CTTTTTTTTTTTTTTAAGTTGTATGCCTTCATGTTAAAAAAGC
1 C-TTTACTTTTTAAAAAGTTATGTGCTTTTGTGTTGAAAGAGC
* * *
12968446 CCTTAATTTTT--AAAGTTATGTGCTTTTCTGTTGAAAGAGC
1 CTTTACTTTTTAAAAAGTTATGTGCTTTTGTGTTGAAAGAGC
12968486 C
1 C
12968487 ATTGATTTTT
Statistics
Matches: 120, Mismatches: 41, Indels: 10
0.70 0.24 0.06
Matches are distributed among these distances:
39 25 0.21
40 27 0.22
41 5 0.04
42 34 0.28
43 29 0.24
ACGTcount: A:0.23, C:0.12, G:0.17, T:0.49
Consensus pattern (42 bp):
CTTTACTTTTTAAAAAGTTATGTGCTTTTGTGTTGAAAGAGC
Found at i:12968410 original size:39 final size:39
Alignment explanation
Indices: 12968285--12968410 Score: 92
Period size: 39 Copynumber: 3.2 Consensus size: 39
12968275 GTCATCTTTA
* * *
12968285 TTTTTTAAAAAGTTATGTGCCTTTGTGTTGAAAAAGCCT
1 TTTTTTAAAAAGTTATGTGCTTTTGTGTTGAAAGACCCT
** * * ** * *
12968324 TTGTTTT-TTAAGTTTTGTTCTTTCATGTTGAAGGAGCCTT
1 TT-TTTTAAAAAGTTATGTGCTTTTGTGTTGAAAGA-CCCT
* *
12968364 TACTTTTTAAAAAGTTGTGTGCTTTTGTGTTGAATGACCCT
1 T--TTTTTAAAAAGTTATGTGCTTTTGTGTTGAAAGACCCT
12968405 TTTTTT
1 TTTTTT
12968411 TTTTTTTAAG
Statistics
Matches: 63, Mismatches: 19, Indels: 10
0.68 0.21 0.11
Matches are distributed among these distances:
39 26 0.41
40 7 0.11
41 8 0.13
42 22 0.35
ACGTcount: A:0.21, C:0.10, G:0.18, T:0.51
Consensus pattern (39 bp):
TTTTTTAAAAAGTTATGTGCTTTTGTGTTGAAAGACCCT
Found at i:12973928 original size:20 final size:21
Alignment explanation
Indices: 12973887--12973941 Score: 60
Period size: 23 Copynumber: 2.6 Consensus size: 21
12973877 TGTTCGAGTT
12973887 TTTAAATCAATTATTAAATTA
1 TTTAAATCAATTATTAAATTA
*
12973908 TTTAAACTCAATTTAATT-TATTA
1 TTTAAA-TCAA-TT-ATTAAATTA
12973931 TTTAAAT-AATT
1 TTTAAATCAATT
12973942 TGAGCTCAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
20 2 0.07
21 8 0.27
22 5 0.17
23 12 0.40
24 3 0.10
ACGTcount: A:0.44, C:0.05, G:0.00, T:0.51
Consensus pattern (21 bp):
TTTAAATCAATTATTAAATTA
Found at i:12974418 original size:19 final size:20
Alignment explanation
Indices: 12974394--12974435 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
12974384 CAAAGAAAGT
*
12974394 AAAGGAAA-AAACAAGGTGA
1 AAAGGAAAGAAACAAGGGGA
*
12974413 AAAGGAAAGAAAGAAGGGGA
1 AAAGGAAAGAAACAAGGGGA
12974433 AAA
1 AAA
12974436 AAAGTGCTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 8 0.40
20 12 0.60
ACGTcount: A:0.64, C:0.02, G:0.31, T:0.02
Consensus pattern (20 bp):
AAAGGAAAGAAACAAGGGGA
Found at i:12974990 original size:22 final size:21
Alignment explanation
Indices: 12974951--12974993 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
12974941 TTTTTATATA
*
12974951 TTATTAATTTTTTATTAAATT
1 TTATTAAATTTTTATTAAATT
*
12974972 TTATTAAAATTTTTGTTAAATT
1 TTATT-AAATTTTTATTAAATT
12974994 ATTTTTTTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 5 0.26
22 14 0.74
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (21 bp):
TTATTAAATTTTTATTAAATT
Done.