Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167937.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_2, 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: 35885061
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 165000 characters in sequence are not A, C, G, or T
File 15 of 195
Found at i:3475096 original size:21 final size:21
Alignment explanation
Indices: 3475072--3475127 Score: 69
Period size: 21 Copynumber: 2.6 Consensus size: 21
3475062 GGTTTGAAAA
*
3475072 GTTTAGAGTTTTGATTTTAGG
1 GTTTAGAGTTTTAATTTTAGG
*
3475093 GTTTATG-GTTTCAATTTTAGG
1 GTTTA-GAGTTTTAATTTTAGG
3475114 GTTTAGAGGTTTTA
1 GTTTAGA-GTTTTA
3475128 GGGCTTAAGT
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
20 1 0.03
21 22 0.76
22 6 0.21
ACGTcount: A:0.20, C:0.02, G:0.27, T:0.52
Consensus pattern (21 bp):
GTTTAGAGTTTTAATTTTAGG
Found at i:3475118 original size:7 final size:7
Alignment explanation
Indices: 3475108--3475263 Score: 57
Period size: 7 Copynumber: 21.4 Consensus size: 7
3475098 TGGTTTCAAT
3475108 TTTAGGG
1 TTTAGGG
3475115 TTTAGAGG
1 TTTAG-GG
3475123 TTTTAGGG
1 -TTTAGGG
* *
3475131 CTTA-AG
1 TTTAGGG
3475137 TTTAGGG
1 TTTAGGG
**
3475144 TTTGAAAAG
1 TTT--AGGG
*
3475153 TTTATGG
1 TTTAGGG
*
3475160 TTTAAGGT
1 TTT-AGGG
*
3475168 TTTA-GT
1 TTTAGGG
*
3475174 TTTAGGT
1 TTTAGGG
3475181 TTTGAGGG
1 TTT-AGGG
3475189 TTTAGGG
1 TTTAGGG
* **
3475196 TTTTGAT
1 TTTAGGG
3475203 TTTAGGG
1 TTTAGGG
3475210 TTT-GAGG
1 TTTAG-GG
*
3475217 TTTAGGT
1 TTTAGGG
3475224 TTTAGAGG
1 TTTAG-GG
*
3475232 ATTTAGGA
1 -TTTAGGG
* **
3475240 TTTTGAT
1 TTTAGGG
3475247 TTTAGGG
1 TTTAGGG
*
3475254 TTTAAGG
1 TTTAGGG
3475261 TTT
1 TTT
3475264 GGAGATTTGA
Statistics
Matches: 110, Mismatches: 27, Indels: 24
0.68 0.17 0.15
Matches are distributed among these distances:
6 11 0.10
7 66 0.60
8 18 0.16
9 15 0.14
ACGTcount: A:0.20, C:0.01, G:0.31, T:0.48
Consensus pattern (7 bp):
TTTAGGG
Found at i:3475140 original size:104 final size:104
Alignment explanation
Indices: 3474954--3475141 Score: 222
Period size: 104 Copynumber: 1.8 Consensus size: 104
3474944 GTTTTAAAAG
* * * * * * *
3474954 TTAGGGTTTTAAGATTTTGGAGTTTTGGATTTTAGGGTTTTGATTTGAGTTTTAAGGATTTTAGG
1 TTAGGGTTTGAAAAGTTTAGAGTTTTGGATTTTAGGGTTTTGATTTCAATTTTAAGGAGTTTAGG
* *
3475019 GTTTGGTCTTAGGGTTTAGAGGATTTTAAAGCTTGAATT
66 GTTTGGGCTTAGAGTTTAGAGGATTTTAAAGCTTGAATT
*
3475058 TTAGGGTTTGAAAAGTTTAGAGTTTT-GATTTTAGGGTTTATGGTTTCAATTTT-AGG-GTTTAG
1 TTAGGGTTTGAAAAGTTTAGAGTTTTGGATTTTAGGGTTT-TGATTTCAATTTTAAGGAGTTTAG
3475120 AGGTTTTAGGGCTTA-AGTTTAG
65 -GG-TTT-GGGCTTAGAGTTTAG
3475142 GGTTTGAAAA
Statistics
Matches: 70, Mismatches: 10, Indels: 8
0.80 0.11 0.09
Matches are distributed among these distances:
102 5 0.07
103 18 0.26
104 41 0.59
105 6 0.09
ACGTcount: A:0.22, C:0.02, G:0.29, T:0.47
Consensus pattern (104 bp):
TTAGGGTTTGAAAAGTTTAGAGTTTTGGATTTTAGGGTTTTGATTTCAATTTTAAGGAGTTTAGG
GTTTGGGCTTAGAGTTTAGAGGATTTTAAAGCTTGAATT
Found at i:3475169 original size:66 final size:66
Alignment explanation
Indices: 3475087--3475214 Score: 159
Period size: 66 Copynumber: 1.9 Consensus size: 66
3475077 GAGTTTTGAT
* *
3475087 TTTAGGGTTTATGGTTTCAATTTTAGGGTTTAGAGGTTTTAGGG-CTTAAGTTTAGGGTTTGAAA
1 TTTAGGGTTTAAGGTTTCAATTTTA-GGTTTAGAGGGTTTAGGGTCTTAAGTTTAGGGTTTGAAA
3475151 AG
65 AG
* * * * * * *
3475153 TTTATGGTTTAAGGTTTTAGTTTTAGGTTTTGAGGGTTTAGGGTTTTGATTTTAGGGTTTGA
1 TTTAGGGTTTAAGGTTTCAATTTTAGGTTTAGAGGGTTTAGGGTCTTAAGTTTAGGGTTTGA
3475215 GGTTTAGGTT
Statistics
Matches: 52, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
65 16 0.31
66 36 0.69
ACGTcount: A:0.20, C:0.02, G:0.30, T:0.48
Consensus pattern (66 bp):
TTTAGGGTTTAAGGTTTCAATTTTAGGTTTAGAGGGTTTAGGGTCTTAAGTTTAGGGTTTGAAAA
G
Found at i:3475177 original size:6 final size:7
Alignment explanation
Indices: 3475153--3475321 Score: 64
Period size: 8 Copynumber: 23.3 Consensus size: 7
3475143 GTTTGAAAAG
3475153 TTTATGGT
1 TTTA-GGT
*
3475161 TTAAGGT
1 TTTAGGT
3475168 TTTA-GT
1 TTTAGGT
3475174 TTTAGGT
1 TTTAGGT
*
3475181 TTTGAGGG
1 TTT-AGGT
3475189 TTTAGGGT
1 TTTA-GGT
*
3475197 TTT-GAT
1 TTTAGGT
3475203 TTTAGGGT
1 TTTA-GGT
*
3475211 TTGAGG-
1 TTTAGGT
3475217 TTTAGGT
1 TTTAGGT
*
3475224 TTTAGAGGA
1 TTT--AGGT
3475233 TTTAGGAT
1 TTTAGG-T
*
3475241 TTT-GAT
1 TTTAGGT
3475247 TTTAGGGT
1 TTTA-GGT
*
3475255 TTAAGG-
1 TTTAGGT
* *
3475261 TTTGGAGA
1 TTTAG-GT
*
3475269 TTT-GAT
1 TTTAGGT
3475275 TTTAGGGT
1 TTTA-GGT
3475283 TTTAAGGT
1 TTT-AGGT
3475291 TTTAGAGT
1 TTTAG-GT
*
3475299 TTT-GAT
1 TTTAGGT
3475305 TTTAGGAT
1 TTTAGG-T
*
3475313 TTGAGGT
1 TTTAGGT
3475320 TT
1 TT
3475322 ATAATTTAGG
Statistics
Matches: 121, Mismatches: 21, Indels: 39
0.67 0.12 0.22
Matches are distributed among these distances:
6 30 0.25
7 32 0.26
8 52 0.43
9 7 0.06
ACGTcount: A:0.19, C:0.00, G:0.30, T:0.51
Consensus pattern (7 bp):
TTTAGGT
Found at i:3475190 original size:29 final size:29
Alignment explanation
Indices: 3475158--3475229 Score: 96
Period size: 29 Copynumber: 2.6 Consensus size: 29
3475148 AAAAGTTTAT
*
3475158 GGTTTAAGGTTTTAG-TTTTAGGTTTTGA
1 GGTTTAAGGTTTTAGATTTTAGGGTTTGA
*
3475186 GGGTTTAGGGTTTT-GATTTTAGGGTTTGA
1 -GGTTTAAGGTTTTAGATTTTAGGGTTTGA
3475215 GGTTT-AGGTTTTAGA
1 GGTTTAAGGTTTTAGA
3475230 GGATTTAGGA
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
27 6 0.16
28 8 0.21
29 24 0.63
ACGTcount: A:0.17, C:0.00, G:0.33, T:0.50
Consensus pattern (29 bp):
GGTTTAAGGTTTTAGATTTTAGGGTTTGA
Found at i:3475192 original size:21 final size:21
Alignment explanation
Indices: 3475168--3475237 Score: 63
Period size: 21 Copynumber: 3.2 Consensus size: 21
3475158 GGTTTAAGGT
3475168 TTTAGTTTTAGGTTTTGAGGG
1 TTTAGTTTTAGGTTTTGAGGG
*
3475189 TTTAGGGTTTT-GATTTT-AGGG
1 TTTA--GTTTTAGGTTTTGAGGG
* *
3475210 TTTGAGGTTTAGGTTTTAGAGGA
1 TTT-AGTTTTAGGTTTT-GAGGG
3475233 TTTAG
1 TTTAG
3475238 GATTTTGATT
Statistics
Matches: 39, Mismatches: 4, Indels: 11
0.72 0.07 0.20
Matches are distributed among these distances:
20 4 0.10
21 16 0.41
22 8 0.21
23 11 0.28
ACGTcount: A:0.17, C:0.00, G:0.33, T:0.50
Consensus pattern (21 bp):
TTTAGTTTTAGGTTTTGAGGG
Found at i:3475248 original size:44 final size:43
Alignment explanation
Indices: 3475160--3475263 Score: 145
Period size: 44 Copynumber: 2.4 Consensus size: 43
3475150 AAGTTTATGG
* * * * *
3475160 TTTAAGGTTTTAGTTTTAGGTTTTGAGGGTTTAGGGTTTTGAT
1 TTTAGGGTTTAAGGTTTAGGTTTTGAGGATTTAGGATTTTGAT
*
3475203 TTTAGGGTTTGAGGTTTAGGTTTTAGAGGATTTAGGATTTTGAT
1 TTTAGGGTTTAAGGTTTAGGTTTT-GAGGATTTAGGATTTTGAT
3475247 TTTAGGGTTTAAGGTTT
1 TTTAGGGTTTAAGGTTT
3475264 GGAGATTTGA
Statistics
Matches: 54, Mismatches: 6, Indels: 1
0.89 0.10 0.02
Matches are distributed among these distances:
43 21 0.39
44 33 0.61
ACGTcount: A:0.18, C:0.00, G:0.31, T:0.51
Consensus pattern (43 bp):
TTTAGGGTTTAAGGTTTAGGTTTTGAGGATTTAGGATTTTGAT
Found at i:3475286 original size:29 final size:29
Alignment explanation
Indices: 3475217--3475321 Score: 115
Period size: 30 Copynumber: 3.6 Consensus size: 29
3475207 GGGTTTGAGG
* *
3475217 TTTAGGTTTTAGAGGATTTAG-GATTTTGAT
1 TTTAGGGTTTA-AGGTTTTAGAGA-TTTGAT
*
3475247 TTTAGGGTTTAAGG-TTTGGAGATTTGAT
1 TTTAGGGTTTAAGGTTTTAGAGATTTGAT
*
3475275 TTTAGGGTTTTAAGGTTTTAGAGTTTTGAT
1 TTTAGGG-TTTAAGGTTTTAGAGATTTGAT
* *
3475305 TTTAGGATTTGAGGTTT
1 TTTAGGGTTTAAGGTTT
3475322 ATAATTTAGG
Statistics
Matches: 66, Mismatches: 6, Indels: 7
0.84 0.08 0.09
Matches are distributed among these distances:
28 17 0.26
29 21 0.32
30 28 0.42
ACGTcount: A:0.21, C:0.00, G:0.29, T:0.50
Consensus pattern (29 bp):
TTTAGGGTTTAAGGTTTTAGAGATTTGAT
Found at i:3475334 original size:14 final size:14
Alignment explanation
Indices: 3475317--3475378 Score: 56
Period size: 14 Copynumber: 4.4 Consensus size: 14
3475307 TAGGATTTGA
3475317 GGTTTATAATTTAG
1 GGTTTATAATTTAG
*
3475331 GGTTTAGAAATTTAG
1 GGTTTA-TAATTTAG
* *
3475346 GATTTCA-ATTTTAG
1 GGTTT-ATAATTTAG
3475360 GGTTT-TGAATTTAG
1 GGTTTAT-AATTTAG
3475374 GGTTT
1 GGTTT
3475379 GAATTTTAAG
Statistics
Matches: 39, Mismatches: 5, Indels: 8
0.75 0.10 0.15
Matches are distributed among these distances:
14 27 0.69
15 11 0.28
16 1 0.03
ACGTcount: A:0.26, C:0.02, G:0.24, T:0.48
Consensus pattern (14 bp):
GGTTTATAATTTAG
Found at i:3475337 original size:58 final size:59
Alignment explanation
Indices: 3475210--3475337 Score: 138
Period size: 58 Copynumber: 2.2 Consensus size: 59
3475200 GATTTTAGGG
* *
3475210 TTTGAGGTTTA-GGTTTTAGAGGATTTAGGATTTTGATTTTAGGGTTTAAGGTTTGGAGA
1 TTTG-GGTTTAGGGTTTTAGAGGATTTAGGATTTTGATTTTAGGATTTAAGGTTTAGAGA
** * * *
3475269 TTTGATTTTAGGGTTTTA-AGGTTTTA-GAGTTTTGATTTTAGGATTTGAGGTTTATA-A
1 TTTGGGTTTAGGGTTTTAGAGGATTTAGGA-TTTTGATTTTAGGATTTAAGGTTTAGAGA
3475326 TTTAGGGTTTAG
1 TTT-GGGTTTAG
3475338 AAATTTAGGA
Statistics
Matches: 57, Mismatches: 9, Indels: 7
0.78 0.12 0.10
Matches are distributed among these distances:
57 6 0.11
58 40 0.70
59 11 0.19
ACGTcount: A:0.22, C:0.00, G:0.29, T:0.49
Consensus pattern (59 bp):
TTTGGGTTTAGGGTTTTAGAGGATTTAGGATTTTGATTTTAGGATTTAAGGTTTAGAGA
Found at i:3475355 original size:28 final size:28
Alignment explanation
Indices: 3475326--3475393 Score: 91
Period size: 28 Copynumber: 2.4 Consensus size: 28
3475316 AGGTTTATAA
3475326 TTTAGGGTTTAGAAATTTAGGATTTCAAT
1 TTTAGGGTTTAG-AATTTAGGATTTCAAT
* * *
3475355 TTTAGGGTTTTGAATTTAGGGTTTGAAT
1 TTTAGGGTTTAGAATTTAGGATTTCAAT
*
3475383 TTTAAGGTTTA
1 TTTAGGGTTTA
3475394 AAGAAAATGC
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
28 23 0.68
29 11 0.32
ACGTcount: A:0.26, C:0.01, G:0.24, T:0.49
Consensus pattern (28 bp):
TTTAGGGTTTAGAATTTAGGATTTCAAT
Found at i:3475386 original size:14 final size:14
Alignment explanation
Indices: 3475326--3475392 Score: 73
Period size: 14 Copynumber: 4.7 Consensus size: 14
3475316 AGGTTTATAA
*
3475326 TTTAGGGTTTAGAAA
1 TTTAGGGTTT-GAAT
* *
3475341 TTTAGGATTTCAAT
1 TTTAGGGTTTGAAT
3475355 TTTAGGGTTTTGAA-
1 TTTAGGG-TTTGAAT
3475369 TTTAGGGTTTGAAT
1 TTTAGGGTTTGAAT
*
3475383 TTTAAGGTTT
1 TTTAGGGTTT
3475393 AAAGAAAATG
Statistics
Matches: 44, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
13 6 0.14
14 24 0.55
15 14 0.32
ACGTcount: A:0.25, C:0.01, G:0.24, T:0.49
Consensus pattern (14 bp):
TTTAGGGTTTGAAT
Found at i:3475539 original size:3 final size:3
Alignment explanation
Indices: 3475533--3475614 Score: 130
Period size: 3 Copynumber: 27.3 Consensus size: 3
3475523 GTTGTTGTTG
3475533 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
* *
3475581 TTA TTA TTA TTT TTA TTG TT- TTA TTA TTTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA T
3475615 CTTTTTTTAT
Statistics
Matches: 74, Mismatches: 3, Indels: 4
0.91 0.04 0.05
Matches are distributed among these distances:
2 2 0.03
3 69 0.93
4 3 0.04
ACGTcount: A:0.29, C:0.00, G:0.01, T:0.70
Consensus pattern (3 bp):
TTA
Found at i:3478710 original size:11 final size:12
Alignment explanation
Indices: 3478682--3478725 Score: 61
Period size: 12 Copynumber: 3.6 Consensus size: 12
3478672 TGGGTTTTGG
*
3478682 AAAAAAAAAACC
1 AAAAAAAAAATC
*
3478694 AAAAAAAAAATAT
1 AAAAAAAAAAT-C
3478707 AAAAAAAAAATC
1 AAAAAAAAAATC
3478719 AAAAAAA
1 AAAAAAA
3478726 GAAGAGCAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
12 17 0.61
13 11 0.39
ACGTcount: A:0.86, C:0.07, G:0.00, T:0.07
Consensus pattern (12 bp):
AAAAAAAAAATC
Found at i:3478736 original size:25 final size:25
Alignment explanation
Indices: 3478681--3478736 Score: 67
Period size: 25 Copynumber: 2.2 Consensus size: 25
3478671 TTGGGTTTTG
*
3478681 GAAAAAAAAAACCAAAAAAAAAATA
1 GAAAAAAAAAACCAAAAAAAAAAGA
* * *
3478706 TAAAAAAAAAATCAAAAAAAGAAGA
1 GAAAAAAAAAACCAAAAAAAAAAGA
*
3478731 GCAAAA
1 GAAAAA
3478737 GGAGAAAAGA
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.80, C:0.07, G:0.07, T:0.05
Consensus pattern (25 bp):
GAAAAAAAAAACCAAAAAAAAAAGA
Found at i:3478954 original size:29 final size:29
Alignment explanation
Indices: 3478910--3479068 Score: 135
Period size: 29 Copynumber: 5.6 Consensus size: 29
3478900 GCAATATAAG
* *
3478910 ATTTAAGCCTAGTTTAATTAACACTTAGA
1 ATTTAAGCCCAGTTTAATTGACACTTAGA
* *
3478939 ATTTAAGCCCAATTTAACTTG-CACATAG-
1 ATTTAAGCCCAGTTTAA-TTGACACTTAGA
* * *
3478967 ATTTAAGCCCAGTTTAACTGGCACTCA-A
1 ATTTAAGCCCAGTTTAATTGACACTTAGA
*
3478995 ATTTAAGCCCAGTTTAGTTGACACTTAGA
1 ATTTAAGCCCAGTTTAATTGACACTTAGA
* ** *** *
3479024 TTTTAAGCTTAGTTTTGCTGGCACTTAGA
1 ATTTAAGCCCAGTTTAATTGACACTTAGA
* *
3479053 TTTTAAGCTCAGTTTA
1 ATTTAAGCCCAGTTTA
3479069 GCTGGTATTC
Statistics
Matches: 106, Mismatches: 20, Indels: 8
0.79 0.15 0.06
Matches are distributed among these distances:
27 2 0.02
28 43 0.41
29 59 0.56
30 2 0.02
ACGTcount: A:0.31, C:0.18, G:0.14, T:0.37
Consensus pattern (29 bp):
ATTTAAGCCCAGTTTAATTGACACTTAGA
Found at i:3479072 original size:29 final size:29
Alignment explanation
Indices: 3478931--3479073 Score: 146
Period size: 29 Copynumber: 5.0 Consensus size: 29
3478921 GTTTAATTAA
* * *
3478931 CACTTAGAATTTAAGCCCAATTTAACTTG
1 CACTTAGAATTTAAGCCCAGTTTAGCTGG
* *
3478960 CACATAG-ATTTAAGCCCAGTTTAACTGG
1 CACTTAGAATTTAAGCCCAGTTTAGCTGG
* * *
3478988 CACTCA-AATTTAAGCCCAGTTTAGTTGA
1 CACTTAGAATTTAAGCCCAGTTTAGCTGG
* ** *
3479016 CACTTAGATTTTAAGCTTAGTTTTGCTGG
1 CACTTAGAATTTAAGCCCAGTTTAGCTGG
* *
3479045 CACTTAGATTTTAAGCTCAGTTTAGCTGG
1 CACTTAGAATTTAAGCCCAGTTTAGCTGG
3479074 TATTCAAATT
Statistics
Matches: 95, Mismatches: 17, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
28 46 0.48
29 49 0.52
ACGTcount: A:0.29, C:0.19, G:0.17, T:0.36
Consensus pattern (29 bp):
CACTTAGAATTTAAGCCCAGTTTAGCTGG
Found at i:3479084 original size:29 final size:29
Alignment explanation
Indices: 3478931--3479073 Score: 121
Period size: 28 Copynumber: 5.0 Consensus size: 29
3478921 GTTTAATTAA
* * *
3478931 CACTTAGAA-TTTAAGCCCAATTTAACTTG
1 CACTTA-AATTTTAAGCCCAGTTTAGCTGG
* * *
3478960 CACATAGA-TTTAAGCCCAGTTTAACTGG
1 CACTTAAATTTTAAGCCCAGTTTAGCTGG
* * *
3478988 CACTCAAA-TTTAAGCCCAGTTTAGTTGA
1 CACTTAAATTTTAAGCCCAGTTTAGCTGG
* ** *
3479016 CACTTAGATTTTAAGCTTAGTTTTGCTGG
1 CACTTAAATTTTAAGCCCAGTTTAGCTGG
* *
3479045 CACTTAGATTTTAAGCTCAGTTTAGCTGG
1 CACTTAAATTTTAAGCCCAGTTTAGCTGG
3479074 TATTCAAATT
Statistics
Matches: 94, Mismatches: 19, Indels: 2
0.82 0.17 0.02
Matches are distributed among these distances:
28 47 0.50
29 47 0.50
ACGTcount: A:0.29, C:0.19, G:0.17, T:0.36
Consensus pattern (29 bp):
CACTTAAATTTTAAGCCCAGTTTAGCTGG
Found at i:3479109 original size:28 final size:28
Alignment explanation
Indices: 3479078--3479132 Score: 85
Period size: 28 Copynumber: 2.0 Consensus size: 28
3479068 AGCTGGTATT
3479078 CAAATTTAAA-TCCAGTTTAACTAGCACA
1 CAAATTTAAACT-CAGTTTAACTAGCACA
*
3479106 CAAATTTAAACTTAGTTTAACTAGCAC
1 CAAATTTAAACTCAGTTTAACTAGCAC
3479133 CCAAGCCTAG
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
28 24 0.96
29 1 0.04
ACGTcount: A:0.42, C:0.20, G:0.07, T:0.31
Consensus pattern (28 bp):
CAAATTTAAACTCAGTTTAACTAGCACA
Found at i:3479165 original size:23 final size:23
Alignment explanation
Indices: 3479130--3479196 Score: 82
Period size: 23 Copynumber: 3.0 Consensus size: 23
3479120 GTTTAACTAG
*
3479130 CACC-CAAGCCTAGATTAGTTGA
1 CACCTCAAGCCTAGATTAGCTGA
* * *
3479152 CACGTCAAGTCTAGATTAACTGA
1 CACCTCAAGCCTAGATTAGCTGA
*
3479175 CACCTTAAGCCTAGATTAGCTG
1 CACCTCAAGCCTAGATTAGCTG
3479197 TCACTTAAGC
Statistics
Matches: 36, Mismatches: 8, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
22 3 0.08
23 33 0.92
ACGTcount: A:0.31, C:0.25, G:0.18, T:0.25
Consensus pattern (23 bp):
CACCTCAAGCCTAGATTAGCTGA
Found at i:3479261 original size:49 final size:51
Alignment explanation
Indices: 3479179--3479288 Score: 134
Period size: 49 Copynumber: 2.2 Consensus size: 51
3479169 AACTGACACC
* * * *
3479179 TTAAGCCTAGATTAGCTGTCACTTAAGCCCAAA-TAGGT-GCACCTAGATT
1 TTAAGCCTAAATTAGCTGGCACCTAAGCCCAAATTAGCTGGCACCTAGATT
* * * *
3479228 TTAAACCTAAATTAGTTGGCACCTAAGCCCAAATTATCTGGCATCTAGATT
1 TTAAGCCTAAATTAGCTGGCACCTAAGCCCAAATTAGCTGGCACCTAGATT
3479279 TTAAGCCTAA
1 TTAAGCCTAA
3479289 TAAAATTGGC
Statistics
Matches: 50, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
49 28 0.56
50 3 0.06
51 19 0.38
ACGTcount: A:0.33, C:0.22, G:0.15, T:0.30
Consensus pattern (51 bp):
TTAAGCCTAAATTAGCTGGCACCTAAGCCCAAATTAGCTGGCACCTAGATT
Found at i:3481575 original size:18 final size:17
Alignment explanation
Indices: 3481552--3481592 Score: 55
Period size: 18 Copynumber: 2.4 Consensus size: 17
3481542 GAAAAAAAGG
*
3481552 GAAAAAATAAAAGAGAAA
1 GAAAAAAAAAAAG-GAAA
*
3481570 GAAAAAAAAAAAGGGAA
1 GAAAAAAAAAAAGGAAA
3481587 GAAAAA
1 GAAAAA
3481593 TGAAGAAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 9 0.43
18 12 0.57
ACGTcount: A:0.78, C:0.00, G:0.20, T:0.02
Consensus pattern (17 bp):
GAAAAAAAAAAAGGAAA
Found at i:3481577 original size:14 final size:14
Alignment explanation
Indices: 3481540--3481577 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
3481530 AAGATTCGAC
*
3481540 AAGAAAAAAAGGGA
1 AAGAAAAAAAGAGA
3481554 AA-AAATAAAAGAGA
1 AAGAAA-AAAAGAGA
3481568 AAGAAAAAAA
1 AAGAAAAAAA
3481578 AAAAGGGAAG
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
13 3 0.14
14 15 0.71
15 3 0.14
ACGTcount: A:0.79, C:0.00, G:0.18, T:0.03
Consensus pattern (14 bp):
AAGAAAAAAAGAGA
Found at i:3481633 original size:18 final size:17
Alignment explanation
Indices: 3481552--3481654 Score: 62
Period size: 17 Copynumber: 5.6 Consensus size: 17
3481542 GAAAAAAAGG
* *
3481552 GAAAAAATAAAAGAGAAA
1 GAAAAAA-AAAAAAAAAA
***
3481570 GAAAAAAAAAAAGGGAA
1 GAAAAAAAAAAAAAAAA
*
3481587 GAAAAATGAAGAAAAAAATTGA
1 GAAAAA--AA-AAAAAAA--AA
*
3481609 GAAAAAAAAATAAAAAA
1 GAAAAAAAAAAAAAAAA
*
3481626 GAAAAAAAAAAGAAAGAA
1 GAAAAAAAAAA-AAAAAA
3481644 GAAGAAAAAAA
1 GAA-AAAAAAA
3481655 GAGAGAAAAC
Statistics
Matches: 67, Mismatches: 11, Indels: 13
0.74 0.12 0.14
Matches are distributed among these distances:
17 24 0.36
18 15 0.22
19 15 0.22
20 6 0.09
22 7 0.10
ACGTcount: A:0.79, C:0.00, G:0.17, T:0.05
Consensus pattern (17 bp):
GAAAAAAAAAAAAAAAA
Found at i:3481651 original size:15 final size:14
Alignment explanation
Indices: 3481615--3481663 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 14
3481605 TTGAGAAAAA
*
3481615 AAAATAAAAAAGAAA
1 AAAA-AAAAAAGAAG
3481630 AAAAAAAGAAAGAAG
1 AAAAAAA-AAAGAAG
*
3481645 AAGAAAAAAAGAGAG
1 AAAAAAAAAAGA-AG
3481660 AAAA
1 AAAA
3481664 CGCCAACTAG
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
14 8 0.28
15 21 0.72
ACGTcount: A:0.82, C:0.00, G:0.16, T:0.02
Consensus pattern (14 bp):
AAAAAAAAAAGAAG
Found at i:3481655 original size:18 final size:17
Alignment explanation
Indices: 3481608--3481661 Score: 63
Period size: 18 Copynumber: 3.1 Consensus size: 17
3481598 AAAAAAATTG
* *
3481608 AGAAAAAAAAATAAAAA
1 AGAAAAAAAAAGAAAGA
3481625 AGAAAAAAAAAAGAAAGA
1 AG-AAAAAAAAAGAAAGA
*
3481643 AGAAGAAAAAAAGAGAGA
1 AGAA-AAAAAAAGAAAGA
3481661 A
1 A
3481662 AACGCCAACT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
17 4 0.12
18 28 0.88
ACGTcount: A:0.81, C:0.00, G:0.17, T:0.02
Consensus pattern (17 bp):
AGAAAAAAAAAGAAAGA
Found at i:3481966 original size:26 final size:26
Alignment explanation
Indices: 3481899--3481948 Score: 84
Period size: 26 Copynumber: 2.0 Consensus size: 26
3481889 CTCGAATCAG
3481899 TTAGCCCAA-CAACCTATTTACTCTC
1 TTAGCCCAACCAACCTATTTACTCTC
*
3481924 TTAGCCCAACCGACCTATTTACTCT
1 TTAGCCCAACCAACCTATTTACTCT
3481949 TCTGGCCCAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 9 0.39
26 14 0.61
ACGTcount: A:0.26, C:0.36, G:0.06, T:0.32
Consensus pattern (26 bp):
TTAGCCCAACCAACCTATTTACTCTC
Found at i:3482882 original size:15 final size:15
Alignment explanation
Indices: 3482853--3482915 Score: 67
Period size: 15 Copynumber: 4.3 Consensus size: 15
3482843 CTAAAACTTC
*
3482853 AAAAT-TAAAATCCT
1 AAAATCTAAAACCCT
3482867 AAAATCTAAAACCCT
1 AAAATCTAAAACCCT
* *
3482882 AGAATCGAAAACTCC-
1 AAAATCTAAAAC-CCT
*
3482897 AAAATCCAAAACCCT
1 AAAATCTAAAACCCT
3482912 AAAA
1 AAAA
3482916 CCTCGAAATT
Statistics
Matches: 41, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
14 7 0.17
15 32 0.78
16 2 0.05
ACGTcount: A:0.56, C:0.24, G:0.03, T:0.17
Consensus pattern (15 bp):
AAAATCTAAAACCCT
Found at i:3482953 original size:29 final size:28
Alignment explanation
Indices: 3482921--3483003 Score: 76
Period size: 29 Copynumber: 2.8 Consensus size: 28
3482911 TAAAACCTCG
*
3482921 AAATTAAAACCTTAAAACCTGAGACCCTA
1 AAATTAAAACCTTAAAACCT-AAACCCTA
* * * *
3482950 AAATCAATACCCTAAAACTCTAAACTCTA
1 AAATTAAAACCTTAAAAC-CTAAACCCTA
*
3482979 AAACTTAAAACCTTGAAACCCTAAA
1 AAA-TTAAAACCTT-AAAACCTAAA
3483004 TTTAGCCAAA
Statistics
Matches: 42, Mismatches: 9, Indels: 5
0.75 0.16 0.09
Matches are distributed among these distances:
29 24 0.57
30 14 0.33
31 4 0.10
ACGTcount: A:0.49, C:0.25, G:0.04, T:0.22
Consensus pattern (28 bp):
AAATTAAAACCTTAAAACCTAAACCCTA
Found at i:3482986 original size:51 final size:53
Alignment explanation
Indices: 3482897--3483003 Score: 141
Period size: 51 Copynumber: 2.1 Consensus size: 53
3482887 CGAAAACTCC
*
3482897 AAAATCCAAAACCCTAAAACCTCGAAATTAAAACCTTAAAACC-TGAGACCCT
1 AAAATCCAAAACCCTAAAACCTCGAAATTAAAACCTTAAAACCTTGAAACCCT
* *
3482949 AAAAT-CAATACCCTAAAA-CTCTAAACTCTAAAA-CTTAAAACCTTGAAACCCT
1 AAAATCCAAAACCCTAAAACCTCGAAA-T-TAAAACCTTAAAACCTTGAAACCCT
3483001 AAA
1 AAA
3483004 TTTAGCCAAA
Statistics
Matches: 49, Mismatches: 3, Indels: 6
0.84 0.05 0.10
Matches are distributed among these distances:
50 6 0.12
51 22 0.45
52 21 0.43
ACGTcount: A:0.50, C:0.27, G:0.04, T:0.20
Consensus pattern (53 bp):
AAAATCCAAAACCCTAAAACCTCGAAATTAAAACCTTAAAACCTTGAAACCCT
Found at i:3485519 original size:2 final size:2
Alignment explanation
Indices: 3485512--3485574 Score: 108
Period size: 2 Copynumber: 31.5 Consensus size: 2
3485502 CTAAGTCATC
*
3485512 AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
3485554 AC AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT A
3485575 GGTTTTAAAC
Statistics
Matches: 57, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 57 1.00
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3487262 original size:31 final size:32
Alignment explanation
Indices: 3487224--3487284 Score: 88
Period size: 31 Copynumber: 1.9 Consensus size: 32
3487214 GATATTAATC
*
3487224 CTTTTATTTCTAGAAG-GAAATTTTAGGTATT
1 CTTTTATTTCTAGAAGACAAATTTTAGGTATT
* *
3487255 CTTTTATTTTTTGAAGACAAATTTTAGGTA
1 CTTTTATTTCTAGAAGACAAATTTTAGGTA
3487285 AACTTAGATT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
31 14 0.54
32 12 0.46
ACGTcount: A:0.30, C:0.07, G:0.15, T:0.49
Consensus pattern (32 bp):
CTTTTATTTCTAGAAGACAAATTTTAGGTATT
Found at i:3488770 original size:2 final size:2
Alignment explanation
Indices: 3488763--3488795 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
3488753 CTTGTTGTCT
*
3488763 TA TA TA TA TA TA TA TA TA TA TA TA TG TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3488796 TAAAATCGGT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3502670 original size:16 final size:16
Alignment explanation
Indices: 3502649--3502683 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
3502639 AATATTTTGT
3502649 ATATATATTTTAA-TAA
1 ATATAT-TTTTAATTAA
3502665 ATATATTTTTAATTAA
1 ATATATTTTTAATTAA
3502681 ATA
1 ATA
3502684 ATGTAAATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 6 0.33
16 12 0.67
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (16 bp):
ATATATTTTTAATTAA
Found at i:3502726 original size:26 final size:26
Alignment explanation
Indices: 3502664--3502753 Score: 80
Period size: 26 Copynumber: 3.5 Consensus size: 26
3502654 TATTTTAATA
*
3502664 AATATATTTTTA-ATTAAAT-AATGT
1 AATATATTTTTATATTAAATAAAAGT
*
3502688 AA-ATTATTATTTTATATTAATTAAAAGT
1 AATA-TA-T-TTTTATATTAAATAAAAGT
* *
3502716 AATATATTTTTAT-TTAAATATATATT
1 AATATATTTTTATATTAAATA-AAAGT
3502742 AATATATTTTTA
1 AATATATTTTTA
3502754 AAAAATTACT
Statistics
Matches: 54, Mismatches: 5, Indels: 12
0.76 0.07 0.17
Matches are distributed among these distances:
23 1 0.02
24 4 0.07
25 7 0.13
26 26 0.48
27 7 0.13
28 8 0.15
29 1 0.02
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.53
Consensus pattern (26 bp):
AATATATTTTTATATTAAATAAAAGT
Found at i:3514202 original size:21 final size:21
Alignment explanation
Indices: 3514176--3514219 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
3514166 ATAATCAATC
*
3514176 AATAAATTAAAAATATAATTA
1 AATAAATTAAAAATAAAATTA
* *
3514197 AATAAATTTAATATAAAATTA
1 AATAAATTAAAAATAAAATTA
3514218 AA
1 AA
3514220 CTAATTCCGC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (21 bp):
AATAAATTAAAAATAAAATTA
Found at i:3514897 original size:132 final size:133
Alignment explanation
Indices: 3514660--3514922 Score: 483
Period size: 132 Copynumber: 2.0 Consensus size: 133
3514650 AGTATTTTTA
3514660 CGTTTTGGTCAAGCCACGTGATATGGTTGGGTATTAATTAACCTTGGTTATGTATGTTATTACAT
1 CGTTTTGGTCAAGCCACGTGATATGGTTGGGTATTAATTAACCTTGGTTATGTATGTTATTACAT
*
3514725 TTGTGCCATCCACCGTGGATTTTAAAAAACCAATCAAAATC-TGTCATTATCTTAAACTAGCAGT
66 TTGTGCCATCCACCGTGGATTTTAAAAAACCAACCAAAATCTTGTCATTATCTTAAACTAGCAGT
3514789 TTG
131 TTG
*
3514792 CGTTTTGGTCAAGCCACGTGATATGGTTGGGTATTAATTAACCTTGGTTATGTATTTTATTACAT
1 CGTTTTGGTCAAGCCACGTGATATGGTTGGGTATTAATTAACCTTGGTTATGTATGTTATTACAT
*
3514857 TTGTGCCATCCACCGTGGATTTTAAAAAACCAACCAAAATCTTTGTCATTGTCTTAAACTAGCAG
66 TTGTGCCATCCACCGTGGATTTTAAAAAACCAACCAAAATC-TTGTCATTATCTTAAACTAGCAG
3514922 T
130 T
3514923 AAAGAAATAG
Statistics
Matches: 126, Mismatches: 3, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
132 104 0.83
134 22 0.17
ACGTcount: A:0.28, C:0.17, G:0.18, T:0.37
Consensus pattern (133 bp):
CGTTTTGGTCAAGCCACGTGATATGGTTGGGTATTAATTAACCTTGGTTATGTATGTTATTACAT
TTGTGCCATCCACCGTGGATTTTAAAAAACCAACCAAAATCTTGTCATTATCTTAAACTAGCAGT
TTG
Found at i:3526140 original size:8 final size:8
Alignment explanation
Indices: 3526129--3526192 Score: 53
Period size: 8 Copynumber: 8.2 Consensus size: 8
3526119 TTTATATACT
3526129 TAATTAAA
1 TAATTAAA
3526137 TAATT-AA
1 TAATTAAA
* *
3526144 TTATTATA
1 TAATTAAA
* *
3526152 TTATTAAT
1 TAATTAAA
3526160 TAA-TAAA
1 TAATTAAA
*
3526167 TTA-TAATA
1 TAATTAA-A
3526175 TAATTAAA
1 TAATTAAA
3526183 TAATTAAA
1 TAATTAAA
3526191 TA
1 TA
3526193 CAAATACATT
Statistics
Matches: 45, Mismatches: 8, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
7 14 0.31
8 28 0.62
9 3 0.07
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (8 bp):
TAATTAAA
Found at i:3526163 original size:23 final size:23
Alignment explanation
Indices: 3526129--3526189 Score: 86
Period size: 23 Copynumber: 2.7 Consensus size: 23
3526119 TTTATATACT
*
3526129 TAATTAAATAATTAATTATTATA
1 TAATTAAATAATTAATTATAATA
* * *
3526152 TTATTAATTAATAAATTATAATA
1 TAATTAAATAATTAATTATAATA
3526175 TAATTAAATAATTAA
1 TAATTAAATAATTAA
3526190 ATACAAATAC
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (23 bp):
TAATTAAATAATTAATTATAATA
Found at i:3526185 original size:20 final size:20
Alignment explanation
Indices: 3526137--3526181 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 20
3526127 CTTAATTAAA
* *
3526137 TAATTAAT-TATTATATTAT
1 TAATTAATAAATTATAATAT
3526156 TAATTAATAAATTATAATA-
1 TAATTAATAAATTATAATAT
3526175 TAATTAA
1 TAATTAA
3526182 ATAATTAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 15 0.65
20 8 0.35
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (20 bp):
TAATTAATAAATTATAATAT
Found at i:3526896 original size:18 final size:17
Alignment explanation
Indices: 3526869--3526929 Score: 63
Period size: 18 Copynumber: 3.5 Consensus size: 17
3526859 TTTATTTAAT
3526869 AAAATT-AATTTATAAA
1 AAAATTAAATTTATAAA
3526885 AAATATTAAATTT-TAAA
1 AAA-ATTAAATTTATAAA
* *
3526902 TCAAATCAAATATTATAAA
1 -AAAATTAAAT-TTATAAA
3526921 AAAATTAAA
1 AAAATTAAA
3526930 ATTAAATTTA
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
16 3 0.08
17 13 0.36
18 16 0.44
19 4 0.11
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.34
Consensus pattern (17 bp):
AAAATTAAATTTATAAA
Found at i:3529498 original size:26 final size:26
Alignment explanation
Indices: 3529458--3529519 Score: 74
Period size: 26 Copynumber: 2.4 Consensus size: 26
3529448 TTCATTCATG
3529458 AATAT-TAAATAAATATATTTAT-AAA
1 AATATATAAATAAATA-ATTTATGAAA
* *
3529483 TATATATAAATGAATAATTTATGAAA
1 AATATATAAATAAATAATTTATGAAA
*
3529509 AATAAATAAAT
1 AATATATAAAT
3529520 TTAAATAAAC
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
25 10 0.32
26 21 0.68
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.37
Consensus pattern (26 bp):
AATATATAAATAAATAATTTATGAAA
Found at i:3546110 original size:3 final size:3
Alignment explanation
Indices: 3546102--3546139 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
3546092 ACACTGATTT
3546102 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
3546140 TGTGGATACT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:3546419 original size:15 final size:15
Alignment explanation
Indices: 3546399--3546431 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
3546389 AACTTTTACT
3546399 AAAAGTTATTTCATA
1 AAAAGTTATTTCATA
*
3546414 AAAAGTTATTTTATA
1 AAAAGTTATTTCATA
3546429 AAA
1 AAA
3546432 GACATCAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.52, C:0.03, G:0.06, T:0.39
Consensus pattern (15 bp):
AAAAGTTATTTCATA
Found at i:3546431 original size:14 final size:14
Alignment explanation
Indices: 3546392--3546432 Score: 55
Period size: 15 Copynumber: 2.8 Consensus size: 14
3546382 TAATGAAAAC
3546392 TTTTACTAAAAGTTA
1 TTTTA-TAAAAGTTA
*
3546407 TTTCATAAAAAGTTA
1 TTTTAT-AAAAGTTA
3546422 TTTTATAAAAG
1 TTTTATAAAAG
3546433 ACATCAAATG
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
14 6 0.26
15 17 0.74
ACGTcount: A:0.44, C:0.05, G:0.07, T:0.44
Consensus pattern (14 bp):
TTTTATAAAAGTTA
Found at i:3550380 original size:36 final size:36
Alignment explanation
Indices: 3550340--3550532 Score: 120
Period size: 46 Copynumber: 4.8 Consensus size: 36
3550330 TATATATTTC
3550340 TTACTTATTCTACTATTTTTTAAGGAAAAACTTTGT
1 TTACTTATTCTACTATTTTTTAAGGAAAAACTTTGT
* *
3550376 TTACTTATTCTCCTATTTTCCCATTTTTTTTAAGGAAATATA-TTT-C
1 TTACTTA-T-T-CTA------C-TATTTTTTAAGGAAA-A-ACTTTGT
3550422 TTACTTATTCTACTATTTTTTAAGGAAAAACTTTGT
1 TTACTTATTCTACTATTTTTTAAGGAAAAACTTTGT
**
3550458 TTACTTATTCTCTTATTTTCCTATTTTTTTTAAGGAAAAACTTTCA
1 TTACTTA-T-TC-TA-----CTA--TTTTTTAAGGAAAAACTTTGT
*
3550504 TTACTTATTCTCCTATTTTTTTAAGGAAA
1 TTACTTATTCTACTA-TTTTTTAAGGAAA
3550533 CACTCTTATT
Statistics
Matches: 126, Mismatches: 7, Indels: 47
0.70 0.04 0.26
Matches are distributed among these distances:
34 1 0.01
35 4 0.03
36 28 0.22
37 17 0.13
38 6 0.05
39 5 0.04
43 4 0.03
44 6 0.05
45 3 0.02
46 47 0.37
47 4 0.03
48 1 0.01
ACGTcount: A:0.27, C:0.14, G:0.06, T:0.52
Consensus pattern (36 bp):
TTACTTATTCTACTATTTTTTAAGGAAAAACTTTGT
Found at i:3550426 original size:46 final size:46
Alignment explanation
Indices: 3550355--3550522 Score: 173
Period size: 46 Copynumber: 3.9 Consensus size: 46
3550345 TATTCTACTA
*
3550355 TTTTTTAAGGAAAAACTTTGTTTACTTATTCTCCTATTTTCCCATT
1 TTTTTTAAGGAAAAACTTTGCTTACTTATTCTCCTATTTTCCCATT
*
3550401 TTTTTTAAGGAAATATA-TTT-CTTACTTA-T-T-CTA------C-TA
1 TTTTTTAAGGAAA-A-ACTTTGCTTACTTATTCTCCTATTTTCCCATT
* * *
3550437 TTTTTTAAGGAAAAACTTTGTTTACTTATTCTCTTATTTTCCTATT
1 TTTTTTAAGGAAAAACTTTGCTTACTTATTCTCCTATTTTCCCATT
3550483 TTTTTTAAGGAAAAACTTT-CATTACTTATTCTCCTATTTT
1 TTTTTTAAGGAAAAACTTTGC-TTACTTATTCTCCTATTTT
3550523 TTTAAGGAAA
Statistics
Matches: 99, Mismatches: 8, Indels: 30
0.72 0.06 0.22
Matches are distributed among these distances:
34 1 0.01
35 4 0.04
36 21 0.21
37 2 0.02
38 1 0.01
39 2 0.02
43 3 0.03
44 1 0.01
45 1 0.01
46 58 0.59
47 4 0.04
48 1 0.01
ACGTcount: A:0.26, C:0.14, G:0.06, T:0.54
Consensus pattern (46 bp):
TTTTTTAAGGAAAAACTTTGCTTACTTATTCTCCTATTTTCCCATT
Found at i:3550431 original size:82 final size:82
Alignment explanation
Indices: 3550331--3550559 Score: 347
Period size: 82 Copynumber: 2.8 Consensus size: 82
3550321 TTGTTTTCTT
*
3550331 ATATATTTCTTACTTATTCTACTATTTTTTAAGGAAAAACTTTGTTTACTTATTCTCCTATTTTC
1 ATATATTTCTTACTTATTCTACTATTTTTTAAGGAAAAACTTTGTTTACTTATTCTCTTATTTTC
3550396 CCATTTTTTTTAAGGAA
66 CCATTTTTTTTAAGGAA
3550413 ATATATTTCTTACTTATTCTACTATTTTTTAAGGAAAAACTTTGTTTACTTATTCTCTTATTTTC
1 ATATATTTCTTACTTATTCTACTATTTTTTAAGGAAAAACTTTGTTTACTTATTCTCTTATTTTC
*
3550478 CTATTTTTTTTAAGGAA
66 CCATTTTTTTTAAGGAA
* * * *
3550495 A-A-ACTTTCATTACTTATTCTCCTATTTTTTTAAGGAAACACTCTT-ATTACTTGTTCTCTTAT
1 ATATA-TTTC-TTACTTATTCTACTA-TTTTTTAAGGAAAAACT-TTGTTTACTTATTCTCTTAT
3550557 TTT
62 TTT
3550560 TTGAAAAATA
Statistics
Matches: 137, Mismatches: 6, Indels: 7
0.91 0.04 0.05
Matches are distributed among these distances:
80 1 0.01
81 5 0.04
82 95 0.69
83 34 0.25
84 2 0.01
ACGTcount: A:0.26, C:0.15, G:0.06, T:0.53
Consensus pattern (82 bp):
ATATATTTCTTACTTATTCTACTATTTTTTAAGGAAAAACTTTGTTTACTTATTCTCTTATTTTC
CCATTTTTTTTAAGGAA
Found at i:3550532 original size:37 final size:37
Alignment explanation
Indices: 3550469--3550709 Score: 147
Period size: 37 Copynumber: 6.5 Consensus size: 37
3550459 TACTTATTCT
*
3550469 CTTATTTTCCTATTTTTTTTAAGGAAAAACT-TTCATTA
1 CTTATTCTCCTA-TTTTTTTAAGGAAAAACTCTT-ATTA
*
3550507 CTTATTCTCCTATTTTTTTAAGGAAACACTCTTATTA
1 CTTATTCTCCTATTTTTTTAAGGAAAAACTCTTATTA
* * * * * *
3550544 CTTGTTCTCTTATTTTTTGAA--AAATATTCATATTA
1 CTTATTCTCCTATTTTTTTAAGGAAAAACTCTTATTA
* * * * *
3550579 CTTGTTTTCTTA-ATTTTTCA-GATAAACACTCTTATTA
1 CTTATTCTCCTATTTTTTTAAGGA-AAA-ACTCTTATTA
* * * **
3550616 CTTGTTCTTCTA-TTTTTT-AGAGAAACACTCGCATTA
1 CTTATTCTCCTATTTTTTTAAG-GAAAAACTCTTATTA
* **
3550652 CTTATTCTCTTATTTTTCTTAAGGGAACCACTCTTATTA
1 CTTATTCTCCTATTTTT-TTAA-GGAAAAACTCTTATTA
* * *
3550691 CTAATT-TTCTAATTTTTTA
1 CTTATTCTCCTATTTTTTTA
3550710 GAGAAATTCT
Statistics
Matches: 161, Mismatches: 32, Indels: 21
0.75 0.15 0.10
Matches are distributed among these distances:
34 5 0.03
35 23 0.14
36 20 0.12
37 70 0.43
38 24 0.15
39 18 0.11
40 1 0.01
ACGTcount: A:0.27, C:0.16, G:0.06, T:0.51
Consensus pattern (37 bp):
CTTATTCTCCTATTTTTTTAAGGAAAAACTCTTATTA
Found at i:3550580 original size:72 final size:73
Alignment explanation
Indices: 3550502--3550711 Score: 221
Period size: 72 Copynumber: 2.9 Consensus size: 73
3550492 GAAAAACTTT
*
3550502 CATTACTTATTCTCCTATTTTTTTAAGGAAACACTCTTATTACTTGTTC-TCTTATTTTTT-GAA
1 CATTACTTATTCTCTTATTTTTTTAAGGAAACACTCTTATTACTTGTTCTTC-TATTTTTTAGAA
* *
3550565 AAATATTCA
65 AAACACTCA
* * * * * * *
3550574 TATTACTTGTTTTCTTA-ATTTTTCAGATAAACACTCTTATTACTTGTTCTTCTATTTTTTAGAG
1 CATTACTTATTCTCTTATTTTTTTAAG-GAAACACTCTTATTACTTGTTCTTCTATTTTTTAGAA
*
3550638 AAACACTCG
65 AAACACTCA
* **
3550647 CATTACTTATTCTCTTATTTTTCTTAAGGGAACCACTCTTATTACTAATT-TTCTAATTTTTTAG
1 CATTACTTATTCTCTTATTTTT-TTAA-GGAAACACTCTTATTACTTGTTCTTCT-ATTTTTTAG
3550711 A
63 A
3550712 GAAATTCTTT
Statistics
Matches: 111, Mismatches: 20, Indels: 11
0.78 0.14 0.08
Matches are distributed among these distances:
71 7 0.06
72 42 0.38
73 24 0.22
74 7 0.06
75 30 0.27
76 1 0.01
ACGTcount: A:0.27, C:0.17, G:0.07, T:0.50
Consensus pattern (73 bp):
CATTACTTATTCTCTTATTTTTTTAAGGAAACACTCTTATTACTTGTTCTTCTATTTTTTAGAAA
AACACTCA
Found at i:3550631 original size:36 final size:36
Alignment explanation
Indices: 3550530--3550669 Score: 149
Period size: 36 Copynumber: 3.9 Consensus size: 36
3550520 TTTTTTAAGG
*
3550530 AAACACTCTTATTACTTGTTCTCTTATTTTT-TGAA
1 AAACACTCTTATTACTTGTTCTCTTATTTTTCAGAA
* * * * *
3550565 AAATATTCATATTACTTGTTTTCTTAATTTTTCAGAT
1 AAACACTCTTATTACTTGTTCTCTT-ATTTTTCAGAA
* *
3550602 AAACACTCTTATTACTTGTTCT-TCTATTTTTTAGAG
1 AAACACTCTTATTACTTGTTCTCT-TATTTTTCAGAA
** *
3550638 AAACACTCGCATTACTTATTCTCTTATTTTTC
1 AAACACTCTTATTACTTGTTCTCTTATTTTTC
3550670 TTAAGGGAAC
Statistics
Matches: 85, Mismatches: 16, Indels: 7
0.79 0.15 0.06
Matches are distributed among these distances:
35 21 0.25
36 42 0.49
37 22 0.26
ACGTcount: A:0.26, C:0.17, G:0.06, T:0.51
Consensus pattern (36 bp):
AAACACTCTTATTACTTGTTCTCTTATTTTTCAGAA
Found at i:3553393 original size:2 final size:2
Alignment explanation
Indices: 3553386--3553420 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
3553376 GATCTATTAC
*
3553386 AT AT AT AT AT AT AT AT AT AT AT AT AT AC AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3553421 ATTACACTAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:3554307 original size:21 final size:20
Alignment explanation
Indices: 3554255--3554319 Score: 68
Period size: 17 Copynumber: 3.5 Consensus size: 20
3554245 TATGTTGAAA
3554255 TTATTTTAAATATATA-ATT
1 TTATTTTAAATATATATATT
*
3554274 TT-TTAT-AATATAT-T-TT
1 TTATTTTAAATATATATATT
*
3554290 ATATTATTAAATATATATATT
1 TTATT-TTAAATATATATATT
3554311 TTATTTTAA
1 TTATTTTAA
3554320 CATGAATGAT
Statistics
Matches: 36, Mismatches: 4, Indels: 11
0.71 0.08 0.22
Matches are distributed among these distances:
16 3 0.08
17 9 0.25
18 4 0.11
19 9 0.25
20 5 0.14
21 6 0.17
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (20 bp):
TTATTTTAAATATATATATT
Found at i:3557373 original size:32 final size:32
Alignment explanation
Indices: 3557326--3557399 Score: 114
Period size: 32 Copynumber: 2.3 Consensus size: 32
3557316 AGATGAAATT
*
3557326 AAATGAAATC-CACGTGCATTAATATTTTATC
1 AAATGAAATCAAACGTGCATTAATATTTTATC
*
3557357 AAATGAAATCAAACGTGTATTAATATTTTATC
1 AAATGAAATCAAACGTGCATTAATATTTTATC
*
3557389 AAATAAAATCA
1 AAATGAAATCA
3557400 TATTTAATGA
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
31 10 0.26
32 29 0.74
ACGTcount: A:0.46, C:0.12, G:0.08, T:0.34
Consensus pattern (32 bp):
AAATGAAATCAAACGTGCATTAATATTTTATC
Found at i:3557404 original size:20 final size:21
Alignment explanation
Indices: 3557379--3557437 Score: 70
Period size: 20 Copynumber: 3.0 Consensus size: 21
3557369 ACGTGTATTA
*
3557379 ATATTTTATCAAATA-AAATC
1 ATATTTAATCAAATATAAATC
*
3557399 ATATTTAATGAAATATAAATC
1 ATATTTAATCAAATATAAATC
*
3557420 -TA-TCAATCAAATATAAAT
1 ATATTTAATCAAATATAAAT
3557438 TAATAAAATA
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
19 14 0.41
20 15 0.44
21 5 0.15
ACGTcount: A:0.53, C:0.08, G:0.02, T:0.37
Consensus pattern (21 bp):
ATATTTAATCAAATATAAATC
Found at i:3557433 original size:19 final size:21
Alignment explanation
Indices: 3557386--3557437 Score: 65
Period size: 19 Copynumber: 2.6 Consensus size: 21
3557376 TTAATATTTT
*
3557386 ATCAAATA-AAATCATATTTA
1 ATCAAATATAAATCATATTCA
*
3557406 ATGAAATATAAATC-TA-TCA
1 ATCAAATATAAATCATATTCA
3557425 ATCAAATATAAAT
1 ATCAAATATAAAT
3557438 TAATAAAATA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
19 14 0.50
20 9 0.32
21 5 0.18
ACGTcount: A:0.56, C:0.10, G:0.02, T:0.33
Consensus pattern (21 bp):
ATCAAATATAAATCATATTCA
Found at i:3558690 original size:270 final size:262
Alignment explanation
Indices: 3558172--3558690 Score: 670
Period size: 259 Copynumber: 1.9 Consensus size: 262
3558162 ATACATGAAA
* *
3558172 TATATCATGAAATACATCAATTACTCAAATGGATATTATATTTAATCAAATATAAATGTATCAAA
1 TATATCATGAAATACATCAATTACT---ATGAATACTATATTTAATCAAATATAAATGTATCAAA
* *
3558237 TAATTAATTAAAGAATCAACTATTTTATAATTGTAATTATAATATTTATAATTTATTAATTATAT
63 TAATTAATTAAAGAATCAACTATTTTATAATTATAATTATAATATTTATAATTTATTAATTATAC
3558302 ATTGATTGATTTAATTTGTCAAAATAAAAAGTTTTAAAATTTTAATATGAATTAAATTGAAAGTG
128 ATTGATTGATTTAATTTGTCAAAATAAAAAGTTTTAAAATTTTAATATGAATTAAATTGAAAGTG
* *
3558367 ATTTAAAATCAATAATAAAAATATAAATATAATCAATTTCGTGTTTTGAATTATATTCGCTTTAT
193 ATTTAAAATCAATAATAAAAACATAAATATAATCAATTTAGTGTTTTGAATTATATTCGCTTTAT
3558432 ATATT
258 ATATT
*
3558437 TATAT-ATGAAATACATCAATTA-T-TGAATACTATATTTAATCAAATATAAATGTATCAAATGA
1 TATATCATGAAATACATCAATTACTATGAATACTATATTTAATCAAATATAAATGTATCAAATAA
* * * * * *
3558499 TTGATTAGAGAATCAACTATTTTATAATTATAATTGTAGTATTTATTGATTTATTAATTCTACAT
66 TTAATTAAAGAATCAACTATTTTATAATTATAATTATAATATTTA-TAATTTATTAATTATACAT
* * *
3558564 TGATTGATTTAATTTGTCATATTAAGAAAATTTAAAAA-TTTTAATACTTTTAATATGAGTTGAA
130 TGATTGATTTAATTTGTC--------AAAA--TAAAAAGTTTTAA-AATTTTAATATGAATTAAA
** * * *
3558628 TTGACAA-TGATTTAATGTTAATAATAAAAACATAAATATAATCAATTTATTTTTTTGAATTAT
184 TTGA-AAGTGATTTAAAATCAATAATAAAAACATAAATATAATCAATTTAGTGTTTTGAATTAT
3558691 TTTTAAATTA
Statistics
Matches: 220, Mismatches: 21, Indels: 21
0.84 0.08 0.08
Matches are distributed among these distances:
259 76 0.35
260 34 0.15
263 1 0.00
264 17 0.08
265 5 0.02
268 4 0.02
269 6 0.03
270 75 0.34
271 2 0.01
ACGTcount: A:0.44, C:0.06, G:0.08, T:0.43
Consensus pattern (262 bp):
TATATCATGAAATACATCAATTACTATGAATACTATATTTAATCAAATATAAATGTATCAAATAA
TTAATTAAAGAATCAACTATTTTATAATTATAATTATAATATTTATAATTTATTAATTATACATT
GATTGATTTAATTTGTCAAAATAAAAAGTTTTAAAATTTTAATATGAATTAAATTGAAAGTGATT
TAAAATCAATAATAAAAACATAAATATAATCAATTTAGTGTTTTGAATTATATTCGCTTTATATA
TT
Found at i:3565652 original size:6 final size:6
Alignment explanation
Indices: 3565641--3565666 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
3565631 AGTACAAGTT
3565641 CAGAAA CAGAAA CAGAAA CAGAAA CA
1 CAGAAA CAGAAA CAGAAA CAGAAA CA
3565667 AATAGATTAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.65, C:0.19, G:0.15, T:0.00
Consensus pattern (6 bp):
CAGAAA
Found at i:3568609 original size:21 final size:21
Alignment explanation
Indices: 3568584--3568623 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
3568574 CCCCTATTTC
*
3568584 TCTCCTCATTATATTACAAGT
1 TCTCCTCATCATATTACAAGT
3568605 TCTCCTCATCATATTACAA
1 TCTCCTCATCATATTACAA
3568624 ATTATTCTGC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.28, G:0.03, T:0.40
Consensus pattern (21 bp):
TCTCCTCATCATATTACAAGT
Found at i:3572153 original size:17 final size:17
Alignment explanation
Indices: 3572131--3572164 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
3572121 TCTAAAACTG
3572131 GAAGTGTAATATTTCCA
1 GAAGTGTAATATTTCCA
3572148 GAAGTGTAATATTTCCA
1 GAAGTGTAATATTTCCA
3572165 TACATTCTGC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.35, C:0.12, G:0.18, T:0.35
Consensus pattern (17 bp):
GAAGTGTAATATTTCCA
Found at i:3574309 original size:26 final size:24
Alignment explanation
Indices: 3574265--3574323 Score: 66
Period size: 25 Copynumber: 2.4 Consensus size: 24
3574255 CTTTCTAACA
* *
3574265 TAATATATAATTATTAATTTAATTG
1 TAATATACAATTATGAA-TTAATTG
3574290 TAATATTACAATTATGAATTAATT-
1 TAATA-TACAATTATGAATTAATTG
3574314 TACATATACA
1 TA-ATATACA
3574324 TGAATTAGTA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
24 6 0.20
25 14 0.47
26 10 0.33
ACGTcount: A:0.46, C:0.05, G:0.03, T:0.46
Consensus pattern (24 bp):
TAATATACAATTATGAATTAATTG
Found at i:3584826 original size:17 final size:17
Alignment explanation
Indices: 3584806--3584841 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
3584796 TTGATTTTTT
3584806 TTTTGTCTCAGAGTTTG
1 TTTTGTCTCAGAGTTTG
*
3584823 TTTTGTCTCAGATTTTG
1 TTTTGTCTCAGAGTTTG
3584840 TT
1 TT
3584842 GAAGTTCTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.11, C:0.11, G:0.19, T:0.58
Consensus pattern (17 bp):
TTTTGTCTCAGAGTTTG
Found at i:3593415 original size:18 final size:16
Alignment explanation
Indices: 3593387--3593421 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
3593377 TTTTTAAAAT
3593387 AAATAAATAATATTTTA
1 AAATAAATAAT-TTTTA
3593404 AAATATAATAATTTTTA
1 AAATA-AATAATTTTTA
3593421 A
1 A
3593422 TTAATTTTCA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 11 0.65
18 6 0.35
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (16 bp):
AAATAAATAATTTTTA
Found at i:3601847 original size:21 final size:21
Alignment explanation
Indices: 3601821--3601873 Score: 72
Period size: 22 Copynumber: 2.5 Consensus size: 21
3601811 AGTTGTACAC
3601821 TGATTTATTATTAAATTATGAA
1 TGATTTATTATTAAATT-TGAA
*
3601843 T-ATTTTATTATTAAATTTTAA
1 TGA-TTTATTATTAAATTTGAA
3601864 TGATTTATTA
1 TGATTTATTA
3601874 AGTTATCGAA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
21 12 0.43
22 16 0.57
ACGTcount: A:0.38, C:0.00, G:0.06, T:0.57
Consensus pattern (21 bp):
TGATTTATTATTAAATTTGAA
Found at i:3602150 original size:3 final size:3
Alignment explanation
Indices: 3602142--3602175 Score: 52
Period size: 3 Copynumber: 11.3 Consensus size: 3
3602132 AATCAAAGTA
3602142 AAT AAT AAT AAT AAT AAT AAAT AA- AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT AAT A
3602176 TTGGTTTAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
2 2 0.07
3 24 0.83
4 3 0.10
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:3603523 original size:38 final size:37
Alignment explanation
Indices: 3603480--3603562 Score: 89
Period size: 38 Copynumber: 2.2 Consensus size: 37
3603470 ATTATTAACA
3603480 ATAAAATAATA-ACAAAAATGGAATAATAACAA-AAAGTG
1 ATAAAATAATATA-AAAAAT-G-ATAATAACAATAAAGTG
* * *
3603518 CTAAAAAAATATTAAAAAATGATAATAAGAATAAAGTG
1 ATAAAATAATA-TAAAAAATGATAATAACAATAAAGTG
3603556 ATAAAAT
1 ATAAAAT
3603563 TTTTTTCCTA
Statistics
Matches: 37, Mismatches: 5, Indels: 6
0.77 0.10 0.12
Matches are distributed among these distances:
37 9 0.24
38 21 0.57
39 6 0.16
40 1 0.03
ACGTcount: A:0.65, C:0.04, G:0.10, T:0.22
Consensus pattern (37 bp):
ATAAAATAATATAAAAAATGATAATAACAATAAAGTG
Found at i:3603926 original size:14 final size:14
Alignment explanation
Indices: 3603909--3603965 Score: 53
Period size: 14 Copynumber: 3.9 Consensus size: 14
3603899 AATTAAACTC
3603909 TCAAAACCTTAAAA
1 TCAAAACCTTAAAA
* *
3603923 TCAAAATCTTAAACTT
1 TCAAAACCTTAAA--A
*
3603939 TCAAAACCCTAAAA
1 TCAAAACCTTAAAA
3603953 -CTAAAACCTTAAA
1 TC-AAAACCTTAAA
3603966 TCCTTTGAAC
Statistics
Matches: 34, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
13 1 0.03
14 22 0.65
16 11 0.32
ACGTcount: A:0.53, C:0.23, G:0.00, T:0.25
Consensus pattern (14 bp):
TCAAAACCTTAAAA
Found at i:3603937 original size:30 final size:30
Alignment explanation
Indices: 3603901--3603965 Score: 87
Period size: 30 Copynumber: 2.2 Consensus size: 30
3603891 AACCCTAAAA
* *
3603901 TTAAACTCTCAAAACCTTAAAA-TCAAAATC
1 TTAAACTCTCAAAACCCTAAAACT-AAAACC
*
3603931 TTAAACTTTCAAAACCCTAAAACTAAAACC
1 TTAAACTCTCAAAACCCTAAAACTAAAACC
3603961 TTAAA
1 TTAAA
3603966 TCCTTTGAAC
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
30 30 0.97
31 1 0.03
ACGTcount: A:0.51, C:0.23, G:0.00, T:0.26
Consensus pattern (30 bp):
TTAAACTCTCAAAACCCTAAAACTAAAACC
Found at i:3603944 original size:16 final size:16
Alignment explanation
Indices: 3603901--3603951 Score: 52
Period size: 16 Copynumber: 3.3 Consensus size: 16
3603891 AACCCTAAAA
*
3603901 TTAAACTCTCAAAACC
1 TTAAACTATCAAAACC
*
3603917 TTAAA--ATCAAAATC
1 TTAAACTATCAAAACC
*
3603931 TTAAACTTTCAAAACC
1 TTAAACTATCAAAACC
*
3603947 CTAAA
1 TTAAA
3603952 ACTAAAACCT
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
14 12 0.43
16 16 0.57
ACGTcount: A:0.49, C:0.24, G:0.00, T:0.27
Consensus pattern (16 bp):
TTAAACTATCAAAACC
Found at i:3604054 original size:21 final size:22
Alignment explanation
Indices: 3604013--3604057 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 22
3604003 CCCTAAATCT
*
3604013 TAAAATTGAAACCATTTAAACCC
1 TAAAATCGAAACCA-TTAAACCC
3604036 TAAAATCGAAACC-TTAAACCC
1 TAAAATCGAAACCATTAAACCC
3604057 T
1 T
3604058 TATAACCCTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 9 0.43
23 12 0.57
ACGTcount: A:0.47, C:0.24, G:0.04, T:0.24
Consensus pattern (22 bp):
TAAAATCGAAACCATTAAACCC
Found at i:3604262 original size:29 final size:29
Alignment explanation
Indices: 3604207--3604264 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
3604197 TTCAAAACCC
***
3604207 TAAAATCCAAAACCTAAAACTTTAAATTT
1 TAAAATCCAAAACCTAAAACCCCAAATTT
*
3604236 TAAAATTCAAAACCTAAAACCCCAAATTT
1 TAAAATCCAAAACCTAAAACCCCAAATTT
3604265 GGTACGCAAT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.52, C:0.21, G:0.00, T:0.28
Consensus pattern (29 bp):
TAAAATCCAAAACCTAAAACCCCAAATTT
Found at i:3605415 original size:21 final size:22
Alignment explanation
Indices: 3605375--3605415 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
3605365 AATCATTTAA
*
3605375 TAATAATGATTTACTACTAAAT
1 TAATAATGATTTAATACTAAAT
*
3605397 TAATAGTGA-TTAATACTAA
1 TAATAATGATTTAATACTAA
3605416 GTTATCATTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 9 0.53
22 8 0.47
ACGTcount: A:0.46, C:0.07, G:0.07, T:0.39
Consensus pattern (22 bp):
TAATAATGATTTAATACTAAAT
Found at i:3606351 original size:21 final size:21
Alignment explanation
Indices: 3606327--3606408 Score: 69
Period size: 21 Copynumber: 3.9 Consensus size: 21
3606317 CTATGAAAAG
3606327 TTACCAAAATTATATCAATGA
1 TTACCAAAATTATATCAATGA
* *
3606348 TTACCAAAAGTATATC-ATAAA
1 TTACCAAAATTATATCAAT-GA
** * *
3606369 TTATTAAAATTGTATAAAATG-
1 TTACCAAAATTATAT-CAATGA
*
3606390 TTACAAAAATTATATCAAT
1 TTACCAAAATTATATCAAT
3606409 AGGTTATCAA
Statistics
Matches: 46, Mismatches: 12, Indels: 7
0.71 0.18 0.11
Matches are distributed among these distances:
20 5 0.11
21 39 0.85
23 2 0.04
ACGTcount: A:0.50, C:0.10, G:0.05, T:0.35
Consensus pattern (21 bp):
TTACCAAAATTATATCAATGA
Found at i:3606630 original size:21 final size:21
Alignment explanation
Indices: 3606587--3606779 Score: 146
Period size: 21 Copynumber: 9.3 Consensus size: 21
3606577 TACAAAAATG
* *
3606587 AAAATTATA-TAAAGGTTATC
1 AAAATTATATTAAAAGTTACC
*
3606607 AAAATTATATTAAAACTTACC
1 AAAATTATATTAAAAGTTACC
* * *
3606628 AAAATTGTACTAAAATTTACC
1 AAAATTATATTAAAAGTTACC
* *
3606649 AACATTATATT-AAAGTTACT
1 AAAATTATATTAAAAGTTACC
* * *
3606669 AAAATTTTATCAAAGGTTACC
1 AAAATTATATTAAAAGTTACC
**
3606690 AAAATTATA-TAAGTGGTTACTC
1 AAAATTATATTAA-AAGTTAC-C
*
3606712 -AAATTATATCATAAA-TTACC
1 AAAATTATATTA-AAAGTTACC
* *
3606732 AAAA-TAGTAGTAAAGGTTACC
1 AAAATTA-TATTAAAAGTTACC
* *
3606753 AAAATTATATTAAAACTTACT
1 AAAATTATATTAAAAGTTACC
3606774 AAAATT
1 AAAATT
3606780 TTATGAAATG
Statistics
Matches: 134, Mismatches: 29, Indels: 19
0.74 0.16 0.10
Matches are distributed among these distances:
20 31 0.23
21 98 0.73
22 4 0.03
23 1 0.01
ACGTcount: A:0.48, C:0.11, G:0.07, T:0.34
Consensus pattern (21 bp):
AAAATTATATTAAAAGTTACC
Found at i:3606689 original size:41 final size:42
Alignment explanation
Indices: 3606587--3606699 Score: 124
Period size: 41 Copynumber: 2.7 Consensus size: 42
3606577 TACAAAAATG
*
3606587 AAAATTATAT-AAAGGTTATCAAAATTATATTAAAACTTACC
1 AAAATTATATCAAAGGTTACCAAAATTATATTAAAACTTACC
* ** * * *
3606628 AAAATTGTA-CTAAAATTTACCAACATTATATT-AAAGTTACT
1 AAAATTATATC-AAAGGTTACCAAAATTATATTAAAACTTACC
*
3606669 AAAATTTTATCAAAGGTTACCAAAATTATAT
1 AAAATTATATCAAAGGTTACCAAAATTATAT
3606700 AAGTGGTTAC
Statistics
Matches: 58, Mismatches: 11, Indels: 6
0.77 0.15 0.08
Matches are distributed among these distances:
41 40 0.69
42 18 0.31
ACGTcount: A:0.49, C:0.11, G:0.05, T:0.35
Consensus pattern (42 bp):
AAAATTATATCAAAGGTTACCAAAATTATATTAAAACTTACC
Found at i:3606752 original size:104 final size:104
Alignment explanation
Indices: 3606587--3606783 Score: 274
Period size: 104 Copynumber: 1.9 Consensus size: 104
3606577 TACAAAAATG
* * * *
3606587 AAAATTATATAAAGGTTATCAAAATTATATTAAAACTTACCAAAATTGTACTAAAATTTACCAAC
1 AAAATTATATAAAGGTTATCAAAATTATATCAAAACTTACCAAAATAGTACTAAAAGTTACCAAA
*
3606652 ATTATATT-AAAGTTACTAAAATTTTATCAAAGGTTACC
66 ATTATATTAAAACTTACTAAAATTTTATCAAAGGTTACC
* * *
3606690 AAAATTATATAAGTGGTTACTC-AAATTATATCATAAA-TTACCAAAATAGTAGTAAAGGTTACC
1 AAAATTATATAA-AGGTTA-TCAAAATTATATCA-AAACTTACCAAAATAGTACTAAAAGTTACC
3606753 AAAATTATATTAAAACTTACTAAAATTTTAT
63 AAAATTATATTAAAACTTACTAAAATTTTAT
3606784 GAAATGCTAT
Statistics
Matches: 82, Mismatches: 8, Indels: 6
0.85 0.08 0.06
Matches are distributed among these distances:
103 12 0.15
104 47 0.57
105 23 0.28
ACGTcount: A:0.48, C:0.11, G:0.07, T:0.35
Consensus pattern (104 bp):
AAAATTATATAAAGGTTATCAAAATTATATCAAAACTTACCAAAATAGTACTAAAAGTTACCAAA
ATTATATTAAAACTTACTAAAATTTTATCAAAGGTTACC
Found at i:3606986 original size:21 final size:22
Alignment explanation
Indices: 3606961--3607029 Score: 58
Period size: 20 Copynumber: 3.3 Consensus size: 22
3606951 TATAAAAGGT
3606961 TTGTATCTCAAA-TTACTAAAA
1 TTGTATCTCAAACTTACTAAAA
* *
3606982 TTGTAT-TAAAAGTTA-TCAAAA
1 TTGTATCTCAAACTTACT-AAAA
*
3607003 -T-TATATCAAACTTACTAAAA
1 TTGTATCTCAAACTTACTAAAA
*
3607023 TTTTATC
1 TTGTATC
3607030 AAAGGTTACC
Statistics
Matches: 38, Mismatches: 4, Indels: 11
0.72 0.08 0.21
Matches are distributed among these distances:
19 3 0.08
20 17 0.45
21 15 0.39
22 3 0.08
ACGTcount: A:0.43, C:0.12, G:0.04, T:0.41
Consensus pattern (22 bp):
TTGTATCTCAAACTTACTAAAA
Found at i:3607024 original size:41 final size:40
Alignment explanation
Indices: 3606968--3607049 Score: 119
Period size: 41 Copynumber: 2.0 Consensus size: 40
3606958 GGTTTGTATC
* *
3606968 TCAAATTACTAAAATTGTATTAAAAGTTATCAAAATTATA
1 TCAAATTACTAAAATTGTATCAAAAGTTACCAAAATTATA
* *
3607008 TCAAACTTACTAAAATTTTATCAAAGGTTACCAAAATTATA
1 TCAAA-TTACTAAAATTGTATCAAAAGTTACCAAAATTATA
3607049 T
1 T
3607050 AAGTGGTTAC
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
40 5 0.14
41 32 0.86
ACGTcount: A:0.48, C:0.11, G:0.05, T:0.37
Consensus pattern (40 bp):
TCAAATTACTAAAATTGTATCAAAAGTTACCAAAATTATA
Found at i:3607043 original size:21 final size:21
Alignment explanation
Indices: 3606973--3607125 Score: 100
Period size: 21 Copynumber: 7.4 Consensus size: 21
3606963 GTATCTCAAA
* * * *
3606973 TTACTAAAATTGTATTAAAAG
1 TTACCAAAATTATATCAAAGG
* *
3606994 TTATCAAAATTATATCAAA-C
1 TTACCAAAATTATATCAAAGG
* *
3607014 TTACTAAAATTTTATCAAAGG
1 TTACCAAAATTATATCAAAGG
*
3607035 TTACCAAAATTATAT-AAGTGG
1 TTACCAAAATTATATCAA-AGG
**
3607056 TTACTTAAATTATATCATAA-G
1 TTACCAAAATTATATCA-AAGG
* *
3607077 TTACTAAAA-TAGTATTAAAGG
1 TTACCAAAATTA-TATCAAAGG
* *
3607098 TTA-CTAAATTATATTAAAGG
1 TTACCAAAATTATATCAAAGG
*
3607118 TTATCAAA
1 TTACCAAA
3607126 CTTTTAACAA
Statistics
Matches: 104, Mismatches: 20, Indels: 16
0.74 0.14 0.11
Matches are distributed among these distances:
20 37 0.36
21 65 0.62
22 1 0.01
23 1 0.01
ACGTcount: A:0.46, C:0.08, G:0.08, T:0.37
Consensus pattern (21 bp):
TTACCAAAATTATATCAAAGG
Found at i:3607072 original size:42 final size:42
Alignment explanation
Indices: 3607014--3607125 Score: 115
Period size: 42 Copynumber: 2.7 Consensus size: 42
3607004 TATATCAAAC
* * *
3607014 TTACTAAAATTTTATCAAAGGTTACCAAAAT--TATATAAGTGG
1 TTACTTAAATTATATCAAAGGTTACCAAAATAGTAT-TAA-AGG
*
3607056 TTACTTAAATTATATCATAA-GTTACTAAAATAGTATTAAAGG
1 TTACTTAAATTATATCA-AAGGTTACCAAAATAGTATTAAAGG
* *
3607098 TTAC-TAAATTATATTAAAGGTTATCAAA
1 TTACTTAAATTATATCAAAGGTTACCAAA
3607126 CTTTTAACAA
Statistics
Matches: 59, Mismatches: 7, Indels: 9
0.79 0.09 0.12
Matches are distributed among these distances:
40 2 0.03
41 18 0.31
42 31 0.53
43 5 0.08
44 3 0.05
ACGTcount: A:0.45, C:0.08, G:0.10, T:0.38
Consensus pattern (42 bp):
TTACTTAAATTATATCAAAGGTTACCAAAATAGTATTAAAGG
Found at i:3607279 original size:22 final size:22
Alignment explanation
Indices: 3607240--3607366 Score: 78
Period size: 22 Copynumber: 5.8 Consensus size: 22
3607230 TTTTATTGAT
* * *
3607240 AATTTACTATTGAGTTATCAAG
1 AATTTACTACTAAATTATCAAG
* *
3607262 AGTTTACTACTAAATTATCAAT
1 AATTTACTACTAAATTATCAAG
* **
3607284 AATTTATTACTAAATTATCACT
1 AATTTACTACTAAATTATCAAG
* * *
3607306 CATTTACTACTAATTTATGAATG
1 AATTTACTACTAAATTATCAA-G
* * *
3607329 -ATTTA-TCGCTAAATTATGAAT
1 AATTTACT-ACTAAATTATCAAG
* *
3607350 AATTTACAACTACATTA
1 AATTTACTACTAAATTA
3607367 GTGATGATTT
Statistics
Matches: 81, Mismatches: 20, Indels: 8
0.74 0.18 0.07
Matches are distributed among these distances:
21 1 0.01
22 80 0.99
ACGTcount: A:0.39, C:0.13, G:0.06, T:0.42
Consensus pattern (22 bp):
AATTTACTACTAAATTATCAAG
Found at i:3607355 original size:44 final size:44
Alignment explanation
Indices: 3607254--3607366 Score: 118
Period size: 44 Copynumber: 2.6 Consensus size: 44
3607244 TACTATTGAG
* * *
3607254 TTATCAAGAGTTTACTACTAAATTATCAATAATTTATTACTAAA
1 TTATCAATAATTTACTACTAAATTATCAATAATTTATCACTAAA
* * * * * *
3607298 TTATCACTCATTTACTACTAATTTATGAATGATTTATCGCTAAA
1 TTATCAATAATTTACTACTAAATTATCAATAATTTATCACTAAA
* * *
3607342 TTATGAATAATTTACAACTACATTA
1 TTATCAATAATTTACTACTAAATTA
3607367 GTGATGATTT
Statistics
Matches: 54, Mismatches: 15, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
44 54 1.00
ACGTcount: A:0.40, C:0.13, G:0.05, T:0.42
Consensus pattern (44 bp):
TTATCAATAATTTACTACTAAATTATCAATAATTTATCACTAAA
Found at i:3607438 original size:22 final size:20
Alignment explanation
Indices: 3607413--3607470 Score: 53
Period size: 22 Copynumber: 2.7 Consensus size: 20
3607403 ATTATTGATT
*
3607413 ATTTACTATAAAGTTATCATTA
1 ATTTACTATAAA-TTATCA-CA
* *
3607435 ATTTATTACTAAATTACTGACA
1 ATTTACTA-TAAATTA-TCACA
3607457 ATTTACTATAAATT
1 ATTTACTATAAATT
3607471 TATCGATGAT
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
21 6 0.20
22 18 0.60
23 6 0.20
ACGTcount: A:0.41, C:0.10, G:0.03, T:0.45
Consensus pattern (20 bp):
ATTTACTATAAATTATCACA
Found at i:3607546 original size:22 final size:22
Alignment explanation
Indices: 3607515--3607637 Score: 104
Period size: 22 Copynumber: 5.5 Consensus size: 22
3607505 ATTGATCATA
*
3607515 ATTAAATTATCACTAATTTAC-
1 ATTAAGTTATCACTAATTTACT
*
3607536 AGTTAAGTTATCAGTAATTTACT
1 A-TTAAGTTATCACTAATTTACT
* * *
3607559 ATTAAGTTATTAGTGATTTACT
1 ATTAAGTTATCACTAATTTACT
* *
3607581 ATTAAATTATCAATAATGATTTACT
1 ATTAAGTTATCACT-A--ATTTACT
* * *
3607606 ATTAAATTATCAATAATTTATT
1 ATTAAGTTATCACTAATTTACT
*
3607628 ATTATGTTAT
1 ATTAAGTTAT
3607638 TATGCATTTA
Statistics
Matches: 86, Mismatches: 11, Indels: 9
0.81 0.10 0.08
Matches are distributed among these distances:
21 1 0.01
22 62 0.72
23 1 0.01
24 1 0.01
25 21 0.24
ACGTcount: A:0.39, C:0.07, G:0.07, T:0.47
Consensus pattern (22 bp):
ATTAAGTTATCACTAATTTACT
Found at i:3607606 original size:25 final size:25
Alignment explanation
Indices: 3607552--3607622 Score: 103
Period size: 25 Copynumber: 3.0 Consensus size: 25
3607542 GTTATCAGTA
* *
3607552 ATTTACTATTAAGTTAT---TAGTG
1 ATTTACTATTAAATTATCAATAATG
3607574 ATTTACTATTAAATTATCAATAATG
1 ATTTACTATTAAATTATCAATAATG
3607599 ATTTACTATTAAATTATCAATAAT
1 ATTTACTATTAAATTATCAATAAT
3607623 TTATTATTAT
Statistics
Matches: 44, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
22 16 0.36
25 28 0.64
ACGTcount: A:0.41, C:0.07, G:0.06, T:0.46
Consensus pattern (25 bp):
ATTTACTATTAAATTATCAATAATG
Found at i:3607769 original size:22 final size:22
Alignment explanation
Indices: 3607530--3607901 Score: 130
Period size: 22 Copynumber: 16.8 Consensus size: 22
3607520 ATTATCACTA
* * *
3607530 ATTTAC-AGTTAAGTTATCAGTA
1 ATTTACTA-TTAAGTTATTATTG
*
3607552 ATTTACTATTAAGTTATTAGTG
1 ATTTACTATTAAGTTATTATTG
* *
3607574 ATTTACTATTAAATTATCAATAATG
1 ATTTACTATTAAGTTAT---TATTG
* * * *
3607599 ATTTACTATTAAATTATCAATA
1 ATTTACTATTAAGTTATTATTG
* *
3607621 ATTTATTATTATGTTATTA-TG
1 ATTTACTATTAAGTTATTATTG
** *
3607642 CATTTAC-AACAATGTTATTATTA
1 -ATTTACTATTAA-GTTATTATTG
* * *
3607665 ATTTACTACTAAATTTTTAATT-
1 ATTTACTATTAAGTTATT-ATTG
** * * *
3607687 ATTTACTACAAAATTCTCATTG
1 ATTTACTATTAAGTTATTATTG
* * * *
3607709 ATTTATTACTAAATCATCTA-TG
1 ATTTACTATTAAGTTAT-TATTG
* ** *
3607731 ATTCACTACCAAATTATTATTG
1 ATTTACTATTAAGTTATTATTG
* *
3607753 ATTTACTTTTAAGTTATCTA-TC
1 ATTTACTATTAAGTTAT-TATTG
** * *
3607775 ATTTACTATTAAACTATCAATG
1 ATTTACTATTAAGTTATTATTG
**
3607797 ATTTACTATTAAGTT-CCATTG
1 ATTTACTATTAAGTTATTATTG
* * * * *
3607818 ATTTATTTTTAAGTTTTTAATA
1 ATTTACTATTAAGTTATTATTG
* * * *
3607840 ATTAATTTTTAAGTTATAAATT-
1 ATTTACTATTAAGTTAT-TATTG
* * *
3607862 ATTTAATATTAAGTTATCATTA
1 ATTTACTATTAAGTTATTATTG
*
3607884 ATTTACTATTAAATTATT
1 ATTTACTATTAAGTTATT
3607902 TATAATTTAC
Statistics
Matches: 269, Mismatches: 64, Indels: 34
0.73 0.17 0.09
Matches are distributed among these distances:
21 29 0.11
22 206 0.77
23 13 0.05
25 21 0.08
ACGTcount: A:0.37, C:0.09, G:0.05, T:0.49
Consensus pattern (22 bp):
ATTTACTATTAAGTTATTATTG
Found at i:3608011 original size:22 final size:22
Alignment explanation
Indices: 3607947--3608013 Score: 64
Period size: 22 Copynumber: 3.0 Consensus size: 22
3607937 TTAAATTGAA
3607947 ACTAATTTAG-TATTAAATTATC
1 ACTAATTT-GCTATTAAATTATC
* * *
3607969 ACTAATTTGCTACTAAGTTATT
1 ACTAATTTGCTATTAAATTATC
* * *
3607991 ATTGATTTGTTATTAAATTATC
1 ACTAATTTGCTATTAAATTATC
3608013 A
1 A
3608014 ATTAATTTTC
Statistics
Matches: 35, Mismatches: 9, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
21 1 0.03
22 34 0.97
ACGTcount: A:0.36, C:0.09, G:0.07, T:0.48
Consensus pattern (22 bp):
ACTAATTTGCTATTAAATTATC
Found at i:3608166 original size:22 final size:21
Alignment explanation
Indices: 3608118--3608195 Score: 68
Period size: 22 Copynumber: 3.6 Consensus size: 21
3608108 TATTATTATG
*
3608118 TTATCACTTATTACTAATAAA
1 TTATCAATTATTACTAATAAA
* * *
3608139 TAATCAATTATGTATTACTAAA
1 TTATCAATTAT-TACTAATAAA
*
3608161 TTATC-ATTGATTTACTATTAAA
1 TTATCAATT-A-TTACTAATAAA
*
3608183 TTATCAATGATTA
1 TTATCAATTATTA
3608196 ATTATTAAGT
Statistics
Matches: 45, Mismatches: 8, Indels: 8
0.74 0.13 0.13
Matches are distributed among these distances:
21 15 0.33
22 27 0.60
23 3 0.07
ACGTcount: A:0.41, C:0.10, G:0.04, T:0.45
Consensus pattern (21 bp):
TTATCAATTATTACTAATAAA
Found at i:3608201 original size:22 final size:22
Alignment explanation
Indices: 3608135--3608217 Score: 69
Period size: 22 Copynumber: 3.8 Consensus size: 22
3608125 TTATTACTAA
* * *
3608135 TAAATAATCAATTATGT-ATTAC
1 TAAATTATCAATGAT-TAATTAT
* * *
3608157 TAAATTATCATTGATTTACTAT
1 TAAATTATCAATGATTAATTAT
3608179 TAAATTATCAATGATTAATTAT
1 TAAATTATCAATGATTAATTAT
* * *
3608201 TAAGTTATGAATAATTA
1 TAAATTATCAATGATTA
3608218 CAACTTATTT
Statistics
Matches: 49, Mismatches: 11, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
21 1 0.02
22 48 0.98
ACGTcount: A:0.43, C:0.06, G:0.06, T:0.45
Consensus pattern (22 bp):
TAAATTATCAATGATTAATTAT
Found at i:3610817 original size:28 final size:27
Alignment explanation
Indices: 3610775--3610827 Score: 79
Period size: 28 Copynumber: 1.9 Consensus size: 27
3610765 ATAAGTAAAA
* *
3610775 TTTGATAACTTTTGATATAATTTTGAT
1 TTTGATAACTCTTGATAAAATTTTGAT
3610802 TTTGATAACATCTTGATAAAATTTTG
1 TTTGATAAC-TCTTGATAAAATTTTG
3610828 GTAACCTTCG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
27 9 0.39
28 14 0.61
ACGTcount: A:0.32, C:0.06, G:0.11, T:0.51
Consensus pattern (27 bp):
TTTGATAACTCTTGATAAAATTTTGAT
Found at i:3610845 original size:21 final size:21
Alignment explanation
Indices: 3610800--3610908 Score: 89
Period size: 21 Copynumber: 5.2 Consensus size: 21
3610790 TATAATTTTG
* * *
3610800 ATTTTGATAACATCTTGATAAA
1 ATTTTGGTAACCT-TTGATATA
*
3610822 ATTTTGGTAACCTTCGATATA
1 ATTTTGGTAACCTTTGATATA
* * *
3610843 ATTTTGATAATCTTTG--GTA
1 ATTTTGGTAACCTTTGATATA
* *
3610862 AGTTTGGTAA-CTTATAATATA
1 ATTTTGGTAACCTT-TGATATA
*
3610883 ATTTTGGTAACCATTGATATA
1 ATTTTGGTAACCTTTGATATA
3610904 ATTTT
1 ATTTT
3610909 AATAATTTTT
Statistics
Matches: 68, Mismatches: 15, Indels: 9
0.74 0.16 0.10
Matches are distributed among these distances:
18 3 0.04
19 11 0.16
21 41 0.60
22 13 0.19
ACGTcount: A:0.33, C:0.08, G:0.13, T:0.46
Consensus pattern (21 bp):
ATTTTGGTAACCTTTGATATA
Found at i:3610929 original size:22 final size:23
Alignment explanation
Indices: 3610896--3610947 Score: 81
Period size: 22 Copynumber: 2.3 Consensus size: 23
3610886 TTGGTAACCA
3610896 TTGAT-ATAATTTTAATAAT-TT
1 TTGATAATAATTTTAATAATCTT
3610917 TTGATAATAATTTTAATAATCTT
1 TTGATAATAATTTTAATAATCTT
*
3610940 TTGGTAAT
1 TTGATAAT
3610948 GTATGATATA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
21 5 0.18
22 14 0.50
23 9 0.32
ACGTcount: A:0.37, C:0.02, G:0.08, T:0.54
Consensus pattern (23 bp):
TTGATAATAATTTTAATAATCTT
Found at i:3611259 original size:22 final size:22
Alignment explanation
Indices: 3611234--3611972 Score: 188
Period size: 22 Copynumber: 33.5 Consensus size: 22
3611224 ATGATTGATA
* *
3611234 ATTAAATTATCATTGATTTATT
1 ATTAAATTATCAATGATTTACT
** *
3611256 ATTATGTTAT-AATAATTTACT
1 ATTAAATTATCAATGATTTACT
* *
3611277 ATTAAGTTATCAATGATATAC-
1 ATTAAATTATCAATGATTTACT
*
3611298 AGTTAAATTAACAATGATTTACT
1 A-TTAAATTATCAATGATTTACT
* * *
3611321 ACTAAATTAGCATTGATTTACT
1 ATTAAATTATCAATGATTTACT
* * *
3611343 ACTAAGTTATAAATGATTTACT
1 ATTAAATTATCAATGATTTACT
* ** *
3611365 ATTAAATTGTTGATAATTTACT
1 ATTAAATTATCAATGATTTACT
* * *
3611387 ATTAAGTTATTAATGATTTAGTGT
1 ATTAAATTATCAATGATTTA--CT
* * * *
3611411 AATTGATTTA-CTATTAATTTA-T
1 -ATTAAATTATC-AATGATTTACT
* * *
3611433 CAATAATTTACTACAA-G--GT--T
1 -ATTAAATTA-T-CAATGATTTACT
* *
3611453 A-TAAATTATTAACTAATTTACT
1 ATTAAATTATCAA-TGATTTACT
* *
3611475 ACTAAATTATCACA-GATTTACA
1 ATTAAATTATCA-ATGATTTACT
* * * * *
3611497 ACTAAGTTATTAGTGATTTATT
1 ATTAAATTATCAATGATTTACT
* *
3611519 ACTAAGTTATCAAT-ATTTTA-T
1 ATTAAATTATCAATGA-TTTACT
*
3611540 ATCTAAATTATCATTGATTTACT
1 AT-TAAATTATCAATGATTTACT
* * * *
3611563 ATTATATTAT-TATAAATTTATT
1 ATTAAATTATCAAT-GATTTACT
* ** * *
3611585 ACTATGTTATCATTTATTTACT
1 ATTAAATTATCAATGATTTACT
* * * *
3611607 ATTTAGTTTTCAATTATTTACT
1 ATTAAATTATCAATGATTTACT
* * * *
3611629 A-AAAACTCAT-TATAGATTTATT
1 ATTAAA-TTATCAAT-GATTTACT
* * * *
3611651 ACTAAATTAACCATGATTTATT
1 ATTAAATTATCAATGATTTACT
* * * *
3611673 ATCAACTTGTCACTGATTTA-T
1 ATTAAATTATCAATGATTTACT
* **
3611694 ATGAAATTATTTATGATTTACT
1 ATTAAATTATCAATGATTTACT
* * *
3611716 ATTAAGTTATCATTGATTAACT
1 ATTAAATTATCAATGATTTACT
** **
3611738 ATTATGTTATTGATGATTAACTACT
1 ATTAAATTATCAATGATT---TACT
* *
3611763 ATTAAGTTAT-AATAATTTACT
1 ATTAAATTATCAATGATTTACT
* * * * *
3611784 TTTAACTT-TAAAATGATTAATT
1 ATTAAATTAT-CAATGATTTACT
* * *
3611806 ACTAAATTATCACTAATTTACT
1 ATTAAATTATCAATGATTTACT
* * **
3611828 ACTAAGTTATTTATGATTTACT
1 ATTAAATTATCAATGATTTACT
* * *
3611850 ATTAAGCTTATCAATTAATTACT
1 ATTAA-ATTATCAATGATTTACT
* *
3611873 ATTAAATTGA--AATTAATTTATT
1 ATTAAATT-ATCAA-TGATTTACT
* * *
3611895 ATTAAGTTATCATTAATTTACT
1 ATTAAATTATCAATGATTTACT
* * *
3611917 ATTAAGTTATCATTGATTTATT
1 ATTAAATTATCAATGATTTACT
* * * *
3611939 ATTAAAATATTAATTATTAACT
1 ATTAAATTATCAATGATTTACT
*
3611961 ATTAAGTTATCA
1 ATTAAATTATCA
3611973 TTTTTTTATT
Statistics
Matches: 521, Mismatches: 155, Indels: 82
0.69 0.20 0.11
Matches are distributed among these distances:
16 2 0.00
17 1 0.00
18 6 0.01
19 1 0.00
20 3 0.01
21 54 0.10
22 379 0.73
23 40 0.08
24 8 0.02
25 27 0.05
ACGTcount: A:0.38, C:0.09, G:0.06, T:0.47
Consensus pattern (22 bp):
ATTAAATTATCAATGATTTACT
Found at i:3611800 original size:90 final size:89
Alignment explanation
Indices: 3611706--3611943 Score: 250
Period size: 89 Copynumber: 2.7 Consensus size: 89
3611696 GAAATTATTT
* * * *
3611706 ATGATTTACTATTAAGTTATCATTGATTAACTATTATGTTATTGATGATTAACTACTATTAAG-T
1 ATGATTTATTATTAAGTTATCATTAATTTACTATTAAGTTATTGATGATT---TACTATTAAGCT
* * *
3611770 TAT-AA-TAATTTACTTTTAACTTTAAA
63 TATCAATTAA-TTACTATTAAATTGAAA
* * * * * *
3611796 ATGATTAATTACTAAATTATCACTAATTTACTACTAAGTTATTTATGATTTACTATTAAGCTTAT
1 ATGATTTATTATTAAGTTATCATTAATTTACTATTAAGTTATTGATGATTTACTATTAAGCTTAT
3611861 CAATTAATTACTATTAAATTGAAA
66 CAATTAATTACTATTAAATTGAAA
* * * *
3611885 TTAATTTATTATTAAGTTATCATTAATTTACTATTAAGTTA-TCATTGATTTATTATTAA
1 ATGATTTATTATTAAGTTATCATTAATTTACTATTAAGTTATTGA-TGATTTACTATTAA
3611944 AATATTAATT
Statistics
Matches: 122, Mismatches: 22, Indels: 9
0.80 0.14 0.06
Matches are distributed among these distances:
87 10 0.08
88 6 0.05
89 63 0.52
90 43 0.35
ACGTcount: A:0.38, C:0.08, G:0.06, T:0.48
Consensus pattern (89 bp):
ATGATTTATTATTAAGTTATCATTAATTTACTATTAAGTTATTGATGATTTACTATTAAGCTTAT
CAATTAATTACTATTAAATTGAAA
Found at i:3611898 original size:11 final size:11
Alignment explanation
Indices: 3611884--3611943 Score: 66
Period size: 11 Copynumber: 5.5 Consensus size: 11
3611874 TTAAATTGAA
3611884 ATTAATTTATT
1 ATTAATTTATT
* *
3611895 ATTAAGTTATC
1 ATTAATTTATT
*
3611906 ATTAATTTACT
1 ATTAATTTATT
* *
3611917 ATTAAGTTATC
1 ATTAATTTATT
*
3611928 ATTGATTTATT
1 ATTAATTTATT
3611939 ATTAA
1 ATTAA
3611944 AATATTAATT
Statistics
Matches: 37, Mismatches: 12, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
11 37 1.00
ACGTcount: A:0.37, C:0.05, G:0.05, T:0.53
Consensus pattern (11 bp):
ATTAATTTATT
Found at i:3612299 original size:22 final size:23
Alignment explanation
Indices: 3612261--3612318 Score: 57
Period size: 22 Copynumber: 2.6 Consensus size: 23
3612251 GATTGATAGT
** *
3612261 TAAATTATCCATT-ATTTATTAC
1 TAAATTATTAATTAATTTACTAC
* *
3612283 TAAGTTA-TAATTAATTTACTAT
1 TAAATTATTAATTAATTTACTAC
3612305 TAAATTATTAATTA
1 TAAATTATTAATTA
3612319 TTAATACTAA
Statistics
Matches: 28, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
21 3 0.11
22 19 0.68
23 6 0.21
ACGTcount: A:0.41, C:0.07, G:0.02, T:0.50
Consensus pattern (23 bp):
TAAATTATTAATTAATTTACTAC
Found at i:3612348 original size:43 final size:44
Alignment explanation
Indices: 3612260--3612420 Score: 105
Period size: 43 Copynumber: 3.7 Consensus size: 44
3612250 TGATTGATAG
* * *
3612260 TTAAATTATCCATTATTTATTACTAAGTTATAATTAATTTACTA
1 TTAAATTATCAATTATTTAATACTAAGTTATAAATAATTTACTA
* * *
3612304 TTAAATTATTAATTA-TTAATACTAA-TGTATAAATGATTTGCTA
1 TTAAATTATCAATTATTTAATACTAAGT-TATAAATAATTTACTA
* * * * * * * * *
3612347 TTAAGTTGTGAATGATTT-ATCATTAGGTTATGAATGATTT-TTA
1 TTAAATTATCAATTATTTAAT-ACTAAGTTATAAATAATTTACTA
** * *
3612390 TTAAATTATTGATGATTTATTACTAAGTTAT
1 TTAAATTATCAATTATTTAATACTAAGTTAT
3612421 TGATGATTTA
Statistics
Matches: 91, Mismatches: 21, Indels: 11
0.74 0.17 0.09
Matches are distributed among these distances:
42 1 0.01
43 59 0.65
44 30 0.33
45 1 0.01
ACGTcount: A:0.37, C:0.05, G:0.09, T:0.49
Consensus pattern (44 bp):
TTAAATTATCAATTATTTAATACTAAGTTATAAATAATTTACTA
Found at i:3612363 original size:22 final size:22
Alignment explanation
Indices: 3612346--3612442 Score: 83
Period size: 22 Copynumber: 4.5 Consensus size: 22
3612336 ATGATTTGCT
*
3612346 ATTAAGTTGTGAATGATTTATC
1 ATTAAGTTATGAATGATTTATC
* *
3612368 ATTAGGTTATGAATGATTT-TT
1 ATTAAGTTATGAATGATTTATC
* *
3612389 ATTAAATTATTG-ATGATTTATT
1 ATTAAGTTA-TGAATGATTTATC
* *
3612411 ACTAAGTTATTG-ATGATTTATT
1 ATTAAGTTA-TGAATGATTTATC
*
3612433 ATAAAGTTAT
1 ATTAAGTTAT
3612443 AACTAATTTA
Statistics
Matches: 64, Mismatches: 9, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
21 16 0.25
22 48 0.75
ACGTcount: A:0.34, C:0.02, G:0.14, T:0.49
Consensus pattern (22 bp):
ATTAAGTTATGAATGATTTATC
Found at i:3612427 original size:43 final size:44
Alignment explanation
Indices: 3612358--3612442 Score: 104
Period size: 43 Copynumber: 2.0 Consensus size: 44
3612348 TAAGTTGTGA
* *
3612358 ATGATTTATCATTAGGTTATGAATGATTT-TTATTAAA-TTATTG
1 ATGATTTATCACTAAGTTATGAATGATTTATTA-TAAAGTTATTG
*
3612401 ATGATTTATTACTAAGTTATTG-ATGATTTATTATAAAGTTAT
1 ATGATTTATCACTAAGTTA-TGAATGATTTATTATAAAGTTAT
3612443 AACTAATTTA
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
43 27 0.75
44 9 0.25
ACGTcount: A:0.34, C:0.02, G:0.13, T:0.51
Consensus pattern (44 bp):
ATGATTTATCACTAAGTTATGAATGATTTATTATAAAGTTATTG
Found at i:3612549 original size:19 final size:19
Alignment explanation
Indices: 3612522--3612563 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
3612512 GTTATTAGTT
*
3612522 ATTTACTATTAAGTTATCA
1 ATTTACTATTAAATTATCA
*
3612541 ATTTGCTATTAAATTATCA
1 ATTTACTATTAAATTATCA
3612560 ATTT
1 ATTT
3612564 TTATTATATT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.36, C:0.10, G:0.05, T:0.50
Consensus pattern (19 bp):
ATTTACTATTAAATTATCA
Found at i:3612713 original size:21 final size:21
Alignment explanation
Indices: 3612689--3612769 Score: 83
Period size: 22 Copynumber: 3.8 Consensus size: 21
3612679 CAGTTATTAG
3612689 TGATTTAC-ATTAAATTATAGA
1 TGATTTACTATTAAATTATA-A
* *
3612710 TGATTTACTATTAAGTTATAT
1 TGATTTACTATTAAATTATAA
* *
3612731 TGATTTACTTTTAAATTTTTAA
1 TGATTTACTATTAAA-TTATAA
* *
3612753 TGATTAACTAATAAATT
1 TGATTTACTATTAAATT
3612770 GTCAATTCTT
Statistics
Matches: 49, Mismatches: 9, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
21 23 0.47
22 26 0.53
ACGTcount: A:0.38, C:0.05, G:0.07, T:0.49
Consensus pattern (21 bp):
TGATTTACTATTAAATTATAA
Found at i:3612905 original size:44 final size:44
Alignment explanation
Indices: 3612857--3612943 Score: 111
Period size: 44 Copynumber: 2.0 Consensus size: 44
3612847 TAAATTGAAA
** * * *
3612857 TTGATCTATTGTTAAATTATTACTAATTTACTATTAAGTTATCT
1 TTGATCTATTGCAAAATTATCAATAATTAACTATTAAGTTATCT
* *
3612901 TTGATTTATTGCAAAATTATCAATAATTAATTATTAAGTTATC
1 TTGATCTATTGCAAAATTATCAATAATTAACTATTAAGTTATC
3612944 ACTTATTTTT
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
44 36 1.00
ACGTcount: A:0.36, C:0.08, G:0.07, T:0.49
Consensus pattern (44 bp):
TTGATCTATTGCAAAATTATCAATAATTAACTATTAAGTTATCT
Found at i:3613052 original size:22 final size:22
Alignment explanation
Indices: 3612985--3613053 Score: 68
Period size: 22 Copynumber: 3.1 Consensus size: 22
3612975 TAATATATTG
*
3612985 TTATGCATTTACAATTATAATA
1 TTATGCATTTACTATTATAATA
* * *
3613007 TAATTG-ATTTACCATTAAAATA
1 TTA-TGCATTTACTATTATAATA
* *
3613029 TTATGCATTTATTATTATATTA
1 TTATGCATTTACTATTATAATA
3613051 TTA
1 TTA
3613054 CTAATTTACT
Statistics
Matches: 37, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
21 2 0.05
22 33 0.89
23 2 0.05
ACGTcount: A:0.39, C:0.07, G:0.04, T:0.49
Consensus pattern (22 bp):
TTATGCATTTACTATTATAATA
Found at i:3613107 original size:22 final size:22
Alignment explanation
Indices: 3613057--3613138 Score: 69
Period size: 22 Copynumber: 3.8 Consensus size: 22
3613047 ATTATTACTA
* *
3613057 ATTTACTAA-AAGTTATCA-AC
1 ATTTACTAATAAATTATCATTC
*
3613077 TATTGACTAATAAATTATCATTC
1 -ATTTACTAATAAATTATCATTC
* * * *
3613100 ATTTACTATTAAGTTATCTTTA
1 ATTTACTAATAAATTATCATTC
*
3613122 ATTTACTACTAAATTAT
1 ATTTACTAATAAATTAT
3613139 ACTAATTACA
Statistics
Matches: 49, Mismatches: 10, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
21 8 0.16
22 40 0.82
23 1 0.02
ACGTcount: A:0.39, C:0.12, G:0.04, T:0.45
Consensus pattern (22 bp):
ATTTACTAATAAATTATCATTC
Found at i:3613966 original size:37 final size:37
Alignment explanation
Indices: 3613916--3613991 Score: 143
Period size: 37 Copynumber: 2.1 Consensus size: 37
3613906 TTGGAAAGAG
3613916 TAAAAAATATTTTAAAGGGTTATAATAGCTCAAATAA
1 TAAAAAATATTTTAAAGGGTTATAATAGCTCAAATAA
*
3613953 TAAAAAATATTTTAAAGGGTTATAATAGTTCAAATAA
1 TAAAAAATATTTTAAAGGGTTATAATAGCTCAAATAA
3613990 TA
1 TA
3613992 TTTAACTCTA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.51, C:0.04, G:0.11, T:0.34
Consensus pattern (37 bp):
TAAAAAATATTTTAAAGGGTTATAATAGCTCAAATAA
Found at i:3616529 original size:15 final size:15
Alignment explanation
Indices: 3616509--3616539 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
3616499 CACTTTTTAG
*
3616509 TCTAATTATAAAAAA
1 TCTAATAATAAAAAA
3616524 TCTAATAATAAAAAA
1 TCTAATAATAAAAAA
3616539 T
1 T
3616540 TCATTTAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.61, C:0.06, G:0.00, T:0.32
Consensus pattern (15 bp):
TCTAATAATAAAAAA
Found at i:3617811 original size:21 final size:21
Alignment explanation
Indices: 3617785--3617838 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
3617775 ATTATTTTTA
3617785 TTAATATTAAAATAGTAATAT
1 TTAATATTAAAATAGTAATAT
* *
3617806 TTAATATTAAAATATTTATAT
1 TTAATATTAAAATAGTAATAT
*
3617827 TTTATATTAAAA
1 TTAATATTAAAA
3617839 GTGTCTATTA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (21 bp):
TTAATATTAAAATAGTAATAT
Found at i:3618035 original size:42 final size:42
Alignment explanation
Indices: 3617988--3618070 Score: 105
Period size: 42 Copynumber: 2.0 Consensus size: 42
3617978 ATTAAGAAAT
* *
3617988 AATATTGTTATATTAT-TTAACCTTAATTATTAAAATAATAAA
1 AATATTATTATA-TATGTTAACATTAATTATTAAAATAATAAA
** *
3618030 AATATTATTATATATGTTATTATTTATTATTAAAATAATAA
1 AATATTATTATATATGTTAACATTAATTATTAAAATAATAA
3618071 TATAATACTA
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
41 3 0.09
42 32 0.91
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.48
Consensus pattern (42 bp):
AATATTATTATATATGTTAACATTAATTATTAAAATAATAAA
Found at i:3619435 original size:3 final size:3
Alignment explanation
Indices: 3619427--3619458 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
3619417 GGTAAGTAAA
*
3619427 AAT AAT AAT AAT AAT CAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
3619459 CCTTTTTTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:3627162 original size:17 final size:17
Alignment explanation
Indices: 3627142--3627176 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
3627132 TGAAAATTAA
3627142 TTAAAA-ATTATTATATT
1 TTAAAATATTATT-TATT
3627159 TTAAAATATTATTTATT
1 TTAAAATATTATTTATT
3627176 T
1 T
3627177 ATTTAAAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 11 0.65
18 6 0.35
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (17 bp):
TTAAAATATTATTTATT
Found at i:3628769 original size:45 final size:45
Alignment explanation
Indices: 3628718--3628808 Score: 173
Period size: 45 Copynumber: 2.0 Consensus size: 45
3628708 GCAATCCACG
3628718 TAACCAAATACACATCATAACCATTTCACACCCAATCCCATATGT
1 TAACCAAATACACATCATAACCATTTCACACCCAATCCCATATGT
*
3628763 TAACCAAATACACATCATAATCATTTCACACCCAATCCCATATGT
1 TAACCAAATACACATCATAACCATTTCACACCCAATCCCATATGT
3628808 T
1 T
3628809 GATGCTACTG
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 45 1.00
ACGTcount: A:0.40, C:0.32, G:0.02, T:0.26
Consensus pattern (45 bp):
TAACCAAATACACATCATAACCATTTCACACCCAATCCCATATGT
Found at i:3635765 original size:15 final size:15
Alignment explanation
Indices: 3635728--3635765 Score: 60
Period size: 16 Copynumber: 2.5 Consensus size: 15
3635718 CAAAGAACTT
3635728 CAAC-AAATCTGAGA
1 CAACAAAATCTGAGA
3635742 CAAACAAAATCTGAGA
1 C-AACAAAATCTGAGA
3635758 CAACAAAA
1 CAACAAAA
3635766 AAAAAAAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 1 0.05
15 10 0.45
16 11 0.50
ACGTcount: A:0.58, C:0.21, G:0.11, T:0.11
Consensus pattern (15 bp):
CAACAAAATCTGAGA
Found at i:3635766 original size:16 final size:16
Alignment explanation
Indices: 3635732--3635765 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
3635722 GAACTTCAAC
3635732 AAATCTGAGACAAACA
1 AAATCTGAGACAAACA
3635748 AAATCTGAGAC-AACA
1 AAATCTGAGACAAACA
3635763 AAA
1 AAA
3635766 AAAAAAAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 7 0.39
16 11 0.61
ACGTcount: A:0.59, C:0.18, G:0.12, T:0.12
Consensus pattern (16 bp):
AAATCTGAGACAAACA
Found at i:3646295 original size:25 final size:25
Alignment explanation
Indices: 3646259--3646315 Score: 64
Period size: 25 Copynumber: 2.3 Consensus size: 25
3646249 CTAATTCATG
* *
3646259 TATATGTA-AATT-AATTCATAATTG
1 TATAT-TACAATTAAATTAATAATTA
3646283 TAATATTACAATTAAATTAATAATTA
1 T-ATATTACAATTAAATTAATAATTA
3646309 TATATTA
1 TATATTA
3646316 TGTTAGAAAG
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
24 3 0.11
25 14 0.50
26 11 0.39
ACGTcount: A:0.47, C:0.04, G:0.04, T:0.46
Consensus pattern (25 bp):
TATATTACAATTAAATTAATAATTA
Found at i:3648432 original size:17 final size:17
Alignment explanation
Indices: 3648410--3648443 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
3648400 GCAGAATGTA
3648410 TGGAAATATTACACTTC
1 TGGAAATATTACACTTC
3648427 TGGAAATATTACACTTC
1 TGGAAATATTACACTTC
3648444 CAGTTTTAGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.35, C:0.18, G:0.12, T:0.35
Consensus pattern (17 bp):
TGGAAATATTACACTTC
Found at i:3651987 original size:21 final size:21
Alignment explanation
Indices: 3651961--3652000 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
3651951 GCAGAATAAT
*
3651961 TTGTAATATGATGAGGAGAAC
1 TTGTAATATAATGAGGAGAAC
3651982 TTGTAATATAATGAGGAGA
1 TTGTAATATAATGAGGAGA
3652001 GAAATAGGGG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.40, C:0.03, G:0.28, T:0.30
Consensus pattern (21 bp):
TTGTAATATAATGAGGAGAAC
Found at i:3654935 original size:6 final size:6
Alignment explanation
Indices: 3654924--3654949 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
3654914 CTAATCTATT
3654924 TGTTTC TGTTTC TGTTTC TGTTTC TG
1 TGTTTC TGTTTC TGTTTC TGTTTC TG
3654950 AACTTGTACT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.00, C:0.15, G:0.19, T:0.65
Consensus pattern (6 bp):
TGTTTC
Found at i:3660561 original size:18 final size:18
Alignment explanation
Indices: 3660538--3660575 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
3660528 CATCTAAACT
3660538 TCTCTTTATCACAGAATC
1 TCTCTTTATCACAGAATC
3660556 TCTCTTTATCACAGAATC
1 TCTCTTTATCACAGAATC
3660574 TC
1 TC
3660576 GTGATATTGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.26, C:0.29, G:0.05, T:0.39
Consensus pattern (18 bp):
TCTCTTTATCACAGAATC
Found at i:3661539 original size:25 final size:26
Alignment explanation
Indices: 3661510--3661565 Score: 78
Period size: 25 Copynumber: 2.2 Consensus size: 26
3661500 CATGATTAAT
* *
3661510 ATTAATATATATATAAAT-AAATATG
1 ATTAATACAAATATAAATAAAATATG
*
3661535 ATTAATACAAATATATATAAAATATG
1 ATTAATACAAATATAAATAAAATATG
3661561 ATTAA
1 ATTAA
3661566 AATAATAAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
25 15 0.56
26 12 0.44
ACGTcount: A:0.57, C:0.02, G:0.04, T:0.38
Consensus pattern (26 bp):
ATTAATACAAATATAAATAAAATATG
Done.