Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr10
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: 57797951
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Warning! 1092422 characters in sequence are not A, C, G, or T
File 13 of 187
Found at i:3314205 original size:21 final size:20
Alignment explanation
Indices: 3314172--3314213 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 20
3314162 GAATTAGGTT
*
3314172 AGGGTTAGGGTTTTTAATTA
1 AGGGTTAGAGTTTTTAATTA
3314192 AGGGTTTAGAGTTTTTAATTA
1 AGGG-TTAGAGTTTTTAATTA
3314213 A
1 A
3314214 ATTAGGCTAG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 4 0.20
21 16 0.80
ACGTcount: A:0.29, C:0.00, G:0.26, T:0.45
Consensus pattern (20 bp):
AGGGTTAGAGTTTTTAATTA
Found at i:3314232 original size:23 final size:23
Alignment explanation
Indices: 3314080--3315155 Score: 804
Period size: 23 Copynumber: 45.5 Consensus size: 23
3314070 AGTTAAGGGT
3314080 TTAGGGTTTTTAAGTT-AATTAGG
1 TTAGGGTTTTTAA-TTAAATTAGG
*
3314103 CTAGGGTTTTTAATTAAATTAGG
1 TTAGGGTTTTTAATTAAATTAGG
* *
3314126 TTAGGATTTTTAAGTT-AA--GGG
1 TTAGGGTTTTTAA-TTAAATTAGG
*
3314147 TTTA-GATTTTTAATTGAATTAGGTTAGGG
1 -TTAGGGTTTTTAATT-AA--A--TTA-GG
*
3314176 TTAGGGTTTTTAATT-AA--GGG
1 TTAGGGTTTTTAATTAAATTAGG
*
3314196 TTTAGAGTTTTTAATTAAATTAGG
1 -TTAGGGTTTTTAATTAAATTAGG
*
3314220 CTAGGGTTTTTAATTAAATTAGG
1 TTAGGGTTTTTAATTAAATTAGG
*
3314243 CTAGGGTTTTTAATTAAATTAGG
1 TTAGGGTTTTTAATTAAATTAGG
*
3314266 TTGGGGTTTTTAATTAAATTAGG
1 TTAGGGTTTTTAATTAAATTAGG
*
3314289 CTAGGGTTTTTAATTAAATTAGG
1 TTAGGGTTTTTAATTAAATTAGG
* *
3314312 CTATGGTTTTTAATTAAATTAGG
1 TTAGGGTTTTTAATTAAATTAGG
*
3314335 TTAGGGTTTTTAAGTT--A-TGGG
1 TTAGGGTTTTTAA-TTAAATTAGG
3314356 TTTAGGGTTTTTAATTGAATTAGGTTAGGG
1 -TTAGGGTTTTTAATT-AA--A--TTA-GG
*
3314386 TTAGGGTTTTTAATT-AA--GGG
1 TTAGGGTTTTTAATTAAATTAGG
3314406 TTTAGGGTTTTTAATTAATTTAGGTTAGG
1 -TTAGGGTTTTTAATTAA---A--TTAGG
*
3314435 CTAGGGTTTTTAATTAAATTAGG
1 TTAGGGTTTTTAATTAAATTAGG
* *
3314458 TTAGGGTTTTTAAGTT-AAGT-GT
1 TTAGGGTTTTTAA-TTAAATTAGG
* *
3314480 TTAGAGTTTTTAATTAAATTAGA
1 TTAGGGTTTTTAATTAAATTAGG
3314503 TTAGGGTTTTTAATTAAATTAGG
1 TTAGGGTTTTTAATTAAATTAGG
*
3314526 TTAGGGTTTTTAAGTT-AA--GGG
1 TTAGGGTTTTTAA-TTAAATTAGG
3314547 TTTAGGGTTTTTAATTGAATTAGGTTAGGG
1 -TTAGGGTTTTTAATT-AA--A--TTA-GG
*
3314577 TTAGGGTTTTTAATT-AA--GGG
1 TTAGGGTTTTTAATTAAATTAGG
3314597 TTTAGGGTTTTTAATTAAATTAGGTTAGG
1 -TTAGGGTTTTTAATT-AA--A--TTAGG
3314626 TTAGGGTTTTTAATTAAATTAGG
1 TTAGGGTTTTTAATTAAATTAGG
3314649 TTAGGGTTTTTAAGTT-AA--AGG
1 TTAGGGTTTTTAA-TTAAATTAGG
*
3314670 TTTAGGGTTTTTAATT-AA--GGG
1 -TTAGGGTTTTTAATTAAATTAGG
3314691 TTTAGGGTTTTTAATTAAATTAGG
1 -TTAGGGTTTTTAATTAAATTAGG
* *
3314715 CTAGGGTTTTTAATTAAATTAGA
1 TTAGGGTTTTTAATTAAATTAGG
*
3314738 TTAGGGTTTTTAAGTT-AA--GGG
1 TTAGGGTTTTTAA-TTAAATTAGG
3314759 TTTAGGGTTTTTAAGTTAATTAGGTTAGGG
1 -TTAGGGTTTTTAA-TTAA--A--TTA-GG
*
3314789 TTAGGGTTTTTAATT-AA--GGG
1 TTAGGGTTTTTAATTAAATTAGG
3314809 TTTAGGGTTTTTAATTAAATTAGGTTAGG
1 -TTAGGGTTTTTAATT-AA--A--TTAGG
3314838 TTAGGGTTTTTAATTAAATTAGG
1 TTAGGGTTTTTAATTAAATTAGG
3314861 TTAGGGTTTTTAAGTT-AA--AGG
1 TTAGGGTTTTTAA-TTAAATTAGG
*
3314882 TTTAGGGTTTTTAATT-AA--GGG
1 -TTAGGGTTTTTAATTAAATTAGG
3314903 TTTAGGGTTTTTAATTAAATTAGG
1 -TTAGGGTTTTTAATTAAATTAGG
* *
3314927 CTAGGGTTTTTAATTAAATTAGA
1 TTAGGGTTTTTAATTAAATTAGG
*
3314950 TTAGGGTTTTTAAGTT-AA--GGG
1 TTAGGGTTTTTAA-TTAAATTAGG
3314971 TTTAGGGTTTTTAAGTTAATTAGGTTAGGG
1 -TTAGGGTTTTTAA-TTAA--A--TTA-GG
*
3315001 TTAGGGTTTTTAATT-AA--GGG
1 TTAGGGTTTTTAATTAAATTAGG
3315021 TTTAGGGTTTTTAATTAAATTAGG
1 -TTAGGGTTTTTAATTAAATTAGG
3315045 TTAGGGTTTTTAATTAAATTAGG
1 TTAGGGTTTTTAATTAAATTAGG
*
3315068 CTAGGGTTTTTAATTAAATTAGCTCATGG
1 TTAGGGTTTTTAATTAAA-T---T-A-GG
* **
3315097 TTTTGGGTTTTTAATTATTTTAGG
1 -TTAGGGTTTTTAATTAAATTAGG
****
3315121 TTAGGGTTTAGGGTTAAATTAGG
1 TTAGGGTTTTTAATTAAATTAGG
3315144 TTAGGGTTTTTA
1 TTAGGGTTTTTA
3315156 TTACATCAAA
Statistics
Matches: 873, Mismatches: 70, Indels: 220
0.75 0.06 0.19
Matches are distributed among these distances:
20 12 0.01
21 148 0.17
22 116 0.13
23 388 0.44
24 28 0.03
25 15 0.02
26 2 0.00
27 10 0.01
28 54 0.06
29 78 0.09
30 22 0.03
ACGTcount: A:0.27, C:0.01, G:0.25, T:0.47
Consensus pattern (23 bp):
TTAGGGTTTTTAATTAAATTAGG
Found at i:3314428 original size:68 final size:63
Alignment explanation
Indices: 3314079--3315089 Score: 516
Period size: 68 Copynumber: 14.4 Consensus size: 63
3314069 AAGTTAAGGG
* * *
3314079 TTTAGGGTTTTTAAGTT-AATTAGGCTAGGGTTTTTAATTAAATTAGG-TTAGGATTTTTAAGTT
1 TTTAGGGTTTTTAA-TTAAATTAGGTTAGGGTTTTTAATT-AA--GGGTTTAGGGTTTTTAA-TT
*
3314142 AAGGG
61 AA--A
* *
3314147 TTTA-GATTTTTAATTGAATTAGGTTAGGGTTAGGGTTTTTAATTAAGGGTTTAGAGTTTTTAAT
1 TTTAGGGTTTTTAATT-AA--A--TTA-GGTTAGGGTTTTTAATTAAGGGTTTAGGGTTTTTAAT
3314211 TAAA
60 TAAA
* * *
3314215 TTAGGCTAGGGTTTTTAATTAAATTAGGCTAGGGTTTTTAATTAAATTAGG-TTGGGGTTTTTAA
1 TT----TAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTAATT-AA--GGGTTTAGGGTTTTTAA
3314279 TTAAA
59 TTAAA
* * *
3314284 TTAGGCTAGGGTTTTTAATTAAATTAGGCTATGGTTTTTAATTAAATTAGG-TTAGGGTTTTTAA
1 TT----TAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTAATT-AA--GGGTTTAGGGTTTTTAA
**
3314348 GTTATGGG
59 -TTA--AA
3314356 TTTAGGGTTTTTAATTGAATTAGGTTAGGGTTAGGGTTTTTAATTAAGGGTTTAGGGTTTTTAAT
1 TTTAGGGTTTTTAATT-AA--A--TTA-GGTTAGGGTTTTTAATTAAGGGTTTAGGGTTTTTAAT
3314421 TAATTTA
60 TAA---A
* *
3314428 GGTTAGGCTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTAAGTTAAGTGTTTAGAGTTTTTAA
1 --TT----TAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTAA-TTAAGGGTTTAGGGTTTTTAA
3314493 TTAAA
59 TTAAA
3314498 TTAGATTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTAAGTTAAGGGTTTAGGGTTTTTAATT
1 -T---TTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTAA-TTAAGGGTTTAGGGTTTTTAATT
3314563 GAATTA
61 -AA--A
* *
3314569 GGTTAGGGTTAGGGTTTTTAATT-AA--GGGTTTAGGGTTTTTAATTAAATTAGGTTAGGTTAGG
1 ---T----TTAGGGTTTTTAATTAAATTAGG-TTAGGGTTTTTAATT--A--AGG---GTTTAGG
3314631 GTTTTTAATTAAA
51 GTTTTTAATTAAA
3314644 TTAGGTTAGGGTTTTTAAGTT-AA--AGGTTTAGGGTTTTTAATTAAGGGTTTAGGGTTTTTAAT
1 -T---TTAGGGTTTTTAA-TTAAATTAGG-TTAGGGTTTTTAATTAAGGGTTTAGGGTTTTTAAT
3314706 TAAA
60 TAAA
*
3314710 TTAGGCTAGGGTTTTTAATTAAATTAGATTAGGGTTTTTAAGTTAAGGGTTTAGGGTTTTTAAGT
1 TT----TAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTAA-TTAAGGGTTTAGGGTTTTTAA-T
3314775 TAATTA
60 TAA--A
* *
3314781 GGTTAGGGTTAGGGTTTTTAATT-AA--GGGTTTAGGGTTTTTAATTAAATTAGGTTAGGTTAGG
1 ---T----TTAGGGTTTTTAATTAAATTAGG-TTAGGGTTTTTAATT--A--AGG---GTTTAGG
3314843 GTTTTTAATTAAA
51 GTTTTTAATTAAA
3314856 TTAGGTTAGGGTTTTTAAGTT-AA--AGGTTTAGGGTTTTTAATTAAGGGTTTAGGGTTTTTAAT
1 -T---TTAGGGTTTTTAA-TTAAATTAGG-TTAGGGTTTTTAATTAAGGGTTTAGGGTTTTTAAT
3314918 TAAA
60 TAAA
*
3314922 TTAGGCTAGGGTTTTTAATTAAATTAGATTAGGGTTTTTAAGTTAAGGGTTTAGGGTTTTTAAGT
1 TT----TAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTAA-TTAAGGGTTTAGGGTTTTTAA-T
3314987 TAATTA
60 TAA--A
* *
3314993 GGTTAGGGTTAGGGTTTTTAATT-AA--GGGTTTAGGGTTTTTAATTAAATTAGG-TTAGGGTTT
1 ---T----TTAGGGTTTTTAATTAAATTAGG-TTAGGGTTTTTAATT-AA--GGGTTTAGGGTTT
3315054 TTAATTAAA
55 TTAATTAAA
3315063 TTAGGCTAGGGTTTTTAATTAAATTAG
1 TT----TAGGGTTTTTAATTAAATTAG
3315090 CTCATGGTTT
Statistics
Matches: 789, Mismatches: 44, Indels: 218
0.75 0.04 0.21
Matches are distributed among these distances:
62 2 0.00
63 1 0.00
65 6 0.01
66 68 0.09
67 65 0.08
68 131 0.17
69 97 0.12
70 16 0.02
71 32 0.04
72 115 0.15
73 128 0.16
74 65 0.08
75 9 0.01
77 8 0.01
78 46 0.06
ACGTcount: A:0.28, C:0.01, G:0.25, T:0.46
Consensus pattern (63 bp):
TTTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTAATTAAGGGTTTAGGGTTTTTAATTAAA
Found at i:3314441 original size:28 final size:28
Alignment explanation
Indices: 3314408--3314462 Score: 101
Period size: 28 Copynumber: 2.0 Consensus size: 28
3314398 ATTAAGGGTT
*
3314408 TAGGGTTTTTAATTAATTTAGGTTAGGC
1 TAGGGTTTTTAATTAAATTAGGTTAGGC
3314436 TAGGGTTTTTAATTAAATTAGGTTAGG
1 TAGGGTTTTTAATTAAATTAGGTTAGG
3314463 GTTTTTAAGT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.27, C:0.02, G:0.25, T:0.45
Consensus pattern (28 bp):
TAGGGTTTTTAATTAAATTAGGTTAGGC
Found at i:3314529 original size:191 final size:188
Alignment explanation
Indices: 3314080--3315089 Score: 935
Period size: 191 Copynumber: 5.4 Consensus size: 188
3314070 AGTTAAGGGT
* *
3314080 TTAGGGTTTTTAAGTT-AATTAGGCTAGGGTTTTTAATTAAATTAGGTTAGGATTTTTAAGTT-A
1 TTAGGGTTTTTAA-TTAAATTAGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTAA-TTAA
* * * *
3314143 A--GGGTTTA-GATTTTTAATTGAATTAGGTTAGGGTTAGGGTTTTTAATT-AA-G---GGTTTA
64 ATTAGG-TTAGGGTTTTTAATT-AA-T--G---GGTTTAGGGTTTTTAATTAAAGGTTAGGGTTA
* * *
3314200 GAGTTTTTAATTAAATTAGG-CTAGGGTTTTTAATTAA--A--TTAGGCTAGGGTTTTTAATTAA
121 GGGTTTTTAATT-AA--GGGTTTAGGGTTTTTAATTAATTAGGTTAGGCTAGGGTTTTTAATTAA
3314260 ATTAGG
183 ATTAGG
* * * *
3314266 TTGGGGTTTTTAATTAAATTAGGCTAGGGTTTTTAATTAAATTAGGCTATGGTTTTTAATTAAAT
1 TTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTAATTAAAT
3314331 TAGGTTAGGGTTTTTAAGTT-ATGGGTTTAGGGTTTTTAATTGAATTAGGTTAGGGTTAGGGTTT
66 TAGGTTAGGGTTTTTAA-TTAATGGGTTTAGGGTTTTTAATT-AA--AGGTTAGGGTTAGGGTTT
3314395 TTAATTAAGGGTTTAGGGTTTTTAATTAATTTAGGTTAGGCTAGGGTTTTTAATTAAATTAGG
127 TTAATTAAGGGTTTAGGGTTTTTAATTAA-TTAGGTTAGGCTAGGGTTTTTAATTAAATTAGG
* * * *
3314458 TTAGGGTTTTTAAGTT-AAGT-GTTTAGAGTTTTTAATTAAATTAGATTAGGGTTTTTAATTAAA
1 TTAGGGTTTTTAA-TTAAATTAGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTAATTAAA
3314521 TTAGGTTAGGGTTTTTAAGTTAA-GGGTTTAGGGTTTTTAATTGAATTAGGTTAGGGTTAGGGTT
65 TTAGGTTAGGGTTTTTAA-TTAATGGGTTTAGGGTTTTTAATT-AA--AGGTTAGGGTTAGGGTT
*
3314585 TTTAATTAAGGGTTTAGGGTTTTTAATTAAATTAGGTTAGGTTAGGGTTTTTAATTAAATTAGG
126 TTTAATTAAGGGTTTAGGGTTTTTAATT-AATTAGGTTAGGCTAGGGTTTTTAATTAAATTAGG
*
3314649 TTAGGGTTTTTAAGTT-AA--AGGTTTAGGGTTTTTAATT-AA--GGGTTTAGGGTTTTTAATTA
1 TTAGGGTTTTTAA-TTAAATTAGG-TTAGGGTTTTTAATTAAATTAGG-TTAGGGTTTTTAATTA
* ** * *
3314708 AATTAGGCTAGGGTTTTTAATTAAATTAGATTAGGGTTTTTAAGTTAAGGGTTTAGGGTTTTTA-
63 AATTAGGTTAGGGTTTTTAATT-AATGGGTTTAGGGTTTTTAA-TTAAAGG-TTAGGG---TTAG
* * * *
3314772 AGTTAATTAGGTT-AGGG-TTAGGGTTTTTAATTAA--GGGTT----TAGGGTTTTTAATTAAAT
122 GGTT-TTTA-ATTAAGGGTTTAGGGTTTTTAATTAATTAGGTTAGGCTAGGGTTTTTAATT-AA-
3314829 TAGGTTAGG
183 -A--TTAGG
3314838 TTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTAAGTT-AA--AGGTTTAGGGTTTTTAATT-A
1 TTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTAA-TTAAATTAGG-TTAGGGTTTTTAATTAA
* * * *
3314899 A--GGGTTTAGGGTTTTTAATTAAATTAGG-CTAGGGTTTTTAATTAAA--TTA-GATTAGGGTT
64 ATTAGG-TTAGGGTTTTTAATT-AA-TGGGTTTAGGGTTTTTAATTAAAGGTTAGGGTTAGGGTT
* *
3314958 TTTAAGTTAAGGGTTTAGGGTTTTTAAGTTAATTAGGTTAGGGTTAGGGTTTTTAATT-AA--GG
126 TTTAA-TTAAGGGTTTAGGGTTTTTAA-TTAATTAGGTTA-GGCTAGGGTTTTTAATTAAATTAG
3315020 G
188 G
*
3315021 TTTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTAATTAAATTAGGCTAGGGTTTTTAATTAAA
1 -TTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTAATTAAA
3315086 TTAG
65 TTAG
3315090 CTCATGGTTT
Statistics
Matches: 711, Mismatches: 48, Indels: 128
0.80 0.05 0.14
Matches are distributed among these distances:
181 25 0.04
182 7 0.01
183 18 0.03
184 58 0.08
185 24 0.03
186 67 0.09
187 22 0.03
188 30 0.04
189 111 0.16
190 39 0.05
191 250 0.35
192 56 0.08
193 4 0.01
ACGTcount: A:0.28, C:0.01, G:0.25, T:0.46
Consensus pattern (188 bp):
TTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTAATTAAAT
TAGGTTAGGGTTTTTAATTAATGGGTTTAGGGTTTTTAATTAAAGGTTAGGGTTAGGGTTTTTAA
TTAAGGGTTTAGGGTTTTTAATTAATTAGGTTAGGCTAGGGTTTTTAATTAAATTAGG
Found at i:3314732 original size:212 final size:209
Alignment explanation
Indices: 3314197--3315085 Score: 1181
Period size: 212 Copynumber: 4.2 Consensus size: 209
3314187 AATTAAGGGT
* *
3314197 TTAGAGTTTTTAATTAAATTAGGCTAGGGTTTTTAATTAAATTAGGCTAGGGTTTTTAATTAAAT
1 TTAGGGTTTTTAATTAAATTAGGCTAGGGTTTTTAATT-AA--AGGTTAGGGTTTTTAATT-AA-
* * ** *
3314262 TAGG-TTGGGGTTTTTAATTAAATTAGGCTAGGGTTTTTAATTAAATTAGGCTATGGTTTTTAA-
61 -GGGTTTAGGGTTTTTAATTAAATTAGGCTAGGGTTTTTAATTAAATTAGATTAGGGTTTTTAAG
* *
3314325 TTAAATTAGG-TTAGGGTTTTTAAGTT-A-TGGGTTTAGGGTT----TTTAATTGAATTAGGTTA
125 TT-AA--GGGTTTAGGGTTTTTAAGTTAATTAGG-TTAGGGTTAGGGTTT--TT-AATTA----A
*
3314383 GGG-TTAGGGTTTTTAATT-A--AGG---GT
179 GGGTTTAGGGTTTTTAATTAATTAGGTTAGG
3314407 TTAGGGTTTTTAATTAATTTAGGTTAGGCTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTAAG
1 TTAGGGTTTTTAATTAA---A--TTAGGCTAGGGTTTTTAATT-AA--AGGTTAGGGTTTTTAA-
* * ** *
3314472 TTAAGTGTTTAGAGTTTTTAATTAAATTAGATTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTT
57 TTAAGGGTTTAGGGTTTTTAATTAAATTAGGCTAGGGTTTTTAATTAAATTAGATTAGGGTTTTT
3314537 AAGTTAAGGGTTTAGGGTTTTTAA-TTGAATTAGGTTAGGGTTAGGGTTTTTAATTAAGGGTTTA
122 AAGTTAAGGGTTTAGGGTTTTTAAGTT-AATTAGGTTAGGGTTAGGGTTTTTAATTAAGGGTTTA
3314601 GGGTTTTTAATTAAATTAGGTTAGG
186 GGGTTTTTAATT-AATTAGGTTAGG
*
3314626 TTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTAAGTTAAAGGTTTAGGGTTTTTAATTAAGGG
1 TTAGGGTTTTTAATTAAATTAGGCTAGGGTTTTTAA-TTAAAGG-TTAGGGTTTTTAATTAAGGG
3314691 TTTAGGGTTTTTAATTAAATTAGGCTAGGGTTTTTAATTAAATTAGATTAGGGTTTTTAAGTTAA
64 TTTAGGGTTTTTAATTAAATTAGGCTAGGGTTTTTAATTAAATTAGATTAGGGTTTTTAAGTTAA
3314756 GGGTTTAGGGTTTTTAAGTTAATTAGGTTAGGGTTAGGGTTTTTAATTAAGGGTTTAGGGTTTTT
129 GGGTTTAGGGTTTTTAAGTTAATTAGGTTAGGGTTAGGGTTTTTAATTAAGGGTTTAGGGTTTTT
3314821 AATTAAATTAGGTTAGG
194 AATT-AATTAGGTTAGG
*
3314838 TTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTAAGTTAAAGGTTTAGGGTTTTTAATTAAGGG
1 TTAGGGTTTTTAATTAAATTAGGCTAGGGTTTTTAA-TTAAAGG-TTAGGGTTTTTAATTAAGGG
3314903 TTTAGGGTTTTTAATTAAATTAGGCTAGGGTTTTTAATTAAATTAGATTAGGGTTTTTAAGTTAA
64 TTTAGGGTTTTTAATTAAATTAGGCTAGGGTTTTTAATTAAATTAGATTAGGGTTTTTAAGTTAA
3314968 GGGTTTAGGGTTTTTAAGTTAATTAGGTTAGGGTTAGGGTTTTTAATTAAGGGTTTAGGGTTTTT
129 GGGTTTAGGGTTTTTAAGTTAATTAGGTTAGGGTTAGGGTTTTTAATTAAGGGTTTAGGGTTTTT
3315033 AATTAA--A--TTAGG
194 AATTAATTAGGTTAGG
3315045 TTAGGGTTTTTAATTAAATTAGGCTAGGGTTTTTAATTAAA
1 TTAGGGTTTTTAATTAAATTAGGCTAGGGTTTTTAATTAAA
3315086 TTAGCTCATG
Statistics
Matches: 632, Mismatches: 20, Indels: 58
0.89 0.03 0.08
Matches are distributed among these distances:
206 5 0.01
207 40 0.06
209 1 0.00
210 16 0.03
211 6 0.01
212 367 0.58
213 30 0.05
214 84 0.13
215 54 0.09
216 8 0.01
218 3 0.00
219 18 0.03
ACGTcount: A:0.28, C:0.01, G:0.25, T:0.46
Consensus pattern (209 bp):
TTAGGGTTTTTAATTAAATTAGGCTAGGGTTTTTAATTAAAGGTTAGGGTTTTTAATTAAGGGTT
TAGGGTTTTTAATTAAATTAGGCTAGGGTTTTTAATTAAATTAGATTAGGGTTTTTAAGTTAAGG
GTTTAGGGTTTTTAAGTTAATTAGGTTAGGGTTAGGGTTTTTAATTAAGGGTTTAGGGTTTTTAA
TTAATTAGGTTAGG
Found at i:3315152 original size:53 final size:53
Alignment explanation
Indices: 3315048--3315153 Score: 122
Period size: 53 Copynumber: 2.0 Consensus size: 53
3315038 AATTAGGTTA
** *
3315048 GGGTTTTTAATTAAATTAGGCTAGGGTTTTTAATTAAATTAGCTCATGGTTTT
1 GGGTTTTTAATTAAATTAGGCTAGGGTTTAGAATTAAATTAGCTCAGGGTTTT
** * ** * *
3315101 GGGTTTTTAATTATTTTAGGTTAGGGTTTAGGGTTAAATTAGGTTAGGGTTTT
1 GGGTTTTTAATTAAATTAGGCTAGGGTTTAGAATTAAATTAGCTCAGGGTTTT
3315154 TATTACATCA
Statistics
Matches: 43, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
53 43 1.00
ACGTcount: A:0.24, C:0.03, G:0.25, T:0.48
Consensus pattern (53 bp):
GGGTTTTTAATTAAATTAGGCTAGGGTTTAGAATTAAATTAGCTCAGGGTTTT
Found at i:3315235 original size:43 final size:45
Alignment explanation
Indices: 3315161--3315246 Score: 140
Period size: 43 Copynumber: 2.0 Consensus size: 45
3315151 TTTTATTACA
*
3315161 TCAAATAAACTTCTATTTTATTACATCAAATAATATCAAAATAAC
1 TCAAATAAACTTCTATTTTATTACATAAAATAATATCAAAATAAC
*
3315206 TCAAA-AAATTTCTATTTT-TTACATAAAATAATATCAAAATA
1 TCAAATAAACTTCTATTTTATTACATAAAATAATATCAAAATA
3315247 TTCAAAATAT
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
43 22 0.56
44 12 0.31
45 5 0.13
ACGTcount: A:0.50, C:0.13, G:0.00, T:0.37
Consensus pattern (45 bp):
TCAAATAAACTTCTATTTTATTACATAAAATAATATCAAAATAAC
Found at i:3315692 original size:18 final size:18
Alignment explanation
Indices: 3315669--3315703 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
3315659 CGGAAAAGGA
*
3315669 TACATATAAGGGTTAGGG
1 TACATATAAGGGCTAGGG
3315687 TACATATAAGGGCTAGG
1 TACATATAAGGGCTAGG
3315704 AAATGCACCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.34, C:0.09, G:0.31, T:0.26
Consensus pattern (18 bp):
TACATATAAGGGCTAGGG
Found at i:3316365 original size:7 final size:7
Alignment explanation
Indices: 3316355--3316379 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
3316345 ATACATACAT
3316355 AATACTA
1 AATACTA
3316362 AATACTA
1 AATACTA
3316369 AATACTA
1 AATACTA
3316376 AATA
1 AATA
3316380 TCAATCAAAT
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:0.60, C:0.12, G:0.00, T:0.28
Consensus pattern (7 bp):
AATACTA
Found at i:3317634 original size:22 final size:22
Alignment explanation
Indices: 3317609--3317659 Score: 93
Period size: 22 Copynumber: 2.3 Consensus size: 22
3317599 AAATATAGAT
*
3317609 TTGAGAGAATTTTGGAAGGAAA
1 TTGAGAGAATTTTGGAAAGAAA
3317631 TTGAGAGAATTTTGGAAAGAAA
1 TTGAGAGAATTTTGGAAAGAAA
3317653 TTGAGAG
1 TTGAGAG
3317660 GAAATATGAG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.41, C:0.00, G:0.31, T:0.27
Consensus pattern (22 bp):
TTGAGAGAATTTTGGAAAGAAA
Found at i:3317637 original size:51 final size:51
Alignment explanation
Indices: 3317522--3317637 Score: 205
Period size: 51 Copynumber: 2.3 Consensus size: 51
3317512 ATTTAAAAAA
* * *
3317522 AAGGAAATTGAGAAGAAATTGAAATTAAATATGGATTTGAGAGAATTTTTG
1 AAGGAAATTGAGAGGAAATTGAAATTAAATATAGATTTGAGAGAATTTTGG
3317573 AAGGAAATTGAGAGGAAATTGAAATTAAATATAGATTTGAGAGAATTTTGG
1 AAGGAAATTGAGAGGAAATTGAAATTAAATATAGATTTGAGAGAATTTTGG
3317624 AAGGAAATTGAGAG
1 AAGGAAATTGAGAG
3317638 AATTTTGGAA
Statistics
Matches: 62, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
51 62 1.00
ACGTcount: A:0.46, C:0.00, G:0.26, T:0.28
Consensus pattern (51 bp):
AAGGAAATTGAGAGGAAATTGAAATTAAATATAGATTTGAGAGAATTTTGG
Found at i:3318051 original size:17 final size:16
Alignment explanation
Indices: 3318018--3318056 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
3318008 TTTAGCATAA
*
3318018 AAAATTGATTAATTAT
1 AAAATTGATTAAGTAT
*
3318034 AAAATTGATTCAGGTAT
1 AAAATTGATT-AAGTAT
3318051 AAAATT
1 AAAATT
3318057 TTGTTTGAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
16 10 0.50
17 10 0.50
ACGTcount: A:0.49, C:0.03, G:0.10, T:0.38
Consensus pattern (16 bp):
AAAATTGATTAAGTAT
Found at i:3325588 original size:23 final size:22
Alignment explanation
Indices: 3325549--3325593 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 22
3325539 AATTATTTTG
*
3325549 GATGTTCATGACTTTGGTATAAT
1 GATGTTAATGACTTTGG-ATAAT
3325572 GATGTTAATGA-TGTTGGATAAT
1 GATGTTAATGACT-TTGGATAAT
3325594 TTGGTATTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 6 0.30
23 14 0.70
ACGTcount: A:0.29, C:0.04, G:0.24, T:0.42
Consensus pattern (22 bp):
GATGTTAATGACTTTGGATAAT
Found at i:3333202 original size:27 final size:27
Alignment explanation
Indices: 3333164--3333512 Score: 414
Period size: 27 Copynumber: 13.0 Consensus size: 27
3333154 ATAGGGTGAT
*
3333164 CGTAATGCCCCTATAGGGTAAAATGAC
1 CGTAATGCCCCTGTAGGGTAAAATGAC
* * *
3333191 CGTAATGCCCCTATAGGATAAAATGAT
1 CGTAATGCCCCTGTAGGGTAAAATGAC
*
3333218 CGTAATACCCCTGTAGGGT-AAATGAC
1 CGTAATGCCCCTGTAGGGTAAAATGAC
* *
3333244 CGTAATGACCCTATAGGGT-AAATGAC
1 CGTAATGCCCCTGTAGGGTAAAATGAC
* * * * *
3333270 CGTAATGTCGCTATAAGGTAAAATCAC
1 CGTAATGCCCCTGTAGGGTAAAATGAC
* * * *
3333297 TGTAATGCCCTTGTATGGTAAAATGAT
1 CGTAATGCCCCTGTAGGGTAAAATGAC
* *
3333324 CGTAATGCCCCTATAGGGTAAAATGAT
1 CGTAATGCCCCTGTAGGGTAAAATGAC
* *
3333351 CGTAATGCCCTTGTAGGTTAAAATGAC
1 CGTAATGCCCCTGTAGGGTAAAATGAC
*
3333378 CGTAACGCCCCTGTAGGGTAAAATGAC
1 CGTAATGCCCCTGTAGGGTAAAATGAC
* *
3333405 CGTAACGCCGCTGTAGGGTAAAATGAC
1 CGTAATGCCCCTGTAGGGTAAAATGAC
** *
3333432 TTTAATGCCCCTGTAGGGTAAAATAAC
1 CGTAATGCCCCTGTAGGGTAAAATGAC
* * * *
3333459 CTTAATGCCCCCGTAAGGTAAAATGAT
1 CGTAATGCCCCTGTAGGGTAAAATGAC
3333486 CGTAATGCCCCTGTAGGGTAAAATGAC
1 CGTAATGCCCCTGTAGGGTAAAATGAC
3333513 TATTTTACCC
Statistics
Matches: 274, Mismatches: 47, Indels: 2
0.85 0.15 0.01
Matches are distributed among these distances:
26 45 0.16
27 229 0.84
ACGTcount: A:0.32, C:0.20, G:0.22, T:0.25
Consensus pattern (27 bp):
CGTAATGCCCCTGTAGGGTAAAATGAC
Found at i:3333663 original size:24 final size:24
Alignment explanation
Indices: 3333530--3333651 Score: 109
Period size: 24 Copynumber: 5.1 Consensus size: 24
3333520 CCCTTTAGGG
* ** *
3333530 TTAAATGATTGATTTACCTATGAT
1 TTAAATGACTGATTTGTCTGTGAT
* * **
3333554 GTAAATGAATGATTTGTCTAAGAT
1 TTAAATGACTGATTTGTCTGTGAT
* * *
3333578 GTAAAAGACTGATTTGTCAGTGAT
1 TTAAATGACTGATTTGTCTGTGAT
* * *
3333602 TTAAATGACTAATTTTTCTGTCAT
1 TTAAATGACTGATTTGTCTGTGAT
*
3333626 TTAAATGATTGATTTGTCTGTGAT
1 TTAAATGACTGATTTGTCTGTGAT
3333650 TT
1 TT
3333652 GTATGAGTGA
Statistics
Matches: 78, Mismatches: 20, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
24 78 1.00
ACGTcount: A:0.31, C:0.07, G:0.17, T:0.44
Consensus pattern (24 bp):
TTAAATGACTGATTTGTCTGTGAT
Found at i:3333856 original size:32 final size:32
Alignment explanation
Indices: 3333811--3333995 Score: 226
Period size: 32 Copynumber: 5.8 Consensus size: 32
3333801 GTGATGCTAT
* *
3333811 TGATGGCTTTGTGCCAATCATATTACCATTAT
1 TGATGGCTTTGTGCCAATCATATTACTATTAC
* * * *
3333843 TGATGGGTGTGTGCCGATCATATTACCATTAC
1 TGATGGCTTTGTGCCAATCATATTACTATTAC
* * *
3333875 TGATGGCTATGTGCCGATCATATTACTACTAC
1 TGATGGCTTTGTGCCAATCATATTACTATTAC
* * *
3333907 TAATGGCTTTGTGTCAATCATACTACTATTAC
1 TGATGGCTTTGTGCCAATCATATTACTATTAC
* * * *
3333939 TGATGGCTGTGTACCGATCATATTACTACTAC
1 TGATGGCTTTGTGCCAATCATATTACTATTAC
3333971 TGATGGCTTTGTGCCAATCATATTA
1 TGATGGCTTTGTGCCAATCATATTA
3333996 TTGTACTTAT
Statistics
Matches: 129, Mismatches: 24, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
32 129 1.00
ACGTcount: A:0.25, C:0.19, G:0.18, T:0.37
Consensus pattern (32 bp):
TGATGGCTTTGTGCCAATCATATTACTATTAC
Found at i:3333977 original size:96 final size:96
Alignment explanation
Indices: 3333813--3333995 Score: 276
Period size: 96 Copynumber: 1.9 Consensus size: 96
3333803 GATGCTATTG
* * * * *
3333813 ATGGCTTTGTGCCAATCATATTACCATTATTGATGGGTGTGTGCCGATCATATTACCATTACTGA
1 ATGGCTTTGTGCCAATCATACTACCATTACTGATGGCTGTGTACCGATCATATTACCACTACTGA
*
3333878 TGGCTATGTGCCGATCATATTACTACTACTA
66 TGGCTATGTGCCAATCATATTACTACTACTA
* * *
3333909 ATGGCTTTGTGTCAATCATACTACTATTACTGATGGCTGTGTACCGATCATATTACTACTACTGA
1 ATGGCTTTGTGCCAATCATACTACCATTACTGATGGCTGTGTACCGATCATATTACCACTACTGA
*
3333974 TGGCTTTGTGCCAATCATATTA
66 TGGCTATGTGCCAATCATATTA
3333996 TTGTACTTAT
Statistics
Matches: 77, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
96 77 1.00
ACGTcount: A:0.25, C:0.20, G:0.18, T:0.37
Consensus pattern (96 bp):
ATGGCTTTGTGCCAATCATACTACCATTACTGATGGCTGTGTACCGATCATATTACCACTACTGA
TGGCTATGTGCCAATCATATTACTACTACTA
Found at i:3334032 original size:22 final size:22
Alignment explanation
Indices: 3334002--3334047 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 22
3333992 ATTATTGTAC
* * *
3334002 TTATGGCTTGTAGCCATTCTGT
1 TTATAGCTTATAGCCATCCTGT
*
3334024 TTATAGCTTATAGCTATCCTGT
1 TTATAGCTTATAGCCATCCTGT
3334046 TT
1 TT
3334048 TCGGCTCTTA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.17, C:0.17, G:0.17, T:0.48
Consensus pattern (22 bp):
TTATAGCTTATAGCCATCCTGT
Found at i:3336130 original size:34 final size:36
Alignment explanation
Indices: 3336051--3336173 Score: 144
Period size: 36 Copynumber: 3.5 Consensus size: 36
3336041 TGATATTCTT
* ** * *
3336051 ATTCGCATGTTAAGCATGCTATTA-AGCTGACTTTG
1 ATTCGCATGTTAAGCATGCCATTATTTCTTATTTTG
* *
3336086 ACTCGCATGTTAAGCATGCC-TT-TTTTTTATTTTG
1 ATTCGCATGTTAAGCATGCCATTATTTCTTATTTTG
* *
3336120 ATTCGTATGTTAAGCATGCCATTATTTCTTATTATG
1 ATTCGCATGTTAAGCATGCCATTATTTCTTATTTTG
3336156 ATTCGCATGTTAAGCATG
1 ATTCGCATGTTAAGCATG
3336174 TCACTCTGTT
Statistics
Matches: 73, Mismatches: 12, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
34 26 0.36
35 20 0.27
36 27 0.37
ACGTcount: A:0.24, C:0.16, G:0.17, T:0.43
Consensus pattern (36 bp):
ATTCGCATGTTAAGCATGCCATTATTTCTTATTTTG
Found at i:3343352 original size:21 final size:19
Alignment explanation
Indices: 3343287--3343380 Score: 134
Period size: 19 Copynumber: 4.8 Consensus size: 19
3343277 AATTTTTGAG
*
3343287 GATATGCAATCTTAGATGT
1 GATATGCAATCTTAGATAT
*
3343306 GATATGCAATCCTAGATAT
1 GATATGCAATCTTAGATAT
3343325 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
*
3343344 GATATATGCAATCTTATATAT
1 G--ATATGCAATCTTAGATAT
*
3343365 GATATGTAATCTTAGA
1 GATATGCAATCTTAGA
3343381 AGATATGATT
Statistics
Matches: 67, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
19 49 0.73
21 18 0.27
ACGTcount: A:0.36, C:0.11, G:0.16, T:0.37
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:3343365 original size:40 final size:38
Alignment explanation
Indices: 3343287--3343387 Score: 134
Period size: 40 Copynumber: 2.7 Consensus size: 38
3343277 AATTTTTGAG
*
3343287 GATATGCAATCTTAGATGTGATATGCAATCCTAGATAT
1 GATATGCAATCTTAGATATGATATGCAATCCTAGATAT
* *
3343325 GATATGCAATCTTAGATATGATATATGCAATCTTATATAT
1 GATATGCAATCTTAGATATG--ATATGCAATCCTAGATAT
*
3343365 GATATGTAATCTTAGA-A-GATATG
1 GATATGCAATCTTAGATATGATATG
3343388 ATTTTGTTAT
Statistics
Matches: 57, Mismatches: 4, Indels: 6
0.85 0.06 0.09
Matches are distributed among these distances:
36 5 0.09
38 20 0.35
39 1 0.02
40 31 0.54
ACGTcount: A:0.37, C:0.10, G:0.17, T:0.37
Consensus pattern (38 bp):
GATATGCAATCTTAGATATGATATGCAATCCTAGATAT
Found at i:3346544 original size:11 final size:11
Alignment explanation
Indices: 3346528--3346552 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
3346518 ACTGTGGAAA
3346528 TATAAATTTAT
1 TATAAATTTAT
3346539 TATAAATTTAT
1 TATAAATTTAT
3346550 TAT
1 TAT
3346553 TCGAATATAT
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:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (11 bp):
TATAAATTTAT
Found at i:3349623 original size:27 final size:27
Alignment explanation
Indices: 3349584--3349751 Score: 115
Period size: 27 Copynumber: 6.3 Consensus size: 27
3349574 GAGTTCACCG
* *
3349584 CAAAGGCTATTCTTTTAGTGTTTGCCT
1 CAAAGGCTATTCTTTTAGAGTTTGCCA
* * **
3349611 TAAAGGCTATTCTTTCAGAGTTTTTCA
1 CAAAGGCTATTCTTTTAGAGTTTGCCA
*
3349638 CAAAGGCTATTCTTTTAGAGTTTTCCA
1 CAAAGGCTATTCTTTTAGAGTTTGCCA
* * * * **
3349665 TAATGACTATT-TTTCAGAGTTCACCA
1 CAAAGGCTATTCTTTTAGAGTTTGCCA
** * *
3349691 CAAAGAAT-TTTTTTTAGAGTTCGCCA
1 CAAAGGCTATTCTTTTAGAGTTTGCCA
* * * * *
3349717 CAATGACTATTCTTTCAAAGTTCGCCA
1 CAAAGGCTATTCTTTTAGAGTTTGCCA
*
3349744 AAAAGGCT
1 CAAAGGCT
3349752 TACAAAATTC
Statistics
Matches: 111, Mismatches: 28, Indels: 4
0.78 0.20 0.03
Matches are distributed among these distances:
25 2 0.02
26 36 0.32
27 73 0.66
ACGTcount: A:0.28, C:0.18, G:0.15, T:0.39
Consensus pattern (27 bp):
CAAAGGCTATTCTTTTAGAGTTTGCCA
Found at i:3349733 original size:53 final size:54
Alignment explanation
Indices: 3349571--3349748 Score: 153
Period size: 54 Copynumber: 3.3 Consensus size: 54
3349561 GGTAGTCCAC
* ** * * ** * *
3349571 TCAGAGTTCACCGCAAAGGCTATTCTTTTAGTGTTTGCCTTAAAGGCTATTCTT
1 TCAGAGTTCACCACAAAGAATATTCTTTTAGAGTTCGCCACAATGACTATTCTT
*** ** ** *
3349625 TCAGAGTTTTTCACAAAGGCTATTCTTTTAGAGTTTTCCATAATGACTATT-TT
1 TCAGAGTTCACCACAAAGAATATTCTTTTAGAGTTCGCCACAATGACTATTCTT
*
3349678 TCAGAGTTCACCACAAAGAAT-TTTTTTTAGAGTTCGCCACAATGACTATTCTT
1 TCAGAGTTCACCACAAAGAATATTCTTTTAGAGTTCGCCACAATGACTATTCTT
* * *
3349731 TCAAAGTTCGCCAAAAAG
1 TCAGAGTTCACCACAAAG
3349749 GCTTACAAAA
Statistics
Matches: 102, Mismatches: 21, Indels: 3
0.81 0.17 0.02
Matches are distributed among these distances:
52 25 0.25
53 35 0.34
54 42 0.41
ACGTcount: A:0.28, C:0.19, G:0.15, T:0.38
Consensus pattern (54 bp):
TCAGAGTTCACCACAAAGAATATTCTTTTAGAGTTCGCCACAATGACTATTCTT
Found at i:3352135 original size:27 final size:27
Alignment explanation
Indices: 3352105--3352189 Score: 71
Period size: 27 Copynumber: 3.1 Consensus size: 27
3352095 ACTTACAGTT
* *
3352105 CCTTCAGAGTTCACCATACATAGTATC
1 CCTTCAGAGTTCACCACACATACTATC
* * * *
3352132 CCTTTAGTGTTCGCCACACATACTATT
1 CCTTCAGAGTTCACCACACATACTATC
* ** * *
3352159 CCTTCAGTGTTTGCCACGCATACTATA
1 CCTTCAGAGTTCACCACACATACTATC
3352186 CCTT
1 CCTT
3352190 TAGAATTATT
Statistics
Matches: 48, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 48 1.00
ACGTcount: A:0.24, C:0.31, G:0.12, T:0.34
Consensus pattern (27 bp):
CCTTCAGAGTTCACCACACATACTATC
Found at i:3352427 original size:54 final size:53
Alignment explanation
Indices: 3352309--3352463 Score: 145
Period size: 54 Copynumber: 2.9 Consensus size: 53
3352299 ATTTTCATTT
* * * *
3352309 GCCACAAGGGTTTTCC-TTTCCTTAGATCACCACAAAGGCTTCTAGTTTATAGATC
1 GCCACAAAGG-TTTCCATTT-CATAGATCGCCACAAAGGCTTCCA-TTTATAGATC
* * * *
3352364 GCCATAAAGGCTTT-CAGTTT-GTAGATCGCCACAAAGGCTTCCATTTAATAGGTT
1 GCCACAAAGG-TTTCCA-TTTCATAGATCGCCACAAAGGCTTCCATTT-ATAGATC
* *
3352418 GCTACAAAGGTTTCCATTTCATAGATTGCCACAAAGGCTTCCATTT
1 GCCACAAAGGTTTCCATTTCATAGATCGCCACAAAGGCTTCCATTT
3352464 CCTGGCGTGT
Statistics
Matches: 83, Mismatches: 12, Indels: 11
0.78 0.11 0.10
Matches are distributed among these distances:
53 9 0.11
54 60 0.72
55 11 0.13
56 3 0.04
ACGTcount: A:0.27, C:0.23, G:0.17, T:0.32
Consensus pattern (53 bp):
GCCACAAAGGTTTCCATTTCATAGATCGCCACAAAGGCTTCCATTTATAGATC
Found at i:3352464 original size:27 final size:26
Alignment explanation
Indices: 3352331--3352463 Score: 140
Period size: 27 Copynumber: 5.0 Consensus size: 26
3352321 TTCCTTTCCT
* *
3352331 TAGATCACCACAAAGGCTTCTAGTTTA
1 TAGATCGCCACAAAGGCTTCCA-TTTA
* * *
3352358 TAGATCGCCATAAAGGCTTTCAGTTTG
1 TAGATCGCCACAAAGGCTTCCA-TTTA
3352385 TAGATCGCCACAAAGGCTTCCATTTAA
1 TAGATCGCCACAAAGGCTTCCATTT-A
* * * *
3352412 TAGGTTGCTACAAAGGTTTCCATTTCA
1 TAGATCGCCACAAAGGCTTCCATTT-A
*
3352439 TAGATTGCCACAAAGGCTTCCATTT
1 TAGATCGCCACAAAGGCTTCCATTT
3352464 CCTGGCGTGT
Statistics
Matches: 89, Mismatches: 16, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
26 3 0.03
27 86 0.97
ACGTcount: A:0.29, C:0.22, G:0.17, T:0.32
Consensus pattern (26 bp):
TAGATCGCCACAAAGGCTTCCATTTA
Found at i:3364882 original size:51 final size:51
Alignment explanation
Indices: 3364764--3365103 Score: 318
Period size: 51 Copynumber: 6.7 Consensus size: 51
3364754 TATCATTCGA
* * **
3364764 TACACGTAGTAGCCTTCACATAGTACTACACACGTGATC--AGTTTTACAA
1 TACACGTAGTAGCCTTCACATAGTACTACACACGTGACCAAAGCTTTACGG
* *
3364813 TTCATGTAGTAGCCTTCACATAGTACTACACACGTGACCAAAGCTTTACGG
1 TACACGTAGTAGCCTTCACATAGTACTACACACGTGACCAAAGCTTTACGG
* *
3364864 CT-CACGTAGTAGCCTTCACATAGTACTACATACGTGACCAAAGCTTTTCGG
1 -TACACGTAGTAGCCTTCACATAGTACTACACACGTGACCAAAGCTTTACGG
* * * * * * ** * *
3364915 TACCCATTGTAGCCTTCACTTAGTACTACACATGTAACCGTAG-ATTACCGA
1 TACACGTAGTAGCCTTCACATAGTACTACACACGTGACCAAAGCTTTA-CGG
* * *
3364966 TACACATAGTAGCATTCACACAGTACTACACACGTG-CTCAAAGC-TTATCGG
1 TACACGTAGTAGCCTTCACATAGTACTACACACGTGAC-CAAAGCTTTA-CGG
* * * * *
3365017 TACACATAGTAGCCTTCACTTAGTACTACACATGTGACCATTA--TTTATCGA
1 TACACGTAGTAGCCTTCACATAGTACTACACACGTGACCA-AAGCTTTA-CGG
* *
3365068 TACACGTAGTAGCCTCCACACAGTACTACACACGTG
1 TACACGTAGTAGCCTTCACATAGTACTACACACGTG
3365104 TTCATCGACA
Statistics
Matches: 238, Mismatches: 43, Indels: 18
0.80 0.14 0.06
Matches are distributed among these distances:
49 36 0.15
50 4 0.02
51 195 0.82
52 3 0.01
ACGTcount: A:0.31, C:0.27, G:0.15, T:0.27
Consensus pattern (51 bp):
TACACGTAGTAGCCTTCACATAGTACTACACACGTGACCAAAGCTTTACGG
Found at i:3364984 original size:102 final size:102
Alignment explanation
Indices: 3364761--3365103 Score: 383
Period size: 102 Copynumber: 3.4 Consensus size: 102
3364751 TTTTATCATT
* * * ** * **
3364761 CGATACACGTAGTAGCCTTCACATAGTACTACACACGTGATC--AG-TTTTACAATTCATGTAGT
1 CGATACACGTAGTAGCCTTCACACAGTACTACACACGTGCTCAAAGCTTAT-CGGTACACATAGT
* * *
3364823 AGCCTTCACATAGTACTACACACGTGACCAAAGCTTTAC
65 AGCCTTCACTTAGTACTACACATGTGACCATAG-TTTAC
* * * * * * *
3364862 GGCT-CACGTAGTAGCCTTCACATAGTACTACATACGTGAC-CAAAGCTTTTCGGTACCCATTGT
1 CGATACACGTAGTAGCCTTCACACAGTACTACACACGTG-CTCAAAGCTTATCGGTACACATAGT
* * *
3364925 AGCCTTCACTTAGTACTACACATGTAACCGTAGATTAC
65 AGCCTTCACTTAGTACTACACATGTGACCATAGTTTAC
* *
3364963 CGATACACATAGTAGCATTCACACAGTACTACACACGTGCTCAAAGCTTATCGGTACACATAGTA
1 CGATACACGTAGTAGCCTTCACACAGTACTACACACGTGCTCAAAGCTTATCGGTACACATAGTA
*
3365028 GCCTTCACTTAGTACTACACATGTGACCATTA-TTTAT
66 GCCTTCACTTAGTACTACACATGTGACCA-TAGTTTAC
*
3365065 CGATACACGTAGTAGCCTCCACACAGTACTACACACGTG
1 CGATACACGTAGTAGCCTTCACACAGTACTACACACGTG
3365104 TTCATCGACA
Statistics
Matches: 202, Mismatches: 33, Indels: 13
0.81 0.13 0.05
Matches are distributed among these distances:
100 34 0.17
101 9 0.04
102 153 0.76
103 6 0.03
ACGTcount: A:0.31, C:0.27, G:0.15, T:0.27
Consensus pattern (102 bp):
CGATACACGTAGTAGCCTTCACACAGTACTACACACGTGCTCAAAGCTTATCGGTACACATAGTA
GCCTTCACTTAGTACTACACATGTGACCATAGTTTAC
Found at i:3365080 original size:153 final size:150
Alignment explanation
Indices: 3364759--3365102 Score: 374
Period size: 153 Copynumber: 2.3 Consensus size: 150
3364749 ATTTTTATCA
* * * * **
3364759 TTCGATACACGTAGTAGCCTTCACATAGTACTACACACGTGATCAGTTTTACAATTCATGTAGTA
1 TTCGATACACGTAGTAGCCTTCACATAGTACTACACACGTAACCAGTATTACAATACACATAGTA
* * *
3364824 GCCTTCACATAGTACTACACACGTGACCAAAGCTTTACGGCTCACGTAGTAGCCTTCACATAGTA
66 GCATTCACACAGTACTACACACGTGACCAAAGCTTTACGGCTCACATAGTAGCCTTCACATAGTA
*
3364889 CTACATACGTGACCAAAGCTT
131 CTACACACGTGACCAAA-CTT
* * * * * * *
3364910 TTCGGTACCCATTGTAGCCTTCACTTAGTACTACACATGTAACC-GTAGATTACCGATACACATA
1 TTCGATACACGTAGTAGCCTTCACATAGTACTACACACGTAACCAGT--ATTA-CAATACACATA
3364974 GTAGCATTCACACAGTACTACACACGTG-CTCAAAGC-TTATCGG-TACACATAGTAGCCTTCAC
63 GTAGCATTCACACAGTACTACACACGTGAC-CAAAGCTTTA-CGGCT-CACATAGTAGCCTTCAC
* * *
3365036 TTAGTACTACACATGTGACCATTA-TT
125 ATAGTACTACACACGTGACCA-AACTT
* *
3365062 TATCGATACACGTAGTAGCCTCCACACAGTACTACACACGT
1 T-TCGATACACGTAGTAGCCTTCACATAGTACTACACACGT
3365103 GTTCATCGAC
Statistics
Matches: 157, Mismatches: 28, Indels: 14
0.79 0.14 0.07
Matches are distributed among these distances:
150 2 0.01
151 36 0.23
152 11 0.07
153 107 0.68
154 1 0.01
ACGTcount: A:0.31, C:0.27, G:0.15, T:0.28
Consensus pattern (150 bp):
TTCGATACACGTAGTAGCCTTCACATAGTACTACACACGTAACCAGTATTACAATACACATAGTA
GCATTCACACAGTACTACACACGTGACCAAAGCTTTACGGCTCACATAGTAGCCTTCACATAGTA
CTACACACGTGACCAAACTT
Found at i:3370481 original size:18 final size:18
Alignment explanation
Indices: 3370443--3370482 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
3370433 AACTGCTGCG
*
3370443 GCTGCAATTGCAATTGCT
1 GCTGCAATTGCAAATGCT
* *
3370461 GCTGCAGTTGCAAATGTT
1 GCTGCAATTGCAAATGCT
3370479 GCTG
1 GCTG
3370483 TTGCTGGGTC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.20, C:0.20, G:0.28, T:0.33
Consensus pattern (18 bp):
GCTGCAATTGCAAATGCT
Found at i:3377964 original size:17 final size:17
Alignment explanation
Indices: 3377942--3377975 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
3377932 AAATTACAAA
3377942 ATCAAATCTTCTAAAAT
1 ATCAAATCTTCTAAAAT
3377959 ATCAAATCTTCTAAAAT
1 ATCAAATCTTCTAAAAT
3377976 TAATTTTCAT
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:0.47, C:0.18, G:0.00, T:0.35
Consensus pattern (17 bp):
ATCAAATCTTCTAAAAT
Found at i:3383726 original size:37 final size:37
Alignment explanation
Indices: 3383676--3383749 Score: 148
Period size: 37 Copynumber: 2.0 Consensus size: 37
3383666 ACCCCTTAAA
3383676 TGATTATAAGCCAAGGACTTAAGTGTATATATATGTT
1 TGATTATAAGCCAAGGACTTAAGTGTATATATATGTT
3383713 TGATTATAAGCCAAGGACTTAAGTGTATATATATGTT
1 TGATTATAAGCCAAGGACTTAAGTGTATATATATGTT
3383750 AGGGTAAGAG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.35, C:0.08, G:0.19, T:0.38
Consensus pattern (37 bp):
TGATTATAAGCCAAGGACTTAAGTGTATATATATGTT
Found at i:3385015 original size:49 final size:50
Alignment explanation
Indices: 3384958--3385075 Score: 132
Period size: 54 Copynumber: 2.3 Consensus size: 50
3384948 TGAGCTTGGA
*
3384958 TTTCTTAATGTAAATTAGCT-TAAATGCTAACATGGGTTGCGGA-GTTGTT
1 TTTCTTAATGTAAATTAGCTATAAATGCTAACATGGGTTGC-AATGTTGTT
* *
3385007 TTTCTTAATGTAAATTGGCTGAAGATCAATGCTAACATGGGTTGCAATGTTGTT
1 TTTCTTAATGTAAATTAGCT----ATAAATGCTAACATGGGTTGCAATGTTGTT
* *
3385061 TTTCTTTATGCAAAT
1 TTTCTTAATGTAAAT
3385076 CTCTCTTTCA
Statistics
Matches: 58, Mismatches: 5, Indels: 7
0.83 0.07 0.10
Matches are distributed among these distances:
49 19 0.33
53 1 0.02
54 38 0.66
ACGTcount: A:0.27, C:0.11, G:0.20, T:0.42
Consensus pattern (50 bp):
TTTCTTAATGTAAATTAGCTATAAATGCTAACATGGGTTGCAATGTTGTT
Found at i:3389056 original size:13 final size:13
Alignment explanation
Indices: 3389038--3389063 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3389028 CGAAACCATA
3389038 ATTATAATAATTT
1 ATTATAATAATTT
3389051 ATTATAATAATTT
1 ATTATAATAATTT
3389064 CGATAAACTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (13 bp):
ATTATAATAATTT
Found at i:3395128 original size:41 final size:40
Alignment explanation
Indices: 3395021--3395131 Score: 111
Period size: 37 Copynumber: 2.8 Consensus size: 40
3395011 TCGGATAGTT
* *
3395021 CGAAGCAATAGTTGACACCCAGTGTCTCATCG-GCCAAGC
1 CGAAGTAATAGTTGACACCCAGTGTCTCATCGAACCAAGC
** ** * * *
3395060 CGAAGT-A-AGTTGGTACCCAGTACCTCATCGAATCTATC
1 CGAAGTAATAGTTGACACCCAGTGTCTCATCGAACCAAGC
3395098 CGAAGTAATAGTATGACACCCAGTGTCTCATCGA
1 CGAAGTAATAGT-TGACACCCAGTGTCTCATCGA
3395132 CTCAAGGTCG
Statistics
Matches: 55, Mismatches: 13, Indels: 6
0.74 0.18 0.08
Matches are distributed among these distances:
37 19 0.35
38 10 0.18
39 6 0.11
40 3 0.05
41 17 0.31
ACGTcount: A:0.30, C:0.27, G:0.21, T:0.23
Consensus pattern (40 bp):
CGAAGTAATAGTTGACACCCAGTGTCTCATCGAACCAAGC
Found at i:3395513 original size:19 final size:19
Alignment explanation
Indices: 3395453--3395527 Score: 77
Period size: 19 Copynumber: 4.0 Consensus size: 19
3395443 AATCAATACA
3395453 CAATTCACATATTCACATAT
1 CAATTCACA-ATTCACATAT
* *
3395473 C--TTCA-AATCTCATATCT
1 CAATTCACAAT-TCACATAT
3395490 CAATTTC-CAATTCACATAT
1 CAA-TTCACAATTCACATAT
3395509 CAATTCACAATTCACATAT
1 CAATTCACAATTCACATAT
3395528 TTACACATAG
Statistics
Matches: 45, Mismatches: 4, Indels: 13
0.73 0.06 0.21
Matches are distributed among these distances:
16 2 0.04
17 8 0.18
18 7 0.16
19 21 0.47
20 7 0.16
ACGTcount: A:0.37, C:0.27, G:0.00, T:0.36
Consensus pattern (19 bp):
CAATTCACAATTCACATAT
Found at i:3396436 original size:9 final size:9
Alignment explanation
Indices: 3396422--3396455 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
3396412 TTCTATTCTG
3396422 TTTCTTTTC
1 TTTCTTTTC
3396431 TTTCTTTT-
1 TTTCTTTTC
*
3396439 TTTCTATTC
1 TTTCTTTTC
3396448 TTTCTTTT
1 TTTCTTTT
3396456 GTTTTATGTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
8 7 0.32
9 15 0.68
ACGTcount: A:0.03, C:0.18, G:0.00, T:0.79
Consensus pattern (9 bp):
TTTCTTTTC
Found at i:3396448 original size:17 final size:17
Alignment explanation
Indices: 3396422--3396455 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
3396412 TTCTATTCTG
*
3396422 TTTCTTTTCTTTCTTTT
1 TTTCTATTCTTTCTTTT
3396439 TTTCTATTCTTTCTTTT
1 TTTCTATTCTTTCTTTT
3396456 GTTTTATGTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.03, C:0.18, G:0.00, T:0.79
Consensus pattern (17 bp):
TTTCTATTCTTTCTTTT
Found at i:3396477 original size:5 final size:5
Alignment explanation
Indices: 3396464--3396535 Score: 62
Period size: 5 Copynumber: 14.4 Consensus size: 5
3396454 TTGTTTTATG
3396464 TATATA TATAA TATAA TATAA TAT-A T-TAA TGATAA TATAA TATAA -A-AA
1 TATA-A TATAA TATAA TATAA TATAA TATAA T-ATAA TATAA TATAA TATAA
* *
3396512 CATAA TCATTAC TATAA TATAA TA
1 TATAA T-A-TAA TATAA TATAA TA
3396536 ATATTTTTAC
Statistics
Matches: 56, Mismatches: 3, Indels: 15
0.76 0.04 0.20
Matches are distributed among these distances:
3 3 0.05
4 6 0.11
5 34 0.61
6 10 0.18
7 3 0.05
ACGTcount: A:0.56, C:0.04, G:0.01, T:0.39
Consensus pattern (5 bp):
TATAA
Found at i:3396489 original size:19 final size:19
Alignment explanation
Indices: 3396465--3396507 Score: 70
Period size: 19 Copynumber: 2.3 Consensus size: 19
3396455 TGTTTTATGT
3396465 ATATATATAAT-ATAATATA
1 ATATAT-TAATGATAATATA
3396484 ATATATTAATGATAATATA
1 ATATATTAATGATAATATA
3396503 ATATA
1 ATATA
3396508 AAAACATAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
18 4 0.17
19 19 0.83
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (19 bp):
ATATATTAATGATAATATA
Found at i:3396517 original size:24 final size:24
Alignment explanation
Indices: 3396471--3396536 Score: 71
Period size: 24 Copynumber: 2.7 Consensus size: 24
3396461 ATGTATATAT
* * *
3396471 ATAATATAATATAATATATTAATG
1 ATAATATAATATAATAAAATAATC
3396495 ATAATATAATATAA-AAACATAATC
1 ATAATATAATATAATAAA-ATAATC
*
3396519 ATTACTATAATATAATAA
1 A-TAATATAATATAATAA
3396537 TATTTTTACA
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
23 2 0.06
24 19 0.54
25 12 0.34
26 2 0.06
ACGTcount: A:0.58, C:0.05, G:0.02, T:0.36
Consensus pattern (24 bp):
ATAATATAATATAATAAAATAATC
Found at i:3398112 original size:12 final size:12
Alignment explanation
Indices: 3398097--3398160 Score: 56
Period size: 12 Copynumber: 5.3 Consensus size: 12
3398087 GATATCCCAG
3398097 AGAAAATCCAAA
1 AGAAAATCCAAA
* * *
3398109 AGAATATCCCAG
1 AGAAAATCCAAA
*
3398121 AGAAAATCCACA
1 AGAAAATCCAAA
* * *
3398133 AGAATATCCCAG
1 AGAAAATCCAAA
*
3398145 AGAAAATCCACA
1 AGAAAATCCAAA
3398157 AGAA
1 AGAA
3398161 GAATATCGCT
Statistics
Matches: 37, Mismatches: 15, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
12 37 1.00
ACGTcount: A:0.55, C:0.22, G:0.12, T:0.11
Consensus pattern (12 bp):
AGAAAATCCAAA
Found at i:3398120 original size:24 final size:24
Alignment explanation
Indices: 3398088--3398160 Score: 137
Period size: 24 Copynumber: 3.0 Consensus size: 24
3398078 GAGATCGATG
*
3398088 ATATCCCAGAGAAAATCCAAAAGA
1 ATATCCCAGAGAAAATCCACAAGA
3398112 ATATCCCAGAGAAAATCCACAAGA
1 ATATCCCAGAGAAAATCCACAAGA
3398136 ATATCCCAGAGAAAATCCACAAGA
1 ATATCCCAGAGAAAATCCACAAGA
3398160 A
1 A
3398161 GAATATCGCT
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
24 48 1.00
ACGTcount: A:0.52, C:0.23, G:0.12, T:0.12
Consensus pattern (24 bp):
ATATCCCAGAGAAAATCCACAAGA
Found at i:3398471 original size:13 final size:13
Alignment explanation
Indices: 3398453--3398480 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
3398443 GATAAAAGAG
3398453 CATATAGAATACC
1 CATATAGAATACC
3398466 CATATAGAATACC
1 CATATAGAATACC
3398479 CA
1 CA
3398481 GAAGAGATCA
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:0.46, C:0.25, G:0.07, T:0.21
Consensus pattern (13 bp):
CATATAGAATACC
Found at i:3399445 original size:22 final size:22
Alignment explanation
Indices: 3399417--3399484 Score: 84
Period size: 22 Copynumber: 3.1 Consensus size: 22
3399407 TATGCACTAT
3399417 TAAACAGAGAGCACTAAAGTGC
1 TAAACAGAGAGCACTAAAGTGC
*
3399439 TATACAGAGAGCAC-AAATGTGC
1 TAAACAGAGAGCACTAAA-GTGC
* * *
3399461 TAAACGGCGAGCACTAACGTGC
1 TAAACAGAGAGCACTAAAGTGC
3399483 TA
1 TA
3399485 GTGATCAGAG
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
21 3 0.08
22 34 0.87
23 2 0.05
ACGTcount: A:0.40, C:0.21, G:0.24, T:0.16
Consensus pattern (22 bp):
TAAACAGAGAGCACTAAAGTGC
Found at i:3399507 original size:25 final size:23
Alignment explanation
Indices: 3399479--3399544 Score: 71
Period size: 22 Copynumber: 2.7 Consensus size: 23
3399469 GAGCACTAAC
3399479 GTGCTAGTGATCAGAGAGCGCCGAT
1 GTGCTA-T-ATCAGAGAGCGCCGAT
* *
3399504 GTGCTA-AACAGAGAGCGCTGAT
1 GTGCTATATCAGAGAGCGCCGAT
3399526 GTGCTAATAATCAGAGAGC
1 GTGCT-AT-ATCAGAGAGC
3399545 ACGCTAAACT
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
22 19 0.54
23 1 0.03
25 15 0.43
ACGTcount: A:0.30, C:0.18, G:0.32, T:0.20
Consensus pattern (23 bp):
GTGCTATATCAGAGAGCGCCGAT
Found at i:3399509 original size:47 final size:45
Alignment explanation
Indices: 3399417--3399546 Score: 136
Period size: 47 Copynumber: 2.8 Consensus size: 45
3399407 TATGCACTAT
3399417 TAAACAGAGAGCACTAAAGTGCTATA-CAGAGAGCACAAATGTGC
1 TAAACAGAGAGCACTAAAGTGCTATATCAGAGAGCACAAATGTGC
* * * * **
3399461 TAAACGGCGAGCACTAACGTGCTAGTGATCAGAGAGCGCCGATGTGC
1 TAAACAGAGAGCACTAAAGTGCTA-T-ATCAGAGAGCACAAATGTGC
* * *
3399508 TAAACAGAGAGCGCTGATGTGCTAATAATCAGAGAGCAC
1 TAAACAGAGAGCACTAAAGTGCT-AT-ATCAGAGAGCAC
3399547 GCTAAACTCC
Statistics
Matches: 69, Mismatches: 13, Indels: 5
0.79 0.15 0.06
Matches are distributed among these distances:
44 21 0.30
45 1 0.01
46 1 0.01
47 45 0.65
48 1 0.01
ACGTcount: A:0.36, C:0.20, G:0.27, T:0.17
Consensus pattern (45 bp):
TAAACAGAGAGCACTAAAGTGCTATATCAGAGAGCACAAATGTGC
Found at i:3399518 original size:22 final size:22
Alignment explanation
Indices: 3399490--3399532 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
3399480 TGCTAGTGAT
3399490 CAGAGAGCGCCGATGTGCTAAA
1 CAGAGAGCGCCGATGTGCTAAA
*
3399512 CAGAGAGCGCTGATGTGCTAA
1 CAGAGAGCGCCGATGTGCTAA
3399533 TAATCAGAGA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.30, C:0.21, G:0.33, T:0.16
Consensus pattern (22 bp):
CAGAGAGCGCCGATGTGCTAAA
Found at i:3400520 original size:17 final size:17
Alignment explanation
Indices: 3400498--3400531 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
3400488 ATGTGGCATG
*
3400498 TACCTAGGTAATGTATA
1 TACCTAAGTAATGTATA
*
3400515 TACCTAAGTGATGTATA
1 TACCTAAGTAATGTATA
3400532 GGGATTAGTC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.35, C:0.12, G:0.18, T:0.35
Consensus pattern (17 bp):
TACCTAAGTAATGTATA
Found at i:3407994 original size:15 final size:15
Alignment explanation
Indices: 3407976--3408031 Score: 85
Period size: 15 Copynumber: 3.7 Consensus size: 15
3407966 ATTATCGGAG
*
3407976 GTGGTGCATACGTTA
1 GTGGTGGATACGTTA
*
3407991 GTGGTGGATACATTA
1 GTGGTGGATACGTTA
*
3408006 GTGGTGGATATGTTA
1 GTGGTGGATACGTTA
3408021 GTGGTGGATAC
1 GTGGTGGATAC
3408032 ATCGGTGTTG
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 36 1.00
ACGTcount: A:0.21, C:0.07, G:0.38, T:0.34
Consensus pattern (15 bp):
GTGGTGGATACGTTA
Found at i:3408021 original size:30 final size:30
Alignment explanation
Indices: 3407976--3408033 Score: 98
Period size: 30 Copynumber: 1.9 Consensus size: 30
3407966 ATTATCGGAG
3407976 GTGGTGCATACGTTAGTGGTGGATACATTA
1 GTGGTGCATACGTTAGTGGTGGATACATTA
* *
3408006 GTGGTGGATATGTTAGTGGTGGATACAT
1 GTGGTGCATACGTTAGTGGTGGATACAT
3408034 CGGTGTTGTC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.22, C:0.07, G:0.36, T:0.34
Consensus pattern (30 bp):
GTGGTGCATACGTTAGTGGTGGATACATTA
Found at i:3410298 original size:21 final size:21
Alignment explanation
Indices: 3410272--3410319 Score: 78
Period size: 21 Copynumber: 2.3 Consensus size: 21
3410262 CGACACATAA
3410272 GTGCCTGAAATGACACACGAG
1 GTGCCTGAAATGACACACGAG
* *
3410293 GTGCCTGATATGACGCACGAG
1 GTGCCTGAAATGACACACGAG
3410314 GTGCCT
1 GTGCCT
3410320 AATATATGAC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.25, C:0.25, G:0.31, T:0.19
Consensus pattern (21 bp):
GTGCCTGAAATGACACACGAG
Found at i:3411456 original size:18 final size:19
Alignment explanation
Indices: 3411433--3411468 Score: 65
Period size: 18 Copynumber: 1.9 Consensus size: 19
3411423 ATTATTTTTC
3411433 TAATAAATATCT-TTTAAA
1 TAATAAATATCTATTTAAA
3411451 TAATAAATATCTATTTAA
1 TAATAAATATCTATTTAA
3411469 TATACAAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 12 0.71
19 5 0.29
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (19 bp):
TAATAAATATCTATTTAAA
Found at i:3411477 original size:19 final size:18
Alignment explanation
Indices: 3411437--3411479 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 18
3411427 TTTTTCTAAT
*
3411437 AAATATCTTTTAAATAAT
1 AAATATCTTTTAAATAAC
3411455 AAATATCTATTT-AATATAC
1 AAATATCT-TTTAAATA-AC
3411474 AAATAT
1 AAATAT
3411480 AAATATTACG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
18 12 0.55
19 10 0.45
ACGTcount: A:0.51, C:0.07, G:0.00, T:0.42
Consensus pattern (18 bp):
AAATATCTTTTAAATAAC
Found at i:3425831 original size:27 final size:26
Alignment explanation
Indices: 3425801--3425913 Score: 100
Period size: 27 Copynumber: 4.2 Consensus size: 26
3425791 ATTTGGAAAA
*
3425801 CTGGGATTTGCCAGTTAATTTGGCGAG
1 CTGGG-TTTACCAGTTAATTTGGCGAG
3425828 CTGGGTTTCACCAGTTAATTTGGCGAG
1 CTGGGTTT-ACCAGTTAATTTGGCGAG
* ** ** *
3425855 CTAGGCTTCGCCAGTTTGTTTGGTGAG
1 CT-GGGTTTACCAGTTAATTTGGCGAG
* * *
3425882 CTAGGGTCTACCAGTGAATTTGGCAAG
1 CT-GGGTTTACCAGTTAATTTGGCGAG
3425909 CTGGG
1 CTGGG
3425914 GTTCACTAGT
Statistics
Matches: 68, Mismatches: 16, Indels: 5
0.76 0.18 0.06
Matches are distributed among these distances:
26 6 0.09
27 58 0.85
28 4 0.06
ACGTcount: A:0.18, C:0.18, G:0.33, T:0.32
Consensus pattern (26 bp):
CTGGGTTTACCAGTTAATTTGGCGAG
Found at i:3425930 original size:54 final size:54
Alignment explanation
Indices: 3425819--3425980 Score: 141
Period size: 54 Copynumber: 3.0 Consensus size: 54
3425809 TGCCAGTTAA
* * * * * *
3425819 TTTGGCGAGCTGGGTTTCACCAGTTAATTTGGCGAGCTAGGCTTCGCCAGTTTG
1 TTTGGTGAGCTGGGTCTCACCAGTGAATTTGGCAAGCTAGGCTTCACCAGTTGG
* * *
3425873 TTTGGTGAGCTAGGGTCT-ACCAGTGAATTTGGCAAGCTGGGGTTCACTAGTTGG
1 TTTGGTGAGCT-GGGTCTCACCAGTGAATTTGGCAAGCTAGGCTTCACCAGTTGG
* * ** * *
3425927 TTTGGTGAGTTATGGT-TCACCAGAT-AGCTTAGCAAGCTAGGGTTCACCAGTTGG
1 TTTGGTGAGCT-GGGTCTCACCAG-TGAATTTGGCAAGCTAGGCTTCACCAGTTGG
3425981 CTTAGCGAAC
Statistics
Matches: 89, Mismatches: 16, Indels: 6
0.80 0.14 0.05
Matches are distributed among these distances:
53 1 0.01
54 82 0.92
55 6 0.07
ACGTcount: A:0.19, C:0.17, G:0.32, T:0.32
Consensus pattern (54 bp):
TTTGGTGAGCTGGGTCTCACCAGTGAATTTGGCAAGCTAGGCTTCACCAGTTGG
Found at i:3426004 original size:27 final size:27
Alignment explanation
Indices: 3425904--3426004 Score: 87
Period size: 27 Copynumber: 3.7 Consensus size: 27
3425894 AGTGAATTTG
* * * *
3425904 GCAAGCTGGGGTTCACTAGTTGGTTTG
1 GCAAGCTAGGGTTCACCAGTTGGCTTA
** * * * *
3425931 GTGAGTTATGGTTCACCAGATAGCTTA
1 GCAAGCTAGGGTTCACCAGTTGGCTTA
3425958 GCAAGCTAGGGTTCACCAGTTGGCTTA
1 GCAAGCTAGGGTTCACCAGTTGGCTTA
*
3425985 GCGAA-CTAGGGTTCGCCAGT
1 GC-AAGCTAGGGTTCACCAGT
3426005 ATAAAGCGAA
Statistics
Matches: 56, Mismatches: 17, Indels: 2
0.75 0.23 0.03
Matches are distributed among these distances:
27 54 0.96
28 2 0.04
ACGTcount: A:0.21, C:0.19, G:0.32, T:0.29
Consensus pattern (27 bp):
GCAAGCTAGGGTTCACCAGTTGGCTTA
Found at i:3430608 original size:19 final size:19
Alignment explanation
Indices: 3430586--3430627 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 19
3430576 TCATTTTTAC
* *
3430586 TTTTGACTTTTTC-TAGAT
1 TTTTTACTTTTTCGTACAT
*
3430604 TTTTTTCTTTTTCGTACAT
1 TTTTTACTTTTTCGTACAT
3430623 TTTTT
1 TTTTT
3430628 TTCTCACCTA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
18 11 0.55
19 9 0.45
ACGTcount: A:0.12, C:0.12, G:0.07, T:0.69
Consensus pattern (19 bp):
TTTTTACTTTTTCGTACAT
Found at i:3430628 original size:19 final size:18
Alignment explanation
Indices: 3430592--3430628 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
3430582 TTACTTTTGA
*
3430592 CTTTTTCTAGATTTTTTT
1 CTTTTTCTACATTTTTTT
3430610 CTTTTTCGTACATTTTTTT
1 CTTTTTC-TACATTTTTTT
3430629 TCTCACCTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.11, C:0.14, G:0.05, T:0.70
Consensus pattern (18 bp):
CTTTTTCTACATTTTTTT
Found at i:3431460 original size:23 final size:27
Alignment explanation
Indices: 3431409--3431467 Score: 74
Period size: 27 Copynumber: 2.3 Consensus size: 27
3431399 AAAATTCTAC
3431409 GACAAA-AAATATAAATTATAATGTAAA
1 GACAAATAAATATAAATTATAATG-AAA
3431436 GA-AAATAAATATAAA-TATAA-G-AA
1 GACAAATAAATATAAATTATAATGAAA
3431459 GACAAATAA
1 GACAAATAA
3431468 GTGTTGATAA
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
23 4 0.13
24 6 0.20
25 1 0.03
26 8 0.27
27 11 0.37
ACGTcount: A:0.66, C:0.03, G:0.08, T:0.22
Consensus pattern (27 bp):
GACAAATAAATATAAATTATAATGAAA
Found at i:3435849 original size:12 final size:12
Alignment explanation
Indices: 3435832--3435865 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
3435822 ATGTCTCAAA
3435832 AAATGAAAATGG
1 AAATGAAAATGG
3435844 AAATGAAAATGG
1 AAATGAAAATGG
*
3435856 AAATGGAAAT
1 AAATGAAAAT
3435866 TTACAATCCT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.59, C:0.00, G:0.24, T:0.18
Consensus pattern (12 bp):
AAATGAAAATGG
Found at i:3435854 original size:18 final size:18
Alignment explanation
Indices: 3435831--3435865 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
3435821 CATGTCTCAA
3435831 AAAATGAAAATGGAAATG
1 AAAATGAAAATGGAAATG
*
3435849 AAAATGGAAATGGAAAT
1 AAAATGAAAATGGAAAT
3435866 TTACAATCCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.60, C:0.00, G:0.23, T:0.17
Consensus pattern (18 bp):
AAAATGAAAATGGAAATG
Found at i:3444086 original size:8 final size:8
Alignment explanation
Indices: 3444073--3444137 Score: 67
Period size: 8 Copynumber: 7.9 Consensus size: 8
3444063 GGTGTTGTTG
3444073 GTTTATTT
1 GTTTATTT
3444081 GTTTATTT
1 GTTTATTT
* *
3444089 GTATGTTT
1 GTTTATTT
3444097 GTTTATTT
1 GTTTATTT
* *
3444105 GTTCAATT
1 GTTTATTT
*
3444113 ATTTCATTT
1 GTTT-ATTT
3444122 CGTTTATTT
1 -GTTTATTT
3444131 GTTTATT
1 GTTTATT
3444138 AAAACGTGAT
Statistics
Matches: 45, Mismatches: 10, Indels: 4
0.76 0.17 0.07
Matches are distributed among these distances:
8 35 0.78
9 7 0.16
10 3 0.07
ACGTcount: A:0.15, C:0.05, G:0.12, T:0.68
Consensus pattern (8 bp):
GTTTATTT
Found at i:3447198 original size:27 final size:27
Alignment explanation
Indices: 3447157--3447225 Score: 84
Period size: 27 Copynumber: 2.6 Consensus size: 27
3447147 GAGGAGGGTA
* **
3447157 TCCCATGGGCAGCACCAAAGGTGCCTT
1 TCCCATGGGCGGCACCAAAGGTGCCCC
* * *
3447184 TCCCATAGGCGGCACCGATGGTGCCCC
1 TCCCATGGGCGGCACCAAAGGTGCCCC
3447211 TCCCATGGGCGGCAC
1 TCCCATGGGCGGCAC
3447226 TGCCCATATA
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 35 1.00
ACGTcount: A:0.17, C:0.38, G:0.29, T:0.16
Consensus pattern (27 bp):
TCCCATGGGCGGCACCAAAGGTGCCCC
Found at i:3447293 original size:10 final size:10
Alignment explanation
Indices: 3447278--3447432 Score: 99
Period size: 10 Copynumber: 15.3 Consensus size: 10
3447268 GAAGGAGAGG
3447278 GAAAGAAGAA
1 GAAAGAAGAA
3447288 GAAAG-A-AA
1 GAAAGAAGAA
*
3447296 GAAAGAAAAA
1 GAAAGAAGAA
*
3447306 GAAAGAAAAA
1 GAAAGAAGAA
* *
3447316 GAAAGGAGAG
1 GAAAGAAGAA
3447326 GAAAG-A-AA
1 GAAAGAAGAA
3447334 GAAA-AAGAA
1 GAAAGAAGAA
3447343 GGAAAGAATAGGAA
1 -GAAAG-A-A-GAA
*
3447357 AAAAGAAGAA
1 GAAAGAAGAA
*
3447367 GAAAAAAGAAA
1 GAAAGAAG-AA
3447378 GAAA-AAGAA
1 GAAAGAAGAA
3447387 GGAAAGAA-AA
1 -GAAAGAAGAA
*
3447397 GGAAAGGAGAA
1 -GAAAGAAGAA
* *
3447408 GAGAAAAAAAA
1 GA-AAGAAGAA
3447419 TGAAAGAAGAA
1 -GAAAGAAGAA
3447430 GAA
1 GAA
3447433 GAGCGAAGGA
Statistics
Matches: 117, Mismatches: 13, Indels: 30
0.73 0.08 0.19
Matches are distributed among these distances:
8 13 0.11
9 7 0.06
10 63 0.54
11 22 0.19
12 4 0.03
13 5 0.04
14 3 0.03
ACGTcount: A:0.71, C:0.00, G:0.28, T:0.01
Consensus pattern (10 bp):
GAAAGAAGAA
Found at i:3447295 original size:4 final size:4
Alignment explanation
Indices: 3447278--3447462 Score: 77
Period size: 4 Copynumber: 49.0 Consensus size: 4
3447268 GAAGGAGAGG
3447278 GAAA G-AA G-AA GAAA GAAA GAAA G-AA -AAA GAAA G-AA -AAA GAAA
1 GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA
* *
3447320 GGAGAG GAAA GAAA G-AA -AAA GAAG GAAA GAATA GGAAA -AAA G-AA
1 -GA-AA GAAA GAAA GAAA GAAA GAAA GAAA GAA-A -GAAA GAAA GAAA
* *
3447364 G-AA GAAA -AAA GAAA G-AA -AAA GAAG GAAA GAAAA GGAAA G-GA GAAGA
1 GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA G-AAA -GAAA GAAA GAA-A
* * * *
3447410 GAAA -AAA -AAT GAAA G-AA G-AA GAAGA GCGAA GGAA GGAA -AAA GAAA
1 GAAA GAAA GAAA GAAA GAAA GAAA GAA-A G-AAA GAAA GAAA GAAA GAAA
3447455 GAAA GAAA
1 GAAA GAAA
3447463 TGTAATTTTT
Statistics
Matches: 144, Mismatches: 12, Indels: 50
0.70 0.06 0.24
Matches are distributed among these distances:
3 49 0.34
4 69 0.48
5 20 0.14
6 6 0.04
ACGTcount: A:0.70, C:0.01, G:0.29, T:0.01
Consensus pattern (4 bp):
GAAA
Found at i:3447295 original size:14 final size:14
Alignment explanation
Indices: 3447278--3447457 Score: 100
Period size: 14 Copynumber: 13.5 Consensus size: 14
3447268 GAAGGAGAGG
3447278 GAAAGAAGAAGAAA
1 GAAAGAAGAAGAAA
3447292 GAAAG-A-AAG-AA
1 GAAAGAAGAAGAAA
3447303 -AAAGAAAGAA-AAA
1 GAAAG-AAGAAGAAA
* *
3447316 GAAAGGAGAGGAAA
1 GAAAGAAGAAGAAA
* *
3447330 GAAAGAAAAAGAAG
1 GAAAGAAGAAGAAA
* *
3447344 GAAAGAATAGGAAA
1 GAAAGAAGAAGAAA
3447358 -AAAGAAGAAGAAA
1 GAAAGAAGAAGAAA
3447371 -AAAGAAAGAA-AAA
1 GAAAG-AAGAAGAAA
* *
3447384 GAAGGAAAGAA-AAG
1 GAAAG-AAGAAGAAA
*
3447398 GAAAGGAGAAGAGAA
1 GAAAGAAGAAGA-AA
*
3447413 -AAA-AA-ATGAAA
1 GAAAGAAGAAGAAA
**
3447424 G-AAGAAGAAGAGC
1 GAAAGAAGAAGAAA
*
3447437 GAAGGAAGGAA-AAA
1 GAAAGAA-GAAGAAA
3447451 GAAAGAA
1 GAAAGAA
3447458 AGAAATGTAA
Statistics
Matches: 126, Mismatches: 25, Indels: 30
0.70 0.14 0.17
Matches are distributed among these distances:
10 4 0.03
11 6 0.05
12 9 0.07
13 35 0.28
14 68 0.54
15 4 0.03
ACGTcount: A:0.69, C:0.01, G:0.29, T:0.01
Consensus pattern (14 bp):
GAAAGAAGAAGAAA
Found at i:3447330 original size:34 final size:33
Alignment explanation
Indices: 3447290--3447386 Score: 110
Period size: 34 Copynumber: 2.9 Consensus size: 33
3447280 AAGAAGAAGA
3447290 AAGAAAGAAAGAAAAAGAAAGAAAAAGAA-AGG
1 AAGAAAGAAAGAAAAAGAAAGAAAAAGAATAGG
*
3447322 AGAGGAAAGAAAGAAAAAG-AAG-GAAAGAATAGG
1 A-A-GAAAGAAAGAAAAAGAAAGAAAAAGAATAGG
*
3447355 AAAAAAGAAGAAGAAAAAAGAAAGAAAAAGAA
1 AAGAAAG-A-AAG-AAAAAGAAAGAAAAAGAA
3447387 GGAAAGAAAA
Statistics
Matches: 54, Mismatches: 3, Indels: 12
0.78 0.04 0.17
Matches are distributed among these distances:
31 4 0.07
32 9 0.17
33 11 0.20
34 21 0.39
35 3 0.06
36 6 0.11
ACGTcount: A:0.73, C:0.00, G:0.26, T:0.01
Consensus pattern (33 bp):
AAGAAAGAAAGAAAAAGAAAGAAAAAGAATAGG
Found at i:3447359 original size:44 final size:43
Alignment explanation
Indices: 3447278--3447457 Score: 167
Period size: 44 Copynumber: 4.2 Consensus size: 43
3447268 GAAGGAGAGG
3447278 GAAAGAAGAAGAAAGAAAG--AAAGAA--AAAGAAA-GAAAAA
1 GAAAGAAGAAGAAAGAAAGAAAAAGAAGGAAAGAAAGGAAAAA
* *
3447316 GAAAGGAGAGGAAAGAAAGAAAAAGAAGGAAAGAATAGGAAAAA
1 GAAAGAAGAAGAAAGAAAGAAAAAGAAGGAAAGAA-AGGAAAAA
* *
3447360 -AGAAGAAGAAAAAAGAAAGAAAAAGAAGGAAAGAAAAGGAAAGGA
1 GA-AAGAAGAAGAAAGAAAGAAAAAGAAGGAAAG-AAAGGAAA-AA
* * * *
3447405 GAAGAGAA-AAAAAATGAAAGAAGAAGAAGAGCGAAGGAAGGAAAAA
1 GAA-AGAAGAAGAAA-GAAAGAAAAAGAAG-G-AAAGAAAGGAAAAA
3447451 GAAAGAA
1 GAAAGAA
3447458 AGAAATGTAA
Statistics
Matches: 118, Mismatches: 10, Indels: 21
0.79 0.07 0.14
Matches are distributed among these distances:
38 17 0.14
40 6 0.05
42 6 0.05
43 2 0.02
44 40 0.34
45 14 0.12
46 22 0.19
47 8 0.07
48 3 0.03
ACGTcount: A:0.69, C:0.01, G:0.29, T:0.01
Consensus pattern (43 bp):
GAAAGAAGAAGAAAGAAAGAAAAAGAAGGAAAGAAAGGAAAAA
Found at i:3447458 original size:10 final size:10
Alignment explanation
Indices: 3447278--3447458 Score: 90
Period size: 10 Copynumber: 17.8 Consensus size: 10
3447268 GAAGGAGAGG
*
3447278 GAAAGAAGAA
1 GAAAGAAAAA
3447288 GAAAG--AAA
1 GAAAGAAAAA
3447296 GAAAGAAAAA
1 GAAAGAAAAA
3447306 GAAAGAAAAA
1 GAAAGAAAAA
3447316 GAAAGGAGAGGAAA
1 GAAA-GA-A--AAA
3447330 GAAAGAAAAA
1 GAAAGAAAAA
*
3447340 G-AAG-GAAA
1 GAAAGAAAAA
*
3447348 GAATAG-GAAA
1 GAA-AGAAAAA
*
3447358 -AAAGAAGAA
1 GAAAGAAAAA
*
3447367 GAAAAAAGAAA
1 GAAAGAA-AAA
*
3447378 GAAA-AAGAAG
1 GAAAGAA-AAA
*
3447388 GAAAGAAAAG
1 GAAAGAAAAA
*
3447398 GAAAGGAGAAGA
1 GAAA-GA-AAAA
3447410 GAAA-AAAAA
1 GAAAGAAAAA
*
3447419 TGAAAGAAGAA
1 -GAAAGAAAAA
** *
3447430 GAAGAGCGAAG
1 GAA-AGAAAAA
*
3447441 GAAGGAAAAA
1 GAAAGAAAAA
3447451 GAAAGAAA
1 GAAAGAAA
3447459 GAAATGTAAT
Statistics
Matches: 134, Mismatches: 20, Indels: 34
0.71 0.11 0.18
Matches are distributed among these distances:
8 13 0.10
9 11 0.08
10 71 0.53
11 22 0.16
12 8 0.06
13 2 0.01
14 7 0.05
ACGTcount: A:0.70, C:0.01, G:0.29, T:0.01
Consensus pattern (10 bp):
GAAAGAAAAA
Found at i:3448308 original size:158 final size:153
Alignment explanation
Indices: 3447792--3448565 Score: 746
Period size: 159 Copynumber: 4.9 Consensus size: 153
3447782 AATAGTATAT
* *
3447792 TTAATAAATTTCAAACATAATGCACTGAAATAATGTAAAATTATAAAAATTAGAATTTATGATAT
1 TTAATAAATTTCAAACATAATGCACTGAAATAATATAAAATTAT-AAAATTAGAAATTATGATAT
* * * *
3447857 TTTTTAAAATAATTAAATGCAGAGAAAAAAATACGAACAAATGGCCAAAGTAAGAGTGTTTTACT
65 TTTTTAAAATAATAAAATGCGGAGAAAAAAATACGAACAAATGGCCGAAGTAAGAGTTTTTTACT
*
3447922 AAAATTTTTTAAAAATTTAGAAAT-AA
130 -AAATTTTTTAAAAA-TCA-AAATAAA
* * * *
3447948 TTAATAAAAATATTTCAAACAAAATGTACTGAAATAATATAAAATAATAAAA-TATGAAAATCAT
1 TTAAT---AA-ATTTCAAACATAATGCACTGAAATAATATAAAATTATAAAATTA-G-AAATTAT
* * * * *
3448012 -ATATTTTTATTAAAAGTAATAAAATTCGG-GAAAATAATACGAGCAAAGGGCAGGAA-TAAGAG
60 GATA-TTTT-TTAAAA-TAATAAAATGCGGAGAAAAAAATACGAACAAATGGC-CGAAGTAAGAG
3448074 TTTTTTTACACTAAATTAATTTTAAAAA--AAAACTAAA
121 -TTTTTT--ACTAAATT--TTTTAAAAATCAAAA-TAAA
3448111 TTAATAAATTTCAAACATAATGCACTGAAATAA-AGTAAAATTATAAAATTAGAAATTATGATAT
1 TTAATAAATTTCAAACATAATGCACTGAAATAATA-TAAAATTATAAAATTAGAAATTATGATAT
* * * * * *
3448175 ATTTTAAAATAATAAAATACGGAGAAAAAAATACGAACAAATGGCTGAAGCAAGAGTGTTTTGCT
65 TTTTTAAAATAATAAAATGCGGAGAAAAAAATACGAACAAATGGCCGAAGTAAGAGTTTTTTACT
3448240 AAATTTTTTAAAAATTCAGAAAT-AA
130 AAATTTTTTAAAAA-TCA-AAATAAA
* * * *
3448265 TTAATACAAATATTTCAAACAAAATGTACTGAAATAATATAAAATAATAAAA-TACGAAAATAAT
1 TTAAT---AA-ATTTCAAACATAATGCACTGAAATAATATAAAATTATAAAATTA-G-AAATTAT
* ** * * * * * *
3448329 -ATATTTAATTGAAGGTAATGAAATTCGG-GAAAATAATACGAGCAAAGGGCGGGAA-TAAGAGT
60 GATATTT--TTTAAAATAATAAAATGCGGAGAAAAAAATACGAACAAATGGC-CGAAGTAAGAG-
* * * *
3448391 TTTTTTTACACTAAATTAATTTAAAAAACACACTAAA
121 -TTTTTT--ACTAAATT-TTTTAAAAATCAAAATAAA
*
3448428 TTAATAAATTTCAAACATAATGCACTGAAATAATGTAAAATTATAAAATTAGAAATTATGATATT
1 TTAATAAATTTCAAACATAATGCACTGAAATAATATAAAATTATAAAATTAGAAATTATGATATT
*
3448493 TTTTAAAGTAATAAAATGCGGAGAAAAAAATACGAACAAATGGCCGAAGTAAGAGTTTTTTACTA
66 TTTTAAAATAATAAAATGCGGAGAAAAAAATACGAACAAATGGCCGAAGTAAGAGTTTTTTACTA
*
3448558 ACTTTTTT
131 AATTTTTT
3448566 TTCAACTTGC
Statistics
Matches: 508, Mismatches: 64, Indels: 95
0.76 0.10 0.14
Matches are distributed among these distances:
152 9 0.02
153 3 0.01
154 21 0.04
155 2 0.00
156 34 0.07
157 53 0.10
158 85 0.17
159 125 0.25
160 68 0.13
161 39 0.08
162 21 0.04
163 28 0.06
164 11 0.02
165 9 0.02
ACGTcount: A:0.51, C:0.07, G:0.11, T:0.31
Consensus pattern (153 bp):
TTAATAAATTTCAAACATAATGCACTGAAATAATATAAAATTATAAAATTAGAAATTATGATATT
TTTTAAAATAATAAAATGCGGAGAAAAAAATACGAACAAATGGCCGAAGTAAGAGTTTTTTACTA
AATTTTTTAAAAATCAAAATAAA
Found at i:3448397 original size:317 final size:317
Alignment explanation
Indices: 3447792--3448565 Score: 1291
Period size: 317 Copynumber: 2.4 Consensus size: 317
3447782 AATAGTATAT
*
3447792 TTAATAAATTTCAAACATAATGCACTGAAATAATGTAAAATTATAAAAATTAGAATTTATGATAT
1 TTAATAAATTTCAAACATAATGCACTGAAATAATGTAAAATTAT-AAAATTAGAAATTATGATAT
* * *
3447857 TTTTTAAAATAATTAAATGCAGAGAAAAAAATACGAACAAATGGCCAAAGTAAGAGTGTTTTACT
65 TTTTTAAAATAATAAAATGCGGAGAAAAAAATACGAACAAATGGCCGAAGTAAGAGTGTTTTACT
*
3447922 AAAATTTTTTAAAAATTTAGAAATAATTAATAAAAATATTTCAAACAAAATGTACTGAAATAATA
130 -AAATTTTTTAAAAATTCAGAAATAATTAATAAAAATATTTCAAACAAAATGTACTGAAATAATA
* * *
3447987 TAAAATAATAAAATATGAAAATCATATATTTTTATTAAAAGTAATAAAATTCGGGAAAATAATAC
194 TAAAATAATAAAATACGAAAATAATATATTTTAATTAAAAGTAATAAAATTCGGGAAAATAATAC
3448052 GAGCAAAGGGCAGGAATAAGAGTTTTTTTACACTAAATTAATTTTAAAAAA-AAACTAAA
259 GAGCAAAGGGCAGGAATAAGAGTTTTTTTACACTAAATTAA-TTTAAAAAACAAACTAAA
* *
3448111 TTAATAAATTTCAAACATAATGCACTGAAATAAAGTAAAATTATAAAATTAGAAATTATGATATA
1 TTAATAAATTTCAAACATAATGCACTGAAATAATGTAAAATTATAAAATTAGAAATTATGATATT
* * * *
3448176 TTTTAAAATAATAAAATACGGAGAAAAAAATACGAACAAATGGCTGAAGCAAGAGTGTTTTGCTA
66 TTTTAAAATAATAAAATGCGGAGAAAAAAATACGAACAAATGGCCGAAGTAAGAGTGTTTTACTA
*
3448241 AATTTTTTAAAAATTCAGAAATAATTAATACAAATATTTCAAACAAAATGTACTGAAATAATATA
131 AATTTTTTAAAAATTCAGAAATAATTAATAAAAATATTTCAAACAAAATGTACTGAAATAATATA
* * *
3448306 AAATAATAAAATACGAAAATAATATA-TTTAATTGAAGGTAATGAAATTCGGGAAAATAATACGA
196 AAATAATAAAATACGAAAATAATATATTTTAATTAAAAGTAATAAAATTCGGGAAAATAATACGA
* *
3448370 GCAAAGGGCGGGAATAAGAGTTTTTTTTACACTAAATTAATTTAAAAAACACACTAAA
261 GCAAAGGGCAGGAATAAGAG-TTTTTTTACACTAAATTAATTTAAAAAACAAACTAAA
3448428 TTAATAAATTTCAAACATAATGCACTGAAATAATGTAAAATTATAAAATTAGAAATTATGATATT
1 TTAATAAATTTCAAACATAATGCACTGAAATAATGTAAAATTATAAAATTAGAAATTATGATATT
* *
3448493 TTTTAAAGTAATAAAATGCGGAGAAAAAAATACGAACAAATGGCCGAAGTAAGAGTTTTTTACTA
66 TTTTAAAATAATAAAATGCGGAGAAAAAAATACGAACAAATGGCCGAAGTAAGAGTGTTTTACTA
*
3448558 ACTTTTTT
131 AATTTTTT
3448566 TTCAACTTGC
Statistics
Matches: 424, Mismatches: 29, Indels: 6
0.92 0.06 0.01
Matches are distributed among these distances:
316 62 0.15
317 243 0.57
318 76 0.18
319 43 0.10
ACGTcount: A:0.51, C:0.07, G:0.11, T:0.31
Consensus pattern (317 bp):
TTAATAAATTTCAAACATAATGCACTGAAATAATGTAAAATTATAAAATTAGAAATTATGATATT
TTTTAAAATAATAAAATGCGGAGAAAAAAATACGAACAAATGGCCGAAGTAAGAGTGTTTTACTA
AATTTTTTAAAAATTCAGAAATAATTAATAAAAATATTTCAAACAAAATGTACTGAAATAATATA
AAATAATAAAATACGAAAATAATATATTTTAATTAAAAGTAATAAAATTCGGGAAAATAATACGA
GCAAAGGGCAGGAATAAGAGTTTTTTTACACTAAATTAATTTAAAAAACAAACTAAA
Found at i:3450235 original size:12 final size:12
Alignment explanation
Indices: 3450220--3450245 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
3450210 GCCCGATTAG
3450220 GAGCCCTAGCCA
1 GAGCCCTAGCCA
3450232 GAGCCCTAGCCA
1 GAGCCCTAGCCA
3450244 GA
1 GA
3450246 TCTGGAACAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.27, C:0.38, G:0.27, T:0.08
Consensus pattern (12 bp):
GAGCCCTAGCCA
Found at i:3450656 original size:14 final size:14
Alignment explanation
Indices: 3450637--3450669 Score: 66
Period size: 14 Copynumber: 2.4 Consensus size: 14
3450627 TTTTTGTATA
3450637 AATTTAATTATTCT
1 AATTTAATTATTCT
3450651 AATTTAATTATTCT
1 AATTTAATTATTCT
3450665 AATTT
1 AATTT
3450670 TAGTTATGCT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.36, C:0.06, G:0.00, T:0.58
Consensus pattern (14 bp):
AATTTAATTATTCT
Found at i:3453798 original size:40 final size:41
Alignment explanation
Indices: 3453707--3453832 Score: 109
Period size: 40 Copynumber: 3.1 Consensus size: 41
3453697 ACTAACACAA
* *
3453707 TAACAATAATAA--TA-GTTTTATACTCAAAATAATACTAAC
1 TAACAATAATAATCTAGGGTTT-TACTAAAAATAATACTAAC
3453746 TAACAATAATAAT-TAGGGTTTTACTAAAAATAATAACTAAC
1 TAACAATAATAATCTAGGGTTTTACTAAAAATAAT-ACTAAC
* * * ** * *
3453787 -CATAATCATAATGCTAGTTTTTTACTAACAATAATACTAAG
1 TAACAATAATAAT-CTAGGGTTTTACTAAAAATAATACTAAC
3453828 TAACA
1 TAACA
3453833 TCTAAACCCT
Statistics
Matches: 70, Mismatches: 11, Indels: 9
0.78 0.12 0.10
Matches are distributed among these distances:
39 12 0.17
40 23 0.33
41 15 0.21
42 20 0.29
ACGTcount: A:0.48, C:0.13, G:0.06, T:0.33
Consensus pattern (41 bp):
TAACAATAATAATCTAGGGTTTTACTAAAAATAATACTAAC
Found at i:3454017 original size:10 final size:10
Alignment explanation
Indices: 3453987--3454025 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
3453977 AAAAAAAACT
3453987 TTTTTTTCTC
1 TTTTTTTCTC
*
3453997 TTCTATTTCTC
1 TT-TTTTTCTC
3454008 TTTTTTTCTC
1 TTTTTTTCTC
*
3454018 TCTTTTTC
1 TTTTTTTC
3454026 CGGCACCACC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
10 16 0.64
11 9 0.36
ACGTcount: A:0.03, C:0.23, G:0.00, T:0.74
Consensus pattern (10 bp):
TTTTTTTCTC
Found at i:3454214 original size:27 final size:27
Alignment explanation
Indices: 3454114--3454203 Score: 146
Period size: 27 Copynumber: 3.3 Consensus size: 27
3454104 AGTGGTGCCA
3454114 CCTATGGGAAAGGCACCT-TGGGTGCTG
1 CCTATGGGAAAGGCACCTCT-GGTGCTG
* *
3454141 CCTATGGGAAAGGCACCTTTGGTGCCG
1 CCTATGGGAAAGGCACCTCTGGTGCTG
3454168 CCTATGGGAAAGGCACCTCTGGTGCTG
1 CCTATGGGAAAGGCACCTCTGGTGCTG
3454195 CCTATGGGA
1 CCTATGGGA
3454204 TACCCTCCTC
Statistics
Matches: 59, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
27 58 0.98
28 1 0.02
ACGTcount: A:0.19, C:0.24, G:0.34, T:0.22
Consensus pattern (27 bp):
CCTATGGGAAAGGCACCTCTGGTGCTG
Found at i:3459449 original size:4 final size:4
Alignment explanation
Indices: 3459427--3459479 Score: 65
Period size: 4 Copynumber: 13.5 Consensus size: 4
3459417 AATGGCATAG
*
3459427 AAAT AATAT AAAC AAAT AAAT AAAT AAAT AAAT AAAT -AA- AAAT AAAT
1 AAAT AA-AT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT
*
3459474 CAAT AA
1 AAAT AA
3459480 CATGCAAAGC
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
3 4 0.10
4 34 0.81
5 4 0.10
ACGTcount: A:0.74, C:0.04, G:0.00, T:0.23
Consensus pattern (4 bp):
AAAT
Found at i:3460436 original size:21 final size:19
Alignment explanation
Indices: 3460400--3460474 Score: 123
Period size: 19 Copynumber: 3.8 Consensus size: 19
3460390 AATCATATCT
3460400 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
*
3460419 TCCAAGATTGCACATATCATA
1 TCTAAGATTG--CATATCATA
3460440 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
3460459 TCTAAGATTGCATATC
1 TCTAAGATTGCATATC
3460475 CTCAAAAATT
Statistics
Matches: 52, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
19 34 0.65
21 18 0.35
ACGTcount: A:0.36, C:0.19, G:0.11, T:0.35
Consensus pattern (19 bp):
TCTAAGATTGCATATCATA
Found at i:3460448 original size:40 final size:38
Alignment explanation
Indices: 3460393--3460470 Score: 129
Period size: 40 Copynumber: 2.0 Consensus size: 38
3460383 ATTACAAAAT
3460393 CATATCTTCTAAGATTGCATATCATATCCAAGATTGCA
1 CATATCTTCTAAGATTGCATATCATATCCAAGATTGCA
*
3460431 CATATCATATCTAAGATTGCATATCATATCTAAGATTGCA
1 CATATC-T-TCTAAGATTGCATATCATATCCAAGATTGCA
3460471 TATCCTCAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 2
0.93 0.03 0.05
Matches are distributed among these distances:
38 6 0.16
39 1 0.03
40 30 0.81
ACGTcount: A:0.36, C:0.19, G:0.10, T:0.35
Consensus pattern (38 bp):
CATATCTTCTAAGATTGCATATCATATCCAAGATTGCA
Found at i:3483618 original size:134 final size:132
Alignment explanation
Indices: 3483380--3483644 Score: 415
Period size: 134 Copynumber: 2.0 Consensus size: 132
3483370 CTTACACATC
* * * *
3483380 TTATTGATTATAATGAAAGCATCTTCTTCTAATGACATTTTGATGTCTCAAATTTACTGCAATCT
1 TTATTCATTATAATGAAAGCATCTTCTTCTAATGACATTTTGATGACCCAAATCTACTGCAATCT
* *
3483445 TCAAAGCATGGAGACATGCAATGGTTTCAATCAGCATATGAGTAGAGAAC-AAAAAGAAGAAAAG
66 TCAAAGCATGGAGACATGCAATGGTTTCAATCACCATATGACTAGAGAACTAAAAA-AAGAAAAG
3483509 TTT
130 TTT
3483512 TTATTCATTATAATGAAAGCATCTTCTTCTAATATGACATTTTGATGACCCAAATCTACTGCAAT
1 TTATTCATTATAATGAAAGCATCTTCTTCT-A-ATGACATTTTGATGACCCAAATCTACTGCAAT
* * *
3483577 CTTCAAAGTATGGAGATATGCAATGGTTTCTATCACCATATGACTAGAGAACTAAAAAAAGAAAA
64 CTTCAAAGCATGGAGACATGCAATGGTTTCAATCACCATATGACTAGAGAACTAAAAAAAGAAAA
3483642 GTT
129 GTT
3483645 ATGTTGAGAT
Statistics
Matches: 121, Mismatches: 9, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
132 29 0.24
133 1 0.01
134 86 0.71
135 5 0.04
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.32
Consensus pattern (132 bp):
TTATTCATTATAATGAAAGCATCTTCTTCTAATGACATTTTGATGACCCAAATCTACTGCAATCT
TCAAAGCATGGAGACATGCAATGGTTTCAATCACCATATGACTAGAGAACTAAAAAAAGAAAAGT
TT
Found at i:3490135 original size:35 final size:33
Alignment explanation
Indices: 3490079--3490154 Score: 84
Period size: 32 Copynumber: 2.3 Consensus size: 33
3490069 GGTCAGATTC
3490079 AATCAAAA-AAAAAGAAAAGAAAAATAAAAATAAAA
1 AATCAAAATAAAAAGAAAAG-AAAA-AAAAA-AAAA
* * *
3490114 AATCAAAATAAAATG-AGAGAAAAAAAGAAAAA
1 AATCAAAATAAAAAGAAAAGAAAAAAAAAAAAA
3490146 AATCAAAAT
1 AATCAAAAT
3490155 CAAAGTCAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
32 13 0.35
33 4 0.11
34 4 0.11
35 11 0.30
36 5 0.14
ACGTcount: A:0.78, C:0.04, G:0.08, T:0.11
Consensus pattern (33 bp):
AATCAAAATAAAAAGAAAAGAAAAAAAAAAAAA
Found at i:3491044 original size:21 final size:21
Alignment explanation
Indices: 3491018--3491066 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
3491008 GCCTTGATTC
3491018 GAAAAAA-AAAAGATGAAAAAT
1 GAAAAAATAAAA-ATGAAAAAT
*
3491039 GAAAAAATGAAAATGAAAAA-
1 GAAAAAATAAAAATGAAAAAT
*
3491059 GTAAAAAT
1 GAAAAAAT
3491067 GAATAGGCTA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 7 0.28
21 15 0.60
22 3 0.12
ACGTcount: A:0.73, C:0.00, G:0.14, T:0.12
Consensus pattern (21 bp):
GAAAAAATAAAAATGAAAAAT
Found at i:3491052 original size:14 final size:14
Alignment explanation
Indices: 3491024--3491069 Score: 56
Period size: 14 Copynumber: 3.1 Consensus size: 14
3491014 ATTCGAAAAA
3491024 AAAAAGATGAAAAATG
1 AAAAA-ATG-AAAATG
3491040 AAAAAATGAAAATG
1 AAAAAATGAAAATG
* *
3491054 AAAAAGTAAAAATG
1 AAAAAATGAAAATG
3491068 AA
1 AA
3491070 TAGGCTAAGG
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
14 20 0.71
15 3 0.11
16 5 0.18
ACGTcount: A:0.72, C:0.00, G:0.15, T:0.13
Consensus pattern (14 bp):
AAAAAATGAAAATG
Found at i:3492380 original size:44 final size:44
Alignment explanation
Indices: 3492325--3492416 Score: 139
Period size: 44 Copynumber: 2.1 Consensus size: 44
3492315 TCCCTAAGCA
* * *
3492325 ACAGTGGAGCAGATTGAAGCCAGAAATCTTATCTTCCTGAGATT
1 ACAGAGGAGCAGATTGAAGCCAGAAATCCTATCTCCCTGAGATT
* *
3492369 ACAGAGGAGCAGATTGAAGCTAGTAATCCTATCTCCCTGAGATT
1 ACAGAGGAGCAGATTGAAGCCAGAAATCCTATCTCCCTGAGATT
3492413 ACAG
1 ACAG
3492417 TGGAACGGAT
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
44 43 1.00
ACGTcount: A:0.33, C:0.20, G:0.23, T:0.25
Consensus pattern (44 bp):
ACAGAGGAGCAGATTGAAGCCAGAAATCCTATCTCCCTGAGATT
Found at i:3492446 original size:44 final size:43
Alignment explanation
Indices: 3492398--3492603 Score: 112
Period size: 44 Copynumber: 4.4 Consensus size: 43
3492388 CTAGTAATCC
3492398 TATCTCCCTGAGATTACAGTGGAACGGATTAAAATAAATGATCT
1 TATCTCCCTGA-ATTACAGTGGAACGGATTAAAATAAATGATCT
* * * *
3492442 TATCTCGCTGAAGTTACAGTAGAGTAGATCGCG--TCAGATGGAAGCCAGGAATCT
1 TATCTCCCTGAA-TTACAGT-G-G-A-A-CG-GATTAAAAT--AA---ATG-ATCT
* * ** * * *
3492496 TATCTCCCTGAGATTACAGCGGAACAGATTGAAGCT-AGTAATCC
1 TATCTCCCTGA-ATTACAGTGGAACGGATT-AAAATAAATGATCT
*
3492540 TATCTCCCTTATATTACAGTGGAACGGATTAAAATAAATGATCT
1 TATCTCCCTGA-ATTACAGTGGAACGGATTAAAATAAATGATCT
*
3492584 TATCTCGCTGAAGTTACAGT
1 TATCTCCCTGAA-TTACAGT
3492604 AGAGTAGATC
Statistics
Matches: 119, Mismatches: 24, Indels: 38
0.66 0.13 0.21
Matches are distributed among these distances:
43 5 0.04
44 67 0.56
45 1 0.01
46 1 0.01
47 1 0.01
48 7 0.06
49 3 0.03
50 5 0.04
51 4 0.03
52 1 0.01
53 3 0.03
54 20 0.17
55 1 0.01
ACGTcount: A:0.33, C:0.18, G:0.20, T:0.29
Consensus pattern (43 bp):
TATCTCCCTGAATTACAGTGGAACGGATTAAAATAAATGATCT
Found at i:3492590 original size:142 final size:142
Alignment explanation
Indices: 3492334--3492653 Score: 568
Period size: 142 Copynumber: 2.3 Consensus size: 142
3492324 AACAGTGGAG
*
3492334 CAGATTGAAGCCAGAAATCTTATCTTCCTGAGATTACAGAGGAGCAGATTGAAGCTAGTAATCCT
1 CAGATTGAAGCCAGAAATCTTATCTTCCTGAGATTACAGAGGAACAGATTGAAGCTAGTAATCCT
3492399 ATCTCCCTGAGATTACAGTGGAACGGATTAAAATAAATGATCTTATCTCGCTGAAGTTACAGTAG
66 ATCTCCCTGAGATTACAGTGGAACGGATTAAAATAAATGATCTTATCTCGCTGAAGTTACAGTAG
*
3492464 AGTAGATCGCGT
131 AGTAGATCGCAT
* * * *
3492476 CAGATGGAAGCCAGGAATCTTATCTCCCTGAGATTACAGCGGAACAGATTGAAGCTAGTAATCCT
1 CAGATTGAAGCCAGAAATCTTATCTTCCTGAGATTACAGAGGAACAGATTGAAGCTAGTAATCCT
* *
3492541 ATCTCCCTTATATTACAGTGGAACGGATTAAAATAAATGATCTTATCTCGCTGAAGTTACAGTAG
66 ATCTCCCTGAGATTACAGTGGAACGGATTAAAATAAATGATCTTATCTCGCTGAAGTTACAGTAG
3492606 AGTAGATCGCAT
131 AGTAGATCGCAT
3492618 CAGATTGAAGCCAGAAATCTTATCTTCCTGAGATTA
1 CAGATTGAAGCCAGAAATCTTATCTTCCTGAGATTA
3492654 TAGTGGAATA
Statistics
Matches: 167, Mismatches: 11, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
142 167 1.00
ACGTcount: A:0.33, C:0.18, G:0.21, T:0.28
Consensus pattern (142 bp):
CAGATTGAAGCCAGAAATCTTATCTTCCTGAGATTACAGAGGAACAGATTGAAGCTAGTAATCCT
ATCTCCCTGAGATTACAGTGGAACGGATTAAAATAAATGATCTTATCTCGCTGAAGTTACAGTAG
AGTAGATCGCAT
Found at i:3492765 original size:50 final size:50
Alignment explanation
Indices: 3492711--3493122 Score: 337
Period size: 50 Copynumber: 8.3 Consensus size: 50
3492701 AGTGGAACAA
* * *
3492711 ATTAAAGCCACATCGGTGAATCTTGCTTCCCCGACATTGCAATTAAAAAG
1 ATTAAAGCCACAACAGTGAATCTTGCTTCCCCGACATTGCAGTTAAAAAG
* * * * * * * ** **
3492761 ATTAAAGTCACAGCGGTGAATCTTACTTCTCTGGCGA-T-CAGTGGAGCAG
1 ATTAAAGCCACAACAGTGAATCTTGCTTCCCCGAC-ATTGCAGTTAAAAAG
* * * *
3492810 ATTAAAACCAAAACGGTGAATCTTGCTTCCCCAACATTGCAGTTAAAAAG
1 ATTAAAGCCACAACAGTGAATCTTGCTTCCCCGACATTGCAGTTAAAAAG
* ** * * * ** ** *
3492860 ATTAAAGCCATAACAACGAATCTTAC-TCCCTAGGCGGTGCAGCGGAACAA-
1 ATTAAAGCCACAACAGTGAATCTTGCTTCCC-CGACATTGCAG-TTAAAAAG
*
3492910 ATTAAAGGCACAACAGTGAATCTTGCTTCCCCGACATTGCAGTTAAAAAG
1 ATTAAAGCCACAACAGTGAATCTTGCTTCCCCGACATTGCAGTTAAAAAG
* * * ** * ** *
3492960 ATTAAAGCTACAACAGCGAATCTTACTTCCCTTACAGTGCAGTGGAACAG
1 ATTAAAGCCACAACAGTGAATCTTGCTTCCCCGACATTGCAGTTAAAAAG
* * * * *
3493010 ATTAAAGCCACATCAATGAATCTTGCCTCCCGGACATTGCAGTTCAAAAG
1 ATTAAAGCCACAACAGTGAATCTTGCTTCCCCGACATTGCAGTTAAAAAG
* * * *
3493060 ATTAAAGCTACAACATTGAATCATGCTTCCCCGACATTGCAATTAAAAAG
1 ATTAAAGCCACAACAGTGAATCTTGCTTCCCCGACATTGCAGTTAAAAAG
3493110 ATTAAAGCCACAA
1 ATTAAAGCCACAA
3493123 TGGCGAATCT
Statistics
Matches: 274, Mismatches: 81, Indels: 14
0.74 0.22 0.04
Matches are distributed among these distances:
48 1 0.00
49 41 0.15
50 223 0.81
51 9 0.03
ACGTcount: A:0.36, C:0.23, G:0.17, T:0.24
Consensus pattern (50 bp):
ATTAAAGCCACAACAGTGAATCTTGCTTCCCCGACATTGCAGTTAAAAAG
Found at i:3492949 original size:100 final size:101
Alignment explanation
Indices: 3492679--3493074 Score: 453
Period size: 100 Copynumber: 4.0 Consensus size: 101
3492669 AAGAATTACA
* * * * * *
3492679 AATCTTATTTCCC-AAGCGATGTAGTGGAACAAATTAAAGCCACATCGGTGAATCTTGCTTCCCC
1 AATCTTACTTCCCTAGGCGGTGCAGTGGAACAAATTAAAGCCACAACAGTGAATCTTGCTTCCCC
* * * * *
3492743 GACATTGCAATTAAAAAGATTAAAGTCACAGCGGTG
66 GACATTGCAGTTAAAAAGATTAAAGCCACAACAGCG
* * * * * * *
3492779 AATCTTACTTCTCT-GGCGAT-CAGTGGAGCAGATTAAAACCAAAACGGTGAATCTTGCTTCCCC
1 AATCTTACTTCCCTAGGCGGTGCAGTGGAACAAATTAAAGCCACAACAGTGAATCTTGCTTCCCC
* * *
3492842 AACATTGCAGTTAAAAAGATTAAAGCCATAACAACG
66 GACATTGCAGTTAAAAAGATTAAAGCCACAACAGCG
* *
3492878 AATCTTAC-TCCCTAGGCGGTGCAGCGGAACAAATTAAAGGCACAACAGTGAATCTTGCTTCCCC
1 AATCTTACTTCCCTAGGCGGTGCAGTGGAACAAATTAAAGCCACAACAGTGAATCTTGCTTCCCC
*
3492942 GACATTGCAGTTAAAAAGATTAAAGCTACAACAGCG
66 GACATTGCAGTTAAAAAGATTAAAGCCACAACAGCG
* * * * *
3492978 AATCTTACTTCCCTTA--CAGTGCAGTGGAACAGATTAAAGCCACATCAATGAATCTTGCCTCCC
1 AATCTTACTTCCC-TAGGCGGTGCAGTGGAACAAATTAAAGCCACAACAGTGAATCTTGCTTCCC
* * *
3493041 GGACATTGCAGTTCAAAAGATTAAAGCTACAACA
65 CGACATTGCAGTTAAAAAGATTAAAGCCACAACA
3493075 TTGAATCATG
Statistics
Matches: 252, Mismatches: 39, Indels: 10
0.84 0.13 0.03
Matches are distributed among these distances:
98 4 0.02
99 78 0.31
100 164 0.65
101 4 0.02
102 2 0.01
ACGTcount: A:0.35, C:0.23, G:0.18, T:0.24
Consensus pattern (101 bp):
AATCTTACTTCCCTAGGCGGTGCAGTGGAACAAATTAAAGCCACAACAGTGAATCTTGCTTCCCC
GACATTGCAGTTAAAAAGATTAAAGCCACAACAGCG
Found at i:3500399 original size:17 final size:19
Alignment explanation
Indices: 3500362--3500401 Score: 57
Period size: 17 Copynumber: 2.2 Consensus size: 19
3500352 GATGAACCAT
3500362 AAAATAAGTTAAAGGAATG
1 AAAATAAGTTAAAGGAATG
*
3500381 AAAATAAG-TAAA-TAATG
1 AAAATAAGTTAAAGGAATG
3500398 AAAA
1 AAAA
3500402 GAAAAAATGA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 8 0.40
18 4 0.20
19 8 0.40
ACGTcount: A:0.65, C:0.00, G:0.15, T:0.20
Consensus pattern (19 bp):
AAAATAAGTTAAAGGAATG
Found at i:3502240 original size:23 final size:23
Alignment explanation
Indices: 3502213--3502257 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
3502203 CGAGAGATAG
*
3502213 TCAAATTGCATAATGTTCCTGTA
1 TCAAATTGCATAATGTACCTGTA
*
3502236 TCAAATTGCATAGTGTACCTGT
1 TCAAATTGCATAATGTACCTGT
3502258 GTCTATTATC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.29, C:0.18, G:0.16, T:0.38
Consensus pattern (23 bp):
TCAAATTGCATAATGTACCTGTA
Found at i:3502585 original size:199 final size:199
Alignment explanation
Indices: 3502236--3502825 Score: 1090
Period size: 199 Copynumber: 3.0 Consensus size: 199
3502226 TGTTCCTGTA
*
3502236 TCAAATTGCATAGTGTACCTGTGTCTATTATCTCTGACCGAGATCCGCGCTTTGCTTCTAGATTC
1 TCAAATTGCATAGTGTACCTGTGTCTATTATCTCTGACCGAGATCCGCGCTTTGCTTCGAGATTC
*
3502301 TAGAAGCATCTACATGAATCTTTAAGTATGAGATTAAATTTCAGCACAACTTTTCATTCTCAGAC
66 TGGAAGCATCTACATGAATCTTTAAGTATGAGATTAAATTTCAGCACAACTTTTCATTCTCAGAC
3502366 AGATGGCCAATCAGAATGGGTATTCAGATATTAGAATATATGTTGTAATCATGTGTAATTGAGAG
131 AGATGGCCAATCAGAATGGGTATTCAGATATTAGAATATATGTTGTAATCATGTGTAATTGAGAG
3502431 ATAG
196 ATAG
3502435 TCAAATTGCATAGTGTACCTGTGTCTATTATCTCTGACCGAGATCCGCGCTTTGCTTCGAGATTC
1 TCAAATTGCATAGTGTACCTGTGTCTATTATCTCTGACCGAGATCCGCGCTTTGCTTCGAGATTC
*
3502500 TGGAAACATCTACATGAATCTTTAAGTATGAGATTAAATTTCAGCACAACTTTTCATTCTCAGAC
66 TGGAAGCATCTACATGAATCTTTAAGTATGAGATTAAATTTCAGCACAACTTTTCATTCTCAGAC
* *
3502565 AGATGGCTAATCATAATGGGTATTCAGATATTAGAATATATGTTGTAATCATGTGTAATTGAGAG
131 AGATGGCCAATCAGAATGGGTATTCAGATATTAGAATATATGTTGTAATCATGTGTAATTGAGAG
3502630 ATAG
196 ATAG
* *
3502634 TCAAATTGCACAGTGTACCTGTGTCTATTATCTCTGATCGAGATCCGCGCTTTGCTTCGAGATTC
1 TCAAATTGCATAGTGTACCTGTGTCTATTATCTCTGACCGAGATCCGCGCTTTGCTTCGAGATTC
* * *
3502699 TGGAAGCACCTACATGAATCTTTAAGTATGAGATTAAATTTCAGCACAACTTTTTATTCTCAGTC
66 TGGAAGCATCTACATGAATCTTTAAGTATGAGATTAAATTTCAGCACAACTTTTCATTCTCAGAC
3502764 AGATGGCCAATCAGAATGGGTATTCAGATATTAGAATATATGTTGTAATCATGTGTAATTGA
131 AGATGGCCAATCAGAATGGGTATTCAGATATTAGAATATATGTTGTAATCATGTGTAATTGA
3502826 TTTTGAATCA
Statistics
Matches: 378, Mismatches: 13, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
199 378 1.00
ACGTcount: A:0.30, C:0.17, G:0.19, T:0.35
Consensus pattern (199 bp):
TCAAATTGCATAGTGTACCTGTGTCTATTATCTCTGACCGAGATCCGCGCTTTGCTTCGAGATTC
TGGAAGCATCTACATGAATCTTTAAGTATGAGATTAAATTTCAGCACAACTTTTCATTCTCAGAC
AGATGGCCAATCAGAATGGGTATTCAGATATTAGAATATATGTTGTAATCATGTGTAATTGAGAG
ATAG
Found at i:3503854 original size:22 final size:23
Alignment explanation
Indices: 3503811--3503856 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 23
3503801 GATGGCTTAT
*
3503811 AATTTTATAAATACTAAGTTATAA
1 AATTTTATAAATAC-AAATTATAA
*
3503835 AATTTTATAATTA-AAATTATAA
1 AATTTTATAAATACAAATTATAA
3503857 TATGGTAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 8 0.40
24 12 0.60
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.43
Consensus pattern (23 bp):
AATTTTATAAATACAAATTATAA
Found at i:3521112 original size:14 final size:14
Alignment explanation
Indices: 3521095--3521124 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
3521085 TGAATGTATT
3521095 ATAATATCTTTTCA
1 ATAATATCTTTTCA
3521109 ATAATATCTTTTCA
1 ATAATATCTTTTCA
3521123 AT
1 AT
3521125 GATGTATGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.37, C:0.13, G:0.00, T:0.50
Consensus pattern (14 bp):
ATAATATCTTTTCA
Found at i:3533877 original size:40 final size:39
Alignment explanation
Indices: 3533846--3534055 Score: 242
Period size: 40 Copynumber: 5.3 Consensus size: 39
3533836 GGACTAAGAT
* *
3533846 CCGAAGGCATTTGTGCGAGATACAAATTCCGGGTTAAGCC
1 CCGAAGGCATTCGTGCGAGATACAAA-TCCGGGTTAAGTC
* *
3533886 CCGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGTC
1 CCGAAGGCATTCGTGCGAGATAC-AAATCCGGGTTAAGTC
* *
3533926 CCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTC
1 CCGAAGGCATTCGTGCGAGATA-CAAATCCGGGTTAAGTC
* * *
3533966 CCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTATGTC
1 CCGAAGGCATTCGTGCGAGATA-CAAATCCGGGTTAAGTC
* * * * *
3534006 CCGAAGGCATT-GTGTGAGTTACTAAAACCGGGCTATGTC
1 CCGAAGGCATTCGTGCGAGATAC-AAATCCGGGTTAAGTC
3534045 CCGAAGGCATT
1 CCGAAGGCATT
3534056 TGAACGAGGA
Statistics
Matches: 156, Mismatches: 11, Indels: 7
0.90 0.06 0.04
Matches are distributed among these distances:
39 34 0.22
40 119 0.76
41 3 0.02
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.26
Consensus pattern (39 bp):
CCGAAGGCATTCGTGCGAGATACAAATCCGGGTTAAGTC
Found at i:3534009 original size:120 final size:120
Alignment explanation
Indices: 3533793--3534055 Score: 309
Period size: 120 Copynumber: 2.2 Consensus size: 120
3533783 TTGAATGCTG
* *
3533793 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAATATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTCGTGCTAAGTGAATAAATCCGGACTAAGATCCGAAGGCATT
* *
3533857 TGTGCGAGATACAAATTCCGGGTTAAGCCCCGAAGGCCTTTGTGCGAGATACTAAA
66 CGTGCGAGATACAAATTCCGGGTTAAGCCCCGAAGG-CATTGTGCGAGATACTAAA
* * * * **
3533913 TCCGGGTTAAGTCCCGAAGGCATTCGTGC-GAGTTATTAAATCCGGGTTAAG-TCCCGAAGGCAT
1 TCCGGGCTAAGTCCCGAAGGCATTCGTGCTAAGTGAATAAATCCGGACTAAGAT-CCGAAGGCAT
* * * * * *
3533976 TCGTGCGAGTTATTAAA-TCCGGGTTATGTCCCGAAGGCATTGTGTGAGTTACTAAA
65 TCGTGCGAGATA-CAAATTCCGGGTTAAGCCCCGAAGGCATTGTGCGAGATACTAAA
* *
3534032 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATT
3534056 TGAACGAGGA
Statistics
Matches: 121, Mismatches: 19, Indels: 7
0.82 0.13 0.05
Matches are distributed among these distances:
119 38 0.31
120 74 0.61
121 9 0.07
ACGTcount: A:0.25, C:0.21, G:0.27, T:0.26
Consensus pattern (120 bp):
TCCGGGCTAAGTCCCGAAGGCATTCGTGCTAAGTGAATAAATCCGGACTAAGATCCGAAGGCATT
CGTGCGAGATACAAATTCCGGGTTAAGCCCCGAAGGCATTGTGCGAGATACTAAA
Found at i:3534075 original size:79 final size:80
Alignment explanation
Indices: 3533794--3534090 Score: 230
Period size: 80 Copynumber: 3.7 Consensus size: 80
3533784 TGAATGCTGT
* ** * * * **
3533794 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAATATATCCGGACTAAGAT-CCGAAGGCATT
1 CCGGGCTAAGTCCCGAAGGCATTCGAAC-GAGTGACTAAATCCGGGTTAAG-TCCCGAAGGCATT
* * *
3533857 TGTGCGAGATAC-AAATT
64 CGTGCGAGTTACTAAA-A
* * * * **
3533874 CCGGGTTAAGCCCCGAAGGCCTTTGTGCGAGAT-ACTAAATCCGGGTTAAGTCCCGAAGGCATTC
1 CCGGGCTAAGTCCCGAAGGCATTCGAACGAG-TGACTAAATCCGGGTTAAGTCCCGAAGGCATTC
* *
3533938 GTGCGAGTTATTAAAT
65 GTGCGAGTTACTAAAA
* ** * * *
3533954 CCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTATGTCCCGAAGGCATT-G
1 CCGGGCTAAGTCCCGAAGGCATTCGAACGAGTGACTAAATCCGGGTTAAGTCCCGAAGGCATTCG
*
3534018 TGTGAGTTACTAAAA
66 TGCGAGTTACTAAAA
* * * *
3534033 CCGGGCTATGTCCCGAAGGCATTTGAACGAG-GAGCTATATCC-GGTTAAATCCCGAAGG
1 CCGGGCTAAGTCCCGAAGGCATTCGAACGAGTGA-CTAAATCCGGGTTAAGTCCCGAAGG
3534091 TACGTGATTT
Statistics
Matches: 183, Mismatches: 28, Indels: 14
0.81 0.12 0.06
Matches are distributed among these distances:
78 15 0.08
79 47 0.26
80 110 0.60
81 11 0.06
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.25
Consensus pattern (80 bp):
CCGGGCTAAGTCCCGAAGGCATTCGAACGAGTGACTAAATCCGGGTTAAGTCCCGAAGGCATTCG
TGCGAGTTACTAAAA
Found at i:3541827 original size:40 final size:39
Alignment explanation
Indices: 3541796--3542005 Score: 233
Period size: 40 Copynumber: 5.3 Consensus size: 39
3541786 GGACTAAGAT
* *
3541796 CCGAAGGCATTTGTGCGAGATACAAATTCCGGGTTAAGCC
1 CCGAAGGCATTCGTGCGAGATACAAA-TCCGGGTTAAGTC
* *
3541836 CCGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGTC
1 CCGAAGGCATTCGTGCGAGATAC-AAATCCGGGTTAAGTC
* *
3541876 CCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTC
1 CCGAAGGCATTCGTGCGAGATA-CAAATCCGGGTTAAGTC
* ** *
3541916 CCGAAGGCATTCGTGCGAGTTGTTAAATCCGGGTTATGTC
1 CCGAAGGCATTCGTGCGAGAT-ACAAATCCGGGTTAAGTC
* * * * *
3541956 CCGAAGGCATT-GTGTGAGTTACTAAAACCGGGCTATGTC
1 CCGAAGGCATTCGTGCGAGATAC-AAATCCGGGTTAAGTC
3541995 CCGAAGGCATT
1 CCGAAGGCATT
3542006 TGAACGAGGA
Statistics
Matches: 153, Mismatches: 13, Indels: 9
0.87 0.07 0.05
Matches are distributed among these distances:
39 33 0.22
40 117 0.76
41 3 0.02
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.26
Consensus pattern (39 bp):
CCGAAGGCATTCGTGCGAGATACAAATCCGGGTTAAGTC
Found at i:3541959 original size:120 final size:120
Alignment explanation
Indices: 3541743--3542005 Score: 300
Period size: 120 Copynumber: 2.2 Consensus size: 120
3541733 TTGAATGCTG
* *
3541743 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAATATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTCGTGCTAAGTGAATAAATCCGGACTAAGATCCGAAGGCATT
* *
3541807 TGTGCGAGATACAAATTCCGGGTTAAGCCCCGAAGGCCTTTGTGCGAGATACTAAA
66 CGTGCGAGATACAAATTCCGGGTTAAGCCCCGAAGG-CATTGTGCGAGATACTAAA
* * * * **
3541863 TCCGGGTTAAGTCCCGAAGGCATTCGTGC-GAGTTATTAAATCCGGGTTAAG-TCCCGAAGGCAT
1 TCCGGGCTAAGTCCCGAAGGCATTCGTGCTAAGTGAATAAATCCGGACTAAGAT-CCGAAGGCAT
* ** * * * *
3541926 TCGTGCGAGTTGTTAAA-TCCGGGTTATGTCCCGAAGGCATTGTGTGAGTTACTAAA
65 TCGTGCGAGAT-ACAAATTCCGGGTTAAGCCCCGAAGGCATTGTGCGAGATACTAAA
* *
3541982 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATT
3542006 TGAACGAGGA
Statistics
Matches: 120, Mismatches: 20, Indels: 7
0.82 0.14 0.05
Matches are distributed among these distances:
119 38 0.32
120 73 0.61
121 9 0.08
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.26
Consensus pattern (120 bp):
TCCGGGCTAAGTCCCGAAGGCATTCGTGCTAAGTGAATAAATCCGGACTAAGATCCGAAGGCATT
CGTGCGAGATACAAATTCCGGGTTAAGCCCCGAAGGCATTGTGCGAGATACTAAA
Found at i:3542025 original size:79 final size:80
Alignment explanation
Indices: 3541796--3542040 Score: 228
Period size: 80 Copynumber: 3.1 Consensus size: 80
3541786 GGACTAAGAT
* * * * * * * ** *
3541796 CCGAAGGCATTTGTGCGAGATAC-AAATTCCGGGTTAAGCCCCGAAGGCCTTTGTGCGA-GATAC
1 CCGAAGGCATTCGTGCGAGTTACTAAA-ACCGGGCTAAGTCCCGAAGGCATTCGAACGAGGA-GC
3541859 TAAATCCGGGTTAAGTC
64 TAAATCCGGGTTAAGTC
* * * ** ** *
3541876 CCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTA
1 CCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCATTCGAACGAGGAGCTA
*
3541941 AATCCGGGTTATGTC
66 AATCCGGGTTAAGTC
* * *
3541956 CCGAAGGCATT-GTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGGCATTTGAACGAGGAGCTA
1 CCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCATTCGAACGAGGAGCTA
* *
3542020 TATCC-GGTTAAATC
66 AATCCGGGTTAAGTC
3542034 CCGAAGG
1 CCGAAGG
3542041 TACGTGATTT
Statistics
Matches: 138, Mismatches: 25, Indels: 6
0.82 0.15 0.04
Matches are distributed among these distances:
78 14 0.10
79 46 0.33
80 75 0.54
81 3 0.02
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.25
Consensus pattern (80 bp):
CCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCATTCGAACGAGGAGCTA
AATCCGGGTTAAGTC
Found at i:3546297 original size:44 final size:44
Alignment explanation
Indices: 3546249--3546437 Score: 127
Period size: 44 Copynumber: 4.3 Consensus size: 44
3546239 AGATAGCAGG
3546249 TCTTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGATGA-CAAA
1 TCTTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGAT-ACCAAA
* * ** *
3546293 TCTTATCTTTCC-AAG-A-TAGTGGGAAGCAGATTTAAGCCACCAAG
1 TCTTATC-TCCCTAAGCAGTAGT-GG-AGCAGATTGAAGATACCAAA
* * * * * * ** **
3546337 CCTTGTCTTCCTGAGCAGCAGTGGAGCAGGTTGAAGATAGTAGG
1 TCTTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGATACCAAA
** * *
3546381 TCTTATCTCCCTAAGCAGTAGTGGAGCAGACAGAAGA-AACTAA
1 TCTTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGATACCAAA
*
3546424 TCCTATCTCCCTAA
1 TCTTATCTCCCTAA
3546438 AGTTGTAGTA
Statistics
Matches: 108, Mismatches: 30, Indels: 15
0.71 0.20 0.10
Matches are distributed among these distances:
42 4 0.04
43 22 0.20
44 73 0.68
45 6 0.06
46 3 0.03
ACGTcount: A:0.31, C:0.21, G:0.23, T:0.25
Consensus pattern (44 bp):
TCTTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGATACCAAA
Found at i:3546446 original size:44 final size:43
Alignment explanation
Indices: 3546384--3546503 Score: 118
Period size: 44 Copynumber: 2.7 Consensus size: 43
3546374 TAGTAGGTCT
**
3546384 TATCTCCCTAAGCAGTAGTGGAGCAGA-CAGAAGAAACTA-ATCC
1 TATCTCCCTAAGTTGTAGTGGAGCAGATCA-AAGAAA-TAGATCC
* * * *
3546427 TATCTCCCTAAAGTTGTAGTAGAGCGGATTAAAGTAATAGATCC
1 TATCTCCCT-AAGTTGTAGTGGAGCAGATCAAAGAAATAGATCC
* *
3546471 TATCTCCCTGAAGTTGCAGTGGAGCGGATCAAA
1 TATCTCCCT-AAGTTGTAGTGGAGCAGATCAAA
3546504 AGGATCTCAT
Statistics
Matches: 64, Mismatches: 10, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
43 11 0.17
44 52 0.81
45 1 0.02
ACGTcount: A:0.33, C:0.20, G:0.23, T:0.24
Consensus pattern (43 bp):
TATCTCCCTAAGTTGTAGTGGAGCAGATCAAAGAAATAGATCC
Found at i:3547004 original size:20 final size:20
Alignment explanation
Indices: 3546971--3547025 Score: 92
Period size: 20 Copynumber: 2.8 Consensus size: 20
3546961 CCGATTACAA
3546971 AAGCCCAAAACCCAACACAG
1 AAGCCCAAAACCCAACACAG
* *
3546991 AAGTCCAAAGCCCAACACAG
1 AAGCCCAAAACCCAACACAG
3547011 AAGCCCAAAACCCAA
1 AAGCCCAAAACCCAA
3547026 GACTTCCCCA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.49, C:0.38, G:0.11, T:0.02
Consensus pattern (20 bp):
AAGCCCAAAACCCAACACAG
Found at i:3554346 original size:15 final size:15
Alignment explanation
Indices: 3554326--3554356 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
3554316 ATCAGCTCGG
3554326 TTGGATGACATTTTA
1 TTGGATGACATTTTA
*
3554341 TTGGATGATATTTTA
1 TTGGATGACATTTTA
3554356 T
1 T
3554357 CTATATGAAA
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:0.26, C:0.03, G:0.19, T:0.52
Consensus pattern (15 bp):
TTGGATGACATTTTA
Found at i:3554845 original size:21 final size:21
Alignment explanation
Indices: 3554815--3554856 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
3554805 TAAATATTGA
*
3554815 GTTATCGTACCCATAGGGACT
1 GTTATCGTACCCACAGGGACT
*
3554836 GTTATTGTACCCACAGGGACT
1 GTTATCGTACCCACAGGGACT
3554857 ATGAAAAGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.24, C:0.24, G:0.24, T:0.29
Consensus pattern (21 bp):
GTTATCGTACCCACAGGGACT
Found at i:3559270 original size:30 final size:30
Alignment explanation
Indices: 3559234--3559293 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
3559224 AATCAATAAA
* *
3559234 CCATCGTTGTCAAGTGATCGGGGTGGTAGG
1 CCATCGTTGCCAAGCGATCGGGGTGGTAGG
*
3559264 CCATCGTTGCCAGGCGATCGGGGTGGTAGG
1 CCATCGTTGCCAAGCGATCGGGGTGGTAGG
3559294 TTATCATTGT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.15, C:0.20, G:0.42, T:0.23
Consensus pattern (30 bp):
CCATCGTTGCCAAGCGATCGGGGTGGTAGG
Found at i:3561440 original size:19 final size:19
Alignment explanation
Indices: 3561412--3561449 Score: 60
Period size: 19 Copynumber: 2.0 Consensus size: 19
3561402 TAGATATGAT
3561412 ATTTTTTTTAT-TTGTTTA
1 ATTTTTTTTATGTTGTTTA
3561430 ATTTCTTTTTATGTTGTTTA
1 ATTT-TTTTTATGTTGTTTA
3561450 TGAACTAAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 4 0.22
19 7 0.39
20 7 0.39
ACGTcount: A:0.16, C:0.03, G:0.08, T:0.74
Consensus pattern (19 bp):
ATTTTTTTTATGTTGTTTA
Found at i:3565520 original size:20 final size:19
Alignment explanation
Indices: 3565497--3565541 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
3565487 TGATTTTAAC
3565497 TAATTTTAAATAATTTCATT
1 TAATTTTAAAT-ATTTCATT
* * *
3565517 TAATTTTCAATTTTTCTTT
1 TAATTTTAAATATTTCATT
3565536 TAATTT
1 TAATTT
3565542 AGACTTAGTA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
19 12 0.55
20 10 0.45
ACGTcount: A:0.31, C:0.07, G:0.00, T:0.62
Consensus pattern (19 bp):
TAATTTTAAATATTTCATT
Found at i:3565594 original size:15 final size:15
Alignment explanation
Indices: 3565576--3565618 Score: 50
Period size: 16 Copynumber: 2.8 Consensus size: 15
3565566 AGATTTTTTT
* *
3565576 TTTAAAATTTTAGTC
1 TTTAATATTTTAGAC
*
3565591 TTTAATTATTTAAGAC
1 TTTAA-TATTTTAGAC
3565607 TTTAATATTTTA
1 TTTAATATTTTA
3565619 TATATGTAGT
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
15 11 0.48
16 12 0.52
ACGTcount: A:0.35, C:0.05, G:0.05, T:0.56
Consensus pattern (15 bp):
TTTAATATTTTAGAC
Found at i:3567826 original size:22 final size:22
Alignment explanation
Indices: 3567801--3567842 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
3567791 GTATTTAGTT
3567801 TATTTCTTGT-TTTCAATCAACA
1 TATTT-TTGTATTTCAATCAACA
*
3567823 TATTTTTTTATTTCAATCAA
1 TATTTTTGTATTTCAATCAA
3567843 TCAATTTACT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 3 0.17
22 15 0.83
ACGTcount: A:0.29, C:0.14, G:0.02, T:0.55
Consensus pattern (22 bp):
TATTTTTGTATTTCAATCAACA
Found at i:3573799 original size:12 final size:13
Alignment explanation
Indices: 3573774--3573804 Score: 55
Period size: 12 Copynumber: 2.5 Consensus size: 13
3573764 TGCAAATGTG
3573774 TCATTTCTCATTT
1 TCATTTCTCATTT
3573787 TCATTTC-CATTT
1 TCATTTCTCATTT
3573799 TCATTT
1 TCATTT
3573805 TAAAAAACCT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 11 0.61
13 7 0.39
ACGTcount: A:0.16, C:0.23, G:0.00, T:0.61
Consensus pattern (13 bp):
TCATTTCTCATTT
Found at i:3580223 original size:40 final size:40
Alignment explanation
Indices: 3580163--3580239 Score: 118
Period size: 40 Copynumber: 1.9 Consensus size: 40
3580153 GTCATGCACA
* ** *
3580163 ATGTATCAAATGGTTGCAACATCTTATACATCATTAATCT
1 ATGTACCAAATGGTCACAACATCTCATACATCATTAATCT
3580203 ATGTACCAAATGGTCACAACATCTCATACATCATTAA
1 ATGTACCAAATGGTCACAACATCTCATACATCATTAA
3580240 ACTCAAAAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
40 33 1.00
ACGTcount: A:0.38, C:0.21, G:0.09, T:0.32
Consensus pattern (40 bp):
ATGTACCAAATGGTCACAACATCTCATACATCATTAATCT
Found at i:3581072 original size:37 final size:37
Alignment explanation
Indices: 3581031--3581101 Score: 101
Period size: 37 Copynumber: 1.9 Consensus size: 37
3581021 TTAATTGCTA
3581031 ATAATTTTT-ATAAATTATTCTTTTTC-TAAATTTTTTT
1 ATAATTTTTAATAAATTA-T-TTTTTCATAAATTTTTTT
*
3581068 ATAATTTTTAATAAGTTATTTTTTCATAAATTTT
1 ATAATTTTTAATAAATTATTTTTTCATAAATTTT
3581102 ATACAAATTC
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
36 6 0.19
37 18 0.58
38 7 0.23
ACGTcount: A:0.32, C:0.04, G:0.01, T:0.62
Consensus pattern (37 bp):
ATAATTTTTAATAAATTATTTTTTCATAAATTTTTTT
Found at i:3581291 original size:11 final size:11
Alignment explanation
Indices: 3581275--3581300 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
3581265 TATGCAATTA
3581275 TTTTAAAATAT
1 TTTTAAAATAT
3581286 TTTTAAAATAT
1 TTTTAAAATAT
3581297 TTTT
1 TTTT
3581301 TCCCACATCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (11 bp):
TTTTAAAATAT
Found at i:3581580 original size:7 final size:7
Alignment explanation
Indices: 3581568--3581606 Score: 78
Period size: 7 Copynumber: 5.6 Consensus size: 7
3581558 CTTGTGCTCT
3581568 TTTAAAA
1 TTTAAAA
3581575 TTTAAAA
1 TTTAAAA
3581582 TTTAAAA
1 TTTAAAA
3581589 TTTAAAA
1 TTTAAAA
3581596 TTTAAAA
1 TTTAAAA
3581603 TTTA
1 TTTA
3581607 GTCCTTATAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 32 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (7 bp):
TTTAAAA
Found at i:3581872 original size:33 final size:33
Alignment explanation
Indices: 3581809--3581872 Score: 78
Period size: 34 Copynumber: 1.9 Consensus size: 33
3581799 TTTTTTCATA
*
3581809 TTTTAAATAAAGAAATATAAAAATTTATAAATT
1 TTTTAAATAAAGAAATATAAAAATTAATAAATT
*
3581842 TTTTAAAATAAA-AAATTATGAAAA-TAATAAA
1 TTTT-AAATAAAGAAA-TATAAAAATTAATAAA
3581873 AACACTTTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
33 13 0.48
34 14 0.52
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (33 bp):
TTTTAAATAAAGAAATATAAAAATTAATAAATT
Found at i:3584641 original size:17 final size:17
Alignment explanation
Indices: 3584596--3584656 Score: 56
Period size: 18 Copynumber: 3.6 Consensus size: 17
3584586 TTATTTTTAA
3584596 TTTT-AAATATTTTA-T
1 TTTTAAAATATTTTATT
3584611 TTTTACTAAA-ATTTTATT
1 TTTTA--AAATATTTTATT
*
3584629 TTTTAAAATATTTTCGTT
1 TTTTAAAATATTTT-ATT
*
3584647 TTTTTAAATA
1 TTTTAAAATA
3584657 AGAAAAATAT
Statistics
Matches: 38, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
15 4 0.11
16 3 0.08
17 11 0.29
18 20 0.53
ACGTcount: A:0.33, C:0.03, G:0.02, T:0.62
Consensus pattern (17 bp):
TTTTAAAATATTTTATT
Found at i:3584919 original size:25 final size:25
Alignment explanation
Indices: 3584890--3584945 Score: 76
Period size: 25 Copynumber: 2.2 Consensus size: 25
3584880 TATTTGCTTT
* *
3584890 GAACCGGCTATACTGGTTATTCTAG
1 GAACCAGCTATACTAGTTATTCTAG
* *
3584915 GAACCAGTTGTACTAGTTATTCTAG
1 GAACCAGCTATACTAGTTATTCTAG
3584940 GAACCA
1 GAACCA
3584946 ATTGGTTAGG
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.29, C:0.20, G:0.21, T:0.30
Consensus pattern (25 bp):
GAACCAGCTATACTAGTTATTCTAG
Done.