Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397269.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_12.1, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 5666189
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 144833 characters in sequence are not A, C, G, or T
File 8 of 14
Found at i:2945352 original size:21 final size:22
Alignment explanation
Indices: 2945319--2945359 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
2945309 ACGGCTGAGG
* *
2945319 TGTCTCCTGCGTCTG-CGTATC
1 TGTCGCCTCCGTCTGACGTATC
2945340 TGTCGCCTCCGTCTGACGTA
1 TGTCGCCTCCGTCTGACGTA
2945360 GAAGTGCCTC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.07, C:0.34, G:0.24, T:0.34
Consensus pattern (22 bp):
TGTCGCCTCCGTCTGACGTATC
Found at i:2965932 original size:281 final size:281
Alignment explanation
Indices: 2965429--2965991 Score: 878
Period size: 281 Copynumber: 2.0 Consensus size: 281
2965419 TAAGAAGGCA
* * *
2965429 ACTTTATAATACTAGATACAGGAACTCGTATAACATCTATAGATGCTCATCAAAGGAAAAGAAGA
1 ACTTTATAATACTAGATACAGGAACTCATATAACATCTATACATGCTCATCAAAGGAAAAGAACA
* *
2965494 AACACAATATTTCTATACGCATATCTATACTTAATCAATTGATACAAACTCCCCAAAAATAATTA
66 AACACAATACTTCTATACACATATCTATACTTAATCAATTGATACAAACTCCCCAAAAATAATTA
* *
2965559 CAATAAAAACCCTAGAATGTGGAGAACCAAGGAAAGACAGGTTACACAAACAAAACCCATGTCCT
131 AAATAAAAACCCTAGAATGTGCAGAACCAAGGAAAGACAGGTTACACAAACAAAACCCATGTCCT
* *
2965624 ATGATGCTCACAGACTAGTACCAGGTAACATAAAAAGGTTCTTCAGTTATTTGAAATCTTTCCTA
196 ATAATGCTCACAGACTAGTACCAGGTAACATAAAAAGGTTCTTCAGTTATTTGAAATCTTTCCGA
2965689 AAGAAA-AGTATATTATTTTCC
261 AAGAAACA-TATATTATTTTCC
* * *
2965710 ACTTTATAATACTAGATATAGGAACTCATGTAACATCTATACATGCTCATCAGAGGAAAAGAACA
1 ACTTTATAATACTAGATACAGGAACTCATATAACATCTATACATGCTCATCAAAGGAAAAGAACA
* * * * * * *
2965775 GACACAATACTTCTATGCACATATCTATACTTATTCAATTGATATAAACTTCTCAAAAATTATTA
66 AACACAATACTTCTATACACATATCTATACTTAATCAATTGATACAAACTCCCCAAAAATAATTA
* * *
2965840 AAATAACAACCCTA-AGATGTGCAGAACCAAGGCAAGACAGGTTACACAAACAAAACCCGTGTCC
131 AAATAAAAACCCTAGA-ATGTGCAGAACCAAGGAAAGACAGGTTACACAAACAAAACCCATGTCC
*
2965904 TATAATGCTCACTGACTAGTACCAGGTAACATAAAAAGGTTCTTCAGTTATTTGAAATCTTTCCG
195 TATAATGCTCACAGACTAGTACCAGGTAACATAAAAAGGTTCTTCAGTTATTTGAAATCTTTCCG
*
2965969 AAGGAAACATATATTATTTTCC
260 AAAGAAACATATATTATTTTCC
2965991 A
1 A
2965992 TAGTCCCCAA
Statistics
Matches: 256, Mismatches: 24, Indels: 4
0.90 0.08 0.01
Matches are distributed among these distances:
280 1 0.00
281 254 0.99
282 1 0.00
ACGTcount: A:0.41, C:0.19, G:0.12, T:0.27
Consensus pattern (281 bp):
ACTTTATAATACTAGATACAGGAACTCATATAACATCTATACATGCTCATCAAAGGAAAAGAACA
AACACAATACTTCTATACACATATCTATACTTAATCAATTGATACAAACTCCCCAAAAATAATTA
AAATAAAAACCCTAGAATGTGCAGAACCAAGGAAAGACAGGTTACACAAACAAAACCCATGTCCT
ATAATGCTCACAGACTAGTACCAGGTAACATAAAAAGGTTCTTCAGTTATTTGAAATCTTTCCGA
AAGAAACATATATTATTTTCC
Found at i:2973931 original size:252 final size:252
Alignment explanation
Indices: 2973592--2974663 Score: 1141
Period size: 252 Copynumber: 4.2 Consensus size: 252
2973582 CCAAAAAATT
* * * * * * * **
2973592 TAAATGTAAATGATTAATTTTGAC-AAAAATTATGTTTATTTTGTATGAAA-TGATTTTTTATGG
1 TAAATGAAAATGATTAATTTTCACTTACAA-TATATTTATTTTAT-TTAAATTGATTTTTTACAG
* * *
2973655 TAACTCTCACTCATTTCCATCAATATTTTAACAATATTTATTTTAACTTTATTAATTTTTATGTT
64 TAACTCTCACTCATTTACATCAATATTTTAACAATATTTATTTTAACTTTATTATTTTTTACGTT
* * * *
2973720 TATTATTATAAATTTATATCAAGATTTTT-AATATTTAATTTTTACTACAGTTATTTTTATCTTT
129 CATTCTTATAAATTTATATCAAGATTTTTAAATATTTAATTTTTACTATAATTATTTTTAT-TTT
* *
2973784 ATTATTATTCACATATAAGTTAAAATTTGTAAATGTTTAAATATTTTTTACTCAATAATA
193 ATTATTATTCACATATAAATTAAAATTTGTAAATGGTTAAATATTTTTTACTCAATAATA
* * * *
2973844 TAAATGAAAATAATTAATTTTCACTTA-AAGTTTATTTATTTTGTTTAGATTGATTTTTTATC-G
1 TAAATGAAAATGATTAATTTTCACTTACAA-TATATTTATTTTATTTAAATTGATTTTTTA-CAG
* * *
2973907 TAACTCTCACTAATTTATATCAATATTTTAACAGA-ACTTATTTTAACTTTATTATTTTTTTACG
64 TAACTCTCACTCATTTACATCAATATTTTAACA-ATATTTATTTTAACTTTATTA-TTTTTTACG
* * *
2973971 TTCGTTCTTATAAATTTATGA-CAAAATTTTTAAATGACTT-ATTTTTACTATAATTATTTTTAT
127 TTCATTCTTATAAATTTAT-ATCAAGATTTTTAAAT-ATTTAATTTTTACTATAATTATTTTTAT
* * **
2974034 TCTTATTATTATTCACATATAAGTTAAAATTATTTAAATGGTTAAATATTTTTTACT-TGTGAAT
190 T-TTATTATTATTCACATATAAATTAAAATT-TGTAAATGGTTAAATATTTTTTACTCAAT-AAT
2974098 A
252 A
* * * * *
2974099 TAAATGAAAATGATTAATTTTCACTTACAATATGTTTATTTTATTTATATTAATTTCTTACGGTA
1 TAAATGAAAATGATTAATTTTCACTTACAATATATTTATTTTATTTAAATTGATTTTTTACAGTA
* * * * *
2974164 ACTTTCATTCATTTACGTCAATA-TTTAAAAATGTTTATTTTAACTTTATTATTTTTTACGTTCA
66 ACTCTCACTCATTTACATCAATATTTTAACAATATTTATTTTAACTTTATTATTTTTTACGTTCA
* *
2974228 TTCTTATAAATTTATATCAAGATTTTTAAATAATTAATTTTTATTATAATTATTTTTATCTTTAT
131 TTCTTATAAATTTATATCAAGATTTTTAAATATTTAATTTTTACTATAATTATTTTTAT-TTTAT
* * * *
2974293 TATTACTCACTTATAAATTAAAATTTGTAAATGGTTAAA-CTTTTTTACTCAAGAATA
195 TATTATTCACATATAAATTAAAATTTGTAAATGGTTAAATATTTTTTACTCAATAATA
* * *
2974350 TAAATGAAAATGATTAATTTTCACTTACAATATCTTTATTATATTTAAATTGACTTTTTACAGTA
1 TAAATGAAAATGATTAATTTTCACTTACAATATATTTATTTTATTTAAATTGATTTTTTACAGTA
* * * * * * *
2974415 ATTTTTACTCATTTATATCAATATTTTAACAATGTTTATTTTAACTTTATTATTTTTTACATTTA
66 ACTCTCACTCATTTACATCAATATTTTAACAATATTTATTTTAACTTTATTATTTTTTACGTTCA
* * * *** * * *
2974480 TTCTTATAAATCTATGTTAA-ACTTTTTAAATGGCTAATTTTCATTATAATTATTTATATTTATA
131 TTCTTATAAATTTATATCAAGA-TTTTTAAATATTTAATTTTTACTATAATTATTTTTATTT-TA
** ** * * *
2974544 TTATTATTCATTTATAAATTAAAATTTGTAAATATTTAAATATTTTTAATTTGAA-AATA
194 TTATTATTCACATATAAATTAAAATTTGTAAATGGTTAAATATTTTTTA-CTCAATAATA
* * * * * *
2974603 TAAAT-ATATAT-AATAATTTTTCAC-AAGAATTATATTTATTTTATCTAAATTGACTTTTTAC
1 TAAATGA-AAATGATTAA-TTTTCACTTACAA-TATATTTATTTTATTTAAATTGATTTTTTAC
2974664 CTCAATATTT
Statistics
Matches: 702, Mismatches: 92, Indels: 51
0.83 0.11 0.06
Matches are distributed among these distances:
251 95 0.14
252 244 0.35
253 177 0.25
254 83 0.12
255 101 0.14
256 2 0.00
ACGTcount: A:0.36, C:0.08, G:0.05, T:0.51
Consensus pattern (252 bp):
TAAATGAAAATGATTAATTTTCACTTACAATATATTTATTTTATTTAAATTGATTTTTTACAGTA
ACTCTCACTCATTTACATCAATATTTTAACAATATTTATTTTAACTTTATTATTTTTTACGTTCA
TTCTTATAAATTTATATCAAGATTTTTAAATATTTAATTTTTACTATAATTATTTTTATTTTATT
ATTATTCACATATAAATTAAAATTTGTAAATGGTTAAATATTTTTTACTCAATAATA
Found at i:2974269 original size:15 final size:15
Alignment explanation
Indices: 2974249--2974286 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
2974239 TTATATCAAG
2974249 ATTTTTA-AATAATT
1 ATTTTTATAATAATT
*
2974263 AATTTTTATTATAATT
1 -ATTTTTATAATAATT
2974279 ATTTTTAT
1 ATTTTTAT
2974287 CTTTATTATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 15 0.71
16 6 0.29
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (15 bp):
ATTTTTATAATAATT
Found at i:2989198 original size:20 final size:21
Alignment explanation
Indices: 2989164--2989205 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
2989154 TTGTATTAAG
2989164 AATATCTAAAGAATTAA-GAA
1 AATATCTAAAGAATTAATGAA
**
2989184 AATATCTAATTAATTAATGAA
1 AATATCTAAAGAATTAATGAA
2989205 A
1 A
2989206 GAAATATTCA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 15 0.79
21 4 0.21
ACGTcount: A:0.57, C:0.05, G:0.07, T:0.31
Consensus pattern (21 bp):
AATATCTAAAGAATTAATGAA
Found at i:2995095 original size:210 final size:215
Alignment explanation
Indices: 2994722--2995130 Score: 530
Period size: 210 Copynumber: 1.9 Consensus size: 215
2994712 TCAGAAGGGG
* * * *
2994722 TAAAAATCAATTTTACAATTTAGATCTATATCAGATTAATACTAAAACAAAAAAAAAGATTGATT
1 TAAAAATCAATTTAACAATTCAGATCAATACCAGATTAATACTAAAAC-AAAAAAAAGATTGATT
* * **
2994787 AAGTTTGATAGGGTGTAAACAATTTTTTTACTCGATTTAATATGAGAACTGAAATAGTCCAAAAC
65 AAGTTTGATAGGGTGAAAACAATTTGTTTACTCGACCTAATATGAGAACTGAAATAGTCCAAAAC
* * *
2994852 AATGTGACCCTTGTCACTGCTTGTTGCAATTTTTTCCTACTTGCAAAA-CCAAATAATAA-AA-A
130 AATGTGACCCTTGCCACTACTTGTTGCAATTTTTTCCTACCTGCAAAAGCCAAATAATAATAATA
2994914 AAAATCATGAGTCAAATTGGC
195 AAAATCATGAGTCAAATTGGC
* * *
2994935 TAAAAATCTATTTAACCATTCAGATCAATACCAGATTAATGCTAAAAC-AAAAAAA-ATTGATTA
1 TAAAAATCAATTTAACAATTCAGATCAATACCAGATTAATACTAAAACAAAAAAAAGATTGATTA
* *
2994998 AGTTTGATGGGGTGAAAACAATTTGTTTACTCGACCTAATAT-AGGAACT-AAATTGGTCCAAAA
66 AGTTTGATAGGGTGAAAACAATTTGTTTACTCGACCTAATATGA-GAACTGAAA-TAGTCCAAAA
* * * *
2995061 CAATGTG-CTTCTTGCCATTACTTGTT-CGAATTTTTTCTTACCTGCAAAAGCTAAATAATAATA
129 CAATGTGAC-CCTTGCCACTACTTGTTGC-AATTTTTTCCTACCTGCAAAAGCCAAATAATAATA
2995124 ATAAAAA
192 ATAAAAA
2995131 AGAAAACAAT
Statistics
Matches: 169, Mismatches: 20, Indels: 14
0.83 0.10 0.07
Matches are distributed among these distances:
209 6 0.04
210 98 0.58
211 17 0.10
212 2 0.01
213 46 0.27
ACGTcount: A:0.41, C:0.14, G:0.12, T:0.32
Consensus pattern (215 bp):
TAAAAATCAATTTAACAATTCAGATCAATACCAGATTAATACTAAAACAAAAAAAAGATTGATTA
AGTTTGATAGGGTGAAAACAATTTGTTTACTCGACCTAATATGAGAACTGAAATAGTCCAAAACA
ATGTGACCCTTGCCACTACTTGTTGCAATTTTTTCCTACCTGCAAAAGCCAAATAATAATAATAA
AAATCATGAGTCAAATTGGC
Found at i:2996205 original size:4 final size:4
Alignment explanation
Indices: 2996196--2996256 Score: 59
Period size: 4 Copynumber: 15.2 Consensus size: 4
2996186 CATTCACTTA
* * * * * * *
2996196 ATAT ATAT ATAT ATAT ATAT ATAC ATAC ATAC ATAC ACAT ACAT ACAT
1 ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT
2996244 ATAT ATAT ATAT A
1 ATAT ATAT ATAT A
2996257 CACACATGAT
Statistics
Matches: 53, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 53 1.00
ACGTcount: A:0.51, C:0.11, G:0.00, T:0.38
Consensus pattern (4 bp):
ATAT
Found at i:2996211 original size:10 final size:10
Alignment explanation
Indices: 2996196--2996256 Score: 59
Period size: 10 Copynumber: 6.1 Consensus size: 10
2996186 CATTCACTTA
2996196 ATATATATAT
1 ATATATATAT
2996206 ATATATATAT
1 ATATATATAT
* *
2996216 ATACATACAT
1 ATATATATAT
* * *
2996226 ACATACACAT
1 ATATATATAT
* *
2996236 ACATACATAT
1 ATATATATAT
2996246 ATATATATAT
1 ATATATATAT
2996256 A
1 A
2996257 CACACATGAT
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
10 43 1.00
ACGTcount: A:0.51, C:0.11, G:0.00, T:0.38
Consensus pattern (10 bp):
ATATATATAT
Found at i:2996909 original size:15 final size:15
Alignment explanation
Indices: 2996891--2996920 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
2996881 AGGAAGAAAG
*
2996891 AAAGACAAAAGAGAA
1 AAAGAAAAAAGAGAA
2996906 AAAGAAAAAAGAGAA
1 AAAGAAAAAAGAGAA
2996921 TAAAATGCAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.77, C:0.03, G:0.20, T:0.00
Consensus pattern (15 bp):
AAAGAAAAAAGAGAA
Found at i:3014856 original size:30 final size:30
Alignment explanation
Indices: 3014791--3014865 Score: 80
Period size: 31 Copynumber: 2.5 Consensus size: 30
3014781 GGGTTAGGGT
* *
3014791 AGGGTTAGGTAGTAAAACTACTACATTTCA
1 AGGGTTAGATAGTAAAACTACTACATGTCA
* *
3014821 TGGGTTATGATAGTAAAACTACTACCTGT-A
1 AGGGTTA-GATAGTAAAACTACTACATGTCA
*
3014851 AGGGTTCGAGTAGTA
1 AGGGTTAGA-TAGTA
3014866 GTCTTAGGGA
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
29 2 0.05
30 17 0.46
31 18 0.49
ACGTcount: A:0.33, C:0.12, G:0.24, T:0.31
Consensus pattern (30 bp):
AGGGTTAGATAGTAAAACTACTACATGTCA
Found at i:3016268 original size:1 final size:1
Alignment explanation
Indices: 3016264--3016289 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
3016254 ATTGGGTGCC
3016264 GGGGGGGGGGGGGGGGGGGGGGGGGG
1 GGGGGGGGGGGGGGGGGGGGGGGGGG
3016290 AGGTGCTGAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:0.00, C:0.00, G:1.00, T:0.00
Consensus pattern (1 bp):
G
Found at i:3018254 original size:55 final size:55
Alignment explanation
Indices: 3018188--3018297 Score: 220
Period size: 55 Copynumber: 2.0 Consensus size: 55
3018178 ATATTCAATA
3018188 ATACACATTAATATACTCATAACTGATATTATCATTATTGTTGTTGGAGGTTCTG
1 ATACACATTAATATACTCATAACTGATATTATCATTATTGTTGTTGGAGGTTCTG
3018243 ATACACATTAATATACTCATAACTGATATTATCATTATTGTTGTTGGAGGTTCTG
1 ATACACATTAATATACTCATAACTGATATTATCATTATTGTTGTTGGAGGTTCTG
3018298 CTGCTTGTTT
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
55 55 1.00
ACGTcount: A:0.31, C:0.13, G:0.15, T:0.42
Consensus pattern (55 bp):
ATACACATTAATATACTCATAACTGATATTATCATTATTGTTGTTGGAGGTTCTG
Found at i:3029730 original size:2 final size:2
Alignment explanation
Indices: 3029725--3029752 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
3029715 TTCTTCTTCT
3029725 TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC
3029753 AGAAGATGGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:3030704 original size:34 final size:34
Alignment explanation
Indices: 3030666--3030733 Score: 118
Period size: 34 Copynumber: 2.0 Consensus size: 34
3030656 ACTAATGTAG
* *
3030666 GGTGAATTTTGTTGTGATTTCATTATATTGTCAA
1 GGTGAATTTTGTTGTGATGTCAGTATATTGTCAA
3030700 GGTGAATTTTGTTGTGATGTCAGTATATTGTCAA
1 GGTGAATTTTGTTGTGATGTCAGTATATTGTCAA
3030734 TCTAGTTATT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 32 1.00
ACGTcount: A:0.24, C:0.06, G:0.24, T:0.47
Consensus pattern (34 bp):
GGTGAATTTTGTTGTGATGTCAGTATATTGTCAA
Found at i:3034026 original size:18 final size:18
Alignment explanation
Indices: 3034003--3034044 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 18
3033993 TTGGTTTTCT
3034003 TTGTTTTGTTCTAATTGG
1 TTGTTTTGTTCTAATTGG
* * *
3034021 TTG-TTTGTTTTCATTTG
1 TTGTTTTGTTCTAATTGG
3034038 TTGTTTT
1 TTGTTTT
3034045 TGTATCATGT
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
17 14 0.70
18 6 0.30
ACGTcount: A:0.07, C:0.05, G:0.19, T:0.69
Consensus pattern (18 bp):
TTGTTTTGTTCTAATTGG
Found at i:3035377 original size:22 final size:20
Alignment explanation
Indices: 3035335--3035389 Score: 67
Period size: 22 Copynumber: 2.6 Consensus size: 20
3035325 TATATAACTA
*
3035335 TAATTAATAATTAATTTTAT
1 TAATTATTAATTAATTTTAT
3035355 TAATTATTAACTTAATTTTTAT
1 TAATTATTAA-TTAA-TTTTAT
3035377 T-ATATATTAATTA
1 TAAT-TATTAATTA
3035390 TAATTAGTTA
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
20 9 0.29
21 9 0.29
22 13 0.42
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (20 bp):
TAATTATTAATTAATTTTAT
Found at i:3038646 original size:21 final size:21
Alignment explanation
Indices: 3038620--3038665 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
3038610 CTCTTAAAGT
*
3038620 AATTTAAAATAAAATAGCATA
1 AATTTAAAATAAAATAACATA
* *
3038641 AATTTAAACTAAAATAACTTA
1 AATTTAAAATAAAATAACATA
3038662 AATT
1 AATT
3038666 AGTTGCTCAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.59, C:0.07, G:0.02, T:0.33
Consensus pattern (21 bp):
AATTTAAAATAAAATAACATA
Found at i:3043538 original size:30 final size:30
Alignment explanation
Indices: 3043463--3043566 Score: 106
Period size: 30 Copynumber: 3.5 Consensus size: 30
3043453 AAAAAAAATT
* * *
3043463 AAATAAGCTCTTATACTTTAATTATG-ATC
1 AAATAAGCTCTTATATTTTTATTTTGAATC
* * * *
3043492 -AATCAAGTTTTTATATTTTTATTTTGAGTT
1 AAAT-AAGCTCTTATATTTTTATTTTGAATC
3043522 AAATAAG-TCATTATATTTTTATTTTGAATC
1 AAATAAGCTC-TTATATTTTTATTTTGAATC
3043552 AAATAAGCTCTTATA
1 AAATAAGCTCTTATA
3043567 ATTAATGATT
Statistics
Matches: 60, Mismatches: 10, Indels: 9
0.76 0.13 0.11
Matches are distributed among these distances:
28 3 0.05
29 18 0.30
30 34 0.57
31 5 0.08
ACGTcount: A:0.36, C:0.09, G:0.08, T:0.48
Consensus pattern (30 bp):
AAATAAGCTCTTATATTTTTATTTTGAATC
Found at i:3047187 original size:26 final size:26
Alignment explanation
Indices: 3047149--3047211 Score: 67
Period size: 26 Copynumber: 2.4 Consensus size: 26
3047139 AAAAAATAAA
3047149 AAATTATTTTGTTGTTATGTTTAATT-
1 AAATTATTTTGTTGTTAT-TTTAATTC
* *
3047175 AAATT-TTTGTGTTTTTATTTTTATTC
1 AAATTATTT-TGTTGTTATTTTAATTC
3047201 AAATTAATTTT
1 AAATT-ATTTT
3047212 TATAATTAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
25 9 0.29
26 18 0.58
27 1 0.03
28 3 0.10
ACGTcount: A:0.27, C:0.02, G:0.08, T:0.63
Consensus pattern (26 bp):
AAATTATTTTGTTGTTATTTTAATTC
Found at i:3047227 original size:20 final size:20
Alignment explanation
Indices: 3047202--3047241 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
3047192 TTTTTATTCA
*
3047202 AATTAATTTTTATAATTAAT
1 AATTAATTATTATAATTAAT
*
3047222 AATTAATTATTATTATTAAT
1 AATTAATTATTATAATTAAT
3047242 TAAAATATCA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (20 bp):
AATTAATTATTATAATTAAT
Found at i:3047231 original size:17 final size:17
Alignment explanation
Indices: 3047211--3047244 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
3047201 AAATTAATTT
3047211 TTATAATTAATAATTAA
1 TTATAATTAATAATTAA
* *
3047228 TTATTATTATTAATTAA
1 TTATAATTAATAATTAA
3047245 AATATCACTT
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:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
TTATAATTAATAATTAA
Found at i:3059705 original size:6 final size:6
Alignment explanation
Indices: 3059694--3059727 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
3059684 CTTGAGCCCA
* *
3059694 AACCAG AACCAG ACCCAG AACCAG AACCCG AACC
1 AACCAG AACCAG AACCAG AACCAG AACCAG AACC
3059728 CGGCTCGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.44, C:0.41, G:0.15, T:0.00
Consensus pattern (6 bp):
AACCAG
Found at i:3062698 original size:28 final size:28
Alignment explanation
Indices: 3062653--3062721 Score: 84
Period size: 28 Copynumber: 2.4 Consensus size: 28
3062643 TAAATAATAA
* *
3062653 AAACATATAACAAATAAATAAATTACACC
1 AAACATA-AATAAGTAAATAAATTACACC
* * *
3062682 AAATATAAATAAGTAAATACATTACATC
1 AAACATAAATAAGTAAATAAATTACACC
3062710 AAACATAAATAA
1 AAACATAAATAA
3062722 AATTTTAAAT
Statistics
Matches: 34, Mismatches: 6, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
28 28 0.82
29 6 0.18
ACGTcount: A:0.62, C:0.13, G:0.01, T:0.23
Consensus pattern (28 bp):
AAACATAAATAAGTAAATAAATTACACC
Found at i:3062791 original size:3 final size:3
Alignment explanation
Indices: 3062783--3062821 Score: 55
Period size: 3 Copynumber: 13.3 Consensus size: 3
3062773 ACATAACTAC
3062783 ATA ATA ATA A-A ATA ATA ATA ATA ATA A-A ATA ATA GATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA -ATA A
3062822 ATAAAAGGAA
Statistics
Matches: 33, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
2 4 0.12
3 26 0.79
4 3 0.09
ACGTcount: A:0.69, C:0.00, G:0.03, T:0.28
Consensus pattern (3 bp):
ATA
Found at i:3062805 original size:17 final size:18
Alignment explanation
Indices: 3062783--3062821 Score: 71
Period size: 17 Copynumber: 2.2 Consensus size: 18
3062773 ACATAACTAC
3062783 ATAATAATAAAATAATA-
1 ATAATAATAAAATAATAG
3062800 ATAATAATAAAATAATAG
1 ATAATAATAAAATAATAG
3062818 ATAA
1 ATAA
3062822 ATAAAAGGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 17 0.81
18 4 0.19
ACGTcount: A:0.69, C:0.00, G:0.03, T:0.28
Consensus pattern (18 bp):
ATAATAATAAAATAATAG
Found at i:3065453 original size:12 final size:12
Alignment explanation
Indices: 3065398--3065459 Score: 79
Period size: 12 Copynumber: 5.2 Consensus size: 12
3065388 GTTTTTCATA
*
3065398 TATATATATATA
1 TATATATATATG
*
3065410 TATATATATATA
1 TATATATATATG
3065422 TATATATATATG
1 TATATATATATG
* *
3065434 TATGTATGTATG
1 TATATATATATG
*
3065446 TATATATGTATG
1 TATATATATATG
3065458 TA
1 TA
3065460 CGCATATATA
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 46 1.00
ACGTcount: A:0.40, C:0.00, G:0.10, T:0.50
Consensus pattern (12 bp):
TATATATATATG
Found at i:3065457 original size:4 final size:4
Alignment explanation
Indices: 3065430--3065459 Score: 51
Period size: 4 Copynumber: 7.5 Consensus size: 4
3065420 TATATATATA
*
3065430 TATG TATG TATG TATG TATA TATG TATG TA
1 TATG TATG TATG TATG TATG TATG TATG TA
3065460 CGCATATATA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.30, C:0.00, G:0.20, T:0.50
Consensus pattern (4 bp):
TATG
Found at i:3065466 original size:16 final size:16
Alignment explanation
Indices: 3065434--3065468 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
3065424 TATATATATG
* *
3065434 TATGTATGTATGTATA
1 TATGTATGTACGCATA
3065450 TATGTATGTACGCATA
1 TATGTATGTACGCATA
3065466 TAT
1 TAT
3065469 ATATAGCAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.31, C:0.06, G:0.17, T:0.46
Consensus pattern (16 bp):
TATGTATGTACGCATA
Found at i:3065469 original size:20 final size:20
Alignment explanation
Indices: 3065423--3065472 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
3065413 ATATATATAT
* *
3065423 ATATATATATGTATGTATGT
1 ATATATATATGTATGTACGC
*
3065443 ATGTATATATGTATGTACGC
1 ATATATATATGTATGTACGC
3065463 ATATATATAT
1 ATATATATAT
3065473 AGCAATTAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.36, C:0.04, G:0.14, T:0.46
Consensus pattern (20 bp):
ATATATATATGTATGTACGC
Found at i:3065472 original size:4 final size:4
Alignment explanation
Indices: 3065395--3065452 Score: 80
Period size: 4 Copynumber: 14.5 Consensus size: 4
3065385 TTTGTTTTTC
* * *
3065395 ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATGT ATGT ATGT
1 ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT
*
3065443 ATGT ATAT AT
1 ATAT ATAT AT
3065453 GTATGTACGC
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
4 52 1.00
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (4 bp):
ATAT
Found at i:3069499 original size:2 final size:2
Alignment explanation
Indices: 3069492--3069525 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
3069482 AATAGGAAAC
3069492 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3069526 CACCTTTAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3070069 original size:49 final size:49
Alignment explanation
Indices: 3069807--3070060 Score: 368
Period size: 49 Copynumber: 5.2 Consensus size: 49
3069797 TCGCTTAATC
* ** *
3069807 TTCGCTTCAAGGGTCTTCACGACTTGACCTTGATCACAAATACTTGATT
1 TTCGCTTCAAGGGTCTTCACGACTTGATCTTGATCATGAACACTTGATT
* *
3069856 GTCGCTTCAAGGTTCTTCACGACTTGATCTTGATCAT-AAGCACTTGATCT
1 TTCGCTTCAAGGGTCTTCACGACTTGATCTTGATCATGAA-CACTTGAT-T
* * *
3069906 AT-GCTTCAAAGGTCTTCACGACTTGATCTTGATCACGAACACTTGATT
1 TTCGCTTCAAGGGTCTTCACGACTTGATCTTGATCATGAACACTTGATT
*
3069954 TTTGCTTCAAGGGTCTTCACGACTTGATCTTGATCATGAACACTTGATT
1 TTCGCTTCAAGGGTCTTCACGACTTGATCTTGATCATGAACACTTGATT
*
3070003 TTCGCTTCAAGGGTCTTTACGACTTGATCTTGATCATGAACACTTGATT
1 TTCGCTTCAAGGGTCTTCACGACTTGATCTTGATCATGAACACTTGATT
*
3070052 TTCACTTCA
1 TTCGCTTCA
3070061 GAAATCTTTT
Statistics
Matches: 186, Mismatches: 15, Indels: 8
0.89 0.07 0.04
Matches are distributed among these distances:
48 4 0.02
49 178 0.96
50 4 0.02
ACGTcount: A:0.24, C:0.23, G:0.17, T:0.37
Consensus pattern (49 bp):
TTCGCTTCAAGGGTCTTCACGACTTGATCTTGATCATGAACACTTGATT
Found at i:3071858 original size:13 final size:14
Alignment explanation
Indices: 3071839--3071873 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
3071829 ATTGCCATGA
*
3071839 TTTTTTTATTGCAC
1 TTTTTTTATTGAAC
3071853 TTTTTTTATTGAA-
1 TTTTTTTATTGAAC
3071866 TTTTTTTA
1 TTTTTTTA
3071874 AAATTGTTGT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 8 0.40
14 12 0.60
ACGTcount: A:0.17, C:0.06, G:0.06, T:0.71
Consensus pattern (14 bp):
TTTTTTTATTGAAC
Found at i:3072048 original size:40 final size:39
Alignment explanation
Indices: 3071992--3072128 Score: 127
Period size: 40 Copynumber: 3.5 Consensus size: 39
3071982 AACTTAAAGT
*
3071992 GGTGCTCTTTATAATAGCACGTGATTTGTTATCCTCAGAG
1 GGTGCTCTTTATAATAGCAC-TAATTTGTTATCCTCAGAG
* * * * ** *
3072032 AGTGCTCTTTATAATAGTACTTA-TTG--ATCATTGGGG
1 GGTGCTCTTTATAATAGCACTAATTTGTTATCCTCAGAG
* * * *
3072068 GGTGTTTTTTAAAATAGCACATAATTTATTATCCTCAGAG
1 GGTGCTCTTTATAATAGCAC-TAATTTGTTATCCTCAGAG
3072108 GGTGCTCTTTATAATAGCACT
1 GGTGCTCTTTATAATAGCACT
3072129 TGTTGATCCT
Statistics
Matches: 72, Mismatches: 21, Indels: 9
0.71 0.21 0.09
Matches are distributed among these distances:
36 21 0.29
37 2 0.03
38 5 0.07
39 3 0.04
40 41 0.57
ACGTcount: A:0.26, C:0.15, G:0.20, T:0.39
Consensus pattern (39 bp):
GGTGCTCTTTATAATAGCACTAATTTGTTATCCTCAGAG
Found at i:3072135 original size:76 final size:76
Alignment explanation
Indices: 3071999--3072247 Score: 318
Period size: 76 Copynumber: 3.3 Consensus size: 76
3071989 AGTGGTGCTC
*** * * * * *
3071999 TTTATAATAGCACGTGATTTGTTATCCTCAGAGAGTGCTCTTTATAATAGTACTTATTGATCATT
1 TTTATAATAGCACACAATTTATTATCCTCAGAGGGTGCTCTTTATAATAGCACTTGTTGATCCTT
*
3072064 GGGGGGTGTTT
66 GGGAGGTGTTT
* *
3072075 TTTAAAATAGCACATAATTTATTATCCTCAGAGGGTGCTCTTTATAATAGCACTTGTTGATCCTT
1 TTTATAATAGCACACAATTTATTATCCTCAGAGGGTGCTCTTTATAATAGCACTTGTTGATCCTT
* *
3072140 GGGACGTGCTT
66 GGGAGGTGTTT
* * ** *
3072151 TTTGTACTAGCACACAATTTATTATCCTTGGAGGGTGCTCTTTATAATAGCAATTGTTGATCCTT
1 TTTATAATAGCACACAATTTATTATCCTCAGAGGGTGCTCTTTATAATAGCACTTGTTGATCCTT
*
3072216 GGGAGGTGTTC
66 GGGAGGTGTTT
*
3072227 TTTATACTAGCACACAATTTA
1 TTTATAATAGCACACAATTTA
3072248 GAATCACCAC
Statistics
Matches: 151, Mismatches: 22, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
76 151 1.00
ACGTcount: A:0.25, C:0.15, G:0.20, T:0.40
Consensus pattern (76 bp):
TTTATAATAGCACACAATTTATTATCCTCAGAGGGTGCTCTTTATAATAGCACTTGTTGATCCTT
GGGAGGTGTTT
Found at i:3072202 original size:40 final size:40
Alignment explanation
Indices: 3071992--3072247 Score: 132
Period size: 36 Copynumber: 6.7 Consensus size: 40
3071982 AACTTAAAGT
*** * **
3071992 GGTGCTCTTTATAATAGCACGTGATTTGTTATCCTCAGAG
1 GGTGCTCTTTATAATAGCACACAATTTATTATCCTTGGAG
* * * *
3072032 AGTGCTCTTTATAATAG--TAC---TTATTGATCATTGGGG
1 GGTGCTCTTTATAATAGCACACAATTTATT-ATCCTTGGAG
* * * * **
3072068 GGTGTTTTTTAAAATAGCACATAATTTATTATCCTCAGAG
1 GGTGCTCTTTATAATAGCACACAATTTATTATCCTTGGAG
*
3072108 GGTGCTCTTTATAATAG--CAC--TTGT-TGATCCTTGG-G
1 GGTGCTCTTTATAATAGCACACAATT-TATTATCCTTGGAG
* * * *
3072143 ACGTGCTTTTTGTACTAGCACACAATTTATTATCCTTGGAG
1 -GGTGCTCTTTATAATAGCACACAATTTATTATCCTTGGAG
*
3072184 GGTGCTCTTTATAATAG----CAATTGT-TGATCCTTGG-G
1 GGTGCTCTTTATAATAGCACACAATT-TATTATCCTTGGAG
* *
3072219 AGGTGTTCTTTATACTAGCACACAATTTA
1 -GGTGCTCTTTATAATAGCACACAATTTA
3072248 GAATCACCAC
Statistics
Matches: 157, Mismatches: 38, Indels: 42
0.66 0.16 0.18
Matches are distributed among these distances:
35 6 0.04
36 70 0.45
37 2 0.01
38 6 0.04
39 2 0.01
40 65 0.41
41 6 0.04
ACGTcount: A:0.25, C:0.16, G:0.20, T:0.39
Consensus pattern (40 bp):
GGTGCTCTTTATAATAGCACACAATTTATTATCCTTGGAG
Found at i:3077422 original size:11 final size:11
Alignment explanation
Indices: 3077406--3077437 Score: 64
Period size: 11 Copynumber: 2.9 Consensus size: 11
3077396 ACAAACTACT
3077406 TCACCATAAGA
1 TCACCATAAGA
3077417 TCACCATAAGA
1 TCACCATAAGA
3077428 TCACCATAAG
1 TCACCATAAG
3077438 TGCCAGCATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.44, C:0.28, G:0.09, T:0.19
Consensus pattern (11 bp):
TCACCATAAGA
Found at i:3078585 original size:2 final size:2
Alignment explanation
Indices: 3078578--3078602 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3078568 CATATTAAGA
3078578 TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG T
3078603 AACCTTAGGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:3083511 original size:22 final size:22
Alignment explanation
Indices: 3083486--3083545 Score: 102
Period size: 22 Copynumber: 2.7 Consensus size: 22
3083476 CTAGTGAGAT
*
3083486 AAAAAACCATATATTTATATTC
1 AAAAAACCATATATTTATATTA
*
3083508 AAAAAACCATATATTTCTATTA
1 AAAAAACCATATATTTATATTA
3083530 AAAAAACCATATATTT
1 AAAAAACCATATATTT
3083546 TCGAAAAAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 36 1.00
ACGTcount: A:0.52, C:0.13, G:0.00, T:0.35
Consensus pattern (22 bp):
AAAAAACCATATATTTATATTA
Found at i:3083554 original size:22 final size:22
Alignment explanation
Indices: 3083486--3083556 Score: 72
Period size: 22 Copynumber: 3.2 Consensus size: 22
3083476 CTAGTGAGAT
** **
3083486 AAAAAACCATATATTTATATTC
1 AAAAAACCATATATTTCGATAA
* *
3083508 AAAAAACCATATATTTCTATTA
1 AAAAAACCATATATTTCGATAA
3083530 AAAAAACCATATATTTTCGA-AA
1 AAAAAACCATATA-TTTCGATAA
3083552 AAAAA
1 AAAAA
3083557 GAAAAGAGCA
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
22 39 0.89
23 5 0.11
ACGTcount: A:0.55, C:0.13, G:0.01, T:0.31
Consensus pattern (22 bp):
AAAAAACCATATATTTCGATAA
Found at i:3099256 original size:17 final size:17
Alignment explanation
Indices: 3099234--3099268 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
3099224 GGCATCTGGG
*
3099234 TAAGCTTTTCTCAGTTT
1 TAAGCTTTTCCCAGTTT
3099251 TAAGCTTTTCCCAGTTT
1 TAAGCTTTTCCCAGTTT
3099268 T
1 T
3099269 TGTCTAATAG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.17, C:0.20, G:0.11, T:0.51
Consensus pattern (17 bp):
TAAGCTTTTCCCAGTTT
Found at i:3106312 original size:22 final size:22
Alignment explanation
Indices: 3106287--3106333 Score: 85
Period size: 22 Copynumber: 2.1 Consensus size: 22
3106277 TGGGTGAACA
3106287 ATGTGTTCAGAATTCACCTAAG
1 ATGTGTTCAGAATTCACCTAAG
*
3106309 ATGTGTTCAGAATTTACCTAAG
1 ATGTGTTCAGAATTCACCTAAG
3106331 ATG
1 ATG
3106334 ACTTCGAATT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.32, C:0.15, G:0.19, T:0.34
Consensus pattern (22 bp):
ATGTGTTCAGAATTCACCTAAG
Found at i:3113102 original size:23 final size:21
Alignment explanation
Indices: 3113068--3113114 Score: 51
Period size: 21 Copynumber: 2.1 Consensus size: 21
3113058 TTAAATGTAA
3113068 TAAAAATATTTATATAAATTTTT
1 TAAAAATATTTA-A-AAATTTTT
*
3113091 TAAAAA-AGTTTAAGAATTTTT
1 TAAAAATA-TTTAAAAATTTTT
3113112 TAA
1 TAA
3113115 GATAAAAATT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
21 10 0.45
22 2 0.09
23 10 0.45
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.47
Consensus pattern (21 bp):
TAAAAATATTTAAAAATTTTT
Found at i:3113126 original size:23 final size:21
Alignment explanation
Indices: 3113084--3113126 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
3113074 TATTTATATA
**
3113084 AATTTTTTAAAAAAGTTTAAG
1 AATTTTTTAAAAAAAATTAAG
3113105 AATTTTTTAAGATAAAAATTAA
1 AATTTTTTAA-A-AAAAATTAA
3113127 ATAAAAAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 10 0.56
22 1 0.06
23 7 0.39
ACGTcount: A:0.51, C:0.00, G:0.07, T:0.42
Consensus pattern (21 bp):
AATTTTTTAAAAAAAATTAAG
Found at i:3116247 original size:30 final size:30
Alignment explanation
Indices: 3116197--3116276 Score: 83
Period size: 31 Copynumber: 2.6 Consensus size: 30
3116187 TTTGGTTCAA
* *
3116197 TTTTTTTC-ATTTAGTCTTCAT-ACTTTATATT
1 TTTTTTTCAATTTAG--TTCATAACTATATA-C
3116228 TTTTTTTCAATTTAGTTCATGAACTATATAC
1 TTTTTTTCAATTTAGTTCAT-AACTATATAC
*
3116259 TTTTATTCAATTTAGTTC
1 TTTTTTTCAATTTAGTTC
3116277 TTATGATGTT
Statistics
Matches: 43, Mismatches: 3, Indels: 6
0.83 0.06 0.12
Matches are distributed among these distances:
30 5 0.12
31 25 0.58
32 13 0.30
ACGTcount: A:0.24, C:0.12, G:0.05, T:0.59
Consensus pattern (30 bp):
TTTTTTTCAATTTAGTTCATAACTATATAC
Found at i:3117465 original size:25 final size:25
Alignment explanation
Indices: 3117435--3117487 Score: 97
Period size: 25 Copynumber: 2.1 Consensus size: 25
3117425 ATGTTTTCAT
3117435 AATCTTCAAGCTTCAAAAAGATTTC
1 AATCTTCAAGCTTCAAAAAGATTTC
*
3117460 AATCTTTAAGCTTCAAAAAGATTTC
1 AATCTTCAAGCTTCAAAAAGATTTC
3117485 AAT
1 AAT
3117488 GATTAGGTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.42, C:0.17, G:0.08, T:0.34
Consensus pattern (25 bp):
AATCTTCAAGCTTCAAAAAGATTTC
Found at i:3117740 original size:53 final size:53
Alignment explanation
Indices: 3117660--3117763 Score: 154
Period size: 53 Copynumber: 2.0 Consensus size: 53
3117650 ATGAAAAACC
* *
3117660 ATGAATGTCCATTCCCTGAAGTAAATGTGACAAATGAGCTACTAATAAAAATT
1 ATGAATGTCCATTCCCTGAAGTAAATGTGACAAACGAGATACTAATAAAAATT
* * * *
3117713 ATGAATGTTCATTCCTTGTAGTGAATGTGACAAACGAGATACTAATAAAAA
1 ATGAATGTCCATTCCCTGAAGTAAATGTGACAAACGAGATACTAATAAAAA
3117764 AATTATAAAT
Statistics
Matches: 45, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
53 45 1.00
ACGTcount: A:0.41, C:0.13, G:0.16, T:0.29
Consensus pattern (53 bp):
ATGAATGTCCATTCCCTGAAGTAAATGTGACAAACGAGATACTAATAAAAATT
Found at i:3117777 original size:53 final size:53
Alignment explanation
Indices: 3117660--3117791 Score: 138
Period size: 53 Copynumber: 2.4 Consensus size: 53
3117650 ATGAAAAACC
* * * *
3117660 ATGAATGTCCATTCCCTGAAGTAAATGTGACAAATGAGCTACTAATAAAAATT
1 ATGAATATTCATTCCCTGAAGTAAATGTGACAAACGAGATACTAATAAAAATT
* * * *
3117713 ATGAATGTTCATTCCTTGTAGTGAATGTGACAAACGAGATACTAATAAAAAAATT
1 ATGAATATTCATTCCCTGAAGTAAATGTGACAAACGAGATACTAAT--AAAAATT
* *
3117768 ATAAATTCATTCATTCACTGAAGT
1 ATGAA-T-ATTCATTCCCTGAAGT
3117792 GAATACGAGA
Statistics
Matches: 64, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
53 40 0.62
55 11 0.17
56 1 0.02
57 12 0.19
ACGTcount: A:0.41, C:0.14, G:0.14, T:0.31
Consensus pattern (53 bp):
ATGAATATTCATTCCCTGAAGTAAATGTGACAAACGAGATACTAATAAAAATT
Found at i:3118548 original size:13 final size:13
Alignment explanation
Indices: 3118497--3118549 Score: 58
Period size: 13 Copynumber: 4.3 Consensus size: 13
3118487 AGATGCTTTA
*
3118497 ATATGTTTTCATT
1 ATATGTTTTAATT
* *
3118510 ATA--TTTAAATG
1 ATATGTTTTAATT
3118521 ATATGTTTT-ATT
1 ATATGTTTTAATT
3118533 ATATGTTTTAATT
1 ATATGTTTTAATT
3118546 ATAT
1 ATAT
3118550 ATTTAATATT
Statistics
Matches: 32, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
11 8 0.25
12 11 0.34
13 13 0.41
ACGTcount: A:0.32, C:0.02, G:0.08, T:0.58
Consensus pattern (13 bp):
ATATGTTTTAATT
Found at i:3119487 original size:24 final size:24
Alignment explanation
Indices: 3119460--3119512 Score: 97
Period size: 24 Copynumber: 2.2 Consensus size: 24
3119450 TTACATATTA
*
3119460 GTTGGAATAACTATTGAACAACCT
1 GTTGCAATAACTATTGAACAACCT
3119484 GTTGCAATAACTATTGAACAACCT
1 GTTGCAATAACTATTGAACAACCT
3119508 GTTGC
1 GTTGC
3119513 TTATGTTTAT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.34, C:0.19, G:0.17, T:0.30
Consensus pattern (24 bp):
GTTGCAATAACTATTGAACAACCT
Found at i:3129342 original size:19 final size:18
Alignment explanation
Indices: 3129297--3129349 Score: 52
Period size: 19 Copynumber: 2.8 Consensus size: 18
3129287 AACTTCCTAC
* *
3129297 TTACAGTTTATTTTGATT
1 TTACAATTTATTTTGATA
*
3129315 TTTCAAATTTATTTTGAGTA
1 TTAC-AATTTATTTTGA-TA
*
3129335 TTACAATTTGTTTTG
1 TTACAATTTATTTTG
3129350 CTGTGTACAC
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
18 3 0.11
19 21 0.75
20 4 0.14
ACGTcount: A:0.25, C:0.06, G:0.11, T:0.58
Consensus pattern (18 bp):
TTACAATTTATTTTGATA
Found at i:3135257 original size:28 final size:28
Alignment explanation
Indices: 3135225--3135361 Score: 107
Period size: 28 Copynumber: 4.9 Consensus size: 28
3135215 CAATTTTAAT
3135225 ATGTTTGTCTTAATTTAGACAAGAAAAC
1 ATGTTTGTCTTAATTTAGACAAGAAAAC
* *
3135253 ATGTTTGGTTTTAATTTAGACAAGAAAAT
1 ATGTTT-GTCTTAATTTAGACAAGAAAAC
* * * * * *
3135282 ATGTTTGTTTTAAATTAAAAATAAAAAAA
1 ATGTTTGTCTTAATTTAGACA-AGAAAAC
* * *
3135311 AT-TGTGTCTT-ATTCTTGATAAGAAAAC
1 ATGTTTGTCTTAATT-TAGACAAGAAAAC
* * *
3135338 ATATTTGCCTCAATTTAGACAAGA
1 ATGTTTGTCTTAATTTAGACAAGA
3135362 TAAAATATTT
Statistics
Matches: 84, Mismatches: 20, Indels: 10
0.74 0.18 0.09
Matches are distributed among these distances:
27 9 0.11
28 39 0.46
29 36 0.43
ACGTcount: A:0.41, C:0.08, G:0.13, T:0.38
Consensus pattern (28 bp):
ATGTTTGTCTTAATTTAGACAAGAAAAC
Found at i:3135297 original size:29 final size:28
Alignment explanation
Indices: 3135222--3135294 Score: 119
Period size: 29 Copynumber: 2.6 Consensus size: 28
3135212 TGACAATTTT
*
3135222 AATATGTTTGTCTTAATTTAGACAAGAA
1 AATATGTTTGTTTTAATTTAGACAAGAA
*
3135250 AACATGTTTGGTTTTAATTTAGACAAGAA
1 AATATGTTT-GTTTTAATTTAGACAAGAA
3135279 AATATGTTTGTTTTAA
1 AATATGTTTGTTTTAA
3135295 ATTAAAAATA
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
28 15 0.37
29 26 0.63
ACGTcount: A:0.37, C:0.05, G:0.15, T:0.42
Consensus pattern (28 bp):
AATATGTTTGTTTTAATTTAGACAAGAA
Found at i:3137055 original size:51 final size:51
Alignment explanation
Indices: 3137000--3137101 Score: 159
Period size: 51 Copynumber: 2.0 Consensus size: 51
3136990 TTGGGAAGTC
* * * *
3137000 CTCGTGTTGATAACAAGTTGTAAAAGAAATAATAGAAATAGGAAGACAAAA
1 CTCGTGCTGATAACAAGTTGTAAAAGAAATAATAAAAATAAGAAGAAAAAA
*
3137051 CTCGTGCTGATAACATGTTGTAAAAGAAATAATAAAAATAAGAAGAAAAAA
1 CTCGTGCTGATAACAAGTTGTAAAAGAAATAATAAAAATAAGAAGAAAAAA
3137102 GAGATATTGA
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
51 46 1.00
ACGTcount: A:0.53, C:0.08, G:0.18, T:0.22
Consensus pattern (51 bp):
CTCGTGCTGATAACAAGTTGTAAAAGAAATAATAAAAATAAGAAGAAAAAA
Found at i:3137310 original size:25 final size:23
Alignment explanation
Indices: 3137260--3137311 Score: 61
Period size: 23 Copynumber: 2.2 Consensus size: 23
3137250 TTTTTAAATT
*
3137260 ATATTATCTTCTTGATAAATCTC
1 ATATTATCTTCTTGATAAATCAC
3137283 ATATTATC-TCTTAGATAATATCCAC
1 ATATTATCTTCTT-GATAA-AT-CAC
3137308 ATAT
1 ATAT
3137312 AGATAAATCT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
22 4 0.16
23 13 0.52
24 2 0.08
25 6 0.24
ACGTcount: A:0.35, C:0.17, G:0.04, T:0.44
Consensus pattern (23 bp):
ATATTATCTTCTTGATAAATCAC
Found at i:3137630 original size:2 final size:2
Alignment explanation
Indices: 3137625--3137666 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
3137615 TATATATATA
*
3137625 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TA TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
3137667 GGTTTTTATT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.02, C:0.00, G:0.48, T:0.50
Consensus pattern (2 bp):
TG
Found at i:3139866 original size:3 final size:3
Alignment explanation
Indices: 3139858--3139883 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
3139848 AACACTTCTG
3139858 TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TT
3139884 TGAAACCTAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:3140362 original size:23 final size:23
Alignment explanation
Indices: 3140279--3140363 Score: 63
Period size: 23 Copynumber: 3.8 Consensus size: 23
3140269 AATTGTCTAA
*
3140279 GTTTATCCAATTATGCTGTATCT
1 GTTTATCCAATTATGCTATATCT
* * **
3140302 GTTTATCCAATCAT-TTAATATGG
1 GTTTATCCAATTATGCT-ATATCT
3140325 GCTTT-T---ATTACTGCTATATCT
1 G-TTTATCCAATTA-TGCTATATCT
3140346 GTTTATCCAATTATGCTA
1 GTTTATCCAATTATGCTA
3140364 AGGAACCTGG
Statistics
Matches: 45, Mismatches: 9, Indels: 16
0.64 0.13 0.23
Matches are distributed among these distances:
20 6 0.13
21 7 0.16
22 2 0.04
23 23 0.51
24 7 0.16
ACGTcount: A:0.25, C:0.16, G:0.12, T:0.47
Consensus pattern (23 bp):
GTTTATCCAATTATGCTATATCT
Found at i:3154555 original size:22 final size:22
Alignment explanation
Indices: 3154530--3154571 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
3154520 GTATTTTTAG
*
3154530 ATTATTAATTAATTATTTATGA
1 ATTAATAATTAATTATTTATGA
* *
3154552 ATTAATATTTATTTATTTAT
1 ATTAATAATTAATTATTTAT
3154572 TCTTTTTTTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (22 bp):
ATTAATAATTAATTATTTATGA
Found at i:3158100 original size:2 final size:2
Alignment explanation
Indices: 3158095--3158129 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
3158085 NNNNNNNTAT
3158095 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
3158130 TGAATACCAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:3181847 original size:166 final size:167
Alignment explanation
Indices: 3181525--3181860 Score: 548
Period size: 166 Copynumber: 2.0 Consensus size: 167
3181515 AACCTACACT
* *
3181525 ACTACATATGTCCGTCATTGCTAATGCCTCCTCCCAAATCATTATATTTCTAAACTCCTTATCTG
1 ACTACATATGTCCATCATTGCTAATGCCTCCTCCCAAATCATCATATTTCTAAACTCCTTATCTG
*
3181590 ATTTGGGCACTAGCAACTTTTTCACTGTCTTCCCTTTTCCCATTTCTCGCACCTTGCGTCCCTTT
66 ATTTGGGCACTAGCAACTTTTTCACTGTCTTCCCTTTTCCCATTTCTCGCACCTTGCATCCCTTT
* *
3181655 CCCCCAATTCATTGTTCTCCATCCCCAAATTCCCATC
131 CCCCCAATTCATTGCTCTCCATCCCCAAATACCCATC
* * * * *
3181692 ACTACATATGTCCATCATTGCTAATGTCTCCTCCCAGATCGTCATATTTCTAAGCTCTTTATCTG
1 ACTACATATGTCCATCATTGCTAATGCCTCCTCCCAAATCATCATATTTCTAAACTCCTTATCTG
* * *
3181757 ATTTGGGCACTAGCAA-TTTTTCACTGTCTTCCTTTTTCCCTTTTTTCGCACCTTGCATCCCTTT
66 ATTTGGGCACTAGCAACTTTTTCACTGTCTTCCCTTTTCCCATTTCTCGCACCTTGCATCCCTTT
3181821 CCCCCAATTCATTGCTCTCCATCCCCAAATACCCATC
131 CCCCCAATTCATTGCTCTCCATCCCCAAATACCCATC
3181858 ACT
1 ACT
3181861 TAATTGCAAA
Statistics
Matches: 156, Mismatches: 13, Indels: 1
0.92 0.08 0.01
Matches are distributed among these distances:
166 82 0.53
167 74 0.47
ACGTcount: A:0.20, C:0.34, G:0.09, T:0.38
Consensus pattern (167 bp):
ACTACATATGTCCATCATTGCTAATGCCTCCTCCCAAATCATCATATTTCTAAACTCCTTATCTG
ATTTGGGCACTAGCAACTTTTTCACTGTCTTCCCTTTTCCCATTTCTCGCACCTTGCATCCCTTT
CCCCCAATTCATTGCTCTCCATCCCCAAATACCCATC
Found at i:3184033 original size:12 final size:12
Alignment explanation
Indices: 3184004--3184063 Score: 52
Period size: 12 Copynumber: 5.0 Consensus size: 12
3183994 ATCCTATCCT
*
3184004 ATGGTTTCTCGC
1 ATGGTTTCTCTC
*
3184016 AAGGTTTCTCTC
1 ATGGTTTCTCTC
*
3184028 ATGGTTCCTCTC
1 ATGGTTTCTCTC
*
3184040 TTGGTTTTCCTCTC
1 ATGG-TTT-CTCTC
3184054 A--GTTTCTCTC
1 ATGGTTTCTCTC
3184064 TAGGACACCC
Statistics
Matches: 39, Mismatches: 7, Indels: 6
0.75 0.13 0.12
Matches are distributed among these distances:
10 5 0.13
11 3 0.08
12 24 0.62
13 2 0.05
14 5 0.13
ACGTcount: A:0.08, C:0.28, G:0.17, T:0.47
Consensus pattern (12 bp):
ATGGTTTCTCTC
Found at i:3187486 original size:30 final size:30
Alignment explanation
Indices: 3187452--3187527 Score: 91
Period size: 30 Copynumber: 2.5 Consensus size: 30
3187442 ATCATTAGTA
*
3187452 ATAAAAGTTTATTTGGA-TCAAAATAAAAAT
1 ATAAAAATTTATTT-GACTCAAAATAAAAAT
*
3187482 ATAAAAATTTATTTGACTCAAAATTAAAAT
1 ATAAAAATTTATTTGACTCAAAATAAAAAT
* * *
3187512 TTAAGAATTTAATTGA
1 ATAAAAATTTATTTGA
3187528 ACGCAATCAA
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
29 2 0.05
30 38 0.95
ACGTcount: A:0.51, C:0.04, G:0.08, T:0.37
Consensus pattern (30 bp):
ATAAAAATTTATTTGACTCAAAATAAAAAT
Found at i:3208368 original size:23 final size:21
Alignment explanation
Indices: 3208334--3208404 Score: 70
Period size: 23 Copynumber: 3.2 Consensus size: 21
3208324 CTATAAGGAG
3208334 GAAAATGGGTTTACTCTATAA
1 GAAAATGGGTTTACTCTATAA
* * *
3208355 GAAAATTTGGGTTTATTTTGTAA
1 GAAAA--TGGGTTTACTCTATAA
* *
3208378 TGAAAATAGATTTACTCTATAA
1 -GAAAATGGGTTTACTCTATAA
3208400 GAAAA
1 GAAAA
3208405 AAAATTTTCA
Statistics
Matches: 39, Mismatches: 8, Indels: 6
0.74 0.15 0.11
Matches are distributed among these distances:
21 10 0.26
22 11 0.28
23 13 0.33
24 5 0.13
ACGTcount: A:0.41, C:0.06, G:0.17, T:0.37
Consensus pattern (21 bp):
GAAAATGGGTTTACTCTATAA
Found at i:3224079 original size:2 final size:2
Alignment explanation
Indices: 3224072--3224099 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
3224062 ACTCAGACAC
3224072 AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG
3224100 GTGGTTGATG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:3229198 original size:17 final size:18
Alignment explanation
Indices: 3229176--3229209 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
3229166 TAAGAGAGTG
*
3229176 AAAGAGATAAA-GAGAAA
1 AAAGAGAAAAAGGAGAAA
3229193 AAAGAGAAAAAGGAGAA
1 AAAGAGAAAAAGGAGAA
3229210 GGGAAAAATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.71, C:0.00, G:0.26, T:0.03
Consensus pattern (18 bp):
AAAGAGAAAAAGGAGAAA
Found at i:3230473 original size:21 final size:21
Alignment explanation
Indices: 3230449--3230489 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
3230439 TACAAACCAA
*
3230449 TTACAAAGAT-ATCAATTTTAG
1 TTACAAA-ATAATCAACTTTAG
3230470 TTACAAAATAATCAACTTTA
1 TTACAAAATAATCAACTTTA
3230490 TTAACACAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 2 0.11
21 16 0.89
ACGTcount: A:0.46, C:0.12, G:0.05, T:0.37
Consensus pattern (21 bp):
TTACAAAATAATCAACTTTAG
Found at i:3231917 original size:19 final size:19
Alignment explanation
Indices: 3231893--3231934 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
3231883 GAAATATAAG
3231893 AGAAAGTATTTAGAGGGAA
1 AGAAAGTATTTAGAGGGAA
* *
3231912 AGAAAGTATTTAGGGGGAG
1 AGAAAGTATTTAGAGGGAA
3231931 AGAA
1 AGAA
3231935 GAAATCTTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.45, C:0.00, G:0.36, T:0.19
Consensus pattern (19 bp):
AGAAAGTATTTAGAGGGAA
Found at i:3232186 original size:14 final size:16
Alignment explanation
Indices: 3232157--3232190 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
3232147 ATGCCTCGCT
3232157 AAAACCTTACTAGGAA
1 AAAACCTTACTAGGAA
3232173 AAAACCTTA-T-GGAA
1 AAAACCTTACTAGGAA
3232187 AAAA
1 AAAA
3232191 AATCCAAGTG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 8 0.44
15 1 0.06
16 9 0.50
ACGTcount: A:0.56, C:0.15, G:0.12, T:0.18
Consensus pattern (16 bp):
AAAACCTTACTAGGAA
Found at i:3236435 original size:25 final size:25
Alignment explanation
Indices: 3236367--3236438 Score: 65
Period size: 25 Copynumber: 2.9 Consensus size: 25
3236357 AAAATTATCT
*
3236367 ATCCACTTTTAGTGGTAAAATTATTC
1 ATCCACTTCTAGTGGTAAAA-TATTC
** * * * *
3236393 -TTAAATTCAAATGATAAAATATTC
1 ATCCACTTCTAGTGGTAAAATATTC
3236417 ATCCACTTCTAGTGGTAAAATA
1 ATCCACTTCTAGTGGTAAAATA
3236439 ATAATTAAAA
Statistics
Matches: 32, Mismatches: 13, Indels: 3
0.67 0.27 0.06
Matches are distributed among these distances:
24 5 0.16
25 27 0.84
ACGTcount: A:0.39, C:0.14, G:0.10, T:0.38
Consensus pattern (25 bp):
ATCCACTTCTAGTGGTAAAATATTC
Found at i:3236617 original size:59 final size:53
Alignment explanation
Indices: 3236549--3236685 Score: 157
Period size: 53 Copynumber: 2.5 Consensus size: 53
3236539 TATTAAATAA
* * * * **
3236549 TGTCGCATTCACTTCAGGAAATGGATGGATTTATAAATTTTTATTATTAGTATCTTGTT
1 TGTCACATTCACTTCAGGAAATGAAT--ATTTATAAA---TT-TTACTAGTAGCTCATT
*
3236608 TGTCACATTCACTTCAGGGAATGAATATTTATAAATTTTACTAGTAGCTCATT
1 TGTCACATTCACTTCAGGAAATGAATATTTATAAATTTTACTAGTAGCTCATT
3236661 TGTCACATTCACTTCAGGAAATGAA
1 TGTCACATTCACTTCAGGAAATGAA
3236686 CATTCATGGT
Statistics
Matches: 70, Mismatches: 8, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
53 36 0.51
54 2 0.03
57 9 0.13
59 23 0.33
ACGTcount: A:0.31, C:0.14, G:0.15, T:0.40
Consensus pattern (53 bp):
TGTCACATTCACTTCAGGAAATGAATATTTATAAATTTTACTAGTAGCTCATT
Found at i:3238383 original size:38 final size:38
Alignment explanation
Indices: 3238304--3238418 Score: 115
Period size: 38 Copynumber: 3.0 Consensus size: 38
3238294 GGACTGTACC
* **
3238304 ATTATCCGTGAAATG-CCTTAAATAGTGGATACCATACT
1 ATTATCCGTGAAATGTCC-TAGATAGTGGGGACCATACT
* * *
3238342 ATTATCCATGAAATGTCCTAGATAGTGGGGACCTTATT
1 ATTATCCGTGAAATGTCCTAGATAGTGGGGACCATACT
** * * *
3238380 ATTATTTGTGAATTGTCCTAGACAGTGGGGATCATACT
1 ATTATCCGTGAAATGTCCTAGATAGTGGGGACCATACT
3238418 A
1 A
3238419 GATAGGGTAT
Statistics
Matches: 62, Mismatches: 14, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
38 60 0.97
39 2 0.03
ACGTcount: A:0.30, C:0.16, G:0.20, T:0.34
Consensus pattern (38 bp):
ATTATCCGTGAAATGTCCTAGATAGTGGGGACCATACT
Found at i:3239591 original size:22 final size:23
Alignment explanation
Indices: 3239544--3239593 Score: 68
Period size: 22 Copynumber: 2.2 Consensus size: 23
3239534 TATGATATAG
3239544 AGTAATTTGAGATTAATTTTGAT
1 AGTAATTTGAGATTAATTTTGAT
*
3239567 AGTAATTT-AGCTTAATTATTG-T
1 AGTAATTTGAGATTAATT-TTGAT
3239589 AGTAA
1 AGTAA
3239594 CACATAGAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
22 14 0.56
23 11 0.44
ACGTcount: A:0.36, C:0.02, G:0.16, T:0.46
Consensus pattern (23 bp):
AGTAATTTGAGATTAATTTTGAT
Found at i:3240116 original size:14 final size:13
Alignment explanation
Indices: 3240086--3240121 Score: 63
Period size: 13 Copynumber: 2.8 Consensus size: 13
3240076 CCCTAACTTT
3240086 AAAACCCTTTGAA
1 AAAACCCTTTGAA
3240099 AAAACCCTTTGAA
1 AAAACCCTTTGAA
*
3240112 AAAAACCTTT
1 AAAACCCTTT
3240122 CAGAAGACTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.47, C:0.22, G:0.06, T:0.25
Consensus pattern (13 bp):
AAAACCCTTTGAA
Found at i:3240914 original size:6 final size:6
Alignment explanation
Indices: 3240903--3240927 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
3240893 TTATCTAAAC
3240903 AATTAA AATTAA AATTAA AATTAA A
1 AATTAA AATTAA AATTAA AATTAA A
3240928 CTAATAAACT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (6 bp):
AATTAA
Found at i:3240935 original size:26 final size:27
Alignment explanation
Indices: 3240897--3240957 Score: 65
Period size: 26 Copynumber: 2.3 Consensus size: 27
3240887 CTTATTTTAT
*
3240897 CTAAAC-AATTAAAATTAA-AATTAAAA
1 CTAAACTAATT-AAACTAATAATTAAAA
*
3240923 TTAAACTAA-TAAACTAATAATTAAAA
1 CTAAACTAATTAAACTAATAATTAAAA
*
3240949 CTAATCTAA
1 CTAAACTAA
3240958 AATATATCAG
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
25 6 0.21
26 21 0.72
27 2 0.07
ACGTcount: A:0.61, C:0.10, G:0.00, T:0.30
Consensus pattern (27 bp):
CTAAACTAATTAAACTAATAATTAAAA
Found at i:3243098 original size:58 final size:58
Alignment explanation
Indices: 3242950--3243091 Score: 169
Period size: 58 Copynumber: 2.4 Consensus size: 58
3242940 GGGACCAACA
** *
3242950 ATGTCTAGCACCATAGCCCTTGCTAGATAGGAATAACAAACATGTGTCTCAACATTACAC
1 ATGTCTAGCACCAT-G-CCTTGCTAGATAGGCCTAACAAACATGTGTCTCAACATTAAAC
* * * * * *
3243010 ATG-CTTAGCACCAAGCCTTGCTAGATAGGCCTCACAAGCATGTGTCTTACCATTAAAT
1 ATGTC-TAGCACCATGCCTTGCTAGATAGGCCTAACAAACATGTGTCTCAACATTAAAC
3243068 ATGTCTAGCACCATGCCTTGCTAG
1 ATGTCTAGCACCATGCCTTGCTAG
3243092 GAAGGCCAAT
Statistics
Matches: 70, Mismatches: 10, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
58 56 0.80
59 3 0.04
60 11 0.16
ACGTcount: A:0.30, C:0.26, G:0.17, T:0.27
Consensus pattern (58 bp):
ATGTCTAGCACCATGCCTTGCTAGATAGGCCTAACAAACATGTGTCTCAACATTAAAC
Found at i:3253389 original size:2 final size:2
Alignment explanation
Indices: 3253382--3253413 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
3253372 GCAGTGAAGC
3253382 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
3253414 AAGAAGTAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:3262991 original size:28 final size:28
Alignment explanation
Indices: 3262951--3263020 Score: 77
Period size: 28 Copynumber: 2.5 Consensus size: 28
3262941 TAAATAATAA
* *
3262951 AAATATATTATAAATAAATAAATTACACC
1 AAATATA-AATAAACAAATAAATTACACC
* * *
3262980 AAATATAAATAAGCAAATACATTACATC
1 AAATATAAATAAACAAATAAATTACACC
*
3263008 AAACATAAATAAA
1 AAATATAAATAAA
3263021 ATTTTAATCT
Statistics
Matches: 34, Mismatches: 7, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
28 27 0.79
29 7 0.21
ACGTcount: A:0.61, C:0.11, G:0.01, T:0.26
Consensus pattern (28 bp):
AAATATAAATAAACAAATAAATTACACC
Found at i:3275144 original size:7 final size:7
Alignment explanation
Indices: 3275132--3275158 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
3275122 AATACCCAAC
3275132 ATTCAAT
1 ATTCAAT
3275139 ATTCAAT
1 ATTCAAT
3275146 ATTCAAT
1 ATTCAAT
3275153 ATTCAA
1 ATTCAA
3275159 CAAACTTTGC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.44, C:0.15, G:0.00, T:0.41
Consensus pattern (7 bp):
ATTCAAT
Found at i:3275252 original size:19 final size:19
Alignment explanation
Indices: 3275228--3275269 Score: 75
Period size: 19 Copynumber: 2.2 Consensus size: 19
3275218 AAACCAGGAA
*
3275228 CAAATTCTAGGATGGAATT
1 CAAATTCTAGGATGAAATT
3275247 CAAATTCTAGGATGAAATT
1 CAAATTCTAGGATGAAATT
3275266 CAAA
1 CAAA
3275270 AGAAAAAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.43, C:0.12, G:0.17, T:0.29
Consensus pattern (19 bp):
CAAATTCTAGGATGAAATT
Found at i:3276856 original size:63 final size:63
Alignment explanation
Indices: 3276721--3276873 Score: 150
Period size: 63 Copynumber: 2.4 Consensus size: 63
3276711 TAGAAGATTT
* * * * *
3276721 GACATCTCAAAATAGAAGAATTGATTCTCTAGAGATAGAAAGCCTCAGACTTTATGAAAAACC
1 GACATCTCAAAATAAAAGAATTGATTCCCCAAAGACAGAAAGCCTCAGACTTTATGAAAAACC
* * * *
3276784 AACATCTCAAAATAAAAGAATTGATTCCCCAAAGGCAGAAAG-TTCTAGACTTTGT-AAAGAACC
1 GACATCTCAAAATAAAAGAATTGATTCCCCAAAGACAGAAAGCCTC-AGACTTTATGAAA-AACC
* * *
3276847 GACAACTCAACAACAAAA-AATCGATTC
1 GACATCTCAA-AATAAAAGAATTGATTC
3276874 TATATATGTG
Statistics
Matches: 74, Mismatches: 13, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
62 5 0.07
63 63 0.85
64 6 0.08
ACGTcount: A:0.45, C:0.20, G:0.14, T:0.22
Consensus pattern (63 bp):
GACATCTCAAAATAAAAGAATTGATTCCCCAAAGACAGAAAGCCTCAGACTTTATGAAAAACC
Found at i:3277451 original size:36 final size:36
Alignment explanation
Indices: 3277368--3277452 Score: 113
Period size: 35 Copynumber: 2.4 Consensus size: 36
3277358 TAGTGTCTTG
*
3277368 ATAAAGGTTATAC-CTGATTCTGATAAAAGGCATGT
1 ATAAAGGTTATGCACTGATTCTGATAAAAGGCATGT
3277403 ATAAAGGTTATGCACTG-TTCT-ATTAAAAGGCATGTT
1 ATAAAGGTTATGCACTGATTCTGA-TAAAAGGCATG-T
*
3277439 GTAAAGGTTATGCA
1 ATAAAGGTTATGCA
3277453 GATCCTGTTG
Statistics
Matches: 45, Mismatches: 2, Indels: 5
0.87 0.04 0.10
Matches are distributed among these distances:
34 1 0.02
35 27 0.60
36 17 0.38
ACGTcount: A:0.35, C:0.11, G:0.21, T:0.33
Consensus pattern (36 bp):
ATAAAGGTTATGCACTGATTCTGATAAAAGGCATGT
Found at i:3287990 original size:14 final size:15
Alignment explanation
Indices: 3287967--3288005 Score: 50
Period size: 13 Copynumber: 2.9 Consensus size: 15
3287957 TTTATCTATG
3287967 AAAAAT-AATTTA-T
1 AAAAATAAATTTACT
3287980 AAAAATAAATTTACT
1 AAAAATAAATTTACT
3287995 --AAATAAATTTA
1 AAAAATAAATTTA
3288006 ATTTAATTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
13 17 0.71
14 6 0.25
15 1 0.04
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.36
Consensus pattern (15 bp):
AAAAATAAATTTACT
Found at i:3290371 original size:29 final size:29
Alignment explanation
Indices: 3290329--3290417 Score: 178
Period size: 29 Copynumber: 3.1 Consensus size: 29
3290319 CAACGTGCAC
3290329 TTGAAAATTCTCATATTCATTAATAGTAA
1 TTGAAAATTCTCATATTCATTAATAGTAA
3290358 TTGAAAATTCTCATATTCATTAATAGTAA
1 TTGAAAATTCTCATATTCATTAATAGTAA
3290387 TTGAAAATTCTCATATTCATTAATAGTAA
1 TTGAAAATTCTCATATTCATTAATAGTAA
3290416 TT
1 TT
3290418 TTATGCGACT
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 60 1.00
ACGTcount: A:0.40, C:0.10, G:0.07, T:0.43
Consensus pattern (29 bp):
TTGAAAATTCTCATATTCATTAATAGTAA
Found at i:3293063 original size:2 final size:2
Alignment explanation
Indices: 3293058--3293088 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
3293048 ACACAAAAAT
3293058 GA GA GA GA GA GA GA -A GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
3293089 TGTGAACACA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
GA
Found at i:3293078 original size:15 final size:15
Alignment explanation
Indices: 3293058--3293086 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
3293048 ACACAAAAAT
3293058 GAGAGAGAGAGAGAA
1 GAGAGAGAGAGAGAA
3293073 GAGAGAGAGAGAGA
1 GAGAGAGAGAGAGA
3293087 GATGTGAACA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (15 bp):
GAGAGAGAGAGAGAA
Found at i:3293123 original size:37 final size:37
Alignment explanation
Indices: 3293076--3293145 Score: 108
Period size: 35 Copynumber: 1.9 Consensus size: 37
3293066 GAGAGAAGAG
*
3293076 AGAGAGAGAGAGATGTG-A-ACACACACACAAATGCA
1 AGAGAAAGAGAGATGTGCACACACACACACAAATGCA
*
3293111 AGAGAAAGAGAGATGTGCACACATACACACAAATG
1 AGAGAAAGAGAGATGTGCACACACACACACAAATG
3293146 AGAGAGAGTG
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
35 16 0.52
36 1 0.03
37 14 0.45
ACGTcount: A:0.49, C:0.17, G:0.24, T:0.10
Consensus pattern (37 bp):
AGAGAAAGAGAGATGTGCACACACACACACAAATGCA
Found at i:3293159 original size:37 final size:35
Alignment explanation
Indices: 3293073--3293160 Score: 115
Period size: 37 Copynumber: 2.5 Consensus size: 35
3293063 AGAGAGAGAA
3293073 GAGAGAGAGAGAGAGATGTGAACACACACACAAAT
1 GAGAGAGAGAGAGAGATGTGAACACACACACAAAT
* *
3293108 GCA-AGAGAAAGAGAGATGTGCACACATACACACAAAT
1 G-AGAGAGAGAGAGAGATGTG-A-ACACACACACAAAT
*
3293145 GAGAGAGAGTGAGAGA
1 GAGAGAGAGAGAGAGA
3293161 GTTAAAACAT
Statistics
Matches: 45, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
35 17 0.38
36 3 0.07
37 25 0.56
ACGTcount: A:0.48, C:0.14, G:0.30, T:0.09
Consensus pattern (35 bp):
GAGAGAGAGAGAGAGATGTGAACACACACACAAAT
Found at i:3298072 original size:15 final size:15
Alignment explanation
Indices: 3298052--3298081 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
3298042 GGGTGTTGTT
*
3298052 ATCATCGTTGTCATC
1 ATCATCGATGTCATC
3298067 ATCATCGATGTCATC
1 ATCATCGATGTCATC
3298082 GGCCCGGCGG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.23, C:0.27, G:0.13, T:0.37
Consensus pattern (15 bp):
ATCATCGATGTCATC
Found at i:3305407 original size:45 final size:45
Alignment explanation
Indices: 3305358--3305447 Score: 162
Period size: 45 Copynumber: 2.0 Consensus size: 45
3305348 TACGCTTCTT
* *
3305358 CTCCTGTTCACATAAAACCCCTTTACAGCAAGCAAGATGAGGTTA
1 CTCCTGTTCACATAAAACCCCTTTACAGCAAGCAAAACGAGGTTA
3305403 CTCCTGTTCACATAAAACCCCTTTACAGCAAGCAAAACGAGGTTA
1 CTCCTGTTCACATAAAACCCCTTTACAGCAAGCAAAACGAGGTTA
3305448 TTTTCAAGTA
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
45 43 1.00
ACGTcount: A:0.34, C:0.28, G:0.14, T:0.23
Consensus pattern (45 bp):
CTCCTGTTCACATAAAACCCCTTTACAGCAAGCAAAACGAGGTTA
Found at i:3306626 original size:31 final size:30
Alignment explanation
Indices: 3306566--3306627 Score: 81
Period size: 30 Copynumber: 2.0 Consensus size: 30
3306556 TATTATAATG
* *
3306566 AAAATTAAATTAAATTTAATAATTAATTTT
1 AAAAATAAATTAAATTTAATAATCAATTTT
3306596 AAAAATAAATTAAAGTTTAA-AATCATATTTT
1 AAAAATAAATTAAA-TTTAATAATCA-ATTTT
3306627 A
1 A
3306628 GATGAATTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
30 17 0.61
31 11 0.39
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.42
Consensus pattern (30 bp):
AAAAATAAATTAAATTTAATAATCAATTTT
Found at i:3308356 original size:38 final size:38
Alignment explanation
Indices: 3308294--3308372 Score: 104
Period size: 38 Copynumber: 2.1 Consensus size: 38
3308284 CAATTAGTTA
* * * *
3308294 TTAGGCATTGAGAGATTGGTTTTTAGGCATTACTTGAC
1 TTAGGCATTAAGAGATTGGCTTTTAAGCATTACATGAC
* *
3308332 TTAGGCATTAAGAGGTTGGCTTTTAAGCATTGCATGAC
1 TTAGGCATTAAGAGATTGGCTTTTAAGCATTACATGAC
3308370 TTA
1 TTA
3308373 ATCATTGTGT
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
38 35 1.00
ACGTcount: A:0.25, C:0.11, G:0.25, T:0.38
Consensus pattern (38 bp):
TTAGGCATTAAGAGATTGGCTTTTAAGCATTACATGAC
Found at i:3308400 original size:22 final size:22
Alignment explanation
Indices: 3308375--3308426 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 22
3308365 ATGACTTAAT
*
3308375 CATTGTGTTTTTCGAACT-TAGG
1 CATTGTGTCTTTCGAA-TGTAGG
* *
3308397 CATTGTGTCTTTGGGATGTAGG
1 CATTGTGTCTTTCGAATGTAGG
3308419 CATTGTGT
1 CATTGTGT
3308427 GACTGGTTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
21 1 0.04
22 25 0.96
ACGTcount: A:0.15, C:0.12, G:0.29, T:0.44
Consensus pattern (22 bp):
CATTGTGTCTTTCGAATGTAGG
Found at i:3308461 original size:22 final size:21
Alignment explanation
Indices: 3308415--3308516 Score: 96
Period size: 22 Copynumber: 4.8 Consensus size: 21
3308405 CTTTGGGATG
3308415 TAGGCATTGTGTGACTGGTTT
1 TAGGCATTGTGTGACTGGTTT
* *
3308436 TAGGTATTTTGTGACTGGTTTT
1 TAGGCATTGTGTGACTGG-TTT
*** **
3308458 TAGGCATTACATGACTAATTT
1 TAGGCATTGTGTGACTGGTTT
* * *
3308479 CAGGCATTGTGTGACTAGATTG
1 TAGGCATTGTGTGACT-GGTTT
3308501 TAGGCATTGTGTGACT
1 TAGGCATTGTGTGACT
3308517 TAATCATTAC
Statistics
Matches: 64, Mismatches: 15, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
21 31 0.48
22 33 0.52
ACGTcount: A:0.21, C:0.11, G:0.27, T:0.41
Consensus pattern (21 bp):
TAGGCATTGTGTGACTGGTTT
Found at i:3308462 original size:43 final size:43
Alignment explanation
Indices: 3308413--3308516 Score: 109
Period size: 43 Copynumber: 2.4 Consensus size: 43
3308403 GTCTTTGGGA
** * * * * *
3308413 TGTAGGCATTGTGTGACTGGTTTTAGGTATTTTGTGACTGGTT
1 TGTAGGCATTGTGTGACTAATTTCAGGCATTGTGTGACTAGAT
* ***
3308456 TTTAGGCATTACATGACTAATTTCAGGCATTGTGTGACTAGAT
1 TGTAGGCATTGTGTGACTAATTTCAGGCATTGTGTGACTAGAT
3308499 TGTAGGCATTGTGTGACT
1 TGTAGGCATTGTGTGACT
3308517 TAATCATTAC
Statistics
Matches: 46, Mismatches: 15, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
43 46 1.00
ACGTcount: A:0.20, C:0.11, G:0.28, T:0.41
Consensus pattern (43 bp):
TGTAGGCATTGTGTGACTAATTTCAGGCATTGTGTGACTAGAT
Found at i:3312169 original size:31 final size:29
Alignment explanation
Indices: 3312102--3312158 Score: 87
Period size: 29 Copynumber: 2.0 Consensus size: 29
3312092 AAGTATTTAT
3312102 AATATCCACTGTAACTAAACAAGATATAC
1 AATATCCACTGTAACTAAACAAGATATAC
** *
3312131 AATATCCACTGTAGTTAAGCAAGATATA
1 AATATCCACTGTAACTAAACAAGATATA
3312159 TTGAATATCC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.46, C:0.18, G:0.11, T:0.26
Consensus pattern (29 bp):
AATATCCACTGTAACTAAACAAGATATAC
Found at i:3313928 original size:14 final size:14
Alignment explanation
Indices: 3313909--3313939 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
3313899 TTTTGGCATG
*
3313909 TCCATGCATAATGT
1 TCCATGCAAAATGT
3313923 TCCATGCAAAATGT
1 TCCATGCAAAATGT
3313937 TCC
1 TCC
3313940 TATCCAGTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.29, C:0.26, G:0.13, T:0.32
Consensus pattern (14 bp):
TCCATGCAAAATGT
Found at i:3315513 original size:21 final size:21
Alignment explanation
Indices: 3315487--3315542 Score: 85
Period size: 21 Copynumber: 2.7 Consensus size: 21
3315477 TTGTTTGACC
* *
3315487 ATCTATTGATAGATTCTATGG
1 ATCTATCGATAGATTCCATGG
3315508 ATCTATCGATAGATTCCATGG
1 ATCTATCGATAGATTCCATGG
*
3315529 ATTTATCGATAGAT
1 ATCTATCGATAGAT
3315543 GTTTCTCACT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.30, C:0.12, G:0.18, T:0.39
Consensus pattern (21 bp):
ATCTATCGATAGATTCCATGG
Found at i:3315854 original size:23 final size:22
Alignment explanation
Indices: 3315812--3315856 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 22
3315802 CTAAGTTACA
*
3315812 CAATGCTTATCAACCGGTCATG
1 CAATGCTTATCAACCAGTCATG
*
3315834 CAATGTCTTATCAACTAGTCATG
1 CAATG-CTTATCAACCAGTCATG
3315857 TGATGCCTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 5 0.25
23 15 0.75
ACGTcount: A:0.29, C:0.24, G:0.16, T:0.31
Consensus pattern (22 bp):
CAATGCTTATCAACCAGTCATG
Found at i:3315868 original size:83 final size:84
Alignment explanation
Indices: 3315729--3316096 Score: 286
Period size: 83 Copynumber: 4.4 Consensus size: 84
3315719 ACTAGTCTCG
* * * *
3315729 CAATGCCTATCAACCAGTCATGTAATGCCTTATCAATTGGTCACGCAATGATTAAAAACCATT-T
1 CAATGCCTATCAACCAGTCATGCAATGCCTTATCAACTAGTCACGCAATGACT-AAAA-CATTGT
*
3315793 -ACGTAATGCCTAAGT-TACA
64 CACGCAATGCCTAAGTCTACA
* * * * ** * *
3315812 CAATGCTTATCAACCGGTCATGCAATGTCTTATCAACTAGTCATGTGATGCCTAAAAGATTGTCA
1 CAATGCCTATCAACCAGTCATGCAATGCCTTATCAACTAGTCACGCAATGACTAAAACATTGTCA
**
3315877 CGCAATGCCTAAGTCTTGA
66 CGCAATGCCTAAGTCTACA
* * * * *
3315896 -AATGCCTATCAACCAGTCTTACAATGCCTTATCAACTACTCACGCAATGCCT-AAAGATTGTCA
1 CAATGCCTATCAACCAGTCATGCAATGCCTTATCAACTAGTCACGCAATGACTAAAACATTGTCA
* * * *
3315959 TGTAATACCTAAGTCT-CG
66 CGCAATGCCTAAGTCTACA
* * * * * * * *
3315977 CAATGCCTATCAATCAGTCACGTAAT-ACTCTATTAACTAGTCATGCAATG-CTCAAAAAATTAT
1 CAATGCCTATCAACCAGTCATGCAATGCCT-TATCAACTAGTCACGCAATGACT-AAAACATTGT
* *
3316040 CACACAATGTCTAAGTCT-CA
64 CACGCAATGCCTAAGTCTACA
* * ***
3316060 TAGTGCCTATCAACCAGTCACATAATGCCTTATCAAC
1 CAATGCCTATCAACCAGTCATGCAATGCCTTATCAAC
3316097 CAGTTAGAGA
Statistics
Matches: 225, Mismatches: 52, Indels: 16
0.77 0.18 0.05
Matches are distributed among these distances:
81 7 0.03
82 66 0.29
83 148 0.66
84 4 0.02
ACGTcount: A:0.33, C:0.25, G:0.13, T:0.29
Consensus pattern (84 bp):
CAATGCCTATCAACCAGTCATGCAATGCCTTATCAACTAGTCACGCAATGACTAAAACATTGTCA
CGCAATGCCTAAGTCTACA
Found at i:3315921 original size:22 final size:23
Alignment explanation
Indices: 3315888--3315931 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
3315878 GCAATGCCTA
3315888 AGTCTTGAAATGCC-TATCAACC
1 AGTCTTGAAATGCCTTATCAACC
3315910 AGTCTT-ACAATGCCTTATCAAC
1 AGTCTTGA-AATGCCTTATCAAC
3315932 TACTCACGCA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
21 1 0.05
22 12 0.60
23 7 0.35
ACGTcount: A:0.32, C:0.27, G:0.11, T:0.30
Consensus pattern (23 bp):
AGTCTTGAAATGCCTTATCAACC
Found at i:3316083 original size:22 final size:23
Alignment explanation
Indices: 3316053--3316100 Score: 71
Period size: 22 Copynumber: 2.1 Consensus size: 23
3316043 ACAATGTCTA
* *
3316053 AGTCTCATAGTGCC-TATCAACC
1 AGTCACATAATGCCTTATCAACC
3316075 AGTCACATAATGCCTTATCAACC
1 AGTCACATAATGCCTTATCAACC
3316098 AGT
1 AGT
3316101 TAGAGAAGGT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 12 0.52
23 11 0.48
ACGTcount: A:0.31, C:0.29, G:0.12, T:0.27
Consensus pattern (23 bp):
AGTCACATAATGCCTTATCAACC
Found at i:3317752 original size:18 final size:18
Alignment explanation
Indices: 3317718--3317752 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
3317708 GTCGAACCAA
* *
3317718 TTGGCTCATTAATATTAG
1 TTGGCTCATCAAGATTAG
3317736 TTGGCTCATCAAGATTA
1 TTGGCTCATCAAGATTA
3317753 ACCCCGTGAG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.29, C:0.14, G:0.17, T:0.40
Consensus pattern (18 bp):
TTGGCTCATCAAGATTAG
Found at i:3320095 original size:23 final size:23
Alignment explanation
Indices: 3320069--3320118 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 23
3320059 ATAGTTATGA
*
3320069 AATGCTTTATAAAACAATCAAGC
1 AATGCCTTATAAAACAATCAAGC
* * *
3320092 AATGCCTTATCAACCAATCATGC
1 AATGCCTTATAAAACAATCAAGC
3320115 AATG
1 AATG
3320119 ACTAAAAATC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.42, C:0.22, G:0.10, T:0.26
Consensus pattern (23 bp):
AATGCCTTATAAAACAATCAAGC
Found at i:3320134 original size:22 final size:22
Alignment explanation
Indices: 3320106--3320184 Score: 79
Period size: 22 Copynumber: 3.6 Consensus size: 22
3320096 CCTTATCAAC
3320106 CAATCATGCAATGACTAAAAAT
1 CAATCATGCAATGACTAAAAAT
* *
3320128 CAATCATGTAATGATTAAAAAT
1 CAATCATGCAATGACTAAAAAT
* * * *
3320150 CGATCACT-TAATGCCTAAAAAC
1 CAATCA-TGCAATGACTAAAAAT
*
3320172 CAATCACGCAATG
1 CAATCATGCAATG
3320185 CCCTATCAAC
Statistics
Matches: 46, Mismatches: 9, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
22 45 0.98
23 1 0.02
ACGTcount: A:0.46, C:0.20, G:0.10, T:0.24
Consensus pattern (22 bp):
CAATCATGCAATGACTAAAAAT
Found at i:3320185 original size:22 final size:22
Alignment explanation
Indices: 3320079--3320186 Score: 74
Period size: 22 Copynumber: 4.9 Consensus size: 22
3320069 AATGCTTTAT
*
3320079 AAAA-CAATCAAGCAATGCCTTA
1 AAAACCAATCACGCAATGCC-TA
** * *
3320101 TCAACCAATCATGCAATGACTA
1 AAAACCAATCACGCAATGCCTA
* * * **
3320123 AAAATCAATCATGTAATGATTA
1 AAAACCAATCACGCAATGCCTA
* * **
3320145 AAAATCGATCACTTAATGCCTA
1 AAAACCAATCACGCAATGCCTA
3320167 AAAACCAATCACGCAATGCC
1 AAAACCAATCACGCAATGCC
3320187 CTATCAACTA
Statistics
Matches: 67, Mismatches: 18, Indels: 2
0.77 0.21 0.02
Matches are distributed among these distances:
22 54 0.81
23 13 0.19
ACGTcount: A:0.45, C:0.23, G:0.09, T:0.22
Consensus pattern (22 bp):
AAAACCAATCACGCAATGCCTA
Found at i:3320435 original size:9 final size:9
Alignment explanation
Indices: 3320421--3320447 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
3320411 TTCAAACAAC
3320421 AAGAATATG
1 AAGAATATG
3320430 AAGAATATG
1 AAGAATATG
3320439 AAGAATATG
1 AAGAATATG
3320448 CTTACCTTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.56, C:0.00, G:0.22, T:0.22
Consensus pattern (9 bp):
AAGAATATG
Found at i:3320487 original size:47 final size:49
Alignment explanation
Indices: 3320412--3320503 Score: 152
Period size: 47 Copynumber: 1.9 Consensus size: 49
3320402 AAATTCAACT
*
3320412 TCAAACAACAAGAATATGAAGAATATGAAGAATATGCTTACCTTTATGC
1 TCAAACAACAAGAATATGAAGAACATGAAGAATATGCTTACCTTTATGC
*
3320461 TCAAA-AACAAGAA-ATGAAGAACATGAAGAATATGCTTATCTTT
1 TCAAACAACAAGAATATGAAGAACATGAAGAATATGCTTACCTTT
3320504 TTGGATATGG
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
47 28 0.68
48 8 0.20
49 5 0.12
ACGTcount: A:0.47, C:0.13, G:0.14, T:0.26
Consensus pattern (49 bp):
TCAAACAACAAGAATATGAAGAACATGAAGAATATGCTTACCTTTATGC
Found at i:3324699 original size:2 final size:2
Alignment explanation
Indices: 3324692--3324722 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
3324682 ATTTTCTTCC
3324692 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
3324723 ACTCACACAC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:3332028 original size:23 final size:23
Alignment explanation
Indices: 3331993--3332041 Score: 80
Period size: 23 Copynumber: 2.1 Consensus size: 23
3331983 ACTATTATCA
*
3331993 AGCAAACGTATCTCATTGTCACT
1 AGCAAACGAATCTCATTGTCACT
*
3332016 AGCAAATGAATCTCATTGTCACT
1 AGCAAACGAATCTCATTGTCACT
3332039 AGC
1 AGC
3332042 GATAAGGTTG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.33, C:0.24, G:0.14, T:0.29
Consensus pattern (23 bp):
AGCAAACGAATCTCATTGTCACT
Found at i:3333302 original size:22 final size:22
Alignment explanation
Indices: 3333260--3333309 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
3333250 TTGTACTTAT
*
3333260 AAACTAGTGACTCAATATTTAA
1 AAACTAGTAACTCAATATTTAA
*
3333282 AAACTAGTAACAT-AATGTTTAA
1 AAACTAGTAAC-TCAATATTTAA
*
3333304 TAACTA
1 AAACTA
3333310 ATTGATTTGC
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 23 0.96
23 1 0.04
ACGTcount: A:0.48, C:0.12, G:0.08, T:0.32
Consensus pattern (22 bp):
AAACTAGTAACTCAATATTTAA
Found at i:3339032 original size:2 final size:2
Alignment explanation
Indices: 3339027--3339063 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
3339017 TGTGTGTGTT
3339027 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3339064 TTTATATGTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:3340286 original size:357 final size:356
Alignment explanation
Indices: 3339590--3340271 Score: 996
Period size: 357 Copynumber: 1.9 Consensus size: 356
3339580 TCTAACTTTC
*
3339590 AAAAACACATAAAAAGTAATAAAAATGAACCCCACTACTCTCCTTTCACTTTAAAAAATATAAAA
1 AAAAAAACATAAAAAGTAATAAAAATGAACCCCACTACTCTCCTTTCACTTTAAAAAATATAAAA
3339655 GGAGAAAGACCACAAGTCCACTCCTAGTTGCAAGGCTATTTCCATGTAAAAGCAACCTTACCTAA
66 GGAGAAAGACCACAAGTCCACTCCTAGTTGCAAGGCTATTTCCATGTAAAAGCAACCTTACCTAA
* * * *
3339720 CATATTTCCAATTCAACTTATGATTAGATTTATAAAGAGCTTTTATTTTTCAAGAAAGTTTAAAC
131 CATATTTCCAATTCAACTTAAGATTAGATTTATAAAGAGCTCTAATTTTCCAAGAAAGTTTAAAC
*
3339785 TTTATAAAAGCATAATATTTTAAAAAATCCTTGAACTATACAAGTAAATTCAAAAAAATGTCATG
196 TTTATAAAAGCATAATATTTTAAAAAATCCTTGAACTATACAAGAAAATTCAAAAAAATGTCATG
** *
3339850 ATTCTTGTATTGTGTTTAATTAACCATTTATATATTTTTTGAACTAAATAGACCTTATAATTAAT
261 ATTCTTGTATTACGTTTAATTAACCATCTATATATTTTTTGAACTAAATAGACCTTATAATTAAT
3339915 AATTGACTAACTATTATTAGTAACATTCATA
326 AATTGACTAACTATTATTAGTAACATTCATA
* * *
3339946 AAAAAAACATACAAAAGTAATGAAAATGGA-CCCACTACTTTCCTTTCACTTTAAAAAATATAAA
1 AAAAAAACATA-AAAAGTAATAAAAATGAACCCCACTACTCTCCTTTCACTTTAAAAAATAT-AA
* * * **********
3340010 AAGGAGAAAGACTAGAAGTCCACTCTTAGTTGCAAGGNNNNNNNNNNGTAAAAGCAACCTTACCT
64 AAGGAGAAAGACCACAAGTCCACTCCTAGTTGCAAGGCTATTTCCATGTAAAAGCAACCTTACCT
* *
3340075 AACGTGTTTCCAATTCAACTTAAGATTAGATTTATAAAGAGCTCTAATTTTCCAAGAAAG-TTAA
129 AACATATTTCCAATTCAACTTAAGATTAGATTTATAAAGAGCTCTAATTTTCCAAGAAAGTTTAA
* * *
3340139 ATTTTATAAAAGCATAATATTTTAAAAAATTCTTGAATTATACAAGAAAATTCAAAAAAA-GTCA
194 ACTTTATAAAAGCATAATATTTTAAAAAATCCTTGAACTATACAAGAAAATTCAAAAAAATGTCA
*
3340203 TGATTCTTTTATTACGTTTAATTAACCATCTATACT-TTTATTTGAACTAAACT-GACTCTTATA
259 TGATTCTTGTATTACGTTTAATTAACCATCTATA-TATTT-TTTGAACTAAA-TAGAC-CTTATA
3340266 ATTAAT
320 ATTAAT
3340272 TATTAGTAAA
Statistics
Matches: 289, Mismatches: 31, Indels: 11
0.87 0.09 0.03
Matches are distributed among these distances:
355 37 0.13
356 115 0.40
357 137 0.47
ACGTcount: A:0.42, C:0.15, G:0.09, T:0.33
Consensus pattern (356 bp):
AAAAAAACATAAAAAGTAATAAAAATGAACCCCACTACTCTCCTTTCACTTTAAAAAATATAAAA
GGAGAAAGACCACAAGTCCACTCCTAGTTGCAAGGCTATTTCCATGTAAAAGCAACCTTACCTAA
CATATTTCCAATTCAACTTAAGATTAGATTTATAAAGAGCTCTAATTTTCCAAGAAAGTTTAAAC
TTTATAAAAGCATAATATTTTAAAAAATCCTTGAACTATACAAGAAAATTCAAAAAAATGTCATG
ATTCTTGTATTACGTTTAATTAACCATCTATATATTTTTTGAACTAAATAGACCTTATAATTAAT
AATTGACTAACTATTATTAGTAACATTCATA
Found at i:3340932 original size:429 final size:429
Alignment explanation
Indices: 3339977--3340948 Score: 1127
Period size: 429 Copynumber: 2.3 Consensus size: 429
3339967 GAAAATGGAC
* * *
3339977 CCACTACTTTCCTTTCACTTTAAAAAATATAAAAAGGAGAAAG-ACTAGAAGTCCACTCTTAGTT
1 CCACTACTCTACTTTCACTTTAAAAAATATAAAAA-GAGAAAGAAC-AAAAGTCCACTCTTAGTT
* ********** *
3340041 GCAAGGNNNNNNNNNNGTAAAAGCAACCTTACCTAACGTGTTTCCAATTCAACTTAAGATTAGAT
64 GCAAAGCTAATTTCATGTAAAAGCAACCTTACCTAACGTATTTCCAATTCAACTTAAGATTAGAT
* * * *
3340106 TTATAAAGAGCTCTAATTTTCCAAGAAAGTTAAATTTTATAAAAGCATAATATTTTAAAAAATTC
129 ATATAAAGAGCTCTAACTTTCCAAGAAAGTTAAAGTTTATAAAAGCATAATATTTT-AAAAATCC
*
3340171 TTGAATTATACAAGAAAATTCAAAAAAAGTCATGATTCTTTTATTACGTTTAATTAACCATCTAT
193 TTGAATTATACAAGAAAATTCAAAAAAAGTCATGATTCTTTTACTACGTTTAATTAACCATCTAT
* * *
3340236 ACTTTTATTTGAACTAAACTGACTCTTATAATTAATTATTAGTAAACTATTGTTAGAAAAAAATA
258 ACTATTATTTGAACTAAACTGACTCTTATAATTAATGATTAGTAAACTATTATTAGAAAAAAATA
* *
3340301 TCATTTGTTATTTGATACTCACATGAAGTCGATGTGGTGTTAAGATGAAAGGTGAAAAATACCAC
323 TCATTTGTCATTTGATACTCACATGAACTCGATGTGGTGTTAAGATGAAAGGTGAAAAATACCAC
* * *
3340366 GTGATCTTGTCATTATGTCACCTCTGCATATCACATTATCAT
388 GTGATCATGTCATCATGTCACATCTGCATATCACATTATCAT
* * *
3340408 CCATTATTCTACTTTCACTTTAGAAAATATAAAAAGAGAAAGAACAAAAGTCCACTCTTAGTTGC
1 CCACTACTCTACTTTCACTTTAAAAAATATAAAAAGAGAAAGAACAAAAGTCCACTCTTAGTTGC
* ********** *
3340473 AAGGNNNNNNNNNNGTAAAAGCAACCTTACCTAACGTATTTCCAATTCAACTTAAGGTTAGATAT
66 AAAGCTAATTTCATGTAAAAGCAACCTTACCTAACGTATTTCCAATTCAACTTAAGATTAGATAT
* *
3340538 ATGAAGAGCTCTTACTTTCCAAGAAAGTTTAAAGTTTATAAAAGCATAATATTTT-AAAATCCTT
131 ATAAAGAGCTCTAACTTTCCAAGAAAG-TTAAAGTTTATAAAAGCATAATATTTTAAAAATCCTT
* * * **
3340602 GACTTATACAAGCAAATTCGAAAAAAAGTCATGATTCTTTTGCTGTGTTTAATTAACCATCTATA
195 GAATTATACAAGAAAATTC-AAAAAAAGTCATGATTCTTTTACTACGTTTAATTAACCATCTATA
* * * *
3340667 C-ATTATTTGAACTAAA-TAGGC-CTTTATGAA-TAGTGATT-GATTAACTATTATTAG-TAAAA
259 CTATTATTTGAACTAAACT-GACTC-TTAT-AATTAATGATTAG-TAAACTATTATTAGAAAAAA
* *
3340726 ATATCATTTGTCATTTTTATACTCACATGACACT-GATGTGGTGTTAAGGTGAAAGGTGAAAAAT
320 ATATCATTTGTCA-TTTGATACTCACATGA-ACTCGATGTGGTGTTAAGATGAAAGGTGAAAAAT
* * * * * * *
3340790 GCCACGTGATCATGTTATCATGTTATATTTGTATATCACATTATCGT
383 ACCACGTGATCATGTCATCATGTCACATCTGCATATCACATTATCAT
* * ** * *
3340837 CTACTACTCTACTTTCACTTTAAAAAATATAAAAGGAGAAAGTCCAGAAGTCTACTCTTAGTTGC
1 CCACTACTCTACTTTCACTTTAAAAAATATAAAAAGAGAAAGAACAAAAGTCCACTCTTAGTTGC
* *
3340902 AAAGCTAATTTCATGTAAACA-CAGCCTTACCTAACATATTTCCAATT
66 AAAGCTAATTTCATGTAAA-AGCAACCTTACCTAACGTATTTCCAATT
3340949 TAGTTTGCCA
Statistics
Matches: 468, Mismatches: 63, Indels: 22
0.85 0.11 0.04
Matches are distributed among these distances:
428 19 0.04
429 232 0.50
430 159 0.34
431 58 0.12
ACGTcount: A:0.37, C:0.15, G:0.12, T:0.34
Consensus pattern (429 bp):
CCACTACTCTACTTTCACTTTAAAAAATATAAAAAGAGAAAGAACAAAAGTCCACTCTTAGTTGC
AAAGCTAATTTCATGTAAAAGCAACCTTACCTAACGTATTTCCAATTCAACTTAAGATTAGATAT
ATAAAGAGCTCTAACTTTCCAAGAAAGTTAAAGTTTATAAAAGCATAATATTTTAAAAATCCTTG
AATTATACAAGAAAATTCAAAAAAAGTCATGATTCTTTTACTACGTTTAATTAACCATCTATACT
ATTATTTGAACTAAACTGACTCTTATAATTAATGATTAGTAAACTATTATTAGAAAAAAATATCA
TTTGTCATTTGATACTCACATGAACTCGATGTGGTGTTAAGATGAAAGGTGAAAAATACCACGTG
ATCATGTCATCATGTCACATCTGCATATCACATTATCAT
Found at i:3341130 original size:79 final size:79
Alignment explanation
Indices: 3340999--3341154 Score: 294
Period size: 79 Copynumber: 2.0 Consensus size: 79
3340989 GTACACAAAT
*
3340999 ACTTTGGATTAGACAACAACTAAATGATTTTGGAATGACTATGCACAAAGTTCCTATATATTGTG
1 ACTTTGGATTAGACAACAACTAAATGATTTTGGAATGACTATACACAAAGTTCCTATATATTGTG
3341064 ATAATATGAGTGAC
66 ATAATATGAGTGAC
*
3341078 ACTTTGGATTAGACAACAACTAAATGATTTTGGAATGGCTATACACAAAGTTCCTATATATTGTG
1 ACTTTGGATTAGACAACAACTAAATGATTTTGGAATGACTATACACAAAGTTCCTATATATTGTG
3341143 ATAATATGAGTG
66 ATAATATGAGTG
3341155 CCATTAATAT
Statistics
Matches: 75, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
79 75 1.00
ACGTcount: A:0.37, C:0.12, G:0.18, T:0.33
Consensus pattern (79 bp):
ACTTTGGATTAGACAACAACTAAATGATTTTGGAATGACTATACACAAAGTTCCTATATATTGTG
ATAATATGAGTGAC
Found at i:3345864 original size:24 final size:24
Alignment explanation
Indices: 3345837--3345885 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
3345827 CATCAACATG
3345837 TTCATTCACAAATTCAATTTCTTT
1 TTCATTCACAAATTCAATTTCTTT
***
3345861 TTCATTCACCCTTTCAATTTCTTT
1 TTCATTCACAAATTCAATTTCTTT
3345885 T
1 T
3345886 CCACTCTATA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.22, C:0.24, G:0.00, T:0.53
Consensus pattern (24 bp):
TTCATTCACAAATTCAATTTCTTT
Found at i:3352138 original size:359 final size:354
Alignment explanation
Indices: 3351483--3352139 Score: 855
Period size: 354 Copynumber: 1.8 Consensus size: 354
3351473 ATAATGTTAA
* * * *
3351483 TTATGTTCCTTATAAATGAACCCAATATATATAAAGTATTGATATTAAAAGACATTACAAATTAA
1 TTATATTCCTTATAAATGAACCCAACATATATAAAGTAATGACATTAAAAGACATTACAAATTAA
* * ** *
3351548 TTAAAATCATAATTTTATTAATTAATTTAATTAATTATATGTTTTATCTTTAATTACATGAAATT
66 TTAAAATCATAATTTCATGAATTAATTTAATTAATTATATAATTTATCCTTAATTACATGAAATT
** * * *
3351613 AAAAAAATAGTTAAATTTCAAAACTATTCTAATCTTACAACTTCTTTTTAGATAATTAAGTTTAT
131 AAAAAAATACCTAAATTTCAAAACTATTCGAATCTCACAACTTCTTTTAAGAT-ATT-AG--T-T
* * *
3351678 ATATTATAAGTTTATATAAATAAAGGTATATATATTTTAATTAATAATTTTATAAGTTATAATAA
191 ATATTATAAGTTTATATAAACAAAGATATATATATTATAATTAATAATTTTATAAGTTATAATAA
3351743 TTGCAATGTTAACACAAAATAGAACATAAATATGTTTATATTTAAAGTGTATATATATTTACACA
256 TTGCAATGTTAACACAAAATAGAACATAAATATGTTTATATTTAAAGTGTATATATATTTACACA
3351808 CATTAAAAGTATTTCACTAAATACATAATAGTAT
321 CATTAAAAGTATTTCACTAAATACATAATAGTAT
* *
3351842 TTATATTCTTTATAAATGAGCCCAACATATATAAAGTAAAT-ACATTAAAAGACATTACAAGA-T
1 TTATATTCCTTATAAATGAACCCAACATATATAAAGT-AATGACATTAAAAGACATTACAA-ATT
* *
3351905 AATTAATAATTATAGTTTCATGAATTAATTTAATTAATTATATAAATTTATCCTTAATTACATGA
64 AATTAA-AATCATAATTTCATGAATTAATTTAATTAATTATAT-AATTTATCCTTAATTACATGA
* * *
3351970 AATTTAAAAAAGA-ACCTAAGTTTTAAAACTATTCGAATCTCGCAACTTCTTTTAAGAT-TT-G-
127 AA-TTAAAAAA-ATACCTAAATTTCAAAACTATTCGAATCTCACAACTTCTTTTAAGATATTAGT
*
3352031 TATATTATAAGTTTATATAAACAAAGATATATATATTATAATTAATAATTTT-TCAAGTTATCAT
190 TATATTATAAGTTTATATAAACAAAGATATATATATTATAATTAATAATTTTAT-AAGTTATAAT
* * * * * *
3352095 -TTTGTAATGTTAACATAAAAT-GAAAAGTAAATATATTTATGTTTA
254 AATTGCAATGTTAACACAAAATAGAACA-TAAATATGTTTATATTTA
3352140 NNNNNNNNNN
Statistics
Matches: 259, Mismatches: 31, Indels: 22
0.83 0.10 0.07
Matches are distributed among these distances:
352 4 0.02
353 35 0.14
354 58 0.22
358 1 0.00
359 58 0.22
360 37 0.14
361 20 0.08
362 45 0.17
363 1 0.00
ACGTcount: A:0.44, C:0.08, G:0.07, T:0.41
Consensus pattern (354 bp):
TTATATTCCTTATAAATGAACCCAACATATATAAAGTAATGACATTAAAAGACATTACAAATTAA
TTAAAATCATAATTTCATGAATTAATTTAATTAATTATATAATTTATCCTTAATTACATGAAATT
AAAAAAATACCTAAATTTCAAAACTATTCGAATCTCACAACTTCTTTTAAGATATTAGTTATATT
ATAAGTTTATATAAACAAAGATATATATATTATAATTAATAATTTTATAAGTTATAATAATTGCA
ATGTTAACACAAAATAGAACATAAATATGTTTATATTTAAAGTGTATATATATTTACACACATTA
AAAGTATTTCACTAAATACATAATAGTAT
Found at i:3355416 original size:1 final size:1
Alignment explanation
Indices: 3355410--3355481 Score: 126
Period size: 1 Copynumber: 72.0 Consensus size: 1
3355400 GAAGAGAAAA
* *
3355410 GGGGGGGGGGGGGGGGGAGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGAGGGGGGGGG
1 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
3355475 GGGGGGG
1 GGGGGGG
3355482 TTATTGCTTT
Statistics
Matches: 67, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
1 67 1.00
ACGTcount: A:0.03, C:0.00, G:0.97, T:0.00
Consensus pattern (1 bp):
G
Found at i:3366712 original size:3 final size:3
Alignment explanation
Indices: 3366698--3366743 Score: 74
Period size: 3 Copynumber: 15.3 Consensus size: 3
3366688 AAATTTTATT
* *
3366698 TCA TCG TCA TCA TCA TCA TCA TCA TCA TCA TCA CCA TCA TCA TCA T
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA T
3366744 TTCCACCACC
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.30, C:0.35, G:0.02, T:0.33
Consensus pattern (3 bp):
TCA
Done.