Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397257.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_95.0, 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: 12062019
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 103452 characters in sequence are not A, C, G, or T
File 25 of 26
Found at i:11012706 original size:23 final size:23
Alignment explanation
Indices: 11012658--11012702 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
11012648 AAATATATAC
*
11012658 ATAATTTATACATAAACATTATT
1 ATAACTTATACATAAACATTATT
*
11012681 ATAACTTATA-ATAAACCTTATT
1 ATAACTTATACATAAACATTATT
11012703 TATATAATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 11 0.55
23 9 0.45
ACGTcount: A:0.47, C:0.11, G:0.00, T:0.42
Consensus pattern (23 bp):
ATAACTTATACATAAACATTATT
Found at i:11013040 original size:220 final size:218
Alignment explanation
Indices: 11012652--11013239 Score: 992
Period size: 220 Copynumber: 2.7 Consensus size: 218
11012642 TGTAATAAAT
* * * * * *
11012652 ATATACATAATTTATACATAAACATTATTATAACTTATAATAAACCTTA-TTTATATAATTACAC
1 ATATACGTAATTTATACATAAATATTATTATAATTTATAATAGA-CTTATTTTATGTGATTACAC
* * * *
11012716 TTAATAACTTTATTAGTTATCACTTTAGTTTTTATAACATATTATTTATAATTAGTTATTATTTA
65 TTAATAACTTTATTAGTTATCACCTTAATTTTTATAACATATTGTCTATAATTAGTTATTATTTA
11012781 TACAAACTTTCATATAAAAATTAAAACATTATAACATATAAGTTATATCGTTAATTTC-ATATAT
130 TACAAACTTTCATATAAAAATTAAAACATTATAACATATAAGTTATATCGTTAA-TTCAATATAT
11012845 ATAATAAAGTAATATAATACATATAC
194 AT-ATAAAGTAATATAATACATATAC
11012871 ATATACGTAATTTATACATAAAATATTATTATAATTTATAATAGACTTATTTTATGTGATTACAC
1 ATATACGTAATTTATACAT-AAATATTATTATAATTTATAATAGACTTATTTTATGTGATTACAC
11012936 TTAATAACTTTATTAGTTATCACCTTAATTTTTATAACATATTGTCTATAATTAGTTATTATTTA
65 TTAATAACTTTATTAGTTATCACCTTAATTTTTATAACATATTGTCTATAATTAGTTATTATTTA
11013001 TACAAACTTTCATATAAAAATTAAAACATTATAACATATAAGTTATATCGTTAATTCAATATATA
130 TACAAACTTTCATATAAAAATTAAAACATTATAACATATAAGTTATATCGTTAATTCAATATATA
11013066 TATAAAGTAATATAATACATATAC
195 TATAAAGTAATATAATACATATAC
11013090 ATATACG---TTTATACATAAATATATATTATAATTTATAATAGACTTATTTTATGTGATTACAC
1 ATATACGTAATTTATACATAAATAT-TATTATAATTTATAATAGACTTATTTTATGTGATTACAC
11013152 TTAATAAC--TATTAGTTATCACCTTAATTTTTATAACATATTGTCTATAATTAGTTATTATTTA
65 TTAATAACTTTATTAGTTATCACCTTAATTTTTATAACATATTGTCTATAATTAGTTATTATTTA
11013215 TACAAACTTTCATATAAAAATTAAA
130 TACAAACTTTCATATAAAAATTAAA
11013240 TAAGTTATAT
Statistics
Matches: 355, Mismatches: 10, Indels: 13
0.94 0.03 0.03
Matches are distributed among these distances:
214 80 0.23
215 6 0.02
216 56 0.16
219 55 0.15
220 158 0.45
ACGTcount: A:0.43, C:0.09, G:0.04, T:0.44
Consensus pattern (218 bp):
ATATACGTAATTTATACATAAATATTATTATAATTTATAATAGACTTATTTTATGTGATTACACT
TAATAACTTTATTAGTTATCACCTTAATTTTTATAACATATTGTCTATAATTAGTTATTATTTAT
ACAAACTTTCATATAAAAATTAAAACATTATAACATATAAGTTATATCGTTAATTCAATATATAT
ATAAAGTAATATAATACATATAC
Found at i:11013340 original size:214 final size:212
Alignment explanation
Indices: 11012686--11013340 Score: 632
Period size: 220 Copynumber: 3.0 Consensus size: 212
11012676 TTATTATAAC
* * * * *
11012686 TTATAATAAACCTTA-TTTATATAATTACACTTAATAACTTTATTAGTTATCACTTTAGTTTTTA
1 TTATAATAGA-CTTATTTTATGTGATTACACTTAATAAC-TTATTAGTTATCACCTTAATTTTTA
* *
11012750 TAACATATTATTTATAATTAGTTATTATTTATACAAACTTTCATATAAAAATTAAAACATTATAA
64 TAACATATTGTCTATAATTAGTTATTATTTATACAAACTTTC--AT----A-TAAAA-A-T-T-A
* * **
11012815 CATATAAGTTATATCGTTAATTTCATATATATAATAAAGTAATATAATACATATACATATACGTA
118 -A-ATAAGTTATATCGTTAATTTCATATATATAATAAAGTAATAT-ATATATATAAATA-ATTTA
* *
11012880 -ATTTATACA-TA--A-AA-TAT--T-ATTATAAT
179 TATATATACATTACTATAACTATAATAATT-TTAT
11012906 TTATAATAGACTTATTTTATGTGATTACACTTAATAACTTTATTAGTTATCACCTTAATTTTTAT
1 TTATAATAGACTTATTTTATGTGATTACACTTAATAAC-TTATTAGTTATCACCTTAATTTTTAT
11012971 AACATATTGTCTATAATTAGTTATTATTTATACAAACTTTCATATAAAAATTAAA-ACA-TTATA
65 AACATATTGTCTATAATTAGTTATTATTTATACAAACTTTCATATAAAAATTAAATA-AGTTATA
* * * * * * *
11013034 ACATATAAGTT-ATATCGT-TAAT----TCAATATATATATA-AAGTAATATAATACATATACAT
129 TCGT-TAATTTCATAT-ATATAATAAAGT-AATATATATATATAAATAAT-TTATATATATACAT
*
11013092 ATACGTTTATAC-ATAAATATATATTATAAT
190 -TAC-TATA-ACTAT-AATA-AT-TT-T-AT
11013122 TTATAATAGACTTATTTTATGTGATTACACTTAATAAC-TATTAGTTATCACCTTAATTTTTATA
1 TTATAATAGACTTATTTTATGTGATTACACTTAATAACTTATTAGTTATCACCTTAATTTTTATA
11013186 ACATATTGTCTATAATTAGTTATTATTTATACAAACTTTCATATAAAAATTAAATAAGTTATATC
66 ACATATTGTCTATAATTAGTTATTATTTATACAAACTTTCATATAAAAATTAAATAAGTTATATC
** *
11013251 GTTAATTTCATATATATAATAAAGTAATATATTTATATATATTTAATTTATATATAAACATTACT
131 GTTAATTTCATATATATAATAAAGTAATATA--TATATATAAATAATTTATATATATACATTACT
11013316 ATAACTTATAATAATTTTAT
194 ATAAC-TATAATAATTTTAT
11013336 TTATA
1 TTATA
11013341 TGATTACACT
Statistics
Matches: 368, Mismatches: 31, Indels: 78
0.77 0.06 0.16
Matches are distributed among these distances:
200 1 0.00
201 4 0.01
202 14 0.04
203 5 0.01
204 2 0.01
206 16 0.04
207 8 0.02
208 2 0.01
209 4 0.01
210 1 0.00
211 1 0.00
212 2 0.01
213 5 0.01
214 98 0.27
215 18 0.05
216 42 0.11
217 4 0.01
218 15 0.04
219 10 0.03
220 111 0.30
221 5 0.01
ACGTcount: A:0.43, C:0.09, G:0.04, T:0.45
Consensus pattern (212 bp):
TTATAATAGACTTATTTTATGTGATTACACTTAATAACTTATTAGTTATCACCTTAATTTTTATA
ACATATTGTCTATAATTAGTTATTATTTATACAAACTTTCATATAAAAATTAAATAAGTTATATC
GTTAATTTCATATATATAATAAAGTAATATATATATATAAATAATTTATATATATACATTACTAT
AACTATAATAATTTTAT
Found at i:11023810 original size:2 final size:2
Alignment explanation
Indices: 11023803--11023840 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
11023793 AAAGAAACAC
11023803 AG AG AG AG AG 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 AG AG AG AG AG
11023841 TGGACCTGGT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:11038032 original size:2 final size:2
Alignment explanation
Indices: 11038027--11038058 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
11038017 GCGCGCGCTT
11038027 TC TC 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 TC TC
11038059 AAAGTAAACG
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:11062158 original size:2 final size:2
Alignment explanation
Indices: 11062151--11062187 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
11062141 ATAGGAATAC
11062151 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
11062188 ATCTCTCTTC
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:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:11067859 original size:6 final size:6
Alignment explanation
Indices: 11067848--11067879 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
11067838 TTGTTTCATT
11067848 TCCATC TCCATC TCCATC TCCATC TCCATC TC
1 TCCATC TCCATC TCCATC TCCATC TCCATC TC
11067880 TCACTCTTGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.16, C:0.50, G:0.00, T:0.34
Consensus pattern (6 bp):
TCCATC
Found at i:11078761 original size:2 final size:2
Alignment explanation
Indices: 11078754--11078794 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
11078744 CCAACTGAAT
11078754 TA TA 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 TA TA T
11078795 TGAACTTTTC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:11108145 original size:4 final size:4
Alignment explanation
Indices: 11108136--11108171 Score: 63
Period size: 4 Copynumber: 8.8 Consensus size: 4
11108126 TATTTTTATA
11108136 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATATC ATA
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA-C ATA
11108172 TATAATTTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
4 27 0.87
5 4 0.13
ACGTcount: A:0.50, C:0.22, G:0.00, T:0.28
Consensus pattern (4 bp):
ATAC
Found at i:11110195 original size:22 final size:22
Alignment explanation
Indices: 11110170--11110211 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
11110160 TCTATGTTAC
* *
11110170 TAAAAAATTTTCAAATTAAATA
1 TAAAAAATGTTAAAATTAAATA
*
11110192 TAAAATATGTTAAAATTAAA
1 TAAAAAATGTTAAAATTAAA
11110212 ATTTTTATCG
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:0.60, C:0.02, G:0.02, T:0.36
Consensus pattern (22 bp):
TAAAAAATGTTAAAATTAAATA
Found at i:11115092 original size:159 final size:162
Alignment explanation
Indices: 11114699--11115109 Score: 451
Period size: 159 Copynumber: 2.5 Consensus size: 162
11114689 ACATAATGAC
* * * * * *
11114699 TAATTATTAAATATACGTGAAAATATTATGAAATGTATTGATTATAA-AAATTAATAAGAGAATT
1 TAATAATTATATATACGTGTAAATATTATAAAAT-TATTGACTA-AAGAAATTAATAAAAGAATT
* * * *
11114763 GAATTTGTCGTGTAATTATAATTTTTGAATTTTTTTTTTCGATCAAAATTTATTATTGGGTACAA
64 GAATTCGTCGTGTAATTATAAATCTTGAA-TTTTTTTTTC-ATCAAAATTCATTATTGGGTACAA
* *
11114828 TTATCATTAATGCTCACATATATGAGATCTAATCAT
127 TTATCATTAATACACACATATATGAGATCTAATCAT
* * * *
11114864 TAAAAATTATATATACGTGTAAATATTATGAAAGTTATTGACTAAACGAAATTAACAAAAAAAAT
1 TAATAATTATATATACGTGTAAATATTAT-AAAATTATTGACTAAA-GAAATTAA-TAAAAGAAT
* *
11114929 TGAATTCGTCGTGCAATTATAAATCTT-AA-TTTTTTTT-AT-AAGAATTCATTATT-GGTCCAA
63 TGAATTCGTCGTGTAATTATAAATCTTGAATTTTTTTTTCATCAA-AATTCATTATTGGGTACAA
*
11114989 TTATCATTCATACACACATATATGAG-T-TAATCAT
127 TTATCATTAATACACACATATATGAGATCTAATCAT
* ** *
11115023 TAATAATTATATATACATGTAAATATTATAAAATATATTGACTAAATGAAATTAATGATCAGAAC
1 TAATAATTATATATACGTGTAAATATTATAAAAT-TATTGACTAAA-GAAATTAAT-AAAAGAAT
*
11115088 TGAATTGGTCGTGTAATTATAA
63 TGAATTCGTCGTGTAATTATAA
11115110 TTGTTGAACC
Statistics
Matches: 209, Mismatches: 30, Indels: 20
0.81 0.12 0.08
Matches are distributed among these distances:
158 4 0.02
159 77 0.37
160 1 0.00
161 31 0.15
162 12 0.06
164 10 0.05
165 33 0.16
166 12 0.06
167 29 0.14
ACGTcount: A:0.42, C:0.08, G:0.11, T:0.40
Consensus pattern (162 bp):
TAATAATTATATATACGTGTAAATATTATAAAATTATTGACTAAAGAAATTAATAAAAGAATTGA
ATTCGTCGTGTAATTATAAATCTTGAATTTTTTTTTCATCAAAATTCATTATTGGGTACAATTAT
CATTAATACACACATATATGAGATCTAATCAT
Found at i:11122420 original size:123 final size:121
Alignment explanation
Indices: 11122293--11122604 Score: 281
Period size: 123 Copynumber: 2.5 Consensus size: 121
11122283 GCCGCACTTG
* * *
11122293 AGGGAAGCACCACATCAGCCATGCTTAATGTGGCTCCATCAGGAATTTCTTCAGATGAAGGTGCT
1 AGGGAA-CACC-CATCAACCTTCCTTAATGTGGCTCCATCAGGAATTTCTTCAGATGAAGGTGCT
** * * * *
11122358 TC-AGCTGAGCTGAGGTTCTCCTGACCTTCACCA-GAAATGGCAATCAGAGGTTCTC-CTA
64 TCTA-AAGAGATGAGGTTCTCCTGACCTTCA-CAGGAAATGACAATCACAGATTCTCTC-A
* * * * * *
11122416 AGGGAACCTGCCCATCAACTTTCCGTAAAT-TGGTTCCATCAGGAACTTCTACAGATGAAGGTGC
1 AGGGAA-C-ACCCATCAACCTTCC-TTAATGTGGCTCCATCAGGAATTTCTTCAGATGAAGGTGC
* *
11122480 TTCTAAAGAGATGAGGTTCTCTTGACCTTCACAGGAAATGACAGTCACAGATTCTCTCA
63 TTCTAAAGAGATGAGGTTCTCCTGACCTTCACAGGAAATGACAATCACAGATTCTCTCA
* * * * * * * *
11122539 AGGGAACATCCTCATCAATCTTTCTTAATGAGTCTCTATTAGAAATTTTTTCAGATGAAGGTGCT
1 AGGGAACA-CC-CATCAACCTTCCTTAATGTGGCTCCATCAGGAATTTCTTCAGATGAAGGTGCT
11122604 T
64 T
11122605 GCAATGAGGC
Statistics
Matches: 149, Mismatches: 32, Indels: 16
0.76 0.16 0.08
Matches are distributed among these distances:
122 9 0.06
123 132 0.89
124 8 0.05
ACGTcount: A:0.28, C:0.23, G:0.21, T:0.29
Consensus pattern (121 bp):
AGGGAACACCCATCAACCTTCCTTAATGTGGCTCCATCAGGAATTTCTTCAGATGAAGGTGCTTC
TAAAGAGATGAGGTTCTCCTGACCTTCACAGGAAATGACAATCACAGATTCTCTCA
Found at i:11138740 original size:2 final size:2
Alignment explanation
Indices: 11138733--11138762 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
11138723 ATTTAGAGTG
11138733 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
11138763 TCCCTTTTCC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:11138929 original size:2 final size:2
Alignment explanation
Indices: 11138922--11138964 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
11138912 TCCCTTATTT
11138922 TA TA TA TA 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 TA TA TA TA
11138964 T
1 T
11138965 GAACTTCGTG
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:11142023 original size:30 final size:30
Alignment explanation
Indices: 11141987--11142055 Score: 120
Period size: 30 Copynumber: 2.3 Consensus size: 30
11141977 TTTCAACAGC
*
11141987 TAGAAGCTCTCCTCGATCTGGCCAAACTGG
1 TAGAAGCTCTCCTCGATCTGGCCAAAATGG
*
11142017 TAGAAGCTCTCCTCGATCTGGTCAAAATGG
1 TAGAAGCTCTCCTCGATCTGGCCAAAATGG
11142047 TAGAAGCTC
1 TAGAAGCTC
11142056 CACAAATTCA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 37 1.00
ACGTcount: A:0.26, C:0.26, G:0.23, T:0.25
Consensus pattern (30 bp):
TAGAAGCTCTCCTCGATCTGGCCAAAATGG
Found at i:11144382 original size:25 final size:24
Alignment explanation
Indices: 11144354--11144401 Score: 69
Period size: 25 Copynumber: 2.0 Consensus size: 24
11144344 TTCATTAATA
* *
11144354 ATTAAATTTACAATATTAAATAAAC
1 ATTAAAATTAAAATA-TAAATAAAC
11144379 ATTAAAATTAAAATATAAATAAA
1 ATTAAAATTAAAATATAAATAAA
11144402 AAATTAGAGT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 8 0.38
25 13 0.62
ACGTcount: A:0.62, C:0.04, G:0.00, T:0.33
Consensus pattern (24 bp):
ATTAAAATTAAAATATAAATAAAC
Found at i:11147978 original size:14 final size:16
Alignment explanation
Indices: 11147955--11147988 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
11147945 GTAAGTCTAG
11147955 TTTTTAATAT-ATTTA
1 TTTTTAATATCATTTA
11147970 TTTTT-ATATCATTTA
1 TTTTTAATATCATTTA
11147985 TTTT
1 TTTT
11147989 ATTTATACTC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 4 0.22
15 14 0.78
ACGTcount: A:0.26, C:0.03, G:0.00, T:0.71
Consensus pattern (16 bp):
TTTTTAATATCATTTA
Found at i:11148381 original size:36 final size:36
Alignment explanation
Indices: 11148341--11148414 Score: 96
Period size: 36 Copynumber: 2.1 Consensus size: 36
11148331 TTCTACGCAA
* **
11148341 TACATGATTTGTTTTCCATCAACAGTTTT-AGTGTCG
1 TACATGATTTATCCTCCATCAACAGTTTTGA-TGTCG
*
11148377 TACATGATTTATCCTCCATCGACAGTTTTGATGTCG
1 TACATGATTTATCCTCCATCAACAGTTTTGATGTCG
11148413 TA
1 TA
11148415 TTTATTCTTC
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
36 32 0.97
37 1 0.03
ACGTcount: A:0.23, C:0.19, G:0.16, T:0.42
Consensus pattern (36 bp):
TACATGATTTATCCTCCATCAACAGTTTTGATGTCG
Found at i:11149536 original size:25 final size:25
Alignment explanation
Indices: 11149500--11149552 Score: 79
Period size: 25 Copynumber: 2.1 Consensus size: 25
11149490 CAATAGTCAA
* *
11149500 ATTGGTTTTAATGTGATGCCTTTTT
1 ATTGGTTATAATGTGATGCCTTCTT
*
11149525 ATTGGTTATAATGTGATGTCTTCTT
1 ATTGGTTATAATGTGATGCCTTCTT
11149550 ATT
1 ATT
11149553 TTTGCTTTAG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.19, C:0.08, G:0.19, T:0.55
Consensus pattern (25 bp):
ATTGGTTATAATGTGATGCCTTCTT
Found at i:11163327 original size:96 final size:95
Alignment explanation
Indices: 11163192--11163384 Score: 350
Period size: 96 Copynumber: 2.0 Consensus size: 95
11163182 TTATGCCTTG
*
11163192 ACCAAAGAAAGGGTTTGTGTTTCCATTTCATTTGTGTCCAACAATTGCATCACCTTTGAAAAGAA
1 ACCAAAGAAAGGGTTTGTGTTTCCATTTCATTTGAGTCCAACAATTGCATCACCTTTGAAAAGAA
*
11163257 AAACTGGGACTCCCCATAGTCTCGCATAGT
66 AAACTGGGACTCCCCATAGTCACGCATAGT
*
11163287 ACCAAAGAAAGGGTTTTGTGTTTCCATTTTATTTGAGTCCAACAATTGCATCACCTTTGAAAAGA
1 ACCAAAGAAAGGG-TTTGTGTTTCCATTTCATTTGAGTCCAACAATTGCATCACCTTTGAAAAGA
11163352 AAAACTGGGACTCCCCATAGTCACGCATAGT
65 AAAACTGGGACTCCCCATAGTCACGCATAGT
11163383 AC
1 AC
11163385 ACGTTTCAAA
Statistics
Matches: 94, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
95 13 0.14
96 81 0.86
ACGTcount: A:0.32, C:0.22, G:0.18, T:0.29
Consensus pattern (95 bp):
ACCAAAGAAAGGGTTTGTGTTTCCATTTCATTTGAGTCCAACAATTGCATCACCTTTGAAAAGAA
AAACTGGGACTCCCCATAGTCACGCATAGT
Found at i:11170483 original size:35 final size:35
Alignment explanation
Indices: 11170437--11170509 Score: 146
Period size: 35 Copynumber: 2.1 Consensus size: 35
11170427 GATGCTCTTA
11170437 GGACAATAATGGTTCAAAACAAGGAAAAGGATAAT
1 GGACAATAATGGTTCAAAACAAGGAAAAGGATAAT
11170472 GGACAATAATGGTTCAAAACAAGGAAAAGGATAAT
1 GGACAATAATGGTTCAAAACAAGGAAAAGGATAAT
11170507 GGA
1 GGA
11170510 AGTTAATTGC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 38 1.00
ACGTcount: A:0.51, C:0.08, G:0.25, T:0.16
Consensus pattern (35 bp):
GGACAATAATGGTTCAAAACAAGGAAAAGGATAAT
Found at i:11175953 original size:18 final size:17
Alignment explanation
Indices: 11175926--11175963 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
11175916 CCCTAATGGG
11175926 GAAAAAATAACA-AAGAA
1 GAAAAAATAA-AGAAGAA
11175943 GAAAAACATAAAGAAGAA
1 GAAAAA-ATAAAGAAGAA
11175961 GAA
1 GAA
11175964 GAAGGAGGAG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 7 0.37
18 12 0.63
ACGTcount: A:0.74, C:0.05, G:0.16, T:0.05
Consensus pattern (17 bp):
GAAAAAATAAAGAAGAA
Found at i:11179164 original size:2 final size:2
Alignment explanation
Indices: 11179157--11179196 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
11179147 ATCTACTTGA
11179157 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
11179197 TAAAAAAGTA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:11183702 original size:18 final size:18
Alignment explanation
Indices: 11183679--11183714 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
11183669 ACGTCGTCAG
* *
11183679 GGACTTCAGTTTCAAGCC
1 GGACTTCACTCTCAAGCC
11183697 GGACTTCACTCTCAAGCC
1 GGACTTCACTCTCAAGCC
11183715 TCCGAGAATC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.22, C:0.33, G:0.19, T:0.25
Consensus pattern (18 bp):
GGACTTCACTCTCAAGCC
Found at i:11188932 original size:2 final size:2
Alignment explanation
Indices: 11188925--11188963 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
11188915 TTCTTAATCC
11188925 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
11188964 GCTGTCTAAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:11195045 original size:17 final size:18
Alignment explanation
Indices: 11195020--11195053 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
11195010 TAACTCTATC
11195020 AAAAATATT-ATTTAATT
1 AAAAATATTAATTTAATT
*
11195037 AAAATTATTAATTTAAT
1 AAAAATATTAATTTAAT
11195054 AAGTATTAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (18 bp):
AAAAATATTAATTTAATT
Found at i:11195052 original size:14 final size:15
Alignment explanation
Indices: 11195026--11195066 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
11195016 TATCAAAAAT
11195026 ATTATTTAA-TTAA-A
1 ATTA-TTAATTTAATA
11195040 ATTATTAATTTAATA
1 ATTATTAATTTAATA
*
11195055 AGTATTAATTTA
1 ATTATTAATTTA
11195067 TAAAGATTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
13 4 0.17
14 8 0.33
15 12 0.50
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.51
Consensus pattern (15 bp):
ATTATTAATTTAATA
Found at i:11201341 original size:32 final size:31
Alignment explanation
Indices: 11201300--11201359 Score: 102
Period size: 32 Copynumber: 1.9 Consensus size: 31
11201290 CAATGGAATA
*
11201300 TAGAAAAAATAAAATAATTATTTTATAAAAT
1 TAGAAAAAATAAAATAATTATTATATAAAAT
11201331 TAGAATAAAATAAAATAATTATTATATAA
1 TAGAA-AAAATAAAATAATTATTATATAA
11201360 TTTGATTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
31 5 0.19
32 22 0.81
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (31 bp):
TAGAAAAAATAAAATAATTATTATATAAAAT
Found at i:11201359 original size:16 final size:16
Alignment explanation
Indices: 11201308--11201359 Score: 50
Period size: 16 Copynumber: 3.2 Consensus size: 16
11201298 TATAGAAAAA
*
11201308 ATAAAATAATTATTTT
1 ATAAAATAATTATTAT
* ** * *
11201324 ATAAAATTAGAATAAA
1 ATAAAATAATTATTAT
11201340 ATAAAATAATTATTAT
1 ATAAAATAATTATTAT
11201356 ATAA
1 ATAA
11201360 TTTGATTTTT
Statistics
Matches: 25, Mismatches: 11, Indels: 0
0.69 0.31 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (16 bp):
ATAAAATAATTATTAT
Found at i:11203037 original size:3 final size:3
Alignment explanation
Indices: 11203029--11203060 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
11203019 CCAAGGGGAG
11203029 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
11203061 GGAGGAGGAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:11203065 original size:3 final size:3
Alignment explanation
Indices: 11203059--11203084 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
11203049 AGAAGAAGAA
11203059 GAG GAG GAG GAG GAG GAG GAG GAG GA
1 GAG GAG GAG GAG GAG GAG GAG GAG GA
11203085 AGAAGCATTG
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:0.35, C:0.00, G:0.65, T:0.00
Consensus pattern (3 bp):
GAG
Found at i:11207272 original size:2 final size:2
Alignment explanation
Indices: 11207267--11207298 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
11207257 TTTTTATTTA
11207267 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
11207299 TAGTTTTATA
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:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:11215131 original size:124 final size:127
Alignment explanation
Indices: 11214971--11215212 Score: 348
Period size: 130 Copynumber: 1.9 Consensus size: 127
11214961 CCGAACAGTA
* *
11214971 TCAGATAGTCTCCCTGACACCGAGGAAAATCCAGAACA-TAGAATTCAAATACATT-TA-GGACC
1 TCAGATAGTCTCCCTGACACCAAGGAAAAACCAGAACACTAGAATTCAAATACATTATACGGACC
* *
11215033 AAAGGAAGTGAAAGCAGAAGCAAACAAATAGATTATATTTACAAATCTTTCACAAACTATTC
66 AAAGGAAATGAAAGCAGAAGCAAACAAATAGATTACATTTACAAATCTTTCACAAACTATTC
11215095 TCAGATTAGTCT-CCTGACACCAAGGAAAAACCAGAACACTAGAATTCAAATACATTCATATCGG
1 TCAGA-TAGTCTCCCTGACACCAAGGAAAAACCAGAACACTAGAATTCAAATACATT-ATA-C-G
* * * *
11215159 GACCACAGGAAATGGAAGCAGAAGCAAACGAATAGATTACATTTATAAATCTTT
62 GACCAAAGGAAATGAAAGCAGAAGCAAACAAATAGATTACATTTACAAATCTTT
11215213 TACTAACTCC
Statistics
Matches: 103, Mismatches: 8, Indels: 8
0.87 0.07 0.07
Matches are distributed among these distances:
124 29 0.28
125 23 0.22
127 2 0.02
130 49 0.48
ACGTcount: A:0.43, C:0.19, G:0.15, T:0.22
Consensus pattern (127 bp):
TCAGATAGTCTCCCTGACACCAAGGAAAAACCAGAACACTAGAATTCAAATACATTATACGGACC
AAAGGAAATGAAAGCAGAAGCAAACAAATAGATTACATTTACAAATCTTTCACAAACTATTC
Found at i:11226650 original size:18 final size:18
Alignment explanation
Indices: 11226608--11226670 Score: 56
Period size: 18 Copynumber: 3.5 Consensus size: 18
11226598 ATAATTATAT
* *
11226608 AAAATTATAAATTAAATTA
1 AAAATT-TAATTTAAAATA
*
11226627 ATAATTTAATTTAAAATA
1 AAAATTTAATTTAAAATA
* *
11226645 AAAATTAAATTT-TAATA
1 AAAATTTAATTTAAAATA
*
11226662 CAAATTTAA
1 AAAATTTAA
11226671 AAAAGAGACT
Statistics
Matches: 36, Mismatches: 8, Indels: 2
0.78 0.17 0.04
Matches are distributed among these distances:
17 11 0.31
18 20 0.56
19 5 0.14
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.40
Consensus pattern (18 bp):
AAAATTTAATTTAAAATA
Found at i:11227426 original size:31 final size:31
Alignment explanation
Indices: 11227391--11227498 Score: 105
Period size: 31 Copynumber: 3.6 Consensus size: 31
11227381 TCAATCATTA
* * *
11227391 TTATAAACATTTATTTGATTTGAAATAAAAT
1 TTATAAAAATTTATTTAATTTAAAATAAAAT
11227422 TTATAAAAATTTATTTAATTTAAAATAAAA-
1 TTATAAAAATTTATTTAATTTAAAATAAAAT
* * * * *
11227452 ATATAAAAATATAATTAA-ATATAATAAAA-
1 TTATAAAAATTTATTTAATTTAAAATAAAAT
* *
11227481 ATATAAAACTTTATTTAA
1 TTATAAAAATTTATTTAA
11227499 AATTTTTTAA
Statistics
Matches: 66, Mismatches: 11, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
29 24 0.36
30 15 0.23
31 27 0.41
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.41
Consensus pattern (31 bp):
TTATAAAAATTTATTTAATTTAAAATAAAAT
Found at i:11227484 original size:11 final size:11
Alignment explanation
Indices: 11227454--11227486 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
11227444 AAATAAAAAT
11227454 ATAAAAATATA
1 ATAAAAATATA
*
11227465 AT-TAAATATA
1 ATAAAAATATA
11227475 ATAAAAATATA
1 ATAAAAATATA
11227486 A
1 A
11227487 AACTTTATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
10 9 0.47
11 10 0.53
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (11 bp):
ATAAAAATATA
Found at i:11228390 original size:29 final size:30
Alignment explanation
Indices: 11228358--11228420 Score: 85
Period size: 30 Copynumber: 2.1 Consensus size: 30
11228348 TTCATTGAAT
*
11228358 AAAATTATATCCAAAA-AT-ATTAATTGAGA
1 AAAATCATATCCAAAAGATGA-TAATTGAGA
*
11228387 AAAATCATATTCAAAAGATGATAATTGAGA
1 AAAATCATATCCAAAAGATGATAATTGAGA
11228417 AAAA
1 AAAA
11228421 ATAACAAGAT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
29 14 0.47
30 15 0.50
31 1 0.03
ACGTcount: A:0.57, C:0.06, G:0.10, T:0.27
Consensus pattern (30 bp):
AAAATCATATCCAAAAGATGATAATTGAGA
Found at i:11229695 original size:17 final size:17
Alignment explanation
Indices: 11229656--11229708 Score: 61
Period size: 18 Copynumber: 3.0 Consensus size: 17
11229646 AATAAAAAAT
* *
11229656 ATTATAATTTTAATAATA
1 ATTAAAATTTTATTAA-A
11229674 ATTAAAATTTTATTAAA
1 ATTAAAATTTTATTAAA
*
11229691 ATTAAAAATTTATATAAA
1 ATTAAAATTTTAT-TAAA
11229709 TATAATTCAA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
17 13 0.42
18 18 0.58
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (17 bp):
ATTAAAATTTTATTAAA
Found at i:11229709 original size:17 final size:17
Alignment explanation
Indices: 11229673--11229708 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
11229663 TTTTAATAAT
*
11229673 AATTAAAATTTTATTAA
1 AATTAAAAATTTATTAA
11229690 AATTAAAAATTTATATAA
1 AATTAAAAATTTAT-TAA
11229708 A
1 A
11229709 TATAATTCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 13 0.76
18 4 0.24
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (17 bp):
AATTAAAAATTTATTAA
Found at i:11230271 original size:14 final size:14
Alignment explanation
Indices: 11230237--11230271 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
11230227 TTTATAATGT
11230237 AACAAGAATTAAAA
1 AACAAGAATTAAAA
*
11230251 AAAAAGAATTAAAA
1 AACAAGAATTAAAA
*
11230265 GACAAGA
1 AACAAGA
11230272 TTTTAATTTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.71, C:0.06, G:0.11, T:0.11
Consensus pattern (14 bp):
AACAAGAATTAAAA
Found at i:11230829 original size:11 final size:11
Alignment explanation
Indices: 11230813--11230837 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
11230803 GTGAGAATAG
11230813 AAATTATTTAT
1 AAATTATTTAT
11230824 AAATTATTTAT
1 AAATTATTTAT
11230835 AAA
1 AAA
11230838 AAATATTTGT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (11 bp):
AAATTATTTAT
Found at i:11232777 original size:2 final size:2
Alignment explanation
Indices: 11232770--11232794 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
11232760 TGATTGGTTT
11232770 TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC T
11232795 TTTAATTGTT
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:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:11246723 original size:11 final size:11
Alignment explanation
Indices: 11246707--11246732 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
11246697 AATGTGCCAC
11246707 TTCCATGCGCA
1 TTCCATGCGCA
11246718 TTCCATGCGCA
1 TTCCATGCGCA
11246729 TTCC
1 TTCC
11246733 CACTCCACAG
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:0.15, C:0.38, G:0.15, T:0.31
Consensus pattern (11 bp):
TTCCATGCGCA
Found at i:11250684 original size:17 final size:16
Alignment explanation
Indices: 11250660--11250691 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
11250650 TTGTATTTTA
11250660 ATTTTTATTTTTAAAT
1 ATTTTTATTTTTAAAT
11250676 ATTTGTTATTTTTAAA
1 ATTT-TTATTTTTAAA
11250692 AAAATAAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.66
Consensus pattern (16 bp):
ATTTTTATTTTTAAAT
Found at i:11250733 original size:13 final size:13
Alignment explanation
Indices: 11250715--11250739 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
11250705 TATTACTTGA
11250715 TTATATAATCATG
1 TTATATAATCATG
11250728 TTATATAATCAT
1 TTATATAATCAT
11250740 TGATCTTAGC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.08, G:0.04, T:0.48
Consensus pattern (13 bp):
TTATATAATCATG
Found at i:11252556 original size:2 final size:2
Alignment explanation
Indices: 11252549--11252577 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
11252539 TACTAGTATG
11252549 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 T
11252578 GTACTTTCAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:11270364 original size:46 final size:46
Alignment explanation
Indices: 11270311--11270404 Score: 188
Period size: 46 Copynumber: 2.0 Consensus size: 46
11270301 CTTATTTCCT
11270311 CTGCCAATCCCTTGTTAGATACAGAAAATATATGGAGTACCCAAAG
1 CTGCCAATCCCTTGTTAGATACAGAAAATATATGGAGTACCCAAAG
11270357 CTGCCAATCCCTTGTTAGATACAGAAAATATATGGAGTACCCAAAG
1 CTGCCAATCCCTTGTTAGATACAGAAAATATATGGAGTACCCAAAG
11270403 CT
1 CT
11270405 TCAAAACCTT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 48 1.00
ACGTcount: A:0.36, C:0.22, G:0.17, T:0.24
Consensus pattern (46 bp):
CTGCCAATCCCTTGTTAGATACAGAAAATATATGGAGTACCCAAAG
Found at i:11271342 original size:67 final size:68
Alignment explanation
Indices: 11271217--11271370 Score: 175
Period size: 67 Copynumber: 2.3 Consensus size: 68
11271207 ATCTTGCTTC
* * **** ***
11271217 GAGGCTTTGTGGAACTTTGGAGGCTTTGATCTTTAGCATCTTTCTTCGATTTTTAGAAT-TTTTT
1 GAGGCTTTGTGGAACTTTGGAGGCTTTGATCTTCAACATCTTTCTTCGATACCCAGAATCTTCCC
*
11271281 TTG
66 TTA
* * * *
11271284 GAGGCTTTGTGGAACTTTGGAGGTTTTGATCTTCAATATCTTTTTTTGATACCCAGAATCTTCCC
1 GAGGCTTTGTGGAACTTTGGAGGCTTTGATCTTCAACATCTTTCTTCGATACCCAGAATCTTCCC
11271349 TTA
66 TTA
11271352 GAGGCTTTGTGGAACTTTG
1 GAGGCTTTGTGGAACTTTG
11271371 AAAGTGAGTC
Statistics
Matches: 72, Mismatches: 14, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
67 49 0.68
68 23 0.32
ACGTcount: A:0.18, C:0.14, G:0.23, T:0.45
Consensus pattern (68 bp):
GAGGCTTTGTGGAACTTTGGAGGCTTTGATCTTCAACATCTTTCTTCGATACCCAGAATCTTCCC
TTA
Found at i:11271775 original size:79 final size:80
Alignment explanation
Indices: 11271633--11271817 Score: 187
Period size: 79 Copynumber: 2.3 Consensus size: 80
11271623 AAATTAGATT
** * * * *
11271633 ATCAAATTTGGATTTTATCTCTATATTCTCTTGATTTATTTAGAGACAAATTAGATTACTAATAA
1 ATCAAATTTAAATATTATCTCTAAATTCTCTTCATTTATTTAGAGACAAATTAGATGACTAATAA
11271698 GTAAATTTTAATT-G
66 GTAAATTTTAATTGG
* * * * * * * *
11271712 ATCAAATTTAAATATTATCTCCAAATTCTTTTCATTTATTTAGTGATAACTTGGATGATTAATAG
1 ATCAAATTTAAATATTATCTCTAAATTCTCTTCATTTATTTAGAGACAAATTAGATGACTAATAA
* *
11271777 GTGAATTTTTATTGG
66 GTAAATTTTAATTGG
*
11271792 TTC-AA-TTAATATATTATCTCTAAATT
1 ATCAAATTTAA-ATATTATCTCTAAATT
11271818 ATTTCAAAAT
Statistics
Matches: 86, Mismatches: 18, Indels: 4
0.80 0.17 0.04
Matches are distributed among these distances:
78 4 0.05
79 79 0.92
80 3 0.03
ACGTcount: A:0.35, C:0.09, G:0.10, T:0.46
Consensus pattern (80 bp):
ATCAAATTTAAATATTATCTCTAAATTCTCTTCATTTATTTAGAGACAAATTAGATGACTAATAA
GTAAATTTTAATTGG
Found at i:11281467 original size:16 final size:15
Alignment explanation
Indices: 11281446--11281475 Score: 51
Period size: 15 Copynumber: 1.9 Consensus size: 15
11281436 TTTCGACTAT
11281446 TTAATTGTTTTTTTCA
1 TTAATT-TTTTTTTCA
11281462 TTAATTTTTTTTTC
1 TTAATTTTTTTTTC
11281476 TTTCTTTTGG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.17, C:0.07, G:0.03, T:0.73
Consensus pattern (15 bp):
TTAATTTTTTTTTCA
Found at i:11282791 original size:16 final size:16
Alignment explanation
Indices: 11282770--11282801 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
11282760 CAATAACATC
11282770 GTAGATGAGATGATGA
1 GTAGATGAGATGATGA
11282786 GTAGATGAGATGATGA
1 GTAGATGAGATGATGA
11282802 ATATCAGGGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.38, C:0.00, G:0.38, T:0.25
Consensus pattern (16 bp):
GTAGATGAGATGATGA
Found at i:11289815 original size:17 final size:16
Alignment explanation
Indices: 11289776--11289815 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 16
11289766 AAATTCAATT
*
11289776 AATAAATTTATATTTA
1 AATAAATTTATATTAA
*
11289792 AACAAATTATATATTAA
1 AATAAATT-TATATTAA
11289809 AATAAAT
1 AATAAAT
11289816 GGTTTATCAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
16 7 0.35
17 13 0.65
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (16 bp):
AATAAATTTATATTAA
Found at i:11292672 original size:16 final size:17
Alignment explanation
Indices: 11292645--11292677 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
11292635 ACCCAAAGCC
11292645 AAAAATTAAAAAAAAAA
1 AAAAATTAAAAAAAAAA
11292662 AAAAATTAAAAAAAAA
1 AAAAATTAAAAAAAAA
11292678 GAGAAGGGTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (17 bp):
AAAAATTAAAAAAAAAA
Found at i:11302809 original size:15 final size:16
Alignment explanation
Indices: 11302789--11302818 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
11302779 CCCCACGCCT
11302789 TCTCCCTC-TCTCTCC
1 TCTCCCTCTTCTCTCC
11302804 TCTCCCTCTTCTCTC
1 TCTCCCTCTTCTCTC
11302819 TCTATGTCGA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.00, C:0.57, G:0.00, T:0.43
Consensus pattern (16 bp):
TCTCCCTCTTCTCTCC
Found at i:11312019 original size:15 final size:15
Alignment explanation
Indices: 11311983--11312022 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
11311973 TGCAAAACTT
11311983 ACAAGGTCACCAGCG
1 ACAAGGTCACCAGCG
*
11311998 -CACAGGTCACCAGGG
1 ACA-AGGTCACCAGCG
11312013 ACAAGGTCAC
1 ACAAGGTCAC
11312023 AATGATACTA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
14 2 0.09
15 18 0.82
16 2 0.09
ACGTcount: A:0.33, C:0.33, G:0.28, T:0.07
Consensus pattern (15 bp):
ACAAGGTCACCAGCG
Found at i:11318674 original size:472 final size:474
Alignment explanation
Indices: 11317760--11318706 Score: 1681
Period size: 472 Copynumber: 2.0 Consensus size: 474
11317750 AAAACCAATT
* *
11317760 CAACATCAATATAAATTCTTACTTGCTGACTCATCCTCAAGACACACATGAAGCTTCTTTTACCT
1 CAACATCAATATAAATTCTTACTTGCTGACTCATCCTCAAGACACACATAAAGCTTCTTTTACAT
11317825 CCAACAATAGAATCTATCAAAGATACCAAAACGATAAACTAACTTGTCTATATTTCATAAAAGGA
66 CCAACAATAGAATCTATCAAAGATACCAAAACGATAAACTAACTTGTCTATATTTCATAAAAGGA
*
11317890 AAATCCCAGACTAATTAACCCCTCCAATATAGTTGGCACGCTGCATTCGTGGCATACTAGCACAA
131 AAATCCCAGACTAATTAACCCCTCCAATATAGTTGGCACGCAGCATTCGTGGCATACTAGCACAA
*
11317955 CTAGCAAAATAAGCTAACAAACAACTTTACAAAGACAGAATTCAACACACAAACAACAGAACATT
196 CTAGCAAAATAAGCTAAAAAACAACTTTACAAAGACAGAATTCAACACACAAACAACAGAACATT
11318020 AAAAATATTCCCTTTTTTCTCTCATACATTTAGCATAAAAAACAGAGTTAAAGGCATCAACTTGC
261 AAAAATATTCCCTTTTTTCTCTCATACATTTAGCATAAAAAACAGAGTTAAAGGCATCAACTTGC
11318085 AAAGCGAAATATTCAAAAACCAATCAAAACGTAACATTTCCAACAATAATCACTCAAAAACGAAA
326 AAAGCGAAATATTCAAAAACCAATCAAAACGTAACATTTCCAACAATAATCACTCAAAAACGAAA
**
11318150 ATAAAATCACATTTAAGCACACAATGCAAGAACCTTTTCAACTTACACGAATATCTCTCGAAAGA
391 ATAAAATCACATTTAAGCACACAAAACAAGAACCTTTTCAACTTACACGAATATCTCTCGAAAGA
*
11318215 GGATGCAAGCAGATAACGC
456 GGATGCAAGCAGAGAACGC
11318234 CAACATCAATATAAATTCTTACTTGCTGACTCATCCTCAAGACACACATAAAGCTTCTTTTACAT
1 CAACATCAATATAAATTCTTACTTGCTGACTCATCCTCAAGACACACATAAAGCTTCTTTTACAT
* *
11318299 CCAACAATCGAATCTATCAAAGGTACCAAAACGATAAACTAACTTGTCTATATTTCATAAAAGGA
66 CCAACAATAGAATCTATCAAAGATACCAAAACGATAAACTAACTTGTCTATATTTCATAAAAGGA
* * *
11318364 AAATCCCAGACTAATTAACCCCTCCAATATAGTT-G-AGGGAGCATTTGTGGCATACCTAGCACA
131 AAATCCCAGACTAATTAACCCCTCCAATATAGTTGGCACGCAGCATTCGTGGCATA-CTAGCACA
*
11318427 ACTAGCAAAATAAGCTACAAAAACAACTTTA-AAAGACAGAAATTCAACA-A-AAACAATAGAAC
195 ACTAGCAAAATAAGCTA-AAAAACAACTTTACAAAGACAG-AATTCAACACACAAACAACAGAAC
*
11318489 ATTAAAAATATT-CCTTTTTTCTCTCATACAATTTAGCATAAAAAACAGAGTTAAAGGCATCACC
258 ATTAAAAATATTCCCTTTTTTCTCTCATAC-ATTTAGCATAAAAAACAGAGTTAAAGGCATCAAC
11318553 TTGCAAAGCGAAATATTCAAAAACCAATCAAAACGTAACATTTCCAACAATAATCACTCAAAAAC
322 TTGCAAAGCGAAATATTCAAAAACCAATCAAAACGTAACATTTCCAACAATAATCACTCAAAAAC
11318618 GAAAATAAAATCACATTTAAGCACACAAAACAAGAACCTTTTCAACTTACACGAATATCTCTCGA
387 GAAAATAAAATCACATTTAAGCACACAAAACAAGAACCTTTTCAACTTACACGAATATCTCTCGA
*
11318683 AAGAGGATGCGAGCAGAGAACGC
452 AAGAGGATGCAAGCAGAGAACGC
11318706 C
1 C
11318707 GGTACAAGTC
Statistics
Matches: 454, Mismatches: 15, Indels: 10
0.95 0.03 0.02
Matches are distributed among these distances:
471 17 0.04
472 221 0.49
473 35 0.08
474 181 0.40
ACGTcount: A:0.44, C:0.23, G:0.10, T:0.24
Consensus pattern (474 bp):
CAACATCAATATAAATTCTTACTTGCTGACTCATCCTCAAGACACACATAAAGCTTCTTTTACAT
CCAACAATAGAATCTATCAAAGATACCAAAACGATAAACTAACTTGTCTATATTTCATAAAAGGA
AAATCCCAGACTAATTAACCCCTCCAATATAGTTGGCACGCAGCATTCGTGGCATACTAGCACAA
CTAGCAAAATAAGCTAAAAAACAACTTTACAAAGACAGAATTCAACACACAAACAACAGAACATT
AAAAATATTCCCTTTTTTCTCTCATACATTTAGCATAAAAAACAGAGTTAAAGGCATCAACTTGC
AAAGCGAAATATTCAAAAACCAATCAAAACGTAACATTTCCAACAATAATCACTCAAAAACGAAA
ATAAAATCACATTTAAGCACACAAAACAAGAACCTTTTCAACTTACACGAATATCTCTCGAAAGA
GGATGCAAGCAGAGAACGC
Found at i:11324338 original size:30 final size:31
Alignment explanation
Indices: 11324271--11324338 Score: 77
Period size: 31 Copynumber: 2.2 Consensus size: 31
11324261 AAGATAATTT
* ** *
11324271 ATAATTTTTTTAAAAAAATAAGACCTATTCA
1 ATAATTTTTTTAAAAAAAAAAGACAAACTCA
11324302 ATAATTTTTTTAAAAAAAAAAG-CAAAGCTCA
1 ATAATTTTTTTAAAAAAAAAAGACAAA-CTCA
11324333 A-AATTT
1 ATAATTT
11324339 AATTTTGGGT
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
30 7 0.22
31 25 0.78
ACGTcount: A:0.51, C:0.09, G:0.04, T:0.35
Consensus pattern (31 bp):
ATAATTTTTTTAAAAAAAAAAGACAAACTCA
Found at i:11325234 original size:13 final size:14
Alignment explanation
Indices: 11325208--11325238 Score: 55
Period size: 13 Copynumber: 2.3 Consensus size: 14
11325198 GGTTGCAATA
11325208 TTCTTTCATTTTCT
1 TTCTTTCATTTTCT
11325222 TTCTTTC-TTTTCT
1 TTCTTTCATTTTCT
11325235 TTCT
1 TTCT
11325239 CTTCCCCTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.59
14 7 0.41
ACGTcount: A:0.03, C:0.23, G:0.00, T:0.74
Consensus pattern (14 bp):
TTCTTTCATTTTCT
Found at i:11325304 original size:19 final size:19
Alignment explanation
Indices: 11325280--11325338 Score: 118
Period size: 19 Copynumber: 3.1 Consensus size: 19
11325270 TTCCCCTTGA
11325280 TTAGCAGACAAAGAAAAAT
1 TTAGCAGACAAAGAAAAAT
11325299 TTAGCAGACAAAGAAAAAT
1 TTAGCAGACAAAGAAAAAT
11325318 TTAGCAGACAAAGAAAAAT
1 TTAGCAGACAAAGAAAAAT
11325337 TT
1 TT
11325339 GGCATTAGTG
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 40 1.00
ACGTcount: A:0.56, C:0.10, G:0.15, T:0.19
Consensus pattern (19 bp):
TTAGCAGACAAAGAAAAAT
Found at i:11326692 original size:2 final size:2
Alignment explanation
Indices: 11326685--11326731 Score: 87
Period size: 2 Copynumber: 24.0 Consensus size: 2
11326675 CCACAAAAGA
11326685 AT AT AT AT AT AT AT AT AT -T AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
11326726 AT AT AT
1 AT AT AT
11326732 TAACTCCTTC
Statistics
Matches: 44, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 43 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:11328048 original size:21 final size:21
Alignment explanation
Indices: 11328023--11328067 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
11328013 CCGGATGCCC
11328023 GTATCCAGGATAACCAGCCAT
1 GTATCCAGGATAACCAGCCAT
* *
11328044 GTATCCAGGGTAACCAGGCAT
1 GTATCCAGGATAACCAGCCAT
11328065 GTA
1 GTA
11328068 CCCGATTCGG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.31, C:0.24, G:0.24, T:0.20
Consensus pattern (21 bp):
GTATCCAGGATAACCAGCCAT
Found at i:11329520 original size:3 final size:3
Alignment explanation
Indices: 11329512--11329557 Score: 56
Period size: 3 Copynumber: 14.3 Consensus size: 3
11329502 TGATGCTTAC
*
11329512 GAT GAT GAT AGAT GGT GGAT GAT GGAT GAT GAT GAT GAT GAT GAT G
1 GAT GAT GAT -GAT GAT -GAT GAT -GAT GAT GAT GAT GAT GAT GAT G
11329558 TATGGGATGC
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
3 30 0.79
4 8 0.21
ACGTcount: A:0.30, C:0.00, G:0.39, T:0.30
Consensus pattern (3 bp):
GAT
Found at i:11344100 original size:12 final size:12
Alignment explanation
Indices: 11344083--11344118 Score: 63
Period size: 12 Copynumber: 3.0 Consensus size: 12
11344073 TGATCAACTA
11344083 GCACACACACGC
1 GCACACACACGC
*
11344095 GCACACACGCGC
1 GCACACACACGC
11344107 GCACACACACGC
1 GCACACACACGC
11344119 ACATAATAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.31, C:0.50, G:0.19, T:0.00
Consensus pattern (12 bp):
GCACACACACGC
Found at i:11344964 original size:28 final size:28
Alignment explanation
Indices: 11344924--11344977 Score: 99
Period size: 28 Copynumber: 1.9 Consensus size: 28
11344914 TGTCATATTG
*
11344924 AAAATATAATTATTACATACTATATTAA
1 AAAAAATAATTATTACATACTATATTAA
11344952 AAAAAATAATTATTACATACTATATT
1 AAAAAATAATTATTACATACTATATT
11344978 GAAGAGAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.54, C:0.07, G:0.00, T:0.39
Consensus pattern (28 bp):
AAAAAATAATTATTACATACTATATTAA
Found at i:11345656 original size:31 final size:33
Alignment explanation
Indices: 11345589--11345656 Score: 86
Period size: 31 Copynumber: 2.1 Consensus size: 33
11345579 GGTTTCAGCC
11345589 TAAAATCAAAAAAATAAAAAGACAATTAAAAAA
1 TAAAATCAAAAAAATAAAAAGACAATTAAAAAA
* * * *
11345622 TAAAA-CAAAATAATAATAA-ACTATTATAAAA
1 TAAAATCAAAAAAATAAAAAGACAATTAAAAAA
11345653 TAAA
1 TAAA
11345657 TCTTAAAAGA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
31 14 0.45
32 12 0.39
33 5 0.16
ACGTcount: A:0.72, C:0.06, G:0.01, T:0.21
Consensus pattern (33 bp):
TAAAATCAAAAAAATAAAAAGACAATTAAAAAA
Found at i:11345696 original size:18 final size:18
Alignment explanation
Indices: 11345673--11345708 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
11345663 AAGACAAATC
*
11345673 AAAGAAAGTATTTAGAGG
1 AAAGAAAGTATGTAGAGG
11345691 AAAGAAAGTATGTAGAGG
1 AAAGAAAGTATGTAGAGG
11345709 GAGTAAGAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.50, C:0.00, G:0.31, T:0.19
Consensus pattern (18 bp):
AAAGAAAGTATGTAGAGG
Found at i:11350132 original size:18 final size:19
Alignment explanation
Indices: 11350111--11350150 Score: 64
Period size: 18 Copynumber: 2.2 Consensus size: 19
11350101 ATATGATGGC
*
11350111 TTATCCACTTTT-GGTGGA
1 TTATCCACTTTTCAGTGGA
11350129 TTATCCACTTTTCAGTGGA
1 TTATCCACTTTTCAGTGGA
11350148 TTA
1 TTA
11350151 AAGCATCTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 12 0.60
19 8 0.40
ACGTcount: A:0.20, C:0.17, G:0.17, T:0.45
Consensus pattern (19 bp):
TTATCCACTTTTCAGTGGA
Found at i:11351935 original size:27 final size:27
Alignment explanation
Indices: 11351905--11351962 Score: 98
Period size: 27 Copynumber: 2.1 Consensus size: 27
11351895 GAGGCCCAAG
* *
11351905 AGGGTGCTAGCCCACTAAGACCCATGT
1 AGGGTGCCAGCCCACCAAGACCCATGT
11351932 AGGGTGCCAGCCCACCAAGACCCATGT
1 AGGGTGCCAGCCCACCAAGACCCATGT
11351959 AGGG
1 AGGG
11351963 ATTTCCCTCC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.26, C:0.31, G:0.29, T:0.14
Consensus pattern (27 bp):
AGGGTGCCAGCCCACCAAGACCCATGT
Found at i:11352026 original size:16 final size:16
Alignment explanation
Indices: 11352013--11352054 Score: 63
Period size: 14 Copynumber: 2.8 Consensus size: 16
11352003 TCCCAAATGG
11352013 TTTTGGA-GGAAAATC
1 TTTTGGAGGGAAAATC
11352028 TTTTGGAGGGAAAA--
1 TTTTGGAGGGAAAATC
11352042 TTTTGGAGGGAAA
1 TTTTGGAGGGAAA
11352055 TGGGTGGGGA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
14 13 0.50
15 7 0.27
16 6 0.23
ACGTcount: A:0.33, C:0.02, G:0.33, T:0.31
Consensus pattern (16 bp):
TTTTGGAGGGAAAATC
Found at i:11353114 original size:2 final size:2
Alignment explanation
Indices: 11353107--11353150 Score: 61
Period size: 2 Copynumber: 22.0 Consensus size: 2
11353097 GAAACCCATT
* * *
11353107 TA TA TA TA CA TA CA TA TA TA TA TA TA TA TA TA TA GA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
11353149 TA
1 TA
11353151 AAGAAAAGCT
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.05, G:0.02, T:0.43
Consensus pattern (2 bp):
TA
Found at i:11360695 original size:12 final size:12
Alignment explanation
Indices: 11360670--11360707 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
11360660 TCTGAATCTC
*
11360670 TCCA-CTATCAA
1 TCCATCTATCCA
11360681 TCCATCTATCCA
1 TCCATCTATCCA
*
11360693 TCCATCCATCCA
1 TCCATCTATCCA
11360705 TCC
1 TCC
11360708 CAAACCTTTC
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
11 4 0.17
12 20 0.83
ACGTcount: A:0.26, C:0.45, G:0.00, T:0.29
Consensus pattern (12 bp):
TCCATCTATCCA
Found at i:11362297 original size:2 final size:2
Alignment explanation
Indices: 11362290--11362321 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
11362280 GCCCTCCCCA
11362290 TC TC 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 TC TC
11362322 CAGCAGAAGT
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:11368257 original size:13 final size:13
Alignment explanation
Indices: 11368239--11368263 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
11368229 TTTGGTAAGT
11368239 AATTATAAAAAAA
1 AATTATAAAAAAA
11368252 AATTATAAAAAA
1 AATTATAAAAAA
11368264 CCAAAAATAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (13 bp):
AATTATAAAAAAA
Found at i:11369185 original size:24 final size:24
Alignment explanation
Indices: 11369154--11369204 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 24
11369144 AAATAATATG
* *
11369154 ATTTTAATATATATTTTATATTA-A
1 ATTTTAATAGATATATTAT-TTATA
11369178 ATTTTAATAGATATATTATTTATA
1 ATTTTAATAGATATATTATTTATA
11369202 ATT
1 ATT
11369205 AAAAATTATT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 3 0.12
24 21 0.88
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (24 bp):
ATTTTAATAGATATATTATTTATA
Found at i:11382315 original size:2 final size:2
Alignment explanation
Indices: 11382308--11382337 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
11382298 TATCTATAAT
*
11382308 TA TA TA TA TA TA TA TA TA TA TA TA TG TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
11382338 ATGTCACTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:11382401 original size:19 final size:19
Alignment explanation
Indices: 11382379--11382427 Score: 71
Period size: 19 Copynumber: 2.6 Consensus size: 19
11382369 TGTAAGCTTG
11382379 ATTTTATTTTGGCATTATA
1 ATTTTATTTTGGCATTATA
* *
11382398 ATTTTATTTTGGTATTATT
1 ATTTTATTTTGGCATTATA
*
11382417 ATTTCATTTTG
1 ATTTTATTTTG
11382428 AGAAGGCATC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.22, C:0.04, G:0.10, T:0.63
Consensus pattern (19 bp):
ATTTTATTTTGGCATTATA
Found at i:11413139 original size:26 final size:26
Alignment explanation
Indices: 11413110--11413191 Score: 82
Period size: 26 Copynumber: 3.2 Consensus size: 26
11413100 TTAATTAGGC
11413110 AAAAAAAATTCTTAAGCAAAAAAGGG
1 AAAAAAAATTCTTAAGCAAAAAAGGG
** **
11413136 AAAAAAAATT-GAAATGC--CCAA-GG
1 AAAAAAAATTCTTAA-GCAAAAAAGGG
11413159 AAAAAAATATTCTTAAGCAAAAAAGGG
1 AAAAAAA-ATTCTTAAGCAAAAAAGGG
11413186 AAAAAA
1 AAAAAA
11413192 GAAAAAGGAA
Statistics
Matches: 42, Mismatches: 8, Indels: 11
0.69 0.13 0.18
Matches are distributed among these distances:
23 9 0.21
24 7 0.17
25 4 0.10
26 14 0.33
27 8 0.19
ACGTcount: A:0.62, C:0.09, G:0.15, T:0.15
Consensus pattern (26 bp):
AAAAAAAATTCTTAAGCAAAAAAGGG
Found at i:11413201 original size:14 final size:15
Alignment explanation
Indices: 11413178--11413210 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
11413168 TTCTTAAGCA
11413178 AAAAAGGGAAAAAAG
1 AAAAAGGGAAAAAAG
*
11413193 AAAAA-GGAAAAAGG
1 AAAAAGGGAAAAAAG
11413207 AAAA
1 AAAA
11413211 GAAGGCTTGG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 12 0.71
15 5 0.29
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (15 bp):
AAAAAGGGAAAAAAG
Found at i:11413207 original size:48 final size:47
Alignment explanation
Indices: 11413110--11413210 Score: 123
Period size: 50 Copynumber: 2.1 Consensus size: 47
11413100 TTAATTAGGC
* ***
11413110 AAAAAAAATTCTTAAGCAAAAAAGGGAAAAAAAATTGAAATGCCCAAGG
1 AAAAAAAATTCTTAAGCAAAAAAGGGAAAAAAAA-T-AAAGGAAAAAGG
11413159 AAAAAAATATTCTTAAGCAAAAAAGGGAAAAAAGAA-AAAGGAAAAAGG
1 AAAAAAA-ATTCTTAAGCAAAAAAGGGAAAAAA-AATAAAGGAAAAAGG
11413207 AAAA
1 AAAA
11413211 GAAGGCTTGG
Statistics
Matches: 46, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
48 12 0.26
49 7 0.15
50 25 0.54
51 2 0.04
ACGTcount: A:0.64, C:0.07, G:0.17, T:0.12
Consensus pattern (47 bp):
AAAAAAAATTCTTAAGCAAAAAAGGGAAAAAAAATAAAGGAAAAAGG
Found at i:11428500 original size:2 final size:2
Alignment explanation
Indices: 11428493--11428518 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
11428483 CTAACAAATT
11428493 CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA
11428519 AAGATACTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:11434339 original size:22 final size:23
Alignment explanation
Indices: 11434314--11434358 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
11434304 TCTAAAGAGG
*
11434314 AAAGAGAGAGGGGTT-GAGGGCA
1 AAAGAAAGAGGGGTTAGAGGGCA
*
11434336 AAAGAAAGAGGGTTTAGAGGGCA
1 AAAGAAAGAGGGGTTAGAGGGCA
11434359 GGAAATGGGA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 13 0.65
23 7 0.35
ACGTcount: A:0.40, C:0.04, G:0.44, T:0.11
Consensus pattern (23 bp):
AAAGAAAGAGGGGTTAGAGGGCA
Found at i:11434674 original size:3 final size:3
Alignment explanation
Indices: 11434666--11434723 Score: 98
Period size: 3 Copynumber: 19.3 Consensus size: 3
11434656 TCAGCGTCGC
* *
11434666 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA CTA TTG TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
11434714 TTA TTA TTA T
1 TTA TTA TTA T
11434724 ATAAAGTCCA
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 51 1.00
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:11462350 original size:26 final size:26
Alignment explanation
Indices: 11462321--11462370 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
11462311 TTATATAAAG
* *
11462321 ATATTTATATATTTTGAGATATTTTA
1 ATATTTATATATATTAAGATATTTTA
*
11462347 ATATTTATGTATATTAAGATATTT
1 ATATTTATATATATTAAGATATTT
11462371 AAAAAAATAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.36, C:0.00, G:0.08, T:0.56
Consensus pattern (26 bp):
ATATTTATATATATTAAGATATTTTA
Found at i:11463877 original size:21 final size:21
Alignment explanation
Indices: 11463838--11463877 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
11463828 AGATCGATTC
*
11463838 ATATTATTTTATTTATTTTAA
1 ATATTATTTTAATTATTTTAA
11463859 ATATTAATTTTAATT-TTTT
1 ATATT-ATTTTAATTATTTT
11463878 GTTATGAAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 9 0.53
22 8 0.47
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (21 bp):
ATATTATTTTAATTATTTTAA
Found at i:11464217 original size:27 final size:27
Alignment explanation
Indices: 11464186--11464309 Score: 77
Period size: 27 Copynumber: 5.3 Consensus size: 27
11464176 TAGGTTAAAT
11464186 ATGAGTTTAGCTTGTTTAAGTAAGTTC
1 ATGAGTTTAGCTTGTTTAAGTAAGTTC
* *
11464213 ATGAG-TT-G--TGGTTCAGT-A----
1 ATGAGTTTAGCTTGTTTAAGTAAGTTC
*
11464231 ATGAGTTCAGCTTGTTTAAGTAAGTTC
1 ATGAGTTTAGCTTGTTTAAGTAAGTTC
* *
11464258 ATGAG-TT-G--TGGTTCAGT-A----
1 ATGAGTTTAGCTTGTTTAAGTAAGTTC
11464276 ATGAGTTTAGCTTGTTTAAGTAAGTTC
1 ATGAGTTTAGCTTGTTTAAGTAAGTTC
11464303 ATGAGTT
1 ATGAGTT
11464310 GTGGTTCAGT
Statistics
Matches: 69, Mismatches: 10, Indels: 36
0.60 0.09 0.31
Matches are distributed among these distances:
18 10 0.14
19 3 0.04
20 2 0.03
22 16 0.23
23 16 0.23
25 2 0.03
26 3 0.04
27 17 0.25
ACGTcount: A:0.25, C:0.07, G:0.26, T:0.42
Consensus pattern (27 bp):
ATGAGTTTAGCTTGTTTAAGTAAGTTC
Found at i:11464250 original size:45 final size:45
Alignment explanation
Indices: 11464186--11464320 Score: 261
Period size: 45 Copynumber: 3.0 Consensus size: 45
11464176 TAGGTTAAAT
11464186 ATGAGTTTAGCTTGTTTAAGTAAGTTCATGAGTTGTGGTTCAGTA
1 ATGAGTTTAGCTTGTTTAAGTAAGTTCATGAGTTGTGGTTCAGTA
*
11464231 ATGAGTTCAGCTTGTTTAAGTAAGTTCATGAGTTGTGGTTCAGTA
1 ATGAGTTTAGCTTGTTTAAGTAAGTTCATGAGTTGTGGTTCAGTA
11464276 ATGAGTTTAGCTTGTTTAAGTAAGTTCATGAGTTGTGGTTCAGTA
1 ATGAGTTTAGCTTGTTTAAGTAAGTTCATGAGTTGTGGTTCAGTA
11464321 TAATACAAGC
Statistics
Matches: 88, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 88 1.00
ACGTcount: A:0.24, C:0.07, G:0.27, T:0.41
Consensus pattern (45 bp):
ATGAGTTTAGCTTGTTTAAGTAAGTTCATGAGTTGTGGTTCAGTA
Found at i:11464436 original size:2 final size:2
Alignment explanation
Indices: 11464429--11464470 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
11464419 AACTCAAGAG
11464429 TA TA TA TA 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 TA TA TA TA
11464471 AAACATATTT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:11501990 original size:14 final size:15
Alignment explanation
Indices: 11501969--11502007 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
11501959 GCACTTTTCG
11501969 ATTAAAATCAAATT-A
1 ATTAAAAT-AAATTCA
11501984 A-TAAAATAAATTCA
1 ATTAAAATAAATTCA
11501998 ATTAAAATAA
1 ATTAAAATAA
11502008 TTTGATTTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
13 5 0.23
14 8 0.36
15 9 0.41
ACGTcount: A:0.64, C:0.05, G:0.00, T:0.31
Consensus pattern (15 bp):
ATTAAAATAAATTCA
Found at i:11518574 original size:15 final size:15
Alignment explanation
Indices: 11518550--11518579 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
11518540 CCCATGCTTT
*
11518550 TCTTTGATAAAATTA
1 TCTTTAATAAAATTA
11518565 TCTTTAATAAAATTA
1 TCTTTAATAAAATTA
11518580 CATTTCATGC
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:0.43, C:0.07, G:0.03, T:0.47
Consensus pattern (15 bp):
TCTTTAATAAAATTA
Found at i:11518931 original size:29 final size:30
Alignment explanation
Indices: 11518865--11518956 Score: 105
Period size: 29 Copynumber: 3.1 Consensus size: 30
11518855 TTAAAAAAGG
* *
11518865 TTGTTACACGTCATGTTGAAAAAAGATATTA
1 TTGTTACACGTCATATTG-AAAAACATATTA
* * *
11518896 TTATTACATGTTATATTGAAAAA-ATATTA
1 TTGTTACACGTCATATTGAAAAACATATTA
* *
11518925 TTGTTACACGTCATATTCAAAAACATTTTA
1 TTGTTACACGTCATATTGAAAAACATATTA
11518955 TT
1 TT
11518957 ACACTTTAAT
Statistics
Matches: 51, Mismatches: 9, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
29 25 0.49
30 12 0.24
31 14 0.27
ACGTcount: A:0.39, C:0.10, G:0.10, T:0.41
Consensus pattern (30 bp):
TTGTTACACGTCATATTGAAAAACATATTA
Found at i:11531920 original size:97 final size:96
Alignment explanation
Indices: 11531628--11532002 Score: 477
Period size: 97 Copynumber: 3.9 Consensus size: 96
11531618 ATTACTGTTC
* * *
11531628 ATAATGATATAACTATTTAATTTGTTTTTATCAGGTAAAACAATTTTTTTTAAAAA-AA-AAATT
1 ATAATAATATAACTATTCAATTTGTTTTTATCAGGTAAAACAATTTTTTTAAAAAATAATAAATT
* *
11531691 AATAATCAAAATTGAGCATCTACACTATTAT
66 AATAATCAAAATCGAACATCTACACTATTAT
* * * * *
11531722 ATAATAATATAACTATCCAATCTGTTTTTATTAGGTAAGACAATTTTTTTAAAATATAATAAATT
1 ATAATAATATAACTATTCAATTTGTTTTTATCAGGTAAAACAATTTTTTTAAAAAATAATAAATT
* * * *
11531787 AGTAGTCAAAATTGAACATCTACACTATTGT
66 AATAATCAAAATCGAACATCTACACTATTAT
* *
11531818 ATAATAATATAACTATTCAATTTGTTTTTAT-TGAGTAAAATAATTTTTTTAAAAAAATAATAAA
1 ATAATAATATAACTATTCAATTTGTTTTTATCAG-GTAAAACAATTTTTTT-AAAAAATAATAAA
* * *
11531882 TAAATAATTAAAATCGAACATCTACACTGTTAT
64 TTAATAATCAAAATCGAACATCTACACTATTAT
* * * * *
11531915 ATAATAAAATAATTATTCAATTTGATTTTATCAGATAAAATAAATTTTTTTAAAAAATAATAAAT
1 ATAATAATATAACTATTCAATTTGTTTTTATCAGGTAAAA-CAATTTTTTTAAAAAATAATAAAT
*
11531980 TAACAATCAAAATCGAACATCTA
65 TAATAATCAAAATCGAACATCTA
11532003 TAGCGTTGCT
Statistics
Matches: 241, Mismatches: 34, Indels: 9
0.85 0.12 0.03
Matches are distributed among these distances:
94 48 0.20
95 3 0.01
96 75 0.31
97 105 0.44
98 10 0.04
ACGTcount: A:0.46, C:0.09, G:0.06, T:0.39
Consensus pattern (96 bp):
ATAATAATATAACTATTCAATTTGTTTTTATCAGGTAAAACAATTTTTTTAAAAAATAATAAATT
AATAATCAAAATCGAACATCTACACTATTAT
Found at i:11540023 original size:25 final size:25
Alignment explanation
Indices: 11539972--11540103 Score: 101
Period size: 25 Copynumber: 5.2 Consensus size: 25
11539962 AAAAGAATGG
* *
11539972 TTTTTAATT-ATTATTTAAATTGATA
1 TTTTT-ATTGATTATTAAAAATGATA
*
11539997 TTTTTATTGATTGTTAAAAATGTTATTA
1 TTTTTATTGATTATTAAAAATG--A-TA
* *
11540025 TTTTTATTGATCATTAGAAATGATA
1 TTTTTATTGATTATTAAAAATGATA
** *
11540050 TTTAGATTGATTGTTAAAAA--ATTA
1 TTTTTATTGATTATTAAAAATGA-TA
*
11540074 TTTTTATT-TTTAATTAAAAATGATA
1 TTTTTATTGATT-ATTAAAAATGATA
11540099 TTTTT
1 TTTTT
11540104 TGAATAGTTT
Statistics
Matches: 84, Mismatches: 15, Indels: 16
0.73 0.13 0.14
Matches are distributed among these distances:
23 3 0.04
24 18 0.21
25 39 0.46
26 2 0.02
27 1 0.01
28 21 0.25
ACGTcount: A:0.36, C:0.01, G:0.08, T:0.55
Consensus pattern (25 bp):
TTTTTATTGATTATTAAAAATGATA
Found at i:11540074 original size:49 final size:50
Alignment explanation
Indices: 11539992--11540101 Score: 132
Period size: 49 Copynumber: 2.2 Consensus size: 50
11539982 TTATTTAAAT
** * *
11539992 TGATATTTTTATTGATTGTTAAAAATGTTATTATTTTTATTGATCATTAGAAA
1 TGATATTTAGATTGATTGTTAAAAA---TATTATTTTTATTGATAATTAAAAA
**
11540045 TGATATTTAGATTGATTGTTAAAAA-ATTATTTTTATTTTTAATTAAAAA
1 TGATATTTAGATTGATTGTTAAAAATATTATTTTTATTGATAATTAAAAA
11540094 TGATATTT
1 TGATATTT
11540102 TTTGAATAGT
Statistics
Matches: 51, Mismatches: 6, Indels: 4
0.84 0.10 0.07
Matches are distributed among these distances:
49 28 0.55
53 23 0.45
ACGTcount: A:0.36, C:0.01, G:0.10, T:0.53
Consensus pattern (50 bp):
TGATATTTAGATTGATTGTTAAAAATATTATTTTTATTGATAATTAAAAA
Found at i:11540257 original size:103 final size:103
Alignment explanation
Indices: 11540143--11540540 Score: 299
Period size: 103 Copynumber: 3.9 Consensus size: 103
11540133 ATGTCAAAAA
* *
11540143 TTATTTCTATCAATCACTAAAAATGATATTTTGATTGATCAATAAAAAAATTACTATTTTTACCG
1 TTATTTCTATCAATCACTAAAAATGATATTTTGATCGATCATTAAAAAAATTACTATTTTTACCG
*
11540208 TTTTTTAAAAGTGATATTTCGATCGATCGTTG-GAAAAG
66 TTATTTAAAAGTGATATTTCGATCGATCGTTGAG-AAAG
* ** * ** * * *
11540246 TTATTTCTATCAATCATTAAAAAAAATATTTCGATCGATTGTTAAAAAGATTACTATTTTGATCG
1 TTATTTCTATCAATCACTAAAAATGATATTTTGATCGATCATTAAAAAAATTACTATTTTTACCG
* * * *
11540311 ATTATTGAAATGTAATATTTCGATCGATTGTTGAGAAAG
66 -TTATTTAAAAGTGATATTTCGATCGATCGTTGAGAAAG
* * * * * * * *
11540350 TTATATCTATTAA-CCCTTAAAAATTAT-TTTTGGATCGATCGTTAAAATAGTTATTA-TTTTA-
1 TTATTTCTATCAATCAC-TAAAAATGATATTTT-GATCGATCATTAAAAAAATTACTATTTTTAC
* * * * * *
11540411 -ATTAATCATAAAGTGATATTTCGATCGATCATTGATAAAT
64 CGTTATTTA-AAAGTGATATTTCGATCGATCGTTGAGAAAG
* * * * * *** *
11540451 TTATTTTTATAAATCA-TCAAAAATGATATATTTTAATAGATCACTAAATCTATTATTATTTTTA
1 TTATTTCTATCAATCACT-AAAAATG--ATATTTTGATCGATCATTAAAAAAATTACTATTTTTA
*
11540515 CTGTT-TCTTAAAAGTGATATTTCGAT
63 CCGTTAT-TTAAAAGTGATATTTCGAT
11540541 ATATGATTAA
Statistics
Matches: 227, Mismatches: 54, Indels: 26
0.74 0.18 0.08
Matches are distributed among these distances:
100 6 0.03
101 41 0.18
102 1 0.00
103 80 0.35
104 78 0.34
105 17 0.07
106 4 0.02
ACGTcount: A:0.37, C:0.10, G:0.11, T:0.43
Consensus pattern (103 bp):
TTATTTCTATCAATCACTAAAAATGATATTTTGATCGATCATTAAAAAAATTACTATTTTTACCG
TTATTTAAAAGTGATATTTCGATCGATCGTTGAGAAAG
Found at i:11540293 original size:26 final size:26
Alignment explanation
Indices: 11540262--11540342 Score: 83
Period size: 28 Copynumber: 3.1 Consensus size: 26
11540252 CTATCAATCA
11540262 TTAAAAAA-AATATTTCGATCGATTG
1 TTAAAAAATAATATTTCGATCGATTG
* * *
11540287 TTAAAAAGATTACTATTTTGATCGATTA
1 TTAAAAA-A-TAATATTTCGATCGATTG
* **
11540315 TTGAAATGTAATATTTCGATCGATTG
1 TTAAAAAATAATATTTCGATCGATTG
11540341 TT
1 TT
11540343 GAGAAAGTTA
Statistics
Matches: 44, Mismatches: 9, Indels: 5
0.76 0.16 0.09
Matches are distributed among these distances:
25 7 0.16
26 18 0.41
28 19 0.43
ACGTcount: A:0.37, C:0.07, G:0.14, T:0.42
Consensus pattern (26 bp):
TTAAAAAATAATATTTCGATCGATTG
Found at i:11540344 original size:26 final size:27
Alignment explanation
Indices: 11540221--11540349 Score: 90
Period size: 25 Copynumber: 4.9 Consensus size: 27
11540211 TTTAAAAGTG
*
11540221 ATATTTCGATCGATCGTTGGAAAAG-T-
1 ATATTTCGATCGATTGTT-GAAAAGATA
* * ** *
11540247 -TATTTCTATCAATCATT-AAAA-AAA
1 ATATTTCGATCGATTGTTGAAAAGATA
*
11540271 ATATTTCGATCGATTGTTAAAAAGATTA
1 ATATTTCGATCGATTGTTGAAAAGA-TA
* * * *
11540299 CTATTTTGATCGATTATTGAAATG-TA
1 ATATTTCGATCGATTGTTGAAAAGATA
11540325 ATATTTCGATCGATTGTTGAGAAAG
1 ATATTTCGATCGATTGTTGA-AAAG
11540350 TTATATCTAT
Statistics
Matches: 78, Mismatches: 18, Indels: 13
0.72 0.17 0.12
Matches are distributed among these distances:
23 4 0.05
25 27 0.35
26 23 0.29
27 4 0.05
28 20 0.26
ACGTcount: A:0.36, C:0.09, G:0.16, T:0.39
Consensus pattern (27 bp):
ATATTTCGATCGATTGTTGAAAAGATA
Found at i:11540370 original size:104 final size:103
Alignment explanation
Indices: 11540138--11540409 Score: 251
Period size: 104 Copynumber: 2.6 Consensus size: 103
11540128 GTATTATGTC
* * * * ** * * ** *
11540138 AAAAATTATTTCTATCAATCACTAAAAATGATATTTTGATTGATCAATAAAAAAATTACTATTTT
1 AAAAGTTATATCTATCAACCATTAAAAAAAATATTTCGATCGATCGTTAAAAAGATTACTATTTT
* * * *
11540203 TACCGTTTTTTAAAAGTGATATTTCGATCGATCGTTGG
66 GACCGTTATTGAAAAGTAATATTTCGATCGATCGTTGG
* * *
11540241 AAAAGTTATTTCTATCAATCATTAAAAAAAATATTTCGATCGATTGTTAAAAAGATTACTATTTT
1 AAAAGTTATATCTATCAACCATTAAAAAAAATATTTCGATCGATCGTTAAAAAGATTACTATTTT
* * *
11540306 GATCGATTATTGAAATGTAATATTTCGATCGATTGTT-G
66 GACCG-TTATTGAAAAGTAATATTTCGATCGATCGTTGG
* * ** * * *
11540344 AGAAAGTTATATCTATTAACCCTTAAAAATTATTTTTGGATCGATCGTTAAAATAG-TTATTATT
1 A-AAAGTTATATCTATCAACCATTAAAAAAAATATTTCGATCGATCGTTAAAA-AGATTACTATT
11540408 TT
64 TT
11540410 AATTAATCAT
Statistics
Matches: 139, Mismatches: 27, Indels: 5
0.81 0.16 0.03
Matches are distributed among these distances:
103 60 0.43
104 77 0.55
105 2 0.01
ACGTcount: A:0.38, C:0.10, G:0.11, T:0.42
Consensus pattern (103 bp):
AAAAGTTATATCTATCAACCATTAAAAAAAATATTTCGATCGATCGTTAAAAAGATTACTATTTT
GACCGTTATTGAAAAGTAATATTTCGATCGATCGTTGG
Found at i:11541537 original size:72 final size:72
Alignment explanation
Indices: 11541417--11541588 Score: 308
Period size: 72 Copynumber: 2.4 Consensus size: 72
11541407 NNNNNNNNNN
* *
11541417 GATTCAAGCTTGGATTCTGCAACAGCCCTCCCAGGGTTGGGTTGAGACTCCCATGCTGCATCTGT
1 GATTCAAGCTTGGATTCTGCAACAGCCCTCCCAGGGTTGGGTTCAGACTCCCATGCTGCAGCTGT
11541482 GTTGATT
66 GTTGATT
*
11541489 GATTCAAGCTTGGATTCTGCAACAGCCCTCCCAGGGTTGGGTTCAGACTCCCATTCTGCAGCTGT
1 GATTCAAGCTTGGATTCTGCAACAGCCCTCCCAGGGTTGGGTTCAGACTCCCATGCTGCAGCTGT
11541554 GTTGATT
66 GTTGATT
*
11541561 GATTCAAGCTTGGGTTCTGCAACAGCCC
1 GATTCAAGCTTGGATTCTGCAACAGCCC
11541589 CGGTAGAGGT
Statistics
Matches: 96, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
72 96 1.00
ACGTcount: A:0.19, C:0.26, G:0.26, T:0.30
Consensus pattern (72 bp):
GATTCAAGCTTGGATTCTGCAACAGCCCTCCCAGGGTTGGGTTCAGACTCCCATGCTGCAGCTGT
GTTGATT
Found at i:11569248 original size:12 final size:12
Alignment explanation
Indices: 11569231--11569269 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
11569221 TCAAAAAAAT
11569231 AAATATAATATA
1 AAATATAATATA
*
11569243 AAATATAATACA
1 AAATATAATATA
* *
11569255 AAATTTAATTTA
1 AAATATAATATA
11569267 AAA
1 AAA
11569270 AAACAATATT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (12 bp):
AAATATAATATA
Found at i:11572872 original size:2 final size:2
Alignment explanation
Indices: 11572867--11572895 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
11572857 ATATATGAGT
11572867 GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
11572896 TAGTTTCTGC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:11578330 original size:24 final size:24
Alignment explanation
Indices: 11578303--11578350 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 24
11578293 GTAAATTTCC
* *
11578303 AATTATTATTACTATATACTAAAG
1 AATTATTAATACTATATAATAAAG
11578327 AATTATTAATACTATATAATAAAG
1 AATTATTAATACTATATAATAAAG
11578351 GAAGGTTCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.50, C:0.06, G:0.04, T:0.40
Consensus pattern (24 bp):
AATTATTAATACTATATAATAAAG
Found at i:11579151 original size:3 final size:3
Alignment explanation
Indices: 11579131--11579182 Score: 68
Period size: 3 Copynumber: 17.3 Consensus size: 3
11579121 CAATTTAACT
* * * *
11579131 GAA GAG GAA GAA GGA GAA GAA GAA GAA GAA GAA GAA GAT GAA GAA GAG
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
11579179 GAA G
1 GAA G
11579183 TATGTTTTTC
Statistics
Matches: 41, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.58, C:0.00, G:0.40, T:0.02
Consensus pattern (3 bp):
GAA
Found at i:11586396 original size:21 final size:21
Alignment explanation
Indices: 11586363--11586402 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
11586353 TCCATTCCTG
*
11586363 TCCCACCCACCCCTCCCCCTT
1 TCCCACCCACCCCCCCCCCTT
* *
11586384 TCCCCCCCCCCCCCCCCCC
1 TCCCACCCACCCCCCCCCC
11586403 CAAAAAAAAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.05, C:0.82, G:0.00, T:0.12
Consensus pattern (21 bp):
TCCCACCCACCCCCCCCCCTT
Found at i:11592785 original size:28 final size:27
Alignment explanation
Indices: 11592749--11592824 Score: 84
Period size: 28 Copynumber: 2.8 Consensus size: 27
11592739 TTAAAATAAA
11592749 ATGTTAAAAATTTAATTATT-GTACATC
1 ATGTTAAAAATTTAATTATTAGTA-ATC
* * *
11592776 ATGTTAAAAA-ATATATTCATTATTAGTC
1 ATGTTAAAAATTTA-ATT-ATTAGTAATC
11592804 ATGTTAAAAATTTAATTATTA
1 ATGTTAAAAATTTAATTATTA
11592825 CGCTATATTA
Statistics
Matches: 41, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
26 2 0.05
27 17 0.41
28 18 0.44
29 4 0.10
ACGTcount: A:0.43, C:0.05, G:0.07, T:0.45
Consensus pattern (27 bp):
ATGTTAAAAATTTAATTATTAGTAATC
Found at i:11601110 original size:2 final size:2
Alignment explanation
Indices: 11601105--11601130 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
11601095 TATAAGGGAA
11601105 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
11601131 TGATCTTTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:11633565 original size:15 final size:15
Alignment explanation
Indices: 11633552--11633602 Score: 66
Period size: 15 Copynumber: 3.3 Consensus size: 15
11633542 TTTTAATATT
11633552 TTATAATGTAATATGA
1 TTATAA-GTAATATGA
*
11633568 TTATAAGTAATGTGA
1 TTATAAGTAATATGA
* *
11633583 TTATAAATAATATAA
1 TTATAAGTAATATGA
11633598 TTATA
1 TTATA
11633603 TAAAAAATAA
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
15 25 0.81
16 6 0.19
ACGTcount: A:0.47, C:0.00, G:0.10, T:0.43
Consensus pattern (15 bp):
TTATAAGTAATATGA
Found at i:11633629 original size:20 final size:20
Alignment explanation
Indices: 11633587--11633646 Score: 57
Period size: 20 Copynumber: 2.9 Consensus size: 20
11633577 ATGTGATTAT
*
11633587 AAATAATATAATTATATAAA
1 AAATAATATAATAATATAAA
*
11633607 AAATAATATTATAATATTTAAA
1 AAATAATATAATAATA--TAAA
* *
11633629 ATATAAATAAAATAATAT
1 AAAT-AATATAATAATAT
11633647 TATAATATTT
Statistics
Matches: 32, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
20 14 0.44
21 1 0.03
22 7 0.22
23 10 0.31
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (20 bp):
AAATAATATAATAATATAAA
Found at i:11633637 original size:23 final size:23
Alignment explanation
Indices: 11633584--11633647 Score: 76
Period size: 23 Copynumber: 2.8 Consensus size: 23
11633574 GTAATGTGAT
*
11633584 TATAAATAATATAATTATATAAAA
1 TATAAATAATATAA-TATTTAAAA
* *
11633608 AAT-AATATTATAATATTTAAAA
1 TATAAATAATATAATATTTAAAA
*
11633630 TATAAATAAAATAATATT
1 TATAAATAATATAATATT
11633648 ATAATATTTG
Statistics
Matches: 33, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
22 10 0.30
23 21 0.64
24 2 0.06
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (23 bp):
TATAAATAATATAATATTTAAAA
Found at i:11633793 original size:5 final size:5
Alignment explanation
Indices: 11633785--11633934 Score: 62
Period size: 5 Copynumber: 30.0 Consensus size: 5
11633775 TAATATCATA
* * * *
11633785 TATTT TATTT T-TATA TATTT TATTTT TATTTT TAATAT AATTT T-TTA
1 TATTT TATTT TAT-TT TATTT TA-TTT TA-TTT T-ATTT TATTT TATTT
* * * * *
11633832 TATTAT ATATTT TATTT TAATT TATTT TA-CT TATAT TATATA AATTT
1 TATT-T -TATTT TATTT TATTT TATTT TATTT TATTT TAT-TT TATTT
* * * * *
11633879 TATTT T-TTA TATTT TATTT TTTTT TATTT T-TTA T-TTT TATAT TA-TA
1 TATTT TATTT TATTT TATTT TATTT TATTT TATTT TATTT TATTT TATTT
11633925 TATTT TATTT
1 TATTT TATTT
11633935 AAATTATAAC
Statistics
Matches: 106, Mismatches: 27, Indels: 24
0.68 0.17 0.15
Matches are distributed among these distances:
4 18 0.17
5 67 0.63
6 16 0.15
7 5 0.05
ACGTcount: A:0.27, C:0.01, G:0.00, T:0.72
Consensus pattern (5 bp):
TATTT
Found at i:11633794 original size:21 final size:20
Alignment explanation
Indices: 11633769--11633832 Score: 76
Period size: 21 Copynumber: 3.1 Consensus size: 20
11633759 TTTTTAAATA
11633769 TATTTTTAATATCATATATTT
1 TATTTTTAATATCATAT-TTT
**
11633790 TATTTTTATATATTTTATTTT
1 TATTTTTA-ATATCATATTTT
*
11633811 TATTTTTAATATAAT-TTTT
1 TATTTTTAATATCATATTTT
11633830 TAT
1 TAT
11633833 ATTATATATT
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
19 7 0.18
20 5 0.13
21 19 0.50
22 7 0.18
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.69
Consensus pattern (20 bp):
TATTTTTAATATCATATTTT
Found at i:11633800 original size:15 final size:15
Alignment explanation
Indices: 11633717--11633920 Score: 111
Period size: 15 Copynumber: 13.3 Consensus size: 15
11633707 TATAAATGTA
11633717 ATATATTTATATTTTT
1 ATATATTT-TATTTTT
*
11633733 -TAT-TATTAATTTTT
1 ATATAT-TTTATTTTT
11633747 ATATATTATTAATTTTT
1 ATATATT-TT-ATTTTT
* * *
11633764 AAATATATTTTTAATATC
1 --ATATA-TTTTATTTTT
11633782 ATATATTTTATTTTT
1 ATATATTTTATTTTT
11633797 ATATATTTTA-TTTT
1 ATATATTTTATTTTT
* *
11633811 -TAT-TTTTA-ATAT
1 ATATATTTTATTTTT
* *
11633823 A-ATTTTTTA-TATT
1 ATATATTTTATTTTT
*
11633836 ATATATTTTATTTTA
1 ATATATTTTATTTTT
*
11633851 ATTTATTTTACTTATATT
1 ATATATTTTA-TT-T-TT
11633869 ATATAAATTTTATTTTT
1 ATAT--ATTTTATTTTT
11633886 -TATATTTTATTTTTTT
1 ATATATTTTA--TTTTT
* *
11633902 TTATTTTTTATTTTT
1 ATATATTTTATTTTT
11633917 ATAT
1 ATAT
11633921 TATATATTTT
Statistics
Matches: 147, Mismatches: 21, Indels: 41
0.70 0.10 0.20
Matches are distributed among these distances:
12 9 0.06
13 10 0.07
14 24 0.16
15 45 0.31
16 17 0.12
17 17 0.12
18 8 0.05
19 9 0.06
20 8 0.05
ACGTcount: A:0.30, C:0.01, G:0.00, T:0.69
Consensus pattern (15 bp):
ATATATTTTATTTTT
Found at i:11633802 original size:22 final size:21
Alignment explanation
Indices: 11633769--11633841 Score: 73
Period size: 21 Copynumber: 3.6 Consensus size: 21
11633759 TTTTTAAATA
11633769 TATTTTTA-ATATCATATATTT
1 TATTTTTATATATCATAT-TTT
**
11633790 TATTTTTATATATTTTATTTT
1 TATTTTTATATATCATATTTT
*
11633811 TATTTTTA-ATATAAT-TTTT
1 TATTTTTATATATCATATTTT
*
11633830 TA-TATTATATAT
1 TATTTTTATATAT
11633842 TTTATTTTAA
Statistics
Matches: 45, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
18 4 0.09
19 10 0.22
20 5 0.11
21 19 0.42
22 7 0.16
ACGTcount: A:0.32, C:0.01, G:0.00, T:0.67
Consensus pattern (21 bp):
TATTTTTATATATCATATTTT
Found at i:11633858 original size:54 final size:53
Alignment explanation
Indices: 11633718--11633918 Score: 169
Period size: 54 Copynumber: 3.7 Consensus size: 53
11633708 ATAAATGTAA
* *
11633718 TATATTTATATTTTTTATTATTAATTTTTATATATTATTAATTTTTAA-ATATATTTTT
1 TATA-TTATATATTTTATT-TTAATTTTT-T-TATT-TTTATTTTTAATATA-ATTTTT
* * * *
11633776 AATATCATATATTTTATTTTTATATATTTTATTTTTATTTTTAATATAATTTTT
1 TATATTATATATTTTATTTTAAT-TTTTTTATTTTTATTTTTAATATAATTTTT
* * * * *
11633830 TATATTATATATTTTATTTTAATTTATTTTACTTATATTATATAAATTTTATTTTT
1 TATATTATATATTTTATTTTAATTT-TTTTATTTTTATT-T-TTAATATAATTTTT
*
11633886 TATATT-T-TATTTT-TTTTTA-TTTTTTATTTTTAT
1 TATATTATATATTTTATTTTAATTTTTTTATTTTTAT
11633919 ATTATATATT
Statistics
Matches: 120, Mismatches: 18, Indels: 17
0.77 0.12 0.11
Matches are distributed among these distances:
51 10 0.08
52 2 0.02
53 6 0.05
54 53 0.44
55 9 0.08
56 22 0.18
57 15 0.12
58 3 0.03
ACGTcount: A:0.30, C:0.01, G:0.00, T:0.69
Consensus pattern (53 bp):
TATATTATATATTTTATTTTAATTTTTTTATTTTTATTTTTAATATAATTTTT
Found at i:11633985 original size:16 final size:17
Alignment explanation
Indices: 11633959--11634012 Score: 58
Period size: 16 Copynumber: 3.1 Consensus size: 17
11633949 TAAAATATTT
11633959 TTAATAAAATAATAAA-A
1 TTAA-AAAATAATAAATA
11633976 TTAAAAAATAA-AAATA
1 TTAAAAAATAATAAATA
11633992 TTATAAAATATAATATAATA
1 TTA-AAAA-ATAATA-AATA
11634012 T
1 T
11634013 AATTATATTA
Statistics
Matches: 32, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
15 3 0.09
16 11 0.34
17 8 0.25
18 4 0.12
19 1 0.03
20 5 0.16
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (17 bp):
TTAAAAAATAATAAATA
Found at i:11653470 original size:2 final size:2
Alignment explanation
Indices: 11653463--11653493 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
11653453 CGTTGTTCCA
11653463 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
11653494 GCGGAGATTA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:11653826 original size:2 final size:2
Alignment explanation
Indices: 11653821--11653850 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
11653811 ACGAAAAAAA
11653821 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
11653851 CCAATGCACA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:11657660 original size:1 final size:1
Alignment explanation
Indices: 11657654--11657684 Score: 62
Period size: 1 Copynumber: 31.0 Consensus size: 1
11657644 CTGTAACAAG
11657654 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
11657685 GAAACCTGCA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 30 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:11664515 original size:17 final size:16
Alignment explanation
Indices: 11664490--11664526 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 16
11664480 TTCTCACCTT
*
11664490 TCTTTCATTCAATCTTC
1 TCTTCCATTCAATC-TC
11664507 TCTTCCATTCAATCTC
1 TCTTCCATTCAATCTC
11664523 TCTT
1 TCTT
11664527 TACTGTCTCT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 6 0.32
17 13 0.68
ACGTcount: A:0.16, C:0.32, G:0.00, T:0.51
Consensus pattern (16 bp):
TCTTCCATTCAATCTC
Found at i:11670822 original size:11 final size:12
Alignment explanation
Indices: 11670806--11670836 Score: 55
Period size: 11 Copynumber: 2.7 Consensus size: 12
11670796 TCTATAATGA
11670806 ATAATTAATAAT
1 ATAATTAATAAT
11670818 A-AATTAATAAT
1 ATAATTAATAAT
11670829 ATAATTAA
1 ATAATTAA
11670837 AAAATTAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 11 0.61
12 7 0.39
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (12 bp):
ATAATTAATAAT
Found at i:11670843 original size:20 final size:20
Alignment explanation
Indices: 11670805--11670858 Score: 60
Period size: 20 Copynumber: 2.8 Consensus size: 20
11670795 TTCTATAATG
*
11670805 AATAAT-TAA-TAATAAATT
1 AATAATATAATTAAAAAATT
11670823 AATAATATAATTAAAAAATT
1 AATAATATAATTAAAAAATT
*
11670843 AA-AATTAAAATTAAAA
1 AATAA-TATAATTAAAA
11670859 TTTCAAATAT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
18 6 0.19
19 5 0.16
20 20 0.65
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (20 bp):
AATAATATAATTAAAAAATT
Done.