Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr9
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: 48574783
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2023350 characters in sequence are not A, C, G, or T
File 113 of 135
Found at i:41436093 original size:17 final size:16
Alignment explanation
Indices: 41436071--41436103 Score: 57
Period size: 17 Copynumber: 2.0 Consensus size: 16
41436061 ACATGAATAC
41436071 TATAAAAATTTATAAAT
1 TATAAAAATTT-TAAAT
41436088 TATAAAAATTTTAAAT
1 TATAAAAATTTTAAAT
41436104 AGATATAAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.31
17 11 0.69
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (16 bp):
TATAAAAATTTTAAAT
Found at i:41436896 original size:20 final size:20
Alignment explanation
Indices: 41436846--41436896 Score: 50
Period size: 20 Copynumber: 2.5 Consensus size: 20
41436836 TCAAATAAAA
*
41436846 AACCCTAAACCTTAAACATAG
1 AACCCTAAA-CTCAAACATAG
* *
41436867 AATCCC-AAACTCCAACATGG
1 AA-CCCTAAACTCAAACATAG
41436887 AACCCTAAAC
1 AACCCTAAAC
41436897 CCTAATCTTA
Statistics
Matches: 25, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
19 3 0.12
20 14 0.56
21 5 0.20
22 3 0.12
ACGTcount: A:0.45, C:0.33, G:0.06, T:0.16
Consensus pattern (20 bp):
AACCCTAAACTCAAACATAG
Found at i:41443198 original size:30 final size:30
Alignment explanation
Indices: 41443162--41443224 Score: 108
Period size: 30 Copynumber: 2.1 Consensus size: 30
41443152 ACTTATTTTA
41443162 TTGTTAATTTTATTATTATTTTAAAGACAT
1 TTGTTAATTTTATTATTATTTTAAAGACAT
* *
41443192 TTGTTAATTTTGTTATTATTTTAGAGACAT
1 TTGTTAATTTTATTATTATTTTAAAGACAT
41443222 TTG
1 TTG
41443225 CTTGTTAAGT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.29, C:0.03, G:0.11, T:0.57
Consensus pattern (30 bp):
TTGTTAATTTTATTATTATTTTAAAGACAT
Found at i:41448119 original size:10 final size:10
Alignment explanation
Indices: 41448104--41448128 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
41448094 AATTTAATTA
41448104 TTAAAAAAAT
1 TTAAAAAAAT
41448114 TTAAAAAAAT
1 TTAAAAAAAT
41448124 TTAAA
1 TTAAA
41448129 TATTTTTTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (10 bp):
TTAAAAAAAT
Found at i:41448375 original size:24 final size:24
Alignment explanation
Indices: 41448347--41448417 Score: 97
Period size: 24 Copynumber: 3.0 Consensus size: 24
41448337 AAGGGTTTAC
*
41448347 AAGAAGATGAAAGGTTAAAGGTTA
1 AAGAAGATGAAAGGTGAAAGGTTA
* *
41448371 AAGAAGATGAAATGTGGAAGGTTA
1 AAGAAGATGAAAGGTGAAAGGTTA
* *
41448395 AGGGAGATGAAAGGTGAAAGGTT
1 AAGAAGATGAAAGGTGAAAGGTT
41448418 GAATATCCAC
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 40 1.00
ACGTcount: A:0.45, C:0.00, G:0.35, T:0.20
Consensus pattern (24 bp):
AAGAAGATGAAAGGTGAAAGGTTA
Found at i:41453602 original size:4 final size:4
Alignment explanation
Indices: 41453593--41453617 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
41453583 GAACGAAACT
41453593 TTTA TTTA TTTA TTTA TTTA TTTA T
1 TTTA TTTA TTTA TTTA TTTA TTTA T
41453618 AAAATTATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TTTA
Found at i:41463226 original size:3 final size:3
Alignment explanation
Indices: 41463218--41463245 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
41463208 TATGTCCATC
41463218 ATG ATG ATG ATG ATG ATG ATG ATG ATG A
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG A
41463246 CAACTTGTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.36, C:0.00, G:0.32, T:0.32
Consensus pattern (3 bp):
ATG
Found at i:41473726 original size:13 final size:13
Alignment explanation
Indices: 41473708--41473732 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
41473698 TCCAGCAACT
41473708 ATGAATTTATTTC
1 ATGAATTTATTTC
41473721 ATGAATTTATTT
1 ATGAATTTATTT
41473733 GATGTTGATT
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:0.32, C:0.04, G:0.08, T:0.56
Consensus pattern (13 bp):
ATGAATTTATTTC
Found at i:41473944 original size:50 final size:50
Alignment explanation
Indices: 41473832--41474080 Score: 291
Period size: 50 Copynumber: 4.8 Consensus size: 50
41473822 ATTTGGGTAA
*
41473832 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTTGAGATCACG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA-CC---A-A-CACG
* * *
41473888 AGAGGTCTCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCAAGACG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCAACACG
* * * *
41473938 AGAGGTCCCATGTAAGACCATGTCTAGGACATGGCATTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCAACACG
* * * * *
41473988 AGAGGTCCCCTATAAGACCATGTCTGGGACATGGCATGGGCACCGACATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCAACACG
** *
41474038 AGAACATCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCA
1 AG-AGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
41474081 TGTTATTATC
Statistics
Matches: 172, Mismatches: 20, Indels: 7
0.86 0.10 0.04
Matches are distributed among these distances:
50 95 0.55
51 35 0.20
52 1 0.01
55 2 0.01
56 39 0.23
ACGTcount: A:0.27, C:0.23, G:0.29, T:0.21
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCAACACG
Found at i:41474021 original size:100 final size:103
Alignment explanation
Indices: 41473832--41474081 Score: 335
Period size: 100 Copynumber: 2.4 Consensus size: 103
41473822 ATTTGGGTAA
*
41473832 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTTGAGATCACGAGAGGTCTC
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCC-TGAGAT--CGAGAGGTCCC
* * * *
41473897 ATGTAAGACCATGTCTGGGACATGGCGTTGGCACCAAGACG
63 ATATAAGACCATGTCTGGGACATGGCATGGGCACCAACACG
* * *
41473938 AGAGGTCCCATGTAAGACCATGTCTAGGACATGGCATTGGCA-CC-GAGAT-GAGAGGTCCCCTA
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTGAGATCGAGAGGTCCCATA
* *
41474000 TAAGACCATGTCTGGGACATGGCATGGGCACCGACATG
66 TAAGACCATGTCTGGGACATGGCATGGGCACCAACACG
* *
41474038 AGAACATCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCAT
1 AG-AGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCAT
41474082 GTTATTATCA
Statistics
Matches: 128, Mismatches: 14, Indels: 8
0.85 0.09 0.05
Matches are distributed among these distances:
100 45 0.35
101 36 0.28
103 5 0.04
105 2 0.02
106 40 0.31
ACGTcount: A:0.27, C:0.23, G:0.29, T:0.21
Consensus pattern (103 bp):
AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTGAGATCGAGAGGTCCCATA
TAAGACCATGTCTGGGACATGGCATGGGCACCAACACG
Found at i:41487713 original size:12 final size:12
Alignment explanation
Indices: 41487696--41487721 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
41487686 CTCGATTTTT
41487696 TTTAAAAATTTA
1 TTTAAAAATTTA
41487708 TTTAAAAATTTA
1 TTTAAAAATTTA
41487720 TT
1 TT
41487722 ATTCCATTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (12 bp):
TTTAAAAATTTA
Found at i:41487930 original size:15 final size:16
Alignment explanation
Indices: 41487907--41487939 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
41487897 TACATTATTT
41487907 TATTTTTTTATGTAAA
1 TATTTTTTTATGTAAA
41487923 TATTTTTTTATGTAAA
1 TATTTTTTTATGTAAA
41487939 T
1 T
41487940 TCAATATTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.30, C:0.00, G:0.06, T:0.64
Consensus pattern (16 bp):
TATTTTTTTATGTAAA
Found at i:41499513 original size:18 final size:19
Alignment explanation
Indices: 41499492--41499533 Score: 68
Period size: 19 Copynumber: 2.3 Consensus size: 19
41499482 TAAAAATTCT
*
41499492 AAAATT-TATAATTTTTAA
1 AAAATTATAAAATTTTTAA
41499510 AAAATTATAAAATTTTTAA
1 AAAATTATAAAATTTTTAA
41499529 AAAAT
1 AAAAT
41499534 CTAACATTGA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 6 0.27
19 16 0.73
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (19 bp):
AAAATTATAAAATTTTTAA
Found at i:41513011 original size:21 final size:23
Alignment explanation
Indices: 41512976--41513019 Score: 65
Period size: 21 Copynumber: 2.0 Consensus size: 23
41512966 TGGTATTAAA
41512976 TTTAAATAGATTTAATTAAAAAT
1 TTTAAATAGATTTAATTAAAAAT
*
41512999 TTTAAA-A-ATTTAATTAGAAAT
1 TTTAAATAGATTTAATTAAAAAT
41513020 AAATTGTAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 13 0.65
22 1 0.05
23 6 0.30
ACGTcount: A:0.52, C:0.00, G:0.05, T:0.43
Consensus pattern (23 bp):
TTTAAATAGATTTAATTAAAAAT
Found at i:41518232 original size:5 final size:5
Alignment explanation
Indices: 41518222--41518257 Score: 72
Period size: 5 Copynumber: 7.2 Consensus size: 5
41518212 GGATGTATGG
41518222 ATGTT ATGTT ATGTT ATGTT ATGTT ATGTT ATGTT A
1 ATGTT ATGTT ATGTT ATGTT ATGTT ATGTT ATGTT A
41518258 ATGTATGGTG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 31 1.00
ACGTcount: A:0.22, C:0.00, G:0.19, T:0.58
Consensus pattern (5 bp):
ATGTT
Found at i:41520251 original size:7 final size:7
Alignment explanation
Indices: 41520239--41520273 Score: 70
Period size: 7 Copynumber: 5.0 Consensus size: 7
41520229 AAATGGTTGC
41520239 TTGAAAG
1 TTGAAAG
41520246 TTGAAAG
1 TTGAAAG
41520253 TTGAAAG
1 TTGAAAG
41520260 TTGAAAG
1 TTGAAAG
41520267 TTGAAAG
1 TTGAAAG
41520274 GTTTAAAATA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 28 1.00
ACGTcount: A:0.43, C:0.00, G:0.29, T:0.29
Consensus pattern (7 bp):
TTGAAAG
Found at i:41520356 original size:20 final size:20
Alignment explanation
Indices: 41520333--41520370 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
41520323 TTTATCTTTA
41520333 TTATTTTTA-ATATAAAATAC
1 TTATTTTTACATA-AAAATAC
41520353 TTATTTTTACATAAAAAT
1 TTATTTTTACATAAAAAT
41520371 TAAAATAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 14 0.82
21 3 0.18
ACGTcount: A:0.45, C:0.05, G:0.00, T:0.50
Consensus pattern (20 bp):
TTATTTTTACATAAAAATAC
Found at i:41523067 original size:207 final size:210
Alignment explanation
Indices: 41522820--41523227 Score: 660
Period size: 211 Copynumber: 2.0 Consensus size: 210
41522810 CCGCTAATCC
41522820 AAATGCAATTATATTTATATAATATCATGCTAGACCTTTTA-TTT-TTAAAT-GTTTTTTCACAT
1 AAATGCAATTATATTTATATAATATCATGCTAGACCTTTTATTTTCTTAAATCGTTTTTTCACAT
* * * *
41522882 ATTATATACAACCACTTCTTAAGAAATTTTATGGAATAAATAGGGATAAAATAAGTATGTAAACT
66 ATTATATAAAACCACCTCCTAAGAAATTTTATGGAATAAATAGGGATAAAATAAGTATATAAACT
* * * *
41522947 TAAATTTAAGGGTCAAAATGGATCTTTCACTTTTATATAATATTTTTTATTAGAATTATAATTGT
131 TAAATTTAAGGGTCAAAATGGATCTTTCACTTTTATATAACAGTTTTTATTAGAATTAAAATTAT
41523012 TTTTATATAATATCA
196 TTTTATATAATATCA
* *
41523027 AAATGCAATTATATTTATATAATATCATGCTAGACCTTTTATTTTTCTTTAATCTTTTTTTCACA
1 AAATGCAATTATATTTATATAATATCATGCTAGACCTTTTA-TTTTCTTAAATCGTTTTTTCACA
* * * *
41523092 TGTTATATAAAACCACCTCCTAGGAAATTTTATGGAATAAATAGGGGTAAAATAGGTATATAAAC
65 TATTATATAAAACCACCTCCTAAGAAATTTTATGGAATAAATAGGGATAAAATAAGTATATAAAC
41523157 TTAAATTTAAGGGTCAAAATGGATCTTTCACTTTTATATAACAGTTTTTATTAGAATTAAAATTA
130 TTAAATTTAAGGGTCAAAATGGATCTTTCACTTTTATATAACAGTTTTTATTAGAATTAAAATTA
41523222 TTTTTA
195 TTTTTA
41523228 AATTTATTAT
Statistics
Matches: 183, Mismatches: 14, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
207 41 0.22
209 3 0.02
210 5 0.03
211 134 0.73
ACGTcount: A:0.38, C:0.10, G:0.10, T:0.43
Consensus pattern (210 bp):
AAATGCAATTATATTTATATAATATCATGCTAGACCTTTTATTTTCTTAAATCGTTTTTTCACAT
ATTATATAAAACCACCTCCTAAGAAATTTTATGGAATAAATAGGGATAAAATAAGTATATAAACT
TAAATTTAAGGGTCAAAATGGATCTTTCACTTTTATATAACAGTTTTTATTAGAATTAAAATTAT
TTTTATATAATATCA
Found at i:41525510 original size:57 final size:56
Alignment explanation
Indices: 41525423--41525533 Score: 177
Period size: 57 Copynumber: 2.0 Consensus size: 56
41525413 AGTATAAATC
* * * *
41525423 AAAATTGGTCCTCCGAAATCTATACGTCGGTGGATTAATTGCTGAATTTTGCCTCT
1 AAAATTGGTCCTCCAAAATCTATACGTCGGTGGATTAATTCCTCAACTTTGCCTCT
41525479 AAAATTGGTCCTCCAAAAATCTATACGTCGGTGGATTAATTCCTCAACTTTGCCT
1 AAAATTGGTCCTCC-AAAATCTATACGTCGGTGGATTAATTCCTCAACTTTGCCT
41525534 TTGGATAATC
Statistics
Matches: 50, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
56 14 0.28
57 36 0.72
ACGTcount: A:0.27, C:0.22, G:0.17, T:0.34
Consensus pattern (56 bp):
AAAATTGGTCCTCCAAAATCTATACGTCGGTGGATTAATTCCTCAACTTTGCCTCT
Found at i:41526330 original size:36 final size:36
Alignment explanation
Indices: 41526289--41526360 Score: 144
Period size: 36 Copynumber: 2.0 Consensus size: 36
41526279 ATTAGAACGA
41526289 TAATTTTCAGTCTATAAAAATCAGGAAATGGGTTTG
1 TAATTTTCAGTCTATAAAAATCAGGAAATGGGTTTG
41526325 TAATTTTCAGTCTATAAAAATCAGGAAATGGGTTTG
1 TAATTTTCAGTCTATAAAAATCAGGAAATGGGTTTG
41526361 GGAGTCGGTT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.36, C:0.08, G:0.19, T:0.36
Consensus pattern (36 bp):
TAATTTTCAGTCTATAAAAATCAGGAAATGGGTTTG
Found at i:41526857 original size:233 final size:233
Alignment explanation
Indices: 41526446--41526915 Score: 933
Period size: 233 Copynumber: 2.0 Consensus size: 233
41526436 CTTAGTGTCG
41526446 ATAA-TTGAAAATTCAAAGAAAATTTAAGATACGATCCCCTTCTTGCATGATTGCAAACTAAATT
1 ATAATTTGAAAATTCAAAGAAAATTTAAGATACGATCCCCTTCTTGCATGATTGCAAACTAAATT
41526510 GAATTTTATGGAAAGAGCCTTCTTATTTCGAGTCAATCGAGAAAAGTATCATGTCCCGTAAGTTA
66 GAATTTTATGGAAAGAGCCTTCTTATTTCGAGTCAATCGAGAAAAGTATCATGTCCCGTAAGTTA
41526575 GGGCACAAATCTCAAATCCTCGAAAATAAGGATTCTCGTTATTTGATTATTCAAATTTAGTCAAG
131 GGGCACAAATCTCAAATCCTCGAAAATAAGGATTCTCGTTATTTGATTATTCAAATTTAGTCAAG
41526640 TGTTGGTACAAAAATAAACGAATATTTAAACATGCTGC
196 TGTTGGTACAAAAATAAACGAATATTTAAACATGCTGC
41526678 ATAATTTGAAAATTCAAAGAAAATTTAAGATACGATCCCCTTCTTGCATGATTGCAAACTAAATT
1 ATAATTTGAAAATTCAAAGAAAATTTAAGATACGATCCCCTTCTTGCATGATTGCAAACTAAATT
41526743 GAATTTTATGGAAAGAGCCTTCTTATTTCGAGTCAATCGAGAAAAGTATCATGTCCCGTAAGTTA
66 GAATTTTATGGAAAGAGCCTTCTTATTTCGAGTCAATCGAGAAAAGTATCATGTCCCGTAAGTTA
41526808 GGGCACAAATCTCAAATCCTCGAAAATAAGGATTCTCGTTATTTGATTATTCAAATTTAGTCAAG
131 GGGCACAAATCTCAAATCCTCGAAAATAAGGATTCTCGTTATTTGATTATTCAAATTTAGTCAAG
41526873 TGTTGGTACAAAAATAAACGAATATTTAAACATGCTGC
196 TGTTGGTACAAAAATAAACGAATATTTAAACATGCTGC
41526911 ATAAT
1 ATAAT
41526916 ATGGAAATGG
Statistics
Matches: 237, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
232 4 0.02
233 233 0.98
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.32
Consensus pattern (233 bp):
ATAATTTGAAAATTCAAAGAAAATTTAAGATACGATCCCCTTCTTGCATGATTGCAAACTAAATT
GAATTTTATGGAAAGAGCCTTCTTATTTCGAGTCAATCGAGAAAAGTATCATGTCCCGTAAGTTA
GGGCACAAATCTCAAATCCTCGAAAATAAGGATTCTCGTTATTTGATTATTCAAATTTAGTCAAG
TGTTGGTACAAAAATAAACGAATATTTAAACATGCTGC
Found at i:41527311 original size:20 final size:20
Alignment explanation
Indices: 41527270--41527311 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
41527260 ATTAAAGGAC
*
41527270 AAAATATAAATAATGAATTA
1 AAAATATAAATAATGAAATA
*
41527290 AAAATACTAAA-AATTAAATA
1 AAAATA-TAAATAATGAAATA
41527310 AA
1 AA
41527312 TAAAAAAGGG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 15 0.79
21 4 0.21
ACGTcount: A:0.69, C:0.02, G:0.02, T:0.26
Consensus pattern (20 bp):
AAAATATAAATAATGAAATA
Found at i:41528867 original size:22 final size:22
Alignment explanation
Indices: 41528834--41528883 Score: 68
Period size: 22 Copynumber: 2.4 Consensus size: 22
41528824 ACAATAATAT
41528834 TTAATA-T-TTAATTATTTTTA
1 TTAATATTATTAATTATTTTTA
* *
41528854 TTGATATTATTAATTGTTTTTA
1 TTAATATTATTAATTATTTTTA
41528876 TTAATATT
1 TTAATATT
41528884 TTTATTGATA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 5 0.20
21 1 0.04
22 19 0.76
ACGTcount: A:0.32, C:0.00, G:0.04, T:0.64
Consensus pattern (22 bp):
TTAATATTATTAATTATTTTTA
Found at i:41531845 original size:20 final size:21
Alignment explanation
Indices: 41531820--41531860 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 21
41531810 TGGGAGTTAG
41531820 TGGGGATATGAGTGG-TTTAA
1 TGGGGATATGAGTGGCTTTAA
*
41531840 TGGGGATATGGGTGGCTTTAA
1 TGGGGATATGAGTGGCTTTAA
41531861 AAAATTATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 14 0.74
21 5 0.26
ACGTcount: A:0.22, C:0.02, G:0.41, T:0.34
Consensus pattern (21 bp):
TGGGGATATGAGTGGCTTTAA
Found at i:41535267 original size:132 final size:132
Alignment explanation
Indices: 41535030--41535276 Score: 327
Period size: 132 Copynumber: 1.9 Consensus size: 132
41535020 CAACTTCAAG
* *
41535030 GAGATAGGAATTCTGGCTTCAATGTACTCCACTGTAACCTCAAGGAGGTAAAATCTGCCATCCTC
1 GAGATAGGAATTCTGGCTTCAATATACTCCACTGTAACCTCAAGGAGGTAAAATCCGCCATCCTC
* * *
41535095 GATCTACTCCACTACCGTCTAGGGAGATAAGTTTTATTATCTTTAATCTATTCCACTGGTGCCCA
66 GATCTACTCCACTACCGTCTAGGAAGATAAGATCTATTATCTTTAATCTATTCCACTGGTGCCCA
41535160 GT
131 GT
* * *
41535162 GAGATA-GAATTACTGGCTTCAATATACTCTATTGTAACCTCAGGGAGGTAAAATCCGCCATCCT
1 GAGATAGGAATT-CTGGCTTCAATATACTCCACTGTAACCTCAAGGAGGTAAAATCCGCCATCCT
* * * * * * *
41535226 TGATCTGCTTCATTACTG-CTTAGGAAGATAAGATCTGTTATCTTTGATCTA
65 CGATCTACTCCACTACCGTC-TAGGAAGATAAGATCTATTATCTTTAATCTA
41535277 CTTCACGCCA
Statistics
Matches: 98, Mismatches: 15, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
131 6 0.06
132 92 0.94
ACGTcount: A:0.28, C:0.22, G:0.18, T:0.32
Consensus pattern (132 bp):
GAGATAGGAATTCTGGCTTCAATATACTCCACTGTAACCTCAAGGAGGTAAAATCCGCCATCCTC
GATCTACTCCACTACCGTCTAGGAAGATAAGATCTATTATCTTTAATCTATTCCACTGGTGCCCA
GT
Found at i:41535399 original size:89 final size:89
Alignment explanation
Indices: 41535248--41535765 Score: 777
Period size: 89 Copynumber: 5.8 Consensus size: 89
41535238 TTACTGCTTA
* *
41535248 GGAAGATAAGATCTGTTATCTTTGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTCT
1 GGAAGACAAGATCTGCTATCTTTGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTCT
*
41535313 TCGATCTGCTTCGCCACCAGTATG
66 TCGATCTACTTCGCCACCAGTATG
* *
41535337 GGAAGACAAGATCTGGTATCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTCT
1 GGAAGACAAGATCTGCTATCTTTGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTCT
* *
41535402 TCGATCTATTTCACCACCAGTATG
66 TCGATCTACTTCGCCACCAGTATG
* * *
41535426 GGAAGACAAGATCTGCTATCTTTGATCTACTTCACTCCAATACATGAAGATAAGATCTGTTTTCT
1 GGAAGACAAGATCTGCTATCTTTGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTCT
*
41535491 TCGATCTACTTTGCCACCAGTATG
66 TCGATCTACTTCGCCACCAGTATG
* * *
41535515 GGAAGACAAGATCTACTATCTTTGATCTACTTCACGCCAATACATGAAGACAAGATATGTTTTCT
1 GGAAGACAAGATCTGCTATCTTTGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTCT
* *
41535580 TTGACCTACTTCGCCACCAGTATG
66 TCGATCTACTTCGCCACCAGTATG
*
41535604 GGAAGACAAGATCTGCTATCTTTGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTATCT
1 GGAAGACAAGATCTGCTATCTTTGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTCT
* * * **
41535669 TTGATCTACTTC-ACACCAATACA
66 TCGATCTACTTCGCCACCAGTATG
* * * * *
41535692 TGAAGACAAGATCCGTTTTCTTTGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTATCT
1 GGAAGACAAGATCTGCTATCTTTGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTCT
*
41535757 TTGATCTAC
66 TCGATCTAC
41535766 CTCACGCCAA
Statistics
Matches: 395, Mismatches: 34, Indels: 1
0.92 0.08 0.00
Matches are distributed among these distances:
88 77 0.19
89 318 0.81
ACGTcount: A:0.30, C:0.24, G:0.16, T:0.31
Consensus pattern (89 bp):
GGAAGACAAGATCTGCTATCTTTGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTCT
TCGATCTACTTCGCCACCAGTATG
Found at i:41535795 original size:44 final size:44
Alignment explanation
Indices: 41535249--41535796 Score: 585
Period size: 44 Copynumber: 12.4 Consensus size: 44
41535239 TACTGCTTAG
* *
41535249 GAAGATAAGATCTGTTATCTTTGATCTACTTCACGCCAATACAT
1 GAAGACAAGATCTGCTATCTTTGATCTACTTCACGCCAATACAT
* * * * * * ***
41535293 GAAGACAAGATCTGCTTTCTTCGATCTGCTTCGCCACCAGTATGG
1 GAAGACAAGATCTGCTATCTTTGATCTACTTC-ACGCCAATACAT
* *
41535338 GAAGACAAGATCTGGTATCTTCGATCTACTTCACGCCAATACAT
1 GAAGACAAGATCTGCTATCTTTGATCTACTTCACGCCAATACAT
* * * * * ***
41535382 GAAGACAAGATCTGCTTTCTTCGATCTATTTCACCACCAGTATGG
1 GAAGACAAGATCTGCTATCTTTGATCTACTTCA-CGCCAATACAT
*
41535427 GAAGACAAGATCTGCTATCTTTGATCTACTTCACTCCAATACAT
1 GAAGACAAGATCTGCTATCTTTGATCTACTTCACGCCAATACAT
* * * * * * ***
41535471 GAAGATAAGATCTGTTTTCTTCGATCTACTTTGC-CACCAGTATGG
1 GAAGACAAGATCTGCTATCTTTGATCTAC-TT-CACGCCAATACAT
*
41535516 GAAGACAAGATCTACTATCTTTGATCTACTTCACGCCAATACAT
1 GAAGACAAGATCTGCTATCTTTGATCTACTTCACGCCAATACAT
* * * * * * * ***
41535560 GAAGACAAGATATGTTTTCTTTGACCTACTTCGCCACCAGTATGG
1 GAAGACAAGATCTGCTATCTTTGATCTACTTC-ACGCCAATACAT
41535605 GAAGACAAGATCTGCTATCTTTGATCTACTTCACGCCAATACAT
1 GAAGACAAGATCTGCTATCTTTGATCTACTTCACGCCAATACAT
*
41535649 GAAGACAAGATCTGCTATCTTTGATCTACTTCACACCAATACAT
1 GAAGACAAGATCTGCTATCTTTGATCTACTTCACGCCAATACAT
* * *
41535693 GAAGACAAGATCCGTTTTCTTTGATCTACTTCACGCCAATACAT
1 GAAGACAAGATCTGCTATCTTTGATCTACTTCACGCCAATACAT
* *
41535737 GAAGACAAGATCTGCTATCTTTGATCTACCTCACGCCAATTCAT
1 GAAGACAAGATCTGCTATCTTTGATCTACTTCACGCCAATACAT
* * *
41535781 AAAAATAAGATCTGCT
1 GAAGACAAGATCTGCT
41535797 GCTTTTCAAC
Statistics
Matches: 409, Mismatches: 89, Indels: 12
0.80 0.17 0.02
Matches are distributed among these distances:
43 1 0.00
44 270 0.66
45 137 0.33
46 1 0.00
ACGTcount: A:0.30, C:0.24, G:0.15, T:0.31
Consensus pattern (44 bp):
GAAGACAAGATCTGCTATCTTTGATCTACTTCACGCCAATACAT
Found at i:41539943 original size:19 final size:20
Alignment explanation
Indices: 41539919--41539958 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
41539909 AAAGGTGTCT
* *
41539919 AATGCACATG-ATGTAATGA
1 AATGCAAATGCATGAAATGA
41539938 AATGCAAATGCATGAAATGA
1 AATGCAAATGCATGAAATGA
41539958 A
1 A
41539959 TGTAAAAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 9 0.50
20 9 0.50
ACGTcount: A:0.47, C:0.10, G:0.20, T:0.23
Consensus pattern (20 bp):
AATGCAAATGCATGAAATGA
Found at i:41547803 original size:15 final size:15
Alignment explanation
Indices: 41547783--41547812 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
41547773 TAACCAAATC
41547783 GAATTAGTATTAACT
1 GAATTAGTATTAACT
41547798 GAATTAGTATTAACT
1 GAATTAGTATTAACT
41547813 AAATCGAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.40, C:0.07, G:0.13, T:0.40
Consensus pattern (15 bp):
GAATTAGTATTAACT
Found at i:41548264 original size:23 final size:22
Alignment explanation
Indices: 41548238--41548298 Score: 59
Period size: 23 Copynumber: 2.6 Consensus size: 22
41548228 AAAGGGGTTA
*
41548238 TAAAGAGATGAAAGTTTAAAGAT
1 TAAAGAGATGAAAGATT-AAGAT
* *
41548261 TAAAGAAAATGAAAGATTAAGGT
1 TAAAG-AGATGAAAGATTAAGAT
*
41548284 CAAGAGAGATGAAAG
1 TAA-AGAGATGAAAG
41548299 GTGAAAGGTT
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
23 19 0.61
24 12 0.39
ACGTcount: A:0.54, C:0.02, G:0.25, T:0.20
Consensus pattern (22 bp):
TAAAGAGATGAAAGATTAAGAT
Found at i:41548814 original size:17 final size:17
Alignment explanation
Indices: 41548765--41548822 Score: 61
Period size: 17 Copynumber: 3.5 Consensus size: 17
41548755 AATTTTATTG
41548765 TTCA-TTTTTTAAAATT
1 TTCAGTTTTTTAAAATT
*
41548781 TTCAGTTTTATT-TAATT
1 TTCAGTTTT-TTAAAATT
41548798 TT-AGTTTGTTTAAAATT
1 TTCAGTTT-TTTAAAATT
41548815 TTCA-TTTT
1 TTCAGTTTT
41548823 AAAATTAGCT
Statistics
Matches: 35, Mismatches: 2, Indels: 10
0.74 0.04 0.21
Matches are distributed among these distances:
16 12 0.34
17 20 0.57
18 3 0.09
ACGTcount: A:0.26, C:0.05, G:0.05, T:0.64
Consensus pattern (17 bp):
TTCAGTTTTTTAAAATT
Found at i:41549718 original size:45 final size:45
Alignment explanation
Indices: 41549654--41549742 Score: 169
Period size: 45 Copynumber: 2.0 Consensus size: 45
41549644 AAGCATAGAA
41549654 CAAATAAATTTGCTTCATAGTTTTTTCTATGTTTGTTTTCAAAAC
1 CAAATAAATTTGCTTCATAGTTTTTTCTATGTTTGTTTTCAAAAC
*
41549699 CAAATAAATTTGCTTCATAGTTTTTTCTATGTTTGTTTTTAAAA
1 CAAATAAATTTGCTTCATAGTTTTTTCTATGTTTGTTTTCAAAA
41549743 TAATGAGTAT
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 43 1.00
ACGTcount: A:0.29, C:0.11, G:0.09, T:0.51
Consensus pattern (45 bp):
CAAATAAATTTGCTTCATAGTTTTTTCTATGTTTGTTTTCAAAAC
Found at i:41550234 original size:9 final size:9
Alignment explanation
Indices: 41550222--41550249 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
41550212 TTTTATTACA
41550222 ACAATTAAT
1 ACAATTAAT
41550231 ACAATTAAT
1 ACAATTAAT
41550240 ACAATTAAT
1 ACAATTAAT
41550249 A
1 A
41550250 ATTTGATAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.57, C:0.11, G:0.00, T:0.32
Consensus pattern (9 bp):
ACAATTAAT
Found at i:41550292 original size:68 final size:66
Alignment explanation
Indices: 41550183--41550333 Score: 275
Period size: 68 Copynumber: 2.3 Consensus size: 66
41550173 AAAATTTTAG
41550183 TTTGATAAATTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATACAATTAA
1 TTTGATAAATTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATT-A-ACAATTAA
41550248 TAA
64 TAA
41550251 TTTGATAAATTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAACAATTAATA
1 TTTGATAAATTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAACAATTAATA
41550316 A
66 A
*
41550317 TTTGATAATTTTACTAA
1 TTTGATAAATTTACTAA
41550334 CAATTAATTT
Statistics
Matches: 82, Mismatches: 1, Indels: 2
0.96 0.01 0.02
Matches are distributed among these distances:
66 27 0.33
67 1 0.01
68 54 0.66
ACGTcount: A:0.46, C:0.09, G:0.05, T:0.41
Consensus pattern (66 bp):
TTTGATAAATTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAACAATTAATA
A
Found at i:41550343 original size:16 final size:16
Alignment explanation
Indices: 41550322--41550363 Score: 66
Period size: 16 Copynumber: 2.6 Consensus size: 16
41550312 AATAATTTGA
*
41550322 TAATTTTACTAACAAT
1 TAATTTTAATAACAAT
41550338 TAATTTTAATAACAAT
1 TAATTTTAATAACAAT
*
41550354 TAGTTTTAAT
1 TAATTTTAAT
41550364 TTTATTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.43, C:0.07, G:0.02, T:0.48
Consensus pattern (16 bp):
TAATTTTAATAACAAT
Found at i:41550347 original size:22 final size:23
Alignment explanation
Indices: 41550337--41550392 Score: 69
Period size: 23 Copynumber: 2.5 Consensus size: 23
41550327 TTACTAACAA
* * *
41550337 TTAATTTTAAT-AACAATTAGTT
1 TTAATTTTAATAAAAAAATAATT
*
41550359 TTAATTTTATTAAAAAAATAATT
1 TTAATTTTAATAAAAAAATAATT
41550382 TTAATTTTAAT
1 TTAATTTTAAT
41550393 TTTAATTAAA
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
22 10 0.36
23 18 0.64
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.52
Consensus pattern (23 bp):
TTAATTTTAATAAAAAAATAATT
Found at i:41550352 original size:59 final size:66
Alignment explanation
Indices: 41550183--41550355 Score: 243
Period size: 68 Copynumber: 2.7 Consensus size: 66
41550173 AAAATTTTAG
41550183 TTTGATAAATTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATACAATTAA
1 TTTGATAAATTTACTAATCAAA-GTTAGATTTTA-TACAACAATTAATACAATTAATACAATTAA
41550248 TAA
64 TAA
41550251 TTTGATAAATTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATT-A-ACAATTAA
1 TTTGATAAATTTACTAATCAAA-GTTAGATTTTA-TACAACAATTAATACAATTAATACAATTAA
41550314 TAA
64 TAA
* *
41550317 TTTGATAATTTTACTAA-C-AA-TTA-ATTTTA-ATAACAATTA
1 TTTGATAAATTTACTAATCAAAGTTAGATTTTATACAACAATTA
41550356 GTTTTAATTT
Statistics
Matches: 103, Mismatches: 2, Indels: 9
0.90 0.02 0.08
Matches are distributed among these distances:
59 9 0.09
61 6 0.06
62 3 0.03
64 2 0.02
65 1 0.01
66 27 0.26
67 1 0.01
68 54 0.52
ACGTcount: A:0.46, C:0.09, G:0.04, T:0.41
Consensus pattern (66 bp):
TTTGATAAATTTACTAATCAAAGTTAGATTTTATACAACAATTAATACAATTAATACAATTAATA
A
Found at i:41556040 original size:30 final size:30
Alignment explanation
Indices: 41556006--41556065 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
41555996 ACTGTAATGT
*
41556006 TTGGTTACTTGCATGCTGCAGTTGTGTTGC
1 TTGGTTACTTGCATGCTGCAGCTGTGTTGC
* *
41556036 TTGGTTTCTTGCATGCTGCTGCTGTGTTGC
1 TTGGTTACTTGCATGCTGCAGCTGTGTTGC
41556066 CACCTTTTAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.07, C:0.18, G:0.30, T:0.45
Consensus pattern (30 bp):
TTGGTTACTTGCATGCTGCAGCTGTGTTGC
Found at i:41573395 original size:17 final size:17
Alignment explanation
Indices: 41573373--41573420 Score: 51
Period size: 17 Copynumber: 2.8 Consensus size: 17
41573363 TTTTATAACG
*
41573373 TATATACTTATATTATA
1 TATATACTTATATAATA
* * *
41573390 TATATATTTTTATAATC
1 TATATACTTATATAATA
*
41573407 TATATACCTATATA
1 TATATACTTATATA
41573421 TGTAAATATT
Statistics
Matches: 24, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.40, C:0.08, G:0.00, T:0.52
Consensus pattern (17 bp):
TATATACTTATATAATA
Found at i:41577520 original size:26 final size:28
Alignment explanation
Indices: 41577485--41577537 Score: 92
Period size: 26 Copynumber: 2.0 Consensus size: 28
41577475 GGTAATTTTC
41577485 TTTCATTTGCTTCATTCATGAC-ATGCT
1 TTTCATTTGCTTCATTCATGACTATGCT
41577512 TTTC-TTTGCTTCATTCATGACTATGC
1 TTTCATTTGCTTCATTCATGACTATGC
41577538 AATGATTGTT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
26 17 0.68
27 8 0.32
ACGTcount: A:0.17, C:0.23, G:0.11, T:0.49
Consensus pattern (28 bp):
TTTCATTTGCTTCATTCATGACTATGCT
Found at i:41586682 original size:14 final size:14
Alignment explanation
Indices: 41586663--41586691 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
41586653 TCATGCATAA
41586663 ATGAAAATGTTCCG
1 ATGAAAATGTTCCG
41586677 ATGAAAATGTTCCG
1 ATGAAAATGTTCCG
41586691 A
1 A
41586692 CATGGTCAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.38, C:0.14, G:0.21, T:0.28
Consensus pattern (14 bp):
ATGAAAATGTTCCG
Found at i:41587485 original size:288 final size:291
Alignment explanation
Indices: 41586955--41587533 Score: 1119
Period size: 288 Copynumber: 2.0 Consensus size: 291
41586945 AAGCTACAAT
41586955 AACAAATATAGCATTTTTTTTTTTAGTGTAACACAATGGTGCTCTATATTCACATATAAAAAGAG
1 AACAAATATAGCA-TTTTTTTTTTAGTGTAACACAATGGTGCTCTATATTCACATATAAAAAGAG
41587020 GAGCAAACTCCGATGGATAAAGACAGAAAATAGAATTATCTTACTTTAACTTGATCTTGAATGTC
65 GAGCAAACTCCGATGGATAAAGACAGAAAATAGAATTATCTTACTTTAACTTGATCTTGAATGTC
41587085 TTCTTTCTGGCCTAATGAATCTTGAATCTTTGATCTCATTGCAGCATTAGCAATAACTTTCTCGC
130 TTCTTTCTGGCCTAATGAATCTTGAATCTTTGATCTCATTGCAGCATTAGCAATAACTTTCTCGC
41587150 GGGTTCCCTCCAGGTGTTTGATTTCTTTAAGGATTCGCTTCTCCTCACTCAACGAGATGCTTTCA
195 GGGTTCCCTCCAGGTGTTTGATTTCTTTAAGGATTCGCTTCTCCTCACTCAACGAGATGCTTTCA
41587215 TGCTGAATGCGGTATTGC-A-CTATGGATCTA
260 TGCTGAATGCGGTATTGCAAGCTATGGATCTA
41587245 AACAAATATAGC-TTTTTTTTTTAGTGTAACACAATGGTGCTCTATATTCACATATAAAAAGAGG
1 AACAAATATAGCATTTTTTTTTTAGTGTAACACAATGGTGCTCTATATTCACATATAAAAAGAGG
*
41587309 AGCAAACTCCGATGGATAAAGGCAGAAAATAGAATTATCTTACTTTAACTTGATCTTGAATGTCT
66 AGCAAACTCCGATGGATAAAGACAGAAAATAGAATTATCTTACTTTAACTTGATCTTGAATGTCT
41587374 TCTTTCTGGCCTAATGAATCTTGAATCTTTGATCTCATTGCAGCATTAGCAATAACTTTCTCGCG
131 TCTTTCTGGCCTAATGAATCTTGAATCTTTGATCTCATTGCAGCATTAGCAATAACTTTCTCGCG
41587439 GGTTCCCTCCAGGTGTTTGATTTCTTTAAGGATTCGCTTCTCCTCACTCAACGAGATGCTTTCAT
196 GGTTCCCTCCAGGTGTTTGATTTCTTTAAGGATTCGCTTCTCCTCACTCAACGAGATGCTTTCAT
41587504 GCTGAATGCGGTATTGCAAGCTATGGATCT
261 GCTGAATGCGGTATTGCAAGCTATGGATCT
41587534 GCAATTCATA
Statistics
Matches: 286, Mismatches: 1, Indels: 4
0.98 0.00 0.01
Matches are distributed among these distances:
288 263 0.92
289 1 0.00
290 22 0.08
ACGTcount: A:0.28, C:0.19, G:0.17, T:0.35
Consensus pattern (291 bp):
AACAAATATAGCATTTTTTTTTTAGTGTAACACAATGGTGCTCTATATTCACATATAAAAAGAGG
AGCAAACTCCGATGGATAAAGACAGAAAATAGAATTATCTTACTTTAACTTGATCTTGAATGTCT
TCTTTCTGGCCTAATGAATCTTGAATCTTTGATCTCATTGCAGCATTAGCAATAACTTTCTCGCG
GGTTCCCTCCAGGTGTTTGATTTCTTTAAGGATTCGCTTCTCCTCACTCAACGAGATGCTTTCAT
GCTGAATGCGGTATTGCAAGCTATGGATCTA
Found at i:41589989 original size:21 final size:22
Alignment explanation
Indices: 41589960--41590000 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
41589950 CAAAAAGAAC
* *
41589960 AGATATGATTAGAATTAATATT
1 AGATATGATCAAAATTAATATT
41589982 AGAT-TGATCAAAATTAATA
1 AGATATGATCAAAATTAATA
41590001 AAAATAATAA
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:0.49, C:0.02, G:0.12, T:0.37
Consensus pattern (22 bp):
AGATATGATCAAAATTAATATT
Found at i:41594359 original size:17 final size:17
Alignment explanation
Indices: 41594337--41594378 Score: 52
Period size: 16 Copynumber: 2.5 Consensus size: 17
41594327 TTATAAAGGC
41594337 TAAAAATAAATTAT-TTT
1 TAAAAA-AAATTATATTT
*
41594354 TAAAAAATA-TATATTT
1 TAAAAAAAATTATATTT
41594370 TAAAAAAAA
1 TAAAAAAAA
41594379 ATAGAGTTAG
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
15 3 0.14
16 13 0.59
17 6 0.27
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (17 bp):
TAAAAAAAATTATATTT
Found at i:41600796 original size:13 final size:13
Alignment explanation
Indices: 41600778--41600803 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
41600768 CTTTTGTAAC
41600778 TTAGTGAAGATGG
1 TTAGTGAAGATGG
41600791 TTAGTGAAGATGG
1 TTAGTGAAGATGG
41600804 CCTCCGGTTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.00, G:0.38, T:0.31
Consensus pattern (13 bp):
TTAGTGAAGATGG
Found at i:41602288 original size:16 final size:16
Alignment explanation
Indices: 41602256--41602289 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
41602246 CAAGAGCGTT
**
41602256 TGCAAAGAAGATTACA
1 TGCAAAGAAGAAGACA
41602272 TGCAAAGAAGAAGACA
1 TGCAAAGAAGAAGACA
41602288 TG
1 TG
41602290 TTTCAATTAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.12, G:0.24, T:0.15
Consensus pattern (16 bp):
TGCAAAGAAGAAGACA
Found at i:41603847 original size:16 final size:17
Alignment explanation
Indices: 41603826--41603858 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
41603816 TTCAATGGTA
41603826 ATTTTGAATTT-ATTTG
1 ATTTTGAATTTAATTTG
*
41603842 ATTTTGCATTTAATTTG
1 ATTTTGAATTTAATTTG
41603859 TCAAATACGG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.24, C:0.03, G:0.12, T:0.61
Consensus pattern (17 bp):
ATTTTGAATTTAATTTG
Found at i:41608458 original size:20 final size:20
Alignment explanation
Indices: 41608433--41608483 Score: 59
Period size: 19 Copynumber: 2.6 Consensus size: 20
41608423 AAATATAAAA
*
41608433 TTTGAAATTTTTATAAATAT
1 TTTGAAATTTTTAAAAATAT
*
41608453 TTTG-AATTTTAAAAAATAT
1 TTTGAAATTTTTAAAAATAT
* *
41608472 TCTGATATTTTT
1 TTTGAAATTTTT
41608484 TTATAATTTT
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
19 16 0.64
20 9 0.36
ACGTcount: A:0.37, C:0.02, G:0.06, T:0.55
Consensus pattern (20 bp):
TTTGAAATTTTTAAAAATAT
Found at i:41610552 original size:20 final size:20
Alignment explanation
Indices: 41610527--41610576 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
41610517 TGATGAAATT
*
41610527 ACTTCATTGTGCTTAGTGGC
1 ACTTCATTGTGCTTAGTGAC
*
41610547 ACTTCATTATGCTTAGTGAC
1 ACTTCATTGTGCTTAGTGAC
*
41610567 ACTTCCTTGT
1 ACTTCATTGT
41610577 TCTTCTGCTT
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:0.18, C:0.22, G:0.18, T:0.42
Consensus pattern (20 bp):
ACTTCATTGTGCTTAGTGAC
Found at i:41611344 original size:2 final size:2
Alignment explanation
Indices: 41611332--41611361 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
41611322 GGAGAAAACG
41611332 TA TA TA T- 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 T
41611362 TTCCCTTGTT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:41612148 original size:17 final size:17
Alignment explanation
Indices: 41612122--41612156 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
41612112 TCAAGCACAC
41612122 CCTTAATGCTAGAATGG
1 CCTTAATGCTAGAATGG
*
41612139 CCTTAGTGCTAGAATGG
1 CCTTAATGCTAGAATGG
41612156 C
1 C
41612157 ATCTTGGTGA
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:0.26, C:0.20, G:0.26, T:0.29
Consensus pattern (17 bp):
CCTTAATGCTAGAATGG
Found at i:41616537 original size:27 final size:27
Alignment explanation
Indices: 41616506--41616557 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
41616496 AAAACTTACA
41616506 AAAAAATTATAATAATTTTCAAAAATC
1 AAAAAATTATAATAATTTTCAAAAATC
* * * *
41616533 AAAAATTTATTATATTTTTTAAAAA
1 AAAAAATTATAATAATTTTCAAAAA
41616558 ATTATAAATT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 21 1.00
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.40
Consensus pattern (27 bp):
AAAAAATTATAATAATTTTCAAAAATC
Found at i:41616574 original size:18 final size:18
Alignment explanation
Indices: 41616548--41616583 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
41616538 TTTATTATAT
*
41616548 TTTTTAAAAAATTATAAA
1 TTTTAAAAAAATTATAAA
*
41616566 TTTTAAAAAAATTCTAAA
1 TTTTAAAAAAATTATAAA
41616584 GAATATATAA
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:0.56, C:0.03, G:0.00, T:0.42
Consensus pattern (18 bp):
TTTTAAAAAAATTATAAA
Found at i:41629442 original size:32 final size:32
Alignment explanation
Indices: 41629399--41629476 Score: 95
Period size: 32 Copynumber: 2.4 Consensus size: 32
41629389 GAGTGTGGCC
* * * *
41629399 GTGTGGACCACACGGGCTAGGCCAGAT-TGGGT
1 GTGTGGGCCACACGAGCAAGGCCA-ATCTGGAT
41629431 GTGTGGGCCACACGAGCAAGGCCAATCTGGAT
1 GTGTGGGCCACACGAGCAAGGCCAATCTGGAT
41629463 GTGTGGGCCCACAC
1 GTGTGGG-CCACAC
41629477 ATTCTAAAAT
Statistics
Matches: 40, Mismatches: 4, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
31 2 0.05
32 32 0.80
33 6 0.15
ACGTcount: A:0.21, C:0.26, G:0.37, T:0.17
Consensus pattern (32 bp):
GTGTGGGCCACACGAGCAAGGCCAATCTGGAT
Found at i:41630935 original size:40 final size:40
Alignment explanation
Indices: 41630880--41631043 Score: 247
Period size: 40 Copynumber: 4.1 Consensus size: 40
41630870 TGTTATACTC
41630880 TCTGTCTGGTGTGTTTCGGTTGGATTAGCTCCTATGAGCT
1 TCTGTCTGGTGTGTTTCGGTTGGATTAGCTCCTATGAGCT
* * *
41630920 TCTGTCTAGTGTGTTTCAGTTGGATTAGCTCCTTTGAGCT
1 TCTGTCTGGTGTGTTTCGGTTGGATTAGCTCCTATGAGCT
* * *
41630960 TCTGTCTGGTGTGTTTTGGTTGGATTAGCTCTTATGAGAT
1 TCTGTCTGGTGTGTTTCGGTTGGATTAGCTCCTATGAGCT
* * *
41631000 TCTGTCTGGTGTGTTTCGGTTGGACTAGCTCTTATGAGCA
1 TCTGTCTGGTGTGTTTCGGTTGGATTAGCTCCTATGAGCT
41631040 TCTG
1 TCTG
41631044 GTGTGTTTTA
Statistics
Matches: 111, Mismatches: 13, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
40 111 1.00
ACGTcount: A:0.12, C:0.16, G:0.29, T:0.44
Consensus pattern (40 bp):
TCTGTCTGGTGTGTTTCGGTTGGATTAGCTCCTATGAGCT
Found at i:41631733 original size:12 final size:12
Alignment explanation
Indices: 41631716--41631754 Score: 60
Period size: 12 Copynumber: 3.2 Consensus size: 12
41631706 TACACAAGCG
*
41631716 TGTGGTCGGCCA
1 TGTGGTTGGCCA
*
41631728 TGTGGTTGGCCG
1 TGTGGTTGGCCA
41631740 TGTGGTTGGCCA
1 TGTGGTTGGCCA
41631752 TGT
1 TGT
41631755 CTTGCACACT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.05, C:0.18, G:0.44, T:0.33
Consensus pattern (12 bp):
TGTGGTTGGCCA
Found at i:41635304 original size:32 final size:32
Alignment explanation
Indices: 41635244--41635304 Score: 79
Period size: 32 Copynumber: 1.9 Consensus size: 32
41635234 TTTTTTAATA
* *
41635244 TTTATATTATATATTAGTATAAATATAAATTT
1 TTTATATTATAAATTAGTATAAACATAAATTT
*
41635276 TTTATGTTATAAATTA-TATAATACATAAA
1 TTTATATTATAAATTAGTATAA-ACATAAA
41635305 AATAACATAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
31 5 0.20
32 20 0.80
ACGTcount: A:0.46, C:0.02, G:0.03, T:0.49
Consensus pattern (32 bp):
TTTATATTATAAATTAGTATAAACATAAATTT
Found at i:41640638 original size:42 final size:42
Alignment explanation
Indices: 41640591--41640671 Score: 144
Period size: 42 Copynumber: 1.9 Consensus size: 42
41640581 CATGGCTTTT
41640591 ATATATACATATCCCAAAATCAAACACATCAAGTATTTAGCC
1 ATATATACATATCCCAAAATCAAACACATCAAGTATTTAGCC
* *
41640633 ATATATATATATCCCAAAATCAAACCCATCAAGTATTTA
1 ATATATACATATCCCAAAATCAAACACATCAAGTATTTA
41640672 ACCAAGAATA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 37 1.00
ACGTcount: A:0.46, C:0.22, G:0.04, T:0.28
Consensus pattern (42 bp):
ATATATACATATCCCAAAATCAAACACATCAAGTATTTAGCC
Found at i:41640683 original size:42 final size:42
Alignment explanation
Indices: 41640599--41640685 Score: 131
Period size: 42 Copynumber: 2.1 Consensus size: 42
41640589 TTATATATAC
* *
41640599 ATATCCCAAAATCAAACACATCAAGTATTTAGCCATATATAT
1 ATATCCCAAAATCAAACACATCAAGTATTTAACCATAAATAT
*
41640641 ATATCCCAAAATCAAACCCATCAAGTATTTAACCA-AGAATAT
1 ATATCCCAAAATCAAACACATCAAGTATTTAACCATA-AATAT
41640683 ATA
1 ATA
41640686 AAACCAAGCT
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
41 1 0.02
42 40 0.98
ACGTcount: A:0.47, C:0.22, G:0.05, T:0.26
Consensus pattern (42 bp):
ATATCCCAAAATCAAACACATCAAGTATTTAACCATAAATAT
Found at i:41647241 original size:18 final size:18
Alignment explanation
Indices: 41647199--41647233 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
41647189 AAGAATCTGT
41647199 GATAGATGAGGAATTTCA
1 GATAGATGAGGAATTTCA
41647217 GATAGATGAGGAATTTC
1 GATAGATGAGGAATTTC
41647234 CGGTAGATTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.37, C:0.06, G:0.29, T:0.29
Consensus pattern (18 bp):
GATAGATGAGGAATTTCA
Found at i:41647511 original size:64 final size:64
Alignment explanation
Indices: 41647410--41647533 Score: 230
Period size: 64 Copynumber: 1.9 Consensus size: 64
41647400 ATATATGTCC
*
41647410 AATATGAATAAATTTGAAGAGTACGTCTCCTTATCCATGTTTAAATATATATCCAACATGTTTA
1 AATATGAATAAATTTGAAGAGTACATCTCCTTATCCATGTTTAAATATATATCCAACATGTTTA
*
41647474 AATATGAATAAATTTGAAGAGTACATCTCCTTATCCATGTTTAAATATGTATCCAACATG
1 AATATGAATAAATTTGAAGAGTACATCTCCTTATCCATGTTTAAATATATATCCAACATG
41647534 GATACAAAGA
Statistics
Matches: 58, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
64 58 1.00
ACGTcount: A:0.38, C:0.15, G:0.11, T:0.36
Consensus pattern (64 bp):
AATATGAATAAATTTGAAGAGTACATCTCCTTATCCATGTTTAAATATATATCCAACATGTTTA
Found at i:41662077 original size:18 final size:18
Alignment explanation
Indices: 41662049--41662084 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
41662039 AAATTTATAT
*
41662049 TTTTTAAAAAATTATAAA
1 TTTTAAAAAAATTATAAA
*
41662067 TTTTAAAAAAATTCTAAA
1 TTTTAAAAAAATTATAAA
41662085 GAATATATAA
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:0.56, C:0.03, G:0.00, T:0.42
Consensus pattern (18 bp):
TTTTAAAAAAATTATAAA
Found at i:41673212 original size:32 final size:32
Alignment explanation
Indices: 41673171--41673236 Score: 123
Period size: 32 Copynumber: 2.1 Consensus size: 32
41673161 GAAGGTTTCA
41673171 AGTTTCTGATTTTAAGTCAAGTCAGCTGTTGT
1 AGTTTCTGATTTTAAGTCAAGTCAGCTGTTGT
*
41673203 AGTTTCTGATTTTAAGTCATGTCAGCTGTTGT
1 AGTTTCTGATTTTAAGTCAAGTCAGCTGTTGT
41673235 AG
1 AG
41673237 GACCTGCCAA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.21, C:0.12, G:0.23, T:0.44
Consensus pattern (32 bp):
AGTTTCTGATTTTAAGTCAAGTCAGCTGTTGT
Found at i:41674934 original size:26 final size:27
Alignment explanation
Indices: 41674888--41674944 Score: 66
Period size: 26 Copynumber: 2.1 Consensus size: 27
41674878 GAATGAAAAG
41674888 AAATTTTATAATTAATATA-TTAATTA
1 AAATTTTATAATTAATATATTTAATTA
*
41674914 AAATTTTAT-A-TAATGAGTATTTAATTG
1 AAATTTTATAATTAAT-A-TATTTAATTA
41674941 AAAT
1 AAAT
41674945 CATAAAAATT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
24 4 0.15
25 2 0.07
26 11 0.41
27 10 0.37
ACGTcount: A:0.47, C:0.00, G:0.05, T:0.47
Consensus pattern (27 bp):
AAATTTTATAATTAATATATTTAATTA
Found at i:41675215 original size:52 final size:52
Alignment explanation
Indices: 41675153--41675257 Score: 192
Period size: 52 Copynumber: 2.0 Consensus size: 52
41675143 CAGCTGCTGG
* *
41675153 ACCTGCCAGGAAAAGTCTTTTGTTTGGACCCAAAATCTGGAAAAATATGTGT
1 ACCTGCCAGGAAAAGTCTTTGGTTTGGACCCAAAAACTGGAAAAATATGTGT
41675205 ACCTGCCAGGAAAAGTCTTTGGTTTGGACCCAAAAACTGGAAAAATATGTGT
1 ACCTGCCAGGAAAAGTCTTTGGTTTGGACCCAAAAACTGGAAAAATATGTGT
41675257 A
1 A
41675258 TCTCCAATGA
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 51 1.00
ACGTcount: A:0.34, C:0.17, G:0.22, T:0.27
Consensus pattern (52 bp):
ACCTGCCAGGAAAAGTCTTTGGTTTGGACCCAAAAACTGGAAAAATATGTGT
Found at i:41680659 original size:22 final size:22
Alignment explanation
Indices: 41680618--41680659 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
41680608 AAAAAATAAC
* *
41680618 TACTATTTTCTTGTTGTTTTGA
1 TACTATTTTCTTATTATTTTGA
41680640 TACTATTTTCTTATTATTTT
1 TACTATTTTCTTATTATTTT
41680660 CTTACTTTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.17, C:0.10, G:0.07, T:0.67
Consensus pattern (22 bp):
TACTATTTTCTTATTATTTTGA
Found at i:41680665 original size:22 final size:22
Alignment explanation
Indices: 41680618--41680670 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 22
41680608 AAAAAATAAC
* * *
41680618 TACTATTTTCTTGTTGTTTTGA
1 TACTATTTTCTTATTATTTTCA
*
41680640 TACTATTTTCTTATTATTTTCT
1 TACTATTTTCTTATTATTTTCA
*
41680662 TACTTTTTT
1 TACTATTTT
41680671 ACTATCATTT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.15, C:0.11, G:0.06, T:0.68
Consensus pattern (22 bp):
TACTATTTTCTTATTATTTTCA
Found at i:41680829 original size:13 final size:13
Alignment explanation
Indices: 41680811--41680835 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
41680801 TATTTAAGTA
41680811 TAAATTTATTTTT
1 TAAATTTATTTTT
41680824 TAAATTTATTTT
1 TAAATTTATTTT
41680836 CAATTTTTTG
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:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (13 bp):
TAAATTTATTTTT
Found at i:41680904 original size:16 final size:17
Alignment explanation
Indices: 41680865--41680906 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 17
41680855 TATTTTAATG
41680865 TTTTTTATA-TTTTAGA
1 TTTTTTATATTTTTAGA
* *
41680881 TGTATTATATTTTTA-A
1 TTTTTTATATTTTTAGA
41680897 TTTTTTATAT
1 TTTTTTATAT
41680907 ATAAAAAATA
Statistics
Matches: 21, Mismatches: 4, Indels: 2
0.78 0.15 0.07
Matches are distributed among these distances:
16 16 0.76
17 5 0.24
ACGTcount: A:0.26, C:0.00, G:0.05, T:0.69
Consensus pattern (17 bp):
TTTTTTATATTTTTAGA
Found at i:41687393 original size:3 final size:3
Alignment explanation
Indices: 41687385--41687431 Score: 85
Period size: 3 Copynumber: 15.7 Consensus size: 3
41687375 CTATTTTTCG
*
41687385 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA CAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
41687432 GTTCGTTAAC
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:41695139 original size:22 final size:22
Alignment explanation
Indices: 41695114--41695156 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
41695104 TATCTTAATA
*
41695114 ATAACAACAAAATTGTAACAAC
1 ATAACAACAAAATAGTAACAAC
* *
41695136 ATAATAATAAAATAGTAACAA
1 ATAACAACAAAATAGTAACAA
41695157 AGTAGTGAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.63, C:0.12, G:0.05, T:0.21
Consensus pattern (22 bp):
ATAACAACAAAATAGTAACAAC
Found at i:41700831 original size:72 final size:71
Alignment explanation
Indices: 41700752--41700960 Score: 222
Period size: 72 Copynumber: 2.9 Consensus size: 71
41700742 GAATTCATCA
* * *
41700752 ACTCAATTGGTTTCTTGACAAGCCTAATTGAGTGAGTTGCAATAGGTTTCCCAATGATTTTGGAA
1 ACTCAATTGG-TTCTTGACAAGCCTAAATGAGTGAGTTGCAAGAGGTTTCCCAATGATCTTGGAA
41700817 TCTGTCC
65 TCTGTCC
* * * * * **
41700824 ACTCAATTGGTTCTAATG-GAAGCTTAAATAAGTGAGTTGCAAGATGTTACCCAATGATCTTAAA
1 ACTCAATTGGTTCT--TGACAAGCCTAAATGAGTGAGTTGCAAGAGGTTTCCCAATGATCTTGGA
*
41700888 ATTTGTCC
64 ATCTGTCC
** * * * *
41700896 ACTCAATTGGTTCACCGACAAGTCTAAATGAGTGAGTTGCAAGAGATTTTCCAGTGATCTTGGAA
1 ACTCAATTGGTTC-TTGACAAGCCTAAATGAGTGAGTTGCAAGAGGTTTCCCAATGATCTTGGAA
41700961 CCGTTGTTGA
Statistics
Matches: 109, Mismatches: 24, Indels: 8
0.77 0.17 0.06
Matches are distributed among these distances:
71 5 0.05
72 102 0.94
73 2 0.02
ACGTcount: A:0.30, C:0.17, G:0.21, T:0.33
Consensus pattern (71 bp):
ACTCAATTGGTTCTTGACAAGCCTAAATGAGTGAGTTGCAAGAGGTTTCCCAATGATCTTGGAAT
CTGTCC
Found at i:41703247 original size:11 final size:11
Alignment explanation
Indices: 41703210--41703283 Score: 50
Period size: 11 Copynumber: 6.8 Consensus size: 11
41703200 ATATTTTTTA
*
41703210 TTTTTAAAAAT
1 TTTTTAAAATT
*
41703221 ATTTTAAAATACT
1 TTTTTAAAAT--T
41703234 TTTTTAAAATT
1 TTTTTAAAATT
41703245 TTTTT---A--
1 TTTTTAAAATT
*
41703251 TTTTTAAAATA
1 TTTTTAAAATT
41703262 TTTTTAAAATACT
1 TTTTTAAAAT--T
41703275 TTTTTAAAA
1 TTTTTAAAA
41703284 ATTGTCTAAA
Statistics
Matches: 50, Mismatches: 4, Indels: 16
0.71 0.06 0.23
Matches are distributed among these distances:
6 5 0.10
8 1 0.02
9 1 0.02
11 24 0.48
13 19 0.38
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.57
Consensus pattern (11 bp):
TTTTTAAAATT
Found at i:41703250 original size:41 final size:41
Alignment explanation
Indices: 41703203--41703283 Score: 146
Period size: 41 Copynumber: 2.0 Consensus size: 41
41703193 TAAATATATA
41703203 TTTTTTATTTTTAAAA-ATATTTTAAAATACTTTTTTAAAAT
1 TTTTTTATTTTTAAAATAT-TTTTAAAATACTTTTTTAAAAT
41703244 TTTTTTATTTTTAAAATATTTTTAAAATACTTTTTTAAAA
1 TTTTTTATTTTTAAAATATTTTTAAAATACTTTTTTAAAA
41703284 ATTGTCTAAA
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
41 37 0.95
42 2 0.05
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.59
Consensus pattern (41 bp):
TTTTTTATTTTTAAAATATTTTTAAAATACTTTTTTAAAAT
Found at i:41703256 original size:17 final size:17
Alignment explanation
Indices: 41703234--41703267 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
41703224 TTAAAATACT
*
41703234 TTTTTAAAATTTTTTTA
1 TTTTTAAAATATTTTTA
41703251 TTTTTAAAATATTTTTA
1 TTTTTAAAATATTTTTA
41703268 AAATACTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (17 bp):
TTTTTAAAATATTTTTA
Found at i:41709741 original size:29 final size:31
Alignment explanation
Indices: 41709708--41709784 Score: 104
Period size: 29 Copynumber: 2.5 Consensus size: 31
41709698 TTTGGTTCAA
*
41709708 GTTACATTTTAGTCACTTATGTT-TGA-AAT
1 GTTACATTTTAGTCACTTATGTTATCATAAT
* *
41709737 GTTACGTTTTAGTCACTTATGTTATCATGAT
1 GTTACATTTTAGTCACTTATGTTATCATAAT
*
41709768 GTAACATTTTAGTCACT
1 GTTACATTTTAGTCACT
41709785 GAGCCGTTAA
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
29 22 0.54
30 2 0.05
31 17 0.41
ACGTcount: A:0.26, C:0.13, G:0.14, T:0.47
Consensus pattern (31 bp):
GTTACATTTTAGTCACTTATGTTATCATAAT
Found at i:41711095 original size:21 final size:21
Alignment explanation
Indices: 41711041--41711096 Score: 60
Period size: 21 Copynumber: 2.6 Consensus size: 21
41711031 TAATTTATAA
41711041 TTTTTTTTATATTTTGAAGAAT
1 TTTTTTTTA-ATTTTGAAGAAT
* * *
41711063 TTTTCTTGAATTTT-AAGATTT
1 TTTTTTTTAATTTTGAAGA-AT
41711084 TTTTTTTTAATTT
1 TTTTTTTTAATTT
41711097 CAAGTGCACA
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
20 4 0.14
21 17 0.61
22 7 0.25
ACGTcount: A:0.23, C:0.02, G:0.07, T:0.68
Consensus pattern (21 bp):
TTTTTTTTAATTTTGAAGAAT
Found at i:41719617 original size:47 final size:47
Alignment explanation
Indices: 41719524--41719621 Score: 126
Period size: 47 Copynumber: 2.1 Consensus size: 47
41719514 TTATATGAAA
* * *
41719524 TATTTTTAAAAATTTTATCAAATAATAAAAAATATTTTACATATATT
1 TATTTTTAAAAATATTATCAAACAATAAAAAATATTTTACACATATT
* **
41719571 TATTTTTAGGAAATATT-TCAAACAATAAAAAATATTTTAGGCATATT
1 TATTTTTA-AAAATATTATCAAACAATAAAAAATATTTTACACATATT
41719618 TATT
1 TATT
41719622 CAAACACAAA
Statistics
Matches: 44, Mismatches: 6, Indels: 2
0.85 0.12 0.04
Matches are distributed among these distances:
47 38 0.86
48 6 0.14
ACGTcount: A:0.46, C:0.05, G:0.04, T:0.45
Consensus pattern (47 bp):
TATTTTTAAAAATATTATCAAACAATAAAAAATATTTTACACATATT
Found at i:41720792 original size:63 final size:63
Alignment explanation
Indices: 41720693--41720818 Score: 243
Period size: 63 Copynumber: 2.0 Consensus size: 63
41720683 TATAGTACTG
41720693 TGATTGACTGTCTTTGTAAGAATGGGTTGGTAAAGGAGGCTCTCGATCTCTCTCGGAAATGAA
1 TGATTGACTGTCTTTGTAAGAATGGGTTGGTAAAGGAGGCTCTCGATCTCTCTCGGAAATGAA
*
41720756 TGATTGACTGTCTTTGTAAGAATGGGTTGGTAAAGGAGGCTCTTGATCTCTCTCGGAAATGAA
1 TGATTGACTGTCTTTGTAAGAATGGGTTGGTAAAGGAGGCTCTCGATCTCTCTCGGAAATGAA
41720819 GGATAAAGGC
Statistics
Matches: 62, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
63 62 1.00
ACGTcount: A:0.25, C:0.13, G:0.29, T:0.33
Consensus pattern (63 bp):
TGATTGACTGTCTTTGTAAGAATGGGTTGGTAAAGGAGGCTCTCGATCTCTCTCGGAAATGAA
Found at i:41725096 original size:16 final size:16
Alignment explanation
Indices: 41725075--41725126 Score: 86
Period size: 16 Copynumber: 3.2 Consensus size: 16
41725065 TTTGGTTCGC
41725075 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
41725091 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
* *
41725107 TGTAATGGAATAGAGG
1 TGTATTGGATTAGAGG
41725123 TGTA
1 TGTA
41725127 ATAGCAAATC
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 34 1.00
ACGTcount: A:0.29, C:0.00, G:0.37, T:0.35
Consensus pattern (16 bp):
TGTATTGGATTAGAGG
Found at i:41725212 original size:39 final size:43
Alignment explanation
Indices: 41725107--41725216 Score: 129
Period size: 45 Copynumber: 2.6 Consensus size: 43
41725097 GGATTAGAGG
41725107 TGTAATGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGTTGAA
1 TGTAATGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGTT--A
* * ***
41725152 TGTAATGGAATAGAGGCGTAATAG-TAATCTTGTGTTTGG-T-
1 TGTAATGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGTTA
41725192 TG-AATGGAATAGAGGTGTAATAGCA
1 TGTAATGGAATAGAGGTGTAATAGCA
41725217 TAATGGAAAA
Statistics
Matches: 57, Mismatches: 7, Indels: 7
0.80 0.10 0.10
Matches are distributed among these distances:
39 20 0.35
40 2 0.04
43 1 0.02
44 11 0.19
45 23 0.40
ACGTcount: A:0.34, C:0.05, G:0.29, T:0.32
Consensus pattern (43 bp):
TGTAATGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGTTA
Found at i:41726718 original size:15 final size:15
Alignment explanation
Indices: 41726698--41726733 Score: 72
Period size: 15 Copynumber: 2.4 Consensus size: 15
41726688 GGTATATGTA
41726698 TAATTGACCTAAAAT
1 TAATTGACCTAAAAT
41726713 TAATTGACCTAAAAT
1 TAATTGACCTAAAAT
41726728 TAATTG
1 TAATTG
41726734 TTGGTATTTG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.44, C:0.11, G:0.08, T:0.36
Consensus pattern (15 bp):
TAATTGACCTAAAAT
Found at i:41730719 original size:9 final size:9
Alignment explanation
Indices: 41730705--41730736 Score: 55
Period size: 9 Copynumber: 3.6 Consensus size: 9
41730695 TATTCATGTA
41730705 TTATGTAAG
1 TTATGTAAG
*
41730714 TTATGTGAG
1 TTATGTAAG
41730723 TTATGTAAG
1 TTATGTAAG
41730732 TTATG
1 TTATG
41730737 ATATTTATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.28, C:0.00, G:0.25, T:0.47
Consensus pattern (9 bp):
TTATGTAAG
Found at i:41732901 original size:28 final size:26
Alignment explanation
Indices: 41732811--41732904 Score: 75
Period size: 28 Copynumber: 3.5 Consensus size: 26
41732801 TAGCATTTAA
* *
41732811 TTAATTTTTTAAAATTTTAAAAAAAATT
1 TTAATTTTTT--AATTTTTAAAATAATT
* * *
41732839 ATAATTTTAT-ATTTTT-TAATAATT
1 TTAATTTTTTAATTTTTAAAATAATT
41732863 TTAATGATTTTTAATTTTTAAAAGTAATTT
1 TTAAT--TTTTTAATTTTTAAAA-TAA-TT
41732893 TTAATTTTTTAA
1 TTAATTTTTTAA
41732905 AATTAAAAAA
Statistics
Matches: 52, Mismatches: 8, Indels: 12
0.72 0.11 0.17
Matches are distributed among these distances:
24 10 0.19
25 5 0.10
26 4 0.08
27 6 0.12
28 17 0.33
29 3 0.06
30 7 0.13
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.57
Consensus pattern (26 bp):
TTAATTTTTTAATTTTTAAAATAATT
Found at i:41735123 original size:13 final size:14
Alignment explanation
Indices: 41735095--41735123 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
41735085 TCAGAAAAGT
41735095 AATTATTTTTTAGA
1 AATTATTTTTTAGA
41735109 AATTATTTTTT-GA
1 AATTATTTTTTAGA
41735122 AA
1 AA
41735124 ACTATTTTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 4 0.27
14 11 0.73
ACGTcount: A:0.38, C:0.00, G:0.07, T:0.55
Consensus pattern (14 bp):
AATTATTTTTTAGA
Found at i:41735631 original size:43 final size:43
Alignment explanation
Indices: 41735579--41735716 Score: 161
Period size: 43 Copynumber: 3.2 Consensus size: 43
41735569 ACGGCACTAT
* * * * *
41735579 AGAATATGACCTTTAGCGGTGCTTTTCTCACAATCACTGCTAA
1 AGAACATGACATTTAGCGGTGCTTTTATCACAATCGCCGCTAA
41735622 AGAACATGACATTTAGCGGCT-CTTTTATCACAATCGCCGCTAA
1 AGAACATGACATTTAGCGG-TGCTTTTATCACAATCGCCGCTAA
* * * * *
41735665 AAAACATGACATTTAGCAGCGTTTTTATCACAAACGCCGCTAA
1 AGAACATGACATTTAGCGGTGCTTTTATCACAATCGCCGCTAA
*
41735708 AGAATATGA
1 AGAACATGA
41735717 TCTTTAGTGA
Statistics
Matches: 81, Mismatches: 12, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
43 80 0.99
44 1 0.01
ACGTcount: A:0.33, C:0.22, G:0.16, T:0.28
Consensus pattern (43 bp):
AGAACATGACATTTAGCGGTGCTTTTATCACAATCGCCGCTAA
Found at i:41735723 original size:43 final size:43
Alignment explanation
Indices: 41735547--41735716 Score: 148
Period size: 43 Copynumber: 4.0 Consensus size: 43
41735537 GTCGCTAAAT
* * * * *
41735547 TTTA-CAGCGTTTTT-TCACATAAACGGCACTATAGAATATGACC
1 TTTAGCAGCGTTTTTATCAC--AAACGCCGCTAAAGAACATGACA
* * * * * * *
41735590 TTTAGCGGTGCTTTTCTCACAATCACTGCTAAAGAACATGACA
1 TTTAGCAGCGTTTTTATCACAAACGCCGCTAAAGAACATGACA
* * *
41735633 TTTAGCGGC-TCTTTTATCACAATCGCCGCTAAAAAACATGACA
1 TTTAGCAGCGT-TTTTATCACAAACGCCGCTAAAGAACATGACA
*
41735676 TTTAGCAGCGTTTTTATCACAAACGCCGCTAAAGAATATGA
1 TTTAGCAGCGTTTTTATCACAAACGCCGCTAAAGAACATGA
41735717 TCTTTAGTGA
Statistics
Matches: 102, Mismatches: 21, Indels: 8
0.78 0.16 0.06
Matches are distributed among these distances:
43 90 0.88
44 8 0.08
45 4 0.04
ACGTcount: A:0.32, C:0.22, G:0.15, T:0.30
Consensus pattern (43 bp):
TTTAGCAGCGTTTTTATCACAAACGCCGCTAAAGAACATGACA
Found at i:41738222 original size:9 final size:9
Alignment explanation
Indices: 41738208--41738246 Score: 60
Period size: 9 Copynumber: 4.3 Consensus size: 9
41738198 TTTATGTATC
41738208 ATGTAAGTT
1 ATGTAAGTT
41738217 ATGTAAGTT
1 ATGTAAGTT
* *
41738226 ACGTGAGTT
1 ATGTAAGTT
41738235 ATGTAAGTT
1 ATGTAAGTT
41738244 ATG
1 ATG
41738247 ATATGATATA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.31, C:0.03, G:0.26, T:0.41
Consensus pattern (9 bp):
ATGTAAGTT
Found at i:41738324 original size:19 final size:19
Alignment explanation
Indices: 41738300--41738336 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
41738290 TTTAATTCTT
41738300 TAAAGTTATGTAAGTTATG
1 TAAAGTTATGTAAGTTATG
41738319 TAAAGTTATGTAAGTTAT
1 TAAAGTTATGTAAGTTAT
41738337 ATATTTTATA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.38, C:0.00, G:0.19, T:0.43
Consensus pattern (19 bp):
TAAAGTTATGTAAGTTATG
Found at i:41738326 original size:10 final size:9
Alignment explanation
Indices: 41738302--41738336 Score: 61
Period size: 9 Copynumber: 3.8 Consensus size: 9
41738292 TAATTCTTTA
41738302 AAGTTATGT
1 AAGTTATGT
41738311 AAGTTATGT
1 AAGTTATGT
41738320 AAAGTTATGT
1 -AAGTTATGT
41738330 AAGTTAT
1 AAGTTAT
41738337 ATATTTTATA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
9 16 0.64
10 9 0.36
ACGTcount: A:0.37, C:0.00, G:0.20, T:0.43
Consensus pattern (9 bp):
AAGTTATGT
Found at i:41742038 original size:8 final size:7
Alignment explanation
Indices: 41742003--41742212 Score: 129
Period size: 7 Copynumber: 30.1 Consensus size: 7
41741993 TTAAAATCAG
41742003 ACCCTAA
1 ACCCTAA
*
41742010 ACACTAA
1 ACCCTAA
*
41742017 ACCATAA
1 ACCCTAA
41742024 ACCCTAA
1 ACCCTAA
41742031 ACCCCTAA
1 A-CCCTAA
*
41742039 ACCATAA
1 ACCCTAA
**
41742046 ACTTTAA
1 ACCCTAA
*
41742053 ACTCTAA
1 ACCCTAA
* *
41742060 ATCTTAA
1 ACCCTAA
*
41742067 GCCCCTAA
1 -ACCCTAA
*
41742075 ACCATAA
1 ACCCTAA
*
41742082 ACACTAA
1 ACCCTAA
*
41742089 ACACTAA
1 ACCCTAA
*
41742096 ACCATAA
1 ACCCTAA
*
41742103 ACACTAA
1 ACCCTAA
*
41742110 ACCATAA
1 ACCCTAA
*
41742117 A-CCTAC
1 ACCCTAA
41742123 ACCCTAA
1 ACCCTAA
*
41742130 ACCGTAA
1 ACCCTAA
*
41742137 ACACTAA
1 ACCCTAA
* *
41742144 ACTCT-T
1 ACCCTAA
*
41742150 ACACTAA
1 ACCCTAA
* *
41742157 ATCATAA
1 ACCCTAA
41742164 ACCCTAA
1 ACCCTAA
*
41742171 ACCTTAA
1 ACCCTAA
*
41742178 ACCCCAA
1 ACCCTAA
* *
41742185 ATCATAA
1 ACCCTAA
*
41742192 A-CCTAC
1 ACCCTAA
41742198 ACCCTAA
1 ACCCTAA
41742205 ACCCTAA
1 ACCCTAA
41742212 A
1 A
41742213 TATATATTAC
Statistics
Matches: 150, Mismatches: 48, Indels: 10
0.72 0.23 0.05
Matches are distributed among these distances:
6 12 0.08
7 127 0.85
8 11 0.07
ACGTcount: A:0.47, C:0.33, G:0.01, T:0.19
Consensus pattern (7 bp):
ACCCTAA
Found at i:41742138 original size:34 final size:34
Alignment explanation
Indices: 41742007--41742212 Score: 133
Period size: 36 Copynumber: 5.7 Consensus size: 34
41741997 AATCAGACCC
* * *
41742007 TAAACACTAAACCATAAACCCTAAACCCCTAAACCA
1 TAAAC-CTAAACCCTAAACCATAAA-CACTAAACCA
* * * * * *
41742043 TAAACTTTAAACTCTAAATCTTAAGCCCCTAAACCA
1 TAAAC-CTAAACCCTAAACCATAA-ACACTAAACCA
*
41742079 TAAACACTAAACACTAAACCATAAACACTAAACCA
1 TAAAC-CTAAACCCTAAACCATAAACACTAAACCA
* *
41742114 TAAACCTACACCCTAAACCGTAAACACTAAACTCTTACA
1 TAAACCTAAACCCTAAACCATAAACACTAAA--C---CA
* * * * *
41742153 CTAAATCATAAACCCTAAACCTTAAACCCCAAATCA
1 -TAAA-CCTAAACCCTAAACCATAAACACTAAACCA
* *
41742189 TAAACCTACACCCTAAACCCTAAA
1 TAAACCTAAACCCTAAACCATAAA
41742213 TATATATTAC
Statistics
Matches: 136, Mismatches: 26, Indels: 18
0.76 0.14 0.10
Matches are distributed among these distances:
34 40 0.29
35 18 0.13
36 50 0.37
39 2 0.01
40 4 0.03
41 22 0.16
ACGTcount: A:0.48, C:0.33, G:0.01, T:0.19
Consensus pattern (34 bp):
TAAACCTAAACCCTAAACCATAAACACTAAACCA
Found at i:41742156 original size:27 final size:26
Alignment explanation
Indices: 41742126--41742176 Score: 66
Period size: 27 Copynumber: 1.9 Consensus size: 26
41742116 AACCTACACC
*
41742126 CTAAACCGTAAACACTAAACTCTTACA
1 CTAAACCATAAACACTAAAC-CTTACA
* *
41742153 CTAAATCATAAACCCTAAACCTTA
1 CTAAACCATAAACACTAAACCTTA
41742177 AACCCCAAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
26 4 0.19
27 17 0.81
ACGTcount: A:0.45, C:0.29, G:0.02, T:0.24
Consensus pattern (26 bp):
CTAAACCATAAACACTAAACCTTACA
Found at i:41742745 original size:107 final size:106
Alignment explanation
Indices: 41742558--41742778 Score: 295
Period size: 107 Copynumber: 2.1 Consensus size: 106
41742548 CGCCACTATT
***
41742558 GCCACTAAAGCTCAACAACAAACGACGTCGTTTTCTCAACTTTTTTTGCAGCGTTTTGTGAAAAG
1 GCCACTAAAGCTCAACAACAAACGACGTCGTTTTCTCAACTTTTTTTGCAGCGTTTTCCAAAAAG
* * *
41742623 TGCCGCTAATTCTCGATCTATTGCGGCGTTATTTTATAAAA-C
66 CGCAGCTAATGCTCGATCTATTGCGGCGTT-TTTTA-AAAAGC
* *
41742665 GCCACTAAAGCTCAACAACAAACGTCGTTGTTTTGCTCAACTTTTTTGTG-A-CGTTTTCCAAAA
1 GCCACTAAAGCTCAACAACAAACGACGTCGTTTT-CTCAACTTTTTT-TGCAGCGTTTTCCAAAA
*
41742728 AGCGCAGCTAATGCTCGATCTATTGTGGCGTTTTTTAAAAAGC
64 AGCGCAGCTAATGCTCGATCTATTGCGGCGTTTTTTAAAAAGC
*
41742771 GCCGCTAA
1 GCCACTAA
41742779 TGCCACTAAA
Statistics
Matches: 101, Mismatches: 10, Indels: 7
0.86 0.08 0.06
Matches are distributed among these distances:
105 4 0.04
106 13 0.13
107 69 0.68
108 13 0.13
109 2 0.02
ACGTcount: A:0.27, C:0.23, G:0.18, T:0.33
Consensus pattern (106 bp):
GCCACTAAAGCTCAACAACAAACGACGTCGTTTTCTCAACTTTTTTTGCAGCGTTTTCCAAAAAG
CGCAGCTAATGCTCGATCTATTGCGGCGTTTTTTAAAAAGC
Found at i:41742892 original size:39 final size:40
Alignment explanation
Indices: 41742849--41742945 Score: 133
Period size: 40 Copynumber: 2.5 Consensus size: 40
41742839 CAAAGTGCTA
* * *
41742849 CTAATGCTCGATCTATAGCGGC-TTTTTCGAGAAGCGCCG
1 CTAATGCTCGATCTATAGCGACGTTTTTCAAAAAGCGCCG
*
41742888 CTAATGCTTGATCTATAGCGACGTTTTTCAAAAAGCGCCG
1 CTAATGCTCGATCTATAGCGACGTTTTTCAAAAAGCGCCG
* *
41742928 CTAATGCTCAACCTATAG
1 CTAATGCTCGATCTATAG
41742946 TGACATTTGT
Statistics
Matches: 50, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
39 20 0.40
40 30 0.60
ACGTcount: A:0.26, C:0.25, G:0.21, T:0.29
Consensus pattern (40 bp):
CTAATGCTCGATCTATAGCGACGTTTTTCAAAAAGCGCCG
Found at i:41749886 original size:24 final size:23
Alignment explanation
Indices: 41749834--41749886 Score: 56
Period size: 22 Copynumber: 2.3 Consensus size: 23
41749824 TATAAAGATC
*
41749834 ATGCATACCAACATAACCATATA
1 ATGCATACCAACACAACCATATA
*
41749857 AT-CATACCATCACAGACACATAT-
1 ATGCATACCAACACA-AC-CATATA
41749880 ATGCATA
1 ATGCATA
41749887 ACTAGATTAC
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
22 10 0.40
23 6 0.24
24 9 0.36
ACGTcount: A:0.45, C:0.26, G:0.06, T:0.23
Consensus pattern (23 bp):
ATGCATACCAACACAACCATATA
Found at i:41751253 original size:3 final size:3
Alignment explanation
Indices: 41751245--41751276 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
41751235 GTCAGTCTGC
41751245 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
41751277 AACAGGTAAA
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:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (3 bp):
TCT
Found at i:41752452 original size:17 final size:17
Alignment explanation
Indices: 41752430--41752464 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
41752420 ATAATCCAAA
*
41752430 AGAGTGAATTTAGGTTC
1 AGAGTGAACTTAGGTTC
41752447 AGAGTGAACTTAGGTTC
1 AGAGTGAACTTAGGTTC
41752464 A
1 A
41752465 AGCAGTGATT
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:0.31, C:0.09, G:0.29, T:0.31
Consensus pattern (17 bp):
AGAGTGAACTTAGGTTC
Found at i:41756835 original size:3 final size:3
Alignment explanation
Indices: 41756827--41756860 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
41756817 TTAGTTTCTT
41756827 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
41756861 CTTTTAAATT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:41760799 original size:25 final size:24
Alignment explanation
Indices: 41760755--41760811 Score: 71
Period size: 25 Copynumber: 2.3 Consensus size: 24
41760745 GGAACTTTGA
41760755 ATTTGTTTGAAATTCTTATGTT-G
1 ATTTGTTTGAAATTCTTATGTTCG
* *
41760778 ATATTGTTGTGGAATTGTTATGTTCG
1 AT-TTGTT-TGAAATTCTTATGTTCG
41760804 ATTTGTTT
1 ATTTGTTT
41760812 AGATGTTGAA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
23 2 0.07
24 6 0.21
25 18 0.62
26 3 0.10
ACGTcount: A:0.19, C:0.04, G:0.21, T:0.56
Consensus pattern (24 bp):
ATTTGTTTGAAATTCTTATGTTCG
Found at i:41770224 original size:15 final size:15
Alignment explanation
Indices: 41770192--41770238 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
41770182 CTAATGTGTG
*
41770192 TATGGCTCCTCC-CTC
1 TATGGCTCCACCAC-C
41770207 TATGGCTCCACCACC
1 TATGGCTCCACCACC
* *
41770222 TATGGTTCCATCACC
1 TATGGCTCCACCACC
41770237 TA
1 TA
41770239 CTTGGACATA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
15 27 0.96
16 1 0.04
ACGTcount: A:0.17, C:0.40, G:0.13, T:0.30
Consensus pattern (15 bp):
TATGGCTCCACCACC
Found at i:41777104 original size:13 final size:12
Alignment explanation
Indices: 41777066--41777115 Score: 59
Period size: 13 Copynumber: 4.2 Consensus size: 12
41777056 ATATTTTTGT
41777066 AATTAATTT-TA
1 AATTAATTTATA
*
41777077 AA-TAATATATCA
1 AATTAATTTAT-A
41777089 AATTAATTTAATA
1 AATTAATTT-ATA
41777102 AATTAATTTATA
1 AATTAATTTATA
41777114 AA
1 AA
41777116 AAAAATATTT
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
10 5 0.15
11 3 0.09
12 8 0.24
13 15 0.45
14 2 0.06
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (12 bp):
AATTAATTTATA
Found at i:41779722 original size:32 final size:32
Alignment explanation
Indices: 41779681--41779744 Score: 128
Period size: 32 Copynumber: 2.0 Consensus size: 32
41779671 TCTATGACTT
41779681 TCCCTTTTATCTTCTTATGTTTGTCATATATA
1 TCCCTTTTATCTTCTTATGTTTGTCATATATA
41779713 TCCCTTTTATCTTCTTATGTTTGTCATATATA
1 TCCCTTTTATCTTCTTATGTTTGTCATATATA
41779745 CGTCTTAGAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.19, C:0.19, G:0.06, T:0.56
Consensus pattern (32 bp):
TCCCTTTTATCTTCTTATGTTTGTCATATATA
Found at i:41803531 original size:98 final size:98
Alignment explanation
Indices: 41803429--41803739 Score: 210
Period size: 104 Copynumber: 3.1 Consensus size: 98
41803419 TAATTCAAAA
41803429 TAACAATAATCGATAGAATTTTTCTATAAAAAAGTGAAAAATGGTATTAAAGAACTAATTACCAT
1 TAACAATAATCGATAGAATTTTTCTATAAAAAAGTGAAAAATGGTATTAAAGAACTAATTACCAT
41803494 TTAATGTTTCAATTAATTTTATTTTATTTATTT
66 TTAATGTTTCAATTAATTTTATTTTATTTATTT
* * * *
41803527 TAACATTATAGTAT-GTTTA-AATTTTTATTTTTTTAGAATAAGATG---AAT--TATTTAAA-A
1 TAACA--ATA--ATCG-ATAGAA---TT-TTTCTATA-AAAAAG-TGAAAAATGGTA-TTAAAGA
* * ** * ** * * ***
41803584 ATTAAAGCTAATATATAAAATTTAAATT--TTTATATACCTCTGATAATTCAAAA
54 ACT-AA-TTACCATTTAATGTTTCAATTAATTT-TAT---T-T--T-ATTTATTT
41803637 TAACAATAATCGATAGAATTTTTCTATAAAAAAGTGAAAAATGGTATTAAAGAACTAATTACCAT
1 TAACAATAATCGATAGAATTTTTCTATAAAAAAGTGAAAAATGGTATTAAAGAACTAATTACCAT
41803702 TTAATGTTTCAATTAATTTTATTTTATTTATTT
66 TTAATGTTTCAATTAATTTTATTTTATTTATTT
41803735 TAACA
1 TAACA
41803740 TTATAGTATG
Statistics
Matches: 149, Mismatches: 32, Indels: 64
0.61 0.13 0.26
Matches are distributed among these distances:
98 14 0.09
99 1 0.01
100 3 0.02
101 6 0.04
102 18 0.12
103 16 0.11
104 38 0.26
105 16 0.11
106 18 0.12
107 6 0.04
108 3 0.02
109 1 0.01
110 9 0.06
ACGTcount: A:0.43, C:0.07, G:0.07, T:0.43
Consensus pattern (98 bp):
TAACAATAATCGATAGAATTTTTCTATAAAAAAGTGAAAAATGGTATTAAAGAACTAATTACCAT
TTAATGTTTCAATTAATTTTATTTTATTTATTT
Found at i:41803654 original size:208 final size:209
Alignment explanation
Indices: 41803395--41803813 Score: 831
Period size: 208 Copynumber: 2.0 Consensus size: 209
41803385 TTTTTCAATG
41803395 ATTTAAATTTTTATATACCTCTGATAATTCAAAATAACAATAATCGATAGAATTTTTCTATAAAA
1 ATTTAAATTTTTATATACCTCTGATAATTCAAAATAACAATAATCGATAGAATTTTTCTATAAAA
41803460 AAGTGAAAAATGGTATTAAAGAACTAATTACCATTTAATGTTTCAATTAATTTTATTTTATTTAT
66 AAGTGAAAAATGGTATTAAAGAACTAATTACCATTTAATGTTTCAATTAATTTTATTTTATTTAT
41803525 TTTAACATTATAGTATGTTTAAATTTTTATTTTTTTAGAATAAGATGAATTATTTAAAAATTAAA
131 TTTAACATTATAGTATGTTTAAATTTTTATTTTTTTAGAATAAGATGAATTATTTAAAAATTAAA
41803590 GCT-AATATATAAA
196 GCTAAATATATAAA
41803603 ATTTAAATTTTTATATACCTCTGATAATTCAAAATAACAATAATCGATAGAATTTTTCTATAAAA
1 ATTTAAATTTTTATATACCTCTGATAATTCAAAATAACAATAATCGATAGAATTTTTCTATAAAA
41803668 AAGTGAAAAATGGTATTAAAGAACTAATTACCATTTAATGTTTCAATTAATTTTATTTTATTTAT
66 AAGTGAAAAATGGTATTAAAGAACTAATTACCATTTAATGTTTCAATTAATTTTATTTTATTTAT
41803733 TTTAACATTATAGTATGTTTAAATTTTTATTTTTTTAGAATAAGATGAATTATTTAAAAATTAAA
131 TTTAACATTATAGTATGTTTAAATTTTTATTTTTTTAGAATAAGATGAATTATTTAAAAATTAAA
41803798 GCTAAATATATAAA
196 GCTAAATATATAAA
41803812 AT
1 AT
41803814 AATATTTTTC
Statistics
Matches: 210, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
208 198 0.94
209 12 0.06
ACGTcount: A:0.43, C:0.06, G:0.07, T:0.44
Consensus pattern (209 bp):
ATTTAAATTTTTATATACCTCTGATAATTCAAAATAACAATAATCGATAGAATTTTTCTATAAAA
AAGTGAAAAATGGTATTAAAGAACTAATTACCATTTAATGTTTCAATTAATTTTATTTTATTTAT
TTTAACATTATAGTATGTTTAAATTTTTATTTTTTTAGAATAAGATGAATTATTTAAAAATTAAA
GCTAAATATATAAA
Found at i:41822333 original size:21 final size:23
Alignment explanation
Indices: 41822295--41822342 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 23
41822285 TAGAAATAAT
* *
41822295 CAAAAAGAATTTATTCAAAAA-A
1 CAAAAAGAAATCATTCAAAAAGA
41822317 CAAAAAGAAATCA-TCAAAAAGA
1 CAAAAAGAAATCATTCAAAAAGA
41822339 CAAA
1 CAAA
41822343 CATGTCTTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 7 0.30
22 16 0.70
ACGTcount: A:0.67, C:0.12, G:0.06, T:0.15
Consensus pattern (23 bp):
CAAAAAGAAATCATTCAAAAAGA
Found at i:41840020 original size:19 final size:19
Alignment explanation
Indices: 41839996--41840056 Score: 113
Period size: 19 Copynumber: 3.2 Consensus size: 19
41839986 AATCATATAT
41839996 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
41840015 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
41840034 TCTAAGATTGCATATACATA
1 TCTAAGATTGCATAT-CATA
41840054 TCT
1 TCT
41840057 TGGAAAATTA
Statistics
Matches: 41, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
19 34 0.83
20 7 0.17
ACGTcount: A:0.36, C:0.16, G:0.10, T:0.38
Consensus pattern (19 bp):
TCTAAGATTGCATATCATA
Found at i:41847479 original size:22 final size:22
Alignment explanation
Indices: 41847451--41847503 Score: 97
Period size: 22 Copynumber: 2.4 Consensus size: 22
41847441 AACCAAAATT
41847451 ATCTCCTAAACTTTAGCATCTA
1 ATCTCCTAAACTTTAGCATCTA
*
41847473 ATCTCCTAAACTTTAGCATTTA
1 ATCTCCTAAACTTTAGCATCTA
41847495 ATCTCCTAA
1 ATCTCCTAA
41847504 TTAAAAGGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.32, C:0.26, G:0.04, T:0.38
Consensus pattern (22 bp):
ATCTCCTAAACTTTAGCATCTA
Found at i:41864233 original size:23 final size:22
Alignment explanation
Indices: 41864201--41864246 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 22
41864191 AATCAAATTT
41864201 AATAAAAATAA-ATAACAAATAAA
1 AATAAAAATAATA-AACAAA-AAA
*
41864224 AATAATAATAATAAACAAAAAA
1 AATAAAAATAATAAACAAAAAA
41864246 A
1 A
41864247 GAGACTAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 4 0.19
23 16 0.76
24 1 0.05
ACGTcount: A:0.78, C:0.04, G:0.00, T:0.17
Consensus pattern (22 bp):
AATAAAAATAATAAACAAAAAA
Found at i:41866567 original size:41 final size:40
Alignment explanation
Indices: 41866521--41866611 Score: 103
Period size: 40 Copynumber: 2.2 Consensus size: 40
41866511 AAACAGGCTT
41866521 TTAGCGGCG-TTTAGACAAAAAACGCCACTAAAAATCAAGCA
1 TTAGCGGCGCTTT-GA-AAAAAACGCCACTAAAAATCAAGCA
* * * ** *
41866562 TTAGCGGCGCTTTTATAAAAACGCCGCTAAATGTCGAGCA
1 TTAGCGGCGCTTTGAAAAAAACGCCACTAAAAATCAAGCA
41866602 TTAGCGGCGC
1 TTAGCGGCGC
41866612 CGCTAAAAAT
Statistics
Matches: 43, Mismatches: 6, Indels: 3
0.83 0.12 0.06
Matches are distributed among these distances:
40 30 0.70
41 10 0.23
42 3 0.07
ACGTcount: A:0.34, C:0.23, G:0.22, T:0.21
Consensus pattern (40 bp):
TTAGCGGCGCTTTGAAAAAAACGCCACTAAAAATCAAGCA
Found at i:41866759 original size:41 final size:41
Alignment explanation
Indices: 41866698--41866937 Score: 345
Period size: 41 Copynumber: 5.9 Consensus size: 41
41866688 TTTTTGGGGG
*
41866698 CTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTCGGGC
1 CTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTCTGGC
* * * * *
41866739 CTTTAGCAGCGCTCTAGAAAAAGCGCCGCTAGTGCTCTGGC
1 CTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTCTGGC
41866780 CTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTCTGGC
1 CTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTCTGGC
* *
41866821 CTTTAGTGGCGTTTTTGAAAAAGCGCCGCTAATGCTCTTGC
1 CTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTCTGGC
* ** * **
41866862 CTTTAGTGGTTTTTTTGGAAAAGCGCCGCTAATGCTCTGTT
1 CTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTCTGGC
*
41866903 CTTTAGCGGCGTTTTTGCAAAAGCGCCGCTAATGC
1 CTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGC
41866938 AAAATACTAT
Statistics
Matches: 176, Mismatches: 23, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
41 176 1.00
ACGTcount: A:0.20, C:0.24, G:0.26, T:0.30
Consensus pattern (41 bp):
CTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTCTGGC
Found at i:41868091 original size:33 final size:33
Alignment explanation
Indices: 41868040--41868111 Score: 81
Period size: 33 Copynumber: 2.2 Consensus size: 33
41868030 TTAAATAATA
* **
41868040 TTTAGGGGTTAGAAATTCAGGGTTGGGTTAGGG
1 TTTAGGGATTAGAAATTCAGGGTCAGGTTAGGG
** * *
41868073 TTTAGGGATTAGGGATTCATGGTCAGGTTTGGG
1 TTTAGGGATTAGAAATTCAGGGTCAGGTTAGGG
41868106 TTTAGG
1 TTTAGG
41868112 ATTTAGATTA
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.19, C:0.04, G:0.40, T:0.36
Consensus pattern (33 bp):
TTTAGGGATTAGAAATTCAGGGTCAGGTTAGGG
Found at i:41873495 original size:43 final size:43
Alignment explanation
Indices: 41873447--41873749 Score: 335
Period size: 43 Copynumber: 7.1 Consensus size: 43
41873437 ATGGCACTTT
* * *
41873447 TAGCGGCGTTTGTGAAAAAAGCGCCGCTAAAAGTTATGATCTA
1 TAGCGGCGTTTGTGAGAAAAGCGCCGCTAAAGGTTCTGATCTA
* * * * *
41873490 TAGCGGCGTTCGTGAGAGAAGCGTCGCTAAAGGTCCTGATATA
1 TAGCGGCGTTTGTGAGAAAAGCGCCGCTAAAGGTTCTGATCTA
* * *
41873533 TAGCAGCGTTTGTGGGAAAAGCGACGCTAAAGG-TCTTGATCTA
1 TAGCGGCGTTTGTGAGAAAAGCGCCGCTAAAGGTTC-TGATCTA
** * *
41873576 TAGCGGCGTTTGTGCCAAAAACGCCACTAAAGG-TCTTGATCTA
1 TAGCGGCGTTTGTGAGAAAAGCGCCGCTAAAGGTTC-TGATCTA
* ** *
41873619 TAGCGGCGTTTGT-ATAAAAAGCATCGCTAAAGGTCCTGATCTA
1 TAGCGGCGTTTGTGA-GAAAAGCGCCGCTAAAGGTTCTGATCTA
* *
41873662 TAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCCTGATCTA
1 TAGCGGCGTTTGTGAGAAAAGCGCCGCTAAAGGTTCTGATCTA
* * *
41873705 TAGCGGCGTTTGTG-GGAAAGCGCTGCTAAAGGTTTTGATCTA
1 TAGCGGCGTTTGTGAGAAAAGCGCCGCTAAAGGTTCTGATCTA
41873747 TAG
1 TAG
41873750 TTCCTGATCT
Statistics
Matches: 220, Mismatches: 36, Indels: 9
0.83 0.14 0.03
Matches are distributed among these distances:
42 28 0.13
43 191 0.87
44 1 0.00
ACGTcount: A:0.27, C:0.18, G:0.29, T:0.26
Consensus pattern (43 bp):
TAGCGGCGTTTGTGAGAAAAGCGCCGCTAAAGGTTCTGATCTA
Found at i:41873606 original size:86 final size:86
Alignment explanation
Indices: 41873447--41873749 Score: 371
Period size: 86 Copynumber: 3.5 Consensus size: 86
41873437 ATGGCACTTT
* * * * *
41873447 TAGCGGCGTTTGTGAAAAAAGCGCCGCTAAAAGT-TATGATCTATAGCGGCGTTCGTGAGAGAAG
1 TAGCGGCGTTTGTGGAAAAAGCGACGCTAAAGGTCT-TGATCTATAGCGGCGTTTGTGAGAAAAG
* *
41873511 CGTCGCTAAAGGTCCTGATATA
65 CGCCGCTAAAGGTCCTGATCTA
* * ** *
41873533 TAGCAGCGTTTGTGGGAAAAGCGACGCTAAAGGTCTTGATCTATAGCGGCGTTTGTGCCAAAAAC
1 TAGCGGCGTTTGTGGAAAAAGCGACGCTAAAGGTCTTGATCTATAGCGGCGTTTGTGAGAAAAGC
* *
41873598 GCCACTAAAGGTCTTGATCTA
66 GCCGCTAAAGGTCCTGATCTA
** * *
41873619 TAGCGGCGTTTGTATAAAAAGC-ATCGCTAAAGGTCCTGATCTATAGCGGCGTTTGTGGGAAAAG
1 TAGCGGCGTTTGTGGAAAAAGCGA-CGCTAAAGGTCTTGATCTATAGCGGCGTTTGTGAGAAAAG
41873683 CGCCGCTAAAGGTCCTGATCTA
65 CGCCGCTAAAGGTCCTGATCTA
* *
41873705 TAGCGGCGTTTGTGG-GAAAGCG-CTGCTAAAGGTTTTGATCTATAG
1 TAGCGGCGTTTGTGGAAAAAGCGAC-GCTAAAGGTCTTGATCTATAG
41873750 TTCCTGATCT
Statistics
Matches: 184, Mismatches: 29, Indels: 9
0.83 0.13 0.04
Matches are distributed among these distances:
84 1 0.01
85 25 0.14
86 157 0.85
87 1 0.01
ACGTcount: A:0.27, C:0.18, G:0.29, T:0.26
Consensus pattern (86 bp):
TAGCGGCGTTTGTGGAAAAAGCGACGCTAAAGGTCTTGATCTATAGCGGCGTTTGTGAGAAAAGC
GCCGCTAAAGGTCCTGATCTA
Found at i:41873677 original size:129 final size:127
Alignment explanation
Indices: 41873447--41873749 Score: 410
Period size: 129 Copynumber: 2.3 Consensus size: 127
41873437 ATGGCACTTT
* * *
41873447 TAGCGGCGTTTGTGAAAAAAGCGCCGCTAAAAGTTATGATCTATAGCGGCGTTCGTGAGAGAAGC
1 TAGCGGCGTTTGTGAAAAAA-CGCCGCTAAAGGTT-TGATCTATAGCGGCGTTCGTGAAAAAAGC
* *
41873512 GTCGCTAAAGGTCCTGATATATAGCAGCGTTTGTGGGAAAAGCGACGCTAAAGGTCTTGATCTA
64 ATCGCTAAAGGTCCTGATATATAGCAGCGTTTGTGGGAAAAGCGACGCTAAAGGTCCTGATCTA
* * *
41873576 TAGCGGCGTTTGTGCCAAAAACGCCACTAAAGGTCTTGATCTATAGCGGCGTTTGT-ATAAAAAG
1 TAGCGGCGTTTGTG-AAAAAACGCCGCTAAAGGT-TTGATCTATAGCGGCGTTCGTGA-AAAAAG
* * *
41873640 CATCGCTAAAGGTCCTGATCTATAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCCTGATCTA
63 CATCGCTAAAGGTCCTGATATATAGCAGCGTTTGTGGGAAAAGCGACGCTAAAGGTCCTGATCTA
** * *
41873705 TAGCGGCGTTTGTGGGAAAGCGCTGCTAAAGGTTTTGATCTATAG
1 TAGCGGCGTTTGTGAAAAAACGCCGCTAAAGG-TTTGATCTATAG
41873750 TTCCTGATCT
Statistics
Matches: 154, Mismatches: 16, Indels: 9
0.86 0.09 0.05
Matches are distributed among these distances:
128 25 0.16
129 123 0.80
130 6 0.04
ACGTcount: A:0.27, C:0.18, G:0.29, T:0.26
Consensus pattern (127 bp):
TAGCGGCGTTTGTGAAAAAACGCCGCTAAAGGTTTGATCTATAGCGGCGTTCGTGAAAAAAGCAT
CGCTAAAGGTCCTGATATATAGCAGCGTTTGTGGGAAAAGCGACGCTAAAGGTCCTGATCTA
Found at i:41874842 original size:38 final size:38
Alignment explanation
Indices: 41874791--41874866 Score: 152
Period size: 38 Copynumber: 2.0 Consensus size: 38
41874781 ACCCCCTGAC
41874791 ATCAAACAATTTCATGTTCAACACATGCTGCCTGGGAT
1 ATCAAACAATTTCATGTTCAACACATGCTGCCTGGGAT
41874829 ATCAAACAATTTCATGTTCAACACATGCTGCCTGGGAT
1 ATCAAACAATTTCATGTTCAACACATGCTGCCTGGGAT
41874867 TTCCGGGTTA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.32, C:0.24, G:0.16, T:0.29
Consensus pattern (38 bp):
ATCAAACAATTTCATGTTCAACACATGCTGCCTGGGAT
Found at i:41884241 original size:75 final size:75
Alignment explanation
Indices: 41884119--41884340 Score: 421
Period size: 75 Copynumber: 3.0 Consensus size: 75
41884109 CAAAAACAGA
41884119 GATGCTTTAAAATTAG--AAAAAAAACTTTTTTATGGTATTCATATATTTATTTCCTATCTTTAT
1 GATGCTTTAAAATTAGAAAAAAAAAAC-TTTTTATGGTATTCATATATTTATTTCCTATCTTTAT
41884182 AGAAATATTCT
65 AGAAATATTCT
41884193 GATGCTTTAAAATTAGAAAAAAAAAACTTTTTATGGTATTCATATATTTATTTCCTATCTTTATA
1 GATGCTTTAAAATTAGAAAAAAAAAACTTTTTATGGTATTCATATATTTATTTCCTATCTTTATA
41884258 GAAATATTCT
66 GAAATATTCT
41884268 GATGCTTTAAAATTAGAAAAAAAAAACTTTTTATGGTATTCATATATTTATTTCCTATCTTTATA
1 GATGCTTTAAAATTAGAAAAAAAAAACTTTTTATGGTATTCATATATTTATTTCCTATCTTTATA
41884333 GAAATATT
66 GAAATATT
41884341 TCTATCTTTA
Statistics
Matches: 146, Mismatches: 0, Indels: 3
0.98 0.00 0.02
Matches are distributed among these distances:
74 16 0.11
75 121 0.83
76 9 0.06
ACGTcount: A:0.38, C:0.09, G:0.08, T:0.45
Consensus pattern (75 bp):
GATGCTTTAAAATTAGAAAAAAAAAACTTTTTATGGTATTCATATATTTATTTCCTATCTTTATA
GAAATATTCT
Found at i:41890039 original size:24 final size:24
Alignment explanation
Indices: 41889994--41890039 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
41889984 TAATTTTATG
*
41889994 ATTTTTTATATTTTTTAAATTTCA
1 ATTTTTTATATTTTTGAAATTTCA
41890018 ATTTTTTAT-TTTTTGAATATTT
1 ATTTTTTATATTTTTGAA-ATTT
41890040 TTATAAATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 7 0.35
24 13 0.65
ACGTcount: A:0.26, C:0.02, G:0.02, T:0.70
Consensus pattern (24 bp):
ATTTTTTATATTTTTGAAATTTCA
Found at i:41922195 original size:22 final size:20
Alignment explanation
Indices: 41922150--41922196 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 20
41922140 TTAATTAACT
* *
41922150 TATTTTCAGGAAAAGTTTCT
1 TATTTTCAGCAAAAGTTTCA
41922170 TATTTTCAGCAAAATGGTTTCA
1 TATTTTCAGCAAAA--GTTTCA
41922192 TATTT
1 TATTT
41922197 AATACATGCT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 13 0.57
22 10 0.43
ACGTcount: A:0.30, C:0.11, G:0.13, T:0.47
Consensus pattern (20 bp):
TATTTTCAGCAAAAGTTTCA
Found at i:41925064 original size:18 final size:19
Alignment explanation
Indices: 41925028--41925064 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
41925018 GTTAAAATTG
41925028 AAACGAAATTAAAAGAAAA
1 AAACGAAATTAAAAGAAAA
*
41925047 AAACGAAA-TAAAATAAAA
1 AAACGAAATTAAAAGAAAA
41925065 TAATGGGACG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 9 0.53
19 8 0.47
ACGTcount: A:0.76, C:0.05, G:0.08, T:0.11
Consensus pattern (19 bp):
AAACGAAATTAAAAGAAAA
Done.