Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold43
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: 2559314
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 13088 characters in sequence are not A, C, G, or T
File 2 of 19
Found at i:162002 original size:18 final size:18
Alignment explanation
Indices: 161979--162058 Score: 61
Period size: 18 Copynumber: 4.3 Consensus size: 18
161969 CTGTACCAGG
* *
161979 GTATGGCCGGAGACCCGA
1 GTATGGCAGGAAACCCGA
*
161997 GTATGGGAGGAAACCCGA
1 GTATGGCAGGAAACCCGA
* ** *
162015 GTATGGGAACAAAGATCCGA
1 GTAT-GGCAGGAA-ACCCGA
* *
162035 ATATGGAAGGAAACCCGA
1 GTATGGCAGGAAACCCGA
162053 GTATGG
1 GTATGG
162059 GGAACAAAGA
Statistics
Matches: 48, Mismatches: 12, Indels: 4
0.75 0.19 0.06
Matches are distributed among these distances:
18 29 0.60
19 11 0.23
20 8 0.17
ACGTcount: A:0.34, C:0.17, G:0.35, T:0.14
Consensus pattern (18 bp):
GTATGGCAGGAAACCCGA
Found at i:162039 original size:20 final size:20
Alignment explanation
Indices: 162011--162079 Score: 70
Period size: 20 Copynumber: 3.5 Consensus size: 20
162001 GGGAGGAAAC
*
162011 CCGAGTATGGGAACAAAGAT
1 CCGAATATGGGAACAAAGAT
** *
162031 CCGAATAT-GGAAGGAA-AC
1 CCGAATATGGGAACAAAGAT
*
162049 CCGAGTATGGGGAACAAAGAT
1 CCGAATAT-GGGAACAAAGAT
162070 CCGAATATGG
1 CCGAATATGG
162080 AAAGCAACCC
Statistics
Matches: 37, Mismatches: 9, Indels: 6
0.71 0.17 0.12
Matches are distributed among these distances:
18 8 0.22
19 6 0.16
20 15 0.41
21 8 0.22
ACGTcount: A:0.39, C:0.16, G:0.30, T:0.14
Consensus pattern (20 bp):
CCGAATATGGGAACAAAGAT
Found at i:162073 original size:39 final size:39
Alignment explanation
Indices: 161993--162100 Score: 164
Period size: 39 Copynumber: 2.8 Consensus size: 39
161983 GGCCGGAGAC
* *
161993 CCGAGTATGGGAGGAAACCCGAGTAT-GGGAACAAAGAT
1 CCGAATATGGAAGGAAACCCGAGTATGGGGAACAAAGAT
162031 CCGAATATGGAAGGAAACCCGAGTATGGGGAACAAAGAT
1 CCGAATATGGAAGGAAACCCGAGTATGGGGAACAAAGAT
* * *
162070 CCGAATATGGAAAGCAACCCGGGTATGGGGA
1 CCGAATATGGAAGGAAACCCGAGTATGGGGA
162101 GTCTGAATCT
Statistics
Matches: 64, Mismatches: 5, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
38 24 0.38
39 40 0.62
ACGTcount: A:0.37, C:0.17, G:0.33, T:0.13
Consensus pattern (39 bp):
CCGAATATGGAAGGAAACCCGAGTATGGGGAACAAAGAT
Found at i:163841 original size:23 final size:23
Alignment explanation
Indices: 163802--163863 Score: 76
Period size: 23 Copynumber: 2.8 Consensus size: 23
163792 AAATTATTTT
*
163802 ATTTAAAA--ATTAATTTTT-AA
1 ATTTAAAATTATTATTTTTTAAA
*
163822 ATTATAAAATTTTTATTTTTTAAA
1 ATT-TAAAATTATTATTTTTTAAA
163846 ATTTAAAATTATTATTTT
1 ATTTAAAATTATTATTTT
163864 ATTTCATTTA
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
20 3 0.09
21 5 0.14
23 22 0.63
24 5 0.14
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (23 bp):
ATTTAAAATTATTATTTTTTAAA
Found at i:164425 original size:20 final size:19
Alignment explanation
Indices: 164383--164434 Score: 58
Period size: 19 Copynumber: 2.9 Consensus size: 19
164373 CATATTTAAA
164383 ATATTTTATATAAATTTTT
1 ATATTTTATATAAATTTTT
164402 ATATTTTA-AT-AA--TTT
1 ATATTTTATATAAATTTTT
* *
164417 GTATTATATATAAATTTT
1 ATATTTTATATAAATTTT
164435 AAAATATATA
Statistics
Matches: 27, Mismatches: 2, Indels: 8
0.73 0.05 0.22
Matches are distributed among these distances:
15 9 0.33
16 2 0.07
17 4 0.15
18 2 0.07
19 10 0.37
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (19 bp):
ATATTTTATATAAATTTTT
Found at i:165232 original size:18 final size:19
Alignment explanation
Indices: 165190--165233 Score: 58
Period size: 18 Copynumber: 2.5 Consensus size: 19
165180 TTGATAGAAT
165190 TAAA-AAAATTAAAATTAA
1 TAAATAAAATTAAAATTAA
*
165208 -AATTAAAATTAAAA-TAA
1 TAAATAAAATTAAAATTAA
165225 TAAATAAAA
1 TAAATAAAA
165234 ACTAAAAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
17 5 0.23
18 17 0.77
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (19 bp):
TAAATAAAATTAAAATTAA
Found at i:165240 original size:6 final size:6
Alignment explanation
Indices: 165194--165222 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
165184 TAGAATTAAA
165194 AAAATT AAAATT AAAATT AAAATT AAAAT
1 AAAATT AAAATT AAAATT AAAATT AAAAT
165223 AATAAATAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (6 bp):
AAAATT
Found at i:165248 original size:18 final size:19
Alignment explanation
Indices: 165193--165249 Score: 55
Period size: 18 Copynumber: 3.1 Consensus size: 19
165183 ATAGAATTAA
* *
165193 AAAAATTAAAATTA-AAAT
1 AAAAACTAAAATAATAAAT
* *
165211 TAAAATTAAAATAATAAAT
1 AAAAACTAAAATAATAAAT
*
165230 AAAAACTAAAA-AATCAAT
1 AAAAACTAAAATAATAAAT
165248 AA
1 AA
165250 TATAAGTTTA
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
18 20 0.61
19 13 0.39
ACGTcount: A:0.72, C:0.04, G:0.00, T:0.25
Consensus pattern (19 bp):
AAAAACTAAAATAATAAAT
Found at i:165319 original size:18 final size:18
Alignment explanation
Indices: 165298--165348 Score: 52
Period size: 17 Copynumber: 2.9 Consensus size: 18
165288 AAAATTTAAC
165298 AAATAATGAAAAAAATAA
1 AAATAATGAAAAAAATAA
* * *
165316 AAATAA-AAAAAAAAGAT
1 AAATAATGAAAAAAATAA
*
165333 AAA-AGTGAAAAAAATA
1 AAATAATGAAAAAAATA
165349 TTTCAGTGCA
Statistics
Matches: 26, Mismatches: 6, Indels: 3
0.74 0.17 0.09
Matches are distributed among these distances:
16 1 0.04
17 19 0.73
18 6 0.23
ACGTcount: A:0.78, C:0.00, G:0.08, T:0.14
Consensus pattern (18 bp):
AAATAATGAAAAAAATAA
Found at i:165328 original size:19 final size:20
Alignment explanation
Indices: 165306--165346 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 20
165296 ACAAATAATG
165306 AAAAAAATAAAAAT-AAAAA
1 AAAAAAATAAAAATGAAAAA
* *
165325 AAAAAGATAAAAGTGAAAAA
1 AAAAAAATAAAAATGAAAAA
165345 AA
1 AA
165347 TATTTCAGTG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 12 0.63
20 7 0.37
ACGTcount: A:0.83, C:0.00, G:0.07, T:0.10
Consensus pattern (20 bp):
AAAAAAATAAAAATGAAAAA
Found at i:168653 original size:3 final size:3
Alignment explanation
Indices: 168645--168705 Score: 122
Period size: 3 Copynumber: 20.3 Consensus size: 3
168635 TAAAATACTG
168645 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
168693 AAT AAT AAT AAT A
1 AAT AAT AAT AAT A
168706 TGAGATAGAT
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 58 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:169577 original size:3 final size:3
Alignment explanation
Indices: 169569--169600 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
169559 TACATGTCTT
169569 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
169601 CAAATGAATT
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:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:170450 original size:43 final size:42
Alignment explanation
Indices: 170320--170451 Score: 103
Period size: 43 Copynumber: 3.1 Consensus size: 42
170310 TTTTGTAAAG
* * *
170320 TTAAATTTAAATT-T-ATAT-TTTAATAATTTAAATTATTTAAT
1 TTAAATTTAAATTATAAAATATTTAATAA--AAAATTATTTATT
* ** * *
170361 TT-AATTTAAATTATTATTTATTTAATAAAATAATAATTTTTAT
1 TTAAATTTAAATTATAAAATATTTAATAAAA-AATTATTTAT-T
170404 TTAAATTT-AATTATAAAATATATTAATATAAAAATTATTTATT
1 TTAAATTTAAATTATAAAATAT-TTAATA-AAAAATTATTTATT
170447 TTAAA
1 TTAAA
170452 ATTTTTAAAT
Statistics
Matches: 73, Mismatches: 10, Indels: 14
0.75 0.10 0.14
Matches are distributed among these distances:
40 10 0.14
41 4 0.05
42 10 0.14
43 27 0.37
44 19 0.26
45 3 0.04
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (42 bp):
TTAAATTTAAATTATAAAATATTTAATAAAAAATTATTTATT
Found at i:170567 original size:15 final size:15
Alignment explanation
Indices: 170547--170579 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
170537 CAATCAATAA
170547 TTATTTTTAAAAAAT
1 TTATTTTTAAAAAAT
*
170562 TTATTTTTAAAAATT
1 TTATTTTTAAAAAAT
170577 TTA
1 TTA
170580 AAAATAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (15 bp):
TTATTTTTAAAAAAT
Found at i:171278 original size:4 final size:4
Alignment explanation
Indices: 171265--171298 Score: 54
Period size: 4 Copynumber: 9.0 Consensus size: 4
171255 TTTTGTTCTT
171265 TTTA -TTA TTTA TTTA TTTA TTTA TTTA TTT- TTTA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA
171299 GGTCTTCAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
3 6 0.21
4 22 0.79
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TTTA
Found at i:173955 original size:19 final size:20
Alignment explanation
Indices: 173912--173955 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
173902 ATTTTTATAT
173912 TAATATTTTTAAAATTTTAA
1 TAATATTTTTAAAATTTTAA
* **
173932 AAATATTTTTATTA-TTTAA
1 TAATATTTTTAAAATTTTAA
173951 TAATA
1 TAATA
173956 ATTTAAATTA
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
19 9 0.45
20 11 0.55
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (20 bp):
TAATATTTTTAAAATTTTAA
Found at i:174166 original size:23 final size:23
Alignment explanation
Indices: 174140--174214 Score: 89
Period size: 23 Copynumber: 3.2 Consensus size: 23
174130 GATAATATTA
*
174140 AATATAAATATATAATAAAAAAT
1 AATATAAATATATAATAAAATAT
*
174163 AATATAAAATATATAATTAAAATTT
1 AATAT-AAATATATAA-TAAAATAT
*
174188 AACATAAA-ATATAATAATAATAT
1 AATATAAATATATAATAA-AATAT
174211 AATA
1 AATA
174215 ATAATAGTAT
Statistics
Matches: 44, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
22 3 0.07
23 18 0.41
24 13 0.30
25 10 0.23
ACGTcount: A:0.65, C:0.01, G:0.00, T:0.33
Consensus pattern (23 bp):
AATATAAATATATAATAAAATAT
Found at i:174226 original size:8 final size:7
Alignment explanation
Indices: 174131--174226 Score: 50
Period size: 7 Copynumber: 14.6 Consensus size: 7
174121 AAAAATTTCG
174131 ATAATAT
1 ATAATAT
174138 -TAA-AT
1 ATAATAT
174143 ATAAATAT
1 AT-AATAT
174151 ATAATA-
1 ATAATAT
174157 A-AA-A-
1 ATAATAT
174161 ATAATAT
1 ATAATAT
*
174168 AAAATAT
1 ATAATAT
174175 ATAAT-T
1 ATAATAT
174181 A-AA-AT
1 ATAATAT
* *
174186 TTAACAT
1 ATAATAT
*
174193 AAAATAT
1 ATAATAT
174200 AATAATAAT
1 -ATAAT-AT
174209 ATAATA-
1 ATAATAT
174215 ATAATAGT
1 ATAATA-T
174223 ATAA
1 ATAA
174227 AAGTTACATA
Statistics
Matches: 69, Mismatches: 7, Indels: 25
0.68 0.07 0.25
Matches are distributed among these distances:
4 2 0.03
5 9 0.13
6 16 0.23
7 23 0.33
8 17 0.25
9 2 0.03
ACGTcount: A:0.64, C:0.01, G:0.01, T:0.34
Consensus pattern (7 bp):
ATAATAT
Found at i:174226 original size:11 final size:11
Alignment explanation
Indices: 174140--174220 Score: 64
Period size: 11 Copynumber: 7.4 Consensus size: 11
174130 GATAATATTA
174140 AATATAAATATAT
1 AATAT-AATA-AT
*
174153 AATA-AAAAAT
1 AATATAATAAT
174163 AATATAA-AAT
1 AATATAATAAT
174173 -ATATAATTAA-
1 AATATAA-TAAT
*
174183 AATTTAACATAA-
1 AATAT-A-ATAAT
174195 AATATAATAAT
1 AATATAATAAT
174206 AATATAATAAT
1 AATATAATAAT
174217 AATA
1 AATA
174221 GTATAAAAGT
Statistics
Matches: 58, Mismatches: 3, Indels: 16
0.75 0.04 0.21
Matches are distributed among these distances:
9 6 0.10
10 13 0.22
11 26 0.45
12 8 0.14
13 5 0.09
ACGTcount: A:0.65, C:0.01, G:0.00, T:0.33
Consensus pattern (11 bp):
AATATAATAAT
Found at i:174872 original size:16 final size:15
Alignment explanation
Indices: 174850--174886 Score: 56
Period size: 16 Copynumber: 2.4 Consensus size: 15
174840 AATATATCAC
174850 AATTAATTATAATAAA
1 AATTAATTATAA-AAA
*
174866 TATTAATTATAAAAA
1 AATTAATTATAAAAA
174881 AATTAA
1 AATTAA
174887 AAATATAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
15 8 0.42
16 11 0.58
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (15 bp):
AATTAATTATAAAAA
Found at i:176313 original size:21 final size:22
Alignment explanation
Indices: 176262--176314 Score: 65
Period size: 21 Copynumber: 2.5 Consensus size: 22
176252 AAAAATATTT
176262 TATTTAAAT-TTAATTAAAAAA
1 TATTTAAATATTAATTAAAAAA
* *
176283 TATATAAATATTAA-TATAAAA
1 TATTTAAATATTAATTAAAAAA
*
176304 TATTTTAATAT
1 TATTTAAATAT
176315 ATTTTAAATG
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 23 0.85
22 4 0.15
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (22 bp):
TATTTAAATATTAATTAAAAAA
Found at i:176689 original size:29 final size:30
Alignment explanation
Indices: 176657--176720 Score: 78
Period size: 29 Copynumber: 2.2 Consensus size: 30
176647 AAATTCTTGA
* *
176657 TTATTTAT-TTTTATTAAATTTTTATAATT
1 TTATTTATATTTAAATAAATTTTTATAATT
**
176686 TTA-TTATATTTAAATAAATTTTTATCTTT
1 TTATTTATATTTAAATAAATTTTTATAATT
176715 TTATTT
1 TTATTT
176721 TATACTCAAG
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
28 4 0.14
29 23 0.79
30 2 0.07
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (30 bp):
TTATTTATATTTAAATAAATTTTTATAATT
Found at i:176702 original size:19 final size:20
Alignment explanation
Indices: 176665--176707 Score: 52
Period size: 19 Copynumber: 2.2 Consensus size: 20
176655 GATTATTTAT
**
176665 TTTTATTAAATTTTTAT-AA
1 TTTTATTAAATTTAAATAAA
*
176684 TTTTATTATATTTAAATAAA
1 TTTTATTAAATTTAAATAAA
176704 TTTT
1 TTTT
176708 TATCTTTTTA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
19 14 0.70
20 6 0.30
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (20 bp):
TTTTATTAAATTTAAATAAA
Found at i:177949 original size:22 final size:22
Alignment explanation
Indices: 177901--177949 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 22
177891 ATCGTATTTA
** *
177901 TATATTTTTTATATTTTATAAT
1 TATATTTAATATATTATATAAT
* *
177923 CATATTTAATATATTATATATT
1 TATATTTAATATATTATATAAT
177945 TATAT
1 TATAT
177950 AAATATTAAT
Statistics
Matches: 21, Mismatches: 6, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (22 bp):
TATATTTAATATATTATATAAT
Found at i:178013 original size:9 final size:8
Alignment explanation
Indices: 177895--178020 Score: 57
Period size: 8 Copynumber: 15.6 Consensus size: 8
177885 AATTTTATCG
177895 TATTTATA
1 TATTTATA
*
177903 TATTTTTTA
1 TA-TTTATA
177912 TATTT-TA
1 TATTTATA
* *
177919 TAATCATA
1 TATTTATA
*
177927 T-TTAATA
1 TATTTATA
177934 TA-TTATA
1 TATTTATA
177941 TATTTATA
1 TATTTATA
**
177949 TAAATAT-
1 TATTTATA
177956 TAATTTAT-
1 T-ATTTATA
*
177964 TAATTA-A
1 TATTTATA
*
177971 AATTATATA
1 TATT-TATA
*
177980 AATTTTAATA
1 TA-TTT-ATA
177990 TATTTATA
1 TATTTATA
*
177998 GATTTATCA
1 TATTTAT-A
178007 TATTTATA
1 TATTTATA
178015 TTATTT
1 -TATTT
178021 TTTATTTCAT
Statistics
Matches: 90, Mismatches: 16, Indels: 23
0.70 0.12 0.18
Matches are distributed among these distances:
7 23 0.26
8 35 0.39
9 26 0.29
10 6 0.07
ACGTcount: A:0.40, C:0.02, G:0.01, T:0.57
Consensus pattern (8 bp):
TATTTATA
Found at i:178038 original size:28 final size:32
Alignment explanation
Indices: 178002--178059 Score: 79
Period size: 31 Copynumber: 1.9 Consensus size: 32
177992 TTTATAGATT
178002 TATCATA-TTT-A-TATTATTTTT-TATTTCA
1 TATCATATTTTAATTATTATTTTTATATTTCA
*
178030 TATCGTATTTTAATTATTATTTTTATATTT
1 TATCATATTTTAATTATTATTTTTATATTT
178060 TATTCTTATA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
28 6 0.24
29 3 0.12
30 1 0.04
31 10 0.40
32 5 0.20
ACGTcount: A:0.28, C:0.05, G:0.02, T:0.66
Consensus pattern (32 bp):
TATCATATTTTAATTATTATTTTTATATTTCA
Found at i:178998 original size:172 final size:171
Alignment explanation
Indices: 178713--179059 Score: 649
Period size: 172 Copynumber: 2.0 Consensus size: 171
178703 ATTTAAATTT
*
178713 AAATATATTAAATTCTTTTAAAAATAAATAAATTATATCAAGTACATACTATATTCGACACTATA
1 AAATATATTAAATTCTTTTAAAAATAAATAAATTATATCAAGTACATACTATATCCGACACTATA
* *
178778 TCTGACACTCGATGAAATTTAGGTAACATGACATAGATGAGTACCTAATCTTTGCGCATTAACAT
66 TCTGAAACTCGATCAAATTTAGGTAACATGACATAGATGAGTACCTAATCTTTGCGCATTAACAT
178843 AATCCAGCCTGTATGCCAGCCTTGGCCAAGAAGCTTATAGC
131 AATCCAGCCTGTATGCCAGCCTTGGCCAAGAAGCTTATAGC
178884 AAATATATTAAATTCTTTTAAAAAATAAATAAATTATATCAAGTACATACTATATCCGACACTAT
1 AAATATATTAAATTCTTTT-AAAAATAAATAAATTATATCAAGTACATACTATATCCGACACTAT
*
178949 ATCTGAAACTCGATCAAATTTAGGTAACATGACATAGATGAGTACCTAATCTTTGTGCATTAACA
65 ATCTGAAACTCGATCAAATTTAGGTAACATGACATAGATGAGTACCTAATCTTTGCGCATTAACA
179014 TAATCCAGCCTGTATGCCAGCCTTGGCCAAGAAGCTTATAGC
130 TAATCCAGCCTGTATGCCAGCCTTGGCCAAGAAGCTTATAGC
179056 AAAT
1 AAAT
179060 GGGATCTCCC
Statistics
Matches: 171, Mismatches: 4, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
171 19 0.11
172 152 0.89
ACGTcount: A:0.39, C:0.18, G:0.12, T:0.31
Consensus pattern (171 bp):
AAATATATTAAATTCTTTTAAAAATAAATAAATTATATCAAGTACATACTATATCCGACACTATA
TCTGAAACTCGATCAAATTTAGGTAACATGACATAGATGAGTACCTAATCTTTGCGCATTAACAT
AATCCAGCCTGTATGCCAGCCTTGGCCAAGAAGCTTATAGC
Found at i:181172 original size:15 final size:15
Alignment explanation
Indices: 181152--181182 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
181142 AATTGATTTT
*
181152 ACTTTAATAATTTAA
1 ACTTTAATAATCTAA
181167 ACTTTAATAATCTAA
1 ACTTTAATAATCTAA
181182 A
1 A
181183 TATCAAATAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.10, G:0.00, T:0.42
Consensus pattern (15 bp):
ACTTTAATAATCTAA
Found at i:181215 original size:16 final size:16
Alignment explanation
Indices: 181196--181253 Score: 66
Period size: 16 Copynumber: 3.6 Consensus size: 16
181186 CAAATATAAG
181196 ATAATTCAAATC-CAAA
1 ATAATT-AAATCTCAAA
*
181212 ATAA-TATAATCTTAAA
1 ATAATTA-AATCTCAAA
*
181228 ATAATTTAATCTCAAA
1 ATAATTAAATCTCAAA
181244 ATAATTAAAT
1 ATAATTAAAT
181254 TTATCACCTC
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
14 1 0.03
15 5 0.14
16 28 0.80
17 1 0.03
ACGTcount: A:0.55, C:0.10, G:0.00, T:0.34
Consensus pattern (16 bp):
ATAATTAAATCTCAAA
Found at i:181792 original size:25 final size:25
Alignment explanation
Indices: 181747--181794 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
181737 TATGTCGAGA
* *
181747 TTATTAATTTATTTTTGTTTTAATT
1 TTATAAATTTATTATTGTTTTAATT
181772 TTATAAATTTAATTATT-TTTTAA
1 TTATAAATTT-ATTATTGTTTTAA
181795 AATATTTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
25 15 0.75
26 5 0.25
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (25 bp):
TTATAAATTTATTATTGTTTTAATT
Found at i:182056 original size:50 final size:45
Alignment explanation
Indices: 181980--182106 Score: 116
Period size: 45 Copynumber: 2.7 Consensus size: 45
181970 GTAATTTAAT
* *
181980 TTTA-AATAAATTAAAATATATTTTATTACTTATGATAATAGTATAATATGA
1 TTTATAATAAATT-ATATA-ATTTTATT-CTTAT-A-AATA-TA-AATATAA
* *
182031 TTTA-ATGTAAATTATATAATTTTATTCTTATAAATATACATATAA
1 TTTATA-ATAAATTATATAATTTTATTCTTATAAATATAAATATAA
182076 TTTATAATAAATTATATAATATTTATT-TTAT
1 TTTATAATAAATTATATAAT-TTTATTCTTAT
182107 TTCAACGTGT
Statistics
Matches: 68, Mismatches: 5, Indels: 12
0.80 0.06 0.14
Matches are distributed among these distances:
45 26 0.38
46 9 0.13
47 4 0.06
48 1 0.01
49 5 0.07
50 8 0.12
51 9 0.13
52 6 0.09
ACGTcount: A:0.45, C:0.02, G:0.03, T:0.50
Consensus pattern (45 bp):
TTTATAATAAATTATATAATTTTATTCTTATAAATATAAATATAA
Found at i:182747 original size:15 final size:15
Alignment explanation
Indices: 182724--182756 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
182714 TTTAAAATAA
182724 TTTTTATTTTT-ATT
1 TTTTTATTTTTAATT
182738 TTTTTAATTTTTAATT
1 TTTTT-ATTTTTAATT
182754 TTT
1 TTT
182757 AAAATTATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 5 0.29
15 6 0.35
16 6 0.35
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (15 bp):
TTTTTATTTTTAATT
Found at i:182748 original size:6 final size:7
Alignment explanation
Indices: 182721--182758 Score: 51
Period size: 7 Copynumber: 5.4 Consensus size: 7
182711 AATTTTAAAA
182721 TAATTTT
1 TAATTTT
182728 T-ATTTT
1 TAATTTT
*
182734 TATTTTTT
1 TA-ATTTT
182742 TAATTTT
1 TAATTTT
182749 TAATTTT
1 TAATTTT
182756 TAA
1 TAA
182759 AATTATTTTG
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
6 6 0.22
7 15 0.56
8 6 0.22
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (7 bp):
TAATTTT
Found at i:183086 original size:6 final size:6
Alignment explanation
Indices: 183075--183101 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
183065 GCAAGAAAAG
183075 AAATTA AAATTA AAATTA AAATTA AAA
1 AAATTA AAATTA AAATTA AAATTA AAA
183102 AAGAATAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (6 bp):
AAATTA
Found at i:183135 original size:13 final size:13
Alignment explanation
Indices: 183105--183153 Score: 53
Period size: 13 Copynumber: 3.6 Consensus size: 13
183095 ATTAAAAAAG
*
183105 AATAAAAAAGTAAGA
1 AATAAAAAAAT-A-A
183120 AATAAAAAAATAA
1 AATAAAAAAATAA
* *
183133 AATTAAAAACTAA
1 AATAAAAAAATAA
183146 AATAAAAA
1 AATAAAAA
183154 TAGAATGTAA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
13 19 0.63
14 1 0.03
15 10 0.33
ACGTcount: A:0.78, C:0.02, G:0.04, T:0.16
Consensus pattern (13 bp):
AATAAAAAAATAA
Found at i:183151 original size:12 final size:12
Alignment explanation
Indices: 183079--183153 Score: 53
Period size: 12 Copynumber: 5.9 Consensus size: 12
183069 GAAAAGAAAT
* *
183079 TAAAATTAAAAT
1 TAAAATAAAAAA
*
183091 TAAAATTAAAAA
1 TAAAATAAAAAA
*
183103 -AGAATAAAAAA
1 TAAAATAAAAAA
183114 GTAAGAAATAAAAAAA
1 -T-A-AAAT-AAAAAA
*
183130 TAAAATTAAAAAC
1 TAAAA-TAAAAAA
183143 TAAAATAAAAA
1 TAAAATAAAAA
183154 TAGAATGTAA
Statistics
Matches: 52, Mismatches: 5, Indels: 12
0.75 0.07 0.17
Matches are distributed among these distances:
11 9 0.17
12 17 0.33
13 13 0.25
14 3 0.06
15 4 0.08
16 6 0.12
ACGTcount: A:0.75, C:0.01, G:0.04, T:0.20
Consensus pattern (12 bp):
TAAAATAAAAAA
Found at i:184161 original size:25 final size:24
Alignment explanation
Indices: 184108--184161 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 24
184098 ATTTTGTTAG
184108 TATATTTTTATTTTGAATAAGCAT
1 TATATTTTTATTTTGAATAAGCAT
* * *
184132 T-TATTTTTATATTTTATTACGCAT
1 TATATTTTTAT-TTTGAATAAGCAT
184156 TATATT
1 TATATT
184162 AAACTTTTAA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
23 9 0.36
24 12 0.48
25 4 0.16
ACGTcount: A:0.30, C:0.06, G:0.06, T:0.59
Consensus pattern (24 bp):
TATATTTTTATTTTGAATAAGCAT
Found at i:184407 original size:17 final size:18
Alignment explanation
Indices: 184385--184433 Score: 57
Period size: 17 Copynumber: 2.8 Consensus size: 18
184375 AAGTCTCAAA
184385 ATTAATAAATAAAAA-TT
1 ATTAATAAATAAAAATTT
**
184402 ATTAATGTATAAAAATTT
1 ATTAATAAATAAAAATTT
184420 ATTTAA-AAATAAAA
1 A-TTAATAAATAAAA
184434 TACTTTAAAT
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
17 13 0.50
18 9 0.35
19 4 0.15
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (18 bp):
ATTAATAAATAAAAATTT
Found at i:184709 original size:19 final size:19
Alignment explanation
Indices: 184687--184778 Score: 61
Period size: 19 Copynumber: 5.1 Consensus size: 19
184677 TATATCATTC
184687 ATATTTAAATATAAATTTA
1 ATATTTAAATATAAATTTA
* * *
184706 ATATATGAATATATATTTA
1 ATATTTAAATATAAATTTA
184725 ATA--TAAATAT--ATTTA
1 ATATTTAAATATAAATTTA
* **
184740 AT-TTATATATATATTTTTA
1 ATATT-TAAATATAAATTTA
*
184759 TATATTTAAA-AAAAATTTA
1 -ATATTTAAATATAAATTTA
184778 A
1 A
184779 AAAATAATAT
Statistics
Matches: 56, Mismatches: 10, Indels: 15
0.69 0.12 0.19
Matches are distributed among these distances:
15 7 0.12
17 12 0.21
18 1 0.02
19 29 0.52
20 5 0.09
21 2 0.04
ACGTcount: A:0.50, C:0.00, G:0.01, T:0.49
Consensus pattern (19 bp):
ATATTTAAATATAAATTTA
Found at i:184733 original size:17 final size:17
Alignment explanation
Indices: 184692--184755 Score: 69
Period size: 19 Copynumber: 3.8 Consensus size: 17
184682 CATTCATATT
*
184692 TAAATATAAATTTAATA
1 TAAATATATATTTAATA
184709 TATGAATATATATTTAATA
1 TA--AATATATATTTAATA
*
184728 T-AA-ATATATTTAATT
1 TAAATATATATTTAATA
*
184743 TATATATATATTT
1 TAAATATATATTT
184756 TTATATATTT
Statistics
Matches: 40, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
15 12 0.30
16 3 0.08
17 10 0.25
19 15 0.38
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (17 bp):
TAAATATATATTTAATA
Found at i:184736 original size:15 final size:15
Alignment explanation
Indices: 184716--184751 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
184706 ATATATGAAT
184716 ATATATTTAATATAA
1 ATATATTTAATATAA
* *
184731 ATATATTTAATTTAT
1 ATATATTTAATATAA
184746 ATATAT
1 ATATAT
184752 ATTTTTATAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (15 bp):
ATATATTTAATATAA
Found at i:188320 original size:16 final size:15
Alignment explanation
Indices: 188268--188314 Score: 58
Period size: 16 Copynumber: 2.9 Consensus size: 15
188258 CAATTAGTTG
*
188268 AATTATTTTCGATTTAA
1 AATTATTTT-AATTT-A
188285 AATTATTTTAATTTA
1 AATTATTTTAATTTA
188300 AATTATTTTTAATTT
1 AATTA-TTTTAATTT
188315 TGATTAATTA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
15 6 0.21
16 13 0.46
17 9 0.32
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.60
Consensus pattern (15 bp):
AATTATTTTAATTTA
Found at i:188502 original size:16 final size:16
Alignment explanation
Indices: 188467--188519 Score: 63
Period size: 16 Copynumber: 3.4 Consensus size: 16
188457 AATTGTACAT
* * *
188467 ATTATTTTAGATTCAG
1 ATTATTTTAAATTTAA
188483 ATTATTTTAAATTTAA
1 ATTATTTTAAATTTAA
*
188499 ATTA-GTTAAATTTAA
1 ATTATTTTAAATTTAA
188514 ATTATT
1 ATTATT
188520 AATTCTTTTA
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
15 14 0.45
16 17 0.55
ACGTcount: A:0.40, C:0.02, G:0.06, T:0.53
Consensus pattern (16 bp):
ATTATTTTAAATTTAA
Found at i:188509 original size:15 final size:14
Alignment explanation
Indices: 188489--188521 Score: 57
Period size: 15 Copynumber: 2.3 Consensus size: 14
188479 TCAGATTATT
188489 TTAAATTTAAATTA
1 TTAAATTTAAATTA
188503 GTTAAATTTAAATTA
1 -TTAAATTTAAATTA
188518 TTAA
1 TTAA
188522 TTCTTTTAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 4 0.22
15 14 0.78
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (14 bp):
TTAAATTTAAATTA
Found at i:189946 original size:21 final size:22
Alignment explanation
Indices: 189915--189955 Score: 59
Period size: 21 Copynumber: 1.9 Consensus size: 22
189905 AATTTAAAAT
189915 TATTATTATA-TTAATATTTATA
1 TATTATTATATTTAA-ATTTATA
189937 TATT-TTATATTTAAATTTA
1 TATTATTATATTTAAATTTA
189956 AATAAAAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 10 0.56
22 8 0.44
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (22 bp):
TATTATTATATTTAAATTTATA
Found at i:190437 original size:27 final size:27
Alignment explanation
Indices: 190407--190458 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
190397 AACTGAAATA
*
190407 AATTTAGGATAAAATTAATTTTTTTTT
1 AATTTAGGACAAAATTAATTTTTTTTT
* *
190434 AATTTCGGACAAAATTGATTTTTTT
1 AATTTAGGACAAAATTAATTTTTTT
190459 ATAGTCACCA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.35, C:0.04, G:0.10, T:0.52
Consensus pattern (27 bp):
AATTTAGGACAAAATTAATTTTTTTTT
Found at i:192406 original size:6 final size:6
Alignment explanation
Indices: 192395--192426 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
192385 AGTCCTACAA
192395 TTCCTC TTCCTC TTCCTC TTCCTC TTCCTC TT
1 TTCCTC TTCCTC TTCCTC TTCCTC TTCCTC TT
192427 TCCCTTCCAG
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:0.00, C:0.47, G:0.00, T:0.53
Consensus pattern (6 bp):
TTCCTC
Found at i:195453 original size:34 final size:31
Alignment explanation
Indices: 195415--195476 Score: 88
Period size: 34 Copynumber: 1.9 Consensus size: 31
195405 TATTAAGGAA
195415 AGAAAGAAAATGAGAAAAGGAAATGAAAGGATGG
1 AGAAAGAAAAT-A-AAAAGGAAA-GAAAGGATGG
*
195449 AGAAAGAAAATAAAAAGGGAAGAAAGGA
1 AGAAAGAAAATAAAAAGGAAAGAAAGGA
195477 AAAAAAGGAA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
31 7 0.26
32 8 0.30
33 1 0.04
34 11 0.41
ACGTcount: A:0.63, C:0.00, G:0.31, T:0.06
Consensus pattern (31 bp):
AGAAAGAAAATAAAAAGGAAAGAAAGGATGG
Found at i:197905 original size:32 final size:31
Alignment explanation
Indices: 197845--197923 Score: 86
Period size: 32 Copynumber: 2.5 Consensus size: 31
197835 AAAATACGAC
*
197845 ATAATATAAATATATAAATATTTAAAATTTTT
1 ATAATAT-AATATATAAATATTTAAAATTTAT
* * *
197877 ATAATATAATTTATTAATATCTTTAAATTTAT
1 ATAATATAATATATAAATAT-TTAAAATTTAT
*
197909 ATAAATATAAAATAT
1 AT-AATATAATATAT
197924 TTTAAGTATG
Statistics
Matches: 39, Mismatches: 6, Indels: 3
0.81 0.12 0.06
Matches are distributed among these distances:
31 11 0.28
32 18 0.46
33 10 0.26
ACGTcount: A:0.52, C:0.01, G:0.00, T:0.47
Consensus pattern (31 bp):
ATAATATAATATATAAATATTTAAAATTTAT
Found at i:207932 original size:14 final size:15
Alignment explanation
Indices: 207899--207929 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
207889 CATGCTGTGG
207899 AATTATTGAGAATAA
1 AATTATTGAGAATAA
*
207914 AATTATTGAGCATAA
1 AATTATTGAGAATAA
207929 A
1 A
207930 TTAAACAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.52, C:0.03, G:0.13, T:0.32
Consensus pattern (15 bp):
AATTATTGAGAATAA
Found at i:209498 original size:8 final size:8
Alignment explanation
Indices: 209487--209554 Score: 65
Period size: 8 Copynumber: 9.1 Consensus size: 8
209477 TTTTTATATT
209487 AATATTTA
1 AATATTTA
209495 AATATTT-
1 AATATTTA
* *
209502 TATAATT-
1 AATATTTA
209509 AA-ATTTA
1 AATATTTA
209516 AATATTT-
1 AATATTTA
*
209523 ATTATTTA
1 AATATTTA
*
209531 AAT-TGTA
1 AATATTTA
209538 AATATTTA
1 AATATTTA
209546 AATATTTA
1 AATATTTA
209554 A
1 A
209555 GTAGATATTT
Statistics
Matches: 48, Mismatches: 8, Indels: 8
0.75 0.12 0.12
Matches are distributed among these distances:
6 3 0.06
7 20 0.42
8 25 0.52
ACGTcount: A:0.47, C:0.00, G:0.01, T:0.51
Consensus pattern (8 bp):
AATATTTA
Found at i:209500 original size:22 final size:21
Alignment explanation
Indices: 209475--209544 Score: 90
Period size: 21 Copynumber: 3.2 Consensus size: 21
209465 ATTAAAAAAT
209475 TATTTTTATATTAATATTTAAA
1 TATTTTTATATTAA-ATTTAAA
209497 TA-TTTTATAATTAAATTTAAA
1 TATTTTTAT-ATTAAATTTAAA
209518 TATTTATTAT-TTAAATTGTAAA
1 TATTT-TTATATTAAATT-TAAA
209540 TATTT
1 TATTT
209545 AAATATTTAA
Statistics
Matches: 44, Mismatches: 0, Indels: 8
0.85 0.00 0.15
Matches are distributed among these distances:
21 22 0.50
22 18 0.41
23 4 0.09
ACGTcount: A:0.41, C:0.00, G:0.01, T:0.57
Consensus pattern (21 bp):
TATTTTTATATTAAATTTAAA
Found at i:209529 original size:15 final size:15
Alignment explanation
Indices: 209485--209554 Score: 65
Period size: 15 Copynumber: 4.7 Consensus size: 15
209475 TATTTTTATA
209485 TTAATATTTAAATAT
1 TTAATATTTAAATAT
* *
209500 TTTATAATTAAAT-T
1 TTAATATTTAAATAT
* *
209514 TAAATATTT-ATTAT
1 TTAATATTTAAATAT
209528 TTAA-ATTGTAAATAT
1 TTAATATT-TAAATAT
209543 TTAAATATTTAA
1 TT-AATATTTAA
209555 GTAGATATTT
Statistics
Matches: 42, Mismatches: 8, Indels: 9
0.71 0.14 0.15
Matches are distributed among these distances:
13 5 0.12
14 12 0.29
15 17 0.40
16 5 0.12
17 3 0.07
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.53
Consensus pattern (15 bp):
TTAATATTTAAATAT
Found at i:209545 original size:22 final size:21
Alignment explanation
Indices: 209507--209554 Score: 69
Period size: 22 Copynumber: 2.2 Consensus size: 21
209497 TATTTTATAA
209507 TTAAATTTAAATATTTATTAT
1 TTAAATTTAAATATTTATTAT
*
209528 TTAAATTGTAAATATTTAAATAT
1 TTAAATT-TAAATATTT-ATTAT
209551 TTAA
1 TTAA
209555 GTAGATATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
21 7 0.29
22 9 0.38
23 8 0.33
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (21 bp):
TTAAATTTAAATATTTATTAT
Found at i:210778 original size:19 final size:20
Alignment explanation
Indices: 210734--210784 Score: 61
Period size: 19 Copynumber: 2.6 Consensus size: 20
210724 ACATATCATC
210734 ATATTTAACAT-TAAAGAATA
1 ATATTTAA-ATATAAAGAATA
*
210754 ATATTTAAATATAAA-AATG
1 ATATTTAAATATAAAGAATA
*
210773 ATATTTATATAT
1 ATATTTAAATAT
210785 TATATACTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
19 16 0.57
20 12 0.43
ACGTcount: A:0.53, C:0.02, G:0.04, T:0.41
Consensus pattern (20 bp):
ATATTTAAATATAAAGAATA
Found at i:210894 original size:9 final size:9
Alignment explanation
Indices: 210879--210911 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
210869 ATTTAAATAT
210879 ATATATTAA
1 ATATATTAA
*
210888 TTATATTAA
1 ATATATTAA
210897 ATATATTAA
1 ATATATTAA
210906 A-ATATT
1 ATATATT
210912 TTTATTTTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
8 5 0.23
9 17 0.77
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (9 bp):
ATATATTAA
Found at i:218831 original size:15 final size:15
Alignment explanation
Indices: 218811--218840 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
218801 AAGAAGTGGC
*
218811 AGCCCTTTGCTTTTT
1 AGCCCTTTCCTTTTT
218826 AGCCCTTTCCTTTTT
1 AGCCCTTTCCTTTTT
218841 CTTCATTTGT
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:0.07, C:0.30, G:0.10, T:0.53
Consensus pattern (15 bp):
AGCCCTTTCCTTTTT
Found at i:219856 original size:16 final size:15
Alignment explanation
Indices: 219818--219957 Score: 63
Period size: 16 Copynumber: 9.9 Consensus size: 15
219808 TTTTAAATTA
*
219818 AATAATAATATTTAT
1 AATAATTATATTTAT
219833 -AT-ATTATATTGTAT
1 AATAATTATATT-TAT
*
219847 AATAATTATATTTAA
1 AATAATTATATTTAT
* *
219862 AATATTTTTTATTTAT
1 AATA-ATTATATTTAT
*
219878 -ATAAATTTTA-TTAT
1 AAT-AATTATATTTAT
219892 -ATAATT-TA--TAT
1 AATAATTATATTTAT
*
219903 AATAA--AAATTT-T
1 AATAATTATATTTAT
219915 AA-AATATATATTTAT
1 AATAAT-TATATTTAT
*
219930 ATTATATTATATTT-T
1 AATA-ATTATATTTAT
* *
219945 AATTATTTTATTT
1 AATAATTATATTT
219958 TTATTAAATA
Statistics
Matches: 98, Mismatches: 12, Indels: 31
0.70 0.09 0.22
Matches are distributed among these distances:
11 6 0.06
12 9 0.09
13 12 0.12
14 24 0.24
15 20 0.20
16 25 0.26
17 2 0.02
ACGTcount: A:0.44, C:0.00, G:0.01, T:0.56
Consensus pattern (15 bp):
AATAATTATATTTAT
Found at i:219899 original size:12 final size:14
Alignment explanation
Indices: 219868--219950 Score: 60
Period size: 14 Copynumber: 5.6 Consensus size: 14
219858 TTAAAATATT
219868 TTTTATTTATATAAA
1 TTTTA-TTATATAAA
219883 TTTTATTATAT-AA
1 TTTTATTATATAAA
* *
219896 TTTATATAATAAAAA
1 TTT-TATTATATAAA
** *
219911 TTTTAAAATATATA
1 TTTTATTATATAAA
*
219925 TTTATATTATATTATA
1 TTT-TATTATA-TAAA
219941 TTTTAATTAT
1 TTTT-ATTAT
219951 TTTATTTTTA
Statistics
Matches: 56, Mismatches: 7, Indels: 9
0.78 0.10 0.12
Matches are distributed among these distances:
13 5 0.09
14 23 0.41
15 16 0.29
16 12 0.21
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (14 bp):
TTTTATTATATAAA
Found at i:219914 original size:45 final size:44
Alignment explanation
Indices: 219826--219942 Score: 105
Period size: 45 Copynumber: 2.6 Consensus size: 44
219816 TAAATAATAA
* *
219826 TATTTATATATTATATTGTATAATAATTATATTTAAAATATTTTT
1 TATTTATATATTATATTATATAAT-ATTATATATAAAATATTTTT
*
219871 TATTTATATAAATTTTATTATATAAT-TTATATAATAAAA-A-TTTT
1 TATTTATAT--ATTATATTATATAATATTATAT-ATAAAATATTTTT
* ** *
219915 AAAATATATATTTATATTATATTATATT
1 TATTTATATA-TTATATTATATAATATT
219943 TTAATTATTT
Statistics
Matches: 59, Mismatches: 8, Indels: 11
0.76 0.10 0.14
Matches are distributed among these distances:
42 1 0.02
43 12 0.20
44 12 0.20
45 16 0.27
46 5 0.08
47 13 0.22
ACGTcount: A:0.44, C:0.00, G:0.01, T:0.56
Consensus pattern (44 bp):
TATTTATATATTATATTATATAATATTATATATAAAATATTTTT
Found at i:220760 original size:18 final size:19
Alignment explanation
Indices: 220729--220771 Score: 70
Period size: 18 Copynumber: 2.3 Consensus size: 19
220719 TCTCACTTAC
220729 TTAAATATTAAAATATATT
1 TTAAATATTAAAATATATT
*
220748 TTAAATA-TAAAATATTTT
1 TTAAATATTAAAATATATT
220766 TTAAAT
1 TTAAAT
220772 TAATGAATAT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 16 0.70
19 7 0.30
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (19 bp):
TTAAATATTAAAATATATT
Found at i:221894 original size:24 final size:24
Alignment explanation
Indices: 221867--221930 Score: 62
Period size: 24 Copynumber: 2.7 Consensus size: 24
221857 AGTGTTATAA
221867 ATTTATA-TAACTTTTTATACATAT
1 ATTTATATTAA-TTTTTATACATAT
*
221891 ATTTTTATTAATTTTTAT--ATAT
1 ATTTATATTAATTTTTATACATAT
*
221913 ATGTTATAGTTATTTTTT
1 AT-TTATA-TTAATTTTT
221931 TGTATTGTAT
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
22 6 0.18
23 4 0.12
24 21 0.62
25 3 0.09
ACGTcount: A:0.31, C:0.03, G:0.03, T:0.62
Consensus pattern (24 bp):
ATTTATATTAATTTTTATACATAT
Found at i:222370 original size:11 final size:11
Alignment explanation
Indices: 222356--222386 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
222346 TGAAATGTTT
222356 TTATATTTATG
1 TTATATTTATG
222367 TTATATTTATG
1 TTATATTTATG
*
222378 TTATTTTTA
1 TTATATTTA
222387 ATATAGTATT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.26, C:0.00, G:0.06, T:0.68
Consensus pattern (11 bp):
TTATATTTATG
Found at i:223341 original size:31 final size:32
Alignment explanation
Indices: 223285--223374 Score: 109
Period size: 30 Copynumber: 2.9 Consensus size: 32
223275 GTATTATAAA
*
223285 TTTATATAAAATTTT-ACACA--TAAATATTTT
1 TTTATAT-ATATTTTAACACATTTAAATATTTT
* *
223315 TTTATGTATATTTTAACATA-TTAAATA-TTT
1 TTTATATATATTTTAACACATTTAAATATTTT
223345 TTTATATATATTTTAACACATTTAAATATT
1 TTTATATATATTTTAACACATTTAAATATT
223375 CATAGTATGC
Statistics
Matches: 51, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
29 6 0.12
30 31 0.61
31 13 0.25
32 1 0.02
ACGTcount: A:0.40, C:0.06, G:0.01, T:0.53
Consensus pattern (32 bp):
TTTATATATATTTTAACACATTTAAATATTTT
Found at i:223738 original size:19 final size:20
Alignment explanation
Indices: 223691--223754 Score: 78
Period size: 20 Copynumber: 3.1 Consensus size: 20
223681 CATTTGTGTA
223691 TTTATATTG-AGTTTATATTAT
1 TTTATATTGTA-TTTATATT-T
223712 TTTCATATTGTATTT-TATTT
1 TTT-ATATTGTATTTATATTT
*
223732 TTTATATTGTATTTGTATTT
1 TTTATATTGTATTTATATTT
223752 TTT
1 TTT
223755 CTCAATTCAT
Statistics
Matches: 40, Mismatches: 0, Indels: 7
0.85 0.00 0.15
Matches are distributed among these distances:
19 11 0.28
20 12 0.30
21 7 0.17
22 9 0.22
23 1 0.03
ACGTcount: A:0.22, C:0.02, G:0.08, T:0.69
Consensus pattern (20 bp):
TTTATATTGTATTTATATTT
Found at i:225581 original size:20 final size:20
Alignment explanation
Indices: 225556--225608 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 20
225546 GGTTGGTTTG
225556 AAAATTTAGATTT-AAGTTAA
1 AAAATTTA-ATTTAAAGTTAA
* *
225576 AAAATTTAAATTTAAATTTAT
1 AAAATTT-AATTTAAAGTTAA
225597 AAAATTTAATTT
1 AAAATTTAATTT
225609 TTTTATATAT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
20 16 0.55
21 13 0.45
ACGTcount: A:0.51, C:0.00, G:0.04, T:0.45
Consensus pattern (20 bp):
AAAATTTAATTTAAAGTTAA
Found at i:225602 original size:21 final size:20
Alignment explanation
Indices: 225556--225605 Score: 64
Period size: 21 Copynumber: 2.5 Consensus size: 20
225546 GGTTGGTTTG
*
225556 AAAATTTAGATTTAAGTTAA
1 AAAATTTAAATTTAAGTTAA
* *
225576 AAAATTTAAATTTAAATTTAT
1 AAAATTTAAATTT-AAGTTAA
225597 AAAATTTAA
1 AAAATTTAA
225606 TTTTTTTATA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
20 12 0.46
21 14 0.54
ACGTcount: A:0.54, C:0.00, G:0.04, T:0.42
Consensus pattern (20 bp):
AAAATTTAAATTTAAGTTAA
Found at i:225942 original size:19 final size:19
Alignment explanation
Indices: 225918--225954 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
225908 TTATAATATA
225918 AATATAACATAT-ATAAAAT
1 AATATAA-ATATAATAAAAT
225937 AATATAAATATAATAAAA
1 AATATAAATATAATAAAA
225955 CGTAATTATA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 4 0.24
19 13 0.76
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.30
Consensus pattern (19 bp):
AATATAAATATAATAAAAT
Found at i:225951 original size:11 final size:11
Alignment explanation
Indices: 225909--225951 Score: 50
Period size: 11 Copynumber: 3.6 Consensus size: 11
225899 TTTTTATTAT
225909 TATAATATAAA
1 TATAATATAAA
225920 TATAACATATATAA
1 TAT-A-ATATA-AA
*
225934 AATAATATAAA
1 TATAATATAAA
225945 TATAATA
1 TATAATA
225952 AAACGTAATT
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
11 11 0.41
12 6 0.22
13 6 0.22
14 4 0.15
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (11 bp):
TATAATATAAA
Found at i:227825 original size:23 final size:22
Alignment explanation
Indices: 227780--227821 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
227770 ATTTATATTT
227780 TAAATTTAATTATAAAAATATA
1 TAAATTTAATTATAAAAATATA
227802 TAAATGTTAA-TATAAAAATA
1 TAAAT-TTAATTATAAAAATA
227822 ATATTTTAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (22 bp):
TAAATTTAATTATAAAAATATA
Found at i:229022 original size:25 final size:25
Alignment explanation
Indices: 228994--229051 Score: 80
Period size: 25 Copynumber: 2.3 Consensus size: 25
228984 GTATTTTAAC
*
228994 ATTTAAATTTCTTTTTAATTATAAA
1 ATTTAAATTTATTTTTAATTATAAA
* *
229019 ATTTTAATTTATTTTTAATTATATA
1 ATTTAAATTTATTTTTAATTATAAA
229044 ATTATAAA
1 ATT-TAAA
229052 AATAAAAAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
25 25 0.89
26 3 0.11
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (25 bp):
ATTTAAATTTATTTTTAATTATAAA
Found at i:229712 original size:15 final size:15
Alignment explanation
Indices: 229671--229712 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
229661 TTAAACACTC
229671 AAAAAGAGAATATGA
1 AAAAAGAGAATATGA
* *
229686 AAAAAAAAAATA-GA
1 AAAAAGAGAATATGA
229700 AACAAAGAGAATA
1 AA-AAAGAGAATA
229713 AAAAAAATGC
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
14 4 0.18
15 18 0.82
ACGTcount: A:0.74, C:0.02, G:0.14, T:0.10
Consensus pattern (15 bp):
AAAAAGAGAATATGA
Found at i:229898 original size:31 final size:32
Alignment explanation
Indices: 229863--229930 Score: 93
Period size: 32 Copynumber: 2.2 Consensus size: 32
229853 AAAATCTAAA
*
229863 ATCTCAA-ATAAGTTTAAACTATATCAATTCT
1 ATCTCAAGATAAGTTTAAACTATATCAAATCT
* * *
229894 ATCTCAAGATAATTTTAAACTCTATTAAATCT
1 ATCTCAAGATAAGTTTAAACTATATCAAATCT
229926 ATCTC
1 ATCTC
229931 TATAAAGTAT
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
31 7 0.22
32 25 0.78
ACGTcount: A:0.40, C:0.18, G:0.03, T:0.40
Consensus pattern (32 bp):
ATCTCAAGATAAGTTTAAACTATATCAAATCT
Found at i:231007 original size:20 final size:20
Alignment explanation
Indices: 230982--231020 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
230972 CTCATTTTAT
230982 AATTATATAATATATATATC
1 AATTATATAATATATATATC
* *
231002 AATTATTTAATTTATATAT
1 AATTATATAATATATATAT
231021 TATGTAATTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (20 bp):
AATTATATAATATATATATC
Found at i:231727 original size:25 final size:24
Alignment explanation
Indices: 231673--231728 Score: 62
Period size: 25 Copynumber: 2.2 Consensus size: 24
231663 AGTTAAGGTG
231673 AACTTAAATAAATATAAATATATC
1 AACTTAAATAAATATAAATATATC
231697 ATACTTAAATATAA-A-AAATTATATC
1 A-ACTTAAATA-AATATAAA-TATATC
231722 TAACTTA
1 -AACTTA
231729 CTATTTATCA
Statistics
Matches: 28, Mismatches: 0, Indels: 7
0.80 0.00 0.20
Matches are distributed among these distances:
24 4 0.14
25 21 0.75
26 3 0.11
ACGTcount: A:0.55, C:0.09, G:0.00, T:0.36
Consensus pattern (24 bp):
AACTTAAATAAATATAAATATATC
Found at i:233621 original size:23 final size:25
Alignment explanation
Indices: 233579--233636 Score: 68
Period size: 23 Copynumber: 2.4 Consensus size: 25
233569 TTGAATAATT
233579 TATTTAAATGTGGTACAAATATT-TA
1 TATTTAAATGTGGTACAAAT-TTATA
*
233604 TATTT-AATGT-GTATAAATTTATA
1 TATTTAAATGTGGTACAAATTTATA
233627 TATTATAAAT
1 TATT-TAAAT
233637 TAAATGATAT
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
22 2 0.07
23 13 0.45
24 6 0.21
25 8 0.28
ACGTcount: A:0.41, C:0.02, G:0.09, T:0.48
Consensus pattern (25 bp):
TATTTAAATGTGGTACAAATTTATA
Found at i:233686 original size:25 final size:25
Alignment explanation
Indices: 233620--233686 Score: 68
Period size: 25 Copynumber: 2.8 Consensus size: 25
233610 ATGTGTATAA
*
233620 ATTTATA--TATTATAAATTAAATG
1 ATTTATATTTATTATAAATAAAATG
* *
233643 ATATTAT-TTTATTAAAAATAAAATT
1 AT-TTATATTTATTATAAATAAAATG
*
233668 ATTTATATTTATTTTAAAT
1 ATTTATATTTATTATAAAT
233687 TTTTTTAATA
Statistics
Matches: 35, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
23 2 0.06
24 8 0.23
25 25 0.71
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.52
Consensus pattern (25 bp):
ATTTATATTTATTATAAATAAAATG
Found at i:233834 original size:19 final size:20
Alignment explanation
Indices: 233790--233834 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
233780 TTTAATTTAA
* *
233790 TTTTAATATATTAAAATTAT
1 TTTTAATATATAAAAAATAT
233810 TATTTAATA-ATAAAAAATAT
1 T-TTTAATATATAAAAAATAT
233830 TTTTA
1 TTTTA
233835 TCTAATTTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
19 4 0.18
20 11 0.50
21 7 0.32
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (20 bp):
TTTTAATATATAAAAAATAT
Found at i:233910 original size:29 final size:28
Alignment explanation
Indices: 233870--233943 Score: 76
Period size: 29 Copynumber: 2.5 Consensus size: 28
233860 AAGTGTTATA
** *
233870 AAAAAATACACTTATTTCTCTAATGTTT
1 AAAAAATACACTTACCTCTCTAAGGTTT
*
233898 AAAAAATGCCACTTACCTCTCTAAGGTTT
1 AAAAAAT-ACACTTACCTCTCTAAGGTTT
233927 AGTTAAAAATACACTTA
1 A---AAAAATACACTTA
233944 TCCCCTAAGC
Statistics
Matches: 37, Mismatches: 5, Indels: 5
0.79 0.11 0.11
Matches are distributed among these distances:
28 7 0.19
29 18 0.49
31 6 0.16
32 6 0.16
ACGTcount: A:0.41, C:0.18, G:0.07, T:0.35
Consensus pattern (28 bp):
AAAAAATACACTTACCTCTCTAAGGTTT
Found at i:234770 original size:13 final size:13
Alignment explanation
Indices: 234752--234785 Score: 52
Period size: 12 Copynumber: 2.7 Consensus size: 13
234742 TAAAAATATT
234752 TAAAAAATTAAAA
1 TAAAAAATTAAAA
234765 TAAAAAA-TAAAA
1 TAAAAAATTAAAA
*
234777 TAAATAATT
1 TAAAAAATT
234786 GATAAATGAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
12 11 0.58
13 8 0.42
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (13 bp):
TAAAAAATTAAAA
Found at i:235028 original size:21 final size:21
Alignment explanation
Indices: 235002--235044 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
234992 GAGTTCGATA
235002 TAGACTTCACCCATAAACCAC
1 TAGACTTCACCCATAAACCAC
235023 TAGACTTCACCCATAAACCAC
1 TAGACTTCACCCATAAACCAC
235044 T
1 T
235045 GATCGCAAGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.37, C:0.37, G:0.05, T:0.21
Consensus pattern (21 bp):
TAGACTTCACCCATAAACCAC
Found at i:252066 original size:2 final size:2
Alignment explanation
Indices: 252055--252095 Score: 68
Period size: 2 Copynumber: 21.5 Consensus size: 2
252045 AAACAAACCC
252055 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
252095 A
1 A
252096 GCTTTGATTT
Statistics
Matches: 37, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
1 2 0.05
2 35 0.95
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:252549 original size:12 final size:12
Alignment explanation
Indices: 252534--252585 Score: 50
Period size: 12 Copynumber: 3.9 Consensus size: 12
252524 ATAAAGTCAT
252534 ATATAATATAAA
1 ATATAATATAAA
252546 ATATAATATAAA
1 ATATAATATAAA
*
252558 GCCATATATATATATAT
1 ---ATATA-ATATA-AA
252575 ATATAATATAA
1 ATATAATATAA
252586 TAAAACCAAG
Statistics
Matches: 34, Mismatches: 1, Indels: 10
0.76 0.02 0.22
Matches are distributed among these distances:
12 13 0.38
13 5 0.15
14 5 0.15
15 5 0.15
16 5 0.15
17 1 0.03
ACGTcount: A:0.58, C:0.04, G:0.02, T:0.37
Consensus pattern (12 bp):
ATATAATATAAA
Found at i:252557 original size:29 final size:29
Alignment explanation
Indices: 252523--252585 Score: 92
Period size: 29 Copynumber: 2.2 Consensus size: 29
252513 AATACCAAAT
*
252523 TATAAAGTCATATATA-ATATAAAATATAA
1 TATAAAGCCATATATATATAT-AAATATAA
*
252552 TATAAAGCCATATATATATATATATATAA
1 TATAAAGCCATATATATATATAAATATAA
252581 TATAA
1 TATAA
252586 TAAAACCAAG
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
29 27 0.87
30 4 0.13
ACGTcount: A:0.56, C:0.05, G:0.03, T:0.37
Consensus pattern (29 bp):
TATAAAGCCATATATATATATAAATATAA
Found at i:252822 original size:22 final size:22
Alignment explanation
Indices: 252778--252818 Score: 59
Period size: 21 Copynumber: 1.9 Consensus size: 22
252768 AAAATTTATT
252778 TAAATTTAATTATAAAAATATA
1 TAAATTTAATTATAAAAATATA
252800 TAAATATTAA-TA-AAAAATA
1 TAAAT-TTAATTATAAAAATA
252819 ATATTTTAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 7 0.39
22 7 0.39
23 4 0.22
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (22 bp):
TAAATTTAATTATAAAAATATA
Found at i:258462 original size:17 final size:17
Alignment explanation
Indices: 258440--258472 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
258430 ATTATTTAAA
*
258440 TTTATTTAATTAAAATT
1 TTTATTTAATAAAAATT
258457 TTTATTTAATAAAAAT
1 TTTATTTAATAAAAAT
258473 AAATTTAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (17 bp):
TTTATTTAATAAAAATT
Found at i:258593 original size:21 final size:21
Alignment explanation
Indices: 258566--258617 Score: 63
Period size: 22 Copynumber: 2.5 Consensus size: 21
258556 AATAATAATA
*
258566 AAATATTTAATTATGT-TTAT
1 AAATATTTAATTAAGTATTAT
258586 AAATTATTTAAATTAAGTATT-T
1 AAA-TATTT-AATTAAGTATTAT
258608 AAATATTTAA
1 AAATATTTAA
258618 ATTTTAATTT
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
20 5 0.18
21 10 0.36
22 11 0.39
23 2 0.07
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (21 bp):
AAATATTTAATTAAGTATTAT
Found at i:258618 original size:21 final size:21
Alignment explanation
Indices: 258566--258620 Score: 69
Period size: 21 Copynumber: 2.6 Consensus size: 21
258556 AATAATAATA
*
258566 AAATATTT-AATTATGTTTAT
1 AAATATTTAAATTAAGTTTAT
258586 AAATTATTTAAATTAAGTATT-T
1 AAA-TATTTAAATTAAGT-TTAT
258608 AAATATTTAAATT
1 AAATATTTAAATT
258621 TTAATTTTTT
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
20 3 0.10
21 15 0.48
22 11 0.35
23 2 0.06
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51
Consensus pattern (21 bp):
AAATATTTAAATTAAGTTTAT
Found at i:259466 original size:3 final size:3
Alignment explanation
Indices: 259458--259508 Score: 95
Period size: 3 Copynumber: 17.3 Consensus size: 3
259448 CCACCTTTAT
259458 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A-A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
259505 ATA A
1 ATA A
259509 ATGTTAATGG
Statistics
Matches: 47, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 2 0.04
3 45 0.96
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:259972 original size:7 final size:7
Alignment explanation
Indices: 259955--259986 Score: 55
Period size: 7 Copynumber: 4.4 Consensus size: 7
259945 TAGACATAAT
259955 TATATAAA
1 TATA-AAA
259963 TATAAAA
1 TATAAAA
259970 TATAAAA
1 TATAAAA
259977 TATAAAA
1 TATAAAA
259984 TAT
1 TAT
259987 CACATAAGAT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 20 0.83
8 4 0.17
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (7 bp):
TATAAAA
Found at i:260044 original size:15 final size:17
Alignment explanation
Indices: 260019--260067 Score: 59
Period size: 16 Copynumber: 3.0 Consensus size: 17
260009 ATTTTAAAAT
260019 TTATATAATATAAATTA
1 TTATATAATATAAATTA
*
260036 TTA-AT-ATATTAAAAT-
1 TTATATAATA-TAAATTA
260051 TTATATAATATAAATTA
1 TTATATAATATAAATTA
260068 AAATATGTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 8
0.72 0.06 0.22
Matches are distributed among these distances:
15 6 0.23
16 14 0.54
17 6 0.23
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
TTATATAATATAAATTA
Found at i:260048 original size:32 final size:32
Alignment explanation
Indices: 259954--260067 Score: 115
Period size: 32 Copynumber: 3.5 Consensus size: 32
259944 TTAGACATAA
* *
259954 TTATATAAATATAAAATA-TAAAATA-TAAAAT
1 TTATAT-AATATAAATTATTAATATATTAAAAT
* * * * * *
259985 ATCACATAAGATGAATGTATAAATATTTTAAAAT
1 -TTATATAATATAAAT-TATTAATATATTAAAAT
260019 TTATATAATATAAATTATTAATATATTAAAAT
1 TTATATAATATAAATTATTAATATATTAAAAT
260051 TTATATAATATAAATTA
1 TTATATAATATAAATTA
260068 AAATATGTTA
Statistics
Matches: 65, Mismatches: 14, Indels: 6
0.76 0.16 0.07
Matches are distributed among these distances:
31 6 0.09
32 38 0.58
33 15 0.23
34 6 0.09
ACGTcount: A:0.55, C:0.02, G:0.03, T:0.40
Consensus pattern (32 bp):
TTATATAATATAAATTATTAATATATTAAAAT
Found at i:260061 original size:17 final size:17
Alignment explanation
Indices: 260012--260061 Score: 61
Period size: 16 Copynumber: 3.1 Consensus size: 17
260002 TATAAATATT
260012 TTAAAATTTATATAATA
1 TTAAAATTTATATAATA
*
260029 -TAAATTATTA-AT-ATA
1 TTAAAAT-TTATATAATA
260044 TTAAAATTTATATAATA
1 TTAAAATTTATATAATA
260061 T
1 T
260062 AAATTAAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 8
0.73 0.05 0.22
Matches are distributed among these distances:
15 6 0.22
16 14 0.52
17 7 0.26
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (17 bp):
TTAAAATTTATATAATA
Found at i:260090 original size:32 final size:32
Alignment explanation
Indices: 259952--260079 Score: 111
Period size: 32 Copynumber: 4.0 Consensus size: 32
259942 TGTTAGACAT
*
259952 AATT-ATATAAATATAAAATATAAA-ATA-TAA
1 AATTAATAT-AATATAAATTATAAATATATTAA
* * * * *
259982 AATATCACATAAGATGAATGTATAAATATTTTAA
1 AAT-TAATATAATATAAAT-TATAAATATATTAA
* *
260016 AATTTATATAATATAAATTATTAATATATTAA
1 AATTAATATAATATAAATTATAAATATATTAA
* *
260048 AATTTATATAATATAAATTA-AAATATGTTAA
1 AATTAATATAATATAAATTATAAATATATTAA
260079 A
1 A
260080 TATAAGTATA
Statistics
Matches: 80, Mismatches: 13, Indels: 9
0.78 0.13 0.09
Matches are distributed among these distances:
30 3 0.04
31 17 0.21
32 41 0.51
33 13 0.16
34 6 0.08
ACGTcount: A:0.56, C:0.02, G:0.03, T:0.39
Consensus pattern (32 bp):
AATTAATATAATATAAATTATAAATATATTAA
Found at i:260234 original size:79 final size:82
Alignment explanation
Indices: 260089--260254 Score: 257
Period size: 80 Copynumber: 2.1 Consensus size: 82
260079 ATATAAGTAT
* * * * *
260089 AAAATTATAAATTATATGAATATAATACGAATTAAAAAAAATTAACTGCTCATTTTTTAAC-CAA
1 AAAATTATAAAATATATAAATATAATACGAATTAAAAAAAATTAACTACTCATTTTCTAACAAAA
260153 AAA-ATGATTAATTATA
66 AAATATGATTAATTATA
*
260169 AAAATTATAAAATATATAAATATAATACGAATT-AAAAAAATTAACTATTCATTTTCTAACAAAA
1 AAAATTATAAAATATATAAATATAATACGAATTAAAAAAAATTAACTACTCATTTTCTAACAAAA
260233 AAATATGATTAATTATA
66 AAATATGATTAATTATA
260250 AAAAT
1 AAAAT
260255 GGTCCCTATG
Statistics
Matches: 78, Mismatches: 6, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
79 24 0.31
80 36 0.46
81 18 0.23
ACGTcount: A:0.55, C:0.07, G:0.04, T:0.34
Consensus pattern (82 bp):
AAAATTATAAAATATATAAATATAATACGAATTAAAAAAAATTAACTACTCATTTTCTAACAAAA
AAATATGATTAATTATA
Found at i:261933 original size:3 final size:3
Alignment explanation
Indices: 261925--261957 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
261915 ATTGATTTCT
261925 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
261958 CCCTTGAGGA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:266792 original size:18 final size:19
Alignment explanation
Indices: 266771--266809 Score: 62
Period size: 18 Copynumber: 2.1 Consensus size: 19
266761 TAATTATTTA
*
266771 TTTAATATTTAGAA-TATT
1 TTTAATATTTAAAATTATT
266789 TTTAATATTTAAAATTATT
1 TTTAATATTTAAAATTATT
266808 TT
1 TT
266810 AATTTAATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 13 0.68
19 6 0.32
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (19 bp):
TTTAATATTTAAAATTATT
Found at i:267241 original size:23 final size:23
Alignment explanation
Indices: 267202--267246 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
267192 AATTTTTTTT
267202 TAAAAAAAAATTATAAT-ATTTA
1 TAAAAAAAAATTATAATGATTTA
267224 TAAAATAAAAATGT-TAATGATTT
1 TAAAA-AAAAAT-TATAATGATTT
267247 TTATAACAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
22 5 0.25
23 10 0.50
24 5 0.25
ACGTcount: A:0.58, C:0.00, G:0.04, T:0.38
Consensus pattern (23 bp):
TAAAAAAAAATTATAATGATTTA
Found at i:267881 original size:2 final size:2
Alignment explanation
Indices: 267874--267917 Score: 81
Period size: 2 Copynumber: 22.5 Consensus size: 2
267864 ACCAGCCCCA
267874 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
267915 AT A
1 AT A
267918 ATTTCAATAG
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.02
2 40 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:268870 original size:20 final size:20
Alignment explanation
Indices: 268847--268884 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
268837 TTTATTTATT
268847 ATATCTAT-TGATTATGTAAC
1 ATATCTATAT-ATTATGTAAC
*
268867 ATATTTATATATTATGTA
1 ATATCTATATATTATGTA
268885 TCTACATATG
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 15 0.94
21 1 0.06
ACGTcount: A:0.37, C:0.05, G:0.08, T:0.50
Consensus pattern (20 bp):
ATATCTATATATTATGTAAC
Found at i:269065 original size:14 final size:14
Alignment explanation
Indices: 269043--269076 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
269033 AACTTAATTA
*
269043 ATTTATAATTAAAT
1 ATTTTTAATTAAAT
*
269057 ATTTTTAATTAAGT
1 ATTTTTAATTAAAT
269071 ATTTTT
1 ATTTTT
269077 CCTTGAAAAG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (14 bp):
ATTTTTAATTAAAT
Found at i:270774 original size:4 final size:4
Alignment explanation
Indices: 270767--270849 Score: 94
Period size: 4 Copynumber: 20.8 Consensus size: 4
270757 ATGAGAAAGA
* * *
270767 ATAT ATAT ATAT ATAT ATGT ATAT GTAT ATAA ATAT ATAT ATAT ATAT
1 ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT
* * ** *
270815 ATAT ATAT GTAT ATAT GTAT GCAT GTAT ATAT ATA
1 ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATA
270850 ATAATGTGAC
Statistics
Matches: 67, Mismatches: 12, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
4 67 1.00
ACGTcount: A:0.45, C:0.01, G:0.07, T:0.47
Consensus pattern (4 bp):
ATAT
Found at i:270776 original size:6 final size:6
Alignment explanation
Indices: 270767--270849 Score: 94
Period size: 6 Copynumber: 13.8 Consensus size: 6
270757 ATGAGAAAGA
* * *
270767 ATATAT ATATAT ATATAT GTATAT GTATAT AAATAT ATATAT ATATAT
1 ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT
* * ** *
270815 ATATAT ATGTAT ATATGT ATGCAT GTATAT ATATA
1 ATATAT ATATAT ATATAT ATATAT ATATAT ATATA
270850 ATAATGTGAC
Statistics
Matches: 63, Mismatches: 14, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
6 63 1.00
ACGTcount: A:0.45, C:0.01, G:0.07, T:0.47
Consensus pattern (6 bp):
ATATAT
Found at i:272183 original size:27 final size:27
Alignment explanation
Indices: 272145--272198 Score: 90
Period size: 27 Copynumber: 2.0 Consensus size: 27
272135 ACTGTTGTCG
*
272145 ATCAATTTTGAAATTAAATTTGAAACA
1 ATCAATTGTGAAATTAAATTTGAAACA
*
272172 ATCAATTGTGAAATTTAATTTGAAACA
1 ATCAATTGTGAAATTAAATTTGAAACA
272199 GTTAAGGTTG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.46, C:0.07, G:0.09, T:0.37
Consensus pattern (27 bp):
ATCAATTGTGAAATTAAATTTGAAACA
Found at i:272622 original size:44 final size:44
Alignment explanation
Indices: 272560--272682 Score: 212
Period size: 44 Copynumber: 2.8 Consensus size: 44
272550 GGTGTTTTTA
*
272560 TTATTTA-TTTTTCGTGGATTGGCATAGTCACCCAATTGCATAT
1 TTATTTATTTTTTCGTGGATTGGCATAGCCACCCAATTGCATAT
272603 TTATTTATTTTTTCGTGGATTGGCATAGCCACCCAATTGCATAT
1 TTATTTATTTTTTCGTGGATTGGCATAGCCACCCAATTGCATAT
* *
272647 TTATTTATTTTTCCATGGATTGGCATAGCCACCCAA
1 TTATTTATTTTTTCGTGGATTGGCATAGCCACCCAA
272683 ATTCTAACAA
Statistics
Matches: 76, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
43 7 0.09
44 69 0.91
ACGTcount: A:0.24, C:0.19, G:0.15, T:0.42
Consensus pattern (44 bp):
TTATTTATTTTTTCGTGGATTGGCATAGCCACCCAATTGCATAT
Found at i:276933 original size:13 final size:13
Alignment explanation
Indices: 276915--276964 Score: 57
Period size: 13 Copynumber: 3.8 Consensus size: 13
276905 CGTTGCCAGC
276915 CAATTTTGAAATT
1 CAATTTTGAAATT
** *
276928 CAATTTAAAACAGT
1 CAATTTTGAA-ATT
276942 CAATTTTGAAATT
1 CAATTTTGAAATT
276955 CAA-TTTGAAA
1 CAATTTTGAAA
276965 CAGTGAAGGT
Statistics
Matches: 30, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
12 7 0.23
13 13 0.43
14 10 0.33
ACGTcount: A:0.44, C:0.10, G:0.08, T:0.38
Consensus pattern (13 bp):
CAATTTTGAAATT
Found at i:276953 original size:27 final size:27
Alignment explanation
Indices: 276915--276968 Score: 99
Period size: 27 Copynumber: 2.0 Consensus size: 27
276905 CGTTGCCAGC
276915 CAATTTTGAAATTCAATTTAAAACAGT
1 CAATTTTGAAATTCAATTTAAAACAGT
*
276942 CAATTTTGAAATTCAATTTGAAACAGT
1 CAATTTTGAAATTCAATTTAAAACAGT
276969 GAAGGTTGCA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.43, C:0.11, G:0.09, T:0.37
Consensus pattern (27 bp):
CAATTTTGAAATTCAATTTAAAACAGT
Found at i:277704 original size:15 final size:15
Alignment explanation
Indices: 277684--277734 Score: 59
Period size: 15 Copynumber: 3.4 Consensus size: 15
277674 TTTGAACTGT
277684 TGGTGCTAGAGGCAG
1 TGGTGCTAGAGGCAG
*
277699 TGGTGCCAGAGGCAG
1 TGGTGCTAGAGGCAG
* *
277714 TGAT-CTACGAGGCAA
1 TGGTGCTA-GAGGCAG
277729 TGGTGC
1 TGGTGC
277735 AGGATTAACC
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
14 2 0.07
15 26 0.90
16 1 0.03
ACGTcount: A:0.22, C:0.18, G:0.41, T:0.20
Consensus pattern (15 bp):
TGGTGCTAGAGGCAG
Found at i:286695 original size:20 final size:20
Alignment explanation
Indices: 286670--286747 Score: 111
Period size: 20 Copynumber: 3.8 Consensus size: 20
286660 TTTTTACCTA
286670 AATGTATCGATACATTCTTC
1 AATGTATCGATACATTCTTC
*
286690 AATGTATCGATACATTCTACCC
1 AATGTATCGATACATTCT--TC
*
286712 AGATGTATCGATACATTATTC
1 A-ATGTATCGATACATTCTTC
286733 AATGTATCGATACAT
1 AATGTATCGATACAT
286748 CTAGTTAAAA
Statistics
Matches: 52, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
20 32 0.62
21 2 0.04
22 2 0.04
23 16 0.31
ACGTcount: A:0.33, C:0.19, G:0.12, T:0.36
Consensus pattern (20 bp):
AATGTATCGATACATTCTTC
Found at i:297538 original size:51 final size:52
Alignment explanation
Indices: 297437--297556 Score: 224
Period size: 51 Copynumber: 2.3 Consensus size: 52
297427 GAAAATTTAT
*
297437 CTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGC
297489 CTGCATGTATCGATACATTT-ATAATGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGC
297540 CTGCATGTATCGATACA
1 CTGCATGTATCGATACA
297557 AAGATCAGTG
Statistics
Matches: 67, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
51 47 0.70
52 20 0.30
ACGTcount: A:0.29, C:0.18, G:0.18, T:0.34
Consensus pattern (52 bp):
CTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGC
Found at i:297583 original size:13 final size:13
Alignment explanation
Indices: 297565--297589 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
297555 CAAAGATCAG
297565 TGTATCGATACAA
1 TGTATCGATACAA
297578 TGTATCGATACA
1 TGTATCGATACA
297590 TGTGAGTAAT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:297671 original size:33 final size:33
Alignment explanation
Indices: 297629--297698 Score: 104
Period size: 33 Copynumber: 2.1 Consensus size: 33
297619 GGCAGTAGCT
297629 TACATTGTATCGATACAAAAAAATATGTATCGA
1 TACATTGTATCGATACAAAAAAATATGTATCGA
* ***
297662 TACATTGTATCGATACAACATTTTATGTATCGA
1 TACATTGTATCGATACAAAAAAATATGTATCGA
297695 TACA
1 TACA
297699 AATCGTTGAA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.40, C:0.14, G:0.11, T:0.34
Consensus pattern (33 bp):
TACATTGTATCGATACAAAAAAATATGTATCGA
Found at i:297672 original size:13 final size:13
Alignment explanation
Indices: 297654--297678 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
297644 CAAAAAAATA
297654 TGTATCGATACAT
1 TGTATCGATACAT
297667 TGTATCGATACA
1 TGTATCGATACA
297679 ACATTTTATG
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:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:298973 original size:114 final size:117
Alignment explanation
Indices: 298696--299138 Score: 336
Period size: 114 Copynumber: 3.8 Consensus size: 117
298686 TTATACTTTG
* * * * * *
298696 GCCATAGCTATAATCGCTCATACATTGGCCTAAGTCACTTATCCGGATAAAAA-AGTTGAATAAT
1 GCCACAGCTATAATCACTTATACATTAGCCTAAGTCACTTATTC--A-AAAAAGGGTTGAATAAT
* * *
298760 TTACTTCATTTAAGGTTAAGATATAATCTCCCTAATGAAGTACATAGTTTCCGTTTG
63 TTACTTCATTTAAGGTTAAGATACAATCT--CTAATGAAGTACATAGATTCCGTTTA
*** * ** *
298817 GCTGTAGCTATAATCACTTATACATTAGCCTAAGTCATTTATT-TGAAAAGGGTTGAATAATTTG
1 GCCACAGCTATAATCACTTATACATTAGCCTAAGTCACTTATTCAAAAAAGGGTTGAATAATTTA
* * *
298881 CTTCATTTAAGGTTGAA-ATACAATCTCT-TTGAAGTAGATA-ATTCCTTTTA
66 CTTCATTTAAGGTT-AAGATACAATCTCTAATGAAGTACATAGATTCCGTTTA
* * * * *
298931 GCCACAGCTATAATTACTTATACATT-GACCTAAGTTACTTATTCAAAAAATGATTGAATAAATT
1 GCCACAGCTATAATCACTTATACATTAG-CCTAAGTCACTTATTCAAAAAAGGGTTGAATAATTT
* * * * * *
298995 AC-TCTATTTAAGGTTAAGATACAATCTCCCTTATG-AGTAGAT--TTTTCTTTCTC
65 ACTTC-ATTTAAGGTTAAGATACAATCT--CTAATGAAGTACATAGATTCCGTT-TA
* * * * *
299048 GCCATAACTATAATCACTTGTATC-TTAGCCATAA-ACACTAATTC-AAAAAGGGTTGAATAATT
1 GCCACAGCTATAATCACTTATA-CATTAGCC-TAAGTCACTTATTCAAAAAAGGGTTGAATAATT
* * *
299110 TACTTTATTTTAGGTTAAGATTCAATCTC
64 TACTTCATTTAAGGTTAAGATACAATCTC
299139 CCTAATTAAA
Statistics
Matches: 262, Mismatches: 46, Indels: 35
0.76 0.13 0.10
Matches are distributed among these distances:
113 1 0.00
114 47 0.18
115 45 0.17
116 46 0.18
117 44 0.17
118 41 0.16
119 2 0.01
121 36 0.14
ACGTcount: A:0.34, C:0.16, G:0.13, T:0.37
Consensus pattern (117 bp):
GCCACAGCTATAATCACTTATACATTAGCCTAAGTCACTTATTCAAAAAAGGGTTGAATAATTTA
CTTCATTTAAGGTTAAGATACAATCTCTAATGAAGTACATAGATTCCGTTTA
Found at i:299138 original size:231 final size:233
Alignment explanation
Indices: 298696--299138 Score: 506
Period size: 231 Copynumber: 1.9 Consensus size: 233
298686 TTATACTTTG
* * * *
298696 GCCATAGCTATAATCGCTCATACATTGGCCTAAGTCACTTATCCGGATAAAAAAGTTGAATAATT
1 GCCACAGCTATAATCACTCATACATTGACCTAAGTCACTTATCC-GATAAAAAAGTTGAATAAAT
* * ** *
298761 TACTTCATTTAAGGTTAAGATATAATCTCCCTAATGAAGTACATAGTTTCCGTTTGGCTGTAGCT
65 TACTTCATTTAAGGTTAAGATACAATCTCCCTAATGAAGTACATA-TTTCCGTTTCGCCATAACT
* * * ** *
298826 ATAATCACTTATACATTAGCCTAAGTCATTTATTTGAAAAGGGTTGAATAATTTGCTTCATTTAA
129 ATAATCACTTATACATTAGCCTAAGACACTAATTCAAAAAGGGTTGAATAATTTACTTCATTTAA
298891 GGTTGAAATACAATCTCTTTGAAGTAGATAATTCCTTTTA
194 GGTTGAAATACAATCTCTTTGAAGTAGATAATTCCTTTTA
* * * * *
298931 GCCACAGCTATAATTACTTATACATTGACCTAAGTTACTTATTC-A-AAAAATGATTGAATAAAT
1 GCCACAGCTATAATCACTCATACATTGACCTAAGTCACTTATCCGATAAAAAAG-TTGAATAAAT
* * * *
298994 TAC-TCTATTTAAGGTTAAGATACAATCTCCCTTATG-AGTAGAT-TTTTCTTTCTCGCCATAAC
65 TACTTC-ATTTAAGGTTAAGATACAATCTCCCTAATGAAGTACATATTTCCGTT-TCGCCATAAC
* *
299056 TATAATCACTTGTATC-TTAGCCATAA-ACACTAATTCAAAAAGGGTTGAATAATTTACTTTATT
128 TATAATCACTTATA-CATTAGCC-TAAGACACTAATTCAAAAAGGGTTGAATAATTTACTTCATT
* *
299119 TTAGGTT-AAGATTCAATCTC
191 TAAGGTTGAA-ATACAATCTC
299139 CCTAATTAAA
Statistics
Matches: 174, Mismatches: 28, Indels: 16
0.80 0.13 0.07
Matches are distributed among these distances:
230 8 0.05
231 70 0.40
232 18 0.10
233 41 0.24
235 37 0.21
ACGTcount: A:0.34, C:0.16, G:0.13, T:0.37
Consensus pattern (233 bp):
GCCACAGCTATAATCACTCATACATTGACCTAAGTCACTTATCCGATAAAAAAGTTGAATAAATT
ACTTCATTTAAGGTTAAGATACAATCTCCCTAATGAAGTACATATTTCCGTTTCGCCATAACTAT
AATCACTTATACATTAGCCTAAGACACTAATTCAAAAAGGGTTGAATAATTTACTTCATTTAAGG
TTGAAATACAATCTCTTTGAAGTAGATAATTCCTTTTA
Found at i:300026 original size:24 final size:24
Alignment explanation
Indices: 299999--300126 Score: 107
Period size: 24 Copynumber: 5.3 Consensus size: 24
299989 AGTAACTAAT
* * *
299999 CCAAAGGTTGTTCTAGGAGTCATG
1 CCAAAAGTTGTTCCAAGAGTCATG
* *
300023 CCAAAAGATGTTCCAAGAGTTATG
1 CCAAAAGTTGTTCCAAGAGTCATG
*
300047 CCAAACGTTGTTCCATA-AGTCATG
1 CCAAAAGTTGTTCCA-AGAGTCATG
** * **
300071 CCAAAAAATGTTCCAGGAGTTGTG
1 CCAAAAGTTGTTCCAAGAGTCATG
*
300095 CCAAATA-TTGTTCCAAGAGTTATG
1 CCAAA-AGTTGTTCCAAGAGTCATG
*
300119 CTAAAAGT
1 CCAAAAGT
300127 ACAAAAAGCT
Statistics
Matches: 82, Mismatches: 18, Indels: 8
0.76 0.17 0.07
Matches are distributed among these distances:
23 1 0.01
24 79 0.96
25 2 0.02
ACGTcount: A:0.33, C:0.18, G:0.21, T:0.28
Consensus pattern (24 bp):
CCAAAAGTTGTTCCAAGAGTCATG
Found at i:300070 original size:48 final size:48
Alignment explanation
Indices: 300016--300109 Score: 143
Period size: 48 Copynumber: 2.0 Consensus size: 48
300006 TTGTTCTAGG
* *
300016 AGTCATGCCAAAAGATGTTCCAAGAGTTATGCCAAACGTTGTTCCATA
1 AGTCATGCCAAAAAATGTTCCAAGAGTTATGCCAAACATTGTTCCATA
* * *
300064 AGTCATGCCAAAAAATGTTCCAGGAGTTGTGCCAAATATTGTTCCA
1 AGTCATGCCAAAAAATGTTCCAAGAGTTATGCCAAACATTGTTCCA
300110 AGAGTTATGC
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
48 41 1.00
ACGTcount: A:0.33, C:0.20, G:0.19, T:0.28
Consensus pattern (48 bp):
AGTCATGCCAAAAAATGTTCCAAGAGTTATGCCAAACATTGTTCCATA
Found at i:302726 original size:16 final size:16
Alignment explanation
Indices: 302694--302742 Score: 62
Period size: 17 Copynumber: 2.9 Consensus size: 16
302684 AAATCAATAG
302694 TTTTAAAAAAATATATT
1 TTTTAAAAAAAT-TATT
302711 TTTTAAAAAAATTATT
1 TTTTAAAAAAATTATT
* *
302727 TCATAAAAAAAATTAT
1 T-TTTAAAAAAATTAT
302743 ATCGAAAGAG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
16 5 0.17
17 24 0.83
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (16 bp):
TTTTAAAAAAATTATT
Found at i:303646 original size:2 final size:2
Alignment explanation
Indices: 303639--303665 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
303629 TCAATCACTT
303639 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 T
303666 TACCATTACA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:303937 original size:29 final size:28
Alignment explanation
Indices: 303904--303960 Score: 78
Period size: 29 Copynumber: 2.0 Consensus size: 28
303894 CTGGTATAGG
* *
303904 TATTTTAACAGAAGTACTTTTAGCACAGT
1 TATTTTAACACAAGTACATTTAG-ACAGT
*
303933 TATTTTAACACAGGTACATTTAGACAGT
1 TATTTTAACACAAGTACATTTAGACAGT
303961 AACGTTTCTT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
28 5 0.20
29 20 0.80
ACGTcount: A:0.35, C:0.14, G:0.14, T:0.37
Consensus pattern (28 bp):
TATTTTAACACAAGTACATTTAGACAGT
Done.