Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008163.1 Hibiscus syriacus cultivar Beakdansim tig00110737_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 266294
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
File 1 of 2
Found at i:4425 original size:24 final size:24
Alignment explanation
Indices: 4393--4442 Score: 57
Period size: 24 Copynumber: 2.1 Consensus size: 24
4383 AATCACATTT
* *
4393 ATTTAAATA-ATTAATTTTTTGAAA
1 ATTTAAATATA-TAATTGTCTGAAA
*
4417 ATTTTAATATATAATTGTCTGAAA
1 ATTTAAATATATAATTGTCTGAAA
4441 AT
1 AT
4443 GAAAGATTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
24 21 0.95
25 1 0.05
ACGTcount: A:0.44, C:0.02, G:0.06, T:0.48
Consensus pattern (24 bp):
ATTTAAATATATAATTGTCTGAAA
Found at i:15479 original size:14 final size:14
Alignment explanation
Indices: 15460--15488 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
15450 ACTTTGGTAT
15460 CCTATAGACTCTAG
1 CCTATAGACTCTAG
15474 CCTATAGACTCTAG
1 CCTATAGACTCTAG
15488 C
1 C
15489 TTTAGCTTGC
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:0.28, C:0.31, G:0.14, T:0.28
Consensus pattern (14 bp):
CCTATAGACTCTAG
Found at i:16317 original size:44 final size:43
Alignment explanation
Indices: 16229--16324 Score: 122
Period size: 44 Copynumber: 2.2 Consensus size: 43
16219 TTGTGCTTCA
*
16229 TGCATCGATACACTAGAGAGTGAACCGATACATCCCTTAAATG
1 TGCATCGATACACCAGAGAGTGAACCGATACATCCCTTAAATG
* * * *
16272 TGCATCGATACACCATGA-AGGTGCACCGATGCATTCCTTGAATG
1 TGCATCGATACACCA-GAGA-GTGAACCGATACATCCCTTAAATG
16316 TGCATCGAT
1 TGCATCGAT
16325 GCACTCTGCT
Statistics
Matches: 46, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
43 15 0.33
44 31 0.67
ACGTcount: A:0.30, C:0.24, G:0.21, T:0.25
Consensus pattern (43 bp):
TGCATCGATACACCAGAGAGTGAACCGATACATCCCTTAAATG
Found at i:16327 original size:23 final size:22
Alignment explanation
Indices: 16254--16324 Score: 72
Period size: 23 Copynumber: 3.2 Consensus size: 22
16244 GAGAGTGAAC
*
16254 CGATACATCCCTTAAATGTGCAT
1 CGATACAT-CCTTGAATGTGCAT
* * *
16277 CGATACA-CCATGAAGGTGCAC
1 CGATACATCCTTGAATGTGCAT
*
16298 CGATGCATTCCTTGAATGTGCAT
1 CGATACA-TCCTTGAATGTGCAT
16321 CGAT
1 CGAT
16325 GCACTCTGCT
Statistics
Matches: 38, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
21 16 0.42
23 22 0.58
ACGTcount: A:0.28, C:0.25, G:0.20, T:0.27
Consensus pattern (22 bp):
CGATACATCCTTGAATGTGCAT
Found at i:18605 original size:21 final size:21
Alignment explanation
Indices: 18580--18627 Score: 96
Period size: 21 Copynumber: 2.3 Consensus size: 21
18570 TTAAAAAATG
18580 ATTTTCAAAGAAAATCTTAAA
1 ATTTTCAAAGAAAATCTTAAA
18601 ATTTTCAAAGAAAATCTTAAA
1 ATTTTCAAAGAAAATCTTAAA
18622 ATTTTC
1 ATTTTC
18628 TTAAATGTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.48, C:0.10, G:0.04, T:0.38
Consensus pattern (21 bp):
ATTTTCAAAGAAAATCTTAAA
Found at i:19023 original size:65 final size:64
Alignment explanation
Indices: 18948--19099 Score: 189
Period size: 65 Copynumber: 2.4 Consensus size: 64
18938 ACCCATTTCA
* * *
18948 AATGCATTTTGTGTACCGATGCAGAAG-CTATGCATCGATGCACTCTTGAATATTTTGAAACATC
1 AATGCATTTTGTGTACCGATGCA-AAGTCCATGCATCGATGCACTCCTGAAT-CTTTGAAACATC
19012 G
64 G
* ** *
19013 AATGCATTTTGTGTACCGATGCACAGTCCATGCATCGATGCACTCCTGGCTCTTTGAAACATTG
1 AATGCATTTTGTGTACCGATGCAAAGTCCATGCATCGATGCACTCCTGAATCTTTGAAACATCG
* * *
19077 AATGTAATTAGTGTACCGATGCA
1 AATGCATTTTGTGTACCGATGCA
19100 CCCCTAGTGT
Statistics
Matches: 76, Mismatches: 10, Indels: 3
0.85 0.11 0.03
Matches are distributed among these distances:
64 33 0.43
65 43 0.57
ACGTcount: A:0.28, C:0.20, G:0.20, T:0.32
Consensus pattern (64 bp):
AATGCATTTTGTGTACCGATGCAAAGTCCATGCATCGATGCACTCCTGAATCTTTGAAACATCG
Found at i:22412 original size:16 final size:16
Alignment explanation
Indices: 22388--22477 Score: 51
Period size: 13 Copynumber: 6.3 Consensus size: 16
22378 ATCGATTTTA
*
22388 ATTACTATATTTATAT
1 ATTATTATATTTATAT
22404 ATTATTATATTT-TA-
1 ATTATTATATTTATAT
22418 ATTATT-TA-TTA-ACT
1 ATTATTATATTTATA-T
*
22432 -TTA--ATAATTA-AT
1 ATTATTATATTTATAT
22444 ATTATTA-A-TTAT-T
1 ATTATTATATTTATAT
* *
22457 ATTATTGTATTTATTT
1 ATTATTATATTTATAT
22473 ATTAT
1 ATTAT
22478 ATTCATTTAA
Statistics
Matches: 60, Mismatches: 2, Indels: 24
0.70 0.02 0.28
Matches are distributed among these distances:
12 6 0.10
13 22 0.37
14 8 0.13
15 7 0.12
16 17 0.28
ACGTcount: A:0.37, C:0.02, G:0.01, T:0.60
Consensus pattern (16 bp):
ATTATTATATTTATAT
Found at i:23204 original size:23 final size:23
Alignment explanation
Indices: 23169--23216 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
23159 ATCAAGTACA
*
23169 ATAATATATTAGGTAACGCTTAT
1 ATAATATAATAGGTAACGCTTAT
* *
23192 ATAATGTAATAGGTAGCGCTTAT
1 ATAATATAATAGGTAACGCTTAT
23215 AT
1 AT
23217 TGATCTATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.38, C:0.08, G:0.17, T:0.38
Consensus pattern (23 bp):
ATAATATAATAGGTAACGCTTAT
Found at i:23947 original size:182 final size:182
Alignment explanation
Indices: 23640--24093 Score: 721
Period size: 182 Copynumber: 2.5 Consensus size: 182
23630 TTTTTACTAT
* *
23640 CGGTTTTATCATTTCGAGACCGGTTTTGTCATATTTTTACCTGTTATATTGTTATGGATTGATAC
1 CGGTTTTGTCATTTCGAGACCGGTTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATAC
* * *
23705 ATTTTTATAAAGTATCGACACTTTATTGGTGCTATAACTTCTTTTCTTTTAAATTCCAAAAGTGT
66 ATTTTTATAAAGTATCGACACTTTATTGCTGCTATAACTTCTTCTCATTTAAATTCCAAAAGTGT
* * * *
23770 TGATACTTATAATAAAGTATCGACACTTTCAACATATCTGGTAGCTCTTTAC
131 CGATACTTATAATAAAGTATCGACACTATCAACATATCCGGTAGCGCTTTAC
* * *
23822 CGGTTTTGTCATTTCGAGACTGATTTTTTCATATTTTTACCTGTTATATTGTTATGGATCGATAC
1 CGGTTTTGTCATTTCGAGACCGGTTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATAC
23887 ATTTTTATAAAGTATCGACACTTTATTAGCT-CTATAACTTCTTCTCATTTAAATTCCAAAAGTG
66 ATTTTTATAAAGTATCGACACTTTATT-GCTGCTATAACTTCTTCTCATTTAAATTCCAAAAGTG
23951 TCGATACTTATAATAAAGTATCGACACTATCAACATATCCGGTAGCGCTTTAC
130 TCGATACTTATAATAAAGTATCGACACTATCAACATATCCGGTAGCGCTTTAC
* ** * * *
24004 CTGTTTTGTCATTTATAGACCGGTTTTGTAATTTTTTTTACCTATTATATTGTTATGGATCGATA
1 CGGTTTTGTCATTTCGAGACCGGTTTTGTCA-TATTTTTACCTGTTATATTGTTATGGATCGATA
24069 CATTTTTATAAAGTATCGACACTTT
65 CATTTTTATAAAGTATCGACACTTT
24094 CAATATATCT
Statistics
Matches: 249, Mismatches: 21, Indels: 3
0.91 0.08 0.01
Matches are distributed among these distances:
182 191 0.77
183 58 0.23
ACGTcount: A:0.27, C:0.16, G:0.13, T:0.44
Consensus pattern (182 bp):
CGGTTTTGTCATTTCGAGACCGGTTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATAC
ATTTTTATAAAGTATCGACACTTTATTGCTGCTATAACTTCTTCTCATTTAAATTCCAAAAGTGT
CGATACTTATAATAAAGTATCGACACTATCAACATATCCGGTAGCGCTTTAC
Found at i:24204 original size:112 final size:112
Alignment explanation
Indices: 23963--24426 Score: 730
Period size: 112 Copynumber: 4.1 Consensus size: 112
23953 GATACTTATA
* * *
23963 ATAAAGTATCGACACTATCAACATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
1 ATAAAGTATCGACACTTTCAATATATCCGATAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
* * *
24028 TTTGTAATTTTTTTTACCTATTATATTGTTATGGATCGATACATTTTT
66 TTTGTCA-TTTTTTTACCTGTTATATTGTTATGGATCAATACATTTTT
* *
24076 ATAAAGTATCGACACTTTCAATATATCTGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
1 ATAAAGTATCGACACTTTCAATATATCCGATAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
*
24141 TTTGTCATTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTT
66 TTTGTCATTTTTTTACCTGTTATATTGTTATGGATCAATACATTTTT
* * * *
24188 ATAAATTATCGACACTTTCAATATATCCAATAGCGCTTTACCTGTTTTGTAATTTATAGACCGAT
1 ATAAAGTATCGACACTTTCAATATATCCGATAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
* *
24253 TTTGTCATTTTTTTACTTGTTATATTGTTATGGATCAATATATTTTT
66 TTTGTCATTTTTTTACCTGTTATATTGTTATGGATCAATACATTTTT
* * *
24300 TTAAAGTATCGACACTTTCAATATATCCGATAGCGCTTTACATGTTTTGTCATTTATAGATCGGT
1 ATAAAGTATCGACACTTTCAATATATCCGATAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
* * *
24365 TTTGTCATTTTTTTACCTGTTATATTGTTATAGATTAATATATTTTT
66 TTTGTCATTTTTTTACCTGTTATATTGTTATGGATCAATACATTTTT
24412 ATAAAGTATCGACAC
1 ATAAAGTATCGACAC
24427 AAACCGACAA
Statistics
Matches: 326, Mismatches: 25, Indels: 1
0.93 0.07 0.00
Matches are distributed among these distances:
112 258 0.79
113 68 0.21
ACGTcount: A:0.26, C:0.14, G:0.13, T:0.46
Consensus pattern (112 bp):
ATAAAGTATCGACACTTTCAATATATCCGATAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
TTTGTCATTTTTTTACCTGTTATATTGTTATGGATCAATACATTTTT
Found at i:28855 original size:35 final size:34
Alignment explanation
Indices: 28770--28856 Score: 97
Period size: 35 Copynumber: 2.5 Consensus size: 34
28760 AAAATAATTT
*
28770 TAAATACAACAAACTTACAATAAGTATTAAATGG
1 TAAATACAACAAAATTACAATAAGTATTAAATGG
* *
28804 TAAATGATAACCAAATTACAATAACTGATATTAAATGG
1 TAAAT-ACAACAAAATTACAATAA--G-TATTAAATGG
28842 T-AATA-AACAAAATTA
1 TAAATACAACAAAATTA
28857 ACTTAAATAC
Statistics
Matches: 45, Mismatches: 4, Indels: 7
0.80 0.07 0.12
Matches are distributed among these distances:
34 5 0.11
35 24 0.53
36 1 0.02
37 4 0.09
38 11 0.24
ACGTcount: A:0.54, C:0.10, G:0.08, T:0.28
Consensus pattern (34 bp):
TAAATACAACAAAATTACAATAAGTATTAAATGG
Found at i:32986 original size:2 final size:2
Alignment explanation
Indices: 32981--33019 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
32971 CACGCATTTA
32981 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
33020 GTCGTGATTT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:33170 original size:17 final size:15
Alignment explanation
Indices: 33148--33202 Score: 53
Period size: 15 Copynumber: 3.7 Consensus size: 15
33138 ATTATTAAAA
33148 ATTATAAAATAAGTTTT
1 ATTATAAAAT-A-TTTT
*
33165 ATTATAAGATATTTT
1 ATTATAAAATATTTT
33180 A-T-TAAAAT-TTTT
1 ATTATAAAATATTTT
33192 ATTATTAAAAT
1 ATTA-TAAAAT
33203 TTATAAAATA
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
12 5 0.15
13 6 0.18
14 1 0.03
15 11 0.33
16 1 0.03
17 9 0.27
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51
Consensus pattern (15 bp):
ATTATAAAATATTTT
Found at i:33191 original size:12 final size:15
Alignment explanation
Indices: 33161--33196 Score: 51
Period size: 12 Copynumber: 2.6 Consensus size: 15
33151 ATAAAATAAG
33161 TTTTATTATAAGATA
1 TTTTATTATAAGATA
33176 TTTTATTA-AA-AT-
1 TTTTATTATAAGATA
33188 TTTTATTAT
1 TTTTATTAT
33197 TAAAATTTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
12 8 0.40
13 2 0.10
14 2 0.10
15 8 0.40
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.61
Consensus pattern (15 bp):
TTTTATTATAAGATA
Found at i:33209 original size:24 final size:24
Alignment explanation
Indices: 33132--33218 Score: 77
Period size: 27 Copynumber: 3.4 Consensus size: 24
33122 TTTATGGATT
* *
33132 ATTTTGATTATTAAAAATTATAAA
1 ATTTTTATTATTAAAATTTATAAA
33156 ATAAGTTTTATTA-TAAGATATTTTATTAAA
1 AT---TTTTATTATTAA-A-A-TTTA-TAAA
33186 ATTTTTATTATTAAAATTTATAAA
1 ATTTTTATTATTAAAATTTATAAA
*
33210 ATATTTATT
1 ATTTTTATT
33219 TAATTATATT
Statistics
Matches: 52, Mismatches: 3, Indels: 16
0.73 0.04 0.23
Matches are distributed among these distances:
24 14 0.27
25 4 0.08
26 4 0.08
27 17 0.33
28 4 0.08
29 3 0.06
30 6 0.12
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (24 bp):
ATTTTTATTATTAAAATTTATAAA
Found at i:33231 original size:26 final size:25
Alignment explanation
Indices: 33173--33236 Score: 67
Period size: 24 Copynumber: 2.5 Consensus size: 25
33163 TTATTATAAG
*
33173 ATATTTTATTAAAATTTTTATTATT
1 ATATTTTATTAAAATATTTATTATT
* *
33198 AAAATTTA-TAAAATATTTATTTAATT
1 ATATTTTATTAAAATATTTA-TT-ATT
33224 ATATTTTAATTAA
1 ATATTTT-ATTAA
33237 TCTGGGTATG
Statistics
Matches: 30, Mismatches: 5, Indels: 5
0.75 0.12 0.12
Matches are distributed among these distances:
24 10 0.33
25 8 0.27
26 8 0.27
27 1 0.03
28 3 0.10
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (25 bp):
ATATTTTATTAAAATATTTATTATT
Found at i:34004 original size:22 final size:23
Alignment explanation
Indices: 33945--33994 Score: 100
Period size: 23 Copynumber: 2.2 Consensus size: 23
33935 GGGTATGAAT
33945 GGTAATTAGATGGAAAAAGGAGG
1 GGTAATTAGATGGAAAAAGGAGG
33968 GGTAATTAGATGGAAAAAGGAGG
1 GGTAATTAGATGGAAAAAGGAGG
33991 GGTA
1 GGTA
33995 TTTGGAGGAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.42, C:0.00, G:0.40, T:0.18
Consensus pattern (23 bp):
GGTAATTAGATGGAAAAAGGAGG
Found at i:34521 original size:15 final size:15
Alignment explanation
Indices: 34498--34533 Score: 63
Period size: 15 Copynumber: 2.4 Consensus size: 15
34488 TCCTTTTGTT
*
34498 CATCCAAAGAAACTC
1 CATCTAAAGAAACTC
34513 CATCTAAAGAAACTC
1 CATCTAAAGAAACTC
34528 CATCTA
1 CATCTA
34534 TCATATTCTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.44, C:0.31, G:0.06, T:0.19
Consensus pattern (15 bp):
CATCTAAAGAAACTC
Found at i:43179 original size:14 final size:15
Alignment explanation
Indices: 43160--43191 Score: 57
Period size: 14 Copynumber: 2.2 Consensus size: 15
43150 CTACTGTGAT
43160 TGTTTCTATATT-TA
1 TGTTTCTATATTGTA
43174 TGTTTCTATATTGTA
1 TGTTTCTATATTGTA
43189 TGT
1 TGT
43192 GGTTATATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 12 0.71
15 5 0.29
ACGTcount: A:0.19, C:0.06, G:0.12, T:0.62
Consensus pattern (15 bp):
TGTTTCTATATTGTA
Found at i:48741 original size:17 final size:17
Alignment explanation
Indices: 48721--48753 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
48711 TAAATGATGC
48721 AAATAAATA-AAAAAAGA
1 AAATAAA-ACAAAAAAGA
48738 AAATAAAACAAAAAAG
1 AAATAAAACAAAAAAG
48754 TGAGAGAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 1 0.07
17 14 0.93
ACGTcount: A:0.82, C:0.03, G:0.06, T:0.09
Consensus pattern (17 bp):
AAATAAAACAAAAAAGA
Found at i:51220 original size:25 final size:25
Alignment explanation
Indices: 51175--51331 Score: 93
Period size: 25 Copynumber: 6.3 Consensus size: 25
51165 CTAAAATCAA
51175 AATA-ATAAATAA-ATAATATAAATAT
1 AATATATAAATAACAT-A-ATAAATAT
*
51200 AATATATAACATAACA-AATAAACAT
1 AATATATAA-ATAACATAATAAATAT
51225 AATACTA-AAATATA-ATATATAATATAT
1 AATA-TATAAATA-ACATA-ATAA-ATAT
*
51252 AATATAT-AATACCATAAT-AATAT
1 AATATATAAATAACATAATAAATAT
*
51275 -ATATAATAAGATAATATAAT-AATAT
1 AATAT-ATAA-ATAACATAATAAATAT
* * *
51300 -ATATATATATAATAT-ATATATAT
1 AATATATAAATAACATAATAAATAT
51323 ATATATATA
1 A-ATATATA
51332 CTATGTAATA
Statistics
Matches: 109, Mismatches: 7, Indels: 32
0.74 0.05 0.22
Matches are distributed among these distances:
22 6 0.06
23 17 0.16
24 9 0.08
25 45 0.41
26 20 0.18
27 11 0.10
28 1 0.01
ACGTcount: A:0.60, C:0.04, G:0.01, T:0.36
Consensus pattern (25 bp):
AATATATAAATAACATAATAAATAT
Found at i:51251 original size:2 final size:2
Alignment explanation
Indices: 51234--51384 Score: 100
Period size: 2 Copynumber: 80.5 Consensus size: 2
51224 TAATACTAAA
*
51234 AT AT A- AT AT AT A- AT AT AT A- AT AT AT A- AT ACC AT A- AT A-
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT
*
51271 AT AT AT AT A- AT A- AG AT A- AT AT A- AT A- AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
51308 AT A- AT AT AT AT AT AT AT AT AT AT ACT AT GT A- AT AT GAT A- AT
1 AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT -AT AT AT
*
51349 AT AT ACT AT A- AT AT AT GT ACT AT A- AT AT AT ACT AT A
1 AT AT A-T AT AT AT AT AT AT A-T AT AT AT AT AT A-T AT A
51385 CTAGACGAAA
Statistics
Matches: 120, Mismatches: 7, Indels: 44
0.70 0.04 0.26
Matches are distributed among these distances:
1 16 0.13
2 93 0.77
3 11 0.09
ACGTcount: A:0.52, C:0.04, G:0.03, T:0.41
Consensus pattern (2 bp):
AT
Found at i:51316 original size:7 final size:7
Alignment explanation
Indices: 51176--51384 Score: 138
Period size: 7 Copynumber: 30.1 Consensus size: 7
51166 TAAAATCAAA
*
51176 ATAATAA
1 ATAATAT
51183 ATAAATAAT
1 AT-AAT-AT
51192 ATAA-AT
1 ATAATAT
51198 ATAATAT
1 ATAATAT
*
51205 ATAACAT
1 ATAATAT
51212 A-ACA-A-
1 ATA-ATAT
*
51217 ATAA-AC
1 ATAATAT
51223 ATAATACT
1 ATAATA-T
51231 A-AA-AT
1 ATAATAT
51236 ATAATAT
1 ATAATAT
51243 ATAATAT
1 ATAATAT
51250 ATAATAT
1 ATAATAT
*
51257 ATAATACC
1 ATAATA-T
51265 ATAATA-
1 ATAATAT
51271 AT-ATAT
1 ATAATAT
*
51277 ATAATAAG
1 ATAAT-AT
51285 ATAATAT
1 ATAATAT
51292 AATAATAT
1 -ATAATAT
51300 ATATATAT
1 ATA-ATAT
51308 ATAATAT
1 ATAATAT
51315 AT-ATAT
1 ATAATAT
51321 ATATATAT
1 ATA-ATAT
*
51329 ATACTAT
1 ATAATAT
*
51336 GTAATAT
1 ATAATAT
51343 GATAATAT
1 -ATAATAT
*
51351 AT-A-CT
1 ATAATAT
51356 ATAATAT
1 ATAATAT
*
51363 AT-GTACT
1 ATAATA-T
51370 ATAATAT
1 ATAATAT
*
51377 ATACTAT
1 ATAATAT
51384 A
1 A
51385 CTAGACGAAA
Statistics
Matches: 164, Mismatches: 15, Indels: 46
0.73 0.07 0.20
Matches are distributed among these distances:
5 11 0.07
6 30 0.18
7 73 0.45
8 47 0.29
9 3 0.02
ACGTcount: A:0.56, C:0.05, G:0.02, T:0.37
Consensus pattern (7 bp):
ATAATAT
Found at i:51364 original size:36 final size:35
Alignment explanation
Indices: 51234--51379 Score: 132
Period size: 36 Copynumber: 4.3 Consensus size: 35
51224 TAATACTAAA
*
51234 ATATA-ATATATAATATATA-AT-ATATA-ATACC
1 ATATATATATATAATATATATATAATATATATACT
* *
51265 ATA-ATA-ATAT-ATATAATAAGATAATATA-ATAAT
1 ATATATATATATAATAT-AT-ATATAATATATATACT
51298 ATATATATATATAATATATATATATATATATATACT
1 ATATATATATATAATATATATATA-ATATATATACT
* *
51334 ATGTA-ATATGATAATATATACTATAATATATGTACT
1 ATATATATAT-ATAATATATA-TATAATATATATACT
51370 ATA-ATATATA
1 ATATATATATA
51380 CTATACTAGA
Statistics
Matches: 95, Mismatches: 7, Indels: 22
0.77 0.06 0.18
Matches are distributed among these distances:
29 4 0.04
30 7 0.07
31 5 0.05
32 2 0.02
33 11 0.12
34 7 0.07
35 17 0.18
36 38 0.40
37 4 0.04
ACGTcount: A:0.53, C:0.03, G:0.03, T:0.41
Consensus pattern (35 bp):
ATATATATATATAATATATATATAATATATATACT
Found at i:51377 original size:54 final size:54
Alignment explanation
Indices: 51182--51384 Score: 181
Period size: 54 Copynumber: 3.8 Consensus size: 54
51172 CAAAATAATA
* * * * * ** *
51182 AATA-AATAATATAAATATAATATATA-AC-ATAACAAATAAACATAATACTAA
1 AATATAATAATATATATATAATATATATACTATAATATATATATATAATAAGAT
*
51233 AATATAAT-ATATAATATATAATATATAATACCATAATA-ATATATATAATAAGAT
1 AATATAATAATAT-ATATATAATATAT-ATACTATAATATATATATATAATAAGAT
* *
51287 AATATAATAATATATATAT-ATATA-ATA-TATATATATATATATATACTATG-T
1 AATATAATAATATATATATAATATATATACTATA-ATATATATATATAATAAGAT
* *
51338 AATATGATAATATATACTATAATATATGTACTATAATATATACTATA
1 AATATAATAATATATA-TATAATATATATACTATAATATATA-TATA
51385 CTAGACGAAA
Statistics
Matches: 127, Mismatches: 12, Indels: 22
0.79 0.07 0.14
Matches are distributed among these distances:
50 3 0.02
51 30 0.24
52 30 0.24
53 11 0.09
54 36 0.28
55 17 0.13
ACGTcount: A:0.56, C:0.05, G:0.02, T:0.37
Consensus pattern (54 bp):
AATATAATAATATATATATAATATATATACTATAATATATATATATAATAAGAT
Found at i:51607 original size:21 final size:20
Alignment explanation
Indices: 51579--51632 Score: 99
Period size: 21 Copynumber: 2.6 Consensus size: 20
51569 CGCAACTCAG
51579 TTTTCAAATTCGCGTTGCGA
1 TTTTCAAATTCGCGTTGCGA
51599 TTTTCCAAATTCGCGTTGCGA
1 TTTT-CAAATTCGCGTTGCGA
51620 TTTTCAAATTCGC
1 TTTTCAAATTCGC
51633 AACACTGAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
20 13 0.39
21 20 0.61
ACGTcount: A:0.20, C:0.22, G:0.17, T:0.41
Consensus pattern (20 bp):
TTTTCAAATTCGCGTTGCGA
Found at i:51662 original size:41 final size:40
Alignment explanation
Indices: 51543--51684 Score: 110
Period size: 41 Copynumber: 3.5 Consensus size: 40
51533 AAATGACCAA
* * *
51543 CAAATTCGCAACACGAACTCCAATTTCGCAACTC-AGTTTT
1 CAAATTCGCAACACGAATTTCAAATTCGCAACTCGA-TTTT
**** * **
51583 CAAATTCGCGTTGCGATTTTCCAAATTCGC-GTTGCGATTTT
1 CAAATTCGCAACACGAATTT-CAAATTCGCAACT-CGATTTT
51624 CAAATTCGCAACACTGAATTTCAAATTCGCAACTCGA-TTT
1 CAAATTCGCAACAC-GAATTTCAAATTCGCAACTCGATTTT
* *
51664 CTGAATTCGCAACGCGAATTT
1 C-AAATTCGCAACACGAATTT
51685 TGTTTTCGCA
Statistics
Matches: 77, Mismatches: 19, Indels: 12
0.71 0.18 0.11
Matches are distributed among these distances:
40 24 0.31
41 46 0.60
42 7 0.09
ACGTcount: A:0.29, C:0.25, G:0.14, T:0.32
Consensus pattern (40 bp):
CAAATTCGCAACACGAATTTCAAATTCGCAACTCGATTTT
Found at i:51888 original size:16 final size:15
Alignment explanation
Indices: 51853--51891 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
51843 TCCCCATCTC
*
51853 TAATTTTTTTTTACA
1 TAATTTTTTTATACA
*
51868 TAATTTTATTTATATA
1 TAATTTT-TTTATACA
51884 TAATTTTT
1 TAATTTTT
51892 CAATGATTTC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
15 8 0.38
16 13 0.62
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.67
Consensus pattern (15 bp):
TAATTTTTTTATACA
Found at i:55227 original size:29 final size:28
Alignment explanation
Indices: 55189--55283 Score: 98
Period size: 29 Copynumber: 3.6 Consensus size: 28
55179 TGAATTCGCA
55189 TTGCGAAAGTCAAATTCATGTTGCGATTG
1 TTGCGAAAGTCAAATTCA-GTTGCGATTG
55218 TTGCGAAAGTCAAATTC----GC-A---
1 TTGCGAAAGTCAAATTCAGTTGCGATTG
**
55238 ACGCGAAAGTCAAATTCACGTTGCGATTG
1 TTGCGAAAGTCAAATTCA-GTTGCGATTG
55267 TTGCGAAAGTCAAATTC
1 TTGCGAAAGTCAAATTC
55284 GAAACGCGAA
Statistics
Matches: 53, Mismatches: 4, Indels: 18
0.71 0.05 0.24
Matches are distributed among these distances:
20 15 0.28
23 1 0.02
24 2 0.04
25 2 0.04
26 1 0.02
29 32 0.60
ACGTcount: A:0.32, C:0.18, G:0.22, T:0.28
Consensus pattern (28 bp):
TTGCGAAAGTCAAATTCAGTTGCGATTG
Found at i:55253 original size:49 final size:49
Alignment explanation
Indices: 55181--55293 Score: 190
Period size: 49 Copynumber: 2.3 Consensus size: 49
55171 GTTTTCCTTG
** *
55181 AATTCGCATTGCGAAAGTCAAATTCATGTTGCGATTGTTGCGAAAGTCA
1 AATTCGCAACGCGAAAGTCAAATTCACGTTGCGATTGTTGCGAAAGTCA
55230 AATTCGCAACGCGAAAGTCAAATTCACGTTGCGATTGTTGCGAAAGTCA
1 AATTCGCAACGCGAAAGTCAAATTCACGTTGCGATTGTTGCGAAAGTCA
*
55279 AATTCGAAACGCGAA
1 AATTCGCAACGCGAA
55294 TTTGACTTTC
Statistics
Matches: 60, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
49 60 1.00
ACGTcount: A:0.34, C:0.19, G:0.22, T:0.26
Consensus pattern (49 bp):
AATTCGCAACGCGAAAGTCAAATTCACGTTGCGATTGTTGCGAAAGTCA
Found at i:55263 original size:20 final size:20
Alignment explanation
Indices: 55217--55263 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
55207 TGTTGCGATT
*
55217 GTTGCGAAAGTCAAATTCGC
1 GTTGCGAAAGTCAAATTCAC
***
55237 AACGCGAAAGTCAAATTCAC
1 GTTGCGAAAGTCAAATTCAC
55257 GTTGCGA
1 GTTGCGA
55264 TTGTTGCGAA
Statistics
Matches: 20, Mismatches: 7, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.34, C:0.21, G:0.23, T:0.21
Consensus pattern (20 bp):
GTTGCGAAAGTCAAATTCAC
Found at i:55357 original size:20 final size:20
Alignment explanation
Indices: 55334--55376 Score: 77
Period size: 20 Copynumber: 2.1 Consensus size: 20
55324 ATCGCAATGT
55334 GAATTTGACTTTCGCGTTGC
1 GAATTTGACTTTCGCGTTGC
*
55354 GAATTTGATTTTCGCGTTGC
1 GAATTTGACTTTCGCGTTGC
55374 GAA
1 GAA
55377 AGTGTACCTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.19, C:0.16, G:0.26, T:0.40
Consensus pattern (20 bp):
GAATTTGACTTTCGCGTTGC
Found at i:55537 original size:64 final size:64
Alignment explanation
Indices: 55435--55602 Score: 282
Period size: 64 Copynumber: 2.6 Consensus size: 64
55425 AATTTAAAAC
*
55435 AACAAATCAACTTTTACAAATCAATTAAACAAGGAAAAAATAAGAATTATTTACACATCAATTA
1 AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAATAAGAATTATTTACACATCAATTA
*** * *
55499 AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAATAATTCTTATTTCCTCATCAATTA
1 AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAATAAGAATTATTTACACATCAATTA
55563 AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAA
1 AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAA
55603 AGTGTACCCC
Statistics
Matches: 98, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
64 98 1.00
ACGTcount: A:0.54, C:0.17, G:0.03, T:0.27
Consensus pattern (64 bp):
AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAATAAGAATTATTTACACATCAATTA
Found at i:56986 original size:21 final size:21
Alignment explanation
Indices: 56962--57063 Score: 102
Period size: 21 Copynumber: 4.9 Consensus size: 21
56952 GTGGGTGAGA
56962 CCTCTTGAACGATGACAGGAG
1 CCTCTTGAACGATGACAGGAG
* * *
56983 CCTCTTGAACGGTGAAAGGGG
1 CCTCTTGAACGATGACAGGAG
* * *
57004 CCTTTTGAAGGATGATAGG-G
1 CCTCTTGAACGATGACAGGAG
57024 CCTCTTGAACGATAGA-A-GAGG
1 CCTCTTGAACGAT-GACAGGA-G
*
57045 CCTCTTGAATGATGACAGG
1 CCTCTTGAACGATGACAGG
57064 TGAATCGGGC
Statistics
Matches: 66, Mismatches: 10, Indels: 9
0.78 0.12 0.11
Matches are distributed among these distances:
19 1 0.02
20 15 0.23
21 49 0.74
22 1 0.02
ACGTcount: A:0.27, C:0.19, G:0.31, T:0.23
Consensus pattern (21 bp):
CCTCTTGAACGATGACAGGAG
Found at i:57047 original size:41 final size:42
Alignment explanation
Indices: 56962--57063 Score: 127
Period size: 41 Copynumber: 2.5 Consensus size: 42
56952 GTGGGTGAGA
* *
56962 CCTCTTGAACGATGACAGGAGCCTCTTGAACGGTGAAAGGGG
1 CCTCTTGAACGATGACAGGAGCCTCTTGAACGATGAAAGAGG
* * *
57004 CCTTTTGAAGGATGATAGG-GCCTCTTGAACGAT-AGAAGAGG
1 CCTCTTGAACGATGACAGGAGCCTCTTGAACGATGA-AAGAGG
*
57045 CCTCTTGAATGATGACAGG
1 CCTCTTGAACGATGACAGG
57064 TGAATCGGGC
Statistics
Matches: 51, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
40 1 0.02
41 34 0.67
42 16 0.31
ACGTcount: A:0.27, C:0.19, G:0.31, T:0.23
Consensus pattern (42 bp):
CCTCTTGAACGATGACAGGAGCCTCTTGAACGATGAAAGAGG
Found at i:57219 original size:4 final size:4
Alignment explanation
Indices: 57203--57244 Score: 57
Period size: 4 Copynumber: 10.5 Consensus size: 4
57193 GGGCCGCTAA
* * *
57203 AAAT AAAT TAAT AAAT AAAT CAAT AAAT AAAC AAAT AAAT AA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AA
57245 TACCGAAAAA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
4 32 1.00
ACGTcount: A:0.71, C:0.05, G:0.00, T:0.24
Consensus pattern (4 bp):
AAAT
Found at i:57491 original size:21 final size:21
Alignment explanation
Indices: 57467--57516 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 21
57457 ACCATTGTCG
* *
57467 TCACGTAAAGTACCGACCTCC
1 TCACGTAAAGCACCGACCTCA
* **
57488 TCACGCAAAGCATTGACCTCA
1 TCACGTAAAGCACCGACCTCA
57509 TCACGTAA
1 TCACGTAA
57517 CTCCCCTAAC
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.32, C:0.34, G:0.14, T:0.20
Consensus pattern (21 bp):
TCACGTAAAGCACCGACCTCA
Found at i:59246 original size:19 final size:20
Alignment explanation
Indices: 59188--59273 Score: 131
Period size: 20 Copynumber: 4.4 Consensus size: 20
59178 TCTAAAACTT
* *
59188 AAAATCACAACGAGAAAATG
1 AAAATCGCAACGCGAAAATG
59208 AAAATCGCAACGCGAAAATG
1 AAAATCGCAACGCGAAAATG
59228 AAAATCGCAACGC-AAAATG
1 AAAATCGCAACGCGAAAATG
*
59247 AAAATCGCAACGCGAAACT-
1 AAAATCGCAACGCGAAAATG
59266 AAAATCGC
1 AAAATCGC
59274 GTTGCGATTT
Statistics
Matches: 62, Mismatches: 3, Indels: 3
0.91 0.04 0.04
Matches are distributed among these distances:
19 27 0.44
20 35 0.56
ACGTcount: A:0.52, C:0.21, G:0.16, T:0.10
Consensus pattern (20 bp):
AAAATCGCAACGCGAAAATG
Found at i:59251 original size:39 final size:39
Alignment explanation
Indices: 59187--59273 Score: 131
Period size: 39 Copynumber: 2.2 Consensus size: 39
59177 TTCTAAAACT
* *
59187 TAAAATCACAACGAGAAAATGAAAATCGCAACGCGAAAA
1 TAAAATCGCAACGACAAAATGAAAATCGCAACGCGAAAA
*
59226 TGAAAATCGCAACG-CAAAATGAAAATCGCAACGCGAAAC
1 T-AAAATCGCAACGACAAAATGAAAATCGCAACGCGAAAA
59265 TAAAATCGC
1 TAAAATCGC
59274 GTTGCGATTT
Statistics
Matches: 44, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
38 8 0.18
39 25 0.57
40 11 0.25
ACGTcount: A:0.52, C:0.21, G:0.16, T:0.11
Consensus pattern (39 bp):
TAAAATCGCAACGACAAAATGAAAATCGCAACGCGAAAA
Found at i:59297 original size:20 final size:20
Alignment explanation
Indices: 59272--59320 Score: 80
Period size: 20 Copynumber: 2.5 Consensus size: 20
59262 AACTAAAATC
59272 GCGTTGCGATTTTCATTTTT
1 GCGTTGCGATTTTCATTTTT
*
59292 GCGTTGCGATTTTTATTTTT
1 GCGTTGCGATTTTCATTTTT
*
59312 GTGTTGCGA
1 GCGTTGCGA
59321 ATTTAAGTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.10, C:0.12, G:0.24, T:0.53
Consensus pattern (20 bp):
GCGTTGCGATTTTCATTTTT
Found at i:59712 original size:22 final size:22
Alignment explanation
Indices: 59657--59714 Score: 98
Period size: 22 Copynumber: 2.6 Consensus size: 22
59647 GATGGAGATA
*
59657 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCGTCGGAGATGGG
59679 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGTCGGAGATGGG
*
59701 GACGGATGTCGTCG
1 GACGGATTTCGTCG
59715 TAGAGAGTGA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 34 1.00
ACGTcount: A:0.17, C:0.17, G:0.45, T:0.21
Consensus pattern (22 bp):
GACGGATTTCGTCGGAGATGGG
Found at i:59887 original size:20 final size:20
Alignment explanation
Indices: 59862--59950 Score: 115
Period size: 20 Copynumber: 4.5 Consensus size: 20
59852 TAAGCACGCT
59862 TTGCGAATTACAGATTCGCG
1 TTGCGAATTACAGATTCGCG
* *
59882 TTGCGATTTACAGATTCACG
1 TTGCGAATTACAGATTCGCG
*
59902 TTGCGATTTACAGATTCGCG
1 TTGCGAATTACAGATTCGCG
** * *
59922 TTGCGAATTTGAAAATCGCG
1 TTGCGAATTACAGATTCGCG
59942 TTGCGAATT
1 TTGCGAATT
59951 TGGAAAATCG
Statistics
Matches: 61, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 61 1.00
ACGTcount: A:0.25, C:0.18, G:0.24, T:0.34
Consensus pattern (20 bp):
TTGCGAATTACAGATTCGCG
Found at i:59944 original size:40 final size:40
Alignment explanation
Indices: 59862--60014 Score: 121
Period size: 41 Copynumber: 3.8 Consensus size: 40
59852 TAAGCACGCT
* * * *
59862 TTGCGAATTACAGATTCGCGTTGCG-ATTT-ACAGATTCACG
1 TTGCGATTTACAGATTCGCATTGCGAATTTGA-A-AATCGCG
*
59902 TTGCGATTTACAGATTCGCGTTGCGAATTTGAAAATCGCG
1 TTGCGATTTACAGATTCGCATTGCGAATTTGAAAATCGCG
** * * ** * *
59942 TTGCGAATTTGGAAAATCGCAACGCGAATTCAGAAAATCGCA
1 TTGCG-ATTTACAGATTCGCATTGCGAATT-TGAAAATCGCG
* *
59984 ATGCGATTTACATATTCGCATTGCGAATTTG
1 TTGCGATTTACAGATTCGCATTGCGAATTTG
60015 GAAACTGAGT
Statistics
Matches: 89, Mismatches: 20, Indels: 8
0.76 0.17 0.07
Matches are distributed among these distances:
40 35 0.39
41 40 0.45
42 14 0.16
ACGTcount: A:0.29, C:0.18, G:0.22, T:0.31
Consensus pattern (40 bp):
TTGCGATTTACAGATTCGCATTGCGAATTTGAAAATCGCG
Found at i:59958 original size:21 final size:21
Alignment explanation
Indices: 59917--60073 Score: 92
Period size: 20 Copynumber: 7.8 Consensus size: 21
59907 ATTTACAGAT
59917 TCGCGTTGCGAATTT-GAAAA
1 TCGCGTTGCGAATTTGGAAAA
59937 TCGCGTTGCGAATTTGGAAAA
1 TCGCGTTGCGAATTTGGAAAA
*** **
59958 TCGCAACGCGAATTCAGAAAA
1 TCGCGTTGCGAATTTGGAAAA
** ** * *
59979 TCGCAATGCG-ATTTACATAT
1 TCGCGTTGCGAATTTGGAAAA
* *
59999 TCGCATTGCGAATTTGGAAAC
1 TCGCGTTGCGAATTTGGAAAA
* * **
60020 T-GAGTTGCGAAATTGG-AGT
1 TCGCGTTGCGAATTTGGAAAA
* *
60039 TCACGTTGCGAATTT-G-AGA
1 TCGCGTTGCGAATTTGGAAAA
*
60058 TCGCGCTGCGAATTTG
1 TCGCGTTGCGAATTTG
60074 TTGGTCATTT
Statistics
Matches: 107, Mismatches: 26, Indels: 8
0.76 0.18 0.06
Matches are distributed among these distances:
19 18 0.17
20 52 0.49
21 37 0.35
ACGTcount: A:0.29, C:0.17, G:0.25, T:0.29
Consensus pattern (21 bp):
TCGCGTTGCGAATTTGGAAAA
Found at i:63845 original size:16 final size:16
Alignment explanation
Indices: 63824--63854 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
63814 ATTGATTGAC
63824 TGTAATTATACCAATA
1 TGTAATTATACCAATA
63840 TGTAATTATACCAAT
1 TGTAATTATACCAAT
63855 TTTGGTAACT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.42, C:0.13, G:0.06, T:0.39
Consensus pattern (16 bp):
TGTAATTATACCAATA
Found at i:65963 original size:23 final size:23
Alignment explanation
Indices: 65915--65963 Score: 55
Period size: 23 Copynumber: 2.1 Consensus size: 23
65905 ATAAAGAACC
*
65915 AAAATAAACTTAAATATACCAGT
1 AAAATAAACTTAAACATACCAGT
* *
65938 AAAATAAAGTTTAAACAT-CCATT
1 AAAATAAA-CTTAAACATACCAGT
65961 AAA
1 AAA
65964 CCAACCATCA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
23 15 0.68
24 7 0.32
ACGTcount: A:0.57, C:0.12, G:0.04, T:0.27
Consensus pattern (23 bp):
AAAATAAACTTAAACATACCAGT
Found at i:71761 original size:14 final size:15
Alignment explanation
Indices: 71739--71804 Score: 98
Period size: 15 Copynumber: 4.5 Consensus size: 15
71729 ATATTTAGTT
*
71739 GGGCGGGCGGATGTG
1 GGGCGGGCGGATGCG
71754 GGGC-GGCGGATGCG
1 GGGCGGGCGGATGCG
*
71768 GGGCGGGTGGATGCG
1 GGGCGGGCGGATGCG
71783 GGGCGGGCGGATGCG
1 GGGCGGGCGGATGCG
*
71798 AGGCGGG
1 GGGCGGG
71805 TAAGGTCTCA
Statistics
Matches: 46, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
14 13 0.28
15 33 0.72
ACGTcount: A:0.08, C:0.17, G:0.67, T:0.09
Consensus pattern (15 bp):
GGGCGGGCGGATGCG
Found at i:71794 original size:30 final size:29
Alignment explanation
Indices: 71739--71805 Score: 98
Period size: 29 Copynumber: 2.3 Consensus size: 29
71729 ATATTTAGTT
* *
71739 GGGCGGGCGGATGTGGGGCGGCGGATGCG
1 GGGCGGGTGGATGCGGGGCGGCGGATGCG
71768 GGGCGGGTGGATGCGGGGCGGGCGGATGCG
1 GGGCGGGTGGATGCGGGGC-GGCGGATGCG
*
71798 AGGCGGGT
1 GGGCGGGT
71806 AAGGTCTCAA
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
29 17 0.50
30 17 0.50
ACGTcount: A:0.07, C:0.16, G:0.66, T:0.10
Consensus pattern (29 bp):
GGGCGGGTGGATGCGGGGCGGCGGATGCG
Found at i:74825 original size:17 final size:17
Alignment explanation
Indices: 74803--74837 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
74793 TGTGGCCCAC
74803 TAGCTTTAACTTGTTGA
1 TAGCTTTAACTTGTTGA
74820 TAGCTTTAACTTGTTGA
1 TAGCTTTAACTTGTTGA
74837 T
1 T
74838 TGATTTGTGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.23, C:0.11, G:0.17, T:0.49
Consensus pattern (17 bp):
TAGCTTTAACTTGTTGA
Found at i:76417 original size:14 final size:14
Alignment explanation
Indices: 76398--76428 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
76388 TAATAAAAAA
76398 ATATAAAGTAAACT
1 ATATAAAGTAAACT
76412 ATATAAAGTAAACT
1 ATATAAAGTAAACT
76426 ATA
1 ATA
76429 CAGAAATAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.58, C:0.06, G:0.06, T:0.29
Consensus pattern (14 bp):
ATATAAAGTAAACT
Found at i:82010 original size:25 final size:25
Alignment explanation
Indices: 81982--82029 Score: 87
Period size: 25 Copynumber: 1.9 Consensus size: 25
81972 AATATAAACC
81982 ATTGGATTTAAGGATTTAATTCCAT
1 ATTGGATTTAAGGATTTAATTCCAT
*
82007 ATTGGATTTGAGGATTTAATTCC
1 ATTGGATTTAAGGATTTAATTCC
82030 GTGTTAAATT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.29, C:0.08, G:0.19, T:0.44
Consensus pattern (25 bp):
ATTGGATTTAAGGATTTAATTCCAT
Found at i:82040 original size:25 final size:25
Alignment explanation
Indices: 81987--82041 Score: 65
Period size: 25 Copynumber: 2.2 Consensus size: 25
81977 AAACCATTGG
* **
81987 ATTTAAGGATTTAATTCCATATTGG
1 ATTTGAGGATTTAATTCCATATTAA
* *
82012 ATTTGAGGATTTAATTCCGTGTTAA
1 ATTTGAGGATTTAATTCCATATTAA
82037 ATTTG
1 ATTTG
82042 GACCATTGGA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.29, C:0.07, G:0.18, T:0.45
Consensus pattern (25 bp):
ATTTGAGGATTTAATTCCATATTAA
Found at i:84431 original size:19 final size:21
Alignment explanation
Indices: 84409--84448 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
84399 TGATCGTTAC
84409 ATATGATA-TTATCATGAACA
1 ATATGATATTTATCATGAACA
84429 TATATGATATTTATCATGAA
1 -ATATGATATTTATCATGAA
84449 TGATATTTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 8 0.44
22 10 0.56
ACGTcount: A:0.42, C:0.07, G:0.10, T:0.40
Consensus pattern (21 bp):
ATATGATATTTATCATGAACA
Found at i:86913 original size:44 final size:45
Alignment explanation
Indices: 86805--86987 Score: 237
Period size: 44 Copynumber: 4.1 Consensus size: 45
86795 ACATATCCAA
*
86805 TATTTTACTAATATACTTACCATTTATTCCATAAGCTCGTAAGCT
1 TATTTTACAAATATACTTACCATTTATTCCATAAGCTCGTAAGCT
* * ** *
86850 TATTTTACAAAAATACTTACTATTTAACCCATAAGCTTGTAAGC-
1 TATTTTACAAATATACTTACCATTTATTCCATAAGCTCGTAAGCT
* *
86894 TATTTTA-ACAATATACTTACCATTTGTTCAATAAGCTCGTAAGCT
1 TATTTTACA-AATATACTTACCATTTATTCCATAAGCTCGTAAGCT
* * *
86939 TATTTTACCAATATACTTGCCA-TTATTCCAGAAGCTCGTAAGCT
1 TATTTTACAAATATACTTACCATTTATTCCATAAGCTCGTAAGCT
86983 TATTT
1 TATTT
86988 GTATGGTTAC
Statistics
Matches: 117, Mismatches: 18, Indels: 7
0.82 0.13 0.05
Matches are distributed among these distances:
43 1 0.01
44 59 0.50
45 57 0.49
ACGTcount: A:0.33, C:0.19, G:0.08, T:0.40
Consensus pattern (45 bp):
TATTTTACAAATATACTTACCATTTATTCCATAAGCTCGTAAGCT
Found at i:86987 original size:89 final size:89
Alignment explanation
Indices: 86805--86987 Score: 244
Period size: 89 Copynumber: 2.1 Consensus size: 89
86795 ACATATCCAA
*
86805 TATTTTACTAATATACTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACAAAAATACTTAC
1 TATTTTACTAATATACTTACCATTTATTCAATAAGCTCGTAAGCTTATTTTACAAAAATACTTAC
* * *
86870 TATTTAACCCATAAGCTTGTAAGC
66 CATTTAACCCAGAAGCTCGTAAGC
* * * *
86894 TATTTTAAC-AATATACTTACCATTTGTTCAATAAGCTCGTAAGCTTATTTTACCAATATACTTG
1 TATTTT-ACTAATATACTTACCATTTATTCAATAAGCTCGTAAGCTTATTTTACAAAAATACTTA
**
86958 CCA-TTATTCCAGAAGCTCGTAAGC
65 CCATTTAACCCAGAAGCTCGTAAGC
86982 TTATTT
1 -TATTT
86988 GTATGGTTAC
Statistics
Matches: 82, Mismatches: 10, Indels: 4
0.85 0.10 0.04
Matches are distributed among these distances:
88 17 0.21
89 63 0.77
90 2 0.02
ACGTcount: A:0.33, C:0.19, G:0.08, T:0.40
Consensus pattern (89 bp):
TATTTTACTAATATACTTACCATTTATTCAATAAGCTCGTAAGCTTATTTTACAAAAATACTTAC
CATTTAACCCAGAAGCTCGTAAGC
Found at i:91133 original size:6 final size:6
Alignment explanation
Indices: 91106--91194 Score: 62
Period size: 6 Copynumber: 15.3 Consensus size: 6
91096 CTCTCATTAT
* * *
91106 TTTTTC TCTTTT- TTTTTC -TTTTC TTTTTC -TATT- TTTTCC TTCTTC
1 TTTTTC T-TTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC
* * * *
91151 GTTTAC TTTTTC TTTTTA TTCTTT- TTATTC TTTTTC TTTTTC TT
1 TTTTTC TTTTTC TTTTTC TT-TTTC TTTTTC TTTTTC TTTTTC TT
91195 ATAATATATT
Statistics
Matches: 63, Mismatches: 13, Indels: 14
0.70 0.14 0.16
Matches are distributed among these distances:
5 16 0.25
6 40 0.63
7 7 0.11
ACGTcount: A:0.04, C:0.17, G:0.01, T:0.78
Consensus pattern (6 bp):
TTTTTC
Found at i:91174 original size:9 final size:9
Alignment explanation
Indices: 91160--91185 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
91150 CGTTTACTTT
91160 TTCTTTTTA
1 TTCTTTTTA
91169 TTCTTTTTA
1 TTCTTTTTA
91178 TTCTTTTT
1 TTCTTTTT
91186 CTTTTTCTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.08, C:0.12, G:0.00, T:0.81
Consensus pattern (9 bp):
TTCTTTTTA
Found at i:93638 original size:21 final size:21
Alignment explanation
Indices: 93597--93640 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
93587 AATTTAAATT
* *
93597 GTGTATCGATGCATTGTTACA
1 GTGTATCGATGCACTGCTACA
*
93618 GTGTATCGATGTACTGCTACA
1 GTGTATCGATGCACTGCTACA
93639 GT
1 GT
93641 AATTTCCGTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.23, C:0.16, G:0.25, T:0.36
Consensus pattern (21 bp):
GTGTATCGATGCACTGCTACA
Found at i:94863 original size:22 final size:22
Alignment explanation
Indices: 94837--94881 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
94827 CCGGTCTAAA
94837 CCGACCCGACCCGACCGTTGAC
1 CCGACCCGACCCGACCGTTGAC
*
94859 CCGACCCGACCCGACTGTTGAC
1 CCGACCCGACCCGACCGTTGAC
94881 C
1 C
94882 GTTGACCGTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.18, C:0.49, G:0.22, T:0.11
Consensus pattern (22 bp):
CCGACCCGACCCGACCGTTGAC
Found at i:95410 original size:20 final size:20
Alignment explanation
Indices: 95372--95410 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
95362 GGTTTTCGCT
*
95372 TATTATTTAAATAATATTTA
1 TATTATTTAAATAAGATTTA
* *
95392 TATTATTTATATTAGATTT
1 TATTATTTAAATAAGATTT
95411 CCAATAAGGA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (20 bp):
TATTATTTAAATAAGATTTA
Found at i:95862 original size:42 final size:42
Alignment explanation
Indices: 95800--95961 Score: 229
Period size: 42 Copynumber: 3.9 Consensus size: 42
95790 GAAGTATTAT
* *
95800 CAGGTCCCTTTGATGTGTGCGAAGGTAAGCCTTACAGTTTCC
1 CAGGTCCCTTTGCTGTGTGCGAAGGTAAGCCTTACAGTTTAC
* *
95842 CATGTCCCTTTGTTGTGTGCGAAGGTAAGCCTTACAGTTTAC
1 CAGGTCCCTTTGCTGTGTGCGAAGGTAAGCCTTACAGTTTAC
*
95884 CAGGTCCCTTTGCTGTGTGC-AAGGGTAAGCCTTACAGTTTGC
1 CAGGTCCCTTTGCTGTGTGCGAA-GGTAAGCCTTACAGTTTAC
* *
95926 CAGGTCCCTTTGCTGTGTG-TAAGGATAAACCTTACA
1 CAGGTCCCTTTGCTGTGTGCGAAGG-TAAGCCTTACA
95962 TTTTTCCTAG
Statistics
Matches: 110, Mismatches: 7, Indels: 6
0.89 0.06 0.05
Matches are distributed among these distances:
41 4 0.04
42 106 0.96
ACGTcount: A:0.20, C:0.23, G:0.25, T:0.32
Consensus pattern (42 bp):
CAGGTCCCTTTGCTGTGTGCGAAGGTAAGCCTTACAGTTTAC
Found at i:102113 original size:22 final size:22
Alignment explanation
Indices: 102059--102119 Score: 88
Period size: 21 Copynumber: 2.8 Consensus size: 22
102049 CCGGTCTGAA
** *
102059 CCGACCCGACCATTGTCCCGAC
1 CCGACCCGACTGTTGACCCGAC
102081 CCGA-CCGACTGTTGACCCGAC
1 CCGACCCGACTGTTGACCCGAC
102102 CCGACCCGACTGTTGACC
1 CCGACCCGACTGTTGACC
102120 GTTGACCGTT
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
21 18 0.51
22 17 0.49
ACGTcount: A:0.18, C:0.46, G:0.21, T:0.15
Consensus pattern (22 bp):
CCGACCCGACTGTTGACCCGAC
Found at i:102652 original size:20 final size:20
Alignment explanation
Indices: 102614--102652 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
102604 GGTTTCCGCT
*
102614 TATTATTTAAATAATATTTA
1 TATTATTTAAATAAGATTTA
* *
102634 TATTATTTATATTAGATTT
1 TATTATTTAAATAAGATTT
102653 CCAATATGGA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (20 bp):
TATTATTTAAATAAGATTTA
Found at i:103101 original size:42 final size:41
Alignment explanation
Indices: 103042--103203 Score: 270
Period size: 42 Copynumber: 3.9 Consensus size: 41
103032 GAAGTATTAT
103042 CAGGTCCCTTTGCTGTGTGCGAAGGTAAGCCTTACAGTTTCC
1 CAGGTCCCTTTGCTGTGTGC-AAGGTAAGCCTTACAGTTTCC
*
103084 CAGGTCCCTTTGCTGTGTGCGAAGGTAAGCCTTACAGTTTAC
1 CAGGTCCCTTTGCTGTGTGC-AAGGTAAGCCTTACAGTTTCC
103126 CAGGTCCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCC
1 CAGGTCCCTTTGCTGTGTGCAA-GGTAAGCCTTACAGTTTCC
*
103168 CAGGTCCCTTTGCTGTGTGCAAGGATAAACCTTACA
1 CAGGTCCCTTTGCTGTGTGCAAGG-TAAGCCTTACA
103204 TTTTTCCTAG
Statistics
Matches: 115, Mismatches: 3, Indels: 4
0.94 0.02 0.03
Matches are distributed among these distances:
41 4 0.03
42 111 0.97
ACGTcount: A:0.19, C:0.25, G:0.25, T:0.30
Consensus pattern (41 bp):
CAGGTCCCTTTGCTGTGTGCAAGGTAAGCCTTACAGTTTCC
Found at i:104586 original size:14 final size:14
Alignment explanation
Indices: 104567--104605 Score: 60
Period size: 14 Copynumber: 2.8 Consensus size: 14
104557 AGTTGACCAA
*
104567 CAGAATCTGTTTTG
1 CAGAATCTGCTTTG
*
104581 CAGAATATGCTTTG
1 CAGAATCTGCTTTG
104595 CAGAATCTGCT
1 CAGAATCTGCT
104606 GTCCGATTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.26, C:0.18, G:0.21, T:0.36
Consensus pattern (14 bp):
CAGAATCTGCTTTG
Found at i:107379 original size:6 final size:6
Alignment explanation
Indices: 107363--107452 Score: 64
Period size: 6 Copynumber: 15.3 Consensus size: 6
107353 CTCATTATTT
* * *
107363 TTTTCTC TTTTTC -TTTTC -TTTTC TTTTTC -TATT- TTTTCC TTCTTC
1 TTTT-TC TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC
* * *
107408 GTTTAC TTTTTC TTTTTA TTCTGTT- TTTTTC TTTTTC TTTTTC TT
1 TTTTTC TTTTTC TTTTTC TT-T-TTC TTTTTC TTTTTC TTTTTC TT
107453 ATAATATATT
Statistics
Matches: 66, Mismatches: 11, Indels: 13
0.73 0.12 0.14
Matches are distributed among these distances:
5 17 0.26
6 40 0.61
7 7 0.11
8 2 0.03
ACGTcount: A:0.03, C:0.18, G:0.02, T:0.77
Consensus pattern (6 bp):
TTTTTC
Found at i:107417 original size:33 final size:34
Alignment explanation
Indices: 107361--107424 Score: 87
Period size: 33 Copynumber: 1.9 Consensus size: 34
107351 ATCTCATTAT
* *
107361 TTTTTTCTCTTTTTCTTTTC-TTTTCTTTTTCTA
1 TTTTTTCTCTTCTTCTTTACTTTTTCTTTTTCTA
107394 TTTTTTC-CTTCTTCGTTTACTTTTTCTTTTT
1 TTTTTTCTCTTCTTC-TTTACTTTTTCTTTTT
107425 ATTCTGTTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
32 6 0.22
33 11 0.41
34 10 0.37
ACGTcount: A:0.03, C:0.19, G:0.02, T:0.77
Consensus pattern (34 bp):
TTTTTTCTCTTCTTCTTTACTTTTTCTTTTTCTA
Found at i:109897 original size:21 final size:21
Alignment explanation
Indices: 109871--109914 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
109861 AATTTAAATT
*
109871 GTGTATCGATGCATTACTACA
1 GTGTATCGATGCACTACTACA
*
109892 GTGTATCGATGCACTGCTACA
1 GTGTATCGATGCACTACTACA
109913 GT
1 GT
109915 AATTTCCGTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.25, C:0.20, G:0.23, T:0.32
Consensus pattern (21 bp):
GTGTATCGATGCACTACTACA
Found at i:112399 original size:31 final size:31
Alignment explanation
Indices: 112361--112430 Score: 131
Period size: 31 Copynumber: 2.3 Consensus size: 31
112351 TTATAAGGAT
*
112361 TTCACTTTCCATTGTAAGTTCGTAACCCTAA
1 TTCACTTTCCATTGTAAGTTCGTAACCCCAA
112392 TTCACTTTCCATTGTAAGTTCGTAACCCCAA
1 TTCACTTTCCATTGTAAGTTCGTAACCCCAA
112423 TTCACTTT
1 TTCACTTT
112431 TTCCCTTATA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 38 1.00
ACGTcount: A:0.24, C:0.27, G:0.09, T:0.40
Consensus pattern (31 bp):
TTCACTTTCCATTGTAAGTTCGTAACCCCAA
Found at i:114077 original size:22 final size:22
Alignment explanation
Indices: 114035--114083 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 22
114025 ACTCTCATTA
* *
114035 TTTTTTTCTCTTTTTCTTTTTC
1 TTTTTTTCTCTTCTTCGTTTTC
114057 TATTTTTTC-CTTCTTCGTTTTC
1 T-TTTTTTCTCTTCTTCGTTTTC
114079 TTTTT
1 TTTTT
114084 ATTTTTATTA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 4 0.17
22 13 0.54
23 7 0.29
ACGTcount: A:0.02, C:0.18, G:0.02, T:0.78
Consensus pattern (22 bp):
TTTTTTTCTCTTCTTCGTTTTC
Found at i:114107 original size:5 final size:6
Alignment explanation
Indices: 114038--114117 Score: 58
Period size: 6 Copynumber: 13.3 Consensus size: 6
114028 CTCATTATTT
* * * * *
114038 TTTTCTC TTTTTC TTTTTC -TATT- TTTTCC TTCTTC GTTTTC TTTTTA
1 TTTT-TC TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC
*
114085 TTTTTA TTATATT- TTTTTC TTTTTC TTTTTC TT
1 TTTTTC TT-T-TTC TTTTTC TTTTTC TTTTTC TT
114118 ATAATATATA
Statistics
Matches: 59, Mismatches: 9, Indels: 11
0.75 0.11 0.14
Matches are distributed among these distances:
5 7 0.12
6 43 0.73
7 7 0.12
8 2 0.03
ACGTcount: A:0.06, C:0.15, G:0.01, T:0.78
Consensus pattern (6 bp):
TTTTTC
Found at i:114132 original size:30 final size:31
Alignment explanation
Indices: 114074--114132 Score: 75
Period size: 30 Copynumber: 1.9 Consensus size: 31
114064 TCCTTCTTCG
* * * *
114074 TTTTCTTTTTATTTTTATTATATTTTTTTCT
1 TTTTCTTTTTACTTATAATATATATTTTTCT
114105 TTTTCTTTTT-CTTATAATATATATTTTT
1 TTTTCTTTTTACTTATAATATATATTTTT
114133 AGCTCTTATG
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
30 14 0.58
31 10 0.42
ACGTcount: A:0.17, C:0.07, G:0.00, T:0.76
Consensus pattern (31 bp):
TTTTCTTTTTACTTATAATATATATTTTTCT
Found at i:116982 original size:45 final size:44
Alignment explanation
Indices: 116918--117091 Score: 204
Period size: 44 Copynumber: 4.1 Consensus size: 44
116908 ACATATCCAA
116918 TATTTTACCAATATACTTACCATTTATTCCATAAGCTCGTAAGCT
1 TATTTTACCAATATACTTACCA-TTATTCCATAAGCTCGTAAGCT
*
116963 TATTTTACCAA-A-A--TA-C-TTA--CCATAAGCTCGTAAG-A
1 TATTTTACCAATATACTTACCATTATTCCATAAGCTCGTAAGCT
* * ** *
116998 TATTTTAACAATATACTTACCATTTGTTCCATAAAATTGTAAGCT
1 TATTTTACCAATATACTTACCA-TTATTCCATAAGCTCGTAAGCT
*
117043 TATTTTACCAATATACTTTCCATTATTCCATAAGCTCGTAAGCT
1 TATTTTACCAATATACTTACCATTATTCCATAAGCTCGTAAGCT
117087 TATTT
1 TATTT
117092 GTATGGTTAC
Statistics
Matches: 106, Mismatches: 13, Indels: 21
0.76 0.09 0.15
Matches are distributed among these distances:
35 10 0.09
36 16 0.15
37 1 0.01
38 3 0.03
39 2 0.02
40 2 0.02
41 2 0.02
42 2 0.02
43 1 0.01
44 36 0.34
45 31 0.29
ACGTcount: A:0.33, C:0.20, G:0.07, T:0.40
Consensus pattern (44 bp):
TATTTTACCAATATACTTACCATTATTCCATAAGCTCGTAAGCT
Found at i:117014 original size:35 final size:36
Alignment explanation
Indices: 116946--117020 Score: 116
Period size: 35 Copynumber: 2.1 Consensus size: 36
116936 ACCATTTATT
* *
116946 CCATAAGCTCGTAAGCTTATTTTACCAAAATACTTA
1 CCATAAGCTCGTAAGCATATTTTAACAAAATACTTA
*
116982 CCATAAGCTCGTAAG-ATATTTTAACAATATACTTA
1 CCATAAGCTCGTAAGCATATTTTAACAAAATACTTA
117017 CCAT
1 CCAT
117021 TTGTTCCATA
Statistics
Matches: 36, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
35 21 0.58
36 15 0.42
ACGTcount: A:0.37, C:0.21, G:0.08, T:0.33
Consensus pattern (36 bp):
CCATAAGCTCGTAAGCATATTTTAACAAAATACTTA
Found at i:117040 original size:44 final size:44
Alignment explanation
Indices: 116992--117075 Score: 116
Period size: 45 Copynumber: 1.9 Consensus size: 44
116982 CCATAAGCTC
*
116992 GTAAG-ATATTTTAACAATATACTTACCATTTGTTCCATAAAATT
1 GTAAGCATATTTTAACAATATACTTACCA-TTATTCCATAAAATT
* * *
117036 GTAAGCTTATTTTACCAATATACTTTCCATTATTCCATAA
1 GTAAGCATATTTTAACAATATACTTACCATTATTCCATAA
117076 GCTCGTAAGC
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
44 15 0.43
45 20 0.57
ACGTcount: A:0.36, C:0.17, G:0.06, T:0.42
Consensus pattern (44 bp):
GTAAGCATATTTTAACAATATACTTACCATTATTCCATAAAATT
Found at i:117050 original size:80 final size:80
Alignment explanation
Indices: 116917--117065 Score: 235
Period size: 80 Copynumber: 1.9 Consensus size: 80
116907 AACATATCCA
* **
116917 ATATTTTACCAATATACTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAAAATACTTA
1 ATATTTTAACAATATACTTACCATTTATTCCATAAAATCGTAAGCTTATTTTACCAAAATACTTA
116982 CCATAAGCTCGTAAG
66 CCATAAGCTCGTAAG
* * * *
116997 ATATTTTAACAATATACTTACCATTTGTTCCATAAAATTGTAAGCTTATTTTACCAATATACTTT
1 ATATTTTAACAATATACTTACCATTTATTCCATAAAATCGTAAGCTTATTTTACCAAAATACTTA
117062 CCAT
66 CCAT
117066 TATTCCATAA
Statistics
Matches: 62, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
80 62 1.00
ACGTcount: A:0.35, C:0.19, G:0.06, T:0.40
Consensus pattern (80 bp):
ATATTTTAACAATATACTTACCATTTATTCCATAAAATCGTAAGCTTATTTTACCAAAATACTTA
CCATAAGCTCGTAAG
Found at i:117215 original size:40 final size:39
Alignment explanation
Indices: 117166--117245 Score: 106
Period size: 40 Copynumber: 2.0 Consensus size: 39
117156 ATAGGAGTCA
* * *
117166 AATATTGCACCAAAGTGCTGAGGTCGAGCTTTGCTCACCT
1 AATAATGCACCAAAGTGCTGAGGTCG-GCTTTACCCACCT
**
117206 AATAATGCACCGTAGTGCTGAGGTCGGCTTTACCCACCT
1 AATAATGCACCAAAGTGCTGAGGTCGGCTTTACCCACCT
117245 A
1 A
117246 GTACACCGTA
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
39 12 0.34
40 23 0.66
ACGTcount: A:0.25, C:0.26, G:0.23, T:0.26
Consensus pattern (39 bp):
AATAATGCACCAAAGTGCTGAGGTCGGCTTTACCCACCT
Found at i:120205 original size:22 final size:21
Alignment explanation
Indices: 120173--120213 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
120163 CCGAAACATC
*
120173 CTTCATAATAAATATCATATAT
1 CTTCATAAT-AACATCATATAT
*
120195 CTTCATGATAACATCATAT
1 CTTCATAATAACATCATAT
120214 GTAACGATCA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 9 0.53
22 8 0.47
ACGTcount: A:0.41, C:0.17, G:0.02, T:0.39
Consensus pattern (21 bp):
CTTCATAATAACATCATATAT
Found at i:125880 original size:112 final size:111
Alignment explanation
Indices: 125680--125912 Score: 367
Period size: 112 Copynumber: 2.1 Consensus size: 111
125670 GTTATAGGTG
* * ** * * *
125680 CATTTTGACATACTTTGTGTATGATTGTATCGATTGATTTTGTTTAATGCATAACGGTGCATTTT
1 CATTTCGACATACTTCGTGTATGAAAGTATCGATCGATTTTGCTTAATGCAAAACGGTGCATTTT
*
125745 CGGCATAAAAGGTGCCACACATGGTATTCATAATGAGGTAAATTAC
66 CGGCATAAAAGGTGCAACACATGGTATTCATAATGAGGTAAATTAC
125791 CATTTCGACATACTTCGTGTATGAAAGTTATCGATCGATTTTGCTTAATGCAAAACGGTGCATTT
1 CATTTCGACATACTTCGTGTATGAAAG-TATCGATCGATTTTGCTTAATGCAAAACGGTGCATTT
* *
125856 TCGGCATAAAAGGTGCAACCCATGGTATTCATAATGAGGTGAATTAC
65 TCGGCATAAAAGGTGCAACACATGGTATTCATAATGAGGTAAATTAC
125903 CATTTCGACA
1 CATTTCGACA
125913 CTTCGGTACA
Statistics
Matches: 111, Mismatches: 10, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
111 23 0.21
112 88 0.79
ACGTcount: A:0.30, C:0.16, G:0.20, T:0.35
Consensus pattern (111 bp):
CATTTCGACATACTTCGTGTATGAAAGTATCGATCGATTTTGCTTAATGCAAAACGGTGCATTTT
CGGCATAAAAGGTGCAACACATGGTATTCATAATGAGGTAAATTAC
Found at i:127610 original size:40 final size:40
Alignment explanation
Indices: 127555--127639 Score: 134
Period size: 40 Copynumber: 2.1 Consensus size: 40
127545 ACACTACAGT
* *
127555 ATATAAGGTGGGTAAAGCTCGACCTCAACACTACGGTGCA
1 ATATTAGGTGAGTAAAGCTCGACCTCAACACTACGGTGCA
* *
127595 TTATTAGGTGAGTAAAGCTCGACCTTAACACTACGGTGCA
1 ATATTAGGTGAGTAAAGCTCGACCTCAACACTACGGTGCA
127635 ATATT
1 ATATT
127640 TTAACTCCTA
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.32, C:0.20, G:0.22, T:0.26
Consensus pattern (40 bp):
ATATTAGGTGAGTAAAGCTCGACCTCAACACTACGGTGCA
Found at i:132449 original size:94 final size:94
Alignment explanation
Indices: 132288--132466 Score: 295
Period size: 94 Copynumber: 1.9 Consensus size: 94
132278 TGGATTGTGA
* * *
132288 ACAACTCAAAAGAGATGGGAAATCAGTTCAATTCAATGAGTTTCACGGTCAAATTTAACCAATAT
1 ACAACTCAAAAGAGATGGGAAATCAGATCAATTCAATAAGTTTCACGGCCAAATTTAACCAATAT
*
132353 TATGACCAATTGTCCATGACTAGTGAAAT
66 TATGACAAATTGTCCATGACTAGTGAAAT
*
132382 ACAACTCAAAAGAGATGGGAAATCAGATCAATTCAATAAGTTTCACGGCCAAATTTAACCACTAT
1 ACAACTCAAAAGAGATGGGAAATCAGATCAATTCAATAAGTTTCACGGCCAAATTTAACCAATAT
* *
132447 TATGGCAAATTGTTCATGAC
66 TATGACAAATTGTCCATGAC
132467 ATTTCAACCA
Statistics
Matches: 78, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
94 78 1.00
ACGTcount: A:0.40, C:0.18, G:0.16, T:0.27
Consensus pattern (94 bp):
ACAACTCAAAAGAGATGGGAAATCAGATCAATTCAATAAGTTTCACGGCCAAATTTAACCAATAT
TATGACAAATTGTCCATGACTAGTGAAAT
Found at i:143453 original size:20 final size:20
Alignment explanation
Indices: 143428--143470 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
143418 TCTAAGAGCC
*
143428 CATTTAAGATCATATAGATG
1 CATTTAAGAGCATATAGATG
* *
143448 CATTTAGGAGCATATAGTTG
1 CATTTAAGAGCATATAGATG
143468 CAT
1 CAT
143471 GTGGTGGAAC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.35, C:0.12, G:0.19, T:0.35
Consensus pattern (20 bp):
CATTTAAGAGCATATAGATG
Found at i:157951 original size:22 final size:21
Alignment explanation
Indices: 157897--157937 Score: 73
Period size: 21 Copynumber: 1.9 Consensus size: 21
157887 AAAAATTGTA
157897 ATAATAATAAATAATATTAACG
1 ATAATAAT-AATAATATTAACG
157919 ATAATAATAATAATATTAA
1 ATAATAATAATAATATTAA
157938 ATTTTAATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 11 0.58
22 8 0.42
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.34
Consensus pattern (21 bp):
ATAATAATAATAATATTAACG
Found at i:158625 original size:20 final size:20
Alignment explanation
Indices: 158512--158628 Score: 58
Period size: 20 Copynumber: 5.7 Consensus size: 20
158502 AAACATCCTT
* *
158512 CCCGAAGGTCTTATTGATGG
1 CCCGAAGGACTTACTGATGG
* * *
158532 CCCGAATGACTTATCAT-CTTG
1 CCCGAAGGACTTA-C-TGATGG
* * * *
158553 CTCGAAAGACTTACAGATGA
1 CCCGAAGGACTTACTGATGG
* *
158573 CCCGAAGGATTTAAGCATCAT-G
1 CCCGAAGGACTT-A-C-TGATGG
* *
158595 CTCGAAAGACTTACTGATGG
1 CCCGAAGGACTTACTGATGG
158615 CCCGAAGGACTTAC
1 CCCGAAGGACTTAC
158629 CAATTTTGGA
Statistics
Matches: 67, Mismatches: 23, Indels: 14
0.64 0.22 0.13
Matches are distributed among these distances:
19 3 0.04
20 36 0.54
21 15 0.22
22 11 0.16
23 2 0.03
ACGTcount: A:0.29, C:0.24, G:0.22, T:0.25
Consensus pattern (20 bp):
CCCGAAGGACTTACTGATGG
Found at i:158669 original size:231 final size:232
Alignment explanation
Indices: 158266--158829 Score: 810
Period size: 231 Copynumber: 2.4 Consensus size: 232
158256 TTTAAAATCC
* *
158266 TGTGAAAACATCCTGCCCGAAGTTCTTATAGATGGCCCGAAGGACTTATCATCTTGCTCGAAAGA
1 TGTGAAAACATCCTTCCCGAAGGTCTTATAGATGGCCCGAAGGACTTATCATCTTGCTCGAAAGA
* * * * *
158331 CTGACAGATAACCCAAAGGATTTAAGCATCATGCTCCAAAAACTTCCTGATGGCCCAAATGACTT
66 CTTACAGATGACCCGAAGGATTTAAGCATCATGCTCCAAAAACTTACTGATGGCCCAAAGGACTT
* *
158396 ACCAATTTTGGAAATAGTTTACTACATAGGAACCTTTTCTTACTTTTAAAAAATTTCAATTTTCA
131 ACCAATTTTGGAAATAGTTTACTACATAAGAAACTTTTCTTACTTTTAAAAAATTTCAATTTTCA
158461 GATTTAAATGAAAAAC-TTCTCATTTTTCGAGACACA
196 GATTTAAATGAAAAACTTTCTCATTTTTCGAGACACA
* *
158497 TGTGAAAACATCCTTCCCGAAGGTCTTATTGATGGCCCGAATGACTTATCATCTTGCTCGAAAGA
1 TGTGAAAACATCCTTCCCGAAGGTCTTATAGATGGCCCGAAGGACTTATCATCTTGCTCGAAAGA
* * *
158562 CTTACAGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTT
66 CTTACAGATGACCCGAAGGATTTAAGCATCATGCTCCAAAAACTTACTGATGGCCCAAAGGACTT
** * *
158627 ACCAATTTTGGAAATAGTTTACTAGGTAAGAAACTTTTCTTACTTTTCAAAAATTTTAATTTTCA
131 ACCAATTTTGGAAATAGTTTACTACATAAGAAACTTTTCTTACTTTTAAAAAATTTCAATTTTCA
* * *
158692 GATTTAAATGAGAAACTTTTCTCATTTTTTGAGAGACA
196 GATTTAAATGAAAAAC-TTTCTCATTTTTCGAGACACA
* * * * **
158730 TGTAAAAACATCCTGT-CCAAAGGTCTTGTGGATTCCCCGAAGGACTTATCATCTT-CGTCGAAA
1 TGTGAAAACATCCT-TCCCGAAGGTCTTATAGATGGCCCGAAGGACTTATCATCTTGC-TCGAAA
* * *
158793 GACTTACAGATGATCTGAAGGATTTAAACATCATGCT
64 GACTTACAGATGACCCGAAGGATTTAAGCATCATGCT
158830 ACCATTTTTG
Statistics
Matches: 298, Mismatches: 31, Indels: 6
0.89 0.09 0.02
Matches are distributed among these distances:
231 192 0.64
232 1 0.00
233 104 0.35
234 1 0.00
ACGTcount: A:0.33, C:0.20, G:0.16, T:0.31
Consensus pattern (232 bp):
TGTGAAAACATCCTTCCCGAAGGTCTTATAGATGGCCCGAAGGACTTATCATCTTGCTCGAAAGA
CTTACAGATGACCCGAAGGATTTAAGCATCATGCTCCAAAAACTTACTGATGGCCCAAAGGACTT
ACCAATTTTGGAAATAGTTTACTACATAAGAAACTTTTCTTACTTTTAAAAAATTTCAATTTTCA
GATTTAAATGAAAAACTTTCTCATTTTTCGAGACACA
Found at i:158982 original size:202 final size:203
Alignment explanation
Indices: 158626--159031 Score: 586
Period size: 202 Copynumber: 2.0 Consensus size: 203
158616 CCGAAGGACT
* * *
158626 TACCAATTTTGGAAATAGTTTACTAGGTAAGAAACTTTTCTTACTTTTCAAAAATTTTAATTTTC
1 TACCAATTTTGGAAATAGTTTACTAGGTAAGAAACTTTTCTAACTTTTAAAAAATTTCAATTTTC
* * *
158691 AGATTTAAATGAGAAACTTTTCTCATTTTTTGAGAGACATGTAAAAACATCCTGTCCAAAGGTCT
66 AGATTTAAATGAGAAACTTTTCTCATTTTTCGAGAGACATATAAAAACATCCTGTCCAAAAGTCT
* * * * *
158756 TGTGGATTCCCCGAAGGACTTATCATCTT-CGTCGAAAGACTTACAGATGA-TCTGAAGGATTTA
131 TGTAGATGCCCCAAAGGACTTATCATCTTGC-TCGAAAGACTTACAAATGACCCT-AAGGATTTA
158819 AACATCATGC
194 AACATCATGC
*
158829 TACCATTTTTGGAAATAGTTTACTAGGTAAGAAAC-TTTCTAACTTTTAAAAAATTTCAATTTTC
1 TACCAATTTTGGAAATAGTTTACTAGGTAAGAAACTTTTCTAACTTTTAAAAAATTTCAATTTTC
* * *
158893 AGATTTAAGTGAGAAACTTTTCTCATTTTTCGAGAGACATATGAAAACATTCTG-CCAAAAAGTC
66 AGATTTAAATGAGAAACTTTTCTCATTTTTCGAGAGACATATAAAAACATCCTGTCC-AAAAGTC
* * *
158957 TTGTAGATGGCCCAAAGGGCTTATCATCTTGCTCGAAAGACTTATAAATGACCCTAAGGATTTAA
130 TTGTAGATGCCCCAAAGGACTTATCATCTTGCTCGAAAGACTTACAAATGACCCTAAGGATTTAA
*
159022 GCATCATGC
195 ACATCATGC
159031 T
1 T
159032 CGAAAGAATT
Statistics
Matches: 181, Mismatches: 19, Indels: 7
0.87 0.09 0.03
Matches are distributed among these distances:
201 2 0.01
202 142 0.78
203 37 0.20
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.35
Consensus pattern (203 bp):
TACCAATTTTGGAAATAGTTTACTAGGTAAGAAACTTTTCTAACTTTTAAAAAATTTCAATTTTC
AGATTTAAATGAGAAACTTTTCTCATTTTTCGAGAGACATATAAAAACATCCTGTCCAAAAGTCT
TGTAGATGCCCCAAAGGACTTATCATCTTGCTCGAAAGACTTACAAATGACCCTAAGGATTTAAA
CATCATGC
Found at i:165792 original size:18 final size:18
Alignment explanation
Indices: 165769--165803 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
165759 ACTGTATATT
165769 TGTCCCAAAGGACCACTA
1 TGTCCCAAAGGACCACTA
*
165787 TGTCCCGAAGGACCACT
1 TGTCCCAAAGGACCACT
165804 CCTTAAAAAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.29, C:0.34, G:0.20, T:0.17
Consensus pattern (18 bp):
TGTCCCAAAGGACCACTA
Found at i:170269 original size:16 final size:16
Alignment explanation
Indices: 170248--170295 Score: 89
Period size: 16 Copynumber: 3.1 Consensus size: 16
170238 CTTTAACATT
170248 TCATATATGTTTACTA
1 TCATATATGTTTACTA
170264 TCATATATGTTTACTA
1 TCATATATGTTTACTA
170280 TCATATATGTTT-CTA
1 TCATATATGTTTACTA
170295 T
1 T
170296 TTACATTTCA
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
15 4 0.12
16 28 0.88
ACGTcount: A:0.29, C:0.12, G:0.06, T:0.52
Consensus pattern (16 bp):
TCATATATGTTTACTA
Found at i:170656 original size:2 final size:2
Alignment explanation
Indices: 170649--170706 Score: 116
Period size: 2 Copynumber: 29.0 Consensus size: 2
170639 TATCTATGTG
170649 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
170691 TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA
170707 GCGTTCACTA
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 56 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:180512 original size:19 final size:19
Alignment explanation
Indices: 180490--180624 Score: 96
Period size: 19 Copynumber: 7.1 Consensus size: 19
180480 AAAATTAAAG
*
180490 TGCAACCCATATTTTAGGT
1 TGCAACACATATTTTAGGT
* * *
180509 TGCAAGATAGATTTTA-GT
1 TGCAACACATATTTTAGGT
* * *
180527 GTGCAACCCATATTTTTGGG
1 -TGCAACACATATTTTAGGT
* *
180547 TGCAAGACAAATTTTA-GT
1 TGCAACACATATTTTAGGT
*
180565 GTGCATCACATATTTTAGGT
1 -TGCAACACATATTTTAGGT
* *
180585 TGCAAGACAGATTTTA-GT
1 TGCAACACATATTTTAGGT
* *
180603 ATGCAACTCATAATTTAGGT
1 -TGCAACACATATTTTAGGT
180623 TG
1 TG
180625 AAACTTGAAT
Statistics
Matches: 85, Mismatches: 25, Indels: 12
0.70 0.20 0.10
Matches are distributed among these distances:
18 5 0.06
19 75 0.88
20 5 0.06
ACGTcount: A:0.30, C:0.14, G:0.20, T:0.36
Consensus pattern (19 bp):
TGCAACACATATTTTAGGT
Found at i:180540 original size:38 final size:38
Alignment explanation
Indices: 180489--180624 Score: 191
Period size: 38 Copynumber: 3.6 Consensus size: 38
180479 TAAAATTAAA
*
180489 GTGCAACCCATATTTTAGGTTGCAAGATAGATTTTAGT
1 GTGCAACCCATATTTTAGGTTGCAAGACAGATTTTAGT
* * *
180527 GTGCAACCCATATTTTTGGGTGCAAGACAAATTTTAGT
1 GTGCAACCCATATTTTAGGTTGCAAGACAGATTTTAGT
* *
180565 GTGCATCACATATTTTAGGTTGCAAGACAGATTTTAGT
1 GTGCAACCCATATTTTAGGTTGCAAGACAGATTTTAGT
* * *
180603 ATGCAACTCATAATTTAGGTTG
1 GTGCAACCCATATTTTAGGTTG
180625 AAACTTGAAT
Statistics
Matches: 85, Mismatches: 13, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
38 85 1.00
ACGTcount: A:0.29, C:0.14, G:0.21, T:0.36
Consensus pattern (38 bp):
GTGCAACCCATATTTTAGGTTGCAAGACAGATTTTAGT
Found at i:180855 original size:40 final size:40
Alignment explanation
Indices: 180694--181016 Score: 176
Period size: 40 Copynumber: 8.2 Consensus size: 40
180684 GTAAGTTGTA
* * * * * *
180694 ATGTATCGTATGGGGTACA-ACATTAATATGAGAGCGCTG
1 ATGTATCATATGAGGTACACACCTAAATATGAAAGCGGTG
* * * * *
180733 ATGTATCATA-CAGGTGCACACCTATAT-TGAGAGCGGTA
1 ATGTATCATATGAGGTACACACCTAAATATGAAAGCGGTG
* ** * * * * *
180771 AGGTATTGTATGGGGTACACACCAAAAAATTAAAGTGGTG
1 ATGTATCATATGAGGTACACACCTAAATATGAAAGCGGTG
* *
180811 ATGTATCATATGAGGTATACACCTAAATATGAAAGCGGTA
1 ATGTATCATATGAGGTACACACCTAAATATGAAAGCGGTG
* * * *
180851 ATGTATCGTACATGA--TACACATCTAATTATGAGAA-CAGTG
1 ATGTATC--ATATGAGGTACACACCTAAATATGA-AAGCGGTG
* * * *
180891 ATGTATCGTATGTGGTACATACCTAAATATGAAATCGGTG
1 ATGTATCATATGAGGTACACACCTAAATATGAAAGCGGTG
* * * * *
180931 ATGTATCGTACTG-GGTGCACATCTCAATATGAAAGTGGTG
1 ATGTATCATA-TGAGGTACACACCTAAATATGAAAGCGGTG
** * * * * *
180971 ACATATCCTACG-GAGTACACACTTAAATAAGAAAGTGGTG
1 ATGTATCATATGAG-GTACACACCTAAATATGAAAGCGGTG
181011 ATGTAT
1 ATGTAT
181017 TGTACGGGAT
Statistics
Matches: 211, Mismatches: 62, Indels: 21
0.72 0.21 0.07
Matches are distributed among these distances:
38 24 0.11
39 29 0.14
40 149 0.71
41 4 0.02
42 5 0.02
ACGTcount: A:0.35, C:0.14, G:0.23, T:0.28
Consensus pattern (40 bp):
ATGTATCATATGAGGTACACACCTAAATATGAAAGCGGTG
Found at i:180952 original size:80 final size:80
Alignment explanation
Indices: 180808--180962 Score: 206
Period size: 80 Copynumber: 1.9 Consensus size: 80
180798 AATTAAAGTG
*
180808 GTGATGTATCATATGAGGTATACACCTAAATATGAAAGCGGTAATGTATCGTACATGATACACAT
1 GTGATGTATCATATGAGGTACACACCTAAATATGAAAGCGGTAATGTATCGTACATGATACACAT
180873 CT-AATTATGAGAACA
66 CTCAA-TATGAGAACA
* * * * * * *
180888 GTGATGTATCGTATGTGGTACATACCTAAATATGAAATCGGTGATGTATCGTAC-TGGGTGCACA
1 GTGATGTATCATATGAGGTACACACCTAAATATGAAAGCGGTAATGTATCGTACAT-GATACACA
180952 TCTCAATATGA
65 TCTCAATATGA
180963 AAGTGGTGAC
Statistics
Matches: 65, Mismatches: 8, Indels: 4
0.84 0.10 0.05
Matches are distributed among these distances:
79 1 0.02
80 62 0.95
81 2 0.03
ACGTcount: A:0.34, C:0.14, G:0.21, T:0.30
Consensus pattern (80 bp):
GTGATGTATCATATGAGGTACACACCTAAATATGAAAGCGGTAATGTATCGTACATGATACACAT
CTCAATATGAGAACA
Found at i:187597 original size:9 final size:9
Alignment explanation
Indices: 187581--187625 Score: 56
Period size: 9 Copynumber: 5.1 Consensus size: 9
187571 ATTTTTCCTT
187581 TTTATATTA
1 TTTATATTA
*
187590 TATATATT-
1 TTTATATTA
*
187598 TTTATACTA
1 TTTATATTA
*
187607 TTAATATTA
1 TTTATATTA
187616 TTTATATTA
1 TTTATATTA
187625 T
1 T
187626 GTTTATACGT
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
8 6 0.21
9 23 0.79
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (9 bp):
TTTATATTA
Found at i:187601 original size:17 final size:17
Alignment explanation
Indices: 187579--187625 Score: 60
Period size: 17 Copynumber: 2.7 Consensus size: 17
187569 TCATTTTTCC
187579 TTTTTATATTA-TATATA
1 TTTTTATATTATTA-ATA
*
187596 TTTTTATACTATTAATA
1 TTTTTATATTATTAATA
187613 TTATTTATATTAT
1 TT-TTTATATTAT
187626 GTTTATACGT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
17 15 0.58
18 11 0.42
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (17 bp):
TTTTTATATTATTAATA
Found at i:187718 original size:2 final size:2
Alignment explanation
Indices: 187713--187740 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
187703 TTTAAATCTT
187713 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
187741 CATTCTTTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:187760 original size:35 final size:35
Alignment explanation
Indices: 187681--187760 Score: 90
Period size: 35 Copynumber: 2.3 Consensus size: 35
187671 TTCTTCTTAC
* *
187681 ATTTTAATATATAAATATATACTTTAAATCTTTAT
1 ATTTTTATATATAAATATATACTATAAATCTTTAT
* * * *
187716 ATATATATATATATATATATA-TATACATTCTTTAT
1 ATTTTTATATATAAATATATACTATA-AATCTTTAT
187751 ATTTTTATAT
1 ATTTTTATAT
187761 TTTATTAATT
Statistics
Matches: 36, Mismatches: 8, Indels: 2
0.78 0.17 0.04
Matches are distributed among these distances:
34 3 0.08
35 33 0.92
ACGTcount: A:0.41, C:0.05, G:0.00, T:0.54
Consensus pattern (35 bp):
ATTTTTATATATAAATATATACTATAAATCTTTAT
Found at i:188077 original size:61 final size:61
Alignment explanation
Indices: 187985--188118 Score: 164
Period size: 61 Copynumber: 2.2 Consensus size: 61
187975 TTAATTTTTG
* * * * *
187985 TTAATATTTTTAAGTTTTTTCAAGCACTTTTAATTTATTAAATTATT-TTTTTATTTTA-TCT
1 TTAATA-TTTTAAGTTCTCTCAAACACTTTTAATTTATTAAA-TATTATTTTAATTTAATTCT
* *
188046 TTAATATTTTAATGTTCTCTCAAACATTTTTAATTTATTAAATATTATTTTAATTTAATTTT
1 TTAATATTTTAA-GTTCTCTCAAACACTTTTAATTTATTAAATATTATTTTAATTTAATTCT
188108 TTAATATTTTA
1 TTAATATTTTA
188119 TAATTATTCT
Statistics
Matches: 63, Mismatches: 7, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
60 10 0.16
61 40 0.63
62 13 0.21
ACGTcount: A:0.31, C:0.06, G:0.02, T:0.60
Consensus pattern (61 bp):
TTAATATTTTAAGTTCTCTCAAACACTTTTAATTTATTAAATATTATTTTAATTTAATTCT
Found at i:188106 original size:25 final size:23
Alignment explanation
Indices: 188074--188123 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 23
188064 CTCAAACATT
*
188074 TTTAATTTATTAAATATTATTTTAA
1 TTTAATTT-TTAAATATT-TTATAA
*
188099 TTTAATTTTTTAATATTTTATAA
1 TTTAATTTTTAAATATTTTATAA
188122 TT
1 TT
188124 ATTCTCAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 7 0.30
24 8 0.35
25 8 0.35
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (23 bp):
TTTAATTTTTAAATATTTTATAA
Found at i:188344 original size:37 final size:37
Alignment explanation
Indices: 188303--188414 Score: 188
Period size: 37 Copynumber: 3.0 Consensus size: 37
188293 AACATAGTGT
188303 TAGAGTTTTACTAGGATTCAAACTCCTAAAAATAGGA
1 TAGAGTTTTACTAGGATTCAAACTCCTAAAAATAGGA
*
188340 TAGAGTTTTACTAGGATTCAAACTCCTAAAAATATGA
1 TAGAGTTTTACTAGGATTCAAACTCCTAAAAATAGGA
* * *
188377 TAGAATTCTACTATGATTCAAACTCCTAAAAATAGGA
1 TAGAGTTTTACTAGGATTCAAACTCCTAAAAATAGGA
188414 T
1 T
188415 CCACAAGCGT
Statistics
Matches: 70, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
37 70 1.00
ACGTcount: A:0.41, C:0.14, G:0.13, T:0.31
Consensus pattern (37 bp):
TAGAGTTTTACTAGGATTCAAACTCCTAAAAATAGGA
Found at i:189041 original size:50 final size:47
Alignment explanation
Indices: 188933--189043 Score: 118
Period size: 48 Copynumber: 2.3 Consensus size: 47
188923 TTAGTATATA
*
188933 TTTTTATTTTTTAGATTACATATATATATATATATGTTATTTTTTAT
1 TTTTTATTTATTAGATTACATATATATATATATATGTTATTTTTTAT
* * *
188980 TATATGT-TTTATTA-ATTTATATATATATATATATATTTACTATTTTTTAT
1 T-T-TTTATTTATTAGA-TTACATATATATATATATATGT--TATTTTTTAT
189030 GTTTTTATTTATTA
1 -TTTTTATTTATTA
189044 TATATTTATT
Statistics
Matches: 52, Mismatches: 5, Indels: 11
0.76 0.07 0.16
Matches are distributed among these distances:
47 2 0.04
48 27 0.52
49 4 0.08
50 18 0.35
51 1 0.02
ACGTcount: A:0.31, C:0.02, G:0.04, T:0.64
Consensus pattern (47 bp):
TTTTTATTTATTAGATTACATATATATATATATATGTTATTTTTTAT
Found at i:189042 original size:4 final size:4
Alignment explanation
Indices: 188969--189135 Score: 57
Period size: 4 Copynumber: 42.5 Consensus size: 4
188959 TATATATATG
* * * * * *
188969 TTAT TT-T TTAT TATAT GT-T TTAT TAAT TTAT ATAT ATAT ATAT ATAT
1 TTAT TTAT TTAT T-TAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT
* * *
189016 TTA- CTAT TT-T TTAT GTT-T TTAT TTA- TTAT ATAT TTAT TATTT TTACT
1 TTAT TTAT TTAT TTAT -TTAT TTAT TTAT TTAT TTAT TTAT T-TAT TTA-T
* * * * *
189063 TT-T TTA- TTA- TTATT TTAT TTAT ATA- TTGT TTCT TCTTT TTCT TTAT
1 TTAT TTAT TTAT TTA-T TTAT TTAT TTAT TTAT TTAT T-TAT TTAT TTAT
* *
189109 TTTT TATAT TTTT TTAT TTAT TTAT TT
1 TTAT T-TAT TTAT TTAT TTAT TTAT TT
189136 TACTTACTAT
Statistics
Matches: 124, Mismatches: 23, Indels: 32
0.69 0.13 0.18
Matches are distributed among these distances:
3 25 0.20
4 79 0.64
5 20 0.16
ACGTcount: A:0.24, C:0.03, G:0.02, T:0.71
Consensus pattern (4 bp):
TTAT
Found at i:189046 original size:33 final size:31
Alignment explanation
Indices: 189009--189075 Score: 91
Period size: 33 Copynumber: 2.1 Consensus size: 31
188999 TATATATATA
189009 TATATATTTACTATTTTTTA-TGTTTTTATTTAT
1 TATATATTTACTA-TTTTTACT-TTTTTA-TTAT
*
189042 TATATATTTATTATTTTTACTTTTTTATTAT
1 TATATATTTACTATTTTTACTTTTTTATTAT
189073 TAT
1 TAT
189076 TTTATTTATA
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
31 7 0.22
32 12 0.38
33 13 0.41
ACGTcount: A:0.25, C:0.03, G:0.01, T:0.70
Consensus pattern (31 bp):
TATATATTTACTATTTTTACTTTTTTATTAT
Found at i:189069 original size:14 final size:15
Alignment explanation
Indices: 189033--189089 Score: 57
Period size: 14 Copynumber: 3.9 Consensus size: 15
189023 TTTTTATGTT
189033 TTTATTTATTATATA-
1 TTTATTTATTAT-TAC
*
189048 TTTA-TTATTTTTAC
1 TTTATTTATTATTAC
*
189062 TTT-TTTATTATTAT
1 TTTATTTATTATTAC
189076 TTTATTTATATATT
1 TTTATTTAT-TATT
189090 GTTTCTTCTT
Statistics
Matches: 35, Mismatches: 3, Indels: 7
0.78 0.07 0.16
Matches are distributed among these distances:
13 2 0.06
14 20 0.57
15 9 0.26
16 4 0.11
ACGTcount: A:0.26, C:0.02, G:0.00, T:0.72
Consensus pattern (15 bp):
TTTATTTATTATTAC
Found at i:189102 original size:43 final size:41
Alignment explanation
Indices: 188986--189134 Score: 109
Period size: 43 Copynumber: 3.7 Consensus size: 41
188976 TTATTATATG
* * * * *
188986 TTTTATTAATTTATATA-TA-TATATA-TATATTTACTATT
1 TTTTATTATTTTATTTATTATTATTTATTATTTTTACTTTT
189024 TTTTATGT-TTTTATTTATTATATATTTATTATTTTTACTTTT
1 TTTTAT-TATTTTATTTATTAT-TATTTATTATTTTTACTTTT
* * *
189066 TTATTATTATTTTATTTATATATTGTTTCTTCTTTTT-CTTTAT
1 TT-TTATTATTTTATTTAT-TATTATTTATTATTTTTACTTT-T
189109 TTTT-TATATTTT-TTTA-T-TTATTTATT
1 TTTTAT-TATTTTATTTATTATTATTTATT
189135 TTACTTACTA
Statistics
Matches: 91, Mismatches: 10, Indels: 20
0.75 0.08 0.17
Matches are distributed among these distances:
38 20 0.22
39 4 0.04
41 10 0.11
42 26 0.29
43 28 0.31
44 3 0.03
ACGTcount: A:0.24, C:0.03, G:0.01, T:0.71
Consensus pattern (41 bp):
TTTTATTATTTTATTTATTATTATTTATTATTTTTACTTTT
Found at i:189164 original size:57 final size:56
Alignment explanation
Indices: 189048--189174 Score: 136
Period size: 56 Copynumber: 2.2 Consensus size: 56
189038 TTATTATATA
* *
189048 TTTATTATTTTTACTTTTTTATTATTATTTTATTTATATATTGTTTCTTCTTTTTC
1 TTTATTATTTTTACTTTTTTATTATTATTTTACTTATATATTGTATCTTCTTTTTC
*
189104 TTTATT-TTTTATATTTTTTTATTTATTTATTTTACTTACTAT-TT-TATCTT-TTCTTTC
1 TTTATTATTTT-TACTTTTTTA-TTA-TTATTTTACTTA-TATATTGTATCTTCTT-TTTC
189161 TTTATCTTATTTTT
1 TTTA--TTATTTTT
189175 TGTTTAATTT
Statistics
Matches: 60, Mismatches: 3, Indels: 13
0.79 0.04 0.17
Matches are distributed among these distances:
55 4 0.07
56 17 0.28
57 16 0.27
58 13 0.22
59 6 0.10
60 4 0.07
ACGTcount: A:0.17, C:0.08, G:0.01, T:0.74
Consensus pattern (56 bp):
TTTATTATTTTTACTTTTTTATTATTATTTTACTTATATATTGTATCTTCTTTTTC
Found at i:193587 original size:116 final size:116
Alignment explanation
Indices: 193245--193595 Score: 465
Period size: 116 Copynumber: 3.0 Consensus size: 116
193235 GCAACTTACA
* *
193245 ATTGGATTTCAACTTCACGACGAAGGATATCCAATTCCAAGGCTCAACTTCACAAC-AGAGGGGT
1 ATTGGATTTCAACTTCACAACGAATGATATCCAATT-CAAGGCTCAACTTCACAACGA-AGGGGT
* * * **
193309 CATCCACAGTTTCAACTTCATGACGAAGGAAATCGTGCTCTAAAAAAACATTC
64 CATCCACAGTTTCAACTTCACGACGAAGGGAATCGTGCTCTACAGCAACATTC
* * *
193362 ATTGGATTTCAATTTCACAACGAATGATATCCAATTCAAGGCTCAACATCACAACGAAGGGGCCA
1 ATTGGATTTCAACTTCACAACGAATGATATCCAATTCAAGGCTCAACTTCACAACGAAGGGGTCA
* * *
193427 TCCACAGTTTCAACTTCACGACAAAGGGAATCATGCTCTACAGCAATATTC
66 TCCACAGTTTCAACTTCACGACGAAGGGAATCGTGCTCTACAGCAACATTC
* * * *
193478 ATTGGATTTTAACTTCATC-ATGAATGATATTCAATTCAAGGCTTAACTTCACAACGAAGGGGTC
1 ATTGGATTTCAACTTCA-CAACGAATGATATCCAATTCAAGGCTCAACTTCACAACGAAGGGGTC
* * *
193542 ATCCACGGTTTCAACTTCACGACGAAGGGAATCGTAC-CCACCAGCAACATTC
65 ATCCACAGTTTCAACTTCACGACGAAGGGAATCGTGCTCTA-CAGCAACATTC
193594 AT
1 AT
193596 CTTCAGGAAC
Statistics
Matches: 205, Mismatches: 26, Indels: 7
0.86 0.11 0.03
Matches are distributed among these distances:
115 2 0.01
116 168 0.82
117 35 0.17
ACGTcount: A:0.34, C:0.24, G:0.17, T:0.25
Consensus pattern (116 bp):
ATTGGATTTCAACTTCACAACGAATGATATCCAATTCAAGGCTCAACTTCACAACGAAGGGGTCA
TCCACAGTTTCAACTTCACGACGAAGGGAATCGTGCTCTACAGCAACATTC
Found at i:193703 original size:37 final size:34
Alignment explanation
Indices: 193657--193796 Score: 154
Period size: 36 Copynumber: 3.9 Consensus size: 34
193647 CACGAGGTCA
* * *
193657 TCTCGCTTGAGACTAATTTACTTAAAACAAAATTTTG
1 TCTCTCTTGAGAC-AGTTT-CTTGAAAC-AAATTTTG
*
193694 TCTCTCTTGAGACAGTTTCTCATGAAACAAATTTTT
1 TCTCTCTTGAGACAGTTTCT--TGAAACAAATTTTG
193730 TCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTTG
1 TCTCTCTTGAGACAGTTT--CTTGAAACAAATTTTG
*
193766 TCTCTTTTGAGACAGTTTCCCTTGAAACAAA
1 TCTCTCTTGAGACAGTTT--CTTGAAACAAA
193797 ATCTTTGAAT
Statistics
Matches: 93, Mismatches: 6, Indels: 9
0.86 0.06 0.08
Matches are distributed among these distances:
35 2 0.02
36 72 0.77
37 17 0.18
38 2 0.02
ACGTcount: A:0.29, C:0.20, G:0.12, T:0.39
Consensus pattern (34 bp):
TCTCTCTTGAGACAGTTTCTTGAAACAAATTTTG
Found at i:193734 original size:36 final size:36
Alignment explanation
Indices: 193681--193796 Score: 187
Period size: 36 Copynumber: 3.2 Consensus size: 36
193671 AATTTACTTA
* *
193681 AAACAAAATTTTGTCTCTCTTGAGACAGTTTCTCATG
1 AAAC-AAATTTTGTCTCTCTTGAGACAGTTTCCCTTG
*
193718 AAACAAATTTTTTCTCTCTTGAGACAGTTTCCCTTG
1 AAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTG
*
193754 AAACAAATTTTGTCTCTTTTGAGACAGTTTCCCTTG
1 AAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTG
193790 AAACAAA
1 AAACAAA
193797 ATCTTTGAAT
Statistics
Matches: 74, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
36 70 0.95
37 4 0.05
ACGTcount: A:0.30, C:0.20, G:0.12, T:0.38
Consensus pattern (36 bp):
AAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTG
Found at i:193880 original size:37 final size:36
Alignment explanation
Indices: 193816--193930 Score: 140
Period size: 36 Copynumber: 3.2 Consensus size: 36
193806 TTTGTTTTCC
* * *
193816 TTGAAACAAATTTTGTCTCCCTCGAGACAGTTTCTT
1 TTGAAAAAAATTTTGTCTCTCTTGAGACAGTTTCTT
** *
193852 TTAGAACTAAGTTTTGTCTCTCTTGAGACAGTTTCTT
1 TT-GAAAAAAATTTTGTCTCTCTTGAGACAGTTTCTT
* * *
193889 TTGAAAAAAAATTTGTCCCTCTTGAGACAGTTTCTC
1 TTGAAAAAAATTTTGTCTCTCTTGAGACAGTTTCTT
193925 TTGAAA
1 TTGAAA
193931 CACAAAAAAA
Statistics
Matches: 67, Mismatches: 11, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
36 36 0.54
37 31 0.46
ACGTcount: A:0.27, C:0.18, G:0.15, T:0.40
Consensus pattern (36 bp):
TTGAAAAAAATTTTGTCTCTCTTGAGACAGTTTCTT
Found at i:193893 original size:102 final size:101
Alignment explanation
Indices: 193716--193900 Score: 255
Period size: 102 Copynumber: 1.8 Consensus size: 101
193706 CAGTTTCTCA
* * * *
193716 TGAAACAAATTTTTTCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCTTTTGAGACAG
1 TGAAACAAATTTTGTCTCCCTCGAGACAGTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAG
*
193781 TTTCCCTTGAAACAAAATCTTTGAATTTGTTTTCCT
66 TTTCCCTTGAAAAAAAATCTTTGAATTTGTTTTCCT
* * *
193817 TGAAACAAATTTTGTCTCCCTCGAGACAGTTT-CTTTTAGAACTAAGTTTTGTCTCTCTTGAGAC
1 TGAAACAAATTTTGTCTCCCTCGAGACAGTTTCCCTTGA-AAC-AAATTTTGTCTCTCTTGAGAC
**
193881 AGTTTCTTTTGAAAAAAAAT
64 AGTTTCCCTTGAAAAAAAAT
193901 TTGTCCCTCT
Statistics
Matches: 72, Mismatches: 10, Indels: 3
0.85 0.12 0.04
Matches are distributed among these distances:
100 4 0.06
101 32 0.44
102 36 0.50
ACGTcount: A:0.28, C:0.18, G:0.13, T:0.41
Consensus pattern (101 bp):
TGAAACAAATTTTGTCTCCCTCGAGACAGTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAG
TTTCCCTTGAAAAAAAATCTTTGAATTTGTTTTCCT
Found at i:193904 original size:138 final size:138
Alignment explanation
Indices: 193681--193932 Score: 355
Period size: 138 Copynumber: 1.8 Consensus size: 138
193671 AATTTACTTA
* * *
193681 AAACAAAATTTTGTCTCTCTTGAGACAGTTTCTCATGAAACAAATTTTTTCTCTCTTGAGACAGT
1 AAACAAAATTTTGTCTCCCTCGAGACAGTTTCTCATGAAACAAATTTTGTCTCTCTTGAGACAGT
* * * *
193746 TTCCCTTGAAACAAATTTTGTCTCTTTTGAGACAGTTTCCCTTGAAACAAAATCTTTGAATTTGT
66 TTCCCTTGAAAAAAAATTTGTCCCTCTTGAGACAGTTTCCCTTGAAACAAAATCTTTGAATTTGT
193811 TTTCCTTG
131 TTTCCTTG
* * *
193819 AAAC-AAATTTTGTCTCCCTCGAGACAGTTTCT-TTTAGAACTAAGTTTTGTCTCTCTTGAGACA
1 AAACAAAATTTTGTCTCCCTCGAGACAGTTTCTCATGA-AAC-AAATTTTGTCTCTCTTGAGACA
** *
193882 GTTTCTTTTGAAAAAAAATTTGTCCCTCTTGAGACAGTTTCTCTTGAAACA
64 GTTTCCCTTGAAAAAAAATTTGTCCCTCTTGAGACAGTTTCCCTTGAAACA
193933 CAAAAAAAAA
Statistics
Matches: 99, Mismatches: 13, Indels: 4
0.85 0.11 0.03
Matches are distributed among these distances:
136 2 0.02
137 29 0.29
138 68 0.69
ACGTcount: A:0.28, C:0.19, G:0.13, T:0.40
Consensus pattern (138 bp):
AAACAAAATTTTGTCTCCCTCGAGACAGTTTCTCATGAAACAAATTTTGTCTCTCTTGAGACAGT
TTCCCTTGAAAAAAAATTTGTCCCTCTTGAGACAGTTTCCCTTGAAACAAAATCTTTGAATTTGT
TTTCCTTG
Found at i:193978 original size:29 final size:30
Alignment explanation
Indices: 193934--193992 Score: 84
Period size: 29 Copynumber: 2.0 Consensus size: 30
193924 CTTGAAACAC
* *
193934 AAAAAAAAACCTTGAAATTGTTTCTCTTGAG
1 AAAAAAAAA-CTTGAAAATATTTCTCTTGAG
193965 AAAAAAAAA-TTGAAAATATTTCTCTTGA
1 AAAAAAAAACTTGAAAATATTTCTCTTGA
193993 AACACAAAGC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
29 17 0.65
31 9 0.35
ACGTcount: A:0.47, C:0.10, G:0.10, T:0.32
Consensus pattern (30 bp):
AAAAAAAAACTTGAAAATATTTCTCTTGAG
Found at i:194135 original size:83 final size:84
Alignment explanation
Indices: 193996--194251 Score: 279
Period size: 83 Copynumber: 3.1 Consensus size: 84
193986 CTCTTGAAAC
* * *
193996 ACAAAG-CCTTCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTGCAGCATAACTCAAGG
1 ACAAAGACCTTCGAGTTCGACTACACTCAGCTTCCAAGGCACATCATTTGCAGCATAACTCAAGG
* *
194060 CTAGAAGGGTTATCTGTCA
66 CAAGAAGGGTTATCAGTCA
* * *
194079 ACAAAGACCTTCGAGTTTGACTACGCTCAGC-TCCAAGGCACATCATTTGCAGCATAACTTAAGG
1 ACAAAGACCTTCGAGTTCGACTACACTCAGCTTCCAAGGCACATCATTTGCAGCATAACTCAAGG
194143 CAAGAAGGGTTATCAGTCA
66 CAAGAAGGGTTATCAGTCA
* * * * * * *
194162 TCAAAGACCTTCGAGTTCGATTACATTCAAC-T-CAGAGGCA-AGTCAAATTTACAGCATAGCTT
1 ACAAAGACCTTCGAGTTCGACTACACTCAGCTTCCA-AGGCACA-TC--ATTTGCAGCATAACTC
* * *
194224 AAGGCAAGAAGGGCTATCTGCCA
62 AAGGCAAGAAGGGTTATCAGTCA
194247 ACAAA
1 ACAAA
194252 ATTATCGAGT
Statistics
Matches: 148, Mismatches: 20, Indels: 8
0.84 0.11 0.05
Matches are distributed among these distances:
82 3 0.02
83 86 0.58
84 21 0.14
85 38 0.26
ACGTcount: A:0.33, C:0.23, G:0.20, T:0.23
Consensus pattern (84 bp):
ACAAAGACCTTCGAGTTCGACTACACTCAGCTTCCAAGGCACATCATTTGCAGCATAACTCAAGG
CAAGAAGGGTTATCAGTCA
Found at i:194789 original size:21 final size:21
Alignment explanation
Indices: 194763--194826 Score: 57
Period size: 21 Copynumber: 3.3 Consensus size: 21
194753 AGAGTTTTAC
194763 TAGGATTCAAACTCCTAAAAA
1 TAGGATTCAAACTCCTAAAAA
* ** *
194784 TAGGA-T-AAAGT--T-TTAC
1 TAGGATTCAAACTCCTAAAAA
194800 TAGGATTCAAACTCCTAAAAA
1 TAGGATTCAAACTCCTAAAAA
194821 TAGGAT
1 TAGGAT
194827 AGAGTTCTAC
Statistics
Matches: 30, Mismatches: 8, Indels: 10
0.62 0.17 0.21
Matches are distributed among these distances:
16 6 0.20
17 2 0.07
18 4 0.13
19 4 0.13
20 2 0.07
21 12 0.40
ACGTcount: A:0.44, C:0.14, G:0.14, T:0.28
Consensus pattern (21 bp):
TAGGATTCAAACTCCTAAAAA
Found at i:194805 original size:37 final size:37
Alignment explanation
Indices: 194755--194863 Score: 182
Period size: 37 Copynumber: 2.9 Consensus size: 37
194745 ATAGCGTTAG
194755 AGTTTTACTAGGATTCAAACTCCTAAAAATAGGATAA
1 AGTTTTACTAGGATTCAAACTCCTAAAAATAGGATAA
*
194792 AGTTTTACTAGGATTCAAACTCCTAAAAATAGGATAG
1 AGTTTTACTAGGATTCAAACTCCTAAAAATAGGATAA
* * *
194829 AGTTCTACTATGATTCAAACTCTTAAAAATAGGAT
1 AGTTTTACTAGGATTCAAACTCCTAAAAATAGGAT
194864 CCACAAGCGT
Statistics
Matches: 68, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 68 1.00
ACGTcount: A:0.41, C:0.14, G:0.14, T:0.31
Consensus pattern (37 bp):
AGTTTTACTAGGATTCAAACTCCTAAAAATAGGATAA
Found at i:195474 original size:2 final size:2
Alignment explanation
Indices: 195467--195537 Score: 63
Period size: 2 Copynumber: 35.5 Consensus size: 2
195457 TTTATTAATT
* * * * * * *
195467 TA TA TA TA TA TA TA TA TA TT TA CTA T- TT TT TA TG TT TT TA TT
1 TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA
195509 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
195538 TATTTTTTTC
Statistics
Matches: 59, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
1 1 0.02
2 56 0.95
3 2 0.03
ACGTcount: A:0.38, C:0.01, G:0.01, T:0.59
Consensus pattern (2 bp):
TA
Found at i:195481 original size:50 final size:48
Alignment explanation
Indices: 195416--195609 Score: 156
Period size: 48 Copynumber: 4.0 Consensus size: 48
195406 TTTTTTTAGA
195416 TTATATATATATATATATATGTGTTATTTTTTATTATCTGTTTTA-TTA-AT
1 TTATATATATATATATATAT-T-TTATTTTTT-TTATCT-TTTTATTTATAT
* *
195466 TTATATATATATATATATA-TTTACTATTTTTTATGTTTTTATTTATAT
1 TTATATATATATATATATATTTTA-TTTTTTTTATCTTTTTATTTATAT
* *
195514 ATATATATATATATATATA-TATATTATTTTTT-TCTTTTT-TATTATTAT
1 TTATATATATATATATATATTTTATT-TTTTTTATCTTTTTAT-TTA-TAT
* * * *
195562 TT-TATTTATATAT-TTTCTTCTTCTTTTTCTTTAT-TTTTTA-TTATAT
1 TTATATATATATATATATATT-TTATTTTT-TTTATCTTTTTATTTATAT
195608 TT
1 TT
195610 TTATTTATTT
Statistics
Matches: 121, Mismatches: 12, Indels: 26
0.76 0.08 0.16
Matches are distributed among these distances:
46 13 0.11
47 38 0.31
48 50 0.41
49 1 0.01
50 19 0.16
ACGTcount: A:0.28, C:0.04, G:0.02, T:0.66
Consensus pattern (48 bp):
TTATATATATATATATATATTTTATTTTTTTTATCTTTTTATTTATAT
Found at i:195586 original size:37 final size:34
Alignment explanation
Indices: 195531--195611 Score: 94
Period size: 37 Copynumber: 2.3 Consensus size: 34
195521 TATATATATA
*
195531 TATATATTATTTTTTTCTTTTT-TATTATTATTTTATT
1 TATATATT-TTTTCTTCTTTTTCT-TTATT-TTTTA-T
195568 TATATATTTTCTTCTTCTTTTTCTTTATTTTTTAT
1 TATATATTTT-TTCTTCTTTTTCTTTATTTTTTAT
195603 TATAT-TTTT
1 TATATATTTT
195612 ATTTATTTTA
Statistics
Matches: 41, Mismatches: 1, Indels: 7
0.84 0.02 0.14
Matches are distributed among these distances:
34 4 0.10
35 6 0.15
36 7 0.17
37 23 0.56
38 1 0.02
ACGTcount: A:0.19, C:0.06, G:0.00, T:0.75
Consensus pattern (34 bp):
TATATATTTTTTCTTCTTTTTCTTTATTTTTTAT
Found at i:195898 original size:333 final size:331
Alignment explanation
Indices: 195547--196545 Score: 1682
Period size: 333 Copynumber: 3.0 Consensus size: 331
195537 TTATTTTTTT
195547 CTTTTTTATTATTATTTTATTTATATATTTTCTTCTTCTTTTTCTTTATTTTTTATTATATTTTT
1 CTTTTTTATTATTATTTTATTTATATATTTT-TTCTTCTTTTTCTTTATTTTTTATTAT-TTTTT
*
195612 ATTTATTTTACTTACTATTTTATCTTTGCTTTCTTTATCTTATCTTTTATTTAATTTATTTTTTC
64 ATTTATTTTACTTACTATTTTATCTTTGTTTTCTTTATCTTATCTTTTATTTAATTTATTTTTTC
*
195677 TTCATTTTAATTTATTTATTTATTTATTTCTTACCTTTTTATCTAATATGGTTTCTTGACCTTCT
129 TTCATTTTAATTTATTTATTTATTTATTTCTTACCTTTTTATCTAACATGGTTTCTTGACCTTCT
* *
195742 TAAGGGCACACCTTTAAAACTATATAAGGTAAGTAATTGGGATCATATTTTTACCTTTTAATTTT
194 TAAGGGCACACCTTTAAAACTATCTAAGGTAAGTAATTGGGATCGTATTTTTACCTTTTAATTTT
*
195807 AAATTACAATTTTCTTAATTTAAGACAATTGGAAATTGCGTAGTACCGAAAGGGAAGTTCAAGGG
259 AAATTACAATTTTCTTAATTTAAGACAACTGGAAATTGCGTAGTACCGAAAGGGAAGTTCAAGGG
195872 TGCTAACA
324 TGCTAACA
*
195880 CTTTTTTATTATTATTTTATTTATATATTTTTTCTTCTTTTTCTTTATTTCTTTATT-TTTTATA
1 CTTTTTTATTATTATTTTATTTATATATTTTTTCTTCTTTTTCTTTATTT-TTTATTATTTTTTA
*
195944 TTTATTTTACTTACTATTTTATCTTTGTTTTCTTTATCTTATCTTTTATTTTATTTTATTTTTTT
65 TTTATTTTACTTACTATTTTATCTTTGTTTTCTTTATCTTATCTTTTA-TTTAATTTA-TTTTTT
* * * *
196009 CTTCATTTTAATTAATTAATTTTTTTATTTCTTACCTTTTTATCTAACATGGTTTCTTGATCTTC
128 CTTCATTTTAATTTATTTATTTATTTATTTCTTACCTTTTTATCTAACATGGTTTCTTGACCTTC
*
196074 TTAAGAGCACACCTTTAAAACTATCTAAGGTAAGTAATTGGGATCGTATTTTTACCTTTTAATTT
193 TTAAGGGCACACCTTTAAAACTATCTAAGGTAAGTAATTGGGATCGTATTTTTACCTTTTAATTT
* *
196139 TAAATTAAAATTTTCTTAATTTAAGACAACTGG-AATTGCGTAGTACCGAAAGGGCAGTTCAAGG
258 TAAATTACAATTTTCTTAATTTAAGACAACTGGAAATTGCGTAGTACCGAAAGGGAAGTTCAAGG
196203 GTGCTAACA
323 GTGCTAACA
196212 CTTTTTTATTATTATTTTATTTATATATTTTTTCTTCTTTTTCTTTATTTTTTA-TATTTTTATA
1 CTTTTTTATTATTATTTTATTTATATATTTTTTCTTCTTTTTCTTTATTTTTTATTATTTTT-TA
* *
196276 TTTATTTTACTTACTATTTTATCTTTGTTTTCTTTATCTTATCTTTTATTTTATTTGTTTTTTTC
65 TTTATTTTACTTACTATTTTATCTTTGTTTTCTTTATCTTATCTTTTATTTAATTT-ATTTTTTC
196341 TTCATTTTAATTTATTTTTTTATTTATTTATTTCTTACCTTTTTATCTAACATGGTTTCTTGACC
129 TTCATTTTAATTTA----TTTATTTATTTATTTCTTACCTTTTTATCTAACATGGTTTCTTGACC
* * *
196406 TTATTAAAGGCACACCTTTAAAACTATCTAAGGTAAGTAATTGGTATCGTATTTTTACCTTTTAA
190 TTCTTAAGGGCACACCTTTAAAACTATCTAAGGTAAGTAATTGGGATCGTATTTTTACCTTTTAA
* *
196471 TTTTAAATTACAATTTTCTTAATTTAAGACAACTGAAAATTGCGTAGTACCG-AAGGGTAGTTCA
255 TTTTAAATTACAATTTTCTTAATTTAAGACAACTGGAAATTGCGTAGTACCGAAAGGGAAGTTCA
196535 AGGGTGCTAAC
320 AGGGTGCTAAC
196546 CCTTCCTTGA
Statistics
Matches: 626, Mismatches: 29, Indels: 20
0.93 0.04 0.03
Matches are distributed among these distances:
330 1 0.00
331 86 0.14
332 167 0.27
333 196 0.31
335 161 0.26
336 15 0.02
ACGTcount: A:0.25, C:0.12, G:0.08, T:0.55
Consensus pattern (331 bp):
CTTTTTTATTATTATTTTATTTATATATTTTTTCTTCTTTTTCTTTATTTTTTATTATTTTTTAT
TTATTTTACTTACTATTTTATCTTTGTTTTCTTTATCTTATCTTTTATTTAATTTATTTTTTCTT
CATTTTAATTTATTTATTTATTTATTTCTTACCTTTTTATCTAACATGGTTTCTTGACCTTCTTA
AGGGCACACCTTTAAAACTATCTAAGGTAAGTAATTGGGATCGTATTTTTACCTTTTAATTTTAA
ATTACAATTTTCTTAATTTAAGACAACTGGAAATTGCGTAGTACCGAAAGGGAAGTTCAAGGGTG
CTAACA
Done.