Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005756.1 Hibiscus syriacus cultivar Beakdansim tig00013475_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: 172372
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Found at i:7620 original size:25 final size:25
Alignment explanation
Indices: 7592--7639 Score: 87
Period size: 25 Copynumber: 1.9 Consensus size: 25
7582 TAGTTTGACC
*
7592 TTTAAATTTTATATAAAATATTATT
1 TTTAAATTTTAGATAAAATATTATT
7617 TTTAAATTTTAGATAAAATATTA
1 TTTAAATTTTAGATAAAATATTA
7640 ATTTAATCTC
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:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (25 bp):
TTTAAATTTTAGATAAAATATTATT
Found at i:9755 original size:20 final size:20
Alignment explanation
Indices: 9723--9768 Score: 53
Period size: 20 Copynumber: 2.4 Consensus size: 20
9713 TACTATACTG
9723 GAAATT-AATGTTT-GAGTGTT
1 GAAATTGAATGTTTGGA-TG-T
9743 GAAATTGAA-GTTTGGATGT
1 GAAATTGAATGTTTGGATGT
9762 GAAATTG
1 GAAATTG
9769 GATTATTTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
19 8 0.33
20 12 0.50
21 4 0.17
ACGTcount: A:0.33, C:0.00, G:0.28, T:0.39
Consensus pattern (20 bp):
GAAATTGAATGTTTGGATGT
Found at i:11233 original size:59 final size:58
Alignment explanation
Indices: 11161--11350 Score: 248
Period size: 59 Copynumber: 3.3 Consensus size: 58
11151 TAGCAGGCTG
*
11161 CATATTCGGGATTGCACTAAAGTATAACTAGTGCATATGATGGGCACGACCTTATGTGT
1 CATATTCGGGATTGCACTAAAGTATAACTAGTGCATATGGTGGG-ACGACCTTATGTGT
* *
11220 CATATTTGGGATTGCACTAAAGTATAACTAGTGCATATGGTGGG--TA---TATGTGT
1 CATATTCGGGATTGCACTAAAGTATAACTAGTGCATATGGTGGGACGACCTTATGTGT
* * *
11273 CATATTCGGGACTGCACTAAAGTATAGCTAGTGCAGATGGTGGGAACGACCTTATGTGT
1 CATATTCGGGATTGCACTAAAGTATAACTAGTGCATATGGTGGG-ACGACCTTATGTGT
*
11332 CATACTCGGG-TTAGCACTA
1 CATATTCGGGATT-GCACTA
11351 CGGTGCATGT
Statistics
Matches: 114, Mismatches: 10, Indels: 14
0.83 0.07 0.10
Matches are distributed among these distances:
53 47 0.41
56 2 0.02
58 1 0.01
59 64 0.56
ACGTcount: A:0.28, C:0.16, G:0.26, T:0.31
Consensus pattern (58 bp):
CATATTCGGGATTGCACTAAAGTATAACTAGTGCATATGGTGGGACGACCTTATGTGT
Found at i:14276 original size:18 final size:18
Alignment explanation
Indices: 14253--14294 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
14243 AATCCTAGGG
*
14253 TGTAACCCTGTAGGTTCT
1 TGTAACACTGTAGGTTCT
*
14271 TGTAACATTGTAGGTTCT
1 TGTAACACTGTAGGTTCT
14289 TGTAAC
1 TGTAAC
14295 GTTAGTATTA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.21, C:0.17, G:0.21, T:0.40
Consensus pattern (18 bp):
TGTAACACTGTAGGTTCT
Found at i:26288 original size:16 final size:17
Alignment explanation
Indices: 26259--26293 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
26249 ATTTTAAAAT
26259 TTTAAAATTACTTTGTA
1 TTTAAAATTACTTTGTA
*
26276 TTTAAAA-TACTTTTTA
1 TTTAAAATTACTTTGTA
26292 TT
1 TT
26294 ATAATTTATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 10 0.59
17 7 0.41
ACGTcount: A:0.34, C:0.06, G:0.03, T:0.57
Consensus pattern (17 bp):
TTTAAAATTACTTTGTA
Found at i:34750 original size:16 final size:16
Alignment explanation
Indices: 34729--34762 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
34719 AATTTTATTA
34729 TTATTTTT-TTTAGTAT
1 TTATTTTTCTTTA-TAT
34745 TTATTTTTCTTTATAT
1 TTATTTTTCTTTATAT
34761 TT
1 TT
34763 TTTAGGCACA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 13 0.76
17 4 0.24
ACGTcount: A:0.18, C:0.03, G:0.03, T:0.76
Consensus pattern (16 bp):
TTATTTTTCTTTATAT
Found at i:36886 original size:21 final size:21
Alignment explanation
Indices: 36862--36912 Score: 70
Period size: 20 Copynumber: 2.5 Consensus size: 21
36852 TCCGATTGAT
*
36862 AAAATTGAAAGATCGATGGCA
1 AAAATTAAAAGATCGATGGCA
*
36883 AAAA-TAAAAGATTGATGGCA
1 AAAATTAAAAGATCGATGGCA
36903 AAAA-TAAAAG
1 AAAATTAAAAG
36913 GACGACATAG
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
20 24 0.86
21 4 0.14
ACGTcount: A:0.57, C:0.06, G:0.20, T:0.18
Consensus pattern (21 bp):
AAAATTAAAAGATCGATGGCA
Found at i:36892 original size:20 final size:20
Alignment explanation
Indices: 36869--36912 Score: 79
Period size: 20 Copynumber: 2.2 Consensus size: 20
36859 GATAAAATTG
36869 AAAGATCGATGGCAAAAATA
1 AAAGATCGATGGCAAAAATA
*
36889 AAAGATTGATGGCAAAAATA
1 AAAGATCGATGGCAAAAATA
36909 AAAG
1 AAAG
36913 GACGACATAG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.57, C:0.07, G:0.20, T:0.16
Consensus pattern (20 bp):
AAAGATCGATGGCAAAAATA
Found at i:37880 original size:4 final size:4
Alignment explanation
Indices: 37871--37895 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
37861 ATTCAAAAAC
37871 ATAA ATAA ATAA ATAA ATAA ATAA A
1 ATAA ATAA ATAA ATAA ATAA ATAA A
37896 CATGTTAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
ATAA
Found at i:39055 original size:2 final size:2
Alignment explanation
Indices: 39044--39080 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
39034 ATGAAAGTAA
39044 AT AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
39081 TAGTTAAAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:53715 original size:14 final size:14
Alignment explanation
Indices: 53698--53736 Score: 53
Period size: 14 Copynumber: 2.8 Consensus size: 14
53688 TTTAAGATAA
53698 TTTATTAATAATAT
1 TTTATTAATAATAT
53712 TTTATATAA-AATAT
1 TTTAT-TAATAATAT
*
53726 TTTATCAATAA
1 TTTATTAATAA
53737 AAATTATATT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
13 2 0.09
14 17 0.77
15 3 0.14
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (14 bp):
TTTATTAATAATAT
Found at i:53939 original size:28 final size:28
Alignment explanation
Indices: 53870--53943 Score: 80
Period size: 28 Copynumber: 2.7 Consensus size: 28
53860 TTTAACCATT
* *
53870 TAAA-AATGAAAAGATATATATTATAAA
1 TAAATAATAAAAAAATATATATTATAAA
**
53897 TAAATTTTAAAAAAATAT-TATTATAAA
1 TAAATAATAAAAAAATATATATTATAAA
*
53924 TAAAATAATAATAAAATATA
1 T-AAATAATAAAAAAATATA
53944 AAAATACAAA
Statistics
Matches: 37, Mismatches: 7, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
27 14 0.38
28 23 0.62
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.34
Consensus pattern (28 bp):
TAAATAATAAAAAAATATATATTATAAA
Found at i:55178 original size:22 final size:22
Alignment explanation
Indices: 55147--55218 Score: 110
Period size: 22 Copynumber: 3.3 Consensus size: 22
55137 CTGAGTGGCA
55147 TATGAAATTTGTCCCGAAGGACC
1 TATG-AATTTGTCCCGAAGGACC
*
55170 TGTGAATTTGTCCCGAAGGACC
1 TATGAATTTGTCCCGAAGGACC
*
55192 TATG-AGTTGTCCCGAAGGACC
1 TATGAATTTGTCCCGAAGGACC
55213 TATGAA
1 TATGAA
55219 ACCCTCGACT
Statistics
Matches: 45, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
21 20 0.44
22 22 0.49
23 3 0.07
ACGTcount: A:0.28, C:0.21, G:0.25, T:0.26
Consensus pattern (22 bp):
TATGAATTTGTCCCGAAGGACC
Found at i:55203 original size:21 final size:21
Alignment explanation
Indices: 55155--55217 Score: 99
Period size: 21 Copynumber: 3.0 Consensus size: 21
55145 CATATGAAAT
* *
55155 TTGTCCCGAAGGACCTGTGAAT
1 TTGTCCCGAAGGACCTATG-AG
55177 TTGTCCCGAAGGACCTATGAG
1 TTGTCCCGAAGGACCTATGAG
55198 TTGTCCCGAAGGACCTATGA
1 TTGTCCCGAAGGACCTATGA
55218 AACCCTCGAC
Statistics
Matches: 39, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
21 21 0.54
22 18 0.46
ACGTcount: A:0.24, C:0.24, G:0.27, T:0.25
Consensus pattern (21 bp):
TTGTCCCGAAGGACCTATGAG
Found at i:56693 original size:64 final size:63
Alignment explanation
Indices: 56594--56754 Score: 182
Period size: 64 Copynumber: 2.5 Consensus size: 63
56584 TAATGAAGGT
* * * *
56594 ATGCATCGATGCACTACACCATGCATAGATGCATAAATCCTATTCGATG-TTTGTATTT-AATGG
1 ATGCATCGATGCACT-C-CTATGCATCGATGCATAAATCATATTCGATGTTTTCTATTTAAAT--
*
56657 GG
62 GC
*
56659 ATGCATCGATGCACTCCTTATGCATCGATGCATAAATCATATTCGATGTTTTCTATTTAAATTC
1 ATGCATCGATGCACTCC-TATGCATCGATGCATAAATCATATTCGATGTTTTCTATTTAAATGC
* *
56723 ATGCATCGATGCACTGCATGTGCATCGATGCA
1 ATGCATCGATGCACT-CCTATGCATCGATGCA
56755 CCTTAAACAA
Statistics
Matches: 84, Mismatches: 8, Indels: 9
0.83 0.08 0.09
Matches are distributed among these distances:
63 1 0.01
64 56 0.67
65 24 0.29
66 3 0.04
ACGTcount: A:0.28, C:0.20, G:0.18, T:0.34
Consensus pattern (63 bp):
ATGCATCGATGCACTCCTATGCATCGATGCATAAATCATATTCGATGTTTTCTATTTAAATGC
Found at i:57431 original size:21 final size:21
Alignment explanation
Indices: 57383--57433 Score: 86
Period size: 21 Copynumber: 2.4 Consensus size: 21
57373 CCCTTTATTT
57383 CCTTTAAT-AATTACTGAATAA
1 CCTTT-ATCAATTACTGAATAA
57404 CCTTTATCAATTACTGAATAA
1 CCTTTATCAATTACTGAATAA
57425 CCTTTATCA
1 CCTTTATCA
57434 TATTTCCAAG
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
20 2 0.07
21 27 0.93
ACGTcount: A:0.37, C:0.20, G:0.04, T:0.39
Consensus pattern (21 bp):
CCTTTATCAATTACTGAATAA
Found at i:59960 original size:22 final size:22
Alignment explanation
Indices: 59929--60000 Score: 110
Period size: 22 Copynumber: 3.3 Consensus size: 22
59919 CTGAGTGGCA
59929 TATGAAATTTGTCCCGAAGGACC
1 TATG-AATTTGTCCCGAAGGACC
*
59952 TGTGAATTTGTCCCGAAGGACC
1 TATGAATTTGTCCCGAAGGACC
*
59974 TATG-AGTTGTCCCGAAGGACC
1 TATGAATTTGTCCCGAAGGACC
59995 TATGAA
1 TATGAA
60001 ACCCTCGACT
Statistics
Matches: 45, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
21 20 0.44
22 22 0.49
23 3 0.07
ACGTcount: A:0.28, C:0.21, G:0.25, T:0.26
Consensus pattern (22 bp):
TATGAATTTGTCCCGAAGGACC
Found at i:59985 original size:21 final size:21
Alignment explanation
Indices: 59937--59999 Score: 99
Period size: 21 Copynumber: 3.0 Consensus size: 21
59927 CATATGAAAT
* *
59937 TTGTCCCGAAGGACCTGTGAAT
1 TTGTCCCGAAGGACCTATG-AG
59959 TTGTCCCGAAGGACCTATGAG
1 TTGTCCCGAAGGACCTATGAG
59980 TTGTCCCGAAGGACCTATGA
1 TTGTCCCGAAGGACCTATGA
60000 AACCCTCGAC
Statistics
Matches: 39, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
21 21 0.54
22 18 0.46
ACGTcount: A:0.24, C:0.24, G:0.27, T:0.25
Consensus pattern (21 bp):
TTGTCCCGAAGGACCTATGAG
Found at i:61473 original size:64 final size:63
Alignment explanation
Indices: 61375--61535 Score: 191
Period size: 64 Copynumber: 2.5 Consensus size: 63
61365 TAATGAAGGT
* * *
61375 ATGCATCGATGCACTACACCATGCATCGATGCATAAATCCTATTCGATG-TTTGTATTT-AATGG
1 ATGCATCGATGCACT-C-CTATGCATCGATGCATAAATCATATTCGATGTTTTCTATTTAAAT--
*
61438 GG
62 GC
*
61440 ATGCATCGATGCACTCCTTATGCATCGATGCATAAATCATATTCGATGTTTTCTATTTAAATTC
1 ATGCATCGATGCACTCC-TATGCATCGATGCATAAATCATATTCGATGTTTTCTATTTAAATGC
* *
61504 ATGCATCGATGCACTGCATGTGCATCGATGCA
1 ATGCATCGATGCACT-CCTATGCATCGATGCA
61536 CCTTAAACAA
Statistics
Matches: 85, Mismatches: 7, Indels: 9
0.84 0.07 0.09
Matches are distributed among these distances:
63 1 0.01
64 57 0.67
65 24 0.28
66 3 0.04
ACGTcount: A:0.27, C:0.21, G:0.18, T:0.34
Consensus pattern (63 bp):
ATGCATCGATGCACTCCTATGCATCGATGCATAAATCATATTCGATGTTTTCTATTTAAATGC
Found at i:68991 original size:2 final size:2
Alignment explanation
Indices: 68984--69014 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
68974 CATACTGTAC
68984 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
69015 GAGAGAGAGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:69019 original size:2 final size:2
Alignment explanation
Indices: 69014--69041 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
69004 ATATATATAT
69014 AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG
69042 GAAATTTCTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:75069 original size:40 final size:40
Alignment explanation
Indices: 75005--75096 Score: 123
Period size: 40 Copynumber: 2.3 Consensus size: 40
74995 GATTGACCGG
** *
75005 TGTCAAAGTATTCCACCTTTATAAGATGGAAGAAGT-GAGA
1 TGTCAAAGTATTCCACCTCAATAAGAAGGAAGAA-TCGAGA
*
75045 TGTCAAAGTATTCCGCCTCAATAAGAAGGAAGAATCGAGA
1 TGTCAAAGTATTCCACCTCAATAAGAAGGAAGAATCGAGA
*
75085 TGTCGAAGTATT
1 TGTCAAAGTATT
75097 AAAAGATAAA
Statistics
Matches: 46, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
39 1 0.02
40 45 0.98
ACGTcount: A:0.37, C:0.14, G:0.23, T:0.26
Consensus pattern (40 bp):
TGTCAAAGTATTCCACCTCAATAAGAAGGAAGAATCGAGA
Found at i:75211 original size:20 final size:20
Alignment explanation
Indices: 75186--75283 Score: 63
Period size: 18 Copynumber: 5.3 Consensus size: 20
75176 TACTTATAAG
*
75186 TTAGTTAACAGAATAGGTAA
1 TTAGTTAACAAAATAGGTAA
* *
75206 TTAGTT--GATAATA---AA
1 TTAGTTAACAAAATAGGTAA
75221 GTTAGTTAACAAAATAGGTAA
1 -TTAGTTAACAAAATAGGTAA
* *
75242 TTAGTT--GATAATA---AA
1 TTAGTTAACAAAATAGGTAA
75257 GTTAGTTAACAAAATAGGTAA
1 -TTAGTTAACAAAATAGGTAA
75278 TTAGTT
1 TTAGTT
75284 GATAATAGAT
Statistics
Matches: 58, Mismatches: 8, Indels: 24
0.64 0.09 0.27
Matches are distributed among these distances:
15 4 0.07
16 12 0.21
18 20 0.34
20 18 0.31
21 4 0.07
ACGTcount: A:0.45, C:0.03, G:0.17, T:0.35
Consensus pattern (20 bp):
TTAGTTAACAAAATAGGTAA
Found at i:75224 original size:36 final size:36
Alignment explanation
Indices: 75183--75290 Score: 207
Period size: 36 Copynumber: 3.0 Consensus size: 36
75173 TAGTACTTAT
*
75183 AAGTTAGTTAACAGAATAGGTAATTAGTTGATAATA
1 AAGTTAGTTAACAAAATAGGTAATTAGTTGATAATA
75219 AAGTTAGTTAACAAAATAGGTAATTAGTTGATAATA
1 AAGTTAGTTAACAAAATAGGTAATTAGTTGATAATA
75255 AAGTTAGTTAACAAAATAGGTAATTAGTTGATAATA
1 AAGTTAGTTAACAAAATAGGTAATTAGTTGATAATA
75291 GATTGTACTT
Statistics
Matches: 71, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
36 71 1.00
ACGTcount: A:0.46, C:0.03, G:0.18, T:0.33
Consensus pattern (36 bp):
AAGTTAGTTAACAAAATAGGTAATTAGTTGATAATA
Found at i:77489 original size:20 final size:20
Alignment explanation
Indices: 77432--77491 Score: 56
Period size: 20 Copynumber: 3.0 Consensus size: 20
77422 ATAGAATATC
*
77432 ATTTA-AATTAAAATTAAAT
1 ATTTATAATTAAATTTAAAT
77451 AATTTCATAA-T--ATTATAAAT
1 -ATTT-ATAATTAAATT-TAAAT
77471 ATTTATAATTAAATTTAAAT
1 ATTTATAATTAAATTTAAAT
77491 A
1 A
77492 GAAACTCAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 12
0.72 0.02 0.26
Matches are distributed among these distances:
18 4 0.12
19 7 0.21
20 15 0.45
21 5 0.15
22 2 0.06
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (20 bp):
ATTTATAATTAAATTTAAAT
Found at i:89619 original size:3 final size:3
Alignment explanation
Indices: 89613--89649 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
89603 TCAAAACCAC
89613 CCT CCT CCT CCT CCT CCT CCT CCT CCT CCT CCT CCT C
1 CCT CCT CCT CCT CCT CCT CCT CCT CCT CCT CCT CCT C
89650 GAGCTGGAGC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.00, C:0.68, G:0.00, T:0.32
Consensus pattern (3 bp):
CCT
Found at i:89687 original size:3 final size:3
Alignment explanation
Indices: 89679--89747 Score: 131
Period size: 3 Copynumber: 23.3 Consensus size: 3
89669 TTAAATGACA
89679 CCT CCT CCT CCT CCT CCT CCT CCT CCT CCT CCT CCT CCT CCT CCT -CT
1 CCT CCT CCT CCT CCT CCT CCT CCT CCT CCT CCT CCT CCT CCT CCT CCT
89726 CCT CCT CCT CCT CCT CCT CCT C
1 CCT CCT CCT CCT CCT CCT CCT C
89748 GAGCTGGAGC
Statistics
Matches: 65, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
2 2 0.03
3 63 0.97
ACGTcount: A:0.00, C:0.67, G:0.00, T:0.33
Consensus pattern (3 bp):
CCT
Found at i:91324 original size:38 final size:40
Alignment explanation
Indices: 91280--91357 Score: 117
Period size: 38 Copynumber: 2.0 Consensus size: 40
91270 ATTTAAAGAA
91280 GAAGAAGAAGAAGAAGA-ACGTGG-TGTTTTTG-AATTTTT
1 GAAGAAGAAGAAGAA-ACACGTGGATGTTTTTGAAATTTTT
*
91318 GAAGAAGAAGAAGAAACATGTGGATGTTTTTGAAATTTTT
1 GAAGAAGAAGAAGAAACACGTGGATGTTTTTGAAATTTTT
91358 TATTATTTAA
Statistics
Matches: 36, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
37 1 0.03
38 20 0.56
39 8 0.22
40 7 0.19
ACGTcount: A:0.38, C:0.03, G:0.27, T:0.32
Consensus pattern (40 bp):
GAAGAAGAAGAAGAAACACGTGGATGTTTTTGAAATTTTT
Found at i:94743 original size:23 final size:20
Alignment explanation
Indices: 94692--94770 Score: 70
Period size: 20 Copynumber: 3.8 Consensus size: 20
94682 AGGGTGTCAA
* * *
94692 AGTGTATCCATGCACCCCTGC
1 AGTGCATCCATGCA-CCATGT
94713 AGTGCATCCATGCACC-TGCCACT
1 AGTGCATCCATGCACCATG----T
*
94736 AGTGCATCGATGCACCATGT
1 AGTGCATCCATGCACCATGT
94756 AGTGCATCCATGCAC
1 AGTGCATCCATGCAC
94771 TCCATTTCGA
Statistics
Matches: 49, Mismatches: 4, Indels: 11
0.77 0.06 0.17
Matches are distributed among these distances:
19 2 0.04
20 17 0.35
21 13 0.27
23 15 0.31
24 2 0.04
ACGTcount: A:0.23, C:0.34, G:0.20, T:0.23
Consensus pattern (20 bp):
AGTGCATCCATGCACCATGT
Found at i:94815 original size:20 final size:20
Alignment explanation
Indices: 94790--94832 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
94780 AATGCAATTA
*
94790 GTGCATCGATGCATCCTGCT
1 GTGCATCGATGCATCCTACT
*
94810 GTGCATCGATGTATCCTACT
1 GTGCATCGATGCATCCTACT
94830 GTG
1 GTG
94833 TATCCATTCA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.16, C:0.26, G:0.26, T:0.33
Consensus pattern (20 bp):
GTGCATCGATGCATCCTACT
Found at i:99509 original size:68 final size:66
Alignment explanation
Indices: 99348--99630 Score: 291
Period size: 68 Copynumber: 4.2 Consensus size: 66
99338 CTCTAAAATA
* * * * ** *
99348 AATATGATTAGGTGCTCTCGTGTGAGTCACTCTAAACCTGCAGGGATCCCGTATGAGTGACCTGA
1 AATATGATTAAGTGCTCTCGTGCGAGTCACTCTAATCCT-C-GGGCTCCCGTGCGAGTCACCTG-
*
99413 AAAT
63 GAAT
* * *
99417 AAATATGATTAAGTGTTCTCGTGCGGGTCACTCTAATTCCTCAGGGCTCCCATGCGAGTCACCTG
1 -AATATGATTAAGTGCTCTCGTGCGAGTCACTCTAA-TCCTC-GGGCTCCCGTGCGAGTCACCTG
99482 GAAT
63 GAAT
** *
99486 AATATGATTAAGTGCTCTCGTGCGAGTCACTCTAATCCTTCGAACTCCCTTGCGAGTCATCC-GG
1 AATATGATTAAGTGCTCTCGTGCGAGTCACTCTAATCC-TCGGGCTCCCGTGCGAGTCA-CCTGG
99550 AAT
64 AAT
* * * *
99553 AATATGATTAGGTTCT-TCCGTGCAAGTCACTCTAATCCCTCGAGGCTCCCGTGCGAGTCACCTA
1 AATATGATTAAGTGCTCT-CGTGCGAGTCACTCTAAT-CCTCG-GGCTCCCGTGCGAGTCACCTG
99617 GAAT
63 GAAT
99621 AATATGATTA
1 AATATGATTA
99631 GGTGTTCCGT
Statistics
Matches: 183, Mismatches: 23, Indels: 16
0.82 0.10 0.07
Matches are distributed among these distances:
66 1 0.01
67 59 0.32
68 67 0.37
69 3 0.02
70 50 0.27
71 3 0.02
ACGTcount: A:0.25, C:0.24, G:0.22, T:0.29
Consensus pattern (66 bp):
AATATGATTAAGTGCTCTCGTGCGAGTCACTCTAATCCTCGGGCTCCCGTGCGAGTCACCTGGAA
T
Found at i:99575 original size:67 final size:65
Alignment explanation
Indices: 99348--99641 Score: 252
Period size: 67 Copynumber: 4.3 Consensus size: 65
99338 CTCTAAAATA
* * * * * * ** *
99348 AATATGATTAGGTGCTCTCGTGTGAGTCACTCTAAACCTGCAGGGATCCCGTATGAGTGACCTGA
1 AATATGATTAGGTTCTC-CGTGCGAGTCACTCTAATCCT-C-GAGCTCCCATGCGAGTCACCTG-
*
99413 AAAT
62 GAAT
* *
99417 AAATATGATTAAGTGTTCT-CGTGCGGGTCACTCTAATTCCTCAGGGCTCCCATGCGAGTCACCT
1 -AATATGATT-AG-GTTCTCCGTGCGAGTCACTCTAA-TCCTC-GAGCTCCCATGCGAGTCACCT
99481 GGAAT
61 GGAAT
* * * *
99486 AATATGATTAAGTGCTCTCGTGCGAGTCACTCTAATCCTTCGAACTCCCTTGCGAGTCATCC-GG
1 AATATGATTAGGTTCTC-CGTGCGAGTCACTCTAATCC-TCGAGCTCCCATGCGAGTCA-CCTGG
99550 AAT
63 AAT
* * *
99553 AATATGATTAGGTTCTTCCGTGCAAGTCACTCTAATCCCTCGAGGCTCCCGTGCGAGTCACCTAG
1 AATATGATTAGGTTC-TCCGTGCGAGTCACTCTAAT-CCTCGA-GCTCCCATGCGAGTCACCTGG
99618 AAT
63 AAT
99621 AATATGATTAGGTGT-TCCGTG
1 AATATGATTAGGT-TCTCCGTG
99642 TACTCCTTGT
Statistics
Matches: 190, Mismatches: 22, Indels: 27
0.79 0.09 0.11
Matches are distributed among these distances:
66 4 0.02
67 66 0.35
68 64 0.34
69 4 0.02
70 43 0.23
71 5 0.03
72 4 0.02
ACGTcount: A:0.24, C:0.24, G:0.22, T:0.29
Consensus pattern (65 bp):
AATATGATTAGGTTCTCCGTGCGAGTCACTCTAATCCTCGAGCTCCCATGCGAGTCACCTGGAAT
Found at i:99631 original size:68 final size:68
Alignment explanation
Indices: 99280--99641 Score: 278
Period size: 70 Copynumber: 5.3 Consensus size: 68
99270 GTCTTAGTAC
* * ** * **
99280 TATGATTAGGCTCTCCCGTGCAAGTCACTCTAAT-TATAC-AGGGATCCCGTATGAGTCACTCTA
1 TATGATTAGGTTCT-CCGTGCGAGTCACTCTAATCCCT-CGAGGGCTCCCGTGCGAGTCAC-CTA
*
99343 AAATAAA
63 GAAT-AA
* * * * ** *
99350 TATGATTAGGTGCTCTCGTGTGAGTCACTCTAA-ACCT-GCAGGGATCCCGTATGAGTGACCTGA
1 TATGATTAGGTTCTC-CGTGCGAGTCACTCTAATCCCTCG-AGGGCTCCCGTGCGAGTCACCT-A
*
99413 AAATAAA
63 GAAT-AA
* * * *
99420 TATGATTAAGTGTTCT-CGTGCGGGTCACTCTAATTCCTC-AGGGCTCCCATGCGAGTCACCTGG
1 TATGATT-AG-GTTCTCCGTGCGAGTCACTCTAATCCCTCGAGGGCTCCCGTGCGAGTCACCTAG
99483 AATAA
64 AATAA
* * * * * *
99488 TATGATTAAGTGCTCTCGTGCGAGTCACTCTAATCCTTCGA--ACTCCCTTGCGAGTCATCC-GG
1 TATGATTAGGTTCTC-CGTGCGAGTCACTCTAATCCCTCGAGGGCTCCCGTGCGAGTCA-CCTAG
99550 AATAA
64 AATAA
*
99555 TATGATTAGGTTCTTCCGTGCAAGTCACTCTAATCCCTCGA-GGCTCCCGTGCGAGTCACCTAGA
1 TATGATTAGGTTC-TCCGTGCGAGTCACTCTAATCCCTCGAGGGCTCCCGTGCGAGTCACCTAGA
99619 ATAA
65 ATAA
99623 TATGATTAGGTGT-TCCGTG
1 TATGATTAGGT-TCTCCGTG
99642 TACTCCTTGT
Statistics
Matches: 243, Mismatches: 32, Indels: 37
0.78 0.10 0.12
Matches are distributed among these distances:
66 4 0.02
67 64 0.26
68 64 0.26
69 8 0.03
70 94 0.39
71 5 0.02
72 4 0.02
ACGTcount: A:0.25, C:0.24, G:0.22, T:0.29
Consensus pattern (68 bp):
TATGATTAGGTTCTCCGTGCGAGTCACTCTAATCCCTCGAGGGCTCCCGTGCGAGTCACCTAGAA
TAA
Found at i:101518 original size:27 final size:25
Alignment explanation
Indices: 101487--101542 Score: 64
Period size: 25 Copynumber: 2.3 Consensus size: 25
101477 GAAATGTGTT
101487 AGATAAACAAGGAAAAGAAAACAAATA
1 AGATAAACAAGGAAAA-AAAA-AAATA
*
101514 AGAT--ACAAGGAAAAAATAAAATA
1 AGATAAACAAGGAAAAAAAAAAATA
101537 A-ATAAA
1 AGATAAA
101543 ATAAATAAGT
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
22 2 0.08
23 6 0.23
24 4 0.15
25 10 0.38
27 4 0.15
ACGTcount: A:0.71, C:0.05, G:0.12, T:0.11
Consensus pattern (25 bp):
AGATAAACAAGGAAAAAAAAAAATA
Found at i:102171 original size:18 final size:17
Alignment explanation
Indices: 102150--102192 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
102140 ATATACACAT
102150 ATAATAATAATAACATGA
1 ATAATAATAATAA-ATGA
*
102168 ATAATAAAAATAAATGA
1 ATAATAATAATAAATGA
102185 ATAA-AATA
1 ATAATAATA
102193 TCCATATAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 3 0.13
17 8 0.35
18 12 0.52
ACGTcount: A:0.67, C:0.02, G:0.05, T:0.26
Consensus pattern (17 bp):
ATAATAATAATAAATGA
Found at i:102598 original size:37 final size:37
Alignment explanation
Indices: 102548--102652 Score: 138
Period size: 37 Copynumber: 2.8 Consensus size: 37
102538 GTGCTTGTGG
* * * *
102548 ATCCTATCTTTAGGAATTTAAATCTTAGTAGAACTCT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAGAACTCT
* * * *
102585 ATCCTATTTTTAGGAGTTTGAATCCTAGCAAAAGTTT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAGAACTCT
102622 ATCCTATTTTTAGGAGTTTGAATCCTAGTAG
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAG
102653 GACGAAAATG
Statistics
Matches: 58, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
37 58 1.00
ACGTcount: A:0.30, C:0.14, G:0.15, T:0.41
Consensus pattern (37 bp):
ATCCTATTTTTAGGAGTTTGAATCCTAGTAGAACTCT
Found at i:102609 original size:21 final size:21
Alignment explanation
Indices: 102585--102648 Score: 57
Period size: 21 Copynumber: 3.3 Consensus size: 21
102575 GTAGAACTCT
102585 ATCCTATTTTTAGGAGTTTGA
1 ATCCTATTTTTAGGAGTTTGA
** **
102606 ATCCTA---GCAAAAGTTT--
1 ATCCTATTTTTAGGAGTTTGA
102622 ATCCTATTTTTAGGAGTTTGA
1 ATCCTATTTTTAGGAGTTTGA
102643 ATCCTA
1 ATCCTA
102649 GTAGGACGAA
Statistics
Matches: 30, Mismatches: 8, Indels: 10
0.62 0.17 0.21
Matches are distributed among these distances:
16 6 0.20
18 6 0.20
19 6 0.20
21 12 0.40
ACGTcount: A:0.28, C:0.14, G:0.16, T:0.42
Consensus pattern (21 bp):
ATCCTATTTTTAGGAGTTTGA
Found at i:103495 original size:105 final size:105
Alignment explanation
Indices: 103195--103825 Score: 891
Period size: 105 Copynumber: 6.0 Consensus size: 105
103185 GTATTGTTCC
* * * * ** *
103195 GAGTCCAATATCCTCCGTCGTGAAATTGAAATTGGCTCT-GGAACCGGGAAATTGTTTGTTGACA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTAAG-ATTGGGAAGTTG-TTGTTGACA
* * * * *
103259 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTC
64 AGCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
103301 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCT--GAAT--GAAATT-TTGTTGACAAG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTAAGATTGGGAAGTTGTTGTTGACAAG
*
103361 CAGCGGTCCCTTCGTCGTGGAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
103401 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTAAGATTGGGAAGTTGTTGTTGACAAG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTAAGATTGGGAAGTTGTTGTTGACAAG
103466 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
103506 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTAAGATTGGGAAGTTGTTGTTGACAAG
*
103571 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGTGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
103611 AAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAA-ATTGAGAAGTTGTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCT-AAGATTGGGAAGTTGTTGTTGACAA
103675 GCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
65 GCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
103716 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTTGCTCTGAA-ATTGAGAAGTTGTTTGTTAACA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCT-AAGATTGGGAAGTTG-TTGTTGACA
* * * * * *
103780 ACCAGCCGTCCCTTCGTTGTAAAGTTGAACTTGTGTTGTCTC
64 AGCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
103822 GAGT
1 GAGT
103826 GTCACGATAT
Statistics
Matches: 485, Mismatches: 33, Indels: 14
0.91 0.06 0.03
Matches are distributed among these distances:
100 82 0.17
102 9 0.02
104 6 0.01
105 305 0.63
106 83 0.17
ACGTcount: A:0.22, C:0.18, G:0.26, T:0.34
Consensus pattern (105 bp):
GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTAAGATTGGGAAGTTGTTGTTGACAAG
CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
Found at i:104072 original size:36 final size:36
Alignment explanation
Indices: 104025--104100 Score: 116
Period size: 36 Copynumber: 2.1 Consensus size: 36
104015 TGTTTGGAGA
* * *
104025 GAAACTGTCTCAAGGGAGACAAAATTCGTTTCAAGG
1 GAAACTATCTCAAGCGAGACAAAATTCATTTCAAGG
*
104061 GAAACTATCTCAAGCGAGATAAAATTCATTTCAAGG
1 GAAACTATCTCAAGCGAGACAAAATTCATTTCAAGG
104097 GAAA
1 GAAA
104101 TGTTTTCAAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.41, C:0.16, G:0.21, T:0.22
Consensus pattern (36 bp):
GAAACTATCTCAAGCGAGACAAAATTCATTTCAAGG
Found at i:104334 original size:105 final size:104
Alignment explanation
Indices: 104000--104318 Score: 527
Period size: 105 Copynumber: 3.1 Consensus size: 104
103990 TTCGTTAAAT
* ** *
104000 TGTTTTCAAAGTTTATGTTTGGAGAGAAACTGTCTCAAGGGAGACAAAA--TTC-GTTTCAAGGG
1 TGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTCTGTTTCGAGGG
* * *
104062 AAACTATCTCAAGCGAGATAAAATTCATTTCAAGGGAAA
66 AAACTATCTCAAGAGAGAAAAAAATCATTTCAAGGGAAA
104101 TGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTCTGTTTCGAGGG
1 TGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTCTGTTTCGAGGG
104166 AAACTATCTCAAGAGAGAAAAAAAATCATTTCAAGGGAAA
66 AAACTATCTCAAGAGAG-AAAAAAATCATTTCAAGGGAAA
104206 TGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTCTGTTTCGAGGG
1 TGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTCTGTTTCGAGGG
* *
104271 AAACTATCTCATGAGAGAAAAAAATAATTTCAAGGGAAA
66 AAACTATCTCAAGAGAGAAAAAAATCATTTCAAGGGAAA
104310 TGTTTTCAA
1 TGTTTTCAA
104319 GAGAAACTAT
Statistics
Matches: 205, Mismatches: 9, Indels: 5
0.94 0.04 0.02
Matches are distributed among these distances:
101 46 0.22
103 3 0.01
104 55 0.27
105 101 0.49
ACGTcount: A:0.37, C:0.12, G:0.20, T:0.30
Consensus pattern (104 bp):
TGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTCTGTTTCGAGGG
AAACTATCTCAAGAGAGAAAAAAATCATTTCAAGGGAAA
Found at i:104475 original size:36 final size:36
Alignment explanation
Indices: 104435--104548 Score: 113
Period size: 36 Copynumber: 3.2 Consensus size: 36
104425 CTTTCGAGTG
* *
104435 AAAACGGTCTCAAGCGAGACAAATCTTGTTTTAAGA
1 AAAACAGTCTCAAGTGAGACAAATCTTGTTTTAAGA
* ** * * * **
104471 AAAACAATCTTGAGTGAAATAAATCTTCTTTCGAGA
1 AAAACAGTCTCAAGTGAGACAAATCTTGTTTTAAGA
*
104507 AAAACAGTCTCAAGTGAGACAAAGT-ATGTTTTAAGA
1 AAAACAGTCTCAAGTGAGACAAA-TCTTGTTTTAAGA
104543 AAAACA
1 AAAACA
104549 AATTTGAGTG
Statistics
Matches: 58, Mismatches: 19, Indels: 2
0.73 0.24 0.03
Matches are distributed among these distances:
36 57 0.98
37 1 0.02
ACGTcount: A:0.44, C:0.14, G:0.17, T:0.25
Consensus pattern (36 bp):
AAAACAGTCTCAAGTGAGACAAATCTTGTTTTAAGA
Found at i:104527 original size:72 final size:74
Alignment explanation
Indices: 104389--104564 Score: 216
Period size: 72 Copynumber: 2.4 Consensus size: 74
104379 TAAAATCTTC
* ** * *
104389 TTAAAAAAAACAGCCTTGAGTGAAATGAAATGCCTTCTTTCGAGTGAAAACGGTCTCAAGCGAGA
1 TTAAGAAAAACAATCTTGAGTGAAAT-AAAT-CCTTCTTTCGAGTAAAAACAGTCTCAAGCGAGA
*
104454 CAAA-TCTTGTT
64 CAAAGT-ATGTT
*
104465 TTAAGAAAAACAATCTTGAGTGAAATAAAT-CTTCTTTCGAG-AAAAACAGTCTCAAGTGAGACA
1 TTAAGAAAAACAATCTTGAGTGAAATAAATCCTTCTTTCGAGTAAAAACAGTCTCAAGCGAGACA
104528 AAGTATGTT
66 AAGTATGTT
*
104537 TTAAGAAAAACAAAT-TTGAGTGAGATAA
1 TTAAGAAAAAC-AATCTTGAGTGAAATAA
104565 TCATCTGCAT
Statistics
Matches: 90, Mismatches: 8, Indels: 8
0.85 0.08 0.08
Matches are distributed among these distances:
72 48 0.53
73 15 0.17
75 4 0.04
76 23 0.26
ACGTcount: A:0.42, C:0.13, G:0.18, T:0.27
Consensus pattern (74 bp):
TTAAGAAAAACAATCTTGAGTGAAATAAATCCTTCTTTCGAGTAAAAACAGTCTCAAGCGAGACA
AAGTATGTT
Found at i:106013 original size:183 final size:183
Alignment explanation
Indices: 105705--106241 Score: 995
Period size: 183 Copynumber: 2.9 Consensus size: 183
105695 ATCAGGTTTA
105705 ACTGAAGGGTTCATCTCATCACAAAGTCTTTGACCTGACAAAAGCAGTGGAGCAAACACCGAATT
1 ACTGAAGGGTTCATCTCATCACAAAGTCTTTGACCTGACAAAAGCAGTGGAGCAAACACCGAATT
* **
105770 GCCAAGTGTCCGAGCAATGTCAT-GATTTGAATGTAATCTATTCATAAAGCCAGGGCTTTCGAGT
66 GCCAAGTGTCCGAGCAGTGTCATAG-TTTGAACATAATCTATTCATAAAGCCAGGGCTTTCGAGT
*
105834 TTCCTCTATAACCAATTGCCTTAGTGGAATAACTCAGCTTTAGAGGGACAAATC
130 TTCCTCTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTAGAGGGACAAATC
*
105888 ACTGAAGGGTTCGTCTCATCACAAAGTCTTTGACCTGACAAAAGCAGTGGAGCAAACACCGAATT
1 ACTGAAGGGTTCATCTCATCACAAAGTCTTTGACCTGACAAAAGCAGTGGAGCAAACACCGAATT
*
105953 GCCAAGTGTCCGAGCAGTGTCATAGTTTGAACATAATCTATTCATAAAGCCAAGGCTTTCGAGTT
66 GCCAAGTGTCCGAGCAGTGTCATAGTTTGAACATAATCTATTCATAAAGCCAGGGCTTTCGAGTT
106018 TCCTCTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTAGAGGGACAAATC
131 TCCTCTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTAGAGGGACAAATC
*
106071 ACTGAAGGGTTCATCTCATCACAAAGTCTTTGGCCTGACAAAAGCAGTGGAGCAAACACCGAATT
1 ACTGAAGGGTTCATCTCATCACAAAGTCTTTGACCTGACAAAAGCAGTGGAGCAAACACCGAATT
106136 GCCAAGTGTCCGAGCAGTGTCATAGTTTGAACATAATCTATTCATAAAGCCAGGGCTTTCGAGTT
66 GCCAAGTGTCCGAGCAGTGTCATAGTTTGAACATAATCTATTCATAAAGCCAGGGCTTTCGAGTT
106201 TCCTCTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTA
131 TCCTCTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTA
106242 CGGATTTAAT
Statistics
Matches: 344, Mismatches: 9, Indels: 2
0.97 0.03 0.01
Matches are distributed among these distances:
183 343 1.00
184 1 0.00
ACGTcount: A:0.31, C:0.22, G:0.20, T:0.27
Consensus pattern (183 bp):
ACTGAAGGGTTCATCTCATCACAAAGTCTTTGACCTGACAAAAGCAGTGGAGCAAACACCGAATT
GCCAAGTGTCCGAGCAGTGTCATAGTTTGAACATAATCTATTCATAAAGCCAGGGCTTTCGAGTT
TCCTCTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTAGAGGGACAAATC
Found at i:110209 original size:18 final size:17
Alignment explanation
Indices: 110186--110242 Score: 60
Period size: 18 Copynumber: 3.2 Consensus size: 17
110176 TTAGATAAAC
110186 AAGATAAAGAAAACAAAT
1 AAGATAAAGAAAA-AAAT
*
110204 AAGATACAAGGAAAAAAT
1 AAGATA-AAGAAAAAAAT
* *
110222 AAAATAAATAAAATAAAT
1 AAGATAAAGAAAA-AAAT
110240 AAG
1 AAG
110243 TAAGATAAGA
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
17 5 0.16
18 21 0.66
19 6 0.19
ACGTcount: A:0.72, C:0.04, G:0.11, T:0.14
Consensus pattern (17 bp):
AAGATAAAGAAAAAAAT
Found at i:110318 original size:2 final size:2
Alignment explanation
Indices: 110307--110338 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
110297 AAGGAAAAAA
*
110307 AT AT AA AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
110339 CAAAGTATTA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:110391 original size:36 final size:38
Alignment explanation
Indices: 110326--110401 Score: 97
Period size: 38 Copynumber: 2.1 Consensus size: 38
110316 TATATATATA
*
110326 TATATATATATATCAAAGTATTAATAAAATA-AATAAGC
1 TATATATATATACCAAAGTATTAATAAAATAGAA-AAGC
110364 TATATATATATACCAAA-TACTT-A-AAAATAGAAAAGC
1 TATATATATATACCAAAGTA-TTAATAAAATAGAAAAGC
110400 TA
1 TA
110402 CCCTCTCAAT
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
36 12 0.34
37 5 0.14
38 18 0.51
ACGTcount: A:0.55, C:0.08, G:0.05, T:0.32
Consensus pattern (38 bp):
TATATATATATACCAAAGTATTAATAAAATAGAAAAGC
Found at i:110820 original size:13 final size:13
Alignment explanation
Indices: 110804--110829 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
110794 AGTAAAAAAA
110804 AAATGAAAATAAT
1 AAATGAAAATAAT
110817 AAATGAAAATAAT
1 AAATGAAAATAAT
110830 TTAATATATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.69, C:0.00, G:0.08, T:0.23
Consensus pattern (13 bp):
AAATGAAAATAAT
Found at i:110874 original size:18 final size:17
Alignment explanation
Indices: 110851--110893 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
110841 ATATACACAT
110851 ATAATAATAATAACATGA
1 ATAATAATAATAA-ATGA
*
110869 ATAATAAAAATAAATGA
1 ATAATAATAATAAATGA
110886 ATAA-AATA
1 ATAATAATA
110894 TCCATATAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 3 0.13
17 8 0.35
18 12 0.52
ACGTcount: A:0.67, C:0.02, G:0.05, T:0.26
Consensus pattern (17 bp):
ATAATAATAATAAATGA
Found at i:111300 original size:37 final size:37
Alignment explanation
Indices: 111250--111354 Score: 138
Period size: 37 Copynumber: 2.8 Consensus size: 37
111240 GTGCTTGTGG
* * * *
111250 ATCCTATCTTTAGGAATTTAAATCTTAGTAGAACTCT
1 ATCCTATTTTTAGGAGTTTGAATCTTAGTAAAACTCT
* *
111287 ATCCTATTTTTAGGAGTTTGAATCTTAGTAAAAGTTT
1 ATCCTATTTTTAGGAGTTTGAATCTTAGTAAAACTCT
* *
111324 ATCCTATTTTTAAGAGTTTGAATCCTAGTAA
1 ATCCTATTTTTAGGAGTTTGAATCTTAGTAA
111355 GACGAAAATG
Statistics
Matches: 60, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 60 1.00
ACGTcount: A:0.31, C:0.12, G:0.13, T:0.43
Consensus pattern (37 bp):
ATCCTATTTTTAGGAGTTTGAATCTTAGTAAAACTCT
Found at i:111349 original size:21 final size:21
Alignment explanation
Indices: 111287--111350 Score: 57
Period size: 19 Copynumber: 3.3 Consensus size: 21
111277 GTAGAACTCT
*
111287 ATCCTATTTTTAGGAGTTTGA
1 ATCCTATTTTTAAGAGTTTGA
** *
111308 AT-C--TTAGTAAAAGTTT--
1 ATCCTATTTTTAAGAGTTTGA
111324 ATCCTATTTTTAAGAGTTTGA
1 ATCCTATTTTTAAGAGTTTGA
111345 ATCCTA
1 ATCCTA
111351 GTAAGACGAA
Statistics
Matches: 31, Mismatches: 7, Indels: 10
0.65 0.15 0.21
Matches are distributed among these distances:
16 2 0.06
17 1 0.03
18 9 0.29
19 10 0.32
20 1 0.03
21 8 0.26
ACGTcount: A:0.30, C:0.11, G:0.14, T:0.45
Consensus pattern (21 bp):
ATCCTATTTTTAAGAGTTTGA
Found at i:117212 original size:20 final size:20
Alignment explanation
Indices: 117187--117280 Score: 100
Period size: 20 Copynumber: 4.7 Consensus size: 20
117177 AATTGGGAAA
117187 ATCGCAATGCGATACTGACT
1 ATCGCAATGCGATACTGACT
*
117207 ATCGCAATGCGATACTTACT
1 ATCGCAATGCGATACTGACT
* *
117227 ATCGCAATGCGATAAT-ACAAA
1 ATCGCAATGCGATACTGAC--T
* *
117248 ATCGCAACGAGATACTGACT
1 ATCGCAATGCGATACTGACT
* *
117268 TTCGCAACGCGAT
1 ATCGCAATGCGAT
117281 TTACATAGCG
Statistics
Matches: 62, Mismatches: 9, Indels: 6
0.81 0.12 0.08
Matches are distributed among these distances:
19 2 0.03
20 45 0.73
21 13 0.21
22 2 0.03
ACGTcount: A:0.34, C:0.24, G:0.18, T:0.23
Consensus pattern (20 bp):
ATCGCAATGCGATACTGACT
Found at i:117859 original size:19 final size:19
Alignment explanation
Indices: 117799--117879 Score: 64
Period size: 19 Copynumber: 4.5 Consensus size: 19
117789 TTCAAGAATG
117799 AAAATCGCAACGCGGAAATA
1 AAAATCGCAACGC-GAAATA
** *
117819 ACTATCGCAA--CGAGAT-
1 AAAATCGCAACGCGAAATA
117835 --AATCGCAACGCGAAATA
1 AAAATCGCAACGCGAAATA
* **
117852 AAAATCGCAAAGCGAAACC
1 AAAATCGCAACGCGAAATA
117871 AAAATCGCA
1 AAAATCGCA
117880 TTGCGATTTT
Statistics
Matches: 48, Mismatches: 8, Indels: 11
0.72 0.12 0.16
Matches are distributed among these distances:
14 7 0.15
16 5 0.10
17 4 0.08
18 1 0.02
19 23 0.48
20 8 0.17
ACGTcount: A:0.48, C:0.23, G:0.17, T:0.11
Consensus pattern (19 bp):
AAAATCGCAACGCGAAATA
Found at i:117957 original size:39 final size:38
Alignment explanation
Indices: 117875--118045 Score: 165
Period size: 39 Copynumber: 4.6 Consensus size: 38
117865 GAAACCAAAA
*
117875 TCGCATTGCGATTTTCATTTCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTTTCATT
* *
117913 TCGCGTTGCGATTTTTATTTCGCGGTTGTGATTTTCATT
1 TCGCGTTGCGATTTTCATTTCGC-GTTGCGATTTTCATT
* **
117952 TCGCGTTGCGATTGTC---T-G-GTCT-CGATAGTCATT
1 TCGCGTTGCGATTTTCATTTCGCGT-TGCGATTTTCATT
** *
117985 TCGCGTTGCGATAGTCATTTCCGCGTTGCGATTCTCATT
1 TCGCGTTGCGATTTTCATTT-CGCGTTGCGATTTTCATT
* *
118024 ATCTCGTTGCAATTTTCATTTC
1 -TCGCGTTGCGATTTTCATTTC
118046 AACCAAAAGA
Statistics
Matches: 108, Mismatches: 15, Indels: 19
0.76 0.11 0.13
Matches are distributed among these distances:
33 25 0.23
34 1 0.01
35 1 0.01
36 2 0.02
38 23 0.21
39 40 0.37
40 16 0.15
ACGTcount: A:0.13, C:0.21, G:0.21, T:0.45
Consensus pattern (38 bp):
TCGCGTTGCGATTTTCATTTCGCGTTGCGATTTTCATT
Found at i:118022 original size:20 final size:19
Alignment explanation
Indices: 117875--118045 Score: 165
Period size: 19 Copynumber: 9.1 Consensus size: 19
117865 GAAACCAAAA
*
117875 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
117894 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
117913 TCGCGTTGCGATTTTTATT
1 TCGCGTTGCGATTTTCATT
*
117932 TCGCGGTTGTGATTTTCATT
1 TCGC-GTTGCGATTTTCATT
*
117952 TCGCGTTGCGATTGTC---
1 TCGCGTTGCGATTTTCATT
**
117968 T-G-GTCT-CGATAGTCATT
1 TCGCGT-TGCGATTTTCATT
**
117985 TCGCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
*
118004 TCCGCGTTGCGATTCTCATT
1 T-CGCGTTGCGATTTTCATT
* *
118024 ATCTCGTTGCAATTTTCATT
1 -TCGCGTTGCGATTTTCATT
118044 TC
1 TC
118046 AACCAAAAGA
Statistics
Matches: 130, Mismatches: 12, Indels: 20
0.80 0.07 0.12
Matches are distributed among these distances:
14 9 0.07
15 2 0.02
16 1 0.01
17 1 0.01
18 2 0.02
19 66 0.51
20 48 0.37
21 1 0.01
ACGTcount: A:0.13, C:0.21, G:0.21, T:0.45
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:120871 original size:12 final size:12
Alignment explanation
Indices: 120854--120878 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
120844 TCTTCAGGGG
120854 CTTTTTCTTCTT
1 CTTTTTCTTCTT
120866 CTTTTTCTTCTT
1 CTTTTTCTTCTT
120878 C
1 C
120879 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:122008 original size:14 final size:16
Alignment explanation
Indices: 121988--122061 Score: 66
Period size: 19 Copynumber: 4.5 Consensus size: 16
121978 TGAAAATCGC
121988 ATTGCGATTTTC-TCG
1 ATTGCGATTTTCTTCG
122003 -TTGCGATTTTCATTTCG
1 ATTGCGATTTTC--TTCG
122020 CATTGCGATTTTCATTTCG
1 -ATTGCGATTTTC--TTCG
122039 CATTGCGATTTTC-TCG
1 -ATTGCGATTTTCTTCG
122055 -TTGCGAT
1 ATTGCGAT
122062 AGCCATTTCG
Statistics
Matches: 54, Mismatches: 0, Indels: 11
0.83 0.00 0.17
Matches are distributed among these distances:
14 18 0.33
16 3 0.06
17 3 0.06
19 30 0.56
ACGTcount: A:0.14, C:0.20, G:0.19, T:0.47
Consensus pattern (16 bp):
ATTGCGATTTTCTTCG
Found at i:122025 original size:19 final size:19
Alignment explanation
Indices: 121984--122051 Score: 101
Period size: 19 Copynumber: 3.8 Consensus size: 19
121974 GAAATGAAAA
121984 TCGCATTGCGATTTTC---
1 TCGCATTGCGATTTTCATT
122000 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
122017 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
122036 TCGCATTGCGATTTTC
1 TCGCATTGCGATTTTC
122052 TCGTTGCGAT
Statistics
Matches: 47, Mismatches: 0, Indels: 7
0.87 0.00 0.13
Matches are distributed among these distances:
14 11 0.23
16 3 0.06
17 3 0.06
19 30 0.64
ACGTcount: A:0.13, C:0.22, G:0.18, T:0.47
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:122027 original size:52 final size:52
Alignment explanation
Indices: 121965--122079 Score: 131
Period size: 52 Copynumber: 2.2 Consensus size: 52
121955 AACGAGAAAA
* ***
121965 TCGCAATGCGAAATGAAAATCGCATTGCGATTTTCTCGTTGCGATTTTCATT
1 TCGCATTGCGAAATGAAAATCGCATTGCGATTTTCTCGTTGCGATAGCCATT
** ** **
122017 TCGCATTGCGATTTTCATTTCGCATTGCGATTTTCTCGTTGCGATAGCCATT
1 TCGCATTGCGAAATGAAAATCGCATTGCGATTTTCTCGTTGCGATAGCCATT
*
122069 TCGCGTTGCGA
1 TCGCATTGCGA
122080 TAGTCTGTTT
Statistics
Matches: 52, Mismatches: 11, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
52 52 1.00
ACGTcount: A:0.19, C:0.22, G:0.21, T:0.38
Consensus pattern (52 bp):
TCGCATTGCGAAATGAAAATCGCATTGCGATTTTCTCGTTGCGATAGCCATT
Found at i:122187 original size:14 final size:14
Alignment explanation
Indices: 122168--122204 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
122158 CATCAATTAA
122168 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
122182 ACAAATCATCTTTT
1 ACAAATCAACATTT
122196 ACAAATCAA
1 ACAAATCAA
122205 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:124107 original size:20 final size:19
Alignment explanation
Indices: 124072--124138 Score: 80
Period size: 19 Copynumber: 3.5 Consensus size: 19
124062 GAAACTTAAA
124072 ATCGCAACGCGAAATGACT
1 ATCGCAACGCGAAATGACT
* *
124091 ATCGCAGCGCGGAAATGGCT
1 ATCGCAACGC-GAAATGACT
* **
124111 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGACT
124130 ATCGCAACG
1 ATCGCAACG
124139 ACAAAATCGC
Statistics
Matches: 39, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
19 23 0.59
20 16 0.41
ACGTcount: A:0.36, C:0.24, G:0.25, T:0.15
Consensus pattern (19 bp):
ATCGCAACGCGAAATGACT
Found at i:124146 original size:14 final size:14
Alignment explanation
Indices: 124127--124166 Score: 80
Period size: 14 Copynumber: 2.9 Consensus size: 14
124117 ATGCGAAATG
124127 AAAATCGCAACGAC
1 AAAATCGCAACGAC
124141 AAAATCGCAACGAC
1 AAAATCGCAACGAC
124155 AAAATCGCAACG
1 AAAATCGCAACG
124167 CGAAACACAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 26 1.00
ACGTcount: A:0.50, C:0.28, G:0.15, T:0.07
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:124219 original size:14 final size:14
Alignment explanation
Indices: 124200--124257 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
124190 TTTCATTTCG
124200 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
124214 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
124230 CGCATTGCGATTTTGT
1 CG--TTGCGATTTTGT
124246 CGTTGCGATTTT
1 CGTTGCGATTTT
124258 TCATTTCTCA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 21 0.55
16 8 0.21
18 9 0.24
ACGTcount: A:0.10, C:0.17, G:0.24, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:124229 original size:32 final size:33
Alignment explanation
Indices: 124187--124274 Score: 142
Period size: 32 Copynumber: 2.7 Consensus size: 33
124177 ATCGCATTGA
*
124187 GATTTTCATTTCGCGTTGCGATTTTGTCGTTGC
1 GATTTTCATTTCGCATTGCGATTTTGTCGTTGC
124220 GA-TTTCATTTCGCATTGCGATTTTGTCGTTGC
1 GATTTTCATTTCGCATTGCGATTTTGTCGTTGC
*
124252 GATTTTTCATTTCTCATTGCGAT
1 GA-TTTTCATTTCGCATTGCGAT
124275 AGCCATTTTC
Statistics
Matches: 51, Mismatches: 2, Indels: 3
0.91 0.04 0.05
Matches are distributed among these distances:
32 31 0.61
33 2 0.04
34 18 0.35
ACGTcount: A:0.12, C:0.18, G:0.20, T:0.49
Consensus pattern (33 bp):
GATTTTCATTTCGCATTGCGATTTTGTCGTTGC
Found at i:124284 original size:20 final size:20
Alignment explanation
Indices: 124261--124305 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
124251 CGATTTTTCA
*
124261 TTTCTCATTGCGATAGCCAT
1 TTTCGCATTGCGATAGCCAT
* *
124281 TTTCGCGTTGCGATAGTCAT
1 TTTCGCATTGCGATAGCCAT
124301 TTTCG
1 TTTCG
124306 TGTTGCGAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.16, C:0.22, G:0.20, T:0.42
Consensus pattern (20 bp):
TTTCGCATTGCGATAGCCAT
Found at i:124310 original size:20 final size:20
Alignment explanation
Indices: 124268--124313 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
124258 TCATTTCTCA
124268 TTGCGATAGCCATTTTCGCG
1 TTGCGATAGCCATTTTCGCG
* *
124288 TTGCGATAGTCATTTTCGTG
1 TTGCGATAGCCATTTTCGCG
124308 TTGCGA
1 TTGCGA
124314 AAGTAAACTA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.15, C:0.20, G:0.26, T:0.39
Consensus pattern (20 bp):
TTGCGATAGCCATTTTCGCG
Found at i:124821 original size:18 final size:18
Alignment explanation
Indices: 124795--124839 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
124785 GTCGATCAGA
*
124795 TGATGGCTCTGGGTGAGG
1 TGATGGCTCTGGGCGAGG
*
124813 TGATAGCTCTGGGCGAGG
1 TGATGGCTCTGGGCGAGG
124831 TGATGGCTC
1 TGATGGCTC
124840 CCGAAGTGGA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.13, C:0.16, G:0.44, T:0.27
Consensus pattern (18 bp):
TGATGGCTCTGGGCGAGG
Found at i:126180 original size:20 final size:20
Alignment explanation
Indices: 126155--126192 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
126145 AATAGTTTCT
126155 GAAAATGAAAATCGCAACAC
1 GAAAATGAAAATCGCAACAC
**
126175 GAAAATGACTATCGCAAC
1 GAAAATGAAAATCGCAAC
126193 GAGAGAATCG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.50, C:0.21, G:0.16, T:0.13
Consensus pattern (20 bp):
GAAAATGAAAATCGCAACAC
Found at i:126483 original size:22 final size:22
Alignment explanation
Indices: 126456--126499 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
126446 GATGGAGATA
126456 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
*
126478 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
126500 TGAGAGAGTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.18, C:0.16, G:0.45, T:0.20
Consensus pattern (22 bp):
GACGGATTTCGCCGGAGATGGG
Found at i:126781 original size:20 final size:20
Alignment explanation
Indices: 126667--126781 Score: 97
Period size: 20 Copynumber: 5.7 Consensus size: 20
126657 CGCTTTGAAA
*
126667 ATCGCATTGCGATTA-TGTATT
1 ATCGCATTGCGA-TAGT-TAGT
* * *
126688 ATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATAGTTAGT
* * *
126708 ATCGCGTTGCGAAAGTAAGT
1 ATCGCATTGCGATAGTTAGT
* ** *
126728 ATCTCATTGCGATTTTTTATT
1 ATCGCATTGCGA-TAGTTAGT
126749 ATCGCATTGCGATAGTTAGT
1 ATCGCATTGCGATAGTTAGT
126769 ATCGCATTGCGAT
1 ATCGCATTGCGAT
126782 TTTCCCAATT
Statistics
Matches: 76, Mismatches: 16, Indels: 5
0.78 0.16 0.05
Matches are distributed among these distances:
20 50 0.66
21 26 0.34
ACGTcount: A:0.24, C:0.17, G:0.23, T:0.37
Consensus pattern (20 bp):
ATCGCATTGCGATAGTTAGT
Found at i:126799 original size:21 final size:21
Alignment explanation
Indices: 126770--126862 Score: 100
Period size: 20 Copynumber: 4.5 Consensus size: 21
126760 ATAGTTAGTA
126770 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGATTTTCCCAAT
* * **
126791 TCGCGTTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTCCCAAT
126811 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGATTTTCCCAAT
* * **
126832 TCGCGTTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTCCCAAT
126852 TCGCATTGCGA
1 TCGCATTGCGA
126863 ATTGGGAAAA
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 32 0.55
21 26 0.45
ACGTcount: A:0.17, C:0.25, G:0.18, T:0.40
Consensus pattern (21 bp):
TCGCATTGCGATTTTCCCAAT
Found at i:126800 original size:41 final size:41
Alignment explanation
Indices: 126709--126843 Score: 150
Period size: 41 Copynumber: 3.3 Consensus size: 41
126699 AAAGTCAGTA
* * * ** *
126709 TCGCGTTGCGAAAGTAAGTATCTCATTGCGATTTT-TTATT
1 TCGCGTTGCGATAGTTAGTATCGCATTGCGATTTTCCCAAT
*
126749 ATCGCATTGCGATAGTTAGTATCGCATTGCGATTTTCCCAAT
1 -TCGCGTTGCGATAGTTAGTATCGCATTGCGATTTTCCCAAT
*
126791 TCGCGTTGCGAT--TTACTTATTCGCATTGCGATTTTCCCAAT
1 TCGCGTTGCGATAGTTA-GTA-TCGCATTGCGATTTTCCCAAT
126832 TCGCGTTGCGAT
1 TCGCGTTGCGAT
126844 TTACTTATTC
Statistics
Matches: 82, Mismatches: 9, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
39 3 0.04
40 2 0.02
41 75 0.91
42 2 0.02
ACGTcount: A:0.20, C:0.21, G:0.20, T:0.39
Consensus pattern (41 bp):
TCGCGTTGCGATAGTTAGTATCGCATTGCGATTTTCCCAAT
Found at i:126814 original size:20 final size:20
Alignment explanation
Indices: 126732--126862 Score: 97
Period size: 20 Copynumber: 6.4 Consensus size: 20
126722 GTAAGTATCT
*
126732 CATTGCGATTT-TTTATTATCG
1 CATTGCGATTTACTTA-T-TCG
*
126753 CATTGCGA--TAGTTAGTATCG
1 CATTGCGATTTACTTA-T-TCG
* **
126773 CATTGCGATTTTCCCAATTCG
1 CATTGCGA-TTTACTTATTCG
*
126794 CGTTGCGATTTACTTATTCG
1 CATTGCGATTTACTTATTCG
* **
126814 CATTGCGATTTTCCCAATTCG
1 CATTGCGA-TTTACTTATTCG
*
126835 CGTTGCGATTTACTTATTCG
1 CATTGCGATTTACTTATTCG
126855 CATTGCGA
1 CATTGCGA
126863 ATTGGGAAAA
Statistics
Matches: 86, Mismatches: 19, Indels: 11
0.74 0.16 0.09
Matches are distributed among these distances:
19 1 0.01
20 48 0.56
21 34 0.40
22 1 0.01
23 2 0.02
ACGTcount: A:0.19, C:0.21, G:0.18, T:0.41
Consensus pattern (20 bp):
CATTGCGATTTACTTATTCG
Found at i:126844 original size:41 final size:41
Alignment explanation
Indices: 126770--126862 Score: 186
Period size: 41 Copynumber: 2.3 Consensus size: 41
126760 ATAGTTAGTA
126770 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
126811 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
126852 TCGCATTGCGA
1 TCGCATTGCGA
126863 ATTGGGAAAA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.17, C:0.25, G:0.18, T:0.40
Consensus pattern (41 bp):
TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
Found at i:130093 original size:39 final size:39
Alignment explanation
Indices: 130029--130103 Score: 123
Period size: 39 Copynumber: 1.9 Consensus size: 39
130019 TGTAACCCCT
* *
130029 TCTTGCCTGGATCATCAAAAGAACTGCATGAATCACTAA
1 TCTTACCTGAATCATCAAAAGAACTGCATGAATCACTAA
*
130068 TCTTACCTGAATCATCAAAAGAACTGCATGCATCAC
1 TCTTACCTGAATCATCAAAAGAACTGCATGAATCAC
130104 CAATTGTGGT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 33 1.00
ACGTcount: A:0.36, C:0.25, G:0.13, T:0.25
Consensus pattern (39 bp):
TCTTACCTGAATCATCAAAAGAACTGCATGAATCACTAA
Found at i:130748 original size:16 final size:17
Alignment explanation
Indices: 130727--130759 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
130717 TTTTTTTCCG
130727 ATTAATTATAT-ATTTT
1 ATTAATTATATCATTTT
*
130743 ATTAATTTTATCATTTT
1 ATTAATTATATCATTTT
130760 TAAAATTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (17 bp):
ATTAATTATATCATTTT
Found at i:134270 original size:21 final size:21
Alignment explanation
Indices: 134246--134306 Score: 70
Period size: 21 Copynumber: 2.9 Consensus size: 21
134236 TTTTTTTTCC
* *
134246 TTTTTTTTCTTTTTCTTTACA
1 TTTTCTTTATTTTTCTTTACA
*
134267 TTTTCTTTATTTTTCTTTAAA
1 TTTTCTTTATTTTTCTTTACA
*
134288 GGTTTCTTTATTTTT-TTTA
1 -TTTTCTTTATTTTTCTTTA
134307 ATAATGCTAA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
21 22 0.63
22 13 0.37
ACGTcount: A:0.13, C:0.10, G:0.03, T:0.74
Consensus pattern (21 bp):
TTTTCTTTATTTTTCTTTACA
Found at i:134293 original size:22 final size:21
Alignment explanation
Indices: 134255--134307 Score: 72
Period size: 21 Copynumber: 2.5 Consensus size: 21
134245 CTTTTTTTTC
* *
134255 TTTTTCTTTACATTTTCTTTA
1 TTTTTCTTTAAAGTTTCTTTA
134276 TTTTTCTTTAAAGGTTTCTTTA
1 TTTTTCTTTAAA-GTTTCTTTA
134298 TTTTT-TTTAA
1 TTTTTCTTTAA
134308 TAATGCTAAG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
21 16 0.55
22 13 0.45
ACGTcount: A:0.17, C:0.09, G:0.04, T:0.70
Consensus pattern (21 bp):
TTTTTCTTTAAAGTTTCTTTA
Found at i:143154 original size:2 final size:2
Alignment explanation
Indices: 143147--143180 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
143137 CATTTCATTA
143147 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
143181 CAAAAAAATT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:144309 original size:19 final size:19
Alignment explanation
Indices: 144287--144324 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
144277 TTAAATTTTC
*
144287 ATAT-TATATTTA-ATAAT
1 ATATATATAATTATATAAT
144304 ATATATATAATTATATAAT
1 ATATATATAATTATATAAT
144323 AT
1 AT
144325 TAACGTTAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 4 0.22
18 7 0.39
19 7 0.39
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (19 bp):
ATATATATAATTATATAAT
Found at i:145920 original size:21 final size:21
Alignment explanation
Indices: 145894--145933 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
145884 TCACGCCTGT
145894 GGCGTGGACTGGCACTCCTTC
1 GGCGTGGACTGGCACTCCTTC
*
145915 GGCGTGGACTGGCGCTCCT
1 GGCGTGGACTGGCACTCCT
145934 GCTCCTACTC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.07, C:0.33, G:0.38, T:0.23
Consensus pattern (21 bp):
GGCGTGGACTGGCACTCCTTC
Found at i:153533 original size:177 final size:175
Alignment explanation
Indices: 153233--153585 Score: 607
Period size: 177 Copynumber: 2.0 Consensus size: 175
153223 GGGGAGTACA
** *
153233 ACAACTTGGATAGTAATCAGTGTTGCAGGACTCCACAAAATGGCTACTGGTGAAGACAACAGGAT
1 ACAACTTGGATAGTAATCAGTGTTGCAGGACTCCACAAAATGGCTACCAGTGAAGACAACAGCAT
*
153298 ATGACATAGGAGATATCAACCCTAAAAGTATCCCACATCAGATAGACAGTAGGAAATCCGGTCTT
66 ATGACATAGGAGATATCAACCCTAAAAGCATCCCACATCAGATAGACAGTAGGAAATCCGGTCTT
*
153363 ATTTTATGATAGATTTTGAACCCAACTTTTCAGGTGAGTTTTGAG
131 ATTTTATGATAGATTTTGAACCCAACTTTTCAGGTGAATTTTGAG
*
153408 ACAACTTTGGATAGTAATCAGTGTTGCAGGACTCCACAAAATGGCTTCCCAGTGAAGACAACAGC
1 ACAAC-TTGGATAGTAATCAGTGTTGCAGGACTCCACAAAATGGC-TACCAGTGAAGACAACAGC
* *
153473 ATATGACATAGGAGATATCAACCCTATAAGCATCCCACTTCAGATAGACAGTAGGAAATCCGGTC
64 ATATGACATAGGAGATATCAACCCTAAAAGCATCCCACATCAGATAGACAGTAGGAAATCCGGTC
*
153538 TTATTTTATGATGGATTTTGAACCCAACTTTTCAGGTGAATTTTGAG
129 TTATTTTATGATAGATTTTGAACCCAACTTTTCAGGTGAATTTTGAG
153585 A
1 A
153586 AGAAAATCAT
Statistics
Matches: 167, Mismatches: 9, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
175 5 0.03
176 39 0.23
177 123 0.74
ACGTcount: A:0.34, C:0.19, G:0.20, T:0.27
Consensus pattern (175 bp):
ACAACTTGGATAGTAATCAGTGTTGCAGGACTCCACAAAATGGCTACCAGTGAAGACAACAGCAT
ATGACATAGGAGATATCAACCCTAAAAGCATCCCACATCAGATAGACAGTAGGAAATCCGGTCTT
ATTTTATGATAGATTTTGAACCCAACTTTTCAGGTGAATTTTGAG
Found at i:160045 original size:23 final size:23
Alignment explanation
Indices: 160019--160066 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
160009 ATAAAGTACA
*
160019 ATAACATACTAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
** *
160042 ATAATGTAATAGGTAGCGTTTAT
1 ATAACATAATAGGTAGCGCTTAT
160065 AT
1 AT
160067 TTACCTATTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.35, C:0.10, G:0.19, T:0.35
Consensus pattern (23 bp):
ATAACATAATAGGTAGCGCTTAT
Found at i:160473 original size:21 final size:22
Alignment explanation
Indices: 160448--160499 Score: 77
Period size: 23 Copynumber: 2.3 Consensus size: 22
160438 ACACTTTACA
*
160448 ATATAACCACTACCTATTACATT
1 ATATAAACA-TACCTATTACATT
160471 ATATAAACGATACCTATTACATT
1 ATATAAAC-ATACCTATTACATT
160494 ATATAA
1 ATATAA
160500 GGGCTACCTA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
23 26 0.96
24 1 0.04
ACGTcount: A:0.44, C:0.19, G:0.02, T:0.35
Consensus pattern (22 bp):
ATATAAACATACCTATTACATT
Found at i:160484 original size:23 final size:23
Alignment explanation
Indices: 160458--160520 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
160448 ATATAACCAC
160458 TACCTATTACATTATATAAACGA
1 TACCTATTACATTATATAAACGA
** *
160481 TACCTATTACATTATATAAGGGC
1 TACCTATTACATTATATAAACGA
*
160504 TACCTATTACATCATAT
1 TACCTATTACATTATAT
160521 GTTTACCTAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.38, C:0.19, G:0.06, T:0.37
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:160977 original size:38 final size:37
Alignment explanation
Indices: 160921--161005 Score: 134
Period size: 38 Copynumber: 2.2 Consensus size: 37
160911 TCAAGTTGTA
* *
160921 GATTTTGATTTCCTTTTGCTTGGCATCATATGAGATTTG
1 GATTTTGA-TTCCTTTTGCTTGGCACCATATGAG-CTTG
160960 GATTTTGATTCCTTTTGCTTGGCACCATATGAGCTTG
1 GATTTTGATTCCTTTTGCTTGGCACCATATGAGCTTG
160997 GATTTTGAT
1 GATTTTGAT
161006 GAGCATCGGA
Statistics
Matches: 44, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
37 12 0.27
38 24 0.55
39 8 0.18
ACGTcount: A:0.18, C:0.14, G:0.21, T:0.47
Consensus pattern (37 bp):
GATTTTGATTCCTTTTGCTTGGCACCATATGAGCTTG
Found at i:161284 original size:18 final size:18
Alignment explanation
Indices: 161261--161297 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
161251 CGAAATATAT
161261 ATTGAAATTCAAACTCAA
1 ATTGAAATTCAAACTCAA
* *
161279 ATTGAAATTTAAATTCAA
1 ATTGAAATTCAAACTCAA
161297 A
1 A
161298 CTCCAATTAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.51, C:0.11, G:0.05, T:0.32
Consensus pattern (18 bp):
ATTGAAATTCAAACTCAA
Found at i:161562 original size:25 final size:25
Alignment explanation
Indices: 161534--161584 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 25
161524 TTAATCCAAA
*
161534 TAATGTACCCATAACAATGTTCAAT
1 TAATGTACCCACAACAATGTTCAAT
*
161559 TAATGTACCCACAACAATGTTTAAT
1 TAATGTACCCACAACAATGTTCAAT
161584 T
1 T
161585 GATTTGTTGT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.39, C:0.20, G:0.08, T:0.33
Consensus pattern (25 bp):
TAATGTACCCACAACAATGTTCAAT
Found at i:161888 original size:23 final size:23
Alignment explanation
Indices: 161860--161919 Score: 84
Period size: 23 Copynumber: 2.6 Consensus size: 23
161850 ATAACCACTA
161860 CTATTACATTATATAAACGATAC
1 CTATTACATTATATAAACGATAC
** *
161883 CTATTACATTATATAAGGGCTAC
1 CTATTACATTATATAAACGATAC
*
161906 CTATTACATCATAT
1 CTATTACATTATAT
161920 GTTTACCTAT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.38, C:0.18, G:0.07, T:0.37
Consensus pattern (23 bp):
CTATTACATTATATAAACGATAC
Found at i:162254 original size:20 final size:20
Alignment explanation
Indices: 162229--162267 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
162219 TCCACAGTGA
* *
162229 AAAAAGTATGGACACTTTAT
1 AAAAAGGATAGACACTTTAT
162249 AAAAAGGATAGACACTTTA
1 AAAAAGGATAGACACTTTA
162268 CAATATAACA
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:0.49, C:0.10, G:0.15, T:0.26
Consensus pattern (20 bp):
AAAAAGGATAGACACTTTAT
Found at i:162309 original size:23 final size:23
Alignment explanation
Indices: 162279--162341 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
162269 AATATAACAC
162279 TACCTATTACATTATATAAACGA
1 TACCTATTACATTATATAAACGA
** *
162302 TACCTATTACATTATATAAGGGC
1 TACCTATTACATTATATAAACGA
*
162325 TACCTATTACATCATAT
1 TACCTATTACATTATAT
162342 GTTTACCTAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.38, C:0.19, G:0.06, T:0.37
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:162401 original size:422 final size:422
Alignment explanation
Indices: 161616--162439 Score: 1498
Period size: 422 Copynumber: 1.9 Consensus size: 422
161606 TTTGAATTAT
161616 TTGATTTAATAATTTCATTTGCACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATAT
1 TTGATTTAATAATTTCATTTGCACAAAAAATTATTTGATTGTTTTGATATTTTAT--AATAATAT
*
161681 TTAGAATTTTTAATTTAATAATAATATCGTAACGTAAAAAATAAATCATTATACGCCTATAATTA
64 TTAGAATTTTTAATTTAATAATAATATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTA
*
161746 TTAAATTAATATCTTAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAA
129 CTAAATTAATATCTTAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAA
161811 GTATGGACACTTTTATAAAAAGGATAGACACTTTACAATATAACCACTACTATTACATTATATAA
194 GTATGGACACTTTTATAAAAAGGATAGACACTTTACAATATAACCACTACTATTACATTATATAA
161876 ACGATACCTATTACATTATATAAGGGCTACCTATTACATCATATGTTTACCTATTATATTGAAAG
259 ACGATACCTATTACATTATATAAGGGCTACCTATTACATCATATGTTTACCTATTATATTGAAAG
*
161941 TGTCCATACTTTTTATAAAAGGATCGATACTTTTTTTAAAAGTTATGTAATTTATGTTTCAA-TT
324 TGTCCATACTTTTTATAAAAGGATCGATACTTTTTTTAAAACTTATGTAATTTATGTTTCAATTT
162005 TTTTAACAGTGTTTCATGTTTTCCACCTACAATA
389 TTTTAACAGTGTTTCATGTTTTCCACCTACAATA
*
162039 TTGATTTAATAATTTCA-TTGCACAAAAAATTATTTGATTGTTTTTATATTTTAT-A-AATATTT
1 TTGATTTAATAATTTCATTTGCACAAAAAATTATTTGATTGTTTTGATATTTTATAATAATATTT
162101 AGAATTTTTAATTTAATAATAATATATACCGTAACGTAAAAAATAAATCATTAGACGCCTATAAT
66 AGAATTTTTAATTTAATAAT-A-ATAT--CGTAACGTAAAAAATAAATCATTAGACGCCTATAAT
162166 TACTAAATTAATATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAA
127 TACTAAATTAATATCTT-AAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAA
162231 AAAGTATGGACAC-TTTATAAAAAGGATAGACACTTTACAATATAA-CACTACCTATTACATTAT
191 AAAGTATGGACACTTTTATAAAAAGGATAGACACTTTACAATATAACCACTA-CTATTACATTAT
162294 ATAAACGATACCTATTACATTATATAAGGGCTACCTATTACATCATATGTTTACCTATTATATTG
255 ATAAACGATACCTATTACATTATATAAGGGCTACCTATTACATCATATGTTTACCTATTATATTG
162359 AAAGTGTCCATACTTTTTATAAAAGGATCGATACTTTTTTTAAAACTTATGTAATTTATGTTTCA
320 AAAGTGTCCATACTTTTTATAAAAGGATCGATACTTTTTTTAAAACTTATGTAATTTATGTTTCA
162424 ATTTTTTTAACAGTGT
385 ATTTTTTTAACAGTGT
162440 ACTGCGAATT
Statistics
Matches: 390, Mismatches: 4, Indels: 14
0.96 0.01 0.03
Matches are distributed among these distances:
418 27 0.07
419 2 0.01
420 4 0.01
421 5 0.01
422 261 0.67
423 91 0.23
ACGTcount: A:0.39, C:0.12, G:0.08, T:0.40
Consensus pattern (422 bp):
TTGATTTAATAATTTCATTTGCACAAAAAATTATTTGATTGTTTTGATATTTTATAATAATATTT
AGAATTTTTAATTTAATAATAATATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACT
AAATTAATATCTTAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGT
ATGGACACTTTTATAAAAAGGATAGACACTTTACAATATAACCACTACTATTACATTATATAAAC
GATACCTATTACATTATATAAGGGCTACCTATTACATCATATGTTTACCTATTATATTGAAAGTG
TCCATACTTTTTATAAAAGGATCGATACTTTTTTTAAAACTTATGTAATTTATGTTTCAATTTTT
TTAACAGTGTTTCATGTTTTCCACCTACAATA
Found at i:166688 original size:3 final size:3
Alignment explanation
Indices: 166680--166772 Score: 87
Period size: 3 Copynumber: 31.0 Consensus size: 3
166670 ACTTGTTTGG
* * * *
166680 ATC ATC ATC TTC ATC ATC ATC ATC ATC ATC GTC ATC GTC ATC ATC TTC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
** * * * * *
166728 ATC GCC AGC TTC ATC GTC ATC ATC ATC ATC ATC GTC ATC TTC ATC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
166773 GTCAGCTTCA
Statistics
Matches: 69, Mismatches: 21, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
3 69 1.00
ACGTcount: A:0.24, C:0.34, G:0.06, T:0.35
Consensus pattern (3 bp):
ATC
Found at i:166697 original size:12 final size:12
Alignment explanation
Indices: 166680--166787 Score: 90
Period size: 12 Copynumber: 9.0 Consensus size: 12
166670 ACTTGTTTGG
166680 ATCATCATCTTC
1 ATCATCATCTTC
*
166692 ATCATCATCATC
1 ATCATCATCTTC
* *
166704 ATCATCGTCATC
1 ATCATCATCTTC
*
166716 GTCATCATCTTC
1 ATCATCATCTTC
** *
166728 ATCGCCAGCTTC
1 ATCATCATCTTC
* *
166740 ATCGTCATCATC
1 ATCATCATCTTC
*
166752 ATCATCATCGTC
1 ATCATCATCTTC
* *
166764 ATCTTCATCGTC
1 ATCATCATCTTC
* *
166776 AGCTTCATCTTC
1 ATCATCATCTTC
166788 TGCGACCGCT
Statistics
Matches: 79, Mismatches: 17, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
12 79 1.00
ACGTcount: A:0.22, C:0.34, G:0.07, T:0.36
Consensus pattern (12 bp):
ATCATCATCTTC
Found at i:166703 original size:18 final size:18
Alignment explanation
Indices: 166680--166784 Score: 102
Period size: 18 Copynumber: 5.8 Consensus size: 18
166670 ACTTGTTTGG
166680 ATCATCATCTTCATCATC
1 ATCATCATCTTCATCATC
* *
166698 ATCATCATCATCGTCATC
1 ATCATCATCTTCATCATC
* **
166716 GTCATCATCTTCATCGCC
1 ATCATCATCTTCATCATC
* * *
166734 AGCTTCATCGTCATCATC
1 ATCATCATCTTCATCATC
* *
166752 ATCATCATCGTCATCTTC
1 ATCATCATCTTCATCATC
* *
166770 ATCGTCAGCTTCATC
1 ATCATCATCTTCATC
166785 TTCTGCGACC
Statistics
Matches: 68, Mismatches: 19, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
18 68 1.00
ACGTcount: A:0.23, C:0.34, G:0.08, T:0.35
Consensus pattern (18 bp):
ATCATCATCTTCATCATC
Found at i:166748 original size:42 final size:42
Alignment explanation
Indices: 166696--166784 Score: 133
Period size: 42 Copynumber: 2.1 Consensus size: 42
166686 ATCTTCATCA
* *
166696 TCATCATCATCATCGTCATCGTCATCATCTTCATCGCCAGCT
1 TCATCATCATCATCATCATCATCATCATCTTCATCGCCAGCT
* * *
166738 TCATCGTCATCATCATCATCATCGTCATCTTCATCGTCAGCT
1 TCATCATCATCATCATCATCATCATCATCTTCATCGCCAGCT
166780 TCATC
1 TCATC
166785 TTCTGCGACC
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.21, C:0.35, G:0.09, T:0.35
Consensus pattern (42 bp):
TCATCATCATCATCATCATCATCATCATCTTCATCGCCAGCT
Found at i:166785 original size:18 final size:18
Alignment explanation
Indices: 166720--166787 Score: 55
Period size: 21 Copynumber: 3.4 Consensus size: 18
166710 GTCATCGTCA
*
166720 TCATCTTCATCGCCAGCT
1 TCATCTTCATCGTCAGCT
* *
166738 TCATCGTCATCATCATCATCAT
1 TCATC-T--TCATCGTCAGC-T
166760 CGTCATCTTCATCGTCAGCT
1 --TCATCTTCATCGTCAGCT
166780 TCATCTTC
1 TCATCTTC
166788 TGCGACCGCT
Statistics
Matches: 39, Mismatches: 5, Indels: 12
0.70 0.09 0.21
Matches are distributed among these distances:
18 13 0.33
19 1 0.03
20 1 0.03
21 17 0.44
22 1 0.03
23 1 0.03
24 5 0.13
ACGTcount: A:0.19, C:0.35, G:0.09, T:0.37
Consensus pattern (18 bp):
TCATCTTCATCGTCAGCT
Found at i:169156 original size:194 final size:195
Alignment explanation
Indices: 168222--170123 Score: 2958
Period size: 193 Copynumber: 9.9 Consensus size: 195
168212 TAATTAGTAG
168222 CGACACAAACTATATTAGTGTCGACACA-TATTTAGACATATTCTCTCATAAAACGGTATAATTG
1 CGACACAAACTATATTAG-GTCGACACATTATTTAGACATA-TCTCTCATAAAACGGTATAATTG
168286 TACCGGTTAGATTGAAAAATTA-ATA-TACATTATACTTTTGGGTTCGATGATTTGTTGGGATCG
64 TACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGA-TT-TTGGGATCG
*
168349 --ACTTTTTATATATGGATCGACACTTTATGGGTGCA-CCTGTTTTCCATTCATTCTGGGGAAAA
127 ACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCT-GGAAAAA
168411 AATAT
191 AATAT
*
168416 CGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGTATAATTG
1 CGACACAAACTATATTAG-GTCGACACATTATTTAGACATA-TCTCTCATAAAACGGTATAATTG
168481 TACCGGTTAGATTGAAAAATTA-ATATTACATTATACTTTTGGGTTCGATGATTTTGGGATCGAC
64 TACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGATCGAC
*
168545 ACTTTTTATATATGGATCGACACTTTATGGGTGCA-CC--TTTTCCATTC-TTCTGGGGAAAAAA
129 ACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCT-GGAAAAAAA
168606 TAT
193 TAT
168609 CGACACAAACTATATTAGTGTCGACACATTATTTAGACAT-TCTCTCATAAAACGGTATAATTGT
1 CGACACAAACTATATTAG-GTCGACACATTATTTAGACATATCTCTCATAAAACGGTATAATTGT
168673 A-CGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGATCGACA
65 ACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGATCGACA
168737 C-TTTTATATATGGATCGACAC-TTAT-GGTGCACCCTG-TTTCCATTCATTCTGGAAAAAAATA
130 CTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAAAAATA
168798 T
195 T
168799 CGACACAAACTATATTAGTGTCGACACATTATTTAGAC-TATCCTCTCATAAAACCGGTATAATT
1 CGACACAAACTATATTAG-GTCGACACATTATTTAGACATAT-CTCTCATAAAA-CGGTATAATT
*
168863 GTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGTTTTCGATGATTTTGGGATCG
63 GTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGG-GTTCGATGATTTTGGGATCG
* **
168928 ACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGAAAAAA
127 ACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGG-AAAAA
168993 AATAT
191 AATAT
168998 CGACACAAACTATATTA-GTCGACACATTATTTAGACATAT-TCTCATAAAACGGTATAATTGTA
1 CGACACAAACTATATTAGGTCGACACATTATTTAGACATATCTCTCATAAAACGGTATAATTGTA
169061 CCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGATCGACAC
66 CCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGATCGACAC
* *
169126 TTTTTATATATGGATCGACACTTTATGGGTG-ACCTTGTTTTCCATTCATTCTGGGGAAAAAATA
131 TTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCT-GGAAAAAAATA
169190 T
195 T
*
169191 AGACACAAACTATATTAGTGTCGACACATTA-TTAGACATAT-TCTCATAAAACCGGTATAATTG
1 CGACACAAACTATATTAG-GTCGACACATTATTTAGACATATCTCTCATAAAA-CGGTATAATTG
169254 TACCGG-TAGATTGAAAAATTACATATTACATTATACTTTTGGGGTTCGATGATTTTGGGATCGA
64 TACCGGTTAGATTGAAAAATTACATATTACATTATACTTTT-GGGTTCGATGATTTTGGGATCGA
*
169318 CACTGTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGG-AAAAAA
128 CACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAAAAA
169382 -AT
193 TAT
169384 CGACACAAACTATATTAGTGTCGACACATTATTTAGACATATC-CTCATAAAACCGGTATAATTG
1 CGACACAAACTATATTAG-GTCGACACATTATTTAGACATATCTCTCATAAAA-CGGTATAATTG
169448 TA-CGGTTAGATTG-AAAA--ACATATTACA-T-TAC-TTTGGGTTCGATGATTTTGGGATCGAC
64 TACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGATCGAC
* *
169506 ACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTT-AATTCATTCTGGAAAAATAA
129 ACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAAA-AA
169570 TAT
193 TAT
169573 CG--AC-AA--ATATTAGTGTCGACACATTATTTAGACATAT-TCTCATAAAACCGGTATAATTG
1 CGACACAAACTATATTAG-GTCGACACATTATTTAGACATATCTCTCATAAAA-CGGTATAATTG
169632 TACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGATCGAC
64 TACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGATCGAC
* * *
169697 ACTTTTTATATATGGATCGACAC-GTAT-GGTGC-CCTTGTTTT-AATTCATTCTGGAAAAAAAA
129 ACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGG-AAAAAAA
169758 TAT
193 TAT
169761 CGACACAAACTATATTAGTGTCGACACATTATTTAGACATATCCTCTCATAAAACGGTATAATTG
1 CGACACAAACTATATTAG-GTCGACACATTATTTAGACATAT-CTCTCATAAAACGGTATAATTG
*
169826 TA-CGGTTAGATTGAAAAA--AAATTATTACATTATACTTTTGGGTTCGATGATTTTGGGATCGG
64 TACCGGTTAGATTGAAAAATTACA-TATTACATTATACTTTTGGGTTCGATGATTTTGGGATC-G
169888 ACACTTTTTATATATGGATCGA-ACTTTATGGGTGCACCCTGTTTTCCA-TCATTCTGGAAAAAA
127 ACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAAAA
169951 ATAT
192 ATAT
*
169955 CGACA-AAACTATATTAGTGTCGACACA-TATTTAGACATATCCTCTCATAAACCGGTATAATTG
1 CGACACAAACTATATTAG-GTCGACACATTATTTAGACATAT-CTCTCATAAAACGGTATAATTG
* * *
170018 TACCGGTTAGATTGAAAAATTACATATTACATTATAC-TTTGGTTTTCGATGTTTTTGGGATTGA
64 TACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGG-GTTCGATGATTTTGGGATCGA
170082 CACTTTTT-TATATGGATCGACACTTTATGGGTGCACCCTGTT
128 CACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTT
170124 GGCCATATTG
Statistics
Matches: 1621, Mismatches: 28, Indels: 119
0.92 0.02 0.07
Matches are distributed among these distances:
184 54 0.03
185 11 0.01
186 17 0.01
187 72 0.04
188 49 0.03
189 25 0.02
190 107 0.07
191 147 0.09
192 102 0.06
193 327 0.20
194 288 0.18
195 252 0.16
196 97 0.06
197 29 0.02
198 17 0.01
199 27 0.02
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (195 bp):
CGACACAAACTATATTAGGTCGACACATTATTTAGACATATCTCTCATAAAACGGTATAATTGTA
CCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGATCGACAC
TTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAAAAATAT
Found at i:172055 original size:29 final size:29
Alignment explanation
Indices: 172022--172081 Score: 84
Period size: 29 Copynumber: 2.1 Consensus size: 29
172012 CTTAATATCA
172022 CCCCTAACACCGAAACTTCTTTCACCACT
1 CCCCTAACACCGAAACTTCTTTCACCACT
* ***
172051 CCCCTCACACCTCTACTTCTTTCACCACT
1 CCCCTAACACCGAAACTTCTTTCACCACT
172080 CC
1 CC
172082 ATCTATTTTT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.22, C:0.50, G:0.02, T:0.27
Consensus pattern (29 bp):
CCCCTAACACCGAAACTTCTTTCACCACT
Done.