Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009616.1 Hibiscus syriacus cultivar Beakdansim tig00117002_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: 692457
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 4
Found at i:13688 original size:2 final size:2
Alignment explanation
Indices: 13683--13722 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
13673 AAATGAAGCA
13683 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
13723 TATTATCATG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:13826 original size:2 final size:2
Alignment explanation
Indices: 13815--13960 Score: 55
Period size: 2 Copynumber: 74.5 Consensus size: 2
13805 ATAAGAATAA
* *
13815 AT AT ACT AT AT A- AGT AT AT AT AT AT AT AT AC A- AT -T AT AC AT
1 AT AT A-T AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * *
13856 AT GAGT AT AT A- AT AT AT AA AT AT AA AT -T AT AT A- AT AA AGT
1 AT -A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T
*
13896 AT AT A- AT A- AT AT A- AA ACT AT AT A- AT AT A- AGT AT AT A- AT
1 AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT A-T AT AT AT AT
* *
13934 AT AT AT GT AT AT AA ACT AT AT AGT AT A
1 AT AT AT AT AT AT AT A-T AT AT A-T AT A
13961 GGCATATAAA
Statistics
Matches: 109, Mismatches: 14, Indels: 42
0.66 0.08 0.25
Matches are distributed among these distances:
1 12 0.11
2 85 0.78
3 11 0.10
4 1 0.01
ACGTcount: A:0.53, C:0.03, G:0.05, T:0.39
Consensus pattern (2 bp):
AT
Found at i:13943 original size:15 final size:15
Alignment explanation
Indices: 13868--13960 Score: 61
Period size: 15 Copynumber: 6.3 Consensus size: 15
13858 GAGTATATAA
*
13868 TATATAAATATAAAT-
1 TATAT-AATATATATG
* *
13883 TATATAATAAAGTATA
1 TATATAATATA-TATG
* **
13899 TA-ATAATATAAAAC
1 TATATAATATATATG
13913 TATATAATATA-A-G
1 TATATAATATATATG
13926 TATATAATATATATG
1 TATATAATATATATG
13941 TATATAA-ACTATATAG
1 TATATAATA-TATAT-G
13957 TATA
1 TATA
13961 GGCATATAAA
Statistics
Matches: 64, Mismatches: 7, Indels: 13
0.76 0.08 0.15
Matches are distributed among these distances:
13 11 0.17
14 11 0.17
15 35 0.55
16 7 0.11
ACGTcount: A:0.55, C:0.02, G:0.04, T:0.39
Consensus pattern (15 bp):
TATATAATATATATG
Found at i:13953 original size:22 final size:21
Alignment explanation
Indices: 13927--13990 Score: 58
Period size: 22 Copynumber: 3.0 Consensus size: 21
13917 TAATATAAGT
*
13927 ATATAATATATATGTATATAA
1 ATATAATATATATGCATATAA
*
13948 ACTAT-ATAGTATAGGCATATAA
1 A-TATAATA-TATATGCATATAA
* *
13970 ATAAGAATATATATTCATATA
1 AT-ATAATATATATGCATATA
13991 TGTACGTATG
Statistics
Matches: 34, Mismatches: 5, Indels: 7
0.74 0.11 0.15
Matches are distributed among these distances:
21 5 0.15
22 26 0.76
23 3 0.09
ACGTcount: A:0.50, C:0.05, G:0.08, T:0.38
Consensus pattern (21 bp):
ATATAATATATATGCATATAA
Found at i:14035 original size:20 final size:21
Alignment explanation
Indices: 14010--14054 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 21
14000 GTATGATGCA
*
14010 TGTATAT-ACTTATGTGTGTG
1 TGTATATAACGTATGTGTGTG
14030 TGTATATACACGTATGTGTGTG
1 TGTATATA-ACGTATGTGTGTG
14052 TGT
1 TGT
14055 GCATGTATGC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 7 0.32
22 15 0.68
ACGTcount: A:0.20, C:0.07, G:0.27, T:0.47
Consensus pattern (21 bp):
TGTATATAACGTATGTGTGTG
Found at i:14215 original size:12 final size:12
Alignment explanation
Indices: 14186--14354 Score: 86
Period size: 12 Copynumber: 13.8 Consensus size: 12
14176 TGTATAGTTA
*
14186 TATATATAAAAG
1 TATATATATAAG
14198 CATATATATATAAG
1 --TATATATATAAG
*
14212 TATATACATAAG
1 TATATATATAAG
**
14224 TATATATGTATGATT
1 TATATA--TAT-AAG
* *
14239 TATGTACATAAG
1 TATATATATAAG
14251 TATAAATATATAAG
1 TAT--ATATATAAG
*
14265 TATAAAGTAT-AG
1 TATATA-TATAAG
14277 -A-ATATATAAG
1 TATATATATAAG
14287 TATATATATAAG
1 TATATATATAAG
14299 TATAAAATATATACA-
1 TAT---ATATATA-AG
14314 TA-AGTATAT-A-
1 TATA-TATATAAG
14324 TATATATATAAG
1 TATATATATAAG
*
14336 --TATATGTAAG
1 TATATATATAAG
14346 TATATATAT
1 TATATATAT
14355 GTGATGTATG
Statistics
Matches: 121, Mismatches: 15, Indels: 40
0.69 0.09 0.23
Matches are distributed among these distances:
9 3 0.02
10 21 0.17
11 5 0.04
12 48 0.40
13 5 0.04
14 23 0.19
15 15 0.12
16 1 0.01
ACGTcount: A:0.50, C:0.02, G:0.09, T:0.38
Consensus pattern (12 bp):
TATATATATAAG
Found at i:14229 original size:14 final size:14
Alignment explanation
Indices: 14134--14354 Score: 101
Period size: 14 Copynumber: 16.1 Consensus size: 14
14124 AGAAAAAATA
*
14134 ATATACGTATATAT
1 ATATAAGTATATAT
14148 AT-TAA-TATTATAT
1 ATATAAGTA-TATAT
**
14161 ATATACTTATGCATAT
1 ATATAAGTAT--ATAT
*
14177 GTAT-AGTTATATAT
1 ATATAAG-TATATAT
* *
14191 ATAAAAGCATATAT
1 ATATAAGTATATAT
14205 ATATAAG--TATAT
1 ATATAAGTATATAT
*
14217 ACATAAGTATATAT
1 ATATAAGTATATAT
* * * *
14231 GTATGA-TTTATGT
1 ATATAAGTATATAT
* *
14244 ACATAAGTATAAAT
1 ATATAAGTATATAT
*
14258 ATATAAGTATAAAGT
1 ATATAAGTATATA-T
*
14273 ATAGAA-TATATA-
1 ATATAAGTATATAT
14285 AGTAT-A-TATATA-
1 A-TATAAGTATATAT
*
14297 AGTATAA-AATATAT
1 A-TATAAGTATATAT
*
14311 ACATAAGTATATAT
1 ATATAAGTATATAT
14325 ATAT-A-TATAAGTAT
1 ATATAAGTAT-A-TAT
*
14339 ATGTAAGTATATAT
1 ATATAAGTATATAT
14353 AT
1 AT
14355 GTGATGTATG
Statistics
Matches: 158, Mismatches: 30, Indels: 38
0.70 0.13 0.17
Matches are distributed among these distances:
12 29 0.18
13 31 0.20
14 73 0.46
15 12 0.08
16 13 0.08
ACGTcount: A:0.48, C:0.03, G:0.09, T:0.40
Consensus pattern (14 bp):
ATATAAGTATATAT
Found at i:14321 original size:27 final size:26
Alignment explanation
Indices: 14256--14323 Score: 79
Period size: 27 Copynumber: 2.6 Consensus size: 26
14246 ATAAGTATAA
*
14256 ATAT-ATAAGTATA-AAGTATAGAAT
1 ATATAATAAGTATATAAGTATAAAAT
14280 ATATAAGTATA-TATATAAGTATAAAAT
1 ATATAA-TA-AGTATATAAGTATAAAAT
14307 ATATACATAAGTATATA
1 ATATA-ATAAGTATATA
14324 TATATATATA
Statistics
Matches: 37, Mismatches: 1, Indels: 9
0.79 0.02 0.19
Matches are distributed among these distances:
24 4 0.11
25 1 0.03
26 7 0.19
27 24 0.65
28 1 0.03
ACGTcount: A:0.54, C:0.01, G:0.09, T:0.35
Consensus pattern (26 bp):
ATATAATAAGTATATAAGTATAAAAT
Found at i:14940 original size:12 final size:13
Alignment explanation
Indices: 14918--14947 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
14908 TAAAACTAAT
14918 TTAATGATTATAA
1 TTAATGATTATAA
14931 TTAA-GATTATAA
1 TTAATGATTATAA
14943 TTAAT
1 TTAAT
14948 ATAAAAAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
12 12 0.75
13 4 0.25
ACGTcount: A:0.47, C:0.00, G:0.07, T:0.47
Consensus pattern (13 bp):
TTAATGATTATAA
Found at i:15174 original size:16 final size:16
Alignment explanation
Indices: 15153--15187 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
15143 TCAATTACAT
*
15153 GTCAGGTTCATATCAG
1 GTCAGGTTCATAACAG
*
15169 GTCAGGTTGATAACAG
1 GTCAGGTTCATAACAG
15185 GTC
1 GTC
15188 GGGTAATACC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.26, C:0.17, G:0.29, T:0.29
Consensus pattern (16 bp):
GTCAGGTTCATAACAG
Found at i:19943 original size:29 final size:29
Alignment explanation
Indices: 19900--19994 Score: 154
Period size: 29 Copynumber: 3.3 Consensus size: 29
19890 GAATTCTACA
* *
19900 GGCGACCTCGTAGGTCGCCATGGCATCCG
1 GGCGACCTTGGAGGTCGCCATGGCATCCG
19929 GGCGACCTTGGAGGTCGCCATGGCATCCG
1 GGCGACCTTGGAGGTCGCCATGGCATCCG
*
19958 GGCGACCTTGGAGGTCGCCATGGCATCCA
1 GGCGACCTTGGAGGTCGCCATGGCATCCG
*
19987 AGCGACCT
1 GGCGACCT
19995 GTGTGGTGTT
Statistics
Matches: 62, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 62 1.00
ACGTcount: A:0.16, C:0.33, G:0.35, T:0.17
Consensus pattern (29 bp):
GGCGACCTTGGAGGTCGCCATGGCATCCG
Found at i:20086 original size:20 final size:20
Alignment explanation
Indices: 20061--20098 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
20051 TGGGGGAGTT
*
20061 GTGGGAGCTGTGCATGGGAC
1 GTGGGAACTGTGCATGGGAC
20081 GTGGGAACTGTGCATGGG
1 GTGGGAACTGTGCATGGG
20099 GCATGGGGGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.16, C:0.13, G:0.50, T:0.21
Consensus pattern (20 bp):
GTGGGAACTGTGCATGGGAC
Found at i:20105 original size:20 final size:20
Alignment explanation
Indices: 20062--20105 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
20052 GGGGGAGTTG
* *
20062 TGGGAGCTGTGCATGGGACG
1 TGGGAACTGTGCATGGGACA
*
20082 TGGGAACTGTGCATGGGGCA
1 TGGGAACTGTGCATGGGACA
20102 TGGG
1 TGGG
20106 GGAGTTGTGG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.16, C:0.14, G:0.50, T:0.20
Consensus pattern (20 bp):
TGGGAACTGTGCATGGGACA
Found at i:20117 original size:51 final size:51
Alignment explanation
Indices: 20048--20154 Score: 214
Period size: 51 Copynumber: 2.1 Consensus size: 51
20038 ATTGGAGCAT
20048 GCATGGGGGAGTTGTGGGAGCTGTGCATGGGACGTGGGAACTGTGCATGGG
1 GCATGGGGGAGTTGTGGGAGCTGTGCATGGGACGTGGGAACTGTGCATGGG
20099 GCATGGGGGAGTTGTGGGAGCTGTGCATGGGACGTGGGAACTGTGCATGGG
1 GCATGGGGGAGTTGTGGGAGCTGTGCATGGGACGTGGGAACTGTGCATGGG
20150 GCATG
1 GCATG
20155 CACGTCGAAC
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
51 56 1.00
ACGTcount: A:0.16, C:0.12, G:0.50, T:0.21
Consensus pattern (51 bp):
GCATGGGGGAGTTGTGGGAGCTGTGCATGGGACGTGGGAACTGTGCATGGG
Found at i:20137 original size:20 final size:20
Alignment explanation
Indices: 20112--20149 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
20102 TGGGGGAGTT
*
20112 GTGGGAGCTGTGCATGGGAC
1 GTGGGAACTGTGCATGGGAC
20132 GTGGGAACTGTGCATGGG
1 GTGGGAACTGTGCATGGG
20150 GCATGCACGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.16, C:0.13, G:0.50, T:0.21
Consensus pattern (20 bp):
GTGGGAACTGTGCATGGGAC
Found at i:20652 original size:21 final size:21
Alignment explanation
Indices: 20627--20670 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
20617 AATCTAGTTA
20627 ATTAGTTTGTTAGTATAAATT
1 ATTAGTTTGTTAGTATAAATT
* *
20648 ATTAGTTTGTTAGTTTAAGTT
1 ATTAGTTTGTTAGTATAAATT
20669 AT
1 AT
20671 ATTATATTAG
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:0.30, C:0.00, G:0.16, T:0.55
Consensus pattern (21 bp):
ATTAGTTTGTTAGTATAAATT
Found at i:20680 original size:28 final size:28
Alignment explanation
Indices: 20647--20737 Score: 155
Period size: 28 Copynumber: 3.2 Consensus size: 28
20637 TAGTATAAAT
*
20647 TATTAGTTTGTTAGTTTAAGTTATATTA
1 TATTAGTTTATTAGTTTAAGTTATATTA
20675 TATTAGTTTATTAGTTTAAGTTATATTA
1 TATTAGTTTATTAGTTTAAGTTATATTA
20703 TATTAGTTTATTAGTTTAAGTTATATATTA
1 TATTAGTTTATTAGTTTAAG-T-TATATTA
20733 TATTA
1 TATTA
20738 TATAAAAAAT
Statistics
Matches: 60, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
28 47 0.78
29 1 0.02
30 12 0.20
ACGTcount: A:0.32, C:0.00, G:0.11, T:0.57
Consensus pattern (28 bp):
TATTAGTTTATTAGTTTAAGTTATATTA
Found at i:20688 original size:8 final size:8
Alignment explanation
Indices: 20646--20720 Score: 53
Period size: 8 Copynumber: 10.4 Consensus size: 8
20636 TTAGTATAAA
20646 TTATTAGT
1 TTATTAGT
*
20654 TTGTTAGT
1 TTATTAGT
20662 TTA--AG-
1 TTATTAGT
20667 TTA-TA-T
1 TTATTAGT
20673 TATATTAGT
1 T-TATTAGT
20682 TTATTAGT
1 TTATTAGT
20690 TTA--AG-
1 TTATTAGT
20695 TTA-TA-T
1 TTATTAGT
20701 TATATTAGT
1 T-TATTAGT
20710 TTATTAGT
1 TTATTAGT
20718 TTA
1 TTA
20721 AGTTATATAT
Statistics
Matches: 55, Mismatches: 2, Indels: 20
0.71 0.03 0.26
Matches are distributed among these distances:
5 6 0.11
6 8 0.15
7 4 0.07
8 33 0.60
9 4 0.07
ACGTcount: A:0.29, C:0.00, G:0.12, T:0.59
Consensus pattern (8 bp):
TTATTAGT
Found at i:20753 original size:56 final size:55
Alignment explanation
Indices: 20647--20757 Score: 127
Period size: 56 Copynumber: 2.0 Consensus size: 55
20637 TAGTATAAAT
* * ** **
20647 TATTAGTTTGTTAGTTTAAGTTATATTATATTAGTTTATTAGTTTAAGTTATATTA
1 TATTAGTTTATTAGTTTAAGTTATATTATATTAGTATAAAAAATTAAGTTA-ATTA
20703 TATTAGTTTATTAGTTTAAGTTATATATTATATTA-TATAAAAAATT-AGTTAATTA
1 TATTAGTTTATTAGTTTAAG-T-TATATTATATTAGTATAAAAAATTAAGTTAATTA
20758 GTTTCTTAGT
Statistics
Matches: 47, Mismatches: 6, Indels: 5
0.81 0.10 0.09
Matches are distributed among these distances:
55 4 0.09
56 24 0.51
57 7 0.15
58 12 0.26
ACGTcount: A:0.36, C:0.00, G:0.10, T:0.54
Consensus pattern (55 bp):
TATTAGTTTATTAGTTTAAGTTATATTATATTAGTATAAAAAATTAAGTTAATTA
Found at i:21287 original size:20 final size:21
Alignment explanation
Indices: 21243--21287 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
21233 AAATATTGTG
**
21243 TTTAAAAATATTTAGTGTTGT
1 TTTAAAAATATTTAGTGTTAA
*
21264 TTTAAAAATATTTTGT-TTAA
1 TTTAAAAATATTTAGTGTTAA
21284 TTTA
1 TTTA
21288 CATTGTATGT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 6 0.29
21 15 0.71
ACGTcount: A:0.36, C:0.00, G:0.09, T:0.56
Consensus pattern (21 bp):
TTTAAAAATATTTAGTGTTAA
Found at i:21577 original size:26 final size:25
Alignment explanation
Indices: 21548--21606 Score: 66
Period size: 26 Copynumber: 2.3 Consensus size: 25
21538 AAATCATATT
*
21548 ATTATTAAATCATTAAATATCAAATC
1 ATTATTAAAT-AGTAAATATCAAATC
*
21574 ATTAGATT-AATAGTAATTATCAAATC
1 ATT--ATTAAATAGTAAATATCAAATC
21600 ATTATTA
1 ATTATTA
21607 GGTTTATTAG
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
24 3 0.11
26 19 0.68
27 3 0.11
28 3 0.11
ACGTcount: A:0.47, C:0.08, G:0.03, T:0.41
Consensus pattern (25 bp):
ATTATTAAATAGTAAATATCAAATC
Found at i:25105 original size:15 final size:14
Alignment explanation
Indices: 25082--25112 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
25072 TACAACACTA
25082 AACTTTAATATAAT
1 AACTTTAATATAAT
25096 AACTTATAATATAAT
1 AACTT-TAATATAAT
25111 AA
1 AA
25113 ACTAATAAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.31
15 11 0.69
ACGTcount: A:0.55, C:0.06, G:0.00, T:0.39
Consensus pattern (14 bp):
AACTTTAATATAAT
Found at i:25237 original size:34 final size:32
Alignment explanation
Indices: 25173--25254 Score: 89
Period size: 34 Copynumber: 2.6 Consensus size: 32
25163 ACTAAACCCT
* *
25173 TAAAC-AACTAATAAAATATTTTTTTATATAA
1 TAAACTAACTAATAAACTATTTTTATATATAA
25204 CTAAAACTAACTAATAAACTATTTTTCAT-TATAA
1 -T-AAACTAACTAATAAACTATTTTT-ATATATAA
*
25238 TATACT-ACTAATAAACT
1 TAAACTAACTAATAAACT
25255 TACTAACTAA
Statistics
Matches: 44, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
31 11 0.25
32 5 0.11
33 5 0.11
34 22 0.50
35 1 0.02
ACGTcount: A:0.49, C:0.12, G:0.00, T:0.39
Consensus pattern (32 bp):
TAAACTAACTAATAAACTATTTTTATATATAA
Found at i:25396 original size:47 final size:48
Alignment explanation
Indices: 25295--25399 Score: 144
Period size: 47 Copynumber: 2.2 Consensus size: 48
25285 CAACAAACAA
*
25295 ATATAACTTAACTATTTAACTAACACAAACTAATTAAATAATTTTTTTT
1 ATATAAC-TAACTATTTAACTAAAACAAACTAATTAAATAATTTTTTTT
*
25344 ATATAACTAACTA-TTAAC-AAAACAAACTAATT-AATTATTTTTTAATT
1 ATATAACTAACTATTTAACTAAAACAAACTAATTAAATAATTTTTT--TT
25391 ATATAACTA
1 ATATAACTA
25400 TCAAACATAT
Statistics
Matches: 52, Mismatches: 2, Indels: 6
0.87 0.03 0.10
Matches are distributed among these distances:
45 10 0.19
46 13 0.25
47 16 0.31
48 6 0.12
49 7 0.13
ACGTcount: A:0.48, C:0.11, G:0.00, T:0.41
Consensus pattern (48 bp):
ATATAACTAACTATTTAACTAAAACAAACTAATTAAATAATTTTTTTT
Found at i:25455 original size:41 final size:40
Alignment explanation
Indices: 25316--25455 Score: 104
Period size: 41 Copynumber: 3.3 Consensus size: 40
25306 CTATTTAACT
* *
25316 AACACAAACTAATTAAATAATTTTT-TTTATATAACTAACTA
1 AACATAAACTAATTAAATAATTTTTAATTATATAACT-A-TA
* * *
25357 TTAACAAAACAAACTAATTAATTATTTTTTAATTATATAACTATCA
1 --AAC---ATAAACTAATTAAATAATTTTTAATTATATAACTAT-A
* *
25403 AACATATACTAATTAAATAATTTTTAATTTATGTATACTAT-
1 AACATAAACTAATTAAATAATTTTTAA-TTATATA-ACTATA
*
25444 AACTTAAACTAA
1 AACATAAACTAA
25456 CAATCATATA
Statistics
Matches: 80, Mismatches: 10, Indels: 16
0.75 0.09 0.15
Matches are distributed among these distances:
41 30 0.38
42 6 0.08
43 8 0.10
44 3 0.04
45 1 0.01
46 22 0.28
47 10 0.12
ACGTcount: A:0.48, C:0.11, G:0.01, T:0.41
Consensus pattern (40 bp):
AACATAAACTAATTAAATAATTTTTAATTATATAACTATA
Found at i:25893 original size:29 final size:29
Alignment explanation
Indices: 25838--25964 Score: 213
Period size: 29 Copynumber: 4.4 Consensus size: 29
25828 GAGCTAGGAG
25838 TACATGGCGACCT--AAGGTCGCCGGGAC
1 TACATGGCGACCTACAAGGTCGCCGGGAC
25865 TACATGGCGACCTACAAGGTCGCCGGGAC
1 TACATGGCGACCTACAAGGTCGCCGGGAC
25894 TACATGGCGACCTACAAGGTCGCCGGGAC
1 TACATGGCGACCTACAAGGTCGCCGGGAC
**
25923 TACATGGCGACCTACAAGGTCGCCCAGAC
1 TACATGGCGACCTACAAGGTCGCCGGGAC
*
25952 TGCATGGCGACCT
1 TACATGGCGACCT
25965 CTCGATTGGC
Statistics
Matches: 95, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
27 13 0.14
29 82 0.86
ACGTcount: A:0.24, C:0.31, G:0.30, T:0.15
Consensus pattern (29 bp):
TACATGGCGACCTACAAGGTCGCCGGGAC
Found at i:26085 original size:21 final size:21
Alignment explanation
Indices: 26059--26105 Score: 85
Period size: 21 Copynumber: 2.2 Consensus size: 21
26049 TATATGCCTT
26059 GTATGGCTCGTATGTCACCCC
1 GTATGGCTCGTATGTCACCCC
*
26080 GTATGGCTCGTATGTCACTCC
1 GTATGGCTCGTATGTCACCCC
26101 GTATG
1 GTATG
26106 TCGCCTGGAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.15, C:0.28, G:0.26, T:0.32
Consensus pattern (21 bp):
GTATGGCTCGTATGTCACCCC
Found at i:26148 original size:29 final size:29
Alignment explanation
Indices: 26106--26165 Score: 111
Period size: 29 Copynumber: 2.1 Consensus size: 29
26096 ACTCCGTATG
26106 TCGCCTGGATTGCATGGCGTCCTACAAGA
1 TCGCCTGGATTGCATGGCGTCCTACAAGA
*
26135 TCGCCTGGATTGCATGGCGTCCTACGAGA
1 TCGCCTGGATTGCATGGCGTCCTACAAGA
26164 TC
1 TC
26166 ACTCTAGAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.18, C:0.28, G:0.28, T:0.25
Consensus pattern (29 bp):
TCGCCTGGATTGCATGGCGTCCTACAAGA
Found at i:26422 original size:29 final size:29
Alignment explanation
Indices: 26380--26439 Score: 111
Period size: 29 Copynumber: 2.1 Consensus size: 29
26370 ATTCTACAGT
26380 GATCTCGTAGGACGCCATGCAATCCAGGC
1 GATCTCGTAGGACGCCATGCAATCCAGGC
*
26409 GATCTTGTAGGACGCCATGCAATCCAGGC
1 GATCTCGTAGGACGCCATGCAATCCAGGC
26438 GA
1 GA
26440 CATACGGAGT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.25, C:0.28, G:0.28, T:0.18
Consensus pattern (29 bp):
GATCTCGTAGGACGCCATGCAATCCAGGC
Found at i:26466 original size:21 final size:21
Alignment explanation
Indices: 26440--26507 Score: 86
Period size: 21 Copynumber: 3.3 Consensus size: 21
26430 ATCCAGGCGA
26440 CATACGGAGTGACATACGAGC
1 CATACGGAGTGACATACGAGC
*
26461 CATACGGGGTGACATACGAGC
1 CATACGGAGTGACATACGAGC
* *
26482 CATAC-AAG-GCATATACGAGC
1 CATACGGAGTG-ACATACGAGC
26502 CATACG
1 CATACG
26508 AGCCAATGGA
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
19 1 0.02
20 15 0.37
21 25 0.61
ACGTcount: A:0.34, C:0.25, G:0.26, T:0.15
Consensus pattern (21 bp):
CATACGGAGTGACATACGAGC
Found at i:26625 original size:29 final size:29
Alignment explanation
Indices: 26581--26678 Score: 155
Period size: 29 Copynumber: 3.4 Consensus size: 29
26571 GCCAATCGAG
* **
26581 AGGTCGCCATGCAGTCTGGGCGACCTTGT
1 AGGTCGCCATGTAGTCCCGGCGACCTTGT
26610 AGGTCGCCATGTAGTCCCGGCGACCTTGT
1 AGGTCGCCATGTAGTCCCGGCGACCTTGT
26639 AGGTCGCCATGTAGTCCCGGCGACC-T-T
1 AGGTCGCCATGTAGTCCCGGCGACCTTGT
26666 AGGTCGCCATGTA
1 AGGTCGCCATGTA
26679 CTCCTAGCTC
Statistics
Matches: 66, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
27 14 0.21
28 1 0.02
29 51 0.77
ACGTcount: A:0.15, C:0.30, G:0.32, T:0.23
Consensus pattern (29 bp):
AGGTCGCCATGTAGTCCCGGCGACCTTGT
Found at i:27192 original size:45 final size:45
Alignment explanation
Indices: 27089--27220 Score: 134
Period size: 45 Copynumber: 3.0 Consensus size: 45
27079 TACATAAATT
*
27089 AAAAATTATTTAATTAGTATATG-TTTG---ATAGTTA--TATAGTTA
1 AAAAATTATTTAATTAGT-T-TGTTTTGTTAATAGTTAGTTATA-TAA
*
27131 AAAAA-TAATTAATTAGTTTGTTTTGTTAATAGTTAGTTATATAA
1 AAAAATTATTTAATTAGTTTGTTTTGTTAATAGTTAGTTATATAA
*
27175 AAAAATTATTTAATTAGTTTGTGTTAGTTAAATAGTTAAGTTATAT
1 AAAAATTATTTAATTAGTTTGT-TTTGTT-AATAGTT-AGTTATAT
27221 TTGTTTGTTG
Statistics
Matches: 76, Mismatches: 4, Indels: 14
0.81 0.04 0.15
Matches are distributed among these distances:
39 2 0.03
40 5 0.07
41 11 0.14
42 5 0.07
43 7 0.09
44 7 0.09
45 19 0.25
46 5 0.07
47 7 0.09
48 8 0.11
ACGTcount: A:0.40, C:0.00, G:0.12, T:0.48
Consensus pattern (45 bp):
AAAAATTATTTAATTAGTTTGTTTTGTTAATAGTTAGTTATATAA
Found at i:30957 original size:26 final size:24
Alignment explanation
Indices: 30899--30957 Score: 64
Period size: 26 Copynumber: 2.3 Consensus size: 24
30889 CTAATAAACC
*
30899 TAATAATGATTTGATAATTACTAT
1 TAATAATGATTTGATAATTAATAT
*
30923 TAATCTAATGATTTGATATTTAATGATT
1 TAA--TAATGATTTGATAATTAAT-A-T
30951 TAATAAT
1 TAATAAT
30958 AATATGATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
24 3 0.10
26 21 0.72
27 1 0.03
28 4 0.14
ACGTcount: A:0.41, C:0.03, G:0.08, T:0.47
Consensus pattern (24 bp):
TAATAATGATTTGATAATTAATAT
Found at i:31752 original size:42 final size:45
Alignment explanation
Indices: 31696--31805 Score: 136
Period size: 47 Copynumber: 2.4 Consensus size: 45
31686 GTTTAAAGAC
* *
31696 ACTAACAAATTAATTAATATTTTTT-TATAT-TTA-ATAACTTAA
1 ACTAACAAACTAATTAATATTTTTTATATATATAATATAACTTAA
*
31738 ACTAAGAAACTAATTAACTAATTTTTTATATATATAATATAACTTAA
1 ACTAACAAACTAATTAA-T-ATTTTTTATATATATAATATAACTTAA
*
31785 ACTAATAAACTAATATAATAT
1 ACTAACAAACTAAT-TAATAT
31806 AACTTAAACT
Statistics
Matches: 58, Mismatches: 4, Indels: 8
0.83 0.06 0.11
Matches are distributed among these distances:
42 15 0.26
43 1 0.02
44 7 0.12
45 5 0.09
46 4 0.07
47 23 0.40
48 3 0.05
ACGTcount: A:0.49, C:0.08, G:0.01, T:0.42
Consensus pattern (45 bp):
ACTAACAAACTAATTAATATTTTTTATATATATAATATAACTTAA
Found at i:31795 original size:8 final size:8
Alignment explanation
Indices: 31782--31856 Score: 53
Period size: 8 Copynumber: 10.4 Consensus size: 8
31772 TAATATAACT
31782 TAAACTAA
1 TAAACTAA
31790 TAAACTAA
1 TAAACTAA
31798 T--A-TAA
1 TAAACTAA
31803 TATAACT--
1 TA-AACTAA
31810 TAAACTAA
1 TAAACTAA
31818 TAAACTAA
1 TAAACTAA
31826 T--A-TAA
1 TAAACTAA
31831 TATAACT--
1 TA-AACTAA
31838 TAAACTAA
1 TAAACTAA
*
31846 CAAACTAA
1 TAAACTAA
31854 TAA
1 TAA
31857 TTTATACTAA
Statistics
Matches: 53, Mismatches: 2, Indels: 24
0.67 0.03 0.30
Matches are distributed among these distances:
5 8 0.15
6 10 0.19
7 4 0.08
8 29 0.55
9 2 0.04
ACGTcount: A:0.59, C:0.12, G:0.00, T:0.29
Consensus pattern (8 bp):
TAAACTAA
Found at i:31862 original size:28 final size:28
Alignment explanation
Indices: 31769--31855 Score: 165
Period size: 28 Copynumber: 3.1 Consensus size: 28
31759 TTTTTTATAT
31769 ATATAATATAACTTAAACTAATAAACTA
1 ATATAATATAACTTAAACTAATAAACTA
31797 ATATAATATAACTTAAACTAATAAACTA
1 ATATAATATAACTTAAACTAATAAACTA
*
31825 ATATAATATAACTTAAACTAACAAACTA
1 ATATAATATAACTTAAACTAATAAACTA
31853 ATA
1 ATA
31856 ATTTATACTA
Statistics
Matches: 58, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
28 58 1.00
ACGTcount: A:0.57, C:0.11, G:0.00, T:0.31
Consensus pattern (28 bp):
ATATAATATAACTTAAACTAATAAACTA
Found at i:31865 original size:21 final size:21
Alignment explanation
Indices: 31832--31880 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
31822 CTAATATAAT
31832 ATAACTTAAACTAACAAACTA
1 ATAACTTAAACTAACAAACTA
* *
31853 ATAATTTATACTAACAAACTA
1 ATAACTTAAACTAACAAACTA
31874 ATTAACT
1 A-TAACT
31881 AGATTTTAGT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.53, C:0.16, G:0.00, T:0.31
Consensus pattern (21 bp):
ATAACTTAAACTAACAAACTA
Found at i:32378 original size:20 final size:20
Alignment explanation
Indices: 32353--32390 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
32343 ACGTGCATGC
*
32353 CCCATGCACAGTTCCCACGT
1 CCCATGCACAGCTCCCACGT
32373 CCCATGCACAGCTCCCAC
1 CCCATGCACAGCTCCCAC
32391 AACTCCCCCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.21, C:0.50, G:0.13, T:0.16
Consensus pattern (20 bp):
CCCATGCACAGCTCCCACGT
Found at i:32408 original size:51 final size:51
Alignment explanation
Indices: 32348--32505 Score: 298
Period size: 51 Copynumber: 3.1 Consensus size: 51
32338 GTTCGACGTG
32348 CATGCCCCATGCACAGTTCCCACGTCCCATGCACAGCTCCCACAACTCCCC
1 CATGCCCCATGCACAGTTCCCACGTCCCATGCACAGCTCCCACAACTCCCC
*
32399 CATGCCCCATGCACAGGTCCCACGTCCCATGCACAGCTCCCACAACTCCCC
1 CATGCCCCATGCACAGTTCCCACGTCCCATGCACAGCTCCCACAACTCCCC
*
32450 CATGCCCCATGCACAGTTCCCTCGTCCCATGCACAGCTCCCACAACTCCCC
1 CATGCCCCATGCACAGTTCCCACGTCCCATGCACAGCTCCCACAACTCCCC
32501 CATGC
1 CATGC
32506 ATGCTCCAAT
Statistics
Matches: 104, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
51 104 1.00
ACGTcount: A:0.21, C:0.51, G:0.13, T:0.16
Consensus pattern (51 bp):
CATGCCCCATGCACAGTTCCCACGTCCCATGCACAGCTCCCACAACTCCCC
Found at i:32427 original size:20 final size:20
Alignment explanation
Indices: 32404--32441 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
32394 TCCCCCATGC
*
32404 CCCATGCACAGGTCCCACGT
1 CCCATGCACAGCTCCCACGT
32424 CCCATGCACAGCTCCCAC
1 CCCATGCACAGCTCCCAC
32442 AACTCCCCCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.21, C:0.50, G:0.16, T:0.13
Consensus pattern (20 bp):
CCCATGCACAGCTCCCACGT
Found at i:32601 original size:29 final size:29
Alignment explanation
Indices: 32559--32671 Score: 199
Period size: 29 Copynumber: 3.9 Consensus size: 29
32549 AACACCACAC
**
32559 AGGTCGCTTGGATGCCATGGCGACCTCCA
1 AGGTCGCCCGGATGCCATGGCGACCTCCA
32588 AGGTCGCCCGGATGCCATGGCGACCTCCA
1 AGGTCGCCCGGATGCCATGGCGACCTCCA
*
32617 AGGTCGCCCGGATGCCATGGCGACCTACA
1 AGGTCGCCCGGATGCCATGGCGACCTCCA
32646 AGGTCGCCCGGATGCCATGGCGACCT
1 AGGTCGCCCGGATGCCATGGCGACCT
32672 ACGAGGTCAC
Statistics
Matches: 81, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 81 1.00
ACGTcount: A:0.18, C:0.35, G:0.32, T:0.16
Consensus pattern (29 bp):
AGGTCGCCCGGATGCCATGGCGACCTCCA
Found at i:40116 original size:21 final size:20
Alignment explanation
Indices: 40038--40136 Score: 72
Period size: 21 Copynumber: 4.8 Consensus size: 20
40028 AATCAGTTTC
40038 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * *
40059 AAAAATCGCAATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
40080 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
40100 CAAGAATCGCAACGCGAATAT
1 CAA-AATCGCAACGCGATTTT
* *
40121 GAAAATCCCAACGCGA
1 CAAAATCGCAACGCGA
40137 ACACATAAAT
Statistics
Matches: 60, Mismatches: 16, Indels: 5
0.74 0.20 0.06
Matches are distributed among these distances:
20 16 0.27
21 44 0.73
ACGTcount: A:0.38, C:0.23, G:0.17, T:0.21
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:40165 original size:20 final size:20
Alignment explanation
Indices: 40142--40332 Score: 215
Period size: 20 Copynumber: 9.6 Consensus size: 20
40132 CGCGAACACA
40142 TAAATCGCAACGCGTATCCG
1 TAAATCGCAACGCGTATCCG
* *
40162 TAAACCGCAACGTGTATCCG
1 TAAATCGCAACGCGTATCCG
*
40182 TAAATAGCAACGCGTATCCG
1 TAAATCGCAACGCGTATCCG
**
40202 TAAATCGCAATACGTATCCG
1 TAAATCGCAACGCGTATCCG
*
40222 TATATCGCAACGCGTATCCG
1 TAAATCGCAACGCGTATCCG
*
40242 TAAATCGCAACG-ATAATCCG
1 TAAATCGCAACGCGT-ATCCG
* * *
40262 TAAATCGCAACGAGAATCTG
1 TAAATCGCAACGCGTATCCG
*
40282 TAAATCGCAACG-ATAATCCG
1 TAAATCGCAACGCGT-ATCCG
* * *
40302 TAAATCGCAACGAGAATCTG
1 TAAATCGCAACGCGTATCCG
*
40322 TAAATCACAAC
1 TAAATCGCAAC
40333 ACTGAAATTT
Statistics
Matches: 144, Mismatches: 23, Indels: 8
0.82 0.13 0.05
Matches are distributed among these distances:
19 1 0.01
20 143 0.99
ACGTcount: A:0.36, C:0.26, G:0.17, T:0.21
Consensus pattern (20 bp):
TAAATCGCAACGCGTATCCG
Found at i:40173 original size:40 final size:40
Alignment explanation
Indices: 40104--40332 Score: 203
Period size: 40 Copynumber: 5.7 Consensus size: 40
40094 GATTTTCAAG
* ** * * *
40104 AATCGCAACGCGAATATGAAAATCCCAACGCG-AACACATA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGTAAC-CGTA
* * *
40144 AATCGCAACGCGTATCCGTAAACCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGTAACCGTA
* ** *
40184 AATAGCAACGCGTATCCGTAAATCGCAATACGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGTAACCGTA
* *
40224 TATCGCAACGCGTATCCGTAAATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGTAA-CCGTA
* * * *
40264 AATCGCAACGAGAATCTGTAAATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGTAA-CCGTA
* * * *
40304 AATCGCAACGAGAATCTGTAAATCACAAC
1 AATCGCAACGCGTATCCGTAAATCGCAAC
40333 ACTGAAATTT
Statistics
Matches: 162, Mismatches: 25, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
39 2 0.01
40 158 0.98
41 2 0.01
ACGTcount: A:0.38, C:0.26, G:0.17, T:0.19
Consensus pattern (40 bp):
AATCGCAACGCGTATCCGTAAATCGCAACGCGTAACCGTA
Found at i:41064 original size:24 final size:24
Alignment explanation
Indices: 41025--41071 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
41015 AAATTTGGTC
41025 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
41049 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
41072 GATGTTTCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (24 bp):
TTGGTCAATATCCGGACTTTGATA
Found at i:41263 original size:12 final size:12
Alignment explanation
Indices: 41246--41270 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
41236 ACATAATCCT
41246 GAAGAAGAAAAA
1 GAAGAAGAAAAA
41258 GAAGAAGAAAAA
1 GAAGAAGAAAAA
41270 G
1 G
41271 TCCCCGAAGA
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:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:43673 original size:72 final size:71
Alignment explanation
Indices: 43564--43801 Score: 276
Period size: 72 Copynumber: 3.4 Consensus size: 71
43554 GCAACGAGAG
* *
43564 AATCGCAATGCGAAATGAAAATCCCAACAAGAAAATCGCAATGCGGAAATGAAAATCGCAATGCG
1 AATCGCAATGCGAAATGAAAATCGCAACGAG-AAATCGCAATGCGGAAATGAAAATCGCAATGCG
43629 AAATGAA
65 AAATGAA
*
43636 AATTGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGGAAATGAAAATCGCAATGCG
1 AATCGCAATGCGAAATGAAAATCGCAACGAGA-AATCGCAATGCGGAAATGAAAATCGCAATGCG
43701 AAATGAA
65 AAATGAA
* * * * * *
43708 AATCGCAACGAGAGAATCG-CAATGTGAAATGA-AAATCGCAATGC-GAAATGAAAATCGCAA--
1 AATCGCAATGCGA-AAT-GAAAAT-CGCAACGAGAAATCGCAATGCGGAAATGAAAATCGCAATG
*
43768 CG--A-GAG
63 CGAAATGAA
43774 AATCGCAATGCGGAAATGAAAATCGCAA
1 AATCGCAATGC-GAAATGAAAATCGCAA
43802 TGCGAAATGA
Statistics
Matches: 144, Mismatches: 16, Indels: 19
0.80 0.09 0.11
Matches are distributed among these distances:
65 4 0.03
66 17 0.12
67 3 0.02
69 2 0.01
71 17 0.12
72 88 0.61
73 7 0.05
74 6 0.04
ACGTcount: A:0.47, C:0.17, G:0.22, T:0.14
Consensus pattern (71 bp):
AATCGCAATGCGAAATGAAAATCGCAACGAGAAATCGCAATGCGGAAATGAAAATCGCAATGCGA
AATGAA
Found at i:43685 original size:53 final size:52
Alignment explanation
Indices: 43550--43819 Score: 397
Period size: 53 Copynumber: 5.1 Consensus size: 52
43540 CGGAAATTAC
*
43550 AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCCCAA--C--AA-GAA
1 AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
* *
43597 AATCGCAATGCGGAAATGAAAATCGCAATGCGAAATGAAAATTGCAATGCGAAATGAA
1 AATCGCAA--C-G--A-GAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
43655 AATCGCAACGAGAGAATCGCAATGCGGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAACGAGAGAATCGCAATGC-GAAATGAAAATCGCAATGCGAAATGAA
*
43708 AATCGCAACGAGAGAATCGCAATGTGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
43760 AATCGCAACGAGAGAATCGCAATGCGGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAACGAGAGAATCGCAATGC-GAAATGAAAATCGCAATGCGAAATGAA
43813 AATCGCA
1 AATCGCA
43820 TTGCGATTCT
Statistics
Matches: 203, Mismatches: 7, Indels: 20
0.88 0.03 0.09
Matches are distributed among these distances:
47 8 0.04
49 1 0.00
50 1 0.00
52 65 0.32
53 112 0.55
55 2 0.01
56 1 0.00
57 2 0.01
58 11 0.05
ACGTcount: A:0.46, C:0.17, G:0.23, T:0.14
Consensus pattern (52 bp):
AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
Found at i:43726 original size:105 final size:109
Alignment explanation
Indices: 43550--43819 Score: 416
Period size: 105 Copynumber: 2.6 Consensus size: 109
43540 CGGAAATTAC
*
43550 AATCGCAACGAGAGAATCGCAATGC-GAAATGAAAATCCCAA--C--AA-GAAAATCGCAATGCG
1 AATCGCAACGAGAGAATCGCAATGCGGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA-GCG
*
43609 GAAATGAAAATCGCAATGCGAAATGAAAATTGCAATGCGAAATGAA
65 G-AATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
43655 AATCGCAACGAGAGAATCGCAATGCGGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA-C-G
1 AATCGCAACGAGAGAATCGCAATGCGGAAATGAAAATCGCAATGCGAAATGAAAATCGCAAGCGG
* *
43718 -A-GAGAATCGCAATGTGAAATGAAAATCGCAATGCGAAATGAA
66 AATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
43760 AATCGCAACGAGAGAATCGCAATGCGGAAATGAAAATCGCAATGCGAAATGAAAATCGCA
1 AATCGCAACGAGAGAATCGCAATGCGGAAATGAAAATCGCAATGCGAAATGAAAATCGCA
43820 TTGCGATTCT
Statistics
Matches: 155, Mismatches: 4, Indels: 12
0.91 0.02 0.07
Matches are distributed among these distances:
105 123 0.79
106 16 0.10
108 2 0.01
109 1 0.01
110 2 0.01
111 11 0.07
ACGTcount: A:0.46, C:0.17, G:0.23, T:0.14
Consensus pattern (109 bp):
AATCGCAACGAGAGAATCGCAATGCGGAAATGAAAATCGCAATGCGAAATGAAAATCGCAAGCGG
AATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
Found at i:43802 original size:72 final size:69
Alignment explanation
Indices: 43531--43824 Score: 262
Period size: 72 Copynumber: 4.2 Consensus size: 69
43521 GCATTTGACT
** * * *
43531 ATCGCAACACGGAAATTACAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCCCAAC--AA
1 ATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGAAA
43594 GAAA
66 GAAA
* *
43598 ATCGCAATGCGGAAATGAAAATCGCAATGCGAAATGAAAATTGCAATGCGAAATGAAAATCGCAA
1 ATCGCAATGCGGAAATGAAAATCGCAA--CG--A-GAGAATCGCAATGCGAAATGAAAATCGCAA
*
43663 CG--AGAGA
61 CGAAAGAAA
* * * * *
43670 ATCGCAATGCGGAAATGAAAATCGCAATGCGA-AAT-GAAAAT-CGCAACGAGAGAATCGCAATG
1 ATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCG-CAATGCGAAATGA-A-AATCGCAA--
*
43732 TGAAATGAAA
61 CGAAA-GAAA
43742 ATCGCAATGC-GAAATGAAAATCGCAACGAGAGAATCGCAATGCGGAAATGAAAATCGCAATGCG
1 ATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGC-GAAATGAAAATCGCAA--CG
43806 AAATGAAA
63 AAA-GAAA
*
43814 ATCGCATTGCG
1 ATCGCAATGCG
43825 ATTCTCTCGT
Statistics
Matches: 186, Mismatches: 22, Indels: 32
0.77 0.09 0.13
Matches are distributed among these distances:
65 7 0.04
66 7 0.04
67 33 0.18
69 3 0.02
70 1 0.01
71 21 0.11
72 106 0.57
73 3 0.02
74 5 0.03
ACGTcount: A:0.45, C:0.18, G:0.22, T:0.15
Consensus pattern (69 bp):
ATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGAAA
GAAA
Found at i:43859 original size:53 final size:52
Alignment explanation
Indices: 43802--43911 Score: 148
Period size: 53 Copynumber: 2.1 Consensus size: 52
43792 AAAATCGCAA
43802 TGCGAAATGAAAATCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCACAT
1 TGCGAAATGAAAATCGCATTGCGATTCTCTCGTTGCGATTTTCATTT-CACAT
** ** ** *
43855 TGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCAT
1 TGCGAAATGAAAATCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCACAT
43907 TGCGA
1 TGCGA
43912 TTTTCATTTC
Statistics
Matches: 50, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
52 9 0.18
53 41 0.82
ACGTcount: A:0.19, C:0.23, G:0.18, T:0.40
Consensus pattern (52 bp):
TGCGAAATGAAAATCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCACAT
Found at i:43876 original size:19 final size:19
Alignment explanation
Indices: 43834--43921 Score: 114
Period size: 19 Copynumber: 4.8 Consensus size: 19
43824 GATTCTCTCG
*
43834 TTGCGATTTTCATTTCCACA
1 TTGCGATTTTCATTT-CGCA
43854 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
43873 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
43887 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
43906 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
43922 AACATAATGC
Statistics
Matches: 60, Mismatches: 3, Indels: 11
0.81 0.04 0.15
Matches are distributed among these distances:
14 6 0.10
16 7 0.12
17 7 0.12
19 25 0.42
20 15 0.25
ACGTcount: A:0.15, C:0.23, G:0.15, T:0.48
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:44031 original size:14 final size:14
Alignment explanation
Indices: 44012--44048 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
44002 CATCAATTAC
44012 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
44026 ACAAATCATCTTTT
1 ACAAATCAACTTTT
44040 ACAAATCAA
1 ACAAATCAA
44049 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:46005 original size:19 final size:19
Alignment explanation
Indices: 45963--46102 Score: 137
Period size: 19 Copynumber: 7.6 Consensus size: 19
45953 TAGTTTACTT
* *
45963 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TCAAAA
* *
45983 TCGCAACGCGAAATGAGAA
1 TCGCAACGCGAAATCAAAA
* *
46002 TCGCAACGAGAAACCAAAA
1 TCGCAACGCGAAATCAAAA
*
46021 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATCAAAA
*
46040 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATCAAAA
*
46059 TCGCAA--CG--A-CAGAA
1 TCGCAACGCGAAATCAAAA
*
46073 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATCAAAA
*
46092 TCGCAATGCGA
1 TCGCAACGCGA
46103 TTTTGGTTTC
Statistics
Matches: 100, Mismatches: 15, Indels: 11
0.79 0.12 0.09
Matches are distributed among these distances:
14 9 0.09
15 1 0.01
16 2 0.02
17 2 0.02
18 1 0.01
19 73 0.73
20 12 0.12
ACGTcount: A:0.46, C:0.25, G:0.19, T:0.10
Consensus pattern (19 bp):
TCGCAACGCGAAATCAAAA
Found at i:46133 original size:14 final size:14
Alignment explanation
Indices: 46114--46172 Score: 64
Period size: 14 Copynumber: 3.9 Consensus size: 14
46104 TTTGGTTTCG
46114 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
46128 CGTTGCGATTTTGGTTT
1 CGTTGCGATTTT-G--T
*
46145 CGCGTTGCGATTCTGT
1 --CGTTGCGATTTTGT
46161 CGTTGCGATTTT
1 CGTTGCGATTTT
46173 CATTTCGCGT
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
14 23 0.61
15 1 0.03
16 1 0.03
17 1 0.03
18 1 0.03
19 11 0.29
ACGTcount: A:0.07, C:0.17, G:0.29, T:0.47
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:46140 original size:33 final size:33
Alignment explanation
Indices: 46098--46221 Score: 185
Period size: 33 Copynumber: 3.7 Consensus size: 33
46088 AAAATCGCAA
*
46098 TGCGATTTTGGTTTCGCGTTGCGATTTTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
46131 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
** *
46164 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
* *
46197 TGCGATTTTAAGTTTCGTGTTGCGA
1 TGCGATTTT-GGTTTCGCGTTGCGA
46222 AAGTAAACTA
Statistics
Matches: 83, Mismatches: 7, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
33 71 0.86
34 12 0.14
ACGTcount: A:0.09, C:0.18, G:0.27, T:0.46
Consensus pattern (33 bp):
TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
Found at i:46152 original size:19 final size:18
Alignment explanation
Indices: 46098--46189 Score: 83
Period size: 19 Copynumber: 5.4 Consensus size: 18
46088 AAAATCGCAA
46098 TGCGATTTTGGTTTCGCGT
1 TGCGATTTT-GTTTCGCGT
46117 TGCGATTTTG--T--CGT
1 TGCGATTTTGTTTCGCGT
46131 TGCGATTTTGGTTTCGCGT
1 TGCGATTTT-GTTTCGCGT
*
46150 TGCGATTCTG--T--CGT
1 TGCGATTTTGTTTCGCGT
*
46164 TGCGATTTTCATTTCGCGT
1 TGCGATTTT-GTTTCGCGT
46183 TGCGATT
1 TGCGATT
46190 CTCTCGTTGC
Statistics
Matches: 60, Mismatches: 3, Indels: 20
0.72 0.04 0.24
Matches are distributed among these distances:
14 23 0.38
15 1 0.02
16 2 0.03
17 2 0.03
18 2 0.03
19 30 0.50
ACGTcount: A:0.08, C:0.17, G:0.28, T:0.47
Consensus pattern (18 bp):
TGCGATTTTGTTTCGCGT
Found at i:46199 original size:14 final size:14
Alignment explanation
Indices: 46147--46203 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
46137 TTTGGTTTCG
*
46147 CGTTGCGATTCTGT
1 CGTTGCGATTCTCT
*
46161 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
46180 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
46194 CGTTGCGATT
1 CGTTGCGATT
46204 TTAAGTTTCG
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
14 20 0.57
16 3 0.09
17 3 0.09
19 9 0.26
ACGTcount: A:0.09, C:0.23, G:0.25, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:46385 original size:83 final size:87
Alignment explanation
Indices: 46269--46541 Score: 333
Period size: 93 Copynumber: 3.1 Consensus size: 87
46259 ATGGATTGCA
* **
46269 TTAC-TTCAACCAATAGACAAAACAAAGACAAATACTGACTT-CAG-G-G-TA-TTAGTTTAGCA
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACT-ACTTACAGTGAGATACACAGTTTAGCA
46328 GAATTGGCAGCAACCGAACAAAT
65 GAATTGGCAGCAACCGAACAAAT
*
46351 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTACTT-ACAGTG----AG-ATACACAGTT
46416 TAGCAGAATTGGCAGCAACCGAACAAAT
60 TAGCAGAATTGGCAGCAACCGAACAAAT
*
46444 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTACTT-ACAGTG----AG-ATACACAGTT
*
46509 TAGCAGAATTGGCAGCAACCGAATAAAT
60 TAGCAGAATTGGCAGCAACCGAACAAAT
46537 TTACT
1 TTACT
46542 AAGCAATCTA
Statistics
Matches: 174, Mismatches: 5, Indels: 13
0.91 0.03 0.07
Matches are distributed among these distances:
82 7 0.04
83 31 0.18
84 3 0.02
85 1 0.01
90 1 0.01
92 2 0.01
93 129 0.74
ACGTcount: A:0.45, C:0.19, G:0.14, T:0.23
Consensus pattern (87 bp):
TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTACTTACAGTGAGATACACAGTTTAGCAG
AATTGGCAGCAACCGAACAAAT
Found at i:46478 original size:93 final size:93
Alignment explanation
Indices: 46319--46541 Score: 437
Period size: 93 Copynumber: 2.4 Consensus size: 93
46309 TCAGGGTATT
46319 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
1 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
46384 TACTATTTCACAGTGTTAAAGAATACAC
66 TACTATTTCACAGTGTTAAAGAATACAC
46412 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
1 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
46477 TACTATTTCACAGTGTTAAAGAATACAC
66 TACTATTTCACAGTGTTAAAGAATACAC
*
46505 AGTTTAGCAGAATTGGCAGCAACCGAATAAATTTACT
1 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACT
46542 AAGCAATCTA
Statistics
Matches: 129, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
93 129 1.00
ACGTcount: A:0.45, C:0.19, G:0.14, T:0.22
Consensus pattern (93 bp):
AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
TACTATTTCACAGTGTTAAAGAATACAC
Found at i:48252 original size:20 final size:20
Alignment explanation
Indices: 48221--48317 Score: 100
Period size: 20 Copynumber: 5.2 Consensus size: 20
48211 TTTTGGTTGA
48221 AATGAAAATCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
***
48241 AATGACTGTCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
48261 AAATGAAAATCGCAAC--GAG
1 -AATGAAAATCGCAACGAGAG
*
48280 -A-G--AATCGCAACGCGA-
1 AATGAAAATCGCAACGAGAG
48295 AATGAAAATCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
48315 AAT
1 AAT
48318 CGCAACGCGA
Statistics
Matches: 62, Mismatches: 7, Indels: 16
0.73 0.08 0.19
Matches are distributed among these distances:
14 9 0.15
16 4 0.06
17 2 0.03
19 15 0.24
20 20 0.32
21 12 0.19
ACGTcount: A:0.46, C:0.18, G:0.25, T:0.11
Consensus pattern (20 bp):
AATGAAAATCGCAACGAGAG
Found at i:48273 original size:21 final size:21
Alignment explanation
Indices: 48219--48283 Score: 96
Period size: 21 Copynumber: 3.1 Consensus size: 21
48209 TCTTTTGGTT
48219 GAAATGAAAATCGCAACGAGA
1 GAAATGAAAATCGCAACGAGA
***
48240 G-AATGACTGTCGCAACGAGA
1 GAAATGAAAATCGCAACGAGA
48260 GAAATGAAAATCGCAACGAGA
1 GAAATGAAAATCGCAACGAGA
48281 GAA
1 GAA
48284 TCGCAACGCG
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
20 17 0.46
21 20 0.54
ACGTcount: A:0.48, C:0.15, G:0.26, T:0.11
Consensus pattern (21 bp):
GAAATGAAAATCGCAACGAGA
Found at i:48287 original size:14 final size:14
Alignment explanation
Indices: 48268--48324 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
48258 GAGAAATGAA
48268 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
48282 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
48301 AATCGCAACGAGAG
1 AATCGCAACGAGAG
48315 AATCGCAACG
1 AATCGCAACG
48325 CGAAATAAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.28
ACGTcount: A:0.44, C:0.23, G:0.25, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:48300 original size:33 final size:33
Alignment explanation
Indices: 48219--48340 Score: 156
Period size: 33 Copynumber: 3.5 Consensus size: 33
48209 TCTTTTGGTT
*
48219 GAAATGAAAATCGCAACGAGAGAATGACTGTCGCAACGAGA
1 GAAATGAAAATCGCAACGAGAG-A--A---TCGCAAC--GC
48260 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
48293 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
48326 GAAAT-AAAATCGCAA
1 GAAATGAAAATCGCAA
48341 TGCGATTTTG
Statistics
Matches: 80, Mismatches: 1, Indels: 9
0.89 0.01 0.10
Matches are distributed among these distances:
32 10 0.12
33 39 0.49
35 7 0.09
38 1 0.01
40 1 0.01
41 22 0.28
ACGTcount: A:0.47, C:0.19, G:0.24, T:0.11
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:48393 original size:21 final size:21
Alignment explanation
Indices: 48368--48441 Score: 96
Period size: 21 Copynumber: 3.5 Consensus size: 21
48358 GTTGCGATTC
48368 TCTCGTTGCGATTTTCATTTT
1 TCTCGTTGCGATTTTCATTTT
**
48389 TCTCGTTGCAGATAGTCA-TTT
1 TCTCGTTGC-GATTTTCATTTT
* *
48410 TCACGTTGCGATTTTCATTTA
1 TCTCGTTGCGATTTTCATTTT
48431 TCTCGTTGCGA
1 TCTCGTTGCGA
48442 CTCTTCTGCA
Statistics
Matches: 44, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
20 6 0.14
21 32 0.73
22 6 0.14
ACGTcount: A:0.15, C:0.20, G:0.18, T:0.47
Consensus pattern (21 bp):
TCTCGTTGCGATTTTCATTTT
Found at i:48563 original size:33 final size:33
Alignment explanation
Indices: 48521--48591 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
48511 AATACTAACT
48521 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
* *
48554 TGAAAATCGCAACGAGAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
48587 TGAAA
1 TGAAA
48592 TCTAAGTGAA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.48, C:0.17, G:0.24, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
Found at i:48997 original size:20 final size:20
Alignment explanation
Indices: 48971--49043 Score: 85
Period size: 20 Copynumber: 3.6 Consensus size: 20
48961 GCTTTAAAAA
48971 TCGCGTTGCGATTTACGGAT
1 TCGCGTTGCGATTTACGGAT
* *
48991 ACGCGTTGCGATTTATGTG-T
1 TCGCGTTGCGATTTACG-GAT
* **
49011 TCGCGTTGCGATTTTCATAT
1 TCGCGTTGCGATTTACGGAT
49031 TCGCGTTGCGATT
1 TCGCGTTGCGATT
49044 CTGGAAAATC
Statistics
Matches: 44, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
20 43 0.98
21 1 0.02
ACGTcount: A:0.14, C:0.19, G:0.27, T:0.40
Consensus pattern (20 bp):
TCGCGTTGCGATTTACGGAT
Found at i:52082 original size:31 final size:30
Alignment explanation
Indices: 52007--52087 Score: 126
Period size: 30 Copynumber: 2.7 Consensus size: 30
51997 AACAGTTACA
*
52007 TTGGGGATTATATTGTAAATGGATTAAATG
1 TTGGGGATTATATTGTAAATGGATTAAAAG
*
52037 TTGGGGATCATATTGTAAATGGATTAAAAG
1 TTGGGGATTATATTGTAAATGGATTAAAAG
*
52067 TTAGGGGATTGTATTGTAAAT
1 TT-GGGGATTATATTGTAAAT
52088 TTTAAAAGTT
Statistics
Matches: 46, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
30 30 0.65
31 16 0.35
ACGTcount: A:0.33, C:0.01, G:0.27, T:0.38
Consensus pattern (30 bp):
TTGGGGATTATATTGTAAATGGATTAAAAG
Found at i:52782 original size:31 final size:31
Alignment explanation
Indices: 52702--52768 Score: 100
Period size: 31 Copynumber: 2.2 Consensus size: 31
52692 TAAAAGTTAC
*
52702 GTTGGG-GAACATATTGTAAATAGAATAAAT
1 GTTGGGAGATCATATTGTAAATAGAATAAAT
* *
52732 TTTGGGAGATCATATTGTAAATAGATTAAAT
1 GTTGGGAGATCATATTGTAAATAGAATAAAT
52763 GTTGGG
1 GTTGGG
52769 GGATTTCATT
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
30 5 0.16
31 27 0.84
ACGTcount: A:0.37, C:0.03, G:0.25, T:0.34
Consensus pattern (31 bp):
GTTGGGAGATCATATTGTAAATAGAATAAAT
Found at i:52815 original size:29 final size:29
Alignment explanation
Indices: 52757--52817 Score: 70
Period size: 29 Copynumber: 2.1 Consensus size: 29
52747 TGTAAATAGA
* * * *
52757 TTAAATGTTGGGGGATTTCATTGTAAGTT
1 TTAAAAGTTAGGGGATTTAAATGTAAGTT
52786 TTAAAAGTTAGGGGATTTAAATG-AATGTT
1 TTAAAAGTTAGGGGATTTAAATGTAA-GTT
52815 TTA
1 TTA
52818 GAAAAGTTTA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
28 2 0.07
29 25 0.93
ACGTcount: A:0.31, C:0.02, G:0.25, T:0.43
Consensus pattern (29 bp):
TTAAAAGTTAGGGGATTTAAATGTAAGTT
Found at i:55094 original size:16 final size:16
Alignment explanation
Indices: 55073--55103 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
55063 ATAAATAAAT
55073 GAACATAAACGAACAC
1 GAACATAAACGAACAC
55089 GAACATAAACGAACA
1 GAACATAAACGAACA
55104 AAATTTTTTT
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:0.58, C:0.23, G:0.13, T:0.06
Consensus pattern (16 bp):
GAACATAAACGAACAC
Found at i:55188 original size:10 final size:10
Alignment explanation
Indices: 55169--55211 Score: 59
Period size: 10 Copynumber: 4.1 Consensus size: 10
55159 CATTTAAATG
*
55169 ATAAATGAAC
1 ATAAACGAAC
55179 ATAAACGAACAC
1 ATAAACG-A-AC
55191 ATAAACGAAC
1 ATAAACGAAC
55201 ATAAACGAAC
1 ATAAACGAAC
55211 A
1 A
55212 ACACAAACAC
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
10 19 0.63
11 2 0.07
12 9 0.30
ACGTcount: A:0.60, C:0.19, G:0.09, T:0.12
Consensus pattern (10 bp):
ATAAACGAAC
Found at i:55194 original size:12 final size:12
Alignment explanation
Indices: 55177--55211 Score: 56
Period size: 12 Copynumber: 3.1 Consensus size: 12
55167 TGATAAATGA
55177 ACATAAACGAAC
1 ACATAAACGAAC
55189 ACATAAACG-A-
1 ACATAAACGAAC
55199 ACATAAACGAAC
1 ACATAAACGAAC
55211 A
1 A
55212 ACACAAACAC
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
10 9 0.43
11 2 0.10
12 10 0.48
ACGTcount: A:0.60, C:0.23, G:0.09, T:0.09
Consensus pattern (12 bp):
ACATAAACGAAC
Found at i:55200 original size:22 final size:22
Alignment explanation
Indices: 55169--55211 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
55159 CATTTAAATG
*
55169 ATAAATGAACATAAACGAACAC
1 ATAAACGAACATAAACGAACAC
55191 ATAAACGAACATAAACGAACA
1 ATAAACGAACATAAACGAACA
55212 ACACAAACAC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.60, C:0.19, G:0.09, T:0.12
Consensus pattern (22 bp):
ATAAACGAACATAAACGAACAC
Found at i:55296 original size:13 final size:16
Alignment explanation
Indices: 55266--55297 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
55256 TTTAAAAATG
55266 TAAACAACAAGAATAA
1 TAAACAACAAGAATAA
*
55282 TAAACAACAAAAATAA
1 TAAACAACAAGAATAA
55298 CAACTTAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.72, C:0.12, G:0.03, T:0.12
Consensus pattern (16 bp):
TAAACAACAAGAATAA
Found at i:57406 original size:207 final size:206
Alignment explanation
Indices: 57031--57444 Score: 735
Period size: 207 Copynumber: 2.0 Consensus size: 206
57021 CTCAATGTTC
*
57031 CACTCCTTTAGACACTTAAAAAGTGAATCATAATATACATACTCCGAATACGATGGAGGCACATC
1 CACTCCTTTAGACACTTAAAAAGTGAATCATAAGATACATACTCCGAATACGATGGAGGCACATC
*
57096 AACAAACTTAAATGCGTTTGTGAAACTTGAAATCATAATCTACAAATGGCATGTACTACCATGTA
66 AACAAACTTAAATGCGTTTGTGAAACTTGAAATCAGAATCTACAAATGGCATGTACTACCATGTA
*
57161 ATGGATGTTTTGATTCGATGTCCACATATCTATAGTGATGCTCACACGCTTGACAGAATGC-TCA
131 ATGGATGTTTTGATTCGATGTCCACATATATATAGTGATGCTCACACGCTTGACAGAATGCATCA
57225 ATTTTTGAACT
196 ATTTTTGAACT
57236 CACTCCTTTAGACACTT-AAAAGTGAATCAT-AGATACATACTCCTGAATACGATGGAGGCACAT
1 CACTCCTTTAGACACTTAAAAAGTGAATCATAAGATACATACTCC-GAATACGATGGAGGCACAT
57299 CAACAAAACTTAATATGCGTTTGTGAAACTTGAAATCAGAATCTACAAATGGCATGTAACTACCA
65 CAAC-AAACTTAA-ATGCGTTTGTGAAACTTGAAATCAGAATCTACAAATGGCATGT-ACTACCA
*
57364 TGTAATGGATGTTTTGATTCGATGTCCACATATATGTAGTGATGCTCACACGCTTGACAGAATGC
127 TGTAATGGATGTTTTGATTCGATGTCCACATATATATAGTGATGCTCACACGCTTGACAGAATGC
57429 ATCAATTTTTGAACT
192 ATCAATTTTTGAACT
57444 C
1 C
57445 TTTTCTTTCC
Statistics
Matches: 200, Mismatches: 4, Indels: 7
0.95 0.02 0.03
Matches are distributed among these distances:
203 12 0.06
204 36 0.18
205 25 0.12
206 42 0.21
207 70 0.35
208 15 0.08
ACGTcount: A:0.35, C:0.19, G:0.16, T:0.30
Consensus pattern (206 bp):
CACTCCTTTAGACACTTAAAAAGTGAATCATAAGATACATACTCCGAATACGATGGAGGCACATC
AACAAACTTAAATGCGTTTGTGAAACTTGAAATCAGAATCTACAAATGGCATGTACTACCATGTA
ATGGATGTTTTGATTCGATGTCCACATATATATAGTGATGCTCACACGCTTGACAGAATGCATCA
ATTTTTGAACT
Found at i:68493 original size:24 final size:24
Alignment explanation
Indices: 68464--68512 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
68454 AAACACTCGA
68464 AAATTTTTGACATTTTACTGCCTG
1 AAATTTTTGACATTTTACTGCCTG
68488 AAATTTTTGACATTTTACTGCCTG
1 AAATTTTTGACATTTTACTGCCTG
68512 A
1 A
68513 TTTTCCTGCT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.27, C:0.16, G:0.12, T:0.45
Consensus pattern (24 bp):
AAATTTTTGACATTTTACTGCCTG
Found at i:74661 original size:147 final size:146
Alignment explanation
Indices: 74395--74687 Score: 550
Period size: 147 Copynumber: 2.0 Consensus size: 146
74385 GTGGTAGAGG
*
74395 CCGTGGTTGTTTTAATAATTCTAATCGACCTCAGTGTCAACTGTGTGGAAATTTGGTCATGTGGT
1 CCGTGGTCGTTTTAATAATTCTAATCGACCTCAGTGTCAACTGTGTGGAAATTTGGTCATGTGGT
74460 TCAGAAGTTCTATCACAGGTTTGATCGTGAGTACACCGGGGTAGGTGACTCCTCTGTGTCAGTTA
66 TCAGAAGTTCTATCACAGGTTTGATCGTGAGTACACCGGGGTAGGTGACTCCTCTGTGTCAGTTA
74525 ATAATGGATCGAAACA
131 ATAATGGATCGAAACA
74541 CCGTGGTCGTTTTAATAATTCTAATCGACCTCAGTGTCAACTGTGTGGAAAATTTGGTCATGTGG
1 CCGTGGTCGTTTTAATAATTCTAATCGACCTCAGTGTCAACTGTGTGG-AAATTTGGTCATGTGG
*
74606 TTCAGAAGTTCTATCACAGGTTTGATCGTGAGTACACCGGGGTAGTTGACTCCTCTGTGTCAGTT
65 TTCAGAAGTTCTATCACAGGTTTGATCGTGAGTACACCGGGGTAGGTGACTCCTCTGTGTCAGTT
*
74671 AATAATGGGTCGAAACA
130 AATAATGGATCGAAACA
74688 GTCTCGCAGT
Statistics
Matches: 143, Mismatches: 3, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
146 47 0.33
147 96 0.67
ACGTcount: A:0.25, C:0.17, G:0.25, T:0.33
Consensus pattern (146 bp):
CCGTGGTCGTTTTAATAATTCTAATCGACCTCAGTGTCAACTGTGTGGAAATTTGGTCATGTGGT
TCAGAAGTTCTATCACAGGTTTGATCGTGAGTACACCGGGGTAGGTGACTCCTCTGTGTCAGTTA
ATAATGGATCGAAACA
Found at i:83560 original size:64 final size:65
Alignment explanation
Indices: 83492--83621 Score: 201
Period size: 64 Copynumber: 2.0 Consensus size: 65
83482 TCCCTAATTT
* * * *
83492 AATATTCTTCACTT-TTTCCTTTTTTATGCCATACCTACAGTTCAATTCATTCAAATTTAA-AAG
1 AATATTCTTCAATTATTT-ATTTTTTATACCATACCTACAATTCAATTCATTCAAATTTAAGAAG
83555 A
65 A
83556 AATATTCTTCAATTATTTATTTTTTATACCATACCTACAATTCAATTCATTCAAATTTAAGAAGA
1 AATATTCTTCAATTATTTATTTTTTATACCATACCTACAATTCAATTCATTCAAATTTAAGAAGA
83621 A
1 A
83622 GGAGAACGTT
Statistics
Matches: 60, Mismatches: 4, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
64 52 0.87
65 8 0.13
ACGTcount: A:0.35, C:0.18, G:0.04, T:0.43
Consensus pattern (65 bp):
AATATTCTTCAATTATTTATTTTTTATACCATACCTACAATTCAATTCATTCAAATTTAAGAAGA
Found at i:86339 original size:65 final size:66
Alignment explanation
Indices: 86261--86387 Score: 184
Period size: 65 Copynumber: 1.9 Consensus size: 66
86251 GTTTTCCTTC
* * * *
86261 TTGAATTTGAATGAATTGAATTGTGGGTATGGTATAAAAAATA-AATAATTGAAGAATATTTCTT
1 TTGAATTTGAATGAATTGAACTGTAGGTATGGTATAAAAAAAAGAATAATAGAAGAATATTTCTT
86325 T
66 T
* *
86326 TTGAATTTTAATGAATTGAACTGTATGTATGGTATAAAAAAAAGGAATAATAGAAGAATATT
1 TTGAATTTGAATGAATTGAACTGTAGGTATGGTATAAAAAAAA-GAATAATAGAAGAATATT
86388 AAATTAGAGA
Statistics
Matches: 54, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
65 38 0.70
67 16 0.30
ACGTcount: A:0.43, C:0.02, G:0.18, T:0.37
Consensus pattern (66 bp):
TTGAATTTGAATGAATTGAACTGTAGGTATGGTATAAAAAAAAGAATAATAGAAGAATATTTCTT
T
Found at i:87262 original size:16 final size:16
Alignment explanation
Indices: 87241--87272 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
87231 TATACAGAGA
87241 TTTTTTCGCAGGGATT
1 TTTTTTCGCAGGGATT
*
87257 TTTTTTTGCAGGGATT
1 TTTTTTCGCAGGGATT
87273 ACTGCCCTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.12, C:0.09, G:0.25, T:0.53
Consensus pattern (16 bp):
TTTTTTCGCAGGGATT
Found at i:101683 original size:35 final size:35
Alignment explanation
Indices: 101643--101710 Score: 127
Period size: 35 Copynumber: 1.9 Consensus size: 35
101633 ATAAAAGTTC
101643 TATAAGGAGGATATGAGTGAAAAGTTGGCTTGCTG
1 TATAAGGAGGATATGAGTGAAAAGTTGGCTTGCTG
*
101678 TATAAGGAGGATATGAGTGAAAGGTTGGCTTGC
1 TATAAGGAGGATATGAGTGAAAAGTTGGCTTGC
101711 CGAGGTTCGT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 32 1.00
ACGTcount: A:0.31, C:0.06, G:0.35, T:0.28
Consensus pattern (35 bp):
TATAAGGAGGATATGAGTGAAAAGTTGGCTTGCTG
Found at i:109070 original size:20 final size:22
Alignment explanation
Indices: 109018--109072 Score: 62
Period size: 20 Copynumber: 2.6 Consensus size: 22
109008 CCTTTTACCA
*
109018 AAGGGATCGATCCTTTTCCTCG
1 AAGGGATCGATCCCTTTCCTCG
* *
109040 AA-GGATTGATCCCTTT-GTC-
1 AAGGGATCGATCCCTTTCCTCG
109059 AAGGGATCGATCCC
1 AAGGGATCGATCCC
109073 AAACTCACTA
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
19 2 0.07
20 12 0.43
21 12 0.43
22 2 0.07
ACGTcount: A:0.22, C:0.25, G:0.24, T:0.29
Consensus pattern (22 bp):
AAGGGATCGATCCCTTTCCTCG
Found at i:109134 original size:16 final size:16
Alignment explanation
Indices: 109113--109156 Score: 52
Period size: 20 Copynumber: 2.5 Consensus size: 16
109103 TTGGTCAAAA
109113 TAAGAGATCCTTTTGC
1 TAAGAGATCCTTTTGC
109129 TAAGAGATTGATCCTTTTGC
1 T-A-AGA--GATCCTTTTGC
109149 TAAGAGAT
1 TAAGAGAT
109157 TGATCCTTTG
Statistics
Matches: 24, Mismatches: 0, Indels: 8
0.75 0.00 0.25
Matches are distributed among these distances:
16 4 0.17
17 1 0.04
18 6 0.25
19 1 0.04
20 12 0.50
ACGTcount: A:0.30, C:0.14, G:0.20, T:0.36
Consensus pattern (16 bp):
TAAGAGATCCTTTTGC
Found at i:109143 original size:20 final size:20
Alignment explanation
Indices: 109118--109165 Score: 96
Period size: 20 Copynumber: 2.4 Consensus size: 20
109108 CAAAATAAGA
109118 GATCCTTTTGCTAAGAGATT
1 GATCCTTTTGCTAAGAGATT
109138 GATCCTTTTGCTAAGAGATT
1 GATCCTTTTGCTAAGAGATT
109158 GATCCTTT
1 GATCCTTT
109166 GAGCTAAAGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.23, C:0.17, G:0.19, T:0.42
Consensus pattern (20 bp):
GATCCTTTTGCTAAGAGATT
Found at i:111987 original size:18 final size:18
Alignment explanation
Indices: 111966--112054 Score: 67
Period size: 18 Copynumber: 4.8 Consensus size: 18
111956 TTTTTTTTCT
111966 TTTTAATAATTTTATATA
1 TTTTAATAATTTTATATA
**
111984 TTTT-ATAAATTAAATATA
1 TTTTAAT-AATTTTATATA
112002 TTTATTAATAAATTTT-TCAT-
1 -TT-TTAAT-AATTTTAT-ATA
*
112022 TTTAAATAATTTTATTATA
1 TTTTAATAATTTTA-TATA
*
112041 TTTAAATAATTTTA
1 TTTTAATAATTTTA
112055 AAATTTGATA
Statistics
Matches: 58, Mismatches: 5, Indels: 15
0.74 0.06 0.19
Matches are distributed among these distances:
17 8 0.14
18 19 0.33
19 19 0.33
20 3 0.05
21 9 0.16
ACGTcount: A:0.42, C:0.01, G:0.00, T:0.57
Consensus pattern (18 bp):
TTTTAATAATTTTATATA
Found at i:119698 original size:19 final size:19
Alignment explanation
Indices: 119674--119712 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
119664 TTTAATTTAC
*
119674 TATTGTGATTGTA-AATATT
1 TATTGTAATT-TAGAATATT
119693 TATTGTAATTTAGAATATT
1 TATTGTAATTTAGAATATT
119712 T
1 T
119713 CATTTTCTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 2 0.11
19 16 0.89
ACGTcount: A:0.33, C:0.00, G:0.13, T:0.54
Consensus pattern (19 bp):
TATTGTAATTTAGAATATT
Found at i:121890 original size:2 final size:2
Alignment explanation
Indices: 121883--121941 Score: 118
Period size: 2 Copynumber: 29.5 Consensus size: 2
121873 GATTTCAATT
121883 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
121925 TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA T
121942 GCAAGAAAAA
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 57 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:131404 original size:41 final size:41
Alignment explanation
Indices: 131359--131518 Score: 302
Period size: 41 Copynumber: 3.9 Consensus size: 41
131349 ATTCGCGTTG
131359 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
1 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
*
131400 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGCTTTTC
1 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
*
131441 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGCTTTTC
1 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
131482 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGAT
1 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGAT
131519 AGTTGAAAAT
Statistics
Matches: 117, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 117 1.00
ACGTcount: A:0.19, C:0.21, G:0.25, T:0.36
Consensus pattern (41 bp):
CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
Found at i:131513 original size:103 final size:103
Alignment explanation
Indices: 131404--131600 Score: 385
Period size: 103 Copynumber: 1.9 Consensus size: 103
131394 ATTTTCCATT
*
131404 TCGCGTTGCGATAGTTGAAAATCGCGTTGCGCTTTTCCATTTCGCGTTGCGATAGTTGAAAATCG
1 TCGCGTTGCGATAGTTGAAAATCACGTTGCGCTTTTCCATTTCGCGTTGCGATAGTTGAAAATCG
131469 CGTTGCGCTTTTCCATTTCGCGTTGCGATAGTTGAAAA
66 CGTTGCGCTTTTCCATTTCGCGTTGCGATAGTTGAAAA
131507 TCGCGTTGCGATAGTTGAAAATCACGTTGCGCTTTTCCATTTCGCGTTGCGATAGTTGAAAATCG
1 TCGCGTTGCGATAGTTGAAAATCACGTTGCGCTTTTCCATTTCGCGTTGCGATAGTTGAAAATCG
131572 CGTTGCGCTTTTCCATTTCGCGTTGCGAT
66 CGTTGCGCTTTTCCATTTCGCGTTGCGAT
131601 TTTCCATTTC
Statistics
Matches: 93, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
103 93 1.00
ACGTcount: A:0.18, C:0.21, G:0.25, T:0.36
Consensus pattern (103 bp):
TCGCGTTGCGATAGTTGAAAATCACGTTGCGCTTTTCCATTTCGCGTTGCGATAGTTGAAAATCG
CGTTGCGCTTTTCCATTTCGCGTTGCGATAGTTGAAAA
Found at i:131552 original size:41 final size:41
Alignment explanation
Indices: 131507--131600 Score: 179
Period size: 41 Copynumber: 2.3 Consensus size: 41
131497 TAGTTGAAAA
131507 TCGCGTTGCGATAGTTGAAAATCACGTTGCGCTTTTCCATT
1 TCGCGTTGCGATAGTTGAAAATCACGTTGCGCTTTTCCATT
*
131548 TCGCGTTGCGATAGTTGAAAATCGCGTTGCGCTTTTCCATT
1 TCGCGTTGCGATAGTTGAAAATCACGTTGCGCTTTTCCATT
131589 TCGCGTTGCGAT
1 TCGCGTTGCGAT
131601 TTTCCATTTC
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.17, C:0.22, G:0.24, T:0.36
Consensus pattern (41 bp):
TCGCGTTGCGATAGTTGAAAATCACGTTGCGCTTTTCCATT
Found at i:131557 original size:82 final size:82
Alignment explanation
Indices: 131366--131537 Score: 245
Period size: 82 Copynumber: 2.1 Consensus size: 82
131356 TTGCATTTCG
*
131366 CGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTTGAAAATCGCGT
1 CGTTGCGATAGTTCAAAATCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTTGAAAATCGCGT
* * * ** *
131431 TGCGCTTTTCCATTTCG
66 TGCGATGTTCAAAATCA
* *
131448 CGTTGCGATAGTTGAAAATCGCGTTGCGCTTTTCCATTTCGCGTTGCGATAGTTGAAAATCGCGT
1 CGTTGCGATAGTTCAAAATCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTTGAAAATCGCGT
*
131513 TGCGATAGTTGAAAATCA
66 TGCGAT-GTTCAAAATCA
131531 CGTTGCG
1 CGTTGCG
131538 CTTTTCCATT
Statistics
Matches: 81, Mismatches: 8, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
82 69 0.85
83 12 0.15
ACGTcount: A:0.20, C:0.20, G:0.26, T:0.34
Consensus pattern (82 bp):
CGTTGCGATAGTTCAAAATCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTTGAAAATCGCGT
TGCGATGTTCAAAATCA
Found at i:131640 original size:22 final size:22
Alignment explanation
Indices: 131612--131683 Score: 87
Period size: 22 Copynumber: 3.4 Consensus size: 22
131602 TTCCATTTCG
131612 CGTTGCGATAGTCTACAGTTGT
1 CGTTGCGATAGTCTACAGTTGT
* * **
131634 CGTTGCGAT--TTTCCAAAT-T
1 CGTTGCGATAGTCTACAGTTGT
131653 CGTTGCGATAGTCTACAGTTGT
1 CGTTGCGATAGTCTACAGTTGT
131675 CGTTGCGAT
1 CGTTGCGAT
131684 TTTCCAAATT
Statistics
Matches: 39, Mismatches: 8, Indels: 6
0.74 0.15 0.11
Matches are distributed among these distances:
19 10 0.26
20 5 0.13
21 5 0.13
22 19 0.49
ACGTcount: A:0.18, C:0.19, G:0.25, T:0.38
Consensus pattern (22 bp):
CGTTGCGATAGTCTACAGTTGT
Found at i:131648 original size:103 final size:101
Alignment explanation
Indices: 131384--131623 Score: 381
Period size: 103 Copynumber: 2.3 Consensus size: 101
131374 TAGTTGAAAA
*
131384 TCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGCTTTTCCATTTCGC
1 TCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTTG-AAATTGCGTTGCGCTTTTCCATTTCGC
131449 GTTGCGATAGTTGAAAATCGCGTTGCGCTTTTCCATT
65 GTTGCGATAGTTGAAAATCGCGTTGCGCTTTTCCATT
* ** ** **
131486 TCGCGTTGCGATAGTTGAAAATCGCGTTGCGATAGTTGAAAATCACGTTGCGCTTTTCCATTTCG
1 TCGCGTTGCGAT-TTTCCATTTCGCGTTGCGATAGTTG-AAATTGCGTTGCGCTTTTCCATTTCG
131551 CGTTGCGATAGTTGAAAATCGCGTTGCGCTTTTCCATT
64 CGTTGCGATAGTTGAAAATCGCGTTGCGCTTTTCCATT
131589 TCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGT
1 TCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGT
131624 CTACAGTTGT
Statistics
Matches: 126, Mismatches: 11, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
102 30 0.24
103 96 0.76
ACGTcount: A:0.17, C:0.22, G:0.24, T:0.37
Consensus pattern (101 bp):
TCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTTGAAATTGCGTTGCGCTTTTCCATTTCGCG
TTGCGATAGTTGAAAATCGCGTTGCGCTTTTCCATT
Found at i:131657 original size:19 final size:19
Alignment explanation
Indices: 131633--131698 Score: 69
Period size: 19 Copynumber: 3.3 Consensus size: 19
131623 TCTACAGTTG
131633 TCGTTGCGATTTTCCAAAT
1 TCGTTGCGATTTTCCAAAT
* * **
131652 TCGTTGCGATAGTCTACAGTT
1 TCGTTGCGAT--TTTCCAAAT
131673 GTCGTTGCGATTTTCCAAAT
1 -TCGTTGCGATTTTCCAAAT
131693 TCGTTG
1 TCGTTG
131699 TGATAGTTAA
Statistics
Matches: 36, Mismatches: 8, Indels: 6
0.72 0.16 0.12
Matches are distributed among these distances:
19 16 0.44
20 5 0.14
21 5 0.14
22 10 0.28
ACGTcount: A:0.18, C:0.20, G:0.21, T:0.41
Consensus pattern (19 bp):
TCGTTGCGATTTTCCAAAT
Found at i:131657 original size:61 final size:60
Alignment explanation
Indices: 131359--131661 Score: 236
Period size: 62 Copynumber: 4.9 Consensus size: 60
131349 ATTCGCGTTG
* * *
131359 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCC-ATTTCGCGTTGCGATAGTTG
1 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCAAATT--CGTTGCGAT-TTTC
* ** * * ** ** * ** * *
131421 AAAATCGCGTTGCGCT-TTTCCATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGCTTTTC
1 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGAT-TTTCCAAAT-TCGTTGCGATTTTC
* ** * *
131482 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATAGTTGAAAATCACGTTGCGCTTTTC
1 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGAT-TTTCCAAAT-TCGTTGCGATTTTC
* *
131544 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGCTTTTCC-ATTTCGCGTTGCGATTTTC
1 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCAAATT--CGTTGCGATTTTC
* * *
131605 CATTTCGCGTTGCGATAGTCT-ACAGTTGTCGTTGCGATTTTCCAAATTCGTTGCGAT
1 CATTTCGCGTTGCGATAGT-TGAAAATCG-CGTTGCGATTTTCCAAATTCGTTGCGAT
131662 AGTCTACAGT
Statistics
Matches: 193, Mismatches: 39, Indels: 19
0.77 0.16 0.08
Matches are distributed among these distances:
60 2 0.01
61 75 0.39
62 111 0.58
63 5 0.03
ACGTcount: A:0.18, C:0.21, G:0.24, T:0.37
Consensus pattern (60 bp):
CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCAAATTCGTTGCGATTTTC
Found at i:131667 original size:41 final size:41
Alignment explanation
Indices: 131592--131705 Score: 185
Period size: 41 Copynumber: 2.8 Consensus size: 41
131582 TTCCATTTCG
*
131592 CGTTGCGATTTTCC-ATTTCGCGTTGCGATAGTCTACAGTTGT
1 CGTTGCGATTTTCCAAATT--CGTTGCGATAGTCTACAGTTGT
131634 CGTTGCGATTTTCCAAATTCGTTGCGATAGTCTACAGTTGT
1 CGTTGCGATTTTCCAAATTCGTTGCGATAGTCTACAGTTGT
*
131675 CGTTGCGATTTTCCAAATTCGTTGTGATAGT
1 CGTTGCGATTTTCCAAATTCGTTGCGATAGT
131706 TAAAAAAAAG
Statistics
Matches: 69, Mismatches: 2, Indels: 3
0.93 0.03 0.04
Matches are distributed among these distances:
41 52 0.75
42 14 0.20
43 3 0.04
ACGTcount: A:0.18, C:0.19, G:0.23, T:0.40
Consensus pattern (41 bp):
CGTTGCGATTTTCCAAATTCGTTGCGATAGTCTACAGTTGT
Found at i:131689 original size:103 final size:100
Alignment explanation
Indices: 131384--131664 Score: 368
Period size: 103 Copynumber: 2.7 Consensus size: 100
131374 TAGTTGAAAA
*
131384 TCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGCTTTTCCATTTCGC
1 TCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTTG-AAATTGCGTTGCGCTTTTCCATTTC-C
131449 GTTGCGATAGTTGAAAATCGCGTTGCGCTTTTCCATT
64 GTTGCGATAGTTGAAAATCGCGTTGCGCTTTTCCATT
* ** ** **
131486 TCGCGTTGCGATAGTTGAAAATCGCGTTGCGATAGTTGAAAATCACGTTGCGCTTTTCCATTTCG
1 TCGCGTTGCGAT-TTTCCATTTCGCGTTGCGATAGTTG-AAATTGCGTTGCGCTTTTCCATTTC-
131551 CGTTGCGATAGTTGAAAATCGCGTTGCGCTTTTCCATT
63 CGTTGCGATAGTTGAAAATCGCGTTGCGCTTTTCCATT
* * *
131589 TCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTCT-ACAGTTGTCGTTGCGATTTTCCAAATT
1 TCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGT-TGA-AATTG-CGTTGCGCTTTTCC-ATTT
131653 -CGTTGCGATAGT
62 CCGTTGCGATAGT
131665 CTACAGTTGT
Statistics
Matches: 158, Mismatches: 16, Indels: 10
0.86 0.09 0.05
Matches are distributed among these distances:
101 1 0.01
102 44 0.28
103 110 0.70
104 3 0.02
ACGTcount: A:0.17, C:0.21, G:0.24, T:0.37
Consensus pattern (100 bp):
TCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTTGAAATTGCGTTGCGCTTTTCCATTTCCGT
TGCGATAGTTGAAAATCGCGTTGCGCTTTTCCATT
Found at i:132227 original size:41 final size:41
Alignment explanation
Indices: 132170--132247 Score: 138
Period size: 41 Copynumber: 1.9 Consensus size: 41
132160 TGGGAACAAC
* *
132170 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTT
1 CATTTCGCGTTGCGATAGGTGAAAATCGCATTGCGATTTTT
132211 CATTTCGCGTTGCGATAGGTGAAAATCGCATTGCGAT
1 CATTTCGCGTTGCGATAGGTGAAAATCGCATTGCGAT
132248 AGTTGAAAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 35 1.00
ACGTcount: A:0.22, C:0.18, G:0.26, T:0.35
Consensus pattern (41 bp):
CATTTCGCGTTGCGATAGGTGAAAATCGCATTGCGATTTTT
Found at i:132276 original size:62 final size:62
Alignment explanation
Indices: 132174--132307 Score: 232
Period size: 62 Copynumber: 2.2 Consensus size: 62
132164 AACAACCATT
132174 TCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTTCATTTCGCGTTGCGATAGGTGAAAA
1 TCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTTCATTTCGCGTTGCGATAGGTGAAAA
* * * *
132236 TCGCATTGCGATAGTTGAAAATCGCGTTGCGCTTTTTCATTTCGCGTTGCTATAGTTGAAAA
1 TCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTTCATTTCGCGTTGCGATAGGTGAAAA
132298 TCGCGTTGCG
1 TCGCGTTGCG
132308 CTTTTCCATT
Statistics
Matches: 67, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
62 67 1.00
ACGTcount: A:0.21, C:0.18, G:0.26, T:0.35
Consensus pattern (62 bp):
TCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTTCATTTCGCGTTGCGATAGGTGAAAA
Found at i:132282 original size:20 final size:20
Alignment explanation
Indices: 132257--132370 Score: 75
Period size: 20 Copynumber: 5.6 Consensus size: 20
132247 TAGTTGAAAA
* *
132257 TCGCGTTGCGCTTTTTCATT
1 TCGCGTTGCGATTTTGCATT
* * * **
132277 TCGCGTTGCTATAGTTGAAAA
1 TCGCGTTGCGAT-TTTGCATT
* *
132298 TCGCGTTGCGCTTTTCCATT
1 TCGCGTTGCGATTTTGCATT
* * **
132318 TCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGAT-TTTGCATT
*
132339 TCGCGTTGCGATTTTTCATT
1 TCGCGTTGCGATTTTGCATT
*
132359 TCGCATTGCGAT
1 TCGCGTTGCGAT
132371 AGTCTACAGT
Statistics
Matches: 66, Mismatches: 26, Indels: 4
0.69 0.27 0.04
Matches are distributed among these distances:
20 38 0.58
21 28 0.42
ACGTcount: A:0.16, C:0.21, G:0.23, T:0.40
Consensus pattern (20 bp):
TCGCGTTGCGATTTTGCATT
Found at i:132296 original size:41 final size:41
Alignment explanation
Indices: 132236--132373 Score: 231
Period size: 41 Copynumber: 3.4 Consensus size: 41
132226 TAGGTGAAAA
132236 TCGCATTGCGATAGTTGAAAATCGCGTTGCGCTTTTTCATT
1 TCGCATTGCGATAGTTGAAAATCGCGTTGCGCTTTTTCATT
* * *
132277 TCGCGTTGCTATAGTTGAAAATCGCGTTGCGCTTTTCCATT
1 TCGCATTGCGATAGTTGAAAATCGCGTTGCGCTTTTTCATT
* *
132318 TCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTTCATT
1 TCGCATTGCGATAGTTGAAAATCGCGTTGCGCTTTTTCATT
132359 TCGCATTGCGATAGT
1 TCGCATTGCGATAGT
132374 CTACAGTTGT
Statistics
Matches: 90, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
41 90 1.00
ACGTcount: A:0.19, C:0.20, G:0.23, T:0.38
Consensus pattern (41 bp):
TCGCATTGCGATAGTTGAAAATCGCGTTGCGCTTTTTCATT
Found at i:132392 original size:22 final size:22
Alignment explanation
Indices: 132364--132433 Score: 74
Period size: 22 Copynumber: 3.3 Consensus size: 22
132354 TCATTTCGCA
132364 TTGCGATAGTCTACAGTTGTCG
1 TTGCGATAGTCTACAGTTGTCG
* * **
132386 TTGCGAT--TTTCCAAAT-TCG
1 TTGCGATAGTCTACAGTTGTCG
*
132405 TTGCGATAGTCTACAGTTGTTG
1 TTGCGATAGTCTACAGTTGTCG
132427 TTGCGAT
1 TTGCGAT
132434 TTTCCAAATT
Statistics
Matches: 36, Mismatches: 9, Indels: 6
0.71 0.18 0.12
Matches are distributed among these distances:
19 10 0.28
20 5 0.14
21 5 0.14
22 16 0.44
ACGTcount: A:0.19, C:0.17, G:0.24, T:0.40
Consensus pattern (22 bp):
TTGCGATAGTCTACAGTTGTCG
Found at i:132396 original size:41 final size:41
Alignment explanation
Indices: 132301--132439 Score: 158
Period size: 41 Copynumber: 3.4 Consensus size: 41
132291 TTGAAAATCG
* * * *
132301 CGTTGCGCTTTTCCATTTCGCGTTGCGATAGT-TGAAAATCG-
1 CGTTGCGATTTTCCATTTCGC-TTGCGATAGTCT-ACAGTTGT
*
132342 CGTTGCGATTTTTCATTTCGCATTGCGATAGTCTACAGTTGT
1 CGTTGCGATTTTCCATTTCGC-TTGCGATAGTCTACAGTTGT
*
132384 CGTTGCGATTTTCCAAATTCG-TTGCGATAGTCTACAGTTGT
1 CGTTGCGATTTTCC-ATTTCGCTTGCGATAGTCTACAGTTGT
*
132425 TGTTGCGATTTTCCA
1 CGTTGCGATTTTCCA
132440 AATTCGTTGT
Statistics
Matches: 86, Mismatches: 9, Indels: 7
0.84 0.09 0.07
Matches are distributed among these distances:
40 1 0.01
41 66 0.77
42 14 0.16
43 5 0.06
ACGTcount: A:0.17, C:0.20, G:0.22, T:0.40
Consensus pattern (41 bp):
CGTTGCGATTTTCCATTTCGCTTGCGATAGTCTACAGTTGT
Found at i:132407 original size:19 final size:19
Alignment explanation
Indices: 132383--132448 Score: 60
Period size: 19 Copynumber: 3.3 Consensus size: 19
132373 TCTACAGTTG
132383 TCGTTGCGATTTTCCAAAT
1 TCGTTGCGATTTTCCAAAT
* * **
132402 TCGTTGCGATAGTCTACAGTT
1 TCGTTGCGAT--TTTCCAAAT
*
132423 GTTGTTGCGATTTTCCAAAT
1 -TCGTTGCGATTTTCCAAAT
132443 TCGTTG
1 TCGTTG
132449 TGATAGTTAA
Statistics
Matches: 34, Mismatches: 10, Indels: 6
0.68 0.20 0.12
Matches are distributed among these distances:
19 15 0.44
20 5 0.15
21 5 0.15
22 9 0.26
ACGTcount: A:0.18, C:0.18, G:0.21, T:0.42
Consensus pattern (19 bp):
TCGTTGCGATTTTCCAAAT
Found at i:132407 original size:82 final size:81
Alignment explanation
Indices: 132241--132414 Score: 226
Period size: 82 Copynumber: 2.1 Consensus size: 81
132231 GAAAATCGCA
* * *
132241 TTGCGATAGTTGAAAATCGCGTTGCGCTTTTTCATTTCGCGTTGCTATAGTTGAAAATCGCGTTG
1 TTGCGATAGTTGAAAATCGCGTTGCGATTTTTCATTTCGCATTGCGATAGTTGAAAATCGCGTTG
* *
132306 CGCTTTTCCATTTCGCG
66 CGATTTTCCAATTC-CG
* * *
132323 TTGCGATAGTTGAAAATCGCGTTGCGATTTTTCATTTCGCATTGCGATAGTCT-ACAGTTGTCGT
1 TTGCGATAGTTGAAAATCGCGTTGCGATTTTTCATTTCGCATTGCGATAGT-TGAAAATCG-CGT
132387 TGCGATTTTCCAAATT-CG
64 TGCGATTTTCC-AATTCCG
132405 TTGCGATAGT
1 TTGCGATAGT
132415 CTACAGTTGT
Statistics
Matches: 81, Mismatches: 8, Indels: 6
0.85 0.08 0.06
Matches are distributed among these distances:
82 64 0.79
83 14 0.17
84 3 0.04
ACGTcount: A:0.19, C:0.19, G:0.23, T:0.39
Consensus pattern (81 bp):
TTGCGATAGTTGAAAATCGCGTTGCGATTTTTCATTTCGCATTGCGATAGTTGAAAATCGCGTTG
CGATTTTCCAATTCCG
Found at i:132440 original size:41 final size:41
Alignment explanation
Indices: 132342--132455 Score: 167
Period size: 41 Copynumber: 2.8 Consensus size: 41
132332 TTGAAAATCG
* *
132342 CGTTGCGATTTTTC-ATTTCGCATTGCGATAGTCTACAGTTGT
1 CGTTGCGATTTTCCAAATTCG--TTGCGATAGTCTACAGTTGT
132384 CGTTGCGATTTTCCAAATTCGTTGCGATAGTCTACAGTTGT
1 CGTTGCGATTTTCCAAATTCGTTGCGATAGTCTACAGTTGT
* *
132425 TGTTGCGATTTTCCAAATTCGTTGTGATAGT
1 CGTTGCGATTTTCCAAATTCGTTGCGATAGT
132456 TAAAAAAAAA
Statistics
Matches: 67, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
41 49 0.73
42 13 0.19
43 5 0.07
ACGTcount: A:0.18, C:0.18, G:0.22, T:0.42
Consensus pattern (41 bp):
CGTTGCGATTTTCCAAATTCGTTGCGATAGTCTACAGTTGT
Found at i:132448 original size:22 final size:22
Alignment explanation
Indices: 132385--132449 Score: 57
Period size: 22 Copynumber: 3.1 Consensus size: 22
132375 TACAGTTGTC
132385 GTTGCGATTTTCCAAATTC---
1 GTTGCGATTTTCCAAATTCGTT
** * *
132404 GTTGCGATAGTCTACAGTT-GTT
1 GTTGCGATTTTCCA-AATTCGTT
132426 GTTGCGATTTTCCAAATTCGTT
1 GTTGCGATTTTCCAAATTCGTT
132448 GT
1 GT
132450 GATAGTTAAA
Statistics
Matches: 33, Mismatches: 8, Indels: 7
0.69 0.17 0.15
Matches are distributed among these distances:
19 11 0.33
20 3 0.09
21 3 0.09
22 16 0.48
ACGTcount: A:0.18, C:0.17, G:0.22, T:0.43
Consensus pattern (22 bp):
GTTGCGATTTTCCAAATTCGTT
Found at i:132561 original size:17 final size:17
Alignment explanation
Indices: 132535--132568 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
132525 CGTATGACCA
132535 CGACCACGACCCAACCC
1 CGACCACGACCCAACCC
* *
132552 CGACCCCGACCCGACCC
1 CGACCACGACCCAACCC
132569 GAGACGAGAC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.24, C:0.62, G:0.15, T:0.00
Consensus pattern (17 bp):
CGACCACGACCCAACCC
Found at i:133195 original size:19 final size:19
Alignment explanation
Indices: 133171--133237 Score: 62
Period size: 19 Copynumber: 3.4 Consensus size: 19
133161 ACGAATTTTT
133171 GCAACGAATTTGGAAAATC
1 GCAACGAATTTGGAAAATC
* **
133190 GCAACGACAATTGTAGACTATC
1 GCAACG--AATT-TGGAAAATC
* *
133212 GCAACAAATTTGAAAAATC
1 GCAACGAATTTGGAAAATC
133231 GCAACGA
1 GCAACGA
133238 CAACTGTAGA
Statistics
Matches: 36, Mismatches: 9, Indels: 6
0.71 0.18 0.12
Matches are distributed among these distances:
19 17 0.47
20 4 0.11
21 4 0.11
22 11 0.31
ACGTcount: A:0.43, C:0.19, G:0.18, T:0.19
Consensus pattern (19 bp):
GCAACGAATTTGGAAAATC
Found at i:133215 original size:22 final size:22
Alignment explanation
Indices: 133187--133258 Score: 80
Period size: 22 Copynumber: 3.4 Consensus size: 22
133177 AATTTGGAAA
133187 ATCGCAACGACAATTGTAGACT
1 ATCGCAACGACAATTGTAGACT
**
133209 ATCGCAAC-A-AATT-T-GAAAA
1 ATCGCAACGACAATTGTAG-ACT
*
133228 ATCGCAACGACAACTGTAGACT
1 ATCGCAACGACAATTGTAGACT
133250 ATCGCAACG
1 ATCGCAACG
133259 CGAAATGGAA
Statistics
Matches: 40, Mismatches: 5, Indels: 10
0.73 0.09 0.18
Matches are distributed among these distances:
18 1 0.03
19 10 0.25
20 5 0.12
21 4 0.10
22 19 0.47
23 1 0.03
ACGTcount: A:0.40, C:0.24, G:0.17, T:0.19
Consensus pattern (22 bp):
ATCGCAACGACAATTGTAGACT
Found at i:133229 original size:41 final size:41
Alignment explanation
Indices: 133171--133257 Score: 147
Period size: 41 Copynumber: 2.1 Consensus size: 41
133161 ACGAATTTTT
* * *
133171 GCAACGAATTTGGAAAATCGCAACGACAATTGTAGACTATC
1 GCAACAAATTTGAAAAATCGCAACGACAACTGTAGACTATC
133212 GCAACAAATTTGAAAAATCGCAACGACAACTGTAGACTATC
1 GCAACAAATTTGAAAAATCGCAACGACAACTGTAGACTATC
133253 GCAAC
1 GCAAC
133258 GCGAAATGGA
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
41 43 1.00
ACGTcount: A:0.41, C:0.22, G:0.17, T:0.20
Consensus pattern (41 bp):
GCAACAAATTTGAAAAATCGCAACGACAACTGTAGACTATC
Found at i:136647 original size:20 final size:21
Alignment explanation
Indices: 136622--136667 Score: 67
Period size: 20 Copynumber: 2.2 Consensus size: 21
136612 AGTGCCCAAC
* *
136622 AATAACATAATCGGTAGAAA-
1 AATAACAAAACCGGTAGAAAT
136642 AATAACAAAACCGGTAGAAAT
1 AATAACAAAACCGGTAGAAAT
136663 AATAA
1 AATAA
136668 TGTTTCCGGT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 18 0.78
21 5 0.22
ACGTcount: A:0.59, C:0.11, G:0.13, T:0.17
Consensus pattern (21 bp):
AATAACAAAACCGGTAGAAAT
Found at i:138607 original size:18 final size:18
Alignment explanation
Indices: 138584--138618 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
138574 AGAGATTATA
138584 AGTGGTCCTTCGGGACAT
1 AGTGGTCCTTCGGGACAT
138602 AGTGGTCCTTCGGGACA
1 AGTGGTCCTTCGGGACA
138619 GATTTTCAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.17, C:0.23, G:0.34, T:0.26
Consensus pattern (18 bp):
AGTGGTCCTTCGGGACAT
Found at i:140339 original size:2 final size:2
Alignment explanation
Indices: 140325--140368 Score: 72
Period size: 2 Copynumber: 22.0 Consensus size: 2
140315 TTTTTTCCTA
140325 AT AT GAT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
140367 AT
1 AT
140369 GAATGATTAT
Statistics
Matches: 40, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
1 1 0.03
2 37 0.93
3 2 0.05
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
AT
Found at i:142125 original size:13 final size:13
Alignment explanation
Indices: 142103--142179 Score: 59
Period size: 13 Copynumber: 5.9 Consensus size: 13
142093 ACGTAGAAAT
*
142103 TAAATGAATATAA
1 TAAATAAATATAA
142116 TAAATAAATATAA
1 TAAATAAATATAA
*
142129 T-AATAATTAGTAA
1 TAAATAAATA-TAA
*
142142 T-ATTAAATATAA
1 TAAATAAATATAA
* *
142154 GAAATAATTAATAA
1 TAAATAAAT-ATAA
* *
142168 TATATAACTATA
1 TAAATAAATATA
142180 GAAATTAAAA
Statistics
Matches: 51, Mismatches: 10, Indels: 6
0.76 0.15 0.09
Matches are distributed among these distances:
12 10 0.20
13 31 0.61
14 10 0.20
ACGTcount: A:0.60, C:0.01, G:0.04, T:0.35
Consensus pattern (13 bp):
TAAATAAATATAA
Found at i:142159 original size:26 final size:27
Alignment explanation
Indices: 142112--142184 Score: 89
Period size: 26 Copynumber: 2.8 Consensus size: 27
142102 TTAAATGAAT
* *
142112 ATAATAAATAAATATAA-TAATAATTA
1 ATAATATATAAATATAAGAAATAATTA
*
142138 GTAATAT-TAAATATAAGAAATAATTA
1 ATAATATATAAATATAAGAAATAATTA
*
142164 ATAATATATAACTAT-AGAAAT
1 ATAATATATAAATATAAGAAAT
142185 TAAAATAGAT
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
25 9 0.22
26 25 0.62
27 6 0.15
ACGTcount: A:0.60, C:0.01, G:0.04, T:0.34
Consensus pattern (27 bp):
ATAATATATAAATATAAGAAATAATTA
Found at i:142169 original size:19 final size:19
Alignment explanation
Indices: 142109--142171 Score: 51
Period size: 16 Copynumber: 3.3 Consensus size: 19
142099 AAATTAAATG
*
142109 AATATAATAAATAAATATAAT
1 AATATAAGAAAT-AAT-TAAT
* *
142130 AATAATTAGTAAT-ATT-A-
1 AAT-ATAAGAAATAATTAAT
142147 AATATAAGAAATAATTAAT
1 AATATAAGAAATAATTAAT
142166 AATATA
1 AATATA
142172 TAACTATAGA
Statistics
Matches: 33, Mismatches: 5, Indels: 10
0.69 0.10 0.21
Matches are distributed among these distances:
16 7 0.21
17 6 0.18
18 2 0.06
19 7 0.21
20 2 0.06
21 3 0.09
22 6 0.18
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (19 bp):
AATATAAGAAATAATTAAT
Found at i:145525 original size:32 final size:31
Alignment explanation
Indices: 145487--145557 Score: 94
Period size: 32 Copynumber: 2.3 Consensus size: 31
145477 TTATATATAT
145487 ATATATATAATATTAATA-A-ATTTAATTTAA
1 ATATATATAATA-TAATATATATTTAATTTAA
145517 AT-TAATATATATATAATATATATTTAATTTAA
1 ATAT-ATATA-ATATAATATATATTTAATTTAA
145549 ATATATATA
1 ATATATATA
145558 CTCAGCCCAA
Statistics
Matches: 36, Mismatches: 0, Indels: 8
0.82 0.00 0.18
Matches are distributed among these distances:
29 1 0.03
30 12 0.33
31 4 0.11
32 18 0.50
33 1 0.03
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (31 bp):
ATATATATAATATAATATATATTTAATTTAA
Found at i:145552 original size:15 final size:15
Alignment explanation
Indices: 145487--145557 Score: 56
Period size: 15 Copynumber: 4.6 Consensus size: 15
145477 TTATATATAT
145487 ATATATATAATATT-A
1 ATATATATAAT-TTAA
* *
145502 ATAAATTTAATTTAA
1 ATATATATAATTTAA
*
145517 AT-TAATATATATATAA
1 ATAT-ATATA-ATTTAA
*
145533 TATATATTTAATTTAA
1 -ATATATATAATTTAA
145549 ATATATATA
1 ATATATATA
145558 CTCAGCCCAA
Statistics
Matches: 43, Mismatches: 8, Indels: 10
0.70 0.13 0.16
Matches are distributed among these distances:
14 2 0.05
15 24 0.56
16 10 0.23
17 6 0.14
18 1 0.02
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
ATATATATAATTTAA
Done.