Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008567.1 Hibiscus syriacus cultivar Beakdansim tig00111484_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: 58335
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:3930 original size:20 final size:20
Alignment explanation
Indices: 3901--3938 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
3891 CAGAACCCCA
*
3901 GGGGGTATCGATTCCCCTGT
1 GGGGGAATCGATTCCCCTGT
*
3921 GGGGGAATCGGTTCCCCT
1 GGGGGAATCGATTCCCCT
3939 TCAAAGGGGA
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:0.11, C:0.26, G:0.37, T:0.26
Consensus pattern (20 bp):
GGGGGAATCGATTCCCCTGT
Found at i:3967 original size:20 final size:20
Alignment explanation
Indices: 3921--3977 Score: 60
Period size: 20 Copynumber: 2.8 Consensus size: 20
3911 ATTCCCCTGT
3921 GGGGGAATCGGTTCCCCTTCAA
1 GGGGGAATCGGTT--CCTTCAA
* *
3943 AGGGGAATCGGTTCCTTGAA
1 GGGGGAATCGGTTCCTTCAA
* *
3963 GGGGGGATCGATTCC
1 GGGGGAATCGGTTCC
3978 CTCTGCACCA
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
20 18 0.60
22 12 0.40
ACGTcount: A:0.19, C:0.21, G:0.37, T:0.23
Consensus pattern (20 bp):
GGGGGAATCGGTTCCTTCAA
Found at i:7829 original size:20 final size:21
Alignment explanation
Indices: 7785--7829 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
7775 GTTTGTTTTC
* *
7785 ATTTTTCAATTTTGAAACATC
1 ATTTTTCAATTTTGAAAAATA
*
7806 ATTTTTCTATTTT-AAAAATA
1 ATTTTTCAATTTTGAAAAATA
7826 ATTT
1 ATTT
7830 CTCATAATCC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 9 0.43
21 12 0.57
ACGTcount: A:0.36, C:0.09, G:0.02, T:0.53
Consensus pattern (21 bp):
ATTTTTCAATTTTGAAAAATA
Found at i:9774 original size:20 final size:21
Alignment explanation
Indices: 9736--9775 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
9726 CGTTATACAA
9736 GGGGGGAATCGGTACTCCCTAT
1 GGGGGGAATCGGTA-TCCCTAT
9758 GGGGGGAATCGGT-TCCCT
1 GGGGGGAATCGGTATCCCT
9776 CCGAGCATAC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 5 0.28
22 13 0.72
ACGTcount: A:0.15, C:0.23, G:0.40, T:0.23
Consensus pattern (21 bp):
GGGGGGAATCGGTATCCCTAT
Found at i:13638 original size:27 final size:27
Alignment explanation
Indices: 13600--13683 Score: 159
Period size: 27 Copynumber: 3.1 Consensus size: 27
13590 TCTTCGCTCA
13600 ACCAGCTACCTCAAAACACTCCGTTTT
1 ACCAGCTACCTCAAAACACTCCGTTTT
13627 ACCAGCTACCTCAAAACACTCCGTTTT
1 ACCAGCTACCTCAAAACACTCCGTTTT
*
13654 ACCAGCTAGCTCAAAACACTCCGTTTT
1 ACCAGCTACCTCAAAACACTCCGTTTT
13681 ACC
1 ACC
13684 CGGCCACCAC
Statistics
Matches: 56, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
27 56 1.00
ACGTcount: A:0.30, C:0.37, G:0.08, T:0.25
Consensus pattern (27 bp):
ACCAGCTACCTCAAAACACTCCGTTTT
Found at i:14239 original size:16 final size:16
Alignment explanation
Indices: 14218--14273 Score: 69
Period size: 16 Copynumber: 3.5 Consensus size: 16
14208 TTCGACTTGT
14218 TATTTACCTGATATGA
1 TATTTACCTGATATGA
* *
14234 TATTTACATGATTTGA
1 TATTTACCTGATATGA
*
14250 TATTTACCTGA-ATTA
1 TATTTACCTGATATGA
14265 TATATTACC
1 TAT-TTACC
14274 ATTGATGAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
15 5 0.15
16 29 0.85
ACGTcount: A:0.32, C:0.12, G:0.09, T:0.46
Consensus pattern (16 bp):
TATTTACCTGATATGA
Found at i:15321 original size:30 final size:31
Alignment explanation
Indices: 15281--15338 Score: 100
Period size: 30 Copynumber: 1.9 Consensus size: 31
15271 GAACTTATCG
15281 AAAAATTAATTTAATAAACAT-AATAAATAT
1 AAAAATTAATTTAATAAACATAAATAAATAT
*
15311 AAAATTTAATTTAATAAACATAAATAAA
1 AAAAATTAATTTAATAAACATAAATAAA
15339 CAAAAGTTAC
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
30 20 0.77
31 6 0.23
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (31 bp):
AAAAATTAATTTAATAAACATAAATAAATAT
Found at i:18779 original size:53 final size:54
Alignment explanation
Indices: 18676--18820 Score: 168
Period size: 53 Copynumber: 2.7 Consensus size: 54
18666 ACATTATCGA
* * **
18676 TTAGGGTTAGAGAAGATGAATAGAAACAAAAGATGAATAGGCTTTGGTTAGAAT
1 TTAGGGTTAGAGAAGATGAACAGAAACAAAAGATAAATAGGCTTCAGTTAGAAT
* * **
18730 TTAGGGTTAGAGAATATGAACA-AGACAAAAGATAAATAGGCTTCAGTTAGGGT
1 TTAGGGTTAGAGAAGATGAACAGAAACAAAAGATAAATAGGCTTCAGTTAGAAT
* *
18783 TTAAGGTTAAAGAAGATGAACAGATAA-AAAAGAATAAA
1 TTAGGGTTAGAGAAGATGAACAGA-AACAAAAG-ATAAA
18821 AAAAATGTTT
Statistics
Matches: 76, Mismatches: 12, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
53 44 0.58
54 26 0.34
55 6 0.08
ACGTcount: A:0.47, C:0.05, G:0.25, T:0.23
Consensus pattern (54 bp):
TTAGGGTTAGAGAAGATGAACAGAAACAAAAGATAAATAGGCTTCAGTTAGAAT
Found at i:19069 original size:106 final size:106
Alignment explanation
Indices: 18898--19104 Score: 251
Period size: 106 Copynumber: 2.0 Consensus size: 106
18888 AAAAAATAGT
* * * * *
18898 TTGGGTTTTGCTTTTGGGTGTTTGTAAGGATCAAACAAGGGTTTGGGGATGAATATGGATGAATA
1 TTGGGTTTTGCTTTTAGGTGTTTGTAAGGATCAAACAAAGGTTTGGGGATGAACATGAATAAATA
* *
18963 A-GTGTTGAGGGTTT-GGG-GTTTGATTGAAAAAATAGGTTGGG
66 ATG-GTTGA--ATTTAGGGTGTTTGATCGAAAAAATAGGTTGGG
* * * *
19004 TTGGGTTTTGGTTTTAGGTGTTTGTAAGGGTTAAAGAAAGGTTTGGGGATGAACACT-AATAAAT
1 TTGGGTTTTGCTTTTAGGTGTTTGTAAGGATCAAACAAAGGTTTGGGGATGAACA-TGAATAAAT
19068 AATGGTTGAATTTAGGGTGTTTGATCGAAAAAATAGG
65 AATGGTTGAATTTAGGGTGTTTGATCGAAAAAATAGG
19105 ATAGAGTTTG
Statistics
Matches: 86, Mismatches: 11, Indels: 8
0.82 0.10 0.08
Matches are distributed among these distances:
104 3 0.03
105 3 0.03
106 78 0.91
107 2 0.02
ACGTcount: A:0.28, C:0.03, G:0.34, T:0.36
Consensus pattern (106 bp):
TTGGGTTTTGCTTTTAGGTGTTTGTAAGGATCAAACAAAGGTTTGGGGATGAACATGAATAAATA
ATGGTTGAATTTAGGGTGTTTGATCGAAAAAATAGGTTGGG
Found at i:19181 original size:101 final size:102
Alignment explanation
Indices: 19007--19241 Score: 282
Period size: 102 Copynumber: 2.3 Consensus size: 102
18997 GGTTGGGTTG
* * * * * * *
19007 GGTTTTGGTTTTAGGTGTTTGTAAGGGTTAAAGAAAGGTTTGGGGATGAACACTAATAAATAATG
1 GGTTTGGGTTTTA-GTGTTTGTAAAGATCAAAGAAAGGTTTGGGGATGAACACTAAAAAACAAGG
19072 GTTGAA-TTTAGGGTGTTTGATCG-AAAAAATAGGATA
65 GTTGAATTTTAGGGTGTTTGATCGAAAAAAATAGGATA
19108 GAGTTTGGGTTTTAGTGTTTGTAAAGATCAAAGAATAAGG-TTGGGGAT-AACAC-AGAAAAACA
1 G-GTTTGGGTTTTAGTGTTTGTAAAGATCAAAG-A-AAGGTTTGGGGATGAACACTA-AAAAACA
* *
19170 AGGGTTTAATTTTGGGGTGTTTGATCGAAAAAAATAGGATA
62 AGGGTTGAATTTTAGGGTGTTTGATCGAAAAAAATAGGATA
* * *
19211 GGTTTGAGTTTTGGTGTTTGTGAAGATCAAA
1 GGTTTGGGTTTTAGTGTTTGTAAAGATCAAA
19242 TGATGGTTTT
Statistics
Matches: 116, Mismatches: 12, Indels: 11
0.83 0.09 0.08
Matches are distributed among these distances:
100 1 0.01
101 34 0.29
102 63 0.54
103 18 0.16
ACGTcount: A:0.33, C:0.04, G:0.29, T:0.34
Consensus pattern (102 bp):
GGTTTGGGTTTTAGTGTTTGTAAAGATCAAAGAAAGGTTTGGGGATGAACACTAAAAAACAAGGG
TTGAATTTTAGGGTGTTTGATCGAAAAAAATAGGATA
Found at i:19732 original size:18 final size:18
Alignment explanation
Indices: 19711--19877 Score: 73
Period size: 18 Copynumber: 9.3 Consensus size: 18
19701 ATTAATAAAC
19711 TATATAATATATAATTTA
1 TATATAATATATAATTTA
* *
19729 TATATAATATATAGTTCA
1 TATATAATATATAATTTA
19747 TATAT-ATAGTTCATAAAGTTTA
1 TATATAATA--T-AT-AA-TTTA
* * *
19769 TAT-TAAT-GA-ACTATA
1 TATATAATATATAATTTA
*
19784 TA-AT-ATATATAGTTTA
1 TATATAATATATAATTTA
* *
19800 TAT-TAATAAATTAATATA
1 TATATAATATA-TAATTTA
* **
19818 TAGT-TTATAT-TAATGAA
1 TA-TATAATATATAATTTA
19835 CTATATAATATATAATTTA
1 -TATATAATATATAATTTA
* * *
19854 TATATAATATTTAGTTCA
1 TATATAATATATAATTTA
19872 TATATA
1 TATATA
19878 TTTGTTCATA
Statistics
Matches: 110, Mismatches: 23, Indels: 32
0.67 0.14 0.19
Matches are distributed among these distances:
14 2 0.02
15 7 0.06
16 8 0.07
17 13 0.12
18 57 0.52
19 11 0.10
20 2 0.02
21 2 0.02
22 8 0.07
ACGTcount: A:0.46, C:0.03, G:0.05, T:0.47
Consensus pattern (18 bp):
TATATAATATATAATTTA
Found at i:19751 original size:13 final size:13
Alignment explanation
Indices: 19735--19761 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
19725 TTTATATATA
19735 ATATATAGTTCAT
1 ATATATAGTTCAT
19748 ATATATAGTTCAT
1 ATATATAGTTCAT
19761 A
1 A
19762 AAGTTTATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.07, G:0.07, T:0.44
Consensus pattern (13 bp):
ATATATAGTTCAT
Found at i:19784 original size:31 final size:29
Alignment explanation
Indices: 19749--19861 Score: 117
Period size: 31 Copynumber: 3.9 Consensus size: 29
19739 ATAGTTCATA
*
19749 TATATAGTTCATAAAGTTTATATTAATGAAC
1 TATATA-TT-ATATAGTTTATATTAATGAAC
19780 TATATAATATATATAGTTTATATTAAT-AA-
1 TATAT-AT-TATATAGTTTATATTAATGAAC
*
19809 -AT-TAATATATAGTTTATATTAATGAAC
1 TATATATTATATAGTTTATATTAATGAAC
* *
19836 TATATAATATATAATTTATATATAAT
1 TATATATTATATAGTTTATAT-TAAT
19862 ATTTAGTTCA
Statistics
Matches: 72, Mismatches: 3, Indels: 15
0.80 0.03 0.17
Matches are distributed among these distances:
25 18 0.25
26 3 0.04
27 1 0.01
28 4 0.06
29 16 0.22
30 6 0.08
31 22 0.31
32 2 0.03
ACGTcount: A:0.46, C:0.03, G:0.05, T:0.46
Consensus pattern (29 bp):
TATATATTATATAGTTTATATTAATGAAC
Found at i:19824 original size:125 final size:126
Alignment explanation
Indices: 19662--19887 Score: 391
Period size: 125 Copynumber: 1.8 Consensus size: 126
19652 ACTAATGGAC
*
19662 TATATATAGTTTATATTAAGAAATTAATACATTGTTTATATTAATAAACTATATAATATATAATT
1 TATATATAGTTTATATTAAGAAATTAATACATAGTTTATATTAATAAACTATATAATATATAATT
19727 TATATATAATATATAGTTCATATATA-TAGTTCATAAAGTTTATATTAATGAACTATATAA
66 TATATATAATATATAGTTCATATATATTAGTTCATAAAGTTTATATTAATGAACTATATAA
* * *
19787 TATATATAGTTTATATTAATAAATTAATATATAGTTTATATTAATGAACTATATAATATATAATT
1 TATATATAGTTTATATTAAGAAATTAATACATAGTTTATATTAATAAACTATATAATATATAATT
* *
19852 TATATATAATATTTAGTTCATATATATTTGTTCATA
66 TATATATAATATATAGTTCATATATATTAGTTCATA
19888 TATAGTAATA
Statistics
Matches: 94, Mismatches: 6, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
125 86 0.91
126 8 0.09
ACGTcount: A:0.44, C:0.04, G:0.05, T:0.47
Consensus pattern (126 bp):
TATATATAGTTTATATTAAGAAATTAATACATAGTTTATATTAATAAACTATATAATATATAATT
TATATATAATATATAGTTCATATATATTAGTTCATAAAGTTTATATTAATGAACTATATAA
Found at i:19875 original size:56 final size:57
Alignment explanation
Indices: 19748--19875 Score: 174
Period size: 56 Copynumber: 2.3 Consensus size: 57
19738 TATAGTTCAT
* *
19748 ATATATAGTTCATAAAGTTTATATTAATGAACTATATAATATATATAGTTTATATTA
1 ATATTTAGTTCATATAGTTTATATTAATGAACTATATAATATATATAGTTTATATTA
* *
19805 ATAAATTA-AT-ATATAGTTTATATTAATGAACTATATAATATATA-A-TTTATATATA
1 AT-ATTTAGTTCATATAGTTTATATTAATGAACTATATAATATATATAGTTTATAT-TA
19860 ATATTTAGTTCATATA
1 ATATTTAGTTCATATA
19876 TATTTGTTCA
Statistics
Matches: 61, Mismatches: 6, Indels: 9
0.80 0.08 0.12
Matches are distributed among these distances:
54 11 0.18
55 6 0.10
56 38 0.62
57 3 0.05
58 3 0.05
ACGTcount: A:0.45, C:0.03, G:0.05, T:0.46
Consensus pattern (57 bp):
ATATTTAGTTCATATAGTTTATATTAATGAACTATATAATATATATAGTTTATATTA
Found at i:19886 original size:14 final size:15
Alignment explanation
Indices: 19855--19891 Score: 58
Period size: 14 Copynumber: 2.5 Consensus size: 15
19845 TATAATTTAT
19855 ATATAATATTTAGTTC
1 ATAT-ATATTTAGTTC
19871 ATATATATTT-GTTC
1 ATATATATTTAGTTC
19885 ATATATA
1 ATATATA
19892 GTAATAAACT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
14 11 0.52
15 6 0.29
16 4 0.19
ACGTcount: A:0.38, C:0.05, G:0.05, T:0.51
Consensus pattern (15 bp):
ATATATATTTAGTTC
Found at i:19906 original size:15 final size:15
Alignment explanation
Indices: 19886--19968 Score: 66
Period size: 15 Copynumber: 5.5 Consensus size: 15
19876 TATTTGTTCA
19886 TATATAGTAATAAAC
1 TATATAGTAATAAAC
* **
19901 TATATAGT-TTATTC
1 TATATAGTAATAAAC
19915 ATATATAGTAATAAAC
1 -TATATAGTAATAAAC
*
19931 TATATAGTTTATTCAAA-
1 TATATAG--TAAT-AAAC
19948 TATA-A-TAATAAAC
1 TATATAGTAATAAAC
19961 TATATAGT
1 TATATAGT
19969 TTATATATAT
Statistics
Matches: 52, Mismatches: 8, Indels: 16
0.68 0.11 0.21
Matches are distributed among these distances:
12 3 0.06
13 7 0.13
14 4 0.08
15 24 0.46
16 4 0.08
17 7 0.13
18 3 0.06
ACGTcount: A:0.47, C:0.06, G:0.06, T:0.41
Consensus pattern (15 bp):
TATATAGTAATAAAC
Found at i:19916 original size:30 final size:30
Alignment explanation
Indices: 19872--19996 Score: 175
Period size: 30 Copynumber: 4.2 Consensus size: 30
19862 ATTTAGTTCA
*
19872 TATATA-TTTGTTCATATATAGTAATAAAC
1 TATATAGTTTATTCATATATAGTAATAAAC
19901 TATATAGTTTATTCATATATAGTAATAAAC
1 TATATAGTTTATTCATATATAGTAATAAAC
* *
19931 TATATAGTTTATTCAAATATAATAATAAAC
1 TATATAGTTTATTCATATATAGTAATAAAC
19961 TATATAGTTTATAT-ATATATA-TATATAAAC
1 TATATAGTTTAT-TCATATATAGTA-ATAAAC
*
19991 AATATA
1 TATATA
19997 TATGTGTGTG
Statistics
Matches: 88, Mismatches: 5, Indels: 5
0.90 0.05 0.05
Matches are distributed among these distances:
29 8 0.09
30 79 0.90
31 1 0.01
ACGTcount: A:0.46, C:0.06, G:0.05, T:0.43
Consensus pattern (30 bp):
TATATAGTTTATTCATATATAGTAATAAAC
Found at i:19935 original size:17 final size:16
Alignment explanation
Indices: 19884--19998 Score: 64
Period size: 15 Copynumber: 7.5 Consensus size: 16
19874 TATATTTGTT
19884 CATATATAGTAATAAA
1 CATATATAGTAATAAA
* **
19900 C-TATATAGT-TTATT
1 CATATATAGTAATAAA
19914 CATATATAGTAATAAA
1 CATATATAGTAATAAA
* **
19930 C-TATATAGT-TTATT
1 CATATATAGTAATAAA
* *
19944 CAAATATAATAATAAA
1 CATATATAGTAATAAA
* *
19960 C-TATATAGT-TTATA
1 CATATATAGTAATAAA
*
19974 TATATATA-TATATAAA
1 CATATATAGTA-ATAAA
19990 CAATATATA
1 C-ATATATA
19999 TGTGTGTGTG
Statistics
Matches: 69, Mismatches: 22, Indels: 15
0.65 0.21 0.14
Matches are distributed among these distances:
14 10 0.14
15 42 0.61
16 10 0.14
17 7 0.10
ACGTcount: A:0.49, C:0.06, G:0.04, T:0.41
Consensus pattern (16 bp):
CATATATAGTAATAAA
Found at i:19962 original size:125 final size:122
Alignment explanation
Indices: 19662--19985 Score: 326
Period size: 125 Copynumber: 2.7 Consensus size: 122
19652 ACTAATGGAC
* * * * * *
19662 TATATATAGTTTATATTAAGAAATTAATACATTGTTTATATTAATAAACTATATAATATATAATT
1 TATATATAGTATATAGTAATAAACTAATATATAGTTTATATTAATAAACTATATAATATATAATT
* *
19727 TATATATAATATATAGTTCATATATATAGTTCATAAAGTTTATATTAATGAACTATATAA
66 TATATATAATATATAGTTCATATATATAGTTCAT-AA--TTATAGTAATAAACTATATAA
* * * *
19787 TATATATAGTTTATATTAATAAATTAATATATAGTTTATATTAATGAACTATATAATATATAATT
1 TATATATAGTATATAGTAATAAACTAATATATAGTTTATATTAATAAACTATATAATATATAATT
* * *
19852 TATATATAATATTTAGTTCATATATATTTGTTCAT-A-TATAGTAATAAACTATATAG
66 TATATATAATATATAGTTCATATATA-TAGTTCATAATTATAGTAATAAACTATATAA
* *
19908 TTTAT-TCA-TATATAGTAATAAAC---TATATAGTTTAT-TCAAATATAA-TA-ATAAACTATA
1 TATATAT-AGTATATAGTAATAAACTAATATATAGTTTATAT-TAATA-AACTATAT-AA-TATA
*
19965 TAGTTTATATATATATATATA
61 TAATTTATATATA-ATATATA
19986 TAAACAATAT
Statistics
Matches: 175, Mismatches: 17, Indels: 20
0.83 0.08 0.09
Matches are distributed among these distances:
116 3 0.02
117 19 0.11
118 18 0.10
119 6 0.03
120 13 0.07
121 22 0.13
124 1 0.01
125 86 0.49
126 7 0.04
ACGTcount: A:0.45, C:0.04, G:0.05, T:0.46
Consensus pattern (122 bp):
TATATATAGTATATAGTAATAAACTAATATATAGTTTATATTAATAAACTATATAATATATAATT
TATATATAATATATAGTTCATATATATAGTTCATAATTATAGTAATAAACTATATAA
Found at i:20117 original size:9 final size:9
Alignment explanation
Indices: 20105--20339 Score: 89
Period size: 9 Copynumber: 25.3 Consensus size: 9
20095 TATGTAAACC
20105 ATATAGTAT
1 ATATAGTAT
20114 ATATAGTTTAT
1 ATATAG--TAT
20125 ATATAGTAT
1 ATATAGTAT
20134 ATATA-TAT
1 ATATAGTAT
*
20142 AGAT-GATAT
1 ATATAG-TAT
20151 ATATAGTAT
1 ATATAGTAT
20160 ATACATAGTTTAT
1 AT--ATAG--TAT
*
20173 ACATA-TATT
1 ATATAGTA-T
* *
20182 TTATAGTTT
1 ATATAGTAT
*
20191 ATATAGTTT
1 ATATAGTAT
20200 ATATAGATTAT
1 ATATAG--TAT
*
20211 ATATGGT-T
1 ATATAGTAT
20219 CATAT-GTAAACT
1 -ATATAGT--A-T
*
20231 ATATAGTGT
1 ATATAGTAT
* *
20240 ATATATTAC
1 ATATAGTAT
*
20249 ATATAGTTT
1 ATATAGTAT
*
20258 ATATA-AATT
1 ATATAGTA-T
20267 ATATAGT-T
1 ATATAGTAT
*
20275 -TATA-CAT
1 ATATAGTAT
*
20282 ATATAGTTT
1 ATATAGTAT
20291 ATATA-TAT
1 ATATAGTAT
20299 AGTATA-TAT
1 A-TATAGTAT
*
20308 GATTTA-TAT
1 -ATATAGTAT
20317 ATATAGTAT
1 ATATAGTAT
20326 ATAAATAGTAT
1 AT--ATAGTAT
20337 ATA
1 ATA
20340 ATTAAGTTAT
Statistics
Matches: 172, Mismatches: 25, Indels: 58
0.67 0.10 0.23
Matches are distributed among these distances:
7 5 0.03
8 23 0.13
9 98 0.57
10 3 0.02
11 36 0.21
12 3 0.02
13 4 0.02
ACGTcount: A:0.41, C:0.03, G:0.09, T:0.47
Consensus pattern (9 bp):
ATATAGTAT
Found at i:20127 original size:11 final size:11
Alignment explanation
Indices: 20111--20634 Score: 112
Period size: 11 Copynumber: 48.7 Consensus size: 11
20101 AACCATATAG
20111 TATATATAGTT
1 TATATATAGTT
20122 TATATATAGTAT
1 TATATATAGT-T
*
20134 ATATATATAGATGA
1 -TATATATAG-T-T
*
20148 TATATATAGTA
1 TATATATAGTT
*
20159 TATACATAGTT
1 TATATATAGTT
*
20170 TATACATA-TAT
1 TATATATAGT-T
20181 T-T-TATAG-T
1 TATATATAGTT
20189 T-TATATAG-T
1 TATATATAGTT
*
20198 T-TATATAGAT
1 TATATATAGTT
*
20208 TATATAT-GGT
1 TATATATAGTT
* *
20218 T-CATAT-GTA
1 TATATATAGTT
*
20227 AACTATATAG--
1 TA-TATATAGTT
*
20237 TGTATATA--T
1 TATATATAGTT
*
20246 TACATATAGTT
1 TATATATAGTT
*
20257 TATATA-AATT
1 TATATATAGTT
* *
20267 ATATAGTTTA-TA
1 -TATA-TATAGTT
*
20279 CATATATAGTT
1 TATATATAGTT
*
20290 TATATATA-TAG
1 TATATATAGT-T
*
20301 TATATATGATTT
1 TATATAT-AGTT
*
20313 ATATATATAGTA
1 -TATATATAGTT
* *
20325 TATAAATAGTA
1 TATATATAGTT
20336 TATA-ATTAAG-T
1 TATATA-T-AGTT
* * *
20347 TATACATTGTA
1 TATATATAGTT
* *
20358 TATAAATA-TA
1 TATATATAGTT
*
20368 AACTATATAG-T
1 TA-TATATAGTT
*
20379 T-TATATAGTA
1 TATATATAGTT
20389 TATATATAGTT
1 TATATATAGTT
* * *
20400 CATAT-TAATA
1 TATATATAGTT
*
20410 AACTATATAGTTT
1 TA-TATATAG-TT
20423 ATATATATAGTT
1 -TATATATAGTT
20435 TATATATAGTT
1 TATATATAGTT
* ***
20446 CATATATACAC
1 TATATATAGTT
20457 TATATA-A-TT
1 TATATATAGTT
*
20466 TATATATAGTA
1 TATATATAGTT
* *
20477 TATAAATA-TA
1 TATATATAGTT
* *
20487 AACTATATAATT
1 TA-TATATAGTT
20499 TATATGTATAG--
1 TATA--TATAGTT
* *
20510 TATACATATTT
1 TATATATAGTT
*
20521 TATATATACTT
1 TATATATAGTT
*
20532 TATATTTATA-TAC
1 TATA--TATAGT-T
*
20545 TACATATAG-T
1 TATATATAGTT
20555 T-TAT-TAGTT
1 TATATATAGTT
20564 TATATATAG--
1 TATATATAGTT
* *
20573 TACATATAATT
1 TATATATAGTT
* *
20584 TATACATA--A
1 TATATATAGTT
20593 TATATATAGTT
1 TATATATAGTT
* *
20604 CATAAATAGTT
1 TATATATAGTT
*
20615 TCTATATAGTT
1 TATATATAGTT
20626 TATAATATA
1 TAT-ATATA
20635 TATAGTTTAC
Statistics
Matches: 378, Mismatches: 81, Indels: 107
0.67 0.14 0.19
Matches are distributed among these distances:
8 6 0.02
9 68 0.18
10 33 0.09
11 200 0.53
12 23 0.06
13 46 0.12
14 2 0.01
ACGTcount: A:0.42, C:0.04, G:0.07, T:0.47
Consensus pattern (11 bp):
TATATATAGTT
Found at i:20139 original size:22 final size:22
Alignment explanation
Indices: 20111--20480 Score: 139
Period size: 22 Copynumber: 17.2 Consensus size: 22
20101 AACCATATAG
20111 TATATATAGTTTATATATAGTATA
1 TATATATAGTTTATATATAG--TA
*
20135 TATATATAGATGATATATATAGTA
1 TATATATAG-T-TTATATATAGTA
* *
20159 TATACATAGTTTATACATA-TA
1 TATATATAGTTTATATATAGTA
*
20180 T-TTTATAG-TT-TATATAGT-
1 TATATATAGTTTATATATAGTA
* *
20198 T-TATATAGATTATATATGGTTCA
1 TATATATAGTTTATATATAG-T-A
* * * *
20221 TATGTAAACTATATAGTGTATA-TA
1 TATATATAGT-T-TA-TATATAGTA
*
20245 TTACATATAGTTTATATA-A--A
1 -TATATATAGTTTATATATAGTA
*
20265 T-TATATAGTTTATACATA-TA
1 TATATATAGTTTATATATAGTA
20285 TAGT-T-TA---TATATATAGTA
1 TA-TATATAGTTTATATATAGTA
20303 TATATGAT--TTATATATATAGTA
1 TATAT-ATAGTT-TATATATAGTA
* *
20325 TATAAATAGTATATA-ATTAAGT-
1 TATATATAGTTTATATA-T-AGTA
* * * *
20347 TATACATTGTATATAAATA-TA
1 TATATATAGTTTATATATAGTA
*
20368 AACTATATAG-TT-TATATAGTA
1 TA-TATATAGTTTATATATAGTA
* *
20389 TATATATAGTTCATAT-TAATA
1 TATATATAGTTTATATATAGTA
* *
20410 AACTATATAGTTTATATATATAGTT
1 TA-TATATAG-TT-TATATATAGTA
* *
20435 TATATATAGTTCATATATA-CA
1 TATATATAGTTTATATATAGTA
20456 CTATATA-A-TTTATATATAGTA
1 -TATATATAGTTTATATATAGTA
20477 TATA
1 TATA
20481 AATATAAACT
Statistics
Matches: 261, Mismatches: 45, Indels: 84
0.67 0.12 0.22
Matches are distributed among these distances:
17 8 0.03
18 30 0.11
19 7 0.03
20 43 0.16
21 23 0.09
22 73 0.28
23 13 0.05
24 36 0.14
25 13 0.05
26 11 0.04
27 4 0.02
ACGTcount: A:0.42, C:0.04, G:0.08, T:0.46
Consensus pattern (22 bp):
TATATATAGTTTATATATAGTA
Found at i:20294 original size:49 final size:48
Alignment explanation
Indices: 20164--20317 Score: 127
Period size: 58 Copynumber: 3.1 Consensus size: 48
20154 TAGTATATAC
* *
20164 ATAGTTTATACATATAT--TTTATAGTTTATATAGTTTATATAGATTAT
1 ATAGTTTATACATATATAGTTTATA-TTCATATAGTTTATATAAATTAT
*
20211 ATATGGTTCATATGTAAACTATATAGTGTATATATTACATATAGTTTATATAAATTAT
1 ATA--GTT--TA--TACA-TATATAGT-T-TATATT-CATATAGTTTATATAAATTAT
* * *
20269 ATAGTTTATACATATATAGTTTATA-T-ATATAGTATATATGATTTAT
1 ATAGTTTATACATATATAGTTTATATTCATATAGTTTATATAAATTAT
20315 ATA
1 ATA
20318 TATAGTATAT
Statistics
Matches: 88, Mismatches: 7, Indels: 25
0.73 0.06 0.21
Matches are distributed among these distances:
46 20 0.23
47 3 0.03
48 1 0.01
49 7 0.08
50 1 0.01
51 10 0.11
52 3 0.03
53 3 0.03
54 7 0.08
56 4 0.05
57 3 0.03
58 26 0.30
ACGTcount: A:0.39, C:0.03, G:0.09, T:0.49
Consensus pattern (48 bp):
ATAGTTTATACATATATAGTTTATATTCATATAGTTTATATAAATTAT
Found at i:20383 original size:33 final size:33
Alignment explanation
Indices: 20258--20383 Score: 87
Period size: 37 Copynumber: 3.6 Consensus size: 33
20248 CATATAGTTT
* * *
20258 ATATAAATTATATAGTTTATACATATATAGTTTAT
1 ATATAAA-TATATAGTTTATACATATGTA-TATAA
* *
20293 ATATATAGTATATATGATTTATATATATAGTATATAA
1 ATATA-AATATATA-G-TTTATACATAT-GTATATAA
*
20330 ATAGTATATA-ATTAAG-TTATACAT-TGTATATAA
1 ATA-TAAATATA-T-AGTTTATACATATGTATATAA
20363 ATATAAACTATATAGTTTATA
1 ATATAAA-TATATAGTTTATA
20384 TAGTATATAT
Statistics
Matches: 72, Mismatches: 9, Indels: 22
0.70 0.09 0.21
Matches are distributed among these distances:
32 5 0.07
33 19 0.26
34 2 0.03
35 18 0.25
36 3 0.04
37 20 0.28
38 5 0.07
ACGTcount: A:0.45, C:0.02, G:0.07, T:0.45
Consensus pattern (33 bp):
ATATAAATATATAGTTTATACATATGTATATAA
Found at i:20451 original size:33 final size:33
Alignment explanation
Indices: 20414--20665 Score: 84
Period size: 33 Copynumber: 7.9 Consensus size: 33
20404 TTAATAAACT
20414 ATATAGTTTATATATATAGTTTATATATAGTTC
1 ATATAGTTTATATATATAGTTTATATATAGTTC
* *
20447 ATATA---TACACTATATAATTTATATATAG-T-
1 ATATAGTTTATA-TATATAGTTTATATATAGTTC
* * * *
20476 ATATAAATATAAACTATATAATTTATATGTATAGTATAC
1 ATAT-AGTTTATA-TATATAGTTTATA--TATAGT-T-C
* *
20515 ATAT--TTTATATATACT--TTATATTTATATACTAC
1 ATATAGTTTATATATA-TAGTT-TA--TATATAGTTC
*
20548 ATATAG--T-T-TAT-TAGTTTATATATAGTAC
1 ATATAGTTTATATATATAGTTTATATATAGTTC
* *
20576 ATATAATTTATACATA-A---TATATATAGTTC
1 ATATAGTTTATATATATAGTTTATATATAGTTC
*
20605 ATAAATAG-TT-TCTATATAGTTTATA-ATA--T-
1 AT--ATAGTTTATATATATAGTTTATATATAGTTC
20634 ATATAGTTTACATACTATATAGTTTATATATA
1 ATATAGTTT--ATA-TATATAGTTTATATATA
20666 TTATATTATT
Statistics
Matches: 168, Mismatches: 15, Indels: 72
0.66 0.06 0.28
Matches are distributed among these distances:
27 4 0.02
28 16 0.10
29 24 0.14
30 12 0.07
31 27 0.16
32 20 0.12
33 35 0.21
34 2 0.01
35 16 0.10
36 5 0.03
37 3 0.02
39 4 0.02
ACGTcount: A:0.41, C:0.06, G:0.06, T:0.48
Consensus pattern (33 bp):
ATATAGTTTATATATATAGTTTATATATAGTTC
Found at i:20486 original size:35 final size:34
Alignment explanation
Indices: 20426--20513 Score: 105
Period size: 31 Copynumber: 2.7 Consensus size: 34
20416 ATAGTTTATA
* *
20426 TATATAGTTTATA-TATAGT-TCAT--ATATACAC
1 TATATAATTTATAGTATAGTAT-ATAAATATAAAC
20457 TATATAATTTATA-TATAGTATATAAATATAAAC
1 TATATAATTTATAGTATAGTATATAAATATAAAC
20490 TATATAATTTATATGTATAGTATA
1 TATATAATTTATA-GTATAGTATA
20514 CATATTTTAT
Statistics
Matches: 50, Mismatches: 2, Indels: 6
0.86 0.03 0.10
Matches are distributed among these distances:
31 20 0.40
32 1 0.02
33 20 0.40
35 9 0.18
ACGTcount: A:0.44, C:0.05, G:0.06, T:0.45
Consensus pattern (34 bp):
TATATAATTTATAGTATAGTATATAAATATAAAC
Found at i:20670 original size:16 final size:16
Alignment explanation
Indices: 20619--20680 Score: 65
Period size: 16 Copynumber: 3.8 Consensus size: 16
20609 ATAGTTTCTA
20619 TATAGTTTATA-ATAT
1 TATAGTTTATATATAT
*
20634 ATATAGTTTACATACTA-
1 -TATAGTTTATATA-TAT
20651 TATAGTTTATATATAT
1 TATAGTTTATATATAT
*
20667 TATATTATTATATA
1 TATAGT-TTATATA
20681 CTTTTTATCT
Statistics
Matches: 39, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
15 2 0.05
16 27 0.69
17 8 0.21
18 2 0.05
ACGTcount: A:0.40, C:0.03, G:0.05, T:0.52
Consensus pattern (16 bp):
TATAGTTTATATATAT
Found at i:21038 original size:6 final size:6
Alignment explanation
Indices: 21027--21068 Score: 50
Period size: 6 Copynumber: 6.8 Consensus size: 6
21017 CATCAATGAT
*
21027 TATTTA TATTTA TTCAATT- TATTTA TATTTA TATTTA TATTT
1 TATTTA TATTTA -T-ATTTA TATTTA TATTTA TATTTA TATTT
21069 TCATATTTGT
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
5 3 0.10
6 24 0.77
7 1 0.03
8 3 0.10
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (6 bp):
TATTTA
Found at i:23163 original size:11 final size:11
Alignment explanation
Indices: 23147--23209 Score: 60
Period size: 11 Copynumber: 5.9 Consensus size: 11
23137 AAAATTACAT
23147 TATTAAAAATA
1 TATTAAAAATA
23158 TATTAAAAATA
1 TATTAAAAATA
* ***
23169 CATTATTGATA
1 TATTAAAAATA
23180 -ATTATAAAAT-
1 TATTA-AAAATA
23190 T-TTAAAAATA
1 TATTAAAAATA
23200 TATTAAAAAT
1 TATTAAAAAT
23210 TCTATAATAC
Statistics
Matches: 41, Mismatches: 7, Indels: 8
0.73 0.12 0.14
Matches are distributed among these distances:
9 5 0.12
10 8 0.20
11 28 0.68
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.40
Consensus pattern (11 bp):
TATTAAAAATA
Found at i:23368 original size:21 final size:22
Alignment explanation
Indices: 23326--23390 Score: 64
Period size: 21 Copynumber: 3.1 Consensus size: 22
23316 AACCCTAAGG
*
23326 CCTAAACCCTAAA-CTCTGAAT
1 CCTAAATCCTAAACCTCTGAAT
*
23347 CCTAAATCCTAAACCT-TTAAT
1 CCTAAATCCTAAACCTCTGAAT
* * *
23368 CCTAAGTGCTAAACC-CTAAAT
1 CCTAAATCCTAAACCTCTGAAT
23389 CC
1 CC
23391 GATTATGTGA
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
21 35 0.95
22 2 0.05
ACGTcount: A:0.37, C:0.32, G:0.05, T:0.26
Consensus pattern (22 bp):
CCTAAATCCTAAACCTCTGAAT
Found at i:24108 original size:75 final size:74
Alignment explanation
Indices: 23963--24112 Score: 282
Period size: 75 Copynumber: 2.0 Consensus size: 74
23953 TGGAGAAGAA
*
23963 CATTTCCTTTTGTTACAAAATTATTAATATTTTAAAAAATATACTTGAAATACATTTCATATAAT
1 CATTTCCTTTTGTTAAAAAATTATTAATATTTTAAAAAATATACTTGAAATACATTTCATATAAT
24028 ATTTTATTT
66 ATTTTATTT
24037 CATTTCCTTTTGTTAAAAAATTATTAATATTTTAAAAAAATATACTTGAAATACATTTCATATAA
1 CATTTCCTTTTGTTAAAAAATTATTAATATTTT-AAAAAATATACTTGAAATACATTTCATATAA
24102 TATTTTATTT
65 TATTTTATTT
24112 C
1 C
24113 TTAAAATTTG
Statistics
Matches: 74, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
74 32 0.43
75 42 0.57
ACGTcount: A:0.40, C:0.09, G:0.03, T:0.48
Consensus pattern (74 bp):
CATTTCCTTTTGTTAAAAAATTATTAATATTTTAAAAAATATACTTGAAATACATTTCATATAAT
ATTTTATTT
Found at i:25404 original size:17 final size:17
Alignment explanation
Indices: 25384--25418 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
25374 ACTTTTGAAA
25384 TTTTTTTGAATTTGAGT
1 TTTTTTTGAATTTGAGT
*
25401 TTTTTTTGAGTTTGAGT
1 TTTTTTTGAATTTGAGT
25418 T
1 T
25419 GAGTTTTAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.14, C:0.00, G:0.20, T:0.66
Consensus pattern (17 bp):
TTTTTTTGAATTTGAGT
Found at i:27249 original size:185 final size:184
Alignment explanation
Indices: 26926--27273 Score: 590
Period size: 185 Copynumber: 1.9 Consensus size: 184
26916 AAAAAAATAT
*
26926 AATTAATTTAATTAATATATAATTATAAAATAAAAATTTCAGATAAATTTTTTAATTAATTAATA
1 AATTAATTTAAATAATATATAATTATAAAATAAAAATTTCAGATAAATTTTTTAATTAATTAATA
26991 TTGATTTAGGTTTAAAAGTTATTGGATATTAAATTATTAATTGAGTTTTAAATGGTTTGAGCTTA
66 TTGATTTAGGTTTAAAAGTTATTGGATATTAAATTATTAATTGAGTTTTAAATGGTTTGAGCTTA
* *
27056 GTTCATATGTTATATATAATATATTTAATATTTTTTAATTAAAAAATAGTTTAC
131 GCTCATATGTTATATATAATATATTTAAAATTTTTTAATTAAAAAATAGTTTAC
* * * *
27110 AATTAATTTAAATAATATATAATTATACAATAAAAATTTTATATAATTTTTTTTAATTAATTAAT
1 AATTAATTTAAATAATATATAATTATAAAATAAAAATTTCAGATAA-ATTTTTTAATTAATTAAT
* *
27175 ATTGATTTAGGTTTAAAAGTTATTGGATCTTAAATTATTAATTGAGTTTTAAATGGTTTG-GGTT
65 ATTGATTTAGGTTTAAAAGTTATTGGATATTAAATTATTAATTGAGTTTTAAATGGTTTGAGCTT
27239 GAGCTCATATGTTATATATAATATATTTAAAATTT
130 -AGCTCATATGTTATATATAATATATTTAAAATTT
27274 AATTTCAATT
Statistics
Matches: 153, Mismatches: 9, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
184 45 0.29
185 108 0.71
ACGTcount: A:0.41, C:0.02, G:0.09, T:0.48
Consensus pattern (184 bp):
AATTAATTTAAATAATATATAATTATAAAATAAAAATTTCAGATAAATTTTTTAATTAATTAATA
TTGATTTAGGTTTAAAAGTTATTGGATATTAAATTATTAATTGAGTTTTAAATGGTTTGAGCTTA
GCTCATATGTTATATATAATATATTTAAAATTTTTTAATTAAAAAATAGTTTAC
Found at i:28303 original size:6 final size:6
Alignment explanation
Indices: 28288--28330 Score: 68
Period size: 6 Copynumber: 7.2 Consensus size: 6
28278 TCGTCTCGGC
* *
28288 TCGTGG TCGAGG TCGAGG TCGTGG TCGTGG TCGTGG TCGTGG T
1 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG T
28331 AATACGTGGA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
6 35 1.00
ACGTcount: A:0.05, C:0.16, G:0.49, T:0.30
Consensus pattern (6 bp):
TCGTGG
Found at i:33941 original size:5 final size:5
Alignment explanation
Indices: 33927--33975 Score: 62
Period size: 5 Copynumber: 9.8 Consensus size: 5
33917 GTCCGTCCGT
* * * *
33927 CTCGT CTCGG CTCGG CACGG CACGG CACGG CTCGG CTCGG CTCGG CTCG
1 CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCG
33976 TGGTCGTGGT
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
5 41 1.00
ACGTcount: A:0.06, C:0.41, G:0.37, T:0.16
Consensus pattern (5 bp):
CTCGG
Found at i:33984 original size:6 final size:6
Alignment explanation
Indices: 33973--34045 Score: 101
Period size: 6 Copynumber: 12.2 Consensus size: 6
33963 TCGGCTCGGC
* * * * *
33973 TCGTGG TCGTGG TCGTGG TCGAGG TCGAGG TCGAGG TCGAGG TCGAGG
1 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG
34021 TCGTGG TCGTGG TCGTGG TCGTGG T
1 TCGTGG TCGTGG TCGTGG TCGTGG T
34046 AATACGTGTC
Statistics
Matches: 65, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 65 1.00
ACGTcount: A:0.07, C:0.16, G:0.49, T:0.27
Consensus pattern (6 bp):
TCGTGG
Found at i:34345 original size:22 final size:22
Alignment explanation
Indices: 34320--34374 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 22
34310 TCAGGAGTTA
* *
34320 CAGGAGTTATTTGATTTAATTC
1 CAGGAGTTATATGATATAATTC
* * *
34342 CAGGGGTTACATGATATAATTT
1 CAGGAGTTATATGATATAATTC
*
34364 CGGGAGTTATA
1 CAGGAGTTATA
34375 ACAGCTAAAT
Statistics
Matches: 25, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.29, C:0.09, G:0.24, T:0.38
Consensus pattern (22 bp):
CAGGAGTTATATGATATAATTC
Found at i:35406 original size:51 final size:49
Alignment explanation
Indices: 35323--35428 Score: 140
Period size: 51 Copynumber: 2.1 Consensus size: 49
35313 TTCTATTGTG
* * **
35323 TTATTAGAACTCATCACGTCAAGATTACGAGTTTTAATAAAAAATATTTTT
1 TTATTAGAACTCATCACGCCAAGATGACGAGTTCCAAT--AAAATATTTTT
* *
35374 TTATTCGAACTCATCACGCCAAGATGATGAGTTCCAATAAAATATTTTT
1 TTATTAGAACTCATCACGCCAAGATGACGAGTTCCAATAAAATATTTTT
35423 TTATTA
1 TTATTA
35429 AAATCTATCA
Statistics
Matches: 48, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
49 16 0.33
51 32 0.67
ACGTcount: A:0.37, C:0.14, G:0.10, T:0.39
Consensus pattern (49 bp):
TTATTAGAACTCATCACGCCAAGATGACGAGTTCCAATAAAATATTTTT
Found at i:39755 original size:31 final size:31
Alignment explanation
Indices: 39717--39793 Score: 111
Period size: 31 Copynumber: 2.5 Consensus size: 31
39707 ATTGTCCTTA
*
39717 TTATATATATTTTTAACAATTTGAAAAATAT
1 TTATATATATTTTTAACAAGTTGAAAAATAT
*
39748 TTATATAT-TTTATTAACAAGTTGGAAAATAT
1 TTATATATATTT-TTAACAAGTTGAAAAATAT
39779 TTATATATATATTTT
1 TTATATATAT-TTTT
39794 TTAAAAATTT
Statistics
Matches: 41, Mismatches: 2, Indels: 5
0.85 0.04 0.10
Matches are distributed among these distances:
30 3 0.07
31 33 0.80
32 3 0.07
33 2 0.05
ACGTcount: A:0.42, C:0.03, G:0.05, T:0.51
Consensus pattern (31 bp):
TTATATATATTTTTAACAAGTTGAAAAATAT
Found at i:40418 original size:75 final size:70
Alignment explanation
Indices: 40257--40420 Score: 170
Period size: 75 Copynumber: 2.2 Consensus size: 70
40247 TGAAATCTGA
* * **
40257 TTTTTTTATATTAATTGTTATTTTATTGAAGATATTTATTCTAAAATTTTATTGTATCAACTCTA
1 TTTTTTTATATTAATTGTTATTTTACTAAAGATATTTACACTAAAATTTTATTGTATCAACTCTA
40322 AAATT
66 AAATT
*
40327 TAAATTTCTTTATATTAATTGTTCATTTTACTAAAGGTATTTACACTAAAATTTTATT-TAT-AT
1 T---TTT-TTTATATTAATTGTT-ATTTTACTAAAGATATTTACACTAAAATTTTATTGTATCA-
40390 ATGCTCTATACAATT
60 A--CTCTA-A-AATT
40405 TTTTTTTACTATTAAT
1 TTTTTTTA-TATTAAT
40421 ACATACGTGT
Statistics
Matches: 78, Mismatches: 5, Indels: 17
0.78 0.05 0.17
Matches are distributed among these distances:
70 1 0.01
73 4 0.05
74 23 0.29
75 39 0.50
76 5 0.06
77 1 0.01
78 5 0.06
ACGTcount: A:0.33, C:0.08, G:0.05, T:0.54
Consensus pattern (70 bp):
TTTTTTTATATTAATTGTTATTTTACTAAAGATATTTACACTAAAATTTTATTGTATCAACTCTA
AAATT
Found at i:45435 original size:71 final size:71
Alignment explanation
Indices: 45358--45500 Score: 277
Period size: 71 Copynumber: 2.0 Consensus size: 71
45348 ACATTCTTAA
*
45358 TCTCTAGAGAAAGATGAATCATTCAAGTGAAACAAGAGGATTTTCAAGTGATTCATTTGGAGTAC
1 TCTCTAGAGAAAGATGAAACATTCAAGTGAAACAAGAGGATTTTCAAGTGATTCATTTGGAGTAC
45423 TTGATG
66 TTGATG
45429 TCTCTAGAGAAAGATGAAACATTCAAGTGAAACAAGAGGATTTTCAAGTGATTCATTTGGAGTAC
1 TCTCTAGAGAAAGATGAAACATTCAAGTGAAACAAGAGGATTTTCAAGTGATTCATTTGGAGTAC
45494 TTGATG
66 TTGATG
45500 T
1 T
45501 AGCTCCATTA
Statistics
Matches: 71, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
71 71 1.00
ACGTcount: A:0.36, C:0.11, G:0.22, T:0.31
Consensus pattern (71 bp):
TCTCTAGAGAAAGATGAAACATTCAAGTGAAACAAGAGGATTTTCAAGTGATTCATTTGGAGTAC
TTGATG
Found at i:50402 original size:35 final size:35
Alignment explanation
Indices: 50348--50470 Score: 156
Period size: 35 Copynumber: 3.5 Consensus size: 35
50338 TTAAAACTTG
50348 CAAAATAATCCTCAATTTCATTCTAAACCCCAAATTC
1 CAAAATAAT--TCAATTTCATTCTAAACCCCAAATTC
* *
50385 CAAAATAATTCAATTTCACTCTAAACCCTAAATTC
1 CAAAATAATTCAATTTCATTCTAAACCCCAAATTC
* * **
50420 TAAAACAATTCAATTAAATTCTAAACCCCAAATTC
1 CAAAATAATTCAATTTCATTCTAAACCCCAAATTC
* *
50455 TAAAATACTTCAATTT
1 CAAAATAATTCAATTT
50471 AAGGTTTAGA
Statistics
Matches: 75, Mismatches: 11, Indels: 2
0.85 0.12 0.02
Matches are distributed among these distances:
35 66 0.88
37 9 0.12
ACGTcount: A:0.44, C:0.24, G:0.00, T:0.32
Consensus pattern (35 bp):
CAAAATAATTCAATTTCATTCTAAACCCCAAATTC
Found at i:52550 original size:35 final size:36
Alignment explanation
Indices: 52502--52594 Score: 127
Period size: 35 Copynumber: 2.6 Consensus size: 36
52492 ATTAAACCTT
* * *
52502 AAATTGAAGTATTTTAGAATTTGAG-GTTTAGAATT
1 AAATTGAATTATTTTGGAATTTGAGAGTTTAGAATG
*
52537 TAATTGAATTATTTTGGAATTT-AGAGTTTAGAATG
1 AAATTGAATTATTTTGGAATTTGAGAGTTTAGAATG
*
52572 AAATTGAATTACTTTGGAATTTG
1 AAATTGAATTATTTTGGAATTTG
52595 GGAATGAAAT
Statistics
Matches: 50, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
34 2 0.04
35 48 0.96
ACGTcount: A:0.35, C:0.01, G:0.19, T:0.44
Consensus pattern (36 bp):
AAATTGAATTATTTTGGAATTTGAGAGTTTAGAATG
Done.