Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007457.1 Hibiscus syriacus cultivar Beakdansim tig00020434_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: 76348
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Found at i:193 original size:23 final size:25
Alignment explanation
Indices: 146--209 Score: 73
Period size: 23 Copynumber: 2.7 Consensus size: 25
136 ATATAATAAT
146 AATTAAATATA--AAAATAAACATA
1 AATTAAATATATTAAAATAAACATA
169 AATTAAATATATTAAAAT-AAC-TA
1 AATTAAATATATTAAAATAAACATA
* *
192 AAATAAATGAAATTAAAA
1 AATTAAAT-ATATTAAAA
210 CTATAATAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
23 20 0.56
24 11 0.31
25 5 0.14
ACGTcount: A:0.67, C:0.03, G:0.02, T:0.28
Consensus pattern (25 bp):
AATTAAATATATTAAAATAAACATA
Found at i:988 original size:26 final size:27
Alignment explanation
Indices: 937--1000 Score: 78
Period size: 26 Copynumber: 2.4 Consensus size: 27
927 AATTATTTAT
* *
937 TAATAATAAT-ATAATAATATTATAAA
1 TAATTATAATAATAATAATAATATAAA
*
963 TATTTATAATAATAATAATAAT-TAAA
1 TAATTATAATAATAATAATAATATAAA
*
989 TAATTAAAATAA
1 TAATTATAATAA
1001 AAATGAAAAA
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
26 22 0.69
27 10 0.31
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (27 bp):
TAATTATAATAATAATAATAATATAAA
Found at i:1235 original size:45 final size:45
Alignment explanation
Indices: 1167--1528 Score: 523
Period size: 45 Copynumber: 8.1 Consensus size: 45
1157 GAGGTTTTAT
* * * * *
1167 CATCTTGCACTGTAGGACTTACAGAGGACCCGAAGATTTTGAAAA
1 CATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAAAA
* *
1212 CATCATGCATTGAAGGGCTTACAGATGACCTGAAGGTTTTGAAAA
1 CATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAAAA
* *
1257 CATCCTGCACTGAAGGACTTACAGATGACCCGAAGGTTTTGAAAA
1 CATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAAAA
* * * *
1302 CATCCTACA-TGAAGGACTTATAGATGACCCGAAGGTTTTG-AAA
1 CATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAAAA
* *
1345 CATCA-GCACTGAAGGGCTTATAGATGACCTGAAGGTTTTGAAAA
1 CATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAAAA
*
1389 CATCATGCACTGAAGGGCTTAAAGATGACCCGAAGGTTTTGAAAA
1 CATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAAAA
* *
1434 CATTATGCACTGAAGGACTTACAGATGACCCGAAGGTTTTGAAAA
1 CATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAAAA
*
1479 CATAATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAAAA
1 CATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAAAA
*
1524 TATCA
1 CATCA
1529 AAAAAACTCC
Statistics
Matches: 288, Mismatches: 26, Indels: 6
0.90 0.08 0.02
Matches are distributed among these distances:
42 2 0.01
43 36 0.12
44 38 0.13
45 212 0.74
ACGTcount: A:0.35, C:0.18, G:0.23, T:0.24
Consensus pattern (45 bp):
CATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAAAA
Found at i:1563 original size:76 final size:74
Alignment explanation
Indices: 1463--1604 Score: 212
Period size: 76 Copynumber: 1.9 Consensus size: 74
1453 TACAGATGAC
*
1463 CCGAAGGTTTTGAAAACATAATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAAAATATC
1 CCGAAGGTTTTGAAAACATAATGCAATGAAGGGCTTACAGATGACCCGAAGGTTTTGAAAATATC
1528 AAAAAAACT
66 AAAAAAACT
* * * **
1537 CCGAAGGCTTTTTGAAAACATCATGCAATGCAGGTCTTATGGATGACCCGAAGGTTTTGAAAATA
1 CCGAAGG--TTTTGAAAACATAATGCAATGAAGGGCTTACAGATGACCCGAAGGTTTTGAAAATA
1602 TCA
64 TCA
1605 TGCATTGAAG
Statistics
Matches: 60, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
74 7 0.12
76 53 0.88
ACGTcount: A:0.37, C:0.17, G:0.21, T:0.25
Consensus pattern (74 bp):
CCGAAGGTTTTGAAAACATAATGCAATGAAGGGCTTACAGATGACCCGAAGGTTTTGAAAATATC
AAAAAAACT
Found at i:1605 original size:45 final size:45
Alignment explanation
Indices: 1537--1963 Score: 642
Period size: 45 Copynumber: 9.5 Consensus size: 45
1527 CAAAAAAACT
* * * **
1537 CCGAAGGCTTTTTGAAAACATCATGCAATGCAGGTCTTATGGATGAC
1 CCGAAGG--TTTTGAAAACATCATGCACTGAAGGGCTTACAGATGAC
* * *
1584 CCGAAGGTTTTGAAAATATCATGCATTGAAGGACTTACAGATGAC
1 CCGAAGGTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGAC
* *
1629 CTGAAGGTTTTG-AAACATCATGTACTGAAGGGCTTACAGATGAC
1 CCGAAGGTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGAC
*
1673 CCGAAGGTTTTGAAAACATCATGCACTGAAGGGATTACAGATGAC
1 CCGAAGGTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGAC
* * *
1718 CCGAAGGTTTTGAAAACATCCTGCACTGAAGGACTTATAGATGAC
1 CCGAAGGTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGAC
1763 CCGAAGGTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGAC
1 CCGAAGGTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGAC
*
1808 CCAAAGGTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGAC
1 CCGAAGGTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGAC
* *
1853 CCGAAGGTTTTG-AAACATCATGCACTGAAGGACTTACAGATGAT
1 CCGAAGGTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGAC
*
1897 CCGAAGGTTTTGAAAACATTCATGCACTGAAGGGATTACAGATGAC
1 CCGAAGGTTTTGAAAACA-TCATGCACTGAAGGGCTTACAGATGAC
*
1943 CCGAAGGTTTTGAAAATATCA
1 CCGAAGGTTTTGAAAACATCA
1964 AAAAGCTCCC
Statistics
Matches: 348, Mismatches: 29, Indels: 8
0.90 0.08 0.02
Matches are distributed among these distances:
44 81 0.23
45 219 0.63
46 41 0.12
47 7 0.02
ACGTcount: A:0.34, C:0.18, G:0.23, T:0.25
Consensus pattern (45 bp):
CCGAAGGTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGAC
Found at i:1639 original size:121 final size:119
Alignment explanation
Indices: 1418--1643 Score: 335
Period size: 121 Copynumber: 1.9 Consensus size: 119
1408 TAAAGATGAC
* *
1418 CCGAAGGTTTTGAAAACATTATGCACTGAAGGACTTACAGATGACCCGAAGGTTTTGAAAACATA
1 CCGAAGGTTTTGAAAACATCATGCAATGAAGGACTTACAGATGACCCGAAGGTTTTGAAAACATA
*
1483 ATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAAAATATCAAAAAAACT
66 ATGCACTGAAGGACTTACAGATGACCCGAAGGTTTTGAAAATATCAAAAAAACT
* * ** *
1537 CCGAAGGCTTTTTGAAAACATCATGCAATGCAGGTCTTATGGATGACCCGAAGGTTTTGAAAATA
1 CCGAAGG--TTTTGAAAACATCATGCAATGAAGGACTTACAGATGACCCGAAGGTTTTGAAAACA
* * *
1602 TCATGCATTGAAGGACTTACAGATGACCTGAAGGTTTTGAAA
64 TAATGCACTGAAGGACTTACAGATGACCCGAAGGTTTTGAAA
1644 CATCATGTAC
Statistics
Matches: 94, Mismatches: 11, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
119 7 0.07
121 87 0.93
ACGTcount: A:0.36, C:0.16, G:0.22, T:0.26
Consensus pattern (119 bp):
CCGAAGGTTTTGAAAACATCATGCAATGAAGGACTTACAGATGACCCGAAGGTTTTGAAAACATA
ATGCACTGAAGGACTTACAGATGACCCGAAGGTTTTGAAAATATCAAAAAAACT
Found at i:1726 original size:300 final size:298
Alignment explanation
Indices: 1248--1957 Score: 962
Period size: 300 Copynumber: 2.3 Consensus size: 298
1238 GACCTGAAGG
* * *
1248 TTTTGAAAACATCCTGCACTGAAGGACTTACAGATGACCCGAAGGTTTTGAAAACATCCTACATG
1 TTTTGAAAACATCATGCAATGAAGGACTTACAGATGACCCGAAGGTTTTGAAAACATCATACATG
* * *
1313 AAGGACTTATAGATGACCCGAAGGTTTTGAAACATCAGCACTGAAGGGCTTATAGATGACCTGAA
66 AAGGACTTACAGATGACCCGAAGGTTTTGAAACATCAGCACTGAAGGGCTTACAGATGACCCGAA
* *
1378 GGTTTTGAAAACATCATGCACTGAAGGGCTTAAAGATGACCCGAAGGTTTTGAAAACATTATGCA
131 GGTTTTGAAAACATCATGCACTGAAGGGATTAAAGATGACCCGAAGGTTTTGAAAACATCATGCA
1443 CTGAAGGACTTACAGATGACCCGAAGGTTTTGAAAACATAATGCACTGAAGGGCTTACAGATGAC
196 CTGAAGGACTTACAGATGACCCGAAGGTTTTGAAAACATAATGCACTGAAGGGCTTACAGATGAC
* *
1508 CCGAAGGTTTTGAAAATATCAAAAAAACTCCGAAGGCT
261 CCAAAGGTTTTGAAAACATCAAAAAAACTCCGAAGGCT
* * ** * *
1546 TTTTGAAAACATCATGCAATGCAGGTCTTATGGATGACCCGAAGGTTTTGAAAATATCATGCATT
1 TTTTGAAAACATCATGCAATGAAGGACTTACAGATGACCCGAAGGTTTTGAAAACATCATACA-T
* *
1611 GAAGGACTTACAGATGACCTGAAGGTTTTGAAACATCATGTACTGAAGGGCTTACAGATGACCCG
65 GAAGGACTTACAGATGACCCGAAGGTTTTGAAACATCA-GCACTGAAGGGCTTACAGATGACCCG
* *
1676 AAGGTTTTGAAAACATCATGCACTGAAGGGATTACAGATGACCCGAAGGTTTTGAAAACATCCTG
129 AAGGTTTTGAAAACATCATGCACTGAAGGGATTAAAGATGACCCGAAGGTTTTGAAAACATCATG
* *
1741 CACTGAAGGACTTATAGATGACCCGAAGGTTTTGAAAACATCATGCACTGAAGGGCTTACAGATG
194 CACTGAAGGACTTACAGATGACCCGAAGGTTTTGAAAACATAATGCACTGAAGGGCTTACAGATG
1806 ACCCAAAGGTTTTGAAAACATCATGCACTGAAGGGCTTACAGA-TGACCCGAAGG--
259 ACCCAAAGGTTTTGAAAACATCA---A---AA------A-A-ACT---CCGAAGGCT
* * *
1860 TTTTG-AAACATCATGCACTGAAGGACTTACAGATGATCCGAAGGTTTTGAAAACATTCATGCAC
1 TTTTGAAAACATCATGCAATGAAGGACTTACAGATGACCCGAAGGTTTTGAAAACA-TCATACA-
1924 TGAAGGGA-TTACAGATGACCCGAAGGTTTTGAAA
64 TGAA-GGACTTACAGATGACCCGAAGGTTTTGAAA
1958 ATATCAAAAA
Statistics
Matches: 360, Mismatches: 31, Indels: 26
0.86 0.07 0.06
Matches are distributed among these distances:
298 54 0.15
299 37 0.10
300 168 0.47
303 1 0.00
306 2 0.01
312 1 0.00
313 45 0.12
314 42 0.12
315 3 0.01
316 7 0.02
ACGTcount: A:0.35, C:0.18, G:0.23, T:0.25
Consensus pattern (298 bp):
TTTTGAAAACATCATGCAATGAAGGACTTACAGATGACCCGAAGGTTTTGAAAACATCATACATG
AAGGACTTACAGATGACCCGAAGGTTTTGAAACATCAGCACTGAAGGGCTTACAGATGACCCGAA
GGTTTTGAAAACATCATGCACTGAAGGGATTAAAGATGACCCGAAGGTTTTGAAAACATCATGCA
CTGAAGGACTTACAGATGACCCGAAGGTTTTGAAAACATAATGCACTGAAGGGCTTACAGATGAC
CCAAAGGTTTTGAAAACATCAAAAAAACTCCGAAGGCT
Found at i:2064 original size:36 final size:37
Alignment explanation
Indices: 2014--2123 Score: 134
Period size: 44 Copynumber: 2.8 Consensus size: 37
2004 GTTATGGATG
2014 ACCCGAA-GTTTTGAAAACATCATGCACTGACGA-TT
1 ACCCGAAGGTTTTGAAAACATCATGCACTGACGACTT
*
2049 ACCCGAAGGTTTTGAAAACATCATGCACTGAAGGACTT
1 ACCCGAAGGTTTTGAAAACATCATGCACTG-ACGACTT
2087 ACATATTACCGAAGGTTTTGAAAACATCATGCACTGA
1 AC------CCGAAGGTTTTGAAAACATCATGCACTGA
2124 AGGGCTTACA
Statistics
Matches: 65, Mismatches: 1, Indels: 10
0.86 0.01 0.13
Matches are distributed among these distances:
35 7 0.11
36 22 0.34
37 3 0.05
38 4 0.06
43 1 0.02
44 28 0.43
ACGTcount: A:0.35, C:0.21, G:0.18, T:0.25
Consensus pattern (37 bp):
ACCCGAAGGTTTTGAAAACATCATGCACTGACGACTT
Found at i:2110 original size:44 final size:45
Alignment explanation
Indices: 2045--2160 Score: 189
Period size: 44 Copynumber: 2.6 Consensus size: 45
2035 ATGCACTGAC
2045 GATTACCCGAAGGTTTTGAAAACATCATGCACTGAAGGACTTACA
1 GATTACCCGAAGGTTTTGAAAACATCATGCACTGAAGGACTTACA
* *
2090 TATTA-CCGAAGGTTTTGAAAACATCATGCACTGAAGGGCTTACA
1 GATTACCCGAAGGTTTTGAAAACATCATGCACTGAAGGACTTACA
* *
2134 GATGACCCGAAGGTTTTGAAAATATCA
1 GATTACCCGAAGGTTTTGAAAACATCA
2161 AAAAGCTCCC
Statistics
Matches: 65, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
44 41 0.63
45 24 0.37
ACGTcount: A:0.35, C:0.18, G:0.21, T:0.26
Consensus pattern (45 bp):
GATTACCCGAAGGTTTTGAAAACATCATGCACTGAAGGACTTACA
Found at i:2125 original size:25 final size:25
Alignment explanation
Indices: 2053--2126 Score: 70
Period size: 25 Copynumber: 3.2 Consensus size: 25
2043 ACGATTACCC
2053 GAAGGTTTTGAAAACATCATGCACT
1 GAAGGTTTTGAAAACATCATGCACT
** * *
2078 GAAGGACTT----ACAT-AT-TACC
1 GAAGGTTTTGAAAACATCATGCACT
2097 GAAGGTTTTGAAAACATCATGCACT
1 GAAGGTTTTGAAAACATCATGCACT
2122 GAAGG
1 GAAGG
2127 GCTTACAGAT
Statistics
Matches: 35, Mismatches: 8, Indels: 12
0.64 0.15 0.22
Matches are distributed among these distances:
19 9 0.26
20 2 0.06
21 4 0.11
23 4 0.11
24 2 0.06
25 14 0.40
ACGTcount: A:0.36, C:0.16, G:0.22, T:0.26
Consensus pattern (25 bp):
GAAGGTTTTGAAAACATCATGCACT
Found at i:6756 original size:32 final size:32
Alignment explanation
Indices: 6715--6776 Score: 106
Period size: 32 Copynumber: 1.9 Consensus size: 32
6705 GAAGAAATGA
* *
6715 TTGTTATGCTTATCTGGTAGAGATACTTCTCG
1 TTGTTATGCTCATCTCGTAGAGATACTTCTCG
6747 TTGTTATGCTCATCTCGTAGAGATACTTCT
1 TTGTTATGCTCATCTCGTAGAGATACTTCT
6777 TATTTCCAGG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.19, C:0.18, G:0.19, T:0.44
Consensus pattern (32 bp):
TTGTTATGCTCATCTCGTAGAGATACTTCTCG
Found at i:7243 original size:9 final size:10
Alignment explanation
Indices: 7222--7247 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
7212 TTTGATTCAA
7222 TTTTTCCCTT
1 TTTTTCCCTT
7232 TTTTTCCCTT
1 TTTTTCCCTT
7242 TTTTTC
1 TTTTTC
7248 TTCTTCAAGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (10 bp):
TTTTTCCCTT
Found at i:10147 original size:15 final size:14
Alignment explanation
Indices: 10122--10162 Score: 59
Period size: 15 Copynumber: 3.0 Consensus size: 14
10112 ATAAAAGTAT
10122 AAATG-AAAATGCA
1 AAATGCAAAATGCA
10135 AAGATGCAAAATGCA
1 AA-ATGCAAAATGCA
10150 AAATGC-AAATGCA
1 AAATGCAAAATGCA
10163 TGTATGAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
13 9 0.35
14 7 0.27
15 10 0.38
ACGTcount: A:0.56, C:0.12, G:0.17, T:0.15
Consensus pattern (14 bp):
AAATGCAAAATGCA
Found at i:10161 original size:6 final size:7
Alignment explanation
Indices: 10122--10162 Score: 59
Period size: 7 Copynumber: 6.0 Consensus size: 7
10112 ATAAAAGTAT
10122 AAATG-A
1 AAATGCA
10128 AAATGCA
1 AAATGCA
10135 AAGATGCA
1 AA-ATGCA
10143 AAATGCA
1 AAATGCA
10150 AAATGC-
1 AAATGCA
10156 AAATGCA
1 AAATGCA
10163 TGTATGAAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
6 11 0.34
7 14 0.44
8 7 0.22
ACGTcount: A:0.56, C:0.12, G:0.17, T:0.15
Consensus pattern (7 bp):
AAATGCA
Found at i:10301 original size:43 final size:43
Alignment explanation
Indices: 10240--10322 Score: 130
Period size: 43 Copynumber: 1.9 Consensus size: 43
10230 TGCATCAAAA
**
10240 AAAACTTTACATAAATGGGACAACTTTCGGTCCTAACTTCAAC
1 AAAACTTTACATAAATGGGACAACTTTCCCTCCTAACTTCAAC
* *
10283 AAAACTTTACATATATGGGATAACTTTCCCTCCTAACTTC
1 AAAACTTTACATAAATGGGACAACTTTCCCTCCTAACTTC
10323 TCTAAAGCCA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
43 36 1.00
ACGTcount: A:0.35, C:0.24, G:0.10, T:0.31
Consensus pattern (43 bp):
AAAACTTTACATAAATGGGACAACTTTCCCTCCTAACTTCAAC
Found at i:12200 original size:2 final size:2
Alignment explanation
Indices: 12193--12243 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
12183 AAATCTATTA
12193 AT 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 AT
12235 AT AT AT AT A
1 AT AT AT AT A
12244 AGATATTTAT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:14093 original size:18 final size:18
Alignment explanation
Indices: 14031--14119 Score: 74
Period size: 18 Copynumber: 5.0 Consensus size: 18
14021 AATGTATTTG
* *
14031 TAATTATT-TATTATTAA
1 TAATTATTATAATAATAA
* *
14048 TAAATATAATAAT-ATAA
1 TAATTATTATAATAATAA
**
14065 TAAACATTTATAATAATAA
1 TAATTA-TTATAATAATAA
* *
14084 TAATTATTATTATTATAA
1 TAATTATTATAATAATAA
*
14102 TAATTATAATAATAATAA
1 TAATTATTATAATAATAA
14120 AATGAAAATG
Statistics
Matches: 56, Mismatches: 13, Indels: 5
0.76 0.18 0.07
Matches are distributed among these distances:
17 14 0.25
18 34 0.61
19 8 0.14
ACGTcount: A:0.54, C:0.01, G:0.00, T:0.45
Consensus pattern (18 bp):
TAATTATTATAATAATAA
Found at i:14114 original size:9 final size:9
Alignment explanation
Indices: 14040--14119 Score: 63
Period size: 9 Copynumber: 8.8 Consensus size: 9
14030 GTAATTATTT
14040 ATTATTAATA
1 ATTA-TAATA
*
14050 AATATAATA
1 ATTATAATA
14059 A-TATAATA
1 ATTATAATA
** *
14067 AACATTTATA
1 ATTA-TAATA
*
14077 ATAATAATA
1 ATTATAATA
* *
14086 ATTATTATT
1 ATTATAATA
14095 ATTATAATA
1 ATTATAATA
14104 ATTATAATA
1 ATTATAATA
*
14113 ATAATAA
1 ATTATAA
14120 AATGAAAATG
Statistics
Matches: 56, Mismatches: 12, Indels: 5
0.77 0.16 0.07
Matches are distributed among these distances:
8 8 0.14
9 39 0.70
10 9 0.16
ACGTcount: A:0.56, C:0.01, G:0.00, T:0.42
Consensus pattern (9 bp):
ATTATAATA
Found at i:16279 original size:23 final size:23
Alignment explanation
Indices: 16252--16313 Score: 79
Period size: 25 Copynumber: 2.6 Consensus size: 23
16242 AATGATTGAA
16252 TACTTGTGTAATTTAAAAAAAAG
1 TACTTGTGTAATTTAAAAAAAAG
***
16275 TACTTGTGTAATTTTTTTTAAAAAG
1 TACTTGTGTAA--TTTAAAAAAAAG
16300 TACTTGTGTAATTT
1 TACTTGTGTAATTT
16314 TTTTTTTAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
23 14 0.41
25 20 0.59
ACGTcount: A:0.35, C:0.05, G:0.13, T:0.47
Consensus pattern (23 bp):
TACTTGTGTAATTTAAAAAAAAG
Found at i:16303 original size:25 final size:25
Alignment explanation
Indices: 16269--16337 Score: 120
Period size: 25 Copynumber: 2.8 Consensus size: 25
16259 GTAATTTAAA
16269 AAAAAGTACTTGTGTAATTTTTTTT
1 AAAAAGTACTTGTGTAATTTTTTTT
16294 AAAAAGTACTTGTGTAATTTTTTTT
1 AAAAAGTACTTGTGTAATTTTTTTT
**
16319 TTAAAGTACTTGTGTAATT
1 AAAAAGTACTTGTGTAATT
16338 ACACATGTGG
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
25 42 1.00
ACGTcount: A:0.32, C:0.04, G:0.13, T:0.51
Consensus pattern (25 bp):
AAAAAGTACTTGTGTAATTTTTTTT
Found at i:17013 original size:101 final size:102
Alignment explanation
Indices: 16838--17044 Score: 353
Period size: 101 Copynumber: 2.0 Consensus size: 102
16828 AAACGACGAC
* *
16838 CTTTCATCTAATGCTTCTAAACAAATCATTAATCGACATAATACTCAATTTAATCCTTAAGTTTT
1 CTTTCATCTAATCCTTCTAAACAAATCATTAATAGACATAATACTCAATTTAATCCTTAAGTTTT
16903 TCCATTAA-TTTTTTTACTTAATCACTGGTATCCGAT
66 TCCATTAATTTTTTTTACTTAATCACTGGTATCCGAT
*
16939 CTTTCATCTAATCCTTCTAAACAAATCATTAATAGACATAATAGTCAATTTAATCCTTAAGTTTT
1 CTTTCATCTAATCCTTCTAAACAAATCATTAATAGACATAATACTCAATTTAATCCTTAAGTTTT
*
17004 TCCATTAATTTTTTTTTTACTTAATCACTGGTGTCCGAT
66 TCCATTAA--TTTTTTTTACTTAATCACTGGTATCCGAT
17043 CT
1 CT
17045 GTTTACAAAG
Statistics
Matches: 99, Mismatches: 4, Indels: 3
0.93 0.04 0.03
Matches are distributed among these distances:
101 70 0.71
104 29 0.29
ACGTcount: A:0.31, C:0.19, G:0.06, T:0.43
Consensus pattern (102 bp):
CTTTCATCTAATCCTTCTAAACAAATCATTAATAGACATAATACTCAATTTAATCCTTAAGTTTT
TCCATTAATTTTTTTTACTTAATCACTGGTATCCGAT
Found at i:17468 original size:32 final size:31
Alignment explanation
Indices: 17414--17475 Score: 74
Period size: 30 Copynumber: 2.0 Consensus size: 31
17404 CCAATATTTA
17414 AATTTTGATCACTCAAATTTAAAACTTTTTTTT
1 AATTTTGATCACTCAAATTT-AAA-TTTTTTTT
*
17447 AATTTT-ATCA-TTAAACTTTAAATTTTTTT
1 AATTTTGATCACTCAAA-TTTAAATTTTTTT
17476 GTCTTAATTA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
30 7 0.26
31 7 0.26
32 7 0.26
33 6 0.22
ACGTcount: A:0.34, C:0.10, G:0.02, T:0.55
Consensus pattern (31 bp):
AATTTTGATCACTCAAATTTAAATTTTTTTT
Found at i:17537 original size:16 final size:16
Alignment explanation
Indices: 17518--17550 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
17508 GTAGCATTAA
17518 AACATTGCGTTTTAGG
1 AACATTGCGTTTTAGG
17534 AACATTGCGTTTTAGG
1 AACATTGCGTTTTAGG
17550 A
1 A
17551 TTCATACATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.27, C:0.12, G:0.24, T:0.36
Consensus pattern (16 bp):
AACATTGCGTTTTAGG
Found at i:18695 original size:182 final size:181
Alignment explanation
Indices: 18347--18994 Score: 856
Period size: 182 Copynumber: 3.6 Consensus size: 181
18337 GATACAAATG
* * * * ** *
18347 AAAAATGTATCGCTCCATAGCAATATAACAGGTAAAAATATGATAAAACTGGTTTC-ATTATGAT
1 AAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAAACCGGTCACGA-AATGAT
* * * *
18411 AAAACCGGTAAACCA-CTACTGGATATATCGAAAGTATCGATTAGATTTAA-ATAAGTATCGACA
65 AAAACCGGTAAA-GAGCTACCGGATATATTGAAAGTGTCGA-TAG--TTAATATAAGTATCGACA
* * * *
18474 CTTTTGGAATTTAAAAGAGAAGAAGTAATAGCACCTATAAAGTGTTGATACTTTAT
126 CTTTTCGAATTTAAAAGAGAAGAAGTTATAGCGCCTATAAAGTGTCGATACTTTAT
* * *
18530 AAAAACGTATCGATCCATAACAATATAACAGGTATAAGTATGACAAAACCGGTCACGAAATGATA
1 AAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAAACCGGTCACGAAATGATA
18595 AAACCGGTAAAGAGCTACCGGATATATTGAAAGTGTCGATACGTTAATATAAGTATCGACACTTT
66 AAACCGGTAAAGAGCTACCGGATATATTGAAAGTGTCGATA-GTTAATATAAGTATCGACACTTT
*
18660 TTGAATTTAAAAGAGAAGAAGTTATAGCGCCTATAAAGTGTCGATACTTTAT
130 TCGAATTTAAAAGAGAAGAAGTTATAGCGCCTATAAAGTGTCGATACTTTAT
* * ** * *
18712 AAAAATGTATCGATCCATAGCAATATAACAGGTAAGAATATGACAAAACAAGTCTCAAAATGATA
1 AAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAAACCGGTCACGAAATGATA
* * *
18777 AAACCGGTAAAAAGCTACCAGATATATTGAAAGTGTCGATAAATTAATATAAGTATCGACAC-TT
66 AAACCGGTAAAGAGCTACCGGATATATTGAAAGTGTCGAT-AGTTAATATAAGTATCGACACTTT
* *
18841 TCGTAATTTAAAAGAGAATAAGTTATAGCGCCTAAAAAGTGTCGATACTTTAT
130 TCG-AATTTAAAAGAGAAGAAGTTATAGCGCCTATAAAGTGTCGATACTTTAT
* * *
18894 GAAAATGTATCGATCCATAACAATATAATAGGTAAAAATATGACAAAACCGGT-ATCGAAATGAC
1 AAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAAACCGGTCA-CGAAATGAT
* * *
18958 AAAACCGGTAAAGCGCTACCGGTTATGTTGAAAGTGT
65 AAAACCGGTAAAGAGCTACCGGATATATTGAAAGTGT
18995 TGGTATTTTA
Statistics
Matches: 411, Mismatches: 47, Indels: 15
0.87 0.10 0.03
Matches are distributed among these distances:
181 8 0.02
182 314 0.76
183 88 0.21
184 1 0.00
ACGTcount: A:0.43, C:0.14, G:0.17, T:0.27
Consensus pattern (181 bp):
AAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAAACCGGTCACGAAATGATA
AAACCGGTAAAGAGCTACCGGATATATTGAAAGTGTCGATAGTTAATATAAGTATCGACACTTTT
CGAATTTAAAAGAGAAGAAGTTATAGCGCCTATAAAGTGTCGATACTTTAT
Found at i:21136 original size:9 final size:9
Alignment explanation
Indices: 21124--21148 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
21114 GTAGAGAAGA
21124 CAGAGGAGG
1 CAGAGGAGG
21133 CAGAGGAGG
1 CAGAGGAGG
21142 CAGAGGA
1 CAGAGGA
21149 AGAGATGGTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.36, C:0.12, G:0.52, T:0.00
Consensus pattern (9 bp):
CAGAGGAGG
Found at i:21190 original size:15 final size:15
Alignment explanation
Indices: 21167--21196 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
21157 TTGGAGGGGT
21167 GGATGACGGTCAGGG
1 GGATGACGGTCAGGG
*
21182 GGATTACGGTCAGGG
1 GGATGACGGTCAGGG
21197 AAAACAGAGT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.20, C:0.13, G:0.50, T:0.17
Consensus pattern (15 bp):
GGATGACGGTCAGGG
Found at i:23065 original size:19 final size:19
Alignment explanation
Indices: 23041--23091 Score: 84
Period size: 19 Copynumber: 2.7 Consensus size: 19
23031 AAATGTATGG
23041 TTAATTTTGTATAAGATTT
1 TTAATTTTGTATAAGATTT
*
23060 TTAATTTTGTATACGATTT
1 TTAATTTTGTATAAGATTT
*
23079 ATAATTTTGTATA
1 TTAATTTTGTATA
23092 TGAATGTAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 30 1.00
ACGTcount: A:0.31, C:0.02, G:0.10, T:0.57
Consensus pattern (19 bp):
TTAATTTTGTATAAGATTT
Found at i:23836 original size:198 final size:197
Alignment explanation
Indices: 23423--24021 Score: 1054
Period size: 198 Copynumber: 3.0 Consensus size: 197
23413 TGGTAAACAT
* *
23423 ATGTGTCGATAAATTTATAAAAAGTATCGATCCTAAAAACATCGAGACCCATAATTATAATGTAA
1 ATGTGTCGATACATTTATAAAAAGTATCGATCCCAAAAACATCGAGACCCATAATTATAATGTAA
* *
23488 TAGGTAAATTATGAATCTAACTGGTCTAAATACACTGGTTTATGAGAAAAAAAGGTGTACATAAA
66 TAGGTAAATTATGAATCTAACCGGTCTAAATACAC-GGTTTATGAG-AAAACAGGTGTACATAAA
23553 GTATCGACACTTATTTAATTTGTGTCGATACTTTGTGTCCAGAATGATTTCCTTACCAAGTGCAT
129 GTATCGACACTTATTTAATTTGTGTCGATACTTTGTGTCCAGAATGATTTCCTTACCAAGTGCAT
23618 GGAA
194 GGAA
* *
23622 ATGTGTCGATACATTTATAAAAAGTATCGATCCCAAAAACATTGAGACACATAATTATAATGTAA
1 ATGTGTCGATACATTTATAAAAAGTATCGATCCCAAAAACATCGAGACCCATAATTATAATGTAA
*
23687 TAGGTAAATTATGAATCTAACCGGTCTAAATACATCGGTTTATGAGAAAACATGTGTACATAAAG
66 TAGGTAAATTATGAATCTAACCGGTCTAAATACA-CGGTTTATGAGAAAACAGGTGTACATAAAG
* * *
23752 TATCGACACTTGTTGAATTTGTGTCGATACTTTGTGTCCGGAATGATTTCCTTACCAAGTGCATG
130 TATCGACACTTATTTAATTTGTGTCGATACTTTGTGTCCAGAATGATTTCCTTACCAAGTGCATG
23817 GAA
195 GAA
*
23820 ATGTGTCGATACATTTATAAAAAGTATCGATCCCAAAAACATCGAGACCCATAATTATAATATAA
1 ATGTGTCGATACATTTATAAAAAGTATCGATCCCAAAAACATCGAGACCCATAATTATAATGTAA
*
23885 TAGGTAAATTATGAATCTAACCAGTCTAAATACACCGGTTTATGAGAAAACAGGTGTACATAAAG
66 TAGGTAAATTATGAATCTAACCGGTCTAAATACA-CGGTTTATGAGAAAACAGGTGTACATAAAG
23950 TATCGACACTTATTTAATTTGTGTCGATACTTTGTGTCCAGAATGATTTCCTTACCAAGTGCATG
130 TATCGACACTTATTTAATTTGTGTCGATACTTTGTGTCCAGAATGATTTCCTTACCAAGTGCATG
24015 GAA
195 GAA
24018 ATGT
1 ATGT
24022 AATAGGTAAA
Statistics
Matches: 380, Mismatches: 19, Indels: 3
0.95 0.05 0.01
Matches are distributed among these distances:
198 275 0.72
199 104 0.27
200 1 0.00
ACGTcount: A:0.37, C:0.15, G:0.17, T:0.32
Consensus pattern (197 bp):
ATGTGTCGATACATTTATAAAAAGTATCGATCCCAAAAACATCGAGACCCATAATTATAATGTAA
TAGGTAAATTATGAATCTAACCGGTCTAAATACACGGTTTATGAGAAAACAGGTGTACATAAAGT
ATCGACACTTATTTAATTTGTGTCGATACTTTGTGTCCAGAATGATTTCCTTACCAAGTGCATGG
AA
Found at i:24302 original size:324 final size:327
Alignment explanation
Indices: 23680--24318 Score: 973
Period size: 324 Copynumber: 1.9 Consensus size: 327
23670 ACATAATTAT
* * *
23680 AATGTAATAGGTAAATTATGAATCTAACCGGTCTAAATACATCGGTTTATGAGAAAACATGTGTA
1 AATGTAATAGGTAAATTATGAATCTAACCGGTCTAAATACACCGGTTTATGAGAAAACAGGTATA
* *
23745 CATAAAGTATCGACACTTGTTGAATTTGTGTCGATACTTTGTGTCCGGAATGATTTCCTTACCAA
66 CATAAAGTATCAACACTTGTTGAATTTGTGTC---AC----TAT-C--AATGATTTCCTTACCAA
*
23810 GTGCATGGAAATGTGTCGATACATTTATAAAAAGTATCGATCCCAAAAACATCGAGACCCATAAT
121 GTGCATGGAAATGTGTCGATACATTTATAAAAAGTATCAATCCCAAAAACATCGAGACCCATAAT
*
23875 TATAATATAATAGGTAAATTATGAATCTAACCAGTCTAAATACACCGGTTTATGAGAAAACAGGT
186 TATAATATAATAGGTAAATTATGAATCTAACCAGTCTAAATACACCAGTTTATGAGAAAACAGGT
* * *
23940 GTACATAAAGTATCGACACTTATTTAATTTGTGTCGATAC-TTTGTGTCCAGAATGATTTCCTTA
251 ATACATAAAGTATCGACACTTATTGAATTTGCGTCGATACGTTT-TGTCCAGAATGATTTCCTTA
24004 CCAAGTGCATGGA
315 CCAAGTGCATGGA
*
24017 AATGTAATAGGTAAATTATGAATCTAATCGGTCTAAATACACCGGTTTATGAGAAAACAGGTATA
1 AATGTAATAGGTAAATTATGAATCTAACCGGTCTAAATACACCGGTTTATGAGAAAACAGGTATA
24082 CATAAAGTATCAACACTTGTTGAATTTGTGTC-C-AT-AATGATTTCCTTACCAAGTGCATGGAA
66 CATAAAGTATCAACACTTGTTGAATTTGTGTCACTATCAATGATTTCCTTACCAAGTGCATGGAA
* * *
24144 ATGTGTCGATACATTTATAATAAGTATCAATCCCAAAAACATCGAGATCCATAATTATAATGTAA
131 ATGTGTCGATACATTTATAAAAAGTATCAATCCCAAAAACATCGAGACCCATAATTATAATATAA
* *
24209 TAGGTAAATTATGAATCTAACCGGTCTAAATACACCAGTTTATGAGAAAACATGTATACATAAAG
196 TAGGTAAATTATGAATCTAACCAGTCTAAATACACCAGTTTATGAGAAAACAGGTATACATAAAG
* *
24274 TATCTACACTCT-TTGACTTTGCGTCGATACGTTTTGTCCAGAATG
261 TATCGACACT-TATTGAATTTGCGTCGATACGTTTTGTCCAGAATG
24319 TAAATGGTCA
Statistics
Matches: 282, Mismatches: 18, Indels: 17
0.89 0.06 0.05
Matches are distributed among these distances:
324 184 0.65
325 4 0.01
328 1 0.00
333 1 0.00
337 92 0.33
ACGTcount: A:0.36, C:0.15, G:0.17, T:0.32
Consensus pattern (327 bp):
AATGTAATAGGTAAATTATGAATCTAACCGGTCTAAATACACCGGTTTATGAGAAAACAGGTATA
CATAAAGTATCAACACTTGTTGAATTTGTGTCACTATCAATGATTTCCTTACCAAGTGCATGGAA
ATGTGTCGATACATTTATAAAAAGTATCAATCCCAAAAACATCGAGACCCATAATTATAATATAA
TAGGTAAATTATGAATCTAACCAGTCTAAATACACCAGTTTATGAGAAAACAGGTATACATAAAG
TATCGACACTTATTGAATTTGCGTCGATACGTTTTGTCCAGAATGATTTCCTTACCAAGTGCATG
GA
Found at i:24807 original size:15 final size:15
Alignment explanation
Indices: 24787--24838 Score: 86
Period size: 15 Copynumber: 3.5 Consensus size: 15
24777 AGAATCGGGG
*
24787 CTCTTCTCAACCCAT
1 CTCTTCTCAACCCAA
*
24802 CTCTTCTCAACCCAC
1 CTCTTCTCAACCCAA
24817 CTCTTCTCAACCCAA
1 CTCTTCTCAACCCAA
24832 CTCTTCT
1 CTCTTCT
24839 GAGGAAATCA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 35 1.00
ACGTcount: A:0.19, C:0.48, G:0.00, T:0.33
Consensus pattern (15 bp):
CTCTTCTCAACCCAA
Found at i:28144 original size:201 final size:201
Alignment explanation
Indices: 27643--28306 Score: 769
Period size: 201 Copynumber: 3.3 Consensus size: 201
27633 ATGTAATCCC
* * * *
27643 GAATGTA-TTTCCAAACCAAGTGT-ACGGACAAAGTGTTGATACATTTATAAAAAGTATCGATCC
1 GAATGTATTTTCAAAACCAAGT-TCAC-GAAAAAGTGTCGATACATTTATAAAAAGTGTCGATCC
* * * *
27706 AAAAAACATCGAGACCCATAATTATAATGTAATAGGTAAAATAACAATGTAACCGGTCTAAATAT
64 CAAAAACATCGAAACACATAATTATAATGTAATAGGTAACATAACAATGTAACCGGTCTAAATAT
* *
27771 ACCGG-TTTATGAGAAAAGAGGTATACATAAAGTATCGACACTTTATACATTTGTGTCGATACTT
129 ACCGGTTTTATGAGAAAATAGGTATACATAATGTATCGACACTTTATACATTTGTGTCGATACTT
*
27835 TGTGTCCA
194 TATGTCCA
* * **
27843 TAATGTATTTTCCAACCAAAACAAGTTCAC-AAATAAGTGTCGATACATTTATATCAAGTGTCGA
1 GAATGTATTTT-C-A--AAACCAAGTTCACGAAA-AAGTGTCGATACATTTATAAAAAGTGTCGA
* * * * * * * *
27907 TCCCAAAAACATCGAAACCCGTAACTATATTGTAATAGGTCACTTTACAATGTAACCGGTATAAA
61 TCCCAAAAACATCGAAACACATAATTATAATGTAATAGGTAACATAACAATGTAACCGGTCTAAA
* * *
27972 TTTACCGGTTTTATGAGAAAATAGGTCTACA-ATATGTATCGACACTTTATTCATTTGTGTCGAT
126 TATACCGGTTTTATGAGAAAATAGGTATACATA-ATGTATCGACACTTTATACATTTGTGTCGAT
28036 ACATGTT-T-TCCA
190 AC-T-TTATGTCCA
* *
28048 GAATGTA-TTTCAAAACCAA-TTGCACGATAAAAATGTCGATACATTTATAACAAGTGTCGATCC
1 GAATGTATTTTCAAAACCAAGTT-CACGA-AAAAGTGTCGATACATTTATAAAAAGTGTCGATCC
* *
28111 CAAAAACATCGAAACACATAATTATAATGTAATAGGTAACATAACAATATAACCAGTCTAAATAT
64 CAAAAACATCGAAACACATAATTATAATGTAATAGGTAACATAACAATGTAACCGGTCTAAATAT
* * * *
28176 ACCGGTTATTA--A-AAAAAATGTATACATAATGTATCGATACTTTATACATTTGTGTCGACACT
129 ACCGGTT-TTATGAGAAAATAGGTATACATAATGTATCGACACTTTATACATTTGTGTCGATACT
28238 TTATGTCCA
193 TTATGTCCA
* ** * *
28247 TAATAAATTTTCGAAA-CAAGTTCACGAAAAAGTGTCGATACATTTAGAAAAAGTGTCGAT
1 GAATGTATTTTCAAAACCAAGTTCACGAAAAAGTGTCGATACATTTATAAAAAGTGTCGAT
28307 ACATTTAGAA
Statistics
Matches: 393, Mismatches: 51, Indels: 42
0.81 0.10 0.09
Matches are distributed among these distances:
197 2 0.01
198 32 0.08
199 59 0.15
200 26 0.07
201 96 0.24
202 7 0.02
203 3 0.01
204 93 0.24
205 71 0.18
206 2 0.01
207 2 0.01
ACGTcount: A:0.39, C:0.16, G:0.14, T:0.31
Consensus pattern (201 bp):
GAATGTATTTTCAAAACCAAGTTCACGAAAAAGTGTCGATACATTTATAAAAAGTGTCGATCCCA
AAAACATCGAAACACATAATTATAATGTAATAGGTAACATAACAATGTAACCGGTCTAAATATAC
CGGTTTTATGAGAAAATAGGTATACATAATGTATCGACACTTTATACATTTGTGTCGATACTTTA
TGTCCA
Found at i:28222 original size:22 final size:21
Alignment explanation
Indices: 28196--28241 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
28186 AAAAAAAATG
*
28196 TATACATAATGTATCGATACTT
1 TATACAT-ATGTATCGACACTT
* *
28218 TATACATTTGTGTCGACACTT
1 TATACATATGTATCGACACTT
28239 TAT
1 TAT
28242 GTCCATAATA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 14 0.67
22 7 0.33
ACGTcount: A:0.30, C:0.15, G:0.11, T:0.43
Consensus pattern (21 bp):
TATACATATGTATCGACACTT
Found at i:28296 original size:21 final size:21
Alignment explanation
Indices: 28272--28327 Score: 112
Period size: 21 Copynumber: 2.7 Consensus size: 21
28262 ACAAGTTCAC
28272 GAAAAAGTGTCGATACATTTA
1 GAAAAAGTGTCGATACATTTA
28293 GAAAAAGTGTCGATACATTTA
1 GAAAAAGTGTCGATACATTTA
28314 GAAAAAGTGTCGAT
1 GAAAAAGTGTCGAT
28328 CCTAAAAATC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.43, C:0.09, G:0.21, T:0.27
Consensus pattern (21 bp):
GAAAAAGTGTCGATACATTTA
Found at i:30220 original size:17 final size:16
Alignment explanation
Indices: 30186--30221 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
30176 CGGTCTAAAT
*
30186 TTTAACCGATCACTTA
1 TTTAACCGATCACCTA
30202 TTTAACCGATCACACTA
1 TTTAACCGATCAC-CTA
30219 TTT
1 TTT
30222 TTTAACCATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 13 0.72
17 5 0.28
ACGTcount: A:0.31, C:0.25, G:0.06, T:0.39
Consensus pattern (16 bp):
TTTAACCGATCACCTA
Found at i:32267 original size:36 final size:36
Alignment explanation
Indices: 32217--32316 Score: 173
Period size: 36 Copynumber: 2.8 Consensus size: 36
32207 CCAACATCTC
*
32217 CGCCACCTCCAGCAGCTACCCCGACACCGACACCAA
1 CGCCACCACCAGCAGCTACCCCGACACCGACACCAA
* *
32253 CGCCACCACAAGCAGCTACCCCGACACCGGCACCAA
1 CGCCACCACCAGCAGCTACCCCGACACCGACACCAA
32289 CGCCACCACCAGCAGCTACCCCGACACC
1 CGCCACCACCAGCAGCTACCCCGACACC
32317 ATCACCATCA
Statistics
Matches: 60, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 60 1.00
ACGTcount: A:0.28, C:0.53, G:0.15, T:0.04
Consensus pattern (36 bp):
CGCCACCACCAGCAGCTACCCCGACACCGACACCAA
Found at i:32316 original size:18 final size:18
Alignment explanation
Indices: 32225--32317 Score: 66
Period size: 18 Copynumber: 5.2 Consensus size: 18
32215 TCCGCCACCT
32225 CCAGCAGCTACCCCGACA
1 CCAGCAGCTACCCCGACA
* * *
32243 CC-GACACCAACGCC-ACCA
1 CCAG-CAGCTACCCCGA-CA
*
32261 CAAGCAGCTACCCCGACA
1 CCAGCAGCTACCCCGACA
* * * *
32279 CCGGCACCAACGCC-ACCA
1 CCAGCAGCTACCCCGA-CA
32297 CCAGCAGCTACCCCGACA
1 CCAGCAGCTACCCCGACA
32315 CCA
1 CCA
32318 TCACCATCAC
Statistics
Matches: 53, Mismatches: 16, Indels: 12
0.65 0.20 0.15
Matches are distributed among these distances:
17 3 0.06
18 47 0.89
19 3 0.06
ACGTcount: A:0.30, C:0.52, G:0.15, T:0.03
Consensus pattern (18 bp):
CCAGCAGCTACCCCGACA
Found at i:33375 original size:3 final size:3
Alignment explanation
Indices: 33367--33425 Score: 118
Period size: 3 Copynumber: 19.7 Consensus size: 3
33357 TATTTAATGA
33367 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
33415 ATT ATT ATT AT
1 ATT ATT ATT AT
33426 CATCATCGTC
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 56 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:34345 original size:3 final size:3
Alignment explanation
Indices: 34337--34374 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
34327 ATACAAGCTG
34337 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
34375 TTGGGTGATA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:35823 original size:21 final size:21
Alignment explanation
Indices: 35799--35850 Score: 95
Period size: 21 Copynumber: 2.5 Consensus size: 21
35789 AAATTAGGAG
35799 TAATTAAAAAGTTAAGTAATT
1 TAATTAAAAAGTTAAGTAATT
35820 TAATTAAAAAGTTAAGTAATT
1 TAATTAAAAAGTTAAGTAATT
*
35841 AAATTAAAAA
1 TAATTAAAAA
35851 AATTAAACTT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.58, C:0.00, G:0.08, T:0.35
Consensus pattern (21 bp):
TAATTAAAAAGTTAAGTAATT
Found at i:42647 original size:3 final size:3
Alignment explanation
Indices: 42639--42670 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
42629 TTCTATATAT
42639 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
42671 GTTGTTGTTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:42901 original size:18 final size:19
Alignment explanation
Indices: 42875--42915 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 19
42865 ACCAACTACA
*
42875 AAATCAAAACATAAAAATC
1 AAATCAAAAAATAAAAATC
*
42894 AAAT-AAAAAATCAAAATC
1 AAATCAAAAAATAAAAATC
42912 AAAT
1 AAAT
42916 TTAATAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 16 0.80
19 4 0.20
ACGTcount: A:0.71, C:0.12, G:0.00, T:0.17
Consensus pattern (19 bp):
AAATCAAAAAATAAAAATC
Found at i:45920 original size:39 final size:39
Alignment explanation
Indices: 45821--45926 Score: 110
Period size: 39 Copynumber: 2.7 Consensus size: 39
45811 CATAACTCTC
* * *
45821 AAATTATTTCAC-TATAACATTCTAAAATCCTAATTTCTT
1 AAATTATTTCACAT-TAACGTTCTAAATTCCTAATTTATT
* *
45860 AAATT-TTGACACCA-TAACGTTCTAAATTCTTAATTTATT
1 AAATTATT-TCA-CATTAACGTTCTAAATTCCTAATTTATT
*
45899 AAATTATTTCACATTAGCGTTCTAAATT
1 AAATTATTTCACATTAACGTTCTAAATT
45927 ATTTTTAAAA
Statistics
Matches: 55, Mismatches: 7, Indels: 10
0.76 0.10 0.14
Matches are distributed among these distances:
38 4 0.07
39 48 0.87
40 3 0.05
ACGTcount: A:0.37, C:0.16, G:0.04, T:0.43
Consensus pattern (39 bp):
AAATTATTTCACATTAACGTTCTAAATTCCTAATTTATT
Found at i:46095 original size:15 final size:15
Alignment explanation
Indices: 46072--46102 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
46062 ATATATATTA
*
46072 TAGATTTTTAAATTT
1 TAGAATTTTAAATTT
46087 TAGAATTTTAAATTT
1 TAGAATTTTAAATTT
46102 T
1 T
46103 TTATATAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.35, C:0.00, G:0.06, T:0.58
Consensus pattern (15 bp):
TAGAATTTTAAATTT
Found at i:46247 original size:22 final size:22
Alignment explanation
Indices: 46193--46248 Score: 60
Period size: 22 Copynumber: 2.5 Consensus size: 22
46183 TAATAAAATT
*
46193 ATATATATATTAATTTAAAAAC
1 ATATTTATATTAATTTAAAAAC
* * *
46215 ATTTTTATATTAATTTATTAAAT
1 ATATTTATATTAATTTA-AAAAC
46238 ATATTT-TATTA
1 ATATTTATATTA
46249 TTAACTTAAT
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
22 20 0.71
23 8 0.29
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.54
Consensus pattern (22 bp):
ATATTTATATTAATTTAAAAAC
Found at i:46310 original size:29 final size:28
Alignment explanation
Indices: 46202--46310 Score: 97
Period size: 27 Copynumber: 4.0 Consensus size: 28
46192 TATATATATA
* *
46202 TTAATTTAAAAACATTTTTATATTAA-T
1 TTAATTTAAAAATATTTTTATTTTAATT
* *
46229 TT-A-TTAAATATA-TTTTATTATTAA-C
1 TTAATTTAAAAATATTTTTATT-TTAATT
46254 TTAATTTAAAAATA-TTTTATGTTT-ATT
1 TTAATTTAAAAATATTTTTAT-TTTAATT
*
46281 TTCATTTAAAAATATTTTTTATTTTAATT
1 TTAATTTAAAAATA-TTTTTATTTTAATT
46310 T
1 T
46311 ATTAAAAGTA
Statistics
Matches: 67, Mismatches: 7, Indels: 14
0.76 0.08 0.16
Matches are distributed among these distances:
24 6 0.09
25 13 0.19
26 3 0.04
27 31 0.46
28 4 0.06
29 10 0.15
ACGTcount: A:0.39, C:0.03, G:0.01, T:0.58
Consensus pattern (28 bp):
TTAATTTAAAAATATTTTTATTTTAATT
Found at i:46941 original size:19 final size:18
Alignment explanation
Indices: 46908--46943 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
46898 TGAAATTTTG
*
46908 ATTAAATTACGTATATAT
1 ATTAAATTACATATATAT
46926 ATTAACATTACATATATA
1 ATTAA-ATTACATATATA
46944 ACAACAAGTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.47, C:0.08, G:0.03, T:0.42
Consensus pattern (18 bp):
ATTAAATTACATATATAT
Found at i:52503 original size:13 final size:13
Alignment explanation
Indices: 52487--52528 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 13
52477 TGCGACATAA
*
52487 ATTTACGACGCGC
1 ATTTATGACGCGC
*
52500 ATTTATGACACGC
1 ATTTATGACGCGC
*
52513 ATTTATGACGCTC
1 ATTTATGACGCGC
52526 ATT
1 ATT
52529 GCGCGTCATT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.26, C:0.24, G:0.17, T:0.33
Consensus pattern (13 bp):
ATTTATGACGCGC
Found at i:52643 original size:85 final size:84
Alignment explanation
Indices: 52500--52665 Score: 244
Period size: 85 Copynumber: 2.0 Consensus size: 84
52490 TACGACGCGC
* * * *
52500 ATTTATGACACGCATTTATGACGCTCATTGCGCGTCATTGAAGCCCCCGTTATAAATGAAGACGA
1 ATTTATGACACACATTTATGACGCTCATTGCGCGACATTGAAACCCCCGTCATAAATGAAGACGA
52565 CACACATTTGTGTGTCATAA
66 CACACA-TTGTGTGTCATAA
* * *
52585 ATTTATGACACACATTTATGAC-TTACATTGCGTGACATTGAAACCCCCGTCATAAATGAAGATG
1 ATTTATGACACACATTTATGACGCT-CATTGCGCGACATTGAAACCCCCGTCATAAATGAAGACG
52649 ACACACATTGTGTGTCA
65 ACACACATTGTGTGTCA
52666 AAGAGTATAT
Statistics
Matches: 73, Mismatches: 7, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
84 11 0.15
85 62 0.85
ACGTcount: A:0.31, C:0.22, G:0.17, T:0.30
Consensus pattern (84 bp):
ATTTATGACACACATTTATGACGCTCATTGCGCGACATTGAAACCCCCGTCATAAATGAAGACGA
CACACATTGTGTGTCATAA
Found at i:52968 original size:18 final size:18
Alignment explanation
Indices: 52945--52981 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
52935 TTACTACATC
52945 AATTCTCATGTTTCTGGG
1 AATTCTCATGTTTCTGGG
52963 AATTCTCATGTTTCTGGG
1 AATTCTCATGTTTCTGGG
52981 A
1 A
52982 GTGAAGAAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.19, C:0.16, G:0.22, T:0.43
Consensus pattern (18 bp):
AATTCTCATGTTTCTGGG
Found at i:71974 original size:12 final size:12
Alignment explanation
Indices: 71957--71991 Score: 70
Period size: 12 Copynumber: 2.9 Consensus size: 12
71947 CCCACCAACA
71957 ATTTTATTTTCG
1 ATTTTATTTTCG
71969 ATTTTATTTTCG
1 ATTTTATTTTCG
71981 ATTTTATTTTC
1 ATTTTATTTTC
71992 AAGAAGGTGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.17, C:0.09, G:0.06, T:0.69
Consensus pattern (12 bp):
ATTTTATTTTCG
Found at i:72513 original size:18 final size:18
Alignment explanation
Indices: 72490--72526 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
72480 AAGGATAAAG
*
72490 TTAACTTAGCTAGGACTC
1 TTAACTTAACTAGGACTC
72508 TTAACTTAACTAGGACTC
1 TTAACTTAACTAGGACTC
72526 T
1 T
72527 AACACCTCTC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.30, C:0.22, G:0.14, T:0.35
Consensus pattern (18 bp):
TTAACTTAACTAGGACTC
Done.