Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002515.1 Hibiscus syriacus cultivar Beakdansim tig00005116_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: 150068
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:1843 original size:17 final size:17
Alignment explanation
Indices: 1821--1858 Score: 76
Period size: 17 Copynumber: 2.2 Consensus size: 17
1811 GGAAGTCAAC
1821 GTCAACGGTCGGGTCGG
1 GTCAACGGTCGGGTCGG
1838 GTCAACGGTCGGGTCGG
1 GTCAACGGTCGGGTCGG
1855 GTCA
1 GTCA
1859 GTCGGGTTGG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.13, C:0.24, G:0.45, T:0.18
Consensus pattern (17 bp):
GTCAACGGTCGGGTCGG
Found at i:1885 original size:10 final size:10
Alignment explanation
Indices: 1870--1947 Score: 58
Period size: 10 Copynumber: 8.1 Consensus size: 10
1860 TCGGGTTGGG
1870 TCAGACCGGT
1 TCAGACCGGT
1880 TCAGA-CGG-
1 TCAGACCGGT
*
1888 TCAAACCGGT
1 TCAGACCGGT
1898 TC-GAACCGGT
1 TCAG-ACCGGT
1908 TCAGACCGG-
1 TCAGACCGGT
* *
1917 TCAAACCGGG
1 TCAGACCGGT
* *
1927 TCAAACC-GA
1 TCAGACCGGT
1936 TCAGAACCGGT
1 TCAG-ACCGGT
1947 T
1 T
1948 GAAAACCGGT
Statistics
Matches: 55, Mismatches: 6, Indels: 13
0.74 0.08 0.18
Matches are distributed among these distances:
8 4 0.07
9 18 0.33
10 30 0.55
11 3 0.05
ACGTcount: A:0.27, C:0.29, G:0.27, T:0.17
Consensus pattern (10 bp):
TCAGACCGGT
Found at i:1925 original size:29 final size:28
Alignment explanation
Indices: 1867--1934 Score: 100
Period size: 29 Copynumber: 2.4 Consensus size: 28
1857 CAGTCGGGTT
*
1867 GGGTCAGACCGGTTCAGACGGTCAAACC
1 GGGTCAAACCGGTTCAGACGGTCAAACC
* *
1895 GGTTCGAACCGGTTCAGACCGGTCAAACC
1 GGGTCAAACCGGTTCAGA-CGGTCAAACC
1924 GGGTCAAACCG
1 GGGTCAAACCG
1935 ATCAGAACCG
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
28 15 0.44
29 19 0.56
ACGTcount: A:0.25, C:0.29, G:0.31, T:0.15
Consensus pattern (28 bp):
GGGTCAAACCGGTTCAGACGGTCAAACC
Found at i:1944 original size:29 final size:28
Alignment explanation
Indices: 1880--1964 Score: 84
Period size: 29 Copynumber: 3.0 Consensus size: 28
1870 TCAGACCGGT
* * *
1880 TCAGA-CGGTCAAACCGGTTCGAACCGGT
1 TCAGACCGGTCAAACCGGGTCAAACC-GA
1908 TCAGACCGGTCAAACCGGGTCAAACCGA
1 TCAGACCGGTCAAACCGGGTCAAACCGA
*
1936 TCAGAACCGGTTGAAAACC-GGTCAAACCG
1 TCAG-ACCGG-T-CAAACCGGGTCAAACCG
1965 GTTTCCAGCC
Statistics
Matches: 49, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
28 10 0.20
29 23 0.47
30 11 0.22
31 5 0.10
ACGTcount: A:0.31, C:0.29, G:0.26, T:0.14
Consensus pattern (28 bp):
TCAGACCGGTCAAACCGGGTCAAACCGA
Found at i:1963 original size:20 final size:19
Alignment explanation
Indices: 1888--1967 Score: 88
Period size: 20 Copynumber: 4.1 Consensus size: 19
1878 GTTCAGACGG
*
1888 TCAAACCGGTTCGAACCGGT
1 TCAAACCGG-TCAAACCGGT
* *
1908 TCAGACCGGTCAAACCGGG
1 TCAAACCGGTCAAACCGGT
*
1927 TCAAACCGATCAGAACCGGT
1 TCAAACCGGTCA-AACCGGT
*
1947 TGAAAACCGGTCAAACCGGT
1 T-CAAACCGGTCAAACCGGT
1967 T
1 T
1968 TCCAGCCCTC
Statistics
Matches: 50, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
19 18 0.36
20 23 0.46
21 9 0.18
ACGTcount: A:0.30, C:0.29, G:0.25, T:0.16
Consensus pattern (19 bp):
TCAAACCGGTCAAACCGGT
Found at i:3196 original size:22 final size:22
Alignment explanation
Indices: 3171--3241 Score: 76
Period size: 22 Copynumber: 3.3 Consensus size: 22
3161 AAAATATTAT
3171 TTAATATTTTTATTAAAAAATA
1 TTAATATTTTTATTAAAAAATA
** *
3193 TTAATATTGATATTACCTAAAATA
1 TTAATATTTTTATTA--AAAAATA
3217 TT-AT-TTTTTA-TAAAAAATA
1 TTAATATTTTTATTAAAAAATA
3236 TTAATA
1 TTAATA
3242 AAAATATTCA
Statistics
Matches: 39, Mismatches: 6, Indels: 9
0.72 0.11 0.17
Matches are distributed among these distances:
19 8 0.21
20 2 0.05
21 2 0.05
22 17 0.44
23 2 0.05
24 8 0.21
ACGTcount: A:0.48, C:0.03, G:0.01, T:0.48
Consensus pattern (22 bp):
TTAATATTTTTATTAAAAAATA
Found at i:3291 original size:20 final size:20
Alignment explanation
Indices: 3239--3301 Score: 65
Period size: 20 Copynumber: 3.0 Consensus size: 20
3229 AAAAATATTA
*
3239 ATAAAAATATTCA-TTTTAGAT
1 ATAAAAATAAT-ATTTTTA-AT
*
3260 ACTAAAATTAATATTTTTAAT
1 A-TAAAAATAATATTTTTAAT
*
3281 ATAAAAATAATATTTTAAAT
1 ATAAAAATAATATTTTTAAT
3301 A
1 A
3302 ATACTCTATC
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
20 18 0.50
21 5 0.14
22 13 0.36
ACGTcount: A:0.52, C:0.03, G:0.02, T:0.43
Consensus pattern (20 bp):
ATAAAAATAATATTTTTAAT
Found at i:3298 original size:19 final size:19
Alignment explanation
Indices: 3239--3302 Score: 67
Period size: 22 Copynumber: 3.2 Consensus size: 19
3229 AAAAATATTA
*
3239 ATAAAAATATTCATTTTAGAT
1 ATAAAAATAAT-ATTTTA-AT
*
3260 ACTAAAATTAATATTTTTAAT
1 A-TAAAAATAATA-TTTTAAT
3281 ATAAAAATAATATTTTAA-
1 ATAAAAATAATATTTTAAT
3299 ATAA
1 ATAA
3303 TACTCTATCA
Statistics
Matches: 38, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
18 4 0.11
19 6 0.16
20 10 0.26
21 5 0.13
22 13 0.34
ACGTcount: A:0.53, C:0.03, G:0.02, T:0.42
Consensus pattern (19 bp):
ATAAAAATAATATTTTAAT
Found at i:38838 original size:18 final size:18
Alignment explanation
Indices: 38807--38858 Score: 68
Period size: 18 Copynumber: 2.8 Consensus size: 18
38797 ATTCAAAATT
38807 AAATAATTGATAAAATATAA
1 AAATAATT--TAAAATATAA
* *
38827 AAATATTTTAAATTATAA
1 AAATAATTTAAAATATAA
38845 AAATAATTTAAAAT
1 AAATAATTTAAAAT
38859 TTCTAAAGAA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
18 21 0.75
20 7 0.25
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.37
Consensus pattern (18 bp):
AAATAATTTAAAATATAA
Found at i:39288 original size:2 final size:2
Alignment explanation
Indices: 39245--39272 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
39235 TATCCGCCAT
39245 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
39273 GTATTCAACT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:39852 original size:9 final size:9
Alignment explanation
Indices: 39825--39857 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
39815 AAAATTTTAA
39825 TTTTTATAT
1 TTTTTATAT
*
39834 ATTTTA-AT
1 TTTTTATAT
39842 TTTTTATAT
1 TTTTTATAT
39851 TTTTTAT
1 TTTTTAT
39858 TGAAAATTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
8 7 0.33
9 14 0.67
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (9 bp):
TTTTTATAT
Found at i:39856 original size:17 final size:16
Alignment explanation
Indices: 39818--39853 Score: 65
Period size: 16 Copynumber: 2.3 Consensus size: 16
39808 TGTCTTTAAA
39818 ATTTTAATTTTTATAT
1 ATTTTAATTTTTATAT
39834 ATTTTAATTTTT-TAT
1 ATTTTAATTTTTATAT
39849 ATTTT
1 ATTTT
39854 TTATTGAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 8 0.40
16 12 0.60
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (16 bp):
ATTTTAATTTTTATAT
Found at i:40214 original size:3 final size:3
Alignment explanation
Indices: 40194--40235 Score: 57
Period size: 3 Copynumber: 14.0 Consensus size: 3
40184 TTTGTTGAGG
* * *
40194 AGA AGG AGA AGG AGA AGA AGA AGA AGA AGA AAA AGA AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
40236 TCCTTTCTCT
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.64, C:0.00, G:0.36, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:41889 original size:2 final size:2
Alignment explanation
Indices: 41842--41870 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
41832 TGTTTTTTTA
41842 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
41871 AACACAGACA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:42943 original size:173 final size:175
Alignment explanation
Indices: 42527--42988 Score: 476
Period size: 179 Copynumber: 2.6 Consensus size: 175
42517 TTGTCGATTA
* * *
42527 TCAAGATTGAAGTTCGGTTTTTTGATCTC-TCTGTGTGAATCCTCATATAGCTTTGAATCACTTG
1 TCAAGATTAAAGTTCGG-TTTTTGATCTCAT-TGTGTGAATCCTCAGATA-CTTTGAATCTCTTG
* ** * * *
42591 GATATCAATCTGGTTTCTAGTATGAAATGTTTATGTTTAATAGTTATTTAGTTGACCATAAAGTA
63 GATATCAATCTGGTTTCTAATATGAAAAATATATGATTAATAG-T-TTTAG-TGAACATAAAGTA
42656 GCTCTTCAAAATGCGATTTTCATTTTCTTTAATCGACTCTTTGTGGTTGGTTT
125 GCTCTTCAAAATGCGA-TTTCATTTTCTTTAATC-ACTCTTTGTGGTTGGTTT
** * *
42709 TCGGGATGAAAGTTC-G-TTTTGATCTCATTGTGCGAATCCTCAGATACCTTTGAATCTCTTGGA
1 TCAAGATTAAAGTTCGGTTTTTGATCTCATTGTGTGAATCCTCAGATA-CTTTGAATCTCTTGGA
* * *
42772 TACCAATCTGGTTTCTAATATGAAACATATATGATTACTAGTTTTA-TGAACATAAAGTAGCTCT
65 TATCAATCTGGTTTCTAATATGAAAAATATATGATTAATAGTTTTAGTGAACATAAAGTAGCTCT
* ** *
42836 TCGAAATTTTG-TTTC-TGTTT-TTT-ATC-TTCTTTGTGGTTGGTTT
130 TC-AAAATGCGATTTCAT-TTTCTTTAATCACTCTTTGTGGTTGGTTT
* *
42879 TCAAGATTAAAGTCCGGTTTTTCGATCTCATTGTGTGAATCCTTAGATACATTTGAATCTCTTGG
1 TCAAGATTAAAGTTCGGTTTTT-GATCTCATTGTGTGAATCCTCAGATAC-TTTGAATCTCTTGG
* * * * *
42944 ACATCAATTTGG-TTCTTCATGTGAAAAATTATATGATTATTAGTT
64 ATATCAATCTGGTTTC-TAATATGAAAAA-TATATGATTAATAGTT
42989 GTTTAGTTGA
Statistics
Matches: 238, Mismatches: 33, Indels: 26
0.80 0.11 0.09
Matches are distributed among these distances:
170 27 0.11
171 1 0.00
172 11 0.05
173 60 0.25
174 22 0.09
175 19 0.08
176 5 0.02
177 4 0.02
178 1 0.00
179 75 0.32
180 1 0.00
181 1 0.00
182 11 0.05
ACGTcount: A:0.25, C:0.14, G:0.17, T:0.44
Consensus pattern (175 bp):
TCAAGATTAAAGTTCGGTTTTTGATCTCATTGTGTGAATCCTCAGATACTTTGAATCTCTTGGAT
ATCAATCTGGTTTCTAATATGAAAAATATATGATTAATAGTTTTAGTGAACATAAAGTAGCTCTT
CAAAATGCGATTTCATTTTCTTTAATCACTCTTTGTGGTTGGTTT
Found at i:45137 original size:17 final size:17
Alignment explanation
Indices: 45117--45149 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
45107 TTCTTAGTTA
*
45117 TTTAAAATTAAAAATAT
1 TTTAAAATAAAAAATAT
45134 TTTAAAATAAAAAATA
1 TTTAAAATAAAAAATA
45150 GAACTTGAAG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (17 bp):
TTTAAAATAAAAAATAT
Found at i:50872 original size:105 final size:105
Alignment explanation
Indices: 50688--50886 Score: 274
Period size: 105 Copynumber: 1.9 Consensus size: 105
50678 TTGTTTCGAA
* ** * * * *
50688 TCAATGCCTCGCTTTATCATTTTGTCAATAATATCTTCAGCTTTAGAGACCATTCCTTCCTTGCA
1 TCAATGCCTCGCTTTACCATTGCGTCAACAATATCTTCAGCTTCAGAAACCATACCTTCCTTGCA
50753 ATGTGCATCAATCAATACATTATACGTGATAACATCAGGC
66 ATGTGCATCAATCAATACATTATACGTGATAACATCAGGC
* *
50793 TCAATGCCTTGCTTTACCATTGCGTCAACAATATGC-TCAGCTTCAGAAACCATACCTTGCTTGC
1 TCAATGCCTCGCTTTACCATTGCGTCAACAATAT-CTTCAGCTTCAGAAACCATACCTTCCTTGC
* * *
50857 AATGTGCATCGATCAATATATTATATGTGA
65 AATGTGCATCAATCAATACATTATACGTGA
50887 AAATATTGAG
Statistics
Matches: 81, Mismatches: 12, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
105 80 0.99
106 1 0.01
ACGTcount: A:0.29, C:0.24, G:0.14, T:0.34
Consensus pattern (105 bp):
TCAATGCCTCGCTTTACCATTGCGTCAACAATATCTTCAGCTTCAGAAACCATACCTTCCTTGCA
ATGTGCATCAATCAATACATTATACGTGATAACATCAGGC
Found at i:55716 original size:105 final size:105
Alignment explanation
Indices: 55576--55767 Score: 242
Period size: 105 Copynumber: 1.8 Consensus size: 105
55566 TAGGTAAAGG
* *** * * * * * *
55576 CATCAGGCTCAATGCCTCGCTTTATCATTTTGTCAATAATAT-CTTCAGCTTTAGAGATCATTCC
1 CATCAGGCTCAATGCCTCGCTTTACCATAGCGTCAACAATATGC-TCACCTTCAGAAACCATACC
55640 TTCCTTGCAATGTGCATCAATCAGAGCAGTATAAGTGATAA
65 TTCCTTGCAATGTGCATCAATCAGAGCAGTATAAGTGATAA
* *
55681 CATCAGGCTCAATGCCTTGCTTTACCATAGCGTCAACAATATGCTCACCTTCGGAAACCATACCT
1 CATCAGGCTCAATGCCTCGCTTTACCATAGCGTCAACAATATGCTCACCTTCAGAAACCATACCT
* *
55746 TGCTTGCAATGTGCATCGATCA
66 TCCTTGCAATGTGCATCAATCA
55768 ATATATTATA
Statistics
Matches: 72, Mismatches: 14, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
105 71 0.99
106 1 0.01
ACGTcount: A:0.28, C:0.26, G:0.16, T:0.31
Consensus pattern (105 bp):
CATCAGGCTCAATGCCTCGCTTTACCATAGCGTCAACAATATGCTCACCTTCAGAAACCATACCT
TCCTTGCAATGTGCATCAATCAGAGCAGTATAAGTGATAA
Found at i:58227 original size:104 final size:105
Alignment explanation
Indices: 58041--58233 Score: 230
Period size: 104 Copynumber: 1.8 Consensus size: 105
58031 TACGTGATAA
* * *
58041 CATCAGGCTCAATGCCTTGCTTTATCATTGTGTCAATAAAATCTTCAGCTTCAGAGATCATCCCT
1 CATCAGGCTCAATGCCTTGCTTCATCATTGTGTCAACAAAATCTTCAGCTTCAGAAATCATCCCT
**
58106 TCCTTGCAAAGTGCATCGA-CAATGTATTATTTGTGACAT
66 TCCTTGCAAAGAACATCGATCAATGTATTATTTGTGACAT
* *** * *
58145 CATCAGGCTCAATGCCTTGCTTCCTCATTGTGTCAACGGTATCTAT-TGCTTTAGAAATCAATCC
1 CATCAGGCTCAATGCCTTGCTTCATCATTGTGTCAACAAAATCT-TCAGCTTCAGAAATC-ATCC
**
58209 C-TCCTTGCACTGAACATCGATCAAT
64 CTTCCTTGCAAAGAACATCGATCAAT
58234 ATACTATACG
Statistics
Matches: 73, Mismatches: 13, Indels: 5
0.80 0.14 0.05
Matches are distributed among these distances:
104 63 0.86
105 10 0.14
ACGTcount: A:0.26, C:0.25, G:0.15, T:0.34
Consensus pattern (105 bp):
CATCAGGCTCAATGCCTTGCTTCATCATTGTGTCAACAAAATCTTCAGCTTCAGAAATCATCCCT
TCCTTGCAAAGAACATCGATCAATGTATTATTTGTGACAT
Found at i:68417 original size:21 final size:20
Alignment explanation
Indices: 68389--68450 Score: 63
Period size: 20 Copynumber: 3.0 Consensus size: 20
68379 AGCAGAACCC
*
68389 CAGGGGGGTATCGATTCCC-
1 CAGGGGGGGATCGATTCCCT
* *
68408 CTGTGGGGGGAATCGGTTCCCT
1 CAG-GGGGGG-ATCGATTCCCT
*
68430 CAGGGGGGGATCGATTTCCT
1 CAGGGGGGGATCGATTCCCT
68450 C
1 C
68451 TGCACCAAAA
Statistics
Matches: 34, Mismatches: 6, Indels: 5
0.76 0.13 0.11
Matches are distributed among these distances:
19 2 0.06
20 15 0.44
21 15 0.44
22 2 0.06
ACGTcount: A:0.13, C:0.24, G:0.39, T:0.24
Consensus pattern (20 bp):
CAGGGGGGGATCGATTCCCT
Found at i:68429 original size:20 final size:21
Alignment explanation
Indices: 68391--68445 Score: 60
Period size: 21 Copynumber: 2.7 Consensus size: 21
68381 CAGAACCCCA
*
68391 GGGGGGTATCGATTCCCCTGT
1 GGGGGGAATCGATTCCCCTGT
* *
68412 GGGGGGAATCGGTTCCCTCAG-
1 GGGGGGAATCGATTCCC-CTGT
68433 GGGGGG-ATCGATT
1 GGGGGGAATCGATT
68446 TCCTCTGCAC
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
20 6 0.21
21 21 0.72
22 2 0.07
ACGTcount: A:0.13, C:0.20, G:0.44, T:0.24
Consensus pattern (21 bp):
GGGGGGAATCGATTCCCCTGT
Found at i:72527 original size:117 final size:117
Alignment explanation
Indices: 72307--72528 Score: 261
Period size: 117 Copynumber: 1.9 Consensus size: 117
72297 CTTTCAAATC
* *
72307 GAAATTTTCTTTTTCAATACTTTCAAATTTCATTTTTGAAAGCTCTAAATCCTTCTTCAAGATTT
1 GAAAATTTCTTTTTCAATACTTTCAAATTTCATTTTTGAAAGCTCTAAATCCTTCTTCAACATTT
* *
72372 CACTTTGATTTTCAAAATCCATTTTCGTTTCTAGAAGAAGTTTGTTTAATTT
66 CACTTTGATTTTCAAAATCCATTTTAGTTTCTAAAAGAAGTTTGTTTAATTT
* * * * *
72424 GAAAATTTCTTTTTCAA-AGTTTTCAGATTTTATTTTTGAAAGCTCTAACTCATT-TCTCAACAT
1 GAAAATTTCTTTTTCAATA-CTTTCAAATTTCATTTTTGAAAGCTCTAAATCCTTCT-TCAACAT
* * * * **
72487 TTTATTTTGATTTTCCAAGTCTGTTTTAGCTTTC-AAAAGAAG
64 TTCACTTTGATTTTCAAAATCCATTTTAG-TTTCTAAAAGAAG
72529 ATCATTTTTA
Statistics
Matches: 87, Mismatches: 15, Indels: 6
0.81 0.14 0.06
Matches are distributed among these distances:
116 2 0.02
117 81 0.93
118 4 0.05
ACGTcount: A:0.28, C:0.15, G:0.09, T:0.47
Consensus pattern (117 bp):
GAAAATTTCTTTTTCAATACTTTCAAATTTCATTTTTGAAAGCTCTAAATCCTTCTTCAACATTT
CACTTTGATTTTCAAAATCCATTTTAGTTTCTAAAAGAAGTTTGTTTAATTT
Found at i:74355 original size:69 final size:68
Alignment explanation
Indices: 74231--74361 Score: 176
Period size: 69 Copynumber: 1.9 Consensus size: 68
74221 TCTAATAATT
* * *
74231 TGAATAAACAATTCAAAATGGTCTAATATAAATTAATCAAAATTTAAAATAATTT-AACTTAATG
1 TGAATAAACAATTCAAAATGCTCTAATACAAATTAATCAAAATTTAAAACAATTTAAACTTAATG
74295 ACC
66 ACC
* *
74298 TGAATAAACAAATTCAAAATGACT-TGAATACGAATTAATCAAAATTTAAAACGATTTAAACTTA
1 TGAATAAAC-AATTCAAAATG-CTCT-AATACAAATTAATCAAAATTTAAAACAATTTAAACTTA
74362 TGGTAACTCG
Statistics
Matches: 55, Mismatches: 5, Indels: 5
0.85 0.08 0.08
Matches are distributed among these distances:
67 9 0.16
68 12 0.22
69 28 0.51
70 6 0.11
ACGTcount: A:0.51, C:0.11, G:0.07, T:0.31
Consensus pattern (68 bp):
TGAATAAACAATTCAAAATGCTCTAATACAAATTAATCAAAATTTAAAACAATTTAAACTTAATG
ACC
Found at i:74819 original size:24 final size:23
Alignment explanation
Indices: 74792--74877 Score: 77
Period size: 24 Copynumber: 3.5 Consensus size: 23
74782 AAATTGAACG
74792 ACCGGTTTTTTTACCGGATTAAAA
1 ACCGGTTTTTTTACCGGA-TAAAA
74816 ACCGGTTTTTTTTCAAACCGGATAAAAA
1 ACCGG-TTTTTTT---ACCGGAT-AAAA
*
74844 ACCAG-TTTTTTATCCGGA-AAAA
1 ACCGGTTTTTTTA-CCGGATAAAA
74866 ATCCGGTTTTTT
1 A-CCGGTTTTTT
74878 AAAAAAACTG
Statistics
Matches: 52, Mismatches: 2, Indels: 16
0.74 0.03 0.23
Matches are distributed among these distances:
22 5 0.10
23 4 0.08
24 15 0.29
25 7 0.13
26 6 0.12
27 1 0.02
28 14 0.27
ACGTcount: A:0.30, C:0.17, G:0.15, T:0.37
Consensus pattern (23 bp):
ACCGGTTTTTTTACCGGATAAAA
Found at i:81412 original size:60 final size:60
Alignment explanation
Indices: 81299--81451 Score: 152
Period size: 60 Copynumber: 2.5 Consensus size: 60
81289 GTATAATTCT
* * **
81299 GGATGAAATT-AGAATGTTCAAAAAGTTTGGGAACCAGTTTAGAATGAATGTCATAGTTTGG
1 GGATGAAATTGA-AATGTTC-AAAAGTTTGGGAACCAGTTTAGAAAGAATGTCATAGATTAA
*
81360 GGATGAAATTGAAATGTTCAAAAGTTTGAGG-A-CTGATTTAGAAAG-ATAGTCATAGATTAA
1 GGATGAAATTGAAATGTTCAAAAGTTTG-GGAACCAG-TTTAGAAAGAAT-GTCATAGATTAA
* * *
81420 GGATGAAATTGGAATATTTAAAAGTTTAGGGA
1 GGATGAAATTGAAATGTTCAAAAGTTT-GGGA
81452 CCAACTTAAA
Statistics
Matches: 78, Mismatches: 8, Indels: 12
0.80 0.08 0.12
Matches are distributed among these distances:
59 4 0.05
60 53 0.68
61 20 0.26
62 1 0.01
ACGTcount: A:0.39, C:0.05, G:0.25, T:0.31
Consensus pattern (60 bp):
GGATGAAATTGAAATGTTCAAAAGTTTGGGAACCAGTTTAGAAAGAATGTCATAGATTAA
Found at i:97003 original size:58 final size:58
Alignment explanation
Indices: 96910--97022 Score: 154
Period size: 58 Copynumber: 1.9 Consensus size: 58
96900 AATACTTCGC
* ** *
96910 TTAGGATGAAAACCCGAGAGGGCGTCCTAAGTTGAAAAAAAAAAAAAAAAAAAAACTT
1 TTAGGATGAAAACCCGAAAGGGCACCCTAAATTGAAAAAAAAAAAAAAAAAAAAACTT
* * * *
96968 TTAGGGTGAAAACCCGAAAGGGCACCCTAAATTGAAAAAGAAAAAAGAGAAAAAA
1 TTAGGATGAAAACCCGAAAGGGCACCCTAAATTGAAAAAAAAAAAAAAAAAAAAA
97023 GAAGAGAAAA
Statistics
Matches: 47, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
58 47 1.00
ACGTcount: A:0.54, C:0.12, G:0.20, T:0.13
Consensus pattern (58 bp):
TTAGGATGAAAACCCGAAAGGGCACCCTAAATTGAAAAAAAAAAAAAAAAAAAAACTT
Found at i:98236 original size:107 final size:107
Alignment explanation
Indices: 98015--98511 Score: 666
Period size: 107 Copynumber: 4.7 Consensus size: 107
98005 GTCATCCGCG
* * * * *
98015 ATTTCAACTCCACGACGGAGGATATCGTGGCACTCGAGACAACACAAGTTCAACTTCACAACGAA
1 ATTTCAACTTCACAACGAAGGATAT--TGG-ACTCCAGACAACACAAGTTCAACTTCACGACGAA
* * *
98080 GGGACGGCTGGTTGTC-AACAAACAACTTCTCAATTTCAGAGCCA
63 GGGACCGCTGATTGTCAAACAAACAACTTCTCAATTTCAGGGCCA
**
98124 ATTTCAACTTCACAACGAAGGATATTGGACT-CAGGACAGTACAAGTTCAACTTCACGACGAAGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCA-GACAACACAAGTTCAACTTCACGACGAAGG
* *
98188 GACCGCTGACTGTCAAACAAATAACTTCTCAATTTCAGGGCCA
65 GACCGCTGATTGTCAAACAAACAACTTCTCAATTTCAGGGCCA
*
98231 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACACAAGTTCAACTTCACGACGAAGGG
* *
98296 ACCGCTGGTTGTC--A-ATA-AA-----CAATTTC----CCA
66 ACCGCTGATTGTCAAACAAACAACTTCTCAATTTCAGGGCCA
**
98325 ATTTCAACTTCACAACGAAGGATATTGGACT-CAGGACAGTACAAGTTCAACTTCACGACGAAGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCA-GACAACACAAGTTCAACTTCACGACGAAGG
*
98389 GACCGCTGACTGTCAAACAAACAACTTCTCAATTTCAGGGCCA
65 GACCGCTGATTGTCAAACAAACAACTTCTCAATTTCAGGGCCA
*
98432 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACACAAGTTCAACTTCACGACGAAGGG
98497 ACCGCTGATTGTCAA
66 ACCGCTGATTGTCAA
98512 CGAACAATAC
Statistics
Matches: 342, Mismatches: 28, Indels: 38
0.84 0.07 0.09
Matches are distributed among these distances:
93 2 0.01
94 73 0.21
96 1 0.00
97 2 0.01
98 9 0.03
103 9 0.03
104 2 0.01
105 2 0.01
106 41 0.12
107 175 0.51
108 4 0.01
109 22 0.06
ACGTcount: A:0.34, C:0.25, G:0.19, T:0.22
Consensus pattern (107 bp):
ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACACAAGTTCAACTTCACGACGAAGGG
ACCGCTGATTGTCAAACAAACAACTTCTCAATTTCAGGGCCA
Found at i:98466 original size:201 final size:204
Alignment explanation
Indices: 98015--98511 Score: 775
Period size: 201 Copynumber: 2.4 Consensus size: 204
98005 GTCATCCGCG
* * * * * *
98015 ATTTCAACTCCACGACGGAGGATATCGTGGCACTCGAGACAACACAAGTTCAACTTCACAACGAA
1 ATTTCAACTTCACAACGAAGGATAT--TGG-ACTCCAGACAACGCAAGTTCAACTTCACGACGAA
*
98080 GGGACGGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGG
63 GGGACCGCTGGTTGTC-A-AAACAA----TCAATTTC--A-CCAATTTCAACTTCACAACGAAGG
*
98145 ATATTGGACTCAGGACAGTACAAGTTCAACTTCACGACGAAGGGACCGCTGACTGTCAAACAAAT
119 ATATTGGACTCAGGACAGTACAAGTTCAACTTCACGACGAAGGGACCGCTGACTGTCAAACAAAC
98210 AACTTCTCAATTTCAGGGCCA
184 AACTTCTCAATTTCAGGGCCA
98231 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
*
98296 ACCGCTGGTTGTCAATA-AA-CAATTTC-CCAATTTCAACTTCACAACGAAGGATATTGGACTCA
66 ACCGCTGGTTGTCAAAACAATCAATTTCACCAATTTCAACTTCACAACGAAGGATATTGGACTCA
98358 GGACAGTACAAGTTCAACTTCACGACGAAGGGACCGCTGACTGTCAAACAAACAACTTCTCAATT
131 GGACAGTACAAGTTCAACTTCACGACGAAGGGACCGCTGACTGTCAAACAAACAACTTCTCAATT
98423 TCAGGGCCA
196 TCAGGGCCA
98432 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
*
98497 ACCGCTGATTGTCAA
66 ACCGCTGGTTGTCAA
98512 CGAACAATAC
Statistics
Matches: 271, Mismatches: 10, Indels: 15
0.92 0.03 0.05
Matches are distributed among these distances:
201 188 0.69
205 7 0.03
210 2 0.01
211 2 0.01
212 1 0.00
213 46 0.17
214 3 0.01
216 22 0.08
ACGTcount: A:0.34, C:0.25, G:0.19, T:0.22
Consensus pattern (204 bp):
ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
ACCGCTGGTTGTCAAAACAATCAATTTCACCAATTTCAACTTCACAACGAAGGATATTGGACTCA
GGACAGTACAAGTTCAACTTCACGACGAAGGGACCGCTGACTGTCAAACAAACAACTTCTCAATT
TCAGGGCCA
Found at i:114006 original size:52 final size:53
Alignment explanation
Indices: 113945--114050 Score: 187
Period size: 52 Copynumber: 2.0 Consensus size: 53
113935 TAAAATGTAA
113945 AGTTTAGGGACTAAATTAAAAAAGAGAACATTTTTAGT-AAAAAATAGGAATT
1 AGTTTAGGGACTAAATTAAAAAAGAGAACATTTTTAGTAAAAAAATAGGAATT
*
113997 AGTTTAGGGACTAAATTAAAAAAGAGAGCATTTTTAGTAAAAAAAATAGGAATT
1 AGTTTAGGGACTAAATTAAAAAAGAGAACATTTTTAGT-AAAAAAATAGGAATT
114051 GAAGTTACAT
Statistics
Matches: 51, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
52 37 0.73
54 14 0.27
ACGTcount: A:0.50, C:0.04, G:0.18, T:0.28
Consensus pattern (53 bp):
AGTTTAGGGACTAAATTAAAAAAGAGAACATTTTTAGTAAAAAAATAGGAATT
Found at i:120364 original size:19 final size:20
Alignment explanation
Indices: 120329--120378 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
120319 TTATATAAAA
120329 ATATAATAAATTATTAAA-AT
1 ATATAAT-AATTATTAAATAT
*
120349 TTATCAATAATT-TTAAATAT
1 ATAT-AATAATTATTAAATAT
120369 ATATAATAAT
1 ATATAATAAT
120379 AAAATATCGA
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
19 11 0.42
20 12 0.46
21 3 0.12
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (20 bp):
ATATAATAATTATTAAATAT
Found at i:121935 original size:2 final size:2
Alignment explanation
Indices: 121928--121953 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
121918 TTCATGAAAC
121928 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
121954 GTCATTATGC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:124353 original size:10 final size:10
Alignment explanation
Indices: 124338--124444 Score: 65
Period size: 10 Copynumber: 11.4 Consensus size: 10
124328 GAGGAGGAGG
124338 AGGAAAGAGA
1 AGGAAAGAGA
124348 AGGAAA-AGA
1 AGGAAAGAGA
*
124357 A--AAGGAGA
1 AGGAAAGAGA
124365 AGGAAAGAGA
1 AGGAAAGAGA
*
124375 AGGAGAGAGA
1 AGGAAAGAGA
124385 A-G-AAGAG-
1 AGGAAAGAGA
124392 AGGAAA-AGGA
1 AGGAAAGA-GA
124402 A-G-AAGAGGAA
1 AGGAAAGA-G-A
124412 AGAGAAAGA-A
1 AG-GAAAGAGA
*
124422 AGGAAAG-CA
1 AGGAAAGAGA
*
124431 AGGAAAAAGA
1 AGGAAAGAGA
124441 AGGA
1 AGGA
124445 CACGTTAGAG
Statistics
Matches: 77, Mismatches: 6, Indels: 28
0.69 0.05 0.25
Matches are distributed among these distances:
7 3 0.04
8 12 0.16
9 24 0.31
10 33 0.43
12 1 0.01
13 4 0.05
ACGTcount: A:0.61, C:0.01, G:0.38, T:0.00
Consensus pattern (10 bp):
AGGAAAGAGA
Found at i:124395 original size:27 final size:27
Alignment explanation
Indices: 124337--124428 Score: 66
Period size: 27 Copynumber: 3.3 Consensus size: 27
124327 GGAGGAGGAG
*
124337 GAGGAAAGAGAAG-GA-AAAGAAAAGGA
1 GAGGAAAGAGAAGAGAGAGAGAAAA-GA
124363 GAAGGAAAGAGAAG-GAGAGAGAAGAAGA
1 G-AGGAAAGAGAAGAGAGAGAGAA-AAGA
*
124391 GAGGAAA-AGGAAGAAGAGGAAAGAGAAAGA
1 GAGGAAAGA-GAAG-AGA-GAGAGA-AAAGA
*
124421 AAGGAAAG
1 GAGGAAAG
124429 CAAGGAAAAA
Statistics
Matches: 54, Mismatches: 3, Indels: 13
0.77 0.04 0.19
Matches are distributed among these distances:
26 2 0.04
27 24 0.44
28 8 0.15
29 4 0.07
30 15 0.28
31 1 0.02
ACGTcount: A:0.60, C:0.00, G:0.40, T:0.00
Consensus pattern (27 bp):
GAGGAAAGAGAAGAGAGAGAGAAAAGA
Found at i:124410 original size:15 final size:16
Alignment explanation
Indices: 124292--124428 Score: 68
Period size: 15 Copynumber: 9.2 Consensus size: 16
124282 GGAGGAGGAA
*
124292 AAAGAGGAAG-AGAAG
1 AAAGAGGAAGAAGAGG
* *
124307 AGAGAGAGAAGAAAAGG
1 AAAGAG-GAAGAAGAGG
* *
124324 AAAGGAGGAGGAGGAGG
1 AAA-GAGGAAGAAGAGG
*
124341 AAAGA-GAAGGAA-AAG
1 AAAGAGGAA-GAAGAGG
124356 AAA-AGG-AG-A-AGG
1 AAAGAGGAAGAAGAGG
124368 AAAGA-GAAG--GA-G
1 AAAGAGGAAGAAGAGG
* *
124380 AGAGAAGAAG-AGAGG
1 AAAGAGGAAGAAGAGG
124395 AAA-AGGAAGAAGAGG
1 AAAGAGGAAGAAGAGG
*
124410 AAAGAGAAAGAA-AGG
1 AAAGAGGAAGAAGAGG
124425 AAAG
1 AAAG
124429 CAAGGAAAAA
Statistics
Matches: 94, Mismatches: 15, Indels: 26
0.70 0.11 0.19
Matches are distributed among these distances:
12 12 0.13
13 9 0.10
14 9 0.10
15 31 0.33
16 15 0.16
17 15 0.16
18 3 0.03
ACGTcount: A:0.58, C:0.00, G:0.42, T:0.00
Consensus pattern (16 bp):
AAAGAGGAAGAAGAGG
Found at i:128716 original size:45 final size:45
Alignment explanation
Indices: 128652--129133 Score: 315
Period size: 45 Copynumber: 11.3 Consensus size: 45
128642 ATATGGCGTT
* *
128652 GGACAATCAGGAGAA-GGTATTGGGTATGGCATTGGACAAGCAGGG
1 GGACAATCAGGA-AATGGTATTGGGTATGGCATTGGACAATCATGG
*
128697 GGACAATTAGGAGAA-GGTATTGGG--T---A-TGG-CAA-C----
1 GGACAATCAGGA-AATGGTATTGGGTATGGCATTGGACAATCATGG
* * * *
128730 GGACAATTAGGAAATGGTATTGGGTACGACATTGGGCAATCATGG
1 GGACAATCAGGAAATGGTATTGGGTATGGCATTGGACAATCATGG
* * *
128775 GGACAGTCAGGAAATGGTATTGGGTACGGCATTGGACAATCAGGG
1 GGACAATCAGGAAATGGTATTGGGTATGGCATTGGACAATCATGG
* * * * ** *
128820 GGTCAGTCAGGAAATAGTATTGGATATGGTGTTGGGCAATCATGG
1 GGACAATCAGGAAATGGTATTGGGTATGGCATTGGACAATCATGG
* **
128865 GGACAATCAGGAAATGGTATTGGATATGGTGTTGGACAATCATGG
1 GGACAATCAGGAAATGGTATTGGGTATGGCATTGGACAATCATGG
* * ** *
128910 GGACAGTCAGGAAATGGTATTGGGTACGGTGTTGGGCAATCA-GTG
1 GGACAATCAGGAAATGGTATTGGGTATGGCATTGGACAATCATG-G
128955 GG---ATCAGG-AA----A-T-GG--T-G--TTGGACAATCATGG
1 GGACAATCAGGAAATGGTATTGGGTATGGCATTGGACAATCATGG
* * * * ** * *
128985 GGACAGTTAAGAAATGGTATTGGGTACGGTGTTGGGCAATCAGGG
1 GGACAATCAGGAAATGGTATTGGGTATGGCATTGGACAATCATGG
* * **
129030 GGACAGTCAGGAAATGGTATTGGATATGGTGTTGGACAATCATGG
1 GGACAATCAGGAAATGGTATTGGGTATGGCATTGGACAATCATGG
* * * **
129075 GGACAGTTAGGAAATGGTATTGGGTACGGTGTTGGACAATCA-GG
1 GGACAATCAGGAAATGGTATTGGGTATGGCATTGGACAATCATGG
* *
129119 AGGTCAATCAAGAAA
1 -GGACAATCAGGAAA
129134 CAATGTTGGA
Statistics
Matches: 361, Mismatches: 45, Indels: 62
0.77 0.10 0.13
Matches are distributed among these distances:
30 13 0.04
31 1 0.00
32 3 0.01
33 24 0.07
34 2 0.01
35 2 0.01
36 1 0.00
37 2 0.01
38 5 0.01
39 7 0.02
40 6 0.02
41 3 0.01
42 5 0.01
43 2 0.01
44 3 0.01
45 282 0.78
ACGTcount: A:0.30, C:0.10, G:0.37, T:0.24
Consensus pattern (45 bp):
GGACAATCAGGAAATGGTATTGGGTATGGCATTGGACAATCATGG
Found at i:128750 original size:78 final size:78
Alignment explanation
Indices: 128652--128818 Score: 203
Period size: 78 Copynumber: 2.1 Consensus size: 78
128642 ATATGGCGTT
* * *
128652 GGACAATCAGGAGAAGGTATTGGGTATGGCATTGGACAAGCAGGGGGACAATTAGGAGAA-GGTA
1 GGACAATCAGGAGAAGGTATTGGGTACGACATTGGACAAGCAGGGGGACAATCAGGA-AATGGTA
*
128716 TTGGGTATGGCAAC
65 TTGGGTACGGCAAC
* * * * *
128730 GGACAATTAGGA-AATGGTATTGGGTACGACATTGGGCAATCATGGGGACAGTCAGGAAATGGTA
1 GGACAATCAGGAGAA-GGTATTGGGTACGACATTGGACAAGCAGGGGGACAATCAGGAAATGGTA
**
128794 TTGGGTACGGCATT
65 TTGGGTACGGCAAC
128808 GGACAATCAGG
1 GGACAATCAGG
128819 GGGTCAGTCA
Statistics
Matches: 75, Mismatches: 12, Indels: 4
0.82 0.13 0.04
Matches are distributed among these distances:
77 4 0.05
78 71 0.95
ACGTcount: A:0.31, C:0.11, G:0.37, T:0.21
Consensus pattern (78 bp):
GGACAATCAGGAGAAGGTATTGGGTACGACATTGGACAAGCAGGGGGACAATCAGGAAATGGTAT
TGGGTACGGCAAC
Found at i:128999 original size:120 final size:119
Alignment explanation
Indices: 128845--129075 Score: 354
Period size: 120 Copynumber: 1.9 Consensus size: 119
128835 AGTATTGGAT
* * * *
128845 ATGGTGTTGGGCAATCATGGGGACAATCAGGAAATGGTATTGGATATGGTGTTGGACAATCATGG
1 ATGGTGTTGGACAATCATGGGGACAATCAAGAAATGGTATTGGATACGGTGTTGGACAATCAGGG
* *
128910 GGACAGTCAGGAAATGGTATTGGGTACGGTGTTGGGCAATCAGTGGGATCAGGAA
66 GGACAGTCAGGAAATGGTATTGGATACGGTGTTGGACAATCA-TGGGATCAGGAA
* * * *
128965 ATGGTGTTGGACAATCATGGGGACAGTTAAGAAATGGTATTGGGTACGGTGTTGGGCAATCAGGG
1 ATGGTGTTGGACAATCATGGGGACAATCAAGAAATGGTATTGGATACGGTGTTGGACAATCAGGG
*
129030 GGACAGTCAGGAAATGGTATTGGATATGGTGTTGGACAATCATGGG
66 GGACAGTCAGGAAATGGTATTGGATACGGTGTTGGACAATCATGGG
129076 GACAGTTAGG
Statistics
Matches: 100, Mismatches: 11, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
119 4 0.04
120 96 0.96
ACGTcount: A:0.27, C:0.10, G:0.38, T:0.26
Consensus pattern (119 bp):
ATGGTGTTGGACAATCATGGGGACAATCAAGAAATGGTATTGGATACGGTGTTGGACAATCAGGG
GGACAGTCAGGAAATGGTATTGGATACGGTGTTGGACAATCATGGGATCAGGAA
Found at i:129018 original size:165 final size:165
Alignment explanation
Indices: 128806--129117 Score: 525
Period size: 165 Copynumber: 1.9 Consensus size: 165
128796 GGGTACGGCA
* * * *
128806 TTGGACAATCAGGGGGTCAGTCAGGAAATAGTATTGGATATGGTGTTGGGCAATCATGGGGACAA
1 TTGGACAATCAGGGGGACAGTCAAGAAATAGTATTGGATACGGTGTTGGGCAATCAGGGGGACAA
128871 TCAGGAAATGGTATTGGATATGGTGTTGGACAATCATGGGGACAGTCAGGAAATGGTATTGGGTA
66 TCAGGAAATGGTATTGGATATGGTGTTGGACAATCATGGGGACAGTCAGGAAATGGTATTGGGTA
*
128936 CGGTGTTGGGCAATCAGTGGGATCAGGAAATGGTG
131 CGGTGTTGGACAATCAGTGGGATCAGGAAATGGTG
* * * * *
128971 TTGGACAATCATGGGGACAGTTAAGAAATGGTATTGGGTACGGTGTTGGGCAATCAGGGGGACAG
1 TTGGACAATCAGGGGGACAGTCAAGAAATAGTATTGGATACGGTGTTGGGCAATCAGGGGGACAA
*
129036 TCAGGAAATGGTATTGGATATGGTGTTGGACAATCATGGGGACAGTTAGGAAATGGTATTGGGTA
66 TCAGGAAATGGTATTGGATATGGTGTTGGACAATCATGGGGACAGTCAGGAAATGGTATTGGGTA
129101 CGGTGTTGGACAATCAG
131 CGGTGTTGGACAATCAG
129118 GAGGTCAATC
Statistics
Matches: 136, Mismatches: 11, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
165 136 1.00
ACGTcount: A:0.28, C:0.10, G:0.37, T:0.26
Consensus pattern (165 bp):
TTGGACAATCAGGGGGACAGTCAAGAAATAGTATTGGATACGGTGTTGGGCAATCAGGGGGACAA
TCAGGAAATGGTATTGGATATGGTGTTGGACAATCATGGGGACAGTCAGGAAATGGTATTGGGTA
CGGTGTTGGACAATCAGTGGGATCAGGAAATGGTG
Found at i:129118 original size:90 final size:90
Alignment explanation
Indices: 128965--129155 Score: 292
Period size: 90 Copynumber: 2.1 Consensus size: 90
128955 GGATCAGGAA
* *
128965 ATGGTGTTGGACAATCATGGGGACAGTTAAGAAATGGTATTGGGTACGGTGTTGGGCAATCAGGG
1 ATGGTGTTGGACAATCATGGGGACAGTTAAGAAATGGTATTGGGTACGGTGTTGGACAATCAGGA
* * ***
129030 GGACAGTCAGGAAATGGTATTGGAT
66 GGACAATCAAGAAACAATATTGGAT
*
129055 ATGGTGTTGGACAATCATGGGGACAGTTAGGAAATGGTATTGGGTACGGTGTTGGACAATCAGGA
1 ATGGTGTTGGACAATCATGGGGACAGTTAAGAAATGGTATTGGGTACGGTGTTGGACAATCAGGA
* *
129120 GGTCAATCAAGAAACAATGTTGGAT
66 GGACAATCAAGAAACAATATTGGAT
129145 ATGGTGTTGGA
1 ATGGTGTTGGA
129156 ATTGGGTCAA
Statistics
Matches: 91, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
90 91 1.00
ACGTcount: A:0.29, C:0.09, G:0.36, T:0.26
Consensus pattern (90 bp):
ATGGTGTTGGACAATCATGGGGACAGTTAAGAAATGGTATTGGGTACGGTGTTGGACAATCAGGA
GGACAATCAAGAAACAATATTGGAT
Found at i:129151 original size:45 final size:45
Alignment explanation
Indices: 128965--129155 Score: 150
Period size: 45 Copynumber: 4.2 Consensus size: 45
128955 GGATCAGGAA
* * *** *
128965 ATGGTGTTGGACAATCATGGGGACAGTTAAGAAATGGTATTGGGT
1 ATGGTGTTGGACAATCATGGGGACAATCAAGAAACAATATTGGAT
* * * * * ***
129010 ACGGTGTTGGGCAATCAGGGGGACAGTCAGGAAATGGTATTGGAT
1 ATGGTGTTGGACAATCATGGGGACAATCAAGAAACAATATTGGAT
* * * *** *
129055 ATGGTGTTGGACAATCATGGGGACAGTTAGGAAATGGTATTGGGT
1 ATGGTGTTGGACAATCATGGGGACAATCAAGAAACAATATTGGAT
* * *
129100 ACGGTGTTGGACAATCA-GGAGGTCAATCAAGAAACAATGTTGGAT
1 ATGGTGTTGGACAATCATGG-GGACAATCAAGAAACAATATTGGAT
129145 ATGGTGTTGGA
1 ATGGTGTTGGA
129156 ATTGGGTCAA
Statistics
Matches: 123, Mismatches: 22, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
44 2 0.02
45 121 0.98
ACGTcount: A:0.29, C:0.09, G:0.36, T:0.26
Consensus pattern (45 bp):
ATGGTGTTGGACAATCATGGGGACAATCAAGAAACAATATTGGAT
Found at i:129153 original size:210 final size:210
Alignment explanation
Indices: 128761--129154 Score: 574
Period size: 210 Copynumber: 1.9 Consensus size: 210
128751 GGGTACGACA
* * *
128761 TTGGGCAATCATGGGGACAGTCAGGAAATGGTATTGGGTACGGCATTGGACAATCAGGGGGTCAG
1 TTGGACAATCATGGGGACAGTCAAGAAATGGTATTGGGTACGGCATTGGACAATCAGGGGGACAG
*
128826 TCAGGAAATAGTATTGGATATGGTGTTGGGCAATCATGGGGACAATCAGGAAATGGTATTGGATA
66 TCAGGAAATAGTATTGGATATGGTGTTGGACAATCATGGGGACAATCAGGAAATGGTATTGGATA
* * * *** *
128891 TGGTGTTGGACAATCATGGGGACAGTCAGGAAATGGTATTGGGTACGGTGTTGGGCAATCAGTGG
131 CGGTGTTGGACAATCATGGGGACAATCAAGAAACAATATTGGATACGGTGTTGGGCAATCAGTGG
128956 GATCAGGAAATGGTG
196 GATCAGGAAATGGTG
* ** *
128971 TTGGACAATCATGGGGACAGTTAAGAAATGGTATTGGGTACGGTGTTGGGCAATCAGGGGGACAG
1 TTGGACAATCATGGGGACAGTCAAGAAATGGTATTGGGTACGGCATTGGACAATCAGGGGGACAG
* * * *
129036 TCAGGAAATGGTATTGGATATGGTGTTGGACAATCATGGGGACAGTTAGGAAATGGTATTGGGTA
66 TCAGGAAATAGTATTGGATATGGTGTTGGACAATCATGGGGACAATCAGGAAATGGTATTGGATA
* * *
129101 CGGTGTTGGACAATCA-GGAGGTCAATCAAGAAACAATGTTGGATATGGTGTTGG
131 CGGTGTTGGACAATCATGG-GGACAATCAAGAAACAATATTGGATACGGTGTTGG
129155 AATTGGGTCA
Statistics
Matches: 161, Mismatches: 22, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
209 2 0.01
210 159 0.99
ACGTcount: A:0.28, C:0.10, G:0.37, T:0.25
Consensus pattern (210 bp):
TTGGACAATCATGGGGACAGTCAAGAAATGGTATTGGGTACGGCATTGGACAATCAGGGGGACAG
TCAGGAAATAGTATTGGATATGGTGTTGGACAATCATGGGGACAATCAGGAAATGGTATTGGATA
CGGTGTTGGACAATCATGGGGACAATCAAGAAACAATATTGGATACGGTGTTGGGCAATCAGTGG
GATCAGGAAATGGTG
Found at i:130530 original size:18 final size:17
Alignment explanation
Indices: 130478--130530 Score: 61
Period size: 18 Copynumber: 2.9 Consensus size: 17
130468 AAAGATACAT
*
130478 ATAAAACTAAGTTCTTTTA
1 ATAAAA-TAAGTT-TTTCA
*
130497 ATAAAATAACTTTTTCA
1 ATAAAATAAGTTTTTCA
130514 ATAAAATTAAGTTTTTC
1 ATAAAA-TAAGTTTTTC
130531 CAAGACTAAC
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
17 10 0.33
18 14 0.47
19 6 0.20
ACGTcount: A:0.43, C:0.09, G:0.04, T:0.43
Consensus pattern (17 bp):
ATAAAATAAGTTTTTCA
Found at i:133196 original size:45 final size:44
Alignment explanation
Indices: 133121--133248 Score: 161
Period size: 45 Copynumber: 2.9 Consensus size: 44
133111 GGAGAAGGTG
* * *
133121 TTGGGTATGGTGTCGGACAATCGGGAGGTCAATCAAGAAATTGTA
1 TTGGGTATGGTGTTGGACAATTGGG-GGTCAATCAAGAAATAGTA
* * *
133166 TTGGATATGGTGTTGGGCAATTAGGGGGTCAATTAAGAAATAGTA
1 TTGGGTATGGTGTTGGACAATT-GGGGGTCAATCAAGAAATAGTA
133211 TTGGGTATGGTGTTGGACAATCT-GGGGTCAATC-AGAAA
1 TTGGGTATGGTGTTGGACAAT-TGGGGGTCAATCAAGAAA
133249 ACAACATTGG
Statistics
Matches: 72, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
43 5 0.07
44 9 0.12
45 54 0.75
46 4 0.06
ACGTcount: A:0.29, C:0.09, G:0.34, T:0.29
Consensus pattern (44 bp):
TTGGGTATGGTGTTGGACAATTGGGGGTCAATCAAGAAATAGTA
Found at i:133291 original size:176 final size:177
Alignment explanation
Indices: 132978--133358 Score: 494
Period size: 176 Copynumber: 2.1 Consensus size: 177
132968 AATGGAAAGG
* * *
132978 GTATCGGATATGGTGTTGGACAATCCGGAGGTCAATCATGAAATAGTATTGGGTATGGTGTTGGA
1 GTATTGGATATGGTGTTGGACAATCAGGAGGTCAATCAAGAAATAGTATTGGGTATGGTGTTGGA
* *
133043 CAATCGGGGGGGGGGGGGGTCAATTAGGAAACAACATTAGATATGGTAATGGAATTGGCAATGGA
66 CAATC--------GGGGGGTCAATCAGAAAACAACATTAGATATGGTAATGGAATTGGCAATGGA
* * *
133108 GATGGAGAAGGTGTTGGGTATGGTGTCGGACAATCGGGAGGTCAATCAAGAAATT
123 GATGGAGAAGGCGTTAGGTACGGTGTCGGACAATCGGGAGGTCAATCAAGAAATT
* * * *
133163 GTATTGGATATGGTGTTGGGCAATTAGGGGGTCAATTAAGAAATAGTATTGGGTATGGTGTTGGA
1 GTATTGGATATGGTGTTGGACAATCAGGAGGTCAATCAAGAAATAGTATTGGGTATGGTGTTGGA
* * *
133228 CAATC-TGGGGTCAATCAGAAAACAACATTGGATATGGTATTGGAATTGGCAATGGAGATGGAGA
66 CAATCGGGGGGTCAATCAGAAAACAACATTAGATATGGTAATGGAATTGGCAATGGAGATGGAGA
* * * *
133292 AGGCGTTAGGTACGGTGTTGGACAATTGGGAGGTCAGTCAGGAAATT
131 AGGCGTTAGGTACGGTGTCGGACAATCGGGAGGTCAATCAAGAAATT
* *
133339 GTGTTGGATATGGTATTGGA
1 GTATTGGATATGGTGTTGGA
133359 ATTGGCAATG
Statistics
Matches: 174, Mismatches: 22, Indels: 9
0.85 0.11 0.04
Matches are distributed among these distances:
176 111 0.64
185 63 0.36
ACGTcount: A:0.29, C:0.08, G:0.36, T:0.27
Consensus pattern (177 bp):
GTATTGGATATGGTGTTGGACAATCAGGAGGTCAATCAAGAAATAGTATTGGGTATGGTGTTGGA
CAATCGGGGGGTCAATCAGAAAACAACATTAGATATGGTAATGGAATTGGCAATGGAGATGGAGA
AGGCGTTAGGTACGGTGTCGGACAATCGGGAGGTCAATCAAGAAATT
Found at i:133349 original size:87 final size:87
Alignment explanation
Indices: 133060--133539 Score: 430
Period size: 87 Copynumber: 5.4 Consensus size: 87
133050 GGGGGGGGGG
* * * * *
133060 GGTCAATTAGGAAACAACATTAGATATGGTAATGGAATTGGCAATGGAGATGGAGAAGGTGTTGG
1 GGTCAATCAGGAAATAGCATTGGATATGGTATTGGAATTGGCAATGGAGATGGAGAAGGTGTTGG
* *
133125 GTATGGTGTCGGACAATCGGGA
66 GTACGGTGTTGGACAATCGGGA
* * * * *** * ** *
133147 GGTCAATCAAGAAATTGTATTGGATATGGTGTTGGGCAATTAGGGGGT-CA-ATTAAGAAATAGT
1 GGTCAATCAGGAAATAGCATTGGATATGGTATT-GG-AATT-GGCAATGGAGATGGAG-AA-GGT
* * *
133210 ATTGGGTATGGTGTTGGACAATCTGG-
61 GTTGGGTACGGTGTTGGACAATCGGGA
* * * * *
133236 GGTCAATCAGAAAACAACATTGGATATGGTATTGGAATTGGCAATGGAGATGGAGAAGGCGTTAG
1 GGTCAATCAGGAAATAGCATTGGATATGGTATTGGAATTGGCAATGGAGATGGAGAAGGTGTTGG
*
133301 GTACGGTGTTGGACAATTGGGA
66 GTACGGTGTTGGACAATCGGGA
* * **
133323 GGTCAGTCAGGAAATTGTGTTGGATATGGTATTGGAATTGGCAATGGAGATGGAGAAGGTGTCGG
1 GGTCAATCAGGAAATAGCATTGGATATGGTATTGGAATTGGCAATGGAGATGGAGAA------GG
133388 TGTTGGGTACGGTGTTGGACAATCGGGA
60 TGTTGGGTACGGTGTTGGACAATCGGGA
* * * * *
133416 GG-CTAATCAGGAAA-AGACGTTGGGTATTGAATTAGAATTGGCAATGGAGATGGAGAAGGTGTT
1 GGTC-AATCAGGAAATAG-CATTGGATATGGTATTGGAATTGGCAATGGAGATGGAGAAGGTGTT
**
133479 GGGTACGGCATTGGACAATCGGGA
64 GGGTACGGTGTTGGACAATCGGGA
* * * *
133503 GGCCAATCAGGAAACAACATTGGATATGGCATTGGAA
1 GGTCAATCAGGAAATAGCATTGGATATGGTATTGGAA
133540 ATGGAAAGGG
Statistics
Matches: 311, Mismatches: 64, Indels: 36
0.76 0.16 0.09
Matches are distributed among these distances:
86 25 0.08
87 136 0.44
88 14 0.05
89 33 0.11
90 28 0.09
92 2 0.01
93 73 0.23
ACGTcount: A:0.30, C:0.09, G:0.35, T:0.26
Consensus pattern (87 bp):
GGTCAATCAGGAAATAGCATTGGATATGGTATTGGAATTGGCAATGGAGATGGAGAAGGTGTTGG
GTACGGTGTTGGACAATCGGGA
Found at i:133528 original size:180 final size:179
Alignment explanation
Indices: 133211--133539 Score: 428
Period size: 180 Copynumber: 1.8 Consensus size: 179
133201 AGAAATAGTA
* * * *
133211 TTGGGTATGGTGTTGGACAATCTGGGGTCAATCAGAAAACAACATTGGATATGGTATTGGAATTG
1 TTGGGTACGGTGTTGGACAATCGGGGGTCAATCAGAAAACAACATTGGATATGGAATTAGAATTG
** * * * ****
133276 GCAATGGAGATGGAGAAGGCGTTAGGTACGGTGTTGGACAATTGGGAGGTCAGTCAGGAAATTGT
66 GCAATGGAGATGGAGAAGGCGTTAGGTACGGCATTGGACAATCGGGAGGCCAATCAGGAAACAAC
* *
133341 GTTGGATATGGTATTGGAATTGGCAATGGAGATGGAGAAGGTGTCGGTG
131 ATTGGATATGGCATTGGAATTGGCAATGGAGATGGAGAAGGTGTCGGTG
* * * *
133390 TTGGGTACGGTGTTGGACAATCGGGAGG-CTAATCAGGAAAA-GACGTTGGGTATTGAATTAGAA
1 TTGGGTACGGTGTTGGACAATCGGG-GGTC-AATCA-GAAAACAACATTGGATATGGAATTAGAA
* *
133453 TTGGCAATGGAGATGGAGAAGGTGTTGGGTACGGCATTGGACAATCGGGAGGCCAATCAGGAAAC
63 TTGGCAATGGAGATGGAGAAGGCGTTAGGTACGGCATTGGACAATCGGGAGGCCAATCAGGAAAC
133518 AACATTGGATATGGCATTGGAA
128 AACATTGGATATGGCATTGGAA
133540 ATGGAAAGGG
Statistics
Matches: 126, Mismatches: 21, Indels: 5
0.83 0.14 0.03
Matches are distributed among these distances:
179 24 0.19
180 97 0.77
181 5 0.04
ACGTcount: A:0.29, C:0.09, G:0.36, T:0.25
Consensus pattern (179 bp):
TTGGGTACGGTGTTGGACAATCGGGGGTCAATCAGAAAACAACATTGGATATGGAATTAGAATTG
GCAATGGAGATGGAGAAGGCGTTAGGTACGGCATTGGACAATCGGGAGGCCAATCAGGAAACAAC
ATTGGATATGGCATTGGAATTGGCAATGGAGATGGAGAAGGTGTCGGTG
Found at i:143333 original size:2 final size:2
Alignment explanation
Indices: 143326--143350 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
143316 TAATGCACCC
143326 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
143351 TGATGAATTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:146927 original size:23 final size:23
Alignment explanation
Indices: 146884--146927 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
146874 TTTAATATGG
*
146884 TTATTATTAAAATTTAGAATTGA
1 TTATTATTAAAAATTAGAATTGA
*
146907 TTATTTTTAATAAATTA-AATT
1 TTATTATTAA-AAATTAGAATT
146928 CAAATTACTC
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
23 13 0.72
24 5 0.28
ACGTcount: A:0.43, C:0.00, G:0.05, T:0.52
Consensus pattern (23 bp):
TTATTATTAAAAATTAGAATTGA
Found at i:147254 original size:24 final size:23
Alignment explanation
Indices: 147202--147254 Score: 63
Period size: 24 Copynumber: 2.3 Consensus size: 23
147192 TGTAGTATTC
147202 AGTTTTTTGCAATTAGATACTCA
1 AGTTTTTTGCAATTAGATACTCA
* *
147225 ATTTTTTGTGCTATTAGATACAT-A
1 AGTTTTT-TGCAATTAGATAC-TCA
147249 AGTTTT
1 AGTTTT
147255 GTTATTTGGT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
23 6 0.24
24 18 0.72
25 1 0.04
ACGTcount: A:0.28, C:0.09, G:0.13, T:0.49
Consensus pattern (23 bp):
AGTTTTTTGCAATTAGATACTCA
Found at i:147571 original size:20 final size:19
Alignment explanation
Indices: 147525--147580 Score: 67
Period size: 19 Copynumber: 2.9 Consensus size: 19
147515 CTCAGTTTCC
*
147525 AAATTCGCAACGCGAATAT
1 AAATTCGCAACGCGATTAT
* *
147544 CAATTCGCAACGCGATTGT
1 AAATTCGCAACGCGATTAT
*
147563 AAGATTCGCAACGTGATT
1 AA-ATTCGCAACGCGATT
147581 TTGAAAAATG
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
19 17 0.55
20 14 0.45
ACGTcount: A:0.34, C:0.21, G:0.20, T:0.25
Consensus pattern (19 bp):
AAATTCGCAACGCGATTAT
Found at i:147609 original size:19 final size:19
Alignment explanation
Indices: 147585--147626 Score: 75
Period size: 19 Copynumber: 2.2 Consensus size: 19
147575 GTGATTTTGA
*
147585 AAAATGTGTTGCGATAGTT
1 AAAATGTGTTGCGATAGTG
147604 AAAATGTGTTGCGATAGTG
1 AAAATGTGTTGCGATAGTG
147623 AAAA
1 AAAA
147627 ATCCAAAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.38, C:0.05, G:0.26, T:0.31
Consensus pattern (19 bp):
AAAATGTGTTGCGATAGTG
Found at i:148026 original size:21 final size:21
Alignment explanation
Indices: 148009--148098 Score: 123
Period size: 21 Copynumber: 4.4 Consensus size: 21
147999 ATTTTGGAAA
148009 ATCGCAACGCGAACTTGGACT
1 ATCGCAACGCGAACTTGGACT
* **
148030 ATCGC-A--CGAATTTGGAAA
1 ATCGCAACGCGAACTTGGACT
148048 ATCGCAACGCGAACTTGGACT
1 ATCGCAACGCGAACTTGGACT
*
148069 ATCGCAACGTGAACTTGGACT
1 ATCGCAACGCGAACTTGGACT
148090 ATCGCAACG
1 ATCGCAACG
148099 AATTTGGACT
Statistics
Matches: 59, Mismatches: 7, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
18 14 0.24
19 1 0.02
20 1 0.02
21 43 0.73
ACGTcount: A:0.31, C:0.26, G:0.23, T:0.20
Consensus pattern (21 bp):
ATCGCAACGCGAACTTGGACT
Done.