Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004675.1 Hibiscus syriacus cultivar Beakdansim tig00010480_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: 61647
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:37 original size:20 final size:20
Alignment explanation
Indices: 12--69 Score: 89
Period size: 20 Copynumber: 2.9 Consensus size: 20
2 TGGCCCTTCA
*
12 GTATCGATACCCCCACTATG
1 GTATCGATACCCCAACTATG
*
32 GTATCGATACCCTAACTATG
1 GTATCGATACCCCAACTATG
*
52 GTATCGATACCCCTACTA
1 GTATCGATACCCCAACTA
70 GTATCAATAC
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.28, C:0.31, G:0.14, T:0.28
Consensus pattern (20 bp):
GTATCGATACCCCAACTATG
Found at i:179 original size:94 final size:93
Alignment explanation
Indices: 10--231 Score: 288
Period size: 94 Copynumber: 2.4 Consensus size: 93
1 CTGGCCCTT
* * *
10 CAGTATCGATACCCCCACTATGGTATCGATACC-CTAACTATGGTATCGATACCCCTACTAGTAT
1 CAGTATCGATACCCTCACCATGGTATCGATACCACTAACTATGGTACCGATACCCCTACTAGTAT
*
74 CAATACCAAAATTAGATTCGATGTGGCC
66 CAATACCAAAATTAGATTCGATGTGACC
* *
102 CAGTATCGATACCCTTACCAAGGTATCGATACCACTATACTATGGTACCGATACCCCTA-TAAGG
1 CAGTATCGATACCCTCACCATGGTATCGATACCACTA-ACTATGGTACCGATACCCCTACT-A-G
* * *
166 TATCGATA-CAAAATTAGGTTCGATGTTACC
63 TATCAATACCAAAATTAGATTCGATGTGACC
* * *
196 CAATATAGATACCCTCACCATGCTATCGATACCACT
1 CAGTATCGATACCCTCACCATGGTATCGATACCACT
232 TCATTAGTAC
Statistics
Matches: 112, Mismatches: 14, Indels: 6
0.85 0.11 0.05
Matches are distributed among these distances:
92 29 0.26
93 4 0.04
94 71 0.63
95 8 0.07
ACGTcount: A:0.32, C:0.27, G:0.14, T:0.27
Consensus pattern (93 bp):
CAGTATCGATACCCTCACCATGGTATCGATACCACTAACTATGGTACCGATACCCCTACTAGTAT
CAATACCAAAATTAGATTCGATGTGACC
Found at i:4171 original size:18 final size:18
Alignment explanation
Indices: 4148--4186 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
4138 TATTTGTCCC
4148 CTGGACCTACCCCATCCT
1 CTGGACCTACCCCATCCT
4166 CTGGACCTACCCCATCCT
1 CTGGACCTACCCCATCCT
4184 CTG
1 CTG
4187 ATTCTATTTG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.15, C:0.49, G:0.13, T:0.23
Consensus pattern (18 bp):
CTGGACCTACCCCATCCT
Found at i:5985 original size:45 final size:46
Alignment explanation
Indices: 5933--6209 Score: 273
Period size: 45 Copynumber: 6.2 Consensus size: 46
5923 AATACATCAT
* **
5933 TATGCATTTTAAACTCTAACATA-TTTTCTGTTGATAATGCACCCA
1 TATGCATTTTCAACTCTAGTATACTTTTCTGTTGATAATGCACCCA
* * * * * *
5978 TATGCA-TTTCAACTATAATATACTTTTATTTTGATAATGTACCTA
1 TATGCATTTTCAACTCTAGTATACTTTTCTGTTGATAATGCACCCA
* * * *
6023 TATAC-GTTTCAAC-CATAGTATATTTTTCTGTTGATAATGTACCCA
1 TATGCATTTTCAACTC-TAGTATACTTTTCTGTTGATAATGCACCCA
* *
6068 TATACA-TTTCAACTCTAGCATACTTTTCTGTTGATAATGCACCCA
1 TATGCATTTTCAACTCTAGTATACTTTTCTGTTGATAATGCACCCA
* *
6113 TATGCA-TTTCAAATCTAGTATACTTTTCTGTTGATAATGCACACA
1 TATGCATTTTCAACTCTAGTATACTTTTCTGTTGATAATGCACCCA
* * * * * *
6158 TATGCA-TTTCAACTCTGGCAT-CCTTTCATGCTCATAATGCACCAA
1 TATGCATTTTCAACTCTAGTATACTTTTC-TGTTGATAATGCACCCA
6203 TATGCAT
1 TATGCAT
6210 AATTCTTTTA
Statistics
Matches: 196, Mismatches: 29, Indels: 13
0.82 0.12 0.05
Matches are distributed among these distances:
44 18 0.09
45 177 0.90
46 1 0.01
ACGTcount: A:0.30, C:0.20, G:0.10, T:0.40
Consensus pattern (46 bp):
TATGCATTTTCAACTCTAGTATACTTTTCTGTTGATAATGCACCCA
Found at i:6172 original size:90 final size:89
Alignment explanation
Indices: 5933--6209 Score: 306
Period size: 90 Copynumber: 3.1 Consensus size: 89
5923 AATACATCAT
* ** * **
5933 TATGCATTTTAAACTCTAACATATTTTCTGTTGATAATGCACCCATATGCATTTCAACTATAATA
1 TATGCATTTCAAA-TCTAGTATATTTTCTGTTGATAATGCACCCATATGCATTTCAACTCTAGCA
* * * *
5998 TACTTTTATTTTGATAATGTACCTA
65 TACTTTTCTGTTGATAATGCACCAA
* * * * *
6023 TATACGTTTC-AACCATAGTATATTTTTCTGTTGATAATGTACCCATATACATTTCAACTCTAGC
1 TATGCATTTCAAATC-TAGTATA-TTTTCTGTTGATAATGCACCCATATGCATTTCAACTCTAGC
*
6087 ATACTTTTCTGTTGATAATGCACCCA
64 ATACTTTTCTGTTGATAATGCACCAA
* *
6113 TATGCATTTCAAATCTAGTATACTTTTCTGTTGATAATGCACACATATGCATTTCAACTCTGGCA
1 TATGCATTTCAAATCTAGTATA-TTTTCTGTTGATAATGCACCCATATGCATTTCAACTCTAGCA
* * *
6178 T-CCTTTCATGCTCATAATGCACCAA
65 TACTTTTC-TGTTGATAATGCACCAA
6203 TATGCAT
1 TATGCAT
6210 AATTCTTTTA
Statistics
Matches: 156, Mismatches: 27, Indels: 8
0.82 0.14 0.04
Matches are distributed among these distances:
88 1 0.01
89 12 0.08
90 140 0.90
91 3 0.02
ACGTcount: A:0.30, C:0.20, G:0.10, T:0.40
Consensus pattern (89 bp):
TATGCATTTCAAATCTAGTATATTTTCTGTTGATAATGCACCCATATGCATTTCAACTCTAGCAT
ACTTTTCTGTTGATAATGCACCAA
Found at i:6195 original size:135 final size:134
Alignment explanation
Indices: 5944--6205 Score: 314
Period size: 135 Copynumber: 1.9 Consensus size: 134
5934 ATGCATTTTA
* *
5944 AACTCTAACATATTTTCTGTTGATAATGCACCCATATGCATTTCAACTATAATATACTTTTATTT
1 AACTCTAACATATTTTCTGTTGATAATGCACCCATATGCATTTCAAATATAATATACTTTTATGT
* * * ** * * * *
6009 TGATAATGTACCTATATACGTTTCAACCATAGTATATTTTTCTGTTGATAATGTACCCATATACA
66 TGATAATGCACCTATATACATTTCAACCATAGCATACCTTTCTGCTCATAATGCACCAATATACA
6074 TTTC
131 TTTC
* * * *
6078 AACTCTAGCATACTTTTCTGTTGATAATGCACCCATATGCATTTCAAATCTAGTATACTTTTCTG
1 AACTCTAACATA-TTTTCTGTTGATAATGCACCCATATGCATTTCAAATATAATATACTTTTATG
* *
6143 TTGATAATGCACAC-ATATGCATTTCAACTC-TGGCAT-CCTTTCATGCTCATAATGCACCAATA
65 TTGATAATGCAC-CTATATACATTTCAAC-CATAGCATACCTTTC-TGCTCATAATGCACCAATA
6205 T
127 T
6206 GCATAATTCT
Statistics
Matches: 107, Mismatches: 17, Indels: 7
0.82 0.13 0.05
Matches are distributed among these distances:
134 15 0.14
135 90 0.84
136 2 0.02
ACGTcount: A:0.30, C:0.21, G:0.10, T:0.40
Consensus pattern (134 bp):
AACTCTAACATATTTTCTGTTGATAATGCACCCATATGCATTTCAAATATAATATACTTTTATGT
TGATAATGCACCTATATACATTTCAACCATAGCATACCTTTCTGCTCATAATGCACCAATATACA
TTTC
Found at i:6749 original size:22 final size:21
Alignment explanation
Indices: 6703--6784 Score: 94
Period size: 22 Copynumber: 3.9 Consensus size: 21
6693 TGTCCCTTCA
*
6703 GTATCGATAC-CCCCACTATG
1 GTATCGATACACCCTACTATG
6723 GTATCGATACTACCCTACTATG
1 GTATCGATAC-ACCCTACTATG
* * *
6745 ATATCTATATTACCCTACTATG
1 GTATCGATA-CACCCTACTATG
*
6767 GTATCGATACCCCCTACT
1 GTATCGATACACCCTACT
6785 TGTATCAATA
Statistics
Matches: 51, Mismatches: 8, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
20 10 0.20
21 7 0.14
22 34 0.67
ACGTcount: A:0.27, C:0.30, G:0.11, T:0.32
Consensus pattern (21 bp):
GTATCGATACACCCTACTATG
Found at i:12328 original size:21 final size:21
Alignment explanation
Indices: 12302--12383 Score: 76
Period size: 21 Copynumber: 3.8 Consensus size: 21
12292 ATAATTTGCA
12302 CCGAAGTG-CCACATAGTTGTC
1 CCGAAG-GACCACATAGTTGTC
12323 CCGAAGGACCACATAGTTGTC
1 CCGAAGGACCACATAGTTGTC
* * *
12344 TCGAAAGACCATATTAGTTTTGTC
1 CCGAAGGACCACA-TAG--TTGTC
* *
12368 CTGAATGACCACATAG
1 CCGAAGGACCACATAG
12384 AACCCTCGAC
Statistics
Matches: 50, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
20 1 0.02
21 29 0.58
22 3 0.06
23 3 0.06
24 14 0.28
ACGTcount: A:0.29, C:0.24, G:0.21, T:0.26
Consensus pattern (21 bp):
CCGAAGGACCACATAGTTGTC
Found at i:18187 original size:20 final size:20
Alignment explanation
Indices: 18150--18188 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
18140 AGATCTCATA
*
18150 TAGGATCATATAGATGCATT
1 TAGGAGCATATAGATGCATT
* *
18170 TAGGAGCATCTAGTTGCAT
1 TAGGAGCATATAGATGCAT
18189 CTAGTTGCAT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.31, C:0.13, G:0.23, T:0.33
Consensus pattern (20 bp):
TAGGAGCATATAGATGCATT
Found at i:22921 original size:43 final size:42
Alignment explanation
Indices: 22780--22921 Score: 155
Period size: 43 Copynumber: 3.4 Consensus size: 42
22770 TGACTAGATC
* * *
22780 TCCTCAACACGAAGGAGCAGTGTCATCCTCAGACAATTAGACT
1 TCCTCAATACGAAGGAGCAATGTCATCCTCATACAA-TAGACT
* * * *
22823 TCCTC-ATCACGAAGGAACAATGTCATCCACATACCA-AGTC-
1 TCCTCAAT-ACGAAGGAGCAATGTCATCCTCATACAATAGACT
*
22863 TCCTCAATGCGAAGGAGCAATGTCATCCTCATACAATCAGACT
1 TCCTCAATACGAAGGAGCAATGTCATCCTCATACAAT-AGACT
*
22906 TCCTCAATGCGAAGGA
1 TCCTCAATACGAAGGA
22922 ACCGTGTTGT
Statistics
Matches: 82, Mismatches: 12, Indels: 10
0.79 0.12 0.10
Matches are distributed among these distances:
40 29 0.35
41 5 0.06
42 4 0.05
43 44 0.54
ACGTcount: A:0.33, C:0.29, G:0.17, T:0.21
Consensus pattern (42 bp):
TCCTCAATACGAAGGAGCAATGTCATCCTCATACAATAGACT
Found at i:23271 original size:139 final size:139
Alignment explanation
Indices: 22817--23276 Score: 661
Period size: 139 Copynumber: 3.3 Consensus size: 139
22807 CTCAGACAAT
* * ** * *
22817 TAGACTTCCTCATCACGAAGGAACAATGTCATCCACATACCAAGTCTCCTCAATGCGAAGGAGCA
1 TAGACGTCCTCATCACGAAGGAACAATGTCGTCCACCGACCAGGTCTCCTCAACGCGAAGGAGCA
* * *
22882 ATGTCATCCTCATACAATCAGACTTCCTCAATGCGAAGGAACCGTGTTGTCTCCAAATTATCCCT
66 GTGTCATCCTCAGACAATCAGACTTCCTCAACGCGAAGGAACCGTGTTGTCTCCAAATTATCCCT
*
22947 AAAGATGGC
131 AAAGACGGC
* * * * *
22956 TAGACTTCCTCATCACGAATGAACAATGTCGTCC-CTTGACCAGATCTCATCAACGCGAAGGAGC
1 TAGACGTCCTCATCACGAAGGAACAATGTCGTCCAC-CGACCAGGTCTCCTCAACGCGAAGGAGC
* * * * * *
23020 AGTGTCATCCTCAGAAAACCAGACTTCCTCATCACGAAGGAACTGTGTTGCCTCCAAATTATCCC
65 AGTGTCATCCTCAGACAATCAGACTTCCTCAACGCGAAGGAACCGTGTTGTCTCCAAATTATCCC
23085 TAAAGACGGC
130 TAAAGACGGC
* * * *
23095 TAGACGTCCTCATCATGAAGGAACAATGTCGTTCACCGACCAGGTCTCCTCAACGCAAAGAAGCA
1 TAGACGTCCTCATCACGAAGGAACAATGTCGTCCACCGACCAGGTCTCCTCAACGCGAAGGAGCA
*
23160 GTGTCATCCTCAGACAATCAGACTTCCTCAACGTGAAGGAACCGTGTTGTCTCCAAATTATCCCT
66 GTGTCATCCTCAGACAATCAGACTTCCTCAACGCGAAGGAACCGTGTTGTCTCCAAATTATCCCT
23225 AAAGACGGC
131 AAAGACGGC
*
23234 TAGACGTCCTCATCACGAAGGAACAATGTCGTCCACCGGCCAG
1 TAGACGTCCTCATCACGAAGGAACAATGTCGTCCACCGACCAG
23277 ATCTTTTTAA
Statistics
Matches: 282, Mismatches: 37, Indels: 4
0.87 0.11 0.01
Matches are distributed among these distances:
138 1 0.00
139 280 0.99
140 1 0.00
ACGTcount: A:0.30, C:0.29, G:0.18, T:0.22
Consensus pattern (139 bp):
TAGACGTCCTCATCACGAAGGAACAATGTCGTCCACCGACCAGGTCTCCTCAACGCGAAGGAGCA
GTGTCATCCTCAGACAATCAGACTTCCTCAACGCGAAGGAACCGTGTTGTCTCCAAATTATCCCT
AAAGACGGC
Found at i:24961 original size:16 final size:16
Alignment explanation
Indices: 24936--25017 Score: 78
Period size: 16 Copynumber: 5.2 Consensus size: 16
24926 CTGCTAACCA
*
24936 CTAACCGCTAACTTTT
1 CTAACAGCTAACTTTT
* *
24952 TTAACAGCTAACATTT
1 CTAACAGCTAACTTTT
* **
24968 CAAACAGCTAA--TCA
1 CTAACAGCTAACTTTT
*
24982 CTAACCGCTAACTTTT
1 CTAACAGCTAACTTTT
*
24998 CTAACAGCTAACCTTT
1 CTAACAGCTAACTTTT
25014 CTAA
1 CTAA
25018 TTGCTAATTA
Statistics
Matches: 51, Mismatches: 13, Indels: 4
0.75 0.19 0.06
Matches are distributed among these distances:
14 10 0.20
16 41 0.80
ACGTcount: A:0.34, C:0.28, G:0.06, T:0.32
Consensus pattern (16 bp):
CTAACAGCTAACTTTT
Found at i:24995 original size:46 final size:46
Alignment explanation
Indices: 24928--25044 Score: 162
Period size: 46 Copynumber: 2.5 Consensus size: 46
24918 TTCAGACTCT
*
24928 GCTAACCACTAACCGCTAACTTTTTTAACAGCTAACATTTCAAACA
1 GCTAATCACTAACCGCTAACTTTTTTAACAGCTAACATTTCAAACA
* * * **
24974 GCTAATCACTAACCGCTAACTTTTCTAACAGCTAACCTTTCTAATT
1 GCTAATCACTAACCGCTAACTTTTTTAACAGCTAACATTTCAAACA
* *
25020 GCTAATTACTAACCGCTAACCTTTT
1 GCTAATCACTAACCGCTAACTTTTT
25045 ATTTATTTAT
Statistics
Matches: 62, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
46 62 1.00
ACGTcount: A:0.32, C:0.28, G:0.07, T:0.32
Consensus pattern (46 bp):
GCTAATCACTAACCGCTAACTTTTTTAACAGCTAACATTTCAAACA
Found at i:25023 original size:16 final size:16
Alignment explanation
Indices: 24936--25043 Score: 71
Period size: 16 Copynumber: 7.0 Consensus size: 16
24926 CTGCTAACCA
* *
24936 CTAACCGCTAACTTTT
1 CTAACAGCTAACCTTT
* *
24952 TTAACAGCTAACATTT
1 CTAACAGCTAACCTTT
* **
24968 CAAACAGCTAA--TCA
1 CTAACAGCTAACCTTT
* *
24982 CTAACCGCTAACTTTT
1 CTAACAGCTAACCTTT
24998 CTAACAGCTAACCTTT
1 CTAACAGCTAACCTTT
** *
25014 CTAATTGCTAA--TTA
1 CTAACAGCTAACCTTT
*
25028 CTAACCGCTAACCTTT
1 CTAACAGCTAACCTTT
25044 TATTTATTTA
Statistics
Matches: 69, Mismatches: 19, Indels: 8
0.72 0.20 0.08
Matches are distributed among these distances:
14 21 0.30
16 48 0.70
ACGTcount: A:0.32, C:0.28, G:0.06, T:0.33
Consensus pattern (16 bp):
CTAACAGCTAACCTTT
Found at i:25256 original size:14 final size:14
Alignment explanation
Indices: 25237--25272 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
25227 ACTTTATTTA
25237 TTTAATTTCAGTCC
1 TTTAATTTCAGTCC
* *
25251 TTTAATTTCATTGC
1 TTTAATTTCAGTCC
25265 TTTAATTT
1 TTTAATTT
25273 TCTGTCTTTC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.22, C:0.14, G:0.06, T:0.58
Consensus pattern (14 bp):
TTTAATTTCAGTCC
Found at i:26296 original size:18 final size:19
Alignment explanation
Indices: 26273--26319 Score: 80
Period size: 18 Copynumber: 2.6 Consensus size: 19
26263 TAATAAAGTC
26273 ATAATTGTTTTTT-AAAAT
1 ATAATTGTTTTTTAAAAAT
26291 ATAATT-TTTTTTAAAAAT
1 ATAATTGTTTTTTAAAAAT
26309 ATAATTGTTTT
1 ATAATTGTTTT
26320 AAAAAAATGG
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
17 6 0.22
18 17 0.63
19 4 0.15
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.57
Consensus pattern (19 bp):
ATAATTGTTTTTTAAAAAT
Found at i:34202 original size:16 final size:16
Alignment explanation
Indices: 34176--34218 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
34166 AAAAGACTTG
*
34176 AACTCGAAAATGACCCA
1 AACTC-AAAATAACCCA
* *
34193 AACTCTAAATAACCCT
1 AACTCAAAATAACCCA
34209 AACTCAAAAT
1 AACTCAAAAT
34219 CATCTGGACT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
16 17 0.77
17 5 0.23
ACGTcount: A:0.49, C:0.28, G:0.05, T:0.19
Consensus pattern (16 bp):
AACTCAAAATAACCCA
Found at i:38205 original size:37 final size:37
Alignment explanation
Indices: 38164--38238 Score: 150
Period size: 37 Copynumber: 2.0 Consensus size: 37
38154 TTTTAAAAAG
38164 ATAAATTTTTAAAATATAAAAATATATTATTAATTGA
1 ATAAATTTTTAAAATATAAAAATATATTATTAATTGA
38201 ATAAATTTTTAAAATATAAAAATATATTATTAATTGA
1 ATAAATTTTTAAAATATAAAAATATATTATTAATTGA
38238 A
1 A
38239 AATATAAAAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.43
Consensus pattern (37 bp):
ATAAATTTTTAAAATATAAAAATATATTATTAATTGA
Found at i:38242 original size:18 final size:18
Alignment explanation
Indices: 38182--38244 Score: 60
Period size: 18 Copynumber: 3.4 Consensus size: 18
38172 TTAAAATATA
38182 AAAATATATTATTAATTG
1 AAAATATATTATTAATTG
*
38200 AATAA-AT-TT-TTAAAATATA
1 AA-AATATATTATT--AAT-TG
38219 AAAATATATTATTAATTG
1 AAAATATATTATTAATTG
38237 AAAATATA
1 AAAATATA
38245 AAAAAGATGT
Statistics
Matches: 36, Mismatches: 2, Indels: 14
0.69 0.04 0.27
Matches are distributed among these distances:
16 2 0.06
17 2 0.06
18 18 0.50
19 10 0.28
20 2 0.06
21 2 0.06
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (18 bp):
AAAATATATTATTAATTG
Found at i:41330 original size:28 final size:28
Alignment explanation
Indices: 41287--41347 Score: 79
Period size: 28 Copynumber: 2.2 Consensus size: 28
41277 GAAAGTACCA
* *
41287 AAAAAATTTCCGAAAATTAAAAAATATAT
1 AAAAAATTACCGAAAATTAAAAAA-ACAT
*
41316 AAAAAATTACC-AAAATTACAAAAACAT
1 AAAAAATTACCGAAAATTAAAAAAACAT
41343 AAAAA
1 AAAAA
41348 GAAGAAAAGA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
27 8 0.28
28 11 0.38
29 10 0.34
ACGTcount: A:0.67, C:0.10, G:0.02, T:0.21
Consensus pattern (28 bp):
AAAAAATTACCGAAAATTAAAAAAACAT
Found at i:41338 original size:29 final size:28
Alignment explanation
Indices: 41286--41347 Score: 81
Period size: 29 Copynumber: 2.2 Consensus size: 28
41276 TGAAAGTACC
* *
41286 AAAAAAATTTCCGAAAATTAAAAAATAT
1 AAAAAAATTACCGAAAATTAAAAAACAT
41314 ATAAAAAATTACC-AAAATTACAAAAACAT
1 A-AAAAAATTACCGAAAATTA-AAAAACAT
41343 AAAAA
1 AAAAA
41348 GAAGAAAAGA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
28 12 0.40
29 18 0.60
ACGTcount: A:0.68, C:0.10, G:0.02, T:0.21
Consensus pattern (28 bp):
AAAAAAATTACCGAAAATTAAAAAACAT
Found at i:48508 original size:22 final size:23
Alignment explanation
Indices: 48478--48522 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
48468 AAATAAAAAC
48478 AAAACGTGCCA-AAAAATAGAGT
1 AAAACGTGCCATAAAAATAGAGT
*
48500 AAAATGTGCCATAAAAATAGAGT
1 AAAACGTGCCATAAAAATAGAGT
48523 TATTAAAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
22 10 0.48
23 11 0.52
ACGTcount: A:0.53, C:0.11, G:0.18, T:0.18
Consensus pattern (23 bp):
AAAACGTGCCATAAAAATAGAGT
Found at i:48850 original size:2 final size:2
Alignment explanation
Indices: 48843--48867 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
48833 AACGTTTGAC
48843 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
48868 TAAGTACTTG
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:49009 original size:29 final size:31
Alignment explanation
Indices: 48952--49015 Score: 87
Period size: 29 Copynumber: 2.1 Consensus size: 31
48942 GTCAAGTCTT
*
48952 ACGTGTCCAAAATATTGATGTTGATATTGTC
1 ACGTGTCCAAAATATTGATGTTAATATTGTC
* *
48983 ACGTGTGCAAAGTA-TGATG-TAATATTGTC
1 ACGTGTCCAAAATATTGATGTTAATATTGTC
49012 ACGT
1 ACGT
49016 CATCATTTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
29 13 0.43
30 5 0.17
31 12 0.40
ACGTcount: A:0.30, C:0.12, G:0.22, T:0.36
Consensus pattern (31 bp):
ACGTGTCCAAAATATTGATGTTAATATTGTC
Found at i:52614 original size:24 final size:23
Alignment explanation
Indices: 52569--52614 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
52559 ATCCCATTTT
*
52569 TTTTTTTTACAATTTTGAATGTA
1 TTTTTTTTACAATTTTAAATGTA
*
52592 TTTTTTTTCCAATTTTAAGATGT
1 TTTTTTTTACAATTTTAA-ATGT
52615 TTGGTAGAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 16 0.80
24 4 0.20
ACGTcount: A:0.24, C:0.07, G:0.09, T:0.61
Consensus pattern (23 bp):
TTTTTTTTACAATTTTAAATGTA
Found at i:53400 original size:20 final size:20
Alignment explanation
Indices: 53375--53417 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
53365 GTTAATTAAC
53375 TAATGATTAATATCCTAAAA
1 TAATGATTAATATCCTAAAA
** *
53395 TAATGATTTTTATCTTAAAA
1 TAATGATTAATATCCTAAAA
53415 TAA
1 TAA
53418 AAATGTTAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.47, C:0.07, G:0.05, T:0.42
Consensus pattern (20 bp):
TAATGATTAATATCCTAAAA
Found at i:54489 original size:60 final size:60
Alignment explanation
Indices: 54422--54583 Score: 159
Period size: 60 Copynumber: 2.7 Consensus size: 60
54412 AAATGTGTCT
*
54422 AAAAGTTTGGGGATCAATTTATAACGAAGATCATAGTTTGAGGAAGAAAATGAAATATTC
1 AAAAGTTTGGGGATCAATTTATAATGAAGATCATAGTTTGAGGAAGAAAATGAAATATTC
** * * * * *
54482 AAAAGTTTGAAGATTAATTTAGAATGATAG-TCATAGTTT-AGGGATGAAATTGAAATATTT
1 AAAAGTTTGGGGATCAATTTATAATGA-AGATCATAGTTTGA-GGAAGAAAATGAAATATTC
* * * * *
54542 AAAACTTTAGGGA-CTAATTTATAATAAAAATCATAATTTGAG
1 AAAAGTTTGGGGATC-AATTTATAATGAAGATCATAGTTTGAG
54584 AACATTAACT
Statistics
Matches: 80, Mismatches: 17, Indels: 10
0.75 0.16 0.09
Matches are distributed among these distances:
59 2 0.03
60 75 0.94
61 3 0.04
ACGTcount: A:0.44, C:0.05, G:0.19, T:0.33
Consensus pattern (60 bp):
AAAAGTTTGGGGATCAATTTATAATGAAGATCATAGTTTGAGGAAGAAAATGAAATATTC
Found at i:59687 original size:34 final size:34
Alignment explanation
Indices: 59644--59733 Score: 137
Period size: 33 Copynumber: 2.7 Consensus size: 34
59634 CCCAGGTGTA
*
59644 AAGTTGGCCACCTACCAAAGATGAATTTTCCAAT
1 AAGTTGGCCACCAACCAAAGATGAATTTTCCAAT
* * *
59678 AAGTTGGCCACAAACC-AAGATTATTTTTCCAAT
1 AAGTTGGCCACCAACCAAAGATGAATTTTCCAAT
59711 AAGTTGGCCACCAACCAAAGATG
1 AAGTTGGCCACCAACCAAAGATG
59734 TCAACTTTGC
Statistics
Matches: 49, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
33 30 0.61
34 19 0.39
ACGTcount: A:0.37, C:0.23, G:0.16, T:0.24
Consensus pattern (34 bp):
AAGTTGGCCACCAACCAAAGATGAATTTTCCAAT
Done.