Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003400.1 Hibiscus syriacus cultivar Beakdansim tig00007155_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: 65920
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:10383 original size:36 final size:36
Alignment explanation
Indices: 10343--10421 Score: 122
Period size: 36 Copynumber: 2.2 Consensus size: 36
10333 GGTAGTCGAT
*
10343 CGAATTAACCGAACTAATTTGATTCGGTCGGTTAAC
1 CGAATTAACCGAACTAATTCGATTCGGTCGGTTAAC
* * *
10379 CGAATTAATCGAACTAATTCGGTTCGGTCGGTTAAT
1 CGAATTAACCGAACTAATTCGATTCGGTCGGTTAAC
10415 CGAATTA
1 CGAATTA
10422 GTTCGAAAAT
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.30, C:0.18, G:0.20, T:0.32
Consensus pattern (36 bp):
CGAATTAACCGAACTAATTCGATTCGGTCGGTTAAC
Found at i:10572 original size:13 final size:13
Alignment explanation
Indices: 10554--10611 Score: 57
Period size: 13 Copynumber: 4.5 Consensus size: 13
10544 AATACAAAAC
*
10554 TTTCATATCTCAT
1 TTTCATATTTCAT
*
10567 TTTCATCTTTCACT
1 TTTCATATTTCA-T
*
10581 TTT-ATA-TTCAC
1 TTTCATATTTCAT
*
10592 TTTCACATTTCAT
1 TTTCATATTTCAT
10605 TTTCATA
1 TTTCATA
10612 ATACATACTT
Statistics
Matches: 35, Mismatches: 7, Indels: 6
0.73 0.15 0.12
Matches are distributed among these distances:
11 3 0.09
12 6 0.17
13 22 0.63
14 4 0.11
ACGTcount: A:0.22, C:0.22, G:0.00, T:0.55
Consensus pattern (13 bp):
TTTCATATTTCAT
Found at i:13812 original size:19 final size:18
Alignment explanation
Indices: 13790--13835 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 18
13780 ACTTAGTGAG
*
13790 ACATTATAGACAATATCAT
1 ACATAATAGAC-ATATCAT
*
13809 ACATAATAGTCATATCAT
1 ACATAATAGACATATCAT
*
13827 ATATAATAG
1 ACATAATAG
13836 TATACACTAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
18 15 0.62
19 9 0.38
ACGTcount: A:0.48, C:0.13, G:0.07, T:0.33
Consensus pattern (18 bp):
ACATAATAGACATATCAT
Found at i:13825 original size:18 final size:18
Alignment explanation
Indices: 13802--13836 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
13792 ATTATAGACA
13802 ATATCATACATAATAGTC
1 ATATCATACATAATAGTC
*
13820 ATATCATATATAATAGT
1 ATATCATACATAATAGT
13837 ATACACTAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.46, C:0.11, G:0.06, T:0.37
Consensus pattern (18 bp):
ATATCATACATAATAGTC
Found at i:14071 original size:24 final size:25
Alignment explanation
Indices: 14022--14096 Score: 75
Period size: 24 Copynumber: 3.0 Consensus size: 25
14012 ACAATACAAA
*
14022 ACTTTCATATCTTATTTTCATC-TTTC
1 ACTTT-ATATATTATTTTCA-CATTTC
14048 ACTTTATAT-TTATTTTCACATTTC
1 ACTTTATATATTATTTTCACATTTC
* * *
14072 A-TTTTTATAATACTTTCACATTTC
1 ACTTTATATATTATTTTCACATTTC
14096 A
1 A
14097 GAACTCATTC
Statistics
Matches: 44, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
23 7 0.16
24 28 0.64
25 4 0.09
26 5 0.11
ACGTcount: A:0.25, C:0.19, G:0.00, T:0.56
Consensus pattern (25 bp):
ACTTTATATATTATTTTCACATTTC
Found at i:14157 original size:18 final size:18
Alignment explanation
Indices: 14093--14162 Score: 68
Period size: 19 Copynumber: 3.8 Consensus size: 18
14083 ACTTTCACAT
*
14093 TTCAGAACTCATTCTCAGA
1 TTCAGAACTTATT-TCAGA
* *
14112 TTCAGAACTTGTTTTCGGA
1 TTCAGAACTT-ATTTCAGA
* *
14131 CTCAAAACTTATTTCAGA
1 TTCAGAACTTATTTCAGA
*
14149 TTCATAACTTATTT
1 TTCAGAACTTATTT
14163 TCAAGTTCAT
Statistics
Matches: 41, Mismatches: 9, Indels: 3
0.77 0.17 0.06
Matches are distributed among these distances:
18 18 0.44
19 21 0.51
20 2 0.05
ACGTcount: A:0.30, C:0.20, G:0.10, T:0.40
Consensus pattern (18 bp):
TTCAGAACTTATTTCAGA
Found at i:16977 original size:30 final size:30
Alignment explanation
Indices: 16932--17006 Score: 82
Period size: 30 Copynumber: 2.5 Consensus size: 30
16922 GCCAAGAACC
* *
16932 TAAA-TTTTAAAAATTACAC-TTTAGGTCCT
1 TAAACTTTTTAAAATTAC-CTTTTAGATCCT
**
16961 TAAACTTTTTAAAATTACCTTTTTTATCCT
1 TAAACTTTTTAAAATTACCTTTTAGATCCT
*
16991 TAAACTTTTTCAAATT
1 TAAACTTTTTAAAATT
17007 TTATACTTTA
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
29 5 0.13
30 34 0.87
ACGTcount: A:0.35, C:0.15, G:0.03, T:0.48
Consensus pattern (30 bp):
TAAACTTTTTAAAATTACCTTTTAGATCCT
Found at i:20229 original size:85 final size:86
Alignment explanation
Indices: 20077--20247 Score: 290
Period size: 85 Copynumber: 2.0 Consensus size: 86
20067 GACAATTCTT
* *
20077 CATTGTTCTATATCATAAGATAAATTGTCTAATTACTATCTAATTTAAAATATTTCTTTACTTTG
1 CATTATTCAATATCATAAGATAAATTGTCTAATTACTATCTAATTTAAAATATTTCTTTACTTTG
*
20142 TCAAAATATAA-TTTTATCTA
66 TCAAAATACAATTTTTATCTA
* *
20162 CATTATTCAATATCATAAGATAAATTGTCTAATTATTTTCTAATTTAAAATATTTCTTTACTTTG
1 CATTATTCAATATCATAAGATAAATTGTCTAATTACTATCTAATTTAAAATATTTCTTTACTTTG
20227 TCAAAATACAATTTTTATCTA
66 TCAAAATACAATTTTTATCTA
20248 AAACACAAAA
Statistics
Matches: 80, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
85 71 0.89
86 9 0.11
ACGTcount: A:0.37, C:0.12, G:0.04, T:0.47
Consensus pattern (86 bp):
CATTATTCAATATCATAAGATAAATTGTCTAATTACTATCTAATTTAAAATATTTCTTTACTTTG
TCAAAATACAATTTTTATCTA
Found at i:27207 original size:25 final size:26
Alignment explanation
Indices: 27171--27222 Score: 72
Period size: 25 Copynumber: 2.0 Consensus size: 26
27161 AAAAAAAAGA
27171 AAAATAATTTATATATATT-TATAAAT
1 AAAATAATTTATATAT-TTATATAAAT
*
27197 AAAAT-ATTTATTTATTTATATAAAT
1 AAAATAATTTATATATTTATATAAAT
27222 A
1 A
27223 TCAAAAAAGG
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
24 2 0.08
25 17 0.71
26 5 0.21
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (26 bp):
AAAATAATTTATATATTTATATAAAT
Found at i:28292 original size:11 final size:11
Alignment explanation
Indices: 28276--28300 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
28266 GAAATTTTGA
28276 TTCCACGGTGG
1 TTCCACGGTGG
28287 TTCCACGGTGG
1 TTCCACGGTGG
28298 TTC
1 TTC
28301 GGCAGCTCTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.08, C:0.28, G:0.32, T:0.32
Consensus pattern (11 bp):
TTCCACGGTGG
Found at i:28881 original size:3 final size:3
Alignment explanation
Indices: 28873--28921 Score: 66
Period size: 3 Copynumber: 16.7 Consensus size: 3
28863 CTGTATTTAT
*
28873 TAA TAA TAA -AA TAA TAA TAA TAA TAA TTA TAA TAA TAA T-A TAAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA
28917 TAA TA
1 TAA TA
28922 TTTAAATGAA
Statistics
Matches: 41, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
2 4 0.10
3 35 0.85
4 2 0.05
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:29424 original size:113 final size:113
Alignment explanation
Indices: 29226--29835 Score: 728
Period size: 113 Copynumber: 5.3 Consensus size: 113
29216 TTGAACAAGC
* ** ** * *
29226 TCTTCTCATTATGAACTTTTTCTGAAAATGTTGATCCATCGAGTGATGAATTCGAGC-AAAAGAT
1 TCTTCTCATTATGAACTCTACCTGGTAATGCTGATCCATCGAATGATGAATTCGAGCAAAAAG-T
*
29290 TGAACAAGTTCTTCTCATTATGAACTTCTTTTTCCTTCTTCAGATGAGT
65 TGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGT
*
29339 TCTTCTCATTATGAACTCTACCTGGTAATGTTGATCCATCGAATGATGAATTCGAGCAAAAAGTT
1 TCTTCTCATTATGAACTCTACCTGGTAATGCTGATCCATCGAATGATGAATTCGAGCAAAAAGTT
* *
29404 GAATAAGTTCTTCTCATTATGAACTTATTCTTCCTTCTTCAGATGAGT
66 GAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGT
* * *
29452 TATTCTCATTATGAACTCTACCTGGCAATACTGATCCATCGAATGATGAATTCGAGCAAAAAGTT
1 TCTTCTCATTATGAACTCTACCTGGTAATGCTGATCCATCGAATGATGAATTCGAGCAAAAAGTT
* *
29517 GAACAAGTTCTTCTCATTATGAACTTATTCTTCCTTCTTTAGATGAGT
66 GAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGT
* * *** *
29565 TCTTCTCATTATGAACTCCT-TCTGGAAATATTGATGCTGATCTATCTCTTTCTGCGAT-AGAGT
1 TCTTCTCATTATGAACT-CTACCTGG---TA---ATGCTGATCCA--TC-GAAT--GATGA-ATT
* * *
29628 CGAGCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTT-CTTCTTCAGATAAGT
53 CGAGCAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGT
* * * * * * *
29688 TCTTCTCATTATGAACT-TTCTCTGGAAATGCTGGTACATC-AAGTGATGGATTTGAGCAAAAGG
1 TCTTCTCATTATGAACTCTAC-CTGGTAATGCTGATCCATCGAA-TGATGAATTCGAGCAAAAAG
*
29751 TTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGT
64 TTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGT
*
29801 TCTTCTCATTATGAACTCTACCTAGTAATGCTGAT
1 TCTTCTCATTATGAACTCTACCTGGTAATGCTGAT
29836 GACCCGAAGA
Statistics
Matches: 433, Mismatches: 44, Indels: 40
0.84 0.09 0.08
Matches are distributed among these distances:
112 49 0.11
113 267 0.62
114 10 0.02
115 2 0.00
116 1 0.00
117 8 0.02
119 9 0.02
120 1 0.00
121 3 0.01
122 1 0.00
123 35 0.08
124 47 0.11
ACGTcount: A:0.27, C:0.20, G:0.15, T:0.38
Consensus pattern (113 bp):
TCTTCTCATTATGAACTCTACCTGGTAATGCTGATCCATCGAATGATGAATTCGAGCAAAAAGTT
GAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGT
Found at i:29768 original size:236 final size:227
Alignment explanation
Indices: 29226--29835 Score: 766
Period size: 236 Copynumber: 2.7 Consensus size: 227
29216 TTGAACAAGC
* * * * *
29226 TCTTCTCATTATGAACTTTTTCTGAAAATGTTGATCCATCGAGTGATGAATTCGAGCAAAAGATT
1 TCTTCTCATTATGAACTTTCTCTGGAAATGCTGATCCATCAAGTGATGAATTCGAGCAAAAGGTT
*
29291 GAACAAGTTCTTCTCATTATGAACTTCTTTTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACT
66 GAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACT
* * * *
29356 -CTACCTGGTAATGTTGATCCATCGAATGATGAATTCGAGCAAAAAGTTGAATAAGTTCTTCTCA
131 CCTACCTGGTAATGCTGATCCATCGAATGATGAAGTCGAGCAAAAAGTTGAACAAGCTCTTCTCA
*
29420 TTATGAACTTATTCTTCCTTCTTCAGATGAGT
196 TTATGAACTTATTCTTCCTTCTTCAGATAAGT
* * * * *
29452 TATTCTCATTATGAACTCTAC-CTGGCAATACTGATCCATCGAA-TGATGAATTCGAGCAAAAAG
1 TCTTCTCATTATGAACT-TTCTCTGGAAATGCTGATCCATC-AAGTGATGAATTCGAGCAAAAGG
* *
29515 TTGAACAAGTTCTTCTCATTATGAACTTATTCTTCCTTCTTTAGATGAGTTCTTCTCATTATGAA
64 TTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
* * *** *
29580 CTCCT-TCTGGAAATATTGATGCTGATCTATCTCTTTCTGCGAT-AGAGTCGAGCAAAAGGTTGA
129 CTCCTACCTGG---TA---ATGCTGATCCA--TC-GAAT--GATGA-AGTCGAGCAAAAAGTTGA
*
29643 ACAAGCTCTTCTCATTATGAACTTCTTCTT-CTTCTTCAGATAAGT
182 ACAAGCTCTTCTCATTATGAACTTATTCTTCCTTCTTCAGATAAGT
* * * *
29688 TCTTCTCATTATGAACTTTCTCTGGAAATGCTGGTACATCAAGTGATGGATTTGAGCAAAAGGTT
1 TCTTCTCATTATGAACTTTCTCTGGAAATGCTGATCCATCAAGTGATGAATTCGAGCAAAAGGTT
*
29753 GAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACT
66 GAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACT
*
29818 -CTACCTAGTAATGCTGAT
131 CCTACCTGGTAATGCTGAT
29836 GACCCGAAGA
Statistics
Matches: 327, Mismatches: 39, Indels: 32
0.82 0.10 0.08
Matches are distributed among these distances:
226 117 0.36
227 4 0.01
229 2 0.01
230 8 0.02
232 9 0.03
233 2 0.01
234 2 0.01
235 7 0.02
236 130 0.40
237 46 0.14
ACGTcount: A:0.27, C:0.20, G:0.15, T:0.38
Consensus pattern (227 bp):
TCTTCTCATTATGAACTTTCTCTGGAAATGCTGATCCATCAAGTGATGAATTCGAGCAAAAGGTT
GAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACT
CCTACCTGGTAATGCTGATCCATCGAATGATGAAGTCGAGCAAAAAGTTGAACAAGCTCTTCTCA
TTATGAACTTATTCTTCCTTCTTCAGATAAGT
Found at i:29959 original size:76 final size:76
Alignment explanation
Indices: 29833--30063 Score: 399
Period size: 76 Copynumber: 3.0 Consensus size: 76
29823 TAGTAATGCT
* ** * * *
29833 GATGACCCGAAGATTTTGAAAACATCAAAAATCTCTCGAAGGCTTTTTGGAAATATCATGCACTG
1 GATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTG
29898 TAGGACTTACA
66 TAGGACTTACA
29909 GATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTG
1 GATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTG
29974 TAGGACTTACA
66 TAGGACTTACA
29985 GATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTG
1 GATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTG
*
30050 CAGGACTTACA
66 TAGGACTTACA
30061 GAT
1 GAT
30064 ATGGGAAATA
Statistics
Matches: 148, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
76 148 1.00
ACGTcount: A:0.35, C:0.21, G:0.19, T:0.25
Consensus pattern (76 bp):
GATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTG
TAGGACTTACA
Found at i:30365 original size:164 final size:165
Alignment explanation
Indices: 30067--30392 Score: 537
Period size: 164 Copynumber: 2.0 Consensus size: 165
30057 TACAGATATG
* * *
30067 GGAAATAGTTTACTAAGTAAGAAACTATGGAAATCGTTTTCTTACTATTCAACAATTTCATTTTC
1 GGAAATAGTTTACTAAGTAAAAAACTAAGAAAATCGTTTTCTTACTATTCAACAATTTCATTTTC
** *
30132 AGAAAAGATTGAATGAGAAACTATGAAAATCGTTTTCTCATTATTTTTCAAAATAACATGTTAAT
66 AGAAAAGATAAAATGAGAAACTATGAAAATCGTTTTCTCATTATTCTTCAAAATAACATGTTAAT
* *
30197 TGGGTAACATGCCCCAATCTTAAGATAATGCTGTT
131 TGGGTAACATGACCCAATCTCAAGATAATGCTGTT
*
30232 GGAAATAGTTTACTAAGTAAAAAACTAAGAAAATCGTTTTCTTACTTTTCAACAATTTCATTTTC
1 GGAAATAGTTTACTAAGTAAAAAACTAAGAAAATCGTTTTCTTACTATTCAACAATTTCATTTTC
* * *
30297 -GAAAAGATAAAATGAGAAACTATGGAAATCGTTTTCTCATTATTCTTCAAAATATCATGTTGAT
66 AGAAAAGATAAAATGAGAAACTATGAAAATCGTTTTCTCATTATTCTTCAAAATAACATGTTAAT
30361 TGGGTAACATGACCCAATCTCAAGATAATGCT
131 TGGGTAACATGACCCAATCTCAAGATAATGCT
30393 CATTCTTGTG
Statistics
Matches: 149, Mismatches: 12, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
164 88 0.59
165 61 0.41
ACGTcount: A:0.38, C:0.14, G:0.13, T:0.35
Consensus pattern (165 bp):
GGAAATAGTTTACTAAGTAAAAAACTAAGAAAATCGTTTTCTTACTATTCAACAATTTCATTTTC
AGAAAAGATAAAATGAGAAACTATGAAAATCGTTTTCTCATTATTCTTCAAAATAACATGTTAAT
TGGGTAACATGACCCAATCTCAAGATAATGCTGTT
Found at i:30925 original size:22 final size:22
Alignment explanation
Indices: 30900--30954 Score: 83
Period size: 22 Copynumber: 2.5 Consensus size: 22
30890 AATAAAGCTT
30900 TCATCTTTGAAAAGAAAATCTA
1 TCATCTTTGAAAAGAAAATCTA
* * *
30922 TCATCTTTAAAAATAGAATCTA
1 TCATCTTTGAAAAGAAAATCTA
30944 TCATCTTTGAA
1 TCATCTTTGAA
30955 GAGTGTAGAT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.42, C:0.15, G:0.07, T:0.36
Consensus pattern (22 bp):
TCATCTTTGAAAAGAAAATCTA
Found at i:33714 original size:114 final size:114
Alignment explanation
Indices: 33514--33739 Score: 380
Period size: 114 Copynumber: 2.0 Consensus size: 114
33504 GATCATGCAG
* * * *
33514 TTCATCTTTCAATTCCAATGATTGGTTCTGGGGTTCCTACCGAATCAGATCAGATAACTCAAAGA
1 TTCATCTTTCAAATCCAATGATTGGTTCTGGGATTCATACCAAATCAGATCAGATAACTCAAAGA
* *
33579 ACACTTTCATAAGATGCTATTGGGTCTCCTTATTTCTACTATGAGAAAA
66 ACACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACTATGAGAAAA
* *
33628 TTCATCTTTCAAATCCAATGATTGGTTTTGGGATTCATACCAAATCAGATCAGATAACTTAAAGA
1 TTCATCTTTCAAATCCAATGATTGGTTCTGGGATTCATACCAAATCAGATCAGATAACTCAAAGA
33693 ACACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACTATGAGAA
66 ACACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACTATGAGAA
33740 CGTGGCACTT
Statistics
Matches: 104, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
114 104 1.00
ACGTcount: A:0.31, C:0.19, G:0.15, T:0.34
Consensus pattern (114 bp):
TTCATCTTTCAAATCCAATGATTGGTTCTGGGATTCATACCAAATCAGATCAGATAACTCAAAGA
ACACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACTATGAGAAAA
Found at i:36044 original size:13 final size:13
Alignment explanation
Indices: 36026--36056 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
36016 TCAATTTTCC
36026 TTTTTCTTCTTCT
1 TTTTTCTTCTTCT
36039 TTTTTCTTCTTCT
1 TTTTTCTTCTTCT
36052 TTTTT
1 TTTTT
36057 TGTTGGATGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (13 bp):
TTTTTCTTCTTCT
Found at i:40827 original size:24 final size:24
Alignment explanation
Indices: 40778--40826 Score: 73
Period size: 24 Copynumber: 2.1 Consensus size: 24
40768 ATGAAATATT
40778 AATAATATATATAAATACTATAAA
1 AATAATATATATAAATACTATAAA
* *
40802 AATAATATGTATATATA-TATAAA
1 AATAATATATATAAATACTATAAA
40825 AA
1 AA
40827 AGAATTATAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 8 0.35
24 15 0.65
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.35
Consensus pattern (24 bp):
AATAATATATATAAATACTATAAA
Found at i:43018 original size:3 final size:3
Alignment explanation
Indices: 43010--43058 Score: 66
Period size: 3 Copynumber: 16.7 Consensus size: 3
43000 CTGTATTTAT
*
43010 TAA TAA TAA -AA TAA TAA TAA TAA TAA TTA TAA TAA TAA T-A TAAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA
43054 TAA TA
1 TAA TA
43059 TTTAAATGAA
Statistics
Matches: 41, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
2 4 0.10
3 35 0.85
4 2 0.05
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:45856 original size:31 final size:31
Alignment explanation
Indices: 45821--45887 Score: 80
Period size: 31 Copynumber: 2.2 Consensus size: 31
45811 CATAATGAGA
*
45821 TATGTTATTATTGGTTAAATACATGATGATG
1 TATGTTATTATTGATTAAATACATGATGATG
* * * * *
45852 TATGTTCTTGTTGATTATATATATGATGATT
1 TATGTTATTATTGATTAAATACATGATGATG
45883 TATGT
1 TATGT
45888 AGATTATGAA
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.28, C:0.03, G:0.18, T:0.51
Consensus pattern (31 bp):
TATGTTATTATTGATTAAATACATGATGATG
Found at i:51900 original size:35 final size:36
Alignment explanation
Indices: 51836--51909 Score: 84
Period size: 35 Copynumber: 2.1 Consensus size: 36
51826 AGGAATTATT
51836 CAAAGAGTATCGATACCAAAGTAGTAGTATC-GATAC
1 CAAAGAGTATCGATACCAAAGTAGTAGTATCAG-TAC
*
51872 CAAAG-GTATCGATACC-AGGATA-TAAGTATCAGTAC
1 CAAAGAGTATCGATACCAAAG-TAGT-AGTATCAGTAC
51907 CAA
1 CAA
51910 TTTTAGAGAT
Statistics
Matches: 34, Mismatches: 1, Indels: 7
0.81 0.02 0.17
Matches are distributed among these distances:
34 3 0.09
35 25 0.74
36 6 0.18
ACGTcount: A:0.42, C:0.18, G:0.19, T:0.22
Consensus pattern (36 bp):
CAAAGAGTATCGATACCAAAGTAGTAGTATCAGTAC
Found at i:52632 original size:23 final size:23
Alignment explanation
Indices: 52598--52669 Score: 99
Period size: 23 Copynumber: 3.1 Consensus size: 23
52588 GAGTCGAGGG
*
52598 TTCTACGCGGTCCTTCGGGACAT
1 TTCTACGTGGTCCTTCGGGACAT
*
52621 TTCTACGTGGTCCTTCGGGACAA
1 TTCTACGTGGTCCTTCGGGACAT
* **
52644 TACTATATGGTCCTTCGGGACAT
1 TTCTACGTGGTCCTTCGGGACAT
52667 TTC
1 TTC
52670 CATGTGGCAC
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 42 1.00
ACGTcount: A:0.17, C:0.26, G:0.24, T:0.33
Consensus pattern (23 bp):
TTCTACGTGGTCCTTCGGGACAT
Found at i:52682 original size:23 final size:23
Alignment explanation
Indices: 52606--52684 Score: 97
Period size: 23 Copynumber: 3.4 Consensus size: 23
52596 GGTTCTACGC
*
52606 GGTCCTTCGGGACATTTCTACGT
1 GGTCCTTCGGGACATTTCTATGT
* * *
52629 GGTCCTTCGGGACAATACTATAT
1 GGTCCTTCGGGACATTTCTATGT
*
52652 GGTCCTTCGGGACATTTCCATGT
1 GGTCCTTCGGGACATTTCTATGT
52675 GG-CACTTCGG
1 GGTC-CTTCGG
52685 TGTAATTTTT
Statistics
Matches: 47, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
22 1 0.02
23 46 0.98
ACGTcount: A:0.16, C:0.25, G:0.27, T:0.32
Consensus pattern (23 bp):
GGTCCTTCGGGACATTTCTATGT
Found at i:52790 original size:26 final size:25
Alignment explanation
Indices: 52747--52806 Score: 61
Period size: 25 Copynumber: 2.4 Consensus size: 25
52737 ACAATATAAA
*
52747 ACTTTCATATCTCGTTTT-CATCTTTC
1 ACTTTCATATCTCCTTTTACA--TTTC
52773 ACTTTCATAT-TCACTTTTACATTTC
1 ACTTTCATATCTC-CTTTTACATTTC
*
52798 ATTTTCATA
1 ACTTTCATA
52807 ATCCATACTT
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
25 14 0.47
26 14 0.47
27 2 0.07
ACGTcount: A:0.22, C:0.23, G:0.02, T:0.53
Consensus pattern (25 bp):
ACTTTCATATCTCCTTTTACATTTC
Found at i:54012 original size:90 final size:90
Alignment explanation
Indices: 53859--54036 Score: 302
Period size: 90 Copynumber: 2.0 Consensus size: 90
53849 ACTAACACAC
* * *
53859 CCTTTTATAGCCAAGTTACCCTAATCATATTAGGGTTTTTATTATTTCCAATTAATTAAATCTAT
1 CCTTTTATAGCCAAGTTACCCTAATCATATCAGGGATTTTATTATTTCAAATTAATTAAATCTAT
* *
53924 ATTTAATTAATTGGAATTTAATAAT
66 ATTTAATTAATTGAAATTAAATAAT
*
53949 CCTTTTATATCCAAGTTACCCTAATCATATCAGGGATTTTATTATTTCAAATTAATTAAATCTAT
1 CCTTTTATAGCCAAGTTACCCTAATCATATCAGGGATTTTATTATTTCAAATTAATTAAATCTAT
54014 ATTTAATTAATTGAAATTAAATA
66 ATTTAATTAATTGAAATTAAATA
54037 TCCGGGATTA
Statistics
Matches: 82, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
90 82 1.00
ACGTcount: A:0.37, C:0.12, G:0.07, T:0.44
Consensus pattern (90 bp):
CCTTTTATAGCCAAGTTACCCTAATCATATCAGGGATTTTATTATTTCAAATTAATTAAATCTAT
ATTTAATTAATTGAAATTAAATAAT
Found at i:58998 original size:30 final size:30
Alignment explanation
Indices: 58962--59083 Score: 99
Period size: 29 Copynumber: 4.0 Consensus size: 30
58952 TCAAAAACCT
*
58962 AACTTTTAAAAATTATACTTTTGGTCCCTA
1 AACTTTTAAAAATTATACTTTTGGTCACTA
* * *
58992 AACTTTT-GAAATT-TGCCTTTTTGGTCCCTTA
1 AACTTTTAAAAATTAT-AC-TTTTGGTCAC-TA
** *
59023 AACTTTTCCAAACTTTATAC-TTTAGTCACTA
1 AACTTTT--AAAAATTATACTTTTGGTCACTA
*
59054 AACTTTTAAAATTTATA-TTTTGGTCACTA
1 AACTTTTAAAAATTATACTTTTGGTCACTA
59083 A
1 A
59084 CTAAAATTTT
Statistics
Matches: 74, Mismatches: 10, Indels: 17
0.73 0.10 0.17
Matches are distributed among these distances:
28 1 0.01
29 26 0.35
30 17 0.23
31 18 0.24
32 7 0.09
34 4 0.05
35 1 0.01
ACGTcount: A:0.30, C:0.17, G:0.07, T:0.45
Consensus pattern (30 bp):
AACTTTTAAAAATTATACTTTTGGTCACTA
Found at i:59056 original size:31 final size:29
Alignment explanation
Indices: 58962--59083 Score: 84
Period size: 30 Copynumber: 4.0 Consensus size: 29
58952 TCAAAAACCT
* * *
58962 AACTTTTAAAAATTATACTTTTGGTCCCTA
1 AACTTTTAAAATTTATAC-TTTAGTCACTA
* * * * *
58992 AACTTTTGAAATTTGCCT-TTTTGGTCCCTTA
1 AACTTTTAAAATTT--ATACTTTAGTCAC-TA
*
59023 AACTTTTCCAAACTTTATACTTTAGTCACTA
1 AACTTTT--AAAATTTATACTTTAGTCACTA
* *
59054 AACTTTTAAAATTTATATTTTGGTCACTA
1 AACTTTTAAAATTTATACTTTAGTCACTA
59083 A
1 A
59084 CTAAAATTTT
Statistics
Matches: 73, Mismatches: 13, Indels: 13
0.74 0.13 0.13
Matches are distributed among these distances:
29 20 0.27
30 21 0.29
31 19 0.26
32 8 0.11
33 5 0.07
ACGTcount: A:0.30, C:0.17, G:0.07, T:0.45
Consensus pattern (29 bp):
AACTTTTAAAATTTATACTTTAGTCACTA
Found at i:61168 original size:13 final size:13
Alignment explanation
Indices: 61150--61179 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
61140 AACAAAAAAT
61150 AATTAAAATTAAA
1 AATTAAAATTAAA
*
61163 AATTAAATTTAAA
1 AATTAAAATTAAA
61176 AATT
1 AATT
61180 CTAAATTATC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (13 bp):
AATTAAAATTAAA
Found at i:62086 original size:22 final size:23
Alignment explanation
Indices: 62061--62106 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
62051 TATTTAATTT
* *
62061 TTAAAA-AATATTAAATTGAATG
1 TTAAAATAATAATAAATTAAATG
*
62083 TTAAAATAGTAATAAATTAAATG
1 TTAAAATAATAATAAATTAAATG
62106 T
1 T
62107 ATTCCACAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
22 6 0.30
23 14 0.70
ACGTcount: A:0.54, C:0.00, G:0.09, T:0.37
Consensus pattern (23 bp):
TTAAAATAATAATAAATTAAATG
Found at i:62513 original size:2 final size:2
Alignment explanation
Indices: 62502--62532 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
62492 AGGTATCGTT
62502 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
62533 ATGCTGTTGT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:62863 original size:2 final size:2
Alignment explanation
Indices: 62858--62896 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
62848 TGTATATATA
62858 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
62897 ATCATTATAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:63115 original size:8 final size:8
Alignment explanation
Indices: 63102--63130 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
63092 ATCTAAAACA
63102 GATTGGTT
1 GATTGGTT
63110 GATTGGTT
1 GATTGGTT
63118 GATTGGTT
1 GATTGGTT
63126 GATTG
1 GATTG
63131 ATGTTTGTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.14, C:0.00, G:0.38, T:0.48
Consensus pattern (8 bp):
GATTGGTT
Done.