Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008518.1 Hibiscus syriacus cultivar Beakdansim tig00111385_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: 39356
ACGTcount: A:0.30, C:0.20, G:0.18, T:0.31
Found at i:4009 original size:17 final size:17
Alignment explanation
Indices: 3987--4028 Score: 75
Period size: 17 Copynumber: 2.5 Consensus size: 17
3977 TTGTTTGGTG
3987 ATAGAATCAAAATTTTA
1 ATAGAATCAAAATTTTA
4004 ATAGAATCAAAATTTTA
1 ATAGAATCAAAATTTTA
*
4021 ATGGAATC
1 ATAGAATC
4029 TCTGGAATAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.50, C:0.07, G:0.10, T:0.33
Consensus pattern (17 bp):
ATAGAATCAAAATTTTA
Found at i:6389 original size:15 final size:15
Alignment explanation
Indices: 6369--6403 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
6359 TGTTCACCAT
*
6369 TCGAACAAACTTCAC
1 TCGAACAAACATCAC
*
6384 TCGAACAAGCATCAC
1 TCGAACAAACATCAC
6399 TCGAA
1 TCGAA
6404 GAGCCTTGCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.40, C:0.31, G:0.11, T:0.17
Consensus pattern (15 bp):
TCGAACAAACATCAC
Found at i:20321 original size:23 final size:23
Alignment explanation
Indices: 20295--20342 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
20285 ATAAAGTACA
*
20295 ATAACATACTAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
**
20318 ATAATGTAATAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
20341 AT
1 AT
20343 TTACCTATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.35, C:0.12, G:0.19, T:0.33
Consensus pattern (23 bp):
ATAACATAATAGGTAGCGCTTAT
Found at i:20747 original size:21 final size:20
Alignment explanation
Indices: 20717--20770 Score: 54
Period size: 23 Copynumber: 2.5 Consensus size: 20
20707 GATAGACACT
*
20717 TTACAATATAACCATTACCTA
1 TTACATTATAACCA-TACCTA
*
20738 TTACATTATATAAACGATACCTA
1 TTACA-T-TAT-AACCATACCTA
20761 TTACATTATA
1 TTACATTATA
20771 TAAGGGCTAC
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
20 1 0.04
21 8 0.29
22 1 0.04
23 14 0.50
24 4 0.14
ACGTcount: A:0.43, C:0.19, G:0.02, T:0.37
Consensus pattern (20 bp):
TTACATTATAACCATACCTA
Found at i:20758 original size:23 final size:23
Alignment explanation
Indices: 20732--20794 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
20722 ATATAACCAT
20732 TACCTATTACATTATATAAACGA
1 TACCTATTACATTATATAAACGA
** *
20755 TACCTATTACATTATATAAGGGC
1 TACCTATTACATTATATAAACGA
*
20778 TACCTATTACATCATAT
1 TACCTATTACATTATAT
20795 GTTTACCTAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.38, C:0.19, G:0.06, T:0.37
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:21111 original size:429 final size:428
Alignment explanation
Indices: 20454--21321 Score: 1679
Period size: 429 Copynumber: 2.0 Consensus size: 428
20444 GGATCGATAC
20454 TTTAACAGTGTTTCATGTTTTCCACCTACAATATTGATTTAATAATTTCATTTGCACAAAAATTA
1 TTTAACAGTGTTTCATGTTTTCCACCTACAATATTGATTTAATAATTTCATTTGCACAAAAATTA
20519 TTTGATTGTTTTTGATATTTTATAAAATATTATTTAGAATTTTTAATTTAATAATAATATACCGT
66 TTTGATTGTTTTTGATATTTTATAAAATATTATTTAGAATTTTTAATTTAATAATAATATACCGT
20584 AACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACTCAAAA
131 AACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACTCAAAA
20649 GATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTTTTATAAAAAGGATAGAC
196 GATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTTTTATAAAAAGGATAGAC
20714 ACTTTACAATATAACCATTACCTATTACATTATATAAACGATACCTATTACATTATATAAGGGCT
261 ACTTTACAATATAACCATTACCTATTACATTATATAAACGATACCTATTACATTATATAAGGGCT
20779 ACCTATTACATCATATGTTTACCTATTATA-TGAAAGTGTCCATACTTTTTATAAAAAGGATCGA
326 ACCTATTACATCATATGTTTACCTATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGA
20843 TAC-TTTTTTAAAACTTATGTAATTTATGTTTCAATTTT
391 TACTTTTTTTAAAACTTATGTAATTTATGTTTCAA-TTT
20881 TTTAACAGTGTTTCATGTTTTCCACCTACAATATTGATTTAATAATTTCATTTGCACCAAAAATT
1 TTTAACAGTGTTTCATGTTTTCCACCTACAATATTGATTTAATAATTTCATTTGCA-CAAAAATT
20946 ATTTGATTG-TTTTGATATTTTATAAAATATTATTTAGAATTTTTAATTTAATAATAATATATAC
65 ATTTGATTGTTTTTGATATTTTATAAAATATTATTTAGAATTTTTAATTTAATAAT-A-ATATAC
21010 CGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACTCA
128 CGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACTCA
21075 AAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTTTTATAAAAAGGATA
193 AAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTTTTATAAAAAGGATA
21140 GACACTTTACAATATAACCATTACCTATTACATTATATAAACGATACCTATTACATTATATAAGG
258 GACACTTTACAATATAACCATTACCTATTACATTATATAAACGATACCTATTACATTATATAAGG
21205 GCTACCTATTACATCATATGTTTACCTATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGAT
323 GCTACCTATTACATCATATGTTTACCTATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGAT
21270 CGATACTTTTTTTAAAACTTATGTAATTTATGTTTCAATTT
388 CGATACTTTTTTTAAAACTTATGTAATTTATGTTTCAATTT
21311 TTTAACAGTGT
1 TTTAACAGTGT
21322 ACTGCGAATT
Statistics
Matches: 436, Mismatches: 0, Indels: 7
0.98 0.00 0.02
Matches are distributed among these distances:
427 102 0.23
428 18 0.04
429 234 0.54
430 51 0.12
431 31 0.07
ACGTcount: A:0.39, C:0.13, G:0.09, T:0.40
Consensus pattern (428 bp):
TTTAACAGTGTTTCATGTTTTCCACCTACAATATTGATTTAATAATTTCATTTGCACAAAAATTA
TTTGATTGTTTTTGATATTTTATAAAATATTATTTAGAATTTTTAATTTAATAATAATATACCGT
AACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACTCAAAA
GATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTTTTATAAAAAGGATAGAC
ACTTTACAATATAACCATTACCTATTACATTATATAAACGATACCTATTACATTATATAAGGGCT
ACCTATTACATCATATGTTTACCTATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGA
TACTTTTTTTAAAACTTATGTAATTTATGTTTCAATTT
Found at i:21176 original size:21 final size:20
Alignment explanation
Indices: 21146--21199 Score: 54
Period size: 23 Copynumber: 2.5 Consensus size: 20
21136 GATAGACACT
*
21146 TTACAATATAACCATTACCTA
1 TTACATTATAACCA-TACCTA
*
21167 TTACATTATATAAACGATACCTA
1 TTACA-T-TAT-AACCATACCTA
21190 TTACATTATA
1 TTACATTATA
21200 TAAGGGCTAC
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
20 1 0.04
21 8 0.29
22 1 0.04
23 14 0.50
24 4 0.14
ACGTcount: A:0.43, C:0.19, G:0.02, T:0.37
Consensus pattern (20 bp):
TTACATTATAACCATACCTA
Found at i:21187 original size:23 final size:23
Alignment explanation
Indices: 21161--21223 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
21151 ATATAACCAT
21161 TACCTATTACATTATATAAACGA
1 TACCTATTACATTATATAAACGA
** *
21184 TACCTATTACATTATATAAGGGC
1 TACCTATTACATTATATAAACGA
*
21207 TACCTATTACATCATAT
1 TACCTATTACATTATAT
21224 GTTTACCTAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.38, C:0.19, G:0.06, T:0.37
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:24296 original size:181 final size:183
Alignment explanation
Indices: 23767--24430 Score: 1214
Period size: 181 Copynumber: 3.7 Consensus size: 183
23757 TTTTAAATGG
*
23767 TATGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCA
1 TATGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCA
*
23832 TAAAACCGGTATATTTATACCGTTATATTACAAAATTATCTATTACATTATAATTATGGGTTCCG
66 TAAGACCGGTATATTTATACCGTTATATTACAAAATTATCTATTACATTATAATTATGGGTTCCG
23897 ATGTGTAAAATGTCGACACTTTTTTAAATTGTATCGACACATTTTTCTTCCAA
131 ATGTGTAAAATGTCGACACTTTTTTAAATTGTATCGACACATTTTTCTTCCAA
23950 TATGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCA
1 TATGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCA
24015 TAAGACCGGTATATTTATACCGTTATATTACAAAATTATCTATTACATTATAATTAT-GGTTCCG
66 TAAGACCGGTATATTTATACCGTTATATTACAAAATTATCTATTACATTATAATTATGGGTTCCG
24079 ATGTGTAAAATGTCGACACTTTTTTAAATTGTATCGACACATTTTTCTTCCAA
131 ATGTGTAAAATGTCGACACTTTTTTAAATTGTATCGACACATTTTTCTTCCAA
24132 TATGGACATAAAGTACCGACACAATATT-AAAAGTGTCGATATAGG-TGTAGACCTATTCGCGCA
1 TATGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCA
24195 TAAGACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTATGGGTTCC
66 TAAGACCGGTATATTTATACC-GTTATATTACAAAATTATCTATTACATTATAATTATGGGTTCC
* *
24260 GATGTGTAAAATGTCGACAC-TTTTTGAATCGTATCGACACATTTTTCTTCCAA
130 GATGTGTAAAATGTCGACACTTTTTTAAATTGTATCGACACATTTTTCTTCCAA
24313 TATGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATT--CGCA
1 TATGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCA
**
24376 TAAGACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTTTATTATAAT
66 TAAGACCGGTATATTTATACC-GTTATATTACAAAATTATCTATTACATTATAAT
24431 ATGTTGAAAG
Statistics
Matches: 471, Mismatches: 6, Indels: 10
0.97 0.01 0.02
Matches are distributed among these distances:
180 39 0.08
181 169 0.36
182 131 0.28
183 132 0.28
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.35
Consensus pattern (183 bp):
TATGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCA
TAAGACCGGTATATTTATACCGTTATATTACAAAATTATCTATTACATTATAATTATGGGTTCCG
ATGTGTAAAATGTCGACACTTTTTTAAATTGTATCGACACATTTTTCTTCCAA
Found at i:25798 original size:9 final size:9
Alignment explanation
Indices: 25783--25830 Score: 60
Period size: 9 Copynumber: 5.3 Consensus size: 9
25773 ACTTGTTTGG
25783 ATCATCATC
1 ATCATCATC
*
25792 TTCATCATC
1 ATCATCATC
*
25801 ATCGTCATC
1 ATCATCATC
25810 ATCATCATC
1 ATCATCATC
* *
25819 GTCATCTTC
1 ATCATCATC
25828 ATC
1 ATC
25831 GTCAGCTTCA
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
9 32 1.00
ACGTcount: A:0.25, C:0.33, G:0.04, T:0.38
Consensus pattern (9 bp):
ATCATCATC
Found at i:25800 original size:12 final size:12
Alignment explanation
Indices: 25783--25842 Score: 63
Period size: 12 Copynumber: 5.2 Consensus size: 12
25773 ACTTGTTTGG
25783 ATCATCATCTTC
1 ATCATCATCTTC
*
25795 ATCATCATCGTC
1 ATCATCATCTTC
25807 ATCATCA---TC
1 ATCATCATCTTC
*
25816 ATCGTCATCTTC
1 ATCATCATCTTC
* *
25828 ATCGTCAGCTTC
1 ATCATCATCTTC
25840 ATC
1 ATC
25843 TTCTGCGACC
Statistics
Matches: 42, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
9 8 0.19
12 34 0.81
ACGTcount: A:0.23, C:0.33, G:0.07, T:0.37
Consensus pattern (12 bp):
ATCATCATCTTC
Found at i:25802 original size:6 final size:6
Alignment explanation
Indices: 25783--25830 Score: 60
Period size: 6 Copynumber: 8.0 Consensus size: 6
25773 ACTTGTTTGG
* * * *
25783 ATCATC ATCTTC ATCATC ATCGTC ATCATC ATCATC GTCATC TTCATC
1 ATCATC ATCATC ATCATC ATCATC ATCATC ATCATC ATCATC ATCATC
25831 GTCAGCTTCA
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
6 36 1.00
ACGTcount: A:0.25, C:0.33, G:0.04, T:0.38
Consensus pattern (6 bp):
ATCATC
Found at i:25803 original size:15 final size:15
Alignment explanation
Indices: 25783--25830 Score: 60
Period size: 15 Copynumber: 3.2 Consensus size: 15
25773 ACTTGTTTGG
*
25783 ATCATCATCTTCATC
1 ATCATCATCATCATC
*
25798 ATCATCGTCATCATC
1 ATCATCATCATCATC
* *
25813 ATCATCGTCATCTTC
1 ATCATCATCATCATC
25828 ATC
1 ATC
25831 GTCAGCTTCA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 30 1.00
ACGTcount: A:0.25, C:0.33, G:0.04, T:0.38
Consensus pattern (15 bp):
ATCATCATCATCATC
Found at i:27298 original size:227 final size:224
Alignment explanation
Indices: 26905--27357 Score: 847
Period size: 227 Copynumber: 2.0 Consensus size: 224
26895 CTAAAGTTCA
26905 GAGTTTCGAAGGACCTGATTTCCTCAGAGAATCGTTTGTTACAGAAGAGGTGGTTGAGAAGAACT
1 GAGTTTCGAAGGACCTGATTTCCTCAGAGAATCGTTTGTTACAGAAGAGGTGGTTGAGAAGAACT
26970 GGGTTGAGAAGAGCTTTGAGAAAGACCTCGCTTCTGACGCTGACGTTTTGGAGCCATTTGGTTGG
66 GGGTTGAGAAGAGCTTTGAGAAAGACCTCGCTTCTGACGCTGACGTTTTGGAGCCATTTGGTTGG
27035 ATGCTACCCCTATACAATGGAACACAAACACATTCAGGATAAAAACTCCAATATAGAAATCAATC
131 ATGCTACCCCTATACAATGGAACACAAACACATTCAGGATAAAAACTCCAATATAGAAATCAATC
27100 AAAACCCATAAAATATCGATAAATTTACCT
196 -AAACCCATAAAATATCGATAAATTTACCT
27130 GAGTTTCGAAGGACCTGATTTCCTCAGAAGAATCGTTTGTTACAGAAGGAGGTGGTTGAGAAGAA
1 GAGTTTCGAAGGACCTGATTTCCTCAG-AGAATCGTTTGTTACAGAA-GAGGTGGTTGAGAAGAA
27195 CTGGGTTGAGAAGAGCTTTGAGAAAGACCTCGCTTCTGACGCTGACGTTTTGGAGCCATTTTGGT
64 CTGGGTTGAGAAGAGCTTTGAGAAAGACCTCGCTTCTGACGCTGACGTTTTGGAGCCA-TTTGGT
27260 TGGATGCTACCCCTATTACAATGG-A-ACAAACACATTCAGGATAAAAACTCCAATATAGAAATC
128 TGGATGCTACCCCTA-TACAATGGAACACAAACACATTCAGGATAAAAACTCCAATATAGAAATC
27323 AATCAAACCCATAAAATATCGATAAATTTACCT
192 AATCAAACCCATAAAATATCGATAAATTTACCT
27356 GA
1 GA
27358 ATATCTGATC
Statistics
Matches: 224, Mismatches: 0, Indels: 7
0.97 0.00 0.03
Matches are distributed among these distances:
225 27 0.12
226 50 0.22
227 117 0.52
228 22 0.10
229 8 0.04
ACGTcount: A:0.34, C:0.18, G:0.22, T:0.26
Consensus pattern (224 bp):
GAGTTTCGAAGGACCTGATTTCCTCAGAGAATCGTTTGTTACAGAAGAGGTGGTTGAGAAGAACT
GGGTTGAGAAGAGCTTTGAGAAAGACCTCGCTTCTGACGCTGACGTTTTGGAGCCATTTGGTTGG
ATGCTACCCCTATACAATGGAACACAAACACATTCAGGATAAAAACTCCAATATAGAAATCAATC
AAACCCATAAAATATCGATAAATTTACCT
Found at i:27435 original size:15 final size:15
Alignment explanation
Indices: 27415--27445 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
27405 AAGATCTGCC
27415 TGCTTGCATTTATGT
1 TGCTTGCATTTATGT
27430 TGCTTGCATTTATGT
1 TGCTTGCATTTATGT
27445 T
1 T
27446 TAGGGTTTCT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.13, C:0.13, G:0.19, T:0.55
Consensus pattern (15 bp):
TGCTTGCATTTATGT
Found at i:28045 original size:197 final size:199
Alignment explanation
Indices: 27507--29107 Score: 2825
Period size: 199 Copynumber: 8.1 Consensus size: 199
27497 TTTAAATTAG
* *
27507 TATCGACACAAA-TATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATT
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
*
27571 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGA-TTTGGGAT
66 ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
* *
27635 CGACAC-GTTT-TATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGG--AA
131 CGACACTTTTTATATATGGATCGACACTTTATGGATGCACCTTGTTTTTAATTCATTCTGGAAAA
27696 AAAA
196 AAAA
*
27700 TATCGACACAAACTATATTA--GTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
*
27763 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTTGGGTTCGATGATTTTGGGA
66 ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATAC-TTTTGGGTTCGATGATTTTGGGA
* * *
27828 TCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTT-TTTCATTCTGGGAA
130 TCGACACTTTTTATATATGGATCGACACTTTATGGATGCACCTTGTTTTTAATTCATTCTGGAAA
27892 AAAAA
195 AAAAA
*
27897 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTTATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
*
27962 ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGTTTCGATGA-TTTGGGAT
66 ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
*
28026 CGACACTTTTTATATATGGATCGACACTTTATTGATGCACCTTG-TTTTAATTCATTCTGGAAAA
131 CGACACTTTTTATATATGGATCGACACTTTATGGATGCACCTTGTTTTTAATTCATTCTGGAAAA
28090 AAAA
196 AAAA
28094 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
28159 ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
*
28224 CGACAC-TTTT-TATATGGATCGACACTTTATTGATGCACCTTGTTTTTAATTCATTCTGGAAAA
131 CGACACTTTTTATATATGGATCGACACTTTATGGATGCACCTTGTTTTTAATTCATTCTGGAAAA
28287 AAAA
196 AAAA
28291 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
28356 ATTGTACCGGTTAGATT-AAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
*
28420 CGACACTTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGGAA
131 CGACAC-TTTTTATATATGGATCGACACTTTATGGATGCACCTTGTTTTTAATTCATTCT-GGAA
28485 AAAAAA
194 AAAAAA
28491 TATCGACAC-AACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
28555 ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
* *
28620 CGACACTTTTT-TATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGGAAA
131 CGACACTTTTTATATATGGATCGACACTTTATGGATGCACCTTGTTTTTAATTCATTCTGGAAAA
28684 AAAA
196 AAAA
28688 TATCGACAC-AAC--TATTAGTGTCGACACATTATTTAGACTTATTCTCTCAT--AACCGG--TA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
*
28746 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
*
28811 CGACACTTTTTATATATGGATCGACACTTTATTGATGCACCTTGTTTTTAATTCATTCTGGAAAA
131 CGACACTTTTTATATATGGATCGACACTTTATGGATGCACCTTGTTTTTAATTCATTCTGGAAAA
28876 AAAA
196 AAAA
28880 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
28945 ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
*
29010 CGACACTTTTTATATATGGATCGACACTTTATTGATGCACCTTGTTTTTAATTCATTCTGGAAAA
131 CGACACTTTTTATATATGGATCGACACTTTATGGATGCACCTTGTTTTTAATTCATTCTGGAAAA
29075 AAAA
196 AAAA
*
29079 TATCGACACAAACTATATTAGTATCGACA
1 TATCGACACAAACTATATTAGTGTCGACA
29108 TGACCCTTAA
Statistics
Matches: 1361, Mismatches: 22, Indels: 44
0.95 0.02 0.03
Matches are distributed among these distances:
191 77 0.06
192 146 0.11
193 36 0.03
194 21 0.02
195 89 0.07
196 126 0.09
197 349 0.26
198 79 0.06
199 366 0.27
200 72 0.05
ACGTcount: A:0.32, C:0.15, G:0.15, T:0.38
Consensus pattern (199 bp):
TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
CGACACTTTTTATATATGGATCGACACTTTATGGATGCACCTTGTTTTTAATTCATTCTGGAAAA
AAAA
Found at i:29026 original size:589 final size:588
Alignment explanation
Indices: 27507--29107 Score: 2821
Period size: 589 Copynumber: 2.7 Consensus size: 588
27497 TTTAAATTAG
* *
27507 TATCGACACAAATATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATTA
1 TATCGACACAAA-CTATTAGTGTCGACACATTATTTAGACTTATTCTCTCAT-AAACCGGTA--A
27572 TTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGA-TTTGGGATC
62 TTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGATC
* * *
27636 GACACGTTTTATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGG--AAAAA
127 GACACTTTTTATATGGATCGACACTTTATTGATGCACCTTGTTTTTAATTCATTCTGGAAAAAAA
*
27699 ATATCGACACAAACTATATTA--GTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTAT
192 ATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTAT
27762 AATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTTGGGTTCGATGATTTTGGG
257 AATTGTACCGGTTAGATT-AAAAATTACATATTACATTATAC-TTTTGGGTTCGATGATTTTGGG
*
27827 ATCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTT-TTTCATTCTGGG-
320 ATCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGGA
*
27890 AAAAAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTTATAAAAC
385 AAAAAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAAC
*
27955 CGGTATAATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGTTTCGATGATT
450 CGGTATAATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATT
*
28020 TGGGATCGACACTTTTTATATATGGATCGACACTTTATTGATGCACCTTGTTTTAATTCATTCTG
515 TGGGATCGACACTTTTTATATATGGATCGACACTTTATGGATGCACCTTGTTTTAATTCATTCTG
28085 GAAAAAAAA
580 GAAAAAAAA
28094 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
1 TATCGACACAAAC--TATTAGTGTCGACACATTATTTAGACTTATTCTCTCAT-AAACCGG--TA
*
28159 ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
61 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
28224 CGACACTTTTTATATGGATCGACACTTTATTGATGCACCTTGTTTTTAATTCATTCTGGAAAAAA
126 CGACACTTTTTATATGGATCGACACTTTATTGATGCACCTTGTTTTTAATTCATTCTGGAAAAAA
28289 AATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTA
191 AATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTA
28354 TAATTGTACCGGTTAGATTAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGA
256 TAATTGTACCGGTTAGATTAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGA
28419 TCGACACTTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGGA
321 TCGACAC-TTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGGA
28484 AAAAAAATATCGACAC-AACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAAC
385 AAAAAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAAC
28548 CGGTATAATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATT
450 CGGTATAATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGA-T
*
28613 TTGGGATCGACACTTTTT-TATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTC
514 TTGGGATCGACACTTTTTATATATGGATCGACACTTTATGGATGCACCTTG-TTTTAATTCATTC
*
28677 TGGGAAAAAAA
578 TGGAAAAAAAA
28688 TATCGACAC-AACTATTAGTGTCGACACATTATTTAGACTTATTCTCTCAT-AACCGGTAATTGT
1 TATCGACACAAACTATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAACCGGTAATTGT
28751 ACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGATCGACA
66 ACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGATCGACA
28816 CTTTTTATATATGGATCGACACTTTATTGATGCACCTTGTTTTTAATTCATTCTGGAAAAAAAAT
131 C-TTTT-TATATGGATCGACACTTTATTGATGCACCTTGTTTTTAATTCATTCTGGAAAAAAAAT
28881 ATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATAA
194 ATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATAA
28946 TTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGATC
259 TTGTACCGGTTAGATT-AAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGATC
* *
29011 GACACTTTTTATATATGGATCGACACTTTATTGATGCACCTTGTTTTTAATTCATTCT-GGAAAA
323 GACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGGAAAA
*
29075 AAAATATCGACACAAACTATATTAGTATCGACA
388 AAAATATCGACACAAACTATATTAGTGTCGACA
29108 TGACCCTTAA
Statistics
Matches: 979, Mismatches: 17, Indels: 34
0.95 0.02 0.03
Matches are distributed among these distances:
587 84 0.09
588 123 0.13
589 278 0.28
590 55 0.06
591 94 0.10
592 66 0.07
593 212 0.22
594 67 0.07
ACGTcount: A:0.32, C:0.15, G:0.15, T:0.38
Consensus pattern (588 bp):
TATCGACACAAACTATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAACCGGTAATTGT
ACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGATCGACA
CTTTTTATATGGATCGACACTTTATTGATGCACCTTGTTTTTAATTCATTCTGGAAAAAAAATAT
CGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATAATT
GTACCGGTTAGATTAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGATCGAC
ACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGGAAAAAAA
ATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTAT
AATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTGGGAT
CGACACTTTTTATATATGGATCGACACTTTATGGATGCACCTTGTTTTAATTCATTCTGGAAAAA
AAA
Found at i:29216 original size:19 final size:19
Alignment explanation
Indices: 29189--29233 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 19
29179 ATTCACATAA
*
29189 AAAAATATAAATCGTATAC
1 AAAATTATAAATCGTATAC
*
29208 AAAATTATAAATCTTATAC
1 AAAATTATAAATCGTATAC
29227 AAAATTA
1 AAAATTA
29234 ACTCGACATT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.58, C:0.09, G:0.02, T:0.31
Consensus pattern (19 bp):
AAAATTATAAATCGTATAC
Found at i:31056 original size:33 final size:33
Alignment explanation
Indices: 31019--31084 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
31009 CATCTTAATA
*
31019 TCACCCCTTAACACCGAAACTTCTTTCACCACT
1 TCACCCCTCAACACCGAAACTTCTTTCACCACT
***
31052 TCACCCCTCAACACCTCTACTTCTTTCACCACT
1 TCACCCCTCAACACCGAAACTTCTTTCACCACT
31085 CCATCTATTT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.24, C:0.45, G:0.02, T:0.29
Consensus pattern (33 bp):
TCACCCCTCAACACCGAAACTTCTTTCACCACT
Found at i:33226 original size:23 final size:24
Alignment explanation
Indices: 33175--33226 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
33165 CCGTTCTATC
33175 TATTTTCAGAGGATATTTAGCTTA
1 TATTTTCAGAGGATATTTAGCTTA
** *
33199 TATTTTCATCGGATATTTA-TTTA
1 TATTTTCAGAGGATATTTAGCTTA
33222 TATTT
1 TATTT
33227 AATCGATACA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
23 8 0.32
24 17 0.68
ACGTcount: A:0.27, C:0.08, G:0.12, T:0.54
Consensus pattern (24 bp):
TATTTTCAGAGGATATTTAGCTTA
Found at i:33417 original size:20 final size:19
Alignment explanation
Indices: 33371--33417 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
33361 TCCGGTATCA
*
33371 TTTTACCGTTTTTATCATT
1 TTTTACCGGTTTTATCATT
*
33390 TTGATACCGGTTTTATCATAT
1 TT-TTACCGGTTTTATCAT-T
33411 TTTTACC
1 TTTTACC
33418 TGTTATATCG
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
19 2 0.09
20 18 0.78
21 3 0.13
ACGTcount: A:0.19, C:0.17, G:0.09, T:0.55
Consensus pattern (19 bp):
TTTTACCGGTTTTATCATT
Found at i:33565 original size:20 final size:20
Alignment explanation
Indices: 33538--33584 Score: 78
Period size: 20 Copynumber: 2.4 Consensus size: 20
33528 ACACTTTTAA
33538 TTTTACCGGTTTTATCAT-T
1 TTTTACCGGTTTTATCATAT
33557 TTGTTACCGGTTTTATCATAT
1 TT-TTACCGGTTTTATCATAT
33578 TTTTACC
1 TTTTACC
33585 TGGTATATCG
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
19 2 0.08
20 21 0.81
21 3 0.12
ACGTcount: A:0.17, C:0.17, G:0.11, T:0.55
Consensus pattern (20 bp):
TTTTACCGGTTTTATCATAT
Found at i:38792 original size:18 final size:19
Alignment explanation
Indices: 38757--38793 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
38747 CACGGAATGT
38757 AAGATTACCAGTGGGAATAA
1 AAGATTACCAG-GGGAATAA
38777 AAGATTACCA-GGGAATA
1 AAGATTACCAGGGGAATA
38794 GGATTACTGG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
20 10 0.59
ACGTcount: A:0.46, C:0.11, G:0.24, T:0.19
Consensus pattern (19 bp):
AAGATTACCAGGGGAATAA
Done.