Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003769.1 Hibiscus syriacus cultivar Beakdansim tig00008073_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: 57627
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
Found at i:1456 original size:175 final size:181
Alignment explanation
Indices: 968--1491 Score: 831
Period size: 175 Copynumber: 2.9 Consensus size: 181
958 ATCAGGTTTA
* *
968 ACTGAAGGGTTCATCTCATCACAAAGTCTTTGACCTGACAAAAGCAGTGGAGCAAACATCGAATT
1 ACTGAAGGGTTCATCTCATCACAAAGTCTTTGGCCTGACAAAAGCAGTGGAGCAAACACCGAATT
**
1033 GCCAAGTGTCCGAGCAATGTCAT-GATTTGAATGTAATCTATTCATAAAGCCAGGGCTTTCGAGT
66 GCCAAGTGTCCGAG--ATGTCATAG-TTTGAACATAATCTATTCATAAAGCCAGGGCTTTCGAGT
1097 TTCCTCTATAACCAA-TGCCTTAGTGGAATAGCTCAGCTTTAAAGGGACCAATC
128 TTCCTCTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTAAAGGGACCAATC
*
1150 ACTGAAGGGTTTCGTCTCATCACAAAGTCTTTGGCCTGACAAAAGCA-TGGAGCAAACACCGAAT
1 ACTGAAGGG-TTCATCTCATCACAAAGTCTTTGGCCTGACAAAAGCAGTGGAGCAAACACCGAAT
* *
1214 TTCCAAGTGTCCG-CATGTCATAGTTTGAACATAATCTATTCATAAAGCCAGGGC-TTCGAGTTT
65 TGCCAAGTGTCCGAGATGTCATAGTTTGAACATAATCTATTCATAAAGCCAGGGCTTTCGAGTTT
*
1277 CCTCTATAA-CAATTGCCTTAGTGGAATAGCTCA-CTTTAGA-GGA-CAATC
130 CCTCTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTAAAGGGACCAATC
1325 ACTGAAGGGTTCATCTCATCACAAAGTCTTTGGCCTGAC-AAAGCAGTGGAGCAAACACACGAAT
1 ACTGAAGGGTTCATCTCATCACAAAGTCTTTGGCCTGACAAAAGCAGTGGAGCAAACAC-CGAAT
1389 TGCCAAGTGTCCGAGAGTGTCATAGTTTGAACATAATCTA-TCAT-AAGCCAGGGCTTTCGAG-T
65 TGCCAAGTGTCCGAGA-TGTCATAGTTTGAACATAATCTATTCATAAAGCCAGGGCTTTCGAGTT
1451 TCCTCTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTA
129 TCCTCTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTA
1492 CGGTTTATTT
Statistics
Matches: 321, Mismatches: 11, Indels: 25
0.90 0.03 0.07
Matches are distributed among these distances:
173 6 0.02
174 41 0.13
175 52 0.16
176 38 0.12
177 37 0.12
178 38 0.12
179 36 0.11
180 1 0.00
182 37 0.12
183 35 0.11
ACGTcount: A:0.31, C:0.22, G:0.20, T:0.27
Consensus pattern (181 bp):
ACTGAAGGGTTCATCTCATCACAAAGTCTTTGGCCTGACAAAAGCAGTGGAGCAAACACCGAATT
GCCAAGTGTCCGAGATGTCATAGTTTGAACATAATCTATTCATAAAGCCAGGGCTTTCGAGTTTC
CTCTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTAAAGGGACCAATC
Found at i:4974 original size:19 final size:20
Alignment explanation
Indices: 4946--4983 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
4936 TGCAGATGAT
*
4946 GGAAATAAAAT-AAAAGAGA
1 GGAAAAAAAATGAAAAGAGA
4965 GGAAAAAAAATGAAAAGAG
1 GGAAAAAAAATGAAAAGAG
4984 TTAGTAAGGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.68, C:0.00, G:0.24, T:0.08
Consensus pattern (20 bp):
GGAAAAAAAATGAAAAGAGA
Found at i:6419 original size:37 final size:37
Alignment explanation
Indices: 6369--6473 Score: 138
Period size: 37 Copynumber: 2.8 Consensus size: 37
6359 GTGCTTGTGG
* * * *
6369 ATCCTATCTTTAGGAATTTAAATCTTAGTAGAACTCT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAGAACTCT
* * * *
6406 ATCCTATTTTTAGGAGTTTGAATCCTAGCAAAATTTT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAGAACTCT
6443 ATCCTATTTTTAGGAGTTTGAATCCTAGTAG
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAG
6474 GACGAAAATG
Statistics
Matches: 58, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
37 58 1.00
ACGTcount: A:0.30, C:0.14, G:0.14, T:0.42
Consensus pattern (37 bp):
ATCCTATTTTTAGGAGTTTGAATCCTAGTAGAACTCT
Found at i:6581 original size:21 final size:19
Alignment explanation
Indices: 6557--6597 Score: 64
Period size: 21 Copynumber: 2.1 Consensus size: 19
6547 TTCCTTTAGA
6557 GGGTATCAGTACCTCCTCATT
1 GGGTATCAGTACC-CCT-ATT
6578 GGGTATCAGTACCCCTATT
1 GGGTATCAGTACCCCTATT
6597 G
1 G
6598 AAATTTGTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 4 0.20
20 3 0.15
21 13 0.65
ACGTcount: A:0.20, C:0.27, G:0.22, T:0.32
Consensus pattern (19 bp):
GGGTATCAGTACCCCTATT
Found at i:11903 original size:19 final size:17
Alignment explanation
Indices: 11879--11923 Score: 54
Period size: 19 Copynumber: 2.5 Consensus size: 17
11869 TATATGGGTT
11879 TATGTGATATGAAAGTGTA
1 TATGTGATATGAAA-TG-A
* *
11898 TATGTGAAATGACATGA
1 TATGTGATATGAAATGA
11915 TATGTGATA
1 TATGTGATA
11924 AAAACCGTGA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
17 9 0.39
18 2 0.09
19 12 0.52
ACGTcount: A:0.38, C:0.02, G:0.24, T:0.36
Consensus pattern (17 bp):
TATGTGATATGAAATGA
Found at i:12228 original size:31 final size:31
Alignment explanation
Indices: 12193--12261 Score: 84
Period size: 31 Copynumber: 2.2 Consensus size: 31
12183 GAGACGTATA
* *
12193 GACAGTTTACATATGTTCTAAGGAATATATG
1 GACAGTTTACATAGGTTCTAAGGAACATATG
* ** *
12224 GACAGTTTACCTAGGTTCTTCGGGACATATG
1 GACAGTTTACATAGGTTCTAAGGAACATATG
12255 GACAGTT
1 GACAGTT
12262 GTCGAGGTTC
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.29, C:0.14, G:0.23, T:0.33
Consensus pattern (31 bp):
GACAGTTTACATAGGTTCTAAGGAACATATG
Found at i:13033 original size:22 final size:22
Alignment explanation
Indices: 13007--13063 Score: 87
Period size: 22 Copynumber: 2.6 Consensus size: 22
12997 TTTTAACATT
13007 CGGTATTGTTCATTAATGTTCA
1 CGGTATTGTTCATTAATGTTCA
* *
13029 TGGTATTGTTCATTACTGTTCA
1 CGGTATTGTTCATTAATGTTCA
*
13051 CGGTACTGTTCAT
1 CGGTATTGTTCAT
13064 ACCATATTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.19, C:0.16, G:0.19, T:0.46
Consensus pattern (22 bp):
CGGTATTGTTCATTAATGTTCA
Found at i:13040 original size:12 final size:12
Alignment explanation
Indices: 13023--13063 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
13013 TGTTCATTAA
*
13023 TGTTCATGGTAT
1 TGTTCATGGTAC
13035 TGTTCAT--TAC
1 TGTTCATGGTAC
*
13045 TGTTCACGGTAC
1 TGTTCATGGTAC
13057 TGTTCAT
1 TGTTCAT
13064 ACCATATTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
10 8 0.33
12 16 0.67
ACGTcount: A:0.17, C:0.17, G:0.20, T:0.46
Consensus pattern (12 bp):
TGTTCATGGTAC
Found at i:19322 original size:15 final size:16
Alignment explanation
Indices: 19302--19342 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
19292 GTTTACTTCA
*
19302 GAATGATT-AAGCGTT
1 GAATGATTCAAACGTT
*
19317 GAATGATTCAAATGTT
1 GAATGATTCAAACGTT
19333 GAATGATTCA
1 GAATGATTCA
19343 GAGACTCTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 8 0.35
16 15 0.65
ACGTcount: A:0.37, C:0.07, G:0.22, T:0.34
Consensus pattern (16 bp):
GAATGATTCAAACGTT
Found at i:20082 original size:23 final size:23
Alignment explanation
Indices: 20056--20103 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
20046 ATAAAGTACA
*
20056 ATAACATACTAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
**
20079 ATAATGTAATAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
20102 AT
1 AT
20104 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:20853 original size:18 final size:18
Alignment explanation
Indices: 20830--20866 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
20820 CGAAATATAT
20830 ATTGAAATTCAAACTCAA
1 ATTGAAATTCAAACTCAA
* *
20848 ATTGAAATTTAAATTCAA
1 ATTGAAATTCAAACTCAA
20866 A
1 A
20867 CTCCAATTAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.51, C:0.11, G:0.05, T:0.32
Consensus pattern (18 bp):
ATTGAAATTCAAACTCAA
Found at i:21096 original size:23 final size:23
Alignment explanation
Indices: 21070--21134 Score: 94
Period size: 23 Copynumber: 2.8 Consensus size: 23
21060 ATGCGAGATA
21070 GATACCTATTACATTATATAAAC
1 GATACCTATTACATTATATAAAC
**
21093 GATACCTATTACATTATATAAGG
1 GATACCTATTACATTATATAAAC
* *
21116 GCTACCTATTACATCATAT
1 GATACCTATTACATTATAT
21135 GTTTACCTAT
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.38, C:0.18, G:0.08, T:0.35
Consensus pattern (23 bp):
GATACCTATTACATTATATAAAC
Found at i:21318 original size:30 final size:29
Alignment explanation
Indices: 21278--21344 Score: 73
Period size: 30 Copynumber: 2.2 Consensus size: 29
21268 TCATTTGCAC
* * *
21278 AAAAAATTATTT-GATTGTTTTATATTTTAT
1 AAAATATTATTTAGAAT-TTTTA-ATTTAAT
21308 AAAATATTATTTAGAATTTTTAATTTAAT
1 AAAATATTATTTAGAATTTTTAATTTAAT
21337 AATAATAT
1 AA-AATAT
21345 ATACCGTAAC
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
29 8 0.25
30 21 0.66
31 3 0.09
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.52
Consensus pattern (29 bp):
AAAATATTATTTAGAATTTTTAATTTAAT
Found at i:21551 original size:23 final size:22
Alignment explanation
Indices: 21489--21560 Score: 90
Period size: 23 Copynumber: 3.2 Consensus size: 22
21479 ACACTTTACA
*
21489 ATATAACCACTACCTATTACATT
1 ATATAA-CGCTACCTATTACATT
*
21512 ATATAACGATACCTATTACATT
1 ATATAACGCTACCTATTACATT
* *
21534 ATATAAGGGCTACCTATTACATC
1 ATATAA-CGCTACCTATTACATT
21557 ATAT
1 ATAT
21561 GTTTACCTAT
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
22 20 0.47
23 23 0.53
ACGTcount: A:0.39, C:0.21, G:0.06, T:0.35
Consensus pattern (22 bp):
ATATAACGCTACCTATTACATT
Found at i:21754 original size:29 final size:29
Alignment explanation
Indices: 21706--21770 Score: 73
Period size: 29 Copynumber: 2.2 Consensus size: 29
21696 TCATTTGCAC
*
21706 AAAA-ATTATTTGATTGTTTTATATTT-AT
1 AAAATATTATTTGAATGTTTTA-ATTTAAT
21734 AAAATATTATTTAGAAT-TTTTAATTTAAT
1 AAAATATTATTT-GAATGTTTTAATTTAAT
21763 AATAATAT
1 AA-AATAT
21771 ATACCGTAAC
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
28 8 0.25
29 16 0.50
30 8 0.25
ACGTcount: A:0.43, C:0.00, G:0.05, T:0.52
Consensus pattern (29 bp):
AAAATATTATTTGAATGTTTTAATTTAAT
Found at i:21866 original size:426 final size:430
Alignment explanation
Indices: 21072--22087 Score: 1981
Period size: 426 Copynumber: 2.4 Consensus size: 430
21062 GCGAGATAGA
21072 TACCTATTACATTATATAAACGATACCTATTACATTATATAAGGGCTACCTATTACATCATATGT
1 TACCTATTACATTATATAAACGATACCTATTACATTATATAAGGGCTACCTATTACATCATATGT
*
21137 TTACCTATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATAC-TTTTTTAAAACTTA
66 TTACCTATTTTATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAACTTA
21201 TGTAATTTATGTTTCAA-TTTTTTAACAGTGTTTCATGTTTTCCACCTACAATATTGATTTAATA
131 TGTAATTTATGTTTCAATTTTTTTAACAGTGTTTCATGTTTTCCACCTACAATATTGATTTAATA
21265 ATTTCATTTGCACAAAAAATTATTTGATTGTTTTATATTTTATAAAATATTATTTAGAATTTTTA
196 ATTTCATTTGCACAAAAAATTATTTGATTGTTTTATATTTTATAAAATATTATTTAGAATTTTTA
21330 ATTTAATAATAATATATACCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTA
261 ATTTAATAATAATATATACCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTA
21395 ATATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGA
326 ATATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGA
21460 CACTTTTAT-AAAAGGATAGACACTTTACAATATAACCAC
391 CACTTTTATAAAAAGGATAGACACTTTACAATATAACCAC
21499 TACCTATTACATTATAT-AACGATACCTATTACATTATATAAGGGCTACCTATTACATCATATGT
1 TACCTATTACATTATATAAACGATACCTATTACATTATATAAGGGCTACCTATTACATCATATGT
21563 TTACCTATTTTATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAACTTA
66 TTACCTATTTTATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAACTTA
21628 TGTAATTTATGTTTCAATTTTTTTAACAGTGTTTCATGTTTTCCACCTACAATATTGATTTAATA
131 TGTAATTTATGTTTCAATTTTTTTAACAGTGTTTCATGTTTTCCACCTACAATATTGATTTAATA
21693 ATTTCATTTGCAC-AAAAATTATTTGATTGTTTTATA-TTTATAAAATATTATTTAGAATTTTTA
196 ATTTCATTTGCACAAAAAATTATTTGATTGTTTTATATTTTATAAAATATTATTTAGAATTTTTA
21756 ATTTAATAATAATATATACCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTA
261 ATTTAATAATAATATATACCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTA
21821 ATATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGA
326 ATATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGA
21886 CACTTTTATAAAAAGGATAGACACTTTACAATATAACCAC
391 CACTTTTATAAAAAGGATAGACACTTTACAATATAACCAC
21926 TACCTATTACATTATATAAACGATACCTATTACATTATATAAGGGCTACCTATTACATCATATGT
1 TACCTATTACATTATATAAACGATACCTATTACATTATATAAGGGCTACCTATTACATCATATGT
21991 TTACCTATTTTATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAACTTA
66 TTACCTATTTTATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAACTTA
22056 TGTAATTTATGTTTCAATTTTTTTAACAGTGT
131 TGTAATTTATGTTTCAATTTTTTTAACAGTGT
22088 ACTGCGAATT
Statistics
Matches: 584, Mismatches: 1, Indels: 7
0.99 0.00 0.01
Matches are distributed among these distances:
426 262 0.45
427 118 0.20
428 204 0.35
ACGTcount: A:0.38, C:0.13, G:0.08, T:0.40
Consensus pattern (430 bp):
TACCTATTACATTATATAAACGATACCTATTACATTATATAAGGGCTACCTATTACATCATATGT
TTACCTATTTTATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAACTTA
TGTAATTTATGTTTCAATTTTTTTAACAGTGTTTCATGTTTTCCACCTACAATATTGATTTAATA
ATTTCATTTGCACAAAAAATTATTTGATTGTTTTATATTTTATAAAATATTATTTAGAATTTTTA
ATTTAATAATAATATATACCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTA
ATATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGA
CACTTTTATAAAAAGGATAGACACTTTACAATATAACCAC
Found at i:21941 original size:21 final size:22
Alignment explanation
Indices: 21916--21967 Score: 77
Period size: 23 Copynumber: 2.3 Consensus size: 22
21906 ACACTTTACA
*
21916 ATATAACCACTACCTATTACATT
1 ATATAAACA-TACCTATTACATT
21939 ATATAAACGATACCTATTACATT
1 ATATAAAC-ATACCTATTACATT
21962 ATATAA
1 ATATAA
21968 GGGCTACCTA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
23 26 0.96
24 1 0.04
ACGTcount: A:0.44, C:0.19, G:0.02, T:0.35
Consensus pattern (22 bp):
ATATAAACATACCTATTACATT
Found at i:21952 original size:23 final size:23
Alignment explanation
Indices: 21926--21988 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
21916 ATATAACCAC
21926 TACCTATTACATTATATAAACGA
1 TACCTATTACATTATATAAACGA
** *
21949 TACCTATTACATTATATAAGGGC
1 TACCTATTACATTATATAAACGA
*
21972 TACCTATTACATCATAT
1 TACCTATTACATTATAT
21989 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:23405 original size:198 final size:200
Alignment explanation
Indices: 23067--24686 Score: 3015
Period size: 199 Copynumber: 8.1 Consensus size: 200
23057 TTTAAATTTG
* *
23067 TATCGACACAAAATATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
23132 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
*
23197 CGACAC-TTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGG-GA
131 CGACACTTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGAAA
23260 AAAAA
196 AAAAA
* *
23265 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACTGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
23330 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
*
23395 CGACAC-TTTTTATATATGGATCGACACTTTATTGGTGCACCTTGTTTTTAATTCATTCTGGAAA
131 CGACACTTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGAAA
23459 AAAAA
196 AAAAA
23464 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
23529 ATTGTACCGGTTAGATT-AAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
23593 CGACACTTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGG-AA
131 CGACACTTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGAAA
23657 AAAAA
196 AAAAA
23662 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
*
23727 ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
23792 CGACACTTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGAAA
131 CGACACTTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGAAA
23857 AAAAA
196 AAAAA
* *
23862 TATCGACACAAAATATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
*
23927 ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
23992 CGACACTTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGAAA
131 CGACACTTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGAAA
24057 AAAAA
196 AAAAA
24062 TATCGACACAAAC--TATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
* *
24125 ATTGTACCAGTTAGATTGAAAAATTACAGATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
24190 CGACAC-TTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGAAA
131 CGACACTTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGAAA
24254 AAAAA
196 AAAAA
*
24259 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCAGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
*
24324 ATTGTACCGGTTAGATTGAAAAATTACAGATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
* *
24389 CGACAC-TTTTTATATATGGATCGACACTTTATTGATGCACCTTGTTTTTAATTCATTCTGGAAA
131 CGACACTTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGAAA
24453 AAAAA
196 AAAAA
24458 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
*
24523 ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
24588 CGACACTTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGAAA
131 CGACACTTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGAAA
24653 AAAAA
196 AAAAA
*
24658 TATCGACACAAACTATATTAGTATCGACA
1 TATCGACACAAACTATATTAGTGTCGACA
24687 TGACCCTTAA
Statistics
Matches: 1391, Mismatches: 24, Indels: 12
0.97 0.02 0.01
Matches are distributed among these distances:
197 76 0.05
198 447 0.32
199 562 0.40
200 306 0.22
ACGTcount: A:0.32, C:0.15, G:0.15, T:0.38
Consensus pattern (200 bp):
TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
CGACACTTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGAAA
AAAAA
Found at i:23800 original size:397 final size:399
Alignment explanation
Indices: 23067--24686 Score: 3011
Period size: 397 Copynumber: 4.1 Consensus size: 399
23057 TTTAAATTTG
*
23067 TATCGACACAAAATATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
23132 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
*
23197 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGG-GAA
131 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGAAAA
* *
23261 AAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACTGG
196 AAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGG
*
23326 TATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTG
261 TATAATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTG
*
23391 GGATCGACAC-TTTTTATATATGGATCGACACTTTATTGGTGCACCTTGTTTTTAATTCATTCTG
326 GGATCGACACTTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTG
23455 GAAAAAAAA
391 GAAAAAAAA
*
23464 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
23529 ATTGTACCGGTTAGATT-AAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
23593 CGACACTTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGG-AA
131 CGACAC-TTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGAAA
23657 AAAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCG
195 AAAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCG
23722 GTATAATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTT
260 GTATAATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTT
23787 GGGATCGACACTTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCT
325 GGGATCGACACTTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCT
23852 GGAAAAAAAA
390 GGAAAAAAAA
*
23862 TATCGACACAAAATATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
*
23927 ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
23992 CGACACTTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGAAA
131 CGACAC-TTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGAAA
24057 AAAAATATCGACACAAAC--TATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCG
195 AAAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCG
* * *
24120 GTATAATTGTACCAGTTAGATTGAAAAATTACAGATTACATTATACTTTTGGGTTCGATGATTTT
260 GTATAATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTT
24185 GGGATCGACAC-TTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCT
325 GGGATCGACACTTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCT
24249 GGAAAAAAAA
390 GGAAAAAAAA
* *
24259 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCAGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
*
24324 ATTGTACCGGTTAGATTGAAAAATTACAGATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
* *
24389 CGACACTTTTTATATATGGATCGACACTTTATTGATGCACCTTGTTTTTAATTCATTCTGGAAAA
131 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGAAAA
24454 AAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGG
196 AAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGG
24519 TATAATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTG
261 TATAATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTG
24584 GGATCGACACTTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTG
326 GGATCGACACTTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTG
24649 GAAAAAAAA
391 GAAAAAAAA
*
24658 TATCGACACAAACTATATTAGTATCGACA
1 TATCGACACAAACTATATTAGTGTCGACA
24687 TGACCCTTAA
Statistics
Matches: 1193, Mismatches: 23, Indels: 12
0.97 0.02 0.01
Matches are distributed among these distances:
396 127 0.11
397 468 0.39
398 378 0.32
399 200 0.17
400 20 0.02
ACGTcount: A:0.32, C:0.15, G:0.15, T:0.38
Consensus pattern (399 bp):
TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGAAAA
AAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGG
TATAATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTG
GGATCGACACTTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTG
GAAAAAAAA
Found at i:24794 original size:19 final size:19
Alignment explanation
Indices: 24767--24811 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 19
24757 TATTCACATA
*
24767 AAAAATATAAATCGTATAC
1 AAAATTATAAATCGTATAC
*
24786 AAAATTATAAATCTTATAC
1 AAAATTATAAATCGTATAC
24805 AAAATTA
1 AAAATTA
24812 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:26637 original size:33 final size:33
Alignment explanation
Indices: 26600--26665 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
26590 CATCTTAATA
*
26600 TCACCCCTTAACACCGAAACTTCTTTCACCACT
1 TCACCCCTCAACACCGAAACTTCTTTCACCACT
***
26633 TCACCCCTCAACACCTCTACTTCTTTCACCACT
1 TCACCCCTCAACACCGAAACTTCTTTCACCACT
26666 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:28803 original size:24 final size:24
Alignment explanation
Indices: 28766--28818 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
28756 CCGTTCTATC
28766 TATTTTCAGAGGATAT-TTAGCTTA
1 TATTTTCAGAGGATATGTTA-CTTA
** *
28790 TATTTTCATCGGATATGTTATTTA
1 TATTTTCAGAGGATATGTTACTTA
28814 TATTT
1 TATTT
28819 AATCGATACA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 22 0.88
25 3 0.12
ACGTcount: A:0.26, C:0.08, G:0.13, T:0.53
Consensus pattern (24 bp):
TATTTTCAGAGGATATGTTACTTA
Found at i:29008 original size:20 final size:19
Alignment explanation
Indices: 28962--29008 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
28952 TCCGGTATCA
*
28962 TTTTACCGTTTTTATCATT
1 TTTTACCGGTTTTATCATT
*
28981 TTGATACCGGTTTTATCATAT
1 TT-TTACCGGTTTTATCAT-T
29002 TTTTACC
1 TTTTACC
29009 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:29155 original size:20 final size:20
Alignment explanation
Indices: 29129--29174 Score: 76
Period size: 20 Copynumber: 2.3 Consensus size: 20
29119 CACTTTTAAA
29129 TTTACCGGTTTTATCAT-TT
1 TTTACCGGTTTTATCATATT
29148 TGTTACCGGTTTTATCATATT
1 T-TTACCGGTTTTATCATATT
29169 TTTACC
1 TTTACC
29175 TGGTATATCG
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
19 1 0.04
20 21 0.84
21 3 0.12
ACGTcount: A:0.17, C:0.17, G:0.11, T:0.54
Consensus pattern (20 bp):
TTTACCGGTTTTATCATATT
Found at i:39075 original size:19 final size:19
Alignment explanation
Indices: 39051--39089 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
39041 TCGAATGCAT
39051 TCCATGCACCGATGCACTC
1 TCCATGCACCGATGCACTC
*
39070 TCCATGCATCGATGCACTC
1 TCCATGCACCGATGCACTC
39089 T
1 T
39090 GAATATTTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.21, C:0.38, G:0.15, T:0.26
Consensus pattern (19 bp):
TCCATGCACCGATGCACTC
Found at i:39214 original size:64 final size:65
Alignment explanation
Indices: 39037--39199 Score: 222
Period size: 65 Copynumber: 2.5 Consensus size: 65
39027 GAATTAATTG
* * * *
39037 AACATCGAATGCATTCCATGCACCGATGCACTCTCCATGCATCGATGCACTCTGAATATTTTCAA
1 AACATCGAATGCATTTCATGCATCGATGCACACTCCATGCATCGATGCACTCAGAATATTTTCAA
* ** **
39102 AACATCGAATGCATTTGATGCATCGATGCACAAGCCATGCATCGATGCAC-CAGGCTATTTTTC-
1 AACATCGAATGCATTTCATGCATCGATGCACACTCCATGCATCGATGCACTCAGAATA-TTTTCA
39165 A
65 A
39166 AACATCGAATGCATTTCATGCATCGATGCACACT
1 AACATCGAATGCATTTCATGCATCGATGCACACT
39200 TGGTGCACCG
Statistics
Matches: 85, Mismatches: 12, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
64 36 0.42
65 49 0.58
ACGTcount: A:0.30, C:0.27, G:0.16, T:0.27
Consensus pattern (65 bp):
AACATCGAATGCATTTCATGCATCGATGCACACTCCATGCATCGATGCACTCAGAATATTTTCAA
Found at i:49485 original size:30 final size:31
Alignment explanation
Indices: 49438--49584 Score: 143
Period size: 30 Copynumber: 5.0 Consensus size: 31
49428 CCCGAAGGAC
* * *
49438 CAGTCCATA-GATTCCGAAGAACCTAGGTAAT
1 CAGTCCATATG-TCCCGAAGAACATAGGTAAA
*
49469 CAGT-CATATGTCCCGAAGGACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
* * *
49499 CAGTCCGTATGTTCCGAAG-A-ATA--TAAT
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
49526 C---CCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
*
49554 CAGTCCATATGTCCAGAA-AACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
49584 C
1 C
49585 CCTCGACCTT
Statistics
Matches: 96, Mismatches: 11, Indels: 19
0.76 0.09 0.15
Matches are distributed among these distances:
24 13 0.14
25 1 0.01
26 3 0.03
27 4 0.04
28 4 0.04
29 3 0.03
30 38 0.40
31 30 0.31
ACGTcount: A:0.37, C:0.22, G:0.19, T:0.22
Consensus pattern (31 bp):
CAGTCCATATGTCCCGAAGAACATAGGTAAA
Found at i:49787 original size:23 final size:24
Alignment explanation
Indices: 49761--49807 Score: 78
Period size: 23 Copynumber: 2.0 Consensus size: 24
49751 ATATACTTGT
*
49761 TTTCACATATATA-TTTCATATCA
1 TTTCACATATACACTTTCATATCA
49784 TTTCACATATACACTTTCATATCA
1 TTTCACATATACACTTTCATATCA
49808 CATGCCATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 12 0.55
24 10 0.45
ACGTcount: A:0.34, C:0.21, G:0.00, T:0.45
Consensus pattern (24 bp):
TTTCACATATACACTTTCATATCA
Found at i:50433 original size:21 final size:21
Alignment explanation
Indices: 50403--50447 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
50393 ATTCTGTCGT
* *
50403 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
50424 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
50445 TTG
1 TTG
50448 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Done.