Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008880.1 Hibiscus syriacus cultivar Beakdansim tig00112124_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: 568240
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
File 3 of 3
Found at i:501931 original size:38 final size:38
Alignment explanation
Indices: 501878--501982 Score: 201
Period size: 38 Copynumber: 2.8 Consensus size: 38
501868 ACAAACGAGT
*
501878 TTGCTTCACTACTCTTTCGTGAAGGCTTATAGATTTAA
1 TTGCTTCACTGCTCTTTCGTGAAGGCTTATAGATTTAA
501916 TTGCTTCACTGCTCTTTCGTGAAGGCTTATAGATTTAA
1 TTGCTTCACTGCTCTTTCGTGAAGGCTTATAGATTTAA
501954 TTGCTTCACTGCTCTTTCGTGAAGGCTTA
1 TTGCTTCACTGCTCTTTCGTGAAGGCTTA
501983 AAATTTACTT
Statistics
Matches: 66, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
38 66 1.00
ACGTcount: A:0.20, C:0.20, G:0.18, T:0.42
Consensus pattern (38 bp):
TTGCTTCACTGCTCTTTCGTGAAGGCTTATAGATTTAA
Found at i:503291 original size:14 final size:14
Alignment explanation
Indices: 503274--503357 Score: 54
Period size: 14 Copynumber: 6.3 Consensus size: 14
503264 ATCTCTTTTT
503274 TTTTCATTTTTCTC
1 TTTTCATTTTTCTC
**
503288 TTTTTGTTTTTCTC
1 TTTTCATTTTTCTC
503302 -TTTCATTTTT-TC
1 TTTTCATTTTTCTC
** *
503314 -CATCATTTTTCTTT
1 TTTTCATTTTTC-TC
503328 TTTTC-TTTTTCT-
1 TTTTCATTTTTCTC
*
503340 TTTTC-TTCTTCTC
1 TTTTCATTTTTCTC
503353 ATTTT
1 -TTTT
503358 TATTATTATT
Statistics
Matches: 55, Mismatches: 10, Indels: 10
0.73 0.13 0.13
Matches are distributed among these distances:
12 21 0.38
13 9 0.16
14 23 0.42
15 2 0.04
ACGTcount: A:0.06, C:0.19, G:0.01, T:0.74
Consensus pattern (14 bp):
TTTTCATTTTTCTC
Found at i:503357 original size:20 final size:20
Alignment explanation
Indices: 503319--503357 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
503309 TTTTCCATCA
* * *
503319 TTTTTCTTTTTTTCTTTTTC
1 TTTTTCTTCTTCTCATTTTC
503339 TTTTTCTTCTTCTCATTTT
1 TTTTTCTTCTTCTCATTTT
503358 TATTATTATT
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:0.03, C:0.18, G:0.00, T:0.79
Consensus pattern (20 bp):
TTTTTCTTCTTCTCATTTTC
Found at i:513104 original size:45 final size:46
Alignment explanation
Indices: 513037--513140 Score: 183
Period size: 45 Copynumber: 2.3 Consensus size: 46
513027 TCATGCTTTG
513037 TTATTCACAAAAATAAATCCTAACCGCATGATATCTAATTCGCATGC
1 TTATTCA-AAAAATAAATCCTAACCGCATGATATCTAATTCGCATGC
*
513084 TTATTCAAAAAATAAA-CCTAACCGCATGATATCTAGTTCGCATGC
1 TTATTCAAAAAATAAATCCTAACCGCATGATATCTAATTCGCATGC
513129 TTATTCAAAAAA
1 TTATTCAAAAAA
513141 CGAAAATAAA
Statistics
Matches: 56, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
45 40 0.71
46 9 0.16
47 7 0.12
ACGTcount: A:0.40, C:0.21, G:0.09, T:0.30
Consensus pattern (46 bp):
TTATTCAAAAAATAAATCCTAACCGCATGATATCTAATTCGCATGC
Found at i:517771 original size:33 final size:34
Alignment explanation
Indices: 517734--517840 Score: 89
Period size: 33 Copynumber: 3.2 Consensus size: 34
517724 GGTAAGAAAT
* * *
517734 TTATTTTTATGTTAGTAT-TTT-TTTAAATAGTTA
1 TTATTTTTATATTAATATATTTATGTAAATA-TTA
517767 TTATTTTTATATTAATATATTTATGTAAATATTA
1 TTATTTTTATATTAATATATTTATGTAAATATTA
* * *
517801 -T-TTTTTAT-TAAAATAATATTTATATAATTATTA
1 TTATTTTTATAT-TAAT-ATATTTATGTAAATATTA
517834 TTTATTT
1 -TTATTT
517841 AGAATTATTA
Statistics
Matches: 61, Mismatches: 6, Indels: 11
0.78 0.08 0.14
Matches are distributed among these distances:
31 1 0.02
32 10 0.16
33 33 0.54
34 6 0.10
35 8 0.13
36 3 0.05
ACGTcount: A:0.35, C:0.00, G:0.04, T:0.62
Consensus pattern (34 bp):
TTATTTTTATATTAATATATTTATGTAAATATTA
Found at i:517818 original size:35 final size:33
Alignment explanation
Indices: 517765--517841 Score: 97
Period size: 33 Copynumber: 2.4 Consensus size: 33
517755 TTTAAATAGT
*
517765 TATTATTTTTATATT--AAT-ATATTTATGTAAA
1 TATTATTTTT-TATTAAAATAATATTTATATAAA
*
517796 TATTATTTTTTATTAAAATAATATTTATATAAT
1 TATTATTTTTTATTAAAATAATATTTATATAAA
517829 TATTATTTATTTA
1 TATTATTT-TTTA
517842 GAATTATTAA
Statistics
Matches: 40, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
30 4 0.10
31 10 0.25
32 3 0.08
33 19 0.47
34 4 0.10
ACGTcount: A:0.39, C:0.00, G:0.01, T:0.60
Consensus pattern (33 bp):
TATTATTTTTTATTAAAATAATATTTATATAAA
Found at i:517831 original size:30 final size:30
Alignment explanation
Indices: 517765--517839 Score: 80
Period size: 30 Copynumber: 2.5 Consensus size: 30
517755 TTTAAATAGT
* *
517765 TATTATTTTTATATTAATATATTTATGTAAA
1 TATTATTTTT-TATTAAAATATATATGTAAA
* *
517796 TATTATTTTTTATTAAAATA-ATATTTATA
1 TATTATTTTTTATTAAAATATATATGTAAA
*
517825 TAATTATTATTTATT
1 T-ATTATTTTTTATT
517840 TAGAATTATT
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
29 7 0.18
30 21 0.55
31 10 0.26
ACGTcount: A:0.39, C:0.00, G:0.01, T:0.60
Consensus pattern (30 bp):
TATTATTTTTTATTAAAATATATATGTAAA
Found at i:518003 original size:17 final size:17
Alignment explanation
Indices: 517981--518034 Score: 54
Period size: 17 Copynumber: 3.2 Consensus size: 17
517971 AATGTTAATA
517981 TTTAAATTTATTTTTAT
1 TTTAAATTTATTTTTAT
* * * *
517998 TTTAAAGTTATTATGAA
1 TTTAAATTTATTTTTAT
* *
518015 TTTATATTAATTTTTAT
1 TTTAAATTTATTTTTAT
518032 TTT
1 TTT
518035 TTATAATATA
Statistics
Matches: 27, Mismatches: 10, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
17 27 1.00
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.65
Consensus pattern (17 bp):
TTTAAATTTATTTTTAT
Found at i:519595 original size:21 final size:21
Alignment explanation
Indices: 519565--519612 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
519555 GCAGGGGTAC
* *
519565 ATGCCCAGCCCTCCACTTCAT
1 ATGCCAAGCCCACCACTTCAT
* *
519586 ATGCCAAGCCCACCAGTTTAT
1 ATGCCAAGCCCACCACTTCAT
519607 ATGCCA
1 ATGCCA
519613 TCTCCGCAGG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.25, C:0.40, G:0.12, T:0.23
Consensus pattern (21 bp):
ATGCCAAGCCCACCACTTCAT
Found at i:519642 original size:21 final size:21
Alignment explanation
Indices: 519616--519709 Score: 120
Period size: 21 Copynumber: 4.5 Consensus size: 21
519606 TATGCCATCT
* *
519616 CCGCAGGGTTACATTCCGAGC
1 CCGCAGGGTTACATGCCTAGC
*
519637 CCGCAGGGTTACATTCCTAGC
1 CCGCAGGGTTACATGCCTAGC
*
519658 CTGCCA-GGTTACATGCCTAGC
1 CCG-CAGGGTTACATGCCTAGC
519679 CCGCCA-GGTTACATGCCTAGC
1 CCG-CAGGGTTACATGCCTAGC
519700 CCGCAGGGTT
1 CCGCAGGGTT
519710 TTATACCATA
Statistics
Matches: 67, Mismatches: 4, Indels: 4
0.89 0.05 0.05
Matches are distributed among these distances:
20 2 0.03
21 63 0.94
22 2 0.03
ACGTcount: A:0.18, C:0.34, G:0.27, T:0.21
Consensus pattern (21 bp):
CCGCAGGGTTACATGCCTAGC
Found at i:520291 original size:33 final size:34
Alignment explanation
Indices: 520232--520328 Score: 133
Period size: 33 Copynumber: 2.9 Consensus size: 34
520222 AAATGTTTTT
*
520232 AAAATACAAATTATATTATTCGAAATTTAAAATA
1 AAAATAAAAATTATATTATTCGAAATTTAAAATA
* * *
520266 AAAATAAAAATAATATTATTC-AAATTTAAATTT
1 AAAATAAAAATTATATTATTCGAAATTTAAAATA
* *
520299 AAAATATAAATTATAGTATTCGAAATTTAA
1 AAAATAAAAATTATATTATTCGAAATTTAA
520329 CATTAAATTT
Statistics
Matches: 55, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
33 28 0.51
34 27 0.49
ACGTcount: A:0.56, C:0.04, G:0.03, T:0.37
Consensus pattern (34 bp):
AAAATAAAAATTATATTATTCGAAATTTAAAATA
Found at i:520335 original size:34 final size:33
Alignment explanation
Indices: 520230--520335 Score: 133
Period size: 34 Copynumber: 3.2 Consensus size: 33
520220 ATAAATGTTT
*
520230 TTAAAATACAAATTATATTATTCGAAATTTAAAA
1 TTAAAATAAAAATTATATTATTCGAAATTT-AAA
* *
520264 TAAAAATAAAAATAATATTATTC-AAATTTAAA
1 TTAAAATAAAAATTATATTATTCGAAATTTAAA
* *
520296 TTTAAAATATAAATTATAGTATTCGAAATTTAACA
1 -TTAAAATAAAAATTATATTATTCGAAATTTAA-A
520331 TTAAA
1 TTAAA
520336 TTTCAACTTA
Statistics
Matches: 62, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
32 3 0.05
33 25 0.40
34 33 0.53
35 1 0.02
ACGTcount: A:0.55, C:0.05, G:0.03, T:0.38
Consensus pattern (33 bp):
TTAAAATAAAAATTATATTATTCGAAATTTAAA
Found at i:521161 original size:128 final size:128
Alignment explanation
Indices: 520719--521351 Score: 1169
Period size: 128 Copynumber: 4.9 Consensus size: 128
520709 AGTTATTCAA
*
520719 ACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCT
1 ACTGATATATCTAGTGTCCCCGAGGGACATGAATGACATAATAGGGCAATGATAACATATTCTCT
*
520784 GACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATATGAATAGTGAACCGATTATAGG
66 GACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATATGAATAGTGAA---ATAATAGG
520849 T
128 T
520850 ACTGATATATCTAGTGTCCCCGAGGGACATGAATGACATAATAGGGCAATGATAACATATTCTCT
1 ACTGATATATCTAGTGTCCCCGAGGGACATGAATGACATAATAGGGCAATGATAACATATTCTCT
520915 GACGAAATAATGGAAGGCGCG-CCCCGGGAACGCGCCTTCATATGAATAGTGAAATAATAGGT
66 GACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATATGAATAGTGAAATAATAGGT
520977 ACTGATATATCTAGTGTCCCCGAGGGACATGAATGACATAATAGGGCAATGATAACATATTCTCT
1 ACTGATATATCTAGTGTCCCCGAGGGACATGAATGACATAATAGGGCAATGATAACATATTCTCT
*
521042 GACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGT
66 GACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATATGAATAGTGAAATAATAGGT
*
521105 ACTGATATATCTAGTGTCCCTGAGGGACATGAATGACATAATAGGGCAATGATAACATATTCTCT
1 ACTGATATATCTAGTGTCCCCGAGGGACATGAATGACATAATAGGGCAATGATAACATATTCTCT
*
521170 GACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGT
66 GACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATATGAATAGTGAAATAATAGGT
* *
521233 AATGATATATCTAGTGTCCTCGAGGGACATGAATGACATAATAGGGCAATGATAACATATTCTCT
1 ACTGATATATCTAGTGTCCCCGAGGGACATGAATGACATAATAGGGCAATGATAACATATTCTCT
521298 GACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATATGAATAGTGAA
66 GACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATATGAATAGTGAA
521352 CCGATTATAG
Statistics
Matches: 493, Mismatches: 8, Indels: 5
0.97 0.02 0.01
Matches are distributed among these distances:
127 94 0.19
128 282 0.57
130 32 0.06
131 85 0.17
ACGTcount: A:0.33, C:0.19, G:0.25, T:0.23
Consensus pattern (128 bp):
ACTGATATATCTAGTGTCCCCGAGGGACATGAATGACATAATAGGGCAATGATAACATATTCTCT
GACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATATGAATAGTGAAATAATAGGT
Found at i:521432 original size:8 final size:8
Alignment explanation
Indices: 521419--521457 Score: 53
Period size: 8 Copynumber: 5.0 Consensus size: 8
521409 TCACAATCTT
521419 TCAAATTC
1 TCAAATTC
521427 TCAAATTC
1 TCAAATTC
* *
521435 CCAAACTC
1 TCAAATTC
521443 T-AAATTC
1 TCAAATTC
521450 TCAAATTC
1 TCAAATTC
521458 CCTGAAAATG
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
7 6 0.23
8 20 0.77
ACGTcount: A:0.38, C:0.28, G:0.00, T:0.33
Consensus pattern (8 bp):
TCAAATTC
Found at i:536037 original size:43 final size:43
Alignment explanation
Indices: 535955--536190 Score: 228
Period size: 42 Copynumber: 5.5 Consensus size: 43
535945 AAGTTAACGA
* *
535955 CATTTTTGGAACAAACGCCACAAAAGGTT-ATATTTATAGCGG
1 CATTTTTGGAACAAACGCCGCAAAAGGTTGATATCTATAGCGG
* ** *
535997 CGTTTTTAGG-GGAAACGCCGCAAAAAGTTGATATCTATAGCGG
1 CATTTTT-GGAACAAACGCCGCAAAAGGTTGATATCTATAGCGG
* *
536040 CATTTTTGGAACAAATGCCGCAAAAGGTTGATATCTATAGCGA
1 CATTTTTGGAACAAACGCCGCAAAAGGTTGATATCTATAGCGG
** * * **
536083 CATTTTTTTGGAACAAACGCCTTAAAA-GTTCAGATCTATAGCTA
1 CA--TTTTTGGAACAAACGCCGCAAAAGGTTGATATCTATAGCGG
* * * *
536127 CGTTTTTTGAACAAACGCCACAAAAGG-TCATATCTATAGCGG
1 CATTTTTGGAACAAACGCCGCAAAAGGTTGATATCTATAGCGG
* *
536169 CGTTTTTTGATACAAACGCCGC
1 CATTTTTGGA-ACAAACGCCGC
536191 TAATTGCCTT
Statistics
Matches: 161, Mismatches: 26, Indels: 13
0.81 0.13 0.06
Matches are distributed among these distances:
42 65 0.40
43 61 0.38
44 15 0.09
45 20 0.12
ACGTcount: A:0.33, C:0.19, G:0.20, T:0.29
Consensus pattern (43 bp):
CATTTTTGGAACAAACGCCGCAAAAGGTTGATATCTATAGCGG
Found at i:536123 original size:130 final size:130
Alignment explanation
Indices: 535957--536190 Score: 292
Period size: 130 Copynumber: 1.8 Consensus size: 130
535947 GTTAACGACA
* * * *** *
535957 TTTTTGGAACAAACGCCACAAAAGGTTATATTTATAGCGGCGTTTTTAGGGGAAACGCCGCAAAA
1 TTTTTGGAACAAACGCCACAAAAGGTTAGATCTATAGCGACGTTTTTAGAACAAACGCCAC-AAA
* * *
536022 AGTTGATATCTATAGCGGCATTTTTGGA-ACAAATGCCGCAAAAGGTTGATATCTATAGCGACAT
65 AGGTCATATCTATAGCGGCATTTTTGGATACAAACGCCGCAAAAGGTTGATATCTATAGCGACAT
536086 T
130 T
** * *
536087 TTTTTGGAACAAACGCCTTAAAA-GTTCAGATCTATAGCTACGTTTTTTGAACAAACGCCACAAA
1 TTTTTGGAACAAACGCCACAAAAGGTT-AGATCTATAGCGACGTTTTTAGAACAAACGCCACAAA
* *
536151 AGGTCATATCTATAGCGGCGTTTTTTGATACAAACGCCGC
65 AGGTCATATCTATAGCGGCATTTTTGGATACAAACGCCGC
536191 TAATTGCCTT
Statistics
Matches: 86, Mismatches: 16, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
129 30 0.35
130 56 0.65
ACGTcount: A:0.32, C:0.18, G:0.20, T:0.29
Consensus pattern (130 bp):
TTTTTGGAACAAACGCCACAAAAGGTTAGATCTATAGCGACGTTTTTAGAACAAACGCCACAAAA
GGTCATATCTATAGCGGCATTTTTGGATACAAACGCCGCAAAAGGTTGATATCTATAGCGACATT
Found at i:541798 original size:21 final size:21
Alignment explanation
Indices: 541747--541799 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
541737 ATTCTGACTA
541747 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTCCAAAT
* * **
541768 TCTCGTTGCGATTTTCTTAAT
1 TCGCATTGCGATTTTCCAAAT
*
541789 TCGCAATGCGA
1 TCGCATTGCGA
541800 ATACGTAAAT
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.21, C:0.23, G:0.17, T:0.40
Consensus pattern (21 bp):
TCGCATTGCGATTTTCCAAAT
Found at i:541814 original size:20 final size:20
Alignment explanation
Indices: 541789--541921 Score: 221
Period size: 20 Copynumber: 6.7 Consensus size: 20
541779 TTTTCTTAAT
541789 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
541809 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
*
541829 TCGCAATACGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
*
541849 TCACAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
*
541869 TCGCAATACGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
541889 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
* *
541909 TCACAACGCGAAT
1 TCGCAATGCGAAT
541922 CTGACTATCG
Statistics
Matches: 105, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 105 1.00
ACGTcount: A:0.42, C:0.21, G:0.17, T:0.20
Consensus pattern (20 bp):
TCGCAATGCGAATACGTAAA
Found at i:541935 original size:20 final size:20
Alignment explanation
Indices: 541921--541990 Score: 131
Period size: 20 Copynumber: 3.5 Consensus size: 20
541911 ACAACGCGAA
541921 TCTGACTATCGCAACGAGAT
1 TCTGACTATCGCAACGAGAT
541941 TCTGACTATCGCAACGAGAT
1 TCTGACTATCGCAACGAGAT
*
541961 TCTGACTATCGCAACGCGAT
1 TCTGACTATCGCAACGAGAT
541981 TCTGACTATC
1 TCTGACTATC
541991 ACAATACTGA
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
20 49 1.00
ACGTcount: A:0.27, C:0.27, G:0.19, T:0.27
Consensus pattern (20 bp):
TCTGACTATCGCAACGAGAT
Found at i:541956 original size:40 final size:40
Alignment explanation
Indices: 541912--541990 Score: 131
Period size: 40 Copynumber: 2.0 Consensus size: 40
541902 ACGTAAATCA
*
541912 CAACGCGAATCTGACTATCGCAACGAGATTCTGACTATCG
1 CAACGAGAATCTGACTATCGCAACGAGATTCTGACTATCG
* *
541952 CAACGAGATTCTGACTATCGCAACGCGATTCTGACTATC
1 CAACGAGAATCTGACTATCGCAACGAGATTCTGACTATC
541991 ACAATACTGA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 36 1.00
ACGTcount: A:0.29, C:0.28, G:0.19, T:0.24
Consensus pattern (40 bp):
CAACGAGAATCTGACTATCGCAACGAGATTCTGACTATCG
Found at i:542411 original size:33 final size:34
Alignment explanation
Indices: 542354--542449 Score: 149
Period size: 33 Copynumber: 2.9 Consensus size: 34
542344 TTTAGTTTCG
542354 CGTTGCGATTTTCATTTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTTCGCATTGCGATTCTCT
542388 CGTTGCGATTTTCA-TTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTTCGCATTGCGATTCTCT
** * *
542421 CGTTGCGATAGTCATTTTTGCGTTGCGAT
1 CGTTGCGATTTTCATTTTCGCATTGCGAT
542450 AGTCTGTTTT
Statistics
Matches: 57, Mismatches: 4, Indels: 2
0.90 0.06 0.03
Matches are distributed among these distances:
33 31 0.54
34 26 0.46
ACGTcount: A:0.12, C:0.22, G:0.21, T:0.45
Consensus pattern (34 bp):
CGTTGCGATTTTCATTTTCGCATTGCGATTCTCT
Found at i:542428 original size:14 final size:14
Alignment explanation
Indices: 542376--542429 Score: 54
Period size: 14 Copynumber: 3.5 Consensus size: 14
542366 CATTTTCGCA
542376 TTGCGATTCTCTCG
1 TTGCGATTCTCTCG
*
542390 TTGCGATTTTCATTTCG
1 TTGCGA--TTC-TCTCG
542407 CATTGCGATTCTCTCG
1 --TTGCGATTCTCTCG
542423 TTGCGAT
1 TTGCGAT
542430 AGTCATTTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
14 13 0.39
16 7 0.21
17 7 0.21
19 6 0.18
ACGTcount: A:0.11, C:0.24, G:0.20, T:0.44
Consensus pattern (14 bp):
TTGCGATTCTCTCG
Found at i:542574 original size:14 final size:14
Alignment explanation
Indices: 542555--542591 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
542545 CATCAATTAA
542555 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
542569 ACAAATCATCTTTT
1 ACAAATCAACATTT
542583 ACAAATCAA
1 ACAAATCAA
542592 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:544011 original size:42 final size:42
Alignment explanation
Indices: 543944--544035 Score: 105
Period size: 42 Copynumber: 2.2 Consensus size: 42
543934 GTGAATCGGG
* * *
543944 CTCTAGAATGTTGGGAGGGACCTCTTCAACGATGACAGTGGC
1 CTCTTGAATGGTGGGAGGGACCTCTTCAACGATGACAGAGGC
* ** *
543986 CTCTTGAATGGTGGGAGGGGA-CTCTTGAGGGATGATAGAGGC
1 CTCTTGAATGGTGGGA-GGGACCTCTTCAACGATGACAGAGGC
544028 CTCTTGAA
1 CTCTTGAA
544036 CGATAGGGGA
Statistics
Matches: 42, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
42 38 0.90
43 4 0.10
ACGTcount: A:0.23, C:0.17, G:0.35, T:0.25
Consensus pattern (42 bp):
CTCTTGAATGGTGGGAGGGACCTCTTCAACGATGACAGAGGC
Found at i:544571 original size:20 final size:20
Alignment explanation
Indices: 544546--544614 Score: 102
Period size: 20 Copynumber: 3.5 Consensus size: 20
544536 GAAACTTAAA
*
544546 ATCGCAACGCAAAAATGACT
1 ATCGCAACGCGAAAATGACT
544566 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
* **
544586 ATCGCAATGCGAATTTGACT
1 ATCGCAACGCGAAAATGACT
544606 ATCGCAACG
1 ATCGCAACG
544615 AGAGAATCGC
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 44 1.00
ACGTcount: A:0.38, C:0.25, G:0.19, T:0.19
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:544688 original size:20 final size:20
Alignment explanation
Indices: 544663--544835 Score: 185
Period size: 20 Copynumber: 9.3 Consensus size: 20
544653 CTCTCGTTGA
**
544663 GATAGTCAAATTCGCATTGC
1 GATAGTCATTTTCGCATTGC
544683 GATAGTCATTTTCGCATTGC
1 GATAGTCATTTTCGCATTGC
544703 GATAGTCATTTTCGCATTGC
1 GATAGTCATTTTCGCATTGC
544723 GATAGTCATTTTCGCATTGC
1 GATAGTCATTTTCGCATTGC
*
544743 GAT--T--TTTTTG--TTGC
1 GATAGTCATTTTCGCATTGC
**
544757 GATTTTCA-TTTCGCATTGC
1 GATAGTCATTTTCGCATTGC
*
544776 GAT--TC--TCTCG--TTGC
1 GATAGTCATTTTCGCATTGC
544790 GATAGTCATTTTCG-AGTTGC
1 GATAGTCATTTTCGCA-TTGC
544810 GATAGTCATTTTCGCATTGC
1 GATAGTCATTTTCGCATTGC
544830 GATAGT
1 GATAGT
544836 AAACTATTCT
Statistics
Matches: 134, Mismatches: 6, Indels: 26
0.81 0.04 0.16
Matches are distributed among these distances:
14 14 0.10
16 12 0.09
17 6 0.04
18 5 0.04
19 7 0.05
20 89 0.66
21 1 0.01
ACGTcount: A:0.19, C:0.18, G:0.21, T:0.42
Consensus pattern (20 bp):
GATAGTCATTTTCGCATTGC
Found at i:544799 original size:33 final size:34
Alignment explanation
Indices: 544679--544812 Score: 146
Period size: 33 Copynumber: 3.8 Consensus size: 34
544669 CAAATTCGCA
544679 TTGCGATAGTCATTTTCGCATTGCGATAGTCATTTTCG
1 TTGCGATAGTCATTTTCGCATTGCGAT--TC--TTTCG
* *
544717 CATTGCGATAGTCATTTTCGCATTGCGATTTTTTTG
1 --TTGCGATAGTCATTTTCGCATTGCGATTCTTTCG
** *
544753 TTGCGATTTTCA-TTTCGCATTGCGATTCTCTCG
1 TTGCGATAGTCATTTTCGCATTGCGATTCTTTCG
544786 TTGCGATAGTCATTTTCG-AGTTGCGAT
1 TTGCGATAGTCATTTTCGCA-TTGCGAT
544813 AGTCATTTTC
Statistics
Matches: 83, Mismatches: 9, Indels: 10
0.81 0.09 0.10
Matches are distributed among these distances:
33 29 0.35
34 22 0.27
36 4 0.05
38 1 0.01
40 27 0.33
ACGTcount: A:0.16, C:0.19, G:0.21, T:0.44
Consensus pattern (34 bp):
TTGCGATAGTCATTTTCGCATTGCGATTCTTTCG
Found at i:546738 original size:20 final size:20
Alignment explanation
Indices: 546715--546755 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
546705 TCTGAAACTT
546715 AAAATCACAACACGAAAATG
1 AAAATCACAACACGAAAATG
*
546735 AAAATCGCAACACGAAAATG
1 AAAATCACAACACGAAAATG
546755 A
1 A
546756 CTACCGTAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.59, C:0.20, G:0.12, T:0.10
Consensus pattern (20 bp):
AAAATCACAACACGAAAATG
Found at i:546770 original size:20 final size:20
Alignment explanation
Indices: 546740--546791 Score: 59
Period size: 20 Copynumber: 2.6 Consensus size: 20
546730 AAATGAAAAT
*
546740 CGCAACACGAAAATGACTAC
1 CGCAACGCGAAAATGACTAC
* ** *
546760 CGTAACGCGAATTTGACTAT
1 CGCAACGCGAAAATGACTAC
546780 CGCAACGCGAAA
1 CGCAACGCGAAA
546792 TGATCGCGAT
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.38, C:0.27, G:0.19, T:0.15
Consensus pattern (20 bp):
CGCAACGCGAAAATGACTAC
Found at i:547171 original size:22 final size:22
Alignment explanation
Indices: 547109--547174 Score: 105
Period size: 22 Copynumber: 3.0 Consensus size: 22
547099 TGACCGTGAA
* *
547109 TGATTTCGCCGGAGATGGAGAC
1 TGATTTCGTCGGAGATGGGGAC
*
547131 TGATATCGTCGGAGATGGGGAC
1 TGATTTCGTCGGAGATGGGGAC
547153 TGATTTCGTCGGAGATGGGGAC
1 TGATTTCGTCGGAGATGGGGAC
547175 GGATGTCGCC
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 40 1.00
ACGTcount: A:0.21, C:0.15, G:0.39, T:0.24
Consensus pattern (22 bp):
TGATTTCGTCGGAGATGGGGAC
Found at i:547444 original size:21 final size:21
Alignment explanation
Indices: 547392--547444 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
547382 ATTTACGTAT
*
547392 TCGCATTGCGAATTAGGAAAA
1 TCGCAATGCGAATTAGGAAAA
* * *
547413 TCGAAACGCGAATTTGGAAAA
1 TCGCAATGCGAATTAGGAAAA
547434 TCGCAATGCGA
1 TCGCAATGCGA
547445 TAGTCAGAAT
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.38, C:0.17, G:0.25, T:0.21
Consensus pattern (21 bp):
TCGCAATGCGAATTAGGAAAA
Found at i:553915 original size:26 final size:26
Alignment explanation
Indices: 553886--553969 Score: 102
Period size: 26 Copynumber: 3.3 Consensus size: 26
553876 TACTTGTTTT
553886 TCATTTATATATTATTAAACTTGATG
1 TCATTTATATATTATTAAACTTGATG
* * * *
553912 TCATTTATTTA-AAGGTAAAC-T-ATT
1 TCATTTATATATTA-TTAAACTTGATG
553936 TCATTTATATATTATTAAACTTGATG
1 TCATTTATATATTATTAAACTTGATG
553962 TCATTTAT
1 TCATTTAT
553970 TTAAGGGTAA
Statistics
Matches: 46, Mismatches: 8, Indels: 8
0.74 0.13 0.13
Matches are distributed among these distances:
24 17 0.37
25 4 0.09
26 25 0.54
ACGTcount: A:0.35, C:0.08, G:0.07, T:0.50
Consensus pattern (26 bp):
TCATTTATATATTATTAAACTTGATG
Found at i:553942 original size:50 final size:50
Alignment explanation
Indices: 553884--553980 Score: 185
Period size: 50 Copynumber: 1.9 Consensus size: 50
553874 TTTACTTGTT
553884 TTTCATTTATATATTATTAAACTTGATGTCATTTATTTAAAGGTAAACTA
1 TTTCATTTATATATTATTAAACTTGATGTCATTTATTTAAAGGTAAACTA
*
553934 TTTCATTTATATATTATTAAACTTGATGTCATTTATTTAAGGGTAAA
1 TTTCATTTATATATTATTAAACTTGATGTCATTTATTTAAAGGTAAA
553981 GTATATAAAT
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
50 46 1.00
ACGTcount: A:0.35, C:0.07, G:0.09, T:0.48
Consensus pattern (50 bp):
TTTCATTTATATATTATTAAACTTGATGTCATTTATTTAAAGGTAAACTA
Found at i:553980 original size:26 final size:26
Alignment explanation
Indices: 553901--553980 Score: 85
Period size: 26 Copynumber: 3.2 Consensus size: 26
553891 TATATATTAT
553901 TAAACTTGATGTCATTTATTTAAAGG
1 TAAACTTGATGTCATTTATTTAAAGG
* * * *
553927 TAAAC-T-ATTTCATTTATATATTA-T
1 TAAACTTGATGTCATTTATTTA-AAGG
*
553951 TAAACTTGATGTCATTTATTTAAGGG
1 TAAACTTGATGTCATTTATTTAAAGG
553977 TAAA
1 TAAA
553981 GTATATAAAT
Statistics
Matches: 41, Mismatches: 9, Indels: 8
0.71 0.16 0.14
Matches are distributed among these distances:
24 17 0.41
25 3 0.07
26 21 0.51
ACGTcount: A:0.36, C:0.07, G:0.11, T:0.45
Consensus pattern (26 bp):
TAAACTTGATGTCATTTATTTAAAGG
Done.