Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003540.1 Hibiscus syriacus cultivar Beakdansim tig00007468_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: 84006
ACGTcount: A:0.34, C:0.16, G:0.18, T:0.32
Found at i:4221 original size:23 final size:23
Alignment explanation
Indices: 4204--4265 Score: 115
Period size: 23 Copynumber: 2.7 Consensus size: 23
4194 AATAACATAC
4204 TAGGTAGCGCTTATATAATGTAA
1 TAGGTAGCGCTTATATAATGTAA
*
4227 TAGGCAGCGCTTATATAATGTAA
1 TAGGTAGCGCTTATATAATGTAA
4250 TAGGTAGCGCTTATAT
1 TAGGTAGCGCTTATAT
4266 TTACATATTT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.32, C:0.11, G:0.23, T:0.34
Consensus pattern (23 bp):
TAGGTAGCGCTTATATAATGTAA
Found at i:4716 original size:23 final size:22
Alignment explanation
Indices: 4690--4746 Score: 87
Period size: 22 Copynumber: 2.5 Consensus size: 22
4680 ATATAACCAC
4690 TACCTATTACATTATATAAACGA
1 TACCTATTACATTATA-AAACGA
* *
4713 TACCTATTACATTATAAAGCGC
1 TACCTATTACATTATAAAACGA
4735 TACCTATTACAT
1 TACCTATTACAT
4747 CATTTTTACC
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
22 16 0.50
23 16 0.50
ACGTcount: A:0.39, C:0.21, G:0.05, T:0.35
Consensus pattern (22 bp):
TACCTATTACATTATAAAACGA
Found at i:4741 original size:22 final size:23
Alignment explanation
Indices: 4680--4746 Score: 91
Period size: 23 Copynumber: 3.0 Consensus size: 23
4670 ATACTTTACA
* *
4680 ATATAACCACTACCTATTACATT
1 ATATAAACGCTACCTATTACATT
*
4703 ATATAAACGATACCTATTACATT
1 ATATAAACGCTACCTATTACATT
*
4726 ATA-AAGCGCTACCTATTACAT
1 ATATAAACGCTACCTATTACAT
4747 CATTTTTACC
Statistics
Matches: 39, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
22 16 0.41
23 23 0.59
ACGTcount: A:0.40, C:0.22, G:0.04, T:0.33
Consensus pattern (23 bp):
ATATAAACGCTACCTATTACATT
Found at i:5122 original size:425 final size:427
Alignment explanation
Indices: 4332--5372 Score: 1865
Period size: 425 Copynumber: 2.5 Consensus size: 427
4322 TATTACATTA
4332 TATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTCTTTTAAAGTTATGTAAT
1 TATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTCTTTTAAAGTTATGTAAT
*
4397 TTATGTTTCAATTTTTTAAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCA
66 TTATGTTTCAATTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCA
4462 TTTGCACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTTTAATTTA
131 TTTGCACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTTTAATTTA
*
4527 ATAATAATATATATCATAACGTAAAAAATAATCATTAGACGCCTATAACTACTAAATTAATATCT
196 ATAATAATATATATCATAACGTAAAAAATAATCATTAGACACCTATAACTACTAAATTAATATCT
4592 TAAAACTCACTCAAAAGATAACCTTAAATTATGTTTTCCACAGTGAAAAAAGTATGGACACTTTT
261 TAAAACTCACTCAAAAGATAACCTTAAATTATGTTTTCCACAGTGAAAAAAGTATGGACACTTTT
4657 ATAAAAAGGATAGATACTTTACAATATAACCACTACCTATTACATTATATAAACGATACCTATTA
326 ATAAAAAGGATAGATACTTTACAATATAACCACTACCTATTACATTATATAAACGATACCTATTA
*
4722 CATTATA-AAGCGCTACCTATTACATC-ATTTTTACC
391 CATTATATAAGCGCTACATATTACATCAATTTTTACC
4757 TATTATATTGAAAGTGTCCATACTTTTTAT-AAAAGGATCGATACTTCTTTTAAAGTTATGTAAT
1 TATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTCTTTTAAAGTTATGTAAT
*
4821 TTATGTTTCAATTTTTTTTAATAGTGTTTCATGTTTTCTACCTACAATATTAATTTAATAATTTC
66 TTATGTTTCAA-TTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTC
*
4886 ATTTGCACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATATTATTTAGAATTTTTAATTT
130 ATTTGCACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTTTAATTT
* *
4951 AATAATAATATATATCGTAACGTAAAAAATAAATCATTAGACACCTATAATTACT-AATTAATAT
195 AATAATAATATATATCATAACGTAAAAAAT-AATCATTAGACACCTATAACTACTAAATTAATAT
5015 CTTAAAACTCACTC-AAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACT
259 CTTAAAACTCACTCAAAAGATAACCTTAAATT-ATGTTTTCCACAGTGAAAAAAGTATGGACACT
5079 TTTATAAAAAGGATAGATACTTTACAATATAACCACTACCTATTACATTATATAAACGATACCTA
323 TTTATAAAAAGGATAGATACTTTACAATATAACCACTACCTATTACATTATATAAACGATACCTA
5144 TTACATTATATAAGCGCTACATATTACATCATATTTTTACC
388 TTACATTATATAAGCGCTACATATTACATCA-ATTTTTACC
*
5185 TATTATATTG-AATTGTCCATACTTTTTATAAAAAGGATCGATACTTCTTTTAAAGTTATGTAAT
1 TATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTCTTTTAAAGTTATGTAAT
*
5249 TTATGTTTCAATTTTTTTAACAGTGTTTCATGTTTTCCACCTAC-A-A-T-A-TTAATAATTTCA
66 TTATGTTTCAATTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCA
*
5309 TTTGCACAAAAAATTATTTGATTGTTTTGATATTTTAT-AAATAATATTTAGAA-TTTAAATTTA
131 TTTGCACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTTTAATTTA
5372 A
196 A
5373 CAACATTAAC
Statistics
Matches: 597, Mismatches: 12, Indels: 19
0.95 0.02 0.03
Matches are distributed among these distances:
420 10 0.02
421 14 0.02
422 50 0.08
423 1 0.00
424 63 0.11
425 305 0.51
426 41 0.07
427 49 0.08
428 64 0.11
ACGTcount: A:0.38, C:0.12, G:0.08, T:0.42
Consensus pattern (427 bp):
TATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTCTTTTAAAGTTATGTAAT
TTATGTTTCAATTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCA
TTTGCACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTTTAATTTA
ATAATAATATATATCATAACGTAAAAAATAATCATTAGACACCTATAACTACTAAATTAATATCT
TAAAACTCACTCAAAAGATAACCTTAAATTATGTTTTCCACAGTGAAAAAAGTATGGACACTTTT
ATAAAAAGGATAGATACTTTACAATATAACCACTACCTATTACATTATATAAACGATACCTATTA
CATTATATAAGCGCTACATATTACATCAATTTTTACC
Found at i:5130 original size:21 final size:22
Alignment explanation
Indices: 5105--5156 Score: 77
Period size: 23 Copynumber: 2.3 Consensus size: 22
5095 ATACTTTACA
*
5105 ATATAACCACTACCTATTACATT
1 ATATAAACA-TACCTATTACATT
5128 ATATAAACGATACCTATTACATT
1 ATATAAAC-ATACCTATTACATT
5151 ATATAA
1 ATATAA
5157 GCGCTACATA
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:5141 original size:23 final size:23
Alignment explanation
Indices: 5115--5177 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
5105 ATATAACCAC
5115 TACCTATTACATTATATAAACGA
1 TACCTATTACATTATATAAACGA
* *
5138 TACCTATTACATTATATAAGCGC
1 TACCTATTACATTATATAAACGA
* *
5161 TACATATTACATCATAT
1 TACCTATTACATTATAT
5178 TTTTACCTAT
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:0.40, C:0.19, G:0.05, T:0.37
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:5645 original size:39 final size:39
Alignment explanation
Indices: 5591--5675 Score: 134
Period size: 39 Copynumber: 2.2 Consensus size: 39
5581 TCAAGTTGTA
* *
5591 GATTTTGATTTCCTTTTGCTTGGCATCATATGAGATTTG
1 GATTTGGATTTCCTTTTGCTTGGCACCATATGAGATTTG
*
5630 GATTTGGATTTCCTTTTGCTTGGCACCATATGAGCTTTG
1 GATTTGGATTTCCTTTTGCTTGGCACCATATGAGATTTG
5669 GACTTTG
1 GA-TTTG
5676 ATGAGCATCA
Statistics
Matches: 42, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
39 38 0.90
40 4 0.10
ACGTcount: A:0.16, C:0.15, G:0.22, T:0.46
Consensus pattern (39 bp):
GATTTGGATTTCCTTTTGCTTGGCACCATATGAGATTTG
Found at i:5966 original size:12 final size:12
Alignment explanation
Indices: 5951--5989 Score: 60
Period size: 12 Copynumber: 3.2 Consensus size: 12
5941 ATATATATTG
* *
5951 AAATTCAAACTC
1 AAATTGAAATTC
5963 AAATTGAAATTC
1 AAATTGAAATTC
5975 AAATTGAAATTC
1 AAATTGAAATTC
5987 AAA
1 AAA
5990 CTCCAATTAC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.54, C:0.13, G:0.05, T:0.28
Consensus pattern (12 bp):
AAATTGAAATTC
Found at i:5972 original size:6 final size:6
Alignment explanation
Indices: 5951--5989 Score: 51
Period size: 6 Copynumber: 6.5 Consensus size: 6
5941 ATATATATTG
* * *
5951 AAATTC AAACTC AAATTG AAATTC AAATTG AAATTC AAA
1 AAATTC AAATTC AAATTC AAATTC AAATTC AAATTC AAA
5990 CTCCAATTAC
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.54, C:0.13, G:0.05, T:0.28
Consensus pattern (6 bp):
AAATTC
Found at i:6408 original size:25 final size:25
Alignment explanation
Indices: 6374--6423 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
6364 ATTATTTTTC
* *
6374 CAAATAATGTACTCATAACAATGTT
1 CAAATAATGTACCCACAACAATGTT
6399 CAAATAATGTACCCACAACAATGTT
1 CAAATAATGTACCCACAACAATGTT
6424 TAATTGATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.44, C:0.20, G:0.08, T:0.28
Consensus pattern (25 bp):
CAAATAATGTACCCACAACAATGTT
Found at i:6677 original size:21 final size:21
Alignment explanation
Indices: 6651--6691 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
6641 CCACAGTGAA
* *
6651 AAAAAGTATGGACACTTTTAT
1 AAAAAGGATAGACACTTTTAT
*
6672 AAAAAGGATAGATACTTTTA
1 AAAAAGGATAGACACTTTTA
6692 CAATATAACC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.46, C:0.07, G:0.15, T:0.32
Consensus pattern (21 bp):
AAAAAGGATAGACACTTTTAT
Found at i:6719 original size:21 final size:22
Alignment explanation
Indices: 6694--6745 Score: 77
Period size: 23 Copynumber: 2.3 Consensus size: 22
6684 TACTTTTACA
*
6694 ATATAACCACTACCTATTACATT
1 ATATAAACA-TACCTATTACATT
6717 ATATAAACGATACCTATTACATT
1 ATATAAAC-ATACCTATTACATT
6740 ATATAA
1 ATATAA
6746 GCGCTACATA
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:6730 original size:23 final size:23
Alignment explanation
Indices: 6704--6766 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
6694 ATATAACCAC
6704 TACCTATTACATTATATAAACGA
1 TACCTATTACATTATATAAACGA
* *
6727 TACCTATTACATTATATAAGCGC
1 TACCTATTACATTATATAAACGA
* *
6750 TACATATTACATCATAT
1 TACCTATTACATTATAT
6767 TTTTACCTAT
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:0.40, C:0.19, G:0.05, T:0.37
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:7112 original size:25 final size:25
Alignment explanation
Indices: 7055--7120 Score: 78
Period size: 25 Copynumber: 2.6 Consensus size: 25
7045 CACTCAAAAG
* *
7055 ATGTATATACCTAGATATGTAGTTA
1 ATGTACATACCTAAATATGTAGTTA
***
7080 ACAAACATACCTAAATATGTAGTTA
1 ATGTACATACCTAAATATGTAGTTA
*
7105 TTGTACATACCTAAAT
1 ATGTACATACCTAAAT
7121 TTAATGATAA
Statistics
Matches: 32, Mismatches: 9, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
25 32 1.00
ACGTcount: A:0.41, C:0.14, G:0.11, T:0.35
Consensus pattern (25 bp):
ATGTACATACCTAAATATGTAGTTA
Found at i:9893 original size:181 final size:181
Alignment explanation
Indices: 9573--10063 Score: 851
Period size: 181 Copynumber: 2.7 Consensus size: 181
9563 TTAAAATTAC
9573 CGACACTTTTTTAAATGGTATCGACACATTTTTCTTCCAATCTGGACATAAAGTACCGACACAAT
1 CGACACTTTTTTAAAT-GTATCGACACATTTTTCTTCCAATCTGGACATAAAGTACCGACACAAT
* *
9638 ATTAGAAAATGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATACTTATACCGGTT
65 ATTA-AAAATGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGTT
* *
9703 ATATTACAAAATTATCTATTACATTATAAATCTGGGTTTCGATGTGTAAATGT
129 ATATTACAAAATTATCTATTACATTATAAATATGGGTTCCGATGTGTAAATGT
9756 CGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAATCTGGACATAAAGTACCGACAC-A-
1 CGACACTTTTTTAAAT-GTATCGACACATTTTTCTTCCAATCTGGACATAAAGTACCGACACAAT
9819 ATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGTT
65 ATTAAAAA-TGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGTT
*
9884 ATATTACAAAATTATCTATTACATTATAATTATGGGTTCCGATGTGTAAATGT
129 ATATTACAAAATTATCTATTACATTATAAATATGGGTTCCGATGTGTAAATGT
*
9937 CGACACTTTTTGACAATGTATCGACACATTTTTCTTCCAATCTGGACATAAAGTACCGACACAAT
1 CGACACTTTTTTA-AATGTATCGACACATTTTTCTTCCAATCTGGACATAAAGTACCGACACAAT
*
10002 ATTAAAAATTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACTGGTATATTTATACCG
65 ATTAAAAA-TGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCG
10064 ATAGCATTGC
Statistics
Matches: 295, Mismatches: 9, Indels: 8
0.95 0.03 0.03
Matches are distributed among these distances:
180 4 0.01
181 165 0.56
182 5 0.02
183 121 0.41
ACGTcount: A:0.33, C:0.18, G:0.15, T:0.34
Consensus pattern (181 bp):
CGACACTTTTTTAAATGTATCGACACATTTTTCTTCCAATCTGGACATAAAGTACCGACACAATA
TTAAAAATGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGTTAT
ATTACAAAATTATCTATTACATTATAAATATGGGTTCCGATGTGTAAATGT
Found at i:10481 original size:23 final size:23
Alignment explanation
Indices: 10455--10517 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
10445 ATATAACCAC
10455 TACCTATTACATTATATAAACGA
1 TACCTATTACATTATATAAACGA
* * *
10478 TACCTATTACATTTTATAAGCGC
1 TACCTATTACATTATATAAACGA
*
10501 TACCTATTACATCATAT
1 TACCTATTACATTATAT
10518 TTTTACCTAT
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.37, C:0.21, G:0.05, T:0.38
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:12119 original size:9 final size:9
Alignment explanation
Indices: 12105--12148 Score: 52
Period size: 9 Copynumber: 4.6 Consensus size: 9
12095 CTTGTTTGGA
12105 TCATCATCT
1 TCATCATCT
12114 TCATCATCAT
1 TCATCATC-T
*
12124 CATCATCATCG
1 --TCATCATCT
12135 TCATCATCT
1 TCATCATCT
12144 TCATC
1 TCATC
12149 GTCAGCTTCA
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
9 21 0.70
10 1 0.03
12 8 0.27
ACGTcount: A:0.25, C:0.34, G:0.02, T:0.39
Consensus pattern (9 bp):
TCATCATCT
Found at i:12123 original size:6 final size:6
Alignment explanation
Indices: 12104--12184 Score: 74
Period size: 6 Copynumber: 13.5 Consensus size: 6
12094 ACTTGTTTGG
* * * *
12104 ATCATC ATCTTC ATCATC ATCATC ATCATC GTCATC ATCTTC ATCGTC
1 ATCATC ATCATC ATCATC ATCATC ATCATC ATCATC ATCATC ATCATC
* * * *
12152 AGCTTC ATCGA-C ATCATC ATCGTC ATCTTC ATC
1 ATCATC ATC-ATC ATCATC ATCATC ATCATC ATC
12185 GTCAGCTTCA
Statistics
Matches: 61, Mismatches: 12, Indels: 4
0.79 0.16 0.05
Matches are distributed among these distances:
5 1 0.02
6 60 0.98
ACGTcount: A:0.25, C:0.33, G:0.06, T:0.36
Consensus pattern (6 bp):
ATCATC
Found at i:12127 original size:18 final size:18
Alignment explanation
Indices: 12108--12199 Score: 76
Period size: 18 Copynumber: 5.1 Consensus size: 18
12098 GTTTGGATCA
* *
12108 TCATCTTCATCATCATCA
1 TCATCATCATCATCATCT
*
12126 TCATCATCGTCATCATCT
1 TCATCATCATCATCATCT
* * * *
12144 TCATCGTCAGCTTCATCG
1 TCATCATCATCATCATCT
* *
12162 ACATCATCATCGTCATCT
1 TCATCATCATCATCATCT
* * *
12180 TCATCGTCAGCTTCATCT
1 TCATCATCATCATCATCT
12198 TC
1 TC
12200 TGCGACTGCT
Statistics
Matches: 57, Mismatches: 17, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
18 57 1.00
ACGTcount: A:0.22, C:0.34, G:0.08, T:0.37
Consensus pattern (18 bp):
TCATCATCATCATCATCT
Found at i:12160 original size:36 final size:36
Alignment explanation
Indices: 12127--12196 Score: 122
Period size: 36 Copynumber: 1.9 Consensus size: 36
12117 TCATCATCAT
*
12127 CATCATCGTCATCATCTTCATCGTCAGCTTCATCGA
1 CATCATCATCATCATCTTCATCGTCAGCTTCATCGA
*
12163 CATCATCATCGTCATCTTCATCGTCAGCTTCATC
1 CATCATCATCATCATCTTCATCGTCAGCTTCATC
12197 TTCTGCGACT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.21, C:0.34, G:0.10, T:0.34
Consensus pattern (36 bp):
CATCATCATCATCATCTTCATCGTCAGCTTCATCGA
Found at i:12195 original size:24 final size:24
Alignment explanation
Indices: 12142--12196 Score: 74
Period size: 24 Copynumber: 2.3 Consensus size: 24
12132 TCGTCATCAT
*
12142 CTTCATCGTCAGCTTCATCGACAT
1 CTTCATCGTCAGCTTCATCGACAG
* * *
12166 CATCATCGTCATCTTCATCGTCAG
1 CTTCATCGTCAGCTTCATCGACAG
12190 CTTCATC
1 CTTCATC
12197 TTCTGCGACT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.20, C:0.35, G:0.11, T:0.35
Consensus pattern (24 bp):
CTTCATCGTCAGCTTCATCGACAG
Found at i:12199 original size:6 final size:6
Alignment explanation
Indices: 12108--12199 Score: 67
Period size: 6 Copynumber: 15.3 Consensus size: 6
12098 GTTTGGATCA
* * * * * * *
12108 TCATCT TCATCA TCATCA TCATCA TCGTCA TCATCT TCATCG TCAGCT
1 TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT
* * * * * *
12156 TCATCG ACATCA TCATCG TCATCT TCATCG TCAGCT TCATCT TC
1 TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT TC
12200 TGCGACTGCT
Statistics
Matches: 68, Mismatches: 18, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
6 68 1.00
ACGTcount: A:0.22, C:0.34, G:0.08, T:0.37
Consensus pattern (6 bp):
TCATCT
Found at i:14034 original size:200 final size:200
Alignment explanation
Indices: 13666--14638 Score: 1842
Period size: 200 Copynumber: 4.9 Consensus size: 200
13656 TAAATTAGTT
13666 TCGACACAAACTAAAA-AGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATACT
1 TCGACACAAACTAAAATAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATACT
13730 TGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGTTTTCGATGTTTTTGGGATC
66 TGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGTTTTCGATGTTTTTGGGATC
* *
13795 GACATTTTTTATATATGGATCGACACTTTATGATTGCACCCTGTTTTCCATTCATTCTGGAACAA
131 GACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGAACAA
13860 AAATA
196 AAATA
* *
13865 TCGACACAAACTAAAATAGTGTCAACACATTATTTAGACATATTCTCTAATAAAACCGGTATACT
1 TCGACACAAACTAAAATAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATACT
*
13930 TGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGTTTTCGATATTTTTGGGATC
66 TGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGTTTTCGATGTTTTTGGGATC
13995 GACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGAACAA
131 GACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGAACAA
14060 AAATA
196 AAATA
*
14065 TCGACACAAACTAAAATAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACTGGTATACT
1 TCGACACAAACTAAAATAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATACT
14130 TGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGTTTTCGATGTTTTTGGGATC
66 TGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGTTTTCGATGTTTTTGGGATC
14195 GACACTTTTTATATATGGATCGACACTTTAT-GTTGCACCCTGTTTTCCATTCATTCTGGAACAA
131 GACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGAACAA
14259 AAATA
196 AAATA
*
14264 TCGACACAAACTAAAATAGTGTCGACACATTATTTAGACATATTCTCTCATAAAAACGGTATACT
1 TCGACACAAACTAAAATAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATACT
14329 TGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGTTTTCGATGTTTTTGGGATC
66 TGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGTTTTCGATGTTTTTGGGATC
*
14394 GACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTTTCATTCATTCTGGAACAA
131 GACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGAACAA
14459 AAATA
196 AAATA
*
14464 TCGACACAAACTAAAATAGTGTCTACACATTATTTAGACATATTCTCTCATAAAACCGGTATACT
1 TCGACACAAACTAAAATAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATACT
*
14529 TATACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGTTTTCGATGTTTTTGGGATC
66 TGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGTTTTCGATGTTTTTGGGATC
14594 GACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTT
131 GACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTT
14639 GGCCATATTG
Statistics
Matches: 757, Mismatches: 15, Indels: 3
0.98 0.02 0.00
Matches are distributed among these distances:
199 213 0.28
200 544 0.72
ACGTcount: A:0.31, C:0.17, G:0.14, T:0.38
Consensus pattern (200 bp):
TCGACACAAACTAAAATAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATACT
TGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGTTTTCGATGTTTTTGGGATC
GACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGAACAA
AAATA
Found at i:14404 original size:399 final size:399
Alignment explanation
Indices: 13666--14638 Score: 1840
Period size: 399 Copynumber: 2.4 Consensus size: 399
13656 TAAATTAGTT
13666 TCGACACAAACTAAAA-AGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATACT
1 TCGACACAAACTAAAATAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATACT
13730 TGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGTTTTCGATGTTTTTGGGATC
66 TGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGTTTTCGATGTTTTTGGGATC
*
13795 GACATTTTTTATATATGGATCGACACTTTATGATTGCACCCTGTTTTCCATTCATTCTGGAACAA
131 GACACTTTTTATATATGGATCGACACTTTATG-TTGCACCCTGTTTTCCATTCATTCTGGAACAA
*
13860 AAATATCGACACAAACTAAAATAGTGTCAACACATTATTTAGACATATTCTCTAATAAAACCGGT
195 AAATATCGACACAAACTAAAATAGTGTCAACACATTATTTAGACATATTCTCTAATAAAAACGGT
13925 ATACTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGTTTTCGATATTTTTG
260 ATACTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGTTTTCGATATTTTTG
13990 GGATCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGG
325 GGATCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGG
14055 AACAAAAATA
390 AACAAAAATA
*
14065 TCGACACAAACTAAAATAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACTGGTATACT
1 TCGACACAAACTAAAATAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATACT
14130 TGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGTTTTCGATGTTTTTGGGATC
66 TGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGTTTTCGATGTTTTTGGGATC
14195 GACACTTTTTATATATGGATCGACACTTTATGTTGCACCCTGTTTTCCATTCATTCTGGAACAAA
131 GACACTTTTTATATATGGATCGACACTTTATGTTGCACCCTGTTTTCCATTCATTCTGGAACAAA
* *
14260 AATATCGACACAAACTAAAATAGTGTCGACACATTATTTAGACATATTCTCTCATAAAAACGGTA
196 AATATCGACACAAACTAAAATAGTGTCAACACATTATTTAGACATATTCTCTAATAAAAACGGTA
*
14325 TACTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGTTTTCGATGTTTTTGG
261 TACTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGTTTTCGATATTTTTGG
*
14390 GATCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTTTCATTCATTCTGGA
326 GATCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGA
14455 ACAAAAATA
391 ACAAAAATA
*
14464 TCGACACAAACTAAAATAGTGTCTACACATTATTTAGACATATTCTCTCATAAAACCGGTATACT
1 TCGACACAAACTAAAATAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATACT
*
14529 TATACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGTTTTCGATGTTTTTGGGATC
66 TGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGTTTTCGATGTTTTTGGGATC
14594 GACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTT
131 GACACTTTTTATATATGGATCGACACTTTAT-GTTGCACCCTGTT
14639 GGCCATATTG
Statistics
Matches: 562, Mismatches: 10, Indels: 3
0.98 0.02 0.01
Matches are distributed among these distances:
399 406 0.72
400 156 0.28
ACGTcount: A:0.31, C:0.17, G:0.14, T:0.38
Consensus pattern (399 bp):
TCGACACAAACTAAAATAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATACT
TGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGTTTTCGATGTTTTTGGGATC
GACACTTTTTATATATGGATCGACACTTTATGTTGCACCCTGTTTTCCATTCATTCTGGAACAAA
AATATCGACACAAACTAAAATAGTGTCAACACATTATTTAGACATATTCTCTAATAAAAACGGTA
TACTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGTTTTCGATATTTTTGG
GATCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGA
ACAAAAATA
Found at i:14803 original size:19 final size:19
Alignment explanation
Indices: 14757--14805 Score: 80
Period size: 19 Copynumber: 2.6 Consensus size: 19
14747 TTATATTCAC
*
14757 ATACAAAAATATAAATCGT
1 ATACAAAATTATAAATCGT
*
14776 ATACAAAATTATAAATCTT
1 ATACAAAATTATAAATCGT
14795 ATACAAAATTA
1 ATACAAAATTA
14806 ACCCTACATT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.57, C:0.10, G:0.02, T:0.31
Consensus pattern (19 bp):
ATACAAAATTATAAATCGT
Found at i:16637 original size:33 final size:33
Alignment explanation
Indices: 16600--16665 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
16590 CATCTTAATA
*
16600 TCACCCCTTAACACCCCAACTTCTTTCACCACT
1 TCACCCCTCAACACCCCAACTTCTTTCACCACT
* *
16633 TCACCCCTCAACACCTCTACTTCTTTCACCACT
1 TCACCCCTCAACACCCCAACTTCTTTCACCACT
16666 CCATCTATTT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.23, C:0.48, G:0.00, T:0.29
Consensus pattern (33 bp):
TCACCCCTCAACACCCCAACTTCTTTCACCACT
Found at i:16724 original size:21 final size:21
Alignment explanation
Indices: 16699--16740 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
16689 CCCCTTATGC
16699 CTCTCAAGTGTATCTTCGACT
1 CTCTCAAGTGTATCTTCGACT
* *
16720 CTCTCAAGTTTCTCTTCGACT
1 CTCTCAAGTGTATCTTCGACT
16741 ATTGATTGTC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.17, C:0.31, G:0.12, T:0.40
Consensus pattern (21 bp):
CTCTCAAGTGTATCTTCGACT
Found at i:16906 original size:18 final size:17
Alignment explanation
Indices: 16883--16918 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
16873 CTCCTTTCTT
*
16883 CTCCTCTACCTCCATTGC
1 CTCCTCTACATCC-TTGC
16901 CTCCTCTACATCCTTGC
1 CTCCTCTACATCCTTGC
16918 C
1 C
16919 AATAACCTTC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 5 0.29
18 12 0.71
ACGTcount: A:0.11, C:0.50, G:0.06, T:0.33
Consensus pattern (17 bp):
CTCCTCTACATCCTTGC
Found at i:18810 original size:24 final size:24
Alignment explanation
Indices: 18773--18825 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
18763 CCGTTCTATC
18773 TATTTTCAGAGGATAT-TTAGCTTA
1 TATTTTCAGAGGATATGTTA-CTTA
** *
18797 TATTTTCATCGGATATGTTATTTA
1 TATTTTCAGAGGATATGTTACTTA
18821 TATTT
1 TATTT
18826 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:18987 original size:17 final size:18
Alignment explanation
Indices: 18965--19007 Score: 61
Period size: 20 Copynumber: 2.3 Consensus size: 18
18955 ATATATCTGG
18965 TATCATTT-TACCGGTTT
1 TATCATTTATACCGGTTT
18982 TATCATTTTGATACCGGTTT
1 TATCA-TTT-ATACCGGTTT
19002 TATCAT
1 TATCAT
19008 ATTTTTACCT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
17 5 0.22
18 3 0.13
19 1 0.04
20 14 0.61
ACGTcount: A:0.21, C:0.16, G:0.12, T:0.51
Consensus pattern (18 bp):
TATCATTTATACCGGTTT
Found at i:19025 original size:20 final size:19
Alignment explanation
Indices: 18970--19016 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 19
18960 TCTGGTATCA
18970 TTTTACCGGTTTTATCATT
1 TTTTACCGGTTTTATCATT
*
18989 TTGATACCGGTTTTATCATAT
1 TT-TTACCGGTTTTATCAT-T
19010 TTTTACC
1 TTTTACC
19017 TGTTATATCG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 2 0.08
20 19 0.79
21 3 0.12
ACGTcount: A:0.19, C:0.17, G:0.11, T:0.53
Consensus pattern (19 bp):
TTTTACCGGTTTTATCATT
Found at i:19250 original size:19 final size:20
Alignment explanation
Indices: 19210--19248 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
19200 GTTATATCGT
19210 TTTGGACCGACACATTTTTTA
1 TTTGGACCGACACA-TTTTTA
*
19231 TTTGGATCGACACATTTT
1 TTTGGACCGACACATTTT
19249 ATAAAATATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.23, C:0.18, G:0.15, T:0.44
Consensus pattern (20 bp):
TTTGGACCGACACATTTTTA
Found at i:19851 original size:11 final size:11
Alignment explanation
Indices: 19835--19859 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
19825 ATCCGGTACT
19835 ACCGTATATTA
1 ACCGTATATTA
19846 ACCGTATATTA
1 ACCGTATATTA
19857 ACC
1 ACC
19860 TGTCTTTCCT
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:0.36, C:0.24, G:0.08, T:0.32
Consensus pattern (11 bp):
ACCGTATATTA
Found at i:20196 original size:32 final size:32
Alignment explanation
Indices: 20155--20216 Score: 97
Period size: 32 Copynumber: 1.9 Consensus size: 32
20145 TATTCCACTC
*
20155 ATAAATTAATGACATATTATATGTTTAAATTT
1 ATAAATTAATGACATATTATATATTTAAATTT
* *
20187 ATAAATTAATTAGATATTATATATTTAAAT
1 ATAAATTAATGACATATTATATATTTAAAT
20217 AAGGACCGGA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.47, C:0.02, G:0.05, T:0.47
Consensus pattern (32 bp):
ATAAATTAATGACATATTATATATTTAAATTT
Found at i:24278 original size:32 final size:32
Alignment explanation
Indices: 24199--24265 Score: 134
Period size: 32 Copynumber: 2.1 Consensus size: 32
24189 ATTTTAAAAT
24199 TAGACAAAAGTTTTTTCTAAACAATACATATA
1 TAGACAAAAGTTTTTTCTAAACAATACATATA
24231 TAGACAAAAGTTTTTTCTAAACAATACATATA
1 TAGACAAAAGTTTTTTCTAAACAATACATATA
24263 TAG
1 TAG
24266 TGAGATTTTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 35 1.00
ACGTcount: A:0.46, C:0.12, G:0.07, T:0.34
Consensus pattern (32 bp):
TAGACAAAAGTTTTTTCTAAACAATACATATA
Found at i:24645 original size:21 final size:21
Alignment explanation
Indices: 24619--24672 Score: 90
Period size: 21 Copynumber: 2.6 Consensus size: 21
24609 GTTTCCAGAT
*
24619 TCGCAACGCGAACTTCGACTA
1 TCGCAATGCGAACTTCGACTA
*
24640 TCGCAATGCGAACTTGGACTA
1 TCGCAATGCGAACTTCGACTA
24661 TCGCAATGCGAA
1 TCGCAATGCGAA
24673 TATGTAAATC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.30, C:0.28, G:0.22, T:0.20
Consensus pattern (21 bp):
TCGCAATGCGAACTTCGACTA
Found at i:24734 original size:21 final size:21
Alignment explanation
Indices: 24681--24726 Score: 83
Period size: 21 Copynumber: 2.2 Consensus size: 21
24671 AATATGTAAA
24681 TCGCAATGCGATAGTCCAAGT
1 TCGCAATGCGATAGTCCAAGT
*
24702 TCGCAATGCGATAGTCGAAGT
1 TCGCAATGCGATAGTCCAAGT
24723 TCGC
1 TCGC
24727 GTTGCGATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.26, C:0.24, G:0.26, T:0.24
Consensus pattern (21 bp):
TCGCAATGCGATAGTCCAAGT
Found at i:25263 original size:19 final size:19
Alignment explanation
Indices: 25235--25313 Score: 68
Period size: 19 Copynumber: 3.9 Consensus size: 19
25225 TCAAAAATAA
*
25235 TATCGCAACGAACTTGGAC
1 TATCGAAACGAACTTGGAC
* *
25254 TATCGAAACGAATTTGGAA
1 TATCGAAACGAACTTGGAC
* *
25273 TAAATCGCAATGCGAACTTTGAC
1 T--ATCG-AA-ACGAACTTGGAC
*
25296 TATCGCAACGAACTTGGA
1 TATCGAAACGAACTTGGA
25314 ATAAATCGCA
Statistics
Matches: 46, Mismatches: 10, Indels: 8
0.72 0.16 0.12
Matches are distributed among these distances:
19 26 0.57
20 1 0.02
21 8 0.17
22 2 0.04
23 9 0.20
ACGTcount: A:0.35, C:0.20, G:0.20, T:0.24
Consensus pattern (19 bp):
TATCGAAACGAACTTGGAC
Found at i:25288 original size:23 final size:23
Alignment explanation
Indices: 25262--25336 Score: 88
Period size: 23 Copynumber: 3.4 Consensus size: 23
25252 ACTATCGAAA
25262 CGAATTTGGAATAAATCGCAATG
1 CGAATTTGGAATAAATCGCAATG
*
25285 CGAACTTT-GACT--ATCGCAA--
1 CGAA-TTTGGAATAAATCGCAATG
*
25304 CGAACTTGGAATAAATCGCAATG
1 CGAATTTGGAATAAATCGCAATG
25327 CGAATTTGGA
1 CGAATTTGGA
25337 CTATCGCAAA
Statistics
Matches: 42, Mismatches: 4, Indels: 12
0.72 0.07 0.21
Matches are distributed among these distances:
18 2 0.05
19 7 0.17
21 14 0.33
23 16 0.38
24 3 0.07
ACGTcount: A:0.36, C:0.17, G:0.21, T:0.25
Consensus pattern (23 bp):
CGAATTTGGAATAAATCGCAATG
Found at i:25291 original size:42 final size:42
Alignment explanation
Indices: 25230--25342 Score: 167
Period size: 42 Copynumber: 2.7 Consensus size: 42
25220 AACATTCAAA
*
25230 AATAATATCGCAA--CGAACTTGGACTATCGAAACGAATTTGG
1 AATAA-ATCGCAATGCGAACTTGGACTATCGAAACGAACTTGG
* *
25271 AATAAATCGCAATGCGAACTTTGACTATCGCAACGAACTTGG
1 AATAAATCGCAATGCGAACTTGGACTATCGAAACGAACTTGG
*
25313 AATAAATCGCAATGCGAATTTGGACTATCG
1 AATAAATCGCAATGCGAACTTGGACTATCG
25343 CAAATTCGAC
Statistics
Matches: 65, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
40 7 0.11
41 5 0.08
42 53 0.82
ACGTcount: A:0.37, C:0.19, G:0.19, T:0.25
Consensus pattern (42 bp):
AATAAATCGCAATGCGAACTTGGACTATCGAAACGAACTTGG
Found at i:25300 original size:21 final size:21
Alignment explanation
Indices: 25276--25345 Score: 74
Period size: 21 Copynumber: 3.3 Consensus size: 21
25266 TTTGGAATAA
25276 ATCGCAATGCGAACTTTGACT
1 ATCGCAATGCGAACTTTGACT
* *
25297 ATCGCAA--CGAACTTGGAAT
1 ATCGCAATGCGAACTTTGACT
25316 AAATCGCAATGCGAA-TTTGGACT
1 --ATCGCAATGCGAACTTT-GACT
25339 ATCGCAA
1 ATCGCAA
25346 ATTCGACTAT
Statistics
Matches: 40, Mismatches: 4, Indels: 10
0.74 0.07 0.19
Matches are distributed among these distances:
19 10 0.25
21 21 0.52
22 2 0.05
23 7 0.17
ACGTcount: A:0.34, C:0.21, G:0.20, T:0.24
Consensus pattern (21 bp):
ATCGCAATGCGAACTTTGACT
Found at i:25439 original size:21 final size:21
Alignment explanation
Indices: 25415--25479 Score: 62
Period size: 21 Copynumber: 3.1 Consensus size: 21
25405 TCGAAGTTCG
*
25415 CGTTGCGATTTATTCCAAATT
1 CGTTGCGATTTATTCGAAATT
* * *
25436 CGTT--GAGTTAGTCGAAGTTT
1 CGTTGCGATTTATTCGAA-ATT
25456 GCGTTGCGATTTATTCGAAATT
1 -CGTTGCGATTTATTCGAAATT
25478 CG
1 CG
25480 CAACGACTGG
Statistics
Matches: 33, Mismatches: 7, Indels: 8
0.69 0.15 0.17
Matches are distributed among these distances:
19 9 0.27
20 2 0.06
21 10 0.30
22 2 0.06
23 10 0.30
ACGTcount: A:0.22, C:0.15, G:0.23, T:0.40
Consensus pattern (21 bp):
CGTTGCGATTTATTCGAAATT
Found at i:25474 original size:23 final size:23
Alignment explanation
Indices: 25405--25474 Score: 67
Period size: 23 Copynumber: 3.2 Consensus size: 23
25395 TTTGCGATAG
*
25405 TCGAAGTTCGCGTTGCGATTTAT
1 TCGAAGTTTGCGTTGCGATTTAT
* * * *
25428 TCCAA-ATT-CGTT--GAGTTAG
1 TCGAAGTTTGCGTTGCGATTTAT
25447 TCGAAGTTTGCGTTGCGATTTAT
1 TCGAAGTTTGCGTTGCGATTTAT
25470 TCGAA
1 TCGAA
25475 ATTCGCAACG
Statistics
Matches: 34, Mismatches: 9, Indels: 8
0.67 0.18 0.16
Matches are distributed among these distances:
19 9 0.26
20 2 0.06
21 8 0.24
22 1 0.03
23 14 0.41
ACGTcount: A:0.21, C:0.16, G:0.24, T:0.39
Consensus pattern (23 bp):
TCGAAGTTTGCGTTGCGATTTAT
Found at i:25575 original size:6 final size:6
Alignment explanation
Indices: 25564--25588 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
25554 GACACATATT
25564 ACCACG ACCACG ACCACG ACCACG A
1 ACCACG ACCACG ACCACG ACCACG A
25589 ACCGACCCGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.36, C:0.48, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:26110 original size:5 final size:5
Alignment explanation
Indices: 26102--26135 Score: 50
Period size: 5 Copynumber: 6.4 Consensus size: 5
26092 TCTTCTCATC
26102 TCGGG TCGGG TCGGG TCGGG TCGTGG TCGTGG TC
1 TCGGG TCGGG TCGGG TCGGG TCG-GG TCG-GG TC
26136 ATGGTCGTGG
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 18 0.64
6 10 0.36
ACGTcount: A:0.00, C:0.21, G:0.53, T:0.26
Consensus pattern (5 bp):
TCGGG
Found at i:26131 original size:6 final size:6
Alignment explanation
Indices: 26105--26146 Score: 54
Period size: 6 Copynumber: 7.5 Consensus size: 6
26095 TCTCATCTCG
*
26105 GGTCG- GGTCG- GGTCG- GGTCGT GGTCGT GGTCAT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
26147 AATACGTGTC
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
5 15 0.44
6 19 0.56
ACGTcount: A:0.02, C:0.17, G:0.52, T:0.29
Consensus pattern (6 bp):
GGTCGT
Found at i:26284 original size:21 final size:20
Alignment explanation
Indices: 26260--26371 Score: 86
Period size: 21 Copynumber: 5.3 Consensus size: 20
26250 CTTGGAATAA
*
26260 ATCGTAACGTGAACTTCGACT
1 ATCGCAACG-GAACTTCGACT
* *
26281 ATCGCAAC-GAACTTGGAAT
1 ATCGCAACGGAACTTCGACT
26300 AAATCGCAACGCGAACTTCGACT
1 --ATCGCAACG-GAACTTCGACT
* *
26323 ATCGCAAC-GAACTTGGAAT
1 ATCGCAACGGAACTTCGACT
26342 AAATCGCAACGCGAACTT-GTACT
1 --ATCGCAACG-GAACTTCG-ACT
26365 ATCGCAA
1 ATCGCAA
26372 TGCGAATATG
Statistics
Matches: 74, Mismatches: 8, Indels: 18
0.74 0.08 0.18
Matches are distributed among these distances:
19 18 0.24
21 38 0.51
22 1 0.01
23 17 0.23
ACGTcount: A:0.35, C:0.25, G:0.19, T:0.21
Consensus pattern (20 bp):
ATCGCAACGGAACTTCGACT
Found at i:26294 original size:19 final size:19
Alignment explanation
Indices: 26270--26336 Score: 80
Period size: 19 Copynumber: 3.3 Consensus size: 19
26260 ATCGTAACGT
26270 GAACTTCGACTATCGCAAC
1 GAACTTCGACTATCGCAAC
* *
26289 GAACTTGGAATAAATCGCAACGC
1 GAACTTCGACT--ATCGCAA--C
26312 GAACTTCGACTATCGCAAC
1 GAACTTCGACTATCGCAAC
26331 GAACTT
1 GAACTT
26337 GGAATAAATC
Statistics
Matches: 40, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
19 16 0.40
21 14 0.35
23 10 0.25
ACGTcount: A:0.34, C:0.27, G:0.18, T:0.21
Consensus pattern (19 bp):
GAACTTCGACTATCGCAAC
Found at i:26294 original size:42 final size:42
Alignment explanation
Indices: 26235--26371 Score: 231
Period size: 42 Copynumber: 3.3 Consensus size: 42
26225 TGCGATTTTG
* * *
26235 GACTATAGCAACGAACTTGGAATAAATCGTAACGTGAACTTC
1 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
26277 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
1 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
26319 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTT-
1 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
26360 GTACTATCGCAA
1 G-ACTATCGCAA
26372 TGCGAATATG
Statistics
Matches: 91, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
41 1 0.01
42 90 0.99
ACGTcount: A:0.36, C:0.23, G:0.19, T:0.21
Consensus pattern (42 bp):
GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
Found at i:26383 original size:21 final size:20
Alignment explanation
Indices: 26341--26396 Score: 60
Period size: 21 Copynumber: 2.8 Consensus size: 20
26331 GAACTTGGAA
*
26341 TAAATCGCAACGCGAACTTG
1 TAAATCGCAATGCGAACTTG
*
26361 TACTATCGCAATGCGAA-TATG
1 TA-AATCGCAATGCGAACT-TG
*
26382 TAAATCGAAATGCGA
1 TAAATCGCAATGCGA
26397 TAGTCGAAGT
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
20 14 0.47
21 16 0.53
ACGTcount: A:0.38, C:0.20, G:0.20, T:0.23
Consensus pattern (20 bp):
TAAATCGCAATGCGAACTTG
Found at i:26469 original size:19 final size:19
Alignment explanation
Indices: 26445--26495 Score: 93
Period size: 19 Copynumber: 2.7 Consensus size: 19
26435 TGATACCGGA
*
26445 GATCGCGTTGCGAATTATC
1 GATCGCATTGCGAATTATC
26464 GATCGCATTGCGAATTATC
1 GATCGCATTGCGAATTATC
26483 GATCGCATTGCGA
1 GATCGCATTGCGA
26496 TTTAGTTGGT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 31 1.00
ACGTcount: A:0.24, C:0.22, G:0.25, T:0.29
Consensus pattern (19 bp):
GATCGCATTGCGAATTATC
Found at i:31657 original size:196 final size:196
Alignment explanation
Indices: 31321--31715 Score: 745
Period size: 196 Copynumber: 2.0 Consensus size: 196
31311 CGTAATCACC
31321 ACATGCCCTCGTAGTTGTTCAGATAATAAAGTACTTTCTCATTCTGCTAAAGAAACTAAACCTAG
1 ACATGCCCTCGTAGTTGTTCAGATAATAAAGTACTTTCTCATTCTGCTAAAGAAACTAAACCTAG
31386 TTGTTACAGTCGTTACTCTGCAACACCTAGGATCCCTCTTTATCATCTCCAATTAGATATAGTGA
66 TTGTTACAGTCGTTACTCTGCAACACCTAGGATCCCTCTTTATCATCTCCAATTAGATATAGTGA
*
31451 AACGTTTGGTTAGATTATCTTCAGTCAGGGCTGTCTTGGCATGTGTTTTTAGAAGAAGTATGTTA
131 AACATTTGGTTAGATTATCTTCAGTCAGGGCTGTCTTGGCATGTGTTTTTAGAAGAAGTATGTTA
31516 T
196 T
31517 ACATGCCCTCGTAGTTGTTCAGATAATAAAGTACTTTCTCATTCTGCTAAAGAAACTAAACCTAG
1 ACATGCCCTCGTAGTTGTTCAGATAATAAAGTACTTTCTCATTCTGCTAAAGAAACTAAACCTAG
* * *
31582 TTGTTACAGTCGTTCCTTTGCAACACCTGGGATCCCTCTTTATCATCTCCAATTAGATATAGTGA
66 TTGTTACAGTCGTTACTCTGCAACACCTAGGATCCCTCTTTATCATCTCCAATTAGATATAGTGA
*
31647 AACATTTGGTTAGATTATCTTCAGTCAGGGCTGTCTTGGCATGTGTTTTTAGAAGCAGTATGTTA
131 AACATTTGGTTAGATTATCTTCAGTCAGGGCTGTCTTGGCATGTGTTTTTAGAAGAAGTATGTTA
31712 T
196 T
31713 ACA
1 ACA
31716 GCGGCAGTGA
Statistics
Matches: 194, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
196 194 1.00
ACGTcount: A:0.27, C:0.19, G:0.18, T:0.36
Consensus pattern (196 bp):
ACATGCCCTCGTAGTTGTTCAGATAATAAAGTACTTTCTCATTCTGCTAAAGAAACTAAACCTAG
TTGTTACAGTCGTTACTCTGCAACACCTAGGATCCCTCTTTATCATCTCCAATTAGATATAGTGA
AACATTTGGTTAGATTATCTTCAGTCAGGGCTGTCTTGGCATGTGTTTTTAGAAGAAGTATGTTA
T
Found at i:33622 original size:132 final size:135
Alignment explanation
Indices: 33381--33648 Score: 479
Period size: 132 Copynumber: 2.0 Consensus size: 135
33371 TTTAGTTTTA
*
33381 TCTCTTATTATATCCAAATCTAGATATTTAGTTGGATATAATAAATAAATAAATAATACCTTATT
1 TCTCTTATTATATCAAAATCTAGATATTTAGTTGGA-ATAATAAATAAATAAATAATACCTTATT
33446 TTTCTCTCTTTTTCTTTAGTTACCGTTAGTTTTTTTCTTCATCTTTCTGATCGACGGCATCATCA
65 TTTCTCTCTTTTTCTTTAGTTACCGTTAGTTTTTTTCTTCATCTTTCTGATCGACGGCATCATCA
33511 ATCTTG
130 ATCTTG
33517 TCTCTTATTATATCAAAATCTAGATATTTAGTTGG-AT-AT-AATAAATAAATAATACCTTATTT
1 TCTCTTATTATATCAAAATCTAGATATTTAGTTGGAATAATAAATAAATAAATAATACCTTATTT
* *
33579 TTCTCTGTTTTTCTTTAGTTACCGTTAGTTTTTTTCTTCATCTTTCTGATCGACGGCATTATCAA
66 TTCTCTCTTTTTCTTTAGTTACCGTTAGTTTTTTTCTTCATCTTTCTGATCGACGGCATCATCAA
33644 TCTTG
131 TCTTG
33649 GTGTAGGTTG
Statistics
Matches: 129, Mismatches: 3, Indels: 4
0.95 0.02 0.03
Matches are distributed among these distances:
132 91 0.71
133 2 0.02
134 2 0.02
136 34 0.26
ACGTcount: A:0.27, C:0.16, G:0.09, T:0.48
Consensus pattern (135 bp):
TCTCTTATTATATCAAAATCTAGATATTTAGTTGGAATAATAAATAAATAAATAATACCTTATTT
TTCTCTCTTTTTCTTTAGTTACCGTTAGTTTTTTTCTTCATCTTTCTGATCGACGGCATCATCAA
TCTTG
Found at i:38364 original size:64 final size:64
Alignment explanation
Indices: 38293--38502 Score: 212
Period size: 64 Copynumber: 3.3 Consensus size: 64
38283 TTGATGCATT
** * *
38293 AGTAGTGCATCGATGCA-CTCTTTTAA-AATAAATACATCGAATGCAATTTGTGCATCGATACAT
1 AGTAGTGCATCGATGCATC-CCATTAATAAGAAA-ACATCGAATGCAATTAGTGCATCGATACAT
38356 A
64 A
* *
38357 AGTAGTGCATCGATGCATCCCATTAATAAGGAAACATCGAATGCAATTAGTGCATCGATGCATA
1 AGTAGTGCATCGATGCATCCCATTAATAAGAAAACATCGAATGCAATTAGTGCATCGATACATA
* * * * * * * * *
38421 AGGCA-TGCATCGATGCATCCCAGTAATAATACAACATCAAATACATTTTA-TGCACCGATGCAT
1 A-GTAGTGCATCGATGCATCCCATTAATAAGAAAACATCGAATGCA-ATTAGTGCATCGATACAT
*
38484 C
64 A
38485 AGTAGTGCATCGATGCAT
1 AGTAGTGCATCGATGCAT
38503 ACCTTCATTA
Statistics
Matches: 124, Mismatches: 17, Indels: 10
0.82 0.11 0.07
Matches are distributed among these distances:
63 2 0.02
64 112 0.90
65 10 0.08
ACGTcount: A:0.35, C:0.20, G:0.18, T:0.27
Consensus pattern (64 bp):
AGTAGTGCATCGATGCATCCCATTAATAAGAAAACATCGAATGCAATTAGTGCATCGATACATA
Found at i:39384 original size:103 final size:103
Alignment explanation
Indices: 39254--39479 Score: 391
Period size: 103 Copynumber: 2.2 Consensus size: 103
39244 GTCAAGGGTC
*
39254 TATGTGGTCCTTCGGGATATATATGTATTCTTTGGAACATGTATGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTATGAAGTCTGGTGAGACACATAC
* *
39319 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
*
39357 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTATGAAGTCTGGTGAGACACATAC
*
39422 TTGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
66 TTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
39460 TATGTGGTCCTTAC-GGACAT
1 TATGTGGTCCTT-CGGGACAT
39480 TATTATATGG
Statistics
Matches: 117, Mismatches: 5, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
103 116 0.99
104 1 0.01
ACGTcount: A:0.27, C:0.14, G:0.23, T:0.36
Consensus pattern (103 bp):
TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTATGAAGTCTGGTGAGACACATAC
TTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
Found at i:39514 original size:23 final size:23
Alignment explanation
Indices: 39488--39550 Score: 72
Period size: 23 Copynumber: 2.7 Consensus size: 23
39478 ATTATTATAT
*
39488 GGCACTACGATGTAATTCTACGC
1 GGCACTACGATGCAATTCTACGC
* * *
39511 GGCACTCCGGTGCAATTCTACGT
1 GGCACTACGATGCAATTCTACGC
* *
39534 GGCACTTCGGTGCAATT
1 GGCACTACGATGCAATT
39551 ATATGAGCTG
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.21, C:0.27, G:0.25, T:0.27
Consensus pattern (23 bp):
GGCACTACGATGCAATTCTACGC
Found at i:44340 original size:64 final size:63
Alignment explanation
Indices: 44272--44492 Score: 248
Period size: 64 Copynumber: 3.5 Consensus size: 63
44262 TTGAAGGTGT
** *
44272 ATCGATGCATTGGTAGTGCATCGATGCACTCTTTTAA-AATAAATACATCGAATGCAATTTGTGC
1 ATCGATGCATAAGTAGTGCATCGATGCA-TCTATTAATAATAAA-ACATCGAATGCAATTTGTGC
* ** *
44336 ATCGATGCATAAGTAGTGCATCGATGCATCCCATTAATAAGGAAACATCGAATGCAATTAGTGC
1 ATCGATGCATAAGTAGTGCATCGATGCAT-CTATTAATAATAAAACATCGAATGCAATTTGTGC
* * * * * *
44400 ATCGATGCATAAGGCA-TGCATCGATGCATCTCAGTAATAATACAACATCGAATACATTTTATGC
1 ATCGATGCATAA-GTAGTGCATCGATGCATCT-ATTAATAATAAAACATCGAATGCAATTTGTGC
* *
44464 ACCGATGCATCAGTAGTGCATCGATGCAT
1 ATCGATGCATAAGTAGTGCATCGATGCAT
44493 ACCTTCATTA
Statistics
Matches: 132, Mismatches: 20, Indels: 10
0.81 0.12 0.06
Matches are distributed among these distances:
63 4 0.03
64 122 0.92
65 6 0.05
ACGTcount: A:0.33, C:0.19, G:0.19, T:0.28
Consensus pattern (63 bp):
ATCGATGCATAAGTAGTGCATCGATGCATCTATTAATAATAAAACATCGAATGCAATTTGTGC
Found at i:45374 original size:103 final size:103
Alignment explanation
Indices: 45244--45469 Score: 364
Period size: 103 Copynumber: 2.2 Consensus size: 103
45234 GTCGAGGGTC
* *
45244 TATGTGGTCCTTCGGGATATATATGTATTCTTTGGAATATGTATGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTATGAAGTCTGGTGAGACACATAC
* * *
45309 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
66 TTCATCCCTAGCATATGTATATGATTCTTAAGGAATGA
*
45347 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTATGAAGTCTGGTGAGACACATAC
*
45412 TTCATCCCTAGTATATGTATATGATTCTTAAGGAATGA
66 TTCATCCCTAGCATATGTATATGATTCTTAAGGAATGA
*
45450 TATATGGTCCTTAC-GGACAT
1 TATGTGGTCCTT-CGGGACAT
45470 TATTATATGG
Statistics
Matches: 114, Mismatches: 8, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
103 113 0.99
104 1 0.01
ACGTcount: A:0.27, C:0.14, G:0.23, T:0.37
Consensus pattern (103 bp):
TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTATGAAGTCTGGTGAGACACATAC
TTCATCCCTAGCATATGTATATGATTCTTAAGGAATGA
Found at i:45505 original size:23 final size:23
Alignment explanation
Indices: 45478--45540 Score: 99
Period size: 23 Copynumber: 2.7 Consensus size: 23
45468 ATTATTATAT
45478 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTCTACGC
* *
45501 GGCACTCCGGTGCAATTCTACGT
1 GGCACTACGGTGCAATTCTACGC
*
45524 GGCACTTCGGTGCAATT
1 GGCACTACGGTGCAATT
45541 ATATGAGCTG
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.19, C:0.29, G:0.27, T:0.25
Consensus pattern (23 bp):
GGCACTACGGTGCAATTCTACGC
Found at i:51745 original size:17 final size:18
Alignment explanation
Indices: 51712--51748 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
51702 ACTCTATTAA
51712 AAACGTTATATTTTCTTT
1 AAACGTTATATTTTCTTT
*
51730 AAACGTTGTA-TTTCTTT
1 AAACGTTATATTTTCTTT
51747 AA
1 AA
51749 CAATTTACGG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 9 0.50
18 9 0.50
ACGTcount: A:0.30, C:0.11, G:0.08, T:0.51
Consensus pattern (18 bp):
AAACGTTATATTTTCTTT
Found at i:52980 original size:24 final size:25
Alignment explanation
Indices: 52948--53012 Score: 75
Period size: 24 Copynumber: 2.7 Consensus size: 25
52938 AATTTTTAAC
*
52948 AATTTTATTTTATTTTTG-ATATTT
1 AATTATATTTTATTTTTGAATATTT
52972 AATTATA-TTTACTTTTTGAATATTT
1 AATTATATTTTA-TTTTTGAATATTT
52997 --TTATATTTTAATTTTT
1 AATTATATTTT-ATTTTT
53013 TTAAAAATCA
Statistics
Matches: 36, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
23 9 0.25
24 20 0.56
25 7 0.19
ACGTcount: A:0.28, C:0.02, G:0.03, T:0.68
Consensus pattern (25 bp):
AATTATATTTTATTTTTGAATATTT
Found at i:52987 original size:23 final size:23
Alignment explanation
Indices: 52950--53004 Score: 71
Period size: 23 Copynumber: 2.4 Consensus size: 23
52940 TTTTTAACAA
52950 TTTTAT-TTTA-TTTTTG-ATAT
1 TTTTATATTTACTTTTTGAATAT
52970 TTAATTATATTTACTTTTTGAATAT
1 TT--TTATATTTACTTTTTGAATAT
52995 TTTTATATTT
1 TTTTATATTT
53005 TAATTTTTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
20 2 0.07
22 4 0.13
23 12 0.40
24 6 0.20
25 6 0.20
ACGTcount: A:0.25, C:0.02, G:0.04, T:0.69
Consensus pattern (23 bp):
TTTTATATTTACTTTTTGAATAT
Found at i:54439 original size:8 final size:7
Alignment explanation
Indices: 54418--54442 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
54408 GAAAACTGAG
54418 ATTAAAA
1 ATTAAAA
54425 ATTAAAA
1 ATTAAAA
54432 ATTAAAA
1 ATTAAAA
54439 ATTA
1 ATTA
54443 TTCACTGAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (7 bp):
ATTAAAA
Found at i:56170 original size:18 final size:17
Alignment explanation
Indices: 56129--56173 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 17
56119 ATAATGTTAT
56129 GTTTGAATTCTAAAATA
1 GTTTGAATTCTAAAATA
*
56146 GTTTGAATAT-TAAAATT
1 GTTTGAAT-TCTAAAATA
56163 GATTTGAATTC
1 G-TTTGAATTC
56174 CGACTTAACA
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
17 16 0.67
18 8 0.33
ACGTcount: A:0.38, C:0.04, G:0.13, T:0.44
Consensus pattern (17 bp):
GTTTGAATTCTAAAATA
Found at i:67260 original size:18 final size:18
Alignment explanation
Indices: 67232--67299 Score: 86
Period size: 18 Copynumber: 3.8 Consensus size: 18
67222 ATTCTAAATG
67232 TTTACAGTTATCAGATGAT
1 TTTACAGTTATCAGAT-AT
67251 TTTA-AGTTATCAGATA-
1 TTTACAGTTATCAGATAT
* *
67267 TTTACAGATATCAAATAT
1 TTTACAGTTATCAGATAT
*
67285 TTTATAGTTATCAGA
1 TTTACAGTTATCAGA
67300 GACATATTAA
Statistics
Matches: 42, Mismatches: 5, Indels: 5
0.81 0.10 0.10
Matches are distributed among these distances:
16 4 0.10
17 11 0.26
18 23 0.55
19 4 0.10
ACGTcount: A:0.37, C:0.09, G:0.12, T:0.43
Consensus pattern (18 bp):
TTTACAGTTATCAGATAT
Found at i:67272 original size:35 final size:35
Alignment explanation
Indices: 67232--67299 Score: 102
Period size: 35 Copynumber: 1.9 Consensus size: 35
67222 ATTCTAAATG
* *
67232 TTTACAGTTATCAGATGATTTTA-AGTTATCAGATA
1 TTTACAGATATCAAAT-ATTTTATAGTTATCAGATA
67267 TTTACAGATATCAAATATTTTATAGTTATCAGA
1 TTTACAGATATCAAATATTTTATAGTTATCAGA
67300 GACATATTAA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
34 6 0.20
35 24 0.80
ACGTcount: A:0.37, C:0.09, G:0.12, T:0.43
Consensus pattern (35 bp):
TTTACAGATATCAAATATTTTATAGTTATCAGATA
Found at i:68293 original size:18 final size:17
Alignment explanation
Indices: 68270--68330 Score: 70
Period size: 17 Copynumber: 3.5 Consensus size: 17
68260 ATGTTTACAG
68270 TTATCAGATGATTTTCAA
1 TTATCAGAT-ATTTTCAA
*
68288 TTATCAGATATTTACAGA
1 TTATCAGATATTTTCA-A
*
68306 -TATCAAATATTTTACAA
1 TTATCAGATATTTT-CAA
68323 TTATCAGA
1 TTATCAGA
68331 CACATATTAA
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
17 18 0.50
18 18 0.50
ACGTcount: A:0.39, C:0.11, G:0.08, T:0.41
Consensus pattern (17 bp):
TTATCAGATATTTTCAA
Found at i:68303 original size:35 final size:35
Alignment explanation
Indices: 68263--68330 Score: 102
Period size: 35 Copynumber: 1.9 Consensus size: 35
68253 ATTCTAAATG
* *
68263 TTTACAGTTATCAGATGATTTT-CAATTATCAGATA
1 TTTACAGATATCAAAT-ATTTTACAATTATCAGATA
68298 TTTACAGATATCAAATATTTTACAATTATCAGA
1 TTTACAGATATCAAATATTTTACAATTATCAGA
68331 CACATATTAA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
34 5 0.17
35 25 0.83
ACGTcount: A:0.38, C:0.12, G:0.09, T:0.41
Consensus pattern (35 bp):
TTTACAGATATCAAATATTTTACAATTATCAGATA
Found at i:71053 original size:44 final size:44
Alignment explanation
Indices: 70969--71276 Score: 480
Period size: 44 Copynumber: 7.1 Consensus size: 44
70959 ACAAAAACGA
* * * *
70969 TAAGGTCTTATCCTTGCACATAGCAAAAGAGCCT-GGGGAAACTG
1 TAAGG-CTTACCCTTGCACACAGCAAAGGAACCTGGGGGAAACTG
*
71013 TAAGGCTTACCCTTGCACACAGCAAAGGAACATGGGGGAAACTG
1 TAAGGCTTACCCTTGCACACAGCAAAGGAACCTGGGGGAAACTG
71057 TAAGGCTTACCCTTGCACACAGCAAAGGAACCTGGGGGAAACTG
1 TAAGGCTTACCCTTGCACACAGCAAAGGAACCTGGGGGAAACTG
71101 TAAGGCTTACCCTTGCACACAGCAAAGGAACCTGGGGGAAACTG
1 TAAGGCTTACCCTTGCACACAGCAAAGGAACCTGGGGGAAACTG
*
71145 TAAGGCTTACCCTTGCACACAGCAAAGGGACCTGGGGG-AACTG
1 TAAGGCTTACCCTTGCACACAGCAAAGGAACCTGGGGGAAACTG
* * *
71188 TAAGGCTTACCCTTGCACACAGTAAAGGGACATGGGGG-AACTG
1 TAAGGCTTACCCTTGCACACAGCAAAGGAACCTGGGGGAAACTG
* *
71231 TAAGGCTTACCCTTGCACACAACAAAGGGACCTGGGGG-AACTG
1 TAAGGCTTACCCTTGCACACAGCAAAGGAACCTGGGGGAAACTG
71274 TAA
1 TAA
71277 CGGTAATTAA
Statistics
Matches: 251, Mismatches: 12, Indels: 3
0.94 0.05 0.01
Matches are distributed among these distances:
43 112 0.45
44 139 0.55
ACGTcount: A:0.31, C:0.23, G:0.28, T:0.18
Consensus pattern (44 bp):
TAAGGCTTACCCTTGCACACAGCAAAGGAACCTGGGGGAAACTG
Found at i:74064 original size:18 final size:17
Alignment explanation
Indices: 74041--74098 Score: 71
Period size: 18 Copynumber: 3.2 Consensus size: 17
74031 ACGGGTCAAC
*
74041 GGTCAACGGTTTGGGTCG
1 GGTCAACGG-TCGGGTCG
74059 GGTCAACGGGTCGGGTCG
1 GGTCAAC-GGTCGGGTCG
*
74077 GGTAAACGAGTCGGGTCG
1 GGTCAACG-GTCGGGTCG
74095 GGTC
1 GGTC
74099 GGGTTATGAC
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
17 1 0.03
18 32 0.91
19 2 0.06
ACGTcount: A:0.14, C:0.19, G:0.47, T:0.21
Consensus pattern (17 bp):
GGTCAACGGTCGGGTCG
Found at i:76121 original size:44 final size:44
Alignment explanation
Indices: 76037--76344 Score: 507
Period size: 44 Copynumber: 7.1 Consensus size: 44
76027 ACAAAAACGA
* * * *
76037 TAAGGTCTTATCCTTGCACATAGCAAAAGAGCCT-GGGGAAACTG
1 TAAGG-CTTACCCTTGCACACAGCAAAGGAACCTGGGGGAAACTG
76081 TAAGGCTTACCCTTGCACACAGCAAAGGAACCTGGGGGAAACTG
1 TAAGGCTTACCCTTGCACACAGCAAAGGAACCTGGGGGAAACTG
76125 TAAGGCTTACCCTTGCACACAGCAAAGGAACCTGGGGGAAACTG
1 TAAGGCTTACCCTTGCACACAGCAAAGGAACCTGGGGGAAACTG
76169 TAAGGCTTACCCTTGCACACAGCAAAGGAACCTGGGGGAAACTG
1 TAAGGCTTACCCTTGCACACAGCAAAGGAACCTGGGGGAAACTG
*
76213 TAAGGCTTACCCTTGCACACAGCAAAGGGACCTGGGGG-AACTG
1 TAAGGCTTACCCTTGCACACAGCAAAGGAACCTGGGGGAAACTG
*
76256 TAAGGCTTACCCTTGCACACAGCAAAGGGACCTGGGGG-AACTG
1 TAAGGCTTACCCTTGCACACAGCAAAGGAACCTGGGGGAAACTG
* *
76299 TAAGGCTTACCCTTGCACACAACAAAGGGACCTGGGGG-AACTG
1 TAAGGCTTACCCTTGCACACAGCAAAGGAACCTGGGGGAAACTG
76342 TAA
1 TAA
76345 CGGTAATTAA
Statistics
Matches: 257, Mismatches: 6, Indels: 3
0.97 0.02 0.01
Matches are distributed among these distances:
43 117 0.46
44 140 0.54
ACGTcount: A:0.31, C:0.24, G:0.28, T:0.17
Consensus pattern (44 bp):
TAAGGCTTACCCTTGCACACAGCAAAGGAACCTGGGGGAAACTG
Found at i:79143 original size:18 final size:18
Alignment explanation
Indices: 79130--79194 Score: 121
Period size: 18 Copynumber: 3.6 Consensus size: 18
79120 GGTCAATGGA
*
79130 TCGGGTCGGGTCAACGGG
1 TCGGGTCGGGTAAACGGG
79148 TCGGGTCGGGTAAACGGG
1 TCGGGTCGGGTAAACGGG
79166 TCGGGTCGGGTAAACGGG
1 TCGGGTCGGGTAAACGGG
79184 TCGGGTCGGGT
1 TCGGGTCGGGT
79195 TATGAACGGT
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
18 46 1.00
ACGTcount: A:0.12, C:0.18, G:0.51, T:0.18
Consensus pattern (18 bp):
TCGGGTCGGGTAAACGGG
Done.