Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001719.1 Hibiscus syriacus cultivar Beakdansim tig00003479_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: 54502
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.34
Found at i:181 original size:20 final size:20
Alignment explanation
Indices: 156--206 Score: 77
Period size: 20 Copynumber: 2.5 Consensus size: 20
146 CCATACAATG
156 GGTATCGATACT-GTAGGTGA
1 GGTATCGATACTCGTAGG-GA
*
176 GGTATCGATACTCGTAGGGT
1 GGTATCGATACTCGTAGGGA
196 GGTATCGATAC
1 GGTATCGATAC
207 CAAGTTCACT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
20 24 0.83
21 5 0.17
ACGTcount: A:0.24, C:0.14, G:0.33, T:0.29
Consensus pattern (20 bp):
GGTATCGATACTCGTAGGGA
Found at i:8210 original size:18 final size:20
Alignment explanation
Indices: 8157--8221 Score: 71
Period size: 20 Copynumber: 3.4 Consensus size: 20
8147 CACTGAATAT
*
8157 TTGTCCCGAAAGACCACTGA
1 TTGTCCCGAAGGACCACTGA
** *
8177 TTGTTTCGAAGAACCACT-A
1 TTGTCCCGAAGGACCACTGA
8196 -TGTCCCGAAGGACCACTGA
1 TTGTCCCGAAGGACCACTGA
*
8215 TTATCCC
1 TTGTCCC
8222 TCGACTCTTG
Statistics
Matches: 35, Mismatches: 8, Indels: 4
0.74 0.17 0.09
Matches are distributed among these distances:
18 14 0.40
19 2 0.06
20 19 0.54
ACGTcount: A:0.28, C:0.29, G:0.18, T:0.25
Consensus pattern (20 bp):
TTGTCCCGAAGGACCACTGA
Found at i:8810 original size:20 final size:18
Alignment explanation
Indices: 8785--8834 Score: 64
Period size: 18 Copynumber: 2.7 Consensus size: 18
8775 CGATGCACTC
*
8785 GCATCGGTGCATCATTCGAT
1 GCATCGATGCATCATT--AT
*
8805 GCATCGATGCATCCTTAT
1 GCATCGATGCATCATTAT
8823 GCATCGATGCAT
1 GCATCGATGCAT
8835 TAATGATATT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
18 14 0.50
20 14 0.50
ACGTcount: A:0.22, C:0.26, G:0.22, T:0.30
Consensus pattern (18 bp):
GCATCGATGCATCATTAT
Found at i:12674 original size:29 final size:28
Alignment explanation
Indices: 12639--12750 Score: 106
Period size: 29 Copynumber: 4.0 Consensus size: 28
12629 TTTATTTAAA
*
12639 TATTTAAAGTATTTTTTAGTTAAAATAAG
1 TATTTAAAGTATTTTTTA-TCAAAATAAG
12668 TATTT-AA-T-TTTTTTATCAAAAT-AG
1 TATTTAAAGTATTTTTTATCAAAATAAG
* * *
12692 AAACTTAAAGTATTTTTTTATCAAAATAGG
1 -TATTTAAAGTA-TTTTTTATCAAAATAAG
* *
12722 TATCTAGAGTATTTTTTGATCAAAATAAG
1 TATTTAAAGTATTTTTT-ATCAAAATAAG
12751 AATATAAATG
Statistics
Matches: 67, Mismatches: 9, Indels: 14
0.74 0.10 0.16
Matches are distributed among these distances:
24 2 0.03
25 9 0.13
26 9 0.13
27 2 0.03
28 8 0.12
29 36 0.54
30 1 0.01
ACGTcount: A:0.40, C:0.04, G:0.10, T:0.46
Consensus pattern (28 bp):
TATTTAAAGTATTTTTTATCAAAATAAG
Found at i:12718 original size:54 final size:58
Alignment explanation
Indices: 12642--12748 Score: 143
Period size: 54 Copynumber: 1.9 Consensus size: 58
12632 ATTTAAATAT
* *
12642 TTAAAGTATTTTTTAGTTAAAATAAGTATTTA-A-T-TTTTTT-ATCAAAATAGAAAC
1 TTAAAGTATTTTTTAGTCAAAATAAGTATCTAGAGTATTTTTTGATCAAAATAGAAAC
*
12696 TTAAAGTATTTTTTTA-TCAAAATAGGTATCTAGAGTATTTTTTGATCAAAATA
1 TTAAAGTA-TTTTTTAGTCAAAATAAGTATCTAGAGTATTTTTTGATCAAAATA
12749 AGAATATAAA
Statistics
Matches: 45, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
54 21 0.47
55 8 0.18
56 1 0.02
57 6 0.13
58 9 0.20
ACGTcount: A:0.40, C:0.05, G:0.09, T:0.46
Consensus pattern (58 bp):
TTAAAGTATTTTTTAGTCAAAATAAGTATCTAGAGTATTTTTTGATCAAAATAGAAAC
Found at i:13005 original size:21 final size:21
Alignment explanation
Indices: 12981--13022 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
12971 ATTTGAATAT
**
12981 TATGAAGGGGTATTGATTCCC
1 TATGAAGGGGTACCGATTCCC
13002 TATGAAGGGGTACCGATTCCC
1 TATGAAGGGGTACCGATTCCC
13023 CCCATTCTGG
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:0.24, C:0.19, G:0.29, T:0.29
Consensus pattern (21 bp):
TATGAAGGGGTACCGATTCCC
Found at i:13084 original size:21 final size:21
Alignment explanation
Indices: 13051--13090 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
13041 TTTTTGCAGA
*
13051 AAAATCATTCCCAAACGGCTCC
1 AAAATCA-TCCCCAACGGCTCC
13073 AAAA-CATCCCCAACGGCT
1 AAAATCATCCCCAACGGCT
13091 AGATATGACT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 11 0.65
21 2 0.12
22 4 0.24
ACGTcount: A:0.38, C:0.38, G:0.10, T:0.15
Consensus pattern (21 bp):
AAAATCATCCCCAACGGCTCC
Found at i:14883 original size:60 final size:60
Alignment explanation
Indices: 14802--14966 Score: 195
Period size: 60 Copynumber: 2.8 Consensus size: 60
14792 CGAAAGATCT
* * *
14802 AAAAGTTTAGGGACCAATTTAGAATGAGATTCATAGTTTGGGGATGAAATTAGAATATTC
1 AAAAGTTTAAGGACTAATTTAGAATGAGAGTCATAGTTTGGGGATGAAATTAGAATATTC
** * ** * * * *
14862 AAAAGTTTAAGGACTGGTTTAGAATAAGAGTCATAGTTTGAAGATGTAATTGGAATGTTT
1 AAAAGTTTAAGGACTAATTTAGAATGAGAGTCATAGTTTGGGGATGAAATTAGAATATTC
* * *
14922 AAAAGTTTAAGGACTAATTTAAAATGAGGGTCATAATTTGGGGAT
1 AAAAGTTTAAGGACTAATTTAGAATGAGAGTCATAGTTTGGGGAT
14967 ATATGATGGA
Statistics
Matches: 85, Mismatches: 20, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
60 85 1.00
ACGTcount: A:0.38, C:0.05, G:0.24, T:0.33
Consensus pattern (60 bp):
AAAAGTTTAAGGACTAATTTAGAATGAGAGTCATAGTTTGGGGATGAAATTAGAATATTC
Found at i:19109 original size:29 final size:29
Alignment explanation
Indices: 19074--19131 Score: 98
Period size: 29 Copynumber: 2.0 Consensus size: 29
19064 GTGTTGACCG
*
19074 TAGGTCGCCATGCCTTCCGGGCGACCTAC
1 TAGGTCGCCATGCCTTCCCGGCGACCTAC
*
19103 TAGGTCGCCATGTCTTCCCGGCGACCTAC
1 TAGGTCGCCATGCCTTCCCGGCGACCTAC
19132 AAGAGATTGC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.14, C:0.38, G:0.26, T:0.22
Consensus pattern (29 bp):
TAGGTCGCCATGCCTTCCCGGCGACCTAC
Found at i:19193 original size:14 final size:14
Alignment explanation
Indices: 19174--19215 Score: 75
Period size: 14 Copynumber: 3.0 Consensus size: 14
19164 CGCTGGGCAT
19174 CCGAGGCCATCCGA
1 CCGAGGCCATCCGA
19188 CCGAGGCCATCCGA
1 CCGAGGCCATCCGA
*
19202 CTGAGGCCATCCGA
1 CCGAGGCCATCCGA
19216 AAGCATTTGA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 27 1.00
ACGTcount: A:0.21, C:0.40, G:0.29, T:0.10
Consensus pattern (14 bp):
CCGAGGCCATCCGA
Found at i:19228 original size:20 final size:20
Alignment explanation
Indices: 19202--19256 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 20
19192 GGCCATCCGA
19202 CTGAGGCCATCCGAAAGCAT
1 CTGAGGCCATCCGAAAGCAT
* * *
19222 TTGAGGCCATCTGAGAGCAT
1 CTGAGGCCATCCGAAAGCAT
* *
19242 CCGAGACCATCCGAA
1 CTGAGGCCATCCGAA
19257 CGAGCTATGT
Statistics
Matches: 27, Mismatches: 8, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.29, C:0.29, G:0.25, T:0.16
Consensus pattern (20 bp):
CTGAGGCCATCCGAAAGCAT
Found at i:24688 original size:18 final size:18
Alignment explanation
Indices: 24665--24704 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
24655 TCACTTGAAC
24665 TATAA-TAAAATATAAAAA
1 TATAATTAAAATA-AAAAA
*
24683 TATAATTATAATAAAAAA
1 TATAATTAAAATAAAAAA
24701 TATA
1 TATA
24705 TTTTATAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 14 0.70
19 6 0.30
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (18 bp):
TATAATTAAAATAAAAAA
Found at i:24698 original size:17 final size:18
Alignment explanation
Indices: 24676--24715 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
24666 ATAATAAAAT
24676 ATAAAAATATA-ATTATA
1 ATAAAAATATATATTATA
*
24693 ATAAAAAATATATTTTATA
1 AT-AAAAATATATATTATA
24712 ATAA
1 ATAA
24716 CTCACTATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
17 2 0.10
18 11 0.55
19 7 0.35
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (18 bp):
ATAAAAATATATATTATA
Found at i:24700 original size:19 final size:20
Alignment explanation
Indices: 24673--24715 Score: 54
Period size: 19 Copynumber: 2.2 Consensus size: 20
24663 ACTATAATAA
*
24673 AATATAAAAATATA-ATTAT
1 AATAAAAAAATATATATTAT
*
24692 AAT-AAAAAATATATTTTAT
1 AATAAAAAAATATATATTAT
24711 AATAA
1 AATAA
24716 CTCACTATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
18 9 0.45
19 10 0.50
20 1 0.05
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (20 bp):
AATAAAAAAATATATATTAT
Found at i:29197 original size:90 final size:90
Alignment explanation
Indices: 29044--29216 Score: 328
Period size: 90 Copynumber: 1.9 Consensus size: 90
29034 AGCTACAGGT
*
29044 TTGTTTCTGTTTTTCTTATTTTCATTTGAAGGCATGGTAGCCAAATTCATGATAGGTAAATTTTT
1 TTGTTTCTGTTTTTCTTATTTTCATTTGAAGGCATGGTAACCAAATTCATGATAGGTAAATTTTT
29109 AGCTGCTGAGATGCGGTGAGCAATC
66 AGCTGCTGAGATGCGGTGAGCAATC
*
29134 TTGTTTCTGTTTTTCTTATTTTCATTTGAAGGCATGGTAACCATATTCATGATAGGTAAATTTTT
1 TTGTTTCTGTTTTTCTTATTTTCATTTGAAGGCATGGTAACCAAATTCATGATAGGTAAATTTTT
29199 AGCTGCTGAGATGCGGTG
66 AGCTGCTGAGATGCGGTG
29217 CAACCTTATG
Statistics
Matches: 81, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
90 81 1.00
ACGTcount: A:0.23, C:0.13, G:0.22, T:0.43
Consensus pattern (90 bp):
TTGTTTCTGTTTTTCTTATTTTCATTTGAAGGCATGGTAACCAAATTCATGATAGGTAAATTTTT
AGCTGCTGAGATGCGGTGAGCAATC
Found at i:29244 original size:90 final size:89
Alignment explanation
Indices: 29060--29244 Score: 230
Period size: 90 Copynumber: 2.1 Consensus size: 89
29050 CTGTTTTTCT
*
29060 TATTTTCATTTGAAGGCATGGTAGCCAAATTCATGATAGGTAAATTTTTAGCTGCTGAGATGCGG
1 TATTTTCATTTGAAGGCATGGTAACCAAATTCATGATAGGTAAATTTTTAGCTGCTGAGATGCGG
* * ** * ** *
29125 TGAGCAATCTTGTTTCTGTTTTTCT
66 T-AGCAACCTTATAGCTCTAATTCA
*
29150 TATTTTCATTTGAAGGCATGGTAACCATATTCATGATAGGTAAATTTTTAGCTGCTGAGATGCGG
1 TATTTTCATTTGAAGGCATGGTAACCAAATTCATGATAGGTAAATTTTTAGCTGCTGAGATGCGG
29215 T-GCAACCTTATGAGCAATCTAATT-A
66 TAGCAACCTTAT-AGC--TCTAATTCA
29240 TATTT
1 TATTT
29245 ATGTCTATAG
Statistics
Matches: 82, Mismatches: 10, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
88 8 0.10
89 1 0.01
90 69 0.84
91 4 0.05
ACGTcount: A:0.26, C:0.14, G:0.21, T:0.39
Consensus pattern (89 bp):
TATTTTCATTTGAAGGCATGGTAACCAAATTCATGATAGGTAAATTTTTAGCTGCTGAGATGCGG
TAGCAACCTTATAGCTCTAATTCA
Found at i:34070 original size:71 final size:67
Alignment explanation
Indices: 34001--34139 Score: 154
Period size: 73 Copynumber: 1.9 Consensus size: 67
33991 AATATTTAAT
*
34001 TTAAAATTATATATAATCTTTGAGTTATAAAT-TAAATTATAAATATTAAATGTGAGTCATTTTA
1 TTAAAATTATATATAATC-TT---TTAT-AATGTAAATCATAAATATTAAA--TGAGTCATTTTA
34065 TTTTAATCTTGAA
59 TTTTAA--TT--A
*
34078 TTAAAATTATATATAATCTTTTATAATGTGAATCATAAATATTAAATGAGTCATTTTATTTT
1 TTAAAATTATATATAATCTTTTATAATGTAAATCATAAATATTAAATGAGTCATTTTATTTT
34140 TAATCTTGAA
Statistics
Matches: 59, Mismatches: 2, Indels: 8
0.86 0.03 0.12
Matches are distributed among these distances:
71 16 0.27
72 3 0.05
73 20 0.34
76 2 0.03
77 18 0.31
ACGTcount: A:0.41, C:0.04, G:0.07, T:0.47
Consensus pattern (67 bp):
TTAAAATTATATATAATCTTTTATAATGTAAATCATAAATATTAAATGAGTCATTTTATTTTAAT
TA
Found at i:34175 original size:73 final size:72
Alignment explanation
Indices: 34001--34153 Score: 211
Period size: 72 Copynumber: 2.1 Consensus size: 72
33991 AATATTTAAT
* *
34001 TTAAAATTATATATAATCTTTGAGTTATAAAT-TAAATTATAAATATTAAATGTGAGTCATTTTA
1 TTAAAATTATATATAATC-TT---TTAT-AATGTGAATCATAAATATTAAA-GTGAGTCATTTTA
34065 TTTTAATCTTGAA
60 TTTTAATCTTGAA
34078 TTAAAATTATATATAATCTTTTATAATGTGAATCATAAATATTAAA-TGAGTCATTTTATTTTTA
1 TTAAAATTATATATAATCTTTTATAATGTGAATCATAAATATTAAAGTGAGTCATTTTA-TTTTA
34142 ATCTTGAA
65 ATCTTGAA
34150 TTAA
1 TTAA
34154 CAATATTTAA
Statistics
Matches: 72, Mismatches: 2, Indels: 9
0.87 0.02 0.11
Matches are distributed among these distances:
71 12 0.17
72 20 0.28
73 20 0.28
76 2 0.03
77 18 0.25
ACGTcount: A:0.41, C:0.05, G:0.07, T:0.47
Consensus pattern (72 bp):
TTAAAATTATATATAATCTTTTATAATGTGAATCATAAATATTAAAGTGAGTCATTTTATTTTAA
TCTTGAA
Found at i:45105 original size:105 final size:105
Alignment explanation
Indices: 44808--45105 Score: 438
Period size: 105 Copynumber: 2.8 Consensus size: 105
44798 CAGGATGCTA
*
44808 GCCTTTGCTAACTTGCCAGCCCA-GATGCTAGCCTCTTCCTTTACTTCCCTCAACTCTTGTTCAA
1 GCCTCTGCTAACTTGCCAG-CCAGGATGCTAGCCTCTTCCTTTACTTCCCTCAACTCTTGTTCAA
* * *
44872 TCTGTATCTTGGTAGTCTGACAACAATCAATAGTTGCTTGG
65 TCTGTATCTTGGAAGTCTGACAATAATCAATAGTCGCTTGG
* * * *
44913 GCTTCTGCTAACTTGCCAACCAGGATGCTAGCCTCTTCCTTTACTT-TCTGCAACTCTTGTTCAG
1 GCCTCTGCTAACTTGCCAGCCAGGATGCTAGCCTCTTCCTTTACTTCCCT-CAACTCTTGTTCAA
* *
44977 TCTGTGTCTTAGAAGTCTGACAATAATCAATAGTCGCTTGG
65 TCTGTATCTTGGAAGTCTGACAATAATCAATAGTCGCTTGG
* * *
45018 GCCTCTGCTAACTTTCCAGCCAGGGTGCTAGCCTCTTCTTTTACTTCCCTCAACTCTTGTTCAAT
1 GCCTCTGCTAACTTGCCAGCCAGGATGCTAGCCTCTTCCTTTACTTCCCTCAACTCTTGTTCAAT
*
45083 CCGTATCTTGGAAGTCTGACAAT
66 CTGTATCTTGGAAGTCTGACAAT
45106 CATCGATATA
Statistics
Matches: 170, Mismatches: 20, Indels: 6
0.87 0.10 0.03
Matches are distributed among these distances:
104 5 0.03
105 163 0.96
106 2 0.01
ACGTcount: A:0.20, C:0.28, G:0.17, T:0.35
Consensus pattern (105 bp):
GCCTCTGCTAACTTGCCAGCCAGGATGCTAGCCTCTTCCTTTACTTCCCTCAACTCTTGTTCAAT
CTGTATCTTGGAAGTCTGACAATAATCAATAGTCGCTTGG
Found at i:50394 original size:20 final size:21
Alignment explanation
Indices: 50366--50404 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
50356 ATAATAATTG
*
50366 TATTTTTTTATAAT-TTTAAT
1 TATTATTTTATAATATTTAAT
50386 TATTATTTTATAATATTTA
1 TATTATTTTATAATATTTA
50405 GATACTATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (21 bp):
TATTATTTTATAATATTTAAT
Found at i:50413 original size:21 final size:21
Alignment explanation
Indices: 50371--50424 Score: 58
Period size: 21 Copynumber: 2.6 Consensus size: 21
50361 AATTGTATTT
*
50371 TTTTATAAT-TTTAATTATTA
1 TTTTATAATATTTAATTACTA
50391 TTTTATAATATTTAGA-TACTA
1 TTTTATAATATTTA-ATTACTA
* *
50412 TTTAATACTATTT
1 TTTTATAATATTT
50425 TTTTTAATAA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
20 9 0.31
21 19 0.66
22 1 0.03
ACGTcount: A:0.35, C:0.04, G:0.02, T:0.59
Consensus pattern (21 bp):
TTTTATAATATTTAATTACTA
Found at i:51637 original size:3 final size:3
Alignment explanation
Indices: 51629--51687 Score: 100
Period size: 3 Copynumber: 19.0 Consensus size: 3
51619 ATTCTCTTAC
51629 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATAT ATT ATT ATTT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT-T ATT ATT A-TT
51676 ATT ATT ATT ATT
1 ATT ATT ATT ATT
51688 GGAAGGGAAG
Statistics
Matches: 54, Mismatches: 0, Indels: 4
0.93 0.00 0.07
Matches are distributed among these distances:
3 48 0.89
4 6 0.11
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:52689 original size:18 final size:17
Alignment explanation
Indices: 52649--52689 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 17
52639 TCTTTTCATC
*
52649 ATTCTGGTTCTACTGAA
1 ATTCTGGTACTACTGAA
52666 AGTTCTGGTACTACTGCAA
1 A-TTCTGGTACTACTG-AA
52685 ATTCT
1 ATTCT
52690 AATGATTCTA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
17 1 0.05
18 17 0.81
19 3 0.14
ACGTcount: A:0.24, C:0.20, G:0.17, T:0.39
Consensus pattern (17 bp):
ATTCTGGTACTACTGAA
Found at i:52802 original size:195 final size:195
Alignment explanation
Indices: 52538--52901 Score: 543
Period size: 195 Copynumber: 1.9 Consensus size: 195
52528 TCCGATTCTT
* * *
52538 CAAATCAAGGTGGTGTTATGGGTCATAGCTCTGCATCTTTCTCACATGCAGGTTCAGCTTCTAGC
1 CAAATCAAGGTGGTATTACGGGTCATAGCTCTGCATCTTTCTCACATGCAAGTTCAGCTTCTAGC
* *
52603 TCATCCTCACATTCCAGTTCAGCTTCACATTCCGCTTCTTTTCATCATTCTGGTTCTACTGAAA-
66 TCATCCTCACATTCCAGTTCAGCTTCACATTCCGCTTCTTTTAATCACTCTGGTTCTA-TGAAAG
* **
52667 GTTCTGGTACTACTGCAAAT-TCTAATGATTCTAAAGGTTCTGGTGAATCATCAATATCTAGTTC
130 GTTCTGGAACTACAACAAATGT-TAATGATTCTAAAGGTTCTGGTGAATCATCAATATCTAGTTC
52731 AG
194 AG
* * *
52733 CAAATCAAGGTGGTATTACGGGTCATGGCTCTTCATCTTTCTCACATTCAAGTTCAGCTTCTAGC
1 CAAATCAAGGTGGTATTACGGGTCATAGCTCTGCATCTTTCTCACATGCAAGTTCAGCTTCTAGC
* * * *
52798 TCATCCTTACATTCCGGTTCAGCTTCACATTCTGCTTCTTTTAATCACTCTGGTTCTATTAAAGG
66 TCATCCTCACATTCCAGTTCAGCTTCACATTCCGCTTCTTTTAATCACTCTGGTTCTATGAAAGG
* *
52863 TTCTGGAACTACAACGAATGTTGATGATTCTAAAGGTTC
131 TTCTGGAACTACAACAAATGTTAATGATTCTAAAGGTTC
52902 AGGCTCTACT
Statistics
Matches: 150, Mismatches: 17, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
194 4 0.03
195 145 0.97
196 1 0.01
ACGTcount: A:0.24, C:0.23, G:0.17, T:0.36
Consensus pattern (195 bp):
CAAATCAAGGTGGTATTACGGGTCATAGCTCTGCATCTTTCTCACATGCAAGTTCAGCTTCTAGC
TCATCCTCACATTCCAGTTCAGCTTCACATTCCGCTTCTTTTAATCACTCTGGTTCTATGAAAGG
TTCTGGAACTACAACAAATGTTAATGATTCTAAAGGTTCTGGTGAATCATCAATATCTAGTTCAG
Found at i:53294 original size:489 final size:489
Alignment explanation
Indices: 52372--54502 Score: 3821
Period size: 489 Copynumber: 4.4 Consensus size: 489
52362 GATTTCTAAG
*
52372 GGTTCTGGAACTACAACGGATGTTGATAACTCTAAAGGTTCCGGTTCTACTGTGACTTCTAACTC
1 GGTTCTGGAACTACAACGGATGTTGATGACTCTAAAGGTTCCGGTTCTACTGTGACTTCTAACTC
* *
52437 TTCATCAGGTTCCGGGGGTTCCGGTTCCACTACAAGTTCTGGTTCTTCATCAGGTTATGGGGTTT
66 TTCATCAGGTTCCGGGGCTTCCGGTTCCTCTACAAGTTCTGGTTCTTCATCAGGTTATGGGGTTT
* * * *
52502 TTAAGGGTTCTGACAACTCCTCACAATCCGATTCTTCAAATCAAGGTGGTGTTATGGGTCATAGC
131 CTAAGGGTTCTGACAATTCCTCACAATCCGATTCTTCAAATCAAGGAGGTGCTATGGGTCATAGC
* *
52567 TCTGCATCTTTCTCACATGCAGGTTCAGCTTCTAGCTCATCCTCACATTCCAGTTCAGCTTCACA
196 TCTGCATCTTTCTCACATGCAGGTTCAGCTTCTAGCGCATCCTCGCATTCCAGTTCAGCTTCACA
*
52632 TTCCGCTTCTTTTCATCATTCTGGTTCTACTGAAAGTTCTGGTACTACTGCAAATTCTAATGATT
261 TTCCGCTTCTTTTCATCATTCTGGTTCTATTGAAAGTTCTGGTACTACTGCAAATTCTAATGATT
* *
52697 CTAAAGGTTCTGGTGAATCATCA-ATATCTAGTTCAGCAAATCAAGGTGGTATTACGGGTCATGG
326 CTAAAGGTTCTGGTGAATCATCACA-ATCTAGTTCAGCAAATCAAGGTGGCATTACGGGTCAAGG
*
52761 CTCTTCATCTTTCTCACATTCAAGTTCAGCTTCTAGCTCATCCTTACATTCCGGTTCAGCTTCAC
390 CTCTTCATCTTTCTCACATTCAAGTTCAGCTTCTAGCTCATCCTTGCATTCCGGTTCAGCTTCAC
52826 ATTCTGCTTCTTTTAATCACTCTGGTTCTATTAAA
455 ATTCTGCTTCTTTTAATCACTCTGGTTCTATTAAA
* * * * **
52861 GGTTCTGGAACTACAACGAATGTTGATGATTCTAAAGGTTCAGGCTCTACTGCAACTTCTAACTC
1 GGTTCTGGAACTACAACGGATGTTGATGACTCTAAAGGTTCCGGTTCTACTGTGACTTCTAACTC
*
52926 TTCATCAGGTTCCGGGGCTTCCGGTTCCACTACAAGTTCTGGTTCTTCATCAGGTTATGGGGTTT
66 TTCATCAGGTTCCGGGGCTTCCGGTTCCTCTACAAGTTCTGGTTCTTCATCAGGTTATGGGGTTT
*
52991 CTAAGGGTTCTGACAATTCCTCACAATCCGATTCTTCAAATCAAGGTGGTGCTATGGGTCATAGC
131 CTAAGGGTTCTGACAATTCCTCACAATCCGATTCTTCAAATCAAGGAGGTGCTATGGGTCATAGC
* *
53056 TCTGCATCTTTCTCCCATGCAGGTTCAGCTTCTAGCGCATCCTCCCATTCCAGTTCAGCTTCACA
196 TCTGCATCTTTCTCACATGCAGGTTCAGCTTCTAGCGCATCCTCGCATTCCAGTTCAGCTTCACA
* *
53121 TTCCGCTTCTTTTCATCACTCTGGTTCTATTGAAAGTTATGGTACTACTGCAAATTCTAATGATT
261 TTCCGCTTCTTTTCATCATTCTGGTTCTATTGAAAGTTCTGGTACTACTGCAAATTCTAATGATT
* * *
53186 CTAAAGGTTCTGGTGAATCATCACAATTTAGTTCAGCAAATCAAGGTGGTATTACGGGTCATGGC
326 CTAAAGGTTCTGGTGAATCATCACAATCTAGTTCAGCAAATCAAGGTGGCATTACGGGTCAAGGC
* *
53251 TCTTCATCTTTCTCACATTCAAGTTCAGCTTCTAGCACATCCTTGCATTCCGGTTCAGATTCACA
391 TCTTCATCTTTCTCACATTCAAGTTCAGCTTCTAGCTCATCCTTGCATTCCGGTTCAGCTTCACA
53316 TTCTGCTTCTTTTAATCACTCTGGTTCTATTAAA
456 TTCTGCTTCTTTTAATCACTCTGGTTCTATTAAA
*
53350 GGTTCTGGAACTACAACGGATGTTGATAACTCTAAAGGTTCCGGTTCTACTGTGACTTCTAACTC
1 GGTTCTGGAACTACAACGGATGTTGATGACTCTAAAGGTTCCGGTTCTACTGTGACTTCTAACTC
* *
53415 TTCATCAGGTTCCGGGGCTTCCGGTTCCTCTACAAGTTCGGGTTCTTCACCAGGTTATGGGGTTT
66 TTCATCAGGTTCCGGGGCTTCCGGTTCCTCTACAAGTTCTGGTTCTTCATCAGGTTATGGGGTTT
*
53480 CTAAGGGTTCTGACAATTCCTCACAATCTGATTCTTCAAATCAAGGAGGTGCTATGGGTCATAGC
131 CTAAGGGTTCTGACAATTCCTCACAATCCGATTCTTCAAATCAAGGAGGTGCTATGGGTCATAGC
*
53545 TCTGTATCTTTCTCACATGCAGGTTCAGCTTCTAGCGCATCCTCGCATTCCAGTTCAGCTTCACA
196 TCTGCATCTTTCTCACATGCAGGTTCAGCTTCTAGCGCATCCTCGCATTCCAGTTCAGCTTCACA
53610 TTCCGCTTCTTTTCATCATTCTGGTTCTATTGAAAGTTCTGGTACTACTGCAAATTCTAATGATT
261 TTCCGCTTCTTTTCATCATTCTGGTTCTATTGAAAGTTCTGGTACTACTGCAAATTCTAATGATT
53675 CT-AAGGTTCTGGTGAATCATCACAATCTAGTTCAGCAAATCAAGGTGGCATTACGGGTCAAGGC
326 CTAAAGGTTCTGGTGAATCATCACAATCTAGTTCAGCAAATCAAGGTGGCATTACGGGTCAAGGC
53739 TCTTCATCTTTCTCACATTCAAGTTCAGCTTCTAGCTCATCCTTGCATTCCGGTTCAGCTTCACA
391 TCTTCATCTTTCTCACATTCAAGTTCAGCTTCTAGCTCATCCTTGCATTCCGGTTCAGCTTCACA
53804 TTCTGCTTCTTTTAATCACTCTGGTTCTATTAAA
456 TTCTGCTTCTTTTAATCACTCTGGTTCTATTAAA
53838 GGTTCTGGAACTACAACGGATGTTGATGACTCTAAAGGTTCCGGTTCTACTGTGACTTCTAACTC
1 GGTTCTGGAACTACAACGGATGTTGATGACTCTAAAGGTTCCGGTTCTACTGTGACTTCTAACTC
*
53903 TTCATCAGGTTCCGGGACTTCCGGTTCCTCTACAAGTTCTGGTTCTTCATCAGGTTATGGGGTTT
66 TTCATCAGGTTCCGGGGCTTCCGGTTCCTCTACAAGTTCTGGTTCTTCATCAGGTTATGGGGTTT
*
53968 CTAAGGGTTCTGACAATTCCTCACAATCTGATTCTTC-AATCAAGGAGGTGCTATGGGTCATAGC
131 CTAAGGGTTCTGACAATTCCTCACAATCCGATTCTTCAAATCAAGGAGGTGCTATGGGTCATAGC
*
54032 TCTGTATCTTTCTCACATGCAGGTTCAGCTTCTAGCGCATCCTCGCATTCCAGTTCAGCTTCACA
196 TCTGCATCTTTCTCACATGCAGGTTCAGCTTCTAGCGCATCCTCGCATTCCAGTTCAGCTTCACA
54097 TTCCGCTTCTTTTCATCATTCTGGTTCTATTGAAAGTTCTGGTACTACTGCAAATTCTAATGATT
261 TTCCGCTTCTTTTCATCATTCTGGTTCTATTGAAAGTTCTGGTACTACTGCAAATTCTAATGATT
54162 CTAAAGGTTCTGGTGAATCATCACAATCTAGTTCAGC-AATCAAGGTGGCATTACGGGTCAAGGC
326 CTAAAGGTTCTGGTGAATCATCACAATCTAGTTCAGCAAATCAAGGTGGCATTACGGGTCAAGGC
54226 TCTTCATCTTTCTCACATTC-AGTTCAGCTTCTAGCTCATCCTTGCATTCCGGTTCAGCTTCACA
391 TCTTCATCTTTCTCACATTCAAGTTCAGCTTCTAGCTCATCCTTGCATTCCGGTTCAGCTTCACA
54290 TTCTGCTTCTTTTAATCACTCTGGTTCTATTAAA
456 TTCTGCTTCTTTTAATCACTCTGGTTCTATTAAA
*
54324 GGTTCTGGAACTACAACGGACGTTGATGACTCTAAAGGTTCCGGTTCTACTGTGACTTCTAACTC
1 GGTTCTGGAACTACAACGGATGTTGATGACTCTAAAGGTTCCGGTTCTACTGTGACTTCTAACTC
54389 TTCATCAGGTTCC-GGGCTTCCGGTTCCTCTACAAGTTCTGGTTCTTCATCAGG-TATGGGGTTT
66 TTCATCAGGTTCCGGGGCTTCCGGTTCCTCTACAAGTTCTGGTTCTTCATCAGGTTATGGGGTTT
* *
54452 CTAAGAGTTCTAACAATTCCT--CAATCCGATTCTTCAAATCAAGGAGGTGCT
131 CTAAGGGTTCTGACAATTCCTCACAATCCGATTCTTCAAATCAAGGAGGTGCT
Statistics
Matches: 1587, Mismatches: 52, Indels: 12
0.96 0.03 0.01
Matches are distributed among these distances:
482 13 0.01
483 15 0.01
484 29 0.02
485 39 0.02
486 155 0.10
487 206 0.13
488 353 0.22
489 776 0.49
490 1 0.00
ACGTcount: A:0.22, C:0.24, G:0.19, T:0.35
Consensus pattern (489 bp):
GGTTCTGGAACTACAACGGATGTTGATGACTCTAAAGGTTCCGGTTCTACTGTGACTTCTAACTC
TTCATCAGGTTCCGGGGCTTCCGGTTCCTCTACAAGTTCTGGTTCTTCATCAGGTTATGGGGTTT
CTAAGGGTTCTGACAATTCCTCACAATCCGATTCTTCAAATCAAGGAGGTGCTATGGGTCATAGC
TCTGCATCTTTCTCACATGCAGGTTCAGCTTCTAGCGCATCCTCGCATTCCAGTTCAGCTTCACA
TTCCGCTTCTTTTCATCATTCTGGTTCTATTGAAAGTTCTGGTACTACTGCAAATTCTAATGATT
CTAAAGGTTCTGGTGAATCATCACAATCTAGTTCAGCAAATCAAGGTGGCATTACGGGTCAAGGC
TCTTCATCTTTCTCACATTCAAGTTCAGCTTCTAGCTCATCCTTGCATTCCGGTTCAGCTTCACA
TTCTGCTTCTTTTAATCACTCTGGTTCTATTAAA
Found at i:53386 original size:195 final size:195
Alignment explanation
Indices: 53027--53390 Score: 480
Period size: 195 Copynumber: 1.9 Consensus size: 195
53017 TCCGATTCTT
* * * *
53027 CAAATCAAGGTGGTGCTATGGGTCATAGCTCTGCATCTTTCTCCCATGCAGGTTCAGCTTCTAGC
1 CAAATCAAGGTGGTACTACGGGTCATAGCTCTGCATCTTTCTCACATGCAAGTTCAGCTTCTAGC
* * *
53092 GCATCCTCCCATTCCAGTTCAGCTTCACATTCCGCTTCTTTTCATCACTCTGGTTCTATTGAAAG
66 ACATCCTCCCATTCCAGTTCAGATTCACATTCCGCTTCTTTTAATCACTCTGGTTCTATTGAAAG
* ** * *
53157 TTATGGTACTACTGCAAATTCTAATGATTCTAAAGGTTCTGGTGAATCATCACAATTTAGTTCAG
131 TTATGGAACTACAACAAATTCTAATAACTCTAAAGGTTCTGGTGAATCATCACAATTTAGTTCAG
* * * *
53222 CAAATCAAGGTGGTATTACGGGTCATGGCTCTTCATCTTTCTCACATTCAAGTTCAGCTTCTAGC
1 CAAATCAAGGTGGTACTACGGGTCATAGCTCTGCATCTTTCTCACATGCAAGTTCAGCTTCTAGC
** * *
53287 ACATCCTTGCATTCCGGTTCAGATTCACATTCTGCTTCTTTTAATCACTCTGGTTCTATT-AAAG
66 ACATCCTCCCATTCCAGTTCAGATTCACATTCCGCTTCTTTTAATCACTCTGGTTCTATTGAAA-
* ** *
53351 GTTCTGGAACTACAACGGATGT-TGATAACTCTAAAGGTTC
130 GTTATGGAACTACAACAAAT-TCTAATAACTCTAAAGGTTC
53391 CGGTTCTACT
Statistics
Matches: 143, Mismatches: 24, Indels: 4
0.84 0.14 0.02
Matches are distributed among these distances:
194 3 0.02
195 139 0.97
196 1 0.01
ACGTcount: A:0.24, C:0.24, G:0.17, T:0.35
Consensus pattern (195 bp):
CAAATCAAGGTGGTACTACGGGTCATAGCTCTGCATCTTTCTCACATGCAAGTTCAGCTTCTAGC
ACATCCTCCCATTCCAGTTCAGATTCACATTCCGCTTCTTTTAATCACTCTGGTTCTATTGAAAG
TTATGGAACTACAACAAATTCTAATAACTCTAAAGGTTCTGGTGAATCATCACAATTTAGTTCAG
Done.