Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008514.1 Hibiscus syriacus cultivar Beakdansim tig00111377_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: 567339
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 3
Found at i:518206 original size:18 final size:19
Alignment explanation
Indices: 518185--518220 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
518175 AATTTAAAAT
*
518185 TAAA-ATTATACCCAAACA
1 TAAACATTATACCAAAACA
518203 TAAACATTATACCAAAAC
1 TAAACATTATACCAAAAC
518221 CCTAATTCAC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 4 0.25
19 12 0.75
ACGTcount: A:0.56, C:0.22, G:0.00, T:0.22
Consensus pattern (19 bp):
TAAACATTATACCAAAACA
Found at i:522744 original size:4 final size:4
Alignment explanation
Indices: 522735--522759 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
522725 ATATATCTTC
522735 CATT CATT CATT CATT CATT CATT C
1 CATT CATT CATT CATT CATT CATT C
522760 TTCTCTCAAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.28, G:0.00, T:0.48
Consensus pattern (4 bp):
CATT
Found at i:526268 original size:2 final size:2
Alignment explanation
Indices: 526261--526285 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
526251 TGATTTTAAG
526261 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
526286 ATTATCTTAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:530722 original size:15 final size:15
Alignment explanation
Indices: 530702--530734 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
530692 TTAGCTGGGT
530702 GGGCGGATGTGGGGC
1 GGGCGGATGTGGGGC
530717 GGGCGGATGTGGGGC
1 GGGCGGATGTGGGGC
530732 GGG
1 GGG
530735 TAATGTCTCA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.06, C:0.12, G:0.70, T:0.12
Consensus pattern (15 bp):
GGGCGGATGTGGGGC
Found at i:538709 original size:15 final size:14
Alignment explanation
Indices: 538687--538716 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
538677 TTTTCCTTTC
538687 TGTTTTTTATTTAT
1 TGTTTTTTATTTAT
538701 TGTTATTTTATTTAT
1 TGTT-TTTTATTTAT
538716 T
1 T
538717 TCATCTAACA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.27
15 11 0.73
ACGTcount: A:0.17, C:0.00, G:0.07, T:0.77
Consensus pattern (14 bp):
TGTTTTTTATTTAT
Found at i:541747 original size:26 final size:27
Alignment explanation
Indices: 541695--541754 Score: 79
Period size: 27 Copynumber: 2.3 Consensus size: 27
541685 TAAAAAGGGC
*
541695 ACAAAAAAAAAGAAGCAATAAACAAAA
1 ACAAAAAAAAAGAAGCAATAAAAAAAA
541722 ACAAAAAAAAAGAA-CAA-AAAGAAAAA
1 ACAAAAAAAAAGAAGCAATAAA-AAAAA
*
541748 AGAAAAA
1 ACAAAAA
541755 GGGACAAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
25 3 0.10
26 13 0.43
27 14 0.47
ACGTcount: A:0.82, C:0.08, G:0.08, T:0.02
Consensus pattern (27 bp):
ACAAAAAAAAAGAAGCAATAAAAAAAA
Found at i:541748 original size:27 final size:27
Alignment explanation
Indices: 541695--541754 Score: 77
Period size: 26 Copynumber: 2.3 Consensus size: 27
541685 TAAAAAGGGC
* *
541695 ACAAAAAAAAAGAAGCAATAAACAAAA
1 ACAAAAAAAAAGAAGCAAAAAAAAAAA
*
541722 ACAAAAAAAAAGAA-CAAAAAGAAAAA
1 ACAAAAAAAAAGAAGCAAAAAAAAAAA
*
541748 AGAAAAA
1 ACAAAAA
541755 GGGACAAAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
26 15 0.52
27 14 0.48
ACGTcount: A:0.82, C:0.08, G:0.08, T:0.02
Consensus pattern (27 bp):
ACAAAAAAAAAGAAGCAAAAAAAAAAA
Found at i:541753 original size:13 final size:13
Alignment explanation
Indices: 541718--541755 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
541708 AGCAATAAAC
541718 AAAAACAAAAA-A
1 AAAAACAAAAAGA
541730 AAAGAACAAAAAGA
1 AAA-AACAAAAAGA
*
541744 AAAAAGAAAAAG
1 AAAAACAAAAAG
541756 GGACAAAAAG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
12 3 0.13
13 16 0.70
14 4 0.17
ACGTcount: A:0.84, C:0.05, G:0.11, T:0.00
Consensus pattern (13 bp):
AAAAACAAAAAGA
Found at i:542382 original size:22 final size:22
Alignment explanation
Indices: 542354--542396 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
542344 GCTACCCCAG
*
542354 CAAACCTTTGAGCATCCAATGC
1 CAAACCTTTGAGCATCAAATGC
542376 CAAACCTTTGAGCATCAAATG
1 CAAACCTTTGAGCATCAAATG
542397 AACAAAAATG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.35, C:0.28, G:0.14, T:0.23
Consensus pattern (22 bp):
CAAACCTTTGAGCATCAAATGC
Found at i:542640 original size:12 final size:12
Alignment explanation
Indices: 542625--542649 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
542615 ACTCTTGATT
542625 AAACATTTTTTG
1 AAACATTTTTTG
542637 AAACATTTTTTG
1 AAACATTTTTTG
542649 A
1 A
542650 TATTTTTAGG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.36, C:0.08, G:0.08, T:0.48
Consensus pattern (12 bp):
AAACATTTTTTG
Found at i:542864 original size:18 final size:18
Alignment explanation
Indices: 542829--542864 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
542819 TCAACATCAA
**
542829 ATATTGGGGCATTTTTGG
1 ATATTGGGGCATCGTTGG
542847 ATATTGGGGCATCGTTGG
1 ATATTGGGGCATCGTTGG
542865 GGATTCAACA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.17, C:0.08, G:0.36, T:0.39
Consensus pattern (18 bp):
ATATTGGGGCATCGTTGG
Found at i:543039 original size:29 final size:29
Alignment explanation
Indices: 543006--543064 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
542996 TACAGCTTTT
543006 AGAGTCAAGTTTCGACTTTAAGACGAAGG
1 AGAGTCAAGTTTCGACTTTAAGACGAAGG
543035 AGAGTCAAGTTTCGACTTTAAGACGAAGG
1 AGAGTCAAGTTTCGACTTTAAGACGAAGG
543064 A
1 A
543065 TACTCGATTC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.36, C:0.14, G:0.27, T:0.24
Consensus pattern (29 bp):
AGAGTCAAGTTTCGACTTTAAGACGAAGG
Found at i:543285 original size:36 final size:36
Alignment explanation
Indices: 543238--543372 Score: 96
Period size: 36 Copynumber: 3.8 Consensus size: 36
543228 CAGATGATTA
* *
543238 TCTCACTTGAGATTGTTTTTCTTAAAACAAGATTTG
1 TCTCGCTTGAGATAGTTTTTCTTAAAACAAGATTTG
** ** * *
543274 TCTCGCTTGAGACCG-TTTTC--ACTAGAAGATTTTA
1 TCTCGCTTGAGATAGTTTTTCTTAAAACAAGA-TTTG
* * **
543308 TCTCGCTTGAGATAGTTTCTCTTGAAACAATCTTTG
1 TCTCGCTTGAGATAGTTTTTCTTAAAACAAGATTTG
* * * *
543344 TCTCCCTTGAGACAGTTTCTCTTGAAACA
1 TCTCGCTTGAGATAGTTTTTCTTAAAACA
543373 TCTACTTTGA
Statistics
Matches: 76, Mismatches: 19, Indels: 8
0.74 0.18 0.08
Matches are distributed among these distances:
33 6 0.08
34 16 0.21
35 9 0.12
36 42 0.55
37 3 0.04
ACGTcount: A:0.24, C:0.20, G:0.16, T:0.40
Consensus pattern (36 bp):
TCTCGCTTGAGATAGTTTTTCTTAAAACAAGATTTG
Found at i:543501 original size:36 final size:36
Alignment explanation
Indices: 543426--543503 Score: 111
Period size: 36 Copynumber: 2.2 Consensus size: 36
543416 GTTTTCCTTA
* ** *
543426 AAACAAATTTTGTCTCCCTTGAGACAGTTTCTTTTG
1 AAACAAATTTTGTCTCCCATGAGACAGTTTCGCTCG
*
543462 AAACAAATTTTGTCTCCCATGAGGCAGTTTCGCTCG
1 AAACAAATTTTGTCTCCCATGAGACAGTTTCGCTCG
543498 AAACAA
1 AAACAA
543504 CACAATGTGC
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.29, C:0.22, G:0.15, T:0.33
Consensus pattern (36 bp):
AAACAAATTTTGTCTCCCATGAGACAGTTTCGCTCG
Found at i:543926 original size:65 final size:65
Alignment explanation
Indices: 543845--544067 Score: 310
Period size: 64 Copynumber: 3.5 Consensus size: 65
543835 TTGGAACTCA
* *
543845 AGACAACACAAGTTCAACTTCACAACGAAGGGGCCGCTGGTTGTTAACAAAAATTTCCCAGTATC
1 AGACAACACAAGTTCAACTTCACAACGAAGGGGCCGCTGGTTGTCAACAAAAATTTCCCAGTTTC
* *
543910 AGACAACACAAGTTCAACTTCACAACGAAGGGGCCGCTGGTTGTCAAC-AAAATTTCCTAGTTTA
1 AGACAACACAAGTTCAACTTCACAACGAAGGGGCCGCTGGTTGTCAACAAAAATTTCCCAGTTTC
* * * * *
543974 AGACAGCATAAGTTCAACTTCACAACGAAGGGGCCGCTGGCTGTCAACAAACAACTTCCCAATTT
1 AGACAACACAAGTTCAACTTCACAACGAAGGGGCCGCTGGTTGTCAACAAA-AATTTCCCAGTTT
544039 C
65 C
* *
544040 AG--AGC-CAATTTCAACTTCACAACGAAGG
1 AGACAACACAAGTTCAACTTCACAACGAAGG
544068 ATATTGGACT
Statistics
Matches: 143, Mismatches: 13, Indels: 6
0.88 0.08 0.04
Matches are distributed among these distances:
63 21 0.15
64 61 0.43
65 49 0.34
66 12 0.08
ACGTcount: A:0.35, C:0.26, G:0.18, T:0.21
Consensus pattern (65 bp):
AGACAACACAAGTTCAACTTCACAACGAAGGGGCCGCTGGTTGTCAACAAAAATTTCCCAGTTTC
Found at i:544026 original size:229 final size:230
Alignment explanation
Indices: 543745--544195 Score: 728
Period size: 235 Copynumber: 1.9 Consensus size: 230
543735 GTGCCACTCG
*
543745 AGACAGCTCAAGTTCAACTTCACAACGAAGGGGCCGCTGACTGTCAACAAACAATTTCCCAA-T-
1 AGACAGCTCAAGTTCAACTTCACAACGAAGGGGCCGCTGACTGTCAACAAACAACTTCCCAATTA
*
543808 CCAATTTCAACTTCACAGCGAAGGATATTGGAACTCAAGACAACACAAGTTCAACTTCACAACGA
66 CCAATTTCAACTTCACAACGAAGGATATTGG-ACTCAAGACAACACAAGTTCAACTTCACAACGA
* * * *
543873 AGGGGCCGCTGGTTGTTAACAAAAATTTCCCAGTATCAGACAACACAAGTTCAACTTCACAACGA
130 AGGGGCCGCTGGTTGTCAACAAAAATTCCCCAGTATAAGACAACACAAGTTCAACTTCACAACAA
*
543938 AGGGGCCGCTGGTTGTCAACAAAATTTCCTAGTTTA
195 AGGGGCCGCTGGCTGTCAACAAAATTTCCTAGTTTA
*
543974 AGACAGCAT-AAGTTCAACTTCACAACGAAGGGGCCGCTGGCTGTCAACAAACAACTTCCCAATT
1 AGACAGC-TCAAGTTCAACTTCACAACGAAGGGGCCGCTGACTGTCAACAAACAACTTCCCAA-T
544038 TCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCAAGACAACACAAGTTCAACTTCAC
64 T---A-CCAATTTCAACTTCACAACGAAGGATATTGGACTCAAGACAACACAAGTTCAACTTCAC
* *
544103 AACGAAGGGGCCGCTGGTTGTCAACAAAAATTCCCCAGTTTAAGACAGCACAAGTTCAACTTCAC
125 AACGAAGGGGCCGCTGGTTGTCAACAAAAATTCCCCAGTATAAGACAACACAAGTTCAACTTCAC
544168 AACAAAGGGGCCGCTGGCTGTCAACAAA
190 AACAAAGGGGCCGCTGGCTGTCAACAAA
544196 CAACTTCCCA
Statistics
Matches: 204, Mismatches: 10, Indels: 10
0.91 0.04 0.04
Matches are distributed among these distances:
229 58 0.28
230 1 0.00
231 1 0.00
235 114 0.56
236 30 0.15
ACGTcount: A:0.35, C:0.26, G:0.18, T:0.20
Consensus pattern (230 bp):
AGACAGCTCAAGTTCAACTTCACAACGAAGGGGCCGCTGACTGTCAACAAACAACTTCCCAATTA
CCAATTTCAACTTCACAACGAAGGATATTGGACTCAAGACAACACAAGTTCAACTTCACAACGAA
GGGGCCGCTGGTTGTCAACAAAAATTCCCCAGTATAAGACAACACAAGTTCAACTTCACAACAAA
GGGGCCGCTGGCTGTCAACAAAATTTCCTAGTTTA
Found at i:544113 original size:170 final size:171
Alignment explanation
Indices: 543910--544245 Score: 584
Period size: 171 Copynumber: 2.0 Consensus size: 171
543900 TCCCAGTATC
* *
543910 AGACAACACAAGTTCAACTTCACAACGAAGGGGCCGCTGGTTGTCAAC-AAAATTTCCTAGTTTA
1 AGACAACACAAGTTCAACTTCACAACGAAGGGGCCGCTGGTTGTCAACAAAAATTCCCCAGTTTA
* *
543974 AGACAGCATAAGTTCAACTTCACAACGAAGGGGCCGCTGGCTGTCAACAAACAACTTCCCAATTT
66 AGACAGCACAAGTTCAACTTCACAACAAAGGGGCCGCTGGCTGTCAACAAACAACTTCCCAATTT
544039 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCA
131 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCA
544080 AGACAACACAAGTTCAACTTCACAACGAAGGGGCCGCTGGTTGTCAACAAAAATTCCCCAGTTTA
1 AGACAACACAAGTTCAACTTCACAACGAAGGGGCCGCTGGTTGTCAACAAAAATTCCCCAGTTTA
*
544145 AGACAGCACAAGTTCAACTTCACAACAAAGGGGCCGCTGGCTGTCAACAAACAACTTCCCAGTTT
66 AGACAGCACAAGTTCAACTTCACAACAAAGGGGCCGCTGGCTGTCAACAAACAACTTCCCAATTT
* * **
544210 CAGAGTCAATTTCAACTTGACAGTGAAGGATATTGG
131 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
544246 CCTCGAAACA
Statistics
Matches: 156, Mismatches: 9, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
170 48 0.31
171 108 0.69
ACGTcount: A:0.35, C:0.25, G:0.19, T:0.21
Consensus pattern (171 bp):
AGACAACACAAGTTCAACTTCACAACGAAGGGGCCGCTGGTTGTCAACAAAAATTCCCCAGTTTA
AGACAGCACAAGTTCAACTTCACAACAAAGGGGCCGCTGGCTGTCAACAAACAACTTCCCAATTT
CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCA
Found at i:544159 original size:65 final size:66
Alignment explanation
Indices: 544079--544209 Score: 212
Period size: 65 Copynumber: 2.0 Consensus size: 66
544069 TATTGGACTC
* *
544079 AAGACAACACAAGTTCAACTTCACAACGAAGGGGCCGCTGGTTGTCAACAAA-AA-TTCCCCAGT
1 AAGACAACACAAGTTCAACTTCACAACAAAGGGGCCGCTGGCTGTCAACAAACAACTT-CCCAGT
544142 TT
65 TT
*
544144 AAGACAGCACAAGTTCAACTTCACAACAAAGGGGCCGCTGGCTGTCAACAAACAACTTCCCAGTT
1 AAGACAACACAAGTTCAACTTCACAACAAAGGGGCCGCTGGCTGTCAACAAACAACTTCCCAGTT
544209 T
66 T
544210 CAGAGTCAAT
Statistics
Matches: 61, Mismatches: 3, Indels: 3
0.91 0.04 0.04
Matches are distributed among these distances:
65 49 0.80
66 10 0.16
67 2 0.03
ACGTcount: A:0.35, C:0.27, G:0.18, T:0.19
Consensus pattern (66 bp):
AAGACAACACAAGTTCAACTTCACAACAAAGGGGCCGCTGGCTGTCAACAAACAACTTCCCAGTT
T
Found at i:544193 original size:106 final size:104
Alignment explanation
Indices: 543974--544175 Score: 255
Period size: 106 Copynumber: 1.9 Consensus size: 104
543964 TCCTAGTTTA
* *
543974 AGACAGCATAAGTTCAACTTCACAACGAAGGGGCCGCTGGCTGTCAACAAACAACTTCCCAATTT
1 AGACAACACAAGTTCAACTTCACAACGAAGGGGCCGCTGGCTGTCAACAAACAACTTCCCAATTT
* * * * *
544039 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACT
66 AAGAGCCAAGTTCAACTTCACAACAAAGGACACTGGACT
* *
544078 CAAGACAACACAAGTTCAACTTCACAACGAAGGGGCCGCTGGTTGTCAACAAA-AA-TTCCCCAG
1 --AGACAACACAAGTTCAACTTCACAACGAAGGGGCCGCTGGCTGTCAACAAACAACTT-CCCAA
544141 TTTAAGACAGCACAAGTTCAACTTCACAACAAAGG
63 TTTAAG--AGC-CAAGTTCAACTTCACAACAAAGG
544176 GGCCGCTGGC
Statistics
Matches: 85, Mismatches: 7, Indels: 6
0.87 0.07 0.06
Matches are distributed among these distances:
104 2 0.02
105 11 0.13
106 48 0.56
107 3 0.04
108 21 0.25
ACGTcount: A:0.37, C:0.26, G:0.18, T:0.19
Consensus pattern (104 bp):
AGACAACACAAGTTCAACTTCACAACGAAGGGGCCGCTGGCTGTCAACAAACAACTTCCCAATTT
AAGAGCCAAGTTCAACTTCACAACAAAGGACACTGGACT
Found at i:545966 original size:15 final size:14
Alignment explanation
Indices: 545944--545973 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
545934 TTTTCCTTTC
545944 TGTTTTTTATTTAT
1 TGTTTTTTATTTAT
545958 TGTTATTTTATTTAT
1 TGTT-TTTTATTTAT
545973 T
1 T
545974 TCATCTAACA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.27
15 11 0.73
ACGTcount: A:0.17, C:0.00, G:0.07, T:0.77
Consensus pattern (14 bp):
TGTTTTTTATTTAT
Found at i:549087 original size:12 final size:12
Alignment explanation
Indices: 549070--549121 Score: 77
Period size: 12 Copynumber: 4.3 Consensus size: 12
549060 AACCAACCAT
549070 TAATATTCAATC
1 TAATATTCAATC
**
549082 TAATATTTGATC
1 TAATATTCAATC
*
549094 TAATATTCAACC
1 TAATATTCAATC
549106 TAATATTCAATC
1 TAATATTCAATC
549118 TAAT
1 TAAT
549122 GTTGATAGAA
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
12 34 1.00
ACGTcount: A:0.40, C:0.15, G:0.02, T:0.42
Consensus pattern (12 bp):
TAATATTCAATC
Found at i:549775 original size:18 final size:17
Alignment explanation
Indices: 549734--549775 Score: 57
Period size: 18 Copynumber: 2.4 Consensus size: 17
549724 AAAATTTATA
549734 AAAAAATATTTAAAAAT
1 AAAAAATATTTAAAAAT
*
549751 ACTAAAATATTTAAAATAT
1 A-AAAAATATTTAAAA-AT
549770 AAAAAA
1 AAAAAA
549776 ATTATTTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
17 1 0.05
18 17 0.81
19 3 0.14
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (17 bp):
AAAAAATATTTAAAAAT
Found at i:560816 original size:29 final size:30
Alignment explanation
Indices: 560759--560819 Score: 106
Period size: 29 Copynumber: 2.1 Consensus size: 30
560749 ATAATAAGTT
*
560759 AACTAATCTATTAGTTTTTAATAAGTAATA
1 AACTAATCTATTAGTTTTTAATAAATAATA
560789 AACTAATCTATTA-TTTTTAATAAATAATA
1 AACTAATCTATTAGTTTTTAATAAATAATA
560818 AA
1 AA
560820 AAATAATAAG
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
29 17 0.57
30 13 0.43
ACGTcount: A:0.48, C:0.07, G:0.03, T:0.43
Consensus pattern (30 bp):
AACTAATCTATTAGTTTTTAATAAATAATA
Found at i:560825 original size:73 final size:73
Alignment explanation
Indices: 560719--560894 Score: 302
Period size: 73 Copynumber: 2.4 Consensus size: 73
560709 ATCTAAATAA
560719 TAAT-TATTAATTTATTAAT-AATAATAAAAAATAATAAGTTAACTAATCTATTAGTTTTTAATA
1 TAATCTATT-ATTT-TTAATAAATAATAAAAAATAATAAGTTAACTAATCTATTAGTTTTTAATA
*
560782 AGTAATAAAC
64 AATAATAAAC
560792 TAATCTATTATTTTTAATAAATAATAAAAAATAATAAGTTAACTAATCTATTAGTTTTTAATAAA
1 TAATCTATTATTTTTAATAAATAATAAAAAATAATAAGTTAACTAATCTATTAGTTTTTAATAAA
560857 TAATAAAC
66 TAATAAAC
560865 TAATCTATTATTTTTTAATAAATAATAAAA
1 TAATCTATTA-TTTTTAATAAATAATAAAA
560895 TATTATTAAT
Statistics
Matches: 99, Mismatches: 1, Indels: 5
0.94 0.01 0.05
Matches are distributed among these distances:
72 5 0.05
73 71 0.72
74 23 0.23
ACGTcount: A:0.51, C:0.05, G:0.03, T:0.42
Consensus pattern (73 bp):
TAATCTATTATTTTTAATAAATAATAAAAAATAATAAGTTAACTAATCTATTAGTTTTTAATAAA
TAATAAAC
Found at i:560866 original size:30 final size:30
Alignment explanation
Indices: 560832--560893 Score: 115
Period size: 30 Copynumber: 2.1 Consensus size: 30
560822 ATAATAAGTT
560832 AACTAATCTATTAGTTTTTAATAAATAATA
1 AACTAATCTATTAGTTTTTAATAAATAATA
*
560862 AACTAATCTATTATTTTTTAATAAATAATA
1 AACTAATCTATTAGTTTTTAATAAATAATA
560892 AA
1 AA
560894 ATATTATTAA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.48, C:0.06, G:0.02, T:0.44
Consensus pattern (30 bp):
AACTAATCTATTAGTTTTTAATAAATAATA
Done.