Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002645.1 Hibiscus syriacus cultivar Beakdansim tig00005396_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: 53765
ACGTcount: A:0.32, C:0.15, G:0.17, T:0.35
Found at i:149 original size:44 final size:45
Alignment explanation
Indices: 11--173 Score: 165
Period size: 44 Copynumber: 3.7 Consensus size: 45
1 ACTAAGTGTG
* *
11 CAAATATAGTAGTAGTACATTTGTTTGTACTATGGCACTATGCGTG
1 CAAAGATAGTAGTAGTACATTTG-TTGTACTATGGCACTATGCGTT
* * * * * *
57 C-AAGA-AGTAGTATTACATTTGTTTTATTATTGCACTATGCATG
1 CAAAGATAGTAGTAGTACATTTGTTGTACTATGGCACTATGCGTT
* * *
100 CAAAGATAGTAGTACTACA-TTGTTGTACTATGGTACTATGTGTT
1 CAAAGATAGTAGTAGTACATTTGTTGTACTATGGCACTATGCGTT
* *
144 TAAAGATGGTAGTAGTACA-TT-TTGTACTAT
1 CAAAGATAGTAGTAGTACATTTGTTGTACTAT
174 AGGACTGTGT
Statistics
Matches: 98, Mismatches: 17, Indels: 7
0.80 0.14 0.06
Matches are distributed among these distances:
43 28 0.29
44 55 0.56
45 14 0.14
46 1 0.01
ACGTcount: A:0.30, C:0.11, G:0.20, T:0.39
Consensus pattern (45 bp):
CAAAGATAGTAGTAGTACATTTGTTGTACTATGGCACTATGCGTT
Found at i:195 original size:43 final size:44
Alignment explanation
Indices: 1--196 Score: 148
Period size: 44 Copynumber: 4.5 Consensus size: 44
* * * * *
1 ACTAAGTGTGCAAATATAGTAGTAGTACATTTGTTTGTACTATGGC
1 ACTATGTGTGCAAAGATGGTAGTACTACA-TTG-TTGTACTATGGT
* * * * * * *
47 ACTATGCGTGC-AAGA-AGTAGTATTACATTTGTTTTATTATTGC
1 ACTATGTGTGCAAAGATGGTAGTACTACA-TTGTTGTACTATGGT
** *
90 ACTATGCATGCAAAGATAGTAGTACTACATTGTTGTACTATGGT
1 ACTATGTGTGCAAAGATGGTAGTACTACATTGTTGTACTATGGT
** *
134 ACTATGTGTTTAAAGATGGTAGTAGTACATT-TTGTACTATAGG-
1 ACTATGTGTGCAAAGATGGTAGTACTACATTGTTGTACTAT-GGT
* *
177 ACTGTGTGTGCAAGGATGGT
1 ACTATGTGTGCAAAGATGGT
197 GTTCAAAAGA
Statistics
Matches: 124, Mismatches: 23, Indels: 9
0.79 0.15 0.06
Matches are distributed among these distances:
43 44 0.35
44 57 0.46
45 14 0.11
46 9 0.07
ACGTcount: A:0.29, C:0.11, G:0.23, T:0.37
Consensus pattern (44 bp):
ACTATGTGTGCAAAGATGGTAGTACTACATTGTTGTACTATGGT
Found at i:4385 original size:20 final size:20
Alignment explanation
Indices: 4347--4385 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
4337 GACGGCTAGA
**
4347 AACATTCAAAAACTCATTCC
1 AACATTCAAAAACAAATTCC
*
4367 AACATTTAAAAACAAATTC
1 AACATTCAAAAACAAATTC
4386 AAGACACTTG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.51, C:0.23, G:0.00, T:0.26
Consensus pattern (20 bp):
AACATTCAAAAACAAATTCC
Found at i:5007 original size:85 final size:85
Alignment explanation
Indices: 4878--5099 Score: 191
Period size: 85 Copynumber: 2.6 Consensus size: 85
4868 TGCTTTTTTA
* * * * *
4878 TTTCTCTAAAGGATG-TAAAATCAGAGAATGGTCTTCCTCATTTCTCTAAAGGGA-GAAAAGTCA
1 TTTCTATAAAGGAAGCT-AAATCAGA-AATGATCTTTCTCCTTTCTCTAAAGGGATGAAAAGTCA
4941 TAATCAAGGGTTGATCTACTCC
64 TAATCAAGGGTTGATCTACTCC
* * * **
4963 TTTCTATAAAGGAAGCTAAATTGAGAAATGATCTTTCTCCTTTCTTTGAA-GGATGCCAAGTCAT
1 TTTCTATAAAGGAAGCTAAA-TCAGAAATGATCTTTCTCCTTTCTCTAAAGGGATGAAAAGTCAT
* * * *
5027 GATCAATGGTTGTTCTGCTCC
65 AATCAAGGGTTGATCTACTCC
* * * * * *
5048 TTTTTTTGAAGGACGCCAAATCAGGAAATGATCTCGT-TCCTTTCTCTAAAGG
1 TTTCTATAAAGGAAGCTAAATCA-GAAATGATCT-TTCTCCTTTCTCTAAAGG
5100 ATGCCAAGTC
Statistics
Matches: 108, Mismatches: 23, Indels: 11
0.76 0.16 0.08
Matches are distributed among these distances:
84 5 0.05
85 96 0.89
86 7 0.06
ACGTcount: A:0.29, C:0.18, G:0.19, T:0.34
Consensus pattern (85 bp):
TTTCTATAAAGGAAGCTAAATCAGAAATGATCTTTCTCCTTTCTCTAAAGGGATGAAAAGTCATA
ATCAAGGGTTGATCTACTCC
Found at i:5100 original size:85 final size:81
Alignment explanation
Indices: 4986--5156 Score: 218
Period size: 85 Copynumber: 2.1 Consensus size: 81
4976 AGCTAAATTG
* * * * *
4986 AGAAATGATCTTTCTCCTTTCTTTGAAGGATGCCAAGTCATGATCAATGGTTGTTCTGCTCCTTT
1 AGAAATGATCTGTCTCCTTTCTCTAAAGGATGCCAAGTCATGATCAATGATTGCTCTG-T--TTT
5051 TTTTGAAGGACGCCAAATCA
63 TTTT-AAGGACGCCAAATCA
* *
5071 GGAAATGATCTCGT-TCCTTTCTCTAAAGGATGCCAAGTCGTGATCAATGATTGCTCTGTTTTTT
1 AGAAATGATCT-GTCTCCTTTCTCTAAAGGATGCCAAGTCATGATCAATGATTGCTCTGTTTTTT
*
5135 TTAAGGATGCCAAATCA
65 TTAAGGACGCCAAATCA
5152 AGAAA
1 AGAAA
5157 AAAATCTTGC
Statistics
Matches: 76, Mismatches: 9, Indels: 6
0.84 0.10 0.07
Matches are distributed among these distances:
81 18 0.24
82 7 0.09
84 1 0.01
85 49 0.64
86 1 0.01
ACGTcount: A:0.27, C:0.19, G:0.19, T:0.35
Consensus pattern (81 bp):
AGAAATGATCTGTCTCCTTTCTCTAAAGGATGCCAAGTCATGATCAATGATTGCTCTGTTTTTTT
TAAGGACGCCAAATCA
Found at i:5177 original size:81 final size:84
Alignment explanation
Indices: 5011--5200 Score: 183
Period size: 85 Copynumber: 2.3 Consensus size: 84
5001 CCTTTCTTTG
* * * *
5011 AAGGATGCCAAGTCATGATCAATGGTTGTTCTGCTCCTTTTTTTGAAGGACGCCAAATCAGGAAA
1 AAGGATGCCAAGTCGTGATCAATGATTGCTCTGCT-CTTTTTTTGAAGGACGCCAAATCAGAAAA
** * ***
5076 TGATCTCGTTCCTTTCTCTA
65 AAATCTCGCTAAGTTCTCTA
*
5096 AAGGATGCCAAGTCGTGATCAATGATTGCTCTG-T-TTTTTTT-AAGGATGCCAAATCAAGAAAA
1 AAGGATGCCAAGTCGTGATCAATGATTGCTCTGCTCTTTTTTTGAAGGACGCCAAATC-AGAAAA
*
5158 AAATCTTGCTAAGTT-TCTA
65 AAATCTCGCTAAGTTCTCTA
* * * *
5177 ATGGACG-TAAGTCGTAATCAATGA
1 AAGGATGCCAAGTCGTGATCAATGA
5201 AAATTCAGTT
Statistics
Matches: 88, Mismatches: 16, Indels: 7
0.79 0.14 0.06
Matches are distributed among these distances:
80 15 0.17
81 22 0.25
82 20 0.23
84 1 0.01
85 30 0.34
ACGTcount: A:0.30, C:0.17, G:0.20, T:0.33
Consensus pattern (84 bp):
AAGGATGCCAAGTCGTGATCAATGATTGCTCTGCTCTTTTTTTGAAGGACGCCAAATCAGAAAAA
AATCTCGCTAAGTTCTCTA
Found at i:7032 original size:195 final size:195
Alignment explanation
Indices: 6693--7079 Score: 472
Period size: 195 Copynumber: 2.0 Consensus size: 195
6683 AGGAATAAAA
* *
6693 GGTATTTTGGGATGGCTTCTTGGGTCAAGATTTAGCACCTCTAATTCTTTTATGTTCCTCGCTCT
1 GGTATTTTGGGATGGCTTCTTGGGTCAAGATTTAGCACCTCTAATTCTTTGATGTTCATCGCTCT
* * * * * * *
6758 AACATGTTCATCTTCTAGAAATGTCCACTGGTTCTAAGCTCTCACAAATGCTTATTGGATGTACG
66 AACATGTTCATCTTCTAGAAATATCCACTAGTTCTAAACTCTCACAAATGCGTATTGAATATAAG
* * * *
6823 ACACTTTTTCAAGAGATTTATAAGCCCACCTCTTGTGAAACAGTTGCACAATTTTAACATTTGAG
131 ACACTTTGTCAAGAGATTTATAAGCCCACCTCTTGTAAAACAGTTGCAAAACTTTAACATTTGAG
* * *
6888 GGTATTTTGGGTTGGCTTCTCT-GGTTAAGATTTAGCACAC-CTAGTTCTTTGATGTTCATCGCT
1 GGTATTTTGGGATGGCTTCT-TGGGTCAAGATTTAGCAC-CTCTAATTCTTTGATGTTCATCGCT
* * * * *** *
6951 GTAGCATGTTCATCTTCTATAAATATCCATTAGTTCTAAACTCTCGTGAATGCGTCTTGAATATA
64 CTAACATGTTCATCTTCTAGAAATATCCACTAGTTCTAAACTCTCACAAATGCGTATTGAATATA
* * * * * *
7016 AGACTCTTTGTCAAGAGTTTTATAAGCTCGCCTCTTGTAAAATAGTTGCAAAACTTTCACATTT
129 AGACACTTTGTCAAGAGATTTATAAGCCCACCTCTTGTAAAACAGTTGCAAAACTTTAACATTT
7080 AACCCGCCTT
Statistics
Matches: 160, Mismatches: 30, Indels: 4
0.82 0.15 0.02
Matches are distributed among these distances:
195 158 0.99
196 2 0.01
ACGTcount: A:0.25, C:0.19, G:0.17, T:0.38
Consensus pattern (195 bp):
GGTATTTTGGGATGGCTTCTTGGGTCAAGATTTAGCACCTCTAATTCTTTGATGTTCATCGCTCT
AACATGTTCATCTTCTAGAAATATCCACTAGTTCTAAACTCTCACAAATGCGTATTGAATATAAG
ACACTTTGTCAAGAGATTTATAAGCCCACCTCTTGTAAAACAGTTGCAAAACTTTAACATTTGAG
Found at i:8803 original size:121 final size:121
Alignment explanation
Indices: 8666--8911 Score: 492
Period size: 121 Copynumber: 2.0 Consensus size: 121
8656 ATTTTAATCC
8666 TATTTTTATATGTTACGTATTATTGTAAATATTTGACATCGGTCACTATATGTTTAATTATTATA
1 TATTTTTATATGTTACGTATTATTGTAAATATTTGACATCGGTCACTATATGTTTAATTATTATA
8731 TTATAGTCACTGACCGTATATTATATTTTATATTTAAATTTGGTCTTAAAATTTAA
66 TTATAGTCACTGACCGTATATTATATTTTATATTTAAATTTGGTCTTAAAATTTAA
8787 TATTTTTATATGTTACGTATTATTGTAAATATTTGACATCGGTCACTATATGTTTAATTATTATA
1 TATTTTTATATGTTACGTATTATTGTAAATATTTGACATCGGTCACTATATGTTTAATTATTATA
8852 TTATAGTCACTGACCGTATATTATATTTTATATTTAAATTTGGTCTTAAAATTTAA
66 TTATAGTCACTGACCGTATATTATATTTTATATTTAAATTTGGTCTTAAAATTTAA
8908 TATT
1 TATT
8912 CTTTTGTTTT
Statistics
Matches: 125, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
121 125 1.00
ACGTcount: A:0.32, C:0.08, G:0.10, T:0.50
Consensus pattern (121 bp):
TATTTTTATATGTTACGTATTATTGTAAATATTTGACATCGGTCACTATATGTTTAATTATTATA
TTATAGTCACTGACCGTATATTATATTTTATATTTAAATTTGGTCTTAAAATTTAA
Found at i:15833 original size:136 final size:136
Alignment explanation
Indices: 15542--16038 Score: 721
Period size: 136 Copynumber: 3.7 Consensus size: 136
15532 TTTAACATTT
*
15542 CCTATCACTCGATTCACGGCATTTCGAATCAGTGATGCCTCGCTTGAGGGATTGACATTTCCAAT
1 CCTATCACTCGATTCACAGCATTTCGAATCAGTGATGCCTCGCTTGAGGGATTGACATTTCCAAT
* * * * * * * *
15607 GGAGAGTTC---ATGGGAATAACTCATCCAACAGAGGGAGAAGAAGTTTATAATGAAAAGAGATT
66 TGAGAGTTCATAATGAGAAGAACTCATTCAATAGAGGGAGAAGAAGTTAATAATGAGAAGAGCTT
*
15669 GTTTGA
131 GTTCGA
* * *
15675 CCTATCACTTGATTTACAGCATTTCGAATCAGTGATGCCTCACTTGAGGGATTGACATTTCCAAT
1 CCTATCACTCGATTCACAGCATTTCGAATCAGTGATGCCTCGCTTGAGGGATTGACATTTCCAAT
* *
15740 TGAAAGTTCATAATGAGAAGAACTCATTCGATAGAGGGAGAAGAAGTTAATAATGAGAAGAGCTT
66 TGAGAGTTCATAATGAGAAGAACTCATTCAATAGAGGGAGAAGAAGTTAATAATGAGAAGAGCTT
*
15805 GTTCAA
131 GTTCGA
* * * *
15811 CCTATCACTTGATTCACGGCATTTCGAATCAGTGACGTCTCGCTTGAGGGATTGACATTTCCAAT
1 CCTATCACTCGATTCACAGCATTTCGAATCAGTGATGCCTCGCTTGAGGGATTGACATTTCCAAT
* * *
15876 TGAGAGTTCATAGTGAGAAGAACTCATTCAATAGAGGGAGAAGAAGATCATAATGAGAAGAGCTT
66 TGAGAGTTCATAATGAGAAGAACTCATTCAATAGAGGGAGAAGAAGTTAATAATGAGAAGAGCTT
15941 GTTCGA
131 GTTCGA
* * * * *
15947 CCTATCACTCGATTCACAACATTTTGAATCTGTGATGCCTCGCTTGAGTGATGGACATTTCCAAT
1 CCTATCACTCGATTCACAGCATTTCGAATCAGTGATGCCTCGCTTGAGGGATTGACATTTCCAAT
16012 TGAGAGTTCATAATGAGAAGAACTCAT
66 TGAGAGTTCATAATGAGAAGAACTCAT
16039 CCTAAAGGAG
Statistics
Matches: 324, Mismatches: 37, Indels: 3
0.89 0.10 0.01
Matches are distributed among these distances:
133 68 0.21
136 256 0.79
ACGTcount: A:0.32, C:0.17, G:0.22, T:0.28
Consensus pattern (136 bp):
CCTATCACTCGATTCACAGCATTTCGAATCAGTGATGCCTCGCTTGAGGGATTGACATTTCCAAT
TGAGAGTTCATAATGAGAAGAACTCATTCAATAGAGGGAGAAGAAGTTAATAATGAGAAGAGCTT
GTTCGA
Found at i:16994 original size:22 final size:24
Alignment explanation
Indices: 16956--17006 Score: 65
Period size: 22 Copynumber: 2.3 Consensus size: 24
16946 TCTGGGTCTT
16956 GGTC-TGC-TGGATCTTGT-ATTG
1 GGTCTTGCTTGGATCTTGTAATTG
*
16977 GG-CTTGCTTGGATGTTGTAATTG
1 GGTCTTGCTTGGATCTTGTAATTG
17000 GGTCTTG
1 GGTCTTG
17007 GGAGAGACTT
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
20 1 0.04
21 5 0.20
22 9 0.36
23 6 0.24
24 4 0.16
ACGTcount: A:0.10, C:0.12, G:0.35, T:0.43
Consensus pattern (24 bp):
GGTCTTGCTTGGATCTTGTAATTG
Found at i:17058 original size:3 final size:3
Alignment explanation
Indices: 17050--17096 Score: 53
Period size: 3 Copynumber: 16.3 Consensus size: 3
17040 TAAACACACT
* * *
17050 TAA TAA TAA TAA TAA TAA TTA TTA TAA T-A TAA T-A TAA TAA TAT TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
17096 T
1 T
17097 TTTTAATATT
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
2 4 0.11
3 34 0.89
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (3 bp):
TAA
Found at i:23345 original size:49 final size:48
Alignment explanation
Indices: 23138--23447 Score: 365
Period size: 49 Copynumber: 6.4 Consensus size: 48
23128 TGAAATGCAC
* * *
23138 GCATTTAACTTTCATTAGTGGTACCTTTTATGTC-GAAATGCACCATTAT
1 GCATTTAACTTGCATTAGTGGCACC-TTTATG-CAAAAATGCACCATTAT
* * * * *
23187 GCA-TT-ACTTTTTCATTAGTAGTACCTTTATGTAAAAAATACACCATTAT
1 GCATTTAAC--TTGCATTAGTGGCACCTTTATG-CAAAAATGCACCATTAT
*
23236 GCATTTAACTTGCATTAGTGGCACCTTTCTGCTAAAAATGCACCATTAT
1 GCATTTAACTTGCATTAGTGGCACCTTTATGC-AAAAATGCACCATTAT
* *
23285 GCATTTCACTTGCATTAGTGGCACCTTTCTGCAAAATATGCACCATTAT
1 GCATTTAACTTGCATTAGTGGCACCTTTATGCAAAA-ATGCACCATTAT
* * * *
23334 GAATTTAACTTGCATTGGTGACACCTTTCTGCCAAAAATGCACCATTAT
1 GCATTTAACTTGCATTAGTGGCACCTTTATG-CAAAAATGCACCATTAT
* *
23383 GCATTCAACTTGCATTAGTGGCAGCTTTATGCAAAAATGCACCATTAT
1 GCATTTAACTTGCATTAGTGGCACCTTTATGCAAAAATGCACCATTAT
*
23431 GCAGTTAACTTGCATTA
1 GCATTTAACTTGCATTA
23448 TAGAGTAGTT
Statistics
Matches: 230, Mismatches: 23, Indels: 17
0.85 0.09 0.06
Matches are distributed among these distances:
47 2 0.01
48 45 0.20
49 174 0.76
50 7 0.03
51 2 0.01
ACGTcount: A:0.30, C:0.21, G:0.14, T:0.36
Consensus pattern (48 bp):
GCATTTAACTTGCATTAGTGGCACCTTTATGCAAAAATGCACCATTAT
Found at i:23796 original size:17 final size:17
Alignment explanation
Indices: 23755--23801 Score: 69
Period size: 17 Copynumber: 2.8 Consensus size: 17
23745 ATTTTCAATT
*
23755 TTTCATAAAATTCATCC
1 TTTCTTAAAATTCATCC
23772 TTTCTTAAAATTCATCC
1 TTTCTTAAAATTCATCC
23789 TATT-TTAAAATTC
1 T-TTCTTAAAATTC
23802 TAGGCTTAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
17 26 0.93
18 2 0.07
ACGTcount: A:0.34, C:0.19, G:0.00, T:0.47
Consensus pattern (17 bp):
TTTCTTAAAATTCATCC
Found at i:25098 original size:32 final size:32
Alignment explanation
Indices: 25056--25117 Score: 83
Period size: 32 Copynumber: 1.9 Consensus size: 32
25046 TTTAAATAGA
25056 TTTTAGTATTTTA-ATTAAGTTTTAGGATATTAT
1 TTTTAGTATTTTATATT-AGTTTTAGG-TATTAT
*
25089 TTTTA-TATTTTATATTTGTTTTAGGTATT
1 TTTTAGTATTTTATATTAGTTTTAGGTATT
25118 TTAAATTAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
31 4 0.15
32 15 0.56
33 8 0.30
ACGTcount: A:0.26, C:0.00, G:0.11, T:0.63
Consensus pattern (32 bp):
TTTTAGTATTTTATATTAGTTTTAGGTATTAT
Found at i:25191 original size:64 final size:66
Alignment explanation
Indices: 25093--25220 Score: 181
Period size: 65 Copynumber: 2.0 Consensus size: 66
25083 TATTATTTTT
*
25093 ATATTTTATATTTGTTTTAGGTATTTTAAATTAAATAGGTTTT-AGTATTTTAATTAGGATTTAG
1 ATATTATATATTTGTTTTAGGTATTTTAAATTAAATAGGTTTTAAGTATTTTAATTAGGATTTAG
25157 A
66 A
** * *
25158 ATATTATATAATTT-TTTT-GGTATTTTAGCTTAAATAGTTTTTAAGTGTTTTAATTAGGATTTA
1 ATATTATAT-ATTTGTTTTAGGTATTTTAAATTAAATAGGTTTTAAGTATTTTAATTAGGATTTA
25221 AGATATTTTA
Statistics
Matches: 56, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
64 21 0.38
65 31 0.55
66 4 0.07
ACGTcount: A:0.31, C:0.01, G:0.13, T:0.55
Consensus pattern (66 bp):
ATATTATATATTTGTTTTAGGTATTTTAAATTAAATAGGTTTTAAGTATTTTAATTAGGATTTAG
A
Found at i:25853 original size:4 final size:4
Alignment explanation
Indices: 25803--25835 Score: 57
Period size: 4 Copynumber: 8.0 Consensus size: 4
25793 CTCCATCTCT
25803 TTTA TTTA TTTA TTTA TTTA TTTA TTTTA TTTA
1 TTTA TTTA TTTA TTTA TTTA TTTA -TTTA TTTA
25836 ATTGTTATCT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 24 0.86
5 4 0.14
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TTTA
Found at i:31237 original size:32 final size:32
Alignment explanation
Indices: 31194--31255 Score: 92
Period size: 32 Copynumber: 1.9 Consensus size: 32
31184 TTTAAATAGG
31194 TTTTAGTATTTTA-ATTAAGTTTTAGGATATTAT
1 TTTTAGTATTTTATATT-AGTTTTA-GATATTAT
31227 TTTTA-TATTTTATATTAGTTTTAGATATT
1 TTTTAGTATTTTATATTAGTTTTAGATATT
31256 TTAAATTAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
31 6 0.21
32 14 0.50
33 8 0.29
ACGTcount: A:0.29, C:0.00, G:0.10, T:0.61
Consensus pattern (32 bp):
TTTTAGTATTTTATATTAGTTTTAGATATTAT
Found at i:31363 original size:63 final size:63
Alignment explanation
Indices: 31236--31356 Score: 165
Period size: 63 Copynumber: 1.9 Consensus size: 63
31226 TTTTTATATT
*
31236 TTATATTAGTTTTAGATATTTTAAATTAAATAGGTTTTAGTATTTTTATTAGGATTTAGAATA
1 TTATATTAGTTTTAGATATTTTAAATTAAATAGGTTTTAGTAGTTTTATTAGGATTTAGAATA
* * **
31299 TTATATTATTTTTTAGGTATTTTAGTTTAAATA-GTTTTAAGT-GTTTTATTAGGATTTA
1 TTATATTA-GTTTTAGATATTTTAAATTAAATAGGTTTT-AGTAGTTTTATTAGGATTTA
31357 AGATATTTTA
Statistics
Matches: 51, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
63 28 0.55
64 23 0.45
ACGTcount: A:0.31, C:0.00, G:0.13, T:0.55
Consensus pattern (63 bp):
TTATATTAGTTTTAGATATTTTAAATTAAATAGGTTTTAGTAGTTTTATTAGGATTTAGAATA
Found at i:31947 original size:4 final size:4
Alignment explanation
Indices: 31938--31970 Score: 57
Period size: 4 Copynumber: 8.0 Consensus size: 4
31928 CTCAATCTCT
31938 TTTA TTTA TTTA TTTA TTTA TTTA TTTTA TTTA
1 TTTA TTTA TTTA TTTA TTTA TTTA -TTTA TTTA
31971 ATTGTTATCT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 24 0.86
5 4 0.14
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TTTA
Found at i:32066 original size:16 final size:15
Alignment explanation
Indices: 32042--32084 Score: 50
Period size: 16 Copynumber: 2.8 Consensus size: 15
32032 TTAATATTTA
*
32042 TTATTTTATTATTTT
1 TTATTTTATTATTAT
* *
32057 TCTTTTTTATAATTAT
1 T-TATTTTATTATTAT
32073 TTATTTTATTAT
1 TTATTTTATTAT
32085 ATCTTTTTAA
Statistics
Matches: 22, Mismatches: 5, Indels: 2
0.76 0.17 0.07
Matches are distributed among these distances:
15 10 0.45
16 12 0.55
ACGTcount: A:0.23, C:0.02, G:0.00, T:0.74
Consensus pattern (15 bp):
TTATTTTATTATTAT
Found at i:34716 original size:49 final size:48
Alignment explanation
Indices: 34658--34999 Score: 371
Period size: 49 Copynumber: 6.9 Consensus size: 48
34648 ACCATGGGTA
** * *
34658 GCACCTTTTATGCTGAAATGCACCGTTATGCATTTAACTTTCATTAGTG
1 GCACC-TTTATGCAAAAATGCACCATTATGCATTTAACTTGCATTAGTG
* ** * * * * * *
34707 GTACCTTTTATGCTCAAATACACCGTTATGCATTAAATTTTCATTAGCG
1 GCACC-TTTATGCAAAAATGCACCATTATGCATTTAACTTGCATTAGTG
* *
34756 GTACCTTTATGCCAAAAATACACCATTATGCATTTAA-TTGCATTAGTG
1 GCACCTTTATG-CAAAAATGCACCATTATGCATTTAACTTGCATTAGTG
* *
34804 ACACCTTTATACCAAAAAAATGCACCATTATGCATTTAACTTGCATTAGTG
1 GCACCTTTAT-GC--AAAAATGCACCATTATGCATTTAACTTGCATTAGTG
* *
34855 GCACCTTTCTGCCAAAAATGCACCATTATGCATTTAACTTGCATTATTG
1 GCACCTTTATG-CAAAAATGCACCATTATGCATTTAACTTGCATTAGTG
* * *
34904 GAACCTTTCTGCCAAAAATGCACCATTATGAATTTAACTTGCATTAGTG
1 GCACCTTTATG-CAAAAATGCACCATTATGCATTTAACTTGCATTAGTG
* *
34953 GCACCTATCTGCAAAAAAATGCACCATTATGCATTTAACTTGCATTA
1 GCACCTTTATGC--AAAAATGCACCATTATGCATTTAACTTGCATTA
35000 TAGAGCAGTT
Statistics
Matches: 259, Mismatches: 26, Indels: 15
0.86 0.09 0.05
Matches are distributed among these distances:
48 25 0.10
49 159 0.61
50 55 0.21
51 20 0.08
ACGTcount: A:0.32, C:0.21, G:0.13, T:0.35
Consensus pattern (48 bp):
GCACCTTTATGCAAAAATGCACCATTATGCATTTAACTTGCATTAGTG
Found at i:34968 original size:148 final size:148
Alignment explanation
Indices: 34673--34999 Score: 435
Period size: 148 Copynumber: 2.2 Consensus size: 148
34663 TTTTATGCTG
* * * *
34673 AAATGCACCGTTATGCATTTAACTTTCATTAGTGGTACCTTTTATGCTCAAATACACCGTTATGC
1 AAATGCACCATTATGCATTTAACTTGCATTAGTGGCACCTTTTATGCTCAAATACACCATTATGC
* * * *
34738 ATTAAATTTTCATTAGCGGTACCTTTATGCCAAAAATACACCATTATGCATTTAATTGCATTAGT
66 ATTAAACTTGCATTAGCGGAACCTTTATGCCAAAAATACACCATTATGAATTTAATTGCATTAGT
*
34803 GACACCTTTATACCAAAA
131 GACACCTATATACCAAAA
* *
34821 AAATGCACCATTATGCATTTAACTTGCATTAGTGGCACC-TTTCTGC-CAAAAATGCACCATTAT
1 AAATGCACCATTATGCATTTAACTTGCATTAGTGGCACCTTTTATGCTC--AAATACACCATTAT
* ** * *
34884 GCATTTAACTTGCATTATTGGAACCTTTCTGCCAAAAATGCACCATTATGAATTTAACTTGCATT
64 GCATTAAACTTGCATTAGCGGAACCTTTATGCCAAAAATACACCATTATGAATTTAA-TTGCATT
* * *
34949 AGTGGCACCTATCT-GCAAAA
128 AGTGACACCTATATACCAAAA
34969 AAATGCACCATTATGCATTTAACTTGCATTA
1 AAATGCACCATTATGCATTTAACTTGCATTA
35000 TAGAGCAGTT
Statistics
Matches: 157, Mismatches: 19, Indels: 6
0.86 0.10 0.03
Matches are distributed among these distances:
146 1 0.01
147 6 0.04
148 132 0.84
149 18 0.11
ACGTcount: A:0.32, C:0.21, G:0.12, T:0.34
Consensus pattern (148 bp):
AAATGCACCATTATGCATTTAACTTGCATTAGTGGCACCTTTTATGCTCAAATACACCATTATGC
ATTAAACTTGCATTAGCGGAACCTTTATGCCAAAAATACACCATTATGAATTTAATTGCATTAGT
GACACCTATATACCAAAA
Found at i:35000 original size:99 final size:98
Alignment explanation
Indices: 34673--34999 Score: 410
Period size: 99 Copynumber: 3.3 Consensus size: 98
34663 TTTTATGCTG
* * * * *
34673 AAATGCACCGTTATGCATTTAACTTTCATTAGTGGTACCTTTTATGCTC--AAATACACCGTTAT
1 AAATGCACCATTATGCATTTAACTTGCATTAGTGGAACC-TTTATGC-CAAAAATGCACCATTAT
* * * * * *
34736 GCATTAAATTTTCATTAGCGGTACCTTTATGCCAA
64 GCATTTAACTTGCATTAGTGGCACCTTTCTGCCAA
* *
34771 AAATACACCATTATGCATTTAA-TTGCATTAGT-GACACCTTTATACCAAAAAAATGCACCATTA
1 AAATGCACCATTATGCATTTAACTTGCATTAGTGGA-ACCTTTATGCC--AAAAATGCACCATTA
34834 TGCATTTAACTTGCATTAGTGGCACCTTTCTGCCAA
63 TGCATTTAACTTGCATTAGTGGCACCTTTCTGCCAA
* * *
34870 AAATGCACCATTATGCATTTAACTTGCATTATTGGAACCTTTCTGCCAAAAATGCACCATTATGA
1 AAATGCACCATTATGCATTTAACTTGCATTAGTGGAACCTTTATGCCAAAAATGCACCATTATGC
* *
34935 ATTTAACTTGCATTAGTGGCACCTATCTGCAAAA
66 ATTTAACTTGCATTAGTGGCACCTTTCTGC-CAA
34969 AAATGCACCATTATGCATTTAACTTGCATTA
1 AAATGCACCATTATGCATTTAACTTGCATTA
35000 TAGAGCAGTT
Statistics
Matches: 201, Mismatches: 20, Indels: 15
0.85 0.08 0.06
Matches are distributed among these distances:
95 1 0.00
96 7 0.03
97 12 0.06
98 66 0.33
99 95 0.47
100 18 0.09
101 2 0.01
ACGTcount: A:0.32, C:0.21, G:0.12, T:0.34
Consensus pattern (98 bp):
AAATGCACCATTATGCATTTAACTTGCATTAGTGGAACCTTTATGCCAAAAATGCACCATTATGC
ATTTAACTTGCATTAGTGGCACCTTTCTGCCAA
Found at i:37894 original size:20 final size:20
Alignment explanation
Indices: 37796--37894 Score: 148
Period size: 20 Copynumber: 5.0 Consensus size: 20
37786 ATCATATTCC
*
37796 CTGGTAATCTTACATTCCCAA
1 CTGGTAATCTTACATT-CCTA
37817 C-GGTAATCTTACATT-CTCA
1 CTGGTAATCTTACATTCCT-A
37836 CTGGTAATCTTACATTCCTA
1 CTGGTAATCTTACATTCCTA
*
37856 CAGGTAATCTTACATTCCTA
1 CTGGTAATCTTACATTCCTA
37876 CTGGTAATCTTACATTCCT
1 CTGGTAATCTTACATTCCT
37895 TGAACCAAAC
Statistics
Matches: 72, Mismatches: 3, Indels: 7
0.88 0.04 0.09
Matches are distributed among these distances:
18 1 0.01
19 2 0.03
20 66 0.92
21 3 0.04
ACGTcount: A:0.26, C:0.26, G:0.10, T:0.37
Consensus pattern (20 bp):
CTGGTAATCTTACATTCCTA
Found at i:38315 original size:11 final size:11
Alignment explanation
Indices: 38286--38319 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
38276 AATATATTTA
*
38286 AAAAGTAAAAT
1 AAAATTAAAAT
38297 ACAAATTAAAAT
1 A-AAATTAAAAT
38309 AAAATTAAAAT
1 AAAATTAAAAT
38320 GAATATAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
11 11 0.52
12 10 0.48
ACGTcount: A:0.71, C:0.03, G:0.03, T:0.24
Consensus pattern (11 bp):
AAAATTAAAAT
Found at i:41571 original size:40 final size:40
Alignment explanation
Indices: 41470--41591 Score: 151
Period size: 40 Copynumber: 3.1 Consensus size: 40
41460 TATCGATTAA
* *
41470 GCACTTTGGTGCATATGGTAGGC-CGACCTTATGTGT-AT
1 GCACTTCGGTGCATATGGTGGGCACGACCTTATGTGTAAT
* * * * * *
41508 TCACTTCAGAGCATATAGAGGGCATGACCTTATGTGTAAT
1 GCACTTCGGTGCATATGGTGGGCACGACCTTATGTGTAAT
41548 GCACTTCGGTGCATATGGTGGGCACGACCTTATGTGTAA-
1 GCACTTCGGTGCATATGGTGGGCACGACCTTATGTGTAAT
41587 GCACT
1 GCACT
41592 ATTGCATTGA
Statistics
Matches: 68, Mismatches: 14, Indels: 3
0.80 0.16 0.04
Matches are distributed among these distances:
38 16 0.24
39 17 0.25
40 35 0.51
ACGTcount: A:0.23, C:0.20, G:0.27, T:0.30
Consensus pattern (40 bp):
GCACTTCGGTGCATATGGTGGGCACGACCTTATGTGTAAT
Found at i:50054 original size:35 final size:36
Alignment explanation
Indices: 50015--50114 Score: 114
Period size: 37 Copynumber: 2.8 Consensus size: 36
50005 GATTTTTAAA
50015 TTCTCTCATCT-CTATT-TTGATTTTAATTATCAAGT
1 TTCTCTC-TCTCCTATTCTTGATTTTAATTATCAAGT
* *
50050 TTCTCTTCTCTCCTCTTCTTGTTTTTAATTATCAAGT
1 TTCTC-TCTCTCCTATTCTTGATTTTAATTATCAAGT
* * *
50087 TTCTCTTCTCTCATCTTCTTGTTTTTAA
1 TTCTC-TCTCTCCTATTCTTGATTTTAA
50115 AGCTTGATCA
Statistics
Matches: 59, Mismatches: 3, Indels: 4
0.89 0.05 0.06
Matches are distributed among these distances:
35 8 0.14
36 6 0.10
37 45 0.76
ACGTcount: A:0.16, C:0.22, G:0.05, T:0.57
Consensus pattern (36 bp):
TTCTCTCTCTCCTATTCTTGATTTTAATTATCAAGT
Found at i:50078 original size:37 final size:37
Alignment explanation
Indices: 50035--50114 Score: 151
Period size: 37 Copynumber: 2.2 Consensus size: 37
50025 TCTATTTTGA
*
50035 TTTTAATTATCAAGTTTCTCTTCTCTCCTCTTCTTGT
1 TTTTAATTATCAAGTTTCTCTTCTCTCATCTTCTTGT
50072 TTTTAATTATCAAGTTTCTCTTCTCTCATCTTCTTGT
1 TTTTAATTATCAAGTTTCTCTTCTCTCATCTTCTTGT
50109 TTTTAA
1 TTTTAA
50115 AGCTTGATCA
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
37 42 1.00
ACGTcount: A:0.16, C:0.21, G:0.05, T:0.57
Consensus pattern (37 bp):
TTTTAATTATCAAGTTTCTCTTCTCTCATCTTCTTGT
Done.