Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000601.1 Hibiscus syriacus cultivar Beakdansim tig00001168_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: 64258
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:5383 original size:19 final size:19
Alignment explanation
Indices: 5359--5398 Score: 71
Period size: 19 Copynumber: 2.1 Consensus size: 19
5349 CAAGATGTAA
5359 AATTTTGAATAACGTCTTG
1 AATTTTGAATAACGTCTTG
*
5378 AATTTTGAATAATGTCTTG
1 AATTTTGAATAACGTCTTG
5397 AA
1 AA
5399 GACAAAGGAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.35, C:0.07, G:0.15, T:0.42
Consensus pattern (19 bp):
AATTTTGAATAACGTCTTG
Found at i:7743 original size:42 final size:41
Alignment explanation
Indices: 7659--7772 Score: 113
Period size: 42 Copynumber: 2.7 Consensus size: 41
7649 TTTCTTACTT
* * * *
7659 AGTAAATCCTTCAGGCCATCAGTAAGTCTTTCGAGCATGATG
1 AGTAAATCCTTCGGGCCATCA-TAAGCCTTTCAAGCAAGATG
* *
7701 AGTAAATCCTTCGGGTCATCTATAAGCCTTTTAAGCAAGATG
1 AGTAAATCCTTCGGGCCATC-ATAAGCCTTTCAAGCAAGATG
* *
7743 A-TAAGTCCTTTGGGCCATCCATAAGACCTT
1 AGTAAATCCTTCGGGCCAT-CATAAG-CCTT
7773 CGGGTAGGAT
Statistics
Matches: 60, Mismatches: 9, Indels: 6
0.80 0.12 0.08
Matches are distributed among these distances:
41 19 0.32
42 40 0.67
43 1 0.02
ACGTcount: A:0.29, C:0.22, G:0.19, T:0.30
Consensus pattern (41 bp):
AGTAAATCCTTCGGGCCATCATAAGCCTTTCAAGCAAGATG
Found at i:8326 original size:134 final size:134
Alignment explanation
Indices: 8097--8650 Score: 743
Period size: 134 Copynumber: 4.1 Consensus size: 134
8087 ACAAATCGAA
* * * * * *
8097 CTCGATTCAATCTTCCCTGAGGAACAGTGGAATGAATCAACATCCCTAGATCTGATTTTTCCT-T
1 CTCGATTCAATCTTCCCTGAGTAATAGTGGAATGAATCAACGTCCCCAGATCTGATTTTCCCTCA
* *
8161 AGTAAGAAGCGGAACAGATCTCTCTCTTTCAATATTTGATATTTCCTGAGTAACAGTGGAACAAG
66 AG-AAGAAGCGGAACAGATCCCTCTCTTTCAAGATTTGATATTTCCTGAGTAACAGTGGAACAAG
8226 TCTGC
130 TCTGC
* * *
8231 CTCGATTCAATCTTCCCTAAGTAATAGTGGAATGAATCAATGTCCCCAGATATGATTTTCCCTCA
1 CTCGATTCAATCTTCCCTGAGTAATAGTGGAATGAATCAACGTCCCCAGATCTGATTTTCCCTCA
* * *
8296 AGAAGAAGCGGAACATATCCCTCTCTTTCAAGATTTGATATTCCCTGAGTAACAGTGGAAAAAGT
66 AGAAGAAGCGGAACAGATCCCTCTCTTTCAAGATTTGATATTTCCTGAGTAACAGTGGAACAAGT
* **
8361 TTAT
131 CTGC
*
8365 CTCGATTCAATCTTCCCTGAGTAATAGTGGAATGAATCAACGTCCCCATATCTGATTTTCCCTCA
1 CTCGATTCAATCTTCCCTGAGTAATAGTGGAATGAATCAACGTCCCCAGATCTGATTTTCCCTCA
* * * * * *
8430 AGAAAAAGCGGAATAGATCCATATCTTTTAAGATTTGATA-TTCCTTGAGTAACAGTTGAACAAG
66 AGAAGAAGCGGAACAGATCCCTCTCTTTCAAGATTTGATATTTCC-TGAGTAACAGTGGAACAAG
*
8494 TCTGT
130 TCTGC
* * * * * *
8499 CTTGATCCAATCTTCCTTGAGTAATAGTGGACTGAATCAACGTCCCCAGATCTAATTTTACCTCA
1 CTCGATTCAATCTTCCCTGAGTAATAGTGGAATGAATCAACGTCCCCAGATCTGATTTTCCCTCA
* * * * * *
8564 AGAAGAAGTGGAACATATCTCTCTCTTTCAAGATTTGATATTTCTTAAGTAACAATGGAACAAGT
66 AGAAGAAGCGGAACAGATCCCTCTCTTTCAAGATTTGATATTTCCTGAGTAACAGTGGAACAAGT
8629 CTGC
131 CTGC
8633 CTCGATTCAATCTTCCCT
1 CTCGATTCAATCTTCCCT
8651 AAAGAACAAT
Statistics
Matches: 362, Mismatches: 55, Indels: 6
0.86 0.13 0.01
Matches are distributed among these distances:
133 3 0.01
134 354 0.98
135 5 0.01
ACGTcount: A:0.31, C:0.21, G:0.16, T:0.32
Consensus pattern (134 bp):
CTCGATTCAATCTTCCCTGAGTAATAGTGGAATGAATCAACGTCCCCAGATCTGATTTTCCCTCA
AGAAGAAGCGGAACAGATCCCTCTCTTTCAAGATTTGATATTTCCTGAGTAACAGTGGAACAAGT
CTGC
Found at i:10583 original size:24 final size:24
Alignment explanation
Indices: 10556--10631 Score: 107
Period size: 24 Copynumber: 3.2 Consensus size: 24
10546 AACTGCCGCT
* *
10556 TAGAATTTGCACCGAAGTGCCACG
1 TAGAATATGCACCGAAGTGCCACA
*
10580 TAGAATATGCACCGAAGTTCCACA
1 TAGAATATGCACCGAAGTGCCACA
* *
10604 TAGAATATGCACCAAAGTGCTACA
1 TAGAATATGCACCGAAGTGCCACA
10628 TAGA
1 TAGA
10632 TTTATCCCGA
Statistics
Matches: 46, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 46 1.00
ACGTcount: A:0.37, C:0.22, G:0.20, T:0.21
Consensus pattern (24 bp):
TAGAATATGCACCGAAGTGCCACA
Found at i:10693 original size:22 final size:23
Alignment explanation
Indices: 10636--10700 Score: 78
Period size: 22 Copynumber: 2.9 Consensus size: 23
10626 CATAGATTTA
*
10636 TCCCGAAGGACCGCGTAGAATTG
1 TCCCGAAGGACCACGTAGAATTG
* * *
10659 TCTCGGAGGACCACATAGAA-TG
1 TCCCGAAGGACCACGTAGAATTG
*
10681 TCCCGAAGAACCACGTAGAA
1 TCCCGAAGGACCACGTAGAA
10701 CCCTCAACTC
Statistics
Matches: 34, Mismatches: 8, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
22 18 0.53
23 16 0.47
ACGTcount: A:0.32, C:0.26, G:0.26, T:0.15
Consensus pattern (23 bp):
TCCCGAAGGACCACGTAGAATTG
Found at i:10839 original size:30 final size:30
Alignment explanation
Indices: 10803--10872 Score: 95
Period size: 30 Copynumber: 2.3 Consensus size: 30
10793 AAGTATCATT
10803 TATTCACATAGAACACATTAACATAAAACA
1 TATTCACATAGAACACATTAACATAAAACA
* * * * *
10833 TTTTCACGTAGAACATATTGACATATAACA
1 TATTCACATAGAACACATTAACATAAAACA
10863 TATTCACATA
1 TATTCACATA
10873 TTAATAAAAC
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.46, C:0.19, G:0.06, T:0.30
Consensus pattern (30 bp):
TATTCACATAGAACACATTAACATAAAACA
Found at i:10873 original size:15 final size:15
Alignment explanation
Indices: 10803--10872 Score: 77
Period size: 15 Copynumber: 4.7 Consensus size: 15
10793 AAGTATCATT
10803 TATTCACATAGAACA
1 TATTCACATAGAACA
* * *
10818 CATTAACATAAAACA
1 TATTCACATAGAACA
* *
10833 TTTTCACGTAGAACA
1 TATTCACATAGAACA
* *
10848 TATTGACATATAACA
1 TATTCACATAGAACA
10863 TATTCACATA
1 TATTCACATA
10873 TTAATAAAAC
Statistics
Matches: 42, Mismatches: 13, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
15 42 1.00
ACGTcount: A:0.46, C:0.19, G:0.06, T:0.30
Consensus pattern (15 bp):
TATTCACATAGAACA
Found at i:18272 original size:22 final size:22
Alignment explanation
Indices: 18242--18283 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
18232 TTATTGATTA
*
18242 AGTAACATTTTAGGTTGGAAGG
1 AGTAACATTTAAGGTTGGAAGG
*
18264 AGTAGCATTTAAGGTTGGAA
1 AGTAACATTTAAGGTTGGAA
18284 CCTAAAATGT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.33, C:0.05, G:0.31, T:0.31
Consensus pattern (22 bp):
AGTAACATTTAAGGTTGGAAGG
Found at i:18440 original size:185 final size:185
Alignment explanation
Indices: 18181--18522 Score: 447
Period size: 185 Copynumber: 1.8 Consensus size: 185
18171 TTTTGATATA
* * * * *
18181 TTTTTTTAATTTGAGAAAGTATGGTAACATTTTAGATTATAACATTTATTCTTATTGATTAAGTA
1 TTTTTTTAATTTGAGAAACTAAGGTAACAGTTTAGATTATAACATTTATTCTTATCGAATAAGTA
* * * *
18246 ACATTTTAGGTTGGAAGGAGTAGCATTTAAGGTTGGAACCTAAAATGTTACATTG-G-ATAATAA
66 ACATTTTAGGTTGAAAGG-GTAACATTTAAGGCT-GAACCTAAAATGCTACATTGTGAATAATAA
* *
18309 ATCATATAGATTGGGTAACATTTTAGGTTTTAACCTAGGCACCATAAGTTTTCAGTT
129 ATAATATAGATTGAGTAACATTTTAGGTTTTAACCTAGGCACCATAAGTTTTCAGTT
* * * *
18366 TTTTTTTCATTTGAGAAACTAAGGTAACAGTTTAGGTTATAAC-TGTTTTTCTTATCGAATACGT
1 TTTTTTTAATTTGAGAAACTAAGGTAACAGTTTAGATTATAACAT-TTATTCTTATCGAATAAGT
* * * *
18430 GACTTTTTAGGTTGAAAGGGTAATATTTTAGGCTGAACCTAAAATGCTACATTGTGAATAATAAA
65 AACATTTTAGGTTGAAAGGGTAACATTTAAGGCTGAACCTAAAATGCTACATTGTGAATAATAAA
* *
18495 TAATGTAGATTGAGTATCATTTTAGGTT
130 TAATATAGATTGAGTAACATTTTAGGTT
18523 GAACCTAAAA
Statistics
Matches: 133, Mismatches: 21, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
183 19 0.14
184 13 0.10
185 101 0.76
ACGTcount: A:0.33, C:0.09, G:0.18, T:0.40
Consensus pattern (185 bp):
TTTTTTTAATTTGAGAAACTAAGGTAACAGTTTAGATTATAACATTTATTCTTATCGAATAAGTA
ACATTTTAGGTTGAAAGGGTAACATTTAAGGCTGAACCTAAAATGCTACATTGTGAATAATAAAT
AATATAGATTGAGTAACATTTTAGGTTTTAACCTAGGCACCATAAGTTTTCAGTT
Found at i:18573 original size:55 final size:57
Alignment explanation
Indices: 18454--18580 Score: 186
Period size: 55 Copynumber: 2.2 Consensus size: 57
18444 AAAGGGTAAT
* *
18454 ATTTTAGGCTGAACCTAAAATGCTACATTGTGAATAATAAATAATGTAGATTGAGTATC
1 ATTTTAGGTTGAACCTAAAATACTACATTGT--ATAATAAATAATGTAGATTGAGTATC
* *
18513 ATTTTAGGTTGAACCTAAAATATTACATTGT-T-ATAAATCATGTAGATTGAGTATC
1 ATTTTAGGTTGAACCTAAAATACTACATTGTATAATAAATAATGTAGATTGAGTATC
18568 ATTTTAGGTTGAA
1 ATTTTAGGTTGAA
18581 AAGCTAAAAA
Statistics
Matches: 64, Mismatches: 4, Indels: 4
0.89 0.06 0.06
Matches are distributed among these distances:
55 35 0.55
56 1 0.02
59 28 0.44
ACGTcount: A:0.37, C:0.09, G:0.17, T:0.38
Consensus pattern (57 bp):
ATTTTAGGTTGAACCTAAAATACTACATTGTATAATAAATAATGTAGATTGAGTATC
Found at i:18791 original size:168 final size:166
Alignment explanation
Indices: 18514--18822 Score: 378
Period size: 168 Copynumber: 1.8 Consensus size: 166
18504 TTGAGTATCA
* *
18514 TTTTAGGTTGAACCTAAAATATTACATTGTTATAAATCATGTAGATTGAGTATCATTTTAGGTTG
1 TTTTAGGTTGAACCTAAAATATTACATTGTTATAAATCATGTAAATTGAGTATCATTTTAAGTTG
* * * *
18579 AAAAGCTAAAAAGTTGCCATGAATTTTGAGTTCTTTTTTTTCATTTGAAAAACCAATGTAACATT
66 AAAACCTAAAAAGTTACCATGAATTTTGAG-TCGTTTTTTTCATTTGAAAAACCAAGGTAACATT
18644 GTAGGTTGTAAACTTTTTTCTAAAAAAATACGTAACT
130 GTAGGTTGTAAACTTTTTTCTAAAAAAATACGTAACT
*
18681 TTTTAGGTTAGAACCTAAAATATTTACGTTGGGTATAATAAATCATGTAAATTG-G-ATACTATT
1 TTTTAGGTT-GAACCTAAAATA-TTACATT--GT-T-ATAAATCATGTAAATTGAGTAT-C-ATT
* * ** *
18744 TTAAGTTG-AAACCTAAAAAGTTATCATGAATTTT-A-T-GTTTTTTTCATTTGAGAAATTAGGG
58 TTAAGTTGAAAACCTAAAAAGTTACCATGAATTTTGAGTCGTTTTTTTCATTTGAAAAACCAAGG
*
18805 TAACATTTTAGGTTGTAA
123 TAACATTGTAGGTTGTAA
18823 TTGTTTTTTA
Statistics
Matches: 121, Mismatches: 13, Indels: 15
0.81 0.09 0.10
Matches are distributed among these distances:
167 9 0.07
168 48 0.40
169 7 0.06
171 5 0.04
172 26 0.21
173 26 0.21
ACGTcount: A:0.35, C:0.09, G:0.15, T:0.41
Consensus pattern (166 bp):
TTTTAGGTTGAACCTAAAATATTACATTGTTATAAATCATGTAAATTGAGTATCATTTTAAGTTG
AAAACCTAAAAAGTTACCATGAATTTTGAGTCGTTTTTTTCATTTGAAAAACCAAGGTAACATTG
TAGGTTGTAAACTTTTTTCTAAAAAAATACGTAACT
Found at i:18999 original size:188 final size:190
Alignment explanation
Indices: 18681--19045 Score: 495
Period size: 187 Copynumber: 1.9 Consensus size: 190
18671 ATACGTAACT
** * **
18681 TTTTAGGTTAGAACCTAAAATATTTACGTTGGGTATAATAAATCATGTAAATTGGATACTATTTT
1 TTTTAGGTTAGAACCTAAAATATTTACGTTGGACATAATAAATCATGTAAATTGAATAAGATTTT
* * * *
18746 AAGTTGAAACCTAAAAAGTTATCATGAATTTTATGTTTTTTTCATTTGAGAAATTAGGGTAACAT
66 AAGTTAAAACCTAAAAAGTTACCATGAATTTTATGTTTTTTTCATTTGAGAAACTAGGATAACAT
* *
18811 TTTAGGTTGTAATTG-TTTT-TTACC-AATTACGTAATTTTTTAGGTTGGAATAGATAAAA
131 TTTAGGTTGTAACTGATTTTCTTACCGAA-TACGTAACTTTTTAGGTTGGAATAGATAAAA
* *
18869 TTTTAGGTTGGAACCTAAAATA-TTACGTTGGACATAATAAATCATGTAGATTGAATAAGATTTT
1 TTTTAGGTTAGAACCTAAAATATTTACGTTGGACATAATAAATCATGTAAATTGAATAAGATTTT
* * ** * *
18933 AGGTTAAAACCTAAAAAGTTACCGTTTATTTTATTTTATTTTTCATTTGAGAAACTATGATAACA
66 AAGTTAAAACCTAAAAAGTTACCATGAATTTTATGTT-TTTTTCATTTGAGAAACTAGGATAACA
* *
18998 TTTTATGTTGTAACTGATTTTCTTACCGAATACTTAACTTTTTAGGTT
130 TTTTAGGTTGTAACTGATTTTCTTACCGAATACGTAACTTTTTAGGTT
19046 AAAACGAGAT
Statistics
Matches: 152, Mismatches: 21, Indels: 6
0.85 0.12 0.03
Matches are distributed among these distances:
187 66 0.43
188 59 0.39
189 4 0.03
190 21 0.14
191 2 0.01
ACGTcount: A:0.34, C:0.08, G:0.15, T:0.43
Consensus pattern (190 bp):
TTTTAGGTTAGAACCTAAAATATTTACGTTGGACATAATAAATCATGTAAATTGAATAAGATTTT
AAGTTAAAACCTAAAAAGTTACCATGAATTTTATGTTTTTTTCATTTGAGAAACTAGGATAACAT
TTTAGGTTGTAACTGATTTTCTTACCGAATACGTAACTTTTTAGGTTGGAATAGATAAAA
Found at i:20552 original size:21 final size:23
Alignment explanation
Indices: 20497--20564 Score: 88
Period size: 23 Copynumber: 3.0 Consensus size: 23
20487 GTACACAAAG
20497 TGCCATAGTACACAAAGTACTCT
1 TGCCATAGTACACAAAGTACTCT
*
20520 TGTCATAGTACACAAAGTACTAC-
1 TGCCATAGTACACAAAGTACT-CT
*
20543 T-CCA-AGTACACGAAGTACTCT
1 TGCCATAGTACACAAAGTACTCT
20564 T
1 T
20565 ACAAAAATAC
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
20 1 0.03
21 15 0.38
22 2 0.05
23 21 0.52
24 1 0.03
ACGTcount: A:0.35, C:0.25, G:0.13, T:0.26
Consensus pattern (23 bp):
TGCCATAGTACACAAAGTACTCT
Found at i:22952 original size:190 final size:191
Alignment explanation
Indices: 22598--23056 Score: 474
Period size: 190 Copynumber: 2.4 Consensus size: 191
22588 AATTTGGGGT
* * *
22598 ATTGCACCATGAGTTTTGAATTTTTTT-A-TTT-GAAAATCGAGGTAATATTTTAGGTTGTAAAT
1 ATTG-ACCATGAG-TTTGAATTTTTTTCATTTTAGAAAATAGA-GTAAAATTTTAGGTTGTAACT
* * *
22660 GTTTTT-TATATCCAAAATACATAACTTTTTTTAGTTTGGAACGATTAATATTTTAGGTTAGAAC
63 GTTTTTCT-TA-CCAAAATACATAAC-TTTTTTAGGTTGAAACGATTAACATTTTAGGTTAGAAC
* * * * *
22724 ATAAAATGTTACGTTTGGTATATAAAAACATGTAGATTG-G-ATACTATTTTAGCTTGAAACCT-
125 ATAAAATGTTACGTTTGGCACATAAAAACATATAGATTGAGTA-AC-ATTTTAGATTAAAACCTA
*
22786 AAAG
188 AAAA
* * *
22790 ATTGACCATGAGTTCTGATTTTTTTTTCATTTTAGAAACTAGAGTAAAATTTTAGGTTGTAACCG
1 ATTGACCATGAGTT-TGA-ATTTTTTTCATTTTAGAAAATAGAGTAAAATTTTAGGTTGTAACTG
* * * *
22855 TTTTTCTTACC-TAATACATAA-TTTTTTAGGTTGAAACGGTTAACATTTTAGGTTGGAATATAA
64 TTTTTCTTACCAAAATACATAACTTTTTTAGGTTGAAACGATTAACATTTTAGGTTAGAACATAA
* *
22918 AATGTTATG-TT-GCACATAATAAATCCTATAGATTGAGTAACATTTTAGATTAAAACCTAAAAA
129 AATGTTACGTTTGGCACATAA-AAA-CATATAGATTGAGTAACATTTTAGATTAAAACCTAAAAA
* * * * * *
22981 ATT-ACCATGAATATTGAGTTTTTTTCATTTGAGAAATTAGGGTAACATTTTAGGTTGTAACTGT
1 ATTGACCATGAGT-TTGAATTTTTTTCATTTTAGAAAATAGAGTAAAATTTTAGGTTGTAACTGT
23045 TTTTCTTACCAA
65 TTTTCTTACCAA
23057 TTACCATGTA
Statistics
Matches: 225, Mismatches: 29, Indels: 28
0.80 0.10 0.10
Matches are distributed among these distances:
188 6 0.03
189 56 0.25
190 81 0.36
191 21 0.09
192 21 0.09
193 3 0.01
194 29 0.13
195 8 0.04
ACGTcount: A:0.34, C:0.10, G:0.15, T:0.42
Consensus pattern (191 bp):
ATTGACCATGAGTTTGAATTTTTTTCATTTTAGAAAATAGAGTAAAATTTTAGGTTGTAACTGTT
TTTCTTACCAAAATACATAACTTTTTTAGGTTGAAACGATTAACATTTTAGGTTAGAACATAAAA
TGTTACGTTTGGCACATAAAAACATATAGATTGAGTAACATTTTAGATTAAAACCTAAAAA
Found at i:27862 original size:43 final size:43
Alignment explanation
Indices: 27814--27896 Score: 148
Period size: 43 Copynumber: 1.9 Consensus size: 43
27804 TACAATTTCC
*
27814 CCATCCACTTTTCAACAATTGTCAACTTGAATTTGGTGCATTT
1 CCATCCACTTTTCAACAATTGTCAACTTGAATTCGGTGCATTT
*
27857 CCATCCACTTTTCAACAATTGTCAGCTTGAATTCGGTGCA
1 CCATCCACTTTTCAACAATTGTCAACTTGAATTCGGTGCA
27897 ATAAATACAC
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
43 38 1.00
ACGTcount: A:0.25, C:0.25, G:0.13, T:0.36
Consensus pattern (43 bp):
CCATCCACTTTTCAACAATTGTCAACTTGAATTCGGTGCATTT
Found at i:28460 original size:10 final size:10
Alignment explanation
Indices: 28442--28472 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
28432 CGTATAACGC
*
28442 TTTTACAAAA
1 TTTTCCAAAA
28452 TTTTCCAAAA
1 TTTTCCAAAA
28462 TTTTCCAAAA
1 TTTTCCAAAA
28472 T
1 T
28473 AGCTCATTGG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.42, C:0.16, G:0.00, T:0.42
Consensus pattern (10 bp):
TTTTCCAAAA
Found at i:31577 original size:9 final size:9
Alignment explanation
Indices: 31565--31615 Score: 52
Period size: 9 Copynumber: 5.7 Consensus size: 9
31555 CGCTTCCTAT
31565 GCTTTTAGC
1 GCTTTTAGC
*
31574 GCTTTTTA-T
1 GC-TTTTAGC
31583 GCTTTTAGC
1 GCTTTTAGC
*
31592 GCTTTTTA-T
1 GC-TTTTAGC
31601 GCTTTTAGC
1 GCTTTTAGC
31610 GCTTTT
1 GCTTTT
31616 CAAGAATTAA
Statistics
Matches: 34, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
8 10 0.29
9 14 0.41
10 10 0.29
ACGTcount: A:0.10, C:0.18, G:0.18, T:0.55
Consensus pattern (9 bp):
GCTTTTAGC
Found at i:31583 original size:18 final size:18
Alignment explanation
Indices: 31562--31615 Score: 108
Period size: 18 Copynumber: 3.0 Consensus size: 18
31552 GCACGCTTCC
31562 TATGCTTTTAGCGCTTTT
1 TATGCTTTTAGCGCTTTT
31580 TATGCTTTTAGCGCTTTT
1 TATGCTTTTAGCGCTTTT
31598 TATGCTTTTAGCGCTTTT
1 TATGCTTTTAGCGCTTTT
31616 CAAGAATTAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 36 1.00
ACGTcount: A:0.11, C:0.17, G:0.17, T:0.56
Consensus pattern (18 bp):
TATGCTTTTAGCGCTTTT
Found at i:32650 original size:142 final size:142
Alignment explanation
Indices: 32394--32677 Score: 559
Period size: 142 Copynumber: 2.0 Consensus size: 142
32384 CAACAGAAAA
32394 ACAACCACGTGAATGAGGAAGAAACCTCAAACAATTCGGCCATTGCTGCATGGCAAAAAGGCTCT
1 ACAACCACGTGAATGAGGAAGAAACCTCAAACAATTCGGCCATTGCTGCATGGCAAAAAGGCTCT
32459 AAAGAATAGGGTTTTTTGCTTTTGCCATCCATATGATGTTATTGCAACACTATGGAGGCTTTCGA
66 AAAGAATAGGGTTTTTTGCTTTTGCCATCCATATGATGTTATTGCAACACTATGGAGGCTTTCGA
32524 TGGGAAGCTTGC
131 TGGGAAGCTTGC
32536 ACAACCACGTGAATGAGGAAGAAACCTCAAACAATTCGGCCATTGCTGCATGGCAAAAAGGCTCT
1 ACAACCACGTGAATGAGGAAGAAACCTCAAACAATTCGGCCATTGCTGCATGGCAAAAAGGCTCT
*
32601 AAAGAATAGGGTTTTTTGCTTTTGCCATCCATATGATGTTATTGCAACACTATGGAGGCTTTTGA
66 AAAGAATAGGGTTTTTTGCTTTTGCCATCCATATGATGTTATTGCAACACTATGGAGGCTTTCGA
32666 TGGGAAGCTTGC
131 TGGGAAGCTTGC
32678 CTTTTCCCAA
Statistics
Matches: 141, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
142 141 1.00
ACGTcount: A:0.30, C:0.19, G:0.23, T:0.27
Consensus pattern (142 bp):
ACAACCACGTGAATGAGGAAGAAACCTCAAACAATTCGGCCATTGCTGCATGGCAAAAAGGCTCT
AAAGAATAGGGTTTTTTGCTTTTGCCATCCATATGATGTTATTGCAACACTATGGAGGCTTTCGA
TGGGAAGCTTGC
Found at i:38024 original size:29 final size:29
Alignment explanation
Indices: 37962--38026 Score: 94
Period size: 29 Copynumber: 2.2 Consensus size: 29
37952 AAATTAATCT
* *
37962 CTAAACTTTTAAATGTTTCAATTTCATTC
1 CTAAACTTTTAAACGTTTCAATTTCATCC
* *
37991 ATAAACTTTTAAACGTTTCAATTTTATCC
1 CTAAACTTTTAAACGTTTCAATTTCATCC
38020 CTAAACT
1 CTAAACT
38027 ATGACTATCA
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.34, C:0.18, G:0.03, T:0.45
Consensus pattern (29 bp):
CTAAACTTTTAAACGTTTCAATTTCATCC
Found at i:38063 original size:60 final size:60
Alignment explanation
Indices: 37992--38148 Score: 176
Period size: 60 Copynumber: 2.6 Consensus size: 60
37982 ATTTCATTCA
* * *
37992 TAAACTTTTAAACGTTTCAATTTTATCCCTAAACTATGA-CTATCATTCTAAATTAGTCCT
1 TAAACTTTTAAACATTTCAATTTCATCCCCAAACTATGACCT-TCATTCTAAATTAGTCCT
* * *
38052 TAAACTTTTAAACATTTTAATTTCATCCCCAAATTATGACCTTCATTCTAAATT-GATCCC
1 TAAACTTTTAAACATTTCAATTTCATCCCCAAACTATGACCTTCATTCTAAATTAG-TCCT
* * * *
38112 TAAACTCTCTAAAAATTCCAATTTC-TTCCCAAACTAT
1 TAAACT-TTTAAACATTTCAATTTCATCCCCAAACTAT
38149 ATGCATATAC
Statistics
Matches: 82, Mismatches: 12, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
59 1 0.01
60 65 0.79
61 16 0.20
ACGTcount: A:0.34, C:0.23, G:0.03, T:0.39
Consensus pattern (60 bp):
TAAACTTTTAAACATTTCAATTTCATCCCCAAACTATGACCTTCATTCTAAATTAGTCCT
Found at i:38697 original size:18 final size:18
Alignment explanation
Indices: 38674--38723 Score: 50
Period size: 19 Copynumber: 2.8 Consensus size: 18
38664 ACCATTATTG
38674 AATTAAATTTTTATAATT
1 AATTAAATTTTTATAATT
* *
38692 AATTAATAGTTTTAAAATT
1 AATTAA-ATTTTTATAATT
*
38711 -A-TATATTTTTATA
1 AATTAAATTTTTATA
38724 TAAATATTTT
Statistics
Matches: 26, Mismatches: 5, Indels: 4
0.74 0.14 0.11
Matches are distributed among these distances:
16 7 0.27
17 2 0.08
18 7 0.27
19 10 0.38
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (18 bp):
AATTAAATTTTTATAATT
Found at i:40866 original size:11 final size:11
Alignment explanation
Indices: 40850--40879 Score: 60
Period size: 11 Copynumber: 2.7 Consensus size: 11
40840 AAGATTAGAT
40850 AAGATAAACAA
1 AAGATAAACAA
40861 AAGATAAACAA
1 AAGATAAACAA
40872 AAGATAAA
1 AAGATAAA
40880 GAAATTGAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.73, C:0.07, G:0.10, T:0.10
Consensus pattern (11 bp):
AAGATAAACAA
Found at i:52141 original size:18 final size:18
Alignment explanation
Indices: 52118--52153 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
52108 CTAAGTCAAG
52118 TCATTGACCCTGACTGAA
1 TCATTGACCCTGACTGAA
* *
52136 TCATTGATCCTGATTGAA
1 TCATTGACCCTGACTGAA
52154 CCGTTGATTT
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:0.28, C:0.22, G:0.17, T:0.33
Consensus pattern (18 bp):
TCATTGACCCTGACTGAA
Found at i:54710 original size:23 final size:23
Alignment explanation
Indices: 54677--54736 Score: 75
Period size: 23 Copynumber: 2.6 Consensus size: 23
54667 AATCTTATAT
* * *
54677 GGCACTACGGTGTAATTCTACGC
1 GGCACTTCGGTGCAATTCTACAC
* *
54700 GGCACTTCGGTGCAATTCTATAT
1 GGCACTTCGGTGCAATTCTACAC
54723 GGCACTTCGGTGCA
1 GGCACTTCGGTGCA
54737 TTTATACGAG
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.20, C:0.25, G:0.27, T:0.28
Consensus pattern (23 bp):
GGCACTTCGGTGCAATTCTACAC
Found at i:60799 original size:21 final size:21
Alignment explanation
Indices: 60748--60815 Score: 115
Period size: 21 Copynumber: 3.4 Consensus size: 21
60738 CTATGTGCAT
60748 CGATGCACATTCAATGTATAC
1 CGATGCACATTCAATGTATAC
60769 CGA-G--CATTCAATGTATAC
1 CGATGCACATTCAATGTATAC
60787 CGATGCACATTCAATGTATAC
1 CGATGCACATTCAATGTATAC
60808 CGATGCAC
1 CGATGCAC
60816 CAAGGAATCC
Statistics
Matches: 44, Mismatches: 0, Indels: 6
0.88 0.00 0.12
Matches are distributed among these distances:
18 17 0.39
19 1 0.02
20 1 0.02
21 25 0.57
ACGTcount: A:0.32, C:0.25, G:0.16, T:0.26
Consensus pattern (21 bp):
CGATGCACATTCAATGTATAC
Found at i:61033 original size:19 final size:20
Alignment explanation
Indices: 61002--61046 Score: 83
Period size: 19 Copynumber: 2.3 Consensus size: 20
60992 ACCAAGGGAA
61002 TGCATCAATACATGGTGTAG
1 TGCATCAATACATGGTGTAG
61022 TGCATC-ATACATGGTGTAG
1 TGCATCAATACATGGTGTAG
61041 TGCATC
1 TGCATC
61047 GATGCATACC
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
19 19 0.76
20 6 0.24
ACGTcount: A:0.27, C:0.18, G:0.24, T:0.31
Consensus pattern (20 bp):
TGCATCAATACATGGTGTAG
Found at i:61612 original size:23 final size:23
Alignment explanation
Indices: 61586--61645 Score: 84
Period size: 23 Copynumber: 2.6 Consensus size: 23
61576 AATCTTATAT
*
61586 GGCACTACGATGCAATTCTATGC
1 GGCACTTCGATGCAATTCTATGC
* * *
61609 GGCACTTTGGTGCAATTCTATGT
1 GGCACTTCGATGCAATTCTATGC
61632 GGCACTTCGATGCA
1 GGCACTTCGATGCA
61646 TTTATACGAG
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.22, C:0.23, G:0.25, T:0.30
Consensus pattern (23 bp):
GGCACTTCGATGCAATTCTATGC
Done.