Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007501.1 Hibiscus syriacus cultivar Beakdansim tig00020796_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: 78722
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.32
Found at i:1957 original size:19 final size:19
Alignment explanation
Indices: 1933--1987 Score: 54
Period size: 19 Copynumber: 3.3 Consensus size: 19
1923 TAGTGTTCCA
1933 TGAGCTGCCATGTTCCTTG
1 TGAGCTGCCATGTTCCTTG
1952 TGA---G-C-TGTT--T-G
1 TGAGCTGCCATGTTCCTTG
1963 TGAGCTGCCATGTTCCTTG
1 TGAGCTGCCATGTTCCTTG
1982 TGAGCT
1 TGAGCT
1988 ATTTGTGAGC
Statistics
Matches: 28, Mismatches: 0, Indels: 16
0.64 0.00 0.36
Matches are distributed among these distances:
11 4 0.14
12 1 0.04
14 5 0.18
15 2 0.07
16 5 0.18
18 1 0.04
19 10 0.36
ACGTcount: A:0.11, C:0.22, G:0.29, T:0.38
Consensus pattern (19 bp):
TGAGCTGCCATGTTCCTTG
Found at i:1968 original size:30 final size:30
Alignment explanation
Indices: 1933--2000 Score: 127
Period size: 30 Copynumber: 2.3 Consensus size: 30
1923 TAGTGTTCCA
*
1933 TGAGCTGCCATGTTCCTTGTGAGCTGTTTG
1 TGAGCTGCCATGTTCCTTGTGAGCTATTTG
1963 TGAGCTGCCATGTTCCTTGTGAGCTATTTG
1 TGAGCTGCCATGTTCCTTGTGAGCTATTTG
1993 TGAGCTGC
1 TGAGCTGC
2001 ATTTAATGTC
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 37 1.00
ACGTcount: A:0.12, C:0.21, G:0.29, T:0.38
Consensus pattern (30 bp):
TGAGCTGCCATGTTCCTTGTGAGCTATTTG
Found at i:4634 original size:14 final size:15
Alignment explanation
Indices: 4605--4637 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
4595 CAACCATCTC
4605 TTTCAATACTTTCTA
1 TTTCAATACTTTCTA
*
4620 TTTCATTAC-TTCTA
1 TTTCAATACTTTCTA
4634 TTTC
1 TTTC
4638 TTAATCCATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 9 0.53
15 8 0.47
ACGTcount: A:0.21, C:0.21, G:0.00, T:0.58
Consensus pattern (15 bp):
TTTCAATACTTTCTA
Found at i:19617 original size:22 final size:23
Alignment explanation
Indices: 19592--19634 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
19582 CAATTCCTTT
*
19592 ATCTT-TTCTTTATCTTGTTTTA
1 ATCTTATTCTTTATATTGTTTTA
*
19614 ATCTTATTTTTTATATTGTTT
1 ATCTTATTCTTTATATTGTTT
19635 CCAGTACTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 5 0.28
23 13 0.72
ACGTcount: A:0.16, C:0.09, G:0.05, T:0.70
Consensus pattern (23 bp):
ATCTTATTCTTTATATTGTTTTA
Found at i:30989 original size:22 final size:23
Alignment explanation
Indices: 30964--31006 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
30954 CAATTCCTTT
*
30964 ATCTT-TTCTTTATCTTGTTTTA
1 ATCTTATTCTTTATATTGTTTTA
*
30986 ATCTTATTTTTTATATTGTTT
1 ATCTTATTCTTTATATTGTTT
31007 CCAGTACTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 5 0.28
23 13 0.72
ACGTcount: A:0.16, C:0.09, G:0.05, T:0.70
Consensus pattern (23 bp):
ATCTTATTCTTTATATTGTTTTA
Found at i:32114 original size:22 final size:21
Alignment explanation
Indices: 32075--32115 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
32065 GTAATGAAAT
*
32075 AAGAAAAAAATTGAAAGAACA
1 AAGAAAAAAATAGAAAGAACA
*
32096 AAGAAATAAAATAGTAAGAA
1 AAGAAA-AAAATAGAAAGAA
32116 AATGAAGATA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 6 0.35
22 11 0.65
ACGTcount: A:0.71, C:0.02, G:0.15, T:0.12
Consensus pattern (21 bp):
AAGAAAAAAATAGAAAGAACA
Found at i:33611 original size:18 final size:18
Alignment explanation
Indices: 33543--33612 Score: 60
Period size: 18 Copynumber: 4.0 Consensus size: 18
33533 GCTTGCTTTC
*
33543 TCTTTTTCTTT-TCTTT-
1 TCTTTTTCTTTCTTTTTG
33559 TC-TTTTC-TTCTTTTCTG
1 TCTTTTTCTTTCTTTT-TG
*
33576 ATTTTTTTCTCTTC-TTTTG
1 -TCTTTTTCT-TTCTTTTTG
33595 TCTTTTTCTTTCTTTTTG
1 TCTTTTTCTTTCTTTTTG
33613 CACTCCAATT
Statistics
Matches: 43, Mismatches: 3, Indels: 14
0.72 0.05 0.23
Matches are distributed among these distances:
14 2 0.05
15 8 0.19
16 3 0.07
17 3 0.07
18 14 0.33
19 7 0.16
20 3 0.07
21 3 0.07
ACGTcount: A:0.01, C:0.19, G:0.04, T:0.76
Consensus pattern (18 bp):
TCTTTTTCTTTCTTTTTG
Found at i:37573 original size:21 final size:21
Alignment explanation
Indices: 37534--37574 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
37524 TAGGAGTCTT
*
37534 TTCTTTCTCTTTTTGTTTTTC
1 TTCTTTCTCTTTTTCTTTTTC
37555 TTCTTTCT-TTTTCTCTTTTT
1 TTCTTTCTCTTTT-TCTTTTT
37575 GTTGCTTTTG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.00, C:0.20, G:0.02, T:0.78
Consensus pattern (21 bp):
TTCTTTCTCTTTTTCTTTTTC
Found at i:38003 original size:35 final size:35
Alignment explanation
Indices: 37958--38033 Score: 134
Period size: 35 Copynumber: 2.2 Consensus size: 35
37948 TAAGGTAATG
*
37958 GTGATGATATAGGTGTGAAATGGTGATAGAAGATA
1 GTGATGATATAGGCGTGAAATGGTGATAGAAGATA
*
37993 GTGATGATATAGGCGTGAAATGGTGATAGAAGATG
1 GTGATGATATAGGCGTGAAATGGTGATAGAAGATA
38028 GTGATG
1 GTGATG
38034 GAAGATGGTG
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
35 39 1.00
ACGTcount: A:0.34, C:0.01, G:0.37, T:0.28
Consensus pattern (35 bp):
GTGATGATATAGGCGTGAAATGGTGATAGAAGATA
Found at i:38046 original size:13 final size:13
Alignment explanation
Indices: 38012--38083 Score: 67
Period size: 13 Copynumber: 5.7 Consensus size: 13
38002 TAGGCGTGAA
*
38012 ATGGTGATAGAAG
1 ATGGTGATGGAAG
38025 ATGGTGATGGAAG
1 ATGGTGATGGAAG
** *
38038 ATGGTGATGTTAT
1 ATGGTGATGGAAG
* * *
38051 A-GGCGGT-GAAA
1 ATGGTGATGGAAG
38062 ATGGTGATGGAAG
1 ATGGTGATGGAAG
38075 ATGGTGATG
1 ATGGTGATG
38084 AACAGATAGT
Statistics
Matches: 45, Mismatches: 12, Indels: 4
0.74 0.20 0.07
Matches are distributed among these distances:
11 2 0.04
12 8 0.18
13 35 0.78
ACGTcount: A:0.31, C:0.01, G:0.42, T:0.26
Consensus pattern (13 bp):
ATGGTGATGGAAG
Found at i:38052 original size:48 final size:50
Alignment explanation
Indices: 37977--38093 Score: 166
Period size: 48 Copynumber: 2.4 Consensus size: 50
37967 TAGGTGTGAA
*
37977 ATGGTGATAGAAGATAGTGATGATATAGGC-GTG-AAATGGTGATAGAAG
1 ATGGTGATGGAAGATAGTGATGATATAGGCGGTGAAAATGGTGATAGAAG
* * *
38025 ATGGTGATGGAAGATGGTGATGTTATAGGCGGTGAAAATGGTGATGGAAG
1 ATGGTGATGGAAGATAGTGATGATATAGGCGGTGAAAATGGTGATAGAAG
*
38075 ATGGTGATGAACAGATAGT
1 ATGGTGATGGA-AGATAGT
38094 ATTTTATAAA
Statistics
Matches: 60, Mismatches: 6, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
48 27 0.45
49 3 0.05
50 24 0.40
51 6 0.10
ACGTcount: A:0.34, C:0.03, G:0.38, T:0.26
Consensus pattern (50 bp):
ATGGTGATGGAAGATAGTGATGATATAGGCGGTGAAAATGGTGATAGAAG
Found at i:38101 original size:50 final size:48
Alignment explanation
Indices: 37977--38101 Score: 155
Period size: 50 Copynumber: 2.6 Consensus size: 48
37967 TAGGTGTGAA
*
37977 ATGGTGAT-AGAAGATAGTGATGATATAGGCGTGAAATGGTGATAGAAG
1 ATGGTGATGA-AAGATAGTGATGTTATAGGCGTGAAATGGTGATAGAAG
* * *
38025 ATGGTGATGGAAGATGGTGATGTTATAGGCGGTGAAAATGGTGATGGAAG
1 ATGGTGATGAAAGATAGTGATGTTATAGGC-GTG-AAATGGTGATAGAAG
*
38075 ATGGTGATGAACAGATAGT-ATTTTATA
1 ATGGTGATGAA-AGATAGTGATGTTATA
38102 AAAATAAGAA
Statistics
Matches: 66, Mismatches: 7, Indels: 6
0.84 0.09 0.08
Matches are distributed among these distances:
48 26 0.39
49 3 0.05
50 31 0.47
51 6 0.09
ACGTcount: A:0.34, C:0.02, G:0.35, T:0.28
Consensus pattern (48 bp):
ATGGTGATGAAAGATAGTGATGTTATAGGCGTGAAATGGTGATAGAAG
Found at i:41461 original size:149 final size:147
Alignment explanation
Indices: 41183--42321 Score: 1310
Period size: 149 Copynumber: 7.9 Consensus size: 147
41173 CCTAAATCAT
*
41183 TTTATTTCACCCGGCCTACTCCACACGTTA-AGGCGCTCGGCGTAAGATCAGGTCATCCTGCCTA
1 TTTATTTCACCCGGCCTACTCCACACGTTAGA-GCGCTCGGCGTAAGACCAGGTCATCCTGCCTA
* *
41247 CTCCCCTCTGGAAGCGCTCGGCATGAACTCTGTCTACCCTGCCTAC-CCCACACGTTGAGGCGCT
65 CTCCCCTCTGGAAGCGCTCGGCATGAACTCTGTCT-CCCTGCCTACTCTCA-ACGTTGAAGCGCT
* * * *
41311 CGACCTGATATTAAAGCGCA
128 CGGCGTGATATTAAGGCACA
* *
41331 TTATATTTCACCCGACCTACTCCACACGTTAGGGCGCTCGGCGTAAGACCAGGTCATCCTGCCTA
1 TT-TATTTCACCCGGCCTACTCCACACGTTAGAGCGCTCGGCGTAAGACCAGGTCATCCTGCCTA
* * * * *
41396 CTCCCCTCTAGAAGCGCTAGGCATGAACTCTGTCTACCCTGCTTACCCT-ACACGTTG-AGATGC
65 CTCCCCTCTGGAAGCGCTCGGCATGAACTCTGTCT-CCCTGCCTACTCTCA-ACGTTGAAG-CGC
41459 TCGGCGTGA-ATCT--GG----
127 TCGGCGTGATAT-TAAGGCACA
* * * * *
41474 --GA---CACCCTGCCTACTCCATACGTTAGAGCGCTCGACGTAAGATCAGGTCATCCTGCCTAC
1 TTTATTTCACCCGGCCTACTCCACACGTTAGAGCGCTCGGCGTAAGACCAGGTCATCCTGCCTAC
* *
41534 TCCCCTTTGGAAGCGCTCGGCATGCACTCTGTCTCCTCTGCCTACTCTCAACGTTGAAGCGCTCG
66 TCCCCTCTGGAAGCGCTCGGCATGAACTCTGTCTCC-CTGCCTACTCTCAACGTTGAAGCGCTCG
*
41599 GCGTGACATTAAGGCACA
130 GCGTGATATTAAGGCACA
41617 TCTTATTTCACCCGGCCTACTCCACACGTTAGAGCGCTCGGCGTAAGACCAGGTCATCCTGCCTA
1 T-TTATTTCACCCGGCCTACTCCACACGTTAGAGCGCTCGGCGTAAGACCAGGTCATCCTGCCTA
* * *
41682 CTTCCCTCTGGAAGCGCTCGGCATGTACTCTGTCTCCTCTGCCTACTCTAAACGTTGAAGCGCTC
65 CTCCCCTCTGGAAGCGCTCGGCATGAACTCTGTCTCC-CTGCCTACTCTCAACGTTGAAGCGCTC
*
41747 GGCGTGACATTAAGGCACA
129 GGCGTGATATTAAGGCACA
*
41766 TCTTGTTTCACCCGGCCTACTCCACACGTTAGAGCGCTCGGCGTAAGACCAGGTCATCCTGCCTA
1 T-TTATTTCACCCGGCCTACTCCACACGTTAGAGCGCTCGGCGTAAGACCAGGTCATCCTGCCTA
* * *
41831 CTCCCCTCTGGAAGCGCTCGGCATGTACTCTGTCCCCCCTGCCTACTCTCAACGTTGAAGTGCTC
65 CTCCCCTCTGGAAGCGCTCGGCATGAACTCTGT-CTCCCTGCCTACTCTCAACGTTGAAGCGCTC
41896 GGCGTGATATTAAGGCACA
129 GGCGTGATATTAAGGCACA
*
41915 TCTTGTTTCACCCGGCCTACTCCACACGTTAGAGCGCTCGGCGTAAGACCAGGTCATCCTGCCTA
1 T-TTATTTCACCCGGCCTACTCCACACGTTAGAGCGCTCGGCGTAAGACCAGGTCATCCTGCCTA
* * *
41980 CTCCCCTCTGGAAGCGCTCGGCATGTACTCTGTCCCCCCTGCCTACTCTCAACGTTGAAGTGCTC
65 CTCCCCTCTGGAAGCGCTCGGCATGAACTCTGT-CTCCCTGCCTACTCTCAACGTTGAAGCGCTC
42045 GGCGTGATATT-------A
129 GGCGTGATATTAAGGCACA
* * ** *
42057 --TA--ACACCCTGCCTACTCCACACGTTAGAGCGC-CTGGCGTAAGATAAAGTCATCCTGCCTA
1 TTTATTTCACCCGGCCTACTCCACACGTTAGAGCGCTC-GGCGTAAGACCAGGTCATCCTGCCTA
* * * * * * *
42117 CTCCCCACTGGAAGCGCTCGGCATGAACTCTATCCCCCTTCCAACTCTTAACGGTGAAGCGCTCG
65 CTCCCCTCTGGAAGCGCTCGGCATGAACTCTGTCTCCCTGCCTACTCTCAACGTTGAAGCGCTCG
* *
42182 GCGTGAAAAT-AGG---A
130 GCGTGATATTAAGGCACA
* * * * * * * *
42196 ---A--T-ACCCTGCCTACCCCATACATTAGAGCGCCCGACGTAAGATCAGGTCATCCGGCCTAC
1 TTTATTTCACCCGGCCTACTCCACACGTTAGAGCGCTCGGCGTAAGACCAGGTCATCCTGCCTAC
* * * * * *
42255 TCCCCACTGGAAGCGCTCGGCATGAACTCTGTCCCCCTTCCAACTCTTAATGTTGAAGCGCTCGG
66 TCCCCTCTGGAAGCGCTCGGCATGAACTCTGTCTCCCTGCCTACTCTCAACGTTGAAGCGCTCGG
42320 CG
131 CG
42322 AAATTCCTTA
Statistics
Matches: 896, Mismatches: 68, Indels: 65
0.87 0.07 0.06
Matches are distributed among these distances:
136 38 0.04
137 302 0.34
138 7 0.01
139 4 0.00
140 1 0.00
142 1 0.00
146 1 0.00
147 1 0.00
148 5 0.01
149 532 0.59
150 4 0.00
ACGTcount: A:0.20, C:0.34, G:0.21, T:0.24
Consensus pattern (147 bp):
TTTATTTCACCCGGCCTACTCCACACGTTAGAGCGCTCGGCGTAAGACCAGGTCATCCTGCCTAC
TCCCCTCTGGAAGCGCTCGGCATGAACTCTGTCTCCCTGCCTACTCTCAACGTTGAAGCGCTCGG
CGTGATATTAAGGCACA
Found at i:42072 original size:435 final size:423
Alignment explanation
Indices: 41190--42321 Score: 1319
Period size: 435 Copynumber: 2.6 Consensus size: 423
41180 CATTTTATTT
41190 CACCCGGCCTACTCCACACGTTA-AGGCGCTCGGCGTAAGATCAGGTCATCCTGCCTACTCCCCT
1 CACCCGGCCTACTCCACACGTTAGA-GCGCTCGGCGTAAGATCAGGTCATCCTGCCTACTCCCCT
* * * * * *
41254 CTGGAAGCGCTCGGCATGAACTCTGTCTACCCTGCCTACCCCACACGTTGAGGCGCTCGACCTGA
65 CTGGAAGCGCTCGGCATGAACTCTGTCT-CCCTGCCTACTCTAAACGTTGAAGCGCTCGGCGTGA
* * * * *
41319 TATTAAAGCGCATTATATTTCACCCGACCTACTCCACACGTTAGGGCGCTCGGCGTAAGACCAGG
129 AATTAAGGCACATT-T-TTTCACCCGGCCTACTCCACACGTTAGAGCGCTCGGCGTAAGACCAGG
* * ** * *
41384 TCATCCTGCCTACTCCCCTCTAGAAGCGCTAGGCATGAACTCTGTCTACCCTGCTTACCCTACAC
192 TCATCCTGCCTACTCCCCTCTGGAAGCGCTCGGCATGAACTCTGTCCCCCCTGCCTACTCTA-AC
* *
41449 GTTG-AGATGCTCGGCGTGAATCTGGGACACCCTGCCTACTCCATACGTTAGAGCGCTCGACGTA
256 GTTGAAG-TGCTCGGCGTGAATCTGGGACACCCGGCCTACTCCACACGTTAGAGCGCTCGACGTA
* * * *
41513 AGATCAGGTCATCCTGCCTACTCCCCTTTGGAAGCGCTCGGCATGCACTCTGTCTCCTCTGCCTA
320 AGACCAGGTCATCCTGCCTACTCCCCTCTGGAAGCGCTCGGCATGCACTCTGTCCCCCCTGCCTA
**
41578 CTCTCAACGTTGAAGCGCTCGGCGTGACATTAAGGCACATCTTATTT
385 CTCTCAACGTTGAAGCGCTCGGCGTGA-ATT-----A-A-CTTATAA
* *
41625 CACCCGGCCTACTCCACACGTTAGAGCGCTCGGCGTAAGACCAGGTCATCCTGCCTACTTCCCTC
1 CACCCGGCCTACTCCACACGTTAGAGCGCTCGGCGTAAGATCAGGTCATCCTGCCTACTCCCCTC
* *
41690 TGGAAGCGCTCGGCATGTACTCTGTCTCCTCTGCCTACTCTAAACGTTGAAGCGCTCGGCGTGAC
66 TGGAAGCGCTCGGCATGAACTCTGTCTCC-CTGCCTACTCTAAACGTTGAAGCGCTCGGCGTGAA
41755 ATTAAGGCACATCTTGTTTCACCCGGCCTACTCCACACGTTAGAGCGCTCGGCGTAAGACCAGGT
130 ATTAAGGCACAT-TT-TTTCACCCGGCCTACTCCACACGTTAGAGCGCTCGGCGTAAGACCAGGT
*
41820 CATCCTGCCTACTCCCCTCTGGAAGCGCTCGGCATGTACTCTGTCCCCCCTGCCTACTCTCAACG
193 CATCCTGCCTACTCCCCTCTGGAAGCGCTCGGCATGAACTCTGTCCCCCCTGCCTACTCT-AACG
*
41885 TTGAAGTGCTCGGCGTGATAT-TAAGGCACATCTTGTTTCACCCGGCCTACTCCACACGTTAGAG
257 TTGAAGTGCTCGGCGTGA-ATCT--GG--------G--ACACCCGGCCTACTCCACACGTTAGAG
* *
41949 CGCTCGGCGTAAGACCAGGTCATCCTGCCTACTCCCCTCTGGAAGCGCTCGGCATGTACTCTGTC
309 CGCTCGACGTAAGACCAGGTCATCCTGCCTACTCCCCTCTGGAAGCGCTCGGCATGCACTCTGTC
*
42014 CCCCCTGCCTACTCTCAACGTTGAAGTGCTCGGCGTG-A-T-A-TTATAA
374 CCCCCTGCCTACTCTCAACGTTGAAGCGCTCGGCGTGAATTAACTTATAA
* * * *
42060 CACCCTGCCTACTCCACACGTTAGAGCGC-CTGGCGTAAGATAAAGTCATCCTGCCTACTCCCCA
1 CACCCGGCCTACTCCACACGTTAGAGCGCTC-GGCGTAAGATCAGGTCATCCTGCCTACTCCCCT
* * * * * *
42124 CTGGAAGCGCTCGGCATGAACTCTATCCCCCTTCCAACTCTTAACGGTGAAGCGCTCGGCGTGAA
65 CTGGAAGCGCTCGGCATGAACTCTGTCTCCCTGCCTACTCTAAACGTTGAAGCGCTCGGCGTGAA
* * * * * * * *
42189 AAT-AGG-A-A-----T-ACCCTGCCTACCCCATACATTAGAGCGCCCGACGTAAGATCAGGTCA
130 ATTAAGGCACATTTTTTCACCCGGCCTACTCCACACGTTAGAGCGCTCGGCGTAAGACCAGGTCA
* * * * *
42245 TCCGGCCTACTCCCCACTGGAAGCGCTCGGCATGAACTCTGT-CCCCCTTCCAACTCTTAATGTT
195 TCCTGCCTACTCCCCTCTGGAAGCGCTCGGCATGAACTCTGTCCCCCCTGCCTACTC-TAACGTT
*
42309 GAAGCGCTCGGCG
259 GAAGTGCTCGGCG
42322 AAATTCCTTA
Statistics
Matches: 614, Mismatches: 63, Indels: 53
0.84 0.09 0.07
Matches are distributed among these distances:
422 29 0.05
423 80 0.13
424 1 0.00
431 1 0.00
432 1 0.00
433 3 0.00
434 35 0.06
435 332 0.54
436 7 0.01
437 3 0.00
444 1 0.00
445 2 0.00
447 119 0.19
ACGTcount: A:0.20, C:0.35, G:0.22, T:0.24
Consensus pattern (423 bp):
CACCCGGCCTACTCCACACGTTAGAGCGCTCGGCGTAAGATCAGGTCATCCTGCCTACTCCCCTC
TGGAAGCGCTCGGCATGAACTCTGTCTCCCTGCCTACTCTAAACGTTGAAGCGCTCGGCGTGAAA
TTAAGGCACATTTTTTCACCCGGCCTACTCCACACGTTAGAGCGCTCGGCGTAAGACCAGGTCAT
CCTGCCTACTCCCCTCTGGAAGCGCTCGGCATGAACTCTGTCCCCCCTGCCTACTCTAACGTTGA
AGTGCTCGGCGTGAATCTGGGACACCCGGCCTACTCCACACGTTAGAGCGCTCGACGTAAGACCA
GGTCATCCTGCCTACTCCCCTCTGGAAGCGCTCGGCATGCACTCTGTCCCCCCTGCCTACTCTCA
ACGTTGAAGCGCTCGGCGTGAATTAACTTATAA
Found at i:50731 original size:21 final size:20
Alignment explanation
Indices: 50707--50745 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
50697 ATGTTTGTTT
50707 ATGGTAATGGAGCTAAGTATG
1 ATGGTAAT-GAGCTAAGTATG
*
50728 ATGGTCATGAGCTAAGTA
1 ATGGTAATGAGCTAAGTA
50746 CATCATCTCC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.33, C:0.08, G:0.31, T:0.28
Consensus pattern (20 bp):
ATGGTAATGAGCTAAGTATG
Found at i:51992 original size:13 final size:13
Alignment explanation
Indices: 51970--51999 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
51960 ACTAAACACC
51970 TTTC-ACATACCT
1 TTTCAACATACCT
51982 TTTCAACATACCT
1 TTTCAACATACCT
51995 TTTCA
1 TTTCA
52000 TCTTTGGCCA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 4 0.24
13 13 0.76
ACGTcount: A:0.27, C:0.30, G:0.00, T:0.43
Consensus pattern (13 bp):
TTTCAACATACCT
Found at i:65459 original size:23 final size:25
Alignment explanation
Indices: 65423--65478 Score: 80
Period size: 23 Copynumber: 2.3 Consensus size: 25
65413 AAAATCCAGC
65423 AAAGAAAATCAAAGCACTC-AAAAG
1 AAAGAAAATCAAAGCACTCAAAAAG
* *
65447 -AAGAAATTGAAAGCACTCAAAAAG
1 AAAGAAAATCAAAGCACTCAAAAAG
65471 AAAGAAAA
1 AAAGAAAA
65479 AGAAAGAAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
23 16 0.59
24 5 0.19
25 6 0.22
ACGTcount: A:0.64, C:0.12, G:0.14, T:0.09
Consensus pattern (25 bp):
AAAGAAAATCAAAGCACTCAAAAAG
Found at i:65480 original size:10 final size:10
Alignment explanation
Indices: 65465--65505 Score: 73
Period size: 10 Copynumber: 4.0 Consensus size: 10
65455 GAAAGCACTC
65465 AAAAAGAAAG
1 AAAAAGAAAG
65475 AAAAAGAAAG
1 AAAAAGAAAG
65485 AAAAAGAAAAG
1 AAAAAG-AAAG
65496 AAAAAGAAAG
1 AAAAAGAAAG
65506 TTGAAGCACT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
10 20 0.67
11 10 0.33
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (10 bp):
AAAAAGAAAG
Found at i:65489 original size:21 final size:21
Alignment explanation
Indices: 65465--65505 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
65455 GAAAGCACTC
65465 AAAAAG-AAAGAAAAAGAAAG
1 AAAAAGAAAAGAAAAAGAAAG
65485 AAAAAGAAAAGAAAAAGAAAG
1 AAAAAGAAAAGAAAAAGAAAG
65506 TTGAAGCACT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 6 0.30
21 14 0.70
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (21 bp):
AAAAAGAAAAGAAAAAGAAAG
Found at i:66965 original size:36 final size:36
Alignment explanation
Indices: 66918--67022 Score: 158
Period size: 36 Copynumber: 2.9 Consensus size: 36
66908 GATACAATCT
66918 GTCCATCACCATTATCATGCCTATATCATCACCATA
1 GTCCATCACCATTATCATGCCTATATCATCACCATA
*
66954 GTCCATCACCATCATCATGCCTATATCATCACCATA
1 GTCCATCACCATTATCATGCCTATATCATCACCATA
* * * *
66990 TTCCACCACCA-TATCACGCCTATATTATCACCA
1 GTCCATCACCATTATCATGCCTATATCATCACCA
67023 ACTTATAAAT
Statistics
Matches: 63, Mismatches: 6, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
35 19 0.30
36 44 0.70
ACGTcount: A:0.30, C:0.36, G:0.05, T:0.29
Consensus pattern (36 bp):
GTCCATCACCATTATCATGCCTATATCATCACCATA
Found at i:72583 original size:23 final size:24
Alignment explanation
Indices: 72538--72583 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 24
72528 AGAAAATAAG
**
72538 CACTCAAAAAGAAGAAATTGAAAA
1 CACTCAAAAAGAAGAAAAAGAAAA
72562 CACTC-AAAAGAAGAAAAAGAAA
1 CACTCAAAAAGAAGAAAAAGAAA
72584 GAAAAGTTGG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 15 0.75
24 5 0.25
ACGTcount: A:0.65, C:0.13, G:0.13, T:0.09
Consensus pattern (24 bp):
CACTCAAAAAGAAGAAAAAGAAAA
Found at i:75332 original size:11 final size:13
Alignment explanation
Indices: 75300--75329 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
75290 TGGCCAAAGA
75300 TGAAAAGGTATGT
1 TGAAAAGGTATGT
75313 TGAAAAGGTATG-
1 TGAAAAGGTATGT
75325 TGAAA
1 TGAAA
75330 GGTGTTTAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 5 0.29
13 12 0.71
ACGTcount: A:0.43, C:0.00, G:0.30, T:0.27
Consensus pattern (13 bp):
TGAAAAGGTATGT
Done.