Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006137.1 Hibiscus syriacus cultivar Beakdansim tig00014556_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: 61609
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.34
Found at i:709 original size:34 final size:35
Alignment explanation
Indices: 656--725 Score: 133
Period size: 34 Copynumber: 2.0 Consensus size: 35
646 TCAGACTCAT
656 TGCCAAAACTTTATCTTCCATCTTCTCAAAAGATG
1 TGCCAAAACTTTATCTTCCATCTTCTCAAAAGATG
691 TGCCAAAAC-TTATCTTCCATCTTCTCAAAAGATG
1 TGCCAAAACTTTATCTTCCATCTTCTCAAAAGATG
725 T
1 T
726 TAAAACACTA
Statistics
Matches: 35, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
34 26 0.74
35 9 0.26
ACGTcount: A:0.31, C:0.26, G:0.09, T:0.34
Consensus pattern (35 bp):
TGCCAAAACTTTATCTTCCATCTTCTCAAAAGATG
Found at i:1200 original size:14 final size:14
Alignment explanation
Indices: 1169--1220 Score: 65
Period size: 14 Copynumber: 3.9 Consensus size: 14
1159 GGCCCTGCAA
1169 AATAA-AAA-AAAT
1 AATAATAAATAAAT
*
1181 ATTAATAAATAAAT
1 AATAATAAATAAAT
1195 AATAAT-AATATAAT
1 AATAATAAATA-AAT
1209 AATAATAAATAA
1 AATAATAAATAA
1221 TTTTTTTAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
12 4 0.12
13 7 0.21
14 19 0.56
15 4 0.12
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (14 bp):
AATAATAAATAAAT
Found at i:1725 original size:168 final size:162
Alignment explanation
Indices: 1476--2042 Score: 555
Period size: 168 Copynumber: 3.5 Consensus size: 162
1466 TGACATATAG
* * * * * *
1476 CCCTTCTCGTCTTGAGTTATGTTGTAAATTTGATTTGCCTCTG-AGTTGAATGTAATCGAACTCG
1 CCCTTCTAGCCTTGAGTTATGTTGCAAA--TGATGTGCCT-TGAAGCTGAGTGTAATCGAACTCG
* *
1540 AAGGA-CTTTGGTTGGCAGATAGCCCTTCTCACCTTAAGCTATAATGAAAATGATGTGCCTTGGA
63 AAGGATCTTTGGTTGGCAGATAGCCCTTCT-ACCTTAAGCTATGATGAAAATGATGTGCCTTTGA
* * * *
1604 GCTGAGAGTATTCGAACTCGAAGGTCTTTTGTTGGCAAATAG
127 GCTGA-AG-AATCGAACTCTAAGGTC---T-TTGGCAGATAA
* * * * *
1646 CCCTTCTTGCCTTGAGCTATGTTGCAAGTGATGTGCCTT-AGAGCTGAGCGTAGTCGAACTCGAA
1 CCCTTCTAGCCTTGAGTTATGTTGCAAATGATGTGCCTTGA-AGCTGAGTGTAATCGAACTCGAA
* * * * * *
1710 -GATCTTTGGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGTTGTAAATGATATGCCTTTGAGC
65 GGATCTTTGGTTGGCAGATAGCCCTTCTA-CCTTAAGCTATGATGAAAATGATGTGCCTTTGAGC
1774 TGAATGGAATCGAACTCTAAGGTCTTTGGCAGATAA
129 TGAA--GAATCGAACTCTAAGGTCTTTGGCAGATAA
*
1810 CCCTTCTAGCCTTGAGTTAT-TCTGCAAATGATGTGCCCTTGAAGCTAAGTGTAATCGAACTCG-
1 CCCTTCTAGCCTTGAGTTATGT-TGCAAATGATGTG-CCTTGAAGCTGAGTGTAATCGAACTCGA
* * * * * **
1873 AGGGTC--T--TTGGCAGATAGCTCTTCTTGCCTTAAGCTATGCTGCAAATGATGCACCTTTGAG
64 AGGATCTTTGGTTGGCAGATAGCCCTTC-TACCTTAAGCTATGATGAAAATGATGTGCCTTTGAG
1934 CTGAATAGAATCGAACTCTAAGGTCTTT-GCAGATAA
128 CTG-A-AGAATCGAACTCTAAGGTCTTTGGCAGATAA
* * *
1970 CCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCCTCGAAGCTGAGTGTAGTCGAACTCGAA
1 CCCTTCTAGCCTTGAGTTATGTTGCAAATGATGTG-CCTTGAAGCTGAGTGTAATCGAACTCGAA
*
2035 TG-TCTTTG
65 GGATCTTTG
2043 TGTTTCAAGA
Statistics
Matches: 335, Mismatches: 44, Indels: 43
0.79 0.10 0.10
Matches are distributed among these distances:
160 68 0.20
161 68 0.20
162 3 0.01
163 3 0.01
164 40 0.12
165 26 0.08
166 1 0.00
167 5 0.01
168 97 0.29
169 1 0.00
170 23 0.07
ACGTcount: A:0.24, C:0.20, G:0.24, T:0.32
Consensus pattern (162 bp):
CCCTTCTAGCCTTGAGTTATGTTGCAAATGATGTGCCTTGAAGCTGAGTGTAATCGAACTCGAAG
GATCTTTGGTTGGCAGATAGCCCTTCTACCTTAAGCTATGATGAAAATGATGTGCCTTTGAGCTG
AAGAATCGAACTCTAAGGTCTTTGGCAGATAA
Found at i:1839 original size:80 final size:80
Alignment explanation
Indices: 1506--2042 Score: 458
Period size: 84 Copynumber: 6.5 Consensus size: 80
1496 GTTGTAAATT
* * * * *
1506 TGATTTGCCTCTGAGTTGAATGTAATCGAACTCGAAGGACTTTGGTTGGCAGATAGCCCTTCTCA
1 TGATGTGCCTTTGAGCTGAATGTAATCGAACTCGAAGG--TCT--TTGGCAGATAACCCTTCT-A
* ** *
1571 -CCTTAAGCTATAATGAAAA
61 GCCTTGAGCTATTCTGCAAA
* * * * *
1590 TGATGTGCCTTGGAGCTGAGA-GTATTCGAACTCGAAGGTCTTTTGTTGGCAAATAGCCCTTCTT
1 TGATGTGCCTTTGAGCTGA-ATGTAATCGAACTCGAAGGTC---T-TTGGCAGATAACCCTTCTA
*
1654 GCCTTGAGCTATGT-TGCAAG
61 GCCTTGAGCTAT-TCTGCAAA
* ** * *
1674 TGATGTGCCTTAGAGCTGAGCGTAGTCGAACTCGAAGATCTTTGGTTGGCAGATAACCCTTCTAG
1 TGATGTGCCTTTGAGCTGAATGTAATCGAACTCGAAGGTC--T--TTGGCAGATAACCCTTCTAG
* *
1739 CCTTGAGTTATGT-TGTAAA
62 CCTTGAGCTAT-TCTGCAAA
* * *
1758 TGATATGCCTTTGAGCTGAATGGAATCGAACTCTAAGGTCTTTGGCAGATAACCCTTCTAGCCTT
1 TGATGTGCCTTTGAGCTGAATGTAATCGAACTCGAAGGTCTTTGGCAGATAACCCTTCTAGCCTT
*
1823 GAGTTATTCTGCAAA
66 GAGCTATTCTGCAAA
* * * * *
1838 TGATGTGCCCTTGAAGCT-AAGTGTAATCGAACTCGAGGGTCTTTGGCAGATAGCTCTTCTTGCC
1 TGATGTGCCTTTG-AGCTGAA-TGTAATCGAACTCGAAGGTCTTTGGCAGATAACCCTTCTAGCC
* *
1902 TTAAGCTATGCTGCAAA
64 TTGAGCTATTCTGCAAA
** *
1919 TGATGCACCTTTGAGCTGAATAG-AATCGAACTCTAAGGTCTTT-GCAGATAACCCTTCTAGCCT
1 TGATGTGCCTTTGAGCTGAAT-GTAATCGAACTCGAAGGTCTTTGGCAGATAACCCTTCTAGCCT
* *
1982 TGAGTTATGCTGCAAA
65 TGAGCTATTCTGCAAA
* * * * *
1998 TGATGTGCCCTCGAAGCTGAGTGTAGTCGAACTCGAATGTCTTTG
1 TGATGTGCCTTTG-AGCTGAATGTAATCGAACTCGAAGGTCTTTG
2043 TGTTTCAAGA
Statistics
Matches: 377, Mismatches: 60, Indels: 35
0.80 0.13 0.07
Matches are distributed among these distances:
79 42 0.11
80 96 0.25
81 68 0.18
82 2 0.01
83 3 0.01
84 164 0.44
85 2 0.01
ACGTcount: A:0.25, C:0.20, G:0.24, T:0.32
Consensus pattern (80 bp):
TGATGTGCCTTTGAGCTGAATGTAATCGAACTCGAAGGTCTTTGGCAGATAACCCTTCTAGCCTT
GAGCTATTCTGCAAA
Found at i:2030 original size:160 final size:161
Alignment explanation
Indices: 1551--2042 Score: 560
Period size: 160 Copynumber: 3.0 Consensus size: 161
1541 AGGACTTTGG
* * *
1551 TTGGCAGATAGCCCTTCTCA-CCTTAAGCTATAATGAAAATGATGTGCCTTGGAGCTG-AGAGTA
1 TTGGCAGATAGCCCTTCT-AGCCTTAAGCTATGATGAAAATGATGTGCCTTTGAGCTGAATAG-A
* * * * * * * *
1614 TTCGAACTCGAAGGTCTTTTGTTGGCAAATAGCCCTTCTTGCCTTGAGCTATGTTGCAAGTGATG
64 ATCGAACTCTAAGGTC---T-TTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATG
* * *
1679 TGCCTTAG-AGCTGAGCGTAGTCGAACTCGAAGATCTTT
125 TGCCCTAGAAGCTGAGTGTAGTCGAACTCGAAGGTC--T
* * * * * * *
1717 GGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGTTGTAAATGATATGCCTTTGAGCTGAATGGA
1 --TTGGCAGATAGCCCTTCTAGCCTTAAGCTATGATGAAAATGATGTGCCTTTGAGCTGAATAGA
*
1782 ATCGAACTCTAAGGTCTTTGGCAGATAACCCTTCTAGCCTTGAGTTATTCTGCAAATGATGTGCC
64 ATCGAACTCTAAGGTCTTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCC
* * * *
1847 CTTGAAGCTAAGTGTAATCGAACTCGAGGGTCT
129 CTAGAAGCTGAGTGTAGTCGAACTCGAAGGTCT
* * * * **
1880 TTGGCAGATAGCTCTTCTTGCCTTAAGCTATGCTGCAAATGATGCACCTTTGAGCTGAATAGAAT
1 TTGGCAGATAGCCCTTCTAGCCTTAAGCTATGATGAAAATGATGTGCCTTTGAGCTGAATAGAAT
1945 CGAACTCTAAGGTCTTT-GCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCCT
66 CGAACTCTAAGGTCTTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCCT
* *
2009 CGAAGCTGAGTGTAGTCGAACTCGAATGTCT
131 AGAAGCTGAGTGTAGTCGAACTCGAAGGTCT
2040 TTG
1 TTG
2043 TGTTTCAAGA
Statistics
Matches: 278, Mismatches: 43, Indels: 14
0.83 0.13 0.04
Matches are distributed among these distances:
160 75 0.27
161 71 0.26
163 1 0.00
164 43 0.15
165 23 0.08
167 1 0.00
168 62 0.22
169 2 0.01
ACGTcount: A:0.25, C:0.20, G:0.24, T:0.32
Consensus pattern (161 bp):
TTGGCAGATAGCCCTTCTAGCCTTAAGCTATGATGAAAATGATGTGCCTTTGAGCTGAATAGAAT
CGAACTCTAAGGTCTTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCCT
AGAAGCTGAGTGTAGTCGAACTCGAAGGTCT
Found at i:2121 original size:34 final size:32
Alignment explanation
Indices: 2043--2155 Score: 142
Period size: 34 Copynumber: 3.5 Consensus size: 32
2033 AATGTCTTTG
*
2043 TGTTTCAAGAGAAAC-ATTTTCAAAG-GTTTTT
1 TGTTTCAAGAGAAACGA-TTTCAAAGTTTTTTT
*
2074 T-TTCCAAGAGAAACGATTTCAAAGTTTTTTTT
1 TGTTTCAAGAGAAACGATTTCAAAG-TTTTTTT
2106 ATGTTTCAAGAGAAACGATTTCAAAGGTTTTTTT
1 -TGTTTCAAGAGAAACGATTTCAAA-GTTTTTTT
2140 GTGTTTCAAGAGAAAC
1 -TGTTTCAAGAGAAAC
2156 TGTCTCCAGG
Statistics
Matches: 72, Mismatches: 4, Indels: 9
0.85 0.05 0.11
Matches are distributed among these distances:
30 20 0.28
31 2 0.03
32 5 0.07
33 1 0.01
34 43 0.60
35 1 0.01
ACGTcount: A:0.33, C:0.11, G:0.17, T:0.40
Consensus pattern (32 bp):
TGTTTCAAGAGAAACGATTTCAAAGTTTTTTT
Found at i:2189 original size:71 final size:67
Alignment explanation
Indices: 2109--2446 Score: 183
Period size: 67 Copynumber: 5.0 Consensus size: 67
2099 TTTTTTTATG
* * *
2109 TTTCAAGAGAAACGAT-TTCAAAGGTTTTTTTGTGTTTCAAGAGAAACTGTCTCCAGGGAGACAA
1 TTTCAAGAGAAA-GATATTCAAAGG----TTGGTGTTTCAAGAGAAACTGTCTCAAGAGAGACAA
*
2173 AATTTTA
61 AACTTTA
* *
2180 TTTCAAGAGAAATATATTCAAAGGTTGGTGTTTCAAGAGAAATTGTCTCAAGAGAGACAAAACTT
1 TTTCAAGAGAAAGATATTCAAAGGTTGGTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTT
*
2245 TG
66 TA
* * * **** * * *
2247 TTTCAAGGGAAA-TTGTCTCAAGAGAGACAAAACTTATTTCTAA-AGAAACAGTCTCAAGGGAGA
1 TTTCAAGAGAAAGATAT-TCAA-AG-G----TTGGTGTTTC-AAGAGAAACTGTCTCAAGAGAGA
* *
2310 CGAAA-TTTG
58 CAAAACTTTA
* * * * *
2319 TTTCAAG-GAAAACATATTCAAAGATT-TTGTTTCAAGGGAAACCGTCTCAAGAGAGACAAAA-T
1 TTTCAAGAG-AAAGATATTCAAAGGTTGGTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACT
*
2381 TTG
65 TTA
* * * ** ** *
2384 TTTCAAGAGAGACAAAGACAAAAATT--T-TTTCAAGAGAAATTGTCTCAAGAGAGACAAAACTT
1 TTTCAAGAGAAAGATATTCAAAGGTTGGTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTT
2446 T
66 T
2447 GTTCCAAAAT
Statistics
Matches: 216, Mismatches: 37, Indels: 35
0.75 0.13 0.12
Matches are distributed among these distances:
63 29 0.13
64 6 0.03
65 50 0.23
66 3 0.01
67 52 0.24
68 2 0.01
69 1 0.00
70 2 0.01
71 23 0.11
72 18 0.08
73 28 0.13
74 2 0.01
ACGTcount: A:0.40, C:0.13, G:0.19, T:0.28
Consensus pattern (67 bp):
TTTCAAGAGAAAGATATTCAAAGGTTGGTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTT
TA
Found at i:2310 original size:36 final size:37
Alignment explanation
Indices: 2210--2329 Score: 122
Period size: 37 Copynumber: 3.3 Consensus size: 37
2200 AAGGTTGGTG
** *
2210 TTTCAAGAGAAATTGTCTCAAGAGAGACAAAACTTTG
1 TTTCAAGAGAAACAGTCTCAAGAGAGACAAAACTTTA
* **
2247 TTTCAAGGGAAATTGTCTCAAGAGAGACAAAAC-TTA
1 TTTCAAGAGAAACAGTCTCAAGAGAGACAAAACTTTA
* * *
2283 TTTCTAA-AGAAACAGTCTCAAGGGAGACGAAA-TTTG
1 TTTC-AAGAGAAACAGTCTCAAGAGAGACAAAACTTTA
2319 TTTCAAG-GAAA
1 TTTCAAGAGAAA
2330 ACATATTCAA
Statistics
Matches: 72, Mismatches: 8, Indels: 8
0.82 0.09 0.09
Matches are distributed among these distances:
35 6 0.08
36 32 0.44
37 34 0.47
ACGTcount: A:0.41, C:0.13, G:0.20, T:0.26
Consensus pattern (37 bp):
TTTCAAGAGAAACAGTCTCAAGAGAGACAAAACTTTA
Found at i:2332 original size:36 final size:35
Alignment explanation
Indices: 2208--2615 Score: 168
Period size: 36 Copynumber: 11.9 Consensus size: 35
2198 CAAAGGTTGG
**
2208 TGTTTCAAGAGAAATTGTCTCAAGAGAGACAAAACTT
1 TGTTTCAAG-GAAACAGTCTCAAGAGAGACAAAA-TT
** *
2245 TGTTTCAAGGGAAATTGTCTCAAGAGAGACAAAACT
1 TGTTTCAA-GGAAACAGTCTCAAGAGAGACAAAATT
* * * *
2281 TATTTCTAAAGAAACAGTCTCAAGGGAGACGAAATT
1 TGTTTC-AAGGAAACAGTCTCAAGAGAGACAAAATT
* *
2317 TGTTTCAAGGAAAACA-TATTC-A-A-AG----ATTT
1 TGTTTCAAGG-AAACAGT-CTCAAGAGAGACAAAATT
*
2346 TGTTTCAAGGGAAACCGTCTCAAGAGAGACAAAATT
1 TGTTTCAA-GGAAACAGTCTCAAGAGAGACAAAATT
* * *
2382 TGTTTCAA-G--AGAG--ACAA-AGACA-AAAATT
1 TGTTTCAAGGAAACAGTCTCAAGAGAGACAAAATT
**
2410 T-TTTCAAGAGAAATTGTCTCAAGAGAGACAAAACTT
1 TGTTTCAAG-GAAACAGTCTCAAGAGAGACAAAA-TT
* ** ** *
2446 TGTTCCAAAATAAATTGTCTCAAGGGAGACAAAATT
1 TGTTTC-AAGGAAACAGTCTCAAGAGAGACAAAATT
* * *
2482 TGTTT-AATGTAAA-AGATATTC-A-A-AG----ATTT
1 TGTTTCAA-GGAAACAG-T-CTCAAGAGAGACAAAATT
2511 TGTTTCAAGGGAAACTA-TCTCAAGAGAGACAAAATT
1 TGTTTCAA-GGAAAC-AGTCTCAAGAGAGACAAAATT
*
2547 TGTTTCAAGAGAAACTA-TCTGAAGAGAGACAAAATTT
1 TGTTTCAAG-GAAAC-AGTCTCAAGAGAGACAAAA-TT
** * * *
2584 TGTTTTGAGTAAATTAGTCTCAAGCGAGACAA
1 TGTTTCAAGGAAA-CAGTCTCAAGAGAGACAA
2616 CCCCTTGTTT
Statistics
Matches: 285, Mismatches: 45, Indels: 82
0.69 0.11 0.20
Matches are distributed among these distances:
27 6 0.02
28 7 0.02
29 32 0.11
30 15 0.05
31 4 0.01
32 7 0.02
33 7 0.02
34 8 0.03
35 16 0.06
36 99 0.35
37 81 0.28
38 3 0.01
ACGTcount: A:0.41, C:0.12, G:0.19, T:0.28
Consensus pattern (35 bp):
TGTTTCAAGGAAACAGTCTCAAGAGAGACAAAATT
Found at i:2441 original size:63 final size:63
Alignment explanation
Indices: 2271--2449 Score: 182
Period size: 65 Copynumber: 2.8 Consensus size: 63
2261 GTCTCAAGAG
* * * * *
2271 AGACAAAACTTATTTCTAA-AGAAACAGTCTCAAGGGAGACGAAATTTGTTTCAAGGAAAACAT
1 AGACAAAAATTTTTTC-AAGAGAAACAGTCTCAAGAGAGACAAAATTTGTTTCAAGGAAAACAA
** * * * *
2334 ATTCAAAGATTTTGTTTCAAGGGAAACCGTCTCAAGAGAGACAAAATTTGTTTCAA-GAGAGACA
1 AGACAAA-AATTT-TTTCAAGAGAAACAGTCTCAAGAGAGACAAAATTTGTTTCAAGGA-AAACA
2398 A
63 A
**
2399 AGACAAAAATTTTTTCAAGAGAAATTGTCTCAAGAGAGACAAAACTTTGTT
1 AGACAAAAATTTTTTCAAGAGAAACAGTCTCAAGAGAGACAAAA-TTTGTT
2450 CCAAAATAAA
Statistics
Matches: 95, Mismatches: 16, Indels: 9
0.79 0.13 0.08
Matches are distributed among these distances:
63 34 0.36
64 17 0.18
65 44 0.46
ACGTcount: A:0.42, C:0.13, G:0.18, T:0.26
Consensus pattern (63 bp):
AGACAAAAATTTTTTCAAGAGAAACAGTCTCAAGAGAGACAAAATTTGTTTCAAGGAAAACAA
Found at i:2503 original size:165 final size:165
Alignment explanation
Indices: 2234--2558 Score: 503
Period size: 165 Copynumber: 2.0 Consensus size: 165
2224 GTCTCAAGAG
* * *
2234 AGACAAAACTTTGTTTCAAGGGAAATTGTCTCAAGAGAGACAAAACTTATTTCTAAAGAAACAGT
1 AGACAAAAATTTGTTTCAAGAGAAATTGTCTCAAGAGAGACAAAACTTATTTCAAAAGAAACAGT
* *
2299 CTCAAGGGAGACGAAATTTGTTTCAAGGAAAACATATTCAAAGATTTTGTTTCAAGGGAAACCGT
66 CTCAAGGGAGACAAAATTTGTTTCAAGGAAAACATATTCAAAGATTTTGTTTCAAGGGAAACCAT
2364 CTCAAGAGAGACAAAATTTGTTTCAAGAGAGACAA
131 CTCAAGAGAGACAAAATTTGTTTCAAGAGAGACAA
* **
2399 AGACAAAAATTT-TTTCAAGAGAAATTGTCTCAAGAGAGACAAAACTT-TGTTCCAAAATAAATT
1 AGACAAAAATTTGTTTCAAGAGAAATTGTCTCAAGAGAGACAAAACTTAT-TT-CAAAAGAAACA
* *
2462 GTCTCAAGGGAGACAAAATTTGTTT-AATGTAAAAGATATTCAAAGATTTTGTTTCAAGGGAAAC
64 GTCTCAAGGGAGACAAAATTTGTTTCAA-GGAAAACATATTCAAAGATTTTGTTTCAAGGGAAAC
*
2526 TATCTCAAGAGAGACAAAATTTGTTTCAAGAGA
128 CATCTCAAGAGAGACAAAATTTGTTTCAAGAGA
2559 AACTATCTGA
Statistics
Matches: 146, Mismatches: 11, Indels: 6
0.90 0.07 0.04
Matches are distributed among these distances:
163 1 0.01
164 38 0.26
165 107 0.73
ACGTcount: A:0.42, C:0.13, G:0.18, T:0.27
Consensus pattern (165 bp):
AGACAAAAATTTGTTTCAAGAGAAATTGTCTCAAGAGAGACAAAACTTATTTCAAAAGAAACAGT
CTCAAGGGAGACAAAATTTGTTTCAAGGAAAACATATTCAAAGATTTTGTTTCAAGGGAAACCAT
CTCAAGAGAGACAAAATTTGTTTCAAGAGAGACAA
Found at i:3240 original size:124 final size:123
Alignment explanation
Indices: 2777--3243 Score: 603
Period size: 124 Copynumber: 3.8 Consensus size: 123
2767 GGCACAATAA
* * ** * * ***
2777 CCTTCTTCGTGAAGTTGAAATCGTGGATGGGTCATTCGTTGTGAAATTGAGCTTTTAATTGGGCA
1 CCTTCGTCGTGAAGTTGAAACCGTGGATGGCCCATTCGTTGTGAAGTTGAGC-CTTAATTGAATA
* * * * * * **
2842 TCCTTCGTCGGGAAGTTGAAATCCAACCTGAAGATGAATGTTGCTGGTGGGTATAATTC
65 TCATTCGTCGTGAAGTTGAAATCCAAGCTGAAGATGAATGTTACTGGTGAGCACGATTC
* * * *
2901 CCTTCGTCGTGAAGTTGAAACCGTTGATGGCCTC-TTCGTTATGAAGTTGAGTCTTGAATTGGAT
1 CCTTCGTCGTGAAGTTGAAACCGTGGATGGCC-CATTCGTTGTGAAGTTGAGCCTT-AATTGAAT
* * * *
2965 ATCCTTCGTCATGAAGTTGAAATCCAATCTAAAGATGAATGTTACTGGTGAGCACGATTC
64 ATCATTCGTCGTGAAGTTGAAATCCAAGCTGAAGATGAATGTTACTGGTGAGCACGATTC
*
3025 CCTTCGTCGTGAAGTTGAAACCGTGGATGGCCCATTTGTTGTGAAGTTGAGCCTTAACTTGAATA
1 CCTTCGTCGTGAAGTTGAAACCGTGGATGGCCCATTCGTTGTGAAGTTGAGCCTTAA-TTGAATA
* **
3090 TCATTCATCGTGAAGTTGAAATCCAAGCTGAAGATGAATGTTACTAATGAGCACGATTC
65 TCATTCGTCGTGAAGTTGAAATCCAAGCTGAAGATGAATGTTACTGGTGAGCACGATTC
* *
3149 CCTTCGTCGTGAAGTTGAAACTGTGGATGGCCCCTTCGTTGTGAAGTTGAGCCTTAACTTGAATA
1 CCTTCGTCGTGAAGTTGAAACCGTGGATGGCCCATTCGTTGTGAAGTTGAGCCTTAA-TTGAATA
3214 TCATTCGTCGTGAAGTTGAAATCCAAGCTG
65 TCATTCGTCGTGAAGTTGAAATCCAAGCTG
3244 TATTGTTTCG
Statistics
Matches: 303, Mismatches: 36, Indels: 8
0.87 0.10 0.02
Matches are distributed among these distances:
123 5 0.02
124 297 0.98
125 1 0.00
ACGTcount: A:0.25, C:0.18, G:0.25, T:0.32
Consensus pattern (123 bp):
CCTTCGTCGTGAAGTTGAAACCGTGGATGGCCCATTCGTTGTGAAGTTGAGCCTTAATTGAATAT
CATTCGTCGTGAAGTTGAAATCCAAGCTGAAGATGAATGTTACTGGTGAGCACGATTC
Found at i:11698 original size:36 final size:34
Alignment explanation
Indices: 11656--11737 Score: 128
Period size: 36 Copynumber: 2.4 Consensus size: 34
11646 TTATTATTAT
11656 ATATATATATATAATATTAATAAATTTAATTTAA
1 ATATATATATATAATATTAATAAATTTAATTTAA
* *
11690 ATTAATATATATATAATATTTATATATTTAATTTAA
1 A-T-ATATATATATAATATTAATAAATTTAATTTAA
11726 ATATATATATAT
1 ATATATATATAT
11738 CCGGCCCGAT
Statistics
Matches: 44, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
34 11 0.25
35 2 0.05
36 31 0.70
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (34 bp):
ATATATATATATAATATTAATAAATTTAATTTAA
Found at i:11715 original size:15 final size:15
Alignment explanation
Indices: 11657--11734 Score: 50
Period size: 15 Copynumber: 5.8 Consensus size: 15
11647 TATTATTATA
11657 TATATATATATAA--
1 TATATATATATAATT
11670 TAT-TA-ATA-AATT
1 TATATATATATAATT
11682 TA-AT-T-TA-AATT
1 TATATATATATAATT
*
11693 AATATATATATAATAT
1 TATATATATATAAT-T
*
11709 T-TATATATTTAATT
1 TATATATATATAATT
*
11723 TAAATATATATA
1 TATATATATATA
11735 TATCCGGCCC
Statistics
Matches: 50, Mismatches: 5, Indels: 18
0.68 0.07 0.25
Matches are distributed among these distances:
10 2 0.04
11 10 0.20
12 7 0.14
13 4 0.08
14 4 0.08
15 22 0.44
16 1 0.02
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
TATATATATATAATT
Found at i:12545 original size:18 final size:18
Alignment explanation
Indices: 12510--12547 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
12500 AAATTTAGAT
12510 AAACATATTAATAATAAA
1 AAACATATTAATAATAAA
*
12528 AAAC-TATTATATACTAAA
1 AAACATATTA-ATAATAAA
12546 AA
1 AA
12548 TTAAAAGTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 5 0.28
18 13 0.72
ACGTcount: A:0.63, C:0.08, G:0.00, T:0.29
Consensus pattern (18 bp):
AAACATATTAATAATAAA
Found at i:22239 original size:24 final size:24
Alignment explanation
Indices: 22212--22284 Score: 67
Period size: 24 Copynumber: 3.0 Consensus size: 24
22202 CGTTCATTTA
22212 CGTTC-GTGAACGTTCGGTTATGTT
1 CGTTCGGT-AACGTTCGGTTATGTT
* * *
22236 CGTTCGGTTATGTTCGTTTATGTT
1 CGTTCGGTAACGTTCGGTTATGTT
* * * *
22260 CGTTCGATTATGTTCGTTTATGTT
1 CGTTCGGTAACGTTCGGTTATGTT
22284 C
1 C
22285 TTTCATTTAT
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
24 42 0.95
25 2 0.05
ACGTcount: A:0.11, C:0.15, G:0.25, T:0.49
Consensus pattern (24 bp):
CGTTCGGTAACGTTCGGTTATGTT
Found at i:22241 original size:14 final size:14
Alignment explanation
Indices: 22222--22277 Score: 75
Period size: 14 Copynumber: 4.3 Consensus size: 14
22212 CGTTCGTGAA
22222 CGTTCGGTTATGTT
1 CGTTCGGTTATGTT
22236 CGTTCGGTTATGTT
1 CGTTCGGTTATGTT
22250 CG-T---TTATGTT
1 CGTTCGGTTATGTT
*
22260 CGTTCGATTATGTT
1 CGTTCGGTTATGTT
22274 CGTT
1 CGTT
22278 TATGTTCTTT
Statistics
Matches: 38, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
10 9 0.24
11 1 0.03
13 1 0.03
14 27 0.71
ACGTcount: A:0.09, C:0.14, G:0.25, T:0.52
Consensus pattern (14 bp):
CGTTCGGTTATGTT
Found at i:22294 original size:24 final size:23
Alignment explanation
Indices: 22223--22297 Score: 96
Period size: 24 Copynumber: 3.1 Consensus size: 23
22213 GTTCGTGAAC
* *
22223 GTTCGGTTATGTTCGTTCGGTTAT
1 GTTCGTTTATGTTCGTTC-ATTAT
22247 GTTCGTTTATGTTCGTTCGATTAT
1 GTTCGTTTATGTTCGTTC-ATTAT
*
22271 GTTCGTTTATGTTCTTTCATTTAT
1 GTTCGTTTATGTTCGTTCA-TTAT
22295 GTT
1 GTT
22298 TAACCCAATC
Statistics
Matches: 47, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
23 1 0.02
24 46 0.98
ACGTcount: A:0.11, C:0.12, G:0.21, T:0.56
Consensus pattern (23 bp):
GTTCGTTTATGTTCGTTCATTAT
Found at i:23296 original size:10 final size:10
Alignment explanation
Indices: 23278--23352 Score: 61
Period size: 10 Copynumber: 7.7 Consensus size: 10
23268 GGGTCTCCAA
*
23278 CGTTGATGTT
1 CGTTTATGTT
23288 CGTTTATGTT
1 CGTTTATGTT
23298 CGTGTTCAT-TT
1 CGT-TT-ATGTT
* *
23309 ATGTTCATGTT
1 -CGTTTATGTT
23320 CGTTTATGTT
1 CGTTTATGTT
23330 CG----TGTT
1 CGTTTATGTT
23336 CGTTTATGTT
1 CGTTTATGTT
23346 CGTTTAT
1 CGTTTAT
23353 TTATTAAATG
Statistics
Matches: 52, Mismatches: 5, Indels: 16
0.71 0.07 0.22
Matches are distributed among these distances:
6 6 0.12
10 35 0.67
11 7 0.13
12 4 0.08
ACGTcount: A:0.11, C:0.12, G:0.21, T:0.56
Consensus pattern (10 bp):
CGTTTATGTT
Found at i:23309 original size:16 final size:16
Alignment explanation
Indices: 23284--23348 Score: 112
Period size: 16 Copynumber: 4.1 Consensus size: 16
23274 CCAACGTTGA
23284 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
* *
23300 TGTTCATTTATGTTCA
1 TGTTCGTTTATGTTCG
23316 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
23332 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
23348 T
1 T
23349 TTATTTATTA
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 45 1.00
ACGTcount: A:0.09, C:0.12, G:0.22, T:0.57
Consensus pattern (16 bp):
TGTTCGTTTATGTTCG
Found at i:23439 original size:16 final size:16
Alignment explanation
Indices: 23418--23450 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
23408 AAAAAAAATT
23418 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
23434 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
23450 T
1 T
23451 CTATTTATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.06, C:0.12, G:0.24, T:0.58
Consensus pattern (16 bp):
TGTTCGTTTATGTTCG
Found at i:31613 original size:9 final size:9
Alignment explanation
Indices: 31599--31632 Score: 50
Period size: 9 Copynumber: 3.7 Consensus size: 9
31589 TTAATTCGAA
31599 AATTAAACG
1 AATTAAACG
31608 AATTAAACG
1 AATTAAACG
*
31617 AATTAACCG
1 AATTAAACG
31626 AAATTAA
1 -AATTAA
31633 TTCGGTTCGA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
9 17 0.74
10 6 0.26
ACGTcount: A:0.56, C:0.12, G:0.09, T:0.24
Consensus pattern (9 bp):
AATTAAACG
Found at i:32942 original size:35 final size:35
Alignment explanation
Indices: 32896--32968 Score: 137
Period size: 35 Copynumber: 2.1 Consensus size: 35
32886 GTGACACGTG
*
32896 TCATATTTATATTTTGACTTAATGTAAAAAAGCAC
1 TCATATTTATATTTTGACTTAATGTAAAAAAACAC
32931 TCATATTTATATTTTGACTTAATGTAAAAAAACAC
1 TCATATTTATATTTTGACTTAATGTAAAAAAACAC
32966 TCA
1 TCA
32969 AACTATACTC
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.41, C:0.12, G:0.07, T:0.40
Consensus pattern (35 bp):
TCATATTTATATTTTGACTTAATGTAAAAAAACAC
Found at i:35085 original size:46 final size:46
Alignment explanation
Indices: 35015--35120 Score: 151
Period size: 46 Copynumber: 2.3 Consensus size: 46
35005 TACACAAAGG
* * *
35015 GTGCATCGATGCATAAAATACATTCGATGTTTTAA-ACAAGCCTGGA
1 GTGCATCGATGCATAAAATACATTCGATGTTTCAATAAAAGCCT-AA
* *
35061 GTGCATCGATGCATAAAATGCATTCGATGTTTCAATAAAATCCTAA
1 GTGCATCGATGCATAAAATACATTCGATGTTTCAATAAAAGCCTAA
35107 GTGCATCGATGCAT
1 GTGCATCGATGCAT
35121 GACTGTTCAT
Statistics
Matches: 54, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
46 48 0.89
47 6 0.11
ACGTcount: A:0.34, C:0.18, G:0.19, T:0.29
Consensus pattern (46 bp):
GTGCATCGATGCATAAAATACATTCGATGTTTCAATAAAAGCCTAA
Found at i:37182 original size:30 final size:31
Alignment explanation
Indices: 37141--37210 Score: 88
Period size: 30 Copynumber: 2.3 Consensus size: 31
37131 CCCGAAGGAC
* *
37141 CTATCCATAGGTCATAAAGAACCTCGG-AAA
1 CTATTCATAGGTCATAAAGAACCTAGGTAAA
* * *
37171 CTGTTCATAGGTCCTGAAGAACCTAGGTAAA
1 CTATTCATAGGTCATAAAGAACCTAGGTAAA
37202 CTATTCATA
1 CTATTCATA
37211 TGTTCCTTAG
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
30 22 0.67
31 11 0.33
ACGTcount: A:0.36, C:0.21, G:0.17, T:0.26
Consensus pattern (31 bp):
CTATTCATAGGTCATAAAGAACCTAGGTAAA
Found at i:37223 original size:31 final size:32
Alignment explanation
Indices: 37157--37244 Score: 92
Period size: 31 Copynumber: 2.8 Consensus size: 32
37147 ATAGGTCATA
* *
37157 AAGAACCTCGG-AAACTGTTCATA-GGTCCTG
1 AAGAACCTAGGTAAACTGTTCATATGTTCCTG
*
37187 AAGAACCTAGGTAAACTATTCATATGTTCCT-
1 AAGAACCTAGGTAAACTGTTCATATGTTCCTG
* * * *
37218 TAGAACATAGGTATACTGTCCATATGT
1 AAGAACCTAGGTAAACTGTTCATATGT
37245 CTCGAAAGAC
Statistics
Matches: 48, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
30 10 0.21
31 33 0.69
32 5 0.10
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.30
Consensus pattern (32 bp):
AAGAACCTAGGTAAACTGTTCATATGTTCCTG
Found at i:37274 original size:32 final size:32
Alignment explanation
Indices: 37194--37294 Score: 111
Period size: 32 Copynumber: 3.2 Consensus size: 32
37184 CTGAAGAACC
* * * *
37194 TAGGTAA-ACTATTCATATGTTCCTTAGAACA
1 TAGGTAATACTGTCCATATGTTCCGTAAAACA
37225 TAGGT-ATACTGTCCATATG-TCTCG-AAAGACA
1 TAGGTAATACTGTCCATATGTTC-CGTAAA-ACA
*
37256 TAGGTAATTCTGTCCATATGTTCCGTAAAACA
1 TAGGTAATACTGTCCATATGTTCCGTAAAACA
37288 TAGGTAA
1 TAGGTAA
37295 ACCCTTGACT
Statistics
Matches: 59, Mismatches: 5, Indels: 11
0.79 0.07 0.15
Matches are distributed among these distances:
30 5 0.08
31 24 0.41
32 25 0.42
33 5 0.08
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.33
Consensus pattern (32 bp):
TAGGTAATACTGTCCATATGTTCCGTAAAACA
Found at i:37517 original size:28 final size:26
Alignment explanation
Indices: 37454--37519 Score: 69
Period size: 28 Copynumber: 2.4 Consensus size: 26
37444 ACATATACCT
37454 TTTCTCATATTCATATAATCATATCA
1 TTTCTCATATTCATATAATCATATCA
* * *
37480 TTTCATTCATATTCGTATATCTCATGTTCA
1 TTTC--TCATATTCATATA-ATCAT-ATCA
37510 TTTCTCATAT
1 TTTCTCATAT
37520 AGTCACATAC
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
26 4 0.12
28 18 0.55
29 4 0.12
30 7 0.21
ACGTcount: A:0.27, C:0.20, G:0.03, T:0.50
Consensus pattern (26 bp):
TTTCTCATATTCATATAATCATATCA
Found at i:37703 original size:16 final size:16
Alignment explanation
Indices: 37682--37719 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
37672 ATGTCACCTC
*
37682 TCATATGATTTCATA-T
1 TCATATGATAT-ATATT
37698 TCATATGATATATATT
1 TCATATGATATATATT
37714 TCATAT
1 TCATAT
37720 TTTTTTCTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 3 0.15
16 17 0.85
ACGTcount: A:0.34, C:0.11, G:0.05, T:0.50
Consensus pattern (16 bp):
TCATATGATATATATT
Found at i:45355 original size:22 final size:21
Alignment explanation
Indices: 45313--45352 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
45303 AAGACTATTT
*
45313 TCATTTTTCAATTTTGAAATA
1 TCATTTTTCAATATTGAAATA
45334 TCATTTTT-ATATATTGAAA
1 TCATTTTTCA-ATATTGAAA
45353 ATAGAGTCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.07, G:0.05, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATATTGAAATA
Found at i:47351 original size:64 final size:65
Alignment explanation
Indices: 47203--47356 Score: 204
Period size: 65 Copynumber: 2.4 Consensus size: 65
47193 TACACTAAGG
* * * * * * *
47203 GTGCATCGATGCATAAAATACATTCGTTGTTTTAAACAAGCCTGGAGTGCATCGATGCATGGTTT
1 GTGCATCGATGCATAAAATGCATTCGATGTTTCAAAAAAGCCTGCAGTGAATCAATGCATGGTTT
*
47268 GTGCATCGATGCATAAAATGCATTCGATGTTTCAATAAAATCCT-CAGTGAATCAATGCATGG-T
1 GTGCATCGATGCATAAAATGCATTCGATGTTTCAA-AAAAGCCTGCAGTGAATCAATGCATGGTT
47331 T
65 T
*
47332 GTGCATCGGTGCATAAAATGCATTC
1 GTGCATCGATGCATAAAATGCATTC
47357 AAAATGGGGT
Statistics
Matches: 79, Mismatches: 9, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
64 26 0.33
65 47 0.59
66 6 0.08
ACGTcount: A:0.30, C:0.18, G:0.21, T:0.31
Consensus pattern (65 bp):
GTGCATCGATGCATAAAATGCATTCGATGTTTCAAAAAAGCCTGCAGTGAATCAATGCATGGTTT
Found at i:48774 original size:36 final size:36
Alignment explanation
Indices: 48723--48792 Score: 95
Period size: 36 Copynumber: 1.9 Consensus size: 36
48713 AAGTCTCTGC
** *
48723 AGGTTCAACTGCGATCAAGCTAGTAATTCCTTATAT
1 AGGTTCAACACCGATCAAGATAGTAATTCCTTATAT
* *
48759 AGGTTCAACACCGATCAAGATGGTAATTTCTTAT
1 AGGTTCAACACCGATCAAGATAGTAATTCCTTAT
48793 GGACCTAAGG
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
36 29 1.00
ACGTcount: A:0.31, C:0.19, G:0.17, T:0.33
Consensus pattern (36 bp):
AGGTTCAACACCGATCAAGATAGTAATTCCTTATAT
Found at i:50120 original size:31 final size:31
Alignment explanation
Indices: 50082--50176 Score: 93
Period size: 32 Copynumber: 3.1 Consensus size: 31
50072 CGTAGGCACT
* * *
50082 TAAAAATGTAATGGAGAAAACATTAGACACC
1 TAAAAATGTAAAGAAAAAAACATTAGACACC
* **
50113 TAAAAATGTAACAAAAAAAAACGGTAGACACC
1 TAAAAATGTAA-AGAAAAAAACATTAGACACC
* * *
50145 TAAAAATATAACGAATAAAACATTAG-CACC
1 TAAAAATGTAAAGAAAAAAACATTAGACACC
50175 TA
1 TA
50177 TTTTTAATAA
Statistics
Matches: 51, Mismatches: 12, Indels: 3
0.77 0.18 0.05
Matches are distributed among these distances:
30 6 0.12
31 21 0.41
32 24 0.47
ACGTcount: A:0.56, C:0.15, G:0.12, T:0.18
Consensus pattern (31 bp):
TAAAAATGTAAAGAAAAAAACATTAGACACC
Found at i:51038 original size:30 final size:30
Alignment explanation
Indices: 51002--51060 Score: 100
Period size: 30 Copynumber: 2.0 Consensus size: 30
50992 CAGTGACCAT
* *
51002 CATAGGTCTCCAGGAGCACATGGCGACCTC
1 CATAGGTCTCCAGGAGCACACGACGACCTC
51032 CATAGGTCTCCAGGAGCACACGACGACCT
1 CATAGGTCTCCAGGAGCACACGACGACCT
51061 ATGGAGCACA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.25, C:0.34, G:0.25, T:0.15
Consensus pattern (30 bp):
CATAGGTCTCCAGGAGCACACGACGACCTC
Found at i:51094 original size:19 final size:19
Alignment explanation
Indices: 51044--51101 Score: 89
Period size: 19 Copynumber: 3.1 Consensus size: 19
51034 TAGGTCTCCA
*
51044 GGAGCACACGACGACCTAT
1 GGAGCACACGGCGACCTAT
51063 GGAGCACACGGCGACCTAT
1 GGAGCACACGGCGACCTAT
**
51082 GGAGCACTTGGCGACCTAT
1 GGAGCACACGGCGACCTAT
51101 G
1 G
51102 AAGCTTCAAC
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 36 1.00
ACGTcount: A:0.26, C:0.29, G:0.31, T:0.14
Consensus pattern (19 bp):
GGAGCACACGGCGACCTAT
Found at i:51715 original size:14 final size:14
Alignment explanation
Indices: 51696--51726 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
51686 TAATATTTGT
51696 CTAAAAGAGCCATA
1 CTAAAAGAGCCATA
51710 CTAAAAGAGCCATA
1 CTAAAAGAGCCATA
51724 CTA
1 CTA
51727 GTGTTTAATC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.48, C:0.23, G:0.13, T:0.16
Consensus pattern (14 bp):
CTAAAAGAGCCATA
Found at i:57628 original size:22 final size:23
Alignment explanation
Indices: 57603--57654 Score: 79
Period size: 23 Copynumber: 2.3 Consensus size: 23
57593 GTGTTTTCAT
57603 AAAAAA-ACCTAAAAGTATTTCG
1 AAAAAATACCTAAAAGTATTTCG
* *
57625 AAAAAATCCCTTAAAGTATTTCG
1 AAAAAATACCTAAAAGTATTTCG
57648 AAAAAAT
1 AAAAAAT
57655 CTTAAAAAAC
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
22 6 0.22
23 21 0.78
ACGTcount: A:0.54, C:0.13, G:0.08, T:0.25
Consensus pattern (23 bp):
AAAAAATACCTAAAAGTATTTCG
Found at i:57658 original size:21 final size:21
Alignment explanation
Indices: 57604--57660 Score: 78
Period size: 23 Copynumber: 2.6 Consensus size: 21
57594 TGTTTTCATA
* *
57604 AAAAAACCTAAAAGTATTTCG
1 AAAAAATCTTAAAGTATTTCG
57625 AAAAAATCCCTTAAAGTATTTCG
1 AAAAAAT--CTTAAAGTATTTCG
57648 AAAAAATCTTAAA
1 AAAAAATCTTAAA
57661 AAACATTTGC
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
21 12 0.38
23 20 0.62
ACGTcount: A:0.53, C:0.14, G:0.07, T:0.26
Consensus pattern (21 bp):
AAAAAATCTTAAAGTATTTCG
Found at i:59632 original size:21 final size:21
Alignment explanation
Indices: 59606--59645 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
59596 CATATTGCTC
59606 AGAGGGAACCGATTCCCCCCA
1 AGAGGGAACCGATTCCCCCCA
* *
59627 AGAGGGTACTGATTCCCCC
1 AGAGGGAACCGATTCCCCC
59646 TGAATGGTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.25, C:0.35, G:0.25, T:0.15
Consensus pattern (21 bp):
AGAGGGAACCGATTCCCCCCA
Done.