Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004772.1 Hibiscus syriacus cultivar Beakdansim tig00010762_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: 157048
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:4861 original size:60 final size:58
Alignment explanation
Indices: 4784--4924 Score: 149
Period size: 58 Copynumber: 2.4 Consensus size: 58
4774 TTTTATGGGT
* *
4784 AAAG-TACACAAATGGTCCCCTAACTATAGGATACTTCTTTGTTGAGTCCCCCGACTATGA
1 AAAGTTACA-AAATGGTCCCCCAACTATAGGA-ACTT-TTTGTTGAGTCACCCGACTATGA
* *** * * *
4844 AAAGTTATAAAATGGTCCCCCGGTTATAGGAAGTTTTTGTTGAGTCACTCGACTATTA
1 AAAGTTACAAAATGGTCCCCCAACTATAGGAACTTTTTGTTGAGTCACCCGACTATGA
* *
4902 AAAGTTACAAAATGATCACCCAA
1 AAAGTTACAAAATGGTCCCCCAA
4925 TTATTCATTA
Statistics
Matches: 66, Mismatches: 14, Indels: 4
0.79 0.17 0.05
Matches are distributed among these distances:
58 38 0.58
59 3 0.05
60 22 0.33
61 3 0.05
ACGTcount: A:0.33, C:0.21, G:0.17, T:0.29
Consensus pattern (58 bp):
AAAGTTACAAAATGGTCCCCCAACTATAGGAACTTTTTGTTGAGTCACCCGACTATGA
Found at i:11264 original size:22 final size:22
Alignment explanation
Indices: 11236--11366 Score: 67
Period size: 22 Copynumber: 5.9 Consensus size: 22
11226 TAATGAAAAT
11236 AAATAAATATAAATAAAATA-AA
1 AAATAAA-ATAAATAAAATATAA
**
11258 AAATAAAATATCTAAAATATAA
1 AAATAAAATAAATAAAATATAA
* **
11280 AAATATAA-AAATATATGTATAA
1 AAATAAAATAAATA-AAATATAA
*
11302 TATAATAAAAT-ACT-AAATAGTAA
1 -A-AATAAAATAAATAAAATA-TAA
* *
11325 CAATAATAATAAAT-AAAT-GAA
1 AAATAA-AATAAATAAAATATAA
* *
11346 AAATAAATATACATATAATAT
1 AAATAAA-ATAAATAAAATAT
11367 TAACTAAAAA
Statistics
Matches: 80, Mismatches: 18, Indels: 21
0.67 0.15 0.18
Matches are distributed among these distances:
20 1 0.01
21 30 0.38
22 31 0.39
23 10 0.12
24 8 0.10
ACGTcount: A:0.66, C:0.03, G:0.02, T:0.28
Consensus pattern (22 bp):
AAATAAAATAAATAAAATATAA
Found at i:11266 original size:23 final size:22
Alignment explanation
Indices: 11236--11294 Score: 57
Period size: 23 Copynumber: 2.5 Consensus size: 22
11226 TAATGAAAAT
11236 AAAT-AAATATAAATAAAATAAA
1 AAATAAAATATAAA-AAAATAAA
* *
11258 AAATAAAATATCTAAAATATAAA
1 AAATAAAATAT-AAAAAAATAAA
11281 AATATAAAAATATA
1 AA-AT-AAAATATA
11295 TGTATAATAT
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
22 4 0.13
23 15 0.50
24 4 0.13
25 7 0.23
ACGTcount: A:0.73, C:0.02, G:0.00, T:0.25
Consensus pattern (22 bp):
AAATAAAATATAAAAAAATAAA
Found at i:11266 original size:31 final size:31
Alignment explanation
Indices: 11231--11290 Score: 77
Period size: 31 Copynumber: 1.9 Consensus size: 31
11221 AAACATAATG
11231 AAAATAAAT-AAATATAAATAAAATAAAAAAT
1 AAAATAAATAAAATATAAA-AAAATAAAAAAT
** *
11262 AAAATATCTAAAATATAAAAATATAAAAA
1 AAAATAAATAAAATATAAAAAAATAAAAA
11291 TATATGTATA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
31 16 0.64
32 9 0.36
ACGTcount: A:0.75, C:0.02, G:0.00, T:0.23
Consensus pattern (31 bp):
AAAATAAATAAAATATAAAAAAATAAAAAAT
Found at i:11284 original size:8 final size:8
Alignment explanation
Indices: 11231--11294 Score: 62
Period size: 8 Copynumber: 8.0 Consensus size: 8
11221 AAACATAATG
11231 AAAATA-A
1 AAAATATA
11238 ATAAATATA
1 A-AAATATA
*
11247 AATAAAATA
1 AA-AATATA
11256 AAAA-AT-
1 AAAATATA
*
11262 AAAATATCT
1 AAAATAT-A
11271 AAAATATA
1 AAAATATA
11279 AAAATATA
1 AAAATATA
11287 AAAATATA
1 AAAATATA
11295 TGTATAATAT
Statistics
Matches: 49, Mismatches: 2, Indels: 11
0.79 0.03 0.18
Matches are distributed among these distances:
6 4 0.08
7 5 0.10
8 24 0.49
9 16 0.33
ACGTcount: A:0.73, C:0.02, G:0.00, T:0.25
Consensus pattern (8 bp):
AAAATATA
Found at i:12052 original size:37 final size:37
Alignment explanation
Indices: 12011--12095 Score: 116
Period size: 37 Copynumber: 2.3 Consensus size: 37
12001 AGTTCTTATC
* *
12011 TTTAGGAGTTTAAATAATAGTAGAACTCTATCCTATT
1 TTTAGGAGTTTAAATAATAGCAAAACTCTATCCTATT
* ** *
12048 TTTAGGAGTTTGAATCCTAGCAAAATTCTATCCTATT
1 TTTAGGAGTTTAAATAATAGCAAAACTCTATCCTATT
12085 TTTAGGAGTTT
1 TTTAGGAGTTT
12096 GAATCCTAGT
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 42 1.00
ACGTcount: A:0.31, C:0.12, G:0.15, T:0.42
Consensus pattern (37 bp):
TTTAGGAGTTTAAATAATAGCAAAACTCTATCCTATT
Found at i:12458 original size:14 final size:14
Alignment explanation
Indices: 12439--12474 Score: 72
Period size: 14 Copynumber: 2.6 Consensus size: 14
12429 TTTAAGTTAT
12439 GTTGCTTGAAAATG
1 GTTGCTTGAAAATG
12453 GTTGCTTGAAAATG
1 GTTGCTTGAAAATG
12467 GTTGCTTG
1 GTTGCTTG
12475 TCACTAAGGC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.22, C:0.08, G:0.31, T:0.39
Consensus pattern (14 bp):
GTTGCTTGAAAATG
Found at i:13057 original size:106 final size:106
Alignment explanation
Indices: 12872--13437 Score: 752
Period size: 106 Copynumber: 5.4 Consensus size: 106
12862 CATTGTTCCA
* * * ** *
12872 AGTCCAATATCCTCCG-TCGTGAAGTTGAAATTGCCTCTGGAACCGGGAAATTGTTTGTTGAAAA
1 AGTCCAATATCCTTCGCT-GTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
12936 CCAG-CTGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCG
65 CCAGTC-GTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCG
* * *
12978 AGTCCAATATCCTTCACTGTGAAGTTGAAATTGGCTCCGAAATTGGGAAATTGTTTGTTGTCAAC
1 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAAC
*
13043 CAGTCATCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCG
66 CAGTCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCG
* *
13084 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAAC
1 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAAC
*
13149 CAGTCGTCCCTTCGTTTGTGAAGTTGAACTTGTGTTGTCTTG
66 CAGTCGTCCCTTCG-TTGTGAAGTTGAACTTGTGTTGTCTCG
** * *
13191 AGTTTAATATCCTTCGCTGTGAAGTTGAAATTGACTCTG-AA-T--GAAA-T-TTTGTTGACAAT
1 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAAC
* * * *
13250 CAGTCGCCCCTTCGTCGTGAAGTTGAGCTTGTGTTGTCTTG
66 CAGTCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCG
* * * * **
13291 GGTCCAAGATCCTTCGCTGAGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAGT
1 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAAC
* * * *
13356 CAGCCGCCCCTTCGCTGTGAAGTTGAACTTGTGCTGTCTCG
66 CAGTCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCG
* *
13397 AGTCTAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAA
1 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAA
13438 TGAAATTTGA
Statistics
Matches: 406, Mismatches: 45, Indels: 18
0.87 0.10 0.04
Matches are distributed among these distances:
100 58 0.14
101 25 0.06
102 2 0.00
103 3 0.01
104 3 0.01
105 2 0.00
106 249 0.61
107 64 0.16
ACGTcount: A:0.22, C:0.19, G:0.24, T:0.35
Consensus pattern (106 bp):
AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAAC
CAGTCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCG
Found at i:13317 original size:207 final size:205
Alignment explanation
Indices: 12892--13445 Score: 766
Period size: 207 Copynumber: 2.7 Consensus size: 205
12882 CCTCCGTCGT
* * ** * *
12892 GAAGTTGAAATTGCCTCTGGAACCGGGAAATTGTTTGTTGAAAACCAGCTGTCCCTTCGTTGTGA
1 GAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAACCAGC-GTCCCTTCGTTGTGA
* * * *
12957 AGTTGAACTTGTGTTGTCTCGAGTCCAATATCCTTCACTGTGAAGTTGAAATTGGCTCCGAAATT
65 AGTTGAACTTGTGTTGTCTCGAGTCTAATATCCTTCGCTGTGAAGTTGAAATTGACTCTG-AA-T
* * *
13022 GGGAAATTGTTTGTTGTCAACCAGTCATCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGT
128 --GAAA-T-TTTGTTGACAACCAGTCACCCCTTCGTCGTGAAGTTGAACTTGTGTTGTCTCGAGT
* *
13087 CCAATATCCTTCGCTGT
189 CCAAGATCCTTCGCTGA
*
13104 GAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAACCAGTCGTCCCTTCGTTTGTG
1 GAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAACCAG-CGTCCCTTCG-TTGTG
* *
13169 AAGTTGAACTTGTGTTGTCTTGAGTTTAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATG
64 AAGTTGAACTTGTGTTGTCTCGAGTCTAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATG
* * * * *
13234 AAATTTTGTTGACAATCAGTCGCCCCTTCGTCGTGAAGTTGAGCTTGTGTTGTCTTGGGTCCAAG
129 AAATTTTGTTGACAACCAGTCACCCCTTCGTCGTGAAGTTGAACTTGTGTTGTCTCGAGTCCAAG
13299 ATCCTTCGCTGA
194 ATCCTTCGCTGA
** * *
13311 GAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAGTCAGCCGCCCCTTCGCTGTGA
1 GAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAACCAG-CGTCCCTTCGTTGTGA
*
13376 AGTTGAACTTGTGCTGTCTCGAGTCTAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGA
65 AGTTGAACTTGTGTTGTCTCGAGTCTAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGA
13441 AATTT
130 AATTT
13446 GAAAAAGTTA
Statistics
Matches: 308, Mismatches: 32, Indels: 10
0.88 0.09 0.03
Matches are distributed among these distances:
206 72 0.23
207 117 0.38
208 1 0.00
209 4 0.01
211 1 0.00
212 52 0.17
213 61 0.20
ACGTcount: A:0.22, C:0.18, G:0.24, T:0.35
Consensus pattern (205 bp):
GAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAACCAGCGTCCCTTCGTTGTGAA
GTTGAACTTGTGTTGTCTCGAGTCTAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAA
ATTTTGTTGACAACCAGTCACCCCTTCGTCGTGAAGTTGAACTTGTGTTGTCTCGAGTCCAAGAT
CCTTCGCTGA
Found at i:14021 original size:16 final size:16
Alignment explanation
Indices: 13996--14034 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
13986 AATGTTTATG
**
13996 TTTC-AAGAGAAACTT
1 TTTCAAAGAGAAACGA
14011 TTTCAAAGAGAAACGA
1 TTTCAAAGAGAAACGA
14027 TTTCAAAG
1 TTTCAAAG
14035 GTTTTTCTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 4 0.19
16 17 0.81
ACGTcount: A:0.44, C:0.13, G:0.15, T:0.28
Consensus pattern (16 bp):
TTTCAAAGAGAAACGA
Found at i:14083 original size:36 final size:36
Alignment explanation
Indices: 14030--14104 Score: 116
Period size: 36 Copynumber: 2.1 Consensus size: 36
14020 GAAACGATTT
*
14030 CAAAGGTTTTTCTAAGGGAAACTGTCTCAAGGGAGA
1 CAAAGGTTTTTCTAAGGGAAACTGTCTCAAGAGAGA
*
14066 CAAAGTTTGTTTC-AAGGGAAACTGTCTCAAGAGAGA
1 CAAAGGTT-TTTCTAAGGGAAACTGTCTCAAGAGAGA
14102 CAA
1 CAA
14105 TGGTGGGCAC
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
36 32 0.89
37 4 0.11
ACGTcount: A:0.36, C:0.15, G:0.25, T:0.24
Consensus pattern (36 bp):
CAAAGGTTTTTCTAAGGGAAACTGTCTCAAGAGAGA
Found at i:14789 original size:24 final size:24
Alignment explanation
Indices: 14760--14820 Score: 104
Period size: 24 Copynumber: 2.5 Consensus size: 24
14750 ATATCAAAAA
14760 AAGAGTTTTGAAAGATGTTTAATC
1 AAGAGTTTTGAAAGATGTTTAATC
*
14784 AAGAGTTTTGAAAGATGTTTAATT
1 AAGAGTTTTGAAAGATGTTTAATC
*
14808 AAAAGTTTTGAAA
1 AAGAGTTTTGAAA
14821 ATATTGTCCC
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 35 1.00
ACGTcount: A:0.41, C:0.02, G:0.20, T:0.38
Consensus pattern (24 bp):
AAGAGTTTTGAAAGATGTTTAATC
Found at i:20560 original size:2 final size:2
Alignment explanation
Indices: 20555--20585 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
20545 ATAAAAAATA
20555 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
20586 ATAGAAAAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:20604 original size:8 final size:9
Alignment explanation
Indices: 20555--20606 Score: 51
Period size: 8 Copynumber: 6.3 Consensus size: 9
20545 ATAAAAAATA
20555 ATATAT-AT
1 ATATATAAT
20563 ATATAT-AT
1 ATATATAAT
20571 ATATAT-AT
1 ATATATAAT
20579 ATATATAAT
1 ATATATAAT
* *
20588 AGA-AAAAT
1 ATATATAAT
20596 A-ATATAAT
1 ATATATAAT
20604 ATA
1 ATA
20607 ACGCAAAGTA
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
7 1 0.03
8 32 0.84
9 5 0.13
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (9 bp):
ATATATAAT
Found at i:21172 original size:37 final size:37
Alignment explanation
Indices: 21078--21179 Score: 132
Period size: 37 Copynumber: 2.8 Consensus size: 37
21068 ATGCTTGTGG
* * ** * *
21078 ATCATATCTTTAGGAGTTTAAATAATAGTAGAACTCT
1 ATCATATTTTTAGGAGTTTGAATCCTAGCAAAACTCT
* *
21115 ATCATATTTTTAGGAATTTGAATCCTAGCAAAATTCT
1 ATCATATTTTTAGGAGTTTGAATCCTAGCAAAACTCT
21152 ATCATATTTTTAGGAGTTTGAATCCTAG
1 ATCATATTTTTAGGAGTTTGAATCCTAG
21180 TAGGACGAAA
Statistics
Matches: 56, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
37 56 1.00
ACGTcount: A:0.34, C:0.12, G:0.14, T:0.40
Consensus pattern (37 bp):
ATCATATTTTTAGGAGTTTGAATCCTAGCAAAACTCT
Found at i:22151 original size:26 final size:26
Alignment explanation
Indices: 22121--22186 Score: 87
Period size: 26 Copynumber: 2.5 Consensus size: 26
22111 ATATGTGCAA
* *
22121 TAACAATATTAATATGAAATACTTTG
1 TAACAATATTAATATGAAATACATCG
**
22147 TAACAATACCAATATGAAATACATCG
1 TAACAATATTAATATGAAATACATCG
*
22173 TAACGATATTAATA
1 TAACAATATTAATA
22187 AAAAGTAATA
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
26 33 1.00
ACGTcount: A:0.48, C:0.12, G:0.08, T:0.32
Consensus pattern (26 bp):
TAACAATATTAATATGAAATACATCG
Found at i:22612 original size:20 final size:20
Alignment explanation
Indices: 22589--22628 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
22579 AATTTGGAAA
22589 TCGCAACAC-ATAAGTCAAAT
1 TCGCAACACGA-AAGTCAAAT
*
22609 TCGCAACGCGAAAGTCAAAT
1 TCGCAACACGAAAGTCAAAT
22629 GTTTTTACGC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 17 0.94
21 1 0.06
ACGTcount: A:0.42, C:0.25, G:0.15, T:0.17
Consensus pattern (20 bp):
TCGCAACACGAAAGTCAAAT
Found at i:23080 original size:25 final size:25
Alignment explanation
Indices: 23046--23095 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
23036 ATTATTTTTC
*
23046 CAAATAATGTACCCATAACAATGTT
1 CAAATAATGTACCCACAACAATGTT
23071 CAAATAATGTACCCACAACAATGTT
1 CAAATAATGTACCCACAACAATGTT
23096 TAATTGATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.44, C:0.22, G:0.08, T:0.26
Consensus pattern (25 bp):
CAAATAATGTACCCACAACAATGTT
Found at i:23187 original size:20 final size:20
Alignment explanation
Indices: 23162--23208 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
23152 GTTGAAGGTA
23162 AAATTCGCAACGCGAAAGTC
1 AAATTCGCAACGCGAAAGTC
* * *
23182 AAATTCGCTACGCTATAGTC
1 AAATTCGCAACGCGAAAGTC
23202 AAATTCG
1 AAATTCG
23209 TAATGCTTAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.36, C:0.23, G:0.17, T:0.23
Consensus pattern (20 bp):
AAATTCGCAACGCGAAAGTC
Found at i:23251 original size:34 final size:34
Alignment explanation
Indices: 23213--23306 Score: 143
Period size: 34 Copynumber: 2.8 Consensus size: 34
23203 AATTCGTAAT
*
23213 GCTTATTTCGCGTTGCGAATTTGACTATCGCAAC
1 GCTTATTTCGCGTTGCGAATTTGACTACCGCAAC
* *
23247 GCTTATTTCACGTTGCGAATTCGACTACCGCAAC
1 GCTTATTTCGCGTTGCGAATTTGACTACCGCAAC
* *
23281 GCTTATTTCGTGTTGCAAATTTGACT
1 GCTTATTTCGCGTTGCGAATTTGACT
23307 TTCGTGTGCG
Statistics
Matches: 53, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
34 53 1.00
ACGTcount: A:0.21, C:0.23, G:0.19, T:0.36
Consensus pattern (34 bp):
GCTTATTTCGCGTTGCGAATTTGACTACCGCAAC
Found at i:23311 original size:20 final size:20
Alignment explanation
Indices: 23286--23334 Score: 73
Period size: 19 Copynumber: 2.5 Consensus size: 20
23276 GCAACGCTTA
23286 TTTCGTGTTGCAAATTTGAC
1 TTTCGTGTTGCAAATTTGAC
* *
23306 TTTCGTG-TGCGAATTTGAT
1 TTTCGTGTTGCAAATTTGAC
23325 TTTCGTGTTG
1 TTTCGTGTTG
23335 ATCTCAACAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
19 17 0.65
20 9 0.35
ACGTcount: A:0.14, C:0.12, G:0.24, T:0.49
Consensus pattern (20 bp):
TTTCGTGTTGCAAATTTGAC
Found at i:25937 original size:24 final size:24
Alignment explanation
Indices: 25910--25956 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
25900 CAAAATCTGA
25910 GTATTGACCAAGATCAAAGTTTGG
1 GTATTGACCAAGATCAAAGTTTGG
*
25934 GTATTGACCAAGATCAAATTTTG
1 GTATTGACCAAGATCAAAGTTTG
25957 AATACTGACT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.34, C:0.13, G:0.21, T:0.32
Consensus pattern (24 bp):
GTATTGACCAAGATCAAAGTTTGG
Found at i:25965 original size:24 final size:24
Alignment explanation
Indices: 25914--25965 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
25904 ATCTGAGTAT
** *
25914 TGACCAAGATCAAAGTTTGGGTAT
1 TGACCAAGATCAAAGTTTGAATAC
*
25938 TGACCAAGATCAAATTTTGAATAC
1 TGACCAAGATCAAAGTTTGAATAC
25962 TGAC
1 TGAC
25966 TAGTACTCAC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.37, C:0.15, G:0.19, T:0.29
Consensus pattern (24 bp):
TGACCAAGATCAAAGTTTGAATAC
Found at i:33265 original size:27 final size:27
Alignment explanation
Indices: 33194--33283 Score: 85
Period size: 27 Copynumber: 3.3 Consensus size: 27
33184 TTTTTAGTTT
*
33194 TTTATTTATTTATTACTATTATATATATC
1 TTTA-TTA-TTATTACCATTATATATATC
* * * *
33223 TTT-TTATTTTTCCCATTGTTTATATC
1 TTTATTATTATTACCATTATATATATC
*
33249 TTTATTATTATTACCATCATATATATTC
1 TTTATTATTATTACCATTATATATA-TC
33277 TTT-TTAT
1 TTTATTAT
33284 ATTCTATATT
Statistics
Matches: 49, Mismatches: 10, Indels: 6
0.75 0.15 0.09
Matches are distributed among these distances:
26 18 0.37
27 23 0.47
28 5 0.10
29 3 0.06
ACGTcount: A:0.26, C:0.11, G:0.01, T:0.62
Consensus pattern (27 bp):
TTTATTATTATTACCATTATATATATC
Found at i:43737 original size:49 final size:50
Alignment explanation
Indices: 43665--43760 Score: 149
Period size: 49 Copynumber: 1.9 Consensus size: 50
43655 AATACTTCGC
* * *
43665 TTAGGATGAAAACCCGAGAGGGCGTCCTAAGTTGAAAAAA-AAAAAACGT
1 TTAGGATGAAAACCCGAAAGGGCGCCCTAAATTGAAAAAAGAAAAAACGT
*
43714 TTAGGGTGAAAACCCGAAAGGGCGCCCTAAATTGAAAAAAGAAAAAA
1 TTAGGATGAAAACCCGAAAGGGCGCCCTAAATTGAAAAAAGAAAAAA
43761 AAAAGAGAAA
Statistics
Matches: 42, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
49 36 0.86
50 6 0.14
ACGTcount: A:0.47, C:0.15, G:0.24, T:0.15
Consensus pattern (50 bp):
TTAGGATGAAAACCCGAAAGGGCGCCCTAAATTGAAAAAAGAAAAAACGT
Found at i:44696 original size:105 final size:105
Alignment explanation
Indices: 44514--45182 Score: 1257
Period size: 105 Copynumber: 6.4 Consensus size: 105
44504 AGGTTTTACC
44514 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
* * * *
44579 ACGAAGGGACCGCTGGTTGTCTACAAGCGTTTCTCAAATT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAGATT
44619 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
44684 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAGATT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAGATT
44724 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
*
44789 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAGATT
44829 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
44894 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAGATT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAGATT
44934 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
* *
44999 ACGAAGGGACCGCTGGTTGTCTACAAGCATTTCTCAGATT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAGATT
*
45039 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAGCTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
*
45104 ATGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAGATT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAGATT
45144 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACT
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACT
45183 AAAAAATAAC
Statistics
Matches: 552, Mismatches: 12, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
105 552 1.00
ACGTcount: A:0.33, C:0.25, G:0.19, T:0.22
Consensus pattern (105 bp):
CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAGATT
Found at i:47135 original size:30 final size:30
Alignment explanation
Indices: 47073--47135 Score: 76
Period size: 30 Copynumber: 2.1 Consensus size: 30
47063 ATAAACATAT
*
47073 TTTTTTCTTTTATTATGTATATTCTTTATA
1 TTTTTTCTTTTATTATGTATATTATTTATA
*
47103 TTTTTT-TTTTACTGTATGTAT-TTATTTTTA
1 TTTTTTCTTTTA-T-TATGTATATTATTTATA
47133 TTT
1 TTT
47136 ATCTCTATAC
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
29 5 0.17
30 17 0.59
31 7 0.24
ACGTcount: A:0.17, C:0.05, G:0.05, T:0.73
Consensus pattern (30 bp):
TTTTTTCTTTTATTATGTATATTATTTATA
Found at i:47490 original size:27 final size:27
Alignment explanation
Indices: 47419--47508 Score: 85
Period size: 27 Copynumber: 3.3 Consensus size: 27
47409 TTTTTAGTTT
*
47419 TTTATTTATTTATTACTATTATATATATC
1 TTTA-TTA-TTATTACCATTATATATATC
* * * *
47448 TTT-TTATTTTTCCCATTGTTTATATC
1 TTTATTATTATTACCATTATATATATC
*
47474 TTTATTATTATTACCATCATATATATTC
1 TTTATTATTATTACCATTATATATA-TC
47502 TTT-TTAT
1 TTTATTAT
47509 ATTCTATATT
Statistics
Matches: 49, Mismatches: 10, Indels: 6
0.75 0.15 0.09
Matches are distributed among these distances:
26 18 0.37
27 23 0.47
28 5 0.10
29 3 0.06
ACGTcount: A:0.26, C:0.11, G:0.01, T:0.62
Consensus pattern (27 bp):
TTTATTATTATTACCATTATATATATC
Found at i:53796 original size:29 final size:29
Alignment explanation
Indices: 53754--53828 Score: 96
Period size: 29 Copynumber: 2.6 Consensus size: 29
53744 AACCCAACCA
**
53754 TAGGTCGCCATGCACTCCCAGCGACCTCC
1 TAGGTCGCCATGCACTCCCAGCGACCAAC
* * *
53783 TAGGTCGCCATGCACGCCCGGCGACCAAG
1 TAGGTCGCCATGCACTCCCAGCGACCAAC
*
53812 GAGGTCGCCATGCACTC
1 TAGGTCGCCATGCACTC
53829 GGGGCGACCA
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 39 1.00
ACGTcount: A:0.19, C:0.40, G:0.27, T:0.15
Consensus pattern (29 bp):
TAGGTCGCCATGCACTCCCAGCGACCAAC
Found at i:53834 original size:29 final size:29
Alignment explanation
Indices: 53755--53842 Score: 95
Period size: 29 Copynumber: 3.0 Consensus size: 29
53745 ACCCAACCAT
* * ****
53755 AGGTCGCCATGCACTCCCAGCGACCTCCT
1 AGGTCGCCATGCACGCCCGGCGACCAAGG
53784 AGGTCGCCATGCACGCCCGGCGACCAAGG
1 AGGTCGCCATGCACGCCCGGCGACCAAGG
* **
53813 AGGTCGCCATGCACTCGGGGCGACCAAGG
1 AGGTCGCCATGCACGCCCGGCGACCAAGG
53842 A
1 A
53843 TTCATGCATG
Statistics
Matches: 50, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 50 1.00
ACGTcount: A:0.20, C:0.38, G:0.31, T:0.11
Consensus pattern (29 bp):
AGGTCGCCATGCACGCCCGGCGACCAAGG
Found at i:54094 original size:29 final size:29
Alignment explanation
Indices: 54059--54145 Score: 120
Period size: 29 Copynumber: 3.0 Consensus size: 29
54049 GTTGGCTGGT
*
54059 AGGTCGCAGGGCATGCATGGCGACCTACC
1 AGGTCGCAGGGCGTGCATGGCGACCTACC
* ***
54088 AGGTCGCTGGGCGTGCATGGCGACCTGGT
1 AGGTCGCAGGGCGTGCATGGCGACCTACC
*
54117 AGGTCGCCGGGCGTGCATGGCGACCTACC
1 AGGTCGCAGGGCGTGCATGGCGACCTACC
54146 CCGGTACTGT
Statistics
Matches: 49, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
29 49 1.00
ACGTcount: A:0.15, C:0.30, G:0.39, T:0.16
Consensus pattern (29 bp):
AGGTCGCAGGGCGTGCATGGCGACCTACC
Found at i:60439 original size:2 final size:2
Alignment explanation
Indices: 60434--60469 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
60424 GCATAGAATA
60434 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
60470 TGAGTGAAAC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:61687 original size:21 final size:21
Alignment explanation
Indices: 61650--61713 Score: 87
Period size: 19 Copynumber: 3.1 Consensus size: 21
61640 TTAAAGATAT
61650 TTTTTTATAAATATTTTTTTA
1 TTTTTTATAAATATTTTTTTA
61671 --TTTTATAAATATTTTTTTA
1 TTTTTTATAAATATTTTTTTA
* *
61690 TTTTTTATTAAATGTTTTTATA
1 TTTTTTA-TAAATATTTTTTTA
61712 TT
1 TT
61714 AAATTTATAA
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
19 19 0.50
21 5 0.13
22 14 0.37
ACGTcount: A:0.28, C:0.00, G:0.02, T:0.70
Consensus pattern (21 bp):
TTTTTTATAAATATTTTTTTA
Found at i:62378 original size:23 final size:23
Alignment explanation
Indices: 62352--62411 Score: 102
Period size: 23 Copynumber: 2.6 Consensus size: 23
62342 ATAGCGAAAT
*
62352 TAACATTTTCGGTAAGAAAAAAG
1 TAACATTTTAGGTAAGAAAAAAG
*
62375 TAACATTTTAAGTAAGAAAAAAG
1 TAACATTTTAGGTAAGAAAAAAG
62398 TAACATTTTAGGTA
1 TAACATTTTAGGTA
62412 GCGCTCTACT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.48, C:0.07, G:0.15, T:0.30
Consensus pattern (23 bp):
TAACATTTTAGGTAAGAAAAAAG
Found at i:66804 original size:62 final size:62
Alignment explanation
Indices: 66707--66842 Score: 245
Period size: 62 Copynumber: 2.2 Consensus size: 62
66697 ACTTTGTCCC
*
66707 ACAGCTCATGTTACTCTTTGGCATCAAAGGTCATTCAAGCACTAAACACGACCAATTCACCT
1 ACAGCCCATGTTACTCTTTGGCATCAAAGGTCATTCAAGCACTAAACACGACCAATTCACCT
* *
66769 ACAGCCCATGTTACTCTTTGGCATCTAAGGTCATTCAAGCACTAAACATGACCAATTCACCT
1 ACAGCCCATGTTACTCTTTGGCATCAAAGGTCATTCAAGCACTAAACACGACCAATTCACCT
66831 ACAGCCCATGTT
1 ACAGCCCATGTT
66843 CTCATCAACT
Statistics
Matches: 71, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
62 71 1.00
ACGTcount: A:0.31, C:0.29, G:0.13, T:0.26
Consensus pattern (62 bp):
ACAGCCCATGTTACTCTTTGGCATCAAAGGTCATTCAAGCACTAAACACGACCAATTCACCT
Found at i:76856 original size:32 final size:32
Alignment explanation
Indices: 76819--76882 Score: 128
Period size: 32 Copynumber: 2.0 Consensus size: 32
76809 AATTAGGTTA
76819 GAGTCGCCACCGATCATTTTAAAAACATTTAG
1 GAGTCGCCACCGATCATTTTAAAAACATTTAG
76851 GAGTCGCCACCGATCATTTTAAAAACATTTAG
1 GAGTCGCCACCGATCATTTTAAAAACATTTAG
76883 ATGGATCGAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.34, C:0.22, G:0.16, T:0.28
Consensus pattern (32 bp):
GAGTCGCCACCGATCATTTTAAAAACATTTAG
Found at i:77204 original size:2 final size:2
Alignment explanation
Indices: 77197--77241 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
77187 GGCGAAAATA
77197 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
77239 AT A
1 AT A
77242 AAGAAAAACA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:78435 original size:73 final size:73
Alignment explanation
Indices: 78358--78713 Score: 488
Period size: 73 Copynumber: 4.9 Consensus size: 73
78348 TAATAAAATA
* *
78358 AAAATATTTTCAAAAACCTATAT-A-ATATATACTTTTAAAAATATTTTAAAAACTATATATTAT
1 AAAATATTTT-AAAAA-CTATATAATATATATATTTTTAAAAATGTTTTAAAAACTATATATTAT
78421 ATTTA-TTTC
64 ATTTATTTTC
* * *
78430 TAAAATATTTTAAAAACTATATAATATATATACTTTTAAAAATATTTTAAAAATTATATATTATA
1 -AAAATATTTTAAAAACTATATAATATATATATTTTTAAAAATGTTTTAAAAACTATATATTATA
*
78495 TTTATTTTA
65 TTTATTTTC
* *
78504 AAAATGTCTTAAAAACTATAT-A-ATATATATTTTTAAAAATGTTTTAAAAACTATATATTATAT
1 AAAATATTTTAAAAACTATATAATATATATATTTTTAAAAATGTTTTAAAAACTATATATTATAT
78567 TTATTTTC
66 TTATTTTC
* * * **
78575 AAAATGTTTTAAAAACTGTATAATATATATATTTTTTAAAATGTTTTAAAAGTTATATATTATAT
1 AAAATATTTTAAAAACTATATAATATATATATTTTTAAAAATGTTTTAAAAACTATATATTATAT
78640 TTATTTTC
66 TTATTTTC
* * * *
78648 AAAATGTTTTAAAAATTATATAATATATATATTTTTCAAACATGTTTTCAAAACTATATATTATA
1 AAAATATTTTAAAAACTATATAATATATATATTTTT-AAAAATGTTTTAAAAACTATATATTATA
78713 T
65 T
78714 ATATGTTTTT
Statistics
Matches: 257, Mismatches: 20, Indels: 11
0.89 0.07 0.04
Matches are distributed among these distances:
71 70 0.27
72 8 0.03
73 152 0.59
74 27 0.11
ACGTcount: A:0.46, C:0.05, G:0.02, T:0.47
Consensus pattern (73 bp):
AAAATATTTTAAAAACTATATAATATATATATTTTTAAAAATGTTTTAAAAACTATATATTATAT
TTATTTTC
Found at i:78557 original size:144 final size:144
Alignment explanation
Indices: 78369--78713 Score: 521
Period size: 144 Copynumber: 2.4 Consensus size: 144
78359 AAATATTTTC
* *
78369 AAAAACCTATATAATATATACTTTTAAAAATATTTTAAAAACTATATATTATATTTA-TTTCTAA
1 AAAAA-CTATATAATATATATTTTTAAAAATGTTTTAAAAACTATATATTATATTTATTTTC-AA
78433 AATATTTTAAAAACTATATAATATATATACTTTTAAAAATATTTTAAAAATTATATATTATATTT
64 AATATTTTAAAAACTATATAATATATATACTTTTAAAAATATTTTAAAAATTATATATTATATTT
78498 ATTTTAAAAATGTCTT
129 ATTTTAAAAATGTCTT
78514 AAAAACTATATAATATATATTTTTAAAAATGTTTTAAAAACTATATATTATATTTATTTTCAAAA
1 AAAAACTATATAATATATATTTTTAAAAATGTTTTAAAAACTATATATTATATTTATTTTCAAAA
* * * * * *
78579 TGTTTTAAAAACTGTATAATATATATATTTTTTAAAATGTTTTAAAAGTTATATATTATATTTAT
66 TATTTTAAAAACTATATAATATATATACTTTTAAAAATATTTTAAAAATTATATATTATATTTAT
* *
78644 TTTCAAAATGTTTT
131 TTTAAAAATGTCTT
* * *
78658 AAAAATTATATAATATATATATTTTTCAAACATGTTTTCAAAACTATATATTATAT
1 AAAAACTATAT-A-ATATATATTTTT-AAAAATGTTTTAAAAACTATATATTATAT
78714 ATATGTTTTT
Statistics
Matches: 183, Mismatches: 13, Indels: 6
0.91 0.06 0.03
Matches are distributed among these distances:
144 134 0.73
145 10 0.05
146 12 0.07
147 27 0.15
ACGTcount: A:0.46, C:0.05, G:0.02, T:0.47
Consensus pattern (144 bp):
AAAAACTATATAATATATATTTTTAAAAATGTTTTAAAAACTATATATTATATTTATTTTCAAAA
TATTTTAAAAACTATATAATATATATACTTTTAAAAATATTTTAAAAATTATATATTATATTTAT
TTTAAAAATGTCTT
Found at i:78714 original size:36 final size:35
Alignment explanation
Indices: 78358--78715 Score: 376
Period size: 36 Copynumber: 9.9 Consensus size: 35
78348 TAATAAAATA
* * * *
78358 AAAATATTTTCAAAAACCTATATAATATATACTTTTA
1 AAAATGTTTT-AAAAA-CTATATATTATATATTTTTC
*
78395 AAAATATTTTAAAAACTATATATTATAT-TTATTTC
1 AAAATGTTTTAAAAACTATATATTATATATT-TTTC
* * *
78430 TAAAATATTTTAAAAACTATATAATATATATACTTTTA
1 -AAAATGTTTTAAAAACTATAT-AT-TATATATTTTTC
* * * *
78468 AAAATATTTTAAAAATTATATATTATATTTATTTTA
1 AAAATGTTTTAAAAACTATATATTATATAT-TTTTC
* * *
78504 AAAATGTCTTAAAAACTATATAATATATATTTTTA
1 AAAATGTTTTAAAAACTATATATTATATATTTTTC
*
78539 AAAATGTTTTAAAAACTATATATTATATTTATTTTC
1 AAAATGTTTTAAAAACTATATATTATATAT-TTTTC
* *
78575 AAAATGTTTTAAAAACTGTATAATATATATATTTTTT
1 AAAATGTTTTAAAAACTATAT-AT-TATATATTTTTC
** *
78612 AAAATGTTTTAAAAGTTATATATTATATTTATTTTC
1 AAAATGTTTTAAAAACTATATATTATATAT-TTTTC
*
78648 AAAATGTTTTAAAAATTATATAATATATATATTTTTC
1 AAAATGTTTTAAAAACTATAT-AT-TATATATTTTTC
*
78685 AAACATGTTTTCAAAACTATATATTATATAT
1 AAA-ATGTTTTAAAAACTATATATTATATAT
78716 ATGTTTTTTT
Statistics
Matches: 279, Mismatches: 29, Indels: 27
0.83 0.09 0.08
Matches are distributed among these distances:
34 1 0.00
35 58 0.21
36 115 0.41
37 68 0.24
38 36 0.13
39 1 0.00
ACGTcount: A:0.46, C:0.05, G:0.02, T:0.47
Consensus pattern (35 bp):
AAAATGTTTTAAAAACTATATATTATATATTTTTC
Found at i:84437 original size:58 final size:57
Alignment explanation
Indices: 84373--84488 Score: 196
Period size: 58 Copynumber: 2.0 Consensus size: 57
84363 AAACCTACAA
84373 AAAAATAATTTTATGTATGATTTTGAAAATAATAATAATAAATAACTAAAATAGAAAC
1 AAAAATAATTTTATGTATGATTTTGAAAA-AATAATAATAAATAACTAAAATAGAAAC
* * *
84431 AAAAATAATTTTATGTATGATTTTGAAAAAATAATAATAAATGATTACAATAGAAAC
1 AAAAATAATTTTATGTATGATTTTGAAAAAATAATAATAAATAACTAAAATAGAAAC
84488 A
1 A
84489 CGAGAATAAG
Statistics
Matches: 55, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
57 26 0.47
58 29 0.53
ACGTcount: A:0.56, C:0.03, G:0.08, T:0.33
Consensus pattern (57 bp):
AAAAATAATTTTATGTATGATTTTGAAAAAATAATAATAAATAACTAAAATAGAAAC
Found at i:98195 original size:49 final size:46
Alignment explanation
Indices: 98099--98207 Score: 119
Period size: 49 Copynumber: 2.3 Consensus size: 46
98089 AATAAGTTAA
*
98099 AAAAAAATAAGTATATACTACATTAAAAAAAATATCAAAGTACACT
1 AAAAAAATAAGTATAAACTACATTAAAAAAAATATCAAAGTACACT
* * * * * *
98145 AAAAAAATATGTATACAATTACATTAAAAGTTAAATGTCAAATTATACT
1 AAAAAAATAAGTATA-AACTACATTAAAA--AAAATATCAAAGTACACT
*
98194 AAAAAAGTAAGTAT
1 AAAAAAATAAGTAT
98208 CGTATTACAT
Statistics
Matches: 51, Mismatches: 9, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
46 14 0.27
47 11 0.22
49 26 0.51
ACGTcount: A:0.58, C:0.08, G:0.06, T:0.28
Consensus pattern (46 bp):
AAAAAAATAAGTATAAACTACATTAAAAAAAATATCAAAGTACACT
Found at i:98568 original size:26 final size:26
Alignment explanation
Indices: 98530--98583 Score: 63
Period size: 26 Copynumber: 2.1 Consensus size: 26
98520 AAAGCATTTT
* * * *
98530 AATTAGTAGTATATATCAGTGTATTA
1 AATTAATAATATATATCAATGTACTA
*
98556 AATTAATAATATATTTCAATGTACTA
1 AATTAATAATATATATCAATGTACTA
98582 AA
1 AA
98584 CTTTAGCAAA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.44, C:0.06, G:0.09, T:0.41
Consensus pattern (26 bp):
AATTAATAATATATATCAATGTACTA
Found at i:98665 original size:19 final size:18
Alignment explanation
Indices: 98627--98662 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
98617 ATAAATGAAT
98627 CTAATTTAATAAAAAAAA
1 CTAATTTAATAAAAAAAA
*
98645 CTAATTTAGTAAAAAAAA
1 CTAATTTAATAAAAAAAA
98663 ACTGAATTGG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.64, C:0.06, G:0.03, T:0.28
Consensus pattern (18 bp):
CTAATTTAATAAAAAAAA
Found at i:100692 original size:16 final size:15
Alignment explanation
Indices: 100671--100700 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
100661 ATCAATTTAA
100671 TTTTTATTAACTTTTT
1 TTTTTATTAA-TTTTT
100687 TTTTTATTAATTTT
1 TTTTTATTAATTTT
100701 GATTATCAGT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.20, C:0.03, G:0.00, T:0.77
Consensus pattern (15 bp):
TTTTTATTAATTTTT
Found at i:101758 original size:17 final size:18
Alignment explanation
Indices: 101736--101769 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
101726 TCTTTAAGTT
101736 ATATTTTATTA-TGTTTA
1 ATATTTTATTAGTGTTTA
*
101753 ATATTTTGTTAGTGTTT
1 ATATTTTATTAGTGTTT
101770 TATTTAACTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.24, C:0.00, G:0.12, T:0.65
Consensus pattern (18 bp):
ATATTTTATTAGTGTTTA
Found at i:101791 original size:16 final size:16
Alignment explanation
Indices: 101772--101803 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
101762 TAGTGTTTTA
101772 TTTAACTATTTAATTT
1 TTTAACTATTTAATTT
*
101788 TTTAACTATTTTATTT
1 TTTAACTATTTAATTT
101804 AATTAATTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.28, C:0.06, G:0.00, T:0.66
Consensus pattern (16 bp):
TTTAACTATTTAATTT
Found at i:115686 original size:6 final size:6
Alignment explanation
Indices: 115675--115705 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
115665 TCGGCACGGC
115675 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG T
1 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG T
115706 AATACGTGTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.00, C:0.16, G:0.48, T:0.35
Consensus pattern (6 bp):
TCGTGG
Found at i:116880 original size:605 final size:605
Alignment explanation
Indices: 115730--116940 Score: 2422
Period size: 605 Copynumber: 2.0 Consensus size: 605
115720 ACACGTCCGC
115730 GCGAACACTATCTTTTTAGAGAAAATTCTTGAGGAATTTCCTTTGAAAGAAACAAATGGAAAAAT
1 GCGAACACTATCTTTTTAGAGAAAATTCTTGAGGAATTTCCTTTGAAAGAAACAAATGGAAAAAT
115795 GTGAAAGATTTCAGCTGCTGAGGACTGTTTAATTTCAAATGATAACAGCTGGTTTATGAGAGTTA
66 GTGAAAGATTTCAGCTGCTGAGGACTGTTTAATTTCAAATGATAACAGCTGGTTTATGAGAGTTA
115860 TCAGAAATTAAACAACTTTTCCTAAATTAAATCAAAAACGTTAAGATGTATCTGGACTGATTTCC
131 TCAGAAATTAAACAACTTTTCCTAAATTAAATCAAAAACGTTAAGATGTATCTGGACTGATTTCC
115925 AGCTTTGTAGAGAGAAGACAAGCTGATAATATCAGGAGTTACAGGAGTTATTTGATTTAATTCCA
196 AGCTTTGTAGAGAGAAGACAAGCTGATAATATCAGGAGTTACAGGAGTTATTTGATTTAATTCCA
115990 TGGGTTACATGATATAATTTCGGGAGTTATAACAACTGAACAATGATGCAATGAACCTGGACTAT
261 TGGGTTACATGATATAATTTCGGGAGTTATAACAACTGAACAATGATGCAATGAACCTGGACTAT
116055 TTTTTAGTCAGGTTCATCTAGACGTTTCAGCTGTTACAAAAGAAGAGATTTAATCCTGAAATTTT
326 TTTTTAGTCAGGTTCATCTAGACGTTTCAGCTGTTACAAAAGAAGAGATTTAATCCTGAAATTTT
116120 ATGGACGATTTTAACCATATTTATAGCCTATAAATAGAGGGTTATATTCAGCTTTTCAACTCACT
391 ATGGACGATTTTAACCATATTTATAGCCTATAAATAGAGGGTTATATTCAGCTTTTCAACTCACT
116185 CCCAAACATTCACAATTCACTTACAAAAGTGTTTTCTACAGTTCTCTATATGAGTTCTCTCTGAG
456 CCCAAACATTCACAATTCACTTACAAAAGTGTTTTCTACAGTTCTCTATATGAGTTCTCTCTGAG
116250 TGCTTTCCAATTAAAAAAGCAATACCACCAGCAGTCCACTCCGGTTTCGGGGGTACGGAATTCGG
521 TGCTTTCCAATTAAAAAAGCAATACCACCAGCAGTCCACTCCGGTTTCGGGGGTACGGAATTCGG
116315 AGCGACCGTGTTAACCTCGG
586 AGCGACCGTGTTAACCTCGG
116335 GCGAACACTATCTTTTTAGAGAAAATTCTTGAGGAATTTCCTTTGAAAGAAACAAATGGAAAAAT
1 GCGAACACTATCTTTTTAGAGAAAATTCTTGAGGAATTTCCTTTGAAAGAAACAAATGGAAAAAT
116400 GTGAAAGATTTCAGCTGCTGAGGACTGTTTAATTTCAAATGATAACAGCTGGTTTATGAGAGTTA
66 GTGAAAGATTTCAGCTGCTGAGGACTGTTTAATTTCAAATGATAACAGCTGGTTTATGAGAGTTA
116465 TCAGAAATTAAACAACTTTTCCTAAATTAAATCAAAAACGTTAAGATGTATCTGGACTGATTTCC
131 TCAGAAATTAAACAACTTTTCCTAAATTAAATCAAAAACGTTAAGATGTATCTGGACTGATTTCC
116530 AGCTTTGTAGAGAGAAGACAAGCTGATAATATCAGGAGTTACAGGAGTTATTTGATTTAATTCCA
196 AGCTTTGTAGAGAGAAGACAAGCTGATAATATCAGGAGTTACAGGAGTTATTTGATTTAATTCCA
116595 TGGGTTACATGATATAATTTCGGGAGTTATAACAACTGAACAATGATGCAATGAACCTGGACTAT
261 TGGGTTACATGATATAATTTCGGGAGTTATAACAACTGAACAATGATGCAATGAACCTGGACTAT
116660 TTTTTAGTCAGGTTCATCTAGACGTTTCAGCTGTTACAAAAGAAGAGATTTAATCCTGAAATTTT
326 TTTTTAGTCAGGTTCATCTAGACGTTTCAGCTGTTACAAAAGAAGAGATTTAATCCTGAAATTTT
116725 ATGGACGATTTTAACCATATTTATAGCCTATAAATAGAGGGTTATATTCAGCTTTTCAACTCACT
391 ATGGACGATTTTAACCATATTTATAGCCTATAAATAGAGGGTTATATTCAGCTTTTCAACTCACT
116790 CCCAAACATTCACAATTCACTTACAAAAGTGTTTTCTACAGTTCTCTATATGAGTTCTCTCTGAG
456 CCCAAACATTCACAATTCACTTACAAAAGTGTTTTCTACAGTTCTCTATATGAGTTCTCTCTGAG
116855 TGCTTTCCAATTAAAAAAGCAATACCACCAGCAGTCCACTCCGGTTTCGGGGGTACGGAATTCGG
521 TGCTTTCCAATTAAAAAAGCAATACCACCAGCAGTCCACTCCGGTTTCGGGGGTACGGAATTCGG
116920 AGCGACCGTGTTAACCTCGG
586 AGCGACCGTGTTAACCTCGG
116940 G
1 G
116941 GGACGGTCCG
Statistics
Matches: 606, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
605 606 1.00
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Consensus pattern (605 bp):
GCGAACACTATCTTTTTAGAGAAAATTCTTGAGGAATTTCCTTTGAAAGAAACAAATGGAAAAAT
GTGAAAGATTTCAGCTGCTGAGGACTGTTTAATTTCAAATGATAACAGCTGGTTTATGAGAGTTA
TCAGAAATTAAACAACTTTTCCTAAATTAAATCAAAAACGTTAAGATGTATCTGGACTGATTTCC
AGCTTTGTAGAGAGAAGACAAGCTGATAATATCAGGAGTTACAGGAGTTATTTGATTTAATTCCA
TGGGTTACATGATATAATTTCGGGAGTTATAACAACTGAACAATGATGCAATGAACCTGGACTAT
TTTTTAGTCAGGTTCATCTAGACGTTTCAGCTGTTACAAAAGAAGAGATTTAATCCTGAAATTTT
ATGGACGATTTTAACCATATTTATAGCCTATAAATAGAGGGTTATATTCAGCTTTTCAACTCACT
CCCAAACATTCACAATTCACTTACAAAAGTGTTTTCTACAGTTCTCTATATGAGTTCTCTCTGAG
TGCTTTCCAATTAAAAAAGCAATACCACCAGCAGTCCACTCCGGTTTCGGGGGTACGGAATTCGG
AGCGACCGTGTTAACCTCGG
Found at i:123862 original size:3 final size:3
Alignment explanation
Indices: 123856--123904 Score: 64
Period size: 3 Copynumber: 16.7 Consensus size: 3
123846 CTTTTTTTAA
** *
123856 TAT TAT TAT TAT TAT CGT TA- TAT TAT TAT TAT TAC TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
123903 TA
1 TA
123905 ATTTACAAAT
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
2 2 0.05
3 37 0.95
ACGTcount: A:0.33, C:0.04, G:0.02, T:0.61
Consensus pattern (3 bp):
TAT
Found at i:125913 original size:22 final size:22
Alignment explanation
Indices: 125888--125931 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
125878 TCAAACGATG
*
125888 CAATGTGTGTTATTTTAAGTGA
1 CAATGTATGTTATTTTAAGTGA
* * *
125910 CAATTTATTTTATTTTATGTGA
1 CAATGTATGTTATTTTAAGTGA
125932 ATGTAAATTT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.27, C:0.05, G:0.16, T:0.52
Consensus pattern (22 bp):
CAATGTATGTTATTTTAAGTGA
Found at i:127513 original size:32 final size:32
Alignment explanation
Indices: 127454--127515 Score: 81
Period size: 32 Copynumber: 1.9 Consensus size: 32
127444 TCTTACCTGT
*
127454 ACTAACTAATTTCTTTTCTTTTCTTTGTGTGC
1 ACTAACTAATTTATTTTCTTTTCTTTGTGTGC
* *
127486 ACTAACTTATTTATTTT-TTGTTGTTTGTGT
1 ACTAACTAATTTATTTTCTT-TTCTTTGTGT
127516 CTTTTTTTCA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
31 2 0.08
32 24 0.92
ACGTcount: A:0.16, C:0.13, G:0.11, T:0.60
Consensus pattern (32 bp):
ACTAACTAATTTATTTTCTTTTCTTTGTGTGC
Found at i:131126 original size:4 final size:4
Alignment explanation
Indices: 131117--131202 Score: 158
Period size: 4 Copynumber: 22.0 Consensus size: 4
131107 AAAAGTATAC
131117 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
131165 ACAT ACAT ACAT ACAT ACAT AC-- ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
131203 GATACATAAA
Statistics
Matches: 80, Mismatches: 0, Indels: 4
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.03
4 78 0.98
ACGTcount: A:0.50, C:0.26, G:0.00, T:0.24
Consensus pattern (4 bp):
ACAT
Found at i:131851 original size:105 final size:105
Alignment explanation
Indices: 131664--131853 Score: 285
Period size: 105 Copynumber: 1.8 Consensus size: 105
131654 TGAGAATTTT
* *
131664 AAAACAAATTGCGTCTCGCTTGAGACATTTTTCCTTTGAGATACAAATTTTGAATTTGATTCACT
1 AAAACAAATTGCGTCTCGCTTGAGACATTTTCCCTTTGAGATACAAATTTCGAATTTGATTCACT
131729 TAAAACAAAATTAATCTCACCTTAGATTGTTGTTTCTTTC
66 TAAAACAAAATTAATCTCACCTTAGATTGTTGTTTCTTTC
* * *
131769 AAAACAAATTTCGTCTCGCTTGAGACCTTTTCCCTTTGAGATCCAAATTTCGAATTTG-TTACAC
1 AAAACAAATTGCGTCTCGCTTGAGACATTTTCCCTTTGAGATACAAATTTCGAATTTGATT-CAC
* *
131833 ATT-AAACAAAGTTGATCTCAC
65 -TTAAAACAAAATTAATCTCAC
131854 TTGAGATCGT
Statistics
Matches: 76, Mismatches: 7, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
104 2 0.03
105 72 0.95
106 2 0.03
ACGTcount: A:0.32, C:0.19, G:0.12, T:0.37
Consensus pattern (105 bp):
AAAACAAATTGCGTCTCGCTTGAGACATTTTCCCTTTGAGATACAAATTTCGAATTTGATTCACT
TAAAACAAAATTAATCTCACCTTAGATTGTTGTTTCTTTC
Found at i:131893 original size:36 final size:36
Alignment explanation
Indices: 131848--131967 Score: 111
Period size: 36 Copynumber: 3.4 Consensus size: 36
131838 ACAAAGTTGA
** *
131848 TCTCACTTGAGATCGTTTTCTC-AAAAATAAACTTTG
1 TCTCACTTGAGA-CAATTTCTCTAAAAACAAACTTTG
* *
131884 TCTCGCTTGAGACAATTTCTCTAAAAACAAATTTTG
1 TCTCACTTGAGACAATTTCTCTAAAAACAAACTTTG
* * * * *
131920 TCTCATTTGAGACTATATCT-T-AAAGCAAATTTTG
1 TCTCACTTGAGACAATTTCTCTAAAAACAAACTTTG
*
131954 TCTCGCTTGAGACA
1 TCTCACTTGAGACA
131968 TCATTTTCTC
Statistics
Matches: 70, Mismatches: 13, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
34 23 0.33
35 8 0.11
36 39 0.56
ACGTcount: A:0.31, C:0.19, G:0.12, T:0.38
Consensus pattern (36 bp):
TCTCACTTGAGACAATTTCTCTAAAAACAAACTTTG
Found at i:132250 original size:28 final size:28
Alignment explanation
Indices: 132212--132315 Score: 129
Period size: 28 Copynumber: 3.6 Consensus size: 28
132202 TCTTGAGACA
* * *
132212 GTTTCTCTTGAGATAAATCTTTGAGTCT
1 GTTTCTTTTGAAAAAAATCTTTGAGTCT
*
132240 GTTCCTTTTGAAAAAAATCTTTGAGT-T
1 GTTTCTTTTGAAAAAAATCTTTGAGTCT
132267 GTTTCTTTTGAAACAAAAATCTTTGAGTCT
1 GTTTCTTTTG-AA-AAAAATCTTTGAGTCT
*
132297 GTTTCTTTGGAAACAAAAT
1 GTTTCTTTTGAAA-AAAAT
132316 TTGGTCTCTC
Statistics
Matches: 66, Mismatches: 6, Indels: 7
0.84 0.08 0.09
Matches are distributed among these distances:
27 10 0.15
28 25 0.38
29 21 0.32
30 10 0.15
ACGTcount: A:0.29, C:0.12, G:0.15, T:0.43
Consensus pattern (28 bp):
GTTTCTTTTGAAAAAAATCTTTGAGTCT
Found at i:132300 original size:30 final size:30
Alignment explanation
Indices: 132226--132381 Score: 149
Period size: 30 Copynumber: 5.1 Consensus size: 30
132216 CTCTTGAGAT
*
132226 AAATCTTTGAGTCTGTTCCTTTTG-AA-AA
1 AAATCTTTGAGTCTGTTTCTTTTGAAACAA
132254 AAATCTTTGAGT-TGTTTCTTTTGAAACAA
1 AAATCTTTGAGTCTGTTTCTTTTGAAACAA
*
132283 AAATCTTTGAGTCTGTTTCTTTGGAAACAA
1 AAATCTTTGAGTCTGTTTCTTTTGAAACAA
* * **
132313 AATTTGGTCTCTCTTAAGAT-AATTTCTTTTGAAACAA
1 AA------ATCT-TTGAG-TCTGTTTCTTTTGAAACAA
*
132350 AAATCTTTGAGTCTGTTTCTTTGGAAACAA
1 AAATCTTTGAGTCTGTTTCTTTTGAAACAA
132380 AA
1 AA
132382 TTTTGTCTCT
Statistics
Matches: 104, Mismatches: 12, Indels: 22
0.75 0.09 0.16
Matches are distributed among these distances:
27 10 0.10
28 14 0.13
29 15 0.14
30 38 0.37
31 3 0.03
36 3 0.03
37 20 0.19
38 1 0.01
ACGTcount: A:0.31, C:0.13, G:0.14, T:0.42
Consensus pattern (30 bp):
AAATCTTTGAGTCTGTTTCTTTTGAAACAA
Found at i:132346 original size:67 final size:67
Alignment explanation
Indices: 132268--132409 Score: 266
Period size: 67 Copynumber: 2.1 Consensus size: 67
132258 CTTTGAGTTG
132268 TTTCTTTTGAAACAAAAATCTTTGAGTCTGTTTCTTTGGAAACAAAATTTGGTCTCTCTTAAGAT
1 TTTCTTTTGAAACAAAAATCTTTGAGTCTGTTTCTTTGGAAACAAAATTTGGTCTCTCTTAAGAT
132333 AA
66 AA
*
132335 TTTCTTTTGAAACAAAAATCTTTGAGTCTGTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGAT
1 TTTCTTTTGAAACAAAAATCTTTGAGTCTGTTTCTTTGGAAACAAAATTTGGTCTCTCTTAAGAT
*
132400 AT
66 AA
132402 TTTCTTTT
1 TTTCTTTT
132410 CTTTTTTTTA
Statistics
Matches: 73, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
67 73 1.00
ACGTcount: A:0.29, C:0.13, G:0.12, T:0.46
Consensus pattern (67 bp):
TTTCTTTTGAAACAAAAATCTTTGAGTCTGTTTCTTTGGAAACAAAATTTGGTCTCTCTTAAGAT
AA
Found at i:133085 original size:28 final size:28
Alignment explanation
Indices: 133039--133117 Score: 99
Period size: 28 Copynumber: 2.7 Consensus size: 28
133029 GAGACAGTTG
133039 CTTTTGAAACACATTATCTTTGAG-CTTGTTT
1 CTTTTGAAACA-A--ATCTTTGAGTC-TGTTT
133070 -TTCTTGAAACAAATCTTTGAGTCTGTTT
1 CTT-TTGAAACAAATCTTTGAGTCTGTTT
133098 CTTTTGAAACAAATCTTTGA
1 CTTTTGAAACAAATCTTTGA
133118 ATCAATTTCT
Statistics
Matches: 45, Mismatches: 0, Indels: 9
0.83 0.00 0.17
Matches are distributed among these distances:
28 31 0.69
29 3 0.07
30 3 0.07
31 8 0.18
ACGTcount: A:0.27, C:0.15, G:0.13, T:0.46
Consensus pattern (28 bp):
CTTTTGAAACAAATCTTTGAGTCTGTTT
Found at i:133126 original size:28 final size:28
Alignment explanation
Indices: 133073--133127 Score: 83
Period size: 28 Copynumber: 2.0 Consensus size: 28
133063 CTTGTTTTTC
* **
133073 TTGAAACAAATCTTTGAGTCTGTTTCTT
1 TTGAAACAAATCTTTGAATCAATTTCTT
133101 TTGAAACAAATCTTTGAATCAATTTCT
1 TTGAAACAAATCTTTGAATCAATTTCT
133128 CCTGAAACCA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.31, C:0.15, G:0.11, T:0.44
Consensus pattern (28 bp):
TTGAAACAAATCTTTGAATCAATTTCTT
Found at i:133133 original size:28 final size:28
Alignment explanation
Indices: 133074--133135 Score: 79
Period size: 28 Copynumber: 2.2 Consensus size: 28
133064 TTGTTTTTCT
* ** **
133074 TGAAACAAATCTTTGAGTCTGTTTCTTT
1 TGAAACAAATCTTTGAATCAATTTCTCC
133102 TGAAACAAATCTTTGAATCAATTTCTCC
1 TGAAACAAATCTTTGAATCAATTTCTCC
133130 TGAAAC
1 TGAAAC
133136 CATGATCCCT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.32, C:0.18, G:0.11, T:0.39
Consensus pattern (28 bp):
TGAAACAAATCTTTGAATCAATTTCTCC
Found at i:133429 original size:133 final size:134
Alignment explanation
Indices: 133164--133492 Score: 509
Period size: 133 Copynumber: 2.5 Consensus size: 134
133154 CCAGTCGTCC
* * * *
133164 TCATCACGTAGGAACCGTGTCATCCCCTGACCAGATCTCCTCATCATGTAGGAGCCATGTCAACC
1 TCATCACGTATGAGCCGTGTCATCCCCTGACCAGATCTCCTCATCACGTAGGAGCCGTGTCAACC
* * * *
133229 ATAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCGCCCTACCTAAAGATGGCCATAA
66 ATAGATAACCAGCCGTCCTCATCACGTAGGAACCGGGTTATCACCCTACCTAAAGATGACCAGAA
133294 CTCT
131 CTCT
* * * *
133298 TCATCACGTATGAGCCGTGCCATCCCCTGACCAGACCTCTTCATCACGTAGGAGCCGTGTCATCC
1 TCATCACGTATGAGCCGTGTCATCCCCTGACCAGATCTCCTCATCACGTAGGAGCCGTGTCAACC
*
133363 -TAGATAACCAGCCGTCCTCATCACGTAGGAATCGGGTTATCACTCCT-CCTAAAGATGACCAGA
66 ATAGATAACCAGCCGTCCTCATCACGTAGGAACCGGGTTATCAC-CCTACCTAAAGATGACCAGA
133426 ACTCT
130 ACTCT
*
133431 TCATCACGTATGAGCAGTGTCATCCCCTGACCAGATCTCCTCATCACGTAGGAGCCGTGTCA
1 TCATCACGTATGAGCCGTGTCATCCCCTGACCAGATCTCCTCATCACGTAGGAGCCGTGTCA
133493 CCCTTAGACG
Statistics
Matches: 177, Mismatches: 17, Indels: 3
0.90 0.09 0.02
Matches are distributed among these distances:
133 117 0.66
134 60 0.34
ACGTcount: A:0.25, C:0.33, G:0.19, T:0.23
Consensus pattern (134 bp):
TCATCACGTATGAGCCGTGTCATCCCCTGACCAGATCTCCTCATCACGTAGGAGCCGTGTCAACC
ATAGATAACCAGCCGTCCTCATCACGTAGGAACCGGGTTATCACCCTACCTAAAGATGACCAGAA
CTCT
Found at i:133534 original size:43 final size:40
Alignment explanation
Indices: 133418--133540 Score: 122
Period size: 40 Copynumber: 3.0 Consensus size: 40
133408 CTCCTAAAGA
133418 TGACCAGAACTCTTCATCACGTATGAGCAGTGTCATCCCC
1 TGACCAGAACTCTTCATCACGTATGAGCAGTGTCATCCCC
* * * * *
133458 TGACCAGATCTCCTCATCACGTAGGAGCCGTGTCA-CCCT
1 TGACCAGAACTCTTCATCACGTATGAGCAGTGTCATCCCC
* ** *
133497 TAGACGACCAGACCTCTTCATTGCGTATGAGCAGTGTCGTCCCC
1 T----GACCAGAACTCTTCATCACGTATGAGCAGTGTCATCCCC
133541 ACCAACAAAA
Statistics
Matches: 65, Mismatches: 13, Indels: 6
0.77 0.15 0.07
Matches are distributed among these distances:
39 4 0.06
40 31 0.48
43 27 0.42
44 3 0.05
ACGTcount: A:0.22, C:0.33, G:0.20, T:0.24
Consensus pattern (40 bp):
TGACCAGAACTCTTCATCACGTATGAGCAGTGTCATCCCC
Found at i:133697 original size:3 final size:3
Alignment explanation
Indices: 133691--133736 Score: 58
Period size: 3 Copynumber: 15.7 Consensus size: 3
133681 TTTTTTTTAA
** *
133691 TAT TAT TAT TAT TAT CGT TA- TAT TAT TAT TAC TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
133737 ATTTACAAAT
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
2 2 0.06
3 34 0.94
ACGTcount: A:0.33, C:0.04, G:0.02, T:0.61
Consensus pattern (3 bp):
TAT
Found at i:135731 original size:22 final size:22
Alignment explanation
Indices: 135706--135749 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
135696 TCAAACGATG
*
135706 CAATGTGTGTTATTTTAAGTGA
1 CAATGTATGTTATTTTAAGTGA
* * *
135728 CAATTTATTTTATTTTATGTGA
1 CAATGTATGTTATTTTAAGTGA
135750 ATGTAAATTT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.27, C:0.05, G:0.16, T:0.52
Consensus pattern (22 bp):
CAATGTATGTTATTTTAAGTGA
Found at i:137755 original size:35 final size:35
Alignment explanation
Indices: 137655--137748 Score: 170
Period size: 35 Copynumber: 2.7 Consensus size: 35
137645 AACAATACCT
*
137655 TTTGTTATATACATCATAGTTAATCGCATTACATG
1 TTTGTTATATACATCAGAGTTAATCGCATTACATG
*
137690 TTTGTTATATACATCAGAGTTCATCGCATTACATG
1 TTTGTTATATACATCAGAGTTAATCGCATTACATG
137725 TTTGTTATATACATCAGAGTTAAT
1 TTTGTTATATACATCAGAGTTAAT
137749 AACATTATAT
Statistics
Matches: 56, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
35 56 1.00
ACGTcount: A:0.31, C:0.14, G:0.13, T:0.43
Consensus pattern (35 bp):
TTTGTTATATACATCAGAGTTAATCGCATTACATG
Found at i:137887 original size:60 final size:60
Alignment explanation
Indices: 137795--137908 Score: 151
Period size: 60 Copynumber: 1.9 Consensus size: 60
137785 AAATAGTCTC
* * *
137795 TAAATTTTTAAATATTTTAACTTTAGCCCTAAATTATGAC-TATCATTCTAAATTTATCCT
1 TAAACTTTTAAATATTTCAACTTTAGCCCTAAACTATGACAT-TCATTCTAAATTTATCCT
* *
137855 TAAACTTTTGAATATTTCAA-TTTCATCCCTAAACTATGACATTCATTCTAAATT
1 TAAACTTTTAAATATTTCAACTTT-AGCCCTAAACTATGACATTCATTCTAAATT
137909 GGTCCCCAAA
Statistics
Matches: 47, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
59 3 0.06
60 43 0.91
61 1 0.02
ACGTcount: A:0.35, C:0.17, G:0.04, T:0.45
Consensus pattern (60 bp):
TAAACTTTTAAATATTTCAACTTTAGCCCTAAACTATGACATTCATTCTAAATTTATCCT
Found at i:137945 original size:30 final size:29
Alignment explanation
Indices: 137911--137979 Score: 77
Period size: 30 Copynumber: 2.3 Consensus size: 29
137901 TCTAAATTGG
*
137911 TCCCCAAATTTTTTGAAAATTCCAATTTTA
1 TCCCCAAATTTTTT-AAAATTCCAATTTCA
* * *
137941 TCCCCAAACATTTTTAACATTCCAGTTTCA
1 TCCCCAAA-TTTTTTAAAATTCCAATTTCA
137971 T-CCCAAATT
1 TCCCCAAATT
137980 ATATGTATAT
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
28 1 0.03
29 6 0.18
30 21 0.64
31 5 0.15
ACGTcount: A:0.32, C:0.26, G:0.03, T:0.39
Consensus pattern (29 bp):
TCCCCAAATTTTTTAAAATTCCAATTTCA
Found at i:140586 original size:174 final size:176
Alignment explanation
Indices: 140287--140638 Score: 656
Period size: 174 Copynumber: 2.0 Consensus size: 176
140277 GAAATTTATT
140287 TTTATTTTTGTTGATAATTTATTTTCCTCACCTAAAATTTAATAAGTTGGTCTCTCCTAAAAAAT
1 TTTATTTTTGTTGATAATTTATTTTCCTCACCTAAAATTTAATAAGTTGGTCTCTCCTAAAAAA-
140352 TATTAGTTCGATCCATAACATAAAAATCTGTGCTCATTCCTGTATATACAAGTGTGTAGGTATTT
65 TATTAGTTCGATCCATAACATAAAAATCTGTGCTCATTCCTGTATATACAAGTGTGTAGGTATTT
*
140417 GAATTTATTTTATTTTTC-ATGTATAATTATTAAA-TATAATGATCC
130 GAATTTATTTTAATTTTCAATGTATAATTATTAAATTATAATGATCC
140462 TTTATTTTTTGTTGATAATTTATTTTCCTCACCTAAAATTTAATAAGTTGGTCTCTCCTAAAAAA
1 TTTA-TTTTTGTTGATAATTTATTTTCCTCACCTAAAATTTAATAAGTTGGTCTCTCCTAAAAAA
140527 -ATTAGTTCGATCCATAACATAAAAATCTGTGCTCATTCCTGTATATACAAGTGTGTAGGTATTT
65 TATTAGTTCGATCCATAACATAAAAATCTGTGCTCATTCCTGTATATACAAGTGTGTAGGTATTT
140591 GAATTTATTTTAATTTTCAATGTATAATTATTAAATTATAATGATCC
130 GAATTTATTTTAATTTTCAATGTATAATTATTAAATTATAATGATCC
140638 T
1 T
140639 GAAGACGCTG
Statistics
Matches: 173, Mismatches: 1, Indels: 5
0.97 0.01 0.03
Matches are distributed among these distances:
174 81 0.47
175 20 0.12
176 72 0.42
ACGTcount: A:0.32, C:0.12, G:0.10, T:0.45
Consensus pattern (176 bp):
TTTATTTTTGTTGATAATTTATTTTCCTCACCTAAAATTTAATAAGTTGGTCTCTCCTAAAAAAT
ATTAGTTCGATCCATAACATAAAAATCTGTGCTCATTCCTGTATATACAAGTGTGTAGGTATTTG
AATTTATTTTAATTTTCAATGTATAATTATTAAATTATAATGATCC
Found at i:141379 original size:30 final size:30
Alignment explanation
Indices: 141343--141410 Score: 127
Period size: 30 Copynumber: 2.2 Consensus size: 30
141333 CATGATTTTG
141343 CCTGTATGTCTTTATGGTTTTCTGTTATTA
1 CCTGTATGTCTTTATGGTTTTCTGTTATTA
141373 CCTGTATGTCTTTATGGTTTTCTGTTATTA
1 CCTGTATGTCTTTATGGTTTTCTGTTATTA
141403 CCATGTAT
1 CC-TGTAT
141411 TTGAATATTG
Statistics
Matches: 37, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
30 32 0.86
31 5 0.14
ACGTcount: A:0.15, C:0.15, G:0.16, T:0.54
Consensus pattern (30 bp):
CCTGTATGTCTTTATGGTTTTCTGTTATTA
Found at i:145848 original size:19 final size:17
Alignment explanation
Indices: 145824--145860 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
145814 AAATAATGAT
145824 CCATATATCGCATAAAA
1 CCATATATCGCATAAAA
145841 CCATATATCGCATAAAA
1 CCATATATCGCATAAAA
145858 CCA
1 CCA
145861 AGTAGATAGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.46, C:0.27, G:0.05, T:0.22
Consensus pattern (17 bp):
CCATATATCGCATAAAA
Found at i:146063 original size:22 final size:21
Alignment explanation
Indices: 146029--146069 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
146019 ATAATTATTT
146029 AAAAAATTAAATAAAAATATC
1 AAAAAATTAAATAAAAATATC
*
146050 AAAAATATTTAATAAAAATA
1 AAAAA-ATTAAATAAAAATA
146070 ATTTTTTATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.27
Consensus pattern (21 bp):
AAAAAATTAAATAAAAATATC
Found at i:150849 original size:21 final size:21
Alignment explanation
Indices: 150825--150865 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
150815 TTAAAATTTA
150825 TTTTTGGTCAAGACTAATTAT
1 TTTTTGGTCAAGACTAATTAT
150846 TTTTTGGTCAAGACTAATTA
1 TTTTTGGTCAAGACTAATTA
150866 CATTTTTTTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.29, C:0.10, G:0.15, T:0.46
Consensus pattern (21 bp):
TTTTTGGTCAAGACTAATTAT
Found at i:150871 original size:21 final size:21
Alignment explanation
Indices: 150826--150871 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
150816 TAAAATTTAT
**
150826 TTTTGGTCAAGACTAATTATT
1 TTTTGGTCAAGACTAATTACA
150847 TTTTGGTCAAGACTAATTACA
1 TTTTGGTCAAGACTAATTACA
150868 TTTT
1 TTTT
150872 TTTCTCGTCA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.28, C:0.11, G:0.13, T:0.48
Consensus pattern (21 bp):
TTTTGGTCAAGACTAATTACA
Found at i:155359 original size:16 final size:16
Alignment explanation
Indices: 155340--155379 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
155330 ATATTTTTAA
*
155340 TATTTTATATTTAATT
1 TATTTAATATTTAATT
*
155356 TATTTAATATTTTATT
1 TATTTAATATTTAATT
*
155372 TAATTAAT
1 TATTTAAT
155380 TTTTTTTGCA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (16 bp):
TATTTAATATTTAATT
Found at i:155369 original size:12 final size:12
Alignment explanation
Indices: 155335--155375 Score: 50
Period size: 12 Copynumber: 3.5 Consensus size: 12
155325 TTATTATATT
155335 TTTAATATTTTA
1 TTTAATATTTTA
*
155347 TATT--TAATTTA
1 T-TTAATATTTTA
155358 TTTAATATTTTA
1 TTTAATATTTTA
155370 TTTAAT
1 TTTAAT
155376 TAATTTTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 6
0.75 0.06 0.19
Matches are distributed among these distances:
10 2 0.08
11 7 0.29
12 13 0.54
13 2 0.08
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (12 bp):
TTTAATATTTTA
Found at i:155371 original size:21 final size:21
Alignment explanation
Indices: 155320--155381 Score: 67
Period size: 21 Copynumber: 3.0 Consensus size: 21
155310 TTTCTAATGT
155320 ATATTTTA-TT-ATATT-TTTA
1 ATATTTTATTTAAT-TTATTTA
155339 ATATTTTATATTTAATTTATTTA
1 ATA-TTT-TATTTAATTTATTTA
*
155362 ATATTTTATTTAATTAATTT
1 ATATTTTATTTAATTTATTT
155382 TTTTTGCAGA
Statistics
Matches: 37, Mismatches: 1, Indels: 8
0.80 0.02 0.17
Matches are distributed among these distances:
19 3 0.08
20 3 0.08
21 15 0.41
22 7 0.19
23 9 0.24
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (21 bp):
ATATTTTATTTAATTTATTTA
Found at i:155384 original size:16 final size:16
Alignment explanation
Indices: 155346--155383 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
155336 TTAATATTTT
* *
155346 ATATTTAATTTATTTA
1 ATATTTTATTTAATTA
155362 ATATTTTATTTAATTA
1 ATATTTTATTTAATTA
155378 AT-TTTT
1 ATATTTT
155384 TTTGCAGATA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
15 4 0.20
16 16 0.80
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (16 bp):
ATATTTTATTTAATTA
Done.