Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007908.1 Hibiscus syriacus cultivar Beakdansim tig00110302_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: 529382
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 3
Found at i:165214 original size:20 final size:20
Alignment explanation
Indices: 165191--165263 Score: 92
Period size: 20 Copynumber: 3.6 Consensus size: 20
165181 CGATAGTCAG
*
165191 ATTCGCGTTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
*
165211 ATTCGCATTACGATTTACGT
1 ATTCGCATTGCGATTTACGT
* *
165231 ATTTGCATTGTGATTTACGT
1 ATTCGCATTGCGATTTACGT
* *
165251 AATCGCAATGCGA
1 ATTCGCATTGCGA
165264 CAGTCAGAAT
Statistics
Matches: 44, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 44 1.00
ACGTcount: A:0.23, C:0.18, G:0.21, T:0.38
Consensus pattern (20 bp):
ATTCGCATTGCGATTTACGT
Found at i:167607 original size:21 final size:21
Alignment explanation
Indices: 167583--167622 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
167573 AGAATCAGAG
167583 AGAGAAGCACAAAGAGAAAAT
1 AGAGAAGCACAAAGAGAAAAT
* *
167604 AGAGAAGCAGAGAGAGAAA
1 AGAGAAGCACAAAGAGAAA
167623 CAACATTTTA
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:0.60, C:0.07, G:0.30, T:0.03
Consensus pattern (21 bp):
AGAGAAGCACAAAGAGAAAAT
Found at i:168137 original size:43 final size:43
Alignment explanation
Indices: 168040--168149 Score: 121
Period size: 43 Copynumber: 2.6 Consensus size: 43
168030 TCTTCCGGGC
* * ** *
168040 ACACCGCTACATATCAAATCGATTGTGGCGTTTGTGACTACAC
1 ACACCGCTAAATATCAAATCTATTACGGCGTTTGTGACTACAA
* *
168083 ACGCCGCTAAATATCAAATCTATTACGGCGTTTGTGATTACAA
1 ACACCGCTAAATATCAAATCTATTACGGCGTTTGTGACTACAA
* * * *
168126 ACACTGTTAAATATCGAACCTATT
1 ACACCGCTAAATATCAAATCTATT
168150 TTGGGAAAAT
Statistics
Matches: 55, Mismatches: 12, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
43 55 1.00
ACGTcount: A:0.32, C:0.23, G:0.15, T:0.30
Consensus pattern (43 bp):
ACACCGCTAAATATCAAATCTATTACGGCGTTTGTGACTACAA
Found at i:169706 original size:131 final size:131
Alignment explanation
Indices: 169462--169814 Score: 379
Period size: 131 Copynumber: 2.7 Consensus size: 131
169452 ATAATTTTAA
* * ** *
169462 GAGAGAAAATGATAATATCTAATTATTTTCATTCAAGAATAAATGACATTTCATACCTTAAAACA
1 GAGAGAGAATGATAATATCTAATTATTTCCAAGCAAGAATAAATGACATCTCATACCTTAAAACA
* * * * * *
169527 ATAATTTATTACTCCAATCGAAATGAGGAGATATTACTATTTCGTCTTAAAATTCAATATCAATT
66 ATAATTTATTACTCCAATCGAAATGAAGAGATATCACAATTCCATCTTAAAAATCAATATCAATT
169592 C
131 C
* * * ** * * *
169593 TAGTGA-AGATGATAATATCTAATGATTTCCAAGCGGGAATAAATGGCCTCTCATACCTTAAAGC
1 GAGAGAGA-ATGATAATATCTAATTATTTCCAAGCAAGAATAAATGACATCTCATACCTTAAAAC
* * * *
169657 AATCATTTATTGCTCCAATTGAAATGAAGAGATATCACAATTCCATCTTAAAAATCAATATTAAT
65 AATAATTTATTACTCCAATCGAAATGAAGAGATATCACAATTCCATCTTAAAAATCAATATCAAT
169722 TC
130 TC
* * ** * *
169724 GAGAGAGAATGATAATATCGAATTATTTCCAATCAA-AATAAATGATC-TCTCATGTCTTAGAGC
1 GAGAGAGAATGATAATATCTAATTATTTCCAAGCAAGAATAAATGA-CATCTCATACCTTAAAAC
* * *
169787 AGTAATTTATTACTCCAACCAAAATGAA
65 AATAATTTATTACTCCAATCGAAATGAA
169815 AAAATATTAC
Statistics
Matches: 180, Mismatches: 39, Indels: 7
0.80 0.17 0.03
Matches are distributed among these distances:
130 44 0.24
131 135 0.75
132 1 0.01
ACGTcount: A:0.41, C:0.15, G:0.12, T:0.32
Consensus pattern (131 bp):
GAGAGAGAATGATAATATCTAATTATTTCCAAGCAAGAATAAATGACATCTCATACCTTAAAACA
ATAATTTATTACTCCAATCGAAATGAAGAGATATCACAATTCCATCTTAAAAATCAATATCAATT
C
Found at i:171437 original size:17 final size:17
Alignment explanation
Indices: 171405--171438 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
171395 TTACAAGCTT
*
171405 TTTGTGTGTGGGTTTGG
1 TTTGTGTGTGGATTTGG
*
171422 TTTGTGTGTTGATTTGG
1 TTTGTGTGTGGATTTGG
171439 GATTTCTGAC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.03, C:0.00, G:0.41, T:0.56
Consensus pattern (17 bp):
TTTGTGTGTGGATTTGG
Found at i:172318 original size:2 final size:2
Alignment explanation
Indices: 172313--172350 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
172303 CACATTTTTT
* *
172313 TA TA TA TA CA TT TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
172351 GTTTACAAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:172463 original size:74 final size:74
Alignment explanation
Indices: 172334--172648 Score: 289
Period size: 74 Copynumber: 4.1 Consensus size: 74
172324 TTATATATAT
** ** *
172334 ATATATATATATATATAGTTTACAAATGATTTTTGAAAATACGTATATGATATATAGTTTTTAAA
1 ATATATATAT-TATATAGTTTTTAAAAAATTTTTGAAAATA--TATATAATATATAGTTTTTAAA
172399 ACATTTTTTGAAA
63 ACA-TTTTTGAAA
* * *
172412 CTATATATATTATATAGTTTTTAAAACATTTTCGAAAAT-TATATAATATATAGTTTTTAAAACA
1 ATATATATATTATATAGTTTTTAAAAAATTTTTGAAAATATATATAATATATAGTTTTTAAAACA
172476 TTTTTAGAAA
66 TTTTT-GAAA
* * ** * *
172486 AT-TATATATTATATAATTTTTGAAATTTTTTTTAAAATATATATAATATATAGTTTTTTAAATC
1 ATATATATATTATATAGTTTTTAAAAAATTTTTGAAAATATATATAATATATAG-TTTTTAAAAC
172550 A-TTTTGAAA
65 ATTTTTGAAA
* * * *
172559 ACT-TATATAATATATTA-TTTTGGAAAAAATATTTATGAAAACAATTATATATTATATAGTTTT
1 A-TATATATATTATA-TAGTTTT-TAAAAAAT-TTT-TGAAAA-TA-TATATAATATATAGTTTT
*
172622 TCAAAAACATGTTTGAAA
59 T--AAAACATTTTTGAAA
172640 ATATATATA
1 ATATATATA
172649 AATTTAAAAT
Statistics
Matches: 198, Mismatches: 25, Indels: 25
0.80 0.10 0.10
Matches are distributed among these distances:
73 40 0.20
74 62 0.31
75 16 0.08
76 3 0.02
77 29 0.15
78 15 0.08
79 13 0.07
80 6 0.03
81 14 0.07
ACGTcount: A:0.43, C:0.04, G:0.06, T:0.46
Consensus pattern (74 bp):
ATATATATATTATATAGTTTTTAAAAAATTTTTGAAAATATATATAATATATAGTTTTTAAAACA
TTTTTGAAA
Found at i:172499 original size:37 final size:36
Alignment explanation
Indices: 172337--172649 Score: 261
Period size: 37 Copynumber: 8.2 Consensus size: 36
172327 TATATATATA
** **
172337 TATATATATATATAGTTTACAAATGATTTTTGAAAAT
1 TATATA-ATATATAGTTTTTAAAACATTTTTGAAAAT
* *
172374 ACGTATATGATATATAGTTTTTAAAACATTTTTTGAAACT
1 ---TATATAATATATAGTTTTTAAAACA-TTTTTGAAAAT
* *
172414 ATATATATTATATAGTTTTTAAAACATTTTCGAAAAT
1 -TATATAATATATAGTTTTTAAAACATTTTTGAAAAT
172451 TATATAATATATAGTTTTTAAAACATTTTTAGAAAAT
1 TATATAATATATAGTTTTTAAAACATTTTT-GAAAAT
* * * ** *
172488 TATATATTATATAATTTTTGAAATTTTTTTTAAAAT
1 TATATAATATATAGTTTTTAAAACATTTTTGAAAAT
*
172524 ATATATAATATATAGTTTTTTAAATCA-TTTTGAAAACT
1 -TATATAATATATAG-TTTTTAAAACATTTTTGAAAA-T
* *
172562 TATATAATATATTA-TTTTGGAAAAAATATTTATGAAAACAAT
1 TATATAATATA-TAGTTTT-TAAAACAT-TTT-TG--AA-AAT
* *
172604 TATATATTATATAGTTTTTCAAAAACATGTTTGAAAAT
1 TATATAATATATAGTTTTT--AAAACATTTTTGAAAAT
172642 ATATATAA
1 -TATATAA
172650 ATTTAAAATA
Statistics
Matches: 222, Mismatches: 34, Indels: 35
0.76 0.12 0.12
Matches are distributed among these distances:
36 37 0.17
37 75 0.34
38 36 0.16
39 26 0.12
40 17 0.08
41 4 0.02
42 19 0.09
43 8 0.04
ACGTcount: A:0.43, C:0.04, G:0.06, T:0.46
Consensus pattern (36 bp):
TATATAATATATAGTTTTTAAAACATTTTTGAAAAT
Found at i:172741 original size:25 final size:26
Alignment explanation
Indices: 172704--172752 Score: 64
Period size: 25 Copynumber: 1.9 Consensus size: 26
172694 AACCATTTTT
172704 AAAATCATATATAAATATAATTTTAA
1 AAAATCATATATAAATATAATTTTAA
* * *
172730 AAAAT-ATTTATATATATATTTTT
1 AAAATCATATATAAATATAATTTT
172753 TCTTTTTTTA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 15 0.75
26 5 0.25
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (26 bp):
AAAATCATATATAAATATAATTTTAA
Found at i:172744 original size:23 final size:25
Alignment explanation
Indices: 172700--172751 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 25
172690 TGAAAACCAT
*
172700 TTTTAAAATCATATATAAATATA-A
1 TTTTAAAATAATATATAAATATATA
* *
172724 TTTTAAAA-AATATTTATATATATA
1 TTTTAAAATAATATATAAATATATA
172748 TTTT
1 TTTT
172752 TTCTTTTTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 11 0.46
24 13 0.54
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (25 bp):
TTTTAAAATAATATATAAATATATA
Found at i:178095 original size:22 final size:20
Alignment explanation
Indices: 178059--178114 Score: 58
Period size: 22 Copynumber: 2.7 Consensus size: 20
178049 TACCGGTAGG
* * *
178059 GGGTATCGGTGCCATAGTAG
1 GGGTATCGATACCATAGTAA
*
178079 GGTAGTATCGATACCATGGTAA
1 GG--GTATCGATACCATAGTAA
178101 GGGTATCGATACCA
1 GGGTATCGATACCA
178115 GGCAACATCG
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
20 14 0.47
22 16 0.53
ACGTcount: A:0.27, C:0.16, G:0.32, T:0.25
Consensus pattern (20 bp):
GGGTATCGATACCATAGTAA
Found at i:178139 original size:95 final size:96
Alignment explanation
Indices: 177967--178172 Score: 240
Period size: 95 Copynumber: 2.2 Consensus size: 96
177957 GATTCAATCA
* * * * * *
177967 GTATCGATACCAAAG-A-GGTAGTATCGATACCGTTATAAGAGGTATCGATGCTAAGAAACATCG
1 GTATCGGTACCATAGTAGGGTAGTATCGATACCATGATAAGAGGTATCGATACCAAGAAACATCG
* *
178030 AATCTAATTTTGGTATCGATAC-CGGTAGGGG
66 AAGCTAATTTTGGTATCGATACTC-GAAGGGG
* * * *
178061 GTATCGGTGCCATAGTAGGGTAGTATCGATACCATGGTAAG-GGTATCGATACCAGGCAACATCG
1 GTATCGGTACCATAGTAGGGTAGTATCGATACCATGATAAGAGGTATCGATACCAAGAAACATCG
* *
178125 AAGCTATTTTTGGTATTGATACTCGAAGGGG
66 AAGCTAATTTTGGTATCGATACTCGAAGGGG
*
178156 GTATCGGTACTATAGTA
1 GTATCGGTACCATAGTA
178173 TAAAAGTATC
Statistics
Matches: 93, Mismatches: 16, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
94 12 0.13
95 60 0.65
96 21 0.23
ACGTcount: A:0.30, C:0.15, G:0.27, T:0.28
Consensus pattern (96 bp):
GTATCGGTACCATAGTAGGGTAGTATCGATACCATGATAAGAGGTATCGATACCAAGAAACATCG
AAGCTAATTTTGGTATCGATACTCGAAGGGG
Found at i:178181 original size:95 final size:96
Alignment explanation
Indices: 177986--178207 Score: 227
Period size: 95 Copynumber: 2.3 Consensus size: 96
177976 CCAAAGAGGT
* ** * * *
177986 AGTATCGATACCGTTATAAGAGGTATCGATGCTAAGAAACATCGAATCTAATTTTGGTATCGATA
1 AGTATCGATACCATGGTAAGAGGTATCGATACCAAGAAACATCGAAGCTAATTTTGGTATCGATA
* * ***
178051 CCGGTAGGGGGTATCGGTGCCATAGTAGGGT
66 CCGGAAGGGGGTATCGGTACCATAGTAGAAA
* * * *
178082 AGTATCGATACCATGGTAAG-GGTATCGATACCAGGCAACATCGAAGCTATTTTTGGTATTGATA
1 AGTATCGATACCATGGTAAGAGGTATCGATACCAAGAAACATCGAAGCTAATTTTGGTATCGATA
* *
178146 CTC-GAAGGGGGTATCGGTACTATAGTATAAA
66 C-CGGAAGGGGGTATCGGTACCATAGTAGAAA
* *
178177 AGTATCGGTACCAGGGT-AGTA-GTATCGATAC
1 AGTATCGATACCATGGTAAG-AGGTATCGATAC
178208 TATAGAGCAA
Statistics
Matches: 104, Mismatches: 19, Indels: 7
0.80 0.15 0.05
Matches are distributed among these distances:
94 2 0.02
95 84 0.81
96 18 0.17
ACGTcount: A:0.30, C:0.15, G:0.27, T:0.28
Consensus pattern (96 bp):
AGTATCGATACCATGGTAAGAGGTATCGATACCAAGAAACATCGAAGCTAATTTTGGTATCGATA
CCGGAAGGGGGTATCGGTACCATAGTAGAAA
Found at i:179025 original size:68 final size:68
Alignment explanation
Indices: 178683--179016 Score: 560
Period size: 68 Copynumber: 4.9 Consensus size: 68
178673 AAAAGATCAA
* *
178683 GAGGCCTAACTATGCATATGACAGAAAGGTGTCATTTATGCTAGTTAGATGAAAGGCTAAGTGCC
1 GAGGCCTAACTGTGCATATGACAGAAAGGTGTCATTTATGCCAGTTAGATGAAAGGCTAAGTGCC
178748 TTT
66 TTT
* * *
178751 GAGGCCTAACTGTGCATATGACAGAAAGGTGTCATTTATGCCAGTTAGATGAAATGTTAAGTGTC
1 GAGGCCTAACTGTGCATATGACAGAAAGGTGTCATTTATGCCAGTTAGATGAAAGGCTAAGTGCC
178816 TTT
66 TTT
*
178819 GAGGCCTAACTGTGCATATGACAGAAAGGTGTCATTTATGCTAGTTAGATGAAAGGCTAAGTGCC
1 GAGGCCTAACTGTGCATATGACAGAAAGGTGTCATTTATGCCAGTTAGATGAAAGGCTAAGTGCC
178884 TTT
66 TTT
*
178887 GAGGCCTAACTGTGCATATGACAGAAATGTGTCATTTATGCCAGTTAGATGAAAGGCTAAGTGCC
1 GAGGCCTAACTGTGCATATGACAGAAAGGTGTCATTTATGCCAGTTAGATGAAAGGCTAAGTGCC
178952 TTT
66 TTT
* * * * *
178955 GAGGCCTAACTGTGCATATGACAGCAATGTGTCATTTATGCCAATTAGATGAACGGTTAAGT
1 GAGGCCTAACTGTGCATATGACAGAAAGGTGTCATTTATGCCAGTTAGATGAAAGGCTAAGT
179017 ATCGTTGAGT
Statistics
Matches: 251, Mismatches: 15, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
68 251 1.00
ACGTcount: A:0.30, C:0.15, G:0.25, T:0.30
Consensus pattern (68 bp):
GAGGCCTAACTGTGCATATGACAGAAAGGTGTCATTTATGCCAGTTAGATGAAAGGCTAAGTGCC
TTT
Found at i:179290 original size:164 final size:163
Alignment explanation
Indices: 178957--179585 Score: 845
Period size: 165 Copynumber: 3.9 Consensus size: 163
178947 GTGCCTTTGA
* * * * *
178957 GGCCTAACTGTGC-ATATGACAGCAATGTGTCATTTATGCCAATTAGATGAACGGTTAAGTATCG
1 GGCCTAACTGTGCAAT-TGACAGAAATGTGTCAATTATGCCAGTTAGATGAATGGTTAAGTACCG
* * * *
179021 TTGAGTAAAAGAAAAAATGTCCTAGCTGTGCAATTGACAGAAATGTGTCATTTATGTCAATTAGA
65 TTGAGTAAAAGAAAAAATGGCCTAGCTGTGCAATTGACAGAAATGTGTCAATTATGCCAGTTAGA
179086 TGAACGGTTAAGTACCGTTGAGTAAAAGAAAAAAT
130 TGAACGGTTAAGTACCGTTGAGTAAAAG-AAAAAT
*
179121 GGCCTAACTGTGCAATTGACAGAAATTTGTCAATTATGCCAGTTAGATGAATGGTTAAGTACCGT
1 GGCCTAACTGTGCAATTGACAGAAATGTGTCAATTATGCCAGTTAGATGAATGGTTAAGTACCGT
* * *
179186 TGAGTAAAAGAAAAAAATCGCCTAGCTGTGCAATTGGCAGAAAGGTGTCAATTATGCCAGTTAGA
66 TGAGTAAAAG-AAAAAATGGCCTAGCTGTGCAATTGACAGAAATGTGTCAATTATGCCAGTTAGA
* *
179251 TGAACGGTTAAGTACCATTGAGTAAAAGAAAATT
130 TGAACGGTTAAGTACCGTTGAGTAAAAGAAAAAT
* * * **
179285 GGCCTAGCTGTGCAATTGACATAAAGGTGTCAATTATTTCAGTTAGATGAATGGTTAAGTACCGT
1 GGCCTAACTGTGCAATTGACAGAAATGTGTCAATTATGCCAGTTAGATGAATGGTTAAGTACCGT
* * * *
179350 TAAGTAAAAGAAAAAAAATGGCCTAGTTGTGCAATTGACAAAAATGTGTCAATTATGCCAGTTAA
66 TGAGTAAAAG--AAAAAATGGCCTAGCTGTGCAATTGACAGAAATGTGTCAATTATGCCAGTTAG
*
179415 ATGAACGGTTAAGTACCGTTGAGTATAAGAAAAAT
129 ATGAACGGTTAAGTACCGTTGAGTAAAAGAAAAAT
** * * *
179450 GGCCTAGTTGTGCAATTTACAGAAATGTGTCAATTATGCCATTTAGATGAATGGTTAAGTATCGT
1 GGCCTAACTGTGCAATTGACAGAAATGTGTCAATTATGCCAGTTAGATGAATGGTTAAGTACCGT
* * * * * * *
179515 TGAGTAAAAG--AAAATGGTCTAACTGTG-GATTGGCAGAAACGTGTCAATTATGACAGTTAGAC
66 TGAGTAAAAGAAAAAATGGCCTAGCTGTGCAATTGACAGAAATGTGTCAATTATGCCAGTTAGAT
179577 GAAC-GTTAA
131 GAACGGTTAA
179586 ACACTGTTGA
Statistics
Matches: 412, Mismatches: 50, Indels: 11
0.87 0.11 0.02
Matches are distributed among these distances:
159 5 0.01
160 32 0.08
161 14 0.03
164 139 0.34
165 222 0.54
ACGTcount: A:0.36, C:0.12, G:0.23, T:0.28
Consensus pattern (163 bp):
GGCCTAACTGTGCAATTGACAGAAATGTGTCAATTATGCCAGTTAGATGAATGGTTAAGTACCGT
TGAGTAAAAGAAAAAATGGCCTAGCTGTGCAATTGACAGAAATGTGTCAATTATGCCAGTTAGAT
GAACGGTTAAGTACCGTTGAGTAAAAGAAAAAT
Found at i:179341 original size:81 final size:82
Alignment explanation
Indices: 178957--179585 Score: 822
Period size: 81 Copynumber: 7.7 Consensus size: 82
178947 GTGCCTTTGA
* * * * *
178957 GGCCTAACTGTGC-ATATGACAGCAATGTGTCATTTATGCCAATTAGATGAACGGTTAAGTATCG
1 GGCCTAGCTGTGCAAT-TGACAGAAATGTGTCAATTATGCCAGTTAGATGAACGGTTAAGTACCG
179021 TTGAGTAAAAGAAAAAAT
65 TTGAGTAAAAGAAAAAAT
* * * *
179039 GTCCTAGCTGTGCAATTGACAGAAATGTGTCATTTATGTCAATTAGATGAACGGTTAAGTACCGT
1 GGCCTAGCTGTGCAATTGACAGAAATGTGTCAATTATGCCAGTTAGATGAACGGTTAAGTACCGT
179104 TGAGTAAAAGAAAAAAT
66 TGAGTAAAAGAAAAAAT
* * *
179121 GGCCTAACTGTGCAATTGACAGAAATTTGTCAATTATGCCAGTTAGATGAATGGTTAAGTACCGT
1 GGCCTAGCTGTGCAATTGACAGAAATGTGTCAATTATGCCAGTTAGATGAACGGTTAAGTACCGT
179186 TGAGTAAAAGAAAAAAAT
66 TGAGTAAAAG-AAAAAAT
* * * *
179204 CGCCTAGCTGTGCAATTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAACGGTTAAGTACCAT
1 GGCCTAGCTGTGCAATTGACAGAAATGTGTCAATTATGCCAGTTAGATGAACGGTTAAGTACCGT
*
179269 TGAGTAAAAG-AAAATT
66 TGAGTAAAAGAAAAAAT
* * ** *
179285 GGCCTAGCTGTGCAATTGACATAAAGGTGTCAATTATTTCAGTTAGATGAATGGTTAAGTACCGT
1 GGCCTAGCTGTGCAATTGACAGAAATGTGTCAATTATGCCAGTTAGATGAACGGTTAAGTACCGT
*
179350 TAAGTAAAAGAAAAAAAAT
66 TGAGTAAAAG--AAAAAAT
* * *
179369 GGCCTAGTTGTGCAATTGACAAAAATGTGTCAATTATGCCAGTTAAATGAACGGTTAAGTACCGT
1 GGCCTAGCTGTGCAATTGACAGAAATGTGTCAATTATGCCAGTTAGATGAACGGTTAAGTACCGT
*
179434 TGAGTATAAG-AAAAAT
66 TGAGTAAAAGAAAAAAT
* * * * *
179450 GGCCTAGTTGTGCAATTTACAGAAATGTGTCAATTATGCCATTTAGATGAATGGTTAAGTATCGT
1 GGCCTAGCTGTGCAATTGACAGAAATGTGTCAATTATGCCAGTTAGATGAACGGTTAAGTACCGT
179515 TGAGTAAAAG--AAAAT
66 TGAGTAAAAGAAAAAAT
* * * * * * *
179530 GGTCTAACTGTG-GATTGGCAGAAACGTGTCAATTATGACAGTTAGACGAAC-GTTAA
1 GGCCTAGCTGTGCAATTGACAGAAATGTGTCAATTATGCCAGTTAGATGAACGGTTAA
179586 ACACTGTTGA
Statistics
Matches: 486, Mismatches: 56, Indels: 14
0.87 0.10 0.03
Matches are distributed among these distances:
78 5 0.01
79 31 0.06
80 14 0.03
81 146 0.30
82 142 0.29
83 77 0.16
84 71 0.15
ACGTcount: A:0.36, C:0.12, G:0.23, T:0.28
Consensus pattern (82 bp):
GGCCTAGCTGTGCAATTGACAGAAATGTGTCAATTATGCCAGTTAGATGAACGGTTAAGTACCGT
TGAGTAAAAGAAAAAAT
Found at i:179482 original size:246 final size:244
Alignment explanation
Indices: 178958--179585 Score: 850
Period size: 246 Copynumber: 2.6 Consensus size: 244
178948 TGCCTTTGAG
* * *
178958 GCCTAACTGTGC-ATATGACAGCAATGTGTCATTTATGCCAATTAGATGAACGGTTAAGTATCGT
1 GCCTAGCTGTGCAAT-TGACAGAAATGTGTCAATTATGCCAATTAGATGAACGGTTAAGTATCGT
* * * *
179022 TGAGTAAAAGAAAAAATGTCCTAGCTGTGCAATTGACAGAAATGTGTCATTTATGTCAATTAGAT
65 TGAGTAAAAG--AAAATGGCCTAGCTGTGCAATTGACAGAAACGTGTCAATTATGTCAGTTAGAT
* * *
179087 GAACGGTTAAGTACCGTTGAGTAAAAGAAAAAATGGCCTAACTGTGCAATTGACAGAAATTTGTC
128 GAACGGTTAAGTACCGTTAAGTAAAAGAAAAAATGGCCTAACTGTGCAATTGACAAAAATGTGTC
* *
179152 AATTATGCCAGTTAGATGAATGGTTAAGTACCGTTGAGTAAAAGAAAAAAATC
193 AATTATGCCAGTTAAATGAACGGTTAAGTACCGTTGAGTAAAAG-AAAAAATC
* * * * *
179205 GCCTAGCTGTGCAATTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAACGGTTAAGTACCATT
1 GCCTAGCTGTGCAATTGACAGAAATGTGTCAATTATGCCAATTAGATGAACGGTTAAGTATCGTT
* * *
179270 GAGTAAAAGAAAATTGGCCTAGCTGTGCAATTGACATAAAGGTGTCAATTATTTCAGTTAGATGA
66 GAGTAAAAGAAAA-TGGCCTAGCTGTGCAATTGACAGAAACGTGTCAATTATGTCAGTTAGATGA
* **
179335 ATGGTTAAGTACCGTTAAGTAAAAGAAAAAAAATGGCCTAGTTGTGCAATTGACAAAAATGTGTC
130 ACGGTTAAGTACCGTTAAGTAAAAG--AAAAAATGGCCTAACTGTGCAATTGACAAAAATGTGTC
* *
179400 AATTATGCCAGTTAAATGAACGGTTAAGTACCGTTGAGTATAAG-AAAAATG
193 AATTATGCCAGTTAAATGAACGGTTAAGTACCGTTGAGTAAAAGAAAAAATC
* * * *
179451 GCCTAGTTGTGCAATTTACAGAAATGTGTCAATTATGCCATTTAGATGAATGGTTAAGTATCGTT
1 GCCTAGCTGTGCAATTGACAGAAATGTGTCAATTATGCCAATTAGATGAACGGTTAAGTATCGTT
* * * * * *
179516 GAGTAAAAGAAAATGGTCTAACTGTG-GATTGGCAGAAACGTGTCAATTATGACAGTTAGACGAA
66 GAGTAAAAGAAAATGGCCTAGCTGTGCAATTGACAGAAACGTGTCAATTATGTCAGTTAGATGAA
179580 C-GTTAA
131 CGGTTAA
179586 ACACTGTTGA
Statistics
Matches: 335, Mismatches: 42, Indels: 12
0.86 0.11 0.03
Matches are distributed among these distances:
243 5 0.01
244 31 0.09
245 15 0.04
246 144 0.43
247 63 0.19
248 77 0.23
ACGTcount: A:0.36, C:0.12, G:0.23, T:0.29
Consensus pattern (244 bp):
GCCTAGCTGTGCAATTGACAGAAATGTGTCAATTATGCCAATTAGATGAACGGTTAAGTATCGTT
GAGTAAAAGAAAATGGCCTAGCTGTGCAATTGACAGAAACGTGTCAATTATGTCAGTTAGATGAA
CGGTTAAGTACCGTTAAGTAAAAGAAAAAATGGCCTAACTGTGCAATTGACAAAAATGTGTCAAT
TATGCCAGTTAAATGAACGGTTAAGTACCGTTGAGTAAAAGAAAAAATC
Found at i:179648 original size:2 final size:2
Alignment explanation
Indices: 179641--179678 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
179631 TGAAGGGATG
179641 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
179679 TGTACAACAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:183457 original size:236 final size:236
Alignment explanation
Indices: 183044--183513 Score: 922
Period size: 236 Copynumber: 2.0 Consensus size: 236
183034 GCCCAAGATC
183044 AAAATAATACCTTCCAACTCTCCTTTTTATTAGTCCATAAAAGAGAAAAACAAAAATTACAACTC
1 AAAATAATACCTTCCAACTCTCCTTTTTATTAGTCCATAAAAGAGAAAAACAAAAATTACAACTC
183109 ATTACCCAATCTTTTACTCTACCACCAGCCCAGGTGAAGGCCTAGCCATAAGTAGCCCCTGAATT
66 ATTACCCAATCTTTTACTCTACCACCAGCCCAGGTGAAGGCCTAGCCATAAGTAGCCCCTGAATT
183174 TTATCTATTTCCTCTCGAGCTTTTCCATGTTCTCTCGGTAGAGCACGTATTGGATTTCAAACTTC
131 TTATCTATTTCCTCTCGAGCTTTTCCATGTTCTCTCGGTAGAGCACGTATTGGATTTCAAACTTC
183239 AATTGAAGATGACGAGTGCTTTTATTTTCTTACTGTCATCT
196 AATTGAAGATGACGAGTGCTTTTATTTTCTTACTGTCATCT
* *
183280 AAAATAATACCTTCCAACTCTCCTTTTTATTAGTCCATAAAAGAGAAAAACCAAAATTATAACTC
1 AAAATAATACCTTCCAACTCTCCTTTTTATTAGTCCATAAAAGAGAAAAACAAAAATTACAACTC
183345 ATTACCCAATCTTTTACTCTACCACCAGCCCAGGTGAAGGCCTAGCCATAAGTAGCCCCTGAATT
66 ATTACCCAATCTTTTACTCTACCACCAGCCCAGGTGAAGGCCTAGCCATAAGTAGCCCCTGAATT
183410 TTATCTATTTCCTCTCGAGCTTTTCCATGTTCTCTCGGTAGAGCACGTATTGGATTTCAAACTTC
131 TTATCTATTTCCTCTCGAGCTTTTCCATGTTCTCTCGGTAGAGCACGTATTGGATTTCAAACTTC
183475 AATTGAAGATGACGAGTGCTTTTATTTTCTTACTGTCAT
196 AATTGAAGATGACGAGTGCTTTTATTTTCTTACTGTCAT
183514 TCTTTACACC
Statistics
Matches: 232, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
236 232 1.00
ACGTcount: A:0.30, C:0.24, G:0.13, T:0.34
Consensus pattern (236 bp):
AAAATAATACCTTCCAACTCTCCTTTTTATTAGTCCATAAAAGAGAAAAACAAAAATTACAACTC
ATTACCCAATCTTTTACTCTACCACCAGCCCAGGTGAAGGCCTAGCCATAAGTAGCCCCTGAATT
TTATCTATTTCCTCTCGAGCTTTTCCATGTTCTCTCGGTAGAGCACGTATTGGATTTCAAACTTC
AATTGAAGATGACGAGTGCTTTTATTTTCTTACTGTCATCT
Found at i:188028 original size:28 final size:27
Alignment explanation
Indices: 187964--188031 Score: 109
Period size: 27 Copynumber: 2.5 Consensus size: 27
187954 TTTTCACCCT
*
187964 AAACCCGACCCAAATATCACACTTAAA
1 AAACCCGACCCGAATATCACACTTAAA
*
187991 AAACTCGACCCGAATATCACACTTAAAA
1 AAACCCGACCCGAATATCACACTT-AAA
188019 AAACCCGACCCGA
1 AAACCCGACCCGA
188032 CCCGAATCCG
Statistics
Matches: 37, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
27 22 0.59
28 15 0.41
ACGTcount: A:0.46, C:0.34, G:0.07, T:0.13
Consensus pattern (27 bp):
AAACCCGACCCGAATATCACACTTAAA
Found at i:188065 original size:31 final size:33
Alignment explanation
Indices: 188030--188092 Score: 96
Period size: 31 Copynumber: 2.0 Consensus size: 33
188020 AACCCGACCC
188030 GACCCGAAT-CCGAAA-TTTA-AAAAAAAAATCT
1 GACCCG-ATCCCGAAATTTTATAAAAAAAAATCT
188061 GACCCGATCCCGAAATTTTATAAAAAAAAATC
1 GACCCGATCCCGAAATTTTATAAAAAAAAATC
188093 CTACTCGAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
30 2 0.07
31 12 0.41
32 4 0.14
33 11 0.38
ACGTcount: A:0.49, C:0.21, G:0.10, T:0.21
Consensus pattern (33 bp):
GACCCGATCCCGAAATTTTATAAAAAAAAATCT
Found at i:196228 original size:16 final size:16
Alignment explanation
Indices: 196207--196255 Score: 71
Period size: 16 Copynumber: 3.1 Consensus size: 16
196197 TGAAAGCTTT
196207 TATTGAATGAACAAAG
1 TATTGAATGAACAAAG
** *
196223 TATTGAAACAACTAAG
1 TATTGAATGAACAAAG
196239 TATTGAATGAACAAAG
1 TATTGAATGAACAAAG
196255 T
1 T
196256 GGAAACAATA
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
16 27 1.00
ACGTcount: A:0.49, C:0.08, G:0.16, T:0.27
Consensus pattern (16 bp):
TATTGAATGAACAAAG
Found at i:215092 original size:8 final size:8
Alignment explanation
Indices: 215079--215103 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
215069 TTTCCATTAC
215079 AAAAAAGA
1 AAAAAAGA
215087 AAAAAAGA
1 AAAAAAGA
215095 AAAAAAGA
1 AAAAAAGA
215103 A
1 A
215104 TAATACGACC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (8 bp):
AAAAAAGA
Found at i:218373 original size:13 final size:13
Alignment explanation
Indices: 218355--218381 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
218345 TCATTTGAGA
218355 TATCAGGTTTCAT
1 TATCAGGTTTCAT
218368 TATCAGGTTTCAT
1 TATCAGGTTTCAT
218381 T
1 T
218382 TAGATGAATC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.22, C:0.15, G:0.15, T:0.48
Consensus pattern (13 bp):
TATCAGGTTTCAT
Found at i:221262 original size:22 final size:22
Alignment explanation
Indices: 221214--221262 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 22
221204 GGTGATTATT
*
221214 ATTTCTCTTGAGTTTATTTTTC
1 ATTTTTCTTGAGTTTATTTTTC
* *
221236 CTTTTTCTTGA-TTTTTTTTTC
1 ATTTTTCTTGAGTTTATTTTTC
*
221257 AATTTT
1 ATTTTT
221263 GAATAAGAAT
Statistics
Matches: 22, Mismatches: 5, Indels: 1
0.79 0.18 0.04
Matches are distributed among these distances:
21 13 0.59
22 9 0.41
ACGTcount: A:0.12, C:0.12, G:0.06, T:0.69
Consensus pattern (22 bp):
ATTTTTCTTGAGTTTATTTTTC
Found at i:221326 original size:24 final size:22
Alignment explanation
Indices: 221279--221335 Score: 62
Period size: 22 Copynumber: 2.5 Consensus size: 22
221269 GAATTTGTCA
*
221279 TTGTGTCACGTTTTTCCTGCTC
1 TTGTGTCACGTTTTTCATGCTC
*
221301 TTGTGTCACGCTTTTTCTATGTTC
1 TTGTGTCACG-TTTTTC-ATGCTC
*
221325 TT-TGGCACGTT
1 TTGTGTCACGTT
221336 CCTTATGACT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
22 12 0.40
23 12 0.40
24 6 0.20
ACGTcount: A:0.07, C:0.23, G:0.19, T:0.51
Consensus pattern (22 bp):
TTGTGTCACGTTTTTCATGCTC
Found at i:227575 original size:114 final size:114
Alignment explanation
Indices: 227375--227595 Score: 442
Period size: 114 Copynumber: 1.9 Consensus size: 114
227365 GTCGGATATG
227375 GAGACTAGAAATTGAAATGATCAGAAAAACACAAAAGCAACATGCAAAGGATTAATACTAATTAT
1 GAGACTAGAAATTGAAATGATCAGAAAAACACAAAAGCAACATGCAAAGGATTAATACTAATTAT
227440 CAAAACAATCTGCCAAGAAGAAACATTACATTTGATTAATTTTACAGTT
66 CAAAACAATCTGCCAAGAAGAAACATTACATTTGATTAATTTTACAGTT
227489 GAGACTAGAAATTGAAATGATCAGAAAAACACAAAAGCAACATGCAAAGGATTAATACTAATTAT
1 GAGACTAGAAATTGAAATGATCAGAAAAACACAAAAGCAACATGCAAAGGATTAATACTAATTAT
227554 CAAAACAATCTGCCAAGAAGAAACATTACATTTGATTAATTT
66 CAAAACAATCTGCCAAGAAGAAACATTACATTTGATTAATTT
227596 ATATTACAGT
Statistics
Matches: 107, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
114 107 1.00
ACGTcount: A:0.49, C:0.14, G:0.13, T:0.24
Consensus pattern (114 bp):
GAGACTAGAAATTGAAATGATCAGAAAAACACAAAAGCAACATGCAAAGGATTAATACTAATTAT
CAAAACAATCTGCCAAGAAGAAACATTACATTTGATTAATTTTACAGTT
Found at i:245549 original size:17 final size:19
Alignment explanation
Indices: 245508--245554 Score: 62
Period size: 21 Copynumber: 2.5 Consensus size: 19
245498 AAGAAAATTT
245508 TAAATTTATTAATTTTTTCTA
1 TAAATTTATTAA--TTTTCTA
245529 TAAATTTATTAA-TTT-TA
1 TAAATTTATTAATTTTCTA
245546 TAAATTTAT
1 TAAATTTAT
245555 CTTTAATATA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
17 11 0.42
18 3 0.12
21 12 0.46
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (19 bp):
TAAATTTATTAATTTTCTA
Found at i:245566 original size:25 final size:26
Alignment explanation
Indices: 245538--245592 Score: 76
Period size: 25 Copynumber: 2.2 Consensus size: 26
245528 ATAAATTTAT
245538 TAATTTTATAAATTTATCTTTAAT-A
1 TAATTTTATAAATTTATCTTTAATAA
* **
245563 TAATTTTTTTTATTTATCTTTAATAA
1 TAATTTTATAAATTTATCTTTAATAA
245589 TAAT
1 TAAT
245593 CTCAGGTAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
25 21 0.81
26 5 0.19
ACGTcount: A:0.36, C:0.04, G:0.00, T:0.60
Consensus pattern (26 bp):
TAATTTTATAAATTTATCTTTAATAA
Found at i:246464 original size:9 final size:9
Alignment explanation
Indices: 246452--246526 Score: 53
Period size: 9 Copynumber: 7.8 Consensus size: 9
246442 GTAAATACAT
246452 AAAATAAAG
1 AAAATAAAG
246461 AAAAATCAAAG
1 -AAAAT-AAAG
*
246472 -AAATAAAAT
1 AAAAT-AAAG
246481 AAAATAAAG
1 AAAATAAAG
246490 ATAAACATAAAG
1 --AAA-ATAAAG
*
246502 AAAATAAAT
1 AAAATAAAG
* *
246511 AAGATAAGG
1 AAAATAAAG
246520 AAAATAA
1 AAAATAA
246527 TAATCATACA
Statistics
Matches: 52, Mismatches: 8, Indels: 11
0.73 0.11 0.15
Matches are distributed among these distances:
9 27 0.52
10 12 0.23
11 7 0.13
12 6 0.12
ACGTcount: A:0.73, C:0.03, G:0.09, T:0.15
Consensus pattern (9 bp):
AAAATAAAG
Found at i:246473 original size:11 final size:10
Alignment explanation
Indices: 246415--246509 Score: 56
Period size: 11 Copynumber: 9.1 Consensus size: 10
246405 ATTACACATG
246415 AGAAAAAGTAA
1 AGAAAAA-TAA
246426 AGATAAAATAA
1 AGA-AAAATAA
*
246437 AGTAAGTAAATAC
1 AG-AA--AAATAA
*
246450 A-TAAAATAA
1 AGAAAAATAA
246459 AGAAAAATCAA
1 AGAAAAAT-AA
246470 AG--AAATAA
1 AGAAAAATAA
246478 A-ATAAAATAA
1 AGA-AAAATAA
246488 AGATAAACATAA
1 AGA-AAA-ATAA
246500 AG-AAAATAA
1 AGAAAAATAA
246509 A
1 A
246510 TAAGATAAGG
Statistics
Matches: 69, Mismatches: 4, Indels: 24
0.71 0.04 0.25
Matches are distributed among these distances:
8 3 0.04
9 15 0.22
10 15 0.22
11 19 0.28
12 11 0.16
13 6 0.09
ACGTcount: A:0.72, C:0.03, G:0.09, T:0.16
Consensus pattern (10 bp):
AGAAAAATAA
Found at i:246475 original size:19 final size:18
Alignment explanation
Indices: 246453--246490 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
246443 TAAATACATA
246453 AAATAAAGA-AAAATCAAAG
1 AAATAAA-ATAAAAT-AAAG
246472 AAATAAAATAAAATAAAG
1 AAATAAAATAAAATAAAG
246490 A
1 A
246491 TAAACATAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 6 0.33
19 12 0.67
ACGTcount: A:0.76, C:0.03, G:0.08, T:0.13
Consensus pattern (18 bp):
AAATAAAATAAAATAAAG
Found at i:246481 original size:33 final size:34
Alignment explanation
Indices: 246418--246511 Score: 103
Period size: 29 Copynumber: 2.9 Consensus size: 34
246408 ACACATGAGA
*
246418 AAAAGTAAAGATAAAATAAAGTAAGTAAATACAT
1 AAAAGTAAAGATAAAATAAAGTAAATAAATACAT
246452 AAAA-TAAAGA-AAAATCAAAG-AAAT-AA-A-AT
1 AAAAGTAAAGATAAAAT-AAAGTAAATAAATACAT
*
246481 AAAA-TAAAGATAAACATAAAGAAAATAAATA
1 AAAAGTAAAGATAAA-ATAAAGTAAATAAATA
246512 AGATAAGGAA
Statistics
Matches: 53, Mismatches: 1, Indels: 13
0.79 0.01 0.19
Matches are distributed among these distances:
29 12 0.23
30 8 0.15
31 8 0.15
32 10 0.19
33 11 0.21
34 4 0.08
ACGTcount: A:0.71, C:0.03, G:0.09, T:0.17
Consensus pattern (34 bp):
AAAAGTAAAGATAAAATAAAGTAAATAAATACAT
Found at i:246483 original size:29 final size:29
Alignment explanation
Indices: 246444--246523 Score: 92
Period size: 30 Copynumber: 2.7 Consensus size: 29
246434 TAAAGTAAGT
*
246444 AAATACATAAAATAAAGAAAA-ATCAAAG-
1 AAATAAATAAAATAAAGAAAACAT-AAAGA
246472 AAATAAAATAAAATAAAGATAAACATAAAGA
1 AAAT-AAATAAAATAAAGA-AAACATAAAGA
* *
246503 AAATAAATAAGATAAGGAAAA
1 AAATAAATAAAATAAAGAAAA
246524 TAATAATCAT
Statistics
Matches: 45, Mismatches: 3, Indels: 7
0.82 0.05 0.13
Matches are distributed among these distances:
28 4 0.09
29 16 0.36
30 19 0.42
31 6 0.13
ACGTcount: A:0.72, C:0.04, G:0.09, T:0.15
Consensus pattern (29 bp):
AAATAAATAAAATAAAGAAAACATAAAGA
Found at i:246501 original size:12 final size:11
Alignment explanation
Indices: 246418--246502 Score: 58
Period size: 11 Copynumber: 7.9 Consensus size: 11
246408 ACACATGAGA
246418 AAAAGTAAAGAT
1 AAAA-TAAAGAT
246430 AAAATAAAG-T
1 AAAATAAAGAT
* *
246440 AAGTAA-ATACAT
1 AA--AATAAAGAT
246452 AAAATAAAGA-
1 AAAATAAAGAT
246462 AAAATCAAAG--
1 AAAAT-AAAGAT
246472 -AAATAAA-AT
1 AAAATAAAGAT
246481 AAAATAAAGAT
1 AAAATAAAGAT
246492 AAACATAAAGA
1 AAA-ATAAAGA
246503 AAATAAATAA
Statistics
Matches: 59, Mismatches: 4, Indels: 20
0.71 0.05 0.24
Matches are distributed among these distances:
8 3 0.05
9 4 0.07
10 17 0.29
11 19 0.32
12 16 0.27
ACGTcount: A:0.71, C:0.04, G:0.09, T:0.16
Consensus pattern (11 bp):
AAAATAAAGAT
Found at i:246772 original size:17 final size:17
Alignment explanation
Indices: 246728--246776 Score: 57
Period size: 17 Copynumber: 2.9 Consensus size: 17
246718 ACGTATAAAC
*
246728 AGAAAAAAATAGAAATA
1 AGAAAAAAATAGAAAGA
246745 A-AATAAAAATAGAAAGA
1 AGAA-AAAAATAGAAAGA
*
246762 AGAAAATAATA-AAAG
1 AGAAAAAAATAGAAAG
246777 GATTAAATTG
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
16 6 0.21
17 20 0.71
18 2 0.07
ACGTcount: A:0.76, C:0.00, G:0.12, T:0.12
Consensus pattern (17 bp):
AGAAAAAAATAGAAAGA
Found at i:248696 original size:83 final size:83
Alignment explanation
Indices: 248552--249661 Score: 1165
Period size: 83 Copynumber: 13.3 Consensus size: 83
248542 TGACATATAG
* * * * * *
248552 CCCTTCTTGCCTTAAGTTATGCTGTAAATTTGATATGCCTTTGAGCTGAATGTAATTGAACTCGA
1 CCCTTCTTACCTTGAGCTATGCTGTAAA--TGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGA
*
248617 AGGTCTTTTGTTGCAGATAG
64 AGGTCTTTTGTTGCAGATAA
* ** *
248637 CCCTTCTCACCTTGAGCTATGCTACAAATGATGTGCCTTTGAGCTGAGTGAAATCGAACTCGAAG
1 CCCTTCTTACCTTGAGCTATGCTGTAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAG
*
248702 GTC-TTTG--GCAGATAG
66 GTCTTTTGTTGCAGATAA
* *
248717 CCCTTCTTACCTTGAGCTATG-TTTAAATGATGCGCCTTTGAGCTGAGTGTAATCGAACTCGAAG
1 CCCTTCTTACCTTGAGCTATGCTGTAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAG
* *
248781 TTCTTTTGATGACAGATAA
66 GTCTTTTGTTG-CAGATAA
* * * * * *
248800 CCCTTC-TAGCCTTGAGTTATGCTGCAAATGATATGCCTCTAAGCTAAGTGTAATCGAACTCGAA
1 CCCTTCTTA-CCTTGAGCTATGCTGTAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAA
*
248864 GGTC-TTTGGTGACAGATAA
65 GGTCTTTTGTTG-CAGATAA
* ** ** * * *
248883 CCCTTCTTGCCTTGATTTATATTGTAAATGATGTGCCTTTGATCTAAGTGTAATCGAACTCAAAG
1 CCCTTCTTACCTTGAGCTATGCTGTAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAG
* *
248948 GTC-TTTGATGACATATAA
66 GTCTTTTGTTG-CAGATAA
* *
248966 CCCTTCTTGCCTTGAGCTATGCTGTAAATGATGTGCCTTCGAGCTGAGTGTAATCGAACTCGAAG
1 CCCTTCTTACCTTGAGCTATGCTGTAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAG
*
249031 GTCTTTTGTTGACATATAA
66 GTCTTTTGTTG-CAGATAA
* * * *
249050 CCCTTCTAACCTTGAGTTATGCTGTAAATGATGTGCCCTTGAGCTGAGTATAATCGAACTCG-AG
1 CCCTTCTTACCTTGAGCTATGCTGTAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAG
*
249114 GTCTTTTGTTAACAGATAA
66 GTCTTTTGTT-GCAGATAA
* *
249133 CCCTTC-TAGCCTTGAGTTATTCTGTAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAA
1 CCCTTCTTA-CCTTGAGCTATGCTGTAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAA
* * *
249197 TGTC-TTTGATGACATATAA
65 GGTCTTTTGTTG-CAGATAA
** * *
249216 CCCTTCTTGTCTTGAGCTATGCTGTAAATGATATGCCTTTGAGCTGAGTGTAATCGAACTCAAAG
1 CCCTTCTTACCTTGAGCTATGCTGTAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAG
* * *
249281 GTCTTATGTTGGAAATAA
66 GTCTTTTGTTGCAGATAA
* * * * * *
249299 CCCTTCTTTCCTTGAGATATGTTGCAAATGATGTGCCTTTGAGCTGAGTGCAATCAAACTCGAAG
1 CCCTTCTTACCTTGAGCTATGCTGTAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAG
*
249364 GTC-TTTG--GCAGATAG
66 GTCTTTTGTTGCAGATAA
* * * *
249379 CCCTTCTTGCCTTGAGCTATGTTGCAAATTATGTGCCTTTGAGCTGAGTGTAATC-ACACTCGAA
1 CCCTTCTTACCTTGAGCTATGCTGTAAATGATGTGCCTTTGAGCTGAGTGTAATCGA-ACTCGAA
*
249443 GGTCTTTT-TTGGCATATAA
65 GGTCTTTTGTT-GCAGATAA
* * * *
249462 CCATTCTTGCCTTGAGCTATGCTGTAAATGATGTTCCTTTGAGTTGAGTGTAATCGAAGTATCGA
1 CCCTTCTTACCTTGAGCTATGCTGTAAATGATGTGCCTTTGAGCTGAGTG---T---A--ATCGA
*
249527 ACTCGAAGGTCTTTTGTTGGCAAATAA
58 ACTCGAAGGTCTTTTGTT-GCAGATAA
* * * * * * *
249554 CCCTTCTCACCTTGAGCTATGTTGCAAATGATGCGCATTTGAGTTGAGTGTAATTGAACTCGAAG
1 CCCTTCTTACCTTGAGCTATGCTGTAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAG
* *
249619 GTC-TTGGCTGACAGATAA
66 GTCTTTTGTTG-CAGATAA
* *
249637 CCCTT-TTCGCCTTGAGTTATGCTGT
1 CCCTTCTT-ACCTTGAGCTATGCTGT
249662 CAATAGTTTT
Statistics
Matches: 876, Mismatches: 118, Indels: 64
0.83 0.11 0.06
Matches are distributed among these distances:
79 42 0.05
80 99 0.11
81 3 0.00
82 13 0.01
83 488 0.56
84 134 0.15
85 22 0.03
86 2 0.00
89 2 0.00
91 18 0.02
92 53 0.06
ACGTcount: A:0.25, C:0.19, G:0.22, T:0.35
Consensus pattern (83 bp):
CCCTTCTTACCTTGAGCTATGCTGTAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAG
GTCTTTTGTTGCAGATAA
Found at i:249081 original size:250 final size:250
Alignment explanation
Indices: 248536--249657 Score: 1329
Period size: 250 Copynumber: 4.5 Consensus size: 250
248526 AACTCGATAA
* * ** * * *
248536 TTTTATTGACATATAGCCCTTCTTGCCTTAAGTTATGCTGTAAATTTGATATGCCTTTGAGCTGA
1 TTTTGTTGACATATAACCCTTCTAACCTTGAGTTATGCTGCAAA--TGATGTGCCTTTGAGCTGA
* * * * ** * * *
248601 ATGTAATTGAACTCGAAGGTCTTTTGTTG-CAGATAGCCCTTCTCACCTTGAGCTATGCTACAAA
64 GTGTAATCGAACTCGAAGGTC-TTTGGTGACAGATAACCCTTCTTGCCTTGAGTTATGTTGCAAA
* * * *
248665 TGATGTGCCTTTGAGCTGAGTGAAATCGAACTCGAAGGTCTTTG--G-CAGATAGCCCTTCTTAC
128 TGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTGATGACATATAACCCTTCTTGC
* * *
248727 CTTGAGCTATG-TTTAAATGATGCGCCTTTGAGCTGAGTGTAATCGAACTCGAAGTTC
193 CTTGAGCTATGCTGTAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTC
* * * * * * *
248784 TTTTGATGACAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATATGCCTCTAAGCTAAGT
1 TTTTGTTGACATATAACCCTTCTAACCTTGAGTTATGCTGCAAATGATGTGCCTTTGAGCTGAGT
* * *
248849 GTAATCGAACTCGAAGGTCTTTGGTGACAGATAACCCTTCTTGCCTTGATTTATATTGTAAATGA
66 GTAATCGAACTCGAAGGTCTTTGGTGACAGATAACCCTTCTTGCCTTGAGTTATGTTGCAAATGA
* * *
248914 TGTGCCTTTGATCTAAGTGTAATCGAACTCAAAGGTCTTTGATGACATATAACCCTTCTTGCCTT
131 TGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTGATGACATATAACCCTTCTTGCCTT
*
248979 GAGCTATGCTGTAAATGATGTGCCTTCGAGCTGAGTGTAATCGAACTCGAAGGTC
196 GAGCTATGCTGTAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTC
* *
249034 TTTTGTTGACATATAACCCTTCTAACCTTGAGTTATGCTGTAAATGATGTGCCCTTGAGCTGAGT
1 TTTTGTTGACATATAACCCTTCTAACCTTGAGTTATGCTGCAAATGATGTGCCTTTGAGCTGAGT
* * * * *
249099 ATAATCGAACTCG-AGGTCTTTTGTTAACAGATAACCCTTCTAGCCTTGAGTTAT-TCTGTAAAT
66 GTAATCGAACTCGAAGGTC-TTTGGTGACAGATAACCCTTCTTGCCTTGAGTTATGT-TGCAAAT
* *
249162 GATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAATGTCTTTGATGACATATAACCCTTCTTGTC
129 GATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTGATGACATATAACCCTTCTTGCC
* *
249227 TTGAGCTATGCTGTAAATGATATGCCTTTGAGCTGAGTGTAATCGAACTCAAAGGTC
194 TTGAGCTATGCTGTAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTC
* ** * *
249284 TTATGTTGGA-A-ATAACCCTTCTTTCCTTGAGATATGTTGCAAATGATGTGCCTTTGAGCTGAG
1 TTTTGTT-GACATATAACCCTTCTAACCTTGAGTTATGCTGCAAATGATGTGCCTTTGAGCTGAG
* * * * *
249347 TGCAATCAAACTCGAAGGTCTTT-G-G-CAGATAGCCCTTCTTGCCTTGAGCTATGTTGCAAATT
65 TGTAATCGAACTCGAAGGTCTTTGGTGACAGATAACCCTTCTTGCCTTGAGTTATGTTGCAAATG
** * *
249409 ATGTGCCTTTGAGCTGAGTGTAATC-ACACTCGAAGGTCTTTTTTGGCATATAACCATTCTTGCC
130 ATGTGCCTTTGAGCTGAGTGTAATCGA-ACTCGAAGGTCTTTGATGACATATAACCCTTCTTGCC
* *
249473 TTGAGCTATGCTGTAAATGATGTTCCTTTGAGTTGAGTGTAATCGAAGTATCGAACTCGAAGGTC
194 TTGAGCTATGCTGTAAATGATGTGCCTTTGAGCTGAGTG---T---A--ATCGAACTCGAAGGTC
* * * * * * * *
249538 TTTTGTTGGCAAATAACCCTTCTCACCTTGAGCTATGTTGCAAATGATGCGCATTTGAGTTGAGT
1 TTTTGTTGACATATAACCCTTCTAACCTTGAGTTATGCTGCAAATGATGTGCCTTTGAGCTGAGT
*
249603 GTAATTGAACTCGAAGGTC-TTGGCTGACAGATAACCCTT-TTCGCCTTGAGTTATG
66 GTAATCGAACTCGAAGGTCTTTGG-TGACAGATAACCCTTCTT-GCCTTGAGTTATG
249658 CTGTCAATAG
Statistics
Matches: 753, Mismatches: 95, Indels: 42
0.85 0.11 0.05
Matches are distributed among these distances:
245 7 0.01
246 223 0.30
247 1 0.00
248 38 0.05
249 92 0.12
250 274 0.36
251 2 0.00
252 1 0.00
253 1 0.00
254 24 0.03
255 64 0.08
257 3 0.00
258 23 0.03
ACGTcount: A:0.25, C:0.19, G:0.21, T:0.35
Consensus pattern (250 bp):
TTTTGTTGACATATAACCCTTCTAACCTTGAGTTATGCTGCAAATGATGTGCCTTTGAGCTGAGT
GTAATCGAACTCGAAGGTCTTTGGTGACAGATAACCCTTCTTGCCTTGAGTTATGTTGCAAATGA
TGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTGATGACATATAACCCTTCTTGCCTT
GAGCTATGCTGTAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTC
Found at i:249218 original size:333 final size:329
Alignment explanation
Indices: 248542--249660 Score: 1309
Period size: 333 Copynumber: 3.4 Consensus size: 329
248532 ATAATTTTAT
* * *
248542 TGACATATAGCCCTTCTTGCCTTAAGTTATGCTGTAAATTTGATATGCCTTTGAGCTGAA-TGTA
1 TGACATATAACCCTTCTTGCCTTGAGCTATGCTGTAAA--TGATATGCCTTTGAGCT-AAGTGTA
* * * ** *
248606 ATTGAACTCGAAGGTCTTTTGTTG-CAGATAGCCCTTCTCACCTTGAGCTATGCTACAAATGATG
63 ATCGAACTCAAAGGTC-TTTGTTGACAGATAACCCTTCTTGCCTTGAGCTATGCTGCAAATGATG
248670 TGCCTTTGAGCTGAGTGAAATCGAACTCGAAGGTCTTTGGCAGATAGCCCTTCTTACCTTGAGCT
127 TGCCTTTGAGCTGAGTGAAATCGAACTCGAAGGTCTTTGGCAGATAGCCCTTCTTACCTTGAGCT
* * * *
248735 ATGTTTAAATGATGCGCCTTTGAGCTGAGTGTAATCGAACTCGAAGTTCTTTTGATGACAGATAA
192 ATGTGTAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGACAGATAA
* * * * *
248800 CCCTTCTAGCCTTGAGTTATGCTGCAAATGATATGCCTCTAAGCTAAGTGTAATCGAACTCGAAG
257 CCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAG
*
248865 GTCTTTGG
322 GTCTTTGA
* ** ** * *
248873 TGACAGATAACCCTTCTTGCCTTGATTTATATTGTAAATGATGTGCCTTTGATCTAAGTGTAATC
1 TGACATATAACCCTTCTTGCCTTGAGCTATGCTGTAAATGATATGCCTTTGAGCTAAGTGTAATC
* * *
248938 GAACTCAAAGGTCTTTGATGACATATAACCCTTCTTGCCTTGAGCTATGCTGTAAATGATGTGCC
66 GAACTCAAAGGTCTTTGTTGACAGATAACCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTGCC
* * * * * *
249003 TTCGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGACATATAACCCTTCTAACCTTGAGTT
131 TTTGAGCTGAGTGAAATCGAACTCGAAGGTC-TTTG--G-CAGATAGCCCTTCTTACCTTGAGCT
* * *
249068 ATGCTGTAAATGATGTGCCCTTGAGCTGAGTATAATCGAACTCG-AGGTCTTTTGTTAACAGATA
192 ATG-TGTAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGACAGATA
*
249132 ACCCTTCTAGCCTTGAGTTATTCTGTAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAA
256 ACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAA
*
249197 TGTCTTTGA
321 GGTCTTTGA
* *
249206 TGACATATAACCCTTCTTGTCTTGAGCTATGCTGTAAATGATATGCCTTTGAGCTGAGTGTAATC
1 TGACATATAACCCTTCTTGCCTTGAGCTATGCTGTAAATGATATGCCTTTGAGCTAAGTGTAATC
* * *
249271 GAACTCAAAGGTCTTATGTTGGA-A-ATAACCCTTCTTTCCTTGAGATATGTTGCAAATGATGTG
66 GAACTCAAAGGTCTT-TGTT-GACAGATAACCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTG
* * *
249334 CCTTTGAGCTGAGTGCAATCAAACTCGAAGGTCTTTGGCAGATAGCCCTTCTTGCCTTGAGCTAT
129 CCTTTGAGCTGAGTGAAATCGAACTCGAAGGTCTTTGGCAGATAGCCCTTCTTACCTTGAGCTAT
* * * *
249399 GTTGCAAATTATGTGCCTTTGAGCTGAGTGTAATC-ACACTCGAAGGTCTTTT-TTGGCATATAA
194 G-TGTAAATGATGTGCCTTTGAGCTGAGTGTAATCGA-ACTCGAAGGTCTTTTGTTGACAGATAA
* * * * *
249462 CCATTCTTGCCTTGAGCTATGCTGTAAATGATGTTCCTTTGAGTTGAGTGTAATCGAAGTATCGA
257 CCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCTTTGAGCTGAGTG---T---A--ATCGA
*
249527 ACTCGAAGGTCTTTTGT
314 ACTCGAAGGTC-TTTGA
* * ** * * ** * * * *
249544 TGGCAAATAACCCTTCTCACCTTGAGCTATGTTGCAAATGATGCGCATTTGAGTTGAGTGTAATT
1 TGACATATAACCCTTCTTGCCTTGAGCTATGCTGTAAATGATATGCCTTTGAGCTAAGTGTAATC
* * * *
249609 GAACTCGAAGGTCTTGGCTGACAGATAACCCTT-TTCGCCTTGAGTTATGCTG
66 GAACTCAAAGGTCTTTGTTGACAGATAACCCTTCTT-GCCTTGAGCTATGCTG
249661 TCAATAGTTT
Statistics
Matches: 671, Mismatches: 94, Indels: 39
0.83 0.12 0.05
Matches are distributed among these distances:
328 9 0.01
329 209 0.31
330 14 0.02
331 32 0.05
332 6 0.01
333 243 0.36
334 40 0.06
335 3 0.00
336 2 0.00
337 20 0.03
338 93 0.14
ACGTcount: A:0.25, C:0.19, G:0.22, T:0.35
Consensus pattern (329 bp):
TGACATATAACCCTTCTTGCCTTGAGCTATGCTGTAAATGATATGCCTTTGAGCTAAGTGTAATC
GAACTCAAAGGTCTTTGTTGACAGATAACCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTGCC
TTTGAGCTGAGTGAAATCGAACTCGAAGGTCTTTGGCAGATAGCCCTTCTTACCTTGAGCTATGT
GTAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGACAGATAACCCT
TCTAGCCTTGAGTTATGCTGTAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCT
TTGA
Found at i:249567 original size:92 final size:91
Alignment explanation
Indices: 249436--249607 Score: 254
Period size: 92 Copynumber: 1.9 Consensus size: 91
249426 GTGTAATCAC
* ** * ** *
249436 ACTCGAAGGTCTTTTTTGGCATATAACCATTCTTGCCTTGAGCTATGCTGTAAATGATGTTCCTT
1 ACTCGAAGGTCTTTTTTGGCAAATAACCATTCTCACCTTGAGCTATGCTGCAAATGATGCGCATT
249501 TGAGTTGAGTGTAATCGAAGTATCGA
66 TGAGTTGAGTGTAATCGAAGTATCGA
* *
249527 ACTCGAAGGTCTTTTGTTGGCAAATAACCCTTCTCACCTTGAGCTATGTTGCAAATGATGCGCAT
1 ACTCGAAGGTCTTTT-TTGGCAAATAACCATTCTCACCTTGAGCTATGCTGCAAATGATGCGCAT
249592 TTGAGTTGAGTGTAAT
65 TTGAGTTGAGTGTAAT
249608 TGAACTCGAA
Statistics
Matches: 71, Mismatches: 9, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
91 15 0.21
92 56 0.79
ACGTcount: A:0.24, C:0.17, G:0.22, T:0.36
Consensus pattern (91 bp):
ACTCGAAGGTCTTTTTTGGCAAATAACCATTCTCACCTTGAGCTATGCTGCAAATGATGCGCATT
TGAGTTGAGTGTAATCGAAGTATCGA
Found at i:254044 original size:23 final size:22
Alignment explanation
Indices: 254018--254062 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
254008 CTGAGTGACA
254018 TATGAAATTTGTCCCGAAGGACC
1 TATG-AATTTGTCCCGAAGGACC
*
254041 TATGTATTTGTCCCGAAGGACC
1 TATGAATTTGTCCCGAAGGACC
254063 ACTGTACATA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
22 17 0.81
23 4 0.19
ACGTcount: A:0.27, C:0.22, G:0.22, T:0.29
Consensus pattern (22 bp):
TATGAATTTGTCCCGAAGGACC
Found at i:254076 original size:22 final size:22
Alignment explanation
Indices: 254029--254080 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 22
254019 ATGAAATTTG
** *
254029 TCCCGAAGGACCTATGTATTTG
1 TCCCGAAGGACCTATGTACATA
254051 TCCCGAAGGACC-ACTGTACATA
1 TCCCGAAGGACCTA-TGTACATA
254073 TCCCGAAG
1 TCCCGAAG
254081 AACCGCGTAG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
21 1 0.04
22 25 0.96
ACGTcount: A:0.27, C:0.29, G:0.21, T:0.23
Consensus pattern (22 bp):
TCCCGAAGGACCTATGTACATA
Found at i:256271 original size:16 final size:16
Alignment explanation
Indices: 256250--256344 Score: 76
Period size: 16 Copynumber: 6.0 Consensus size: 16
256240 TACACATGAG
256250 ATAAAGTAAAGATAAA
1 ATAAAGTAAAGATAAA
*
256266 ATAAAGTAAA-AT-AC
1 ATAAAGTAAAGATAAA
256280 ATAAA-TAAAGA-AAA
1 ATAAAGTAAAGATAAA
*
256294 ATCAAAGAAATAGAGATAAA
1 AT-AAAG---TAAAGATAAA
*
256314 ATAAAATAAAGATAAA
1 ATAAAGTAAAGATAAA
256330 CATAAAG-AAA-ATAAA
1 -ATAAAGTAAAGATAAA
256345 TAAGATAAGG
Statistics
Matches: 64, Mismatches: 6, Indels: 19
0.72 0.07 0.21
Matches are distributed among these distances:
13 4 0.06
14 10 0.16
15 10 0.16
16 22 0.34
17 5 0.08
19 8 0.12
20 5 0.08
ACGTcount: A:0.71, C:0.03, G:0.09, T:0.17
Consensus pattern (16 bp):
ATAAAGTAAAGATAAA
Found at i:256336 original size:12 final size:11
Alignment explanation
Indices: 256248--256337 Score: 66
Period size: 11 Copynumber: 8.3 Consensus size: 11
256238 ATTACACATG
*
256248 AGATAAAGTAA
1 AGATAAAATAA
256259 AGATAAAATAA
1 AGATAAAATAA
256270 AG-TAAAAT--
1 AGATAAAATAA
*
256278 ACAT-AAATAA
1 AGATAAAATAA
256288 AGA-AAAATCAA
1 AGATAAAAT-AA
*
256299 AGAAATAGAGATAA
1 AG--ATA-AAATAA
256313 A-ATAAAATAA
1 AGATAAAATAA
256323 AGATAAACATAA
1 AGATAAA-ATAA
256335 AGA
1 AGA
256338 AAATAAATAA
Statistics
Matches: 63, Mismatches: 5, Indels: 21
0.71 0.06 0.24
Matches are distributed among these distances:
8 5 0.08
9 1 0.02
10 18 0.29
11 24 0.38
12 7 0.11
13 1 0.02
14 4 0.06
15 3 0.05
ACGTcount: A:0.69, C:0.03, G:0.11, T:0.17
Consensus pattern (11 bp):
AGATAAAATAA
Found at i:256346 original size:30 final size:30
Alignment explanation
Indices: 256250--256352 Score: 86
Period size: 30 Copynumber: 3.3 Consensus size: 30
256240 TACACATGAG
* * *
256250 ATAAAGTAAAGATAAAATAAAGTAAAATAC
1 ATAAAATAAAGATAAAATAAAGAAAAATAA
256280 AT-AAATAAAGA-AAAATCAAAGAAATAGAGATAAA
1 ATAAAATAAAGATAAAAT-AAAG-AA-A-A-AT-AA
256314 ATAAAATAAAGATAAACATAAAG-AAAATAA
1 ATAAAATAAAGATAAA-ATAAAGAAAAATAA
*
256344 ATAAGATAA
1 ATAAAATAA
256353 GGAAAATAAT
Statistics
Matches: 60, Mismatches: 4, Indels: 18
0.73 0.05 0.22
Matches are distributed among these distances:
28 5 0.08
29 12 0.20
30 13 0.22
31 3 0.05
32 2 0.03
33 3 0.05
34 4 0.07
35 9 0.15
36 7 0.12
37 2 0.03
ACGTcount: A:0.70, C:0.03, G:0.10, T:0.17
Consensus pattern (30 bp):
ATAAAATAAAGATAAAATAAAGAAAAATAA
Found at i:256976 original size:20 final size:20
Alignment explanation
Indices: 256947--256987 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
256937 CCGCTGCCTA
* * *
256947 GTCGGTCGTCGTTGATCGGC
1 GTCGGCCGTCGGTCATCGGC
256967 GTCGGCCGTCGGTCATCGGC
1 GTCGGCCGTCGGTCATCGGC
256987 G
1 G
256988 GCAAAACAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.05, C:0.29, G:0.41, T:0.24
Consensus pattern (20 bp):
GTCGGCCGTCGGTCATCGGC
Found at i:258643 original size:23 final size:24
Alignment explanation
Indices: 258617--258666 Score: 59
Period size: 22 Copynumber: 2.2 Consensus size: 24
258607 CAAACAGTCA
* *
258617 AAAAATGTGTCAT-AAGGCAAAAG
1 AAAAACGTATCATAAAGGCAAAAG
*
258640 -AAAACGTATCATAAAGGCAGAAG
1 AAAAACGTATCATAAAGGCAAAAG
258663 AAAA
1 AAAA
258667 CATGCTATAA
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
22 10 0.45
23 9 0.41
24 3 0.14
ACGTcount: A:0.56, C:0.10, G:0.20, T:0.14
Consensus pattern (24 bp):
AAAAACGTATCATAAAGGCAAAAG
Found at i:258667 original size:23 final size:23
Alignment explanation
Indices: 258626--258698 Score: 71
Period size: 23 Copynumber: 3.2 Consensus size: 23
258616 AAAAAATGTG
*
258626 TCAT-AAGGCAAAAGAAAACGTA
1 TCATAAAGGCAGAAGAAAACGTA
258648 TCATAAAGGCAGAAGAAAAC--A
1 TCATAAAGGCAGAAGAAAACGTA
** *
258669 TGCTATAAAGATAGAGGAAAACGTA
1 T-C-ATAAAGGCAGAAGAAAACGTA
258694 TCATA
1 TCATA
258699 CAAGTATACT
Statistics
Matches: 42, Mismatches: 4, Indels: 9
0.76 0.07 0.16
Matches are distributed among these distances:
21 2 0.05
22 5 0.12
23 32 0.76
24 1 0.02
25 2 0.05
ACGTcount: A:0.52, C:0.12, G:0.19, T:0.16
Consensus pattern (23 bp):
TCATAAAGGCAGAAGAAAACGTA
Found at i:259694 original size:34 final size:33
Alignment explanation
Indices: 259651--259715 Score: 103
Period size: 34 Copynumber: 1.9 Consensus size: 33
259641 ATATAATTAT
259651 TTTATTAAAAAACAAGTATGCTTCACAAATTTG
1 TTTATTAAAAAACAAGTATGCTTCACAAATTTG
* *
259684 TTTATTTAAAAAATAAGTATGCTTCATAAATT
1 TTTA-TTAAAAAACAAGTATGCTTCACAAATT
259716 AAAATTGATG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
33 4 0.14
34 25 0.86
ACGTcount: A:0.43, C:0.09, G:0.08, T:0.40
Consensus pattern (33 bp):
TTTATTAAAAAACAAGTATGCTTCACAAATTTG
Found at i:274361 original size:24 final size:22
Alignment explanation
Indices: 274317--274361 Score: 54
Period size: 24 Copynumber: 2.0 Consensus size: 22
274307 TTATCTTTGT
**
274317 GTTTAGTATTTTATTTTAAATA
1 GTTTAGTATTTTATTAGAAATA
274339 GTTTAAGTATTATTATTAGAAAT
1 GTTT-AGTATT-TTATTAGAAAT
274362 TAACTCTTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 4 0.21
23 6 0.32
24 9 0.47
ACGTcount: A:0.36, C:0.00, G:0.11, T:0.53
Consensus pattern (22 bp):
GTTTAGTATTTTATTAGAAATA
Found at i:278464 original size:22 final size:22
Alignment explanation
Indices: 278413--278464 Score: 54
Period size: 22 Copynumber: 2.4 Consensus size: 22
278403 TCACTTTAAA
*
278413 TTTATTTATTTAATTATTTATT
1 TTTATTTATGTAATTATTTATT
*
278435 TTCT-TTTATGTACTT-TTTATCT
1 TT-TATTTATGTAATTATTTAT-T
278457 TTTATTTA
1 TTTATTTA
278465 AAAAACAACT
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
21 6 0.24
22 18 0.72
23 1 0.04
ACGTcount: A:0.21, C:0.06, G:0.02, T:0.71
Consensus pattern (22 bp):
TTTATTTATGTAATTATTTATT
Found at i:280270 original size:32 final size:31
Alignment explanation
Indices: 280184--280307 Score: 135
Period size: 31 Copynumber: 4.0 Consensus size: 31
280174 CTCGAATGAC
* *
280184 CTGTCCATATGT-TCCTAAGAACATAGGTAAA
1 CTGTCCATATGTCTCCAAAG-ACATAGGTAAT
*
280215 CTGTTCATATGTC-CCAAAGGACATAGGTAAT
1 CTGTCCATATGTCTCCAAA-GACATAGGTAAT
* *
280246 CATGTCCATATGTCTCGAAAGACATAGGCAAT
1 C-TGTCCATATGTCTCCAAAGACATAGGTAAT
** *
280278 CTGTTTATATGTCTCGAAAGACATAGGTAA
1 CTGTCCATATGTCTCCAAAGACATAGGTAA
280308 CCCTCGACTC
Statistics
Matches: 80, Mismatches: 9, Indels: 8
0.82 0.09 0.08
Matches are distributed among these distances:
31 52 0.65
32 24 0.30
33 4 0.05
ACGTcount: A:0.34, C:0.19, G:0.19, T:0.29
Consensus pattern (31 bp):
CTGTCCATATGTCTCCAAAGACATAGGTAAT
Found at i:280271 original size:63 final size:63
Alignment explanation
Indices: 280185--280307 Score: 160
Period size: 63 Copynumber: 2.0 Consensus size: 63
280175 TCGAATGACC
* *
280185 TGTCCATATGTTCCTAAGAACATAGGTAAACTGTTCATATGTC-CCAAAGGACATAGGTAATCA
1 TGTCCATATGTTCCAAAGAACATAGGCAAACTGTTCATATGTCTCCAAA-GACATAGGTAATCA
* * * *
280248 TGTCCATATGTCTCGAAAG-ACATAGGCAATCTGTTTATATGTCTCGAAAGACATAGGTAA
1 TGTCCATATGT-TCCAAAGAACATAGGCAAACTGTTCATATGTCTCCAAAGACATAGGTAA
280308 CCCTCGACTC
Statistics
Matches: 52, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
63 43 0.83
64 9 0.17
ACGTcount: A:0.34, C:0.18, G:0.19, T:0.29
Consensus pattern (63 bp):
TGTCCATATGTTCCAAAGAACATAGGCAAACTGTTCATATGTCTCCAAAGACATAGGTAATCA
Found at i:284822 original size:31 final size:31
Alignment explanation
Indices: 284787--284889 Score: 118
Period size: 31 Copynumber: 3.3 Consensus size: 31
284777 TTGAAGGACG
* *
284787 TGTCCATATATTCCTATGAACATAGGTAAAC
1 TGTCCATATATTCCAAAGAACATAGGTAAAC
* * *
284818 TGTCCATATGTCCCAAAGAACATAGGTAATCC
1 TGTCCATATATTCCAAAGAACATAGGTAA-AC
* *
284850 TGTCCATATATCTCAAAAG-ACATAGGTAATC
1 TGTCCATATAT-TCCAAAGAACATAGGTAAAC
284881 TGTCCATAT
1 TGTCCATAT
284890 GTCTCGAAGG
Statistics
Matches: 61, Mismatches: 9, Indels: 4
0.82 0.12 0.05
Matches are distributed among these distances:
31 35 0.57
32 21 0.34
33 5 0.08
ACGTcount: A:0.35, C:0.21, G:0.14, T:0.30
Consensus pattern (31 bp):
TGTCCATATATTCCAAAGAACATAGGTAAAC
Found at i:284903 original size:31 final size:31
Alignment explanation
Indices: 284806--284909 Score: 145
Period size: 31 Copynumber: 3.3 Consensus size: 31
284796 ATTCCTATGA
* * *
284806 ACATAGGTAAACTGTCCATATGTCCCAAAGA
1 ACATAGGTAATCTGTCCATATGTCTCAAAGG
* *
284837 ACATAGGTAATCCTGTCCATATATCTCAAAAG
1 ACATAGGTAAT-CTGTCCATATGTCTCAAAGG
*
284869 ACATAGGTAATCTGTCCATATGTCTCGAAGG
1 ACATAGGTAATCTGTCCATATGTCTCAAAGG
284900 ACATAGGTAA
1 ACATAGGTAA
284910 CCTTCGACTC
Statistics
Matches: 64, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
31 37 0.58
32 27 0.42
ACGTcount: A:0.37, C:0.20, G:0.17, T:0.26
Consensus pattern (31 bp):
ACATAGGTAATCTGTCCATATGTCTCAAAGG
Found at i:285886 original size:23 final size:22
Alignment explanation
Indices: 285860--285902 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 22
285850 TGTTCCATAG
285860 CATATATCA-CATATGCATATAAT
1 CATATAT-ATCATAT-CATATAAT
285883 CATATATATCATATCATATA
1 CATATATATCATATCATATA
285903 GCTTATTCTT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
22 7 0.37
23 12 0.63
ACGTcount: A:0.44, C:0.16, G:0.02, T:0.37
Consensus pattern (22 bp):
CATATATATCATATCATATAAT
Found at i:286661 original size:12 final size:12
Alignment explanation
Indices: 286644--286668 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
286634 TCTTGACAAG
286644 TTAAATTTAGCT
1 TTAAATTTAGCT
286656 TTAAATTTAGCT
1 TTAAATTTAGCT
286668 T
1 T
286669 ATCAACTCTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.32, C:0.08, G:0.08, T:0.52
Consensus pattern (12 bp):
TTAAATTTAGCT
Found at i:289233 original size:15 final size:16
Alignment explanation
Indices: 289213--289256 Score: 56
Period size: 15 Copynumber: 2.9 Consensus size: 16
289203 TTTAGCATAC
289213 TTTATTTCATTTTAA-
1 TTTATTTCATTTTAAT
*
289228 TTTATTTCA-TTCAAT
1 TTTATTTCATTTTAAT
*
289243 TTTATTTTATTTTA
1 TTTATTTCATTTTA
289257 TCAGATACTT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
14 4 0.17
15 17 0.71
16 3 0.12
ACGTcount: A:0.25, C:0.07, G:0.00, T:0.68
Consensus pattern (16 bp):
TTTATTTCATTTTAAT
Found at i:289255 original size:5 final size:5
Alignment explanation
Indices: 289213--289282 Score: 50
Period size: 5 Copynumber: 13.6 Consensus size: 5
289203 TTTAGCATAC
* * * ** ** *
289213 TTTAT TTCAT TTTAA TTTAT TTCAT TCAAT TTTAT TTTAT TTTAT CAGATAC
1 TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT --TTTAT
289265 TTTAT TTTAT TTTAT TTT
1 TTTAT TTTAT TTTAT TTT
289283 TCTATGAATA
Statistics
Matches: 48, Mismatches: 15, Indels: 4
0.72 0.22 0.06
Matches are distributed among these distances:
5 46 0.96
7 2 0.04
ACGTcount: A:0.24, C:0.07, G:0.01, T:0.67
Consensus pattern (5 bp):
TTTAT
Found at i:290362 original size:53 final size:51
Alignment explanation
Indices: 290210--290421 Score: 264
Period size: 54 Copynumber: 4.0 Consensus size: 51
290200 TTTCAGTTAT
* * *
290210 CATCAAGAAACTCCTAAAAATTAGGCTTAGTTTCTTTAAAAATTCATTTAAAAA
1 CATCAAGAAACCCCT-AAAATTAGGCTTAATTTCTTT-AAAATTCATTT-GAAA
* ** *
290264 TATCAAGAAAACCCCTAAAAACCAGGCTTAATTTCTTTGAAATTCATTTGAAA
1 CATCAAG-AAACCCCT-AAAATTAGGCTTAATTTCTTTAAAATTCATTTGAAA
*
290317 CATCAAGAAACCCCTAAAATTCAGGTTTAATTTCTTTAAAAATTCATTTGAAAA
1 CATCAAGAAACCCCTAAAATT-AGGCTTAATTTCTTT-AAAATTCATTTG-AAA
290371 CATCAAGAAACCCCTAAAATTAGGCTT-ATCTTCTTTAAAATTCATTTGAAA
1 CATCAAGAAACCCCTAAAATTAGGCTTAAT-TTCTTTAAAATTCATTTGAAA
290422 ATTGTCAAGA
Statistics
Matches: 140, Mismatches: 13, Indels: 13
0.84 0.08 0.08
Matches are distributed among these distances:
51 7 0.05
52 36 0.26
53 31 0.22
54 40 0.29
55 26 0.19
ACGTcount: A:0.42, C:0.17, G:0.08, T:0.33
Consensus pattern (51 bp):
CATCAAGAAACCCCTAAAATTAGGCTTAATTTCTTTAAAATTCATTTGAAA
Found at i:290431 original size:53 final size:54
Alignment explanation
Indices: 290211--290434 Score: 280
Period size: 52 Copynumber: 4.2 Consensus size: 54
290201 TTCAGTTATC
* * *
290211 ATCAAGAAACTCCTAAAAATTAGGCTTAGTTTCTTTAAAAATTCATTTAAAAAT
1 ATCAAGAAACCCCTAAAAATTAGGCTTAATTTCTTTAAAAATTCATTTGAAAAT
** * *
290265 ATCAAGAAAACCCCTAAAAACCAGGCTTAATTTCTTT-GAAATTCATTTG-AAAC
1 ATCAAG-AAACCCCTAAAAATTAGGCTTAATTTCTTTAAAAATTCATTTGAAAAT
* *
290318 ATCAAGAAACCCCT-AAAATTCAGGTTTAATTTCTTTAAAAATTCATTTGAAAAC
1 ATCAAGAAACCCCTAAAAATT-AGGCTTAATTTCTTTAAAAATTCATTTGAAAAT
290372 ATCAAGAAACCCCT-AAAATTAGGCTT-ATCTTCTTT-AAAATTCATTTGAAAATT
1 ATCAAGAAACCCCTAAAAATTAGGCTTAAT-TTCTTTAAAAATTCATTTGAAAA-T
*
290425 GTCAAGAAAC
1 ATCAAGAAAC
290435 TTCTGAAAAA
Statistics
Matches: 150, Mismatches: 14, Indels: 13
0.85 0.08 0.07
Matches are distributed among these distances:
51 4 0.03
52 40 0.27
53 40 0.27
54 40 0.27
55 26 0.17
ACGTcount: A:0.42, C:0.17, G:0.08, T:0.32
Consensus pattern (54 bp):
ATCAAGAAACCCCTAAAAATTAGGCTTAATTTCTTTAAAAATTCATTTGAAAAT
Found at i:290465 original size:107 final size:107
Alignment explanation
Indices: 290210--290458 Score: 308
Period size: 107 Copynumber: 2.3 Consensus size: 107
290200 TTTCAGTTAT
* *
290210 CATCAAGAAACTCCTAAAAATTAGGCTTAGTTTCTTTAAAAATTCATTTAAAAATATCAAGAAAA
1 CATCAAGAAACTCCTAAAAATCAGGCTTAGTTTCTTTAAAAATTCATTTAAAAACATCAAGAAAA
*
290275 CCCCTAAAAACCAGGCTTAATTTCTTTGAAATTCATTTGAAA
66 CCCCTAAAAACCAGGCTTAATTTCTTTAAAATTCATTTGAAA
* * * * *
290317 CATCAAGAAACCCCTAAAATTCAGGTTTAATTTCTTTAAAAATTCATTTGAAAACATCAAG-AAA
1 CATCAAGAAACTCCTAAAAATCAGGCTTAGTTTCTTTAAAAATTCATTTAAAAACATCAAGAAAA
**
290381 CCCCT-AAAATTAGGCTT-ATCTTCTTTAAAATTCATTTGAAA
66 CCCCTAAAAACCAGGCTTAAT-TTCTTTAAAATTCATTTGAAA
* * *
290422 -ATTGTCAAGAAACTTCTGAAAAATCAGACATAGTTTC
1 CA---TCAAGAAACTCCT-AAAAATCAGGCTTAGTTTC
290459 AAAAAAACAC
Statistics
Matches: 120, Mismatches: 17, Indels: 9
0.82 0.12 0.06
Matches are distributed among these distances:
104 3 0.03
105 30 0.25
106 8 0.07
107 65 0.54
108 14 0.12
ACGTcount: A:0.42, C:0.17, G:0.09, T:0.32
Consensus pattern (107 bp):
CATCAAGAAACTCCTAAAAATCAGGCTTAGTTTCTTTAAAAATTCATTTAAAAACATCAAGAAAA
CCCCTAAAAACCAGGCTTAATTTCTTTAAAATTCATTTGAAA
Found at i:290630 original size:2 final size:2
Alignment explanation
Indices: 290623--291670 Score: 1983
Period size: 2 Copynumber: 529.5 Consensus size: 2
290613 AAAATATGTA
290623 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
290665 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
290707 TG TG TG TG TG TG TG TG T- TG TG TG TG TG TG TG TG T- TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
290747 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
290789 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG -G TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
290830 TG TG TG TG TG TG TG TG TG TG T- TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
*
290871 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG GG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
290913 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
290955 TG -G TG TG TG TG TG TG TG TG TG TG TG TG -G TG TG TG T- TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
290994 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
291036 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
291078 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
291120 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T- TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
291161 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
291203 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
291245 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
291287 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
291329 TG TG TG TG TG TG TG TG TG TG TG TG TG -G TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
291370 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
291412 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
291454 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
291496 TG TG TG TG TG -G TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
291537 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
291579 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
* * *
291621 TG TG TG TG T- TG TG TG TG TG TG TG TG TA TG TG TG TA TG TA TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
291662 TG TG TG TG T
1 TG TG TG TG T
291671 ATGTATGCAT
Statistics
Matches: 1027, Mismatches: 8, Indels: 22
0.97 0.01 0.02
Matches are distributed among these distances:
1 11 0.01
2 1016 0.99
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:291675 original size:4 final size:4
Alignment explanation
Indices: 291644--291840 Score: 261
Period size: 4 Copynumber: 49.5 Consensus size: 4
291634 TGTGTGTGTG
* * * * *
291644 TGTA TGTG TGTA TGTA TGTG TGTG TGTA TGTA TGCA TGCA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
291692 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
* * * * * * *
291740 TGCA TGTA TGCA TGTA TGCA TGTA TGCA TGCA TGCA TGCA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
* *
291788 TGTA TATA TATA TGTA T-TA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
291835 TGTA TG
1 TGTA TG
291841 CGTGCGTGCG
Statistics
Matches: 176, Mismatches: 16, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
3 3 0.02
4 173 0.98
ACGTcount: A:0.24, C:0.05, G:0.25, T:0.46
Consensus pattern (4 bp):
TGTA
Found at i:291846 original size:4 final size:4
Alignment explanation
Indices: 291839--291892 Score: 108
Period size: 4 Copynumber: 13.5 Consensus size: 4
291829 TATGTATGTA
291839 TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG
1 TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG
291887 TGCG TG
1 TGCG TG
291893 TGTGTGTGCA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 50 1.00
ACGTcount: A:0.00, C:0.24, G:0.50, T:0.26
Consensus pattern (4 bp):
TGCG
Found at i:293634 original size:7 final size:7
Alignment explanation
Indices: 293622--293709 Score: 61
Period size: 8 Copynumber: 11.3 Consensus size: 7
293612 TATTTTCTTC
293622 TTCTTTT
1 TTCTTTT
293629 TTCTTTT
1 TTCTTTT
293636 TTCCTTTT
1 TT-CTTTT
*
293644 TTTTATTT
1 TTCT-TTT
*
293652 TTTTATTT
1 TTCT-TTT
293660 TTCTATTT
1 TTCT-TTT
293668 CTT-TTTT
1 -TTCTTTT
293675 TCTCATTTT
1 T-TC-TTTT
293684 CTTCCTTTT
1 -TT-CTTTT
293693 TTCTTTT
1 TTCTTTT
293700 TTCCTTTT
1 TT-CTTTT
293708 TT
1 TT
293710 TACTCATTTT
Statistics
Matches: 70, Mismatches: 2, Indels: 17
0.79 0.02 0.19
Matches are distributed among these distances:
6 1 0.01
7 21 0.30
8 35 0.50
9 11 0.16
10 2 0.03
ACGTcount: A:0.05, C:0.16, G:0.00, T:0.80
Consensus pattern (7 bp):
TTCTTTT
Found at i:293736 original size:36 final size:35
Alignment explanation
Indices: 293613--293735 Score: 120
Period size: 34 Copynumber: 3.7 Consensus size: 35
293603 GGATCTGCCT
293613 ATTTTCTTCTTCTTTTTTCTTTTTTCCTTTTTTT-T-
1 ATTTTCTTC--CTTTTTTCTTTTTTCCTTTTTTTCTC
*
293648 ATTTT-TT--TATTTTTC-TATTT-CTTTTTTTCTC
1 ATTTTCTTCCT-TTTTTCTTTTTTCCTTTTTTTCTC
293679 ATTTTCTTCCTTTTTTCTTTTTTCCTTTTTTTACTC
1 ATTTTCTTCCTTTTTTCTTTTTTCCTTTTTTT-CTC
* *
293715 ATTTT-TTTC-TTCTTCTTTTTT
1 ATTTTCTTCCTTTTTTCTTTTTT
293736 TGTTTTTGCT
Statistics
Matches: 75, Mismatches: 4, Indels: 19
0.77 0.04 0.19
Matches are distributed among these distances:
29 8 0.11
30 6 0.08
31 11 0.15
32 2 0.03
33 6 0.08
34 18 0.24
35 16 0.21
36 8 0.11
ACGTcount: A:0.06, C:0.17, G:0.00, T:0.77
Consensus pattern (35 bp):
ATTTTCTTCCTTTTTTCTTTTTTCCTTTTTTTCTC
Found at i:298997 original size:31 final size:29
Alignment explanation
Indices: 298955--299013 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
298945 TACTATGTAT
* *
298955 GCACCTAAAAGTGTAATAGAAAAAATATTAG
1 GCACCTAAAA--GTAACAAAAAAAATATTAG
*
298986 GCACCTTAAAGTAACAAAAAAAATATTA
1 GCACCTAAAAGTAACAAAAAAAATATTA
299014 AATGTTTATT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 16 0.64
31 9 0.36
ACGTcount: A:0.54, C:0.12, G:0.12, T:0.22
Consensus pattern (29 bp):
GCACCTAAAAGTAACAAAAAAAATATTAG
Found at i:299290 original size:4 final size:4
Alignment explanation
Indices: 299281--299307 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
299271 GTTGAGCCAA
299281 AAAG AAAG AAAG AAAG AAAG AAAG AAA
1 AAAG AAAG AAAG AAAG AAAG AAAG AAA
299308 AAGCACTTGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (4 bp):
AAAG
Found at i:300224 original size:32 final size:32
Alignment explanation
Indices: 300138--300240 Score: 172
Period size: 31 Copynumber: 3.2 Consensus size: 32
300128 CATGTTTTGG
300138 CTTTTGCCCATTTCAAGAAAAAAAAAAAGTTGT
1 CTTTTGCCCATTTCAAG-AAAAAAAAAAGTTGT
* *
300171 CTTCTACCCATTTCAAG-AAAAAAAAAGTTGT
1 CTTTTGCCCATTTCAAGAAAAAAAAAAGTTGT
300202 CTTTTGCCCATTTCAAGAAAAAAAAAAGTTGT
1 CTTTTGCCCATTTCAAGAAAAAAAAAAGTTGT
300234 CTTTTGC
1 CTTTTGC
300241 TTTATGTGTA
Statistics
Matches: 65, Mismatches: 4, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
31 29 0.45
32 21 0.32
33 15 0.23
ACGTcount: A:0.39, C:0.17, G:0.12, T:0.32
Consensus pattern (32 bp):
CTTTTGCCCATTTCAAGAAAAAAAAAAGTTGT
Found at i:301674 original size:33 final size:33
Alignment explanation
Indices: 301634--301701 Score: 136
Period size: 33 Copynumber: 2.1 Consensus size: 33
301624 AATTAATTTG
301634 TACTCTTTATTTGTTTGAGCAGAAATAATTAAT
1 TACTCTTTATTTGTTTGAGCAGAAATAATTAAT
301667 TACTCTTTATTTGTTTGAGCAGAAATAATTAAT
1 TACTCTTTATTTGTTTGAGCAGAAATAATTAAT
301700 TA
1 TA
301702 ATATAATTAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.34, C:0.09, G:0.12, T:0.46
Consensus pattern (33 bp):
TACTCTTTATTTGTTTGAGCAGAAATAATTAAT
Found at i:303863 original size:80 final size:80
Alignment explanation
Indices: 303748--303907 Score: 284
Period size: 80 Copynumber: 2.0 Consensus size: 80
303738 TGGTAGCAAG
303748 ACCCTGCTTTTCTTTTGCGGACAAAGTTAAACTACCATGTTTATCCGCATTCATTGATGTTTTTA
1 ACCCTGCTTTTCTTTTGCGGACAAAGTTAAACTACCATGTTTATCCGCATTCATTGATGTTTTTA
**
303813 TGTCTTGCTTTGACA
66 TACCTTGCTTTGACA
* *
303828 ACCCTGCTTTTCTTTTGCGGACAAATTTAAGCTACCATGTTTATCCGCATTCATTGATGTTTTTA
1 ACCCTGCTTTTCTTTTGCGGACAAAGTTAAACTACCATGTTTATCCGCATTCATTGATGTTTTTA
303893 TACCTTGCTTTGACA
66 TACCTTGCTTTGACA
303908 GCCTCGAGAC
Statistics
Matches: 76, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
80 76 1.00
ACGTcount: A:0.21, C:0.22, G:0.14, T:0.42
Consensus pattern (80 bp):
ACCCTGCTTTTCTTTTGCGGACAAAGTTAAACTACCATGTTTATCCGCATTCATTGATGTTTTTA
TACCTTGCTTTGACA
Found at i:306528 original size:80 final size:84
Alignment explanation
Indices: 306429--306593 Score: 232
Period size: 80 Copynumber: 2.0 Consensus size: 84
306419 TCTCCAAACC
* * *
306429 CTATCACTAACCCATCGCCGTCGCCCTTT-TCGATCACAACCACTACCATCG-AT-GT-A-GTCA
1 CTATCACTAACCCACCGCCGTCGCCCTTTCT-GACCACAACCACCACCATCGAATAGTCATGTCA
306489 TCATCATAGTTATAAGTCGT
65 TCATCATAGTTATAAGTCGT
*
306509 CTATCACTAACCCACCGCCGTCGCCCTTTCTGGCCACAACCACCACCATCGACATAGTCATTGTC
1 CTATCACTAACCCACCGCCGTCGCCCTTTCTGACCACAACCACCACCATCGA-ATAGTCA-TGTC
306574 ATCATCATAGTTATAAGTCG
64 ATCATCATAGTTATAAGTCG
306594 CCATAGTTGT
Statistics
Matches: 74, Mismatches: 4, Indels: 8
0.86 0.05 0.09
Matches are distributed among these distances:
80 45 0.61
81 1 0.01
82 2 0.03
83 2 0.03
84 1 0.01
86 23 0.31
ACGTcount: A:0.26, C:0.35, G:0.13, T:0.27
Consensus pattern (84 bp):
CTATCACTAACCCACCGCCGTCGCCCTTTCTGACCACAACCACCACCATCGAATAGTCATGTCAT
CATCATAGTTATAAGTCGT
Found at i:312377 original size:21 final size:21
Alignment explanation
Indices: 312352--312419 Score: 100
Period size: 21 Copynumber: 3.2 Consensus size: 21
312342 AGTCGCTTGT
*
312352 CGTCCGCCGTCCTCCGACCAT
1 CGTCCGCCGTCCTCCGACCAC
*
312373 CGTCCGCCGTCCTCCAACCAC
1 CGTCCGCCGTCCTCCGACCAC
* *
312394 CGTTCGCCGTCTTCCGACCAC
1 CGTCCGCCGTCCTCCGACCAC
312415 CGTCC
1 CGTCC
312420 ACCGCCGCAC
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 41 1.00
ACGTcount: A:0.10, C:0.53, G:0.18, T:0.19
Consensus pattern (21 bp):
CGTCCGCCGTCCTCCGACCAC
Found at i:323221 original size:37 final size:37
Alignment explanation
Indices: 323177--323272 Score: 174
Period size: 37 Copynumber: 2.6 Consensus size: 37
323167 TCCTAAATTT
323177 ATATTTTAAGTTTAATATTTTTTTTCTTTCGAAACTC
1 ATATTTTAAGTTTAATATTTTTTTTCTTTCGAAACTC
* *
323214 ATATTTTAAGTTTAATATTTTTTTTCTTTCTAAATTC
1 ATATTTTAAGTTTAATATTTTTTTTCTTTCGAAACTC
323251 ATATTTTAAGTTTAATATTTTT
1 ATATTTTAAGTTTAATATTTTT
323273 GTCAAACCTC
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 57 1.00
ACGTcount: A:0.28, C:0.07, G:0.04, T:0.60
Consensus pattern (37 bp):
ATATTTTAAGTTTAATATTTTTTTTCTTTCGAAACTC
Found at i:324981 original size:26 final size:24
Alignment explanation
Indices: 324934--324982 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
324924 ATAACATTTC
*
324934 ATAAAAAAATATTAAAATTTAATG
1 ATAAAAAAATATTAAAACTTAATG
324958 ATAAAAAAATATTAAACGACTTAAT
1 ATAAAAAAATATTAAA--ACTTAAT
324983 TAATATAATT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 16 0.73
26 6 0.27
ACGTcount: A:0.61, C:0.04, G:0.04, T:0.31
Consensus pattern (24 bp):
ATAAAAAAATATTAAAACTTAATG
Found at i:332042 original size:144 final size:142
Alignment explanation
Indices: 331816--332102 Score: 475
Period size: 144 Copynumber: 2.0 Consensus size: 142
331806 TCTTAAAGTA
* * * *
331816 CATAAAACACCATAATAAAATATAATTAAAGTCTAGAAACATAAATGGCAAACACATAATGTTTT
1 CATAAAACACCATAATAAAACATAATTAAAGCCTAGAAACATAAATGACAAACACATAATATTTT
* * *
331881 TGTTCTTTGGCACAACATTCTAAAATTTCAGGCAATACTTGTGACATCTGATACTATAGTATTAC
66 TATTCTTTGGCACAACATTCTAAAATTTCAAGCAATACTTGTGACATCTGATACTACAGTATTAC
331946 AATCATCATTCT
131 AATCATCATTCT
331958 CATAAAACACCATAATAAAAGACATAATTAAAGCCTAGAAACATAAATGACAAACACATAATATT
1 CATAAAACACCATAAT-AAA-ACATAATTAAAGCCTAGAAACATAAATGACAAACACATAATATT
* *
332023 TTTATTCTTTGGCACAACATTCTCAAATTTCAAGCAATACTTGTGACATCTGATACTCCAGTATT
64 TTTATTCTTTGGCACAACATTCTAAAATTTCAAGCAATACTTGTGACATCTGATACTACAGTATT
332088 ACAATCATCATTCT
129 ACAATCATCATTCT
332102 C
1 C
332103 TATTTCCTCC
Statistics
Matches: 134, Mismatches: 9, Indels: 2
0.92 0.06 0.01
Matches are distributed among these distances:
142 16 0.12
143 3 0.02
144 115 0.86
ACGTcount: A:0.41, C:0.19, G:0.09, T:0.31
Consensus pattern (142 bp):
CATAAAACACCATAATAAAACATAATTAAAGCCTAGAAACATAAATGACAAACACATAATATTTT
TATTCTTTGGCACAACATTCTAAAATTTCAAGCAATACTTGTGACATCTGATACTACAGTATTAC
AATCATCATTCT
Found at i:355780 original size:42 final size:42
Alignment explanation
Indices: 355721--355804 Score: 168
Period size: 42 Copynumber: 2.0 Consensus size: 42
355711 TTTTCCAACC
355721 ATTCTCTCTTTTTCCCAAAAGGGTAAGGTCTCGTGCAAGCTT
1 ATTCTCTCTTTTTCCCAAAAGGGTAAGGTCTCGTGCAAGCTT
355763 ATTCTCTCTTTTTCCCAAAAGGGTAAGGTCTCGTGCAAGCTT
1 ATTCTCTCTTTTTCCCAAAAGGGTAAGGTCTCGTGCAAGCTT
355805 CAAGTATGCC
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.21, C:0.24, G:0.19, T:0.36
Consensus pattern (42 bp):
ATTCTCTCTTTTTCCCAAAAGGGTAAGGTCTCGTGCAAGCTT
Found at i:357713 original size:14 final size:14
Alignment explanation
Indices: 357696--357746 Score: 56
Period size: 14 Copynumber: 3.9 Consensus size: 14
357686 TGAACGTTCA
357696 GTTATGTTCGTTTG
1 GTTATGTTCGTTTG
357710 GTTATGTTCG--T-
1 GTTATGTTCGTTTG
*
357721 -TTATGTTCGTTCG
1 GTTATGTTCGTTTG
*
357734 ATTATGTTCGTTT
1 GTTATGTTCGTTT
357747 ATGTTCATTC
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
10 9 0.29
12 1 0.03
14 21 0.68
ACGTcount: A:0.10, C:0.10, G:0.24, T:0.57
Consensus pattern (14 bp):
GTTATGTTCGTTTG
Found at i:357718 original size:24 final size:24
Alignment explanation
Indices: 357697--357752 Score: 94
Period size: 24 Copynumber: 2.3 Consensus size: 24
357687 GAACGTTCAG
* *
357697 TTATGTTCGTTTGGTTATGTTCGT
1 TTATGTTCGTTCGATTATGTTCGT
357721 TTATGTTCGTTCGATTATGTTCGT
1 TTATGTTCGTTCGATTATGTTCGT
357745 TTATGTTC
1 TTATGTTC
357753 ATTCTTTTAT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.11, C:0.11, G:0.21, T:0.57
Consensus pattern (24 bp):
TTATGTTCGTTCGATTATGTTCGT
Found at i:357762 original size:24 final size:24
Alignment explanation
Indices: 357697--357765 Score: 84
Period size: 24 Copynumber: 2.9 Consensus size: 24
357687 GAACGTTCAG
* * *
357697 TTATGTTCGTTTGGTTATGTTCGT
1 TTATGTTCATTCGATTATGTTCGT
*
357721 TTATGTTCGTTCGATTATGTTCGT
1 TTATGTTCATTCGATTATGTTCGT
**
357745 TTATGTTCATTCTTTTATGTT
1 TTATGTTCATTCGATTATGTT
357766 TAACACAATC
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 40 1.00
ACGTcount: A:0.12, C:0.10, G:0.19, T:0.59
Consensus pattern (24 bp):
TTATGTTCATTCGATTATGTTCGT
Found at i:358862 original size:16 final size:16
Alignment explanation
Indices: 358841--358902 Score: 85
Period size: 16 Copynumber: 4.1 Consensus size: 16
358831 CTCCAACGTT
358841 TGTTCGTGTTCATTTA
1 TGTTCGTGTTCATTTA
*
358857 TGTTCGTGTTCGTTTA
1 TGTTCGTGTTCATTTA
*
358873 TG-TCGTGTTCGTTTA
1 TGTTCGTGTTCATTTA
358888 TGTTCGT-TT-ATTTA
1 TGTTCGTGTTCATTTA
358902 T
1 T
358903 TAAATGAACG
Statistics
Matches: 43, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
14 5 0.12
15 17 0.40
16 21 0.49
ACGTcount: A:0.10, C:0.11, G:0.21, T:0.58
Consensus pattern (16 bp):
TGTTCGTGTTCATTTA
Found at i:358880 original size:15 final size:15
Alignment explanation
Indices: 358844--358890 Score: 76
Period size: 15 Copynumber: 3.1 Consensus size: 15
358834 CAACGTTTGT
*
358844 TCGTGTTCATTTATG
1 TCGTGTTCGTTTATG
358859 TTCGTGTTCGTTTATG
1 -TCGTGTTCGTTTATG
358875 TCGTGTTCGTTTATG
1 TCGTGTTCGTTTATG
358890 T
1 T
358891 TCGTTTATTT
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
15 16 0.53
16 14 0.47
ACGTcount: A:0.09, C:0.13, G:0.23, T:0.55
Consensus pattern (15 bp):
TCGTGTTCGTTTATG
Found at i:358984 original size:16 final size:16
Alignment explanation
Indices: 358963--358995 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
358953 AAAAAATTTT
358963 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
358979 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
358995 T
1 T
358996 TTATTTATTA
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:359163 original size:20 final size:18
Alignment explanation
Indices: 359140--359204 Score: 62
Period size: 18 Copynumber: 3.5 Consensus size: 18
359130 TATGTGTTAT
359140 ATTTTAATTCATATATTTAA
1 ATTTTAATT-AT-TATTTAA
*
359160 ATTTTTATTATTATTTAA
1 ATTTTAATTATTATTTAA
*
359178 ATTATT--TTATTATGTTAT
1 ATT-TTAATTATTAT-TTAA
359196 ATTTTAATT
1 ATTTTAATT
359205 CATATATTAT
Statistics
Matches: 39, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
17 9 0.23
18 16 0.41
19 6 0.15
20 8 0.21
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.63
Consensus pattern (18 bp):
ATTTTAATTATTATTTAA
Found at i:360514 original size:14 final size:14
Alignment explanation
Indices: 360495--360586 Score: 84
Period size: 14 Copynumber: 6.6 Consensus size: 14
360485 TTTGTCCTGG
*
360495 TTATAAATATTATA
1 TTATAATTATTATA
360509 TTATAATTATTACTA
1 TTATAATTATTA-TA
360524 TTAT-ATTA-T-TA
1 TTATAATTATTATA
*
360535 TTATATTTATGT-TA
1 TTATAATTAT-TATA
**
360549 TTATAACAATTATA
1 TTATAATTATTATA
360563 TTATAATTATTAGTA
1 TTATAATTATTA-TA
*
360578 TTATTATTA
1 TTATAATTA
360587 ATATCATTTA
Statistics
Matches: 64, Mismatches: 8, Indels: 11
0.77 0.10 0.13
Matches are distributed among these distances:
11 6 0.09
12 3 0.05
13 2 0.03
14 37 0.58
15 16 0.25
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.55
Consensus pattern (14 bp):
TTATAATTATTATA
Found at i:360525 original size:20 final size:19
Alignment explanation
Indices: 360502--360586 Score: 72
Period size: 20 Copynumber: 4.5 Consensus size: 19
360492 TGGTTATAAA
360502 TATTATATTATAATTATTAC
1 TATTATATTAT-ATTATTAC
360522 TATTATA-T-TATTATTA-
1 TATTATATTATATTATTAC
*
360538 TATT-TATGT-TATTATAAC
1 TATTATAT-TATATTATTAC
* *
360556 AATTATATTATAATTATTAG
1 TATTATATTAT-ATTATTAC
360576 TATTATTATTA
1 TATTA-TATTA
360587 ATATCATTTA
Statistics
Matches: 53, Mismatches: 5, Indels: 13
0.75 0.07 0.18
Matches are distributed among these distances:
15 2 0.04
16 4 0.08
17 15 0.28
18 5 0.09
19 5 0.09
20 17 0.32
21 5 0.09
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.56
Consensus pattern (19 bp):
TATTATATTATATTATTAC
Found at i:360533 original size:3 final size:3
Alignment explanation
Indices: 360502--360586 Score: 54
Period size: 3 Copynumber: 29.7 Consensus size: 3
360492 TGGTTATAAA
* * *
360502 TAT TA- TAT TAT AAT TAT TAC TAT TA- TAT TAT TAT TA- TAT T-T ATGT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT -TAT
* * * * *
360547 TAT TAT AAC AAT TA- TAT TAT AAT TAT TAG TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
360587 ATATCATTTA
Statistics
Matches: 63, Mismatches: 13, Indels: 12
0.72 0.15 0.14
Matches are distributed among these distances:
2 9 0.14
3 53 0.84
4 1 0.02
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.56
Consensus pattern (3 bp):
TAT
Found at i:360554 original size:54 final size:53
Alignment explanation
Indices: 360495--360600 Score: 153
Period size: 54 Copynumber: 2.0 Consensus size: 53
360485 TTTGTCCTGG
*
360495 TTATAA-ATATTATATTATAATTATTACTATTATATTATTATTAT-ATTTATGTTA
1 TTATAACA-ATTATATTATAATTATTACTA-T-TATTATTAATATCATTTATGTTA
*
360549 TTATAACAATTATATTATAATTATTAGTATTATTATTAATATCATTTATGTT
1 TTATAACAATTATATTATAATTATTACTATTATTATTAATATCATTTATGTT
360601 CTTGTAGGTT
Statistics
Matches: 48, Mismatches: 2, Indels: 5
0.87 0.04 0.09
Matches are distributed among these distances:
52 11 0.23
53 10 0.21
54 26 0.54
55 1 0.02
ACGTcount: A:0.39, C:0.03, G:0.03, T:0.56
Consensus pattern (53 bp):
TTATAACAATTATATTATAATTATTACTATTATTATTAATATCATTTATGTTA
Found at i:363689 original size:14 final size:14
Alignment explanation
Indices: 363670--363714 Score: 54
Period size: 14 Copynumber: 3.1 Consensus size: 14
363660 ATTTTGCTTG
363670 AGGAAAATTAAAAA
1 AGGAAAATTAAAAA
363684 AGGAAAAAATTAAAAA
1 AGG--AAAATTAAAAA
**
363700 AATAAAATTAAAAA
1 AGGAAAATTAAAAA
363714 A
1 A
363715 ATTAAAAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
14 15 0.56
16 12 0.44
ACGTcount: A:0.76, C:0.00, G:0.09, T:0.16
Consensus pattern (14 bp):
AGGAAAATTAAAAA
Found at i:363699 original size:9 final size:9
Alignment explanation
Indices: 363687--363766 Score: 75
Period size: 9 Copynumber: 9.7 Consensus size: 9
363677 TTAAAAAAGG
363687 AAAAAATTA
1 AAAAAATTA
363696 AAAAAA-T-
1 AAAAAATTA
363703 --AAAATTA
1 AAAAAATTA
363710 AAAAAATTA
1 AAAAAATTA
363719 AAAAAATT-
1 AAAAAATTA
363727 AAAAAA-T-
1 AAAAAATTA
* *
363734 AAAAAGTGA
1 AAAAAATTA
*
363743 AAAAAATAA
1 AAAAAATTA
*
363752 AAAAAATGA
1 AAAAAATTA
363761 AAAAAA
1 AAAAAA
363767 GAATAAAATG
Statistics
Matches: 60, Mismatches: 5, Indels: 12
0.78 0.06 0.16
Matches are distributed among these distances:
5 4 0.07
6 1 0.02
7 6 0.10
8 7 0.12
9 42 0.70
ACGTcount: A:0.80, C:0.00, G:0.04, T:0.16
Consensus pattern (9 bp):
AAAAAATTA
Found at i:363706 original size:23 final size:23
Alignment explanation
Indices: 363673--363757 Score: 89
Period size: 24 Copynumber: 3.6 Consensus size: 23
363663 TTGCTTGAGG
* *
363673 AAAATTAAAAAAGGAAAAAATTAA
1 AAAAATAAAAAA-AAAAAAATTAA
**
363697 AAAAATAAAATTAAAAAAATTAA
1 AAAAATAAAAAAAAAAAAATTAA
* * *
363720 AAAAATTAAAAAATAAAAAGTGAA
1 AAAAA-TAAAAAAAAAAAAATTAA
363744 AAAAATAAAAAAAA
1 AAAAATAAAAAAAA
363758 TGAAAAAAAG
Statistics
Matches: 50, Mismatches: 10, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
23 23 0.46
24 27 0.54
ACGTcount: A:0.79, C:0.00, G:0.05, T:0.16
Consensus pattern (23 bp):
AAAAATAAAAAAAAAAAAATTAA
Found at i:363723 original size:32 final size:34
Alignment explanation
Indices: 363687--363766 Score: 112
Period size: 33 Copynumber: 2.4 Consensus size: 34
363677 TTAAAAAAGG
* *
363687 AAAAAATTAAAAAAAT-AAAA-TTAAAAAAATTA
1 AAAAAATTAAAAAAATAAAAAGTGAAAAAAATAA
363719 AAAAAATT-AAAAAATAAAAAGTGAAAAAAATAA
1 AAAAAATTAAAAAAATAAAAAGTGAAAAAAATAA
*
363752 AAAAAATGAAAAAAA
1 AAAAAATTAAAAAAA
363767 GAATAAAATG
Statistics
Matches: 42, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
31 7 0.17
32 12 0.29
33 17 0.40
34 6 0.14
ACGTcount: A:0.80, C:0.00, G:0.04, T:0.16
Consensus pattern (34 bp):
AAAAAATTAAAAAAATAAAAAGTGAAAAAAATAA
Found at i:363756 original size:24 final size:22
Alignment explanation
Indices: 363679--363766 Score: 52
Period size: 26 Copynumber: 3.7 Consensus size: 22
363669 GAGGAAAATT
* *
363679 AAAAAAGGAAAAAATTAAAAAA
1 AAAAAATGAAAAAAATAAAAAA
* *
363701 ATAAAATTAAAAAAATTAAAAAAA
1 AAAAAATGAAAAAAA-T-AAAAAA
*
363725 TTAAAAAAT-AAAAAGTGAAAAAAATAA
1 --AAAAAATGAAAAA---AATAAAA-AA
363752 AAAAAATGAAAAAAA
1 AAAAAATGAAAAAAA
363767 GAATAAAATG
Statistics
Matches: 51, Mismatches: 6, Indels: 17
0.69 0.08 0.23
Matches are distributed among these distances:
22 11 0.22
23 3 0.06
24 6 0.12
25 12 0.24
26 15 0.29
27 2 0.04
28 2 0.04
ACGTcount: A:0.80, C:0.00, G:0.06, T:0.15
Consensus pattern (22 bp):
AAAAAATGAAAAAAATAAAAAA
Found at i:363774 original size:9 final size:8
Alignment explanation
Indices: 363673--363766 Score: 68
Period size: 8 Copynumber: 11.6 Consensus size: 8
363663 TTGCTTGAGG
*
363673 AAAATTAA
1 AAAAATAA
**
363681 AAAAGGAA
1 AAAAATAA
*
363689 AAAATTAA
1 AAAAATAA
363697 AAAAAT--
1 AAAAATAA
*
363703 AAAATTAA
1 AAAAATAA
363711 AAAAATTAA
1 AAAAA-TAA
*
363720 AAAAATTA
1 AAAAATAA
363728 AAAAAT-A
1 AAAAATAA
*
363735 AAAAGTGAA
1 AAAAAT-AA
363744 AAAAATAAA
1 AAAAAT-AA
363753 AAAAATGAA
1 AAAAAT-AA
363762 AAAAA
1 AAAAA
363767 GAATAAAATG
Statistics
Matches: 69, Mismatches: 12, Indels: 9
0.77 0.13 0.10
Matches are distributed among these distances:
6 5 0.07
7 6 0.09
8 29 0.42
9 29 0.42
ACGTcount: A:0.79, C:0.00, G:0.05, T:0.16
Consensus pattern (8 bp):
AAAAATAA
Found at i:363774 original size:18 final size:18
Alignment explanation
Indices: 363727--363774 Score: 62
Period size: 18 Copynumber: 2.6 Consensus size: 18
363717 TAAAAAAATT
363727 AAAAAATAAAAAGTGAAA
1 AAAAAATAAAAAGTGAAA
*
363745 AAAATAA-AAAAAATGAAA
1 AAAA-AATAAAAAGTGAAA
363763 AAAAGAATAAAA
1 AAAA-AATAAAA
363775 TGAGTGTTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
18 20 0.77
19 6 0.23
ACGTcount: A:0.81, C:0.00, G:0.08, T:0.10
Consensus pattern (18 bp):
AAAAAATAAAAAGTGAAA
Found at i:364813 original size:55 final size:55
Alignment explanation
Indices: 364747--365208 Score: 822
Period size: 55 Copynumber: 8.4 Consensus size: 55
364737 TTGAAGCATC
*
364747 AAGATTGTTCGAGTCTTATACTCTCTGAAGGAATAAGGAGCAGACACGATTGTTG
1 AAGATTGTTCGAGTCTTATACTCTCTGAAGGAATAGGGAGCAGACACGATTGTTG
* *
364802 AAGATTGTTCGAGTCTTATACTCTCTTAAGGAATAGGGAGTAGACAC-ACTTGTTG
1 AAGATTGTTCGAGTCTTATACTCTCTGAAGGAATAGGGAGCAGACACGA-TTGTTG
*
364857 AAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTGTTG
1 AAGATTGTTCGAGTCTTATACTCTCTGAAGGAATAGGGAGCAGACACGATTGTTG
*
364912 AAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTGTTG
1 AAGATTGTTCGAGTCTTATACTCTCTGAAGGAATAGGGAGCAGACACGATTGTTG
364967 AAGATTGTTCGAGTCTTATACTCTCTGAAGGAATAGGGAGCAGACACGATTGTTG
1 AAGATTGTTCGAGTCTTATACTCTCTGAAGGAATAGGGAGCAGACACGATTGTTG
*
365022 AAGATTGTTCGAGTCTTATACTCTCTGAAGGAATAGGGAGCAGATACGATTGTTG
1 AAGATTGTTCGAGTCTTATACTCTCTGAAGGAATAGGGAGCAGACACGATTGTTG
*
365077 AAGATTGTTCGAGTCTTATACTCTCTAAAGGAATAGGGAGCAGACACGATTGTTG
1 AAGATTGTTCGAGTCTTATACTCTCTGAAGGAATAGGGAGCAGACACGATTGTTG
365132 AAGATTGTTCGAGTCTTATACTCTCTGAAGGAATAGGGAGCAGACACGATTGTTG
1 AAGATTGTTCGAGTCTTATACTCTCTGAAGGAATAGGGAGCAGACACGATTGTTG
365187 AAGA-TGTTCGAGT-TCTATACTC
1 AAGATTGTTCGAGTCT-TATACTC
365209 CCTAAAGAAA
Statistics
Matches: 393, Mismatches: 11, Indels: 7
0.96 0.03 0.02
Matches are distributed among these distances:
53 1 0.00
54 17 0.04
55 374 0.95
56 1 0.00
ACGTcount: A:0.30, C:0.15, G:0.26, T:0.30
Consensus pattern (55 bp):
AAGATTGTTCGAGTCTTATACTCTCTGAAGGAATAGGGAGCAGACACGATTGTTG
Found at i:365260 original size:55 final size:56
Alignment explanation
Indices: 365193--365455 Score: 329
Period size: 56 Copynumber: 4.8 Consensus size: 56
365183 GTTGAAGATG
* *
365193 TTCGAGTTCTATACTCCCT-AAAGAAAGAGGGGGCGAACCCGTAGGAAGAAGATTA
1 TTCGAGTTCTATACTCCCTGAAAGAAAGAGGGAGCGAACCCGTAGGCAGAAGATTA
* * *
365248 TTCGAGTTCTATACTCCCTGAAAGAAAAAGGGATCAAACCCGTTA-GCAGAAGATTA
1 TTCGAGTTCTATACTCCCTGAAAGAAAGAGGGAGCGAACCCG-TAGGCAGAAGATTA
* * *
365304 TTCGAGTTCTATACTCCCTGAAAGAAAGAGGGAGCGAACTCGTAGGTAGAAGATTG
1 TTCGAGTTCTATACTCCCTGAAAGAAAGAGGGAGCGAACCCGTAGGCAGAAGATTA
* * * * *
365360 TTCGAGTTC-CTACTCCCT-AAAAAAAGAGGGAGCGAACCTGTTGGCAGAAGATTG
1 TTCGAGTTCTATACTCCCTGAAAGAAAGAGGGAGCGAACCCGTAGGCAGAAGATTA
* * *
365414 TTCGAGTTCCATACTCCCAGAAAGCAAA-AGGAAGCGAACCCG
1 TTCGAGTTCTATACTCCCTGAAAG-AAAGAGGGAGCGAACCCG
365456 CTGATCGAAG
Statistics
Matches: 180, Mismatches: 22, Indels: 11
0.85 0.10 0.05
Matches are distributed among these distances:
54 40 0.22
55 36 0.20
56 99 0.55
57 5 0.03
ACGTcount: A:0.34, C:0.20, G:0.25, T:0.21
Consensus pattern (56 bp):
TTCGAGTTCTATACTCCCTGAAAGAAAGAGGGAGCGAACCCGTAGGCAGAAGATTA
Found at i:365280 original size:110 final size:110
Alignment explanation
Indices: 364747--365366 Score: 693
Period size: 110 Copynumber: 5.6 Consensus size: 110
364737 TTGAAGCATC
* * * * * * *
364747 AAGATTGTTCGAGTCTTATACTCTCTGAAGGAATAAGGAGCAGACACGATTGTTGAAGATTGTTC
1 AAGATTGTTCGAGTCTTATACTCCCTAAAGAAAGAGGGAGCAGACACGATGGTAGAAGATTGTTC
* * *
364812 GAGTCTTATACTCTCTTAAGGAATAGGGAGTAGACAC-ACTTGTTG
66 GAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGA-TTGTTG
* * * * *
364857 AAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTGTTGAAGATTGTTC
1 AAGATTGTTCGAGTCTTATACTCCCTAAAGAAAGAGGGAGCAGACACGATGGTAGAAGATTGTTC
364922 GAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTGTTG
66 GAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTGTTG
* * * * * *
364967 AAGATTGTTCGAGTCTTATACTCTCTGAAGGAATAGGGAGCAGACACGATTGTTGAAGATTGTTC
1 AAGATTGTTCGAGTCTTATACTCCCTAAAGAAAGAGGGAGCAGACACGATGGTAGAAGATTGTTC
* *
365032 GAGTCTTATACTCTCTGAAGGAATAGGGAGCAGATACGATTGTTG
66 GAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTGTTG
* * * * *
365077 AAGATTGTTCGAGTCTTATACTCTCTAAAGGAATAGGGAGCAGACACGATTGTTGAAGATTGTTC
1 AAGATTGTTCGAGTCTTATACTCCCTAAAGAAAGAGGGAGCAGACACGATGGTAGAAGATTGTTC
*
365142 GAGTCTTATACTCTCTGAAGGAATAGGGAGCAGACACGATTGTTG
66 GAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTGTTG
* * * *
365187 AAGA-TGTTCGAGT-TCTATACTCCCTAAAGAAAGAGGGGGC-GAACCCG-TAGGAAGAAGATTA
1 AAGATTGTTCGAGTCT-TATACTCCCTAAAGAAAGAGGGAGCAG-ACACGAT-GGTAGAAGATTG
* * * * * **
365248 TTCGAGT-TCTATACTCCCTGAAAGAAAAAGGGATCAAACCCG-TTAGCAG
63 TTCGAGTCT-TATACTCTCTG-AAGAAATAGGGAGCAGACACGATT-GTTG
* *
365297 AAGATTATTCGAGT-TCTATACTCCCTGAAAGAAAGAGGGAGC-GAACTCG-TAGGTAGAAGATT
1 AAGATTGTTCGAGTCT-TATACTCCCT-AAAGAAAGAGGGAGCAG-ACACGAT-GGTAGAAGATT
365359 GTTCGAGT
62 GTTCGAGT
365367 TCCTACTCCC
Statistics
Matches: 469, Mismatches: 32, Indels: 16
0.91 0.06 0.03
Matches are distributed among these distances:
108 4 0.01
109 61 0.13
110 344 0.73
111 21 0.04
112 39 0.08
ACGTcount: A:0.31, C:0.15, G:0.26, T:0.28
Consensus pattern (110 bp):
AAGATTGTTCGAGTCTTATACTCCCTAAAGAAAGAGGGAGCAGACACGATGGTAGAAGATTGTTC
GAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTGTTG
Found at i:365302 original size:165 final size:167
Alignment explanation
Indices: 364747--365444 Score: 748
Period size: 165 Copynumber: 4.2 Consensus size: 167
364737 TTGAAGCATC
* * *
364747 AAGATTGTTCGAGTCTTATACTCTCTGAAGGAATAA-GGAGCAGACACGATTGTTGAAGATTGTT
1 AAGATTGTTCGAGTCTTATACTCCCTGAAAGAAAAAGGGAGCAGACACGATTGTTGAAGATTGTT
* *
364811 CGAGTCTTATACTCTCTTAAGGAATAGGGAGTAGACAC-ACTTGTTGAAGATTGTTCGAGTCTTA
66 CGAGTCTTATACTCTCTGAAGGAATAGGGAGCAGACACGA-TTGTTGAAGATTGTTCGAGTCTTA
* * * * * *
364875 TACTCTCTGAAGAAATAGGGAGC-AGACACGATTGTTG
130 TACTCCCTAAAGAAAGAGGGAGCGAGACCCGATGGTAG
* *
364912 AAGATTGTTCGAGTCTTATACTCTCTG-AAGAAATAGGGAGCAGACACGATTGTTGAAGATTGTT
1 AAGATTGTTCGAGTCTTATACTCCCTGAAAGAAAAAGGGAGCAGACACGATTGTTGAAGATTGTT
364976 CGAGTCTTATACTCTCTGAAGGAATAGGGAGCAGACACGATTGTTGAAGATTGTTCGAGTCTTAT
66 CGAGTCTTATACTCTCTGAAGGAATAGGGAGCAGACACGATTGTTGAAGATTGTTCGAGTCTTAT
* * * * ** * *
365041 ACTCTCTGAAGGAATAGGGAGC-AGATACGATTGTTG
131 ACTCCCTAAAGAAAGAGGGAGCGAGACCCGATGGTAG
* * *
365077 AAGATTGTTCGAGTCTTATACTCTCT-AAAGGAATAGGGAGCAGACACGATTGTTGAAGATTGTT
1 AAGATTGTTCGAGTCTTATACTCCCTGAAAGAAAAAGGGAGCAGACACGATTGTTGAAGATTGTT
365141 CGAGTCTTATACTCTCTGAAGGAATAGGGAGCAGACACGATTGTTGAAGA-TGTTCGAGT-TCTA
66 CGAGTCTTATACTCTCTGAAGGAATAGGGAGCAGACACGATTGTTGAAGATTGTTCGAGTCT-TA
* *
365204 TACTCCCTAAAGAAAGAGGGGGCGA-ACCCG-TAGGAAG
130 TACTCCCTAAAGAAAGAGGGAGCGAGACCCGAT-GGTAG
* * * * ** *
365241 AAGATTATTCGAGT-TCTATACTCCCTGAAAGAAAAAGGGATCAAACCCG-TTAGCAGAAGATTA
1 AAGATTGTTCGAGTCT-TATACTCCCTGAAAGAAAAAGGGAGCAGACACGATT-GTTGAAGATTG
* * * * * *
365304 TTCGAGT-TCTATACTCCCTGAAAGAAAGAGGGAGC-GAACTCG-TAGGTAGAAGATTGTTCGAG
64 TTCGAGTCT-TATACTCTCTG-AAGGAATAGGGAGCAG-ACACGAT-TGTTGAAGATTGTTCGAG
** * * * *
365366 T-TCCTACTCCCTAAAAAAAGAGGGAGCGA-ACCTGTTGGCAG
125 TCTTATACTCCCTAAAGAAAGAGGGAGCGAGACCCGATGGTAG
* * *
365407 AAGATTGTTCGAGT-TCCATACTCCCAGAAAGCAAAAGG
1 AAGATTGTTCGAGTCT-TATACTCCCTGAAAGAAAAAGG
365445 AAGCGAACCC
Statistics
Matches: 474, Mismatches: 44, Indels: 29
0.87 0.08 0.05
Matches are distributed among these distances:
163 3 0.01
164 64 0.14
165 307 0.65
166 89 0.19
167 11 0.02
ACGTcount: A:0.32, C:0.16, G:0.26, T:0.27
Consensus pattern (167 bp):
AAGATTGTTCGAGTCTTATACTCCCTGAAAGAAAAAGGGAGCAGACACGATTGTTGAAGATTGTT
CGAGTCTTATACTCTCTGAAGGAATAGGGAGCAGACACGATTGTTGAAGATTGTTCGAGTCTTAT
ACTCCCTAAAGAAAGAGGGAGCGAGACCCGATGGTAG
Found at i:365466 original size:110 final size:111
Alignment explanation
Indices: 364856--365472 Score: 361
Period size: 110 Copynumber: 5.6 Consensus size: 111
364846 CACACTTGTT
* * * * *
364856 GAAGATTGTTCGAG-TCTTATACTCTCTG-AAGAAATAGGGAGC-AGACACGATTG-TTGAAGAT
1 GAAGATTGTTCGAGTTC-TATACTC-CCGAAAGAAAGAGGGAGCGA-ACCCG-TAGATAGAAGAT
* * * * **
364917 TGTTCGAG-TCTTATACTCTCTG-AAGAAATAGGGAGCAGACACGATT-GTT
62 TGTTCGAGTTC-TATACTCCCTGAAAGAAAAAGGGAGCAAACCCG-TTAGCA
* * * * * *
364966 GAAGATTGTTCGAG-TCTTATACTCTCTG-AAGGAATAGGGAGC-AGACACGATTG-TTGAAGAT
1 GAAGATTGTTCGAGTTC-TATACTC-CCGAAAGAAAGAGGGAGCGA-ACCCG-TAGATAGAAGAT
* * * * ** **
365027 TGTTCGAG-TCTTATACTCTCTG-AAGGAATAGGGAGCAGATACGATT-GTT
62 TGTTCGAGTTC-TATACTCCCTGAAAGAAAAAGGGAGCAAACCCG-TTAGCA
* * * * * * *
365076 GAAGATTGTTCGAG-TCTTATACTCTCTAAAGGAATAGGGAGC-AGACACGATTG-TTGAAGATT
1 GAAGATTGTTCGAGTTC-TATACTCCCGAAAGAAAGAGGGAGCGA-ACCCG-TAGATAGAAGATT
* * * * * **
365138 GTTCGAG-TCTTATACTCTCTG-AAGGAATAGGGAGCAGACACGATT-GTT
63 GTTCGAGTTC-TATACTCCCTGAAAGAAAAAGGGAGCAAACCCG-TTAGCA
* * *
365186 GAAGA-TGTTCGAGTTCTATACTCCCTAAAGAAAGAGGGGGCGAACCCGTAGGA-AGAAGATTAT
1 GAAGATTGTTCGAGTTCTATACTCCCGAAAGAAAGAGGGAGCGAACCCGTA-GATAGAAGATTGT
*
365249 TCGAGTTCTATACTCCCTGAAAGAAAAAGGGATCAAACCCGTTAGCA
65 TCGAGTTCTATACTCCCTGAAAGAAAAAGGGAGCAAACCCGTTAGCA
* * *
365296 GAAGATTATTCGAGTTCTATACTCCCTGAAAGAAAGAGGGAGCGAACTCGTAGGTAGAAGATTGT
1 GAAGATTGTTCGAGTTCTATACTCCC-GAAAGAAAGAGGGAGCGAACCCGTAGATAGAAGATTGT
* * * *
365361 TCGAGTTC-CTACTCCCT-AAA-AAAAGAGGGAGCGAACCTGTTGGCA
65 TCGAGTTCTATACTCCCTGAAAGAAAA-AGGGAGCAAACCCGTTAGCA
* * *
365406 GAAGATTGTTCGAGTTCCATACTCCCAGAAAGCAAA-AGGAAGCGAACCCGCT-GATCGAAGATT
1 GAAGATTGTTCGAGTTCTATACTCCC-GAAAG-AAAGAGGGAGCGAACCCG-TAGATAGAAGATT
365469 GTTC
63 GTTC
365473 AAAGAAGAGG
Statistics
Matches: 452, Mismatches: 41, Indels: 28
0.87 0.08 0.05
Matches are distributed among these distances:
108 1 0.00
109 63 0.14
110 317 0.70
111 32 0.07
112 39 0.09
ACGTcount: A:0.32, C:0.17, G:0.26, T:0.26
Consensus pattern (111 bp):
GAAGATTGTTCGAGTTCTATACTCCCGAAAGAAAGAGGGAGCGAACCCGTAGATAGAAGATTGTT
CGAGTTCTATACTCCCTGAAAGAAAAAGGGAGCAAACCCGTTAGCA
Found at i:365639 original size:14 final size:14
Alignment explanation
Indices: 365620--365714 Score: 72
Period size: 14 Copynumber: 6.9 Consensus size: 14
365610 TTTATCCTGG
*
365620 TTATAAATATTATA
1 TTATAATTATTATA
365634 TTATAATTATTATTA
1 TTATAATTATTA-TA
365649 TTAT-ATTA-T-TA
1 TTATAATTATTATA
*
365660 TTAT-ATTATTGTTA
1 TTATAATTATT-ATA
**
365674 TTATAACAATTATA
1 TTATAATTATTATA
*
365688 TTATAATAATTATTA
1 TTATAATTATTA-TA
* *
365703 GTATTATTATTA
1 TTATAATTATTA
365715 ATATCATTTA
Statistics
Matches: 67, Mismatches: 8, Indels: 11
0.78 0.09 0.13
Matches are distributed among these distances:
11 10 0.15
12 1 0.01
13 1 0.01
14 34 0.51
15 21 0.31
ACGTcount: A:0.41, C:0.01, G:0.02, T:0.56
Consensus pattern (14 bp):
TTATAATTATTATA
Found at i:365647 original size:3 final size:3
Alignment explanation
Indices: 365627--365714 Score: 76
Period size: 3 Copynumber: 30.7 Consensus size: 3
365617 TGGTTATAAA
* *
365627 TAT TA- TAT TAT AAT TAT TAT TAT TA- TAT TAT TAT TA- TAT TAT TGT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * * * * *
365672 TAT TAT AAC AAT TA- TAT TAT AAT AAT TAT TAG TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
365715 ATATCATTTA
Statistics
Matches: 69, Mismatches: 12, Indels: 8
0.78 0.13 0.09
Matches are distributed among these distances:
2 8 0.12
3 61 0.88
ACGTcount: A:0.40, C:0.01, G:0.02, T:0.57
Consensus pattern (3 bp):
TAT
Found at i:370172 original size:13 final size:13
Alignment explanation
Indices: 370154--370178 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
370144 GTAATAAACA
370154 AAATTAACAAAAT
1 AAATTAACAAAAT
370167 AAATTAACAAAA
1 AAATTAACAAAA
370179 AGTCCAACAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.72, C:0.08, G:0.00, T:0.20
Consensus pattern (13 bp):
AAATTAACAAAAT
Found at i:372382 original size:28 final size:29
Alignment explanation
Indices: 372349--372420 Score: 89
Period size: 28 Copynumber: 2.6 Consensus size: 29
372339 AAAAAATAAT
*
372349 TATTAAATAAAATATTA-AAAAT-TTAAA
1 TATTAAATAAAATATAACAAAATATTAAA
372376 TAATTAAATAAAATACTAACAAAATATTAAA
1 T-ATTAAATAAAATA-TAACAAAATATTAAA
372407 TA-T-AATAAAATATA
1 TATTAAATAAAATATA
372421 CCTTAAAAAT
Statistics
Matches: 40, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
27 3 0.08
28 22 0.55
29 3 0.08
30 6 0.15
31 6 0.15
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (29 bp):
TATTAAATAAAATATAACAAAATATTAAA
Found at i:372418 original size:17 final size:18
Alignment explanation
Indices: 372386--372419 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
372376 TAATTAAATA
372386 AAATACTAACAAAATATT
1 AAATACTAACAAAATATT
*
372404 AAATA-TAATAAAATAT
1 AAATACTAACAAAATAT
372420 ACCTTAAAAA
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:0.65, C:0.06, G:0.00, T:0.29
Consensus pattern (18 bp):
AAATACTAACAAAATATT
Found at i:372459 original size:10 final size:10
Alignment explanation
Indices: 372434--372476 Score: 50
Period size: 10 Copynumber: 4.3 Consensus size: 10
372424 TAAAAATCTA
*
372434 TGAGAGAATA
1 TGAGAGAATT
* *
372444 TAAGAGTATT
1 TGAGAGAATT
*
372454 TGAGAGAAGT
1 TGAGAGAATT
372464 TGAGAGAATT
1 TGAGAGAATT
372474 TGA
1 TGA
372477 TGTGATGAAA
Statistics
Matches: 26, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
10 26 1.00
ACGTcount: A:0.42, C:0.00, G:0.30, T:0.28
Consensus pattern (10 bp):
TGAGAGAATT
Found at i:377999 original size:24 final size:24
Alignment explanation
Indices: 377972--378020 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
377962 AAATGGTCAC
377972 TAATATTTAAATAAATTTTCATTT
1 TAATATTTAAATAAATTTTCATTT
* * *
377996 TAATGTTTGAATAAATTTTCGTTT
1 TAATATTTAAATAAATTTTCATTT
378020 T
1 T
378021 CCTTATTAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.35, C:0.04, G:0.06, T:0.55
Consensus pattern (24 bp):
TAATATTTAAATAAATTTTCATTT
Found at i:381899 original size:2 final size:2
Alignment explanation
Indices: 381892--381916 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
381882 AAATAGTGAT
381892 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
381917 TAAAAAATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:382104 original size:23 final size:24
Alignment explanation
Indices: 382052--382105 Score: 58
Period size: 25 Copynumber: 2.2 Consensus size: 24
382042 ATGAATTTAT
382052 TTTAATATTTATATTTTCTTATCAA
1 TTTAATATTTATATTTTCTTA-CAA
* *
382077 ATTAATATTTAT-TTTTAGTTA-AA
1 TTTAATATTTATATTTT-CTTACAA
382100 TTTAAT
1 TTTAAT
382106 TTTCAACCTT
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
23 7 0.28
24 4 0.16
25 14 0.56
ACGTcount: A:0.35, C:0.04, G:0.02, T:0.59
Consensus pattern (24 bp):
TTTAATATTTATATTTTCTTACAA
Found at i:389459 original size:37 final size:37
Alignment explanation
Indices: 389418--389491 Score: 148
Period size: 37 Copynumber: 2.0 Consensus size: 37
389408 AAACAATTTG
389418 TATAAATAAAAGTATAGTGAGTGAACAGTTGAGTGGC
1 TATAAATAAAAGTATAGTGAGTGAACAGTTGAGTGGC
389455 TATAAATAAAAGTATAGTGAGTGAACAGTTGAGTGGC
1 TATAAATAAAAGTATAGTGAGTGAACAGTTGAGTGGC
389492 CATCCGACCA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.41, C:0.05, G:0.27, T:0.27
Consensus pattern (37 bp):
TATAAATAAAAGTATAGTGAGTGAACAGTTGAGTGGC
Found at i:395786 original size:20 final size:20
Alignment explanation
Indices: 395759--395809 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
395749 CAAATTTCTG
* *
395759 TTTCGCAACTCGATTTTCGAA
1 TTTCGCAACTCGAATTT-AAA
*
395780 TTT-GCAACGCGAATTTAAA
1 TTTCGCAACTCGAATTTAAA
395799 TTTCGCAACTC
1 TTTCGCAACTC
395810 AGCTTTTAAT
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
19 5 0.20
20 17 0.68
21 3 0.12
ACGTcount: A:0.27, C:0.24, G:0.14, T:0.35
Consensus pattern (20 bp):
TTTCGCAACTCGAATTTAAA
Found at i:396800 original size:24 final size:24
Alignment explanation
Indices: 396749--396802 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
396739 GTATTCGAAA
*
396749 TTTGATCTTGGTCAATACCCAGAC
1 TTTGATCTTGGTCAATACCCAAAC
* *
396773 TTTGATCTTGGTCAATACTCAAAT
1 TTTGATCTTGGTCAATACCCAAAC
396797 TTTGAT
1 TTTGAT
396803 TGTGTTTCAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.26, C:0.19, G:0.15, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCAAAC
Found at i:397050 original size:3 final size:3
Alignment explanation
Indices: 397042--397072 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
397032 ATATAATCCT
397042 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA G
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA G
397073 TTCCCAAAGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:399180 original size:12 final size:12
Alignment explanation
Indices: 399163--399196 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
399153 AGTTAAGGGA
399163 AATCAAAATCAC
1 AATCAAAATCAC
399175 AATCAAAATCAC
1 AATCAAAATCAC
*
399187 AATCACAATC
1 AATCAAAATC
399197 GCCTTCACCT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.56, C:0.26, G:0.00, T:0.18
Consensus pattern (12 bp):
AATCAAAATCAC
Found at i:399185 original size:18 final size:18
Alignment explanation
Indices: 399162--399196 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
399152 AAGTTAAGGG
399162 AAATCAAAATCACAATCA
1 AAATCAAAATCACAATCA
*
399180 AAATCACAATCACAATC
1 AAATCAAAATCACAATC
399197 GCCTTCACCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.57, C:0.26, G:0.00, T:0.17
Consensus pattern (18 bp):
AAATCAAAATCACAATCA
Found at i:399410 original size:26 final size:26
Alignment explanation
Indices: 399380--399444 Score: 130
Period size: 26 Copynumber: 2.5 Consensus size: 26
399370 TTCACTATGT
399380 TGTTACAGACATAGCTGATTCATTGA
1 TGTTACAGACATAGCTGATTCATTGA
399406 TGTTACAGACATAGCTGATTCATTGA
1 TGTTACAGACATAGCTGATTCATTGA
399432 TGTTACAGACATA
1 TGTTACAGACATA
399445 ACATGGTGGT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 39 1.00
ACGTcount: A:0.32, C:0.15, G:0.18, T:0.34
Consensus pattern (26 bp):
TGTTACAGACATAGCTGATTCATTGA
Found at i:400245 original size:20 final size:20
Alignment explanation
Indices: 400220--400313 Score: 76
Period size: 20 Copynumber: 5.0 Consensus size: 20
400210 ACAAATTTGC
400220 AACTCAAATTCGCAACTCGA
1 AACTCAAATTCGCAACTCGA
*
400240 AACTCAAATTCGCAACACG-
1 AACTCAAATTCGCAACTCGA
400259 -A---AAA-TCGCAACTCGA
1 AACTCAAATTCGCAACTCGA
* *
400274 AAATGAAATTCGCAAC-CGA
1 AACTCAAATTCGCAACTCGA
** **
400293 ATTTTGAATTCGCAACTCGA
1 AACTCAAATTCGCAACTCGA
400313 A
1 A
400314 TTTCATTTTC
Statistics
Matches: 61, Mismatches: 6, Indels: 14
0.75 0.07 0.17
Matches are distributed among these distances:
14 9 0.15
15 3 0.05
16 1 0.02
18 1 0.02
19 18 0.30
20 29 0.48
ACGTcount: A:0.41, C:0.26, G:0.13, T:0.20
Consensus pattern (20 bp):
AACTCAAATTCGCAACTCGA
Found at i:400272 original size:34 final size:33
Alignment explanation
Indices: 400211--400293 Score: 105
Period size: 34 Copynumber: 2.5 Consensus size: 33
400201 TGTAACAAGA
* * *
400211 CAAATTTGCAACTC-AAATTCGCAACTCGAAACT
1 CAAATTCGCAAC-CGAAAATCGCAACTCGAAAAT
400244 CAAATTCGCAACACGAAAATCGCAACTCGAAAAT
1 CAAATTCGCAAC-CGAAAATCGCAACTCGAAAAT
*
400278 GAAATTCGCAACCGAA
1 CAAATTCGCAACCGAA
400294 TTTTGAATTC
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
33 16 0.36
34 28 0.64
ACGTcount: A:0.43, C:0.27, G:0.12, T:0.18
Consensus pattern (33 bp):
CAAATTCGCAACCGAAAATCGCAACTCGAAAAT
Found at i:400341 original size:20 final size:20
Alignment explanation
Indices: 400318--400357 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
400308 CTCGAATTTC
400318 ATTTTCGAGTTGCGATTTTT
1 ATTTTCGAGTTGCGATTTTT
*
400338 ATTTTTGAGTTGCGATTTTT
1 ATTTTCGAGTTGCGATTTTT
400358 GAGTTGCGAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.15, C:0.07, G:0.20, T:0.57
Consensus pattern (20 bp):
ATTTTCGAGTTGCGATTTTT
Done.