Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032248.1 Gossypioides kirkii chromosome KI_06
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: 60359545
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 900 characters in sequence are not A, C, G, or T
File 110 of 193
Found at i:35322524 original size:38 final size:39
Alignment explanation
Indices: 35322481--35322557 Score: 129
Period size: 38 Copynumber: 2.0 Consensus size: 39
35322471 AAAATTGGGT
35322481 AAGATAAAAAATTTGGACTTTGA-GGAAAATGGGTGAAG
1 AAGATAAAAAATTTGGACTTTGAGGGAAAATGGGTGAAG
* *
35322519 AAGATAAAAAGTTTGGGCTTTGAGGGAAAATGGGTGAAG
1 AAGATAAAAAATTTGGACTTTGAGGGAAAATGGGTGAAG
35322558 TAAATTGGAC
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
38 21 0.58
39 15 0.42
ACGTcount: A:0.42, C:0.03, G:0.32, T:0.23
Consensus pattern (39 bp):
AAGATAAAAAATTTGGACTTTGAGGGAAAATGGGTGAAG
Found at i:35324698 original size:85 final size:85
Alignment explanation
Indices: 35324498--35324678 Score: 303
Period size: 84 Copynumber: 2.1 Consensus size: 85
35324488 TAAAAATAAA
* *
35324498 AATTGAATAAATCTATTTCGAGATTTATTCCCTTCATTCAACAAAATTTTATTCTATATTTGGAT
1 AATTGAATAATTCTATTTCGAGATTTATTCCCGTCATTCAACAAAATTTTATTCTATATTTGGAT
35324563 TTTGTTTCCAAATAATAATT
66 TTTGTTTCCAAATAATAATT
* *
35324583 AATTGAATAATTCTATTTCGAGATTTATTCCCGTCATTCAA-TAGATTTTATTCTATATTTGGAT
1 AATTGAATAATTCTATTTCGAGATTTATTCCCGTCATTCAACAAAATTTTATTCTATATTTGGAT
35324647 TTTGTTTCCAAATAATAATT
66 TTTGTTTCCAAATAATAATT
35324667 AA-TGAATTAATT
1 AATTGAA-TAATT
35324679 ATTGTTTCAG
Statistics
Matches: 91, Mismatches: 4, Indels: 3
0.93 0.04 0.03
Matches are distributed among these distances:
83 4 0.04
84 48 0.53
85 39 0.43
ACGTcount: A:0.34, C:0.12, G:0.08, T:0.46
Consensus pattern (85 bp):
AATTGAATAATTCTATTTCGAGATTTATTCCCGTCATTCAACAAAATTTTATTCTATATTTGGAT
TTTGTTTCCAAATAATAATT
Found at i:35324950 original size:81 final size:83
Alignment explanation
Indices: 35324779--35324954 Score: 177
Period size: 81 Copynumber: 2.2 Consensus size: 83
35324769 ACAGATTTAA
* * * * *
35324779 TTTGATTTTGATTTTGTTTCCAAACAAGAATTAATTGAATAATTCTGTTTGGGATTTATTCTTAT
1 TTTGATTTTGATTTTGTTTCAAAACAAGAAATAATTAAATAATTCTGTTTAGGATTTAATCTTAT
* *
35324844 CGTTTAAACAAATTTTAT
66 CGATTAAACAAATTTGAT
* * *
35324862 TCT-ATTTT-TTTTTGTTTCAAAACAATAAATAA-TAAATAATTCTGTTTCAGGATTTAATCTTG
1 TTTGATTTTGATTTTGTTTCAAAACAAGAAATAATTAAATAATTCTGTTT-AGGATTTAATCTT-
*
35324924 A-C-ATTCAACAGAA-TTGAT
64 ATCGATTAAACA-AATTTGAT
35324942 TTTGATTTT-ATTT
1 TTTGATTTTGATTT
35324955 CAGAATTTTA
Statistics
Matches: 76, Mismatches: 13, Indels: 10
0.77 0.13 0.10
Matches are distributed among these distances:
80 26 0.34
81 42 0.55
82 6 0.08
83 2 0.03
ACGTcount: A:0.32, C:0.09, G:0.10, T:0.49
Consensus pattern (83 bp):
TTTGATTTTGATTTTGTTTCAAAACAAGAAATAATTAAATAATTCTGTTTAGGATTTAATCTTAT
CGATTAAACAAATTTGAT
Found at i:35327737 original size:52 final size:52
Alignment explanation
Indices: 35327638--35327739 Score: 127
Period size: 53 Copynumber: 2.0 Consensus size: 52
35327628 AATTGTTTTC
*
35327638 AGATCTGATGTTTTAAAAAAATATAAATATTTATTTAATTTGTTTTTGTTTA
1 AGATCTGATGTTTTAAAAAAATATAAATATTTATTTAATTTGATTTTGTTTA
* * * *
35327690 AGATCTTATGTTATTATATAAATATAAATATTTGTTT-ATATT-ATTTTGTT
1 AGATCTGATGTT-TTAAAAAAATATAAATATTTATTTAAT-TTGATTTTGTT
35327740 GATATCTTGT
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
52 20 0.47
53 23 0.53
ACGTcount: A:0.35, C:0.02, G:0.09, T:0.54
Consensus pattern (52 bp):
AGATCTGATGTTTTAAAAAAATATAAATATTTATTTAATTTGATTTTGTTTA
Found at i:35330440 original size:91 final size:91
Alignment explanation
Indices: 35330223--35330442 Score: 259
Period size: 91 Copynumber: 2.4 Consensus size: 91
35330213 ATTATATTGG
* *
35330223 ACATTTTTAAAGTACAAATACCACATCAAATATTTTATAAAAATACAAGTATTAAATAATACATA
1 ACATTTTTAAAGTACAAATACCACATCAAATATTTTATAAAAATACAAGTACTAAATAATACACA
*
35330288 AATTGATAATTTAAGTATCACATTAA
66 AATTGATAAGTTAAGTATCACATTAA
* * * *
35330314 ACATTTTTAAAGTATAAGTACCACATCAAACATTTTATAAAAATA-TAGATACTAAATAATACAC
1 ACATTTTTAAAGTACAAATACCACATCAAATATTTTATAAAAATACAAG-TACTAAATAATACAC
* *
35330378 AAATT-A-ACAGTTCAGATATCACATTAC
65 AAATTGATA-AGTTAAG-TATCACATTAA
* * * *
35330405 ATATTTTTAAAATACAAATA-CATTATCCAATATTTTAT
1 ACATTTTTAAAGTACAAATACCA-CATCAAATATTTTAT
35330443 TAGGGTAGAG
Statistics
Matches: 109, Mismatches: 16, Indels: 8
0.82 0.12 0.06
Matches are distributed among these distances:
89 1 0.01
90 10 0.09
91 98 0.90
ACGTcount: A:0.49, C:0.13, G:0.04, T:0.35
Consensus pattern (91 bp):
ACATTTTTAAAGTACAAATACCACATCAAATATTTTATAAAAATACAAGTACTAAATAATACACA
AATTGATAAGTTAAGTATCACATTAA
Found at i:35330621 original size:15 final size:15
Alignment explanation
Indices: 35330601--35330634 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
35330591 TATTTAATCA
* *
35330601 AATTTTTATTATTAT
1 AATTTTAATTATAAT
35330616 AATTTTAATTATAAT
1 AATTTTAATTATAAT
35330631 AATT
1 AATT
35330635 AAAGTAAAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (15 bp):
AATTTTAATTATAAT
Found at i:35332506 original size:96 final size:92
Alignment explanation
Indices: 35332395--35332576 Score: 294
Period size: 97 Copynumber: 1.9 Consensus size: 92
35332385 ACTTAGTCGG
35332395 ACACATTATATATGGTATAGATAATT-AAATAAATATAATTATTCAATAAATATATAGATATCAA
1 ACACATTATATATGGTATAGATAATTAAAATAAATATAATTATTCAATAAATATATAG--A--AA
*
35332459 GCAAAATGAAAATAAGATCAAATTCTTGACGA
62 -CAAAATGAAAATAAGATAAAATTCTTGACGA
35332491 ACACATTATATATGGTATAGATAATTAAAATAAATATAATTATTCAATAAATATATAGAAACAAA
1 ACACATTATATATGGTATAGATAATTAAAATAAATATAATTATTCAATAAATATATAGAAACAAA
*
35332556 ATGAAAATAAGGTAAAATTCT
66 ATGAAAATAAGATAAAATTCT
35332577 ATTATTAGTC
Statistics
Matches: 83, Mismatches: 2, Indels: 6
0.91 0.02 0.07
Matches are distributed among these distances:
92 23 0.28
93 2 0.02
95 1 0.01
96 26 0.31
97 31 0.37
ACGTcount: A:0.53, C:0.07, G:0.09, T:0.31
Consensus pattern (92 bp):
ACACATTATATATGGTATAGATAATTAAAATAAATATAATTATTCAATAAATATATAGAAACAAA
ATGAAAATAAGATAAAATTCTTGACGA
Found at i:35333315 original size:28 final size:28
Alignment explanation
Indices: 35333284--35333342 Score: 100
Period size: 28 Copynumber: 2.1 Consensus size: 28
35333274 AAATGTTCAT
35333284 TGTGGTATTTATATTTGAAAATATCCAA
1 TGTGGTATTTATATTTGAAAATATCCAA
* *
35333312 TGTGGTATTTGTATTTGAAAATGTCCAA
1 TGTGGTATTTATATTTGAAAATATCCAA
35333340 TGT
1 TGT
35333343 AGTACCTAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.31, C:0.07, G:0.19, T:0.44
Consensus pattern (28 bp):
TGTGGTATTTATATTTGAAAATATCCAA
Found at i:35333430 original size:62 final size:62
Alignment explanation
Indices: 35333329--35333467 Score: 197
Period size: 62 Copynumber: 2.2 Consensus size: 62
35333319 TTTGTATTTG
* *
35333329 AAAATGTCCAATGTAGTACCTAAACTATCAATTTATGTATTATTTGGAACTTATACTTTCAT
1 AAAATATCCAATGTGGTACCTAAACTATCAATTTATGTATTATTTGGAACTTATACTTTCAT
* * * * *
35333391 AAAATATCCAATGTGGTACCTAAACTATCAATTTGTGTATTATTTGGTATTTGTGCTTTCAT
1 AAAATATCCAATGTGGTACCTAAACTATCAATTTATGTATTATTTGGAACTTATACTTTCAT
* *
35333453 AAAATTTTCAATGTG
1 AAAATATCCAATGTG
35333468 TTACTTATAT
Statistics
Matches: 68, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
62 68 1.00
ACGTcount: A:0.33, C:0.13, G:0.12, T:0.42
Consensus pattern (62 bp):
AAAATATCCAATGTGGTACCTAAACTATCAATTTATGTATTATTTGGAACTTATACTTTCAT
Found at i:35333849 original size:21 final size:20
Alignment explanation
Indices: 35333810--35333849 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
35333800 AGAAATTTTG
* *
35333810 AGTTAAAATTTGTTTTTTAA
1 AGTTAAAATATGTTGTTTAA
35333830 AGTTAAACATATGTTGTTTA
1 AGTTAAA-ATATGTTGTTTA
35333850 GTTTTAGTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.35, C:0.03, G:0.12, T:0.50
Consensus pattern (20 bp):
AGTTAAAATATGTTGTTTAA
Found at i:35334306 original size:91 final size:91
Alignment explanation
Indices: 35334030--35334287 Score: 396
Period size: 89 Copynumber: 2.9 Consensus size: 91
35334020 ACCTCATTGA
* * * * * ** *
35334030 ACATTTTCAAAGTATAAATACCACATTAGACATTTTATGAAAGTATATGTA-TCAAATAATACAA
1 ACATTTTTAAAGTATAGATACCACATCAAACATTTTATGAAAGTACAAATACT-AAATAATACAT
35334094 AAATTAATAGTTCAAGTATCATGTTGG
65 AAATTAATAGTTCAAGTATCATGTTGG
*
35334121 ACATTTTT-AAGTA-AGATACCACATCAAACATTTTATGAAAGTACAAATACCAAATAATACATA
1 ACATTTTTAAAGTATAGATACCACATCAAACATTTTATGAAAGTACAAATACTAAATAATACATA
35334184 AATTAATAGTTCAAGTATCATGTTGG
66 AATTAATAGTTCAAGTATCATGTTGG
*
35334210 ACATTTTTAAAGTATAGATACCACATCAAACATTTTATGAAAGTACAAATACTAAATAATATATA
1 ACATTTTTAAAGTATAGATACCACATCAAACATTTTATGAAAGTACAAATACTAAATAATACATA
35334275 AATTAATAGTTCA
66 AATTAATAGTTCA
35334288 TGCACCACAT
Statistics
Matches: 153, Mismatches: 11, Indels: 6
0.90 0.06 0.04
Matches are distributed among these distances:
89 75 0.49
90 10 0.07
91 68 0.44
ACGTcount: A:0.46, C:0.12, G:0.09, T:0.33
Consensus pattern (91 bp):
ACATTTTTAAAGTATAGATACCACATCAAACATTTTATGAAAGTACAAATACTAAATAATACATA
AATTAATAGTTCAAGTATCATGTTGG
Found at i:35335990 original size:14 final size:14
Alignment explanation
Indices: 35335971--35336016 Score: 60
Period size: 14 Copynumber: 3.4 Consensus size: 14
35335961 AGTTAACTGA
35335971 TCGATTAATCAAAT
1 TCGATTAATCAAAT
*
35335985 TCGATTAA-CCAA-
1 TCGATTAATCAAAT
*
35335997 CCGATTAATCAAAT
1 TCGATTAATCAAAT
35336011 TCGATT
1 TCGATT
35336017 GATTAACCGA
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
12 7 0.27
13 6 0.23
14 13 0.50
ACGTcount: A:0.39, C:0.20, G:0.09, T:0.33
Consensus pattern (14 bp):
TCGATTAATCAAAT
Found at i:35338193 original size:5 final size:6
Alignment explanation
Indices: 35338179--35338203 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
35338169 GCTTTTTCCC
35338179 TTTTAT TTTTAT TTTTAT TTTTAT T
1 TTTTAT TTTTAT TTTTAT TTTTAT T
35338204 GTTTTAGTCA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (6 bp):
TTTTAT
Found at i:35338865 original size:128 final size:128
Alignment explanation
Indices: 35338637--35338895 Score: 500
Period size: 128 Copynumber: 2.0 Consensus size: 128
35338627 GAGATAGATG
35338637 CTTAAGTGTATATATAAAGAACAAAGAGAGTATTAATGAAAAGACCATATCTTTGTACAATTGAC
1 CTTAAGTGTATATATAAAGAACAAAGAGAGTATTAATGAAAAGACCATATCTTTGTACAATTGAC
*
35338702 TTTACAAATTTCTTTCTTGTCTTCAATATGGAGATATTGACTTGTATTTATGCTTTCTAACAA
66 TTTACAAATTTCTTTCTTGTCTTCAATATGGAGATATTGACTTGTATTTATGCCTTCTAACAA
*
35338765 CTTAAGTGTATATATAAAGAACAAAGAGAGTATTAATGAAAAGACCATATTTTTGTACAATTGAC
1 CTTAAGTGTATATATAAAGAACAAAGAGAGTATTAATGAAAAGACCATATCTTTGTACAATTGAC
35338830 TTTACAAATTTCTTTCTTGTCTTCAATATGGAGATATTGACTTGTATTTATGCCTTCTAACAA
66 TTTACAAATTTCTTTCTTGTCTTCAATATGGAGATATTGACTTGTATTTATGCCTTCTAACAA
35338893 CTT
1 CTT
35338896 TAGGGACTTT
Statistics
Matches: 129, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
128 129 1.00
ACGTcount: A:0.36, C:0.13, G:0.13, T:0.39
Consensus pattern (128 bp):
CTTAAGTGTATATATAAAGAACAAAGAGAGTATTAATGAAAAGACCATATCTTTGTACAATTGAC
TTTACAAATTTCTTTCTTGTCTTCAATATGGAGATATTGACTTGTATTTATGCCTTCTAACAA
Found at i:35340599 original size:232 final size:237
Alignment explanation
Indices: 35340185--35340643 Score: 822
Period size: 232 Copynumber: 1.9 Consensus size: 237
35340175 TCACTTATGT
* *
35340185 GCCATAATTCATGTTTTTAATTAATAACTGTTTTATTTTTATAGAGTAAATTTTGAATTTATAAA
1 GCCATAATTCATGTTTTTAATTAATAACTGTTTTATTTATATAGAGTAAATTCTGAATTTATAAA
35340250 TATATGAAAATATATTTTTTCAATGTATCATTATGTTGAATATATTTTATTTATTAAATTAACTA
66 TATATGAAAATATATTTTTTCAA--TATCATTA-GTTGAATATATTTTATTTATTAAATTAACTA
35340315 TTTATTTTGATATATTTTTTCTTATATATTTCTTATAAAATAAAACATAAATAAAAACAATATCA
128 TTTATTTTGATATATTTTTTCTTATATATTTCTTATAAAATAAAACATAAATAAAAACAATATCA
35340380 ATTAAACATATTTAATGAAACGGATAATTGGAAATTTCAGCCCAC
193 ATTAAACATATTTAATGAAACGGATAATTGGAAATTTCAGCCCAC
35340425 GCCATAATTCATGTTTTTAATTAATAACTGTTTTATTTATATAGAGTAAATTCTGAATTTATAAA
1 GCCATAATTCATGTTTTTAATTAATAACTGTTTTATTTATATAGAGTAAATTCTGAATTTATAAA
35340490 TATATGATAAATATATTTTTTC-A-AT-A-TA-TT-AATATATTTTATTTATTAAATTAACTATT
66 TATATGA-AAATATATTTTTTCAATATCATTAGTTGAATATATTTTATTTATTAAATTAACTATT
35340549 TATTTTGATATATTTTTTCTTATATATTTCTTATAAAATAAAACATAAATAAAAACAATATCAAT
130 TATTTTGATATATTTTTTCTTATATATTTCTTATAAAATAAAACATAAATAAAAACAATATCAAT
35340614 TAAACATATTTAATGAAACGGATAATTGGA
195 TAAACATATTTAATGAAACGGATAATTGGA
35340644 CATGTGTTGA
Statistics
Matches: 216, Mismatches: 2, Indels: 10
0.95 0.01 0.04
Matches are distributed among these distances:
232 124 0.57
233 2 0.01
235 2 0.01
236 1 0.00
237 2 0.01
240 71 0.33
241 14 0.06
ACGTcount: A:0.41, C:0.07, G:0.07, T:0.45
Consensus pattern (237 bp):
GCCATAATTCATGTTTTTAATTAATAACTGTTTTATTTATATAGAGTAAATTCTGAATTTATAAA
TATATGAAAATATATTTTTTCAATATCATTAGTTGAATATATTTTATTTATTAAATTAACTATTT
ATTTTGATATATTTTTTCTTATATATTTCTTATAAAATAAAACATAAATAAAAACAATATCAATT
AAACATATTTAATGAAACGGATAATTGGAAATTTCAGCCCAC
Found at i:35353773 original size:26 final size:26
Alignment explanation
Indices: 35353733--35353787 Score: 76
Period size: 26 Copynumber: 2.1 Consensus size: 26
35353723 GATGTAATTT
**
35353733 GTTATGCCTTTAATTATTA-GAAGGTA
1 GTTATGCCTCCAATTATTACG-AGGTA
35353759 GTTATGCCTCCAATTATTACGAGGTA
1 GTTATGCCTCCAATTATTACGAGGTA
35353785 GTT
1 GTT
35353788 GTTCTTGAAC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
26 25 0.96
27 1 0.04
ACGTcount: A:0.27, C:0.13, G:0.20, T:0.40
Consensus pattern (26 bp):
GTTATGCCTCCAATTATTACGAGGTA
Found at i:35356618 original size:16 final size:16
Alignment explanation
Indices: 35356597--35356651 Score: 101
Period size: 16 Copynumber: 3.4 Consensus size: 16
35356587 GTTTGGTTCG
35356597 CTGTAATGGAATAGAA
1 CTGTAATGGAATAGAA
*
35356613 CTGTAATGGAATAGAG
1 CTGTAATGGAATAGAA
35356629 CTGTAATGGAATAGAA
1 CTGTAATGGAATAGAA
35356645 CTGTAAT
1 CTGTAAT
35356652 CAGTAATTCA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 37 1.00
ACGTcount: A:0.40, C:0.07, G:0.25, T:0.27
Consensus pattern (16 bp):
CTGTAATGGAATAGAA
Found at i:35356847 original size:59 final size:56
Alignment explanation
Indices: 35356777--35356923 Score: 179
Period size: 59 Copynumber: 2.5 Consensus size: 56
35356767 AATTTTAATG
* *
35356777 ATTATTATTAAATATAATTTAATAAAAATATTTAATTTATTTAATTATATTTTAACATA
1 ATTATTATTAAATATAATTTAATAAAAATATGTAATTTA-ATAA-TAT-TTTTAACATA
* *
35356836 ATTATTATTAAATACAATTTAATAAAATAATATGTAATTTAATAATATTTTTAATATA
1 ATTATTATTAAATATAATTTAAT-AAA-AATATGTAATTTAATAATATTTTTAACATA
*
35356894 ATTATTATTAAAATATGAA-TTAGTAAAAAT
1 ATTATTATT-AAATAT-AATTTAATAAAAAT
35356924 TATAATATAT
Statistics
Matches: 78, Mismatches: 6, Indels: 10
0.83 0.06 0.11
Matches are distributed among these distances:
57 3 0.04
58 21 0.27
59 34 0.44
60 8 0.10
61 12 0.15
ACGTcount: A:0.50, C:0.01, G:0.02, T:0.47
Consensus pattern (56 bp):
ATTATTATTAAATATAATTTAATAAAAATATGTAATTTAATAATATTTTTAACATA
Found at i:35356896 original size:58 final size:59
Alignment explanation
Indices: 35356777--35356905 Score: 183
Period size: 59 Copynumber: 2.2 Consensus size: 59
35356767 AATTTTAATG
* * *
35356777 ATTATTATTAAATATAATTTAATAAAAATATTTAATTTATTTAATTATATTTTAACATA
1 ATTATTATTAAATACAATTTAATAAAAATATGTAATTTATATAATTATATTTTAACATA
*
35356836 ATTATTATTAAATACAATTTAATAAAATAATATGTAATTTA-ATAA-TAT-TTTTAATATA
1 ATTATTATTAAATACAATTTAAT-AAA-AATATGTAATTTATATAATTATATTTTAACATA
35356894 ATTATTATTAAA
1 ATTATTATTAAA
35356906 ATATGAATTA
Statistics
Matches: 64, Mismatches: 4, Indels: 5
0.88 0.05 0.07
Matches are distributed among these distances:
58 21 0.33
59 25 0.39
60 6 0.09
61 12 0.19
ACGTcount: A:0.49, C:0.02, G:0.01, T:0.49
Consensus pattern (59 bp):
ATTATTATTAAATACAATTTAATAAAAATATGTAATTTATATAATTATATTTTAACATA
Found at i:35359106 original size:18 final size:18
Alignment explanation
Indices: 35359083--35359120 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
35359073 TTAGAAGAAA
35359083 GGGGTAAATTAAAATTTT
1 GGGGTAAATTAAAATTTT
35359101 GGGGTAAATTAAAATTTT
1 GGGGTAAATTAAAATTTT
35359119 GG
1 GG
35359121 CCAACTTTCC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.37, C:0.00, G:0.26, T:0.37
Consensus pattern (18 bp):
GGGGTAAATTAAAATTTT
Found at i:35380315 original size:41 final size:42
Alignment explanation
Indices: 35380264--35380380 Score: 168
Period size: 41 Copynumber: 2.9 Consensus size: 42
35380254 TGCTTTCCAC
*
35380264 AAAGCGCCGCTAAAGGTCGGGTCATTAGCGGCGCTTA-TAGA
1 AAAGCGCCGCTAAAGGTCGTGTCATTAGCGGCGCTTATTAGA
* *
35380305 AAAGCACCGCTAAAGGTCTTGTCATTAGCGGCGCTTATTAGA
1 AAAGCGCCGCTAAAGGTCGTGTCATTAGCGGCGCTTATTAGA
* *
35380347 AAAGCGCCACTAAAGGT-GTG-AATTAGCGGCGCTT
1 AAAGCGCCGCTAAAGGTCGTGTCATTAGCGGCGCTT
35380381 TCCCATAAGC
Statistics
Matches: 68, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
40 13 0.19
41 36 0.53
42 19 0.28
ACGTcount: A:0.28, C:0.21, G:0.28, T:0.22
Consensus pattern (42 bp):
AAAGCGCCGCTAAAGGTCGTGTCATTAGCGGCGCTTATTAGA
Found at i:35381909 original size:66 final size:66
Alignment explanation
Indices: 35381803--35381959 Score: 260
Period size: 66 Copynumber: 2.4 Consensus size: 66
35381793 CAAATTGCTC
*
35381803 AACTTAAAGAGGAGGCTGCAGCGAGAGAAGCAGAGGCTCAAAAAAAATATGATGAACTCCATCTA
1 AACTTAAAGAGGAGGCTGCAGCGAGAGAAGCAGAGGCTCAAAAAAAATATGAAGAACTCCATCTA
35381868 A
66 A
* *
35381869 AACTTAAAGAGGAGGCTGCAGTGAGAGAAGCAGAGTCTCAAAAAAAATATGAAGAACTCCATCTA
1 AACTTAAAGAGGAGGCTGCAGCGAGAGAAGCAGAGGCTCAAAAAAAATATGAAGAACTCCATCTA
*
35381934 C
66 A
* *
35381935 AACTTAAAGTGGAGGCAGCAGCGAG
1 AACTTAAAGAGGAGGCTGCAGCGAG
35381960 GCAAGCGAAG
Statistics
Matches: 84, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
66 84 1.00
ACGTcount: A:0.43, C:0.17, G:0.25, T:0.15
Consensus pattern (66 bp):
AACTTAAAGAGGAGGCTGCAGCGAGAGAAGCAGAGGCTCAAAAAAAATATGAAGAACTCCATCTA
A
Found at i:35382320 original size:43 final size:42
Alignment explanation
Indices: 35382259--35382399 Score: 192
Period size: 43 Copynumber: 3.3 Consensus size: 42
35382249 ATTTGTTATA
*
35382259 TTAGCGGCGCTTGTGGAGAAAGCGCCGCTAAAGAACATGAGCT
1 TTAGCGGCGCTTGTGGAGAAAGCGCCGCTAAAGAACATG-CCT
* * *
35382302 TTAGCGGCACTTGTGGAGAAAGCGCTGCTAAAAAAACATGCCT
1 TTAGCGGCGCTTGTGGAGAAAGCGCCGCT-AAAGAACATGCCT
* * *
35382345 TTAGCAGCGCTTGTGGAGAAAGCGCCGTTAAAGAACATGTTCT
1 TTAGCGGCGCTTGTGGAGAAAGCGCCGCTAAAGAACATG-CCT
35382388 TTAGCGGCGCTT
1 TTAGCGGCGCTT
35382400 TTTCGCATAA
Statistics
Matches: 85, Mismatches: 11, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
42 9 0.11
43 67 0.79
44 9 0.11
ACGTcount: A:0.28, C:0.21, G:0.29, T:0.23
Consensus pattern (42 bp):
TTAGCGGCGCTTGTGGAGAAAGCGCCGCTAAAGAACATGCCT
Found at i:35385745 original size:15 final size:15
Alignment explanation
Indices: 35385696--35385746 Score: 52
Period size: 15 Copynumber: 3.5 Consensus size: 15
35385686 TTCTCTAAGA
*
35385696 TTATATTTTAGTCAC
1 TTATATTTTAGTCAT
**
35385711 TTATA-TTT-GAAAT
1 TTATATTTTAGTCAT
35385724 GTTATATTTTAGTCAT
1 -TTATATTTTAGTCAT
35385740 TTATATT
1 TTATATT
35385747 ATCGTTCTGT
Statistics
Matches: 28, Mismatches: 5, Indels: 6
0.72 0.13 0.15
Matches are distributed among these distances:
13 2 0.07
14 8 0.29
15 15 0.54
16 3 0.11
ACGTcount: A:0.29, C:0.06, G:0.08, T:0.57
Consensus pattern (15 bp):
TTATATTTTAGTCAT
Found at i:35387203 original size:7 final size:7
Alignment explanation
Indices: 35387156--35387235 Score: 51
Period size: 7 Copynumber: 11.4 Consensus size: 7
35387146 TTAATAGTTA
*
35387156 ATATATA
1 ATATATT
*
35387163 ATATACT
1 ATATATT
35387170 AT-TATT
1 ATATATT
35387176 ATATA-T
1 ATATATT
*
35387182 A-ACGATT
1 ATA-TATT
35387189 ATTATATT
1 A-TATATT
35387197 ATATATT
1 ATATATT
35387204 ATATATT
1 ATATATT
*
35387211 GTATGA-T
1 ATAT-ATT
35387218 ATAATATT
1 AT-ATATT
*
35387226 ATATAGT
1 ATATATT
35387233 ATA
1 ATA
35387236 GTGAGAAGAA
Statistics
Matches: 57, Mismatches: 8, Indels: 16
0.70 0.10 0.20
Matches are distributed among these distances:
5 1 0.02
6 8 0.14
7 37 0.65
8 10 0.18
9 1 0.02
ACGTcount: A:0.44, C:0.03, G:0.05, T:0.49
Consensus pattern (7 bp):
ATATATT
Found at i:35390621 original size:23 final size:24
Alignment explanation
Indices: 35390595--35390639 Score: 67
Period size: 23 Copynumber: 1.9 Consensus size: 24
35390585 CCAATTAGGA
35390595 AATTAT-TGTTTAG-ATTTAATTCT
1 AATTATCT-TTTAGAATTTAATTCT
35390618 AATTATCTTTTAGAATTTAATT
1 AATTATCTTTTAGAATTTAATT
35390640 TGGATCCAAC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
23 11 0.55
24 9 0.45
ACGTcount: A:0.33, C:0.04, G:0.07, T:0.56
Consensus pattern (24 bp):
AATTATCTTTTAGAATTTAATTCT
Found at i:35392191 original size:11 final size:11
Alignment explanation
Indices: 35392177--35392252 Score: 52
Period size: 11 Copynumber: 6.8 Consensus size: 11
35392167 GATAATCACT
35392177 TTAATATTAAA
1 TTAATATTAAA
35392188 TTAATA--AAA
1 TTAATATTAAA
*
35392197 -TATTATTAAAA
1 TTAATATT-AAA
*
35392208 TAAATATTAAA
1 TTAATATTAAA
35392219 TTAA-ATTTAATA
1 TTAATA-TTAA-A
35392231 TTAAACTATTAAA
1 TT-AA-TATTAAA
*
35392244 ATAATATTA
1 TTAATATTA
35392253 TTTTTGGAAT
Statistics
Matches: 51, Mismatches: 5, Indels: 18
0.69 0.07 0.24
Matches are distributed among these distances:
8 4 0.08
9 3 0.06
10 1 0.02
11 24 0.47
12 10 0.20
13 4 0.08
14 4 0.08
15 1 0.02
ACGTcount: A:0.57, C:0.01, G:0.00, T:0.42
Consensus pattern (11 bp):
TTAATATTAAA
Found at i:35392221 original size:68 final size:75
Alignment explanation
Indices: 35392092--35392234 Score: 192
Period size: 68 Copynumber: 2.0 Consensus size: 75
35392082 TGATTAAGCT
*
35392092 TAATCACTTTAATATTAAATTAATATAATAAAATGTATATCTACAAGATAAACATTAAATTAAAT
1 TAATCACTTTAATATT-AA-TAATATAATAAAATATATATCTACAAGATAAACATTAAATTAAAT
35392157 ATAATATTAAGA
64 ATAATATTAAGA
* *
35392169 TAATCACTTTAATATT-A-AAT-TAATAAAATAT-TAT-TA-AA-ATAAATATTAAATTAAATTT
1 TAATCACTTTAATATTAATAATATAATAAAATATATATCTACAAGATAAACATTAAATTAAATAT
35392227 AATATTAA
66 AATATTAA
35392235 ACTATTAAAA
Statistics
Matches: 63, Mismatches: 3, Indels: 9
0.84 0.04 0.12
Matches are distributed among these distances:
68 26 0.41
69 2 0.03
70 2 0.03
71 3 0.05
72 10 0.16
73 3 0.05
75 1 0.02
77 16 0.25
ACGTcount: A:0.54, C:0.05, G:0.02, T:0.39
Consensus pattern (75 bp):
TAATCACTTTAATATTAATAATATAATAAAATATATATCTACAAGATAAACATTAAATTAAATAT
AATATTAAGA
Found at i:35397727 original size:24 final size:24
Alignment explanation
Indices: 35397699--35397758 Score: 84
Period size: 24 Copynumber: 2.5 Consensus size: 24
35397689 TAAACTAATA
* *
35397699 AGAGTTTGACTGAATCAAATAAAC
1 AGAGTTTAACTGAAACAAATAAAC
*
35397723 AGAGTTTAATTGAAACAAATAAAC
1 AGAGTTTAACTGAAACAAATAAAC
*
35397747 ATAGTTTAACTG
1 AGAGTTTAACTG
35397759 GATTATTATT
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.47, C:0.10, G:0.15, T:0.28
Consensus pattern (24 bp):
AGAGTTTAACTGAAACAAATAAAC
Found at i:35401400 original size:22 final size:23
Alignment explanation
Indices: 35401375--35401421 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 23
35401365 ACTTTAACTT
* *
35401375 TTATTTTTATTTTTTC-ATTAGG
1 TTATTATTATTATTTCTATTAGG
*
35401397 TTATTATTATTATTTCTATTTGG
1 TTATTATTATTATTTCTATTAGG
35401420 TT
1 TT
35401422 TTTGGACTGT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
22 14 0.67
23 7 0.33
ACGTcount: A:0.19, C:0.04, G:0.09, T:0.68
Consensus pattern (23 bp):
TTATTATTATTATTTCTATTAGG
Found at i:35405385 original size:17 final size:17
Alignment explanation
Indices: 35405365--35405419 Score: 51
Period size: 17 Copynumber: 3.2 Consensus size: 17
35405355 ATTGTCCCTA
35405365 CATTATTAATGTCATTG
1 CATTATTAATGTCATTG
* * *
35405382 CATTTTTATTGTCACTG
1 CATTATTAATGTCATTG
35405399 CATCTA--AATTGTCATTG
1 CAT-TATTAA-TGTCATTG
35405416 CATT
1 CATT
35405420 TCCATATATA
Statistics
Matches: 30, Mismatches: 6, Indels: 5
0.73 0.15 0.12
Matches are distributed among these distances:
16 2 0.07
17 27 0.90
18 1 0.03
ACGTcount: A:0.25, C:0.16, G:0.11, T:0.47
Consensus pattern (17 bp):
CATTATTAATGTCATTG
Found at i:35406007 original size:26 final size:26
Alignment explanation
Indices: 35405971--35406020 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
35405961 CAGTCACCTG
* * *
35405971 AAAAAGAAAAAAATGAGAAAAAAAAA
1 AAAAAAAAAAAAAAGACAAAAAAAAA
35405997 AAAAAAAAAAAAAAGACAAAAAAA
1 AAAAAAAAAAAAAAGACAAAAAAA
35406021 TTGTTTATTA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.88, C:0.02, G:0.08, T:0.02
Consensus pattern (26 bp):
AAAAAAAAAAAAAAGACAAAAAAAAA
Found at i:35406017 original size:24 final size:24
Alignment explanation
Indices: 35405971--35406020 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 24
35405961 CAGTCACCTG
* **
35405971 AAAAAGAAAAAAATGAGAAAAAAA
1 AAAAAAAAAAAAAAAAGAAAAAAA
*
35405995 AAAAAAAAAAAAAAAAGACAAAAA
1 AAAAAAAAAAAAAAAAGAAAAAAA
35406019 AA
1 AA
35406021 TTGTTTATTA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.88, C:0.02, G:0.08, T:0.02
Consensus pattern (24 bp):
AAAAAAAAAAAAAAAAGAAAAAAA
Found at i:35417120 original size:54 final size:54
Alignment explanation
Indices: 35417038--35417155 Score: 218
Period size: 54 Copynumber: 2.2 Consensus size: 54
35417028 AGGAGTTTCG
35417038 TGGAGTACCGATGACATATTAAGATCGCATTATCTGTAGTCAGTGCACTGCATT
1 TGGAGTACCGATGACATATTAAGATCGCATTATCTGTAGTCAGTGCACTGCATT
* *
35417092 TGGAGTACCGATGACATATTAAGATCGCATTATTTGTAGTCAGTGTACTGCATT
1 TGGAGTACCGATGACATATTAAGATCGCATTATCTGTAGTCAGTGCACTGCATT
35417146 TGGAGTACCG
1 TGGAGTACCG
35417156 GGGATTGACA
Statistics
Matches: 62, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
54 62 1.00
ACGTcount: A:0.27, C:0.17, G:0.24, T:0.32
Consensus pattern (54 bp):
TGGAGTACCGATGACATATTAAGATCGCATTATCTGTAGTCAGTGCACTGCATT
Found at i:35419268 original size:21 final size:22
Alignment explanation
Indices: 35419222--35419266 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
35419212 AATCAATGAG
*
35419222 AATTGAAATCACCAAAATTAAA
1 AATTGAAATAACCAAAATTAAA
35419244 AATTGAAA-AACCAAAACTTAAA
1 AATTGAAATAACCAAAA-TTAAA
35419266 A
1 A
35419267 TTTAATATAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 7 0.33
22 14 0.67
ACGTcount: A:0.62, C:0.13, G:0.04, T:0.20
Consensus pattern (22 bp):
AATTGAAATAACCAAAATTAAA
Found at i:35419968 original size:17 final size:17
Alignment explanation
Indices: 35419948--35420003 Score: 55
Period size: 17 Copynumber: 3.3 Consensus size: 17
35419938 CTCTTGACCT
35419948 TTAACCTTCCATCTTCC
1 TTAACCTTCCATCTTCC
*
35419965 TTAATC-TCC--CTTGACC
1 TTAACCTTCCATCTT--CC
35419981 TTTAACCTTCCATCTTCC
1 -TTAACCTTCCATCTTCC
35419999 TTAAC
1 TTAAC
35420004 TTTTCATATT
Statistics
Matches: 31, Mismatches: 2, Indels: 12
0.69 0.04 0.27
Matches are distributed among these distances:
14 3 0.10
16 5 0.16
17 15 0.48
18 5 0.16
20 3 0.10
ACGTcount: A:0.20, C:0.38, G:0.02, T:0.41
Consensus pattern (17 bp):
TTAACCTTCCATCTTCC
Found at i:35419978 original size:34 final size:34
Alignment explanation
Indices: 35419934--35420002 Score: 129
Period size: 34 Copynumber: 2.0 Consensus size: 34
35419924 TCAACCTTTC
*
35419934 ATCTCTCTTGACCTTTAACCTTCCATCTTCCTTA
1 ATCTCCCTTGACCTTTAACCTTCCATCTTCCTTA
35419968 ATCTCCCTTGACCTTTAACCTTCCATCTTCCTTA
1 ATCTCCCTTGACCTTTAACCTTCCATCTTCCTTA
35420002 A
1 A
35420003 CTTTTCATAT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.19, C:0.36, G:0.03, T:0.42
Consensus pattern (34 bp):
ATCTCCCTTGACCTTTAACCTTCCATCTTCCTTA
Found at i:35420549 original size:34 final size:33
Alignment explanation
Indices: 35420485--35420549 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
35420475 GCTTGCAAGT
* * * *
35420485 TTTGTTAAGGGATTACTTATGTTTACTTAAAAG
1 TTTGTTAAAGGACTACTTATATTTAATTAAAAG
35420518 TTTGTTAAAGGACTACTTATATTTATATTAAA
1 TTTGTTAAAGGACTACTTATATTTA-ATTAAA
35420550 TTTATATTGT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
33 22 0.81
34 5 0.19
ACGTcount: A:0.34, C:0.06, G:0.14, T:0.46
Consensus pattern (33 bp):
TTTGTTAAAGGACTACTTATATTTAATTAAAAG
Found at i:35425453 original size:17 final size:17
Alignment explanation
Indices: 35425431--35425485 Score: 62
Period size: 17 Copynumber: 3.2 Consensus size: 17
35425421 TTCTTGACTT
35425431 TTAACCTTCCATCTTCC
1 TTAACCTTCCATCTTCC
35425448 TTAACC-TCC--CTTGACC
1 TTAACCTTCCATCTT--CC
35425464 TTTAACCTTCCATCTTCC
1 -TTAACCTTCCATCTTCC
35425482 TTAA
1 TTAA
35425486 TCTCCCTTGA
Statistics
Matches: 32, Mismatches: 0, Indels: 12
0.73 0.00 0.27
Matches are distributed among these distances:
14 3 0.09
16 5 0.16
17 16 0.50
18 5 0.16
20 3 0.09
ACGTcount: A:0.20, C:0.38, G:0.02, T:0.40
Consensus pattern (17 bp):
TTAACCTTCCATCTTCC
Found at i:35425468 original size:34 final size:34
Alignment explanation
Indices: 35425423--35425520 Score: 160
Period size: 34 Copynumber: 2.9 Consensus size: 34
35425413 TTTCATCTTT
*
35425423 CTTGACTTTTAACCTTCCATCTTCCTTAACCTCC
1 CTTGACCTTTAACCTTCCATCTTCCTTAACCTCC
*
35425457 CTTGACCTTTAACCTTCCATCTTCCTTAATCTCC
1 CTTGACCTTTAACCTTCCATCTTCCTTAACCTCC
* *
35425491 CTTGACCTTTAGCCTTCCATCTTTCTTAAC
1 CTTGACCTTTAACCTTCCATCTTCCTTAAC
35425521 TTTTCATATT
Statistics
Matches: 59, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
34 59 1.00
ACGTcount: A:0.17, C:0.37, G:0.04, T:0.42
Consensus pattern (34 bp):
CTTGACCTTTAACCTTCCATCTTCCTTAACCTCC
Found at i:35426024 original size:20 final size:20
Alignment explanation
Indices: 35425984--35426024 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
35425974 TAAATTAAAA
35425984 TTAATAAAAATATAAATTTT
1 TTAATAAAAATATAAATTTT
35426004 TTAATTAAATAATAT-AATTTT
1 TTAA-TAAA-AATATAAATTTT
35426025 ATTGTAAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 4 0.21
21 10 0.53
22 5 0.26
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (20 bp):
TTAATAAAAATATAAATTTT
Found at i:35426334 original size:5 final size:5
Alignment explanation
Indices: 35426320--35426370 Score: 86
Period size: 5 Copynumber: 10.4 Consensus size: 5
35426310 ATTTTTAAAT
*
35426320 ATATA ATATA CTATA ATATA ATATA ATATA ATAT- ATATA ATATA ATATA
1 ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA
35426369 AT
1 AT
35426371 GTTTTTATTA
Statistics
Matches: 43, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
4 4 0.09
5 39 0.91
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (5 bp):
ATATA
Found at i:35427308 original size:7 final size:7
Alignment explanation
Indices: 35427296--35427323 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
35427286 TAAATCAAAT
35427296 GTGTTGA
1 GTGTTGA
35427303 GTGTTGA
1 GTGTTGA
35427310 GTGTTGA
1 GTGTTGA
35427317 GTGTTGA
1 GTGTTGA
35427324 ATATTTAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.14, C:0.00, G:0.43, T:0.43
Consensus pattern (7 bp):
GTGTTGA
Found at i:35429442 original size:17 final size:17
Alignment explanation
Indices: 35429406--35429452 Score: 53
Period size: 17 Copynumber: 2.8 Consensus size: 17
35429396 TGTAGTAAAC
*
35429406 TAAGAGAAATGCAGTGA
1 TAAGAAAAATGCAGTGA
35429423 TAATG-AAAATGCAG-GCA
1 TAA-GAAAAATGCAGTG-A
35429440 TAAGAAAAATGCA
1 TAAGAAAAATGCA
35429453 TGAAAACTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
16 2 0.08
17 23 0.88
18 1 0.04
ACGTcount: A:0.51, C:0.09, G:0.23, T:0.17
Consensus pattern (17 bp):
TAAGAAAAATGCAGTGA
Found at i:35429901 original size:12 final size:13
Alignment explanation
Indices: 35429883--35429928 Score: 51
Period size: 12 Copynumber: 3.5 Consensus size: 13
35429873 TCAGTTTCAG
35429883 TTTCTTCCTTCTC
1 TTTCTTCCTTCTC
35429896 -TTCTTCCTTC-C
1 TTTCTTCCTTCTC
*
35429907 TTTCTTCTTCTTCTT
1 TTTCTTC--CTTCTC
35429922 TTTCTTC
1 TTTCTTC
35429929 ATCCTTCTCT
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
11 1 0.04
12 16 0.57
14 4 0.14
15 7 0.25
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (13 bp):
TTTCTTCCTTCTC
Found at i:35440667 original size:21 final size:21
Alignment explanation
Indices: 35440643--35440712 Score: 81
Period size: 21 Copynumber: 3.3 Consensus size: 21
35440633 AAGCAATTTA
35440643 GAAACAATGTAAACTTCTACC
1 GAAACAATGTAAACTTCTACC
* *
35440664 GAAAC-TTGTAATAGTTCTACC
1 GAAACAATGTAA-ACTTCTACC
*
35440685 GATACAAGTGT-AACTTCTACC
1 GAAACAA-TGTAAACTTCTACC
35440706 GAAACAA
1 GAAACAA
35440713 GTCATGCTTC
Statistics
Matches: 40, Mismatches: 6, Indels: 6
0.77 0.12 0.12
Matches are distributed among these distances:
20 5 0.12
21 31 0.77
22 1 0.03
23 3 0.08
ACGTcount: A:0.40, C:0.21, G:0.13, T:0.26
Consensus pattern (21 bp):
GAAACAATGTAAACTTCTACC
Found at i:35440724 original size:42 final size:42
Alignment explanation
Indices: 35440646--35440731 Score: 104
Period size: 42 Copynumber: 2.0 Consensus size: 42
35440636 CAATTTAGAA
**
35440646 ACAATGTAAACTTCTACCGAAACTTGTAATAGTTCTACCGAT
1 ACAATGTAAACTTCTACCGAAACAAGTAATAGTTCTACCGAT
* *
35440688 ACAAGTGT-AACTTCTACCGAAACAAGTCAT-GCTTCTACTGAT
1 ACAA-TGTAAACTTCTACCGAAACAAGTAATAG-TTCTACCGAT
35440730 AC
1 AC
35440732 TAAAAACTCC
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
41 1 0.03
42 34 0.89
43 3 0.08
ACGTcount: A:0.35, C:0.23, G:0.13, T:0.29
Consensus pattern (42 bp):
ACAATGTAAACTTCTACCGAAACAAGTAATAGTTCTACCGAT
Found at i:35443541 original size:26 final size:26
Alignment explanation
Indices: 35443490--35443541 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
35443480 CTTAAGTTAT
*
35443490 ATATTATTTGATATTCAATAGTTTTA
1 ATATTATTTGATATTCAATAATTTTA
*
35443516 ATATTATTTGAT-TTTAATAATATTTA
1 ATATTATTTGATATTCAATAAT-TTTA
35443542 CATAATTGTG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
25 7 0.30
26 16 0.70
ACGTcount: A:0.37, C:0.02, G:0.06, T:0.56
Consensus pattern (26 bp):
ATATTATTTGATATTCAATAATTTTA
Found at i:35443839 original size:25 final size:23
Alignment explanation
Indices: 35443786--35443836 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 23
35443776 ATTTAATTAG
35443786 AAAATATATTTTTAAAAATTATA
1 AAAATATATTTTTAAAAATTATA
*
35443809 AAAATATTTTATTTAATAAATT-TA
1 AAAATATATT-TTTAA-AAATTATA
35443833 AAAA
1 AAAA
35443837 ATAAATATAT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
23 9 0.36
24 11 0.44
25 5 0.20
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (23 bp):
AAAATATATTTTTAAAAATTATA
Found at i:35444743 original size:17 final size:17
Alignment explanation
Indices: 35444711--35444744 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
35444701 TTACATTCAT
*
35444711 AATAATTTTTAATATAA
1 AATAATTTTGAATATAA
*
35444728 AATAATTTTGATTATAA
1 AATAATTTTGAATATAA
35444745 TCATGATTTT
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:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (17 bp):
AATAATTTTGAATATAA
Found at i:35445589 original size:44 final size:45
Alignment explanation
Indices: 35445513--35445597 Score: 109
Period size: 44 Copynumber: 1.9 Consensus size: 45
35445503 ATTAAAGCAA
* ** *
35445513 AATAGAAAATTGTGATAATTGTACATTGAAAAATAGTTATAATTT
1 AATAGAAAATTATGATAATTACACATTGAAAAATAATTATAATTT
* *
35445558 AATA-AAAATTATGATAATTACATATTTAAAAATAATTATA
1 AATAGAAAATTATGATAATTACACATTGAAAAATAATTATA
35445598 TTTTTAACTT
Statistics
Matches: 34, Mismatches: 6, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
44 30 0.88
45 4 0.12
ACGTcount: A:0.52, C:0.02, G:0.08, T:0.38
Consensus pattern (45 bp):
AATAGAAAATTATGATAATTACACATTGAAAAATAATTATAATTT
Found at i:35455521 original size:17 final size:17
Alignment explanation
Indices: 35455491--35455531 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 17
35455481 AAACTAAAAT
35455491 GAATGCAACGACAATCAA
1 GAATGCAACGACAAT-AA
35455509 -AATGCAA-GCACAATAA
1 GAATGCAACG-ACAATAA
35455525 GAATGCA
1 GAATGCA
35455532 TGAAAACTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
16 3 0.14
17 18 0.86
ACGTcount: A:0.51, C:0.20, G:0.17, T:0.12
Consensus pattern (17 bp):
GAATGCAACGACAATAA
Found at i:35467905 original size:18 final size:19
Alignment explanation
Indices: 35467882--35467917 Score: 65
Period size: 18 Copynumber: 1.9 Consensus size: 19
35467872 TATATTATAC
35467882 ATTAATTAA-TTAATTAAG
1 ATTAATTAACTTAATTAAG
35467900 ATTAATTAACTTAATTAA
1 ATTAATTAACTTAATTAA
35467918 AGTTTTGTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 9 0.53
19 8 0.47
ACGTcount: A:0.50, C:0.03, G:0.03, T:0.44
Consensus pattern (19 bp):
ATTAATTAACTTAATTAAG
Found at i:35471771 original size:18 final size:18
Alignment explanation
Indices: 35471748--35471782 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
35471738 GAGTTAAACG
*
35471748 AATCGAGTTGTTCGAGTT
1 AATCGAGTTATTCGAGTT
35471766 AATCGAGTTATTCGAGT
1 AATCGAGTTATTCGAGT
35471783 CAACTTGAAT
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:0.26, C:0.11, G:0.26, T:0.37
Consensus pattern (18 bp):
AATCGAGTTATTCGAGTT
Found at i:35471853 original size:18 final size:18
Alignment explanation
Indices: 35471832--35471868 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
35471822 TGAGTTTTTG
* *
35471832 AATTCGAATAACTCGAAT
1 AATTCAAATAAATCGAAT
35471850 AATTCAAATAAATCGAAT
1 AATTCAAATAAATCGAAT
35471868 A
1 A
35471869 TCAAACTATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.51, C:0.14, G:0.08, T:0.27
Consensus pattern (18 bp):
AATTCAAATAAATCGAAT
Found at i:35472110 original size:30 final size:30
Alignment explanation
Indices: 35472060--35472118 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
35472050 AAACTTTTTA
*
35472060 TTTCCCCTCAAAACTTTACT-CCCTCTCAC
1 TTTCCCCTAAAAACTTTACTCCCCTCTCAC
*
35472089 TTTCTCCCTAAAAATTTTACTCCCCTCTCA
1 TTTC-CCCTAAAAACTTTACTCCCCTCTCA
35472119 GCCCACCCCC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
29 4 0.15
30 14 0.54
31 8 0.31
ACGTcount: A:0.22, C:0.41, G:0.00, T:0.37
Consensus pattern (30 bp):
TTTCCCCTAAAAACTTTACTCCCCTCTCAC
Found at i:35472402 original size:17 final size:18
Alignment explanation
Indices: 35472380--35472426 Score: 62
Period size: 17 Copynumber: 2.7 Consensus size: 18
35472370 CACATTTTGT
35472380 ATTATTTATATTAT-TTA
1 ATTATTTATATTATATTA
*
35472397 ATTATTTA-ATCATATTA
1 ATTATTTATATTATATTA
*
35472414 AATATTTATATTA
1 ATTATTTATATTA
35472427 AAATTGAATT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
16 4 0.16
17 18 0.72
18 3 0.12
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.57
Consensus pattern (18 bp):
ATTATTTATATTATATTA
Found at i:35473974 original size:5 final size:5
Alignment explanation
Indices: 35473961--35473990 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
35473951 ACACCATTTC
*
35473961 AATAT AATAA AATAA AATAA AATAA AATAA
1 AATAA AATAA AATAA AATAA AATAA AATAA
35473991 CATGCACAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (5 bp):
AATAA
Found at i:35489597 original size:15 final size:15
Alignment explanation
Indices: 35489577--35489609 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
35489567 TTTAGTATTA
35489577 TTGAGATATTAATTC
1 TTGAGATATTAATTC
35489592 TTGAGATATTAATTC
1 TTGAGATATTAATTC
35489607 TTG
1 TTG
35489610 TTTGATGTGC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.30, C:0.06, G:0.15, T:0.48
Consensus pattern (15 bp):
TTGAGATATTAATTC
Found at i:35490266 original size:6 final size:6
Alignment explanation
Indices: 35490255--35490317 Score: 54
Period size: 6 Copynumber: 9.7 Consensus size: 6
35490245 ACTTTAGCCA
* *
35490255 TTTTAT TTTTAT TATTTAT TTTTATT TTATTAT TTTTAG TTTAATT TTTCTAT
1 TTTTAT TTTTAT T-TTTAT TTTTA-T TT-TTAT TTTTAT TTTTA-T TTT-TAT
*
35490308 TTTAAT TTTT
1 TTTTAT TTTT
35490318 CCCTTTTTGC
Statistics
Matches: 46, Mismatches: 6, Indels: 10
0.74 0.10 0.16
Matches are distributed among these distances:
6 23 0.50
7 19 0.41
8 4 0.09
ACGTcount: A:0.21, C:0.02, G:0.02, T:0.76
Consensus pattern (6 bp):
TTTTAT
Found at i:35490292 original size:14 final size:14
Alignment explanation
Indices: 35490257--35490311 Score: 60
Period size: 13 Copynumber: 4.0 Consensus size: 14
35490247 TTTAGCCATT
*
35490257 TTATTTTTATTAT-
1 TTATTTTTATTTTA
35490270 TTATTTTTATTTTA
1 TTATTTTTATTTTA
*
35490284 TTATTTTTAGTTTAA
1 TTATTTTTA-TTTTA
*
35490299 TT-TTTCTATTTTA
1 TTATTTTTATTTTA
35490312 ATTTTTCCCT
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
13 16 0.44
14 14 0.39
15 6 0.17
ACGTcount: A:0.22, C:0.02, G:0.02, T:0.75
Consensus pattern (14 bp):
TTATTTTTATTTTA
Found at i:35490312 original size:14 final size:14
Alignment explanation
Indices: 35490273--35490318 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 14
35490263 TTATTATTTA
35490273 TTTT-TATTTT-AT
1 TTTTCTATTTTAAT
* *
35490285 TATTTTTAGTTTAAT
1 T-TTTCTATTTTAAT
35490300 TTTTCTATTTTAAT
1 TTTTCTATTTTAAT
35490314 TTTTC
1 TTTTC
35490319 CCTTTTTGCT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
12 1 0.04
13 3 0.11
14 21 0.75
15 3 0.11
ACGTcount: A:0.20, C:0.04, G:0.02, T:0.74
Consensus pattern (14 bp):
TTTTCTATTTTAAT
Found at i:35493099 original size:11 final size:11
Alignment explanation
Indices: 35493083--35493116 Score: 54
Period size: 11 Copynumber: 3.3 Consensus size: 11
35493073 TCATGTTTTT
35493083 AAAAAAATTGA
1 AAAAAAATTGA
35493094 AAAAAAA-T-A
1 AAAAAAATTGA
35493103 AAAAAAATTGA
1 AAAAAAATTGA
35493114 AAA
1 AAA
35493117 GTTCAAAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
9 8 0.38
10 2 0.10
11 11 0.52
ACGTcount: A:0.79, C:0.00, G:0.06, T:0.15
Consensus pattern (11 bp):
AAAAAAATTGA
Found at i:35493185 original size:22 final size:23
Alignment explanation
Indices: 35493138--35493186 Score: 91
Period size: 22 Copynumber: 2.2 Consensus size: 23
35493128 ATTTAATATA
35493138 TTTATTTTCATTTTTATTTTTAT
1 TTTATTTTCATTTTTATTTTTAT
35493161 TTTATTTT-ATTTTTATTTTTAT
1 TTTATTTTCATTTTTATTTTTAT
35493183 TTTA
1 TTTA
35493187 ATTATGTACT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
22 18 0.69
23 8 0.31
ACGTcount: A:0.18, C:0.02, G:0.00, T:0.80
Consensus pattern (23 bp):
TTTATTTTCATTTTTATTTTTAT
Found at i:35493186 original size:5 final size:6
Alignment explanation
Indices: 35493138--35493185 Score: 73
Period size: 6 Copynumber: 8.3 Consensus size: 6
35493128 ATTTAATATA
*
35493138 TTTATT TTCATT TTTATT TTTA-T TTTA-T TTTATT TTTATT TTTATT
1 TTTATT TTTATT TTTATT TTTATT TTTATT TTTATT TTTATT TTTATT
35493184 TT
1 TT
35493186 AATTATGTAC
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
5 10 0.26
6 29 0.74
ACGTcount: A:0.17, C:0.02, G:0.00, T:0.81
Consensus pattern (6 bp):
TTTATT
Found at i:35493199 original size:22 final size:22
Alignment explanation
Indices: 35493152--35493210 Score: 66
Period size: 22 Copynumber: 2.6 Consensus size: 22
35493142 TTTTCATTTT
* **
35493152 TATTTTTATTTTATTTTATTTT
1 TATTTTTATTTTATATTATTAC
35493174 TATTTTTATTTTA-ATTATGTAC
1 TATTTTTATTTTATATTAT-TAC
35493196 TATTTTTATTCTTAT
1 TATTTTTATT-TTAT
35493211 GTTTTTTTTT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
21 4 0.13
22 24 0.77
23 3 0.10
ACGTcount: A:0.22, C:0.03, G:0.02, T:0.73
Consensus pattern (22 bp):
TATTTTTATTTTATATTATTAC
Found at i:35493199 original size:28 final size:28
Alignment explanation
Indices: 35493140--35493210 Score: 79
Period size: 28 Copynumber: 2.5 Consensus size: 28
35493130 TTAATATATT
* * * **
35493140 TATTTTCATTTTTATTTTTATTTTATTT
1 TATTTTTATTTTTATTTTAATTATATAC
*
35493168 TATTTTTATTTTTATTTTAATTATGTAC
1 TATTTTTATTTTTATTTTAATTATATAC
*
35493196 TATTTTTATTCTTAT
1 TATTTTTATTTTTAT
35493211 GTTTTTTTTT
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
28 36 1.00
ACGTcount: A:0.21, C:0.04, G:0.01, T:0.73
Consensus pattern (28 bp):
TATTTTTATTTTTATTTTAATTATATAC
Found at i:35494133 original size:15 final size:13
Alignment explanation
Indices: 35494113--35494185 Score: 58
Period size: 14 Copynumber: 5.3 Consensus size: 13
35494103 TTTATTATTT
35494113 AAAAAAATCGAAAA
1 AAAAAAAT-GAAAA
35494127 GAAAAAAATGAAAA
1 -AAAAAAATGAAAA
*
35494141 AAAAGAATTGAAAA
1 AAAA-AAATGAAAA
**
35494155 AAAATTGA-GAAAA
1 AAAA-AAATGAAAA
*
35494168 AAAGAAAAAGAAAA
1 AAA-AAAATGAAAA
35494182 AAAA
1 AAAA
35494186 GAAGAAGACA
Statistics
Matches: 48, Mismatches: 7, Indels: 8
0.76 0.11 0.13
Matches are distributed among these distances:
13 14 0.29
14 26 0.54
15 8 0.17
ACGTcount: A:0.78, C:0.01, G:0.12, T:0.08
Consensus pattern (13 bp):
AAAAAAATGAAAA
Found at i:35494180 original size:27 final size:24
Alignment explanation
Indices: 35494113--35494185 Score: 76
Period size: 24 Copynumber: 2.9 Consensus size: 24
35494103 TTTATTATTT
*
35494113 AAAAAAATCGAAAAG-AAAAAAATG
1 AAAAAAA-AGAAAAGAAAAAAAATG
**
35494137 AAAAAAAAGAATTGAAAAAAAATTG
1 AAAAAAAAGAAAAGAAAAAAAA-TG
35494162 AGAAAAAAAGAAAAAGAAAAAAAA
1 A-AAAAAAAG-AAAAGAAAAAAAA
35494186 GAAGAAGACA
Statistics
Matches: 40, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
23 4 0.10
24 14 0.35
25 3 0.08
26 8 0.20
27 11 0.28
ACGTcount: A:0.78, C:0.01, G:0.12, T:0.08
Consensus pattern (24 bp):
AAAAAAAAGAAAAGAAAAAAAATG
Found at i:35494186 original size:15 final size:16
Alignment explanation
Indices: 35494164--35494198 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
35494154 AAAAATTGAG
35494164 AAAAAAAGAAAAAGA-
1 AAAAAAAGAAAAAGAC
*
35494179 AAAAAAAGAAGAAGAC
1 AAAAAAAGAAAAAGAC
35494195 AAAA
1 AAAA
35494199 GTGTGTTTGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 14 0.78
16 4 0.22
ACGTcount: A:0.83, C:0.03, G:0.14, T:0.00
Consensus pattern (16 bp):
AAAAAAAGAAAAAGAC
Found at i:35495250 original size:23 final size:25
Alignment explanation
Indices: 35495224--35495269 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
35495214 CCAATTAGGG
35495224 AATTAT-TGTTTAG-ATTTAATTCT
1 AATTATCTGTTTAGAATTTAATTCT
*
35495247 AATTATCTTTTTAGAATTTAATT
1 AATTATCTGTTTAGAATTTAATT
35495270 TGGATCCAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 6 0.30
25 8 0.40
ACGTcount: A:0.33, C:0.04, G:0.07, T:0.57
Consensus pattern (25 bp):
AATTATCTGTTTAGAATTTAATTCT
Found at i:35519913 original size:20 final size:20
Alignment explanation
Indices: 35519888--35519940 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 20
35519878 TTTTTCGAAA
*
35519888 AAAGTCAACGATTAACGGTC
1 AAAGTCAACGATCAACGGTC
35519908 AAAGTCAACGATCAACGGTC
1 AAAGTCAACGATCAACGGTC
35519928 --AGTCAACGATCAA
1 AAAGTCAACGATCAA
35519941 TGGTTGGTCA
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
18 13 0.41
20 19 0.59
ACGTcount: A:0.42, C:0.23, G:0.19, T:0.17
Consensus pattern (20 bp):
AAAGTCAACGATCAACGGTC
Found at i:35519933 original size:18 final size:18
Alignment explanation
Indices: 35519890--35520000 Score: 98
Period size: 18 Copynumber: 6.0 Consensus size: 18
35519880 TTTCGAAAAA
*
35519890 AGTCAACGATTAACGGTC
1 AGTCAACGATCAACGGTC
35519908 AAAGTCAACGATCAACGGTC
1 --AGTCAACGATCAACGGTC
* *
35519928 AGTCAACGATCAATGGTT
1 AGTCAACGATCAACGGTC
* **
35519946 GGTCAACGATCAATAGTC
1 AGTCAACGATCAACGGTC
* * *
35519964 AGTCAATGGTCAACAGTC
1 AGTCAACGATCAACGGTC
35519982 -GATCAACGATCAAACGGTC
1 AG-TCAACGATC-AACGGTC
35520001 GATCAACAGT
Statistics
Matches: 76, Mismatches: 13, Indels: 5
0.81 0.14 0.05
Matches are distributed among these distances:
17 1 0.01
18 52 0.68
19 6 0.08
20 17 0.22
ACGTcount: A:0.35, C:0.23, G:0.22, T:0.21
Consensus pattern (18 bp):
AGTCAACGATCAACGGTC
Found at i:35522180 original size:22 final size:22
Alignment explanation
Indices: 35522151--35522208 Score: 109
Period size: 22 Copynumber: 2.7 Consensus size: 22
35522141 TTTTATATGG
35522151 AATT-TTGAATTAAAGAATTTT
1 AATTATTGAATTAAAGAATTTT
35522172 AATTATTGAATTAAAGAATTTT
1 AATTATTGAATTAAAGAATTTT
35522194 AATTATTGAATTAAA
1 AATTATTGAATTAAA
35522209 ATTTAGTATA
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
21 4 0.11
22 32 0.89
ACGTcount: A:0.47, C:0.00, G:0.09, T:0.45
Consensus pattern (22 bp):
AATTATTGAATTAAAGAATTTT
Found at i:35523372 original size:16 final size:16
Alignment explanation
Indices: 35523351--35523382 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
35523341 GATGATTTTT
*
35523351 ATGTTAAAGGACTAAA
1 ATGTTAAAGGAATAAA
35523367 ATGTTAAAGGAATAAA
1 ATGTTAAAGGAATAAA
35523383 TTTGTAAGGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.53, C:0.03, G:0.19, T:0.25
Consensus pattern (16 bp):
ATGTTAAAGGAATAAA
Found at i:35524301 original size:195 final size:198
Alignment explanation
Indices: 35523862--35524306 Score: 487
Period size: 195 Copynumber: 2.3 Consensus size: 198
35523852 ACGCGATAGT
* * *
35523862 TGAGGTACCACATATGTTGCGAGTCCTCGACAGCAT-GTGTGAGCAGCATCGTGAGTCGGGAAAT
1 TGAGGTACCGCATATGTTGCGAGTCCTCGACAGC-TCGTGTGAGCAGCATCGTGACTCGAGAAAT
* * *
35523926 GAGAAAAAAAATCCAAGAATGGATTATAGGGCCTACGATGGTTGAGATTTATGCATAAGTGCATA
65 GAGAAAAAAAATCCAAGAATGGATTATAGGCCCTACGATGGTTGAGATCTATCCATAAGTGCATA
* * * * * * *
35523991 TTCTCGACAGCTCGTGTGAGCATCATCATCGTTAGGGAACAGTTATATGCACAGATATCGTATCG
130 CTCTCGACAGCTCGTATGAG-ATCATCATCATTAGGGAACAGTTATATACACAGACACCGTACCG
35524056 ATGGC
194 ATGGC
* *
35524061 TGAGGTACCGCATATGTTGCAAGTCCTCGACAGCTCGTATGAGCAGCATCGTGACTCGAGAAA-G
1 TGAGGTACCGCATATGTTGCGAGTCCTCGACAGCTCGTGTGAGCAGCATCGTGACTCGAGAAATG
* *** * * * *
35524125 AG-ATATGGATCCTA-AATGGATTATAGGCCCTACGATGGTTGGGA-CTATCCTTTA-TGCATAC
66 AGAAAAAAAATCCAAGAATGGATTATAGGCCCTACGATGGTTGAGATCTATCCATAAGTGCATAC
* *
35524186 TCTCGATAGCTCGTATGAG-T-AGT-ATCATTAGGGAACAGTTTATAGTACAAACAGGCACCGTA
131 TCTCGACAGCTCGTATGAGATCA-TCATCATTAGGGAACAG-TTATA-TAC--ACAGACACCGTA
35524248 CCGATGGC
191 CCGATGGC
** * *
35524256 TTG-GGTACTTCATACGTTGCGAGTCCTCGACATCTCGTGTGAGCAGCATCG
1 -TGAGGTACCGCATATGTTGCGAGTCCTCGACAGCTCGTGTGAGCAGCATCG
35524307 AGCACTGGTA
Statistics
Matches: 208, Mismatches: 31, Indels: 18
0.81 0.12 0.07
Matches are distributed among these distances:
191 15 0.07
192 7 0.03
193 2 0.01
194 23 0.11
195 64 0.31
196 30 0.14
197 7 0.03
198 4 0.02
199 56 0.27
ACGTcount: A:0.28, C:0.20, G:0.26, T:0.26
Consensus pattern (198 bp):
TGAGGTACCGCATATGTTGCGAGTCCTCGACAGCTCGTGTGAGCAGCATCGTGACTCGAGAAATG
AGAAAAAAAATCCAAGAATGGATTATAGGCCCTACGATGGTTGAGATCTATCCATAAGTGCATAC
TCTCGACAGCTCGTATGAGATCATCATCATTAGGGAACAGTTATATACACAGACACCGTACCGAT
GGC
Found at i:35527143 original size:18 final size:18
Alignment explanation
Indices: 35527101--35527145 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 18
35527091 ATCCAACAGT
*
35527101 TGCGAGCTCATTCGAAGG
1 TGCGAGCTCACTCGAAGG
35527119 TGCGAGCTCACTC-AAGG
1 TGCGAGCTCACTCGAAGG
*
35527136 CTGTGAGCTC
1 -TGCGAGCTC
35527146 GACCTAGTTG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
17 4 0.17
18 20 0.83
ACGTcount: A:0.20, C:0.27, G:0.31, T:0.22
Consensus pattern (18 bp):
TGCGAGCTCACTCGAAGG
Found at i:35540694 original size:19 final size:19
Alignment explanation
Indices: 35540660--35540696 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
35540650 CAGCAATTTA
**
35540660 TTCTTTTTCTTTTTTTTTC
1 TTCTTTTTCTCATTTTTTC
35540679 TTCTTTTTCTCATTTTTT
1 TTCTTTTTCTCATTTTTT
35540697 ATTTTCAAGT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.03, C:0.16, G:0.00, T:0.81
Consensus pattern (19 bp):
TTCTTTTTCTCATTTTTTC
Found at i:35541307 original size:17 final size:17
Alignment explanation
Indices: 35541285--35541322 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
35541275 AACTAAAATG
*
35541285 AATGCAA-CGACAATTAA
1 AATGCAAGC-ACAATAAA
35541302 AATGCAAGCACAATAAA
1 AATGCAAGCACAATAAA
35541319 AATG
1 AATG
35541323 TATGAAAACC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 18 0.95
18 1 0.05
ACGTcount: A:0.55, C:0.16, G:0.13, T:0.16
Consensus pattern (17 bp):
AATGCAAGCACAATAAA
Found at i:35554858 original size:27 final size:28
Alignment explanation
Indices: 35554802--35554910 Score: 123
Period size: 28 Copynumber: 3.8 Consensus size: 28
35554792 CAAATGATTT
35554802 TAAAATTATTAAAATTATTTTTTAAAATA
1 TAAAATTATTAAAATTA-TTTTTAAAATA
* * *
35554831 T-AAATTTTTTAAGTTATTTTTAAAATA
1 TAAAATTATTAAAATTATTTTTAAAATA
35554858 TAAAATTATTAAAATTATTTTTTTAAAATAA
1 TAAAATTATTAAAATTA--TTTTTAAAAT-A
* *
35554889 TAAAATTCTT-AAATAATTTTTA
1 TAAAATTATTAAAATTATTTTTA
35554911 TTTTCAATTT
Statistics
Matches: 68, Mismatches: 8, Indels: 9
0.80 0.09 0.11
Matches are distributed among these distances:
27 12 0.18
28 30 0.44
29 1 0.01
30 15 0.22
31 10 0.15
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.50
Consensus pattern (28 bp):
TAAAATTATTAAAATTATTTTTAAAATA
Found at i:35555739 original size:29 final size:29
Alignment explanation
Indices: 35555706--35555809 Score: 108
Period size: 29 Copynumber: 3.6 Consensus size: 29
35555696 AAAATTATTT
35555706 AATAATTT-ATTATTTTATTATTTTAAAAA
1 AATAATTTAATTATTTTA-TATTTTAAAAA
* *
35555735 AATAAATTTAATAATTTTGTATTTT-AAAA
1 AAT-AATTTAATTATTTTATATTTTAAAAA
* *
35555764 AATAATTTAAATTTTTTTATATTTT-TAAA
1 AATAATTT-AATTATTTTATATTTTAAAAA
*
35555793 AA-AATTTAATAATTTTA
1 AATAATTTAATTATTTTA
35555810 AAATTATTTG
Statistics
Matches: 64, Mismatches: 8, Indels: 8
0.80 0.10 0.10
Matches are distributed among these distances:
27 8 0.12
28 10 0.16
29 28 0.44
30 11 0.17
31 7 0.11
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.53
Consensus pattern (29 bp):
AATAATTTAATTATTTTATATTTTAAAAA
Found at i:35555818 original size:19 final size:19
Alignment explanation
Indices: 35555764--35555818 Score: 51
Period size: 19 Copynumber: 3.0 Consensus size: 19
35555754 TATTTTAAAA
*
35555764 AATAA-TTT-AAATTTTTT
1 AATAATTTTAAAATTATTT
* * **
35555781 TATATTTTTAAAAAAATTT
1 AATAATTTTAAAATTATTT
35555800 AATAATTTTAAAATTATTT
1 AATAATTTTAAAATTATTT
35555819 GCTGACGTGA
Statistics
Matches: 27, Mismatches: 9, Indels: 2
0.71 0.24 0.05
Matches are distributed among these distances:
17 3 0.11
18 3 0.11
19 21 0.78
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (19 bp):
AATAATTTTAAAATTATTT
Found at i:35566087 original size:16 final size:16
Alignment explanation
Indices: 35566066--35566097 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
35566056 GGCACATGCT
*
35566066 CGTGTGTCAGTCCGTG
1 CGTGTGTCAGCCCGTG
35566082 CGTGTGTCAGCCCGTG
1 CGTGTGTCAGCCCGTG
35566098 TGGCTCACAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.06, C:0.28, G:0.38, T:0.28
Consensus pattern (16 bp):
CGTGTGTCAGCCCGTG
Found at i:35569653 original size:21 final size:24
Alignment explanation
Indices: 35569607--35569654 Score: 66
Period size: 22 Copynumber: 2.1 Consensus size: 24
35569597 CGTCGCAACA
35569607 ATAATGGCTAGTGTCGTGACATCC
1 ATAATGGCTAGTGTCGTGACATCC
*
35569631 ATAA-GGCTA-TGTTGTGAC-TCC
1 ATAATGGCTAGTGTCGTGACATCC
35569652 ATA
1 ATA
35569655 GGCAAAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
21 6 0.26
22 8 0.35
23 5 0.22
24 4 0.17
ACGTcount: A:0.27, C:0.19, G:0.23, T:0.31
Consensus pattern (24 bp):
ATAATGGCTAGTGTCGTGACATCC
Found at i:35574068 original size:870 final size:872
Alignment explanation
Indices: 35572383--35574112 Score: 3238
Period size: 870 Copynumber: 2.0 Consensus size: 872
35572373 ATATGATTGA
* *
35572383 TTCCATTACCTTTTGGTTATTTGTTCATTTAGTCCTAATTAGTTTAAGACTAAATTGAAAATAAG
1 TTCCATTACCTTTTGGTTATTTATTCATTTAGTCCTAATTAGTTTAAGACTAAATTGAAAATAAA
*
35572448 TTTGTTTAATTTAAATTTAAAATAATTAAAGGACAAAATATAAAATTGGACTCTCTTCAAATGGC
66 TTTGTTTAATCTAAATTTAAAATAATTAAAGGACAAAATATAAAATTGGAC-CTCTTC--A-GGC
35572513 CTAATAATAGAATTGGTATAAAACTCTTTAGATTTTGGCAAATGCAATTAGAACCTAATAAAATG
127 CTAATAATAGAATTGGTATAAAACTCTTTAGATTTTGGCAAATGCAATTAGAACCTAATAAAATG
*
35572578 AGGATTTACTAATTAGTTTAATTTAGTATGATCAAGAATGGTGGTTTTGAGGCCACAAATTCGAT
192 AGGATTTACTAATTAGTTTAATTTAGTATGATCAAGAATGGTGGTTTTGAGGCAACAAATTCGAT
35572643 GTGTTAGATCGTAAATATTAATTATTTAATATTTATGAGGTCATTAGTATAGTATTAAATTTTGG
257 GTGTTAGATCGTAAATATTAATTATTTAATATTTATGAGGTCATTAGTATAGTATTAAATTTTGG
*
35572708 TTAAGAAATTCTATCATTTAGTTAGTTAATTACGTAAAAAGGATTAAATCGTAAAAGGTAAAAAA
322 TTAAGAAATTCTATCATTTAGGTAGTTAATTACGTAAAAAGGATTAAATCGTAAAAGGTAAAAAA
* *
35572773 GTTGAATTCTATAAATTGAAGGGTAAGTTAAGGTACTTGAATGGTAATTATACCATTGGAAGAGT
387 GTTAAATTCTATAAATTGAAAGGTAAGTTAAGGTACTTGAATGGTAATTATACCATTGGAAGAGT
35572838 AGTGAGCGGCTTTGGCTATTCTTTTAGCTAAAATTCATGTGTGAACAAAGGATAAAATGGTAATT
452 AGTGAGCGGCTTTGGCTATTCTTTTAGCTAAAATTCATGTGTGAACAAAGGATAAAATGGTAATT
35572903 AAGTAAATAAATGTTATAAAATAAAATTAAAAAGGAAAGAAAAAAGGTTATCTTCTTCATTTTTT
517 AAGTAAATAAATGTTATAAAATAAAATTAAAAAGGAAAGAAAAAAGGTTATCTTCTTCATTTTTT
35572968 ACTTTCTCCAAAGCCAAAACTTAAAAGAAGAACAAGGTTAGGAATGACCAAGCTTTGGATCATTC
582 ACTTTCTCCAAAGCCAAAACTTAAAAGAAGAACAAGGTTAGGAATGACCAAGCTTTGGATCATTC
35573033 TAGGTGAGTGAAATCTCGCCCGTTTTTAGTAATTTTTATGTTTTGAGTCCATATTAGCTTAATCT
647 TAGGTGAGTGAAATCTCGCCCGTTTTTAGTAATTTTTATGTTTTGAGTCCATATTAGCTTAATCT
35573098 AGCTAGCTCAAGGACTAATTTCTGATTATGTCAAATGTTATAAATTTTTCCATTGATGAATAAGC
712 AGCTAGCTCAAGGACTAATTTCTGATTATGTCAAATGTTATAAATTTTTCCATTGATGAATAAGC
35573163 TTGTTTTTGAAATATTATGGAAGATTTATAAGCTTGGTTGTTAGATTTGATTATTTTTTAAAGTA
777 TTGTTTTTGAAATATTATGGAAGATTTATAAGCTTGGTTGTTAGATTTGATTATTTTTTAAAGTA
35573228 GTTTTTGATGATTTTTCCATTAAACTTATTT
842 GTTTTTGATGATTTTTCCATTAAACTTATTT
35573259 TTCCATTACCTTTTGGTTATTTATTCATTTAGTCCTAATTAGTTTAAGACTAAATTGAAAATAAA
1 TTCCATTACCTTTTGGTTATTTATTCATTTAGTCCTAATTAGTTTAAGACTAAATTGAAAATAAA
35573324 TTTGTTTAATCTAAATTTAAAATAATTAAAGGACAAAATATAAAATTGGA-CTC-TC-GGCCTAA
66 TTTGTTTAATCTAAATTTAAAATAATTAAAGGACAAAATATAAAATTGGACCTCTTCAGGCCTAA
*
35573386 TAATAGAATTGGTATAAAACTCTTTAGATTTTGGCAAATTGCAATTATAACCTAATAAAATGAGG
131 TAATAGAATTGGTATAAAACTCTTTAGATTTTGGCAAA-TGCAATTAGAACCTAATAAAATGAGG
35573451 ATTTACTAATTAGTTTAATTTAGTATGATCAAGAATGGTGGTTTTGAGGCAACAAATTCGATGTG
195 ATTTACTAATTAGTTTAATTTAGTATGATCAAGAATGGTGGTTTTGAGGCAACAAATTCGATGTG
35573516 TTAGATCGTAAATATTAATTATTTAATATTTATGAGGTCATTAGTATAGTATTAAATTTTTTGGT
260 TTAGATCGTAAATATTAATTATTTAATATTTATGAGGTCATTAGTATAGTATTAAA--TTTTGGT
35573581 TAAGAAATTCTATCATTTAGGTAGTTAATTACGTAAAAAGGATTAAATCGTAAAAGGTAAAAAAG
323 TAAGAAATTCTATCATTTAGGTAGTTAATTACGTAAAAAGGATTAAATCGTAAAAGGTAAAAAAG
*
35573646 TTAAATTCTATTAATTGAAAGGTAAGTTAAGGTACTTGAATGGTAATTATACCATTGGAAGAGTA
388 TTAAATTCTATAAATTGAAAGGTAAGTTAAGGTACTTGAATGGTAATTATACCATTGGAAGAGTA
35573711 GTGAGCGGCTTTGGCTATTCTTTTAGCTAAAATTCATGTGTGAACAAAGGATAAAATGGTAATTA
453 GTGAGCGGCTTTGGCTATTCTTTTAGCTAAAATTCATGTGTGAACAAAGGATAAAATGGTAATTA
*
35573776 AGTAAATAAATGTTAT-AAATAAAATTAAAAAGG-AAGAAAAGAGGTTATCTTCTTCATTTTTTA
518 AGTAAATAAATGTTATAAAATAAAATTAAAAAGGAAAGAAAAAAGGTTATCTTCTTCATTTTTTA
* *
35573839 CTTTCTCCAAAGCCAAAACTTAAAAGAAGAACAAGGTTAGGAATGGCCAAGCTTTGGATCATTTT
583 CTTTCTCCAAAGCCAAAACTTAAAAGAAGAACAAGGTTAGGAATGACCAAGCTTTGGATCATTCT
35573904 AGGTGAGTGAAATCTCGCCCGTTTTTAGTAATTTTTATGTTTTTGAGTCCATATTAGCTTAATCT
648 AGGTGAGTGAAATCTCGCCCGTTTTTAGTAATTTTTATG-TTTTGAGTCCATATTAGCTTAATCT
35573969 AGCTAGCTCAAGGACTAATTTCTGATTATGTCAAATGTTATAAA-TTTTCCATTGATGAATAAGC
712 AGCTAGCTCAAGGACTAATTTCTGATTATGTCAAATGTTATAAATTTTTCCATTGATGAATAAGC
35574033 TTGTTTTTGAAATATTATGGAAGATTTATAAGCTTGGTTGTTAGATTTGATTATTTTTTAAAGTA
777 TTGTTTTTGAAATATTATGGAAGATTTATAAGCTTGGTTGTTAGATTTGATTATTTTTTAAAGTA
35574098 GTTTTTGATGATTTT
842 GTTTTTGATGATTTT
35574113 AATGTTTAAG
Statistics
Matches: 838, Mismatches: 12, Indels: 14
0.97 0.01 0.02
Matches are distributed among these distances:
869 45 0.05
870 376 0.45
871 86 0.10
872 214 0.26
873 2 0.00
874 3 0.00
876 112 0.13
ACGTcount: A:0.36, C:0.09, G:0.17, T:0.38
Consensus pattern (872 bp):
TTCCATTACCTTTTGGTTATTTATTCATTTAGTCCTAATTAGTTTAAGACTAAATTGAAAATAAA
TTTGTTTAATCTAAATTTAAAATAATTAAAGGACAAAATATAAAATTGGACCTCTTCAGGCCTAA
TAATAGAATTGGTATAAAACTCTTTAGATTTTGGCAAATGCAATTAGAACCTAATAAAATGAGGA
TTTACTAATTAGTTTAATTTAGTATGATCAAGAATGGTGGTTTTGAGGCAACAAATTCGATGTGT
TAGATCGTAAATATTAATTATTTAATATTTATGAGGTCATTAGTATAGTATTAAATTTTGGTTAA
GAAATTCTATCATTTAGGTAGTTAATTACGTAAAAAGGATTAAATCGTAAAAGGTAAAAAAGTTA
AATTCTATAAATTGAAAGGTAAGTTAAGGTACTTGAATGGTAATTATACCATTGGAAGAGTAGTG
AGCGGCTTTGGCTATTCTTTTAGCTAAAATTCATGTGTGAACAAAGGATAAAATGGTAATTAAGT
AAATAAATGTTATAAAATAAAATTAAAAAGGAAAGAAAAAAGGTTATCTTCTTCATTTTTTACTT
TCTCCAAAGCCAAAACTTAAAAGAAGAACAAGGTTAGGAATGACCAAGCTTTGGATCATTCTAGG
TGAGTGAAATCTCGCCCGTTTTTAGTAATTTTTATGTTTTGAGTCCATATTAGCTTAATCTAGCT
AGCTCAAGGACTAATTTCTGATTATGTCAAATGTTATAAATTTTTCCATTGATGAATAAGCTTGT
TTTTGAAATATTATGGAAGATTTATAAGCTTGGTTGTTAGATTTGATTATTTTTTAAAGTAGTTT
TTGATGATTTTTCCATTAAACTTATTT
Found at i:35574697 original size:52 final size:52
Alignment explanation
Indices: 35574611--35574953 Score: 445
Period size: 52 Copynumber: 6.6 Consensus size: 52
35574601 AAATGCAAAA
* *
35574611 AGGTTCGATGACTATGTGTTATCGTGAGTATATGAATCCTTTACGGATTATG
1 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATG
* * * * *
35574663 AGGTCCTATGACTAAGTGTCATCGTGAGTCTATGAATCATTTACAGATTATG
1 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATG
* *
35574715 AGGTCTGATGACTATGTGTCATCGTGAGTATATGGATCCTTTACGGATTATG
1 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATG
* * * *
35574767 AGGTTCGATGACTGTGTGTCATTGTGAGTATATGAATTCTTTACGGATTATG
1 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATG
* * *
35574819 AGGTCTGATGACTGTGTGTCATCGTGAGTATATGAATCCTTTATGGATTATG
1 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATG
* * * * * *
35574871 AGATCAGATAACTATGTGTCATCGTGAGTATATGGATCCTATTACAGATT-TA
1 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCT-TTACGGATTATG
* * *
35574923 AGGTCCGAAGACTTTGTGTCATCATGAGTAT
1 AGGTCCGATGACTATGTGTCATCGTGAGTAT
35574954 TAAATGGGAA
Statistics
Matches: 251, Mismatches: 39, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
52 244 0.97
53 7 0.03
ACGTcount: A:0.26, C:0.13, G:0.24, T:0.37
Consensus pattern (52 bp):
AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATG
Found at i:35579421 original size:24 final size:24
Alignment explanation
Indices: 35579385--35579439 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 24
35579375 CTCGAATGAT
** *
35579385 GAGCTAATTTATCTAGGTTCGTAA
1 GAGCTAACCTATCTAGGCTCGTAA
* *
35579409 GAGCTAACCTATCTGGGCTCGTAT
1 GAGCTAACCTATCTAGGCTCGTAA
35579433 GAGCTAA
1 GAGCTAA
35579440 TTTTTTTTGG
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.27, C:0.18, G:0.24, T:0.31
Consensus pattern (24 bp):
GAGCTAACCTATCTAGGCTCGTAA
Found at i:35579457 original size:25 final size:25
Alignment explanation
Indices: 35579420--35579495 Score: 100
Period size: 25 Copynumber: 3.0 Consensus size: 25
35579410 AGCTAACCTA
*
35579420 TCTGGGCTCGTATGAGCTAATTTTT
1 TCTGGGCTTGTATGAGCTAATTTTT
* *
35579445 TTTGGGCTTGTATGAGCTAATTTTG
1 TCTGGGCTTGTATGAGCTAATTTTT
*
35579470 TCTGGG-TTCGTATGAGCTAAATTTT
1 TCTGGGCTT-GTATGAGCTAATTTTT
35579495 T
1 T
35579496 GAAAGACTCA
Statistics
Matches: 44, Mismatches: 6, Indels: 2
0.85 0.12 0.04
Matches are distributed among these distances:
24 2 0.05
25 42 0.95
ACGTcount: A:0.17, C:0.12, G:0.25, T:0.46
Consensus pattern (25 bp):
TCTGGGCTTGTATGAGCTAATTTTT
Found at i:35580648 original size:2 final size:2
Alignment explanation
Indices: 35580641--35580665 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
35580631 AATGATTGAA
35580641 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
35580666 ATTGACTACT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:35583197 original size:26 final size:26
Alignment explanation
Indices: 35583168--35583249 Score: 64
Period size: 26 Copynumber: 3.2 Consensus size: 26
35583158 TGTGTCATCG
35583168 TGAGTATATGAATCCTTTACGGATTA
1 TGAGTATATGAATCCTTTACGGATTA
* * *
35583194 TGAGGTCATATGATTAT-GTGT-C--ATCA
1 TGA-GT-ATATGA--ATCCTTTACGGATTA
*
35583220 TGAGTATATGAATCCTTTATGGATTA
1 TGAGTATATGAATCCTTTACGGATTA
35583246 TGAG
1 TGAG
35583250 GTCCGATGAC
Statistics
Matches: 41, Mismatches: 7, Indels: 16
0.64 0.11 0.25
Matches are distributed among these distances:
22 2 0.05
23 2 0.05
24 6 0.15
25 2 0.05
26 16 0.39
27 2 0.05
28 7 0.17
29 2 0.05
30 2 0.05
ACGTcount: A:0.29, C:0.10, G:0.22, T:0.39
Consensus pattern (26 bp):
TGAGTATATGAATCCTTTACGGATTA
Found at i:35583234 original size:52 final size:52
Alignment explanation
Indices: 35583150--35583484 Score: 464
Period size: 52 Copynumber: 6.5 Consensus size: 52
35583140 AAAAAGATCC
35583150 GATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATGAGGTCA
1 GATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATGAGGTCA
* * * * *
35583202 TATGATTATGTGTCATCATGAGTATATGAATCCTTTATGGATTATGAGGTCC
1 GATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATGAGGTCA
* *
35583254 GATGACTATGTTTCATCGTGAGTATATGAATCATTTACGGATTATGAGGGTC-
1 GATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATGA-GGTCA
*
35583306 GATAACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATGAGGTTC-
1 GATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATGAGG-TCA
* * * *
35583358 GATGACTATGTGTCATCATGAGTATCTGAATCCTTTACGGATTATGAAGTCC
1 GATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATGAGGTCA
* * * *
35583410 GATGACTATGTGTCATCGTGAGTATATGGATCCTATTACAGATT-TAAGGTCC
1 GATGACTATGTGTCATCGTGAGTATATGAATCCT-TTACGGATTATGAGGTCA
35583462 GATGAC--TGTGTCATCGTGAGTAT
1 GATGACTATGTGTCATCGTGAGTAT
35583485 TAAATGGGAA
Statistics
Matches: 255, Mismatches: 24, Indels: 10
0.88 0.08 0.03
Matches are distributed among these distances:
50 17 0.07
51 4 0.02
52 222 0.87
53 12 0.05
ACGTcount: A:0.27, C:0.14, G:0.24, T:0.36
Consensus pattern (52 bp):
GATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATGAGGTCA
Found at i:35587023 original size:43 final size:43
Alignment explanation
Indices: 35586968--35587060 Score: 172
Period size: 43 Copynumber: 2.2 Consensus size: 43
35586958 GGTATCCACT
35586968 ATGAAT-T-CTTCAACCAATGGGCTTAAGACCCATCCCTTTCG
1 ATGAATCTACTTCAACCAATGGGCTTAAGACCCATCCCTTTCG
35587009 ATGAATCTACTTCAACCAATGGGCTTAAGACCCATCCCTTTCG
1 ATGAATCTACTTCAACCAATGGGCTTAAGACCCATCCCTTTCG
35587052 ATGAATCTA
1 ATGAATCTA
35587061 GAACCAATTT
Statistics
Matches: 50, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
41 6 0.12
42 1 0.02
43 43 0.86
ACGTcount: A:0.29, C:0.28, G:0.14, T:0.29
Consensus pattern (43 bp):
ATGAATCTACTTCAACCAATGGGCTTAAGACCCATCCCTTTCG
Found at i:35591622 original size:36 final size:36
Alignment explanation
Indices: 35591582--35591660 Score: 131
Period size: 36 Copynumber: 2.2 Consensus size: 36
35591572 TTGTGAAAGT
*
35591582 AAATATGTGGGTATGTTATTCATGTCATTTGACAAC
1 AAATATGTGGGTATGTTATTCATGTCATGTGACAAC
**
35591618 AAATATGTGGGTATGTTATTCATGTCATGTGACAGT
1 AAATATGTGGGTATGTTATTCATGTCATGTGACAAC
35591654 AAATATG
1 AAATATG
35591661 AGATAGTAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
36 40 1.00
ACGTcount: A:0.32, C:0.09, G:0.22, T:0.38
Consensus pattern (36 bp):
AAATATGTGGGTATGTTATTCATGTCATGTGACAAC
Found at i:35591679 original size:86 final size:86
Alignment explanation
Indices: 35591579--35591746 Score: 282
Period size: 86 Copynumber: 2.0 Consensus size: 86
35591569 TTGTTGTGAA
* * *
35591579 AGTAAATATGTGGGTATGTTATTCATGTCATTTGACAACAAATATGTGGGTATGTTATTCATGTC
1 AGTAAATATGTGGGTATGTTATTCATGCCATGTGACAACAAATACGTGGGTATGTTATTCATGTC
*
35591644 ATGTGACAGTAAATATGAGAT
66 ATGTAACAGTAAATATGAGAT
*
35591665 AGTAAATATGTGGGTATGTTATTCATGCCATGTGACAATAAATACGTGGGTATGTTATTCATGTC
1 AGTAAATATGTGGGTATGTTATTCATGCCATGTGACAACAAATACGTGGGTATGTTATTCATGTC
*
35591730 ATGTAATAGTAAATATG
66 ATGTAACAGTAAATATG
35591747 TGGGTATGTT
Statistics
Matches: 76, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
86 76 1.00
ACGTcount: A:0.33, C:0.08, G:0.22, T:0.37
Consensus pattern (86 bp):
AGTAAATATGTGGGTATGTTATTCATGCCATGTGACAACAAATACGTGGGTATGTTATTCATGTC
ATGTAACAGTAAATATGAGAT
Found at i:35591714 original size:36 final size:36
Alignment explanation
Indices: 35591662--35591879 Score: 319
Period size: 36 Copynumber: 6.1 Consensus size: 36
35591652 GTAAATATGA
35591662 GATAGTAAATATGTGGGTATGTTATTCATGCCATGT
1 GATAGTAAATATGTGGGTATGTTATTCATGCCATGT
* * * *
35591698 GACAATAAATACGTGGGTATGTTATTCATGTCATGT
1 GATAGTAAATATGTGGGTATGTTATTCATGCCATGT
* *
35591734 AATAGTAAATATGTGGGTATGTTATTCATGCCATGA
1 GATAGTAAATATGTGGGTATGTTATTCATGCCATGT
**
35591770 GATAGTAAATATGTGGGTATGTTATTCATGTAATGT
1 GATAGTAAATATGTGGGTATGTTATTCATGCCATGT
* *
35591806 GATAGTAAATATATGGGTGTGTTATTCATGCCATGT
1 GATAGTAAATATGTGGGTATGTTATTCATGCCATGT
* * *
35591842 GAGAGTAAATATGTGGGTATATTTTTCATGCCATGT
1 GATAGTAAATATGTGGGTATGTTATTCATGCCATGT
35591878 GA
1 GA
35591880 CAGTGATTAT
Statistics
Matches: 159, Mismatches: 23, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
36 159 1.00
ACGTcount: A:0.30, C:0.08, G:0.24, T:0.38
Consensus pattern (36 bp):
GATAGTAAATATGTGGGTATGTTATTCATGCCATGT
Found at i:35592453 original size:61 final size:59
Alignment explanation
Indices: 35592353--35592486 Score: 178
Period size: 61 Copynumber: 2.2 Consensus size: 59
35592343 ATATGATTAT
* *
35592353 ATGTGATTAATATGTGATGTGATAAATGCTGAAATATTCATGTGATTAAATGTGACTAA
1 ATGTGATTAATATGTGATGTGATAAATGCTGAAACATTCATATGATTAAATGTGACTAA
* * *
35592412 ATGTTATTAATATGTGATGTGTGATAAATGTTGAAACATTCATATGATTAAATGTGATTAA
1 ATGTGATTAATATGTGA--TGTGATAAATGCTGAAACATTCATATGATTAAATGTGACTAA
*
35592473 TATTTGATGTAATA
1 -ATGTGAT-TAATA
35592487 ATTGTTGAAA
Statistics
Matches: 64, Mismatches: 7, Indels: 4
0.85 0.09 0.05
Matches are distributed among these distances:
59 16 0.25
61 38 0.59
62 5 0.08
63 5 0.08
ACGTcount: A:0.37, C:0.04, G:0.19, T:0.40
Consensus pattern (59 bp):
ATGTGATTAATATGTGATGTGATAAATGCTGAAACATTCATATGATTAAATGTGACTAA
Found at i:35592471 original size:110 final size:107
Alignment explanation
Indices: 35592343--35592585 Score: 346
Period size: 110 Copynumber: 2.3 Consensus size: 107
35592333 TTTATCATAA
* *
35592343 ATATGATTATATGTGATTAATATGTGATGTGATAAATGCTGAAATATTCATGTGATTAAATGTGA
1 ATATGATTAAATGTGATTAATATGTGATGTAATAAATGCTGAAATATTCATGTGATT-AATGTGA
* * *
35592408 CTAAATGTTATTAATATGTGATGTGTGATAAATGTTGAAACATTC
65 CTAAATATGATTAATATGTGA--TGTGATAAATATTGAAACATTC
* * *
35592453 ATATGATTAAATGTGATTAATATTTGATGTAATAATTGTTGAAATATTCATGTGATTAATGTGAC
1 ATATGATTAAATGTGATTAATATGTGATGTAATAAATGCTGAAATATTCATGTGATTAATGTGAC
**
35592518 TAAATATGATTAATATGTGATGTGATAAATATTGAAGTATTC
66 TAAATATGATTAATATGTGATGTGATAAATATTGAAACATTC
*
35592560 ATATGACT-AATGTGATTAA-ATGTGAT
1 ATATGATTAAATGTGATTAATATGTGAT
35592586 TATATGTGGT
Statistics
Matches: 121, Mismatches: 12, Indels: 5
0.88 0.09 0.04
Matches are distributed among these distances:
105 6 0.05
106 11 0.09
107 26 0.21
109 26 0.21
110 52 0.43
ACGTcount: A:0.37, C:0.04, G:0.18, T:0.41
Consensus pattern (107 bp):
ATATGATTAAATGTGATTAATATGTGATGTAATAAATGCTGAAATATTCATGTGATTAATGTGAC
TAAATATGATTAATATGTGATGTGATAAATATTGAAACATTC
Found at i:35592511 original size:49 final size:49
Alignment explanation
Indices: 35592402--35592532 Score: 142
Period size: 49 Copynumber: 2.7 Consensus size: 49
35592392 ATGTGATTAA
* * * *
35592402 ATGTGACTAAATGTTATTAATATGTGATGTGTGATAAATGTTGAAACATTC
1 ATGTGATTAAATGTGATTAATATATGA--TGTAATAAATGTTGAAACATTC
* * * *
35592453 ATATGATTAAATGTGATTAATATTTGATGTAATAATTGTTGAAATATTC
1 ATGTGATTAAATGTGATTAATATATGATGTAATAAATGTTGAAACATTC
*
35592502 ATGTGATT-AATGTGACTAA-ATATGAT-TAATA
1 ATGTGATTAAATGTGATTAATATATGATGTAATA
35592533 TGTGATGTGA
Statistics
Matches: 70, Mismatches: 10, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
46 5 0.07
47 6 0.09
48 10 0.14
49 26 0.37
51 23 0.33
ACGTcount: A:0.38, C:0.04, G:0.17, T:0.41
Consensus pattern (49 bp):
ATGTGATTAAATGTGATTAATATATGATGTAATAAATGTTGAAACATTC
Found at i:35592512 original size:24 final size:24
Alignment explanation
Indices: 35592431--35592511 Score: 69
Period size: 24 Copynumber: 3.4 Consensus size: 24
35592421 ATATGTGATG
*
35592431 TGTGA-TAAATGTTGAAACATTCA
1 TGTGATTAAATGTTGAAATATTCA
* *
35592454 TATGATTAAATG-TGATTAATATTTGA
1 TGTGATTAAATGTTGA--AATA-TTCA
* *
35592480 TGT-AATAATTGTTGAAATATTCA
1 TGTGATTAAATGTTGAAATATTCA
35592503 TGTGATTAA
1 TGTGATTAA
35592512 TGTGACTAAA
Statistics
Matches: 44, Mismatches: 8, Indels: 11
0.70 0.13 0.17
Matches are distributed among these distances:
23 13 0.30
24 14 0.32
25 9 0.20
26 8 0.18
ACGTcount: A:0.38, C:0.04, G:0.16, T:0.42
Consensus pattern (24 bp):
TGTGATTAAATGTTGAAATATTCA
Found at i:35592531 original size:58 final size:58
Alignment explanation
Indices: 35592353--35592593 Score: 223
Period size: 58 Copynumber: 4.3 Consensus size: 58
35592343 ATATGATTAT
* ** * *
35592353 ATGTGATTAATATGTGATGTGATAAATGCTGAAATATTCATGTGATTAAATGTGACTAA
1 ATGTGATTAATATGTGATGTAATAAATATTGAAATATTCATATGACT-AATGTGACTAA
* * * *
35592412 ATGTTATTAATATGTGATGTGTGATAAATGTTGAAACATTCATATG----A--T---TAA
1 ATGTGATTAATATGTGA--TGTAATAAATATTGAAATATTCATATGACTAATGTGACTAA
* * * * *
35592463 ATGTGATTAATATTTGATGTAATAATTGTTGAAATATTCATGTGATTAATGTGACTAA
1 ATGTGATTAATATGTGATGTAATAAATATTGAAATATTCATATGACTAATGTGACTAA
* * * *
35592521 ATATGATTAATATGTGATGTGATAAATATTGAAGTATTCATATGACTAATGTGATTAA
1 ATGTGATTAATATGTGATGTAATAAATATTGAAATATTCATATGACTAATGTGACTAA
35592579 ATGTGATT-ATATGTG
1 ATGTGATTAATATGTG
35592594 GTTAAATGTG
Statistics
Matches: 151, Mismatches: 20, Indels: 24
0.77 0.10 0.12
Matches are distributed among these distances:
49 23 0.15
51 18 0.12
53 1 0.01
54 1 0.01
55 1 0.01
56 1 0.01
57 7 0.05
58 59 0.39
59 16 0.11
61 24 0.16
ACGTcount: A:0.37, C:0.04, G:0.19, T:0.41
Consensus pattern (58 bp):
ATGTGATTAATATGTGATGTAATAAATATTGAAATATTCATATGACTAATGTGACTAA
Found at i:35592583 original size:10 final size:10
Alignment explanation
Indices: 35592568--35592629 Score: 81
Period size: 10 Copynumber: 6.3 Consensus size: 10
35592558 TCATATGACT
35592568 AATGTGATTA
1 AATGTGATTA
35592578 AATGTGATTA
1 AATGTGATTA
* *
35592588 TATGTGGTTA
1 AATGTGATTA
*
35592598 AATGTGGTTA
1 AATGTGATTA
35592608 AATGTGATTA
1 AATGTGATTA
*
35592618 TATGTG-TTA
1 AATGTGATTA
35592627 AAT
1 AAT
35592630 ATTAATGTGA
Statistics
Matches: 46, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
9 5 0.11
10 41 0.89
ACGTcount: A:0.34, C:0.00, G:0.23, T:0.44
Consensus pattern (10 bp):
AATGTGATTA
Found at i:35592609 original size:30 final size:29
Alignment explanation
Indices: 35592568--35592629 Score: 106
Period size: 30 Copynumber: 2.1 Consensus size: 29
35592558 TCATATGACT
35592568 AATGTGATTAAATGTGATTATATGTGGTTA
1 AATGTGATTAAATGTGATTATATGT-GTTA
*
35592598 AATGTGGTTAAATGTGATTATATGTGTTA
1 AATGTGATTAAATGTGATTATATGTGTTA
35592627 AAT
1 AAT
35592630 ATTAATGTGA
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
29 7 0.23
30 24 0.77
ACGTcount: A:0.34, C:0.00, G:0.23, T:0.44
Consensus pattern (29 bp):
AATGTGATTAAATGTGATTATATGTGTTA
Found at i:35592657 original size:23 final size:23
Alignment explanation
Indices: 35592608--35592714 Score: 151
Period size: 23 Copynumber: 4.6 Consensus size: 23
35592598 AATGTGGTTA
*
35592608 AATGTGATTATATGTGTTAAATATT
1 AATGTGATT-TATG-CTTAAATATT
* *
35592633 AATGTGATTTAAGCTTAAATGTT
1 AATGTGATTTATGCTTAAATATT
* *
35592656 AATATGATTTATGCTTAAATTTT
1 AATGTGATTTATGCTTAAATATT
35592679 AATGTGATTTATGCTTAAATATT
1 AATGTGATTTATGCTTAAATATT
35592702 AATGTGATTTATG
1 AATGTGATTTATG
35592715 TTGGAAAATA
Statistics
Matches: 74, Mismatches: 8, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
23 62 0.84
24 3 0.04
25 9 0.12
ACGTcount: A:0.35, C:0.03, G:0.15, T:0.48
Consensus pattern (23 bp):
AATGTGATTTATGCTTAAATATT
Found at i:35596928 original size:23 final size:23
Alignment explanation
Indices: 35596898--35596947 Score: 82
Period size: 23 Copynumber: 2.2 Consensus size: 23
35596888 TTTTCCAACA
*
35596898 ATTTATGCTTAAATGTTAATATG
1 ATTTATGCTTAAATATTAATATG
*
35596921 ATTTATGCTTAAATATTAATGTG
1 ATTTATGCTTAAATATTAATATG
35596944 ATTT
1 ATTT
35596948 GTGATGAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.34, C:0.04, G:0.12, T:0.50
Consensus pattern (23 bp):
ATTTATGCTTAAATATTAATATG
Found at i:35596957 original size:23 final size:23
Alignment explanation
Indices: 35596898--35596960 Score: 63
Period size: 23 Copynumber: 2.7 Consensus size: 23
35596888 TTTTCCAACA
* * *
35596898 ATTTATGCTTAAATGTTAATATG
1 ATTTATGATGAAATATTAATATG
* * *
35596921 ATTTATGCTTAAATATTAATGTG
1 ATTTATGATGAAATATTAATATG
*
35596944 ATTTGTGATGAAATATT
1 ATTTATGATGAAATATT
35596961 CAGTTGATTA
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.35, C:0.03, G:0.14, T:0.48
Consensus pattern (23 bp):
ATTTATGATGAAATATTAATATG
Found at i:35597666 original size:39 final size:39
Alignment explanation
Indices: 35597438--35597664 Score: 294
Period size: 39 Copynumber: 5.8 Consensus size: 39
35597428 ATAGACTAGT
* * * *
35597438 AGTGTTTACAGTGTCACT-ATTGCCTCAGTATAACGTTGC
1 AGTGTTTACAGTGTCACTGCTAG-TTCAGTATAACATTGC
* * *
35597477 GGTGTTTACGGTATCACTGCTAGTTCAGTATAACATTGC
1 AGTGTTTACAGTGTCACTGCTAGTTCAGTATAACATTGC
* * * *
35597516 AGTGTTTACAGTGTCATTGCCAGTTTAGTATAGCATTGC
1 AGTGTTTACAGTGTCACTGCTAGTTCAGTATAACATTGC
* *
35597555 AGTGTTTACAATGTCACTGCTAGTTCAGTATAGCATTGC
1 AGTGTTTACAGTGTCACTGCTAGTTCAGTATAACATTGC
*
35597594 AGTGTTTACAGTGTCACTGCTAGTTCAGTATATCATTGC
1 AGTGTTTACAGTGTCACTGCTAGTTCAGTATAACATTGC
* *
35597633 AGTGTTTACAGTGTCACTACCAGTTCAGTATA
1 AGTGTTTACAGTGTCACTGCTAGTTCAGTATA
35597665 TCCCCATTGT
Statistics
Matches: 165, Mismatches: 22, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
39 163 0.99
40 2 0.01
ACGTcount: A:0.24, C:0.18, G:0.21, T:0.37
Consensus pattern (39 bp):
AGTGTTTACAGTGTCACTGCTAGTTCAGTATAACATTGC
Found at i:35599176 original size:25 final size:27
Alignment explanation
Indices: 35599106--35599176 Score: 71
Period size: 25 Copynumber: 2.8 Consensus size: 27
35599096 GCCTTACAAA
*
35599106 ATGTGACTAAATGTGATT-AATATGTG
1 ATGTGACTAAATGTGATTAAATATGTC
* * *
35599132 ATGTGA-TAAACGTTA-AAAATAT-TC
1 ATGTGACTAAATGTGATTAAATATGTC
35599156 ATGTGACT-AATGTGATTAAAT
1 ATGTGACTAAATGTGATTAAAT
35599177 GTGATTATAT
Statistics
Matches: 35, Mismatches: 7, Indels: 7
0.71 0.14 0.14
Matches are distributed among these distances:
24 12 0.34
25 17 0.49
26 6 0.17
ACGTcount: A:0.39, C:0.06, G:0.18, T:0.37
Consensus pattern (27 bp):
ATGTGACTAAATGTGATTAAATATGTC
Found at i:35599179 original size:10 final size:10
Alignment explanation
Indices: 35599164--35599210 Score: 67
Period size: 10 Copynumber: 4.6 Consensus size: 10
35599154 TCATGTGACT
35599164 AATGTGATTA
1 AATGTGATTA
35599174 AATGTGATTA
1 AATGTGATTA
* *
35599184 TATGTGATCA
1 AATGTGATTA
35599194 AATGTGATTA
1 AATGTGATTA
35599204 ATATGTG
1 A-ATGTG
35599211 TTGTATTAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
10 27 0.84
11 5 0.16
ACGTcount: A:0.36, C:0.02, G:0.21, T:0.40
Consensus pattern (10 bp):
AATGTGATTA
Found at i:35599190 original size:20 final size:20
Alignment explanation
Indices: 35599156--35599210 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 20
35599146 AAAAATATTC
* *
35599156 ATGTGACTA-ATGTGATTAA
1 ATGTGATTATATGTGATCAA
35599175 ATGTGATTATATGTGATCAA
1 ATGTGATTATATGTGATCAA
35599195 ATGTGATTAATATGTG
1 ATGTGATT-ATATGTG
35599211 TTGTATTAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
19 8 0.25
20 17 0.53
21 7 0.22
ACGTcount: A:0.35, C:0.04, G:0.22, T:0.40
Consensus pattern (20 bp):
ATGTGATTATATGTGATCAA
Found at i:35604646 original size:18 final size:18
Alignment explanation
Indices: 35604620--35604654 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
35604610 AAATAGTTGC
* *
35604620 AAAATAATACATAAAAGA
1 AAAACAATACACAAAAGA
35604638 AAAACAATACACAAAAG
1 AAAACAATACACAAAAG
35604655 TTGAAAATAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.71, C:0.11, G:0.06, T:0.11
Consensus pattern (18 bp):
AAAACAATACACAAAAGA
Found at i:35612076 original size:30 final size:30
Alignment explanation
Indices: 35612007--35612077 Score: 74
Period size: 30 Copynumber: 2.4 Consensus size: 30
35611997 CTTTGATCTA
* * * *
35612007 ATGTGCAATGTTATATATGAATTTTGATTTT
1 ATGT-CAATTTTATACATGAATTTTAATTTG
35612038 ATGT-AATTTTATACATGAAATTTTAATTTG
1 ATGTCAATTTTATACATG-AATTTTAATTTG
35612068 AT-TCAATTTT
1 ATGTCAATTTT
35612078 TATTGATTTA
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
29 12 0.35
30 18 0.53
31 4 0.12
ACGTcount: A:0.32, C:0.04, G:0.11, T:0.52
Consensus pattern (30 bp):
ATGTCAATTTTATACATGAATTTTAATTTG
Found at i:35614754 original size:21 final size:21
Alignment explanation
Indices: 35614713--35614754 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
35614703 CTTTAGGTAC
* *
35614713 AAAGGTGATATCTTTATACTT
1 AAAGATGATATCTTTAAACTT
35614734 AAAGATGATATCTTTAAACTT
1 AAAGATGATATCTTTAAACTT
35614755 GAGGAGTAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.38, C:0.10, G:0.12, T:0.40
Consensus pattern (21 bp):
AAAGATGATATCTTTAAACTT
Found at i:35621610 original size:22 final size:21
Alignment explanation
Indices: 35621569--35621611 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
35621559 GTTTTGAATA
*
35621569 AATTTTAAAGACTTTTAATTT
1 AATTTTAAAGACTTTAAATTT
*
35621590 AATTTTTAAGACTTGTAAATTT
1 AATTTTAAAGACTT-TAAATTT
35621612 TTTGGGATGT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 13 0.68
22 6 0.32
ACGTcount: A:0.37, C:0.05, G:0.07, T:0.51
Consensus pattern (21 bp):
AATTTTAAAGACTTTAAATTT
Found at i:35624487 original size:15 final size:17
Alignment explanation
Indices: 35624455--35624499 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 17
35624445 CTTCTTATTT
* *
35624455 TCCTCTTGTCTTTCTTCT
1 TCCTCTTCTC-TTCTTCC
35624473 TCTCTCTTCTCTTCTTCC
1 TC-CTCTTCTCTTCTTCC
35624491 TCCTCTTCT
1 TCCTCTTCT
35624500 TTAACACCCA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
17 7 0.29
18 10 0.42
19 7 0.29
ACGTcount: A:0.00, C:0.40, G:0.02, T:0.58
Consensus pattern (17 bp):
TCCTCTTCTCTTCTTCC
Found at i:35644331 original size:19 final size:20
Alignment explanation
Indices: 35644284--35644331 Score: 50
Period size: 19 Copynumber: 2.5 Consensus size: 20
35644274 TTGATAATTC
35644284 TTAA-TATTA-AATTATAAA
1 TTAATTATTATAATTATAAA
*
35644302 TTAAATT-TTATAATT-TATA
1 TT-AATTATTATAATTATAAA
35644321 TTAATTATTAT
1 TTAATTATTAT
35644332 CAAGAGTTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
18 6 0.24
19 14 0.56
20 5 0.20
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (20 bp):
TTAATTATTATAATTATAAA
Found at i:35644994 original size:25 final size:25
Alignment explanation
Indices: 35644961--35645018 Score: 73
Period size: 25 Copynumber: 2.3 Consensus size: 25
35644951 ATTCATCTTC
* *
35644961 TAATTTTTAATTT-ATTTAATTTAT
1 TAATATTTAATTTAATTTAAATTAT
*
35644985 TAACTATTTAATTTAATTTAAATTGT
1 TAA-TATTTAATTTAATTTAAATTAT
35645011 TAATATTT
1 TAATATTT
35645019 TATAGCACGC
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
24 3 0.10
25 14 0.48
26 12 0.41
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.60
Consensus pattern (25 bp):
TAATATTTAATTTAATTTAAATTAT
Found at i:35645020 original size:26 final size:25
Alignment explanation
Indices: 35644961--35645020 Score: 70
Period size: 26 Copynumber: 2.4 Consensus size: 25
35644951 ATTCATCTTC
*
35644961 TAAT-TTTTAATTTATTTAATTTAT
1 TAATATTTTAATTTATTTAAATTAT
*
35644985 TAACTA-TTTAATTTAATTTAAATTGT
1 TAA-TATTTTAATTT-ATTTAAATTAT
35645011 TAATATTTTA
1 TAATATTTTA
35645021 TAGCACGCAA
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
24 3 0.10
25 11 0.37
26 16 0.53
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.60
Consensus pattern (25 bp):
TAATATTTTAATTTATTTAAATTAT
Found at i:35658872 original size:16 final size:15
Alignment explanation
Indices: 35658838--35658873 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
35658828 ATATTTAAAG
35658838 AAAAATGAATATTGT
1 AAAAATGAATATTGT
* *
35658853 AAAAATGGATGTTGT
1 AAAAATGAATATTGT
35658868 AAAAAT
1 AAAAAT
35658874 CTTGATTTTG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.53, C:0.00, G:0.17, T:0.31
Consensus pattern (15 bp):
AAAAATGAATATTGT
Found at i:35670918 original size:17 final size:16
Alignment explanation
Indices: 35670896--35670930 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
35670886 ATTGAAAATT
35670896 TTTAATTAATAAATTTA
1 TTTAATTAA-AAATTTA
*
35670913 TTTAATTAAAGATTTA
1 TTTAATTAAAAATTTA
35670929 TT
1 TT
35670931 CTCATTTCAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 8 0.47
17 9 0.53
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (16 bp):
TTTAATTAAAAATTTA
Found at i:35674940 original size:28 final size:28
Alignment explanation
Indices: 35674897--35675073 Score: 196
Period size: 28 Copynumber: 6.4 Consensus size: 28
35674887 AAGACTTAAG
*
35674897 AGAGCGTTATTCTGTAATATGGCTCGAA
1 AGAGCGTTATTCTGTAATCTGGCTCGAA
* * *
35674925 AGAGCGTTATTTTGTATTTTGGCTCGAA
1 AGAGCGTTATTCTGTAATCTGGCTCGAA
*
35674953 AGAGCGTTATTCTGTAATATGGCTCG-A
1 AGAGCGTTATTCTGTAATCTGGCTCGAA
* * *
35674980 AGAGTGTTATTCTGTATTCTGGCTCAAA
1 AGAGCGTTATTCTGTAATCTGGCTCGAA
* * * *
35675008 AGAGTGCTACTCTGTATTCTGGCTCGAA
1 AGAGCGTTATTCTGTAATCTGGCTCGAA
* * *
35675036 AGAGCGTTACTCT-AAATCTAGCTCGAA
1 AGAGCGTTATTCTGTAATCTGGCTCGAA
*
35675063 AGAGCATTATT
1 AGAGCGTTATT
35675074 TTGGGTTGGT
Statistics
Matches: 128, Mismatches: 20, Indels: 3
0.85 0.13 0.02
Matches are distributed among these distances:
27 43 0.34
28 85 0.66
ACGTcount: A:0.27, C:0.16, G:0.23, T:0.34
Consensus pattern (28 bp):
AGAGCGTTATTCTGTAATCTGGCTCGAA
Done.