Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D07
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: 58101237
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1550000 characters in sequence are not A, C, G, or T
File 188 of 199
Found at i:54554619 original size:44 final size:45
Alignment explanation
Indices: 54554570--54554660 Score: 121
Period size: 45 Copynumber: 2.0 Consensus size: 45
54554560 ACCTCTATTC
* * *
54554570 CATTCAACCAAACACAAGATTA-CTATTACGCCTCTATTCCATTA
1 CATTCAACCAAACACAAGATTAGCTATTACACCTCTAATCCAATA
***
54554614 CATTCAACCAAACAGTGGATTAGCTATTACACCTCTAATCCAATA
1 CATTCAACCAAACACAAGATTAGCTATTACACCTCTAATCCAATA
54554659 CA
1 CA
54554661 CCTCTAATCC
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
44 19 0.47
45 21 0.52
ACGTcount: A:0.37, C:0.29, G:0.07, T:0.27
Consensus pattern (45 bp):
CATTCAACCAAACACAAGATTAGCTATTACACCTCTAATCCAATA
Found at i:54554662 original size:16 final size:16
Alignment explanation
Indices: 54554641--54554709 Score: 129
Period size: 16 Copynumber: 4.2 Consensus size: 16
54554631 GATTAGCTAT
54554641 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
54554657 TACACCTCTAATCCCAA
1 TACACCTCTAAT-CCAA
54554674 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
54554690 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
54554706 TACA
1 TACA
54554710 GCGAACCAAA
Statistics
Matches: 52, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
16 36 0.69
17 16 0.31
ACGTcount: A:0.38, C:0.38, G:0.00, T:0.25
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:54554683 original size:33 final size:32
Alignment explanation
Indices: 54554641--54554709 Score: 129
Period size: 33 Copynumber: 2.1 Consensus size: 32
54554631 GATTAGCTAT
54554641 TACACCTCTAATCCAATACACCTCTAATCCCAA
1 TACACCTCTAATCCAATACACCTCTAAT-CCAA
54554674 TACACCTCTAATCCAATACACCTCTAATCCAA
1 TACACCTCTAATCCAATACACCTCTAATCCAA
54554706 TACA
1 TACA
54554710 GCGAACCAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
32 8 0.22
33 28 0.78
ACGTcount: A:0.38, C:0.38, G:0.00, T:0.25
Consensus pattern (32 bp):
TACACCTCTAATCCAATACACCTCTAATCCAA
Found at i:54555725 original size:128 final size:129
Alignment explanation
Indices: 54555497--54555760 Score: 512
Period size: 128 Copynumber: 2.1 Consensus size: 129
54555487 ACATTTCTCG
54555497 AGAAGAAAATAAAATCACAAATAGTCTCGTTAAGATGGTTCATGACATAAGAACAAGATTACTTT
1 AGAAGAAAATAAAATCACAAATAGTCTCGTTAAGATGGTTCATGACATAAGAACAAGATTACTTT
*
54555562 TGATTGAGAATTTAGGGATTAGTTTAGTTTCTTACATTTGTCTTGCACTC-TTTTTTTCAAAGA
66 TGATTGAGAATTTAGGGATTAGTTTAATTTCTTACATTTGTCTTGCACTCTTTTTTTTCAAAGA
54555625 AGAAGAAAATAAAATCACAAATAGTCTCGTTAAGATGGTTCATGACATAAGAACAAGATTACTTT
1 AGAAGAAAATAAAATCACAAATAGTCTCGTTAAGATGGTTCATGACATAAGAACAAGATTACTTT
54555690 TGATTGAGAATTTAGGGATTAGTTTAATTTCTTACATTTGTCTTGCACTCTTTTTTTTCAAAGA
66 TGATTGAGAATTTAGGGATTAGTTTAATTTCTTACATTTGTCTTGCACTCTTTTTTTTCAAAGA
54555754 AGAAGAA
1 AGAAGAA
54555761 GAAGAAGAAG
Statistics
Matches: 134, Mismatches: 1, Indels: 1
0.99 0.01 0.01
Matches are distributed among these distances:
128 114 0.85
129 20 0.15
ACGTcount: A:0.36, C:0.11, G:0.16, T:0.36
Consensus pattern (129 bp):
AGAAGAAAATAAAATCACAAATAGTCTCGTTAAGATGGTTCATGACATAAGAACAAGATTACTTT
TGATTGAGAATTTAGGGATTAGTTTAATTTCTTACATTTGTCTTGCACTCTTTTTTTTCAAAGA
Found at i:54555756 original size:3 final size:3
Alignment explanation
Indices: 54555750--54555781 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
54555740 TTTTTTTTCA
54555750 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
54555782 AATTAACATA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:54556610 original size:24 final size:24
Alignment explanation
Indices: 54556582--54556635 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
54556572 TCTTTCTAAA
** *
54556582 ATATTTATTATTTATTAGTATAAT
1 ATATTTAGCATTTATTAGCATAAT
54556606 ATATTTAGCATTTATTAGCATAAT
1 ATATTTAGCATTTATTAGCATAAT
*
54556630 TTATTT
1 ATATTT
54556636 GGCCTACGAA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.35, C:0.04, G:0.06, T:0.56
Consensus pattern (24 bp):
ATATTTAGCATTTATTAGCATAAT
Found at i:54561846 original size:19 final size:20
Alignment explanation
Indices: 54561818--54561856 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
54561808 TAGATTTTTA
*
54561818 GAAAA-TTTTAGAATCTTAT
1 GAAAACTTTAAGAATCTTAT
*
54561837 GAAAACTTTAAGAATTTTAT
1 GAAAACTTTAAGAATCTTAT
54561857 TGGTTTTTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.44, C:0.05, G:0.10, T:0.41
Consensus pattern (20 bp):
GAAAACTTTAAGAATCTTAT
Found at i:54561856 original size:20 final size:19
Alignment explanation
Indices: 54561803--54561856 Score: 56
Period size: 18 Copynumber: 2.8 Consensus size: 19
54561793 GTTTGTTTGG
* *
54561803 AATTTTAGATTTTTA-GAA
1 AATTTAAGAATTTTATGAA
* *
54561821 AATTTTAGAATCTTATGAA
1 AATTTAAGAATTTTATGAA
54561840 AACTTTAAGAATTTTAT
1 AA-TTTAAGAATTTTAT
54561857 TGGTTTTTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
18 13 0.43
19 5 0.17
20 12 0.40
ACGTcount: A:0.41, C:0.04, G:0.09, T:0.46
Consensus pattern (19 bp):
AATTTAAGAATTTTATGAA
Found at i:54566219 original size:46 final size:47
Alignment explanation
Indices: 54566150--54566261 Score: 154
Period size: 46 Copynumber: 2.4 Consensus size: 47
54566140 ATTTTATTTG
* *
54566150 GCCTTTGTGGCGTATTCTGTATGTTGCGTTTGTGGCATACTCTGTTA
1 GCCTTTGTGGCGTATTCTGTATGTTGCCTTTGTGGCATACTCTGATA
* * **
54566197 GCCTTTGT-TCGTATTCTTTATGTTGCCTTTGTGGTGTACTCTGATA
1 GCCTTTGTGGCGTATTCTGTATGTTGCCTTTGTGGCATACTCTGATA
*
54566243 GCCTTTGTGGCGTACTCTG
1 GCCTTTGTGGCGTATTCTG
54566262 ATAACCTTTG
Statistics
Matches: 55, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
46 40 0.73
47 15 0.27
ACGTcount: A:0.10, C:0.19, G:0.26, T:0.46
Consensus pattern (47 bp):
GCCTTTGTGGCGTATTCTGTATGTTGCCTTTGTGGCATACTCTGATA
Found at i:54566249 original size:22 final size:22
Alignment explanation
Indices: 54566150--54566278 Score: 98
Period size: 22 Copynumber: 5.6 Consensus size: 22
54566140 ATTTTATTTG
* *
54566150 GCCTTTGTGGCGTATTCTGTATGTT
1 GCCTTTGTGGCGTACTCTG-A--TA
* * *
54566175 GCGTTTGTGGCATACTCTGTTA
1 GCCTTTGTGGCGTACTCTGATA
* * * *
54566197 GCCTTTGT-TCGTATTCTTTATGTT
1 GCCTTTGTGGCGTACTC-TGA--TA
*
54566221 GCCTTTGTGGTGTACTCTGATA
1 GCCTTTGTGGCGTACTCTGATA
54566243 GCCTTTGTGGCGTACTCTGATA
1 GCCTTTGTGGCGTACTCTGATA
*
54566265 ACCTTTGTGGCGTA
1 GCCTTTGTGGCGTA
54566279 TTTTGTCTGG
Statistics
Matches: 81, Mismatches: 19, Indels: 11
0.73 0.17 0.10
Matches are distributed among these distances:
21 5 0.06
22 44 0.54
24 11 0.14
25 21 0.26
ACGTcount: A:0.12, C:0.19, G:0.26, T:0.44
Consensus pattern (22 bp):
GCCTTTGTGGCGTACTCTGATA
Found at i:54569912 original size:29 final size:30
Alignment explanation
Indices: 54569866--54569933 Score: 79
Period size: 29 Copynumber: 2.4 Consensus size: 30
54569856 AATAAACTTA
*
54569866 AAATTTT-AAAGTAAAAAAGTAAAAAGATT
1 AAATTTTCAAAGTAAAAAAATAAAAAGATT
* * *
54569895 AAATTTTCAAA-TATAAAAATATAAATATT
1 AAATTTTCAAAGTAAAAAAATAAAAAGATT
54569924 AAA-TTTCAAA
1 AAATTTTCAAA
54569934 CATAGAAGCA
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
28 7 0.21
29 24 0.71
30 3 0.09
ACGTcount: A:0.60, C:0.03, G:0.04, T:0.32
Consensus pattern (30 bp):
AAATTTTCAAAGTAAAAAAATAAAAAGATT
Found at i:54576482 original size:20 final size:20
Alignment explanation
Indices: 54576457--54576498 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
54576447 AAGAAGTTAA
54576457 AACATTAGGTGCAAAAATAT
1 AACATTAGGTGCAAAAATAT
54576477 AACATTAGGTGCAAAAATAT
1 AACATTAGGTGCAAAAATAT
54576497 AA
1 AA
54576499 TTTTGTAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.52, C:0.10, G:0.14, T:0.24
Consensus pattern (20 bp):
AACATTAGGTGCAAAAATAT
Found at i:54578912 original size:157 final size:148
Alignment explanation
Indices: 54578684--54579082 Score: 541
Period size: 157 Copynumber: 2.6 Consensus size: 148
54578674 ATAACCTTAT
* *
54578684 TTTGAAATAGTT-AAAAAAATCAAAACTTTGTTTTAAAATTTTAAACTTTCCTTTAAAATGACTT
1 TTTGAAATAGTTGAAAAAAATCAAAACTTTGTTTAAAAATTTTAAACTTTCCTTTAAAATGACTA
* * *
54578748 AAAAAAACAAATTTTTATTTTTCAAAATCTAAACTTTCTCCTTTTTTTTAAAAACAAACACTATT
66 AAAAAAACATATTTTTATTTTTCAAAATCTAAA-GTT-T-C--TTCTTTAAAAA-AAACACTATT
* *
54578813 TTTCTTAAAGTTTAAAGATTTTAT
125 TTTCTTAAAGATTAAAGATTTTAC
** *
54578837 TTTGATGTAGTTGAAAAAAAAAATTAAAACTTTGTTTAAAAATTTTAAACTTTCCTTTAAAATGA
1 TTTGAAATAGTTG---AAAAAAATCAAAACTTTGTTTAAAAATTTTAAACTTTCCTTTAAAATGA
54578902 CTAAAAAAAACATATTTTTATTTTTCAAAATCTAAAGTTTCTTCTTTAAAAAAAACACTATTTTT
63 CTAAAAAAAACATATTTTTATTTTTCAAAATCTAAAGTTTCTTCTTTAAAAAAAACACTATTTTT
*
54578967 CTTAAAGATTAAAGCTTTTAC
128 CTTAAAGATTAAAGATTTTAC
* * *
54578988 TTTGAAATAGTTGAAAAAAATCAAAATTTTGTTTTAAAAA-TTTAAAATTTCCTTTAAAATAACT
1 TTTGAAATAGTTGAAAAAAATCAAAACTTTG-TTTAAAAATTTTAAACTTTCCTTTAAAATGACT
* **
54579052 AAGAAAAACATATTTTTATTTTAGAAAATCT
65 AAAAAAAACATATTTTTATTTTTCAAAATCT
54579083 CTTTTTTTTA
Statistics
Matches: 221, Mismatches: 20, Indels: 15
0.86 0.08 0.06
Matches are distributed among these distances:
148 66 0.30
149 8 0.04
151 42 0.19
152 10 0.05
153 10 0.05
154 1 0.00
155 1 0.00
156 2 0.01
157 81 0.37
ACGTcount: A:0.43, C:0.10, G:0.05, T:0.42
Consensus pattern (148 bp):
TTTGAAATAGTTGAAAAAAATCAAAACTTTGTTTAAAAATTTTAAACTTTCCTTTAAAATGACTA
AAAAAAACATATTTTTATTTTTCAAAATCTAAAGTTTCTTCTTTAAAAAAAACACTATTTTTCTT
AAAGATTAAAGATTTTAC
Found at i:54582141 original size:26 final size:25
Alignment explanation
Indices: 54582097--54582145 Score: 80
Period size: 26 Copynumber: 1.9 Consensus size: 25
54582087 TCTCATCCCA
54582097 ATTTTACTCAAGTAAAATTTTGACG
1 ATTTTACTCAAGTAAAATTTTGACG
*
54582122 ATTTTACTCCTAGTAAAATTTTGA
1 ATTTTACT-CAAGTAAAATTTTGA
54582146 GAAAATTTGT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 8 0.36
26 14 0.64
ACGTcount: A:0.35, C:0.12, G:0.10, T:0.43
Consensus pattern (25 bp):
ATTTTACTCAAGTAAAATTTTGACG
Found at i:54588407 original size:21 final size:21
Alignment explanation
Indices: 54588381--54588429 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 21
54588371 AGAATCCCAG
*
54588381 AACCCTAATAAACCC-AACTCT
1 AACCCTAAT-AACCCTAACCCT
*
54588402 AACCCTAATCACCCTAACCCT
1 AACCCTAATAACCCTAACCCT
54588423 AACCCTA
1 AACCCTA
54588430 TTAATTCTTC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 4 0.16
21 21 0.84
ACGTcount: A:0.39, C:0.43, G:0.00, T:0.18
Consensus pattern (21 bp):
AACCCTAATAACCCTAACCCT
Found at i:54611609 original size:349 final size:349
Alignment explanation
Indices: 54610970--54611674 Score: 1358
Period size: 349 Copynumber: 2.0 Consensus size: 349
54610960 TCTGGGTCCG
54610970 TCAATTCATATTCATGTGCGTACATTTCCATTTCAGAGAGCACACTCCCGCGAACCTCATCCTTA
1 TCAATTCATATTCATGTGCGTACATTTCCATTTCAGAGAGCACACTCCCGCGAACCTCATCCTTA
54611035 CAGCGGGATTACCAGTCCAGGCTAAATCCCCTGTAATATAAACTCATAGAGTATTGTCGGGATTA
66 CAGCGGGATTACCAGTCCAGGCTAAATCCCCTGTAATATAAACTCATAGAGTATTGTCGGGATTA
54611100 CCAGTCCAGGCTAAATCCCCTGCAACGACAATTACTCTAATGAGCTTGGATCTGAATTACCAATC
131 CCAGTCCAGGCTAAATCCCCTGCAACGACAATTACTCTAATGAGCTTGGATCTGAATTACCAATC
* *
54611165 CAGGCTAAATTCAGACCCTAATTCGGATTACCCGTCCGGGCTAAATCCATTTTCCATATATTCTT
196 CAGGCTAAATTCAGACCCTAATTCAGATTACCCGTCCGGGCTAAATCCATTTTCCACATATTCTT
*
54611230 TGGGAGGGCTATATTAGGATAGGATCACCCGTCTGGGCTAGATCCTTTTTACCGTCAATTCATTT
261 CGGGAGGGCTATATTAGGATAGGATCACCCGTCTGGGCTAGATCCTTTTTACCGTCAATTCATTT
54611295 TTAGGGATCCATCGAATTTTCCTT
326 TTAGGGATCCATCGAATTTTCCTT
*
54611319 TCAATTCATATTCATGTGCGTACATTTTCATTTCAGAGAGCACACTCCCGCGAACCTCATCCTTA
1 TCAATTCATATTCATGTGCGTACATTTCCATTTCAGAGAGCACACTCCCGCGAACCTCATCCTTA
54611384 CAGCGGGATTACCAGTCCAGGCTAAATCCCCTGTAATATAAACTCATAGAGTATTGTCGGGATTA
66 CAGCGGGATTACCAGTCCAGGCTAAATCCCCTGTAATATAAACTCATAGAGTATTGTCGGGATTA
*
54611449 CCAGTCCAGGCTAAATCCCCTGCAACGACAATTACTCTACTGAGCTTGGATCTGAATTACCAATC
131 CCAGTCCAGGCTAAATCCCCTGCAACGACAATTACTCTAATGAGCTTGGATCTGAATTACCAATC
54611514 CAGGCTAAATTCAGACCCTAATTCAGATTACCCGTCCGGGCTAAATCCATTTTCCACATATTCTT
196 CAGGCTAAATTCAGACCCTAATTCAGATTACCCGTCCGGGCTAAATCCATTTTCCACATATTCTT
54611579 CGGGAGGGCTATATTAGGATAGGATCACCCGTCTGGGCTAGATCCTTTTTACCGTCAATTCATTT
261 CGGGAGGGCTATATTAGGATAGGATCACCCGTCTGGGCTAGATCCTTTTTACCGTCAATTCATTT
54611644 TTAGGGATCCATCGAATTTTCCTT
326 TTAGGGATCCATCGAATTTTCCTT
54611668 TC-ATTCA
1 TCAATTCA
54611675 ACCGAGATTT
Statistics
Matches: 351, Mismatches: 5, Indels: 1
0.98 0.01 0.00
Matches are distributed among these distances:
348 5 0.01
349 346 0.99
ACGTcount: A:0.27, C:0.26, G:0.17, T:0.30
Consensus pattern (349 bp):
TCAATTCATATTCATGTGCGTACATTTCCATTTCAGAGAGCACACTCCCGCGAACCTCATCCTTA
CAGCGGGATTACCAGTCCAGGCTAAATCCCCTGTAATATAAACTCATAGAGTATTGTCGGGATTA
CCAGTCCAGGCTAAATCCCCTGCAACGACAATTACTCTAATGAGCTTGGATCTGAATTACCAATC
CAGGCTAAATTCAGACCCTAATTCAGATTACCCGTCCGGGCTAAATCCATTTTCCACATATTCTT
CGGGAGGGCTATATTAGGATAGGATCACCCGTCTGGGCTAGATCCTTTTTACCGTCAATTCATTT
TTAGGGATCCATCGAATTTTCCTT
Found at i:54619348 original size:20 final size:18
Alignment explanation
Indices: 54619301--54619349 Score: 57
Period size: 20 Copynumber: 2.7 Consensus size: 18
54619291 TAAGATAAAC
54619301 ATTAAATTAA-ATTTAAT
1 ATTAAATTAATATTTAAT
54619318 ATTAAGA-TAATCACTTTAAT
1 ATTAA-ATTAAT-A-TTTAAT
54619338 ATTAAATTAATA
1 ATTAAATTAATA
54619350 AAATACTATT
Statistics
Matches: 27, Mismatches: 0, Indels: 8
0.77 0.00 0.23
Matches are distributed among these distances:
17 8 0.30
18 1 0.04
19 3 0.11
20 15 0.56
ACGTcount: A:0.51, C:0.04, G:0.02, T:0.43
Consensus pattern (18 bp):
ATTAAATTAATATTTAAT
Found at i:54621943 original size:19 final size:17
Alignment explanation
Indices: 54621909--54621943 Score: 52
Period size: 19 Copynumber: 1.9 Consensus size: 17
54621899 CTAAAATAGT
54621909 AACAAAGTTAACAATAA
1 AACAAAGTTAACAATAA
54621926 AACAAGAGTTATACAATA
1 AACAA-AGTTA-ACAATA
54621944 TCCAAACAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 5 0.31
18 5 0.31
19 6 0.38
ACGTcount: A:0.60, C:0.11, G:0.09, T:0.20
Consensus pattern (17 bp):
AACAAAGTTAACAATAA
Found at i:54629615 original size:12 final size:12
Alignment explanation
Indices: 54629598--54629630 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
54629588 CAGGCCGCCC
54629598 ATATTAATTTTT
1 ATATTAATTTTT
54629610 ATATT-ATTTTT
1 ATATTAATTTTT
54629621 ATA-TAATTTT
1 ATATTAATTTT
54629631 AAAATATATA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
10 1 0.05
11 14 0.70
12 5 0.25
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (12 bp):
ATATTAATTTTT
Found at i:54629798 original size:30 final size:30
Alignment explanation
Indices: 54629754--54629816 Score: 90
Period size: 30 Copynumber: 2.1 Consensus size: 30
54629744 ACTTAACTAG
* *
54629754 CAAATATTTCTAAAATAATAACAAAATTAA
1 CAAATATTTCTAAAAAAACAACAAAATTAA
* *
54629784 CAAATGTTTTTAAAAAAACAACAAAATTAA
1 CAAATATTTCTAAAAAAACAACAAAATTAA
54629814 CAA
1 CAA
54629817 TAAAATAAGT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.60, C:0.11, G:0.02, T:0.27
Consensus pattern (30 bp):
CAAATATTTCTAAAAAAACAACAAAATTAA
Found at i:54638205 original size:53 final size:53
Alignment explanation
Indices: 54638138--54638244 Score: 187
Period size: 53 Copynumber: 2.0 Consensus size: 53
54638128 TTGTACCATG
** *
54638138 AATTGCTTTGAGTGTGGACTTAACCAATTGAATCAAAATACAGAACTAGAAAA
1 AATTGCTTCAAGTGTGGACTTAACCAATTGAATCAAAACACAGAACTAGAAAA
54638191 AATTGCTTCAAGTGTGGACTTAACCAATTGAATCAAAACACAGAACTAGAAAA
1 AATTGCTTCAAGTGTGGACTTAACCAATTGAATCAAAACACAGAACTAGAAAA
54638244 A
1 A
54638245 GTTTTCTCTC
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
53 51 1.00
ACGTcount: A:0.45, C:0.15, G:0.16, T:0.24
Consensus pattern (53 bp):
AATTGCTTCAAGTGTGGACTTAACCAATTGAATCAAAACACAGAACTAGAAAA
Found at i:54638947 original size:12 final size:12
Alignment explanation
Indices: 54638930--54638954 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
54638920 TGCAAACGGA
54638930 TCATTTCCATTT
1 TCATTTCCATTT
54638942 TCATTTCCATTT
1 TCATTTCCATTT
54638954 T
1 T
54638955 TGAAAACCTA
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:0.16, C:0.24, G:0.00, T:0.60
Consensus pattern (12 bp):
TCATTTCCATTT
Found at i:54648630 original size:3 final size:3
Alignment explanation
Indices: 54648622--54648646 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
54648612 TACACTATTT
54648622 ATC ATC ATC ATC ATC ATC ATC ATC A
1 ATC ATC ATC ATC ATC ATC ATC ATC A
54648647 ACTTATCTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.36, C:0.32, G:0.00, T:0.32
Consensus pattern (3 bp):
ATC
Found at i:54655695 original size:22 final size:22
Alignment explanation
Indices: 54655670--54655712 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
54655660 ATTTTTTTAC
*
54655670 AAAATAAT-TTTTGTATAAAAAT
1 AAAA-AATGTTTTGTAAAAAAAT
*
54655692 AAAAATTGTTTTGTAAAAAAA
1 AAAAAATGTTTTGTAAAAAAA
54655713 ATATAAGATA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 2 0.11
22 16 0.89
ACGTcount: A:0.56, C:0.00, G:0.07, T:0.37
Consensus pattern (22 bp):
AAAAAATGTTTTGTAAAAAAAT
Found at i:54655980 original size:29 final size:30
Alignment explanation
Indices: 54655954--54656013 Score: 81
Period size: 29 Copynumber: 2.1 Consensus size: 30
54655944 TCTCGTAAGT
*
54655954 TTTTAAAAAATTG-GTCTATTTTTGTAATA
1 TTTTAAAAAAATGAGTCTATTTTTGTAATA
*
54655983 TTTTAAAAAAATGAGTTTATTTTT-TAA-A
1 TTTTAAAAAAATGAGTCTATTTTTGTAATA
54656011 TTT
1 TTT
54656014 AATTCGAGCA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
28 4 0.14
29 15 0.54
30 9 0.32
ACGTcount: A:0.37, C:0.02, G:0.08, T:0.53
Consensus pattern (30 bp):
TTTTAAAAAAATGAGTCTATTTTTGTAATA
Found at i:54656656 original size:27 final size:27
Alignment explanation
Indices: 54656599--54656657 Score: 66
Period size: 28 Copynumber: 2.1 Consensus size: 27
54656589 AGGGAGGGAG
* * *
54656599 AAAAAATTAATAATTGGTGATTAAATTA
1 AAAAAATTAATAATTAGTGACT-AATGA
54656627 AAAAAATTAATAATTAGTGACCT-ATGA
1 AAAAAATTAATAATTAGTGA-CTAATGA
54656654 AAAA
1 AAAA
54656658 GAGAAATAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
27 7 0.26
28 19 0.70
29 1 0.04
ACGTcount: A:0.56, C:0.03, G:0.10, T:0.31
Consensus pattern (27 bp):
AAAAAATTAATAATTAGTGACTAATGA
Found at i:54659614 original size:37 final size:37
Alignment explanation
Indices: 54659573--54659785 Score: 372
Period size: 37 Copynumber: 5.8 Consensus size: 37
54659563 TTTGAGTACT
54659573 TCTGATCAAGAAACAAAGTGATAAGTGGCTACACTTA
1 TCTGATCAAGAAACAAAGTGATAAGTGGCTACACTTA
54659610 TCTGATCAAGAAACAAAGTGATAAGTGGCTACACTTA
1 TCTGATCAAGAAACAAAGTGATAAGTGGCTACACTTA
*
54659647 TCTGATCAAGAAACAAAGTGATAAGTGGTTACACTTA
1 TCTGATCAAGAAACAAAGTGATAAGTGGCTACACTTA
*
54659684 TCTGATCAAGAAACAAAGTGATAAGTGGTTACACTTA
1 TCTGATCAAGAAACAAAGTGATAAGTGGCTACACTTA
*
54659721 TCTGATCAAGAGACAAAGTGATAAGTGGCTACACTTA
1 TCTGATCAAGAAACAAAGTGATAAGTGGCTACACTTA
** *
54659758 TCTGATCAAGTGATAAAGTGATAAGTGG
1 TCTGATCAAGAAACAAAGTGATAAGTGG
54659786 TAGCTTCAGC
Statistics
Matches: 171, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 171 1.00
ACGTcount: A:0.39, C:0.14, G:0.21, T:0.26
Consensus pattern (37 bp):
TCTGATCAAGAAACAAAGTGATAAGTGGCTACACTTA
Found at i:54659857 original size:45 final size:46
Alignment explanation
Indices: 54659748--54659871 Score: 200
Period size: 46 Copynumber: 2.8 Consensus size: 46
54659738 GTGATAAGTG
* *
54659748 GCTACACTTATCTGATCAAGTGATAAAGTGATAAGTGGTAGCTTCA
1 GCTACACTTATCTGATCAAGTGACAAAGTGATAAGTGGTAGCCTCA
*
54659794 GCTACACTTATCTGATCAAGTGGCAAAGTGATAAGTGGTAGCCT-A
1 GCTACACTTATCTGATCAAGTGACAAAGTGATAAGTGGTAGCCTCA
54659839 GCTACACTTATCTGATCAAG-GAC-AAGTGATAAG
1 GCTACACTTATCTGATCAAGTGACAAAGTGATAAG
54659872 AGGTCATATG
Statistics
Matches: 74, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
43 10 0.14
44 2 0.03
45 21 0.28
46 41 0.55
ACGTcount: A:0.33, C:0.17, G:0.23, T:0.27
Consensus pattern (46 bp):
GCTACACTTATCTGATCAAGTGACAAAGTGATAAGTGGTAGCCTCA
Found at i:54667386 original size:37 final size:37
Alignment explanation
Indices: 54667290--54667497 Score: 327
Period size: 37 Copynumber: 5.8 Consensus size: 37
54667280 TTTGAGTACT
54667290 TCTGATCAAG-AACAAAGTGATAAGTGGCTACACTTA
1 TCTGATCAAGAAACAAAGTGATAAGTGGCTACACTTA
54667326 TCTGATC---AAA-AAAGTGATAAGTGGCTACACTTA
1 TCTGATCAAGAAACAAAGTGATAAGTGGCTACACTTA
*
54667359 TCTGATCAAGAAACAAAGTGATAAGTGGTTACACTTA
1 TCTGATCAAGAAACAAAGTGATAAGTGGCTACACTTA
*
54667396 TCTGATCAAGAAACAAAGTGATAAGTGGTTACACTTA
1 TCTGATCAAGAAACAAAGTGATAAGTGGCTACACTTA
*
54667433 TCTGATCAAGAGACAAAGTGATAAGTGGCTACACTTA
1 TCTGATCAAGAAACAAAGTGATAAGTGGCTACACTTA
** *
54667470 TCTGATCAAGTGATAAAGTGATAAGTGG
1 TCTGATCAAGAAACAAAGTGATAAGTGG
54667498 TAGCTTCAGC
Statistics
Matches: 162, Mismatches: 5, Indels: 9
0.92 0.03 0.05
Matches are distributed among these distances:
33 30 0.19
34 2 0.01
36 10 0.06
37 120 0.74
ACGTcount: A:0.39, C:0.14, G:0.21, T:0.26
Consensus pattern (37 bp):
TCTGATCAAGAAACAAAGTGATAAGTGGCTACACTTA
Found at i:54667569 original size:45 final size:46
Alignment explanation
Indices: 54667460--54667583 Score: 191
Period size: 46 Copynumber: 2.8 Consensus size: 46
54667450 GTGATAAGTG
* * *
54667460 GCTACACTTATCTGATCAAGTGATAAAGTGATAAGTGGTAGCTTCA
1 GCTACACTTATCTGATCAAGTGACAAAGTGATAAGTGGCAGCCTCA
*
54667506 GCTACACTTATCTGATCAAGTGGCAAAGTGATAAGTGGCAGCCT-A
1 GCTACACTTATCTGATCAAGTGACAAAGTGATAAGTGGCAGCCTCA
54667551 GCTACACTTATCTGATCAAG-GAC-AAGTGATAAG
1 GCTACACTTATCTGATCAAGTGACAAAGTGATAAG
54667584 AGGTCATATG
Statistics
Matches: 73, Mismatches: 5, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
43 10 0.14
44 2 0.03
45 21 0.29
46 40 0.55
ACGTcount: A:0.33, C:0.18, G:0.23, T:0.27
Consensus pattern (46 bp):
GCTACACTTATCTGATCAAGTGACAAAGTGATAAGTGGCAGCCTCA
Found at i:54688948 original size:37 final size:37
Alignment explanation
Indices: 54688865--54689045 Score: 272
Period size: 37 Copynumber: 4.8 Consensus size: 37
54688855 TTTGAGTACT
*
54688865 TCTGATCAAGAAACAAAGTGATAAGTGCTTGGCTACACTTA
1 TCTGATCAAGAAACAAAGTGATAA--G--TGGTTACACTTA
54688906 TCTGATCAAGAAACAAAGTGATAAGTGGTTACACTTA
1 TCTGATCAAGAAACAAAGTGATAAGTGGTTACACTTA
54688943 TCTGATCAAGAAACAAAGTGATAAGTGGTTACACTTA
1 TCTGATCAAGAAACAAAGTGATAAGTGGTTACACTTA
* *
54688980 TCTGATCAAGAGACAAAGTGATAAGTGGCTACACTTA
1 TCTGATCAAGAAACAAAGTGATAAGTGGTTACACTTA
** *
54689017 TCTGATCAAGTGATAAAGTGATAAGTGGT
1 TCTGATCAAGAAACAAAGTGATAAGTGGT
54689046 AGCTTCAGCT
Statistics
Matches: 134, Mismatches: 6, Indels: 4
0.93 0.04 0.03
Matches are distributed among these distances:
37 109 0.81
39 1 0.01
41 24 0.18
ACGTcount: A:0.38, C:0.14, G:0.21, T:0.27
Consensus pattern (37 bp):
TCTGATCAAGAAACAAAGTGATAAGTGGTTACACTTA
Found at i:54689116 original size:45 final size:46
Alignment explanation
Indices: 54689007--54689130 Score: 200
Period size: 46 Copynumber: 2.8 Consensus size: 46
54688997 GTGATAAGTG
* *
54689007 GCTACACTTATCTGATCAAGTGATAAAGTGATAAGTGGTAGCTTCA
1 GCTACACTTATCTGATCAAGTGACAAAGTGATAAGTGGTAGCCTCA
*
54689053 GCTACACTTATCTGATCAAGTGGCAAAGTGATAAGTGGTAGCCT-A
1 GCTACACTTATCTGATCAAGTGACAAAGTGATAAGTGGTAGCCTCA
54689098 GCTACACTTATCTGATCAAG-GAC-AAGTGATAAG
1 GCTACACTTATCTGATCAAGTGACAAAGTGATAAG
54689131 AGGTCATATG
Statistics
Matches: 74, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
43 10 0.14
44 2 0.03
45 21 0.28
46 41 0.55
ACGTcount: A:0.33, C:0.17, G:0.23, T:0.27
Consensus pattern (46 bp):
GCTACACTTATCTGATCAAGTGACAAAGTGATAAGTGGTAGCCTCA
Found at i:54705729 original size:21 final size:21
Alignment explanation
Indices: 54705704--54705760 Score: 60
Period size: 21 Copynumber: 2.7 Consensus size: 21
54705694 TACCATATTT
*
54705704 AATACCCTCACCAACTTTTTC
1 AATACCCTCACCAACATTTTC
* * * *
54705725 CATACACTGACCAGCATTTTC
1 AATACCCTCACCAACATTTTC
*
54705746 AATACCCTTACCAAC
1 AATACCCTCACCAAC
54705761 CTTTACATGG
Statistics
Matches: 27, Mismatches: 9, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.32, C:0.37, G:0.04, T:0.28
Consensus pattern (21 bp):
AATACCCTCACCAACATTTTC
Found at i:54706294 original size:16 final size:16
Alignment explanation
Indices: 54706273--54706306 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
54706263 ATAACAGGTT
54706273 AATATAATATTCTTTC
1 AATATAATATTCTTTC
54706289 AATATAATATTCTTTC
1 AATATAATATTCTTTC
54706305 AA
1 AA
54706307 GAATAAAACC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.41, C:0.12, G:0.00, T:0.47
Consensus pattern (16 bp):
AATATAATATTCTTTC
Found at i:54706552 original size:32 final size:33
Alignment explanation
Indices: 54706495--54706557 Score: 101
Period size: 33 Copynumber: 1.9 Consensus size: 33
54706485 TTTTGTTTGA
* *
54706495 TTAAATCAAGATTAAAAAAGGGGTTAGGGTTAG
1 TTAAATCAAGATTAAAAAAGAGGTTAAGGTTAG
54706528 TTAAATCAAGATTAAAAAA-AGGTTAAGGTT
1 TTAAATCAAGATTAAAAAAGAGGTTAAGGTT
54706558 TTTTGATTCG
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
32 9 0.32
33 19 0.68
ACGTcount: A:0.46, C:0.03, G:0.22, T:0.29
Consensus pattern (33 bp):
TTAAATCAAGATTAAAAAAGAGGTTAAGGTTAG
Found at i:54706617 original size:32 final size:32
Alignment explanation
Indices: 54706506--54706638 Score: 101
Period size: 32 Copynumber: 4.1 Consensus size: 32
54706496 TAAATCAAGA
**
54706506 TTAAAAAAGGGGTTAGGGTTAGTTAAATCAAGA-
1 TTAAAAAAGGGGTTAGGGTTCTTTAAATC--GAT
* * * * *
54706539 TTAAAAAA-AGGTTAAGGTTTTTTGATTCGACT
1 TTAAAAAAGGGGTTAGGGTTCTTTAAATCGA-T
* * *
54706571 GTACAAAAAAGGGGTTATGGTTTTTTAAAT-GAT
1 -T-TAAAAAAGGGGTTAGGGTTCTTTAAATCGAT
54706604 TTAAAAAAGGGGGTTAGGGTTCTTTAAATCGAT
1 TTAAAAAA-GGGGTTAGGGTTCTTTAAATCGAT
54706637 TT
1 TT
54706639 CGCACTTTCA
Statistics
Matches: 79, Mismatches: 14, Indels: 14
0.74 0.13 0.13
Matches are distributed among these distances:
30 2 0.03
31 6 0.08
32 33 0.42
33 15 0.19
34 8 0.10
35 15 0.19
ACGTcount: A:0.36, C:0.05, G:0.24, T:0.35
Consensus pattern (32 bp):
TTAAAAAAGGGGTTAGGGTTCTTTAAATCGAT
Found at i:54713085 original size:17 final size:16
Alignment explanation
Indices: 54713063--54713102 Score: 53
Period size: 18 Copynumber: 2.4 Consensus size: 16
54713053 ATCTTCCTGA
*
54713063 ACAAAAAATTAGATATG
1 ACAAAAAATTA-AGATG
54713080 ACAAAAAAATTAAGATG
1 AC-AAAAAATTAAGATG
54713097 ACAAAA
1 ACAAAA
54713103 TGAGAAAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
16 4 0.19
17 8 0.38
18 9 0.43
ACGTcount: A:0.65, C:0.07, G:0.10, T:0.17
Consensus pattern (16 bp):
ACAAAAAATTAAGATG
Found at i:54713088 original size:18 final size:17
Alignment explanation
Indices: 54713065--54713102 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
54713055 CTTCCTGAAC
*
54713065 AAAAAATTAGATATGACA
1 AAAAAATTA-AGATGACA
54713083 AAAAAATTAAGATGACA
1 AAAAAATTAAGATGACA
54713100 AAA
1 AAA
54713103 TGAGAAAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 10 0.53
18 9 0.47
ACGTcount: A:0.66, C:0.05, G:0.11, T:0.18
Consensus pattern (17 bp):
AAAAAATTAAGATGACA
Found at i:54717203 original size:34 final size:30
Alignment explanation
Indices: 54717149--54717219 Score: 81
Period size: 30 Copynumber: 2.2 Consensus size: 30
54717139 TTAGTTTGAG
*
54717149 AGAAATATTTTTTCTCTAAAAAAATAGCTTGTTT
1 AGAAATATTTTGTCTCT--AAAAAT-GCTT-TTT
54717183 AGAAATACTTTTGTCT-TAAAAATGCTTTTT
1 AGAAATA-TTTTGTCTCTAAAAATGCTTTTT
54717213 AGAAATA
1 AGAAATA
54717220 ATACTAAACT
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
30 10 0.29
31 4 0.11
32 6 0.17
34 8 0.23
35 7 0.20
ACGTcount: A:0.39, C:0.08, G:0.10, T:0.42
Consensus pattern (30 bp):
AGAAATATTTTGTCTCTAAAAATGCTTTTT
Found at i:54734801 original size:38 final size:37
Alignment explanation
Indices: 54734758--54734861 Score: 108
Period size: 38 Copynumber: 2.8 Consensus size: 37
54734748 AAAATTATTA
54734758 TTTTAGAAAATTTTTTAAATTTAAATTTTTTA-ATATAT
1 TTTTAGAAAATTTTTTAAATTTAAATTTTTTATA-AT-T
**
54734796 TTTTAGATTATTTTTTAAATTTTATAATTTTTTATAATT
1 TTTTAGAAAATTTTTTAAA-TTTA-AATTTTTTATAATT
* *
54734835 TTTTA-AAAA--TATAAAATTTAAATTTTT
1 TTTTAGAAAATTTTTTAAATTTAAATTTTT
54734862 GAAAATTATT
Statistics
Matches: 57, Mismatches: 6, Indels: 10
0.78 0.08 0.14
Matches are distributed among these distances:
34 7 0.12
35 4 0.07
36 5 0.09
38 19 0.33
39 10 0.18
40 11 0.19
41 1 0.02
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (37 bp):
TTTTAGAAAATTTTTTAAATTTAAATTTTTTATAATT
Found at i:54734828 original size:10 final size:10
Alignment explanation
Indices: 54734777--54734839 Score: 53
Period size: 10 Copynumber: 6.4 Consensus size: 10
54734767 ATTTTTTAAA
54734777 TTTA-AATTT
1 TTTATAATTT
54734786 TTTAATATATTT
1 TTT-ATA-ATTT
* *
54734798 TTAGATTATTT
1 TT-TATAATTT
54734809 TTTA-AA--T
1 TTTATAATTT
54734816 TTTATAATTT
1 TTTATAATTT
54734826 TTTATAATTT
1 TTTATAATTT
54734836 TTTA
1 TTTA
54734840 AAAATATAAA
Statistics
Matches: 43, Mismatches: 4, Indels: 13
0.72 0.07 0.22
Matches are distributed among these distances:
7 5 0.12
8 2 0.05
9 4 0.09
10 17 0.40
11 7 0.16
12 8 0.19
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.67
Consensus pattern (10 bp):
TTTATAATTT
Found at i:54737884 original size:12 final size:12
Alignment explanation
Indices: 54737869--54737898 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
54737859 ACAATAATAC
54737869 TATATATAAATG
1 TATATATAAATG
*
54737881 TATATATATATG
1 TATATATAAATG
54737893 TATATA
1 TATATA
54737899 ATAGAAATAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.47, C:0.00, G:0.07, T:0.47
Consensus pattern (12 bp):
TATATATAAATG
Found at i:54738004 original size:19 final size:17
Alignment explanation
Indices: 54737980--54738026 Score: 51
Period size: 16 Copynumber: 2.7 Consensus size: 17
54737970 AATTAAAGTA
*
54737980 ATAAAAAATAATACTATAT
1 ATAAAAAAT-ATA-TATAC
*
54737999 ATAAAATATATATATAC
1 ATAAAAAATATATATAC
54738016 AT-AAAAATATA
1 ATAAAAAATATA
54738027 CACTAATATA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
16 8 0.32
17 6 0.24
18 3 0.12
19 8 0.32
ACGTcount: A:0.64, C:0.04, G:0.00, T:0.32
Consensus pattern (17 bp):
ATAAAAAATATATATAC
Found at i:54738022 original size:18 final size:19
Alignment explanation
Indices: 54737983--54738031 Score: 59
Period size: 17 Copynumber: 2.7 Consensus size: 19
54737973 TAAAGTAATA
*
54737983 AAAAATA-ATACTATATAT
1 AAAAATATATACTATACAT
54738001 -AAAATATATA-TATACAT
1 AAAAATATATACTATACAT
*
54738018 AAAAATATACACTA
1 AAAAATATATACTA
54738032 ATATATAATA
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
17 12 0.46
18 12 0.46
19 2 0.08
ACGTcount: A:0.61, C:0.08, G:0.00, T:0.31
Consensus pattern (19 bp):
AAAAATATATACTATACAT
Found at i:54738258 original size:3 final size:3
Alignment explanation
Indices: 54738245--54738328 Score: 59
Period size: 3 Copynumber: 28.3 Consensus size: 3
54738235 GAGGGCATAT
* * * *
54738245 ATA AT- ATA ATA ATA AT- ATA AAA ATA ATA TATA CATG AGA AAA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA -ATA -ATA ATA ATA ATA
* *
54738290 ATA ATA AT- ATAA ATA ATA GTA AAA ATA ATA A-A ATA ATA A
1 ATA ATA ATA AT-A ATA ATA ATA ATA ATA ATA ATA ATA ATA A
54738329 AACAAAGCTC
Statistics
Matches: 63, Mismatches: 12, Indels: 12
0.72 0.14 0.14
Matches are distributed among these distances:
2 8 0.13
3 48 0.76
4 7 0.11
ACGTcount: A:0.67, C:0.01, G:0.04, T:0.29
Consensus pattern (3 bp):
ATA
Found at i:54738261 original size:11 final size:11
Alignment explanation
Indices: 54738245--54738328 Score: 57
Period size: 11 Copynumber: 7.4 Consensus size: 11
54738235 GAGGGCATAT
54738245 ATAATATAATA
1 ATAATATAATA
*
54738256 ATAATATAAAA
1 ATAATATAATA
54738267 ATAATAT-ATA
1 ATAATATAATA
*
54738277 CATGAGA-AAAATA
1 -AT-A-ATATAATA
54738290 ATAATA-ATATAA
1 ATAATATA-AT-A
*
54738302 ATAATAGTAAAA
1 ATAATA-TAATA
*
54738314 ATAATAAAATA
1 ATAATATAATA
54738325 ATAA
1 ATAA
54738329 AACAAAGCTC
Statistics
Matches: 58, Mismatches: 6, Indels: 18
0.71 0.07 0.22
Matches are distributed among these distances:
10 4 0.07
11 30 0.52
12 18 0.31
13 5 0.09
14 1 0.02
ACGTcount: A:0.67, C:0.01, G:0.04, T:0.29
Consensus pattern (11 bp):
ATAATATAATA
Found at i:54738297 original size:26 final size:26
Alignment explanation
Indices: 54738245--54738324 Score: 73
Period size: 24 Copynumber: 3.2 Consensus size: 26
54738235 GAGGGCATAT
* *
54738245 ATAATATAATAATAATATAAA-AATA
1 ATAATATAATAATAGTAAAAATAATA
*
54738270 AT-ATATACAT--GAG-AAAAATAATA
1 ATAATATA-ATAATAGTAAAAATAATA
54738293 ATAATATAAATAATAGTAAAAATAATA
1 ATAATAT-AATAATAGTAAAAATAATA
54738320 A-AATA
1 ATAATA
54738325 ATAAAACAAA
Statistics
Matches: 44, Mismatches: 4, Indels: 13
0.72 0.07 0.21
Matches are distributed among these distances:
22 4 0.09
23 7 0.16
24 11 0.25
25 5 0.11
26 6 0.14
27 11 0.25
ACGTcount: A:0.66, C:0.01, G:0.04, T:0.29
Consensus pattern (26 bp):
ATAATATAATAATAGTAAAAATAATA
Found at i:54738319 original size:15 final size:15
Alignment explanation
Indices: 54738252--54738330 Score: 65
Period size: 15 Copynumber: 5.1 Consensus size: 15
54738242 TATATAATAT
54738252 AATAATAAT-ATAAA
1 AATAATAATAATAAA
54738266 AATAATATATACATGAGAAA
1 AATAATA-ATA-AT---AAA
*
54738286 AATAATAATAATATA
1 AATAATAATAATAAA
*
54738301 AATAATAGTAA-AAA
1 AATAATAATAATAAA
54738315 TAATAA-AATAATAAA
1 -AATAATAATAATAAA
54738330 A
1 A
54738331 CAAAGCTCTC
Statistics
Matches: 53, Mismatches: 4, Indels: 16
0.73 0.05 0.22
Matches are distributed among these distances:
14 14 0.26
15 22 0.42
17 2 0.04
18 2 0.04
19 3 0.06
20 10 0.19
ACGTcount: A:0.68, C:0.01, G:0.04, T:0.27
Consensus pattern (15 bp):
AATAATAATAATAAA
Found at i:54738718 original size:23 final size:20
Alignment explanation
Indices: 54738655--54738719 Score: 60
Period size: 20 Copynumber: 3.0 Consensus size: 20
54738645 AACCTTTTTT
*
54738655 ACAAAAAAACACCTC-CAAAAA
1 ACAAAAAAA-ACCTCTC-CAAA
54738676 ACAAAAAAAACCTCTCCAAA
1 ACAAAAAAAACCTCTCCAAA
*
54738696 ACAAAGAACAATCCTTCTCCAAA
1 ACAAA-AA-AAACC-TCTCCAAA
54738719 A
1 A
54738720 AACCAAAAAC
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
20 13 0.34
21 12 0.32
22 4 0.11
23 9 0.24
ACGTcount: A:0.58, C:0.29, G:0.02, T:0.11
Consensus pattern (20 bp):
ACAAAAAAAACCTCTCCAAA
Found at i:54738866 original size:38 final size:38
Alignment explanation
Indices: 54738812--54738910 Score: 173
Period size: 38 Copynumber: 2.6 Consensus size: 38
54738802 GGTGGCCAAG
*
54738812 GGTGGTGGAGTTGGTGGCTAAGGTGGGTGGCCAACAAA
1 GGTGGTGGAGTAGGTGGCTAAGGTGGGTGGCCAACAAA
54738850 GGTGGTGGAGTAGGTGGCTAAGGTGGGTGGCCAACAAA
1 GGTGGTGGAGTAGGTGGCTAAGGTGGGTGGCCAACAAA
*
54738888 GG-GGTGGAGTAGGTGGCCAAGGT
1 GGTGGTGGAGTAGGTGGCTAAGGT
54738911 TTTTATTTAT
Statistics
Matches: 59, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
37 20 0.34
38 39 0.66
ACGTcount: A:0.21, C:0.10, G:0.49, T:0.19
Consensus pattern (38 bp):
GGTGGTGGAGTAGGTGGCTAAGGTGGGTGGCCAACAAA
Found at i:54739268 original size:40 final size:40
Alignment explanation
Indices: 54739224--54739375 Score: 196
Period size: 40 Copynumber: 3.8 Consensus size: 40
54739214 GTGTTTTTAG
*
54739224 TCTGCTCCACTACTACTTAGGGAGATAAGACTTGATGCGA
1 TCTGCTCCACTACTGCTTAGGGAGATAAGACTTGATGCGA
* * * * ***
54739264 TCTGCTTCACTATTGCTTAGGGAAATAAGATCTGTGGTTTTA
1 TCTGCTCCACTACTGCTTAGGGAGATAAGA-CT-TGATGCGA
*
54739306 TCTGCTCCACTACTGCTTAGGGAGATAAGACTTAATGCGA
1 TCTGCTCCACTACTGCTTAGGGAGATAAGACTTGATGCGA
*
54739346 TCTACTCCACTACTGCTTAGGGAGATAAGA
1 TCTGCTCCACTACTGCTTAGGGAGATAAGA
54739376 TTGTAATCTT
Statistics
Matches: 93, Mismatches: 17, Indels: 4
0.82 0.15 0.04
Matches are distributed among these distances:
40 58 0.62
41 4 0.04
42 31 0.33
ACGTcount: A:0.27, C:0.20, G:0.22, T:0.31
Consensus pattern (40 bp):
TCTGCTCCACTACTGCTTAGGGAGATAAGACTTGATGCGA
Found at i:54739315 original size:82 final size:83
Alignment explanation
Indices: 54739208--54739376 Score: 259
Period size: 82 Copynumber: 2.0 Consensus size: 83
54739198 CATGGGGATG
* * * * *
54739208 AGATTTGTGTTTTTAGTCTGCTCCACTACTACTTAGGGAGATAAGACTTGATGCGATCTGCTTCA
1 AGATCTGTGGTTTTAGTCTGCTCCACTACTACTTAGGGAGATAAGACTTAATGCGATCTACTCCA
*
54739273 CTATTGCTTAGGGAAATA
66 CTACTGCTTAGGGAAATA
*
54739291 AGATCTGTGGTTTTA-TCTGCTCCACTACTGCTTAGGGAGATAAGACTTAATGCGATCTACTCCA
1 AGATCTGTGGTTTTAGTCTGCTCCACTACTACTTAGGGAGATAAGACTTAATGCGATCTACTCCA
*
54739355 CTACTGCTTAGGGAGATA
66 CTACTGCTTAGGGAAATA
54739373 AGAT
1 AGAT
54739377 TGTAATCTTC
Statistics
Matches: 78, Mismatches: 8, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
82 65 0.83
83 13 0.17
ACGTcount: A:0.26, C:0.18, G:0.22, T:0.34
Consensus pattern (83 bp):
AGATCTGTGGTTTTAGTCTGCTCCACTACTACTTAGGGAGATAAGACTTAATGCGATCTACTCCA
CTACTGCTTAGGGAAATA
Found at i:54739614 original size:45 final size:45
Alignment explanation
Indices: 54739563--54739761 Score: 111
Period size: 45 Copynumber: 4.4 Consensus size: 45
54739553 GATCTGCAAT
*
54739563 CTTCAATCTATTCCACTGCCAGATACAGGGAGATAGAGTTATCGG
1 CTTCAATCTATTCCACTGCCAGATACAGGGAGATAGAGTTATCAG
* * * * * * * *
54739608 CTTCAATGTACTCCACTG-TAG-TCACAGGGAGGTAAAATCTACCAT
1 CTTCAATCTATTCCACTGCCAGAT-ACAGGGAGATAGAGT-TATCAG
* * * * ** * * *
54739653 CTTCGATCTGCTT-CGCTGCCTA-ATACAGGAAGGCA-AGATCTGCAAT
1 CTTCAATCT-ATTCCACTGCC-AGATACAGGGAGATAGAGTTAT-C-AG
* *
54739699 CTTCAATCTATTCCACTGCCAGATACAGTGAGATAGAGTTATCGG
1 CTTCAATCTATTCCACTGCCAGATACAGGGAGATAGAGTTATCAG
* *
54739744 CTTCAATGTACTCCACTG
1 CTTCAATCTATTCCACTG
54739762 TAGTCAGGGA
Statistics
Matches: 109, Mismatches: 34, Indels: 22
0.66 0.21 0.13
Matches are distributed among these distances:
43 1 0.01
44 15 0.14
45 51 0.47
46 36 0.33
47 6 0.06
ACGTcount: A:0.28, C:0.25, G:0.20, T:0.28
Consensus pattern (45 bp):
CTTCAATCTATTCCACTGCCAGATACAGGGAGATAGAGTTATCAG
Found at i:54739846 original size:134 final size:133
Alignment explanation
Indices: 54739536--54740109 Score: 977
Period size: 134 Copynumber: 4.3 Consensus size: 133
54739526 CCACTTCCTA
* *
54739536 CCAATATAGGAAGGCAGGATCTGCAATCTTCAATCTATTCCACTGCCAGATACAGGGAGATAGAG
1 CCAATACAGGAAGGCAAGATCTGCAATCTTCAATCTATTCCACTGCCAGATACAGGGAGATAGAG
*
54739601 TTATCGGCTTCAATGTACTCCACTGTAGTCACAGGGAGGTAAAATCTACCATCTTCGATCTGCTT
66 TTATCGGCTTCAATGTACTCCACTGTAGT--CAGGGAGGTAAAATCTGCCATCTTCGATCTGCTT
54739666 CGCTG
129 CGCTG
*
54739671 CCTAATACAGGAAGGCAAGATCTGCAATCTTCAATCTATTCCACTGCCAGATACAGTGAGATAGA
1 CC-AATACAGGAAGGCAAGATCTGCAATCTTCAATCTATTCCACTGCCAGATACAGGGAGATAGA
54739736 GTTATCGGCTTCAATGTACTCCACTGTAGTCAGGGAGGTAAAATCTGCCATCTTCGATCTGCTTC
65 GTTATCGGCTTCAATGTACTCCACTGTAGTCAGGGAGGTAAAATCTGCCATCTTCGATCTGCTTC
54739801 GCTG
130 GCTG
* *
54739805 CCGAATACAGGAAGGCAAGATCTGCAATATTCAATCTATTCCACTGCCAGATACAGTGAGATAGA
1 CC-AATACAGGAAGGCAAGATCTGCAATCTTCAATCTATTCCACTGCCAGATACAGGGAGATAGA
* *
54739870 GTTATCGGCTTCAATGTACTCCACTGTGGTCAGGGAGGTAAAATCTGCCATCTTTGATCTGCTTC
65 GTTATCGGCTTCAATGTACTCCACTGTAGTCAGGGAGGTAAAATCTGCCATCTTCGATCTGCTTC
54739935 GCTG
130 GCTG
* *
54739939 CCAATACAGGAAGGCAAGATCTGCAATCTTCAATCTATTCCACTGCCAAATACAGGGAGATAGAA
1 CCAATACAGGAAGGCAAGATCTGCAATCTTCAATCTATTCCACTGCCAGATACAGGGAGATAGAG
* * * *
54740004 TTATCGGCTTCAGTGTACTCCACTGTGGTCAGGAAGGTAAAATCTGCCATCTTTGATCTGCTTCG
66 TTATCGGCTTCAATGTACTCCACTGTAGTCAGGGAGGTAAAATCTGCCATCTTCGATCTGCTTCG
54740069 CTG
131 CTG
54740072 CCAAATACAGGAAGGCAAGATCTGCAATCTTCAATCTA
1 CC-AATACAGGAAGGCAAGATCTGCAATCTTCAATCTA
54740110 CTTCACCACC
Statistics
Matches: 423, Mismatches: 14, Indels: 5
0.96 0.03 0.01
Matches are distributed among these distances:
133 127 0.30
134 205 0.48
135 2 0.00
136 89 0.21
ACGTcount: A:0.29, C:0.23, G:0.21, T:0.27
Consensus pattern (133 bp):
CCAATACAGGAAGGCAAGATCTGCAATCTTCAATCTATTCCACTGCCAGATACAGGGAGATAGAG
TTATCGGCTTCAATGTACTCCACTGTAGTCAGGGAGGTAAAATCTGCCATCTTCGATCTGCTTCG
CTG
Found at i:54740044 original size:267 final size:269
Alignment explanation
Indices: 54739538--54740109 Score: 986
Period size: 267 Copynumber: 2.1 Consensus size: 269
54739528 ACTTCCTACC
* *
54739538 AATATAGGAAGGCAGGATCTGCAATCTTCAATCTATTCCACTGCCAGATACAGGGAGATAGAGTT
1 AATACAGGAAGGCAAGATCTGCAATCTTCAATCTATTCCACTGCCAGATACAGGGAGATAGAGTT
54739603 ATCGGCTTCAATGTACTCCACTGTAGTCACAGGGAGGTAAAATCTACCATCTTCGATCTGCTTCG
66 ATCGGCTTCAATGTACTCCACTGTAGT-ACAGGGAGGTAAAATCTACCATCTTCGATCTGCTTCG
* *
54739668 CTGCCTAATACAGGAAGGCAAGATCTGCAATCTTCAATCTATTCCACTGCCAGATACAGTGAGAT
130 CTGCCTAATACAGGAAGGCAAGATCTGCAATCTTCAATCTATTCCACTGCCAAATACAGGGAGAT
* *
54739733 AGAGTTATCGGCTTCAATGTACTCCACTGTAGTCAGGGAGGTAAAATCTGCCATCTTCGATCTGC
195 AGAATTATCGGCTTCAATGTACTCCACTGTAGTCAGGAAGGTAAAATCTGCCATCTTCGATCTGC
*
54739798 TTCGCTGCCG
260 TTCGCTGCCA
* *
54739808 AATACAGGAAGGCAAGATCTGCAATATTCAATCTATTCCACTGCCAGATACAGTGAGATAGAGTT
1 AATACAGGAAGGCAAGATCTGCAATCTTCAATCTATTCCACTGCCAGATACAGGGAGATAGAGTT
* * *
54739873 ATCGGCTTCAATGTACTCCACTGTGGT-CAGGGAGGTAAAATCTGCCATCTTTGATCTGCTTCGC
66 ATCGGCTTCAATGTACTCCACTGTAGTACAGGGAGGTAAAATCTACCATCTTCGATCTGCTTCGC
54739937 TGCC-AATACAGGAAGGCAAGATCTGCAATCTTCAATCTATTCCACTGCCAAATACAGGGAGATA
131 TGCCTAATACAGGAAGGCAAGATCTGCAATCTTCAATCTATTCCACTGCCAAATACAGGGAGATA
* * *
54740001 GAATTATCGGCTTCAGTGTACTCCACTGTGGTCAGGAAGGTAAAATCTGCCATCTTTGATCTGCT
196 GAATTATCGGCTTCAATGTACTCCACTGTAGTCAGGAAGGTAAAATCTGCCATCTTCGATCTGCT
54740066 TCGCTGCCA
261 TCGCTGCCA
54740075 AATACAGGAAGGCAAGATCTGCAATCTTCAATCTA
1 AATACAGGAAGGCAAGATCTGCAATCTTCAATCTA
54740110 CTTCACCACC
Statistics
Matches: 286, Mismatches: 16, Indels: 3
0.94 0.05 0.01
Matches are distributed among these distances:
267 160 0.56
268 39 0.14
270 87 0.30
ACGTcount: A:0.29, C:0.23, G:0.21, T:0.27
Consensus pattern (269 bp):
AATACAGGAAGGCAAGATCTGCAATCTTCAATCTATTCCACTGCCAGATACAGGGAGATAGAGTT
ATCGGCTTCAATGTACTCCACTGTAGTACAGGGAGGTAAAATCTACCATCTTCGATCTGCTTCGC
TGCCTAATACAGGAAGGCAAGATCTGCAATCTTCAATCTATTCCACTGCCAAATACAGGGAGATA
GAATTATCGGCTTCAATGTACTCCACTGTAGTCAGGAAGGTAAAATCTGCCATCTTCGATCTGCT
TCGCTGCCA
Found at i:54740141 original size:44 final size:44
Alignment explanation
Indices: 54740081--54740598 Score: 398
Period size: 44 Copynumber: 11.8 Consensus size: 44
54740071 GCCAAATACA
* * * *
54740081 GGAAGGCAAGATCTGCAATCTTCAATCTACTTCACCACCAGTAT
1 GGAAGACAAGATCTGCTATCTTCGATCTACTTCACCACCAATAT
* * * * *
54740125 GGGAGACAAGATCTGC-ATCTTGGATCGACTTC-CTATCAATAT
1 GGAAGACAAGATCTGCTATCTTCGATCTACTTCACCACCAATAT
* * * *
54740167 AGGAAGATAGGACCTGCTATCTTCGATCTACTTCA-CGCCAATACAT
1 -GGAAGACAAGATCTGCTATCTTCGATCTACTTCACCACCAAT--AT
* * *
54740213 -GAAGACAAGATCTGCTTTCTGCGATCTACTTCGCCACCAATAT
1 GGAAGACAAGATCTGCTATCTTCGATCTACTTCACCACCAATAT
* * * * *
54740256 GGGAAGACAAGATCTGC-ATATTGGATCCACTTC-CTATCAATAT
1 -GGAAGACAAGATCTGCTATCTTCGATCTACTTCACCACCAATAT
* * *
54740299 AGGAAGATAGGATCTGCTATCTTCGATCTACTTCA-CGCCAATACAT
1 -GGAAGACAAGATCTGCTATCTTCGATCTACTTCACCACCAAT--AT
* * * *
54740345 -GAAGACAATATCTGCTTTCTGCGATCTACTTCGCCACCAATAT
1 GGAAGACAAGATCTGCTATCTTCGATCTACTTCACCACCAATAT
* *
54740388 GGGAAGACAAGATCTGC-ATCTTCGATCCACTTC-CTACCAATAT
1 -GGAAGACAAGATCTGCTATCTTCGATCTACTTCACCACCAATAT
* * * * *
54740431 AGAAAGATAGGATCTGCTACCTTCGATCTACTTCA-CGCCAATACAT
1 -GGAAGACAAGATCTGCTATCTTCGATCTACTTCACCACCAAT--AT
* * *
54740477 -GAAGACAAGATCTGCTTTCTGCGATCTACTTCGCCACCAATAT
1 GGAAGACAAGATCTGCTATCTTCGATCTACTTCACCACCAATAT
* * * * *
54740520 GGGAAGACAAGATCTGC-ATCCTGGATCCACTTC-CTATCAATAT
1 -GGAAGACAAGATCTGCTATCTTCGATCTACTTCACCACCAATAT
* * * *
54740563 AGGAAGATAGGACCTGCTATCTTCGATCTGCTTCAC
1 -GGAAGACAAGATCTGCTATCTTCGATCTACTTCAC
54740599 GCTAATACAT
Statistics
Matches: 367, Mismatches: 83, Indels: 47
0.74 0.17 0.09
Matches are distributed among these distances:
42 7 0.02
43 96 0.26
44 195 0.53
45 63 0.17
46 6 0.02
ACGTcount: A:0.30, C:0.26, G:0.17, T:0.27
Consensus pattern (44 bp):
GGAAGACAAGATCTGCTATCTTCGATCTACTTCACCACCAATAT
Found at i:54740294 original size:132 final size:132
Alignment explanation
Indices: 54740047--54740626 Score: 910
Period size: 132 Copynumber: 4.4 Consensus size: 132
54740037 AAGGTAAAAT
* * * * * * ** * *
54740047 CTGCCATCTTTGATCTGCTTCGCTGCCAAATACAGGAAGGCAAGATCTGCAATCTTCAATCTACT
1 CTGCTATCTTCGATCTACTTCAC-GCC-AATACATGAAGACAAGATCTGCTTTCTGCGATCTACT
* * *
54740112 TCACCACCAGTATGGG-AGACAAGATCTGCATCTTGGATCGACTTCCTATCAATATAGGAAGATA
64 TCGCCACCAATATGGGAAGACAAGATCTGCATCTTGGATCCACTTCCTATCAATATAGGAAGATA
54740176 GGAC
129 GGAC
54740180 CTGCTATCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTCTGCGATCTACTTC
1 CTGCTATCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTCTGCGATCTACTTC
*
54740245 GCCACCAATATGGGAAGACAAGATCTGCATATTGGATCCACTTCCTATCAATATAGGAAGATAGG
66 GCCACCAATATGGGAAGACAAGATCTGCATCTTGGATCCACTTCCTATCAATATAGGAAGATAGG
*
54740310 AT
131 AC
*
54740312 CTGCTATCTTCGATCTACTTCACGCCAATACATGAAGACAATATCTGCTTTCTGCGATCTACTTC
1 CTGCTATCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTCTGCGATCTACTTC
* * *
54740377 GCCACCAATATGGGAAGACAAGATCTGCATCTTCGATCCACTTCCTACCAATATAGAAAGATAGG
66 GCCACCAATATGGGAAGACAAGATCTGCATCTTGGATCCACTTCCTATCAATATAGGAAGATAGG
*
54740442 AT
131 AC
*
54740444 CTGCTACCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTCTGCGATCTACTTC
1 CTGCTATCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTCTGCGATCTACTTC
*
54740509 GCCACCAATATGGGAAGACAAGATCTGCATCCTGGATCCACTTCCTATCAATATAGGAAGATAGG
66 GCCACCAATATGGGAAGACAAGATCTGCATCTTGGATCCACTTCCTATCAATATAGGAAGATAGG
54740574 AC
131 AC
* * *
54740576 CTGCTATCTTCGATCTGCTTCACGCTAATACATGAAGACAAGATCTACTTT
1 CTGCTATCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTT
54740627 AATGACTTCA
Statistics
Matches: 415, Mismatches: 31, Indels: 3
0.92 0.07 0.01
Matches are distributed among these distances:
131 45 0.11
132 351 0.85
133 19 0.05
ACGTcount: A:0.30, C:0.26, G:0.17, T:0.28
Consensus pattern (132 bp):
CTGCTATCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTCTGCGATCTACTTC
GCCACCAATATGGGAAGACAAGATCTGCATCTTGGATCCACTTCCTATCAATATAGGAAGATAGG
AC
Found at i:54752780 original size:12 final size:12
Alignment explanation
Indices: 54752765--54752794 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
54752755 ACAATAATAC
54752765 TATATATAAATG
1 TATATATAAATG
*
54752777 TATATATATATG
1 TATATATAAATG
54752789 TATATA
1 TATATA
54752795 ATAGAAATAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.47, C:0.00, G:0.07, T:0.47
Consensus pattern (12 bp):
TATATATAAATG
Found at i:54752900 original size:19 final size:17
Alignment explanation
Indices: 54752876--54752922 Score: 51
Period size: 16 Copynumber: 2.7 Consensus size: 17
54752866 AATTAAAGTA
*
54752876 ATAAAAAATAATACTATAT
1 ATAAAAAAT-ATA-TATAC
*
54752895 ATAAAATATATATATAC
1 ATAAAAAATATATATAC
54752912 AT-AAAAATATA
1 ATAAAAAATATA
54752923 CACTAATATA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
16 8 0.32
17 6 0.24
18 3 0.12
19 8 0.32
ACGTcount: A:0.64, C:0.04, G:0.00, T:0.32
Consensus pattern (17 bp):
ATAAAAAATATATATAC
Found at i:54752918 original size:18 final size:19
Alignment explanation
Indices: 54752879--54752927 Score: 59
Period size: 17 Copynumber: 2.7 Consensus size: 19
54752869 TAAAGTAATA
*
54752879 AAAAATA-ATACTATATAT
1 AAAAATATATACTATACAT
54752897 -AAAATATATA-TATACAT
1 AAAAATATATACTATACAT
*
54752914 AAAAATATACACTA
1 AAAAATATATACTA
54752928 ATATATAATA
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
17 12 0.46
18 12 0.46
19 2 0.08
ACGTcount: A:0.61, C:0.08, G:0.00, T:0.31
Consensus pattern (19 bp):
AAAAATATATACTATACAT
Found at i:54753154 original size:3 final size:3
Alignment explanation
Indices: 54753141--54753223 Score: 54
Period size: 3 Copynumber: 28.3 Consensus size: 3
54753131 GAGGGCATAT
54753141 ATA AT- ATA ATA ATA AT- ATA A-A A-A ATA ATA TATA CATGA GA-A ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA -ATA -AT-A -ATA ATA
* *
54753185 ATA ATA AT- ATAA ATA ATA GTA AAA ATA ATA A-A ATA ATA A
1 ATA ATA ATA AT-A ATA ATA ATA ATA ATA ATA ATA ATA ATA A
54753224 AACAAAGCTC
Statistics
Matches: 65, Mismatches: 6, Indels: 18
0.73 0.07 0.20
Matches are distributed among these distances:
2 13 0.20
3 43 0.66
4 7 0.11
5 2 0.03
ACGTcount: A:0.66, C:0.01, G:0.04, T:0.29
Consensus pattern (3 bp):
ATA
Found at i:54753588 original size:23 final size:23
Alignment explanation
Indices: 54753553--54753625 Score: 71
Period size: 23 Copynumber: 3.2 Consensus size: 23
54753543 CCTTTTTTAC
*
54753553 AAAAAAA-CACCTCCAAAAAACA
1 AAAAAAACCTCCTCCAAAAAACA
54753575 AAAAAAACCTCCTCC--AAAACA
1 AAAAAAACCTCCTCCAAAAAACA
* * *
54753596 AAGAACAATCCTTCTCCAAAAAACC
1 AA-AA-AAACCTCCTCCAAAAAACA
54753621 AAAAA
1 AAAAA
54753626 CCCACCCTAA
Statistics
Matches: 42, Mismatches: 4, Indels: 9
0.76 0.07 0.16
Matches are distributed among these distances:
21 8 0.19
22 9 0.21
23 16 0.38
24 2 0.05
25 7 0.17
ACGTcount: A:0.60, C:0.29, G:0.01, T:0.10
Consensus pattern (23 bp):
AAAAAAACCTCCTCCAAAAAACA
Found at i:54753593 original size:21 final size:21
Alignment explanation
Indices: 54753551--54753616 Score: 62
Period size: 21 Copynumber: 3.0 Consensus size: 21
54753541 AACCTTTTTT
**
54753551 ACAAAAAAACACCTCC-AAAAA
1 ACAAAAAAA-ACCTCCTCCAAA
54753572 ACAAAAAAAACCTCCTCCAAA
1 ACAAAAAAAACCTCCTCCAAA
* *
54753593 ACAAAGAACAATCCTTCTCCAAA
1 ACAAA-AA-AAACCTCCTCCAAA
54753616 A
1 A
54753617 AACCAAAAAC
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
20 6 0.16
21 17 0.45
22 2 0.05
23 13 0.34
ACGTcount: A:0.58, C:0.30, G:0.02, T:0.11
Consensus pattern (21 bp):
ACAAAAAAAACCTCCTCCAAA
Found at i:54753762 original size:38 final size:38
Alignment explanation
Indices: 54753708--54753807 Score: 182
Period size: 38 Copynumber: 2.6 Consensus size: 38
54753698 GGTGGCCAAG
*
54753708 GGTGGTGGAGTTGGTGGCTAAGGTGGGTGGCCAACAAA
1 GGTGGTGGAGTAGGTGGCTAAGGTGGGTGGCCAACAAA
54753746 GGTGGTGGAGTAGGTGGCTAAGGTGGGTGGCCAACAAA
1 GGTGGTGGAGTAGGTGGCTAAGGTGGGTGGCCAACAAA
*
54753784 GGTGGTGGAGTAGGTGGCCAAGGT
1 GGTGGTGGAGTAGGTGGCTAAGGT
54753808 TTTTTTATTT
Statistics
Matches: 60, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 60 1.00
ACGTcount: A:0.21, C:0.10, G:0.49, T:0.20
Consensus pattern (38 bp):
GGTGGTGGAGTAGGTGGCTAAGGTGGGTGGCCAACAAA
Found at i:54755019 original size:21 final size:20
Alignment explanation
Indices: 54754984--54755028 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 20
54754974 TTAAATAGGG
*
54754984 AAACTTTAGGTTTTTACATGAA
1 AAACTTGAGGTTTTTAC--GAA
54755006 AAACTTGA-GTTTTTACGAA
1 AAACTTGAGGTTTTTACGAA
54755025 AAAC
1 AAAC
54755029 CAGATTCTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
19 7 0.32
21 8 0.36
22 7 0.32
ACGTcount: A:0.40, C:0.11, G:0.13, T:0.36
Consensus pattern (20 bp):
AAACTTGAGGTTTTTACGAA
Found at i:54756638 original size:14 final size:15
Alignment explanation
Indices: 54756609--54756641 Score: 50
Period size: 14 Copynumber: 2.2 Consensus size: 15
54756599 AGTCTTAACA
54756609 AATCAGATCATATCAG
1 AATCAGAT-ATATCAG
54756625 AATCAGAT-TATCAG
1 AATCAGATATATCAG
54756639 AAT
1 AAT
54756642 ATACGATATG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 9 0.53
16 8 0.47
ACGTcount: A:0.45, C:0.15, G:0.12, T:0.27
Consensus pattern (15 bp):
AATCAGATATATCAG
Found at i:54774033 original size:19 final size:17
Alignment explanation
Indices: 54774009--54774055 Score: 51
Period size: 16 Copynumber: 2.7 Consensus size: 17
54773999 AATTAAAGTA
*
54774009 ATAAAAAATAATACTATAT
1 ATAAAAAAT-ATA-TATAC
*
54774028 ATAAAATATATATATAC
1 ATAAAAAATATATATAC
54774045 AT-AAAAATATA
1 ATAAAAAATATA
54774056 CACTAATATA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
16 8 0.32
17 6 0.24
18 3 0.12
19 8 0.32
ACGTcount: A:0.64, C:0.04, G:0.00, T:0.32
Consensus pattern (17 bp):
ATAAAAAATATATATAC
Found at i:54774051 original size:18 final size:19
Alignment explanation
Indices: 54774012--54774060 Score: 59
Period size: 17 Copynumber: 2.7 Consensus size: 19
54774002 TAAAGTAATA
*
54774012 AAAAATA-ATACTATATAT
1 AAAAATATATACTATACAT
54774030 -AAAATATATA-TATACAT
1 AAAAATATATACTATACAT
*
54774047 AAAAATATACACTA
1 AAAAATATATACTA
54774061 ATATATAATA
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
17 12 0.46
18 12 0.46
19 2 0.08
ACGTcount: A:0.61, C:0.08, G:0.00, T:0.31
Consensus pattern (19 bp):
AAAAATATATACTATACAT
Found at i:54774287 original size:3 final size:3
Alignment explanation
Indices: 54774274--54774355 Score: 57
Period size: 3 Copynumber: 27.3 Consensus size: 3
54774264 GAGGGCATAT
*
54774274 ATA AT- ATA ATA ATA AT- ATA AAA ATA ATA TATA CATGA GA-A ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA -ATA -AT-A -ATA ATA ATA
* *
54774320 ATA AT- ATAA ATA ATA GTA AAA ATA ATA A-A ATA ATA A
1 ATA ATA AT-A ATA ATA ATA ATA ATA ATA ATA ATA ATA A
54774356 AACAAAGCTC
Statistics
Matches: 63, Mismatches: 8, Indels: 16
0.72 0.09 0.18
Matches are distributed among these distances:
2 9 0.14
3 45 0.71
4 7 0.11
5 2 0.03
ACGTcount: A:0.66, C:0.01, G:0.04, T:0.29
Consensus pattern (3 bp):
ATA
Found at i:54774290 original size:11 final size:11
Alignment explanation
Indices: 54774274--54774355 Score: 71
Period size: 11 Copynumber: 7.4 Consensus size: 11
54774264 GAGGGCATAT
54774274 ATAATATAATA
1 ATAATATAATA
*
54774285 ATAATATAAAA
1 ATAATATAATA
54774296 ATAATAT-ATA
1 ATAATATAATA
*
54774306 CATGAGAAATAATA
1 -AT-A-ATATAATA
54774320 ATAATAT-A-A
1 ATAATATAATA
*
54774329 ATAATAGTAAAA
1 ATAATA-TAATA
*
54774341 ATAATAAAATA
1 ATAATATAATA
54774352 ATAA
1 ATAA
54774356 AACAAAGCTC
Statistics
Matches: 58, Mismatches: 6, Indels: 14
0.74 0.08 0.18
Matches are distributed among these distances:
9 7 0.12
10 4 0.07
11 30 0.52
12 9 0.16
13 5 0.09
14 3 0.05
ACGTcount: A:0.66, C:0.01, G:0.04, T:0.29
Consensus pattern (11 bp):
ATAATATAATA
Found at i:54774320 original size:27 final size:28
Alignment explanation
Indices: 54774290--54774356 Score: 70
Period size: 27 Copynumber: 2.5 Consensus size: 28
54774280 TAATAATAAT
* *
54774290 ATAAAAATAATATATACAT-G-AGAAATA
1 ATAAAAATAATAAATA-ATAGTAAAAATA
*
54774317 ATAATAAT-ATAAATAATAGTAAAAATA
1 ATAAAAATAATAAATAATAGTAAAAATA
54774344 AT-AAAATAATAAA
1 ATAAAAATAATAAA
54774357 ACAAAGCTCT
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
25 2 0.06
26 11 0.33
27 20 0.61
ACGTcount: A:0.67, C:0.01, G:0.04, T:0.27
Consensus pattern (28 bp):
ATAAAAATAATAAATAATAGTAAAAATA
Found at i:54774343 original size:24 final size:24
Alignment explanation
Indices: 54774274--54774352 Score: 69
Period size: 24 Copynumber: 3.4 Consensus size: 24
54774264 GAGGGCATAT
54774274 ATAATATAATAATAATA-TAAAAATA
1 ATAATAT-A-AATAATAGTAAAAATA
* *
54774299 AT-ATATACAT--GAG-AAATAATA
1 ATAATATAAATAATAGTAAA-AATA
54774320 ATAATATAAATAATAGTAAAAATA
1 ATAATATAAATAATAGTAAAAATA
*
54774344 ATAAAATAA
1 ATAATATAA
54774353 TAAAACAAAG
Statistics
Matches: 43, Mismatches: 5, Indels: 13
0.70 0.08 0.21
Matches are distributed among these distances:
20 4 0.09
21 6 0.14
22 9 0.21
23 1 0.02
24 18 0.42
25 5 0.12
ACGTcount: A:0.66, C:0.01, G:0.04, T:0.29
Consensus pattern (24 bp):
ATAATATAAATAATAGTAAAAATA
Found at i:54774719 original size:23 final size:23
Alignment explanation
Indices: 54774684--54774756 Score: 71
Period size: 23 Copynumber: 3.2 Consensus size: 23
54774674 CCTTTTTTAC
*
54774684 AAAAAAA-CACCTCCAAAAAACA
1 AAAAAAACCTCCTCCAAAAAACA
54774706 AAAAAAACCTCCTCC--AAAACA
1 AAAAAAACCTCCTCCAAAAAACA
* * *
54774727 AAGAACAATCCTTCTCCAAAAAACC
1 AA-AA-AAACCTCCTCCAAAAAACA
54774752 AAAAA
1 AAAAA
54774757 CCCACCTCTA
Statistics
Matches: 42, Mismatches: 4, Indels: 9
0.76 0.07 0.16
Matches are distributed among these distances:
21 8 0.19
22 9 0.21
23 16 0.38
24 2 0.05
25 7 0.17
ACGTcount: A:0.60, C:0.29, G:0.01, T:0.10
Consensus pattern (23 bp):
AAAAAAACCTCCTCCAAAAAACA
Found at i:54774724 original size:21 final size:21
Alignment explanation
Indices: 54774682--54774747 Score: 62
Period size: 21 Copynumber: 3.0 Consensus size: 21
54774672 AACCTTTTTT
**
54774682 ACAAAAAAACACCTCC-AAAAA
1 ACAAAAAAA-ACCTCCTCCAAA
54774703 ACAAAAAAAACCTCCTCCAAA
1 ACAAAAAAAACCTCCTCCAAA
* *
54774724 ACAAAGAACAATCCTTCTCCAAA
1 ACAAA-AA-AAACCTCCTCCAAA
54774747 A
1 A
54774748 AACCAAAAAC
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
20 6 0.16
21 17 0.45
22 2 0.05
23 13 0.34
ACGTcount: A:0.58, C:0.30, G:0.02, T:0.11
Consensus pattern (21 bp):
ACAAAAAAAACCTCCTCCAAA
Found at i:54774894 original size:38 final size:38
Alignment explanation
Indices: 54774840--54774939 Score: 182
Period size: 38 Copynumber: 2.6 Consensus size: 38
54774830 GGTGGCCAAG
*
54774840 GGTGGTGGAGTTGGTGGCTAAGGTGGGTGGCCAACAAA
1 GGTGGTGGAGTAGGTGGCTAAGGTGGGTGGCCAACAAA
54774878 GGTGGTGGAGTAGGTGGCTAAGGTGGGTGGCCAACAAA
1 GGTGGTGGAGTAGGTGGCTAAGGTGGGTGGCCAACAAA
*
54774916 GGTGGTGGAGTAGGTGGCCAAGGT
1 GGTGGTGGAGTAGGTGGCTAAGGT
54774940 TTTTATTTAT
Statistics
Matches: 60, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 60 1.00
ACGTcount: A:0.21, C:0.10, G:0.49, T:0.20
Consensus pattern (38 bp):
GGTGGTGGAGTAGGTGGCTAAGGTGGGTGGCCAACAAA
Found at i:54781630 original size:7 final size:7
Alignment explanation
Indices: 54781615--54781644 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
54781605 CCAAAAGCCT
*
54781615 CCAGATG
1 CCAGCTG
54781622 CCAGCTG
1 CCAGCTG
54781629 CCAGCTG
1 CCAGCTG
54781636 CCAGCTG
1 CCAGCTG
54781643 CC
1 CC
54781645 GTTTGGTGGC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.17, C:0.43, G:0.27, T:0.13
Consensus pattern (7 bp):
CCAGCTG
Found at i:54785473 original size:16 final size:16
Alignment explanation
Indices: 54785454--54785511 Score: 50
Period size: 16 Copynumber: 3.8 Consensus size: 16
54785444 CTTTTTAATT
54785454 TTTTTTAAATTTATAC
1 TTTTTTAAATTTATAC
* * *
54785470 TTTTTTAATTTTAAAA
1 TTTTTTAAATTTATAC
54785486 TATTTTTAAA---ATAC
1 T-TTTTTAAATTTATAC
*
54785500 TTTTTTTAATTT
1 TTTTTTAAATTT
54785512 TTTAAAATTT
Statistics
Matches: 31, Mismatches: 7, Indels: 8
0.67 0.15 0.17
Matches are distributed among these distances:
13 7 0.23
14 3 0.10
16 14 0.45
17 7 0.23
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (16 bp):
TTTTTTAAATTTATAC
Found at i:54785490 original size:25 final size:25
Alignment explanation
Indices: 54785402--54785490 Score: 58
Period size: 24 Copynumber: 3.4 Consensus size: 25
54785392 CCCGATATAA
*
54785402 TAAATATATTTAT--TTTTTTTATTT
1 TAAA-ATATTTATACTTTTTTAATTT
*
54785426 TAAAATATTTTTTACATACTTTTTAATTTTT
1 TAAAATA-TTTATAC-T--TTTTTAA--TTT
**
54785457 TTTAA-ATTTATACTTTTTTAATTT
1 TAAAATATTTATACTTTTTTAATTT
54785481 TAAAATATTT
1 TAAAATATTT
54785491 TTAAAATACT
Statistics
Matches: 49, Mismatches: 7, Indels: 17
0.67 0.10 0.23
Matches are distributed among these distances:
23 3 0.06
24 14 0.29
25 4 0.08
26 7 0.14
27 1 0.02
28 1 0.02
29 12 0.24
30 1 0.02
31 6 0.12
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (25 bp):
TAAAATATTTATACTTTTTTAATTT
Found at i:54785492 original size:33 final size:31
Alignment explanation
Indices: 54785466--54785529 Score: 96
Period size: 31 Copynumber: 2.1 Consensus size: 31
54785456 TTTTAAATTT
54785466 ATAC-TTTTTTAA-TTTTAAAATATTTTTAAA
1 ATACTTTTTTTAATTTTTAAAA-ATTTTTAAA
*
54785496 ATACTTTTTTTAATTTTTTAAAATTTTTAAA
1 ATACTTTTTTTAATTTTTAAAAATTTTTAAA
54785527 ATA
1 ATA
54785530 AAAATGGGCC
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
30 4 0.13
31 20 0.65
32 7 0.23
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (31 bp):
ATACTTTTTTTAATTTTTAAAAATTTTTAAA
Found at i:54788142 original size:32 final size:31
Alignment explanation
Indices: 54788099--54788164 Score: 89
Period size: 31 Copynumber: 2.1 Consensus size: 31
54788089 TTTTCTCATA
54788099 AAAATAATTAAAAAATATTTAAAAATATAAAAT
1 AAAATAATT-AAAAATATTTAAAAAT-TAAAAT
* *
54788132 AAAA-AATTAAAAATATTTTAAAATTAATAT
1 AAAATAATTAAAAATATTTAAAAATTAAAAT
54788162 AAA
1 AAA
54788165 CTTATAACAA
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
30 8 0.26
31 15 0.48
32 4 0.13
33 4 0.13
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (31 bp):
AAAATAATTAAAAATATTTAAAAATTAAAAT
Found at i:54788192 original size:10 final size:10
Alignment explanation
Indices: 54788098--54788222 Score: 51
Period size: 10 Copynumber: 12.4 Consensus size: 10
54788088 ATTTTCTCAT
54788098 AAAAATAATTA
1 AAAAATAA-TA
*
54788109 AAAAATATTTA
1 AAAAATA-ATA
54788120 AAAATATAA-A
1 AAAA-ATAATA
*
54788130 ATAAAA-AATT
1 A-AAAATAATA
* *
54788140 AAAAATATTTT
1 AAAAATA-ATA
*
54788151 AAAATTAATA
1 AAAAATAATA
* * *
54788161 TAAACTTAT-
1 AAAAATAATA
* *
54788170 AACAATCATA
1 AAAAATAATA
54788180 AAAAATAATA
1 AAAAATAATA
* *
54788190 AAAACTTAT-
1 AAAAATAATA
* *
54788199 AACAATCATA
1 AAAAATAATA
54788209 AAAAATAATA
1 AAAAATAATA
54788219 AAAA
1 AAAA
54788223 CTTATTAATA
Statistics
Matches: 83, Mismatches: 23, Indels: 17
0.67 0.19 0.14
Matches are distributed among these distances:
9 17 0.20
10 39 0.47
11 24 0.29
12 3 0.04
ACGTcount: A:0.67, C:0.05, G:0.00, T:0.28
Consensus pattern (10 bp):
AAAAATAATA
Found at i:54788194 original size:29 final size:29
Alignment explanation
Indices: 54788151--54788227 Score: 136
Period size: 29 Copynumber: 2.7 Consensus size: 29
54788141 AAAATATTTT
* *
54788151 AAAATTAATATAAACTTATAACAATCATA
1 AAAAATAATAAAAACTTATAACAATCATA
54788180 AAAAATAATAAAAACTTATAACAATCATA
1 AAAAATAATAAAAACTTATAACAATCATA
54788209 AAAAATAATAAAAACTTAT
1 AAAAATAATAAAAACTTAT
54788228 TAATATTATA
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 46 1.00
ACGTcount: A:0.64, C:0.09, G:0.00, T:0.27
Consensus pattern (29 bp):
AAAAATAATAAAAACTTATAACAATCATA
Found at i:54788238 original size:29 final size:28
Alignment explanation
Indices: 54788112--54788243 Score: 106
Period size: 29 Copynumber: 4.5 Consensus size: 28
54788102 ATAATTAAAA
* *
54788112 AATATT-TAAAAATATAAAATAAAAAATTAAA
1 AATATTATAAAAA-AT--AATAAAAACTT-AT
* * *
54788143 AATATT-TTAAAATTAATATAAACTTAT
1 AATATTATAAAAAATAATAAAAACTTAT
* *
54788170 AACAATCATAAAAAATAATAAAAACTTAT
1 AA-TATTATAAAAAATAATAAAAACTTAT
* *
54788199 AACAATCATAAAAAATAATAAAAACTTATT
1 AA-TATTATAAAAAATAATAAAAACTTA-T
54788229 AATATTATAAAAAAT
1 AATATTATAAAAAAT
54788244 CTAAAAAATT
Statistics
Matches: 86, Mismatches: 12, Indels: 8
0.81 0.11 0.08
Matches are distributed among these distances:
27 3 0.03
28 11 0.13
29 57 0.66
30 4 0.05
31 11 0.13
ACGTcount: A:0.64, C:0.05, G:0.00, T:0.31
Consensus pattern (28 bp):
AATATTATAAAAAATAATAAAAACTTAT
Found at i:54788267 original size:29 final size:29
Alignment explanation
Indices: 54788112--54788259 Score: 92
Period size: 29 Copynumber: 5.1 Consensus size: 29
54788102 ATAATTAAAA
**
54788112 AATATT-TAAAAATATAAAATAAAAAATTAAA
1 AATATTATAAAAA-AT--AATAAAAAATTATT
* * * *
54788143 AATATT-TTAAAATTAATATAAACTTA-T
1 AATATTATAAAAAATAATAAAAAATTATT
* * *
54788170 AACAATCATAAAAAATAATAAAAACTTA-T
1 AA-TATTATAAAAAATAATAAAAAATTATT
* * *
54788199 AACAATCATAAAAAATAATAAAAACTTATT
1 AA-TATTATAAAAAATAATAAAAAATTATT
*
54788229 AATATTATAAAAAAT-CTAAAAAATT-TT
1 AATATTATAAAAAATAATAAAAAATTATT
54788256 AATA
1 AATA
54788260 AATTATAATT
Statistics
Matches: 100, Mismatches: 14, Indels: 10
0.81 0.11 0.08
Matches are distributed among these distances:
27 8 0.08
28 20 0.20
29 57 0.57
30 4 0.04
31 11 0.11
ACGTcount: A:0.63, C:0.05, G:0.00, T:0.32
Consensus pattern (29 bp):
AATATTATAAAAAATAATAAAAAATTATT
Found at i:54788347 original size:19 final size:18
Alignment explanation
Indices: 54788325--54788409 Score: 55
Period size: 20 Copynumber: 4.3 Consensus size: 18
54788315 TACAAATTCT
54788325 TAAAAACTTATAAAAATCA
1 TAAAAA-TTATAAAAATCA
*
54788344 TAAAAAATTATTAAGAA-CA
1 T-AAAAATTA-TAAAAATCA
* * *
54788363 TTAAAATTGATACAAACTTA
1 TAAAAATT-ATA-AAAATCA
54788383 TAAAAATTATTTAAAAAATCA
1 TAAAAATTA--T-AAAAATCA
54788404 TAAAAA
1 TAAAAA
54788410 CTTGATTTAG
Statistics
Matches: 50, Mismatches: 8, Indels: 14
0.69 0.11 0.19
Matches are distributed among these distances:
18 8 0.16
19 11 0.22
20 18 0.36
21 12 0.24
22 1 0.02
ACGTcount: A:0.61, C:0.07, G:0.02, T:0.29
Consensus pattern (18 bp):
TAAAAATTATAAAAATCA
Found at i:54788919 original size:11 final size:10
Alignment explanation
Indices: 54788903--54788987 Score: 57
Period size: 10 Copynumber: 8.3 Consensus size: 10
54788893 ATAGTTCATG
54788903 TTTTTATGATT
1 TTTTTAT-ATT
*
54788914 TTTTTA-ATA
1 TTTTTATATT
* *
54788923 ATTTTATATCA
1 TTTTTATAT-T
54788934 TTTTTAT-TT
1 TTTTTATATT
54788943 ATTTTTATATT
1 -TTTTTATATT
**
54788954 TTTCAATATT
1 TTTTTATATT
54788964 TTTTTATGATT
1 TTTTTAT-ATT
* *
54788975 TTTATATGTT
1 TTTTTATATT
54788985 TTT
1 TTT
54788988 AAGAAATTTT
Statistics
Matches: 59, Mismatches: 10, Indels: 11
0.74 0.12 0.14
Matches are distributed among these distances:
9 7 0.12
10 28 0.47
11 24 0.41
ACGTcount: A:0.24, C:0.02, G:0.04, T:0.71
Consensus pattern (10 bp):
TTTTTATATT
Found at i:54788976 original size:39 final size:41
Alignment explanation
Indices: 54788903--54788988 Score: 104
Period size: 39 Copynumber: 2.1 Consensus size: 41
54788893 ATAGTTCATG
* *
54788903 TTTTTATGATTTTTTTAATAATTTTATATCATTTTTATTTA
1 TTTTTATGATTTTTTCAATAATTTTATATCATTTTTATATA
* * * *
54788944 TTTTTAT-A-TTTTTCAATATTTTTTTATGATTTTTATATG
1 TTTTTATGATTTTTTCAATAATTTTATATCATTTTTATATA
54788983 TTTTTA
1 TTTTTA
54788989 AGAAATTTTA
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
39 31 0.79
40 1 0.03
41 7 0.18
ACGTcount: A:0.24, C:0.02, G:0.03, T:0.70
Consensus pattern (41 bp):
TTTTTATGATTTTTTCAATAATTTTATATCATTTTTATATA
Found at i:54788986 original size:10 final size:10
Alignment explanation
Indices: 54788903--54788988 Score: 70
Period size: 11 Copynumber: 8.6 Consensus size: 10
54788893 ATAGTTCATG
*
54788903 TTTTTATGATT
1 TTTTTAT-ATA
54788914 TTTTTA-ATA
1 TTTTTATATA
*
54788923 ATTTTATATCA
1 TTTTTATAT-A
*
54788934 TTTTTATTTA
1 TTTTTATATA
54788944 TTTTTATAT-
1 TTTTTATATA
*
54788953 TTTTCA-ATA
1 TTTTTATATA
*
54788962 TTTTTTTATGA
1 TTTTTATAT-A
*
54788973 TTTTTATATG
1 TTTTTATATA
54788983 TTTTTA
1 TTTTTA
54788989 AGAAATTTTA
Statistics
Matches: 60, Mismatches: 10, Indels: 11
0.74 0.12 0.14
Matches are distributed among these distances:
8 2 0.03
9 16 0.27
10 19 0.32
11 23 0.38
ACGTcount: A:0.24, C:0.02, G:0.03, T:0.70
Consensus pattern (10 bp):
TTTTTATATA
Found at i:54788986 original size:21 final size:21
Alignment explanation
Indices: 54788903--54788987 Score: 70
Period size: 21 Copynumber: 4.1 Consensus size: 21
54788893 ATAGTTCATG
* *
54788903 TTTTTATGATTTTTTTAATAAT
1 TTTTTATGATTTTTAT-ATATT
* * *
54788925 TTTATATCATTTTTAT-T-TA
1 TTTTTATGATTTTTATATATT
54788944 TTTTTAT-ATTTTTCA-ATATT
1 TTTTTATGATTTTT-ATATATT
*
54788964 TTTTTATGATTTTTATATGTT
1 TTTTTATGATTTTTATATATT
54788985 TTT
1 TTT
54788988 AAGAAATTTT
Statistics
Matches: 50, Mismatches: 8, Indels: 11
0.72 0.12 0.16
Matches are distributed among these distances:
18 6 0.12
19 8 0.16
20 10 0.20
21 13 0.26
22 13 0.26
ACGTcount: A:0.24, C:0.02, G:0.04, T:0.71
Consensus pattern (21 bp):
TTTTTATGATTTTTATATATT
Found at i:54789072 original size:19 final size:18
Alignment explanation
Indices: 54789045--54789172 Score: 75
Period size: 19 Copynumber: 6.9 Consensus size: 18
54789035 TAATGTTACA
54789045 AATTGTTTATAATTGTTTAT
1 AATT-TTTATAATT-TTTAT
* *
54789065 TATTTTTATAA-TATTAT
1 AATTTTTATAATTTTTAT
54789082 AAGTTTTTATTAATTTTTAT
1 AA-TTTTTA-TAATTTTTAT
* *
54789102 AATTTTATATAATCTTAAT
1 AATTTT-TATAATTTTTAT
* *
54789121 -ATTCTT-TAATATTTAAT
1 AATTTTTATAAT-TTTTAT
* *
54789138 GATTTTTATGATTTTTTAT
1 AATTTTTAT-AATTTTTAT
*
54789157 GATTTTT-TAATATTTT
1 AATTTTTATAAT-TTTT
54789173 TATGGGAAAA
Statistics
Matches: 87, Mismatches: 12, Indels: 20
0.73 0.10 0.17
Matches are distributed among these distances:
16 4 0.05
17 13 0.15
18 21 0.24
19 35 0.40
20 14 0.16
ACGTcount: A:0.31, C:0.02, G:0.05, T:0.62
Consensus pattern (18 bp):
AATTTTTATAATTTTTAT
Found at i:54789109 original size:8 final size:9
Alignment explanation
Indices: 54789045--54789172 Score: 75
Period size: 10 Copynumber: 13.8 Consensus size: 9
54789035 TAATGTTACA
54789045 AATTGTTTAT
1 AATT-TTTAT
54789055 AATTGTTTAT
1 AATT-TTTAT
*
54789065 TATTTTTAT
1 AATTTTTAT
*
54789074 AA-TATTAT
1 AATTTTTAT
54789082 AAGTTTTTATT
1 AA-TTTTTA-T
54789093 AATTTTTAT
1 AATTTTTAT
54789102 AATTTTATAT
1 AATTTT-TAT
* *
54789112 AATCTTAAT
1 AATTTTTAT
*
54789121 -ATTCTT-T
1 AATTTTTAT
*
54789128 AATATTTAAT
1 AAT-TTTTAT
*
54789138 GATTTTTAT
1 AATTTTTAT
*
54789147 GATTTTTTAT
1 -AATTTTTAT
*
54789157 GATTTTT-T
1 AATTTTTAT
54789165 AATATTTT
1 AAT-TTTT
54789173 TATGGGAAAA
Statistics
Matches: 91, Mismatches: 18, Indels: 19
0.71 0.14 0.15
Matches are distributed among these distances:
7 1 0.01
8 15 0.16
9 31 0.34
10 41 0.45
11 3 0.03
ACGTcount: A:0.31, C:0.02, G:0.05, T:0.62
Consensus pattern (9 bp):
AATTTTTAT
Found at i:54789109 original size:28 final size:27
Alignment explanation
Indices: 54789050--54789110 Score: 88
Period size: 28 Copynumber: 2.2 Consensus size: 27
54789040 TTACAAATTG
54789050 TTTATAATTGTTTATTATTTTTATAAT
1 TTTATAATTGTTTATTATTTTTATAAT
*
54789077 ATTATAAGTT-TTTATTAATTTTTATAAT
1 TTTATAA-TTGTTTATT-ATTTTTATAAT
54789105 TTTATA
1 TTTATA
54789111 TAATCTTAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
27 12 0.40
28 18 0.60
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (27 bp):
TTTATAATTGTTTATTATTTTTATAAT
Found at i:54792109 original size:30 final size:30
Alignment explanation
Indices: 54792066--54792123 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 30
54792056 TTTTATATAC
*
54792066 TATATAATTTATAACAC-ATAATCTAAATT
1 TATATAATATATAACACTATAATCTAAATT
* *
54792095 TATAGTAATATATAATACTATAATGTAAA
1 TATA-TAATATATAACACTATAATCTAAA
54792124 CATTAAAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 4 0.17
30 11 0.46
31 9 0.38
ACGTcount: A:0.50, C:0.07, G:0.03, T:0.40
Consensus pattern (30 bp):
TATATAATATATAACACTATAATCTAAATT
Found at i:54794382 original size:28 final size:27
Alignment explanation
Indices: 54794342--54794399 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 27
54794332 ATTATGGTCA
*
54794342 AAGTTGTTACTAAAGTCACTTAGCAGTT
1 AAGTGGTTACT-AAGTCACTTAGCAGTT
***
54794370 AAGTGGTTACTAAGTTGGTTAGCAGTT
1 AAGTGGTTACTAAGTCACTTAGCAGTT
54794397 AAG
1 AAG
54794400 AAGTTAGCTA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
27 16 0.62
28 10 0.38
ACGTcount: A:0.31, C:0.10, G:0.24, T:0.34
Consensus pattern (27 bp):
AAGTGGTTACTAAGTCACTTAGCAGTT
Found at i:54803543 original size:27 final size:28
Alignment explanation
Indices: 54803493--54803550 Score: 82
Period size: 27 Copynumber: 2.1 Consensus size: 28
54803483 ATTATGGTCA
*
54803493 AAGTTGTTACTAAAGTCAGTTAGCAGTT
1 AAGTGGTTACTAAAGTCAGTTAGCAGTT
**
54803521 AAGTGGTTACT-AAGTTGGTTAGCAGTT
1 AAGTGGTTACTAAAGTCAGTTAGCAGTT
54803548 AAG
1 AAG
54803551 AAGTTAGCTA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
27 17 0.63
28 10 0.37
ACGTcount: A:0.31, C:0.09, G:0.26, T:0.34
Consensus pattern (28 bp):
AAGTGGTTACTAAAGTCAGTTAGCAGTT
Found at i:54804524 original size:18 final size:19
Alignment explanation
Indices: 54804487--54804524 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
54804477 AAGTTCGTAA
**
54804487 TTTATTATATTATGTTATT
1 TTTATTATATTATGCAATT
54804506 TTTA-TATATTATGCAATT
1 TTTATTATATTATGCAATT
54804524 T
1 T
54804525 ATAACATATA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 13 0.76
19 4 0.24
ACGTcount: A:0.29, C:0.03, G:0.05, T:0.63
Consensus pattern (19 bp):
TTTATTATATTATGCAATT
Found at i:54806448 original size:31 final size:31
Alignment explanation
Indices: 54806413--54806493 Score: 126
Period size: 31 Copynumber: 2.6 Consensus size: 31
54806403 CGCCCGTATG
*
54806413 TATACAATTGAATCAAAATCAAAATTTTATA
1 TATACAATTGAATCAAAATCAAAATTTAATA
*
54806444 TATACATTTGAATCAAAATCAAAATTTAATA
1 TATACAATTGAATCAAAATCAAAATTTAATA
* *
54806475 TATATAATTGAATAAAAAT
1 TATACAATTGAATCAAAAT
54806494 AAAGATCAAA
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 45 1.00
ACGTcount: A:0.53, C:0.07, G:0.04, T:0.36
Consensus pattern (31 bp):
TATACAATTGAATCAAAATCAAAATTTAATA
Found at i:54806816 original size:9 final size:9
Alignment explanation
Indices: 54806791--54806823 Score: 52
Period size: 8 Copynumber: 3.9 Consensus size: 9
54806781 TAATATAAAT
54806791 ATAATTTTA
1 ATAATTTTA
54806800 AT-ATTTTA
1 ATAATTTTA
54806808 ATAATTTT-
1 ATAATTTTA
54806816 ATAATTTT
1 ATAATTTT
54806824 CAAAAGATTA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
8 16 0.70
9 7 0.30
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (9 bp):
ATAATTTTA
Found at i:54809553 original size:3 final size:3
Alignment explanation
Indices: 54809547--54809573 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
54809537 GGGTGATGAT
54809547 GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA
54809574 AGGGGTAAAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:54815999 original size:12 final size:12
Alignment explanation
Indices: 54815921--54816000 Score: 54
Period size: 12 Copynumber: 6.2 Consensus size: 12
54815911 AAAAAATTTC
54815921 AAAAAAA-TCGAA
1 AAAAAAAGT-GAA
**
54815933 AAAAAAAGAAAA
1 AAAAAAAGTGAA
54815945 AAAAAGAAGTGACA
1 AAAAA-AAGTGA-A
*
54815959 AAAAAATCGAGTTAA
1 AAAAAA---AGTGAA
*
54815974 AAAAAAAGAAGAA
1 AAAAAAAG-TGAA
54815987 AAAAAAAGTGAA
1 AAAAAAAGTGAA
54815999 AA
1 AA
54816001 GGCTTGCGAG
Statistics
Matches: 53, Mismatches: 8, Indels: 14
0.71 0.11 0.19
Matches are distributed among these distances:
12 21 0.40
13 15 0.28
14 6 0.11
15 7 0.13
16 4 0.08
ACGTcount: A:0.75, C:0.04, G:0.14, T:0.07
Consensus pattern (12 bp):
AAAAAAAGTGAA
Found at i:54817102 original size:14 final size:13
Alignment explanation
Indices: 54817083--54817120 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 13
54817073 AAAAGTGAGA
54817083 GAAAAAGAAAA-T
1 GAAAAAGAAAATT
54817095 GAAGAAAAGAAAATT
1 G-A-AAAAGAAAATT
54817110 GAAAAAGAAAA
1 GAAAAAGAAAA
54817121 AGCAAAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
12 1 0.04
13 10 0.43
14 10 0.43
15 2 0.09
ACGTcount: A:0.74, C:0.00, G:0.18, T:0.08
Consensus pattern (13 bp):
GAAAAAGAAAATT
Found at i:54817113 original size:27 final size:27
Alignment explanation
Indices: 54817083--54817144 Score: 81
Period size: 27 Copynumber: 2.3 Consensus size: 27
54817073 AAAAGTGAGA
* *
54817083 GAAAAAGAAAATG-AAGAAAAGAAAATT
1 GAAAAAGAAAAAGCAAAAAAAG-AAATT
*
54817110 GAAAAAGAAAAAGCAAAAAAAGAATTT
1 GAAAAAGAAAAAGCAAAAAAAGAAATT
54817137 GAAAAAGA
1 GAAAAAGA
54817145 GTTTGAAAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
27 24 0.77
28 7 0.23
ACGTcount: A:0.71, C:0.02, G:0.18, T:0.10
Consensus pattern (27 bp):
GAAAAAGAAAAAGCAAAAAAAGAAATT
Found at i:54817117 original size:13 final size:12
Alignment explanation
Indices: 54817001--54817120 Score: 63
Period size: 12 Copynumber: 10.0 Consensus size: 12
54816991 AGAAAAAGAT
*
54817001 TGAAAAAGAAAT
1 TGAAAAAGAAAA
54817013 TG--AAAGAAAA
1 TGAAAAAGAAAA
*
54817023 -CAAAAAGAAAA
1 TGAAAAAGAAAA
*
54817034 CGAAAAAGAAAA
1 TGAAAAAGAAAA
* **
54817046 AGAAATTGCAAAA
1 TGAAAAAG-AAAA
54817059 -GAAAAAG-AAA
1 TGAAAAAGAAAA
* * *
54817069 TCAAAAAAGTGAGA
1 T-GAAAAAG-AAAA
54817083 -GAAAAAGAAAA
1 TGAAAAAGAAAA
54817094 TGAAGAAAAGAAAA
1 TG-A-AAAAGAAAA
54817108 TTGAAAAAGAAAA
1 -TGAAAAAGAAAA
54817121 AGCAAAAAAA
Statistics
Matches: 83, Mismatches: 13, Indels: 23
0.70 0.11 0.19
Matches are distributed among these distances:
10 10 0.12
11 10 0.12
12 35 0.42
13 14 0.17
14 12 0.14
15 2 0.02
ACGTcount: A:0.71, C:0.03, G:0.17, T:0.08
Consensus pattern (12 bp):
TGAAAAAGAAAA
Found at i:54817127 original size:7 final size:6
Alignment explanation
Indices: 54817015--54817128 Score: 70
Period size: 6 Copynumber: 18.5 Consensus size: 6
54817005 AAAGAAATTG
* * ** *
54817015 AAAG-A AAACAA AAAGAA AACGAA AAAGAA AAAGAA ATTGCA AAAGAA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA
* ** * * *
54817062 AAAGAA ATCA-AA AAAGTG AGAGAA AAAGAA AATGAAGA AAAGAA AATTGAA
1 AAAGAA A-AAGAA AAAGAA AAAGAA AAAGAA AAAG-A-A AAAGAA AA-AGAA
54817113 AAAGAA AAAGCAA AAA
1 AAAGAA AAAG-AA AAA
54817129 AAGAATTTGA
Statistics
Matches: 80, Mismatches: 22, Indels: 12
0.70 0.19 0.11
Matches are distributed among these distances:
5 4 0.05
6 59 0.74
7 13 0.16
8 4 0.05
ACGTcount: A:0.73, C:0.04, G:0.17, T:0.06
Consensus pattern (6 bp):
AAAGAA
Found at i:54817157 original size:12 final size:12
Alignment explanation
Indices: 54817126--54817157 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
54817116 GAAAAAGCAA
*
54817126 AAAAAGAATTTG
1 AAAAAGAGTTTG
54817138 AAAAAGAGTTTG
1 AAAAAGAGTTTG
54817150 AAAAAGAG
1 AAAAAGAG
54817158 AAGAGTGAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.59, C:0.00, G:0.22, T:0.19
Consensus pattern (12 bp):
AAAAAGAGTTTG
Found at i:54821527 original size:5 final size:5
Alignment explanation
Indices: 54821517--54821572 Score: 53
Period size: 5 Copynumber: 11.4 Consensus size: 5
54821507 AGAATAGGAC
* * *
54821517 ATGAT ATGAT ATGTT TTGAT -TCGAT ATGAT ATGAT ACG-T ATGAT ATGAT
1 ATGAT ATGAT ATGAT ATGAT AT-GAT ATGAT ATGAT ATGAT ATGAT ATGAT
*
54821566 AAGAT AT
1 ATGAT AT
54821573 AAGTTAGCTT
Statistics
Matches: 41, Mismatches: 7, Indels: 6
0.76 0.13 0.11
Matches are distributed among these distances:
4 4 0.10
5 36 0.88
6 1 0.02
ACGTcount: A:0.36, C:0.04, G:0.20, T:0.41
Consensus pattern (5 bp):
ATGAT
Found at i:54822650 original size:17 final size:17
Alignment explanation
Indices: 54822628--54822661 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
54822618 TATAAACATG
*
54822628 TTAATTTAATTTATTTT
1 TTAATTTAATGTATTTT
*
54822645 TTAATTTGATGTATTTT
1 TTAATTTAATGTATTTT
54822662 GTAGTTTTTT
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:0.26, C:0.00, G:0.06, T:0.68
Consensus pattern (17 bp):
TTAATTTAATGTATTTT
Found at i:54832323 original size:106 final size:106
Alignment explanation
Indices: 54832019--54832440 Score: 711
Period size: 106 Copynumber: 4.0 Consensus size: 106
54832009 TGGATTTAGA
* * *
54832019 TTTAATAGGATATTTGGCTATTTGGTCGAACGAGAAATCGAAACCCAGCACGTTAGGGCACATTC
1 TTTAAAAGGATATTTGGCTATTTGGTCGAACGAGAAATCGAAACCCAGCACGTTAGGGCACGTTT
*
54832084 TCTTGAATTTCCAAACGCAAAATATTGCCTTACTTTGAAAG
66 TCTCGAATTTCCAAACGCAAAATATTGCCTTACTTTGAAAG
*
54832125 TTTAAAAGGGATATTTGGCTATTTGGTCGAACGAGAAATCAAAACCCAGCACGTTAGGGCACGTT
1 TTTAAAA-GGATATTTGGCTATTTGGTCGAACGAGAAATCGAAACCCAGCACGTTAGGGCACGTT
*
54832190 TTCTCGAATTTTCAAAC-CAAAATATTGCCTTACTTTGAAAG
65 TTCTCGAATTTCCAAACGCAAAATATTGCCTTACTTTGAAAG
54832231 TTTAAAAGGATATTTGGCTATTTGGTCGAACGAGAAATCGAAACCCAGCACGTTAGGGCACGTTT
1 TTTAAAAGGATATTTGGCTATTTGGTCGAACGAGAAATCGAAACCCAGCACGTTAGGGCACGTTT
* *
54832296 TCTCGAATTTCCAAACGCGAAATATTGCCTTACTTTGAAAT
66 TCTCGAATTTCCAAACGCAAAATATTGCCTTACTTTGAAAG
* * * *
54832337 TTTGAAAGAATATTCGGCTATTTGGTCGAACGAGAAATCGAAACCCAACACGTTAGGGCACGTTT
1 TTTAAAAGGATATTTGGCTATTTGGTCGAACGAGAAATCGAAACCCAGCACGTTAGGGCACGTTT
*
54832402 TCTCGAATTTCCAAACGCAAAATATTGTCTTACTTTGAA
66 TCTCGAATTTCCAAACGCAAAATATTGCCTTACTTTGAA
54832441 TTTTTTTTGA
Statistics
Matches: 298, Mismatches: 16, Indels: 4
0.94 0.05 0.01
Matches are distributed among these distances:
105 72 0.24
106 157 0.53
107 69 0.23
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.30
Consensus pattern (106 bp):
TTTAAAAGGATATTTGGCTATTTGGTCGAACGAGAAATCGAAACCCAGCACGTTAGGGCACGTTT
TCTCGAATTTCCAAACGCAAAATATTGCCTTACTTTGAAAG
Found at i:54840809 original size:25 final size:24
Alignment explanation
Indices: 54840751--54840809 Score: 64
Period size: 25 Copynumber: 2.4 Consensus size: 24
54840741 ATAGAATTTT
* * *
54840751 TTTTAAATTATAAAAAAATTAGAA
1 TTTTAAAATATAAAAAAATAAAAA
*
54840775 TTTTAAAAATATATAAAAATAAAAA
1 TTTT-AAAATATAAAAAAATAAAAA
54840800 TTATTAAAAT
1 TT-TTAAAAT
54840810 TCATTTAAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
24 4 0.14
25 23 0.79
26 2 0.07
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (24 bp):
TTTTAAAATATAAAAAAATAAAAA
Found at i:54840854 original size:18 final size:17
Alignment explanation
Indices: 54840824--54840857 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
54840814 TTAAAATAGT
*
54840824 ATAAAATTGCAAAAAAA
1 ATAAAATTACAAAAAAA
54840841 ATAAAATTTACAAAAAA
1 ATAAAA-TTACAAAAAA
54840858 TATATATTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.71, C:0.06, G:0.03, T:0.21
Consensus pattern (17 bp):
ATAAAATTACAAAAAAA
Found at i:54840857 original size:16 final size:16
Alignment explanation
Indices: 54840836--54840893 Score: 50
Period size: 16 Copynumber: 3.7 Consensus size: 16
54840826 AAAATTGCAA
54840836 AAAAAATAAAATTTAC
1 AAAAAATAAAATTTAC
*
54840852 AAAAAAT-ATATATTA-
1 AAAAAATAAAAT-TTAC
* *
54840867 AAATTATTAAAATTT-C
1 AAA-AAATAAAATTTAC
54840883 AAAAAATAAAA
1 AAAAAATAAAA
54840894 ATAAAAAGTT
Statistics
Matches: 32, Mismatches: 6, Indels: 9
0.68 0.13 0.19
Matches are distributed among these distances:
15 12 0.38
16 17 0.53
17 3 0.09
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.29
Consensus pattern (16 bp):
AAAAAATAAAATTTAC
Found at i:54841261 original size:32 final size:33
Alignment explanation
Indices: 54841215--54841295 Score: 94
Period size: 32 Copynumber: 2.5 Consensus size: 33
54841205 AAATCAGGTG
* * *
54841215 AAAATTTTTATAATTTTTTATAAATTTAT-TTTT
1 AAAA-TTTTATAATTTTTGAAAAATTCATATTTT
**
54841248 CTAATTTTATAATTTTTGAAAAATTCATATTTT
1 AAAATTTTATAATTTTTGAAAAATTCATATTTT
54841281 AAAATTTTA-AATTTT
1 AAAATTTTATAATTTT
54841296 CTATTCTTTT
Statistics
Matches: 40, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
32 27 0.68
33 13 0.32
ACGTcount: A:0.38, C:0.02, G:0.01, T:0.58
Consensus pattern (33 bp):
AAAATTTTATAATTTTTGAAAAATTCATATTTT
Found at i:54841313 original size:18 final size:19
Alignment explanation
Indices: 54841285--54841331 Score: 62
Period size: 19 Copynumber: 2.6 Consensus size: 19
54841275 TATTTTAAAA
*
54841285 TTTTA-AATTTTCT-ATTC
1 TTTTATAATTTTATGATTC
*
54841302 TTTTATAATTTTATGATTT
1 TTTTATAATTTTATGATTC
54841321 TTTTATAATTT
1 TTTTATAATTT
54841332 GTTTTTATCA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
17 5 0.19
18 7 0.27
19 14 0.54
ACGTcount: A:0.26, C:0.04, G:0.02, T:0.68
Consensus pattern (19 bp):
TTTTATAATTTTATGATTC
Found at i:54842195 original size:52 final size:52
Alignment explanation
Indices: 54842117--54842223 Score: 178
Period size: 52 Copynumber: 2.1 Consensus size: 52
54842107 GAGAAAAATT
* * *
54842117 TAGTGCTTTCCATTGCCCTAAATTTTTCTTTGAGCCATTTACACCTTTCCTC
1 TAGTGCTTTCCATTGCCATAAATTTTTCTTTGACCCATTTACACCTTTCCCC
*
54842169 TAGTGGTTTCCATTGCCATAAATTTTTCTTTGACCCATTTACACCTTTCCCC
1 TAGTGCTTTCCATTGCCATAAATTTTTCTTTGACCCATTTACACCTTTCCCC
54842221 TAG
1 TAG
54842224 CCATTTACCA
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
52 51 1.00
ACGTcount: A:0.19, C:0.28, G:0.10, T:0.43
Consensus pattern (52 bp):
TAGTGCTTTCCATTGCCATAAATTTTTCTTTGACCCATTTACACCTTTCCCC
Found at i:54843287 original size:17 final size:16
Alignment explanation
Indices: 54843264--54843311 Score: 53
Period size: 17 Copynumber: 2.9 Consensus size: 16
54843254 TAATATATAT
54843264 ATATAAAATACAAAAAA
1 ATATAAAATA-AAAAAA
*
54843281 GTATAAACATAAAAAAA
1 ATATAAA-ATAAAAAAA
54843298 A-ATAAAAATAAAAA
1 ATAT-AAAATAAAAA
54843312 TATTTTTTAC
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
16 9 0.33
17 15 0.56
18 3 0.11
ACGTcount: A:0.77, C:0.04, G:0.02, T:0.17
Consensus pattern (16 bp):
ATATAAAATAAAAAAA
Found at i:54843296 original size:16 final size:16
Alignment explanation
Indices: 54843268--54843311 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 16
54843258 ATATATATAT
*
54843268 AAAATACAAAAAAGTATA
1 AAAATA-AAAAAA-AATA
*
54843286 AACATAAAAAAAAATA
1 AAAATAAAAAAAAATA
54843302 AAAATAAAAA
1 AAAATAAAAA
54843312 TATTTTTTAC
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
16 12 0.52
17 6 0.26
18 5 0.22
ACGTcount: A:0.80, C:0.05, G:0.02, T:0.14
Consensus pattern (16 bp):
AAAATAAAAAAAAATA
Found at i:54843440 original size:11 final size:12
Alignment explanation
Indices: 54843408--54843440 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
54843398 ATTCCCCTCT
54843408 CTTCTCT-TTCC
1 CTTCTCTCTTCC
54843419 CTTCTCTCTTCC
1 CTTCTCTCTTCC
54843431 C-TCTCTCTTC
1 CTTCTCTCTTC
54843441 TTTTTTTCTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 16 0.76
12 5 0.24
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (12 bp):
CTTCTCTCTTCC
Found at i:54843939 original size:3 final size:3
Alignment explanation
Indices: 54843905--54843967 Score: 54
Period size: 3 Copynumber: 20.3 Consensus size: 3
54843895 AATATCCTTG
* * * *
54843905 TTA TTT TTA TTA GTA TTA TTA GTA TTA CTA TTA TTA TTA TGTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA
* *
54843951 GTA TATA TTT TTA TTA T
1 TTA T-TA TTA TTA TTA T
54843968 GTACGTGTAT
Statistics
Matches: 46, Mismatches: 12, Indels: 4
0.74 0.19 0.06
Matches are distributed among these distances:
3 40 0.87
4 6 0.13
ACGTcount: A:0.30, C:0.02, G:0.06, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:54843977 original size:23 final size:23
Alignment explanation
Indices: 54843912--54843978 Score: 61
Period size: 23 Copynumber: 3.0 Consensus size: 23
54843902 TTGTTATTTT
*
54843912 TATTAGTATTAT-TAGTA-T-TA
1 TATTATTATTATGTAGTAGTATA
*
54843932 CTATTATTATTATGTATTAGTATA
1 -TATTATTATTATGTAGTAGTATA
*
54843956 TATTTTTATTATGTACGT-GTATA
1 TATTATTATTATGTA-GTAGTATA
54843979 CATATATATA
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
21 11 0.29
22 4 0.11
23 20 0.53
24 3 0.08
ACGTcount: A:0.31, C:0.03, G:0.10, T:0.55
Consensus pattern (23 bp):
TATTATTATTATGTAGTAGTATA
Found at i:54844080 original size:3 final size:3
Alignment explanation
Indices: 54844067--54844102 Score: 63
Period size: 3 Copynumber: 12.0 Consensus size: 3
54844057 TATTCCAATG
*
54844067 TTA TCA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
54844103 GTTTATGTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (3 bp):
TTA
Done.