Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr10
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: 21822658
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.32
Warning! 1067834 characters in sequence are not A, C, G, or T
File 45 of 59
Found at i:16294618 original size:27 final size:28
Alignment explanation
Indices: 16294561--16294618 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 28
16294551 GGAAAAATGT
*
16294561 CCTGGTGGTGGAAAATTACAATTTTGCC
1 CCTGGTGGTGGAAAATTACAATTTTGAC
*
16294589 CCTGG-GGTGGCAAAATTACCATTTT-AC
1 CCTGGTGGTGG-AAAATTACAATTTTGAC
16294616 CCT
1 CCT
16294619 TTTACTCCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
27 9 0.33
28 18 0.67
ACGTcount: A:0.24, C:0.22, G:0.22, T:0.31
Consensus pattern (28 bp):
CCTGGTGGTGGAAAATTACAATTTTGAC
Found at i:16294689 original size:20 final size:20
Alignment explanation
Indices: 16294672--16294709 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
16294662 CCTCAAATCT
16294672 TACTCCAATAAGTCAAATTA
1 TACTCCAATAAGTCAAATTA
16294692 TACTCCAATAAGTCAAAT
1 TACTCCAATAAGTCAAAT
16294710 GGGGCCAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.45, C:0.21, G:0.05, T:0.29
Consensus pattern (20 bp):
TACTCCAATAAGTCAAATTA
Found at i:16296412 original size:58 final size:57
Alignment explanation
Indices: 16296316--16296434 Score: 175
Period size: 58 Copynumber: 2.1 Consensus size: 57
16296306 ACAATCATCT
* * * *
16296316 AAAGTAGTTTGCATGTGATAGATTTATTTTATATGATTTAATTAATGCTATGCAATGC
1 AAAGTAGTATACATGTGATAGATTTATTTTATACGATTTAATAAATGCTATGC-ATGC
* *
16296374 AAAGTAGTATACATGTGATAGATTTATTTTATGCGATTTGATAAATGCTATGCATGC
1 AAAGTAGTATACATGTGATAGATTTATTTTATACGATTTAATAAATGCTATGCATGC
16296431 AAAG
1 AAAG
16296435 ATGAGACCTT
Statistics
Matches: 55, Mismatches: 6, Indels: 1
0.89 0.10 0.02
Matches are distributed among these distances:
57 8 0.15
58 47 0.85
ACGTcount: A:0.34, C:0.08, G:0.18, T:0.39
Consensus pattern (57 bp):
AAAGTAGTATACATGTGATAGATTTATTTTATACGATTTAATAAATGCTATGCATGC
Found at i:16320389 original size:22 final size:23
Alignment explanation
Indices: 16320355--16320405 Score: 77
Period size: 22 Copynumber: 2.3 Consensus size: 23
16320345 TCAATATGTT
*
16320355 TAAAAAAGAATAAGAAAAGAATC
1 TAAAAAAGAATAAGAAAAAAATC
*
16320378 TAAAAAA-TATAAGAAAAAAATC
1 TAAAAAAGAATAAGAAAAAAATC
16320400 TAAAAA
1 TAAAAA
16320406 TTACTCTTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
22 19 0.73
23 7 0.27
ACGTcount: A:0.73, C:0.04, G:0.08, T:0.16
Consensus pattern (23 bp):
TAAAAAAGAATAAGAAAAAAATC
Found at i:16320502 original size:41 final size:41
Alignment explanation
Indices: 16320445--16320526 Score: 121
Period size: 41 Copynumber: 2.0 Consensus size: 41
16320435 AACTTAATTT
* * *
16320445 TAATGGAAGAAGAGGAGAAGAAGTTGATGGTGTTGGAGAGA
1 TAATGGAAGAAGAGGAGAAAAAGATGATGGAGTTGGAGAGA
16320486 TAATGGACA-AAGAGGAGAAAAAGATGATGGAGTTGGAGAGA
1 TAATGGA-AGAAGAGGAGAAAAAGATGATGGAGTTGGAGAGA
16320527 GATAAAAGAT
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
41 36 0.97
42 1 0.03
ACGTcount: A:0.43, C:0.01, G:0.39, T:0.17
Consensus pattern (41 bp):
TAATGGAAGAAGAGGAGAAAAAGATGATGGAGTTGGAGAGA
Found at i:16326111 original size:29 final size:30
Alignment explanation
Indices: 16326078--16326154 Score: 79
Period size: 29 Copynumber: 2.6 Consensus size: 30
16326068 ATTCAAGAGA
*
16326078 ATTCAAATAAAGT-TTTATTTTTTTA-TTAG
1 ATTCAAATAAA-TCTTTATATTTTTATTTAG
*
16326107 ATTC-AATCAAATCTTTATATTTTTATTTTG
1 ATTCAAAT-AAATCTTTATATTTTTATTTAG
* *
16326137 AATCAAATAAACCTTTAT
1 ATTCAAATAAATCTTTAT
16326155 GACTGATGAT
Statistics
Matches: 40, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
28 4 0.10
29 18 0.45
30 15 0.38
31 3 0.08
ACGTcount: A:0.36, C:0.09, G:0.04, T:0.51
Consensus pattern (30 bp):
ATTCAAATAAATCTTTATATTTTTATTTAG
Found at i:16326153 original size:30 final size:29
Alignment explanation
Indices: 16326075--16326154 Score: 72
Period size: 30 Copynumber: 2.7 Consensus size: 29
16326065 ATTATTCAAG
** *
16326075 AGAATTCAAATAAAGTTTTATTTTTTTATT
1 AGAA-TCAAATAAACCTTTATATTTTTATT
* *
16326105 AGATTC-AATCAAATCTTTATATTTTTATTT
1 AGAATCAAAT-AAACCTTTATATTTTTA-TT
*
16326135 TGAATCAAATAAACCTTTAT
1 AGAATCAAATAAACCTTTAT
16326155 GACTGATGAT
Statistics
Matches: 40, Mismatches: 7, Indels: 6
0.75 0.13 0.11
Matches are distributed among these distances:
28 3 0.08
29 16 0.40
30 18 0.45
31 3 0.08
ACGTcount: A:0.38, C:0.09, G:0.05, T:0.49
Consensus pattern (29 bp):
AGAATCAAATAAACCTTTATATTTTTATT
Found at i:16328274 original size:249 final size:246
Alignment explanation
Indices: 16327956--16328451 Score: 845
Period size: 244 Copynumber: 2.0 Consensus size: 246
16327946 TCTACTCTAT
*
16327956 TTTGTTTCACAAGCATTGGGTGTCACAAAAACTTTAACAAAGTTTAACTCATTCAGATTTGTTTT
1 TTTGTTTCACAAGCATTGAGTGTCACAAAAACTTTAACAAAGTTTAACTCATTCAGATTTGTTTT
16328021 CCTTTCTCAGGTTACATTTAGACCAGCAAG-AAGAAAAGGGTGAGGGGACAACCCTGAGCGAAGC
66 CCTTTCTCA-G----A-TTAGACCAGCAAGAAAGAAAAGGGTGAGGGGACAACCCTGAGCGAAGC
*
16328085 ATCTGTTAATTCATTTTGAATCCTTAGGCTCAACATTTACAAATT-A-ATTAGTATGCATCCTCT
125 ATCTGTTAATTCATTTTGAATCCTTAGGCCCAACATTTACAAATTAATATTAGTATGCATCCTCT
16328148 GCCCTAAATGCAACTGGCAACAGGTCAGCAGACACAGCGAAAGCCACCTTAACGGCA
190 GCCCTAAATGCAACTGGCAACAGGTCAGCAGACACAGCGAAAGCCACCTTAACGGCA
* *
16328205 TTTGTTTCACAAGCATTGATTGTCACAAAAACTTTAACAAAGTTTAACTCATTCGGATTTGTTTT
1 TTTGTTTCACAAGCATTGAGTGTCACAAAAACTTTAACAAAGTTTAACTCATTCAGATTTGTTTT
*
16328270 CCTTTCTCAGATTAGACCAGCAAGAAAGAAAAGGGTGAGGGGACAACCCTGAGCGAAGCCTCTGT
66 CCTTTCTCAGATTAGACCAGCAAGAAAGAAAAGGGTGAGGGGACAACCCTGAGCGAAGCATCTGT
*
16328335 TAATTCATTTTGAATCCTTAGGCCCAACATTTACAAATTAATTATTAGTATGCGTCCTCTGCCCT
131 TAATTCATTTTGAATCCTTAGGCCCAACATTTACAAATTAA-TATTAGTATGCATCCTCTGCCCT
*
16328400 AAATGCAACTGGCAACAGGTCAGCAGACACAGCTAAAGCCACCTTAACGGCA
195 AAATGCAACTGGCAACAGGTCAGCAGACACAGCGAAAGCCACCTTAACGGCA
16328452 AGCCAACACA
Statistics
Matches: 236, Mismatches: 7, Indels: 10
0.93 0.03 0.04
Matches are distributed among these distances:
243 13 0.06
244 78 0.33
245 1 0.00
247 72 0.31
248 1 0.00
249 71 0.30
ACGTcount: A:0.32, C:0.22, G:0.18, T:0.28
Consensus pattern (246 bp):
TTTGTTTCACAAGCATTGAGTGTCACAAAAACTTTAACAAAGTTTAACTCATTCAGATTTGTTTT
CCTTTCTCAGATTAGACCAGCAAGAAAGAAAAGGGTGAGGGGACAACCCTGAGCGAAGCATCTGT
TAATTCATTTTGAATCCTTAGGCCCAACATTTACAAATTAATATTAGTATGCATCCTCTGCCCTA
AATGCAACTGGCAACAGGTCAGCAGACACAGCGAAAGCCACCTTAACGGCA
Found at i:16334836 original size:26 final size:26
Alignment explanation
Indices: 16334758--16334836 Score: 97
Period size: 26 Copynumber: 3.0 Consensus size: 26
16334748 TAGAATCTAA
*
16334758 GGATAATTTTGCCACCAGAAGTGGAT
1 GGATAATTTTGCCACCAAAAGTGGAT
* *
16334784 AGATAATTTTGCCACCAATAA-TAGAT
1 GGATAATTTTGCCACCAA-AAGTGGAT
* *
16334810 GGGTAATTTTACCACCAAAAGTGGAT
1 GGATAATTTTGCCACCAAAAGTGGAT
16334836 G
1 G
16334837 AATACCGTAA
Statistics
Matches: 44, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
25 2 0.05
26 40 0.91
27 2 0.05
ACGTcount: A:0.35, C:0.15, G:0.22, T:0.28
Consensus pattern (26 bp):
GGATAATTTTGCCACCAAAAGTGGAT
Found at i:16336420 original size:18 final size:19
Alignment explanation
Indices: 16336396--16336439 Score: 81
Period size: 18 Copynumber: 2.4 Consensus size: 19
16336386 CTTCTTTTTT
16336396 ATATTATTTCTTTTACAAC
1 ATATTATTTCTTTTACAAC
16336415 -TATTATTTCTTTTACAAC
1 ATATTATTTCTTTTACAAC
16336433 ATATTAT
1 ATATTAT
16336440 CAGCACGAGG
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
18 18 0.75
19 6 0.25
ACGTcount: A:0.32, C:0.14, G:0.00, T:0.55
Consensus pattern (19 bp):
ATATTATTTCTTTTACAAC
Found at i:16338238 original size:32 final size:32
Alignment explanation
Indices: 16338202--16338350 Score: 122
Period size: 35 Copynumber: 4.5 Consensus size: 32
16338192 TTTACCGGGA
*
16338202 TCAACTAAAACCCAAAGTGGTTTTTCAAAGGC
1 TCAACCAAAACCCAAAGTGGTTTTTCAAAGGC
* **
16338234 TCAACCACAACCTGTCACAA-TGGTTTTTCACGGGC
1 TCAACCAAAACC---CA-AAGTGGTTTTTCAAAGGC
**
16338269 TCAACCAAAAATCAAAGTGGTTTTTCAAAGGC
1 TCAACCAAAACCCAAAGTGGTTTTTCAAAGGC
* * * *
16338301 TCAACCACAACCTACAACAATGGTTTTTCACTAGAC
1 TCAACCAAAACC--CAA-AGTGGTTTTTCA-AAGGC
16338337 T-AACCAAAACCCAA
1 TCAACCAAAACCCAA
16338351 CAACTAACTT
Statistics
Matches: 92, Mismatches: 16, Indels: 17
0.74 0.13 0.14
Matches are distributed among these distances:
31 2 0.02
32 34 0.37
33 3 0.03
34 3 0.03
35 44 0.48
36 6 0.07
ACGTcount: A:0.37, C:0.27, G:0.13, T:0.23
Consensus pattern (32 bp):
TCAACCAAAACCCAAAGTGGTTTTTCAAAGGC
Found at i:16338258 original size:35 final size:34
Alignment explanation
Indices: 16338219--16338330 Score: 131
Period size: 35 Copynumber: 3.3 Consensus size: 34
16338209 AAACCCAAAG
16338219 TGGTTTTTCAAAGGCTCAACCACAACCTGTCACAA
1 TGGTTTTTCAAAGGCTCAACCACAACCT-TCACAA
** **
16338254 TGGTTTTTCACGGGCTCAACCA-AA-AATCA-AA
1 TGGTTTTTCAAAGGCTCAACCACAACCTTCACAA
*
16338285 GTGGTTTTTCAAAGGCTCAACCACAACCTACAACAA
1 -TGGTTTTTCAAAGGCTCAACCACAACCTTC-ACAA
16338321 TGGTTTTTCA
1 TGGTTTTTCA
16338331 CTAGACTAAC
Statistics
Matches: 63, Mismatches: 9, Indels: 10
0.77 0.11 0.12
Matches are distributed among these distances:
31 2 0.03
32 23 0.37
33 2 0.03
34 3 0.05
35 31 0.49
36 2 0.03
ACGTcount: A:0.32, C:0.25, G:0.15, T:0.28
Consensus pattern (34 bp):
TGGTTTTTCAAAGGCTCAACCACAACCTTCACAA
Found at i:16338342 original size:67 final size:67
Alignment explanation
Indices: 16338214--16338345 Score: 205
Period size: 67 Copynumber: 2.0 Consensus size: 67
16338204 AACTAAAACC
* * *
16338214 CAAAGTGGTTTTTCAAAGGCTCAACCACAACCTGTCACAATGGTTTTTCACGGGCTCAACCAAAA
1 CAAAGTGGTTTTTCAAAGGCTCAACCACAACCTGACACAATGGTTTTTCACAGACTCAACCAAAA
16338279 AT
66 AT
16338281 CAAAGTGGTTTTTCAAAGGCTCAACCACAACCT-ACAACAATGGTTTTTCACTAGACT-AACCAA
1 CAAAGTGGTTTTTCAAAGGCTCAACCACAACCTGAC-ACAATGGTTTTTCAC-AGACTCAACCAA
16338344 AA
64 AA
16338346 CCCAACAACT
Statistics
Matches: 60, Mismatches: 3, Indels: 4
0.90 0.04 0.06
Matches are distributed among these distances:
66 1 0.02
67 56 0.93
68 3 0.05
ACGTcount: A:0.36, C:0.25, G:0.14, T:0.25
Consensus pattern (67 bp):
CAAAGTGGTTTTTCAAAGGCTCAACCACAACCTGACACAATGGTTTTTCACAGACTCAACCAAAA
AT
Found at i:16339739 original size:55 final size:53
Alignment explanation
Indices: 16339647--16339832 Score: 187
Period size: 55 Copynumber: 3.4 Consensus size: 53
16339637 GTTAGAGTTA
*
16339647 TTTTAGCGTGTCACGACTATTCTTGGTGTGTTG-TGGGTTAACTAATTATTTGGGT
1 TTTTAGCGTGTCACGACTGTTCTTGG-GTG-TGCTGGGTTAACTAATT-TTTGGGT
* * * * *
16339702 TGTTAGCGTATCACGGCTGTTCTTAGGGTGTGCTGGGTTAATTGAATTTATGGGT
1 TTTTAGCGTGTCACGACTGTTCTT-GGGTGTGCTGGGTTAACT-AATTTTTGGGT
* * * *
16339757 TTTTGGCGTGTCACGGCTGTTCCT-GGTGTGTCGTGGGTTAACTGATTTTTTGGGT
1 TTTTAGCGTGTCACGACTGTTCTTGGGTGTG-C-TGGGTTAACT-AATTTTTGGGT
*
16339812 TTTTAGTGTGTCACGACTGTT
1 TTTTAGCGTGTCACGACTGTT
16339833 GGTGTAACCA
Statistics
Matches: 110, Mismatches: 16, Indels: 10
0.81 0.12 0.07
Matches are distributed among these distances:
53 6 0.05
54 3 0.03
55 95 0.86
56 6 0.05
ACGTcount: A:0.13, C:0.12, G:0.31, T:0.44
Consensus pattern (53 bp):
TTTTAGCGTGTCACGACTGTTCTTGGGTGTGCTGGGTTAACTAATTTTTGGGT
Found at i:16339937 original size:31 final size:31
Alignment explanation
Indices: 16339902--16339983 Score: 94
Period size: 31 Copynumber: 2.6 Consensus size: 31
16339892 AACAATACTG
*
16339902 ATGCATGGCGTGTCACGACATTTGACT-TGAT
1 ATGCATGGCGTGTCACAACATTTGA-TGTGAT
* * *
16339933 ATGCATGGCGTGTTACAACATTTTATGTTAT
1 ATGCATGGCGTGTCACAACATTTGATGTGAT
* *
16339964 ATGCATGGCATGTAACAACA
1 ATGCATGGCGTGTCACAACA
16339984 CGACTGACAA
Statistics
Matches: 44, Mismatches: 6, Indels: 2
0.85 0.12 0.04
Matches are distributed among these distances:
30 1 0.02
31 43 0.98
ACGTcount: A:0.28, C:0.17, G:0.22, T:0.33
Consensus pattern (31 bp):
ATGCATGGCGTGTCACAACATTTGATGTGAT
Found at i:16343503 original size:31 final size:31
Alignment explanation
Indices: 16343457--16343640 Score: 221
Period size: 31 Copynumber: 6.0 Consensus size: 31
16343447 AATAAGGAAT
*
16343457 AAATG-TGAGACACGCCATGCATAACAAGTA
1 AAATGTTGTGACACGCCATGCATAACAAGTA
* * *
16343487 AAATGTTGTGACACGCCGTGCATATCAAATA
1 AAATGTTGTGACACGCCATGCATAACAAGTA
* * *
16343518 AAATATT-TGGACACGCCATGCATAAGAAGAA
1 AAATGTTGT-GACACGCCATGCATAACAAGTA
* * *
16343549 AAATTTTATGACACGCCGTGCATAACAAGTA
1 AAATGTTGTGACACGCCATGCATAACAAGTA
*
16343580 AAATGTTGTGACACGCCATGTATAACAAGTA
1 AAATGTTGTGACACGCCATGCATAACAAGTA
*
16343611 AATTG-TGCTGACACGCCATGCATAACAAGT
1 AAATGTTG-TGACACGCCATGCATAACAAGT
16343641 TCTGGTGTGT
Statistics
Matches: 130, Mismatches: 20, Indels: 7
0.83 0.13 0.04
Matches are distributed among these distances:
30 8 0.06
31 121 0.93
32 1 0.01
ACGTcount: A:0.39, C:0.19, G:0.19, T:0.23
Consensus pattern (31 bp):
AAATGTTGTGACACGCCATGCATAACAAGTA
Found at i:16343583 original size:93 final size:92
Alignment explanation
Indices: 16343465--16343635 Score: 254
Period size: 93 Copynumber: 1.8 Consensus size: 92
16343455 ATAAATGTGA
* * *
16343465 GACACGCCATGCATAACAAGTAAAATGTTGTGACACGCCGTGCATATCAAATAAAATATTTG-GA
1 GACACGCCATGCATAACAAGTAAAATGTTGTGACACGCCATGCATAACAAAT-AAAT-TGTGCGA
16343529 CACGCCATGCATAAGAAGAAAAATTTTAT
64 CACGCCATGCATAAGAAGAAAAATTTTAT
* * *
16343558 GACACGCCGTGCATAACAAGTAAAATGTTGTGACACGCCATGTATAACAAGTAAATTGTGCTGAC
1 GACACGCCATGCATAACAAGTAAAATGTTGTGACACGCCATGCATAACAAATAAATTGTGC-GAC
16343623 ACGCCATGCATAA
65 ACGCCATGCATAA
16343636 CAAGTTCTGG
Statistics
Matches: 70, Mismatches: 6, Indels: 4
0.88 0.08 0.05
Matches are distributed among these distances:
91 3 0.04
92 4 0.06
93 63 0.90
ACGTcount: A:0.39, C:0.20, G:0.19, T:0.23
Consensus pattern (92 bp):
GACACGCCATGCATAACAAGTAAAATGTTGTGACACGCCATGCATAACAAATAAATTGTGCGACA
CGCCATGCATAAGAAGAAAAATTTTAT
Found at i:16344751 original size:14 final size:15
Alignment explanation
Indices: 16344732--16344792 Score: 63
Period size: 14 Copynumber: 4.1 Consensus size: 15
16344722 TATATCTGTT
*
16344732 TACAATGAAT-TGTA
1 TACAATAAATGTGTA
16344746 TACAATAAACTGTGTA
1 TACAATAAA-TGTGTA
*
16344762 TACAAAAAATGTGTA
1 TACAATAAATGTGTA
* *
16344777 TAAAATGAAT-TGTA
1 TACAATAAATGTGTA
16344791 TA
1 TA
16344793 TAAAAATTTC
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
14 14 0.35
15 14 0.35
16 12 0.30
ACGTcount: A:0.48, C:0.07, G:0.13, T:0.33
Consensus pattern (15 bp):
TACAATAAATGTGTA
Found at i:16344776 original size:15 final size:16
Alignment explanation
Indices: 16344742--16344778 Score: 58
Period size: 15 Copynumber: 2.4 Consensus size: 16
16344732 TACAATGAAT
*
16344742 TGTATACAATAAACTG
1 TGTATACAATAAAATG
16344758 TGTATACAA-AAAATG
1 TGTATACAATAAAATG
16344773 TGTATA
1 TGTATA
16344779 AAATGAATTG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 11 0.55
16 9 0.45
ACGTcount: A:0.46, C:0.08, G:0.14, T:0.32
Consensus pattern (16 bp):
TGTATACAATAAAATG
Found at i:16346317 original size:31 final size:31
Alignment explanation
Indices: 16346279--16346574 Score: 301
Period size: 31 Copynumber: 9.5 Consensus size: 31
16346269 AACCATAGAT
*
16346279 AGTAAAATGTTGTGACACG-CAGTGCATACCA
1 AGTAAAATGTTGTGACACGCCA-TGCATAACA
* *
16346310 AGTAAAATGTTGTCACACGCCATGCAAAACA
1 AGTAAAATGTTGTGACACGCCATGCATAACA
*
16346341 AGTAAAATGTCGTGACACGCCATGCATAACA
1 AGTAAAATGTTGTGACACGCCATGCATAACA
* * * * *
16346372 AGATAAACT-TGGTGACACGCCAAGGATAACG
1 AG-TAAAATGTTGTGACACGCCATGCATAACA
* * * *
16346403 AGGAAAATGTTGTGACACTCCATGCAAAATA
1 AGTAAAATGTTGTGACACGCCATGCATAACA
16346434 AGTAAAATGTTGTGACACGCCATGCATAACA
1 AGTAAAATGTTGTGACACGCCATGCATAACA
* * * * *
16346465 AGATAAACT-TGGTGACACGTCAAGGATAACA
1 AG-TAAAATGTTGTGACACGCCATGCATAACA
* * **
16346496 AGCAAAATGTTTTGACACGCCATGCATGTCA
1 AGTAAAATGTTGTGACACGCCATGCATAACA
* * * *
16346527 AATCAAACGTTGTGACACGCCATGAATAACA
1 AGTAAAATGTTGTGACACGCCATGCATAACA
*
16346558 AGTAAAATATTGTGACA
1 AGTAAAATGTTGTGACA
16346575 TGCTAAAGCT
Statistics
Matches: 210, Mismatches: 50, Indels: 10
0.78 0.19 0.04
Matches are distributed among these distances:
30 8 0.04
31 190 0.90
32 12 0.06
ACGTcount: A:0.40, C:0.19, G:0.20, T:0.21
Consensus pattern (31 bp):
AGTAAAATGTTGTGACACGCCATGCATAACA
Found at i:16346449 original size:93 final size:93
Alignment explanation
Indices: 16346308--16346563 Score: 354
Period size: 93 Copynumber: 2.8 Consensus size: 93
16346298 CAGTGCATAC
* * * *
16346308 CAAGTAAAATGTTGTCACACGCCATGCAAAACAAGTAAAATGTCGTGACACGCCATGCATAACAA
1 CAAGCAAAATGTTGTGACACGCCATGCAAAATAAGTAAAATGTTGTGACACGCCATGCATAACAA
16346373 GATAAACTTGGTGACACGCCAAGGATAA
66 GATAAACTTGGTGACACGCCAAGGATAA
* * *
16346401 CGAGGAAAATGTTGTGACACTCCATGCAAAATAAGTAAAATGTTGTGACACGCCATGCATAACAA
1 CAAGCAAAATGTTGTGACACGCCATGCAAAATAAGTAAAATGTTGTGACACGCCATGCATAACAA
*
16346466 GATAAACTTGGTGACACGTCAAGGATAA
66 GATAAACTTGGTGACACGCCAAGGATAA
* ** * * * *
16346494 CAAGCAAAATGTTTTGACACGCCATGC-ATGTCAAATCAAACGTTGTGACACGCCATGAATAACA
1 CAAGCAAAATGTTGTGACACGCCATGCAAAAT-AAGTAAAATGTTGTGACACGCCATGCATAACA
16346558 AG-TAAA
65 AGATAAA
16346564 ATATTGTGAC
Statistics
Matches: 145, Mismatches: 17, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
92 6 0.04
93 139 0.96
ACGTcount: A:0.40, C:0.20, G:0.20, T:0.20
Consensus pattern (93 bp):
CAAGCAAAATGTTGTGACACGCCATGCAAAATAAGTAAAATGTTGTGACACGCCATGCATAACAA
GATAAACTTGGTGACACGCCAAGGATAA
Found at i:16346573 original size:93 final size:92
Alignment explanation
Indices: 16346281--16346574 Score: 333
Period size: 93 Copynumber: 3.2 Consensus size: 92
16346271 CCATAGATAG
* * * * *
16346281 TAAAATGTTGTGACACGC-AGTGCATACCAAGTAAAATGTTGTCACACGCCATGCAAAACAAGTA
1 TAAAAT-TGGTGACACGCAAG-G-ATAACAAGCAAAATGTTGTGACACGCCATGCAAATCAAGTA
*
16346345 AAATGTCGTGACACGCCATGCATAACAAGA
63 AAATGTTGTGACACGCCATGCATAACAAGA
* * * *
16346375 TAAACTTGGTGACACGCCAAGGATAACGAGGAAAATGTTGTGACACTCCATGCAAAAT-AAGTAA
1 TAAAATTGGTGACACG-CAAGGATAACAAGCAAAATGTTGTGACACGCCATGC-AAATCAAGTAA
16346439 AATGTTGTGACACGCCATGCATAACAAGA
64 AATGTTGTGACACGCCATGCATAACAAGA
* * ** * *
16346468 TAAACTTGGTGACACGTCAAGGATAACAAGCAAAATGTTTTGACACGCCATGCATGTCAAATCAA
1 TAAAATTGGTGACACG-CAAGGATAACAAGCAAAATGTTGTGACACGCCATGCAAATCAAGTAAA
* *
16346533 ACGTTGTGACACGCCATGAATAACAAG-
65 ATGTTGTGACACGCCATGCATAACAAGA
*
16346560 TAAAATATTGTGACA
1 TAAAAT-TGGTGACA
16346575 TGCTAAAGCT
Statistics
Matches: 173, Mismatches: 22, Indels: 11
0.84 0.11 0.05
Matches are distributed among these distances:
92 7 0.04
93 154 0.89
94 10 0.06
95 2 0.01
ACGTcount: A:0.39, C:0.19, G:0.20, T:0.21
Consensus pattern (92 bp):
TAAAATTGGTGACACGCAAGGATAACAAGCAAAATGTTGTGACACGCCATGCAAATCAAGTAAAA
TGTTGTGACACGCCATGCATAACAAGA
Found at i:16347227 original size:156 final size:156
Alignment explanation
Indices: 16346943--16347237 Score: 450
Period size: 156 Copynumber: 1.9 Consensus size: 156
16346933 CTACAATAAC
* *
16346943 ATATATAACTGTGTTATTCAATAATCATATATGGAATTGATGAACATTAACCGTTATAACTTTAA
1 ATATATAACTGTGTTATTCAATAATCATATATGGAATTGATGAACATGAACCGTTACAACTTTAA
* * *
16347008 TATCCTAACCGACGGCTCGTTAGCAGTTTGTGGTGGAGCTGGACCGATCGGTGCTTGAAGACCTG
66 TATCCTAACCGACGACTCGTTAGCAGTCTGCGGTGGAGCTGGACCGATCGGTGCTTGAAGACCTG
16347073 TCGTCACTTCCGCATGCTGCAATTAG
131 TCGTCACTTCCGCATGCTGCAATTAG
* *
16347099 ATATATAACTGTGTTATTCAATAATCATGTATGGAATTGTTGAACATGAACCGTTACAACTTTAA
1 ATATATAACTGTGTTATTCAATAATCATATATGGAATTGATGAACATGAACCGTTACAACTTTAA
* * * **
16347164 TATCCTTACC-ACCTACTCGTTAGCTGTCTGCGGTGGAG-TCGGACCGATCGGTGCTTGTGGACC
66 TATCCTAACCGA-CGACTCGTTAGCAGTCTGCGGTGGAGCT-GGACCGATCGGTGCTTGAAGACC
16347227 TGTCGTCACTT
129 TGTCGTCACTT
16347238 TTGCACCGAC
Statistics
Matches: 125, Mismatches: 12, Indels: 4
0.89 0.09 0.03
Matches are distributed among these distances:
155 2 0.02
156 123 0.98
ACGTcount: A:0.26, C:0.20, G:0.21, T:0.33
Consensus pattern (156 bp):
ATATATAACTGTGTTATTCAATAATCATATATGGAATTGATGAACATGAACCGTTACAACTTTAA
TATCCTAACCGACGACTCGTTAGCAGTCTGCGGTGGAGCTGGACCGATCGGTGCTTGAAGACCTG
TCGTCACTTCCGCATGCTGCAATTAG
Found at i:16348860 original size:31 final size:31
Alignment explanation
Indices: 16348822--16349087 Score: 284
Period size: 31 Copynumber: 8.6 Consensus size: 31
16348812 AATAAGGAAT
* **
16348822 AAATGTTGTGACATGCCATGCATTGCAA-TCA
1 AAATGTTGTGACACGCCATGCATAACAAGT-A
*
16348853 AAATGTTGTGACACGCCATGTATAACAAGTA
1 AAATGTTGTGACACGCCATGCATAACAAGTA
* *
16348884 AAATGTTGTGACACGCCATGAATAACAAGTT
1 AAATGTTGTGACACGCCATGCATAACAAGTA
* * *
16348915 AAACGTTATGACACGCCATGCATATCAAGTA
1 AAATGTTGTGACACGCCATGCATAACAAGTA
* *
16348946 AAATGCTGTCACACGCCATGCATAACAAGTA
1 AAATGTTGTGACACGCCATGCATAACAAGTA
* * * *
16348977 AAAT-TCTATGACATGACATGCATATCAAGTA
1 AAATGT-TGTGACACGCCATGCATAACAAGTA
* * * *
16349008 AAATGCTGTCACACACCATGCATATCAAGTA
1 AAATGTTGTGACACGCCATGCATAACAAGTA
* * * *
16349039 AAATGCTGTCACACGCTATGCATATCAAGTA
1 AAATGTTGTGACACGCCATGCATAACAAGTA
*
16349070 AAATGTTGTCACACGCCA
1 AAATGTTGTGACACGCCA
16349088 ATAACTAACT
Statistics
Matches: 200, Mismatches: 32, Indels: 6
0.84 0.13 0.03
Matches are distributed among these distances:
31 199 1.00
32 1 0.00
ACGTcount: A:0.38, C:0.21, G:0.17, T:0.25
Consensus pattern (31 bp):
AAATGTTGTGACACGCCATGCATAACAAGTA
Found at i:16349621 original size:53 final size:52
Alignment explanation
Indices: 16349553--16349664 Score: 152
Period size: 53 Copynumber: 2.1 Consensus size: 52
16349543 TCTATTTCAA
* * * *
16349553 ACCATGACGTGTCAGCTGCTCAAGCACTGTCGTGTCACACACTCTAAACCATG
1 ACCATGGCGTATCAGCTGCTCAAGCAATGCCGTGTCACACACTCTAAA-CATG
**
16349606 ACCATGGCGTATCAGCTTTTCAAGCAATGCCGTGTCACACACTCTAAACATG
1 ACCATGGCGTATCAGCTGCTCAAGCAATGCCGTGTCACACACTCTAAACATG
*
16349658 ATCATGG
1 ACCATGG
16349665 GTTGTCACCA
Statistics
Matches: 52, Mismatches: 7, Indels: 1
0.87 0.12 0.02
Matches are distributed among these distances:
52 10 0.19
53 42 0.81
ACGTcount: A:0.28, C:0.29, G:0.19, T:0.24
Consensus pattern (52 bp):
ACCATGGCGTATCAGCTGCTCAAGCAATGCCGTGTCACACACTCTAAACATG
Found at i:16349740 original size:47 final size:47
Alignment explanation
Indices: 16349669--16350032 Score: 326
Period size: 47 Copynumber: 7.8 Consensus size: 47
16349659 TCATGGGTTG
* * * **
16349669 TCACCAACTCTGAACTCTGGCGTGTCACAGATTCCCTCCATGTAGTC
1 TCACCAACTTTGAACGCTGACGTGTCACAGATTCCCTCCATGGCGTC
* * *
16349716 TCACCAACTTTGAACGCTGACGTGTCACAGATTCTCTCCATGGTGTG
1 TCACCAACTTTGAACGCTGACGTGTCACAGATTCCCTCCATGGCGTC
* * * ** *
16349763 TCACCAACTCTT-AACTCT-AGCATCTCACAGATTCAATCCATGGCGTT
1 TCACCAACT-TTGAACGCTGA-CGTGTCACAGATTCCCTCCATGGCGTC
* * *
16349810 TCACCAACTTTGAACGCTTGA-GTGTCACAGGTTCCCTCCATGCCGTG
1 TCACCAACTTTGAACGC-TGACGTGTCACAGATTCCCTCCATGGCGTC
** *
16349857 TCACCAACTCTT-AA-TTTGGCGTGTCACAGATTCCCTCCATGGCGTC
1 TCACCAACT-TTGAACGCTGACGTGTCACAGATTCCCTCCATGGCGTC
* * * * *
16349903 TCACTAACTCTGAACGCTG-CTGTGTCACAGATTCCCACCATGGCATG
1 TCACCAACTTTGAACGCTGAC-GTGTCACAGATTCCCTCCATGGCGTC
* * ** *
16349950 TCACCAACTCTGAACTCTGGTGTCTCACAGATTCCCTCCATGGCGTC
1 TCACCAACTTTGAACGCTGACGTGTCACAGATTCCCTCCATGGCGTC
** * * *
16349997 TCACCAACTTTGAGTGGTGTCGTGTCACACATTCCC
1 TCACCAACTTTGAACGCTGACGTGTCACAGATTCCC
16350033 AACATGACGT
Statistics
Matches: 255, Mismatches: 51, Indels: 22
0.78 0.16 0.07
Matches are distributed among these distances:
45 3 0.01
46 37 0.15
47 209 0.82
48 5 0.02
49 1 0.00
ACGTcount: A:0.21, C:0.32, G:0.18, T:0.29
Consensus pattern (47 bp):
TCACCAACTTTGAACGCTGACGTGTCACAGATTCCCTCCATGGCGTC
Found at i:16349821 original size:94 final size:94
Alignment explanation
Indices: 16349667--16350032 Score: 459
Period size: 94 Copynumber: 3.9 Consensus size: 94
16349657 GATCATGGGT
* **
16349667 TGTCACCAACTCTGAACTCTGGCGTGTCACAGATTCCCTCCATGTAGTCTCACCAACTTTGAACG
1 TGTCACCAACTCTGAACTCTGGCGTCTCACAGATTCCCTCCATGGCGTCTCACCAACTTTGAACG
* *
16349732 CTGACGTGTCACAGATTCTCTCCATGGTG
66 CTGACGTGTCACAGATTCCCTCCATGGCG
* * * ** *
16349761 TGTCACCAACTCTTAACTCTAGCATCTCACAGATTCAATCCATGGCGTTTCACCAACTTTGAACG
1 TGTCACCAACTCTGAACTCTGGCGTCTCACAGATTCCCTCCATGGCGTCTCACCAACTTTGAACG
* *
16349826 CTTGA-GTGTCACAGGTTCCCTCCATGCCG
66 C-TGACGTGTCACAGATTCCCTCCATGGCG
* * * * *
16349855 TGTCACCAACTCTTAA-TTTGGCGTGTCACAGATTCCCTCCATGGCGTCTCACTAACTCTGAACG
1 TGTCACCAACTCTGAACTCTGGCGTCTCACAGATTCCCTCCATGGCGTCTCACCAACTTTGAACG
* *
16349919 CTG-CTGTGTCACAGATTCCCACCATGGCA
66 CTGAC-GTGTCACAGATTCCCTCCATGGCG
* **
16349948 TGTCACCAACTCTGAACTCTGGTGTCTCACAGATTCCCTCCATGGCGTCTCACCAACTTTGAGTG
1 TGTCACCAACTCTGAACTCTGGCGTCTCACAGATTCCCTCCATGGCGTCTCACCAACTTTGAACG
* * *
16350013 GTGTCGTGTCACACATTCCC
66 CTGACGTGTCACAGATTCCC
16350033 AACATGACGT
Statistics
Matches: 231, Mismatches: 36, Indels: 10
0.83 0.13 0.04
Matches are distributed among these distances:
92 2 0.01
93 75 0.32
94 150 0.65
95 4 0.02
ACGTcount: A:0.21, C:0.32, G:0.18, T:0.29
Consensus pattern (94 bp):
TGTCACCAACTCTGAACTCTGGCGTCTCACAGATTCCCTCCATGGCGTCTCACCAACTTTGAACG
CTGACGTGTCACAGATTCCCTCCATGGCG
Found at i:16350025 original size:187 final size:188
Alignment explanation
Indices: 16349667--16350009 Score: 510
Period size: 187 Copynumber: 1.8 Consensus size: 188
16349657 GATCATGGGT
* *
16349667 TGTCACCAACTCTGAACTCTGGCGTGTCACAGATTCCCTCCATGTAGTCTCACCAACTTTGAACG
1 TGTCACCAACTCTGAACTCTGGCGTGTCACAGATTCCCTCCATGGAGTCTCACCAACTCTGAACG
* * ** *
16349732 CTGACGTGTCACAGATTCTCTCCATGGTGTGTCACCAACTCTTAACTCTAGCATCTCACAGATTC
66 CTGACGTGTCACAGATTCCCACCATGGCATGTCACCAACTCTGAACTCTAGCATCTCACAGATTC
*
16349797 AATCCATGGCGTTTCACCAACTTTGAACGCTTGAGTGTCACAGGTTCCCTCCATGCCG
131 AATCCATGGCGTCTCACCAACTTTGAACGCTTGAGTGTCACAGGTTCCCTCCATGCCG
* * * *
16349855 TGTCACCAACTCTTAA-TTTGGCGTGTCACAGATTCCCTCCATGGCGTCTCACTAACTCTGAACG
1 TGTCACCAACTCTGAACTCTGGCGTGTCACAGATTCCCTCCATGGAGTCTCACCAACTCTGAACG
* **
16349919 CTG-CTGTGTCACAGATTCCCACCATGGCATGTCACCAACTCTGAACTCTGGTGTCTCACAGATT
66 CTGAC-GTGTCACAGATTCCCACCATGGCATGTCACCAACTCTGAACTCTAGCATCTCACAGATT
**
16349983 CCCTCCATGGCGTCTCACCAACTTTGA
130 CAATCCATGGCGTCTCACCAACTTTGA
16350010 GTGGTGTCGT
Statistics
Matches: 137, Mismatches: 17, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
186 1 0.01
187 121 0.88
188 15 0.11
ACGTcount: A:0.22, C:0.32, G:0.17, T:0.29
Consensus pattern (188 bp):
TGTCACCAACTCTGAACTCTGGCGTGTCACAGATTCCCTCCATGGAGTCTCACCAACTCTGAACG
CTGACGTGTCACAGATTCCCACCATGGCATGTCACCAACTCTGAACTCTAGCATCTCACAGATTC
AATCCATGGCGTCTCACCAACTTTGAACGCTTGAGTGTCACAGGTTCCCTCCATGCCG
Found at i:16350804 original size:144 final size:143
Alignment explanation
Indices: 16350543--16350830 Score: 558
Period size: 144 Copynumber: 2.0 Consensus size: 143
16350533 TCAACATTCT
*
16350543 CTATCTCTTATTTTTTATGATCACAAAACACTCCAAGATTAATAATGCAATGTCTATGTTCAATA
1 CTATCTCTTATTTTTGATGATCACAAAACACTCCAAGATTAATAATGCAATGTCTATGTTCAATA
16350608 TGAATGTTTCAAATCTTTATGCATAATGAGGTGCTCCCCCTTAGTCAATGCATCTACTTTTCTTT
66 TGAATGTTTCAAATCTTTATGCATAATGAGGTGCTCCCCCTTAGTCAATGCATCTACTTTTCTTT
16350673 ACATAATATTCAA
131 ACATAATATTCAA
16350686 CNTATCTCTTATTTTTGATGATCACAAAACACTCCAAGATTAATAATGCAATGTCTATGTTCAAT
1 C-TATCTCTTATTTTTGATGATCACAAAACACTCCAAGATTAATAATGCAATGTCTATGTTCAAT
16350751 ATGAATGTTTCAAATCTTTATGCATAATGAGGTGCTCCCCCTTAGTCAATGCATCTACTTTTCTT
65 ATGAATGTTTCAAATCTTTATGCATAATGAGGTGCTCCCCCTTAGTCAATGCATCTACTTTTCTT
16350816 TACATAATATTCAA
130 TACATAATATTCAA
16350830 C
1 C
16350831 AAAACCAAAA
Statistics
Matches: 143, Mismatches: 1, Indels: 1
0.99 0.01 0.01
Matches are distributed among these distances:
143 1 0.01
144 142 0.99
ACGTcount: A:0.31, C:0.20, G:0.10, T:0.39
Consensus pattern (143 bp):
CTATCTCTTATTTTTGATGATCACAAAACACTCCAAGATTAATAATGCAATGTCTATGTTCAATA
TGAATGTTTCAAATCTTTATGCATAATGAGGTGCTCCCCCTTAGTCAATGCATCTACTTTTCTTT
ACATAATATTCAA
Found at i:16351843 original size:19 final size:19
Alignment explanation
Indices: 16351801--16351843 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 19
16351791 AGAGAAGAGA
* *
16351801 CAATTATAAAGCTTGATGC
1 CAATTATAAAGCTAGATAC
* *
16351820 TAATTTTAAAGCTAGATAC
1 CAATTATAAAGCTAGATAC
16351839 CAATT
1 CAATT
16351844 GAGAAAACTT
Statistics
Matches: 19, Mismatches: 5, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.40, C:0.14, G:0.12, T:0.35
Consensus pattern (19 bp):
CAATTATAAAGCTAGATAC
Found at i:16357552 original size:67 final size:67
Alignment explanation
Indices: 16357444--16357582 Score: 217
Period size: 67 Copynumber: 2.1 Consensus size: 67
16357434 ACTTAGCCAA
* *
16357444 AACCTTTCACAATAGTTTTTATCGGGATCAACTAAAACCCAAAGTGGTTTTTCAAAAGTTCAACC
1 AACCTTTCACAATAGTTTTTATCGGGATCAACCAAAACCCAAAGTGGTTTTTCAAAAGCTCAACC
16357509 AC
66 AC
* * *
16357511 AACCTTTCATAATAGTTTTTCA-CGGGCTCAACCAAAACCCAAAGTGGTTTTTCAAAGGCTCAAC
1 AACCTTTCACAATAGTTTTT-ATCGGGATCAACCAAAACCCAAAGTGGTTTTTCAAAAGCTCAAC
16357575 CAC
65 CAC
16357578 AACCT
1 AACCT
16357583 ACACTAACTT
Statistics
Matches: 66, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
67 65 0.98
68 1 0.02
ACGTcount: A:0.35, C:0.25, G:0.12, T:0.28
Consensus pattern (67 bp):
AACCTTTCACAATAGTTTTTATCGGGATCAACCAAAACCCAAAGTGGTTTTTCAAAAGCTCAACC
AC
Found at i:16357571 original size:32 final size:32
Alignment explanation
Indices: 16357471--16357581 Score: 107
Period size: 32 Copynumber: 3.4 Consensus size: 32
16357461 TTTATCGGGA
* * *
16357471 TCAACTAAAACCCAAAGTGGTTTTTCAAAAGT
1 TCAACCAAAACCCAAAGTGGTTTTTCAAAGGC
* * **
16357503 TCAACCACAACCTTTCATAA-TAGTTTTTCACGGGC
1 TCAACCAAAACC---CA-AAGTGGTTTTTCAAAGGC
16357538 TCAACCAAAACCCAAAGTGGTTTTTCAAAGGC
1 TCAACCAAAACCCAAAGTGGTTTTTCAAAGGC
*
16357570 TCAACCACAACC
1 TCAACCAAAACC
16357582 TACACTAACT
Statistics
Matches: 62, Mismatches: 12, Indels: 10
0.74 0.14 0.12
Matches are distributed among these distances:
31 2 0.03
32 35 0.56
35 23 0.37
36 2 0.03
ACGTcount: A:0.36, C:0.27, G:0.12, T:0.25
Consensus pattern (32 bp):
TCAACCAAAACCCAAAGTGGTTTTTCAAAGGC
Found at i:16361787 original size:2 final size:2
Alignment explanation
Indices: 16361780--16361834 Score: 51
Period size: 2 Copynumber: 27.5 Consensus size: 2
16361770 TTTATGTTTT
* * *
16361780 TA TA TA TA TA TA TA TNA AA TA TT TA TA -A GT- TT TA TA TA TA TA
1 TA TA TA TA TA TA TA T-A TA TA TA TA TA TA -TA TA TA TA TA TA TA
16361822 TA TA TA TA TA TA T
1 TA TA TA TA TA TA T
16361835 TCATGTACTA
Statistics
Matches: 44, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
1 2 0.05
2 41 0.93
3 1 0.02
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.51
Consensus pattern (2 bp):
TA
Found at i:16362797 original size:73 final size:73
Alignment explanation
Indices: 16362700--16362844 Score: 186
Period size: 73 Copynumber: 2.0 Consensus size: 73
16362690 GAAGTTGGCG
* *
16362700 GGTTCAGAAACAGAGACAACTTAATCGACTAAAAAACATAGTTAGTCGACTAAAAGCTTACTG-C
1 GGTTCAGAAACAGAGACAACTTAATCGACTAAAAAACATAGTTAGTCAACTAAAAGCTCACTGTC
16362764 TAGAAACTA
66 TA-AAACTA
* * * * * *
16362773 GGTTCA-AAGACAGAGACGACTTAATCGACTCAGAAGCATTGTTAGTCAACTAAGAGCTCACTGT
1 GGTTCAGAA-ACAGAGACAACTTAATCGACTAAAAAACATAGTTAGTCAACTAAAAGCTCACTGT
16362837 CTAAAACT
65 CTAAAACT
16362845 GGGGTAAGAA
Statistics
Matches: 62, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
72 2 0.03
73 57 0.92
74 3 0.05
ACGTcount: A:0.40, C:0.19, G:0.18, T:0.23
Consensus pattern (73 bp):
GGTTCAGAAACAGAGACAACTTAATCGACTAAAAAACATAGTTAGTCAACTAAAAGCTCACTGTC
TAAAACTA
Found at i:16373600 original size:42 final size:42
Alignment explanation
Indices: 16373553--16373678 Score: 198
Period size: 42 Copynumber: 3.0 Consensus size: 42
16373543 CAGCTCATAT
* * * *
16373553 GCATCGGCTTATGCGCACTCCCACTCACACATAGTCGGGTCA
1 GCATCGACTTATGCACACTCCCACTCGCACATAGCCGGGTCA
*
16373595 GCATCGACTTATACACACTCCCACTCGCACATAGCCGGGTCA
1 GCATCGACTTATGCACACTCCCACTCGCACATAGCCGGGTCA
*
16373637 GCATCGACTTATGCACACTCCTACTCGCACATAGCCGGGTCA
1 GCATCGACTTATGCACACTCCCACTCGCACATAGCCGGGTCA
16373679 ATATCATTAC
Statistics
Matches: 77, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 77 1.00
ACGTcount: A:0.24, C:0.37, G:0.19, T:0.21
Consensus pattern (42 bp):
GCATCGACTTATGCACACTCCCACTCGCACATAGCCGGGTCA
Found at i:16377068 original size:21 final size:20
Alignment explanation
Indices: 16377044--16377091 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 20
16377034 ATCTTACCTT
*
16377044 TTTTTCACTTGTTTCCTTGAA
1 TTTTTCACTT-TTCCCTTGAA
*
16377065 TTTTCACACTTTTCCCTTGAA
1 TTTT-TCACTTTTCCCTTGAA
16377086 TTTTTC
1 TTTTTC
16377092 CACCCAGGGT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
20 1 0.04
21 17 0.74
22 5 0.22
ACGTcount: A:0.15, C:0.23, G:0.06, T:0.56
Consensus pattern (20 bp):
TTTTTCACTTTTCCCTTGAA
Found at i:16377091 original size:22 final size:22
Alignment explanation
Indices: 16377049--16377089 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
16377039 ACCTTTTTTT
*
16377049 CACTTGTTTCCTTGAATTTTCA
1 CACTTGTTCCCTTGAATTTTCA
16377071 CACTT-TTCCCTTGAATTTT
1 CACTTGTTCCCTTGAATTTT
16377090 TCCACCCAGG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.17, C:0.24, G:0.07, T:0.51
Consensus pattern (22 bp):
CACTTGTTCCCTTGAATTTTCA
Found at i:16400763 original size:2 final size:2
Alignment explanation
Indices: 16400756--16400799 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
16400746 NNNNNNNNNN
16400756 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
16400798 AT
1 AT
16400800 GGAAGTTTTG
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:16402391 original size:11 final size:12
Alignment explanation
Indices: 16402363--16402393 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
16402353 CCAAATCATA
16402363 ATTTATTTTTCT
1 ATTTATTTTTCT
16402375 ATTTATTTTTCT
1 ATTTATTTTTCT
16402387 A-TTATTT
1 ATTTATTT
16402394 CTTTCCTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 6 0.32
12 13 0.68
ACGTcount: A:0.19, C:0.06, G:0.00, T:0.74
Consensus pattern (12 bp):
ATTTATTTTTCT
Found at i:16402583 original size:31 final size:31
Alignment explanation
Indices: 16402531--16402589 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
16402521 CTCACCTTTC
16402531 ATTCTTTCTTTCTTTACTTCTTTATTCCTTG
1 ATTCTTTCTTTCTTTACTTCTTTATTCCTTG
* *
16402562 ATTCTTT-TTTTTTTCATTTCTTTATTCC
1 ATTCTTTCTTTCTTT-ACTTCTTTATTCC
16402590 ATGCTCCATG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 6 0.24
31 19 0.76
ACGTcount: A:0.10, C:0.20, G:0.02, T:0.68
Consensus pattern (31 bp):
ATTCTTTCTTTCTTTACTTCTTTATTCCTTG
Found at i:16408448 original size:13 final size:13
Alignment explanation
Indices: 16408430--16408454 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
16408420 TTTCAGAAAA
16408430 TTTATAAAATCAT
1 TTTATAAAATCAT
16408443 TTTATAAAATCA
1 TTTATAAAATCA
16408455 CAATTTCTCC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.08, G:0.00, T:0.44
Consensus pattern (13 bp):
TTTATAAAATCAT
Found at i:16411796 original size:15 final size:14
Alignment explanation
Indices: 16411776--16411826 Score: 66
Period size: 15 Copynumber: 3.4 Consensus size: 14
16411766 TTCTTAAAAC
16411776 AACTTTAAAATCGAA
1 AACTTTAAAATC-AA
16411791 AACTTTAAAATTCAA
1 AACTTTAAAA-TCAA
*
16411806 AGCTTTAAAATCAA
1 AACTTTAAAATCAA
16411820 AATCTTT
1 AA-CTTT
16411827 GATATTTAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
14 5 0.16
15 25 0.78
16 2 0.06
ACGTcount: A:0.49, C:0.14, G:0.04, T:0.33
Consensus pattern (14 bp):
AACTTTAAAATCAA
Found at i:16415813 original size:67 final size:67
Alignment explanation
Indices: 16415741--16415876 Score: 188
Period size: 67 Copynumber: 2.0 Consensus size: 67
16415731 AAGCTTTTAC
*
16415741 AATGGCTTTTCACAA-GCTTC-GCCACAACCTTTAACAATGGTTTTTCACGA-GATCAACCAAAA
1 AATGGCTTTTCA-AAGGC-TCAACCACAACCTTTAACAATGGTTTTTCA-GAGGATCAACCAAAA
16415803 CCCAA
63 CCCAA
* * *
16415808 AATGGCTTTTCAAAGGCTCAACCATAACCTTTAACAATGGTTTTTCATAGGATCAACCAAAACTC
1 AATGGCTTTTCAAAGGCTCAACCACAACCTTTAACAATGGTTTTTCAGAGGATCAACCAAAACCC
16415873 AA
66 AA
16415875 AA
1 AA
16415877 ACTAACTTTT
Statistics
Matches: 62, Mismatches: 4, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
66 5 0.08
67 57 0.92
ACGTcount: A:0.37, C:0.25, G:0.12, T:0.26
Consensus pattern (67 bp):
AATGGCTTTTCAAAGGCTCAACCACAACCTTTAACAATGGTTTTTCAGAGGATCAACCAAAACCC
AA
Found at i:16415853 original size:35 final size:35
Alignment explanation
Indices: 16415766--16415870 Score: 119
Period size: 35 Copynumber: 3.1 Consensus size: 35
16415756 GCTTCGCCAC
*
16415766 AACCTTTAACAATGGTTTTTC-ACGAGATCAACCAA
1 AACCTTTAACAATGGTTTTTCAAAG-GATCAACCAA
* * * *
16415801 AACC--CAA-AATGGCTTTTCAAAGGCTCAACCAT
1 AACCTTTAACAATGGTTTTTCAAAGGATCAACCAA
*
16415833 AACCTTTAACAATGGTTTTTCATAGGATCAACCAA
1 AACCTTTAACAATGGTTTTTCAAAGGATCAACCAA
16415868 AAC
1 AAC
16415871 TCAAAAACTA
Statistics
Matches: 56, Mismatches: 10, Indels: 8
0.76 0.14 0.11
Matches are distributed among these distances:
32 22 0.39
33 4 0.07
34 2 0.04
35 28 0.50
ACGTcount: A:0.38, C:0.24, G:0.11, T:0.27
Consensus pattern (35 bp):
AACCTTTAACAATGGTTTTTCAAAGGATCAACCAA
Found at i:16416443 original size:72 final size:73
Alignment explanation
Indices: 16416263--16416446 Score: 199
Period size: 73 Copynumber: 2.5 Consensus size: 73
16416253 CTTAGTCAAT
* * * * *
16416263 TAACTATGCTTCTTAGTCGATTAAGTCGTCTTTGTCTCTGAACCCAGTCTCTGGCAGTAAGCTTT
1 TAACAATGCTTCTTAGTCGATTAAGTCGTCTCTGTTTCTAAACCCAGTCTCTGGCAGTAAGCTCT
* *
16416328 TAGTTGAT
66 TAGATGAC
* * * * * *
16416336 TAACAATGCTTATTAGTCAATTAAGTCATCTCTGTTTCTAAACCCAGTTTCTGGTATTAAGCTCT
1 TAACAATGCTTCTTAGTCGATTAAGTCGTCTCTGTTTCTAAACCCAGTCTCTGGCAGTAAGCTCT
*
16416401 TA-ATGGC
66 TAGATGAC
* * * *
16416408 TAACCATTCTTCTTAGTTGACTAAGTCGTCTCTGTTTCT
1 TAACAATGCTTCTTAGTCGATTAAGTCGTCTCTGTTTCT
16416447 GAACTGGCCA
Statistics
Matches: 90, Mismatches: 21, Indels: 1
0.80 0.19 0.01
Matches are distributed among these distances:
72 34 0.38
73 56 0.62
ACGTcount: A:0.23, C:0.21, G:0.16, T:0.41
Consensus pattern (73 bp):
TAACAATGCTTCTTAGTCGATTAAGTCGTCTCTGTTTCTAAACCCAGTCTCTGGCAGTAAGCTCT
TAGATGAC
Found at i:16423333 original size:35 final size:35
Alignment explanation
Indices: 16423281--16423401 Score: 117
Period size: 35 Copynumber: 3.5 Consensus size: 35
16423271 TTCCACTAAG
* *
16423281 CTTTTACAATGGCTTTTCACAAGTTCAGCCACAAC
1 CTTTAACAATGGCTTTTCACAAGTTCAACCACAAC
* * * *
16423316 CTTTAACAATGGTTTTTCACGAGATCAACCAAAAC
1 CTTTAACAATGGCTTTTCACAAGTTCAACCACAAC
*
16423351 C--CAA-AATGGCTTTTCA-AAGGCTT-AACCACAAC
1 CTTTAACAATGGCTTTTCACAA-G-TTCAACCACAAC
*
16423383 CTTTAACAATGGTTTTTCA
1 CTTTAACAATGGCTTTTCA
16423402 TAAGATCATC
Statistics
Matches: 68, Mismatches: 13, Indels: 10
0.75 0.14 0.11
Matches are distributed among these distances:
31 1 0.01
32 21 0.31
33 3 0.04
34 2 0.03
35 41 0.60
ACGTcount: A:0.33, C:0.25, G:0.12, T:0.31
Consensus pattern (35 bp):
CTTTAACAATGGCTTTTCACAAGTTCAACCACAAC
Found at i:16423396 original size:67 final size:67
Alignment explanation
Indices: 16423288--16423423 Score: 204
Period size: 67 Copynumber: 2.0 Consensus size: 67
16423278 AAGCTTTTAC
* *
16423288 AATGGCTTTTCACAAGTTCAGCCACAACCTTTAACAATGGTTTTTCACGAGATCAACCAAAACCC
1 AATGGCTTTTCACAAGTTCAACCACAACCTTTAACAATGGTTTTTCACAAGATCAACCAAAACCC
16423353 AA
66 AA
* *
16423355 AATGGCTTTTCA-AAGGCTT-AACCACAACCTTTAACAATGGTTTTTCATAAGATCATCCAAAAC
1 AATGGCTTTTCACAA-G-TTCAACCACAACCTTTAACAATGGTTTTTCACAAGATCAACCAAAAC
16423418 CCAA
64 CCAA
16423422 AA
1 AA
16423424 ACTAAGTTTT
Statistics
Matches: 63, Mismatches: 4, Indels: 4
0.89 0.06 0.06
Matches are distributed among these distances:
66 2 0.03
67 59 0.94
68 2 0.03
ACGTcount: A:0.38, C:0.25, G:0.11, T:0.26
Consensus pattern (67 bp):
AATGGCTTTTCACAAGTTCAACCACAACCTTTAACAATGGTTTTTCACAAGATCAACCAAAACCC
AA
Found at i:16423895 original size:73 final size:73
Alignment explanation
Indices: 16423812--16423977 Score: 251
Period size: 73 Copynumber: 2.3 Consensus size: 73
16423802 CAGAATGCTT
* * * * * *
16423812 TTAGTCGACTAACTATGCTTTTTAGTTGATTAATTCATCTTTGTCTCTGAACCTAGTCTCTAGCA
1 TTAGTTGACTAACAATGCTTTTTAGTCGATTAAGTCATCTTTGTCTCTGAACCCAGTCTCTAACA
*
16423877 GTAAGCTC
66 ATAAGCTC
* *
16423885 TTAGTTGACTAACAATGCTTTTTAGTCGATTAAGTCATCTTTGTTTCTGAACCCAGTTTCTAACA
1 TTAGTTGACTAACAATGCTTTTTAGTCGATTAAGTCATCTTTGTCTCTGAACCCAGTCTCTAACA
16423950 ATAAGCTC
66 ATAAGCTC
16423958 TTAGTTGACTAACAATGCTT
1 TTAGTTGACTAACAATGCTT
16423978 CTTGGTCAAC
Statistics
Matches: 84, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
73 84 1.00
ACGTcount: A:0.26, C:0.19, G:0.14, T:0.40
Consensus pattern (73 bp):
TTAGTTGACTAACAATGCTTTTTAGTCGATTAAGTCATCTTTGTCTCTGAACCCAGTCTCTAACA
ATAAGCTC
Found at i:16423992 original size:73 final size:73
Alignment explanation
Indices: 16423812--16424007 Score: 221
Period size: 73 Copynumber: 2.7 Consensus size: 73
16423802 CAGAATGCTT
* * * ** * * * * *
16423812 TTAGTCGACTAACTATGCTTTTTAGTTGATTAATTCATCTTTGTCTCTGAACCTAGTCTCTAGCA
1 TTAGTTGACTAACAATGCTTCTTAGTCAACTAAGTCATCTTTGTTTCTGAACCCAGTCTCTAACA
*
16423877 GTAAGCTC
66 ATAAGCTC
* * * *
16423885 TTAGTTGACTAACAATGCTTTTTAGTCGATTAAGTCATCTTTGTTTCTGAACCCAGTTTCTAACA
1 TTAGTTGACTAACAATGCTTCTTAGTCAACTAAGTCATCTTTGTTTCTGAACCCAGTCTCTAACA
16423950 ATAAGCTC
66 ATAAGCTC
* ** *
16423958 TTAGTTGACTAACAATGCTTCTTGGTCAACTAAGTCGCCTCTGTTTCTGA
1 TTAGTTGACTAACAATGCTTCTTAGTCAACTAAGTCATCTTTGTTTCTGA
16424008 TCCGGCCATC
Statistics
Matches: 107, Mismatches: 16, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
73 107 1.00
ACGTcount: A:0.24, C:0.20, G:0.15, T:0.40
Consensus pattern (73 bp):
TTAGTTGACTAACAATGCTTCTTAGTCAACTAAGTCATCTTTGTTTCTGAACCCAGTCTCTAACA
ATAAGCTC
Found at i:16426841 original size:74 final size:74
Alignment explanation
Indices: 16426725--16426864 Score: 226
Period size: 74 Copynumber: 1.9 Consensus size: 74
16426715 AAATCTATAC
* * *
16426725 TTATAAATATGTATTCTTTAAATGATGATCATCGAAACATTTTTTATTATAATTATTAGTAAGAT
1 TTATAAATATGTATTCATCAAATGATCATCATCGAAACATTTTTTATTATAATTATTAGTAAGAT
16426790 TCAAACTTA
66 TCAAACTTA
* * *
16426799 TTATAAATGTGTATTCATCAAATGATCATCATTGAAATATTTTTTATTATAATTATTAGTAAGAT
1 TTATAAATATGTATTCATCAAATGATCATCATCGAAACATTTTTTATTATAATTATTAGTAAGAT
16426864 T
66 T
16426865 TATTCCATTT
Statistics
Matches: 60, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
74 60 1.00
ACGTcount: A:0.39, C:0.07, G:0.09, T:0.46
Consensus pattern (74 bp):
TTATAAATATGTATTCATCAAATGATCATCATCGAAACATTTTTTATTATAATTATTAGTAAGAT
TCAAACTTA
Found at i:16428168 original size:185 final size:178
Alignment explanation
Indices: 16427854--16428210 Score: 464
Period size: 185 Copynumber: 2.0 Consensus size: 178
16427844 CTCTTTATTG
* * * *
16427854 AGTCTTAATTAGATTCACAAATTAATTAATCATTGACTAGACAATCAAAAGCATTAAGAACAAGT
1 AGTCTCAATTAGATTCACAAATCAATTAATCATTGACCAGACAATCAAAAGCATTAAAAACAAGT
* *
16427919 TTGAATAAGCAACCCATTCATAGTAAATAAAAGAGAAATAAATATTCAAACCACATGTTGAAATC
66 TTGAATAAGCAACCCATTCATAGTAAATAAAAAAGAAACAAATATTCAAACCACATGTTGAAATC
* *
16427984 CACCACAATCCTAAAAAAATAGTTTAGCTCAAAATATTTAATTTGTCA
131 AACCACAATCCTAAAAAAATAGTTTAGCTCAAAATATCTAATTTGTCA
* ** *
16428032 AGTCTCAATTAGATTCACAAATCAGTTAATTGTTGGCCAGACAATCAAAAGCATTAAAAACATA-
1 AGTCTCAATTAGATTCACAAATCAATTAATCATTGACCAGACAATCAAAAGCATTAAAAACA-AG
* *
16428096 TTTGAATAAGTAAAACTATACCCATTCATAGTAAATAAAAAAGAAACCAATATTCAAACTACATG
65 TTTGAATAAG-----C-A-ACCCATTCATAGTAAATAAAAAAGAAACAAATATTCAAACCACATG
* * * * *
16428161 TTGAAATCAATCATAATCTTAGAAAAATAGTTTAGCTCATAATATCTAAT
123 TTGAAATCAACCACAATCCTAAAAAAATAGTTTAGCTCAAAATATCTAAT
16428211 AAAAACTTCA
Statistics
Matches: 152, Mismatches: 19, Indels: 9
0.84 0.11 0.05
Matches are distributed among these distances:
178 64 0.42
179 1 0.01
183 1 0.01
184 1 0.01
185 85 0.56
ACGTcount: A:0.46, C:0.15, G:0.10, T:0.29
Consensus pattern (178 bp):
AGTCTCAATTAGATTCACAAATCAATTAATCATTGACCAGACAATCAAAAGCATTAAAAACAAGT
TTGAATAAGCAACCCATTCATAGTAAATAAAAAAGAAACAAATATTCAAACCACATGTTGAAATC
AACCACAATCCTAAAAAAATAGTTTAGCTCAAAATATCTAATTTGTCA
Found at i:16429009 original size:20 final size:20
Alignment explanation
Indices: 16428960--16429011 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
16428950 CAAAAATATA
*
16428960 AAAATAAACATAAGTAACAT
1 AAAATAAACATTAGTAACAT
* *
16428980 AAAACT-AACATTATTAACTT
1 AAAA-TAAACATTAGTAACAT
16429000 AAAATAAACATT
1 AAAATAAACATT
16429012 TAAATATAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
19 1 0.04
20 25 0.93
21 1 0.04
ACGTcount: A:0.60, C:0.12, G:0.02, T:0.27
Consensus pattern (20 bp):
AAAATAAACATTAGTAACAT
Found at i:16433339 original size:20 final size:20
Alignment explanation
Indices: 16433314--16433369 Score: 60
Period size: 20 Copynumber: 2.8 Consensus size: 20
16433304 CTCCTACCAA
16433314 AACATAAAATAAACATAAAT
1 AACATAAAATAAACATAAAT
* * *
16433334 AACATACAACT-AACATTATT
1 AACATA-AAATAAACATAAAT
*
16433354 AACTTAAAATAAACAT
1 AACATAAAATAAACAT
16433370 CTAAATATAA
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
19 3 0.10
20 23 0.79
21 3 0.10
ACGTcount: A:0.61, C:0.14, G:0.00, T:0.25
Consensus pattern (20 bp):
AACATAAAATAAACATAAAT
Found at i:16440574 original size:8 final size:9
Alignment explanation
Indices: 16440558--16440625 Score: 54
Period size: 8 Copynumber: 7.8 Consensus size: 9
16440548 TGTAGACACC
16440558 TAAA-AAAA
1 TAAATAAAA
16440566 TAAAT-AAA
1 TAAATAAAA
*
16440574 TAATTAAAA
1 TAAATAAAA
16440583 TATAATAAAA
1 TA-AATAAAA
*
16440593 T-AA-AATA
1 TAAATAAAA
16440600 TAAAGTAAAA
1 TAAA-TAAAA
*
16440610 TAATTAAAA
1 TAAATAAAA
*
16440619 AAAATAA
1 TAAATAA
16440626 CCAAAAAAAA
Statistics
Matches: 47, Mismatches: 7, Indels: 11
0.72 0.11 0.17
Matches are distributed among these distances:
7 4 0.09
8 15 0.32
9 15 0.32
10 13 0.28
ACGTcount: A:0.74, C:0.00, G:0.01, T:0.25
Consensus pattern (9 bp):
TAAATAAAA
Found at i:16441746 original size:3 final size:3
Alignment explanation
Indices: 16441732--16441760 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
16441722 GAGGCTTGCA
16441732 AAT AAT AA- AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
16441761 TCATGATACA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.08
3 23 0.92
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:16442229 original size:21 final size:19
Alignment explanation
Indices: 16442188--16442233 Score: 56
Period size: 21 Copynumber: 2.3 Consensus size: 19
16442178 TAGAAAACCA
*
16442188 AAAAAATAAAAAAATATAT
1 AAAAAATAAAAAAATACAT
*
16442207 AAAAAATAATAAATAATCCAT
1 AAAAAATAA-AAA-AATACAT
16442228 AAAAAA
1 AAAAAA
16442234 ATTATTATTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 9 0.39
20 3 0.13
21 11 0.48
ACGTcount: A:0.76, C:0.04, G:0.00, T:0.20
Consensus pattern (19 bp):
AAAAAATAAAAAAATACAT
Found at i:16442232 original size:22 final size:18
Alignment explanation
Indices: 16442187--16442235 Score: 53
Period size: 19 Copynumber: 2.4 Consensus size: 18
16442177 ATAGAAAACC
16442187 AAAAAAATAAAAAAATAT
1 AAAAAAATAAAAAAATAT
16442205 ATAAAAAATAATAAATAATCCAT
1 A-AAAAAATAA-AAA-AAT--AT
16442228 AAAAAAAT
1 AAAAAAAT
16442236 TATTATTAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
18 1 0.04
19 9 0.35
20 3 0.12
21 3 0.12
22 7 0.27
23 3 0.12
ACGTcount: A:0.76, C:0.04, G:0.00, T:0.20
Consensus pattern (18 bp):
AAAAAAATAAAAAAATAT
Found at i:16452480 original size:185 final size:180
Alignment explanation
Indices: 16452232--16452652 Score: 565
Period size: 185 Copynumber: 2.3 Consensus size: 180
16452222 TGGGAATTTT
* * * * *
16452232 AATCAAACCTATTATGAGATAGGTCGAGTCTAAATTTAGTTTAAGAATTTCAATTTTGTTTAAAT
1 AATC-AACCTATTGTGAGATAGGTCGAGCCTAAATTAAGTTTAGGAATTTTAATTTTGTTTAAAT
* * *
16452297 CAAAACTGTTGTGAGATAGGTCGAGCCTAGATTTAAGTCTAGAAATTTTAATTTTGTTTAAATCG
65 CAAAACTGTTGTGAGATAGGCCGAGCCTAGA-TTAAGTCTAGAAATTTCAA---T-TTTAAATCA
*
16452362 AACCTGTTGTGAGATAGGTCGAGCCTAGATTAAGTCTAGAAATTTCAA-TTGTTTA
125 AACCTGTTGTGAGATAAGTCGAGCCTAGATTAAGTCTAGAAATTTCAATTTGTTTA
16452417 AATCGAACCTATTGTGAGATAGGTCGAGCCTAAATTAAGTTTAGGAATTTTAATTTTGTTTAAAT
1 AATC-AACCTATTGTGAGATAGGTCGAGCCTAAATTAAGTTTAGGAATTTTAATTTTGTTTAAAT
* * * *
16452482 CGAACCTGTTGTGAGATAGGCCGAGCCTAGATTAAGTCTAGGAATTTCAATTTTAAATCAAATCT
65 CAAAACTGTTGTGAGATAGGCCGAGCCTAGATTAAGTCTAGAAATTTCAATTTTAAATCAAACCT
* * *
16452547 GTTGTGAGATAAGTTGAGCCTAGATTAAGTCTAGGAATTTTAATTTTGTTTA
130 GTTGTGAGATAAGTCGAGCCTAGATTAAGTCTAGAAATTTCAA-TTTGTTTA
* * * * *
16452599 AATCAGACCTGTTGTGAGATAGGTCAAGCTTAGATTAAGTCTAGGAATTTTAAT
1 AATCA-ACCTATTGTGAGATAGGTCGAGCCTAAATTAAGTTTAGGAATTTTAAT
16452653 CGAATTTGTT
Statistics
Matches: 211, Mismatches: 22, Indels: 9
0.87 0.09 0.04
Matches are distributed among these distances:
180 51 0.24
181 2 0.01
182 54 0.26
184 17 0.08
185 87 0.41
ACGTcount: A:0.33, C:0.11, G:0.20, T:0.37
Consensus pattern (180 bp):
AATCAACCTATTGTGAGATAGGTCGAGCCTAAATTAAGTTTAGGAATTTTAATTTTGTTTAAATC
AAAACTGTTGTGAGATAGGCCGAGCCTAGATTAAGTCTAGAAATTTCAATTTTAAATCAAACCTG
TTGTGAGATAAGTCGAGCCTAGATTAAGTCTAGAAATTTCAATTTGTTTA
Found at i:16452617 original size:120 final size:122
Alignment explanation
Indices: 16452232--16452648 Score: 588
Period size: 120 Copynumber: 3.4 Consensus size: 122
16452222 TGGGAATTTT
* * * * * * * *
16452232 AATCAAACCTATTATGAGATAGGTCGAGTCTAAATTTAGTTTAAGAATTTCAATTTTGTTTAAAT
1 AATCGAACCTGTTGTGAGATAGGTCGAGCCTAGATTAAGTCTAGGAATTTCAA--TTGTTTAAAT
*
16452297 CAAAACTGTTGTGAGATAGGTCGAGCCTAGATTTAAGTCTAGAAATTTTAATTTTGTTTA
64 CAAAACTGTTGTGAGATAGGTCGAGCCTAGA-TTAAGTCTAGGAATTTTAATTTTGTTTA
* *
16452357 AATCGAACCTGTTGTGAGATAGGTCGAGCCTAGATTAAGTCTAGAAATTTCAATTGTTTAAATCG
1 AATCGAACCTGTTGTGAGATAGGTCGAGCCTAGATTAAGTCTAGGAATTTCAATTGTTTAAATCA
* * * *
16452422 AACCTATTGTGAGATAGGTCGAGCCTAAATTAAGTTTAGGAATTTTAATTTTGTTTA
66 AAACTGTTGTGAGATAGGTCGAGCCTAGATTAAGTCTAGGAATTTTAATTTTGTTTA
*
16452479 AATCGAACCTGTTGTGAGATAGGCCGAGCCTAGATTAAGTCTAGGAATTTCAA-T-TTTAAATCA
1 AATCGAACCTGTTGTGAGATAGGTCGAGCCTAGATTAAGTCTAGGAATTTCAATTGTTTAAATCA
* * *
16452542 AATCTGTTGTGAGATAAGTTGAGCCTAGATTAAGTCTAGGAATTTTAATTTTGTTTA
66 AAACTGTTGTGAGATAGGTCGAGCCTAGATTAAGTCTAGGAATTTTAATTTTGTTTA
* *
16452599 AATC-AGACCTGTTGTGAGATAGGTCAAGCTTAGATTAAGTCTAGGAATTT
1 AATCGA-ACCTGTTGTGAGATAGGTCGAGCCTAGATTAAGTCTAGGAATTT
16452649 TAATCGAATT
Statistics
Matches: 264, Mismatches: 27, Indels: 7
0.89 0.09 0.02
Matches are distributed among these distances:
119 1 0.00
120 104 0.39
121 1 0.00
122 77 0.29
123 37 0.14
125 44 0.17
ACGTcount: A:0.33, C:0.11, G:0.20, T:0.36
Consensus pattern (122 bp):
AATCGAACCTGTTGTGAGATAGGTCGAGCCTAGATTAAGTCTAGGAATTTCAATTGTTTAAATCA
AAACTGTTGTGAGATAGGTCGAGCCTAGATTAAGTCTAGGAATTTTAATTTTGTTTA
Found at i:16452649 original size:62 final size:62
Alignment explanation
Indices: 16452232--16452652 Score: 518
Period size: 62 Copynumber: 6.9 Consensus size: 62
16452222 TGGGAATTTT
* * * * * * * * *
16452232 AATCAAACCTATTATGAGATAGGTCGAGTCTAAATTTAGTTTAAGAATTTCAATTTTGTTTA
1 AATCAGACCTGTTGTGAGATAGGTCGAGCCTAGATTAAGTCTAGGAATTTTAATTTTGTTTA
* * *
16452294 AATCAAAACTGTTGTGAGATAGGTCGAGCCTAGATTTAAGTCTAGAAATTTTAATTTTGTTTA
1 AATCAGACCTGTTGTGAGATAGGTCGAGCCTAGA-TTAAGTCTAGGAATTTTAATTTTGTTTA
* *
16452357 AATC-GAACCTGTTGTGAGATAGGTCGAGCCTAGATTAAGTCTAGAAATTTCAA--TTGTTTA
1 AATCAG-ACCTGTTGTGAGATAGGTCGAGCCTAGATTAAGTCTAGGAATTTTAATTTTGTTTA
* * *
16452417 AATC-GAACCTATTGTGAGATAGGTCGAGCCTAAATTAAGTTTAGGAATTTTAATTTTGTTTA
1 AATCAG-ACCTGTTGTGAGATAGGTCGAGCCTAGATTAAGTCTAGGAATTTTAATTTTGTTTA
* *
16452479 AATC-GAACCTGTTGTGAGATAGGCCGAGCCTAGATTAAGTCTAGGAATTTCAA---T-TTTA
1 AATCAG-ACCTGTTGTGAGATAGGTCGAGCCTAGATTAAGTCTAGGAATTTTAATTTTGTTTA
* * * *
16452537 AATCAAATCTGTTGTGAGATAAGTTGAGCCTAGATTAAGTCTAGGAATTTTAATTTTGTTTA
1 AATCAGACCTGTTGTGAGATAGGTCGAGCCTAGATTAAGTCTAGGAATTTTAATTTTGTTTA
* *
16452599 AATCAGACCTGTTGTGAGATAGGTCAAGCTTAGATTAAGTCTAGGAATTTTAAT
1 AATCAGACCTGTTGTGAGATAGGTCGAGCCTAGATTAAGTCTAGGAATTTTAAT
16452653 CGAATTTGTT
Statistics
Matches: 315, Mismatches: 35, Indels: 18
0.86 0.10 0.05
Matches are distributed among these distances:
58 50 0.16
59 1 0.00
60 55 0.17
61 1 0.00
62 154 0.49
63 54 0.17
ACGTcount: A:0.33, C:0.11, G:0.20, T:0.37
Consensus pattern (62 bp):
AATCAGACCTGTTGTGAGATAGGTCGAGCCTAGATTAAGTCTAGGAATTTTAATTTTGTTTA
Found at i:16452889 original size:12 final size:12
Alignment explanation
Indices: 16452872--16452896 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
16452862 TTAAAATATA
16452872 ATAAAATAAAAT
1 ATAAAATAAAAT
16452884 ATAAAATAAAAT
1 ATAAAATAAAAT
16452896 A
1 A
16452897 ATTAAAAAAA
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:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (12 bp):
ATAAAATAAAAT
Found at i:16452904 original size:22 final size:21
Alignment explanation
Indices: 16452847--16452905 Score: 66
Period size: 22 Copynumber: 2.7 Consensus size: 21
16452837 GACACCTAAA
16452847 AAAATAAATAAAAAATTAAAAT
1 AAAAT-AATAAAAAATTAAAAT
*
16452869 ATAATAA-AATAAAATATAAAAT
1 AAAATAATAA-AAAAT-TAAAAT
16452891 AAAATAATTAAAAAA
1 AAAATAA-TAAAAAA
16452906 AGAGAATAAC
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
20 2 0.06
21 7 0.23
22 16 0.52
23 4 0.13
24 2 0.06
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (21 bp):
AAAATAATAAAAAATTAAAAT
Found at i:16452904 original size:27 final size:26
Alignment explanation
Indices: 16452845--16452905 Score: 70
Period size: 28 Copynumber: 2.2 Consensus size: 26
16452835 TAGACACCTA
16452845 AAAAAATAAATAAAAAATTAAAATAT
1 AAAAAATAAATAAAAAATTAAAATAT
*
16452871 AATAAAATAAAATATAAAA-TAAAATAATT
1 AA-AAAAT-AAATAAAAAATTAAAAT-A-T
16452900 AAAAAA
1 AAAAAA
16452906 AGAGAATAAC
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
26 2 0.07
27 11 0.37
28 14 0.47
29 3 0.10
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (26 bp):
AAAAAATAAATAAAAAATTAAAATAT
Found at i:16452906 original size:17 final size:18
Alignment explanation
Indices: 16452847--16452903 Score: 66
Period size: 17 Copynumber: 3.2 Consensus size: 18
16452837 GACACCTAAA
16452847 AAAATAAATAAAA-AATT
1 AAAATAAATAAAATAATT
16452864 AAAATATAATAAAATAA--
1 AAAATA-AATAAAATAATT
*
16452881 AATATAAAATAAAATAATT
1 AAAAT-AAATAAAATAATT
16452900 AAAA
1 AAAA
16452904 AAAGAGAATA
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
17 20 0.61
18 8 0.24
19 5 0.15
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (18 bp):
AAAATAAATAAAATAATT
Found at i:16453215 original size:15 final size:13
Alignment explanation
Indices: 16453158--16453217 Score: 52
Period size: 13 Copynumber: 4.4 Consensus size: 13
16453148 TAGCCCAAGC
*
16453158 AAAAAGAAATACA
1 AAAAACAAATACA
16453171 AAAAACAACGAT-CA
1 AAAAACAA--ATACA
16453185 AAAAACATAATA-A
1 AAAAACA-AATACA
16453198 AAAAACAGATATACA
1 AAAAACA-A-ATACA
16453213 AAAAA
1 AAAAA
16453218 ATGAGAGAGG
Statistics
Matches: 39, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
13 18 0.46
14 12 0.31
15 9 0.23
ACGTcount: A:0.73, C:0.12, G:0.05, T:0.10
Consensus pattern (13 bp):
AAAAACAAATACA
Found at i:16453962 original size:21 final size:21
Alignment explanation
Indices: 16453938--16453977 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
16453928 TTAAAAAAAA
16453938 TATAAAAAAAATAAAAATATT
1 TATAAAAAAAATAAAAATATT
* * *
16453959 TATATAAATAATAACAATA
1 TATAAAAAAAATAAAAATA
16453978 ACAATAATAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.30
Consensus pattern (21 bp):
TATAAAAAAAATAAAAATATT
Found at i:16454046 original size:3 final size:3
Alignment explanation
Indices: 16454033--16454061 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
16454023 GAGGCTTGCA
16454033 AAT AA- AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
16454062 TCATGATACA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.08
3 23 0.92
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:16456403 original size:28 final size:28
Alignment explanation
Indices: 16456371--16456425 Score: 85
Period size: 28 Copynumber: 2.0 Consensus size: 28
16456361 TAATTGAAAG
*
16456371 TTTATTTATGTTTAG-TGTAATTTATTTT
1 TTTATTTATATTT-GTTGTAATTTATTTT
16456399 TTTATTTATATTTGTTGTAATTTATTT
1 TTTATTTATATTTGTTGTAATTTATTT
16456426 ATTCTAACAT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
27 1 0.04
28 24 0.96
ACGTcount: A:0.22, C:0.00, G:0.09, T:0.69
Consensus pattern (28 bp):
TTTATTTATATTTGTTGTAATTTATTTT
Found at i:16457002 original size:33 final size:32
Alignment explanation
Indices: 16456957--16457018 Score: 81
Period size: 33 Copynumber: 1.9 Consensus size: 32
16456947 ATTAATTTAG
* *
16456957 TTATTTGAATTTGATTATTTGGATAAAATTAAA
1 TTATTTGAATTTGAATATTTAG-TAAAATTAAA
16456990 TTATTCTG-ATTTGAATATTTAGTAAAATT
1 TTATT-TGAATTTGAATATTTAGTAAAATT
16457019 TTAAATCAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
32 7 0.27
33 17 0.65
34 2 0.08
ACGTcount: A:0.37, C:0.02, G:0.11, T:0.50
Consensus pattern (32 bp):
TTATTTGAATTTGAATATTTAGTAAAATTAAA
Found at i:16464623 original size:16 final size:16
Alignment explanation
Indices: 16464602--16464639 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
16464592 GAGAAGCTTA
* *
16464602 AAAGCTTGAAGCTAAG
1 AAAGCTTGAAACCAAG
16464618 AAAGCTTGAAACCAAG
1 AAAGCTTGAAACCAAG
16464634 AAAGCT
1 AAAGCT
16464640 AATGGCTCAG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.47, C:0.16, G:0.21, T:0.16
Consensus pattern (16 bp):
AAAGCTTGAAACCAAG
Found at i:16474410 original size:18 final size:19
Alignment explanation
Indices: 16474384--16474421 Score: 51
Period size: 18 Copynumber: 2.0 Consensus size: 19
16474374 AGGTATAGTG
*
16474384 CAAATACCTA-TTTTTAGA
1 CAAACACCTACTTTTTAGA
16474402 CAAACACCTACCTTTTTAGA
1 CAAACACCTA-CTTTTTAGA
16474422 TGACTTAATG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 9 0.53
20 8 0.47
ACGTcount: A:0.37, C:0.24, G:0.05, T:0.34
Consensus pattern (19 bp):
CAAACACCTACTTTTTAGA
Found at i:16495228 original size:29 final size:29
Alignment explanation
Indices: 16495186--16495241 Score: 112
Period size: 29 Copynumber: 1.9 Consensus size: 29
16495176 AAATTGATCA
16495186 AATGGAGGCAGCTGGAAGCACTAACACAT
1 AATGGAGGCAGCTGGAAGCACTAACACAT
16495215 AATGGAGGCAGCTGGAAGCACTAACAC
1 AATGGAGGCAGCTGGAAGCACTAACAC
16495242 CACATTTGTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.38, C:0.21, G:0.29, T:0.12
Consensus pattern (29 bp):
AATGGAGGCAGCTGGAAGCACTAACACAT
Found at i:16496226 original size:22 final size:22
Alignment explanation
Indices: 16496201--16496247 Score: 85
Period size: 22 Copynumber: 2.1 Consensus size: 22
16496191 AATTTGAGGT
16496201 CATCTTAGGTAAATTCTGAACA
1 CATCTTAGGTAAATTCTGAACA
*
16496223 CATCTTAGGTGAATTCTGAACA
1 CATCTTAGGTAAATTCTGAACA
16496245 CAT
1 CAT
16496248 TGTTCACCCG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.34, C:0.19, G:0.15, T:0.32
Consensus pattern (22 bp):
CATCTTAGGTAAATTCTGAACA
Found at i:16506886 original size:23 final size:23
Alignment explanation
Indices: 16506860--16506912 Score: 106
Period size: 23 Copynumber: 2.3 Consensus size: 23
16506850 CTTTTTTTAA
16506860 TTCTTCTTTCTCCTTTTTCAGTT
1 TTCTTCTTTCTCCTTTTTCAGTT
16506883 TTCTTCTTTCTCCTTTTTCAGTT
1 TTCTTCTTTCTCCTTTTTCAGTT
16506906 TTCTTCT
1 TTCTTCT
16506913 ATCTACACTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.04, C:0.26, G:0.04, T:0.66
Consensus pattern (23 bp):
TTCTTCTTTCTCCTTTTTCAGTT
Found at i:16514924 original size:6 final size:6
Alignment explanation
Indices: 16514913--16514979 Score: 53
Period size: 6 Copynumber: 10.8 Consensus size: 6
16514903 TTTCCTTATA
* * * * *
16514913 CATATG CATATG TATATA CATATG CATATG TATATATG CATATG TATATA
1 CATATG CATATG CATATG CATATG CATATG --CATATG CATATG CATATG
* *
16514963 TATATG CATATG TATAT
1 CATATG CATATG CATAT
16514980 ATAATATATA
Statistics
Matches: 48, Mismatches: 11, Indels: 4
0.76 0.17 0.06
Matches are distributed among these distances:
6 43 0.90
8 5 0.10
ACGTcount: A:0.37, C:0.09, G:0.12, T:0.42
Consensus pattern (6 bp):
CATATG
Found at i:16514948 original size:2 final size:2
Alignment explanation
Indices: 16514938--16515022 Score: 84
Period size: 2 Copynumber: 43.5 Consensus size: 2
16514928 ATACATATGC
* ** * ** *
16514938 AT AT GT AT AT AT GC AT AT GT AT AT AT AT AT GC AT AT GT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
16514980 AT A- AT AT AT AT A- AT AT AT AT AT AT AT AT AT AT GT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
16515020 AT A
1 AT A
16515023 GGCTGACTGA
Statistics
Matches: 65, Mismatches: 16, Indels: 4
0.76 0.19 0.05
Matches are distributed among these distances:
1 2 0.03
2 63 0.97
ACGTcount: A:0.45, C:0.02, G:0.07, T:0.46
Consensus pattern (2 bp):
AT
Found at i:16514951 original size:14 final size:13
Alignment explanation
Indices: 16514914--16515019 Score: 64
Period size: 12 Copynumber: 8.3 Consensus size: 13
16514904 TTCCTTATAC
16514914 ATATGCATATGTAT
1 ATAT-CATATGTAT
16514928 ATA-CATATGCATAT
1 ATATCATATG--TAT
* *
16514942 GTAT-ATATGCAT
1 ATATCATATGTAT
*
16514954 ATGT-ATA--TAT
1 ATATCATATGTAT
16514964 ATATGCATATGTAT
1 ATAT-CATATGTAT
* *
16514978 ATATAATATATAT
1 ATATCATATGTAT
*
16514991 AATAT-ATATATAT
1 -ATATCATATGTAT
16515004 ATAT-ATATGTAT
1 ATATCATATGTAT
16515016 ATAT
1 ATAT
16515020 ATAGGCTGAC
Statistics
Matches: 75, Mismatches: 9, Indels: 18
0.74 0.09 0.18
Matches are distributed among these distances:
10 5 0.07
12 31 0.41
13 15 0.20
14 24 0.32
ACGTcount: A:0.42, C:0.05, G:0.08, T:0.44
Consensus pattern (13 bp):
ATATCATATGTAT
Found at i:16514955 original size:32 final size:29
Alignment explanation
Indices: 16514920--16515018 Score: 123
Period size: 32 Copynumber: 3.4 Consensus size: 29
16514910 ATACATATGC
16514920 ATATGTATATACATATGCATATGTATATAT
1 ATATGTATATA-ATATGCATATGTATATAT
16514950 GCATATGTATATATATATGCATATGTATATAT
1 --ATATGTATATA-ATATGCATATGTATATAT
* *
16514982 A-ATATATATAATAT--ATATATATATAT
1 ATATGTATATAATATGCATATGTATATAT
16515008 ATATGTATATA
1 ATATGTATATA
16515019 TATAGGCTGA
Statistics
Matches: 62, Mismatches: 4, Indels: 7
0.85 0.05 0.10
Matches are distributed among these distances:
26 12 0.19
27 8 0.13
28 4 0.06
29 8 0.13
30 1 0.02
32 29 0.47
ACGTcount: A:0.43, C:0.04, G:0.08, T:0.44
Consensus pattern (29 bp):
ATATGTATATAATATGCATATGTATATAT
Found at i:16514981 original size:18 final size:18
Alignment explanation
Indices: 16514909--16515022 Score: 119
Period size: 18 Copynumber: 6.4 Consensus size: 18
16514899 ATATTTTCCT
*
16514909 TATACATATGCATATGTA
1 TATATATATGCATATGTA
*
16514927 TATACATATGCATATG--
1 TATATATATGCATATGTA
16514943 --TATATATGCATATGTA
1 TATATATATGCATATGTA
16514959 TATATATATGCATATGTA
1 TATATATATGCATATGTA
** *
16514977 TATATAATATATATAATATA
1 TATAT-ATATGCAT-ATGTA
**
16514997 TATATATATATATATGTA
1 TATATATATGCATATGTA
16515015 TATATATA
1 TATATATA
16515023 GGCTGACTGA
Statistics
Matches: 85, Mismatches: 5, Indels: 12
0.83 0.05 0.12
Matches are distributed among these distances:
14 13 0.15
18 49 0.58
19 14 0.16
20 9 0.11
ACGTcount: A:0.43, C:0.05, G:0.08, T:0.44
Consensus pattern (18 bp):
TATATATATGCATATGTA
Found at i:16517177 original size:16 final size:16
Alignment explanation
Indices: 16517140--16517178 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
16517130 ACACAACTAC
*
16517140 ACATACAAACATGAAT
1 ACATATAAACATGAAT
16517156 ACATATAAACAT-AGAT
1 ACATATAAACATGA-AT
16517172 ACATATA
1 ACATATA
16517179 TAACTATATA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 1 0.05
16 20 0.95
ACGTcount: A:0.56, C:0.15, G:0.05, T:0.23
Consensus pattern (16 bp):
ACATATAAACATGAAT
Found at i:16521292 original size:29 final size:30
Alignment explanation
Indices: 16521226--16521292 Score: 70
Period size: 27 Copynumber: 2.3 Consensus size: 30
16521216 ACAACATTTT
*
16521226 AAATTTAAAATATATTTATTGAATAATATA
1 AAATTTAAAATATATATATTGAATAATATA
*
16521256 AAA-ATAAAA-A-ATATATT-AATATATATA
1 AAATTTAAAATATATATATTGAATA-ATATA
16521283 ATAATTTAAA
1 A-AATTTAAA
16521293 TTCATATTAA
Statistics
Matches: 31, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
26 4 0.13
27 12 0.39
28 3 0.10
29 9 0.29
30 3 0.10
ACGTcount: A:0.60, C:0.00, G:0.01, T:0.39
Consensus pattern (30 bp):
AAATTTAAAATATATATATTGAATAATATA
Found at i:16522680 original size:22 final size:22
Alignment explanation
Indices: 16522652--16522701 Score: 93
Period size: 22 Copynumber: 2.3 Consensus size: 22
16522642 ATATAATGTT
16522652 AGAAAAAACTCTTAAATTATTC
1 AGAAAAAACTCTTAAATTATTC
16522674 AGAAAAAACTCTTAAATTATTC
1 AGAAAAAACTCTTAAATTATTC
16522696 A-AAAAA
1 AGAAAAA
16522702 TTTAAATAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
21 5 0.18
22 23 0.82
ACGTcount: A:0.56, C:0.12, G:0.04, T:0.28
Consensus pattern (22 bp):
AGAAAAAACTCTTAAATTATTC
Found at i:16530572 original size:16 final size:16
Alignment explanation
Indices: 16530535--16530573 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
16530525 ACACAACTAC
*
16530535 ACATACAAACATGAAT
1 ACATATAAACATGAAT
16530551 ACATATAAACAT-AGAT
1 ACATATAAACATGA-AT
16530567 ACATATA
1 ACATATA
16530574 TAACTATATA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 1 0.05
16 20 0.95
ACGTcount: A:0.56, C:0.15, G:0.05, T:0.23
Consensus pattern (16 bp):
ACATATAAACATGAAT
Found at i:16532671 original size:10 final size:10
Alignment explanation
Indices: 16532656--16532680 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
16532646 TTATTGAATA
16532656 ATATAAAAAT
1 ATATAAAAAT
16532666 ATATAAAAAT
1 ATATAAAAAT
16532676 ATATA
1 ATATA
16532681 TAATAATTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (10 bp):
ATATAAAAAT
Found at i:16539715 original size:21 final size:21
Alignment explanation
Indices: 16539666--16539706 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
16539656 AGAGCGGTTG
*
16539666 AGAGAGAGGGGAAGACGGGTA
1 AGAGAGAGGGGAAGACGGATA
16539687 AGAGAGAGGGGAAGACGGAT
1 AGAGAGAGGGGAAGACGGAT
16539707 GGGTGAGAGA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.39, C:0.05, G:0.51, T:0.05
Consensus pattern (21 bp):
AGAGAGAGGGGAAGACGGATA
Found at i:16542892 original size:2 final size:2
Alignment explanation
Indices: 16542885--16542931 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
16542875 TATGTTTTGA
16542885 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
16542927 AT AT A
1 AT AT A
16542932 GATTATACGT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:16544764 original size:2 final size:2
Alignment explanation
Indices: 16544757--16544783 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
16544747 ATGGTGTAAT
16544757 TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC T
16544784 AAGACACCCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:16554754 original size:26 final size:26
Alignment explanation
Indices: 16554717--16554768 Score: 63
Period size: 26 Copynumber: 2.0 Consensus size: 26
16554707 GATTAGCCTG
*
16554717 TCATTTAGCAAAGT-TACTTAACAACT
1 TCATTTAGCAAAATCTACTTAA-AACT
16554743 TCATTT-GACAAAATCTACTTAAAACT
1 TCATTTAG-CAAAATCTACTTAAAACT
16554769 AATATTAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
25 1 0.04
26 15 0.65
27 7 0.30
ACGTcount: A:0.40, C:0.19, G:0.06, T:0.35
Consensus pattern (26 bp):
TCATTTAGCAAAATCTACTTAAAACT
Found at i:16556760 original size:16 final size:18
Alignment explanation
Indices: 16556739--16556776 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
16556729 ATTAATTCTA
16556739 TTTTA-TCTT-TTCATTT
1 TTTTATTCTTATTCATTT
*
16556755 TTTTATTCTTATTCCTTT
1 TTTTATTCTTATTCATTT
16556773 TTTT
1 TTTT
16556777 GAAATAATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 5 0.26
17 4 0.21
18 10 0.53
ACGTcount: A:0.11, C:0.13, G:0.00, T:0.76
Consensus pattern (18 bp):
TTTTATTCTTATTCATTT
Found at i:16558040 original size:19 final size:19
Alignment explanation
Indices: 16558016--16558052 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
16558006 CCATTTGACT
16558016 TATTGGAGTATGATTTGAG
1 TATTGGAGTATGATTTGAG
16558035 TATTGGAGTATGATTTGA
1 TATTGGAGTATGATTTGA
16558053 AGTTTAGAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.27, C:0.00, G:0.30, T:0.43
Consensus pattern (19 bp):
TATTGGAGTATGATTTGAG
Found at i:16561682 original size:357 final size:358
Alignment explanation
Indices: 16561026--16561744 Score: 1323
Period size: 357 Copynumber: 2.0 Consensus size: 358
16561016 AAATAATCCC
16561026 TCTTAAATCACATGATAGTTTGCACATCTCTACACCTTTCATGATGGGAAACAACTATTTATTTT
1 TCTTAAATCACATGATAGTTTGCACATCTCTACACCTTTCATGATGGGAAACAACTATTTATTTT
* * *
16561091 GACACCTTTATACAATTAGATCTATTTTAGTTTCATTTTTGATATTCATATAGTAGATTTGCTAA
66 GACACCTTTATACAATTAGATCTATTTTAGTTTCATTTTTGATATTCATATAATACATTTACTAA
*
16561156 TTTAGTTTGTCCTACCAATTCCCTTTGGAAAATGCAGCATCAAATTGTTCTTAAACAAAATTATG
131 TTTAGTTTGTACTACCAATTCCCTTTGGAAAATGCAGCATCAAATTGTTCTTAAACAAAATTATG
16561221 TAATTTTTTTTATATACGTTGTCCATCTAGGATTATGTCATGGTAACTATGGAGATTCAAAACCG
196 TAATTTTTTTTATATACGTTGTCCATCTAGGATTATGTCATGGTAACTATGGAGATTCAAAACCG
*
16561286 AACAATGTAATTTTCAATGACGTTTTGAAGAGAACAACAAATATAATTGAAGTAAGACTTTCGAT
261 AACAATGTAATTTTCAATGACGTATTGAAGAGAACAACAAATATAATTGAAGTAAGACTTTCGAT
16561351 TCTGTTCTGGTTATCTTCCAACTGTGGATATGG
326 TCTGTTCTGGTTATCTTCCAACTGTGGATATGG
*
16561384 TCTTAAATCACATGATAGTTTGCACATCTCTACACCTTTCATGATGGGAAGCAACTATTTATTTT
1 TCTTAAATCACATGATAGTTTGCACATCTCTACACCTTTCATGATGGGAAACAACTATTTATTTT
* *
16561449 GACACCTTTATACAATTAGATCTATTTTAGTTTCATTTTTGATGTTCATGTAATACATTTACTAA
66 GACACCTTTATACAATTAGATCTATTTTAGTTTCATTTTTGATATTCATATAATACATTTACTAA
*
16561514 TTTAGTTTTTACTACCAA-TCCCTTTGGAAAATGCAGCATCAAATTGTTCTTAAACAAAATTATG
131 TTTAGTTTGTACTACCAATTCCCTTTGGAAAATGCAGCATCAAATTGTTCTTAAACAAAATTATG
* * *
16561578 TAATTTTTTTTATTTACGTTGTCCATCTAGGATTATGTCATGGTAACTATGGATATTCAAAATCG
196 TAATTTTTTTTATATACGTTGTCCATCTAGGATTATGTCATGGTAACTATGGAGATTCAAAACCG
16561643 AACAATGTAATTTTCAATGACGTATTGAAGAGAACAACAAATATAATTGAAGTAAGACTTTCGAT
261 AACAATGTAATTTTCAATGACGTATTGAAGAGAACAACAAATATAATTGAAGTAAGACTTTCGAT
16561708 TCTGTTCTGGTTATCTTCCAACTGTGGATATGG
326 TCTGTTCTGGTTATCTTCCAACTGTGGATATGG
16561741 TCTT
1 TCTT
16561745 TTGCTATTTA
Statistics
Matches: 349, Mismatches: 12, Indels: 1
0.96 0.03 0.00
Matches are distributed among these distances:
357 209 0.60
358 140 0.40
ACGTcount: A:0.31, C:0.15, G:0.14, T:0.39
Consensus pattern (358 bp):
TCTTAAATCACATGATAGTTTGCACATCTCTACACCTTTCATGATGGGAAACAACTATTTATTTT
GACACCTTTATACAATTAGATCTATTTTAGTTTCATTTTTGATATTCATATAATACATTTACTAA
TTTAGTTTGTACTACCAATTCCCTTTGGAAAATGCAGCATCAAATTGTTCTTAAACAAAATTATG
TAATTTTTTTTATATACGTTGTCCATCTAGGATTATGTCATGGTAACTATGGAGATTCAAAACCG
AACAATGTAATTTTCAATGACGTATTGAAGAGAACAACAAATATAATTGAAGTAAGACTTTCGAT
TCTGTTCTGGTTATCTTCCAACTGTGGATATGG
Found at i:16574089 original size:12 final size:12
Alignment explanation
Indices: 16574058--16574091 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
16574048 GTTTCGGGTT
*
16574058 CAGGCACAGGCA
1 CAGGCACGGGCA
16574070 CAGGCACGGGCA
1 CAGGCACGGGCA
*
16574082 CGGGCACGGG
1 CAGGCACGGG
16574092 TGGAGGGTTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.24, C:0.32, G:0.44, T:0.00
Consensus pattern (12 bp):
CAGGCACGGGCA
Found at i:16575685 original size:17 final size:17
Alignment explanation
Indices: 16575663--16575704 Score: 66
Period size: 17 Copynumber: 2.5 Consensus size: 17
16575653 ACTAAATATG
16575663 TGATATTTACCAATCAC
1 TGATATTTACCAATCAC
*
16575680 TGATATTTACTAATCAC
1 TGATATTTACCAATCAC
*
16575697 TAATATTT
1 TGATATTT
16575705 TGTGAACATA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.36, C:0.17, G:0.05, T:0.43
Consensus pattern (17 bp):
TGATATTTACCAATCAC
Found at i:16587007 original size:11 final size:11
Alignment explanation
Indices: 16586993--16587025 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
16586983 TAATTATTTT
*
16586993 ATATTTATATA
1 ATATTGATATA
16587004 ATATTGATATA
1 ATATTGATATA
16587015 ATATTGA-ATA
1 ATATTGATATA
16587025 A
1 A
16587026 AAGGTGAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
10 4 0.19
11 17 0.81
ACGTcount: A:0.48, C:0.00, G:0.06, T:0.45
Consensus pattern (11 bp):
ATATTGATATA
Found at i:16590766 original size:23 final size:22
Alignment explanation
Indices: 16590723--16590780 Score: 55
Period size: 23 Copynumber: 2.5 Consensus size: 22
16590713 AAATACAAAC
* **
16590723 ATATTTTTATTATAATTTAATA
1 ATATTTTTATTAGAAGATAATA
16590745 ATATTTTGTATTAGAAGATAATTA
1 ATATTTT-TATTAGAAGATAA-TA
16590769 A-ACTTTTTATTA
1 ATA-TTTTTATTA
16590781 TAATTAAATA
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
22 7 0.23
23 16 0.53
24 7 0.23
ACGTcount: A:0.40, C:0.02, G:0.05, T:0.53
Consensus pattern (22 bp):
ATATTTTTATTAGAAGATAATA
Found at i:16590923 original size:44 final size:42
Alignment explanation
Indices: 16590831--16590926 Score: 113
Period size: 44 Copynumber: 2.2 Consensus size: 42
16590821 TTCATTCAAT
*
16590831 TTAAATAATACTAAATAATATTCTTTATTACATTCATTATAA
1 TTAAATAATAATAAATAATATTCTTTATTACATTCATTATAA
* * * *
16590873 TCAAATAATAATATTAATAATATTCTTTA-TAGTATTTATTATAG
1 TTAAATAATAATA--AATAATATTCTTTATTA-CATTCATTATAA
16590917 TTAAATAATA
1 TTAAATAATA
16590927 TTAATATATT
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
42 11 0.24
43 2 0.04
44 32 0.71
ACGTcount: A:0.46, C:0.06, G:0.02, T:0.46
Consensus pattern (42 bp):
TTAAATAATAATAAATAATATTCTTTATTACATTCATTATAA
Found at i:16590937 original size:8 final size:8
Alignment explanation
Indices: 16590924--16590954 Score: 62
Period size: 8 Copynumber: 3.9 Consensus size: 8
16590914 TAGTTAAATA
16590924 ATATTAAT
1 ATATTAAT
16590932 ATATTAAT
1 ATATTAAT
16590940 ATATTAAT
1 ATATTAAT
16590948 ATATTAA
1 ATATTAA
16590955 ATAATATTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (8 bp):
ATATTAAT
Found at i:16591722 original size:30 final size:29
Alignment explanation
Indices: 16591682--16591784 Score: 118
Period size: 30 Copynumber: 3.5 Consensus size: 29
16591672 ATTATTAGTC
*
16591682 ATAAGGGCTTATTTGATTCAAAATAAAAAT
1 ATAAGAGCTTATTTGA-TCAAAATAAAAAT
16591712 ATAAGAGCTTATTTGACTCAAAATAAAAAT
1 ATAAGAGCTTATTTGA-TCAAAATAAAAAT
* ** *
16591742 ATAAGAACTTGA-TTGATCGTAATAAAAGT
1 ATAAGAGCTT-ATTTGATCAAAATAAAAAT
*
16591771 ATAATAGCTTATTT
1 ATAAGAGCTTATTT
16591785 AAATTTTCTT
Statistics
Matches: 63, Mismatches: 8, Indels: 5
0.83 0.11 0.07
Matches are distributed among these distances:
28 1 0.02
29 20 0.32
30 41 0.65
31 1 0.02
ACGTcount: A:0.46, C:0.08, G:0.13, T:0.34
Consensus pattern (29 bp):
ATAAGAGCTTATTTGATCAAAATAAAAAT
Found at i:16593609 original size:17 final size:17
Alignment explanation
Indices: 16593587--16593619 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
16593577 TCTTCATGTC
*
16593587 AAATTAAATACAAAATT
1 AAATTAAAAACAAAATT
16593604 AAATTAAAAACAAAAT
1 AAATTAAAAACAAAAT
16593620 ATATATGATC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.70, C:0.06, G:0.00, T:0.24
Consensus pattern (17 bp):
AAATTAAAAACAAAATT
Found at i:16594305 original size:35 final size:35
Alignment explanation
Indices: 16594149--16594360 Score: 211
Period size: 35 Copynumber: 6.1 Consensus size: 35
16594139 TTAATTGTTT
* * * *
16594149 AATTTAATCAATTAAGCTCAATAACTTAATTAAAT
1 AATTTAATCAATTAGGCACAATGACTTAATTAAAC
* *
16594184 AATTTAATTAATTAAGCAACAAT---TTAATTAAAC
1 AATTTAATCAATTAGGC-ACAATGACTTAATTAAAC
*** *
16594217 AATTTTAATCAATTAGGTTTAATGACTTAATTGAAC
1 AA-TTTAATCAATTAGGCACAATGACTTAATTAAAC
* *
16594253 AATTTTAATCAAATAGGCACAATGACTTAGTTAAAC
1 AA-TTTAATCAATTAGGCACAATGACTTAATTAAAC
* * *
16594289 AATTTAATTAATTAGGCTCAATGATTTAATTAAAC
1 AATTTAATCAATTAGGCACAATGACTTAATTAAAC
*
16594324 AATTTAATTAATTAGGCAC-A--ACTTAATTAAAC
1 AATTTAATCAATTAGGCACAATGACTTAATTAAAC
16594356 AATTT
1 AATTT
16594361 TAGAGCATGT
Statistics
Matches: 150, Mismatches: 22, Indels: 13
0.81 0.12 0.07
Matches are distributed among these distances:
32 16 0.11
33 14 0.09
34 13 0.09
35 62 0.41
36 45 0.30
ACGTcount: A:0.45, C:0.10, G:0.07, T:0.37
Consensus pattern (35 bp):
AATTTAATCAATTAGGCACAATGACTTAATTAAAC
Found at i:16602832 original size:16 final size:16
Alignment explanation
Indices: 16602813--16602843 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
16602803 GATTCGCTGA
16602813 TGGAATTTTTCGTTGT
1 TGGAATTTTTCGTTGT
*
16602829 TGGAATTTTTTGTTG
1 TGGAATTTTTCGTTG
16602844 AAACTTTCTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.13, C:0.03, G:0.26, T:0.58
Consensus pattern (16 bp):
TGGAATTTTTCGTTGT
Found at i:16604700 original size:12 final size:12
Alignment explanation
Indices: 16604683--16604712 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
16604673 AAAATATTCT
*
16604683 TAATATGCTTTC
1 TAATATGCTATC
16604695 TAATATGCTATC
1 TAATATGCTATC
16604707 TAATAT
1 TAATAT
16604713 TCCAACCAAA
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:0.33, C:0.13, G:0.07, T:0.47
Consensus pattern (12 bp):
TAATATGCTATC
Found at i:16607294 original size:15 final size:15
Alignment explanation
Indices: 16607274--16607304 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
16607264 CACGTTTTAG
*
16607274 TATTTATTATTTACT
1 TATTTATTATTAACT
16607289 TATTTATTATTAACT
1 TATTTATTATTAACT
16607304 T
1 T
16607305 TTCTATCCCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.29, C:0.06, G:0.00, T:0.65
Consensus pattern (15 bp):
TATTTATTATTAACT
Found at i:16609112 original size:19 final size:19
Alignment explanation
Indices: 16609090--16609129 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
16609080 TATATTAAAT
16609090 AAAAAATCAT-ATTACTTTA
1 AAAAAAT-ATCATTACTTTA
*
16609109 AAAAAATATCATTTCTTTA
1 AAAAAATATCATTACTTTA
16609128 AA
1 AA
16609130 CCAAGCATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 2 0.11
19 17 0.89
ACGTcount: A:0.53, C:0.10, G:0.00, T:0.38
Consensus pattern (19 bp):
AAAAAATATCATTACTTTA
Found at i:16614492 original size:24 final size:24
Alignment explanation
Indices: 16614430--16614493 Score: 58
Period size: 24 Copynumber: 2.7 Consensus size: 24
16614420 CCAAACAGTG
*
16614430 GAAGAGCGACGG-AGAGAAAGAGGG
1 GAAGAGCGA-GGAAGAGAAAGAGGA
* ** **
16614454 GAAAAATGATTAAGAGAAAGAGGA
1 GAAGAGCGAGGAAGAGAAAGAGGA
16614478 GAAGAGCGAGGAAGAG
1 GAAGAGCGAGGAAGAG
16614494 CAATGGAGAG
Statistics
Matches: 28, Mismatches: 11, Indels: 2
0.68 0.27 0.05
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.48, C:0.05, G:0.42, T:0.05
Consensus pattern (24 bp):
GAAGAGCGAGGAAGAGAAAGAGGA
Found at i:16614684 original size:48 final size:48
Alignment explanation
Indices: 16614499--16614746 Score: 216
Period size: 48 Copynumber: 5.2 Consensus size: 48
16614489 AAGAGCAATG
* * *
16614499 GAGAGA-AAGAGGGGAAGAGCGACTGAGAGAAAGAGGGGAAAAGCAGCG
1 GAGAGAGAA-AGGGGAAGAGCGACTGAGAGAAAGAGGGGAAGAGCGGCT
* ** * * *
16614547 GAGAGA-AAGAGGGGAAAAGCGGTTGAGAGAAAGAGGGAAAGAACAGCT
1 GAGAGAGAA-AGGGGAAGAGCGACTGAGAGAAAGAGGGGAAGAGCGGCT
* * * * * *
16614595 GAGAAAGAGAGGGGAAAAGGGACTGAGAGAAAGAGGCGAAGAGCGGTT
1 GAGAGAGAAAGGGGAAGAGCGACTGAGAGAAAGAGGGGAAGAGCGGCT
* *
16614643 GAGAGAGAAAGGGGAAGAGCGACAGAGAGAAAGAGGGGAAGAACGGCT
1 GAGAGAGAAAGGGGAAGAGCGACTGAGAGAAAGAGGGGAAGAGCGGCT
* * * * * * * * *
16614691 AAAAGAAAAAAGGGAAGAGCGGCTGAGAG-ATGAGGGAAAG-GAGGAT
1 GAGAGAGAAAGGGGAAGAGCGACTGAGAGAAAGAGGGGAAGAGCGGCT
16614737 GAGAGAGAAA
1 GAGAGAGAAA
16614747 AAATTATTTT
Statistics
Matches: 160, Mismatches: 39, Indels: 4
0.79 0.19 0.02
Matches are distributed among these distances:
46 10 0.06
47 9 0.06
48 140 0.88
49 1 0.01
ACGTcount: A:0.45, C:0.06, G:0.44, T:0.04
Consensus pattern (48 bp):
GAGAGAGAAAGGGGAAGAGCGACTGAGAGAAAGAGGGGAAGAGCGGCT
Found at i:16614697 original size:24 final size:24
Alignment explanation
Indices: 16614499--16614720 Score: 193
Period size: 24 Copynumber: 9.2 Consensus size: 24
16614489 AAGAGCAATG
* *
16614499 GAGAGAAAGAGGGGAAGAGCGACT
1 GAGAGAAAGAGGGGAAGAACGGCT
* *
16614523 GAGAGAAAGAGGGGAA-AAGCAGCG
1 GAGAGAAAGAGGGGAAGAA-CGGCT
*
16614547 GAGAGAAAGAGGGGAA-AAGCGGTT
1 GAGAGAAAGAGGGGAAGAA-CGGCT
* *
16614571 GAGAGAAAGAGGGAAAGAACAGCT
1 GAGAGAAAGAGGGGAAGAACGGCT
*
16614595 GAGA-AAGAGAGGGGAA-AAGGGACT
1 GAGAGAA-AGAGGGGAAGAACGG-CT
* * *
16614619 GAGAGAAAGAGGCGAAGAGCGGTT
1 GAGAGAAAGAGGGGAAGAACGGCT
* * *
16614643 GAGAGAGAA-AGGGGAAGAGCGACA
1 GAGAGA-AAGAGGGGAAGAACGGCT
16614667 GAGAGAAAGAGGGGAAGAACGGCT
1 GAGAGAAAGAGGGGAAGAACGGCT
* * * * *
16614691 AAAAGAAAAAAGGGAAGAGCGGCT
1 GAGAGAAAGAGGGGAAGAACGGCT
16614715 GAGAGA
1 GAGAGA
16614721 TGAGGGAAAG
Statistics
Matches: 159, Mismatches: 31, Indels: 16
0.77 0.15 0.08
Matches are distributed among these distances:
23 8 0.05
24 142 0.89
25 9 0.06
ACGTcount: A:0.45, C:0.07, G:0.44, T:0.04
Consensus pattern (24 bp):
GAGAGAAAGAGGGGAAGAACGGCT
Found at i:16614698 original size:72 final size:70
Alignment explanation
Indices: 16614499--16614720 Score: 243
Period size: 72 Copynumber: 3.1 Consensus size: 70
16614489 AAGAGCAATG
* * *
16614499 GAGAGAAAGAGGGGAAGAGCGACTGAGAGAAAGAGGGGAAAAGCAGCGGAGAGAAAGAGGGGAAA
1 GAGAGAAAGAGGGGAAGAGCGACTGAGAGAAAGAGGGGAAAA-CGGCTGAGAGAAAGA-GGGAAG
16614564 AGCGGTT
64 AGCGGTT
* * *
16614571 GAGAGAAAGAGGGAAAGAAC-AGCTGAGA-AAGAGAGGGGAAAAGGGACTGAGAGAAAGAGGCGA
1 GAGAGAAAGAGGGGAAGAGCGA-CTGAGAGAA-AGAGGGGAAAACGG-CTGAGAGAAAGAGG-GA
16614634 AGAGCGGTT
62 AGAGCGGTT
* * * *
16614643 GAGAGAGAA-AGGGGAAGAGCGACAGAGAGAAAGAGGGGAAGAACGGCTAAAAGAAAAAAGGGAA
1 GAGAGA-AAGAGGGGAAGAGCGACTGAGAGAAAGAGGGGAA-AACGGCTGAGAG-AAAGAGGGAA
*
16614707 GAGCGGCT
63 GAGCGGTT
16614715 GAGAGA
1 GAGAGA
16614721 TGAGGGAAAG
Statistics
Matches: 127, Mismatches: 14, Indels: 18
0.80 0.09 0.11
Matches are distributed among these distances:
71 6 0.05
72 106 0.83
73 15 0.12
ACGTcount: A:0.45, C:0.07, G:0.44, T:0.04
Consensus pattern (70 bp):
GAGAGAAAGAGGGGAAGAGCGACTGAGAGAAAGAGGGGAAAACGGCTGAGAGAAAGAGGGAAGAG
CGGTT
Found at i:16615265 original size:14 final size:14
Alignment explanation
Indices: 16615246--16615280 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
16615236 TGATGGCTAA
*
16615246 AAACCAAAATAAAG
1 AAACCAAAAAAAAG
*
16615260 AAACCAAAAAAAAT
1 AAACCAAAAAAAAG
16615274 AAACCAA
1 AAACCAA
16615281 CAACAAAGTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.74, C:0.17, G:0.03, T:0.06
Consensus pattern (14 bp):
AAACCAAAAAAAAG
Found at i:16619623 original size:34 final size:34
Alignment explanation
Indices: 16619580--16619647 Score: 109
Period size: 34 Copynumber: 2.0 Consensus size: 34
16619570 AATAACTAGG
* *
16619580 TTGACAATATACTGACATCACAACAAAATTCACC
1 TTGACAATATAATGAAATCACAACAAAATTCACC
*
16619614 TTGACAATATAATGAAATCACAACAAACTTCACC
1 TTGACAATATAATGAAATCACAACAAAATTCACC
16619648 CTACATTAGT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
34 31 1.00
ACGTcount: A:0.46, C:0.25, G:0.06, T:0.24
Consensus pattern (34 bp):
TTGACAATATAATGAAATCACAACAAAATTCACC
Found at i:16620608 original size:2 final size:2
Alignment explanation
Indices: 16620603--16620628 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
16620593 GAGGGGGGGN
16620603 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
16620629 GAGAGAGAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:16620633 original size:2 final size:2
Alignment explanation
Indices: 16620628--16620659 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
16620618 ATATATATAT
16620628 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
16620660 GAGGGAGGGG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:16626545 original size:2 final size:2
Alignment explanation
Indices: 16626538--16626562 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
16626528 CACCAAAATA
16626538 TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG T
16626563 ACACCAAATG
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:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:16635117 original size:17 final size:17
Alignment explanation
Indices: 16635089--16635136 Score: 69
Period size: 17 Copynumber: 2.8 Consensus size: 17
16635079 TCTAGACACT
*
16635089 ACCCATTAAATACTCGA
1 ACCCATTAAATACCCGA
* *
16635106 ACTCATTTAATACCCGA
1 ACCCATTAAATACCCGA
16635123 ACCCATTAAATACC
1 ACCCATTAAATACC
16635137 AAATTAAAAT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
17 26 1.00
ACGTcount: A:0.40, C:0.31, G:0.04, T:0.25
Consensus pattern (17 bp):
ACCCATTAAATACCCGA
Found at i:16635335 original size:20 final size:22
Alignment explanation
Indices: 16635293--16635337 Score: 58
Period size: 20 Copynumber: 2.1 Consensus size: 22
16635283 TTATAAAGAA
*
16635293 TTAATATATATAAAACTAATAT
1 TTAATATATATAAAACCAATAT
*
16635315 TTAATAT-TA-AAAACCATTAT
1 TTAATATATATAAAACCAATAT
16635335 TTA
1 TTA
16635338 TAATTGGGTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 12 0.57
21 2 0.10
22 7 0.33
ACGTcount: A:0.51, C:0.07, G:0.00, T:0.42
Consensus pattern (22 bp):
TTAATATATATAAAACCAATAT
Found at i:16640775 original size:2 final size:2
Alignment explanation
Indices: 16640758--16640793 Score: 54
Period size: 2 Copynumber: 17.5 Consensus size: 2
16640748 GTTGTTTGTG
*
16640758 TA TA CTA TA CA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
16640794 GTAAAATGTT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
2 29 0.94
3 2 0.06
ACGTcount: A:0.47, C:0.06, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:16641234 original size:25 final size:25
Alignment explanation
Indices: 16641200--16641257 Score: 89
Period size: 25 Copynumber: 2.3 Consensus size: 25
16641190 CGGTCTGTAA
* *
16641200 TTATACGTGGTAAGGGCACGAGTTG
1 TTATACGTGGCAAGGCCACGAGTTG
16641225 TTATACGTGGCAAGGCCACGAGTTG
1 TTATACGTGGCAAGGCCACGAGTTG
*
16641250 ATATACGT
1 TTATACGT
16641258 AGTTGCGACC
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 30 1.00
ACGTcount: A:0.26, C:0.16, G:0.31, T:0.28
Consensus pattern (25 bp):
TTATACGTGGCAAGGCCACGAGTTG
Found at i:16643519 original size:76 final size:73
Alignment explanation
Indices: 16643397--16643556 Score: 216
Period size: 76 Copynumber: 2.2 Consensus size: 73
16643387 AGAGCGCATC
* * *
16643397 TATTTTAATTTTGGGTAATTCATAAAAAAAAATTGTTCCTTACTTTAAAAGCAATTCCTAAAATT
1 TATTTTAATTTTGGATAATTAATAAAAAAAAATTGTTCCTTACTTTAAAAGAAATTCCTAAAATT
16643462 AAGGATAGA
66 AAGGATA-A
* *
16643471 -ATTTTAATTTTGGATGATTAATAAAAATAGGAAATTGTTTCC-TACTTTAAAAGAAATTCTTAA
1 TATTTTAATTTTGGATAATTAATAAAAA-A--AAATTG-TTCCTTACTTTAAAAGAAATTCCTAA
16643534 AATTAAGGATAA
62 AATTAAGGATAA
16643546 TATTTTAATTT
1 TATTTTAATTT
16643557 AGAAAATTCA
Statistics
Matches: 76, Mismatches: 5, Indels: 8
0.85 0.06 0.09
Matches are distributed among these distances:
73 24 0.32
74 1 0.01
75 1 0.01
76 46 0.61
77 4 0.05
ACGTcount: A:0.42, C:0.07, G:0.11, T:0.41
Consensus pattern (73 bp):
TATTTTAATTTTGGATAATTAATAAAAAAAAATTGTTCCTTACTTTAAAAGAAATTCCTAAAATT
AAGGATAA
Found at i:16650389 original size:2 final size:2
Alignment explanation
Indices: 16650382--16650421 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
16650372 NNNNNNNNNN
16650382 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
16650422 TGTCATTTAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:16651221 original size:26 final size:26
Alignment explanation
Indices: 16651185--16651243 Score: 109
Period size: 26 Copynumber: 2.3 Consensus size: 26
16651175 CGCCATACTT
*
16651185 AATGACATATCTAGGATATTTGATAA
1 AATGACTTATCTAGGATATTTGATAA
16651211 AATGACTTATCTAGGATATTTGATAA
1 AATGACTTATCTAGGATATTTGATAA
16651237 AATGACT
1 AATGACT
16651244 ATATTGCACT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 32 1.00
ACGTcount: A:0.41, C:0.08, G:0.15, T:0.36
Consensus pattern (26 bp):
AATGACTTATCTAGGATATTTGATAA
Done.