Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr2
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: 41236440
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 2030548 characters in sequence are not A, C, G, or T
File 36 of 106
Found at i:13777005 original size:25 final size:25
Alignment explanation
Indices: 13776977--13777028 Score: 86
Period size: 25 Copynumber: 2.1 Consensus size: 25
13776967 ATATATGATT
*
13776977 AACTAACAATTGAAAACTATTCCAC
1 AACTAACAATTAAAAACTATTCCAC
*
13777002 AACTAACAATTAAAAACTATTCTAC
1 AACTAACAATTAAAAACTATTCCAC
13777027 AA
1 AA
13777029 TTAAAATCAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.52, C:0.21, G:0.02, T:0.25
Consensus pattern (25 bp):
AACTAACAATTAAAAACTATTCCAC
Found at i:13777508 original size:86 final size:86
Alignment explanation
Indices: 13777394--13777662 Score: 394
Period size: 86 Copynumber: 3.1 Consensus size: 86
13777384 AAACATTGTT
* * * * * *
13777394 GTTTGCATCCTAGTTAAAGAAATATAAATTAATTTTACATTTTTTAATTTACAAGTTTAACTAAA
1 GTTTGCATCATAGTTCAAGTAATATAAATTAATTTTACATTTATTAGTTTACAAGTTTAACTAAT
13777459 ATTAAAATTTTATATATTTAA
66 ATTAAAATTTTATATATTTAA
* *
13777480 GTTTGCATCATAGTTCAAGTAATATAAATTAATTTTACATTTATTAGTTTACAAATTCAACTAAT
1 GTTTGCATCATAGTTCAAGTAATATAAATTAATTTTACATTTATTAGTTTACAAGTTTAACTAAT
*
13777545 ATTAAAATTTTATATTTTTAA
66 ATTAAAATTTTATATATTTAA
* * * *
13777566 GATTACATCATAGTTCAAGTAATATAAATTACTTTTACATTTGTTAGTTTACAAGTTTAACTAAT
1 GTTTGCATCATAGTTCAAGTAATATAAATTAATTTTACATTTATTAGTTTACAAGTTTAACTAAT
* * *
13777631 ATAAAAATTTTATATATGTAC
66 ATTAAAATTTTATATATTTAA
13777652 GTTTGCATCAT
1 GTTTGCATCAT
13777663 TGTGTTGGGT
Statistics
Matches: 162, Mismatches: 21, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
86 162 1.00
ACGTcount: A:0.39, C:0.09, G:0.07, T:0.45
Consensus pattern (86 bp):
GTTTGCATCATAGTTCAAGTAATATAAATTAATTTTACATTTATTAGTTTACAAGTTTAACTAAT
ATTAAAATTTTATATATTTAA
Found at i:13777509 original size:48 final size:46
Alignment explanation
Indices: 13777457--13777596 Score: 127
Period size: 46 Copynumber: 3.1 Consensus size: 46
13777447 AGTTTAACTA
13777457 AAATTAAAATTTTATATATTTAAGTTTGCATCATAGTTCAAGTAATAT
1 AAATTAAAATTTTATAT-TTTAAGTTT-CATCATAGTTCAAGTAATAT
* * * *
13777505 AAATT--AATTTTACATTTATTAGTTT-A-CA-AATTCAACT-A-AT
1 AAATTAAAATTTTATATTT-TAAGTTTCATCATAGTTCAAGTAATAT
*
13777545 --ATTAAAATTTTATATTTTTAAGATTACATCATAGTTCAAGTAATAT
1 AAATTAAAATTTTATA-TTTTAAG-TTTCATCATAGTTCAAGTAATAT
13777591 AAATTA
1 AAATTA
13777597 CTTTTACATT
Statistics
Matches: 71, Mismatches: 9, Indels: 24
0.68 0.09 0.23
Matches are distributed among these distances:
38 3 0.04
40 13 0.18
41 6 0.08
42 8 0.11
43 4 0.06
44 8 0.11
45 3 0.04
46 17 0.24
48 9 0.13
ACGTcount: A:0.43, C:0.07, G:0.06, T:0.44
Consensus pattern (46 bp):
AAATTAAAATTTTATATTTTAAGTTTCATCATAGTTCAAGTAATAT
Found at i:13777545 original size:42 final size:39
Alignment explanation
Indices: 13777414--13777642 Score: 161
Period size: 42 Copynumber: 5.4 Consensus size: 39
13777404 TAGTTAAAGA
* *
13777414 AATATAAATTAATTTTACATTTTTTAATTTACAAGTTTAACT
1 AATATAAA--AATTTTACA-TTTTTAGTTTACAAGTTCAACT
* * * * *
13777456 AAAATTAAAATTTTATATATTTAAGTTTGCATCATAGTTCAAGT
1 AATATAAAAATTTTACAT-TTTTAGTTT--A-CA-AGTTCAACT
*
13777500 AATATAAATTAATTTTACATTTATTAGTTTACAAATTCAACT
1 AATATAAA--AATTTTACATTT-TTAGTTTACAAGTTCAACT
* * * *
13777542 AATATTAAAATTTTATATTTTTAAGATTACATCATAGTTCAAGT
1 AATATAAAAATTTTACATTTTT-AG-TT-TA-CA-AGTTCAACT
* *
13777586 AATATAAATTACTTTTACATTTGTTAGTTTACAAGTTTAACT
1 AATATAAA--AATTTTACATTT-TTAGTTTACAAGTTCAACT
13777628 AATATAAAAATTTTA
1 AATATAAAAATTTTA
13777643 TATATGTACG
Statistics
Matches: 146, Mismatches: 25, Indels: 34
0.71 0.12 0.17
Matches are distributed among these distances:
39 3 0.02
40 34 0.23
41 2 0.01
42 37 0.25
43 8 0.05
44 29 0.20
45 4 0.03
46 27 0.18
47 2 0.01
ACGTcount: A:0.41, C:0.07, G:0.05, T:0.46
Consensus pattern (39 bp):
AATATAAAAATTTTACATTTTTAGTTTACAAGTTCAACT
Found at i:13778415 original size:36 final size:35
Alignment explanation
Indices: 13778308--13778622 Score: 312
Period size: 35 Copynumber: 8.9 Consensus size: 35
13778298 AGTTCTTAAG
**** *
13778308 AAGCCCAATTAACTTAATTGTTTAATTTAATCGATT
1 AAGCCCAA-TAACTTAATTAAACAATTTAATCAATT
* * *
13778344 AGGCCCAATAACTTAATTAAATAATTTAATTAATT
1 AAGCCCAATAACTTAATTAAACAATTTAATCAATT
* *
13778379 AAGCCCAACAATTTAATTAAACAATTTTAATCAATT
1 AAGCCCAATAACTTAATTAAACAA-TTTAATCAATT
*
13778415 AAGCCCAATGACTTAATTAAACGAATTTAATCAATT
1 AAGCCCAATAACTTAATTAAAC-AATTTAATCAATT
* *
13778451 AAGTCCAATGACTTAATTAAACGAATTTAATCAATT
1 AAGCCCAATAACTTAATTAAAC-AATTTAATCAATT
**** *
13778487 AAGCCCAATAACTTAATTGTTTAATTTAATTAATT
1 AAGCCCAATAACTTAATTAAACAATTTAATCAATT
* * * *
13778522 AGGCTCAATGACTTAATTAAACAATTTAATTAATT
1 AAGCCCAATAACTTAATTAAACAATTTAATCAATT
* * * * *
13778557 AGGCCCAATGATTTAATTAAATAATTTAATTAATT
1 AAGCCCAATAACTTAATTAAACAATTTAATCAATT
*
13778592 -AG-GC-ATAACTTAATTAAACAATTTTAATCAA
1 AAGCCCAATAACTTAATTAAACAA-TTTAATCAA
13778623 GTGCTTGAGA
Statistics
Matches: 238, Mismatches: 38, Indels: 9
0.84 0.13 0.03
Matches are distributed among these distances:
32 14 0.06
33 9 0.04
34 1 0.00
35 114 0.48
36 98 0.41
37 2 0.01
ACGTcount: A:0.43, C:0.13, G:0.07, T:0.37
Consensus pattern (35 bp):
AAGCCCAATAACTTAATTAAACAATTTAATCAATT
Found at i:13778432 original size:18 final size:18
Alignment explanation
Indices: 13778411--13778470 Score: 50
Period size: 18 Copynumber: 3.3 Consensus size: 18
13778401 AATTTTAATC
*
13778411 AATTAAGCCCAATGACTT
1 AATTAAGACCAATGACTT
* * * *
13778429 AATTAA-ACGAATTTAATC
1 AATTAAGACCAA-TGACTT
*
13778447 AATTAAGTCCAATGACTT
1 AATTAAGACCAATGACTT
13778465 AATTAA
1 AATTAA
13778471 ACGAATTTAA
Statistics
Matches: 30, Mismatches: 10, Indels: 4
0.68 0.23 0.09
Matches are distributed among these distances:
17 3 0.10
18 24 0.80
19 3 0.10
ACGTcount: A:0.45, C:0.15, G:0.08, T:0.32
Consensus pattern (18 bp):
AATTAAGACCAATGACTT
Found at i:13778486 original size:18 final size:18
Alignment explanation
Indices: 13778429--13778488 Score: 59
Period size: 18 Copynumber: 3.3 Consensus size: 18
13778419 CCAATGACTT
13778429 AATTAAACGAATTTAATC
1 AATTAAACGAATTTAATC
* * * * *
13778447 AATTAAGTCCAA-TGACTT
1 AATTAA-ACGAATTTAATC
13778465 AATTAAACGAATTTAATC
1 AATTAAACGAATTTAATC
13778483 AATTAA
1 AATTAA
13778489 GCCCAATAAC
Statistics
Matches: 30, Mismatches: 10, Indels: 4
0.68 0.23 0.09
Matches are distributed among these distances:
17 3 0.10
18 24 0.80
19 3 0.10
ACGTcount: A:0.48, C:0.12, G:0.07, T:0.33
Consensus pattern (18 bp):
AATTAAACGAATTTAATC
Found at i:13780720 original size:38 final size:40
Alignment explanation
Indices: 13780632--13780734 Score: 120
Period size: 38 Copynumber: 2.6 Consensus size: 40
13780622 ACCCAGCTCA
* * *
13780632 TGTGCATCCCCACACATCGTGCACATAGCCAGAGTCATCG
1 TGTGCATCCCCCCACATCGTGCACATAGACAGAGCCATCG
* * *
13780672 TGTGCGTCCCCCCACATCGTGCACA-A-ATAGTGCCATCG
1 TGTGCATCCCCCCACATCGTGCACATAGACAGAGCCATCG
* *
13780710 TGTGCATCCCCCTACATCATGCACA
1 TGTGCATCCCCCCACATCGTGCACA
13780735 CGGGCACTTT
Statistics
Matches: 54, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
38 30 0.56
39 1 0.02
40 23 0.43
ACGTcount: A:0.23, C:0.37, G:0.18, T:0.21
Consensus pattern (40 bp):
TGTGCATCCCCCCACATCGTGCACATAGACAGAGCCATCG
Found at i:13780858 original size:2 final size:2
Alignment explanation
Indices: 13780851--13780905 Score: 110
Period size: 2 Copynumber: 27.5 Consensus size: 2
13780841 AATGCACAAC
13780851 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
13780893 AT AT AT AT AT AT A
1 AT AT AT AT AT AT A
13780906 NNNNNNNNNN
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:13781724 original size:23 final size:23
Alignment explanation
Indices: 13781698--13781742 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
13781688 AGGAAGAAGA
13781698 AGAAGAAGCTACTGGAAAATGAG
1 AGAAGAAGCTACTGGAAAATGAG
*
13781721 AGAAGAAGCTACTGGAAGATGA
1 AGAAGAAGCTACTGGAAAATGA
13781743 TATTTATAAC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.47, C:0.09, G:0.31, T:0.13
Consensus pattern (23 bp):
AGAAGAAGCTACTGGAAAATGAG
Found at i:13786228 original size:180 final size:180
Alignment explanation
Indices: 13786014--13786342 Score: 518
Period size: 180 Copynumber: 1.8 Consensus size: 180
13786004 TTAATAGCCT
* * * *
13786014 AAATCAGCTTGTTTGGCCATGAAAATTTCCAGAAATAATCCTCATTGAACATTTTAATAAAGATA
1 AAATCAGCATATTTGACCATGAAAATTTCCAGAAATAATCCTCATTAAACATTTTAATAAAGATA
* *
13786079 ATTTT-TCTGGAATTTTTCAGAATTAATTTTCC-AGAGTTTCTTGTCAATTAAAACTGAAATTCA
66 GTTTTCT-TGGAATTTTTCAGAATTAA-TTTCCAAGACTTTCTTGTCAATTAAAACTGAAATTCA
13786142 TGCCAAAACAGTGAGCTGGACAGATTTATATTTGCACCAATTTTCTTGCTCG
129 TGCCAAAACAGTGAGCTGGACAGATTTATATTTGCACCAATTTTCTTGCTCG
* * *
13786194 AAATCAGCATATTTGACCATGATATTTTCCAGAAATAATCCTTATTAAACATTTTAATAAAGATA
1 AAATCAGCATATTTGACCATGAAAATTTCCAGAAATAATCCTCATTAAACATTTTAATAAAGATA
*
13786259 GTTTTCTTGGAATTTTTCAGAATTAATTTCCAAGACTTTCTTGTTAATTAAAACTGAAATTCATG
66 GTTTTCTTGGAATTTTTCAGAATTAATTTCCAAGACTTTCTTGTCAATTAAAACTGAAATTCATG
* *
13786324 TCATAACAGTGAGCTGGAC
131 CCAAAACAGTGAGCTGGAC
13786343 TGCTTTCACT
Statistics
Matches: 135, Mismatches: 12, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
179 5 0.04
180 129 0.96
181 1 0.01
ACGTcount: A:0.35, C:0.15, G:0.13, T:0.37
Consensus pattern (180 bp):
AAATCAGCATATTTGACCATGAAAATTTCCAGAAATAATCCTCATTAAACATTTTAATAAAGATA
GTTTTCTTGGAATTTTTCAGAATTAATTTCCAAGACTTTCTTGTCAATTAAAACTGAAATTCATG
CCAAAACAGTGAGCTGGACAGATTTATATTTGCACCAATTTTCTTGCTCG
Found at i:13786369 original size:180 final size:180
Alignment explanation
Indices: 13786014--13786386 Score: 511
Period size: 180 Copynumber: 2.1 Consensus size: 180
13786004 TTAATAGCCT
* * * *
13786014 AAATCAGCTTGTTTGGCCATGAAAATTTCCAGAAATAATCCTCATTGAACATTTTAATAAAGATA
1 AAATCAGCATATTTGACCATGAAAATTTCCAGAAATAATCCTCATTAAACATTTTAATAAAGATA
*
13786079 ATTTTTCTGGAATTTTTCAGAATTAATTTTCCAGAGTTTCTTGTCAATTAAAACTGAAATTCATG
66 ATTTTTCTGGAATTTTTCAGAATTAATTTTCCAGACTTTCTTGTCAATTAAAACTGAAATTCATG
* *
13786144 CCAAAACAGTGAGCTGGACAGATTTATATTTGCACCAATTTTCTTGCTCG
131 CCAAAACAGTGAGCTGGACAGATTTATATTTGCACCAAATTTCTTGCTCA
* * *
13786194 AAATCAGCATATTTGACCATGATATTTTCCAGAAATAATCCTTATTAAACATTTTAATAAAGAT-
1 AAATCAGCATATTTGACCATGAAAATTTCCAGAAATAATCCTCATTAAACATTTTAATAAAGATA
* *
13786258 AGTTTTCTTGGAATTTTTCAGAATTAA-TTTCCAAGACTTTCTTGTTAATTAAAACTGAAATTCA
66 ATTTTTC-TGGAATTTTTCAGAATTAATTTTCC-AGACTTTCTTGTCAATTAAAACTGAAATTCA
* * * * * *
13786322 TGTCATAACAGTGAGCTGGACTGCTTTCACT-TTTGC-TCAAATTTCTTGCTTA
129 TGCCAAAACAGTGAGCTGGACAGATTT-A-TATTTGCACCAAATTTCTTGCTCA
*
13786374 AAATCAGCCTATT
1 AAATCAGCATATT
13786387 CAATCATGAA
Statistics
Matches: 170, Mismatches: 19, Indels: 8
0.86 0.10 0.04
Matches are distributed among these distances:
179 11 0.06
180 152 0.89
181 6 0.04
182 1 0.01
ACGTcount: A:0.33, C:0.16, G:0.13, T:0.38
Consensus pattern (180 bp):
AAATCAGCATATTTGACCATGAAAATTTCCAGAAATAATCCTCATTAAACATTTTAATAAAGATA
ATTTTTCTGGAATTTTTCAGAATTAATTTTCCAGACTTTCTTGTCAATTAAAACTGAAATTCATG
CCAAAACAGTGAGCTGGACAGATTTATATTTGCACCAAATTTCTTGCTCA
Found at i:13787113 original size:35 final size:35
Alignment explanation
Indices: 13787088--13787300 Score: 243
Period size: 35 Copynumber: 6.1 Consensus size: 35
13787078 TTAATTGTTT
*
13787088 AATTTAATCAATTAGGCCCAATAACTTAATTAAAC
1 AATTTAATTAATTAGGCCCAATAACTTAATTAAAC
* * *
13787123 AATTTAATTAATTAAGCCCAACAATTTAATTAAAC
1 AATTTAATTAATTAGGCCCAATAACTTAATTAAAC
* ****
13787158 AAATTTAATCAATTAGGCCCAATAACTTAATTGTTT
1 -AATTTAATTAATTAGGCCCAATAACTTAATTAAAC
* *
13787194 AATTTAATTAATTATGCCCAATGACTTAATTAAAC
1 AATTTAATTAATTAGGCCCAATAACTTAATTAAAC
* * * * *
13787229 AATTTAATTAATTAGGCCCATTGATTTAATGAAAT
1 AATTTAATTAATTAGGCCCAATAACTTAATTAAAC
*
13787264 AATTTAATTAATTAGG--C-ACAACTTAATTAAAC
1 AATTTAATTAATTAGGCCCAATAACTTAATTAAAC
13787296 AATTT
1 AATTT
13787301 TAACCAAGTG
Statistics
Matches: 147, Mismatches: 30, Indels: 5
0.81 0.16 0.03
Matches are distributed among these distances:
32 14 0.10
33 1 0.01
35 105 0.71
36 27 0.18
ACGTcount: A:0.44, C:0.13, G:0.07, T:0.37
Consensus pattern (35 bp):
AATTTAATTAATTAGGCCCAATAACTTAATTAAAC
Found at i:13787182 original size:71 final size:71
Alignment explanation
Indices: 13787088--13787303 Score: 269
Period size: 71 Copynumber: 3.1 Consensus size: 71
13787078 TTAATTGTTT
* *
13787088 AATTTAATCAATTAGGCCCAATAACTTAATTAAACAATTTAATTAATTAAGCCCAACAATTTAAT
1 AATTTAATCAATTAGGCCCAATAACTTAATTAAATAATTTAATTAATTAAGCCCAACAACTTAAT
13787153 TAAACA
66 TAAACA
*** * **
13787159 AATTTAATCAATTAGGCCCAATAACTTAATTGTTTAATTTAATTAATTATGCCCAATGACTTAAT
1 AATTTAATCAATTAGGCCCAATAACTTAATTAAATAATTTAATTAATTAAGCCCAACAACTTAAT
13787224 TAAAC-
66 TAAACA
* * * * * *
13787229 AATTTAATTAATTAGGCCCATTGATTTAATGAAATAATTTAATTAATT-AG-GC-ACAACTTAAT
1 AATTTAATCAATTAGGCCCAATAACTTAATTAAATAATTTAATTAATTAAGCCCAACAACTTAAT
13787291 TAAACA
66 TAAACA
*
13787297 ATTTTAA
1 AATTTAA
13787304 CCAAGTGCTT
Statistics
Matches: 123, Mismatches: 21, Indels: 5
0.83 0.14 0.03
Matches are distributed among these distances:
67 13 0.11
68 7 0.06
69 1 0.01
70 40 0.33
71 62 0.50
ACGTcount: A:0.44, C:0.13, G:0.06, T:0.37
Consensus pattern (71 bp):
AATTTAATCAATTAGGCCCAATAACTTAATTAAATAATTTAATTAATTAAGCCCAACAACTTAAT
TAAACA
Found at i:13787184 original size:106 final size:105
Alignment explanation
Indices: 13787068--13787280 Score: 318
Period size: 106 Copynumber: 2.0 Consensus size: 105
13787058 TCCTTAAGAA
*
13787068 GCCCATTAACTTAATTGTTTAATTTAATCAATTAGGCCCAATAACTTAATTAAACAATTTAATTA
1 GCCCAATAACTTAATTGTTTAATTTAATCAATTAGGCCCAATAACTTAATTAAACAATTTAATTA
*
13787133 ATTAAGCCCAACAATTTAATTAAACAAATTTAATCAATTAG
66 ATTAAGCCCAACAATTTAATGAAA-AAATTTAATCAATTAG
* * *
13787174 GCCCAATAACTTAATTGTTTAATTTAATTAATTATGCCCAATGACTTAATTAAACAATTTAATTA
1 GCCCAATAACTTAATTGTTTAATTTAATCAATTAGGCCCAATAACTTAATTAAACAATTTAATTA
* *** * *
13787239 ATTAGGCCCATTGATTTAATGAAATAATTTAATTAATTAG
66 ATTAAGCCCAACAATTTAATGAAAAAATTTAATCAATTAG
13787279 GC
1 GC
13787281 ACAACTTAAT
Statistics
Matches: 96, Mismatches: 11, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
105 16 0.17
106 80 0.83
ACGTcount: A:0.41, C:0.14, G:0.08, T:0.38
Consensus pattern (105 bp):
GCCCAATAACTTAATTGTTTAATTTAATCAATTAGGCCCAATAACTTAATTAAACAATTTAATTA
ATTAAGCCCAACAATTTAATGAAAAAATTTAATCAATTAG
Found at i:13799420 original size:2 final size:2
Alignment explanation
Indices: 13799413--13799437 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
13799403 AAGAAAACAA
13799413 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
13799438 AAAGTTAAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:13801287 original size:20 final size:22
Alignment explanation
Indices: 13801262--13801307 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
13801252 CTTTAAGATC
13801262 AAAA-AATGAGTTAAGGAAAAAA
1 AAAAGAATGAGTTAAGG-AAAAA
*
13801284 AAAAGAATGAGTTATGGAAAAA
1 AAAAGAATGAGTTAAGGAAAAA
13801306 AA
1 AA
13801308 GGGAAAAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 11 0.50
23 11 0.50
ACGTcount: A:0.65, C:0.00, G:0.20, T:0.15
Consensus pattern (22 bp):
AAAAGAATGAGTTAAGGAAAAA
Found at i:13801294 original size:23 final size:22
Alignment explanation
Indices: 13801262--13801307 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 22
13801252 CTTTAAGATC
13801262 AAAAAATGAGTTAAGGAAAAAA
1 AAAAAATGAGTTAAGGAAAAAA
*
13801284 AAAAGAATGAGTTATGGAAAAAA
1 AAAA-AATGAGTTAAGGAAAAAA
13801307 A
1 A
13801308 GGGAAAAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
22 4 0.18
23 18 0.82
ACGTcount: A:0.65, C:0.00, G:0.20, T:0.15
Consensus pattern (22 bp):
AAAAAATGAGTTAAGGAAAAAA
Found at i:13801358 original size:51 final size:51
Alignment explanation
Indices: 13801302--13801448 Score: 192
Period size: 51 Copynumber: 2.9 Consensus size: 51
13801292 GAGTTATGGA
* *
13801302 AAAAAAGGGAAAAAAAGAAAAGAAAAATAATTCCAAAATTTGGGTCTAAATG
1 AAAAAAGAGAAAAAAAGAAAAGAAAAATAATTCCAAAATTTGGGTCT-AAGG
* *
13801354 AAAAAGAAAGAAAAAAAG-AAA-AAAAATAATTCCAAAATTTGAG-CTAAGG
1 AAAAA-AGAGAAAAAAAGAAAAGAAAAATAATTCCAAAATTTGGGTCTAAGG
* *
13801403 AAAAAATGAGAAAAAAGGAAAAGAAAAATAATTACAAAATTTGGGT
1 AAAAAA-GAGAAAAAAAGAAAAGAAAAATAATTCCAAAATTTGGGT
13801449 TTAGATAGCA
Statistics
Matches: 82, Mismatches: 8, Indels: 10
0.82 0.08 0.10
Matches are distributed among these distances:
48 1 0.01
49 17 0.21
50 5 0.06
51 41 0.50
52 8 0.10
53 10 0.12
ACGTcount: A:0.63, C:0.05, G:0.16, T:0.16
Consensus pattern (51 bp):
AAAAAAGAGAAAAAAAGAAAAGAAAAATAATTCCAAAATTTGGGTCTAAGG
Found at i:13804510 original size:12 final size:12
Alignment explanation
Indices: 13804495--13804529 Score: 61
Period size: 12 Copynumber: 2.9 Consensus size: 12
13804485 AAAAATGAGG
*
13804495 AAAAAAAGACAA
1 AAAAAAAGAAAA
13804507 AAAAAAAGAAAA
1 AAAAAAAGAAAA
13804519 AAAAAAAGAAA
1 AAAAAAAGAAA
13804530 GTCTTTTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.89, C:0.03, G:0.09, T:0.00
Consensus pattern (12 bp):
AAAAAAAGAAAA
Found at i:13809337 original size:80 final size:80
Alignment explanation
Indices: 13809252--13809404 Score: 254
Period size: 80 Copynumber: 1.9 Consensus size: 80
13809242 TCATACTCAA
* *
13809252 CCCATAGTGTATATGACTGT-CTCAACTCATACATCACATGGCATACATTTCATAACCTCATAAA
1 CCCATAGTGTATATGA-TATACTCAACACATACATCACATGGCATACATTTCATAACCTCATAAA
13809316 TCACTTACATGCCCAG
65 TCACTTACATGCCCAG
* *
13809332 CCCATAGTGTATATGATATACTTAACACATACATCTCATGGCATACATTTCATAACCTCATAAAT
1 CCCATAGTGTATATGATATACTCAACACATACATCACATGGCATACATTTCATAACCTCATAAAT
13809397 CACTTACA
66 CACTTACA
13809405 AGCATCCAAC
Statistics
Matches: 68, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
79 2 0.03
80 66 0.97
ACGTcount: A:0.35, C:0.27, G:0.08, T:0.30
Consensus pattern (80 bp):
CCCATAGTGTATATGATATACTCAACACATACATCACATGGCATACATTTCATAACCTCATAAAT
CACTTACATGCCCAG
Found at i:13814628 original size:21 final size:22
Alignment explanation
Indices: 13814603--13814643 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
13814593 CCTAGGTGGA
*
13814603 AAAATTCAAGGGAA-AAGTGTG
1 AAAATTCAAGGAAACAAGTGTG
13814624 AAAATTCAAGGAAACAAGTG
1 AAAATTCAAGGAAACAAGTG
13814644 AAAAAAAAGT
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:0.51, C:0.07, G:0.24, T:0.17
Consensus pattern (22 bp):
AAAATTCAAGGAAACAAGTGTG
Found at i:13814644 original size:20 final size:21
Alignment explanation
Indices: 13814603--13814647 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 21
13814593 CCTAGGTGGA
*
13814603 AAAATTCAAGGGAAAAGTGTG
1 AAAATTCAAGGGAAAAGAGTG
13814624 AAAATTCAA-GGAAACA-AGTG
1 AAAATTCAAGGGAAA-AGAGTG
13814644 AAAA
1 AAAA
13814648 AAAAGTAAGA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
20 12 0.55
21 10 0.45
ACGTcount: A:0.56, C:0.07, G:0.22, T:0.16
Consensus pattern (21 bp):
AAAATTCAAGGGAAAAGAGTG
Found at i:13814648 original size:21 final size:20
Alignment explanation
Indices: 13814601--13814648 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 20
13814591 ACCCTAGGTG
*
13814601 GAAAAATTCAAGGGAAAAGT
1 GAAAAATTCAAGGAAAAAGT
*
13814621 GTGAAAATTCAAGGAAACAAGT
1 G-AAAAATTCAAGGAAA-AAGT
13814643 GAAAAA
1 GAAAAA
13814649 AAAGTAAGAT
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:0.56, C:0.06, G:0.23, T:0.15
Consensus pattern (20 bp):
GAAAAATTCAAGGAAAAAGT
Found at i:13826590 original size:20 final size:20
Alignment explanation
Indices: 13826565--13826602 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
13826555 AAATGATGCT
13826565 AACAAAACGAAAAACAAAAC
1 AACAAAACGAAAAACAAAAC
**
13826585 AACAAAGGGAAAAACAAA
1 AACAAAACGAAAAACAAA
13826603 GAAAAATCAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.74, C:0.16, G:0.11, T:0.00
Consensus pattern (20 bp):
AACAAAACGAAAAACAAAAC
Found at i:13826974 original size:8 final size:7
Alignment explanation
Indices: 13826928--13826997 Score: 52
Period size: 8 Copynumber: 9.1 Consensus size: 7
13826918 TGGAAGTTGC
13826928 AAAAAGA
1 AAAAAGA
13826935 AAAAGAGA
1 AAAA-AGA
13826943 TGAAAAA-A
1 --AAAAAGA
13826951 AAAGAAGA
1 AAA-AAGA
*
13826959 AGAAAGA
1 AAAAAGA
13826966 AACAAAGA
1 AA-AAAGA
13826974 AAATAAGA
1 AAA-AAGA
*
13826982 AATAAATA
1 AA-AAAGA
13826990 AAAAAGA
1 AAAAAGA
13826997 A
1 A
13826998 CNNNNNNNNN
Statistics
Matches: 51, Mismatches: 4, Indels: 16
0.72 0.06 0.23
Matches are distributed among these distances:
6 3 0.06
7 17 0.33
8 25 0.49
9 2 0.04
10 4 0.08
ACGTcount: A:0.77, C:0.01, G:0.16, T:0.06
Consensus pattern (7 bp):
AAAAAGA
Found at i:13827185 original size:17 final size:19
Alignment explanation
Indices: 13827137--13827175 Score: 71
Period size: 19 Copynumber: 2.1 Consensus size: 19
13827127 TGGAAGTTGC
13827137 AAAAAGAAAAAGAGATGAA
1 AAAAAGAAAAAGAGATGAA
13827156 AAAAAGAAAAAGAGA-GAA
1 AAAAAGAAAAAGAGATGAA
13827174 AA
1 AA
13827176 GAAACAAAGA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 5 0.25
19 15 0.75
ACGTcount: A:0.77, C:0.00, G:0.21, T:0.03
Consensus pattern (19 bp):
AAAAAGAAAAAGAGATGAA
Found at i:13831189 original size:20 final size:20
Alignment explanation
Indices: 13831166--13831209 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
13831156 AAGCATAAAT
* *
13831166 TTCTAATTTCCAGCAGCTTC
1 TTCTAACTTCCAGCAACTTC
*
13831186 TTCTAGCTTCCAGCAACTTC
1 TTCTAACTTCCAGCAACTTC
13831206 TTCT
1 TTCT
13831210 TCTTCCTCAC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.18, C:0.32, G:0.09, T:0.41
Consensus pattern (20 bp):
TTCTAACTTCCAGCAACTTC
Found at i:13832210 original size:35 final size:35
Alignment explanation
Indices: 13832171--13832272 Score: 119
Period size: 35 Copynumber: 3.1 Consensus size: 35
13832161 AAGAATGCTT
* *
13832171 ATGATGATACTAAAATGTGCGAGTAGGGAGTGCAC
1 ATGATGATATTGAAATGTGCGAGTAGGGAGTGCAC
13832206 ATGATGATATTGAAATGT---A--A--GAGTGCAC
1 ATGATGATATTGAAATGTGCGAGTAGGGAGTGCAC
* *
13832234 ATGATGATATTGAAATGTGCGTGTAGGGAGTGTAC
1 ATGATGATATTGAAATGTGCGAGTAGGGAGTGCAC
13832269 ATGA
1 ATGA
13832273 GCTGAATGAA
Statistics
Matches: 56, Mismatches: 4, Indels: 14
0.76 0.05 0.19
Matches are distributed among these distances:
28 26 0.46
30 1 0.02
32 1 0.02
33 1 0.02
35 27 0.48
ACGTcount: A:0.34, C:0.08, G:0.30, T:0.27
Consensus pattern (35 bp):
ATGATGATATTGAAATGTGCGAGTAGGGAGTGCAC
Found at i:13832238 original size:28 final size:28
Alignment explanation
Indices: 13832198--13832251 Score: 108
Period size: 28 Copynumber: 1.9 Consensus size: 28
13832188 TGCGAGTAGG
13832198 GAGTGCACATGATGATATTGAAATGTAA
1 GAGTGCACATGATGATATTGAAATGTAA
13832226 GAGTGCACATGATGATATTGAAATGT
1 GAGTGCACATGATGATATTGAAATGT
13832252 GCGTGTAGGG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.37, C:0.07, G:0.26, T:0.30
Consensus pattern (28 bp):
GAGTGCACATGATGATATTGAAATGTAA
Found at i:13833590 original size:21 final size:18
Alignment explanation
Indices: 13833548--13833580 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
13833538 TCATTTTTCC
13833548 ACCAT-TCAATCATGCAT
1 ACCATGTCAATCATGCAT
13833565 A-CATGTCAATCATGCA
1 ACCATGTCAATCATGCA
13833581 CATGACCATG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 3 0.20
17 12 0.80
ACGTcount: A:0.36, C:0.27, G:0.09, T:0.27
Consensus pattern (18 bp):
ACCATGTCAATCATGCAT
Found at i:13833804 original size:21 final size:21
Alignment explanation
Indices: 13833778--13833875 Score: 81
Period size: 22 Copynumber: 4.6 Consensus size: 21
13833768 AAGCCTCCTG
*
13833778 GTACATTTTCAAAACCTTAAA
1 GTACATTTTCAAAACCTTCAA
* * *
13833799 GTACATCTTCAACACC-TCCA
1 GTACATTTTCAAAACCTTCAA
** *
13833819 GTACACCTTCAAATCCTTCAA
1 GTACATTTTCAAAACCTTCAA
* *
13833840 GTATAATTTTGAAAACCTTCAA
1 GTA-CATTTTCAAAACCTTCAA
*
13833862 GTAACAATTTCAAA
1 GT-ACATTTTCAAA
13833876 TCTTCTAAGT
Statistics
Matches: 58, Mismatches: 16, Indels: 5
0.73 0.20 0.06
Matches are distributed among these distances:
20 15 0.26
21 20 0.34
22 22 0.38
23 1 0.02
ACGTcount: A:0.39, C:0.24, G:0.06, T:0.31
Consensus pattern (21 bp):
GTACATTTTCAAAACCTTCAA
Found at i:13834153 original size:22 final size:22
Alignment explanation
Indices: 13834113--13834179 Score: 71
Period size: 22 Copynumber: 3.0 Consensus size: 22
13834103 ATCTTGAAAT
* *
13834113 CCTCTAAATACATTTTCCAAAA
1 CCTCTAAGTACATTCTCCAAAA
*
13834135 CCTTTAAGTACATTCTCCAAAA
1 CCTCTAAGTACATTCTCCAAAA
* * * *
13834157 TCTCTAGGTACAATCTACAAAA
1 CCTCTAAGTACATTCTCCAAAA
13834179 C
1 C
13834180 TTCCGGGTAC
Statistics
Matches: 36, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
22 36 1.00
ACGTcount: A:0.39, C:0.27, G:0.04, T:0.30
Consensus pattern (22 bp):
CCTCTAAGTACATTCTCCAAAA
Found at i:13834190 original size:44 final size:43
Alignment explanation
Indices: 13834142--13834256 Score: 108
Period size: 44 Copynumber: 2.6 Consensus size: 43
13834132 AAACCTTTAA
* * *
13834142 GTACATTCTCCAAAATCTCTAGGTACAATCTACAAAACTTCCGG
1 GTACATT-TCCAAAATCTCTAGGTACAATATACAAAACCTCCAG
* * *
13834186 GTACATTTTCTAAAA-CATCTAGGTATAATATTCAAAACCTCCAG
1 GTACA-TTTCCAAAATC-TCTAGGTACAATATACAAAACCTCCAG
*
13834230 GTACAATTTTCAAAATCT-TCAGGTACA
1 GTAC-ATTTCCAAAATCTCT-AGGTACA
13834257 TTTTTTGAAA
Statistics
Matches: 57, Mismatches: 9, Indels: 10
0.75 0.12 0.13
Matches are distributed among these distances:
43 2 0.04
44 51 0.89
45 4 0.07
ACGTcount: A:0.37, C:0.23, G:0.10, T:0.30
Consensus pattern (43 bp):
GTACATTTCCAAAATCTCTAGGTACAATATACAAAACCTCCAG
Found at i:13834399 original size:67 final size:67
Alignment explanation
Indices: 13834322--13834470 Score: 181
Period size: 67 Copynumber: 2.2 Consensus size: 67
13834312 ATTTGGTTAC
* ** *
13834322 AATCTCCAAAACCTCCAAGTATATTCTTTAAAACCTCAAGGCAGTTATTTTCAAAACCTCTAAGT
1 AATCTCCAAAACCTCCAAGTACATTCTCCAAAACCTCAAGGCAATTATTTTCAAAACCTCTAAGT
13834387 AT
66 AT
* ** * ** * *
13834389 AATCTTCAAAACCTTTAAGTACATTCTCCAAAATCTGGAGGTAATTATTTTCAAAACCTCTAGGT
1 AATCTCCAAAACCTCCAAGTACATTCTCCAAAACCTCAAGGCAATTATTTTCAAAACCTCTAAGT
13834454 AT
66 AT
*
13834456 ATTCTCCAAAACCTC
1 AATCTCCAAAACCTC
13834471 TAGATACATC
Statistics
Matches: 67, Mismatches: 15, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
67 67 1.00
ACGTcount: A:0.36, C:0.23, G:0.08, T:0.32
Consensus pattern (67 bp):
AATCTCCAAAACCTCCAAGTACATTCTCCAAAACCTCAAGGCAATTATTTTCAAAACCTCTAAGT
AT
Found at i:13834471 original size:22 final size:22
Alignment explanation
Indices: 13834328--13834473 Score: 107
Period size: 22 Copynumber: 6.5 Consensus size: 22
13834318 TTACAATCTC
* *
13834328 CAAAACCTCCAAGTATATTCTT
1 CAAAACCTCTAGGTATATTCTT
* * *
13834350 TAAAACCTCAAGGCAGTTATT-TT
1 CAAAACCTCTAGGTA--TATTCTT
* *
13834373 CAAAACCTCTAAGTATAATCTT
1 CAAAACCTCTAGGTATATTCTT
* * * *
13834395 CAAAACCTTTAAGTACATTCTC
1 CAAAACCTCTAGGTATATTCTT
* **
13834417 CAAAATCTGGAGGTAATTATT-TT
1 CAAAACCTCTAGGT-A-TATTCTT
*
13834440 CAAAACCTCTAGGTATATTCTC
1 CAAAACCTCTAGGTATATTCTT
13834462 CAAAACCTCTAG
1 CAAAACCTCTAG
13834474 ATACATCTGT
Statistics
Matches: 95, Mismatches: 23, Indels: 12
0.73 0.18 0.09
Matches are distributed among these distances:
21 7 0.07
22 55 0.58
23 26 0.27
24 7 0.07
ACGTcount: A:0.36, C:0.23, G:0.09, T:0.32
Consensus pattern (22 bp):
CAAAACCTCTAGGTATATTCTT
Found at i:13834507 original size:43 final size:43
Alignment explanation
Indices: 13834460--13834564 Score: 120
Period size: 43 Copynumber: 2.4 Consensus size: 43
13834450 AGGTATATTC
*
13834460 TCCAAAACCTCTAGATACATCTGTAAAACCTTCAAGTAACAAT
1 TCCAAAACCTCTAGATACATCTCTAAAACCTTCAAGTAACAAT
* * * * * *
13834503 TCCAAAACCTCTAGGTAAATCTCTAAAGCCTTCGAGTAATAGT
1 TCCAAAACCTCTAGATACATCTCTAAAACCTTCAAGTAACAAT
** *
13834546 TTTAAAACCTCAAGATACA
1 TCCAAAACCTCTAGATACA
13834565 ATCTTCAAAG
Statistics
Matches: 50, Mismatches: 12, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
43 50 1.00
ACGTcount: A:0.40, C:0.24, G:0.10, T:0.27
Consensus pattern (43 bp):
TCCAAAACCTCTAGATACATCTCTAAAACCTTCAAGTAACAAT
Found at i:13834520 original size:22 final size:22
Alignment explanation
Indices: 13834128--13834525 Score: 92
Period size: 22 Copynumber: 18.1 Consensus size: 22
13834118 AAATACATTT
* * *
13834128 TCCAAAACCTTTAAGTACATTC
1 TCCAAAACCTCTAGGTACAATC
*
13834150 TCCAAAATCTCTAGGTACAATC
1 TCCAAAACCTCTAGGTACAATC
* * ** * *
13834172 TACAAAACTTCCGGGTACATTT
1 TCCAAAACCTCTAGGTACAATC
* * * *
13834194 TCTAAAACATCTAGGTATAATA
1 TCCAAAACCTCTAGGTACAATC
* * *
13834216 TTCAAAACCTCCAGGTACAATT
1 TCCAAAACCTCTAGGTACAATC
* * * *
13834238 TTCAAAATCT-TCAGGTACATTT
1 TCCAAAACCTCT-AGGTACAATC
*** * *
13834260 TTTGAAA-CTTTAAGGAACAATC
1 TCCAAAACCTCT-AGGTACAATC
* * * * *
13834282 TTCAAAACGTCTAGATACATTT
1 TCCAAAACCTCTAGGTACAATC
* * * *
13834304 TTCGAAACAT-TTGGTTACAATC
1 TCCAAAACCTCTAGG-TACAATC
* * * *
13834326 TCCAAAACCTCCAAGTATATTC
1 TCCAAAACCTCTAGGTACAATC
** * * ** *
13834348 TTTAAAACCTCAAGGCAGTTATT
1 TCCAAAACCTCTAGGTA-CAATC
* * *
13834371 TTCAAAACCTCTAAGTATAATC
1 TCCAAAACCTCTAGGTACAATC
* * * *
13834393 TTCAAAACCTTTAAGTACATTC
1 TCCAAAACCTCTAGGTACAATC
* ** *
13834415 TCCAAAATCTGGAGGTA-ATTATT
1 TCCAAAACCTCTAGGTACA--ATC
* * *
13834438 TTCAAAACCTCTAGGTATATTC
1 TCCAAAACCTCTAGGTACAATC
*
13834460 TCCAAAACCTCTAGATAC-ATC
1 TCCAAAACCTCTAGGTACAATC
** *
13834481 TGTAAAACCT-TCAAGTAACAAT-
1 TCCAAAACCTCT-AGGT-ACAATC
13834503 TCCAAAACCTCTAGGTA-AATC
1 TCCAAAACCTCTAGGTACAATC
13834524 TC
1 TC
13834526 TAAAGCCTTC
Statistics
Matches: 265, Mismatches: 97, Indels: 29
0.68 0.25 0.07
Matches are distributed among these distances:
20 4 0.02
21 20 0.08
22 205 0.77
23 35 0.13
24 1 0.00
ACGTcount: A:0.37, C:0.22, G:0.09, T:0.32
Consensus pattern (22 bp):
TCCAAAACCTCTAGGTACAATC
Found at i:13834601 original size:22 final size:23
Alignment explanation
Indices: 13834441--13834630 Score: 98
Period size: 22 Copynumber: 8.7 Consensus size: 23
13834431 AATTATTTTC
* * **
13834441 AAAACCTCTAGGT-ATATTCTCC
1 AAAACCTCTAGGTAACAATCTTT
* *
13834463 AAAACCTCTAGAT-AC-ATCTGT
1 AAAACCTCTAGGTAACAATCTTT
* **
13834484 AAAACCT-TCAAGTAACAAT-TCC
1 AAAACCTCT-AGGTAACAATCTTT
*
13834506 AAAACCTCTAGGT-A-AATCTCT
1 AAAACCTCTAGGTAACAATCTTT
* * * *
13834527 AAAGCCT-TCGAGTAATAGT-TTT
1 AAAACCTCTAG-GTAACAATCTTT
* * *
13834549 AAAACCTCAAGAT-ACAATCTTC
1 AAAACCTCTAGGTAACAATCTTT
*
13834571 AAAGCCTCTAGGTAACAAT-TTT
1 AAAACCTCTAGGTAACAATCTTT
*
13834593 AAAACCTCTGGGTAA-AATCTTT
1 AAAACCTCTAGGTAACAATCTTT
*
13834615 AAAACCTTTAGGTAAC
1 AAAACCTCTAGGTAAC
13834631 CTTTTCAAAA
Statistics
Matches: 125, Mismatches: 30, Indels: 25
0.69 0.17 0.14
Matches are distributed among these distances:
20 6 0.05
21 29 0.23
22 79 0.63
23 11 0.09
ACGTcount: A:0.38, C:0.22, G:0.11, T:0.29
Consensus pattern (23 bp):
AAAACCTCTAGGTAACAATCTTT
Found at i:13834612 original size:44 final size:43
Alignment explanation
Indices: 13834495--13834630 Score: 123
Period size: 44 Copynumber: 3.1 Consensus size: 43
13834485 AAACCTTCAA
** *
13834495 GTAACAATTCCAAAACCTCTAGGT-AAATC-TCTAAAGCCTTCG
1 GTAACAATTTTAAAACCTCTAGGTAAAATCTTC-AAAGCCTTAG
* * * * *
13834537 AGTAATAGTTTTAAAACCTCAAGATACAATCTTCAAAGCCTCTAG
1 -GTAACAATTTTAAAACCTCTAGGTAAAATCTTCAAAGCCT-TAG
* * *
13834582 GTAACAATTTTAAAACCTCTGGGTAAAATCTTTAAAACCTTTAG
1 GTAACAATTTTAAAACCTCTAGGTAAAATCTTCAAAGCC-TTAG
13834626 GTAAC
1 GTAAC
13834631 CTTTTCAAAA
Statistics
Matches: 73, Mismatches: 16, Indels: 7
0.76 0.17 0.07
Matches are distributed among these distances:
43 18 0.25
44 50 0.68
45 5 0.07
ACGTcount: A:0.38, C:0.21, G:0.12, T:0.29
Consensus pattern (43 bp):
GTAACAATTTTAAAACCTCTAGGTAAAATCTTCAAAGCCTTAG
Found at i:13834831 original size:5 final size:5
Alignment explanation
Indices: 13834822--13834851 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
13834812 ATTTAAGGCA
*
13834822 ATTTT TTTTT ATTTT ATTTT ATTTT ATTTT
1 ATTTT ATTTT ATTTT ATTTT ATTTT ATTTT
13834852 GTTTCATATA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (5 bp):
ATTTT
Found at i:13842915 original size:42 final size:42
Alignment explanation
Indices: 13842860--13842993 Score: 178
Period size: 42 Copynumber: 3.2 Consensus size: 42
13842850 ACCATCCAAC
* * *
13842860 CATCATCAGCTCATGTGCACTCCCACTCGCACATAGCTGGGT
1 CATCATCAGCTCATGTGCACTCCTACACGCACATGGCTGGGT
* * * *
13842902 CAGCATCAACTCATATGCACTCCTACACGTACATGGCTGGGT
1 CATCATCAGCTCATGTGCACTCCTACACGCACATGGCTGGGT
* * *
13842944 CATCATCAGCTCATGTGTACTTCTACACGCACATGGTTGGGT
1 CATCATCAGCTCATGTGCACTCCTACACGCACATGGCTGGGT
13842986 CATCATCA
1 CATCATCA
13842994 TCACAAAAAA
Statistics
Matches: 78, Mismatches: 14, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
42 78 1.00
ACGTcount: A:0.24, C:0.31, G:0.19, T:0.26
Consensus pattern (42 bp):
CATCATCAGCTCATGTGCACTCCTACACGCACATGGCTGGGT
Found at i:13844884 original size:23 final size:22
Alignment explanation
Indices: 13844857--13844907 Score: 75
Period size: 23 Copynumber: 2.3 Consensus size: 22
13844847 TCAAGAGCAA
* *
13844857 TTTTTAGATTCTTTTCTTTTTTT
1 TTTTTAGATTCTTTT-TTATTCT
13844880 TTTTTAGATTCTTTTTTATTCT
1 TTTTTAGATTCTTTTTTATTCT
13844902 TTTTTA
1 TTTTTA
13844908 AAGAGATTGA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
22 11 0.42
23 15 0.58
ACGTcount: A:0.12, C:0.08, G:0.04, T:0.76
Consensus pattern (22 bp):
TTTTTAGATTCTTTTTTATTCT
Found at i:13848570 original size:17 final size:17
Alignment explanation
Indices: 13848526--13848579 Score: 58
Period size: 17 Copynumber: 3.2 Consensus size: 17
13848516 AATTACTATA
13848526 TTAAATATATACTAATACT
1 TTAAATATATA-T-ATACT
* *
13848545 TTTAGTATATATATACT
1 TTAAATATATATATACT
13848562 TTAAATATA-ATATA-T
1 TTAAATATATATATACT
13848577 TTA
1 TTA
13848580 TTTTTTATTT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
15 4 0.13
16 5 0.16
17 12 0.39
18 1 0.03
19 9 0.29
ACGTcount: A:0.44, C:0.06, G:0.02, T:0.48
Consensus pattern (17 bp):
TTAAATATATATATACT
Found at i:13848625 original size:15 final size:17
Alignment explanation
Indices: 13848595--13848627 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 17
13848585 TATTTTATCT
13848595 TAACATTATAAAAATTA
1 TAACATTATAAAAATTA
13848612 TAAC-TTAT-AAAATTA
1 TAACATTATAAAAATTA
13848627 T
1 T
13848628 TAATTGTAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 8 0.50
16 4 0.25
17 4 0.25
ACGTcount: A:0.55, C:0.06, G:0.00, T:0.39
Consensus pattern (17 bp):
TAACATTATAAAAATTA
Found at i:13848690 original size:2 final size:2
Alignment explanation
Indices: 13848636--13848674 Score: 60
Period size: 2 Copynumber: 19.5 Consensus size: 2
13848626 ATTAATTGTA
* *
13848636 AT AT AT AT GT TT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
13848675 CACTTTATAG
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (2 bp):
AT
Found at i:13849204 original size:40 final size:40
Alignment explanation
Indices: 13849118--13849256 Score: 161
Period size: 40 Copynumber: 3.5 Consensus size: 40
13849108 TATAATTTTT
* * *
13849118 GTTATTTAAGTTTATGTTATTTGTTTGGATCTTTGTGTTTA
1 GTTATTTAAGTTTATGTT-GTTGTTTGGATATTTATGTTTA
* * *
13849159 GTTATTTAAGTTTATGTTGTTATTTGGGTATTTATGTATA
1 GTTATTTAAGTTTATGTTGTTGTTTGGATATTTATGTTTA
* * * * * *
13849199 ATTATTTAAGTTTATATAGTTGTATGGATATTTATTTTTT
1 GTTATTTAAGTTTATGTTGTTGTTTGGATATTTATGTTTA
13849239 GTTATTTAAGTTTATGTT
1 GTTATTTAAGTTTATGTT
13849257 TGAGATCTTT
Statistics
Matches: 80, Mismatches: 18, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
40 62 0.77
41 18 0.22
ACGTcount: A:0.22, C:0.01, G:0.17, T:0.60
Consensus pattern (40 bp):
GTTATTTAAGTTTATGTTGTTGTTTGGATATTTATGTTTA
Found at i:13850490 original size:27 final size:27
Alignment explanation
Indices: 13850452--13850505 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
13850442 TCGATACTTG
13850452 GTACCTAGAAATCATTCTATTTAAAAT
1 GTACCTAGAAATCATTCTATTTAAAAT
13850479 GTACCTAGAAATCATTCTATTTAAAAT
1 GTACCTAGAAATCATTCTATTTAAAAT
13850506 ATATTTATAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.41, C:0.15, G:0.07, T:0.37
Consensus pattern (27 bp):
GTACCTAGAAATCATTCTATTTAAAAT
Found at i:13851190 original size:15 final size:16
Alignment explanation
Indices: 13851170--13851207 Score: 53
Period size: 15 Copynumber: 2.5 Consensus size: 16
13851160 TAGAGATTTT
13851170 GATTTTAAAGCTTT-G
1 GATTTTAAAGCTTTCG
*
13851185 GATTTTAAAGTTTTCG
1 GATTTTAAAGCTTTCG
13851201 G-TTTTAA
1 GATTTTAA
13851208 CGTTGTTTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 19 0.90
16 2 0.10
ACGTcount: A:0.26, C:0.05, G:0.18, T:0.50
Consensus pattern (16 bp):
GATTTTAAAGCTTTCG
Found at i:13855629 original size:43 final size:43
Alignment explanation
Indices: 13855566--13855791 Score: 194
Period size: 43 Copynumber: 5.3 Consensus size: 43
13855556 TCGTGACAAG
* * *
13855566 GTAAATCTTTCCCTTAATGATAATGTGTATGGGTATTGATTAT
1 GTAAATCTTACCCTTGATGATAATGTGAATGGGTATTGATTAT
* * * *
13855609 CTAAATCTTACCCATGATGATAATGTGAATGGATGTTGATTAT
1 GTAAATCTTACCCTTGATGATAATGTGAATGGGTATTGATTAT
* * * *
13855652 GGAAAT-TCTACCCTTGATGATAATGTGCATAGGTAATGATTAT
1 GTAAATCT-TACCCTTGATGATAATGTGAATGGGTATTGATTAT
* * * * **
13855695 GAAAATCTTA-CCTTGA-GCGTAAGGCGAATGGGTATTGATGGT
1 GTAAATCTTACCCTTGATG-ATAATGTGAATGGGTATTGATTAT
* * *
13855737 GAAAATC-TA-CCTTAAATGATAATGTGAATGGGTATTGATTAC
1 GTAAATCTTACCCTT-GATGATAATGTGAATGGGTATTGATTAT
*
13855779 ATAAATC-TACCCT
1 GTAAATCTTACCCT
13855792 ACTATGATTA
Statistics
Matches: 144, Mismatches: 33, Indels: 12
0.76 0.17 0.06
Matches are distributed among these distances:
41 7 0.05
42 56 0.39
43 80 0.56
44 1 0.01
ACGTcount: A:0.32, C:0.12, G:0.20, T:0.35
Consensus pattern (43 bp):
GTAAATCTTACCCTTGATGATAATGTGAATGGGTATTGATTAT
Found at i:13855785 original size:42 final size:40
Alignment explanation
Indices: 13855577--13855789 Score: 133
Period size: 42 Copynumber: 5.0 Consensus size: 40
13855567 TAAATCTTTC
* *
13855577 CCTTAATGATAATGTGTATGGGTATTGATTATCTAAATCTTA
1 CCTTAATGATAATGTGAATGGGTATTGATTA-CAAAATC-TA
* * * * * *
13855619 CCCATGATGATAATGTGAATGGATGTTGATTATGGAAATTCTA
1 -CCTTAATGATAATGTGAATGGGTATTGATTA--CAAAATCTA
* * * * *
13855662 CCCTTGATGATAATGTGCATAGGTAATGATTATGAAAATCTTA
1 -CCTTAATGATAATGTGAATGGGTATTGATTA-CAAAATC-TA
* * * * *
13855705 CCTTGA-GCGTAAGGCGAATGGGTATTGATGGT-GAAAATCTA
1 CCTTAATG-ATAATGTGAATGGGTATTGAT--TACAAAATCTA
13855746 CCTTAAATGATAATGTGAATGGGTATTGATTACATAAATCTA
1 CCTT-AATGATAATGTGAATGGGTATTGATTACA-AAATCTA
13855788 CC
1 CC
13855790 CTACTATGAT
Statistics
Matches: 133, Mismatches: 28, Indels: 19
0.74 0.16 0.11
Matches are distributed among these distances:
40 1 0.01
41 8 0.06
42 62 0.47
43 57 0.43
44 5 0.04
ACGTcount: A:0.33, C:0.11, G:0.21, T:0.35
Consensus pattern (40 bp):
CCTTAATGATAATGTGAATGGGTATTGATTACAAAATCTA
Found at i:13865557 original size:2 final size:2
Alignment explanation
Indices: 13865550--13865592 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
13865540 TTTGATGATT
13865550 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
13865592 T
1 T
13865593 GTTGTGCATG
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:13876398 original size:29 final size:29
Alignment explanation
Indices: 13876334--13876398 Score: 121
Period size: 29 Copynumber: 2.2 Consensus size: 29
13876324 ATAAATGACC
*
13876334 ATGTTTACCACAATTATAACATCTAGGTA
1 ATGTTTTCCACAATTATAACATCTAGGTA
13876363 ATGTTTTCCACAATTATAACATCTAGGTA
1 ATGTTTTCCACAATTATAACATCTAGGTA
13876392 ATGTTTT
1 ATGTTTT
13876399 AGCTAAATTT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 35 1.00
ACGTcount: A:0.34, C:0.15, G:0.11, T:0.40
Consensus pattern (29 bp):
ATGTTTTCCACAATTATAACATCTAGGTA
Found at i:13884217 original size:43 final size:43
Alignment explanation
Indices: 13884120--13884287 Score: 196
Period size: 43 Copynumber: 3.9 Consensus size: 43
13884110 TCATTCATTG
* * *
13884120 TCATGTGCACTCCCTAC-TCGCACATGGTCGGGTCATCATCGGC
1 TCATGTGCACTCCC-ACATCGCACATAGCCGGGTCATCATCAGC
* ** *
13884163 TTATGCACACTCTCTAC-TCGCACATAGCCGGGTCATCATCAGC
1 TCATGTGCACTC-CCACATCGCACATAGCCGGGTCATCATCAGC
* * *
13884206 TCATGTGCACTCCCACATCGTACATAACTGGGTCATCATCAGC
1 TCATGTGCACTCCCACATCGCACATAGCCGGGTCATCATCAGC
**
13884249 TCATGTGCACTCCCACATCGCACATAGTTGGGTCATCAT
1 TCATGTGCACTCCCACATCGCACATAGCCGGGTCATCAT
13884288 TATCACACAA
Statistics
Matches: 106, Mismatches: 17, Indels: 4
0.83 0.13 0.03
Matches are distributed among these distances:
42 3 0.03
43 102 0.96
44 1 0.01
ACGTcount: A:0.22, C:0.33, G:0.18, T:0.26
Consensus pattern (43 bp):
TCATGTGCACTCCCACATCGCACATAGCCGGGTCATCATCAGC
Found at i:13887787 original size:27 final size:27
Alignment explanation
Indices: 13887751--13887815 Score: 94
Period size: 27 Copynumber: 2.4 Consensus size: 27
13887741 AATTGGAAAG
* *
13887751 AAAAAAAATATCGGAGGACTAAATTGA
1 AAAAAAAATATCAGAGGACTAAATGGA
*
13887778 AAAAAAAATATTAGAGGACTAAATGGA
1 AAAAAAAATATCAGAGGACTAAATGGA
13887805 AAAGAAAAATA
1 AAA-AAAAATA
13887816 AATTATTTAG
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
27 27 0.79
28 7 0.21
ACGTcount: A:0.62, C:0.05, G:0.17, T:0.17
Consensus pattern (27 bp):
AAAAAAAATATCAGAGGACTAAATGGA
Found at i:13887845 original size:31 final size:30
Alignment explanation
Indices: 13887739--13887847 Score: 111
Period size: 31 Copynumber: 3.7 Consensus size: 30
13887729 GGAAAAGGTT
* *
13887739 TAAATTGGAAAGAAAAA-AAATATCGGAGGAC
1 TAAATTGAAAAGAAAAATAAAT-T-AGAGGAC
13887770 TAAATTGAAAA-AAAAAT--ATTAGAGGAC
1 TAAATTGAAAAGAAAAATAAATTAGAGGAC
* *
13887797 TAAATGGAAAAGAAAAATAAATTATTTA-GAC
1 TAAATTGAAAAGAAAAATAAATTA--GAGGAC
13887828 TAAATTGAAAAGAAAAATAA
1 TAAATTGAAAAGAAAAATAA
13887848 GGAATGAGGT
Statistics
Matches: 67, Mismatches: 5, Indels: 12
0.80 0.06 0.14
Matches are distributed among these distances:
27 16 0.24
28 7 0.10
29 2 0.03
30 9 0.13
31 32 0.48
32 1 0.01
ACGTcount: A:0.60, C:0.04, G:0.16, T:0.21
Consensus pattern (30 bp):
TAAATTGAAAAGAAAAATAAATTAGAGGAC
Found at i:13895908 original size:20 final size:21
Alignment explanation
Indices: 13895874--13895916 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 21
13895864 GGCATAAATA
* *
13895874 TCAAAGTTTCTAGCAAGTTCT
1 TCAAAGTTTCCAGCAACTTCT
13895895 TCAAA-TTTCCAGCAACTTCT
1 TCAAAGTTTCCAGCAACTTCT
13895915 TC
1 TC
13895917 TTCTTCTTCT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 15 0.75
21 5 0.25
ACGTcount: A:0.28, C:0.26, G:0.09, T:0.37
Consensus pattern (21 bp):
TCAAAGTTTCCAGCAACTTCT
Found at i:13896095 original size:21 final size:21
Alignment explanation
Indices: 13896069--13896109 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
13896059 ACCTTAAAAC
13896069 CCTCAAAAGTCTTTGTTCAGT
1 CCTCAAAAGTCTTTGTTCAGT
13896090 CCTCAAAAGTCTTTGTTCAG
1 CCTCAAAAGTCTTTGTTCAG
13896110 CACTTTCTCT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.24, C:0.24, G:0.15, T:0.37
Consensus pattern (21 bp):
CCTCAAAAGTCTTTGTTCAGT
Found at i:13898372 original size:90 final size:90
Alignment explanation
Indices: 13898214--13898393 Score: 252
Period size: 90 Copynumber: 2.0 Consensus size: 90
13898204 CTTTTTATGC
* * * *
13898214 CAACTATGAGTATCAGTTTTATCACCATGGTCAGTGTATTGTAAAACGTGTGTCTTTATCTTTTA
1 CAACTAAGAGTATCAATTTTATCACCATGGTCAGTATATTGTAAAACGTGTGTCTTTATCTTTGA
*
13898279 ACTGTAGAAGGTTTGTTATTTCTTA
66 ACTGTAAAAGGTTTGTTATTTCTTA
* * * ***
13898304 CAACTAAGAGTGTCAATTTTATCACTATGGTTAGTATATTGTTTTACGTGTGTCTTTATCTTTGA
1 CAACTAAGAGTATCAATTTTATCACCATGGTCAGTATATTGTAAAACGTGTGTCTTTATCTTTGA
*
13898369 ACTGTAAAAGGTTTGTTGTTTCTTA
66 ACTGTAAAAGGTTTGTTATTTCTTA
13898394 TTCTTTTGCC
Statistics
Matches: 78, Mismatches: 12, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
90 78 1.00
ACGTcount: A:0.25, C:0.12, G:0.18, T:0.45
Consensus pattern (90 bp):
CAACTAAGAGTATCAATTTTATCACCATGGTCAGTATATTGTAAAACGTGTGTCTTTATCTTTGA
ACTGTAAAAGGTTTGTTATTTCTTA
Found at i:13902489 original size:2 final size:2
Alignment explanation
Indices: 13902484--13902532 Score: 82
Period size: 2 Copynumber: 25.0 Consensus size: 2
13902474 ATATATATAT
*
13902484 AG AG AG AG AG AG AG AG AG A- AG AG AG CG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
13902525 AG AG AG AG
1 AG AG AG AG
13902533 GAATTGGCTG
Statistics
Matches: 44, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
1 1 0.02
2 43 0.98
ACGTcount: A:0.49, C:0.02, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:13904707 original size:134 final size:134
Alignment explanation
Indices: 13904512--13904781 Score: 540
Period size: 134 Copynumber: 2.0 Consensus size: 134
13904502 TTCCATCAAA
13904512 TATACTTACCTAGTATTGACCATGTTGATTGATGTTGACGTCATGTTGATTGTGTTGATTGATAT
1 TATACTTACCTAGTATTGACCATGTTGATTGATGTTGACGTCATGTTGATTGTGTTGATTGATAT
13904577 TAGCACGGCATGGCATTGACTAAAAATATTTTTTATTTTAGAAATTAAAATAAACCAAAAATAAA
66 TAGCACGGCATGGCATTGACTAAAAATATTTTTTATTTTAGAAATTAAAATAAACCAAAAATAAA
13904642 TTTT
131 TTTT
13904646 TATACTTACCTAGTATTGACCATGTTGATTGATGTTGACGTCATGTTGATTGTGTTGATTGATAT
1 TATACTTACCTAGTATTGACCATGTTGATTGATGTTGACGTCATGTTGATTGTGTTGATTGATAT
13904711 TAGCACGGCATGGCATTGACTAAAAATATTTTTTATTTTAGAAATTAAAATAAACCAAAAATAAA
66 TAGCACGGCATGGCATTGACTAAAAATATTTTTTATTTTAGAAATTAAAATAAACCAAAAATAAA
13904776 TTTT
131 TTTT
13904780 TA
1 TA
13904782 AAAAAATTCC
Statistics
Matches: 136, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
134 136 1.00
ACGTcount: A:0.34, C:0.10, G:0.16, T:0.40
Consensus pattern (134 bp):
TATACTTACCTAGTATTGACCATGTTGATTGATGTTGACGTCATGTTGATTGTGTTGATTGATAT
TAGCACGGCATGGCATTGACTAAAAATATTTTTTATTTTAGAAATTAAAATAAACCAAAAATAAA
TTTT
Found at i:13906616 original size:35 final size:35
Alignment explanation
Indices: 13906571--13906638 Score: 91
Period size: 35 Copynumber: 1.9 Consensus size: 35
13906561 GACAAAGTTT
* ** *
13906571 AACCCATCTACATTTTCTATGGTTAAGGTATAATC
1 AACCAATCTACATTTTAAATGGCTAAGGTATAATC
*
13906606 AACCAATCTACCTTTTAAATGGCTAAGGTATAA
1 AACCAATCTACATTTTAAATGGCTAAGGTATAA
13906639 CTAATATCAA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
35 28 1.00
ACGTcount: A:0.35, C:0.19, G:0.12, T:0.34
Consensus pattern (35 bp):
AACCAATCTACATTTTAAATGGCTAAGGTATAATC
Found at i:13907045 original size:60 final size:60
Alignment explanation
Indices: 13906975--13907109 Score: 148
Period size: 60 Copynumber: 2.2 Consensus size: 60
13906965 AAAACCCATG
* * * ** *
13906975 AAAATATATCGATACAGTTTGAAATTTATCTATACATTTTTTATCAAAACCA-T-ACTGCTT
1 AAAATTTATCGATACAGTTTGAAATGTATCAATACATTTTCGATCAAAAACATTCACT--TT
* * * *
13907035 AAAATTTATCGATACATTTTGGAATGTATCAATATATTTTCGGTCAAAAACATTCACTTT
1 AAAATTTATCGATACAGTTTGAAATGTATCAATACATTTTCGATCAAAAACATTCACTTT
13907095 AAAATTTATCGATAC
1 AAAATTTATCGATAC
13907110 TTTTCATAAT
Statistics
Matches: 63, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
60 59 0.94
61 1 0.02
62 3 0.05
ACGTcount: A:0.39, C:0.14, G:0.08, T:0.39
Consensus pattern (60 bp):
AAAATTTATCGATACAGTTTGAAATGTATCAATACATTTTCGATCAAAAACATTCACTTT
Found at i:13907121 original size:60 final size:59
Alignment explanation
Indices: 13907018--13907173 Score: 172
Period size: 60 Copynumber: 2.6 Consensus size: 59
13907008 ACATTTTTTA
* * * *
13907018 TCAAAACCATACTGCTTAAAATTTATCGATACATTTTGGAATGTATCAATATATTTTCGG
1 TCAAAACTATTCTACTTAAAATTTATCGATAC-TTTTAGAATGTATCAATATATTTTCGG
* **
13907078 TCAAAAAC-ATTC-ACTTTAAAATTTATCGATACTTTTCATAATGTATGGATATATTTTCGG
1 TC-AAAACTATTCTAC-TTAAAATTTATCGATACTTTT-AGAATGTATCAATATATTTTCGG
* * *
13907138 TCAGAACTATTCTACTTAAAATCTATCAATACTTTT
1 TCAAAACTATTCTACTTAAAATTTATCGATACTTTT
13907174 GGGCCAAATA
Statistics
Matches: 82, Mismatches: 9, Indels: 10
0.81 0.09 0.10
Matches are distributed among these distances:
59 9 0.11
60 66 0.80
61 7 0.09
ACGTcount: A:0.35, C:0.15, G:0.09, T:0.40
Consensus pattern (59 bp):
TCAAAACTATTCTACTTAAAATTTATCGATACTTTTAGAATGTATCAATATATTTTCGG
Found at i:13910134 original size:19 final size:19
Alignment explanation
Indices: 13910110--13910151 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
13910100 CTTCTTCACC
13910110 TTCATGCTCCCACGCCATT
1 TTCATGCTCCCACGCCATT
* *
13910129 TTCATGCTTCCATGCCATT
1 TTCATGCTCCCACGCCATT
13910148 TTCA
1 TTCA
13910152 CCTTGCCACC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.17, C:0.36, G:0.10, T:0.38
Consensus pattern (19 bp):
TTCATGCTCCCACGCCATT
Found at i:13910264 original size:16 final size:14
Alignment explanation
Indices: 13910241--13910286 Score: 58
Period size: 16 Copynumber: 3.1 Consensus size: 14
13910231 ATCAGTTGGA
13910241 AAAAAGGAGAAAGG
1 AAAAAGGAGAAAGG
13910255 AAAGAAAGGAGAAA-G
1 -AA-AAAGGAGAAAGG
13910270 AAAAAGAGAGAAAGG
1 AAAAAG-GAGAAAGG
13910285 AA
1 AA
13910287 GAAAAAGCTT
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
13 4 0.14
14 8 0.29
15 6 0.21
16 10 0.36
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (14 bp):
AAAAAGGAGAAAGG
Found at i:13913438 original size:35 final size:35
Alignment explanation
Indices: 13913365--13913467 Score: 116
Period size: 35 Copynumber: 2.9 Consensus size: 35
13913355 TCTGAATATT
* * * * *
13913365 TGTGTGATACAACGCCCCACATCTGGCCCTTGTTA
1 TGTGTGATATAACGCCCTACATCTAGCCCTTATCA
* *
13913400 TGTGTGATATAACGCCCTATATCTAGCCTTTATCA
1 TGTGTGATATAACGCCCTACATCTAGCCCTTATCA
* * *
13913435 TGTGTGGTATAACACCTTACATCTAGCCCTTAT
1 TGTGTGATATAACGCCCTACATCTAGCCCTTAT
13913468 TCTCATATAA
Statistics
Matches: 56, Mismatches: 12, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
35 56 1.00
ACGTcount: A:0.23, C:0.26, G:0.17, T:0.34
Consensus pattern (35 bp):
TGTGTGATATAACGCCCTACATCTAGCCCTTATCA
Found at i:13918413 original size:17 final size:17
Alignment explanation
Indices: 13918362--13918403 Score: 61
Period size: 16 Copynumber: 2.5 Consensus size: 17
13918352 TTTTTTTATA
13918362 ATTTTACTTAAT-AAATT
1 ATTTTA-TTAATAAAATT
13918379 -TTTTATTAATAAAATT
1 ATTTTATTAATAAAATT
13918395 ATTTTATTA
1 ATTTTATTA
13918404 TTTAATTTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
15 5 0.22
16 10 0.43
17 8 0.35
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.57
Consensus pattern (17 bp):
ATTTTATTAATAAAATT
Found at i:13918429 original size:21 final size:23
Alignment explanation
Indices: 13918400--13918447 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 23
13918390 AAATTATTTT
*
13918400 ATTATTTAATTT-ATAAATTAAA
1 ATTATTTAATTTGATAAATAAAA
*
13918422 ATTA-TTAATTTGATAAGTAAAA
1 ATTATTTAATTTGATAAATAAAA
13918444 ATTA
1 ATTA
13918448 AACACATTGA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 7 0.30
22 16 0.70
ACGTcount: A:0.50, C:0.00, G:0.04, T:0.46
Consensus pattern (23 bp):
ATTATTTAATTTGATAAATAAAA
Found at i:13919458 original size:19 final size:20
Alignment explanation
Indices: 13919423--13919475 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 20
13919413 AACTTTACCC
13919423 ATATTAATATTTGTAAATAA-A
1 ATATTAATA--TGTAAATAACA
13919444 ATATTAATATGTAAATAATCA
1 ATATTAATATGTAAATAA-CA
13919465 ATTATTAATAT
1 A-TATTAATAT
13919476 TTTAAACAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
19 9 0.31
21 11 0.38
22 9 0.31
ACGTcount: A:0.51, C:0.02, G:0.04, T:0.43
Consensus pattern (20 bp):
ATATTAATATGTAAATAACA
Found at i:13919581 original size:122 final size:127
Alignment explanation
Indices: 13919443--13919756 Score: 409
Period size: 122 Copynumber: 2.5 Consensus size: 127
13919433 TTGTAAATAA
* *
13919443 AATATTAATATGTAAATAATCAATTATTAATATTTTAAACAAATTATAAATTATTAATA-TTAAA
1 AATATTAATATTTAAATTATCAATTATTAATATTTTAAACAAATTATAAATTATTAATATTTAAA
* * *
13919507 TAATAAAATAATAATAAATAAT-A-A-CAT-TT-AAATTATAAATAAAATAATAATATTTTAT
66 T-ATAAAATAAAAATAAATAATCATATAATATTGAAATTAAAAATAAAATAATAATATTTTAT
* *
13919565 AATATTAATATTTAAATTATCAATTAATAATATTTTAAATAAATTATAAATTATTAATATTTAAA
1 AATATTAATATTTAAATTATCAATTATTAATATTTTAAACAAATTATAAATTATTAATATTTAAA
13919630 TATAAAATAAAAATAAATAATCATATTAATATTGAAATTAAAAATAAAATAATAATATTTTAT
66 TATAAAATAAAAATAAATAATCATA-TAATATTGAAATTAAAAATAAAATAATAATATTTTAT
* * *
13919693 AATATTAATGA-TTAAATTATAAAAATATTAATA-TTT----AAATTATCAATTATTAATATTTT
1 AATATTAAT-ATTTAAATTAT-CAATTATTAATATTTTAAACAAATTATAAATTATTAATA-TTT
13919752 AAATA
63 AAATA
13919757 AATTATAATT
Statistics
Matches: 171, Mismatches: 11, Indels: 17
0.86 0.06 0.09
Matches are distributed among these distances:
122 74 0.43
123 7 0.04
124 19 0.11
125 8 0.05
126 2 0.01
127 2 0.01
128 49 0.29
129 10 0.06
ACGTcount: A:0.55, C:0.02, G:0.01, T:0.42
Consensus pattern (127 bp):
AATATTAATATTTAAATTATCAATTATTAATATTTTAAACAAATTATAAATTATTAATATTTAAA
TATAAAATAAAAATAAATAATCATATAATATTGAAATTAAAAATAAAATAATAATATTTTAT
Found at i:13919639 original size:26 final size:27
Alignment explanation
Indices: 13919586--13919785 Score: 73
Period size: 27 Copynumber: 6.8 Consensus size: 27
13919576 TTAAATTATC
*
13919586 AATTAATAATATTTTAAATAAATTATA
1 AATTAATAATATTTTAAATAAATAATA
* *
13919613 AATTATTAATATTTAAATATAAAATAA-A
1 AATTAATAATATTTTAA-AT-AAATAATA
* *
13919641 AATAAATAATCATATTAATATTGAAATTAAAAATA
1 AATTAATAAT-ATTTTAA-A-T-AAA-T---AATA
* *
13919676 AAATAATAATATTTTATAATATTAATGATTA
1 AATTAATAATATTTTA-AATA--AAT-AATA
* * * *
13919707 AATT-ATAAAAATATTAATATTTAAATTATC
1 AATTAAT-AATATTTTAA-A--TAAATAATA
* *
13919737 AATTATTAATATTTTAAATAAATTAT-
1 AATTAATAATATTTTAAATAAATAATA
* *
13919763 AATTATTAATATTTAAAAATAAA
1 AATTAATAATATTT-TAAATAAA
13919786 ATAAAATAAA
Statistics
Matches: 132, Mismatches: 23, Indels: 36
0.69 0.12 0.19
Matches are distributed among these distances:
26 14 0.11
27 30 0.23
28 11 0.08
29 13 0.10
30 20 0.15
31 19 0.14
32 1 0.01
33 4 0.03
34 10 0.08
35 10 0.08
ACGTcount: A:0.56, C:0.01, G:0.01, T:0.42
Consensus pattern (27 bp):
AATTAATAATATTTTAAATAAATAATA
Found at i:13919660 original size:37 final size:35
Alignment explanation
Indices: 13919616--13919685 Score: 97
Period size: 37 Copynumber: 1.9 Consensus size: 35
13919606 AATTATAAAT
*
13919616 TATTAATATTTAAA-TATAAAATAAAAATAAATAATCA
1 TATTAATATTGAAATTA-AAAAT-AAAAT-AATAATCA
13919653 TATTAATATTGAAATTAAAAATAAAATAATAAT
1 TATTAATATTGAAATTAAAAATAAAATAATAAT
13919686 ATTTTATAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
35 6 0.19
36 5 0.16
37 18 0.58
38 2 0.06
ACGTcount: A:0.61, C:0.01, G:0.01, T:0.36
Consensus pattern (35 bp):
TATTAATATTGAAATTAAAAATAAAATAATAATCA
Found at i:13919698 original size:42 final size:42
Alignment explanation
Indices: 13919625--13919716 Score: 105
Period size: 42 Copynumber: 2.2 Consensus size: 42
13919615 TTATTAATAT
* *
13919625 TTAAATATAAAATAAAAATAAATAATCATATTAAT-ATTGAAA
1 TTAAAAATAAAATAAAAATAAATAATAATATTAATGATT-AAA
* ** *
13919667 TTAAAAATAAAATAATAATATTTTATAATATTAATGATTAAA
1 TTAAAAATAAAATAAAAATAAATAATAATATTAATGATTAAA
13919709 TTATAAAA
1 TTA-AAAA
13919717 ATATTAATAT
Statistics
Matches: 42, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
42 35 0.83
43 7 0.17
ACGTcount: A:0.60, C:0.01, G:0.02, T:0.37
Consensus pattern (42 bp):
TTAAAAATAAAATAAAAATAAATAATAATATTAATGATTAAA
Found at i:13919752 original size:23 final size:23
Alignment explanation
Indices: 13919693--13919779 Score: 79
Period size: 23 Copynumber: 3.7 Consensus size: 23
13919683 AATATTTTAT
13919693 AATATTAATGA-TTAAATTATAAA
1 AATATTAAT-ATTTAAATTATAAA
*
13919716 AATATTAATATTTAAATTAT-CA
1 AATATTAATATTTAAATTATAAA
* * *
13919738 ATTATTAATATTTTAAATAAATTATA
1 AATATTAATA-TTTAAAT-TA-TAAA
*
13919764 ATTATTAATATTTAAA
1 AATATTAATATTTAAA
13919780 AATAAAATAA
Statistics
Matches: 55, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
22 11 0.20
23 25 0.45
24 1 0.02
25 7 0.13
26 11 0.20
ACGTcount: A:0.52, C:0.01, G:0.01, T:0.46
Consensus pattern (23 bp):
AATATTAATATTTAAATTATAAA
Found at i:13922538 original size:8 final size:8
Alignment explanation
Indices: 13922525--13922555 Score: 53
Period size: 8 Copynumber: 3.9 Consensus size: 8
13922515 GTGTACATGA
13922525 ATATATAC
1 ATATATAC
13922533 ATATATAC
1 ATATATAC
*
13922541 ATATATCC
1 ATATATAC
13922549 ATATATA
1 ATATATA
13922556 TGTATGTATA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.48, C:0.13, G:0.00, T:0.39
Consensus pattern (8 bp):
ATATATAC
Found at i:13943087 original size:15 final size:15
Alignment explanation
Indices: 13943067--13943101 Score: 70
Period size: 15 Copynumber: 2.3 Consensus size: 15
13943057 TCACACCTTT
13943067 GAACCCTTTTGACTA
1 GAACCCTTTTGACTA
13943082 GAACCCTTTTGACTA
1 GAACCCTTTTGACTA
13943097 GAACC
1 GAACC
13943102 TTTGAATTCT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.29, C:0.29, G:0.14, T:0.29
Consensus pattern (15 bp):
GAACCCTTTTGACTA
Found at i:13943831 original size:43 final size:43
Alignment explanation
Indices: 13943768--13943879 Score: 163
Period size: 43 Copynumber: 2.6 Consensus size: 43
13943758 TATTGACTTG
* *
13943768 GCTATGTGCGGGTAGGGAGTGCGCATAAGCCGAGGATGACCC-
1 GCTATGTGCGAGTAGGGAGTGCGCATAACCCGAGGATGACCCA
* *
13943810 GATTATGTGCGAGTAGGGAGTGCGCATAACCCGATGATGACCCA
1 G-CTATGTGCGAGTAGGGAGTGCGCATAACCCGAGGATGACCCA
*
13943854 GCCATGTGCGAGTAGGGAGTGCGCAT
1 GCTATGTGCGAGTAGGGAGTGCGCAT
13943880 GAGCTGGTGA
Statistics
Matches: 62, Mismatches: 6, Indels: 3
0.87 0.08 0.04
Matches are distributed among these distances:
42 1 0.02
43 60 0.97
44 1 0.02
ACGTcount: A:0.23, C:0.21, G:0.38, T:0.19
Consensus pattern (43 bp):
GCTATGTGCGAGTAGGGAGTGCGCATAACCCGAGGATGACCCA
Found at i:13943891 original size:43 final size:43
Alignment explanation
Indices: 13943771--13943892 Score: 149
Period size: 43 Copynumber: 2.8 Consensus size: 43
13943761 TGACTTGGCT
* **
13943771 ATGTGCGGGTAGGGAGTGCGCATAAGCCGAG-GATGACCCGATT
1 ATGTGCGAGTAGGGAGTGCGCATAAGCCG-GTGATGACCCGACC
* *
13943814 ATGTGCGAGTAGGGAGTGCGCATAACCCGATGATGACCC-AGCC
1 ATGTGCGAGTAGGGAGTGCGCATAAGCCGGTGATGACCCGA-CC
* *
13943857 ATGTGCGAGTAGGGAGTGCGCATGAGCTGGTGATGA
1 ATGTGCGAGTAGGGAGTGCGCATAAGCCGGTGATGA
13943893 TGATGATGGG
Statistics
Matches: 68, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
42 1 0.01
43 67 0.99
ACGTcount: A:0.24, C:0.19, G:0.39, T:0.19
Consensus pattern (43 bp):
ATGTGCGAGTAGGGAGTGCGCATAAGCCGGTGATGACCCGACC
Found at i:13943940 original size:2 final size:2
Alignment explanation
Indices: 13943933--13943965 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
13943923 GGTATATGCG
*
13943933 TA TA TA TA TA TA TA TA TA TA TA TA TA TA CA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
13943966 GTAAATATGT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:13944304 original size:39 final size:39
Alignment explanation
Indices: 13944250--13944336 Score: 113
Period size: 39 Copynumber: 2.2 Consensus size: 39
13944240 TTCTCGCTGT
* * *
13944250 AGCGAGAAACTTTCTGTTT-TTGGGTAGCAATTTCACTGC
1 AGCGAGAAACCTTCTGTTTCTAGGGTA-CAATTTCACCGC
*
13944289 AGCGAGAAACCTTCTGTTTCTAGGTTACAATTTCACCGC
1 AGCGAGAAACCTTCTGTTTCTAGGGTACAATTTCACCGC
*
13944328 AGTGAGAAA
1 AGCGAGAAA
13944337 GAATCTCGCT
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
39 37 0.88
40 5 0.12
ACGTcount: A:0.28, C:0.20, G:0.22, T:0.31
Consensus pattern (39 bp):
AGCGAGAAACCTTCTGTTTCTAGGGTACAATTTCACCGC
Found at i:13945347 original size:15 final size:15
Alignment explanation
Indices: 13945327--13945389 Score: 54
Period size: 15 Copynumber: 4.2 Consensus size: 15
13945317 ATCTTTCTAG
13945327 TAATCACATTCTCAA
1 TAATCACATTCTCAA
* * *
13945342 TAATCATATACCCAA
1 TAATCACATTCTCAA
* * *
13945357 CAATCACATTCACGA
1 TAATCACATTCTCAA
* *
13945372 TAATAACATTTTCAA
1 TAATCACATTCTCAA
13945387 TAA
1 TAA
13945390 AATACCAAAC
Statistics
Matches: 35, Mismatches: 13, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
15 35 1.00
ACGTcount: A:0.44, C:0.24, G:0.02, T:0.30
Consensus pattern (15 bp):
TAATCACATTCTCAA
Found at i:13949362 original size:20 final size:20
Alignment explanation
Indices: 13949337--13949377 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
13949327 ATAGGCCTTG
*
13949337 TTGATTTTTATGAAATGAAA
1 TTGATTTATATGAAATGAAA
13949357 TTGATTTATATGAAATGAAA
1 TTGATTTATATGAAATGAAA
13949377 T
1 T
13949378 GAGATTGGAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.41, C:0.00, G:0.15, T:0.44
Consensus pattern (20 bp):
TTGATTTATATGAAATGAAA
Found at i:13949393 original size:25 final size:25
Alignment explanation
Indices: 13949346--13949395 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
13949336 GTTGATTTTT
*
13949346 ATGAAATGAAATTGATTTATATGAA
1 ATGAAATGAAATTGATGTATATGAA
*
13949371 ATGAAATGAGATTGGATGT-TATGAA
1 ATGAAATGAAATT-GATGTATATGAA
13949396 TCATATTATG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 18 0.82
26 4 0.18
ACGTcount: A:0.44, C:0.00, G:0.22, T:0.34
Consensus pattern (25 bp):
ATGAAATGAAATTGATGTATATGAA
Found at i:13965502 original size:22 final size:20
Alignment explanation
Indices: 13965471--13965515 Score: 54
Period size: 22 Copynumber: 2.1 Consensus size: 20
13965461 ATAAATAAAA
13965471 TATTAATATTTAAATGATTAAT
1 TATTAATATTTAAA--ATTAAT
* *
13965493 TATTAGTATTTTAAATTAAT
1 TATTAATATTTAAAATTAAT
13965513 TAT
1 TAT
13965516 AAATGATTGA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 9 0.43
22 12 0.57
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.53
Consensus pattern (20 bp):
TATTAATATTTAAAATTAAT
Found at i:13965620 original size:42 final size:41
Alignment explanation
Indices: 13965573--13965654 Score: 112
Period size: 41 Copynumber: 2.0 Consensus size: 41
13965563 TAATAACATT
* *
13965573 TAAATTATAAATT-AATTATTAATATTTTAAAATATTAATTAC
1 TAAATTAT-AATTAAAATATTAATA-TTTAAAATATAAATTAC
*
13965615 TAAATTATAATTAAAATATTAATATTTAAATTATAAATTA
1 TAAATTATAATTAAAATATTAATATTTAAAATATAAATTA
13965655 TGAATTTTTT
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
41 18 0.50
42 18 0.50
ACGTcount: A:0.52, C:0.01, G:0.00, T:0.46
Consensus pattern (41 bp):
TAAATTATAATTAAAATATTAATATTTAAAATATAAATTAC
Found at i:13965632 original size:26 final size:26
Alignment explanation
Indices: 13965599--13965650 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 26
13965589 TATTAATATT
13965599 TTAAAATATTAAT-TACTAAATTATAA
1 TTAAAATATTAATAT-CTAAATTATAA
*
13965625 TTAAAATATTAATATTTAAATTATAA
1 TTAAAATATTAATATCTAAATTATAA
13965651 ATTATGAATT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
26 23 0.96
27 1 0.04
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (26 bp):
TTAAAATATTAATATCTAAATTATAA
Found at i:13972302 original size:89 final size:89
Alignment explanation
Indices: 13972143--13972311 Score: 241
Period size: 89 Copynumber: 1.9 Consensus size: 89
13972133 GGTGTTTGTA
* * * **
13972143 GGTTATCACTTGATCTCGTTAAAAAGCAAGAATCCCTTTGTGGATTGTGTAAGGGTTATTGCTTG
1 GGTTATCACTTGATCCCATTAAAAAGCAAGAATCACTTTGTGGATTGTGTAAGGGTTATCACTTG
13972208 ATCCCGTGAAAAAGTTATTGTGAG
66 ATCCCGTGAAAAAGTTATTGTGAG
* * *
13972232 GGTTATCGCTTGATCCCATTAAAAAGCAAGAATCACTTTGTGGATTGTGTGAGTGTTATCACTTT
1 GGTTATCACTTGATCCCATTAAAAAGCAAGAATCACTTTGTGGATTGTGTAAGGGTTATCAC-TT
*
13972297 G-TCCCGTTAAAAAGT
65 GATCCCGTGAAAAAGT
13972312 AAGAGTCCTT
Statistics
Matches: 70, Mismatches: 9, Indels: 2
0.86 0.11 0.02
Matches are distributed among these distances:
89 67 0.96
90 3 0.04
ACGTcount: A:0.27, C:0.15, G:0.23, T:0.35
Consensus pattern (89 bp):
GGTTATCACTTGATCCCATTAAAAAGCAAGAATCACTTTGTGGATTGTGTAAGGGTTATCACTTG
ATCCCGTGAAAAAGTTATTGTGAG
Found at i:13972745 original size:139 final size:139
Alignment explanation
Indices: 13972524--13972805 Score: 501
Period size: 139 Copynumber: 2.0 Consensus size: 139
13972514 TAGCTAGCAA
13972524 TTAAACTTAAGAAAAATATTTTACTTTGATAGATTATTTTTATGCTTAATGATTTATTGTTGGAA
1 TTAAACTTAAGAAAAATATTTTACTTTGATAGATTATTTTTATGCTTAATGATTTATTGTTGGAA
* *
13972589 ACTTGATTTTGATGCTAGAAAATATATTTGGGTGAAGAAGTTTTGATTTTTTTAATTAGATTTTC
66 ACTTGATTTTGATGCTAGAAAATATATTTGGGTGAAAAAGTTTTGATTTTTATAATTAGATTTTC
*
13972654 AAGAAATTT
131 AAGAAAATT
* *
13972663 TTAAACTTAGGAAAAATATTTTACTTTGATTGATTATTTTTATGCTTAATGATTTATTGTTGGAA
1 TTAAACTTAAGAAAAATATTTTACTTTGATAGATTATTTTTATGCTTAATGATTTATTGTTGGAA
**
13972728 TTTTGATTTTGATGCTAGAAAATATATTTGGGTGAAAAAGTTTTGATTTTTATAATTAGATTTTC
66 ACTTGATTTTGATGCTAGAAAATATATTTGGGTGAAAAAGTTTTGATTTTTATAATTAGATTTTC
13972793 AAGAAAATT
131 AAGAAAATT
13972802 TTAA
1 TTAA
13972806 TATATCAATT
Statistics
Matches: 136, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
139 136 1.00
ACGTcount: A:0.34, C:0.04, G:0.15, T:0.47
Consensus pattern (139 bp):
TTAAACTTAAGAAAAATATTTTACTTTGATAGATTATTTTTATGCTTAATGATTTATTGTTGGAA
ACTTGATTTTGATGCTAGAAAATATATTTGGGTGAAAAAGTTTTGATTTTTATAATTAGATTTTC
AAGAAAATT
Found at i:13976761 original size:57 final size:54
Alignment explanation
Indices: 13976671--13976783 Score: 199
Period size: 57 Copynumber: 2.0 Consensus size: 54
13976661 TTTCAAATAC
13976671 TTTTAACATTCACAAATTTCTAAGGTATCTACCAATTTATGCTTTTCCACAAAATT
1 TTTTAACATTCACAAATTTCTAAGGTATCTACCAATTTATGC-TTTCCAC-AAATT
13976727 TTNTTAACATTCACAAATTTCTAAGGTATCTACCAATTTATGCTTTCCACAAATT
1 TT-TTAACATTCACAAATTTCTAAGGTATCTACCAATTTATGCTTTCCACAAATT
13976782 TT
1 TT
13976784 CATTTAAAAT
Statistics
Matches: 56, Mismatches: 0, Indels: 3
0.95 0.00 0.05
Matches are distributed among these distances:
55 7 0.12
56 9 0.16
57 40 0.71
ACGTcount: A:0.33, C:0.19, G:0.05, T:0.42
Consensus pattern (54 bp):
TTTTAACATTCACAAATTTCTAAGGTATCTACCAATTTATGCTTTCCACAAATT
Found at i:13976812 original size:2 final size:2
Alignment explanation
Indices: 13976805--13976879 Score: 132
Period size: 2 Copynumber: 37.5 Consensus size: 2
13976795 AATCAACACG
13976805 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* *
13976847 TA TA TG TA TA TA TA TA TA TA TA TA CA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
13976880 GGAAATAGCG
Statistics
Matches: 69, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 69 1.00
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.49
Consensus pattern (2 bp):
TA
Found at i:13977327 original size:4 final size:4
Alignment explanation
Indices: 13977316--13977389 Score: 64
Period size: 4 Copynumber: 19.2 Consensus size: 4
13977306 TCCTTACCTT
* * * *
13977316 TTTC -TTC TTTC -TCC TTTC TTTC TTTC TTCC TTTC TTCC TTTC -TCC
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC
* * *
13977361 TTTC TTTC TTTC TTCC CTTC TTCC TTTC T
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC T
13977390 CCTTTCCTTC
Statistics
Matches: 53, Mismatches: 14, Indels: 6
0.73 0.19 0.08
Matches are distributed among these distances:
3 7 0.13
4 46 0.87
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (4 bp):
TTTC
Found at i:13977338 original size:15 final size:15
Alignment explanation
Indices: 13977316--13977395 Score: 108
Period size: 15 Copynumber: 5.3 Consensus size: 15
13977306 TCCTTACCTT
13977316 TTTC-TTCTTTCTCC
1 TTTCTTTCTTTCTCC
13977330 TTTCTTTCTTTCTTCC
1 TTTCTTTCTTTC-TCC
*
13977346 TTTCTTCCTTTCTCC
1 TTTCTTTCTTTCTCC
13977361 TTTCTTTCTTTCTTCC
1 TTTCTTTCTTTC-TCC
* *
13977377 CTTCTTCCTTTCTCC
1 TTTCTTTCTTTCTCC
13977392 TTTC
1 TTTC
13977396 CTTCCAAGCC
Statistics
Matches: 58, Mismatches: 5, Indels: 5
0.85 0.07 0.07
Matches are distributed among these distances:
14 4 0.07
15 27 0.47
16 27 0.47
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (15 bp):
TTTCTTTCTTTCTCC
Found at i:13977342 original size:8 final size:8
Alignment explanation
Indices: 13977316--13977400 Score: 106
Period size: 8 Copynumber: 11.0 Consensus size: 8
13977306 TCCTTACCTT
13977316 TTTCTT-C
1 TTTCTTCC
13977323 TTTC-TCC
1 TTTCTTCC
*
13977330 TTTCTTTC
1 TTTCTTCC
13977338 TTTCTTCC
1 TTTCTTCC
13977346 TTTCTTCC
1 TTTCTTCC
13977354 TTTC-TCC
1 TTTCTTCC
*
13977361 TTTCTTTC
1 TTTCTTCC
13977369 TTTCTTCC
1 TTTCTTCC
*
13977377 CTTCTTCC
1 TTTCTTCC
13977385 TTTC-TCC
1 TTTCTTCC
13977392 TTTCCTTCC
1 TTT-CTTCC
13977401 AAGCCGATCT
Statistics
Matches: 67, Mismatches: 6, Indels: 8
0.83 0.07 0.10
Matches are distributed among these distances:
6 1 0.01
7 22 0.33
8 41 0.61
9 3 0.04
ACGTcount: A:0.00, C:0.38, G:0.00, T:0.62
Consensus pattern (8 bp):
TTTCTTCC
Found at i:13977359 original size:31 final size:31
Alignment explanation
Indices: 13977316--13977395 Score: 144
Period size: 31 Copynumber: 2.6 Consensus size: 31
13977306 TCCTTACCTT
13977316 TTTCTT-CTTTCTCCTTTCTTTCTTTCTTCC
1 TTTCTTCCTTTCTCCTTTCTTTCTTTCTTCC
13977346 TTTCTTCCTTTCTCCTTTCTTTCTTTCTTCC
1 TTTCTTCCTTTCTCCTTTCTTTCTTTCTTCC
*
13977377 CTTCTTCCTTTCTCCTTTC
1 TTTCTTCCTTTCTCCTTTC
13977396 CTTCCAAGCC
Statistics
Matches: 48, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
30 6 0.12
31 42 0.88
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (31 bp):
TTTCTTCCTTTCTCCTTTCTTTCTTTCTTCC
Found at i:13979298 original size:23 final size:22
Alignment explanation
Indices: 13979266--13979308 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
13979256 AACCTATCTT
* *
13979266 AATAATATTAACACCAAATTAAG
1 AATAAAATTAAC-CAAAATTAAG
13979289 AATAAAATTAACCAAAATTA
1 AATAAAATTAACCAAAATTA
13979309 GATTGACTCA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 7 0.39
23 11 0.61
ACGTcount: A:0.60, C:0.12, G:0.02, T:0.26
Consensus pattern (22 bp):
AATAAAATTAACCAAAATTAAG
Found at i:13980290 original size:18 final size:19
Alignment explanation
Indices: 13980263--13980312 Score: 52
Period size: 18 Copynumber: 2.8 Consensus size: 19
13980253 ACACGTTTAC
* *
13980263 TTAATCGTGTTAT-CGTGT
1 TTAAACGTGTTATACGTAT
*
13980281 TTAAATGTG-TATACGTAT
1 TTAAACGTGTTATACGTAT
13980299 TTAAACGTG-TATAC
1 TTAAACGTGTTATAC
13980313 ATGACATGTT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
17 3 0.11
18 24 0.89
ACGTcount: A:0.28, C:0.10, G:0.18, T:0.44
Consensus pattern (19 bp):
TTAAACGTGTTATACGTAT
Found at i:13980566 original size:9 final size:9
Alignment explanation
Indices: 13980549--13980632 Score: 114
Period size: 9 Copynumber: 9.3 Consensus size: 9
13980539 ATATTTTTAT
13980549 TTAATCGTG
1 TTAATCGTG
*
13980558 TTAAACGTG
1 TTAATCGTG
13980567 TTAATCGTG
1 TTAATCGTG
*
13980576 TTAAACGTG
1 TTAATCGTG
*
13980585 CTAATCGTG
1 TTAATCGTG
*
13980594 TTAATCATG
1 TTAATCGTG
*
13980603 TTAAACGTG
1 TTAATCGTG
13980612 TTAATCGTG
1 TTAATCGTG
*
13980621 TTAAACGTG
1 TTAATCGTG
13980630 TTA
1 TTA
13980633 TTAATCGTAT
Statistics
Matches: 64, Mismatches: 11, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
9 64 1.00
ACGTcount: A:0.29, C:0.12, G:0.20, T:0.39
Consensus pattern (9 bp):
TTAATCGTG
Found at i:13981839 original size:8 final size:8
Alignment explanation
Indices: 13981821--13981880 Score: 61
Period size: 8 Copynumber: 7.8 Consensus size: 8
13981811 TTTTTTTTGT
13981821 TGGGT-AA
1 TGGGTAAA
13981828 TGGGTAAA
1 TGGGTAAA
* *
13981836 TGGGTTAG
1 TGGGTAAA
*
13981844 TGGGTAAG
1 TGGGTAAA
*
13981852 TGGGTAAG
1 TGGGTAAA
*
13981860 GGGGTAAA
1 TGGGTAAA
13981868 TGGGT-AA
1 TGGGTAAA
13981875 TGGGTA
1 TGGGTA
13981881 GTCCACATGA
Statistics
Matches: 45, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
7 12 0.27
8 33 0.73
ACGTcount: A:0.27, C:0.00, G:0.47, T:0.27
Consensus pattern (8 bp):
TGGGTAAA
Found at i:13981849 original size:16 final size:16
Alignment explanation
Indices: 13981821--13981880 Score: 79
Period size: 16 Copynumber: 3.9 Consensus size: 16
13981811 TTTTTTTTGT
13981821 TGGGTAA-TGGGTAAA
1 TGGGTAAGTGGGTAAA
* *
13981836 TGGGTTAGTGGGTAAG
1 TGGGTAAGTGGGTAAA
*
13981852 TGGGTAAGGGGGTAAA
1 TGGGTAAGTGGGTAAA
13981868 TGGGTAA-TGGGTA
1 TGGGTAAGTGGGTA
13981881 GTCCACATGA
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
15 11 0.29
16 27 0.71
ACGTcount: A:0.27, C:0.00, G:0.47, T:0.27
Consensus pattern (16 bp):
TGGGTAAGTGGGTAAA
Found at i:13982337 original size:17 final size:17
Alignment explanation
Indices: 13982302--13982336 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
13982292 TTAATAATTT
*
13982302 AATAATTAAATAAATAA
1 AATAATTAAAAAAATAA
13982319 AATAA-TAAAAAAATAA
1 AATAATTAAAAAAATAA
13982335 AA
1 AA
13982337 AGAAAGTAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 12 0.71
17 5 0.29
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (17 bp):
AATAATTAAAAAAATAA
Found at i:13983755 original size:21 final size:21
Alignment explanation
Indices: 13983704--13983767 Score: 92
Period size: 21 Copynumber: 3.0 Consensus size: 21
13983694 TTGAATGGAG
* * *
13983704 GCATCAGTCCTTATCATAAAT
1 GCATCAGTCTTTGTCATGAAT
*
13983725 GCATCAGTCTTTGTTATGAAT
1 GCATCAGTCTTTGTCATGAAT
13983746 GCATCAGTCTTTGTCATGAAT
1 GCATCAGTCTTTGTCATGAAT
13983767 G
1 G
13983768 TGAGACCTCG
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 38 1.00
ACGTcount: A:0.27, C:0.19, G:0.17, T:0.38
Consensus pattern (21 bp):
GCATCAGTCTTTGTCATGAAT
Found at i:13985070 original size:42 final size:42
Alignment explanation
Indices: 13985011--13985101 Score: 164
Period size: 42 Copynumber: 2.2 Consensus size: 42
13985001 TTATGTGATA
*
13985011 ATGATGACCCAGCTATGTGCGTGTGGGAGTGCACATGAGCTG
1 ATGATGACCCAACTATGTGCGTGTGGGAGTGCACATGAGCTG
*
13985053 ATGATGACCCAATTATGTGCGTGTGGGAGTGCACATGAGCTG
1 ATGATGACCCAACTATGTGCGTGTGGGAGTGCACATGAGCTG
13985095 ATGATGA
1 ATGATGA
13985102 TGGGATGGTA
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
42 47 1.00
ACGTcount: A:0.24, C:0.16, G:0.34, T:0.25
Consensus pattern (42 bp):
ATGATGACCCAACTATGTGCGTGTGGGAGTGCACATGAGCTG
Found at i:13985462 original size:39 final size:39
Alignment explanation
Indices: 13985402--13985499 Score: 153
Period size: 39 Copynumber: 2.5 Consensus size: 39
13985392 TCATTCTTGT
* *
13985402 TGCAGTGAGAAACTTTCTGTTTTG-CTGCTTGAATTTCGC
1 TGCAGCGAGAAACTTTCTGTTTTGCCT-CTTGAATCTCGC
*
13985441 TGTAGCGAGAAACTTTCTGTTTTGCCTCTTGAATCTCGC
1 TGCAGCGAGAAACTTTCTGTTTTGCCTCTTGAATCTCGC
13985480 TGCAGCGAGAAACTTTCTGT
1 TGCAGCGAGAAACTTTCTGT
13985500 CCAGCATGCT
Statistics
Matches: 54, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
39 52 0.96
40 2 0.04
ACGTcount: A:0.19, C:0.20, G:0.22, T:0.38
Consensus pattern (39 bp):
TGCAGCGAGAAACTTTCTGTTTTGCCTCTTGAATCTCGC
Found at i:13989337 original size:19 final size:19
Alignment explanation
Indices: 13989313--13989378 Score: 107
Period size: 19 Copynumber: 3.5 Consensus size: 19
13989303 TAATATTTTC
*
13989313 ATATTATTTTACTCATAAA
1 ATATTATTTTATTCATAAA
13989332 ATATTATTTTATTCATAAA
1 ATATTATTTTATTCATAAA
13989351 ATATTATTTTATTC-TAAA
1 ATATTATTTTATTCATAAA
*
13989369 ATATTCTTTT
1 ATATTATTTT
13989379 CACCGGTCAC
Statistics
Matches: 45, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
18 13 0.29
19 32 0.71
ACGTcount: A:0.38, C:0.08, G:0.00, T:0.55
Consensus pattern (19 bp):
ATATTATTTTATTCATAAA
Found at i:13989793 original size:24 final size:24
Alignment explanation
Indices: 13989765--13989811 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
13989755 TTTGATTAAA
*
13989765 CATTTATGTGAATATATTTGTATG
1 CATTTATGTGAATATATGTGTATG
13989789 CATTTATGTGAATATATGTGTAT
1 CATTTATGTGAATATATGTGTAT
13989812 TTGTTGATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.30, C:0.04, G:0.17, T:0.49
Consensus pattern (24 bp):
CATTTATGTGAATATATGTGTATG
Found at i:13990873 original size:26 final size:27
Alignment explanation
Indices: 13990839--13990891 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 27
13990829 CGAGTATAAG
* *
13990839 GGGCAAAATAGTCATTTGC-CACCCAA
1 GGGCAAAATAGTAATTTACACACCCAA
*
13990865 GGGCAAAATTGTAATTTACACACCCAA
1 GGGCAAAATAGTAATTTACACACCCAA
13990892 CACTTGTCAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
26 16 0.70
27 7 0.30
ACGTcount: A:0.38, C:0.25, G:0.17, T:0.21
Consensus pattern (27 bp):
GGGCAAAATAGTAATTTACACACCCAA
Found at i:13991169 original size:21 final size:22
Alignment explanation
Indices: 13991144--13991184 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
13991134 CCTAGGTGGA
*
13991144 AAAATTCAAGGGAA-AAGTGTG
1 AAAATTCAAGGAAACAAGTGTG
13991165 AAAATTCAAGGAAACAAGTG
1 AAAATTCAAGGAAACAAGTG
13991185 AAAAAANNNN
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:0.51, C:0.07, G:0.24, T:0.17
Consensus pattern (22 bp):
AAAATTCAAGGAAACAAGTGTG
Found at i:13991185 original size:20 final size:21
Alignment explanation
Indices: 13991144--13991188 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 21
13991134 CCTAGGTGGA
*
13991144 AAAATTCAAGGGAAAAGTGTG
1 AAAATTCAAGGGAAAAGAGTG
13991165 AAAATTCAA-GGAAACA-AGTG
1 AAAATTCAAGGGAAA-AGAGTG
13991185 AAAA
1 AAAA
13991189 AANNNNNNNN
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
20 12 0.55
21 10 0.45
ACGTcount: A:0.56, C:0.07, G:0.22, T:0.16
Consensus pattern (21 bp):
AAAATTCAAGGGAAAAGAGTG
Found at i:13991189 original size:21 final size:20
Alignment explanation
Indices: 13991142--13991189 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 20
13991132 ACCCTAGGTG
*
13991142 GAAAAATTCAAGGGAAAAGT
1 GAAAAATTCAAGGAAAAAGT
*
13991162 GTGAAAATTCAAGGAAACAAGT
1 G-AAAAATTCAAGGAAA-AAGT
13991184 GAAAAA
1 GAAAAA
13991190 ANNNNNNNNN
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:0.56, C:0.06, G:0.23, T:0.15
Consensus pattern (20 bp):
GAAAAATTCAAGGAAAAAGT
Found at i:14011749 original size:2 final size:2
Alignment explanation
Indices: 14011742--14011772 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
14011732 ACTTTCTATA
14011742 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
14011773 TATATATATA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:14011777 original size:2 final size:2
Alignment explanation
Indices: 14011772--14011796 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
14011762 ACACACACAC
14011772 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
14011797 CATACATCAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:14011893 original size:37 final size:37
Alignment explanation
Indices: 14011846--14011927 Score: 155
Period size: 37 Copynumber: 2.2 Consensus size: 37
14011836 AATGCAATAT
14011846 CATCATCATGTGTGCACTCCCTACTCACACACTCCAA
1 CATCATCATGTGTGCACTCCCTACTCACACACTCCAA
*
14011883 CATCATCATGTGTGCACTCCCTACTCACACACTTCAA
1 CATCATCATGTGTGCACTCCCTACTCACACACTCCAA
14011920 CATCATCA
1 CATCATCA
14011928 CATAACATTA
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
37 44 1.00
ACGTcount: A:0.28, C:0.39, G:0.07, T:0.26
Consensus pattern (37 bp):
CATCATCATGTGTGCACTCCCTACTCACACACTCCAA
Found at i:14021427 original size:26 final size:26
Alignment explanation
Indices: 14021398--14021535 Score: 75
Period size: 27 Copynumber: 5.1 Consensus size: 26
14021388 CATCGGTCAT
14021398 CAGCTCATGTGCACTCCCACACCGCA
1 CAGCTCATGTGCACTCCCACACCGCA
* * * *
14021424 CAGC-AATGATGTA-TACAACCACCGGTCA
1 CAGCTCATG-TGCACTCCCA-CACC-G-CA
14021452 TCAGCTCATGTGCACTCCCACACCGCA
1 -CAGCTCATGTGCACTCCCACACCGCA
* * ** ** *
14021479 CAGTAATCATATATACAACCAC-CGGTCA
1 CAG--CTCATGTGCACTCCCACACCG-CA
14021507 TCAGCTCATGTGCACTCCCACACCGCA
1 -CAGCTCATGTGCACTCCCACACCGCA
14021534 CA
1 CA
14021536 TAGCTGGAAT
Statistics
Matches: 78, Mismatches: 22, Indels: 24
0.63 0.18 0.19
Matches are distributed among these distances:
25 6 0.08
26 16 0.21
27 18 0.23
28 18 0.23
29 14 0.18
30 6 0.08
ACGTcount: A:0.29, C:0.38, G:0.14, T:0.18
Consensus pattern (26 bp):
CAGCTCATGTGCACTCCCACACCGCA
Found at i:14021464 original size:55 final size:55
Alignment explanation
Indices: 14021376--14021535 Score: 275
Period size: 55 Copynumber: 2.9 Consensus size: 55
14021366 ATCTCTATAG
* *
14021376 CATATATACACCCATCGGTCATCAGCTCATGTGCACTCCCACACCGCACAGCAAT
1 CATATATACAACCACCGGTCATCAGCTCATGTGCACTCCCACACCGCACAGCAAT
* * *
14021431 GATGTATACAACCACCGGTCATCAGCTCATGTGCACTCCCACACCGCACAGTAAT
1 CATATATACAACCACCGGTCATCAGCTCATGTGCACTCCCACACCGCACAGCAAT
14021486 CATATATACAACCACCGGTCATCAGCTCATGTGCACTCCCACACCGCACA
1 CATATATACAACCACCGGTCATCAGCTCATGTGCACTCCCACACCGCACA
14021536 TAGCTGGAAT
Statistics
Matches: 98, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
55 98 1.00
ACGTcount: A:0.29, C:0.38, G:0.14, T:0.19
Consensus pattern (55 bp):
CATATATACAACCACCGGTCATCAGCTCATGTGCACTCCCACACCGCACAGCAAT
Found at i:14021475 original size:29 final size:29
Alignment explanation
Indices: 14021391--14021531 Score: 88
Period size: 29 Copynumber: 5.1 Consensus size: 29
14021381 ATACACCCAT
14021391 CGGTCATCAGCTCATGTGCACTCCCACAC
1 CGGTCATCAGCTCATGTGCACTCCCACAC
* * * *
14021420 C-G-CA-CAGC-AATGATGTA-TACAACCAC
1 CGGTCATCAGCTCATG-TGCACTCCCA-CAC
14021446 CGGTCATCAGCTCATGTGCACTCCCACAC
1 CGGTCATCAGCTCATGTGCACTCCCACAC
* * * *
14021475 C-G-CA-CAGTAATCATAT--A-TACAACCAC
1 CGGTCATCAG--CTCATGTGCACTCCCA-CAC
14021501 CGGTCATCAGCTCATGTGCACTCCCACAC
1 CGGTCATCAGCTCATGTGCACTCCCACAC
14021530 CG
1 CG
14021532 CACATAGCTG
Statistics
Matches: 80, Mismatches: 16, Indels: 32
0.62 0.12 0.25
Matches are distributed among these distances:
25 9 0.11
26 19 0.24
27 11 0.14
28 11 0.14
29 21 0.26
30 9 0.11
ACGTcount: A:0.28, C:0.38, G:0.16, T:0.19
Consensus pattern (29 bp):
CGGTCATCAGCTCATGTGCACTCCCACAC
Found at i:14021645 original size:2 final size:2
Alignment explanation
Indices: 14021628--14021678 Score: 84
Period size: 2 Copynumber: 25.0 Consensus size: 2
14021618 TTATCAATAC
*
14021628 AT AT CAT AT AT CT 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
14021671 AT AT AT AT
1 AT AT AT AT
14021679 CAACATAACA
Statistics
Matches: 46, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
2 44 0.96
3 2 0.04
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:14026285 original size:38 final size:38
Alignment explanation
Indices: 14026198--14026339 Score: 187
Period size: 38 Copynumber: 3.7 Consensus size: 38
14026188 CACCCGGCTA
* * * *
14026198 ATGTACATCCCCCCACATTGTGTACATAGCCG-GCACCATC
1 ATGTACATCCCCCCACATCGTGCACA-ATCAGTG--CCATC
*
14026238 ATGTGCATCCCCCCACATCGTGCACAATCAGTGCCATC
1 ATGTACATCCCCCCACATCGTGCACAATCAGTGCCATC
*
14026276 ATGTACATCCCCCCACATTGTGCACAATCAGTGCCATC
1 ATGTACATCCCCCCACATCGTGCACAATCAGTGCCATC
*
14026314 GTGTACATCCCCCCACATCGTGCACA
1 ATGTACATCCCCCCACATCGTGCACA
14026340 TGGGCACTAT
Statistics
Matches: 92, Mismatches: 9, Indels: 4
0.88 0.09 0.04
Matches are distributed among these distances:
38 65 0.71
39 3 0.03
40 24 0.26
ACGTcount: A:0.25, C:0.39, G:0.15, T:0.22
Consensus pattern (38 bp):
ATGTACATCCCCCCACATCGTGCACAATCAGTGCCATC
Found at i:14026334 original size:19 final size:19
Alignment explanation
Indices: 14026199--14026340 Score: 63
Period size: 19 Copynumber: 7.4 Consensus size: 19
14026189 ACCCGGCTAA
*
14026199 TGTACATCCCCCCACATTG
1 TGTACATCCCCCCACATCG
* ** *
14026218 TGTACATAGCCGGCACCATCA
1 TGTACAT-CCCCCCA-CATCG
*
14026239 TGTGCATCCCCCCACATCG
1 TGTACATCCCCCCACATCG
* **** *
14026258 TGCACAATCAGTGC-CATCA
1 TGTAC-ATCCCCCCACATCG
*
14026277 TGTACATCCCCCCACATTG
1 TGTACATCCCCCCACATCG
* ****
14026296 TGCACAATCAGTGC-CATCG
1 TGTAC-ATCCCCCCACATCG
14026315 TGTACATCCCCCCACATCG
1 TGTACATCCCCCCACATCG
*
14026334 TGCACAT
1 TGTACAT
14026341 GGGCACTATC
Statistics
Matches: 81, Mismatches: 36, Indels: 12
0.63 0.28 0.09
Matches are distributed among these distances:
18 8 0.10
19 48 0.59
20 16 0.20
21 9 0.11
ACGTcount: A:0.24, C:0.39, G:0.15, T:0.23
Consensus pattern (19 bp):
TGTACATCCCCCCACATCG
Found at i:14034174 original size:38 final size:40
Alignment explanation
Indices: 14034090--14034191 Score: 118
Period size: 38 Copynumber: 2.6 Consensus size: 40
14034080 CCGGCTCAGG
* *
14034090 TACATCCCCTCACATCGTGCACATAGCCAGGGCCATCATG
1 TACATCCCCCCACATCGTGCACATAGCCAGGGCCATCATA
* ** * *
14034130 TGCATCCCCCCACATCGTGCACA-A-TTAGTGCCATCCTA
1 TACATCCCCCCACATCGTGCACATAGCCAGGGCCATCATA
*
14034168 TACATCCCCCTACATCGTGCACAT
1 TACATCCCCCCACATCGTGCACAT
14034192 GGGCACTATC
Statistics
Matches: 52, Mismatches: 9, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
38 30 0.58
39 1 0.02
40 21 0.40
ACGTcount: A:0.25, C:0.39, G:0.14, T:0.23
Consensus pattern (40 bp):
TACATCCCCCCACATCGTGCACATAGCCAGGGCCATCATA
Done.