Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr4
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: 31929104
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 1434590 characters in sequence are not A, C, G, or T
File 17 of 82
Found at i:5716896 original size:36 final size:38
Alignment explanation
Indices: 5716849--5716941 Score: 118
Period size: 38 Copynumber: 2.5 Consensus size: 38
5716839 TGTCGTGTGT
* *
5716849 GGTGTGGGAGTGCACATGACGGT-G-ATGGTGAGGTGC
1 GGTGTGGGAGTGCACATGACGATAGTATGGTAAGGTGC
* * * *
5716885 GGTGTGGGAGTGCACTTGATGATAGTATTGTAATGTGC
1 GGTGTGGGAGTGCACATGACGATAGTATGGTAAGGTGC
5716923 GGTGTGGGAGTGCACATGA
1 GGTGTGGGAGTGCACATGA
5716942 GCCGGGGGAG
Statistics
Matches: 48, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
36 20 0.42
37 1 0.02
38 27 0.56
ACGTcount: A:0.19, C:0.10, G:0.44, T:0.27
Consensus pattern (38 bp):
GGTGTGGGAGTGCACATGACGATAGTATGGTAAGGTGC
Found at i:5720179 original size:154 final size:153
Alignment explanation
Indices: 5719899--5720205 Score: 587
Period size: 154 Copynumber: 2.0 Consensus size: 153
5719889 ACCTCTCCCT
5719899 ATATGTTCATCCAGCAAGAGATCCATCATATAATCATGAATTTCATCCATGAAAATAAGAAAGAA
1 ATATGTTCATCCAGCAAGAGATCCATCATATAATCATGAATTTCATCCATGAAAATAAGAAAGAA
*
5719964 TGCTTAGGAAAGATAGATCTCAAGCTAGAATTGGAAAATCTTACCTTTTGTCACTTGATTCTTTG
66 TGCTTAGGAAAGATAGATCTCAAGCTAGAATTGAAAAATCTTACCTTTTGTCACTTGATTCTTTG
5720029 AAATTTGGTGAATTTCTCTTGAA
131 AAATTTGGTGAATTTCTCTTGAA
5720052 NATATGTTCATCCAGCAAGAGATCCATCATATAATCATGAATTTCATCCATGAAAATAAGAAAGA
1 -ATATGTTCATCCAGCAAGAGATCCATCATATAATCATGAATTTCATCCATGAAAATAAGAAAGA
5720117 ATGCTTAGGAAAGATAGATCTCAAGCTAGAATTGAAAAATCTTACCTTTTGTCACTTGATTCTTT
65 ATGCTTAGGAAAGATAGATCTCAAGCTAGAATTGAAAAATCTTACCTTTTGTCACTTGATTCTTT
*
5720182 GAAATTTTGTGAATTTCTCTTGAA
130 GAAATTTGGTGAATTTCTCTTGAA
5720206 TTTCTTAGCT
Statistics
Matches: 151, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
154 151 1.00
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.34
Consensus pattern (153 bp):
ATATGTTCATCCAGCAAGAGATCCATCATATAATCATGAATTTCATCCATGAAAATAAGAAAGAA
TGCTTAGGAAAGATAGATCTCAAGCTAGAATTGAAAAATCTTACCTTTTGTCACTTGATTCTTTG
AAATTTGGTGAATTTCTCTTGAA
Found at i:5722914 original size:19 final size:19
Alignment explanation
Indices: 5722886--5722923 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
5722876 TTATATTACT
5722886 GTTTTGAAAA-CAAATAAAA
1 GTTTTGAAAATC-AATAAAA
*
5722905 GTTTTTAAAATCAATAAAA
1 GTTTTGAAAATCAATAAAA
5722924 AATTAAATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 16 0.94
20 1 0.06
ACGTcount: A:0.55, C:0.05, G:0.08, T:0.32
Consensus pattern (19 bp):
GTTTTGAAAATCAATAAAA
Found at i:5726957 original size:15 final size:15
Alignment explanation
Indices: 5726937--5726969 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
5726927 GTTTCTCTCC
5726937 TCTTCCATGAAAGCT
1 TCTTCCATGAAAGCT
5726952 TCTTCCATGAAAGCT
1 TCTTCCATGAAAGCT
5726967 TCT
1 TCT
5726970 CTCAAGCTTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.24, C:0.27, G:0.12, T:0.36
Consensus pattern (15 bp):
TCTTCCATGAAAGCT
Found at i:5727685 original size:2 final size:2
Alignment explanation
Indices: 5727668--5727705 Score: 53
Period size: 2 Copynumber: 19.5 Consensus size: 2
5727658 CATGTGTTTC
5727668 TA TA TA -A TA T- TGA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA T
5727706 TATGTCATAA
Statistics
Matches: 33, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
1 2 0.06
2 30 0.91
3 1 0.03
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:5727873 original size:41 final size:40
Alignment explanation
Indices: 5727816--5727962 Score: 201
Period size: 41 Copynumber: 3.6 Consensus size: 40
5727806 ATATTACTCG
5727816 TGTGCACGATGTGGGGGGATGCACACGATGATGATGTCACT
1 TGTGCACGATGTGGGGGGATGCACACGATGATGAT-TCACT
*
5727857 TGTGCACAATGTGGGGGGATGCACACGATGATGATATCACT
1 TGTGCACGATGTGGGGGGATGCACACGATGATGAT-TCACT
* *
5727898 TGTGCACGATGTGGGGGGATGCATGAAGCGAT-AT-ATT-GCT
1 TGTGCACGATGTGGGGGGATGCA--CA-CGATGATGATTCACT
5727938 TGTGCACGATGTGGGGGGATGCACA
1 TGTGCACGATGTGGGGGGATGCACA
5727963 TGAGCTGGGT
Statistics
Matches: 97, Mismatches: 6, Indels: 9
0.87 0.05 0.08
Matches are distributed among these distances:
38 1 0.01
40 25 0.26
41 62 0.64
42 2 0.02
43 3 0.03
44 4 0.04
ACGTcount: A:0.23, C:0.16, G:0.37, T:0.24
Consensus pattern (40 bp):
TGTGCACGATGTGGGGGGATGCACACGATGATGATTCACT
Found at i:5728003 original size:54 final size:53
Alignment explanation
Indices: 5727938--5728141 Score: 275
Period size: 54 Copynumber: 3.8 Consensus size: 53
5727928 ATATATTGCT
5727938 TGTGCACGATGTGGGGGGATGCACATGAGCTGGGTGAGATGGAGTGTCTGGCTA
1 TGTGCACGATGTGGGGGGATGCACATGAGCTGGGTGAGATGG-GTGTCTGGCTA
* * * *
5727992 TGTGCATGATGTGGGGGGATGCATATGAGCTAGATGAGATGGGGTGTCTGGCTA
1 TGTGCACGATGTGGGGGGATGCACATGAGCTGGGTGAGAT-GGGTGTCTGGCTA
* * * **
5728046 TGTGCACGATGTAGGGGGATACACATGAGCTGGGTGAGACAGGGTGT-TCGATTA
1 TGTGCACGATGTGGGGGGATGCACATGAGCTGGGTGAGA-TGGGTGTCT-GGCTA
*
5728100 TGTGCACGATATGGGGGGATGCACATGAGCTGGGTGAGATGG
1 TGTGCACGATGTGGGGGGATGCACATGAGCTGGGTGAGATGG
5728142 TGGTGTATGT
Statistics
Matches: 130, Mismatches: 17, Indels: 7
0.84 0.11 0.05
Matches are distributed among these distances:
53 3 0.02
54 125 0.96
55 2 0.02
ACGTcount: A:0.21, C:0.12, G:0.43, T:0.25
Consensus pattern (53 bp):
TGTGCACGATGTGGGGGGATGCACATGAGCTGGGTGAGATGGGTGTCTGGCTA
Found at i:5751874 original size:61 final size:62
Alignment explanation
Indices: 5751809--5752030 Score: 249
Period size: 61 Copynumber: 3.6 Consensus size: 62
5751799 AGTGAATGCG
* ** ** *
5751809 ATTTCTATTGATACATTGTCCAAATGTATCAATAGATTTGAATGGGGAAGTATTTT--ACGTA
1 ATTTCTATCGATACATTGTCCAAATGTATCAATAGATTTGAAAAGGGAAACATTTTGAATG-A
* *
5751870 ATTTCTATCGATGCATTATCCAAATGTATCAATAGATTTGAAAAGGGAAACATTTTGAATGA
1 ATTTCTATCGATACATTGTCCAAATGTATCAATAGATTTGAAAAGGGAAACATTTTGAATGA
* *
5751932 A-TTCTATCAATACATTGTCCAAATGTATCAATAGATTTGAAGAA-GGAAACA-TTCGAGATGA
1 ATTTCTATCGATACATTGTCCAAATGTATCAATAGATTTGAA-AAGGGAAACATTTTGA-ATGA
* * **
5751993 A-TTCTATCGATACATTCTGCAAATGTATTGATAGATTT
1 ATTTCTATCGATACATTGTCCAAATGTATCAATAGATTT
5752031 TAGGTAGAAA
Statistics
Matches: 140, Mismatches: 17, Indels: 8
0.85 0.10 0.05
Matches are distributed among these distances:
60 4 0.03
61 130 0.93
62 4 0.03
63 2 0.01
ACGTcount: A:0.36, C:0.12, G:0.16, T:0.36
Consensus pattern (62 bp):
ATTTCTATCGATACATTGTCCAAATGTATCAATAGATTTGAAAAGGGAAACATTTTGAATGA
Found at i:5753480 original size:45 final size:44
Alignment explanation
Indices: 5753372--5753526 Score: 120
Period size: 45 Copynumber: 3.5 Consensus size: 44
5753362 TACCATTTAT
*
5753372 TAGG-AGATTACTCCGGATGATGATTATG-TAATGATGCCA-C-
1 TAGGAAGATTACTCCAGATGATGATTATGTTAATGATGCCATCG
* * * * *
5753412 TAGTCAAGACTACTCTAGGTGATGATTATGTTTATGATGCCATCCG
1 TAG-GAAGATTACTCCAGATGATGATTATGTTAATGATGCCAT-CG
* * ** * * *
5753458 TTGGGAGATTACTCCAGATGATGATTACATTGATGATACCATTTG
1 TAGGAAGATTACTCCAGATGATGATTATGTTAATGATGCCA-TCG
* *
5753503 TCGAAAGATTACTCCAGATGATGA
1 TAGGAAGATTACTCCAGATGATGA
5753527 CTTGACCTTT
Statistics
Matches: 88, Mismatches: 20, Indels: 9
0.75 0.17 0.08
Matches are distributed among these distances:
40 3 0.03
42 20 0.23
43 10 0.11
45 52 0.59
46 3 0.03
ACGTcount: A:0.30, C:0.15, G:0.23, T:0.32
Consensus pattern (44 bp):
TAGGAAGATTACTCCAGATGATGATTATGTTAATGATGCCATCG
Found at i:5766591 original size:23 final size:23
Alignment explanation
Indices: 5766545--5766591 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 23
5766535 CATCTTGCAG
* *
5766545 AGTTCTAGTACTTTTCATAGGTA
1 AGTTCTAGTACTTTTCACAAGTA
5766568 AGTTCTAGTACTTTTCACAAGTA
1 AGTTCTAGTACTTTTCACAAGTA
5766591 A
1 A
5766592 TTCATCAATG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.40
Consensus pattern (23 bp):
AGTTCTAGTACTTTTCACAAGTA
Found at i:5773346 original size:2 final size:2
Alignment explanation
Indices: 5773339--5773401 Score: 57
Period size: 2 Copynumber: 34.0 Consensus size: 2
5773329 GTCAGAGGAG
* *
5773339 TA TA TA TA TA TA T- TA TA TA TA -A TT TCA AA T- TA TA TA -A TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA TA TA TA TA TA
5773378 TA -A TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
5773402 GATCGTGGGC
Statistics
Matches: 50, Mismatches: 4, Indels: 14
0.74 0.06 0.21
Matches are distributed among these distances:
1 6 0.12
2 44 0.88
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:5774974 original size:25 final size:25
Alignment explanation
Indices: 5774946--5775081 Score: 96
Period size: 25 Copynumber: 5.4 Consensus size: 25
5774936 TGTGATTGAA
*
5774946 TGTAAGTCATTGCGTGACTGTTATC
1 TGTAAGGCATTGCGTGACTGTTATC
* * * *
5774971 TGTATTGG-ATTGCATGA-TCGTTTTA
1 TGTA-AGGCATTGCGTGACT-GTTATC
* * *
5774996 TGTAGGGCATTGCGTAACTGCTATC
1 TGTAAGGCATTGCGTGACTGTTATC
* * * *
5775021 TATAGGGCATTACATGACTGTTATC
1 TGTAAGGCATTGCGTGACTGTTATC
* * *
5775046 TGTATGGAAGTGCGTGACTGTTATC
1 TGTAAGGCATTGCGTGACTGTTATC
*
5775071 TGTATGGCATT
1 TGTAAGGCATT
5775082 TCAAGAATTT
Statistics
Matches: 83, Mismatches: 24, Indels: 8
0.72 0.21 0.07
Matches are distributed among these distances:
24 3 0.04
25 78 0.94
26 2 0.02
ACGTcount: A:0.21, C:0.14, G:0.26, T:0.39
Consensus pattern (25 bp):
TGTAAGGCATTGCGTGACTGTTATC
Found at i:5775007 original size:50 final size:51
Alignment explanation
Indices: 5774953--5775081 Score: 131
Period size: 50 Copynumber: 2.6 Consensus size: 51
5774943 GAATGTAAGT
* * *
5774953 CATTGCGTGACTGTTATCTGTATTGG-ATTGCATGA-TCGTTTTATGTAGGG
1 CATTGCGTGACTGTTATCTGTATGGGCATTACATGACT-GTTATATGTAGGG
* * * * *
5775003 CATTGCGTAACTGCTATCTATA-GGGCATTACATGACTGTTATCTGTATGG
1 CATTGCGTGACTGTTATCTGTATGGGCATTACATGACTGTTATATGTAGGG
* *
5775053 AAGTGCGTGACTGTTATCTGTAT-GGCATT
1 CATTGCGTGACTGTTATCTGTATGGGCATT
5775082 TCAAGAATTT
Statistics
Matches: 63, Mismatches: 13, Indels: 6
0.77 0.16 0.07
Matches are distributed among these distances:
49 2 0.03
50 60 0.95
51 1 0.02
ACGTcount: A:0.21, C:0.15, G:0.26, T:0.39
Consensus pattern (51 bp):
CATTGCGTGACTGTTATCTGTATGGGCATTACATGACTGTTATATGTAGGG
Found at i:5777861 original size:20 final size:19
Alignment explanation
Indices: 5777836--5777876 Score: 64
Period size: 20 Copynumber: 2.1 Consensus size: 19
5777826 TAATTTAAAA
5777836 TAAAATAACATAAATTTAAC
1 TAAAATAACATAAA-TTAAC
*
5777856 TAAAATAACTTAAATTAAC
1 TAAAATAACATAAATTAAC
5777875 TA
1 TA
5777877 CTCAACATGT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
19 7 0.35
20 13 0.65
ACGTcount: A:0.59, C:0.10, G:0.00, T:0.32
Consensus pattern (19 bp):
TAAAATAACATAAATTAAC
Found at i:5779757 original size:2 final size:2
Alignment explanation
Indices: 5779750--5779797 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
5779740 TCATCCATCA
5779750 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
5779792 AT AT AT
1 AT AT AT
5779798 NNNNNNNNNN
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5785233 original size:26 final size:26
Alignment explanation
Indices: 5785173--5785234 Score: 106
Period size: 26 Copynumber: 2.4 Consensus size: 26
5785163 ACCATATACC
*
5785173 CATCATCAACATGCACACCATCCCAT
1 CATCATCATCATGCACACCATCCCAT
*
5785199 CATCATCATCATGCACATCATCCCAT
1 CATCATCATCATGCACACCATCCCAT
5785225 CATCATCATC
1 CATCATCATC
5785235 TCATATGCAA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 34 1.00
ACGTcount: A:0.32, C:0.40, G:0.03, T:0.24
Consensus pattern (26 bp):
CATCATCATCATGCACACCATCCCAT
Found at i:5788057 original size:20 final size:20
Alignment explanation
Indices: 5788032--5788074 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
5788022 GGAAGGAAAA
* * *
5788032 AGAAGAAGCTGCTGGAAGTT
1 AGAAGAAACTACTGGAAATT
5788052 AGAAGAAACTACTGGAAATT
1 AGAAGAAACTACTGGAAATT
5788072 AGA
1 AGA
5788075 TATTTATATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.44, C:0.09, G:0.28, T:0.19
Consensus pattern (20 bp):
AGAAGAAACTACTGGAAATT
Found at i:5791712 original size:188 final size:188
Alignment explanation
Indices: 5791395--5791771 Score: 630
Period size: 188 Copynumber: 2.0 Consensus size: 188
5791385 ATAAACTAAC
* *
5791395 AAACTAAATAAGTTGAGAAAAGTAGTATATTAAATAGCTAGGATTATGGGTTCATTCAACATTTC
1 AAACTAAATAAGTTGAGAAAAGTAGTATATTAAATACCTAGGATTATAGGTTCATTCAACATTTC
* * * * *
5791460 ATCTGATATCAGCTTTTTTGTTATTTATCTTTCTTAGGTGATTTTACTAACCTAGAATCCAAAGC
66 ATCTGATACCAGCTTTTCTATTATTTATCTTTCCTAGGTGATTTTACTAACATAGAATCCAAAGC
*
5791525 TATGGACAAGTCTCCGTCGAGTTGCTTGTACAAATATCTAA-TGTAATTAGTTCACTAT
131 TATGGACAAGTCTCCGTCGAGTTGCTTGTACAAATACCTAACT-TAATTAGTTCACTAT
5791583 AAACTAAATAAGTTGAGAAAAGTAGTATATTAAATACCTAGGATTATAGGTTCATTCAACATTTC
1 AAACTAAATAAGTTGAGAAAAGTAGTATATTAAATACCTAGGATTATAGGTTCATTCAACATTTC
* * *
5791648 ATCTGATACCAGCTTTTCTATTATTTATCTTTCCTGGGTGGTTTTGCTAACATAGAATCCAAAGC
66 ATCTGATACCAGCTTTTCTATTATTTATCTTTCCTAGGTGATTTTACTAACATAGAATCCAAAGC
*
5791713 TATGGACAAGTCTCTGTCGAGTTGCTTGTACAAATACCTAACTTAATTAGTTCACTAT
131 TATGGACAAGTCTCCGTCGAGTTGCTTGTACAAATACCTAACTTAATTAGTTCACTAT
5791771 A
1 A
5791772 TGTCTATACG
Statistics
Matches: 176, Mismatches: 12, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
188 175 0.99
189 1 0.01
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.37
Consensus pattern (188 bp):
AAACTAAATAAGTTGAGAAAAGTAGTATATTAAATACCTAGGATTATAGGTTCATTCAACATTTC
ATCTGATACCAGCTTTTCTATTATTTATCTTTCCTAGGTGATTTTACTAACATAGAATCCAAAGC
TATGGACAAGTCTCCGTCGAGTTGCTTGTACAAATACCTAACTTAATTAGTTCACTAT
Found at i:5793009 original size:21 final size:21
Alignment explanation
Indices: 5792985--5793029 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
5792975 TTAAAGTAAT
5792985 TTAAAAC-AAAATAACATAAAA
1 TTAAAACTAAAATAAC-TAAAA
*
5793006 TT-AAACTAAAATAACTTAAA
1 TTAAAACTAAAATAACTAAAA
5793026 TTAA
1 TTAA
5793030 CTATTCAACA
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
20 10 0.48
21 11 0.52
ACGTcount: A:0.64, C:0.09, G:0.00, T:0.27
Consensus pattern (21 bp):
TTAAAACTAAAATAACTAAAA
Found at i:5793026 original size:20 final size:20
Alignment explanation
Indices: 5792988--5793029 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
5792978 AAGTAATTTA
5792988 AAACAAAATAACATAAAATT
1 AAACAAAATAACATAAAATT
*
5793008 AAACTAAAATAAC-TTAAATT
1 AAAC-AAAATAACATAAAATT
5793028 AA
1 AA
5793030 CTATTCAACA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 12 0.60
21 8 0.40
ACGTcount: A:0.67, C:0.10, G:0.00, T:0.24
Consensus pattern (20 bp):
AAACAAAATAACATAAAATT
Found at i:5797374 original size:15 final size:16
Alignment explanation
Indices: 5797347--5797376 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
5797337 TTGTCCAAAG
5797347 CATACATATCACAACA
1 CATACATATCACAACA
5797363 CATACA-ATCACAAC
1 CATACATATCACAAC
5797377 TATATATATA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.50, C:0.33, G:0.00, T:0.17
Consensus pattern (16 bp):
CATACATATCACAACA
Found at i:5804515 original size:41 final size:41
Alignment explanation
Indices: 5804458--5804546 Score: 169
Period size: 41 Copynumber: 2.2 Consensus size: 41
5804448 CTTTGGAAAC
5804458 AAGAATCGATTCCCTAGAGATAGAAAGTTTCAAACTTTATG
1 AAGAATCGATTCCCTAGAGATAGAAAGTTTCAAACTTTATG
*
5804499 AAGAATTGATTCCCTAGAGATAGAAAGTTTCAAACTTTATG
1 AAGAATCGATTCCCTAGAGATAGAAAGTTTCAAACTTTATG
5804540 AAGAATC
1 AAGAATC
5804547 AACATCTTAA
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 46 1.00
ACGTcount: A:0.40, C:0.13, G:0.17, T:0.29
Consensus pattern (41 bp):
AAGAATCGATTCCCTAGAGATAGAAAGTTTCAAACTTTATG
Found at i:5805892 original size:32 final size:32
Alignment explanation
Indices: 5805833--5805893 Score: 77
Period size: 32 Copynumber: 1.9 Consensus size: 32
5805823 TGACATGGCA
* *
5805833 TGCCACGTGGCACCAATGTGATGATGTGGTAG
1 TGCCACGTGGCACCAATATGATAATGTGGTAG
* * *
5805865 TGCCATGTGGCACTAATATGCTAATGTGG
1 TGCCACGTGGCACCAATATGATAATGTGG
5805894 CAATGTTGAT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
32 24 1.00
ACGTcount: A:0.23, C:0.18, G:0.31, T:0.28
Consensus pattern (32 bp):
TGCCACGTGGCACCAATATGATAATGTGGTAG
Found at i:5807525 original size:19 final size:19
Alignment explanation
Indices: 5807501--5807538 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
5807491 CCATTTGACT
*
5807501 TATTGGAGTATGATTTGAG
1 TATTGGAGTATAATTTGAG
5807520 TATTGGAGTATAATTTGAG
1 TATTGGAGTATAATTTGAG
5807539 GGTTTGGCAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.29, C:0.00, G:0.29, T:0.42
Consensus pattern (19 bp):
TATTGGAGTATAATTTGAG
Found at i:5814419 original size:169 final size:169
Alignment explanation
Indices: 5814140--5814467 Score: 611
Period size: 169 Copynumber: 1.9 Consensus size: 169
5814130 ATTTTGGCAC
5814140 TTTCTTTGTATACACATTACATCCCATGTAATTGTATCACCAAAAAATTGTATTCACTCTTACTA
1 TTTCTTTGTATACACATTACATCCCATGTAATTGTATCACCAAAAAATTGTATTCACTCTTACTA
* * *
5814205 ACCTCTTTTTGTGTATGAGATAAGTACACTTGTACATTTTATTAAATCCAACCCTTTGGATCCCA
66 ACCTCCTTTTGTGTATAAGATAAGTACACTTATACATTTTATTAAATCCAACCCTTTGGATCCCA
5814270 TTTAATACAACAAAGTGTATAACTCCAATAAAAGACGTA
131 TTTAATACAACAAAGTGTATAACTCCAATAAAAGACGTA
* *
5814309 TTTCTTTGTATACACATTACATCCCATGTAATTGTATCATCAAAGAATTGTATTCACTCTTACTA
1 TTTCTTTGTATACACATTACATCCCATGTAATTGTATCACCAAAAAATTGTATTCACTCTTACTA
5814374 ACCTCCTTTTGTGTATAAGATAAGTACACTTATACATTTTATTAAATCCAACCCTTTGGATCCCA
66 ACCTCCTTTTGTGTATAAGATAAGTACACTTATACATTTTATTAAATCCAACCCTTTGGATCCCA
5814439 TTTAATACAACAAAGTGTATAACTCCAAT
131 TTTAATACAACAAAGTGTATAACTCCAAT
5814468 GAAGACATAT
Statistics
Matches: 154, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
169 154 1.00
ACGTcount: A:0.34, C:0.20, G:0.09, T:0.37
Consensus pattern (169 bp):
TTTCTTTGTATACACATTACATCCCATGTAATTGTATCACCAAAAAATTGTATTCACTCTTACTA
ACCTCCTTTTGTGTATAAGATAAGTACACTTATACATTTTATTAAATCCAACCCTTTGGATCCCA
TTTAATACAACAAAGTGTATAACTCCAATAAAAGACGTA
Found at i:5815983 original size:19 final size:19
Alignment explanation
Indices: 5815959--5815997 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
5815949 GCTAGAGGAA
5815959 AATTTTAGAATAAAATAAT
1 AATTTTAGAATAAAATAAT
* *
5815978 AATTTTTGGATAAAATAAT
1 AATTTTAGAATAAAATAAT
5815997 A
1 A
5815998 TTAAAATAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.54, C:0.00, G:0.08, T:0.38
Consensus pattern (19 bp):
AATTTTAGAATAAAATAAT
Found at i:5816325 original size:29 final size:29
Alignment explanation
Indices: 5816292--5816353 Score: 74
Period size: 28 Copynumber: 2.1 Consensus size: 29
5816282 TAAGAAATTG
*
5816292 AAGGGTGGAA-TTGTAAATAATGAAAAGTT-
1 AAGGGT-GAAGTTGT-AATAATCAAAAGTTC
*
5816321 AAGGGTGAAGTTGTAATTATCAAAAGTTC
1 AAGGGTGAAGTTGTAATAATCAAAAGTTC
5816350 AAGG
1 AAGG
5816354 TTCAACTTGC
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
28 15 0.52
29 14 0.48
ACGTcount: A:0.42, C:0.03, G:0.27, T:0.27
Consensus pattern (29 bp):
AAGGGTGAAGTTGTAATAATCAAAAGTTC
Found at i:5817832 original size:25 final size:25
Alignment explanation
Indices: 5817797--5817845 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
5817787 AGCATGATGT
*
5817797 TTTATATACTACTATTCGT-GAAAGA
1 TTTATAAACTACTATT-GTGGAAAGA
*
5817822 TTTATAAACTATTATTGTGGAAAG
1 TTTATAAACTACTATTGTGGAAAG
5817846 CATGAGCTAG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 2 0.10
25 19 0.90
ACGTcount: A:0.37, C:0.08, G:0.14, T:0.41
Consensus pattern (25 bp):
TTTATAAACTACTATTGTGGAAAGA
Found at i:5820074 original size:57 final size:58
Alignment explanation
Indices: 5819976--5820154 Score: 265
Period size: 57 Copynumber: 3.1 Consensus size: 58
5819966 AGGGTCTTAT
* ** *
5819976 CTTTGCA-TGCATAGCATTTATTAAATCACATAAAATAAATCTATCACATGCATACTA
1 CTTTGCATTGCATAACATTTATTAAATTGCATAAAATAAATCTATCACATGCAAACTA
5820033 CTTTGCATTGCATAACATTTATTAAATTGCAT-AAATAAATCTATCACATGCAAACTA
1 CTTTGCATTGCATAACATTTATTAAATTGCATAAAATAAATCTATCACATGCAAACTA
*
5820090 C-TTGAGATNTTGCATAACATTTATTAAATTGCATAAAATAAATCTATCACATGCAAACTA
1 CTTTG-CA--TTGCATAACATTTATTAAATTGCATAAAATAAATCTATCACATGCAAACTA
5820150 CTTTG
1 CTTTG
5820155 GATGATTATG
Statistics
Matches: 111, Mismatches: 5, Indels: 8
0.90 0.04 0.06
Matches are distributed among these distances:
56 3 0.03
57 33 0.30
58 21 0.19
59 25 0.23
60 26 0.23
61 3 0.03
ACGTcount: A:0.40, C:0.17, G:0.08, T:0.35
Consensus pattern (58 bp):
CTTTGCATTGCATAACATTTATTAAATTGCATAAAATAAATCTATCACATGCAAACTA
Found at i:5825348 original size:20 final size:20
Alignment explanation
Indices: 5825303--5825351 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 20
5825293 TATTCTTATA
* *
5825303 TTAAATTAAAGCAAATTAAG
1 TTAAATTAAAGCAAAATAAC
*
5825323 TAAAATTAAA-CTAAAATAAC
1 TTAAATTAAAGC-AAAATAAC
5825343 TTAAATTAA
1 TTAAATTAA
5825352 TTACACAACA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
19 1 0.04
20 23 0.96
ACGTcount: A:0.59, C:0.06, G:0.04, T:0.31
Consensus pattern (20 bp):
TTAAATTAAAGCAAAATAAC
Found at i:5829704 original size:2 final size:2
Alignment explanation
Indices: 5829697--5829724 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
5829687 TGGACGTTTT
5829697 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
5829725 GTTTTCCATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:5830438 original size:36 final size:36
Alignment explanation
Indices: 5830398--5830490 Score: 132
Period size: 36 Copynumber: 2.6 Consensus size: 36
5830388 TGCCTATGCG
* * * *
5830398 CGATGTGAGGGTGCACATGATGGCATTTGTTGTGCA
1 CGATGTGGGGGTGCACACGATGGCATTAGCTGTGCA
*
5830434 CGATGTGGGGGTGCACACGATGGTATTAGCTGTGCA
1 CGATGTGGGGGTGCACACGATGGCATTAGCTGTGCA
*
5830470 CAATGTGGGGGTGCACACGAT
1 CGATGTGGGGGTGCACACGAT
5830491 AACTTCGACT
Statistics
Matches: 51, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
36 51 1.00
ACGTcount: A:0.20, C:0.16, G:0.38, T:0.26
Consensus pattern (36 bp):
CGATGTGGGGGTGCACACGATGGCATTAGCTGTGCA
Found at i:5833052 original size:77 final size:77
Alignment explanation
Indices: 5832815--5833040 Score: 298
Period size: 77 Copynumber: 2.9 Consensus size: 77
5832805 AATGCCATTT
* * * * *
5832815 ATTTTAATTTTGTGTGATTCATAAAAAATCGGAAAATG-TTCCTACTTT-AAAGTGAATTCCTAA
1 ATTTTAATTTTGAGTGATTCATAAAGAATAGGAAATTGTTTCCTACTTTAAAAG-AAATTCCTAA
*
5832878 ACTTAAGGATAGA
65 AATTAAGGATAGA
*
5832891 ATTTTAA-TTTGAGGTGATTCATAAAGAATTA-GAAATTGTTTCCTAGTTTAAAAGAAATTCCTA
1 ATTTTAATTTTGA-GTGATTCATAAAGAA-TAGGAAATTGTTTCCTACTTTAAAAGAAATTCCTA
* *
5832954 AAATCAAGGGTAGA
64 AAATTAAGGATAGA
* *
5832968 ATTTTAATTTTGAGTGATTCATAAAGAATAGGAAATTGTTTCATACTTTAAAAGAAATTCTTAAA
1 ATTTTAATTTTGAGTGATTCATAAAGAATAGGAAATTGTTTCCTACTTTAAAAGAAATTCCTAAA
5833033 ATTAAGGA
66 ATTAAGGA
5833041 CATCATTTTA
Statistics
Matches: 130, Mismatches: 14, Indels: 11
0.84 0.09 0.07
Matches are distributed among these distances:
75 4 0.03
76 29 0.22
77 88 0.68
78 9 0.07
ACGTcount: A:0.40, C:0.08, G:0.15, T:0.37
Consensus pattern (77 bp):
ATTTTAATTTTGAGTGATTCATAAAGAATAGGAAATTGTTTCCTACTTTAAAAGAAATTCCTAAA
ATTAAGGATAGA
Found at i:5842019 original size:11 final size:11
Alignment explanation
Indices: 5842007--5842079 Score: 55
Period size: 10 Copynumber: 6.6 Consensus size: 11
5841997 ACTAAACTTT
5842007 TTTTTTCCTT-
1 TTTTTTCCTTC
5842017 TTTTTT-C-TC
1 TTTTTTCCTTC
*
5842026 TTTTCTCTCTTC
1 TTTTTTC-CTTC
5842038 TTTTTT-CTTC
1 TTTTTTCCTTC
*
5842048 TTTTTTCTCTCTT
1 TTTTTTC-CT-TC
5842061 TTTTTTCCCTTC
1 TTTTTT-CCTTC
*
5842073 TGTTTTC
1 TTTTTTC
5842080 TTTTTCTTCT
Statistics
Matches: 50, Mismatches: 5, Indels: 15
0.71 0.07 0.21
Matches are distributed among these distances:
8 1 0.02
9 6 0.12
10 16 0.32
11 2 0.04
12 15 0.30
13 9 0.18
14 1 0.02
ACGTcount: A:0.00, C:0.25, G:0.01, T:0.74
Consensus pattern (11 bp):
TTTTTTCCTTC
Found at i:5842048 original size:24 final size:24
Alignment explanation
Indices: 5842014--5842067 Score: 85
Period size: 24 Copynumber: 2.3 Consensus size: 24
5842004 TTTTTTTTTC
5842014 CTTTTTT-TTCTCTTTTCTCTCTT
1 CTTTTTTCTTCTCTTTTCTCTCTT
*
5842037 CTTTTTTCTTCTTTTTTCTCTCTT
1 CTTTTTTCTTCTCTTTTCTCTCTT
5842061 -TTTTTTC
1 CTTTTTTC
5842068 CCTTCTGTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
23 14 0.48
24 15 0.52
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (24 bp):
CTTTTTTCTTCTCTTTTCTCTCTT
Found at i:5842052 original size:41 final size:41
Alignment explanation
Indices: 5842007--5842108 Score: 120
Period size: 41 Copynumber: 2.5 Consensus size: 41
5841997 ACTAAACTTT
**
5842007 TTTTTTCCT-TTTTTTTCTCTTTTCTCTCTTCTTTTTTCTTC
1 TTTTTTCCTATTTTTTTCTCCCTTCTCTCTTC-TTTTTCTTC
* * *
5842048 TTTTTTCTCTCTTTTTTT-TCCCTTCTGTTTTCTTTTTCTTC
1 TTTTTTC-CTATTTTTTTCTCCCTTCTCTCTTCTTTTTCTTC
5842089 -TTTTTCCTATTTTTTTCTCC
1 TTTTTTCCTATTTTTTTCTCC
5842109 TTCATAAGCA
Statistics
Matches: 53, Mismatches: 5, Indels: 7
0.82 0.08 0.11
Matches are distributed among these distances:
39 9 0.17
40 9 0.17
41 16 0.30
42 12 0.23
43 7 0.13
ACGTcount: A:0.01, C:0.25, G:0.01, T:0.74
Consensus pattern (41 bp):
TTTTTTCCTATTTTTTTCTCCCTTCTCTCTTCTTTTTCTTC
Found at i:5842052 original size:42 final size:40
Alignment explanation
Indices: 5842006--5842111 Score: 119
Period size: 42 Copynumber: 2.6 Consensus size: 40
5841996 TACTAAACTT
*
5842006 TTTTTTTCCTTTTTTTTCTCTTTTCTCTCTTCTTTTTTCTTC
1 TTTTTTTCCTTTTTTTTCTC-CTTCTCTCTTC-TTTTTCTTC
* *
5842048 TTTTTTCTCTCTTTTTTTTC-CCTTCTGTTTTCTTTTTCTTC
1 TTTTTT-TC-CTTTTTTTTCTCCTTCTCTCTTCTTTTTCTTC
5842089 --TTTTTCCTATTTTTTTCTCCTTC
1 TTTTTTTCCT-TTTTTTTCTCCTTC
5842112 ATAAGCATAC
Statistics
Matches: 57, Mismatches: 3, Indels: 11
0.80 0.04 0.15
Matches are distributed among these distances:
37 2 0.04
38 10 0.18
39 9 0.16
41 9 0.16
42 14 0.25
43 3 0.05
44 10 0.18
ACGTcount: A:0.01, C:0.25, G:0.01, T:0.74
Consensus pattern (40 bp):
TTTTTTTCCTTTTTTTTCTCCTTCTCTCTTCTTTTTCTTC
Found at i:5842139 original size:73 final size:73
Alignment explanation
Indices: 5842061--5842204 Score: 177
Period size: 73 Copynumber: 2.0 Consensus size: 73
5842051 TTTCTCTCTT
*
5842061 TTTTTTCCCTTCTGTTTT-CTTT-TTCTTCTTTTTCCTATTT-TTTTCTCCTTCATAAGCATACT
1 TTTTTTCCCTTCTATTTTCCTTTATT-TTCTTTTT--T-TTTATTTTCTCCTTCATAAGCATACT
5842123 AAACCATTTCAA
62 AAACCATTTCAA
** * * *
5842135 TTTTTTTTCTTTTATTTTCCTTTATTTTCTTTTTTTTTATTTTCTCCTTTATAAGTATACTAAAC
1 TTTTTTCCCTTCTATTTTCCTTTATTTTCTTTTTTTTTATTTTCTCCTTCATAAGCATACTAAAC
5842200 CATTT
66 CATTT
5842205 TATTATTTAT
Statistics
Matches: 61, Mismatches: 6, Indels: 7
0.82 0.08 0.09
Matches are distributed among these distances:
72 3 0.05
73 30 0.49
74 14 0.23
75 12 0.20
76 2 0.03
ACGTcount: A:0.17, C:0.19, G:0.02, T:0.62
Consensus pattern (73 bp):
TTTTTTCCCTTCTATTTTCCTTTATTTTCTTTTTTTTTATTTTCTCCTTCATAAGCATACTAAAC
CATTTCAA
Found at i:5842172 original size:10 final size:10
Alignment explanation
Indices: 5842135--5842177 Score: 52
Period size: 10 Copynumber: 4.4 Consensus size: 10
5842125 ACCATTTCAA
5842135 TTTT-TTTTC
1 TTTTATTTTC
5842144 TTTTATTTTC
1 TTTTATTTTC
*
5842154 CTTTATTTTC
1 TTTTATTTTC
* *
5842164 TTTTTTTTTA
1 TTTTATTTTC
5842174 TTTT
1 TTTT
5842178 CTCCTTTATA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
9 4 0.14
10 25 0.86
ACGTcount: A:0.07, C:0.09, G:0.00, T:0.84
Consensus pattern (10 bp):
TTTTATTTTC
Found at i:5842231 original size:9 final size:9
Alignment explanation
Indices: 5842210--5842248 Score: 62
Period size: 9 Copynumber: 4.3 Consensus size: 9
5842200 CATTTTATTA
5842210 TTTATTC-T
1 TTTATTCTT
5842218 TTTATTCTT
1 TTTATTCTT
5842227 TTTATTCTTT
1 TTTATTC-TT
5842237 TTTATTCTT
1 TTTATTCTT
5842246 TTT
1 TTT
5842249 GTAAATTTAA
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
8 7 0.24
9 13 0.45
10 9 0.31
ACGTcount: A:0.10, C:0.10, G:0.00, T:0.79
Consensus pattern (9 bp):
TTTATTCTT
Found at i:5842240 original size:10 final size:10
Alignment explanation
Indices: 5842217--5842248 Score: 57
Period size: 10 Copynumber: 3.3 Consensus size: 10
5842207 TTATTTATTC
5842217 TTTTATTC-T
1 TTTTATTCTT
5842226 TTTTATTCTT
1 TTTTATTCTT
5842236 TTTTATTCTT
1 TTTTATTCTT
5842246 TTT
1 TTT
5842249 GTAAATTTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
9 8 0.36
10 14 0.64
ACGTcount: A:0.09, C:0.09, G:0.00, T:0.81
Consensus pattern (10 bp):
TTTTATTCTT
Found at i:5842242 original size:67 final size:69
Alignment explanation
Indices: 5842101--5842239 Score: 167
Period size: 73 Copynumber: 2.0 Consensus size: 69
5842091 TTTCCTATTT
*
5842101 TTTTCTCCTTCATAAGCATACTAAACCATTTCAATTTTTTTTCTTTTATTTTCCTTTATTTTCTT
1 TTTTCTCCTTCATAAGCATACTAAACCATTTCAATTTTTATTCTTTTATTTT-CTTTA-TTTC--
5842166 TTTTTTTA
62 TTTTTTTA
* * *
5842174 TTTTCTCCTTTATAAGTATACTAAACCATTT-TATTATTTATTCTTTTATTCTT-TTTA-TTCTT
1 TTTTCTCCTTCATAAGCATACTAAACCATTTCAATT-TTTATTCTTTTATT-TTCTTTATTTCTT
5842236 TTTT
64 TTTT
5842240 ATTCTTTTTG
Statistics
Matches: 60, Mismatches: 4, Indels: 9
0.82 0.05 0.12
Matches are distributed among these distances:
68 6 0.10
70 3 0.05
72 7 0.12
73 42 0.70
74 2 0.03
ACGTcount: A:0.20, C:0.16, G:0.01, T:0.63
Consensus pattern (69 bp):
TTTTCTCCTTCATAAGCATACTAAACCATTTCAATTTTTATTCTTTTATTTTCTTTATTTCTTTT
TTTA
Found at i:5842411 original size:18 final size:19
Alignment explanation
Indices: 5842380--5842421 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 19
5842370 AACGCTCATA
*
5842380 TTTAAATTATTAATAAAAT
1 TTTATATTATTAATAAAAT
**
5842399 TTTATATTA-TAATTTAAT
1 TTTATATTATTAATAAAAT
5842417 TTTAT
1 TTTAT
5842422 TTTAAAAATA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
18 12 0.60
19 8 0.40
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (19 bp):
TTTATATTATTAATAAAAT
Found at i:5842441 original size:22 final size:23
Alignment explanation
Indices: 5842407--5842450 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
5842397 ATTTTATATT
5842407 ATAATTTAA-TTTTATTTTAAAA
1 ATAATTTAATTTTTATTTTAAAA
5842429 ATAA-TTAATTTTTTATTTTAAA
1 ATAATTTAA-TTTTTATTTTAAA
5842451 TTAAATAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
21 4 0.20
22 4 0.20
23 12 0.60
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (23 bp):
ATAATTTAATTTTTATTTTAAAA
Found at i:5842459 original size:22 final size:23
Alignment explanation
Indices: 5842416--5842460 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
5842406 TATAATTTAA
*
5842416 TTTTATTTTAAAAATAATTAATT
1 TTTTATTTTAAAAATAAATAATT
*
5842439 TTTTATTTT-AAATTAAATAATT
1 TTTTATTTTAAAAATAAATAATT
5842461 GACTGGATCC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 11 0.55
23 9 0.45
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (23 bp):
TTTTATTTTAAAAATAAATAATT
Found at i:5846962 original size:31 final size:31
Alignment explanation
Indices: 5846926--5846993 Score: 104
Period size: 31 Copynumber: 2.2 Consensus size: 31
5846916 ACCCCCATCA
*
5846926 ACCTTGGGCTTG-CAATGTATATCCCCATTGC
1 ACCTTGGGC-TGACAACGTATATCCCCATTGC
5846957 ACCTTGGGCTGACAACGTATATCCCCATTGC
1 ACCTTGGGCTGACAACGTATATCCCCATTGC
5846988 -CCTTGG
1 ACCTTGG
5846994 AAATTTTATG
Statistics
Matches: 35, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
30 8 0.23
31 27 0.77
ACGTcount: A:0.19, C:0.31, G:0.21, T:0.29
Consensus pattern (31 bp):
ACCTTGGGCTGACAACGTATATCCCCATTGC
Found at i:5847283 original size:68 final size:65
Alignment explanation
Indices: 5847126--5847297 Score: 209
Period size: 68 Copynumber: 2.6 Consensus size: 65
5847116 GTTGACTCAT
* * * * * *
5847126 CTCATAAGGTATATGGAATTTACATCATATACATAATCTCATGGCATTTATGCTTGCTTAATCAT
1 CTCATATGGTATATGGAATTTACATCATATACATAATCTCATGACATTTATGCGTACTTAAACAC
* * * * *
5847191 CTCATGTAGTATATGGAATATACATTATATACATATTCTCATGACATTAATTATGCGTACTTAAA
1 CTCATATGGTATATGGAATTTACATCATATACATAATCTCATGACA-T--TTATGCGTACTTAAA
5847256 CAC
63 CAC
*
5847259 CTCATATGGTATATGAAATTTACATCATATACATAATCT
1 CTCATATGGTATATGGAATTTACATCATATACATAATCT
5847298 TATGGAATTC
Statistics
Matches: 87, Mismatches: 17, Indels: 3
0.81 0.16 0.03
Matches are distributed among these distances:
65 39 0.45
66 1 0.01
68 47 0.54
ACGTcount: A:0.35, C:0.16, G:0.10, T:0.38
Consensus pattern (65 bp):
CTCATATGGTATATGGAATTTACATCATATACATAATCTCATGACATTTATGCGTACTTAAACAC
Found at i:5854103 original size:43 final size:43
Alignment explanation
Indices: 5854050--5854196 Score: 188
Period size: 43 Copynumber: 3.4 Consensus size: 43
5854040 TTGACTCGGC
* * *
5854050 TATGTACGAGTAGGGAGTGCGCATAAGCCGATGATGACCCAGT
1 TATGTGCGAGTAGGGAGTGCGCATAACCCGGTGATGACCCAGT
* *
5854093 TATGTGCGAGTAGGGAGTGCCCATAACCCGGTGATGACTC-GAT
1 TATGTGCGAGTAGGGAGTGCGCATAACCCGGTGATGACCCAG-T
* * * *
5854136 TATGTGCAAGTAAGGAGTGCGCATAACCCGGTGATGACCTAGC
1 TATGTGCGAGTAGGGAGTGCGCATAACCCGGTGATGACCCAGT
*
5854179 CATGTGCGAGTAGGGAGT
1 TATGTGCGAGTAGGGAGT
5854197 ACGTATGAGT
Statistics
Matches: 88, Mismatches: 14, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
42 1 0.01
43 86 0.98
44 1 0.01
ACGTcount: A:0.26, C:0.19, G:0.33, T:0.22
Consensus pattern (43 bp):
TATGTGCGAGTAGGGAGTGCGCATAACCCGGTGATGACCCAGT
Found at i:5857889 original size:27 final size:29
Alignment explanation
Indices: 5857858--5857918 Score: 90
Period size: 27 Copynumber: 2.2 Consensus size: 29
5857848 GATCAAGCCC
5857858 AACCTATCTACCTTTT-C-AAGGAGGTAT
1 AACCTATCTACCTTTTACTAAGGAGGTAT
* *
5857885 AACCTTTCTACCTTTTACTATGGAGGTAT
1 AACCTATCTACCTTTTACTAAGGAGGTAT
5857914 AACCT
1 AACCT
5857919 TACAAAAATG
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
27 15 0.50
28 1 0.03
29 14 0.47
ACGTcount: A:0.28, C:0.23, G:0.13, T:0.36
Consensus pattern (29 bp):
AACCTATCTACCTTTTACTAAGGAGGTAT
Found at i:5862231 original size:21 final size:21
Alignment explanation
Indices: 5862183--5862231 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 21
5862173 TTTTAGCCTC
5862183 TTATTTTCATTTTCCAAATCAA
1 TTATTTTCATTTTCCAAA-CAA
*
5862205 TT-TTTTCATTTTTCAAA-AA
1 TTATTTTCATTTTCCAAACAA
5862224 TTCATTTT
1 TT-ATTTT
5862232 TGACACTAAG
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
19 4 0.17
21 18 0.75
22 2 0.08
ACGTcount: A:0.29, C:0.14, G:0.00, T:0.57
Consensus pattern (21 bp):
TTATTTTCATTTTCCAAACAA
Found at i:5878591 original size:43 final size:43
Alignment explanation
Indices: 5878534--5878652 Score: 143
Period size: 43 Copynumber: 2.8 Consensus size: 43
5878524 GTAATTATAT
* *
5878534 TGACTCGACTATGTGCGAGTAGGGAGTGTGCATAAGC-CGAG-GA
1 TGACCCGACTATGTGCGAGTAGGGAGTGCGCATAA-CTCG-GTGA
* * *
5878577 TGACCCGATTATGTGCGAGTAGGAAGTACGCATAACTCGGTGA
1 TGACCCGACTATGTGCGAGTAGGGAGTGCGCATAACTCGGTGA
* *
5878620 TGACCCAACCATGTGCGAGTAGGGAGTGCGCAT
1 TGACCCGACTATGTGCGAGTAGGGAGTGCGCAT
5878653 GAGCTGGTAA
Statistics
Matches: 64, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
42 2 0.03
43 62 0.97
ACGTcount: A:0.26, C:0.19, G:0.34, T:0.21
Consensus pattern (43 bp):
TGACCCGACTATGTGCGAGTAGGGAGTGCGCATAACTCGGTGA
Found at i:5878692 original size:23 final size:23
Alignment explanation
Indices: 5878662--5878721 Score: 84
Period size: 23 Copynumber: 2.6 Consensus size: 23
5878652 TGAGCTGGTA
* *
5878662 ATGATGATGATGGGATGGTGTGT
1 ATGATGATGATGGGATGGTATGC
*
5878685 ATGATGATGATGAGATGGTATGC
1 ATGATGATGATGGGATGGTATGC
*
5878708 ATAATGATGATGGG
1 ATGATGATGATGGG
5878722 TATATACGTA
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.28, C:0.02, G:0.38, T:0.32
Consensus pattern (23 bp):
ATGATGATGATGGGATGGTATGC
Found at i:5879142 original size:60 final size:60
Alignment explanation
Indices: 5879064--5879271 Score: 233
Period size: 60 Copynumber: 3.5 Consensus size: 60
5879054 CAAAATTCAT
* * * * * * *
5879064 TCTCACTGCAGCGAGAAACTTTTTGTTTCTGGGTTAGAATTTCACTGTAGCGAGAATGAA
1 TCTCGCTGCAGCAAGAAACTTTCTGTTTCTGGGTTAAAATTTCGCTGCAGCGAGAATAAA
* ** * *
5879124 TCTCGCTGCAGCAAGAAACTTTCTGTTTCTGGGTTACAATTTCGCTGCAATGA-AATTCAT
1 TCTCGCTGCAGCAAGAAACTTTCTGTTTCTGGGTTAAAATTTCGCTGCAGCGAGAA-TAAA
* * *
5879184 TCTCGCTGCAGCGAGAAACCTTCTGTTTCTGGGTTACAAATTT-GCTGCAGCGAGATTAAA
1 TCTCGCTGCAGCAAGAAACTTTCTGTTTCTGGGTTA-AAATTTCGCTGCAGCGAGAATAAA
5879244 TCTCGCTGCAGCGAA-AAACTTTCTGTTT
1 TCTCGCTGCAGC-AAGAAACTTTCTGTTT
5879272 TGGTCTCCTA
Statistics
Matches: 124, Mismatches: 20, Indels: 8
0.82 0.13 0.05
Matches are distributed among these distances:
59 2 0.02
60 115 0.93
61 7 0.06
ACGTcount: A:0.25, C:0.21, G:0.21, T:0.33
Consensus pattern (60 bp):
TCTCGCTGCAGCAAGAAACTTTCTGTTTCTGGGTTAAAATTTCGCTGCAGCGAGAATAAA
Found at i:5879263 original size:120 final size:120
Alignment explanation
Indices: 5879056--5879271 Score: 328
Period size: 120 Copynumber: 1.8 Consensus size: 120
5879046 CACTGCAGCA
* * * *
5879056 AAATTCATTCTCACTGCAGCGAGAAACTTTTTGTTTCTGGGTTAGAATTTCACTGTAGCGAGAAT
1 AAATTCATTCTCACTGCAGCGAGAAACCTTCTGTTTCTGGGTTAAAATTTCACTGCAGCGAGAAT
*
5879121 GAATCTCGCTGCAGCAAGAAACTTTCTGTTTCTGGGTTACAATTTCGCTGCAATG
66 AAATCTCGCTGCAGCAAGAAACTTTCTGTTTCTGGGTTACAATTTCGCTGCAATG
* * *
5879176 AAATTCATTCTCGCTGCAGCGAGAAACCTTCTGTTTCTGGGTTACAAATTT-GCTGCAGCGAGAT
1 AAATTCATTCTCACTGCAGCGAGAAACCTTCTGTTTCTGGGTTA-AAATTTCACTGCAGCGAGAA
5879240 TAAATCTCGCTGCAGCGAA-AAACTTTCTGTTT
65 TAAATCTCGCTGCAGC-AAGAAACTTTCTGTTT
5879272 TGGTCTCCTA
Statistics
Matches: 86, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
120 79 0.92
121 7 0.08
ACGTcount: A:0.26, C:0.20, G:0.20, T:0.33
Consensus pattern (120 bp):
AAATTCATTCTCACTGCAGCGAGAAACCTTCTGTTTCTGGGTTAAAATTTCACTGCAGCGAGAAT
AAATCTCGCTGCAGCAAGAAACTTTCTGTTTCTGGGTTACAATTTCGCTGCAATG
Found at i:5881042 original size:20 final size:20
Alignment explanation
Indices: 5880985--5881047 Score: 92
Period size: 20 Copynumber: 3.2 Consensus size: 20
5880975 TATATACCCA
*
5880985 TCATCATCATC-TCACCAAC
1 TCATCATCATCATCACCAGC
* *
5881004 CCATTATCATCATCACCAGC
1 TCATCATCATCATCACCAGC
5881024 TCATCATCATCATCACCAGC
1 TCATCATCATCATCACCAGC
5881044 TCAT
1 TCAT
5881048 GCGTACTCCC
Statistics
Matches: 38, Mismatches: 5, Indels: 1
0.86 0.11 0.02
Matches are distributed among these distances:
19 9 0.24
20 29 0.76
ACGTcount: A:0.30, C:0.40, G:0.03, T:0.27
Consensus pattern (20 bp):
TCATCATCATCATCACCAGC
Found at i:5881099 original size:43 final size:43
Alignment explanation
Indices: 5881046--5881155 Score: 159
Period size: 43 Copynumber: 2.6 Consensus size: 43
5881036 TCACCAGCTC
* ** * *
5881046 ATGCGTACTCCCTACTCGCACATGGCTGGGTCATCAC-CGGGTT
1 ATGCGCACTCCCTACTCGCACATAACCGGGTCATC-CTCGGCTT
5881089 ATGCGCACTCCCTACTCGCACATAACCGGGTCATCCTCGGCTT
1 ATGCGCACTCCCTACTCGCACATAACCGGGTCATCCTCGGCTT
5881132 ATGCGCACTCCCTACTCGCACATA
1 ATGCGCACTCCCTACTCGCACATA
5881156 GTCGAGTCAA
Statistics
Matches: 61, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
42 1 0.02
43 60 0.98
ACGTcount: A:0.19, C:0.37, G:0.20, T:0.24
Consensus pattern (43 bp):
ATGCGCACTCCCTACTCGCACATAACCGGGTCATCCTCGGCTT
Found at i:5884274 original size:2 final size:2
Alignment explanation
Indices: 5884267--5884300 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
5884257 AACATTATTC
*
5884267 AT AT AT AT AT AC 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
5884301 CAACATAATG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:5893713 original size:15 final size:16
Alignment explanation
Indices: 5893693--5893727 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
5893683 AGTTCGTATC
*
5893693 AAAGCTTTTGG-TTTA
1 AAAGCTTATGGTTTTA
5893708 AAAGCTTATGGTTTTA
1 AAAGCTTATGGTTTTA
5893724 AAAG
1 AAAG
5893728 AAGTTTTTGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 10 0.56
16 8 0.44
ACGTcount: A:0.34, C:0.06, G:0.20, T:0.40
Consensus pattern (16 bp):
AAAGCTTATGGTTTTA
Found at i:5904203 original size:43 final size:43
Alignment explanation
Indices: 5904135--5904246 Score: 138
Period size: 43 Copynumber: 2.6 Consensus size: 43
5904125 TATTGACTCG
* *
5904135 GCTATGTGCGAGTAGGGAGTACGCATAAGCCGAG-GATGACCC-
1 GCTATGTGCGAGTAGGGAGTGCGCATAACCCG-GTGATGACCCA
* *
5904177 GATTATGTACGAGTAGGGAGTGCGCATAACCCGGTGATGACCCA
1 G-CTATGTGCGAGTAGGGAGTGCGCATAACCCGGTGATGACCCA
* *
5904221 GCCATGTGCGAGTAGGGAGTGTGCAT
1 GCTATGTGCGAGTAGGGAGTGCGCAT
5904247 GAGCTGGTGG
Statistics
Matches: 59, Mismatches: 8, Indels: 5
0.82 0.11 0.07
Matches are distributed among these distances:
42 2 0.03
43 56 0.95
44 1 0.02
ACGTcount: A:0.25, C:0.20, G:0.36, T:0.20
Consensus pattern (43 bp):
GCTATGTGCGAGTAGGGAGTGCGCATAACCCGGTGATGACCCA
Found at i:5905553 original size:2 final size:2
Alignment explanation
Indices: 5905546--5905577 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
5905536 GGTCGTGACA
5905546 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
5905578 CAACATAATG
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:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5915923 original size:58 final size:57
Alignment explanation
Indices: 5915834--5915953 Score: 197
Period size: 58 Copynumber: 2.1 Consensus size: 57
5915824 AAGGTCTCAG
5915834 CTTTGCATGCATAGCATTTATTAAATTGCATAAAATAAATCGATCACATGCATAA-TA
1 CTTTGCATGCATAGCATTTATTAAATTGCATAAAATAAATCGATCACATGCA-AACTA
**
5915891 CTTTGCATTGCATAGCATTTATTAAATTGCATAAAATAAATTTATCACATGCAAACTA
1 CTTTGCA-TGCATAGCATTTATTAAATTGCATAAAATAAATCGATCACATGCAAACTA
5915949 CTTTG
1 CTTTG
5915954 GATGATTATG
Statistics
Matches: 59, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
57 9 0.15
58 50 0.85
ACGTcount: A:0.38, C:0.16, G:0.10, T:0.36
Consensus pattern (57 bp):
CTTTGCATGCATAGCATTTATTAAATTGCATAAAATAAATCGATCACATGCAAACTA
Found at i:5917289 original size:42 final size:42
Alignment explanation
Indices: 5917196--5917318 Score: 140
Period size: 42 Copynumber: 3.0 Consensus size: 42
5917186 AATGATATTA
** * *
5917196 ACCCGACTATGTGCGAGT-ACAATGTGCATAAGCTGATGCTG
1 ACCCGACTATGTGCGAGTGGGAATGCGCATAAGCCGATGCTG
* * *
5917237 ACCCGGCTATGTGCGAGTGGGAGTGCGCATAAGCCGATGCTT
1 ACCCGACTATGTGCGAGTGGGAATGCGCATAAGCCGATGCTG
* * * *
5917279 ACTCGACTATGTGCGAGTGGGAATACACATAAGTCGATGC
1 ACCCGACTATGTGCGAGTGGGAATGCGCATAAGCCGATGC
5917319 ATATAAGCTA
Statistics
Matches: 68, Mismatches: 13, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
41 17 0.25
42 51 0.75
ACGTcount: A:0.25, C:0.22, G:0.30, T:0.23
Consensus pattern (42 bp):
ACCCGACTATGTGCGAGTGGGAATGCGCATAAGCCGATGCTG
Found at i:5922669 original size:42 final size:42
Alignment explanation
Indices: 5922610--5922776 Score: 208
Period size: 42 Copynumber: 4.0 Consensus size: 42
5922600 CTCCCATCAT
* * * *
5922610 CATCAGCTCATATGCACTCCCACTAGCACATGGCTGGGTCAG
1 CATCAGCTTATGTGCACTCCCACTCGCACATAGCTGGGTCAG
** * * * * *
5922652 CATTGGCTTATGTGCACTCCCACTCACATAGAGCTGGGTTAA
1 CATCAGCTTATGTGCACTCCCACTCGCACATAGCTGGGTCAG
*
5922694 CATCAGCTTATGCGCACTCCCACTCGCACATAGCTGGGTCAG
1 CATCAGCTTATGTGCACTCCCACTCGCACATAGCTGGGTCAG
* *
5922736 CATCAGCTTACGTGCACTCCTACTCGCACATAGCTGGGTCA
1 CATCAGCTTATGTGCACTCCCACTCGCACATAGCTGGGTCA
5922777 ATATCATTAC
Statistics
Matches: 103, Mismatches: 22, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
42 103 1.00
ACGTcount: A:0.23, C:0.32, G:0.21, T:0.24
Consensus pattern (42 bp):
CATCAGCTTATGTGCACTCCCACTCGCACATAGCTGGGTCAG
Found at i:5930432 original size:42 final size:42
Alignment explanation
Indices: 5930318--5930436 Score: 166
Period size: 42 Copynumber: 2.8 Consensus size: 42
5930308 TGTGGGCCTA
** * *
5930318 GCTATGTGCGAGTAATAGTGCACATAAGCCATTACTAACCCG
1 GCTATGTGCGAGTAGGAGTGCACATAAGCCGTTGCTAACCCG
* * *
5930360 GCTATGTACGAGTGGGAGTGCACATAAGCCGTTGCTGACCCG
1 GCTATGTGCGAGTAGGAGTGCACATAAGCCGTTGCTAACCCG
*
5930402 GCTATGTGCGAGTAGGAGTGCGCATAAGCCGTTGC
1 GCTATGTGCGAGTAGGAGTGCACATAAGCCGTTGC
5930437 ATATGAGATG
Statistics
Matches: 67, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
42 67 1.00
ACGTcount: A:0.24, C:0.23, G:0.30, T:0.23
Consensus pattern (42 bp):
GCTATGTGCGAGTAGGAGTGCACATAAGCCGTTGCTAACCCG
Found at i:5930485 original size:2 final size:2
Alignment explanation
Indices: 5930478--5930512 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
5930468 TGATGATTGT
5930478 TA TA TA TA TA 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
5930513 GGTATATGGT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:5938234 original size:60 final size:60
Alignment explanation
Indices: 5938135--5938297 Score: 159
Period size: 60 Copynumber: 2.7 Consensus size: 60
5938125 AGATCAAAAT
* * *** * *
5938135 AGAAGGTTTTTCGCTGCAGTGAGATTGAATCTCGTTGCAGCGAAATTGTAACCCA-GAAAC
1 AGAAGGTTTCTCGCTGCAGCGAGATTTTTTCTCGCTGCAGCGAAATT-CAACCCATGAAAC
* * * * **
5938195 AGAAGGTTTCTCGCTGCAGGGAGATTTTTTGTCGCTGCAGCAAAATTCAGCTGATGAAAC
1 AGAAGGTTTCTCGCTGCAGCGAGATTTTTTCTCGCTGCAGCGAAATTCAACCCATGAAAC
* *
5938255 AG-AGAGTTTCTCGCTGCAACGAGATTTTTTTTCGCTGCAGCGA
1 AGAAG-GTTTCTCGCTGCAGCGAGATTTTTTCTCGCTGCAGCGA
5938298 GAAGCTACAG
Statistics
Matches: 85, Mismatches: 16, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
59 5 0.06
60 80 0.94
ACGTcount: A:0.26, C:0.19, G:0.26, T:0.29
Consensus pattern (60 bp):
AGAAGGTTTCTCGCTGCAGCGAGATTTTTTCTCGCTGCAGCGAAATTCAACCCATGAAAC
Found at i:5949890 original size:14 final size:14
Alignment explanation
Indices: 5949873--5949914 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
5949863 TTTAGAATAA
*
5949873 AATAATATTATATT
1 AATAATATAATATT
*
5949887 AATAAAATAATATT
1 AATAATATAATATT
5949901 AA-AATATAAATATT
1 AATAATAT-AATATT
5949915 TTATTAATTG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
13 4 0.17
14 20 0.83
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (14 bp):
AATAATATAATATT
Found at i:5950839 original size:7 final size:6
Alignment explanation
Indices: 5950827--5950909 Score: 52
Period size: 5 Copynumber: 13.7 Consensus size: 6
5950817 GTCCATAGCC
5950827 AAAGAGG AAAGAG AAAG-G AGAAGCAAG AAAGAAG AAATGAG AAAG-G
1 AAAGA-G AAAGAG AAAGAG A-AAG--AG AAAG-AG AAA-GAG AAAGAG
*
5950873 AAAG-G AAAG-G AAAGAA AAAGAG AGAA-AG AAAG-G AAAG
1 AAAGAG AAAGAG AAAGAG AAAGAG A-AAGAG AAAGAG AAAG
5950910 GCACGATTTG
Statistics
Matches: 66, Mismatches: 2, Indels: 18
0.77 0.02 0.21
Matches are distributed among these distances:
5 24 0.36
6 18 0.27
7 18 0.27
8 4 0.06
9 2 0.03
ACGTcount: A:0.64, C:0.01, G:0.34, T:0.01
Consensus pattern (6 bp):
AAAGAG
Found at i:5950888 original size:33 final size:29
Alignment explanation
Indices: 5950836--5950910 Score: 86
Period size: 28 Copynumber: 2.7 Consensus size: 29
5950826 CAAAGAGGAA
*
5950836 AGAGAAAGGAGAA-GCAA-GAAAGAAGAAA-
1 AGAGAAAGGA-AAGGAAAGGAAAGAA-AAAG
*
5950864 TGAGAAAGGAAAGGAAAGGAAAGAAAAAG
1 AGAGAAAGGAAAGGAAAGGAAAGAAAAAG
5950893 AGAGAAA-GAAAGGAAAGG
1 AGAGAAAGGAAAGGAAAGG
5950911 CACGATTTGC
Statistics
Matches: 41, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
27 2 0.05
28 26 0.63
29 13 0.32
ACGTcount: A:0.63, C:0.01, G:0.35, T:0.01
Consensus pattern (29 bp):
AGAGAAAGGAAAGGAAAGGAAAGAAAAAG
Found at i:5954342 original size:43 final size:43
Alignment explanation
Indices: 5954292--5954403 Score: 136
Period size: 43 Copynumber: 2.6 Consensus size: 43
5954282 TATTGACTCG
*
5954292 GCTATGTGTGAGTAGGGAGTGCGCATAAGCCAAG-GATAACTCA
1 GCTATGTGTGAGTAGGGAGTGCGCATAA-CCAAGTGATAACCCA
* * * ** *
5954335 GTTATGTGCGAGTAAGGAGTGCGCATAACCCGGTGATGACCCA
1 GCTATGTGTGAGTAGGGAGTGCGCATAACCAAGTGATAACCCA
*
5954378 GCCATGTGTGAGTAGGGAGTGCGCAT
1 GCTATGTGTGAGTAGGGAGTGCGCAT
5954404 GAGTTGGTGA
Statistics
Matches: 57, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
42 3 0.05
43 54 0.95
ACGTcount: A:0.26, C:0.18, G:0.35, T:0.21
Consensus pattern (43 bp):
GCTATGTGTGAGTAGGGAGTGCGCATAACCAAGTGATAACCCA
Found at i:5954833 original size:39 final size:40
Alignment explanation
Indices: 5954754--5954842 Score: 119
Period size: 39 Copynumber: 2.2 Consensus size: 40
5954744 AAATACATTC
* *
5954754 TCGCTGCAACGAGAAACTTTCTGTTTTCTGGGATGCAATT
1 TCGCTGCAGCGAGAAACTTTCTGTTTTCTGGGATGAAATT
* *
5954794 TTGCTGCAGCGAGAAACATTT-TG-TTTCTGGGTTGAAATT
1 TCGCTGCAGCGAGAAAC-TTTCTGTTTTCTGGGATGAAATT
5954833 TCGCTGCAGC
1 TCGCTGCAGC
5954843 AAGATTGAAT
Statistics
Matches: 43, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
39 23 0.53
40 17 0.40
41 3 0.07
ACGTcount: A:0.21, C:0.19, G:0.25, T:0.35
Consensus pattern (40 bp):
TCGCTGCAGCGAGAAACTTTCTGTTTTCTGGGATGAAATT
Found at i:5956144 original size:63 final size:63
Alignment explanation
Indices: 5955997--5956148 Score: 196
Period size: 63 Copynumber: 2.4 Consensus size: 63
5955987 CGGCATGTGT
* ** * * *
5955997 ACTGCCCACTCTGCACATGCACAGTTGTAAATGTCACAATATCATCATTCGACCGGTATATGC
1 ACTGCCCACTCCGCACATGCATGGTTGTAAATGTCACAACATCATCATTCAACCGGGATATGC
* * ** * *
5956060 ACTGCCCACTCCACATATGCATGGTTGTAGTTGTCACAACATCGTCATTCAATCGGGATATGC
1 ACTGCCCACTCCGCACATGCATGGTTGTAAATGTCACAACATCATCATTCAACCGGGATATGC
5956123 ACTGCCCACTCCGCACATGCATGGTT
1 ACTGCCCACTCCGCACATGCATGGTT
5956149 ACATCAATTA
Statistics
Matches: 75, Mismatches: 14, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
63 75 1.00
ACGTcount: A:0.26, C:0.30, G:0.18, T:0.27
Consensus pattern (63 bp):
ACTGCCCACTCCGCACATGCATGGTTGTAAATGTCACAACATCATCATTCAACCGGGATATGC
Found at i:5968784 original size:35 final size:35
Alignment explanation
Indices: 5968735--5968801 Score: 107
Period size: 35 Copynumber: 1.9 Consensus size: 35
5968725 GTTCAACCAA
*
5968735 AACCCTCAACAATGCCTTTTAATGGGAGCAAGTAT
1 AACCCTCAACAATGCCTTTTAATGGAAGCAAGTAT
* *
5968770 AACCCTCAATAATGCCTTTTCATGGAAGCAAG
1 AACCCTCAACAATGCCTTTTAATGGAAGCAAG
5968802 CACAACTCAC
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 29 1.00
ACGTcount: A:0.34, C:0.24, G:0.16, T:0.25
Consensus pattern (35 bp):
AACCCTCAACAATGCCTTTTAATGGAAGCAAGTAT
Found at i:5970791 original size:23 final size:26
Alignment explanation
Indices: 5970764--5970823 Score: 72
Period size: 26 Copynumber: 2.3 Consensus size: 26
5970754 CAACCATATA
5970764 CCCATCATCA-A-CATGCACACCATC
1 CCCATCATCACATCATGCACACCATC
5970788 CCATCATCATCATCATCATGCACACCAT-
1 CC--CATCATCA-CATCATGCACACCATC
5970816 CCCATCAT
1 CCCATCAT
5970824 TATCATCTCA
Statistics
Matches: 31, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
24 2 0.06
26 14 0.45
28 3 0.10
29 12 0.39
ACGTcount: A:0.32, C:0.43, G:0.03, T:0.22
Consensus pattern (26 bp):
CCCATCATCACATCATGCACACCATC
Found at i:5970808 original size:29 final size:29
Alignment explanation
Indices: 5970766--5970834 Score: 113
Period size: 29 Copynumber: 2.4 Consensus size: 29
5970756 ACCATATACC
*
5970766 CATCATCAACATGCACACCATCCCATCAT
1 CATCATCATCATGCACACCATCCCATCAT
5970795 CATCATCATCATGCACACCATCCCATCAT
1 CATCATCATCATGCACACCATCCCATCAT
*
5970824 TATCATC-TCAT
1 CATCATCATCAT
5970835 ATGCAACGGC
Statistics
Matches: 38, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
28 4 0.11
29 34 0.89
ACGTcount: A:0.32, C:0.39, G:0.03, T:0.26
Consensus pattern (29 bp):
CATCATCATCATGCACACCATCCCATCAT
Found at i:5970918 original size:42 final size:42
Alignment explanation
Indices: 5970855--5970991 Score: 195
Period size: 42 Copynumber: 3.3 Consensus size: 42
5970845 TTATGTGCAT
* * * *
5970855 ATAGCCAGGTCAGTAACGGCTTATGTGCACTCCCACTCACAC
1 ATAGCCGGGTCAGCAACGGCTTATGTGCACTCCTACTCGCAC
*
5970897 ATAGCCGGGTC-GACAATGGCTTATGTGCACTCCTACTCGCAC
1 ATAGCCGGGTCAG-CAACGGCTTATGTGCACTCCTACTCGCAC
*
5970939 ATAGCCTGGTCAGCAACGGCTTATGTGCACTCCTACTCGCAC
1 ATAGCCGGGTCAGCAACGGCTTATGTGCACTCCTACTCGCAC
*
5970981 ATAGCTGGGTC
1 ATAGCCGGGTC
5970992 CAAATCAACA
Statistics
Matches: 84, Mismatches: 9, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
41 1 0.01
42 82 0.98
43 1 0.01
ACGTcount: A:0.23, C:0.31, G:0.23, T:0.23
Consensus pattern (42 bp):
ATAGCCGGGTCAGCAACGGCTTATGTGCACTCCTACTCGCAC
Found at i:5976796 original size:25 final size:24
Alignment explanation
Indices: 5976744--5976801 Score: 116
Period size: 24 Copynumber: 2.4 Consensus size: 24
5976734 TAAAAATAAG
5976744 AAAAAAAATAGTTTTCTTTGTCTT
1 AAAAAAAATAGTTTTCTTTGTCTT
5976768 AAAAAAAATAGTTTTCTTTGTCTT
1 AAAAAAAATAGTTTTCTTTGTCTT
5976792 AAAAAAAATA
1 AAAAAAAATA
5976802 AAACTCAGCA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 34 1.00
ACGTcount: A:0.47, C:0.07, G:0.07, T:0.40
Consensus pattern (24 bp):
AAAAAAAATAGTTTTCTTTGTCTT
Found at i:5979819 original size:28 final size:28
Alignment explanation
Indices: 5979788--5979843 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
5979778 GTGGGGGGAT
5979788 GTACATGAGCCGGGTGTGATTATGATGA
1 GTACATGAGCCGGGTGTGATTATGATGA
5979816 GTACATGAGCCGGGTGTGATTATGATGA
1 GTACATGAGCCGGGTGTGATTATGATGA
5979844 TATTGATGCT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.25, C:0.11, G:0.36, T:0.29
Consensus pattern (28 bp):
GTACATGAGCCGGGTGTGATTATGATGA
Found at i:5981460 original size:29 final size:29
Alignment explanation
Indices: 5981426--5981491 Score: 82
Period size: 29 Copynumber: 2.3 Consensus size: 29
5981416 GAAAAGTTAG
* *
5981426 TATGGGTTTGTGGTGAGCT-AGTTAAAAAAC
1 TATGGGTTTGTGATGAACTCA-TT-AAAAAC
5981456 -ATGGGTTTGTGATGAACTCATTAAAAAC
1 TATGGGTTTGTGATGAACTCATTAAAAAC
5981484 TATGGGTT
1 TATGGGTT
5981492 ATTGCTTGAT
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
28 6 0.19
29 25 0.78
30 1 0.03
ACGTcount: A:0.30, C:0.08, G:0.27, T:0.35
Consensus pattern (29 bp):
TATGGGTTTGTGATGAACTCATTAAAAAC
Found at i:5981601 original size:50 final size:50
Alignment explanation
Indices: 5981543--5981712 Score: 198
Period size: 50 Copynumber: 3.4 Consensus size: 50
5981533 TGATCCCATG
*
5981543 AAAAAGCAAGAATCCTTTTGTGGATTGTGTAAAGGTTATTGCTTCTTGTC
1 AAAAAGCAAGAATCCTTTTGTGGATTGTGTAAAGGTTATCGCTTCTTGTC
* * * *
5981593 AAAAAGCAAAAATCCCTTTATGGATTGTGTAAGGGTTATCGCTTCTTGTC
1 AAAAAGCAAGAATCCTTTTGTGGATTGTGTAAAGGTTATCGCTTCTTGTC
* * ** * * *
5981643 AAAAAGCAAGAATCTTTTTTGTAGATTGTGTAAAAATTATCACTTC-CGATT
1 AAAAAGCAAGAATC-CTTTTGTGGATTGTGTAAAGGTTATCGCTTCTTG-TC
*
5981694 AAAAAACAAGAATCCTTTT
1 AAAAAGCAAGAATCCTTTT
5981713 AGTATATTAT
Statistics
Matches: 100, Mismatches: 18, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
50 63 0.63
51 37 0.37
ACGTcount: A:0.34, C:0.14, G:0.17, T:0.35
Consensus pattern (50 bp):
AAAAAGCAAGAATCCTTTTGTGGATTGTGTAAAGGTTATCGCTTCTTGTC
Found at i:5986994 original size:29 final size:29
Alignment explanation
Indices: 5986947--5987115 Score: 200
Period size: 29 Copynumber: 5.8 Consensus size: 29
5986937 TTAAGAAAAC
* * *
5986947 TCTTGTCCTTAATTAAGACAAAACATATTA
1 TCTTGT-CTAAATTAAGACAAAACATGTTT
* *
5986977 TCTTGTCTAAATTGAGAC-AAATATGTTT
1 TCTTGTCTAAATTAAGACAAAACATGTTT
* * *
5987005 TCTTGTCTAGATTTAGACAAAACATATTT
1 TCTTGTCTAAATTAAGACAAAACATGTTT
*
5987034 TCCTTATCTTAAATTAAGAC-AAACATGTTT
1 T-CTTGTC-TAAATTAAGACAAAACATGTTT
5987064 TCTTGTCTAAATTCAA-ACAAAACATGTTT
1 TCTTGTCTAAATT-AAGACAAAACATGTTT
5987093 TCTTGTCTAAATTAAGACAAAAC
1 TCTTGTCTAAATTAAGACAAAAC
5987116 GTGTAAAAAC
Statistics
Matches: 119, Mismatches: 14, Indels: 13
0.82 0.10 0.09
Matches are distributed among these distances:
28 33 0.28
29 56 0.47
30 21 0.18
31 9 0.08
ACGTcount: A:0.37, C:0.15, G:0.09, T:0.38
Consensus pattern (29 bp):
TCTTGTCTAAATTAAGACAAAACATGTTT
Found at i:5987062 original size:59 final size:57
Alignment explanation
Indices: 5986947--5987113 Score: 217
Period size: 59 Copynumber: 2.9 Consensus size: 57
5986937 TTAAGAAAAC
* * * * *
5986947 TCTTGTCCTTAATTAAGACAAAACATATTATCTTGTCTAAATTGAGACAAATATGTTT
1 TCTTGT-CTAAATTCAGACAAAACATATTTTCTTGTCTAAATTAAGACAAACATGTTT
* * *
5987005 TCTTGTCTAGATTTAGACAAAACATATTTTCCTTATCTTAAATTAAGACAAACATGTTT
1 TCTTGTCTAAATTCAGACAAAACATATTTT-CTTGTC-TAAATTAAGACAAACATGTTT
* *
5987064 TCTTGTCTAAATTCAAACAAAACATGTTTTCTTGTCTAAATTAAGACAAA
1 TCTTGTCTAAATTCAGACAAAACATATTTTCTTGTCTAAATTAAGACAAA
5987114 ACGTGTAAAA
Statistics
Matches: 95, Mismatches: 12, Indels: 5
0.85 0.11 0.04
Matches are distributed among these distances:
57 34 0.36
58 16 0.17
59 45 0.47
ACGTcount: A:0.37, C:0.15, G:0.09, T:0.39
Consensus pattern (57 bp):
TCTTGTCTAAATTCAGACAAAACATATTTTCTTGTCTAAATTAAGACAAACATGTTT
Found at i:5992037 original size:42 final size:42
Alignment explanation
Indices: 5991947--5992079 Score: 214
Period size: 42 Copynumber: 3.1 Consensus size: 42
5991937 ATCATCCCAC
*
5991947 CATCATCAGCTCATGTGCACTCCCCACTCGTACATAGTTGGGT
1 CATCATCAGCTCATGTGCACT-CCCACACGTACATAGTTGGGT
*
5991990 CATCATCAGCTCATGTGCACT-CCACACCGCACATAGTTGGGT
1 CATCATCAGCTCATGTGCACTCCCACA-CGTACATAGTTGGGT
*
5992032 CATCATCAGCTCATGTGCACTCCCACACGTACATAGCTGGGT
1 CATCATCAGCTCATGTGCACTCCCACACGTACATAGTTGGGT
5992074 CATCAT
1 CATCAT
5992080 TATCACATAA
Statistics
Matches: 84, Mismatches: 4, Indels: 5
0.90 0.04 0.05
Matches are distributed among these distances:
41 4 0.05
42 54 0.64
43 26 0.31
ACGTcount: A:0.23, C:0.33, G:0.18, T:0.26
Consensus pattern (42 bp):
CATCATCAGCTCATGTGCACTCCCACACGTACATAGTTGGGT
Found at i:5999705 original size:2 final size:2
Alignment explanation
Indices: 5999698--5999736 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
5999688 TGTATGTATG
5999698 TA TA TA TA TA TA TA 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 TA TA T
5999737 CAATCATTAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:5999834 original size:42 final size:42
Alignment explanation
Indices: 5999788--5999910 Score: 129
Period size: 42 Copynumber: 2.9 Consensus size: 42
5999778 GCACATGGTT
* * **
5999788 GGGTCATCATCGGCTTATGCGCACTCTTACTTGCACATAACC
1 GGGTCAACATCGGCTTATGCGCACTCATACTCACACATAACC
* * ** **
5999830 GGGTCAACATCGGCTTCTACGCACTCCCACTCACACATTGCC
1 GGGTCAACATCGGCTTATGCGCACTCATACTCACACATAACC
* * *
5999872 TGGTCAGCATCAGCTTATGCGCACTCATACTCACACATA
1 GGGTCAACATCGGCTTATGCGCACTCATACTCACACATA
5999911 GCTAGGTCAA
Statistics
Matches: 64, Mismatches: 17, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
42 64 1.00
ACGTcount: A:0.24, C:0.34, G:0.17, T:0.25
Consensus pattern (42 bp):
GGGTCAACATCGGCTTATGCGCACTCATACTCACACATAACC
Found at i:6003850 original size:19 final size:19
Alignment explanation
Indices: 6003826--6003863 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
6003816 TTCATGAAAC
6003826 ATGGTGTTTAAACACATTT
1 ATGGTGTTTAAACACATTT
6003845 ATGGTGTTTAAACACATTT
1 ATGGTGTTTAAACACATTT
6003864 TAAATAGCAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.32, C:0.11, G:0.16, T:0.42
Consensus pattern (19 bp):
ATGGTGTTTAAACACATTT
Found at i:6013104 original size:13 final size:13
Alignment explanation
Indices: 6013086--6013112 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
6013076 GTCTACTTTC
6013086 TAACTTATCCATA
1 TAACTTATCCATA
6013099 TAACTTATCCATA
1 TAACTTATCCATA
6013112 T
1 T
6013113 TAGTATTGCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.37, C:0.22, G:0.00, T:0.41
Consensus pattern (13 bp):
TAACTTATCCATA
Found at i:6014434 original size:58 final size:57
Alignment explanation
Indices: 6014327--6014438 Score: 206
Period size: 58 Copynumber: 1.9 Consensus size: 57
6014317 TAGGACACTC
6014327 AAATGCATGTAAGTGTTTTCTTTTTTTTTTTCATAGTCAAGCTGATTTAGTGATCTA
1 AAATGCATGTAAGTGTTTTCTTTTTTTTTTTCATAGTCAAGCTGATTTAGTGATCTA
*
6014384 AAATGCATGTAAGTGTTTTATTTTTTTTTTTTCATAGTCAAGCTGATTTAGTGAT
1 AAATGCATGTAAGTGTTTT-CTTTTTTTTTTTCATAGTCAAGCTGATTTAGTGAT
6014439 TTGAAGTTGT
Statistics
Matches: 53, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
57 19 0.36
58 34 0.64
ACGTcount: A:0.25, C:0.09, G:0.16, T:0.50
Consensus pattern (57 bp):
AAATGCATGTAAGTGTTTTCTTTTTTTTTTTCATAGTCAAGCTGATTTAGTGATCTA
Found at i:6015832 original size:262 final size:262
Alignment explanation
Indices: 6015310--6015802 Score: 792
Period size: 261 Copynumber: 1.9 Consensus size: 262
6015300 GACAAATTCT
6015310 AAATTAATTAGTGGACCATATATGGCTATTTTTGAAAAAAATAAAGTGAATCATAACTTTTGTTT
1 AAATTAATTAGTGGACCATATATGGCTATTTTTGAAAAAAATAAAGTGAATCATAACTTTTGTTT
* * * *
6015375 GGAATAATAATTAGTTTAAGTAAGGTGATATGTATAAATAATTAATTATATTTATTTGGCTAAAA
66 GGAATAATAATTAGTTTAAGTAAGGTGATACGTATAAATAATTAATGACATTTATTTGGATAAAA
* * *
6015440 ATAGTAACTTATGTAAGATTTTTGCCTGATAATGGGGTAATTTTGTAATTTCATAACTTTTGGGG
131 ATAGTAACTAATGTAAGATTTTTGCCTGATAATGGGGCAATTTTGTAATTTCATAACTTTTGGGC
* * *
6015505 TTTCTTTTATCATTGCCAAGTGTCAAGCAAGGAAGCCCCAAAAGGCTTCCTTTAAATATAGTTAT
196 CTTCTTTTATCATTACCAAGTGTCAAGCAAGGAAACCCCAAAAGGCTTCCTTTAAATATAGTTAT
6015570 AA
261 AA
* * *
6015572 AAATTAATTAGTGGACCATATATGGCTTTTTTTGAAAAAAA-AAGGTGAGTCATAACTTTTGTTT
1 AAATTAATTAGTGGACCATATATGGCTATTTTTGAAAAAAATAAAGTGAATCATAACTTTTGTTT
* *
6015636 GGAATAATAATTAGTTTAAGTAAGGTGATACGTATAAATAGTTAATGCCATTTATTTGGATAAAA
66 GGAATAATAATTAGTTTAAGTAAGGTGATACGTATAAATAATTAATGACATTTATTTGGATAAAA
* * *
6015701 ATAGTAACTAATTTAAGATTTTTGCTTGATAATGGGGCAATTTTGTAATTTCATAATTTTTGGAG
131 ATAGTAACTAATGTAAGATTTTTGCCTGATAATGGGGCAATTTTGTAATTTCATAACTTTTGG-G
6015766 CCCTT-TTTTATCATTACCAAGTGTCAAGCAAGGAAAC
195 -CCTTCTTTTATCATTACCAAGTGTCAAGCAAGGAAAC
6015803 TCTTTGGGGC
Statistics
Matches: 211, Mismatches: 18, Indels: 4
0.91 0.08 0.02
Matches are distributed among these distances:
261 138 0.65
262 71 0.34
263 2 0.01
ACGTcount: A:0.36, C:0.09, G:0.17, T:0.38
Consensus pattern (262 bp):
AAATTAATTAGTGGACCATATATGGCTATTTTTGAAAAAAATAAAGTGAATCATAACTTTTGTTT
GGAATAATAATTAGTTTAAGTAAGGTGATACGTATAAATAATTAATGACATTTATTTGGATAAAA
ATAGTAACTAATGTAAGATTTTTGCCTGATAATGGGGCAATTTTGTAATTTCATAACTTTTGGGC
CTTCTTTTATCATTACCAAGTGTCAAGCAAGGAAACCCCAAAAGGCTTCCTTTAAATATAGTTAT
AA
Found at i:6016169 original size:21 final size:21
Alignment explanation
Indices: 6016147--6016184 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
6016137 TATTTTTTCT
6016147 CTCTT-TTTTTT-TTCTTTTG
1 CTCTTATTTTTTGTTCTTTTG
6016166 CTCTTATTTTTTGTTCTTT
1 CTCTTATTTTTTGTTCTTT
6016185 ATAACTCACT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 5 0.29
20 6 0.35
21 6 0.35
ACGTcount: A:0.03, C:0.16, G:0.05, T:0.76
Consensus pattern (21 bp):
CTCTTATTTTTTGTTCTTTTG
Found at i:6018414 original size:17 final size:17
Alignment explanation
Indices: 6018392--6018435 Score: 61
Period size: 17 Copynumber: 2.6 Consensus size: 17
6018382 AATTAATTAT
6018392 ATTAAAAATATATAAAA
1 ATTAAAAATATATAAAA
*
6018409 ATTAAAAAAATATAAAA
1 ATTAAAAATATATAAAA
* *
6018426 GTAAAAAATA
1 ATTAAAAATA
6018436 ATTAATAAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.73, C:0.00, G:0.02, T:0.25
Consensus pattern (17 bp):
ATTAAAAATATATAAAA
Found at i:6019553 original size:19 final size:19
Alignment explanation
Indices: 6019508--6019544 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
6019498 CTTTCTCTTG
6019508 ATGCTTGCATCTTCTCTCA
1 ATGCTTGCATCTTCTCTCA
6019527 ATGCTTGCATCTTCTCTC
1 ATGCTTGCATCTTCTCTC
6019545 TTAGCTTGCT
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:0.14, C:0.32, G:0.11, T:0.43
Consensus pattern (19 bp):
ATGCTTGCATCTTCTCTCA
Found at i:6021430 original size:2 final size:2
Alignment explanation
Indices: 6021418--6021453 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
6021408 ATGATGATTG
* *
6021418 AT AT CT AT AT AT AT AT AT AT AT AT AT AT AC AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
6021454 GGTATATGGT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.47, C:0.06, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:6032528 original size:122 final size:122
Alignment explanation
Indices: 6032288--6032511 Score: 421
Period size: 122 Copynumber: 1.8 Consensus size: 122
6032278 CGATACTTTT
**
6032288 GTAGAATTCAAGAAGATTTCTCACTTAGAAATTTCAAGAAAACAACCACTTGTAATTTTCTTGAA
1 GTAGAATTCAAGAAGATTTCTCACTTAGAAATTTCAAGAAAACAACCACTTCAAATTTTCTTGAA
6032353 ATTTCATCATTTAATCATATTTAATTAAATAATTTCAGACTAAATACACTAAATTTG
66 ATTTCATCATTTAATCATATTTAATTAAATAATTTCAGACTAAATACACTAAATTTG
6032410 GTAGAATTCAAGAAGATTTCTCACTTAGAAATTTCAAGAAAACAACCACTTCAAATTTTCTTGAA
1 GTAGAATTCAAGAAGATTTCTCACTTAGAAATTTCAAGAAAACAACCACTTCAAATTTTCTTGAA
*
6032475 ATTTCATCATTTAATCGTATTTAATTAAATAATTTCA
66 ATTTCATCATTTAATCATATTTAATTAAATAATTTCA
6032512 TAGTAAGTTC
Statistics
Matches: 99, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
122 99 1.00
ACGTcount: A:0.41, C:0.14, G:0.08, T:0.37
Consensus pattern (122 bp):
GTAGAATTCAAGAAGATTTCTCACTTAGAAATTTCAAGAAAACAACCACTTCAAATTTTCTTGAA
ATTTCATCATTTAATCATATTTAATTAAATAATTTCAGACTAAATACACTAAATTTG
Found at i:6034167 original size:86 final size:86
Alignment explanation
Indices: 6034061--6034328 Score: 527
Period size: 86 Copynumber: 3.1 Consensus size: 86
6034051 TTGTTTTAAA
*
6034061 TTCTATTTCTTGAATTAGTTTAGTTTCACTTGTTTTGAAGAGTTAGATTTCAATCAAGATTATCT
1 TTCTCTTTCTTGAATTAGTTTAGTTTCACTTGTTTTGAAGAGTTAGATTTCAATCAAGATTATCT
6034126 ATTTTGTTCATCTTGTTTCTC
66 ATTTTGTTCATCTTGTTTCTC
6034147 TTCTCTTTCTTGAATTAGTTTAGTTTCACTTGTTTTGAAGAGTTAGATTTCAATCAAGATTATCT
1 TTCTCTTTCTTGAATTAGTTTAGTTTCACTTGTTTTGAAGAGTTAGATTTCAATCAAGATTATCT
6034212 ATTTTGTTCATCTTGTTTCTC
66 ATTTTGTTCATCTTGTTTCTC
6034233 TTCTCTTTCTTGAATTAGTTTAGTTTCACTTGTTTTGAAGAGTTAGATTTCAATCAAGATTATCT
1 TTCTCTTTCTTGAATTAGTTTAGTTTCACTTGTTTTGAAGAGTTAGATTTCAATCAAGATTATCT
6034298 ATTTTGTTCATCTTGTTTCTC
66 ATTTTGTTCATCTTGTTTCTC
6034319 TTCTCTTTCT
1 TTCTCTTTCT
6034329 AATTTTCCTT
Statistics
Matches: 181, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
86 181 1.00
ACGTcount: A:0.21, C:0.14, G:0.12, T:0.53
Consensus pattern (86 bp):
TTCTCTTTCTTGAATTAGTTTAGTTTCACTTGTTTTGAAGAGTTAGATTTCAATCAAGATTATCT
ATTTTGTTCATCTTGTTTCTC
Found at i:6035044 original size:12 final size:12
Alignment explanation
Indices: 6035018--6035050 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
6035008 TCCTTATAAA
6035018 ATTTAAAATATT
1 ATTTAAAATATT
6035030 A-TTAAAATAATT
1 ATTTAAAAT-ATT
6035042 ATTTAAAAT
1 ATTTAAAAT
6035051 TATTTAAGTA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 7 0.37
12 5 0.26
13 7 0.37
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (12 bp):
ATTTAAAATATT
Found at i:6074571 original size:68 final size:68
Alignment explanation
Indices: 6074468--6074716 Score: 212
Period size: 68 Copynumber: 3.7 Consensus size: 68
6074458 TCTCATAAGG
* * ** * *
6074468 TATATGGAAGATACATCATATACATAATCTAATGGCATTCATCATGCTTTCTCAATAATCTCATG
1 TATATGGAATATATATCATATACATAATCTAATGGCATTCATCATGCTTAATCAATAACCTCATA
6074533 TAA
66 TAA
* * * *
6074536 TATATGGAATATATATCATATACATTATCTCATGGCATTCATCATGCTTAATTAATCACCTCATA
1 TATATGGAATATATATCATATACATAATCTAATGGCATTCATCATGCTTAATCAATAACCTCATA
**
6074601 TGG
66 TAA
* * * * * * * * * * *
6074604 TATATGGAATTTATATCATATACACAATCTTATAGTATACATCATGCATACTTAATCATCTCATA
1 TATATGGAATATATATCATATACATAATCTAATGGCATTCATCATGCTTAATCAATAACCTCATA
**
6074669 TGG
66 TAA
* * * * *
6074672 TGTATGAAAT-TCACATCATATACATAATCTTATGGCAATCATCAT
1 TATATGGAATAT-ATATCATATACATAATCTAATGGCATTCATCAT
6074717 ACTAAACATG
Statistics
Matches: 150, Mismatches: 30, Indels: 2
0.82 0.16 0.01
Matches are distributed among these distances:
67 1 0.01
68 149 0.99
ACGTcount: A:0.36, C:0.17, G:0.10, T:0.37
Consensus pattern (68 bp):
TATATGGAATATATATCATATACATAATCTAATGGCATTCATCATGCTTAATCAATAACCTCATA
TAA
Found at i:6075725 original size:12 final size:12
Alignment explanation
Indices: 6075689--6075725 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
6075679 TTTGGGGAAA
6075689 ATGTATCGATAC
1 ATGTATCGATAC
6075701 AT-TAT-GA-AC
1 ATGTATCGATAC
6075710 ATGTATCGATAC
1 ATGTATCGATAC
6075722 ATGT
1 ATGT
6075726 TCATCTGGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
9 4 0.18
10 5 0.23
11 5 0.23
12 8 0.36
ACGTcount: A:0.35, C:0.14, G:0.16, T:0.35
Consensus pattern (12 bp):
ATGTATCGATAC
Found at i:6075986 original size:16 final size:16
Alignment explanation
Indices: 6075962--6075992 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
6075952 TAAAAATATT
6075962 AAAAAAATCAAAATCC
1 AAAAAAATCAAAATCC
*
6075978 AAAAGAATCAAAATC
1 AAAAAAATCAAAATC
6075993 TAATTTTTTT
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:0.68, C:0.16, G:0.03, T:0.13
Consensus pattern (16 bp):
AAAAAAATCAAAATCC
Found at i:6076465 original size:16 final size:16
Alignment explanation
Indices: 6076441--6076471 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
6076431 TAAAAATATT
6076441 AAAAAAATCAAAATCC
1 AAAAAAATCAAAATCC
*
6076457 AAAAGAATCAAAATC
1 AAAAAAATCAAAATC
6076472 TAATTTTTTT
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:0.68, C:0.16, G:0.03, T:0.13
Consensus pattern (16 bp):
AAAAAAATCAAAATCC
Found at i:6076762 original size:477 final size:478
Alignment explanation
Indices: 6075840--6076800 Score: 1748
Period size: 477 Copynumber: 2.0 Consensus size: 478
6075830 TACCCAGCTT
6075840 ACTTACATTAAATACCATTTAAGTAAATGTCTTCTTTATTTATTTATTTTTACTCTTCATTTACT
1 ACTTACATTAAATACCATTTAAGTAAATGTCTTCTTTATTTATTTATTTTTACTCTTCATTTACT
* *
6075905 TAATAAATTTAATGTAAATAAGCAAACAACCCTCCTTTTAGATTCAATAAAAATATTAAAAAAAT
66 TAATAAATTAAATGTAAATAAGCAAACAACCCCCCTTTTAGATTCAATAAAAATATTAAAAAAAT
*
6075970 CAAAATCCAAAAGAATCAAAATCTAATTTTTTTTGTTTCAAGAACAAAATTGAAAAAGTTTGATT
131 CAAAATCCAAAAGAATCAAAATCTAATTTTTTTTATTTCAAGAACAAAATTGAAAAAGTTTGATT
* *
6076035 GAAATTAAATTTGCAGTTTCAATTACCATAGCAAATGTACTCCAAAAATTATGAAAAAAAAATCA
196 GAAATTAAATTTGCAGTTCCAATTACCATAACAAATGTACTCCAAAAATTATG-AAAAAAAATCA
**
6076100 TTTTTGATCATTTAAAAATCAAGAAAATCATTACCACCAATTTTTAATTCCAAAAAGATTATTCT
260 TTTTTGATCATTTAAAAATCAAGAAAATCATTACCACCAATTTTTAATTCCAAAAAGATTATTAA
6076165 ATGAAAATCACATATTTGACCCCTTCAAGACATAGAAAATTTTTTGCTTCAAAAATGACAAACAA
325 ATGAAAATCACATATTTGACCCCTTCAAGACATAGAAAATTTTTTGCTTCAAAAATGACAAACAA
* *
6076230 TAGAAAGTGTCAATGGATTTCTTTTGAAGGTTAAAACTAAGTTTGATGTTCAAAATATGTAATCT
390 CAGAAAGTGTCAACGGATTTCTTTTGAAGGTTAAAACTAAGTTTGATGTTCAAAATATGTAATCT
6076295 ATATGCTCATCTAAGGATTTCCTA
455 ATATGCTCATCTAAGGATTTCCTA
6076319 ACTTACATTAAATACCATTTAAGTAAATGTCTTCTTTATTTATTTATTTTTACTC-TCTATTTAC
1 ACTTACATTAAATACCATTTAAGTAAATGTCTTCTTTATTTATTTATTTTTACTCTTC-ATTTAC
*
6076383 TTAATAAATTAAATGTAAATAAGCAAACAACCCCCCTTTTGGATTCAATAAAAATATTAAAAAAA
65 TTAATAAATTAAATGTAAATAAGCAAACAACCCCCCTTTTAGATTCAATAAAAATATTAAAAAAA
6076448 TCAAAATCCAAAAGAATCAAAATCTAA-TTTTTTTATTTCAAGAACAAAATTGAAAAAGTTTGAT
130 TCAAAATCCAAAAGAATCAAAATCTAATTTTTTTTATTTCAAGAACAAAATTGAAAAAGTTTGAT
*
6076512 TGAAATTAAATTTGCAGTTCCCATTTACCATAACAAATGTACTCCAAAAATTATG-AAAAAAATC
195 TGAAATTAAATTTGCAGTT-CCAATTACCATAACAAATGTACTCCAAAAATTATGAAAAAAAATC
*
6076576 ATTTTTGATCATTTAAAAATCAAGAAAATCATTACCACCAATTTTTAATTCTAAAAAGATTATTA
259 ATTTTTGATCATTTAAAAATCAAGAAAATCATTACCACCAATTTTTAATTCCAAAAAGATTATTA
*
6076641 AATGAAAATCACATATTTGACCCCTTCAAGACATAGAAAATTTTTTGCTTCAAAAGTGACAAACA
324 AATGAAAATCACATATTTGACCCCTTCAAGACATAGAAAATTTTTTGCTTCAAAAATGACAAACA
*
6076706 ACGGAAAGTGTCAACGGATTTCTTTTGAAGGTTAAAACTAAGTTTGATGTTCAAAATATGTAATC
389 ACAGAAAGTGTCAACGGATTTCTTTTGAAGGTTAAAACTAAGTTTGATGTTCAAAATATGTAATC
6076771 TATATGCTCATCTAAGGATTTCCTA
454 TATATGCTCATCTAAGGATTTCCTA
6076796 ACTTA
1 ACTTA
6076801 TCCTCTTACT
Statistics
Matches: 466, Mismatches: 14, Indels: 6
0.96 0.03 0.01
Matches are distributed among these distances:
477 227 0.49
478 57 0.12
479 182 0.39
ACGTcount: A:0.42, C:0.14, G:0.09, T:0.35
Consensus pattern (478 bp):
ACTTACATTAAATACCATTTAAGTAAATGTCTTCTTTATTTATTTATTTTTACTCTTCATTTACT
TAATAAATTAAATGTAAATAAGCAAACAACCCCCCTTTTAGATTCAATAAAAATATTAAAAAAAT
CAAAATCCAAAAGAATCAAAATCTAATTTTTTTTATTTCAAGAACAAAATTGAAAAAGTTTGATT
GAAATTAAATTTGCAGTTCCAATTACCATAACAAATGTACTCCAAAAATTATGAAAAAAAATCAT
TTTTGATCATTTAAAAATCAAGAAAATCATTACCACCAATTTTTAATTCCAAAAAGATTATTAAA
TGAAAATCACATATTTGACCCCTTCAAGACATAGAAAATTTTTTGCTTCAAAAATGACAAACAAC
AGAAAGTGTCAACGGATTTCTTTTGAAGGTTAAAACTAAGTTTGATGTTCAAAATATGTAATCTA
TATGCTCATCTAAGGATTTCCTA
Found at i:6091300 original size:34 final size:34
Alignment explanation
Indices: 6091241--6091337 Score: 92
Period size: 35 Copynumber: 2.8 Consensus size: 34
6091231 ACCATTATTA
*
6091241 AAGGGTTTTCACTTGAT-TCAATGAAAAAGTATTGT
1 AAGGG-TTTCACTTGATCTC-GTGAAAAAGTATTGT
** * *
6091276 -AGGAGTTTTGCTTGATCTTGTGAAAAAACTATTGT
1 AAGG-GTTTCACTTGATCTCGTG-AAAAAGTATTGT
6091311 AAGGGTTTCACTTGATCTCGT-AAAAAG
1 AAGGGTTTCACTTGATCTCGTGAAAAAG
6091338 CACATTTCCC
Statistics
Matches: 49, Mismatches: 9, Indels: 10
0.72 0.13 0.15
Matches are distributed among these distances:
33 5 0.10
34 14 0.29
35 27 0.55
36 3 0.06
ACGTcount: A:0.32, C:0.10, G:0.22, T:0.36
Consensus pattern (34 bp):
AAGGGTTTCACTTGATCTCGTGAAAAAGTATTGT
Found at i:6094631 original size:43 final size:43
Alignment explanation
Indices: 6094570--6094819 Score: 325
Period size: 43 Copynumber: 6.0 Consensus size: 43
6094560 TGTGATAATT
6094570 ATGACCCAGCCATGTGCGAGTAGGGAGTGCACATGAGCTGATG
1 ATGACCCAGCCATGTGCGAGTAGGGAGTGCACATGAGCTGATG
*
6094613 ATGACCCAGCTATGTGCGAGTAGGGAGTGCACATGAGCTGATG
1 ATGACCCAGCCATGTGCGAGTAGGGAGTGCACATGAGCTGATG
* * *
6094656 ATGACCCAGCCATGTGTG-G-A-GGAGTACACATGAGCTTATG
1 ATGACCCAGCCATGTGCGAGTAGGGAGTGCACATGAGCTGATG
** *
6094696 ATGACCCAGTTATGTGCGAGTAAGGAGTGCACATGAGCTGATG
1 ATGACCCAGCCATGTGCGAGTAGGGAGTGCACATGAGCTGATG
* * *
6094739 ATGACCCAACCATGTGTG-G-A-GGAGTACACATGAGCTGATG
1 ATGACCCAGCCATGTGCGAGTAGGGAGTGCACATGAGCTGATG
* * *
6094779 ATGACCCAGCTATATGCGATGT-GGGAGTGCACATAAGCTGA
1 ATGACCCAGCCATGTGCGA-GTAGGGAGTGCACATGAGCTGA
6094820 GAGAGAGTTG
Statistics
Matches: 179, Mismatches: 21, Indels: 14
0.84 0.10 0.07
Matches are distributed among these distances:
40 66 0.37
41 3 0.02
42 4 0.02
43 106 0.59
ACGTcount: A:0.28, C:0.19, G:0.32, T:0.21
Consensus pattern (43 bp):
ATGACCCAGCCATGTGCGAGTAGGGAGTGCACATGAGCTGATG
Found at i:6094712 original size:83 final size:83
Alignment explanation
Indices: 6094570--6094819 Score: 385
Period size: 83 Copynumber: 3.0 Consensus size: 83
6094560 TGTGATAATT
* *
6094570 ATGACCCAGCCATGTGCGAGTAGGGAGTGCACATGAGCTGATGATGACCCAGCTATGTGCGAGTA
1 ATGACCCAGCCATGTGTG-G-A-GGAGTACACATGAGCTGATGATGACCCAGCTATGTGCGAGTA
6094635 GGGAGTGCACATGAGCTGATG
63 GGGAGTGCACATGAGCTGATG
* * *
6094656 ATGACCCAGCCATGTGTGGAGGAGTACACATGAGCTTATGATGACCCAGTTATGTGCGAGTAAGG
1 ATGACCCAGCCATGTGTGGAGGAGTACACATGAGCTGATGATGACCCAGCTATGTGCGAGTAGGG
6094721 AGTGCACATGAGCTGATG
66 AGTGCACATGAGCTGATG
* *
6094739 ATGACCCAACCATGTGTGGAGGAGTACACATGAGCTGATGATGACCCAGCTATATGCGATGT-GG
1 ATGACCCAGCCATGTGTGGAGGAGTACACATGAGCTGATGATGACCCAGCTATGTGCGA-GTAGG
*
6094803 GAGTGCACATAAGCTGA
65 GAGTGCACATGAGCTGA
6094820 GAGAGAGTTG
Statistics
Matches: 152, Mismatches: 11, Indels: 5
0.90 0.07 0.03
Matches are distributed among these distances:
83 131 0.86
84 3 0.02
85 1 0.01
86 17 0.11
ACGTcount: A:0.28, C:0.19, G:0.32, T:0.21
Consensus pattern (83 bp):
ATGACCCAGCCATGTGTGGAGGAGTACACATGAGCTGATGATGACCCAGCTATGTGCGAGTAGGG
AGTGCACATGAGCTGATG
Found at i:6107568 original size:34 final size:36
Alignment explanation
Indices: 6107507--6107611 Score: 101
Period size: 35 Copynumber: 3.0 Consensus size: 36
6107497 GGTTATTGAG
* *
6107507 CTCATGAAAAACCACTGTTG-AAGGGTTTCGCTTGATT
1 CTCATGAAAAA--ACTATTGTAAAGGTTTCGCTTGATT
* *
6107544 C-CAT-AAAAAAGTATTGTAAAGGTTTCGCTTTA-T
1 CTCATGAAAAAACTATTGTAAAGGTTTCGCTTGATT
* * *
6107577 CTTATGAAAAAACTATTGTAAGGGTTTTGCTTGAT
1 CTCATGAAAAAACTATTGTAAAGGTTTCGCTTGAT
6107612 CTCGTAAAAA
Statistics
Matches: 55, Mismatches: 9, Indels: 9
0.75 0.12 0.12
Matches are distributed among these distances:
33 7 0.13
34 15 0.27
35 29 0.53
36 3 0.05
37 1 0.02
ACGTcount: A:0.31, C:0.13, G:0.19, T:0.36
Consensus pattern (36 bp):
CTCATGAAAAAACTATTGTAAAGGTTTCGCTTGATT
Found at i:6107801 original size:52 final size:52
Alignment explanation
Indices: 6107745--6107844 Score: 155
Period size: 52 Copynumber: 1.9 Consensus size: 52
6107735 ATTGTGATTT
* * *
6107745 ATTGCTTGCATTTAGCTTAGGAAAATTTTTTACCTTTATTTATTATTTATGC
1 ATTGCTTGCATTTAGATTAGGAAAATATTTTACCTTGATTTATTATTTATGC
* *
6107797 ATTGCTTGCATTTGGATTAGGAAAATATTTTACCTTGCTTTATTATTT
1 ATTGCTTGCATTTAGATTAGGAAAATATTTTACCTTGATTTATTATTT
6107845 GTTTTTTTTT
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
52 43 1.00
ACGTcount: A:0.25, C:0.11, G:0.13, T:0.51
Consensus pattern (52 bp):
ATTGCTTGCATTTAGATTAGGAAAATATTTTACCTTGATTTATTATTTATGC
Found at i:6115524 original size:16 final size:18
Alignment explanation
Indices: 6115498--6115536 Score: 55
Period size: 17 Copynumber: 2.3 Consensus size: 18
6115488 CAATCCAACA
*
6115498 TAAATAATT-AATTAAAC
1 TAAATAATTAAATAAAAC
6115515 TAAA-AATTAAATAAAAC
1 TAAATAATTAAATAAAAC
6115532 TAAAT
1 TAAAT
6115537 CACAATAAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
16 4 0.21
17 15 0.79
ACGTcount: A:0.64, C:0.05, G:0.00, T:0.31
Consensus pattern (18 bp):
TAAATAATTAAATAAAAC
Found at i:6118603 original size:30 final size:33
Alignment explanation
Indices: 6118568--6118651 Score: 111
Period size: 35 Copynumber: 2.6 Consensus size: 33
6118558 CTTCAATATA
**
6118568 TTTTCTTTCTTTTCAATT-TGGTTCT-CC-AAC
1 TTTTCTTTCTTTTCAATTATCCTTCTCCCAAAC
6118598 TTTTCTTTCTTTTCAATTTAATCCTTCTCCCAAAC
1 TTTTCTTTCTTTTCAA-TT-ATCCTTCTCCCAAAC
6118633 TTTTCTTTCTTTTCAATTA
1 TTTTCTTTCTTTTCAATTA
6118652 AGTCCTGCTA
Statistics
Matches: 47, Mismatches: 2, Indels: 7
0.84 0.04 0.12
Matches are distributed among these distances:
30 16 0.34
31 2 0.04
33 6 0.13
34 4 0.09
35 19 0.40
ACGTcount: A:0.17, C:0.24, G:0.02, T:0.57
Consensus pattern (33 bp):
TTTTCTTTCTTTTCAATTATCCTTCTCCCAAAC
Found at i:6119043 original size:43 final size:43
Alignment explanation
Indices: 6118978--6119101 Score: 212
Period size: 43 Copynumber: 2.9 Consensus size: 43
6118968 GGTGTTATAT
* *
6118978 CATAGAATCAATCTCTTTTCTTCAAAAGATTGATTCTTCTTAA
1 CATAGAATCAATCTCTTCTCTTCAAAAGATTGATTCTTCTCAA
*
6119021 CATAGAATCAATCTCGTCTCTTCAAAAGATTGATTCTTCTCAA
1 CATAGAATCAATCTCTTCTCTTCAAAAGATTGATTCTTCTCAA
*
6119064 CATAGAATCAATCTCTTCTTTTCAAAAGATTGATTCTT
1 CATAGAATCAATCTCTTCTCTTCAAAAGATTGATTCTT
6119102 GTTGAAACAA
Statistics
Matches: 76, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
43 76 1.00
ACGTcount: A:0.32, C:0.20, G:0.08, T:0.40
Consensus pattern (43 bp):
CATAGAATCAATCTCTTCTCTTCAAAAGATTGATTCTTCTCAA
Found at i:6119080 original size:22 final size:22
Alignment explanation
Indices: 6119012--6119082 Score: 60
Period size: 22 Copynumber: 3.3 Consensus size: 22
6119002 AAAGATTGAT
*
6119012 TCTTCTTAACATAGAATCAATC
1 TCTTCTCAACATAGAATCAATC
**
6119034 TCGTCTCTTCAA-A-AG-ATTGAT-
1 TC-T-TC-TCAACATAGAATCAATC
6119055 TCTTCTCAACATAGAATCAATC
1 TCTTCTCAACATAGAATCAATC
6119077 TCTTCT
1 TCTTCT
6119083 TTTCAAAAGA
Statistics
Matches: 37, Mismatches: 5, Indels: 14
0.66 0.09 0.25
Matches are distributed among these distances:
18 4 0.11
19 3 0.08
20 3 0.08
21 6 0.16
22 12 0.32
23 3 0.08
24 3 0.08
25 3 0.08
ACGTcount: A:0.31, C:0.24, G:0.07, T:0.38
Consensus pattern (22 bp):
TCTTCTCAACATAGAATCAATC
Found at i:6122184 original size:95 final size:95
Alignment explanation
Indices: 6122021--6122214 Score: 388
Period size: 95 Copynumber: 2.0 Consensus size: 95
6122011 CTCCTAAGAC
6122021 TTCATTATATAGGTTGAGTATATAGAAATTTAAATATTTTAATAAATTTTAGTAGATAGATATTT
1 TTCATTATATAGGTTGAGTATATAGAAATTTAAATATTTTAATAAATTTTAGTAGATAGATATTT
6122086 TTATTGAAAATTACAACTAAGTTTCCACTG
66 TTATTGAAAATTACAACTAAGTTTCCACTG
6122116 TTCATTATATAGGTTGAGTATATAGAAATTTAAATATTTTAATAAATTTTAGTAGATAGATATTT
1 TTCATTATATAGGTTGAGTATATAGAAATTTAAATATTTTAATAAATTTTAGTAGATAGATATTT
6122181 TTATTGAAAATTACAACTAAGTTTCCACTG
66 TTATTGAAAATTACAACTAAGTTTCCACTG
6122211 TTCA
1 TTCA
6122215 ATAAGTATGA
Statistics
Matches: 99, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
95 99 1.00
ACGTcount: A:0.39, C:0.07, G:0.11, T:0.43
Consensus pattern (95 bp):
TTCATTATATAGGTTGAGTATATAGAAATTTAAATATTTTAATAAATTTTAGTAGATAGATATTT
TTATTGAAAATTACAACTAAGTTTCCACTG
Found at i:6123937 original size:23 final size:23
Alignment explanation
Indices: 6123906--6123954 Score: 64
Period size: 23 Copynumber: 2.0 Consensus size: 23
6123896 ATTTTTTTCA
6123906 ATTTATATTATTATC-ATTTTTATTT
1 ATTTAT-TTATT-TCTA-TTTTATTT
6123931 ATTTATTTATTTCTATTTTATTT
1 ATTTATTTATTTCTATTTTATTT
6123954 A
1 A
6123955 CTCATATGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
23 11 0.48
24 6 0.26
25 6 0.26
ACGTcount: A:0.27, C:0.04, G:0.00, T:0.69
Consensus pattern (23 bp):
ATTTATTTATTTCTATTTTATTT
Found at i:6124613 original size:41 final size:41
Alignment explanation
Indices: 6124536--6124615 Score: 108
Period size: 41 Copynumber: 2.0 Consensus size: 41
6124526 TATAAGTTTA
* * *
6124536 AGCCTATCATAACATATTCTATCTTAACATTCCAACCTAAT
1 AGCCTATCATAACATATTATATCTCAAAATTCCAACCTAAT
*
6124577 AGCCTATCATTACATATTATATCTCAATAATT-CAACCTA
1 AGCCTATCATAACATATTATATCTCAA-AATTCCAACCTA
6124616 TAACCCAATA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
41 31 0.91
42 3 0.09
ACGTcount: A:0.38, C:0.25, G:0.03, T:0.35
Consensus pattern (41 bp):
AGCCTATCATAACATATTATATCTCAAAATTCCAACCTAAT
Found at i:6126167 original size:31 final size:31
Alignment explanation
Indices: 6126129--6126226 Score: 101
Period size: 31 Copynumber: 3.2 Consensus size: 31
6126119 CGTATGAACG
* *
6126129 AAATTAAACAAAATTGTAAAGTAC-ATGGATT
1 AAATTAAACAAAATTCTAAAGTACAAT-GACT
* * *
6126160 AAATTAAACAAAACTCTATAGTCCAATGACT
1 AAATTAAACAAAATTCTAAAGTACAATGACT
* *
6126191 AAATTAAACAAAATTCTACAA-TATAATGATT
1 AAATTAAACAAAATTCTA-AAGTACAATGACT
6126222 AAATT
1 AAATT
6126227 GAGCAAGCTT
Statistics
Matches: 55, Mismatches: 10, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
31 52 0.95
32 3 0.05
ACGTcount: A:0.52, C:0.11, G:0.07, T:0.30
Consensus pattern (31 bp):
AAATTAAACAAAATTCTAAAGTACAATGACT
Found at i:6129026 original size:2 final size:2
Alignment explanation
Indices: 6129019--6129068 Score: 91
Period size: 2 Copynumber: 25.0 Consensus size: 2
6129009 TTTGTTCATC
*
6129019 AT AT AT AT AN 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
6129061 AT AT AT AT
1 AT AT AT AT
6129069 TTTCATGCAT
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:6138143 original size:15 final size:16
Alignment explanation
Indices: 6138123--6138165 Score: 52
Period size: 16 Copynumber: 2.7 Consensus size: 16
6138113 ACATAAAATT
*
6138123 AAAATAACTCACT-TA
1 AAAATAACTAACTATA
*
6138138 AAAATAAACTAATTATA
1 AAAAT-AACTAACTATA
6138155 AAAATAACTAA
1 AAAATAACTAA
6138166 AAATAAATAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
15 5 0.21
16 12 0.50
17 7 0.29
ACGTcount: A:0.63, C:0.12, G:0.00, T:0.26
Consensus pattern (16 bp):
AAAATAACTAACTATA
Found at i:6151316 original size:4 final size:4
Alignment explanation
Indices: 6151309--6151446 Score: 141
Period size: 4 Copynumber: 34.5 Consensus size: 4
6151299 TGTGTGTGTT
* * * *
6151309 TATA TATA TATA TATA TATG TATG TATA TATA TATA TATG TATG TATA
1 TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA
* * * * *
6151357 TATA TATA TATA TGTA TGTA TATA TATA TATA TGTA TGTA TGTA TATA
1 TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA
* * * * * *
6151405 TATA TGTA TGTA TGTA TATA TATA TATG TATG TATG TATA TA
1 TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TA
6151447 CAAATGGGCA
Statistics
Matches: 122, Mismatches: 12, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
4 122 1.00
ACGTcount: A:0.39, C:0.00, G:0.11, T:0.50
Consensus pattern (4 bp):
TATA
Found at i:6151338 original size:20 final size:20
Alignment explanation
Indices: 6151313--6151446 Score: 214
Period size: 20 Copynumber: 6.5 Consensus size: 20
6151303 TGTGTTTATA
6151313 TATATATATATATATGTATG
1 TATATATATATATATGTATG
6151333 TATATATATATATATGTATG
1 TATATATATATATATGTATG
6151353 TATATATATATATATATGTATG
1 --TATATATATATATATGTATG
6151375 TATATATATATATATGTATG
1 TATATATATATATATGTATG
*
6151395 TATGTATATATATATGTATG
1 TATATATATATATATGTATG
6151415 TATGTATATATATATATGTATG
1 TA--TATATATATATATGTATG
*
6151437 TATGTATATA
1 TATATATATA
6151447 CAAATGGGCA
Statistics
Matches: 107, Mismatches: 3, Indels: 8
0.91 0.03 0.07
Matches are distributed among these distances:
20 68 0.64
22 39 0.36
ACGTcount: A:0.39, C:0.00, G:0.11, T:0.50
Consensus pattern (20 bp):
TATATATATATATATGTATG
Found at i:6151370 original size:42 final size:42
Alignment explanation
Indices: 6151311--6151446 Score: 227
Period size: 42 Copynumber: 3.1 Consensus size: 42
6151301 TGTGTGTTTA
6151311 TATATATATATATATATGTATGTATATATATATATATGTATG
1 TATATATATATATATATGTATGTATATATATATATATGTATG
6151353 TATATATATATATATATGTATGTATATATATATATATGTATG
1 TATATATATATATATATGTATGTATATATATATATATGTATG
*
6151395 TATGTATATATATATGTATGTATGTATATATATATATGTATGTATG
1 TA--TATATATATATATATGTATGTATATATATATA--TATGTATG
6151441 TATATA
1 TATATA
6151447 CAAATGGGCA
Statistics
Matches: 89, Mismatches: 1, Indels: 6
0.93 0.01 0.06
Matches are distributed among these distances:
42 44 0.49
44 35 0.39
46 10 0.11
ACGTcount: A:0.39, C:0.00, G:0.11, T:0.50
Consensus pattern (42 bp):
TATATATATATATATATGTATGTATATATATATATATGTATG
Found at i:6151998 original size:57 final size:58
Alignment explanation
Indices: 6151937--6152061 Score: 144
Period size: 57 Copynumber: 2.2 Consensus size: 58
6151927 TCACGCAGTA
* ** * * *
6151937 CACATGTTTAGCATTAAGCCTTGTTAGATAGACAT-CAAGCATGTATCTTACTCATTG
1 CACATGTCTAGCACCAAGCCTTGCTAGATAGACATCCAAGCACGTATCTTACTCACTG
* * *
6151994 CACATGTCTAGCACCAAGCCTTGCTATATAGGCATCCCAAGCACGTGTCTTACTCACTG
1 CACATGTCTAGCACCAAGCCTTGCTAGATAGACAT-CCAAGCACGTATCTTACTCACTG
*
6152053 CACGTGTCT
1 CACATGTCT
6152062 GATTATATAT
Statistics
Matches: 56, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
57 29 0.52
59 27 0.48
ACGTcount: A:0.26, C:0.26, G:0.17, T:0.30
Consensus pattern (58 bp):
CACATGTCTAGCACCAAGCCTTGCTAGATAGACATCCAAGCACGTATCTTACTCACTG
Done.