Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr11
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: 61124829
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1263459 characters in sequence are not A, C, G, or T
File 203 of 205
Found at i:60194075 original size:20 final size:20
Alignment explanation
Indices: 60194047--60194093 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
60194037 ATGATTACAT
* *
60194047 ATATATATATAAATTATAAA
1 ATATATATAGAAAGTATAAA
* *
60194067 ATATGTATAGAAAGTATAAT
1 ATATATATAGAAAGTATAAA
60194087 ATATATA
1 ATATATA
60194094 CGTACATATA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.55, C:0.00, G:0.06, T:0.38
Consensus pattern (20 bp):
ATATATATAGAAAGTATAAA
Found at i:60194119 original size:50 final size:50
Alignment explanation
Indices: 60193959--60194120 Score: 118
Period size: 50 Copynumber: 3.1 Consensus size: 50
60193949 AGAAATTATA
* *
60193959 AAATATGGATAGAAAGTATAATATATATATATACGTACATATATATATAAGTTAAT
1 AAATATGTATAGAAAG--T-ATA-ATATATATACGTAC--ATATATATAAGATAAT
* * * * *
60194015 AAATATATAGATCATAAAG-A-AA-ATGAT-TACATATATATATATAA-ATTAT
1 AAATATGT--AT-AGAAAGTATAATAT-ATATACGTACATATATATAAGATAAT
*
60194064 AAAATATGTATAGAAAGTATAATATATATACGTACATATATATAAGGTAAT
1 -AAATATGTATAGAAAGTATAATATATATACGTACATATATATAAGATAAT
60194115 AAATAT
1 AAATAT
60194121 ATAAATCATA
Statistics
Matches: 83, Mismatches: 13, Indels: 26
0.68 0.11 0.21
Matches are distributed among these distances:
47 5 0.06
48 3 0.04
49 7 0.08
50 40 0.48
51 3 0.04
52 7 0.08
53 3 0.04
54 1 0.01
55 1 0.01
56 6 0.07
58 2 0.02
59 5 0.06
ACGTcount: A:0.52, C:0.04, G:0.09, T:0.35
Consensus pattern (50 bp):
AAATATGTATAGAAAGTATAATATATATACGTACATATATATAAGATAAT
Found at i:60194123 original size:100 final size:104
Alignment explanation
Indices: 60193939--60194151 Score: 301
Period size: 100 Copynumber: 2.1 Consensus size: 104
60193929 AATAAAAAAA
*
60193939 ATATACATATAGAAATTATAAAATATGGATAGAAAGTATAATATATATATATACGTACATATATA
1 ATATATATATAGAAATTATAAAATATGGATAGAAAG-ATAATATATATATATACGTACA-ATATA
* * *
60194004 TATAAGTTAATAAATATATAGATCATAAAGAA-AATGATTAC
64 TATAAGGTAATAAATATATAAATCATAAA-AATAATAATTAC
* *
60194045 ATATATATATATAAATTATAAAATATGTATAGAAAG-T-ATA-ATATATATACGTAC-ATATATA
1 ATATATATATAGAAATTATAAAATATGGATAGAAAGATAATATATATATATACGTACAATATATA
*
60194106 TAAGGTAATAAATATATAAATCATAAAAATAATAATTAT
66 TAAGGTAATAAATATATAAATCATAAAAATAATAATTAC
60194145 ATATATA
1 ATATATA
60194152 AACTTAAAAA
Statistics
Matches: 99, Mismatches: 7, Indels: 8
0.87 0.06 0.07
Matches are distributed among these distances:
99 2 0.02
100 46 0.46
102 14 0.14
103 3 0.03
104 1 0.01
106 33 0.33
ACGTcount: A:0.54, C:0.04, G:0.08, T:0.35
Consensus pattern (104 bp):
ATATATATATAGAAATTATAAAATATGGATAGAAAGATAATATATATATATACGTACAATATATA
TAAGGTAATAAATATATAAATCATAAAAATAATAATTAC
Found at i:60194735 original size:19 final size:19
Alignment explanation
Indices: 60194711--60194802 Score: 121
Period size: 19 Copynumber: 4.8 Consensus size: 19
60194701 AATCATATCT
*
60194711 TCTAAGATTGTATATCATA
1 TCTAAGATTGCATATCATA
*
60194730 TCTAAGATTACATATCATA
1 TCTAAGATTGCATATCATA
** *
60194749 TCTAAGATTATATATTATA
1 TCTAAGATTGCATATCATA
* *
60194768 TCTAAGATTGCATATAATG
1 TCTAAGATTGCATATCATA
60194787 TCTAAGATTGCATATC
1 TCTAAGATTGCATATC
60194803 CCTAAAGATT
Statistics
Matches: 64, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 64 1.00
ACGTcount: A:0.38, C:0.12, G:0.10, T:0.40
Consensus pattern (19 bp):
TCTAAGATTGCATATCATA
Found at i:60194763 original size:38 final size:38
Alignment explanation
Indices: 60194688--60194795 Score: 126
Period size: 38 Copynumber: 2.7 Consensus size: 38
60194678 AAATTAAATC
* *
60194688 TCTAAGATTACAAAATCATATCTTCTAAGATTGTATATCATA
1 TCTAAGATTAC-ATATCATA---TCTAAGATTATATATCATA
*
60194730 TCTAAGATTACATATCATATCTAAGATTATATATTATA
1 TCTAAGATTACATATCATATCTAAGATTATATATCATA
* * *
60194768 TCTAAGATTGCATATAATGTCTAAGATT
1 TCTAAGATTACATATCATATCTAAGATT
60194796 GCATATCCCT
Statistics
Matches: 60, Mismatches: 6, Indels: 4
0.86 0.09 0.06
Matches are distributed among these distances:
38 42 0.70
41 7 0.12
42 11 0.18
ACGTcount: A:0.40, C:0.12, G:0.08, T:0.40
Consensus pattern (38 bp):
TCTAAGATTACATATCATATCTAAGATTATATATCATA
Found at i:60202729 original size:19 final size:17
Alignment explanation
Indices: 60202705--60202750 Score: 56
Period size: 20 Copynumber: 2.5 Consensus size: 17
60202695 TATTCTTTAG
*
60202705 AATTTTTTTAAACTATTAT
1 AATTTTTTTAAA--AATAT
60202724 AATTTTTTTTAAAAATAT
1 AA-TTTTTTTAAAAATAT
60202742 AATTTTTTT
1 AATTTTTTT
60202751 GAATTTTTGA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
17 7 0.28
18 6 0.24
19 2 0.08
20 10 0.40
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (17 bp):
AATTTTTTTAAAAATAT
Found at i:60202742 original size:18 final size:19
Alignment explanation
Indices: 60202707--60202750 Score: 63
Period size: 18 Copynumber: 2.3 Consensus size: 19
60202697 TTCTTTAGAA
*
60202707 TTTTTTTAAACTATTATAAT
1 TTTTTTTAAAC-AATATAAT
60202727 TTTTTTTAAA-AATATAAT
1 TTTTTTTAAACAATATAAT
60202745 TTTTTT
1 TTTTTT
60202751 GAATTTTTGA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 13 0.57
20 10 0.43
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (19 bp):
TTTTTTTAAACAATATAAT
Found at i:60202768 original size:11 final size:11
Alignment explanation
Indices: 60202742--60202792 Score: 54
Period size: 13 Copynumber: 4.6 Consensus size: 11
60202732 TTAAAAATAT
60202742 AATTTTTTTG-
1 AATTTTTTTGA
60202752 AA--TTTTTGAA
1 AATTTTTTTG-A
60202762 AATTTTTTTGA
1 AATTTTTTTGA
60202773 AATTTTTTTTTGA
1 AA--TTTTTTTGA
60202786 AATTTTT
1 AATTTTT
60202793 GTTAAGAGAG
Statistics
Matches: 35, Mismatches: 0, Indels: 11
0.76 0.00 0.24
Matches are distributed among these distances:
8 6 0.17
10 4 0.11
11 8 0.23
12 6 0.17
13 11 0.31
ACGTcount: A:0.27, C:0.00, G:0.08, T:0.65
Consensus pattern (11 bp):
AATTTTTTTGA
Found at i:60202771 original size:12 final size:12
Alignment explanation
Indices: 60202754--60202792 Score: 53
Period size: 12 Copynumber: 3.2 Consensus size: 12
60202744 TTTTTTTGAA
60202754 TTTTTGAAAATT
1 TTTTTGAAAATT
*
60202766 TTTTTGAAATTTT
1 TTTTTGAAA-ATT
60202779 TTTTTG-AAATT
1 TTTTTGAAAATT
60202790 TTT
1 TTT
60202793 GTTAAGAGAG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
11 5 0.21
12 11 0.46
13 8 0.33
ACGTcount: A:0.26, C:0.00, G:0.08, T:0.67
Consensus pattern (12 bp):
TTTTTGAAAATT
Found at i:60202780 original size:13 final size:13
Alignment explanation
Indices: 60202754--60202792 Score: 62
Period size: 13 Copynumber: 3.1 Consensus size: 13
60202744 TTTTTTTGAA
*
60202754 TTTTTGAAA-ATT
1 TTTTTGAAATTTT
60202766 TTTTTGAAATTTT
1 TTTTTGAAATTTT
60202779 TTTTTGAAATTTT
1 TTTTTGAAATTTT
60202792 T
1 T
60202793 GTTAAGAGAG
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
12 9 0.36
13 16 0.64
ACGTcount: A:0.26, C:0.00, G:0.08, T:0.67
Consensus pattern (13 bp):
TTTTTGAAATTTT
Found at i:60208685 original size:2 final size:2
Alignment explanation
Indices: 60208678--60208702 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
60208668 CTCATCCTCA
60208678 TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC T
60208703 GAGTTTTATG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:60208858 original size:2 final size:2
Alignment explanation
Indices: 60208853--60208896 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
60208843 ATATACCCCT
60208853 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
60208895 CA
1 CA
60208897 TATATTTATA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:60215462 original size:38 final size:38
Alignment explanation
Indices: 60215420--60215492 Score: 130
Period size: 38 Copynumber: 1.9 Consensus size: 38
60215410 GTAATAGAAC
60215420 AATTCAACACTAGCAGTCA-ACATGCTTAACATGTATTT
1 AATTCAACACTAGCAGT-AGACATGCTTAACATGTATTT
60215458 AATTCAACACTAGCAGTAGACATGCTTAACATGTA
1 AATTCAACACTAGCAGTAGACATGCTTAACATGTA
60215493 ATCAGTAGGG
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
37 1 0.03
38 33 0.97
ACGTcount: A:0.38, C:0.21, G:0.12, T:0.29
Consensus pattern (38 bp):
AATTCAACACTAGCAGTAGACATGCTTAACATGTATTT
Found at i:60230066 original size:20 final size:20
Alignment explanation
Indices: 60230037--60230076 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
60230027 TTTTCCATAG
* *
60230037 AATAATATAACATTAAAATA
1 AATAAAATAAAATTAAAATA
*
60230057 AATAAAATAAAATTAGAATA
1 AATAAAATAAAATTAAAATA
60230077 TTGAATTGAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.68, C:0.03, G:0.03, T:0.28
Consensus pattern (20 bp):
AATAAAATAAAATTAAAATA
Found at i:60230987 original size:15 final size:16
Alignment explanation
Indices: 60230958--60231003 Score: 51
Period size: 15 Copynumber: 2.9 Consensus size: 16
60230948 ATTCTTGACT
* *
60230958 CTTATAAATTCAAAAA
1 CTTAAAAATTAAAAAA
60230974 -TTAAAAATTAAAAAA
1 CTTAAAAATTAAAAAA
60230989 CTTTAAAAA-TAAAAA
1 C-TTAAAAATTAAAAA
60231004 TTATTTAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
15 13 0.50
16 6 0.23
17 7 0.27
ACGTcount: A:0.65, C:0.07, G:0.00, T:0.28
Consensus pattern (16 bp):
CTTAAAAATTAAAAAA
Found at i:60234379 original size:16 final size:16
Alignment explanation
Indices: 60234358--60234425 Score: 109
Period size: 16 Copynumber: 4.2 Consensus size: 16
60234348 TTTGGTTCGC
*
60234358 TGTATTAGATTAGAGG
1 TGTATTGGATTAGAGG
60234374 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
*
60234390 TGTAATGGATTAGAGG
1 TGTATTGGATTAGAGG
*
60234406 TGTATTGGAATAGAGG
1 TGTATTGGATTAGAGG
60234422 TGTA
1 TGTA
60234426 ATAGCAAATC
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 48 1.00
ACGTcount: A:0.29, C:0.00, G:0.35, T:0.35
Consensus pattern (16 bp):
TGTATTGGATTAGAGG
Found at i:60234465 original size:45 final size:41
Alignment explanation
Indices: 60234406--60234515 Score: 116
Period size: 45 Copynumber: 2.6 Consensus size: 41
60234396 GGATTAGAGG
*
60234406 TGTATTGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGTT
1 TGTAATGGAATAGAGGTGTAATAGCAAATCAACTGTTTGG-T
* * ***
60234448 GAATGTAATGGAATAGAGGCGTAATAG-TAATCTTGTGTTTGGT
1 ---TGTAATGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGT
60234491 TG-AATGGAATAGAGGTGTAATAGCA
1 TGTAATGGAATAGAGGTGTAATAGCA
60234516 TAATGGAAAA
Statistics
Matches: 56, Mismatches: 8, Indels: 7
0.79 0.11 0.10
Matches are distributed among these distances:
39 20 0.36
40 2 0.04
43 1 0.02
44 11 0.20
45 22 0.39
ACGTcount: A:0.33, C:0.05, G:0.29, T:0.33
Consensus pattern (41 bp):
TGTAATGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGT
Found at i:60234678 original size:16 final size:16
Alignment explanation
Indices: 60234641--60234682 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
60234631 TTAATCATAT
*
60234641 TTAAACATA-ATTATTA
1 TTAAA-ATATATTATAA
60234657 TT-AAATATATTATAA
1 TTAAAATATATTATAA
60234672 TTAAAATATAT
1 TTAAAATATAT
60234683 AATTTAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 3 0.13
15 10 0.43
16 10 0.43
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (16 bp):
TTAAAATATATTATAA
Found at i:60234689 original size:14 final size:15
Alignment explanation
Indices: 60234650--60234691 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
60234640 TTTAAACATA
*
60234650 ATTATTATTAAATAT
1 ATTATAATTAAATAT
60234665 ATTATAATTAAA-AT
1 ATTATAATTAAATAT
*
60234679 A-TATAATTTAATA
1 ATTATAATTAAATA
60234692 AAATTCTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 9 0.38
14 4 0.17
15 11 0.46
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
ATTATAATTAAATAT
Found at i:60234809 original size:14 final size:15
Alignment explanation
Indices: 60234760--60234811 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
60234750 ATAAAATATA
60234760 AATTAACATA-ATTAT
1 AATTAA-ATATATTAT
*
60234775 TATTAAATATATTAT
1 AATTAAATATATTAT
60234790 AATTAAA-ATA-TAT
1 AATTAAATATATTAT
*
60234803 AATTTAATA
1 AATTAAATA
60234812 AAATTCTTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
13 9 0.28
14 7 0.22
15 16 0.50
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (15 bp):
AATTAAATATATTAT
Found at i:60237831 original size:11 final size:11
Alignment explanation
Indices: 60237815--60237840 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
60237805 TCGGGAGGCA
60237815 AAGGTAGAACG
1 AAGGTAGAACG
60237826 AAGGTAGAACG
1 AAGGTAGAACG
60237837 AAGG
1 AAGG
60237841 AAGAGGCGAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.46, C:0.08, G:0.38, T:0.08
Consensus pattern (11 bp):
AAGGTAGAACG
Found at i:60247794 original size:18 final size:17
Alignment explanation
Indices: 60247773--60247828 Score: 51
Period size: 18 Copynumber: 3.2 Consensus size: 17
60247763 CAAATAAGAC
*
60247773 AATAATAACAATAATGAA
1 AATAATAA-AATAATAAA
*
60247791 AATAAATAAAATTATAAA
1 AAT-AATAAAATAATAAA
*
60247809 AATAA-AAATAAAATAAA
1 AATAATAAA-ATAATAAA
60247826 AAT
1 AAT
60247829 CTATGTATAT
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
16 3 0.09
17 11 0.34
18 13 0.41
19 5 0.16
ACGTcount: A:0.73, C:0.02, G:0.02, T:0.23
Consensus pattern (17 bp):
AATAATAAAATAATAAA
Found at i:60247977 original size:6 final size:6
Alignment explanation
Indices: 60247966--60247994 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
60247956 TTAAAAACAT
60247966 ATATAG ATATAG ATATAG ATATAG ATATA
1 ATATAG ATATAG ATATAG ATATAG ATATA
60247995 TAGGTGCGTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.14, T:0.34
Consensus pattern (6 bp):
ATATAG
Found at i:60248306 original size:28 final size:28
Alignment explanation
Indices: 60248241--60248308 Score: 68
Period size: 28 Copynumber: 2.4 Consensus size: 28
60248231 ATTATTATAC
*
60248241 ATGAAAGTATATGTAAGTATGTATTAAAAT
1 ATGAAA-TATATGTAAGTA-GTATAAAAAT
* *
60248271 ATG-TATATATGTAGGTA-TATAAAAATT
1 ATGAAATATATGTAAGTAGTATAAAAA-T
60248298 ATGAAATATAT
1 ATGAAATATAT
60248309 AAAAAAAGAT
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
26 7 0.22
27 4 0.12
28 17 0.53
29 1 0.03
30 3 0.09
ACGTcount: A:0.47, C:0.00, G:0.15, T:0.38
Consensus pattern (28 bp):
ATGAAATATATGTAAGTAGTATAAAAAT
Found at i:60250857 original size:23 final size:23
Alignment explanation
Indices: 60250831--60250878 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
60250821 TAGGGTTGAT
60250831 TTAATAAAAGTTAATCAACTTTC
1 TTAATAAAAGTTAATCAACTTTC
60250854 TTAATAAAAGTTAATCAACTTTC
1 TTAATAAAAGTTAATCAACTTTC
60250877 TT
1 TT
60250879 TTGGTATTCT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.42, C:0.12, G:0.04, T:0.42
Consensus pattern (23 bp):
TTAATAAAAGTTAATCAACTTTC
Found at i:60252326 original size:43 final size:43
Alignment explanation
Indices: 60252278--60252440 Score: 229
Period size: 43 Copynumber: 3.8 Consensus size: 43
60252268 TACAAAAACA
* *
60252278 CCGCTAAAGAACATGATCTTTAGCGGCGCTTTTGTAGCAAATG
1 CCGCTAAAGAACATGACCTTTAGCGGCGCTTTTATAGCAAATG
* * * *
60252321 CCGCTAAAGAACAGGACCTTTAGCGGCGCTTTTCTAGTAAACG
1 CCGCTAAAGAACATGACCTTTAGCGGCGCTTTTATAGCAAATG
* * *
60252364 CTGCTAAAGAACATGATCTTTAGCGGCGTTTTTATCA-CAAATG
1 CCGCTAAAGAACATGACCTTTAGCGGCGCTTTTAT-AGCAAATG
60252407 CCGCTAAAGAACATGACCTTTAGCGGCGCTTTTA
1 CCGCTAAAGAACATGACCTTTAGCGGCGCTTTTA
60252441 ACGACGCTTT
Statistics
Matches: 104, Mismatches: 15, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
43 103 0.99
44 1 0.01
ACGTcount: A:0.28, C:0.23, G:0.21, T:0.28
Consensus pattern (43 bp):
CCGCTAAAGAACATGACCTTTAGCGGCGCTTTTATAGCAAATG
Found at i:60252380 original size:86 final size:86
Alignment explanation
Indices: 60252280--60252439 Score: 277
Period size: 86 Copynumber: 1.9 Consensus size: 86
60252270 CAAAAACACC
*
60252280 GCTAAAGAACATGATCTTTAGCGGCGCTTTTGT-AGCAAATGCCGCTAAAGAACAGGACCTTTAG
1 GCTAAAGAACATGATCTTTAGCGGCGCTTTTATCA-CAAATGCCGCTAAAGAACAGGACCTTTAG
60252344 CGGCGCTTTTCTAGTAAACGCT
65 CGGCGCTTTTCTAGTAAACGCT
* *
60252366 GCTAAAGAACATGATCTTTAGCGGCGTTTTTATCACAAATGCCGCTAAAGAACATGACCTTTAGC
1 GCTAAAGAACATGATCTTTAGCGGCGCTTTTATCACAAATGCCGCTAAAGAACAGGACCTTTAGC
60252431 GGCGCTTTT
66 GGCGCTTTT
60252440 AACGACGCTT
Statistics
Matches: 70, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
86 69 0.99
87 1 0.01
ACGTcount: A:0.28, C:0.22, G:0.22, T:0.28
Consensus pattern (86 bp):
GCTAAAGAACATGATCTTTAGCGGCGCTTTTATCACAAATGCCGCTAAAGAACAGGACCTTTAGC
GGCGCTTTTCTAGTAAACGCT
Found at i:60252775 original size:21 final size:21
Alignment explanation
Indices: 60252751--60252800 Score: 100
Period size: 21 Copynumber: 2.4 Consensus size: 21
60252741 TTCTACTCTG
60252751 CTCTGCTTCCCTCGTTGCTGC
1 CTCTGCTTCCCTCGTTGCTGC
60252772 CTCTGCTTCCCTCGTTGCTGC
1 CTCTGCTTCCCTCGTTGCTGC
60252793 CTCTGCTT
1 CTCTGCTT
60252801 TAAGTTGTAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.00, C:0.42, G:0.18, T:0.40
Consensus pattern (21 bp):
CTCTGCTTCCCTCGTTGCTGC
Found at i:60258343 original size:43 final size:43
Alignment explanation
Indices: 60258294--60258445 Score: 188
Period size: 43 Copynumber: 3.6 Consensus size: 43
60258284 TATAATTAAA
* *
60258294 TTATGTAACTTATGATATGATATATATTTATGTATTATGCAAG
1 TTATGTAAGTTATGATATGATATATATTTATGTATTATGTAAG
* * *
60258337 TTATGTAAGTTATGATATGATATACA--TAAG--TTATGTGAG
1 TTATGTAAGTTATGATATGATATATATTTATGTATTATGTAAG
* *
60258376 TTATGTAAGTTACGATATGATATATTTTTATGTATTATGTAAG
1 TTATGTAAGTTATGATATGATATATATTTATGTATTATGTAAG
*
60258419 TTATGTAAGTTGA-GTTATGATATATAT
1 TTATGTAAGTT-ATGATATGATATATAT
60258446 AAGTTATTAA
Statistics
Matches: 92, Mismatches: 12, Indels: 10
0.81 0.11 0.09
Matches are distributed among these distances:
39 30 0.33
41 6 0.07
43 55 0.60
44 1 0.01
ACGTcount: A:0.34, C:0.03, G:0.17, T:0.46
Consensus pattern (43 bp):
TTATGTAAGTTATGATATGATATATATTTATGTATTATGTAAG
Found at i:60258346 original size:9 final size:9
Alignment explanation
Indices: 60258328--60258489 Score: 73
Period size: 9 Copynumber: 17.7 Consensus size: 9
60258318 TATTTATGTA
*
60258328 TTATGCAAG
1 TTATGTAAG
60258337 TTATGTAAG
1 TTATGTAAG
*
60258346 TTATGATATG
1 TTATG-TAAG
**
60258356 ATATACATAAG
1 -T-TATGTAAG
*
60258367 TTATGTGAG
1 TTATGTAAG
60258376 TTATGTAAG
1 TTATGTAAG
* *
60258385 TTACGATATG
1 TTATG-TAAG
* * **
60258395 ATATAT-TT
1 TTATGTAAG
60258403 TTATGT-A-
1 TTATGTAAG
60258410 TTATGTAAG
1 TTATGTAAG
60258419 TTATGTAAG
1 TTATGTAAG
*
60258428 TTGA-GTTATG
1 TT-ATG-TAAG
*
60258438 ATATATATAAG
1 -T-TATGTAAG
60258449 TTAT-TAAG
1 TTATGTAAG
*
60258457 TTATGTATG
1 TTATGTAAG
*
60258466 TTATGTGAG
1 TTATGTAAG
*
60258475 TTATGTATG
1 TTATGTAAG
60258484 TTATGT
1 TTATGT
60258490 GGAAATTAGT
Statistics
Matches: 115, Mismatches: 26, Indels: 24
0.70 0.16 0.15
Matches are distributed among these distances:
7 6 0.05
8 14 0.12
9 69 0.60
10 14 0.12
11 9 0.08
12 3 0.03
ACGTcount: A:0.32, C:0.02, G:0.20, T:0.46
Consensus pattern (9 bp):
TTATGTAAG
Found at i:60258438 original size:82 final size:81
Alignment explanation
Indices: 60258279--60258468 Score: 256
Period size: 82 Copynumber: 2.3 Consensus size: 81
60258269 ATGGTTATTT
* * *
60258279 ATAAGTATAATTAAATTATGTAACTTATGATATGATATATATTTATGTATTATGCAAGTTATGTA
1 ATAAGT-T-ATTAAGTTATGTAAGTTACGATATGATATATATTTATGTATTATGCAAGTTATGTA
60258344 AGTTATGATATGATATAC
64 AGTTATGATATGATATAC
* * *
60258362 ATAAGTTATGTGAGTTATGTAAGTTACGATATGATATATTTTTATGTATTATGTAAGTTATGTAA
1 ATAAGTTAT-TAAGTTATGTAAGTTACGATATGATATATATTTATGTATTATGCAAGTTATGTAA
* *
60258427 GTTGA-GTTATGATATAT
65 GTT-ATGATATGATATAC
*
60258444 ATAAGTTATTAAGTTATGTATGTTA
1 ATAAGTTATTAAGTTATGTAAGTTA
60258469 TGTGAGTTAT
Statistics
Matches: 95, Mismatches: 10, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
81 16 0.17
82 72 0.76
83 7 0.07
ACGTcount: A:0.36, C:0.02, G:0.16, T:0.45
Consensus pattern (81 bp):
ATAAGTTATTAAGTTATGTAAGTTACGATATGATATATATTTATGTATTATGCAAGTTATGTAAG
TTATGATATGATATAC
Found at i:60258469 original size:47 final size:44
Alignment explanation
Indices: 60258294--60258477 Score: 124
Period size: 43 Copynumber: 4.3 Consensus size: 44
60258284 TATAATTAAA
* * *
60258294 TTATGTAACTTATGATATGATATATAT-TTATGT-A-TTATGCAAG
1 TTATGTAAGTTACGATATGATATAT-TGTTATGTAAGTTATG-TAG
* *
60258337 TTATGTAAGTTATGATATGATATA----CA--TAAGTTATGTGAG
1 TTATGTAAGTTACGATATGATATATTGTTATGTAAGTTATGT-AG
*
60258376 TTATGTAAGTTACGATATGATATATTTTTATGT-A-TTATGTAAG
1 TTATGTAAGTTACGATATGATATATTGTTATGTAAGTTATGT-AG
*
60258419 TTATGTAAGTTGA-GTTATGATATATATAAGTTAT-TAAGTTATGTATG
1 TTATGTAAGTT-ACGATATGATATAT-T--GTTATGTAAGTTATGTA-G
*
60258466 TTATGTGAGTTA
1 TTATGTAAGTTA
60258478 TGTATGTTAT
Statistics
Matches: 116, Mismatches: 9, Indels: 29
0.75 0.06 0.19
Matches are distributed among these distances:
37 1 0.01
38 1 0.01
39 31 0.27
43 54 0.47
44 3 0.03
45 2 0.02
46 7 0.06
47 17 0.15
ACGTcount: A:0.34, C:0.02, G:0.18, T:0.46
Consensus pattern (44 bp):
TTATGTAAGTTACGATATGATATATTGTTATGTAAGTTATGTAG
Found at i:60258652 original size:34 final size:34
Alignment explanation
Indices: 60258614--60258678 Score: 94
Period size: 34 Copynumber: 1.9 Consensus size: 34
60258604 ATAATATTTA
* *
60258614 AAAATAAATAATTATATATAATATTTAAAAATAT
1 AAAATAAAGAATTATATATAAAATTTAAAAATAT
* *
60258648 AAAATAAAGAATTATGTTTAAAATTTAAAAA
1 AAAATAAAGAATTATATATAAAATTTAAAAA
60258679 GTTAATAGTA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
34 27 1.00
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (34 bp):
AAAATAAAGAATTATATATAAAATTTAAAAATAT
Found at i:60260544 original size:11 final size:12
Alignment explanation
Indices: 60260511--60260544 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
60260501 AACAAACGGC
60260511 CCAAGCAAAAATG
1 CCAA-CAAAAATG
60260524 CCAACAAAAATG
1 CCAACAAAAATG
60260536 CCAACAAAA
1 CCAACAAAA
60260545 GAATATGACC
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 17 0.81
13 4 0.19
ACGTcount: A:0.59, C:0.26, G:0.09, T:0.06
Consensus pattern (12 bp):
CCAACAAAAATG
Found at i:60260681 original size:23 final size:22
Alignment explanation
Indices: 60260655--60260776 Score: 113
Period size: 23 Copynumber: 5.3 Consensus size: 22
60260645 CAGGTCAGTT
60260655 GGGAAATTGGGGAAATGAAATCG
1 GGGAAATTGGGGAAATGAAAT-G
*
60260678 GGGAAATTAGGGGAAAATG-AATT
1 GGGAAATT-GGGG-AAATGAAATG
*
60260701 GGGAAATTGGGGAAATTAAATCG
1 GGGAAATTGGGGAAATGAAAT-G
** *
60260724 AAGAAATTGGGGGAATAGGAAAT-
1 GGGAAATT-GGGGAA-ATGAAATG
*
60260747 GGGAAATTAGGGAAATGAAATTG
1 GGGAAATTGGGGAAATGAAA-TG
60260770 GGGAAAT
1 GGGAAAT
60260777 CTGAGTGGGG
Statistics
Matches: 80, Mismatches: 11, Indels: 16
0.75 0.10 0.15
Matches are distributed among these distances:
21 9 0.11
22 13 0.16
23 35 0.44
24 13 0.16
25 10 0.12
ACGTcount: A:0.43, C:0.02, G:0.36, T:0.20
Consensus pattern (22 bp):
GGGAAATTGGGGAAATGAAATG
Found at i:60260722 original size:46 final size:46
Alignment explanation
Indices: 60260653--60260776 Score: 167
Period size: 46 Copynumber: 2.7 Consensus size: 46
60260643 GACAGGTCAG
*
60260653 TTGGGAAATTGGGGAAATGAAATCGGGGAAATTAGGGGAAAATGAA
1 TTGGGAAATTGGGGAAATGAAATCGGGGAAATTAGGGGAAAAGGAA
* ** * *
60260699 TTGGGAAATTGGGGAAATTAAATCGAAGAAATTGGGGGAATAGGAA
1 TTGGGAAATTGGGGAAATGAAATCGGGGAAATTAGGGGAAAAGGAA
* * *
60260745 ATGGGAAATTAGGGAAATGAAATTGGGGAAAT
1 TTGGGAAATTGGGGAAATGAAATCGGGGAAAT
60260777 CTGAGTGGGG
Statistics
Matches: 66, Mismatches: 12, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
46 66 1.00
ACGTcount: A:0.42, C:0.02, G:0.35, T:0.21
Consensus pattern (46 bp):
TTGGGAAATTGGGGAAATGAAATCGGGGAAATTAGGGGAAAAGGAA
Found at i:60260987 original size:74 final size:75
Alignment explanation
Indices: 60260894--60261032 Score: 226
Period size: 74 Copynumber: 1.9 Consensus size: 75
60260884 ATCACAGTTA
*
60260894 AAAACGACAACGTTTAGCAAACACTTAAAACATAATTGCGGC-ATTTTAGTAAAAACGCCACTAA
1 AAAACGACAACGTCTAGCAAACACTTAAAACATAATTGCGGCGATTTTAGTAAAAACGCCACTAA
60260958 AAACGTATAT
66 AAACGTATAT
* * * *
60260968 AAAACGACAATGTCTAGCAAACACTTAAAACATAATTGTGGCGTTTTTCGTAAAAACGCCACTAA
1 AAAACGACAACGTCTAGCAAACACTTAAAACATAATTGCGGCGATTTTAGTAAAAACGCCACTAA
60261033 CACATATCCT
Statistics
Matches: 59, Mismatches: 5, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
74 39 0.66
75 20 0.34
ACGTcount: A:0.44, C:0.19, G:0.13, T:0.24
Consensus pattern (75 bp):
AAAACGACAACGTCTAGCAAACACTTAAAACATAATTGCGGCGATTTTAGTAAAAACGCCACTAA
AAACGTATAT
Found at i:60261136 original size:116 final size:115
Alignment explanation
Indices: 60260929--60261298 Score: 422
Period size: 116 Copynumber: 3.3 Consensus size: 115
60260919 TAAAACATAA
* * * * * *
60260929 TTGCGGCATTTTAGTAAAAACGCCACTAAAAACGTATATAAAACGACAATGTCTAGCAAACACTT
1 TTGCGGCGTTTTAGTAAAAACGCCACTAAAAACGCAAACAAAACAACAACGTCTAGCAAACACTT
* * *
60260994 AAAACATAATTGTGGCGTTTTTCGTAAAAACGCCACTAACACATATCCTT
66 AAAACATAATTGCGGCGTTTTGCGTAAAAACACCACTAACACATATCCTT
*
60261044 TTGCGGCGTTTTAGTAAAAACGCCACTAAAAACGCAGAACAAAACAACAACGTTTAGCAAACACT
1 TTGCGGCGTTTTAGTAAAAACGCCACTAAAAACGCA-AACAAAACAACAACGTCTAGCAAACACT
* *
60261109 TAAAACATAATTGCGGCGTTTTGCGTAAAAATACCACTAGCACATATCCTT
65 TAAAACATAATTGCGGCGTTTTGCGTAAAAACACCACTAACACATATCCTT
** * * *
60261160 TTGTAGCGTTTTAGTAAAAACG---C-----A-G---ATAAAACGACAATGTCTAGCAAACACTT
1 TTGCGGCGTTTTAGTAAAAACGCCACTAAAAACGCAAACAAAACAACAACGTCTAGCAAACACTT
* * *** *
60261213 AAAACATGATTGCGGCATTTTTTTTAAAAACGCCACTAACACATATCCTT
66 AAAACATAATTGCGGCGTTTTGCGTAAAAACACCACTAACACATATCCTT
* *
60261263 TTGCAGCATTTTAGTAAAAACGCCACTAAAAACGCA
1 TTGCGGCGTTTTAGTAAAAACGCCACTAAAAACGCA
60261299 GATAAAACGA
Statistics
Matches: 215, Mismatches: 28, Indels: 25
0.80 0.10 0.09
Matches are distributed among these distances:
103 86 0.40
106 1 0.00
107 1 0.00
108 1 0.00
111 1 0.00
112 1 0.00
113 1 0.00
115 34 0.16
116 89 0.41
ACGTcount: A:0.39, C:0.21, G:0.14, T:0.26
Consensus pattern (115 bp):
TTGCGGCGTTTTAGTAAAAACGCCACTAAAAACGCAAACAAAACAACAACGTCTAGCAAACACTT
AAAACATAATTGCGGCGTTTTGCGTAAAAACACCACTAACACATATCCTT
Found at i:60261263 original size:103 final size:104
Alignment explanation
Indices: 60261070--60261285 Score: 299
Period size: 103 Copynumber: 2.1 Consensus size: 104
60261060 AAAACGCCAC
* *
60261070 TAAAAACGCAGAACAAAACAACAACGTTTAGCAAACACTTAAAACATAATTGCGGCGTTTTGCGT
1 TAAAAACGCAGAACAAAACAACAACGTCTAGCAAACACTTAAAACATAATTGCGGCATTTTGCGT
* * * *
60261135 AAAAATACCACTAGCACATATCCTTTTGTAGCGTTTTAG
66 AAAAACACCACTAACACATATCCTTTTGCAGCATTTTAG
* * * * ***
60261174 TAAAAACGCAG-ATAAAACGACAATGTCTAGCAAACACTTAAAACATGATTGCGGCATTTTTTTT
1 TAAAAACGCAGAACAAAACAACAACGTCTAGCAAACACTTAAAACATAATTGCGGCATTTTGCGT
*
60261238 AAAAACGCCACTAACACATATCCTTTTGCAGCATTTTAG
66 AAAAACACCACTAACACATATCCTTTTGCAGCATTTTAG
60261277 TAAAAACGC
1 TAAAAACGC
60261286 CACTAAAAAC
Statistics
Matches: 98, Mismatches: 14, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
103 87 0.89
104 11 0.11
ACGTcount: A:0.40, C:0.20, G:0.13, T:0.26
Consensus pattern (104 bp):
TAAAAACGCAGAACAAAACAACAACGTCTAGCAAACACTTAAAACATAATTGCGGCATTTTGCGT
AAAAACACCACTAACACATATCCTTTTGCAGCATTTTAG
Found at i:60261495 original size:7 final size:7
Alignment explanation
Indices: 60261485--60261859 Score: 109
Period size: 7 Copynumber: 52.7 Consensus size: 7
60261475 ATATAAAATT
60261485 TAAACCC
1 TAAACCC
*
60261492 TAAACCA
1 TAAACCC
*
60261499 TAAGCCCC
1 TAA-ACCC
60261507 T-AACCC
1 TAAACCC
*
60261513 ATAAACCT
1 -TAAACCC
*
60261521 TAAGCCC
1 TAAACCC
*
60261528 ATAACCCC
1 -TAAACCC
**
60261536 TAAAATC
1 TAAACCC
* *
60261543 TAAGCTCT
1 TAAAC-CC
60261551 TAAACCC
1 TAAACCC
60261558 TAAACCC
1 TAAACCC
*
60261565 TAAACAC
1 TAAACCC
*
60261572 TAAACCA
1 TAAACCC
60261579 TAAA-CC
1 TAAACCC
* *
60261585 TATACCT
1 TAAACCC
*
60261592 TAAACCA
1 TAAACCC
*
60261599 TAAACAC
1 TAAACCC
*
60261606 TAAACTC
1 TAAACCC
* *
60261613 TTAACAC
1 TAAACCC
* *
60261620 TAAATCA
1 TAAACCC
* *
60261627 TAAAACT
1 TAAACCC
**
60261634 TAAACTT
1 TAAACCC
*
60261641 TAAACCA
1 TAAACCC
60261648 TAAA-CC
1 TAAACCC
*
60261654 TACACCC
1 TAAACCC
**
60261661 TAAACTA
1 TAAACCC
*
60261668 TAAACAC
1 TAAACCC
60261675 TAAACCC
1 TAAACCC
* *
60261682 TAAGCCAA
1 TAAACC-C
*
60261690 TAACCCC
1 TAAACCC
*
60261697 TAGACCC
1 TAAACCC
*
60261704 TAAGCCC
1 TAAACCC
60261711 -ATAACCC
1 TA-AACCC
*
60261718 TTAAACCA
1 -TAAACCC
*
60261726 TAAATCCT
1 TAAA-CCC
60261734 TAAACCC
1 TAAACCC
* *
60261741 TAAATCT
1 TAAACCC
*
60261748 TAAGCCAC
1 TAAACC-C
60261756 T-AACCC
1 TAAACCC
*
60261762 TAGACCC
1 TAAACCC
*
60261769 TAAGCCC
1 TAAACCC
60261776 -ATAACCC
1 TA-AACCC
60261783 TTAAACCC
1 -TAAACCC
**
60261791 TAAGTTCC
1 TAA-ACCC
*
60261799 T-AACCTT
1 TAAACC-C
*
60261806 TAAACAC
1 TAAACCC
*
60261813 TAAACAC
1 TAAACCC
*
60261820 TAAACCA
1 TAAACCC
*
60261827 TAAACTAC
1 TAAAC-CC
**
60261835 -AAACTG
1 TAAACCC
*
60261841 TAAACCA
1 TAAACCC
60261848 TAAACCC
1 TAAACCC
60261855 TAAAC
1 TAAAC
60261860 TCAAAACTCT
Statistics
Matches: 260, Mismatches: 86, Indels: 44
0.67 0.22 0.11
Matches are distributed among these distances:
6 16 0.06
7 198 0.76
8 44 0.17
9 2 0.01
ACGTcount: A:0.44, C:0.33, G:0.03, T:0.21
Consensus pattern (7 bp):
TAAACCC
Found at i:60261567 original size:22 final size:22
Alignment explanation
Indices: 60261484--60261608 Score: 80
Period size: 22 Copynumber: 5.8 Consensus size: 22
60261474 AATATAAAAT
*
60261484 TTAAACCCTAAACCATAAGCCC
1 TTAAACCCTAAACCCTAAGCCC
* *
60261506 CT-AACCCATAAACCTTAAGCCC
1 TTAAACCC-TAAACCCTAAGCCC
* * ** *
60261528 ATAACCCCTAAAATCTAAGCTC
1 TTAAACCCTAAACCCTAAGCCC
* *
60261550 TTAAACCCTAAACCCTAAACAC
1 TTAAACCCTAAACCCTAAGCCC
*
60261572 -TAAACCATAAA-CCTATA--CC
1 TTAAACCCTAAACCCTA-AGCCC
* *
60261591 TTAAACCATAAACACTAA
1 TTAAACCCTAAACCCTAA
60261609 ACTCTTAACA
Statistics
Matches: 81, Mismatches: 17, Indels: 12
0.74 0.15 0.11
Matches are distributed among these distances:
19 1 0.01
20 16 0.20
21 19 0.23
22 41 0.51
23 4 0.05
ACGTcount: A:0.44, C:0.34, G:0.02, T:0.20
Consensus pattern (22 bp):
TTAAACCCTAAACCCTAAGCCC
Found at i:60261595 original size:20 final size:21
Alignment explanation
Indices: 60261549--60261616 Score: 77
Period size: 20 Copynumber: 3.2 Consensus size: 21
60261539 AATCTAAGCT
*
60261549 CTTAAACCCTAAACCCTAAACA
1 CTTAAACCATAAA-CCTAAACA
*
60261571 C-TAAACCATAAACCTATAC-
1 CTTAAACCATAAACCTAAACA
*
60261590 CTTAAACCATAAACACTAAACT
1 CTTAAACCATAAAC-CTAAACA
60261612 CTTAA
1 CTTAA
60261617 CACTAAATCA
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
19 1 0.03
20 18 0.45
21 15 0.38
22 6 0.15
ACGTcount: A:0.47, C:0.31, G:0.00, T:0.22
Consensus pattern (21 bp):
CTTAAACCATAAACCTAAACA
Found at i:60261610 original size:48 final size:48
Alignment explanation
Indices: 60261551--60261665 Score: 142
Period size: 48 Copynumber: 2.4 Consensus size: 48
60261541 TCTAAGCTCT
*
60261551 TAAACCCTAAACCCTAAACACTAAACCAT-AAACCTATACCTTAAACCA
1 TAAA-CCTAAACCCTAAACACTAAACCATAAAACCTAAACCTTAAACCA
* * * * *
60261599 TAAACACTAAACTCTTAACACTAAATCATAAAACTTAAACTTTAAACCA
1 TAAAC-CTAAACCCTAAACACTAAACCATAAAACCTAAACCTTAAACCA
*
60261648 TAAACCTACACCCTAAAC
1 TAAACCTAAACCCTAAAC
60261666 TATAAACACT
Statistics
Matches: 56, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
47 1 0.02
48 34 0.61
49 21 0.38
ACGTcount: A:0.49, C:0.30, G:0.00, T:0.22
Consensus pattern (48 bp):
TAAACCTAAACCCTAAACACTAAACCATAAAACCTAAACCTTAAACCA
Found at i:60261703 original size:22 final size:22
Alignment explanation
Indices: 60261674--60261794 Score: 102
Period size: 22 Copynumber: 5.5 Consensus size: 22
60261664 ACTATAAACA
60261674 CTAAACCCTAAGCCAATAACCC
1 CTAAACCCTAAGCCAATAACCC
* *
60261696 CTAGACCCTAAGCCCATAACCC
1 CTAAACCCTAAGCCAATAACCC
* * * * *
60261718 TTAAACCATAAATCC-TTAAACC
1 CTAAACCCT-AAGCCAATAACCC
* * *
60261740 CTAAATCTTAAGCCACTAA-CC
1 CTAAACCCTAAGCCAATAACCC
* *
60261761 CTAGACCCTAAGCCCATAACCC
1 CTAAACCCTAAGCCAATAACCC
*
60261783 TTAAACCCTAAG
1 CTAAACCCTAAG
60261795 TTCCTAACCT
Statistics
Matches: 76, Mismatches: 20, Indels: 6
0.75 0.20 0.06
Matches are distributed among these distances:
21 20 0.26
22 52 0.68
23 4 0.05
ACGTcount: A:0.38, C:0.37, G:0.06, T:0.19
Consensus pattern (22 bp):
CTAAACCCTAAGCCAATAACCC
Found at i:60261758 original size:15 final size:16
Alignment explanation
Indices: 60261716--60261758 Score: 56
Period size: 15 Copynumber: 2.9 Consensus size: 16
60261706 AGCCCATAAC
60261716 CCTTAAACCA-TAAAT
1 CCTTAAACCACTAAAT
60261731 CCTTAAACC-CTAAAT
1 CCTTAAACCACTAAAT
*
60261746 -CTTAAGCCACTAA
1 CCTTAAACCACTAA
60261759 CCCTAGACCC
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
14 7 0.28
15 18 0.72
ACGTcount: A:0.42, C:0.30, G:0.02, T:0.26
Consensus pattern (16 bp):
CCTTAAACCACTAAAT
Found at i:60261802 original size:22 final size:21
Alignment explanation
Indices: 60261675--60261815 Score: 97
Period size: 22 Copynumber: 6.5 Consensus size: 21
60261665 CTATAAACAC
* *
60261675 TAAACCCTAAGCCAATAACCCC
1 TAAACCCTAAGCC-CTAACCCT
*
60261697 TAGACCCTAAGCCCATAACCCT
1 TAAACCCTAAGCCC-TAACCCT
* * *
60261719 TAAACCATAAATCCTTAAACCC-
1 TAAACCCT-AAGCCCT-AACCCT
* *
60261741 TAAATCTTAAGCCACTAACCC-
1 TAAACCCTAAGCC-CTAACCCT
*
60261762 TAGACCCTAAGCCCATAACCCT
1 TAAACCCTAAGCCC-TAACCCT
* *
60261784 TAAACCCTAAGTTCCTAACCTT
1 TAAACCCTAAG-CCCTAACCCT
*
60261806 TAAACACTAA
1 TAAACCCTAA
60261816 ACACTAAACC
Statistics
Matches: 94, Mismatches: 18, Indels: 14
0.75 0.14 0.11
Matches are distributed among these distances:
20 1 0.01
21 25 0.27
22 57 0.61
23 11 0.12
ACGTcount: A:0.38, C:0.35, G:0.05, T:0.21
Consensus pattern (21 bp):
TAAACCCTAAGCCCTAACCCT
Found at i:60261860 original size:21 final size:21
Alignment explanation
Indices: 60261806--60261866 Score: 70
Period size: 21 Copynumber: 2.9 Consensus size: 21
60261796 TCCTAACCTT
*
60261806 TAAACACTAAACACTAAACCA
1 TAAACACTAAACTCTAAACCA
*
60261827 TAAACTAC-AAACTGTAAACCA
1 TAAAC-ACTAAACTCTAAACCA
* *
60261848 TAAACCCTAAACTCAAAAC
1 TAAACACTAAACTCTAAAC
60261867 TCTAATCCCA
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
20 1 0.03
21 30 0.91
22 2 0.06
ACGTcount: A:0.54, C:0.28, G:0.02, T:0.16
Consensus pattern (21 bp):
TAAACACTAAACTCTAAACCA
Found at i:60266820 original size:46 final size:46
Alignment explanation
Indices: 60266763--60266860 Score: 160
Period size: 46 Copynumber: 2.1 Consensus size: 46
60266753 GCTATTTGCT
* *
60266763 GTGTAGGTTCAATCCTAACGGATGACCAGACACTATTATTTGATTC
1 GTGTAGGTTCAACCCTAACGGATGACCAGACACTATTATCTGATTC
* *
60266809 GTGTAGGTTCAACCCTAATGGATGACCAGACACTATTATCTGATTT
1 GTGTAGGTTCAACCCTAACGGATGACCAGACACTATTATCTGATTC
60266855 GTGTAG
1 GTGTAG
60266861 TATGATTTCT
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
46 48 1.00
ACGTcount: A:0.28, C:0.18, G:0.21, T:0.33
Consensus pattern (46 bp):
GTGTAGGTTCAACCCTAACGGATGACCAGACACTATTATCTGATTC
Found at i:60268953 original size:494 final size:494
Alignment explanation
Indices: 60268026--60269013 Score: 1976
Period size: 494 Copynumber: 2.0 Consensus size: 494
60268016 GGTTGTGATA
60268026 TAAAATGGTTAAAAACTTTTATATGAATTGTATTTGAATTGAATTTATTGAATTGCAGGTGCAAA
1 TAAAATGGTTAAAAACTTTTATATGAATTGTATTTGAATTGAATTTATTGAATTGCAGGTGCAAA
60268091 TAAGGGCATATTGGTTGTATGTTAAAATGATTAGGTGAATTGGTGTTTTAGATTTGAATTATGAA
66 TAAGGGCATATTGGTTGTATGTTAAAATGATTAGGTGAATTGGTGTTTTAGATTTGAATTATGAA
60268156 TGTTTTGGTGTTGGTTTGAATAGCATGAAATGACATCATAGGTCACTTAAGGAAATGGTATGAAA
131 TGTTTTGGTGTTGGTTTGAATAGCATGAAATGACATCATAGGTCACTTAAGGAAATGGTATGAAA
60268221 GCTTGCTCAAATAGGTCATTTTTGTTGCACATGGGCTACCACACGATCGTGTGTCACACATGGTT
196 GCTTGCTCAAATAGGTCATTTTTGTTGCACATGGGCTACCACACGATCGTGTGTCACACATGGTT
60268286 GGATGACACAGCTGTGTGTTCAACATGTTCAGGGTGATATTTAGGTCACACGGCTACAGAGAGTT
261 GGATGACACAGCTGTGTGTTCAACATGTTCAGGGTGATATTTAGGTCACACGGCTACAGAGAGTT
60268351 ACACGGCCTAGCGACACGGCCGTATAACCCTACACACACGGTCTGAGTTGTTTCGCACAGCCGTG
326 ACACGGCCTAGCGACACGGCCGTATAACCCTACACACACGGTCTGAGTTGTTTCGCACAGCCGTG
60268416 TGACCCCTATTTTACTATTTACCTATCTTTTTGTAAAAGTTTCAAAATGGTCCTAATTTAGTTTC
391 TGACCCCTATTTTACTATTTACCTATCTTTTTGTAAAAGTTTCAAAATGGTCCTAATTTAGTTTC
60268481 AAGCCGATTTAAGAGCTTTTTTAAGCTTGATTAAGACTC
456 AAGCCGATTTAAGAGCTTTTTTAAGCTTGATTAAGACTC
60268520 TAAAATGGTTAAAAACTTTTATATGAATTGTATTTGAATTGAATTTATTGAATTGCAGGTGCAAA
1 TAAAATGGTTAAAAACTTTTATATGAATTGTATTTGAATTGAATTTATTGAATTGCAGGTGCAAA
60268585 TAAGGGCATATTGGTTGTATGTTAAAATGATTAGGTGAATTGGTGTTTTAGATTTGAATTATGAA
66 TAAGGGCATATTGGTTGTATGTTAAAATGATTAGGTGAATTGGTGTTTTAGATTTGAATTATGAA
60268650 TGTTTTGGTGTTGGTTTGAATAGCATGAAATGACATCATAGGTCACTTAAGGAAATGGTATGAAA
131 TGTTTTGGTGTTGGTTTGAATAGCATGAAATGACATCATAGGTCACTTAAGGAAATGGTATGAAA
60268715 GCTTGCTCAAATAGGTCATTTTTGTTGCACATGGGCTACCACACGATCGTGTGTCACACATGGTT
196 GCTTGCTCAAATAGGTCATTTTTGTTGCACATGGGCTACCACACGATCGTGTGTCACACATGGTT
60268780 GGATGACACAGCTGTGTGTTCAACATGTTCAGGGTGATATTTAGGTCACACGGCTACAGAGAGTT
261 GGATGACACAGCTGTGTGTTCAACATGTTCAGGGTGATATTTAGGTCACACGGCTACAGAGAGTT
60268845 ACACGGCCTAGCGACACGGCCGTATAACCCTACACACACGGTCTGAGTTGTTTCGCACAGCCGTG
326 ACACGGCCTAGCGACACGGCCGTATAACCCTACACACACGGTCTGAGTTGTTTCGCACAGCCGTG
60268910 TGACCCCTATTTTACTATTTACCTATCTTTTTGTAAAAGTTTCAAAATGGTCCTAATTTAGTTTC
391 TGACCCCTATTTTACTATTTACCTATCTTTTTGTAAAAGTTTCAAAATGGTCCTAATTTAGTTTC
60268975 AAGCCGATTTAAGAGCTTTTTTAAGCTTGATTAAGACTC
456 AAGCCGATTTAAGAGCTTTTTTAAGCTTGATTAAGACTC
60269014 AATTTTTGTT
Statistics
Matches: 494, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
494 494 1.00
ACGTcount: A:0.29, C:0.15, G:0.22, T:0.34
Consensus pattern (494 bp):
TAAAATGGTTAAAAACTTTTATATGAATTGTATTTGAATTGAATTTATTGAATTGCAGGTGCAAA
TAAGGGCATATTGGTTGTATGTTAAAATGATTAGGTGAATTGGTGTTTTAGATTTGAATTATGAA
TGTTTTGGTGTTGGTTTGAATAGCATGAAATGACATCATAGGTCACTTAAGGAAATGGTATGAAA
GCTTGCTCAAATAGGTCATTTTTGTTGCACATGGGCTACCACACGATCGTGTGTCACACATGGTT
GGATGACACAGCTGTGTGTTCAACATGTTCAGGGTGATATTTAGGTCACACGGCTACAGAGAGTT
ACACGGCCTAGCGACACGGCCGTATAACCCTACACACACGGTCTGAGTTGTTTCGCACAGCCGTG
TGACCCCTATTTTACTATTTACCTATCTTTTTGTAAAAGTTTCAAAATGGTCCTAATTTAGTTTC
AAGCCGATTTAAGAGCTTTTTTAAGCTTGATTAAGACTC
Found at i:60274412 original size:30 final size:30
Alignment explanation
Indices: 60274376--60274434 Score: 118
Period size: 30 Copynumber: 2.0 Consensus size: 30
60274366 TTCTTTGTCA
60274376 TGTTTGTTAGTTAATTTTAGTTTTTAATCG
1 TGTTTGTTAGTTAATTTTAGTTTTTAATCG
60274406 TGTTTGTTAGTTAATTTTAGTTTTTAATC
1 TGTTTGTTAGTTAATTTTAGTTTTTAATC
60274435 AATCACTCGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.20, C:0.03, G:0.15, T:0.61
Consensus pattern (30 bp):
TGTTTGTTAGTTAATTTTAGTTTTTAATCG
Found at i:60274895 original size:46 final size:46
Alignment explanation
Indices: 60274842--60275164 Score: 513
Period size: 46 Copynumber: 7.0 Consensus size: 46
60274832 ACATTGCTAT
*
60274842 AACTCAGTATGGTTTTCTTCA-CGAAAATACCATACCTACTTTTCAC
1 AACTCAGTATGGTTTTCTTCACCG-AAACACCATACCTACTTTTCAC
* * * *
60274888 AACTCAGTATGGTTTTCTTTACCGAAATACCATACATAATTTTCAC
1 AACTCAGTATGGTTTTCTTCACCGAAACACCATACCTACTTTTCAC
* *
60274934 AACTCAGTATGGTTTTCTTTACCGAAACACCATACCTACTTTTAAC
1 AACTCAGTATGGTTTTCTTCACCGAAACACCATACCTACTTTTCAC
** *
60274980 AACTCAGTATGGTTTTCTTCAAGGAAATACCATACCTACTTTTCAC
1 AACTCAGTATGGTTTTCTTCACCGAAACACCATACCTACTTTTCAC
** *
60275026 AACTCAGTATGGTTTTCTTCATTGAAACACCATACCTACTTTTCAT
1 AACTCAGTATGGTTTTCTTCACCGAAACACCATACCTACTTTTCAC
60275072 AACTCAGTATGGTTTTCTTCACCGAAACACCATACCTACTTTTCAC
1 AACTCAGTATGGTTTTCTTCACCGAAACACCATACCTACTTTTCAC
60275118 AACTCAGTATGGTTTTCTTCACCGAAACACCATACCTACTTTTCAC
1 AACTCAGTATGGTTTTCTTCACCGAAACACCATACCTACTTTTCAC
60275164 A
1 A
60275165 CTTTGCCATG
Statistics
Matches: 257, Mismatches: 19, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
46 255 0.99
47 2 0.01
ACGTcount: A:0.30, C:0.26, G:0.09, T:0.35
Consensus pattern (46 bp):
AACTCAGTATGGTTTTCTTCACCGAAACACCATACCTACTTTTCAC
Found at i:60281908 original size:60 final size:60
Alignment explanation
Indices: 60281791--60281911 Score: 145
Period size: 60 Copynumber: 2.0 Consensus size: 60
60281781 AGTTGAGTGG
* *** *
60281791 CCATTTTGTAACTTTTCGTAGTTGGATGACCAAAAAAGAAATTTACTAAAAGCTGGATGA
1 CCATTTTGTAACTTTTCATAGTTGGATGACCAAAAAAGAAAAAAAATAAAAGCTGGATGA
* * * *
60281851 CCATTTTGTAACTTTTCATAGTTGCG-TGACCAAAAAGGAAAAAAAATCATAGTTGGATGA
1 CCATTTTGTAACTTTTCATAGTTG-GATGACCAAAAAAGAAAAAAAATAAAAGCTGGATGA
60281911 C
1 C
60281912 TATCAAAGTA
Statistics
Matches: 51, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
60 50 0.98
61 1 0.02
ACGTcount: A:0.37, C:0.14, G:0.18, T:0.31
Consensus pattern (60 bp):
CCATTTTGTAACTTTTCATAGTTGGATGACCAAAAAAGAAAAAAAATAAAAGCTGGATGA
Found at i:60289042 original size:21 final size:22
Alignment explanation
Indices: 60289013--60289059 Score: 78
Period size: 21 Copynumber: 2.2 Consensus size: 22
60289003 CAGAAGGAGT
*
60289013 GAGTAGTACTTCGCAGCAGGTG
1 GAGTAGTACTCCGCAGCAGGTG
60289035 GAGT-GTACTCCGCAGCAGGTG
1 GAGTAGTACTCCGCAGCAGGTG
60289056 GAGT
1 GAGT
60289060 TTGAGCAGAG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.21, C:0.19, G:0.38, T:0.21
Consensus pattern (22 bp):
GAGTAGTACTCCGCAGCAGGTG
Found at i:60294843 original size:3 final size:3
Alignment explanation
Indices: 60294837--60294917 Score: 54
Period size: 3 Copynumber: 27.0 Consensus size: 3
60294827 TAAAAAAATT
** * * * * *
60294837 TAA TAA TAA TAA TAA TAA TAA TGG TAT TAT TAA TAA TAA TGA TGA TGA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* ** * *
60294885 TGA TGG TAT TAA TAA TAA TAA TAA CAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
60294918 AAATCTTAAA
Statistics
Matches: 66, Mismatches: 12, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
3 66 1.00
ACGTcount: A:0.53, C:0.01, G:0.10, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:60296646 original size:21 final size:21
Alignment explanation
Indices: 60296622--60296664 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
60296612 CCGCCAGTGA
*
60296622 TCATGTCGTTGCGGGTGTTCC
1 TCATGTCGCTGCGGGTGTTCC
* *
60296643 TCATGTCGCTGCTGTTGTTCC
1 TCATGTCGCTGCGGGTGTTCC
60296664 T
1 T
60296665 TCTATCGTTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.05, C:0.26, G:0.28, T:0.42
Consensus pattern (21 bp):
TCATGTCGCTGCGGGTGTTCC
Found at i:60297986 original size:29 final size:29
Alignment explanation
Indices: 60297932--60298013 Score: 119
Period size: 29 Copynumber: 2.8 Consensus size: 29
60297922 GCATTTAAAA
*
60297932 ACACACGGTCATGTGAACAGCCCGTGTGTG
1 ACACACGGTCGTGTG-ACAGCCCGTGTGTG
* *
60297962 ACACACGGTTGTGTGGCAGCCCGTGTGTG
1 ACACACGGTCGTGTGACAGCCCGTGTGTG
*
60297991 ACACATGGTCGTGTGACAGCCCG
1 ACACACGGTCGTGTGACAGCCCG
60298014 GGTCTTAAGC
Statistics
Matches: 46, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
29 33 0.72
30 13 0.28
ACGTcount: A:0.20, C:0.27, G:0.33, T:0.21
Consensus pattern (29 bp):
ACACACGGTCGTGTGACAGCCCGTGTGTG
Found at i:60298328 original size:29 final size:29
Alignment explanation
Indices: 60298286--60298343 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
60298276 ATCATTCATC
60298286 CATTTCAACTTCAAATAAACACAAATCAA
1 CATTTCAACTTCAAATAAACACAAATCAA
60298315 CATTTCAACTTCAAATAAACACAAATCAA
1 CATTTCAACTTCAAATAAACACAAATCAA
60298344 GTCAAGAATC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.52, C:0.24, G:0.00, T:0.24
Consensus pattern (29 bp):
CATTTCAACTTCAAATAAACACAAATCAA
Found at i:60304490 original size:10 final size:10
Alignment explanation
Indices: 60304472--60304519 Score: 53
Period size: 10 Copynumber: 4.9 Consensus size: 10
60304462 TTTTTAGCAT
60304472 TTTAT-TTTA
1 TTTATCTTTA
60304481 TTTATCTTTA
1 TTTATCTTTA
60304491 TTTATCTTTA
1 TTTATCTTTA
* ** *
60304501 ATTAAATGTA
1 TTTATCTTTA
60304511 TTTATCTTT
1 TTTATCTTT
60304520 TAGGAATTTA
Statistics
Matches: 30, Mismatches: 8, Indels: 1
0.77 0.21 0.03
Matches are distributed among these distances:
9 5 0.17
10 25 0.83
ACGTcount: A:0.25, C:0.06, G:0.02, T:0.67
Consensus pattern (10 bp):
TTTATCTTTA
Found at i:60307392 original size:23 final size:23
Alignment explanation
Indices: 60307366--60307455 Score: 105
Period size: 23 Copynumber: 4.0 Consensus size: 23
60307356 GGCTCTGCCG
*
60307366 ATCAGGCACTTTATGTGTCGTAT
1 ATCAGGCACTTTATGTGTCATAT
60307389 ATCAGGCACTTTATGTGTCATAT
1 ATCAGGCACTTTATGTGTCATAT
* * ** *
60307412 TTCAGGCACCTCGTGTGTCGT-T
1 ATCAGGCACTTTATGTGTCATAT
60307434 -TCAGGCAC-TTATGTGTCATAT
1 ATCAGGCACTTTATGTGTCATAT
60307455 A
1 A
60307456 CTGATCAAGT
Statistics
Matches: 56, Mismatches: 9, Indels: 5
0.80 0.13 0.07
Matches are distributed among these distances:
20 8 0.14
21 9 0.16
22 1 0.02
23 38 0.68
ACGTcount: A:0.21, C:0.20, G:0.21, T:0.38
Consensus pattern (23 bp):
ATCAGGCACTTTATGTGTCATAT
Found at i:60307420 original size:46 final size:43
Alignment explanation
Indices: 60307367--60307454 Score: 122
Period size: 46 Copynumber: 2.0 Consensus size: 43
60307357 GCTCTGCCGA
* *
60307367 TCAGGCACTTTATGTGTCGTATATCAGGCACTTTATGTGTCATATT
1 TCAGGCACCTCATGTGTCGT-T-TCAGGCAC-TTATGTGTCATATT
*
60307413 TCAGGCACCTCGTGTGTCGTTTCAGGCACTTATGTGTCATAT
1 TCAGGCACCTCATGTGTCGTTTCAGGCACTTATGTGTCATAT
60307455 ACTGATCAAG
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
43 13 0.33
44 8 0.21
45 1 0.03
46 17 0.44
ACGTcount: A:0.19, C:0.20, G:0.22, T:0.39
Consensus pattern (43 bp):
TCAGGCACCTCATGTGTCGTTTCAGGCACTTATGTGTCATATT
Found at i:60314662 original size:32 final size:30
Alignment explanation
Indices: 60314609--60314675 Score: 75
Period size: 32 Copynumber: 2.1 Consensus size: 30
60314599 CTAAAACTAT
60314609 TTAAAATAATATAAAATATTATATTT-AAAAGA
1 TTAAAAT-ATATAAAATATTAT-TTTCAAAA-A
60314641 TTAAAAT-TATAAAATAAATTATTTTCAAAAA
1 TTAAAATATATAAAAT--ATTATTTTCAAAAA
60314672 TTAA
1 TTAA
60314676 GATTTATTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
30 8 0.25
31 8 0.25
32 16 0.50
ACGTcount: A:0.58, C:0.01, G:0.01, T:0.39
Consensus pattern (30 bp):
TTAAAATATATAAAATATTATTTTCAAAAA
Found at i:60317877 original size:18 final size:18
Alignment explanation
Indices: 60317854--60317891 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
60317844 TTAAACCTTT
60317854 TTGGCTTGTGTTTGGATG
1 TTGGCTTGTGTTTGGATG
60317872 TTGGCTTGTGTTTGGATG
1 TTGGCTTGTGTTTGGATG
60317890 TT
1 TT
60317892 AAGTGTATTG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.05, C:0.05, G:0.37, T:0.53
Consensus pattern (18 bp):
TTGGCTTGTGTTTGGATG
Found at i:60322490 original size:3 final size:3
Alignment explanation
Indices: 60322482--60322509 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
60322472 TTCTCTAGAG
60322482 AGA AGA AGA AGA AGA AGA AGA AGA AGA A
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA A
60322510 ACTGATACAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:60326068 original size:15 final size:16
Alignment explanation
Indices: 60326036--60326070 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
60326026 ACGGATTTAC
60326036 AAATAATATAAGTAAA
1 AAATAATATAAGTAAA
*
60326052 AAATAATAT-ATTAAA
1 AAATAATATAAGTAAA
60326067 AAAT
1 AAAT
60326071 GTGGTATTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 9 0.50
16 9 0.50
ACGTcount: A:0.69, C:0.00, G:0.03, T:0.29
Consensus pattern (16 bp):
AAATAATATAAGTAAA
Found at i:60329673 original size:16 final size:16
Alignment explanation
Indices: 60329652--60329685 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
60329642 TATGTTTAGT
*
60329652 ATAGAAGATAAGAAAA
1 ATAGAAGAAAAGAAAA
60329668 ATAGAAGAAAAGAAAA
1 ATAGAAGAAAAGAAAA
60329684 AT
1 AT
60329686 GTTTGTAATG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.71, C:0.00, G:0.18, T:0.12
Consensus pattern (16 bp):
ATAGAAGAAAAGAAAA
Found at i:60332184 original size:14 final size:14
Alignment explanation
Indices: 60332141--60332187 Score: 55
Period size: 14 Copynumber: 3.5 Consensus size: 14
60332131 AATTTAATTT
60332141 ATTTTTACAATTAC
1 ATTTTTACAATTAC
*
60332155 ATTTAT-C-A-TAC
1 ATTTTTACAATTAC
60332166 TATTTTTACAATTAC
1 -ATTTTTACAATTAC
60332181 ATTTTTA
1 ATTTTTA
60332188 TAATATAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 8
0.73 0.05 0.22
Matches are distributed among these distances:
11 3 0.11
12 6 0.22
13 2 0.07
14 13 0.48
15 3 0.11
ACGTcount: A:0.34, C:0.13, G:0.00, T:0.53
Consensus pattern (14 bp):
ATTTTTACAATTAC
Found at i:60334450 original size:1 final size:1
Alignment explanation
Indices: 60334441--60334471 Score: 53
Period size: 1 Copynumber: 31.0 Consensus size: 1
60334431 TTTTTTTTTT
*
60334441 GGGGAGGGGGGGGGGGGGGGGGGGGGGGGGG
1 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
60334472 TTGGGAAATC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
1 28 1.00
ACGTcount: A:0.03, C:0.00, G:0.97, T:0.00
Consensus pattern (1 bp):
G
Found at i:60337461 original size:16 final size:17
Alignment explanation
Indices: 60337440--60337473 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
60337430 GAAGAAGAAA
60337440 ATATTAAATT-ATTTTT
1 ATATTAAATTAATTTTT
*
60337456 ATATTATATTAATTTTT
1 ATATTAAATTAATTTTT
60337473 A
1 A
60337474 AATAATTAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (17 bp):
ATATTAAATTAATTTTT
Found at i:60341584 original size:44 final size:44
Alignment explanation
Indices: 60341521--60341608 Score: 167
Period size: 44 Copynumber: 2.0 Consensus size: 44
60341511 TTTATAATGC
60341521 AATAAGGGCCAGTTATACCCGAATAGGAGAGAAACCATCAACTT
1 AATAAGGGCCAGTTATACCCGAATAGGAGAGAAACCATCAACTT
*
60341565 AATAAGGGCTAGTTATACCCGAATAGGAGAGAAACCATCAACTT
1 AATAAGGGCCAGTTATACCCGAATAGGAGAGAAACCATCAACTT
60341609 TCTCCACTTG
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 43 1.00
ACGTcount: A:0.41, C:0.19, G:0.20, T:0.19
Consensus pattern (44 bp):
AATAAGGGCCAGTTATACCCGAATAGGAGAGAAACCATCAACTT
Found at i:60352089 original size:19 final size:18
Alignment explanation
Indices: 60352057--60352102 Score: 60
Period size: 19 Copynumber: 2.6 Consensus size: 18
60352047 TACCTTCTTT
60352057 TATATA-AT-ATATGAGA
1 TATATATATGATATGAGA
*
60352073 TATATGATATGATATGATA
1 TATAT-ATATGATATGAGA
60352092 TATATATATGA
1 TATATATATGA
60352103 CAGTTGCATG
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
16 5 0.19
17 1 0.04
18 8 0.31
19 12 0.46
ACGTcount: A:0.46, C:0.00, G:0.13, T:0.41
Consensus pattern (18 bp):
TATATATATGATATGAGA
Found at i:60365822 original size:36 final size:36
Alignment explanation
Indices: 60365775--60365848 Score: 139
Period size: 36 Copynumber: 2.1 Consensus size: 36
60365765 ACTTGATTAC
*
60365775 TATTTTATAGTAATTGACTTTTCATTAAGGAATATG
1 TATTTTATAGTAATTGACTTTTCATTAAGGAAGATG
60365811 TATTTTATAGTAATTGACTTTTCATTAAGGAAGATG
1 TATTTTATAGTAATTGACTTTTCATTAAGGAAGATG
60365847 TA
1 TA
60365849 ATGGTTACCA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.34, C:0.05, G:0.15, T:0.46
Consensus pattern (36 bp):
TATTTTATAGTAATTGACTTTTCATTAAGGAAGATG
Found at i:60374321 original size:31 final size:31
Alignment explanation
Indices: 60374296--60374414 Score: 105
Period size: 31 Copynumber: 3.8 Consensus size: 31
60374286 ACCACTTCAG
* * *
60374296 ATTGCCTAACAATGATGGTTTACCACCCTGA
1 ATTGCCCAACAACGATGGTTTACCACCCAGA
*
60374327 ATTGCCCAACAACGATGGTTTACCACCCCGA
1 ATTGCCCAACAACGATGGTTTACCACCCAGA
* * ** *
60374358 ATTGTCCGACAACGATGACTTACCATCTCA-A
1 ATTGCCCAACAACGATGGTTTACCA-CCCAGA
* * * *
60374389 ATTGCACGATAATGATGGTTTACCAC
1 ATTGCCCAACAACGATGGTTTACCAC
60374415 GGTAGTTAGA
Statistics
Matches: 72, Mismatches: 15, Indels: 3
0.80 0.17 0.03
Matches are distributed among these distances:
30 1 0.01
31 69 0.96
32 2 0.03
ACGTcount: A:0.30, C:0.28, G:0.16, T:0.26
Consensus pattern (31 bp):
ATTGCCCAACAACGATGGTTTACCACCCAGA
Found at i:60376466 original size:19 final size:19
Alignment explanation
Indices: 60376444--60376495 Score: 70
Period size: 19 Copynumber: 2.7 Consensus size: 19
60376434 CATACAAAAC
*
60376444 GCATCTTGGCGCACAAAGT
1 GCATCTTGGCACACAAAGT
*
60376463 GCATAC-TAGCACACAAAGT
1 GCAT-CTTGGCACACAAAGT
60376482 GCATCTTGGCACAC
1 GCATCTTGGCACAC
60376496 GGAGCGCGTA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
18 1 0.04
19 26 0.93
20 1 0.04
ACGTcount: A:0.31, C:0.29, G:0.21, T:0.19
Consensus pattern (19 bp):
GCATCTTGGCACACAAAGT
Found at i:60388146 original size:22 final size:20
Alignment explanation
Indices: 60388108--60388147 Score: 53
Period size: 22 Copynumber: 1.9 Consensus size: 20
60388098 TAACCATAAG
*
60388108 CTTAATTATTTATTTTTTAA
1 CTTAATTATTTAGTTTTTAA
60388128 CTTAATTTCATTTAGTTTTT
1 CTTAA-TT-ATTTAGTTTTT
60388148 CATATAATGT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 5 0.29
21 2 0.12
22 10 0.59
ACGTcount: A:0.25, C:0.07, G:0.03, T:0.65
Consensus pattern (20 bp):
CTTAATTATTTAGTTTTTAA
Found at i:60388270 original size:13 final size:13
Alignment explanation
Indices: 60388252--60388278 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
60388242 TGTTAACACT
60388252 AGGTACTATAATA
1 AGGTACTATAATA
60388265 AGGTACTATAATA
1 AGGTACTATAATA
60388278 A
1 A
60388279 AACACATTGA
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:0.48, C:0.07, G:0.15, T:0.30
Consensus pattern (13 bp):
AGGTACTATAATA
Found at i:60388420 original size:17 final size:17
Alignment explanation
Indices: 60388398--60388431 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
60388388 TAGAATTGGG
60388398 TTGAAAATTTTATTTAA
1 TTGAAAATTTTATTTAA
60388415 TTGAAAATTTTATTTAA
1 TTGAAAATTTTATTTAA
60388432 ATTAATTTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.41, C:0.00, G:0.06, T:0.53
Consensus pattern (17 bp):
TTGAAAATTTTATTTAA
Found at i:60394179 original size:42 final size:42
Alignment explanation
Indices: 60394111--60394229 Score: 143
Period size: 42 Copynumber: 2.8 Consensus size: 42
60394101 ATGCTAAATG
* * *
60394111 GAAACCTATAAGGGTTGAACGGAAGCTCATATGAGCTGAAC-
1 GAAACCCATTAGGGTTAAACGGAAGCTCATATGAGCTGAACT
* * *
60394152 GAAAACCCA-TAGGAGTTAAACTGAAGCTCAAAAGAGCTGAACT
1 G-AAACCCATTAGG-GTTAAACGGAAGCTCATATGAGCTGAACT
*
60394195 GAAACCCATTAGGGTTAAACGGAAACTCATATGAG
1 GAAACCCATTAGGGTTAAACGGAAGCTCATATGAG
60394230 TTAACTGGAG
Statistics
Matches: 64, Mismatches: 10, Indels: 7
0.79 0.12 0.09
Matches are distributed among these distances:
41 4 0.06
42 55 0.86
43 5 0.08
ACGTcount: A:0.40, C:0.18, G:0.24, T:0.18
Consensus pattern (42 bp):
GAAACCCATTAGGGTTAAACGGAAGCTCATATGAGCTGAACT
Found at i:60394232 original size:21 final size:21
Alignment explanation
Indices: 60394128--60394233 Score: 61
Period size: 21 Copynumber: 5.0 Consensus size: 21
60394118 ATAAGGGTTG
* * *
60394128 AACGGAAGCTCATATGAGCTG
1 AACGGAAACTCATATGAGTTA
* * *
60394149 AACGAAAACCCATAGGAGTTA
1 AACGGAAACTCATATGAGTTA
* * * * * *
60394170 AACTGAAGCTCAAAAGAGCTG
1 AACGGAAACTCATATGAGTTA
* * *
60394191 AACTGAAACCCAT-TAGGGTTA
1 AACGGAAACTCATAT-GAGTTA
60394212 AACGGAAACTCATATGAGTTA
1 AACGGAAACTCATATGAGTTA
60394233 A
1 A
60394234 CTGGAGCTCA
Statistics
Matches: 59, Mismatches: 24, Indels: 4
0.68 0.28 0.05
Matches are distributed among these distances:
21 58 0.98
22 1 0.02
ACGTcount: A:0.42, C:0.18, G:0.22, T:0.19
Consensus pattern (21 bp):
AACGGAAACTCATATGAGTTA
Found at i:60395976 original size:15 final size:15
Alignment explanation
Indices: 60395956--60396012 Score: 55
Period size: 15 Copynumber: 3.8 Consensus size: 15
60395946 TAGGTTGGAT
60395956 AATTAAATAATTATA
1 AATTAAATAATTATA
* *
60395971 AATTAAATAAATAAA
1 AATTAAATAATTATA
*
60395986 ATATTAATATAAGTAT-
1 A-ATTAA-ATAATTATA
60396002 AATTAAA-AATT
1 AATTAAATAATT
60396013 TTAGGTTAAG
Statistics
Matches: 35, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
13 3 0.09
14 1 0.03
15 19 0.54
16 6 0.17
17 6 0.17
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (15 bp):
AATTAAATAATTATA
Found at i:60401546 original size:20 final size:20
Alignment explanation
Indices: 60401482--60401549 Score: 59
Period size: 20 Copynumber: 3.4 Consensus size: 20
60401472 AAGTTAATAA
60401482 TTGGTATA-GTTTCATAATTT
1 TTGGTATATG-TTCATAATTT
* * **
60401502 TT-TTATATTTTCTCATAATAA
1 TTGGTATA-TGT-TCATAATTT
60401523 TTGGTATATGTTCATAATTT
1 TTGGTATATGTTCATAATTT
60401543 TTGGTAT
1 TTGGTAT
60401550 TCCCTTAGAT
Statistics
Matches: 36, Mismatches: 8, Indels: 8
0.69 0.15 0.15
Matches are distributed among these distances:
19 4 0.11
20 17 0.47
21 11 0.31
22 4 0.11
ACGTcount: A:0.26, C:0.06, G:0.12, T:0.56
Consensus pattern (20 bp):
TTGGTATATGTTCATAATTT
Found at i:60404197 original size:20 final size:20
Alignment explanation
Indices: 60404174--60404751 Score: 149
Period size: 20 Copynumber: 29.2 Consensus size: 20
60404164 CCCCTTACAA
60404174 TTTTTGGTACTTCCTCATAT
1 TTTTTGGTACTTCCTCATAT
* *
60404194 TTTTTTGTA-TTCCTTCATAA
1 TTTTTGGTACTTCC-TCATAT
*
60404214 TTTTTGGTACTTTCTCAT-T
1 TTTTTGGTACTTCCTCATAT
*
60404233 TTTTTAGTACTTCCTCATAT
1 TTTTTGGTACTTCCTCATAT
* * *
60404253 TTTATAGTA-TTCTCTTATAAT
1 TTTTTGGTACTTC-CTCAT-AT
* *
60404274 TTTTT-GTACTTTCTCTTAT
1 TTTTTGGTACTTCCTCATAT
* * * *
60404293 TTTTT-TTAATATTCCCTCGTAA
1 TTTTTGGT-A-CTT-CCTCATAT
* * *
60404315 TTTTTGGTATTTTCTCATAA
1 TTTTTGGTACTTCCTCATAT
** * *
60404335 TTTTTAATACATCATCATA-
1 TTTTTGGTACTTCCTCATAT
*
60404354 -TTTT--TACATCCTCATATT
1 TTTTTGGTACTTCCTCATA-T
** * *
60404372 TTTTTTATACTTTCTC-TTT
1 TTTTTGGTACTTCCTCATAT
*
60404391 GTTTTTGGTA-TTCTCTCATAA
1 -TTTTTGGTACTTC-CTCATAT
*
60404412 TCTTTGGATACTTCCTCATAT
1 TTTTTGG-TACTTCCTCATAT
* * * *
60404433 GTTTTGATA-TACCCTTC-TAA
1 TTTTTGGTACT-TCC-TCATAT
* * *
60404453 TTTTTAGTACATCTTCAT-T
1 TTTTTGGTACTTCCTCATAT
** * * *
60404472 TTTTTTATTCTTTCTCAGAT
1 TTTTTGGTACTTCCTCATAT
* *
60404492 TTTATAGTA-TTCTCTCATAAT
1 TTTTTGGTACTTC-CTCAT-AT
*
60404513 TTTTT-TTACTT-CTCA-ATT
1 TTTTTGGTACTTCCTCATA-T
*
60404531 TTTTTAGTA-TTCCCTCATAT
1 TTTTTGGTACTT-CCTCATAT
60404551 TTTTT-GTA-TTCTCTCATAAT
1 TTTTTGGTACTTC-CTCAT-AT
* * * *
60404571 GTTTT-ATACATCTTCATAAT
1 TTTTTGGTACTTCCTCAT-AT
* * * *
60404591 TTTTT-GTGCATCCTCGTAG
1 TTTTTGGTACTTCCTCATAT
*
60404610 TTTTTGGTA-TCCCTCATAAT
1 TTTTTGGTACTTCCTCAT-AT
60404630 TTTTT-GTACTTCCTCATATT
1 TTTTTGGTACTTCCTCATA-T
*
60404650 TTTTTGGTA-TTCCCTCGTGA-
1 TTTTTGGTACTT-CCTCAT-AT
* *
60404670 TTTTTGATACAT-CT-A-A-
1 TTTTTGGTACTTCCTCATAT
* * * *
60404686 GTTTTGGCACTCCCTCATAA
1 TTTTTGGTACTTCCTCATAT
*
60404706 TTTTTGGTAATTCCT-AGTAT
1 TTTTTGGTACTTCCTCA-TAT
**
60404726 TTTTTTATACTTCCTCATAAT
1 TTTTTGGTACTTCCTCAT-AT
60404747 TTTTT
1 TTTTT
60404752 ATACATCATC
Statistics
Matches: 407, Mismatches: 100, Indels: 101
0.67 0.16 0.17
Matches are distributed among these distances:
16 19 0.05
17 3 0.01
18 14 0.03
19 89 0.22
20 201 0.49
21 65 0.16
22 15 0.04
23 1 0.00
ACGTcount: A:0.20, C:0.17, G:0.07, T:0.56
Consensus pattern (20 bp):
TTTTTGGTACTTCCTCATAT
Found at i:60404250 original size:59 final size:60
Alignment explanation
Indices: 60404174--60404653 Score: 234
Period size: 59 Copynumber: 8.1 Consensus size: 60
60404164 CCCCTTACAA
* *
60404174 TTTTTGGTACTTCCTCATATTTTTTTGTATTCCT-TCATAATTTTTGGTACTTTCTCATT
1 TTTTTAGTACTTCCTCATATTTTTTTGTATTCCTCTCATAATTTTTTGTACTTTCTCATT
* * *
60404233 TTTTTAGTACTTCCTCATATTTTATAGTATT-CTCTTATAATTTTTTGTACTTTCTCTTATTT
1 TTTTTAGTACTTCCTCATATTTTTTTGTATTCCTCTCATAATTTTTTGTACTTTCTC--A-TT
* * * * * ** *
60404295 TTTTTAATA-TTCCCTCGTAATTTTTGGTATT-TTCTCATAATTTTTAATAC-ATCATCA-T
1 TTTTTAGTACTT-CCTCATATTTTTTTGTATTCCTCTCATAATTTTTTGTACTTTC-TCATT
* * * * * ** * *
60404353 ATTTT--TACATCCTCATATTTTTTT-TATACTTTCTCTTTGTTTTTGGTA-TTCTCTCATAA
1 TTTTTAGTACTTCCTCATATTTTTTTGTATTC-CTCTCATAATTTTTTGTACTT-TCTCAT-T
* * * * * *
60404412 TCTTTGGATACTTCCTCATA-TGTTTTGATATACC-CTTC-TAATTTTTAGTAC-ATCTTCATTT
1 TTTTTAG-TACTTCCTCATATTTTTTTG-TATTCCTC-TCATAATTTTTTGTACTTTC-TCA-TT
* * * * * *
60404473 TTTTTA-TTCTTTCTCAGATTTTATAGTATT-CTCTCATAATTTTTTTTAC-TTCTCAATT
1 TTTTTAGTACTTCCTCATATTTTTTTGTATTCCTCTCATAATTTTTTGTACTTTCTC-ATT
* * *
60404531 TTTTTAGTA-TTCCCTCATA-TTTTTTGTATT-CTCTCATAATGTTTTATACATCTTCAT-AAT
1 TTTTTAGTACTT-CCTCATATTTTTTTGTATTCCTCTCATAATTTTTTGTAC-T-TTC-TCATT
* * * * * *
60404591 TTTTT-GTGCATCCTCGTAGTTTTTGGTA-TCC-CTCATAATTTTTTGTACTTCCTCATAT
1 TTTTTAGTACTTCCTCATATTTTTTTGTATTCCTCTCATAATTTTTTGTACTTTCTCAT-T
60404649 TTTTT
1 TTTTT
60404654 TGGTATTCCC
Statistics
Matches: 318, Mismatches: 66, Indels: 75
0.69 0.14 0.16
Matches are distributed among these distances:
55 3 0.01
56 14 0.04
57 20 0.06
58 57 0.18
59 108 0.34
60 24 0.08
61 30 0.09
62 57 0.18
63 5 0.02
ACGTcount: A:0.20, C:0.17, G:0.06, T:0.57
Consensus pattern (60 bp):
TTTTTAGTACTTCCTCATATTTTTTTGTATTCCTCTCATAATTTTTTGTACTTTCTCATT
Found at i:60404306 original size:42 final size:42
Alignment explanation
Indices: 60404233--60404339 Score: 101
Period size: 42 Copynumber: 2.6 Consensus size: 42
60404223 CTTTCTCATT
* * * * * *
60404233 TTTTTAGTACTTCCTCAT-A-TTTTATAGTATTCTCTTATAA
1 TTTTTGGTACTTTCTCATAATTTTTTTAATATTCCCTCATAA
* * * *
60404273 TTTTTTGTACTTTCTCTTATTTTTTTTAATATTCCCTCGTAA
1 TTTTTGGTACTTTCTCATAATTTTTTTAATATTCCCTCATAA
*
60404315 TTTTTGGTATTTTCTCATAATTTTT
1 TTTTTGGTACTTTCTCATAATTTTT
60404340 AATACATCAT
Statistics
Matches: 52, Mismatches: 13, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
40 15 0.29
42 37 0.71
ACGTcount: A:0.20, C:0.14, G:0.06, T:0.61
Consensus pattern (42 bp):
TTTTTGGTACTTTCTCATAATTTTTTTAATATTCCCTCATAA
Found at i:60404363 original size:16 final size:16
Alignment explanation
Indices: 60404342--60404374 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
60404332 TAATTTTTAA
60404342 TACATCATCATATTTT
1 TACATCATCATATTTT
*
60404358 TACATCCTCATATTTT
1 TACATCATCATATTTT
60404374 T
1 T
60404375 TTTATACTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.27, C:0.21, G:0.00, T:0.52
Consensus pattern (16 bp):
TACATCATCATATTTT
Found at i:60404566 original size:39 final size:40
Alignment explanation
Indices: 60404469--60404566 Score: 112
Period size: 39 Copynumber: 2.5 Consensus size: 40
60404459 GTACATCTTC
*
60404469 ATTTTTTTTATTCTTTCTCAGATTTTATAGTATTCTCTCATA
1 ATTTTTTTTATTC--TCTCAGATTTTATAGTATTCCCTCATA
* *
60404511 ATTTTTTTTACT-TCTCA-ATTTTTTTAGTATTCCCTCAT-
1 ATTTTTTTTATTCTCTCAGA-TTTTATAGTATTCCCTCATA
*
60404549 ATTTTTTGTATTCTCTCA
1 ATTTTTTTTATTCTCTCA
60404567 TAATGTTTTA
Statistics
Matches: 49, Mismatches: 5, Indels: 7
0.80 0.08 0.11
Matches are distributed among these distances:
38 11 0.22
39 27 0.55
42 11 0.22
ACGTcount: A:0.19, C:0.16, G:0.04, T:0.60
Consensus pattern (40 bp):
ATTTTTTTTATTCTCTCAGATTTTATAGTATTCCCTCATA
Found at i:60404748 original size:21 final size:20
Alignment explanation
Indices: 60404726--60404770 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
60404716 TTCCTAGTAT
* *
60404726 TTTTTTATACTTCCTCATAA
1 TTTTTTATACATCATCATAA
60404746 TTTTTTATACATCATCATAA
1 TTTTTTATACATCATCATAA
60404766 GTTTT
1 -TTTT
60404771 GGTGCTTTCT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 18 0.82
21 4 0.18
ACGTcount: A:0.27, C:0.16, G:0.02, T:0.56
Consensus pattern (20 bp):
TTTTTTATACATCATCATAA
Found at i:60404751 original size:77 final size:75
Alignment explanation
Indices: 60404611--60404758 Score: 176
Period size: 77 Copynumber: 1.9 Consensus size: 75
60404601 TCCTCGTAGT
* * * * * *
60404611 TTTTGGTATCCCTCATAATTTTTTGTACTTCCTCATATTTTTTTGGTATTCCCTCGTGATTTTTG
1 TTTTGGCATCCCTCATAATTTTTGGTAATTCCTCATATTTTTTTGATATTCCCTCATAATTTTT-
60404676 ATACATCTAAG
65 ATACATCTAAG
60404687 TTTTGGCACTCCCTCATAATTTTTGGTAATTCCT-AGTATTTTTTT-ATACTT-CCTCATAATTT
1 TTTTGGCA-TCCCTCATAATTTTTGGTAATTCCTCA-TATTTTTTTGATA-TTCCCTCATAA-TT
60404749 TTTATACATC
62 TTTATACATC
60404759 ATCATAAGTT
Statistics
Matches: 62, Mismatches: 6, Indels: 8
0.82 0.08 0.11
Matches are distributed among these distances:
76 23 0.37
77 39 0.63
ACGTcount: A:0.20, C:0.19, G:0.09, T:0.51
Consensus pattern (75 bp):
TTTTGGCATCCCTCATAATTTTTGGTAATTCCTCATATTTTTTTGATATTCCCTCATAATTTTTA
TACATCTAAG
Found at i:60405045 original size:22 final size:22
Alignment explanation
Indices: 60405020--60405068 Score: 89
Period size: 22 Copynumber: 2.2 Consensus size: 22
60405010 ATCCCTCACA
*
60405020 ATTTTTGGTATCTCCTCGTGTT
1 ATTTGTGGTATCTCCTCGTGTT
60405042 ATTTGTGGTATCTCCTCGTGTT
1 ATTTGTGGTATCTCCTCGTGTT
60405064 ATTTG
1 ATTTG
60405069 GACTTCTCTT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.10, C:0.16, G:0.20, T:0.53
Consensus pattern (22 bp):
ATTTGTGGTATCTCCTCGTGTT
Found at i:60405107 original size:20 final size:21
Alignment explanation
Indices: 60405084--60405173 Score: 55
Period size: 21 Copynumber: 4.4 Consensus size: 21
60405074 CTCTTATAGT
*
60405084 TTTTTTGTACTT-CTTCATTC
1 TTTTTTGTACTTACTTCATAC
* * *
60405104 TTTTTTGGT-GTTAATTCATAA
1 TTTTTT-GTACTTACTTCATAC
*
60405125 TTTTTTATACTT-CTTCATAC
1 TTTTTTGTACTTACTTCATAC
* * *
60405145 ATTTTTTATACTTCCTT-AT-T
1 -TTTTTTGTACTTACTTCATAC
60405165 TTTTTTGTA
1 TTTTTTGTA
60405174 TTTCCTCAAA
Statistics
Matches: 55, Mismatches: 10, Indels: 11
0.72 0.13 0.14
Matches are distributed among these distances:
19 8 0.15
20 15 0.27
21 29 0.53
22 3 0.05
ACGTcount: A:0.18, C:0.13, G:0.06, T:0.63
Consensus pattern (21 bp):
TTTTTTGTACTTACTTCATAC
Found at i:60405148 original size:21 final size:20
Alignment explanation
Indices: 60405118--60405158 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 20
60405108 TTGGTGTTAA
60405118 TTCATAATTTTTTATACTTC
1 TTCATAATTTTTTATACTTC
60405138 TTCATACATTTTTTATACTTC
1 TTCATA-ATTTTTTATACTTC
60405159 CTTATTTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 6 0.30
21 14 0.70
ACGTcount: A:0.24, C:0.17, G:0.00, T:0.59
Consensus pattern (20 bp):
TTCATAATTTTTTATACTTC
Found at i:60405495 original size:21 final size:21
Alignment explanation
Indices: 60405448--60405496 Score: 55
Period size: 20 Copynumber: 2.4 Consensus size: 21
60405438 GCTTTCTTAT
* *
60405448 AATTTTTTTGGATTCTCTTAA
1 AATTTTTTAGGATTCTCTCAA
* *
60405469 AA-TTTTTAGTATTTTCTCAA
1 AATTTTTTAGGATTCTCTCAA
60405489 AATTTTTT
1 AATTTTTT
60405497 GTACTTCCTC
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
20 16 0.70
21 7 0.30
ACGTcount: A:0.27, C:0.08, G:0.06, T:0.59
Consensus pattern (21 bp):
AATTTTTTAGGATTCTCTCAA
Found at i:60405507 original size:20 final size:20
Alignment explanation
Indices: 60405467--60405521 Score: 56
Period size: 20 Copynumber: 2.8 Consensus size: 20
60405457 GGATTCTCTT
* *
60405467 AAAATTTTTAGTATTTTCTC
1 AAAATTTTTAGTACTTCCTC
*
60405487 AAAATTTTTTGTACTTCCTC
1 AAAATTTTTAGTACTTCCTC
* * *
60405507 ATATTTTTTAATACT
1 AAAATTTTTAGTACT
60405522 ATTAACTTTT
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.29, C:0.13, G:0.04, T:0.55
Consensus pattern (20 bp):
AAAATTTTTAGTACTTCCTC
Found at i:60429136 original size:43 final size:44
Alignment explanation
Indices: 60429088--60429220 Score: 130
Period size: 43 Copynumber: 3.0 Consensus size: 44
60429078 ACAATAAATA
*
60429088 AAAATTATAAAAATAT-AATATATATGTGTATGTATATATACAT
1 AAAATTATAAAAATATAAAAATATATGTGTATGTATATATACAT
* * **
60429131 AAAATTATAAAAATATGGAGAATATA--TGTATGTATATATATTTT
1 AAAATTATAAAAATAT-AAAAATATATGTGTATGTATATATA-CAT
** *
60429175 AAAATTAT-GCAATATAAAAATATATGTAAGTATGTATATAAACAT
1 AAAATTATAAAAATATAAAAATATATGT--GTATGTATATATACAT
60429220 A
1 A
60429221 TATGTGTATG
Statistics
Matches: 72, Mismatches: 11, Indels: 12
0.76 0.12 0.13
Matches are distributed among these distances:
42 7 0.10
43 35 0.49
44 10 0.14
45 8 0.11
46 12 0.17
ACGTcount: A:0.51, C:0.02, G:0.09, T:0.38
Consensus pattern (44 bp):
AAAATTATAAAAATATAAAAATATATGTGTATGTATATATACAT
Found at i:60429171 original size:45 final size:43
Alignment explanation
Indices: 60429088--60429171 Score: 107
Period size: 45 Copynumber: 1.9 Consensus size: 43
60429078 ACAATAAATA
* *
60429088 AAAATTATAAAAATATAATATATATGTGTATGTATATATACAT
1 AAAATTATAAAAATATAATATATATGTATATATATATATACAT
*
60429131 AAAATTATAAAAATATGGAGA-ATATATGTATGTATATATAT
1 AAAATTATAAAAATAT--A-ATATATATGTATATATATATAT
60429172 TTTAAAATTA
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
43 16 0.46
45 18 0.51
46 1 0.03
ACGTcount: A:0.51, C:0.01, G:0.10, T:0.38
Consensus pattern (43 bp):
AAAATTATAAAAATATAATATATATGTATATATATATATACAT
Found at i:60429212 original size:22 final size:22
Alignment explanation
Indices: 60429187--60429256 Score: 60
Period size: 22 Copynumber: 3.2 Consensus size: 22
60429177 AATTATGCAA
60429187 TATAAAAATATATGTAAGTATG
1 TATAAAAATATATGTAAGTATG
60429209 TATATAAACATATATGT--GTATG
1 TATA-AAA-ATATATGTAAGTATG
60429231 TA-AATTAAA-ATATGTATA-TATG
1 TATAA--AAATATATGTA-AGTATG
60429253 TATA
1 TATA
60429257 TAGATGAATA
Statistics
Matches: 40, Mismatches: 0, Indels: 15
0.73 0.00 0.27
Matches are distributed among these distances:
20 7 0.17
21 2 0.05
22 19 0.47
23 4 0.10
24 8 0.20
ACGTcount: A:0.47, C:0.01, G:0.11, T:0.40
Consensus pattern (22 bp):
TATAAAAATATATGTAAGTATG
Found at i:60430612 original size:7 final size:7
Alignment explanation
Indices: 60430600--60430632 Score: 52
Period size: 7 Copynumber: 5.0 Consensus size: 7
60430590 AAAGTATTTT
60430600 AAAAATA
1 AAAAATA
60430607 AAAAAT-
1 AAAAATA
60430613 AAAAAT-
1 AAAAATA
60430619 AAAAATA
1 AAAAATA
60430626 AAAAATA
1 AAAAATA
60430633 TATATTTATT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
6 12 0.48
7 13 0.52
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (7 bp):
AAAAATA
Found at i:60430616 original size:5 final size:6
Alignment explanation
Indices: 60430599--60430629 Score: 53
Period size: 6 Copynumber: 5.0 Consensus size: 6
60430589 AAAAGTATTT
60430599 TAAAAA TAAAAAA TAAAAA TAAAAA TAAAAA
1 TAAAAA T-AAAAA TAAAAA TAAAAA TAAAAA
60430630 ATATATATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 18 0.75
7 6 0.25
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (6 bp):
TAAAAA
Found at i:60430628 original size:36 final size:36
Alignment explanation
Indices: 60430553--60430628 Score: 100
Period size: 36 Copynumber: 2.1 Consensus size: 36
60430543 TAAACATTAA
* ***
60430553 AAAATTATTTTAAAAATAAAAAATAAAAAATATTTT
1 AAAAGTATTTTAAAAATAAAAAATAAAAAATAAAAT
60430589 AAAAGTATTTTAAAAATAAAAAAT-AAAAATAAAAAT
1 AAAAGTATTTTAAAAATAAAAAATAAAAAAT-AAAAT
60430625 AAAA
1 AAAA
60430629 AATATATATT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
35 6 0.17
36 29 0.83
ACGTcount: A:0.70, C:0.00, G:0.01, T:0.29
Consensus pattern (36 bp):
AAAAGTATTTTAAAAATAAAAAATAAAAAATAAAAT
Found at i:60437631 original size:17 final size:16
Alignment explanation
Indices: 60437611--60437666 Score: 53
Period size: 16 Copynumber: 3.4 Consensus size: 16
60437601 AATATATACA
60437611 TTTATATTTGTAATTAT
1 TTTATATTT-TAATTAT
60437628 TTTAT-TTTTAA-TAT
1 TTTATATTTTAATTAT
* *
60437642 TTAATAATTTTATATTTT
1 TTTAT-ATTTTA-ATTAT
60437660 TTTATAT
1 TTTATAT
60437667 AATCATCTTA
Statistics
Matches: 32, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
14 7 0.22
15 3 0.09
16 8 0.25
17 8 0.25
18 6 0.19
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (16 bp):
TTTATATTTTAATTAT
Found at i:60437669 original size:23 final size:22
Alignment explanation
Indices: 60437621--60437684 Score: 65
Period size: 22 Copynumber: 2.9 Consensus size: 22
60437611 TTTATATTTG
* ** *
60437621 TAATTATTTTATTTTTAATATT
1 TAATAATTTTATTTTTTTTATA
60437643 TAATAATTTTATATTTTTTTATA
1 TAATAATTTTAT-TTTTTTTATA
* *
60437666 TAATCATCTTATTTTTTTT
1 TAATAATTTTATTTTTTTT
60437685 GTTTACATTA
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
22 18 0.51
23 17 0.49
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.67
Consensus pattern (22 bp):
TAATAATTTTATTTTTTTTATA
Found at i:60445487 original size:23 final size:23
Alignment explanation
Indices: 60445441--60445487 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
60445431 AAAAAATCCT
*
60445441 AAACCGATAAACCCTAAACACTA
1 AAACCGATAAAACCTAAACACTA
* * *
60445464 AAACCTATAAAACCTTAACTCTA
1 AAACCGATAAAACCTAAACACTA
60445487 A
1 A
60445488 CTCCACCTTA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.51, C:0.28, G:0.02, T:0.19
Consensus pattern (23 bp):
AAACCGATAAAACCTAAACACTA
Found at i:60449852 original size:21 final size:21
Alignment explanation
Indices: 60449827--60449866 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
60449817 AGCCGCAGCA
*
60449827 TCGCCTCCAACGCCGCCTCAG
1 TCGCCTCCAACGCAGCCTCAG
*
60449848 TCGCCTCCACCGCAGCCTC
1 TCGCCTCCAACGCAGCCTC
60449867 CTAAGGCTGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.12, C:0.55, G:0.17, T:0.15
Consensus pattern (21 bp):
TCGCCTCCAACGCAGCCTCAG
Found at i:60450051 original size:18 final size:18
Alignment explanation
Indices: 60450028--60450069 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
60450018 ACCACCTCCA
*
60450028 CCTCCACCTCATCCACCG
1 CCTCCACCTCAGCCACCG
* *
60450046 CCTCCACCTCCGCCGCCG
1 CCTCCACCTCAGCCACCG
60450064 CCTCCA
1 CCTCCA
60450070 ATATCTGGGT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.12, C:0.64, G:0.10, T:0.14
Consensus pattern (18 bp):
CCTCCACCTCAGCCACCG
Found at i:60450247 original size:3 final size:3
Alignment explanation
Indices: 60450239--60450263 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
60450229 CCACCCCCAT
60450239 CGC CGC CGC CGC CGC CGC CGC CGC C
1 CGC CGC CGC CGC CGC CGC CGC CGC C
60450264 ACCTCCACCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.00, C:0.68, G:0.32, T:0.00
Consensus pattern (3 bp):
CGC
Found at i:60453773 original size:123 final size:124
Alignment explanation
Indices: 60453415--60453782 Score: 569
Period size: 124 Copynumber: 3.0 Consensus size: 124
60453405 TTTTAAGTCC
*** *
60453415 TGGAAGAAATAATTTCGAGTTAACGTTTCTGATCAAATAGTATAAAATCGCTTCTAGCTGGATGC
1 TGGAAGAAATAATTT-TTTTTAACGTTTCTGAGCAAATAGTATAAAATCGCTTCTAGCTGGATGC
*
60453480 TATTTGAGAAGAATTTGTGAAATCACGCCCTCGTGGACACGCTTTTGCTACAGTAGGTCA
65 TATTTGAGAAGAATTTGTGAAATCGCGCCCTCGTGGACACGCTTTTGCTACAGTAGGTCA
* * *
60453540 TGGAAGAAATAATTTTTTTTGACGTTTCTGAGGAAATAGTATAAAATCGCATCTAGCTGGATGCT
1 TGGAAGAAATAATTTTTTTTAACGTTTCTGAGCAAATAGTATAAAATCGCTTCTAGCTGGATGCT
* * * * *
60453605 ATTTGGGAAGAATTTGTGAAATCGCGCCCTCGTGGTCACGATTTTGCTACTGTTGGTCA
66 ATTTGAGAAGAATTTGTGAAATCGCGCCCTCGTGGACACGCTTTTGCTACAGTAGGTCA
*
60453664 TGGAAGAAATAATTTTTTTTAACGTTTCTGAGCAAATAGTAT-AAATCGCTTCTAG-TAGGACGC
1 TGGAAGAAATAATTTTTTTTAACGTTTCTGAGCAAATAGTATAAAATCGCTTCTAGCT-GGATGC
*
60453727 TATTTGAGAAGAATTTGTGAAATCGCGCCCTCGTGGACGCGCTTTTGCTACAGTAG
65 TATTTGAGAAGAATTTGTGAAATCGCGCCCTCGTGGACACGCTTTTGCTACAGTAG
60453783 CATGTTTGGG
Statistics
Matches: 219, Mismatches: 23, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
122 1 0.00
123 67 0.31
124 136 0.62
125 15 0.07
ACGTcount: A:0.29, C:0.16, G:0.23, T:0.33
Consensus pattern (124 bp):
TGGAAGAAATAATTTTTTTTAACGTTTCTGAGCAAATAGTATAAAATCGCTTCTAGCTGGATGCT
ATTTGAGAAGAATTTGTGAAATCGCGCCCTCGTGGACACGCTTTTGCTACAGTAGGTCA
Found at i:60456663 original size:25 final size:25
Alignment explanation
Indices: 60456635--60456814 Score: 134
Period size: 25 Copynumber: 7.6 Consensus size: 25
60456625 TAAGCTCATG
60456635 TTATTACATCAAATAAACTTCTATT
1 TTATTACATCAAATAAACTTCTATT
*
60456660 TTATTATATCAAAT-AA-TATC-A--
1 TTATTACATCAAATAAACT-TCTATT
** * * *
60456681 AAATAAC-TCAAAAAAATTTCTATT
1 TTATTACATCAAATAAACTTCTATT
60456705 TTATTACATCAAATAAACTTCTATT
1 TTATTACATCAAATAAACTTCTATT
60456730 TTATTACATCAAAT-AA-TATC-A--
1 TTATTACATCAAATAAACT-TCTATT
** * * *
60456751 AAATAAC-TCAAA-AAAATTTTATT
1 TTATTACATCAAATAAACTTCTATT
60456774 TTATTACATCAAATAAACTTCTATT
1 TTATTACATCAAATAAACTTCTATT
* *
60456799 TTAGTACATAAAATAA
1 TTATTACATCAAATAA
60456815 TATCAAAATA
Statistics
Matches: 118, Mismatches: 22, Indels: 30
0.69 0.13 0.18
Matches are distributed among these distances:
20 13 0.11
21 13 0.11
22 2 0.02
23 8 0.07
24 17 0.14
25 65 0.55
ACGTcount: A:0.47, C:0.13, G:0.01, T:0.39
Consensus pattern (25 bp):
TTATTACATCAAATAAACTTCTATT
Found at i:60456807 original size:69 final size:70
Alignment explanation
Indices: 60456635--60456824 Score: 346
Period size: 70 Copynumber: 2.7 Consensus size: 70
60456625 TAAGCTCATG
*
60456635 TTATTACATCAAATAAACTTCTATTTTATTATATCAAATAATATCAAAATAACTCAAAAAAATTT
1 TTATTACATCAAATAAACTTCTATTTTATTACATCAAATAATATCAAAATAACTCAAAAAAATTT
60456700 CTATT
66 CTATT
60456705 TTATTACATCAAATAAACTTCTATTTTATTACATCAAATAATATCAAAATAACTCAAAAAAATTT
1 TTATTACATCAAATAAACTTCTATTTTATTACATCAAATAATATCAAAATAACTCAAAAAAATTT
60456770 -TATT
66 CTATT
* *
60456774 TTATTACATCAAATAAACTTCTATTTTAGTACATAAAATAATATCAAAATA
1 TTATTACATCAAATAAACTTCTATTTTATTACATCAAATAATATCAAAATA
60456825 TTTAAAATAT
Statistics
Matches: 117, Mismatches: 3, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
69 53 0.45
70 64 0.55
ACGTcount: A:0.48, C:0.13, G:0.01, T:0.39
Consensus pattern (70 bp):
TTATTACATCAAATAAACTTCTATTTTATTACATCAAATAATATCAAAATAACTCAAAAAAATTT
CTATT
Found at i:60458139 original size:20 final size:20
Alignment explanation
Indices: 60458114--60458151 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
60458104 TTTATTTTTA
60458114 AAAATCT-ATATAATAATTGT
1 AAAATCTAATATAA-AATTGT
60458134 AAAATCTAATATAAAATT
1 AAAATCTAATATAAAATT
60458152 TACCTCGTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.55, C:0.05, G:0.03, T:0.37
Consensus pattern (20 bp):
AAAATCTAATATAAAATTGT
Found at i:60459182 original size:12 final size:12
Alignment explanation
Indices: 60459144--60459185 Score: 52
Period size: 12 Copynumber: 3.7 Consensus size: 12
60459134 TAAATATGGA
*
60459144 TTTGAGAGAAAT
1 TTTGAGAGGAAT
60459156 TTTGA-AGGAA-
1 TTTGAGAGGAAT
*
60459166 ATTGAGAGGAAT
1 TTTGAGAGGAAT
60459178 TTTGAGAG
1 TTTGAGAG
60459186 ATGATTAGTT
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
10 4 0.16
11 9 0.36
12 12 0.48
ACGTcount: A:0.38, C:0.00, G:0.31, T:0.31
Consensus pattern (12 bp):
TTTGAGAGGAAT
Found at i:60463157 original size:17 final size:18
Alignment explanation
Indices: 60463132--60463177 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
60463122 TATAAGAATA
*
60463132 ATTATATTA-AGAATTTT
1 ATTAAATTATAGAATTTT
* *
60463149 ATTAAATTATATATTTTT
1 ATTAAATTATAGAATTTT
60463167 ATTAAATTATA
1 ATTAAATTATA
60463178 TTTAATAATT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
17 8 0.32
18 17 0.68
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.54
Consensus pattern (18 bp):
ATTAAATTATAGAATTTT
Found at i:60463294 original size:120 final size:120
Alignment explanation
Indices: 60463080--60463438 Score: 641
Period size: 120 Copynumber: 3.0 Consensus size: 120
60463070 TAGATTATAT
* *
60463080 ATTAT-TTTTATAGTATTATATATTATGATTTTACTAAATTCATATAAGAATAATT-ATATTAAG
1 ATTATATTTTATAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATTAAG
*
60463143 AATTTTATTAAATTATATATTTTTATTAAATTATATTTAATAATTATTATTTTAA
66 AATTTTATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATTTTAA
* *
60463198 ATTATATTTTACAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATTAAA
1 ATTATATTTTATAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATTAAG
60463263 AATTTTATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATTTTAA
66 AATTTTATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATTTTAA
*
60463318 ATTATATTTTATAATATTATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATTAAG
1 ATTATATTTTATAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATTAAG
*
60463383 AATTTTATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATGTTAA
66 AATTTTATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATTTTAA
60463438 A
1 A
60463439 ATATGATTAA
Statistics
Matches: 230, Mismatches: 9, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
118 5 0.02
119 47 0.20
120 178 0.77
ACGTcount: A:0.43, C:0.01, G:0.04, T:0.52
Consensus pattern (120 bp):
ATTATATTTTATAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATTAAG
AATTTTATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATTTTAA
Found at i:60463317 original size:26 final size:25
Alignment explanation
Indices: 60463279--60463337 Score: 82
Period size: 26 Copynumber: 2.3 Consensus size: 25
60463269 ATTAAATTAT
*
60463279 ATATTTTTATTAAATTATATTTAATA
1 ATATTATT-TTAAATTATATTTAATA
*
60463305 ATAATTATTTTAAATTATATTTTATA
1 AT-ATTATTTTAAATTATATTTAATA
60463331 ATATTAT
1 ATATTAT
60463338 ATATTATGAT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
25 5 0.17
26 20 0.67
27 5 0.17
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (25 bp):
ATATTATTTTAAATTATATTTAATA
Found at i:60463343 original size:22 final size:24
Alignment explanation
Indices: 60463318--60463364 Score: 64
Period size: 23 Copynumber: 2.0 Consensus size: 24
60463308 ATTATTTTAA
60463318 ATTAT-ATTTTA-TAATATT-ATAT
1 ATTATGATTTTAGTAA-ATTCATAT
60463340 ATTATGATTTTAGTAAATTCATAT
1 ATTATGATTTTAGTAAATTCATAT
60463364 A
1 A
60463365 AGAATATTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
22 5 0.23
23 9 0.41
24 8 0.36
ACGTcount: A:0.40, C:0.02, G:0.04, T:0.53
Consensus pattern (24 bp):
ATTATGATTTTAGTAAATTCATAT
Found at i:60463388 original size:38 final size:36
Alignment explanation
Indices: 60463330--60463401 Score: 92
Period size: 37 Copynumber: 1.9 Consensus size: 36
60463320 TATATTTTAT
*
60463330 AATATTATATATTATGATTTTAGTAAATTCATATAAG
1 AATATTATATATTAAGATTTTAGTAAATT-ATATAAG
*
60463367 AATATT-TAATATTAAGAATTTTATTAAATTATATA
1 AATATTAT-ATATTAAG-ATTTTAGTAAATTATATA
60463402 TTTTTATTAA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
36 1 0.03
37 18 0.58
38 12 0.39
ACGTcount: A:0.46, C:0.01, G:0.06, T:0.47
Consensus pattern (36 bp):
AATATTATATATTAAGATTTTAGTAAATTATATAAG
Found at i:60463562 original size:15 final size:15
Alignment explanation
Indices: 60463542--60463575 Score: 61
Period size: 14 Copynumber: 2.3 Consensus size: 15
60463532 GGTATTCTAG
60463542 TCATTTTAATTTTTT
1 TCATTTTAATTTTTT
60463557 TCA-TTTAATTTTTT
1 TCATTTTAATTTTTT
60463571 TCATT
1 TCATT
60463576 ATGCTATTAC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 14 0.78
15 4 0.22
ACGTcount: A:0.21, C:0.09, G:0.00, T:0.71
Consensus pattern (15 bp):
TCATTTTAATTTTTT
Found at i:60466326 original size:31 final size:29
Alignment explanation
Indices: 60466250--60466326 Score: 84
Period size: 29 Copynumber: 2.6 Consensus size: 29
60466240 TGGGGGAATA
* *
60466250 TTTTAGAAGTTATTTATATAAAGGTTAAG
1 TTTTTGAAGATATTTATATAAAGGTTAAG
* *
60466279 TTTTTAAAAATATTTATAT-AAGGTTTAAG
1 TTTTTGAAGATATTTATATAAAGG-TTAAG
60466308 TTTATTCGAAGATATTTAT
1 TTT-TT-GAAGATATTTAT
60466327 TTAGGGCTTT
Statistics
Matches: 39, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
28 4 0.10
29 23 0.59
30 2 0.05
31 10 0.26
ACGTcount: A:0.38, C:0.01, G:0.13, T:0.48
Consensus pattern (29 bp):
TTTTTGAAGATATTTATATAAAGGTTAAG
Found at i:60471220 original size:27 final size:27
Alignment explanation
Indices: 60471182--60471248 Score: 116
Period size: 27 Copynumber: 2.5 Consensus size: 27
60471172 CCTATCAGGT
*
60471182 AGGCGCCAATGAAGGTGTCTCACAGAG
1 AGGCGCCAATGAAGGTGCCTCACAGAG
*
60471209 AGGCGCCAATGAAGGTGCCTCATAGAG
1 AGGCGCCAATGAAGGTGCCTCACAGAG
60471236 AGGCGCCAATGAA
1 AGGCGCCAATGAA
60471249 TATTGTAATT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
27 38 1.00
ACGTcount: A:0.31, C:0.22, G:0.33, T:0.13
Consensus pattern (27 bp):
AGGCGCCAATGAAGGTGCCTCACAGAG
Found at i:60471268 original size:19 final size:19
Alignment explanation
Indices: 60471244--60471354 Score: 88
Period size: 19 Copynumber: 5.6 Consensus size: 19
60471234 AGAGGCGCCA
60471244 ATGAATATTGTAATTTTGT
1 ATGAATATTGTAATTTTGT
*
60471263 ATGAATATTGTAATTATTTT
1 ATGAATATTGTAATT-TTGT
60471283 AT-AATTAAATT-TATATTTATAGTT
1 ATGAA-T--ATTGTA-ATTT-T-G-T
*
60471307 TTGGAATA--GT-ATTTTGT
1 AT-GAATATTGTAATTTTGT
60471324 ATGAATATTGTAATTTTGT
1 ATGAATATTGTAATTTTGT
60471343 ATGAATATTGTA
1 ATGAATATTGTA
60471355 GTTATTTTAT
Statistics
Matches: 74, Mismatches: 4, Indels: 28
0.70 0.04 0.26
Matches are distributed among these distances:
16 5 0.07
17 2 0.03
18 3 0.04
19 37 0.50
20 10 0.14
21 3 0.04
22 8 0.11
23 1 0.01
24 2 0.03
25 1 0.01
26 2 0.03
ACGTcount: A:0.34, C:0.00, G:0.14, T:0.52
Consensus pattern (19 bp):
ATGAATATTGTAATTTTGT
Found at i:60471420 original size:60 final size:60
Alignment explanation
Indices: 60471350--60471471 Score: 165
Period size: 60 Copynumber: 2.0 Consensus size: 60
60471340 TGTATGAATA
* * * * * *
60471350 TTGTAGTTATTTTATAA-TTAATTTGTTAGTAATTTAGGATTATGTTATAAATTTTTGTGT
1 TTGTAATTA-TTTAAAATTTAATTTATTAGTAATTTAGGATTAAGCTATAAATTGTTGTGT
*
60471410 TTGTAATTATTTAAAATTTAATTTATTAGTAATTTAGGATTAAGCTATAAGTTGTTGTGT
1 TTGTAATTATTTAAAATTTAATTTATTAGTAATTTAGGATTAAGCTATAAATTGTTGTGT
60471470 TT
1 TT
60471472 AGTTTAATAT
Statistics
Matches: 54, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
59 6 0.11
60 48 0.89
ACGTcount: A:0.30, C:0.01, G:0.15, T:0.54
Consensus pattern (60 bp):
TTGTAATTATTTAAAATTTAATTTATTAGTAATTTAGGATTAAGCTATAAATTGTTGTGT
Found at i:60471549 original size:38 final size:38
Alignment explanation
Indices: 60471504--60471585 Score: 164
Period size: 38 Copynumber: 2.2 Consensus size: 38
60471494 CATATAAAGT
60471504 TTATAAAAAAATTAAAAATCATTTTATTAAAAGTTTAA
1 TTATAAAAAAATTAAAAATCATTTTATTAAAAGTTTAA
60471542 TTATAAAAAAATTAAAAATCATTTTATTAAAAGTTTAA
1 TTATAAAAAAATTAAAAATCATTTTATTAAAAGTTTAA
60471580 TTATAA
1 TTATAA
60471586 CTGACTTTTT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 44 1.00
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.40
Consensus pattern (38 bp):
TTATAAAAAAATTAAAAATCATTTTATTAAAAGTTTAA
Done.