Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007293.1 Hibiscus syriacus cultivar Beakdansim tig00019391_pilon, whole genome shotgun sequence
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: 160342
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Found at i:11904 original size:62 final size:62
Alignment explanation
Indices: 11834--11961 Score: 202
Period size: 62 Copynumber: 2.1 Consensus size: 62
11824 ACAACCTACT
* * *
11834 TGGAAAAGGTATTCATAACTCATTCATACATGTCGATAAACGTCGAGATGCACATTCTGGAA
1 TGGAAAAGGTATTCATAACTCACTCATAAATGTCGATAAACATCGAGATGCACATTCTGGAA
* * *
11896 TGGAAAAGGTATTCATAACTCACTCGTAAATGTCTATAAACATTGAGATGCACATTCTGGAA
1 TGGAAAAGGTATTCATAACTCACTCATAAATGTCGATAAACATCGAGATGCACATTCTGGAA
11958 TGGA
1 TGGA
11962 GGGAATAGAT
Statistics
Matches: 60, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
62 60 1.00
ACGTcount: A:0.36, C:0.16, G:0.20, T:0.28
Consensus pattern (62 bp):
TGGAAAAGGTATTCATAACTCACTCATAAATGTCGATAAACATCGAGATGCACATTCTGGAA
Found at i:14624 original size:11 final size:11
Alignment explanation
Indices: 14608--14642 Score: 61
Period size: 11 Copynumber: 3.2 Consensus size: 11
14598 CTAAAGATAA
14608 GGAGGGGTGGG
1 GGAGGGGTGGG
14619 GGAGGGGTGGG
1 GGAGGGGTGGG
*
14630 GGAGGGGAGGG
1 GGAGGGGTGGG
14641 GG
1 GG
14643 GGACAACTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
11 23 1.00
ACGTcount: A:0.11, C:0.00, G:0.83, T:0.06
Consensus pattern (11 bp):
GGAGGGGTGGG
Found at i:32390 original size:16 final size:19
Alignment explanation
Indices: 32357--32392 Score: 51
Period size: 16 Copynumber: 2.1 Consensus size: 19
32347 ACTCGTATTT
32357 AAATAATATGAAATTTAAA
1 AAATAATATGAAATTTAAA
32376 AAAT-ATAT-AAA-TTAAA
1 AAATAATATGAAATTTAAA
32392 A
1 A
32393 TTTATTAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
16 6 0.35
17 3 0.18
18 4 0.24
19 4 0.24
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.31
Consensus pattern (19 bp):
AAATAATATGAAATTTAAA
Found at i:35909 original size:13 final size:13
Alignment explanation
Indices: 35871--35914 Score: 54
Period size: 13 Copynumber: 3.3 Consensus size: 13
35861 TTCTATATAT
*
35871 TATTTTA-ATAAAT
1 TATTTTATA-AAAA
35884 TATTTATATAAAAA
1 TATTT-TATAAAAA
35898 TATTTTATAAAAA
1 TATTTTATAAAAA
35911 TATT
1 TATT
35915 AATTTTATTT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
13 17 0.61
14 10 0.36
15 1 0.04
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (13 bp):
TATTTTATAAAAA
Found at i:35923 original size:22 final size:22
Alignment explanation
Indices: 35898--35945 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
35888 TATATAAAAA
35898 TATTTTA-TAAAAATATTAATTT
1 TATTTTACTAAAAATATT-ATTT
*
35920 TATTTTACTAAAATTATTATTT
1 TATTTTACTAAAAATATTATTT
35942 TATT
1 TATT
35946 ATTTATATAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
22 15 0.62
23 9 0.38
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (22 bp):
TATTTTACTAAAAATATTATTT
Found at i:36113 original size:60 final size:61
Alignment explanation
Indices: 36013--36144 Score: 146
Period size: 60 Copynumber: 2.2 Consensus size: 61
36003 GCATCATATG
* * * * *
36013 TCCTCAAATTATGATATTCTTTTTAAATTGGACCCTAAAC-TTTTAAATATTCCAATTTTA
1 TCCTAAAATTATGATATTCATTCTAAATTGGACCCTAAACTTTTTAAACATTCCAATTTCA
* * *
36073 TCCTTAAATTATGACTA-TCATTCTAAATTGG-TCCTAAAACTTTTTGAACATTCCAATTTCA
1 TCCTAAAATTATGA-TATTCATTCTAAATTGGACCCT-AAACTTTTTAAACATTCCAATTTCA
36134 TCC-AAAATTAT
1 TCCTAAAATTAT
36145 ATGTATATAT
Statistics
Matches: 61, Mismatches: 8, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
59 3 0.05
60 36 0.59
61 22 0.36
ACGTcount: A:0.34, C:0.18, G:0.05, T:0.42
Consensus pattern (61 bp):
TCCTAAAATTATGATATTCATTCTAAATTGGACCCTAAACTTTTTAAACATTCCAATTTCA
Found at i:43209 original size:19 final size:19
Alignment explanation
Indices: 43185--43224 Score: 71
Period size: 19 Copynumber: 2.1 Consensus size: 19
43175 TTTATCTAAT
43185 TATTAATTTAAATATTAAA
1 TATTAATTTAAATATTAAA
*
43204 TATTAATTTAAATTTTAAA
1 TATTAATTTAAATATTAAA
43223 TA
1 TA
43225 GAATATGTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (19 bp):
TATTAATTTAAATATTAAA
Found at i:48517 original size:30 final size:29
Alignment explanation
Indices: 48477--48538 Score: 79
Period size: 30 Copynumber: 2.1 Consensus size: 29
48467 TTTATGACAC
*
48477 GATACCTGATTTTCTGAATATTGTTTATAT
1 GATACCTGATTTACTGAAT-TTGTTTATAT
* * *
48507 GATACTTGATTTACTGTATTTTTTTATAT
1 GATACCTGATTTACTGAATTTGTTTATAT
48536 GAT
1 GAT
48539 CTCTGGTTAC
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
29 12 0.43
30 16 0.57
ACGTcount: A:0.26, C:0.08, G:0.13, T:0.53
Consensus pattern (29 bp):
GATACCTGATTTACTGAATTTGTTTATAT
Found at i:48549 original size:28 final size:29
Alignment explanation
Indices: 48500--48574 Score: 82
Period size: 28 Copynumber: 2.6 Consensus size: 29
48490 CTGAATATTG
* *
48500 TTTATATGATACT-TGATTTACTGTATTTT
1 TTTATATGAT-CTCTGAGTTACTATATTTT
48529 TTTATATGATCTCTG-GTTACTATATTTT
1 TTTATATGATCTCTGAGTTACTATATTTT
* * *
48557 TGTATCTGATTTCTGAGT
1 TTTATATGATCTCTGAGT
48575 ATGAAATATT
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
28 25 0.64
29 14 0.36
ACGTcount: A:0.21, C:0.09, G:0.13, T:0.56
Consensus pattern (29 bp):
TTTATATGATCTCTGAGTTACTATATTTT
Found at i:49959 original size:101 final size:102
Alignment explanation
Indices: 49784--49974 Score: 285
Period size: 101 Copynumber: 1.9 Consensus size: 102
49774 ACAATTAATT
* * * * * *
49784 TTTTTAATGATTTTGTTAATAGAGAACATGATTAGCATATACTGATAATGTAGAGGTAAAATAAA
1 TTTTTAACGATTTTATCAATAGAGAACATGATTAGCATATACTAATAATATAGAGATAAAATAAA
* *
49849 AATGTTCAAAAGTTTAGAGA-TAATATGATAATTTAA
66 AATATTCAAAAATTTAGAGACTAATATGATAATTTAA
*
49885 TTTTTAACGATTTTATCAATAGAGAACATGATTAGCATATGCTAATAATATAGAGATAAAATAAA
1 TTTTTAACGATTTTATCAATAGAGAACATGATTAGCATATACTAATAATATAGAGATAAAATAAA
*
49950 AATATTCAAAAATTTATAGACTAAT
66 AATATTCAAAAATTTAGAGACTAAT
49975 TTAGAATGAT
Statistics
Matches: 79, Mismatches: 10, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
101 75 0.95
102 4 0.05
ACGTcount: A:0.46, C:0.06, G:0.13, T:0.36
Consensus pattern (102 bp):
TTTTTAACGATTTTATCAATAGAGAACATGATTAGCATATACTAATAATATAGAGATAAAATAAA
AATATTCAAAAATTTAGAGACTAATATGATAATTTAA
Found at i:50311 original size:18 final size:17
Alignment explanation
Indices: 50285--50318 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
50275 TCAATAAAAA
50285 TATAAAAAATATTTAAAT
1 TATAAAAAA-ATTTAAAT
*
50303 TATATAAAAATTTAAA
1 TATAAAAAAATTTAAA
50319 CTTTTCAAGG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (17 bp):
TATAAAAAAATTTAAAT
Found at i:50983 original size:185 final size:184
Alignment explanation
Indices: 50648--51018 Score: 620
Period size: 185 Copynumber: 2.0 Consensus size: 184
50638 AAATTAAATG
*
50648 TTTTTAATTCAAAAAAAGTTTATAATTAATTTAAATAATATATAATTATAAAATAAAAATTTCAG
1 TTTTTAATTCAAAAAAAGTTTACAATTAATTTAAATAATATATAATTATAAAATAAAAATTTCAG
50713 ATAAATTTTTTAATTAATTAATATTGATTTAGATTTAAAAGTTATTGGATCTTAAATTATTAATT
66 ATAAATTTTTTAATTAATTAATATTGATTTAGATTTAAAAGTTATTGGATCTTAAATTATTAATT
* *
50778 GAGTTTTAAATTGTTTGGGCTTAGCCCAAATGTTATATATAATATATATAATAT
131 GAGTTTTAAATAGTTTGGGCTGAGCCCAAATGTTATATATAATATATATAATAT
50832 TTTTTAATT-AAGAAAACAGTTTACAATTAATTTAAATAATATATAATTATAAAATAAAAAATTT
1 TTTTTAATTCAA-AAAA-AGTTTACAATTAATTTAAATAATATATAATTATAAAAT-AAAAATTT
* * *
50896 -ATATAATTTTTTTAATTAATTAATATTGATTTAGGTTTAAAAGTTATTGGATCTTAAATTATTA
63 CAGATAAATTTTTTAATTAATTAATATTGATTTAGATTTAAAAGTTATTGGATCTTAAATTATTA
* * *
50960 ATTGGGTTTTAAATAGTTTGGGCTGAGCCCATATGTTATATATAATATATTTAATAT
128 ATTGAGTTTTAAATAGTTTGGGCTGAGCCCAAATGTTATATATAATATATATAATAT
51017 TT
1 TT
51019 AATTTTGGTT
Statistics
Matches: 175, Mismatches: 9, Indels: 5
0.93 0.05 0.03
Matches are distributed among these distances:
183 2 0.01
184 13 0.07
185 152 0.87
186 8 0.05
ACGTcount: A:0.42, C:0.04, G:0.09, T:0.46
Consensus pattern (184 bp):
TTTTTAATTCAAAAAAAGTTTACAATTAATTTAAATAATATATAATTATAAAATAAAAATTTCAG
ATAAATTTTTTAATTAATTAATATTGATTTAGATTTAAAAGTTATTGGATCTTAAATTATTAATT
GAGTTTTAAATAGTTTGGGCTGAGCCCAAATGTTATATATAATATATATAATAT
Found at i:52216 original size:44 final size:42
Alignment explanation
Indices: 52167--52265 Score: 98
Period size: 42 Copynumber: 2.4 Consensus size: 42
52157 TTTCATTCCT
* * *
52167 TAATATTTTATAAATTCT-CTCTTAATTTTATAGGTTCGATTCTC
1 TAATA-TTTA-AAATT-TACTCTTAATTTTATAAGTTCCATACTC
*
52211 TAATA-TTAAAGTTTACCTCTTAATTTTATAAGTTCCATACTC
1 TAATATTTAAAATTTA-CTCTTAATTTTATAAGTTCCATACTC
52253 TAATA--TAAAATTT
1 TAATATTTAAAATTT
52266 TACTTCTATC
Statistics
Matches: 48, Mismatches: 5, Indels: 7
0.80 0.08 0.12
Matches are distributed among these distances:
40 1 0.02
41 11 0.23
42 31 0.65
44 5 0.10
ACGTcount: A:0.33, C:0.13, G:0.05, T:0.48
Consensus pattern (42 bp):
TAATATTTAAAATTTACTCTTAATTTTATAAGTTCCATACTC
Found at i:52233 original size:42 final size:42
Alignment explanation
Indices: 52185--52268 Score: 123
Period size: 42 Copynumber: 2.0 Consensus size: 42
52175 TATAAATTCT
* * * *
52185 CTCTTAATTTTATAGGTTCGATTCTCTAATATTAAAGTTTAC
1 CTCTTAATTTTATAAGTTCCATACTCTAATATAAAAGTTTAC
*
52227 CTCTTAATTTTATAAGTTCCATACTCTAATATAAAATTTTAC
1 CTCTTAATTTTATAAGTTCCATACTCTAATATAAAAGTTTAC
52269 TTCTATCCCT
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 37 1.00
ACGTcount: A:0.32, C:0.15, G:0.06, T:0.46
Consensus pattern (42 bp):
CTCTTAATTTTATAAGTTCCATACTCTAATATAAAAGTTTAC
Found at i:52243 original size:21 final size:21
Alignment explanation
Indices: 52171--52245 Score: 57
Period size: 20 Copynumber: 3.6 Consensus size: 21
52161 ATTCCTTAAT
* *
52171 ATTTTATAAATTC-TCTCTTA
1 ATTTTATAAGTTCGACTCTTA
* *
52191 ATTTTATAGGTTCGATTCTCTA
1 ATTTTATAAGTTCGACTCT-TA
* *
52213 ATATTA-AAGTT-TACCTCTTA
1 ATTTTATAAGTTCGA-CTCTTA
52233 ATTTTATAAGTTC
1 ATTTTATAAGTTC
52246 CATACTCTAA
Statistics
Matches: 41, Mismatches: 9, Indels: 8
0.71 0.16 0.14
Matches are distributed among these distances:
20 19 0.46
21 15 0.37
22 7 0.17
ACGTcount: A:0.29, C:0.13, G:0.07, T:0.51
Consensus pattern (21 bp):
ATTTTATAAGTTCGACTCTTA
Found at i:52426 original size:73 final size:73
Alignment explanation
Indices: 52341--52485 Score: 290
Period size: 73 Copynumber: 2.0 Consensus size: 73
52331 GCAAGGCATC
52341 CATATCCCTACCTACCTTCTGTCTCAACCGACAGAGCATATCAATCCATAACACCACCACCACTC
1 CATATCCCTACCTACCTTCTGTCTCAACCGACAGAGCATATCAATCCATAACACCACCACCACTC
52406 CATAGATT
66 CATAGATT
52414 CATATCCCTACCTACCTTCTGTCTCAACCGACAGAGCATATCAATCCATAACACCACCACCACTC
1 CATATCCCTACCTACCTTCTGTCTCAACCGACAGAGCATATCAATCCATAACACCACCACCACTC
52479 CATAGAT
66 CATAGAT
52486 AGAAAGAGTT
Statistics
Matches: 72, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
73 72 1.00
ACGTcount: A:0.32, C:0.39, G:0.07, T:0.23
Consensus pattern (73 bp):
CATATCCCTACCTACCTTCTGTCTCAACCGACAGAGCATATCAATCCATAACACCACCACCACTC
CATAGATT
Found at i:56104 original size:19 final size:20
Alignment explanation
Indices: 56072--56109 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
56062 GTGTGAACAC
56072 ATATAATAATAACA-AAATT
1 ATATAATAATAACATAAATT
56091 ATATAA-AATAAACATAAAT
1 ATATAATAAT-AACATAAAT
56110 AAAATTTTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
18 3 0.18
19 10 0.59
20 4 0.24
ACGTcount: A:0.66, C:0.05, G:0.00, T:0.29
Consensus pattern (20 bp):
ATATAATAATAACATAAATT
Found at i:57505 original size:24 final size:23
Alignment explanation
Indices: 57473--57528 Score: 69
Period size: 24 Copynumber: 2.3 Consensus size: 23
57463 AAGGAACGTA
57473 TCACAAGATCA-AAAAAAATAAGTG
1 TCACAAGATCAGAAAAAAA-AA-TG
*
57497 TCACAAGATCAGTAAAAAAACATG
1 TCACAAGATCAG-AAAAAAAAATG
57521 TCACAAGA
1 TCACAAGA
57529 ATAACGATTG
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
24 21 0.72
25 1 0.03
26 7 0.24
ACGTcount: A:0.55, C:0.16, G:0.12, T:0.16
Consensus pattern (23 bp):
TCACAAGATCAGAAAAAAAAATG
Found at i:58656 original size:19 final size:20
Alignment explanation
Indices: 58632--58682 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
58622 AATGACCAAT
58632 AAAATCGCAACGCGATAT-C
1 AAAATCGCAACGCGATATAC
* *
58651 AAAATCGCAACGCGATTTAG
1 AAAATCGCAACGCGATATAC
58671 AAAATCGCAACG
1 AAAATCGCAACG
58683 TTAAAAAGAA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 17 0.59
20 12 0.41
ACGTcount: A:0.43, C:0.24, G:0.18, T:0.16
Consensus pattern (20 bp):
AAAATCGCAACGCGATATAC
Found at i:58676 original size:20 final size:20
Alignment explanation
Indices: 58632--58898 Score: 115
Period size: 20 Copynumber: 13.1 Consensus size: 20
58622 AATGACCAAT
* *
58632 AAAATCGCAACGCGATAT-C
1 AAAATCGCAACGCGATTTAG
58651 AAAATCGCAACGCGATTTAG
1 AAAATCGCAACGCGATTTAG
** ***
58671 AAAATCGCAACGTTAAAAAG
1 AAAATCGCAACGCGATTTAG
***
58691 AAAATCGCAACG-GACAAAAG
1 AAAATCGCAACGCGA-TTTAG
* * **
58711 AAAATCGCAACACGAGCTTCC
1 AAAATCGCAACGCGA-TTTAG
**
58732 AAGTTCGCAACGCGATTTAGAAG
1 AAAATCGCAACGCGATTT---AG
* * * *
58755 AAAATCGTAATGCGATTGAT
1 AAAATCGCAACGCGATTTAG
** * *
58775 TGAATCGCAATGCGATTTAT
1 AAAATCGCAACGCGATTTAG
* * *
58795 AGAATCGCAATGCGATTGAG
1 AAAATCGCAACGCGATTTAG
* *
58815 AGAGTCGCAACGCGATTTAG
1 AAAATCGCAACGCGATTTAG
* * *
58835 AAGAGAATCGCAATGCGACTGAG
1 -A-A-AATCGCAACGCGATTTAG
* * * *
58858 AGAATCGCAATGCGACTGAG
1 AAAATCGCAACGCGATTTAG
*
58878 AGAATCGCAACGCGATTTAG
1 AAAATCGCAACGCGATTTAG
58898 A
1 A
58899 TTTGTTTCTT
Statistics
Matches: 193, Mismatches: 46, Indels: 17
0.75 0.18 0.07
Matches are distributed among these distances:
19 18 0.09
20 132 0.68
21 15 0.08
22 1 0.01
23 27 0.14
ACGTcount: A:0.39, C:0.19, G:0.23, T:0.19
Consensus pattern (20 bp):
AAAATCGCAACGCGATTTAG
Found at i:58843 original size:63 final size:63
Alignment explanation
Indices: 58776--58898 Score: 201
Period size: 63 Copynumber: 2.0 Consensus size: 63
58766 GCGATTGATT
* * * * *
58776 GAATCGCAATGCGATTTATAGAATCGCAATGCGATTGAGAGAGTCGCAACGCGATTTAGAAGA
1 GAATCGCAATGCGACTGAGAGAATCGCAATGCGACTGAGAGAATCGCAACGCGATTTAGAAGA
58839 GAATCGCAATGCGACTGAGAGAATCGCAATGCGACTGAGAGAATCGCAACGCGATTTAGA
1 GAATCGCAATGCGACTGAGAGAATCGCAATGCGACTGAGAGAATCGCAACGCGATTTAGA
58899 TTTGTTTCTT
Statistics
Matches: 55, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
63 55 1.00
ACGTcount: A:0.35, C:0.18, G:0.28, T:0.20
Consensus pattern (63 bp):
GAATCGCAATGCGACTGAGAGAATCGCAATGCGACTGAGAGAATCGCAACGCGATTTAGAAGA
Found at i:58844 original size:83 final size:83
Alignment explanation
Indices: 58736--58894 Score: 237
Period size: 83 Copynumber: 1.9 Consensus size: 83
58726 GCTTCCAAGT
* * ** * * *
58736 TCGCAACGCGATTTAGAAGAAAATCGTAATGCGATTGATTGAATCGCAATGCGATTTATAGAATC
1 TCGCAACGCGATTTAGAAGAAAATCGCAATGCGACTGAGAGAATCGCAATGCGACTGAGAGAATC
*
58801 GCAATGCGATTGAGAGAG
66 GCAACGCGATTGAGAGAG
*
58819 TCGCAACGCGATTTAGAAGAGAATCGCAATGCGACTGAGAGAATCGCAATGCGACTGAGAGAATC
1 TCGCAACGCGATTTAGAAGAAAATCGCAATGCGACTGAGAGAATCGCAATGCGACTGAGAGAATC
58884 GCAACGCGATT
66 GCAACGCGATT
58895 TAGATTTGTT
Statistics
Matches: 67, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
83 67 1.00
ACGTcount: A:0.35, C:0.18, G:0.26, T:0.21
Consensus pattern (83 bp):
TCGCAACGCGATTTAGAAGAAAATCGCAATGCGACTGAGAGAATCGCAATGCGACTGAGAGAATC
GCAACGCGATTGAGAGAG
Found at i:58974 original size:6 final size:6
Alignment explanation
Indices: 58963--59067 Score: 210
Period size: 6 Copynumber: 17.5 Consensus size: 6
58953 GACACGTATT
58963 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
59011 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
59059 ACCACG ACC
1 ACCACG ACC
59068 CGAGACGGCG
Statistics
Matches: 99, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 99 1.00
ACGTcount: A:0.33, C:0.50, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:59774 original size:6 final size:6
Alignment explanation
Indices: 59753--59813 Score: 108
Period size: 6 Copynumber: 10.5 Consensus size: 6
59743 TCTCGTCTCG
59753 GGTCG- GGTCG- GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
59799 GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGT
59814 AATACGTGTC
Statistics
Matches: 55, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
5 10 0.18
6 45 0.82
ACGTcount: A:0.00, C:0.16, G:0.52, T:0.31
Consensus pattern (6 bp):
GGTCGT
Found at i:59916 original size:20 final size:20
Alignment explanation
Indices: 59891--59930 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
59881 TTTTTAACTA
*
59891 TTCTTTTGACCGTTGCGATT
1 TTCTTTTGAACGTTGCGATT
*
59911 TTCTTTTTAACGTTGCGATT
1 TTCTTTTGAACGTTGCGATT
59931 CTCTAAATCG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.12, C:0.17, G:0.17, T:0.53
Consensus pattern (20 bp):
TTCTTTTGAACGTTGCGATT
Found at i:59944 original size:20 final size:20
Alignment explanation
Indices: 59923--60114 Score: 195
Period size: 20 Copynumber: 9.3 Consensus size: 20
59913 CTTTTTAACG
*
59923 TTGCGATTCTCTAAATCGCG
1 TTGCGATTCTCTAAATCGCA
* *
59943 TTGCGATTCTCTAACTCGCG
1 TTGCGATTCTCTAAATCGCA
* *
59963 TTGCGATTCTCTCAGTCGCA
1 TTGCGATTCTCTAAATCGCA
* *
59983 TTGCGATTCTCTTAGTCGCA
1 TTGCGATTCTCTAAATCGCA
*
60003 TTGCGATTCTCTTCTAAATCGCG
1 TTGCGA-T-TC-TCTAAATCGCA
* *
60026 TTGCGACTCTCTCAATCGCA
1 TTGCGATTCTCTAAATCGCA
*
60046 TTGCGATTCTATAAATCGCA
1 TTGCGATTCTCTAAATCGCA
** *
60066 TTGCGATTCAATCAATCGCA
1 TTGCGATTCTCTAAATCGCA
*
60086 TTGCGATTTTCTTCTAAATCGCG
1 TTGCGA--TTC-TCTAAATCGCA
60109 TTGCGA
1 TTGCGA
60115 ACTTGGAAGC
Statistics
Matches: 146, Mismatches: 20, Indels: 9
0.83 0.11 0.05
Matches are distributed among these distances:
20 111 0.76
21 3 0.02
22 5 0.03
23 27 0.18
ACGTcount: A:0.20, C:0.26, G:0.18, T:0.36
Consensus pattern (20 bp):
TTGCGATTCTCTAAATCGCA
Found at i:60045 original size:63 final size:62
Alignment explanation
Indices: 59923--60074 Score: 218
Period size: 63 Copynumber: 2.5 Consensus size: 62
59913 CTTTTTAACG
* * * *
59923 TTGCGATTCTCTAAATCGCGTTGCGA-T-TCTCTAACTCGCGTTGCGATTCTCTCAGTCGCA
1 TTGCGATTCTCTAAATCGCATTGCGATTCTCTCTAAATCGCGTTGCGACTCTCTCAATCGCA
* *
59983 TTGCGATTCTCTTAGTCGCATTGCGATTCTCTTCTAAATCGCGTTGCGACTCTCTCAATCGCA
1 TTGCGATTCTCTAAATCGCATTGCGATTCTC-TCTAAATCGCGTTGCGACTCTCTCAATCGCA
*
60046 TTGCGATTCTATAAATCGCATTGCGATTC
1 TTGCGATTCTCTAAATCGCATTGCGATTC
60075 AATCAATCGC
Statistics
Matches: 80, Mismatches: 9, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
60 23 0.29
61 1 0.01
62 2 0.03
63 54 0.68
ACGTcount: A:0.18, C:0.27, G:0.18, T:0.36
Consensus pattern (62 bp):
TTGCGATTCTCTAAATCGCATTGCGATTCTCTCTAAATCGCGTTGCGACTCTCTCAATCGCA
Found at i:60050 original size:83 final size:83
Alignment explanation
Indices: 59932--60114 Score: 260
Period size: 83 Copynumber: 2.2 Consensus size: 83
59922 GTTGCGATTC
* * * * * ** *
59932 TCTAAATCGCGTTGCGATTCTCTAACTCGCGTTGCGATTCTCTCAGTCGCATTGCGATTCTCTTA
1 TCTAAATCGCGTTGCGACTCTCTAACTCGCATTGCGATTCTATAAATCGCATTGCGATTCAATCA
*
59997 GTCGCATTGCGATTCTCT
66 ATCGCATTGCGATTCTCT
60015 TCTAAATCGCGTTGCGACTCTCTCAA-TCGCATTGCGATTCTATAAATCGCATTGCGATTCAATC
1 TCTAAATCGCGTTGCGACTCTCT-AACTCGCATTGCGATTCTATAAATCGCATTGCGATTCAATC
*
60079 AATCGCATTGCGATTTTCT
65 AATCGCATTGCGATTCTCT
60098 TCTAAATCGCGTTGCGA
1 TCTAAATCGCGTTGCGA
60115 ACTTGGAAGC
Statistics
Matches: 89, Mismatches: 10, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
83 87 0.98
84 2 0.02
ACGTcount: A:0.20, C:0.26, G:0.18, T:0.36
Consensus pattern (83 bp):
TCTAAATCGCGTTGCGACTCTCTAACTCGCATTGCGATTCTATAAATCGCATTGCGATTCAATCA
ATCGCATTGCGATTCTCT
Found at i:60191 original size:20 final size:20
Alignment explanation
Indices: 59921--60322 Score: 184
Period size: 20 Copynumber: 19.6 Consensus size: 20
59911 TTCTTTTTAA
*
59921 CGTTGCGATTCTCTAAATCG
1 CGTTGCGATTTTCTAAATCG
* *
59941 CGTTGCGATTCTCTAACTCG
1 CGTTGCGATTTTCTAAATCG
* * *
59961 CGTTGCGATTCTCTCAGTCG
1 CGTTGCGATTTTCTAAATCG
* * * *
59981 CATTGCGATTCTCTTAGTCG
1 CGTTGCGATTTTCTAAATCG
*
60001 CATTGCGATTCTCTTCTAAATCG
1 CGTTGCGA-T-T-TTCTAAATCG
* * *
60024 CGTTGCGACTCTCTCAATCG
1 CGTTGCGATTTTCTAAATCG
* * *
60044 CATTGCGATTCTATAAATCG
1 CGTTGCGATTTTCTAAATCG
* *** *
60064 CATTGCGATTCAATCAATCG
1 CGTTGCGATTTTCTAAATCG
*
60084 CATTGCGATTTTCTTCTAAATCG
1 CGTTGCGA--TT-TTCTAAATCG
** ** *
60107 CGTTGCGAACTTGGAAGCTCG
1 CGTTGCGATTTTCTAA-ATCG
* *
60128 CGTTGCGATTTTCT--TTTG
1 CGTTGCGATTTTCTAAATCG
*** **
60146 ACCGTTGCGATTTTCTTTTTAA
1 --CGTTGCGATTTTCTAAATCG
60168 CGTTGCGATTTTCTAAATCG
1 CGTTGCGATTTTCTAAATCG
* *
60188 CGTTGCGATTTT-GATATACG
1 CGTTGCGATTTTCTAAAT-CG
* **
60208 CGTTGCGATTTATGT-GTTCG
1 CGTTGCGATTT-TCTAAATCG
*
60228 CGTTGCGATTTTC-ATATTCG
1 CGTTGCGATTTTCTA-AATCG
**
60248 CGTTGCGATTTTGGAAAATCG
1 CGTTGCGATTTT-CTAAATCG
** * * *
60269 CAATGCGAATTTGTACTATCG
1 CGTTGCGATTTTCTA-AATCG
* *
60290 CATTGCGATTTTCAAGAATCG
1 CGTTGCGATTTTCTA-AATCG
60311 CGTTGCGATTTT
1 CGTTGCGATTTT
60323 GGAAACTGAT
Statistics
Matches: 301, Mismatches: 62, Indels: 37
0.75 0.16 0.09
Matches are distributed among these distances:
18 2 0.01
19 4 0.01
20 202 0.67
21 60 0.20
22 6 0.02
23 27 0.09
ACGTcount: A:0.19, C:0.22, G:0.21, T:0.38
Consensus pattern (20 bp):
CGTTGCGATTTTCTAAATCG
Found at i:60275 original size:21 final size:21
Alignment explanation
Indices: 60245--60327 Score: 78
Period size: 21 Copynumber: 4.0 Consensus size: 21
60235 ATTTTCATAT
*
60245 TCGCGTTGCGATTTTGGAAAA
1 TCGCATTGCGATTTTGGAAAA
* * * **
60266 TCGCAATGCGAATTTGTACTA
1 TCGCATTGCGATTTTGGAAAA
*
60287 TCGCATTGCGATTTT-CAAGAA
1 TCGCATTGCGATTTTGGAA-AA
*
60308 TCGCGTTGCGATTTTGGAAA
1 TCGCATTGCGATTTTGGAAA
60328 CTGATTTGCG
Statistics
Matches: 47, Mismatches: 13, Indels: 4
0.73 0.20 0.06
Matches are distributed among these distances:
20 1 0.02
21 44 0.94
22 2 0.04
ACGTcount: A:0.25, C:0.17, G:0.24, T:0.34
Consensus pattern (21 bp):
TCGCATTGCGATTTTGGAAAA
Found at i:61749 original size:3 final size:3
Alignment explanation
Indices: 61741--61772 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
61731 GATAAGAGAT
61741 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
61773 TTTTGATAAC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:61967 original size:3 final size:3
Alignment explanation
Indices: 61959--61989 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
61949 CATGTGATGG
61959 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
61990 TGAGCTTTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:66204 original size:2 final size:2
Alignment explanation
Indices: 66197--66224 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
66187 AAAGCATGTT
66197 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
66225 ATTATGTAAA
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:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:67773 original size:44 final size:44
Alignment explanation
Indices: 67724--67810 Score: 149
Period size: 44 Copynumber: 2.0 Consensus size: 44
67714 ATGGTATTCG
*
67724 TGTTCGTTTATTTTTTGTTCGCGAA-AATGTTCATTTAATGTTTT
1 TGTTCGTTTATTTTTTGTTCGCGAACAAT-ATCATTTAATGTTTT
67768 TGTTCGTTTATTTTTTGTTCGCGAACAATATCATTTAATGTTT
1 TGTTCGTTTATTTTTTGTTCGCGAACAATATCATTTAATGTTT
67811 GCAAACATGT
Statistics
Matches: 41, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
44 38 0.93
45 3 0.07
ACGTcount: A:0.20, C:0.10, G:0.15, T:0.55
Consensus pattern (44 bp):
TGTTCGTTTATTTTTTGTTCGCGAACAATATCATTTAATGTTTT
Found at i:67861 original size:23 final size:23
Alignment explanation
Indices: 67831--67875 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
67821 TTGTTTATAT
*
67831 GTTCACGAACATATTCATTTAGC
1 GTTCACGAAAATATTCATTTAGC
*
67854 GTTCACGAAAATGTTCATTTAG
1 GTTCACGAAAATATTCATTTAG
67876 TATTCGTTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.31, C:0.18, G:0.16, T:0.36
Consensus pattern (23 bp):
GTTCACGAAAATATTCATTTAGC
Found at i:69580 original size:2 final size:2
Alignment explanation
Indices: 69573--69621 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
69563 GTTGTTTCTG
69573 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
69615 AT AT AT A
1 AT AT AT A
69622 ATGTATGTTG
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:75446 original size:21 final size:20
Alignment explanation
Indices: 75421--75519 Score: 81
Period size: 21 Copynumber: 4.8 Consensus size: 20
75411 AATCAGTTTC
75421 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * *
75442 GAAAATCGCAATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
75463 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
75483 CCAAAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
75504 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
75520 ACACATAAAT
Statistics
Matches: 61, Mismatches: 15, Indels: 5
0.75 0.19 0.06
Matches are distributed among these distances:
20 16 0.26
21 45 0.74
ACGTcount: A:0.37, C:0.23, G:0.18, T:0.21
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:75548 original size:20 final size:20
Alignment explanation
Indices: 75486--75679 Score: 203
Period size: 20 Copynumber: 9.7 Consensus size: 20
75476 CGATTTTCCA
* ** *
75486 AAATCGCAACGCGAATATGA
1 AAATCGCAACGCGTATCCGT
* *
75506 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTATC-CGT
75526 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
75546 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGT
**
75566 AAATCGCAACGCGTATGGGT
1 AAATCGCAACGCGTATCCGT
* * *
75586 AAATCGTAATGCATATCCGT
1 AAATCGCAACGCGTATCCGT
*
75606 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
* * *
75626 AAATCGCAACG-ATAATACAT
1 AAATCGCAACGCGT-ATCCGT
75646 AAAATCGCAACGCGTATCCGT
1 -AAATCGCAACGCGTATCCGT
75667 AAATCGCAACGCG
1 AAATCGCAACGCG
75680 ATATTTAAAG
Statistics
Matches: 142, Mismatches: 27, Indels: 10
0.79 0.15 0.06
Matches are distributed among these distances:
19 2 0.01
20 122 0.86
21 17 0.12
22 1 0.01
ACGTcount: A:0.36, C:0.25, G:0.19, T:0.20
Consensus pattern (20 bp):
AAATCGCAACGCGTATCCGT
Found at i:75570 original size:60 final size:60
Alignment explanation
Indices: 75486--75679 Score: 235
Period size: 60 Copynumber: 3.2 Consensus size: 60
75476 CGATTTTCCA
* ** * *
75486 AAATCGCAACGCGAATATGAAAATCGCAACGCGAACACATAAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
* * *** * * *
75546 AAATCGCAACGTGTATCCGTAAATCGCAACGCGTATGGGTAAATCGTAATGCATATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
* **
75606 ATATCGCAACGCGTATCCGTAAATCGCAACGATAATACATAAAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACAT-AAATCGCAACGCGTATCCGT
75667 AAATCGCAACGCG
1 AAATCGCAACGCG
75680 ATATTTAAAG
Statistics
Matches: 108, Mismatches: 25, Indels: 1
0.81 0.19 0.01
Matches are distributed among these distances:
60 79 0.73
61 29 0.27
ACGTcount: A:0.36, C:0.25, G:0.19, T:0.20
Consensus pattern (60 bp):
AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
Found at i:76095 original size:32 final size:32
Alignment explanation
Indices: 76057--76125 Score: 111
Period size: 32 Copynumber: 2.2 Consensus size: 32
76047 ATTTCACTTA
*
76057 GATTTCATTTCGCGTTACGATTCTGTCGTTGC
1 GATTTCATTTCGCGTTACGATTCTCTCGTTGC
* *
76089 GATTTCATTTCGCGTTGCTATTCTCTCGTTGC
1 GATTTCATTTCGCGTTACGATTCTCTCGTTGC
76121 GATTT
1 GATTT
76126 TCAAGTTAGT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.12, C:0.22, G:0.20, T:0.46
Consensus pattern (32 bp):
GATTTCATTTCGCGTTACGATTCTCTCGTTGC
Found at i:76106 original size:18 final size:18
Alignment explanation
Indices: 76057--76106 Score: 54
Period size: 18 Copynumber: 3.0 Consensus size: 18
76047 ATTTCACTTA
*
76057 GATTTCATTTCGCGTTAC
1 GATTTCATTTCGCGTTGC
*
76075 GA-TTC-TGT--CGTTGC
1 GATTTCATTTCGCGTTGC
76089 GATTTCATTTCGCGTTGC
1 GATTTCATTTCGCGTTGC
76107 TATTCTCTCG
Statistics
Matches: 25, Mismatches: 3, Indels: 8
0.69 0.08 0.22
Matches are distributed among these distances:
14 7 0.28
15 3 0.12
16 4 0.16
17 3 0.12
18 8 0.32
ACGTcount: A:0.12, C:0.22, G:0.22, T:0.44
Consensus pattern (18 bp):
GATTTCATTTCGCGTTGC
Found at i:76252 original size:20 final size:20
Alignment explanation
Indices: 76208--76317 Score: 108
Period size: 21 Copynumber: 5.8 Consensus size: 20
76198 TGCAGAAGAG
*
76208 TCGCAACGAGATAAATGAAAA
1 TCGCAACGAGA-GAATGAAAA
***
76229 TCGCAACGAGAGAATGACTG
1 TCGCAACGAGAGAATGAAAA
76249 TCGCAACGAGAGAAATGAAAA
1 TCGCAACGAGAG-AATGAAAA
76270 TCGCAAC--GAG-A-G--AA
1 TCGCAACGAGAGAATGAAAA
*
76284 TCGCAACGCGA-AATGAAAA
1 TCGCAACGAGAGAATGAAAA
76303 TCGCAACGAGAGAAT
1 TCGCAACGAGAGAAT
76318 CGCAACGCGA
Statistics
Matches: 73, Mismatches: 8, Indels: 17
0.74 0.08 0.17
Matches are distributed among these distances:
14 9 0.12
16 4 0.05
17 2 0.03
19 15 0.21
20 20 0.27
21 23 0.32
ACGTcount: A:0.45, C:0.18, G:0.25, T:0.12
Consensus pattern (20 bp):
TCGCAACGAGAGAATGAAAA
Found at i:76265 original size:41 final size:38
Alignment explanation
Indices: 76201--76317 Score: 145
Period size: 41 Copynumber: 3.1 Consensus size: 38
76191 TTCAATTTGC
* *
76201 AGAAGAGTCGCAACGAGATAAATGAAAATCGCAACGAG
1 AGAATAGTCGCAACGAGAGAAATGAAAATCGCAACGAG
76239 AGAATGACTGTCGCAACGAGAGAAATGAAAATCGCAACGAG
1 AGAAT-A--GTCGCAACGAGAGAAATGAAAATCGCAACGAG
*
76280 AG-A-A-TCGCAAC--GCGAAATGAAAATCGCAACGAG
1 AGAATAGTCGCAACGAGAGAAATGAAAATCGCAACGAG
76313 AGAAT
1 AGAAT
76318 CGCAACGCGA
Statistics
Matches: 71, Mismatches: 3, Indels: 13
0.82 0.03 0.15
Matches are distributed among these distances:
33 23 0.32
34 1 0.01
35 7 0.10
38 5 0.07
39 1 0.01
40 1 0.01
41 33 0.46
ACGTcount: A:0.46, C:0.17, G:0.26, T:0.11
Consensus pattern (38 bp):
AGAATAGTCGCAACGAGAGAAATGAAAATCGCAACGAG
Found at i:76287 original size:14 final size:14
Alignment explanation
Indices: 76268--76324 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
76258 GAGAAATGAA
76268 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
76282 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
76301 AATCGCAACGAGAG
1 AATCGCAACGAGAG
76315 AATCGCAACG
1 AATCGCAACG
76325 CGAAACCAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.28
ACGTcount: A:0.44, C:0.23, G:0.25, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:76300 original size:33 final size:33
Alignment explanation
Indices: 76260--76340 Score: 144
Period size: 33 Copynumber: 2.5 Consensus size: 33
76250 CGCAACGAGA
76260 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
76293 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
**
76326 GAAACCAAAATCGCA
1 GAAATGAAAATCGCA
76341 TTGCGATTTT
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 46 1.00
ACGTcount: A:0.47, C:0.22, G:0.22, T:0.09
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:76363 original size:19 final size:19
Alignment explanation
Indices: 76341--76433 Score: 71
Period size: 19 Copynumber: 5.4 Consensus size: 19
76331 CAAAATCGCA
76341 TTGCGATTTTCATTTTGCG
1 TTGCGATTTTCATTTTGCG
*
76360 TTGCGA--TTC--TCT-CG
1 TTGCGATTTTCATTTTGCG
*
76374 TTGCGATTTTCATTTCGCG
1 TTGCGATTTTCATTTTGCG
*
76393 TTGCGA--TTC--TCT-CG
1 TTGCGATTTTCATTTTGCG
* *
76407 TTGCGATTGTCATTTCGCG
1 TTGCGATTTTCATTTTGCG
76426 TTGCGATT
1 TTGCGATT
76434 CTCTCGTTGC
Statistics
Matches: 56, Mismatches: 8, Indels: 20
0.67 0.10 0.24
Matches are distributed among these distances:
14 16 0.29
15 3 0.05
16 5 0.09
17 6 0.11
18 2 0.04
19 24 0.43
ACGTcount: A:0.10, C:0.22, G:0.23, T:0.46
Consensus pattern (19 bp):
TTGCGATTTTCATTTTGCG
Found at i:76375 original size:14 final size:14
Alignment explanation
Indices: 76358--76447 Score: 72
Period size: 14 Copynumber: 5.7 Consensus size: 14
76348 TTTCATTTTG
76358 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
76372 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
76391 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
76405 CGTTGCGATTGTCATTTCG
1 CGTTGCGA-T-TC---TCT
76424 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
76438 CGTTGCGATT
1 CGTTGCGATT
76448 TTCATTTCAA
Statistics
Matches: 62, Mismatches: 4, Indels: 20
0.72 0.05 0.23
Matches are distributed among these distances:
14 30 0.48
15 1 0.02
16 5 0.08
17 5 0.08
18 1 0.02
19 20 0.32
ACGTcount: A:0.09, C:0.24, G:0.23, T:0.43
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:76383 original size:33 final size:33
Alignment explanation
Indices: 76341--76455 Score: 212
Period size: 33 Copynumber: 3.5 Consensus size: 33
76331 CAAAATCGCA
*
76341 TTGCGATTTTCATTTTGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
76374 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
*
76407 TTGCGATTGTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
76440 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
76456 AACCAAAAGA
Statistics
Matches: 79, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 79 1.00
ACGTcount: A:0.10, C:0.23, G:0.21, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:78306 original size:93 final size:93
Alignment explanation
Indices: 78147--78522 Score: 727
Period size: 93 Copynumber: 4.1 Consensus size: 93
78137 TAGATTGCTT
* *
78147 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGAGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
78212 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
78240 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
78305 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
78333 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
78398 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
78426 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
78491 TTTGTCTTTGTTTTGTCTTTTGGTTG-A
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
78518 AGTAA
1 AGTAA
78523 TGCAATCCAT
Statistics
Matches: 281, Mismatches: 2, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
92 6 0.02
93 275 0.98
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:78610 original size:19 final size:19
Alignment explanation
Indices: 78570--78698 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
78560 TAGTTTACTT
* *
78570 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-CAAAA
78590 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
**
78609 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAACCAAAA
*
78628 TCGCAA--CG--A-CAGAA
1 TCGCAACGCGAAACCAAAA
78642 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
*
78661 TCGCAA--CG--A-CAAGA
1 TCGCAACGCGAAACCAAAA
78675 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
78694 TCGCA
1 TCGCA
78699 TTGCGATTTT
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 19 0.21
15 2 0.02
16 4 0.04
17 4 0.04
18 2 0.02
19 46 0.51
20 13 0.14
ACGTcount: A:0.46, C:0.29, G:0.17, T:0.09
Consensus pattern (19 bp):
TCGCAACGCGAAACCAAAA
Found at i:78649 original size:33 final size:32
Alignment explanation
Indices: 78606--78698 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 32
78596 CGCGAAACCA
**
78606 AAATCGCAACGCGAAATGAAAATCGCAACGAC
1 AAATCGCAACGCGAAACCAAAATCGCAACGAC
78638 AGAATCGCAACGCGAAACCAAAATCGCAACGAC
1 A-AATCGCAACGCGAAACCAAAATCGCAACGAC
78671 AAGATCGCAACGCGAAACCAAAATCGCA
1 AA-ATCGCAACGCGAAACCAAAATCGCA
78699 TTGCGATTTT
Statistics
Matches: 57, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
32 2 0.04
33 55 0.96
ACGTcount: A:0.46, C:0.28, G:0.18, T:0.08
Consensus pattern (32 bp):
AAATCGCAACGCGAAACCAAAATCGCAACGAC
Found at i:78696 original size:52 final size:52
Alignment explanation
Indices: 78570--78698 Score: 140
Period size: 52 Copynumber: 2.5 Consensus size: 52
78560 TAGTTTACTT
**
78570 TCGCAACACGAAACTTAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
1 TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
* * *
78622 T-G-AAAATCGCAACGACAGAATCGCAACGCGAAACCAAAATCGCAACGAC-AAGA
1 TCGCAACA-CGAAAC-ACAAAATCGCAACGCGAAACCAAAATCGCAACG-CGAA-A
*
78675 TCGCAACGCGAAAC-CAAAATCGCA
1 TCGCAACACGAAACACAAAATCGCA
78699 TTGCGATTTT
Statistics
Matches: 62, Mismatches: 9, Indels: 12
0.75 0.11 0.14
Matches are distributed among these distances:
50 3 0.05
51 6 0.10
52 42 0.68
53 3 0.05
54 6 0.10
55 2 0.03
ACGTcount: A:0.46, C:0.29, G:0.17, T:0.09
Consensus pattern (52 bp):
TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
Found at i:78716 original size:19 final size:19
Alignment explanation
Indices: 78694--78828 Score: 128
Period size: 19 Copynumber: 7.6 Consensus size: 19
78684 GAAACCAAAA
*
78694 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
78713 TCGCGTTGCGA--TTC-TT
1 TCGCGTTGCGATTTTCATT
78729 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* *
78746 TCGCATTGCGA--TTC-TG
1 TCGCGTTGCGATTTTCATT
78762 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
78779 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
*
78798 TCGCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTTCA-TT
*
78818 TCGTGTTGCGA
1 TCGCGTTGCGA
78829 AAGTAAACTA
Statistics
Matches: 95, Mismatches: 10, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 15 0.16
16 11 0.12
17 11 0.12
19 46 0.48
20 12 0.13
ACGTcount: A:0.11, C:0.19, G:0.24, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:78735 original size:14 final size:14
Alignment explanation
Indices: 78716--78772 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
78706 TTTCATTTCG
78716 CGTTGCGATTCTTT
1 CGTTGCGATTCTTT
78730 CGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-TTT
*
78747 CGCATTGCGATTCTGT
1 CG--TTGCGATTCTTT
78763 CGTTGCGATT
1 CGTTGCGATT
78773 TTCATTTCGC
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 16 0.43
16 7 0.19
17 8 0.22
19 6 0.16
ACGTcount: A:0.11, C:0.21, G:0.23, T:0.46
Consensus pattern (14 bp):
CGTTGCGATTCTTT
Found at i:78741 original size:33 final size:33
Alignment explanation
Indices: 78699--78791 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
78689 CAAAATCGCA
*
78699 TTGCGATTTTCATTTCGCGTTGCGATTCTTTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
*
78732 TTGCGATTTTCATTTCGCATTGCGATTCTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
78765 TTGCGATTTTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCGTTGCGATT
78792 TTGGTTTCGC
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.11, C:0.20, G:0.22, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
Found at i:80765 original size:14 final size:14
Alignment explanation
Indices: 80746--80781 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
80736 ATTGTTTAAT
80746 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
80760 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
80774 TGATTTGT
1 TGATTTGT
80782 GTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:80903 original size:19 final size:19
Alignment explanation
Indices: 80887--80984 Score: 143
Period size: 19 Copynumber: 5.4 Consensus size: 19
80877 AAAAATGACT
80887 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
80906 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
80925 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
80939 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
80958 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
80978 ATCGCAA
1 ATCGCAA
80985 CGAGAGAATC
Statistics
Matches: 71, Mismatches: 2, Indels: 11
0.85 0.02 0.13
Matches are distributed among these distances:
14 10 0.14
15 1 0.01
16 2 0.03
17 2 0.03
18 1 0.01
19 39 0.55
20 16 0.23
ACGTcount: A:0.46, C:0.17, G:0.22, T:0.14
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:81016 original size:53 final size:53
Alignment explanation
Indices: 80887--81002 Score: 225
Period size: 53 Copynumber: 2.2 Consensus size: 53
80877 AAAAATGACT
80887 ATCGCAATGCGAAATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
80939 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
80992 ATCGCAATGCG
1 ATCGCAATGCG
81003 TTTATAATTT
Statistics
Matches: 63, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
52 29 0.46
53 34 0.54
ACGTcount: A:0.44, C:0.18, G:0.24, T:0.14
Consensus pattern (53 bp):
ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
Found at i:81247 original size:157 final size:154
Alignment explanation
Indices: 81009--81321 Score: 583
Period size: 157 Copynumber: 2.0 Consensus size: 154
80999 TGCGTTTATA
81009 ATTTCGCATTGCGATTCTCTCGTTGCGATTTCATTTCGCATTGCGATTTCATTTCGCATTGCGAT
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTCATTTCGCATTGCGATTTCATTTCGCATTGCGAT
81074 TCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGA
66 TCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGA
81139 TTTTCATTT-CGCATTGCGATTTTC
131 -TTTCATTTCCGCATTGCGATTTTC
81163 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATTTCGCATTGC
1 ATTTCGCATTGCGATTCTCTCGTTGCGA-TTTCATTT-CGCATTGCGA-TTTCATTTCGCATTGC
81228 GATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTG
63 GATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTG
81293 CGATTTCATTTCCGCATTGCGATTTTC
128 CGATTTCATTTCCGCATTGCGATTTTC
81320 AT
1 AT
81322 GTTGGGATTT
Statistics
Matches: 155, Mismatches: 0, Indels: 5
0.97 0.00 0.03
Matches are distributed among these distances:
154 28 0.18
155 8 0.05
156 18 0.12
157 101 0.65
ACGTcount: A:0.14, C:0.24, G:0.17, T:0.45
Consensus pattern (154 bp):
ATTTCGCATTGCGATTCTCTCGTTGCGATTTCATTTCGCATTGCGATTTCATTTCGCATTGCGAT
TCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGA
TTTCATTTCCGCATTGCGATTTTC
Found at i:81349 original size:52 final size:52
Alignment explanation
Indices: 81009--81321 Score: 587
Period size: 52 Copynumber: 6.0 Consensus size: 52
80999 TGCGTTTATA
81009 ATTTCGCATTGCGATTCTCTCGTTGCGA-TTTCATTTCGCATTGCGA-TTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
81059 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
81111 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
81163 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTT-CGCATTGCGATTTTC
81216 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
81268 ATTTCGCATTGCGATTCTCTCGTTGCGA-TTTCATTTCCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTT-CGCATTGCGATTTTC
81320 AT
1 AT
81322 GTTGGGATTT
Statistics
Matches: 259, Mismatches: 0, Indels: 6
0.98 0.00 0.02
Matches are distributed among these distances:
50 28 0.11
51 26 0.10
52 153 0.59
53 52 0.20
ACGTcount: A:0.14, C:0.24, G:0.17, T:0.45
Consensus pattern (52 bp):
ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
Found at i:81371 original size:33 final size:33
Alignment explanation
Indices: 81049--81363 Score: 270
Period size: 33 Copynumber: 9.2 Consensus size: 33
81039 TCATTTCGCA
81049 TTGCGA-TTTCATTTCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
*
81081 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCG
1 TTGCGATTTTCATTTCGCATTGCGA--TTC-TCTCG
* * * * *
81117 CATTGCGATTCTCTCGTTGCG-ATTTTC-ATT-TCGCA
1 --TTGCGATT-T-TCATTTCGCA-TTGCGATTCTCTCG
81152 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
*
81185 TTGCGATTTTCATTTCCGCATTGCGATTTTCATTTCG
1 TTGCGATTTTCATTT-CGCATTGCGA--TTC-TCTCG
* * * * *
81222 CATTGCGATTCTCTCGTTGCG-ATTTTC-ATT-TCGCA
1 --TTGCGATT-T-TCATTTCGCA-TTGCGATTCTCTCG
81257 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
*
81290 TTGCGA-TTTCATTTCCGCATTGCGATTTTCAT-G
1 TTGCGATTTTCATTT-CGCATTGCGATTCTC-TCG
*
81323 TTGGGATTTTCATTTCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
81356 TTGCGATT
1 TTGCGATT
81364 GTAATTTCCG
Statistics
Matches: 227, Mismatches: 28, Indels: 55
0.73 0.09 0.18
Matches are distributed among these distances:
31 18 0.08
32 25 0.11
33 103 0.45
34 19 0.08
35 7 0.03
36 7 0.03
37 8 0.04
38 8 0.04
39 13 0.06
40 15 0.07
41 4 0.02
ACGTcount: A:0.13, C:0.23, G:0.18, T:0.46
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
Found at i:83877 original size:24 final size:24
Alignment explanation
Indices: 83843--83889 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
83833 CTGAAACATC
83843 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
83867 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
83890 GACCAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGGATATTGACCAAT
Found at i:84597 original size:20 final size:20
Alignment explanation
Indices: 84569--84798 Score: 221
Period size: 20 Copynumber: 11.5 Consensus size: 20
84559 AAATTTCAGT
* * *
84569 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
84589 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
* *
84609 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
84629 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
*
84649 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
* *
84669 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATTCGC
* ** * *
84689 ATTGCGATTTACCCATACGT
1 GTTGCGATTTACGGATTCGC
* *
84709 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATTCGC
*
84729 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
*
84749 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATTCGC
**
84769 GTTGCGATTTTA-ATATTCGC
1 GTTGCGA-TTTACGGATTCGC
84789 GTTGCGATTT
1 GTTGCGATTT
84799 TGGAAAATCG
Statistics
Matches: 181, Mismatches: 26, Indels: 7
0.85 0.12 0.03
Matches are distributed among these distances:
19 3 0.02
20 173 0.96
21 5 0.03
ACGTcount: A:0.20, C:0.18, G:0.25, T:0.37
Consensus pattern (20 bp):
GTTGCGATTTACGGATTCGC
Found at i:84799 original size:20 final size:20
Alignment explanation
Indices: 84765--84862 Score: 83
Period size: 21 Copynumber: 4.8 Consensus size: 20
84755 ATTTATGTGT
*
84765 TCGCGTTGCGATTTTAATAT
1 TCGCGTTGCGATTTTAATAA
84785 TCGCGTTGCGATTTTGGAA-AA
1 TCGCGTTGCGATTTT--AATAA
** *
84806 TCGCAATGCGAATTTGTACT-A
1 TCGCGTTGCG-ATTT-TAATAA
* *
84827 TCGCATTGCGATTTTCAAGAA
1 TCGCGTTGCGATTTT-AATAA
84848 TCGCGTTGCGATTTT
1 TCGCGTTGCGATTTT
84863 GGAAACTGAT
Statistics
Matches: 63, Mismatches: 8, Indels: 13
0.75 0.10 0.15
Matches are distributed among these distances:
19 1 0.02
20 20 0.32
21 35 0.56
22 6 0.10
23 1 0.02
ACGTcount: A:0.22, C:0.17, G:0.22, T:0.38
Consensus pattern (20 bp):
TCGCGTTGCGATTTTAATAA
Found at i:84858 original size:42 final size:43
Alignment explanation
Indices: 84765--84863 Score: 107
Period size: 42 Copynumber: 2.4 Consensus size: 43
84755 ATTTATGTGT
* *
84765 TCGCGTTGCG-ATTT-TAATATTCGCGTTGCGATTTTGGAAAA
1 TCGCGTTGCGAATTTGTAATATTCGCATTGCGATTTTGCAAAA
** *
84806 TCGCAATGCGAATTTGTACTA-TCGCATTGCGATTTT-CAAGAA
1 TCGCGTTGCGAATTTGTAATATTCGCATTGCGATTTTGCAA-AA
*
84848 TCGCGTTGCGATTTTG
1 TCGCGTTGCGAATTTG
84864 GAAACTGATT
Statistics
Matches: 47, Mismatches: 8, Indels: 5
0.78 0.13 0.08
Matches are distributed among these distances:
41 10 0.21
42 33 0.70
43 4 0.09
ACGTcount: A:0.22, C:0.17, G:0.23, T:0.37
Consensus pattern (43 bp):
TCGCGTTGCGAATTTGTAATATTCGCATTGCGATTTTGCAAAA
Found at i:85746 original size:48 final size:48
Alignment explanation
Indices: 85672--85776 Score: 192
Period size: 48 Copynumber: 2.2 Consensus size: 48
85662 TTCAAATAGA
85672 AAATTAAATTAAAGACCTAAACTATAACCTAAATAGCTAAAAGGAACT
1 AAATTAAATTAAAGACCTAAACTATAACCTAAATAGCTAAAAGGAACT
* *
85720 AAATTAAATTAAATACCTAAAGTATAACCTAAATAGCTAAAAGGAACT
1 AAATTAAATTAAAGACCTAAACTATAACCTAAATAGCTAAAAGGAACT
85768 AAATTAAAT
1 AAATTAAAT
85777 AAAAATAAAA
Statistics
Matches: 55, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
48 55 1.00
ACGTcount: A:0.55, C:0.12, G:0.08, T:0.25
Consensus pattern (48 bp):
AAATTAAATTAAAGACCTAAACTATAACCTAAATAGCTAAAAGGAACT
Found at i:92980 original size:40 final size:40
Alignment explanation
Indices: 92936--93016 Score: 162
Period size: 40 Copynumber: 2.0 Consensus size: 40
92926 TTCCATACAT
92936 GAATTCTTGAAGTTCTTCTGCATTATTCAACACTGTGTTA
1 GAATTCTTGAAGTTCTTCTGCATTATTCAACACTGTGTTA
92976 GAATTCTTGAAGTTCTTCTGCATTATTCAACACTGTGTTA
1 GAATTCTTGAAGTTCTTCTGCATTATTCAACACTGTGTTA
93016 G
1 G
93017 GTTTAGGAAG
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 41 1.00
ACGTcount: A:0.25, C:0.17, G:0.16, T:0.42
Consensus pattern (40 bp):
GAATTCTTGAAGTTCTTCTGCATTATTCAACACTGTGTTA
Found at i:94115 original size:16 final size:17
Alignment explanation
Indices: 94082--94115 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
94072 ATCTGTTACC
*
94082 TAAAACATATTATTATT
1 TAAAACAAATTATTATT
94099 TAAAACAAATT-TTATT
1 TAAAACAAATTATTATT
94115 T
1 T
94116 TTGTTAAATG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.47, C:0.06, G:0.00, T:0.47
Consensus pattern (17 bp):
TAAAACAAATTATTATT
Found at i:94193 original size:36 final size:36
Alignment explanation
Indices: 94146--94219 Score: 148
Period size: 36 Copynumber: 2.1 Consensus size: 36
94136 GGCTATTAGC
94146 TCAGTTGGTTAGAGCGTCGTGCTAATAACGCGAAGG
1 TCAGTTGGTTAGAGCGTCGTGCTAATAACGCGAAGG
94182 TCAGTTGGTTAGAGCGTCGTGCTAATAACGCGAAGG
1 TCAGTTGGTTAGAGCGTCGTGCTAATAACGCGAAGG
94218 TC
1 TC
94220 GCAGGTTCGA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 38 1.00
ACGTcount: A:0.24, C:0.18, G:0.32, T:0.26
Consensus pattern (36 bp):
TCAGTTGGTTAGAGCGTCGTGCTAATAACGCGAAGG
Found at i:96435 original size:313 final size:308
Alignment explanation
Indices: 95866--96489 Score: 926
Period size: 313 Copynumber: 2.0 Consensus size: 308
95856 GATTTGTGTC
*
95866 GATTTACCTTCCAAGAGGACTGGAGTTTTGTCAAGATGTCTTTTCCTTTTCCAGTGTATAAGCAT
1 GATTTACCTTCCAAGAGGACTGGAGTTCTGTCAAGATGTCTTTTCCTTTTCCAGTGTATAAGCAT
95931 GTCTAGACCTTCCTTACCTGTAAAGTCCTCGTGGAGCATTAAGTTGCTGTACAATTCTAACGGGC
66 GTCTAGACCTTCCTTACCTGTAAAGTCCTCGTGGAGCATTAAGTTGCTGTACAATTCTAACGGGC
* *
95996 CTGACCTTTTCTGTTGCGGAGTGTGCCTCCTTTGTTTCTAATCATTAGCATACAATTTTCTGGGC
131 CTGACCTTTTCTGTTGCGGAGTGTGCCACCTTTGTCTCTAATCATTAGCATACAATTTTCTGGGC
* ** *
96061 TACTATGTTCCAAATGATGGTAAAGAGCAGCTGTGTGTGCACGGACGATAATGTAGTTTTCCTGA
196 CACTATGTTCCAAATGATGACAAAGAGCAGCTGTGTGTGCACGCACGATAATGTAGTTTTCCTGA
* * *
96126 GGGCGGTGTTAATTGCTTTTGGATGGGATTGGTATCATCATATCGGTT
261 GGGCAGTGTTAATCGCTTTTGGATGGGATTGGTATCATCATATCGGCT
* *
96174 GATTTGCCTTCCAAGAGGACTGGAGTTCTGTCAAGATGTCTTTTCCTTTTCTAGTGTATATGAAA
1 GATTTACCTTCCAAGAGGACTGGAGTTCTGTCAAGATGTCTTTTCCTTTTCCAGTG--TAT--AA
* * * * * *
96239 GCATGTCTAGACCTTCCTTACTTGTGAAGTCCTTGTGGAGCCTTAAGTTGCTGTACAATTCTCAT
62 GCATGTCTAGACCTTCCTTACCTGTAAAGTCCTCGTGGAGCATTAAGTTGCTGTACAATTCTAAC
* * * * * * *
96304 GTGCTTGACCTTTTTTTGTTGCGGAGTGTGCCACCTTTGTCTCTACTCGTTTGCGTACAATTTTC
127 GGGCCTGACC-TTTTCTGTTGCGGAGTGTGCCACCTTTGTCTCTAATCATTAGCATACAATTTTC
* * * *
96369 TGGGCCACTATGTTCCAGATGATGACAAAGAGCAGCTGTGTAGT-CATGCATGATTATGTAGTTT
191 TGGGCCACTATGTTCCAAATGATGACAAAGAGCAGCTGTGT-GTGCACGCACGATAATGTAGTTT
96433 TCCTGAGGGCAGTGTTAATCGCTTTTGGATGGGATTGGTATCATCATATCGGCT
255 TCCTGAGGGCAGTGTTAATCGCTTTTGGATGGGATTGGTATCATCATATCGGCT
96487 GAT
1 GAT
96490 GTGGTTAGTG
Statistics
Matches: 281, Mismatches: 29, Indels: 7
0.89 0.09 0.02
Matches are distributed among these distances:
308 53 0.19
310 3 0.01
312 69 0.25
313 154 0.55
314 2 0.01
ACGTcount: A:0.21, C:0.19, G:0.24, T:0.37
Consensus pattern (308 bp):
GATTTACCTTCCAAGAGGACTGGAGTTCTGTCAAGATGTCTTTTCCTTTTCCAGTGTATAAGCAT
GTCTAGACCTTCCTTACCTGTAAAGTCCTCGTGGAGCATTAAGTTGCTGTACAATTCTAACGGGC
CTGACCTTTTCTGTTGCGGAGTGTGCCACCTTTGTCTCTAATCATTAGCATACAATTTTCTGGGC
CACTATGTTCCAAATGATGACAAAGAGCAGCTGTGTGTGCACGCACGATAATGTAGTTTTCCTGA
GGGCAGTGTTAATCGCTTTTGGATGGGATTGGTATCATCATATCGGCT
Found at i:102603 original size:23 final size:23
Alignment explanation
Indices: 102576--102623 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
102566 TCTTATTGGA
102576 ACTATTAAGACATAAACATAACT
1 ACTATTAAGACATAAACATAACT
102599 ACTATTAAGACATAAACATAACT
1 ACTATTAAGACATAAACATAACT
102622 AC
1 AC
102624 ATGGAAACTA
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:0.52, C:0.19, G:0.04, T:0.25
Consensus pattern (23 bp):
ACTATTAAGACATAAACATAACT
Found at i:102807 original size:20 final size:18
Alignment explanation
Indices: 102770--102810 Score: 55
Period size: 20 Copynumber: 2.2 Consensus size: 18
102760 TTAAAAGTAA
*
102770 ATTTTTTTTATATTTTAT
1 ATTTTTTTTATATATTAT
102788 ATTTTTCTTTAATATATTAT
1 ATTTTT-TTT-ATATATTAT
102808 ATT
1 ATT
102811 AAATTTCATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 6 0.30
19 3 0.15
20 11 0.55
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.71
Consensus pattern (18 bp):
ATTTTTTTTATATATTAT
Found at i:105294 original size:25 final size:26
Alignment explanation
Indices: 105256--105307 Score: 72
Period size: 25 Copynumber: 2.0 Consensus size: 26
105246 AGGTACACCA
*
105256 TTCTCCTTTCCTTT-TCTTTTGTAGGT
1 TTCTCCTTTACTTTCT-TTTTGTAGGT
105282 TTCT-CTTTACTTTCTTTTTGTAGGT
1 TTCTCCTTTACTTTCTTTTTGTAGGT
105307 T
1 T
105308 ATTCATCTCC
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
25 19 0.79
26 5 0.21
ACGTcount: A:0.06, C:0.19, G:0.12, T:0.63
Consensus pattern (26 bp):
TTCTCCTTTACTTTCTTTTTGTAGGT
Found at i:115394 original size:29 final size:29
Alignment explanation
Indices: 115346--115408 Score: 101
Period size: 29 Copynumber: 2.2 Consensus size: 29
115336 AGTGTTGGCC
*
115346 GTAGGTCGCCATGCCTTCCGGGCGACCTT
1 GTAGGTCGCCATGACTTCCGGGCGACCTT
115375 GTAGGTCGCCATGAAC-TCCGGGCGACCTT
1 GTAGGTCGCCATG-ACTTCCGGGCGACCTT
115404 GTAGG
1 GTAGG
115409 CCCAACACAT
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
29 31 0.97
30 1 0.03
ACGTcount: A:0.14, C:0.30, G:0.33, T:0.22
Consensus pattern (29 bp):
GTAGGTCGCCATGACTTCCGGGCGACCTT
Found at i:115549 original size:23 final size:22
Alignment explanation
Indices: 115500--115590 Score: 77
Period size: 20 Copynumber: 4.2 Consensus size: 22
115490 CCTCGGATTC
* *
115500 CCTCGCATAGCTCGCTCGGCTGC
1 CCTCGCATAGCTCG-TCGGATGG
115523 CCTCGCATAGCTCGTTCGGATGG
1 CCTCGCATAGCTCG-TCGGATGG
115546 CCTCAG-AT-GCTC-TCGGATGG
1 CCTC-GCATAGCTCGTCGGATGG
*
115566 CCTCTG-AT-GCTC-TCGGATAG
1 CCTC-GCATAGCTCGTCGGATGG
115586 CCTCG
1 CCTCG
115591 GTCGGATGGC
Statistics
Matches: 62, Mismatches: 5, Indels: 6
0.85 0.07 0.08
Matches are distributed among these distances:
19 1 0.02
20 30 0.48
22 4 0.06
23 26 0.42
24 1 0.02
ACGTcount: A:0.12, C:0.35, G:0.27, T:0.25
Consensus pattern (22 bp):
CCTCGCATAGCTCGTCGGATGG
Found at i:115563 original size:20 final size:20
Alignment explanation
Indices: 115538--115589 Score: 86
Period size: 20 Copynumber: 2.6 Consensus size: 20
115528 CATAGCTCGT
115538 TCGGATGGCCTCAGATGCTC
1 TCGGATGGCCTCAGATGCTC
*
115558 TCGGATGGCCTCTGATGCTC
1 TCGGATGGCCTCAGATGCTC
*
115578 TCGGATAGCCTC
1 TCGGATGGCCTC
115590 GGTCGGATGG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.13, C:0.31, G:0.29, T:0.27
Consensus pattern (20 bp):
TCGGATGGCCTCAGATGCTC
Found at i:115686 original size:29 final size:29
Alignment explanation
Indices: 115649--115711 Score: 90
Period size: 29 Copynumber: 2.2 Consensus size: 29
115639 GCTATCTCTT
**
115649 GTAGCTCGCGGGGAAGACATGGCGACCTA
1 GTAGCTCGCCCGGAAGACATGGCGACCTA
* *
115678 GTAGGTCGCCCGGAAGGCATGGCGACCTA
1 GTAGCTCGCCCGGAAGACATGGCGACCTA
115707 GTAGC
1 GTAGC
115712 CAATACTGTG
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.22, C:0.25, G:0.38, T:0.14
Consensus pattern (29 bp):
GTAGCTCGCCCGGAAGACATGGCGACCTA
Found at i:119678 original size:21 final size:21
Alignment explanation
Indices: 119649--119688 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
119639 AAACGTTAAT
* *
119649 AATATTAATGTTTTAGGTAAA
1 AATAATAATATTTTAGGTAAA
*
119670 AATAATAATATTTTCGGTA
1 AATAATAATATTTTAGGTA
119689 GTTTTTACAG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.42, C:0.03, G:0.12, T:0.42
Consensus pattern (21 bp):
AATAATAATATTTTAGGTAAA
Found at i:121575 original size:16 final size:16
Alignment explanation
Indices: 121550--121582 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
121540 ATTCATACAT
121550 AACATCTGAATCATTC
1 AACATCTGAATCATTC
*
121566 AACATTTGAATCATTC
1 AACATCTGAATCATTC
121582 A
1 A
121583 GCGCTTAATC
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:0.39, C:0.21, G:0.06, T:0.33
Consensus pattern (16 bp):
AACATCTGAATCATTC
Found at i:124076 original size:27 final size:27
Alignment explanation
Indices: 124044--124103 Score: 77
Period size: 27 Copynumber: 2.2 Consensus size: 27
124034 TTAACAAAAC
*
124044 TTGACTAGACT-AGAAAAATCGATATTT
1 TTGACTAGACTCA-AAAAATCAATATTT
* *
124071 TTGACTAGATTCAAAAAATCAATCTTT
1 TTGACTAGACTCAAAAAATCAATATTT
124098 TTGACT
1 TTGACT
124104 CGACATGATT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
27 28 0.97
28 1 0.03
ACGTcount: A:0.38, C:0.13, G:0.12, T:0.37
Consensus pattern (27 bp):
TTGACTAGACTCAAAAAATCAATATTT
Found at i:138680 original size:13 final size:13
Alignment explanation
Indices: 138662--138686 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
138652 ATATGACATC
138662 GTTTTAAAATTTA
1 GTTTTAAAATTTA
138675 GTTTTAAAATTT
1 GTTTTAAAATTT
138687 TTATAAAGTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.00, G:0.08, T:0.56
Consensus pattern (13 bp):
GTTTTAAAATTTA
Found at i:139677 original size:20 final size:19
Alignment explanation
Indices: 139639--139693 Score: 58
Period size: 20 Copynumber: 2.8 Consensus size: 19
139629 AACGAAAGAA
*
139639 AAATGAAGAACAATAAAA-G
1 AAATGAAAAACAA-AAAAGG
139658 AACATGAAAAACAAAGAAAGG
1 AA-ATGAAAAACAAA-AAAGG
*
139679 AAATGAATAACAAAA
1 AAATGAAAAACAAAA
139694 GAATAACACA
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
19 4 0.13
20 24 0.77
21 3 0.10
ACGTcount: A:0.69, C:0.07, G:0.15, T:0.09
Consensus pattern (19 bp):
AAATGAAAAACAAAAAAGG
Found at i:144838 original size:14 final size:14
Alignment explanation
Indices: 144819--144848 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
144809 TCAATTGATT
144819 GTGAGAAAGAACAA
1 GTGAGAAAGAACAA
144833 GTGAGAAAGAACAA
1 GTGAGAAAGAACAA
144847 GT
1 GT
144849 CAACAACATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.53, C:0.07, G:0.30, T:0.10
Consensus pattern (14 bp):
GTGAGAAAGAACAA
Found at i:145820 original size:5 final size:5
Alignment explanation
Indices: 145810--145853 Score: 70
Period size: 5 Copynumber: 8.8 Consensus size: 5
145800 TCCTTTGTTC
* *
145810 TTTCA TTTCA TTTCA TTTAA TTTAA TTTCA TTTCA TTTCA TTTC
1 TTTCA TTTCA TTTCA TTTCA TTTCA TTTCA TTTCA TTTCA TTTC
145854 TTCCTTCATC
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
5 37 1.00
ACGTcount: A:0.23, C:0.16, G:0.00, T:0.61
Consensus pattern (5 bp):
TTTCA
Found at i:149390 original size:2 final size:2
Alignment explanation
Indices: 149383--149410 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
149373 TTTTGTTGTA
149383 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
149411 GTAATATGTG
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:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:149748 original size:30 final size:30
Alignment explanation
Indices: 149687--149749 Score: 99
Period size: 31 Copynumber: 2.1 Consensus size: 30
149677 AAAAAAATTG
*
149687 AATATTTTATGTACCTATTTTGACAAAAAA
1 AATATTTTAAGTACCTATTTTGACAAAAAA
*
149717 AATACTTTTAAGTATCTATTTTGACAAAAAA
1 AATA-TTTTAAGTACCTATTTTGACAAAAAA
149748 AA
1 AA
149750 ACAACTTCAA
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
30 4 0.13
31 26 0.87
ACGTcount: A:0.46, C:0.10, G:0.06, T:0.38
Consensus pattern (30 bp):
AATATTTTAAGTACCTATTTTGACAAAAAA
Found at i:149762 original size:32 final size:30
Alignment explanation
Indices: 149701--149793 Score: 93
Period size: 31 Copynumber: 3.1 Consensus size: 30
149691 TTTTATGTAC
* *
149701 CTATTTTGACAAAAAAAATAC-TTTTAAGTA
1 CTATTTTGACAAAAAAAA-ACACTTCAAGTA
149731 TCTATTTTGACAAAAAAAAACAACTTCAAGTA
1 -CTATTTTGACAAAAAAAAAC-ACTTCAAGTA
* *
149763 CTTAATTTG--ATAAAAAAACACTTCAAGTA
1 C-TATTTTGACAAAAAAAAACACTTCAAGTA
149792 CT
1 CT
149794 TTGATGAAGA
Statistics
Matches: 55, Mismatches: 4, Indels: 9
0.81 0.06 0.13
Matches are distributed among these distances:
28 1 0.02
29 11 0.20
30 11 0.20
31 19 0.35
32 13 0.24
ACGTcount: A:0.47, C:0.14, G:0.06, T:0.32
Consensus pattern (30 bp):
CTATTTTGACAAAAAAAAACACTTCAAGTA
Found at i:151078 original size:12 final size:12
Alignment explanation
Indices: 151061--151085 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
151051 CTGGAAACAC
151061 TGAGAATAAGTA
1 TGAGAATAAGTA
151073 TGAGAATAAGTA
1 TGAGAATAAGTA
151085 T
1 T
151086 ATGGACGGAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.48, C:0.00, G:0.24, T:0.28
Consensus pattern (12 bp):
TGAGAATAAGTA
Found at i:153431 original size:29 final size:28
Alignment explanation
Indices: 153373--153439 Score: 73
Period size: 29 Copynumber: 2.3 Consensus size: 28
153363 ATTAACTCTG
*
153373 AAATCTATAAAGAATTATAAATTTTATTA
1 AAAT-TATAAAGAATTATAAATATTATTA
*
153402 AAATTATACAGAGATTATAAATAATT-TTA
1 AAATTATAAAGA-ATTATAAAT-ATTATTA
153431 ACAATTATA
1 A-AATTATA
153440 TAAAAATAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
28 7 0.21
29 17 0.52
30 9 0.27
ACGTcount: A:0.52, C:0.04, G:0.04, T:0.39
Consensus pattern (28 bp):
AAATTATAAAGAATTATAAATATTATTA
Found at i:153644 original size:21 final size:19
Alignment explanation
Indices: 153604--153644 Score: 55
Period size: 21 Copynumber: 2.1 Consensus size: 19
153594 ATTTAATTGA
*
153604 AATTTTAAAATATTTTTAT
1 AATTTTAAAATATGTTTAT
153623 AATTATTAAAATTATGTTTAT
1 AATT-TTAAAA-TATGTTTAT
153644 A
1 A
153645 TATCAAATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 4 0.21
20 6 0.32
21 9 0.47
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (19 bp):
AATTTTAAAATATGTTTAT
Done.