Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013793.1 Corchorus capsularis cultivar CVL-1 contig13814, 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: 133846
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.32
Found at i:7 original size:2 final size:2
Alignment explanation
Indices: 1--88 Score: 167
Period size: 2 Copynumber: 44.0 Consensus size: 2
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
*
43 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CC CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
85 CT CT
1 CT CT
89 TTATCAAATA
Statistics
Matches: 84, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
2 84 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:445 original size:64 final size:64
Alignment explanation
Indices: 370--497 Score: 247
Period size: 64 Copynumber: 2.0 Consensus size: 64
360 CACTTGGGCC
370 TGTTATATTTTTTGAATTTCCTATACCATTTTCAGTTAGAGACTTATTTGATTAAATTTCAACT
1 TGTTATATTTTTTGAATTTCCTATACCATTTTCAGTTAGAGACTTATTTGATTAAATTTCAACT
*
434 TGTTATATTTTTTGAATTTCTTATACCATTTTCAGTTAGAGACTTATTTGATTAAATTTCAACT
1 TGTTATATTTTTTGAATTTCCTATACCATTTTCAGTTAGAGACTTATTTGATTAAATTTCAACT
498 ACTAAAAACT
Statistics
Matches: 63, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
64 63 1.00
ACGTcount: A:0.28, C:0.12, G:0.09, T:0.51
Consensus pattern (64 bp):
TGTTATATTTTTTGAATTTCCTATACCATTTTCAGTTAGAGACTTATTTGATTAAATTTCAACT
Found at i:6171 original size:16 final size:15
Alignment explanation
Indices: 6147--6184 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
6137 ATTTTCTTAT
6147 TTTAA-TTGTTTTCTA
1 TTTAATTTG-TTTCTA
6162 TTTAATTTGTTTCTA
1 TTTAATTTGTTTCTA
*
6177 CTTAATTT
1 TTTAATTT
6185 AATTTGAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 18 0.86
16 3 0.14
ACGTcount: A:0.21, C:0.08, G:0.05, T:0.66
Consensus pattern (15 bp):
TTTAATTTGTTTCTA
Found at i:15895 original size:25 final size:29
Alignment explanation
Indices: 15867--15922 Score: 75
Period size: 25 Copynumber: 2.1 Consensus size: 29
15857 AATTATAGCT
15867 GAATAATCAAG-CAAG-CA-AA-TTTGAA
1 GAATAATCAAGTCAAGACAGAATTTTGAA
*
15892 GAATACTCAAGTCAAGACAGAATTTTGAA
1 GAATAATCAAGTCAAGACAGAATTTTGAA
15921 GA
1 GA
15923 TACTGAAAGA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
25 10 0.38
26 4 0.15
27 2 0.08
28 2 0.08
29 8 0.31
ACGTcount: A:0.48, C:0.12, G:0.18, T:0.21
Consensus pattern (29 bp):
GAATAATCAAGTCAAGACAGAATTTTGAA
Found at i:16029 original size:28 final size:28
Alignment explanation
Indices: 15989--16057 Score: 138
Period size: 28 Copynumber: 2.5 Consensus size: 28
15979 AAAACAAACA
15989 GTACGGACACGCTGAAGCGATCAACGTC
1 GTACGGACACGCTGAAGCGATCAACGTC
16017 GTACGGACACGCTGAAGCGATCAACGTC
1 GTACGGACACGCTGAAGCGATCAACGTC
16045 GTACGGACACGCT
1 GTACGGACACGCT
16058 AAGGCTGTTA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 41 1.00
ACGTcount: A:0.28, C:0.29, G:0.29, T:0.14
Consensus pattern (28 bp):
GTACGGACACGCTGAAGCGATCAACGTC
Found at i:19410 original size:27 final size:28
Alignment explanation
Indices: 19380--19446 Score: 127
Period size: 28 Copynumber: 2.4 Consensus size: 28
19370 GGTCGTCCAG
19380 GGGCATTTTGGTCA-TTTTTGCACCCGA
1 GGGCATTTTGGTCATTTTTTGCACCCGA
19407 GGGCATTTTGGTCATTTTTTGCACCCGA
1 GGGCATTTTGGTCATTTTTTGCACCCGA
19435 GGGCATTTTGGT
1 GGGCATTTTGGT
19447 AAATTGGTGG
Statistics
Matches: 39, Mismatches: 0, Indels: 1
0.98 0.00 0.03
Matches are distributed among these distances:
27 14 0.36
28 25 0.64
ACGTcount: A:0.13, C:0.19, G:0.28, T:0.39
Consensus pattern (28 bp):
GGGCATTTTGGTCATTTTTTGCACCCGA
Found at i:20119 original size:11 final size:11
Alignment explanation
Indices: 20093--20126 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
20083 ACCCATTTTA
*
20093 AATAAA-AAAC
1 AATAAATAAAT
20103 AATAAATAAAT
1 AATAAATAAAT
20114 AATAAATAAAT
1 AATAAATAAAT
20125 AA
1 AA
20127 ATACATTCCA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
10 6 0.27
11 16 0.73
ACGTcount: A:0.76, C:0.03, G:0.00, T:0.21
Consensus pattern (11 bp):
AATAAATAAAT
Found at i:20123 original size:15 final size:15
Alignment explanation
Indices: 20091--20129 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
20081 AAACCCATTT
20091 TAAATAAA-AAACAA
1 TAAATAAATAAACAA
20105 TAAATAAATAATA-AA
1 TAAATAAATAA-ACAA
20120 TAAATAAATA
1 TAAATAAATA
20130 CATTCCACCC
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 8 0.35
15 14 0.61
16 1 0.04
ACGTcount: A:0.74, C:0.03, G:0.00, T:0.23
Consensus pattern (15 bp):
TAAATAAATAAACAA
Found at i:23500 original size:38 final size:38
Alignment explanation
Indices: 23445--23520 Score: 134
Period size: 38 Copynumber: 2.0 Consensus size: 38
23435 AGATTAGTCA
*
23445 GAGTCAAGGTAAAAGTAATTAGTAAATCAGTAATTAAG
1 GAGTCAAGGTAAAAGTAATCAGTAAATCAGTAATTAAG
*
23483 GAGTCAAGGTAATAGTAATCAGTAAATCAGTAATTAAG
1 GAGTCAAGGTAAAAGTAATCAGTAAATCAGTAATTAAG
23521 TAAAAAGAGA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 36 1.00
ACGTcount: A:0.46, C:0.07, G:0.21, T:0.26
Consensus pattern (38 bp):
GAGTCAAGGTAAAAGTAATCAGTAAATCAGTAATTAAG
Found at i:23639 original size:43 final size:43
Alignment explanation
Indices: 23587--23780 Score: 278
Period size: 43 Copynumber: 4.7 Consensus size: 43
23577 TAAACCGGTG
* *
23587 GGTAAACAACTTGATTCAGTGTAATTAAGTGAATTGGTAATTT
1 GGTAAACAACTTAATTCGGTGTAATTAAGTGAATTGGTAATTT
*
23630 GTTAAACAACTTAATTCGGTGTAATTAAGTGAATTGGTAATTT
1 GGTAAACAACTTAATTCGGTGTAATTAAGTGAATTGGTAATTT
* *
23673 GGTAAACAACTTAATTCGGTGTAATTAAGTAAATTGGCAATTT
1 GGTAAACAACTTAATTCGGTGTAATTAAGTGAATTGGTAATTT
23716 GGTAAACAACTTAATTCGGTGTAATTAAGT-AA---G--A-TT
1 GGTAAACAACTTAATTCGGTGTAATTAAGTGAATTGGTAATTT
*
23752 -GTAATCAACTTAATTCGGTGTAATTAAGT
1 GGTAAACAACTTAATTCGGTGTAATTAAGT
23781 AAAATTGATA
Statistics
Matches: 144, Mismatches: 7, Indels: 8
0.91 0.04 0.05
Matches are distributed among these distances:
35 28 0.19
36 2 0.01
37 1 0.01
39 1 0.01
42 2 0.01
43 110 0.76
ACGTcount: A:0.36, C:0.08, G:0.19, T:0.37
Consensus pattern (43 bp):
GGTAAACAACTTAATTCGGTGTAATTAAGTGAATTGGTAATTT
Found at i:23761 original size:35 final size:35
Alignment explanation
Indices: 23717--23792 Score: 125
Period size: 35 Copynumber: 2.1 Consensus size: 35
23707 TGGCAATTTG
* *
23717 GTAAACAACTTAATTCGGTGTAATTAAGTAAGATT
1 GTAATCAACTTAATTCGGTGTAATTAAGTAAAATT
23752 GTAATCAACTTAATTCGGTGTAATTAAGTAAAATT
1 GTAATCAACTTAATTCGGTGTAATTAAGTAAAATT
23787 GATAAT
1 G-TAAT
23793 TAAATTAAGT
Statistics
Matches: 38, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
35 34 0.89
36 4 0.11
ACGTcount: A:0.41, C:0.08, G:0.16, T:0.36
Consensus pattern (35 bp):
GTAATCAACTTAATTCGGTGTAATTAAGTAAAATT
Found at i:23813 original size:57 final size:51
Alignment explanation
Indices: 23752--23878 Score: 182
Period size: 57 Copynumber: 2.4 Consensus size: 51
23742 AAGTAAGATT
*
23752 GTAATCAACTTAATTCGGTGTAATTAAGTAAAATTGATAATTAAATTAAGTCATTTG
1 GTAATCAACTTAATTCGGTGTAATTAAGT-AAATTGATAACTAAA-T-A---ATTTG
*
23809 GTAATCAACTTAATTCGGTGTAATTAAGTAAATTGGTAACTAAATAATTTG
1 GTAATCAACTTAATTCGGTGTAATTAAGTAAATTGATAACTAAATAATTTG
23860 GTAATCAACTTAATTCGGT
1 GTAATCAACTTAATTCGGT
23879 AAGATGGTAA
Statistics
Matches: 68, Mismatches: 2, Indels: 6
0.89 0.03 0.08
Matches are distributed among these distances:
51 24 0.35
54 1 0.01
55 1 0.01
56 13 0.19
57 29 0.43
ACGTcount: A:0.39, C:0.09, G:0.15, T:0.38
Consensus pattern (51 bp):
GTAATCAACTTAATTCGGTGTAATTAAGTAAATTGATAACTAAATAATTTG
Found at i:23888 original size:76 final size:76
Alignment explanation
Indices: 23807--24036 Score: 370
Period size: 76 Copynumber: 2.9 Consensus size: 76
23797 TTAAGTCATT
23807 TGGTAATCAACTTAATTCGGTGTAATTAAGTAAATTGGTAACTAAATAATTTGGTAATCAACTTA
1 TGGTAATCAACTTAATTCGGTGTAATTAAGTAAATTGGTAACTAAATAATTTGGTAATCAACTTA
23872 ATTCGGTAAGA
66 ATTCGGTAAGA
*
23883 TGGTAATCAACTTAATTCGGTGTAATTAAGAAAATTGGTAACTAAATAATTTGGTAATCAACTTA
1 TGGTAATCAACTTAATTCGGTGTAATTAAGTAAATTGGTAACTAAATAATTTGGTAATCAACTTA
*
23948 ATTCGGTAAGG
66 ATTCGGTAAGA
* *
23959 TGGTAATCAACTTAATTCGGTGCAATTAAGTAAATTGGTAATTAAATTAAGTAATGTGGTAATCA
1 TGGTAATCAACTTAATTCGGTGTAATTAAGTAAATTGGTAACTAAA-TAA-T--T-TGGTAATCA
24024 ACTTAAATTCGGT
61 ACTT-AATTCGGT
24037 GTAATTAAGT
Statistics
Matches: 143, Mismatches: 5, Indels: 6
0.93 0.03 0.04
Matches are distributed among these distances:
76 117 0.82
77 3 0.02
78 1 0.01
80 1 0.01
81 13 0.09
82 8 0.06
ACGTcount: A:0.38, C:0.09, G:0.18, T:0.35
Consensus pattern (76 bp):
TGGTAATCAACTTAATTCGGTGTAATTAAGTAAATTGGTAACTAAATAATTTGGTAATCAACTTA
ATTCGGTAAGA
Found at i:23912 original size:133 final size:129
Alignment explanation
Indices: 23738--24186 Score: 399
Period size: 133 Copynumber: 3.4 Consensus size: 129
23728 AATTCGGTGT
* *
23738 AATTAAGTAAGATTGTAATCAACTTAATTCGGTGTAATTAAGTAAAATTGATAATTAAATTAAGT
1 AATTAAGTAAGATGGTAATCAACTTAATTCGGTGTAATTAAGTAAAATTGGTAATTAAA-TAAGT
*
23803 CATTTGGTAATCAACTTAATTCGGTGTAATTAAGTAAATT-GGT-AACTAAATAATTTGGTAATC
65 -ATTTGGTAATCAACTTAATTCGGTGTAATTAAGTAAATTCGGTCAACTAAATAAATTGGTAATC
23866 A
129 A
* *
23867 ACTTAATTCGGTAAGATGGTAATCAACTTAATTCGGTGTAATTAAG-AAAATTGGTAACTAAAT-
1 AATTAA----GTAAGATGGTAATCAACTTAATTCGGTGTAATTAAGTAAAATTGGTAATTAAATA
* * * * *
23930 A--ATTTGGTAATCAACTTAATTCGGTAAGGTGGTAATCAACTTAATTCGGTGCAATTAAGTAAA
62 AGTATTTGGTAATCAACTTAATTC-----GGT-GTAATTAAGTAAATTCGGT-CAACTAAATAAA
*
23993 TTGGTAATTA
120 TTGGTAATCA
* * *
24003 AATTAAGTAATG-TGGTAATCAACTTAAATTCGGTGTAATTAAGT-AAATTGGTGATTAGACTAG
1 AATTAAGTAA-GATGGTAATCAACTT-AATTCGGTGTAATTAAGTAAAATTGGTAATTA-AATAA
* * * *
24066 GTAATTTGGTAATTAACTTAATTCGGTGTAATTAAGTAAA-TCAGT-AA-TCAACTTAATTCGGT
63 GT-ATTTGGTAATCAACTTAATTCGGTGTAATTAAGTAAATTCGGTCAACT-AAATAAATT-GGT
*
24128 -GT--
125 AATCA
* * * *
24130 AATTAAGCAA-ATTGGTAATTAACTTAATTTGGTGTAATTAAGT-AAATCGGTAATTAA
1 AATTAAGTAAGA-TGGTAATCAACTTAATTCGGTGTAATTAAGTAAAATTGGTAATTAA
24187 CTTAATTCAG
Statistics
Matches: 266, Mismatches: 29, Indels: 54
0.76 0.08 0.15
Matches are distributed among these distances:
125 1 0.00
126 28 0.11
127 42 0.16
128 1 0.00
129 15 0.06
130 4 0.02
131 5 0.02
132 44 0.17
133 79 0.30
134 5 0.02
136 22 0.08
138 20 0.08
ACGTcount: A:0.39, C:0.08, G:0.17, T:0.36
Consensus pattern (129 bp):
AATTAAGTAAGATGGTAATCAACTTAATTCGGTGTAATTAAGTAAAATTGGTAATTAAATAAGTA
TTTGGTAATCAACTTAATTCGGTGTAATTAAGTAAATTCGGTCAACTAAATAAATTGGTAATCA
Found at i:24006 original size:21 final size:21
Alignment explanation
Indices: 23982--24021 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
23972 AATTCGGTGC
23982 AATTAAGTAAAT-TGGTAATTA
1 AATTAAGT-AATGTGGTAATTA
24003 AATTAAGTAATGTGGTAAT
1 AATTAAGTAATGTGGTAAT
24022 CAACTTAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 3 0.17
21 15 0.83
ACGTcount: A:0.45, C:0.00, G:0.17, T:0.38
Consensus pattern (21 bp):
AATTAAGTAATGTGGTAATTA
Found at i:24029 original size:21 final size:21
Alignment explanation
Indices: 23982--24029 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
23972 AATTCGGTGC
*
23982 AATTAAGTAAATTGGTAATTA
1 AATTAAGTAAATTGGTAATCA
24003 AATTAAGT-AATGTGGTAATCA
1 AATTAAGTAAAT-TGGTAATCA
*
24024 ACTTAA
1 AATTAA
24030 ATTCGGTGTA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 3 0.12
21 21 0.88
ACGTcount: A:0.46, C:0.04, G:0.15, T:0.35
Consensus pattern (21 bp):
AATTAAGTAAATTGGTAATCA
Found at i:24041 original size:76 final size:73
Alignment explanation
Indices: 23807--24211 Score: 318
Period size: 76 Copynumber: 5.5 Consensus size: 73
23797 TTAAGTCATT
*
23807 TGGTAATCAACTTAATTCGGTGTAATTAAGTAAATTGGTAACTAAA-TAATTTGGTAATCAACTT
1 TGGTAATCAACTTAATTCGGTGTAATTAAGTAAATTGGTAATTAAATTAATTTGGTAATCAACTT
23871 AATTCGGTAAG
66 AATTCGG---G
* *
23882 ATGGTAATCAACTTAATTCGGTGTAATTAAGAAAATTGGTAACTAAA-TAATTTGGTAATCAACT
1 -TGGTAATCAACTTAATTCGGTGTAATTAAGTAAATTGGTAATTAAATTAATTTGGTAATCAACT
23946 TAATTCGGTAAGG
65 TAATTC-G---GG
*
23959 TGGTAATCAACTTAATTCGGTGCAATTAAGTAAATTGGTAATTAAATTAAGTAATGTGGTAATCA
1 TGGTAATCAACTTAATTCGGTGTAATTAAGTAAATTGGTAATTAAATTAA-T--T-TGGTAATCA
24024 ACTTAAATTC-GG
62 ACTT-AATTCGGG
* * * * * * * * *
24036 T-GTAATTAAGTAAATT-GGTGATTAGACTAGGTAATTTGGTAATTAACTTAATTCGGTGTAATT
1 TGGTAATCAACTTAATTCGGTG--TA-ATTAAGTAAATTGGTAATTAAATTAATT-TG-GTAATC
* *
24099 AA-GTAAATC---
61 AACTTAATTCGGG
* * * *
24108 -AGTAATCAACTTAATTCGGTGTAATTAAGCAAATTGGTAATTAACTTAATTTGGTGTAATTAA-
1 TGGTAATCAACTTAATTCGGTGTAATTAAGTAAATTGGTAATTAAATTAATTT-G-GTAATCAAC
* *
24171 GTAAATC---
64 TTAATTCGGG
* *
24178 -GGTAATTAACTTAATTCAGTGTAATTAAGTAAAT
1 TGGTAATCAACTTAATTCGGTGTAATTAAGTAAAT
24212 CAGTAGTTAC
Statistics
Matches: 283, Mismatches: 29, Indels: 40
0.80 0.08 0.11
Matches are distributed among these distances:
70 71 0.25
71 2 0.01
72 12 0.04
73 4 0.01
74 4 0.01
75 7 0.02
76 130 0.46
77 10 0.04
78 23 0.08
80 2 0.01
81 13 0.05
82 5 0.02
ACGTcount: A:0.38, C:0.08, G:0.18, T:0.36
Consensus pattern (73 bp):
TGGTAATCAACTTAATTCGGTGTAATTAAGTAAATTGGTAATTAAATTAATTTGGTAATCAACTT
AATTCGGG
Found at i:24045 original size:57 final size:56
Alignment explanation
Indices: 23953--24106 Score: 227
Period size: 57 Copynumber: 2.7 Consensus size: 56
23943 ACTTAATTCG
* * *
23953 GTAAGGTGGTAATCAACTTAATTCGGTGCAATTAAGTAAATTGGTAATTAAATTAA
1 GTAATGTGGTAATCAACTTAATTCGGTGTAATTAAGTAAATTGGTAATTAAACTAA
* * *
24009 GTAATGTGGTAATCAACTTAAATTCGGTGTAATTAAGTAAATTGGTGATTAGACTAG
1 GTAATGTGGTAATCAACTT-AATTCGGTGTAATTAAGTAAATTGGTAATTAAACTAA
* *
24066 GTAATTTGGTAATTAACTTAATTCGGTGTAATTAAGTAAAT
1 GTAATGTGGTAATCAACTTAATTCGGTGTAATTAAGTAAAT
24107 CAGTAATCAA
Statistics
Matches: 89, Mismatches: 8, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
56 40 0.45
57 49 0.55
ACGTcount: A:0.37, C:0.06, G:0.20, T:0.36
Consensus pattern (56 bp):
GTAATGTGGTAATCAACTTAATTCGGTGTAATTAAGTAAATTGGTAATTAAACTAA
Found at i:24120 original size:35 final size:35
Alignment explanation
Indices: 24074--24246 Score: 256
Period size: 35 Copynumber: 4.9 Consensus size: 35
24064 AGGTAATTTG
24074 GTAATTAACTTAATTCGGTGTAATTAAGTAAATCA
1 GTAATTAACTTAATTCGGTGTAATTAAGTAAATCA
* * **
24109 GTAATCAACTTAATTCGGTGTAATTAAGCAAATTG
1 GTAATTAACTTAATTCGGTGTAATTAAGTAAATCA
* *
24144 GTAATTAACTTAATTTGGTGTAATTAAGTAAATCG
1 GTAATTAACTTAATTCGGTGTAATTAAGTAAATCA
*
24179 GTAATTAACTTAATTCAGTGTAATTAAGTAAATCA
1 GTAATTAACTTAATTCGGTGTAATTAAGTAAATCA
* * *
24214 GTAGTTACCTTAATTCGGTATAATTAAGTAAAT
1 GTAATTAACTTAATTCGGTGTAATTAAGTAAAT
24247 AAAGGGCTTA
Statistics
Matches: 123, Mismatches: 15, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
35 123 1.00
ACGTcount: A:0.39, C:0.09, G:0.15, T:0.38
Consensus pattern (35 bp):
GTAATTAACTTAATTCGGTGTAATTAAGTAAATCA
Found at i:26305 original size:21 final size:21
Alignment explanation
Indices: 26279--26327 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 21
26269 TGTCCCTGGG
*
26279 CGCCCAGATGAA-ATGCCTAGC
1 CGCCCAGATGAACA-ACCTAGC
*
26300 CGCCCAGATTAACAACCTAGC
1 CGCCCAGATGAACAACCTAGC
26321 CGCCCAG
1 CGCCCAG
26328 GTCATCTGGA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 24 0.96
22 1 0.04
ACGTcount: A:0.29, C:0.39, G:0.20, T:0.12
Consensus pattern (21 bp):
CGCCCAGATGAACAACCTAGC
Found at i:39038 original size:20 final size:21
Alignment explanation
Indices: 38999--39044 Score: 60
Period size: 20 Copynumber: 2.3 Consensus size: 21
38989 AGATTCACTT
38999 ACTCTTTCCTCTTCCCGAAAA
1 ACTCTTTCCTCTTCCCGAAAA
* *
39020 ACTCTTT-CTTTTTCCGAAAA
1 ACTCTTTCCTCTTCCCGAAAA
39040 A-TCTT
1 ACTCTT
39045 CTTGTATTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 4 0.17
20 12 0.52
21 7 0.30
ACGTcount: A:0.24, C:0.30, G:0.04, T:0.41
Consensus pattern (21 bp):
ACTCTTTCCTCTTCCCGAAAA
Found at i:46076 original size:34 final size:34
Alignment explanation
Indices: 46013--46089 Score: 118
Period size: 35 Copynumber: 2.2 Consensus size: 34
46003 TCCAAGAATT
* *
46013 AGTTTTTGTTTTTCCGTTTTTTCTAAAAAAAAAA
1 AGTTTTTCTTTTTCCGATTTTTCTAAAAAAAAAA
46047 AGTTTTTCCTTTTTCCGATTTTTCTAAAAAAAAAA
1 AGTTTTT-CTTTTTCCGATTTTTCTAAAAAAAAAA
46082 AGATTTTT
1 AG-TTTTT
46090 GCGATTTAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
34 7 0.18
35 27 0.69
36 5 0.13
ACGTcount: A:0.32, C:0.10, G:0.08, T:0.49
Consensus pattern (34 bp):
AGTTTTTCTTTTTCCGATTTTTCTAAAAAAAAAA
Found at i:46143 original size:28 final size:27
Alignment explanation
Indices: 46056--46143 Score: 74
Period size: 25 Copynumber: 3.2 Consensus size: 27
46046 AAGTTTTTCC
*
46056 TTTTTCCGATTTTTCTAAAAAAAAA-AAGA
1 TTTTTCCGA-TTTT-TAAAAAAAAATTA-A
* *
46085 TTTTTGCGA--TTTAAAAAAAAATTAG
1 TTTTTCCGATTTTTAAAAAAAAATTAA
**
46110 GGTTTCCGATTTTTGAAAAAAAAATTAA
1 TTTTTCCGATTTTT-AAAAAAAAATTAA
46138 TTTTTC
1 TTTTTC
46144 TTTTCCGTTT
Statistics
Matches: 46, Mismatches: 9, Indels: 9
0.72 0.14 0.14
Matches are distributed among these distances:
25 16 0.35
26 3 0.07
27 3 0.07
28 16 0.35
29 8 0.17
ACGTcount: A:0.41, C:0.08, G:0.10, T:0.41
Consensus pattern (27 bp):
TTTTTCCGATTTTTAAAAAAAAATTAA
Found at i:49422 original size:21 final size:21
Alignment explanation
Indices: 49398--49465 Score: 70
Period size: 21 Copynumber: 3.2 Consensus size: 21
49388 AGCCAGGCCA
49398 CTGCCGCGCCATCCGTGCCGC
1 CTGCCGCGCCATCCGTGCCGC
* *
49419 CTGCC-CGGCCCAGCCAG-GCC-A
1 CTGCCGC-G-CCATCC-GTGCCGC
49440 CTGCCGCGCCATCCGTGCCGC
1 CTGCCGCGCCATCCGTGCCGC
49461 CTGCC
1 CTGCC
49466 CGGCCATGCT
Statistics
Matches: 37, Mismatches: 4, Indels: 12
0.70 0.08 0.23
Matches are distributed among these distances:
19 1 0.03
20 9 0.24
21 17 0.46
22 9 0.24
23 1 0.03
ACGTcount: A:0.07, C:0.53, G:0.28, T:0.12
Consensus pattern (21 bp):
CTGCCGCGCCATCCGTGCCGC
Found at i:49427 original size:42 final size:42
Alignment explanation
Indices: 49368--49470 Score: 206
Period size: 42 Copynumber: 2.5 Consensus size: 42
49358 CCAGCCGATG
49368 CCGTGCCGCCTGCCCGGCCCAGCCAGGCCACTGCCGCGCCAT
1 CCGTGCCGCCTGCCCGGCCCAGCCAGGCCACTGCCGCGCCAT
49410 CCGTGCCGCCTGCCCGGCCCAGCCAGGCCACTGCCGCGCCAT
1 CCGTGCCGCCTGCCCGGCCCAGCCAGGCCACTGCCGCGCCAT
49452 CCGTGCCGCCTGCCCGGCC
1 CCGTGCCGCCTGCCCGGCC
49471 ATGCTCGGCC
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 61 1.00
ACGTcount: A:0.08, C:0.53, G:0.29, T:0.10
Consensus pattern (42 bp):
CCGTGCCGCCTGCCCGGCCCAGCCAGGCCACTGCCGCGCCAT
Found at i:54900 original size:19 final size:18
Alignment explanation
Indices: 54876--54912 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
54866 TTGAAGATTT
54876 CTTGAAGATAATTTGAAGA
1 CTTGAAGATAA-TTGAAGA
*
54895 CTTGAAGATCATTGAAGA
1 CTTGAAGATAATTGAAGA
54913 ATTATTTCCA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.41, C:0.08, G:0.22, T:0.30
Consensus pattern (18 bp):
CTTGAAGATAATTGAAGA
Found at i:56892 original size:17 final size:17
Alignment explanation
Indices: 56870--56902 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
56860 ATAATCTAGT
*
56870 AAAATCGAAAATGAAAA
1 AAAATCAAAAATGAAAA
56887 AAAATCAAAAATGAAA
1 AAAATCAAAAATGAAA
56903 GTGAAAAGTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.73, C:0.06, G:0.09, T:0.12
Consensus pattern (17 bp):
AAAATCAAAAATGAAAA
Found at i:57428 original size:17 final size:17
Alignment explanation
Indices: 57406--57448 Score: 51
Period size: 12 Copynumber: 2.8 Consensus size: 17
57396 AAAATTCAAA
57406 ATTCAAAACAAAATTTC
1 ATTCAAAACAAAATTTC
57423 ATT-----CAAAATTTC
1 ATTCAAAACAAAATTTC
57435 ATTCAAAACAAAAT
1 ATTCAAAACAAAAT
57449 ACATTAGCAC
Statistics
Matches: 21, Mismatches: 0, Indels: 10
0.68 0.00 0.32
Matches are distributed among these distances:
12 12 0.57
17 9 0.43
ACGTcount: A:0.53, C:0.16, G:0.00, T:0.30
Consensus pattern (17 bp):
ATTCAAAACAAAATTTC
Found at i:57429 original size:12 final size:12
Alignment explanation
Indices: 57414--57442 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
57404 AAATTCAAAA
57414 CAAAATTTCATT
1 CAAAATTTCATT
57426 CAAAATTTCATT
1 CAAAATTTCATT
57438 CAAAA
1 CAAAA
57443 CAAAATACAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.48, C:0.17, G:0.00, T:0.34
Consensus pattern (12 bp):
CAAAATTTCATT
Found at i:63877 original size:18 final size:19
Alignment explanation
Indices: 63850--63887 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
63840 TAGATTCGTA
*
63850 TCAATTGGTAAATC-ATCT
1 TCAATCGGTAAATCTATCT
63868 TCAATCGGTAAATCTATCT
1 TCAATCGGTAAATCTATCT
63887 T
1 T
63888 TTTACTCATC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 13 0.72
19 5 0.28
ACGTcount: A:0.32, C:0.18, G:0.11, T:0.39
Consensus pattern (19 bp):
TCAATCGGTAAATCTATCT
Found at i:69430 original size:33 final size:33
Alignment explanation
Indices: 69393--69489 Score: 106
Period size: 33 Copynumber: 2.9 Consensus size: 33
69383 AGCACTTGTG
69393 ACCGGCCACGCAACTTGGAGATGCCC-GCACAAC
1 ACCGGCCACGCAACTTGGAGATGCCCGGC-CAAC
* * * *
69426 ACCGGGCATGCGACTTGGAGATGCCCGGCCATC
1 ACCGGCCACGCAACTTGGAGATGCCCGGCCAAC
* * **
69459 ACCGGCCACGCGACATGGCCATGCCCGGCCA
1 ACCGGCCACGCAACTTGGAGATGCCCGGCCA
69490 CAACCAGCCA
Statistics
Matches: 54, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
33 52 0.96
34 2 0.04
ACGTcount: A:0.22, C:0.39, G:0.29, T:0.10
Consensus pattern (33 bp):
ACCGGCCACGCAACTTGGAGATGCCCGGCCAAC
Found at i:69535 original size:33 final size:33
Alignment explanation
Indices: 69446--69537 Score: 125
Period size: 33 Copynumber: 2.8 Consensus size: 33
69436 CGACTTGGAG
**
69446 ATGCCCGGCCATC-ACCGGCCACGCGACATGGCC
1 ATGCCCGGCCA-CAACCGGCCACATGACATGGCC
*
69479 ATGCCCGGCCACAACCAGCCACATGAC-TCGGCC
1 ATGCCCGGCCACAACCGGCCACATGACAT-GGCC
69512 ATGCCCGGCCACAACCGGCCACATGA
1 ATGCCCGGCCACAACCGGCCACATGA
69538 TCCTTTAGCT
Statistics
Matches: 53, Mismatches: 4, Indels: 4
0.87 0.07 0.07
Matches are distributed among these distances:
32 2 0.04
33 51 0.96
ACGTcount: A:0.23, C:0.45, G:0.24, T:0.09
Consensus pattern (33 bp):
ATGCCCGGCCACAACCGGCCACATGACATGGCC
Found at i:75708 original size:19 final size:18
Alignment explanation
Indices: 75684--75720 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
75674 TTTGAGATTT
75684 CTTGAAGATAATTTGAAGA
1 CTTGAAGATAA-TTGAAGA
*
75703 CTTGAAGATCATTGAAGA
1 CTTGAAGATAATTGAAGA
75721 ATTATTTCCA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.41, C:0.08, G:0.22, T:0.30
Consensus pattern (18 bp):
CTTGAAGATAATTGAAGA
Found at i:84130 original size:21 final size:21
Alignment explanation
Indices: 84106--84158 Score: 63
Period size: 21 Copynumber: 2.6 Consensus size: 21
84096 GCACTGGAGT
*
84106 ACATGGGGCGCGAAGCAAACC
1 ACATGGGGCGCCAAGCAAACC
* **
84127 ACATGGGGTGCCAAGCATGCC
1 ACATGGGGCGCCAAGCAAACC
84148 ACAT-GGGCGCC
1 ACATGGGGCGCC
84159 CAGCGCTAAT
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
20 6 0.22
21 21 0.78
ACGTcount: A:0.26, C:0.30, G:0.34, T:0.09
Consensus pattern (21 bp):
ACATGGGGCGCCAAGCAAACC
Found at i:92924 original size:61 final size:61
Alignment explanation
Indices: 92697--93134 Score: 532
Period size: 61 Copynumber: 7.2 Consensus size: 61
92687 AATTTTCTTA
* * *
92697 AAATTAAAAATAGCGACGTCTAGACGCCGCTATATTAAAGGGTTTTTATAAAAAAAAATCTC
1 AAATTAAAAATAGCGGCGTCTAGACGCCGCTATATTTAAGGGTTTTT-TTAAAAAAAATCTC
** * * * *
92759 AAATTAAAAATAGCGGCGTCTAGACGTTGCTATA-TTAA-AG-TGTTTT-ACAAAAATCTA
1 AAATTAAAAATAGCGGCGTCTAGACGCCGCTATATTTAAGGGTTTTTTTAAAAAAAATCTC
**
92816 AAATTAAAAATAGCGGCGTCTAGACGCCGCTATATTTAAGGGTTTTTTTTTTAAAAAATCTC
1 AAATTAAAAATAGCGGCGTCTAGACGCCGCTATATTTAAGGG-TTTTTTTAAAAAAAATCTC
* *
92878 AATTTAAAAATAGCAGCGTCTAGACGCCGCTATATTTAAGGGTTTTTTTAAAAAAAATCTC
1 AAATTAAAAATAGCGGCGTCTAGACGCCGCTATATTTAAGGGTTTTTTTAAAAAAAATCTC
* * * *
92939 AAATTAAAAATAACGGCGTCTAGAAGCCGCTATA-TTAA-AG-TGTTTT-AAAAAAATCTC
1 AAATTAAAAATAGCGGCGTCTAGACGCCGCTATATTTAAGGGTTTTTTTAAAAAAAATCTC
* ** ** *
92996 AAATTAAATATAGCGGTATCTAGACGCCGCTATATTTAAGGGTTTTTAAAAAAAAAATCTT
1 AAATTAAAAATAGCGGCGTCTAGACGCCGCTATATTTAAGGGTTTTTTTAAAAAAAATCTC
* * *
93057 AAGTTAAATATAGCGGCGTTTAGACGCCGCTATATTTAAGGGTTTTTTTAAAAAAAAAAATCTC
1 AAATTAAAAATAGCGGCGTCTAGACGCCGCTATATTTAAGGGTTTTTTT---AAAAAAAATCTC
*
93121 AAATTAAATATAGC
1 AAATTAAAAATAGC
93135 TATTATGACT
Statistics
Matches: 320, Mismatches: 44, Indels: 22
0.83 0.11 0.06
Matches are distributed among these distances:
57 81 0.25
58 14 0.04
59 6 0.02
60 8 0.03
61 108 0.34
62 79 0.25
64 24 0.08
ACGTcount: A:0.40, C:0.13, G:0.15, T:0.32
Consensus pattern (61 bp):
AAATTAAAAATAGCGGCGTCTAGACGCCGCTATATTTAAGGGTTTTTTTAAAAAAAATCTC
Found at i:93003 original size:180 final size:178
Alignment explanation
Indices: 92700--93128 Score: 615
Period size: 180 Copynumber: 2.4 Consensus size: 178
92690 TTTCTTAAAA
* *
92700 TTAAAAATAGCGACGTCTAGACGCCGCTATATTAAAGGGTTTTTATAAAAAAAAATCTCAAATTA
1 TTAAAAATAGCG-CGTCTAGACGCCGCTATATTTAAGGGTTTTT-TTAAAAAAAATCTCAAATTA
* * ** *
92765 AAAATAGCGGCGTCTAGACGTTGCTATATTAAAGTGTTTTACAAAAATCTAAAATTAAAAATAGC
64 AAAATAACGGCGTCTAGAAGCCGCTATATTAAAGTGTTTTAAAAAAATCTAAAATTAAAAATAGC
* **** *
92830 GGCGTCTAGACGCCGCTATATTTAAGGGTTTTTTTTTTAAAAAATCTCAAT
129 GGCATCTAGACGCCGCTATATTTAAGGG-TTTTTAAAAAAAAAATCTCAAG
92881 TTAAAAATAGCAGCGTCTAGACGCCGCTATATTTAAGGGTTTTTTTAAAAAAAATCTCAAATTAA
1 TTAAAAATAGC-GCGTCTAGACGCCGCTATATTTAAGGGTTTTTTTAAAAAAAATCTCAAATTAA
* *
92946 AAATAACGGCGTCTAGAAGCCGCTATATTAAAGTGTTTTAAAAAAATCTCAAATTAAATATAGCG
65 AAATAACGGCGTCTAGAAGCCGCTATATTAAAGTGTTTTAAAAAAATCTAAAATTAAAAATAGCG
* *
93011 GTATCTAGACGCCGCTATATTTAAGGGTTTTTAAAAAAAAAATCTTAAG
130 GCATCTAGACGCCGCTATATTTAAGGGTTTTTAAAAAAAAAATCTCAAG
* *
93060 TTAAATATAGCGGCGTTTAGACGCCGCTATATTTAAGGGTTTTTTTAAAAAAAAAAATCTCAAAT
1 TTAAAAATAGC-GCGTCTAGACGCCGCTATATTTAAGGGTTTTTTT---AAAAAAAATCTCAAAT
93125 TAAA
62 TAAA
93129 TATAGCTATT
Statistics
Matches: 224, Mismatches: 20, Indels: 7
0.89 0.08 0.03
Matches are distributed among these distances:
179 59 0.26
180 103 0.46
181 41 0.18
182 21 0.09
ACGTcount: A:0.40, C:0.13, G:0.15, T:0.32
Consensus pattern (178 bp):
TTAAAAATAGCGCGTCTAGACGCCGCTATATTTAAGGGTTTTTTTAAAAAAAATCTCAAATTAAA
AATAACGGCGTCTAGAAGCCGCTATATTAAAGTGTTTTAAAAAAATCTAAAATTAAAAATAGCGG
CATCTAGACGCCGCTATATTTAAGGGTTTTTAAAAAAAAAATCTCAAG
Found at i:96864 original size:31 final size:31
Alignment explanation
Indices: 96829--96911 Score: 105
Period size: 31 Copynumber: 2.7 Consensus size: 31
96819 CCTCCATTTC
* *
96829 GCGGCGTCTGG-TTTCTAAACGCTGTAGATTA
1 GCGGCGTCTGGATTTC-AAACGCCGCAGATTA
96860 GCGGCGTCTGGATTTCAAACGCCGCAGATTA
1 GCGGCGTCTGGATTTCAAACGCCGCAGATTA
* * *
96891 GCGGAGTCTGGAGTCCAAACG
1 GCGGCGTCTGGATTTCAAACG
96912 TCACTATTTA
Statistics
Matches: 46, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
31 42 0.91
32 4 0.09
ACGTcount: A:0.22, C:0.23, G:0.31, T:0.24
Consensus pattern (31 bp):
GCGGCGTCTGGATTTCAAACGCCGCAGATTA
Found at i:97112 original size:31 final size:31
Alignment explanation
Indices: 97074--97140 Score: 109
Period size: 31 Copynumber: 2.2 Consensus size: 31
97064 TCTTATCTAA
*
97074 ACGCCACTAAATAGCGGCGTCTGAATA-TAAG
1 ACGCCACTAAATAACGGCGTCT-AATATTAAG
97105 ACGCCACTAAATAACGGCGTCTAATATTAAG
1 ACGCCACTAAATAACGGCGTCTAATATTAAG
97136 ACGCC
1 ACGCC
97141 GTTATCTTCA
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
30 4 0.12
31 30 0.88
ACGTcount: A:0.36, C:0.25, G:0.19, T:0.19
Consensus pattern (31 bp):
ACGCCACTAAATAACGGCGTCTAATATTAAG
Found at i:100761 original size:12 final size:12
Alignment explanation
Indices: 100744--100769 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
100734 TTTTTATTTT
100744 TTATAAGTTTAA
1 TTATAAGTTTAA
100756 TTATAAGTTTAA
1 TTATAAGTTTAA
100768 TT
1 TT
100770 TAGGAAATTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.38, C:0.00, G:0.08, T:0.54
Consensus pattern (12 bp):
TTATAAGTTTAA
Found at i:101157 original size:12 final size:14
Alignment explanation
Indices: 101129--101160 Score: 50
Period size: 12 Copynumber: 2.4 Consensus size: 14
101119 ACATAAATTC
101129 AATGTTATAACATA
1 AATGTTATAACATA
101143 AATGTTAT-A-ATA
1 AATGTTATAACATA
101155 AATGTT
1 AATGTT
101161 CTAGAATTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 9 0.50
13 1 0.06
14 8 0.44
ACGTcount: A:0.47, C:0.03, G:0.09, T:0.41
Consensus pattern (14 bp):
AATGTTATAACATA
Found at i:103215 original size:21 final size:21
Alignment explanation
Indices: 103173--103215 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
103163 TTAATTATAT
*
103173 ATATATAAAATAAATCTGAAA
1 ATATATAAAATAAATCTCAAA
*
103194 ATATATAAACTAAAATC-CAAA
1 ATATATAAAAT-AAATCTCAAA
103215 A
1 A
103216 CCTAAAAAGC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 14 0.74
22 5 0.26
ACGTcount: A:0.63, C:0.09, G:0.02, T:0.26
Consensus pattern (21 bp):
ATATATAAAATAAATCTCAAA
Found at i:104067 original size:50 final size:50
Alignment explanation
Indices: 103996--104134 Score: 208
Period size: 50 Copynumber: 2.8 Consensus size: 50
103986 GACAACACCG
* * *
103996 AGCTATCCCGAAGCTCA-AACAAGTGCTCCCCGCACTGATCACAAACCTA
1 AGCTTTCCCCAAGCTTAGAACAAGTGCTCCCCGCACTGATCACAAACCTA
* * * *
104045 TGCTTTCCCCAAGCTTAGAACAAGTGCTCGCCGCACTAATTACAAACCTA
1 AGCTTTCCCCAAGCTTAGAACAAGTGCTCCCCGCACTGATCACAAACCTA
104095 AGCTTTCCCCAAGCTTAGAACAAGTGCTCCCCGCACTGAT
1 AGCTTTCCCCAAGCTTAGAACAAGTGCTCCCCGCACTGAT
104135 TAAACCAAAG
Statistics
Matches: 79, Mismatches: 10, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
49 13 0.16
50 66 0.84
ACGTcount: A:0.29, C:0.35, G:0.15, T:0.21
Consensus pattern (50 bp):
AGCTTTCCCCAAGCTTAGAACAAGTGCTCCCCGCACTGATCACAAACCTA
Found at i:112038 original size:50 final size:50
Alignment explanation
Indices: 111956--112099 Score: 227
Period size: 50 Copynumber: 2.9 Consensus size: 50
111946 GACAACACCG
* * *
111956 AGCTTTCCCCAAGCTCA-AACAAGCGCTCCCCGCACTGATCACGAACCTA
1 AGCTTTCCCCAAGCTTAGAACAAGTGCTCCCCGCACTGATCACAAACCTA
*
112005 AGCTTTCCCCAAGCTTAGAACAAGTGCTCCCCGCACTGATTACAAACCTA
1 AGCTTTCCCCAAGCTTAGAACAAGTGCTCCCCGCACTGATCACAAACCTA
* *
112055 AGCTTTCCCCAAGCTTAGAACAAGTGATCCCCGCACTGATTACAA
1 AGCTTTCCCCAAGCTTAGAACAAGTGCTCCCCGCACTGATCACAA
112100 TCAAAGAGAT
Statistics
Matches: 89, Mismatches: 5, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
49 16 0.18
50 73 0.82
ACGTcount: A:0.30, C:0.35, G:0.15, T:0.20
Consensus pattern (50 bp):
AGCTTTCCCCAAGCTTAGAACAAGTGCTCCCCGCACTGATCACAAACCTA
Found at i:126047 original size:21 final size:21
Alignment explanation
Indices: 125980--126052 Score: 62
Period size: 21 Copynumber: 3.6 Consensus size: 21
125970 AGACACAAAA
* *
125980 TTAAACATGCAAACAAGAAAA
1 TTAAATATGCAAACAAGAAAT
* * *
126001 TTAAATCT--AAACATGCAAT
1 TTAAATATGCAAACAAGAAAT
*
126020 CCT-AATATGCAAACAAGAAAT
1 -TTAAATATGCAAACAAGAAAT
126041 TTAAATATGCAA
1 TTAAATATGCAA
126053 GATAGATAAA
Statistics
Matches: 38, Mismatches: 10, Indels: 8
0.68 0.18 0.14
Matches are distributed among these distances:
19 12 0.32
20 2 0.05
21 24 0.63
ACGTcount: A:0.53, C:0.15, G:0.08, T:0.23
Consensus pattern (21 bp):
TTAAATATGCAAACAAGAAAT
Found at i:129165 original size:26 final size:27
Alignment explanation
Indices: 129136--129217 Score: 80
Period size: 26 Copynumber: 3.1 Consensus size: 27
129126 AATTTTGTTT
129136 TTGCGCTTTTT-CTATAAAAAAAAAAA
1 TTGCGCTTTTTCCTATAAAAAAAAAAA
*
129162 TTGCG-TTTTTCCCTAAAAAGAAAAAAAA
1 TTGCGCTTTTT-CCTATAAA-AAAAAAAA
* * * *
129190 TT-TGCTTTTTGCGATTAAAAAAAAAA
1 TTGCGCTTTTTCCTATAAAAAAAAAAA
129216 TT
1 TT
129218 TGCGAAAAAA
Statistics
Matches: 46, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
25 5 0.11
26 15 0.33
27 11 0.24
28 15 0.33
ACGTcount: A:0.44, C:0.11, G:0.10, T:0.35
Consensus pattern (27 bp):
TTGCGCTTTTTCCTATAAAAAAAAAAA
Found at i:129178 original size:25 final size:27
Alignment explanation
Indices: 129136--129187 Score: 72
Period size: 25 Copynumber: 2.0 Consensus size: 27
129126 AATTTTGTTT
*
129136 TTGCGCTTTTTCTATAAAAA-AAAAAA
1 TTGCGCTTTTTCCATAAAAAGAAAAAA
*
129162 TTGCG-TTTTTCCCTAAAAAGAAAAAA
1 TTGCGCTTTTTCCATAAAAAGAAAAAA
129188 AATTTGCTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
25 12 0.52
26 11 0.48
ACGTcount: A:0.44, C:0.13, G:0.10, T:0.33
Consensus pattern (27 bp):
TTGCGCTTTTTCCATAAAAAGAAAAAA
Found at i:129213 original size:28 final size:27
Alignment explanation
Indices: 129151--129215 Score: 69
Period size: 28 Copynumber: 2.3 Consensus size: 27
129141 CTTTTTCTAT
*
129151 AAAAAAAAAAATTGCGTTTTTCCCTAA
1 AAAAAAAAAAATTGCGTTTTTCCATAA
* *
129178 AAAGAAAAAAAATTTGC-TTTTTGCGATTA
1 AAA-AAAAAAAA-TTGCGTTTTT-CCATAA
129207 AAAAAAAAA
1 AAAAAAAAA
129216 TTTGCGAAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
27 3 0.09
28 19 0.59
29 10 0.31
ACGTcount: A:0.54, C:0.09, G:0.09, T:0.28
Consensus pattern (27 bp):
AAAAAAAAAAATTGCGTTTTTCCATAA
Found at i:133345 original size:35 final size:35
Alignment explanation
Indices: 133306--133446 Score: 180
Period size: 35 Copynumber: 4.0 Consensus size: 35
133296 TTACTGATTG
*
133306 CCATTTCTT-TTTACTGATTAATATTTTACTCTTTA
1 CCATTTCTTCTTTACTGATTACT-TTTTACTCTTTA
* *
133341 CCATTTTTTTCTTTACTGATTACTCTTTACTCTTTA
1 CCA-TTTCTTCTTTACTGATTACTTTTTACTCTTTA
* * *
133377 CCATTT-TTCTTTACTGATTTCTCTATAACTCTTTA
1 CCATTTCTTCTTTACTGATTACT-TTTTACTCTTTA
133412 CCATTTC-TCTTTACTGATTACTTTTTACTCTTTA
1 CCATTTCTTCTTTACTGATTACTTTTTACTCTTTA
133446 C
1 C
133447 TGATTACCAT
Statistics
Matches: 92, Mismatches: 10, Indels: 9
0.83 0.09 0.08
Matches are distributed among these distances:
34 26 0.28
35 35 0.38
36 19 0.21
37 12 0.13
ACGTcount: A:0.19, C:0.22, G:0.03, T:0.56
Consensus pattern (35 bp):
CCATTTCTTCTTTACTGATTACTTTTTACTCTTTA
Found at i:133370 original size:7 final size:7
Alignment explanation
Indices: 133350--133482 Score: 55
Period size: 7 Copynumber: 19.1 Consensus size: 7
133340 ACCATTTTTT
133350 TCTTTAC
1 TCTTTAC
**
133357 TGATTAC
1 TCTTTAC
133364 TCTTTAC
1 TCTTTAC
133371 TCTTTAC
1 TCTTTAC
*
133378 -CATTT-T
1 TC-TTTAC
133384 TCTTTAC
1 TCTTTAC
*
133391 TGATTT-C
1 T-CTTTAC
*
133398 TCTATAAC
1 TCT-TTAC
133406 TCTTTAC
1 TCTTTAC
133413 -CATTT-C
1 TC-TTTAC
133419 TCTTTAC
1 TCTTTAC
**
133426 TGATTAC
1 TCTTTAC
*
133433 TTTTTAC
1 TCTTTAC
133440 TCTTTAC
1 TCTTTAC
**
133447 TGATTAC
1 TCTTTAC
*
133454 -CATTAC
1 TCTTTAC
*
133460 TTTTTAC
1 TCTTTAC
133467 -CATTTTAC
1 TC--TTTAC
133475 TCTTTAC
1 TCTTTAC
133482 T
1 T
133483 GATTGCCTTT
Statistics
Matches: 92, Mismatches: 21, Indels: 26
0.66 0.15 0.19
Matches are distributed among these distances:
6 15 0.16
7 64 0.70
8 12 0.13
9 1 0.01
ACGTcount: A:0.20, C:0.23, G:0.03, T:0.54
Consensus pattern (7 bp):
TCTTTAC
Found at i:133477 original size:69 final size:71
Alignment explanation
Indices: 133328--133481 Score: 165
Period size: 69 Copynumber: 2.2 Consensus size: 71
133318 ACTGATTAAT
* ** *
133328 ATTTTACTCTTTACCATTTTTTTCTTTACTGATTACTCTTTACTCTTTACCATTTTTCTTTACTG
1 ATTTTACTCTTTACCA-TTTTCTCTTTACTGATTACTCTTTACTCTTTACCATTTACCATTACTG
133393 ATTTCTC
65 ATTTCTC
* * * *
133400 -TATAACTCTTTACCA-TTTCTCTTTACTGATTACTTTTTACTCTTTACTGA-TTACCATTACT-
1 ATTTTACTCTTTACCATTTTCTCTTTACTGATTACTCTTTACTCTTTAC-CATTTACCATTACTG
*
133461 TTTTAC-C
65 ATTT-CTC
133468 ATTTTACTCTTTAC
1 ATTTTACTCTTTAC
133482 TGATTGCCTT
Statistics
Matches: 68, Mismatches: 11, Indels: 9
0.77 0.12 0.10
Matches are distributed among these distances:
68 4 0.06
69 50 0.74
70 1 0.01
71 13 0.19
ACGTcount: A:0.19, C:0.23, G:0.03, T:0.55
Consensus pattern (71 bp):
ATTTTACTCTTTACCATTTTCTCTTTACTGATTACTCTTTACTCTTTACCATTTACCATTACTGA
TTTCTC
Found at i:133580 original size:26 final size:26
Alignment explanation
Indices: 133551--133773 Score: 188
Period size: 26 Copynumber: 8.4 Consensus size: 26
133541 CTTTATTGAC
133551 TACT-ATTACGCTTTTCTTACTCTTTT
1 TACTGATTAC-CTTTTCTTACTCTTTT
* *
133577 TACTGAATA-TTGTTTCTTACTCTTTT
1 TACTGATTACCT-TTTCTTACTCTTTT
*
133603 TACTGATGACTCTTTTTCTTACTCTTTT
1 TACTGATTAC-C-TTTTCTTACTCTTTT
*
133631 TACTGAATA-CTGTTTCTTACTC-TTT
1 TACTGATTACCT-TTTCTTACTCTTTT
**
133656 TACTGATGGCTCTTTTCTTACTCTTTT
1 TACTGATTAC-CTTTTCTTACTCTTTT
* * *
133683 TACTGAATA-TTGTTTCTTACTCTATT
1 TACTGATTACCT-TTTCTTACTCTTTT
*
133709 TACTGATGACCCTTTTCTTACTCTTTT
1 TACTGATTA-CCTTTTCTTACTCTTTT
* * *
133736 TACTGAATA-TTGGTTTTTTACTCTTTTT
1 TACTGATTACCT--TTTCTTACTC-TTTT
133764 TACTGATTAC
1 TACTGATTAC
133774 TGATTACTAT
Statistics
Matches: 157, Mismatches: 24, Indels: 29
0.75 0.11 0.14
Matches are distributed among these distances:
25 13 0.08
26 66 0.42
27 43 0.27
28 34 0.22
29 1 0.01
ACGTcount: A:0.17, C:0.19, G:0.08, T:0.55
Consensus pattern (26 bp):
TACTGATTACCTTTTCTTACTCTTTT
Found at i:133616 original size:16 final size:15
Alignment explanation
Indices: 133594--133651 Score: 59
Period size: 16 Copynumber: 3.9 Consensus size: 15
133584 TATTGTTTCT
133594 TACTCTTTTTACTGA
1 TACTCTTTTTACTGA
133609 TGACTCTTTTT-CT--
1 T-ACTCTTTTTACTGA
133622 TACTCTTTTTACTGAA
1 TACTCTTTTTACTG-A
*
133638 TACTGTTTCTTACT
1 TACTCTTT-TTACT
133652 CTTTTACTGA
Statistics
Matches: 36, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
12 9 0.25
13 3 0.08
15 3 0.08
16 16 0.44
17 5 0.14
ACGTcount: A:0.17, C:0.21, G:0.07, T:0.55
Consensus pattern (15 bp):
TACTCTTTTTACTGA
Found at i:133618 original size:53 final size:53
Alignment explanation
Indices: 133561--133770 Score: 341
Period size: 53 Copynumber: 3.9 Consensus size: 53
133551 TACTATTACG
133561 CTTTTCTTACTCTTTTTACTGAATATTGTTTCTTACTCTTTTTACTGATGACT
1 CTTTTCTTACTCTTTTTACTGAATATTGTTTCTTACTCTTTTTACTGATGACT
* *
133614 CTTTTTCTTACTCTTTTTACTGAATACTGTTTCTTACTC-TTTTACTGATGGCT
1 C-TTTTCTTACTCTTTTTACTGAATATTGTTTCTTACTCTTTTTACTGATGACT
* *
133667 CTTTTCTTACTCTTTTTACTGAATATTGTTTCTTACTCTATTTACTGATGACC
1 CTTTTCTTACTCTTTTTACTGAATATTGTTTCTTACTCTTTTTACTGATGACT
*
133720 CTTTTCTTACTCTTTTTACTGAATATTGGTTTTTTACTCTTTTTTACTGAT
1 CTTTTCTTACTCTTTTTACTGAATATT-GTTTCTTACTC-TTTTTACTGAT
133771 TACTGATTAC
Statistics
Matches: 145, Mismatches: 8, Indels: 6
0.91 0.05 0.04
Matches are distributed among these distances:
52 36 0.25
53 53 0.37
54 46 0.32
55 10 0.07
ACGTcount: A:0.17, C:0.19, G:0.08, T:0.56
Consensus pattern (53 bp):
CTTTTCTTACTCTTTTTACTGAATATTGTTTCTTACTCTTTTTACTGATGACT
Done.