Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020280.1 Corchorus olitorius cultivar O-4 contig20313, 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: 73637
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:140 original size:31 final size:31
Alignment explanation
Indices: 105--272 Score: 125
Period size: 31 Copynumber: 5.5 Consensus size: 31
95 TTTCGATGTC
105 AGGCCCTTATTTGAGCATTTTGGCAAACGTT
1 AGGCCCTTATTTGAGCATTTTGGCAAACGTT
** * *
136 AGGCCCTTATTTG-GCCAAATT---AAAAGAT
1 AGGCCCTTATTTGAG-CATTTTGGCAAACGTT
*
164 CGAGCCCTTATTTGAGCATTTTGGCAAACGTT
1 AG-GCCCTTATTTGAGCATTTTGGCAAACGTT
* ** * *
196 AGGCCCTTATTTGATCAAATT---AAAAGATC
1 AGGCCCTTATTTGAGCATTTTGGCAAACG-TT
** *
225 ATACCCTTATTTGAGCATTTTGGCAAACATT
1 AGGCCCTTATTTGAGCATTTTGGCAAACGTT
**
256 AAACCCTTATTTGAGCA
1 AGGCCCTTATTTGAGCA
273 ATTAGCCTAT
Statistics
Matches: 103, Mismatches: 24, Indels: 20
0.70 0.16 0.14
Matches are distributed among these distances:
28 10 0.10
29 32 0.31
30 2 0.02
31 50 0.49
32 9 0.09
ACGTcount: A:0.30, C:0.20, G:0.17, T:0.33
Consensus pattern (31 bp):
AGGCCCTTATTTGAGCATTTTGGCAAACGTT
Found at i:180 original size:60 final size:60
Alignment explanation
Indices: 107--269 Score: 256
Period size: 60 Copynumber: 2.7 Consensus size: 60
97 TCGATGTCAG
*
107 GCCCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTGGCCAAATTAAAAGATCGA-
1 GCCCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTGACCAAATTAAAAGATC-AT
*
167 GCCCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTGATCAAATTAAAAGATCAT
1 GCCCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTGACCAAATTAAAAGATCAT
* * **
227 ACCCTTATTTGAGCATTTTGGCAAACATTAAACCCTTATTTGA
1 GCCCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTGA
270 GCAATTAGCC
Statistics
Matches: 96, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
59 1 0.01
60 95 0.99
ACGTcount: A:0.29, C:0.20, G:0.17, T:0.34
Consensus pattern (60 bp):
GCCCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTGACCAAATTAAAAGATCAT
Found at i:2816 original size:84 final size:84
Alignment explanation
Indices: 2675--2849 Score: 305
Period size: 84 Copynumber: 2.1 Consensus size: 84
2665 CTTCTCCTTC
2675 TGATGATTTTATGGCAAAATTTTGGTCTTTACATGAGAAGGAGAATGAAAGAGGATCAATTGAGA
1 TGATGATTTTATGGCAAAATTTTGGTCTTTACATGAGAAGGAGAATGAAAGAGGATCAATTGAGA
2740 TTGAAGAATATGTTGATAA
66 TTGAAGAATATGTTGATAA
* * *
2759 TGATGATTTTATGGCTAATTTTTGGTCTTTACATGAGAAGGAGAATGAAAGAGGATCAGTTGAGA
1 TGATGATTTTATGGCAAAATTTTGGTCTTTACATGAGAAGGAGAATGAAAGAGGATCAATTGAGA
* *
2824 TTGGAGAATATGTTGATGA
66 TTGAAGAATATGTTGATAA
2843 TGATGAT
1 TGATGAT
2850 AATTAAATTC
Statistics
Matches: 86, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
84 86 1.00
ACGTcount: A:0.35, C:0.05, G:0.27, T:0.34
Consensus pattern (84 bp):
TGATGATTTTATGGCAAAATTTTGGTCTTTACATGAGAAGGAGAATGAAAGAGGATCAATTGAGA
TTGAAGAATATGTTGATAA
Found at i:10890 original size:18 final size:15
Alignment explanation
Indices: 10869--10911 Score: 50
Period size: 18 Copynumber: 2.7 Consensus size: 15
10859 GAAGATGATC
10869 ATGATGATCATGTCTACG
1 ATGATGATCATGT-T--G
*
10887 ATGATGATGATGTTG
1 ATGATGATCATGTTG
10902 ATGATGATCA
1 ATGATGATCA
10912 ATGTGGTCTT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
15 10 0.43
17 1 0.04
18 12 0.52
ACGTcount: A:0.30, C:0.09, G:0.26, T:0.35
Consensus pattern (15 bp):
ATGATGATCATGTTG
Found at i:19861 original size:29 final size:29
Alignment explanation
Indices: 19819--19877 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
19809 TCACTAAAAC
19819 AATCTTCTTCGTTCGTCGGCCTTAGATGA
1 AATCTTCTTCGTTCGTCGGCCTTAGATGA
19848 AATCTTCTTCGTTCGTCGGCCTTAGATGA
1 AATCTTCTTCGTTCGTCGGCCTTAGATGA
19877 A
1 A
19878 CAATTAGACC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.19, C:0.24, G:0.20, T:0.37
Consensus pattern (29 bp):
AATCTTCTTCGTTCGTCGGCCTTAGATGA
Found at i:21446 original size:54 final size:54
Alignment explanation
Indices: 21364--21471 Score: 216
Period size: 54 Copynumber: 2.0 Consensus size: 54
21354 TTGAACAATC
21364 TTTTCATTGTATTGCTAGCTTGATTAGATCTAGATTGAATGGATTTAAGAGAGT
1 TTTTCATTGTATTGCTAGCTTGATTAGATCTAGATTGAATGGATTTAAGAGAGT
21418 TTTTCATTGTATTGCTAGCTTGATTAGATCTAGATTGAATGGATTTAAGAGAGT
1 TTTTCATTGTATTGCTAGCTTGATTAGATCTAGATTGAATGGATTTAAGAGAGT
21472 AGCTAAGGAT
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
54 54 1.00
ACGTcount: A:0.28, C:0.07, G:0.22, T:0.43
Consensus pattern (54 bp):
TTTTCATTGTATTGCTAGCTTGATTAGATCTAGATTGAATGGATTTAAGAGAGT
Found at i:35929 original size:32 final size:32
Alignment explanation
Indices: 35888--35951 Score: 128
Period size: 32 Copynumber: 2.0 Consensus size: 32
35878 AACACTTCCA
35888 GGGCATTTTCTTGCATCTCGTTTAAGGAATCT
1 GGGCATTTTCTTGCATCTCGTTTAAGGAATCT
35920 GGGCATTTTCTTGCATCTCGTTTAAGGAATCT
1 GGGCATTTTCTTGCATCTCGTTTAAGGAATCT
35952 TACGCTTATC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.19, C:0.19, G:0.22, T:0.41
Consensus pattern (32 bp):
GGGCATTTTCTTGCATCTCGTTTAAGGAATCT
Found at i:40215 original size:24 final size:26
Alignment explanation
Indices: 40168--40216 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
40158 AAAACCATGA
*
40168 CTAATAAATAATCAATTGATATCAACC
1 CTAATAAAAAATCAATTGA-ATCAACC
40195 CTAA-AAAAAATCAATTG-ATCAA
1 CTAATAAAAAATCAATTGAATCAA
40217 GGTGGTAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 5 0.24
26 12 0.57
27 4 0.19
ACGTcount: A:0.53, C:0.16, G:0.04, T:0.27
Consensus pattern (26 bp):
CTAATAAAAAATCAATTGAATCAACC
Found at i:42981 original size:6 final size:6
Alignment explanation
Indices: 42970--43007 Score: 53
Period size: 6 Copynumber: 6.5 Consensus size: 6
42960 ATTTTGTTGG
42970 TTTTGT TTTTGT TTTTG- TTTTGT TTTT-T ATTTTGT TTT
1 TTTTGT TTTTGT TTTTGT TTTTGT TTTTGT -TTTTGT TTT
43008 ATTTTGTCAC
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
5 6 0.21
6 22 0.76
7 1 0.03
ACGTcount: A:0.03, C:0.00, G:0.13, T:0.84
Consensus pattern (6 bp):
TTTTGT
Found at i:42991 original size:17 final size:17
Alignment explanation
Indices: 42969--43012 Score: 63
Period size: 17 Copynumber: 2.6 Consensus size: 17
42959 TATTTTGTTG
42969 GTTTTGTTTTTGT-TTTT
1 GTTTTGTTTTT-TATTTT
42986 GTTTTGTTTTTTATTTT
1 GTTTTGTTTTTTATTTT
*
43003 GTTTTATTTT
1 GTTTTGTTTT
43013 GTCACATGAT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
16 1 0.04
17 24 0.96
ACGTcount: A:0.05, C:0.00, G:0.14, T:0.82
Consensus pattern (17 bp):
GTTTTGTTTTTTATTTT
Found at i:43473 original size:6 final size:6
Alignment explanation
Indices: 43464--43495 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
43454 TATATATATC
43464 ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT AT
1 ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT AT
43496 TGAGAATTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (6 bp):
ATAAAT
Found at i:56280 original size:9 final size:8
Alignment explanation
Indices: 56262--56307 Score: 56
Period size: 8 Copynumber: 5.8 Consensus size: 8
56252 TTTACATGCC
56262 AAATAAAA
1 AAATAAAA
56270 AAATAAAA
1 AAATAAAA
**
56278 AAATAATT
1 AAATAAAA
* *
56286 TAATTAAA
1 AAATAAAA
56294 AAATAAAA
1 AAATAAAA
56302 AAATAA
1 AAATAA
56308 TTTCTTATAA
Statistics
Matches: 30, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
8 30 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (8 bp):
AAATAAAA
Found at i:57120 original size:21 final size:21
Alignment explanation
Indices: 57096--57162 Score: 57
Period size: 21 Copynumber: 3.2 Consensus size: 21
57086 AATTCTTTGT
57096 AAATTAAGAAATACTCAACTC
1 AAATTAAGAAATACTCAACTC
* * ** *
57117 AAATCATAGAAA-ATTC-TTTGT
1 AAATTA-AGAAATACTCAACT-C
57138 AAATTAAGAAATACTCAACTC
1 AAATTAAGAAATACTCAACTC
57159 AAAT
1 AAAT
57163 CCTGATCCTT
Statistics
Matches: 32, Mismatches: 10, Indels: 8
0.64 0.20 0.16
Matches are distributed among these distances:
20 6 0.19
21 20 0.62
22 6 0.19
ACGTcount: A:0.51, C:0.15, G:0.06, T:0.28
Consensus pattern (21 bp):
AAATTAAGAAATACTCAACTC
Found at i:57142 original size:42 final size:42
Alignment explanation
Indices: 57083--57163 Score: 162
Period size: 42 Copynumber: 1.9 Consensus size: 42
57073 GCTAAGTCTT
57083 GAAAATTCTTTGTAAATTAAGAAATACTCAACTCAAATCATA
1 GAAAATTCTTTGTAAATTAAGAAATACTCAACTCAAATCATA
57125 GAAAATTCTTTGTAAATTAAGAAATACTCAACTCAAATC
1 GAAAATTCTTTGTAAATTAAGAAATACTCAACTCAAATC
57164 CTGATCCTTA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 39 1.00
ACGTcount: A:0.47, C:0.15, G:0.07, T:0.31
Consensus pattern (42 bp):
GAAAATTCTTTGTAAATTAAGAAATACTCAACTCAAATCATA
Found at i:57325 original size:56 final size:57
Alignment explanation
Indices: 57229--57343 Score: 187
Period size: 56 Copynumber: 2.0 Consensus size: 57
57219 TTTATTTTGT
* *
57229 AGAATAATTAAGTATAAATGGGGGGGATAGGATTTATTATAACATTTATTGTGTGAA
1 AGAATAATTAAGTACAAATGAGGGGGATAGGATTTATTATAACATTTATTGTGTGAA
* *
57286 AGAATAATTAAGTACAGAT-AGGGGGATATGATTTATTATAACATTTATTGTGTGAA
1 AGAATAATTAAGTACAAATGAGGGGGATAGGATTTATTATAACATTTATTGTGTGAA
57342 AG
1 AG
57344 GAAACAGATA
Statistics
Matches: 54, Mismatches: 4, Indels: 1
0.92 0.07 0.02
Matches are distributed among these distances:
56 37 0.69
57 17 0.31
ACGTcount: A:0.39, C:0.03, G:0.23, T:0.35
Consensus pattern (57 bp):
AGAATAATTAAGTACAAATGAGGGGGATAGGATTTATTATAACATTTATTGTGTGAA
Found at i:59239 original size:37 final size:37
Alignment explanation
Indices: 59187--59260 Score: 94
Period size: 37 Copynumber: 2.0 Consensus size: 37
59177 CCCAAAGGTT
* * **
59187 GATGGTCAAACCACAAAAAGCGTTTCTTTGTATATGC
1 GATGGTAAAACCACAAAAAGCATTTCAATGTATATGC
* *
59224 GATGGTAAAAGCACAAAATGCATTTCAATGTATATGC
1 GATGGTAAAACCACAAAAAGCATTTCAATGTATATGC
59261 ATGATCAAAA
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
37 31 1.00
ACGTcount: A:0.36, C:0.16, G:0.19, T:0.28
Consensus pattern (37 bp):
GATGGTAAAACCACAAAAAGCATTTCAATGTATATGC
Found at i:59435 original size:21 final size:21
Alignment explanation
Indices: 59394--59451 Score: 55
Period size: 21 Copynumber: 2.7 Consensus size: 21
59384 ACAACATTGT
*
59394 ACATGCATGGGTAAACT-CCAAA
1 ACATG-AT-GGTAAAATCCCAAA
* *
59416 GCATGATGGTCAAATCCCAAA
1 ACATGATGGTAAAATCCCAAA
*
59437 ACTTGATGGTAAAAT
1 ACATGATGGTAAAAT
59452 TCCGAAGTTT
Statistics
Matches: 29, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
20 6 0.21
21 19 0.66
22 4 0.14
ACGTcount: A:0.40, C:0.19, G:0.19, T:0.22
Consensus pattern (21 bp):
ACATGATGGTAAAATCCCAAA
Found at i:59909 original size:130 final size:133
Alignment explanation
Indices: 59641--59909 Score: 302
Period size: 130 Copynumber: 2.0 Consensus size: 133
59631 ATGATCATAC
* * *
59641 AAAAAACATTTTATTGAAAATGCATGGTCAAACTCCAAATTTTGATAGTCAAACCACAAAAAACA
1 AAAAAACATTTCATTGAAAATGCATGGTCAAACTCCAAAGTTTGATAGTCAAAACACAAAAAACA
*** * * ** *
59706 TCATTGTACATGCATGGTCAAACCCCAAAGGATGATGGCCAAAGTTCATAGTTTTGATAGTTAAA
66 TCATTGTACATGCATGGTCAAACCCCAAAGGATGATGGCCAAACCCCATAATATCAATAGTCAAA
59771 CCA
131 CCA
* *
59774 CAAAAAGCATTTCATT-ATAAATTCATGGT-AAA-TCTCAAAGTTTGATAGT-AAAACAC-AAAA
1 -AAAAAACATTTCATTGA-AAATGCATGGTCAAACTC-CAAAGTTTGATAGTCAAAACACAAAAA
* *
59834 A-TTCATTGTACATGCATGGTCAAACCCCGAAA-GATGATGGTCAAACCCCA-AATATCAATAGT
63 ACATCATTGTACATGCATGGTCAAACCCC-AAAGGATGATGGCCAAACCCCATAATATCAATAGT
59896 CAAACCA
127 CAAACCA
59903 TAAAAAA
1 -AAAAAA
59910 TATCGTTGTA
Statistics
Matches: 115, Mismatches: 17, Indels: 11
0.80 0.12 0.08
Matches are distributed among these distances:
129 19 0.17
130 40 0.35
131 8 0.07
132 8 0.07
133 17 0.15
134 23 0.20
ACGTcount: A:0.43, C:0.18, G:0.13, T:0.25
Consensus pattern (133 bp):
AAAAAACATTTCATTGAAAATGCATGGTCAAACTCCAAAGTTTGATAGTCAAAACACAAAAAACA
TCATTGTACATGCATGGTCAAACCCCAAAGGATGATGGCCAAACCCCATAATATCAATAGTCAAA
CCA
Found at i:59920 original size:76 final size:75
Alignment explanation
Indices: 59809--59985 Score: 209
Period size: 76 Copynumber: 2.4 Consensus size: 75
59799 TGGTAAATCT
** * * *
59809 CAAAGTTTGATAGT-AAAACAC-AAAAATTCATTGTACATGCATGGTCAAACCCCGAAA-GATGA
1 CAAAGTTCAATAGTCAAACCACAAAAAATTCATTGTACATACATGATCAAACCCC-AAAGGATGA
*
59871 TGGTCAAACCC
65 TGGTAAAACCC
* *
59882 CAAA-TATCAATAGTCAAACCATAAAAAATATCGTTGTACATACATGATCAAACCCCAAAGGATG
1 CAAAGT-TCAATAGTCAAACCACAAAAAAT-TCATTGTACATACATGATCAAACCCCAAAGGATG
59946 ATGGTAAAACCC
64 ATGGTAAAACCC
* *
59958 TAAAGTTCGATAGTCAAACCACAAAAAA
1 CAAAGTTCAATAGTCAAACCACAAAAAA
59986 CATTTCATTC
Statistics
Matches: 87, Mismatches: 11, Indels: 9
0.81 0.10 0.08
Matches are distributed among these distances:
72 1 0.01
73 10 0.11
74 5 0.06
75 9 0.10
76 61 0.70
77 1 0.01
ACGTcount: A:0.45, C:0.20, G:0.14, T:0.21
Consensus pattern (75 bp):
CAAAGTTCAATAGTCAAACCACAAAAAATTCATTGTACATACATGATCAAACCCCAAAGGATGAT
GGTAAAACCC
Found at i:60019 original size:206 final size:207
Alignment explanation
Indices: 59656--60150 Score: 599
Period size: 206 Copynumber: 2.4 Consensus size: 207
59646 ACATTTTATT
* * *
59656 GAAA-ATGCATGGTCAAACTCCAAATTTTGATAGTCAAACCACAAAAAACATCATTGTACATGCA
1 GAAAGATG-ATGGTCAAACCCCAAA-TTCGATAGTCAAACCACAAAAAACATCGTTGTACATGCA
* ** * * * *
59720 TGGTCAAACCCCAAAGGATGATGGCCAAAGTTCATAGTTTTGATAGTTAAACCACAAAAAGCATT
64 TGGTCAAACCCCAAAGGATGATGGCAAAACCTCAAAGTTTCGATAGTCAAACCACAAAAAACATT
* * * * * *
59785 TCATTATAAATTCATGGTAAATCTCAAAGTTTGATAGT-AAAACACAAAAA-TTCATTGTACATG
129 TCATTAGAAATGCATGGTAAACCTCAAAGTTTGATAGTCAAAACACAAAAACATAATTATACATG
59848 CATGGTCAAAC-CCC
194 CATGGTC-AACGCCC
* * * *
59862 GAAAGATGATGGTCAAACCCCAAATATCAATAGTCAAACCATAAAAAATATCGTTGTACATACAT
1 GAAAGATGATGGTCAAACCCCAAAT-TCGATAGTCAAACCACAAAAAACATCGTTGTACATGCAT
* *
59927 GATCAAACCCCAAAGGATGATGGTAAAACC-CTAAAG-TTCGATAGTCAAACCACAAAAAACATT
65 GGTCAAACCCCAAAGGATGATGGCAAAACCTC-AAAGTTTCGATAGTCAAACCACAAAAAACATT
* * *
59990 TCATTCGAACTGCATGGTCAAACCTCAAAGTTTGATAGTCAAACCACAAAAACATAATTATACAT
129 TCATTAGAAATGCATGGT-AAACCTCAAAGTTTGATAGTCAAAACACAAAAACATAATTATACAT
60055 GCATGGTCAACGCCC
193 GCATGGTCAACGCCC
* *
60070 -AAAGGATGATGGTCAAACCCCAAAGTTCGATAGGCAAACCACAAAAAACACTTCGTTGTATATG
1 GAAA-GATGATGGTCAAACCCCAAA-TTCGATAGTCAAACCACAAAAAACA--TCGTTGTACATG
*
60134 CATGGTCAAACCACAAA
62 CATGGTCAAACCCCAAA
60151 AACATCATTG
Statistics
Matches: 245, Mismatches: 33, Indels: 18
0.83 0.11 0.06
Matches are distributed among these distances:
205 40 0.16
206 99 0.40
207 20 0.08
208 60 0.24
209 1 0.00
210 25 0.10
ACGTcount: A:0.42, C:0.21, G:0.14, T:0.23
Consensus pattern (207 bp):
GAAAGATGATGGTCAAACCCCAAATTCGATAGTCAAACCACAAAAAACATCGTTGTACATGCATG
GTCAAACCCCAAAGGATGATGGCAAAACCTCAAAGTTTCGATAGTCAAACCACAAAAAACATTTC
ATTAGAAATGCATGGTAAACCTCAAAGTTTGATAGTCAAAACACAAAAACATAATTATACATGCA
TGGTCAACGCCC
Found at i:60108 original size:132 final size:132
Alignment explanation
Indices: 59891--60150 Score: 348
Period size: 132 Copynumber: 2.0 Consensus size: 132
59881 CCAAATATCA
* * *
59891 ATAGTCAAACCATAAAAAATATCGTTGTACATACATGATCAAACCCCAAAGGATGATGGTAAAAC
1 ATAGTCAAACCACAAAAAATA-CATTATACATACATGATCAAACCCCAAAGGATGATGGTAAAAC
* * * *
59956 CCTAAAGTTCGATAGTCAAACCACAAAAAACATTTCATTCG-A-ACTGCATGGTCAAACCTCAAA
65 CCCAAAGTTCGATAGGCAAACCACAAAAAACACTTCATT-GTATA-TGCATGGTCAAACCACAAA
60019 GTTTG
128 GTTTG
* * *
60024 ATAGTCAAACCACAAAAACATA-ATTATACATGCATGGTC-AACGCCCAAAGGATGATGGTCAAA
1 ATAGTCAAACCACAAAAA-ATACATTATACATACATGATCAAAC-CCCAAAGGATGATGGTAAAA
*
60087 CCCCAAAGTTCGATAGGCAAACCACAAAAAACACTTCGTTGTATATGCATGGTCAAACCACAAA
64 CCCCAAAGTTCGATAGGCAAACCACAAAAAACACTTCATTGTATATGCATGGTCAAACCACAAA
60151 AACATCATTG
Statistics
Matches: 112, Mismatches: 11, Indels: 9
0.85 0.08 0.07
Matches are distributed among these distances:
131 4 0.04
132 87 0.78
133 18 0.16
134 3 0.03
ACGTcount: A:0.42, C:0.22, G:0.14, T:0.21
Consensus pattern (132 bp):
ATAGTCAAACCACAAAAAATACATTATACATACATGATCAAACCCCAAAGGATGATGGTAAAACC
CCAAAGTTCGATAGGCAAACCACAAAAAACACTTCATTGTATATGCATGGTCAAACCACAAAGTT
TG
Found at i:60168 original size:33 final size:34
Alignment explanation
Indices: 60104--60184 Score: 110
Period size: 33 Copynumber: 2.4 Consensus size: 34
60094 GTTCGATAGG
* *
60104 CAAACCACAAAAAACACTTCGTTGTATATGCATGGT
1 CAAACCAC-AAAAACAC-TCATTGTACATGCATGGT
60140 CAAACCACAAAAACA-TCATTGTACATGCATGGT
1 CAAACCACAAAAACACTCATTGTACATGCATGGT
*
60173 CAAACCGCAAAA
1 CAAACCACAAAA
60185 TTCGATAGTC
Statistics
Matches: 42, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
33 27 0.64
35 7 0.17
36 8 0.19
ACGTcount: A:0.43, C:0.25, G:0.12, T:0.20
Consensus pattern (34 bp):
CAAACCACAAAAACACTCATTGTACATGCATGGT
Found at i:60233 original size:57 final size:53
Alignment explanation
Indices: 60138--60242 Score: 129
Period size: 57 Copynumber: 1.9 Consensus size: 53
60128 TATATGCATG
*
60138 GTCAAACCACAAAAACATCATTGTACATGCATGGTCAAACCGCAAAATTCGATA
1 GTCAAACCACAAAAACATCATTGTACATGCATGATCAAACC-CAAAATTCGATA
** * *
60192 GTCAAACCACAAAAAACATTTTGTTGTATATGCATGATCAAATCCAAAATT
1 GTCAAACCAC-AAAAACA--TCATTGTACATGCATGATCAAACCCAAAATT
60243 TGGTCAAACC
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
54 10 0.23
55 7 0.16
56 7 0.16
57 19 0.44
ACGTcount: A:0.43, C:0.21, G:0.11, T:0.25
Consensus pattern (53 bp):
GTCAAACCACAAAAACATCATTGTACATGCATGATCAAACCCAAAATTCGATA
Found at i:60271 original size:21 final size:21
Alignment explanation
Indices: 60246--60292 Score: 76
Period size: 21 Copynumber: 2.2 Consensus size: 21
60236 CAAAATTTGG
*
60246 TCAAACCCCAAATTTTTATAA
1 TCAAACCCCAAATTTTGATAA
*
60267 TCAAACCCCAAATTTTGATAG
1 TCAAACCCCAAATTTTGATAA
60288 TCAAA
1 TCAAA
60293 TCACGTTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.43, C:0.23, G:0.04, T:0.30
Consensus pattern (21 bp):
TCAAACCCCAAATTTTGATAA
Found at i:62012 original size:28 final size:28
Alignment explanation
Indices: 61975--62043 Score: 129
Period size: 28 Copynumber: 2.5 Consensus size: 28
61965 TTGTACGTAG
*
61975 AAAATCATTTCTCTTTTTTGTCTGTACA
1 AAAATAATTTCTCTTTTTTGTCTGTACA
62003 AAAATAATTTCTCTTTTTTGTCTGTACA
1 AAAATAATTTCTCTTTTTTGTCTGTACA
62031 AAAATAATTTCTC
1 AAAATAATTTCTC
62044 CTTCTTTTAA
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
28 40 1.00
ACGTcount: A:0.30, C:0.16, G:0.06, T:0.48
Consensus pattern (28 bp):
AAAATAATTTCTCTTTTTTGTCTGTACA
Found at i:65535 original size:8 final size:8
Alignment explanation
Indices: 65522--65567 Score: 56
Period size: 8 Copynumber: 5.8 Consensus size: 8
65512 TTTACATGCC
65522 AAATAAAA
1 AAATAAAA
65530 AAATAAAA
1 AAATAAAA
* **
65538 AACTAATT
1 AAATAAAA
*
65546 TAATAAAA
1 AAATAAAA
65554 AAATAAAA
1 AAATAAAA
65562 AAATAA
1 AAATAA
65568 TTTGTTATAA
Statistics
Matches: 30, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
8 30 1.00
ACGTcount: A:0.78, C:0.02, G:0.00, T:0.20
Consensus pattern (8 bp):
AAATAAAA
Found at i:65555 original size:24 final size:24
Alignment explanation
Indices: 65523--65570 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
65513 TTACATGCCA
*
65523 AATAAAAAAATAAAAAACTAATTT
1 AATAAAAAAATAAAAAAATAATTT
65547 AATAAAAAAATAAAAAAATAATTT
1 AATAAAAAAATAAAAAAATAATTT
65571 GTTATAAGGT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.73, C:0.02, G:0.00, T:0.25
Consensus pattern (24 bp):
AATAAAAAAATAAAAAAATAATTT
Found at i:67263 original size:57 final size:57
Alignment explanation
Indices: 67200--67350 Score: 198
Period size: 55 Copynumber: 2.7 Consensus size: 57
67190 TATTTTTCCC
* * *
67200 AAAAACATTTCAGTGTACATGCATGGTCAAACCTCAAAGTTTAATGGTCAAACAACA
1 AAAAACATTTCATTGTACATGCATGGTCAAACCACAAAGGTTAATGGTCAAACAACA
* * *
67257 AAAAACA--TCATTGTACATGCACGGTCAAACCCCAAAGGTTAATGGTCAAACCACA
1 AAAAACATTTCATTGTACATGCATGGTCAAACCACAAAGGTTAATGGTCAAACAACA
* * *
67312 AAAAGCATTTCTTTGTATATGCGATGGTCAAACCACAAA
1 AAAAACATTTCATTGTACATGC-ATGGTCAAACCACAAA
67351 ATGCATTTCA
Statistics
Matches: 81, Mismatches: 10, Indels: 5
0.84 0.10 0.05
Matches are distributed among these distances:
55 49 0.60
57 18 0.22
58 14 0.17
ACGTcount: A:0.41, C:0.21, G:0.15, T:0.23
Consensus pattern (57 bp):
AAAAACATTTCATTGTACATGCATGGTCAAACCACAAAGGTTAATGGTCAAACAACA
Found at i:67348 original size:37 final size:36
Alignment explanation
Indices: 67298--67379 Score: 119
Period size: 37 Copynumber: 2.2 Consensus size: 36
67288 CCAAAGGTTA
**
67298 ATGGTCAAACCACAAAAAGCATTTCTTTGTATATGC
1 ATGGTCAAACCACAAAAAGCATTTCAATGTATATGC
*
67334 GATGGTCAAACCACAAAATGCATTTCAATGTATATGC
1 -ATGGTCAAACCACAAAAAGCATTTCAATGTATATGC
*
67371 ATGATCAAA
1 ATGGTCAAA
67380 ACTCAAATTT
Statistics
Matches: 41, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
36 8 0.20
37 33 0.80
ACGTcount: A:0.39, C:0.18, G:0.15, T:0.28
Consensus pattern (36 bp):
ATGGTCAAACCACAAAAAGCATTTCAATGTATATGC
Found at i:67535 original size:21 final size:21
Alignment explanation
Indices: 67504--67556 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
67494 ACAACATTGT
* *
67504 ACATGCATGGTTAAACTCCAAA
1 ACATG-ATGGTCAAACCCCAAA
*
67526 GCATGATGGTCAAACCCCAAA
1 ACATGATGGTCAAACCCCAAA
*
67547 ACTTGATGGT
1 ACATGATGGT
67557 AAAATTCCGA
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
21 22 0.85
22 4 0.15
ACGTcount: A:0.36, C:0.23, G:0.19, T:0.23
Consensus pattern (21 bp):
ACATGATGGTCAAACCCCAAA
Found at i:67805 original size:21 final size:21
Alignment explanation
Indices: 67779--67830 Score: 95
Period size: 21 Copynumber: 2.5 Consensus size: 21
67769 TATGCATGGT
67779 AAACCCCAAATTTTGATAGTC
1 AAACCCCAAATTTTGATAGTC
67800 AAACCCCAAATTTTGATAGTC
1 AAACCCCAAATTTTGATAGTC
*
67821 AAACCACAAA
1 AAACCCCAAA
67831 AAACATCATT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.44, C:0.25, G:0.08, T:0.23
Consensus pattern (21 bp):
AAACCCCAAATTTTGATAGTC
Found at i:67831 original size:109 final size:109
Alignment explanation
Indices: 67639--67850 Score: 277
Period size: 109 Copynumber: 1.9 Consensus size: 109
67629 TAGTCAAACC
* *** *
67639 ACAAAAAACATTTTGTTTTTTATGCATGATCAAACCCCGAATTTTGATAAGCAAACCCCAAAGTT
1 ACAAAAAACATTTTATTGAATATGCATGATCAAACCCCAAATTTTGATAAGCAAACCCCAAAGTT
* *
67704 TGATTAAAAAACCACAAAAAACATTTATTGTATATGCATGATCAT
66 TGATTAAAAAACCACAAAAAACA-TCATTGTACATGCATGATCAT
* *
67749 ACAAAAAACATTTTATTGAATATGCATGGT-AAACCCCAAATTTTGAT-AGTCAAACCCCAAATT
1 ACAAAAAACATTTTATTGAATATGCATGATCAAACCCCAAATTTTGATAAG-CAAACCCCAAAGT
**
67812 TTGA-TAGTCAAACCACAAAAAACATCATTGTACATGCAT
65 TTGATTA-AAAAACCACAAAAAACATCATTGTACATGCAT
67851 AGTCAAACCC
Statistics
Matches: 89, Mismatches: 11, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
108 17 0.19
109 47 0.53
110 25 0.28
ACGTcount: A:0.42, C:0.18, G:0.10, T:0.29
Consensus pattern (109 bp):
ACAAAAAACATTTTATTGAATATGCATGATCAAACCCCAAATTTTGATAAGCAAACCCCAAAGTT
TGATTAAAAAACCACAAAAAACATCATTGTACATGCATGATCAT
Found at i:68068 original size:208 final size:207
Alignment explanation
Indices: 67770--68252 Score: 591
Period size: 208 Copynumber: 2.3 Consensus size: 207
67760 TTTATTGAAT
*** * *
67770 ATGCATGGT-AAACCCCAAATTTTGATAGTCAAACCCCAAATTTTGATAGTCAAACCACAAAAAA
1 ATGCATGGTCAAACCCCAAAGGATGATGGTCAAACCCCAAA-TTCGATAGTCAAACCACAAAAAA
* * * * *
67834 CATCATTGTACATGCATAGTCAAACCCCAAAGGATGATGGCCAAA-GCTCATAGTTTTGATAGTC
65 CATCATTGTACATACATAGTCAAACCCCAAAGGATGATGGCAAAACCCT-AAAG-TTCGATAGTC
* * *
67898 AAACCACAAAAAGCATTTCATTATAAATTCATGGT-AAATCTCAAAGTTTAATAGTCAAACCACA
128 AAACCACAAAAAACATTTCATTATAAATGCATGGTCAAACCTCAAAGTTTAATAGTCAAACCACA
* *
67962 AAAA-ATTCATTGTAC
193 AAAACA-TAATTATAC
* * * *
67977 ATGCATGGTCAAACCCCAAAGGATGATGGTCAAATCCCAAATATCAATAGTTAAACCATAAAAAA
1 ATGCATGGTCAAACCCCAAAGGATGATGGTCAAACCCCAAAT-TCGATAGTCAAACCACAAAAAA
* * *
68042 CATCGTTCG-ACATACATGGTCAAACCCCAAAGGATGATGGTAAAACCCTAAAGTTCGATAGTCA
65 CATCATT-GTACATACATAGTCAAACCCCAAAGGATGATGGCAAAACCCTAAAGTTCGATAGTCA
* * *
68106 AACCACAAAAAACATTTCATTCTAACTGCATGGTCAAACCTCAAAGTTTGATAGTCAAACCACAA
129 AACCACAAAAAACATTTCATTATAAATGCATGGTCAAACCTCAAAGTTTAATAGTCAAACCACAA
68171 AAACATAATTATAC
194 AAACATAATTATAC
* * * *
68185 ATGCATTGAC-AACGCCCAAAGGATGATGATCAAACCCCAAAGTTCGATAGGCAAACCACAAAAA
1 ATGCATGGTCAAAC-CCCAAAGGATGATGGTCAAACCCCAAA-TTCGATAGTCAAACCACAAAAA
68249 ACAT
64 ACAT
68253 TTCGTTGTAT
Statistics
Matches: 235, Mismatches: 33, Indels: 15
0.83 0.12 0.05
Matches are distributed among these distances:
207 53 0.23
208 177 0.75
209 5 0.02
ACGTcount: A:0.42, C:0.22, G:0.13, T:0.23
Consensus pattern (207 bp):
ATGCATGGTCAAACCCCAAAGGATGATGGTCAAACCCCAAATTCGATAGTCAAACCACAAAAAAC
ATCATTGTACATACATAGTCAAACCCCAAAGGATGATGGCAAAACCCTAAAGTTCGATAGTCAAA
CCACAAAAAACATTTCATTATAAATGCATGGTCAAACCTCAAAGTTTAATAGTCAAACCACAAAA
ACATAATTATAC
Found at i:68073 original size:76 final size:76
Alignment explanation
Indices: 67940--68120 Score: 235
Period size: 76 Copynumber: 2.4 Consensus size: 76
67930 GGTAAATCTC
* * * *
67940 AAAGTTTAATAGTCAAACCACAAAAAA-TTCATT-GTACATGCATGGTCAAACCCCAAAGGATGA
1 AAAGTTCAATAGTCAAACCACAAAAAACATCGTTCG-ACATACATGGTCAAACCCCAAAGGATGA
*
68003 TGGTCAAATCCC-
65 TGGT-AAAACCCT
* *
68015 AAA-TATCAATAGTTAAACCATAAAAAACATCGTTCGACATACATGGTCAAACCCCAAAGGATGA
1 AAAGT-TCAATAGTCAAACCACAAAAAACATCGTTCGACATACATGGTCAAACCCCAAAGGATGA
68079 TGGTAAAACCCT
65 TGGTAAAACCCT
*
68091 AAAGTTCGATAGTCAAACCACAAAAAACAT
1 AAAGTTCAATAGTCAAACCACAAAAAACAT
68121 TTCATTCTAA
Statistics
Matches: 91, Mismatches: 10, Indels: 9
0.83 0.09 0.08
Matches are distributed among these distances:
74 1 0.01
75 28 0.31
76 60 0.66
77 2 0.02
ACGTcount: A:0.45, C:0.21, G:0.13, T:0.21
Consensus pattern (76 bp):
AAAGTTCAATAGTCAAACCACAAAAAACATCGTTCGACATACATGGTCAAACCCCAAAGGATGAT
GGTAAAACCCT
Found at i:68300 original size:33 final size:34
Alignment explanation
Indices: 68236--68316 Score: 110
Period size: 33 Copynumber: 2.4 Consensus size: 34
68226 GTTCGATAGG
* *
68236 CAAACCACAAAAAACATTTCGTTGTATATGCATGGT
1 CAAACCAC-AAAAACA-TTCATTGTACATGCATGGT
68272 CAAACCACAAAAACA-TCATTGTACATGCATGGT
1 CAAACCACAAAAACATTCATTGTACATGCATGGT
*
68305 CAAACCCCAAAA
1 CAAACCACAAAA
68317 TTCGATAGTC
Statistics
Matches: 42, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
33 27 0.64
35 7 0.17
36 8 0.19
ACGTcount: A:0.43, C:0.25, G:0.11, T:0.21
Consensus pattern (34 bp):
CAAACCACAAAAACATTCATTGTACATGCATGGT
Found at i:69175 original size:25 final size:27
Alignment explanation
Indices: 69106--69175 Score: 65
Period size: 27 Copynumber: 2.6 Consensus size: 27
69096 AACTTTTTCA
*
69106 ATATAATT-ATAAGATTTTAAAATATTCT
1 ATAT-ATTAATAA-ATTATAAAATATTCT
**
69134 ATATATTAATACTTTATAAAATATT-T
1 ATATATTAATAAATTATAAAATATTCT
*
69160 A-ATGTTAATAAATTAT
1 ATATATTAATAAATTAT
69176 TTCTAGTCAT
Statistics
Matches: 35, Mismatches: 6, Indels: 5
0.76 0.13 0.11
Matches are distributed among these distances:
25 12 0.34
26 2 0.06
27 14 0.40
28 7 0.20
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (27 bp):
ATATATTAATAAATTATAAAATATTCT
Found at i:70420 original size:17 final size:17
Alignment explanation
Indices: 70379--70420 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
70369 CATGCAAAAT
70379 AAAAA-AATAAAAATAA
1 AAAAATAATAAAAATAA
* **
70395 TAATTTAATAAAAATAA
1 AAAAATAATAAAAATAA
70412 AAAAATAAT
1 AAAAATAAT
70421 TTCTTATAAG
Statistics
Matches: 19, Mismatches: 6, Indels: 1
0.73 0.23 0.04
Matches are distributed among these distances:
16 2 0.11
17 17 0.89
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (17 bp):
AAAAATAATAAAAATAA
Found at i:72110 original size:57 final size:57
Alignment explanation
Indices: 72047--72193 Score: 174
Period size: 55 Copynumber: 2.6 Consensus size: 57
72037 TTTTTTTCCC
* * * *
72047 AAAAACATTTCACTGTACATGCATGGTCAAATCTCAAAGTTTAATAGTCAAACCACA
1 AAAAACATTTCATTGTACATGCATGGTCAAACCACAAAGGTTAATAGTCAAACCACA
* *
72104 AAAAACA--TCATTGTACATGCACT-GTCAAACCACAAAGGTTGATGGTCAAACCACA
1 AAAAACATTTCATTGTACATGCA-TGGTCAAACCACAAAGGTTAATAGTCAAACCACA
* * *
72159 AAAAGCATTTCTTTGTATATGCGATGGTCAAACCA
1 AAAAACATTTCATTGTACATGC-ATGGTCAAACCA
72194 TAAAATGCAT
Statistics
Matches: 76, Mismatches: 9, Indels: 9
0.81 0.10 0.10
Matches are distributed among these distances:
55 46 0.61
56 1 0.01
57 19 0.25
58 10 0.13
ACGTcount: A:0.40, C:0.21, G:0.14, T:0.25
Consensus pattern (57 bp):
AAAAACATTTCATTGTACATGCATGGTCAAACCACAAAGGTTAATAGTCAAACCACA
Found at i:72204 original size:37 final size:37
Alignment explanation
Indices: 72144--72226 Score: 114
Period size: 37 Copynumber: 2.3 Consensus size: 37
72134 CACAAAGGTT
**
72144 GATGGTCAAACCACAAAAAGCATTTCTTTGTATATGC
1 GATGGTCAAACCACAAAAAGCATTTCAATGTATATGC
* *
72181 GATGGTCAAACCATAAAATGCATTTCAATGTATATGC
1 GATGGTCAAACCACAAAAAGCATTTCAATGTATATGC
*
72218 -ATGATCAAA
1 GATGGTCAAA
72227 ACTCAAATTT
Statistics
Matches: 41, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
36 8 0.20
37 33 0.80
ACGTcount: A:0.39, C:0.17, G:0.16, T:0.29
Consensus pattern (37 bp):
GATGGTCAAACCACAAAAAGCATTTCAATGTATATGC
Found at i:72382 original size:21 final size:22
Alignment explanation
Indices: 72352--72392 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
72342 CAACATTGTA
* *
72352 CATGCATGGTTAAACTCCAAAG
1 CATGCATGGTCAAACCCCAAAG
72374 CATG-ATGGTCAAACCCCAA
1 CATGCATGGTCAAACCCCAA
72393 GACTTGATGG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.37, C:0.27, G:0.17, T:0.20
Consensus pattern (22 bp):
CATGCATGGTCAAACCCCAAAG
Found at i:72868 original size:132 final size:132
Alignment explanation
Indices: 72598--72872 Score: 331
Period size: 132 Copynumber: 2.1 Consensus size: 132
72588 ATTATCATAC
* * * * * * *
72598 AAAAAACATTTTATTGA-ATATGCATGGTCAAACCCCAAATTTTGATAGTCGAACCACAAAAAAC
1 AAAAAACATTTCATT-ATAAATTCATGGT-AAATCTCAAAGTTTGATAGTCAAACCACAAAAAAC
* * * * **
72662 ATCATTGTACATGCATGGTCAAAACCCAAAGGATGATGGCCAAAGCTCATAGTTTTGATAGTCAA
64 ATCATTGTACATGCATGGTCAAAACCCAAAGGATGATGGCCAAACCCCATAATATCAATAGTCAA
*
72727 ACCAC
129 A-CAA
* *
72732 AAAAAGCATTTCATTATAAATTCATGGTAAATCTCAAAGTTTGATAGTCAAACCACAAAAAA-TT
1 AAAAAACATTTCATTATAAATTCATGGTAAATCTCAAAGTTTGATAGTCAAACCACAAAAAACAT
* *
72796 CATTGTACATGCATGGTCAAACCCCAAAGGATGATGGTCAAACCCCA-AATATCAATAGTCAAAC
66 CATTGTACATGCATGGTCAAAACCCAAAGGATGATGGCCAAACCCCATAATATCAATAGTCAAAC
72860 AA
131 AA
72862 TAAAAAACATT
1 -AAAAAACATT
72873 GTTGTACATA
Statistics
Matches: 120, Mismatches: 19, Indels: 7
0.82 0.13 0.05
Matches are distributed among these distances:
130 2 0.02
131 21 0.17
132 44 0.37
133 31 0.26
134 22 0.18
ACGTcount: A:0.43, C:0.19, G:0.13, T:0.25
Consensus pattern (132 bp):
AAAAAACATTTCATTATAAATTCATGGTAAATCTCAAAGTTTGATAGTCAAACCACAAAAAACAT
CATTGTACATGCATGGTCAAAACCCAAAGGATGATGGCCAAACCCCATAATATCAATAGTCAAAC
AA
Found at i:72887 original size:76 final size:76
Alignment explanation
Indices: 72775--72948 Score: 228
Period size: 76 Copynumber: 2.3 Consensus size: 76
72765 TCAAAGTTTG
* * * * *
72775 ATAGTCAAACCAC-AAAAA-ATTCATTGTACATGCATGGTCAAACCCCAAAGGATGATGGTCAAA
1 ATAGTCAAACAACAAAAAACATT-GTTGTACATACATGGTCAAACCCCAAAGGATGATGATAAAA
72838 CCCC-AAATATCA
65 CCCCAAAAT-TCA
*
72850 ATAGTCAAACAATAAAAAACATTGTTGTACATACATGGTCAAACCCCAAAGGATGATGATAAAAC
1 ATAGTCAAACAACAAAAAACATTGTTGTACATACATGGTCAAACCCCAAAGGATGATGATAAAAC
* *
72915 CTCAAAATTCG
66 CCCAAAATTCA
*
72926 ATAGTCAAACCACAAAAAACATT
1 ATAGTCAAACAACAAAAAACATT
72949 TCACTCTAAC
Statistics
Matches: 86, Mismatches: 10, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
75 11 0.13
76 68 0.79
77 7 0.08
ACGTcount: A:0.46, C:0.21, G:0.12, T:0.21
Consensus pattern (76 bp):
ATAGTCAAACAACAAAAAACATTGTTGTACATACATGGTCAAACCCCAAAGGATGATGATAAAAC
CCCAAAATTCA
Found at i:72979 original size:208 final size:206
Alignment explanation
Indices: 72621--73109 Score: 597
Period size: 208 Copynumber: 2.3 Consensus size: 206
72611 TTGAATATGC
* * * ** *
72621 ATGGTCAAACCCCAAATTTTGATAGTCGAACCACAAAAAACATCATTGTACATGCATGGTCAAAA
1 ATGGTCAAACCCCAAA-TTCGATAGTC-AAACAAAAAAAACATTGTTGTACATGCATGGTCAAAC
* * * ** * * *
72686 CCCAAAGGATGATGGCCAAAGCTCATAGTTTTGATAGTCAAACCACAAAAAGCATTTCATTATAA
64 CCCAAAGGATGATGACAAAACCTCATAAATTCGATAGTCAAACCACAAAAAACATTTCACTATAA
* * * *
72751 ATTCATGGTAAATCTCAAAGTTTGATAGTCAAACCACAAAAA-ATTCATTGTACATGCATGGTCA
129 ATGCATGGTAAACCTCAAAGTTTGATAGTCAAACCACAAAAACA-TAATTATACATGCATGGTC-
72815 AAC-CCCAAAGGATG
192 AACGCCCAAAGGATG
* *
72829 ATGGTCAAACCCCAAATATCAATAGTCAAACAATAAAAAACATTGTTGTACATACATGGTCAAAC
1 ATGGTCAAACCCCAAAT-TCGATAGTCAAACAA-AAAAAACATTGTTGTACATGCATGGTCAAAC
* *
72894 CCCAAAGGATGATGATAAAACCTCA-AAATTCGATAGTCAAACCACAAAAAACATTTCACTCTAA
64 CCCAAAGGATGATGACAAAACCTCATAAATTCGATAGTCAAACCACAAAAAACATTTCACTATAA
* *
72958 CTGCATGGTCAAACCTCAAAGTTTGATAGTCAAACCACAAAAACATAATTATGCATGCATGGTCA
129 ATGCATGGT-AAACCTCAAAGTTTGATAGTCAAACCACAAAAACATAATTATACATGCATGGTCA
73023 ACGCCCAAAGGATG
193 ACGCCCAAAGGATG
* * * *
73037 ATGATCGAACCCCAAAGTTCGATAGGCAAACCAAAAAAAACATTTCGTTGTATATGCATGGTCAA
1 ATGGTCAAACCCCAAA-TTCGATAGTCAAA-CAAAAAAAACA-TT-GTTGTACATGCATGGTCAA
*
73102 ACCACAAA
62 ACCCCAAA
73110 AACATCATTG
Statistics
Matches: 241, Mismatches: 31, Indels: 16
0.84 0.11 0.06
Matches are distributed among these distances:
207 48 0.20
208 162 0.67
209 7 0.03
210 24 0.10
ACGTcount: A:0.42, C:0.21, G:0.14, T:0.23
Consensus pattern (206 bp):
ATGGTCAAACCCCAAATTCGATAGTCAAACAAAAAAAACATTGTTGTACATGCATGGTCAAACCC
CAAAGGATGATGACAAAACCTCATAAATTCGATAGTCAAACCACAAAAAACATTTCACTATAAAT
GCATGGTAAACCTCAAAGTTTGATAGTCAAACCACAAAAACATAATTATACATGCATGGTCAACG
CCCAAAGGATG
Found at i:73103 original size:36 final size:33
Alignment explanation
Indices: 73063--73137 Score: 96
Period size: 33 Copynumber: 2.2 Consensus size: 33
73053 GTTCGATAGG
* *
73063 CAAACCAAAAAAAACATTTCGTTGTATATGCATGGT
1 CAAACC-AAAAAAACA--TCATTGTACATGCATGGT
*
73099 CAAACCACAAAAACATCATTGTACATGCATGGT
1 CAAACCAAAAAAACATCATTGTACATGCATGGT
73132 CAAACC
1 CAAACC
73138 CCAAAATTCG
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
33 22 0.61
35 8 0.22
36 6 0.17
ACGTcount: A:0.43, C:0.23, G:0.12, T:0.23
Consensus pattern (33 bp):
CAAACCAAAAAAACATCATTGTACATGCATGGT
Found at i:73235 original size:18 final size:18
Alignment explanation
Indices: 73194--73238 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
73184 ATGATCAAAT
*
73194 CCAAATTTTGTTCAAACC
1 CCAAATTTTGGTCAAACC
**
73212 TAAAATTTTGGTCAAACC
1 CCAAATTTTGGTCAAACC
73230 CCAAATTTT
1 CCAAATTTT
73239 TATAATCAAA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.36, C:0.22, G:0.07, T:0.36
Consensus pattern (18 bp):
CCAAATTTTGGTCAAACC
Found at i:73249 original size:21 final size:21
Alignment explanation
Indices: 73223--73269 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
73213 AAAATTTTGG
* *
73223 TCAAACCCCAAATTTTTATAA
1 TCAAACCCCAAAGTTTGATAA
*
73244 TCAAACCCCAAAGTTTGATAG
1 TCAAACCCCAAAGTTTGATAA
73265 TCAAA
1 TCAAA
73270 TCACGTTAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.43, C:0.23, G:0.06, T:0.28
Consensus pattern (21 bp):
TCAAACCCCAAAGTTTGATAA
Done.