Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014969.1 Corchorus olitorius cultivar O-4 contig15002, 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: 106099
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.30
Found at i:5747 original size:84 final size:85
Alignment explanation
Indices: 5653--5933 Score: 440
Period size: 84 Copynumber: 3.3 Consensus size: 85
5643 CCAATAACCA
* * * *
5653 AAAGTCCCCAAACACATATATAACACATGGGCACCTCTATTCCAAAGTCCTTAAACACATATGTA
1 AAAGTCCCCAAACACATATATAACACAGGGGCACCTCTATTACAAAGTCCTCAAACACATATATA
* *
5718 ACACAGAGACACCTATATTC
66 ACACAGAGGCATCTATATTC
5738 -AAGTCCCCAAACACATATATAACACAGGGGCACCTCTATTACAAAGTCCTCAAACACATATATA
1 AAAGTCCCCAAACACATATATAACACAGGGGCACCTCTATTACAAAGTCCTCAAACACATATATA
5802 ACACAGAGGCATCTATA-TC
66 ACACAGAGGCATCTATATTC
*
5821 AAAGTCCCCAAACACATATATAACACAGGGGCAACTCTATTACAAAGTCCTCAAACACATATATA
1 AAAGTCCCCAAACACATATATAACACAGGGGCACCTCTATTACAAAGTCCTCAAACACATATATA
* *
5886 ACACAGGGGCATCTCTATTAC
66 ACACAGAGGCATCTATATT-C
**
5907 AAAGTCTTCAAACACATATATAACACA
1 AAAGTCCCCAAACACATATATAACACA
5934 AAGGCATTTT
Statistics
Matches: 182, Mismatches: 11, Indels: 5
0.92 0.06 0.03
Matches are distributed among these distances:
83 2 0.01
84 153 0.84
85 1 0.01
86 26 0.14
ACGTcount: A:0.42, C:0.27, G:0.10, T:0.21
Consensus pattern (85 bp):
AAAGTCCCCAAACACATATATAACACAGGGGCACCTCTATTACAAAGTCCTCAAACACATATATA
ACACAGAGGCATCTATATTC
Found at i:5799 original size:127 final size:127
Alignment explanation
Indices: 5653--5940 Score: 404
Period size: 127 Copynumber: 2.3 Consensus size: 127
5643 CCAATAACCA
* ** *
5653 AAAGTCCCCAAACACATATATAACACATG-GGCACCTCTAT-TCCAAAGTCCTTAAACACATATG
1 AAAGTCCTCAAACACATATATAACACA-GAGGCA--TCTATAT-CAAAGTCCCCAAACACATATA
*
5716 TAACACAGAGACACCTATATT-C-AAGTCCCCAAACACATATATAACACAGGGGCACCTCTATTA
62 TAACACAGAGACAACTATATTACAAAGTCCCCAAACACATATATAACACAGGGGCACCTCTATTA
5779 C
127 C
5780 AAAGTCCTCAAACACATATATAACACAGAGGCATCTATATCAAAGTCCCCAAACACATATATAAC
1 AAAGTCCTCAAACACATATATAACACAGAGGCATCTATATCAAAGTCCCCAAACACATATATAAC
* * * * *
5845 ACAGGGGCAACTCTATTACAAAGTCCTCAAACACATATATAACACAGGGGCATCTCTATTAC
66 ACAGAGACAACTATATTACAAAGTCCCCAAACACATATATAACACAGGGGCACCTCTATTAC
* *
5907 AAAGTCTTCAAACACATATATAACACAAAGGCAT
1 AAAGTCCTCAAACACATATATAACACAGAGGCAT
5941 TTTTCCTTAT
Statistics
Matches: 145, Mismatches: 12, Indels: 8
0.88 0.07 0.05
Matches are distributed among these distances:
125 40 0.28
126 3 0.02
127 102 0.70
ACGTcount: A:0.42, C:0.27, G:0.10, T:0.21
Consensus pattern (127 bp):
AAAGTCCTCAAACACATATATAACACAGAGGCATCTATATCAAAGTCCCCAAACACATATATAAC
ACAGAGACAACTATATTACAAAGTCCCCAAACACATATATAACACAGGGGCACCTCTATTAC
Found at i:5940 original size:43 final size:43
Alignment explanation
Indices: 5653--5933 Score: 392
Period size: 43 Copynumber: 6.6 Consensus size: 43
5643 CCAATAACCA
* * *
5653 AAAGTCCCCAAACACATATATAACACATGGGCACCTCTATTCC
1 AAAGTCCTCAAACACATATATAACACAGGGGCACCTCTATTAC
* * * * *
5696 AAAGTCCTTAAACACATATGTAACACAGAGACACCTATATT-C
1 AAAGTCCTCAAACACATATATAACACAGGGGCACCTCTATTAC
*
5738 -AAGTCCCCAAACACATATATAACACAGGGGCACCTCTATTAC
1 AAAGTCCTCAAACACATATATAACACAGGGGCACCTCTATTAC
*
5780 AAAGTCCTCAAACACATATATAACACAGAGGCA--TCTA-TATC
1 AAAGTCCTCAAACACATATATAACACAGGGGCACCTCTATTA-C
* *
5821 AAAGTCCCCAAACACATATATAACACAGGGGCAACTCTATTAC
1 AAAGTCCTCAAACACATATATAACACAGGGGCACCTCTATTAC
*
5864 AAAGTCCTCAAACACATATATAACACAGGGGCATCTCTATTAC
1 AAAGTCCTCAAACACATATATAACACAGGGGCACCTCTATTAC
*
5907 AAAGTCTTCAAACACATATATAACACA
1 AAAGTCCTCAAACACATATATAACACA
5934 AAGGCATTTT
Statistics
Matches: 212, Mismatches: 20, Indels: 12
0.87 0.08 0.05
Matches are distributed among these distances:
40 2 0.01
41 70 0.33
42 2 0.01
43 136 0.64
44 2 0.01
ACGTcount: A:0.42, C:0.27, G:0.10, T:0.21
Consensus pattern (43 bp):
AAAGTCCTCAAACACATATATAACACAGGGGCACCTCTATTAC
Found at i:9228 original size:96 final size:96
Alignment explanation
Indices: 9064--9253 Score: 344
Period size: 96 Copynumber: 2.0 Consensus size: 96
9054 AAATATATTA
*
9064 ATTTAATTAGATTATATTAGAATTAAATTAAATTTACTCACAACCAATTAAATTTGGACAAATGT
1 ATTTAATTAGATTATATTAGAATTAAATTAAATTCACTCACAACCAATTAAATTTGGACAAATGT
9129 CAGAAGGAGAAAAACCAAAAACTAAGCATGC
66 CAGAAGGAGAAAAACCAAAAACTAAGCATGC
*
9160 ATTTAATTAGATTATATTAGAATTAAATTAAATTCACTCACAACCAATTAACTTTGGACAAATGT
1 ATTTAATTAGATTATATTAGAATTAAATTAAATTCACTCACAACCAATTAAATTTGGACAAATGT
* *
9225 CAGAAGGAGAAAAACCAAATACTTAGCAT
66 CAGAAGGAGAAAAACCAAAAACTAAGCAT
9254 ACAGCAACTT
Statistics
Matches: 90, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
96 90 1.00
ACGTcount: A:0.47, C:0.13, G:0.11, T:0.29
Consensus pattern (96 bp):
ATTTAATTAGATTATATTAGAATTAAATTAAATTCACTCACAACCAATTAAATTTGGACAAATGT
CAGAAGGAGAAAAACCAAAAACTAAGCATGC
Found at i:12527 original size:9 final size:9
Alignment explanation
Indices: 12505--12559 Score: 51
Period size: 9 Copynumber: 6.2 Consensus size: 9
12495 GGATCATTGG
*
12505 AATATTATAT
1 AATA-TATAA
12515 AATATATAA
1 AATATATAA
*
12524 AATATATAT
1 AATATATAA
*
12533 AATAAATAA
1 AATATATAA
*
12542 AA-ATAAAA
1 AATATATAA
12550 AATA-ATAA
1 AATATATAA
12558 AA
1 AA
12560 GATGACGTGT
Statistics
Matches: 37, Mismatches: 7, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
8 11 0.30
9 22 0.59
10 4 0.11
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (9 bp):
AATATATAA
Found at i:12533 original size:18 final size:19
Alignment explanation
Indices: 12505--12543 Score: 62
Period size: 18 Copynumber: 2.1 Consensus size: 19
12495 GGATCATTGG
*
12505 AATATTATATAATATATAA
1 AATATTATATAATAAATAA
12524 AATA-TATATAATAAATAA
1 AATATTATATAATAAATAA
12542 AA
1 AA
12544 ATAAAAAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 15 0.79
19 4 0.21
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (19 bp):
AATATTATATAATAAATAA
Found at i:30816 original size:30 final size:30
Alignment explanation
Indices: 30780--30877 Score: 142
Period size: 30 Copynumber: 3.3 Consensus size: 30
30770 TGCTGACATC
* *
30780 TCAAAATCTTCCTCGGGATCCTCATCTGGG
1 TCAAAATCCTCCTCGGGATCCTCATCCGGG
* * *
30810 TCAAAATCCTCTTCAGGATCCTCGTCCGGG
1 TCAAAATCCTCCTCGGGATCCTCATCCGGG
*
30840 TCGAAATCCTCCTCGGGATCCTCATCCGGG
1 TCAAAATCCTCCTCGGGATCCTCATCCGGG
30870 TCAAAATC
1 TCAAAATC
30878 ATCTTCAGAA
Statistics
Matches: 58, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 58 1.00
ACGTcount: A:0.21, C:0.33, G:0.19, T:0.27
Consensus pattern (30 bp):
TCAAAATCCTCCTCGGGATCCTCATCCGGG
Found at i:33963 original size:14 final size:14
Alignment explanation
Indices: 33944--33971 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
33934 AGAAAGATCT
33944 GTACCAACTACCAA
1 GTACCAACTACCAA
33958 GTACCAACTACCAA
1 GTACCAACTACCAA
33972 ACTCCAAAGC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.36, G:0.07, T:0.14
Consensus pattern (14 bp):
GTACCAACTACCAA
Found at i:36251 original size:21 final size:21
Alignment explanation
Indices: 36227--36290 Score: 112
Period size: 21 Copynumber: 3.1 Consensus size: 21
36217 CCTTAGGCAA
36227 CTCCAATGAGCTTGAAACCTT
1 CTCCAATGAGCTTGAAACCTT
*
36248 CTCCAATGAGCTTGAAACTTT
1 CTCCAATGAGCTTGAAACCTT
36269 CTCCAATGAGCTTGAAA-CTT
1 CTCCAATGAGCTTGAAACCTT
36289 CT
1 CT
36291 TTGTGTGAAT
Statistics
Matches: 41, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
20 4 0.10
21 37 0.90
ACGTcount: A:0.28, C:0.27, G:0.14, T:0.31
Consensus pattern (21 bp):
CTCCAATGAGCTTGAAACCTT
Found at i:41240 original size:31 final size:31
Alignment explanation
Indices: 41162--41267 Score: 196
Period size: 31 Copynumber: 3.5 Consensus size: 31
41152 AAAACAAAAA
41162 GGGGCCAAACGTTTGTCGCGATGCTCGATTT
1 GGGGCCAAACGTTTGTCGCGATGCTCGATTT
*
41193 GGGG-CAAATGTTTGTCGCGATGCTCGATTT
1 GGGGCCAAACGTTTGTCGCGATGCTCGATTT
41223 GGGGCCAAACGTTTGTCGCGATGCTCGATTT
1 GGGGCCAAACGTTTGTCGCGATGCTCGATTT
41254 GGGGCCAAACGTTT
1 GGGGCCAAACGTTT
41268 CAATTTAAAC
Statistics
Matches: 72, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
30 29 0.40
31 43 0.60
ACGTcount: A:0.17, C:0.21, G:0.33, T:0.29
Consensus pattern (31 bp):
GGGGCCAAACGTTTGTCGCGATGCTCGATTT
Found at i:42501 original size:13 final size:13
Alignment explanation
Indices: 42485--42510 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
42475 AAGAAGGAGG
42485 AAAAAAAGAAAAA
1 AAAAAAAGAAAAA
42498 AAAAAAAGAAAAA
1 AAAAAAAGAAAAA
42511 GAGAAGGAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (13 bp):
AAAAAAAGAAAAA
Found at i:44187 original size:21 final size:21
Alignment explanation
Indices: 44163--44202 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
44153 TCTTGCTCTT
* *
44163 TTCATTGGAGCTAATGGCATC
1 TTCAATGGAGCAAATGGCATC
*
44184 TTCAATGGATCAAATGGCA
1 TTCAATGGAGCAAATGGCA
44203 CCTTAGGCAA
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:0.30, C:0.17, G:0.23, T:0.30
Consensus pattern (21 bp):
TTCAATGGAGCAAATGGCATC
Found at i:44237 original size:21 final size:21
Alignment explanation
Indices: 44213--44276 Score: 112
Period size: 21 Copynumber: 3.1 Consensus size: 21
44203 CCTTAGGCAA
44213 CTCCAATGAGCTTGAAACCTT
1 CTCCAATGAGCTTGAAACCTT
*
44234 CTCCAATGAGCTTGAAACTTT
1 CTCCAATGAGCTTGAAACCTT
44255 CTCCAATGAGCTTGAAA-CTT
1 CTCCAATGAGCTTGAAACCTT
44275 CT
1 CT
44277 TTGTGTGAAT
Statistics
Matches: 41, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
20 4 0.10
21 37 0.90
ACGTcount: A:0.28, C:0.27, G:0.14, T:0.31
Consensus pattern (21 bp):
CTCCAATGAGCTTGAAACCTT
Found at i:47029 original size:2 final size:2
Alignment explanation
Indices: 47017--47103 Score: 60
Period size: 2 Copynumber: 46.0 Consensus size: 2
47007 TATAAATTAT
* * * *
47017 TA TA AA TA TA TA TT TA TA TA TA TA AA GA -A T- TA TA TA -A T-
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * *
47055 TA TA AA TA TA TC TGA TA TA T- TA TA TA TT TA TA TA TA TA TA TA
1 TA TA TA TA TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA TA TA
47097 T- TA TA TA
1 TA TA TA TA
47104 AACGGTCGGT
Statistics
Matches: 66, Mismatches: 12, Indels: 14
0.72 0.13 0.15
Matches are distributed among these distances:
1 6 0.09
2 59 0.89
3 1 0.02
ACGTcount: A:0.48, C:0.01, G:0.02, T:0.48
Consensus pattern (2 bp):
TA
Found at i:47032 original size:24 final size:25
Alignment explanation
Indices: 47005--47086 Score: 62
Period size: 24 Copynumber: 3.2 Consensus size: 25
46995 GTATTTTAAT
47005 TTTATAAATTATTATA-AATATATA
1 TTTATAAATTATTATAGAATATATA
* *
47029 TTTATATA-TA-TAAAGAATTATATA
1 TTTATAAATTATTATAGAA-TATATA
* * *
47053 ATTATAAATATATCTGATATATTATATA
1 TTTATAAAT-TAT-T-ATAGAATATATA
47081 TTTATA
1 TTTATA
47087 TATATATATA
Statistics
Matches: 43, Mismatches: 8, Indels: 10
0.70 0.13 0.16
Matches are distributed among these distances:
22 3 0.07
23 4 0.09
24 19 0.44
26 2 0.05
28 12 0.28
29 3 0.07
ACGTcount: A:0.48, C:0.01, G:0.02, T:0.49
Consensus pattern (25 bp):
TTTATAAATTATTATAGAATATATA
Found at i:47041 original size:30 final size:30
Alignment explanation
Indices: 47007--47105 Score: 83
Period size: 30 Copynumber: 3.2 Consensus size: 30
46997 ATTTTAATTT
*
47007 TATAAATTATTATAAATATATATTTATATA
1 TATAAATTATTATAAATATATATATATATA
** * *
47037 TATAAAGAATTATATAAT-TATAAATATATC
1 TATAAATTATTATA-AATATATATATATATA
* **
47067 TGATATATTATATATTTATATATATATATATTA
1 T-ATAAATTAT-TATAAATATATATATATA-TA
47100 TATAAA
1 TATAAA
47106 CGGTCGGTTC
Statistics
Matches: 51, Mismatches: 13, Indels: 8
0.71 0.18 0.11
Matches are distributed among these distances:
30 22 0.43
31 11 0.22
32 16 0.31
33 2 0.04
ACGTcount: A:0.49, C:0.01, G:0.02, T:0.47
Consensus pattern (30 bp):
TATAAATTATTATAAATATATATATATATA
Found at i:47101 original size:28 final size:27
Alignment explanation
Indices: 47023--47102 Score: 85
Period size: 28 Copynumber: 3.0 Consensus size: 27
47013 TTATTATAAA
*
47023 TATATATTTATATATATA-A-AGA-AT
1 TATATATTTATATATATATATATATAT
* * *
47047 TATATAATTATAAATATATCTGATATAT
1 TATATATTTATATATATATAT-ATATAT
47075 TATATATTTATATATATATATATTATAT
1 TATATATTTATATATATATATA-TATAT
47103 AAACGGTCGG
Statistics
Matches: 44, Mismatches: 7, Indels: 6
0.77 0.12 0.11
Matches are distributed among these distances:
24 16 0.36
27 3 0.07
28 25 0.57
ACGTcount: A:0.46, C:0.01, G:0.03, T:0.50
Consensus pattern (27 bp):
TATATATTTATATATATATATATATAT
Found at i:49534 original size:3 final size:3
Alignment explanation
Indices: 49526--49553 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
49516 TGGATGACAT
49526 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
49554 CCTATGTACC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:50130 original size:44 final size:44
Alignment explanation
Indices: 50061--50149 Score: 133
Period size: 44 Copynumber: 2.0 Consensus size: 44
50051 TGTCCTATGA
* * * *
50061 TTCTGAGTAAACTAGGGCTCGTTAGAGAGAACCCTACGATCTCC
1 TTCTAAGTAAACTAGGGCTCATTAGAGAGAACCCAACGAACTCC
*
50105 TTCTAAGTAAACTTGGGCTCATTAGAGAGAACCCAACGAACTCC
1 TTCTAAGTAAACTAGGGCTCATTAGAGAGAACCCAACGAACTCC
50149 T
1 T
50150 AGAGTTAAGT
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
44 40 1.00
ACGTcount: A:0.30, C:0.25, G:0.20, T:0.25
Consensus pattern (44 bp):
TTCTAAGTAAACTAGGGCTCATTAGAGAGAACCCAACGAACTCC
Found at i:51645 original size:44 final size:44
Alignment explanation
Indices: 51576--51664 Score: 124
Period size: 44 Copynumber: 2.0 Consensus size: 44
51566 TGTCCTATGA
* *
51576 TTCTGAGTAAACTAGGGCTCATTAGAGAGAACCCTACGATCTCC
1 TTCTAAGTAAACTAGGGCTCATTAGAGAGAACCCAACGATCTCC
* ** *
51620 TTCTAAGTAAACTTGGGCTTGTTAGAGAGAACGCAACGATCTCC
1 TTCTAAGTAAACTAGGGCTCATTAGAGAGAACCCAACGATCTCC
51664 T
1 T
51665 AGAGTTAAGT
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
44 39 1.00
ACGTcount: A:0.29, C:0.22, G:0.21, T:0.27
Consensus pattern (44 bp):
TTCTAAGTAAACTAGGGCTCATTAGAGAGAACCCAACGATCTCC
Found at i:51792 original size:22 final size:22
Alignment explanation
Indices: 51764--51808 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
51754 CAGCAACTAA
*
51764 ACTACCCTCCTAGAACACAGCC
1 ACTACCCTCCTAAAACACAGCC
51786 ACTACCCTCCTAAAACACAGCC
1 ACTACCCTCCTAAAACACAGCC
51808 A
1 A
51809 TAAAATTATT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.36, C:0.44, G:0.07, T:0.13
Consensus pattern (22 bp):
ACTACCCTCCTAAAACACAGCC
Found at i:52205 original size:3 final size:3
Alignment explanation
Indices: 52199--52273 Score: 141
Period size: 3 Copynumber: 24.7 Consensus size: 3
52189 TTATTAAAAA
52199 AAG AAG AAG AAAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG -AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
52245 AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
52274 AAGGAAACTG
Statistics
Matches: 71, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
3 68 0.96
4 3 0.04
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:59013 original size:2 final size:2
Alignment explanation
Indices: 58969--58994 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
58959 AACTAGAGTG
58969 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
58995 TACTTTTCAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:78123 original size:30 final size:31
Alignment explanation
Indices: 78088--78160 Score: 94
Period size: 30 Copynumber: 2.4 Consensus size: 31
78078 GGAGAAAATG
*
78088 CAATTCAGGATACACCGTTACCA-CTTGTGT
1 CAATTCAGGATACAACGTTACCAGCTTGTGT
* * * *
78118 CAATTCAGCATATAACGTTATCAGGTTGTGT
1 CAATTCAGGATACAACGTTACCAGCTTGTGT
78149 CAATTCAGGATA
1 CAATTCAGGATA
78161 AAAATCAGAC
Statistics
Matches: 36, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
30 19 0.53
31 17 0.47
ACGTcount: A:0.30, C:0.21, G:0.18, T:0.32
Consensus pattern (31 bp):
CAATTCAGGATACAACGTTACCAGCTTGTGT
Found at i:80358 original size:52 final size:52
Alignment explanation
Indices: 80301--80405 Score: 192
Period size: 52 Copynumber: 2.0 Consensus size: 52
80291 TTTTTCTTTC
*
80301 CGCAACAACTTCTGTCCCGAAGTTGAACAAGTTCTGGGCTGAAGTTGTCCTG
1 CGCAACAACTTCTGTCCCGAAGTTGAACAAGTTCTGGGCCGAAGTTGTCCTG
*
80353 CGCAACAACTTTTGTCCCGAAGTTGAACAAGTTCTGGGCCGAAGTTGTCCTG
1 CGCAACAACTTCTGTCCCGAAGTTGAACAAGTTCTGGGCCGAAGTTGTCCTG
80405 C
1 C
80406 AATTCTTGTT
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 51 1.00
ACGTcount: A:0.23, C:0.26, G:0.25, T:0.27
Consensus pattern (52 bp):
CGCAACAACTTCTGTCCCGAAGTTGAACAAGTTCTGGGCCGAAGTTGTCCTG
Found at i:86452 original size:21 final size:22
Alignment explanation
Indices: 86422--86463 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
86412 GTCCTGCGCT
*
86422 ACAACTTCTGTCCCGAAGTTGA
1 ACAACTTCTGGCCCGAAGTTGA
*
86444 ACAA-TTCTGGGCCGAAGTTG
1 ACAACTTCTGGCCCGAAGTTG
86464 TCCTGCAATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.26, C:0.24, G:0.24, T:0.26
Consensus pattern (22 bp):
ACAACTTCTGGCCCGAAGTTGA
Found at i:86469 original size:51 final size:52
Alignment explanation
Indices: 86370--86469 Score: 166
Period size: 52 Copynumber: 1.9 Consensus size: 52
86360 TCTTTCCGCA
* * *
86370 ACAACTTCTGTCCTGAAGTTGAGCAAGTTCTGGGCTGAAGTTGTCCTGCGCT
1 ACAACTTCTGTCCCGAAGTTGAACAAGTTCTGGGCCGAAGTTGTCCTGCGCT
86422 ACAACTTCTGTCCCGAAGTTGAACAA-TTCTGGGCCGAAGTTGTCCTGC
1 ACAACTTCTGTCCCGAAGTTGAACAAGTTCTGGGCCGAAGTTGTCCTGC
86470 AATTCTTGTT
Statistics
Matches: 45, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
51 21 0.47
52 24 0.53
ACGTcount: A:0.21, C:0.25, G:0.25, T:0.29
Consensus pattern (52 bp):
ACAACTTCTGTCCCGAAGTTGAACAAGTTCTGGGCCGAAGTTGTCCTGCGCT
Found at i:91409 original size:1 final size:1
Alignment explanation
Indices: 91403--91431 Score: 58
Period size: 1 Copynumber: 29.0 Consensus size: 1
91393 CTAGAAGGAC
91403 TTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTT
91432 CCAGAGGGAC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 28 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:92282 original size:20 final size:21
Alignment explanation
Indices: 92259--92301 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 21
92249 CAAATCAAGG
*
92259 AATAAGCAATC-AATCAAAGC
1 AATAAGCAATCAAAGCAAAGC
*
92279 AATAATCAATCAAAGCAAAGC
1 AATAAGCAATCAAAGCAAAGC
92300 AA
1 AA
92302 AAGAAGAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 10 0.50
21 10 0.50
ACGTcount: A:0.58, C:0.19, G:0.09, T:0.14
Consensus pattern (21 bp):
AATAAGCAATCAAAGCAAAGC
Found at i:92287 original size:16 final size:16
Alignment explanation
Indices: 92266--92296 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
92256 AGGAATAAGC
92266 AATCAATCAAAGCAAT
1 AATCAATCAAAGCAAT
92282 AATCAATCAAAGCAA
1 AATCAATCAAAGCAA
92297 AGCAAAAGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.58, C:0.19, G:0.06, T:0.16
Consensus pattern (16 bp):
AATCAATCAAAGCAAT
Found at i:94499 original size:6 final size:6
Alignment explanation
Indices: 94482--94522 Score: 73
Period size: 6 Copynumber: 6.8 Consensus size: 6
94472 AGTGCAAATC
*
94482 AAAAAG ATAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAA
1 AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAA
94523 AAATTAACGC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 33 1.00
ACGTcount: A:0.83, C:0.00, G:0.15, T:0.02
Consensus pattern (6 bp):
AAAAAG
Found at i:102157 original size:86 final size:84
Alignment explanation
Indices: 102004--102162 Score: 221
Period size: 86 Copynumber: 1.9 Consensus size: 84
101994 ATAATTGATA
* * * *
102004 AATAATAATGAGAATATTTTCTAAATCTTGCCAAATTGTGGAAGGTTTAGGAGATATTTTAAGAA
1 AATAATAATGAGAATATTTTCTAAATCTTGCCAAATTGTGGAAGATTTA-GAAAAATATTAAGAA
102069 ATAAATAAATTATAAAGATTG
65 AT-AATAAATTATAAAGATTG
* *
102090 AATAATAATGAGAATATTTTCTGAATCTTGCCAAATTGTGGGAGATTT-GAAAAATATTAAGTAA
1 AATAATAATGAGAATATTTTCTAAATCTTGCCAAATTGTGGAAGATTTAGAAAAATATTAAG--A
102154 AATAATAAA
64 AATAATAAA
102163 AAAGAAGTTA
Statistics
Matches: 65, Mismatches: 6, Indels: 5
0.86 0.08 0.07
Matches are distributed among these distances:
84 10 0.15
85 6 0.09
86 49 0.75
ACGTcount: A:0.45, C:0.05, G:0.16, T:0.34
Consensus pattern (84 bp):
AATAATAATGAGAATATTTTCTAAATCTTGCCAAATTGTGGAAGATTTAGAAAAATATTAAGAAA
TAATAAATTATAAAGATTG
Found at i:105768 original size:25 final size:28
Alignment explanation
Indices: 105723--105787 Score: 75
Period size: 26 Copynumber: 2.4 Consensus size: 28
105713 GAGGAAAAGA
*
105723 AAAAAGAAAA-ATGAAGAAAAGAA-TTG
1 AAAAAGAAAAGATAAAGAAAAGAAGTTG
105749 AAAAAGAAAAGA-AAAG-AAAGAAGTTG
1 AAAAAGAAAAGATAAAGAAAAGAAGTTG
*
105775 AAAATGCAAAAGA
1 AAAAAG-AAAAGA
105788 CGGAGGAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
25 6 0.18
26 21 0.62
27 7 0.21
ACGTcount: A:0.69, C:0.02, G:0.20, T:0.09
Consensus pattern (28 bp):
AAAAAGAAAAGATAAAGAAAAGAAGTTG
Done.