Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022458.1 Corchorus olitorius cultivar O-4 contig22491, 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: 119722
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.31
Found at i:2285 original size:21 final size:21
Alignment explanation
Indices: 2244--2298 Score: 78
Period size: 21 Copynumber: 2.7 Consensus size: 21
2234 TTGGCAACTG
*
2244 TACAGATGAGATTA--CACTA
1 TACAGATGAGATTATGTACTA
*
2263 TACAGATTAGATTATGTACTA
1 TACAGATGAGATTATGTACTA
2284 TACAGATGAGATTAT
1 TACAGATGAGATTAT
2299 TAGAGCAGCG
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
19 13 0.42
21 18 0.58
ACGTcount: A:0.40, C:0.11, G:0.16, T:0.33
Consensus pattern (21 bp):
TACAGATGAGATTATGTACTA
Found at i:17364 original size:14 final size:14
Alignment explanation
Indices: 17345--17390 Score: 55
Period size: 14 Copynumber: 3.6 Consensus size: 14
17335 CTCATAAATA
17345 AAAATAAAACAATC
1 AAAATAAAACAATC
17359 AAAAT--AA-AAT-
1 AAAATAAAACAATC
*
17369 AAAAAAAAACAATC
1 AAAATAAAACAATC
17383 AAAATAAA
1 AAAATAAA
17391 GTACCTTCGT
Statistics
Matches: 26, Mismatches: 2, Indels: 8
0.72 0.06 0.22
Matches are distributed among these distances:
10 4 0.15
11 3 0.12
12 4 0.15
13 3 0.12
14 12 0.46
ACGTcount: A:0.78, C:0.09, G:0.00, T:0.13
Consensus pattern (14 bp):
AAAATAAAACAATC
Found at i:17365 original size:24 final size:23
Alignment explanation
Indices: 17338--17390 Score: 88
Period size: 24 Copynumber: 2.2 Consensus size: 23
17328 AATAATTCTC
17338 ATAAATAAAAATAAAACAATCAAA
1 ATAAATAAAAA-AAAACAATCAAA
17362 ATAAAATAAAAAAAAACAATCAAA
1 AT-AAATAAAAAAAAACAATCAAA
17386 ATAAA
1 ATAAA
17391 GTACCTTCGT
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
23 3 0.11
24 16 0.57
25 9 0.32
ACGTcount: A:0.77, C:0.08, G:0.00, T:0.15
Consensus pattern (23 bp):
ATAAATAAAAAAAAACAATCAAA
Found at i:35297 original size:145 final size:138
Alignment explanation
Indices: 35023--35311 Score: 465
Period size: 145 Copynumber: 2.1 Consensus size: 138
35013 GTTCCATGTG
35023 ATTA-TAGATTAAAAGGGTACCTGAACCTACATTCCAAGCACTTATCCATTGTGATATCAACTAA
1 ATTATTAGATTAAAAGGGTACCTGAACCTACATTCCAAGCACTTATCCATTGTGATATCAACTAA
35087 ACCTAAGCTACCAACTATGGAAAAAATTGCAAATGAAGTTTTGGTACGCCAATAGTAAGTATAAA
66 ACCTAAGCTACCAACTATGGAAAAAATTGCAAATGAAGTTTTGGTACGCCAATAGTAAGTATAAA
35152 TCATAGTA
131 TCATAGTA
*
35160 ATTATTAGATTAAAAGGGTACCTGAACCTACATTCCAAGCAGTTATCCATTGTGAATTTGTAATA
1 ATTATTAGATTAAAAGGGTACCTGAACCTACATTCCAAGCACTTATCCA-T-TG----TG--ATA
* *
35225 TCAACTAAACCTAAGCTACCAACTATTG-AAAAATTGCAAATGAATTTTTGGTACGCCAATAGTA
58 TCAACTAAACCTAAGCTACCAACTATGGAAAAAATTGCAAATGAAGTTTTGGTACGCCAATAGTA
35289 AGTATAAATCATAGTA
123 AGTATAAATCATAGTA
35305 ATTATTA
1 ATTATTA
35312 ATGCAGCTAC
Statistics
Matches: 140, Mismatches: 3, Indels: 10
0.92 0.02 0.07
Matches are distributed among these distances:
137 4 0.03
138 43 0.31
139 1 0.01
140 2 0.01
144 2 0.01
145 58 0.41
146 30 0.21
ACGTcount: A:0.40, C:0.16, G:0.14, T:0.30
Consensus pattern (138 bp):
ATTATTAGATTAAAAGGGTACCTGAACCTACATTCCAAGCACTTATCCATTGTGATATCAACTAA
ACCTAAGCTACCAACTATGGAAAAAATTGCAAATGAAGTTTTGGTACGCCAATAGTAAGTATAAA
TCATAGTA
Found at i:40700 original size:14 final size:15
Alignment explanation
Indices: 40683--40711 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
40673 CTTTTTAATC
40683 ATTTTT-TTTAAAAA
1 ATTTTTATTTAAAAA
40697 ATTTTTATTTAAAAA
1 ATTTTTATTTAAAAA
40712 TATATAACCA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
ATTTTTATTTAAAAA
Found at i:40791 original size:11 final size:11
Alignment explanation
Indices: 40767--40801 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
40757 TTGACGACGC
40767 AACAAAAACAA
1 AACAAAAACAA
* *
40778 AACGAAAACGA
1 AACAAAAACAA
40789 AACAAAAACAA
1 AACAAAAACAA
40800 AA
1 AA
40802 AACAGAAAAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.77, C:0.17, G:0.06, T:0.00
Consensus pattern (11 bp):
AACAAAAACAA
Found at i:47127 original size:33 final size:33
Alignment explanation
Indices: 47040--47134 Score: 172
Period size: 33 Copynumber: 2.9 Consensus size: 33
47030 ATCAGCATGG
*
47040 ATGCCACCTCAGTCACTGCCTCATGCATCGGGA
1 ATGCCACCTCAGTCACTGCCTTATGCATCGGGA
47073 ATGCCACCTCAGTCACTGCCTTATGCATCGGGA
1 ATGCCACCTCAGTCACTGCCTTATGCATCGGGA
*
47106 ATGCCACCTCAGTCACTGCCTTATTCATC
1 ATGCCACCTCAGTCACTGCCTTATGCATC
47135 AGCAATTCCA
Statistics
Matches: 60, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 60 1.00
ACGTcount: A:0.21, C:0.36, G:0.18, T:0.25
Consensus pattern (33 bp):
ATGCCACCTCAGTCACTGCCTTATGCATCGGGA
Found at i:59816 original size:21 final size:21
Alignment explanation
Indices: 59792--59835 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
59782 GTTGCCCCGA
59792 CTCATTAGCCAGAGCAAAACT
1 CTCATTAGCCAGAGCAAAACT
*
59813 CTCATTAGTCAGAGCAAAACT
1 CTCATTAGCCAGAGCAAAACT
59834 CT
1 CT
59836 GGATACCGGA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.36, C:0.27, G:0.14, T:0.23
Consensus pattern (21 bp):
CTCATTAGCCAGAGCAAAACT
Found at i:61780 original size:21 final size:21
Alignment explanation
Indices: 61754--61828 Score: 62
Period size: 21 Copynumber: 3.3 Consensus size: 21
61744 ATGGATAAAT
61754 TGGTGGAGGTGGTGAATGTGG
1 TGGTGGAGGTGGTGAATGTGG
*
61775 TGGTGGTGGTGGTGGAGAGTGTGG
1 TGGTGGAGGTGGT-GA-A-TGTGG
*
61799 TGGCGGTGGAGGTGAGT-ATTGTGG
1 T---GGTGGAGGTG-GTGAATGTGG
61823 TGGTGG
1 TGGTGG
61829 TGGGGAGTTA
Statistics
Matches: 44, Mismatches: 3, Indels: 14
0.72 0.05 0.23
Matches are distributed among these distances:
21 17 0.39
22 2 0.05
23 1 0.02
24 12 0.27
26 1 0.02
27 9 0.20
28 2 0.05
ACGTcount: A:0.11, C:0.01, G:0.59, T:0.29
Consensus pattern (21 bp):
TGGTGGAGGTGGTGAATGTGG
Found at i:61788 original size:24 final size:24
Alignment explanation
Indices: 61754--61831 Score: 95
Period size: 24 Copynumber: 3.2 Consensus size: 24
61744 ATGGATAAAT
61754 TGGTGGAGGTGGTGAATGTGGTGG
1 TGGTGGAGGTGGTGAATGTGGTGG
* * *
61778 TGGTGGTGGTGGAGAGTGTGGTGG
1 TGGTGGAGGTGGTGAATGTGGTGG
* *
61802 CGGTGGAGGTGAGT-ATTGTGGTGG
1 TGGTGGAGGTG-GTGAATGTGGTGG
61826 TGGTGG
1 TGGTGG
61832 GGAGTTATAG
Statistics
Matches: 45, Mismatches: 8, Indels: 2
0.82 0.15 0.04
Matches are distributed among these distances:
24 44 0.98
25 1 0.02
ACGTcount: A:0.10, C:0.01, G:0.59, T:0.29
Consensus pattern (24 bp):
TGGTGGAGGTGGTGAATGTGGTGG
Found at i:61836 original size:21 final size:21
Alignment explanation
Indices: 61775--61836 Score: 70
Period size: 21 Copynumber: 3.0 Consensus size: 21
61765 GTGAATGTGG
*
61775 TGGTGGTGGTGGTGGAGAGTG
1 TGGTGGTGGTGGTGGAGAGTA
* * *
61796 TGGTGGCGGTGGAGGTGAGTA
1 TGGTGGTGGTGGTGGAGAGTA
* *
61817 TTGTGGTGGTGGTGGGGAGT
1 TGGTGGTGGTGGTGGAGAGT
61837 TATAGTAATA
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.10, C:0.02, G:0.60, T:0.29
Consensus pattern (21 bp):
TGGTGGTGGTGGTGGAGAGTA
Found at i:62164 original size:66 final size:66
Alignment explanation
Indices: 62094--62217 Score: 167
Period size: 66 Copynumber: 1.9 Consensus size: 66
62084 TGGTGGTGGG
* * * * *
62094 GAAGGAGGTGGAGGTGAGGGAGGTGGTGGAGGAGGTGAATAAACTGGTGGTGGAGGTGGGGGAGG
1 GAAGGAGGTGGAGGTGAGGGAGGAGGGGGAGGAGGAGAATAAACAGGAGGTGGAGGTGGGGGAGG
62159 T
66 T
* * * *
62160 GAAGGAGGTGGCGGTGAGGGTGGAGGGGGAGGTGGAGAGTAAACAGGAGGTGGAGGTG
1 GAAGGAGGTGGAGGTGAGGGAGGAGGGGGAGGAGGAGAATAAACAGGAGGTGGAGGTG
62218 ATGGCGGAGG
Statistics
Matches: 49, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
66 49 1.00
ACGTcount: A:0.23, C:0.02, G:0.60, T:0.15
Consensus pattern (66 bp):
GAAGGAGGTGGAGGTGAGGGAGGAGGGGGAGGAGGAGAATAAACAGGAGGTGGAGGTGGGGGAGG
T
Found at i:62191 original size:42 final size:43
Alignment explanation
Indices: 62162--62259 Score: 137
Period size: 42 Copynumber: 2.3 Consensus size: 43
62152 GGGGAGGTGA
* *
62162 AGGAGGTGGCGGTGAGGGTGGAGGGGGAGGT-GGAGAGTAAAC
1 AGGAGGTGGAGGTGAGGGCGGAGGGGGAGGTGGGAGAGTAAAC
*
62204 AGGAGGTGGAGGTGATGGCGGAGGGGGAGGT-GGAGAGTAAAC
1 AGGAGGTGGAGGTGAGGGCGGAGGGGGAGGTGGGAGAGTAAAC
* *
62246 AGGCGGCGGAGGTG
1 AGGAGGTGGAGGTG
62260 GTGGAGAGTA
Statistics
Matches: 51, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
42 51 1.00
ACGTcount: A:0.23, C:0.06, G:0.59, T:0.11
Consensus pattern (43 bp):
AGGAGGTGGAGGTGAGGGCGGAGGGGGAGGTGGGAGAGTAAAC
Found at i:62208 original size:24 final size:24
Alignment explanation
Indices: 62181--62260 Score: 75
Period size: 24 Copynumber: 3.6 Consensus size: 24
62171 CGGTGAGGGT
62181 GGAGGGGGAGGTGGAGAGTAAACA
1 GGAGGGGGAGGTGGAGAGTAAACA
*
62205 GGAGGTGGAGGT-GATG-G----C-
1 GGAGGGGGAGGTGGA-GAGTAAACA
62223 GGAGGGGGAGGTGGAGAGTAAACA
1 GGAGGGGGAGGTGGAGAGTAAACA
* *
62247 GGCGGCGGAGGTGG
1 GGAGGGGGAGGTGG
62261 TGGAGAGTAA
Statistics
Matches: 44, Mismatches: 4, Indels: 16
0.69 0.06 0.25
Matches are distributed among these distances:
18 12 0.27
19 4 0.09
23 4 0.09
24 24 0.55
ACGTcount: A:0.25, C:0.06, G:0.59, T:0.10
Consensus pattern (24 bp):
GGAGGGGGAGGTGGAGAGTAAACA
Found at i:62233 original size:66 final size:65
Alignment explanation
Indices: 62096--62238 Score: 155
Period size: 66 Copynumber: 2.2 Consensus size: 65
62086 GTGGTGGGGA
* * * * *
62096 AGGAGGTGGAGGTGAGGGAGGTGGTGGAGGAGGTGAATAAACTGGTGGTGGAGGTGGGGGAGGTG
1 AGGAGGTGGAGGTGAGGGAGGAGGGGGAGGAGGAGAATAAACAGGAGGTGGAGGTGGGGGAGGTG
* * * *
62161 AAGGAGGTGGCGGTGAGGGTGGAGGGGGAGGTGGAGAGTAAACAGGAGGTGGAGGTGATGGCGGA
1 -AGGAGGTGGAGGTGAGGGAGGAGGGGGAGGAGGAGAATAAACAGGAGGTGGAGGTG--GG-GGA
62226 GG-G
62 GGTG
62229 -GGAGGTGGAG
1 AGGAGGTGGAG
62239 AGTAAACAGG
Statistics
Matches: 64, Mismatches: 10, Indels: 6
0.80 0.12 0.08
Matches are distributed among these distances:
66 56 0.88
68 3 0.05
69 5 0.08
ACGTcount: A:0.22, C:0.03, G:0.61, T:0.14
Consensus pattern (65 bp):
AGGAGGTGGAGGTGAGGGAGGAGGGGGAGGAGGAGAATAAACAGGAGGTGGAGGTGGGGGAGGTG
Found at i:62262 original size:27 final size:27
Alignment explanation
Indices: 62232--62308 Score: 136
Period size: 27 Copynumber: 2.9 Consensus size: 27
62222 CGGAGGGGGA
*
62232 GGTGGAGAGTAAACAGGCGGCGGAGGT
1 GGTGGAGAGTAAACTGGCGGCGGAGGT
*
62259 GGTGGAGAGTAAACTGGCGGCGGTGGT
1 GGTGGAGAGTAAACTGGCGGCGGAGGT
62286 GGTGGAGAGTAAACTGGCGGCGG
1 GGTGGAGAGTAAACTGGCGGCGG
62309 CGGAGGCGGT
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 48 1.00
ACGTcount: A:0.22, C:0.12, G:0.52, T:0.14
Consensus pattern (27 bp):
GGTGGAGAGTAAACTGGCGGCGGAGGT
Found at i:62360 original size:21 final size:21
Alignment explanation
Indices: 62336--62395 Score: 84
Period size: 21 Copynumber: 2.9 Consensus size: 21
62326 GAGGAGTATA
*
62336 AACAGGTGGCGAAGGCACAAC
1 AACAGGTGGAGAAGGCACAAC
* * *
62357 AACAGGTGGTGACGGCACTAC
1 AACAGGTGGAGAAGGCACAAC
62378 AACAGGTGGAGAAGGCAC
1 AACAGGTGGAGAAGGCAC
62396 CGGGATTGGC
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.35, C:0.22, G:0.35, T:0.08
Consensus pattern (21 bp):
AACAGGTGGAGAAGGCACAAC
Found at i:63785 original size:15 final size:15
Alignment explanation
Indices: 63762--63791 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
63752 ATGAAAAGCT
*
63762 TGGGTTTTTTGCAAA
1 TGGGGTTTTTGCAAA
63777 TGGGGTTTTTGCAAA
1 TGGGGTTTTTGCAAA
63792 CAAAACGATA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.20, C:0.07, G:0.30, T:0.43
Consensus pattern (15 bp):
TGGGGTTTTTGCAAA
Found at i:66698 original size:3 final size:3
Alignment explanation
Indices: 66690--66714 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
66680 ATCAAGCTTC
66690 ATG ATG ATG ATG ATG ATG ATG ATG A
1 ATG ATG ATG ATG ATG ATG ATG ATG A
66715 AGAAGAAGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.36, C:0.00, G:0.32, T:0.32
Consensus pattern (3 bp):
ATG
Found at i:84928 original size:25 final size:25
Alignment explanation
Indices: 84900--84953 Score: 108
Period size: 25 Copynumber: 2.2 Consensus size: 25
84890 TCTCTTGGCT
84900 TAATTAGCAAAGTGATAAATTATGA
1 TAATTAGCAAAGTGATAAATTATGA
84925 TAATTAGCAAAGTGATAAATTATGA
1 TAATTAGCAAAGTGATAAATTATGA
84950 TAAT
1 TAAT
84954 ATAGTGGGGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.48, C:0.04, G:0.15, T:0.33
Consensus pattern (25 bp):
TAATTAGCAAAGTGATAAATTATGA
Found at i:88377 original size:18 final size:19
Alignment explanation
Indices: 88340--88377 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 19
88330 GCTCCCGTTG
88340 TGATGCTCCCACTTTTCAATA
1 TGATGCTCCCA--TTTCAATA
88361 TGATGCTCCCA-TTCAAT
1 TGATGCTCCCATTTCAAT
88378 TCTAACCATT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
18 6 0.35
21 11 0.65
ACGTcount: A:0.24, C:0.29, G:0.11, T:0.37
Consensus pattern (19 bp):
TGATGCTCCCATTTCAATA
Found at i:94164 original size:13 final size:13
Alignment explanation
Indices: 94146--94172 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
94136 CATGATCTTA
94146 TTCCCACTAAATT
1 TTCCCACTAAATT
94159 TTCCCACTAAATT
1 TTCCCACTAAATT
94172 T
1 T
94173 GAAATGAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.30, G:0.00, T:0.41
Consensus pattern (13 bp):
TTCCCACTAAATT
Found at i:99844 original size:31 final size:32
Alignment explanation
Indices: 99774--99853 Score: 92
Period size: 31 Copynumber: 2.5 Consensus size: 32
99764 TCCTCCGTCA
* * *
99774 AGGGTAAAATATCTTGAATTTCGGAAGTTCAG
1 AGGGCAAAATATCCTGAACTTCGGAAGTTCAG
*
99806 -GGAGCAAAATATCCTGAACTT-GGAAGTTTAG
1 AGG-GCAAAATATCCTGAACTTCGGAAGTTCAG
*
99837 AGGGCAAAATGTCCTGA
1 AGGGCAAAATATCCTGA
99854 TCTAAAGTTC
Statistics
Matches: 41, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
31 24 0.59
32 17 0.41
ACGTcount: A:0.35, C:0.12, G:0.26, T:0.26
Consensus pattern (32 bp):
AGGGCAAAATATCCTGAACTTCGGAAGTTCAG
Found at i:102007 original size:22 final size:23
Alignment explanation
Indices: 101979--102026 Score: 71
Period size: 24 Copynumber: 2.1 Consensus size: 23
101969 GGTTAATAAT
101979 TTCCTTG-TTTTGTTCAATGCTA
1 TTCCTTGTTTTTGTTCAATGCTA
*
102001 TTCCTTGTTTTTTGTTCAATTCTA
1 TTCCTTG-TTTTTGTTCAATGCTA
102025 TT
1 TT
102027 GGCTAAAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 7 0.30
24 16 0.70
ACGTcount: A:0.12, C:0.17, G:0.10, T:0.60
Consensus pattern (23 bp):
TTCCTTGTTTTTGTTCAATGCTA
Found at i:113957 original size:31 final size:31
Alignment explanation
Indices: 113922--114061 Score: 163
Period size: 31 Copynumber: 4.5 Consensus size: 31
113912 TTTGTGCACG
* *
113922 TGGCATGCCACATGTCACTTTTTGAAACACA
1 TGGCGTGCCACATGTCACTTTTTGATACACA
* *
113953 TGGCATGCCACGTGTCACTTTTTGATACACA
1 TGGCGTGCCACATGTCACTTTTTGATACACA
** * * **
113984 TGGCGTGATACGTGTCACTTTTTGGTACATG
1 TGGCGTGCCACATGTCACTTTTTGATACACA
* * *
114015 TGACGTGCCACATGTCACTTTTTGGTACATA
1 TGGCGTGCCACATGTCACTTTTTGATACACA
114046 TGGCGTGCCACATGTC
1 TGGCGTGCCACATGTC
114062 GCTTGGCATG
Statistics
Matches: 95, Mismatches: 14, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 95 1.00
ACGTcount: A:0.21, C:0.24, G:0.22, T:0.33
Consensus pattern (31 bp):
TGGCGTGCCACATGTCACTTTTTGATACACA
Found at i:115722 original size:18 final size:18
Alignment explanation
Indices: 115699--115733 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
115689 CATATTGAAC
115699 TCTAATTAATATGAAATG
1 TCTAATTAATATGAAATG
115717 TCTAATTAATATGAAAT
1 TCTAATTAATATGAAAT
115734 TGAGTCGAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.46, C:0.06, G:0.09, T:0.40
Consensus pattern (18 bp):
TCTAATTAATATGAAATG
Found at i:116330 original size:5 final size:5
Alignment explanation
Indices: 116320--116363 Score: 74
Period size: 5 Copynumber: 9.2 Consensus size: 5
116310 GAAAATTGAG
116320 ATTTT ATTTT ATTTT A-TTT ATTTT ATTTT A-TTT ATTTT ATTTT A
1 ATTTT ATTTT ATTTT ATTTT ATTTT ATTTT ATTTT ATTTT ATTTT A
116364 CAAGAAATAC
Statistics
Matches: 37, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
4 8 0.22
5 29 0.78
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (5 bp):
ATTTT
Found at i:116341 original size:9 final size:9
Alignment explanation
Indices: 116322--116361 Score: 55
Period size: 9 Copynumber: 4.3 Consensus size: 9
116312 AAATTGAGAT
116322 TTTATTTTA
1 TTTATTTTA
116331 TTT-TATTTA
1 TTTAT-TTTA
116340 TTTTATTTTA
1 -TTTATTTTA
116350 TTTATTTTA
1 TTTATTTTA
116359 TTT
1 TTT
116362 TACAAGAAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
8 1 0.04
9 19 0.68
10 7 0.25
11 1 0.04
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (9 bp):
TTTATTTTA
Found at i:116341 original size:14 final size:14
Alignment explanation
Indices: 116322--116363 Score: 84
Period size: 14 Copynumber: 3.0 Consensus size: 14
116312 AAATTGAGAT
116322 TTTATTTTATTTTA
1 TTTATTTTATTTTA
116336 TTTATTTTATTTTA
1 TTTATTTTATTTTA
116350 TTTATTTTATTTTA
1 TTTATTTTATTTTA
116364 CAAGAAATAC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 28 1.00
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (14 bp):
TTTATTTTATTTTA
Found at i:116344 original size:19 final size:19
Alignment explanation
Indices: 116320--116363 Score: 72
Period size: 19 Copynumber: 2.3 Consensus size: 19
116310 GAAAATTGAG
116320 ATTTTATTTTATTTTATTT
1 ATTTTATTTTATTTTATTT
116339 ATTTTATTTTA-TTTATTTT
1 ATTTTATTTTATTTTA-TTT
116358 ATTTTA
1 ATTTTA
116364 CAAGAAATAC
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
18 4 0.17
19 20 0.83
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (19 bp):
ATTTTATTTTATTTTATTT
Found at i:117900 original size:17 final size:18
Alignment explanation
Indices: 117868--117902 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
117858 TATATTTATA
*
117868 TAATTACTTAATATAATT
1 TAATTACTTAAAATAATT
117886 TAATT-CTTAAAATAATT
1 TAATTACTTAAAATAATT
117903 ATTAAAAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.46, C:0.06, G:0.00, T:0.49
Consensus pattern (18 bp):
TAATTACTTAAAATAATT
Found at i:119465 original size:43 final size:42
Alignment explanation
Indices: 119404--119485 Score: 137
Period size: 42 Copynumber: 1.9 Consensus size: 42
119394 GCTAAGTCTT
119404 GAAAATTCTTTGTAAATTAAAAAAATACTCAACTCAAATCATA
1 GAAAATTCTTTGTAAATT-AAAAAATACTCAACTCAAATCATA
**
119447 GAAAATTCTTTGTAAATTAAGCAATACTCAACTCAAATC
1 GAAAATTCTTTGTAAATTAAAAAATACTCAACTCAAATC
119486 CTGATCCTTA
Statistics
Matches: 37, Mismatches: 2, Indels: 1
0.93 0.05 0.03
Matches are distributed among these distances:
42 19 0.51
43 18 0.49
ACGTcount: A:0.48, C:0.16, G:0.06, T:0.30
Consensus pattern (42 bp):
GAAAATTCTTTGTAAATTAAAAAATACTCAACTCAAATCATA
Found at i:119620 original size:55 final size:55
Alignment explanation
Indices: 119550--119660 Score: 222
Period size: 55 Copynumber: 2.0 Consensus size: 55
119540 TTTATTTTGT
119550 AGAATAATTAAGTAGAGATAGGGGATAGGATTTATTATAACATTTATTGTGTGAA
1 AGAATAATTAAGTAGAGATAGGGGATAGGATTTATTATAACATTTATTGTGTGAA
119605 AGAATAATTAAGTAGAGATAGGGGATAGGATTTATTATAACATTTATTGTGTGAA
1 AGAATAATTAAGTAGAGATAGGGGATAGGATTTATTATAACATTTATTGTGTGAA
119660 A
1 A
119661 AGGAAACACA
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
55 56 1.00
ACGTcount: A:0.41, C:0.02, G:0.23, T:0.34
Consensus pattern (55 bp):
AGAATAATTAAGTAGAGATAGGGGATAGGATTTATTATAACATTTATTGTGTGAA
Done.