Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold4728.1
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: 46697
ACGTcount: A:0.27, C:0.14, G:0.14, T:0.26
Warning! 8887 characters in sequence are not A, C, G, or T
Found at i:1818 original size:86 final size:87
Alignment explanation
Indices: 1708--2118 Score: 565
Period size: 86 Copynumber: 4.7 Consensus size: 87
1698 CAGAAATTAA
* * *
1708 AAGGCTCTACTCACCTCTCGCAATATGAGTTGAGTTTTGAAAACATGAATT-AAAACAGAAATTG
1 AAGGCTCAACTCACTTCTCGCAATATGAGTTGAGTTTTGAAAACATAAATTAAAAACAGAAATTG
* * *
1772 GAAATACCTCAGCATGTGAGCC
66 AAAATACCTCGGCATGCGAGCC
* * *
1794 GAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTGAAAAACATAAATTAAAAATAGAAATT
1 AAGGCTCAACTCACTTCTCGCAATATGAGTTGAGTTTTG-AAAACATAAATTAAAAACAGAAATT
1859 GAAAATACCTCGGCATGCGAGCC
65 GAAAATACCTCGGCATGCGAGCC
* * *
1882 AAGGCTCAACTCACTTCTCGCAATATGAGTTGAGTTTTTGAAAAGTAAAAATTAAAAACAGAATT
1 AAGGCTCAACTCACTTCTCGCAATATGAGTTGAG-TTTTGAAAA-CATAAATTAAAAACAGAAAT
* * *
1947 TGAAAATACCTCGACATGTGACCC
64 TGAAAATACCTCGGCATGCGAGCC
* * * *
1971 GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAACATGAATT-AAAACAGAAATTG
1 AAGGCTCAACTCACTTCTCGCAATATGAGTTGAGTTTTGAAAACATAAATTAAAAACAGAAATTG
2035 AAAATACCTCGGCATGCGAGCC
66 AAAATACCTCGGCATGCGAGCC
* * *
2057 AAGGCTCAACTCACTTCTCGCAAAATGAGTTGAGTTTTTGAAAAGTAAAAATTAAAAACAGA
1 AAGGCTCAACTCACTTCTCGCAATATGAGTTGAG-TTTTGAAAA-CATAAATTAAAAACAGA
2119 GTTTGAAAGA
Statistics
Matches: 283, Mismatches: 35, Indels: 11
0.86 0.11 0.03
Matches are distributed among these distances:
86 96 0.34
87 25 0.09
88 81 0.29
89 81 0.29
ACGTcount: A:0.38, C:0.18, G:0.17, T:0.26
Consensus pattern (87 bp):
AAGGCTCAACTCACTTCTCGCAATATGAGTTGAGTTTTGAAAACATAAATTAAAAACAGAAATTG
AAAATACCTCGGCATGCGAGCC
Found at i:1888 original size:88 final size:88
Alignment explanation
Indices: 1708--2460 Score: 575
Period size: 88 Copynumber: 8.4 Consensus size: 88
1698 CAGAAATTAA
* * * *
1708 AAGGCTCTACTCACCTCTCGCAATATGAGTTGAGTTTTG-AAAACATGAATT-AAAACAGAAATT
1 AAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTGAAAAACATAAATTAAAAACAGAAATT
* * *
1771 GGAAATACCTCAGCATGTGAGCC
66 GAAAATACCTCGGCATGCGAGCC
* *
1794 GAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTGAAAAACATAAATTAAAAATAGAAATT
1 AAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTGAAAAACATAAATTAAAAACAGAAATT
1859 GAAAATACCTCGGCATGCGAGCC
66 GAAAATACCTCGGCATGCGAGCC
** * *
1882 AAGGCTCAACTCACTTCTCGCAATATGAGTTGAGTTTTTGAAAAGTAAAAATTAAAAACAGAATT
1 AAGGCTCAACTCACTTCTCGCAATATGAGTTGA-TTTTTGAAAAACATAAATTAAAAACAGAAAT
* * *
1947 TGAAAATACCTCGACATGTGACCC
65 TGAAAATACCTCGGCATGCGAGCC
* * *
1971 GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTG-AAAACATGAATT-AAAACAGAAATT
1 AAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTGAAAAACATAAATTAAAAACAGAAATT
2034 GAAAATACCTCGGCATGCGAGCC
66 GAAAATACCTCGGCATGCGAGCC
* ** * **
2057 AAGGCTCAACTCACTTCTCGCAAAATGAGTTGAGTTTTTGAAAAGTAAAAATTAAAAACAGAGTT
1 AAGGCTCAACTCACTTCTCGCAATATGAGTTGA-TTTTTGAAAAACATAAATTAAAAACAGAAAT
* ** * ** * ** *
2122 TGAAAGACAGAATTTGAAAATACCTCGGC
65 TG-AA-A-ATACCTCG-GCAT-GCGAGCC
* * * ** *
2151 ATGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTAAAATATAAATTGAAA
1 AAG-G-CTC-A-ACTC-ACT----TCTCGCAATATGAGTTGATTTTTGAAAAACATAAATT--AA
*
2216 AAACAGAAATTGAAAATACCT---CA-GCGTGTCC
55 AAACAGAAATTGAAAATACCTCGGCATGCGAG-CC
* * * * * * **
2247 TGAGGCTCAATTCACCTCTCGCGATATGAGTTGATTTTTTGAAAAGCAGAAATTGAAAAGTAGAA
1 -AAGGCTCAACTCACTTCTCGCAATATGAGTTGA-TTTTTGAAAAACATAAATT-AAAAACAGAA
* *
2312 ATTGAAAATACCTCAGCGTGC---CC
63 ATTGAAAATACCTCGGCATGCGAGCC
* * * * *** *
2335 TGAGGCTCAACTCACCTCTCGTAATATGAGTCGATTTTTTTTTAAACAGAAATTGAAAAACA-AA
1 -AAGGCTCAACTCACTTCTCGCAATATGAGTTGA-TTTTTGAAAAACATAAATT-AAAAACAGAA
*
2399 TATTGAAAATACCT---CA-GCGTGTCC
63 -ATTGAAAATACCTCGGCATGCGAG-CC
* *
2423 TAAGGCTCGACCCACTTCTCGCAATATGAGTTGATTTT
1 -AAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTT
2461 GCATGTGACC
Statistics
Matches: 535, Mismatches: 98, Indels: 67
0.76 0.14 0.10
Matches are distributed among these distances:
84 2 0.00
85 1 0.00
86 96 0.18
87 31 0.06
88 212 0.40
89 103 0.19
90 2 0.00
91 2 0.00
92 8 0.01
93 4 0.01
94 6 0.01
95 5 0.01
96 4 0.01
97 3 0.01
98 3 0.01
99 3 0.01
101 3 0.01
102 16 0.03
103 19 0.04
104 12 0.02
ACGTcount: A:0.37, C:0.19, G:0.17, T:0.27
Consensus pattern (88 bp):
AAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTGAAAAACATAAATTAAAAACAGAAATT
GAAAATACCTCGGCATGCGAGCC
Found at i:2065 original size:175 final size:176
Alignment explanation
Indices: 1540--2460 Score: 807
Period size: 176 Copynumber: 5.2 Consensus size: 176
1530 GTGATCTTGA
* * * * * * *
1540 GCTCAACCCATTTCTTGCAATATGAATTGA-TTATTT-AAAAACAGACATT-AAAAACAGAAATT
1 GCTCAACTCACTTCTCGCAATATGAGTTGAGTT-TTTGAAAAGCAAAAATTAAAAAACAGAAATT
* * * * * * * *
1602 GAGAATAGCTCAGCACGTGAGCCAAGGCGCAATTCACCTCTCGCAATATGAGTTGTTCTTTTTTG
65 GAAAATACCTCAGCATGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTG--ATTTTTTG
* * ** ** * * ***
1667 -AAACTTAATTTGAAAAGTAGATTTTGAAAA-A---CAG-AAATTAAAAG
128 AAAACATAAATT-AAAAACAGAAATTGAAAATACCTCAGCGAGTCCTAAG
* * **
1711 GCTCTACTCACCTCTCGCAATATGAGTTGAG-TTTTGAAAA-CATGAATT--AAAACAGAAATTG
1 GCTCAACTCACTTCTCGCAATATGAGTTGAGTTTTTGAAAAGCAAAAATTAAAAAACAGAAATTG
* * *
1772 GAAATACCTCAGCATGTGAGCCGAGGCTCAACTCACTTCTCGCAATATGAGTTGA-TTTTTGAAA
66 AAAATACCTCAGCATGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTG-AA
*
1836 AACATAAATTAAAAATAGAAATTGAAAATACCTCGGCATGCGAG-CC-AAG
130 AACATAAATTAAAAACAGAAATTGAAAATACCT---CA-GCGAGTCCTAAG
* *
1885 GCTCAACTCACTTCTCGCAATATGAGTTGAGTTTTTGAAAAGTAAAAATT-AAAAACAGAATTTG
1 GCTCAACTCACTTCTCGCAATATGAGTTGAGTTTTTGAAAAGCAAAAATTAAAAAACAGAAATTG
1949 AAAATACCTC-GACATGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTGAA
66 AAAATACCTCAG-CATGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAA
*
2012 AACATGAATT-AAAACAGAAATTGAAAATACCTCGGCATGCGAG-CC-AAG
130 AACATAAATTAAAAACAGAAATTGAAAATACCT---CA-GCGAGTCCTAAG
* *
2060 GCTCAACTCACTTCTCGCAAAATGAGTTGAGTTTTTGAAAAGTAAAAATTAAAAACAGAGTTTGA
1 GCTCAACTCACTTCTCGCAATATGAGTTGAGTTTTTGAAAAGCAAAAATT------A-A-----A
* *
2125 AAGACAGAATTTGAAAATACCTCGGCATGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGT
54 AA-ACAGAAATTGAAAATACCTCAGCATGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGT
* * * *
2190 TGATTTTTTTAAAATATAAATTGAAAAAACAGAAATTGAAAATACCTCAGCGTGTCCTGAG
118 TGATTTTTTGAAAACATAAATT--AAAAACAGAAATTGAAAATACCTCAGCGAGTCCTAAG
* * * * * * **
2251 GCTCAATTCACCTCTCGCGATATGAGTTGATTTTTTGAAAAGCAGAAATTGAAAAGTAGAAATTG
1 GCTCAACTCACTTCTCGCAATATGAGTTGAGTTTTTGAAAAGCAAAAATTAAAAAACAGAAATTG
* * **
2316 AAAATACCTCAGC--GTG-CCCTGAGGCTCAACTCACCTCTCGTAATATGAGTCGATTTTTTTTT
66 AAAATACCTCAGCATGTGACCC-GAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTTGA
* *
2378 AAACAGAAATTGAAAAACA-AATATTGAAAATACCTCAGCGTGTCCTAAG
129 AAACATAAATT-AAAAACAGAA-ATTGAAAATACCTCAGCGAGTCCTAAG
* *
2427 GCTCGACCCACTTCTCGCAATATGAGTTGA-TTTT
1 GCTCAACTCACTTCTCGCAATATGAGTTGAGTTTT
2461 GCATGTGACC
Statistics
Matches: 641, Mismatches: 68, Indels: 78
0.81 0.09 0.10
Matches are distributed among these distances:
166 6 0.01
167 15 0.02
168 10 0.02
169 59 0.09
170 8 0.01
171 29 0.05
174 34 0.05
175 105 0.16
176 110 0.17
177 84 0.13
178 19 0.03
179 3 0.00
183 1 0.00
184 1 0.00
188 3 0.00
189 67 0.10
190 20 0.03
191 45 0.07
193 22 0.03
ACGTcount: A:0.37, C:0.18, G:0.17, T:0.28
Consensus pattern (176 bp):
GCTCAACTCACTTCTCGCAATATGAGTTGAGTTTTTGAAAAGCAAAAATTAAAAAACAGAAATTG
AAAATACCTCAGCATGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAA
ACATAAATTAAAAACAGAAATTGAAAATACCTCAGCGAGTCCTAAG
Found at i:2217 original size:103 final size:104
Alignment explanation
Indices: 2025--2222 Score: 292
Period size: 103 Copynumber: 1.9 Consensus size: 104
2015 ATGAATTAAA
* *
2025 ACAGAAATTGAAAATACCTCGGCATGCGAGCCAAGGCTCAACTCACTTCTCGCAAAATGAGTTGA
1 ACAGAAATTGAAAATACCTCGGCATGCGACCCAAGGCTCAACTCACCTCTCGCAAAATGAGTTGA
2090 GTTTTTGAAAAGTAAAAATT-AAAAACAGAGTTTGAAAG
66 GTTTTTGAAAAGTAAAAATTAAAAAACAGAGTTTGAAAG
* * * *
2128 ACAGAATTTGAAAATACCTCGGCATGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGA
1 ACAGAAATTGAAAATACCTCGGCATGCGACCCAAGGCTCAACTCACCTCTCGCAAAATGAGTTGA
* * *
2193 TTTTTTTAAAA-TATAAATTGAAAAAACAGA
66 GTTTTTGAAAAGTAAAAATT-AAAAAACAGA
2223 AATTGAAAAT
Statistics
Matches: 84, Mismatches: 9, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
102 7 0.08
103 68 0.81
104 9 0.11
ACGTcount: A:0.39, C:0.18, G:0.18, T:0.25
Consensus pattern (104 bp):
ACAGAAATTGAAAATACCTCGGCATGCGACCCAAGGCTCAACTCACCTCTCGCAAAATGAGTTGA
GTTTTTGAAAAGTAAAAATTAAAAAACAGAGTTTGAAAG
Found at i:2304 original size:14 final size:14
Alignment explanation
Indices: 2285--2319 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
2275 AGTTGATTTT
2285 TTGAAAAGCAGAAA
1 TTGAAAAGCAGAAA
*
2299 TTGAAAAGTAGAAA
1 TTGAAAAGCAGAAA
2313 TTGAAAA
1 TTGAAAA
2320 TACCTCAGCG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.57, C:0.03, G:0.20, T:0.20
Consensus pattern (14 bp):
TTGAAAAGCAGAAA
Found at i:2529 original size:14 final size:14
Alignment explanation
Indices: 2510--2543 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
2500 GTTGATTTTT
2510 TTGAAAAGCAAAAA
1 TTGAAAAGCAAAAA
*
2524 TTGAAAAGCAGAAA
1 TTGAAAAGCAAAAA
2538 TTGAAA
1 TTGAAA
2544 TTACCTCAGC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.59, C:0.06, G:0.18, T:0.18
Consensus pattern (14 bp):
TTGAAAAGCAAAAA
Found at i:2586 original size:137 final size:137
Alignment explanation
Indices: 2336--2599 Score: 370
Period size: 137 Copynumber: 1.9 Consensus size: 137
2326 AGCGTGCCCT
* ** *
2336 GAGGCTCAACTCACCTCTCGTAATATGAGTCGATTTTTTTTTAAACAGAAATTGAAAAACAAATA
1 GAGGCTCAACTCACCTCTCGCAATATGAGTCGATTTTTTTGAAAACAAAAATTGAAAAACAAATA
* * * *
2401 TTGAAAATACCTCAGCGTGTCCTAAGGCTCGACCCACTTCTCGCAATATGAGTTGAT-TTTGCAT
66 TTGAAAATACCTCAGCGTGCCCCAAGGCTCAACCCACCTCTCGCAATATGAGTTGATATTTGCAT
2465 GTGACCC
131 GTGACCC
* *
2472 GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAAGCAAAAATTGAAAAGCAGAA
1 GAGGCTCAACTCACCTCTCGCAATATGAGTCGATTTTTTTGAAAA-CAAAAATTGAAAAACA-AA
* * * *
2537 -ATTGAAATTACCTCAGCGTGCCCCGAGGCTCAACTCACCTCTCGTAATATGAGTTGATATTTG
64 TATTGAAAATACCTCAGCGTGCCCCAAGGCTCAACCCACCTCTCGCAATATGAGTTGATATTTG
2600 AAAAATATAG
Statistics
Matches: 111, Mismatches: 14, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
136 41 0.37
137 64 0.58
138 6 0.05
ACGTcount: A:0.31, C:0.22, G:0.18, T:0.29
Consensus pattern (137 bp):
GAGGCTCAACTCACCTCTCGCAATATGAGTCGATTTTTTTGAAAACAAAAATTGAAAAACAAATA
TTGAAAATACCTCAGCGTGCCCCAAGGCTCAACCCACCTCTCGCAATATGAGTTGATATTTGCAT
GTGACCC
Found at i:2652 original size:87 final size:87
Alignment explanation
Indices: 2472--2860 Score: 435
Period size: 87 Copynumber: 4.5 Consensus size: 87
2462 CATGTGACCC
* * *
2472 GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAAGCAAAAATTGAAAAGCAGAA
1 GAGGCTCAACTCACCTCTCGCAATATGAGTTGA--TTTTTGAAAAACAAAAATTAAAAAACAGAA
* *
2537 ATTGAAATTACCTCAGCGTGCCCC
64 ATTGAAAATACCTCAGCGTGCCCT
* * * * *
2561 GAGGCTCAACTCACCTCTCGTAATATGAGTTGATATTTGAAAAATATAGATTAAAAAACAGAAAT
1 GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAAAAATTAAAAAACAGAAAT
2626 TGAAAATACCTCAGCGTGCCCT
66 TGAAAATACCTCAGCGTGCCCT
* * *** * *
2648 GAGGCTCAACTCACCTCTCGTAATATGAGTCGATTTTTTTTTAAACAGAAATTGAAAAACA-AAT
1 GAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTGAAAAACAAAAATTAAAAAACAGAA-
*
2712 ATTGAAAATACCTCAGCGTGTCCT
64 ATTGAAAATACCTCAGCGTGCCCT
* * * * ** * * *
2736 AAGGCTCGACCCACTTCTCGCAATATGAGTTGA-TTTTG--AAACATCAATTGAAAATATAGAAG
1 GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAAAAATT-AAAAAACAGAAA
*
2798 TTGAAAATACCTCAGCGTGTCCT
65 TTGAAAATACCTCAGCGTGCCCT
* *
2821 GAGGCTCAACTTACCTCTCGCGATATGAGTTGATTTTTGA
1 GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGA
2861 CAAGCAGAAA
Statistics
Matches: 255, Mismatches: 39, Indels: 14
0.83 0.13 0.05
Matches are distributed among these distances:
84 9 0.04
85 55 0.22
86 11 0.04
87 79 0.31
88 69 0.27
89 32 0.13
ACGTcount: A:0.34, C:0.20, G:0.17, T:0.29
Consensus pattern (87 bp):
GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAAAAATTAAAAAACAGAAAT
TGAAAATACCTCAGCGTGCCCT
Found at i:2675 original size:224 final size:224
Alignment explanation
Indices: 2248--2684 Score: 644
Period size: 224 Copynumber: 2.0 Consensus size: 224
2238 AGCGTGTCCT
* * * *
2248 GAGGCTCAATTCACCTCTCGCGATATGAGTTGATTTTTTGAAAAGCAGAAATTGAAAAGTAGAAA
1 GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAAGCAAAAATTGAAAAGCAGAAA
* * ***
2313 TTGAAAATACCTCAGCGTGCCCTGAGGCTCAACTCACCTCTCGTAATATGAGTCGATTTTTTTTT
66 TTGAAAATACCTCAGCGTGCCCCGAGGCTCAACTCACCTCTCGTAATATGAGTCGATTATTTGAA
* * * *
2378 AAACAGAAATTGAAAAACAAATATTGAAAATACCTCAGCGTGTCCTAAGGCTCGACCCACTTCTC
131 AAACAGAAATTAAAAAACAAATATTGAAAATACCTCAGCGTGCCCTAAGGCTCAACCCACCTCTC
*
2443 GCAATATGAGTTGATTTTGCATGTGACCC
196 GCAATATGAGTCGATTTTGCATGTGACCC
2472 GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAAGCAAAAATTGAAAAGCAGAA
1 GAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTTGAAAAGCAAAAATTGAAAAGCAGAA
* *
2537 ATTGAAATTACCTCAGCGTGCCCCGAGGCTCAACTCACCTCTCGTAATATGAGTTGA-TATTTGA
65 ATTGAAAATACCTCAGCGTGCCCCGAGGCTCAACTCACCTCTCGTAATATGAGTCGATTATTTGA
* * * * *
2601 AAAATATAGATTAAAAAACAGAA-ATTGAAAATACCTCAGCGTGCCCTGAGGCTCAACTCACCTC
130 AAAACAGAAATTAAAAAACA-AATATTGAAAATACCTCAGCGTGCCCTAAGGCTCAACCCACCTC
*
2665 TCGTAATATGAGTCGATTTT
194 TCGCAATATGAGTCGATTTT
2685 TTTTTAAACA
Statistics
Matches: 189, Mismatches: 22, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
224 104 0.55
225 85 0.45
ACGTcount: A:0.33, C:0.21, G:0.18, T:0.28
Consensus pattern (224 bp):
GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAAGCAAAAATTGAAAAGCAGAAA
TTGAAAATACCTCAGCGTGCCCCGAGGCTCAACTCACCTCTCGTAATATGAGTCGATTATTTGAA
AAACAGAAATTAAAAAACAAATATTGAAAATACCTCAGCGTGCCCTAAGGCTCAACCCACCTCTC
GCAATATGAGTCGATTTTGCATGTGACCC
Found at i:2714 original size:312 final size:312
Alignment explanation
Indices: 2149--2773 Score: 1065
Period size: 312 Copynumber: 2.0 Consensus size: 312
2139 AAATACCTCG
* *
2149 GCATGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTAAAATATAAATTGA
1 GCATGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTAAAACAAAAATTGA
* * * *
2214 AAAAACAGAAATTGAAAATACCTCAGCGTGTCCTGAGGCTCAATTCACCTCTCGCGATATGAGTT
66 AAAAACAGAAATTGAAAATACCTCAGCGTGCCCCGAGGCTCAACTCACCTCTCGCAATATGAGTT
* * * **
2279 GATTTTTTGAAAAGCAGAAATTGAAAAGTAGAAATTGAAAATACCTCAGCGTGCCCTGAGGCTCA
131 GATTATTTGAAAAACAGAAATTAAAAAACAGAAATTGAAAATACCTCAGCGTGCCCTGAGGCTCA
2344 ACTCACCTCTCGTAATATGAGTCGATTTTTTTTTAAACAGAAATTGAAAAACAAATATTGAAAAT
196 ACTCACCTCTCGTAATATGAGTCGATTTTTTTTTAAACAGAAATTGAAAAACAAATATTGAAAAT
2409 ACCTCAGCGTGTCCTAAGGCTCGACCCACTTCTCGCAATATGAGTTGATTTT
261 ACCTCAGCGTGTCCTAAGGCTCGACCCACTTCTCGCAATATGAGTTGATTTT
2461 GCATGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAAGCAAAAATT
1 GCATGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTT-AAAA-CAAAAATT
* * *
2526 G-AAAAGCAGAAATTGAAATTACCTCAGCGTGCCCCGAGGCTCAACTCACCTCTCGTAATATGAG
64 GAAAAAACAGAAATTGAAAATACCTCAGCGTGCCCCGAGGCTCAACTCACCTCTCGCAATATGAG
* * *
2590 TTGA-TATTTGAAAAATATAGATTAAAAAACAGAAATTGAAAATACCTCAGCGTGCCCTGAGGCT
129 TTGATTATTTGAAAAACAGAAATTAAAAAACAGAAATTGAAAATACCTCAGCGTGCCCTGAGGCT
2654 CAACTCACCTCTCGTAATATGAGTCGATTTTTTTTTAAACAGAAATTGAAAAACAAATATTGAAA
194 CAACTCACCTCTCGTAATATGAGTCGATTTTTTTTTAAACAGAAATTGAAAAACAAATATTGAAA
2719 ATACCTCAGCGTGTCCTAAGGCTCGACCCACTTCTCGCAATATGAGTTGATTTT
259 ATACCTCAGCGTGTCCTAAGGCTCGACCCACTTCTCGCAATATGAGTTGATTTT
2773 G
1 G
2774 AAACATCAAT
Statistics
Matches: 294, Mismatches: 17, Indels: 4
0.93 0.05 0.01
Matches are distributed among these distances:
312 223 0.76
313 64 0.22
314 7 0.02
ACGTcount: A:0.34, C:0.20, G:0.17, T:0.28
Consensus pattern (312 bp):
GCATGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTAAAACAAAAATTGA
AAAAACAGAAATTGAAAATACCTCAGCGTGCCCCGAGGCTCAACTCACCTCTCGCAATATGAGTT
GATTATTTGAAAAACAGAAATTAAAAAACAGAAATTGAAAATACCTCAGCGTGCCCTGAGGCTCA
ACTCACCTCTCGTAATATGAGTCGATTTTTTTTTAAACAGAAATTGAAAAACAAATATTGAAAAT
ACCTCAGCGTGTCCTAAGGCTCGACCCACTTCTCGCAATATGAGTTGATTTT
Found at i:2849 original size:173 final size:176
Alignment explanation
Indices: 2472--2858 Score: 523
Period size: 173 Copynumber: 2.2 Consensus size: 176
2462 CATGTGACCC
*
2472 GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAAGCAAAAATTGAAAAGCAGAA
1 GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAAGCAAAAATTGAAAAACAGAA
* * * *
2537 ATTGAAATTACCTCAGCGTGCCCCGAGGCTCAACTCACCTCTCGTAATATGAGTTGATATTTGAA
66 ATTGAAAATACCTCAGCGTGCCCCAAGGCTCAACCCACCTCTCGCAATATGAGTTGATATTTGAA
*
2602 AAATATAGATTAAAAAACAGAAATTGAAAATACCTCAGCGTGCCCT
131 AAATACAGATTAAAAAACAGAAATTGAAAATACCTCAGCGTGCCCT
* * ** *
2648 GAGGCTCAACTCACCTCTCGTAATATGAGTCGATTTTTTTTTAAA-CAGAAATTGAAAAACA-AA
1 GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAAGCAAAAATTGAAAAACAGAA
* * * *
2711 TATTGAAAATACCTCAGCGTGTCCTAAGGCTCGACCCACTTCTCGCAATATGAGTTGAT-TTTGA
66 -ATTGAAAATACCTCAGCGTGCCCCAAGGCTCAACCCACCTCTCGCAATATGAGTTGATATTTGA
* * * * *
2775 AACAT-CA-ATTGAAAATATAGAAGTTGAAAATACCTCAGCGTGTCCT
130 AAAATACAGATT-AAAAAACAGAAATTGAAAATACCTCAGCGTGCCCT
* *
2821 GAGGCTCAACTTACCTCTCGCGATATGAGTTGATTTTT
1 GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTT
2859 GACAAGCAGA
Statistics
Matches: 185, Mismatches: 24, Indels: 7
0.86 0.11 0.03
Matches are distributed among these distances:
172 3 0.02
173 66 0.36
174 11 0.06
175 64 0.35
176 41 0.22
ACGTcount: A:0.34, C:0.20, G:0.17, T:0.29
Consensus pattern (176 bp):
GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAAGCAAAAATTGAAAAACAGAA
ATTGAAAATACCTCAGCGTGCCCCAAGGCTCAACCCACCTCTCGCAATATGAGTTGATATTTGAA
AAATACAGATTAAAAAACAGAAATTGAAAATACCTCAGCGTGCCCT
Found at i:7820 original size:26 final size:26
Alignment explanation
Indices: 7791--7846 Score: 103
Period size: 26 Copynumber: 2.2 Consensus size: 26
7781 TGATACAAAT
*
7791 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTCCA
7817 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
7843 TGAT
1 TGAT
7847 GGGAATTTCA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.30, C:0.05, G:0.27, T:0.38
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:26753 original size:80 final size:76
Alignment explanation
Indices: 26643--26812 Score: 270
Period size: 80 Copynumber: 2.2 Consensus size: 76
26633 AATAATATAT
*
26643 ATAATTAAT-AAAAATAAAAATAAGGAAACATGTATGATATGTATATAAACCTATATGATATATA
1 ATAA-TAATAAAAAATAAAAATAAAGAAACATGTATGATATGTATATAAACCTATATG--ATATA
26707 TATTTATATTAGAAA
63 TATTTATATTAG-AA
26722 ATAACTAATAAAAAATAAAAATAAAGAAACATGTATGATATGTATATAAACCTATATGATATATA
1 ATAA-TAATAAAAAATAAAAATAAAGAAACATGTATGATATGTATATAAACCTATATGATATATA
26787 TTTATATTAGAA
65 TTTATATTAGAA
*
26799 ATGATAATAAAAAA
1 ATAATAATAAAAAA
26813 GGACTATTTG
Statistics
Matches: 87, Mismatches: 3, Indels: 5
0.92 0.03 0.05
Matches are distributed among these distances:
76 10 0.11
77 5 0.06
78 17 0.20
79 8 0.09
80 47 0.54
ACGTcount: A:0.55, C:0.04, G:0.08, T:0.32
Consensus pattern (76 bp):
ATAATAATAAAAAATAAAAATAAAGAAACATGTATGATATGTATATAAACCTATATGATATATAT
TTATATTAGAA
Found at i:29763 original size:37 final size:37
Alignment explanation
Indices: 29722--29798 Score: 145
Period size: 37 Copynumber: 2.1 Consensus size: 37
29712 AACTAAAAAA
29722 TTAAATAAGTTTGATGGTCAAGTACCATTGTCATATT
1 TTAAATAAGTTTGATGGTCAAGTACCATTGTCATATT
*
29759 TTAAATAAGTTTGATGGTTAAGTACCATTGTCATATT
1 TTAAATAAGTTTGATGGTCAAGTACCATTGTCATATT
29796 TTA
1 TTA
29799 GAGGTTTAGT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
37 39 1.00
ACGTcount: A:0.32, C:0.09, G:0.16, T:0.43
Consensus pattern (37 bp):
TTAAATAAGTTTGATGGTCAAGTACCATTGTCATATT
Found at i:31429 original size:41 final size:42
Alignment explanation
Indices: 31283--31428 Score: 118
Period size: 43 Copynumber: 3.4 Consensus size: 42
31273 TCTATGAATT
* * * *
31283 TACTAGCAGCTTTTATTTACAAATATGTTGTGCACTCACAACC
1 TACTAGCAGC-TTTATCTACAAATATGTTGTACATTCAAAACC
* * * * *
31326 TACTGGCAG-TTTATCTACAAACACTGGTGGTTCATATGC-AAACT
1 TACTAGCAGCTTTATCTACAAATA-T-GTTGTACAT-T-CAAAACC
* *
31370 TACTAACAGCTTTTATCTGCAAATATGTTGTACATTCAAAACC
1 TACTAGCAGC-TTTATCTACAAATATGTTGTACATTCAAAACC
31413 TACTAGCAG-TTTATCT
1 TACTAGCAGCTTTATCT
31429 GAATTTTCCC
Statistics
Matches: 80, Mismatches: 16, Indels: 16
0.71 0.14 0.14
Matches are distributed among these distances:
41 19 0.24
42 2 0.03
43 27 0.34
44 18 0.22
45 2 0.03
46 12 0.15
ACGTcount: A:0.31, C:0.21, G:0.13, T:0.35
Consensus pattern (42 bp):
TACTAGCAGCTTTATCTACAAATATGTTGTACATTCAAAACC
Found at i:36460 original size:26 final size:26
Alignment explanation
Indices: 36431--36512 Score: 146
Period size: 26 Copynumber: 3.2 Consensus size: 26
36421 TGATACAAAT
*
36431 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTCCA
36457 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
36483 TGATAATGTGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
36509 TGAT
1 TGAT
36513 GGGCATTTCA
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 54 1.00
ACGTcount: A:0.30, C:0.06, G:0.26, T:0.38
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:37075 original size:16 final size:15
Alignment explanation
Indices: 37037--37075 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
37027 AATGAAATAT
37037 ACAAATTGAAATAAA
1 ACAAATTGAAATAAA
*
37052 ACTTAATTGAAATAAA
1 AC-AAATTGAAATAAA
37068 ATCAAATT
1 A-CAAATT
37076 AGAAGGGATA
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
15 2 0.10
16 17 0.85
17 1 0.05
ACGTcount: A:0.59, C:0.08, G:0.05, T:0.28
Consensus pattern (15 bp):
ACAAATTGAAATAAA
Found at i:41908 original size:112 final size:112
Alignment explanation
Indices: 41677--41910 Score: 431
Period size: 112 Copynumber: 2.1 Consensus size: 112
41667 GGCCTATTAC
41677 ACACA-AATAATAATAAATGAAGTGACGTAAACCTGATGTTAAAAATACTAATAGTGCTATATAC
1 ACACATAATAATAATAAATGAAGTGACGTAAACCTGATGTTAAAAATACTAATAGTGCTATATAC
41741 AAATATATATATATTTAAAATATGTACGTAATAGGAATGAAAAATGT
66 AAATATATATATATTTAAAATATGTACGTAATAGGAATGAAAAATGT
41788 ACACATAATAATAATAAATGAAGTGACGTAAACCTGATGTTAAAAATACTAATAGTGCTATATAC
1 ACACATAATAATAATAAATGAAGTGACGTAAACCTGATGTTAAAAATACTAATAGTGCTATATAC
*
41853 -AA-ATATATATA-TTAAAATATGTACGTAATAGGATTGAAAAATGT
66 AAATATATATATATTTAAAATATGTACGTAATAGGAATGAAAAATGT
41897 ACACATAATAATAA
1 ACACATAATAATAA
41911 ATATATACAT
Statistics
Matches: 121, Mismatches: 1, Indels: 4
0.96 0.01 0.03
Matches are distributed among these distances:
109 46 0.38
110 9 0.07
111 7 0.06
112 59 0.49
ACGTcount: A:0.50, C:0.09, G:0.12, T:0.29
Consensus pattern (112 bp):
ACACATAATAATAATAAATGAAGTGACGTAAACCTGATGTTAAAAATACTAATAGTGCTATATAC
AAATATATATATATTTAAAATATGTACGTAATAGGAATGAAAAATGT
Found at i:41998 original size:3 final size:3
Alignment explanation
Indices: 41985--42020 Score: 54
Period size: 3 Copynumber: 12.0 Consensus size: 3
41975 AATATATCTC
* *
41985 TAA TGA TAA TAA TAA TAA TAA TAA TAG TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
42021 AAAGATGTAT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.61, C:0.00, G:0.06, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:42431 original size:79 final size:79
Alignment explanation
Indices: 42337--42488 Score: 295
Period size: 79 Copynumber: 1.9 Consensus size: 79
42327 AAAATAATAC
42337 TATATATATGCATACATATATAATAAAACATACACTAATATTATATATGTGATAATACTAGAAAT
1 TATATATATGCATACATATATAATAAAACATACACTAATATTATATATGTGATAATACTAGAAAT
42402 AATAATAACCTATA
66 AATAATAACCTATA
*
42416 TATATATATGCATACATGTATAATAAAACATACACTAATATTATATATGTGATAATACTAGAAAT
1 TATATATATGCATACATATATAATAAAACATACACTAATATTATATATGTGATAATACTAGAAAT
42481 AATAATAA
66 AATAATAA
42489 TTAGTAATAA
Statistics
Matches: 72, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
79 72 1.00
ACGTcount: A:0.51, C:0.09, G:0.06, T:0.34
Consensus pattern (79 bp):
TATATATATGCATACATATATAATAAAACATACACTAATATTATATATGTGATAATACTAGAAAT
AATAATAACCTATA
Found at i:42464 original size:39 final size:39
Alignment explanation
Indices: 42339--42464 Score: 143
Period size: 39 Copynumber: 3.2 Consensus size: 39
42329 AATAATACTA
42339 TATATATGCATACATATATAATAAAACATACACTAATAT
1 TATATATGCATACATATATAATAAAACATACACTAATAT
* * *
42378 TATATATGTGATA-ATACTAGAAATAATA-ATA-ACCT-ATAT
1 TATATATG-CATACATA-TA-TAATAAAACATACA-CTAATAT
*
42417 ATATATATGCATACATGTATAATAAAACATACACTAATAT
1 -TATATATGCATACATATATAATAAAACATACACTAATAT
42457 TATATATG
1 TATATATG
42465 TGATAATACT
Statistics
Matches: 71, Mismatches: 7, Indels: 18
0.74 0.07 0.19
Matches are distributed among these distances:
38 6 0.08
39 34 0.48
40 25 0.35
41 6 0.08
ACGTcount: A:0.49, C:0.10, G:0.06, T:0.35
Consensus pattern (39 bp):
TATATATGCATACATATATAATAAAACATACACTAATAT
Found at i:42499 original size:16 final size:17
Alignment explanation
Indices: 42474--42521 Score: 71
Period size: 16 Copynumber: 2.8 Consensus size: 17
42464 GTGATAATAC
42474 TAGAAATAATAATA-AT
1 TAGAAATAATAATACAT
*
42490 TAGTAATAATAATACAT
1 TAGAAATAATAATACAT
42507 TAGAAATACATAATA
1 TAGAAATA-ATAATA
42522 GAGGAAATAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
16 13 0.46
17 9 0.32
18 6 0.21
ACGTcount: A:0.58, C:0.04, G:0.06, T:0.31
Consensus pattern (17 bp):
TAGAAATAATAATACAT
Done.