Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold6442.1
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: 11717
ACGTcount: A:0.27, C:0.22, G:0.19, T:0.32
Found at i:761 original size:76 final size:77
Alignment explanation
Indices: 603--794 Score: 293
Period size: 76 Copynumber: 2.5 Consensus size: 77
593 TGTGAACCCA
* *
603 AGGCTCAACTCACATCTCGCAATATGAGTTGA---TTTTTGAAAAACAGAAATTTAAAAATACCT
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTTAAAAACAGAAATTTAAAAATACCT
665 CAGCGTGTCCTG
66 CAGCGTGTCCTG
* * * *
677 AGGCTCAACTCACCTCTCGCAATTTGAGTTGATTTTTTTTTAACAACAGAAA-TTGAAATTACCT
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTTAAAAACAGAAATTTAAAAATACCT
741 CAGCGTGTCCTG
66 CAGCGTGTCCTG
*
753 AGGCTCAACTCACCTCTAGCAATATGAGTTGATTTTTTTTTA
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTTA
795 CACTCACCTC
Statistics
Matches: 107, Mismatches: 8, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
74 30 0.28
76 62 0.58
77 15 0.14
ACGTcount: A:0.30, C:0.21, G:0.16, T:0.33
Consensus pattern (77 bp):
AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTTAAAAACAGAAATTTAAAAATACCT
CAGCGTGTCCTG
Found at i:975 original size:89 final size:92
Alignment explanation
Indices: 855--1090 Score: 297
Period size: 89 Copynumber: 2.6 Consensus size: 92
845 TCGGCGTGCC
* * * *
855 CCAAGGCACAACTCACTTCTCGCAATATGAGTTGATTTTTTTTGAAACATAAATTAAAAAAACGA
1 CCAAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTATGAAACATAAATTAAAAAAACCA
920 -AAATTGAAAATACCTCAGCGTGT-A-
66 GAAATTGAAAATACCTCAGCGTGTGAG
** * * * * *
944 CTGAGGCTCAACTCACCTCTCGCAATATGAGTCGATTTTTGA-AAAACAGAAATT--GAAAACCA
1 CCAAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTATGAAACATAAATTAAAAAAACCA
1006 GAAATTGAAAATACCTCAGCGTGTGAG
66 GAAATTGAAAATACCTCAGCGTGTGAG
* * *
1033 CCAAGGCTCAACTCACCTCTTGCAATATGAGCTAATTTTTTATG-AACATAAATTAAAA
1 CCAAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTATGAAACATAAATTAAAA
1091 CCACCTCAGC
Statistics
Matches: 120, Mismatches: 21, Indels: 10
0.79 0.14 0.07
Matches are distributed among these distances:
86 6 0.05
87 23 0.19
88 11 0.09
89 79 0.66
91 1 0.01
ACGTcount: A:0.39, C:0.19, G:0.15, T:0.27
Consensus pattern (92 bp):
CCAAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTATGAAACATAAATTAAAAAAACCA
GAAATTGAAAATACCTCAGCGTGTGAG
Found at i:1001 original size:14 final size:14
Alignment explanation
Indices: 982--1016 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
972 GAGTCGATTT
982 TTGAAAAACAGAAA
1 TTGAAAAACAGAAA
*
996 TTGAAAACCAGAAA
1 TTGAAAAACAGAAA
1010 TTGAAAA
1 TTGAAAA
1017 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:0.60, C:0.09, G:0.14, T:0.17
Consensus pattern (14 bp):
TTGAAAAACAGAAA
Found at i:1128 original size:73 final size:73
Alignment explanation
Indices: 1036--1658 Score: 828
Period size: 73 Copynumber: 8.5 Consensus size: 73
1026 GTGTGAGCCA
1036 AGGCTCAACTCACCTCTTGCAATATGAGCTAATTTTTTATGAACATAAATTAAAACCACCTCAGC
1 AGGCTCAACTCACCTCTTGCAATATGAGCTAATTTTTTATGAACATAAATTAAAACCACCTCAGC
1101 GTGTCCTG
66 GTGTCCTG
1109 AGGCTCAACTCACCTCTTGCAATATGAGCTAATTTTTTATGAACATAAATTAAAACCACCTCAGC
1 AGGCTCAACTCACCTCTTGCAATATGAGCTAATTTTTTATGAACATAAATTAAAACCACCTCAGC
1174 GTGTCCTG
66 GTGTCCTG
1182 AGGCTCAACTCACCTCTTGCAATATGAGCTAATTTTTTATGAACATAAATTAAAACCACCTCAGC
1 AGGCTCAACTCACCTCTTGCAATATGAGCTAATTTTTTATGAACATAAATTAAAACCACCTCAGC
1247 GTGTCCTG
66 GTGTCCTG
1255 AGGCTCAACTCACCTCTTGCAATATGAGCTAATTTTTTATGAACATAAATTAAAACCACCTCAGC
1 AGGCTCAACTCACCTCTTGCAATATGAGCTAATTTTTTATGAACATAAATTAAAACCACCTCAGC
1320 GTGTCCTG
66 GTGTCCTG
1328 AGGCTCAACTCACCTCTTGCAATATGAGCTAATTTTTTATGAACATAAATTAAAACCACCTCAGC
1 AGGCTCAACTCACCTCTTGCAATATGAGCTAATTTTTTATGAACATAAATTAAAACCACCTCAGC
1393 GTGTCCTG
66 GTGTCCTG
* * * * ** * * **
1401 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGACAAACAAAAATTGAAATTACCTCAGC
1 AGGCTCAACTCACCTCTTGCAATATGAGCTAATTTTTTATGAACATAAATTAAAACCACCTCAGC
*
1466 --GTCTTG
66 GTGTCCTG
* * * * ** * *
1472 AGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTTTTAAAAAAACAGAAATTGAAAA-TACC
1 AGGCTCAACTCACCTCTTGCAATATGAGCT-A-ATTTTTT--ATGAACATAAATT-AAAACCACC
**
1536 TCAGCATGTGAACTG
61 TCAGC--GTGTCCTG
* * * ** * *
1551 AGGCTCAACTCACCTCTCGCAATATGAGTTGAA---ATTAAAACACAAAAATTGAAAA-TACCTC
1 AGGCTCAACTCACCTCTTGCAATATGAGCT-AATTTTTTATGA-ACATAAATT-AAAACCACCTC
* *
1612 AGCGTGCCCCG
63 AGCGTGTCCTG
*
1623 AGGCTCAACTCACCTCTTGCAATATGAGCTGATTTT
1 AGGCTCAACTCACCTCTTGCAATATGAGCTAATTTT
1659 GAAAAAGTAG
Statistics
Matches: 505, Mismatches: 32, Indels: 25
0.90 0.06 0.04
Matches are distributed among these distances:
71 35 0.07
72 33 0.07
73 356 0.70
74 22 0.04
75 22 0.04
76 3 0.01
79 34 0.07
ACGTcount: A:0.33, C:0.24, G:0.14, T:0.29
Consensus pattern (73 bp):
AGGCTCAACTCACCTCTTGCAATATGAGCTAATTTTTTATGAACATAAATTAAAACCACCTCAGC
GTGTCCTG
Found at i:1415 original size:219 final size:217
Alignment explanation
Indices: 1036--2864 Score: 1264
Period size: 219 Copynumber: 8.5 Consensus size: 217
1026 GTGTGAGCCA
1036 AGGCTCAACTCACCTCTTGCAATATGAGCTAATTTTTTATGAACATAAATTAAAACCACCTCAGC
1 AGGCTCAACTCACCTCTTGCAATATGAGCTAATTTTTTATGAACATAAATTAAAACCACCTCAGC
1101 GTGTCCTGAGGCTCAACTCACCTCTTGCAATATGAGCTAATTTTTTATGAACATAAATTAAAACC
66 GTGTCCTGAGGCTCAACTCACCTCTTGCAATATGAGCTAATTTTTTATGAACATAAATTAAAACC
* * ** *
1166 ACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTTGCAATATGAGCTAATTTTTTATGAACATAAA
131 ACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTTGCAATATGAGCTGATTTTTGACAAACAAAAA
1231 TTAAAACCACCTCAGCGTGTCCTG
196 TTAAAACCACCTCAGC--GTCCTG
1255 AGGCTCAACTCACCTCTTGCAATATGAGCTAATTTTTTATGAACATAAATTAAAACCACCTCAGC
1 AGGCTCAACTCACCTCTTGCAATATGAGCTAATTTTTTATGAACATAAATTAAAACCACCTCAGC
1320 GTGTCCTGAGGCTCAACTCACCTCTTGCAATATGAGCTAATTTTTTATGAACATAAATTAAAACC
66 GTGTCCTGAGGCTCAACTCACCTCTTGCAATATGAGCTAATTTTTTATGAACATAAATTAAAACC
* *
1385 ACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGACAAACAAAAA
131 ACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTTGCAATATGAGCTGATTTTTGACAAACAAAAA
* ** *
1450 TTGAAATTACCTCAGCGTCTTG
196 TTAAAACCACCTCAGCGTCCTG
* * * * ** * *
1472 AGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTTTTAAAAAAACAGAAATTGAAAA-TACC
1 AGGCTCAACTCACCTCTTGCAATATGAGCT-A-ATTTTTT--ATGAACATAAATT-AAAACCACC
** * * * ** *
1536 TCAGCATGTGAACTGAGGCTCAACTCACCTCTCGCAATATGAGTTGAA---ATTAAAACACAAAA
61 TCAGC--GTGTCCTGAGGCTCAACTCACCTCTTGCAATATGAGCT-AATTTTTTATGA-ACATAA
* * *
1598 ATTGAAAA-TACCTCAGCGTGCCCCGAGGCTCAACTCACCTCTTGCAATATGAGCTGA-TTTTGA
122 ATT-AAAACCACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTTGCAATATGAGCTGATTTTTGA
* * *
1661 AAAAGTAGAAATT--AA--A----AG-G---T-
186 CAAA-CAAAAATTAAAACCACCTCAGCGTCCTG
* * * * * * * ** * * ** *
1681 ----TCAACCCAGCTCTCGCAATATGAGTTGATTCTTGACAAACAGAAATTGAAATTACCTCATC
1 AGGCTCAACTCACCTCTTGCAATATGAGCTAATTTTTTATGAACATAAATTAAAACCACCTCAGC
* *
1742 GTGTCCTGAGGCTCAACTCACCTCTCGCAATAT--G--AA-----T-TG-A-A-AAA--AATACC
66 GTGTCCTGAGGCTCAACTCACCTCTTGCAATATGAGCTAATTTTTTATGAACATAAATTAAAACC
* * * * * * *
1792 A---CAGTGTGTAATCTGAAGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTAAAAAAA
131 ACCTCAGCGTGT--CCTGAGGCTCAACTCACCTCTTGCAATATGAGCTGA---TTTTT-GACAAA
* *
1854 CAGAAATTGAAAA-TACCTCAGCATGTGAACC-G
190 CAAAAATT-AAAACCACCTCAGC--GT---CCTG
* * * * * * *
1886 AGGCTCAACTCACCTCTCGCAATATAAGTTGATTTTTTTTTTGAAAACAGAAATTGAAAA-TACC
1 AGGCTCAACTCACCTCTTGCAATATGAGCT-A-ATTTTTTATG--AACATAAATT-AAAACCACC
* * ** * * * * * *
1950 TCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATAAGTTGAA-TTTTGA-AAACAGAAATT
61 TCAGCGTGTCCTGAGGCTCAACTCACCTCTTGCAATATGAGCT-AATTTTTTATGAACATAAATT
* ** * * * *
2013 GAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTACG
125 AAAACCACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTTGCAATATGAGCTGA--TTTTTGACA
* * *
2078 AACAGAAATT-GAA--ACCTCAGCGTGCCCCG
188 AACAAAAATTAAAACCACCTCAGCGT--CCTG
*
2107 AGGCTCAACTCACCTCTTGCAATATGAGCTAATTTTTGATGAACATAAATTAAAACCACCTCA--
1 AGGCTCAACTCACCTCTTGCAATATGAGCTAATTTTTTATGAACATAAATTAAAACCACCTCAGC
* * * * ** *
2170 GTATCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGAA---ATTAAAACACAAAAATTGAAA
66 GTGTCCTGAGGCTCAACTCACCTCTTGCAATATGAGCT-AATTTTTTATGA-ACATAAATT-AAA
* * * * ** *
2232 A-TACCTCAGCGTGCCCCGAGGCTCAACTCACCTCTTGCAATATGAGCTAATTTTTGATGAACAT
128 ACCACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTTGCAATATGAGCTGATTTTTGACAAACAA
**
2296 AAATTAAAACCACCTCAGTATCCTG
193 AAATTAAAACCACCTCAGCGTCCTG
* * * ** * *
2321 AGGCTCAACTCACCTCTCGCAATATGAGTTGAA---ATTAAAACACAAAAATTGAAAA-TACCTC
1 AGGCTCAACTCACCTCTTGCAATATGAGCT-AATTTTTTATGA-ACATAAATT-AAAACCACCTC
* * *
2382 AGCGTGAGCC-AAGGCTCAACTCACCTCTTGCAATATGAGCTAATTTTTGATGAACATAAATTAA
63 AGCGTG-TCCTGAGGCTCAACTCACCTCTTGCAATATGAGCTAATTTTTTATGAACATAAATTAA
* * *
2446 AACCACCTCA--GTATCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGACAAACA
127 AACCACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTTGCAATATGAGCTGATTTTTGACAAACA
* ** * *
2509 AAAATTGAAATTACCTCATCGTCTTG
192 AAAATTAAAACCACCTCAGCGTCCTG
* * * * ** * *
2535 AGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTTTTAAAAAAACAGAAATTGAAAA-TACC
1 AGGCTCAACTCACCTCTTGCAATATGAGCT-A-ATTTTTT--ATGAACATAAATT-AAAACCACC
* * * * ** *
2599 TCAGCATGTGAACC-GAGGCTCAACTCACCTCTCGCAATATGAGTTGAA---ATTAAAACACAAA
61 TCAGC--GTG-TCCTGAGGCTCAACTCACCTCTTGCAATATGAGCT-AATTTTTTATGA-ACATA
* * * *
2660 AATTGAAAA-TACCTCAGCGTGCCCCGAGGCTCAACTCACCTCTTGCAATATGAGCTAATTTTTG
121 AATT-AAAACCACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTTGCAATATGAGCTGATTTTTG
** * **
2724 ATGAACATAAATTAAAACCACCTCAGTATCCTG
185 ACAAACAAAAATTAAAACCACCTCAGCGTCCTG
* * * ** * *
2757 AGGCTCAACTCACCTCTCGCAATATGAGTTGAA---ATTAAAACACAAAAATTGAAAA-TACCTC
1 AGGCTCAACTCACCTCTTGCAATATGAGCT-AATTTTTTATGA-ACATAAATT-AAAACCACCTC
* * *
2818 AGCGTGCCCCGAGGCTCAACTCACCTCTTGCAATATGAGCTGATTTT
63 AGCGTGTCCTGAGGCTCAACTCACCTCTTGCAATATGAGCTAATTTT
2865 GAAAAACAAA
Statistics
Matches: 1316, Mismatches: 193, Indels: 204
0.77 0.11 0.12
Matches are distributed among these distances:
182 6 0.00
184 34 0.03
185 1 0.00
187 3 0.00
188 12 0.01
189 6 0.00
191 2 0.00
192 2 0.00
194 2 0.00
196 2 0.00
197 1 0.00
199 32 0.02
200 3 0.00
201 20 0.02
203 4 0.00
205 23 0.02
209 23 0.02
210 1 0.00
211 4 0.00
212 3 0.00
213 81 0.06
214 143 0.11
215 157 0.12
216 35 0.03
217 72 0.05
218 8 0.01
219 239 0.18
220 23 0.02
221 99 0.08
222 158 0.12
223 47 0.04
224 5 0.00
225 3 0.00
226 11 0.01
227 10 0.01
228 34 0.03
230 7 0.01
ACGTcount: A:0.34, C:0.23, G:0.15, T:0.28
Consensus pattern (217 bp):
AGGCTCAACTCACCTCTTGCAATATGAGCTAATTTTTTATGAACATAAATTAAAACCACCTCAGC
GTGTCCTGAGGCTCAACTCACCTCTTGCAATATGAGCTAATTTTTTATGAACATAAATTAAAACC
ACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTTGCAATATGAGCTGATTTTTGACAAACAAAAA
TTAAAACCACCTCAGCGTCCTG
Found at i:2030 original size:72 final size:72
Alignment explanation
Indices: 1809--2882 Score: 906
Period size: 72 Copynumber: 14.7 Consensus size: 72
1799 GTAATCTGAA
* * *
1809 GCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTAAAAAAACAGAAATTGAAAATACCTCA
1 GCTCAACTCACCTCTCGCAATATGAGTTGA---ATTTT--GAAAACAAAAATTGAAAATACCTCA
**
1874 GCATGTGAACCGAG
61 GC--GTGTCCCGAG
* * *
1888 GCTCAACTCACCTCTCGCAATATAAGTTGATTTTTTTTTTGAAAACAGAAATTGAAAATACCTCA
1 GCTCAACTCACCTCTCGCAATATGAGTTGA-----ATTTTGAAAACAAAAATTGAAAATACCTCA
* **
1953 ACGTGTCTTGAG
61 GCGTGTCCCGAG
** * * *
1965 GCTCAACTCATTTCTCGCAATATAAGTTGAATTTTGAAAACAGAAATTGAAATTACCTCAGCGTG
1 GCTCAACTCACCTCTCGCAATATGAGTTGAATTTTGAAAACAAAAATTGAAAATACCTCAGCGTG
*
2030 TCCTGAG
66 TCCCGAG
* * * *
2037 GCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTACGAACAGAAATTG--AA-ACCTCAGC
1 GCTCAACTCACCTCTCGCAATATGAGTTGA--ATTTTGA-AAACAAAAATTGAAAATACCTCAGC
*
2099 GTGCCCCGAG
63 GTGTCCCGAG
* * * * *
2109 GCTCAACTCACCTCTTGCAATATGAGCT-AATTTTTGATGAACATAAATT-AAAACCACCTCA--
1 GCTCAACTCACCTCTCGCAATATGAGTTGAA-TTTTGA-AAACAAAAATTGAAAA-TACCTCAGC
* *
2170 GTATCCTGAG
63 GTGTCCCGAG
* *
2180 GCTCAACTCACCTCTCGCAATATGAGTTGAA-ATTAAAACACAAAAATTGAAAATACCTCAGCGT
1 GCTCAACTCACCTCTCGCAATATGAGTTGAATTTTGAAA-ACAAAAATTGAAAATACCTCAGCGT
*
2244 GCCCCGAG
65 GTCCCGAG
* * * * *
2252 GCTCAACTCACCTCTTGCAATATGAGCT-AATTTTTGATGAACATAAATT-AAAACCACCTCA--
1 GCTCAACTCACCTCTCGCAATATGAGTTGAA-TTTTGA-AAACAAAAATTGAAAA-TACCTCAGC
* *
2313 GTATCCTGAG
63 GTGTCCCGAG
* *
2323 GCTCAACTCACCTCTCGCAATATGAGTTGAA-ATTAAAACACAAAAATTGAAAATACCTCAGCGT
1 GCTCAACTCACCTCTCGCAATATGAGTTGAATTTTGAAA-ACAAAAATTGAAAATACCTCAGCGT
** *
2387 GAGCCAAG
65 GTCCCGAG
* * * * *
2395 GCTCAACTCACCTCTTGCAATATGAGCT-AATTTTTGATGAACATAAATT-AAAACCACCTCA--
1 GCTCAACTCACCTCTCGCAATATGAGTTGAA-TTTTGA-AAACAAAAATTGAAAA-TACCTCAGC
* *
2456 GTATCCTGAG
63 GTGTCCCGAG
* * *
2466 GCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGACAAACAAAAATTGAAATTACCTCATC--
1 GCTCAACTCACCTCTCGCAATATGAGTTGAATTTTGA-AAACAAAAATTGAAAATACCTCAGCGT
**
2529 GTCTTGAG
65 GTCCCGAG
* * * *
2537 GCTCAACTCACTTCTCGCAATATGAGTTGATTTTTTTTAAAAAAACAGAAATTGAAAATACCTCA
1 GCTCAACTCACCTCTCGCAATATGAGTTGA---ATTTT--GAAAACAAAAATTGAAAATACCTCA
**
2602 GCATGTGAACCGAG
61 GC--GTGTCCCGAG
* *
2616 GCTCAACTCACCTCTCGCAATATGAGTTGAA-ATTAAAACACAAAAATTGAAAATACCTCAGCGT
1 GCTCAACTCACCTCTCGCAATATGAGTTGAATTTTGAAA-ACAAAAATTGAAAATACCTCAGCGT
*
2680 GCCCCGAG
65 GTCCCGAG
* * * * *
2688 GCTCAACTCACCTCTTGCAATATGAGCT-AATTTTTGATGAACATAAATT-AAAACCACCTCA--
1 GCTCAACTCACCTCTCGCAATATGAGTTGAA-TTTTGA-AAACAAAAATTGAAAA-TACCTCAGC
* *
2749 GTATCCTGAG
63 GTGTCCCGAG
* *
2759 GCTCAACTCACCTCTCGCAATATGAGTTGAA-ATTAAAACACAAAAATTGAAAATACCTCAGCGT
1 GCTCAACTCACCTCTCGCAATATGAGTTGAATTTTGAAA-ACAAAAATTGAAAATACCTCAGCGT
*
2823 GCCCCGAG
65 GTCCCGAG
* *
2831 GCTCAACTCACCTCTTGCAATATGAGCTG-ATTTTGAAAAACAAAAATT-AAAA
1 GCTCAACTCACCTCTCGCAATATGAGTTGAATTTTG-AAAACAAAAATTGAAAA
2883 GGCTTAACTC
Statistics
Matches: 818, Mismatches: 124, Indels: 114
0.77 0.12 0.11
Matches are distributed among these distances:
69 3 0.00
70 66 0.08
71 212 0.26
72 272 0.33
73 65 0.08
74 35 0.04
75 35 0.04
76 1 0.00
77 34 0.04
79 87 0.11
81 8 0.01
ACGTcount: A:0.35, C:0.23, G:0.15, T:0.27
Consensus pattern (72 bp):
GCTCAACTCACCTCTCGCAATATGAGTTGAATTTTGAAAACAAAAATTGAAAATACCTCAGCGTG
TCCCGAG
Found at i:2206 original size:143 final size:142
Alignment explanation
Indices: 1936--2882 Score: 1212
Period size: 143 Copynumber: 6.6 Consensus size: 142
1926 TTGAAAACAG
* * ** ** * * *
1936 AAATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATAAGTTGAA-TTTT
1 AAATTG-AAATACCTCAGCGTGCCCCGAGGCTCAACTCACCTCTTGCAATATGAGCT-AATTTTT
* * * ** *
2000 GA-AAACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGT
64 GATGAACATAAATTAAAACCACCTCA--GTATCCTGAGGCTCAACTCACCTCTCGCAATATGAGT
** *** *
2064 TGATTTTTTTTACGAACAG
127 TGA-AATTAAAAC--ACAA
2083 AAATTG-AA-ACCTCAGCGTGCCCCGAGGCTCAACTCACCTCTTGCAATATGAGCTAATTTTTGA
1 AAATTGAAATACCTCAGCGTGCCCCGAGGCTCAACTCACCTCTTGCAATATGAGCTAATTTTTGA
2146 TGAACATAAATTAAAACCACCTCAGTATCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGAA
66 TGAACATAAATTAAAACCACCTCAGTATCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGAA
2211 ATTAAAACACAA
131 ATTAAAACACAA
2223 AAATTGAAAATACCTCAGCGTGCCCCGAGGCTCAACTCACCTCTTGCAATATGAGCTAATTTTTG
1 AAATTG-AAATACCTCAGCGTGCCCCGAGGCTCAACTCACCTCTTGCAATATGAGCTAATTTTTG
2288 ATGAACATAAATTAAAACCACCTCAGTATCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA
65 ATGAACATAAATTAAAACCACCTCAGTATCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA
2353 AATTAAAACACAA
130 AATTAAAACACAA
** *
2366 AAATTGAAAATACCTCAGCGTGAGCCAAGGCTCAACTCACCTCTTGCAATATGAGCTAATTTTTG
1 AAATTG-AAATACCTCAGCGTGCCCCGAGGCTCAACTCACCTCTTGCAATATGAGCTAATTTTTG
2431 ATGAACATAAATTAAAACCACCTCAGTATCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA
65 ATGAACATAAATTAAAACCACCTCAGTATCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA
** *
2496 TTTTTGACAA-ACAA
130 -AATT-AAAACACAA
* ** * * * *
2510 AAATTGAAATTACCTCATCGT--CTTGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTT
1 AAATTGAAA-TACCTCAGCGTGCCCCGAGGCTCAACTCACCTCTTGCAATATGAGCT-A--ATTT
* ** * * *
2573 TTAAAAAAACAGAAATTGAAAA-TACCTCAGCATGTGAACC-GAGGCTCAACTCACCTCTCGCAA
62 TT-GATGAACATAAATT-AAAACCACCT---CA-GT-ATCCTGAGGCTCAACTCACCTCTCGCAA
2636 TATGAGTTGAAATTAAAACACAA
120 TATGAGTTGAAATTAAAACACAA
2659 AAATTGAAAATACCTCAGCGTGCCCCGAGGCTCAACTCACCTCTTGCAATATGAGCTAATTTTTG
1 AAATTG-AAATACCTCAGCGTGCCCCGAGGCTCAACTCACCTCTTGCAATATGAGCTAATTTTTG
2724 ATGAACATAAATTAAAACCACCTCAGTATCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA
65 ATGAACATAAATTAAAACCACCTCAGTATCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA
2789 AATTAAAACACAA
130 AATTAAAACACAA
*
2802 AAATTGAAAATACCTCAGCGTGCCCCGAGGCTCAACTCACCTCTTGCAATATGAGCTGA-TTTTG
1 AAATTG-AAATACCTCAGCGTGCCCCGAGGCTCAACTCACCTCTTGCAATATGAGCTAATTTTTG
** *
2866 AAAAACAAAAATTAAAA
65 ATGAACATAAATTAAAA
2883 GGCTTAACTC
Statistics
Matches: 714, Mismatches: 62, Indels: 53
0.86 0.07 0.06
Matches are distributed among these distances:
140 9 0.01
142 55 0.08
143 410 0.57
144 67 0.09
145 28 0.04
146 18 0.03
147 24 0.03
148 8 0.01
149 24 0.03
150 39 0.05
151 32 0.04
ACGTcount: A:0.35, C:0.23, G:0.15, T:0.27
Consensus pattern (142 bp):
AAATTGAAATACCTCAGCGTGCCCCGAGGCTCAACTCACCTCTTGCAATATGAGCTAATTTTTGA
TGAACATAAATTAAAACCACCTCAGTATCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGAA
ATTAAAACACAA
Found at i:2654 original size:436 final size:426
Alignment explanation
Indices: 1936--2882 Score: 1346
Period size: 436 Copynumber: 2.2 Consensus size: 426
1926 TTGAAAACAG
* * *** ** * * *
1936 AAATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATAAGTTGAATTTTG
1 AAATTGAAAATACCTCAGCGTGACCCAAGGCTCAACTCACCTCTTGCAATATGAGCT-AATTTTG
* * ** *
2001 -AAAACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTT
65 AAAAACAAAAATTAAAACCACCTCA--GTATCCTGAGGCTCAACTCACCTCTCGCAATATGAGTT
* * * *
2065 GATTTTTTTTACGAACAGAAATTGAAACCTCAGCGTGCCCCGAGGCTCAACTCACCTCTTGCAAT
128 GA-TTTTTTGACAAACAAAAATTGAAACCTCAGCGT-CCCCGAGGCTCAACTCACCTCTCGCAAT
* ** * *
2130 ATGAGCTAATTTTTGATGAACATAAATTAAAACCACCTCAGTATCCTGAGGCTCAACTCACCTCT
191 ATGAGCTAATTTTTAAAAAACAGAAATTAAAACCACCTCAGTAACCTGAGGCTCAACTCACCTCT
2195 CGCAATATGAGTTGAAATTAAAACACAAAAATTGAAAATACCTCAGCGTGCCCCGAGGCTCAACT
256 CGCAATATGAGTTGAAATTAAAACACAAAAATTGAAAATACCTCAGCGTGCCCCGAGGCTCAACT
2260 CACCTCTTGCAATATGAGCTAATTTTTGATGAACATAAATTAAAACCACCTCAGTATCCTGAGGC
321 CACCTCTTGCAATATGAGCTAATTTTTGATGAACATAAATTAAAACCACCTCAGTATCCTGAGGC
2325 TCAACTCACCTCTCGCAATATGAGTTGAAATTAAAACACAA
386 TCAACTCACCTCTCGCAATATGAGTTGAAATTAAAACACAA
*
2366 AAATTGAAAATACCTCAGCGTGAGCCAAGGCTCAACTCACCTCTTGCAATATGAGCTAATTTTTG
1 AAATTGAAAATACCTCAGCGTGACCCAAGGCTCAACTCACCTCTTGCAATATGAGCTAA-TTTTG
** *
2431 ATGAACATAAATTAAAACCACCTCAGTATCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA
65 AAAAACAAAAATTAAAACCACCTCAGTATCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA
* ** *
2496 -TTTTTGACAAACAAAAATTGAAATTACCTCATCGT-CTTGAGGCTCAACTCACTTCTCGCAATA
130 TTTTTTGACAAACAAAAATTG-AA--ACCTCAGCGTCCCCGAGGCTCAACTCACCTCTCGCAATA
* * *
2559 TGAGTTGATTTTTTTTAAAAAAACAGAAATTGAAAA-TACCTCAGCATGTGAACC-GAGGCTCAA
192 TGAGCT-A--ATTTTT-AAAAAACAGAAATT-AAAACCACCT---CA-GT-AACCTGAGGCTCAA
2622 CTCACCTCTCGCAATATGAGTTGAAATTAAAACACAAAAATTGAAAATACCTCAGCGTGCCCCGA
247 CTCACCTCTCGCAATATGAGTTGAAATTAAAACACAAAAATTGAAAATACCTCAGCGTGCCCCGA
2687 GGCTCAACTCACCTCTTGCAATATGAGCTAATTTTTGATGAACATAAATTAAAACCACCTCAGTA
312 GGCTCAACTCACCTCTTGCAATATGAGCTAATTTTTGATGAACATAAATTAAAACCACCTCAGTA
2752 TCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGAAATTAAAACACAA
377 TCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGAAATTAAAACACAA
* * *
2802 AAATTGAAAATACCTCAGCGTGCCCCGAGGCTCAACTCACCTCTTGCAATATGAGCTGATTTTGA
1 AAATTGAAAATACCTCAGCGTGACCCAAGGCTCAACTCACCTCTTGCAATATGAGCTAATTTTGA
2867 AAAACAAAAATTAAAA
66 AAAACAAAAATTAAAA
2883 GGCTTAACTC
Statistics
Matches: 461, Mismatches: 41, Indels: 25
0.87 0.08 0.05
Matches are distributed among these distances:
427 17 0.04
428 31 0.07
429 42 0.09
430 60 0.13
431 23 0.05
432 14 0.03
433 4 0.01
435 21 0.05
436 246 0.53
437 3 0.01
ACGTcount: A:0.35, C:0.23, G:0.15, T:0.27
Consensus pattern (426 bp):
AAATTGAAAATACCTCAGCGTGACCCAAGGCTCAACTCACCTCTTGCAATATGAGCTAATTTTGA
AAAACAAAAATTAAAACCACCTCAGTATCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGAT
TTTTTGACAAACAAAAATTGAAACCTCAGCGTCCCCGAGGCTCAACTCACCTCTCGCAATATGAG
CTAATTTTTAAAAAACAGAAATTAAAACCACCTCAGTAACCTGAGGCTCAACTCACCTCTCGCAA
TATGAGTTGAAATTAAAACACAAAAATTGAAAATACCTCAGCGTGCCCCGAGGCTCAACTCACCT
CTTGCAATATGAGCTAATTTTTGATGAACATAAATTAAAACCACCTCAGTATCCTGAGGCTCAAC
TCACCTCTCGCAATATGAGTTGAAATTAAAACACAA
Found at i:2977 original size:122 final size:123
Alignment explanation
Indices: 2757--3002 Score: 345
Period size: 122 Copynumber: 2.0 Consensus size: 123
2747 CAGTATCCTG
* *
2757 AGGCTCAACTCACCTCTCGCAATATGAGTTGAAATTAAAACACAAAAATTGAAAATACCTCAGCG
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGAAATTAAAACACAAAAACTAAAAATACCTCAGCG
* * *
2822 TGCCCCGAGGCTCAACTCACCTCTTGCAATATGAGCTGATTTTGAAAAACAAAAATTAAA
66 TGCCCCAAGGCACAACTCACCTCTCGCAATATGAGCTGATTTTG-AAAA-AAAAATTAAA
* * * * *
2882 AGGCTTAACTCACCTCTCGCAATATGAG-T-CAATTTAAA-ACATAAACTAAAAATACCTCGGCG
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGAAATTAAAACACAAAAACTAAAAATACCTCAGCG
* *
2944 TGCCCCAAGGCACAACTCACTTCTCGCAATATGAGTTGATTTTGAAAAAAAAATTAAA
66 TGCCCCAAGGCACAACTCACCTCTCGCAATATGAGCTGATTTTGAAAAAAAAATTAAA
3002 A
1 A
3003 ATACCTCAAC
Statistics
Matches: 109, Mismatches: 12, Indels: 5
0.87 0.10 0.04
Matches are distributed among these distances:
120 11 0.10
121 4 0.04
122 59 0.54
123 7 0.06
124 1 0.01
125 27 0.25
ACGTcount: A:0.39, C:0.23, G:0.14, T:0.24
Consensus pattern (123 bp):
AGGCTCAACTCACCTCTCGCAATATGAGTTGAAATTAAAACACAAAAACTAAAAATACCTCAGCG
TGCCCCAAGGCACAACTCACCTCTCGCAATATGAGCTGATTTTGAAAAAAAAATTAAA
Found at i:3032 original size:70 final size:70
Alignment explanation
Indices: 2881--3056 Score: 196
Period size: 70 Copynumber: 2.5 Consensus size: 70
2871 CAAAAATTAA
* * * * * **
2881 AAGGCTTAACTCACCTCTCGCAATATGAG-TCAATTTAAAACATAAACTAAAAATACCTCGGCGT
1 AAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTAAAACAAAAACTAAAAATACCTCAACGT
2945 GCCCC
66 GCCCC
* *
2950 AAGGCACAACTCACTTCTCGCAATATGAGTTGATTTTGAAAA-AAAAATTAAAAATACCTCAACG
1 AAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTT-AAAACAAAAACTAAAAATACCTCAACG
* **
3014 TGTCTT
65 TGCCCC
*
3020 GAGGCTCAACTCA-TCTCTCGCAATATGAGTTGATTTT
1 AAGGCTCAACTCACT-TCTCGCAATATGAGTTGATTTT
3057 CCTTGGAAAG
Statistics
Matches: 90, Mismatches: 14, Indels: 5
0.83 0.13 0.05
Matches are distributed among these distances:
69 27 0.30
70 59 0.66
71 4 0.04
ACGTcount: A:0.35, C:0.23, G:0.14, T:0.28
Consensus pattern (70 bp):
AAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTAAAACAAAAACTAAAAATACCTCAACGT
GCCCC
Found at i:11131 original size:12 final size:12
Alignment explanation
Indices: 11111--11158 Score: 87
Period size: 12 Copynumber: 4.0 Consensus size: 12
11101 TCGGATATGC
*
11111 AATGTATGAATG
1 AATGCATGAATG
11123 AATGCATGAATG
1 AATGCATGAATG
11135 AATGCATGAATG
1 AATGCATGAATG
11147 AATGCATGAATG
1 AATGCATGAATG
11159 TCAAATGAAT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
12 35 1.00
ACGTcount: A:0.42, C:0.06, G:0.25, T:0.27
Consensus pattern (12 bp):
AATGCATGAATG
Found at i:11169 original size:4 final size:4
Alignment explanation
Indices: 11111--11158 Score: 60
Period size: 4 Copynumber: 12.0 Consensus size: 4
11101 TCGGATATGC
* * * *
11111 AATG TATG AATG AATG CATG AATG AATG CATG AATG AATG CATG AATG
1 AATG AATG AATG AATG AATG AATG AATG AATG AATG AATG AATG AATG
11159 TCAAATGAAT
Statistics
Matches: 36, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
4 36 1.00
ACGTcount: A:0.42, C:0.06, G:0.25, T:0.27
Consensus pattern (4 bp):
AATG
Done.