Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Cotton_A_33942
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: 4982
ACGTcount: A:0.41, C:0.14, G:0.28, T:0.17
Found at i:684 original size:111 final size:111
Alignment explanation
Indices: 552--771 Score: 307
Period size: 111 Copynumber: 2.0 Consensus size: 111
542 TAAAGGAGGC
* ** * * *
552 TGAAGCTGAGAAGGTATCAAAACTGATTTTGGCTGAAAAGAAGAAACTTGATGA-GCAGCCCAAG
1 TGAAGCTGAGAAGGTACCAAAACTGAAGTTGGCTGAAAAGAAGAAACCTGAAGAGGCA-ACCAAG
* * **
616 GAGGAAAGTGTTGAGAAAAATGTGCCAAAACAAAAGTTGGTCGAAGA
65 GAGGAAAGCGTTGAGAAAAAGGTAACAAAACAAAAGTTGGTCGAAGA
*
663 TGAAGCTGAGAAGGTACCAAAACTGAAGTTGGCTGAAAAGAAGAAACCTGAAGAGGTAACCAAGG
1 TGAAGCTGAGAAGGTACCAAAACTGAAGTTGGCTGAAAAGAAGAAACCTGAAGAGGCAACCAAGG
* *
728 AGGAAAGCGTTGAGCAAAAGGTAACAAAACAGAAGTTGGTCGAA
66 AGGAAAGCGTTGAGAAAAAGGTAACAAAACAAAAGTTGGTCGAA
772 AAGGAGGCTG
Statistics
Matches: 95, Mismatches: 13, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
111 93 0.98
112 2 0.02
ACGTcount: A:0.43, C:0.12, G:0.29, T:0.16
Consensus pattern (111 bp):
TGAAGCTGAGAAGGTACCAAAACTGAAGTTGGCTGAAAAGAAGAAACCTGAAGAGGCAACCAAGG
AGGAAAGCGTTGAGAAAAAGGTAACAAAACAAAAGTTGGTCGAAGA
Found at i:893 original size:129 final size:129
Alignment explanation
Indices: 663--896 Score: 357
Period size: 129 Copynumber: 1.8 Consensus size: 129
653 TGGTCGAAGA
* * * *
663 TGAAGCTGAGAAGGTACCAAAACTGAAGTTGGCTGAAAAGAAGAAACCTGAAGAGGTAACCAAGG
1 TGAAGATGAGAAGGTACCAAAACTGAAATTAGCTGAAAAGAAGAAACATGAAGAGGTAACCAAGG
*
728 AGGAAAGCGTTGAGCAAAAGGTAACAAAACAGAAGTTGGTCGAAAAGGAGGCTGAAGTTGCAGC
66 AGGAAAGCGTTGAGCAAAAGGCAACAAAACAGAAGTTGGTCGAAAAGGAGGCTGAAGTTGCAGC
792 TGAAGATGAGAAGGTACCAAAACTGAAATTAGCTGAAAAGAAGAAACATGAAGAGG-AA-CAGAT
1 TGAAGATGAGAAGGTACCAAAACTGAAATTAGCTGAAAAGAAGAAACATGAAGAGGTAACCA-A-
**
855 GGAGGAAAGCGTTGAGCAAAAGGCGCCAAAACTA-AAGTTGGT
64 GGAGGAAAGCGTTGAGCAAAAGGCAACAAAAC-AGAAGTTGGT
897 AGAAGCTGAA
Statistics
Matches: 95, Mismatches: 7, Indels: 6
0.88 0.06 0.06
Matches are distributed among these distances:
127 2 0.02
128 3 0.03
129 89 0.94
130 1 0.01
ACGTcount: A:0.44, C:0.12, G:0.30, T:0.14
Consensus pattern (129 bp):
TGAAGATGAGAAGGTACCAAAACTGAAATTAGCTGAAAAGAAGAAACATGAAGAGGTAACCAAGG
AGGAAAGCGTTGAGCAAAAGGCAACAAAACAGAAGTTGGTCGAAAAGGAGGCTGAAGTTGCAGC
Found at i:973 original size:240 final size:238
Alignment explanation
Indices: 550--2273 Score: 1452
Period size: 240 Copynumber: 7.4 Consensus size: 238
540 CGTAAAGGAG
* * ** * * * * *
550 GCTGAAGCTGAGAAGGTATCAAAACTGATTTTGGCTGAAAAGAAGAAACTTGATGAGCAGCCCAA
1 GCTGAAGATGAGAAGGTACCAAAACTGAAATTGGCTGAAAAGAAGAAACATGAAGAGGAACACAA
* * * * * * *
615 GGAGGAAAGTGTTGAGAAAAATGTGCCAAAACAAAAGTTGGTCGAAGATGAAGCTGAGAAGGTAC
66 GGAGGAAAGCGTTGAGCAAAAGGTGCCAAAACCAAAGTTGGTAGAAGCTGAAACTGAGAAGGTAC
*
680 CAAAACTGAAGTTGGCTGAAAAGAAGAAACCTGAAGAGGTAACCAAGGAGGAAAGCGTTGAGCAA
131 CAAAACTGATGTTGGCTGAAAAGAAGAAACCTGAAGAGGTAACCAAGGAGGAAAGCGTTGAGCAA
745 AAGGTAACAAAACAGAAGTTGGTCGAAAAGGAGGCTGAAGTTGCA
196 AAGGT-ACAAAACAGAAGTTGGTCGAAAAGGAGGCTGAAG-TGCA
* * *
790 GCTGAAGATGAGAAGGTACCAAAACTGAAATTAGCTGAAAAGAAGAAACATGAAGAGGAACAGAT
1 GCTGAAGATGAGAAGGTACCAAAACTGAAATTGGCTGAAAAGAAGAAACATGAAGAGGAACACAA
* * *
855 GGAGGAAAGCGTTGAGCAAAAGGCGCCAAAACTAAAGTTGGTAGAAGCTGAAACTGAGAAAGTAC
66 GGAGGAAAGCGTTGAGCAAAAGGTGCCAAAACCAAAGTTGGTAGAAGCTGAAACTGAGAAGGTAC
*
920 CAAAACTGATGTTGGCAGAAAAGAAGAAACCTGAAGAGGTAACCAAGGAGGAAAGCGTTGAGCAA
131 CAAAACTGATGTTGGCTGAAAAGAAGAAACCTGAAGAGGTAACCAAGGAGGAAAGCGTTGAGCAA
* *
985 AAGGTGCGAAAACAGAAGTTGATCGAAAAGGAGGCTGAAGTCGCA
196 AAGGTAC-AAAACAGAAGTTGGTCGAAAAGGAGGCTGAAGT-GCA
* * *
1030 GCTGAAGATGAGAAGGTACCAAAACTGAAATTGGCTGAAAAGAAGAAACATGAAGAGGTACAGAT
1 GCTGAAGATGAGAAGGTACCAAAACTGAAATTGGCTGAAAAGAAGAAACATGAAGAGGAACACAA
* * * *
1095 GGAGGAAAACGTTGAGCAAAAGGGGCCAAAACCAAAGCTGGTCGATGCTGAAGCTGAAGCTGAGA
66 GGAGGAAAGCGTTGAGCAAAAGGTGCCAAAACCAAAGTTGGT--A----GAAGCTGAAACTGAGA
* * * *
1160 AGGTACCAAAACTGACGTTGGCTGAAAAGAAGAAACCTGAAGAGGTAACCAAGGACGACAGCATT
125 AGGTACCAAAACTGATGTTGGCTGAAAAGAAGAAACCTGAAGAGGTAACCAAGGAGGAAAGCGTT
* *
1225 GAGCAAAAGGTGCCCAAACCA-AAGTTGGTCG-AAA--A-G--GAA--G-A
190 GAGCAAAAGGT--ACAAAACAGAAGTTGGTCGAAAAGGAGGCTGAAGTGCA
* * * * ** * * * *
1266 --TGAGGCTGAGAAGGTACCAAAACAGATGA-TGGCTGAACTGAAGAAACTTGAGGAGGTACCCA
1 GCTGAAGATGAGAAGGTACCAAAACTGA-AATTGGCTGAAAAGAAGAAACATGAAGAGGAACACA
* * * * *
1328 AGGAGGAAAGTGTTGAGCAAAAGGTACCAAAACCACAGTTGGTCGAAGCTGAAGA-AGAGAAGGT
65 AGGAGGAAAGCGTTGAGCAAAAGGTGCCAAAACCAAAGTTGGTAGAAGCTGAA-ACTGAGAAGGT
** * * * *
1392 ACCGCAATTGATAG-TGGTTGAAAAGAAGAAACCTGAAGAGTTACCCAAGGAGGAAAGCGTTGAG
129 ACCAAAACTGAT-GTTGGCTGAAAAGAAGAAACCTGAAGAGGTAACCAAGGAGGAAAGCGTTGAG
* *
1456 CAAAAGTTGCCAAAACCA-AAGTTGGTC---AA--A-GCTG-A----A
193 CAAAAGGT-ACAAAA-CAGAAGTTGGTCGAAAAGGAGGCTGAAGTGCA
** * * * * *
1492 GC------TGAGAAGGTACCAAAACTGATGTTGGCGGAAAAGAAGAAACCTAAAGAGGTACCCAA
1 GCTGAAGATGAGAAGGTACCAAAACTGAAATTGGCTGAAAAGAAGAAACATGAAGAGGAACACAA
* * * * *
1551 GGAGGAAAGTGTTGAGCAAAAGGTGCCAAAACCAAAGTTGGTCGATGCTGAAGCTGAGAAAGTAC
66 GGAGGAAAGCGTTGAGCAAAAGGTGCCAAAACCAAAGTTGGTAGAAGCTGAAACTGAGAAGGTAC
* * * *
1616 CAAAACTGATGTTGTCTGAAAAGAAGAATCCTAAAGAGGTAACC---GAGGAAAGCGTTCAGCAA
131 CAAAACTGATGTTGGCTGAAAAGAAGAAACCTGAAGAGGTAACCAAGGAGGAAAGCGTTGAGCAA
** * *
1678 AAGATGCCCAAACCA-AAGTTGGTCGAAAAGAAGGCTGAA---C-
196 AAG--GTACAAAACAGAAGTTGGTCGAAAAGGAGGCTGAAGTGCA
* * * * *
1718 -C------TGAGAAGGTACCAAAACAGATGA-TGGCTGCAAAGAAGAAACTTGAAGAGGTAGC-C
1 GCTGAAGATGAGAAGGTACCAAAACTGA-AATTGGCTGAAAAGAAGAAACATGAAGAGG-AACAC
* * *
1774 AAGGAGGAAAGTGTTGAGCAAAAGGTGCCAAAACCAAAGTTGGTCGAAGCTGAAGCTGAGAAGGT
64 AAGGAGGAAAGCGTTGAGCAAAAGGTGCCAAAACCAAAGTTGGTAGAAGCTGAAACTGAGAAGGT
* * * *
1839 ACCAAAATTGATATT-GCTTGAAAAGAAGAAACCTGAAGAGGTAACCAAGGAGGAAACCTTTGAG
129 ACCAAAACTGATGTTGGC-TGAAAAGAAGAAACCTGAAGAGGTAACCAAGGAGGAAAGCGTTGAG
* *
1903 CAAAAGTTGCCAAAACCA-AAGTTGGTC---AA--A-GCTG-A----A
193 CAAAAGGT-ACAAAA-CAGAAGTTGGTCGAAAAGGAGGCTGAAGTGCA
** * * *
1939 GC------TGAGAAGGTACCAAAACTGATGTTGGCTGAAACGAAGAAATC-TGAAGAGGTACCCA
1 GCTGAAGATGAGAAGGTACCAAAACTGAAATTGGCTGAAAAGAAGAAA-CATGAAGAGGAACACA
* * * * * *
1997 AGGTGGAAAGTGTTGAGCAAGAGGTCCCAAAACCAAAGTTGGTCCATGCTGAAGCTGAAGCAGAG
65 AGGAGGAAAGCGTTGAGCAAAAGGTGCCAAAACCAAAGTTGGT--A----GAAGCTGAAACTGAG
* * * * * *
2062 AAGGTACCTAAACTGATGTTGGCTGAAAACAAGAAACATGAAGAGGTACCCAAGGAGGAAAGTGC
124 AAGGTACCAAAACTGATGTTGGCTGAAAAGAAGAAACCTGAAGAGGTAACCAAGGAGGAAAGCGT
* *
2127 TGAGCAAAAGGTGCCAAAAACA-AAGTTGGTTG---A--A-GCTG-A----A
189 TGAGCAAAAGGT-AC-AAAACAGAAGTTGGTCGAAAAGGAGGCTGAAGTGCA
* * * * * * *
2167 GCTGAAGCTGAGACGGTACCAAAACTGAAGTTGGCTGAAAAGAAGAAACCTGAAAAGGTACCCAA
1 GCTGAAGATGAGAAGGTACCAAAACTGAAATTGGCTGAAAAGAAGAAACATGAAGAGGAACACAA
* * *
2232 GAAGGAAAACGTTGAGCAAAAGGTGCCAAAACCAAAGCTGGT
66 GGAGGAAAGCGTTGAGCAAAAGGTGCCAAAACCAAAGTTGGT
2274 CAAAAATAAG
Statistics
Matches: 1265, Mismatches: 159, Indels: 126
0.82 0.10 0.08
Matches are distributed among these distances:
219 31 0.02
220 5 0.00
221 3 0.00
222 229 0.18
223 2 0.00
224 2 0.00
225 152 0.12
226 7 0.01
227 11 0.01
228 217 0.17
229 7 0.01
233 1 0.00
234 172 0.14
235 1 0.00
236 1 0.00
237 1 0.00
239 2 0.00
240 315 0.25
242 2 0.00
243 1 0.00
245 3 0.00
246 94 0.07
247 5 0.00
248 1 0.00
ACGTcount: A:0.41, C:0.15, G:0.29, T:0.15
Consensus pattern (238 bp):
GCTGAAGATGAGAAGGTACCAAAACTGAAATTGGCTGAAAAGAAGAAACATGAAGAGGAACACAA
GGAGGAAAGCGTTGAGCAAAAGGTGCCAAAACCAAAGTTGGTAGAAGCTGAAACTGAGAAGGTAC
CAAAACTGATGTTGGCTGAAAAGAAGAAACCTGAAGAGGTAACCAAGGAGGAAAGCGTTGAGCAA
AAGGTACAAAACAGAAGTTGGTCGAAAAGGAGGCTGAAGTGCA
Found at i:983 original size:111 final size:112
Alignment explanation
Indices: 789--2273 Score: 1260
Period size: 111 Copynumber: 13.0 Consensus size: 112
779 CTGAAGTTGC
* ** * *
789 AGCTGAAGATGAGAAGGTACCAAAACTGAAATTAGCTGAAAAGAAGAAACATGAAGAGG-AA-CA
1 AGCTGAAGCTGAGAAGGTACCAAAACTGATGTTGGCTGAAAAGAAGAAACCTGAAGAGGTAACCA
* *
852 GATGGAGGAAAGCGTTGAGCAAAAGGCGCCAAAACTAAAGTTGGT-AGA
66 -A-GGAGGAAAGCGTTGAGCAAAAGGTGCCAAAACCAAAGTTGGTAAGA
* * *
900 AGCTGAAACTGAGAAAGTACCAAAACTGATGTTGGCAGAAAAGAAGAAACCTGAAGAGGTAACCA
1 AGCTGAAGCTGAGAAGGTACCAAAACTGATGTTGGCTGAAAAGAAGAAACCTGAAGAGGTAACCA
* *
965 AGGAGGAAAGCGTTGAGCAAAAGGTGCGAAAA-CAGAAGTTGATCGAA-A
66 AGGAGGAAAGCGTTGAGCAAAAGGTGCCAAAACCA-AAGTTGGT--AAGA
* * * * ** * *
1013 AG--GAGGCT--GAA-GT-CGC--AGCTGAAGATGAGAAGGTACCAAA-ACTGAAATTGGCTGAA
1 AGCTGAAGCTGAGAAGGTAC-CAAAACTGATGTTG-G-CTG-A--AAAGA-AGAAA---CCTG--
* * * * * * * *
1069 AAGAAG-AAACATGAAGAGGTACAG-ATGGAGGAAAACGTTGAGCAAAAGGGGCCAAAACCAAAG
54 AAGAGGTAACCA--AGGAGG-AAAGCGTTGA-GCAAA-----------AGGTGCCAAAACCAAAG
* *
1132 CTGGT-CGA
104 TTGGTAAGA
* *
1140 TGCTGAAGCTGAAGCTGAGAAGGTACCAAAACTGACGTTGGCTGAAAAGAAGAAACCTGAAGAGG
1 AGCTGAAGCTG-A---GA--AGGTACCAAAACTGATGTTGGCTGAAAAGAAGAAACCTGAAGAGG
* * * *
1205 TAACCAAGGACGACAGCATTGAGCAAAAGGTGCCCAAACCAAAGTTGGTCGAAAAGGA
60 TAACCAAGGAGGAAAGCGTTGAGCAAAAGGTGCCAAAACCAAAGTTGGT----AA-GA
* * * * ** * * *
1263 AGATGAGGCTGAGAAGGTACCAAAACAGATGATGGCTGAACTGAAGAAACTTGAGGAGGTACCCA
1 AGCTGAAGCTGAGAAGGTACCAAAACTGATGTTGGCTGAAAAGAAGAAACCTGAAGAGGTAACCA
* * * *
1328 AGGAGGAAAGTGTTGAGCAAAAGGTACCAAAACCACAGTTGGT-CGA
66 AGGAGGAAAGCGTTGAGCAAAAGGTGCCAAAACCAAAGTTGGTAAGA
** ** * * * *
1374 AGCTGAAGAAGAGAAGGTACCGCAATTGATAG-TGGTTGAAAAGAAGAAACCTGAAGAGTTACCC
1 AGCTGAAGCTGAGAAGGTACCAAAACTGAT-GTTGGCTGAAAAGAAGAAACCTGAAGAGGTAACC
* *
1438 AAGGAGGAAAGCGTTGAGCAAAAGTTGCCAAAACCAAAGTTGGTCA-A
65 AAGGAGGAAAGCGTTGAGCAAAAGGTGCCAAAACCAAAGTTGGTAAGA
* * *
1485 AGCTGAAGCTGAGAAGGTACCAAAACTGATGTTGGCGGAAAAGAAGAAACCTAAAGAGGTACCCA
1 AGCTGAAGCTGAGAAGGTACCAAAACTGATGTTGGCTGAAAAGAAGAAACCTGAAGAGGTAACCA
* *
1550 AGGAGGAAAGTGTTGAGCAAAAGGTGCCAAAACCAAAGTTGGT-CGA
66 AGGAGGAAAGCGTTGAGCAAAAGGTGCCAAAACCAAAGTTGGTAAGA
* * * * *
1596 TGCTGAAGCTGAGAAAGTACCAAAACTGATGTTGTCTGAAAAGAAGAATCCTAAAGAGGTAACC-
1 AGCTGAAGCTGAGAAGGTACCAAAACTGATGTTGGCTGAAAAGAAGAAACCTGAAGAGGTAACCA
* * *
1660 --GAGGAAAGCGTTCAGCAAAAGATGCCCAAACCAAAGTTGGTCGAAAAGA
66 AGGAGGAAAGCGTTGAGCAAAAGGTGCCAAAACCAAAGTTGGT----AAGA
* * * * * *
1709 AGGCTGAACCTGAGAAGGTACCAAAACAGATGATGGCTGCAAAGAAGAAACTTGAAGAGGTAGCC
1 A-GCTGAAGCTGAGAAGGTACCAAAACTGATGTTGGCTGAAAAGAAGAAACCTGAAGAGGTAACC
* *
1774 AAGGAGGAAAGTGTTGAGCAAAAGGTGCCAAAACCAAAGTTGGT-CGA
65 AAGGAGGAAAGCGTTGAGCAAAAGGTGCCAAAACCAAAGTTGGTAAGA
* *
1821 AGCTGAAGCTGAGAAGGTACCAAAATTGATATT-GCTTGAAAAGAAGAAACCTGAAGAGGTAACC
1 AGCTGAAGCTGAGAAGGTACCAAAACTGATGTTGGC-TGAAAAGAAGAAACCTGAAGAGGTAACC
* * * *
1885 AAGGAGGAAACCTTTGAGCAAAAGTTGCCAAAACCAAAGTTGGTCA-A
65 AAGGAGGAAAGCGTTGAGCAAAAGGTGCCAAAACCAAAGTTGGTAAGA
* * *
1932 AGCTGAAGCTGAGAAGGTACCAAAACTGATGTTGGCTGAAACGAAGAAATCTGAAGAGGTACCCA
1 AGCTGAAGCTGAGAAGGTACCAAAACTGATGTTGGCTGAAAAGAAGAAACCTGAAGAGGTAACCA
* * * * *
1997 AGGTGGAAAGTGTTGAGCAAGAGGTCCCAAAACCAAAGTTGGTCCATGCTGA
66 AGGAGGAAAGCGTTGAGCAAAAGGTGCCAAAACCAAAGTTGGT--A---AGA
* * * * *
2049 AGCTGAAGCAGAGAAGGTACCTAAACTGATGTTGGCTGAAAACAAGAAACATGAAGAGGTACCCA
1 AGCTGAAGCTGAGAAGGTACCAAAACTGATGTTGGCTGAAAAGAAGAAACCTGAAGAGGTAACCA
* * *
2114 AGGAGGAAAGTGCTGAGCAAAAGGTGCCAAAAACAAAGTTGGTTGAAGCTGA
66 AGGAGGAAAGCGTTGAGCAAAAGGTGCCAAAACCAAAGTTGG-T-AA---GA
* * * *
2166 AGCTGAAGCTGAGACGGTACCAAAACTGAAGTTGGCTGAAAAGAAGAAACCTGAAAAGGTACCCA
1 AGCTGAAGCTGAGAAGGTACCAAAACTGATGTTGGCTGAAAAGAAGAAACCTGAAGAGGTAACCA
* * *
2231 AGAAGGAAAACGTTGAGCAAAAGGTGCCAAAACCAAAGCTGGT
66 AGGAGGAAAGCGTTGAGCAAAAGGTGCCAAAACCAAAGTTGGT
2274 CAAAAATAAG
Statistics
Matches: 1108, Mismatches: 182, Indels: 163
0.76 0.13 0.11
Matches are distributed among these distances:
106 8 0.01
107 2 0.00
108 41 0.04
109 4 0.00
110 5 0.00
111 529 0.48
112 9 0.01
113 7 0.01
114 57 0.05
115 4 0.00
116 6 0.01
117 337 0.30
118 8 0.01
119 2 0.00
122 1 0.00
123 10 0.01
127 2 0.00
128 8 0.01
129 28 0.03
130 7 0.01
131 4 0.00
132 3 0.00
135 9 0.01
136 1 0.00
137 2 0.00
138 4 0.00
139 2 0.00
140 8 0.01
ACGTcount: A:0.41, C:0.15, G:0.28, T:0.15
Consensus pattern (112 bp):
AGCTGAAGCTGAGAAGGTACCAAAACTGATGTTGGCTGAAAAGAAGAAACCTGAAGAGGTAACCA
AGGAGGAAAGCGTTGAGCAAAAGGTGCCAAAACCAAAGTTGGTAAGA
Found at i:1244 original size:117 final size:117
Alignment explanation
Indices: 1029--2274 Score: 1439
Period size: 117 Copynumber: 10.9 Consensus size: 117
1019 CTGAAGTCGC
* ** * **
1029 AGCTGAAGATGAGAAGGTACCAAAACTGAAATTGGCTGAAAAGAAGAAACATGAAGAGGTACAGA
1 AGCTGAAGCTGAGAAGGTACCAAAACTGATGTTGGCTGAAAAGAAGAAACCTGAAGAGGTACCCA
* * * *
1094 TGGAGGAAAACGTTGAGCAAAAGGGGCCAAAACCAAAGCTGGTCGATGCTGA
66 AGGAGGAAAGCGTTGAGCAAAAGGTGCCAAAACCAAAGTTGGTCGATGCTGA
* *
1146 AGCTGAAGCTGAGAAGGTACCAAAACTGACGTTGGCTGAAAAGAAGAAACCTGAAGAGGTAACCA
1 AGCTGAAGCTGAGAAGGTACCAAAACTGATGTTGGCTGAAAAGAAGAAACCTGAAGAGGTACCCA
* * * * ****
1211 AGGACGACAGCATTGAGCAAAAGGTGCCCAAACCAAAGTTGGTCGAAAAGGA
66 AGGAGGAAAGCGTTGAGCAAAAGGTGCCAAAACCAAAGTTGGTCGATGCTGA
* * * * ** * *
1263 AGATGAGGCTGAGAAGGTACCAAAACAGATGATGGCTGAACTGAAGAAACTTGAGGAGGTACCCA
1 AGCTGAAGCTGAGAAGGTACCAAAACTGATGTTGGCTGAAAAGAAGAAACCTGAAGAGGTACCCA
* * * *
1328 AGGAGGAAAGTGTTGAGCAAAAGGTACCAAAACCACAGTTGGTCGAAGCTGA
66 AGGAGGAAAGCGTTGAGCAAAAGGTGCCAAAACCAAAGTTGGTCGATGCTGA
** * * *
1380 A---GAA---GAGAAGGTACCGCAATTGATAG-TGGTTGAAAAGAAGAAACCTGAAGAGTTACCC
1 AGCTGAAGCTGAGAAGGTACCAAAACTGAT-GTTGGCTGAAAAGAAGAAACCTGAAGAGGTACCC
*
1438 AAGGAGGAAAGCGTTGAGCAAAAGTTGCCAAAACCAAAGTTGGTC-A-----A
65 AAGGAGGAAAGCGTTGAGCAAAAGGTGCCAAAACCAAAGTTGGTCGATGCTGA
* *
1485 AGCTGAAGCTGAGAAGGTACCAAAACTGATGTTGGCGGAAAAGAAGAAACCTAAAGAGGTACCCA
1 AGCTGAAGCTGAGAAGGTACCAAAACTGATGTTGGCTGAAAAGAAGAAACCTGAAGAGGTACCCA
*
1550 AGGAGGAAAGTGTTGAGCAAAAGGTGCCAAAACCAAAGTTGGTCGATGCTGA
66 AGGAGGAAAGCGTTGAGCAAAAGGTGCCAAAACCAAAGTTGGTCGATGCTGA
* * * *
1602 AGCTG-A---GA-AA-GTACCAAAACTGATGTTGTCTGAAAAGAAGAATCCTAAAGAGGTAACC-
1 AGCTGAAGCTGAGAAGGTACCAAAACTGATGTTGGCTGAAAAGAAGAAACCTGAAGAGGTACCCA
* * * ***
1660 --GAGGAAAGCGTTCAGCAAAAGATGCCCAAACCAAAGTTGGTCGA-AAAGA
66 AGGAGGAAAGCGTTGAGCAAAAGGTGCCAAAACCAAAGTTGGTCGATGCTGA
* * * * * *
1709 AGGCTGAACCTGAGAAGGTACCAAAACAGATGATGGCTGCAAAGAAGAAACTTGAAGAGGTAGCC
1 A-GCTGAAGCTGAGAAGGTACCAAAACTGATGTTGGCTGAAAAGAAGAAACCTGAAGAGGTACCC
*
1774 AAGGAGGAAAGTGTTGAGCAAAAGGTGCCAAAACCAAAGTT-G--G-T-C-GA
65 AAGGAGGAAAGCGTTGAGCAAAAGGTGCCAAAACCAAAGTTGGTCGATGCTGA
* * *
1821 AGCTGAAGCTGAGAAGGTACCAAAATTGATATT-GCTTGAAAAGAAGAAACCTGAAGAGGTAACC
1 AGCTGAAGCTGAGAAGGTACCAAAACTGATGTTGGC-TGAAAAGAAGAAACCTGAAGAGGTACCC
* * *
1885 AAGGAGGAAACCTTTGAGCAAAAGTTGCCAAAACCAAAGTTGGTC-A-----A
65 AAGGAGGAAAGCGTTGAGCAAAAGGTGCCAAAACCAAAGTTGGTCGATGCTGA
* *
1932 AGCTGAAGCTGAGAAGGTACCAAAACTGATGTTGGCTGAAACGAAGAAATCTGAAGAGGTACCCA
1 AGCTGAAGCTGAGAAGGTACCAAAACTGATGTTGGCTGAAAAGAAGAAACCTGAAGAGGTACCCA
* * * * *
1997 AGGTGGAAAGTGTTGAGCAAGAGGTCCCAAAACCAAAGTTGGTCCATGCTGA
66 AGGAGGAAAGCGTTGAGCAAAAGGTGCCAAAACCAAAGTTGGTCGATGCTGA
* * * *
2049 AGCTGAAGCAGAGAAGGTACCTAAACTGATGTTGGCTGAAAACAAGAAACATGAAGAGGTACCCA
1 AGCTGAAGCTGAGAAGGTACCAAAACTGATGTTGGCTGAAAAGAAGAAACCTGAAGAGGTACCCA
* * * * *
2114 AGGAGGAAAGTGCTGAGCAAAAGGTGCCAAAAACAAAGTTGGTTGAAGCTGA
66 AGGAGGAAAGCGTTGAGCAAAAGGTGCCAAAACCAAAGTTGGTCGATGCTGA
* * *
2166 AGCTGAAGCTGAGACGGTACCAAAACTGAAGTTGGCTGAAAAGAAGAAACCTGAAAAGGTACCCA
1 AGCTGAAGCTGAGAAGGTACCAAAACTGATGTTGGCTGAAAAGAAGAAACCTGAAGAGGTACCCA
* * *
2231 AGAAGGAAAACGTTGAGCAAAAGGTGCCAAAACCAAAGCTGGTC
66 AGGAGGAAAGCGTTGAGCAAAAGGTGCCAAAACCAAAGTTGGTC
2275 AAAAATAAGG
Statistics
Matches: 953, Mismatches: 139, Indels: 74
0.82 0.12 0.06
Matches are distributed among these distances:
105 2 0.00
107 3 0.00
108 47 0.05
109 1 0.00
110 4 0.00
111 399 0.42
112 13 0.01
113 4 0.00
114 43 0.05
116 2 0.00
117 435 0.46
ACGTcount: A:0.41, C:0.16, G:0.28, T:0.15
Consensus pattern (117 bp):
AGCTGAAGCTGAGAAGGTACCAAAACTGATGTTGGCTGAAAAGAAGAAACCTGAAGAGGTACCCA
AGGAGGAAAGCGTTGAGCAAAAGGTGCCAAAACCAAAGTTGGTCGATGCTGA
Found at i:1872 original size:447 final size:450
Alignment explanation
Indices: 550--2274 Score: 1973
Period size: 447 Copynumber: 3.7 Consensus size: 450
540 CGTAAAGGAG
* * * * *
550 GCTGAAGCTGAGAAGGTATCAAAACTGATTTTGGCTGAAAAGAAGAAACTTGATGA-GCAGCCCA
1 GCTGAAGCTGAGAAGGTACCAAAACTGATGTTGGCTGAAAAGAAGAAACCTGAAGAGGTA-CCCA
* * * * *
614 AGGAGGAAAGTGTTGAGAAAAATGTGCCAAAACAAAAGTTGGTCGAAGATGAAGCT---GAGAAG
65 AGGAGGAAAGTGTTGAGCAAAAGGTGCCAAAACCAAAGTTGGTCGATGCTGAAGCTGAAGAGAAG
*
676 GTACCAAAACTGAAGTTGGCTGAAAAGAAGAAACCTGAAGAGGTAACCAAGGAGGAAAGCGTTGA
130 GTACCAAAACTGATGTTGGCTGAAAAGAAGAAACCTGAAGAGGTAACC-A-GAGGAAAGCGTTGA
** *
741 GCAAAAGGT-AACAAAACAGAAGTTGGTCGAAAAGGAGGCTGAAGTTGCAGCTGAAGATGAGAAG
193 GCAAAAGGTGCCCAAAACA-AAGTTGGTCGAAAA-GAAGCTGAA----C--C------TGAGAAG
* * * * * ** *
805 GTACCAAAACTGA-AATTAGCTGAAAAGAAGAAACATGAAGAGGAACAGATGGAGGAAAGCGTTG
244 GTACCAAAACAGATGA-TGGCTGAAAAGAAGAAACTTGAAGAGGTACCCAAGGAGGAAAGCGTTG
* * * * * * *
869 AGCAAAAGGCGCCAAAACTAAAGTTGGTAGAAGCTGAAACTGAGAAAGTACCAAAACTGATGTTG
308 AGCAAAAGGTGCCAAAACCAAAGTTGGTCGAAGCTGAAGCTGAGAAGGTACCAAAATTGATATT-
* * *
934 GC-AGAAAAGAAGAAACCTGAAGAGGTAACCAAGGAGGAAAGCGTTGAGCAAAAGGTGCGAAAA-
372 GCTTGAAAAGAAGAAACCTGAAGAGGTAACCAAGGAGGAAAGCGTTGAGCAAAAGTTGCCAAAAC
*
997 CAGAAGTTGATCGAAAAGGA
437 CA-AAGTTGGTC---AA--A
** *
1017 GGCTGAAGTCGCAGCTGAAGATGAGAAGGTACCAAAACTGAAATTGGCTGAAAAGAAGAAACATG
1 -GCTG-A-----AGC------TGAGAAGGTACCAAAACTGATGTTGGCTGAAAAGAAGAAACCTG
** * ** * *
1082 AAGAGGTACAGATGGAGGAAAACGTTGAGCAAAAGGGGCCAAAACCAAAGCTGGTCGATGCTGAA
53 AAGAGGTACCCAAGGAGGAAAGTGTTGAGCAAAAGGTGCCAAAACCAAAGTTGGTCGATGCTGAA
*
1147 GCTGAAGCTGAGAAGGTACCAAAACTGACGTTGGCTGAAAAGAAGAAACCTGAAGAGGTAACCA-
118 GCTGAA---GAGAAGGTACCAAAACTGATGTTGGCTGAAAAGAAGAAACCTGAAGAGGTAACCAG
* * * **
1211 AGGACGACAGCATTGAGCAAAAGGTGCCCAAACCAAAGTTGGTCGAAAAGGAAGATGAGGCTGAG
180 AGGA--A-AGCGTTGAGCAAAAGGTGCCCAAAACAAAGTTGGTCGAAAA-GAAGCTGAACCTGAG
** * *
1276 AAGGTACCAAAACAGATGATGGCTGAACTGAAGAAACTTGAGGAGGTACCCAAGGAGGAAAGTGT
241 AAGGTACCAAAACAGATGATGGCTGAAAAGAAGAAACTTGAAGAGGTACCCAAGGAGGAAAGCGT
* * ** ** *
1341 TGAGCAAAAGGTACCAAAACCACAGTTGGTCGAAGCTGAAGAAGAGAAGGTACCGCAATTGATAG
306 TGAGCAAAAGGTGCCAAAACCAAAGTTGGTCGAAGCTGAAGCTGAGAAGGTACCAAAATTGATAT
* * *
1406 TGGTTGAAAAGAAGAAACCTGAAGAGTTACCCAAGGAGGAAAGCGTTGAGCAAAAGTTGCCAAAA
371 TGCTTGAAAAGAAGAAACCTGAAGAGGTAACCAAGGAGGAAAGCGTTGAGCAAAAGTTGCCAAAA
1471 CCAAAGTTGGTCAAA
436 CCAAAGTTGGTCAAA
* *
1486 GCTGAAGCTGAGAAGGTACCAAAACTGATGTTGGCGGAAAAGAAGAAACCTAAAGAGGTACCCAA
1 GCTGAAGCTGAGAAGGTACCAAAACTGATGTTGGCTGAAAAGAAGAAACCTGAAGAGGTACCCAA
1551 GGAGGAAAGTGTTGAGCAAAAGGTGCCAAAACCAAAGTTGGTCGATGCTGAAGCTG-AGA-AA-G
66 GGAGGAAAGTGTTGAGCAAAAGGTGCCAAAACCAAAGTTGGTCGATGCTGAAGCTGAAGAGAAGG
* * * *
1613 TACCAAAACTGATGTTGTCTGAAAAGAAGAATCCTAAAGAGGTAACC-GAGGAAAGCGTTCAGCA
131 TACCAAAACTGATGTTGGCTGAAAAGAAGAAACCTGAAGAGGTAACCAGAGGAAAGCGTTGAGCA
* *
1677 AAAGATGCCCAAACCAAAGTTGGTCGAAAAGAAGGCTGAACCTGAGAAGGTACCAAAACAGATGA
196 AAAGGTGCCCAAAACAAAGTTGGTCGAAAAGAA-GCTGAACCTGAGAAGGTACCAAAACAGATGA
* * *
1742 TGGCTGCAAAGAAGAAACTTGAAGAGGTAGCCAAGGAGGAAAGTGTTGAGCAAAAGGTGCCAAAA
260 TGGCTGAAAAGAAGAAACTTGAAGAGGTACCCAAGGAGGAAAGCGTTGAGCAAAAGGTGCCAAAA
1807 CCAAAGTTGGTCGAAGCTGAAGCTGAGAAGGTACCAAAATTGATATTGCTTGAAAAGAAGAAACC
325 CCAAAGTTGGTCGAAGCTGAAGCTGAGAAGGTACCAAAATTGATATTGCTTGAAAAGAAGAAACC
* *
1872 TGAAGAGGTAACCAAGGAGGAAACCTTTGAGCAAAAGTTGCCAAAACCAAAGTTGGTCAAA
390 TGAAGAGGTAACCAAGGAGGAAAGCGTTGAGCAAAAGTTGCCAAAACCAAAGTTGGTCAAA
* *
1933 GCTGAAGCTGAGAAGGTACCAAAACTGATGTTGGCTGAAACGAAGAAATCTGAAGAGGTACCCAA
1 GCTGAAGCTGAGAAGGTACCAAAACTGATGTTGGCTGAAAAGAAGAAACCTGAAGAGGTACCCAA
* * * *
1998 GGTGGAAAGTGTTGAGCAAGAGGTCCCAAAACCAAAGTTGGTCCATGCTGAAGCTGAAGCAGAGA
66 GGAGGAAAGTGTTGAGCAAAAGGTGCCAAAACCAAAGTTGGTCGATGCTGAAGCTG-A--AGAGA
* * * * * *
2063 AGGTACCTAAACTGATGTTGGCTGAAAACAAGAAACATGAAGAGGTACCCAAGGAGGAAAGTGCT
128 AGGTACCAAAACTGATGTTGGCTGAAAAGAAGAAACCTGAAGAGGTAACC-A-GAGGAAAGCGTT
* * ** * * *
2128 GAGCAAAAGGTGCCAAAAACAAAGTTGGTTGAAGCTGAAGCTGAAGCTGAGACGGTACCAAAACT
191 GAGCAAAAGGTGCCCAAAACAAAGTTGGTCGAA-AAGAAGCTGAACCTGAGAAGGTACCAAAACA
* * * * * *
2193 GAAGTTGGCTGAAAAGAAGAAACCTGAAAAGGTACCCAAGAAGGAAAACGTTGAGCAAAAGGTGC
255 GATGATGGCTGAAAAGAAGAAACTTGAAGAGGTACCCAAGGAGGAAAGCGTTGAGCAAAAGGTGC
*
2258 CAAAACCAAAGCTGGTC
320 CAAAACCAAAGTTGGTC
2275 AAAAATAAGG
Statistics
Matches: 1083, Mismatches: 136, Indels: 88
0.83 0.10 0.07
Matches are distributed among these distances:
446 3 0.00
447 353 0.33
448 1 0.00
450 48 0.04
451 5 0.00
452 4 0.00
453 41 0.04
455 1 0.00
456 234 0.22
457 3 0.00
462 3 0.00
467 1 0.00
468 8 0.01
469 2 0.00
471 2 0.00
473 1 0.00
474 174 0.16
475 3 0.00
480 92 0.08
481 2 0.00
483 4 0.00
485 2 0.00
486 90 0.08
487 6 0.01
ACGTcount: A:0.41, C:0.15, G:0.29, T:0.15
Consensus pattern (450 bp):
GCTGAAGCTGAGAAGGTACCAAAACTGATGTTGGCTGAAAAGAAGAAACCTGAAGAGGTACCCAA
GGAGGAAAGTGTTGAGCAAAAGGTGCCAAAACCAAAGTTGGTCGATGCTGAAGCTGAAGAGAAGG
TACCAAAACTGATGTTGGCTGAAAAGAAGAAACCTGAAGAGGTAACCAGAGGAAAGCGTTGAGCA
AAAGGTGCCCAAAACAAAGTTGGTCGAAAAGAAGCTGAACCTGAGAAGGTACCAAAACAGATGAT
GGCTGAAAAGAAGAAACTTGAAGAGGTACCCAAGGAGGAAAGCGTTGAGCAAAAGGTGCCAAAAC
CAAAGTTGGTCGAAGCTGAAGCTGAGAAGGTACCAAAATTGATATTGCTTGAAAAGAAGAAACCT
GAAGAGGTAACCAAGGAGGAAAGCGTTGAGCAAAAGTTGCCAAAACCAAAGTTGGTCAAA
Found at i:2453 original size:72 final size:71
Alignment explanation
Indices: 2362--4022 Score: 1191
Period size: 72 Copynumber: 23.2 Consensus size: 71
2352 TGAAACCAAT
* * * * * *
2362 GAACCTAAAGAGGTACCCAAGGAGGAGACTATTGAGGAACAGGTACCAAAACCAAAGTCGGCTGA
1 GAACCTGAAGAGGTACCCAAGGTGGAGAGTGTTGAGGAAAAGGTACCAAAACCAAAGTTGG-TGA
2427 GAAGAAG
65 GAAGAAG
** *
2434 GAACCAAAAGAGGTACCCAAGGTGGAGAGTGTTGAGGAAAAGGTACCAAAATCAAAGTTGGTTGA
1 GAACCTGAAGAGGTACCCAAGGTGGAGAGTGTTGAGGAAAAGGTACCAAAACCAAAGTTGG-TGA
*
2499 TAAGAAG
65 GAAGAAG
* * ** * * * *
2506 GAATCTGAAGAAGTACGTAAGG-GGAACAATGTTGAGGAAAAGGTACCAAAATCAAAGTTGGT-T
1 GAACCTGAAGAGGTACCCAAGGTGG-AGAGTGTTGAGGAAAAGGTACCAAAACCAAAGTTGGTGA
2569 G-AGAAG
65 GAAGAAG
* * * * *
2575 GAACCTGAAGAGGTACGCAAGGTGGAGAGTGTTGGGGAAAAGGTACCAGAACAAAATTTGGTTGA
1 GAACCTGAAGAGGTACCCAAGGTGGAGAGTGTTGAGGAAAAGGTACCAAAACCAAAGTTGG-TGA
2640 GAAGAAG
65 GAAGAAG
*
2647 GAACCTGAAGAGGTACCCAAGGTGGAGAGTGTTGAGGAAAAGGTACCAGAACCAAAGTTGGTAGA
1 GAACCTGAAGAGGTACCCAAGGTGGAGAGTGTTGAGGAAAAGGTACCAAAACCAAAGTTGGT-GA
2712 GAAGAAG
65 GAAGAAG
* * * * * *
2719 AAACTTGAAGAGGCACCCAAGGGGGAGAGTGTTGAGGAAAA---AGC---AGCAAAGTTGGTTGA
1 GAACCTGAAGAGGTACCCAAGGTGGAGAGTGTTGAGGAAAAGGTACCAAAACCAAAGTTGG-TGA
* *
2778 AAAGAAA
65 GAAGAAG
* * * * *
2785 AAACTTGAAGAGGTACCCAAGGTGGAGAGTGTTGA-GAAGAAGGCACCAAAACCAAAGTTGATCA
1 GAACCTGAAGAGGTACCCAAGGTGGAGAGTGTTGAGGAA-AAGGTACCAAAACCAAAGTTGGT-G
*
2849 AGAAAAAG
64 AGAAGAAG
*** *
2857 GAACCTGAAGACACACCCAAGGTGGAGATTGTTGAGGAAAAGGTACCAAAACCAAAGTTGGTTGA
1 GAACCTGAAGAGGTACCCAAGGTGGAGAGTGTTGAGGAAAAGGTACCAAAACCAAAGTTGG-TGA
*
2922 GAAGGAG
65 GAAGAAG
* * * ** ** * *** * *
2929 GTACC-CAAG-GTGGA-GAAACCTGAAGAGAAATCCCAAGAGGAGAATGTTGAGGAAAAAGTAGC
1 GAACCTGAAGAG-GTACCCAAGGTG--GAG-AGT--GTTGAGGA-AA-----AGG---T---ACC
* *
2991 AAAACTAAAGTTGGTTGAGAAGAAA
48 AAAACCAAAGTTGG-TGAGAAGAAG
* * * * *
3016 AAACCTGAAGAGGTACACAAGGTGAAGAGTGTTGA-GAAGAAGGTACCAAAA-CAAAATTCGATT
1 GAACCTGAAGAGGTACCCAAGGTGGAGAGTGTTGAGGAA-AAGGTACCAAAACCAAAGTT-G-GT
*
3079 GAGAAGAAA
63 GAGAAGAAG
* * * * * *
3088 GAACCTAAAGACGCATCGAAGGGGGAGAGTGTTGAGGAAAAGGTACCAAAACCAAAGTTGGTCGA
1 GAACCTGAAGAGGTACCCAAGGTGGAGAGTGTTGAGGAAAAGGTACCAAAACCAAAGTTGGT-GA
3153 GAAGAAG
65 GAAGAAG
* * * * ** * **
3160 GAACTTGAAGTGATACCCAAGGTGGAGAGTGGTGA-GAAGAAGGTTTCAAAACCGAAGTTAATCG
1 GAACCTGAAGAGGTACCCAAGGTGGAGAGTGTTGAGGAA-AAGGTACCAAAACCAAAGTTGGT-G
* *
3224 AGGAGGAG
64 AGAAGAAG
* * * * * * * * *
3232 GAAACTGAGGACGCATCCAAGGGGGTGAGTGTTGAAGAAAAGGTATCAAAACCAAAGTTGGTTGA
1 GAACCTGAAGAGGTACCCAAGGTGGAGAGTGTTGAGGAAAAGGTACCAAAACCAAAGTTGG-TGA
3297 GAAGAAG
65 GAAGAAG
* * * *
3304 GAACCTGAAGAGGTACCCAAGGTGGAGACTGTTGAGAAAAAAGTACCAAAATCAAAGTTGGT---
1 GAACCTGAAGAGGTACCCAAGGTGGAGAGTGTTGAGGAAAAGGTACCAAAACCAAAGTTGGTGAG
3366 ------
66 AAGAAG
* * * * * *
3366 --TCCTGAAGAGGTACCCAAGGGGGAGATTGTTGAGAAAAAAGTACCAAAATCAAAGTTGGTTGA
1 GAACCTGAAGAGGTACCCAAGGTGGAGAGTGTTGAGGAAAAGGTACCAAAACCAAAGTTGG-TGA
*
3429 GAAAAAG
65 GAAGAAG
* * ** * *
3436 GAACCTGAAGAGATACCCAAGGTGGAGGGTGTTGA-GAAGAAATTACCAAAACCGAAGTTGATTG
1 GAACCTGAAGAGGTACCCAAGGTGGAGAGTGTTGAGGAA-AAGGTACCAAAACCAAAGTTG-GTG
3500 AGAAGAAG
64 AGAAGAAG
* * * * * * *
3508 GAACCTAAAGATGCACCCAAGG-GGAGAGTGTTGAGGAAAAGGAATCAAAACCAAATTTGGT-TG
1 GAACCTGAAGAGGTACCCAAGGTGGAGAGTGTTGAGGAAAAGGTACCAAAACCAAAGTTGGTGAG
3571 -AGAAG
66 AAGAAG
* ** * * *
3576 GAGCCT-AAGGAGGTACCCAAGGTGGAGACCGATGAGGAAAAGGTACCAAAACCAAATTTGGTTA
1 GAACCTGAA-GAGGTACCCAAGGTGGAGAGTGTTGAGGAAAAGGTACCAAAACCAAAGTTGG-TG
3640 AGAAGAAG
64 AGAAGAAG
* * * * * * * *
3648 AAACCT-AATGAGGCACCCAAGGAGGAGAGGGTTCAGGAAAAAGTACCAAAATCAAAGTTAGTTG
1 GAACCTGAA-GAGGTACCCAAGGTGGAGAGTGTTGAGGAAAAGGTACCAAAACCAAAGTT-GGTG
3712 AGAAGAAG
64 AGAAGAAG
* * * * *** *
3720 GAACTTGAAGAGATACCTAAGGTGGAGAGTATTGA-GAAGAAGGTATGGAAACCAAAGTTGATTG
1 GAACCTGAAGAGGTACCCAAGGTGGAGAGTGTTGAGGAA-AAGGTACCAAAACCAAAGTTG-GTG
3784 AGAAGAAG
64 AGAAGAAG
* * * ** * * * * * *
3792 GAACTTGAAGACGCACCCAAGAAGGGGAATGTTGAGGAAAATGTACCAAAATCAAGGCTGGTTGA
1 GAACCTGAAGAGGTACCCAAGGTGGAGAGTGTTGAGGAAAAGGTACCAAAACCAAAGTTGG-TGA
*
3857 -AACTAAG
65 GAA-GAAG
* * *
3864 GAACCTGAAGAGGAACCCAAAGG-GGAGAGTATTGAGGAAAAGGTACCAAAACTAAAGTTGGTTG
1 GAACCTGAAGAGGTACCC-AAGGTGGAGAGTGTTGAGGAAAAGGTACCAAAACCAAAGTTGG-TG
3928 AGAAGAAG
64 AGAAGAAG
* * * *
3936 GAACCTGGAA-AGGCAACCAAGGAGGAGAGTCTTGAGGAAAAGGTACCAAAACCAAAGTTGGTTG
1 GAACCT-GAAGAGGTACCCAAGGTGGAGAGTGTTGAGGAAAAGGTACCAAAACCAAAGTTGG-TG
* *
4000 AAAATAAG
64 AGAAGAAG
*
4008 GAACTTGAAGAGGTA
1 GAACCTGAAGAGGTA
4023 TCTAAGGAGA
Statistics
Matches: 1250, Mismatches: 260, Indels: 158
0.75 0.16 0.09
Matches are distributed among these distances:
60 56 0.04
61 1 0.00
65 3 0.00
66 52 0.04
67 3 0.00
68 21 0.02
69 91 0.07
70 9 0.01
71 62 0.05
72 859 0.69
73 33 0.03
75 5 0.00
76 2 0.00
78 3 0.00
81 3 0.00
82 1 0.00
83 3 0.00
84 2 0.00
86 2 0.00
87 29 0.02
88 5 0.00
89 5 0.00
ACGTcount: A:0.41, C:0.12, G:0.31, T:0.16
Consensus pattern (71 bp):
GAACCTGAAGAGGTACCCAAGGTGGAGAGTGTTGAGGAAAAGGTACCAAAACCAAAGTTGGTGAG
AAGAAG
Found at i:3380 original size:60 final size:60
Alignment explanation
Indices: 3307--3426 Score: 222
Period size: 60 Copynumber: 2.0 Consensus size: 60
3297 GAAGAAGGAA
*
3307 CCTGAAGAGGTACCCAAGGTGGAGACTGTTGAGAAAAAAGTACCAAAATCAAAGTTGGTT
1 CCTGAAGAGGTACCCAAGGGGGAGACTGTTGAGAAAAAAGTACCAAAATCAAAGTTGGTT
*
3367 CCTGAAGAGGTACCCAAGGGGGAGATTGTTGAGAAAAAAGTACCAAAATCAAAGTTGGTT
1 CCTGAAGAGGTACCCAAGGGGGAGACTGTTGAGAAAAAAGTACCAAAATCAAAGTTGGTT
3427 GAGAAAAAGG
Statistics
Matches: 58, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
60 58 1.00
ACGTcount: A:0.38, C:0.14, G:0.28, T:0.20
Consensus pattern (60 bp):
CCTGAAGAGGTACCCAAGGGGGAGACTGTTGAGAAAAAAGTACCAAAATCAAAGTTGGTT
Found at i:3485 original size:132 final size:132
Alignment explanation
Indices: 3248--3495 Score: 363
Period size: 132 Copynumber: 1.9 Consensus size: 132
3238 GAGGACGCAT
* * * *
3248 CCAAGGGGGTGAGTGTTGAAGAAAAGGTATCAAAACCAAAGTTGGTTGAGAAGAAGGAACCTGAA
1 CCAAGGGGGAGAGTGTTGAAGAAAAAGTACCAAAACCAAAGTTGGTTGAGAAAAAGGAACCTGAA
* *
3313 GAGGTACCCAAGGTGGAGACTGTTGAGAAAAAAGTACCAAAATCAAAGTTGGTTCCTGAAGAGGT
66 GAGATACCCAAGGTGGAGACTGTTGAGAAAAAAGTACCAAAACCAAAGTTGGTTCCTGAAGAGGT
3378 AC
131 AC
* *
3380 CCAAGGGGGAGATTGTTG-AGAAAAAAGTACCAAAATCAAAGTTGGTTGAGAAAAAGGAACCTGA
1 CCAAGGGGGAGAGTGTTGAAG-AAAAAGTACCAAAACCAAAGTTGGTTGAGAAAAAGGAACCTGA
** * * *
3444 AGAGATACCCAAGGTGGAGGGTGTTGAGAAGAAATTACCAAAACCGAAGTTG
65 AGAGATACCCAAGGTGGAGACTGTTGAGAAAAAAGTACCAAAACCAAAGTTG
3496 ATTGAGAAGA
Statistics
Matches: 102, Mismatches: 13, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
131 2 0.02
132 100 0.98
ACGTcount: A:0.40, C:0.12, G:0.30, T:0.18
Consensus pattern (132 bp):
CCAAGGGGGAGAGTGTTGAAGAAAAAGTACCAAAACCAAAGTTGGTTGAGAAAAAGGAACCTGAA
GAGATACCCAAGGTGGAGACTGTTGAGAAAAAAGTACCAAAACCAAAGTTGGTTCCTGAAGAGGT
AC
Done.