Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold1518
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, 969
Length: 1616
ACGTcount: A:0.24, C:0.18, G:0.29, T:0.30
Found at i:68 original size:46 final size:46
Alignment explanation
Indices: 1--1193 Score: 1577
Period size: 46 Copynumber: 25.9 Consensus size: 46
* * *
1 CGAAGATGGCAGATCTTGTCTTCCTGTATTTGCCAGCGGAGGAGAT
1 CGAAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGGGGAT
* * * *
47 CGAAGATAGAAGATCTTGTCTTCTTGAATTTGGCAGCGGAAGGGAT
1 CGAAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGGGGAT
* * * *
93 CGAAGATATCAGATCTTGTCTTCCTGTCTTTGGCCGCGGATGGGAT
1 CGAAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGGGGAT
* * * *
139 CGAAGATATCAGATCTTGTCTTCCTGTCTTTGGCCGCGGATGGGAT
1 CGAAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGGGGAT
* * * *
185 CGAAGATATCAGATCTTGTCTTCCTGTCTTTGGCCGCGGATGGGAT
1 CGAAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGGGGAT
* * * *
231 CGAAGATATCAGATCTTGTCTTCCTGTCTTTGGCCGCGGATGGGAT
1 CGAAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGGGGAT
* * * *
277 CGAAGATATCAGATCTTGTCTTCCTGTCTTTGGCCGCGGATGGGAT
1 CGAAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGGGGAT
* * * *
323 CGAAGATATCAGATCTTGTCTTCCTGTCTTTGGCCGCGGATGGGAT
1 CGAAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGGGGAT
* *
369 CGAAGATATCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGGGGAA
1 CGAAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGGGGAT
* * *
415 CGAAGATATCAGATCTTGTCTTCCTGTCTTTGGCAGCGGATGGGAT
1 CGAAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGGGGAT
* *
461 CGAAGATATCAGATCTTGTCTTCCTATATTTGGCAGCGGAGGGGAT
1 CGAAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGGGGAT
* * *
507 CGAGGATACCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGGGGAA
1 CGAAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGGGGAT
* * * *
553 CGAAGATATCAGATCTTGTCTTCCTGTATTTGGCAGTGGAAGAGAT
1 CGAAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGGGGAT
* * * *
599 CGAAGATAGCAGATCTTATCTTCCTGTATTTGGCAGCAGAGGAGTT
1 CGAAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGGGGAT
* * *
645 CGAGGATAGCAGATCTGGTCTTCCTGTATATGGCAGCGGAGGGGAT
1 CGAAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGGGGAT
* * * * *
691 CGACGATAACAGATCTGGTCTTCCTGTGTTTGGCAGCGGAGGAGAT
1 CGAAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGGGGAT
* *
737 CGAAGATAGCAGTTCTTGTCTTCCTGTATCTT-GCAGAGGAGGGGAT
1 CGAAGATAGCAGATCTTGTCTTCCTGTAT-TTGGCAGCGGAGGGGAT
* * * *
783 CGAAGATAGCAAATCTTGTCTTCCTATATTTGGCAGCGGAAGAGAT
1 CGAAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGGGGAT
829 CGAAGATA-CTAGATCTTGTCTTCCTGTATTTGGCAG-GAGAGGGGAT
1 CGAAGATAGC-AGATCTTGTCTTCCTGTATTTGGCAGCG-GAGGGGAT
* * * *
875 CGAAGATATCAGATCATGTCTTCCTGTATTTGGCAGCGAAGGAGAT
1 CGAAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGGGGAT
** * * *
921 TAAAGATAGCAGATCATGTTTTCCTGTATTTGGCAGCAGAGGGGAT
1 CGAAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGGGGAT
*
967 CGGACAGA-A-CAGATCTTGTCTTCCTGTATTTGGCAGCGGAGGAGAT
1 C-GA-AGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGGGGAT
*
1013 CGAAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGAAGGGGAT
1 CGAAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGGGGAT
*
1059 CGAAGATAGCAGATCTTGTCTTCCTATATTTGGCAGCGGAGGGGAT
1 CGAAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGGGGAT
* * *
1105 CGAAGATAGCAGACCTTGTCTTCCAGTATTTGGCAGCGGAGGAGAT
1 CGAAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGGGGAT
* * *
1151 CAAAGACAGCAGATCTTGTCTTCCTGTATTTGGCAGCAGAGGG
1 CGAAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGGG
1194 TGTCTTCCTG
Statistics
Matches: 1038, Mismatches: 99, Indels: 20
0.90 0.09 0.02
Matches are distributed among these distances:
44 3 0.00
45 7 0.01
46 1019 0.98
47 6 0.01
48 3 0.00
ACGTcount: A:0.23, C:0.19, G:0.29, T:0.29
Consensus pattern (46 bp):
CGAAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGGGGAT
Found at i:249 original size:138 final size:137
Alignment explanation
Indices: 1--1616 Score: 1655
Period size: 138 Copynumber: 11.5 Consensus size: 137
** * *
1 CGAAGATGGCAGATCTTGTCTTCCTGTATTTGCCAGCGGAGGAGATCGAAGATAGAAGATCTTGT
1 CGAAGATATCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGG-GATCGAAGATAGCAGATCTTGT
* * * * * *
66 CTTCTTGAATTTGGCAGCGGAAGGGATCGAAGATATCAGATCTTGTCTTCCTGTCTTTGGCCGCG
65 CTTCCTGTATTTGGCAGCGGAGGGGATCGAAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCG
*
131 GATGGGAT
130 GAGGGGAT
* * *
139 CGAAGATATCAGATCTTGTCTTCCTGTCTTTGGCCGCGGATGGGATCGAAGATATCAGATCTTGT
1 CGAAGATATCAGATCTTGTCTTCCTGTATTTGGCAGCGGA-GGGATCGAAGATAGCAGATCTTGT
* * * * * *
204 CTTCCTGTCTTTGGCCGCGGATGGGATCGAAGATATCAGATCTTGTCTTCCTGTCTTTGGCCGCG
65 CTTCCTGTATTTGGCAGCGGAGGGGATCGAAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCG
*
269 GATGGGAT
130 GAGGGGAT
* * *
277 CGAAGATATCAGATCTTGTCTTCCTGTCTTTGGCCGCGGATGGGATCGAAGATATCAGATCTTGT
1 CGAAGATATCAGATCTTGTCTTCCTGTATTTGGCAGCGGA-GGGATCGAAGATAGCAGATCTTGT
* * * *
342 CTTCCTGTCTTTGGCCGCGGATGGGATCGAAGATATCAGATCTTGTCTTCCTGTATTTGGCAGCG
65 CTTCCTGTATTTGGCAGCGGAGGGGATCGAAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCG
*
407 GAGGGGAA
130 GAGGGGAT
* *
415 CGAAGATATCAGATCTTGTCTTCCTGTCTTTGGCAGCGGATGGGATCGAAGATATCAGATCTTGT
1 CGAAGATATCAGATCTTGTCTTCCTGTATTTGGCAGCGGA-GGGATCGAAGATAGCAGATCTTGT
* * *
480 CTTCCTATATTTGGCAGCGGAGGGGATCGAGGATACCAGATCTTGTCTTCCTGTATTTGGCAGCG
65 CTTCCTGTATTTGGCAGCGGAGGGGATCGAAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCG
*
545 GAGGGGAA
130 GAGGGGAT
* * *
553 CGAAGATATCAGATCTTGTCTTCCTGTATTTGGCAGTGGAAGAGATCGAAGATAGCAGATCTTAT
1 CGAAGATATCAGATCTTGTCTTCCTGTATTTGGCAGCGG-AGGGATCGAAGATAGCAGATCTTGT
* * * * * *
618 CTTCCTGTATTTGGCAGCAGAGGAGTTCGAGGATAGCAGATCTGGTCTTCCTGTATATGGCAGCG
65 CTTCCTGTATTTGGCAGCGGAGGGGATCGAAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCG
683 GAGGGGAT
130 GAGGGGAT
* * * * *
691 CGACGATAACAGATCTGGTCTTCCTGTGTTTGGCAGCGGAGGAGATCGAAGATAGCAGTTCTTGT
1 CGAAGATATCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGG-GATCGAAGATAGCAGATCTTGT
* * *
756 CTTCCTGTATCTT-GCAGAGGAGGGGATCGAAGATAGCAAATCTTGTCTTCCTATATTTGGCAGC
65 CTTCCTGTAT-TTGGCAGCGGAGGGGATCGAAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGC
* *
820 GGAAGAGAT
129 GGAGGGGAT
* *
829 CGAAGATA-CTAGATCTTGTCTTCCTGTATTTGGCAG-GAGAGGGGATCGAAGATATCAGATCAT
1 CGAAGATATC-AGATCTTGTCTTCCTGTATTTGGCAGCG-GA-GGGATCGAAGATAGCAGATCTT
* * ** * *
892 GTCTTCCTGTATTTGGCAGCGAAGGAGATTAAAGATAGCAGATCATGTTTTCCTGTATTTGGCAG
63 GTCTTCCTGTATTTGGCAGCGGAGGGGATCGAAGATAGCAGATCTTGTCTTCCTGTATTTGGCAG
*
957 CAGAGGGGAT
128 CGGAGGGGAT
967 CGGACAGA-A-CAGATCTTGTCTTCCTGTATTTGGCAGCGGAGGAGATCGAAGATAGCAGATCTT
1 C-GA-AGATATCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGG-GATCGAAGATAGCAGATCTT
* *
1030 GTCTTCCTGTATTTGGCAGCGAAGGGGATCGAAGATAGCAGATCTTGTCTTCCTATATTTGGCAG
63 GTCTTCCTGTATTTGGCAGCGGAGGGGATCGAAGATAGCAGATCTTGTCTTCCTGTATTTGGCAG
1095 CGGAGGGGAT
128 CGGAGGGGAT
* * * * *
1105 CGAAGATAGCAGACCTTGTCTTCCAGTATTTGGCAGCGGAGGAGATCAAAGACAGCAGATCTTGT
1 CGAAGATATCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGG-GATCGAAGATAGCAGATCTTGT
* * ** * ** *** **
1170 CTTCCTGTATTTGGCAGCAGAGGGTGTCTTCCTGAATTTGGCAACGAAAGGGATTGAAGATATTA
65 CTTCCTGTATTTGGCAGCGGAGGG-G--AT-C-GAAGATAGC-A-G--A--TCTTG-TCTTCCT-
* ** * **
1235 G-ATCTTGTCTTCCTGTATTTGG--
117 GTAT-TTGGC-AGC-GGA-GGGGAT
** **** * * * * *
1257 CAGCGGAGGGGATCGAAGATAGCAGATCTTGTCTTCCTGAATTTGGCAACGAAAGGGATTGAAGA
1 C-GAAGATATCA-G-----------ATCTTGTCTTCCTGTATTTGGCAGCG-GAGGGATCGAAGA
**
1322 TATTAGATCTTGTCTTCCTGTATTTGGCAGCGGAGGGGATCGAAGATAGCAGATCTTGTCTTCCT
52 TAGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGGGGATCGAAGATAGCAGATCTTGTCTTCCT
* * * *
1387 GAATTTGGCAACGAAAGGGAT
117 GTATTTGGCAGCGGAGGGGAT
* *
1408 TGAAGATATTAGATCTTGTCTTCCTGTATTTGGCAGCGGAGGGGATCGAAGATAGCAGATCTTGT
1 CGAAGATATCAGATCTTGTCTTCCTGTATTTGGCAGCGGA-GGGATCGAAGATAGCAGATCTTGT
* * * * * **
1473 CTTCCTGAATTTGGCAACGAAAGGGATTGAAGATATTAGATCTTGTCTTCCTGTATTTGGCAGCG
65 CTTCCTGTATTTGGCAGCGGAGGGGATCGAAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCG
1538 GAGGGGAT
130 GAGGGGAT
* * ** * * **
1546 CGAAGATAGCAGATCTTGTCTTCCTGAAACTGGCAGCGAAAGGGATTGAAGATATTAGATCTTGT
1 CGAAGATATCAGATCTTGTCTTCCTGTATTTGGCAGCG-GAGGGATCGAAGATAGCAGATCTTGT
1611 CTTCCT
65 CTTCCT
Statistics
Matches: 1253, Mismatches: 175, Indels: 100
0.82 0.11 0.07
Matches are distributed among these distances:
136 3 0.00
137 12 0.01
138 1090 0.87
139 14 0.01
140 3 0.00
141 1 0.00
142 1 0.00
143 6 0.00
144 1 0.00
145 1 0.00
147 1 0.00
149 5 0.00
150 10 0.01
151 5 0.00
152 7 0.01
153 11 0.01
154 5 0.00
156 1 0.00
158 1 0.00
159 1 0.00
160 6 0.00
161 1 0.00
162 1 0.00
164 1 0.00
165 62 0.05
166 3 0.00
ACGTcount: A:0.24, C:0.18, G:0.29, T:0.30
Consensus pattern (137 bp):
CGAAGATATCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGGGATCGAAGATAGCAGATCTTGTC
TTCCTGTATTTGGCAGCGGAGGGGATCGAAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGG
AGGGGAT
Found at i:1269 original size:46 final size:46
Alignment explanation
Indices: 1194--1616 Score: 576
Period size: 46 Copynumber: 9.2 Consensus size: 46
1184 CAGCAGAGGG
*
1194 TGTCTTCCTGAATTTGGCAACGAAAGGGATTGAAGATATTAGATCT
1 TGTCTTCCTGAATTTGGCAGCGAAAGGGATTGAAGATATTAGATCT
* * * * **
1240 TGTCTTCCTGTATTTGGCAGCGGAGGGGATCGAAGATAGCAGATCT
1 TGTCTTCCTGAATTTGGCAGCGAAAGGGATTGAAGATATTAGATCT
*
1286 TGTCTTCCTGAATTTGGCAACGAAAGGGATTGAAGATATTAGATCT
1 TGTCTTCCTGAATTTGGCAGCGAAAGGGATTGAAGATATTAGATCT
* * * * **
1332 TGTCTTCCTGTATTTGGCAGCGGAGGGGATCGAAGATAGCAGATCT
1 TGTCTTCCTGAATTTGGCAGCGAAAGGGATTGAAGATATTAGATCT
*
1378 TGTCTTCCTGAATTTGGCAACGAAAGGGATTGAAGATATTAGATCT
1 TGTCTTCCTGAATTTGGCAGCGAAAGGGATTGAAGATATTAGATCT
* * * * **
1424 TGTCTTCCTGTATTTGGCAGCGGAGGGGATCGAAGATAGCAGATCT
1 TGTCTTCCTGAATTTGGCAGCGAAAGGGATTGAAGATATTAGATCT
*
1470 TGTCTTCCTGAATTTGGCAACGAAAGGGATTGAAGATATTAGATCT
1 TGTCTTCCTGAATTTGGCAGCGAAAGGGATTGAAGATATTAGATCT
* * * * **
1516 TGTCTTCCTGTATTTGGCAGCGGAGGGGATCGAAGATAGCAGATCT
1 TGTCTTCCTGAATTTGGCAGCGAAAGGGATTGAAGATATTAGATCT
**
1562 TGTCTTCCTGAAACTGGCAGCGAAAGGGATTGAAGATATTAGATCT
1 TGTCTTCCTGAATTTGGCAGCGAAAGGGATTGAAGATATTAGATCT
1608 TGTCTTCCT
1 TGTCTTCCT
Statistics
Matches: 320, Mismatches: 57, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
46 320 1.00
ACGTcount: A:0.26, C:0.16, G:0.28, T:0.31
Consensus pattern (46 bp):
TGTCTTCCTGAATTTGGCAGCGAAAGGGATTGAAGATATTAGATCT
Found at i:1281 original size:119 final size:119
Alignment explanation
Indices: 1075--1304 Score: 336
Period size: 119 Copynumber: 1.9 Consensus size: 119
1065 TAGCAGATCT
* * *
1075 TGTCTTCCTATATTTGGCAGCGGAGGGGATCGAAGATAGCAGACCTTGTCTTCCAGTATTTGGCA
1 TGTCTTCCTATATTTGGCAACGAAAGGGATCGAAGATAGCAGACCTTGTCTTCCAGTATTTGGCA
*
1140 GCGGAGGAGATCAAAGACAGCAGATCTTGTCTTCCTGTATTTGGCAGCAGAGGG
66 GCGGAGGAGATCAAAGACAGCAGATCTTGTCTTCCTGAATTTGGCAGCAGAGGG
* ** * *
1194 TGTCTTCCTGA-ATTTGGCAACGAAAGGGATTGAAGATATTAGATCTTGTCTTCCTGTATTTGGC
1 TGTCTTCCT-ATATTTGGCAACGAAAGGGATCGAAGATAGCAGACCTTGTCTTCCAGTATTTGGC
* * *
1258 AGCGGAGGGGATCGAAGATAGCAGATCTTGTCTTCCTGAATTTGGCA
65 AGCGGAGGAGATCAAAGACAGCAGATCTTGTCTTCCTGAATTTGGCA
1305 ACGAAAGGGA
Statistics
Matches: 98, Mismatches: 12, Indels: 2
0.88 0.11 0.02
Matches are distributed among these distances:
119 97 0.99
120 1 0.01
ACGTcount: A:0.24, C:0.18, G:0.29, T:0.30
Consensus pattern (119 bp):
TGTCTTCCTATATTTGGCAACGAAAGGGATCGAAGATAGCAGACCTTGTCTTCCAGTATTTGGCA
GCGGAGGAGATCAAAGACAGCAGATCTTGTCTTCCTGAATTTGGCAGCAGAGGG
Found at i:1303 original size:165 final size:165
Alignment explanation
Indices: 1029--1542 Score: 501
Period size: 165 Copynumber: 3.0 Consensus size: 165
1019 TAGCAGATCT
* * *
1029 TGTCTTCCTGTATTTGGCAGCGAAGGGGATCGAAGATAGCAGATCTTGTCTTCCTATATTTGGCA
1 TGTCTTCCTGAATTTGGCAACGAAAGGGATCGAAGATAGCAGATCTTGTCTTCCTATATTTGGCA
* * *
1094 GCGGAGGGGATCGAAGATAGCAGACCTTGTCTTCCAGTATTTGGCAGCG-GAGGAGATCAAAGAC
66 GCGGAGGGGATCGAAGATAGCAGACCTTGTCTTCCAGAATTTGGCAACGAAAGG-GATCAAAGAC
1158 AGCAGATCTTGTCTTCCTGTATTTGGCAGCAGAGGG
130 AGCAGATCTTGTCTTCCTGTATTTGGCAGCAGAGGG
* ** *
1194 TGTCTTCCTGAATTTGGCAACGAAAGGGATTGAAGATATTAGATCTTGTCTTCCTGTATTTGGCA
1 TGTCTTCCTGAATTTGGCAACGAAAGGGATCGAAGATAGCAGATCTTGTCTTCCTATATTTGGCA
* * ** *
1259 GCGGAGGGGATCGAAGATAGCAGATCTTGTCTTCCTGAATTTGGCAACGAAAGGGATTGAAGATA
66 GCGGAGGGGATCGAAGATAGCAGACCTTGTCTTCCAGAATTTGGCAACGAAAGGGATCAAAGACA
** *
1324 TTAGATCTTGTCTTCCTGTATTTGGCAGCGGAGGG
131 GCAGATCTTGTCTTCCTGTATTTGGCAGCAGAGGG
**** * * * **
1359 -GATCGAAGATAGCAGATCTTGTCTTCCTGAATTTGGCAACGAAAGGGATTGAAGATATTAGATC
1 TG-TC-TTCCT-G-A-AT-TTG----GC--AA-----CGA--AA-GGGATCGAAGATAGCAGATC
* * *
1423 TTGTCTTCCTGTATTTGGCAGCGGAGGGGATCGAAGATAGCAGATCTTGTCTTCCTGAATTTGGC
46 TTGTCTTCCTATATTTGGCAGCGGAGGGGATCGAAGATAGCAGACCTTGTCTTCCAGAATTTGGC
** * ** *
1488 AACGAAAGGGATTGAAGATATTAGATCTTGTCTTCCTGTATTTGGCAGCGGAGGG
111 AACGAAAGGGATCAAAGACAGCAGATCTTGTCTTCCTGTATTTGGCAGCAGAGGG
1543 GATCGAAGAT
Statistics
Matches: 304, Mismatches: 24, Indels: 23
0.87 0.07 0.07
Matches are distributed among these distances:
164 1 0.00
165 145 0.48
166 4 0.01
167 1 0.00
168 1 0.00
169 2 0.01
170 3 0.01
174 1 0.00
176 2 0.01
181 2 0.01
183 2 0.01
184 140 0.46
ACGTcount: A:0.25, C:0.16, G:0.29, T:0.30
Consensus pattern (165 bp):
TGTCTTCCTGAATTTGGCAACGAAAGGGATCGAAGATAGCAGATCTTGTCTTCCTATATTTGGCA
GCGGAGGGGATCGAAGATAGCAGACCTTGTCTTCCAGAATTTGGCAACGAAAGGGATCAAAGACA
GCAGATCTTGTCTTCCTGTATTTGGCAGCAGAGGG
Found at i:1342 original size:92 final size:92
Alignment explanation
Indices: 1194--1616 Score: 819
Period size: 92 Copynumber: 4.6 Consensus size: 92
1184 CAGCAGAGGG
1194 TGTCTTCCTGAATTTGGCAACGAAAGGGATTGAAGATATTAGATCTTGTCTTCCTGTATTTGGCA
1 TGTCTTCCTGAATTTGGCAACGAAAGGGATTGAAGATATTAGATCTTGTCTTCCTGTATTTGGCA
1259 GCGGAGGGGATCGAAGATAGCAGATCT
66 GCGGAGGGGATCGAAGATAGCAGATCT
1286 TGTCTTCCTGAATTTGGCAACGAAAGGGATTGAAGATATTAGATCTTGTCTTCCTGTATTTGGCA
1 TGTCTTCCTGAATTTGGCAACGAAAGGGATTGAAGATATTAGATCTTGTCTTCCTGTATTTGGCA
1351 GCGGAGGGGATCGAAGATAGCAGATCT
66 GCGGAGGGGATCGAAGATAGCAGATCT
1378 TGTCTTCCTGAATTTGGCAACGAAAGGGATTGAAGATATTAGATCTTGTCTTCCTGTATTTGGCA
1 TGTCTTCCTGAATTTGGCAACGAAAGGGATTGAAGATATTAGATCTTGTCTTCCTGTATTTGGCA
1443 GCGGAGGGGATCGAAGATAGCAGATCT
66 GCGGAGGGGATCGAAGATAGCAGATCT
1470 TGTCTTCCTGAATTTGGCAACGAAAGGGATTGAAGATATTAGATCTTGTCTTCCTGTATTTGGCA
1 TGTCTTCCTGAATTTGGCAACGAAAGGGATTGAAGATATTAGATCTTGTCTTCCTGTATTTGGCA
1535 GCGGAGGGGATCGAAGATAGCAGATCT
66 GCGGAGGGGATCGAAGATAGCAGATCT
** *
1562 TGTCTTCCTGAAACTGGCAGCGAAAGGGATTGAAGATATTAGATCTTGTCTTCCT
1 TGTCTTCCTGAATTTGGCAACGAAAGGGATTGAAGATATTAGATCTTGTCTTCCT
Statistics
Matches: 328, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
92 328 1.00
ACGTcount: A:0.26, C:0.16, G:0.28, T:0.31
Consensus pattern (92 bp):
TGTCTTCCTGAATTTGGCAACGAAAGGGATTGAAGATATTAGATCTTGTCTTCCTGTATTTGGCA
GCGGAGGGGATCGAAGATAGCAGATCT
Found at i:1347 original size:211 final size:211
Alignment explanation
Indices: 983--1569 Score: 656
Period size: 211 Copynumber: 2.7 Consensus size: 211
973 GAACAGATCT
* * *
983 TGTCTTCCTGTATTTGGCAGCGGAGGAGATCGAAGATAGCAGATCTTGTCTTCCTGTATTTGGCA
1 TGTCTTCCTGAATTTGGCAACGAAGGAGATCGAAGATAGCAGATCTTGTCTTCCTGTATTTGGCA
* * *
1048 GCGAAGGGGATCGAAGATAGCAGATCTTGTCTTCCTATATTTGGCAGCGGAGGGGATCGAAGATA
66 GCGAAGGGGATCGAAGATAGCAGATCTTGTCTTCCTATATTTGGCAACGAAAGGGATCGAAGATA
*
1113 GCAGACCTTGTCTTCCAGTATTTGGCAGCGGAGGAGATCAAAGACAGCAGATCTTGTCTTCCTGT
131 GCAGACCTTGTCTTCCAGTATTTGGCAGCGGAGGAGATCAAAGACAGCAGATCTTGTCTTCCTGA
1178 ATTTGGCAGCAGAGGG
196 ATTTGGCAGCAGAGGG
* **
1194 TGTCTTCCTGAATTTGGCAACGAAAGG-GATTGAAGATATTAGATCTTGTCTTCCTGTATTTGGC
1 TGTCTTCCTGAATTTGGCAACG-AAGGAGATCGAAGATAGCAGATCTTGTCTTCCTGTATTTGGC
* *
1258 AGCGGAGGGGATCGAAGATAGCAGATCTTGTCTTCCTGA-ATTTGGCAACGAAAGGGATTGAAGA
65 AGCGAAGGGGATCGAAGATAGCAGATCTTGTCTTCCT-ATATTTGGCAACGAAAGGGATCGAAGA
** * * * * *
1322 TATTAGATCTTGTCTTCCTGTATTTGGCAGCGGAGGGGATCGAAGATAGCAGATCTTGTCTTCCT
129 TAGCAGACCTTGTCTTCCAGTATTTGGCAGCGGAGGAGATCAAAGACAGCAGATCTTGTCTTCCT
*
1387 GAATTTGGCAACGAAAGGGATTGAAGATATTAG
194 GAATTTGGC-A-G-CA--GA--G--G------G
* * * * *
1420 ATCTTGTCTTCCTGTATTTGGCAGCGGAGGGGATCGAAGATAGCAGATCTTGTCTTCCTGAATTT
1 ----TGTCTTCCTGAATTTGGCAACGAAGGAGATCGAAGATAGCAGATCTTGTCTTCCTGTATTT
* * * ** * * * *
1485 GGCAACGAAAGGGATTGAAGATATTAGATCTTGTCTTCCTGTATTTGGCAGCGGAGGGGATCGAA
62 GGCAGCGAAGGGGATCGAAGATAGCAGATCTTGTCTTCCTATATTTGGCAACGAAAGGGATCGAA
*
1550 GATAGCAGATCTTGTCTTCC
127 GATAGCAGACCTTGTCTTCC
1570 TGAAACTGGC
Statistics
Matches: 313, Mismatches: 40, Indels: 27
0.82 0.11 0.07
Matches are distributed among these distances:
211 177 0.57
212 5 0.02
213 1 0.00
214 1 0.00
216 2 0.01
218 1 0.00
220 1 0.00
226 1 0.00
229 3 0.01
230 121 0.39
ACGTcount: A:0.25, C:0.17, G:0.29, T:0.30
Consensus pattern (211 bp):
TGTCTTCCTGAATTTGGCAACGAAGGAGATCGAAGATAGCAGATCTTGTCTTCCTGTATTTGGCA
GCGAAGGGGATCGAAGATAGCAGATCTTGTCTTCCTATATTTGGCAACGAAAGGGATCGAAGATA
GCAGACCTTGTCTTCCAGTATTTGGCAGCGGAGGAGATCAAAGACAGCAGATCTTGTCTTCCTGA
ATTTGGCAGCAGAGGG
Done.