Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold6529.1
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: 11220
ACGTcount: A:0.29, C:0.21, G:0.19, T:0.31
Found at i:83 original size:30 final size:30
Alignment explanation
Indices: 4--104 Score: 114
Period size: 30 Copynumber: 3.4 Consensus size: 30
1 CAA
* * **
4 GTGTGGTTAGTGGAGTAGGTAATGGAGCAA-
1 GTGTGGCTAGTGGAGTTGGTGGTGGAG-AAG
*
34 GTGTGGCTAGTGGATTTGGTGGTGGAGAAG
1 GTGTGGCTAGTGGAGTTGGTGGTGGAGAAG
*
64 GTGTGGCTAGTGGAGTTGGTGGTGGAAAAG
1 GTGTGGCTAGTGGAGTTGGTGGTGGAGAAG
**
94 AAGTGGCTAGT
1 GTGTGGCTAGT
105 TGAGAAAAGT
Statistics
Matches: 61, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
29 2 0.03
30 59 0.97
ACGTcount: A:0.22, C:0.04, G:0.47, T:0.28
Consensus pattern (30 bp):
GTGTGGCTAGTGGAGTTGGTGGTGGAGAAG
Found at i:810 original size:30 final size:30
Alignment explanation
Indices: 774--834 Score: 97
Period size: 30 Copynumber: 2.0 Consensus size: 30
764 TTTGAAAAAT
774 AGAAATT-AAAAGACTCAACTCAACTCTCGC
1 AGAAATTAAAAAG-CTCAACTCAACTCTCGC
*
804 AGAAATTAAAAAGCTCAACTCACCTCTCGC
1 AGAAATTAAAAAGCTCAACTCAACTCTCGC
834 A
1 A
835 ATATGAGTTG
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
30 24 0.83
31 5 0.17
ACGTcount: A:0.43, C:0.28, G:0.10, T:0.20
Consensus pattern (30 bp):
AGAAATTAAAAAGCTCAACTCAACTCTCGC
Found at i:1156 original size:77 final size:77
Alignment explanation
Indices: 957--1197 Score: 266
Period size: 79 Copynumber: 3.1 Consensus size: 77
947 AAAATAGATT
* ** * * * * *
957 TTGAAAATACCTCGACATGTGACCCGAGGCTCAACTCACATCTCGCAATGTAAGTTAATTTTTTT
1 TTGAAAATACCTCAACGCGTGAGCCAAGGCTCAACTCACCTCTCGCAATATGAGTTAATTTTTTT
* * *
1022 GAAAAATATAAA
66 GAAAGACAGAAA
* * * * *
1034 TTGAAAAAATACCTCAATGTGTGATCTAAAGCTCAACTCACCTCTCGCAATATGAGTTAATTTTT
1 TTG--AAAATACCTCAACGCGTGAGCCAAGGCTCAACTCACCTCTCGCAATATGAGTTAATTTTT
1099 TTGAAAGACAGAAA
64 TTGAAAGACAGAAA
* * *
1113 TTGAAAATAGCTCAGCGCGTGAGCCAAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTT
1 TTGAAAATACCTCAACGCGTGAGCCAAGGCTCAACTCACCTCTCGCAATATGAGTT-AATTTTTT
* *
1178 TTAAAGGCAGAAA
65 TGAAAGACAGAAA
1191 TTGAAAA
1 TTGAAAA
1198 ACAGAAAATG
Statistics
Matches: 138, Mismatches: 23, Indels: 5
0.83 0.14 0.03
Matches are distributed among these distances:
77 49 0.36
78 25 0.18
79 64 0.46
ACGTcount: A:0.36, C:0.19, G:0.16, T:0.29
Consensus pattern (77 bp):
TTGAAAATACCTCAACGCGTGAGCCAAGGCTCAACTCACCTCTCGCAATATGAGTTAATTTTTTT
GAAAGACAGAAA
Found at i:1210 original size:92 final size:92
Alignment explanation
Indices: 1099--1269 Score: 227
Period size: 92 Copynumber: 1.9 Consensus size: 92
1089 GTTAATTTTT
* * * *
1099 TTGAAAGACAGAAATTGAAAATAGCTCAGCGCGTGAGCC-AAGGCTCAACTCACCTCTCGCAATA
1 TTGAAAAACAGAAAATGAAAATACCTCAGCGCGTGA-CCTAAGGCTCAACTCACCTCTCACAATA
* *
1163 TGAGTTGATTTTTTTTTAAAGGCAGAAA
65 CGAGTTGATTGTTTTTTAAAGGCAGAAA
** * * *
1191 TTGAAAAACAGAAAATGAAAATACCTTGGCGTGTGACCTGAGGCTCAACTCGCCTCTCACAATAC
1 TTGAAAAACAGAAAATGAAAATACCTCAGCGCGTGACCTAAGGCTCAACTCACCTCTCACAATAC
1256 GAGTTGATTGTTTT
66 GAGTTGATTGTTTT
1270 GACAACAGAA
Statistics
Matches: 67, Mismatches: 11, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
91 2 0.03
92 65 0.97
ACGTcount: A:0.33, C:0.19, G:0.20, T:0.27
Consensus pattern (92 bp):
TTGAAAAACAGAAAATGAAAATACCTCAGCGCGTGACCTAAGGCTCAACTCACCTCTCACAATAC
GAGTTGATTGTTTTTTAAAGGCAGAAA
Found at i:1353 original size:76 final size:76
Alignment explanation
Indices: 1191--1589 Score: 475
Period size: 76 Copynumber: 5.2 Consensus size: 76
1181 AAGGCAGAAA
* ** * * *
1191 TTGAAAAACAGAAAATGAAAATACCTTGGCGTGTGACCTGAGGCTCAACTCGCCTCTCACAATAC
1 TTGAAAAACAGAAATTGAAAATACCTCAGCGTGT--CCTGAGGCTCAACTCACCTCTCGCAATAT
*
1256 GAGTTGA-TTGTT
64 GAGTTGATTTTTT
* *
1268 TTG-ACAACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGA
1 TTGAAAAACAGAAATTGAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGA
1332 GTTGATTTTTT
66 GTTGATTTTTT
* ** ** *
1343 TTGAAAAACAGAAATTGAAAATACCTCAGCATGTTTTGAGGCTCAACTCATTTCTCACAATATGA
1 TTGAAAAACAGAAATTGAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGA
1408 GTTGATTTTTTT
66 GTTGA-TTTTTT
* * * * * *
1420 TTGAAGAACAGAAATTGAAAATACCTCGGCGTGTGACCTAAGGCTCAACTCGCCGCTCGCAATAC
1 TTGAAAAACAGAAATTGAAAATACCTCAGCGTGT--CCTGAGGCTCAACTCACCTCTCGCAATAT
1485 GAGTTGA-TTTTT
64 GAGTTGATTTTTT
* * *
1497 TTG-ACAACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTAGCAATATGA
1 TTGAAAAACAGAAATTGAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGA
*
1561 GTTCATTTTTT
66 GTTGATTTTTT
**
1572 TT-ATGAACAGAAATTGAA
1 TTGAAAAACAGAAATTGAA
1590 GAACAGAAAT
Statistics
Matches: 275, Mismatches: 40, Indels: 16
0.83 0.12 0.05
Matches are distributed among these distances:
74 63 0.23
75 27 0.10
76 110 0.40
77 48 0.17
79 27 0.10
ACGTcount: A:0.32, C:0.20, G:0.18, T:0.30
Consensus pattern (76 bp):
TTGAAAAACAGAAATTGAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGA
GTTGATTTTTT
Found at i:1506 original size:153 final size:152
Alignment explanation
Indices: 1191--2399 Score: 534
Period size: 182 Copynumber: 7.5 Consensus size: 152
1181 AAGGCAGAAA
* ** * * *
1191 TTGAAAAACAGAAAATGAAAATACCTTGGCGTGTGACCTGAGGCTCAACTCGCCTCTCACAATAC
1 TTGAAAAACAGAAATTGAAAATACCTCAGCATGT--CCTGAGGCTCAACTCACCTCTCACAATAT
* * * *
1256 GAGTTGA-TTGTTTTG-ACAACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACC
64 GAGTTGATTTTTTTTGAAGAACAGAAATTGAAAATACCTCAGCGTGTCCTAAGGCTCAACTCACC
* *
1319 TCTCGCAATATGAGTTGATTTTTT
129 GCTCGCAATACGAGTTGATTTTTT
** **
1343 TTGAAAAACAGAAATTGAAAATACCTCAGCATGTTTTGAGGCTCAACTCATTTCTCACAATATGA
1 TTGAAAAACAGAAATTGAAAATACCTCAGCATGTCCTGAGGCTCAACTCACCTCTCACAATATGA
* *
1408 GTTGATTTTTTTTTGAAGAACAGAAATTGAAAATACCTCGGCGTGTGACCTAAGGCTCAACTCGC
66 GTTGA-TTTTTTTTGAAGAACAGAAATTGAAAATACCTCAGCGTGT--CCTAAGGCTCAACTCAC
1473 CGCTCGCAATACGAGTTGA-TTTTT
128 CGCTCGCAATACGAGTTGATTTTTT
* * *
1497 TTG-ACAACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCT-AGCAATATG
1 TTGAAAAACAGAAATTGAAAATACCTCAGCATGTCCTGAGGCTCAACTCACCTCTCA-CAATATG
* * *
1560 AGTTCATTTTTTTTATGAACAGAAATTGAAGAACAGAAATTGAAAAGACCTCAGCATGTGAGCC-
65 AGTTGA---TTTTT-T---------TTGAAGAACAGAAATTGAAAATACCTCAGC--GTG-TCCT
* * * * *
1624 GAGGCTCAACTCACCTCTAGCAATATGAGTTCATTTTTTT
114 AAGGCTCAACTCACCGCTCGCAATACGAGTTGA-TTTTTT
*
1664 TATGAACAGAAATTGAAGAACAGAAATTGAAAAGACCTCAGCATGTGAGCC-GAGGCTCAACTCA
1 T-T-----G--A---AA-AACAGAAATTGAAAATACCTCAGCATGT---CCTGAGGCTCAACTCA
* *
1728 CCTCT-AGCAATATGAGTTCATTTTTTTTATGAACAGAAATTGAAGAACAGAAATTGAAAAGACC
51 CCTCTCA-CAATATGAGTTGA---TTTTT-T---------TTGAAGAACAGAAATTGAAAATACC
* * * * * *
1792 TCAGCATGTGAGCC-GAGGCTCAACTCACCTCTAGCAATATGAGTTCATTTTTTT
102 TCAGC--GTG-TCCTAAGGCTCAACTCACCGCTCGCAATACGAGTTGA-TTTTTT
* * *
1846 TATGAACAGAAATTGAAGAACAGAAATTGAAAAGACCTCAGCATGTGAGAC-GAGGCTCAAATCA
1 T-T-----G--A---AA-AACAGAAATTGAAAATACCTCAGCATGT---CCTGAGGCTCAACTCA
* * * * **
1910 CCTCTCGCAATATGAGTT-A--ATTTTTGACA-AACAGAAATTGAAATTACCTCAGCATGTCCCG
51 CCTCTCACAATATGAGTTGATTTTTTTTGA-AGAACAGAAATTGAAAATACCTCAGCGTGTCCTA
* * * *
1971 AGGCTCAACTCACCTCTCGCAATATGAGTCGATTTTTGAAAAACAGAAA
115 AGGCTCAACTCACCGCTCGCAATACGAGTTGATTTTT-----------T
* * * **
2020 TTGAAAACCAGAAATTGAAAATACCTCAGCGTGTGAGCC-AAGGCTCAACTCACCTCTTGCAATA
1 TTGAAAAACAGAAATTGAAAATACCTCAGCATGT---CCTGAGGCTCAACTCACCTCTCACAATA
* * * * * *
2084 TGAGCT-A--ATTTTTGATGAACATAAATT-AAAACCACCTCAGCGTGTCCTGAGGCTCAACTCA
63 TGAGTTGATTTTTTTTGAAGAACAGAAATTGAAAA-TACCTCAGCGTGTCCTAAGGCTCAACTCA
* *
2145 CCTCTCGCAATATGAGTTGA----TT
127 CCGCTCGCAATACGAGTTGATTTTTT
* * * * * *
2167 TTGACAAACAAAAATTGAAATTACCTCAGC--GTCTTGAGGCTCAACTCACTTCTCGCAATATGA
1 TTGAAAAACAGAAATTGAAAATACCTCAGCATGTCCTGAGGCTCAACTCACCTCTCACAATATGA
* * *
2230 GTTGATTTTTTTTGAAACATAAATTTAAAAAATGAAAATTGAAAATACCTCAGCGTGTCCTGAGG
66 GTTGATTTTTTTTG--------A---AGAACA-G-AAATTGAAAATACCTCAGCGTGTCCTAAGG
* * **
2295 CTCAACTCACCTCTCGCAATATGAGTTGA----AA
118 CTCAACTCACCGCTCGCAATACGAGTTGATTTTTT
* * ** * **
2326 TT-AAAACACAAAAATTGAAAATACCTCAGCGTACCCCGAGGCTCAACTCACCTCTTGCAATATG
1 TTGAAAA-ACAGAAATTGAAAATACCTCAGCATGTCCTGAGGCTCAACTCACCTCTCACAATATG
*
2390 AGCTGATTTT
65 AGTTGATTTT
2400 GAAAAAGTAG
Statistics
Matches: 888, Mismatches: 93, Indels: 143
0.79 0.08 0.13
Matches are distributed among these distances:
142 1 0.00
143 27 0.03
144 1 0.00
145 2 0.00
146 6 0.01
147 26 0.03
150 30 0.03
152 38 0.04
153 83 0.09
154 9 0.01
155 38 0.04
156 1 0.00
157 3 0.00
158 4 0.00
159 77 0.09
160 4 0.00
161 38 0.04
162 119 0.13
163 9 0.01
164 32 0.04
165 55 0.06
166 29 0.03
167 10 0.01
168 2 0.00
173 2 0.00
174 1 0.00
175 1 0.00
176 2 0.00
179 1 0.00
180 25 0.03
181 1 0.00
182 209 0.24
183 2 0.00
ACGTcount: A:0.34, C:0.21, G:0.17, T:0.28
Consensus pattern (152 bp):
TTGAAAAACAGAAATTGAAAATACCTCAGCATGTCCTGAGGCTCAACTCACCTCTCACAATATGA
GTTGATTTTTTTTGAAGAACAGAAATTGAAAATACCTCAGCGTGTCCTAAGGCTCAACTCACCGC
TCGCAATACGAGTTGATTTTTT
Found at i:1595 original size:14 final size:14
Alignment explanation
Indices: 1576--1603 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1566 TTTTTTTTAT
1576 GAACAGAAATTGAA
1 GAACAGAAATTGAA
1590 GAACAGAAATTGAA
1 GAACAGAAATTGAA
1604 AAGACCTCAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.57, C:0.07, G:0.21, T:0.14
Consensus pattern (14 bp):
GAACAGAAATTGAA
Found at i:1655 original size:91 final size:91
Alignment explanation
Indices: 1502--1934 Score: 773
Period size: 91 Copynumber: 4.8 Consensus size: 91
1492 TTTTTTTGAC
** *
1502 AACAGAAATTGAAATTACCTCAGC--GTG-TCCTGAGGCTCAACTCACCTCTAGCAATATGAGTT
1 AACAGAAATTGAAAAGACCTCAGCATGTGAGCC-GAGGCTCAACTCACCTCTAGCAATATGAGTT
1564 CATTTTTTTTATGAACAGAAATTGAAG
65 CATTTTTTTTATGAACAGAAATTGAAG
1591 AACAGAAATTGAAAAGACCTCAGCATGTGAGCCGAGGCTCAACTCACCTCTAGCAATATGAGTTC
1 AACAGAAATTGAAAAGACCTCAGCATGTGAGCCGAGGCTCAACTCACCTCTAGCAATATGAGTTC
1656 ATTTTTTTTATGAACAGAAATTGAAG
66 ATTTTTTTTATGAACAGAAATTGAAG
1682 AACAGAAATTGAAAAGACCTCAGCATGTGAGCCGAGGCTCAACTCACCTCTAGCAATATGAGTTC
1 AACAGAAATTGAAAAGACCTCAGCATGTGAGCCGAGGCTCAACTCACCTCTAGCAATATGAGTTC
1747 ATTTTTTTTATGAACAGAAATTGAAG
66 ATTTTTTTTATGAACAGAAATTGAAG
1773 AACAGAAATTGAAAAGACCTCAGCATGTGAGCCGAGGCTCAACTCACCTCTAGCAATATGAGTTC
1 AACAGAAATTGAAAAGACCTCAGCATGTGAGCCGAGGCTCAACTCACCTCTAGCAATATGAGTTC
1838 ATTTTTTTTATGAACAGAAATTGAAG
66 ATTTTTTTTATGAACAGAAATTGAAG
* * * *
1864 AACAGAAATTGAAAAGACCTCAGCATGTGAGACGAGGCTCAAATCACCTCTCGCAATATGAGTTA
1 AACAGAAATTGAAAAGACCTCAGCATGTGAGCCGAGGCTCAACTCACCTCTAGCAATATGAGTTC
1929 ATTTTT
66 ATTTTT
1935 GACAAACAGA
Statistics
Matches: 334, Mismatches: 7, Indels: 4
0.97 0.02 0.01
Matches are distributed among these distances:
89 22 0.07
91 310 0.93
92 2 0.01
ACGTcount: A:0.36, C:0.19, G:0.18, T:0.27
Consensus pattern (91 bp):
AACAGAAATTGAAAAGACCTCAGCATGTGAGCCGAGGCTCAACTCACCTCTAGCAATATGAGTTC
ATTTTTTTTATGAACAGAAATTGAAG
Found at i:1686 original size:14 final size:14
Alignment explanation
Indices: 1667--1694 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1657 TTTTTTTTAT
1667 GAACAGAAATTGAA
1 GAACAGAAATTGAA
1681 GAACAGAAATTGAA
1 GAACAGAAATTGAA
1695 AAGACCTCAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.57, C:0.07, G:0.21, T:0.14
Consensus pattern (14 bp):
GAACAGAAATTGAA
Found at i:1777 original size:14 final size:14
Alignment explanation
Indices: 1758--1785 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1748 TTTTTTTTAT
1758 GAACAGAAATTGAA
1 GAACAGAAATTGAA
1772 GAACAGAAATTGAA
1 GAACAGAAATTGAA
1786 AAGACCTCAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.57, C:0.07, G:0.21, T:0.14
Consensus pattern (14 bp):
GAACAGAAATTGAA
Found at i:1807 original size:182 final size:182
Alignment explanation
Indices: 1502--2096 Score: 808
Period size: 182 Copynumber: 3.4 Consensus size: 182
1492 TTTTTTTGAC
** *
1502 AACAGAAATTGAAATTACCTCAGC--GTG-TCCTGAGGCTCAACTCACCTCTAGCAATATGAGTT
1 AACAGAAATTGAAAAGACCTCAGCATGTGAGCC-GAGGCTCAACTCACCTCTAGCAATATGAGTT
1564 CATTTTTTTTATGAACAGAAATTGAAGAACAGAAATTGAAAAGACCTCAGCATGTGAGCCGAGGC
65 CATTTTTTTTATGAACAGAAATTGAAGAACAGAAATTGAAAAGACCTCAGCATGTGAGCCGAGGC
1629 TCAACTCACCTCTAGCAATATGAGTTCATTTTTTTTATGAACAGAAATTGAAG
130 TCAACTCACCTCTAGCAATATGAGTTCATTTTTTTTATGAACAGAAATTGAAG
1682 AACAGAAATTGAAAAGACCTCAGCATGTGAGCCGAGGCTCAACTCACCTCTAGCAATATGAGTTC
1 AACAGAAATTGAAAAGACCTCAGCATGTGAGCCGAGGCTCAACTCACCTCTAGCAATATGAGTTC
1747 ATTTTTTTTATGAACAGAAATTGAAGAACAGAAATTGAAAAGACCTCAGCATGTGAGCCGAGGCT
66 ATTTTTTTTATGAACAGAAATTGAAGAACAGAAATTGAAAAGACCTCAGCATGTGAGCCGAGGCT
1812 CAACTCACCTCTAGCAATATGAGTTCATTTTTTTTATGAACAGAAATTGAAG
131 CAACTCACCTCTAGCAATATGAGTTCATTTTTTTTATGAACAGAAATTGAAG
* * *
1864 AACAGAAATTGAAAAGACCTCAGCATGTGAGACGAGGCTCAAATCACCTCTCGCAATATGAGTT-
1 AACAGAAATTGAAAAGACCTCAGCATGTGAGCCGAGGCTCAACTCACCTCTAGCAATATGAGTTC
* ** *
1928 A---ATTTT-TG-AC---------A-AACAGAAATTGAAATTACCTCAGCATGT--CCCGAGGCT
66 ATTTTTTTTATGAACAGAAATTGAAGAACAGAAATTGAAAAGACCTCAGCATGTGAGCCGAGGCT
* * **
1976 CAACTCACCTCTCGCAATATGAG-TCGA--TTTTTGAAAAACAGAAATTGAA-
131 CAACTCACCTCTAGCAATATGAGTTC-ATTTTTTTTATGAACAGAAATTGAAG
* * * * *
2025 AACCAGAAATTGAAAATACCTCAGCGTGTGAGCCAAGGCTCAACTCACCTCTTGCAATATGAGCT
1 AA-CAGAAATTGAAAAGACCTCAGCATGTGAGCCGAGGCTCAACTCACCTCTAGCAATATGAGTT
*
2090 AATTTTT
65 CATTTTT
2097 GATGAACATA
Statistics
Matches: 384, Mismatches: 22, Indels: 32
0.88 0.05 0.07
Matches are distributed among these distances:
161 2 0.01
162 74 0.19
163 3 0.01
164 31 0.08
166 27 0.07
167 1 0.00
176 2 0.01
177 2 0.01
178 4 0.01
180 22 0.06
181 1 0.00
182 213 0.55
183 2 0.01
ACGTcount: A:0.36, C:0.20, G:0.18, T:0.26
Consensus pattern (182 bp):
AACAGAAATTGAAAAGACCTCAGCATGTGAGCCGAGGCTCAACTCACCTCTAGCAATATGAGTTC
ATTTTTTTTATGAACAGAAATTGAAGAACAGAAATTGAAAAGACCTCAGCATGTGAGCCGAGGCT
CAACTCACCTCTAGCAATATGAGTTCATTTTTTTTATGAACAGAAATTGAAG
Found at i:1868 original size:14 final size:14
Alignment explanation
Indices: 1849--1876 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1839 TTTTTTTTAT
1849 GAACAGAAATTGAA
1 GAACAGAAATTGAA
1863 GAACAGAAATTGAA
1 GAACAGAAATTGAA
1877 AAGACCTCAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.57, C:0.07, G:0.21, T:0.14
Consensus pattern (14 bp):
GAACAGAAATTGAA
Found at i:1995 original size:73 final size:74
Alignment explanation
Indices: 1858--2026 Score: 241
Period size: 73 Copynumber: 2.3 Consensus size: 74
1848 TGAACAGAAA
* *
1858 TTGAAGAACAGAAATTGAAAAGACCTCAGCATGTGAGACGAGGCTCAAATCACCTCTCGCAATAT
1 TTGAAAAACAGAAATTGAAAAGACCTCAGCATGT-ACACGAGGCTCAAATCACCTCTCGCAATAT
*
1923 GAGTTAATTT
65 GAGTCAATTT
* ** * *
1933 TTGACAAACAGAAATTGAAATTACCTCAGCATGT-CCCGAGGCTCAACTCACCTCTCGCAATATG
1 TTGAAAAACAGAAATTGAAAAGACCTCAGCATGTACACGAGGCTCAAATCACCTCTCGCAATATG
*
1997 AGTCGATTT
66 AGTCAATTT
2006 TTGAAAAACAGAAATTGAAAA
1 TTGAAAAACAGAAATTGAAAA
2027 CCAGAAATTG
Statistics
Matches: 83, Mismatches: 11, Indels: 2
0.86 0.11 0.02
Matches are distributed among these distances:
73 53 0.64
75 30 0.36
ACGTcount: A:0.38, C:0.20, G:0.18, T:0.24
Consensus pattern (74 bp):
TTGAAAAACAGAAATTGAAAAGACCTCAGCATGTACACGAGGCTCAAATCACCTCTCGCAATATG
AGTCAATTT
Found at i:2025 original size:14 final size:14
Alignment explanation
Indices: 2006--2040 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
1996 GAGTCGATTT
2006 TTGAAAAACAGAAA
1 TTGAAAAACAGAAA
*
2020 TTGAAAACCAGAAA
1 TTGAAAAACAGAAA
2034 TTGAAAA
1 TTGAAAA
2041 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:2075 original size:162 final size:161
Alignment explanation
Indices: 1773--2186 Score: 528
Period size: 162 Copynumber: 2.5 Consensus size: 161
1763 GAAATTGAAG
* * *
1773 AACAGAAATTGAAAAGACCTCAGCATGTGAGCCGAGGCTCAACTCACCTCTAGCAATATGAGTTC
1 AACAGAAATTGAAAACACCTCAGCATGT--CCCGAGGCTCAACTCACCTCTCGCAATATGAG-TC
* ** *
1838 -ATTTTTTTTATGAACAGAAATTGAAGAACAGAAATTGAAAAGACCTCAGCATGTGAGACGAGGC
63 GA--TTTTTGAAAAACAGAAATTGAA-AACAGAAATTGAAAAGACCTCAGCATGTGAGACAAGGC
*
1902 TCAAATCACCTCTCGCAATATGAGTTAATTTTTGACA
125 TCAAATCACCTCTCGCAATATGAGCTAATTTTTGACA
**
1939 AACAGAAATTGAAATTACCTCAGCATGTCCCGAGGCTCAACTCACCTCTCGCAATATGAGTCGAT
1 AACAGAAATTGAAAACACCTCAGCATGTCCCGAGGCTCAACTCACCTCTCGCAATATGAGTCGAT
* * * *
2004 TTTTGAAAAACAGAAATTGAAAACCAGAAATTGAAAATACCTCAGCGTGTGAGCCAAGGCTCAAC
66 TTTTGAAAAACAGAAATTGAAAA-CAGAAATTGAAAAGACCTCAGCATGTGAGACAAGGCTCAAA
* **
2069 TCACCTCTTGCAATATGAGCTAATTTTTGATG
130 TCACCTCTCGCAATATGAGCTAATTTTTGACA
* * * *
2101 AACATAAATT-AAAACCACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA
1 AACAGAAATTGAAAA-CACCTCAGCATGTCCCGAGGCTCAACTCACCTCTCGCAATATGAGTCGA
* *
2165 -TTTTGACAAACAAAAATTGAAA
65 TTTTTGAAAAACAGAAATTGAAA
2187 TTACCTCAGC
Statistics
Matches: 221, Mismatches: 24, Indels: 11
0.86 0.09 0.04
Matches are distributed among these distances:
161 25 0.11
162 137 0.62
163 2 0.01
164 31 0.14
166 26 0.12
ACGTcount: A:0.36, C:0.21, G:0.17, T:0.25
Consensus pattern (161 bp):
AACAGAAATTGAAAACACCTCAGCATGTCCCGAGGCTCAACTCACCTCTCGCAATATGAGTCGAT
TTTTGAAAAACAGAAATTGAAAACAGAAATTGAAAAGACCTCAGCATGTGAGACAAGGCTCAAAT
CACCTCTCGCAATATGAGCTAATTTTTGACA
Found at i:2095 original size:89 final size:87
Alignment explanation
Indices: 1933--2117 Score: 232
Period size: 89 Copynumber: 2.1 Consensus size: 87
1923 GAGTTAATTT
* *
1933 TTGACAAA-CAGAAATTGAAATTACCTCAGCATGTCCCGAGGCTCAACTCACCTCTCGCAATATG
1 TTGA-AAACCAGAAATTGAAAATACCTCAGCATGTCCCAAGGCTCAACTCACCTCTCGCAATATG
*
1997 AGTCGATTTTTGAAAAACAGAAA
65 AGTCAATTTTTGAAAAACAGAAA
* * *
2020 TTGAAAACCAGAAATTGAAAATACCTCAGCGTGTGAGCCAAGGCTCAACTCACCTCTTGCAATAT
1 TTGAAAACCAGAAATTGAAAATACCTCAGCATGT--CCCAAGGCTCAACTCACCTCTCGCAATAT
** *
2085 GAG-CTAATTTTTGATGAACATAAA
64 GAGTC-AATTTTTGAAAAACAGAAA
2109 TT-AAAACCA
1 TTGAAAACCA
2118 CCTCAGCGTG
Statistics
Matches: 85, Mismatches: 9, Indels: 7
0.84 0.09 0.07
Matches are distributed among these distances:
86 3 0.04
87 28 0.33
88 8 0.09
89 46 0.54
ACGTcount: A:0.38, C:0.22, G:0.16, T:0.25
Consensus pattern (87 bp):
TTGAAAACCAGAAATTGAAAATACCTCAGCATGTCCCAAGGCTCAACTCACCTCTCGCAATATGA
GTCAATTTTTGAAAAACAGAAA
Found at i:2155 original size:73 final size:71
Alignment explanation
Indices: 2060--2259 Score: 240
Period size: 70 Copynumber: 2.8 Consensus size: 71
2050 GTGTGAGCCA
* * *
2060 AGGCTCAACTCACCTCTTGCAATATGAGCTAATTTTTGATGAACATAAATTAAAACCACCTCAGC
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGATGAACATAAATTAAAACCACCTCAGC
2125 GTGTCCTG
66 --GTCCTG
** * * **
2133 AGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTGACAAACAAAAATTGAAATTACCTCAGC
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGATGAACATAAATTAAAACCACCTCAGC
*
2197 GTCTTG
66 GTCCTG
* **
2203 AGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTTTTGAAACATAAATTTAAAA
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGATG-AACATAAA-TTAAAA
2260 AATGAAAATT
Statistics
Matches: 107, Mismatches: 17, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
70 36 0.34
71 4 0.04
72 33 0.31
73 34 0.32
ACGTcount: A:0.33, C:0.21, G:0.14, T:0.31
Consensus pattern (71 bp):
AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGATGAACATAAATTAAAACCACCTCAGC
GTCCTG
Found at i:2417 original size:159 final size:156
Alignment explanation
Indices: 2117--2418 Score: 419
Period size: 159 Copynumber: 1.9 Consensus size: 156
2107 AATTAAAACC
** *
2117 ACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTGACAAACAAAAAT
1 ACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGAAATTGAAAAACAAAAAT
* ** * *
2182 TGAAATTACCTCAGCGTCTTGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTTTTGAAA
66 TGAAAATACCTCAGCGTCCCGAGGCTCAACTCACCTCTCGCAATATGAGCTGA---TTTTTGAAA
* *
2247 CATAAATTTAAAAAATGAAAATTGAAAAT
128 AATAAAATTAAAAAATGAAAATTGAAAAT
2276 ACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGAAATT-AAAACACAAAAA
1 ACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGAAATTGAAAA-ACAAAAA
*
2340 TTGAAAATACCTCAGCGTACCCCGAGGCTCAACTCACCTCTTGCAATATGAGCTGA-TTTTGAAA
65 TTGAAAATACCTCAGCGT--CCCGAGGCTCAACTCACCTCTCGCAATATGAGCTGATTTTTGAAA
2404 AAGTAGAAATTAAAA
128 AA-TA-AAATTAAAA
2419 GGTTCAACCC
Statistics
Matches: 127, Mismatches: 11, Indels: 10
0.86 0.07 0.07
Matches are distributed among these distances:
157 9 0.07
158 5 0.04
159 82 0.65
161 31 0.24
ACGTcount: A:0.35, C:0.22, G:0.16, T:0.27
Consensus pattern (156 bp):
ACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGAAATTGAAAAACAAAAAT
TGAAAATACCTCAGCGTCCCGAGGCTCAACTCACCTCTCGCAATATGAGCTGATTTTTGAAAAAT
AAAATTAAAAAATGAAAATTGAAAAT
Found at i:2553 original size:74 final size:75
Alignment explanation
Indices: 2422--2772 Score: 385
Period size: 76 Copynumber: 4.7 Consensus size: 75
2412 ATTAAAAGGT
* * * *
2422 TCAACCCACCTCTCGCAATATGAGTTGA----TTTTGACAAACAAAAATTGAAATTACCTCAGC-
1 TCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTGAAAAACAGAAATTGAAAATACCTCAGCT
*
2482 GTCTTGAGGC
66 GTCCTGAGGC
*
2492 TCAACTCACTTCTCGCAATATGAGTTGATTTTTTTTGAAAAACAGAAATTGAAAATACCTCAGCA
1 TCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTGAAAAACAGAAATTGAAAATACCTCAGC-
**
2557 TGTTTTGAGGC
65 TGTCCTGAGGC
** * * *
2568 TCAACTCATTTCTCACAATATGAGTTGATTTTTTTTTGAAGAACAGAAATTGAAAATACCTCGGC
1 TCAACTCACCTCTCGCAATATGAGTTGA-TTTTTTTTGAAAAACAGAAATTGAAAATACCTCAGC
*
2633 GTGTGACCTAAGGC
65 -TGT--CCTGAGGC
* * * * *
2647 TCAACTCGCCGCTCGCAATACGAGTTGA-TTTTTTTG-ACAACAGAAATTGAAATTACCTCAGCG
1 TCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTGAAAAACAGAAATTGAAAATACCTCAGC-
2710 TGTCCTGAGGC
65 TGTCCTGAGGC
* * **
2721 TCAACTCACCTCTAGCAATATGAGTTCATTTTTTTT-ATGAACAGAAATTGAA
1 TCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTGAAAAACAGAAATTGAA
2773 GAACAGAAAT
Statistics
Matches: 239, Mismatches: 31, Indels: 17
0.83 0.11 0.06
Matches are distributed among these distances:
70 26 0.11
74 59 0.25
75 20 0.08
76 62 0.26
77 45 0.19
79 27 0.11
ACGTcount: A:0.32, C:0.20, G:0.17, T:0.32
Consensus pattern (75 bp):
TCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTGAAAAACAGAAATTGAAAATACCTCAGCT
GTCCTGAGGC
Found at i:2719 original size:153 final size:156
Alignment explanation
Indices: 2488--2912 Score: 495
Period size: 164 Copynumber: 2.7 Consensus size: 156
2478 CAGCGTCTTG
* * *
2488 AGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTTTTGAAAAACAGAAATTGAAAATACCTC
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTTTG-ACAACAGAAATTGAAATTACCTC
* ** **
2553 AGCATGTTTTGAGGCTCAACTCATTTCTCACAATATGAGTTGA-TTTTTT-T-TTGAAGAACAGA
64 AGCGTGTCCTGAGGCTCAACTCACCTCTCACAATATGAGTTGATTTTTTTATATTGAAGAACAGA
* * *
2615 AATTGAAAATACCTCGGCGTGTGA-CCTA
129 AATTGAAAAGACCTCAGCATGTGAGCC-A
* * *
2643 AGGCTCAACTCGCCGCTCGCAATACGAGTTGATTTTTTTGACAACAGAAATTGAAATTACCTCAG
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGACAACAGAAATTGAAATTACCTCAG
*
2708 CGTGTCCTGAGGCTCAACTCACCTCT-AGCAATATGAGTTCATTTTTTTTATGAACAGAAATTGA
66 CGTGTCCTGAGGCTCAACTCACCTCTCA-CAATATGAGTTGA-TTTTTTTAT--------ATTGA
*
2772 AGAACAGAAATTGAAAAGACCTCAGCATGTGAGCCG
121 AGAACAGAAATTGAAAAGACCTCAGCATGTGAGCCA
*
2808 AGGCTCAACTCACCTCTCGCAATATGAGTT-A-ATTTTTGACAAACAGAAATTGAAATTACCTCA
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAC-AACAGAAATTGAAATTACCTCA
* * *
2871 TCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAATTGA
65 GCGTGTCCTGAGGCTCAACTCACCTCTCACAATATGAGTTGA
2913 AAAAAATACC
Statistics
Matches: 230, Mismatches: 24, Indels: 23
0.83 0.09 0.08
Matches are distributed among these distances:
152 1 0.00
153 56 0.24
154 8 0.03
155 34 0.15
156 1 0.00
163 8 0.03
164 60 0.26
165 60 0.26
166 2 0.01
ACGTcount: A:0.32, C:0.21, G:0.17, T:0.30
Consensus pattern (156 bp):
AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGACAACAGAAATTGAAATTACCTCAG
CGTGTCCTGAGGCTCAACTCACCTCTCACAATATGAGTTGATTTTTTTATATTGAAGAACAGAAA
TTGAAAAGACCTCAGCATGTGAGCCA
Found at i:2778 original size:14 final size:14
Alignment explanation
Indices: 2759--2786 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
2749 TTTTTTTTAT
2759 GAACAGAAATTGAA
1 GAACAGAAATTGAA
2773 GAACAGAAATTGAA
1 GAACAGAAATTGAA
2787 AAGACCTCAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.57, C:0.07, G:0.21, T:0.14
Consensus pattern (14 bp):
GAACAGAAATTGAA
Found at i:2854 original size:89 final size:89
Alignment explanation
Indices: 2685--2861 Score: 234
Period size: 89 Copynumber: 2.0 Consensus size: 89
2675 TTTTTTTGAC
** *
2685 AACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTAGCAATATGAGTTCAT
1 AACAGAAATTGAAAAGACCTCAGCGTGGCCTGAGGCTCAACTCACCTCTAGCAATATGAGTTCAT
* * **
2750 TTTTTTTATGAACAGAAATTGAAG
66 ATTTTTGACAAACAGAAATTGAAG
*
2774 AACAGAAATTGAAAAGACCTCAGCATGTGAGCC-GAGGCTCAACTCACCTCTCGCAATATGAGTT
1 AACAGAAATTGAAAAGACCTCAGC--GTG-GCCTGAGGCTCAACTCACCTCTAGCAATATGAGTT
2838 -A-ATTTTTGACAAACAGAAATTGAA
63 CATATTTTTGACAAACAGAAATTGAA
2862 ATTACCTCAT
Statistics
Matches: 77, Mismatches: 8, Indels: 6
0.85 0.09 0.07
Matches are distributed among these distances:
89 41 0.53
90 1 0.01
91 33 0.43
92 2 0.03
ACGTcount: A:0.36, C:0.20, G:0.18, T:0.27
Consensus pattern (89 bp):
AACAGAAATTGAAAAGACCTCAGCGTGGCCTGAGGCTCAACTCACCTCTAGCAATATGAGTTCAT
ATTTTTGACAAACAGAAATTGAAG
Found at i:2890 original size:164 final size:165
Alignment explanation
Indices: 2603--2907 Score: 481
Period size: 165 Copynumber: 1.9 Consensus size: 165
2593 TGATTTTTTT
* * * *
2603 TTGAAGAACAGAAATTGAAAATACCTCGGCGTGTGACCTAAGGCTCAACTCGCCGCTCGCAATAC
1 TTGAAGAACAGAAATTGAAAAGACCTCAGCATGTGACCTAAGGCTCAACTCACCGCTCGCAATAC
*
2668 GAGTTGATTTTTTTGACAACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTC
66 GAGTTGATATTTTTGACAACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTC
2733 TAGCAATATGAGTTCATTTTTTTTATGAACAGAAA
131 TAGCAATATGAGTTCATTTTTTTTATGAACAGAAA
* *
2768 TTGAAGAACAGAAATTGAAAAGACCTCAGCATGTGAGCC-GAGGCTCAACTCACCTCTCGCAATA
1 TTGAAGAACAGAAATTGAAAAGACCTCAGCATGTGA-CCTAAGGCTCAACTCACCGCTCGCAATA
* *
2832 TGAGTT-A-ATTTTTGACAAACAGAAATTGAAATTACCTCATCGTGTCCTGAGGCTCAACTCACC
65 CGAGTTGATATTTTTGAC-AACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACC
*
2895 TCTCGCAATATGA
129 TCTAGCAATATGA
2908 ATTGAAAAAA
Statistics
Matches: 128, Mismatches: 10, Indels: 5
0.90 0.07 0.03
Matches are distributed among these distances:
163 8 0.06
164 58 0.45
165 60 0.47
166 2 0.02
ACGTcount: A:0.32, C:0.22, G:0.18, T:0.27
Consensus pattern (165 bp):
TTGAAGAACAGAAATTGAAAAGACCTCAGCATGTGACCTAAGGCTCAACTCACCGCTCGCAATAC
GAGTTGATATTTTTGACAACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTC
TAGCAATATGAGTTCATTTTTTTTATGAACAGAAA
Found at i:3023 original size:78 final size:76
Alignment explanation
Indices: 2940--3220 Score: 358
Period size: 72 Copynumber: 3.7 Consensus size: 76
2930 GTAATCTGAA
*
2940 GCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTTAAAAACAGAAATTGAAAATACCTCAG
1 GCTCAACTCACCTCTCGCAATATAAGTTGATTTTTTTTTAAAAACAGAAATTGAAAATACCTCAG
*
3005 CATGTGAACCGAG
66 CA-GTG-TCCGAG
* *
3018 GCTCAACTCACCTCTCGCAATATAAGTTGATTTTTTTTTGAAAACAGAAATTGAAAATACCTCAA
1 GCTCAACTCACCTCTCGCAATATAAGTTGATTTTTTTTTAAAAACAGAAATTGAAAATACCTCAG
*
3083 C-GTGTCTTGAG
66 CAGTGTC-CGAG
** * * *
3094 GCTCAACTCATTTCTCGCAATATAAGTTGA----ATTTTGAAAACAGAAATTGAAATTACCTCAG
1 GCTCAACTCACCTCTCGCAATATAAGTTGATTTTTTTTTAAAAACAGAAATTGAAAATACCTCAG
3155 C-GTGTCCTGAG
66 CAGTGTCC-GAG
* * **
3166 GCTCAACTCACCTCTCGCAAAATGAGTTGATTTTTTTTTACGAACAGAAATTGAA
1 GCTCAACTCACCTCTCGCAATATAAGTTGATTTTTTTTTAAAAACAGAAATTGAA
3221 GAACAGAAAT
Statistics
Matches: 178, Mismatches: 19, Indels: 14
0.84 0.09 0.07
Matches are distributed among these distances:
72 63 0.35
75 1 0.01
76 51 0.29
78 63 0.35
ACGTcount: A:0.33, C:0.20, G:0.15, T:0.31
Consensus pattern (76 bp):
GCTCAACTCACCTCTCGCAATATAAGTTGATTTTTTTTTAAAAACAGAAATTGAAAATACCTCAG
CAGTGTCCGAG
Found at i:3112 original size:76 final size:75
Alignment explanation
Indices: 2934--3220 Score: 359
Period size: 78 Copynumber: 3.8 Consensus size: 75
2924 CAGTGTGTAA
* * *
2934 TCTGAAGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTTAAAAACAGAAATTGAAAATA
1 TCTGAGGCTCAACTCACCTCTCGCAATATAAGTTGATTTTTTTTTGAAAACAGAAATTGAAAATA
*
2999 CCTCAGCATGTG
66 CCTCA--ACGTG
* *
3011 AACCGAGGCTCAACTCACCTCTCGCAATATAAGTTGATTTTTTTTTGAAAACAGAAATTGAAAAT
1 -TCTGAGGCTCAACTCACCTCTCGCAATATAAGTTGATTTTTTTTTGAAAACAGAAATTGAAAAT
3076 ACCTCAACGTG
65 ACCTCAACGTG
** * *
3087 TCTTGAGGCTCAACTCATTTCTCGCAATATAAGTTGA----ATTTTGAAAACAGAAATTGAAATT
1 TC-TGAGGCTCAACTCACCTCTCGCAATATAAGTTGATTTTTTTTTGAAAACAGAAATTGAAAAT
*
3148 ACCTCAGCGTG
65 ACCTCAACGTG
* * *
3159 TCCTGAGGCTCAACTCACCTCTCGCAAAATGAGTTGATTTTTTTTT-ACGAACAGAAATTGAA
1 T-CTGAGGCTCAACTCACCTCTCGCAATATAAGTTGATTTTTTTTTGA-AAACAGAAATTGAA
3221 GAACAGAAAT
Statistics
Matches: 183, Mismatches: 19, Indels: 16
0.84 0.09 0.07
Matches are distributed among these distances:
72 63 0.34
73 1 0.01
75 2 0.01
76 52 0.28
78 65 0.36
ACGTcount: A:0.33, C:0.20, G:0.15, T:0.31
Consensus pattern (75 bp):
TCTGAGGCTCAACTCACCTCTCGCAATATAAGTTGATTTTTTTTTGAAAACAGAAATTGAAAATA
CCTCAACGTG
Found at i:3226 original size:14 final size:14
Alignment explanation
Indices: 3207--3234 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
3197 TTTTTTTTAC
3207 GAACAGAAATTGAA
1 GAACAGAAATTGAA
3221 GAACAGAAATTGAA
1 GAACAGAAATTGAA
3235 ATTACCTCAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.57, C:0.07, G:0.21, T:0.14
Consensus pattern (14 bp):
GAACAGAAATTGAA
Found at i:3316 original size:14 final size:14
Alignment explanation
Indices: 3297--3324 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
3287 TTTTTTTTAC
3297 GAACAGAAATTGAA
1 GAACAGAAATTGAA
3311 GAACAGAAATTGAA
1 GAACAGAAATTGAA
3325 AAGACCTCAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.57, C:0.07, G:0.21, T:0.14
Consensus pattern (14 bp):
GAACAGAAATTGAA
Found at i:3373 original size:92 final size:90
Alignment explanation
Indices: 3127--3382 Score: 426
Period size: 90 Copynumber: 2.8 Consensus size: 90
3117 AAGTTGAATT
3127 TTGAA-AACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAAAATGA
1 TTGAAGAACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAAAATGA
3191 GTTGATTTTTTTTTACGAACAGAAA
66 GTTGATTTTTTTTTACGAACAGAAA
3216 TTGAAGAACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAAAATGA
1 TTGAAGAACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAAAATGA
3281 GTTGATTTTTTTTTACGAACAGAAA
66 GTTGATTTTTTTTTACGAACAGAAA
** * *
3306 TTGAAGAACAGAAATTGAAAAGACCTCAGCATGTGAGCC-GAGGCTCAACTCACCTCTCGCAATA
1 TTGAAGAACAGAAATTGAAATTACCTCAGC--GTG-TCCTGAGGCTCAACTCACCTCTCGCAAAA
*
3370 TGAGTTAATTTTT
63 TGAGTTGATTTTT
3383 GACAAACAGA
Statistics
Matches: 158, Mismatches: 5, Indels: 5
0.94 0.03 0.03
Matches are distributed among these distances:
89 5 0.03
90 112 0.71
92 39 0.25
93 2 0.01
ACGTcount: A:0.34, C:0.20, G:0.18, T:0.28
Consensus pattern (90 bp):
TTGAAGAACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAAAATGA
GTTGATTTTTTTTTACGAACAGAAA
Found at i:3566 original size:72 final size:73
Alignment explanation
Indices: 3312--3599 Score: 409
Period size: 73 Copynumber: 3.9 Consensus size: 73
3302 GAAATTGAAG
** *
3312 AACAGAAATTGAAAAGACCTCAGCATGTGAGCC-GAGGCTCAACTCACCTCTCGCAATATGAGTT
1 AACAGAAATTGAAATTACCTCAGC--GTG-TCCTGAGGCTCAACTCACCTCTCGCAATATGAGTT
*
3376 AATTTTTGACA
63 GATTTTTGACA
* *
3387 AACAGAAATTGAAATTACCTCAGCGTGTCCCGAGGCTCAACTCACCTTTCGCAATATGAGTTGAT
1 AACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGAT
3452 TTTTGACA
66 TTTTGACA
*
3460 AACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTAGCAATATGAGTTGA-
1 AACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGAT
*
3524 TTTTGAAA
66 TTTTGACA
* * * * * *
3532 AACAAAAATTAAAAGTACCTCAACGTGTCTTGAGGCTCAACTCATCTCTCGCAATATGAGTTGAT
1 AACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGAT
3597 TTT
66 TTT
3600 CCTTGAAAAG
Statistics
Matches: 195, Mismatches: 16, Indels: 6
0.90 0.07 0.03
Matches are distributed among these distances:
72 66 0.34
73 107 0.55
75 22 0.11
ACGTcount: A:0.33, C:0.22, G:0.17, T:0.28
Consensus pattern (73 bp):
AACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGAT
TTTTGACA
Found at i:3584 original size:145 final size:147
Alignment explanation
Indices: 3312--3599 Score: 411
Period size: 145 Copynumber: 2.0 Consensus size: 147
3302 GAAATTGAAG
*
3312 AACAGAAATTGAAAAGACCTCAGCATGTGAGCCGAGGCTCAACTCACCTCTCGCAATATGAGTTA
1 AACAGAAATTGAAAAGACCTCAGCA-GTGAGCCGAGGCTCAACTCACCTCTAGCAATATGAGTTA
* * * * * *
3377 ATTTTTGACAAACAGAAATTGAAATTACCTCAGCGTGTCCCGAGGCTCAACTCACCTTTCGCAAT
65 ATTTTTGAAAAACAAAAATTAAAAGTACCTCAACGTGTCCCGAGGCTCAACTCACCTCTCGCAAT
3442 ATGAGTTGATTTTTGACA
130 ATGAGTTGATTTTTGACA
** * *
3460 AACAGAAATTGAAATTACCTCAGC-GTG-TCCTGAGGCTCAACTCACCTCTAGCAATATGAGTTG
1 AACAGAAATTGAAAAGACCTCAGCAGTGAGCC-GAGGCTCAACTCACCTCTAGCAATATGAGTTA
** *
3523 A-TTTTGAAAAACAAAAATTAAAAGTACCTCAACGTGTCTTGAGGCTCAACTCATCTCTCGCAAT
65 ATTTTTGAAAAACAAAAATTAAAAGTACCTCAACGTGTCCCGAGGCTCAACTCACCTCTCGCAAT
3587 ATGAGTTGATTTT
130 ATGAGTTGATTTT
3600 CCTTGAAAAG
Statistics
Matches: 125, Mismatches: 14, Indels: 5
0.87 0.10 0.03
Matches are distributed among these distances:
145 69 0.55
146 34 0.27
148 22 0.18
ACGTcount: A:0.33, C:0.22, G:0.17, T:0.28
Consensus pattern (147 bp):
AACAGAAATTGAAAAGACCTCAGCAGTGAGCCGAGGCTCAACTCACCTCTAGCAATATGAGTTAA
TTTTTGAAAAACAAAAATTAAAAGTACCTCAACGTGTCCCGAGGCTCAACTCACCTCTCGCAATA
TGAGTTGATTTTTGACA
Found at i:11136 original size:14 final size:15
Alignment explanation
Indices: 11106--11138 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
11096 AAACTAAACC
*
11106 AAAATTAAAACCATA
1 AAAATTAAAAACATA
11121 AAAATTAAAAAC-TA
1 AAAATTAAAAACATA
11135 AAAA
1 AAAA
11139 ACAACCAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 6 0.35
15 11 0.65
ACGTcount: A:0.73, C:0.09, G:0.00, T:0.18
Consensus pattern (15 bp):
AAAATTAAAAACATA
Done.