Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023745.1 Corchorus olitorius cultivar O-4 contig23778, whole genome shotgun sequence
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: 16696
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.31
Found at i:387 original size:50 final size:50
Alignment explanation
Indices: 306--402 Score: 131
Period size: 50 Copynumber: 1.9 Consensus size: 50
296 AATGTTTTAC
* * ** *
306 AATAAAATTGCTTTCCATTTGCGAGTTCAAGATCAAAGTTCGCTTTTAAA
1 AATAAAATTGCATTCCATATGCGAGACCAAGACCAAAGTTCGCTTTTAAA
* *
356 AATAAGATTGCATTCCATATGTGAGACCAAGACCAAAGTTCGCTTTT
1 AATAAAATTGCATTCCATATGCGAGACCAAGACCAAAGTTCGCTTTT
403 CGAAGGGCAT
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
50 40 1.00
ACGTcount: A:0.34, C:0.18, G:0.15, T:0.33
Consensus pattern (50 bp):
AATAAAATTGCATTCCATATGCGAGACCAAGACCAAAGTTCGCTTTTAAA
Found at i:1210 original size:119 final size:119
Alignment explanation
Indices: 999--1223 Score: 326
Period size: 119 Copynumber: 1.9 Consensus size: 119
989 CGAATGCTTC
* * * * * * * * *
999 GGCTTTTCCATAAGTCAAACTCGTTTCCATACGAGTCAGTTTAAGCCTTGGTTCCATCCAAGCCA
1 GGCTTTTACACAAGGCAAACTCGTTTCAATACAAGTCAGCTCAAGCCTTGGTTCCACCCAAGCAA
*
1064 CGTAGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTAGCAACGTA
66 CGTAGGCTTTTCCACAAGCCAAACTCGTTTCCATACAAGTCAATTAGCAACGTA
*
1118 GGCTTTTACACAAGGCAAACTCGTTTCAATACAAGTCTGCTCAAGCCTTGGTTCCACCCAAGCAA
1 GGCTTTTACACAAGGCAAACTCGTTTCAATACAAGTCAGCTCAAGCCTTGGTTCCACCCAAGCAA
*
1183 CAG-GGGCTTTTCCACAAGCCAAACTCGTTTCCATACAAGTC
66 C-GTAGGCTTTTCCACAAGCCAAACTCGTTTCCATACAAGTC
1224 TGCTCAAGCC
Statistics
Matches: 93, Mismatches: 12, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
119 92 0.99
120 1 0.01
ACGTcount: A:0.28, C:0.29, G:0.17, T:0.27
Consensus pattern (119 bp):
GGCTTTTACACAAGGCAAACTCGTTTCAATACAAGTCAGCTCAAGCCTTGGTTCCACCCAAGCAA
CGTAGGCTTTTCCACAAGCCAAACTCGTTTCCATACAAGTCAATTAGCAACGTA
Found at i:1220 original size:69 final size:69
Alignment explanation
Indices: 1118--1342 Score: 353
Period size: 69 Copynumber: 3.3 Consensus size: 69
1108 TAGCAACGTA
* * *
1118 GGCTTTTACACAAGGCAAACTCGTTTCAATACAAGTCTGCTCAAGCCTTGGTTCCACCCAAGCAA
1 GGCTTTTCCACAAGCCAAACTCGTTTCCATACAAGTCTGCTCAAGCCTTGGTTCCACCCAAGCAA
1183 CAGG
66 CAGG
1187 GGCTTTTCCACAAGCCAAACTCGTTTCCATACAAGTCTGCTCAAGCCTTGGTTCCACCCAAGCAA
1 GGCTTTTCCACAAGCCAAACTCGTTTCCATACAAGTCTGCTCAAGCCTTGGTTCCACCCAAGCAA
1252 CAGG
66 CAGG
* * * * *
1256 GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAG-TAGAAGCCTTGGTTCCACCAAAGCG
1 GGCTTTTCCACAAGCCAAACTCGTTTCCATACAAGTCTGCT-CAAGCCTTGGTTCCACCCAAGCA
1320 ACAGG
65 ACAGG
*
1325 GGCTTTTCCATAAGCCAA
1 GGCTTTTCCACAAGCCAA
1343 GTTCATTTCC
Statistics
Matches: 146, Mismatches: 9, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
68 1 0.01
69 145 0.99
ACGTcount: A:0.28, C:0.30, G:0.19, T:0.23
Consensus pattern (69 bp):
GGCTTTTCCACAAGCCAAACTCGTTTCCATACAAGTCTGCTCAAGCCTTGGTTCCACCCAAGCAA
CAGG
Found at i:1457 original size:69 final size:69
Alignment explanation
Indices: 1377--1529 Score: 243
Period size: 69 Copynumber: 2.2 Consensus size: 69
1367 TTCCAAGACT
1377 AAACTCATTTCCATACGAGTCAGTTCAAGCCTTGGTTCCACCCAAGCAACAAGGGCTTTTCCACA
1 AAACTCATTTCCATACGAGTCAGTTCAAGCCTTGGTTCCACCCAAGCAACAAGGGCTTTTCCACA
1442 AGCC
66 AGCC
* * * * *
1446 AAACTCGTTTCCATACGAGTCAGTTGAAGCCTTGGTTCCACCCAAGCGACATGGGCTTTTCCATA
1 AAACTCATTTCCATACGAGTCAGTTCAAGCCTTGGTTCCACCCAAGCAACAAGGGCTTTTCCACA
1511 AGCC
66 AGCC
**
1515 AAGTTCATTTCCATA
1 AAACTCATTTCCATA
1530 TGAATTCAGT
Statistics
Matches: 76, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
69 76 1.00
ACGTcount: A:0.27, C:0.29, G:0.17, T:0.26
Consensus pattern (69 bp):
AAACTCATTTCCATACGAGTCAGTTCAAGCCTTGGTTCCACCCAAGCAACAAGGGCTTTTCCACA
AGCC
Found at i:1457 original size:105 final size:105
Alignment explanation
Indices: 1272--1460 Score: 288
Period size: 105 Copynumber: 1.8 Consensus size: 105
1262 TCCACAAGCC
* * * * *
1272 AAACTCGTTTCCATACGAGTCAGTAGAAGCCTTGGTTCCACCAAAGCGACAGGGGCTTTTCCATA
1 AAACTCATTTCCATACGAGTCAGTACAAGCCTTGGTTCCACCAAAGCAACAAGGGCTTTTCCACA
**
1337 AGCCAAGTTCATTTCCATATGAATTCAGTCTTCCAAGACT
66 AGCCAAACTCATTTCCATATGAATTCAGTCTTCCAAGACT
* *
1377 AAACTCATTTCCATACGAGTCAGTTCAAGCCTTGGTTCCACCCAAGCAACAAGGGCTTTTCCACA
1 AAACTCATTTCCATACGAGTCAGTACAAGCCTTGGTTCCACCAAAGCAACAAGGGCTTTTCCACA
*
1442 AGCCAAACTCGTTTCCATA
66 AGCCAAACTCATTTCCATA
1461 CGAGTCAGTT
Statistics
Matches: 74, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
105 74 1.00
ACGTcount: A:0.29, C:0.28, G:0.16, T:0.26
Consensus pattern (105 bp):
AAACTCATTTCCATACGAGTCAGTACAAGCCTTGGTTCCACCAAAGCAACAAGGGCTTTTCCACA
AGCCAAACTCATTTCCATATGAATTCAGTCTTCCAAGACT
Found at i:1504 original size:174 final size:174
Alignment explanation
Indices: 1203--1636 Score: 751
Period size: 174 Copynumber: 2.5 Consensus size: 174
1193 TCCACAAGCC
* * * * *
1203 AAACTCGTTTCCATACAAGTCTGCTCAAGCCTTGGTTCCACCCAAGCAACAGGGGCTTTTCCACA
1 AAACTCATTTCCATACGAGTCAGTTCAAGCCTTGGTTCCACCCAAGCAACAAGGGCTTTTCCACA
1268 AGCCAAACTCGTTTCCATACGAGTCAGTAGAAGCCTTGGTTCCACCAAAGCGACAGGGGCTTTTC
66 AGCCAAACTCGTTTCCATACGAGTCAGTAGAAGCCTTGGTTCCACCAAAGCGACAGGGGCTTTTC
1333 CATAAGCCAAGTTCATTTCCATATGAATTCAGTCTTCCAAGACT
131 CATAAGCCAAGTTCATTTCCATATGAATTCAGTCTTCCAAGACT
1377 AAACTCATTTCCATACGAGTCAGTTCAAGCCTTGGTTCCACCCAAGCAACAAGGGCTTTTCCACA
1 AAACTCATTTCCATACGAGTCAGTTCAAGCCTTGGTTCCACCCAAGCAACAAGGGCTTTTCCACA
* * *
1442 AGCCAAACTCGTTTCCATACGAGTCAGTTGAAGCCTTGGTTCCACCCAAGCGACATGGGCTTTTC
66 AGCCAAACTCGTTTCCATACGAGTCAGTAGAAGCCTTGGTTCCACCAAAGCGACAGGGGCTTTTC
1507 CATAAGCCAAGTTCATTTCCATATGAATTCAGTCTTCCAAGACT
131 CATAAGCCAAGTTCATTTCCATATGAATTCAGTCTTCCAAGACT
* * **
1551 AAACTCATTTCCATACGAGTCAGTTCAAACCTTGGTTCCATCCAAGCAGTAAGGGCTTTTCCACA
1 AAACTCATTTCCATACGAGTCAGTTCAAGCCTTGGTTCCACCCAAGCAACAAGGGCTTTTCCACA
*
1616 AGCCAAATTCGTTTCCATACG
66 AGCCAAACTCGTTTCCATACG
1637 GTGCATTACC
Statistics
Matches: 247, Mismatches: 13, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
174 247 1.00
ACGTcount: A:0.28, C:0.29, G:0.17, T:0.27
Consensus pattern (174 bp):
AAACTCATTTCCATACGAGTCAGTTCAAGCCTTGGTTCCACCCAAGCAACAAGGGCTTTTCCACA
AGCCAAACTCGTTTCCATACGAGTCAGTAGAAGCCTTGGTTCCACCAAAGCGACAGGGGCTTTTC
CATAAGCCAAGTTCATTTCCATATGAATTCAGTCTTCCAAGACT
Found at i:1564 original size:105 final size:105
Alignment explanation
Indices: 1446--1634 Score: 283
Period size: 105 Copynumber: 1.8 Consensus size: 105
1436 TCCACAAGCC
* * *
1446 AAACTCGTTTCCATACGAGTCAGTTGAAGCCTTGGTTCCACCCAAGC-G-ACATGGGCTTTTCCA
1 AAACTCATTTCCATACGAGTCAGTTCAAACCTTGGTTCCACCCAAGCAGTA-A-GGGCTTTTCCA
* *
1509 TAAGCCAAGTTCATTTCCATATGAATTCAGTCTTCCAAGACT
64 CAAGCCAAATTCATTTCCATATGAATTCAGTCTTCCAAGACT
*
1551 AAACTCATTTCCATACGAGTCAGTTCAAACCTTGGTTCCATCCAAGCAGTAAGGGCTTTTCCACA
1 AAACTCATTTCCATACGAGTCAGTTCAAACCTTGGTTCCACCCAAGCAGTAAGGGCTTTTCCACA
*
1616 AGCCAAATTCGTTTCCATA
66 AGCCAAATTCATTTCCATA
1635 CGGTGCATTA
Statistics
Matches: 75, Mismatches: 7, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
105 72 0.96
106 2 0.03
107 1 0.01
ACGTcount: A:0.28, C:0.27, G:0.16, T:0.29
Consensus pattern (105 bp):
AAACTCATTTCCATACGAGTCAGTTCAAACCTTGGTTCCACCCAAGCAGTAAGGGCTTTTCCACA
AGCCAAATTCATTTCCATATGAATTCAGTCTTCCAAGACT
Found at i:1911 original size:73 final size:73
Alignment explanation
Indices: 1661--1901 Score: 446
Period size: 73 Copynumber: 3.3 Consensus size: 73
1651 TCTCGATTGG
* *
1661 ACTCGGTGAGCTCGTTGTAGCAAATCTTCAAATAGATCAGATTGATTCGGTGAATCAAGTCAATG
1 ACTCGGTGAGCTCGGTGCAGCAAATCTTCAAATAGATCAGATTGATTCGGTGAATCAAGTCAATG
1726 CGGTGCAA
66 CGGTGCAA
*
1734 ACTCGGTGAGCTCGGTGCAGCAAATCTTTAAATAGATCAGATTGATTCGGTGAATCAAGTCAATG
1 ACTCGGTGAGCTCGGTGCAGCAAATCTTCAAATAGATCAGATTGATTCGGTGAATCAAGTCAATG
1799 CGGTGCAA
66 CGGTGCAA
*
1807 ACTCAGTGAGCTCGGTGCAGCAAATCTTCAAATAGATCAGATTGATTCGGTGAATCAAGTCAATG
1 ACTCGGTGAGCTCGGTGCAGCAAATCTTCAAATAGATCAGATTGATTCGGTGAATCAAGTCAATG
1872 CGGTGCAA
66 CGGTGCAA
1880 ACTCGGTGAGCTCGGTGCAGCA
1 ACTCGGTGAGCTCGGTGCAGCA
1902 CGTTTTCAAA
Statistics
Matches: 162, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
73 162 1.00
ACGTcount: A:0.29, C:0.19, G:0.26, T:0.25
Consensus pattern (73 bp):
ACTCGGTGAGCTCGGTGCAGCAAATCTTCAAATAGATCAGATTGATTCGGTGAATCAAGTCAATG
CGGTGCAA
Found at i:1949 original size:146 final size:146
Alignment explanation
Indices: 1661--1951 Score: 408
Period size: 146 Copynumber: 2.0 Consensus size: 146
1651 TCTCGATTGG
* * *
1661 ACTCGGTGAGCTCGTTGTAGCAAATCTTCAAATAGATCAGATTGATTCGGTGAATCAAGTCAATG
1 ACTCAGTGAGCTCGGTGCAGCAAATCTTCAAATAGATCAGATTGATTCGGTGAATCAAGTCAATG
* * * * *
1726 CGGTGCAAACTCGGTGAGCTCGGTGCAGCAAATCTTTAAATAGATCAGATTGATTCGGTGAATCA
66 CGGTGCAAACTCGGTGAGCTCGGTGCAGCAAATCTTTAAACAGATAAGATCGATTCAGTAAATCA
*
1791 AGTCAATGCGGTGCAA
131 AGTCAATACGGTGCAA
1807 ACTCAGTGAGCTCGGTGCAGCAAATCTTCAAATAGATCAGATTGATTCGGTGAATCAAGTCAATG
1 ACTCAGTGAGCTCGGTGCAGCAAATCTTCAAATAGATCAGATTGATTCGGTGAATCAAGTCAATG
**
1872 CGGTGCAAACTCGGTGAGCTCGGTGCAGCACGT-TTTCAAACA-ATTAAAGA-CGATTCAGTAAA
66 CGGTGCAAACTCGGTGAGCTCGGTGCAGCAAATCTTT-AAACAGA-T-AAGATCGATTCAGTAAA
* * *
1934 TTAAGTTACTACGGTGCA
128 TCAAGTCAATACGGTGCA
1952 GTATTTCTTC
Statistics
Matches: 128, Mismatches: 14, Indels: 6
0.86 0.09 0.04
Matches are distributed among these distances:
145 4 0.03
146 121 0.95
147 3 0.02
ACGTcount: A:0.31, C:0.19, G:0.24, T:0.26
Consensus pattern (146 bp):
ACTCAGTGAGCTCGGTGCAGCAAATCTTCAAATAGATCAGATTGATTCGGTGAATCAAGTCAATG
CGGTGCAAACTCGGTGAGCTCGGTGCAGCAAATCTTTAAACAGATAAGATCGATTCAGTAAATCA
AGTCAATACGGTGCAA
Found at i:6148 original size:30 final size:30
Alignment explanation
Indices: 6112--6169 Score: 98
Period size: 30 Copynumber: 1.9 Consensus size: 30
6102 CGTTTCGACA
6112 CATGGTCTTGCAAATGACACCAAAAGTTGT
1 CATGGTCTTGCAAATGACACCAAAAGTTGT
* *
6142 CATGGTCTTGCAACTGACACCAGAAGTT
1 CATGGTCTTGCAAATGACACCAAAAGTT
6170 ACCATGAAGT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.31, C:0.22, G:0.21, T:0.26
Consensus pattern (30 bp):
CATGGTCTTGCAAATGACACCAAAAGTTGT
Found at i:6192 original size:41 final size:40
Alignment explanation
Indices: 6135--6281 Score: 161
Period size: 41 Copynumber: 3.9 Consensus size: 40
6125 ATGACACCAA
* *
6135 AAGTTGTCATGGTCTTGCAACTGACACCAGAAGTTACCATG
1 AAGTTGTCATGATCTTGCAATTGACACCAGAAGTTA-CATG
6176 AAGTTGTCATGATCTTGCAATTG--A-C---A---ACA-G
1 AAGTTGTCATGATCTTGCAATTGACACCAGAAGTTACATG
* * *
6206 AAGTTGTCATGGTCTTGCAAATGACACCAGAAGTTGTCATG
1 AAGTTGTCATGATCTTGCAATTGACACCAGAAGTT-ACATG
6247 AAGTTGTCATGATCTTGCAATTGACACCAGAAGTT
1 AAGTTGTCATGATCTTGCAATTGACACCAGAAGTT
6282 GTCATGGTCT
Statistics
Matches: 88, Mismatches: 7, Indels: 22
0.75 0.06 0.19
Matches are distributed among these distances:
30 22 0.25
31 2 0.02
32 2 0.02
33 1 0.01
35 1 0.01
36 1 0.01
38 1 0.01
39 1 0.01
40 2 0.02
41 55 0.62
ACGTcount: A:0.31, C:0.18, G:0.22, T:0.29
Consensus pattern (40 bp):
AAGTTGTCATGATCTTGCAATTGACACCAGAAGTTACATG
Found at i:6211 original size:30 final size:30
Alignment explanation
Indices: 6175--6247 Score: 119
Period size: 30 Copynumber: 2.4 Consensus size: 30
6165 AAGTTACCAT
*
6175 GAAGTTGTCATGATCTTGCAATTGACAACA
1 GAAGTTGTCATGATCTTGCAAATGACAACA
* *
6205 GAAGTTGTCATGGTCTTGCAAATGACACCA
1 GAAGTTGTCATGATCTTGCAAATGACAACA
6235 GAAGTTGTCATGA
1 GAAGTTGTCATGA
6248 AGTTGTCATG
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 39 1.00
ACGTcount: A:0.32, C:0.16, G:0.23, T:0.29
Consensus pattern (30 bp):
GAAGTTGTCATGATCTTGCAAATGACAACA
Found at i:6233 original size:71 final size:71
Alignment explanation
Indices: 6112--6431 Score: 333
Period size: 71 Copynumber: 4.8 Consensus size: 71
6102 CGTTTCGACA
* * * *
6112 CATGGTCTTGCAAATGACACCAAAAGTTGTCATGGTCTTGCAACTGACACCAGAAGTTACCATGA
1 CATGATCTTGCAATTGACACCAGAAGTTGTCATGGTCTTGCAAATGACACCAGAAGTTACCATGA
6177 AGTTGT
66 AGTTGT
* **
6183 CATGATCTTGCAATTGACAACAGAAGTTGTCATGGTCTTGCAAATGACACCAGAAGTTGTCATGA
1 CATGATCTTGCAATTGACACCAGAAGTTGTCATGGTCTTGCAAATGACACCAGAAGTTACCATGA
6248 AGTTGT
66 AGTTGT
*
6254 CATGATCTTGCAATTGACACCAGAAGTTGTCATGGTCTTGCAATTG--A-C-------ACCA-GA
1 CATGATCTTGCAATTGACACCAGAAGTTGTCATGGTCTTGCAAATGACACCAGAAGTTACCATGA
6308 AGTTGT
66 AGTTGT
* * *
6314 CATGGTCTTGCAAATGACACCAGAAGTTGTCATGGTCTTGCAATTGACA-C------T---A-GA
1 CATGATCTTGCAATTGACACCAGAAGTTGTCATGGTCTTGCAAATGACACCAGAAGTTACCATGA
*
6368 AATTGT
66 AGTTGT
* * * * *
6374 CATGGTCTTGCAATTGACACCAGAAGTTGTCATGATTTTGCAATTGGCACCAGAAGTT
1 CATGATCTTGCAATTGACACCAGAAGTTGTCATGGTCTTGCAAATGACACCAGAAGTT
6432 GTCATGATTT
Statistics
Matches: 221, Mismatches: 18, Indels: 24
0.84 0.07 0.09
Matches are distributed among these distances:
60 105 0.48
61 3 0.01
62 2 0.01
67 1 0.00
68 1 0.00
69 1 0.00
71 108 0.49
ACGTcount: A:0.30, C:0.19, G:0.22, T:0.29
Consensus pattern (71 bp):
CATGATCTTGCAATTGACACCAGAAGTTGTCATGGTCTTGCAAATGACACCAGAAGTTACCATGA
AGTTGT
Found at i:6280 original size:30 final size:30
Alignment explanation
Indices: 6246--6651 Score: 560
Period size: 30 Copynumber: 13.5 Consensus size: 30
6236 AAGTTGTCAT
6246 GAAGTTGTCATGATCTTGCAATTGACACCA
1 GAAGTTGTCATGATCTTGCAATTGACACCA
*
6276 GAAGTTGTCATGGTCTTGCAATTGACACCA
1 GAAGTTGTCATGATCTTGCAATTGACACCA
* *
6306 GAAGTTGTCATGGTCTTGCAAATGACACCA
1 GAAGTTGTCATGATCTTGCAATTGACACCA
* *
6336 GAAGTTGTCATGGTCTTGCAATTGACACTA
1 GAAGTTGTCATGATCTTGCAATTGACACCA
* *
6366 GAAATTGTCATGGTCTTGCAATTGACACCA
1 GAAGTTGTCATGATCTTGCAATTGACACCA
* *
6396 GAAGTTGTCATGATTTTGCAATTGGCACCA
1 GAAGTTGTCATGATCTTGCAATTGACACCA
* *
6426 GAAGTTGTCATGATTTTGCAATTGACACCC
1 GAAGTTGTCATGATCTTGCAATTGACACCA
*
6456 GAAGTTGTCATGATTTTGCAATTGACACCA
1 GAAGTTGTCATGATCTTGCAATTGACACCA
* *
6486 GAAGCTGTCATGATGTTGCAATTGACACCA
1 GAAGTTGTCATGATCTTGCAATTGACACCA
* *
6516 GAAGCTATCATGATCTTGCAATTGACACCA
1 GAAGTTGTCATGATCTTGCAATTGACACCA
* *
6546 TAAGTTGTCATGATTTTGCAATTGACACCA
1 GAAGTTGTCATGATCTTGCAATTGACACCA
* ***
6576 TAAGTTGTCATGATCTTGCAATTGACAATT
1 GAAGTTGTCATGATCTTGCAATTGACACCA
* * * *
6606 GAAGATGTCATAATTTTATTCAATTGACACCA
1 GAAGTTGTCATGA-TCT-TGCAATTGACACCA
6638 GAAGTTGTCATGAT
1 GAAGTTGTCATGAT
6652 AAATTTCCAA
Statistics
Matches: 339, Mismatches: 35, Indels: 3
0.90 0.09 0.01
Matches are distributed among these distances:
30 315 0.93
31 3 0.01
32 21 0.06
ACGTcount: A:0.30, C:0.18, G:0.20, T:0.32
Consensus pattern (30 bp):
GAAGTTGTCATGATCTTGCAATTGACACCA
Found at i:6632 original size:32 final size:32
Alignment explanation
Indices: 6594--6700 Score: 108
Period size: 32 Copynumber: 3.3 Consensus size: 32
6584 CATGATCTTG
*
6594 CAATTGACAATTGAAGATGTCATAATTTTATT
1 CAATTGACACTTGAAGATGTCATAATTTTATT
** * ** *
6626 CAATTGACACCAGAAGTTGTCATGATAAATT-TC
1 CAATTGACACTTGAAGATGTCAT-A-ATTTTATT
* *
6659 CAATAGACACTTGAAGATGCCATAATTTTATT
1 CAATTGACACTTGAAGATGTCATAATTTTATT
6691 CAATTGACAC
1 CAATTGACAC
6701 CAGAAGTAAC
Statistics
Matches: 56, Mismatches: 16, Indels: 6
0.72 0.21 0.08
Matches are distributed among these distances:
31 3 0.05
32 30 0.54
33 20 0.36
34 3 0.05
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.34
Consensus pattern (32 bp):
CAATTGACACTTGAAGATGTCATAATTTTATT
Found at i:6694 original size:65 final size:62
Alignment explanation
Indices: 6384--6707 Score: 214
Period size: 60 Copynumber: 5.3 Consensus size: 62
6374 CATGGTCTTG
* * * * *** * * * *
6384 CAATTGACACCAGAAGTTGTCATGATTTTGCAATTGGCACCAGAAGTTGTCATGA-TTT-TG
1 CAATTGACACCAGAAGTTGTCATGATCTTCCAATAGACAATTGAAGATGCCATAATTTTATT
* * * * *** * * * * *
6444 CAATTGACACCCGAAGTTGTCATGATTTTGCAATTGACACCAGAAGCTGTCATGA-TGT-TG
1 CAATTGACACCAGAAGTTGTCATGATCTTCCAATAGACAATTGAAGATGCCATAATTTTATT
* * * * * * * *
6504 CAATTGACACCAGAAGCTATCATGATCTTGCAATTGACACCA-T-AAGTTGTCATGA-TTT-TG
1 CAATTGACACCAGAAGTTGTCATGATCTTCCAATAGACA--ATTGAAGATGCCATAATTTTATT
* * * *
6564 CAATTGACACCATAAGTTGTCATGATCTTGCAATTGACAATTGAAGATGTCATAATTTTATT
1 CAATTGACACCAGAAGTTGTCATGATCTTCCAATAGACAATTGAAGATGCCATAATTTTATT
* *
6626 CAATTGACACCAGAAGTTGTCATGATAAATTTCCAATAGACACTTGAAGATGCCATAATTTTATT
1 CAATTGACACCAGAAGTTGTCATGAT---CTTCCAATAGACAATTGAAGATGCCATAATTTTATT
6691 CAATTGACACCAGAAGT
1 CAATTGACACCAGAAGT
6708 AACGATTTTA
Statistics
Matches: 231, Mismatches: 24, Indels: 13
0.86 0.09 0.05
Matches are distributed among these distances:
58 1 0.00
59 1 0.00
60 152 0.66
61 3 0.01
62 26 0.11
65 48 0.21
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Consensus pattern (62 bp):
CAATTGACACCAGAAGTTGTCATGATCTTCCAATAGACAATTGAAGATGCCATAATTTTATT
Found at i:6733 original size:65 final size:64
Alignment explanation
Indices: 6564--6707 Score: 166
Period size: 65 Copynumber: 2.3 Consensus size: 64
6554 CATGATTTTG
* ** * * * * *
6564 CAATTGACACCATAAGTTGTCATGAT--CTTGCAATTGACAATTGAAGATGTCATAATTTTATT
1 CAATTGACACCAGAAGTTAACATGATAAATTTCAAATGACACTTGAAGATGCCATAATTTTATT
** *
6626 CAATTGACACCAGAAGTTGTCATGATAAATTTCCAATAGACACTTGAAGATGCCATAATTTTATT
1 CAATTGACACCAGAAGTTAACATGATAAATTTCAAAT-GACACTTGAAGATGCCATAATTTTATT
6691 CAATTGACACCAGAAGT
1 CAATTGACACCAGAAGT
6708 AACGATTTTA
Statistics
Matches: 72, Mismatches: 7, Indels: 3
0.88 0.09 0.04
Matches are distributed among these distances:
62 25 0.35
64 5 0.07
65 42 0.58
ACGTcount: A:0.36, C:0.17, G:0.15, T:0.33
Consensus pattern (64 bp):
CAATTGACACCAGAAGTTAACATGATAAATTTCAAATGACACTTGAAGATGCCATAATTTTATT
Found at i:9569 original size:15 final size:16
Alignment explanation
Indices: 9536--9575 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
9526 TTACTTTGTT
9536 TTGTTTTCTAGTATAA
1 TTGTTTTCTAGTATAA
*
9552 TTGTTTTCT-GTTTAA
1 TTGTTTTCTAGTATAA
*
9567 TTGCTTTCT
1 TTGTTTTCT
9576 TTCAACCTCT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 13 0.59
16 9 0.41
ACGTcount: A:0.15, C:0.10, G:0.12, T:0.62
Consensus pattern (16 bp):
TTGTTTTCTAGTATAA
Found at i:12986 original size:21 final size:21
Alignment explanation
Indices: 12941--12992 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
12931 CCATTCACCG
* *
12941 TGCCACCACCGGTTAAGCCCG
1 TGCCACCACCGGCTAAGCCCA
12962 TGCCACCACCGGCTATA-CCCA
1 TGCCACCACCGGCTA-AGCCCA
*
12983 TGCCATCACC
1 TGCCACCACC
12993 ATTTAGGGCC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
21 26 0.96
22 1 0.04
ACGTcount: A:0.21, C:0.46, G:0.17, T:0.15
Consensus pattern (21 bp):
TGCCACCACCGGCTAAGCCCA
Found at i:16329 original size:15 final size:16
Alignment explanation
Indices: 16305--16344 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
16295 AGAGGTTGAA
*
16305 AGAAAGCAATTAAAC-
1 AGAAAACAATTAAACT
*
16320 AGAAAACAATTATACT
1 AGAAAACAATTAAACT
16336 AGAAAACAA
1 AGAAAACAA
16345 AGCAAAGTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 13 0.59
16 9 0.41
ACGTcount: A:0.62, C:0.12, G:0.10, T:0.15
Consensus pattern (16 bp):
AGAAAACAATTAAACT
Done.