Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014045.1 Corchorus olitorius cultivar O-4 contig14078, 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: 68832
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:1339 original size:22 final size:22
Alignment explanation
Indices: 1248--1330 Score: 78
Period size: 22 Copynumber: 3.8 Consensus size: 22
1238 GTCATTGTGT
* *
1248 GGTTATCAAAATTCCATAAT-AA
1 GGTTATCAAAATTTCAT-ATGGA
* * * *
1270 GATTATTAAAAATTCATAAGGA
1 GGTTATCAAAATTTCATATGGA
* *
1292 TGTCATCAAAATTTCATATGGA
1 GGTTATCAAAATTTCATATGGA
1314 GGTTATCAAAATTTCAT
1 GGTTATCAAAATTTCAT
1331 TGTATGGTTT
Statistics
Matches: 46, Mismatches: 14, Indels: 2
0.74 0.23 0.03
Matches are distributed among these distances:
21 1 0.02
22 45 0.98
ACGTcount: A:0.42, C:0.11, G:0.12, T:0.35
Consensus pattern (22 bp):
GGTTATCAAAATTTCATATGGA
Found at i:1524 original size:6 final size:6
Alignment explanation
Indices: 1513--1538 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
1503 TAAAGTCAAG
1513 AAATAC AAATAC AAATAC AAATAC AA
1 AAATAC AAATAC AAATAC AAATAC AA
1539 TGAAGTATAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.69, C:0.15, G:0.00, T:0.15
Consensus pattern (6 bp):
AAATAC
Found at i:2780 original size:2 final size:2
Alignment explanation
Indices: 2773--2804 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
2763 GAGCTAGTTA
2773 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2805 TTGGTGATGG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5202 original size:26 final size:26
Alignment explanation
Indices: 5145--5203 Score: 73
Period size: 26 Copynumber: 2.2 Consensus size: 26
5135 GATATATTAG
* * *
5145 ATTTTTTAAATATATTTCTTACTCTT
1 ATTTTTCAAATATATTTCTTAATCTC
*
5171 ATTTTTCAAATATATTTCTTAAATGTC
1 ATTTTTCAAATATATTTCTT-AATCTC
5198 ATTTTT
1 ATTTTT
5204 AAACTTTTAC
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
26 19 0.68
27 9 0.32
ACGTcount: A:0.29, C:0.10, G:0.02, T:0.59
Consensus pattern (26 bp):
ATTTTTCAAATATATTTCTTAATCTC
Found at i:5310 original size:125 final size:126
Alignment explanation
Indices: 5178--5416 Score: 329
Period size: 126 Copynumber: 1.9 Consensus size: 126
5168 CTTATTTTTC
* * ** *
5178 AAATATATTTCTTAAATGTCATT-TTTAAACTTTTACAATTTTACTCAATTAAAAACTCTATTTT
1 AAATATATTTCTTAAATGACATTATTTAAAATTTTACAATTTTACTCAACCAAAAACTCTATTCT
* *
5242 TATTTAATCAAA-TCTAATATATTTATAATTATTTTATTTTTACCATTTTACTATTTTAATT
66 TATTTAATCAAATTC-AATATATTTATAACTATTTTATCTTTACCATTTTACTATTTTAATT
* * ** *
5303 AAATATATTTCTTAAATGACATTATTTAAAATTTTACAGTTTTATTTTACCAAAAATTCTATTCT
1 AAATATATTTCTTAAATGACATTATTTAAAATTTTACAATTTTACTCAACCAAAAACTCTATTCT
* *
5368 TATTTAATTAAATTCAATATTTTTATAACTATTTTATCTTTACCATTTT
66 TATTTAATCAAATTCAATATATTTATAACTATTTTATCTTTACCATTTT
5417 TTTAGGGATT
Statistics
Matches: 98, Mismatches: 14, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
125 22 0.22
126 74 0.76
127 2 0.02
ACGTcount: A:0.36, C:0.10, G:0.01, T:0.52
Consensus pattern (126 bp):
AAATATATTTCTTAAATGACATTATTTAAAATTTTACAATTTTACTCAACCAAAAACTCTATTCT
TATTTAATCAAATTCAATATATTTATAACTATTTTATCTTTACCATTTTACTATTTTAATT
Found at i:5596 original size:31 final size:31
Alignment explanation
Indices: 5560--5684 Score: 218
Period size: 31 Copynumber: 4.1 Consensus size: 31
5550 ACTAAATACT
5560 AAAAAAATCCCTTATGTTTTTCTTTTGGGAC
1 AAAAAAATCCCTTATGTTTTTCTTTTGGGAC
5591 -AAAAAATCCCTTATGTTTTTCTTTTGGGAC
1 AAAAAAATCCCTTATGTTTTTCTTTTGGGAC
5621 AAAAAAATCCCTTATGTTTTTCTTTTGGGAC
1 AAAAAAATCCCTTATGTTTTTCTTTTGGGAC
* *
5652 AGATAAATCCCTTATGTTTTT-TTTTGGGAC
1 AAAAAAATCCCTTATGTTTTTCTTTTGGGAC
5682 AAA
1 AAA
5685 TTAGTCCCTT
Statistics
Matches: 90, Mismatches: 3, Indels: 3
0.94 0.03 0.03
Matches are distributed among these distances:
30 41 0.46
31 49 0.54
ACGTcount: A:0.29, C:0.15, G:0.14, T:0.42
Consensus pattern (31 bp):
AAAAAAATCCCTTATGTTTTTCTTTTGGGAC
Found at i:5693 original size:30 final size:31
Alignment explanation
Indices: 5564--5694 Score: 212
Period size: 30 Copynumber: 4.3 Consensus size: 31
5554 AATACTAAAA
5564 AAATCCCTTATGTTTTTCTTTTGGGACAAA-
1 AAATCCCTTATGTTTTTCTTTTGGGACAAAT
*
5594 AAATCCCTTATGTTTTTCTTTTGGGACAAAA
1 AAATCCCTTATGTTTTTCTTTTGGGACAAAT
*
5625 AAATCCCTTATGTTTTTCTTTTGGGACAGAT
1 AAATCCCTTATGTTTTTCTTTTGGGACAAAT
5656 AAATCCCTTATGTTTTT-TTTTGGGACAAAT
1 AAATCCCTTATGTTTTTCTTTTGGGACAAAT
* *
5686 TAGTCCCTT
1 AAATCCCTT
5695 GCTGAGGTGG
Statistics
Matches: 95, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
30 49 0.52
31 46 0.48
ACGTcount: A:0.25, C:0.17, G:0.14, T:0.44
Consensus pattern (31 bp):
AAATCCCTTATGTTTTTCTTTTGGGACAAAT
Found at i:5694 original size:61 final size:61
Alignment explanation
Indices: 5560--5684 Score: 225
Period size: 61 Copynumber: 2.0 Consensus size: 61
5550 ACTAAATACT
5560 AAAAAAATCCCTTATGTTTTTCTTTTGGGACAAAAAATCCCTTATGTTTTTCTTTTGGGAC
1 AAAAAAATCCCTTATGTTTTTCTTTTGGGACAAAAAATCCCTTATGTTTTTCTTTTGGGAC
*
5621 AAAAAAATCCCTTATGTTTTTCTTTTGGGACAGATAAATCCCTTATGTTTTT-TTTTGGGAC
1 AAAAAAATCCCTTATGTTTTTCTTTTGGGACA-AAAAATCCCTTATGTTTTTCTTTTGGGAC
5682 AAA
1 AAA
5685 TTAGTCCCTT
Statistics
Matches: 62, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
61 44 0.71
62 18 0.29
ACGTcount: A:0.29, C:0.15, G:0.14, T:0.42
Consensus pattern (61 bp):
AAAAAAATCCCTTATGTTTTTCTTTTGGGACAAAAAATCCCTTATGTTTTTCTTTTGGGAC
Found at i:15089 original size:19 final size:22
Alignment explanation
Indices: 15048--15092 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 22
15038 ATTATAAATT
*
15048 GCTACCCCTAGAAAAATTATTG
1 GCTACCCCTAGAAAAAATATTG
15070 GCTACCCC-A-AAAAAAT-TTG
1 GCTACCCCTAGAAAAAATATTG
15089 GCTA
1 GCTA
15093 TTAATATTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
19 7 0.32
20 6 0.27
21 1 0.05
22 8 0.36
ACGTcount: A:0.38, C:0.24, G:0.13, T:0.24
Consensus pattern (22 bp):
GCTACCCCTAGAAAAAATATTG
Found at i:16645 original size:35 final size:35
Alignment explanation
Indices: 16594--16751 Score: 183
Period size: 35 Copynumber: 4.5 Consensus size: 35
16584 CTTAAAGACA
*
16594 AATCAAT-AGGACCAACAAGCAACATGGAAAGCTT
1 AATCAATAAGGGCCAACAAGCAACATGGAAAGCTT
* * *
16628 ACTCAATAAGGGCCAACAAGCATCATGGATAGCTT
1 AATCAATAAGGGCCAACAAGCAACATGGAAAGCTT
* *
16663 AATCATTAAGGGCCAATAAGCAACATGGAAAGCTT
1 AATCAATAAGGGCCAACAAGCAACATGGAAAGCTT
* * * * *
16698 AATCAACAAAGGCCAAGAAGCACCATGGAAAACTT
1 AATCAATAAGGGCCAACAAGCAACATGGAAAGCTT
* * *
16733 AGTTAATAAGAGCCAACAA
1 AATCAATAAGGGCCAACAA
16752 CCACCATTGT
Statistics
Matches: 102, Mismatches: 21, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
34 6 0.06
35 96 0.94
ACGTcount: A:0.45, C:0.20, G:0.18, T:0.16
Consensus pattern (35 bp):
AATCAATAAGGGCCAACAAGCAACATGGAAAGCTT
Found at i:19067 original size:17 final size:17
Alignment explanation
Indices: 19042--19078 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
19032 GGGTATTAAA
19042 CCATAATGGTTTAATAC
1 CCATAATGGTTTAATAC
*
19059 CCATTATGGTTTAATAC
1 CCATAATGGTTTAATAC
19076 CCA
1 CCA
19079 AATTAGCCCC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.32, C:0.22, G:0.11, T:0.35
Consensus pattern (17 bp):
CCATAATGGTTTAATAC
Found at i:19848 original size:29 final size:29
Alignment explanation
Indices: 19825--19885 Score: 81
Period size: 29 Copynumber: 2.1 Consensus size: 29
19815 TATTTTGTTT
19825 CCTGAACTTT-AATTTTGGACATTTTACTC
1 CCTGAA-TTTCAATTTTGGACATTTTACTC
*
19854 CCTGAATTTCAATTTTGGGACGTTTTAC-C
1 CCTGAATTTCAATTTT-GGACATTTTACTC
19883 CCT
1 CCT
19886 TCAGCCTAAC
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
28 3 0.10
29 16 0.55
30 10 0.34
ACGTcount: A:0.21, C:0.23, G:0.13, T:0.43
Consensus pattern (29 bp):
CCTGAATTTCAATTTTGGACATTTTACTC
Found at i:20098 original size:29 final size:29
Alignment explanation
Indices: 20065--20124 Score: 95
Period size: 29 Copynumber: 2.1 Consensus size: 29
20055 AAACGTCCCC
*
20065 AAATTGAAGTTCAAGGGA-CAAAATATCCA
1 AAATTGAAATTC-AGGGAGCAAAATATCCA
20094 AAATTGAAATTCAGGGAGCAAAATATCCA
1 AAATTGAAATTCAGGGAGCAAAATATCCA
20123 AA
1 AA
20125 CGCTACAAGT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
28 5 0.17
29 24 0.83
ACGTcount: A:0.50, C:0.13, G:0.17, T:0.20
Consensus pattern (29 bp):
AAATTGAAATTCAGGGAGCAAAATATCCA
Found at i:30646 original size:14 final size:14
Alignment explanation
Indices: 30627--30660 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
30617 TTTTATAATT
30627 ATTTTATTTTTACC
1 ATTTTATTTTTACC
*
30641 ATTTTATTTTTACT
1 ATTTTATTTTTACC
30655 ATTTTA
1 ATTTTA
30661 ATTTAAAAGA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.24, C:0.09, G:0.00, T:0.68
Consensus pattern (14 bp):
ATTTTATTTTTACC
Found at i:31170 original size:25 final size:26
Alignment explanation
Indices: 31114--31175 Score: 108
Period size: 25 Copynumber: 2.4 Consensus size: 26
31104 CGAGCCAATC
31114 TCTTGGGTTTGATCGGGCTCAGGTAA
1 TCTTGGGTTTGATCGGGCTCAGGTAA
31140 TCTTGGGTTTGATCGGG-TCAGGTAA
1 TCTTGGGTTTGATCGGGCTCAGGTAA
*
31165 TTTTGGGTTTG
1 TCTTGGGTTTG
31176 GGTCGTTTCA
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
25 18 0.51
26 17 0.49
ACGTcount: A:0.13, C:0.11, G:0.35, T:0.40
Consensus pattern (26 bp):
TCTTGGGTTTGATCGGGCTCAGGTAA
Found at i:31592 original size:26 final size:26
Alignment explanation
Indices: 31556--31608 Score: 97
Period size: 26 Copynumber: 2.0 Consensus size: 26
31546 AGTCTCAAAC
*
31556 TCTCTCCTCAATTTTGGGATTCTTCG
1 TCTCACCTCAATTTTGGGATTCTTCG
31582 TCTCACCTCAATTTTGGGATTCTTCG
1 TCTCACCTCAATTTTGGGATTCTTCG
31608 T
1 T
31609 ATAATTAGAG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.13, C:0.26, G:0.15, T:0.45
Consensus pattern (26 bp):
TCTCACCTCAATTTTGGGATTCTTCG
Found at i:32901 original size:18 final size:17
Alignment explanation
Indices: 32868--32901 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
32858 GGGTCCCACA
*
32868 TAAAAATATTTTAAAAT
1 TAAAAATATTTCAAAAT
32885 TAAAAATATTTCCAAAA
1 TAAAAATATTT-CAAAA
32902 GAAAAAAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.59, C:0.06, G:0.00, T:0.35
Consensus pattern (17 bp):
TAAAAATATTTCAAAAT
Found at i:36961 original size:2 final size:2
Alignment explanation
Indices: 36954--37035 Score: 52
Period size: 2 Copynumber: 44.5 Consensus size: 2
36944 GTTTAATAAT
* * *
36954 TA TA TA TA TT TA T- TA T- TA TA TA TA TT TA TA TA TA TA TA TC
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * *
36994 TA -A TA T- TA T- TA TA -A TA T- TT TA TA TA AA TT TA AA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
37031 TA TA T
1 TA TA T
37036 TAGTAAACGG
Statistics
Matches: 60, Mismatches: 13, Indels: 14
0.69 0.15 0.16
Matches are distributed among these distances:
1 7 0.12
2 53 0.88
ACGTcount: A:0.44, C:0.01, G:0.00, T:0.55
Consensus pattern (2 bp):
TA
Found at i:36973 original size:16 final size:15
Alignment explanation
Indices: 36952--37036 Score: 79
Period size: 14 Copynumber: 5.8 Consensus size: 15
36942 CGGTTTAATA
36952 ATTATATATATTTATT
1 ATTATATATATTTA-T
36968 ATTATATATATTTAT
1 ATTATATATATTTAT
*
36983 A-TATATATATCTAAT
1 ATTATATATAT-TTAT
*
36998 ATTAT-TATA-ATAT
1 ATTATATATATTTAT
* *
37011 TTTATATAAATTTA-
1 ATTATATATATTTAT
*
37025 AATATATATATT
1 ATTATATATATT
37037 AGTAAACGGT
Statistics
Matches: 56, Mismatches: 9, Indels: 10
0.75 0.12 0.13
Matches are distributed among these distances:
13 6 0.11
14 21 0.38
15 12 0.21
16 17 0.30
ACGTcount: A:0.44, C:0.01, G:0.00, T:0.55
Consensus pattern (15 bp):
ATTATATATATTTAT
Found at i:38205 original size:325 final size:324
Alignment explanation
Indices: 37748--38399 Score: 1243
Period size: 325 Copynumber: 2.0 Consensus size: 324
37738 TCAATTCAGA
*
37748 ATTTTATATTAAATTAATTTTGATAAGCACATAATGATCAACATAATAATTAAACACTCTATATT
1 ATTTTATATAAAATTAATTTTGATAAGCACATAATGATCAACATAATAATTAAACACTCTATATT
37813 TCAAAATATCACACTTTAAAGAACTTTATATTACCCAAAATATCCATCACTTTAGATAACAAATA
66 TCAAAATATCACACTTTAAAGAACTTTATATTACCCAAAATATCCATCACTTTAGATAACAAATA
37878 AATCATTAATTTTTTTAGTAGTATTTATGTTACAATGTATATTTGAAAATTTTCATTATATTATT
131 AATCATTAATTTTTTTAGTAGTATTTATGTTACAATGTATATTTGAAAATTTTCATTATATTATT
37943 ATTGCTCGCAAAAGTAATAGTATTAATGTACTAAATTATTTTTTATCCTCTCAAATAAATATTTT
196 ATTGCTCGCAAAAGTAATAGTATTAATGTACTAAATTATTTTTTATCCTCTCAAATAAATA-TTT
*
38008 TTGCATTAAATTATTCCCTAAAATTATAAGAAAAATTGTAAGATACATT-AAAGTTTCTTTTTAT
260 TTGCATTAAATTATTCCCTAAAATTAAAAGAAAAATTGTAAGATACATTAAAAG-TTCTTTTTAT
38072 G
324 G
38073 ATTTTATATAAAATTAATTTTGATAAGCACATAATGATCAACATAATAATTAAACACTCTATATT
1 ATTTTATATAAAATTAATTTTGATAAGCACATAATGATCAACATAATAATTAAACACTCTATATT
*
38138 TCAAAATATCTCACTTTAAAGAACTTTATATTACCCAAAATATCCATCACTTTAGATAACAAATA
66 TCAAAATATCACACTTTAAAGAACTTTATATTACCCAAAATATCCATCACTTTAGATAACAAATA
*
38203 AATCATTAATTTTTTTAGTAGTATTTATGTTACAATGTATCTTTGAAAATTTTCATTATATTATT
131 AATCATTAATTTTTTTAGTAGTATTTATGTTACAATGTATATTTGAAAATTTTCATTATATTATT
38268 ATTGCTCGCAAAAGTAATAGTATTAATGTACTAAATTATTTTTTATCCTCTCAAATAAATATTTT
196 ATTGCTCGCAAAAGTAATAGTATTAATGTACTAAATTATTTTTTATCCTCTCAAATAAATATTTT
38333 TGCATTAAATTATTCCCTAAAATTAAAAGAAAAATTGTAAGATACATTAAAAGTTCTTTTTATG
261 TGCATTAAATTATTCCCTAAAATTAAAAGAAAAATTGTAAGATACATTAAAAGTTCTTTTTATG
38397 ATT
1 ATT
38400 AATTTTAGCT
Statistics
Matches: 322, Mismatches: 4, Indels: 3
0.98 0.01 0.01
Matches are distributed among these distances:
324 65 0.20
325 257 0.80
ACGTcount: A:0.40, C:0.12, G:0.06, T:0.42
Consensus pattern (324 bp):
ATTTTATATAAAATTAATTTTGATAAGCACATAATGATCAACATAATAATTAAACACTCTATATT
TCAAAATATCACACTTTAAAGAACTTTATATTACCCAAAATATCCATCACTTTAGATAACAAATA
AATCATTAATTTTTTTAGTAGTATTTATGTTACAATGTATATTTGAAAATTTTCATTATATTATT
ATTGCTCGCAAAAGTAATAGTATTAATGTACTAAATTATTTTTTATCCTCTCAAATAAATATTTT
TGCATTAAATTATTCCCTAAAATTAAAAGAAAAATTGTAAGATACATTAAAAGTTCTTTTTATG
Found at i:39684 original size:22 final size:22
Alignment explanation
Indices: 39656--39698 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
39646 ATTGTTATGG
* *
39656 AAGAATGGAGGGAAGGAAGAGA
1 AAGAATGGAGAGAAGAAAGAGA
*
39678 AAGAATGTAGAGAAGAAAGAG
1 AAGAATGGAGAGAAGAAAGAG
39699 GAAGGGGCGG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.53, C:0.00, G:0.40, T:0.07
Consensus pattern (22 bp):
AAGAATGGAGAGAAGAAAGAGA
Found at i:40775 original size:31 final size:31
Alignment explanation
Indices: 40695--40776 Score: 89
Period size: 29 Copynumber: 2.7 Consensus size: 31
40685 TGATCCGACG
* *
40695 TGGCCTTGCCACGTGACATTTTGGTACTATG
1 TGGCATTGCCACGTGACATTTTGGTACTATA
* *
40726 TGACA-TG-GACGTGACATTTTGGTA-TGATA
1 TGGCATTGCCACGTGACATTTTGGTACT-ATA
*
40755 TGGCATTGCCACGTGTCATTTT
1 TGGCATTGCCACGTGACATTTT
40777 TGGTCCGACG
Statistics
Matches: 41, Mismatches: 7, Indels: 6
0.76 0.13 0.11
Matches are distributed among these distances:
28 1 0.02
29 22 0.54
30 4 0.10
31 14 0.34
ACGTcount: A:0.20, C:0.18, G:0.26, T:0.37
Consensus pattern (31 bp):
TGGCATTGCCACGTGACATTTTGGTACTATA
Found at i:45873 original size:36 final size:36
Alignment explanation
Indices: 45824--45899 Score: 134
Period size: 36 Copynumber: 2.1 Consensus size: 36
45814 CAAGGAAAAG
* *
45824 GAAAGGGGGTTAATTTGGATGGATAAAGATGTTTAT
1 GAAAAGGGGTTAATTTGGATGGATAAAGATGATTAT
45860 GAAAAGGGGTTAATTTGGATGGATAAAGATGATTAT
1 GAAAAGGGGTTAATTTGGATGGATAAAGATGATTAT
45896 GAAA
1 GAAA
45900 CAAAGCAGTA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 38 1.00
ACGTcount: A:0.38, C:0.00, G:0.32, T:0.30
Consensus pattern (36 bp):
GAAAAGGGGTTAATTTGGATGGATAAAGATGATTAT
Found at i:57045 original size:2 final size:2
Alignment explanation
Indices: 57040--57065 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
57030 GAGGGAGAAT
57040 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
57066 CTTGTCCCAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:57437 original size:27 final size:25
Alignment explanation
Indices: 57371--57438 Score: 64
Period size: 27 Copynumber: 2.5 Consensus size: 25
57361 ACAATGGGCC
57371 TTAGTAATTAATTATTGGTTTATTAT
1 TTAGTAA-TAATTATTGGTTTATTAT
* * *
57397 TCACATAAAAAATTATTGGTTTATTAT
1 TTA-GT-AATAATTATTGGTTTATTAT
57424 GATTAGTAATAATTA
1 --TTAGTAATAATTA
57439 ATTACAAGTC
Statistics
Matches: 32, Mismatches: 6, Indels: 7
0.71 0.13 0.16
Matches are distributed among these distances:
26 2 0.06
27 25 0.78
28 3 0.09
29 2 0.06
ACGTcount: A:0.38, C:0.03, G:0.10, T:0.49
Consensus pattern (25 bp):
TTAGTAATAATTATTGGTTTATTAT
Found at i:58852 original size:199 final size:199
Alignment explanation
Indices: 58512--58884 Score: 674
Period size: 199 Copynumber: 1.9 Consensus size: 199
58502 AGTTGAACCG
* * * * *
58512 GTCGGTGGAGTTTAGCAGACTGCACAAGCGGGTCTTGAAGGGTGACATGTGTCCCCTAGGGACTA
1 GTCGGTGGAGTTTAGCAAACTACACAAGCGGGTCTTAAAGGGTGACATGTGTCACCTAGAGACTA
58577 GATTGAAATATTTAAAATTTAATTAATTTAGAAAATGGACATGTGTAAACTCCACAACCCGCTTG
66 GATTGAAATATTTAAAATTTAATTAATTTAGAAAATGGACATGTGTAAACTCCACAACCCGCTTG
58642 TGGAGTCCAAGATTTACACCGCCGGTGTATCAAATAATTTCCCTTATAAGGGTTTATATATAATA
131 TGGAGTCCAAGATTTACACCGCCGGTGTATCAAATAATTTCCCTTATAAGGGTTTATATATAATA
58707 CACC
196 CACC
*
58711 GTCGGTGGAGTTTAGCAAACTACACAAGCGGGTTTTAAAGGGTGACATGTGTCACCTAGAGACTA
1 GTCGGTGGAGTTTAGCAAACTACACAAGCGGGTCTTAAAGGGTGACATGTGTCACCTAGAGACTA
* *
58776 GATTGAAATATTTAAAATTTAATTAATTTAGAAAATGGACATGTGTCAACTCCACAACCCGTTTG
66 GATTGAAATATTTAAAATTTAATTAATTTAGAAAATGGACATGTGTAAACTCCACAACCCGCTTG
58841 TGGAGTCCAAGATTTACACCGCCGGTGTATCAAATAATTTCCCT
131 TGGAGTCCAAGATTTACACCGCCGGTGTATCAAATAATTTCCCT
58885 AATTATAATA
Statistics
Matches: 166, Mismatches: 8, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
199 166 1.00
ACGTcount: A:0.32, C:0.18, G:0.21, T:0.29
Consensus pattern (199 bp):
GTCGGTGGAGTTTAGCAAACTACACAAGCGGGTCTTAAAGGGTGACATGTGTCACCTAGAGACTA
GATTGAAATATTTAAAATTTAATTAATTTAGAAAATGGACATGTGTAAACTCCACAACCCGCTTG
TGGAGTCCAAGATTTACACCGCCGGTGTATCAAATAATTTCCCTTATAAGGGTTTATATATAATA
CACC
Found at i:58924 original size:25 final size:25
Alignment explanation
Indices: 58896--58948 Score: 88
Period size: 25 Copynumber: 2.1 Consensus size: 25
58886 ATTATAATAC
*
58896 AAAATACTTGGAAAGAATATCATTA
1 AAAATACTTAGAAAGAATATCATTA
*
58921 AAAATACTTAGAAAGAATATCGTTA
1 AAAATACTTAGAAAGAATATCATTA
58946 AAA
1 AAA
58949 TTTTAATTGG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.55, C:0.08, G:0.11, T:0.26
Consensus pattern (25 bp):
AAAATACTTAGAAAGAATATCATTA
Found at i:61302 original size:57 final size:57
Alignment explanation
Indices: 61214--61329 Score: 223
Period size: 57 Copynumber: 2.0 Consensus size: 57
61204 CCATTGCAGA
*
61214 AAACTCCATTATCTAAACTTACACCTTCCTTCGAATCGAATTCGATTTTGGATGAAC
1 AAACTCCATGATCTAAACTTACACCTTCCTTCGAATCGAATTCGATTTTGGATGAAC
61271 AAACTCCATGATCTAAACTTACACCTTCCTTCGAATCGAATTCGATTTTGGATGAAC
1 AAACTCCATGATCTAAACTTACACCTTCCTTCGAATCGAATTCGATTTTGGATGAAC
61328 AA
1 AA
61330 CAAGGATTAG
Statistics
Matches: 58, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
57 58 1.00
ACGTcount: A:0.33, C:0.24, G:0.11, T:0.32
Consensus pattern (57 bp):
AAACTCCATGATCTAAACTTACACCTTCCTTCGAATCGAATTCGATTTTGGATGAAC
Done.