Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012293.1 Corchorus olitorius cultivar O-4 contig12326, 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: 49959
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31
Found at i:3933 original size:44 final size:41
Alignment explanation
Indices: 3842--4113 Score: 292
Period size: 41 Copynumber: 6.5 Consensus size: 41
3832 CAAGGATCAA
* * * * * *
3842 ATGACTTGGTCTTTAATTAACAATCTAATTCAAGGGTCTTG
1 ATGACTTGATCTTGAATTGATAATTTAATTCAAGGGTCTCG
* * * * *
3883 ACGACTTGGTCTTGAATTGATAATAATTCGATTCAAGAGACTCG
1 ATGACTTGATCTTGAATTGATAAT--TT-AATTCAAGGGTCTCG
* ** *
3927 ATGACTTGGTCTTGAATTGATAACAATTCGATTCAAGAGTCTCG
1 ATGACTTGATCTTGAATTGAT---AATTTAATTCAAGGGTCTCG
* *
3971 ATGACTTGTTCTTGAATTGATAATTTAATTCGAGGGTCTCG
1 ATGACTTGATCTTGAATTGATAATTTAATTCAAGGGTCTCG
**
4012 ATGACTCAATCTTGAATTGATAATTTAATTCAAGGGTCTCG
1 ATGACTTGATCTTGAATTGATAATTTAATTCAAGGGTCTCG
**
4053 ATGACTCAATCTTGAATTGATAATTTAATTCAAGGGTCTCG
1 ATGACTTGATCTTGAATTGATAATTTAATTCAAGGGTCTCG
*
4094 ATGACTTGTTCTTGAATTGA
1 ATGACTTGATCTTGAATTGA
4114 ATTGATAATT
Statistics
Matches: 201, Mismatches: 24, Indels: 12
0.85 0.10 0.05
Matches are distributed among these distances:
41 131 0.65
43 1 0.00
44 65 0.32
45 1 0.00
47 3 0.01
ACGTcount: A:0.29, C:0.14, G:0.19, T:0.37
Consensus pattern (41 bp):
ATGACTTGATCTTGAATTGATAATTTAATTCAAGGGTCTCG
Found at i:4621 original size:21 final size:21
Alignment explanation
Indices: 4595--4636 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
4585 ATCTTTTCCT
4595 TCCTTCCCCGGCAACGACGCC
1 TCCTTCCCCGGCAACGACGCC
*
4616 TCCTTCCCCGGCAACGGCGCC
1 TCCTTCCCCGGCAACGACGCC
4637 AAAATTGTGA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.12, C:0.52, G:0.21, T:0.14
Consensus pattern (21 bp):
TCCTTCCCCGGCAACGACGCC
Found at i:5151 original size:27 final size:27
Alignment explanation
Indices: 5110--5200 Score: 128
Period size: 27 Copynumber: 3.4 Consensus size: 27
5100 GCTACTTCTT
* * *
5110 ATTTTGGCCACTTGCATGTCCAGGGGC
1 ATTTTGGTCATTTGCACGTCCAGGGGC
*
5137 ATTTTGGTCATTTGCACGCCCAGGGGC
1 ATTTTGGTCATTTGCACGTCCAGGGGC
* *
5164 ATTTTGGTCATTTGCGCATCCAGGGGC
1 ATTTTGGTCATTTGCACGTCCAGGGGC
5191 ATTTTGGTCA
1 ATTTTGGTCA
5201 CTTCAAGTAC
Statistics
Matches: 57, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 57 1.00
ACGTcount: A:0.15, C:0.23, G:0.29, T:0.33
Consensus pattern (27 bp):
ATTTTGGTCATTTGCACGTCCAGGGGC
Found at i:8946 original size:36 final size:36
Alignment explanation
Indices: 8858--9506 Score: 606
Period size: 35 Copynumber: 18.4 Consensus size: 36
8848 CATATGCTAA
* * * *
8858 AGTTAATTTCAAGATGATCCGGGGCGATC-TTTCTTT
1 AGTTTATTTC-AGTTGATCCAGGGCGATCTTTTCTTC
* ** * *
8894 GGTTTATACCATTTGATCCAGGGCGATCTTTTATTC
1 AGTTTATTTCAGTTGATCCAGGGCGATCTTTTCTTC
* * *
8930 AGTTTATTTCAGTTGATCTAGGGTGAT-ATTTCTTC
1 AGTTTATTTCAGTTGATCCAGGGCGATCTTTTCTTC
** * * * * *
8965 AGAATATTTCAGTCGACCCAGGGAGGTC-TTTCTCC
1 AGTTTATTTCAGTTGATCCAGGGCGATCTTTTCTTC
* * *
9000 AATTTATTTCAGTTGATCCAGGGCGGTC-TTTCTTT
1 AGTTTATTTCAGTTGATCCAGGGCGATCTTTTCTTC
* ** * *
9035 AGTTTATTTTAGGCGA-CCTAGGGTGGTC-TTTCTTC
1 AGTTTATTTCAGTTGATCC-AGGGCGATCTTTTCTTC
*
9070 AGTTTA--T---TTGATCCAAGGCGATCTTTTCTTC
1 AGTTTATTTCAGTTGATCCAGGGCGATCTTTTCTTC
9101 AAGTTTATTTCAGTTGATCCAGGGCGATCTTTTCTTC
1 -AGTTTATTTCAGTTGATCCAGGGCGATCTTTTCTTC
* *
9138 AGTTTATTTTAGTTGATCCAGGGCGATCCTTTCTTC
1 AGTTTATTTCAGTTGATCCAGGGCGATCTTTTCTTC
*
9174 AAG-TTATTTCAGTTGACCCAGGGCGATCTTTTCTTC
1 -AGTTTATTTCAGTTGATCCAGGGCGATCTTTTCTTC
* *
9210 AGTTTATTTAAGTTGATCCAGGGCGATCCTTTCTTC
1 AGTTTATTTCAGTTGATCCAGGGCGATCTTTTCTTC
* * * *
9246 AAG-TTATTTTAGTTGACCCAGGGCGGTC-TTTCTCC
1 -AGTTTATTTCAGTTGATCCAGGGCGATCTTTTCTTC
*
9281 AATTTATTTCAGTTGATCCAGGGCGATC-TTTCTTC
1 AGTTTATTTCAGTTGATCCAGGGCGATCTTTTCTTC
** * *
9316 AGTTTATTTCAGGCGA-CCTAGGGTGGTC-TTTCTTC
1 AGTTTATTTCAGTTGATCC-AGGGCGATCTTTTCTTC
9351 AGTTTA--T---TTGATCCAGGGCGATCTTTTCTTC
1 AGTTTATTTCAGTTGATCCAGGGCGATCTTTTCTTC
*
9382 AAAGTTTATTTCAGTTGATCCAGGGCGATCCTTTCTTC
1 --AGTTTATTTCAGTTGATCCAGGGCGATCTTTTCTTC
** *
9420 AGTTTATTTCAAATGATCCAGGGCGATC-TTTCCTC
1 AGTTTATTTCAGTTGATCCAGGGCGATCTTTTCTTC
* * * * *
9455 AATTTACTTCAATTGATCCAGGGCGATCTTCTCTGC
1 AGTTTATTTCAGTTGATCCAGGGCGATCTTTTCTTC
9491 AGTTTATTTCAGTTGA
1 AGTTTATTTCAGTTGA
9507 CCGTAAATTG
Statistics
Matches: 503, Mismatches: 84, Indels: 52
0.79 0.13 0.08
Matches are distributed among these distances:
30 17 0.03
31 18 0.04
32 6 0.01
33 8 0.02
34 6 0.01
35 207 0.41
36 191 0.38
37 27 0.05
38 23 0.05
ACGTcount: A:0.19, C:0.20, G:0.20, T:0.41
Consensus pattern (36 bp):
AGTTTATTTCAGTTGATCCAGGGCGATCTTTTCTTC
Found at i:9478 original size:281 final size:280
Alignment explanation
Indices: 8906--9506 Score: 945
Period size: 281 Copynumber: 2.1 Consensus size: 280
8896 TTTATACCAT
* * *
8906 TTGATCCAGGGCGATCTTTTATTCAGTTTATTTCAGTTGATCTAGGGTGATATTTCTTCAGAATA
1 TTGATCCAGGGCGATCTTTTCTTCAGTTTATTTCAGTTGATCCAGGGCGATATTTCTTCAGAATA
* *
8971 TTTCAGTCGACCCAGGGAGGTCTTTCTCCAATTTATTTCAGTTGATCCAGGGCGGTCTTTCTTTA
66 TTTCAGTCGACCCAGGGAGGTCTTTCTCCAATTTATTTCAGTTGATCCAGGGCGATCTTTCTTCA
*
9036 GTTTATTTTAGGCGACCTAGGGTGGTCTTTCTTCAGTTTATTTGATCCAAGGCGATCTTTTCTTC
131 GTTTATTTCAGGCGACCTAGGGTGGTCTTTCTTCAGTTTATTTGATCCAAGGCGATCTTTTCTTC
* * **
9101 AAGTTTATTTCAGTTGATCCAGGGCGATCTTTTCTTCAGTTTATTTTAGTTGATCCAGGGCGATC
196 AAGTTTATTTCAGTTGATCCAGGGCGATCCTTTCTTCAGTTTATTTCAAATGATCCAGGGCGATC
* * *
9166 CTTTCTTCAAGTTATTTCAG
261 CTTTCCTCAAGTTACTTCAA
* * * *
9186 TTGACCCAGGGCGATCTTTTCTTCAGTTTATTTAAGTTGATCCAGGGCGATCCTTTCTTCA-AGT
1 TTGATCCAGGGCGATCTTTTCTTCAGTTTATTTCAGTTGATCCAGGGCGAT-ATTTCTTCAGA-A
* * *
9250 TATTTTAGTTGACCCAGGGCGGTCTTTCTCCAATTTATTTCAGTTGATCCAGGGCGATCTTTCTT
64 TATTTCAGTCGACCCAGGGAGGTCTTTCTCCAATTTATTTCAGTTGATCCAGGGCGATCTTTCTT
*
9315 CAGTTTATTTCAGGCGACCTAGGGTGGTCTTTCTTCAGTTTATTTGATCCAGGGCGATCTTTTCT
129 CAGTTTATTTCAGGCGACCTAGGGTGGTCTTTCTTCAGTTTATTTGATCCAAGGCGATCTTTTCT
9380 TCAAAGTTTATTTCAGTTGATCCAGGGCGATCCTTTCTTCAGTTTATTTCAAATGATCCAGGGCG
194 TC-AAGTTTATTTCAGTTGATCCAGGGCGATCCTTTCTTCAGTTTATTTCAAATGATCCAGGGCG
*
9445 AT-CTTTCCTCAATTTACTTCAA
258 ATCCTTTCCTCAAGTTACTTCAA
* *
9467 TTGATCCAGGGCGATCTTCTCTGCAGTTTATTTCAGTTGA
1 TTGATCCAGGGCGATCTTTTCTTCAGTTTATTTCAGTTGA
9507 CCGTAAATTG
Statistics
Matches: 292, Mismatches: 26, Indels: 5
0.90 0.08 0.02
Matches are distributed among these distances:
280 47 0.16
281 185 0.63
282 60 0.21
ACGTcount: A:0.19, C:0.20, G:0.20, T:0.41
Consensus pattern (280 bp):
TTGATCCAGGGCGATCTTTTCTTCAGTTTATTTCAGTTGATCCAGGGCGATATTTCTTCAGAATA
TTTCAGTCGACCCAGGGAGGTCTTTCTCCAATTTATTTCAGTTGATCCAGGGCGATCTTTCTTCA
GTTTATTTCAGGCGACCTAGGGTGGTCTTTCTTCAGTTTATTTGATCCAAGGCGATCTTTTCTTC
AAGTTTATTTCAGTTGATCCAGGGCGATCCTTTCTTCAGTTTATTTCAAATGATCCAGGGCGATC
CTTTCCTCAAGTTACTTCAA
Found at i:9703 original size:30 final size:30
Alignment explanation
Indices: 9667--10071 Score: 444
Period size: 30 Copynumber: 13.4 Consensus size: 30
9657 TCAGAGTTTG
* * *
9667 CATTGCTTCATTTTAATCCCGTTTAAGGGT
1 CATTGCTTCATTTTAATCCTGTTTGAGGAT
* *
9697 CATTGCTTCATTTCAATCCTGGTTGAGGAT
1 CATTGCTTCATTTTAATCCTGTTTGAGGAT
* *
9727 CATTGCTTTATTTTAATCCTGGTTGAGGAT
1 CATTGCTTCATTTTAATCCTGTTTGAGGAT
* *
9757 CATTGCTTTATTTTAATCCTGTTTGAAGAT
1 CATTGCTTCATTTTAATCCTGTTTGAGGAT
*
9787 CATTGCTTCATTTTAATCCTGGTTGAGGAT
1 CATTGCTTCATTTTAATCCTGTTTGAGGAT
* *
9817 CATTGCTTTATGAGTTAATCCTGTTTGAGGAT
1 CATTGCTTCAT--TTTAATCCTGTTTGAGGAT
*
9849 CATTGCTTCATTTTAGTCCTGTTTGAGGAT
1 CATTGCTTCATTTTAATCCTGTTTGAGGAT
*
9879 CATTGCTTCATTTTAATCCTGGTTGAGGAT
1 CATTGCTTCATTTTAATCCTGTTTGAGGAT
*
9909 CGTTGCGTT-ATTTTAATCCTAG-TTGAGGAT
1 CATTGC-TTCATTTTAATCCT-GTTTGAGGAT
* * * *
9939 CATTGTTTTATTTTAATCCTGGTTGAAGAT
1 CATTGCTTCATTTTAATCCTGTTTGAGGAT
* * *
9969 CGTTG-TTTATTTTTCAATCCTGGTTGAGGAT
1 CATTGCTTCA-TTTT-AATCCTGTTTGAGGAT
* *
10000 CATTGCTTCATTTCAATCCTGGTCT-AGGAT
1 CATTGCTTCATTTTAATCCT-GTTTGAGGAT
* *
10030 CGTTG-TTTATTTTTCAATCCTGGTTT-AGGAT
1 CATTGCTTCA-TTTT-AATCCT-GTTTGAGGAT
10061 CATTGCTTCAT
1 CATTGCTTCAT
10072 CAGTTAATCC
Statistics
Matches: 325, Mismatches: 37, Indels: 25
0.84 0.10 0.06
Matches are distributed among these distances:
29 10 0.03
30 235 0.72
31 47 0.14
32 33 0.10
ACGTcount: A:0.20, C:0.16, G:0.19, T:0.45
Consensus pattern (30 bp):
CATTGCTTCATTTTAATCCTGTTTGAGGAT
Found at i:9760 original size:60 final size:60
Alignment explanation
Indices: 9667--10071 Score: 492
Period size: 60 Copynumber: 6.7 Consensus size: 60
9657 TCAGAGTTTG
* * * * * *
9667 CATTGCTTCATTTTAATCCCGTTTAAGGGTCATTGCTTCATTTCAATCCTGGTTGAGGAT
1 CATTGCTTTATTTTAATCCTGGTTGAGGATCATTGCTTCATTTTAATCCTGGTTGAGGAT
* * *
9727 CATTGCTTTATTTTAATCCTGGTTGAGGATCATTGCTTTATTTTAATCCTGTTTGAAGAT
1 CATTGCTTTATTTTAATCCTGGTTGAGGATCATTGCTTCATTTTAATCCTGGTTGAGGAT
* * * *
9787 CATTGCTTCATTTTAATCCTGGTTGAGGATCATTGCTTTATGAGTTAATCCTGTTTGAGGAT
1 CATTGCTTTATTTTAATCCTGGTTGAGGATCATTGCTTCAT--TTTAATCCTGGTTGAGGAT
* * *
9849 CATTGCTTCATTTTAGTCCTGTTTGAGGATCATTGCTTCATTTTAATCCTGGTTGAGGAT
1 CATTGCTTTATTTTAATCCTGGTTGAGGATCATTGCTTCATTTTAATCCTGGTTGAGGAT
* * * * * *
9909 CGTTGCGTTATTTTAATCCTAGTTGAGGATCATTGTTTTATTTTAATCCTGGTTGAAGAT
1 CATTGCTTTATTTTAATCCTGGTTGAGGATCATTGCTTCATTTTAATCCTGGTTGAGGAT
* *
9969 CGTTG-TTTATTTTTCAATCCTGGTTGAGGATCATTGCTTCATTTCAATCCTGGTCT-AGGAT
1 CATTGCTTTA-TTTT-AATCCTGGTTGAGGATCATTGCTTCATTTTAATCCTGGT-TGAGGAT
* *
10030 CGTTG-TTTATTTTTCAATCCTGGTTTAGGATCATTGCTTCAT
1 CATTGCTTTA-TTTT-AATCCTGGTTGAGGATCATTGCTTCAT
10072 CAGTTAATCC
Statistics
Matches: 307, Mismatches: 33, Indels: 9
0.88 0.09 0.03
Matches are distributed among these distances:
59 3 0.01
60 168 0.55
61 80 0.26
62 56 0.18
ACGTcount: A:0.20, C:0.16, G:0.19, T:0.45
Consensus pattern (60 bp):
CATTGCTTTATTTTAATCCTGGTTGAGGATCATTGCTTCATTTTAATCCTGGTTGAGGAT
Found at i:9955 original size:152 final size:150
Alignment explanation
Indices: 9679--10066 Score: 512
Period size: 152 Copynumber: 2.6 Consensus size: 150
9669 TTGCTTCATT
* * * *
9679 TTAATCCCGTTTAAGGGTCATTGCTTCATTTCAATCCTGGTTGAGGATCATTGCTTTATTTTAAT
1 TTAATCCTGTTTGAGGATCATTGCTTCATTTCAATCCTGTTTGAGGATCATTGCTTTATTTTAAT
*
9744 CCTGGTTGAGGATCATTGCTTTATTTTAATCCTGTTTGAAGATCATTGCTTCATTTTAATCCTGG
66 CCTGGTTGAGGATCATTGCGTTATTTTAATCCTGTTTGAAGATCATTGCTTCATTTTAATCCTGG
*
9809 TTGAGGATCATTGCTTTATGAG
131 TTGAAGATCATTG-TTTAT-AG
* * *
9831 TTAATCCTGTTTGAGGATCATTGCTTCATTTTAGTCCTGTTTGAGGATCATTGCTTCATTTTAAT
1 TTAATCCTGTTTGAGGATCATTGCTTCATTTCAATCCTGTTTGAGGATCATTGCTTTATTTTAAT
* * * *
9896 CCTGGTTGAGGATCGTTGCGTTATTTTAATCCTAG-TTGAGGATCATTGTTTTATTTTAATCCTG
66 CCTGGTTGAGGATCATTGCGTTATTTTAATCCT-GTTTGAAGATCATTGCTTCATTTTAATCCTG
* **
9960 GTTGAAGATCGTTGTTTATTT
130 GTTGAAGATCATTGTTTATAG
* * *
9981 TTCAATCCTGGTTGAGGATCATTGCTTCATTTCAATCCTGGTCT-AGGATCGTTG-TTTATTTTT
1 TT-AATCCTGTTTGAGGATCATTGCTTCATTTCAATCCT-GTTTGAGGATCATTGCTTTA-TTTT
*
10044 CAATCCTGGTTTAGGATCATTGC
63 -AATCCTGGTTGAGGATCATTGC
10067 TTCATCAGTT
Statistics
Matches: 207, Mismatches: 24, Indels: 10
0.86 0.10 0.04
Matches are distributed among these distances:
150 5 0.02
151 51 0.25
152 150 0.72
153 1 0.00
ACGTcount: A:0.20, C:0.15, G:0.20, T:0.45
Consensus pattern (150 bp):
TTAATCCTGTTTGAGGATCATTGCTTCATTTCAATCCTGTTTGAGGATCATTGCTTTATTTTAAT
CCTGGTTGAGGATCATTGCGTTATTTTAATCCTGTTTGAAGATCATTGCTTCATTTTAATCCTGG
TTGAAGATCATTGTTTATAG
Found at i:13977 original size:44 final size:45
Alignment explanation
Indices: 13863--13985 Score: 169
Period size: 44 Copynumber: 2.8 Consensus size: 45
13853 AGATCAATTT
* * * *
13863 TATTAATTTCCAAAATCTTCTTTTGG-ATGTACTTGAATTGAAAAC
1 TATTACTTTCCAAAATCTTCTTTTGGAAT-TACTTGAAATAAAAAA
13908 TATTACTTTCCAAAATCTTCTTTTGGAATTACTT-AAATAAAAAA
1 TATTACTTTCCAAAATCTTCTTTTGGAATTACTTGAAATAAAAAA
* *
13952 TTTTATTTTCCAAAATCTTCTTTTGGAATTACTT
1 TATTACTTTCCAAAATCTTCTTTTGGAATTACTT
13986 TAAAAACGTT
Statistics
Matches: 71, Mismatches: 6, Indels: 3
0.89 0.08 0.04
Matches are distributed among these distances:
44 39 0.55
45 30 0.42
46 2 0.03
ACGTcount: A:0.33, C:0.14, G:0.07, T:0.46
Consensus pattern (45 bp):
TATTACTTTCCAAAATCTTCTTTTGGAATTACTTGAAATAAAAAA
Found at i:19225 original size:13 final size:13
Alignment explanation
Indices: 19207--19232 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
19197 GGTTCTGATG
19207 CAAACAATAACTA
1 CAAACAATAACTA
19220 CAAACAATAACTA
1 CAAACAATAACTA
19233 GCATATGACT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.62, C:0.23, G:0.00, T:0.15
Consensus pattern (13 bp):
CAAACAATAACTA
Found at i:21154 original size:32 final size:31
Alignment explanation
Indices: 21113--21174 Score: 106
Period size: 32 Copynumber: 2.0 Consensus size: 31
21103 GGCCTGTTGC
*
21113 GCGGCATGGCTAGGCCATGGTCGGGCTGTGGT
1 GCGGCATGGCTAGGCCAT-GCCGGGCTGTGGT
21145 GCGGCATGGCTAGGCCATGCCGGGCTGTGG
1 GCGGCATGGCTAGGCCATGCCGGGCTGTGG
21175 CCTGGCCATG
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
31 11 0.38
32 18 0.62
ACGTcount: A:0.10, C:0.24, G:0.47, T:0.19
Consensus pattern (31 bp):
GCGGCATGGCTAGGCCATGCCGGGCTGTGGT
Found at i:34035 original size:32 final size:32
Alignment explanation
Indices: 33994--34057 Score: 110
Period size: 32 Copynumber: 2.0 Consensus size: 32
33984 TTATGCAATC
* *
33994 CAAAATATGATATGCTATTGTAATATAGAACT
1 CAAAATATGATATGCTACTGTAACATAGAACT
34026 CAAAATATGATATGCTACTGTAACATAGAACT
1 CAAAATATGATATGCTACTGTAACATAGAACT
34058 AACATGAGAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.44, C:0.12, G:0.12, T:0.31
Consensus pattern (32 bp):
CAAAATATGATATGCTACTGTAACATAGAACT
Found at i:34955 original size:18 final size:20
Alignment explanation
Indices: 34910--34948 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
34900 GCATAACTTA
*
34910 CAATCGATTGAAACTGTTTTC
1 CAATTGATTGAAACTG-TTTC
34931 CAATTGATTGAAACTGTT
1 CAATTGATTGAAACTGTT
34949 CAATTGAAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 2 0.12
21 15 0.88
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (20 bp):
CAATTGATTGAAACTGTTTC
Found at i:36223 original size:6 final size:6
Alignment explanation
Indices: 36212--36261 Score: 100
Period size: 6 Copynumber: 8.3 Consensus size: 6
36202 AACGTTTTCA
36212 TTGTTT TTGTTT TTGTTT TTGTTT TTGTTT TTGTTT TTGTTT TTGTTT
1 TTGTTT TTGTTT TTGTTT TTGTTT TTGTTT TTGTTT TTGTTT TTGTTT
36260 TT
1 TT
36262 ACATATTGAA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 44 1.00
ACGTcount: A:0.00, C:0.00, G:0.16, T:0.84
Consensus pattern (6 bp):
TTGTTT
Found at i:36458 original size:22 final size:21
Alignment explanation
Indices: 36416--36458 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
36406 TGTTTCTGTT
* *
36416 TCAACCTTATGAAGGTCGAAC
1 TCAACCTTATAAAAGTCGAAC
36437 TCAACCTTAATAAAAGTCGAAC
1 TCAACCTT-ATAAAAGTCGAAC
36459 CAGCAACATA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 8 0.42
22 11 0.58
ACGTcount: A:0.40, C:0.23, G:0.14, T:0.23
Consensus pattern (21 bp):
TCAACCTTATAAAAGTCGAAC
Found at i:44372 original size:5 final size:5
Alignment explanation
Indices: 44336--44370 Score: 52
Period size: 5 Copynumber: 7.0 Consensus size: 5
44326 ACACACCACT
* *
44336 CCAAA CCAAA CCAAA CCAAA CCAAA ACAAA ACAAA
1 CCAAA CCAAA CCAAA CCAAA CCAAA CCAAA CCAAA
44371 ACTTATGCAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
5 29 1.00
ACGTcount: A:0.66, C:0.34, G:0.00, T:0.00
Consensus pattern (5 bp):
CCAAA
Found at i:45389 original size:53 final size:54
Alignment explanation
Indices: 45306--45413 Score: 150
Period size: 53 Copynumber: 2.0 Consensus size: 54
45296 GCCTGCATCA
* *
45306 CCCAGGTGTGTCAAAAGAGATACGCATAAATGAGT-AGAAGGT-AAAGGCTATCT
1 CCCAGGTGTGCCAAAAGAGATACGAATAAATGAGTGA-AAGGTGAAAGGCTATCT
*
45359 CCCAGGTGTGCCAAAAGTGATAC-AAGTAAATGAGTGAAAGGTGAAAGGCTATCT
1 CCCAGGTGTGCCAAAAGAGATACGAA-TAAATGAGTGAAAGGTGAAAGGCTATCT
45413 C
1 C
45414 TTTTTATCAT
Statistics
Matches: 49, Mismatches: 3, Indels: 5
0.86 0.05 0.09
Matches are distributed among these distances:
52 1 0.02
53 35 0.71
54 13 0.27
ACGTcount: A:0.37, C:0.16, G:0.27, T:0.20
Consensus pattern (54 bp):
CCCAGGTGTGCCAAAAGAGATACGAATAAATGAGTGAAAGGTGAAAGGCTATCT
Found at i:46630 original size:1 final size:1
Alignment explanation
Indices: 46626--46654 Score: 58
Period size: 1 Copynumber: 29.0 Consensus size: 1
46616 AATTAAATTT
46626 AAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAA
46655 CAAGATGTAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 28 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:47649 original size:15 final size:14
Alignment explanation
Indices: 47622--47661 Score: 53
Period size: 15 Copynumber: 2.8 Consensus size: 14
47612 AGAGCCCTTG
*
47622 GAGAAGGAGAAGAA
1 GAGAAGAAGAAGAA
*
47636 GTGAAAGAAGAAGAA
1 GAG-AAGAAGAAGAA
47651 GAGAAGAAGAA
1 GAGAAGAAGAA
47662 AATCGGAGGA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
14 10 0.45
15 12 0.55
ACGTcount: A:0.60, C:0.00, G:0.38, T:0.03
Consensus pattern (14 bp):
GAGAAGAAGAAGAA
Found at i:49430 original size:13 final size:13
Alignment explanation
Indices: 49412--49441 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
49402 CCATCTCCTC
49412 TCTCTTTTCCCTA
1 TCTCTTTTCCCTA
*
49425 TCTCTTTTCCCTG
1 TCTCTTTTCCCTA
49438 TCTC
1 TCTC
49442 CATTCATAGG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.03, C:0.40, G:0.03, T:0.53
Consensus pattern (13 bp):
TCTCTTTTCCCTA
Found at i:49920 original size:2 final size:2
Alignment explanation
Indices: 49913--49948 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
49903 TCGGAGATCA
49913 AT AT 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 AT AT
49949 CGTCTTATTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.