Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014288.1 Corchorus olitorius cultivar O-4 contig14321, 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: 25136
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.35
Found at i:2264 original size:15 final size:15
Alignment explanation
Indices: 2246--2290 Score: 56
Period size: 15 Copynumber: 3.0 Consensus size: 15
2236 CATAAATTTG
2246 GGTGCCATCATCTTC
1 GGTGCCATCATCTTC
* *
2261 GGTGCCGTCGAT-TTT
1 GGTGCCATC-ATCTTC
2276 GGTGCCATCATCTTC
1 GGTGCCATCATCTTC
2291 TTCCATGACA
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
14 2 0.08
15 20 0.83
16 2 0.08
ACGTcount: A:0.11, C:0.29, G:0.24, T:0.36
Consensus pattern (15 bp):
GGTGCCATCATCTTC
Found at i:2264 original size:30 final size:30
Alignment explanation
Indices: 2228--2290 Score: 81
Period size: 30 Copynumber: 2.1 Consensus size: 30
2218 AGTAAACACT
2228 TTCGGTGACATAAATTTGGGTGCCATCATC
1 TTCGGTGACATAAATTTGGGTGCCATCATC
* * ** *
2258 TTCGGTGCCGTCGATTTTGGTGCCATCATC
1 TTCGGTGACATAAATTTGGGTGCCATCATC
2288 TTC
1 TTC
2291 TTCCATGACA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.16, C:0.24, G:0.24, T:0.37
Consensus pattern (30 bp):
TTCGGTGACATAAATTTGGGTGCCATCATC
Found at i:3540 original size:18 final size:18
Alignment explanation
Indices: 3519--3578 Score: 93
Period size: 18 Copynumber: 3.3 Consensus size: 18
3509 AACTTGGTGC
3519 GGTGCGGCCACTTGTTGT
1 GGTGCGGCCACTTGTTGT
3537 GGTGCGGCCACTTGTTGT
1 GGTGCGGCCACTTGTTGT
* * *
3555 GGTGCGACCACTTGATGC
1 GGTGCGGCCACTTGTTGT
3573 GGTGCG
1 GGTGCG
3579 ATTTGCTGTT
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 39 1.00
ACGTcount: A:0.08, C:0.23, G:0.40, T:0.28
Consensus pattern (18 bp):
GGTGCGGCCACTTGTTGT
Found at i:3579 original size:18 final size:18
Alignment explanation
Indices: 3510--3579 Score: 86
Period size: 18 Copynumber: 3.9 Consensus size: 18
3500 AAGTGTGGCA
* *
3510 ACTTGGTGCGGTGCGGCC
1 ACTTGTTGCGGTGCGACC
* *
3528 ACTTGTTGTGGTGCGGCC
1 ACTTGTTGCGGTGCGACC
*
3546 ACTTGTTGTGGTGCGACC
1 ACTTGTTGCGGTGCGACC
*
3564 ACTTGATGCGGTGCGA
1 ACTTGTTGCGGTGCGA
3580 TTTGCTGTTG
Statistics
Matches: 47, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 47 1.00
ACGTcount: A:0.10, C:0.23, G:0.39, T:0.29
Consensus pattern (18 bp):
ACTTGTTGCGGTGCGACC
Found at i:4316 original size:159 final size:158
Alignment explanation
Indices: 3981--4272 Score: 433
Period size: 159 Copynumber: 1.8 Consensus size: 158
3971 AAAAGTAGTA
* *
3981 AAGAAAATAAACCTTTTAACAACACCAAAATGAGATCTGAATCCTTGTGAGTCCCACCGGGCGTG
1 AAGAAAA-AATCCTTTTAACAACACCAAAATGAGATCTAAATCCTTGTGAGTCCCACCGGGCGTG
*
4046 CCAAAAAGAGATGTTGGTGCGCTAAGTGGGGCGAAAGTAAAAATAAAAAGAACAAAGTTGGGGAT
65 CCAAAAAGAGATGTTCGTGCGCTAAGTGGGGCGAAAGTAAAAATAAAAAGAACAAAGTTGGGGAT
* * *
4111 CGCCAACTTGAAAGTAAAAATCAAGAAAAAC
130 CGCCAAATAGAAACTAAAAATCAAG--AAAC
* * * * *
4142 AAGAAAAAATCCTTTTAACAGCACCGAGATGAGATCTAAATCCTTGT-AGTCCCGCTGGGCGTGC
1 AAGAAAAAATCCTTTTAACAACACCAAAATGAGATCTAAATCCTTGTGAGTCCCACCGGGCGTGC
*
4206 CAAAATGAGATGTTCGTGCGCTAAGTGGGGCGAAAGTAAAAATAAAAAGAACAAAGTTGGGTGAT
66 CAAAAAGAGATGTTCGTGCGCTAAGTGGGGCGAAAGTAAAAATAAAAAGAACAAAGTTGGG-GAT
4271 CG
130 CG
4273 AGCCAAAATA
Statistics
Matches: 121, Mismatches: 9, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
159 74 0.61
160 40 0.33
161 7 0.06
ACGTcount: A:0.40, C:0.17, G:0.24, T:0.20
Consensus pattern (158 bp):
AAGAAAAAATCCTTTTAACAACACCAAAATGAGATCTAAATCCTTGTGAGTCCCACCGGGCGTGC
CAAAAAGAGATGTTCGTGCGCTAAGTGGGGCGAAAGTAAAAATAAAAAGAACAAAGTTGGGGATC
GCCAAATAGAAACTAAAAATCAAGAAAC
Found at i:5150 original size:11 final size:11
Alignment explanation
Indices: 5134--5159 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
5124 AGATAATTTC
5134 TTTTCTTCTAG
1 TTTTCTTCTAG
5145 TTTTCTTCTAG
1 TTTTCTTCTAG
5156 TTTT
1 TTTT
5160 TTAGGCAAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.08, C:0.15, G:0.08, T:0.69
Consensus pattern (11 bp):
TTTTCTTCTAG
Found at i:7067 original size:18 final size:18
Alignment explanation
Indices: 7046--7124 Score: 131
Period size: 18 Copynumber: 4.4 Consensus size: 18
7036 AACTTGGTGC
*
7046 GGTGCGGCCACTTGTTGT
1 GGTGCGACCACTTGTTGT
7064 GGTGCGACCACTTGTTGT
1 GGTGCGACCACTTGTTGT
7082 GGTGCGACCACTTGTTGT
1 GGTGCGACCACTTGTTGT
* *
7100 GGTGCGACCACTTGATGC
1 GGTGCGACCACTTGTTGT
7118 GGTGCGA
1 GGTGCGA
7125 TTTGCTGTTG
Statistics
Matches: 58, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 58 1.00
ACGTcount: A:0.11, C:0.23, G:0.37, T:0.29
Consensus pattern (18 bp):
GGTGCGACCACTTGTTGT
Found at i:7134 original size:36 final size:36
Alignment explanation
Indices: 7037--7124 Score: 140
Period size: 36 Copynumber: 2.4 Consensus size: 36
7027 AAGTGTGGCA
* *
7037 ACTTGGTGCGGTGCGGCCACTTGTTGTGGTGCGACC
1 ACTTGATGCGGTGCGACCACTTGTTGTGGTGCGACC
* *
7073 ACTTGTTGTGGTGCGACCACTTGTTGTGGTGCGACC
1 ACTTGATGCGGTGCGACCACTTGTTGTGGTGCGACC
7109 ACTTGATGCGGTGCGA
1 ACTTGATGCGGTGCGA
7125 TTTGCTGTTG
Statistics
Matches: 47, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
36 47 1.00
ACGTcount: A:0.11, C:0.23, G:0.36, T:0.30
Consensus pattern (36 bp):
ACTTGATGCGGTGCGACCACTTGTTGTGGTGCGACC
Found at i:7832 original size:159 final size:159
Alignment explanation
Indices: 7526--7924 Score: 618
Period size: 159 Copynumber: 2.5 Consensus size: 159
7516 AAAAGCAGTA
* * * * *
7526 AAGAAAATAAACCTTTTAACAACACCAAAATGAGATCTGAATCCTTGTGAGTCCCACCGGGCGTG
1 AAGAAAA-AATCCTTTTAACAGCACCAAGATGAGATCTAAATCCTTGT-AGTCCCACTGGGCGTG
* ** *
7591 CTAAAAAGAGATGTTGGTGCGCTAAGTGAGGCGAAAGTAAAAATAAAAAGAACAAAGTTGGGGAT
64 CCAAAAAGAGATGTTCATGCGCTAAGTGAGGCAAAAGTAAAAATAAAAAGAACAAAGTTGGGGAT
7656 CGCCAACTTGAAAGTAAAAATCAAGAAAAAC
129 CGCCAACTTGAAAGTAAAAATCAAGAAAAAC
*
7687 AAGAAAAAATCCTTTTAACAGCACCAAGATGAGATCTAAATCCTTGTAGTCCCGCTGGGCGTGCC
1 AAGAAAAAATCCTTTTAACAGCACCAAGATGAGATCTAAATCCTTGTAGTCCCACTGGGCGTGCC
* * *
7752 AAAATGAGATGTTCATGCGCTAAGTGGGGCAAAAGTAAAAGTAAAAAGAACAAAGTTGGGGATCG
66 AAAAAGAGATGTTCATGCGCTAAGTGAGGCAAAAGTAAAAATAAAAAGAACAAAGTTGGGGATCG
* *
7817 CCAACTTGGATGTAAAAATCAAGAAAAAC
131 CCAACTTGAAAGTAAAAATCAAGAAAAAC
* * *
7846 AAGAAAAAATCCTTTTAACAGCATCGAGATGAGATCTAAATCCTTGTAGTCCCACTGGGTGTGCC
1 AAGAAAAAATCCTTTTAACAGCACCAAGATGAGATCTAAATCCTTGTAGTCCCACTGGGCGTGCC
7911 AAAAAGAGATGTTC
66 AAAAAGAGATGTTC
7925 GTGCCAAAAA
Statistics
Matches: 218, Mismatches: 20, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
159 175 0.80
160 36 0.17
161 7 0.03
ACGTcount: A:0.41, C:0.17, G:0.22, T:0.21
Consensus pattern (159 bp):
AAGAAAAAATCCTTTTAACAGCACCAAGATGAGATCTAAATCCTTGTAGTCCCACTGGGCGTGCC
AAAAAGAGATGTTCATGCGCTAAGTGAGGCAAAAGTAAAAATAAAAAGAACAAAGTTGGGGATCG
CCAACTTGAAAGTAAAAATCAAGAAAAAC
Found at i:10802 original size:15 final size:15
Alignment explanation
Indices: 10782--10810 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
10772 GTTGTTTCCA
10782 ATGTGAACAATATAT
1 ATGTGAACAATATAT
10797 ATGTGAACAATATA
1 ATGTGAACAATATA
10811 AAACATGCAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.48, C:0.07, G:0.14, T:0.31
Consensus pattern (15 bp):
ATGTGAACAATATAT
Found at i:12785 original size:16 final size:16
Alignment explanation
Indices: 12754--12792 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
12744 TATTTTAAAT
*
12754 TTAATAA-ATTATAAC
1 TTAATAATATAATAAC
12769 TTAATAATATAATAAC
1 TTAATAATATAATAAC
12785 TTAATAAT
1 TTAATAAT
12793 CTTAATAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
15 7 0.32
16 15 0.68
ACGTcount: A:0.54, C:0.05, G:0.00, T:0.41
Consensus pattern (16 bp):
TTAATAATATAATAAC
Found at i:12816 original size:25 final size:26
Alignment explanation
Indices: 12763--12817 Score: 71
Period size: 25 Copynumber: 2.2 Consensus size: 26
12753 TTTAATAAAT
12763 TATAA-CTTAATAATATAATAACTTA
1 TATAATCTTAATAATATAATAACTTA
* *
12788 -ATAATCTTAATAATATTATTA-TTA
1 TATAATCTTAATAATATAATAACTTA
12812 TATAAT
1 TATAAT
12818 TTCTAAATAG
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
24 7 0.27
25 19 0.73
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.45
Consensus pattern (26 bp):
TATAATCTTAATAATATAATAACTTA
Found at i:15676 original size:19 final size:20
Alignment explanation
Indices: 15649--15686 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
15639 TACTATTATT
15649 TTTTGAATTT-AATATTTTAC
1 TTTTGAATTTCAAT-TTTTAC
15669 TTTT-AATTTCAATTTTTA
1 TTTTGAATTTCAATTTTTA
15687 AATGTCAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.29, C:0.05, G:0.03, T:0.63
Consensus pattern (20 bp):
TTTTGAATTTCAATTTTTAC
Found at i:16035 original size:22 final size:22
Alignment explanation
Indices: 15853--16028 Score: 108
Period size: 22 Copynumber: 7.9 Consensus size: 22
15843 TGTCTCTGTG
* * *
15853 TGGTTATCAAAATTTAATAAGA
1 TGGTTATTAAAATTTCATAGGA
*
15875 TGGTTATTATAATTTCATGAGGA
1 TGGTTATTAAAATTTCAT-AGGA
* * *
15898 -GGTTATCAATATTCCATAGTG-
1 TGGTTATTAAAATTTCATAG-GA
** *
15919 TGGTTACCAAAATTTCACATGGA
1 TGGTTATTAAAATTTCATA-GGA
* *
15942 -AGTTATCAAAATTTCATAGTG-
1 TGGTTATTAAAATTTCATAG-GA
**
15963 TGGTTACCAAAATTTCATAGGA
1 TGGTTATTAAAATTTCATAGGA
**
15985 TCAGGTTATTAAAATTTTTTAGGA
1 T--GGTTATTAAAATTTCATAGGA
* *
16009 AGGTTATTGAAATTTCATAG
1 TGGTTATTAAAATTTCATAG
16029 TGTGGTTTTC
Statistics
Matches: 119, Mismatches: 25, Indels: 20
0.73 0.15 0.12
Matches are distributed among these distances:
21 4 0.03
22 94 0.79
23 4 0.03
24 17 0.14
ACGTcount: A:0.35, C:0.09, G:0.18, T:0.38
Consensus pattern (22 bp):
TGGTTATTAAAATTTCATAGGA
Found at i:16093 original size:22 final size:22
Alignment explanation
Indices: 16068--16127 Score: 68
Period size: 22 Copynumber: 2.7 Consensus size: 22
16058 ATCAAAGAGA
*
16068 TTATCAAAATGTCATAGCGAGG
1 TTATCAAAATTTCATAGCGAGG
* *
16090 TTAT-AAGAATTTCATAGTGTGG
1 TTATCAA-AATTTCATAGCGAGG
*
16112 TTAACAAAATTTCATA
1 TTATCAAAATTTCATA
16128 AGGAGGTAGG
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
21 2 0.06
22 28 0.88
23 2 0.06
ACGTcount: A:0.38, C:0.10, G:0.17, T:0.35
Consensus pattern (22 bp):
TTATCAAAATTTCATAGCGAGG
Found at i:16182 original size:74 final size:74
Alignment explanation
Indices: 16064--16201 Score: 188
Period size: 74 Copynumber: 1.9 Consensus size: 74
16054 GTTTATCAAA
16064 GAGATTATCAAAATGTCATAGCGAGGTTATAAGAATTTCATAGTGTGGTTAACAAAATTTCATAA
1 GAGATTATCAAAATGTCATAGCGAGGTTATAAGAATTTCATAGTGTGGTTAACAAAATTTCATAA
16129 GGAGGTAGG
66 GGAGGTAGG
* * * * * ** *
16138 GAGATTATCAAATTTTCATAGTGTGGTTATTAA-TATTTTTTAGTGTGGTTATCAAAATTTCATA
1 GAGATTATCAAAATGTCATAGCGAGGTTA-TAAGAATTTCATAGTGTGGTTAACAAAATTTCATA
16202 TGAAGGTTAT
Statistics
Matches: 55, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
74 52 0.95
75 3 0.05
ACGTcount: A:0.35, C:0.07, G:0.20, T:0.38
Consensus pattern (74 bp):
GAGATTATCAAAATGTCATAGCGAGGTTATAAGAATTTCATAGTGTGGTTAACAAAATTTCATAA
GGAGGTAGG
Found at i:16197 original size:22 final size:23
Alignment explanation
Indices: 16142--16201 Score: 72
Period size: 22 Copynumber: 2.7 Consensus size: 23
16132 GGTAGGGAGA
16142 TTATC-AAATTTTCATAGTGTGG
1 TTATCAAAATTTTCATAGTGTGG
* * *
16164 TTATTAATATTTT-TTAGTGTGG
1 TTATCAAAATTTTCATAGTGTGG
16186 TTATCAAAA-TTTCATA
1 TTATCAAAATTTTCATA
16202 TGAAGGTTAT
Statistics
Matches: 30, Mismatches: 6, Indels: 4
0.75 0.15 0.10
Matches are distributed among these distances:
21 3 0.10
22 21 0.70
23 6 0.20
ACGTcount: A:0.30, C:0.07, G:0.13, T:0.50
Consensus pattern (23 bp):
TTATCAAAATTTTCATAGTGTGG
Found at i:16209 original size:22 final size:21
Alignment explanation
Indices: 16184--16492 Score: 96
Period size: 22 Copynumber: 13.9 Consensus size: 21
16174 TTTTTAGTGT
16184 GGTTATCAAAATTTCATATGAA
1 GGTTATCAAAATTTCATA-GAA
* *
16206 GGTTAT-AAAAGTCTTAATTTCATAA
1 GGTTATCAAAA-T-TTCA--T-AGAA
* * *
16231 GGAGTACCAAAATTTGATAGAA
1 GG-TTATCAAAATTTCATAGAA
*
16253 GGTTATC-AAATCTCATAG-A
1 GGTTATCAAAATTTCATAGAA
* *
16272 GTGATCATCGAAATTTCATAGAGA
1 G-G-TTATCAAAATTTCATAGA-A
16296 TCGGATTAT-AGAAATTT-ATAGGAA
1 --GG-TTATCA-AAATTTCATA-GAA
* *
16320 GATTATCAAAATTTCATAG-T
1 GGTTATCAAAATTTCATAGAA
* * *
16340 GTTGTTATCAATATTTCAAAGTGA
1 G--GTTATCAAAATTTCATAG-AA
* *
16364 GGTTATCCAAATTACATAATGAA
1 GGTTATCAAAATTTCAT-A-GAA
** *
16387 -AATATCAAAATTTCATAGAGG
1 GGTTATCAAAATTTCATAGA-A
* * * *
16408 GGTAAACAAAATTTTATAAAGA
1 GGTTATCAAAATTTCATAGA-A
*
16430 GGTTATCAAAATTTCATAAAGA
1 GGTTATCAAAATTTCATAGA-A
*
16452 GGTTATCAAATTTTCA-A-AA
1 GGTTATCAAAATTTCATAGAA
*
16471 TGTGATTACCAAAATTTCATAG
1 -G-G-TTATCAAAATTTCATAG
16493 TCGTATTTAT
Statistics
Matches: 213, Mismatches: 43, Indels: 60
0.67 0.14 0.19
Matches are distributed among these distances:
19 3 0.01
20 15 0.07
21 25 0.12
22 126 0.59
23 7 0.03
24 7 0.03
25 21 0.10
26 5 0.02
27 4 0.02
ACGTcount: A:0.42, C:0.10, G:0.15, T:0.33
Consensus pattern (21 bp):
GGTTATCAAAATTTCATAGAA
Found at i:16837 original size:126 final size:129
Alignment explanation
Indices: 16587--16856 Score: 287
Period size: 126 Copynumber: 2.1 Consensus size: 129
16577 AAATTTCAGG
* ** *
16587 GAGGATATCAAAATTTCATATGAAGGTTATCAAAATTTCGTAGTTTATTTTCAAAATTTCATAAG
1 GAGGTTATCAAAAAATCATAGGAAGGTTATCAAAATTTCGTAGTTTA--TTCAAAATTTCATAAG
* * * **
16652 AGGGTTACCAAAATTTCATAGTATGTAGATCAAAATTTCATAGGGAGATTAACAAAATTTCATAA
64 AAGGTTACCAAAATTTCATAGGAGGTAGATCAAAATTTCATAGCAAGATTAACAAAATTTCATAA
16717 T
129 T
* *
16718 GAGGTTATCAAAAAATCATAGGGAGGTTATCAAAATTT-GTAG-TTA-TCAAGATTTCATAAGAA
1 GAGGTTATCAAAAAATCATAGGAAGGTTATCAAAATTTCGTAGTTTATTCAAAATTTCATAAGAA
* * ** * * * * *
16780 GGTTA-TAAAATTTTATAAGGAGGTTTATCAAAATTTTATAGCAAGGTTATCACAATTTCATAGT
66 GGTTACCAAAATTTCAT-AGGAGGTAGATCAAAATTTCATAGCAAGATTAACAAAATTTCATAAT
* *
16844 GTGATTATCAAAA
1 GAGGTTATCAAAA
16857 TTTCAGAGTG
Statistics
Matches: 116, Mismatches: 22, Indels: 7
0.80 0.15 0.05
Matches are distributed among these distances:
125 9 0.08
126 67 0.58
129 3 0.03
130 4 0.03
131 33 0.28
ACGTcount: A:0.40, C:0.09, G:0.16, T:0.35
Consensus pattern (129 bp):
GAGGTTATCAAAAAATCATAGGAAGGTTATCAAAATTTCGTAGTTTATTCAAAATTTCATAAGAA
GGTTACCAAAATTTCATAGGAGGTAGATCAAAATTTCATAGCAAGATTAACAAAATTTCATAAT
Found at i:16984 original size:45 final size:45
Alignment explanation
Indices: 16911--17040 Score: 122
Period size: 45 Copynumber: 2.9 Consensus size: 45
16901 TTTCATAACG
* * *
16911 TGGTTATCAATATATCATATGAAGGTTATCAACATCTCATAGTGT
1 TGGTTATCAAAATATCATAGGAAGGTTATCAAAATCTCATAGTGT
* *
16956 TGGTTATCAAAATTTCATTAGGAA-GTTATCAAAATTTCATAGTG-
1 TGGTTATCAAAATATCA-TAGGAAGGTTATCAAAATCTCATAGTGT
* * * * * *
17000 AGGTTTTTAAAAT-TCCGTAGGGAGGTTATCAAAATTTCATA
1 TGGTTATCAAAATAT-CATAGGAAGGTTATCAAAATCTCATA
17041 AGGAGGTTAA
Statistics
Matches: 72, Mismatches: 10, Indels: 7
0.81 0.11 0.08
Matches are distributed among these distances:
43 6 0.08
44 28 0.39
45 33 0.46
46 5 0.07
ACGTcount: A:0.35, C:0.11, G:0.17, T:0.38
Consensus pattern (45 bp):
TGGTTATCAAAATATCATAGGAAGGTTATCAAAATCTCATAGTGT
Found at i:17055 original size:22 final size:22
Alignment explanation
Indices: 16573--17049 Score: 229
Period size: 22 Copynumber: 22.0 Consensus size: 22
16563 CTATGGAGTA
* *
16573 ATCAAAATTTC--AGGGAGGAT
1 ATCAAAATTTCATAAGGAGGTT
* *
16593 ATCAAAATTTCATATGAAGGTT
1 ATCAAAATTTCATAAGGAGGTT
* ****
16615 ATCAAAATTTCGT-AGTTTATT
1 ATCAAAATTTCATAAGGAGGTT
*
16636 TTCAAAATTTCATAA-GAGGGTT
1 ATCAAAATTTCATAAGGA-GGTT
* * * *
16658 ACCAAAATTTCAT-AGTATGTAG
1 ATCAAAATTTCATAAGGAGGT-T
* *
16680 ATCAAAATTTCATAGGGAGATT
1 ATCAAAATTTCATAAGGAGGTT
* *
16702 AACAAAATTTCATAATGAGGTT
1 ATCAAAATTTCATAAGGAGGTT
** *
16724 ATCAAAAAATCATAGGGAGGTT
1 ATCAAAATTTCATAAGGAGGTT
*
16746 ATCAAAA-TT--T--GTA-GTT
1 ATCAAAATTTCATAAGGAGGTT
* *
16762 ATCAAGATTTCATAAGAAGGTT
1 ATCAAAATTTCATAAGGAGGTT
*
16784 AT-AAAATTTTATAAGGAGGTTT
1 ATCAAAATTTCATAAGGAGG-TT
* *
16806 ATCAAAATTTTAT-AGCAAGGTT
1 ATCAAAATTTCATAAG-GAGGTT
* * *
16828 ATCACAATTTCAT-AGTGTGATT
1 ATCAAAATTTCATAAG-GAGGTT
* * *
16850 ATCAAAATTTCA-GAGTGTGATT
1 ATCAAAATTTCATAAG-GAGGTT
*
16872 A-CTAACAA-TTCA-AATGAAGGTT
1 ATC-AA-AATTTCATAA-GGAGGTT
* * * * *
16894 CTTAAATTTTCATAACGTGGTT
1 ATCAAAATTTCATAAGGAGGTT
* * * *
16916 ATCAATATATCATATGAAGGTT
1 ATCAAAATTTCATAAGGAGGTT
* * *
16938 ATCAACATCTCAT-AGTGTTGGTT
1 ATCAAAATTTCATAAG-G-AGGTT
* *
16961 ATCAAAATTTCATTAGGAAGTT
1 ATCAAAATTTCATAAGGAGGTT
16983 ATCAAAATTTCAT-AGTGAGGTT
1 ATCAAAATTTCATAAG-GAGGTT
* * * * *
17005 TTTAAAATTCCGTAGGGAGGTT
1 ATCAAAATTTCATAAGGAGGTT
17027 ATCAAAATTTCATAAGGAGGTT
1 ATCAAAATTTCATAAGGAGGTT
17049 A
1 A
17050 AAAAAAATTT
Statistics
Matches: 340, Mismatches: 89, Indels: 54
0.70 0.18 0.11
Matches are distributed among these distances:
16 9 0.03
17 4 0.01
19 2 0.01
20 11 0.03
21 39 0.11
22 235 0.69
23 38 0.11
24 2 0.01
ACGTcount: A:0.38, C:0.10, G:0.17, T:0.35
Consensus pattern (22 bp):
ATCAAAATTTCATAAGGAGGTT
Found at i:17525 original size:29 final size:31
Alignment explanation
Indices: 17483--17549 Score: 77
Period size: 31 Copynumber: 2.2 Consensus size: 31
17473 GCTCAATTCC
* * *
17483 AGCCTAAATCTTTA-AAGAGC-TCCAAATTG
1 AGCCTAAATCTTTACAAAACCAACCAAATTG
17512 AGCCTAAA-CATTTACAAAACCAACCAAATTG
1 AGCCTAAATC-TTTACAAAACCAACCAAATTG
17543 AGCCTAA
1 AGCCTAA
17550 GTTGGATGAA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
28 1 0.03
29 12 0.38
30 4 0.12
31 15 0.47
ACGTcount: A:0.43, C:0.24, G:0.10, T:0.22
Consensus pattern (31 bp):
AGCCTAAATCTTTACAAAACCAACCAAATTG
Found at i:18617 original size:16 final size:15
Alignment explanation
Indices: 18590--18619 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
18580 AAGCGCAGGG
18590 AAGAAAGAAGAAAAT
1 AAGAAAGAAGAAAAT
18605 AAGAAAGGAAGAAAA
1 AAGAAA-GAAGAAAA
18620 GAAAAAATTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.73, C:0.00, G:0.23, T:0.03
Consensus pattern (15 bp):
AAGAAAGAAGAAAAT
Found at i:20614 original size:22 final size:22
Alignment explanation
Indices: 20584--20811 Score: 143
Period size: 22 Copynumber: 10.6 Consensus size: 22
20574 TCCAAAGTAG
*
20584 AAATATTGATAACCACACTGTGA
1 AAAT-TTGATAACCACACTATGA
* *
20607 AAATTTGATAACCTCATTAT-A
1 AAATTTGATAACCACACTATGA
* * *
20628 AAATTCCGATAATCTCACTATGA
1 AAATT-TGATAACCACACTATGA
*
20651 AAATTTGATAACCACACTGTGA
1 AAATTTGATAACCACACTATGA
* *
20673 AATTTTGATGACCACACTATGA
1 AAATTTGATAACCACACTATGA
* * * *
20695 AATTTTGATAACCTCAATGTGA
1 AAATTTGATAACCACACTATGA
* *
20717 AATTTTGAT-A--A-TCTAT-A
1 AAATTTGATAACCACACTATGA
* ***
20734 AAA-TTGGTAATTGCACTATGA
1 AAATTTGATAACCACACTATGA
*
20755 AAATTTTGATAACCTC-CTCAT-A
1 AAA-TTTGATAACCACACT-ATGA
* *
20777 AATTTTGATAACCACACCATG-
1 AAATTTGATAACCACACTATGA
20798 AAATTTCGATAACC
1 AAATTT-GATAACC
20812 CCCTAATTAT
Statistics
Matches: 159, Mismatches: 33, Indels: 27
0.73 0.15 0.12
Matches are distributed among these distances:
16 4 0.03
17 4 0.03
18 2 0.01
20 4 0.03
21 29 0.18
22 97 0.61
23 19 0.12
ACGTcount: A:0.39, C:0.17, G:0.11, T:0.33
Consensus pattern (22 bp):
AAATTTGATAACCACACTATGA
Found at i:20698 original size:66 final size:66
Alignment explanation
Indices: 20584--20727 Score: 180
Period size: 66 Copynumber: 2.2 Consensus size: 66
20574 TCCAAAGTAG
* * * *
20584 AAATATTGATAACCACACTGTGAAAATTTGATAACCTCATTATAAAATTCCGATAATCTCACTAT
1 AAAT-TTGATAACCACACTGTGAAAATTTGATAACCACACTATAAAATTCCGATAACCTCAATAT
20649 GA
65 GA
* * * ** *
20651 AAATTTGATAACCACACTGTGAAATTTTGATGACCACACTATGAAATTTTGATAACCTCAATGTG
1 AAATTTGATAACCACACTGTGAAAATTTGATAACCACACTATAAAATTCCGATAACCTCAATATG
20716 A
66 A
*
20717 AATTTTGATAA
1 AAATTTGATAA
20728 TCTATAAAAT
Statistics
Matches: 66, Mismatches: 11, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
66 62 0.94
67 4 0.06
ACGTcount: A:0.40, C:0.16, G:0.11, T:0.33
Consensus pattern (66 bp):
AAATTTGATAACCACACTGTGAAAATTTGATAACCACACTATAAAATTCCGATAACCTCAATATG
A
Found at i:20716 original size:44 final size:44
Alignment explanation
Indices: 20583--20727 Score: 173
Period size: 44 Copynumber: 3.3 Consensus size: 44
20573 CTCCAAAGTA
* * * *
20583 GAAATATTGATAACCACACTGTGAAAATTTGATAACCTCATTAT
1 GAAATTTTGATAACCACACTATGAAAATTTGATAACCTCAATGT
* ** * * * *
20627 AAAATTCCGATAATCTCACTATGAAAATTTGATAACCACACTGT
1 GAAATTTTGATAACCACACTATGAAAATTTGATAACCTCAATGT
* *
20671 GAAATTTTGATGACCACACTATGAAATTTTGATAACCTCAATGT
1 GAAATTTTGATAACCACACTATGAAAATTTGATAACCTCAATGT
20715 GAAATTTTGATAA
1 GAAATTTTGATAA
20728 TCTATAAAAT
Statistics
Matches: 81, Mismatches: 20, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
44 81 1.00
ACGTcount: A:0.40, C:0.16, G:0.12, T:0.32
Consensus pattern (44 bp):
GAAATTTTGATAACCACACTATGAAAATTTGATAACCTCAATGT
Found at i:20779 original size:21 final size:22
Alignment explanation
Indices: 20755--20811 Score: 73
Period size: 21 Copynumber: 2.6 Consensus size: 22
20745 TGCACTATGA
*
20755 AAATTTTGATAACCTC-CTCAT-
1 AAATTTTGATAACCACAC-CATG
20776 AAATTTTGATAACCACACCATG
1 AAATTTTGATAACCACACCATG
*
20798 AAATTTCGATAACC
1 AAATTTTGATAACC
20812 CCCTAATTAT
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
21 18 0.56
22 14 0.44
ACGTcount: A:0.39, C:0.23, G:0.07, T:0.32
Consensus pattern (22 bp):
AAATTTTGATAACCACACCATG
Found at i:20951 original size:26 final size:22
Alignment explanation
Indices: 20830--20936 Score: 99
Period size: 22 Copynumber: 4.9 Consensus size: 22
20820 ATGAAAATGA
* * *
20830 AAATTGTGATATCCTCTCTATG
1 AAATTTTGATAACCTCCCTATG
* * *
20852 TAATGTTGATAACCTCTCC-ATA
1 AAATTTTGATAACCTC-CCTATG
* *
20874 AAATTTTCATAGCCTCCCTATG
1 AAATTTTGATAACCTCCCTATG
* * *
20896 AAATTTTGTTAACCTCCATAGG
1 AAATTTTGATAACCTCCCTATG
20918 AAATTTTGATAACCTCCCT
1 AAATTTTGATAACCTCCCT
20937 CCCTATGAAA
Statistics
Matches: 65, Mismatches: 18, Indels: 4
0.75 0.21 0.05
Matches are distributed among these distances:
21 2 0.03
22 62 0.95
23 1 0.02
ACGTcount: A:0.30, C:0.22, G:0.10, T:0.37
Consensus pattern (22 bp):
AAATTTTGATAACCTCCCTATG
Found at i:21092 original size:22 final size:22
Alignment explanation
Indices: 21067--21167 Score: 103
Period size: 22 Copynumber: 4.6 Consensus size: 22
21057 TCACACTATA
* *
21067 AAATTTCGATAACCTTGGTATG
1 AAATTTTGATAACCTTTGTATG
* * * **
21089 AAATTTTGTTAACCTCTCTAAA
1 AAATTTTGATAACCTTTGTATG
* *
21111 AAATTTTGATAACCTTTATGTG
1 AAATTTTGATAACCTTTGTATG
*
21133 AAATTTTGGTAACCTTTGTATG
1 AAATTTTGATAACCTTTGTATG
*
21155 AAATTCTGATAAC
1 AAATTTTGATAAC
21168 TACACTATAA
Statistics
Matches: 61, Mismatches: 18, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
22 61 1.00
ACGTcount: A:0.34, C:0.13, G:0.13, T:0.41
Consensus pattern (22 bp):
AAATTTTGATAACCTTTGTATG
Found at i:21137 original size:66 final size:66
Alignment explanation
Indices: 21067--21191 Score: 162
Period size: 66 Copynumber: 1.9 Consensus size: 66
21057 TCACACTATA
* * *
21067 AAATTTCGATAACCTTGGTATGAAATTTTGTTAACCT-CTCTAAAAAATTTTGATAACCTTTATG
1 AAATTTCGATAACCTTGGTATGAAATTCTGATAA-CTACACTAAAAAATTTTGATAACCTTTATG
21131 TG
65 TG
* * * * *
21133 AAATTTTGGTAACCTTTGTATGAAATTCTGATAACTACACTATAAAGTTTTGATAACCT
1 AAATTTCGATAACCTTGGTATGAAATTCTGATAACTACACTAAAAAATTTTGATAACCT
21192 ATGTAATTTT
Statistics
Matches: 50, Mismatches: 8, Indels: 2
0.83 0.13 0.03
Matches are distributed among these distances:
65 2 0.04
66 48 0.96
ACGTcount: A:0.34, C:0.14, G:0.12, T:0.40
Consensus pattern (66 bp):
AAATTTCGATAACCTTGGTATGAAATTCTGATAACTACACTAAAAAATTTTGATAACCTTTATGT
G
Found at i:21159 original size:44 final size:44
Alignment explanation
Indices: 21041--21147 Score: 124
Period size: 44 Copynumber: 2.4 Consensus size: 44
21031 TGCGGGCTCT
* * * * * * *
21041 TATGAAATTTTGATAATCACACTATAAAATTTCGATAACCTTGG
1 TATGAAATTTTGGTAACCTCTCTAAAAAATTTTGATAACCTTGA
* *
21085 TATGAAATTTTGTTAACCTCTCTAAAAAATTTTGATAACCTTTA
1 TATGAAATTTTGGTAACCTCTCTAAAAAATTTTGATAACCTTGA
*
21129 TGTGAAATTTTGGTAACCT
1 TATGAAATTTTGGTAACCT
21148 TTGTATGAAA
Statistics
Matches: 53, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
44 53 1.00
ACGTcount: A:0.36, C:0.13, G:0.11, T:0.40
Consensus pattern (44 bp):
TATGAAATTTTGGTAACCTCTCTAAAAAATTTTGATAACCTTGA
Found at i:24049 original size:11 final size:11
Alignment explanation
Indices: 24033--24063 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
24023 TCTGTTTTTT
24033 GTTTTTGTTTC
1 GTTTTTGTTTC
*
24044 GTTTTTGTTTT
1 GTTTTTGTTTC
24055 GTTTTTGTT
1 GTTTTTGTT
24064 AGGCTGTCAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.00, C:0.03, G:0.19, T:0.77
Consensus pattern (11 bp):
GTTTTTGTTTC
Done.