Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017313.1 Corchorus olitorius cultivar O-4 contig17346, 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: 43045
ACGTcount: A:0.34, C:0.19, G:0.16, T:0.31
Found at i:3834 original size:2 final size:2
Alignment explanation
Indices: 3822--3851 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
3812 GAAAAATCCT
*
3822 CA CA AA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
3852 TGTTTACCAC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.53, C:0.47, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:4273 original size:16 final size:16
Alignment explanation
Indices: 4252--4299 Score: 87
Period size: 16 Copynumber: 3.0 Consensus size: 16
4242 TACAATTCAG
*
4252 AAAGCAGAGAAGCTCT
1 AAAGCAGAAAAGCTCT
4268 AAAGCAGAAAAGCTCT
1 AAAGCAGAAAAGCTCT
4284 AAAGCAGAAAAGCTCT
1 AAAGCAGAAAAGCTCT
4300 GAAGTATTTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
16 31 1.00
ACGTcount: A:0.48, C:0.19, G:0.21, T:0.12
Consensus pattern (16 bp):
AAAGCAGAAAAGCTCT
Found at i:4457 original size:36 final size:36
Alignment explanation
Indices: 4399--4507 Score: 128
Period size: 41 Copynumber: 2.9 Consensus size: 36
4389 TTTTCGTTTG
** * *
4399 TTCAAGATCAAGTTATCAAGACCCTTGAATTATCAA
1 TTCAAGATTGAGTCATCGAGACCCTTGAATTATCAA
*
4435 TTCAAGATTGAGTCATTGAGACCCTTGAATTAAATTATCAA
1 TTCAAGATTGAGTCATCGAGACCCTTG-----AATTATCAA
4476 TTCAAGATTGAGTCATCGAGACCCTTGAATTA
1 TTCAAGATTGAGTCATCGAGACCCTTGAATTA
4508 AATTATCAAT
Statistics
Matches: 62, Mismatches: 6, Indels: 10
0.79 0.08 0.13
Matches are distributed among these distances:
36 27 0.44
41 35 0.56
ACGTcount: A:0.36, C:0.17, G:0.15, T:0.32
Consensus pattern (36 bp):
TTCAAGATTGAGTCATCGAGACCCTTGAATTATCAA
Found at i:4483 original size:41 final size:41
Alignment explanation
Indices: 4426--4635 Score: 226
Period size: 41 Copynumber: 5.1 Consensus size: 41
4416 AAGACCCTTG
* * *
4426 AATTATCAATTCAAGATTGAGTCATTGAGACCCTTGAATTA
1 AATTATCAATTCAAGAATAAGTCATCGAGACCCTTGAATTA
* *
4467 AATTATCAATTCAAGATTGAGTCATCGAGACCCTTGAATTA
1 AATTATCAATTCAAGAATAAGTCATCGAGACCCTTGAATTA
* * *
4508 AATTATCAATTCAAGAACAAGTCCTCGAGACCCTTGAATCGA
1 AATTATCAATTCAAGAATAAGTCATCGAGACCCTTGAAT-TA
* * * *
4550 ATTATTATCAATTCAAGACTAAGTCATCAACACCCTTAAATTA
1 A--ATTATCAATTCAAGAATAAGTCATCGAGACCCTTGAATTA
* * * *
4593 GATTGTCAATTCAAGAACAAGTCATTC-A-ACCCTTGAATCA
1 AATTATCAATTCAAGAATAAGTCA-TCGAGACCCTTGAATTA
4633 AAT
1 AAT
4636 CAAATCAAAG
Statistics
Matches: 145, Mismatches: 20, Indels: 9
0.83 0.11 0.05
Matches are distributed among these distances:
40 12 0.08
41 96 0.66
42 4 0.03
43 1 0.01
44 32 0.22
ACGTcount: A:0.39, C:0.20, G:0.12, T:0.30
Consensus pattern (41 bp):
AATTATCAATTCAAGAATAAGTCATCGAGACCCTTGAATTA
Found at i:4602 original size:85 final size:84
Alignment explanation
Indices: 4426--4635 Score: 243
Period size: 85 Copynumber: 2.5 Consensus size: 84
4416 AAGACCCTTG
*** * * * *
4426 AATTATCAATTCAAGATTGAGTCA-TTGAGACCCTTGAAT-TAAATTATCAATTCAAGATTGAGT
1 AATTATCAATTCAAGAACAAGTCACTCGAGACCCTTGAATCGAAATTATCAATTCAAGACTAAGT
* * *
4489 CATCGAGACCCTTGAATTA
66 CATCAACACCCTTAAATTA
4508 AATTATCAATTCAAGAACAAGTC-CTCGAGACCCTTGAATCGAATTATTATCAATTCAAGACTAA
1 AATTATCAATTCAAGAACAAGTCACTCGAGACCCTTGAATCGAA--ATTATCAATTCAAGACTAA
4572 GTCATCAACACCCTTAAATTA
64 GTCATCAACACCCTTAAATTA
* * *
4593 GATTGTCAATTCAAGAACAAGTCATTC-A-ACCCTTGAATC-AAAT
1 AATTATCAATTCAAGAACAAGTCACTCGAGACCCTTGAATCGAAAT
4636 CAAATCAAAG
Statistics
Matches: 110, Mismatches: 13, Indels: 11
0.82 0.10 0.08
Matches are distributed among these distances:
81 2 0.02
82 34 0.31
83 4 0.04
84 11 0.10
85 57 0.52
86 2 0.02
ACGTcount: A:0.39, C:0.20, G:0.12, T:0.30
Consensus pattern (84 bp):
AATTATCAATTCAAGAACAAGTCACTCGAGACCCTTGAATCGAAATTATCAATTCAAGACTAAGT
CATCAACACCCTTAAATTA
Found at i:6514 original size:76 final size:75
Alignment explanation
Indices: 6365--6505 Score: 230
Period size: 76 Copynumber: 1.9 Consensus size: 75
6355 ACTGCCCAAC
*
6365 AAAATAAAAAAAGAAGCTCGCTAAGTTGAAAATCCTTTAAAGGACGGCTTAGACAAAAGTTAGAG
1 AAAATAAAAAAAGAAGCTCGCTAAGTTGAAAATCCTGTAAAGGACGGCTTAGACAAAAGTTAGAG
6430 CGAAAAAAAG
66 CGAAAAAAAG
* *
6440 AAAA-AAAAAAAGAAAAGCTCGCTAAGTTGAAAATCCTGTAAAGGATGGCTTAGGCAAAAGTTAG
1 AAAATAAAAAAAG--AAGCTCGCTAAGTTGAAAATCCTGTAAAGGACGGCTTAGACAAAAGTTAG
6504 AG
64 AG
6506 GGGGAAAAAA
Statistics
Matches: 61, Mismatches: 3, Indels: 3
0.91 0.04 0.04
Matches are distributed among these distances:
74 8 0.13
75 4 0.07
76 49 0.80
ACGTcount: A:0.50, C:0.11, G:0.21, T:0.18
Consensus pattern (75 bp):
AAAATAAAAAAAGAAGCTCGCTAAGTTGAAAATCCTGTAAAGGACGGCTTAGACAAAAGTTAGAG
CGAAAAAAAG
Found at i:7280 original size:16 final size:16
Alignment explanation
Indices: 7247--7282 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
7237 CACAATTCAA
* *
7247 AAAGCAGAAAAGCTCT
1 AAAGCAGAAAAACACT
7263 AAAGCAGAAAAACACT
1 AAAGCAGAAAAACACT
7279 AAAG
1 AAAG
7283 TATTTTCAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.58, C:0.17, G:0.17, T:0.08
Consensus pattern (16 bp):
AAAGCAGAAAAACACT
Found at i:7435 original size:41 final size:41
Alignment explanation
Indices: 7378--7602 Score: 297
Period size: 41 Copynumber: 5.4 Consensus size: 41
7368 TTTTCGTTTG
*
7378 TTCAAGATCAAGTCATCAAGACCCTTGAATTAAATTATCAA
1 TTCAAGATCAAGTCATCGAGACCCTTGAATTAAATTATCAA
**
7419 TTCAAGATTGAGTCATCGAGACCCTTGAATTAAATTATCAA
1 TTCAAGATCAAGTCATCGAGACCCTTGAATTAAATTATCAA
**
7460 TTCAAGATTGAGTCATCGAGTACCCTTGAATTAAATTATCAA
1 TTCAAGATCAAGTCATCGAG-ACCCTTGAATTAAATTATCAA
* *
7502 TTCAAGAACAAGTCATCGAGACCCTTGAATCGAATTATTATCAA
1 TTCAAGATCAAGTCATCGAGACCCTTGAAT-TAA--ATTATCAA
* * * * *
7546 TTCAAGACCAAGTCGTCAAGACCCTTGAATTAGATTGTCAA
1 TTCAAGATCAAGTCATCGAGACCCTTGAATTAAATTATCAA
*
7587 TTCAAGAACAAGTCAT
1 TTCAAGATCAAGTCAT
7603 TCGACTCTTG
Statistics
Matches: 165, Mismatches: 15, Indels: 8
0.88 0.08 0.04
Matches are distributed among these distances:
41 89 0.54
42 40 0.24
43 1 0.01
44 35 0.21
ACGTcount: A:0.38, C:0.19, G:0.14, T:0.29
Consensus pattern (41 bp):
TTCAAGATCAAGTCATCGAGACCCTTGAATTAAATTATCAA
Found at i:7495 original size:83 final size:84
Alignment explanation
Indices: 7378--7602 Score: 319
Period size: 83 Copynumber: 2.7 Consensus size: 84
7368 TTTTCGTTTG
***
7378 TTCAAGATCAAGTCATCAAGACCCTTGAATTAAATTATCAATTCAAGATTGAGTCATCGAGACCC
1 TTCAAGATCAAGTCATCAAGACCCTTGAATTAAATTATCAATTCAAGAACAAGTCATCGAGACCC
*
7443 TTGAAT-TAA-ATTATCAA
66 TTGAATCGAATATTATCAA
** *
7460 TTCAAGATTGAGTCATCGAGTACCCTTGAATTAAATTATCAATTCAAGAACAAGTCATCGAGACC
1 TTCAAGATCAAGTCATCAAG-ACCCTTGAATTAAATTATCAATTCAAGAACAAGTCATCGAGACC
7525 CTTGAATCGAATTATTATCAA
65 CTTGAATCGAA-TATTATCAA
* * * *
7546 TTCAAGACCAAGTCGTCAAGACCCTTGAATTAGATTGTCAATTCAAGAACAAGTCAT
1 TTCAAGATCAAGTCATCAAGACCCTTGAATTAAATTATCAATTCAAGAACAAGTCAT
7603 TCGACTCTTG
Statistics
Matches: 125, Mismatches: 14, Indels: 5
0.87 0.10 0.03
Matches are distributed among these distances:
82 17 0.14
83 48 0.38
84 2 0.02
85 35 0.28
86 23 0.18
ACGTcount: A:0.38, C:0.19, G:0.14, T:0.29
Consensus pattern (84 bp):
TTCAAGATCAAGTCATCAAGACCCTTGAATTAAATTATCAATTCAAGAACAAGTCATCGAGACCC
TTGAATCGAATATTATCAA
Found at i:7628 original size:127 final size:123
Alignment explanation
Indices: 7378--7620 Score: 283
Period size: 127 Copynumber: 2.0 Consensus size: 123
7368 TTTTCGTTTG
* * *** *
7378 TTCAAGATCAAGTCATCAAGACCCTTGAATTAAATTATCAATTCAAGATTGAGTCATCGAGACCC
1 TTCAAGAACAAGTCATCAAGACCCTTGAATGAAATTATCAATTCAAGACCAAGTCATCAAGACCC
*** * *
7443 TTGAATTAAATTATCAATTCAAGATTGAGTCATCGAGTACCCTTGAATTAAATTATCAA
66 TTGAATTAAATTATCAATTCAAGAACAAGTCATC-AGTACCCTTGAATCAAATAATCAA
* *
7502 TTCAAGAACAAGTCATCGAGACCCTTGAATCGAATTATTATCAATTCAAGACCAAGTCGTCAAGA
1 TTCAAGAACAAGTCATCAAGACCCTTGAAT-GAA--ATTATCAATTCAAGACCAAGTCATCAAGA
* * *
7567 CCCTTGAATTAGATTGTCAATTCAAGAACAAGTCATTC-G-ACTCTTGAATCAAAT
63 CCCTTGAATTAAATTATCAATTCAAGAACAAGTCA-TCAGTACCCTTGAATCAAAT
7621 CAAATCAAAG
Statistics
Matches: 100, Mismatches: 15, Indels: 7
0.82 0.12 0.06
Matches are distributed among these distances:
124 28 0.28
125 15 0.15
126 1 0.01
127 54 0.54
128 2 0.02
ACGTcount: A:0.37, C:0.19, G:0.14, T:0.30
Consensus pattern (123 bp):
TTCAAGAACAAGTCATCAAGACCCTTGAATGAAATTATCAATTCAAGACCAAGTCATCAAGACCC
TTGAATTAAATTATCAATTCAAGAACAAGTCATCAGTACCCTTGAATCAAATAATCAA
Found at i:13378 original size:20 final size:22
Alignment explanation
Indices: 13327--13382 Score: 89
Period size: 22 Copynumber: 2.6 Consensus size: 22
13317 GATTGAAGAA
*
13327 AATGCTCTGCAAAGTGAAAAAT
1 AATGCTCTGCAAAGTGAAAAAG
13349 AATGCTCTGCAAAGTG-AAAAG
1 AATGCTCTGCAAAGTGAAAAAG
13370 AAT-CTCTGCAAAG
1 AATGCTCTGCAAAG
13383 ATGTTTCCAA
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
20 10 0.30
21 7 0.21
22 16 0.48
ACGTcount: A:0.43, C:0.16, G:0.20, T:0.21
Consensus pattern (22 bp):
AATGCTCTGCAAAGTGAAAAAG
Found at i:13417 original size:74 final size:74
Alignment explanation
Indices: 13338--13527 Score: 334
Period size: 74 Copynumber: 2.6 Consensus size: 74
13328 ATGCTCTGCA
13338 AAGTGAAAAATAATGCTCTGCAAAGTGAAAAGAATCTCTGCAAAGATGTTTCCAATAGTGCAAAG
1 AAGTGAAAAATAATGCTCTGCAAAGTGAAAAGAATCTCTGCAAAGATGTTTCCAATAGTGCAAAG
13403 CTGAAGTTG
66 CTGAAGTTG
*
13412 AAGTGAAAAATAATGCTCTGCAAAGTGGAAAGAATCTCTGCAAAGATGTTTCCAATAGTGCAAAG
1 AAGTGAAAAATAATGCTCTGCAAAGTGAAAAGAATCTCTGCAAAGATGTTTCCAATAGTGCAAAG
13477 CTGAAGTTG
66 CTGAAGTTG
13486 AA--G-AAAATAATGCTCTGCAAAGTGAAAA-AATGCTCTGCAAAG
1 AAGTGAAAAATAATGCTCTGCAAAGTGAAAAGAAT-CTCTGCAAAG
13528 TGGAGAATAA
Statistics
Matches: 113, Mismatches: 2, Indels: 5
0.94 0.02 0.04
Matches are distributed among these distances:
70 3 0.03
71 34 0.30
72 1 0.01
74 75 0.66
ACGTcount: A:0.42, C:0.14, G:0.22, T:0.23
Consensus pattern (74 bp):
AAGTGAAAAATAATGCTCTGCAAAGTGAAAAGAATCTCTGCAAAGATGTTTCCAATAGTGCAAAG
CTGAAGTTG
Found at i:13542 original size:22 final size:20
Alignment explanation
Indices: 13490--13569 Score: 108
Period size: 20 Copynumber: 3.9 Consensus size: 20
13480 AAGTTGAAGA
13490 AAATAATGCTCTGCAAAGTG
1 AAATAATGCTCTGCAAAGTG
*
13510 AAAAAATGCTCTGCAAAGTGG
1 AAATAATGCTCTGCAAAGT-G
13531 AGAATAATGCTCTGCAAAGTAG
1 A-AATAATGCTCTGCAAAGT-G
*
13553 AAAGAAT-CTCTGCAAAG
1 AAATAATGCTCTGCAAAG
13570 ATGTTTCCAA
Statistics
Matches: 54, Mismatches: 4, Indels: 4
0.87 0.06 0.06
Matches are distributed among these distances:
20 28 0.52
21 7 0.13
22 19 0.35
ACGTcount: A:0.42, C:0.15, G:0.21, T:0.21
Consensus pattern (20 bp):
AAATAATGCTCTGCAAAGTG
Found at i:13792 original size:15 final size:15
Alignment explanation
Indices: 13772--13805 Score: 68
Period size: 15 Copynumber: 2.3 Consensus size: 15
13762 TTTTCTTATT
13772 TCTTACTTTTATTAC
1 TCTTACTTTTATTAC
13787 TCTTACTTTTATTAC
1 TCTTACTTTTATTAC
13802 TCTT
1 TCTT
13806 CAAAGTATCA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.18, C:0.21, G:0.00, T:0.62
Consensus pattern (15 bp):
TCTTACTTTTATTAC
Found at i:13896 original size:21 final size:21
Alignment explanation
Indices: 13870--13945 Score: 127
Period size: 21 Copynumber: 3.6 Consensus size: 21
13860 GGTATCAGAG
13870 CCTTCTCCAATGAGCTTGGAA
1 CCTTCTCCAATGAGCTTGGAA
*
13891 CCTTCTCCAATAAGCTTGGAA
1 CCTTCTCCAATGAGCTTGGAA
13912 CCTTCTCCAATGAGCTTGGAA
1 CCTTCTCCAATGAGCTTGGAA
13933 -CTTGCTCCAATGA
1 CCTT-CTCCAATGA
13946 ACTCCTACTA
Statistics
Matches: 52, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
20 3 0.06
21 49 0.94
ACGTcount: A:0.25, C:0.29, G:0.17, T:0.29
Consensus pattern (21 bp):
CCTTCTCCAATGAGCTTGGAA
Found at i:15798 original size:33 final size:33
Alignment explanation
Indices: 15761--15865 Score: 115
Period size: 33 Copynumber: 3.2 Consensus size: 33
15751 ATTAGCATCC
*
15761 AAAACAGAATTT-GTTTCATCACAAACAACACCT
1 AAAACAG-ATTTAGTGTCATCACAAACAACACCT
15794 AAAACAGATTTAGTGTCATCACAAACAACA-CT
1 AAAACAGATTTAGTGTCATCACAAACAACACCT
** * * * *
15826 CAAATTAGTTTTAGTATCATCACTAACAACATCT
1 -AAAACAGATTTAGTGTCATCACAAACAACACCT
15860 AAAACA
1 AAAACA
15866 CTCTTTCCAA
Statistics
Matches: 61, Mismatches: 8, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
32 6 0.10
33 53 0.87
34 2 0.03
ACGTcount: A:0.46, C:0.22, G:0.07, T:0.26
Consensus pattern (33 bp):
AAAACAGATTTAGTGTCATCACAAACAACACCT
Found at i:18429 original size:21 final size:21
Alignment explanation
Indices: 18317--18413 Score: 167
Period size: 21 Copynumber: 4.6 Consensus size: 21
18307 CTTAGGCAAT
*
18317 TCCAATGAGCTTGAAACCTTC
1 TCCAATGAGCTTGGAACCTTC
18338 TCCAATGAGCTTGGAACCTTC
1 TCCAATGAGCTTGGAACCTTC
*
18359 TCCAATGAGCTTGGAACCTTG
1 TCCAATGAGCTTGGAACCTTC
*
18380 TCCAATAAGCTTGGAACCTTC
1 TCCAATGAGCTTGGAACCTTC
18401 TCCAATGAGCTTG
1 TCCAATGAGCTTG
18414 AAACTTGCTT
Statistics
Matches: 71, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 71 1.00
ACGTcount: A:0.26, C:0.27, G:0.19, T:0.29
Consensus pattern (21 bp):
TCCAATGAGCTTGGAACCTTC
Found at i:27052 original size:21 final size:21
Alignment explanation
Indices: 27028--27071 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
27018 CCTCTTCTCC
*
27028 TTTTGTCATGAAAACACTTTT
1 TTTTGTCATGAAAACAATTTT
* *
27049 TTTTTTTATGAAAACAATTTT
1 TTTTGTCATGAAAACAATTTT
27070 TT
1 TT
27072 AACTACCCTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.30, C:0.09, G:0.07, T:0.55
Consensus pattern (21 bp):
TTTTGTCATGAAAACAATTTT
Found at i:27360 original size:14 final size:12
Alignment explanation
Indices: 27332--27357 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
27322 TGCAAAAATC
27332 AATTTTTTTCAA
1 AATTTTTTTCAA
27344 AATTTTTTTCAA
1 AATTTTTTTCAA
27356 AA
1 AA
27358 AATGGGGAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.38, C:0.08, G:0.00, T:0.54
Consensus pattern (12 bp):
AATTTTTTTCAA
Found at i:30029 original size:21 final size:21
Alignment explanation
Indices: 30003--30044 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
29993 GCATCTTAGG
30003 CAACTCCGA-TGAGCTTGAAAC
1 CAACTCC-ATTGAGCTTGAAAC
30024 CAACTCCATTGAGCTTGAAAC
1 CAACTCCATTGAGCTTGAAAC
30045 TTCTTTGTGC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 1 0.05
21 19 0.95
ACGTcount: A:0.33, C:0.29, G:0.17, T:0.21
Consensus pattern (21 bp):
CAACTCCATTGAGCTTGAAAC
Found at i:32814 original size:33 final size:33
Alignment explanation
Indices: 32777--32840 Score: 94
Period size: 33 Copynumber: 1.9 Consensus size: 33
32767 ATTAGCATCC
* *
32777 AAAACAGAATTT-GTTTCATCCCAAACAACACCT
1 AAAACAG-ATTTAGTGTCATCACAAACAACACCT
32810 AAAACAGATTTAGTGTCATCACAAACAACAC
1 AAAACAGATTTAGTGTCATCACAAACAACAC
32841 TCAAATTCGT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
32 4 0.14
33 24 0.86
ACGTcount: A:0.45, C:0.25, G:0.08, T:0.22
Consensus pattern (33 bp):
AAAACAGATTTAGTGTCATCACAAACAACACCT
Found at i:35201 original size:65 final size:65
Alignment explanation
Indices: 35092--35221 Score: 215
Period size: 65 Copynumber: 2.0 Consensus size: 65
35082 GGAAAAATTG
* * *
35092 GTCCTACCCATGCATGGGGTACCCTTGGCTTACACACGCCTGGGCTAGTGCAGAAAGTTTGAATC
1 GTCCAACCCATGCATGGGGTACCCTTGGCCTACACACGCCTGGGCTAGTGCAGAAAGTTGGAATC
* *
35157 GTCCAACCCATGCATGGGGTACCCTTGTCCTACCCACGCCTGGGCTAGTGCAGAAAGTTGGAATC
1 GTCCAACCCATGCATGGGGTACCCTTGGCCTACACACGCCTGGGCTAGTGCAGAAAGTTGGAATC
35222 AATAGCAAGC
Statistics
Matches: 60, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
65 60 1.00
ACGTcount: A:0.22, C:0.29, G:0.26, T:0.23
Consensus pattern (65 bp):
GTCCAACCCATGCATGGGGTACCCTTGGCCTACACACGCCTGGGCTAGTGCAGAAAGTTGGAATC
Found at i:35437 original size:21 final size:21
Alignment explanation
Indices: 35411--35452 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
35401 ACATCTTAGG
*
35411 CAACTCCGATAAGCTTGAAAC
1 CAACTCCAATAAGCTTGAAAC
*
35432 CAACTCCAATGAGCTTGAAAC
1 CAACTCCAATAAGCTTGAAAC
35453 TTCTTTGTGC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.38, C:0.29, G:0.14, T:0.19
Consensus pattern (21 bp):
CAACTCCAATAAGCTTGAAAC
Found at i:42549 original size:2 final size:2
Alignment explanation
Indices: 42542--42577 Score: 56
Period size: 2 Copynumber: 18.0 Consensus size: 2
42532 CACCACCAAA
42542 AT AT AT AT AT AT AT AT AT AT AT GA- 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
42578 TACACCCTCA
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 1 0.03
2 30 0.94
3 1 0.03
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Done.