Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015397.1 Corchorus capsularis cultivar CVL-1 contig15418, 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: 9261
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.30
Found at i:437 original size:27 final size:26
Alignment explanation
Indices: 402--479 Score: 79
Period size: 27 Copynumber: 2.9 Consensus size: 26
392 AAGTAGACTT
*
402 AAAACGACCAAAATGCCCCTGAATGTG-C
1 AAAATGACCAAAATGCCCCTG---GTGCC
* *
430 -AAATGACCAGAATACCCCTGGTGCC
1 AAAATGACCAAAATGCCCCTGGTGCC
455 AAAATGACCAAAATGCCCCTAGGTG
1 AAAATGACCAAAATGCCCCT-GGTG
480 ACCCTAATGG
Statistics
Matches: 42, Mismatches: 5, Indels: 7
0.78 0.09 0.13
Matches are distributed among these distances:
24 3 0.07
25 1 0.02
26 17 0.40
27 21 0.50
ACGTcount: A:0.37, C:0.28, G:0.19, T:0.15
Consensus pattern (26 bp):
AAAATGACCAAAATGCCCCTGGTGCC
Found at i:901 original size:90 final size:89
Alignment explanation
Indices: 785--1032 Score: 345
Period size: 90 Copynumber: 2.7 Consensus size: 89
775 GCACCGCAGT
*
785 AACTTGA-TCTACGGAATCATCCTGAACTATTTGAAAACGTTCTGCACCGAGCTCACCGAATCCA
1 AACTTGATTC-ACCGAATCATCCTGAACTATTTGAAAA-GTTCTGCACCGAGCTCACCGAATCCA
849 ATCTTGAAGAAATAAGGCACCGCCTC
64 ATCTTGAAGAAATAAGGCACCGCCTC
* * *
875 AACTTGATTCACCGAATCATCCTGAACTATTTGAAGATGTGCTACACCGAGCTCACCGAATCCAA
1 AACTTGATTCACCGAATCATCCTGAACTATTTGAA-AAGTTCTGCACCGAGCTCACCGAATCCAA
940 TCTTGAAGAAATAAGGCACCGCCTC
65 TCTTGAAGAAATAAGGCACCGCCTC
* * * * * *
965 AATCTAGATTAACCGAATCATCCTTAACTGTTTGAAAATTTGCTGCACCGAGCTCACTGAATTCC
1 AA-CTTGATTCACCGAATCATCCTGAACTATTTGAAAAGTT-CTGCACCGAGCTCACCGAA-TCC
1030 AAT
63 AAT
1033 AGATGCACCA
Statistics
Matches: 140, Mismatches: 13, Indels: 8
0.87 0.08 0.05
Matches are distributed among these distances:
90 85 0.61
91 49 0.35
92 6 0.04
ACGTcount: A:0.32, C:0.27, G:0.16, T:0.25
Consensus pattern (89 bp):
AACTTGATTCACCGAATCATCCTGAACTATTTGAAAAGTTCTGCACCGAGCTCACCGAATCCAAT
CTTGAAGAAATAAGGCACCGCCTC
Found at i:3081 original size:81 final size:84
Alignment explanation
Indices: 2946--3188 Score: 330
Period size: 81 Copynumber: 2.9 Consensus size: 84
2936 CCAATCTTTG
2946 AATAGATGCACCACATTAACTTGATTCACCGAATAACCATGATCTATTTGAAAATTTACTGCACC
1 AATAGATGCACCACATTAACTTGATTCACCGAATAACCATGATCTATTTGAAAATTTACTGCACC
3011 GAGCTCACCGAATT-C-C-
66 GAGCTCACCGAATTCCACT
* * * * *
3027 AATAGATGCACCACATTAACTTGATTCACTGAATTACCCTGATCTGTGTGAAAATTTACTGCACC
1 AATAGATGCACCACATTAACTTGATTCACCGAATAACCATGATCTATTTGAAAATTTACTGCACC
*
3092 GAGCTCACCGTATTCCAATCTTT
66 GAGCTCACCGAATTCC-A-C--T
** * *
3115 GAATAGATGCACCGTATTAACTTGATTCACCGAATAACCATGATCTATTTGAAAATATGCTGCAC
1 -AATAGATGCACCACATTAACTTGATTCACCGAATAACCATGATCTATTTGAAAATTTACTGCAC
3180 CGAGCTCAC
65 CGAGCTCAC
3189 AAATCCAATC
Statistics
Matches: 139, Mismatches: 15, Indels: 8
0.86 0.09 0.05
Matches are distributed among these distances:
81 73 0.53
82 1 0.01
85 1 0.01
89 64 0.46
ACGTcount: A:0.33, C:0.25, G:0.14, T:0.29
Consensus pattern (84 bp):
AATAGATGCACCACATTAACTTGATTCACCGAATAACCATGATCTATTTGAAAATTTACTGCACC
GAGCTCACCGAATTCCACT
Found at i:3329 original size:91 final size:90
Alignment explanation
Indices: 3044--3408 Score: 461
Period size: 91 Copynumber: 4.1 Consensus size: 90
3034 GCACCACATT
* * * * * * * * *
3044 AACTTGATTCACTGAATTACCCTGATCTGTGTGAAAATTTACTGCACCGAGCTCACCGTATTCCA
1 AACTTGATTCACCGAATCACCATGAACTATTTGAAAATATGCTGCACCGAGCTCACCG-AATCCA
*
3109 ATCTTT--G-AATAGATGCACCGTATT
65 ATCTTTGAGAAATA-ATGCACCGTATC
* * *
3133 AACTTGATTCACCGAATAACCATGATCTATTTGAAAATATGCTGCACCGAGCTCA-CAAATCCAA
1 AACTTGATTCACCGAATCACCATGAACTATTTGAAAATATGCTGCACCGAGCTCACCGAATCCAA
*
3197 TCTTTGAAGAAATAATGCACTGTATC
66 TCTTTG-AGAAATAATGCACCGTATC
*
3223 AACTTGATTCACCGAATCACCATGAACTATTTGAAAATATGTTGCACCGAGCTCACCGAATCCAA
1 AACTTGATTCACCGAATCACCATGAACTATTTGAAAATATGCTGCACCGAGCTCACCGAATCCAA
3288 TCTTTGAAGAAATAATGCACCGTATC
66 TCTTTG-AGAAATAATGCACCGTATC
* * * *
3314 AACTTGATTCACCGAATCATCTTGAACTGTTTGAAAATATGCTGCACCGAGCTCACCGACTCCAA
1 AACTTGATTCACCGAATCACCATGAACTATTTGAAAATATGCTGCACCGAGCTCACCGAATCCAA
* *
3379 TC-TTGAGAAATAATTCACCGAATCC
66 TCTTTGAGAAATAATGCACCGTAT-C
3404 AACTT
1 AACTT
3409 TGAGGATACA
Statistics
Matches: 247, Mismatches: 23, Indels: 11
0.88 0.08 0.04
Matches are distributed among these distances:
87 11 0.04
88 1 0.00
89 64 0.26
90 72 0.29
91 99 0.40
ACGTcount: A:0.33, C:0.24, G:0.14, T:0.28
Consensus pattern (90 bp):
AACTTGATTCACCGAATCACCATGAACTATTTGAAAATATGCTGCACCGAGCTCACCGAATCCAA
TCTTTGAGAAATAATGCACCGTATC
Found at i:3349 original size:181 final size:178
Alignment explanation
Indices: 2926--3392 Score: 517
Period size: 170 Copynumber: 2.7 Consensus size: 178
2916 GACACGATCA
* ** * *
2926 TCACCGTATTCCAATCTTTGAATAGATGCACCACATTAACTTGATTCACCGAATAACCATGATCT
1 TCACCGTAATCCAATCTTTGAATAGATGCACCGTATCAACTTGATTCACCGAATAACCATGAACT
* * * *** *
2991 ATTTGAAAATTTACTGCACCGAGCTCACCGAATTCCAA---T-AG-----ATGCACCACATTAAC
66 ATTTGAAAATATGCTGCACCGAGCTCACC-AAATCCAATCTTGAGAAATAATGCACTGTATCAAC
* * * * * *
3047 TTGATTCACTGAATTACCCTGATCTGTGTGAAAATTTACTGCACCGAGC
130 TTGATTCACCGAATCACCATGAACTATGTGAAAATATACTGCACCGAGC
* * *
3096 TCACCGTATTCCAATCTTTGAATAGATGCACCGTATTAACTTGATTCACCGAATAACCATGATCT
1 TCACCGTAATCCAATCTTTGAATAGATGCACCGTATCAACTTGATTCACCGAATAACCATGAACT
3161 ATTTGAAAATATGCTGCACCGAGCTCA-CAAATCCAATCTTTGAAGAAATAATGCACTGTATCAA
66 ATTTGAAAATATGCTGCACCGAGCTCACCAAATCCAATC-TTG-AGAAATAATGCACTGTATCAA
* **
3225 CTTGATTCACCGAATCACCATGAACTATTTGAAAATATGTTGCACCGAGC
129 CTTGATTCACCGAATCACCATGAACTATGTGAAAATATACTGCACCGAGC
* * *
3275 TCACCG-AATCCAATCTTTGAAGAAATA-ATGCACCGTATCAACTTGATTCACCGAATCATCTTG
1 TCACCGTAATCCAATCTTT---G-AATAGATGCACCGTATCAACTTGATTCACCGAATAACCATG
* * *
3338 AACTGTTTGAAAATATGCTGCACCGAGCTCACCGACTCCAATCTTGAGAAATAAT
62 AACTATTTGAAAATATGCTGCACCGAGCTCACCAAATCCAATCTTGAGAAATAAT
3393 TCACCGAATC
Statistics
Matches: 254, Mismatches: 27, Indels: 22
0.84 0.09 0.07
Matches are distributed among these distances:
168 7 0.03
169 1 0.00
170 88 0.35
172 1 0.00
174 2 0.01
178 11 0.04
179 57 0.22
180 9 0.04
181 65 0.26
182 13 0.05
ACGTcount: A:0.33, C:0.24, G:0.14, T:0.29
Consensus pattern (178 bp):
TCACCGTAATCCAATCTTTGAATAGATGCACCGTATCAACTTGATTCACCGAATAACCATGAACT
ATTTGAAAATATGCTGCACCGAGCTCACCAAATCCAATCTTGAGAAATAATGCACTGTATCAACT
TGATTCACCGAATCACCATGAACTATGTGAAAATATACTGCACCGAGC
Found at i:3499 original size:35 final size:35
Alignment explanation
Indices: 3396--3608 Score: 248
Period size: 35 Copynumber: 6.0 Consensus size: 35
3386 AAATAATTCA
* * * *
3396 CCGAATCCAACTTTGAGGATAC-ACCATCGAGTGAT
1 CCGAATCCAACTTTGAAGATGCTA-CACCGAGTCAT
** * *
3431 CTAAATCCAACTTTGAAACATGCTACACTGAGTCAT
1 CCGAATCCAACTTTG-AAGATGCTACACCGAGTCAT
3467 CCGAATCCAACTTTGAAGATGCTACACCGAGTCAT
1 CCGAATCCAACTTTGAAGATGCTACACCGAGTCAT
* * * * *
3502 CTGAAACCAGCATTAAAGATGCTACACCGAGTCAT
1 CCGAATCCAACTTTGAAGATGCTACACCGAGTCAT
* *
3537 CCGAATCCAACTTTGAAAACGCTACACCGAGTCAT
1 CCGAATCCAACTTTGAAGATGCTACACCGAGTCAT
*
3572 CCAAATCCAACTTTGAAAGATGCTACACCGAGTCAT
1 CCGAATCCAACTTTG-AAGATGCTACACCGAGTCAT
3608 C
1 C
3609 TGGAACAAAC
Statistics
Matches: 148, Mismatches: 27, Indels: 5
0.82 0.15 0.03
Matches are distributed among these distances:
35 103 0.70
36 44 0.30
37 1 0.01
ACGTcount: A:0.34, C:0.28, G:0.15, T:0.23
Consensus pattern (35 bp):
CCGAATCCAACTTTGAAGATGCTACACCGAGTCAT
Found at i:3541 original size:70 final size:71
Alignment explanation
Indices: 3396--3608 Score: 288
Period size: 70 Copynumber: 3.0 Consensus size: 71
3386 AAATAATTCA
* * * * * *
3396 CCGAATCCAACTTTGAGGATAC-ACCATCGAGTGATCTAAATCCAACTTTGAAACATGCTACACT
1 CCGAATCCAACTTTGAAGATGCTA-CACCGAGTCATCTAAATCCAACTTTGAAAGATGCTACACC
3460 GAGTCAT
65 GAGTCAT
* *
3467 CCGAATCCAACTTTGAAGATGCTACACCGAGTCATCTGAAA-CCAGCATT-AAAGATGCTACACC
1 CCGAATCCAACTTTGAAGATGCTACACCGAGTCATCT-AAATCCAACTTTGAAAGATGCTACACC
3530 GAGTCAT
65 GAGTCAT
* * *
3537 CCGAATCCAACTTTGAAAACGCTACACCGAGTCATCCAAATCCAACTTTGAAAGATGCTACACCG
1 CCGAATCCAACTTTGAAGATGCTACACCGAGTCATCTAAATCCAACTTTGAAAGATGCTACACCG
3602 AGTCAT
66 AGTCAT
3608 C
1 C
3609 TGGAACAAAC
Statistics
Matches: 125, Mismatches: 13, Indels: 8
0.86 0.09 0.05
Matches are distributed among these distances:
69 3 0.02
70 59 0.47
71 59 0.47
72 4 0.03
ACGTcount: A:0.34, C:0.28, G:0.15, T:0.23
Consensus pattern (71 bp):
CCGAATCCAACTTTGAAGATGCTACACCGAGTCATCTAAATCCAACTTTGAAAGATGCTACACCG
AGTCAT
Found at i:3626 original size:36 final size:36
Alignment explanation
Indices: 3434--3629 Score: 265
Period size: 35 Copynumber: 5.5 Consensus size: 36
3424 GAGTGATCTA
* *
3434 AATCCAACTTTGAAACATGCTACACTGAGTCATCCG
1 AATCCAACTTTGAAAGATGCTACACCGAGTCATCCG
*
3470 AATCCAACTTTG-AAGATGCTACACCGAGTCATCTG
1 AATCCAACTTTGAAAGATGCTACACCGAGTCATCCG
* * *
3505 AAACCAGCATT-AAAGATGCTACACCGAGTCATCCG
1 AATCCAACTTTGAAAGATGCTACACCGAGTCATCCG
* *
3540 AATCCAACTTTGAAA-ACGCTACACCGAGTCATCCA
1 AATCCAACTTTGAAAGATGCTACACCGAGTCATCCG
*
3575 AATCCAACTTTGAAAGATGCTACACCGAGTCATCTGG
1 AATCCAACTTTGAAAGATGCTACACCGAGTCATC-CG
*
3612 AA-CAAACTTTGAAAGATG
1 AATCCAACTTTGAAAGATG
3630 TTCACTGGAT
Statistics
Matches: 140, Mismatches: 16, Indels: 8
0.85 0.10 0.05
Matches are distributed among these distances:
35 91 0.65
36 47 0.34
37 2 0.01
ACGTcount: A:0.36, C:0.26, G:0.16, T:0.22
Consensus pattern (36 bp):
AATCCAACTTTGAAAGATGCTACACCGAGTCATCCG
Found at i:3699 original size:54 final size:54
Alignment explanation
Indices: 3632--4080 Score: 509
Period size: 54 Copynumber: 8.4 Consensus size: 54
3622 GAAAGATGTT
* * * * * * * **
3632 CACTGGATTACTTGAAGATGAACTTAAATCACCGGAAACTCTCATAATTGTTCG
1 CACTGGATCACTTGAAGATAAACTTAAACCACTGGAAACTTTCTTGATTGACCG
* *
3686 CACTGGATCACTTGAAGATAAACTTAAACCACTAGAGACTTTCTTGATTGACCG
1 CACTGGATCACTTGAAGATAAACTTAAACCACTGGAAACTTTCTTGATTGACCG
* * * *
3740 CACTCGATCACTTGAAGATCAACTTAAACCACTGGAGACTTTTTTGATTGACCG
1 CACTGGATCACTTGAAGATAAACTTAAACCACTGGAAACTTTCTTGATTGACCG
* * * **
3794 CACTGGATCACTTGAGGATAAACTTTAGCCACTGGAAACTTTCAAGATTGACCG
1 CACTGGATCACTTGAAGATAAACTTAAACCACTGGAAACTTTCTTGATTGACCG
* * * *
3848 CACTGAACCACTTGAAGATAAACTTTAGCCACTGGAAACTTTCTTGATTGACCG
1 CACTGGATCACTTGAAGATAAACTTAAACCACTGGAAACTTTCTTGATTGACCG
* *
3902 CACTGGATCACTT--A-A-AGA--T--ACCACTGGAAACTTTCTCGATTGACCG
1 CACTGGATCACTTGAAGATAAACTTAAACCACTGGAAACTTTCTTGATTGACCG
* * *
3948 CATTGGATTACTTGAAGATAAACTTAAACCACTGGAAAATTTCTTGATTGACCG
1 CACTGGATCACTTGAAGATAAACTTAAACCACTGGAAACTTTCTTGATTGACCG
* * * *
4002 CACTGGATCACTTGAAGATAAACTCAATATCACTGTAAACTTCCTTGATTGACCG
1 CACTGGATCACTTGAAGATAAACTTAA-ACCACTGGAAACTTTCTTGATTGACCG
* * *
4057 TATTGGATCACTTGAGGATAAACT
1 CACTGGATCACTTGAAGATAAACT
4081 CAATATCACT
Statistics
Matches: 337, Mismatches: 49, Indels: 17
0.84 0.12 0.04
Matches are distributed among these distances:
46 36 0.11
48 2 0.01
49 1 0.00
50 4 0.01
51 1 0.00
52 2 0.01
54 247 0.73
55 44 0.13
ACGTcount: A:0.32, C:0.22, G:0.17, T:0.29
Consensus pattern (54 bp):
CACTGGATCACTTGAAGATAAACTTAAACCACTGGAAACTTTCTTGATTGACCG
Found at i:3943 original size:46 final size:46
Alignment explanation
Indices: 3876--4021 Score: 166
Period size: 46 Copynumber: 3.0 Consensus size: 46
3866 TAAACTTTAG
3876 CCACTGGAAACTTTCTTGATTGACCGCACTGGATCACTTAAAGATA
1 CCACTGGAAACTTTCTTGATTGACCGCACTGGATCACTTAAAGATA
* * * *
3922 CCACTGGAAACTTTCTCGATTGACCGCATTGGATTACTTGAAGATAAACTTAAA
1 CCACTGGAAACTTTCTTGATTGACCGCACTGGATCACTT--A-A-AGA--T--A
* *
3976 CCACTGGAAAATTTCTTGATTGACCGCACTGGATCACTTGAAGATA
1 CCACTGGAAACTTTCTTGATTGACCGCACTGGATCACTTAAAGATA
4022 AACTCAATAT
Statistics
Matches: 82, Mismatches: 10, Indels: 16
0.76 0.09 0.15
Matches are distributed among these distances:
46 37 0.45
48 2 0.02
49 1 0.01
50 4 0.05
51 1 0.01
52 1 0.01
54 36 0.44
ACGTcount: A:0.32, C:0.22, G:0.18, T:0.29
Consensus pattern (46 bp):
CCACTGGAAACTTTCTTGATTGACCGCACTGGATCACTTAAAGATA
Found at i:3995 original size:100 final size:100
Alignment explanation
Indices: 3822--4021 Score: 310
Period size: 100 Copynumber: 2.0 Consensus size: 100
3812 TAAACTTTAG
* * *
3822 CCACTGGAAACTTTCAAGATTGACCGCACTGAACCACTTGAAGATAAACTTTAGCCACTGGAAAC
1 CCACTGGAAACTTTCAAGATTGACCGCACTGAACCACTTGAAGATAAACTTAAACCACTGGAAAA
3887 TTTCTTGATTGACCGCACTGGATCACTTAAAGATA
66 TTTCTTGATTGACCGCACTGGATCACTTAAAGATA
** * * **
3922 CCACTGGAAACTTTCTCGATTGACCGCATTGGATTACTTGAAGATAAACTTAAACCACTGGAAAA
1 CCACTGGAAACTTTCAAGATTGACCGCACTGAACCACTTGAAGATAAACTTAAACCACTGGAAAA
*
3987 TTTCTTGATTGACCGCACTGGATCACTTGAAGATA
66 TTTCTTGATTGACCGCACTGGATCACTTAAAGATA
4022 AACTCAATAT
Statistics
Matches: 90, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
100 90 1.00
ACGTcount: A:0.33, C:0.23, G:0.17, T:0.28
Consensus pattern (100 bp):
CCACTGGAAACTTTCAAGATTGACCGCACTGAACCACTTGAAGATAAACTTAAACCACTGGAAAA
TTTCTTGATTGACCGCACTGGATCACTTAAAGATA
Found at i:3997 original size:154 final size:154
Alignment explanation
Indices: 3767--4069 Score: 410
Period size: 154 Copynumber: 2.0 Consensus size: 154
3757 ATCAACTTAA
* * * * * *
3767 ACCACTGGAGACTTTTTTGATTGACCGCACTGGATCACTTGAGGATAAACTTTAGCCACTGGAAA
1 ACCACTGGAAACTTTCTCGATTGACCGCACTGGATCACTTGAAGATAAACTTAAACCACTGGAAA
* * *
3832 CTTTCAAGATTGACCGCACTGAACCACTTGAAGATAAACT-TTAGCCACTGGAAACTTTCTTGAT
66 ATTTCAAGATTGACCGCACTGAACCACTTGAAGATAAACTAATA-CCACTGGAAACTTCCTTGAT
3896 TGACCGCACTGGATCACTTAAAGAT
130 TGACCGCACTGGATCACTTAAAGAT
* *
3921 ACCACTGGAAACTTTCTCGATTGACCGCATTGGATTACTTGAAGATAAACTTAAACCACTGGAAA
1 ACCACTGGAAACTTTCTCGATTGACCGCACTGGATCACTTGAAGATAAACTTAAACCACTGGAAA
** * * * *
3986 ATTTCTTGATTGACCGCACTGGATCACTTGAAGATAAACTCAATATCACTGTAAACTTCCTTGAT
66 ATTTCAAGATTGACCGCACTGAACCACTTGAAGATAAACT-AATACCACTGGAAACTTCCTTGAT
* *
4051 TGACCGTATTGGATCACTT
130 TGACCGCACTGGATCACTT
4070 GAGGATAAAC
Statistics
Matches: 128, Mismatches: 19, Indels: 3
0.85 0.13 0.02
Matches are distributed among these distances:
154 92 0.72
155 34 0.27
156 2 0.02
ACGTcount: A:0.31, C:0.22, G:0.17, T:0.29
Consensus pattern (154 bp):
ACCACTGGAAACTTTCTCGATTGACCGCACTGGATCACTTGAAGATAAACTTAAACCACTGGAAA
ATTTCAAGATTGACCGCACTGAACCACTTGAAGATAAACTAATACCACTGGAAACTTCCTTGATT
GACCGCACTGGATCACTTAAAGAT
Found at i:4064 original size:55 final size:55
Alignment explanation
Indices: 3923--4091 Score: 241
Period size: 55 Copynumber: 3.1 Consensus size: 55
3913 TTAAAGATAC
* * * *
3923 CACTGGAAACTTTCTCGATTGACCGCATTGGATTACTTGAAGATAAACTTAA-AC
1 CACTGGAAACTTTCTTGATTGACCGCATTGGATCACTTGAAGATAAACTCAATAT
* *
3977 CACTGGAAAATTTCTTGATTGACCGCACTGGATCACTTGAAGATAAACTCAATAT
1 CACTGGAAACTTTCTTGATTGACCGCATTGGATCACTTGAAGATAAACTCAATAT
* * * *
4032 CACTGTAAACTTCCTTGATTGACCGTATTGGATCACTTGAGGATAAACTCAATAT
1 CACTGGAAACTTTCTTGATTGACCGCATTGGATCACTTGAAGATAAACTCAATAT
4087 CACTG
1 CACTG
4092 ATCGTGTCGT
Statistics
Matches: 102, Mismatches: 12, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
54 47 0.46
55 55 0.54
ACGTcount: A:0.33, C:0.21, G:0.17, T:0.30
Consensus pattern (55 bp):
CACTGGAAACTTTCTTGATTGACCGCATTGGATCACTTGAAGATAAACTCAATAT
Found at i:4297 original size:21 final size:20
Alignment explanation
Indices: 4258--4302 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
4248 AATTATCAAT
* *
4258 TAAAAAGAAAGCAATTAAAC
1 TAAAAACAAAGCAAGTAAAC
*
4278 TAAAAACAAAGCAAAGTAAAT
1 TAAAAACAAAGC-AAGTAAAC
4299 TAAA
1 TAAA
4303 TCTAAATCTA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 11 0.52
21 10 0.48
ACGTcount: A:0.67, C:0.09, G:0.09, T:0.16
Consensus pattern (20 bp):
TAAAAACAAAGCAAGTAAAC
Found at i:5744 original size:19 final size:18
Alignment explanation
Indices: 5711--5746 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
5701 TTGAAATAAT
5711 TCTTCAATGATCTTCAAA
1 TCTTCAATGATCTTCAAA
*
5729 TCTTCAAATTATCTTCAA
1 TCTTC-AATGATCTTCAA
5747 TAAATCTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.33, C:0.22, G:0.03, T:0.42
Consensus pattern (18 bp):
TCTTCAATGATCTTCAAA
Found at i:7359 original size:21 final size:19
Alignment explanation
Indices: 7327--7365 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 19
7317 CAATCAAGCA
7327 AATCAAGATTCAAAGCATC
1 AATCAAGATTCAAAGCATC
*
7346 AATCATAGCATTCATAGCAT
1 AATCA-AG-ATTCAAAGCAT
7366 ATGAGTCATA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 5 0.29
20 2 0.12
21 10 0.59
ACGTcount: A:0.44, C:0.21, G:0.10, T:0.26
Consensus pattern (19 bp):
AATCAAGATTCAAAGCATC
Found at i:8147 original size:17 final size:18
Alignment explanation
Indices: 8125--8158 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
8115 TCCTAATAAG
8125 AAAAAC-AAAAACAAAAA
1 AAAAACTAAAAACAAAAA
*
8142 AAAAACTAAAAAGAAAA
1 AAAAACTAAAAACAAAA
8159 TTACAACGTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.85, C:0.09, G:0.03, T:0.03
Consensus pattern (18 bp):
AAAAACTAAAAACAAAAA
Done.