Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013007.1 Corchorus olitorius cultivar O-4 contig13040, 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: 47569
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.32
Found at i:402 original size:123 final size:128
Alignment explanation
Indices: 264--519 Score: 405
Period size: 123 Copynumber: 2.0 Consensus size: 128
254 CATTGTTTAA
* *
264 ACTTTTATAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATAT-CTT-TA-T
1 ACTTTTACAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCCAATATCCTTATACT
326 A-ATTTTTACCATTTTACTATTTTAATT-AAAAAACTTATATATATTAGAATTTTTTAAATAT
66 ATATTTTTACCATTTTACTATTTTAATTAAAAAAACTTATATATATTAGAATTTTTTAAATAT
* *
387 ACTTTTACAGTTTTACTCAACTAAAAACTCTATTTTTATTTATTTAATTCCAATATCCTTATACT
1 ACTTTTACAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCCAATATCCTTATAC-
452 TATTTTATTTTTACCATTTTACTATTTTAATTAAAAAAACTTATATATATTAGAATTTTTTAAAT
65 TA---TATTTTTACCATTTTACTATTTTAATTAAAAAAACTTATATATATTAGAATTTTTTAAAT
517 AT
127 AT
519 A
1 A
520 TTTCTTAAAT
Statistics
Matches: 120, Mismatches: 4, Indels: 9
0.90 0.03 0.07
Matches are distributed among these distances:
123 52 0.43
124 3 0.03
125 2 0.02
127 2 0.02
131 26 0.22
132 35 0.29
ACGTcount: A:0.37, C:0.11, G:0.02, T:0.50
Consensus pattern (128 bp):
ACTTTTACAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCCAATATCCTTATACT
ATATTTTTACCATTTTACTATTTTAATTAAAAAAACTTATATATATTAGAATTTTTTAAATAT
Found at i:541 original size:14 final size:13
Alignment explanation
Indices: 505--543 Score: 51
Period size: 14 Copynumber: 2.9 Consensus size: 13
495 TATATATTAG
505 AATTTTTTAAATA
1 AATTTTTTAAATA
* *
518 TATTTCTTAAATGA
1 AATTTTTTAAAT-A
532 AATTTTTTAAAT
1 AATTTTTTAAAT
544 TTTACAATTT
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
13 10 0.48
14 11 0.52
ACGTcount: A:0.41, C:0.03, G:0.03, T:0.54
Consensus pattern (13 bp):
AATTTTTTAAATA
Found at i:8172 original size:60 final size:60
Alignment explanation
Indices: 8096--8215 Score: 222
Period size: 60 Copynumber: 2.0 Consensus size: 60
8086 TTTGACCAAA
8096 TCAAAATCTGCATTAAACGTGGGGGATACGCTTACTTATATATAAAAACTCACCTTAACT
1 TCAAAATCTGCATTAAACGTGGGGGATACGCTTACTTATATATAAAAACTCACCTTAACT
* *
8156 TCAAAATTTGCATTAAACGTGGGGGATACGCTTGCTTATATATAAAAACTCACCTTAACT
1 TCAAAATCTGCATTAAACGTGGGGGATACGCTTACTTATATATAAAAACTCACCTTAACT
8216 AATTAGAATC
Statistics
Matches: 58, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
60 58 1.00
ACGTcount: A:0.36, C:0.19, G:0.14, T:0.31
Consensus pattern (60 bp):
TCAAAATCTGCATTAAACGTGGGGGATACGCTTACTTATATATAAAAACTCACCTTAACT
Found at i:8568 original size:20 final size:20
Alignment explanation
Indices: 8543--8580 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
8533 TCTAGTATGT
*
8543 CTTTTTATTTCTTTAATTCC
1 CTTTTTATTTCCTTAATTCC
8563 CTTTTTATTTCCTTAATT
1 CTTTTTATTTCCTTAATT
8581 AACTCCCCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.16, C:0.18, G:0.00, T:0.66
Consensus pattern (20 bp):
CTTTTTATTTCCTTAATTCC
Found at i:8683 original size:16 final size:18
Alignment explanation
Indices: 8662--8694 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
8652 TATTCTCCCA
8662 AATAA-TTAATT-AAGAC
1 AATAATTTAATTCAAGAC
8678 AATAATTTAATTCAAGA
1 AATAATTTAATTCAAGA
8695 TTTAGCCCCT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
17 6 0.40
18 4 0.27
ACGTcount: A:0.55, C:0.06, G:0.06, T:0.33
Consensus pattern (18 bp):
AATAATTTAATTCAAGAC
Found at i:36909 original size:6 final size:6
Alignment explanation
Indices: 36892--36922 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
36882 GTACTTTTTA
36892 ATATAG -TATAG ATATAG ATATAG ATATAG AT
1 ATATAG ATATAG ATATAG ATATAG ATATAG AT
36923 GATGATTAGT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
5 5 0.21
6 19 0.79
ACGTcount: A:0.48, C:0.00, G:0.16, T:0.35
Consensus pattern (6 bp):
ATATAG
Found at i:38932 original size:8 final size:8
Alignment explanation
Indices: 38921--38945 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
38911 ACCCCCTCTT
38921 CCCCACCA
1 CCCCACCA
38929 CCCCACCA
1 CCCCACCA
38937 CCCCACCA
1 CCCCACCA
38945 C
1 C
38946 ATACATACAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.24, C:0.76, G:0.00, T:0.00
Consensus pattern (8 bp):
CCCCACCA
Found at i:40149 original size:40 final size:40
Alignment explanation
Indices: 40085--40161 Score: 120
Period size: 40 Copynumber: 1.9 Consensus size: 40
40075 CACATAAATA
*
40085 TTATAATAAATCTCATCCCCCTTAATTATCTAGAATTATG
1 TTATAATAAATCTCATCCACCTTAATTATCTAGAATTATG
*
40125 TTATAATAAATC-CTATCCATCTTAATTATCTAGAATT
1 TTATAATAAATCTC-ATCCACCTTAATTATCTAGAATT
40162 GTAACCTCTC
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
39 1 0.03
40 33 0.97
ACGTcount: A:0.36, C:0.18, G:0.04, T:0.42
Consensus pattern (40 bp):
TTATAATAAATCTCATCCACCTTAATTATCTAGAATTATG
Found at i:43231 original size:33 final size:33
Alignment explanation
Indices: 43189--43254 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
43179 TTTATCTTGA
*
43189 GACCACCATGACAAATCAGG-TCATTTGCTTTGC
1 GACCACCATGACAAA-CAGGACCATTTGCTTTGC
*
43222 GACCACCATGACAAACCGGACCATTTGCTTTGC
1 GACCACCATGACAAACAGGACCATTTGCTTTGC
43255 AAGAAGTTTG
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
32 3 0.10
33 27 0.90
ACGTcount: A:0.27, C:0.30, G:0.18, T:0.24
Consensus pattern (33 bp):
GACCACCATGACAAACAGGACCATTTGCTTTGC
Found at i:45095 original size:75 final size:74
Alignment explanation
Indices: 44976--45414 Score: 630
Period size: 75 Copynumber: 5.9 Consensus size: 74
44966 GTTTGACATT
44976 AAGATTCCATACTCAGCAAGGATCGTAGCCATAAGTGCCTTTCCTTGTTGATGCTTCTGGCCTAT
1 AAGATTCCATACTCAGCAAGGATCGTAGCCATAAGTG-CTTTCCTTGTTGATGCTTCTGGCCTAT
*
45041 GTAGCCCATT
65 GTAGCCCATC
45051 AAGATTCCATACTCAGCAAGGATCGTAGCCATAAGTGTCTTTCCTTGTTGATGCTTCTGGCC--T
1 AAGATTCCATACTCAGCAAGGATCGTAGCCATAAGTG-CTTTCCTTGTTGATGCTTCTGGCCTAT
45114 GTAGCCCATC
65 GTAGCCCATC
* ** **
45124 AAGATTCCATGCTCAGCAAGGATAATAGCCATAAGTTTATTTCCTTGTTGATGCTTCTGGCCTAT
1 AAGATTCCATACTCAGCAAGGATCGTAGCCATAAG-TGCTTTCCTTGTTGATGCTTCTGGCCTAT
45189 GTAGCCCATC
65 GTAGCCCATC
* * * * * *
45199 AAGATTCCATACTCGGCAAGGATCGTAACCATAAATGCCTTTCGTTGTTGATGTTTCTGGCCTTT
1 AAGATTCCATACTCAGCAAGGATCGTAGCCATAAGTG-CTTTCCTTGTTGATGCTTCTGGCCTAT
45264 GTAGCCCATC
65 GTAGCCCATC
* * *
45274 CAGATTCCATACTAAGCAAGGATCGTAGCCATAAATGCATTTCCTTGTTGATGCTTCTGGCCTAT
1 AAGATTCCATACTCAGCAAGGATCGTAGCCATAAGTGC-TTTCCTTGTTGATGCTTCTGGCCTAT
45339 GTAGCCCATC
65 GTAGCCCATC
* * * * *
45349 AAAATTCCATAATCAACAAGGATCGTAGCCATAAGTGCATTTCCTTCTTGATGCTTCTAGCCTAT
1 AAGATTCCATACTCAGCAAGGATCGTAGCCATAAGTGC-TTTCCTTGTTGATGCTTCTGGCCTAT
45414 G
65 G
45415 CAGCTTAAAA
Statistics
Matches: 326, Mismatches: 33, Indels: 10
0.88 0.09 0.03
Matches are distributed among these distances:
73 65 0.20
74 3 0.01
75 258 0.79
ACGTcount: A:0.25, C:0.24, G:0.19, T:0.32
Consensus pattern (74 bp):
AAGATTCCATACTCAGCAAGGATCGTAGCCATAAGTGCTTTCCTTGTTGATGCTTCTGGCCTATG
TAGCCCATC
Found at i:45609 original size:109 final size:109
Alignment explanation
Indices: 45409--45833 Score: 455
Period size: 109 Copynumber: 3.8 Consensus size: 109
45399 ATGCTTCTAG
* * *
45409 CCTATGCAGCTTAAAAGAAGGCGTGCACAACGCCTATAGCCTATGCAGCTTAAAAGAAAAGGCTT
1 CCTATGTAGCTTAAAAGAGGGCGT--ACAACACCTATAGCCTATGCAGCTT-AAA-AAAAGGCTT
* * *
45474 ACAACGCCAATAACCTATGCAGCTTAATAAGGGCTTACAGTGCCCGCAA
62 ACAACGCCTAT-ACCTATGCAGCTTAAAAAGGGCTTACAATGCCCGCAA
* * * *
45523 CCTATGTAGCTTAAAA-TGGGCGTAGAACACCTATAGCCCATGCGGCTTAAAAAAAGGCTTACAA
1 CCTATGTAGCTTAAAAGAGGGCGTACAACACCTATAGCCTATGCAGCTTAAAAAAAGGCTTACAA
*
45587 CGCCTATAGCCTATGCAACTTAAAAAGGGCTTACAATGCCCGCAA
66 CGCCTATA-CCTATGCAGCTTAAAAAGGGCTTACAATGCCCGCAA
* ** * * *
45632 CCTATGTAGCTTAAAAGAGGGGGTACAACGTCTATTGCCTATGTAGCTTAAAAAAGGGCTTACAA
1 CCTATGTAGCTTAAAAGAGGGCGTACAACACCTATAGCCTATGCAGCTTAAAAAAAGGCTTACAA
* ** *
45697 CGCC--TA-CTATGCAGCTTAAAAAAAGGCTTACAAATGCCTACAG
66 CGCCTATACCTATGCAGCTT-AAAAAGGGCTTAC-AATGCCCGCAA
* * *
45740 CCTGTGTAGCTTAAAAAAAGGGAGGCGTACAACACCTATA-CCTATGCAGCTTCAAAAAAGGCTT
1 CCTATGTAGCTT---AAAAGAG-GGCGTACAACACCTATAGCCTATGCAGCTTAAAAAAAGGCTT
* * *
45804 ACAACGCCTACATCCTATGTAGGTTAAAAA
62 ACAACGCCTATA-CCTATGCAGCTTAAAAA
45834 AGGATTAAGC
Statistics
Matches: 261, Mismatches: 38, Indels: 24
0.81 0.12 0.07
Matches are distributed among these distances:
106 10 0.04
107 12 0.05
108 22 0.08
109 68 0.26
110 45 0.17
111 56 0.21
112 13 0.05
113 6 0.02
114 20 0.08
115 9 0.03
ACGTcount: A:0.36, C:0.23, G:0.20, T:0.22
Consensus pattern (109 bp):
CCTATGTAGCTTAAAAGAGGGCGTACAACACCTATAGCCTATGCAGCTTAAAAAAAGGCTTACAA
CGCCTATACCTATGCAGCTTAAAAAGGGCTTACAATGCCCGCAA
Found at i:45619 original size:36 final size:37
Alignment explanation
Indices: 45406--45836 Score: 306
Period size: 36 Copynumber: 11.6 Consensus size: 37
45396 TTGATGCTTC
*
45406 TAGCCTATGCAGCTTAAAAGAA-GGCGTGCACAACGCCTA
1 TAGCCTATGCAGCTTAAAA-AAGGGC-T-TACAACGCCTA
* *
45445 TAGCCTATGCAGCTTAAAAGAAAAGGCTTACAACGCCAA
1 TAGCCTATGCAGCTT-AAA-AAAGGGCTTACAACGCCTA
* * ** **
45484 TAACCTATGCAGCTT-AATAAGGGCTTACAGTGCCCG
1 TAGCCTATGCAGCTTAAAAAAGGGCTTACAACGCCTA
* * * * * * *
45520 CAACCTATGTAGCTT-AAAATGGGCGTAGAACACCTA
1 TAGCCTATGCAGCTTAAAAAAGGGCTTACAACGCCTA
* * *
45556 TAGCCCATGCGGCTTAAAAAAAGGCTTACAACGCCTA
1 TAGCCTATGCAGCTTAAAAAAGGGCTTACAACGCCTA
* * **
45593 TAGCCTATGCAACTT-AAAAAGGGCTTACAATGCCCG
1 TAGCCTATGCAGCTTAAAAAAGGGCTTACAACGCCTA
* * * * ** *
45629 CAACCTATGTAGCTTAAAAGAGGGGGTACAACGTCTA
1 TAGCCTATGCAGCTTAAAAAAGGGCTTACAACGCCTA
* *
45666 TTGCCTATGTAGCTTAAAAAAGGGCTTACAACGCC--
1 TAGCCTATGCAGCTTAAAAAAGGGCTTACAACGCCTA
* *
45701 TA--CTATGCAGCTTAAAAAAAGGCTTACAAATGCCTA
1 TAGCCTATGCAGCTTAAAAAAGGGCTTAC-AACGCCTA
* * * * *
45737 CAGCCTGTGTAGCTTAAAAAAAGGGAGGCGTACAACACCTA
1 TAGCCTATGCAGCTT-AAAAAA--G-GGCTTACAACGCCTA
45778 TA-CCTATGCAGCTTCAAAAAA-GGCTTACAACGCCTA
1 TAGCCTATGCAGCTT-AAAAAAGGGCTTACAACGCCTA
* * * *
45814 CATCCTATGTAGGTTAAAAAAGG
1 TAGCCTATGCAGCTTAAAAAAGG
45837 ATTAAGCGAA
Statistics
Matches: 301, Mismatches: 75, Indels: 34
0.73 0.18 0.08
Matches are distributed among these distances:
33 23 0.08
34 5 0.02
35 1 0.00
36 97 0.32
37 83 0.28
38 9 0.03
39 44 0.15
40 22 0.07
41 11 0.04
42 6 0.02
ACGTcount: A:0.35, C:0.23, G:0.20, T:0.22
Consensus pattern (37 bp):
TAGCCTATGCAGCTTAAAAAAGGGCTTACAACGCCTA
Found at i:45644 original size:73 final size:69
Alignment explanation
Indices: 45410--45833 Score: 247
Period size: 73 Copynumber: 5.8 Consensus size: 69
45400 TGCTTCTAGC
* * * *
45410 CTATGCAGCTTAAAAGAAGGCGTGCACAACGCCTATAGCCTATGCAGCTTAAAAGAAAAGGCTTA
1 CTATGCAGCTTAAAAAAAGGC-T-TACAACGCCTATAGCCTATGTAGCTT--AA-AAAGGGCTTA
*
45475 CAACGCCAATAA
61 CAAC-CC--CAA
* * ** *** * * * *
45487 CCTATGCAGCTT-AATAAGGGCTTACAGTGCCCGCAACCTATGTAGCTTAAAATGGGCGTAGAAC
1 -CTATGCAGCTTAAAAAAAGGCTTACAACGCCTATAGCCTATGTAGCTTAAAAAGGGCTTACAAC
*
45551 ACCTATA
65 -CCCA-A
* * * *
45558 GCCCATGCGGCTTAAAAAAAGGCTTACAACGCCTATAGCCTATGCAACTTAAAAAGGGCTTACAA
1 --CTATGCAGCTTAAAAAAAGGCTTACAACGCCTATAGCCTATGTAGCTTAAAAAGGGCTTACAA
45623 TGCCCGCAA
64 --CCC-CAA
* * * ** * *
45632 CCTATGTAGCTTAAAAGAGGGGGTACAACGTCTATTGCCTATGTAGCTTAAAAAAGGGCTTACAA
1 -CTATGCAGCTTAAAAAAAGGCTTACAACGCCTATAGCCTATGTAGCTT-AAAAAGGGCTTACAA
* *
45697 CGCCTA
64 CCCCAA
* * * *
45703 CTATGCAGCTTAAAAAAAGGCTTACAAATGCCTACAGCCTGTGTAGCTTAAAAAAAGGGAGGCGT
1 CTATGCAGCTTAAAAAAAGGCTTAC-AACGCCTATAGCCTATGTAGCTT--AAAAA--G-GGCTT
*
45768 ACAACACCTATA
60 ACAAC-CCCA-A
* * * *
45780 CCTATGCAGCTTCAAAAAAGGCTTACAACGCCTACATCCTATGTAGGTTAAAAA
1 -CTATGCAGCTTAAAAAAAGGCTTACAACGCCTATAGCCTATGTAGCTTAAAAA
45834 AGGATTAAGC
Statistics
Matches: 267, Mismatches: 64, Indels: 33
0.73 0.18 0.09
Matches are distributed among these distances:
70 22 0.08
71 21 0.08
72 30 0.11
73 78 0.29
74 19 0.07
75 34 0.13
76 2 0.01
77 26 0.10
78 35 0.13
ACGTcount: A:0.36, C:0.23, G:0.20, T:0.22
Consensus pattern (69 bp):
CTATGCAGCTTAAAAAAAGGCTTACAACGCCTATAGCCTATGTAGCTTAAAAAGGGCTTACAACC
CCAA
Found at i:45736 original size:34 final size:33
Alignment explanation
Indices: 45562--45814 Score: 112
Period size: 37 Copynumber: 7.0 Consensus size: 33
45552 CCTATAGCCC
*
45562 ATGCGGCTTAAAAAAAGGCTTACAACGCCTATAGCCT
1 ATGCAGCTTAAAAAAAGGCTTACAACGCC--TA--CT
* * * *
45599 ATGCAACTT-AAAAAGGGCTTACAATGCCCGCAACCT
1 ATGCAGCTTAAAAAAAGGCTTACAA--CGC-CTA-CT
* * * ** *
45635 ATGTAGCTTAAAAGAGGGGGTACAACGTCTATTGCCT
1 ATGCAGCTTAAAAAAAGGCTTACAACGCCTA----CT
* *
45672 ATGTAGCTTAAAAAAGGGCTTACAACGCCTACT
1 ATGCAGCTTAAAAAAAGGCTTACAACGCCTACT
*
45705 ATGCAGCTTAAAAAAAGGCTTACAAATGCCTACAGCCT
1 ATGCAGCTTAAAAAAAGGCTTAC-AACGCCT--A--CT
* * * *
45743 GTGTAGCTTAAAAAAAGGGAGGCGTACAACACCTATACCT
1 ATGCAGCTT-AAAAAA---AGGCTTACAACGCC--TA-CT
*
45783 ATGCAGCTTCAAAAAAGGCTTACAACGCCTAC
1 ATGCAGCTTAAAAAAAGGCTTACAACGCCTAC
45815 ATCCTATGTA
Statistics
Matches: 168, Mismatches: 30, Indels: 40
0.71 0.13 0.17
Matches are distributed among these distances:
33 24 0.14
34 10 0.06
35 1 0.01
36 37 0.22
37 50 0.30
38 11 0.07
39 12 0.07
40 10 0.06
41 5 0.03
42 7 0.04
43 1 0.01
ACGTcount: A:0.36, C:0.23, G:0.19, T:0.22
Consensus pattern (33 bp):
ATGCAGCTTAAAAAAAGGCTTACAACGCCTACT
Found at i:46187 original size:44 final size:44
Alignment explanation
Indices: 46124--46421 Score: 438
Period size: 44 Copynumber: 6.8 Consensus size: 44
46114 ATAAAAAACG
46124 TATGGTGTTCGCGAAACTATCACCCTCTTTCAATGTCAAAGGAA
1 TATGGTGTTCGCGAAACTATCACCCTCTTTCAATGTCAAAGGAA
* *
46168 TATGGTGTTCGCGAAACTATCACCCTCTTTCAATGTCAAAAGCA
1 TATGGTGTTCGCGAAACTATCACCCTCTTTCAATGTCAAAGGAA
*
46212 TATGGTGTTCGCGAAACTATCACCCTCTTTCAATGTCAAAGGCA
1 TATGGTGTTCGCGAAACTATCACCCTCTTTCAATGTCAAAGGAA
46256 TATGGTGTTCGCGAAACTATCACCCTCTTTCAATGTCAAA-GACA
1 TATGGTGTTCGCGAAACTATCACCCTCTTTCAATGTCAAAGGA-A
** *
46300 TATGGTGTTCGCGAAACTATCACCCTCTCCCAATGTCAAAGGCA
1 TATGGTGTTCGCGAAACTATCACCCTCTTTCAATGTCAAAGGAA
* * * * *
46344 TATGGTGTTGGCGAAATTAT-AACCTTTTTCCAATGTCAAAAGAA
1 TATGGTGTTCGCGAAACTATCACCCTCTTT-CAATGTCAAAGGAA
* **
46388 TATGGTGTTTGCGAAACTATCACTTTCTTTCAAT
1 TATGGTGTTCGCGAAACTATCACCCTCTTTCAAT
46422 AACAAAGGGT
Statistics
Matches: 229, Mismatches: 21, Indels: 8
0.89 0.08 0.03
Matches are distributed among these distances:
43 6 0.03
44 217 0.95
45 6 0.03
ACGTcount: A:0.29, C:0.23, G:0.17, T:0.31
Consensus pattern (44 bp):
TATGGTGTTCGCGAAACTATCACCCTCTTTCAATGTCAAAGGAA
Found at i:47127 original size:51 final size:54
Alignment explanation
Indices: 47068--47176 Score: 134
Period size: 56 Copynumber: 2.0 Consensus size: 54
47058 ATGAGGCTAT
* *
47068 AAGGTGTTACTCT-C-CA-ATAACTCCATAGGGTGCCACTAACACCATACTTCC
1 AAGGTGTTACTCTCCACACATAACTCCAGAGGGTGCCACCAACACCATACTTCC
* * *
47119 AAGGTGTTACTTTCCAACACCATAACTCCAGAGGGTGTCGCCAACACCATACTTCC
1 AAGGTGTTACTCTCC-ACA-CATAACTCCAGAGGGTGCCACCAACACCATACTTCC
47175 AA
1 AA
47177 AGGATTACCA
Statistics
Matches: 48, Mismatches: 5, Indels: 5
0.83 0.09 0.09
Matches are distributed among these distances:
51 12 0.25
52 1 0.02
54 2 0.04
56 33 0.69
ACGTcount: A:0.30, C:0.31, G:0.15, T:0.24
Consensus pattern (54 bp):
AAGGTGTTACTCTCCACACATAACTCCAGAGGGTGCCACCAACACCATACTTCC
Done.