Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007438.1 Corchorus capsularis cultivar CVL-1 contig07459, 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: 49098
ACGTcount: A:0.29, C:0.21, G:0.19, T:0.31
Found at i:91 original size:51 final size:50
Alignment explanation
Indices: 7--124 Score: 164
Period size: 51 Copynumber: 2.3 Consensus size: 50
1 AAAAAA
* **
7 AAAATTCCATCTTTTAGTCAAAAGGTTACATCTTTATAAACTAATTATTT
1 AAAATTCAATCTTTTAGTCAAAAGGTTACATCTTTATAAACTAATTACAT
* **
57 AAAAGTTCAATCTTTTATTCAAAAGGTTACATCTTTATTTACTAATTACAT
1 AAAA-TTCAATCTTTTAGTCAAAAGGTTACATCTTTATAAACTAATTACAT
108 AAATATTCAATCTTTTA
1 AAA-ATTCAATCTTTTA
125 ACATAAAGAT
Statistics
Matches: 60, Mismatches: 6, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
50 4 0.07
51 55 0.92
52 1 0.02
ACGTcount: A:0.38, C:0.14, G:0.05, T:0.43
Consensus pattern (50 bp):
AAAATTCAATCTTTTAGTCAAAAGGTTACATCTTTATAAACTAATTACAT
Found at i:3073 original size:27 final size:27
Alignment explanation
Indices: 3000--3073 Score: 112
Period size: 27 Copynumber: 2.7 Consensus size: 27
2990 GAACCTAAAG
* *
3000 ATGACTAAAATGCCCCTGAGTGCAAAA
1 ATGACCAAAATGCCCCTGGGTGCAAAA
3027 ATGACCAAAATGCCCCTGGGTGCAAAA
1 ATGACCAAAATGCCCCTGGGTGCAAAA
* *
3054 ATGACCAAAATACCCTTGGG
1 ATGACCAAAATGCCCCTGGG
3074 CGACCCTAAT
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 43 1.00
ACGTcount: A:0.38, C:0.24, G:0.20, T:0.18
Consensus pattern (27 bp):
ATGACCAAAATGCCCCTGGGTGCAAAA
Found at i:4739 original size:2 final size:2
Alignment explanation
Indices: 4732--4762 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
4722 CGTGGGTTAC
4732 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
4763 ATAAAACGAC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:8113 original size:46 final size:46
Alignment explanation
Indices: 8046--8145 Score: 200
Period size: 46 Copynumber: 2.2 Consensus size: 46
8036 ATGGATAAAG
8046 CTCTTGATCCAGTGTGAATTATCCCTTTTATTCTTTAGACAATCAC
1 CTCTTGATCCAGTGTGAATTATCCCTTTTATTCTTTAGACAATCAC
8092 CTCTTGATCCAGTGTGAATTATCCCTTTTATTCTTTAGACAATCAC
1 CTCTTGATCCAGTGTGAATTATCCCTTTTATTCTTTAGACAATCAC
8138 CTCTTGAT
1 CTCTTGAT
8146 AATTACCCAA
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 54 1.00
ACGTcount: A:0.23, C:0.24, G:0.11, T:0.42
Consensus pattern (46 bp):
CTCTTGATCCAGTGTGAATTATCCCTTTTATTCTTTAGACAATCAC
Found at i:8670 original size:18 final size:17
Alignment explanation
Indices: 8647--8682 Score: 63
Period size: 18 Copynumber: 2.1 Consensus size: 17
8637 CTCAACCTAA
8647 AACTAGAAGAAAAACTAG
1 AACTAGAAGAAAAA-TAG
8665 AACTAGAAGAAAAATAG
1 AACTAGAAGAAAAATAG
8682 A
1 A
8683 TGAAGAGAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 4 0.22
18 14 0.78
ACGTcount: A:0.64, C:0.08, G:0.17, T:0.11
Consensus pattern (17 bp):
AACTAGAAGAAAAATAG
Found at i:9291 original size:18 final size:19
Alignment explanation
Indices: 9268--9306 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
9258 TTCTTGAAAT
9268 AATTCTTC-AATGATCTTC
1 AATTCTTCAAATGATCTTC
*
9286 AATTCTTCAAATTATCTTC
1 AATTCTTCAAATGATCTTC
9305 AA
1 AA
9307 ATAATCTTCA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 8 0.42
19 11 0.58
ACGTcount: A:0.33, C:0.21, G:0.03, T:0.44
Consensus pattern (19 bp):
AATTCTTCAAATGATCTTC
Found at i:9305 original size:11 final size:11
Alignment explanation
Indices: 9259--9320 Score: 60
Period size: 11 Copynumber: 5.9 Consensus size: 11
9249 AATTCTTGCT
*
9259 TCTTGAAATAA
1 TCTTCAAATAA
*
9270 TTCTTC-AATGA
1 -TCTTCAAATAA
9281 TCTTC-AAT--
1 TCTTCAAATAA
*
9289 TCTTCAAATTA
1 TCTTCAAATAA
9300 TCTTCAAATAA
1 TCTTCAAATAA
9311 TCTTCAAATA
1 TCTTCAAATA
9321 TGAACTTCGA
Statistics
Matches: 44, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
8 5 0.11
9 3 0.07
10 8 0.18
11 24 0.55
12 4 0.09
ACGTcount: A:0.37, C:0.18, G:0.03, T:0.42
Consensus pattern (11 bp):
TCTTCAAATAA
Found at i:9317 original size:22 final size:22
Alignment explanation
Indices: 9259--9319 Score: 67
Period size: 22 Copynumber: 2.9 Consensus size: 22
9249 AATTCTTGCT
*
9259 TCTTGAAATAATTCTTC-AATGA
1 TCTTCAAATAA-TCTTCAAATGA
*
9281 TCTTC-AAT--TCTTCAAATTA
1 TCTTCAAATAATCTTCAAATGA
9300 TCTTCAAATAATCTTCAAAT
1 TCTTCAAATAATCTTCAAAT
9320 ATGAACTTCG
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
18 5 0.15
19 9 0.27
20 3 0.09
21 3 0.09
22 13 0.39
ACGTcount: A:0.36, C:0.18, G:0.03, T:0.43
Consensus pattern (22 bp):
TCTTCAAATAATCTTCAAATGA
Found at i:10401 original size:18 final size:19
Alignment explanation
Indices: 10378--10415 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
10368 CTCCTCTTGC
10378 ATGAAAACAC-TTCTTTTT
1 ATGAAAACACATTCTTTTT
*
10396 ATGAAAACACATTTTTTTT
1 ATGAAAACACATTCTTTTT
10415 A
1 A
10416 ACTACCCTCT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 10 0.56
19 8 0.44
ACGTcount: A:0.37, C:0.13, G:0.05, T:0.45
Consensus pattern (19 bp):
ATGAAAACACATTCTTTTT
Found at i:10927 original size:21 final size:19
Alignment explanation
Indices: 10895--10933 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 19
10885 CAATCAAGCA
10895 AATCAAGATTCAAAGCATC
1 AATCAAGATTCAAAGCATC
*
10914 AATCATAGCATTCATAGCAT
1 AATCA-AG-ATTCAAAGCAT
10934 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:13045 original size:24 final size:25
Alignment explanation
Indices: 13018--13076 Score: 77
Period size: 25 Copynumber: 2.4 Consensus size: 25
13008 TTTAAATCGC
13018 AAAAAGCAAAT-TTTTTTTTAAGAA
1 AAAAAGCAAATATTTTTTTTAAGAA
*
13042 AAAAA-CACAATATTTTTTTTTAGAA
1 AAAAAGCA-AATATTTTTTTTAAGAA
*
13067 AAAACGCAAA
1 AAAAAGCAAA
13077 AACAAAACTT
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
23 2 0.07
24 8 0.27
25 18 0.60
26 2 0.07
ACGTcount: A:0.53, C:0.08, G:0.07, T:0.32
Consensus pattern (25 bp):
AAAAAGCAAATATTTTTTTTAAGAA
Found at i:25008 original size:6 final size:6
Alignment explanation
Indices: 24997--25021 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
24987 CGAAGCTTTT
24997 GGTGCA GGTGCA GGTGCA GGTGCA G
1 GGTGCA GGTGCA GGTGCA GGTGCA G
25022 CATTTTTCTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.16, G:0.52, T:0.16
Consensus pattern (6 bp):
GGTGCA
Found at i:29121 original size:18 final size:17
Alignment explanation
Indices: 29098--29133 Score: 63
Period size: 18 Copynumber: 2.1 Consensus size: 17
29088 CTCAACCTAA
29098 AACTAGAAGAAAAACTAG
1 AACTAGAAGAAAAA-TAG
29116 AACTAGAAGAAAAATAG
1 AACTAGAAGAAAAATAG
29133 A
1 A
29134 TGAAGAGAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 4 0.22
18 14 0.78
ACGTcount: A:0.64, C:0.08, G:0.17, T:0.11
Consensus pattern (17 bp):
AACTAGAAGAAAAATAG
Found at i:29748 original size:18 final size:19
Alignment explanation
Indices: 29725--29763 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
29715 TTCTTGAAAT
29725 AATTCTTC-AATGATCTTC
1 AATTCTTCAAATGATCTTC
*
29743 AATTCTTCAAATTATCTTC
1 AATTCTTCAAATGATCTTC
29762 AA
1 AA
29764 ATAATCTTCA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 8 0.42
19 11 0.58
ACGTcount: A:0.33, C:0.21, G:0.03, T:0.44
Consensus pattern (19 bp):
AATTCTTCAAATGATCTTC
Found at i:29762 original size:11 final size:11
Alignment explanation
Indices: 29716--29777 Score: 60
Period size: 11 Copynumber: 5.9 Consensus size: 11
29706 AATTCTTGCT
*
29716 TCTTGAAATAA
1 TCTTCAAATAA
*
29727 TTCTTC-AATGA
1 -TCTTCAAATAA
29738 TCTTC-AAT--
1 TCTTCAAATAA
*
29746 TCTTCAAATTA
1 TCTTCAAATAA
29757 TCTTCAAATAA
1 TCTTCAAATAA
29768 TCTTCAAATA
1 TCTTCAAATA
29778 CGAACTTCGA
Statistics
Matches: 44, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
8 5 0.11
9 3 0.07
10 8 0.18
11 24 0.55
12 4 0.09
ACGTcount: A:0.37, C:0.18, G:0.03, T:0.42
Consensus pattern (11 bp):
TCTTCAAATAA
Found at i:29774 original size:22 final size:22
Alignment explanation
Indices: 29716--29776 Score: 67
Period size: 22 Copynumber: 2.9 Consensus size: 22
29706 AATTCTTGCT
*
29716 TCTTGAAATAATTCTTC-AATGA
1 TCTTCAAATAA-TCTTCAAATGA
*
29738 TCTTC-AAT--TCTTCAAATTA
1 TCTTCAAATAATCTTCAAATGA
29757 TCTTCAAATAATCTTCAAAT
1 TCTTCAAATAATCTTCAAAT
29777 ACGAACTTCG
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
18 5 0.15
19 9 0.27
20 3 0.09
21 3 0.09
22 13 0.39
ACGTcount: A:0.36, C:0.18, G:0.03, T:0.43
Consensus pattern (22 bp):
TCTTCAAATAATCTTCAAATGA
Found at i:32753 original size:7 final size:7
Alignment explanation
Indices: 32741--32773 Score: 50
Period size: 7 Copynumber: 4.9 Consensus size: 7
32731 GGCAACCCAA
32741 TTTTAAT
1 TTTTAAT
32748 TTTTAAT
1 TTTTAAT
*
32755 TTTTAGT
1 TTTTAAT
32762 TTTT-AT
1 TTTTAAT
32768 TTTTAA
1 TTTTAA
32774 AGTTTTATGA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
6 5 0.22
7 18 0.78
ACGTcount: A:0.24, C:0.00, G:0.03, T:0.73
Consensus pattern (7 bp):
TTTTAAT
Found at i:33645 original size:37 final size:41
Alignment explanation
Indices: 33599--33701 Score: 144
Period size: 37 Copynumber: 2.6 Consensus size: 41
33589 ACCAATTTTA
*
33599 TTATTTTCCAAAAGTCTTCTCTTGGATTT-C-AAAA-A-TT
1 TTATTTTCCAAAAGTCTTCTCTTGGATTTGCTAAAAGACAT
*
33636 TTATTTTCCAAAAGTCTTCTTTTGGATTTGCTAAAAGACAT
1 TTATTTTCCAAAAGTCTTCTCTTGGATTTGCTAAAAGACAT
*
33677 TCA-TTTCCAAAAGTCTTCTCTTGGA
1 TTATTTTCCAAAAGTCTTCTCTTGGA
33702 ATTGTGTAAA
Statistics
Matches: 58, Mismatches: 4, Indels: 5
0.87 0.06 0.07
Matches are distributed among these distances:
37 28 0.48
38 1 0.02
39 4 0.07
40 22 0.38
41 3 0.05
ACGTcount: A:0.28, C:0.17, G:0.11, T:0.44
Consensus pattern (41 bp):
TTATTTTCCAAAAGTCTTCTCTTGGATTTGCTAAAAGACAT
Found at i:33907 original size:25 final size:26
Alignment explanation
Indices: 33839--33907 Score: 90
Period size: 25 Copynumber: 2.8 Consensus size: 26
33829 ATTTTTATTA
*
33839 CATCTTTTTAATTTTC-TCACTTTTC
1 CATCTTTTTCATTTTCTTCACTTTTC
*
33864 CATTTTTTTCATTTT-TTCACTTTTC
1 CATCTTTTTCATTTTCTTCACTTTTC
*
33889 C-TCTTTTTCTTTTTCTTCA
1 CATCTTTTTCATTTTCTTCA
33908 AATTCTAACC
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
24 11 0.29
25 27 0.71
ACGTcount: A:0.12, C:0.23, G:0.00, T:0.65
Consensus pattern (26 bp):
CATCTTTTTCATTTTCTTCACTTTTC
Found at i:34727 original size:32 final size:32
Alignment explanation
Indices: 34664--34765 Score: 89
Period size: 32 Copynumber: 3.1 Consensus size: 32
34654 CTTTATTGAC
* * * *
34664 TTTACTTAATTACCTTAAATCAAGTTCTTTAT
1 TTTACTTAATTACCCTGAATTAAGCTCTTTAT
34696 TTTACTTAATTACCCTGAATTAAGC-CTTTTAT
1 TTTACTTAATTACCCTGAATTAAGCTC-TTTAT
* * *
34728 TGATCTCACTTAATTACACTGAATTAAGTTCTTAAT
1 T--T-T-ACTTAATTACCCTGAATTAAGCTCTTTAT
34764 TT
1 TT
34766 CCTTGCTTGA
Statistics
Matches: 57, Mismatches: 7, Indels: 10
0.77 0.09 0.14
Matches are distributed among these distances:
31 1 0.02
32 27 0.47
34 2 0.04
35 1 0.02
36 25 0.44
37 1 0.02
ACGTcount: A:0.30, C:0.17, G:0.06, T:0.47
Consensus pattern (32 bp):
TTTACTTAATTACCCTGAATTAAGCTCTTTAT
Found at i:34818 original size:35 final size:35
Alignment explanation
Indices: 34771--34891 Score: 136
Period size: 36 Copynumber: 3.4 Consensus size: 35
34761 AATTTCCTTG
* * * * *
34771 CTTGAAATTAAGCCTGTGTCTTTTTACTTAATTTC
1 CTTGAAACTAAGCCTGTCTTTTTTTACCTAGTTTC
*
34806 CATGAAACTAAG-CTAGTCTTTTTTTTACCTAGTTTC
1 CTTGAAACTAAGCCT-GTC-TTTTTTTACCTAGTTTC
* *
34842 CTTGAAACTAAGTCAGTCTTTTCTTTACCTAGTTTC
1 CTTGAAACTAAGCCTGTCTTTT-TTTACCTAGTTTC
34878 CTTGAAACTAAGCC
1 CTTGAAACTAAGCC
34892 AATCTATCTT
Statistics
Matches: 73, Mismatches: 9, Indels: 7
0.82 0.10 0.08
Matches are distributed among these distances:
34 2 0.03
35 16 0.22
36 54 0.74
37 1 0.01
ACGTcount: A:0.25, C:0.21, G:0.12, T:0.43
Consensus pattern (35 bp):
CTTGAAACTAAGCCTGTCTTTTTTTACCTAGTTTC
Found at i:34842 original size:36 final size:37
Alignment explanation
Indices: 34791--34890 Score: 150
Period size: 36 Copynumber: 2.8 Consensus size: 37
34781 AGCCTGTGTC
* * *
34791 TTTTTACTTAATTTCCATGAAACTAAGCT-AGTCTTT
1 TTTTTACCTAGTTTCCTTGAAACTAAGCTCAGTCTTT
34827 TTTTTACCTAGTTTCCTTGAAACTAAG-TCAGTCTTT
1 TTTTTACCTAGTTTCCTTGAAACTAAGCTCAGTCTTT
*
34863 TCTTTACCTAGTTTCCTTGAAACTAAGC
1 TTTTTACCTAGTTTCCTTGAAACTAAGC
34891 CAATCTATCT
Statistics
Matches: 58, Mismatches: 4, Indels: 3
0.89 0.06 0.05
Matches are distributed among these distances:
35 1 0.02
36 57 0.98
ACGTcount: A:0.25, C:0.20, G:0.10, T:0.45
Consensus pattern (37 bp):
TTTTTACCTAGTTTCCTTGAAACTAAGCTCAGTCTTT
Found at i:34918 original size:35 final size:35
Alignment explanation
Indices: 34793--34931 Score: 134
Period size: 36 Copynumber: 3.9 Consensus size: 35
34783 CCTGTGTCTT
* * * * * * *
34793 TTTACTTAATTTCCATGAAACTAAGCTAGTCTTTTT
1 TTTACCTAGTTTCCTTGAAACTAAGCCAATC-TATC
* * *
34829 TTTACCTAGTTTCCTTGAAACTAAGTCAGTCTTTTC
1 TTTACCTAGTTTCCTTGAAACTAAGCCAATC-TATC
34865 TTTACCTAGTTTCCTTGAAACTAAGCCAATCTATC
1 TTTACCTAGTTTCCTTGAAACTAAGCCAATCTATC
* ** *
34900 TTTACCTAATTTTTTTGAAATTAAGCCAATCT
1 TTTACCTAGTTTCCTTGAAACTAAGCCAATCT
34932 TTTATCAGTC
Statistics
Matches: 90, Mismatches: 13, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
35 31 0.34
36 59 0.66
ACGTcount: A:0.27, C:0.20, G:0.09, T:0.44
Consensus pattern (35 bp):
TTTACCTAGTTTCCTTGAAACTAAGCCAATCTATC
Found at i:34952 original size:11 final size:11
Alignment explanation
Indices: 34936--35175 Score: 100
Period size: 11 Copynumber: 22.1 Consensus size: 11
34926 CAATCTTTTA
34936 TCAGTCTAATT
1 TCAGTCTAATT
**
34947 TCAGTCTTCTT
1 TCAGTCTAATT
* *
34958 TCAGCCTGATT
1 TCAGTCTAATT
*
34969 TCAGTTTAATAT
1 TCAGTCTAAT-T
34981 TC-GTCCT--TT
1 TCAGT-CTAATT
34990 TCAGTCTAATT
1 TCAGTCTAATT
** *
35001 TCAGTCTTCTA
1 TCAGTCTAATT
* **
35012 TCAGTTTTCTT
1 TCAGTCTAATT
* *
35023 TCAGTCTGAGT
1 TCAGTCTAATT
*
35034 TCAGTTTAATAT
1 TCAGTCTAAT-T
35046 TC-GTCCT--TT
1 TCAGT-CTAATT
35055 TCAGTCTAATT
1 TCAGTCTAATT
** *
35066 TCAGTCTTCTA
1 TCAGTCTAATT
* **
35077 TCAGTTTTCTT
1 TCAGTCTAATT
35088 TCAGTCTAATT
1 TCAGTCTAATT
* *
35099 TCAGTTTAATA
1 TCAGTCTAATT
*
35110 TCCGTCCT--TT
1 TCAGT-CTAATT
35120 TCAGTCTAATT
1 TCAGTCTAATT
* ** *
35131 TTAGTCTTCTA
1 TCAGTCTAATT
* **
35142 TCAGTTTTCTT
1 TCAGTCTAATT
*
35153 TCAGTCTTATT
1 TCAGTCTAATT
35164 TCAGTCTAATT
1 TCAGTCTAATT
35175 T
1 T
35176 TCAATCCTCT
Statistics
Matches: 170, Mismatches: 46, Indels: 26
0.70 0.19 0.11
Matches are distributed among these distances:
9 12 0.07
10 11 0.06
11 138 0.81
12 9 0.05
ACGTcount: A:0.19, C:0.20, G:0.10, T:0.50
Consensus pattern (11 bp):
TCAGTCTAATT
Found at i:35040 original size:65 final size:65
Alignment explanation
Indices: 34947--35173 Score: 382
Period size: 65 Copynumber: 3.5 Consensus size: 65
34937 CAGTCTAATT
* *
34947 TCAGTCTTCTTTCAGCCTGATTTCAGTTTAATATTCGTCCTTTTCAGTCTAATTTCAGTCTTCTA
1 TCAGTTTTCTTTCAGTCTGATTTCAGTTTAATATTCGTCCTTTTCAGTCTAATTTCAGTCTTCTA
*
35012 TCAGTTTTCTTTCAGTCTGAGTTCAGTTTAATATTCGTCCTTTTCAGTCTAATTTCAGTCTTCTA
1 TCAGTTTTCTTTCAGTCTGATTTCAGTTTAATATTCGTCCTTTTCAGTCTAATTTCAGTCTTCTA
* * *
35077 TCAGTTTTCTTTCAGTCTAATTTCAGTTTAATATCCGTCCTTTTCAGTCTAATTTTAGTCTTCTA
1 TCAGTTTTCTTTCAGTCTGATTTCAGTTTAATATTCGTCCTTTTCAGTCTAATTTCAGTCTTCTA
* *
35142 TCAGTTTTCTTTCAGTCTTATTTCAGTCTAAT
1 TCAGTTTTCTTTCAGTCTGATTTCAGTTTAAT
35174 TTTCAATCCT
Statistics
Matches: 153, Mismatches: 9, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
65 153 1.00
ACGTcount: A:0.19, C:0.21, G:0.11, T:0.50
Consensus pattern (65 bp):
TCAGTTTTCTTTCAGTCTGATTTCAGTTTAATATTCGTCCTTTTCAGTCTAATTTCAGTCTTCTA
Found at i:35368 original size:49 final size:49
Alignment explanation
Indices: 35315--35427 Score: 122
Period size: 49 Copynumber: 2.3 Consensus size: 49
35305 AATAAGATCC
* *
35315 ACTTCTCTTAATTTCCTTTA-TGTCCCTTTA-TTTCACTGAATTAAGATTT
1 ACTTCTCTTAATTTCCTTTATTGTCCC-TAACTTT-ACTGAATTAAGAATT
* * * *
35364 ACTTCTCTCAATTTCTTTTATTTTCCCTAACTTTGCTGAATTAAGAATT
1 ACTTCTCTTAATTTCCTTTATTGTCCCTAACTTTACTGAATTAAGAATT
*
35413 ACTTTTTCTTAATTT
1 AC-TTCTCTTAATTT
35428 TCTTCAATCA
Statistics
Matches: 53, Mismatches: 8, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
49 35 0.66
50 18 0.34
ACGTcount: A:0.23, C:0.19, G:0.05, T:0.52
Consensus pattern (49 bp):
ACTTCTCTTAATTTCCTTTATTGTCCCTAACTTTACTGAATTAAGAATT
Done.