Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017034.1 Corchorus olitorius cultivar O-4 contig17067, 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: 50072
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.31
Found at i:3950 original size:17 final size:17
Alignment explanation
Indices: 3928--3961 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
3918 TGTTGTTTTT
3928 TATGATAACAAAATAAA
1 TATGATAACAAAATAAA
3945 TATGATAACAAAATAAA
1 TATGATAACAAAATAAA
3962 CCTAAATATG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.65, C:0.06, G:0.06, T:0.24
Consensus pattern (17 bp):
TATGATAACAAAATAAA
Found at i:11695 original size:27 final size:28
Alignment explanation
Indices: 11663--11719 Score: 78
Period size: 29 Copynumber: 2.0 Consensus size: 28
11653 AAAATGAAAT
* *
11663 AAAAAAAATGAAGAAAGAAAAAAAGAGAG
1 AAAAGAAATGAAAAAAG-AAAAAAGAGAG
11692 AAAATGAAATGAAAAAAGAAAAAAGAGA
1 AAAA-GAAATGAAAAAAGAAAAAAGAGA
11720 AATTTGAAAC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 14 0.56
30 11 0.44
ACGTcount: A:0.75, C:0.00, G:0.19, T:0.05
Consensus pattern (28 bp):
AAAAGAAATGAAAAAAGAAAAAAGAGAG
Found at i:11721 original size:39 final size:38
Alignment explanation
Indices: 11644--11717 Score: 98
Period size: 39 Copynumber: 1.9 Consensus size: 38
11634 AAAAAAGTAG
11644 AAAAGGATGAAAATGAAATAAAAAAAATGAAGAAAGAAA
1 AAAAGGATGAAAATGAAATAAAAAAAA-GAAGAAAGAAA
* *
11683 AAAAGAGA-GAAAATGAAAT-GAAAAAAGAAAAAAGA
1 AAAAG-GATGAAAATGAAATAAAAAAAAGAAGAAAGA
11718 GAAATTTGAA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
37 8 0.25
38 6 0.19
39 16 0.50
40 2 0.06
ACGTcount: A:0.73, C:0.00, G:0.19, T:0.08
Consensus pattern (38 bp):
AAAAGGATGAAAATGAAATAAAAAAAAGAAGAAAGAAA
Found at i:12097 original size:9 final size:9
Alignment explanation
Indices: 12061--12120 Score: 57
Period size: 9 Copynumber: 6.6 Consensus size: 9
12051 AAGTGCCAAA
12061 AAAAAAAAG
1 AAAAAAAAG
* *
12070 AAGAAGAAG
1 AAAAAAAAG
* *
12079 AAGAAGAAG
1 AAAAAAAAG
12088 AAAAAAAAG
1 AAAAAAAAG
12097 AAAAAAAAAG
1 -AAAAAAAAG
* *
12107 AAAGAAAAT
1 AAAAAAAAG
12116 AAAAA
1 AAAAA
12121 TATAAGGGAA
Statistics
Matches: 43, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
9 34 0.79
10 9 0.21
ACGTcount: A:0.82, C:0.00, G:0.17, T:0.02
Consensus pattern (9 bp):
AAAAAAAAG
Found at i:12429 original size:5 final size:5
Alignment explanation
Indices: 12415--12468 Score: 51
Period size: 5 Copynumber: 11.0 Consensus size: 5
12405 AAAATGGCTT
* *
12415 CAAAA AAAAA CAAAAA CAAAA CAAAA C-AAA C-AAA CAAAGA AAAAA C-AAA
1 CAAAA CAAAA C-AAAA CAAAA CAAAA CAAAA CAAAA CAAA-A CAAAA CAAAA
12464 CAAAA
1 CAAAA
12469 AAGAAAAGGA
Statistics
Matches: 41, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
4 12 0.29
5 20 0.49
6 9 0.22
ACGTcount: A:0.81, C:0.17, G:0.02, T:0.00
Consensus pattern (5 bp):
CAAAA
Found at i:12430 original size:11 final size:11
Alignment explanation
Indices: 12416--12475 Score: 66
Period size: 11 Copynumber: 5.3 Consensus size: 11
12406 AAATGGCTTC
12416 AAAAAAAAACA
1 AAAAAAAAACA
*
12427 AAAACAAAACA
1 AAAAAAAAACA
12438 AAACAAACAAACA
1 AAA-AAA-AAACA
*
12451 AAGAAAAAACA
1 AAAAAAAAACA
* *
12462 AACAAAAAAGA
1 AAAAAAAAACA
12473 AAA
1 AAA
12476 GGAAAAATTT
Statistics
Matches: 41, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
11 29 0.71
12 5 0.12
13 7 0.17
ACGTcount: A:0.83, C:0.13, G:0.03, T:0.00
Consensus pattern (11 bp):
AAAAAAAAACA
Found at i:27852 original size:26 final size:26
Alignment explanation
Indices: 27818--27907 Score: 65
Period size: 26 Copynumber: 3.4 Consensus size: 26
27808 AAGTTCCCAC
27818 CAGTCTTCAAAGTATTCAATTTAACT
1 CAGTCTTCAAAGTATTCAATTTAACT
* * **** **
27844 CAGTTTTCAAATTGGGAAAGTTCCCAC-
1 CAGTCTTCAAAGTATTCAA-TT-TAACT
*
27871 CAGTCTTCAAAGTATTCAATTTAGCT
1 CAGTCTTCAAAGTATTCAATTTAACT
*
27897 CAGTTTTCAAA
1 CAGTCTTCAAA
27908 TTGGGAAAGT
Statistics
Matches: 43, Mismatches: 18, Indels: 6
0.64 0.27 0.09
Matches are distributed among these distances:
25 1 0.02
26 25 0.58
27 15 0.35
28 2 0.05
ACGTcount: A:0.32, C:0.20, G:0.12, T:0.36
Consensus pattern (26 bp):
CAGTCTTCAAAGTATTCAATTTAACT
Found at i:27855 original size:53 final size:53
Alignment explanation
Indices: 27792--28137 Score: 484
Period size: 52 Copynumber: 6.5 Consensus size: 53
27782 ATCATGTTTA
* *
27792 AGTTTTCAAATTGGGAAAGTTCCCACCAGTCTTCAAAGTATTCAATTTAACTC
1 AGTTTTCAAATTGGGAAAGTTCCCACCAGTCTTCAAAGTATTCAATCTAGCTC
*
27845 AGTTTTCAAATTGGGAAAGTTCCCACCAGTCTTCAAAGTATTCAATTTAGCTC
1 AGTTTTCAAATTGGGAAAGTTCCCACCAGTCTTCAAAGTATTCAATCTAGCTC
* *
27898 AGTTTTCAAATTGGGAAAGTTTCCACCAGTTTTCAAAGTATTCAATCTAGCTC
1 AGTTTTCAAATTGGGAAAGTTCCCACCAGTCTTCAAAGTATTCAATCTAGCTC
** * *
27951 TTTTTTTTCAAATTGGGAAAGTTCCCACCAATCTTCAAAGTTTTCAATCTAGCTC
1 --AGTTTTCAAATTGGGAAAGTTCCCACCAGTCTTCAAAGTATTCAATCTAGCTC
* * * *
28006 -TTTTTCAAATTGGGAGAGTTCCCACCAGTCTTTAAAGTATTCAATCTAGCAC
1 AGTTTTCAAATTGGGAAAGTTCCCACCAGTCTTCAAAGTATTCAATCTAGCTC
* * *
28058 -TTTTTCAAATTGGGAAAGTTCCCACCAGGT-TTCAAAGTATTCAATTTCGCTC
1 AGTTTTCAAATTGGGAAAGTTCCCACCA-GTCTTCAAAGTATTCAATCTAGCTC
*
28110 TG-TTTCAAATTGGGAAAGTTCCCACCAG
1 AGTTTTCAAATTGGGAAAGTTCCCACCAG
28138 GTTTTAGTTT
Statistics
Matches: 268, Mismatches: 21, Indels: 10
0.90 0.07 0.03
Matches are distributed among these distances:
51 1 0.00
52 116 0.43
53 104 0.39
55 47 0.18
ACGTcount: A:0.29, C:0.21, G:0.15, T:0.35
Consensus pattern (53 bp):
AGTTTTCAAATTGGGAAAGTTCCCACCAGTCTTCAAAGTATTCAATCTAGCTC
Found at i:27929 original size:27 final size:27
Alignment explanation
Indices: 27792--27934 Score: 89
Period size: 27 Copynumber: 5.4 Consensus size: 27
27782 ATCATGTTTA
*
27792 AGTTTTCAAATTGGGAAAGTTCCCACC
1 AGTTTTCAAATTGGGAAAGTTTCCACC
* * **** *
27819 AGTCTTCAAAGTATTCAA-TTT-AACTC
1 AGTTTTCAAATTGGGAAAGTTTCCAC-C
*
27845 AGTTTTCAAATTGGGAAAGTTCCCACC
1 AGTTTTCAAATTGGGAAAGTTTCCACC
* * ****
27872 AGTCTTCAAAGTATTCAA-TTT--AGCTC
1 AGTTTTCAAATTGGGAAAGTTTCCA-C-C
27898 AGTTTTCAAATTGGGAAAGTTTCCACC
1 AGTTTTCAAATTGGGAAAGTTTCCACC
27925 AGTTTTCAAA
1 AGTTTTCAAA
27935 GTATTCAATC
Statistics
Matches: 79, Mismatches: 29, Indels: 16
0.64 0.23 0.13
Matches are distributed among these distances:
24 1 0.01
25 3 0.04
26 30 0.38
27 41 0.52
28 3 0.04
29 1 0.01
ACGTcount: A:0.31, C:0.20, G:0.15, T:0.34
Consensus pattern (27 bp):
AGTTTTCAAATTGGGAAAGTTTCCACC
Found at i:29044 original size:27 final size:27
Alignment explanation
Indices: 29014--29065 Score: 95
Period size: 27 Copynumber: 1.9 Consensus size: 27
29004 GCACTTAGGT
*
29014 CATTTAGGGGCATTTTGGTCATTTTTA
1 CATTCAGGGGCATTTTGGTCATTTTTA
29041 CATTCAGGGGCATTTTGGTCATTTT
1 CATTCAGGGGCATTTTGGTCATTTT
29066 AAATTCACAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.17, C:0.13, G:0.23, T:0.46
Consensus pattern (27 bp):
CATTCAGGGGCATTTTGGTCATTTTTA
Found at i:29072 original size:26 final size:27
Alignment explanation
Indices: 29019--29072 Score: 92
Period size: 27 Copynumber: 2.0 Consensus size: 27
29009 TAGGTCATTT
*
29019 AGGGGCATTTTGGTCATTTTTACATTC
1 AGGGGCATTTTGGTCATTTTTAAATTC
29046 AGGGGCATTTTGGTCA-TTTTAAATTC
1 AGGGGCATTTTGGTCATTTTTAAATTC
29072 A
1 A
29073 CATTATTTAG
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
26 10 0.38
27 16 0.62
ACGTcount: A:0.22, C:0.13, G:0.22, T:0.43
Consensus pattern (27 bp):
AGGGGCATTTTGGTCATTTTTAAATTC
Found at i:34316 original size:19 final size:21
Alignment explanation
Indices: 34272--34311 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
34262 GATTTCCTTT
34272 CTCTTTCCTCTTCCCGAAAAA
1 CTCTTTCCTCTTCCCGAAAAA
*
34293 CTCTTT-CTCTTCCCCAAAA
1 CTCTTTCCTCTTCCCGAAAA
34312 TTCTTCTTCT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.23, C:0.40, G:0.03, T:0.35
Consensus pattern (21 bp):
CTCTTTCCTCTTCCCGAAAAA
Found at i:35280 original size:24 final size:25
Alignment explanation
Indices: 35246--35298 Score: 81
Period size: 25 Copynumber: 2.2 Consensus size: 25
35236 ATTATTTAAA
35246 TAAATTAATTATA-TTTTTAAATCC
1 TAAATTAATTATAGTTTTTAAATCC
* *
35270 TAAATTGATTATAGTTTTTAAATCT
1 TAAATTAATTATAGTTTTTAAATCC
35295 TAAA
1 TAAA
35299 ATATATTAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
24 12 0.46
25 14 0.54
ACGTcount: A:0.42, C:0.06, G:0.04, T:0.49
Consensus pattern (25 bp):
TAAATTAATTATAGTTTTTAAATCC
Found at i:36935 original size:25 final size:27
Alignment explanation
Indices: 36900--36950 Score: 70
Period size: 25 Copynumber: 2.0 Consensus size: 27
36890 AATAGTAATT
*
36900 ATAAAGAAAAG-CAATTAAA-CTAAAA
1 ATAAAGAAAAGTAAATTAAATCTAAAA
*
36925 ATAAAGCAAAGTAAATTAAATCTAAA
1 ATAAAGAAAAGTAAATTAAATCTAAA
36951 CTATGGCAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 10 0.45
26 7 0.32
27 5 0.23
ACGTcount: A:0.65, C:0.08, G:0.08, T:0.20
Consensus pattern (27 bp):
ATAAAGAAAAGTAAATTAAATCTAAAA
Found at i:38585 original size:38 final size:38
Alignment explanation
Indices: 38501--38705 Score: 202
Period size: 38 Copynumber: 5.3 Consensus size: 38
38491 TTTCCCCTAA
* * *
38501 TTGAAAAC-TGAATGAGATCTTTTCCTAAATTAAAAACCT
1 TTGAAAACTTG-ATGGGATCTTTCCCTAAATTGAAAA-CT
*** *
38540 AAAAAAACTTGATGGGATCTTTCCCTAAATTGAAAATT
1 TTGAAAACTTGATGGGATCTTTCCCTAAATTGAAAACT
*
38578 TTGAAAAC-TGATGGGATCTTTCCCTAAATTGAAAACC
1 TTGAAAACTTGATGGGATCTTTCCCTAAATTGAAAACT
* * *
38615 TTAAAAACTGGATGGGATCTTTCCCTAAATTGAAATCT
1 TTGAAAACTTGATGGGATCTTTCCCTAAATTGAAAACT
38653 TTGAAAAACTTCTTGATGGGATCTTT-CC-AAATTTGAAAAACT
1 TTG-AAAA---CTTGATGGGATCTTTCCCTAAA-TTG-AAAACT
*
38695 TTGAAGACTTG
1 TTGAAAACTTG
38706 GATTGAATAC
Statistics
Matches: 138, Mismatches: 20, Indels: 17
0.79 0.11 0.10
Matches are distributed among these distances:
37 34 0.25
38 38 0.28
39 31 0.22
40 5 0.04
41 8 0.06
42 22 0.16
ACGTcount: A:0.37, C:0.15, G:0.15, T:0.33
Consensus pattern (38 bp):
TTGAAAACTTGATGGGATCTTTCCCTAAATTGAAAACT
Found at i:38599 original size:37 final size:37
Alignment explanation
Indices: 38501--38699 Score: 195
Period size: 37 Copynumber: 5.1 Consensus size: 37
38491 TTTCCCCTAA
* * *
38501 TTGAAAACTGAATGAGATCTTTTCCTAAATTAAAAACCT
1 TTGAAAACTG-ATGGGATCTTTCCCTAAATTGAAAA-CT
*** *
38540 AAAAAAACTTGATGGGATCTTTCCCTAAATTGAAAATT
1 TTGAAAAC-TGATGGGATCTTTCCCTAAATTGAAAACT
*
38578 TTGAAAACTGATGGGATCTTTCCCTAAATTGAAAACC
1 TTGAAAACTGATGGGATCTTTCCCTAAATTGAAAACT
* *
38615 TTAAAAACTGGATGGGATCTTTCCCTAAATTGAAATCT
1 TTGAAAACT-GATGGGATCTTTCCCTAAATTGAAAACT
38653 TTGAAAAACTTCTTGATGGGATCTTT-CC-AAATTTGAAAAACT
1 TTG-AAAA---C-TGATGGGATCTTTCCCTAAA-TTG-AAAACT
38695 TTGAA
1 TTGAA
38700 GACTTGGATT
Statistics
Matches: 134, Mismatches: 17, Indels: 16
0.80 0.10 0.10
Matches are distributed among these distances:
37 35 0.26
38 34 0.25
39 31 0.23
40 5 0.04
41 7 0.05
42 21 0.16
43 1 0.01
ACGTcount: A:0.38, C:0.15, G:0.14, T:0.33
Consensus pattern (37 bp):
TTGAAAACTGATGGGATCTTTCCCTAAATTGAAAACT
Found at i:38639 original size:75 final size:77
Alignment explanation
Indices: 38501--38659 Score: 243
Period size: 75 Copynumber: 2.1 Consensus size: 77
38491 TTTCCCCTAA
* *
38501 TTGAAAACTGAATGAGATCTTTTCCTAAATTAAAAACCTAAAAAAACTTGATGGGATCTTTCCCT
1 TTGAAAACTGAATGAGATCTTTCCCTAAATTAAAAACCTAAAAAAACTGGATGGGATCTTTCCCT
38566 AAATTGAAAAT-T
66 AAATTG-AAATCT
* * *
38578 TTGAAAACTG-ATGGGATCTTTCCCTAAATTGAAAACCT-TAAAAACTGGATGGGATCTTTCCCT
1 TTGAAAACTGAATGAGATCTTTCCCTAAATTAAAAACCTAAAAAAACTGGATGGGATCTTTCCCT
38641 AAATTGAAATCT
66 AAATTGAAATCT
38653 TTGAAAA
1 TTGAAAA
38660 ACTTCTTGAT
Statistics
Matches: 76, Mismatches: 5, Indels: 4
0.89 0.06 0.05
Matches are distributed among these distances:
74 4 0.05
75 37 0.49
76 25 0.33
77 10 0.13
ACGTcount: A:0.39, C:0.15, G:0.14, T:0.32
Consensus pattern (77 bp):
TTGAAAACTGAATGAGATCTTTCCCTAAATTAAAAACCTAAAAAAACTGGATGGGATCTTTCCCT
AAATTGAAATCT
Found at i:39551 original size:3 final size:3
Alignment explanation
Indices: 39543--39612 Score: 140
Period size: 3 Copynumber: 23.3 Consensus size: 3
39533 GTGCCAACCC
39543 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
39591 CTT CTT CTT CTT CTT CTT CTT C
1 CTT CTT CTT CTT CTT CTT CTT C
39613 ACCCGTTCGA
Statistics
Matches: 67, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 67 1.00
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (3 bp):
CTT
Found at i:42670 original size:40 final size:40
Alignment explanation
Indices: 42626--42708 Score: 139
Period size: 40 Copynumber: 2.1 Consensus size: 40
42616 GCACTTACCC
42626 AAAAGCAGATGAAGATATAAAAAGAAATGAGATAAAGAGA
1 AAAAGCAGATGAAGATATAAAAAGAAATGAGATAAAGAGA
* * *
42666 AAAAGCAGATGAAGATATAAATATAAATGAGATAAAGGGA
1 AAAAGCAGATGAAGATATAAAAAGAAATGAGATAAAGAGA
42706 AAA
1 AAA
42709 TGAATTATGC
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.61, C:0.02, G:0.22, T:0.14
Consensus pattern (40 bp):
AAAAGCAGATGAAGATATAAAAAGAAATGAGATAAAGAGA
Found at i:44081 original size:31 final size:30
Alignment explanation
Indices: 44041--44145 Score: 106
Period size: 31 Copynumber: 3.5 Consensus size: 30
44031 TCTTTGGCTG
* * *
44041 AAATCTCAAATAAGTCCCCGAACTTTGCCAT
1 AAATATCAAATAAGGCCCCGAACTTTG-CAA
*
44072 AAATATCAAATAAGGGCCCGAACTTTG-AA
1 AAATATCAAATAAGGCCCCGAACTTTGCAA
* *
44101 AAAGATCAAATAAGGGCCCC-AACTTCGCGAA
1 AAATATCAAATAA-GGCCCCGAACTTTGC-AA
*
44132 AAATCTCAAATAAG
1 AAATATCAAATAAG
44146 TCCACTCCGT
Statistics
Matches: 62, Mismatches: 9, Indels: 7
0.79 0.12 0.09
Matches are distributed among these distances:
29 19 0.31
30 6 0.10
31 37 0.60
ACGTcount: A:0.43, C:0.23, G:0.14, T:0.20
Consensus pattern (30 bp):
AAATATCAAATAAGGCCCCGAACTTTGCAA
Found at i:44280 original size:13 final size:13
Alignment explanation
Indices: 44264--44288 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
44254 AACTTAAAGA
44264 AAAAATACAAAAC
1 AAAAATACAAAAC
44277 AAAAATACAAAA
1 AAAAATACAAAA
44289 TAATGAAATA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.80, C:0.12, G:0.00, T:0.08
Consensus pattern (13 bp):
AAAAATACAAAAC
Found at i:44918 original size:2 final size:2
Alignment explanation
Indices: 44911--44940 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
44901 TTATGCATCA
44911 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
44941 TCTAGTGTGG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:45121 original size:2 final size:2
Alignment explanation
Indices: 45114--45149 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
45104 AAGGAACAGA
45114 AT AT AT AT AT AT AT AT AT AT AT AT 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
45150 TAAGAAATGG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:46138 original size:24 final size:24
Alignment explanation
Indices: 46111--46181 Score: 106
Period size: 24 Copynumber: 3.0 Consensus size: 24
46101 GAGGCACATG
*
46111 TAGATGCTGTTAATGATGTTGGTT
1 TAGATGCTGTTAATGATGCTGGTT
*
46135 TAGATGATGTTAATGATGCTGGTT
1 TAGATGCTGTTAATGATGCTGGTT
* *
46159 TAGATGCTGATACTGATGCTGGT
1 TAGATGCTGTTAATGATGCTGGT
46182 AAGGAGGGAG
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 42 1.00
ACGTcount: A:0.23, C:0.07, G:0.30, T:0.41
Consensus pattern (24 bp):
TAGATGCTGTTAATGATGCTGGTT
Found at i:48751 original size:21 final size:21
Alignment explanation
Indices: 48727--48767 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
48717 ACAGATGAAA
48727 CAAACCCTACAAACATGCCAG
1 CAAACCCTACAAACATGCCAG
* *
48748 CAAACGCTTCAAACATGCCA
1 CAAACCCTACAAACATGCCA
48768 ACAGACCTGC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.41, C:0.37, G:0.10, T:0.12
Consensus pattern (21 bp):
CAAACCCTACAAACATGCCAG
Found at i:48882 original size:14 final size:15
Alignment explanation
Indices: 48854--48888 Score: 63
Period size: 14 Copynumber: 2.4 Consensus size: 15
48844 AGGCCAATGT
48854 TGCTGCAATTGTTTC
1 TGCTGCAATTGTTTC
48869 TGCTGCAA-TGTTTC
1 TGCTGCAATTGTTTC
48883 TGCTGC
1 TGCTGC
48889 TCAAGCTGCT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 12 0.60
15 8 0.40
ACGTcount: A:0.11, C:0.23, G:0.23, T:0.43
Consensus pattern (15 bp):
TGCTGCAATTGTTTC
Done.