Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024224.1 Corchorus olitorius cultivar O-4 contig24257, 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: 74270
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.34
Found at i:691 original size:16 final size:15
Alignment explanation
Indices: 653--694 Score: 66
Period size: 15 Copynumber: 2.7 Consensus size: 15
643 ACAGAGATTG
*
653 ACAGAAAGCAATTAA
1 ACAGAAAACAATTAA
668 ACAGAAAACAATTAA
1 ACAGAAAACAATTAA
683 ACTAGAAAACAA
1 AC-AGAAAACAA
695 AGCAAAGTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
15 16 0.64
16 9 0.36
ACGTcount: A:0.64, C:0.14, G:0.10, T:0.12
Consensus pattern (15 bp):
ACAGAAAACAATTAA
Found at i:5941 original size:35 final size:34
Alignment explanation
Indices: 5896--6035 Score: 165
Period size: 35 Copynumber: 4.0 Consensus size: 34
5886 TAAAAATGAC
*
5896 GGAACTTTCCCTAAATTGAAAAC-TAAAATCTGATG
1 GGAACTTTCCC-AATTTGAAAACTTAAAA-CTGATG
* *
5931 GGAACTTTCCCAATTTAAAAACTTTGAAAAGTGAATG
1 GGAACTTTCCCAATTTGAAAAC-TT-AAAACTG-ATG
* *
5968 GAAACTTTCCCAATTTGAAAACTTAAAAACTGGTG
1 GGAACTTTCCCAATTTGAAAACTT-AAAACTGATG
*
6003 GGAACTTTCCCAATTTGAAAACTTAAACCTGAT
1 GGAACTTTCCCAATTTGAAAACTTAAAACTGAT
6036 AAAATTCTTT
Statistics
Matches: 90, Mismatches: 11, Indels: 9
0.82 0.10 0.08
Matches are distributed among these distances:
34 16 0.18
35 36 0.40
36 11 0.12
37 27 0.30
ACGTcount: A:0.39, C:0.17, G:0.14, T:0.29
Consensus pattern (34 bp):
GGAACTTTCCCAATTTGAAAACTTAAAACTGATG
Found at i:6008 original size:72 final size:71
Alignment explanation
Indices: 5853--6027 Score: 210
Period size: 72 Copynumber: 2.4 Consensus size: 71
5843 AAATATTTTT
* *
5853 TGGTGGGAACTTTCCCAATTTAAAAGCTAAAGCTAAAAATGACGGAACTTTCCCTAAATTGAAAA
1 TGGTGGGAACTTTCCCAATTTAAAAACT-TAGC-AAAAATGACGGAACTTTCCCTAAATTGAAAA
*
5918 CTAAAATC
64 CTAAAAAC
* * * * *
5926 TGATGGGAACTTTCCCAATTTAAAAACTTTG-AAAAGTGAATGGAAACTTTCCC-AATTTGAAAA
1 TGGTGGGAACTTTCCCAATTTAAAAACTTAGCAAAAATG-ACGG-AACTTTCCCTAAATTGAAAA
5989 CTTAAAAAC
64 C-TAAAAAC
*
5998 TGGTGGGAACTTTCCCAATTTGAAAACTTA
1 TGGTGGGAACTTTCCCAATTTAAAAACTTA
6028 AACCTGATAA
Statistics
Matches: 88, Mismatches: 11, Indels: 7
0.83 0.10 0.07
Matches are distributed among these distances:
70 6 0.07
71 13 0.15
72 43 0.49
73 26 0.30
ACGTcount: A:0.39, C:0.17, G:0.15, T:0.29
Consensus pattern (71 bp):
TGGTGGGAACTTTCCCAATTTAAAAACTTAGCAAAAATGACGGAACTTTCCCTAAATTGAAAACT
AAAAAC
Found at i:6802 original size:15 final size:15
Alignment explanation
Indices: 6779--6809 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
6769 CCAAGCCCAA
*
6779 ATCATGAAATAAACC
1 ATCAAGAAATAAACC
6794 ATCAAGAAATAAACC
1 ATCAAGAAATAAACC
6809 A
1 A
6810 AGCCCAAGTC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.58, C:0.19, G:0.06, T:0.16
Consensus pattern (15 bp):
ATCAAGAAATAAACC
Found at i:7875 original size:9 final size:8
Alignment explanation
Indices: 7853--7878 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
7843 CTAATCCCCT
7853 TGTTTTTC
1 TGTTTTTC
7861 TGTTTTTC
1 TGTTTTTC
7869 TGTTTTTC
1 TGTTTTTC
7877 TG
1 TG
7879 GTTCAAGGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.00, C:0.12, G:0.15, T:0.73
Consensus pattern (8 bp):
TGTTTTTC
Found at i:10647 original size:21 final size:22
Alignment explanation
Indices: 10620--10675 Score: 71
Period size: 21 Copynumber: 2.6 Consensus size: 22
10610 GCATTCGTGG
10620 CTTCTTCTCGGCGCTTT-GCCT
1 CTTCTTCTCGGCGCTTTCGCCT
* *
10641 TTTCTTCACGGCG-TTTCGCCT
1 CTTCTTCTCGGCGCTTTCGCCT
*
10662 CTTCATCTCGGCGC
1 CTTCTTCTCGGCGC
10676 ACTAATTCTT
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
20 3 0.11
21 25 0.89
ACGTcount: A:0.04, C:0.38, G:0.20, T:0.39
Consensus pattern (22 bp):
CTTCTTCTCGGCGCTTTCGCCT
Found at i:12777 original size:8 final size:8
Alignment explanation
Indices: 12764--12788 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
12754 CATTAGGGAA
12764 GACATCTT
1 GACATCTT
12772 GACATCTT
1 GACATCTT
12780 GACATCTT
1 GACATCTT
12788 G
1 G
12789 TGGAGTGTTT
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:0.24, G:0.16, T:0.36
Consensus pattern (8 bp):
GACATCTT
Found at i:21442 original size:22 final size:21
Alignment explanation
Indices: 21404--21444 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
21394 CCAAAAAATA
21404 TGATAATAAATAATATTATAT
1 TGATAATAAATAATATTATAT
*
21425 TGATTATAAATTAATATTAT
1 TGATAATAAA-TAATATTAT
21445 TATAGTAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.49, C:0.00, G:0.05, T:0.46
Consensus pattern (21 bp):
TGATAATAAATAATATTATAT
Found at i:21849 original size:21 final size:21
Alignment explanation
Indices: 21825--21867 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
21815 GGTTTAACAT
** *
21825 GGTTTGAGGATCAAACTTTGG
1 GGTTTGACCATCAAAATTTGG
21846 GGTTTGACCATCAAAATTTGG
1 GGTTTGACCATCAAAATTTGG
21867 G
1 G
21868 CAAAAACACA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.26, C:0.12, G:0.30, T:0.33
Consensus pattern (21 bp):
GGTTTGACCATCAAAATTTGG
Found at i:21945 original size:101 final size:101
Alignment explanation
Indices: 21770--21968 Score: 317
Period size: 101 Copynumber: 2.0 Consensus size: 101
21760 AATTTACCTT
* * *
21770 AAACACAATTTTGGGCAAAAATGTAGTGGGTGCTTCAATTGATAAGGTTTAACATGGTTTGAGGA
1 AAACACAATTTTGGGCAAAAATGTAGCGAGTGCTTCAATTGATAAGGTTTAACATGATTTGAGGA
21835 TCAAACTTTGGGGTTTGACCATCAAAATTTGGGCAA
66 TCAAACTTTGGGGTTTGACCATCAAAATTTGGGCAA
* * **
21871 AAACACAGTTTTGGGCAAAAATGTGGCGAGTGCTTCAATTGATAAGGTTTAACATGATTTGATTA
1 AAACACAATTTTGGGCAAAAATGTAGCGAGTGCTTCAATTGATAAGGTTTAACATGATTTGAGGA
* *
21936 TCAAACTTTGGGGTTTGACCATTAAACTTTGGG
66 TCAAACTTTGGGGTTTGACCATCAAAATTTGGG
21969 GTTTGACCAT
Statistics
Matches: 89, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
101 89 1.00
ACGTcount: A:0.32, C:0.12, G:0.24, T:0.32
Consensus pattern (101 bp):
AAACACAATTTTGGGCAAAAATGTAGCGAGTGCTTCAATTGATAAGGTTTAACATGATTTGAGGA
TCAAACTTTGGGGTTTGACCATCAAAATTTGGGCAA
Found at i:21962 original size:21 final size:21
Alignment explanation
Indices: 21935--22010 Score: 125
Period size: 21 Copynumber: 3.6 Consensus size: 21
21925 TGATTTGATT
*
21935 ATCAAACTTTGGGGTTTGACC
1 ATCAAAATTTGGGGTTTGACC
* *
21956 ATTAAACTTTGGGGTTTGACC
1 ATCAAAATTTGGGGTTTGACC
21977 ATCAAAATTTGGGGTTTGACC
1 ATCAAAATTTGGGGTTTGACC
21998 ATCAAAATTTGGG
1 ATCAAAATTTGGG
22011 TAAAAACACA
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 52 1.00
ACGTcount: A:0.28, C:0.14, G:0.24, T:0.34
Consensus pattern (21 bp):
ATCAAAATTTGGGGTTTGACC
Found at i:22083 original size:143 final size:143
Alignment explanation
Indices: 21825--22153 Score: 514
Period size: 143 Copynumber: 2.3 Consensus size: 143
21815 GGTTTAACAT
**
21825 GGTTTGAGGATCAAACTTTGGGGTTTGACCATCAAAATTTGGGCAAAAACACAGTTTTGGGCAAA
1 GGTTTGACCATCAAACTTTGGGGTTTGACCATCAAAATTTGGGCAAAAACACAGTTTTGGGCAAA
*
21890 AATGTGGCGAGTGCTTCAATTGATAAGGTTTAACATGATTTGATTATCAAACTTTGGGGTTTGAC
66 AATGTGGCGAGTGCTTCAATTGATAAGGTTTAACATGATTTGACTATCAAACTTTGGGGTTTGAC
* *
21955 CATTAAACTTTGG
131 CATCAAACTTTAG
* * * *
21968 GGTTTGACCATCAAAATTTGGGGTTTGACCATCAAAATTTGGGTAAAAACACAGTTTTTGGTAAA
1 GGTTTGACCATCAAACTTTGGGGTTTGACCATCAAAATTTGGGCAAAAACACAGTTTTGGGCAAA
* * *
22033 AATGTGGTGGGTGCTTCAATTGATAAGGTTTAACATGGTTTGACTATCAAACTTTGGGGTTTGAC
66 AATGTGGCGAGTGCTTCAATTGATAAGGTTTAACATGATTTGACTATCAAACTTTGGGGTTTGAC
22098 CATCAAACTTTAG
131 CATCAAACTTTAG
* * * *
22111 GGTTTAACTATCAAACTTTGGGGTTTGACTATCAAACTTTGGG
1 GGTTTGACCATCAAACTTTGGGGTTTGACCATCAAAATTTGGG
22154 GTTTGACCAT
Statistics
Matches: 169, Mismatches: 17, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
143 169 1.00
ACGTcount: A:0.29, C:0.13, G:0.24, T:0.34
Consensus pattern (143 bp):
GGTTTGACCATCAAACTTTGGGGTTTGACCATCAAAATTTGGGCAAAAACACAGTTTTGGGCAAA
AATGTGGCGAGTGCTTCAATTGATAAGGTTTAACATGATTTGACTATCAAACTTTGGGGTTTGAC
CATCAAACTTTAG
Found at i:22093 original size:21 final size:21
Alignment explanation
Indices: 22069--22174 Score: 167
Period size: 21 Copynumber: 5.0 Consensus size: 21
22059 GGTTTAACAT
22069 GGTTTGACTATCAAACTTTGG
1 GGTTTGACTATCAAACTTTGG
* *
22090 GGTTTGACCATCAAACTTTAG
1 GGTTTGACTATCAAACTTTGG
*
22111 GGTTTAACTATCAAACTTTGG
1 GGTTTGACTATCAAACTTTGG
22132 GGTTTGACTATCAAACTTTGG
1 GGTTTGACTATCAAACTTTGG
* *
22153 GGTTTGACCATCAAAATTTGG
1 GGTTTGACTATCAAACTTTGG
22174 G
1 G
22175 TAACTGAAAT
Statistics
Matches: 77, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 77 1.00
ACGTcount: A:0.26, C:0.15, G:0.23, T:0.36
Consensus pattern (21 bp):
GGTTTGACTATCAAACTTTGG
Found at i:33207 original size:14 final size:15
Alignment explanation
Indices: 33188--33216 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
33178 CAATATATGA
33188 AAGAAAAATT-AATT
1 AAGAAAAATTCAATT
33202 AAGAAAAATTCAATT
1 AAGAAAAATTCAATT
33217 CAATTAAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.62, C:0.03, G:0.07, T:0.28
Consensus pattern (15 bp):
AAGAAAAATTCAATT
Found at i:34956 original size:42 final size:42
Alignment explanation
Indices: 34901--34982 Score: 110
Period size: 42 Copynumber: 2.0 Consensus size: 42
34891 ATGACATTTT
* * *
34901 CATGACATGTCATCATGTCAAGTGATATCTTAGATGATATGG
1 CATGACATATCATCATGTCAAGTGACATCATAGATGATATGG
* * *
34943 CATGTCATATCATCATGTCACGTGACATGATAGATGATAT
1 CATGACATATCATCATGTCAAGTGACATCATAGATGATAT
34983 ATGGACATGC
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
42 34 1.00
ACGTcount: A:0.32, C:0.16, G:0.20, T:0.33
Consensus pattern (42 bp):
CATGACATATCATCATGTCAAGTGACATCATAGATGATATGG
Found at i:37672 original size:13 final size:13
Alignment explanation
Indices: 37651--37686 Score: 54
Period size: 13 Copynumber: 2.7 Consensus size: 13
37641 TTGTTTTGTA
*
37651 TTGTATTTTGTTT
1 TTGTTTTTTGTTT
37664 TTGTTTTTTGTTT
1 TTGTTTTTTGTTT
37677 TTGTGTTTTT
1 TTGT-TTTTT
37687 CTTTACTTTG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
13 16 0.76
14 5 0.24
ACGTcount: A:0.03, C:0.00, G:0.17, T:0.81
Consensus pattern (13 bp):
TTGTTTTTTGTTT
Found at i:44288 original size:164 final size:163
Alignment explanation
Indices: 44010--44447 Score: 684
Period size: 164 Copynumber: 2.7 Consensus size: 163
44000 AACGCCGCTA
* *
44010 AAACGCCGCTATATATTATAGGCGTAGAGTTGGAAAATTTCTTTGTTTTA--GGAGGAGGGAATT
1 AAACGCCGCTATATATTATAGGTGTAGAGTTGTAAAATTTCTTTGTTTTAGTGGA-GAGGGAATT
*
44073 TTTCCCTCCAAAAAAAGGG-AAAAAAATCTCTCCCTCAATTATATTAAAATAGCGGCGTTTCCTT
65 TTTCCCTCCAAAAAAAGGGAAAAAAAATCTCTCCCTCCA-TATATTAAAATAGCGGCGTTTCCTT
* *
44137 TTCTAGATGCCACTAATCAGCGGCGTCTGATGTCC
129 TCCTAGACGCCACTAATCAGCGGCGTCTGATGTCC
* * * *
44172 AAACGTCGTTATATATTATAGGTGTAGATTTGTAAAATTTCTTTGTTTTAGTGGAGAGAGAATTT
1 AAACGCCGCTATATATTATAGGTGTAGAGTTGTAAAATTTCTTTGTTTTAGTGGAGAGGGAA-TT
*
44237 TTTCCCTCCAAAAAAAGGGAAAAAAAATCTCTCCCTCCATATATTAAAATAGCGGCGTTTCGTTT
65 TTTCCCTCCAAAAAAAGGGAAAAAAAATCTCTCCCTCCATATATTAAAATAGCGGCGTTTCCTTT
*
44302 CCTAGACGCCACTAATTAGCGGCGTCTGATGTCC
130 CCTAGACGCCACTAATCAGCGGCGTCTGATGTCC
* * *
44336 AAACGCCGCTATATATTATAGGTGTAGAGTTGTAAACTTTCTTTGTTTTAGTGGGGAGGGAACTT
1 AAACGCCGCTATATATTATAGGTGTAGAGTTGTAAAATTTCTTTGTTTTAGTGGAGAGGGAATTT
*
44401 TTCCCTCCAAAAAAAGGAGAAAAAAAATCTCTCCCTCCATAGATTAA
66 TTCCCTCCAAAAAAAGG-GAAAAAAAATCTCTCCCTCCATATATTAA
44448 TATGTCGGCG
Statistics
Matches: 252, Mismatches: 19, Indels: 8
0.90 0.07 0.03
Matches are distributed among these distances:
162 45 0.18
163 25 0.10
164 164 0.65
165 18 0.07
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32
Consensus pattern (163 bp):
AAACGCCGCTATATATTATAGGTGTAGAGTTGTAAAATTTCTTTGTTTTAGTGGAGAGGGAATTT
TTCCCTCCAAAAAAAGGGAAAAAAAATCTCTCCCTCCATATATTAAAATAGCGGCGTTTCCTTTC
CTAGACGCCACTAATCAGCGGCGTCTGATGTCC
Found at i:47751 original size:20 final size:21
Alignment explanation
Indices: 47726--47767 Score: 59
Period size: 23 Copynumber: 2.0 Consensus size: 21
47716 AACTAAACAG
47726 TTTG-AAGAATCAAACCAGAT
1 TTTGAAAGAATCAAACCAGAT
47746 TTTGAAAAAGAATCAAACCAGA
1 TTTG--AAAGAATCAAACCAGA
47768 AACTAAAAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 4 0.21
23 15 0.79
ACGTcount: A:0.50, C:0.14, G:0.14, T:0.21
Consensus pattern (21 bp):
TTTGAAAGAATCAAACCAGAT
Found at i:47776 original size:23 final size:23
Alignment explanation
Indices: 47730--47776 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
47720 AAACAGTTTG
*** *
47730 AAGAATCAAACCAGATTTTGAAA
1 AAGAATCAAACCAGAAACTAAAA
47753 AAGAATCAAACCAGAAACTAAAA
1 AAGAATCAAACCAGAAACTAAAA
47776 A
1 A
47777 CAAAGCCAAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.60, C:0.15, G:0.11, T:0.15
Consensus pattern (23 bp):
AAGAATCAAACCAGAAACTAAAA
Found at i:53709 original size:106 final size:107
Alignment explanation
Indices: 53554--53977 Score: 735
Period size: 107 Copynumber: 4.0 Consensus size: 107
53544 ACTTGGGGCC
53554 CTTGGGCCTTGGGCTCTTAAATGACTTAAAATTTTTGCTAAGTCTAAAAGTTTTTGTTTCCAACA
1 CTTGGGCCTTGGGCTCTTAAATGACTTAAAATTTTTGCTAAGTCTAAAAGTTTTTGTTTCCAACA
* *
53619 AGTATTTTTGGAAAAGAGGCA-TTTTTTGAATATAATAAGCG
66 AGTATTTTCGGATAAGAGGCATTTTTTTGAATATAATAAGCG
53660 CTTGGGCCTTGGGCTCTTAAATGACTTAAAATTTTTGCTAAGTCTAAAAGTTTTTGTTTCCAACA
1 CTTGGGCCTTGGGCTCTTAAATGACTTAAAATTTTTGCTAAGTCTAAAAGTTTTTGTTTCCAACA
53725 AGTATTTTCGGATAAGAGGCATTTTTTTGAATATAATAAGCG
66 AGTATTTTCGGATAAGAGGCATTTTTTTGAATATAATAAGCG
* * *
53767 CTTGGGCTTTGGGCTCTTAAATGACTTAGAATTTTTGCTAAGTCTAAACGTTTTTGTTTCCAACA
1 CTTGGGCCTTGGGCTCTTAAATGACTTAAAATTTTTGCTAAGTCTAAAAGTTTTTGTTTCCAACA
* *
53832 AGTATTTTCAGATAAGAGGCATTTTTTTTGAATATAATAAGCT
66 AGTATTTTCGGATAAGAGGCA-TTTTTTTGAATATAATAAGCG
* *
53875 TTTGGGCCTTGGGCTCTTAAATGACTTAGAATTTTTGCTAAGTCTAAAAGTTTTTGTTTCCAACA
1 CTTGGGCCTTGGGCTCTTAAATGACTTAAAATTTTTGCTAAGTCTAAAAGTTTTTGTTTCCAACA
*
53940 AGTATTTTCGCATAAGAGGCA-TTTTTTGAATATAATAA
66 AGTATTTTCGGATAAGAGGCATTTTTTTGAATATAATAA
53978 ACTGTCAAAA
Statistics
Matches: 304, Mismatches: 12, Indels: 4
0.95 0.04 0.01
Matches are distributed among these distances:
106 101 0.33
107 102 0.34
108 101 0.33
ACGTcount: A:0.29, C:0.13, G:0.18, T:0.40
Consensus pattern (107 bp):
CTTGGGCCTTGGGCTCTTAAATGACTTAAAATTTTTGCTAAGTCTAAAAGTTTTTGTTTCCAACA
AGTATTTTCGGATAAGAGGCATTTTTTTGAATATAATAAGCG
Found at i:54430 original size:178 final size:178
Alignment explanation
Indices: 54131--54452 Score: 572
Period size: 178 Copynumber: 1.8 Consensus size: 178
54121 CTCTAGATGT
54131 TTTTAAGCGGCTTTGTTGTATCCCAAATACAACTTACTTGAAATAGTCTGACAATATTGTATTTG
1 TTTTAAGCGGCTTTGTTGTATCCCAAATACAACTTACTTGAAATAGTCTGACAATATTGTATTTG
*
54196 AGAAACCTTGCCTCCTCAAAGTCTTGTTTTTTCTCTCTTAGTTTTCAGAAATTTTCTAACATCAT
66 AGAAACCTTACCTCCTCAAAGTCTTGTTTTTTCTCTCTTAGTTTTCAGAAATTTTCTAACATCAT
*
54261 ACATACAATATATATATATATATATATATCTTGTTTTTTCTCTTTTAG
131 ACATACAAAATATATATATATATATATATCTTGTTTTTTCTCTTTTAG
* * ** *
54309 TTTTAAGTGGTTTTGTTGTATCCCAAATACAACTTGTTTGAAATAGTCTGAGAATATTGTATTTG
1 TTTTAAGCGGCTTTGTTGTATCCCAAATACAACTTACTTGAAATAGTCTGACAATATTGTATTTG
*
54374 AGAAACCTTACCTCCTCAAAGTCTTGTTTTTTCTCTCTTAGTTTTCATAAATTTTCTAACATCAT
66 AGAAACCTTACCTCCTCAAAGTCTTGTTTTTTCTCTCTTAGTTTTCAGAAATTTTCTAACATCAT
54439 ACATACAAAATATA
131 ACATACAAAATATA
54453 CAAATAATAG
Statistics
Matches: 136, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
178 136 1.00
ACGTcount: A:0.30, C:0.16, G:0.11, T:0.43
Consensus pattern (178 bp):
TTTTAAGCGGCTTTGTTGTATCCCAAATACAACTTACTTGAAATAGTCTGACAATATTGTATTTG
AGAAACCTTACCTCCTCAAAGTCTTGTTTTTTCTCTCTTAGTTTTCAGAAATTTTCTAACATCAT
ACATACAAAATATATATATATATATATATCTTGTTTTTTCTCTTTTAG
Found at i:65571 original size:15 final size:15
Alignment explanation
Indices: 65541--65582 Score: 66
Period size: 15 Copynumber: 2.7 Consensus size: 15
65531 TTACTTTGCT
65541 TTGTTTTCTAGTTTAA
1 TTGTTTTCT-GTTTAA
65557 TTGTTTTCTGTTTAA
1 TTGTTTTCTGTTTAA
*
65572 TTGCTTTCTGT
1 TTGTTTTCTGT
65583 CAATCTCTGT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
15 16 0.64
16 9 0.36
ACGTcount: A:0.12, C:0.10, G:0.14, T:0.64
Consensus pattern (15 bp):
TTGTTTTCTGTTTAA
Found at i:66790 original size:10 final size:10
Alignment explanation
Indices: 66775--66800 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
66765 CTTTTCTTTC
66775 TTCTTTGTTT
1 TTCTTTGTTT
66785 TTCTTTGTTT
1 TTCTTTGTTT
66795 TTCTTT
1 TTCTTT
66801 CTTTCTTTCT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.00, C:0.12, G:0.08, T:0.81
Consensus pattern (10 bp):
TTCTTTGTTT
Done.