Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold782
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: 6641
ACGTcount: A:0.32, C:0.15, G:0.14, T:0.29
Warning! 741 characters in sequence are not A, C, G, or T
Found at i:1027 original size:47 final size:47
Alignment explanation
Indices: 774--1001 Score: 447
Period size: 47 Copynumber: 4.9 Consensus size: 47
764 ATACATAGGT
*
774 TTTTTTAAGTTATATTTATAAAAATTAGATAAAATTAAAAAATTTAG
1 TTTTTTAAGTAATATTTATAAAAATTAGATAAAATTAAAAAATTTAG
821 TTTTTTAAGTAATATTTATAAAAATTAGATAAAATTAAAAAATTTAG
1 TTTTTTAAGTAATATTTATAAAAATTAGATAAAATTAAAAAATTTAG
868 TTTTTTAAGTAATATTTATAAAAATTAGATAAAATTAAAAAATTTAG
1 TTTTTTAAGTAATATTTATAAAAATTAGATAAAATTAAAAAATTTAG
915 TTTTTTAAGTAATATTTATAAAAATTAGATAAAATTAAAAAATTTAG
1 TTTTTTAAGTAATATTTATAAAAATTAGATAAAATTAAAAAATTTAG
962 TTTTTTAAGTAATATTTATAAAAATTAGATAAAATTAAAA
1 TTTTTTAAGTAATATTTATAAAAATTAGATAAAATTAAAA
1002 GTTTAATGTT
Statistics
Matches: 180, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
47 180 1.00
ACGTcount: A:0.51, C:0.00, G:0.06, T:0.43
Consensus pattern (47 bp):
TTTTTTAAGTAATATTTATAAAAATTAGATAAAATTAAAAAATTTAG
Found at i:2262 original size:114 final size:114
Alignment explanation
Indices: 1821--2476 Score: 1023
Period size: 115 Copynumber: 5.8 Consensus size: 114
1811 NNNNNNNNNN
* *
1821 AAAAACGCCGCTAAATCCCCGAAAGCTCACAAAACAGCATCGTTTTGGATTAGGTTTTTTGCGGC
1 AAAAACGCCGCTAAATCCACGAAAGCTCACAAAACTGCATCGTTTTGGATTAGGTTTTTTGCGGC
* *
1886 GCTTTCCCAAAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTTCTT
66 GCTTTCTC-AAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTCCTT
* *
1936 AAAAACGCCGCTAAATCCCCGAAAGCTCACAAAACAGCATCGTTTTGGATTAGGTTTTTTGCGGC
1 AAAAACGCCGCTAAATCCACGAAAGCTCACAAAACTGCATCGTTTTGGATTAGGTTTTTTGCGGC
* *
2001 GCTTTCCCAAAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTTCTT
66 GCTTTCTC-AAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTCCTT
* * **
2051 AAAAACGCCGCTAAATCCCCGAAAGCTCACAAAAACTGCGTCGTTTTACATTAGGTTTTTTGCGG
1 AAAAACGCCGCTAAATCCACGAAAGCTCAC-AAAACTGCATCGTTTTGGATTAGGTTTTTTGCGG
* * * * *
2116 TGCTATCTCAAAAACGCCGCTAAAGCCATGAGCATTAGCGACACTTCCTT
65 CGCTTTCTCAAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTCCTT
2166 AAAAACGCCGCTAAATCCAC-AAAGCTCACAAAACTGCATCGTTTTGGATTAGGTTTTTCTGCGG
1 AAAAACGCCGCTAAATCCACGAAAGCTCACAAAACTGCATCGTTTTGGATTAGGTTTTT-TGCGG
2230 CGCTTTCTCAAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTCCTT
65 CGCTTTCTCAAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTCCTT
* *
2280 AAAAACGCCACTAAATCCAC--AAGCTCACAAAACTGCGTCGTTTTGGATTAGGTTTTTTGCGGC
1 AAAAACGCCGCTAAATCCACGAAAGCTCACAAAACTGCATCGTTTTGGATTAGGTTTTTTGCGGC
2343 GCTTTCTCAAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTCCTT
66 GCTTTCTCAAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTCCTT
* * * *
2392 AAAAACGCTGCTAAATCCAC-AAAGCTCACAAATCTGCGTCGTTTTGGATTAGGTTTTTTGCAGC
1 AAAAACGCCGCTAAATCCACGAAAGCTCACAAAACTGCATCGTTTTGGATTAGGTTTTTTGCGGC
* *
2456 GCTTTTTAAAAAACGCCGCTA
66 GCTTTCTCAAAAACGCCGCTA
2477 TTGCTTATTG
Statistics
Matches: 510, Mismatches: 28, Indels: 8
0.93 0.05 0.01
Matches are distributed among these distances:
112 73 0.14
113 122 0.24
114 78 0.15
115 201 0.39
116 36 0.07
ACGTcount: A:0.28, C:0.27, G:0.19, T:0.26
Consensus pattern (114 bp):
AAAAACGCCGCTAAATCCACGAAAGCTCACAAAACTGCATCGTTTTGGATTAGGTTTTTTGCGGC
GCTTTCTCAAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTCCTT
Found at i:3982 original size:30 final size:29
Alignment explanation
Indices: 3948--4041 Score: 95
Period size: 30 Copynumber: 3.2 Consensus size: 29
3938 TTATTTTTTG
*
3948 CATTTTAACCCATGTACTTTTC-AAAATTTA
1 CATTTTAACCCA--AACTTTTCTAAAATTTA
*
3978 CATTTTGACCCCAAACTTTTCTAAAATTTA
1 CATTTT-AACCCAAACTTTTCTAAAATTTA
*
4008 CATTTTGACCCCAAAAC-TTTCTAAAA-TTA
1 CATTTT-AACCC-AAACTTTTCTAAAATTTA
4037 CATTT
1 CATTT
4042 CGACCCTTAG
Statistics
Matches: 59, Mismatches: 2, Indels: 7
0.87 0.03 0.10
Matches are distributed among these distances:
29 15 0.25
30 35 0.59
31 9 0.15
ACGTcount: A:0.34, C:0.22, G:0.03, T:0.40
Consensus pattern (29 bp):
CATTTTAACCCAAACTTTTCTAAAATTTA
Found at i:3995 original size:29 final size:31
Alignment explanation
Indices: 3963--4047 Score: 133
Period size: 30 Copynumber: 2.9 Consensus size: 31
3953 TAACCCATGT
3963 ACTTTTC-AAAATTTACATTTTGACCCC-AA
1 ACTTTTCTAAAATTTACATTTTGACCCCAAA
3992 ACTTTTCTAAAATTTACATTTTGACCCCAAA
1 ACTTTTCTAAAATTTACATTTTGACCCCAAA
*
4023 AC-TTTCTAAAA-TTACATTTCGACCC
1 ACTTTTCTAAAATTTACATTTTGACCC
4048 TTAGACTTTC
Statistics
Matches: 53, Mismatches: 1, Indels: 4
0.91 0.02 0.07
Matches are distributed among these distances:
29 20 0.38
30 29 0.55
31 4 0.08
ACGTcount: A:0.34, C:0.25, G:0.04, T:0.38
Consensus pattern (31 bp):
ACTTTTCTAAAATTTACATTTTGACCCCAAA
Found at i:4703 original size:11 final size:11
Alignment explanation
Indices: 4681--4747 Score: 59
Period size: 11 Copynumber: 6.1 Consensus size: 11
4671 AGCCCCGAAG
4681 AGGAAGGAAAAA
1 AGGAA-GAAAAA
4693 AGGAAGAAAAA
1 AGGAAGAAAAA
*
4704 AAGAAG-AAAA
1 AGGAAGAAAAA
*
4714 A-GAGAGAACAA
1 AGGA-AGAAAAA
4725 AGGAAGGAAAAA
1 AGGAA-GAAAAA
*
4737 A-AAAGAAAAA
1 AGGAAGAAAAA
4747 A
1 A
4748 AAATATATTT
Statistics
Matches: 47, Mismatches: 4, Indels: 10
0.77 0.07 0.16
Matches are distributed among these distances:
9 2 0.04
10 14 0.30
11 18 0.38
12 13 0.28
ACGTcount: A:0.73, C:0.01, G:0.25, T:0.00
Consensus pattern (11 bp):
AGGAAGAAAAA
Found at i:4865 original size:13 final size:13
Alignment explanation
Indices: 4849--4873 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
4839 AAACGCCCAA
4849 AAAAAAAAACAGC
1 AAAAAAAAACAGC
4862 AAAAAAAAACAG
1 AAAAAAAAACAG
4874 GATAGCAAAA
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:0.08, T:0.00
Consensus pattern (13 bp):
AAAAAAAAACAGC
Found at i:4866 original size:16 final size:16
Alignment explanation
Indices: 4829--4870 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
4819 GCAGCCCCAA
4829 AAAAAAAACAAAACGCC
1 AAAAAAAA-AAAACGCC
*
4846 CAAAAAAAAAAACAG-C
1 AAAAAAAAAAAAC-GCC
4862 AAAAAAAAA
1 AAAAAAAAA
4871 CAGGATAGCA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
16 14 0.64
17 8 0.36
ACGTcount: A:0.79, C:0.17, G:0.05, T:0.00
Consensus pattern (16 bp):
AAAAAAAAAAAACGCC
Found at i:5723 original size:26 final size:25
Alignment explanation
Indices: 5671--5726 Score: 67
Period size: 26 Copynumber: 2.2 Consensus size: 25
5661 GTTTCAAAAA
* *
5671 TTTTCGTGTTTTCAAAATTTTAATG
1 TTTTCGTGTTTTAAAAATTCTAATG
**
5696 TTTTCGTGTTTTAAAAAATTCTCGTG
1 TTTTCGTGTTTT-AAAAATTCTAATG
5722 TTTTC
1 TTTTC
5727 AAAAAATTTT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
25 12 0.46
26 14 0.54
ACGTcount: A:0.21, C:0.11, G:0.12, T:0.55
Consensus pattern (25 bp):
TTTTCGTGTTTTAAAAATTCTAATG
Found at i:5748 original size:17 final size:18
Alignment explanation
Indices: 5559--6150 Score: 309
Period size: 17 Copynumber: 31.7 Consensus size: 18
5549 ACTTTTAACA
* *
5559 TTTTCAAGAGTTTTCGTG
1 TTTTCAAAAATTTTCGTG
* * *
5577 -TTTCACAAATGTTAGTG
1 TTTTCAAAAATTTTCGTG
*
5594 TTTT--AAAATTTTTGTG
1 TTTTCAAAAATTTTCGTG
5610 -TTTCAAAAATTTTCGTG
1 TTTTCAAAAATTTTCGTG
*
5627 TTTTCAAAATTTTTCGTG
1 TTTTCAAAAATTTTCGTG
** *
5645 TCAT-AAAAATTCTCGTG
1 TTTTCAAAAATTTTCGTG
5662 -TTTCAAAAATTTTCGTG
1 TTTTCAAAAATTTTCGTG
5679 TTTTCAAAATTTTAATGTTTTCGTG
1 TTTTC-AAA----AA--TTTTCGTG
* *
5704 TTTTAAAAAATTCTCGTG
1 TTTTCAAAAATTTTCGTG
5722 TTTTCAAAAAATTTTCGTG
1 TTTTC-AAAAATTTTCGTG
5741 -TTTCAAAAATTTTCGTG
1 TTTTCAAAAATTTTCGTG
*
5758 TTTTCAAAATTTTCATGTTTTCGTA
1 TTTTCAAAA-----A--TTTTCGTG
*
5783 TTTTCAAAAAAAAATTCTCGTG
1 TTTTC----AAAAATTTTCGTG
**
5805 TTTT-AAAAAAATTCGTG
1 TTTTCAAAAATTTTCGTG
* *
5822 TTTT-AAAAA-ATTCATG
1 TTTTCAAAAATTTTCGTG
*
5838 TTTTC-GAAATTTTCGTG
1 TTTTCAAAAATTTTCGTG
* *
5855 TTTTCAAAATTTTTTGTG
1 TTTTCAAAAATTTTCGTG
*** *
5873 -TCAGAAAAATTCTCGTG
1 TTTTCAAAAATTTTCGTG
5890 -TTTCAAAAATTTTCGTG
1 TTTTCAAAAATTTTCGTG
*
5907 TTTTCAAAATTTTCATGTTTTTGTG
1 TTTTCAAAA-----A--TTTTCGTG
*
5932 TTTTCAAAAAAAATTCTCGTG
1 TTTTC---AAAAATTTTCGTG
* *
5953 TTTTTAAAAAAATTTCGTG
1 -TTTTCAAAAATTTTCGTG
* ** * *
5972 TTTTAAAAAAAATACATG
1 TTTTCAAAAATTTTCGTG
*
5990 TTTTC-GAAATTTTCGTG
1 TTTTCAAAAATTTTCGTG
* *
6007 TTTTCAAAATTTTTTGTG
1 TTTTCAAAAATTTTCGTG
*** *
6025 -TCAGAAAAATTCTCGTG
1 TTTTCAAAAATTTTCGTG
6042 -TTTCAAAAATTTTCGTG
1 TTTTCAAAAATTTTCGTG
*
6059 TTTTCAAAATTTTCATGTTTTCGGG
1 TTTTCAAAA-----A--TTTTCGTG
*
6084 TTTTCAAAAAATTCTCGTG
1 TTTTC-AAAAATTTTCGTG
*
6103 TTTTCAAAAAATTTTTGTG
1 TTTTC-AAAAATTTTCGTG
*
6122 -TTTCAAAAATCTTCGTG
1 TTTTCAAAAATTTTCGTG
6139 TTTTCAAAAATT
1 TTTTCAAAAATT
6151 ATTATTTTGT
Statistics
Matches: 442, Mismatches: 80, Indels: 104
0.71 0.13 0.17
Matches are distributed among these distances:
15 3 0.01
16 23 0.05
17 159 0.36
18 115 0.26
19 49 0.11
20 2 0.00
21 7 0.02
22 14 0.03
23 6 0.01
24 4 0.01
25 48 0.11
26 4 0.01
28 4 0.01
29 4 0.01
ACGTcount: A:0.30, C:0.11, G:0.12, T:0.47
Consensus pattern (18 bp):
TTTTCAAAAATTTTCGTG
Found at i:5750 original size:79 final size:79
Alignment explanation
Indices: 5619--5859 Score: 287
Period size: 79 Copynumber: 3.1 Consensus size: 79
5609 GTTTCAAAAA
* * * *
5619 TTTTCGTGTTTTCAAAATTTTTCGTG---TCATAAAAATTCTCGTGTTTCAAAAATTTTCGTGTT
1 TTTTCGTGTTTTAAAAAATTCTCGTGTTTTCA-AAAAATTTTCGTGTTTCAAAAATTTTCGTGTT
*
5681 TTCAAAATTTTAATG
65 TTCAAAATTTTCATG
5696 TTTTCGTGTTTTAAAAAATTCTCGTGTTTTCAAAAAATTTTCGTGTTTCAAAAATTTTCGTGTTT
1 TTTTCGTGTTTTAAAAAATTCTCGTGTTTTCAAAAAATTTTCGTGTTTCAAAAATTTTCGTGTTT
5761 TCAAAATTTTCATG
66 TCAAAATTTTCATG
* * * * *
5775 TTTTCGTATTTTCAAAAAAAAATTCTCGTGTTTT-AAAAAA-ATTCGTGTTTTAAAAA-ATTCAT
1 TTTTCGTGTTTT----AAAAAATTCTCGTGTTTTCAAAAAATTTTCGTGTTTCAAAAATTTTCGT
* *
5837 GTTTTCGAAATTTTCGTG
62 GTTTTCAAAATTTTCATG
5855 TTTTC
1 TTTTC
5860 AAAATTTTTT
Statistics
Matches: 145, Mismatches: 12, Indels: 11
0.86 0.07 0.07
Matches are distributed among these distances:
77 23 0.16
79 56 0.39
80 28 0.19
81 14 0.10
82 6 0.04
83 18 0.12
ACGTcount: A:0.29, C:0.11, G:0.11, T:0.49
Consensus pattern (79 bp):
TTTTCGTGTTTTAAAAAATTCTCGTGTTTTCAAAAAATTTTCGTGTTTCAAAAATTTTCGTGTTT
TCAAAATTTTCATG
Found at i:5829 original size:16 final size:17
Alignment explanation
Indices: 5790--5841 Score: 70
Period size: 16 Copynumber: 3.0 Consensus size: 17
5780 GTATTTTCAA
5790 AAAAAAATTCTCGTGTTTT
1 AAAAAAA-T-TCGTGTTTT
5809 AAAAAAATTCGTGTTTT
1 AAAAAAATTCGTGTTTT
*
5826 -AAAAAATTCATGTTTT
1 AAAAAAATTCGTGTTTT
5842 CGAAATTTTC
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
16 15 0.47
17 9 0.28
18 1 0.03
19 7 0.22
ACGTcount: A:0.40, C:0.08, G:0.10, T:0.42
Consensus pattern (17 bp):
AAAAAAATTCGTGTTTT
Found at i:5850 original size:64 final size:64
Alignment explanation
Indices: 5727--5851 Score: 171
Period size: 64 Copynumber: 2.0 Consensus size: 64
5717 TCGTGTTTTC
* ** ** *
5727 AAAAAATTTTCGTGTTTCAAAAATTTTCGTGTTTTCAAAATTTTCATGTTTTCGTATTTTCAAA
1 AAAAAATTCTCGTGTTTCAAAAAAATTCGTGTTTTCAAAAAATTCATGTTTTCGAATTTTCAAA
*
5791 AAAAAATTCTCGTGTTTTAAAAAAATTCGTGTTTT-AAAAAATTCATGTTTTCGAAATTTTC
1 AAAAAATTCTCGTGTTTCAAAAAAATTCGTGTTTTCAAAAAATTCATGTTTTCG-AATTTTC
5852 GTGTTTTCAA
Statistics
Matches: 53, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
63 16 0.30
64 37 0.70
ACGTcount: A:0.34, C:0.10, G:0.10, T:0.46
Consensus pattern (64 bp):
AAAAAATTCTCGTGTTTCAAAAAAATTCGTGTTTTCAAAAAATTCATGTTTTCGAATTTTCAAA
Found at i:5867 original size:81 final size:83
Alignment explanation
Indices: 5649--5927 Score: 238
Period size: 79 Copynumber: 3.4 Consensus size: 83
5639 TTCGTGTCAT
* * * ***
5649 AAAAAT-TCTCGTGTTTCAAAAATTTTCGTGTTTTCAAAATTTTAATGTTTTCGTGTTTT----A
1 AAAAATAT-TCGTGTTTCAAAAATATTCATGTTTTCAAAATTTTCATGTTTTCAAATTTTCAAAA
5709 AAAAATTCTCGTGTTTTCA
65 AAAAATTCTCGTGTTTTCA
* * * **
5728 AAAAATTTTCGTGTTTCAAAAATTTTCGTGTTTTCAAAATTTTCATGTTTTCGTATTTTCAAAAA
1 AAAAATATTCGTGTTTCAAAAATATTCATGTTTTCAAAATTTTCATGTTTTCAAATTTTCAAAAA
5793 AAAATTCTCGTGTTTT-A
66 AAAATTCTCGTGTTTTCA
* * * *
5810 AAAAA-ATTCGTGTTTTAAAAA-ATTCATGTTTTCGAAATTTTCGTGTTTTCAAAATTTTTTGTG
1 AAAAATATTCGTGTTTCAAAAATATTCATGTTTTCAAAATTTTCATGTTTTC-AAA---TTT-TC
** *
5873 TCAGAAAAATTCTCGTG-TTTC-
61 AAAAAAAAATTCTCGTGTTTTCA
* *
5894 AAAAATTTTCGTGTTTTC-AAAATTTTCATGTTTT
1 AAAAATATTCGTG-TTTCAAAAATATTCATGTTTT
5928 TGTGTTTTCA
Statistics
Matches: 169, Mismatches: 17, Indels: 21
0.82 0.08 0.10
Matches are distributed among these distances:
79 55 0.33
80 26 0.15
81 15 0.09
82 6 0.04
83 18 0.11
84 11 0.07
85 25 0.15
86 13 0.08
ACGTcount: A:0.30, C:0.11, G:0.11, T:0.48
Consensus pattern (83 bp):
AAAAATATTCGTGTTTCAAAAATATTCATGTTTTCAAAATTTTCATGTTTTCAAATTTTCAAAAA
AAAATTCTCGTGTTTTCA
Found at i:5955 original size:21 final size:19
Alignment explanation
Indices: 5929--5984 Score: 85
Period size: 19 Copynumber: 2.8 Consensus size: 19
5919 TCATGTTTTT
5929 GTGTTTTCAAAAAAAATTCTC
1 GTGTTTT-AAAAAAAATT-TC
*
5950 GTGTTTTTAAAAAAATTTC
1 GTGTTTTAAAAAAAATTTC
5969 GTGTTTTAAAAAAAAT
1 GTGTTTTAAAAAAAAT
5985 ACATGTTTTC
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
19 17 0.52
20 9 0.27
21 7 0.21
ACGTcount: A:0.41, C:0.07, G:0.11, T:0.41
Consensus pattern (19 bp):
GTGTTTTAAAAAAAATTTC
Found at i:6047 original size:152 final size:152
Alignment explanation
Indices: 5728--6130 Score: 674
Period size: 152 Copynumber: 2.7 Consensus size: 152
5718 CGTGTTTTCA
* *
5728 AAAAATTTTCGTGTTTCAAAAATTTTCGTGTTTTCAAAATTTTCATGTTTTCGTATTTTCAAAAA
1 AAAAATTCTCGTGTTTCAAAAATTTTCGTGTTTTCAAAATTTTCATGTTTTCGTGTTTTC-AAAA
*
5793 AAAATTCTCGTG-TTTTAAAAAAA-TTCGTGTTTT--AAAAAATTCATGTTTTCGAAATTTTCGT
65 AAAATTCTCGTGTTTTTAAAAAAATTTCGTGTTTTAAAAAAAATACATGTTTTCGAAATTTTCGT
5854 GTTTTCAAAATTTTTTGTGTCAG
130 GTTTTCAAAATTTTTTGTGTCAG
*
5877 AAAAATTCTCGTGTTTCAAAAATTTTCGTGTTTTCAAAATTTTCATGTTTTTGTGTTTTCAAAAA
1 AAAAATTCTCGTGTTTCAAAAATTTTCGTGTTTTCAAAATTTTCATGTTTTCGTGTTTTCAAAAA
5942 AAATTCTCGTGTTTTTAAAAAAATTTCGTGTTTTAAAAAAAATACATGTTTTCGAAATTTTCGTG
66 AAATTCTCGTGTTTTTAAAAAAATTTCGTGTTTTAAAAAAAATACATGTTTTCGAAATTTTCGTG
6007 TTTTCAAAATTTTTTGTGTCAG
131 TTTTCAAAATTTTTTGTGTCAG
*
6029 AAAAATTCTCGTGTTTCAAAAATTTTCGTGTTTTCAAAATTTTCATGTTTTCGGGTTTTC--AAA
1 AAAAATTCTCGTGTTTCAAAAATTTTCGTGTTTTCAAAATTTTCATGTTTTCGTGTTTTCAAAAA
* * * *
6092 AAATTCTCGTGTTTTCAAAAAATTTTTGTGTTTCAAAAA
66 AAATTCTCGTGTTTTTAAAAAAATTTCGTGTTTTAAAAA
6131 TCTTCGTGTT
Statistics
Matches: 240, Mismatches: 10, Indels: 7
0.93 0.04 0.03
Matches are distributed among these distances:
148 16 0.07
149 68 0.28
150 48 0.20
152 108 0.45
ACGTcount: A:0.32, C:0.10, G:0.12, T:0.46
Consensus pattern (152 bp):
AAAAATTCTCGTGTTTCAAAAATTTTCGTGTTTTCAAAATTTTCATGTTTTCGTGTTTTCAAAAA
AAATTCTCGTGTTTTTAAAAAAATTTCGTGTTTTAAAAAAAATACATGTTTTCGAAATTTTCGTG
TTTTCAAAATTTTTTGTGTCAG
Found at i:6094 original size:27 final size:25
Alignment explanation
Indices: 6051--6107 Score: 69
Period size: 27 Copynumber: 2.2 Consensus size: 25
6041 GTTTCAAAAA
* *
6051 TTTTCGTGTTTTCAAAATTTTCATG
1 TTTTCGGGTTTTCAAAATTCTCATG
*
6076 TTTTCGGGTTTTCAAAAAATTCTCGTG
1 TTTTCGGGTTTTC--AAAATTCTCATG
6103 TTTTC
1 TTTTC
6108 AAAAAATTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
25 12 0.44
27 15 0.56
ACGTcount: A:0.19, C:0.14, G:0.14, T:0.53
Consensus pattern (25 bp):
TTTTCGGGTTTTCAAAATTCTCATG
Done.