Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3036
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: 54167
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:160 original size:30 final size:30
Alignment explanation
Indices: 126--222 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
116 AGCTCACTCC
126 TAGCTCATA-TTTAGCTCACGAGCTAAACCT
1 TAGCTCA-ACTTTAGCTCACGAGCTAAACCT
* * * * * *
156 TAGCTCAACTTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
* *
186 CAGCTCAACTTTAGCTCACGAGCTAAAGCT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
216 TAGCTCA
1 TAGCTCA
223 TTTTAGTTTA
Statistics
Matches: 51, Mismatches: 15, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
29 1 0.02
30 50 0.98
ACGTcount: A:0.28, C:0.27, G:0.16, T:0.29
Consensus pattern (30 bp):
TAGCTCAACTTTAGCTCACGAGCTAAACCT
Found at i:2184 original size:13 final size:13
Alignment explanation
Indices: 2166--2194 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
2156 CGGCTAACCT
2166 ACATAATTAAATA
1 ACATAATTAAATA
2179 ACATAATTAAATA
1 ACATAATTAAATA
2192 ACA
1 ACA
2195 CACAACTATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.62, C:0.10, G:0.00, T:0.28
Consensus pattern (13 bp):
ACATAATTAAATA
Found at i:7449 original size:20 final size:19
Alignment explanation
Indices: 7426--7490 Score: 51
Period size: 20 Copynumber: 3.3 Consensus size: 19
7416 AAGCTCAAAC
7426 GAGCTAAAGTAAGCTAAATT
1 GAGCTAAAGT-AGCTAAATT
7446 GAGCTCAAACG-AGCTAAATT
1 GAGCT-AAA-GTAGCTAAATT
* * * *
7466 AAGCTCATGTGAGCTAAATC
1 GAGCTAAAGT-AGCTAAATT
7486 GAGCT
1 GAGCT
7491 GGGAAAAACT
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 30 0.83
21 3 0.08
22 1 0.03
ACGTcount: A:0.38, C:0.17, G:0.22, T:0.23
Consensus pattern (19 bp):
GAGCTAAAGTAGCTAAATT
Found at i:9301 original size:33 final size:33
Alignment explanation
Indices: 9263--9325 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
9253 GATTACTCAC
9263 TTCACTCG-TTTCTTTT-ACAGACTCTCTTTCTTT
1 TTCACTCGATTTCTTTTCA-AG-CTCTCTTTCTTT
*
9296 TTCACTTGATTTCTTTTCAAGCTCTCTTTC
1 TTCACTCGATTTCTTTTCAAGCTCTCTTTC
9326 AATTTCTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
33 16 0.59
34 10 0.37
35 1 0.04
ACGTcount: A:0.13, C:0.27, G:0.06, T:0.54
Consensus pattern (33 bp):
TTCACTCGATTTCTTTTCAAGCTCTCTTTCTTT
Found at i:9352 original size:21 final size:21
Alignment explanation
Indices: 9323--9378 Score: 51
Period size: 21 Copynumber: 2.7 Consensus size: 21
9313 CAAGCTCTCT
*
9323 TTCAATTTCTTTTTTCGCTTT-
1 TTCATTTTCTTTTTTC-CTTTC
* ** *
9344 TTCTTTTTCAATTTTCTTTTC
1 TTCATTTTCTTTTTTCCTTTC
9365 TTCATTTTCTTTTT
1 TTCATTTTCTTTTT
9379 CTCTCACTTT
Statistics
Matches: 26, Mismatches: 8, Indels: 2
0.72 0.22 0.06
Matches are distributed among these distances:
20 3 0.12
21 23 0.88
ACGTcount: A:0.09, C:0.18, G:0.02, T:0.71
Consensus pattern (21 bp):
TTCATTTTCTTTTTTCCTTTC
Found at i:9371 original size:14 final size:14
Alignment explanation
Indices: 9322--9378 Score: 57
Period size: 14 Copynumber: 4.1 Consensus size: 14
9312 TCAAGCTCTC
9322 TTTCAA-TTTCTTT
1 TTTCAATTTTCTTT
**
9335 TTTCGCTTTT-TCTT
1 TTTCAATTTTCT-TT
9349 TTTCAATTTTCTTT
1 TTTCAATTTTCTTT
9363 TCTTC-ATTTTCTTT
1 T-TTCAATTTTCTTT
9377 TT
1 TT
9379 CTCTCACTTT
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
13 6 0.17
14 26 0.72
15 4 0.11
ACGTcount: A:0.09, C:0.18, G:0.02, T:0.72
Consensus pattern (14 bp):
TTTCAATTTTCTTT
Found at i:9406 original size:18 final size:18
Alignment explanation
Indices: 9385--9442 Score: 73
Period size: 18 Copynumber: 3.3 Consensus size: 18
9375 TTTTCTCTCA
9385 CTTTTTCGATTTCTTTTT
1 CTTTTTCGATTTCTTTTT
* *
9403 CTTTTGCAATTTCTTTTT
1 CTTTTTCGATTTCTTTTT
*
9421 C-TTTTCGTTTTCTTTTT
1 CTTTTTCGATTTCTTTTT
*
9438 GTTTT
1 CTTTT
9443 CTTTCAATTT
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
17 13 0.39
18 20 0.61
ACGTcount: A:0.05, C:0.16, G:0.07, T:0.72
Consensus pattern (18 bp):
CTTTTTCGATTTCTTTTT
Found at i:9431 original size:11 final size:11
Alignment explanation
Indices: 9412--9446 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
9402 TCTTTTGCAA
*
9412 TTTCTTTTTCT
1 TTTCGTTTTCT
9423 TTTCGTTTTCT
1 TTTCGTTTTCT
*
9434 TTTTGTTTTCT
1 TTTCGTTTTCT
9445 TT
1 TT
9447 CAATTTCTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.00, C:0.14, G:0.06, T:0.80
Consensus pattern (11 bp):
TTTCGTTTTCT
Found at i:9459 original size:6 final size:6
Alignment explanation
Indices: 9340--9446 Score: 65
Period size: 6 Copynumber: 17.7 Consensus size: 6
9330 TCTTTTTTCG
* * * **
9340 CTTTTT CTTTTT CAATTTT CTTTTCTT CATTTT CTTTTT CTCTCA CTTTTT
1 CTTTTT CTTTTT C-TTTTT C-TTT-TT CTTTTT CTTTTT CTTTTT CTTTTT
** * ** *
9391 CGATTT CTTTTT CTTTTG CAATTT CTTTTT C-TTTT CGTTTT CTTTTT
1 CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT
*
9438 -GTTTT CTTT
1 CTTTTT CTTT
9447 CAATTTCTTT
Statistics
Matches: 73, Mismatches: 24, Indels: 8
0.70 0.23 0.08
Matches are distributed among these distances:
5 9 0.12
6 52 0.71
7 9 0.12
8 3 0.04
ACGTcount: A:0.07, C:0.19, G:0.04, T:0.71
Consensus pattern (6 bp):
CTTTTT
Found at i:10852 original size:27 final size:27
Alignment explanation
Indices: 10821--10872 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
10811 ACAAGTGAGG
10821 AAAAAGAAAAAGAGAATGAAAAAGAGC
1 AAAAAGAAAAAGAGAATGAAAAAGAGC
* ** *
10848 AAAAAGAGATTGAGAGTGAAAAAGA
1 AAAAAGAAAAAGAGAATGAAAAAGA
10873 AATTGAAGAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 21 1.00
ACGTcount: A:0.65, C:0.02, G:0.25, T:0.08
Consensus pattern (27 bp):
AAAAAGAAAAAGAGAATGAAAAAGAGC
Found at i:18880 original size:28 final size:28
Alignment explanation
Indices: 18840--18898 Score: 118
Period size: 28 Copynumber: 2.1 Consensus size: 28
18830 GCTTATATTA
18840 ACTCTTCCAGTTCACCTCGCAACTTGCT
1 ACTCTTCCAGTTCACCTCGCAACTTGCT
18868 ACTCTTCCAGTTCACCTCGCAACTTGCT
1 ACTCTTCCAGTTCACCTCGCAACTTGCT
18896 ACT
1 ACT
18899 AGTTCAGATT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.19, C:0.39, G:0.10, T:0.32
Consensus pattern (28 bp):
ACTCTTCCAGTTCACCTCGCAACTTGCT
Found at i:21814 original size:30 final size:30
Alignment explanation
Indices: 21733--21825 Score: 79
Period size: 30 Copynumber: 3.2 Consensus size: 30
21723 TAAACTAAAA
*
21733 TGAGCTAAGCTTTAGCTCGTGAGC----GT
1 TGAGCTAAGGTTTAGCTCGTGAGCTGAAGT
* * * * * *
21759 TGAGCTGAGGCTAAACTCCTAAGCTGAAGT
1 TGAGCTAAGGTTTAGCTCGTGAGCTGAAGT
21789 TGAGCTAAGGTTTAGCTCGTGAGCTGAA-T
1 TGAGCTAAGGTTTAGCTCGTGAGCTGAAGT
21818 ATGAGCTA
1 -TGAGCTA
21826 GGAGTGAGCT
Statistics
Matches: 49, Mismatches: 13, Indels: 6
0.72 0.19 0.09
Matches are distributed among these distances:
26 17 0.35
29 1 0.02
30 31 0.63
ACGTcount: A:0.26, C:0.17, G:0.29, T:0.28
Consensus pattern (30 bp):
TGAGCTAAGGTTTAGCTCGTGAGCTGAAGT
Found at i:23999 original size:30 final size:30
Alignment explanation
Indices: 23928--24010 Score: 89
Period size: 30 Copynumber: 2.7 Consensus size: 30
23918 CTTTTGTTTC
* *
23928 AATTTCTTTTTCATCTTCTTTTTCACTCTCA
1 AATTTCTTTTTCTTC-TCTTTTTCAATCTCA
23959 AATTTC-TTTTCGTTCTCTTTTTCAATCTC-
1 AATTTCTTTTTC-TTCTCTTTTTCAATCTCA
* *
23988 ATTTTCTTTTTCTTTTTCTTTTT
1 AATTTCTTTTTC-TTCTCTTTTT
24011 TCTTTTCAAA
Statistics
Matches: 45, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
29 5 0.11
30 32 0.71
31 8 0.18
ACGTcount: A:0.12, C:0.22, G:0.01, T:0.65
Consensus pattern (30 bp):
AATTTCTTTTTCTTCTCTTTTTCAATCTCA
Found at i:24111 original size:25 final size:24
Alignment explanation
Indices: 24083--24141 Score: 66
Period size: 25 Copynumber: 2.4 Consensus size: 24
24073 TGCCTCTCTT
24083 TTCTTTT-TATTTCATTTTCATTTTC
1 TTCTTTTCTATTTC-TTTTC-TTTTC
*
24108 TTCTTTTGCTTTTTCTTTTCTTTTC
1 TTCTTTT-CTATTTCTTTTCTTTTC
*
24133 TTGTTTTCT
1 TTCTTTTCT
24142 CTTTACAAGA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
24 2 0.07
25 18 0.60
26 5 0.17
27 5 0.17
ACGTcount: A:0.05, C:0.17, G:0.03, T:0.75
Consensus pattern (24 bp):
TTCTTTTCTATTTCTTTTCTTTTC
Found at i:35494 original size:19 final size:19
Alignment explanation
Indices: 35470--35507 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
35460 TGGCTTAGAA
35470 AATGACTCTTGAGTTGTCC
1 AATGACTCTTGAGTTGTCC
35489 AATGACTCTTGAGTTGTCC
1 AATGACTCTTGAGTTGTCC
35508 TTGGCTAGTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.21, C:0.21, G:0.21, T:0.37
Consensus pattern (19 bp):
AATGACTCTTGAGTTGTCC
Found at i:37880 original size:19 final size:18
Alignment explanation
Indices: 37844--37883 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
37834 TTTCCACTCG
*
37844 TTTCTTTTTCAACTTCTC
1 TTTCTTTTTCAACATCTC
*
37862 TTTCTTTTTCCACAATCTC
1 TTTCTTTTTCAAC-ATCTC
37881 TTT
1 TTT
37884 GTTTGTTGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 12 0.63
19 7 0.37
ACGTcount: A:0.12, C:0.28, G:0.00, T:0.60
Consensus pattern (18 bp):
TTTCTTTTTCAACATCTC
Found at i:38948 original size:14 final size:14
Alignment explanation
Indices: 38929--38976 Score: 89
Period size: 14 Copynumber: 3.5 Consensus size: 14
38919 ACTAGCTCTC
38929 TTTTTTTTCACAAT
1 TTTTTTTTCACAAT
38943 TTTTTTTTCACAAT
1 TTTTTTTTCACAAT
38957 TTTTTTTTCA-AAT
1 TTTTTTTTCACAAT
38970 TTTTTTT
1 TTTTTTT
38977 ACAACTTGAT
Statistics
Matches: 34, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
13 10 0.29
14 24 0.71
ACGTcount: A:0.19, C:0.10, G:0.00, T:0.71
Consensus pattern (14 bp):
TTTTTTTTCACAAT
Found at i:39039 original size:12 final size:12
Alignment explanation
Indices: 39022--39077 Score: 87
Period size: 12 Copynumber: 4.8 Consensus size: 12
39012 AACCAAATTT
39022 TTTTTTTTTGAA
1 TTTTTTTTTGAA
*
39034 TTTTTTTTTGAC
1 TTTTTTTTTGAA
39046 TTTTTTTTTGAA
1 TTTTTTTTTGAA
*
39058 -TTTTTTTTGAG
1 TTTTTTTTTGAA
39069 TTTTTTTTT
1 TTTTTTTTT
39078 CGAGAAACTA
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
11 10 0.25
12 30 0.75
ACGTcount: A:0.11, C:0.02, G:0.09, T:0.79
Consensus pattern (12 bp):
TTTTTTTTTGAA
Found at i:39054 original size:24 final size:23
Alignment explanation
Indices: 39022--39077 Score: 94
Period size: 23 Copynumber: 2.4 Consensus size: 23
39012 AACCAAATTT
39022 TTTTTTTTTGAATTTTTTTTTGAC
1 TTTTTTTTTGAA-TTTTTTTTGAC
*
39046 TTTTTTTTTGAATTTTTTTTGAG
1 TTTTTTTTTGAATTTTTTTTGAC
39069 TTTTTTTTT
1 TTTTTTTTT
39078 CGAGAAACTA
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
23 19 0.61
24 12 0.39
ACGTcount: A:0.11, C:0.02, G:0.09, T:0.79
Consensus pattern (23 bp):
TTTTTTTTTGAATTTTTTTTGAC
Found at i:41581 original size:15 final size:16
Alignment explanation
Indices: 41551--41585 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
41541 CACACTCATT
41551 TTCTCAATGTTTTTTC
1 TTCTCAATGTTTTTTC
*
41567 TTCTCCATG-TTTTTC
1 TTCTCAATGTTTTTTC
41582 TTCT
1 TTCT
41586 TTTTCTACCT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 10 0.56
16 8 0.44
ACGTcount: A:0.09, C:0.23, G:0.06, T:0.63
Consensus pattern (16 bp):
TTCTCAATGTTTTTTC
Found at i:47575 original size:19 final size:18
Alignment explanation
Indices: 47539--47578 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
47529 TTTCCACTCG
*
47539 TTTCTTTTTCAACTTCTC
1 TTTCTTTTTCAACATCTC
*
47557 TTTCTTTTTCCACAATCTC
1 TTTCTTTTTCAAC-ATCTC
47576 TTT
1 TTT
47579 GTTTGTTGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 12 0.63
19 7 0.37
ACGTcount: A:0.12, C:0.28, G:0.00, T:0.60
Consensus pattern (18 bp):
TTTCTTTTTCAACATCTC
Found at i:48645 original size:13 final size:13
Alignment explanation
Indices: 48627--48676 Score: 77
Period size: 12 Copynumber: 3.9 Consensus size: 13
48617 TAGCTCTCTC
48627 TTTTTTTCACAATT
1 TTTTTTTCACAA-T
48641 TTTTTTTCACAAT
1 TTTTTTTCACAAT
48654 TTTTTTTCA-AAT
1 TTTTTTTCACAAT
48666 TTTTTTT-ACAA
1 TTTTTTTCACAA
48677 CTTGATATCC
Statistics
Matches: 35, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
11 1 0.03
12 12 0.34
13 10 0.29
14 12 0.34
ACGTcount: A:0.24, C:0.12, G:0.00, T:0.64
Consensus pattern (13 bp):
TTTTTTTCACAAT
Found at i:48646 original size:14 final size:14
Alignment explanation
Indices: 48627--48672 Score: 78
Period size: 13 Copynumber: 3.4 Consensus size: 14
48617 TAGCTCTCTC
48627 TTTTTTTCACAATT
1 TTTTTTTCACAATT
48641 TTTTTTTCACAA-T
1 TTTTTTTCACAATT
48654 TTTTTTTCA-AATT
1 TTTTTTTCACAATT
48667 TTTTTT
1 TTTTTT
48673 ACAACTTGAT
Statistics
Matches: 31, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
12 2 0.06
13 17 0.55
14 12 0.39
ACGTcount: A:0.20, C:0.11, G:0.00, T:0.70
Consensus pattern (14 bp):
TTTTTTTCACAATT
Found at i:48732 original size:13 final size:13
Alignment explanation
Indices: 48714--48765 Score: 79
Period size: 13 Copynumber: 4.1 Consensus size: 13
48704 TGGAAACCAA
48714 AATTTTTTTTTTG
1 AATTTTTTTTTTG
48727 AA-TTTTTTTTTG
1 AATTTTTTTTTTG
*
48739 AATTTTTTTTTCG
1 AATTTTTTTTTTG
*
48752 AGTTTTTTTTTTG
1 AATTTTTTTTTTG
48765 A
1 A
48766 GAAACTACTA
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
12 12 0.34
13 23 0.66
ACGTcount: A:0.15, C:0.02, G:0.10, T:0.73
Consensus pattern (13 bp):
AATTTTTTTTTTG
Found at i:48734 original size:12 final size:12
Alignment explanation
Indices: 48717--48762 Score: 74
Period size: 12 Copynumber: 3.8 Consensus size: 12
48707 AAACCAAAAT
48717 TTTTTTTTTGAA
1 TTTTTTTTTGAA
48729 TTTTTTTTTGAA
1 TTTTTTTTTGAA
*
48741 TTTTTTTTTCGAG
1 TTTTTTTTT-GAA
48754 TTTTTTTTT
1 TTTTTTTTT
48763 TGAGAAACTA
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
12 21 0.66
13 11 0.34
ACGTcount: A:0.11, C:0.02, G:0.09, T:0.78
Consensus pattern (12 bp):
TTTTTTTTTGAA
Found at i:48742 original size:25 final size:25
Alignment explanation
Indices: 48714--48762 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 25
48704 TGGAAACCAA
*
48714 AATTTTTTTTTTGAATTTTTTTTTG
1 AATTTTTTTTTCGAATTTTTTTTTG
*
48739 AATTTTTTTTTCGAGTTTTTTTTT
1 AATTTTTTTTTCGAATTTTTTTTT
48763 TGAGAAACTA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.14, C:0.02, G:0.08, T:0.76
Consensus pattern (25 bp):
AATTTTTTTTTCGAATTTTTTTTTG
Found at i:48939 original size:65 final size:66
Alignment explanation
Indices: 48834--48964 Score: 219
Period size: 65 Copynumber: 2.0 Consensus size: 66
48824 GATACCAATT
* * *
48834 TGATACGAACTCATTTTGTGATTGATTCGAGTCGTTAGTGTTTGCTC-ATCGTGAATTTGAGTAA
1 TGATACAAACTCATTTAGTGATTGATTCGAGTCGTGAGTGTTTGCTCGATCGTGAATTTGAGTAA
48898 G
66 G
*
48899 TGATACAAACTCGTTTAGTGATTGATTCGAGTCGTGAGTGTTTGCTCGATCGTGAATTTGAGTAA
1 TGATACAAACTCATTTAGTGATTGATTCGAGTCGTGAGTGTTTGCTCGATCGTGAATTTGAGTAA
48964 G
66 G
48965 GCTAAGTTTG
Statistics
Matches: 61, Mismatches: 4, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
65 43 0.70
66 18 0.30
ACGTcount: A:0.24, C:0.12, G:0.26, T:0.38
Consensus pattern (66 bp):
TGATACAAACTCATTTAGTGATTGATTCGAGTCGTGAGTGTTTGCTCGATCGTGAATTTGAGTAA
G
Found at i:52484 original size:11 final size:11
Alignment explanation
Indices: 52468--52529 Score: 94
Period size: 10 Copynumber: 5.9 Consensus size: 11
52458 GAATACAACT
52468 GAATTTTTTTC
1 GAATTTTTTTC
52479 GAA-TTTTTTC
1 GAATTTTTTTC
52489 GAATTTTTTTC
1 GAATTTTTTTC
*
52500 GAATTTTTTTT
1 GAATTTTTTTC
52511 G-ATTTTTTTC
1 GAATTTTTTTC
52521 G-ATTTTTTT
1 GAATTTTTTT
52530 TTCACCAACC
Statistics
Matches: 48, Mismatches: 2, Indels: 3
0.91 0.04 0.06
Matches are distributed among these distances:
10 27 0.56
11 21 0.44
ACGTcount: A:0.16, C:0.06, G:0.10, T:0.68
Consensus pattern (11 bp):
GAATTTTTTTC
Found at i:52485 original size:10 final size:10
Alignment explanation
Indices: 52472--52528 Score: 71
Period size: 11 Copynumber: 5.6 Consensus size: 10
52462 ACAACTGAAT
52472 TTTTTTCGAA
1 TTTTTTCGAA
52482 TTTTTTCGAA
1 TTTTTTCGAA
52492 TTTTTTTCGAA
1 -TTTTTTCGAA
* *
52503 TTTTTTTTGAT
1 -TTTTTTCGAA
52514 TTTTTTCG-A
1 TTTTTTCGAA
52523 TTTTTT
1 TTTTTT
52529 TTTCACCAAC
Statistics
Matches: 42, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
9 6 0.14
10 17 0.40
11 19 0.45
ACGTcount: A:0.14, C:0.07, G:0.09, T:0.70
Consensus pattern (10 bp):
TTTTTTCGAA
Found at i:52531 original size:21 final size:21
Alignment explanation
Indices: 52467--52530 Score: 94
Period size: 21 Copynumber: 3.0 Consensus size: 21
52457 TGAATACAAC
*
52467 TGAATTTTTTTCGAATTTTTT
1 TGAATTTTTTTCGATTTTTTT
*
52488 CGAATTTTTTTCGAATTTTTTT
1 TGAATTTTTTTCG-ATTTTTTT
52510 TG-ATTTTTTTCGATTTTTTT
1 TGAATTTTTTTCGATTTTTTT
52530 T
1 T
52531 TCACCAACCT
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
20 9 0.23
21 22 0.56
22 8 0.21
ACGTcount: A:0.16, C:0.06, G:0.09, T:0.69
Consensus pattern (21 bp):
TGAATTTTTTTCGATTTTTTT
Done.