Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold242
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: 61083
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32
Found at i:2702 original size:23 final size:22
Alignment explanation
Indices: 2650--2702 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
2640 TCCACGTCTT
*
2650 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
2672 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
2695 TTTCTTTT
1 TTTCTTTT
2703 TCACTCTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 3 0.12
22 5 0.19
23 12 0.46
24 6 0.23
ACGTcount: A:0.09, C:0.19, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTCTTTTCTTTCTTTTTCTAA
Found at i:5610 original size:59 final size:59
Alignment explanation
Indices: 5537--5655 Score: 220
Period size: 59 Copynumber: 2.0 Consensus size: 59
5527 TAACCAAAAC
5537 AATGTTTCCTTACAAACTATTTATAGGCATTATTATGAATATTCAAATTCAACATTTAT
1 AATGTTTCCTTACAAACTATTTATAGGCATTATTATGAATATTCAAATTCAACATTTAT
* *
5596 AATGTTTTCTTACAAACTATTTATAGGCATTATTATGACTATTCAAATTCAACATTTAT
1 AATGTTTCCTTACAAACTATTTATAGGCATTATTATGAATATTCAAATTCAACATTTAT
5655 A
1 A
5656 TCAGCTATTA
Statistics
Matches: 58, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
59 58 1.00
ACGTcount: A:0.37, C:0.13, G:0.07, T:0.43
Consensus pattern (59 bp):
AATGTTTCCTTACAAACTATTTATAGGCATTATTATGAATATTCAAATTCAACATTTAT
Found at i:7256 original size:20 final size:19
Alignment explanation
Indices: 7233--7297 Score: 51
Period size: 20 Copynumber: 3.3 Consensus size: 19
7223 AAGCTCAAAC
7233 GAGCTAAAGTAAGCTAAATT
1 GAGCTAAAGT-AGCTAAATT
7253 GAGCTCAAACG-AGCTAAATT
1 GAGCT-AAA-GTAGCTAAATT
* * * *
7273 AAGCTCATGTGAGCTAAATC
1 GAGCTAAAGT-AGCTAAATT
7293 GAGCT
1 GAGCT
7298 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:11761 original size:27 final size:26
Alignment explanation
Indices: 11717--11767 Score: 66
Period size: 27 Copynumber: 1.9 Consensus size: 26
11707 CTCGCTGCAA
*
11717 TTTGGTGGCCTCGCCACATATATCTGT
1 TTTGGTGACCTCGCCACA-ATATCTGT
* *
11744 TTTGGTGACTTCGTCACAATATCT
1 TTTGGTGACCTCGCCACAATATCT
11768 AGCAGCCTCG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
26 6 0.29
27 15 0.71
ACGTcount: A:0.18, C:0.24, G:0.20, T:0.39
Consensus pattern (26 bp):
TTTGGTGACCTCGCCACAATATCTGT
Found at i:11836 original size:26 final size:27
Alignment explanation
Indices: 11807--11865 Score: 84
Period size: 27 Copynumber: 2.2 Consensus size: 27
11797 CCACATATAT
*
11807 ATATCTAT-TCTGGTGGCCTAGTCACA
1 ATATCTATATCTGGTGACCTAGTCACA
* *
11833 ATATCTATATCTGGTGACTTCGTCACA
1 ATATCTATATCTGGTGACCTAGTCACA
11860 ATATCT
1 ATATCT
11866 GGCAGCCTCG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
26 8 0.28
27 21 0.72
ACGTcount: A:0.25, C:0.22, G:0.15, T:0.37
Consensus pattern (27 bp):
ATATCTATATCTGGTGACCTAGTCACA
Found at i:21872 original size:13 final size:13
Alignment explanation
Indices: 21856--21905 Score: 55
Period size: 13 Copynumber: 3.6 Consensus size: 13
21846 AAAAAAAATC
21856 AAAAAAAAATTTG
1 AAAAAAAAATTTG
21869 AAAAAAAAATTTG
1 AAAAAAAAATTTG
* *
21882 ATTGAAAAAAAAATTC
1 A---AAAAAAAATTTG
21898 AAAAAAAA
1 AAAAAAAA
21906 TCGAAAAAAG
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
13 21 0.66
16 11 0.34
ACGTcount: A:0.72, C:0.02, G:0.06, T:0.20
Consensus pattern (13 bp):
AAAAAAAAATTTG
Found at i:22961 original size:12 final size:12
Alignment explanation
Indices: 22940--22991 Score: 56
Period size: 12 Copynumber: 4.6 Consensus size: 12
22930 AGAAAAGGAG
*
22940 AAAGAGATTGAA
1 AAAGAAATTGAA
22952 AAAGAAATTG--
1 AAAGAAATTGAA
*
22962 AAAGAAAAT-AA
1 AAAGAAATTGAA
*
22973 AAAGAAATTGCA
1 AAAGAAATTGAA
22985 AAAGAAA
1 AAAGAAA
22992 AAGAAATCAA
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
10 8 0.24
11 8 0.24
12 17 0.52
ACGTcount: A:0.67, C:0.02, G:0.17, T:0.13
Consensus pattern (12 bp):
AAAGAAATTGAA
Found at i:22976 original size:21 final size:22
Alignment explanation
Indices: 22950--22992 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 22
22940 AAAGAGATTG
22950 AAAAAGAAATTG-AAAGAAAAT
1 AAAAAGAAATTGAAAAGAAAAT
22971 AAAAAGAAATTGCAAAAGAAAA
1 AAAAAGAAATTG-AAAAGAAAA
22993 AGAAATCAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 12 0.60
23 8 0.40
ACGTcount: A:0.72, C:0.02, G:0.14, T:0.12
Consensus pattern (22 bp):
AAAAAGAAATTGAAAAGAAAAT
Found at i:23031 original size:14 final size:13
Alignment explanation
Indices: 23012--23049 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 13
23002 AAAAGTGAGA
23012 GAAAAAGAAAA-T
1 GAAAAAGAAAATT
23024 GAAGAAAAGAAAATT
1 G-A-AAAAGAAAATT
23039 GAAAAAGAAAA
1 GAAAAAGAAAA
23050 AGCGAAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
12 1 0.04
13 10 0.43
14 10 0.43
15 2 0.09
ACGTcount: A:0.74, C:0.00, G:0.18, T:0.08
Consensus pattern (13 bp):
GAAAAAGAAAATT
Found at i:23046 original size:13 final size:12
Alignment explanation
Indices: 22948--23049 Score: 50
Period size: 12 Copynumber: 8.0 Consensus size: 12
22938 AGAAAGAGAT
*
22948 TGAAAAAGAAAT
1 TGAAAAAGAAAA
22960 TG--AAAGAAAA
1 TGAAAAAGAAAA
*
22970 T-AAAAAGAAAT
1 TGAAAAAGAAAA
*
22981 TGCAAAAGAAAA
1 TGAAAAAGAAAA
*
22993 AGAAATCAA-AAAA
1 TGAAA--AAGAAAA
23006 GTGAGAGAAAAAGAAAA
1 -T----GAAAAAGAAAA
23023 TGAAGAAAAGAAAA
1 TG-A-AAAAGAAAA
23037 TTGAAAAAGAAAA
1 -TGAAAAAGAAAA
23050 AGCGAAAAAA
Statistics
Matches: 69, Mismatches: 7, Indels: 27
0.67 0.07 0.26
Matches are distributed among these distances:
10 8 0.12
11 8 0.12
12 14 0.20
13 14 0.20
14 12 0.17
15 2 0.03
16 3 0.04
17 4 0.06
18 4 0.06
ACGTcount: A:0.70, C:0.02, G:0.18, T:0.11
Consensus pattern (12 bp):
TGAAAAAGAAAA
Found at i:23063 original size:21 final size:21
Alignment explanation
Indices: 23013--23063 Score: 50
Period size: 21 Copynumber: 2.4 Consensus size: 21
23003 AAAGTGAGAG
*
23013 AAAAAGAAAATGAAGAAAAGA
1 AAAAAGAAAAAGAAGAAAAGA
** *
23034 AAATTGAAAAAGAA-AAAGCGA
1 AAAAAGAAAAAGAAGAAA-AGA
23055 AAAAAGAAA
1 AAAAAGAAA
23064 TTGAAAGAGA
Statistics
Matches: 23, Mismatches: 6, Indels: 2
0.74 0.19 0.06
Matches are distributed among these distances:
20 3 0.13
21 20 0.87
ACGTcount: A:0.75, C:0.02, G:0.18, T:0.06
Consensus pattern (21 bp):
AAAAAGAAAAAGAAGAAAAGA
Found at i:23103 original size:33 final size:33
Alignment explanation
Indices: 23066--23128 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
23056 AAAAGAAATT
23066 GAAAGAGAG-CT-TGAAAAGAAATCAAGTGAAAAA
1 GAAAGAGAGTCTGT-AAAAGAAA-CAAGTGAAAAA
*
23099 GAAAGAGAGTCTGTAAAAGAAACGAGTGAA
1 GAAAGAGAGTCTGTAAAAGAAACAAGTGAA
23129 GTGAGTAATC
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:0.54, C:0.06, G:0.27, T:0.13
Consensus pattern (33 bp):
GAAAGAGAGTCTGTAAAAGAAACAAGTGAAAAA
Found at i:24927 original size:20 final size:20
Alignment explanation
Indices: 24904--24957 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
24894 AGTTTTTCCC
*
24904 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTCACATG
* ***
24924 AGCTTAATTTAGCTCGTTTG
1 AGCTCAATTTAGCTCACATG
24944 AGCTCAATTTAGCT
1 AGCTCAATTTAGCT
24958 TACTTTAGCT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.24, C:0.20, G:0.19, T:0.37
Consensus pattern (20 bp):
AGCTCAATTTAGCTCACATG
Found at i:24939 original size:30 final size:30
Alignment explanation
Indices: 24904--24977 Score: 98
Period size: 30 Copynumber: 2.5 Consensus size: 30
24894 AGTTTTTCCC
24904 AGCTCGATTT-AGCTCACA-TGAGCTTAATTT
1 AGCTCG-TTTGAGCTCA-ATTGAGCTTAATTT
* *
24934 AGCTCGTTTGAGCTCAATTTAGCTTACTTT
1 AGCTCGTTTGAGCTCAATTGAGCTTAATTT
24964 AGCTCGTTTGAGCT
1 AGCTCGTTTGAGCT
24978 TGGCTTAAGT
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
29 4 0.10
30 36 0.90
ACGTcount: A:0.22, C:0.20, G:0.19, T:0.39
Consensus pattern (30 bp):
AGCTCGTTTGAGCTCAATTGAGCTTAATTT
Found at i:24967 original size:20 final size:20
Alignment explanation
Indices: 24904--24968 Score: 53
Period size: 20 Copynumber: 3.2 Consensus size: 20
24894 AGTTTTTCCC
* * * *
24904 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTTACTTT
*
24924 AGCTTAATTTAGC-T-CGTTT
1 AGCTCAATTTAGCTTAC-TTT
24943 GAGCTCAATTTAGCTTACTTT
1 -AGCTCAATTTAGCTTACTTT
24964 AGCTC
1 AGCTC
24969 GTTTGAGCTT
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 28 0.80
21 4 0.11
22 1 0.03
ACGTcount: A:0.23, C:0.22, G:0.17, T:0.38
Consensus pattern (20 bp):
AGCTCAATTTAGCTTACTTT
Found at i:26657 original size:13 final size:13
Alignment explanation
Indices: 26639--26663 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
26629 GGAAATTTGA
26639 AAAAAAAAAATTC
1 AAAAAAAAAATTC
26652 AAAAAAAAAATT
1 AAAAAAAAAATT
26664 TTGAAGTATA
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:0.04, G:0.00, T:0.16
Consensus pattern (13 bp):
AAAAAAAAAATTC
Found at i:27645 original size:18 final size:18
Alignment explanation
Indices: 27589--27646 Score: 62
Period size: 18 Copynumber: 3.1 Consensus size: 18
27579 AGTGCGAGCG
27589 AGAAAAAGAAATCAAAAGAAA
1 AGAAAAAGAAATC--AA-AAA
* **
27610 AGAAAAAGAGATTGAAAA
1 AGAAAAAGAAATCAAAAA
27628 AGAAAAAGAAATCAAAAA
1 AGAAAAAGAAATCAAAAA
27646 A
1 A
27647 CAGAGTGAGG
Statistics
Matches: 31, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
18 19 0.61
19 1 0.03
21 11 0.35
ACGTcount: A:0.74, C:0.03, G:0.16, T:0.07
Consensus pattern (18 bp):
AGAAAAAGAAATCAAAAA
Found at i:29707 original size:16 final size:16
Alignment explanation
Indices: 29686--29717 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
29676 TAATGTGTTT
29686 TGCTGCTGTTGTTTAA
1 TGCTGCTGTTGTTTAA
29702 TGCTGCTGTTGTTTAA
1 TGCTGCTGTTGTTTAA
29718 ATGCAGAATG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.12, C:0.12, G:0.25, T:0.50
Consensus pattern (16 bp):
TGCTGCTGTTGTTTAA
Found at i:34778 original size:21 final size:21
Alignment explanation
Indices: 34752--34801 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
34742 ACATTCTTGT
34752 AAAGAAAAAACAAAGAAAAG-A
1 AAAGAAAAAACAAA-AAAAGAA
* *
34773 AAAGAAAAAGCAAAAGAAGAA
1 AAAGAAAAAACAAAAAAAGAA
34794 AAAGAAAA
1 AAAGAAAA
34802 TGAAATAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
20 4 0.15
21 22 0.85
ACGTcount: A:0.80, C:0.04, G:0.16, T:0.00
Consensus pattern (21 bp):
AAAGAAAAAACAAAAAAAGAA
Found at i:34787 original size:6 final size:5
Alignment explanation
Indices: 34752--34819 Score: 59
Period size: 5 Copynumber: 13.0 Consensus size: 5
34742 ACATTCTTGT
* *
34752 AAAGA AAAAA CAAAGA AAAGA AAAGAA AAAGCA AAAGA AGA-A AAAGA
1 AAAGA AAAGA -AAAGA AAAGA AAAG-A AAAG-A AAAGA AAAGA AAAGA
34799 AAATGA AATA-A AAAGA AAAGA
1 AAA-GA AA-AGA AAAGA AAAGA
34820 GAGGCAAAAG
Statistics
Matches: 52, Mismatches: 5, Indels: 12
0.75 0.07 0.17
Matches are distributed among these distances:
4 4 0.08
5 29 0.56
6 18 0.35
7 1 0.02
ACGTcount: A:0.78, C:0.03, G:0.16, T:0.03
Consensus pattern (5 bp):
AAAGA
Found at i:34792 original size:15 final size:14
Alignment explanation
Indices: 34763--34819 Score: 60
Period size: 16 Copynumber: 3.7 Consensus size: 14
34753 AAGAAAAAAC
34763 AAAGAAAAGAAAAGAA
1 AAAGAAAAG--AAGAA
34779 AAAGCAAAAGAAGAA
1 AAAG-AAAAGAAGAA
*
34794 AAAGAAAATGAAATAA
1 AAAGAAAA-G-AAGAA
34810 AAAGAAAAGA
1 AAAGAAAAGA
34820 GAGGCAAAAG
Statistics
Matches: 37, Mismatches: 1, Indels: 8
0.80 0.02 0.17
Matches are distributed among these distances:
14 5 0.14
15 11 0.30
16 16 0.43
17 5 0.14
ACGTcount: A:0.77, C:0.02, G:0.18, T:0.04
Consensus pattern (14 bp):
AAAGAAAAGAAGAA
Found at i:34909 original size:18 final size:18
Alignment explanation
Indices: 34882--34937 Score: 51
Period size: 18 Copynumber: 3.1 Consensus size: 18
34872 AAAGCCTTTG
*
34882 AAAAGCAAAAAGAAAATGA
1 AAAAG-AAAATGAAAATGA
* * *
34901 AAATGAAAATGAGATTGA
1 AAAAGAAAATGAAAATGA
*
34919 AAAAGAGAATGAAAA-GA
1 AAAAGAAAATGAAAATGA
34936 AA
1 AA
34938 TTTGAGAGAG
Statistics
Matches: 29, Mismatches: 8, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
17 4 0.14
18 21 0.72
19 4 0.14
ACGTcount: A:0.68, C:0.02, G:0.20, T:0.11
Consensus pattern (18 bp):
AAAAGAAAATGAAAATGA
Found at i:34922 original size:30 final size:30
Alignment explanation
Indices: 34888--34969 Score: 85
Period size: 30 Copynumber: 2.7 Consensus size: 30
34878 TTTGAAAAGC
**
34888 AAAAAGAAAATGAAAATGAAA-ATGAGATTG
1 AAAAAGAAAATGAAAA-GAAATATGAGAGAG
* *
34918 AAAAAGAGAATGAAAAGAAATTTGAGAGAG
1 AAAAAGAAAATGAAAAGAAATATGAGAGAG
**
34948 AAAAAGAAGTTGAAAAAGAAAT
1 AAAAAGAAAATG-AAAAGAAAT
34970 TGAAAAAGAG
Statistics
Matches: 43, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
29 4 0.09
30 30 0.70
31 9 0.21
ACGTcount: A:0.63, C:0.00, G:0.22, T:0.15
Consensus pattern (30 bp):
AAAAAGAAAATGAAAAGAAATATGAGAGAG
Found at i:34964 original size:12 final size:12
Alignment explanation
Indices: 34947--34991 Score: 56
Period size: 12 Copynumber: 3.8 Consensus size: 12
34937 ATTTGAGAGA
*
34947 GAAAAAGAAGTT
1 GAAAAAGAAATT
34959 GAAAAAGAAATT
1 GAAAAAGAAATT
*
34971 GAAAAAGAGATT
1 GAAAAAGAAATT
*
34983 -AAAGAGAAA
1 GAAAAAGAAA
34992 GAAATTGAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
11 7 0.24
12 22 0.76
ACGTcount: A:0.64, C:0.00, G:0.22, T:0.13
Consensus pattern (12 bp):
GAAAAAGAAATT
Found at i:44869 original size:13 final size:13
Alignment explanation
Indices: 44851--44891 Score: 55
Period size: 13 Copynumber: 3.0 Consensus size: 13
44841 AAACCGTATG
44851 CAATTTTTTTTTT
1 CAATTTTTTTTTT
44864 CAATTTTTTTTTT
1 CAATTTTTTTTTT
*
44877 GAACTTCTTTTTTTT
1 CAA-TT-TTTTTTTT
44892 ACGTACCTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
13 15 0.60
14 2 0.08
15 8 0.32
ACGTcount: A:0.15, C:0.10, G:0.02, T:0.73
Consensus pattern (13 bp):
CAATTTTTTTTTT
Found at i:45220 original size:22 final size:22
Alignment explanation
Indices: 45190--45233 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
45180 TTTGGTATTT
45190 GGGAATTGGTACGAAATGGTAA
1 GGGAATTGGTACGAAATGGTAA
*
45212 GGGATTTGGTACGAAATGGTAA
1 GGGAATTGGTACGAAATGGTAA
45234 TGGTTCAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.34, C:0.05, G:0.36, T:0.25
Consensus pattern (22 bp):
GGGAATTGGTACGAAATGGTAA
Found at i:46832 original size:19 final size:19
Alignment explanation
Indices: 46808--46847 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
46798 AGCTCCCATG
46808 TAGCTCCACACCAGCTCAT
1 TAGCTCCACACCAGCTCAT
***
46827 TAGCTCGGGACCAGCTCAT
1 TAGCTCCACACCAGCTCAT
46846 TA
1 TA
46848 TCAGCTCACG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.25, C:0.35, G:0.17, T:0.23
Consensus pattern (19 bp):
TAGCTCCACACCAGCTCAT
Found at i:50951 original size:30 final size:30
Alignment explanation
Indices: 50915--50975 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
50905 TTCTTAACTC
*
50915 AAACTTTGGCAAAATTACAATTTTTCTCCT
1 AAACTTTGGCAAAATTACAATTTTGCTCCT
* * * *
50945 AAACTTTTGCATATTTACACTTTTGCTCCT
1 AAACTTTGGCAAAATTACAATTTTGCTCCT
50975 A
1 A
50976 GGCTCGGGAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.30, C:0.21, G:0.07, T:0.43
Consensus pattern (30 bp):
AAACTTTGGCAAAATTACAATTTTGCTCCT
Found at i:54823 original size:10 final size:10
Alignment explanation
Indices: 54790--54838 Score: 55
Period size: 10 Copynumber: 4.8 Consensus size: 10
54780 AAAAAGTAAT
*
54790 GAGCTGAAAC
1 GAGCTCAAAC
54800 GAGCT-AAATTC
1 GAGCTCAAA--C
54811 GAGCTCAAAC
1 GAGCTCAAAC
*
54821 GAGCTAAAAC
1 GAGCTCAAAC
54831 GAGCTCAA
1 GAGCTCAA
54839 GTAAGCTGAT
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
9 3 0.09
10 22 0.65
11 6 0.18
12 3 0.09
ACGTcount: A:0.41, C:0.22, G:0.22, T:0.14
Consensus pattern (10 bp):
GAGCTCAAAC
Done.