Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold822
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: 41369
ACGTcount: A:0.35, C:0.18, G:0.15, T:0.32
Found at i:1835 original size:64 final size:65
Alignment explanation
Indices: 1655--1835 Score: 216
Period size: 64 Copynumber: 2.9 Consensus size: 65
1645 GCAAACAAAC
*
1655 ATTTGAACCACATATGTATA-AT--TTACA-ACATTAAATTTCAGCTCAAAGAA-TTTGTAACCT
1 ATTTGAACCACATATGTATATATAATT-CATACATTAAATTACAGCTC-AAGAACTTTGTAACCT
1715 AT
64 AT
* * * * *
1717 ATTCGAACCTCATATGTATGTAAAATTCATACATTAAATTCCA-CTCAA-ACACTTTGTAACCTA
1 ATTTGAACCACATATGTATATATAATTCATACATTAAATTACAGCTCAAGA-ACTTTGTAACCTA
1780 T
65 T
*
1781 ATTTGAAACACATATGTATATATAATTCATACATTAAA-TACAGCTCAAGAACTTT
1 ATTTGAACCACATATGTATATATAATTCATACATTAAATTACAGCTCAAGAACTTT
1836 AAATATATAT
Statistics
Matches: 100, Mismatches: 11, Indels: 14
0.80 0.09 0.11
Matches are distributed among these distances:
62 18 0.18
63 7 0.07
64 60 0.60
65 15 0.15
ACGTcount: A:0.40, C:0.18, G:0.07, T:0.35
Consensus pattern (65 bp):
ATTTGAACCACATATGTATATATAATTCATACATTAAATTACAGCTCAAGAACTTTGTAACCTAT
Found at i:1950 original size:21 final size:22
Alignment explanation
Indices: 1909--1951 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
1899 TCAAAGAACT
1909 TATATCATACATTCAAACTTTA
1 TATATCATACATTCAAACTTTA
1931 TATAT-ATA-ATTCACAACTTTA
1 TATATCATACATTCA-AACTTTA
1952 AATTCAACTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
20 5 0.25
21 10 0.50
22 5 0.25
ACGTcount: A:0.42, C:0.16, G:0.00, T:0.42
Consensus pattern (22 bp):
TATATCATACATTCAAACTTTA
Found at i:2561 original size:28 final size:28
Alignment explanation
Indices: 2530--2583 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 28
2520 CATGCATTTC
* *
2530 ATTTA-TTTCATATTTTAGTCCCTAAAAA
1 ATTTATTTTCACAATTTAG-CCCTAAAAA
2558 ATTTATTTTCACAATTTAGCCCTAAA
1 ATTTATTTTCACAATTTAGCCCTAAA
2584 TACTCAAGTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
28 12 0.52
29 11 0.48
ACGTcount: A:0.35, C:0.17, G:0.04, T:0.44
Consensus pattern (28 bp):
ATTTATTTTCACAATTTAGCCCTAAAAA
Found at i:7430 original size:42 final size:44
Alignment explanation
Indices: 7365--7449 Score: 122
Period size: 43 Copynumber: 2.0 Consensus size: 44
7355 GCAGGCCACC
7365 TAAAATATACTATCTAAAGAAGTAA-TTTATT-ATTTAATTTAAT
1 TAAAATATACTATCTAAAGAAGTAATTTTATTAATTT-ATTTAAT
* *
7408 TAAAATATAGT-TCTAAATAAGTAATTTTATTAATTTATTTAA
1 TAAAATATACTATCTAAAGAAGTAATTTTATTAATTTATTTAA
7450 ACATAAATTA
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
42 12 0.32
43 22 0.58
44 4 0.11
ACGTcount: A:0.46, C:0.04, G:0.05, T:0.46
Consensus pattern (44 bp):
TAAAATATACTATCTAAAGAAGTAATTTTATTAATTTATTTAAT
Found at i:8072 original size:8 final size:8
Alignment explanation
Indices: 8061--8105 Score: 54
Period size: 8 Copynumber: 5.1 Consensus size: 8
8051 TATATTTAAA
8061 TATATTTT
1 TATATTTT
8069 TATATTTT
1 TATATTTT
8077 TATATTTTT
1 TATA-TTTT
8086 TATAAATTTT
1 TAT--ATTTT
8096 TATATATTT
1 TATAT-TTT
8105 T
1 T
8106 TTTCAAAATA
Statistics
Matches: 33, Mismatches: 0, Indels: 7
0.82 0.00 0.17
Matches are distributed among these distances:
8 14 0.42
9 11 0.33
10 7 0.21
11 1 0.03
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (8 bp):
TATATTTT
Found at i:8073 original size:10 final size:10
Alignment explanation
Indices: 8046--8106 Score: 74
Period size: 10 Copynumber: 6.4 Consensus size: 10
8036 GTTTTAGTGA
8046 TTTTATATAT
1 TTTTATATAT
**
8056 TTAAATATA-
1 TTTTATATAT
8065 TTTT-TATAT
1 TTTTATATAT
8074 TTTTATAT-T
1 TTTTATATAT
*
8083 TTTTATAAAT
1 TTTTATATAT
8093 TTTTATATAT
1 TTTTATATAT
8103 TTTT
1 TTTT
8107 TTCAAAATAC
Statistics
Matches: 42, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
8 4 0.10
9 14 0.33
10 24 0.57
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (10 bp):
TTTTATATAT
Found at i:8177 original size:25 final size:26
Alignment explanation
Indices: 8123--8179 Score: 64
Period size: 26 Copynumber: 2.2 Consensus size: 26
8113 ATACTATAAG
* *
8123 ATTTTTATATATTTGTAATTGTATGC
1 ATTTTTATATATTTATAATTGTATAC
*
8149 ATTTTTATA-ATTTTATAATT-TATAT
1 ATTTTTATATA-TTTATAATTGTATAC
8174 ATTTTT
1 ATTTTT
8180 TAAAATATTA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
25 10 0.37
26 17 0.63
ACGTcount: A:0.30, C:0.02, G:0.05, T:0.63
Consensus pattern (26 bp):
ATTTTTATATATTTATAATTGTATAC
Found at i:9102 original size:31 final size:31
Alignment explanation
Indices: 9043--9132 Score: 114
Period size: 31 Copynumber: 2.9 Consensus size: 31
9033 TATGTGATAG
* * *
9043 TACAGGGTTTGAATATG-AAATATTAATGA-
1 TACATGGTATGAATATGAAAATATGAATGAT
9072 TA-ATAGGATATGAATATGAAAATATGAATGAT
1 TACAT-GG-TATGAATATGAAAATATGAATGAT
9104 TACATGGTATGAATATGAAAATATGAATG
1 TACATGGTATGAATATGAAAATATGAATG
9133 GTTGATACCA
Statistics
Matches: 53, Mismatches: 3, Indels: 8
0.83 0.05 0.12
Matches are distributed among these distances:
28 1 0.02
29 4 0.08
30 9 0.17
31 33 0.62
32 4 0.08
33 2 0.04
ACGTcount: A:0.46, C:0.02, G:0.20, T:0.32
Consensus pattern (31 bp):
TACATGGTATGAATATGAAAATATGAATGAT
Found at i:13093 original size:26 final size:26
Alignment explanation
Indices: 13035--13099 Score: 78
Period size: 26 Copynumber: 2.5 Consensus size: 26
13025 ATAAGAGCAA
* * *
13035 TAATCAAGAAGTTCACAAAGAACTTT
1 TAATCAGGAAGCTCACAAAGAACCTT
* *
13061 TAATCAGGAAGCTCACGAAGAGCCTT
1 TAATCAGGAAGCTCACAAAGAACCTT
13087 TAATCAGG-AGCTC
1 TAATCAGGAAGCTC
13100 CGGATAGCCA
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
25 5 0.15
26 29 0.85
ACGTcount: A:0.38, C:0.20, G:0.18, T:0.23
Consensus pattern (26 bp):
TAATCAGGAAGCTCACAAAGAACCTT
Found at i:13998 original size:13 final size:12
Alignment explanation
Indices: 13980--14015 Score: 54
Period size: 13 Copynumber: 2.9 Consensus size: 12
13970 GATTTATAGC
13980 TTTTATTTTTTT
1 TTTTATTTTTTT
*
13992 TTGTTATTTTTAT
1 TT-TTATTTTTTT
14005 TTTTATTTTTT
1 TTTTATTTTTT
14016 ACAAACAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
12 10 0.48
13 11 0.52
ACGTcount: A:0.11, C:0.00, G:0.03, T:0.86
Consensus pattern (12 bp):
TTTTATTTTTTT
Found at i:14004 original size:6 final size:6
Alignment explanation
Indices: 13980--14014 Score: 52
Period size: 6 Copynumber: 5.7 Consensus size: 6
13970 GATTTATAGC
*
13980 TTTTAT TTTTTT TTGTTAT TTTTAT TTTTAT TTTT
1 TTTTAT TTTTAT TT-TTAT TTTTAT TTTTAT TTTT
14015 TACAAACAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
6 21 0.81
7 5 0.19
ACGTcount: A:0.11, C:0.00, G:0.03, T:0.86
Consensus pattern (6 bp):
TTTTAT
Found at i:14626 original size:3 final size:3
Alignment explanation
Indices: 14612--14664 Score: 54
Period size: 3 Copynumber: 17.3 Consensus size: 3
14602 AAATTGTTAT
* *
14612 TTA TTA TCA TTA TTA TTA TTA TTTA TTA TTA TTA TCT- TTA TTT TTA
1 TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA T-TA TTA TTA TTA
*
14658 TTT TTA T
1 TTA TTA T
14665 ATTCATGCGC
Statistics
Matches: 41, Mismatches: 6, Indels: 6
0.77 0.11 0.11
Matches are distributed among these distances:
2 1 0.02
3 36 0.88
4 4 0.10
ACGTcount: A:0.26, C:0.04, G:0.00, T:0.70
Consensus pattern (3 bp):
TTA
Found at i:14634 original size:22 final size:22
Alignment explanation
Indices: 14608--14659 Score: 72
Period size: 22 Copynumber: 2.4 Consensus size: 22
14598 TAGAAAATTG
14608 TTATTTATTATCATTAT-TATTA
1 TTATTTATTATCATTATCT-TTA
*
14630 TTATTTATTATTATTATCTTTA
1 TTATTTATTATCATTATCTTTA
14652 TT-TTTATT
1 TTATTTATT
14660 TTTATATTCA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
21 6 0.21
22 21 0.75
23 1 0.04
ACGTcount: A:0.27, C:0.04, G:0.00, T:0.69
Consensus pattern (22 bp):
TTATTTATTATCATTATCTTTA
Found at i:14646 original size:28 final size:27
Alignment explanation
Indices: 14612--14664 Score: 79
Period size: 28 Copynumber: 1.9 Consensus size: 27
14602 AAATTGTTAT
14612 TTATTATCATTATTATTATTATTTATTA
1 TTATTATCATTATTATTATT-TTTATTA
* *
14640 TTATTATCTTTATTTTTATTTTTAT
1 TTATTATCATTATTATTATTTTTAT
14665 ATTCATGCGC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
27 5 0.22
28 18 0.78
ACGTcount: A:0.26, C:0.04, G:0.00, T:0.70
Consensus pattern (27 bp):
TTATTATCATTATTATTATTTTTATTA
Found at i:15101 original size:23 final size:23
Alignment explanation
Indices: 15075--15118 Score: 56
Period size: 23 Copynumber: 1.9 Consensus size: 23
15065 CGATTTTGTT
15075 TATT-CATT-TATTCATATTATTTC
1 TATTCCATTGTATT-AT-TTATTTC
15098 TATTCCATTGTATTATTTATT
1 TATTCCATTGTATTATTTATT
15119 ATTGCATTGT
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
23 9 0.47
24 6 0.32
25 4 0.21
ACGTcount: A:0.25, C:0.11, G:0.02, T:0.61
Consensus pattern (23 bp):
TATTCCATTGTATTATTTATTTC
Found at i:15126 original size:20 final size:20
Alignment explanation
Indices: 15089--15135 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
15079 CATTTATTCA
15089 TATTATTT-CTATTCCATTG
1 TATTATTTACTATTCCATTG
* *
15108 TATTATTTATTATTGCATTG
1 TATTATTTACTATTCCATTG
15128 TA-TATTTA
1 TATTATTTA
15136 ATGTAGCATC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 14 0.56
20 11 0.44
ACGTcount: A:0.26, C:0.09, G:0.06, T:0.60
Consensus pattern (20 bp):
TATTATTTACTATTCCATTG
Found at i:15144 original size:19 final size:20
Alignment explanation
Indices: 15103--15144 Score: 50
Period size: 19 Copynumber: 2.1 Consensus size: 20
15093 ATTTCTATTC
* *
15103 CATTGTATTATTTATTATTG
1 CATTGTATTATTTAATATAG
*
15123 CATTGTA-TATTTAATGTAG
1 CATTGTATTATTTAATATAG
15142 CAT
1 CAT
15145 CACATCATTT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
19 12 0.63
20 7 0.37
ACGTcount: A:0.29, C:0.07, G:0.12, T:0.52
Consensus pattern (20 bp):
CATTGTATTATTTAATATAG
Found at i:17798 original size:44 final size:44
Alignment explanation
Indices: 17720--17804 Score: 109
Period size: 44 Copynumber: 1.9 Consensus size: 44
17710 ACCTCCAACT
* * * *
17720 TGGACAAAGGTAGAAGAAAATATTAGTGGATCCCCTACTCCTAA
1 TGGACAAAGGTAAAAGAAAATATAAATGGATCCCCCACTCCTAA
*
17764 TGGACAAATGTAAAAGAAAATATCAAATGG-TCCCCCACTCC
1 TGGACAAAGGTAAAAGAAAATAT-AAATGGATCCCCCACTCC
17805 CAACGTTGCC
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
44 31 0.89
45 4 0.11
ACGTcount: A:0.40, C:0.21, G:0.18, T:0.21
Consensus pattern (44 bp):
TGGACAAAGGTAAAAGAAAATATAAATGGATCCCCCACTCCTAA
Found at i:19941 original size:42 final size:44
Alignment explanation
Indices: 19876--19960 Score: 122
Period size: 43 Copynumber: 2.0 Consensus size: 44
19866 GCAGGCCACC
19876 TAAAATATACTATCTAAAGAAGTAA-TTTATT-ATTTAATTTAAT
1 TAAAATATACTATCTAAAGAAGTAATTTTATTAATTT-ATTTAAT
* *
19919 TAAAATATAGT-TCTAAATAAGTAATTTTATTAATTTATTTAA
1 TAAAATATACTATCTAAAGAAGTAATTTTATTAATTTATTTAA
19961 ACATAAATTA
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
42 12 0.32
43 22 0.58
44 4 0.11
ACGTcount: A:0.46, C:0.04, G:0.05, T:0.46
Consensus pattern (44 bp):
TAAAATATACTATCTAAAGAAGTAATTTTATTAATTTATTTAAT
Found at i:20164 original size:16 final size:15
Alignment explanation
Indices: 20147--20192 Score: 60
Period size: 13 Copynumber: 3.1 Consensus size: 15
20137 AATTGCATAT
20147 TTTAAAAAATAAATA
1 TTTAAAAAATAAATA
*
20162 TTTATAATAATAAATA
1 TTTA-AAAAATAAATA
20178 --TAAAAAATAAATA
1 TTTAAAAAATAAATA
20191 TT
1 TT
20193 GATAGTAACT
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
13 10 0.38
14 2 0.08
15 4 0.15
16 10 0.38
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (15 bp):
TTTAAAAAATAAATA
Found at i:20582 original size:8 final size:8
Alignment explanation
Indices: 20571--20615 Score: 54
Period size: 8 Copynumber: 5.1 Consensus size: 8
20561 TATATTTAAA
20571 TATATTTT
1 TATATTTT
20579 TATATTTT
1 TATATTTT
20587 TATATTTTT
1 TATA-TTTT
20596 TATAAATTTT
1 TAT--ATTTT
20606 TATATATTT
1 TATAT-TTT
20615 T
1 T
20616 TTTTCAAAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 7
0.82 0.00 0.17
Matches are distributed among these distances:
8 14 0.42
9 11 0.33
10 7 0.21
11 1 0.03
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (8 bp):
TATATTTT
Found at i:20583 original size:10 final size:10
Alignment explanation
Indices: 20556--20616 Score: 74
Period size: 10 Copynumber: 6.4 Consensus size: 10
20546 GTTTTAGTGA
20556 TTTTATATAT
1 TTTTATATAT
**
20566 TTAAATATA-
1 TTTTATATAT
20575 TTTT-TATAT
1 TTTTATATAT
20584 TTTTATAT-T
1 TTTTATATAT
*
20593 TTTTATAAAT
1 TTTTATATAT
20603 TTTTATATAT
1 TTTTATATAT
20613 TTTT
1 TTTT
20617 TTTCAAAATA
Statistics
Matches: 42, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
8 4 0.10
9 14 0.33
10 24 0.57
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (10 bp):
TTTTATATAT
Found at i:20688 original size:25 final size:26
Alignment explanation
Indices: 20634--20690 Score: 64
Period size: 26 Copynumber: 2.2 Consensus size: 26
20624 ATACTATAAG
* *
20634 ATTTTTATATATTTGTAATTGTATGC
1 ATTTTTATATATTTATAATTGTATAC
*
20660 ATTTTTATA-ATTTTATAATT-TATAT
1 ATTTTTATATA-TTTATAATTGTATAC
20685 ATTTTT
1 ATTTTT
20691 TAAAATATTA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
25 10 0.37
26 17 0.63
ACGTcount: A:0.30, C:0.02, G:0.05, T:0.63
Consensus pattern (26 bp):
ATTTTTATATATTTATAATTGTATAC
Found at i:21625 original size:31 final size:30
Alignment explanation
Indices: 21549--21635 Score: 101
Period size: 31 Copynumber: 3.0 Consensus size: 30
21539 TATGTGATAG
* * *
21549 TACAGGGTTTGAATATG-AAATATTAATGA
1 TACATGGTATGAATATGAAAATATGAATGA
21578 TA-ATAGG-AT-AATATGAAAATATGAATGA
1 TACAT-GGTATGAATATGAAAATATGAATGA
21606 TTACATGGTATGAATATGAAAATATGAATG
1 -TACATGGTATGAATATGAAAATATGAATG
21636 GTTGATACCA
Statistics
Matches: 49, Mismatches: 3, Indels: 10
0.79 0.05 0.16
Matches are distributed among these distances:
27 6 0.12
28 13 0.27
29 8 0.16
30 4 0.08
31 18 0.37
ACGTcount: A:0.46, C:0.02, G:0.20, T:0.32
Consensus pattern (30 bp):
TACATGGTATGAATATGAAAATATGAATGA
Found at i:25412 original size:23 final size:23
Alignment explanation
Indices: 25382--25431 Score: 82
Period size: 23 Copynumber: 2.2 Consensus size: 23
25372 TACATACGTA
*
25382 ATCAGGAAGCTCACAAAGAGCCT
1 ATCAGGAAGCTCACAAAAAGCCT
*
25405 ATCAGGAAGCTCACAAAAAGCTT
1 ATCAGGAAGCTCACAAAAAGCCT
25428 ATCA
1 ATCA
25432 TCCATTAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.42, C:0.24, G:0.18, T:0.16
Consensus pattern (23 bp):
ATCAGGAAGCTCACAAAAAGCCT
Found at i:25582 original size:26 final size:26
Alignment explanation
Indices: 25550--25614 Score: 80
Period size: 26 Copynumber: 2.5 Consensus size: 26
25540 ATGAGAGCAA
* *
25550 TAATCAGGAAGTTCAC-AATGAACTTT
1 TAATCAGGAAGCTCACGAA-GAACCTT
*
25576 TAATCAGGAAGCTCACGAAGAGCCTT
1 TAATCAGGAAGCTCACGAAGAACCTT
25602 TAATCAGG-AGCTC
1 TAATCAGGAAGCTC
25615 CGGATAGCCA
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
25 5 0.14
26 28 0.80
27 2 0.06
ACGTcount: A:0.35, C:0.20, G:0.20, T:0.25
Consensus pattern (26 bp):
TAATCAGGAAGCTCACGAAGAACCTT
Found at i:28080 original size:64 final size:65
Alignment explanation
Indices: 27955--28128 Score: 200
Period size: 64 Copynumber: 2.8 Consensus size: 65
27945 GCAAACAAAC
* *
27955 ATTCGAACCACATATGTAT---AATTTACA-ACATTAAATTTCAGCTCAAAGAATTTGTAACCTA
1 ATTCGAACCACATATGTATAGAAAATT-CATACATTAAATTCCAGCTCAAAGAATTTGTAACCTA
28016 T
65 T
* *
28017 ATTCGAACCTCATATGTATGGAAAATTCATACATTAAATTCCA-CTCAAA-AATTTTGTAACCTA
1 ATTCGAACCACATATGTATAGAAAATTCATACATTAAATTCCAGCTCAAAGAA-TTTGTAACCTA
28080 T
65 T
* * * * *
28081 ATTTGAACCACATATGTATATATAATTCATACATTGAA-TACAGCTCAA
1 ATTCGAACCACATATGTATAGAAAATTCATACATTAAATTCCAGCTCAA
28129 GAACTTTAAA
Statistics
Matches: 96, Mismatches: 10, Indels: 10
0.83 0.09 0.09
Matches are distributed among these distances:
62 18 0.19
63 5 0.05
64 57 0.59
65 16 0.17
ACGTcount: A:0.40, C:0.18, G:0.08, T:0.34
Consensus pattern (65 bp):
ATTCGAACCACATATGTATAGAAAATTCATACATTAAATTCCAGCTCAAAGAATTTGTAACCTAT
Found at i:28248 original size:21 final size:22
Alignment explanation
Indices: 28207--28249 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
28197 TCAAAGAACT
28207 TATATCATACATTCAAACTTTA
1 TATATCATACATTCAAACTTTA
28229 TATAT-ATA-ATTCACAACTTTA
1 TATATCATACATTCA-AACTTTA
28250 AATTCAACTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
20 5 0.25
21 10 0.50
22 5 0.25
ACGTcount: A:0.42, C:0.16, G:0.00, T:0.42
Consensus pattern (22 bp):
TATATCATACATTCAAACTTTA
Found at i:35941 original size:63 final size:65
Alignment explanation
Indices: 35829--35974 Score: 199
Period size: 63 Copynumber: 2.3 Consensus size: 65
35819 TATATTTACA
* * * *
35829 ACATTAAATTTCAGCTCAAAGAATTTGTAACCTATATTCGAACCTCATATGTATGTAAAATTCAT
1 ACATTAAATTCCAGCTCAAAGAATTTGTAACCTATATTCGAAACACATATGTATATAAAATTCAT
* * *
35894 ACATTAAATTCCA-CTCAAA-ACTTTGTAACCTATATTTGAAACACATATGTATATATAATTCAT
1 ACATTAAATTCCAGCTCAAAGAATTTGTAACCTATATTCGAAACACATATGTATATAAAATTCAT
*
35957 ACATTAAA-TACAGCTCAA
1 ACATTAAATTCCAGCTCAA
35975 GAACTTTAAA
Statistics
Matches: 72, Mismatches: 8, Indels: 4
0.86 0.10 0.05
Matches are distributed among these distances:
62 3 0.04
63 51 0.71
64 6 0.08
65 12 0.17
ACGTcount: A:0.41, C:0.18, G:0.07, T:0.34
Consensus pattern (65 bp):
ACATTAAATTCCAGCTCAAAGAATTTGTAACCTATATTCGAAACACATATGTATATAAAATTCAT
Found at i:35991 original size:63 final size:61
Alignment explanation
Indices: 35829--36013 Score: 167
Period size: 63 Copynumber: 2.9 Consensus size: 61
35819 TATATTTACA
* * * * * *
35829 ACATTAAATTTCAGCTCAAAGAATTTGTAACCTATATTCGAACCTCATATGTATGTAAAATTCAT
1 ACATTAAATTACA-CTCAAA-ACTTTGAAACATATATTCGAA-C-CATATGTATATATAATTCAT
* * * *
35894 ACATTAAATTCCACTCAAAACTTTGTAACCTATATTTGAAACACATATGTATATATAATTCAT
1 ACATTAAATTACACTCAAAACTTTGAAACATATATTCG-AAC-CATATGTATATATAATTCAT
*
35957 ACATTAAA-TACAGCTCAAGAACTTT-AAATATATATTCGAACCATATGTGCATATATA
1 ACATTAAATTACA-CTCAA-AACTTTGAAACATATATTCGAACCATATGT--ATATATA
36014 TATAAAATTC
Statistics
Matches: 104, Mismatches: 11, Indels: 12
0.82 0.09 0.09
Matches are distributed among these distances:
61 7 0.07
62 6 0.06
63 65 0.62
64 14 0.13
65 12 0.12
ACGTcount: A:0.41, C:0.17, G:0.08, T:0.35
Consensus pattern (61 bp):
ACATTAAATTACACTCAAAACTTTGAAACATATATTCGAACCATATGTATATATAATTCAT
Found at i:36092 original size:21 final size:22
Alignment explanation
Indices: 36051--36093 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
36041 TCAAAGAACT
36051 TATATCATACATTCAAACTTTA
1 TATATCATACATTCAAACTTTA
36073 TATAT-ATA-ATTCACAACTTTA
1 TATATCATACATTCA-AACTTTA
36094 AATTCAACTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
20 5 0.25
21 10 0.50
22 5 0.25
ACGTcount: A:0.42, C:0.16, G:0.00, T:0.42
Consensus pattern (22 bp):
TATATCATACATTCAAACTTTA
Found at i:36700 original size:28 final size:28
Alignment explanation
Indices: 36669--36722 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 28
36659 CATGCATTTC
* *
36669 ATTTA-TTTCATATTTTAGTCCCTAAAAA
1 ATTTATTTTCACAATTTAG-CCCTAAAAA
36697 ATTTATTTTCACAATTTAGCCCTAAA
1 ATTTATTTTCACAATTTAGCCCTAAA
36723 TACTCAAGTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
28 12 0.52
29 11 0.48
ACGTcount: A:0.35, C:0.17, G:0.04, T:0.44
Consensus pattern (28 bp):
ATTTATTTTCACAATTTAGCCCTAAAAA
Done.