Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3746
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: 167119
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Found at i:3446 original size:13 final size:13
Alignment explanation
Indices: 3428--3459 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
3418 TTTCCAGCAA
3428 TTATGAATTTATT
1 TTATGAATTTATT
3441 TTATGAATTTATT
1 TTATGAATTTATT
*
3454 TGATGA
1 TTATGA
3460 TGATCCAAGC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.31, C:0.00, G:0.12, T:0.56
Consensus pattern (13 bp):
TTATGAATTTATT
Found at i:3679 original size:50 final size:50
Alignment explanation
Indices: 3557--3794 Score: 295
Period size: 50 Copynumber: 4.7 Consensus size: 50
3547 GGGTAAGAGA
*
3557 CCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTAAGATCATGAGAGGTC
1 CCATGTAAGACCATGTCTGGGACATGGCATTGGCA-CC-GAGA-C--GAGAGGTC
* *
3612 CCCTGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACGAGAGGTC
1 CCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGACGAGAGGTC
* *
3662 CCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAGAGGTC
1 CCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGACGAGAGGTC
* * **
3712 CC-TATAAGACCATGTCTGGGACATGGCA-TGGCACC-ATCACGAGAACAT-
1 CCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGA-GACGAG-AGGTC
*
3760 CCATGTAAGACCATGTCTGGGACATGGCTTTGGCA
1 CCATGTAAGACCATGTCTGGGACATGGCATTGGCA
3795 TGTTATTATC
Statistics
Matches: 164, Mismatches: 15, Indels: 13
0.85 0.08 0.07
Matches are distributed among these distances:
47 1 0.01
48 13 0.08
49 50 0.30
50 61 0.37
52 1 0.01
53 3 0.02
54 2 0.01
55 33 0.20
ACGTcount: A:0.26, C:0.24, G:0.29, T:0.21
Consensus pattern (50 bp):
CCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGACGAGAGGTC
Found at i:3781 original size:98 final size:103
Alignment explanation
Indices: 3557--3795 Score: 330
Period size: 98 Copynumber: 2.3 Consensus size: 103
3547 GGGTAAGAGA
*
3557 CCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTAAGATCATGAGAGGTCCCCTGTAAGA
1 CCATGTAAGACCATGTCTGGGACATGGCATTGGCATCC--AGATCATGAGAGGTCCCCTATAAGA
* **
3622 CCATGTCTGGGACATGGCATGGGCACCGAGACGAGAGGTC
64 CCATGTCTGGGACATGGCATGGGCACCGACACGAGACATC
* *
3662 CCATGTAAGACCATGTCTGGGACATGGCGTTGGCA-CC-GA-GATGAGAGGT-CCCTATAAGACC
1 CCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCAGATCATGAGAGGTCCCCTATAAGACC
3723 ATGTCTGGGACATGGCAT-GGCACC-ATCACGAGAACAT-
66 ATGTCTGGGACATGGCATGGGCACCGA-CACGAG-ACATC
*
3760 CCATGTAAGACCATGTCTGGGACATGGCTTTGGCAT
1 CCATGTAAGACCATGTCTGGGACATGGCATTGGCAT
3796 GTTATTATCA
Statistics
Matches: 124, Mismatches: 7, Indels: 12
0.87 0.05 0.08
Matches are distributed among these distances:
97 1 0.01
98 45 0.36
99 31 0.25
100 9 0.07
101 2 0.02
104 2 0.02
105 34 0.27
ACGTcount: A:0.26, C:0.24, G:0.29, T:0.21
Consensus pattern (103 bp):
CCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCAGATCATGAGAGGTCCCCTATAAGACC
ATGTCTGGGACATGGCATGGGCACCGACACGAGACATC
Found at i:8062 original size:10 final size:11
Alignment explanation
Indices: 8042--8079 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
8032 CTATATATTT
*
8042 AAAACATATAA
1 AAAATATATAA
8053 AAAATA-ATAA
1 AAAATATATAA
8063 TAAAATATATAA
1 -AAAATATATAA
8075 AAAAT
1 AAAAT
8080 TACCTTTTTC
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
10 4 0.17
11 16 0.67
12 4 0.17
ACGTcount: A:0.74, C:0.03, G:0.00, T:0.24
Consensus pattern (11 bp):
AAAATATATAA
Found at i:23772 original size:55 final size:50
Alignment explanation
Indices: 23703--23941 Score: 245
Period size: 50 Copynumber: 4.7 Consensus size: 50
23693 GTAAAGAGAT
23703 CCATGTAAGACCATGTCT-GGACATGGCATTGGCATCCTTAAGATCATGAGAGGTC
1 CCATGTAAGACCATGTCTGGGACATGGCATTGGCA-CC--AAGA-C--GAGAGGTC
* * *
23758 CCCTGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACGAGAGGTC
1 CCATGTAAGACCATGTCTGGGACATGGCATTGGCACCAAGACGAGAGGTC
* * *
23808 CCATGTAAGACCATGTCTGGGA-ATGGCGTTGGCACCGAGATG-GAAGGTC
1 CCATGTAAGACCATGTCTGGGACATGGCATTGGCACCAAGACGAG-AGGTC
* * ** **
23857 CC-TATAA-ACCATGTCTGGGACATGGCATGGGCACCATCACGAGAACATC
1 CCATGTAAGACCATGTCTGGGACATGGCATTGGCACCAAGACGAG-AGGTC
*
23906 CCATGTAAGACCATGTTCTGGGACATGGCTTTGGCA
1 CCATGTAAGACCATG-TCTGGGACATGGCATTGGCA
23942 TGTTATTATC
Statistics
Matches: 158, Mismatches: 19, Indels: 17
0.81 0.10 0.09
Matches are distributed among these distances:
47 13 0.08
48 19 0.12
49 31 0.20
50 33 0.21
51 6 0.04
52 19 0.12
53 3 0.02
55 19 0.12
56 15 0.09
ACGTcount: A:0.26, C:0.24, G:0.29, T:0.21
Consensus pattern (50 bp):
CCATGTAAGACCATGTCTGGGACATGGCATTGGCACCAAGACGAGAGGTC
Found at i:23808 original size:50 final size:51
Alignment explanation
Indices: 23703--23934 Score: 246
Period size: 49 Copynumber: 4.5 Consensus size: 51
23693 GTAAAGAGAT
* *
23703 CCATGTAAGACCATGTCT-GGACATGGCATTGGCATCCTTAAGATC-ATGAGAGGTC
1 CCATGTAAGACCATGTCTGGGACATGGCATGGGCA-CC--GAGA-CGA-GA-AGGTC
*
23758 CCCTGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACGAG-AGGTC
1 CCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACGAGAAGGTC
* * *
23808 CCATGTAAGACCATGTCTGGGA-ATGGCGTTGGCACCGAGATG-GAAGGTC
1 CCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACGAGAAGGTC
* * **
23857 CC-TATAA-ACCATGTCTGGGACATGGCATGGGCACC-ATCACGAGAACATC
1 CCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGA-GACGAGAAGGTC
23906 CCATGTAAGACCATGTTCTGGGACATGGC
1 CCATGTAAGACCATG-TCTGGGACATGGC
23935 TTTGGCATGT
Statistics
Matches: 153, Mismatches: 15, Indels: 21
0.81 0.08 0.11
Matches are distributed among these distances:
47 14 0.09
48 19 0.12
49 31 0.20
50 30 0.20
51 6 0.04
52 15 0.10
53 4 0.03
55 19 0.12
56 15 0.10
ACGTcount: A:0.26, C:0.24, G:0.29, T:0.21
Consensus pattern (51 bp):
CCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACGAGAAGGTC
Found at i:23882 original size:97 final size:105
Alignment explanation
Indices: 23703--23942 Score: 302
Period size: 97 Copynumber: 2.3 Consensus size: 105
23693 GTAAAGAGAT
* *
23703 CCATGTAAGACCATGTCT-GGACATGGCATTGGCATCCTTAAGATCATGAGAGGTCCCCTGTAAG
1 CCATGTAAGACCATGTCTGGGACATGGCATTGGCATCC-TAAGAT-AGGAGAGGTCCCCTATAAG
* **
23767 ACCATGTCTGGGACATGGCATGGGCACCGA-GACGAG-AGGTC
64 ACCATGTCTGGGACATGGCATGGGCACC-ATCACGAGAACATC
* *
23808 CCATGTAAGACCATGTCTGGGA-ATGGCGTTGGCA-CC-GAGAT-GGA-AGGT-CCCTATAA-AC
1 CCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTAAGATAGGAGAGGTCCCCTATAAGAC
23866 CATGTCTGGGACATGGCATGGGCACCATCACGAGAACATC
66 CATGTCTGGGACATGGCATGGGCACCATCACGAGAACATC
*
23906 CCATGTAAGACCATGTTCTGGGACATGGCTTTGGCAT
1 CCATGTAAGACCATG-TCTGGGACATGGCATTGGCAT
23943 GTTATTATCA
Statistics
Matches: 121, Mismatches: 8, Indels: 16
0.83 0.06 0.11
Matches are distributed among these distances:
96 1 0.01
97 33 0.27
98 25 0.21
99 11 0.09
100 13 0.11
102 4 0.03
104 2 0.02
105 29 0.24
106 3 0.02
ACGTcount: A:0.26, C:0.24, G:0.29, T:0.22
Consensus pattern (105 bp):
CCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTAAGATAGGAGAGGTCCCCTATAAGAC
CATGTCTGGGACATGGCATGGGCACCATCACGAGAACATC
Found at i:26072 original size:23 final size:23
Alignment explanation
Indices: 26045--26089 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
26035 AGGTACTCTG
26045 TGTACCG-ATACTGTTACTGTTAT
1 TGTACCGCA-ACTGTTACTGTTAT
*
26068 TGTACTGCAACTGTTACTGTTA
1 TGTACCGCAACTGTTACTGTTA
26090 CGGTGTATTC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 19 0.95
24 1 0.05
ACGTcount: A:0.22, C:0.18, G:0.18, T:0.42
Consensus pattern (23 bp):
TGTACCGCAACTGTTACTGTTAT
Found at i:28360 original size:10 final size:11
Alignment explanation
Indices: 28339--28379 Score: 50
Period size: 10 Copynumber: 3.9 Consensus size: 11
28329 CCCCCCTCCC
28339 TTCTCTCTTCT
1 TTCTCTCTTCT
28350 TTCTC-CTTCT
1 TTCTCTCTTCT
* *
28360 TT-TTTTTTCT
1 TTCTCTCTTCT
28370 TTCTCTCTTC
1 TTCTCTCTTC
28380 AAAATGATTT
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
9 1 0.04
10 13 0.54
11 10 0.42
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (11 bp):
TTCTCTCTTCT
Found at i:32621 original size:29 final size:30
Alignment explanation
Indices: 32562--32619 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
32552 TCCGAGCCTT
*
32562 GGGGCAAAAATGTAATTATGTAAAAGTTTA
1 GGGGCAAAAATGTAATTATGAAAAAGTTTA
* *
32592 GGGGCAAAATTGTAATTTTGAAAAAGTT
1 GGGGCAAAAATGTAATTATGAAAAAGTT
32620 AGAGTCGAGG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.41, C:0.03, G:0.24, T:0.31
Consensus pattern (30 bp):
GGGGCAAAAATGTAATTATGAAAAAGTTTA
Found at i:32848 original size:13 final size:13
Alignment explanation
Indices: 32830--32861 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
32820 TTTCCAGCAA
32830 TTATGAATTTATT
1 TTATGAATTTATT
32843 TTATGAATTTATT
1 TTATGAATTTATT
*
32856 TGATGA
1 TTATGA
32862 TGATCCAAGC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.31, C:0.00, G:0.12, T:0.56
Consensus pattern (13 bp):
TTATGAATTTATT
Found at i:33046 original size:50 final size:50
Alignment explanation
Indices: 32955--33195 Score: 270
Period size: 50 Copynumber: 4.7 Consensus size: 50
32945 CATTTGGGTA
* * *
32955 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTTAAGATCATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATCGGCA-CC----GA-GATG
* * *
33011 AGAGGTCCCCTGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATCGGCACCGAGATG
* *
33061 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATCGGCACCGAGATG
* * * *
33111 AGAGGTCCC-TATAAGACCATGTCTGGGACATGGCATGGGCACC-ATCACG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATCGGCACCGA-GATG
**
33160 AGAACATCCCATGTAAGACCATGTCTGGGACATGGC
1 AG-AGGTCCCATGTAAGACCATGTCTGGGACATGGC
33196 TTTGGCATGT
Statistics
Matches: 165, Mismatches: 17, Indels: 11
0.85 0.09 0.06
Matches are distributed among these distances:
48 1 0.01
49 35 0.21
50 62 0.38
51 26 0.16
55 2 0.01
56 39 0.24
ACGTcount: A:0.27, C:0.24, G:0.29, T:0.20
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATCGGCACCGAGATG
Found at i:33161 original size:99 final size:103
Alignment explanation
Indices: 32955--33203 Score: 355
Period size: 100 Copynumber: 2.4 Consensus size: 103
32945 CATTTGGGTA
32955 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTTAAGATCATGAGAGGTCCC
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCC---AGATCATGAGAGGTCCC
* *
33020 CTGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
63 CTATAAGACCATGTCTGGGACATGGCATGGGCACCGACACG
* * *
33061 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCA-CC-GA-GATGAGAGGT-CCCTA
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCAGATCATGAGAGGTCCCCTA
33122 TAAGACCATGTCTGGGACATGGCATGGGCACC-ATCACG
66 TAAGACCATGTCTGGGACATGGCATGGGCACCGA-CACG
* *
33160 AGAACATCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCAT
1 AG-AGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCAT
33204 GTTATTATCA
Statistics
Matches: 132, Mismatches: 8, Indels: 11
0.87 0.05 0.07
Matches are distributed among these distances:
98 1 0.01
99 41 0.31
100 46 0.35
101 2 0.02
105 2 0.02
106 40 0.30
ACGTcount: A:0.26, C:0.24, G:0.29, T:0.21
Consensus pattern (103 bp):
AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCAGATCATGAGAGGTCCCCTA
TAAGACCATGTCTGGGACATGGCATGGGCACCGACACG
Found at i:35346 original size:6 final size:6
Alignment explanation
Indices: 35335--35373 Score: 51
Period size: 6 Copynumber: 6.5 Consensus size: 6
35325 TGTGTACCGA
* * *
35335 TACTGT TACTGT TATTGT TACTGC AACTGT TACTGT TAC
1 TACTGT TACTGT TACTGT TACTGT TACTGT TACTGT TAC
35374 GGTGTATTCC
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.21, C:0.18, G:0.15, T:0.46
Consensus pattern (6 bp):
TACTGT
Found at i:42573 original size:20 final size:20
Alignment explanation
Indices: 42548--42587 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
42538 TTGCCAAAAG
42548 GTAAATGAAAGCTTCTATTT
1 GTAAATGAAAGCTTCTATTT
42568 GTAAATGAAAGCTTCTATTT
1 GTAAATGAAAGCTTCTATTT
42588 TCGCTCTCTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.35, C:0.10, G:0.15, T:0.40
Consensus pattern (20 bp):
GTAAATGAAAGCTTCTATTT
Found at i:45042 original size:15 final size:15
Alignment explanation
Indices: 45022--45050 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
45012 TCGTCCTCAG
45022 CCTCTCCTTCATCTC
1 CCTCTCCTTCATCTC
45037 CCTCTCCTTCATCT
1 CCTCTCCTTCATCT
45051 TCTTTGTCTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.07, C:0.52, G:0.00, T:0.41
Consensus pattern (15 bp):
CCTCTCCTTCATCTC
Found at i:51601 original size:16 final size:17
Alignment explanation
Indices: 51562--51602 Score: 59
Period size: 16 Copynumber: 2.5 Consensus size: 17
51552 ATAGTAAAAA
51562 TATAATTTTATTATTTT
1 TATAATTTTATTATTTT
*
51579 AAT-ATTTTA-TATTTT
1 TATAATTTTATTATTTT
51594 TATAATTTT
1 TATAATTTT
51603 TAAAAGATTA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
15 8 0.38
16 11 0.52
17 2 0.10
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (17 bp):
TATAATTTTATTATTTT
Found at i:51624 original size:46 final size:46
Alignment explanation
Indices: 51532--51632 Score: 109
Period size: 46 Copynumber: 2.2 Consensus size: 46
51522 GGAGCTAAAA
* **
51532 TTAA-ATTTTATATTTTTATAATAGTAAAAATATAATTTTATTATT
1 TTAATATTTTATATTTTTATAATAGTAAAAATATAATATTAAAATT
**
51577 TTAATATTTTATATTTTTATAATTTTTAAAAGAT-TAA-ATTAAAATT
1 TTAATATTTTATATTTTTATAA-TAGTAAAA-ATATAATATTAAAATT
*
51623 TTATTATTTT
1 TTAATATTTT
51633 CAAAAATAAA
Statistics
Matches: 47, Mismatches: 6, Indels: 5
0.81 0.10 0.09
Matches are distributed among these distances:
45 4 0.09
46 32 0.68
47 9 0.19
48 2 0.04
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (46 bp):
TTAATATTTTATATTTTTATAATAGTAAAAATATAATATTAAAATT
Found at i:51632 original size:30 final size:28
Alignment explanation
Indices: 51591--51654 Score: 74
Period size: 30 Copynumber: 2.2 Consensus size: 28
51581 TATTTTATAT
* *
51591 TTTTATAATTTTTAAAAGATTAAATTAAAA
1 TTTTATAATTTTCAAAA-A-TAAAATAAAA
* *
51621 TTTTATTATTTTCAAAAATAAAATATAA
1 TTTTATAATTTTCAAAAATAAAATAAAA
51649 TTTTAT
1 TTTTAT
51655 CGTTACTAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
28 14 0.47
29 1 0.03
30 15 0.50
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.50
Consensus pattern (28 bp):
TTTTATAATTTTCAAAAATAAAATAAAA
Found at i:53169 original size:24 final size:23
Alignment explanation
Indices: 53142--53187 Score: 65
Period size: 24 Copynumber: 2.0 Consensus size: 23
53132 AGAGAGCAGG
*
53142 GGAAAGAAAGAAGGAAGGGAAAAA
1 GGAAAGAAAGAA-AAAGGGAAAAA
*
53166 GGAAAGAAGGAAAAAGGGAAAA
1 GGAAAGAAAGAAAAAGGGAAAA
53188 TTAGATTTCA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 9 0.45
24 11 0.55
ACGTcount: A:0.63, C:0.00, G:0.37, T:0.00
Consensus pattern (23 bp):
GGAAAGAAAGAAAAAGGGAAAAA
Found at i:54893 original size:45 final size:45
Alignment explanation
Indices: 54829--54925 Score: 149
Period size: 45 Copynumber: 2.2 Consensus size: 45
54819 ATGTGTCGGC
* * *
54829 TACTGTTACTGTTACCGATTCGGCACTTTGTGTGTCGAATATTGT
1 TACTGTTACCGTTACCGATTCAGCACTTTGTGTGTCGAATACTGT
* *
54874 TACTGTTACCGTTATCGATTCAGCACTTTGTGTGTTGAATACTGT
1 TACTGTTACCGTTACCGATTCAGCACTTTGTGTGTCGAATACTGT
54919 TACTGTT
1 TACTGTT
54926 GCTGTTCTGA
Statistics
Matches: 47, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
45 47 1.00
ACGTcount: A:0.19, C:0.18, G:0.21, T:0.43
Consensus pattern (45 bp):
TACTGTTACCGTTACCGATTCAGCACTTTGTGTGTCGAATACTGT
Found at i:56401 original size:29 final size:30
Alignment explanation
Indices: 56364--56420 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
56354 TCCGAGCCTT
*
56364 GGGGAAAAA-TGTAATTATGTAAAAGTTTA
1 GGGGAAAAATTGTAATTATGAAAAAGTTTA
* *
56393 GGGGCAAAATTGTAATTTTGAAAAAGTT
1 GGGGAAAAATTGTAATTATGAAAAAGTT
56421 AGAGTCGAGG
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 8 0.33
30 16 0.67
ACGTcount: A:0.42, C:0.02, G:0.25, T:0.32
Consensus pattern (30 bp):
GGGGAAAAATTGTAATTATGAAAAAGTTTA
Found at i:56650 original size:13 final size:13
Alignment explanation
Indices: 56632--56663 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
56622 TTTCCAGCAA
56632 TTATGAATTTATT
1 TTATGAATTTATT
56645 TTATGAATTTATT
1 TTATGAATTTATT
*
56658 TGATGA
1 TTATGA
56664 TGATCCAAGC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.31, C:0.00, G:0.12, T:0.56
Consensus pattern (13 bp):
TTATGAATTTATT
Found at i:56871 original size:50 final size:50
Alignment explanation
Indices: 56758--56999 Score: 297
Period size: 50 Copynumber: 4.7 Consensus size: 50
56748 ATTTGGGTAA
* * *
56758 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTTAAGATCATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCA-CC--GAGA-C--G
*
56814 AGAGGTCCCCTGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
* * *
56864 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
* * *
56914 AGAGGTCCCCTATAAGACCATGTCTGGGACATGGCATGGGCACC-ATCACG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGA-GACG
**
56964 AGAACATCCCATGTAAGACCATGTCTGGGACATGGC
1 AG-AGGTCCCATGTAAGACCATGTCTGGGACATGGC
57000 TTTGGCATGT
Statistics
Matches: 166, Mismatches: 18, Indels: 9
0.86 0.09 0.05
Matches are distributed among these distances:
49 1 0.01
50 91 0.55
51 29 0.17
52 1 0.01
53 3 0.02
55 2 0.01
56 39 0.23
ACGTcount: A:0.26, C:0.24, G:0.29, T:0.20
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
Found at i:56947 original size:100 final size:103
Alignment explanation
Indices: 56758--57007 Score: 364
Period size: 100 Copynumber: 2.4 Consensus size: 103
56748 ATTTGGGTAA
56758 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTTAAGATCATGAGAGGTCCC
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCC---AGATCATGAGAGGTCCC
* *
56823 CTGTAAGACCATGTCTGGGACATGGCATGGGCACCGA-GACG
63 CTATAAGACCATGTCTGGGACATGGCATGGGCACC-ATCACG
* * *
56864 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCA-CC-GA-GATGAGAGGTCCCCTA
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCAGATCATGAGAGGTCCCCTA
56926 TAAGACCATGTCTGGGACATGGCATGGGCACCATCACG
66 TAAGACCATGTCTGGGACATGGCATGGGCACCATCACG
* *
56964 AGAACATCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCAT
1 AG-AGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCAT
57008 GTTATTATCA
Statistics
Matches: 133, Mismatches: 8, Indels: 10
0.88 0.05 0.07
Matches are distributed among these distances:
99 1 0.01
100 51 0.38
101 39 0.29
105 2 0.02
106 40 0.30
ACGTcount: A:0.26, C:0.24, G:0.29, T:0.21
Consensus pattern (103 bp):
AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCAGATCATGAGAGGTCCCCTA
TAAGACCATGTCTGGGACATGGCATGGGCACCATCACG
Found at i:61672 original size:29 final size:29
Alignment explanation
Indices: 61639--61702 Score: 76
Period size: 30 Copynumber: 2.2 Consensus size: 29
61629 TAATCCACCA
61639 CCCAACTTTTTG-AAAATTACAATTTTGCC
1 CCCAAC-TTTTGCAAAATTACAATTTTGCC
* * *
61668 CCCAAACTTTTGCATAATTACACTTTTGTC
1 CCC-AACTTTTGCAAAATTACAATTTTGCC
61698 CCCAA
1 CCCAA
61703 GCTCGAAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
29 10 0.33
30 20 0.67
ACGTcount: A:0.30, C:0.28, G:0.06, T:0.36
Consensus pattern (29 bp):
CCCAACTTTTGCAAAATTACAATTTTGCC
Found at i:61676 original size:30 final size:30
Alignment explanation
Indices: 61646--61702 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
61636 CCACCCAACT
61646 TTTTG-AAAATTACAATTTTGCCCCCAAAC
1 TTTTGCAAAATTACAATTTTGCCCCCAAAC
* * *
61675 TTTTGCATAATTACACTTTTGTCCCCAA
1 TTTTGCAAAATTACAATTTTGCCCCCAA
61703 GCTCGAAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 5 0.21
30 19 0.79
ACGTcount: A:0.30, C:0.25, G:0.07, T:0.39
Consensus pattern (30 bp):
TTTTGCAAAATTACAATTTTGCCCCCAAAC
Found at i:72513 original size:114 final size:114
Alignment explanation
Indices: 72313--72541 Score: 440
Period size: 114 Copynumber: 2.0 Consensus size: 114
72303 AAATTCATCC
*
72313 TGCCTCACCTCACCTTATCTTATCCCACCCAACATCCACTTTTCAAAAAGAAAAAAACTCAATCT
1 TGCCTCACCTCACCTTATCTTATCCCACACAACATCCACTTTTCAAAAAGAAAAAAACTCAATCT
72378 ATCAAGTAAGGATTAATTCGAAATAAATTGGATCATTCGAGTTTTGTTA
66 ATCAAGTAAGGATTAATTCGAAATAAATTGGATCATTCGAGTTTTGTTA
*
72427 TGCCTCACCTCACCTTATCTTATCCCACACTACATCCACTTTTCAAAAAGAAAAAAACTCAATCT
1 TGCCTCACCTCACCTTATCTTATCCCACACAACATCCACTTTTCAAAAAGAAAAAAACTCAATCT
72492 ATCAAGTAAGGATTAATTCGAAATAAATTGGATCATTCGAGTTTTGTTA
66 ATCAAGTAAGGATTAATTCGAAATAAATTGGATCATTCGAGTTTTGTTA
72541 T
1 T
72542 TCCTATTTTC
Statistics
Matches: 113, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
114 113 1.00
ACGTcount: A:0.36, C:0.23, G:0.10, T:0.31
Consensus pattern (114 bp):
TGCCTCACCTCACCTTATCTTATCCCACACAACATCCACTTTTCAAAAAGAAAAAAACTCAATCT
ATCAAGTAAGGATTAATTCGAAATAAATTGGATCATTCGAGTTTTGTTA
Found at i:73084 original size:21 final size:22
Alignment explanation
Indices: 73058--73111 Score: 76
Period size: 21 Copynumber: 2.5 Consensus size: 22
73048 AACAGCGGTG
73058 GCGGTGAGATTAAG-TACTGTA
1 GCGGTGAGATTAAGATACTGTA
*
73079 GCGGTGAGATT-GGATACTGTA
1 GCGGTGAGATTAAGATACTGTA
*
73100 GCAGTGAGATTA
1 GCGGTGAGATTA
73112 GAAACAGCAG
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
20 1 0.03
21 28 0.97
ACGTcount: A:0.28, C:0.09, G:0.35, T:0.28
Consensus pattern (22 bp):
GCGGTGAGATTAAGATACTGTA
Found at i:73249 original size:19 final size:18
Alignment explanation
Indices: 73225--73271 Score: 58
Period size: 19 Copynumber: 2.6 Consensus size: 18
73215 CGAAGTTTTT
*
73225 AAAATTATTTAACAATTA
1 AAAATTATTAAACAATTA
* *
73243 CAAAATTAATAAAGAATTA
1 -AAAATTATTAAACAATTA
73262 AAAATTATTA
1 AAAATTATTA
73272 CAATTATATT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
18 9 0.38
19 15 0.62
ACGTcount: A:0.60, C:0.04, G:0.02, T:0.34
Consensus pattern (18 bp):
AAAATTATTAAACAATTA
Found at i:73320 original size:30 final size:30
Alignment explanation
Indices: 73280--73336 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
73270 TACAATTATA
*
73280 TTTATTTGTATTGC-TCTTACAAAAATACCT
1 TTTATGTGTATTGCGT-TTACAAAAATACCT
73310 TTTATGTGTATTGCGTTTACAAAAATA
1 TTTATGTGTATTGCGTTTACAAAAATA
73337 TTGAATATAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
30 24 0.96
31 1 0.04
ACGTcount: A:0.32, C:0.12, G:0.11, T:0.46
Consensus pattern (30 bp):
TTTATGTGTATTGCGTTTACAAAAATACCT
Found at i:76348 original size:6 final size:6
Alignment explanation
Indices: 76337--76362 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
76327 TTTGCAACCA
76337 AAGGGG AAGGGG AAGGGG AAGGGG AA
1 AAGGGG AAGGGG AAGGGG AAGGGG AA
76363 AGGAGAGAAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.38, C:0.00, G:0.62, T:0.00
Consensus pattern (6 bp):
AAGGGG
Found at i:86521 original size:21 final size:20
Alignment explanation
Indices: 86495--86539 Score: 72
Period size: 21 Copynumber: 2.2 Consensus size: 20
86485 CAACGTGGCA
86495 AGTTAACTGGCCACATCAGC
1 AGTTAACTGGCCACATCAGC
*
86515 TAGTTAACTTGCCACATCAGC
1 -AGTTAACTGGCCACATCAGC
86536 AGTT
1 AGTT
86540 CTGTTAAAAC
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 4 0.17
21 19 0.83
ACGTcount: A:0.29, C:0.27, G:0.18, T:0.27
Consensus pattern (20 bp):
AGTTAACTGGCCACATCAGC
Found at i:88380 original size:3 final size:3
Alignment explanation
Indices: 88372--88414 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
88362 TGTTCTCTGC
88372 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA A
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA A
88415 TAAAAGAGGA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:94569 original size:39 final size:39
Alignment explanation
Indices: 94511--94631 Score: 215
Period size: 39 Copynumber: 3.1 Consensus size: 39
94501 AATTATATTA
*
94511 CCAGCACAAAGCCTGCGGGACTTTAGCCCGGATACATTT
1 CCAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTT
* *
94550 CCTGCACGAAGCCTACGGGACTTTAGCCCGGATACATTT
1 CCAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTT
94589 CCAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTT
1 CCAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTT
94628 CCAG
1 CCAG
94632 TATCTTGCAT
Statistics
Matches: 77, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
39 77 1.00
ACGTcount: A:0.24, C:0.31, G:0.24, T:0.21
Consensus pattern (39 bp):
CCAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTT
Found at i:97318 original size:55 final size:53
Alignment explanation
Indices: 97190--97381 Score: 217
Period size: 55 Copynumber: 3.6 Consensus size: 53
97180 TTGAACTTTC
* * *
97190 CAATGTCATGTCTTGACATGGTCTTACGTGGTATCCTTGCCTTAT-GAACTCAC-
1 CAATGCCATGCCTTGACATGGTCTTACATGGTA-CCTTGCCTTATAGAACTC-CT
* *
97243 CAATGCCATGCCTTGGCATGGTCTTACATGGGACCTTCGCCTTATAGTAACTCCT
1 CAATGCCATGCCTTGACATGGTCTTACATGGTACCTT-GCCTTATAG-AACTCCT
* * * * **
97298 CAATGCCATGTCTTGACATGGTCTTACATGATTTCCTTGCCTTATAGAATTTAT
1 CAATGCCATGCCTTGACATGGTCTTACATG-GTACCTTGCCTTATAGAACTCCT
*
97352 CAATGCCATGCCTTGGCATGGTCTTACATG
1 CAATGCCATGCCTTGACATGGTCTTACATG
97382 ATATCCTTAT
Statistics
Matches: 119, Mismatches: 15, Indels: 9
0.83 0.10 0.06
Matches are distributed among these distances:
52 4 0.03
53 35 0.29
54 34 0.29
55 42 0.35
56 4 0.03
ACGTcount: A:0.21, C:0.25, G:0.19, T:0.35
Consensus pattern (53 bp):
CAATGCCATGCCTTGACATGGTCTTACATGGTACCTTGCCTTATAGAACTCCT
Found at i:97646 original size:44 final size:44
Alignment explanation
Indices: 97579--97665 Score: 122
Period size: 44 Copynumber: 2.0 Consensus size: 44
97569 GTATCCTTAA
* *
97579 CCGTCAATTCCTCCTTAAATGCCATGTTATGAA-CATGGACTTTT
1 CCGTCAATTCCTCCTTAAATGCCATGGTA-CAACCATGGACTTTT
* *
97623 CCGTCAATTCTTCCTTAATTGCCATGGTACAACCATGGACTTT
1 CCGTCAATTCCTCCTTAAATGCCATGGTACAACCATGGACTTT
97666 GAGATATCAA
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
43 2 0.05
44 36 0.95
ACGTcount: A:0.24, C:0.26, G:0.14, T:0.36
Consensus pattern (44 bp):
CCGTCAATTCCTCCTTAAATGCCATGGTACAACCATGGACTTTT
Found at i:98106 original size:7 final size:7
Alignment explanation
Indices: 98094--98121 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
98084 CCAACTTTCC
98094 CGATTTT
1 CGATTTT
98101 CGATTTT
1 CGATTTT
98108 CGATTTT
1 CGATTTT
98115 CGATTTT
1 CGATTTT
98122 TCTCTCGTTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.14, C:0.14, G:0.14, T:0.57
Consensus pattern (7 bp):
CGATTTT
Found at i:101841 original size:3 final size:3
Alignment explanation
Indices: 101833--101866 Score: 50
Period size: 3 Copynumber: 11.3 Consensus size: 3
101823 AGAAGGCGAC
* *
101833 GAA GAA GAA GAT GAT GAA GAA GAA GAA GAA GAA G
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA G
101867 GTTGAGATAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.59, C:0.00, G:0.35, T:0.06
Consensus pattern (3 bp):
GAA
Found at i:110474 original size:19 final size:20
Alignment explanation
Indices: 110431--110472 Score: 70
Period size: 18 Copynumber: 2.2 Consensus size: 20
110421 ACATCAGCCA
110431 TTTTATCTTAAATTTTAATT
1 TTTTATCTTAAATTTTAATT
110451 TTTTAT-TTAAA-TTTAATT
1 TTTTATCTTAAATTTTAATT
110469 TTTT
1 TTTT
110473 TAAATAAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
18 11 0.50
19 5 0.23
20 6 0.27
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69
Consensus pattern (20 bp):
TTTTATCTTAAATTTTAATT
Found at i:110480 original size:19 final size:19
Alignment explanation
Indices: 110439--110480 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
110429 CATTTTATCT
**
110439 TAAATTTTAATTTTTTATT
1 TAAATTTTAATTTTTTAAA
110458 TAAA-TTTAATTTTTTTAAA
1 TAAATTTTAA-TTTTTTAAA
110477 TAAA
1 TAAA
110481 AAAATTGATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
18 5 0.25
19 15 0.75
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (19 bp):
TAAATTTTAATTTTTTAAA
Found at i:111551 original size:7 final size:7
Alignment explanation
Indices: 111539--111573 Score: 70
Period size: 7 Copynumber: 5.0 Consensus size: 7
111529 CAAAGAGGGT
111539 GTAGGCC
1 GTAGGCC
111546 GTAGGCC
1 GTAGGCC
111553 GTAGGCC
1 GTAGGCC
111560 GTAGGCC
1 GTAGGCC
111567 GTAGGCC
1 GTAGGCC
111574 ACTGGTGCTG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 28 1.00
ACGTcount: A:0.14, C:0.29, G:0.43, T:0.14
Consensus pattern (7 bp):
GTAGGCC
Found at i:114623 original size:2 final size:2
Alignment explanation
Indices: 114618--114649 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
114608 AATATATGGA
114618 AG AG AG AG AG AG AG AG AG AG AG AG AG AG -G AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
114650 TATTATGGGA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:115761 original size:18 final size:18
Alignment explanation
Indices: 115738--115772 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
115728 TAATTACCAT
115738 TTTAATTACATTATAAGG
1 TTTAATTACATTATAAGG
**
115756 TTTAATTGTATTATAAG
1 TTTAATTACATTATAAG
115773 CTAGCTTTTG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.37, C:0.03, G:0.11, T:0.49
Consensus pattern (18 bp):
TTTAATTACATTATAAGG
Found at i:121795 original size:8 final size:7
Alignment explanation
Indices: 121774--121798 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
121764 GCATCACTAT
121774 ATTAAAA
1 ATTAAAA
121781 ATTAAAA
1 ATTAAAA
121788 ATTAAAA
1 ATTAAAA
121795 ATTA
1 ATTA
121799 CAAACAAGAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (7 bp):
ATTAAAA
Found at i:133262 original size:18 final size:18
Alignment explanation
Indices: 133239--133273 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
133229 TCATACCTTA
*
133239 TAATTTTTTATTGAATAC
1 TAATTTCTTATTGAATAC
*
133257 TAATTTCTTATTTAATA
1 TAATTTCTTATTGAATA
133274 AATTGTTCAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.34, C:0.06, G:0.03, T:0.57
Consensus pattern (18 bp):
TAATTTCTTATTGAATAC
Found at i:133613 original size:22 final size:23
Alignment explanation
Indices: 133574--133623 Score: 68
Period size: 22 Copynumber: 2.2 Consensus size: 23
133564 ATTATAATGA
*
133574 AATAAAACTGAAAATAAATATT-T
1 AATAAAAATGAAAATAAA-ATTAT
133597 AATAAAAATG-AAATAAAATTAT
1 AATAAAAATGAAAATAAAATTAT
133619 AATAA
1 AATAA
133624 TATAAAATAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
21 3 0.12
22 13 0.52
23 9 0.36
ACGTcount: A:0.66, C:0.02, G:0.04, T:0.28
Consensus pattern (23 bp):
AATAAAAATGAAAATAAAATTAT
Found at i:134122 original size:20 final size:20
Alignment explanation
Indices: 134085--134123 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
134075 TTAAATAAAC
*
134085 TATTTTTTTAAAAGAAAAAG
1 TATTTTTCTAAAAGAAAAAG
* *
134105 TATTTTTCTCAAATAAAAA
1 TATTTTTCTAAAAGAAAAA
134124 AATTAACCCA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.49, C:0.05, G:0.05, T:0.41
Consensus pattern (20 bp):
TATTTTTCTAAAAGAAAAAG
Found at i:137282 original size:8 final size:8
Alignment explanation
Indices: 137240--137264 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
137230 ATATAGACTA
137240 AATAAAAT
1 AATAAAAT
137248 AATAAAAT
1 AATAAAAT
137256 AATAAAAT
1 AATAAAAT
137264 A
1 A
137265 TCTTATTAAA
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:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (8 bp):
AATAAAAT
Found at i:137564 original size:29 final size:30
Alignment explanation
Indices: 137507--137574 Score: 75
Period size: 30 Copynumber: 2.3 Consensus size: 30
137497 CACCCTTAAA
* * * *
137507 ATATTTTCACTATTAGTCCTTCAACTTTTC
1 ATATTTACACTATTAATCCCTCAAATTTTC
*
137537 ATATTTACACT-TTAATCCCTCAAATTTTG
1 ATATTTACACTATTAATCCCTCAAATTTTC
137566 AGTATTTAC
1 A-TATTTAC
137575 TCTTGGGCCA
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
29 15 0.47
30 17 0.53
ACGTcount: A:0.28, C:0.21, G:0.04, T:0.47
Consensus pattern (30 bp):
ATATTTACACTATTAATCCCTCAAATTTTC
Found at i:138154 original size:3 final size:3
Alignment explanation
Indices: 138148--138219 Score: 80
Period size: 3 Copynumber: 25.0 Consensus size: 3
138138 ATCTAAGATT
* **
138148 TTA TTA TTA TTA TTAA TTA TTA GTA TGG TT- TTA -TA TTA TTA TTA
1 TTA TTA TTA TTA TT-A TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
138192 TTA TTA TTA TTA TTA TTA TT- TTA -TA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
138220 AGTTAAAGAT
Statistics
Matches: 59, Mismatches: 5, Indels: 10
0.80 0.07 0.14
Matches are distributed among these distances:
2 8 0.14
3 48 0.81
4 3 0.05
ACGTcount: A:0.32, C:0.00, G:0.04, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:138338 original size:25 final size:24
Alignment explanation
Indices: 138293--138351 Score: 86
Period size: 25 Copynumber: 2.5 Consensus size: 24
138283 ATAATGAAAA
138293 TTGTAAT-AAAAATATTGGTACAT
1 TTGTAATAAAAAATATTGGTACAT
138316 TTGTAATAAATAAATATAT-GTACAT
1 TTGTAATAAA-AAATAT-TGGTACAT
138341 TTGTAATAAAA
1 TTGTAATAAAA
138352 TAATTAAGTT
Statistics
Matches: 33, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
23 7 0.21
24 3 0.09
25 22 0.67
26 1 0.03
ACGTcount: A:0.47, C:0.03, G:0.10, T:0.39
Consensus pattern (24 bp):
TTGTAATAAAAAATATTGGTACAT
Found at i:141358 original size:14 final size:15
Alignment explanation
Indices: 141341--141369 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
141331 GAGTATGGTA
141341 AAATA-TTAAAAAAT
1 AAATATTTAAAAAAT
141355 AAATATTTAAAAAAT
1 AAATATTTAAAAAAT
141370 TACTAATAGT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 5 0.36
15 9 0.64
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (15 bp):
AAATATTTAAAAAAT
Found at i:141683 original size:27 final size:29
Alignment explanation
Indices: 141625--141682 Score: 77
Period size: 27 Copynumber: 2.1 Consensus size: 29
141615 AAATTAAATT
* *
141625 AAATAATTAAAAAATTAATAAGTATTGTA
1 AAATAATTAAAAAATAAATAAATATTGTA
141654 AAAT-ATT-AAAAATAAATAAATATT-TA
1 AAATAATTAAAAAATAAATAAATATTGTA
141680 AAA
1 AAA
141683 AAGATATATT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
26 5 0.19
27 15 0.56
28 3 0.11
29 4 0.15
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (29 bp):
AAATAATTAAAAAATAAATAAATATTGTA
Found at i:145244 original size:20 final size:20
Alignment explanation
Indices: 145219--145268 Score: 70
Period size: 17 Copynumber: 2.6 Consensus size: 20
145209 TGGCTTAAAA
145219 TTGGTAGTGGATTGTTGTTG
1 TTGGTAGTGGATTGTTGTTG
145239 TTGGTAGTGG---GTTGTTG
1 TTGGTAGTGGATTGTTGTTG
*
145256 GTGGTAGTGGATT
1 TTGGTAGTGGATT
145269 AGTGGATGGT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
17 16 0.62
20 10 0.38
ACGTcount: A:0.10, C:0.00, G:0.44, T:0.46
Consensus pattern (20 bp):
TTGGTAGTGGATTGTTGTTG
Found at i:149883 original size:20 final size:20
Alignment explanation
Indices: 149858--149907 Score: 70
Period size: 17 Copynumber: 2.6 Consensus size: 20
149848 TGGCTTAAAA
149858 TTGGTAGTGGATTGTTGTTG
1 TTGGTAGTGGATTGTTGTTG
149878 TTGGTAGTGG---GTTGTTG
1 TTGGTAGTGGATTGTTGTTG
*
149895 GTGGTAGTGGATT
1 TTGGTAGTGGATT
149908 AGTGGATGGT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
17 16 0.62
20 10 0.38
ACGTcount: A:0.10, C:0.00, G:0.44, T:0.46
Consensus pattern (20 bp):
TTGGTAGTGGATTGTTGTTG
Found at i:155786 original size:27 final size:28
Alignment explanation
Indices: 155728--155786 Score: 70
Period size: 27 Copynumber: 2.1 Consensus size: 28
155718 AACTAAGAAT
*
155728 AAAATTATAAAAATATTAATAATTATTT
1 AAAATTATAAAAATATTAATAATTATTC
155756 AAAATT-TAAAAA-ATTAAATAATT-TTAC
1 AAAATTATAAAAATATT-AATAATTATT-C
155783 AAAA
1 AAAA
155787 ATAATTTTCG
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
26 5 0.18
27 17 0.61
28 6 0.21
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (28 bp):
AAAATTATAAAAATATTAATAATTATTC
Found at i:157650 original size:15 final size:15
Alignment explanation
Indices: 157602--157651 Score: 57
Period size: 15 Copynumber: 3.3 Consensus size: 15
157592 CTCCTCATCT
*
157602 TCATCGTCATCCTCA
1 TCATCTTCATCCTCA
* *
157617 TCATCTTCATCAAT-T
1 TCATCTTCATC-CTCA
157632 TCATCTTCATCCTCA
1 TCATCTTCATCCTCA
157647 TCATC
1 TCATC
157652 CAACTCAAGC
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
14 1 0.04
15 26 0.93
16 1 0.04
ACGTcount: A:0.22, C:0.36, G:0.02, T:0.40
Consensus pattern (15 bp):
TCATCTTCATCCTCA
Found at i:157666 original size:30 final size:29
Alignment explanation
Indices: 157602--157667 Score: 71
Period size: 30 Copynumber: 2.2 Consensus size: 29
157592 CTCCTCATCT
* **
157602 TCATCGTCATCCTCATCATCTTCATCAATT
1 TCATCTTCATCCTCATCATC-TCATCAAGC
157632 TCATCTTCATCCTCATCATC-CAACTCAAGC
1 TCATCTTCATCCTCATCATCTC-A-TCAAGC
157662 TCATCT
1 TCATCT
157668 CCCTGAATAG
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
28 1 0.03
29 1 0.03
30 29 0.94
ACGTcount: A:0.24, C:0.36, G:0.03, T:0.36
Consensus pattern (29 bp):
TCATCTTCATCCTCATCATCTCATCAAGC
Found at i:165089 original size:30 final size:30
Alignment explanation
Indices: 165053--165113 Score: 104
Period size: 30 Copynumber: 2.0 Consensus size: 30
165043 GATATACTCT
165053 TAGATGATGCTGTAGTATCAGAAAAAAAGG
1 TAGATGATGCTGTAGTATCAGAAAAAAAGG
* *
165083 TAGATGATGCTGTGGTATCAGGAAAAAAGG
1 TAGATGATGCTGTAGTATCAGAAAAAAAGG
165113 T
1 T
165114 GGAGGAGACG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.39, C:0.07, G:0.30, T:0.25
Consensus pattern (30 bp):
TAGATGATGCTGTAGTATCAGAAAAAAAGG
Done.