Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_216
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: 127576
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:3357 original size:30 final size:30
Alignment explanation
Indices: 3323--3384 Score: 124
Period size: 30 Copynumber: 2.1 Consensus size: 30
3313 TTTTAAATGA
3323 TGGTTGATTAAGTATGAAATGCTAAGTAAT
1 TGGTTGATTAAGTATGAAATGCTAAGTAAT
3353 TGGTTGATTAAGTATGAAATGCTAAGTAAT
1 TGGTTGATTAAGTATGAAATGCTAAGTAAT
3383 TG
1 TG
3385 TATTTGAATG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.35, C:0.03, G:0.24, T:0.37
Consensus pattern (30 bp):
TGGTTGATTAAGTATGAAATGCTAAGTAAT
Found at i:7472 original size:13 final size:13
Alignment explanation
Indices: 7456--7502 Score: 67
Period size: 13 Copynumber: 3.5 Consensus size: 13
7446 AAAAAAATAT
7456 AAAAAAATTCGAA
1 AAAAAAATTCGAA
*
7469 AAAAAAATTTTGAA
1 AAAAAAA-TTCGAA
*
7483 AAAAAAATTCCAA
1 AAAAAAATTCGAA
7496 AAAAAAA
1 AAAAAAA
7503 GTTTGTATTC
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
13 18 0.60
14 12 0.40
ACGTcount: A:0.72, C:0.06, G:0.04, T:0.17
Consensus pattern (13 bp):
AAAAAAATTCGAA
Found at i:7475 original size:14 final size:14
Alignment explanation
Indices: 7456--7502 Score: 60
Period size: 14 Copynumber: 3.4 Consensus size: 14
7446 AAAAAAATAT
7456 AAAAAAATTCGAAA
1 AAAAAAATTCGAAA
* *
7470 AAAAAATTTTG-AA
1 AAAAAAATTCGAAA
*
7483 AAAAAAATTCCAAA
1 AAAAAAATTCGAAA
7497 AAAAAA
1 AAAAAA
7503 GTTTGTATTC
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
13 10 0.37
14 17 0.63
ACGTcount: A:0.72, C:0.06, G:0.04, T:0.17
Consensus pattern (14 bp):
AAAAAAATTCGAAA
Found at i:7497 original size:27 final size:27
Alignment explanation
Indices: 7456--7507 Score: 86
Period size: 27 Copynumber: 1.9 Consensus size: 27
7446 AAAAAAATAT
* *
7456 AAAAAAATTCGAAAAAAAAATTTTGAA
1 AAAAAAATTCCAAAAAAAAAGTTTGAA
7483 AAAAAAATTCCAAAAAAAAAGTTTG
1 AAAAAAATTCCAAAAAAAAAGTTTG
7508 TATTCAATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.65, C:0.06, G:0.08, T:0.21
Consensus pattern (27 bp):
AAAAAAATTCCAAAAAAAAAGTTTGAA
Found at i:7606 original size:27 final size:28
Alignment explanation
Indices: 7551--7616 Score: 89
Period size: 27 Copynumber: 2.3 Consensus size: 28
7541 TTGAAGAAAA
* *
7551 AAAAAGAAGAAGAAAAAAAATTCAGAATT-
1 AAAAA-AA-AAGAAAAAAAAATCAAAATTG
7580 AAAAAAAAAGAAAAAAAAATCAAAATTG
1 AAAAAAAAAGAAAAAAAAATCAAAATTG
7608 AAAAAAAAA
1 AAAAAAAAA
7617 AGAGTGATTG
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
27 18 0.53
28 11 0.32
29 5 0.15
ACGTcount: A:0.77, C:0.03, G:0.09, T:0.11
Consensus pattern (28 bp):
AAAAAAAAAGAAAAAAAAATCAAAATTG
Found at i:8483 original size:6 final size:6
Alignment explanation
Indices: 8474--8509 Score: 54
Period size: 6 Copynumber: 6.0 Consensus size: 6
8464 AAAAAAGAAT
* *
8474 TTGAGA TTGAGA TTGAGA TTGATA TTGATA TTGAGA
1 TTGAGA TTGAGA TTGAGA TTGAGA TTGAGA TTGAGA
8510 AAAAAATTGA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.33, C:0.00, G:0.28, T:0.39
Consensus pattern (6 bp):
TTGAGA
Found at i:8484 original size:26 final size:27
Alignment explanation
Indices: 8420--8485 Score: 80
Period size: 26 Copynumber: 2.5 Consensus size: 27
8410 ACGAATCTTG
* *
8420 AATGAAATTGAGAGAAGAAAAAAAGAA
1 AATGAGATTGAGAAAAGAAAAAAAGAA
*
8447 AATGAGAGTGAGAAAAG-AAAAAAGAA
1 AATGAGATTGAGAAAAGAAAAAAAGAA
**
8473 TTTGAGATTGAGA
1 AATGAGATTGAGA
8486 TTGAGATTGA
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
26 19 0.58
27 14 0.42
ACGTcount: A:0.59, C:0.00, G:0.26, T:0.15
Consensus pattern (27 bp):
AATGAGATTGAGAAAAGAAAAAAAGAA
Found at i:13779 original size:20 final size:20
Alignment explanation
Indices: 13733--13779 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
13723 AGCTCGTTTC
13733 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCGAGCTCAAGT
* *
13753 CAACTCACTCGAGCTCAATT
1 CAGCTCACTCGAGCTCAAGT
13773 CAGCTCA
1 CAGCTCA
13780 ATCTTAACCC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.28, C:0.36, G:0.15, T:0.21
Consensus pattern (20 bp):
CAGCTCACTCGAGCTCAAGT
Found at i:15946 original size:47 final size:47
Alignment explanation
Indices: 15868--15972 Score: 133
Period size: 47 Copynumber: 2.2 Consensus size: 47
15858 GAGTGTCATG
* *
15868 GAAAAAGAAATTGAGATTGAAAAAGGATGTGA-AAAGAGAAAGAAATC
1 GAAAAAGAAATTGAGATTGAAAAAAGATGTGAGAAAAAGAAA-AAATC
* *
15915 GAAAAAGAAATTGAGATTGAACAAAAG-TGTGAGGAAAAAGAGAAAATT
1 GAAAAAGAAATTGAGATTGAA-AAAAGATGTGA-GAAAAAGAAAAAATC
15963 GAAAAAGAAA
1 GAAAAAGAAA
15973 GAAAAGACAA
Statistics
Matches: 51, Mismatches: 4, Indels: 5
0.85 0.07 0.08
Matches are distributed among these distances:
47 26 0.51
48 18 0.35
49 7 0.14
ACGTcount: A:0.59, C:0.02, G:0.25, T:0.14
Consensus pattern (47 bp):
GAAAAAGAAATTGAGATTGAAAAAAGATGTGAGAAAAAGAAAAAATC
Found at i:17685 original size:20 final size:20
Alignment explanation
Indices: 17639--17685 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
17629 AGCTCGTTTC
17639 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCGAGCTCAAGT
* *
17659 CAACTCACTCGAGCTCAATT
1 CAGCTCACTCGAGCTCAAGT
17679 CAGCTCA
1 CAGCTCA
17686 ATCTTAACCT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.28, C:0.36, G:0.15, T:0.21
Consensus pattern (20 bp):
CAGCTCACTCGAGCTCAAGT
Found at i:20885 original size:30 final size:28
Alignment explanation
Indices: 20832--20887 Score: 76
Period size: 30 Copynumber: 1.9 Consensus size: 28
20822 TTCTTCCACG
* *
20832 CTTTCTTTTTGCTCACTCTCTTTTTCAA
1 CTTTCTTTTTGCACACACTCTTTTTCAA
20860 CTTTACTTTCTTGCACACACTCTTTTTC
1 CTTT-CTTT-TTGCACACACTCTTTTTC
20888 TTTTTCGCTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 4 0.17
29 4 0.17
30 16 0.67
ACGTcount: A:0.12, C:0.30, G:0.04, T:0.54
Consensus pattern (28 bp):
CTTTCTTTTTGCACACACTCTTTTTCAA
Found at i:21972 original size:22 final size:22
Alignment explanation
Indices: 21947--21988 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
21937 TTTTCAGAAT
*
21947 TTTTGTTTGAAATTTTTTTTCG
1 TTTTGTTTCAAATTTTTTTTCG
* *
21969 TTTTTTTTCAATTTTTTTTT
1 TTTTGTTTCAAATTTTTTTT
21989 GAAACTTACT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.12, C:0.05, G:0.07, T:0.76
Consensus pattern (22 bp):
TTTTGTTTCAAATTTTTTTTCG
Found at i:22273 original size:29 final size:29
Alignment explanation
Indices: 22207--22263 Score: 96
Period size: 29 Copynumber: 2.0 Consensus size: 29
22197 GATTCAAAGA
*
22207 TGGGTTTATGGATATGAAGTTTATGTAGT
1 TGGGTTTATGGATATAAAGTTTATGTAGT
*
22236 TGGGTTTATGGATATAAAGTTTTTGTAG
1 TGGGTTTATGGATATAAAGTTTATGTAG
22264 GTTTGGTTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.25, C:0.00, G:0.30, T:0.46
Consensus pattern (29 bp):
TGGGTTTATGGATATAAAGTTTATGTAGT
Found at i:26650 original size:70 final size:69
Alignment explanation
Indices: 26550--26740 Score: 242
Period size: 70 Copynumber: 2.8 Consensus size: 69
26540 AATTGATGAG
* * * * *
26550 TTGTTATATTAAAAATGTCTTCATTTACGTTCGATTTAAATGCTTAATGTGTTGCTGTAAAGTGC
1 TTGTTATCTTAAAAATGTGTTCATTTACGTTCAATTTAAATGCTTAATGTGCTGCTGTAAAGGGC
26615 TAAT
66 TAAT
* * *
26619 TTGTTATCTTAAAAAATGTGTTCACTCACGTT-AATTTTAGATGCTTAATGTGCTGCTGTAAAGG
1 TTGTTATCTT-AAAAATGTGTTCATTTACGTTCAA-TTTAAATGCTTAATGTGCTGCTGTAAAGG
*
26683 GCTGAT
64 GCTAAT
* * *
26689 TTGTTGTCTTGAAAATGTGTTCATTTACG-TCCATTTAAATGCTTAATGTGCT
1 TTGTTATCTTAAAAATGTGTTCATTTACGTTCAATTTAAATGCTTAATGTGCT
26741 TTCCAAAAAT
Statistics
Matches: 104, Mismatches: 15, Indels: 7
0.83 0.12 0.06
Matches are distributed among these distances:
68 19 0.18
69 27 0.26
70 58 0.56
ACGTcount: A:0.27, C:0.12, G:0.18, T:0.43
Consensus pattern (69 bp):
TTGTTATCTTAAAAATGTGTTCATTTACGTTCAATTTAAATGCTTAATGTGCTGCTGTAAAGGGC
TAAT
Found at i:30930 original size:22 final size:22
Alignment explanation
Indices: 30902--30945 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
30892 TTTTGAACCA
30902 TTACCATTTCGTACCAAATCCC
1 TTACCATTTCGTACCAAATCCC
*
30924 TTACCATTTCGTACCAATTCCC
1 TTACCATTTCGTACCAAATCCC
30946 AAATACCAAA
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:0.25, C:0.36, G:0.05, T:0.34
Consensus pattern (22 bp):
TTACCATTTCGTACCAAATCCC
Found at i:32550 original size:64 final size:64
Alignment explanation
Indices: 32469--32651 Score: 167
Period size: 67 Copynumber: 2.8 Consensus size: 64
32459 AGACATTATG
* * *
32469 ATGTAGCTAGGTTGCATGGGAGATACTATGTGTACACCATGTAGACAAGAGAGCTACGGGATAT
1 ATGTAGCTAGGTCGCATGGGAGATACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATAA
* * * * * * *
32533 ATGTAGCTAGGTCGCATGCGTGATTCCAGGTGAAGGACACCATGTAGACAAAAGAGCTACGAGAT
1 ATGTAGCTAGGTCGCATGGGAGATACTA--TG-TGTACACCATGTAGACAAGAGAGCTACGAGAT
32598 AA
63 AA
* * *
32600 ACTG--GCTAGGTCACATGGGTAG-TACTAAGTGTTCACCATGT-GTACAAGAGAG
1 A-TGTAGCTAGGTCGCATGGG-AGATACTATGTGTACACCATGTAG-ACAAGAGAG
32652 TCGAACTATA
Statistics
Matches: 93, Mismatches: 20, Indels: 13
0.74 0.16 0.10
Matches are distributed among these distances:
62 1 0.01
63 17 0.18
64 24 0.26
66 18 0.19
67 31 0.33
68 2 0.02
ACGTcount: A:0.32, C:0.16, G:0.29, T:0.23
Consensus pattern (64 bp):
ATGTAGCTAGGTCGCATGGGAGATACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATAA
Found at i:34213 original size:20 final size:20
Alignment explanation
Indices: 34174--34234 Score: 61
Period size: 20 Copynumber: 3.0 Consensus size: 20
34164 CCAATAAAAT
* *
34174 AAATGAGCTGAATTGTAGCT-
1 AAATGACCTCAATTG-AGCTG
*
34194 AAATTGACCTCGATTGAGCTG
1 AAA-TGACCTCAATTGAGCTG
*
34215 AAATGAGCTCAATTGAGCTG
1 AAATGACCTCAATTGAGCTG
34235 GTCGGAGTTG
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
20 22 0.65
21 12 0.35
ACGTcount: A:0.33, C:0.15, G:0.25, T:0.28
Consensus pattern (20 bp):
AAATGACCTCAATTGAGCTG
Found at i:36326 original size:18 final size:18
Alignment explanation
Indices: 36305--36339 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
36295 TTTTTCTTTT
36305 TCAATTT-TTTTCTCAATC
1 TCAATTTCTTTT-TCAATC
36323 TCAATTTCTTTTTCAAT
1 TCAATTTCTTTTTCAAT
36340 TTTCTTTTCT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.23, C:0.20, G:0.00, T:0.57
Consensus pattern (18 bp):
TCAATTTCTTTTTCAATC
Found at i:37238 original size:14 final size:14
Alignment explanation
Indices: 37219--37282 Score: 60
Period size: 15 Copynumber: 4.5 Consensus size: 14
37209 AGACTTTTCA
37219 CTTTTTTTTTCCTT
1 CTTTTTTTTTCCTT
**
37233 CTTTTTTTTAAC-T
1 CTTTTTTTTTCCTT
*
37246 CGATTTTTTTGTCACTT
1 C--TTTTTTTTTC-CTT
37263 CTTTTTTTTTCCTT
1 CTTTTTTTTTCCTT
37277 -TTTTTT
1 CTTTTTT
37283 CAATTTTTTT
Statistics
Matches: 40, Mismatches: 6, Indels: 9
0.73 0.11 0.16
Matches are distributed among these distances:
13 8 0.20
14 13 0.32
15 16 0.40
16 1 0.03
17 2 0.05
ACGTcount: A:0.06, C:0.17, G:0.03, T:0.73
Consensus pattern (14 bp):
CTTTTTTTTTCCTT
Found at i:37301 original size:12 final size:12
Alignment explanation
Indices: 37286--37310 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
37276 TTTTTTTCAA
37286 TTTTTTTGAATT
1 TTTTTTTGAATT
37298 TTTTTTTGAATT
1 TTTTTTTGAATT
37310 T
1 T
37311 CTTCTCTTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.00, G:0.08, T:0.76
Consensus pattern (12 bp):
TTTTTTTGAATT
Found at i:38718 original size:20 final size:20
Alignment explanation
Indices: 38679--38739 Score: 61
Period size: 20 Copynumber: 3.0 Consensus size: 20
38669 CCAATAAAAT
* *
38679 AAATGAGCTGAATTGTAGCT-
1 AAATGACCTCAATTG-AGCTG
*
38699 AAATTGACCTCGATTGAGCTG
1 AAA-TGACCTCAATTGAGCTG
*
38720 AAATGAGCTCAATTGAGCTG
1 AAATGACCTCAATTGAGCTG
38740 GTCGGAGTTG
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
20 22 0.65
21 12 0.35
ACGTcount: A:0.33, C:0.15, G:0.25, T:0.28
Consensus pattern (20 bp):
AAATGACCTCAATTGAGCTG
Found at i:42675 original size:30 final size:29
Alignment explanation
Indices: 42641--42724 Score: 78
Period size: 30 Copynumber: 2.8 Consensus size: 29
42631 TAAACTAAAA
*
42641 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAG-TTTAGCTCGTGAGCTAAAGC
* * * * * *
42671 TGAGCTGAGATTAAACTCCTAAGCTGAAGC
1 TGAGCTAAG-TTTAGCTCGTGAGCTAAAGC
*
42701 TGAGCTAAGTTTAGCTTGTGAGCT
1 TGAGCTAAGTTTAGCTCGTGAGCT
42725 GAATATGAGC
Statistics
Matches: 40, Mismatches: 14, Indels: 1
0.73 0.25 0.02
Matches are distributed among these distances:
29 10 0.25
30 30 0.75
ACGTcount: A:0.27, C:0.17, G:0.26, T:0.30
Consensus pattern (29 bp):
TGAGCTAAGTTTAGCTCGTGAGCTAAAGC
Found at i:43933 original size:30 final size:30
Alignment explanation
Indices: 43899--43995 Score: 97
Period size: 30 Copynumber: 3.2 Consensus size: 30
43889 AGCTCACTCC
*
43899 TAGCTCATA-TTCAGCCCACGAGCTAAACCT
1 TAGCTCA-ACTTCAGCTCACGAGCTAAACCT
* * * * *
43929 TAGCTCAACTTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTCAGCTCACGAGCTAAACCT
* * *
43959 CAGCTCAACTTTAGCTCACGAGCTAAAGCT
1 TAGCTCAACTTCAGCTCACGAGCTAAACCT
43989 TAGCTCA
1 TAGCTCA
43996 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:0.29, G:0.16, T:0.27
Consensus pattern (30 bp):
TAGCTCAACTTCAGCTCACGAGCTAAACCT
Found at i:44884 original size:22 final size:20
Alignment explanation
Indices: 44852--44900 Score: 53
Period size: 20 Copynumber: 2.3 Consensus size: 20
44842 GCCAAATTTA
44852 TGAACTATTTTAATACATTAGTG
1 TGAAC-ATTTTAAT-CATT-GTG
* *
44875 TGAACATTTTTATTATTGTG
1 TGAACATTTTAATCATTGTG
44895 TGAACA
1 TGAACA
44901 CCTAGATGTC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 9 0.38
21 3 0.12
22 7 0.29
23 5 0.21
ACGTcount: A:0.33, C:0.08, G:0.14, T:0.45
Consensus pattern (20 bp):
TGAACATTTTAATCATTGTG
Found at i:46540 original size:9 final size:10
Alignment explanation
Indices: 46533--46589 Score: 55
Period size: 11 Copynumber: 5.5 Consensus size: 10
46523 AAGAGAAAAC
46533 AAAGAAAAGA
1 AAAGAAAAGA
46543 AAAGAAAAAGTA
1 AAAG-AAAAG-A
*
46555 AAAGAAGA-A
1 AAAGAAAAGA
46564 AAAGAAAACGA
1 AAAGAAAA-GA
46575 AATA-AAAAGA
1 AA-AGAAAAGA
46585 AAAGA
1 AAAGA
46590 GAGGCAAGAG
Statistics
Matches: 39, Mismatches: 2, Indels: 12
0.74 0.04 0.23
Matches are distributed among these distances:
9 9 0.23
10 9 0.23
11 15 0.38
12 6 0.15
ACGTcount: A:0.77, C:0.02, G:0.18, T:0.04
Consensus pattern (10 bp):
AAAGAAAAGA
Found at i:46557 original size:6 final size:5
Alignment explanation
Indices: 46533--46589 Score: 55
Period size: 5 Copynumber: 11.0 Consensus size: 5
46523 AAGAGAAAAC
*
46533 AAAGA AAAGA AAAGAA AAAGTA AAAGA AGA-A AAAGA AAACGA AATA-A
1 AAAGA AAAGA AAAG-A AAAG-A AAAGA AAAGA AAAGA AAA-GA AA-AGA
46580 AAAGA AAAGA
1 AAAGA AAAGA
46590 GAGGCAAGAG
Statistics
Matches: 44, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
4 4 0.09
5 25 0.57
6 14 0.32
7 1 0.02
ACGTcount: A:0.77, C:0.02, G:0.18, T:0.04
Consensus pattern (5 bp):
AAAGA
Found at i:46564 original size:15 final size:14
Alignment explanation
Indices: 46533--46589 Score: 60
Period size: 16 Copynumber: 3.7 Consensus size: 14
46523 AAGAGAAAAC
46533 AAAGAAAAGAAAAGAA
1 AAAGAAAAG--AAGAA
46549 AAAGTAAAAGAAGAA
1 AAAG-AAAAGAAGAA
*
46564 AAAGAAAACGAAATAA
1 AAAGAAAA-G-AAGAA
46580 AAAGAAAAGA
1 AAAGAAAAGA
46590 GAGGCAAGAG
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:46782 original size:20 final size:20
Alignment explanation
Indices: 46759--46812 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
46749 AGTTTTTCCC
*
46759 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTCACATG
* ***
46779 AGCTTAATTTAGCTCGTTTG
1 AGCTCAATTTAGCTCACATG
46799 AGCTCAATTTAGCT
1 AGCTCAATTTAGCT
46813 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:46794 original size:30 final size:30
Alignment explanation
Indices: 46759--46832 Score: 98
Period size: 30 Copynumber: 2.5 Consensus size: 30
46749 AGTTTTTCCC
46759 AGCTCGATTT-AGCTCACA-TGAGCTTAATTT
1 AGCTCG-TTTGAGCTCA-ATTGAGCTTAATTT
* *
46789 AGCTCGTTTGAGCTCAATTTAGCTTACTTT
1 AGCTCGTTTGAGCTCAATTGAGCTTAATTT
46819 AGCTCGTTTGAGCT
1 AGCTCGTTTGAGCT
46833 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:46822 original size:20 final size:20
Alignment explanation
Indices: 46759--46823 Score: 53
Period size: 20 Copynumber: 3.2 Consensus size: 20
46749 AGTTTTTCCC
* * * *
46759 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTTACTTT
*
46779 AGCTTAATTTAGC-T-CGTTT
1 AGCTCAATTTAGCTTAC-TTT
46798 GAGCTCAATTTAGCTTACTTT
1 -AGCTCAATTTAGCTTACTTT
46819 AGCTC
1 AGCTC
46824 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:49572 original size:18 final size:18
Alignment explanation
Indices: 49546--49604 Score: 82
Period size: 18 Copynumber: 3.3 Consensus size: 18
49536 AAATTGAAAG
* *
49546 AAAACAAAAAGAAAGCGA
1 AAAAGAAAAAGAAATCGA
* *
49564 AAAAGAAAAAGAAATTGC
1 AAAAGAAAAAGAAATCGA
49582 AAAAGAAAAAGAAATCGA
1 AAAAGAAAAAGAAATCGA
49600 AAAAG
1 AAAAG
49605 TGAGAGAAAA
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 35 1.00
ACGTcount: A:0.71, C:0.07, G:0.17, T:0.05
Consensus pattern (18 bp):
AAAAGAAAAAGAAATCGA
Found at i:49644 original size:13 final size:12
Alignment explanation
Indices: 49520--49675 Score: 55
Period size: 12 Copynumber: 13.6 Consensus size: 12
49510 AGAAAAGGAG
*
49520 AAAGAGATTGAA
1 AAAGAAATTGAA
49532 AAAGAAATTG--
1 AAAGAAATTGAA
**
49542 AAAGAAA-ACAA
1 AAAGAAATTGAA
**
49553 AAAGAAAGCGAA
1 AAAGAAATTGAA
**
49565 AAAGAAAAAGAA
1 AAAGAAATTGAA
** *
49577 ATTGCAAA-AGAA
1 AAAG-AAATTGAA
*
49589 AAAGAAATCGAA
1 AAAGAAATTGAA
** **
49601 AAAGTGAGAGAA
1 AAAGAAATTGAA
*
49613 AAAGAAAATGAAGA
1 AAAGAAATTG-A-A
49627 AAAGATAATTGAA
1 AAAGA-AATTGAA
49640 AAAGAAATTG--
1 AAAGAAATTGAA
49650 --AG-AA-TGAA
1 AAAGAAATTGAA
49658 AAA-AAATTGAA
1 AAAGAAATTGAA
49669 AAAGAAA
1 AAAGAAA
49676 AAGCGGAAAA
Statistics
Matches: 108, Mismatches: 21, Indels: 30
0.68 0.13 0.19
Matches are distributed among these distances:
6 2 0.02
7 2 0.02
8 2 0.02
10 10 0.09
11 17 0.16
12 54 0.50
13 10 0.09
14 7 0.06
15 4 0.04
ACGTcount: A:0.67, C:0.03, G:0.19, T:0.11
Consensus pattern (12 bp):
AAAGAAATTGAA
Found at i:49664 original size:17 final size:18
Alignment explanation
Indices: 49636--49678 Score: 61
Period size: 17 Copynumber: 2.4 Consensus size: 18
49626 AAAAGATAAT
*
49636 TGAAAAAGAAATTGAGAA
1 TGAAAAAGAAATTGAAAA
49654 TGAAAAA-AAATTGAAAA
1 TGAAAAAGAAATTGAAAA
*
49671 AGAAAAAG
1 TGAAAAAG
49679 CGGAAAAAGA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
17 15 0.68
18 7 0.32
ACGTcount: A:0.67, C:0.00, G:0.19, T:0.14
Consensus pattern (18 bp):
TGAAAAAGAAATTGAAAA
Found at i:49690 original size:6 final size:6
Alignment explanation
Indices: 49542--49678 Score: 53
Period size: 6 Copynumber: 22.7 Consensus size: 6
49532 AAAGAAATTG
* ** ** *
49542 AAAG-A AAACAA AAAGAA AGCGAA AAAGAA AAAGAA ATTGCA AAAGAA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA
** ** * * **
49589 AAAGAA ATCGAA AAAGTG AGAGAA AAAGAA AATGAAGA AAAGATA ATTGAA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAG-A-A AAAGA-A AAAGAA
** * * **
49640 AAAGAA ATTGAG AATGAA AAA-AA ATTGAA AAAGAA AAAG
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAG
49679 CGGAAAAAGA
Statistics
Matches: 89, Mismatches: 39, Indels: 7
0.66 0.29 0.05
Matches are distributed among these distances:
5 6 0.07
6 73 0.82
7 6 0.07
8 4 0.04
ACGTcount: A:0.69, C:0.03, G:0.19, T:0.09
Consensus pattern (6 bp):
AAAGAA
Found at i:51552 original size:20 final size:20
Alignment explanation
Indices: 51529--51582 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
51519 AGTTTTTCCC
*
51529 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTCACATG
* ***
51549 AGCTTAATTTAGCTCGTTTG
1 AGCTCAATTTAGCTCACATG
51569 AGCTCAATTTAGCT
1 AGCTCAATTTAGCT
51583 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:51564 original size:30 final size:30
Alignment explanation
Indices: 51529--51602 Score: 98
Period size: 30 Copynumber: 2.5 Consensus size: 30
51519 AGTTTTTCCC
51529 AGCTCGATTT-AGCTCACA-TGAGCTTAATTT
1 AGCTCG-TTTGAGCTCA-ATTGAGCTTAATTT
* *
51559 AGCTCGTTTGAGCTCAATTTAGCTTACTTT
1 AGCTCGTTTGAGCTCAATTGAGCTTAATTT
51589 AGCTCGTTTGAGCT
1 AGCTCGTTTGAGCT
51603 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:51592 original size:20 final size:20
Alignment explanation
Indices: 51529--51593 Score: 53
Period size: 20 Copynumber: 3.2 Consensus size: 20
51519 AGTTTTTCCC
* * * *
51529 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTTACTTT
*
51549 AGCTTAATTTAGC-T-CGTTT
1 AGCTCAATTTAGCTTAC-TTT
51568 GAGCTCAATTTAGCTTACTTT
1 -AGCTCAATTTAGCTTACTTT
51589 AGCTC
1 AGCTC
51594 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:53080 original size:11 final size:12
Alignment explanation
Indices: 53048--53078 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
53038 TTGAGAGAAC
53048 TTGAAAAAGCCT
1 TTGAAAAAGCCT
53060 TTGAAAAAGCCT
1 TTGAAAAAGCCT
53072 TTGAAAA
1 TTGAAAA
53079 GCAAAAAGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.45, C:0.13, G:0.16, T:0.26
Consensus pattern (12 bp):
TTGAAAAAGCCT
Found at i:53115 original size:30 final size:30
Alignment explanation
Indices: 53081--53148 Score: 84
Period size: 30 Copynumber: 2.3 Consensus size: 30
53071 TTTGAAAAGC
*
53081 AAAAAGAAAAAGAAAATGAAA-ATGAGATTG
1 AAAAAGAAAAAGAAAA-GAAATATGAGAGTG
* * *
53111 AAAAAGAGAACGAAAAGAAATTTGAGAGTG
1 AAAAAGAAAAAGAAAAGAAATATGAGAGTG
53141 AAAAAGAA
1 AAAAAGAA
53149 GTTGAAAAAG
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
29 4 0.12
30 28 0.88
ACGTcount: A:0.65, C:0.01, G:0.22, T:0.12
Consensus pattern (30 bp):
AAAAAGAAAAAGAAAAGAAATATGAGAGTG
Found at i:53135 original size:24 final size:24
Alignment explanation
Indices: 53086--53132 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
53076 AAAGCAAAAA
* *
53086 GAAAAAGAAAATGAAAATGAGATT
1 GAAAAAGAAAACGAAAATGAAATT
*
53110 GAAAAAGAGAACGAAAA-GAAATT
1 GAAAAAGAAAACGAAAATGAAATT
53133 TGAGAGTGAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
23 5 0.25
24 15 0.75
ACGTcount: A:0.64, C:0.02, G:0.21, T:0.13
Consensus pattern (24 bp):
GAAAAAGAAAACGAAAATGAAATT
Found at i:54897 original size:22 final size:22
Alignment explanation
Indices: 54867--54910 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
54857 TTTGGTATTT
54867 GGGAATTGGTACGAAATGGTAA
1 GGGAATTGGTACGAAATGGTAA
*
54889 GGGATTTGGTACGAAATGGTAA
1 GGGAATTGGTACGAAATGGTAA
54911 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:56329 original size:20 final size:20
Alignment explanation
Indices: 56283--56329 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
56273 AGCTCGTTTC
*
56283 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* *
56303 CAACTCACTCAAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
56323 CAGCTCA
1 CAGCTCA
56330 ATTTTAACCC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.30, C:0.36, G:0.13, T:0.21
Consensus pattern (20 bp):
CAGCTCACTCAAGCTCAAGT
Found at i:58476 original size:30 final size:30
Alignment explanation
Indices: 58442--58538 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
58432 AGCTCACTCC
58442 TAGCTCATA-TTCAGCTCACGAGCTAAACCT
1 TAGCTCA-ACTTCAGCTCACGAGCTAAACCT
* * * * *
58472 TAGCTCAACTTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTCAGCTCACGAGCTAAACCT
* * *
58502 CAGCTCAACTTTAGCTCACGAGCTAAAGCT
1 TAGCTCAACTTCAGCTCACGAGCTAAACCT
58532 TAGCTCA
1 TAGCTCA
58539 TTTTAGTTTA
Statistics
Matches: 52, Mismatches: 14, Indels: 2
0.76 0.21 0.03
Matches are distributed among these distances:
29 1 0.02
30 51 0.98
ACGTcount: A:0.28, C:0.28, G:0.16, T:0.28
Consensus pattern (30 bp):
TAGCTCAACTTCAGCTCACGAGCTAAACCT
Found at i:61605 original size:29 final size:29
Alignment explanation
Indices: 61572--61628 Score: 96
Period size: 29 Copynumber: 2.0 Consensus size: 29
61562 ATAACCAAAC
*
61572 CTACAAAAACTTTATATCCATAAACCCAA
1 CTACAAAAACTTCATATCCATAAACCCAA
*
61601 CTACATAAACTTCATATCCATAAACCCA
1 CTACAAAAACTTCATATCCATAAACCCA
61629 TCTTTGAATC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.46, C:0.30, G:0.00, T:0.25
Consensus pattern (29 bp):
CTACAAAAACTTCATATCCATAAACCCAA
Found at i:62280 original size:21 final size:20
Alignment explanation
Indices: 62236--62284 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
62226 TCAGCTCCCA
* *
62236 TCAGCTCACTTGAGCTCGAT
1 TCAGCTCGCTTGAGCTAGAT
*
62256 TCAGCTCGTTTGAGCTAGAAT
1 TCAGCTCGCTTGAGCTAG-AT
62277 TCAGCTCG
1 TCAGCTCG
62285 ATCTAGCTCA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
20 15 0.60
21 10 0.40
ACGTcount: A:0.20, C:0.27, G:0.22, T:0.31
Consensus pattern (20 bp):
TCAGCTCGCTTGAGCTAGAT
Found at i:63877 original size:30 final size:30
Alignment explanation
Indices: 63791--63888 Score: 97
Period size: 30 Copynumber: 3.3 Consensus size: 30
63781 TTAAACTAAA
* *
63791 ATGAGCTAAGCTTTAGCTCGTGAGCTAAAG
1 ATGAGCTAAGATTTAGCTCGTGAGCTGAAG
* * * * * *
63821 TTGAGCTGAGATTAAACTCCTAAGCTGAAG
1 ATGAGCTAAGATTTAGCTCGTGAGCTGAAG
* * *
63851 CTGAGCTAAGGTTTAGCTCGTGAGCTGAAT
1 ATGAGCTAAGATTTAGCTCGTGAGCTGAAG
63881 ATGAGCTA
1 ATGAGCTA
63889 GGAGTGAGCT
Statistics
Matches: 51, Mismatches: 17, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
30 51 1.00
ACGTcount: A:0.30, C:0.16, G:0.27, T:0.28
Consensus pattern (30 bp):
ATGAGCTAAGATTTAGCTCGTGAGCTGAAG
Found at i:66191 original size:30 final size:30
Alignment explanation
Indices: 66120--66202 Score: 89
Period size: 30 Copynumber: 2.7 Consensus size: 30
66110 CTTTTGTTTC
* *
66120 AATTTCTTTTTCATCTTCTTTTTCACTCTCA
1 AATTTCTTTTTCTTC-TCTTTTTCAATCTCA
66151 AATTTC-TTTTCGTTCTCTTTTTCAATCTC-
1 AATTTCTTTTTC-TTCTCTTTTTCAATCTCA
* *
66180 ATTTTCTTTTTCATTTTCTTTTT
1 AATTTCTTTTTC-TTCTCTTTTT
66203 GCTTTTCAAA
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:0.13, C:0.22, G:0.01, T:0.64
Consensus pattern (30 bp):
AATTTCTTTTTCTTCTCTTTTTCAATCTCA
Found at i:66202 original size:18 final size:18
Alignment explanation
Indices: 66153--66208 Score: 51
Period size: 18 Copynumber: 3.1 Consensus size: 18
66143 CACTCTCAAA
* *
66153 TTTC-TTTTCGTTCTCTT
1 TTTCATTTTCATTTTCTT
* *
66170 TTTCAATCTCATTTTCTT
1 TTTCATTTTCATTTTCTT
*
66188 TTTCATTTTCTTTTTGCTT
1 TTTCATTTTCATTTT-CTT
66207 TT
1 TT
66209 CAAAAGCTTT
Statistics
Matches: 30, Mismatches: 7, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
17 4 0.13
18 21 0.70
19 5 0.17
ACGTcount: A:0.07, C:0.20, G:0.04, T:0.70
Consensus pattern (18 bp):
TTTCATTTTCATTTTCTT
Found at i:66209 original size:12 final size:12
Alignment explanation
Indices: 66178--66202 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
66168 TTTTTCAATC
66178 TCATTTTCTTTT
1 TCATTTTCTTTT
66190 TCATTTTCTTTT
1 TCATTTTCTTTT
66202 T
1 T
66203 GCTTTTCAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.08, C:0.16, G:0.00, T:0.76
Consensus pattern (12 bp):
TCATTTTCTTTT
Found at i:66321 original size:15 final size:14
Alignment explanation
Indices: 66271--66320 Score: 57
Period size: 15 Copynumber: 3.4 Consensus size: 14
66261 CTCTTGCCTC
*
66271 TCTTTTCTTTTTATT
1 TCTTTTCTTTTT-CT
66286 TCATTTTCTTTTTCT
1 TC-TTTTCTTTTTCT
66301 TCTTTTGCTTTTTCT
1 TCTTTT-CTTTTTCT
66316 T-TTTT
1 TCTTTT
66321 TTTCTTTATT
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
14 8 0.25
15 14 0.44
16 10 0.31
ACGTcount: A:0.04, C:0.16, G:0.02, T:0.78
Consensus pattern (14 bp):
TCTTTTCTTTTTCT
Found at i:66337 original size:21 final size:21
Alignment explanation
Indices: 66269--66338 Score: 65
Period size: 20 Copynumber: 3.3 Consensus size: 21
66259 GCCTCTTGCC
66269 TCTCTTTTCTTTTTATTTCATTT
1 TCTCTTTTCTTTTT-TTT-ATTT
* **
66292 TCT-TTTTCTTCTTTTGCTTT
1 TCTCTTTTCTTTTTTTTATTT
66312 T-TCTTTT-TTTTTCTTTATTT
1 TCTCTTTTCTTTTT-TTTATTT
66332 TCTCTTT
1 TCTCTTT
66339 ACAAGAATGT
Statistics
Matches: 38, Mismatches: 6, Indels: 8
0.73 0.12 0.15
Matches are distributed among these distances:
19 5 0.13
20 14 0.37
21 7 0.18
22 9 0.24
23 3 0.08
ACGTcount: A:0.04, C:0.17, G:0.01, T:0.77
Consensus pattern (21 bp):
TCTCTTTTCTTTTTTTTATTT
Found at i:67201 original size:4 final size:4
Alignment explanation
Indices: 67192--67219 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
67182 AAGTTTTATT
67192 TTTA TTTA TTTA TTTA TTTA TTTA TTTA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA
67220 CTTAGCTTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (4 bp):
TTTA
Found at i:72459 original size:18 final size:17
Alignment explanation
Indices: 72426--72459 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
72416 ACAACTTGAA
*
72426 TTTTTTTTAATTCGAAT
1 TTTTTTTTAATACGAAT
72443 TTTTTTTTAACTACGAA
1 TTTTTTTTAA-TACGAA
72460 CCTATTTCGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.26, C:0.09, G:0.06, T:0.59
Consensus pattern (17 bp):
TTTTTTTTAATACGAAT
Found at i:73998 original size:30 final size:30
Alignment explanation
Indices: 73912--74009 Score: 90
Period size: 30 Copynumber: 3.3 Consensus size: 30
73902 TTAAACTAAA
* *
73912 ATGAGCTAAGCTTTAGCTCGTGAGCTAAAG
1 ATGAGCTAAGATTTAGCTCGTGAGCTGAAG
* * * * *
73942 TTGAGCTGAA-ATTAAACTCCTAAGCTGAAG
1 ATGAGCT-AAGATTTAGCTCGTGAGCTGAAG
* * *
73972 CTGAGCTAAGGTTTAGCTCGTGAGCTGAAT
1 ATGAGCTAAGATTTAGCTCGTGAGCTGAAG
74002 ATGAGCTA
1 ATGAGCTA
74010 GGAGTGAGCT
Statistics
Matches: 51, Mismatches: 15, Indels: 4
0.73 0.21 0.06
Matches are distributed among these distances:
29 2 0.04
30 47 0.92
31 2 0.04
ACGTcount: A:0.31, C:0.16, G:0.26, T:0.28
Consensus pattern (30 bp):
ATGAGCTAAGATTTAGCTCGTGAGCTGAAG
Found at i:75440 original size:21 final size:20
Alignment explanation
Indices: 75401--75440 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
75391 ATCAGCTCAC
*
75401 TTGAGCTCGATTCAGCTCGT
1 TTGAGCTAGATTCAGCTCGT
*
75421 TTGAGCTAGAATTTAGCTCG
1 TTGAGCTAG-ATTCAGCTCG
75441 ATCTAGCTCA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.20, C:0.20, G:0.25, T:0.35
Consensus pattern (20 bp):
TTGAGCTAGATTCAGCTCGT
Found at i:77911 original size:21 final size:20
Alignment explanation
Indices: 77883--77942 Score: 59
Period size: 21 Copynumber: 2.9 Consensus size: 20
77873 TTGTAATGAT
77883 AAAACAAAGAAAAG-AAAAGA
1 AAAACAAA-AAAAGAAAAAGA
*
77903 AAAAGCAAAAGAAGAAAAAGA
1 AAAA-CAAAAAAAGAAAAAGA
*
77924 AAACAAAATAAAAAGAAAA
1 AAA-ACAA-AAAAAGAAAA
77943 GAGAGGCAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
20 8 0.24
21 15 0.45
22 10 0.30
ACGTcount: A:0.80, C:0.05, G:0.13, T:0.02
Consensus pattern (20 bp):
AAAACAAAAAAAGAAAAAGA
Found at i:77912 original size:6 final size:5
Alignment explanation
Indices: 77888--77944 Score: 53
Period size: 5 Copynumber: 11.0 Consensus size: 5
77878 ATGATAAAAC
* * *
77888 AAAGA AAAGA AAAGAA AAAGCA AAAGA AGA-A AAAGA AAACA AAATAA
1 AAAGA AAAGA AAAG-A AAAG-A AAAGA AAAGA AAAGA AAAGA AAA-GA
77935 AAAGA AAAGA
1 AAAGA AAAGA
77945 GAGGCAAAAG
Statistics
Matches: 43, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
4 3 0.07
5 26 0.60
6 14 0.33
ACGTcount: A:0.79, C:0.04, G:0.16, T:0.02
Consensus pattern (5 bp):
AAAGA
Found at i:77937 original size:25 final size:25
Alignment explanation
Indices: 77892--77940 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 25
77882 TAAAACAAAG
*
77892 AAAAGAAAAGAAAAAGCAAAAGAAGA
1 AAAAGAAAACAAAAA-CAAAAGAAGA
77918 AAAAGAAAACAAAATA-AAAAGAA
1 AAAAGAAAACAAAA-ACAAAAGAA
77941 AAGAGAGGCA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
25 7 0.33
26 13 0.62
27 1 0.05
ACGTcount: A:0.80, C:0.04, G:0.14, T:0.02
Consensus pattern (25 bp):
AAAAGAAAACAAAAACAAAAGAAGA
Found at i:78023 original size:13 final size:12
Alignment explanation
Indices: 77992--78023 Score: 64
Period size: 12 Copynumber: 2.7 Consensus size: 12
77982 TTGAGAGACC
77992 TTGAAAAAGCCT
1 TTGAAAAAGCCT
78004 TTGAAAAAGCCT
1 TTGAAAAAGCCT
78016 TTGAAAAA
1 TTGAAAAA
78024 CAAAAAGAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.47, C:0.12, G:0.16, T:0.25
Consensus pattern (12 bp):
TTGAAAAAGCCT
Found at i:78056 original size:12 final size:12
Alignment explanation
Indices: 78031--78073 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
78021 AAACAAAAAG
* *
78031 AAAAGAAAAAGA
1 AAAAGAGAATGA
* *
78043 AAATGAGATTGA
1 AAAAGAGAATGA
78055 AAAAGAGAATGA
1 AAAAGAGAATGA
78067 AAAAGAG
1 AAAAGAG
78074 TTTCAGAGAG
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.67, C:0.00, G:0.23, T:0.09
Consensus pattern (12 bp):
AAAAGAGAATGA
Found at i:80269 original size:24 final size:24
Alignment explanation
Indices: 80239--80317 Score: 90
Period size: 24 Copynumber: 3.3 Consensus size: 24
80229 GAAATGAAAA
*
80239 AAAAAGAAAAAGAGATTGAGAGTG
1 AAAAAGAAAAAGAGATTGAGAGAG
*
80263 AAAAAGAAAATA-AGATTGA-AAAG
1 AAAAAGAAAA-AGAGATTGAGAGAG
* * *
80286 AGAATGAAAAAGAGTTTGAGAGAG
1 AAAAAGAAAAAGAGATTGAGAGAG
80310 AAAAAGAA
1 AAAAAGAA
80318 TGTGAACAAG
Statistics
Matches: 44, Mismatches: 8, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
22 1 0.02
23 16 0.36
24 26 0.59
25 1 0.02
ACGTcount: A:0.62, C:0.00, G:0.25, T:0.13
Consensus pattern (24 bp):
AAAAAGAAAAAGAGATTGAGAGAG
Found at i:85343 original size:30 final size:30
Alignment explanation
Indices: 85258--85354 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
85248 TAAACTAAAA
* *
85258 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGGTTTAGCTCGTGAGCTGAAGT
* * * * * *
85288 TGAGCTGAGGCTAAACTCCTAAGCTGAAGT
1 TGAGCTAAGGTTTAGCTCGTGAGCTGAAGT
85318 TGAGCTAAGGTTTAGCTCGTGAGCTGAA-T
1 TGAGCTAAGGTTTAGCTCGTGAGCTGAAGT
85347 ATGAGCTA
1 -TGAGCTA
85355 GGAGTGAGCT
Statistics
Matches: 52, Mismatches: 14, Indels: 2
0.76 0.21 0.03
Matches are distributed among these distances:
29 1 0.02
30 51 0.98
ACGTcount: A:0.28, C:0.16, G:0.28, T:0.28
Consensus pattern (30 bp):
TGAGCTAAGGTTTAGCTCGTGAGCTGAAGT
Found at i:87455 original size:15 final size:15
Alignment explanation
Indices: 87437--87486 Score: 54
Period size: 15 Copynumber: 3.5 Consensus size: 15
87427 GAATCACTCG
87437 TTTCTTTTATTTCAA
1 TTTCTTTTATTTCAA
87452 TTTCTTTCTATTT-AA
1 TTTCTTT-TATTTCAA
*
87467 --TCTCTT-TTTCAA
1 TTTCTTTTATTTCAA
87479 TTTCTTTT
1 TTTCTTTT
87487 TCAACTTCTT
Statistics
Matches: 29, Mismatches: 2, Indels: 9
0.73 0.05 0.22
Matches are distributed among these distances:
11 3 0.10
12 3 0.10
13 4 0.14
14 5 0.17
15 9 0.31
16 5 0.17
ACGTcount: A:0.16, C:0.16, G:0.00, T:0.68
Consensus pattern (15 bp):
TTTCTTTTATTTCAA
Found at i:87486 original size:12 final size:12
Alignment explanation
Indices: 87446--87500 Score: 56
Period size: 12 Copynumber: 4.3 Consensus size: 12
87436 GTTTCTTTTA
87446 TTTCAATTTCTTT
1 TTTCAATTTC-TT
* *
87459 CTATTTAATCTCTT
1 -T-TTCAATTTCTT
87473 TTTCAATTTCTT
1 TTTCAATTTCTT
*
87485 TTTCAACTTCTT
1 TTTCAATTTCTT
87497 TTTC
1 TTTC
87501 TCTCTCAAAT
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
12 24 0.69
13 1 0.03
14 3 0.09
15 7 0.20
ACGTcount: A:0.16, C:0.20, G:0.00, T:0.64
Consensus pattern (12 bp):
TTTCAATTTCTT
Found at i:90190 original size:30 final size:30
Alignment explanation
Indices: 90105--90201 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
90095 TAAACTAAAA
* *
90105 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGGTTTAGCTCGTGAGCTGAAGT
* * * * * *
90135 TGAGCTGAGGCTAAACTCCTAAGCTGAAGT
1 TGAGCTAAGGTTTAGCTCGTGAGCTGAAGT
90165 TGAGCTAAGGTTTAGCTCGTGAGCTGAA-T
1 TGAGCTAAGGTTTAGCTCGTGAGCTGAAGT
90194 ATGAGCTA
1 -TGAGCTA
90202 GGAGTGAGCT
Statistics
Matches: 52, Mismatches: 14, Indels: 2
0.76 0.21 0.03
Matches are distributed among these distances:
29 1 0.02
30 51 0.98
ACGTcount: A:0.28, C:0.16, G:0.28, T:0.28
Consensus pattern (30 bp):
TGAGCTAAGGTTTAGCTCGTGAGCTGAAGT
Found at i:91530 original size:21 final size:20
Alignment explanation
Indices: 91486--91534 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
91476 TCAGCTCCCA
* *
91486 TCAGCTCACTTGAGCTCGAT
1 TCAGCTCGCTTGAGCTAGAT
*
91506 TCAGCTCGTTTGAGCTAGAAT
1 TCAGCTCGCTTGAGCTAG-AT
91527 TCAGCTCG
1 TCAGCTCG
91535 ATCTAGCTCA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
20 15 0.60
21 10 0.40
ACGTcount: A:0.20, C:0.27, G:0.22, T:0.31
Consensus pattern (20 bp):
TCAGCTCGCTTGAGCTAGAT
Found at i:94979 original size:33 final size:33
Alignment explanation
Indices: 94941--95003 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
94931 GATTACTCAC
94941 TTCACTCG-TTTCTTTT-ATAGACTCTCTTTCTTT
1 TTCACTCGATTTCTTTTCA-AG-CTCTCTTTCTTT
*
94974 TTCACTTGATTTCTTTTCAAGCTCTCTTTC
1 TTCACTCGATTTCTTTTCAAGCTCTCTTTC
95004 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:0.25, G:0.06, T:0.56
Consensus pattern (33 bp):
TTCACTCGATTTCTTTTCAAGCTCTCTTTCTTT
Found at i:95030 original size:27 final size:27
Alignment explanation
Indices: 95000--95086 Score: 97
Period size: 27 Copynumber: 3.1 Consensus size: 27
94990 TCAAGCTCTC
*
95000 TTTCAATTTCTTTT-TTCGCTTTTTCTT
1 TTTCAATTTCTTTTCTTC-CATTTTCTT
* *
95027 TTTCAATTTTTTTTCATTCTCAATTTCTT
1 TTTCAATTTCTTTTC-TTC-CATTTTCTT
95056 TTTCAATTTTCTTTTCTT-CATTTTCTT
1 TTTCAA-TTTCTTTTCTTCCATTTTCTT
95083 TTTC
1 TTTC
95087 TCTCACTTTT
Statistics
Matches: 51, Mismatches: 6, Indels: 6
0.81 0.10 0.10
Matches are distributed among these distances:
27 25 0.49
29 18 0.35
30 8 0.16
ACGTcount: A:0.11, C:0.18, G:0.01, T:0.69
Consensus pattern (27 bp):
TTTCAATTTCTTTTCTTCCATTTTCTT
Found at i:95041 original size:17 final size:18
Alignment explanation
Indices: 95018--95060 Score: 61
Period size: 17 Copynumber: 2.4 Consensus size: 18
95008 TCTTTTTTCG
* *
95018 CTTTTTCTTTTTCAATTT
1 CTTTTTCATTCTCAATTT
95036 -TTTTTCATTCTCAATTT
1 CTTTTTCATTCTCAATTT
95053 CTTTTTCA
1 CTTTTTCA
95061 ATTTTCTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
17 15 0.68
18 7 0.32
ACGTcount: A:0.14, C:0.19, G:0.00, T:0.67
Consensus pattern (18 bp):
CTTTTTCATTCTCAATTT
Found at i:95062 original size:29 final size:27
Alignment explanation
Indices: 95021--95086 Score: 89
Period size: 29 Copynumber: 2.4 Consensus size: 27
95011 TTTTTCGCTT
95021 TTTCTTTTTCAATTTT-TTTTCATTCTCAA
1 TTTCTTTTTCAATTTTCTTTTC--T-TCAA
*
95050 TTTCTTTTTCAATTTTCTTTTCTTCAT
1 TTTCTTTTTCAATTTTCTTTTCTTCAA
95077 TTTCTTTTTC
1 TTTCTTTTTC
95087 TCTCACTTTT
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
27 13 0.37
28 1 0.03
29 16 0.46
30 5 0.14
ACGTcount: A:0.12, C:0.18, G:0.00, T:0.70
Consensus pattern (27 bp):
TTTCTTTTTCAATTTTCTTTTCTTCAA
Found at i:95070 original size:12 final size:12
Alignment explanation
Indices: 95021--95118 Score: 50
Period size: 12 Copynumber: 8.6 Consensus size: 12
95011 TTTTTCGCTT
95021 TTTCTTTTTCAA
1 TTTCTTTTTCAA
95033 TTT-TTTTTC-A
1 TTTCTTTTTCAA
95043 -TTC----TCAA
1 TTTCTTTTTCAA
95050 TTTCTTTTTCAA
1 TTTCTTTTTCAA
*
95062 TTTTCTTTTCTTCAT
1 -TTTC-TTT-TTCAA
**
95077 TTTCTTTTTCTC
1 TTTCTTTTTCAA
** *
95089 TCACTTTTT-GA
1 TTTCTTTTTCAA
95100 TTTCTTTTTCAA
1 TTTCTTTTTCAA
*
95112 TCTCTTT
1 TTTCTTT
95119 CTCCTTTTCT
Statistics
Matches: 64, Mismatches: 11, Indels: 22
0.66 0.11 0.23
Matches are distributed among these distances:
6 2 0.03
7 1 0.02
8 3 0.05
9 2 0.03
10 1 0.02
11 13 0.20
12 24 0.38
13 7 0.11
14 7 0.11
15 4 0.06
ACGTcount: A:0.12, C:0.19, G:0.01, T:0.67
Consensus pattern (12 bp):
TTTCTTTTTCAA
Found at i:96129 original size:11 final size:10
Alignment explanation
Indices: 96113--96151 Score: 53
Period size: 10 Copynumber: 3.8 Consensus size: 10
96103 AGACTTTTCA
96113 CTTTTTTTGTT
1 CTTTTTTT-TT
96124 CTTTTTTTTT
1 CTTTTTTTTT
96134 AC-TTTTTTTT
1 -CTTTTTTTTT
96144 CTTTTTTT
1 CTTTTTTT
96152 GCTCACTTCT
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
9 1 0.04
10 16 0.62
11 9 0.35
ACGTcount: A:0.03, C:0.10, G:0.03, T:0.85
Consensus pattern (10 bp):
CTTTTTTTTT
Found at i:96132 original size:22 final size:21
Alignment explanation
Indices: 96107--96167 Score: 70
Period size: 20 Copynumber: 2.8 Consensus size: 21
96097 CTCGCAAGAC
96107 TTTTCACTTTTTTTGTTCTTTT
1 TTTTCACTTTTTTT-TTCTTTT
*
96129 TTTTTAC-TTTTTTTTCTTTT
1 TTTTCACTTTTTTTTTCTTTT
96149 TTTGCTCACTTCTTTTTTT
1 TTT--TCACTT-TTTTTTT
96168 TTTGAATTTC
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
20 10 0.30
21 6 0.18
22 9 0.27
23 1 0.03
24 7 0.21
ACGTcount: A:0.05, C:0.15, G:0.03, T:0.77
Consensus pattern (21 bp):
TTTTCACTTTTTTTTTCTTTT
Found at i:98237 original size:18 final size:19
Alignment explanation
Indices: 98200--98247 Score: 62
Period size: 18 Copynumber: 2.5 Consensus size: 19
98190 AATAGTCCAT
*
98200 TCATGAACTTAATGATTAAG
1 TCATGAACCTAA-GATTAAG
98220 TCATGAACCTAA-ATTAAG
1 TCATGAACCTAAGATTAAG
*
98238 ACATGAACCT
1 TCATGAACCT
98248 TCTAGAAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
18 15 0.58
20 11 0.42
ACGTcount: A:0.42, C:0.17, G:0.12, T:0.29
Consensus pattern (19 bp):
TCATGAACCTAAGATTAAG
Found at i:101818 original size:11 final size:11
Alignment explanation
Indices: 101797--101827 Score: 53
Period size: 11 Copynumber: 2.7 Consensus size: 11
101787 TGCAATTTTT
101797 TTTTCTTTTCAA
1 TTTT-TTTTCAA
101809 TTTTTTTTCAA
1 TTTTTTTTCAA
101820 TTTTTTTT
1 TTTTTTTT
101828 ACGTACCTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 15 0.79
12 4 0.21
ACGTcount: A:0.13, C:0.10, G:0.00, T:0.77
Consensus pattern (11 bp):
TTTTTTTTCAA
Found at i:104245 original size:20 final size:20
Alignment explanation
Indices: 104220--104266 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
104210 AGTTCCGTCC
104220 AGCTCAATTCAGCTCATTTG
1 AGCTCAATTCAGCTCATTTG
* *
104240 AGCTCAGTTCAGCTCGTTTG
1 AGCTCAATTCAGCTCATTTG
104260 AGCTCAA
1 AGCTCAA
104267 CCGAGCTTAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.23, C:0.26, G:0.19, T:0.32
Consensus pattern (20 bp):
AGCTCAATTCAGCTCATTTG
Found at i:105796 original size:15 final size:15
Alignment explanation
Indices: 105776--105823 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 15
105766 TCAAAGATGG
105776 GTTTATGGATATGAA
1 GTTTATGGATATGAA
* * *
105791 GTTTATGTAGATGGA
1 GTTTATGGATATGAA
*
105806 -TTTATGGATATAAA
1 GTTTATGGATATGAA
105820 GTTT
1 GTTT
105824 TTGTAGGTTT
Statistics
Matches: 25, Mismatches: 7, Indels: 2
0.74 0.21 0.06
Matches are distributed among these distances:
14 10 0.40
15 15 0.60
ACGTcount: A:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (15 bp):
GTTTATGGATATGAA
Found at i:105803 original size:29 final size:29
Alignment explanation
Indices: 105770--105829 Score: 93
Period size: 29 Copynumber: 2.1 Consensus size: 29
105760 AAGGATTCAA
* *
105770 AGATGGGTTTATGGATATGAAGTTTATGT
1 AGATGGATTTATGGATATAAAGTTTATGT
*
105799 AGATGGATTTATGGATATAAAGTTTTTGT
1 AGATGGATTTATGGATATAAAGTTTATGT
105828 AG
1 AG
105830 GTTTGGTTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.30, C:0.00, G:0.28, T:0.42
Consensus pattern (29 bp):
AGATGGATTTATGGATATAAAGTTTATGT
Found at i:110884 original size:29 final size:29
Alignment explanation
Indices: 110851--110907 Score: 96
Period size: 29 Copynumber: 2.0 Consensus size: 29
110841 ATAACCAAAC
*
110851 CTACAAAAACTTTATATCCATAAACCCAA
1 CTACAAAAACTTCATATCCATAAACCCAA
*
110880 CTACATAAACTTCATATCCATAAACCCA
1 CTACAAAAACTTCATATCCATAAACCCA
110908 TCTTTGAATC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.46, C:0.30, G:0.00, T:0.25
Consensus pattern (29 bp):
CTACAAAAACTTCATATCCATAAACCCAA
Found at i:116802 original size:20 final size:19
Alignment explanation
Indices: 116779--116843 Score: 51
Period size: 20 Copynumber: 3.3 Consensus size: 19
116769 AAGCTCAAAC
116779 GAGCTAAAGTAAGCTAAATT
1 GAGCTAAAGT-AGCTAAATT
116799 GAGCTCAAACG-AGCTAAATT
1 GAGCT-AAA-GTAGCTAAATT
* * * *
116819 AAGCTCATGTGAGCTAAATC
1 GAGCTAAAGT-AGCTAAATT
116839 GAGCT
1 GAGCT
116844 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:118655 original size:33 final size:33
Alignment explanation
Indices: 118617--118679 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
118607 GATTACTCAC
118617 TTCACTCG-TTTCTTTT-ATAGACTCTCTTTCTTT
1 TTCACTCGATTTCTTTTCA-AG-CTCTCTTTCTTT
*
118650 TTCACTTGATTTCTTTTCAAGCTCTCTTTC
1 TTCACTCGATTTCTTTTCAAGCTCTCTTTC
118680 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:0.25, G:0.06, T:0.56
Consensus pattern (33 bp):
TTCACTCGATTTCTTTTCAAGCTCTCTTTCTTT
Found at i:118691 original size:12 final size:12
Alignment explanation
Indices: 118658--118794 Score: 51
Period size: 12 Copynumber: 10.7 Consensus size: 12
118648 TTTTCACTTG
118658 ATTTC-TTTTCA
1 ATTTCTTTTTCA
** *
118669 AGCTCTCTTTCA
1 ATTTCTTTTTCA
*
118681 ATTTCTTTTTCGCT
1 ATTTCTTTTT--CA
*
118695 TTTTCTTTTTCA
1 ATTTCTTTTTCA
*
118707 ATTTTTTTTTCA
1 ATTTCTTTTTCA
118719 TTCTCATTTCTTTTTCA
1 -----ATTTCTTTTTCA
118736 ATTTTCTTTTCTTCA
1 A-TTTC-TTT-TTCA
* *
118751 TTTTCTTTTTCT
1 ATTTCTTTTTCA
* ** *
118763 CTCACTTTTTCG
1 ATTTCTTTTTCA
*
118775 ATTTCTCTTTCA
1 ATTTCTTTTTCA
*
118787 ATCTCTTT
1 ATTTCTTT
118795 CTCCTTTTCT
Statistics
Matches: 90, Mismatches: 25, Indels: 21
0.66 0.18 0.15
Matches are distributed among these distances:
11 3 0.03
12 48 0.53
13 7 0.08
14 17 0.19
15 4 0.04
17 11 0.12
ACGTcount: A:0.12, C:0.22, G:0.02, T:0.64
Consensus pattern (12 bp):
ATTTCTTTTTCA
Found at i:118736 original size:29 final size:27
Alignment explanation
Indices: 118695--118761 Score: 91
Period size: 29 Copynumber: 2.4 Consensus size: 27
118685 CTTTTTCGCT
*
118695 TTTTCTTTTTCAATTTTTTTTTCATTC-
1 TTTTCTTTTTCAATTTTCTTTTC-TTCA
118722 TCATTTCTTTTTCAATTTTCTTTTCTTCA
1 T--TTTCTTTTTCAATTTTCTTTTCTTCA
118751 TTTTCTTTTTC
1 TTTTCTTTTTC
118762 TCTCACTTTT
Statistics
Matches: 36, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
27 11 0.31
28 3 0.08
29 22 0.61
ACGTcount: A:0.10, C:0.18, G:0.00, T:0.72
Consensus pattern (27 bp):
TTTTCTTTTTCAATTTTCTTTTCTTCA
Found at i:119806 original size:13 final size:12
Alignment explanation
Indices: 119782--119847 Score: 53
Period size: 12 Copynumber: 5.2 Consensus size: 12
119772 CTCGCAAGAC
*
119782 TTTTCACTTTTT
1 TTTTCTCTTTTT
119794 TTTTCTTCTTTTT
1 TTTTC-TCTTTTT
*
119807 TTTAACTCGATTTTT
1 TTT-TCTC--TTTTT
* *
119822 TTGTCACTTTTT
1 TTTTCTCTTTTT
119834 TTTTCT-TTTTT
1 TTTTCTCTTTTT
119845 TTT
1 TTT
119848 CGATTTTTTT
Statistics
Matches: 43, Mismatches: 7, Indels: 9
0.73 0.12 0.15
Matches are distributed among these distances:
11 8 0.19
12 14 0.33
13 11 0.26
14 3 0.07
15 7 0.16
ACGTcount: A:0.08, C:0.14, G:0.03, T:0.76
Consensus pattern (12 bp):
TTTTCTCTTTTT
Found at i:119845 original size:22 final size:22
Alignment explanation
Indices: 119817--119859 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
119807 TTTAACTCGA
119817 TTTTTTTGTC-ACTTTTTTTTTC
1 TTTTTTTGTCGA-TTTTTTTTTC
*
119839 TTTTTTTTTCGATTTTTTTTT
1 TTTTTTTGTCGATTTTTTTTT
119860 GAATTTTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 18 0.95
23 1 0.05
ACGTcount: A:0.05, C:0.09, G:0.05, T:0.81
Consensus pattern (22 bp):
TTTTTTTGTCGATTTTTTTTTC
Found at i:119854 original size:12 final size:12
Alignment explanation
Indices: 119813--119870 Score: 61
Period size: 12 Copynumber: 5.0 Consensus size: 12
119803 TTTTTTTAAC
*
119813 TCGATTTTTTTG
1 TCGATTTTTTTT
119825 TC-ACTTTTTTTT
1 TCGA-TTTTTTTT
119837 TC--TTTTTTTT
1 TCGATTTTTTTT
119847 TCGATTTTTTTT
1 TCGATTTTTTTT
119859 T-GAATTTTTTTT
1 TCG-ATTTTTTTT
119871 GAATTTCTTC
Statistics
Matches: 41, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
10 10 0.24
11 2 0.05
12 29 0.71
ACGTcount: A:0.09, C:0.09, G:0.07, T:0.76
Consensus pattern (12 bp):
TCGATTTTTTTT
Found at i:119871 original size:11 final size:11
Alignment explanation
Indices: 119840--119876 Score: 56
Period size: 11 Copynumber: 3.3 Consensus size: 11
119830 TTTTTTTTCT
*
119840 TTTTTTTTCGAT
1 TTTTTTTT-GAA
119852 TTTTTTTTGAA
1 TTTTTTTTGAA
119863 TTTTTTTTGAA
1 TTTTTTTTGAA
119874 TTT
1 TTT
119877 CTTCTCTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
11 16 0.67
12 8 0.33
ACGTcount: A:0.14, C:0.03, G:0.08, T:0.76
Consensus pattern (11 bp):
TTTTTTTTGAA
Found at i:121514 original size:20 final size:20
Alignment explanation
Indices: 121491--121544 Score: 72
Period size: 20 Copynumber: 2.7 Consensus size: 20
121481 AGCTAAAGTA
121491 AGCTAAATTGAGCTCAAACG
1 AGCTAAATTGAGCTCAAACG
* * *
121511 AGCTAAATTAAGCTCATATG
1 AGCTAAATTGAGCTCAAACG
*
121531 AGCTAAATCGAGCT
1 AGCTAAATTGAGCT
121545 GGGAAAAACT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.39, C:0.19, G:0.19, T:0.24
Consensus pattern (20 bp):
AGCTAAATTGAGCTCAAACG
Done.