Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold35_ERROPOS97344
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: 97344
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.32
Found at i:1025 original size:20 final size:20
Alignment explanation
Indices: 979--1025 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
969 AGCTCGTTTC
*
979 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* *
999 CAACTCACTCAAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
1019 CAGCTCA
1 CAGCTCA
1026 ATCTTAACCC
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:5148 original size:20 final size:20
Alignment explanation
Indices: 5125--5171 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
5115 GGGTTAAGAT
*
5125 TGAGCTGAATTGAGCTTGAA
1 TGAGCTGAATTGAGCTCGAA
* * *
5145 TGAGTTGACTTGAGCTCGAG
1 TGAGCTGAATTGAGCTCGAA
5165 TGAGCTG
1 TGAGCTG
5172 GAAACGAGCT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.23, C:0.13, G:0.34, T:0.30
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCGAA
Found at i:8015 original size:11 final size:10
Alignment explanation
Indices: 8001--8038 Score: 58
Period size: 10 Copynumber: 3.7 Consensus size: 10
7991 ACTTTTCACT
8001 TTTTTTTGTTC
1 TTTTTTT-TTC
*
8012 TTTTTTTTAC
1 TTTTTTTTTC
8022 TTTTTTTTTC
1 TTTTTTTTTC
8032 TTTTTTT
1 TTTTTTT
8039 GCTCACTTCT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
10 18 0.72
11 7 0.28
ACGTcount: A:0.03, C:0.08, G:0.03, T:0.87
Consensus pattern (10 bp):
TTTTTTTTTC
Found at i:8046 original size:23 final size:21
Alignment explanation
Indices: 7993--8054 Score: 72
Period size: 20 Copynumber: 2.8 Consensus size: 21
7983 CTCGCAAGAC
7993 TTTTCACTTTTTTTTGTTCTTTT
1 TTTTCAC-TTTTTTT-TTCTTTT
8016 TTTT-ACTTTTTTTTTCTTTT
1 TTTTCACTTTTTTTTTCTTTT
8036 TTTGCTCACTTCTTTTTTT
1 TTT--TCACTT-TTTTTTT
8055 TTTGAATTTC
Statistics
Matches: 35, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
20 10 0.29
21 7 0.20
22 3 0.09
23 8 0.23
24 7 0.20
ACGTcount: A:0.05, C:0.15, G:0.03, T:0.77
Consensus pattern (21 bp):
TTTTCACTTTTTTTTTCTTTT
Found at i:9609 original size:20 final size:20
Alignment explanation
Indices: 9586--9632 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
9576 GGGTTAAGAT
*
9586 TGAGCTGAATTGAGCTTGAA
1 TGAGCTGAATTGAGCTCGAA
* * *
9606 TGAGTTGACTTGAGCTCGAG
1 TGAGCTGAATTGAGCTCGAA
9626 TGAGCTG
1 TGAGCTG
9633 GAAACGAGCT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.23, C:0.13, G:0.34, T:0.30
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCGAA
Found at i:11469 original size:18 final size:18
Alignment explanation
Indices: 11443--11492 Score: 64
Period size: 18 Copynumber: 2.8 Consensus size: 18
11433 AAATTGAAAG
*
11443 AAAACAAAAAGAAAACGA
1 AAAAGAAAAAGAAAACGA
** *
11461 AAAAGAAAAAGAAATTGC
1 AAAAGAAAAAGAAAACGA
11479 AAAAGAAAAAGAAA
1 AAAAGAAAAAGAAA
11493 TCAAAATAGT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.76, C:0.06, G:0.14, T:0.04
Consensus pattern (18 bp):
AAAAGAAAAAGAAAACGA
Found at i:11471 original size:6 final size:6
Alignment explanation
Indices: 11439--11492 Score: 56
Period size: 6 Copynumber: 9.2 Consensus size: 6
11429 AAAGAAATTG
* * ** *
11439 AAAG-A AAACAA AAAGAA AACGAA AAAGAA AAAGAA ATTGCA AAAGAA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA
11486 AAAGAA A
1 AAAGAA A
11493 TCAAAATAGT
Statistics
Matches: 38, Mismatches: 10, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
5 3 0.08
6 35 0.92
ACGTcount: A:0.76, C:0.06, G:0.15, T:0.04
Consensus pattern (6 bp):
AAAGAA
Found at i:11542 original size:27 final size:28
Alignment explanation
Indices: 11507--11573 Score: 84
Period size: 29 Copynumber: 2.4 Consensus size: 28
11497 AATAGTGAGA
11507 GAAAAAGAAAATGA-A-GAAAAGAAAATT
1 GAAAAAGAAAATGAGATGAAAA-AAAATT
* *
11534 GAAAAAGAAATTGAGATTGAGAAAAAATT
1 GAAAAAGAAAATGAGA-TGAAAAAAAATT
11563 GAAAAAGAAAA
1 GAAAAAGAAAA
11574 AGATTTTGAA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
27 13 0.38
28 1 0.03
29 16 0.47
30 4 0.12
ACGTcount: A:0.67, C:0.00, G:0.19, T:0.13
Consensus pattern (28 bp):
GAAAAAGAAAATGAGATGAAAAAAAATT
Found at i:11563 original size:17 final size:18
Alignment explanation
Indices: 11531--11564 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
11521 AGAAAAGAAA
11531 ATTGAAAAAGAAATTGAG
1 ATTGAAAAAGAAATTGAG
*
11549 ATTGAGAAA-AAATTGA
1 ATTGAAAAAGAAATTGA
11565 AAAAGAAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.56, C:0.00, G:0.21, T:0.24
Consensus pattern (18 bp):
ATTGAAAAAGAAATTGAG
Found at i:13649 original size:10 final size:10
Alignment explanation
Indices: 13633--13690 Score: 64
Period size: 10 Copynumber: 5.7 Consensus size: 10
13623 CAACTCCGAC
13633 CAGCTCAATT
1 CAGCTCAATT
* *
13643 GAGCTCATTT
1 CAGCTCAATT
13653 CAGCTCAA-T
1 CAGCTCAATT
13662 CGAGCTCAATT
1 C-AGCTCAATT
*
13673 TAGCTACAATT
1 CAGCT-CAATT
13684 CAGCTCA
1 CAGCTCA
13691 TTTATTTTAT
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
9 2 0.05
10 27 0.69
11 10 0.26
ACGTcount: A:0.29, C:0.28, G:0.14, T:0.29
Consensus pattern (10 bp):
CAGCTCAATT
Found at i:13656 original size:20 final size:20
Alignment explanation
Indices: 13633--13693 Score: 79
Period size: 20 Copynumber: 3.0 Consensus size: 20
13623 CAACTCCGAC
13633 CAGCTCAATTGAGCTCATTT
1 CAGCTCAATTGAGCTCATTT
*
13653 CAGCTCAATCGAGCTCAATTT
1 CAGCTCAATTGAGCTC-ATTT
*
13674 -AGCTACAATTCAGCTCATTT
1 CAGCT-CAATTGAGCTCATTT
13694 ATTTTATTGG
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
20 23 0.64
21 13 0.36
ACGTcount: A:0.28, C:0.26, G:0.13, T:0.33
Consensus pattern (20 bp):
CAGCTCAATTGAGCTCATTT
Found at i:18304 original size:21 final size:23
Alignment explanation
Indices: 18259--18305 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
18249 TCACCTGCAA
* *
18259 TAAACACATTAAAATGAGTTTAT
1 TAAACACATTAAAATCAGCTTAT
18282 TAAACACATTAAAA-CA-CTTAT
1 TAAACACATTAAAATCAGCTTAT
18303 TAA
1 TAA
18306 TCATAACACA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 7 0.32
22 1 0.05
23 14 0.64
ACGTcount: A:0.51, C:0.13, G:0.04, T:0.32
Consensus pattern (23 bp):
TAAACACATTAAAATCAGCTTAT
Found at i:23637 original size:15 final size:16
Alignment explanation
Indices: 23616--23657 Score: 77
Period size: 15 Copynumber: 2.7 Consensus size: 16
23606 TAGCTTCTTC
23616 TTTTTTTTTCACGAAA
1 TTTTTTTTTCACGAAA
23632 TTTTTTTTTCACG-AA
1 TTTTTTTTTCACGAAA
23647 TTTTTTTTTCA
1 TTTTTTTTTCA
23658 ACTTGATATC
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
15 13 0.50
16 13 0.50
ACGTcount: A:0.19, C:0.12, G:0.05, T:0.64
Consensus pattern (16 bp):
TTTTTTTTTCACGAAA
Found at i:23712 original size:12 final size:11
Alignment explanation
Indices: 23695--23727 Score: 57
Period size: 12 Copynumber: 2.9 Consensus size: 11
23685 ATGGAAACCA
23695 AATTTTTTTTT
1 AATTTTTTTTT
23706 GAATTTTTTTTT
1 -AATTTTTTTTT
23718 AATTTTTTTT
1 AATTTTTTTT
23728 GAAGAAACTA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 10 0.48
12 11 0.52
ACGTcount: A:0.18, C:0.00, G:0.03, T:0.79
Consensus pattern (11 bp):
AATTTTTTTTT
Found at i:23714 original size:11 final size:11
Alignment explanation
Indices: 23698--23730 Score: 57
Period size: 11 Copynumber: 3.0 Consensus size: 11
23688 GAAACCAAAT
23698 TTTTTTTTGAA
1 TTTTTTTTGAA
*
23709 TTTTTTTTTAA
1 TTTTTTTTGAA
23720 TTTTTTTTGAA
1 TTTTTTTTGAA
23731 GAAACTACTA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.18, C:0.00, G:0.06, T:0.76
Consensus pattern (11 bp):
TTTTTTTTGAA
Found at i:24765 original size:21 final size:23
Alignment explanation
Indices: 24720--24766 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
24710 TCACCTGCAA
* *
24720 TAAACACATTAAAATGAGTTTAT
1 TAAACACATTAAAATCAGCTTAT
24743 TAAACACATTAAAA-CA-CTTAT
1 TAAACACATTAAAATCAGCTTAT
24764 TAA
1 TAA
24767 TCATAGCACA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 7 0.32
22 1 0.05
23 14 0.64
ACGTcount: A:0.51, C:0.13, G:0.04, T:0.32
Consensus pattern (23 bp):
TAAACACATTAAAATCAGCTTAT
Found at i:28258 original size:13 final size:12
Alignment explanation
Indices: 28240--28281 Score: 54
Period size: 10 Copynumber: 3.7 Consensus size: 12
28230 TGTGAGCGAG
28240 AAAAGAACATTGA
1 AAAAGAA-ATTGA
28253 AAAAGAAATTG-
1 AAAAGAAATTGA
28264 -AAAGAAA-TGA
1 AAAAGAAATTGA
28274 AAAAGAAA
1 AAAAGAAA
28282 AAATATGAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
9 2 0.07
10 7 0.26
11 7 0.26
12 4 0.15
13 7 0.26
ACGTcount: A:0.69, C:0.02, G:0.17, T:0.12
Consensus pattern (12 bp):
AAAAGAAATTGA
Found at i:29269 original size:20 final size:20
Alignment explanation
Indices: 29223--29269 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
29213 AGCTCGTTTC
*
29223 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* *
29243 CAACTCACTCAAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
29263 CAGCTCA
1 CAGCTCA
29270 ATCTTAACCC
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:30794 original size:14 final size:14
Alignment explanation
Indices: 30770--30824 Score: 67
Period size: 14 Copynumber: 3.8 Consensus size: 14
30760 AAAAAAAATC
30770 AAAAAAAAAATTTG
1 AAAAAAAAAATTTG
30784 AAAAAAAAAATTTG
1 AAAAAAAAAATTTG
*
30798 ATTGAAAAAAAAA-TTC
1 A---AAAAAAAAATTTG
30814 AAAAAAAAAAT
1 AAAAAAAAAAT
30825 CGAGCAAAAA
Statistics
Matches: 36, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
13 9 0.25
14 15 0.42
16 3 0.08
17 9 0.25
ACGTcount: A:0.73, C:0.02, G:0.05, T:0.20
Consensus pattern (14 bp):
AAAAAAAAAATTTG
Found at i:31891 original size:11 final size:12
Alignment explanation
Indices: 31875--31993 Score: 66
Period size: 12 Copynumber: 9.6 Consensus size: 12
31865 AAAGAAATTG
31875 AAAGAAAAC-AA
1 AAAGAAAACGAA
31886 AAAGAAAACGAA
1 AAAGAAAACGAA
*
31898 GAAGAAAA-GAA
1 AAAGAAAACGAA
**
31909 ATTGCAAAA-GAA
1 AAAG-AAAACGAA
*
31921 AAAGAAATCGAA
1 AAAGAAAACGAA
* *
31933 AAAGTGAGA-GAA
1 AAAG-AAAACGAA
*
31945 AAAGAAAATGAAGA
1 AAAGAAAACG-A-A
*
31959 AAAGAAAATTGAA
1 AAAGAAAA-CGAA
31972 AAAGAAAAAGCGAAA
1 AAAG-AAAA-CG-AA
31987 AAAGAAA
1 AAAGAAA
31994 TTGAAAGAGA
Statistics
Matches: 84, Mismatches: 14, Indels: 17
0.73 0.12 0.15
Matches are distributed among these distances:
11 18 0.21
12 33 0.39
13 7 0.08
14 18 0.21
15 8 0.10
ACGTcount: A:0.71, C:0.04, G:0.19, T:0.06
Consensus pattern (12 bp):
AAAGAAAACGAA
Found at i:31924 original size:56 final size:55
Alignment explanation
Indices: 31862--31981 Score: 136
Period size: 57 Copynumber: 2.1 Consensus size: 55
31852 GAAAGAGATT
* *
31862 GAAAAAGAAATTGAAAGAA-A-ACAAAAAGAAAACGAAGAAGAAAAGAAATTGCAAAA
1 GAAAAAGAAATCGAAA-AAGAGACAAAAAGAAAACGAAGAA-AAAA-AAATTGAAAAA
* * *
31918 GAAAAAGAAATCGAAAAAGTGAGAGAAAAAGAAAATGAAGAAAAGAAAATTGAAAAA
1 GAAAAAGAAATCGAAAAA--GAGACAAAAAGAAAACGAAGAAAAAAAAATTGAAAAA
31975 GAAAAAG
1 GAAAAAG
31982 CGAAAAAAGA
Statistics
Matches: 55, Mismatches: 5, Indels: 7
0.82 0.07 0.10
Matches are distributed among these distances:
55 2 0.04
56 15 0.27
57 17 0.31
58 4 0.07
59 17 0.31
ACGTcount: A:0.69, C:0.03, G:0.20, T:0.07
Consensus pattern (55 bp):
GAAAAAGAAATCGAAAAAGAGACAAAAAGAAAACGAAGAAAAAAAAATTGAAAAA
Found at i:31925 original size:6 final size:6
Alignment explanation
Indices: 31875--31981 Score: 56
Period size: 6 Copynumber: 17.7 Consensus size: 6
31865 AAAGAAATTG
* * * ** *
31875 AAAG-A AAACAA AAAGAA AACGAA GAAG-A AAAGAA ATTGCA AAAGAA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA
** ** * * *
31921 AAAGAA ATCGAA AAAGTG AGAGAA AAAGAA AATGAAGA AAAGAA AATTGAA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAG-A-A AAAGAA AA-AGAA
31972 AAAGAA AAAG
1 AAAGAA AAAG
31982 CGAAAAAAGA
Statistics
Matches: 71, Mismatches: 26, Indels: 9
0.67 0.25 0.08
Matches are distributed among these distances:
5 7 0.10
6 53 0.75
7 7 0.10
8 4 0.06
ACGTcount: A:0.70, C:0.04, G:0.20, T:0.07
Consensus pattern (6 bp):
AAAGAA
Found at i:31934 original size:17 final size:17
Alignment explanation
Indices: 31878--31934 Score: 62
Period size: 17 Copynumber: 3.3 Consensus size: 17
31868 GAAATTGAAA
* *
31878 GAAAACAAAAAGAAAAC
1 GAAAAGAAAAAGAAATC
*
31895 GAAGAAG-AAAAGAAATT
1 GAA-AAGAAAAAGAAATC
31912 GCAAAAGAAAAAGAAATC
1 G-AAAAGAAAAAGAAATC
31930 GAAAA
1 GAAAA
31935 AGTGAGAGAA
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
17 19 0.58
18 14 0.42
ACGTcount: A:0.70, C:0.07, G:0.18, T:0.05
Consensus pattern (17 bp):
GAAAAGAAAAAGAAATC
Found at i:31963 original size:14 final size:13
Alignment explanation
Indices: 31942--31979 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 13
31932 AAAAGTGAGA
31942 GAAAAAGAAAA-T
1 GAAAAAGAAAATT
31954 GAAGAAAAGAAAATT
1 G-A-AAAAGAAAATT
31969 GAAAAAGAAAA
1 GAAAAAGAAAA
31980 AGCGAAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
12 1 0.04
13 10 0.43
14 10 0.43
15 2 0.09
ACGTcount: A:0.74, C:0.00, G:0.18, T:0.08
Consensus pattern (13 bp):
GAAAAAGAAAATT
Found at i:31976 original size:13 final size:12
Alignment explanation
Indices: 31861--31979 Score: 63
Period size: 12 Copynumber: 10.0 Consensus size: 12
31851 AGAAAGAGAT
*
31861 TGAAAAAGAAAT
1 TGAAAAAGAAAA
31873 TG--AAAGAAAA
1 TGAAAAAGAAAA
*
31883 -CAAAAAGAAAA
1 TGAAAAAGAAAA
* *
31894 CGAAGAAGAAAA
1 TGAAAAAGAAAA
**
31906 -GAAATTGCAAAA
1 TGAAAAAG-AAAA
31918 -GAAAAAG-AAA
1 TGAAAAAGAAAA
* *
31928 TCGAAAAAGTGAGA
1 T-GAAAAAG-AAAA
31942 -GAAAAAGAAAA
1 TGAAAAAGAAAA
31953 TGAAGAAAAGAAAA
1 TG-A-AAAAGAAAA
31967 TTGAAAAAGAAAA
1 -TGAAAAAGAAAA
31980 AGCGAAAAAA
Statistics
Matches: 83, Mismatches: 12, Indels: 23
0.70 0.10 0.19
Matches are distributed among these distances:
10 10 0.12
11 14 0.17
12 35 0.42
13 10 0.12
14 12 0.14
15 2 0.02
ACGTcount: A:0.69, C:0.03, G:0.19, T:0.08
Consensus pattern (12 bp):
TGAAAAAGAAAA
Found at i:31993 original size:21 final size:21
Alignment explanation
Indices: 31943--31993 Score: 50
Period size: 21 Copynumber: 2.4 Consensus size: 21
31933 AAAGTGAGAG
*
31943 AAAAAGAAAATGAAGAAAAGA
1 AAAAAGAAAAAGAAGAAAAGA
** *
31964 AAATTGAAAAAGAA-AAAGCGA
1 AAAAAGAAAAAGAAGAAA-AGA
31985 AAAAAGAAA
1 AAAAAGAAA
31994 TTGAAAGAGA
Statistics
Matches: 23, Mismatches: 6, Indels: 2
0.74 0.19 0.06
Matches are distributed among these distances:
20 3 0.13
21 20 0.87
ACGTcount: A:0.75, C:0.02, G:0.18, T:0.06
Consensus pattern (21 bp):
AAAAAGAAAAAGAAGAAAAGA
Found at i:33879 original size:20 final size:20
Alignment explanation
Indices: 33833--33879 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
33823 AGCTCGTTTC
*
33833 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* *
33853 CAACTCACTCAAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
33873 CAGCTCA
1 CAGCTCA
33880 ATCTTAACCC
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:37770 original size:32 final size:32
Alignment explanation
Indices: 37699--37777 Score: 95
Period size: 32 Copynumber: 2.5 Consensus size: 32
37689 AACAGCAGCA
* * * *
37699 AAAACACATTAAGTAGCAGCATTAAATTCGTC
1 AAAACACATTAAATAACAGCATTAAATACGAC
* * *
37731 CAGACACATTAAATAACAGCATTAACTACGAC
1 AAAACACATTAAATAACAGCATTAAATACGAC
37763 AAAACACATTAAATA
1 AAAACACATTAAATA
37778 GACTTAAGAC
Statistics
Matches: 38, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
32 38 1.00
ACGTcount: A:0.49, C:0.20, G:0.09, T:0.22
Consensus pattern (32 bp):
AAAACACATTAAATAACAGCATTAAATACGAC
Found at i:37966 original size:20 final size:19
Alignment explanation
Indices: 37935--37972 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
37925 AGCTAGTAAC
*
37935 GAGCTCAATGAGTTGAATT
1 GAGCTCAATGAGCTGAATT
37954 GAGCTCGAATGAGCTGAAT
1 GAGCTC-AATGAGCTGAAT
37973 CGAAAATGTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.32, C:0.13, G:0.29, T:0.26
Consensus pattern (19 bp):
GAGCTCAATGAGCTGAATT
Found at i:39365 original size:12 final size:12
Alignment explanation
Indices: 39348--39373 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
39338 TTTAACTTGC
39348 TGTTTGTGTCTT
1 TGTTTGTGTCTT
39360 TGTTTGTGTCTT
1 TGTTTGTGTCTT
39372 TG
1 TG
39374 CTGGTTTGGG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.00, C:0.08, G:0.27, T:0.65
Consensus pattern (12 bp):
TGTTTGTGTCTT
Found at i:41411 original size:14 final size:13
Alignment explanation
Indices: 41345--41418 Score: 64
Period size: 12 Copynumber: 5.8 Consensus size: 13
41335 TTCAACATCT
41345 TTTTCTTTTTCAA
1 TTTTCTTTTTCAA
*
41358 TTTT-TTTCTCAA
1 TTTTCTTTTTCAA
* ** *
41370 -TCTCAATCTCAA
1 TTTTCTTTTTCAA
41382 -TTTCTTTTTCAA
1 TTTTCTTTTTCAA
*
41394 TTTTCTTTTCTTAA
1 TTTTCTTTT-TCAA
41408 TTTTCTTTTTC
1 TTTTCTTTTTC
41419 TCTCACTTTT
Statistics
Matches: 48, Mismatches: 10, Indels: 6
0.75 0.16 0.09
Matches are distributed among these distances:
11 2 0.04
12 21 0.44
13 13 0.27
14 12 0.25
ACGTcount: A:0.16, C:0.19, G:0.00, T:0.65
Consensus pattern (13 bp):
TTTTCTTTTTCAA
Found at i:41445 original size:18 final size:18
Alignment explanation
Indices: 41424--41478 Score: 65
Period size: 18 Copynumber: 3.1 Consensus size: 18
41414 TTTTCTCTCA
*
41424 CTTTTTTGATTTCTTTTT
1 CTTTTTCGATTTCTTTTT
* * *
41442 CTTTTGCAATTTATTTTT
1 CTTTTTCGATTTCTTTTT
*
41460 CTTTTTCGTTTTCTTTTT
1 CTTTTTCGATTTCTTTTT
41478 C
1 C
41479 GATTTCATTA
Statistics
Matches: 29, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.07, C:0.15, G:0.05, T:0.73
Consensus pattern (18 bp):
CTTTTTCGATTTCTTTTT
Found at i:42327 original size:15 final size:16
Alignment explanation
Indices: 42307--42346 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 16
42297 AACTTCACAC
42307 TCTTTTTTTTT-AATT
1 TCTTTTTTTTTGAATT
42322 TCTTTTTTTTTTGAATT
1 TC-TTTTTTTTTGAATT
42339 TCCTTTTT
1 T-CTTTTT
42347 CTTCAAATTT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
15 2 0.09
16 9 0.41
17 10 0.45
18 1 0.05
ACGTcount: A:0.10, C:0.10, G:0.03, T:0.78
Consensus pattern (16 bp):
TCTTTTTTTTTGAATT
Found at i:42331 original size:17 final size:18
Alignment explanation
Indices: 42309--42346 Score: 62
Period size: 16 Copynumber: 2.2 Consensus size: 18
42299 CTTCACACTC
42309 TTTTTTTTT-AATTT-CT
1 TTTTTTTTTGAATTTCCT
42325 TTTTTTTTTGAATTTCCT
1 TTTTTTTTTGAATTTCCT
42343 TTTT
1 TTTT
42347 CTTCAAATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 9 0.45
17 5 0.25
18 6 0.30
ACGTcount: A:0.11, C:0.08, G:0.03, T:0.79
Consensus pattern (18 bp):
TTTTTTTTTGAATTTCCT
Found at i:43951 original size:20 final size:20
Alignment explanation
Indices: 43928--43991 Score: 65
Period size: 20 Copynumber: 3.2 Consensus size: 20
43918 AGCTCAAACA
*
43928 AGCTAAAGTAAGCTAAATTG
1 AGCTAAAGTGAGCTAAATTG
** *
43948 AGCTAAAACGAGCTAAATTA
1 AGCTAAAGTGAGCTAAATTG
* * *
43968 AGCTCATGTGAGCTAAATCG
1 AGCTAAAGTGAGCTAAATTG
43988 AGCT
1 AGCT
43992 GGGAAAAACT
Statistics
Matches: 34, Mismatches: 10, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.41, C:0.16, G:0.20, T:0.23
Consensus pattern (20 bp):
AGCTAAAGTGAGCTAAATTG
Found at i:43964 original size:30 final size:30
Alignment explanation
Indices: 43918--43991 Score: 87
Period size: 30 Copynumber: 2.5 Consensus size: 30
43908 ACTTAAGCCA
* *
43918 AGCTCAAACAAGCTAAAGTAAGCTAAAT-TG
1 AGCTAAAACGAGCTAAAGTAAGCT-AATGTG
* *
43948 AGCTAAAACGAGCTAAATTAAGCTCATGTG
1 AGCTAAAACGAGCTAAAGTAAGCTAATGTG
*
43978 AGCTAAATCGAGCT
1 AGCTAAAACGAGCT
43992 GGGAAAAACT
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
29 2 0.05
30 36 0.95
ACGTcount: A:0.42, C:0.18, G:0.19, T:0.22
Consensus pattern (30 bp):
AGCTAAAACGAGCTAAAGTAAGCTAATGTG
Found at i:45802 original size:33 final size:33
Alignment explanation
Indices: 45764--45826 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
45754 GATTACTCAC
45764 TTCACTCG-TTTCTTTT-ACAGACTCTCTTTCTTT
1 TTCACTCGATTTCTTTTCA-AG-CTCTCTTTCTTT
*
45797 TTCACTTGATTTCTTTTCAAGCTCTCTTTC
1 TTCACTCGATTTCTTTTCAAGCTCTCTTTC
45827 AATTTCTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
33 16 0.59
34 10 0.37
35 1 0.04
ACGTcount: A:0.13, C:0.27, G:0.06, T:0.54
Consensus pattern (33 bp):
TTCACTCGATTTCTTTTCAAGCTCTCTTTCTTT
Found at i:45838 original size:12 final size:12
Alignment explanation
Indices: 45805--45996 Score: 79
Period size: 12 Copynumber: 15.7 Consensus size: 12
45795 TTTTCACTTG
45805 ATTTC-TTTTCA
1 ATTTCTTTTTCA
** *
45816 AGCTCTCTTTCA
1 ATTTCTTTTTCA
*
45828 ATTTCTTTTTCGCT
1 ATTTCTTTTT--CA
*
45842 TTTTCTTTTTCA
1 ATTTCTTTTTCA
*
45854 ATTTTTTCATTCTCA
1 ATTTCTT--TT-TCA
45869 ATTTCTTTTTCA
1 ATTTCTTTTTCA
45881 ATTTTCTTTTCTTCA
1 A-TTTC-TTT-TTCA
* *
45896 TTTTCTTTTTCT
1 ATTTCTTTTTCA
* ** *
45908 CTCACTTTTTCG
1 ATTTCTTTTTCA
45920 ATTTCTTTTTC-
1 ATTTCTTTTTCA
* ** *
45931 TTTTGCAATTTCT
1 ATTT-CTTTTTCA
*
45944 TTTTCTTTTTCA
1 ATTTCTTTTTCA
*
45956 TTTTCTTTTT--
1 ATTTCTTTTTCA
* *
45966 GTTT-TCTTTCA
1 ATTTCTTTTTCA
45977 ATTTCTTTTTCA
1 ATTTCTTTTTCA
*
45989 ATCTCTTT
1 ATTTCTTT
45997 CTCCTTTTCT
Statistics
Matches: 135, Mismatches: 32, Indels: 27
0.70 0.16 0.14
Matches are distributed among these distances:
9 4 0.03
10 3 0.02
11 9 0.07
12 74 0.55
13 13 0.10
14 19 0.14
15 13 0.10
ACGTcount: A:0.11, C:0.20, G:0.03, T:0.66
Consensus pattern (12 bp):
ATTTCTTTTTCA
Found at i:45859 original size:15 final size:15
Alignment explanation
Indices: 45841--45885 Score: 51
Period size: 15 Copynumber: 3.2 Consensus size: 15
45831 TCTTTTTCGC
45841 TTTTTCTTTTTCAAT
1 TTTTTCTTTTTCAAT
* *
45856 TTTTTCATTCTCAA-
1 TTTTTCTTTTTCAAT
45870 --TTTCTTTTTCAAT
1 TTTTTCTTTTTCAAT
45883 TTT
1 TTT
45886 CTTTTCTTCA
Statistics
Matches: 23, Mismatches: 4, Indels: 6
0.70 0.12 0.18
Matches are distributed among these distances:
12 10 0.43
15 13 0.57
ACGTcount: A:0.16, C:0.16, G:0.00, T:0.69
Consensus pattern (15 bp):
TTTTTCTTTTTCAAT
Found at i:45881 original size:27 final size:27
Alignment explanation
Indices: 45843--45906 Score: 87
Period size: 27 Copynumber: 2.4 Consensus size: 27
45833 TTTTTCGCTT
45843 TTTCTTTTTCAATTTT-TTCATTC-TCAA
1 TTTCTTTTTCAATTTTCTT--TTCTTCAA
*
45870 TTTCTTTTTCAATTTTCTTTTCTTCAT
1 TTTCTTTTTCAATTTTCTTTTCTTCAA
45897 TTTCTTTTTC
1 TTTCTTTTTC
45907 TCTCACTTTT
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
26 3 0.09
27 29 0.85
28 2 0.06
ACGTcount: A:0.12, C:0.19, G:0.00, T:0.69
Consensus pattern (27 bp):
TTTCTTTTTCAATTTTCTTTTCTTCAA
Found at i:45965 original size:18 final size:18
Alignment explanation
Indices: 45842--45970 Score: 89
Period size: 18 Copynumber: 6.8 Consensus size: 18
45832 CTTTTTCGCT
45842 TTTTCTTTTTCAATTTTTTCA
1 TTTTCTTTTTC---TTTTTCA
* **
45863 TTCTCAATTTCTTTTTCAA
1 TTTTCTTTTTCTTTTTC-A
* *
45882 TTTTCTTTTCTTCATTTTCT
1 TTTTC-TTT-TTCTTTTTCA
* **
45902 TTTTCTCTCACTTTTTCGA
1 TTTTCTTTTTCTTTTTC-A
*
45921 -TTTCTTTTTCTTTTGCA
1 TTTTCTTTTTCTTTTTCA
*
45938 ATTTCTTTTTCTTTTTCA
1 TTTTCTTTTTCTTTTTCA
*
45956 TTTTCTTTTTGTTTT
1 TTTTCTTTTTCTTTT
45971 CTTTCAATTT
Statistics
Matches: 83, Mismatches: 20, Indels: 13
0.72 0.17 0.11
Matches are distributed among these distances:
17 1 0.01
18 53 0.64
19 7 0.08
20 6 0.07
21 16 0.19
ACGTcount: A:0.10, C:0.18, G:0.02, T:0.70
Consensus pattern (18 bp):
TTTTCTTTTTCTTTTTCA
Found at i:45970 original size:11 final size:12
Alignment explanation
Indices: 45823--45988 Score: 85
Period size: 12 Copynumber: 13.4 Consensus size: 12
45813 TCAAGCTCTC
*
45823 TTTCAATTTCTT
1 TTTCATTTTCTT
*
45835 TTTCGCTTTTTCTT
1 TTT--CATTTTCTT
45849 TTTCAATTTT-TT
1 TTTC-ATTTTCTT
*
45861 CATTCTCAATTTCTT
1 --TT-TCATTTTCTT
45876 TTTCAATTTTCTTT
1 TTTC-ATTTTC-TT
45890 TCTTCATTTTCTT
1 T-TTCATTTTCTT
**
45903 TTTC-TCTCACTT
1 TTTCAT-TTTCTT
45915 TTTCGA-TTTCTT
1 TTTC-ATTTTCTT
**
45927 TTTC-TTTTGCAA
1 TTTCATTTT-CTT
*
45939 TTTCTTTTTCTT
1 TTTCATTTTCTT
45951 TTTCATTTTCTT
1 TTTCATTTTCTT
*
45963 TTT-GTTTTC--
1 TTTCATTTTCTT
*
45972 TTTCAATTTCTT
1 TTTCATTTTCTT
45984 TTTCA
1 TTTCA
45989 ATCTCTTTCT
Statistics
Matches: 118, Mismatches: 17, Indels: 38
0.68 0.10 0.22
Matches are distributed among these distances:
9 3 0.03
10 4 0.03
11 9 0.08
12 52 0.44
13 18 0.15
14 25 0.21
15 7 0.06
ACGTcount: A:0.11, C:0.19, G:0.02, T:0.68
Consensus pattern (12 bp):
TTTCATTTTCTT
Found at i:45987 original size:6 final size:6
Alignment explanation
Indices: 45829--45974 Score: 69
Period size: 6 Copynumber: 23.2 Consensus size: 6
45819 TCTCTTTCAA
* * ** *
45829 TTTCTT TTTCGCTT TTTCTT TTTCAATTT TTTCAT TCTCAA TTTCTT TTTCAAT
1 TTTCTT TTT--CTT TTTCTT TTTC---TT TTTCTT TTTCTT TTTCTT TTTC-TT
* * ** **
45883 TTTCTTT TCTTCAT TTTCTT TTTCTC TCACTT TTTCGA TTTCTT TTTCTT
1 TTTC-TT T-TTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT
* ** * *
45933 TTGCAA TTTCTT TTTCTT TTTCAT TTTCTT TTT-GT TTTCTT T
1 TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT T
45975 CAATTTCTTT
Statistics
Matches: 101, Mismatches: 31, Indels: 16
0.68 0.21 0.11
Matches are distributed among these distances:
5 4 0.04
6 73 0.72
7 9 0.09
8 9 0.09
9 6 0.06
ACGTcount: A:0.09, C:0.18, G:0.03, T:0.70
Consensus pattern (6 bp):
TTTCTT
Found at i:48579 original size:47 final size:47
Alignment explanation
Indices: 48516--48872 Score: 496
Period size: 47 Copynumber: 7.6 Consensus size: 47
48506 CCCTTCGGGA
* * *
48516 CTTATCACATTTATACACTTCCACATCCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
*
48563 CTTATCACATATATACACTGTCACATTCAT--CA----CCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
* *
48604 CTTATCTCATATATGCA-TGTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACT-TTCACATTCATCACATTGGCCATTCGGC
* *
48651 CTTATCACACATACACA-TGTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACT-TTCACATTCATCACATTGGCCATTCGGC
48698 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATTGGCCATTCGGC
* *
48747 CTTATCACATATATACACTTTCACATTCATCACATTGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
* *
48794 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
48841 CTTATCACATATATATACACTTTCACATTCAT
1 CTTATCAC--ATATATACACTTTCACATTCAT
48873 TCAAATATAC
Statistics
Matches: 281, Mismatches: 17, Indels: 22
0.88 0.05 0.07
Matches are distributed among these distances:
40 1 0.00
41 34 0.12
43 2 0.01
45 2 0.01
47 176 0.63
49 65 0.23
50 1 0.00
ACGTcount: A:0.28, C:0.29, G:0.08, T:0.34
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
Found at i:48729 original size:96 final size:95
Alignment explanation
Indices: 48516--48872 Score: 493
Period size: 96 Copynumber: 3.8 Consensus size: 95
48506 CCCTTCGGGA
* * *
48516 CTTATCACATTTATACACTTCCACATCCATCACATTGGCCATTCGGCCTTATCACATATATACAC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATACAC
48581 TG-TCACATTCAT--CA----CCATTCGGC
66 TGTTCACATTCATCACATTGGCCATTCGGC
* * * *
48604 CTTATCTCATATATGCA-TGTTCACATTCATCACATTGGCCATTCGGCCTTATCACACATACACA
1 CTTATCACATATATACACT-TTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATACA
48668 -TGTTCACATTCATCACATTGGCCATTCGGC
65 CTGTTCACATTCATCACATTGGCCATTCGGC
48698 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATAC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATAC
* *
48763 ACT-TTCACATTCATCACATTGGCTATTAGGC
64 ACTGTTCACATTCATCACATTGGCCATTCGGC
* *
48794 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATAC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCAC--ATATATAC
48859 ACT-TTCACATTCAT
64 ACTGTTCACATTCAT
48873 TCAAATATAC
Statistics
Matches: 240, Mismatches: 15, Indels: 20
0.87 0.05 0.07
Matches are distributed among these distances:
87 3 0.01
88 65 0.27
90 2 0.01
94 61 0.25
96 107 0.45
97 2 0.01
ACGTcount: A:0.28, C:0.29, G:0.08, T:0.34
Consensus pattern (95 bp):
CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATACAC
TGTTCACATTCATCACATTGGCCATTCGGC
Found at i:48795 original size:143 final size:137
Alignment explanation
Indices: 48516--48872 Score: 488
Period size: 143 Copynumber: 2.6 Consensus size: 137
48506 CCCTTCGGGA
** * * *
48516 CTTATCACATTTATACACTTCCACATCCATCACATTGGCCATTCGGCCTTATCAC--ATATATAC
1 CTTATCACACATACACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATATAC
* * *
48579 ACTGTCACATTCATCACCATTCGGCCTTATCTCATATATGCATGTTCACATTCATCACATTGGCC
66 ACTTTCACATTCATCACCATTCGGCCTTATCACATATATACATGTTCACATTCATCACATTGGCC
*
48644 ATTCGGC
131 ATTAGGC
48651 CTTATCACACATACACA-TGTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATATA
1 CTTATCACACATACACACT-TTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATATA
48715 CACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATACACT-TTCACATTCATCA
65 CACTTTCACATTCAT--CA----CCATTCGGCCTTATCACATATATACA-TGTTCACATTCATCA
*
48779 CATTGGCTATTAGGC
123 CATTGGCCATTAGGC
* * * *
48794 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATAC
1 CTTATCACACATACACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATATAC
48859 ACTTTCACATTCAT
66 ACTTTCACATTCAT
48873 TCAAATATAC
Statistics
Matches: 197, Mismatches: 14, Indels: 14
0.88 0.06 0.06
Matches are distributed among these distances:
134 1 0.01
135 48 0.24
137 21 0.11
139 2 0.01
143 123 0.62
144 2 0.01
ACGTcount: A:0.28, C:0.29, G:0.08, T:0.34
Consensus pattern (137 bp):
CTTATCACACATACACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATATAC
ACTTTCACATTCATCACCATTCGGCCTTATCACATATATACATGTTCACATTCATCACATTGGCC
ATTAGGC
Found at i:51490 original size:40 final size:40
Alignment explanation
Indices: 51458--51801 Score: 427
Period size: 40 Copynumber: 8.6 Consensus size: 40
51448 CCAGCATGAT
* * * *
51458 TGCTCTTCGGGACCTAGCCCGGATATAACACCAGAACGAA
1 TGCTCTTCGGGACTTAGCCCGGATATATCACTAGCACGAA
* * * *
51498 TGCTCTTTGGAACTTAGCACAGATATATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATATATCACTAGCACGAA
* * * *
51538 TGCTCTTCGGAACTTAGTCCAGATACATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATATATCACTAGCACGAA
* *
51578 TGCTCTTTGGGATTTAGCCCGGATATATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATATATCACTAGCACGAA
* * * *
51618 TGCTCTTCAGAACTTAGTCCGGATATATCCCTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATATATCACTAGCACGAA
* * *
51658 TGCTCTTCGGAACTTAGTCCAGATATATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATATATCACTAGCACGAA
* * * *
51698 TGCTCTTCGGGACTTAGCCCGGACACATCACTAGTATGAA
1 TGCTCTTCGGGACTTAGCCCGGATATATCACTAGCACGAA
* * * *
51738 TGCTCTTCGGGACTTAGCTCGGGTACATCACTAGCATGAA
1 TGCTCTTCGGGACTTAGCCCGGATATATCACTAGCACGAA
51778 TGCTCTTCGGGACTTAGCCCGGAT
1 TGCTCTTCGGGACTTAGCCCGGAT
51802 CATCGTCGAG
Statistics
Matches: 264, Mismatches: 40, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
40 264 1.00
ACGTcount: A:0.27, C:0.26, G:0.21, T:0.26
Consensus pattern (40 bp):
TGCTCTTCGGGACTTAGCCCGGATATATCACTAGCACGAA
Found at i:52280 original size:17 final size:17
Alignment explanation
Indices: 52260--52294 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
52250 TGCTGGAATA
52260 AATTAATTAATTAAGTT
1 AATTAATTAATTAAGTT
* *
52277 AATTAGTTAATTTAGTT
1 AATTAATTAATTAAGTT
52294 A
1 A
52295 CAGCTCTTAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.43, C:0.00, G:0.09, T:0.49
Consensus pattern (17 bp):
AATTAATTAATTAAGTT
Found at i:53747 original size:11 final size:11
Alignment explanation
Indices: 53733--53771 Score: 60
Period size: 11 Copynumber: 3.5 Consensus size: 11
53723 AAAAAAAAAG
53733 AAAAATTCAAA
1 AAAAATTCAAA
53744 AAAAATTCAAA
1 AAAAATTCAAA
*
53755 AAAAAATCGAAA
1 AAAAATTC-AAA
53767 AAAAA
1 AAAAA
53772 AAAATGAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
11 18 0.69
12 8 0.31
ACGTcount: A:0.77, C:0.08, G:0.03, T:0.13
Consensus pattern (11 bp):
AAAAATTCAAA
Found at i:53748 original size:12 final size:12
Alignment explanation
Indices: 53728--53772 Score: 58
Period size: 12 Copynumber: 3.8 Consensus size: 12
53718 ATTGAAAAAA
53728 AAAAGAAAAATTC
1 AAAA-AAAAATTC
53741 -AAAAAAAATTC
1 AAAAAAAAATTC
53752 AAAAAAAAA-TC
1 AAAAAAAAATTC
53763 GAAAAAAAAA
1 -AAAAAAAAA
53773 AAATGAAAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
11 10 0.33
12 20 0.67
ACGTcount: A:0.78, C:0.07, G:0.04, T:0.11
Consensus pattern (12 bp):
AAAAAAAAATTC
Found at i:53770 original size:15 final size:14
Alignment explanation
Indices: 53752--53784 Score: 57
Period size: 15 Copynumber: 2.3 Consensus size: 14
53742 AAAAAAATTC
53752 AAAAAAAAATCGAAA
1 AAAAAAAAAT-GAAA
53767 AAAAAAAAATGAAA
1 AAAAAAAAATGAAA
53781 AAAA
1 AAAA
53785 TCAAGTTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 8 0.44
15 10 0.56
ACGTcount: A:0.85, C:0.03, G:0.06, T:0.06
Consensus pattern (14 bp):
AAAAAAAAATGAAA
Found at i:58375 original size:39 final size:40
Alignment explanation
Indices: 58250--58473 Score: 244
Period size: 40 Copynumber: 5.7 Consensus size: 40
58240 GCTACTCGTT
* *
58250 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAAT-TAGTAACTCGCA
* * *
58290 CAAATGCCTTCGGGACTTAACCCAGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTAACTCGCA
* *
58330 CCAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTAACTCGCA
* * *
58369 CAAATGCCTTCAGG-CTTAGCCTGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTAACTCGCA
* * * *
58408 CAAATGCCTTC-GGATCTTAGTCCGG-ATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGAAT-TAGTAAC-TCGCA
58449 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
58474 CATCATTCGA
Statistics
Matches: 159, Mismatches: 18, Indels: 13
0.84 0.09 0.07
Matches are distributed among these distances:
38 2 0.01
39 70 0.44
40 74 0.47
41 13 0.08
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATTAGTAACTCGCA
Found at i:60812 original size:47 final size:47
Alignment explanation
Indices: 60749--61111 Score: 532
Period size: 47 Copynumber: 7.6 Consensus size: 47
60739 CCCTTCGGGA
* * *
60749 CTTATCACATTTATACACTTCCACATCCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
*
60796 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGAC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
* *
60843 CTTATCTCATATATGCA-TGTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACT-TTCACATTCATCACATTGGCCATTCGGC
* * *
60890 CTTATCACACATACACA-TGTTCACATTCATCACATGGGCCATTCGGC
1 CTTATCACATATATACACT-TTCACATTCATCACATTGGCCATTCGGC
60937 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATTGGCCATTCGGC
* * *
60986 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
* *
61033 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
61080 CTTATCACATATATATACACTTTCACATTCAT
1 CTTATCAC--ATATATACACTTTCACATTCAT
61112 TCAAATATAC
Statistics
Matches: 291, Mismatches: 19, Indels: 10
0.91 0.06 0.03
Matches are distributed among these distances:
46 1 0.00
47 225 0.77
49 64 0.22
50 1 0.00
ACGTcount: A:0.28, C:0.29, G:0.09, T:0.34
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
Found at i:61009 original size:143 final size:143
Alignment explanation
Indices: 60749--61111 Score: 536
Period size: 143 Copynumber: 2.6 Consensus size: 143
60739 CCCTTCGGGA
** * * * *
60749 CTTATCACATTTATACACTTCCACATCCATCACATTGGCCATTCGGCCTTATCAC--ATATATAC
1 CTTATCACACATACACACTTTCACATTCATCACATCGGCCATTCGGCCTTATCACATATATATAC
* *
60812 ACTTTCACATTCATCACATTGGCCATTCGACCTTATCTCATATATGCATGTTCACATTCATCACA
66 ACTTTCACATTCATCACATTGGCCATTCGACCTTATCACATATATACATGTTCACATTCATCACA
* *
60877 TTGGCCATTCGGC
131 TCGGCCATTAGGC
*
60890 CTTATCACACATACACA-TGTTCACATTCATCACATGGGCCATTCGGCCTTATCACATATATATA
1 CTTATCACACATACACACT-TTCACATTCATCACATCGGCCATTCGGCCTTATCACATATATATA
*
60954 CACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATACACT-TTCACATTCATCA
65 CACTTTCACATTCATCACATTGGCCATTCGACCTTATCACATATATACA-TGTTCACATTCATCA
*
61018 CATCGGCTATTAGGC
129 CATCGGCCATTAGGC
* * *
61033 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATAC
1 CTTATCACACATACACACTTTCACATTCATCACATCGGCCATTCGGCCTTATCACATATATATAC
61098 ACTTTCACATTCAT
66 ACTTTCACATTCAT
61112 TCAAATATAC
Statistics
Matches: 201, Mismatches: 16, Indels: 8
0.89 0.07 0.04
Matches are distributed among these distances:
140 1 0.00
141 47 0.23
143 151 0.75
144 2 0.01
ACGTcount: A:0.28, C:0.29, G:0.09, T:0.34
Consensus pattern (143 bp):
CTTATCACACATACACACTTTCACATTCATCACATCGGCCATTCGGCCTTATCACATATATATAC
ACTTTCACATTCATCACATTGGCCATTCGACCTTATCACATATATACATGTTCACATTCATCACA
TCGGCCATTAGGC
Found at i:64626 original size:20 final size:20
Alignment explanation
Indices: 64603--64656 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
64593 AGTTTTTCCC
*
64603 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTCACATG
* ***
64623 AGCTTAATTTAGCTCGTTTG
1 AGCTCAATTTAGCTCACATG
64643 AGCTCAATTTAGCT
1 AGCTCAATTTAGCT
64657 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:64638 original size:30 final size:30
Alignment explanation
Indices: 64603--64676 Score: 98
Period size: 30 Copynumber: 2.5 Consensus size: 30
64593 AGTTTTTCCC
64603 AGCTCGATTT-AGCTCACA-TGAGCTTAATTT
1 AGCTCG-TTTGAGCTCA-ATTGAGCTTAATTT
* *
64633 AGCTCGTTTGAGCTCAATTTAGCTTACTTT
1 AGCTCGTTTGAGCTCAATTGAGCTTAATTT
64663 AGCTCGTTTGAGCT
1 AGCTCGTTTGAGCT
64677 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:64666 original size:20 final size:20
Alignment explanation
Indices: 64603--64667 Score: 53
Period size: 20 Copynumber: 3.2 Consensus size: 20
64593 AGTTTTTCCC
* * * *
64603 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTTACTTT
*
64623 AGCTTAATTTAGC-T-CGTTT
1 AGCTCAATTTAGCTTAC-TTT
64642 GAGCTCAATTTAGCTTACTTT
1 -AGCTCAATTTAGCTTACTTT
64663 AGCTC
1 AGCTC
64668 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:66285 original size:12 final size:11
Alignment explanation
Indices: 66261--66324 Score: 51
Period size: 11 Copynumber: 5.7 Consensus size: 11
66251 TTGGAGTAAC
*
66261 AAAAAAA-TCA
1 AAAAAAATTGA
*
66271 AAAAAATTTGA
1 AAAAAAATTGA
66282 AAAAAAATTGATTA
1 AAAAAAATTG---A
*
66296 AAAAAAATT-C
1 AAAAAAATTGA
*
66306 AAAAAAAGTGA
1 AAAAAAATTGA
66317 AAAAAAAT
1 AAAAAAAT
66325 CGAGCAAAAA
Statistics
Matches: 42, Mismatches: 7, Indels: 9
0.72 0.12 0.16
Matches are distributed among these distances:
10 14 0.33
11 18 0.43
14 10 0.24
ACGTcount: A:0.72, C:0.03, G:0.06, T:0.19
Consensus pattern (11 bp):
AAAAAAATTGA
Found at i:66334 original size:35 final size:35
Alignment explanation
Indices: 66261--66337 Score: 102
Period size: 35 Copynumber: 2.2 Consensus size: 35
66251 TTGGAGTAAC
* * **
66261 AAAAAAATCAAAAAAATTTGAAAAAAAATTGATTA
1 AAAAAAATCAAAAAAATGTGAAAAAAAATCGAGCA
66296 AAAAAAATTCAAAAAAA-GTGAAAAAAAATCGAGCA
1 AAAAAAA-TCAAAAAAATGTGAAAAAAAATCGAGCA
66331 AAAAAAA
1 AAAAAAA
66338 AGAAAAGAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
35 28 0.76
36 9 0.24
ACGTcount: A:0.71, C:0.05, G:0.08, T:0.16
Consensus pattern (35 bp):
AAAAAAATCAAAAAAATGTGAAAAAAAATCGAGCA
Found at i:67396 original size:6 final size:6
Alignment explanation
Indices: 67387--67497 Score: 80
Period size: 6 Copynumber: 18.0 Consensus size: 6
67377 GAAAGAGATT
* ** *
67387 GAAAAA GAAAAAA AAAAAA GAAAAA GAAAAA GAAATT GCAAAA G-AAAA
1 GAAAAA G-AAAAA GAAAAA GAAAAA GAAAAA GAAAAA GAAAAA GAAAAA
** ** * * *
67435 GAAATC GAAAAA GTGAGA GAAAAA GAAAAT GAAGAAAA GAAAATT GAAAAA
1 GAAAAA GAAAAA GAAAAA GAAAAA GAAAAA G-A-AAAA GAAAA-A GAAAAA
67486 GAAAAA GAAAAA
1 GAAAAA GAAAAA
67498 AAAGAAATTG
Statistics
Matches: 79, Mismatches: 21, Indels: 10
0.72 0.19 0.09
Matches are distributed among these distances:
5 5 0.06
6 58 0.73
7 12 0.15
8 4 0.05
ACGTcount: A:0.74, C:0.02, G:0.18, T:0.06
Consensus pattern (6 bp):
GAAAAA
Found at i:67474 original size:14 final size:13
Alignment explanation
Indices: 67454--67498 Score: 56
Period size: 13 Copynumber: 3.4 Consensus size: 13
67444 AAAGTGAGAG
67454 AAAAAGAAAATGA
1 AAAAAGAAAATGA
67467 AGAAAAGAAAATTG-
1 A-AAAAGAAAA-TGA
*
67481 AAAAAGAAAAAGA
1 AAAAAGAAAATGA
67494 AAAAA
1 AAAAA
67499 AAGAAATTGA
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
12 1 0.04
13 15 0.54
14 10 0.36
15 2 0.07
ACGTcount: A:0.78, C:0.00, G:0.16, T:0.07
Consensus pattern (13 bp):
AAAAAGAAAATGA
Found at i:67483 original size:27 final size:27
Alignment explanation
Indices: 67453--67510 Score: 82
Period size: 27 Copynumber: 2.1 Consensus size: 27
67443 AAAAGTGAGA
* *
67453 GAAAAAGAAAATG-AAGAAAAGAAAATT
1 GAAAAAGAAAAAGAAAAAAAAG-AAATT
67480 GAAAAAGAAAAAGAAAAAAAAGAAATT
1 GAAAAAGAAAAAGAAAAAAAAGAAATT
67507 GAAA
1 GAAA
67511 GAGAGCTTGA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
27 21 0.75
28 7 0.25
ACGTcount: A:0.74, C:0.00, G:0.17, T:0.09
Consensus pattern (27 bp):
GAAAAAGAAAAAGAAAAAAAAGAAATT
Found at i:67501 original size:66 final size:66
Alignment explanation
Indices: 67387--67510 Score: 162
Period size: 66 Copynumber: 1.9 Consensus size: 66
67377 GAAAGAGATT
**
67387 GAAAAAGAAAAAAAAAAAAGAAAAAGAAAAAGAAATTGCAAAAGAAAAGAAATCGAAAAAGTGAG
1 GAAAAAGAAAAAAAAAAAAGAAAAAGAAAAAGAAAAAGCAAAAGAAAAGAAATCGAAAAAGTGAG
67452 A
66 A
* * * *
67453 GAAAAAGAAAATGAAGAAAAGAAAATTGAAAAAGAAAAAG-AAAA-AAAAGAAATTGAAA
1 GAAAAAGAAAA-AAAAAAAAGAAAA-AGAAAAAGAAAAAGCAAAAGAAAAGAAATCGAAA
67511 GAGAGCTTGA
Statistics
Matches: 50, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
66 24 0.48
67 15 0.30
68 11 0.22
ACGTcount: A:0.73, C:0.02, G:0.18, T:0.07
Consensus pattern (66 bp):
GAAAAAGAAAAAAAAAAAAGAAAAAGAAAAAGAAAAAGCAAAAGAAAAGAAATCGAAAAAGTGAG
A
Found at i:67523 original size:66 final size:65
Alignment explanation
Indices: 67377--67527 Score: 150
Period size: 66 Copynumber: 2.3 Consensus size: 65
67367 GAGAAAAGGA
**
67377 GAAAGAGA-TTGAAAAAGAAAAAAAAAAAAGAAAAAGAAAAAGAAATTGCAAAAGAAAAGAAATC
1 GAAAGAGAGTTGAAAAAGAAAAAAAAAAAAGAAAAAGAAAAAGAAAAAGCAAAAGAAAAGAAATC
* * * * *
67441 GAAAAAGTGAG-AGAAAAAGAAAATGAAGAAAAGAAAATTGAAAAAGAAAAAG-AAAA-AAAAGA
1 G--AAAGAGAGTTGAAAAAGAAAA-AAAAAAAAGAAAA-AGAAAAAGAAAAAGCAAAAGAAAAGA
*
67503 AATT
62 AATC
67507 GAAAGAGAGCTTG-AAAAGAAA
1 GAAAGAGAG-TTGAAAAAGAAA
67528 TCAAGTGAAA
Statistics
Matches: 70, Mismatches: 10, Indels: 13
0.75 0.11 0.14
Matches are distributed among these distances:
64 8 0.11
65 8 0.11
66 28 0.40
67 15 0.21
68 11 0.16
ACGTcount: A:0.70, C:0.02, G:0.20, T:0.09
Consensus pattern (65 bp):
GAAAGAGAGTTGAAAAAGAAAAAAAAAAAAGAAAAAGAAAAAGAAAAAGCAAAAGAAAAGAAATC
Found at i:67544 original size:33 final size:33
Alignment explanation
Indices: 67507--67569 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
67497 AAAAGAAATT
67507 GAAAGAGAG-CT-TGAAAAGAAATCAAGTGAAAAA
1 GAAAGAGAGTCTAT-AAAAGAAA-CAAGTGAAAAA
*
67540 GAAAGAGAGTCTATAAAAGAAACGAGTGAA
1 GAAAGAGAGTCTATAAAAGAAACAAGTGAA
67570 GTGAGTAATC
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
33 16 0.59
34 10 0.37
35 1 0.04
ACGTcount: A:0.56, C:0.06, G:0.25, T:0.13
Consensus pattern (33 bp):
GAAAGAGAGTCTATAAAAGAAACAAGTGAAAAA
Found at i:69366 original size:20 final size:20
Alignment explanation
Indices: 69343--69396 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
69333 AGTTTTTCCC
*
69343 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTCACATG
* ***
69363 AGCTTAATTTAGCTCGTTTG
1 AGCTCAATTTAGCTCACATG
69383 AGCTCAATTTAGCT
1 AGCTCAATTTAGCT
69397 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:69378 original size:30 final size:30
Alignment explanation
Indices: 69343--69416 Score: 98
Period size: 30 Copynumber: 2.5 Consensus size: 30
69333 AGTTTTTCCC
69343 AGCTCGATTT-AGCTCACA-TGAGCTTAATTT
1 AGCTCG-TTTGAGCTCA-ATTGAGCTTAATTT
* *
69373 AGCTCGTTTGAGCTCAATTTAGCTTACTTT
1 AGCTCGTTTGAGCTCAATTGAGCTTAATTT
69403 AGCTCGTTTGAGCT
1 AGCTCGTTTGAGCT
69417 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:69406 original size:20 final size:20
Alignment explanation
Indices: 69343--69407 Score: 53
Period size: 20 Copynumber: 3.2 Consensus size: 20
69333 AGTTTTTCCC
* * * *
69343 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTTACTTT
*
69363 AGCTTAATTTAGC-T-CGTTT
1 AGCTCAATTTAGCTTAC-TTT
69382 GAGCTCAATTTAGCTTACTTT
1 -AGCTCAATTTAGCTTACTTT
69403 AGCTC
1 AGCTC
69408 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:72205 original size:23 final size:22
Alignment explanation
Indices: 72153--72205 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
72143 TCCACGTCTT
*
72153 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
72175 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
72198 TTTCTTTT
1 TTTCTTTT
72206 TCACTCTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 3 0.12
22 5 0.19
23 12 0.46
24 6 0.23
ACGTcount: A:0.09, C:0.19, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTCTTTTCTTTCTTTTTCTAA
Found at i:75560 original size:43 final size:43
Alignment explanation
Indices: 75432--75578 Score: 158
Period size: 43 Copynumber: 3.4 Consensus size: 43
75422 CAATGTCATA
* * * *
75432 TCCCAGACATGGTTTTACATGTTATCA-CATATCGATGCCACTG
1 TCCCAGACATGGTCTTACATATAAT-ATCATATCGATGCCAATG
* * *
75475 TTCTAGACAAGGTCTT--ATATGAA-ATCATATACGATGCCAATG
1 TCCCAGACATGGTCTTACATAT-AATATCATAT-CGATGCCAATG
*
75517 TCCCAGACATGGTCTTACAAATAATATCATATCGATGCCAATG
1 TCCCAGACATGGTCTTACATATAATATCATATCGATGCCAATG
*
75560 TCCCAGGCATGGTCTTACA
1 TCCCAGACATGGTCTTACA
75579 CGAAATCACA
Statistics
Matches: 86, Mismatches: 12, Indels: 12
0.78 0.11 0.11
Matches are distributed among these distances:
40 1 0.01
41 8 0.09
42 24 0.28
43 43 0.50
44 10 0.12
ACGTcount: A:0.31, C:0.23, G:0.16, T:0.30
Consensus pattern (43 bp):
TCCCAGACATGGTCTTACATATAATATCATATCGATGCCAATG
Found at i:77656 original size:10 final size:10
Alignment explanation
Indices: 77640--77697 Score: 64
Period size: 10 Copynumber: 5.7 Consensus size: 10
77630 CAACTCCGAC
77640 CAGCTCAATT
1 CAGCTCAATT
* *
77650 GAGCTCATTT
1 CAGCTCAATT
77660 CAGCTCAA-T
1 CAGCTCAATT
77669 CGAGCTCAATT
1 C-AGCTCAATT
*
77680 TAGCTACAATT
1 CAGCT-CAATT
77691 CAGCTCA
1 CAGCTCA
77698 TTTATTTTAT
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
9 2 0.05
10 27 0.69
11 10 0.26
ACGTcount: A:0.29, C:0.28, G:0.14, T:0.29
Consensus pattern (10 bp):
CAGCTCAATT
Found at i:77663 original size:20 final size:20
Alignment explanation
Indices: 77640--77700 Score: 79
Period size: 20 Copynumber: 3.0 Consensus size: 20
77630 CAACTCCGAC
77640 CAGCTCAATTGAGCTCATTT
1 CAGCTCAATTGAGCTCATTT
*
77660 CAGCTCAATCGAGCTCAATTT
1 CAGCTCAATTGAGCTC-ATTT
*
77681 -AGCTACAATTCAGCTCATTT
1 CAGCT-CAATTGAGCTCATTT
77701 ATTTTATTGG
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
20 23 0.64
21 13 0.36
ACGTcount: A:0.28, C:0.26, G:0.13, T:0.33
Consensus pattern (20 bp):
CAGCTCAATTGAGCTCATTT
Found at i:78957 original size:11 final size:10
Alignment explanation
Indices: 78941--78970 Score: 51
Period size: 10 Copynumber: 2.9 Consensus size: 10
78931 GTTCGTAATG
78941 AAAAAAAAGTC
1 AAAAAAAA-TC
78952 AAAAAAAATC
1 AAAAAAAATC
78962 AAAAAAAAT
1 AAAAAAAAT
78971 TTGAGTTGGA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 11 0.58
11 8 0.42
ACGTcount: A:0.80, C:0.07, G:0.03, T:0.10
Consensus pattern (10 bp):
AAAAAAAATC
Found at i:79065 original size:11 final size:11
Alignment explanation
Indices: 79043--79090 Score: 51
Period size: 11 Copynumber: 4.3 Consensus size: 11
79033 AAAAGAGAAG
79043 AAATTCAAAAAA
1 AAATT-AAAAAA
79055 AAATTAAAAAA
1 AAATTAAAAAA
**
79066 AAATCGAAAAA
1 AAATTAAAAAA
**
79077 AAAGGAAAAAA
1 AAATTAAAAAA
79088 AAA
1 AAA
79091 GAAGTGACAA
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
11 26 0.84
12 5 0.16
ACGTcount: A:0.79, C:0.04, G:0.06, T:0.10
Consensus pattern (11 bp):
AAATTAAAAAA
Found at i:80178 original size:18 final size:18
Alignment explanation
Indices: 80152--80201 Score: 64
Period size: 18 Copynumber: 2.8 Consensus size: 18
80142 AAATTGAAAG
*
80152 AAAACAAAAAGAAAACGA
1 AAAAGAAAAAGAAAACGA
** *
80170 AAAAGAAAAAGAAATTGC
1 AAAAGAAAAAGAAAACGA
80188 AAAAGAAAAAGAAA
1 AAAAGAAAAAGAAA
80202 TCAAAATAGT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.76, C:0.06, G:0.14, T:0.04
Consensus pattern (18 bp):
AAAAGAAAAAGAAAACGA
Found at i:80180 original size:6 final size:6
Alignment explanation
Indices: 80148--80201 Score: 56
Period size: 6 Copynumber: 9.2 Consensus size: 6
80138 AAAGAAATTG
* * ** *
80148 AAAG-A AAACAA AAAGAA AACGAA AAAGAA AAAGAA ATTGCA AAAGAA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA
80195 AAAGAA A
1 AAAGAA A
80202 TCAAAATAGT
Statistics
Matches: 38, Mismatches: 10, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
5 3 0.08
6 35 0.92
ACGTcount: A:0.76, C:0.06, G:0.15, T:0.04
Consensus pattern (6 bp):
AAAGAA
Found at i:80261 original size:18 final size:18
Alignment explanation
Indices: 80240--80274 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
80230 AGAAAAGAAA
80240 ATTGA-AAAAGAAATTGAG
1 ATTGAGAAAA-AAATTGAG
80258 ATTGAGAAAAAAATTGA
1 ATTGAGAAAAAAATTGA
80275 AAAAGAAAAA
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:0.57, C:0.00, G:0.20, T:0.23
Consensus pattern (18 bp):
ATTGAGAAAAAAATTGAG
Found at i:82310 original size:20 final size:20
Alignment explanation
Indices: 82287--82332 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
82277 CCAGCTCGAA
*
82287 TTAGCTCACATGAGCTTAAT
1 TTAGCTCACATGAGCTCAAT
***
82307 TTAGCTCGTTTGAGCTCAAT
1 TTAGCTCACATGAGCTCAAT
82327 TTAGCT
1 TTAGCT
82333 TACTTTAGCT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.24, C:0.20, G:0.17, T:0.39
Consensus pattern (20 bp):
TTAGCTCACATGAGCTCAAT
Found at i:82314 original size:30 final size:30
Alignment explanation
Indices: 82279--82352 Score: 80
Period size: 30 Copynumber: 2.5 Consensus size: 30
82269 AGTTTTTCCC
82279 AGCTCGAATT-AGCTCACA-TGAGCTTAATTT
1 AGCTCG-ATTGAGCTCA-ATTGAGCTTAATTT
* * *
82309 AGCTCGTTTGAGCTCAATTTAGCTTACTTT
1 AGCTCGATTGAGCTCAATTGAGCTTAATTT
*
82339 AGCTCGTTTGAGCT
1 AGCTCGATTGAGCT
82353 TGGCTTAAGT
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
29 3 0.08
30 36 0.92
ACGTcount: A:0.23, C:0.20, G:0.19, T:0.38
Consensus pattern (30 bp):
AGCTCGATTGAGCTCAATTGAGCTTAATTT
Found at i:83980 original size:10 final size:10
Alignment explanation
Indices: 83964--84021 Score: 71
Period size: 10 Copynumber: 5.7 Consensus size: 10
83954 CAACTCCGAC
83964 CAGCTCAATT
1 CAGCTCAATT
* *
83974 GAGCTCATTT
1 CAGCTCAATT
83984 CAGCTCAATT
1 CAGCTCAATT
*
83994 GAGCTCAATT
1 CAGCTCAATT
*
84004 TAGCTACAATT
1 CAGCT-CAATT
84015 CAGCTCA
1 CAGCTCA
84022 TTTATTTTAT
Statistics
Matches: 40, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
10 31 0.77
11 9 0.22
ACGTcount: A:0.29, C:0.26, G:0.14, T:0.31
Consensus pattern (10 bp):
CAGCTCAATT
Found at i:83987 original size:20 final size:20
Alignment explanation
Indices: 83964--84024 Score: 88
Period size: 20 Copynumber: 3.0 Consensus size: 20
83954 CAACTCCGAC
83964 CAGCTCAATTGAGCTCATTT
1 CAGCTCAATTGAGCTCATTT
83984 CAGCTCAATTGAGCTCAATTT
1 CAGCTCAATTGAGCTC-ATTT
*
84005 -AGCTACAATTCAGCTCATTT
1 CAGCT-CAATTGAGCTCATTT
84025 ATTTTATTGG
Statistics
Matches: 38, Mismatches: 1, Indels: 4
0.88 0.02 0.09
Matches are distributed among these distances:
20 24 0.63
21 14 0.37
ACGTcount: A:0.28, C:0.25, G:0.13, T:0.34
Consensus pattern (20 bp):
CAGCTCAATTGAGCTCATTT
Found at i:85953 original size:21 final size:21
Alignment explanation
Indices: 85915--85954 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
85905 CCACGTCTTT
*
85915 TTCATTTGTTTCTTTTTCTAA
1 TTCATTTGTCTCTTTTTCTAA
85936 TTCATTT-TCTCTTCTTTCT
1 TTCATTTGTCTCTT-TTTCT
85955 TCAATTTCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.10, C:0.20, G:0.03, T:0.68
Consensus pattern (21 bp):
TTCATTTGTCTCTTTTTCTAA
Done.