Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1092
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: 788722
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 5
Found at i:6372 original size:31 final size:31
Alignment explanation
Indices: 6315--6497 Score: 123
Period size: 31 Copynumber: 5.8 Consensus size: 31
6305 AAGCAATGAT
* * *
6315 TTGCCACTGATTTGTGTCGGCTTTAAAAGGG
1 TTGCCACCGACTTGTGTGGGCTTTAAAAGGG
* * * *
6346 TTGCCACCGACTTATGTGGGCATTAAAGAAAGT
1 TTGCCACCGACTTGTGTGGGC-TTTAA-AAGGG
* * *
6379 TTGCCACCGACTTGTGTAGCCTTTAGAAGGG
1 TTGCCACCGACTTGTGTGGGCTTTAAAAGGG
* * ** * *
6410 TTGTCTCTAACTTTTGTGGGCTTTAGAGAAAGG
1 TTGCCACCGACTTGTGTGGGCTTTA-A-AAGGG
* * *
6443 TTTCCATCGACTTGTGTGGGCTTTAGAAGGG
1 TTGCCACCGACTTGTGTGGGCTTTAAAAGGG
* * * *
6474 TTGCTACCAACTTGTCTAGGCTTT
1 TTGCCACCGACTTGTGTGGGCTTT
6498 GTGGACTTTG
Statistics
Matches: 110, Mismatches: 38, Indels: 8
0.71 0.24 0.05
Matches are distributed among these distances:
31 60 0.55
32 7 0.06
33 43 0.39
ACGTcount: A:0.21, C:0.18, G:0.27, T:0.34
Consensus pattern (31 bp):
TTGCCACCGACTTGTGTGGGCTTTAAAAGGG
Found at i:6466 original size:33 final size:32
Alignment explanation
Indices: 6326--6475 Score: 103
Period size: 33 Copynumber: 4.7 Consensus size: 32
6316 TGCCACTGAT
* * *
6326 TTGTGTCGGCTTTAA-AAGGGTTGCCACCGAC
1 TTGTGTGGGCTTTAAGAAAGGTTTCCACCGAC
* *
6357 TTATGTGGGCATTAAAGAAA-GTTTGCCACCGAC
1 TTGTGTGGGC-TTTAAGAAAGGTTT-CCACCGAC
* * * * **
6390 TTGTGTAGCCTTT-AGAAGGGTTGT-CTCTAAC
1 TTGTGTGGGCTTTAAGAAAGGTT-TCCACCGAC
* *
6421 TTTTGTGGGCTTTAGAGAAAGGTTTCCATCGAC
1 TTGTGTGGGCTTTA-AGAAAGGTTTCCACCGAC
*
6454 TTGTGTGGGCTTT-AGAAGGGTT
1 TTGTGTGGGCTTTAAGAAAGGTT
6476 GCTACCAACT
Statistics
Matches: 88, Mismatches: 23, Indels: 16
0.69 0.18 0.13
Matches are distributed among these distances:
31 34 0.39
32 13 0.15
33 41 0.47
ACGTcount: A:0.21, C:0.16, G:0.29, T:0.34
Consensus pattern (32 bp):
TTGTGTGGGCTTTAAGAAAGGTTTCCACCGAC
Found at i:6497 original size:64 final size:64
Alignment explanation
Indices: 6314--6486 Score: 197
Period size: 64 Copynumber: 2.7 Consensus size: 64
6304 CAAGCAATGA
* * * * * * *
6314 TTTGCCACTGATTTGTGTCGGCTTTAAAAGGGTTGCCACCGACTTATGTGGGCATTAAAGAAAG
1 TTTGCCACCGACTTGTGTAGGCTTTAGAAGGGTTGCTACCAACTTATGTGGGCTTTAAAGAAAG
* * * *
6378 TTTGCCACCGACTTGTGTAGCCTTTAGAAGGGTTGTCT-CTAACTTTTGTGGGCTTTAGAGAAAG
1 TTTGCCACCGACTTGTGTAGGCTTTAGAAGGGTTG-CTACCAACTTATGTGGGCTTTAAAGAAA-
6442 G
64 G
* *
6443 TTT-CCATCGACTTGTGTGGGCTTTAGAAGGGTTGCTACCAACTT
1 TTTGCCACCGACTTGTGTAGGCTTTAGAAGGGTTGCTACCAACTT
6487 GTCTAGGCTT
Statistics
Matches: 91, Mismatches: 15, Indels: 6
0.81 0.13 0.05
Matches are distributed among these distances:
63 2 0.02
64 84 0.92
65 5 0.05
ACGTcount: A:0.21, C:0.18, G:0.27, T:0.34
Consensus pattern (64 bp):
TTTGCCACCGACTTGTGTAGGCTTTAGAAGGGTTGCTACCAACTTATGTGGGCTTTAAAGAAAG
Found at i:6577 original size:34 final size:33
Alignment explanation
Indices: 6496--6672 Score: 182
Period size: 35 Copynumber: 5.3 Consensus size: 33
6486 TGTCTAGGCT
**
6496 TTGTGGACTTTGAA-GAAAAAGGTGCCA-AGAAG
1 TTGTGGACTTAAAAGGAAAAAGGTGCCATAG-AG
* *
6528 TTGTGGACTTAAAAAGGAAAAAAGGTGCTATAGCG
1 TTGTGGACTT-AAAAGG-AAAAAGGTGCCATAGAG
**
6563 TTGTGGACTTAAAA-GAAAAA-GTGCCACGGAG
1 TTGTGGACTTAAAAGGAAAAAGGTGCCATAGAG
*
6594 TTGTGGACTTTAAAAGGACAAAGGTGCCATAGAG
1 TTGTGGAC-TTAAAAGGAAAAAGGTGCCATAGAG
* *
6628 TTATGGACTTAAAAGGGAAAAAGGGTGCCATGGAG
1 TTGTGGACTTAAAA-GGAAAAA-GGTGCCATAGAG
*
6663 TCGTGGACTT
1 TTGTGGACTT
6673 TGAGAAGAGA
Statistics
Matches: 120, Mismatches: 16, Indels: 15
0.79 0.11 0.10
Matches are distributed among these distances:
31 15 0.12
32 21 0.17
33 14 0.12
34 27 0.22
35 41 0.34
36 2 0.02
ACGTcount: A:0.36, C:0.11, G:0.31, T:0.23
Consensus pattern (33 bp):
TTGTGGACTTAAAAGGAAAAAGGTGCCATAGAG
Found at i:7694 original size:12 final size:14
Alignment explanation
Indices: 7668--7697 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
7658 TGAGGTGAAA
7668 TTTTTCTCTTCTTT
1 TTTTTCTCTTCTTT
7682 TTTTTCTCTT-TTT
1 TTTTTCTCTTCTTT
7695 TTT
1 TTT
7698 AAGACCAGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 6 0.38
14 10 0.62
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (14 bp):
TTTTTCTCTTCTTT
Found at i:10917 original size:20 final size:20
Alignment explanation
Indices: 10873--10930 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 20
10863 ATTTCAACGA
***
10873 TTTGTATCGATACATAAAAT
1 TTTGTATCGATACATATTTT
*
10893 GTTGTATCGATACATATTTT
1 TTTGTATCGATACATATTTT
10913 TTTGTATCGATACA-ATTT
1 TTTGTATCGATACATATTT
10931 AAGCTACTGC
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
19 4 0.12
20 29 0.88
ACGTcount: A:0.31, C:0.10, G:0.12, T:0.47
Consensus pattern (20 bp):
TTTGTATCGATACATATTTT
Found at i:10989 original size:13 final size:13
Alignment explanation
Indices: 10971--10995 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
10961 ATTACTCACA
10971 TGTATCGATACAT
1 TGTATCGATACAT
10984 TGTATCGATACA
1 TGTATCGATACA
10996 CTGATCTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:11132 original size:52 final size:52
Alignment explanation
Indices: 11004--11124 Score: 224
Period size: 52 Copynumber: 2.3 Consensus size: 52
10994 CACTGATCTT
*
11004 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACATTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
*
11056 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
11108 TGTATCGATACATGCAG
1 TGTATCGATACATGCAG
11125 ATAAATTTTC
Statistics
Matches: 67, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
52 67 1.00
ACGTcount: A:0.35, C:0.18, G:0.18, T:0.29
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
Found at i:16972 original size:20 final size:20
Alignment explanation
Indices: 16947--17000 Score: 83
Period size: 20 Copynumber: 2.7 Consensus size: 20
16937 GTTACAAGCA
*
16947 ATGTATCGATACAAT-TCATC
1 ATGTATCGATACAATGT-ACC
16967 ATGTATCGATACAATGTACC
1 ATGTATCGATACAATGTACC
16987 ATGTATCGATACAA
1 ATGTATCGATACAA
17001 ACAGTGGTAG
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
20 31 0.97
21 1 0.03
ACGTcount: A:0.37, C:0.19, G:0.13, T:0.31
Consensus pattern (20 bp):
ATGTATCGATACAATGTACC
Found at i:17068 original size:13 final size:13
Alignment explanation
Indices: 17050--17076 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
17040 ACAATTGTCC
17050 ATGTATCGATACA
1 ATGTATCGATACA
17063 ATGTATCGATACA
1 ATGTATCGATACA
17076 A
1 A
17077 AGCATAATGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:24199 original size:18 final size:18
Alignment explanation
Indices: 24178--24212 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
24168 TTCGAGTCAC
24178 CATCATCATCATCATTGT
1 CATCATCATCATCATTGT
*
24196 CATCTTCATCATCATTG
1 CATCATCATCATCATTG
24213 ATGGTTGACT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.26, C:0.29, G:0.06, T:0.40
Consensus pattern (18 bp):
CATCATCATCATCATTGT
Found at i:25821 original size:20 final size:20
Alignment explanation
Indices: 25796--25849 Score: 83
Period size: 20 Copynumber: 2.7 Consensus size: 20
25786 GTTACAAGCA
*
25796 ATGTATCGATACAAT-TCATC
1 ATGTATCGATACAATGT-ACC
25816 ATGTATCGATACAATGTACC
1 ATGTATCGATACAATGTACC
25836 ATGTATCGATACAA
1 ATGTATCGATACAA
25850 ATAATGGTAG
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
20 31 0.97
21 1 0.03
ACGTcount: A:0.37, C:0.19, G:0.13, T:0.31
Consensus pattern (20 bp):
ATGTATCGATACAATGTACC
Found at i:25910 original size:20 final size:20
Alignment explanation
Indices: 25877--25932 Score: 71
Period size: 19 Copynumber: 2.9 Consensus size: 20
25867 ACTGCCAGTT
*
25877 TCATTTATCAATACAATTG-
1 TCATGTATCAATACAATTGA
*
25896 TCCATGTATCGATACAA-TGA
1 T-CATGTATCAATACAATTGA
25916 TCATGTATCAATACAAT
1 TCATGTATCAATACAAT
25933 GTATCGATAC
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
19 17 0.55
20 14 0.45
ACGTcount: A:0.38, C:0.18, G:0.09, T:0.36
Consensus pattern (20 bp):
TCATGTATCAATACAATTGA
Found at i:29101 original size:21 final size:21
Alignment explanation
Indices: 29050--29123 Score: 105
Period size: 21 Copynumber: 3.6 Consensus size: 21
29040 ATTTGAGACA
*
29050 TGTATCGATACATTCACTTA-
1 TGTATCGATACATTCACTAAT
*
29070 TGTATCTATACATTCACTAAT
1 TGTATCGATACATTCACTAAT
*
29091 TATATCGATACATTCACTAAT
1 TGTATCGATACATTCACTAAT
*
29112 TGTATCCATACA
1 TGTATCGATACA
29124 AATCGTAGAA
Statistics
Matches: 47, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
20 18 0.38
21 29 0.62
ACGTcount: A:0.34, C:0.20, G:0.07, T:0.39
Consensus pattern (21 bp):
TGTATCGATACATTCACTAAT
Found at i:35893 original size:15 final size:15
Alignment explanation
Indices: 35875--35903 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
35865 AAAAAGAGAA
35875 AAAAACAAAAAAAAC
1 AAAAACAAAAAAAAC
35890 AAAAACAAAAAAAA
1 AAAAACAAAAAAAA
35904 TGCAAAAGCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.90, C:0.10, G:0.00, T:0.00
Consensus pattern (15 bp):
AAAAACAAAAAAAAC
Found at i:37058 original size:24 final size:24
Alignment explanation
Indices: 37031--37107 Score: 74
Period size: 24 Copynumber: 3.4 Consensus size: 24
37021 TTATTCCATA
37031 TGCATTTGCCCTTCTATTGATGTT
1 TGCATTTGCCCTTCTATTGATGTT
* * *
37055 TGCATTTG--CAT-TATTCCA--TA
1 TGCATTTGCCCTTCTATT-GATGTT
*
37075 TGCATTTTCCCTTCTATTGATGTT
1 TGCATTTGCCCTTCTATTGATGTT
37099 TGCATTTGC
1 TGCATTTGC
37108 ATTATTTCAT
Statistics
Matches: 39, Mismatches: 8, Indels: 12
0.66 0.14 0.20
Matches are distributed among these distances:
20 8 0.21
21 4 0.10
22 6 0.15
23 4 0.10
24 17 0.44
ACGTcount: A:0.16, C:0.21, G:0.14, T:0.49
Consensus pattern (24 bp):
TGCATTTGCCCTTCTATTGATGTT
Found at i:37062 original size:44 final size:44
Alignment explanation
Indices: 37014--37119 Score: 194
Period size: 44 Copynumber: 2.4 Consensus size: 44
37004 TAACATTGGT
37014 ATTTGCATTATTCCATATGCATTTGCCCTTCTATTGATGTTTGC
1 ATTTGCATTATTCCATATGCATTTGCCCTTCTATTGATGTTTGC
*
37058 ATTTGCATTATTCCATATGCATTTTCCCTTCTATTGATGTTTGC
1 ATTTGCATTATTCCATATGCATTTGCCCTTCTATTGATGTTTGC
*
37102 ATTTGCATTATTTCATAT
1 ATTTGCATTATTCCATAT
37120 ACATCTGCAC
Statistics
Matches: 60, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
44 60 1.00
ACGTcount: A:0.20, C:0.19, G:0.11, T:0.50
Consensus pattern (44 bp):
ATTTGCATTATTCCATATGCATTTGCCCTTCTATTGATGTTTGC
Found at i:38319 original size:48 final size:48
Alignment explanation
Indices: 38207--38319 Score: 172
Period size: 48 Copynumber: 2.4 Consensus size: 48
38197 GTACCTAGCT
*
38207 AAACTCTTTTCTTCCCTCATTTAACCGTATTGGTGTTAGGGCCTAGTC
1 AAACTCTTTTCTTTCCTCATTTAACCGTATTGGTGTTAGGGCCTAGTC
* * * *
38255 AAACTCTTTTCATTCCTCCTTTGACTGTATTGGTGTTAGGGCCTAGTC
1 AAACTCTTTTCTTTCCTCATTTAACCGTATTGGTGTTAGGGCCTAGTC
*
38303 AAACTCTTCTCTTTCCT
1 AAACTCTTTTCTTTCCT
38320 ATCTGACGTA
Statistics
Matches: 58, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
48 58 1.00
ACGTcount: A:0.18, C:0.26, G:0.15, T:0.42
Consensus pattern (48 bp):
AAACTCTTTTCTTTCCTCATTTAACCGTATTGGTGTTAGGGCCTAGTC
Found at i:38632 original size:42 final size:42
Alignment explanation
Indices: 38471--38690 Score: 144
Period size: 42 Copynumber: 5.2 Consensus size: 42
38461 ATGCCTTTGG
* * * * *
38471 TCTTTTGTCTGCTCGTCGGCTTAGACCTAAG-AGACTTTTTTTA
1 TCTTTTGTCTGCCCGTCGACTTTGA-CTCAGTAGAC-TTCTTTA
* * * * * *
38514 CCCTTTATCTGCCCGTCGACTTAGAC-CCGAAGACTT-TTCTA
1 TCTTTTGTCTGCCCGTCGACTTTGACTCAGTAGACTTCTT-TA
** * * * * * * *
38555 TCTTTTGTCTGTTCATTGGCTTAGACCCGGAAGACTTCTTTA
1 TCTTTTGTCTGCCCGTCGACTTTGACTCAGTAGACTTCTTTA
*
38597 TCTTTTGTCTGCCCGTCGA-TTTAGGCTCAAG-AGACTTCTTTA
1 TCTTTTGTCTGCCCGTCGACTTT-GACTC-AGTAGACTTCTTTA
* * *
38639 TCCTTTATCTGCCCGTCGACTTTGACTCAGTAGACTCCTTTA
1 TCTTTTGTCTGCCCGTCGACTTTGACTCAGTAGACTTCTTTA
38681 TCTTTTGTCT
1 TCTTTTGTCT
38691 ACCTGTTGGC
Statistics
Matches: 138, Mismatches: 31, Indels: 17
0.74 0.17 0.09
Matches are distributed among these distances:
40 2 0.01
41 27 0.20
42 83 0.60
43 26 0.19
ACGTcount: A:0.16, C:0.26, G:0.17, T:0.41
Consensus pattern (42 bp):
TCTTTTGTCTGCCCGTCGACTTTGACTCAGTAGACTTCTTTA
Found at i:38700 original size:126 final size:126
Alignment explanation
Indices: 38471--38703 Score: 285
Period size: 126 Copynumber: 1.8 Consensus size: 126
38461 ATGCCTTTGG
* * *
38471 TCTTTTGTCTGCTCGTCGGCTTAGACCTAAGAGACTTTTTTTACCCTTTATCTGCCCGTCGACTT
1 TCTTTTGTCTGCCCGTCGACTTAGACCTAAGAGACTTTCTTTACCCTTTATCTGCCCGTCGACTT
* * **
38536 AGACCCGAAGACTTTTCTATCTTTTGTCTGTTCATTGGCTTAGACCCGGAAGACTTCTTTA
66 AGACCAGAAGACTCTTCTATCTTTTGTCTCCTCATTGGCTTAGACCCGGAAGACTTCTTTA
* * *
38597 TCTTTTGTCTGCCCGTCGATTTAG-GCTCAAGAGAC-TTCTTTATCCTTTATCTGCCCGTCGACT
1 TCTTTTGTCTGCCCGTCGACTTAGACCT-AAGAGACTTTCTTTACCCTTTATCTGCCCGTCGACT
* * *
38660 TTGACTCAGTAGACTCCTT-TATCTTTTGTCTACCT-GTTGGCTTA
65 TAGAC-CAGAAGACT-CTTCTATCTTTTGTCT-CCTCATTGGCTTA
38704 AACCTGGGGG
Statistics
Matches: 90, Mismatches: 13, Indels: 8
0.81 0.12 0.07
Matches are distributed among these distances:
125 32 0.36
126 55 0.61
127 3 0.03
ACGTcount: A:0.16, C:0.26, G:0.17, T:0.41
Consensus pattern (126 bp):
TCTTTTGTCTGCCCGTCGACTTAGACCTAAGAGACTTTCTTTACCCTTTATCTGCCCGTCGACTT
AGACCAGAAGACTCTTCTATCTTTTGTCTCCTCATTGGCTTAGACCCGGAAGACTTCTTTA
Found at i:38776 original size:43 final size:42
Alignment explanation
Indices: 38727--39275 Score: 428
Period size: 43 Copynumber: 12.8 Consensus size: 42
38717 ACTTCATCTC
* * *
38727 AAGTCTGCCTGTCGGCTTTAACCCTAGAGACTTCCTTGCCCTC
1 AAGTCTGCCTGTCGGCTTTGACCCTAGAGACTT-CTTACCCTT
* **
38770 AAGTCTGCCTATCGGCTTTGA-CCT--TCACTTTCTTCACCCTT
1 AAGTCTGCCTGTCGGCTTTGACCCTAGAGAC-TTCTT-ACCCTT
* * * *
38811 AAGTCTGCTTATCGACTTTGACCCTGGAGACTTCCTTACCCTT
1 AAGTCTGCCTGTCGGCTTTGACCCTAGAGACTT-CTTACCCTT
* *
38854 AAGTCTGTCTGTCGGCTTT-ATCCCTGGAGACTTTCTTCACCCTT
1 AAGTCTGCCTGTCGGCTTTGA-CCCTAGAGAC-TTCTT-ACCCTT
*
38898 AAGTCTGCCTGTCAGCTTTGACCCTAGAGACTTCTT-CGCCTTT
1 AAGTCTGCCTGTCGGCTTTGACCCTAGAGACTTCTTAC-CC-TT
** * * **
38941 AAGTCTGCCTGTCAACTTTGACCCTGGAGAATTCTTCACTTTTT
1 AAGTCTGCCTGTCGGCTTTGACCCTAGAGACTTCTT-AC-CCTT
* * * * * *
38985 AAATCTGCTTGTCAGCTTTGACCCTGGAGATTTCTTCCCCTTT
1 AAGTCTGCCTGTCGGCTTTGACCCTAGAGACTTCTTACCC-TT
* * * * * *
39028 AAGTCTGCCTATCAGCTTTGACCTTGGGGACTTCTTTGCCCTT
1 AAGTCTGCCTGTCGGCTTTGACCCTAGAGACTTC-TTACCCTT
* * * * *
39071 AAGTCTACCTATCAGCTTTAACCTTAGAGACTTCTT-CCTCTTT
1 AAGTCTGCCTGTCGGCTTTGACCCTAGAGACTTCTTACC-C-TT
* * *
39114 AAGTTTGCCTGTCGGCTTTGACTCTAGAGATTTCTTCACCCTT
1 AAGTCTGCCTGTCGGCTTTGACCCTAGAGACTTCTT-ACCCTT
* * * *
39157 AAGTCTGCCTGTCGGCTTTAACCCTAGAGACTTTTTCATCCTA
1 AAGTCTGCCTGTCGGCTTTGACCCTAGAGACTTCTT-ACCCTT
* * * *
39200 AAGTCTACCTGTCGGCTTTGACCTTGGAGA-TTCATTCCCCCTT
1 AAGTCTGCCTGTCGGCTTTGACCCTAGAGACTTC-TT-ACCCTT
* * *
39243 AAGTCTACCTGTTGGCTTTGACCTTAGAGACTT
1 AAGTCTGCCTGTCGGCTTTGACCCTAGAGACTT
39276 TTTCATCCAT
Statistics
Matches: 418, Mismatches: 66, Indels: 43
0.79 0.13 0.08
Matches are distributed among these distances:
40 5 0.01
41 28 0.07
42 14 0.03
43 286 0.68
44 81 0.19
45 4 0.01
ACGTcount: A:0.17, C:0.29, G:0.17, T:0.37
Consensus pattern (42 bp):
AAGTCTGCCTGTCGGCTTTGACCCTAGAGACTTCTTACCCTT
Found at i:38919 original size:87 final size:85
Alignment explanation
Indices: 38727--39275 Score: 511
Period size: 86 Copynumber: 6.4 Consensus size: 85
38717 ACTTCATCTC
* * * *
38727 AAGTCTGCCTGTCGGCTTTAACCCTAGAGACTTCCTTGCCC-TCAAGTCTGCCTATCGGCTTTGA
1 AAGTCTGCCTGTCAGCTTTGACCCTAGAGACTT-CTT-CCCTTTAAGTCTGCCTGTCGGCTTTGA
** *
38791 -CCTTCA-CTTTCTTCACCCTT
64 CCCTGGAGATTTCTTCACCCTT
* * * *
38811 AAGTCTGCTTATC-GACTTTGACCCTGGAGACTTCCTTACCC-TTAAGTCTGTCTGTCGGCTTT-
1 AAGTCTGCCTGTCAG-CTTTGACCCTAGAGACTT-CTT-CCCTTTAAGTCTGCCTGTCGGCTTTG
38873 ATCCCTGGAGACTTTCTTCACCCTT
63 A-CCCTGGAGA-TTTCTTCACCCTT
**
38898 AAGTCTGCCTGTCAGCTTTGACCCTAGAGACTTCTTCGCCTTTAAGTCTGCCTGTCAACTTTGAC
1 AAGTCTGCCTGTCAGCTTTGACCCTAGAGACTTCTTC-CCTTTAAGTCTGCCTGTCGGCTTTGAC
* **
38963 CCTGGAGAATTCTTCACTTTTT
65 CCTGGAGATTTCTTCAC-CCTT
* * * * * *
38985 AAATCTGCTTGTCAGCTTTGACCCTGGAGATTTCTTCCCCTTTAAGTCTGCCTATCAGCTTTGAC
1 AAGTCTGCCTGTCAGCTTTGACCCTAGAGACTTCTT-CCCTTTAAGTCTGCCTGTCGGCTTTGAC
* * * **
39050 CTTGGGGACTTCTTTGCCCTT
65 CCTGGAGATTTCTTCACCCTT
* * * * *
39071 AAGTCTACCTATCAGCTTTAACCTTAGAGACTTCTTCCTCTTTAAGTTTGCCTGTCGGCTTTGAC
1 AAGTCTGCCTGTCAGCTTTGACCCTAGAGACTTCTTCC-CTTTAAGTCTGCCTGTCGGCTTTGAC
* *
39136 TCTAGAGATTTCTTCACCCTT
65 CCTGGAGATTTCTTCACCCTT
* * * * *
39157 AAGTCTGCCTGTCGGCTTTAACCCTAGAGACTTTTTCATCC-TAAAGTCTACCTGTCGGCTTTGA
1 AAGTCTGCCTGTCAGCTTTGACCCTAGAGACTTCTTC--CCTTTAAGTCTGCCTGTCGGCTTTGA
* *
39221 CCTTGGAGA-TTCATTCCCCCTT
64 CCCTGGAGATTTC-TTCACCCTT
* ** *
39243 AAGTCTACCTGTTGGCTTTGACCTTAGAGACTT
1 AAGTCTGCCTGTCAGCTTTGACCCTAGAGACTT
39276 TTTCATCCAT
Statistics
Matches: 383, Mismatches: 67, Indels: 28
0.80 0.14 0.06
Matches are distributed among these distances:
83 2 0.01
84 52 0.14
85 10 0.03
86 175 0.46
87 140 0.37
88 4 0.01
ACGTcount: A:0.17, C:0.29, G:0.17, T:0.37
Consensus pattern (85 bp):
AAGTCTGCCTGTCAGCTTTGACCCTAGAGACTTCTTCCCTTTAAGTCTGCCTGTCGGCTTTGACC
CTGGAGATTTCTTCACCCTT
Found at i:39315 original size:42 final size:42
Alignment explanation
Indices: 39268--39514 Score: 185
Period size: 42 Copynumber: 5.9 Consensus size: 42
39258 CTTTGACCTT
*
39268 AGAGACTTTTTCATCCATCATCTGCCCATCGGCTTAAACCCG
1 AGAGACTTCTTCATCCATCATCTGCCCATCGGCTTAAACCCG
* * *
39310 AGAGACTTCTTCATCCATCGTCTGCCCATCGACTTAAA-CCT
1 AGAGACTTCTTCATCCATCATCTGCCCATCGGCTTAAACCCG
*** *
39351 AGGAGACTTCTTCATTTTTCATCTGCCCATCGGCTTAGACCCG
1 A-GAGACTTCTTCATCCATCATCTGCCCATCGGCTTAAACCCG
* ** * * * * **
39394 GGAGACTTCTTCATCTTTCATCTACCCGTCGACTCAGTCCCG
1 AGAGACTTCTTCATCCATCATCTGCCCATCGGCTTAAACCCG
* * * * * **
39436 GGAGATTTCCTTTA-CCGATCAT-TTCCCTGTCAACTTAAACCCG
1 AGAGACTT-CTTCATCC-ATCATCTGCCC-ATCGGCTTAAACCCG
* ** *
39479 GGAGACTTCTTCATCTTTCATCTGCCCATTGGCTTA
1 AGAGACTTCTTCATCCATCATCTGCCCATCGGCTTA
39515 GACTTAGGAG
Statistics
Matches: 162, Mismatches: 36, Indels: 14
0.76 0.17 0.07
Matches are distributed among these distances:
41 3 0.02
42 126 0.78
43 33 0.20
ACGTcount: A:0.21, C:0.32, G:0.15, T:0.32
Consensus pattern (42 bp):
AGAGACTTCTTCATCCATCATCTGCCCATCGGCTTAAACCCG
Found at i:39729 original size:42 final size:42
Alignment explanation
Indices: 39269--39743 Score: 130
Period size: 42 Copynumber: 11.2 Consensus size: 42
39259 TTTGACCTTA
* * * * * * *
39269 GAGACTTTTTCATCCATCATCTGCCCATCGGCTTAAACCCGA
1 GAGACTTCTTCATCCACCGTCTACCCATCGGCTTAGACCTGG
* * * * *
39311 GAGACTTCTTCATCCATCGTCTGCCCATCGACTTAAACCTAG
1 GAGACTTCTTCATCCACCGTCTACCCATCGGCTTAGACCTGG
**** * * *
39353 GAGACTTCTTCATTTTTCATCTGCCCATCGGCTTAGACCCGG
1 GAGACTTCTTCATCCACCGTCTACCCATCGGCTTAGACCTGG
*** * * * * * *
39395 GAGACTTCTTCATCTTTCATCTACCCGTCGACTCAGTCCCGG
1 GAGACTTCTTCATCCACCGTCTACCCATCGGCTTAGACCTGG
* * * * * * ** * *
39437 GAGATTTCCTTTA-CCGATCAT-TTCCCTGTCAACTTAAACCCGG
1 GAGACTT-CTTCATCC-ACCGTCTACCC-ATCGGCTTAGACCTGG
*** * * * * *
39480 GAGACTTCTTCATCTTTCATCTGCCCATTGGCTTAGACTTAG
1 GAGACTTCTTCATCCACCGTCTACCCATCGGCTTAGACCTGG
* * * ** * * * *
39522 GAGACTTCTTAATCCACCTGTCTGCCCTTCAACTAAGTCCCGA
1 GAGACTTCTTCATCCACC-GTCTACCCATCGGCTTAGACCTGG
* * * * * ** *
39565 GAGACTTTCTTTATCAACCATCTGCCTATCGATTTAGATGC-GG
1 GAGAC-TTCTTCATCCACCGTCTACCCATCGGCTTAGA-CCTGG
*** * ** * * * *
39608 GAGACTTCTTCATCTTTCATAGACTCGTTGGCTTAGACCCT-A
1 GAGACTTCTTCATCCACCGTCTACCCATCGGCTTAGA-CCTGG
* * * *
39650 GAGACTTCTTTATCCACCGTCTACCCGTCGACATAGACCTGG
1 GAGACTTCTTCATCCACCGTCTACCCATCGGCTTAGACCTGG
* ** *
39692 GAGACTTCTTCATCCACCGTTTTTCCATCGGCTTAGACCCGG
1 GAGACTTCTTCATCCACCGTCTACCCATCGGCTTAGACCTGG
39734 GAGACTTCTT
1 GAGACTTCTT
39744 TTATCAACTA
Statistics
Matches: 319, Mismatches: 104, Indels: 20
0.72 0.23 0.05
Matches are distributed among these distances:
41 3 0.01
42 237 0.74
43 67 0.21
44 12 0.04
ACGTcount: A:0.21, C:0.31, G:0.17, T:0.32
Consensus pattern (42 bp):
GAGACTTCTTCATCCACCGTCTACCCATCGGCTTAGACCTGG
Found at i:42112 original size:15 final size:16
Alignment explanation
Indices: 42089--42123 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
42079 ATCAAATTTG
*
42089 AAAAGAAAAG-AAAGA
1 AAAAAAAAAGAAAAGA
42104 AAAAAAAAAGAAAAGA
1 AAAAAAAAAGAAAAGA
42120 AAAA
1 AAAA
42124 GGATGCAATG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 9 0.50
16 9 0.50
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (16 bp):
AAAAAAAAAGAAAAGA
Found at i:42584 original size:36 final size:36
Alignment explanation
Indices: 42532--42602 Score: 106
Period size: 36 Copynumber: 2.0 Consensus size: 36
42522 TTGGCAACAA
* * *
42532 AGCAACTTGAGTAATAAATCGGCAACAGCTGCTGGC
1 AGCAACGTGAGAAATAAATCGGCAACAGCTACTGGC
*
42568 AGCAACGTGAGAAATAAATTGGCAACAGCTACTGG
1 AGCAACGTGAGAAATAAATCGGCAACAGCTACTGG
42603 TGACAAAGAG
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.37, C:0.20, G:0.25, T:0.18
Consensus pattern (36 bp):
AGCAACGTGAGAAATAAATCGGCAACAGCTACTGGC
Found at i:45075 original size:155 final size:155
Alignment explanation
Indices: 44442--45132 Score: 642
Period size: 157 Copynumber: 4.4 Consensus size: 155
44432 TCATCATACC
** ** * * * * *
44442 TAGT-CTTTTTAAGTTTTTTAGGGTTGTCGGGGTACTTTTACGTTGAAGGTATACCTTTAGGAGC
1 TAGTCCTTTTTAAGTCCTTTAGGG-TACCGGGATACTTTCACGTTGAAGGTATCCCCTAAGG-GC
* * * * ** * *
44506 ATTTTTGTAATTTTTTAGAACCAACTCCTAGGTCACCA-TCGGGTCTGCTTTTATGCCGAAAGTG
64 ATTTTTGTAATTTTTTAGAACCGAGTCCTAGGTTATCACT-GGGTCCACTTTTATGTCGAAGGTG
* *
44570 GGTATTTAGGATAGGTCCA-CCTATTTTA
128 GGCATTTAGGATAGGTTCACCCT-TTTTA
** * * *
44598 TAGTTTTTTTTAAGTCCTTTTAGGGGTACCGGGATACTTTCACGTTGAAGGTATCCCTTAGGGGT
1 TAGTCCTTTTTAAGTCC-TTTA-GGGTACCGGGATACTTTCACGTTGAAGGTATCCCCTAAGGGC
* * * * * ** *
44663 ATTTTTGTAATTTCTTAGAATCGAGTCTTAGGTTGTCACTAGGTCTGCTTTTATGTTGAAGGTGG
64 ATTTTTGTAATTTTTTAGAACCGAGTCCTAGGTTATCACTGGGTCCACTTTTATGTCGAAGGTGG
* *
44728 GCATTTAGGATAGGTTCACCCCTTTTC
129 GCATTTAGGATAGGTTCACCCTTTTTA
* * * * * *
44755 TAGT-CTTTTTAGGGCCTTTAAGGTTACCGGGATACTTTCACGTCGAAGGTATCCCCTAATGGTA
1 TAGTCCTTTTTAAGTCCTTT-AGGGTACCGGGATACTTTCACGTTGAAGGTATCCCCTAAGGGCA
** * * * *
44819 TTTTCATAATTTTTCTTAGAACCGAGTCCTAGGTTGTCATTTGGTCCACTTTTATG-CTGAAGGC
65 TTTTTGTAA-TTTT-TTAGAACCGAGTCCTAGGTTATCACTGGGTCCACTTTTATGTC-GAAGGT
* * *
44883 AGGCATTTAGGATAGGTTCATCACC-ATTTC
127 GGGCATTTAGGATAGGTTCA-C-CCTTTTTA
* * *
44913 TAG-CCTTTTTAAGTCCTTTAGGGTACAGGGATACTTTCGCATTGAAGGTATCCCCTAAGGGCAT
1 TAGTCCTTTTTAAGTCCTTTAGGGTACCGGGATACTTTCACGTTGAAGGTATCCCCTAAGGGCAT
* * *
44977 TTTTGTAATTTTTTAGAATCGAGTCCTAGGTTAACACTGGGTCCACTTTTATGTCGAAGGTGGGT
66 TTTTGTAATTTTTTAGAACCGAGTCCTAGGTTATCACTGGGTCCACTTTTATGTCGAAGGTGGGC
*
45042 ATTTAAGATAGGTTCACCCTTTTTA
131 ATTTAGGATAGGTTCACCCTTTTTA
* ** ** *
45067 TAGTCCTTTTTAAG-CCTTTTTGGGGTACCAAGATACTTTCACGTCAAAGGTATCCCCTAGGGGC
1 TAGTCCTTTTTAAGTCC--TTTAGGGTACCGGGATACTTTCACGTTGAAGGTATCCCCTAAGGGC
45131 AT
64 AT
45133 GTTCATAATT
Statistics
Matches: 439, Mismatches: 79, Indels: 34
0.80 0.14 0.06
Matches are distributed among these distances:
153 2 0.00
154 9 0.02
155 116 0.26
156 61 0.14
157 188 0.43
158 58 0.13
159 5 0.01
ACGTcount: A:0.22, C:0.17, G:0.22, T:0.39
Consensus pattern (155 bp):
TAGTCCTTTTTAAGTCCTTTAGGGTACCGGGATACTTTCACGTTGAAGGTATCCCCTAAGGGCAT
TTTTGTAATTTTTTAGAACCGAGTCCTAGGTTATCACTGGGTCCACTTTTATGTCGAAGGTGGGC
ATTTAGGATAGGTTCACCCTTTTTA
Found at i:51080 original size:20 final size:20
Alignment explanation
Indices: 51057--51155 Score: 76
Period size: 20 Copynumber: 4.8 Consensus size: 20
51047 ACACACTCCT
51057 ATGTATCGATACAATTTATA
1 ATGTATCGATACAATTTATA
*
51077 ATGTATCGATACAATGTAT-
1 ATGTATCGATACAATTTATA
* * * * *
51096 TTGAAATTCTA-ACCATTGATCTCA
1 ATG-TA-TCGATACAATT--TAT-A
*
51120 ATGTATCGATACAATTTATT
1 ATGTATCGATACAATTTATA
51140 ATGTATCGATACAATT
1 ATGTATCGATACAATT
51156 ATAGCCATTG
Statistics
Matches: 59, Mismatches: 13, Indels: 14
0.69 0.15 0.16
Matches are distributed among these distances:
19 2 0.03
20 39 0.66
21 5 0.08
22 5 0.08
23 6 0.10
24 2 0.03
ACGTcount: A:0.36, C:0.13, G:0.11, T:0.39
Consensus pattern (20 bp):
ATGTATCGATACAATTTATA
Found at i:51175 original size:52 final size:52
Alignment explanation
Indices: 51108--51207 Score: 173
Period size: 52 Copynumber: 1.9 Consensus size: 52
51098 GAAATTCTAA
* *
51108 CCATTGATCTCAATGTATCGATACAATTTATTATGTATCGATACAATTATAG
1 CCATTGAGCTCAATGTATCGATACAATTTATCATGTATCGATACAATTATAG
*
51160 CCATTGAGCTTAATGTATCGATACAATTTATCATGTATCGATACAATT
1 CCATTGAGCTCAATGTATCGATACAATTTATCATGTATCGATACAATT
51208 CACTTAGGGT
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 45 1.00
ACGTcount: A:0.34, C:0.16, G:0.12, T:0.38
Consensus pattern (52 bp):
CCATTGAGCTCAATGTATCGATACAATTTATCATGTATCGATACAATTATAG
Found at i:52705 original size:164 final size:163
Alignment explanation
Indices: 52524--52875 Score: 451
Period size: 164 Copynumber: 2.2 Consensus size: 163
52514 CTCTTTCTCG
** ** * *
52524 AAAAAAT-CATTTCGTACCTTAATAAAAACCTGAAAAGATATGAAAATTTTTTGAAACCTTTTAT
1 AAAAAATACATTTCGTACCTTAATAAAAACCCAAAAAGATACAAAAAGTTTTTGAAACATTTTAT
** * * * *
52588 ACCCCTACAGATTCCCAG-AGAAATATAAAAGATTGAAAATATGATTTATATTTATTTCAATCAT
66 ACCCCTACAGACCCCCAGAAG-AATATAAAAGATTAAAAAAATAATTAATATTTATTTCAATCA-
52652 TG-AAGTGTTAACTTAATTTTATTTATTTATTATT-
129 TGAAAGTGTTAACTTAATTTTATTTATTTATT-TTC
** *
52686 AAAAAATACTATTTCGTACCTTAATGGAAACCCAAAAAGATACAAAAAGTTTTTGAAATATTTTA
1 AAAAAATAC-ATTTCGTACCTTAATAAAAACCCAAAAAGATACAAAAAGTTTTTGAAACATTTTA
** *
52751 TACCCCTATGGACCCCCATAAGAATATAAAAGATTAAAAAAATAATTAATATTTATTTCAATCAT
65 TACCCCTACAGACCCCCAGAAGAATATAAAAGATTAAAAAAATAATTAATATTTATTTCAATCAT
*
52816 GAAAGTGTTAATTTAATTTTATTTATTTATTTTC
130 GAAAGTGTTAACTTAATTTTATTTATTTATTTTC
*
52850 GAAAAATACCATTTCGTACCTTAATA
1 AAAAAATA-CATTTCGTACCTTAATA
52876 GATGTAGAGA
Statistics
Matches: 163, Mismatches: 21, Indels: 10
0.84 0.11 0.05
Matches are distributed among these distances:
162 7 0.04
163 5 0.03
164 148 0.91
165 3 0.02
ACGTcount: A:0.42, C:0.12, G:0.08, T:0.37
Consensus pattern (163 bp):
AAAAAATACATTTCGTACCTTAATAAAAACCCAAAAAGATACAAAAAGTTTTTGAAACATTTTAT
ACCCCTACAGACCCCCAGAAGAATATAAAAGATTAAAAAAATAATTAATATTTATTTCAATCATG
AAAGTGTTAACTTAATTTTATTTATTTATTTTC
Found at i:53280 original size:20 final size:20
Alignment explanation
Indices: 53234--53271 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
53224 CTGCCAAGAA
53234 AATGTATCGATACATTGAAT
1 AATGTATCGATACATTGAAT
53254 AATGTATCGATACATTGA
1 AATGTATCGATACATTGA
53272 TCTTTGTATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.39, C:0.11, G:0.16, T:0.34
Consensus pattern (20 bp):
AATGTATCGATACATTGAAT
Found at i:56728 original size:164 final size:158
Alignment explanation
Indices: 56374--56792 Score: 604
Period size: 164 Copynumber: 2.6 Consensus size: 158
56364 ACGTTACGAC
* * *
56374 AATAGAAACCCAAAAAGATACGAAAAGTTTTTAAAATCTTCTATATCCCTACGAACCCCTATAGG
1 AATAGAAA-CCAAAAAGATACAAAAAGTTTTTAAAATCTTTTATACCCCTACGAA-CCC-ATAGG
56439 AATATAAAAGATAAAAAATGATTAATATTTATTTCAACCATGAAAATGTTAATTTAAATTTTTTA
63 AATATAAAAGATAAAAAATGATTAATATTTATTTCAACCATGAAAATGTTAATTTAAATTTTTTA
* *
56504 TTTATTTTCGAAAAATATCATTTCGTATCTT
128 TTTATTTTCGAAAAATACCATTTCGTACCTT
*
56535 AATAGAAACTCGAAAAGATACAAAAAGTTTTTAAAATCTTTTATACCCCTACGAAGCCTCATAGG
1 AATAGAAAC-CAAAAAGATACAAAAAGTTTTTAAAATCTTTTATACCCCTACGAA-CC-CATAGG
* * *
56600 AATATAAAAGATCAAAAAAATGATTAATATTTATTTCAATCATGAAAGTGTTAATTTAATTTTGT
63 AATATAAAAGAT--AAAAAATGATTAATATTTATTTCAACCATGAAAATGTTAATTTAAATTT-T
*
56665 TTCTTTATTTTCGAAAAATACCATTTCGTACCTT
125 TTATTTATTTTCGAAAAATACCATTTCGTACCTT
* * * *
56699 AATGGAAACCAAAAAAGATACAAAAAGTTTTTAAAATCTTTTATACCCTTATGGAACCCATAAGA
1 AATAGAAACC-AAAAAGATACAAAAAGTTTTTAAAATCTTTTATACCCCTA-CGAACCCATAGGA
56764 ATATAAAAGATTAAAAAATGATTAATATT
64 ATATAAAAGA-TAAAAAATGATTAATATT
56793 GAAATATCTT
Statistics
Matches: 234, Mismatches: 16, Indels: 15
0.88 0.06 0.06
Matches are distributed among these distances:
160 1 0.00
161 68 0.29
162 18 0.08
163 63 0.27
164 81 0.35
165 3 0.01
ACGTcount: A:0.44, C:0.13, G:0.09, T:0.34
Consensus pattern (158 bp):
AATAGAAACCAAAAAGATACAAAAAGTTTTTAAAATCTTTTATACCCCTACGAACCCATAGGAAT
ATAAAAGATAAAAAATGATTAATATTTATTTCAACCATGAAAATGTTAATTTAAATTTTTTATTT
ATTTTCGAAAAATACCATTTCGTACCTT
Found at i:57625 original size:22 final size:23
Alignment explanation
Indices: 57558--57625 Score: 72
Period size: 22 Copynumber: 3.1 Consensus size: 23
57548 AGCTTAGTTT
*
57558 TTTCTATTTTTCTACCTATTTTC
1 TTTCTATTTTTCTTCCTATTTTC
* *
57581 TTT-TATTTTTCTTGC--TTTCC
1 TTTCTATTTTTCTTCCTATTTTC
*
57601 TTTCTCTTTTT-TTCCTATTTTC
1 TTTCTATTTTTCTTCCTATTTTC
57623 TTT
1 TTT
57626 TCAGCCGATC
Statistics
Matches: 36, Mismatches: 6, Indels: 7
0.73 0.12 0.14
Matches are distributed among these distances:
20 10 0.28
21 6 0.17
22 17 0.47
23 3 0.08
ACGTcount: A:0.07, C:0.21, G:0.01, T:0.71
Consensus pattern (23 bp):
TTTCTATTTTTCTTCCTATTTTC
Found at i:58423 original size:166 final size:167
Alignment explanation
Indices: 58240--58673 Score: 508
Period size: 166 Copynumber: 2.6 Consensus size: 167
58230 GACAATACAG
* *
58240 AGAAGAAAACTTCGTATTTTGGATATAGGAAAATTTTAAGAAAAAAATTCAAAAACTCATGAAAA
1 AGAAGAAAACTTCGTATTTTGGAAATAGGAAAATTTTAAG-AAAAAATTCAAAAACTCAAGAAAA
* * *
58305 TGAATGAATTTTT-AAAACTAATTTAATATAAATTAA-ATAACAATATTTTATGAATTTTAAAAA
65 TGAATAAATTTTTGAAAACTAATTTAATATAAATTAATA-AACAATATTTGATGAATTTAAAAAA
* *
58368 ATAAAAACCAAGAAAAATTCTCCC-AAAAAAATTTACGA
129 ACAAAAACCAAGAAAAATCCTCCCAAAAAAAATTTACGA
*
58406 AGTAA-AAAACTTCGTATTTTGGAAATAGGAAAATTTTAAGGAAAAATTCAAAAACTCAAGAAAA
1 AG-AAGAAAACTTCGTATTTTGGAAATAGGAAAATTTTAAGAAAAAATTCAAAAACTCAAGAAAA
* ** * *
58470 TGAATAAATTTTTGAAAACTGATTTGCTATGAATTAATAAATAATATTTGATGAATTTAAAAAAA
65 TGAATAAATTTTTGAAAACTAATTTAATATAAATTAATAAACAATATTTGATGAATTTAAAAAAA
*
58535 CAAAAACTAAGAAAAATCCTCCCAAAAAAAATTTACGA
130 CAAAAACCAAGAAAAATCCTCCCAAAAAAAATTTACGA
** * * * * * *
58573 AGAAGAAAACCCCGTAATTTGAAAATATGAGAAATTTCAA-AAGAAAATT-AATAACTTAAG-AA
1 AGAAGAAAACTTCGTATTTTGGAAATAGGA-AAATTTTAAGAA-AAAATTCAAAAACTCAAGAAA
* * *
58635 AT-AAAAAGATTTTTTTAAAACTGATTTAATA-AAAGTTAA
64 ATGAATAA-A-TTTTTGAAAACTAATTTAATATAAA-TTAA
58674 ATGATAAAAT
Statistics
Matches: 230, Mismatches: 28, Indels: 19
0.83 0.10 0.07
Matches are distributed among these distances:
165 38 0.17
166 107 0.47
167 71 0.31
168 14 0.06
ACGTcount: A:0.53, C:0.08, G:0.10, T:0.29
Consensus pattern (167 bp):
AGAAGAAAACTTCGTATTTTGGAAATAGGAAAATTTTAAGAAAAAATTCAAAAACTCAAGAAAAT
GAATAAATTTTTGAAAACTAATTTAATATAAATTAATAAACAATATTTGATGAATTTAAAAAAAC
AAAAACCAAGAAAAATCCTCCCAAAAAAAATTTACGA
Found at i:59519 original size:20 final size:20
Alignment explanation
Indices: 59494--59567 Score: 96
Period size: 20 Copynumber: 3.7 Consensus size: 20
59484 TCCCATAGCC
*
59494 ATGTATCGATATAATTCATA
1 ATGTATCGATACAATTCATA
*
59514 ATGTATCGATACAATTCATC
1 ATGTATCGATACAATTCATA
**
59534 ATGTATCGATACAATGT-ACC
1 ATGTATCGATACAAT-TCATA
59554 ATGTATCGATACAA
1 ATGTATCGATACAA
59568 ACAGTGGTAG
Statistics
Matches: 50, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
20 49 0.98
21 1 0.02
ACGTcount: A:0.38, C:0.16, G:0.12, T:0.34
Consensus pattern (20 bp):
ATGTATCGATACAATTCATA
Found at i:59634 original size:13 final size:13
Alignment explanation
Indices: 59616--59642 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
59606 TACAATGAAC
59616 ATGTATCGATACA
1 ATGTATCGATACA
59629 ATGTATCGATACA
1 ATGTATCGATACA
59642 A
1 A
59643 AGCATAATGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:68358 original size:13 final size:13
Alignment explanation
Indices: 68340--68392 Score: 55
Period size: 13 Copynumber: 4.5 Consensus size: 13
68330 CCGTTAGAAG
68340 CAATGTATCGATA
1 CAATGTATCGATA
68353 CAATGTATCGATA
1 CAATGTATCGATA
*
68366 CGA-G--TC-AT-
1 CAATGTATCGATA
68374 C-ATGTATCGATA
1 CAATGTATCGATA
68386 CAATGTA
1 CAATGTA
68393 CCATGTATCG
Statistics
Matches: 33, Mismatches: 1, Indels: 12
0.72 0.02 0.26
Matches are distributed among these distances:
7 1 0.03
8 2 0.06
9 2 0.06
10 4 0.12
11 2 0.06
12 2 0.06
13 20 0.61
ACGTcount: A:0.36, C:0.17, G:0.17, T:0.30
Consensus pattern (13 bp):
CAATGTATCGATA
Found at i:68380 original size:20 final size:20
Alignment explanation
Indices: 68355--68408 Score: 74
Period size: 20 Copynumber: 2.7 Consensus size: 20
68345 TATCGATACA
* *
68355 ATGTATCGATACGA-GTCATC
1 ATGTATCGATACAATGT-ACC
68375 ATGTATCGATACAATGTACC
1 ATGTATCGATACAATGTACC
68395 ATGTATCGATACAA
1 ATGTATCGATACAA
68409 ACAGTGGTAG
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
20 29 0.94
21 2 0.06
ACGTcount: A:0.35, C:0.19, G:0.17, T:0.30
Consensus pattern (20 bp):
ATGTATCGATACAATGTACC
Found at i:68462 original size:20 final size:20
Alignment explanation
Indices: 68437--68491 Score: 60
Period size: 19 Copynumber: 2.8 Consensus size: 20
68427 CTACCAGTTT
***
68437 CATGTATCGATACAATTGTC
1 CATGTATCGATACAATTAAA
68457 CATGTA-CTGATACAA-TAAA
1 CATGTATC-GATACAATTAAA
68476 CATGTATCGATACAAT
1 CATGTATCGATACAAT
68492 GTATTGATAC
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
19 15 0.52
20 14 0.48
ACGTcount: A:0.38, C:0.18, G:0.13, T:0.31
Consensus pattern (20 bp):
CATGTATCGATACAATTAAA
Found at i:69644 original size:32 final size:31
Alignment explanation
Indices: 69595--69690 Score: 115
Period size: 32 Copynumber: 3.0 Consensus size: 31
69585 CCTTACAATA
69595 CTATC-TTTCAAGGCTAAGATAGAAACCTCC
1 CTATCTTTTCAAGGCTAAGATAGAAACCTCC
*
69625 CTATCTTTTCACAGGCTAAGATAGAACCTCTCTCC
1 CTATCTTTTCA-AGGCTAAGATAGAA--AC-CTCC
69660 CTATCTTTTTCAAAGGCTAAGATA-AAACCTC
1 CTATC-TTTTC-AAGGCTAAGATAGAAACCTC
69691 TCAATCACTT
Statistics
Matches: 57, Mismatches: 2, Indels: 12
0.80 0.03 0.17
Matches are distributed among these distances:
30 5 0.09
31 5 0.09
32 17 0.30
33 1 0.02
34 1 0.02
35 11 0.19
36 16 0.28
37 1 0.02
ACGTcount: A:0.31, C:0.27, G:0.11, T:0.30
Consensus pattern (31 bp):
CTATCTTTTCAAGGCTAAGATAGAAACCTCC
Found at i:69677 original size:36 final size:35
Alignment explanation
Indices: 69595--69692 Score: 125
Period size: 36 Copynumber: 2.9 Consensus size: 35
69585 CCTTACAATA
*
69595 CTATC-TTTC-AAGGCTAAGATAGAA--AC-CTCC
1 CTATCTTTTCAAAGGCTAAGATAGAACCTCTCTCC
*
69625 CTATCTTTTCACAGGCTAAGATAGAACCTCTCTCC
1 CTATCTTTTCAAAGGCTAAGATAGAACCTCTCTCC
*
69660 CTATCTTTTTCAAAGGCTAAGATAAAACCTCTC
1 CTATC-TTTTCAAAGGCTAAGATAGAACCTCTC
69693 AATCACTTAG
Statistics
Matches: 58, Mismatches: 4, Indels: 6
0.85 0.06 0.09
Matches are distributed among these distances:
30 5 0.09
31 4 0.07
32 14 0.24
34 1 0.02
35 9 0.16
36 25 0.43
ACGTcount: A:0.31, C:0.28, G:0.11, T:0.31
Consensus pattern (35 bp):
CTATCTTTTCAAAGGCTAAGATAGAACCTCTCTCC
Found at i:70156 original size:13 final size:13
Alignment explanation
Indices: 70138--70163 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
70128 ACTATTCACC
70138 ATGTATCGATACA
1 ATGTATCGATACA
70151 ATGTATCGATACA
1 ATGTATCGATACA
70164 TGAACAGTGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:74559 original size:36 final size:35
Alignment explanation
Indices: 74476--74573 Score: 100
Period size: 36 Copynumber: 2.9 Consensus size: 35
74466 CCTTACAACA
*
74476 CTATC-TTTC-AAGGCTTAGATAGAAACCTC-CT--
1 CTATCTTTTCAAAGGCTAAGATAG-AACCTCTCTCC
** *
74507 -TATCTTTTCACGGGCTAAGATAGAATCTCTCTCC
1 CTATCTTTTCAAAGGCTAAGATAGAACCTCTCTCC
74541 CTATCTATTTCAAAGGCTAAGATAGAACCTCTC
1 CTATCT-TTTCAAAGGCTAAGATAGAACCTCTC
74574 AATCACTTAA
Statistics
Matches: 53, Mismatches: 7, Indels: 9
0.77 0.10 0.13
Matches are distributed among these distances:
30 4 0.08
31 9 0.17
32 12 0.23
35 5 0.09
36 23 0.43
ACGTcount: A:0.29, C:0.26, G:0.13, T:0.33
Consensus pattern (35 bp):
CTATCTTTTCAAAGGCTAAGATAGAACCTCTCTCC
Found at i:75177 original size:13 final size:13
Alignment explanation
Indices: 75159--75196 Score: 58
Period size: 13 Copynumber: 2.9 Consensus size: 13
75149 TACCAAAAAC
*
75159 ATGTATCGATATA
1 ATGTATCGATACA
75172 ATGTATCGATACA
1 ATGTATCGATACA
*
75185 ATGTATCCATAC
1 ATGTATCGATAC
75197 TAAGCAATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.34
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:77295 original size:166 final size:165
Alignment explanation
Indices: 76887--77516 Score: 709
Period size: 167 Copynumber: 3.8 Consensus size: 165
76877 GGGTTTTTTT
* * *
76887 CTCCGTAAATTTTTT-T-AGGAGGATTTTTCTTCGTTCTTAATTTTTAAAATTTATCAAATATTA
1 CTCCGTAAATTTTTTCTGA-G-GGATTTTTCTTGGTTTTTAATTTTTAAAATTCATCAAATATTA
* *** * * ** * *
76950 TTATTTATTTCATATTGAATCGGATTTCAAAAGTTCATTTATTTTTAGGAGTTTTTGAATTTGTT
64 TTATTTATTTCATATTAAATCATTTTTCAAAAATTCATTCATTTCCATGAG-TTTTAAATTT-TT
* * * *
77015 TCTTAAAATTCTTCTTGTTTTTCGAAAAACAAAGTTTTGTA
127 TCTTAAAATT-TTCCTATTTTT-GAAAAACGAAGTTTTCTA
* * *
77056 CTCCGTAAATCTTTTC-GGGGTGCTTTTTCTTAGG-TTTTAA--TTTAAAATTCATCAAATATTA
1 CTCCGTAAATTTTTTCTGAGG-GATTTTTCTT-GGTTTTTAATTTTTAAAATTCATCAAATATTA
*
77117 TTATTTATTTCATATTAAATTATTTTTCAAAAATT-ATTTCATTTCCATGAGTTTTTAAATTTTT
64 TTATTTATTTCATATTAAATCATTTTTCAAAAATTCA-TTCATTTCCATGAG-TTTTAAATTTTT
*
77181 TCTTAAAATTTTCCTATTTTTGAAAAACGGAGTTTTCTA
127 TCTTAAAATTTTCCTATTTTTGAAAAACGAAGTTTTCTA
* * * *
77220 TTTCGTAAATTTTTTCTGAGGGATTTTTCTTGGTTTTTAATTTCTAAAATTCATAAAATATTATT
1 CTCCGTAAATTTTTTCTGAGGGATTTTTCTTGGTTTTTAATTTTTAAAATTCATCAAATATTATT
* * **
77285 ATTTATTTCATATTAAATCACTTTTCAAAAGTTCATTCATTTTTATGAGTTTTAAATTTTTTCCT
66 ATTTATTTCATATTAAATCATTTTTCAAAAATTCATTCATTTCCATGAGTTTTAAATTTTTT-CT
* * *
77350 TAAAATTCT-CTTTTTTCTGAAAAATGAAGTTTTCTA
130 TAAAATTTTCCTATTTT-TGAAAAACGAAGTTTTCTA
* * * * * * *
77386 CTCCATAAATAATTTTCAGGGGGATTTTTCTTGGTTTTAAATTTTTAAAATTCATCCATTATTAT
1 CTCCGTAAAT-TTTTTCTGAGGGATTTTTCTTGGTTTTTAATTTTTAAAATTCATCAAATATTAT
* *
77451 TATTTATTTCATATTAAATCATTTTTCAAAAATTCAATCATTTCCATGAGTTTTGAATTTTTTCT
65 TATTTATTTCATATTAAATCATTTTTCAAAAATTCATTCATTTCCATGAGTTTTAAATTTTTTCT
77516 T
130 T
77517 TGAAATCCCC
Statistics
Matches: 393, Mismatches: 55, Indels: 29
0.82 0.12 0.06
Matches are distributed among these distances:
163 2 0.01
164 43 0.11
165 31 0.08
166 113 0.29
167 173 0.44
168 1 0.00
169 29 0.07
170 1 0.00
ACGTcount: A:0.29, C:0.11, G:0.09, T:0.51
Consensus pattern (165 bp):
CTCCGTAAATTTTTTCTGAGGGATTTTTCTTGGTTTTTAATTTTTAAAATTCATCAAATATTATT
ATTTATTTCATATTAAATCATTTTTCAAAAATTCATTCATTTCCATGAGTTTTAAATTTTTTCTT
AAAATTTTCCTATTTTTGAAAAACGAAGTTTTCTA
Found at i:77496 original size:333 final size:332
Alignment explanation
Indices: 76890--77516 Score: 878
Period size: 333 Copynumber: 1.9 Consensus size: 332
76880 TTTTTTTCTC
* * *
76890 CGTAAATTTTTTTAGGAGGATTTTTCTTCGTTCTTAATTTTTAAAATTTATCAAATATTATTATT
1 CGTAAATTTTTTTAGGAGGATTTTTCTTCGTTCTTAATTTCTAAAATTCATAAAATATTATTATT
* ** * *
76955 TATTTCATATTGAATCGGATTTCAAAAGTTCATTTATTTTTAGGAGTTTTTGAATTTGTTTCTTA
66 TATTTCATATTAAATCACATTTCAAAAGTTCATTCATTTTTAGGAGTTTTTAAATTTGTTTCTTA
* * * *
77020 AAATTCTTCTTGTTTTTCGAAAAACAAAGTTTTGTACTCCGTAAATCTTTTCGGGGTGCTTTTTC
131 AAATTCTTCTTGTTTTTCGAAAAACAAAGTTTTCTACTCCATAAATATTTTCGGGGTGATTTTTC
*
77085 TTAGGTTTTAATTTAAAATTCATCAAATATTATTATTTATTTCATATTAAATTATTTTTCAAAAA
196 TTAGGTTTTAATTTAAAATTCATCAAATATTATTATTTATTTCATATTAAATCATTTTTCAAAAA
*
77150 TTATTTCATTTCCATGAGTTTTTAAATTTTTTCTTAAAATTTTCCTATTTTTGAAAAACGGAGTT
261 TTATATCATTTCCATGAG-TTTTAAATTTTTTCTTAAAATTTTCCTATTTTTGAAAAACGGAGTT
77215 TTCTATTT
325 TTCTATTT
* *
77223 CGTAAATTTTTTCT--GAGGGATTTTTCTTGGTTTTTAATTTCTAAAATTCATAAAATATTATTA
1 CGTAAATTTTTT-TAGGA-GGATTTTTCTTCGTTCTTAATTTCTAAAATTCATAAAATATTATTA
* *
77286 TTTATTTCATATTAAATCACTTTTCAAAAGTTCATTCATTTTTATGAG-TTTTAAATTT-TTTCC
64 TTTATTTCATATTAAATCACATTTCAAAAGTTCATTCATTTTTAGGAGTTTTTAAATTTGTTT-C
**
77349 TTAAAATTC-TC-T-TTTTTCTGAAAAATGAAGTTTTCTACTCCATAAATAATTTTCAGGGG-GA
128 TTAAAATTCTTCTTGTTTTTC-GAAAAACAAAGTTTTCTACTCCATAAAT-ATTTTC-GGGGTGA
* *
77410 TTTTTCTT-GGTTTTAAATTTTTAAAATTCATCCATTATTATTATTTATTTCATATTAAATCATT
190 TTTTTCTTAGGTTTT-AA--TTTAAAATTCATCAAATATTATTATTTATTTCATATTAAATCATT
*
77474 TTTCAAAAATTCA-ATCATTTCCATGAGTTTTGAATTTTTTCTT
252 TTTCAAAAATT-ATATCATTTCCATGAGTTTTAAATTTTTTCTT
77517 TGAAATCCCC
Statistics
Matches: 261, Mismatches: 23, Indels: 21
0.86 0.08 0.07
Matches are distributed among these distances:
329 6 0.02
330 31 0.12
331 21 0.08
332 40 0.15
333 161 0.62
334 2 0.01
ACGTcount: A:0.29, C:0.11, G:0.09, T:0.51
Consensus pattern (332 bp):
CGTAAATTTTTTTAGGAGGATTTTTCTTCGTTCTTAATTTCTAAAATTCATAAAATATTATTATT
TATTTCATATTAAATCACATTTCAAAAGTTCATTCATTTTTAGGAGTTTTTAAATTTGTTTCTTA
AAATTCTTCTTGTTTTTCGAAAAACAAAGTTTTCTACTCCATAAATATTTTCGGGGTGATTTTTC
TTAGGTTTTAATTTAAAATTCATCAAATATTATTATTTATTTCATATTAAATCATTTTTCAAAAA
TTATATCATTTCCATGAGTTTTAAATTTTTTCTTAAAATTTTCCTATTTTTGAAAAACGGAGTTT
TCTATTT
Found at i:78177 original size:12 final size:12
Alignment explanation
Indices: 78160--78208 Score: 50
Period size: 12 Copynumber: 4.2 Consensus size: 12
78150 GCAAGCAAGC
78160 AAAAAAGAGAGA
1 AAAAAAGAGAGA
78172 AAAAAA-A-A-A
1 AAAAAAGAGAGA
*
78181 AGAAAAAGAAAGA
1 A-AAAAAGAGAGA
*
78194 AAAAAAGTGAGA
1 AAAAAAGAGAGA
78206 AAA
1 AAA
78209 TAGAAAGATT
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
9 2 0.06
10 6 0.19
11 2 0.06
12 19 0.61
13 2 0.06
ACGTcount: A:0.80, C:0.00, G:0.18, T:0.02
Consensus pattern (12 bp):
AAAAAAGAGAGA
Found at i:86148 original size:246 final size:246
Alignment explanation
Indices: 85714--86207 Score: 916
Period size: 246 Copynumber: 2.0 Consensus size: 246
85704 GTAGAACCAA
*
85714 TTAATGAAATTTGGCCTAGTCAACTTATTAGCATCAAGTATGCTGCAAAGTGACAAGTTTGTAGT
1 TTAATGAAATTTGGCCTAGTCAACTTATTAGCATCAAGTATGCTACAAAGTGACAAGTTTGTAGT
85779 TATCTTCACTTGTTTATATCTTTTATGAATAAAACATTTATGGTGTCAATTATTTCCAATAGGTA
66 TATCTTCACTTGTTTATATCTTTTATGAATAAAACATTTATGGTGTCAATTATTTCCAATAGGTA
*
85844 ATCATTAAGTTAGGTTTTAATACTATAATAATTATTTTCATTATTTTATGTTAGCTCAAAATAGG
131 ATCATTAACTTAGGTTTTAATACTATAATAATTATTTTCATTATTTTATGTTAGCTCAAAATAGG
*
85909 GATTAAACCAGGAGGAGGGGTGAATTGGATCTAATGGAAAATTAAAAACTT
196 GATTAAACCAAGAGGAGGGGTGAATTGGATCTAATGGAAAATTAAAAACTT
*
85960 TTAATGAAATTTGGCCTAGTCAACTTGTTAGCATCAAGTATGCTACAAAGTGACAAGTTTGTAGT
1 TTAATGAAATTTGGCCTAGTCAACTTATTAGCATCAAGTATGCTACAAAGTGACAAGTTTGTAGT
86025 TATCTTCACTTGTTTATATCTTTTATGAATAAAACATTTATGGTGTCAATTATTTCCAATAGGTA
66 TATCTTCACTTGTTTATATCTTTTATGAATAAAACATTTATGGTGTCAATTATTTCCAATAGGTA
*
86090 ATCATTAACTTAGGTTTTAATACTATAATAATTATTTTCATTATTTTGTGTTAGCTCAAAATAGG
131 ATCATTAACTTAGGTTTTAATACTATAATAATTATTTTCATTATTTTATGTTAGCTCAAAATAGG
* * *
86155 GATTGAACCAAGAGGAGGGGTGAATTGGTTTTAATGGAAAATTAAAAACTT
196 GATTAAACCAAGAGGAGGGGTGAATTGGATCTAATGGAAAATTAAAAACTT
86206 TT
1 TT
86208 TCATAAGCAA
Statistics
Matches: 240, Mismatches: 8, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
246 240 1.00
ACGTcount: A:0.34, C:0.11, G:0.17, T:0.39
Consensus pattern (246 bp):
TTAATGAAATTTGGCCTAGTCAACTTATTAGCATCAAGTATGCTACAAAGTGACAAGTTTGTAGT
TATCTTCACTTGTTTATATCTTTTATGAATAAAACATTTATGGTGTCAATTATTTCCAATAGGTA
ATCATTAACTTAGGTTTTAATACTATAATAATTATTTTCATTATTTTATGTTAGCTCAAAATAGG
GATTAAACCAAGAGGAGGGGTGAATTGGATCTAATGGAAAATTAAAAACTT
Found at i:87005 original size:32 final size:31
Alignment explanation
Indices: 86931--87064 Score: 187
Period size: 32 Copynumber: 4.2 Consensus size: 31
86921 TACTATTCAC
*
86931 ATGTATCGATAGATGAACAGTGATGAACAGT
1 ATGTATCGATACATGAACAGTGATGAACAGT
* *
86962 ATGTATCGATACATGAATAGTGATGAATAGT
1 ATGTATCGATACATGAACAGTGATGAACAGT
*
86993 GATGTATTGATACATGAACAGTGATGAACAGT
1 -ATGTATCGATACATGAACAGTGATGAACAGT
* *
87025 AATGTATCGATACATGAACAGTGATCAACAGCA
1 -ATGTATCGATACATGAACAGTGATGAACAG-T
87058 ATGTATC
1 ATGTATC
87065 AATTAAAAGT
Statistics
Matches: 91, Mismatches: 10, Indels: 3
0.88 0.10 0.03
Matches are distributed among these distances:
31 28 0.31
32 63 0.69
ACGTcount: A:0.39, C:0.11, G:0.22, T:0.28
Consensus pattern (31 bp):
ATGTATCGATACATGAACAGTGATGAACAGT
Found at i:95349 original size:58 final size:58
Alignment explanation
Indices: 95173--95357 Score: 178
Period size: 58 Copynumber: 3.2 Consensus size: 58
95163 ACTTACCAAT
*** * * * *
95173 TTCATGCA-TTTAGAGTTATTTTAATCATTTTTCATAATTTAGGGACTATTATGT-AA
1 TTCATGCATTTTAGAACCATTTTAGTCATTTTTTATGATTTAGGGACAATTATGTAAA
* * * * * * *
95229 TTCATGCATTTTAGGACCACTTTAGTCAATTTCTATGATTTAAGGATAATTATGTAAT
1 TTCATGCATTTTAGAACCATTTTAGTCATTTTTTATGATTTAGGGACAATTATGTAAA
* * * *
95287 TTCATACATTTT-GAAACCATTTTAGTCATTTTTTATGATTTAGGGACCACTATATAAA
1 TTCATGCATTTTAG-AACCATTTTAGTCATTTTTTATGATTTAGGGACAATTATGTAAA
95345 TTCATGCATTTTA
1 TTCATGCATTTTA
95358 AGGTCAATAG
Statistics
Matches: 99, Mismatches: 26, Indels: 5
0.76 0.20 0.04
Matches are distributed among these distances:
56 8 0.08
57 34 0.34
58 57 0.58
ACGTcount: A:0.31, C:0.12, G:0.12, T:0.45
Consensus pattern (58 bp):
TTCATGCATTTTAGAACCATTTTAGTCATTTTTTATGATTTAGGGACAATTATGTAAA
Found at i:96272 original size:20 final size:19
Alignment explanation
Indices: 96246--96301 Score: 67
Period size: 19 Copynumber: 2.9 Consensus size: 19
96236 CTACCAGTTT
* *
96246 CATGTATCGATACAATTATG
1 CATGTATCGATACAATGA-A
* *
96266 TATGTATCGGTACAATGAA
1 CATGTATCGATACAATGAA
96285 CATGTATCGATACAATG
1 CATGTATCGATACAATG
96302 TATCGATACA
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
19 15 0.50
20 15 0.50
ACGTcount: A:0.36, C:0.14, G:0.18, T:0.32
Consensus pattern (19 bp):
CATGTATCGATACAATGAA
Found at i:96304 original size:13 final size:13
Alignment explanation
Indices: 96286--96312 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
96276 TACAATGAAC
96286 ATGTATCGATACA
1 ATGTATCGATACA
96299 ATGTATCGATACA
1 ATGTATCGATACA
96312 A
1 A
96313 AGCATGATGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:97828 original size:19 final size:19
Alignment explanation
Indices: 97804--97853 Score: 91
Period size: 19 Copynumber: 2.6 Consensus size: 19
97794 AAACAGAAAA
97804 TGTATCGATACATAAGTGT
1 TGTATCGATACATAAGTGT
*
97823 TGTATCGATACATAAGTTT
1 TGTATCGATACATAAGTGT
97842 TGTATCGATACA
1 TGTATCGATACA
97854 ATGTATCGCT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 30 1.00
ACGTcount: A:0.32, C:0.12, G:0.18, T:0.38
Consensus pattern (19 bp):
TGTATCGATACATAAGTGT
Found at i:97904 original size:21 final size:21
Alignment explanation
Indices: 97878--97918 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
97868 AGCTACTGCC
97878 AAGGAAATGTATCGATACATT
1 AAGGAAATGTATCGATACATT
97899 AAGGAAATGTATCGATACAT
1 AAGGAAATGTATCGATACAT
97919 CGATCTTTGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.44, C:0.10, G:0.20, T:0.27
Consensus pattern (21 bp):
AAGGAAATGTATCGATACATT
Found at i:100337 original size:51 final size:53
Alignment explanation
Indices: 100280--100402 Score: 180
Period size: 51 Copynumber: 2.4 Consensus size: 53
100270 CAATTCTCTG
* * *
100280 CAATCGGAGATATTCCAACTCCGATTTTATTT-TC-AAAACACCAA-TTTTCTA
1 CAATCGGGGATACTCCAACTCCGATTTTATTTCCCAAAAACACCAATTTTTC-A
*
100331 TAATCGGGGATACTCCAACTCCGATTTTATTTCCCAAAAACACCAATTTTTCA
1 CAATCGGGGATACTCCAACTCCGATTTTATTTCCCAAAAACACCAATTTTTCA
100384 CAATCGGGGATACTCCAAC
1 CAATCGGGGATACTCCAAC
100403 CCCGTTAATC
Statistics
Matches: 64, Mismatches: 5, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
51 29 0.45
52 1 0.02
53 29 0.45
54 5 0.08
ACGTcount: A:0.33, C:0.26, G:0.11, T:0.31
Consensus pattern (53 bp):
CAATCGGGGATACTCCAACTCCGATTTTATTTCCCAAAAACACCAATTTTTCA
Found at i:100456 original size:28 final size:27
Alignment explanation
Indices: 100386--100461 Score: 100
Period size: 27 Copynumber: 2.8 Consensus size: 27
100376 ATTTTTCACA
100386 ATCGGGGATACTCCAACCCCGTTAATC
1 ATCGGGGATACTCCAACCCCGTTAATC
* *
100413 ATCGGGGATACTCCAACCCTGTT-ATT
1 ATCGGGGATACTCCAACCCCGTTAATC
*
100439 TTCGAGGGGATACTCCAACCCCG
1 ATC--GGGGATACTCCAACCCCG
100462 GTTTTAATTC
Statistics
Matches: 43, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
26 4 0.09
27 22 0.51
28 17 0.40
ACGTcount: A:0.24, C:0.32, G:0.21, T:0.24
Consensus pattern (27 bp):
ATCGGGGATACTCCAACCCCGTTAATC
Found at i:100508 original size:79 final size:76
Alignment explanation
Indices: 100413--100588 Score: 235
Period size: 79 Copynumber: 2.3 Consensus size: 76
100403 CCCGTTAATC
* * * *
100413 ATCGGGGATACTCCAACCCTGTTATTTTCGAGGGGATACTCCAACCCCGGTTTTAATTCTAAAAT
1 ATCGGGGATACTCCAACCCTGTTACTTCCGAGGGGATACTCCAACCCCGATTTTAATTCTAAAAC
*
100478 ATTAATTTCTCATA
66 ATCAATTT-T--TA
* * * *
100492 ATCGGGGATACTCCAACCCCGTTACTTCCGAGGGGATACTTCAATCCCGATTTTATTTCTAAAAC
1 ATCGGGGATACTCCAACCCTGTTACTTCCGAGGGGATACTCCAACCCCGATTTTAATTCTAAAAC
*
100557 ATCAATTTTTC
66 ATCAATTTTTA
100568 ATCGGGGATACTCCAACCCTG
1 ATCGGGGATACTCCAACCCTG
100589 GCTTTATTTC
Statistics
Matches: 86, Mismatches: 11, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
76 21 0.24
78 1 0.01
79 64 0.74
ACGTcount: A:0.27, C:0.26, G:0.16, T:0.32
Consensus pattern (76 bp):
ATCGGGGATACTCCAACCCTGTTACTTCCGAGGGGATACTCCAACCCCGATTTTAATTCTAAAAC
ATCAATTTTTA
Found at i:100627 original size:51 final size:51
Alignment explanation
Indices: 100568--100689 Score: 190
Period size: 51 Copynumber: 2.4 Consensus size: 51
100558 TCAATTTTTC
* * *
100568 ATCGGGGATACTCCAACCCTGGCTTTATTTCCAAAATATTGATTTCTCACA
1 ATCGGGGATACTCCAACCCCGGCCTTATTTCCAAAATATCGATTTCTCACA
* * *
100619 ATCGGGGATACTTCAACCCCGGCCTTATTTCTAAAATATCGATTTCTCATA
1 ATCGGGGATACTCCAACCCCGGCCTTATTTCCAAAATATCGATTTCTCACA
100670 ATCGGGGATACTCCAACCCC
1 ATCGGGGATACTCCAACCCC
100690 ATTATTTTCA
Statistics
Matches: 64, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
51 64 1.00
ACGTcount: A:0.27, C:0.28, G:0.15, T:0.30
Consensus pattern (51 bp):
ATCGGGGATACTCCAACCCCGGCCTTATTTCCAAAATATCGATTTCTCACA
Found at i:100653 original size:178 final size:181
Alignment explanation
Indices: 100444--100769 Score: 498
Period size: 178 Copynumber: 1.8 Consensus size: 181
100434 TTATTTTCGA
** *
100444 GGGGATACTCCAACCCCGGTTTTAATTCTAAAATATTAATTTCTCATAATCGGGGATACTCCAAC
1 GGGGATACTCCAACCCCGGCCTTAATTCTAAAATATCAATTTCTCATAATCGGGGATACTCCAAC
* * * *
100509 CCCGTTACTTCCGA-GGGGATACTTCAATCCCGATTTTATTTCTAAAACATCAA-TTT-T-TCAT
66 CCCATTACTTCC-ACGGGGATACTCCAACCCCGATTTTATTTCTAAAACATCAATTTTCTATAAT
100570 CGGGGATACTCCAACCCTGGCTTTATTTCCAAAATATTGATTTCTCACAATC
130 CGGGGATACTCCAACCCTGGCTTTATTTCCAAAATATTGATTTCTCACAATC
* * *
100622 GGGGATACTTCAACCCCGGCCTTATTTCTAAAATATCGATTTCTCATAATCGGGGATACTCCAAC
1 GGGGATACTCCAACCCCGGCCTTAATTCTAAAATATCAATTTCTCATAATCGGGGATACTCCAAC
* * *
100687 CCCATTATTTTCACGGGGATACTCCAACCCCGATTTTATTTTTAAAACATCAATTTTCTATAATC
66 CCCATTACTTCCACGGGGATACTCCAACCCCGATTTTATTTCTAAAACATCAATTTTCTATAATC
100752 GGGGATACTCCAACCCTG
131 GGGGATACTCCAACCCTG
100770 TTACTATCTC
Statistics
Matches: 131, Mismatches: 13, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
177 1 0.01
178 104 0.79
179 3 0.02
180 1 0.01
181 22 0.17
ACGTcount: A:0.28, C:0.25, G:0.14, T:0.33
Consensus pattern (181 bp):
GGGGATACTCCAACCCCGGCCTTAATTCTAAAATATCAATTTCTCATAATCGGGGATACTCCAAC
CCCATTACTTCCACGGGGATACTCCAACCCCGATTTTATTTCTAAAACATCAATTTTCTATAATC
GGGGATACTCCAACCCTGGCTTTATTTCCAAAATATTGATTTCTCACAATC
Found at i:100752 original size:79 final size:79
Alignment explanation
Indices: 100621--100767 Score: 215
Period size: 79 Copynumber: 1.9 Consensus size: 79
100611 TTCTCACAAT
* * * *
100621 CGGGGATACTTCAACCCCGGCCTTATTTCTAAAATATCGATTTCTCATAATCGGGGATACTCCAA
1 CGGGGATACTCCAACCCCGACCTTATTTCTAAAACATCAATTTCTCATAATCGGGGATACTCCAA
100686 CCCCATTATTTTCA
66 CCCCATTATTTTCA
** *
100700 CGGGGATACTCCAACCCCGATTTTATTTTTAAAACATCAATTT-TCTATAATCGGGGATACTCCA
1 CGGGGATACTCCAACCCCGACCTTATTTCTAAAACATCAATTTCTC-ATAATCGGGGATACTCCA
100764 ACCC
65 ACCC
100768 TGTTACTATC
Statistics
Matches: 60, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
78 2 0.03
79 58 0.97
ACGTcount: A:0.28, C:0.27, G:0.14, T:0.31
Consensus pattern (79 bp):
CGGGGATACTCCAACCCCGACCTTATTTCTAAAACATCAATTTCTCATAATCGGGGATACTCCAA
CCCCATTATTTTCA
Found at i:107049 original size:21 final size:21
Alignment explanation
Indices: 107023--107071 Score: 55
Period size: 22 Copynumber: 2.3 Consensus size: 21
107013 ATATTATTAA
* *
107023 TATTTT-TCATTTGATTCAATT
1 TATTTTCTAATTTGACT-AATT
107044 TATTTTCTAATTTGACTAATT
1 TATTTTCTAATTTGACTAATT
107065 TCATTTT
1 T-ATTTT
107072 AAGCTCATTA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 11 0.46
22 13 0.54
ACGTcount: A:0.24, C:0.10, G:0.04, T:0.61
Consensus pattern (21 bp):
TATTTTCTAATTTGACTAATT
Found at i:109365 original size:19 final size:20
Alignment explanation
Indices: 109320--109375 Score: 69
Period size: 20 Copynumber: 2.9 Consensus size: 20
109310 CTACCAGTTT
* *
109320 CATGTATCGATACAATTATG
1 CATGTATCGATACAATGATA
*
109340 TATGTATCGATACAATGA-A
1 CATGTATCGATACAATGATA
*
109359 CATGTATTGATACAATG
1 CATGTATCGATACAATG
109376 TATCGATACA
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
19 15 0.48
20 16 0.52
ACGTcount: A:0.38, C:0.12, G:0.16, T:0.34
Consensus pattern (20 bp):
CATGTATCGATACAATGATA
Found at i:114459 original size:5 final size:5
Alignment explanation
Indices: 114449--114477 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
114439 AATTTTAAAT
114449 TTTTA TTTTA TTTTA TTTTA TTTTA TTTT
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTT
114478 TAAACTAGTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (5 bp):
TTTTA
Found at i:115466 original size:157 final size:156
Alignment explanation
Indices: 115186--115468 Score: 399
Period size: 157 Copynumber: 1.8 Consensus size: 156
115176 TGAGCAACCT
* * *
115186 TGCTTGGCCGAAAGTCCCTAGTGCCATAAGAGGATTATTTCATGCATTTTTAAACACATTTTAGG
1 TGCTTAGCCGAAAGTCCCTAGTACCATAAGAGGATTATTTCATGCATTTCTAAACACATTTTAGG
* * *
115251 TTTTTTAGCATTTTAAGGGCCTTTTTGCAAATTGTAGAAAGTTCAAAGACTAAGTTGCAAAAAAA
66 CTTTTTA-CATTTTAAGGGCCTTTTTGCAAATTGTAGAAAGTTCAAAGACGAACTTGCAAAAAAA
115316 GTTAAAATTTTTTTCTTTAGGTATCCA
130 GTTAAAATTTTTTTCTTTAGGTATCCA
* * *
115343 TGCTTAGCCGAGAGTCCCTAGTACCATAAGAGGATTGTTTCATGCATTTCTAAACATATTTTAGG
1 TGCTTAGCCGAAAGTCCCTAGTACCATAAGAGGATTATTTCATGCATTTCTAAACACATTTTAGG
* * **
115408 CTTTTTA-ATGTATT-AGGGACCTTTTTGTAAATTTTAGAAAGTTCATGGACGAACTTGCAAA
66 CTTTTTACAT-T-TTAAGGG-CCTTTTTGCAAATTGTAGAAAGTTCAAAGACGAACTTGCAAA
115469 TTTTGAAAGA
Statistics
Matches: 110, Mismatches: 13, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
155 2 0.02
156 5 0.05
157 103 0.94
ACGTcount: A:0.30, C:0.14, G:0.18, T:0.37
Consensus pattern (156 bp):
TGCTTAGCCGAAAGTCCCTAGTACCATAAGAGGATTATTTCATGCATTTCTAAACACATTTTAGG
CTTTTTACATTTTAAGGGCCTTTTTGCAAATTGTAGAAAGTTCAAAGACGAACTTGCAAAAAAAG
TTAAAATTTTTTTCTTTAGGTATCCA
Found at i:117149 original size:13 final size:13
Alignment explanation
Indices: 117131--117187 Score: 51
Period size: 13 Copynumber: 3.9 Consensus size: 13
117121 CATAAAGTGT
117131 TGTATCGATACAA
1 TGTATCGATACAA
117144 TGTATCGATACATAA
1 TGTATCGATAC--AA
*
117159 GTGTTGTATTGATACAA
1 ----TGTATCGATACAA
117176 TGTATCGATACA
1 TGTATCGATACA
117188 TAAGTTTTGT
Statistics
Matches: 36, Mismatches: 2, Indels: 12
0.72 0.04 0.24
Matches are distributed among these distances:
13 22 0.61
15 2 0.06
17 2 0.06
19 10 0.28
ACGTcount: A:0.35, C:0.12, G:0.18, T:0.35
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:117166 original size:32 final size:32
Alignment explanation
Indices: 117113--117211 Score: 171
Period size: 32 Copynumber: 3.1 Consensus size: 32
117103 CAACGATTTT
117113 TATCGATACATAAAGTGTTGTATCGATACAATG
1 TATCGATACAT-AAGTGTTGTATCGATACAATG
*
117146 TATCGATACATAAGTGTTGTATTGATACAATG
1 TATCGATACATAAGTGTTGTATCGATACAATG
*
117178 TATCGATACATAAGTTTTGTATCGATACAATG
1 TATCGATACATAAGTGTTGTATCGATACAATG
117210 TA
1 TA
117212 AGCTACTACC
Statistics
Matches: 63, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
32 52 0.83
33 11 0.17
ACGTcount: A:0.35, C:0.11, G:0.17, T:0.36
Consensus pattern (32 bp):
TATCGATACATAAGTGTTGTATCGATACAATG
Found at i:117200 original size:19 final size:18
Alignment explanation
Indices: 117113--117206 Score: 73
Period size: 19 Copynumber: 5.6 Consensus size: 18
117103 CAACGATTTT
117113 TATCGATACATAAAGTGTTG
1 TATCGATACAT-AAGT-TTG
117133 TATCGATAC--AA---TG
1 TATCGATACATAAGTTTG
117146 TATCGATACATAAGTGTTG
1 TATCGATACATAAGT-TTG
*
117165 TATTGATAC--AA---TG
1 TATCGATACATAAGTTTG
117178 TATCGATACATAAGTTTTG
1 TATCGATACATAAG-TTTG
117197 TATCGATACA
1 TATCGATACA
117207 ATGTAAGCTA
Statistics
Matches: 60, Mismatches: 2, Indels: 25
0.69 0.02 0.29
Matches are distributed among these distances:
13 21 0.35
15 4 0.07
17 4 0.07
19 22 0.37
20 9 0.15
ACGTcount: A:0.35, C:0.12, G:0.17, T:0.36
Consensus pattern (18 bp):
TATCGATACATAAGTTTG
Found at i:117374 original size:32 final size:32
Alignment explanation
Indices: 117333--117409 Score: 154
Period size: 32 Copynumber: 2.4 Consensus size: 32
117323 ACATTATAAA
117333 ATGTATCGATACATGCAGGCAAATTTGCCCAG
1 ATGTATCGATACATGCAGGCAAATTTGCCCAG
117365 ATGTATCGATACATGCAGGCAAATTTGCCCAG
1 ATGTATCGATACATGCAGGCAAATTTGCCCAG
117397 ATGTATCGATACA
1 ATGTATCGATACA
117410 CTATGAAATG
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 45 1.00
ACGTcount: A:0.32, C:0.21, G:0.21, T:0.26
Consensus pattern (32 bp):
ATGTATCGATACATGCAGGCAAATTTGCCCAG
Found at i:117384 original size:84 final size:84
Alignment explanation
Indices: 117282--117442 Score: 295
Period size: 84 Copynumber: 1.9 Consensus size: 84
117272 CACTGATCTT
*
117282 TGTATCGATACATACAGGCAAATTTGCCCAGATGTATCGATACATTATAAAATGTATCGATACAT
1 TGTATCGATACATACAGGCAAATTTGCCCAGATGTATCGATACACTATAAAATGTATCGATACAT
117347 GCAGGCAAATTTGCCCAGA
66 GCAGGCAAATTTGCCCAGA
* *
117366 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATGAAATGTATCGATACAT
1 TGTATCGATACATACAGGCAAATTTGCCCAGATGTATCGATACACTATAAAATGTATCGATACAT
117431 GCAGGCAAATTT
66 GCAGGCAAATTT
117443 TCATATTTCG
Statistics
Matches: 74, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
84 74 1.00
ACGTcount: A:0.35, C:0.19, G:0.19, T:0.28
Consensus pattern (84 bp):
TGTATCGATACATACAGGCAAATTTGCCCAGATGTATCGATACACTATAAAATGTATCGATACAT
GCAGGCAAATTTGCCCAGA
Found at i:128642 original size:22 final size:22
Alignment explanation
Indices: 128615--128671 Score: 96
Period size: 22 Copynumber: 2.6 Consensus size: 22
128605 ATGTATAGTG
*
128615 ATGAACAGTGATGTATCGATAC
1 ATGAACAGTGATGTATCAATAC
128637 ATGAACAGTGATGTATCAATAC
1 ATGAACAGTGATGTATCAATAC
*
128659 ATGAGCAGTGATG
1 ATGAACAGTGATG
128672 AACAGTAAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.37, C:0.12, G:0.25, T:0.26
Consensus pattern (22 bp):
ATGAACAGTGATGTATCAATAC
Found at i:129482 original size:48 final size:48
Alignment explanation
Indices: 129430--129525 Score: 149
Period size: 48 Copynumber: 2.0 Consensus size: 48
129420 TTTTGGGAAA
* *
129430 TTATTATTTTGGAAAATTTTTGAGTTTTCTTAAA-AGGCATGATGAAGC
1 TTATTATTTTGGAAAAATTTTGAGTTTTCTTAAAGA-GCATGATAAAGC
*
129478 TTATTGTTTTGGAAAAATTTTGAGTTTTCTTAAAGAGCATGATAAAGC
1 TTATTATTTTGGAAAAATTTTGAGTTTTCTTAAAGAGCATGATAAAGC
129526 AATCAACTAA
Statistics
Matches: 44, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
48 43 0.98
49 1 0.02
ACGTcount: A:0.32, C:0.06, G:0.19, T:0.43
Consensus pattern (48 bp):
TTATTATTTTGGAAAAATTTTGAGTTTTCTTAAAGAGCATGATAAAGC
Found at i:131221 original size:13 final size:13
Alignment explanation
Indices: 131203--131228 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
131193 TACAGCAAGT
131203 ATGTATCGATACA
1 ATGTATCGATACA
131216 ATGTATCGATACA
1 ATGTATCGATACA
131229 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:133477 original size:21 final size:21
Alignment explanation
Indices: 133444--133488 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
133434 TTGCAAGTTG
*
133444 AAATAAAGAAGTTGGCTAATGA
1 AAATAAAGAAGTTAGCTAA-GA
*
133466 AAATAATG-AGTTAGCTAAGA
1 AAATAAAGAAGTTAGCTAAGA
133486 AAA
1 AAA
133489 ATGAAAACTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 9 0.43
22 7 0.33
ACGTcount: A:0.53, C:0.04, G:0.20, T:0.22
Consensus pattern (21 bp):
AAATAAAGAAGTTAGCTAAGA
Found at i:135313 original size:15 final size:15
Alignment explanation
Indices: 135293--135328 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
135283 TAAAAATGTC
*
135293 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
135308 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
*
135323 CCAAAT
1 CAAAAT
135329 AAAATTGATG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.50, C:0.17, G:0.19, T:0.14
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:137420 original size:13 final size:13
Alignment explanation
Indices: 137402--137427 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
137392 CATTTTTTCT
137402 TTGTATCGATACA
1 TTGTATCGATACA
137415 TTGTATCGATACA
1 TTGTATCGATACA
137428 GGGTGATTAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:139253 original size:56 final size:56
Alignment explanation
Indices: 139191--139312 Score: 244
Period size: 56 Copynumber: 2.2 Consensus size: 56
139181 CTATAACAAA
139191 AAGGGGGAGAGAAAATAGATATGTGCAAATAAATTTTTGATATGAATTACTTGATT
1 AAGGGGGAGAGAAAATAGATATGTGCAAATAAATTTTTGATATGAATTACTTGATT
139247 AAGGGGGAGAGAAAATAGATATGTGCAAATAAATTTTTGATATGAATTACTTGATT
1 AAGGGGGAGAGAAAATAGATATGTGCAAATAAATTTTTGATATGAATTACTTGATT
139303 AAGGGGGAGA
1 AAGGGGGAGA
139313 ATTATTAATA
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
56 66 1.00
ACGTcount: A:0.41, C:0.03, G:0.26, T:0.30
Consensus pattern (56 bp):
AAGGGGGAGAGAAAATAGATATGTGCAAATAAATTTTTGATATGAATTACTTGATT
Found at i:141674 original size:50 final size:49
Alignment explanation
Indices: 141551--141852 Score: 282
Period size: 50 Copynumber: 6.0 Consensus size: 49
141541 AGGGTAAAGC
* * * * *
141551 CTTATAAAGTCAAAGGTCTACACAAGTTAGCACCCGATAGGAAGGTAAAAT
1 CTTATAAAGTCAAA-GTCCACACTAGCTAGCACCTGATA-GAAGGTCAAAT
* *
141602 CTTATAAAGTTAAAAGTTCACACTAGCTAGCACCTGATAGAAGGGTCAAAT
1 CTTATAAAG-TCAAAGTCCACACTAGCTAGCACCTGATAGAA-GGTCAAAT
* * * * * *
141653 CTTATAGAGTCAAAGTCCACACTAACTGGGA-CTCGATATGAGGGTCAAGT
1 CTTATAAAGTCAAAGTCCACACTAGCTAGCACCT-GATA-GAAGGTCAAAT
* *
141703 CTTCTAAAGTCAAAGTCCACACTAGCTAGCACCTAATAAGAAGGTCAAAT
1 CTTATAAAGTCAAAGTCCACACTAGCTAGCACCTGAT-AGAAGGTCAAAT
* * * * * *
141753 CTTATAAAATCAAATTCCACACTAGTTGGCACCTAATAGGAAAGTCAAAT
1 CTTATAAAGTCAAAGTCCACACTAGCTAGCACCTGATA-GAAGGTCAAAT
* * ** *
141803 CTAATAGAGTCAAAGTCCACACTAATTAGCACTTGATAAGAAGGTCAAAT
1 CTTATAAAGTCAAAGTCCACACTAGCTAGCACCTGAT-AGAAGGTCAAAT
141853 ACTATAGAGC
Statistics
Matches: 205, Mismatches: 38, Indels: 17
0.79 0.15 0.07
Matches are distributed among these distances:
49 3 0.01
50 149 0.73
51 49 0.24
52 4 0.02
ACGTcount: A:0.39, C:0.20, G:0.17, T:0.24
Consensus pattern (49 bp):
CTTATAAAGTCAAAGTCCACACTAGCTAGCACCTGATAGAAGGTCAAAT
Found at i:141800 original size:100 final size:100
Alignment explanation
Indices: 141551--141852 Score: 329
Period size: 100 Copynumber: 3.0 Consensus size: 100
141541 AGGGTAAAGC
* * * * * *
141551 CTTATAAAGTCAAAGGTCTACACAAGTTAGCACCCGATAGGAAGGTAAAATCTTATAAAGTTAAA
1 CTTATAAAGTCAAA-GTCCACACTAGTTGGCACCTGATAGGAAGGTCAAATCTTATAAAG-TCAA
*
141616 AGTTCACACTAGCTAGCACCTGAT-AGAAGGGTCAAAT
64 AGTCCACACTAGCTAGCACCTGATAAGAA-GGTCAAAT
* ** * * * * *
141653 CTTATAGAGTCAAAGTCCACACTAACTGGGA-CTCGATATGAGGGTCAAGTCTTCTAAAGTCAAA
1 CTTATAAAGTCAAAGTCCACACTAGTTGGCACCT-GATAGGAAGGTCAAATCTTATAAAGTCAAA
*
141717 GTCCACACTAGCTAGCACCTAATAAGAAGGTCAAAT
65 GTCCACACTAGCTAGCACCTGATAAGAAGGTCAAAT
* * * * * *
141753 CTTATAAAATCAAATTCCACACTAGTTGGCACCTAATAGGAAAGTCAAATCTAATAGAGTCAAAG
1 CTTATAAAGTCAAAGTCCACACTAGTTGGCACCTGATAGGAAGGTCAAATCTTATAAAGTCAAAG
** *
141818 TCCACACTAATTAGCACTTGATAAGAAGGTCAAAT
66 TCCACACTAGCTAGCACCTGATAAGAAGGTCAAAT
141853 ACTATAGAGC
Statistics
Matches: 163, Mismatches: 34, Indels: 8
0.80 0.17 0.04
Matches are distributed among these distances:
100 113 0.69
101 37 0.23
102 13 0.08
ACGTcount: A:0.39, C:0.20, G:0.17, T:0.24
Consensus pattern (100 bp):
CTTATAAAGTCAAAGTCCACACTAGTTGGCACCTGATAGGAAGGTCAAATCTTATAAAGTCAAAG
TCCACACTAGCTAGCACCTGATAAGAAGGTCAAAT
Found at i:141850 original size:150 final size:152
Alignment explanation
Indices: 141555--141850 Score: 366
Period size: 150 Copynumber: 2.0 Consensus size: 152
141545 TAAAGCCTTA
* * * * *
141555 TAAAGTCAAAGGTCTACACAAGTTAGCACCCGATAGGAAGGTAAAATCTTATAAAGTTAAAAGTT
1 TAAAGTCAAAGGTCCACACAAGCTAGCACCCAATAAGAAGGTAAAATCTTATAAAGATAAAAGTT
* * * * *
141620 CACACTAGCTAGCACCTGATAGAAGGGTCAAATCTTATAGAGTCAAAGTCCACACTAACTGGGAC
66 CACACTAGCTAGCACCTAATAGAAGAGTCAAATCTAATAGAGTCAAAGTCCACACTAACTAGCAC
* *
141685 TCGATATGAGGGTCAAGTCTTC
131 TCGATAAGAAGGTCAAGTCTTC
* * * *
141707 TAAAGTCAAA-GTCCACACTAGCTAGCACCTAATAAGAAGGTCAAATCTTATAAA-ATCAAA-TT
1 TAAAGTCAAAGGTCCACACAAGCTAGCACCCAATAAGAAGGTAAAATCTTATAAAGATAAAAGTT
* * *
141769 CCACACTAGTTGGCACCTAATAGGAA-AGTCAAATCTAATAGAGTCAAAGTCCACACTAATTAGC
66 -CACACTAGCTAGCACCTAATA-GAAGAGTCAAATCTAATAGAGTCAAAGTCCACACTAACTAGC
*
141833 ACTTGATAAGAAGGTCAA
129 ACTCGATAAGAAGGTCAA
141851 ATACTATAGA
Statistics
Matches: 122, Mismatches: 20, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
149 2 0.02
150 70 0.57
151 40 0.33
152 10 0.08
ACGTcount: A:0.40, C:0.20, G:0.18, T:0.23
Consensus pattern (152 bp):
TAAAGTCAAAGGTCCACACAAGCTAGCACCCAATAAGAAGGTAAAATCTTATAAAGATAAAAGTT
CACACTAGCTAGCACCTAATAGAAGAGTCAAATCTAATAGAGTCAAAGTCCACACTAACTAGCAC
TCGATAAGAAGGTCAAGTCTTC
Found at i:146504 original size:16 final size:16
Alignment explanation
Indices: 146483--146513 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
146473 TACATATTGC
146483 TTAGTATCAATACATT
1 TTAGTATCAATACATT
*
146499 TTAGTATCGATACAT
1 TTAGTATCAATACAT
146514 GTTCATAGTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.13, G:0.10, T:0.42
Consensus pattern (16 bp):
TTAGTATCAATACATT
Found at i:146524 original size:19 final size:17
Alignment explanation
Indices: 146466--146531 Score: 71
Period size: 19 Copynumber: 3.6 Consensus size: 17
146456 ACACCCAGAT
146466 GTATCGATACATATTGCTTA
1 GTATCGATACAT-TT-C-TA
*
146486 GTATCAATACATTT-TA
1 GTATCGATACATTTCTA
146502 GTATCGATACATGTTCATA
1 GTATCGATACAT-TTC-TA
146521 GTATCGATACA
1 GTATCGATACA
146532 CCCTGAAAAA
Statistics
Matches: 41, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
16 13 0.32
17 2 0.05
19 15 0.37
20 11 0.27
ACGTcount: A:0.33, C:0.15, G:0.14, T:0.38
Consensus pattern (17 bp):
GTATCGATACATTTCTA
Found at i:152658 original size:20 final size:20
Alignment explanation
Indices: 152633--152687 Score: 92
Period size: 20 Copynumber: 2.8 Consensus size: 20
152623 AATTTCCCAG
152633 AATGTATCGATACATTGAAT
1 AATGTATCGATACATTGAAT
152653 AATGTATCGATACATTGAAT
1 AATGTATCGATACATTGAAT
* *
152673 AATGTGTCAATACAT
1 AATGTATCGATACAT
152688 ATGGAAAACC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.40, C:0.11, G:0.15, T:0.35
Consensus pattern (20 bp):
AATGTATCGATACATTGAAT
Found at i:155320 original size:20 final size:20
Alignment explanation
Indices: 155295--155332 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
155285 AGATAAGTTT
155295 AAATGTGTTTTCAA-TAAATC
1 AAATGT-TTTTCAAGTAAATC
155315 AAATGTTTTTCAAGTAAA
1 AAATGTTTTTCAAGTAAA
155333 AATAATCCAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 7 0.41
20 10 0.59
ACGTcount: A:0.42, C:0.08, G:0.11, T:0.39
Consensus pattern (20 bp):
AAATGTTTTTCAAGTAAATC
Found at i:155993 original size:22 final size:23
Alignment explanation
Indices: 155955--155998 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 23
155945 GCATTCAACC
155955 TTTGGGTACAATCTCTT-AAGAA
1 TTTGGGTACAATCTCTTGAAGAA
*
155977 TTTGGGATATAAT-TCTTGAAGA
1 TTTGGG-TACAATCTCTTGAAGA
155999 GATTGAGAGG
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
22 10 0.53
23 9 0.47
ACGTcount: A:0.32, C:0.09, G:0.20, T:0.39
Consensus pattern (23 bp):
TTTGGGTACAATCTCTTGAAGAA
Found at i:167850 original size:18 final size:18
Alignment explanation
Indices: 167824--167866 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
167814 TCTGATAGTG
* *
167824 ATGAGGACAATGGAAAGT
1 ATGATGACAATGGAAAAT
167842 ATGATGACAATGGAAAAT
1 ATGATGACAATGGAAAAT
167860 ATGATGA
1 ATGATGA
167867 TGATGATATA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.47, C:0.05, G:0.28, T:0.21
Consensus pattern (18 bp):
ATGATGACAATGGAAAAT
Found at i:172261 original size:22 final size:21
Alignment explanation
Indices: 172225--172265 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
172215 TTTTATTAAA
172225 TTAATAAATAATATTAATTAT
1 TTAATAAATAATATTAATTAT
*
172246 TTAATAAATTATTATTAATT
1 TTAATAAA-TAATATTAATT
172266 TATATTTATG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 8 0.44
22 10 0.56
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (21 bp):
TTAATAAATAATATTAATTAT
Found at i:175049 original size:16 final size:16
Alignment explanation
Indices: 175028--175058 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
175018 AATTCGTGTA
*
175028 TTATTTTATGTTTATG
1 TTATTTTATATTTATG
175044 TTATTTTATATTTAT
1 TTATTTTATATTTAT
175059 ACCTATTTGA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.23, C:0.00, G:0.06, T:0.71
Consensus pattern (16 bp):
TTATTTTATATTTATG
Found at i:176707 original size:17 final size:18
Alignment explanation
Indices: 176681--176714 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
176671 ACTTGTTTAT
*
176681 ATAATTAGAGA-AAAAAA
1 ATAATAAGAGAGAAAAAA
176698 ATAATAAGAGAGAAAAA
1 ATAATAAGAGAGAAAAA
176715 CTCATTCCTT
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:0.71, C:0.00, G:0.15, T:0.15
Consensus pattern (18 bp):
ATAATAAGAGAGAAAAAA
Found at i:181486 original size:29 final size:29
Alignment explanation
Indices: 181453--181510 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
181443 AAAACCATTA
181453 ACCTTTTGATTAAAGATCACCTCTTGATC
1 ACCTTTTGATTAAAGATCACCTCTTGATC
181482 ACCTTTTGATTAAAGATCACCTCTTGATC
1 ACCTTTTGATTAAAGATCACCTCTTGATC
181511 TACCAACTAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.28, C:0.24, G:0.10, T:0.38
Consensus pattern (29 bp):
ACCTTTTGATTAAAGATCACCTCTTGATC
Found at i:183369 original size:5 final size:5
Alignment explanation
Indices: 183359--183389 Score: 62
Period size: 5 Copynumber: 6.2 Consensus size: 5
183349 TTTGATTGGG
183359 GCCTT GCCTT GCCTT GCCTT GCCTT GCCTT G
1 GCCTT GCCTT GCCTT GCCTT GCCTT GCCTT G
183390 GCGGGACTAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.00, C:0.39, G:0.23, T:0.39
Consensus pattern (5 bp):
GCCTT
Found at i:184451 original size:43 final size:40
Alignment explanation
Indices: 184364--184451 Score: 97
Period size: 43 Copynumber: 2.1 Consensus size: 40
184354 AATCACTATT
* *
184364 TATTAATAAAAAATATATTTTTATTTAAATTTAATTATATAA
1 TATTAATAAAAAATATATTTTTATTT--ATTTAATAATAAAA
184406 TATTAATATAAAAATAATATTTTTAGTTT-TTTAAATAATAAAA
1 TATTAATA-AAAAAT-ATATTTTTA-TTTATTT-AATAATAAAA
184449 TAT
1 TAT
184452 GTCGTTGAGC
Statistics
Matches: 40, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
42 11 0.28
43 17 0.43
44 9 0.22
45 3 0.08
ACGTcount: A:0.50, C:0.00, G:0.01, T:0.49
Consensus pattern (40 bp):
TATTAATAAAAAATATATTTTTATTTATTTAATAATAAAA
Found at i:185639 original size:13 final size:13
Alignment explanation
Indices: 185621--185679 Score: 55
Period size: 13 Copynumber: 4.0 Consensus size: 13
185611 ACATTATGCT
185621 TTGTATCGATACA
1 TTGTATCGATACA
185634 TTGTATCGATACACA
1 TTGTATCGAT--ACA
185649 CCTAGATGTATCGATACA
1 --T---TGTATCGATACA
185667 TTGTATCGATACA
1 TTGTATCGATACA
185680 CACCTAGATG
Statistics
Matches: 39, Mismatches: 0, Indels: 14
0.74 0.00 0.26
Matches are distributed among these distances:
13 22 0.56
15 3 0.08
16 1 0.03
17 1 0.03
18 3 0.08
20 9 0.23
ACGTcount: A:0.32, C:0.19, G:0.15, T:0.34
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:185644 original size:33 final size:32
Alignment explanation
Indices: 185622--185700 Score: 140
Period size: 33 Copynumber: 2.4 Consensus size: 32
185612 CATTATGCTT
185622 TGTATCGATACATTGTATCGATACACACCTAGA
1 TGTATCGATACATTGTATCGATACACACCTA-A
185655 TGTATCGATACATTGTATCGATACACACCTAGA
1 TGTATCGATACATTGTATCGATACACACCTA-A
185688 TGTATCGATACAT
1 TGTATCGATACAT
185701 ATTCATTGTA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 46 1.00
ACGTcount: A:0.33, C:0.20, G:0.15, T:0.32
Consensus pattern (32 bp):
TGTATCGATACATTGTATCGATACACACCTAA
Found at i:185660 original size:20 final size:20
Alignment explanation
Indices: 185635--185699 Score: 81
Period size: 20 Copynumber: 3.6 Consensus size: 20
185625 ATCGATACAT
185635 TGTATCGATACACACCTAGA
1 TGTATCGATACACACCTAGA
185655 TGTATCGAT--ACA--T---
1 TGTATCGATACACACCTAGA
185668 TGTATCGATACACACCTAGA
1 TGTATCGATACACACCTAGA
185688 TGTATCGATACA
1 TGTATCGATACA
185700 TATTCATTGT
Statistics
Matches: 38, Mismatches: 0, Indels: 14
0.73 0.00 0.27
Matches are distributed among these distances:
13 9 0.24
15 3 0.08
16 1 0.03
17 1 0.03
18 3 0.08
20 21 0.55
ACGTcount: A:0.34, C:0.22, G:0.15, T:0.29
Consensus pattern (20 bp):
TGTATCGATACACACCTAGA
Found at i:185712 original size:19 final size:20
Alignment explanation
Indices: 185688--185739 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
185678 CACACCTAGA
**
185688 TGTATCGATACATATTC-AT
1 TGTATCGATACATAGACAAT
* *
185707 TGTATCGATATATGGACAAT
1 TGTATCGATACATAGACAAT
185727 TGTATCGATACAT
1 TGTATCGATACAT
185740 GAAATTGGCA
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
19 13 0.48
20 14 0.52
ACGTcount: A:0.33, C:0.13, G:0.15, T:0.38
Consensus pattern (20 bp):
TGTATCGATACATAGACAAT
Found at i:185794 original size:20 final size:19
Alignment explanation
Indices: 185769--185835 Score: 74
Period size: 20 Copynumber: 3.7 Consensus size: 19
185759 CTACCACTGT
185769 TTGTATCGATACATGGTACA
1 TTGTATCGATACATGGTA-A
185789 TTGTATCGATAC-----AA
1 TTGTATCGATACATGGTAA
185803 -TGTATCGATACATGGTGAA
1 TTGTATCGATACATGGT-AA
185822 TTGTATCGATACAT
1 TTGTATCGATACAT
185836 TACTTCTAAT
Statistics
Matches: 40, Mismatches: 0, Indels: 14
0.74 0.00 0.26
Matches are distributed among these distances:
13 11 0.28
14 1 0.03
15 1 0.03
19 2 0.05
20 25 0.62
ACGTcount: A:0.31, C:0.13, G:0.19, T:0.36
Consensus pattern (19 bp):
TTGTATCGATACATGGTAA
Found at i:185806 original size:13 final size:13
Alignment explanation
Indices: 185785--185814 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
185775 CGATACATGG
*
185785 TACATTGTATCGA
1 TACAATGTATCGA
185798 TACAATGTATCGA
1 TACAATGTATCGA
185811 TACA
1 TACA
185815 TGGTGAATTG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.37, C:0.17, G:0.13, T:0.33
Consensus pattern (13 bp):
TACAATGTATCGA
Found at i:185812 original size:33 final size:33
Alignment explanation
Indices: 185770--185834 Score: 114
Period size: 33 Copynumber: 2.0 Consensus size: 33
185760 TACCACTGTT
185770 TGTATCGATACATGGT-ACATTGTATCGATACAA
1 TGTATCGATACATGGTGA-ATTGTATCGATACAA
185803 TGTATCGATACATGGTGAATTGTATCGATACA
1 TGTATCGATACATGGTGAATTGTATCGATACA
185835 TTACTTCTAA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
33 30 0.97
34 1 0.03
ACGTcount: A:0.32, C:0.14, G:0.20, T:0.34
Consensus pattern (33 bp):
TGTATCGATACATGGTGAATTGTATCGATACAA
Found at i:194512 original size:13 final size:13
Alignment explanation
Indices: 194494--194520 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
194484 ACATTATGCT
194494 TTGTATCGATACA
1 TTGTATCGATACA
194507 TTGTATCGATACA
1 TTGTATCGATACA
194520 T
1 T
194521 GGACAATTGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:197587 original size:18 final size:17
Alignment explanation
Indices: 197545--197599 Score: 65
Period size: 17 Copynumber: 3.1 Consensus size: 17
197535 TATCTAATTT
* *
197545 TATAATTATTAGATAAT
1 TATATTTATTAGATAAA
*
197562 TATATTTATTAGGTAAA
1 TATATTTATTAGATAAA
197579 TATTATTTATTAAGATAAA
1 TA-TATTTATT-AGATAAA
197598 TA
1 TA
197600 AGGAGTTTAA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
17 16 0.50
18 8 0.25
19 8 0.25
ACGTcount: A:0.45, C:0.00, G:0.07, T:0.47
Consensus pattern (17 bp):
TATATTTATTAGATAAA
Found at i:202141 original size:17 final size:16
Alignment explanation
Indices: 202101--202141 Score: 64
Period size: 17 Copynumber: 2.5 Consensus size: 16
202091 AAAAAAAAAG
202101 AAAAAAAAACAAAACA
1 AAAAAAAAACAAAACA
202117 AAACAAAAAACAAAACA
1 AAA-AAAAAACAAAACA
*
202134 AAGAAAAA
1 AAAAAAAA
202142 GAGAGAAAAG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 8 0.35
17 15 0.65
ACGTcount: A:0.85, C:0.12, G:0.02, T:0.00
Consensus pattern (16 bp):
AAAAAAAAACAAAACA
Found at i:203347 original size:176 final size:172
Alignment explanation
Indices: 203120--204245 Score: 1183
Period size: 176 Copynumber: 6.4 Consensus size: 172
203110 TCCTTCCGCT
* * *
203120 TTTCAGTCCTCAAAGAGTAGGAC-ACCTTTTAAAGCCCACACAAGTTGGTGGCACTTCCTAGTCC
1 TTTCCGTCCTCAAAGAGCAGGACTCCCTTTTAAAGCCCACACAAGTTGGTGGCACTTCC-AGTCC
*
203184 TCAAAGAGCAGGACGCCTTCTCCTTTTAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAA
65 TCAAAGAGCAGGACGCCTTCTCCTTTTAAAGCCCACACAAGTTGGTGGCACTTTCCAGTCCTCAA
* * * *
203249 AGAGCGGGATGCCTTTTCTTTCAAAGCCCACACAAGTTGGTGGCACC
130 AGAGCAGGACGCC---CCTTTTAAAGCCCACACAAGTTGGTGGCA-C
*
203296 TTTCCGTCCCCAAAGAGCAGGAC-CCCTTTTAAAGCCCACACAAGTTGGTGGCACTTCCCAGTCC
1 TTTCCGTCCTCAAAGAGCAGGACTCCCTTTTAAAGCCCACACAAGTTGGTGGCACTT-CCAGTCC
* * *
203360 TCAAAGAGTAGGACACCTTCTCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTTCC-GTCCCCA
65 TCAAAGAGCAGGACGCCTTCTCCTTTTAAAGCCCACACAAGTTGGTGGCA-CTTTCCAGTCCTCA
203424 AAGAGCAGGA--CCCCTTTTAAAGCCCACACAAGTTGGTGGCAC
129 AAGAGCAGGACGCCCCTTTTAAAGCCCACACAAGTTGGTGGCAC
* *
203466 TTCCCAGTCCTCAAAGAGCAGGACATTTTCTCCTTTTAAAGCCCACACAAGTTGGTGGCATTTTC
1 TTTCC-GTCCTCAAAGAGCAGGAC----TC-CCTTTTAAAGCCCACACAAGTTGGTGGCA-CTTC
* * *
203531 CAGTCCTCAAAGAGCGGGACGCCTT-TTCTTTCAAAGCCCACACAAGTTGGTGGCACCTTTCC-G
59 CAGTCCTCAAAGAGCAGGACGCCTTCTCCTTTTAAAGCCCACACAAGTTGGTGGCA-CTTTCCAG
*
203594 TCCCCAAAGAGCAGGA--CCCCTTTTAAAGCCCACACAAGTTGGTGGCAC
123 TCCTCAAAGAGCAGGACGCCCCTTTTAAAGCCCACACAAGTTGGTGGCAC
* * *
203642 ATCCCAGTCCTCAAAGAGCAGGATGCCTTCTCCTTTCAAAGCCCACACAAGTTGGTGGCACCTTT
1 TTTCC-GTCCTCAAAGAGCAGGA---C-TC-CCTTTTAAAGCCCACACAAGTTGGTGGCA-C-TT
* *
203707 CC-GTCCCCAAAGAGCAGGA---C--C-CC-TTTAAAGCCCACACAAGTTGGTGGCACTTCCCAG
58 CCAGTCCTCAAAGAGCAGGACGCCTTCTCCTTTTAAAGCCCACACAAGTTGGTGGCACTTTCCAG
*
203764 TCCTCAAAGAGCAGGACGTCTTCTCCTTTTAAAGCCCACACAAGTTGGTGGCAT
123 TCCTCAAAGAGCAGGACG-C--C-CCTTTTAAAGCCCACACAAGTTGGTGGCAC
* * * *
203818 TTTCTAGTCCTCAAAGAGCGGGACGCCTTTTCTTTCAAAGCCCACACAAGTTGGTGGCACCTTTC
1 TTTC-CGTCCTCAAAGAGCAGGACTCC----CTTTTAAAGCCCACACAAGTTGGTGGCA-C-TTC
* * * * *
203883 C-GTCCCCAAAGAGCAGGA---C--C-CCTTTTAAAGCCCATACAAGTTGGTGGCACATCCCAAT
59 CAGTCCTCAAAGAGCAGGACGCCTTCTCCTTTTAAAGCCCACACAAGTTGGTGGCACTTTCCAGT
* *
203941 CCTCAAAGAGCAGGACGCCTTCTCCTTTTAAAGCCCACACAAATTGGTGGCAT
124 CCTCAAAGAGCAGGACG-C--C-CCTTTTAAAGCCCACACAAGTTGGTGGCAC
* * * *
203994 TTTCCAGTCCTCAAAGAGCGGGACACCTTTTCTTTTAAAGCCCACACAAGTTGATGGCACCTCCA
1 TTTCC-GTCCTCAAAGAGCAGGACTCC----CTTTTAAAGCCCACACAAGTTGGTGGCACTTCCA
* * * *
204059 GTCCTCAAAGAGCGGGACGCCTT-TTCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCC
61 GTCCTCAAAGAGCAGGACGCCTTCTCCTTTTAAAGCCCACACAAGTTGGTGGCACTTTCCAGTCC
* * *
204123 TCAAAGAGCAGGA--CACCTCTTAAAGCCAACACAAGTTGGTGGCACC
126 TCAAAGAGCAGGACGCCCCTTTTAAAGCCCACACAAGTTGGTGGCA-C
* * * * **
204169 TTTCAGTCCTCAAAGAGCAGGAC-GCCTTTCAAAGCCCACACGAGTTGGTGGCACTTTTTAGTCC
1 TTTCCGTCCTCAAAGAGCAGGACTCCCTTTTAAAGCCCACACAAGTTGGTGGCAC-TTCCAGTCC
204233 TCAAAGAGCAGGA
65 TCAAAGAGCAGGA
204246 TACACTTTAT
Statistics
Matches: 843, Mismatches: 69, Indels: 82
0.85 0.07 0.08
Matches are distributed among these distances:
169 31 0.04
170 64 0.08
171 46 0.05
172 1 0.00
173 4 0.00
174 48 0.06
175 77 0.09
176 458 0.54
177 64 0.08
178 3 0.00
179 1 0.00
180 46 0.05
ACGTcount: A:0.26, C:0.30, G:0.20, T:0.24
Consensus pattern (172 bp):
TTTCCGTCCTCAAAGAGCAGGACTCCCTTTTAAAGCCCACACAAGTTGGTGGCACTTCCAGTCCT
CAAAGAGCAGGACGCCTTCTCCTTTTAAAGCCCACACAAGTTGGTGGCACTTTCCAGTCCTCAAA
GAGCAGGACGCCCCTTTTAAAGCCCACACAAGTTGGTGGCAC
Found at i:203654 original size:292 final size:292
Alignment explanation
Indices: 203120--204245 Score: 1784
Period size: 292 Copynumber: 3.9 Consensus size: 292
203110 TCCTTCCGCT
* * * * *
203120 TTTCAGTCCTCAAAGAGTAGGACACCTTTTAAAGCCCACACAAGTTGGTGGCACTTCCTAGTCCT
1 TTTCCGTCCCCAAAGAGCAGGACCCCTTTTAAAGCCCACACAAGTTGGTGGCACTTCCCAGTCCT
203185 CAAAGAGCAGGACGCCTTCTCCTTTTAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAA
66 CAAAGAGCAGGACGCCTTCTCCTTTTAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAA
*
203250 GAGCGGGATGCCTTTTCTTTCAAAGCCCACACAAGTTGGTGGCACCTTTCCGTCCCCAAAGAGCA
131 GAGCGGGACGCCTTTTCTTTCAAAGCCCACACAAGTTGGTGGCACCTTTCCGTCCCCAAAGAGCA
* * *
203315 GGACCCCTTTTAAAGCCCACACAAGTTGGTGGCACTTCCCAGTCCTCAAAGAGTAGGACACCTTC
196 GGACCCCTTTTAAAGCCCACACAAGTTGGTGGCACATCCCAGTCCTCAAAGAGCAGGACGCCTTC
203380 TCCTTTTAAAGCCCACACAAGTTGGTGGCACC
261 TCCTTTTAAAGCCCACACAAGTTGGTGGCACC
203412 TTTCCGTCCCCAAAGAGCAGGACCCCTTTTAAAGCCCACACAAGTTGGTGGCACTTCCCAGTCCT
1 TTTCCGTCCCCAAAGAGCAGGACCCCTTTTAAAGCCCACACAAGTTGGTGGCACTTCCCAGTCCT
***
203477 CAAAGAGCAGGACATTTTCTCCTTTTAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAA
66 CAAAGAGCAGGACGCCTTCTCCTTTTAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAA
203542 GAGCGGGACGCCTTTTCTTTCAAAGCCCACACAAGTTGGTGGCACCTTTCCGTCCCCAAAGAGCA
131 GAGCGGGACGCCTTTTCTTTCAAAGCCCACACAAGTTGGTGGCACCTTTCCGTCCCCAAAGAGCA
*
203607 GGACCCCTTTTAAAGCCCACACAAGTTGGTGGCACATCCCAGTCCTCAAAGAGCAGGATGCCTTC
196 GGACCCCTTTTAAAGCCCACACAAGTTGGTGGCACATCCCAGTCCTCAAAGAGCAGGACGCCTTC
*
203672 TCCTTTCAAAGCCCACACAAGTTGGTGGCACC
261 TCCTTTTAAAGCCCACACAAGTTGGTGGCACC
203704 TTTCCGTCCCCAAAGAGCAGGACCCC-TTTAAAGCCCACACAAGTTGGTGGCACTTCCCAGTCCT
1 TTTCCGTCCCCAAAGAGCAGGACCCCTTTTAAAGCCCACACAAGTTGGTGGCACTTCCCAGTCCT
* *
203768 CAAAGAGCAGGACGTCTTCTCCTTTTAAAGCCCACACAAGTTGGTGGCATTTTCTAGTCCTCAAA
66 CAAAGAGCAGGACGCCTTCTCCTTTTAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAA
203833 GAGCGGGACGCCTTTTCTTTCAAAGCCCACACAAGTTGGTGGCACCTTTCCGTCCCCAAAGAGCA
131 GAGCGGGACGCCTTTTCTTTCAAAGCCCACACAAGTTGGTGGCACCTTTCCGTCCCCAAAGAGCA
* *
203898 GGACCCCTTTTAAAGCCCATACAAGTTGGTGGCACATCCCAATCCTCAAAGAGCAGGACGCCTTC
196 GGACCCCTTTTAAAGCCCACACAAGTTGGTGGCACATCCCAGTCCTCAAAGAGCAGGACGCCTTC
* *
203963 TCCTTTTAAAGCCCACACAAATTGGTGGCA-T
261 TCCTTTTAAAGCCCACACAAGTTGGTGGCACC
* * * *
203994 TTTCCAGTCCTCAAAGAGCGGGACACCTTTTCTTTTAAAGCCCACACAAGTTGATGGCACCT-CC
1 TTTCC-GTCCCCAAAGAGCAGGAC-CC----CTTTTAAAGCCCACACAAGTTGGTGGCACTTCCC
* * *
204058 AGTCCTCAAAGAGCGGGACGCCTT-TTCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTC
60 AGTCCTCAAAGAGCAGGACGCCTTCTCCTTTTAAAGCCCACACAAGTTGGTGGCATTTTCCAGTC
* * * * *
204122 CTCAAAGAGCAGGACACC---TC-TT-AAAGCCAACACAAGTTGGTGGCACCTTTCAGTCCTCAA
125 CTCAAAGAGCGGGACGCCTTTTCTTTCAAAGCCCACACAAGTTGGTGGCACCTTTCCGTCCCCAA
* * * * ***
204182 AGAGCAGGACGCCTTTCAAAGCCCACACGAGTTGGTGGCACTTTTTAGTCCTCAAAGAGCAGGA
190 AGAGCAGGACCCCTTTTAAAGCCCACACAAGTTGGTGGCACATCCCAGTCCTCAAAGAGCAGGA
204246 TACACTTTAT
Statistics
Matches: 781, Mismatches: 46, Indels: 16
0.93 0.05 0.02
Matches are distributed among these distances:
290 95 0.12
291 273 0.35
292 308 0.39
295 53 0.07
296 25 0.03
297 27 0.03
ACGTcount: A:0.26, C:0.30, G:0.20, T:0.24
Consensus pattern (292 bp):
TTTCCGTCCCCAAAGAGCAGGACCCCTTTTAAAGCCCACACAAGTTGGTGGCACTTCCCAGTCCT
CAAAGAGCAGGACGCCTTCTCCTTTTAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAA
GAGCGGGACGCCTTTTCTTTCAAAGCCCACACAAGTTGGTGGCACCTTTCCGTCCCCAAAGAGCA
GGACCCCTTTTAAAGCCCACACAAGTTGGTGGCACATCCCAGTCCTCAAAGAGCAGGACGCCTTC
TCCTTTTAAAGCCCACACAAGTTGGTGGCACC
Found at i:204966 original size:21 final size:21
Alignment explanation
Indices: 204942--205018 Score: 111
Period size: 21 Copynumber: 3.7 Consensus size: 21
204932 AATTTATCCA
204942 AATGTATCGATACATTTGTAG
1 AATGTATCGATACATTTGTAG
*
204963 AATGTATCGATACATTTGTGG
1 AATGTATCGATACATTTGTAG
* *
204984 AATGTATCGATACA-TTCTACA
1 AATGTATCGATACATTTGTA-G
205005 AATGTATCGATACA
1 AATGTATCGATACA
205019 GGGTCCTAAC
Statistics
Matches: 51, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
20 3 0.06
21 48 0.94
ACGTcount: A:0.35, C:0.13, G:0.17, T:0.35
Consensus pattern (21 bp):
AATGTATCGATACATTTGTAG
Found at i:205147 original size:13 final size:13
Alignment explanation
Indices: 205129--205154 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
205119 CATTTTTCTG
205129 TGTATCGATACAT
1 TGTATCGATACAT
205142 TGTATCGATACAT
1 TGTATCGATACAT
205155 GGATCTTTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:205151 original size:33 final size:33
Alignment explanation
Indices: 205109--205175 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
205099 GCCAAGGAAA
***
205109 TGTATCGATACATTTTTCTGTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
*
205142 TGTATCGATACATGGATCTTTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
205175 T
1 T
205176 TGGAAATTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.25, C:0.15, G:0.16, T:0.43
Consensus pattern (33 bp):
TGTATCGATACATGGATCTGTGTATCGATACAT
Found at i:207628 original size:55 final size:51
Alignment explanation
Indices: 207511--207898 Score: 175
Period size: 52 Copynumber: 7.4 Consensus size: 51
207501 CAATTCTCCG
* * *
207511 CAATCGGGGATATTCCATCTCCGATTTTATTTTCAAAACACTAATTTTCTA
1 CAATCGGGGATACTCCAACTCCGATTTTATTTTCAAAACACAAATTTTCTA
* *
207562 TAATTGGGGATACTCCAACTCCGATTTTATTTTCAAAAAAAACACAAATTTT-TCA
1 CAATCGGGGATACTCCAACTCCGATTTTATTTTC----AAAACACAAATTTTCT-A
* * * ** * * * * *
207617 CAATCGGGGATACGCCAACCCCG--TTAATCATCGGGGATACTCCAACCCCGTTATT-TC
1 CAATCGGGGATACTCCAACTCCGATTTTATTTTC---AAAAC-ACAA----ATT-TTCTA
* * * * ***
207674 CGA--GGGGATACTCCAACCCCTG-CTTTATTCTT-AAAATATTGA-TTTCTCA
1 CAATCGGGGATACTCCAACTCC-GATTTTATT-TTCAAAACACAAATTTTCT-A
* * * * *
207723 TAATCGGGGATACTCCAACCCCGATTTTA-TTGCTAAAACACTAATTTTTCCA
1 CAATCGGGGATACTCCAACTCCGATTTTATTTTC-AAAACAC-AAATTTTCTA
* * * *
207775 CAATCGGGGATACTCCAACCCCGATTTTATTTTTAAAACACCAATTTTCCTT
1 CAATCGGGGATACTCCAACTCCGATTTTATTTTCAAAACACAAATTTT-CTA
* * * * *
207827 TAATCGGGGATACTCCAGCTCCGATTTTATTTCCAAAAACACCAATTTTTTCA
1 CAATCGGGGATACTCCAACTCCGATTTTATTTTC-AAAACACAAATTTTCT-A
*
207880 CAATCGAGGATACTCCAAC
1 CAATCGGGGATACTCCAAC
207899 CTCGTTATTT
Statistics
Matches: 249, Mismatches: 61, Indels: 52
0.69 0.17 0.14
Matches are distributed among these distances:
47 2 0.01
48 2 0.01
49 2 0.01
50 2 0.01
51 61 0.24
52 70 0.28
53 45 0.18
54 3 0.01
55 49 0.20
56 1 0.00
57 8 0.03
58 4 0.02
ACGTcount: A:0.30, C:0.25, G:0.12, T:0.32
Consensus pattern (51 bp):
CAATCGGGGATACTCCAACTCCGATTTTATTTTCAAAACACAAATTTTCTA
Found at i:207688 original size:28 final size:27
Alignment explanation
Indices: 207622--207693 Score: 90
Period size: 27 Copynumber: 2.6 Consensus size: 27
207612 TTTCACAATC
* **
207622 GGGGATACGCCAACCCCGTTAATCATC
1 GGGGATACTCCAACCCCGTTAATCAGA
* *
207649 GGGGATACTCCAACCCCGTTATTTCCGA
1 GGGGATACTCCAACCCCGTTA-ATCAGA
207677 GGGGATACTCCAACCCC
1 GGGGATACTCCAACCCC
207694 TGCTTTATTC
Statistics
Matches: 39, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
27 20 0.51
28 19 0.49
ACGTcount: A:0.24, C:0.35, G:0.22, T:0.19
Consensus pattern (27 bp):
GGGGATACTCCAACCCCGTTAATCAGA
Found at i:207739 original size:51 final size:52
Alignment explanation
Indices: 207677--207899 Score: 193
Period size: 52 Copynumber: 4.3 Consensus size: 52
207667 TTATTTCCGA
* * * *
207677 GGGGATACTCCAACCCCTG-CTTTATT-CTTAAAATATTGATTTCT-CATAATC
1 GGGGATACTCCAACCCC-GACTTTATTGC-TAAAACACTAATTTCTCCACAATC
* *
207728 GGGGATACTCCAACCCCGATTTTATTGCTAAAACACTAATTTTTCCACAATC
1 GGGGATACTCCAACCCCGACTTTATTGCTAAAACACTAATTTCTCCACAATC
* ** * **
207780 GGGGATACTCCAACCCCGATTTTATTTTTAAAACACCAATTT-TCCTTTAATC
1 GGGGATACTCCAACCCCGACTTTATTGCTAAAACACTAATTTCTCC-ACAATC
* * * * * * * *
207832 GGGGATACTCCAGCTCCGATTTTATTTCCAAAAACACCAATTTTTTCACAATC
1 GGGGATACTCCAACCCCGACTTTA-TTGCTAAAACACTAATTTCTCCACAATC
*
207885 GAGGATACTCCAACC
1 GGGGATACTCCAACC
207900 TCGTTATTTC
Statistics
Matches: 144, Mismatches: 22, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
50 1 0.01
51 38 0.26
52 72 0.50
53 31 0.22
54 2 0.01
ACGTcount: A:0.30, C:0.26, G:0.12, T:0.33
Consensus pattern (52 bp):
GGGGATACTCCAACCCCGACTTTATTGCTAAAACACTAATTTCTCCACAATC
Found at i:207891 original size:53 final size:52
Alignment explanation
Indices: 207724--207899 Score: 230
Period size: 52 Copynumber: 3.4 Consensus size: 52
207714 GATTTCTCAT
* * *
207724 AATCGGGGATACTCCAACCCCGATTTTATTGCTAAAACACTAATTTTTCCAC
1 AATCGGGGATACTCCAACCCCGATTTTATTTCTAAAACACCAATTTTTTCAC
* *
207776 AATCGGGGATACTCCAACCCCGATTTTATTTTTAAAACACCAATTTTCCTT--T
1 AATCGGGGATACTCCAACCCCGATTTTATTTCTAAAACACCAATTTT--TTCAC
* * *
207828 AATCGGGGATACTCCAGCTCCGATTTTATTTCCAAAAACACCAATTTTTTCAC
1 AATCGGGGATACTCCAACCCCGATTTTATTT-CTAAAACACCAATTTTTTCAC
*
207881 AATCGAGGATACTCCAACC
1 AATCGGGGATACTCCAACC
207900 TCGTTATTTC
Statistics
Matches: 106, Mismatches: 13, Indels: 9
0.83 0.10 0.07
Matches are distributed among these distances:
51 2 0.02
52 73 0.69
53 30 0.28
54 1 0.01
ACGTcount: A:0.31, C:0.27, G:0.11, T:0.31
Consensus pattern (52 bp):
AATCGGGGATACTCCAACCCCGATTTTATTTCTAAAACACCAATTTTTTCAC
Found at i:207910 original size:31 final size:28
Alignment explanation
Indices: 207882--207958 Score: 86
Period size: 28 Copynumber: 2.8 Consensus size: 28
207872 TTTTTTCACA
*
207882 ATCGAGGATACTCCAACCTCGTTATTTC
1 ATCGAGGATACTCCAACCCCGTTATTTC
* **
207910 ATCGGGGATACTCCAACCCCGTTACCTC
1 ATCGAGGATACTCCAACCCCGTTATTTC
207938 --CGAGGGGATACTCCAACCCCG
1 ATCGA--GGATACTCCAACCCCG
207959 GCTTTATTCC
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
26 2 0.05
28 40 0.95
ACGTcount: A:0.23, C:0.35, G:0.19, T:0.22
Consensus pattern (28 bp):
ATCGAGGATACTCCAACCCCGTTATTTC
Found at i:207982 original size:264 final size:264
Alignment explanation
Indices: 207511--208009 Score: 768
Period size: 264 Copynumber: 1.9 Consensus size: 264
207501 CAATTCTCCG
* * * * *
207511 CAATCGGGGATATTCCATCTCCGATTTTATTTTCAAAACACTAATTTTCTATAATTGGGGATACT
1 CAATCGGGGATACTCCAACCCCGATTTTATTTTCAAAACACCAATTTTCTATAATCGGGGATACT
*
207576 CCAACTCCGATTTTATTTTCAAAAAAAACACAAATTTTTCACAATCGGGGATACGCCAACCCCGT
66 CCAACTCCGATTTTATTTTCAAAAAAAACACAAATTTTTCACAATCGAGGATACGCCAACCCCGT
** * **
207641 TAATCATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCTGCTTTATTCTT
131 TAATCATCGGGGATACTCCAACCCCGTTACCTCCGAGGGGATACTCCAACCCCGGCTTTATTCCC
207706 AAAATATTGATTTCTCATAATCGGGGATACTCCAACCCCGATTTTATTGCTAAAACACTAATTTT
196 AAAATATTGATTTCTCATAATCGGGGATACTCCAACCCCGATTTTATTGCTAAAACACTAATTTT
207771 TCCA
261 TCCA
* *
207775 CAATCGGGGATACTCCAACCCCGATTTTATTTTTAAAACACCAATTTTCCTTTAATCGGGGATAC
1 CAATCGGGGATACTCCAACCCCGATTTTATTTTCAAAACACCAATTTT-CTATAATCGGGGATAC
* * * * * *
207840 TCCAGCTCCGATTTTA-TTTCCAAAAACAC-CAATTTTTTCACAATCGAGGATACTCCAACCTCG
65 TCCAACTCCGATTTTATTTTCAAAAAAAACACAAATTTTTCACAATCGAGGATACGCCAACCCCG
*
207903 TTATTTCATCGGGGATACTCCAACCCCGTTACCTCCGAGGGGATACTCCAACCCCGGCTTTATTC
130 TTA-ATCATCGGGGATACTCCAACCCCGTTACCTCCGAGGGGATACTCCAACCCCGGCTTTATTC
* *
207968 CCAAAATTTTGATTTCTCATAATTGGGGATACTCCAACCCCG
194 CCAAAATATTGATTTCTCATAATCGGGGATACTCCAACCCCG
208010 TTATTTTCGA
Statistics
Matches: 211, Mismatches: 22, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
263 33 0.16
264 149 0.71
265 29 0.14
ACGTcount: A:0.28, C:0.27, G:0.13, T:0.31
Consensus pattern (264 bp):
CAATCGGGGATACTCCAACCCCGATTTTATTTTCAAAACACCAATTTTCTATAATCGGGGATACT
CCAACTCCGATTTTATTTTCAAAAAAAACACAAATTTTTCACAATCGAGGATACGCCAACCCCGT
TAATCATCGGGGATACTCCAACCCCGTTACCTCCGAGGGGATACTCCAACCCCGGCTTTATTCCC
AAAATATTGATTTCTCATAATCGGGGATACTCCAACCCCGATTTTATTGCTAAAACACTAATTTT
TCCA
Found at i:209508 original size:30 final size:29
Alignment explanation
Indices: 209460--209537 Score: 86
Period size: 30 Copynumber: 2.7 Consensus size: 29
209450 AAGAATGATT
* **
209460 AGGGTGAAA-TGTAAGTCAATAGGGTAACC
1 AGGGTGAAACT-TAAGTCAAAAAAGTAACC
*
209489 AGGGTGAAACTTAAAGTCAAAAAAGTAACT
1 AGGGTGAAACTT-AAGTCAAAAAAGTAACC
*
209519 AGGATGAAACTTAAGTCAA
1 AGGGTGAAACTTAAGTCAA
209538 GAAGGTGATG
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
29 17 0.40
30 25 0.60
ACGTcount: A:0.45, C:0.10, G:0.24, T:0.21
Consensus pattern (29 bp):
AGGGTGAAACTTAAGTCAAAAAAGTAACC
Found at i:209589 original size:31 final size:33
Alignment explanation
Indices: 209554--209625 Score: 89
Period size: 31 Copynumber: 2.3 Consensus size: 33
209544 GATGAGGGTG
*
209554 AAACCTAATAA-TCAA-AAGGATGACCAAGGCA
1 AAACCTAATAAGTCAAGAAGAATGACCAAGGCA
* *
209585 AAACCT--TAAGTCAAGAAGAATGACTAAGGCG
1 AAACCTAATAAGTCAAGAAGAATGACCAAGGCA
209616 AAACCTAATA
1 AAACCTAATA
209626 GTTAAAAAAC
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
29 3 0.09
30 4 0.12
31 25 0.74
33 2 0.06
ACGTcount: A:0.50, C:0.18, G:0.17, T:0.15
Consensus pattern (33 bp):
AAACCTAATAAGTCAAGAAGAATGACCAAGGCA
Found at i:209765 original size:31 final size:31
Alignment explanation
Indices: 209686--209831 Score: 113
Period size: 31 Copynumber: 4.8 Consensus size: 31
209676 CTATGGCTGG
* *
209686 ACCTATTAATTATAAGGATGATTAAGGCAAA
1 ACCTATTAATTAAAAGGATGACTAAGGCAAA
* * * * *
209717 A-TTAATTAGTCAAAAGGATTACTAGGGCAAA
1 ACCT-ATTAATTAAAAGGATGACTAAGGCAAA
* * *
209748 ACCTATTAATTAGAAGGAT-AATAAACGCAAA
1 ACCTATTAATTAAAAGGATGACT-AAGGCAAA
* *
209779 ACCTATT-AGTAAAA-AATGACTAA-GCAAA
1 ACCTATTAATTAAAAGGATGACTAAGGCAAA
* *
209807 ACTTATTAATCAAAAGGATGACTAA
1 ACCTATTAATTAAAAGGATGACTAA
209832 CTTATTAGTG
Statistics
Matches: 87, Mismatches: 22, Indels: 13
0.71 0.18 0.11
Matches are distributed among these distances:
28 11 0.13
29 9 0.10
30 18 0.21
31 48 0.55
32 1 0.01
ACGTcount: A:0.49, C:0.12, G:0.14, T:0.25
Consensus pattern (31 bp):
ACCTATTAATTAAAAGGATGACTAAGGCAAA
Found at i:209821 original size:28 final size:29
Alignment explanation
Indices: 209743--209831 Score: 74
Period size: 30 Copynumber: 3.0 Consensus size: 29
209733 GATTACTAGG
* * *
209743 GCAAAACCTATTAATTAGAAGGAT-AATAAA
1 GCAAAACCTATTAA-TAAAAAGATGACT-AA
*
209773 CGCAAAACCTATTAGTAAAAA-ATGACTAA
1 -GCAAAACCTATTAATAAAAAGATGACTAA
* *
209802 GCAAAACTTATTAATCAAAAGGATGACTAA
1 GCAAAACCTATTAAT-AAAAAGATGACTAA
209832 CTTATTAGTG
Statistics
Matches: 48, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
28 13 0.27
29 8 0.17
30 14 0.29
31 13 0.27
ACGTcount: A:0.52, C:0.13, G:0.12, T:0.22
Consensus pattern (29 bp):
GCAAAACCTATTAATAAAAAGATGACTAA
Found at i:209892 original size:29 final size:31
Alignment explanation
Indices: 209834--209900 Score: 93
Period size: 29 Copynumber: 2.2 Consensus size: 31
209824 ATGACTAACT
*
209834 TATTAGTGAGAAAGATGACTAGAGTAAAACG
1 TATTAGTGAGAAAGATGACTAGAGTAAAACC
* *
209865 TATTAGT-AGAAAG-TGATTAGGGTAAAACC
1 TATTAGTGAGAAAGATGACTAGAGTAAAACC
209894 TATTAGT
1 TATTAGT
209901 TAAAAAGGTT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
29 20 0.61
30 6 0.18
31 7 0.21
ACGTcount: A:0.42, C:0.06, G:0.24, T:0.28
Consensus pattern (31 bp):
TATTAGTGAGAAAGATGACTAGAGTAAAACC
Found at i:210230 original size:60 final size:60
Alignment explanation
Indices: 210157--210272 Score: 133
Period size: 60 Copynumber: 1.9 Consensus size: 60
210147 TTAAAAGGTG
* * * *
210157 ACTAAGGTAAAACCTAAACTTAAGAAGATGACTAGGGCAAAACCTTCAATCAAAAAAGTA
1 ACTAAGATAAAACCTAAACTAAAAAAGATGACGAGGGCAAAACCTTCAATCAAAAAAGTA
* * * * * * *
210217 ACTAAGATGAAACCTTAAGTAAAAAAGGTGACGATGGCAAAACTTTCAATCGAAAA
1 ACTAAGATAAAACCTAAACTAAAAAAGATGACGAGGGCAAAACCTTCAATCAAAAA
210273 GGTGATTTAG
Statistics
Matches: 45, Mismatches: 11, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
60 45 1.00
ACGTcount: A:0.49, C:0.16, G:0.16, T:0.19
Consensus pattern (60 bp):
ACTAAGATAAAACCTAAACTAAAAAAGATGACGAGGGCAAAACCTTCAATCAAAAAAGTA
Found at i:210689 original size:20 final size:21
Alignment explanation
Indices: 210645--210698 Score: 74
Period size: 20 Copynumber: 2.6 Consensus size: 21
210635 TTTTACAATT
*
210645 TGTATCAATACAAAGAGTGAA
1 TGTATCAATACATAGAGTGAA
*
210666 TGTATCAATACATA-AGTGAG
1 TGTATCAATACATAGAGTGAA
*
210686 TGTATCGATACAT
1 TGTATCAATACAT
210699 GTCTGAAATG
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 17 0.57
21 13 0.43
ACGTcount: A:0.41, C:0.11, G:0.19, T:0.30
Consensus pattern (21 bp):
TGTATCAATACATAGAGTGAA
Found at i:220593 original size:139 final size:138
Alignment explanation
Indices: 220438--220821 Score: 456
Period size: 139 Copynumber: 2.8 Consensus size: 138
220428 TTGTAAATTT
* * *
220438 TAAAAATCTCATTTCGTACCTTAATAGAGAATCAAAAGATATAAAAACTTTTGAAGATTTCTATA
1 TAAAAAT-TCATTTCGTACCTTAATGGAGAATCAAAAGATATAAAAAGTTTTGAAGAATTCTATA
* * *
220503 CCCTTACGGAAAACCTTAAGAATATTAGAAATCTTGAAAAATTAAGATAATAATTTTTATTTAAT
65 CCCTTACGGATAACCATAAGAATATTAGAAATCTTAAAAAATTAAGATAATAA-TTTTATTTAA-
220568 TTTTAATCT-C
128 TTTTAATCTCC
* * * * ** *
220578 TAAAAATTTATTTCGTACCTTAATGGAAAACCAAAAAGTTACGAAAAGTTTT-AAAAACTTCTAT
1 TAAAAATTCATTTCGTACCTTAATGGAGAATC-AAAAGATATAAAAAGTTTTGAAGAA-TTCTAT
* *
220642 ACTCC-TACGGATAACCAT-AGTAATATTAGCAATCTTAAAAAATTAAGATAATTATTTTATTTA
64 AC-CCTTACGGATAACCATAAG-AATATTAGAAATCTTAAAAAATTAAGATAATAATTTTATTTA
220705 ATTTTAATCTCC
127 ATTTTAATCTCC
* *
220717 AAAAAATTCATTTCGTACCTTAATGGAGAATCGAAA-ATATACGAAAAGTTTTGAAGAATTCTAT
1 TAAAAATTCATTTCGTACCTTAATGGAGAATCAAAAGATATA--AAAAGTTTTGAAGAATTCTAT
* * *
220781 A-CCTTACGGATAACCATAGGAATAATAGAAATATATAAAAA
64 ACCCTTACGGATAACCATAAGAATATTAGAAATCT-TAAAAA
220822 TGGTTAATTT
Statistics
Matches: 205, Mismatches: 28, Indels: 23
0.80 0.11 0.09
Matches are distributed among these distances:
137 4 0.02
138 36 0.18
139 88 0.43
140 75 0.37
141 2 0.01
ACGTcount: A:0.44, C:0.12, G:0.10, T:0.34
Consensus pattern (138 bp):
TAAAAATTCATTTCGTACCTTAATGGAGAATCAAAAGATATAAAAAGTTTTGAAGAATTCTATAC
CCTTACGGATAACCATAAGAATATTAGAAATCTTAAAAAATTAAGATAATAATTTTATTTAATTT
TAATCTCC
Done.