Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006967.1 Hibiscus syriacus cultivar Beakdansim tig00017934_pilon, whole genome shotgun sequence
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: 107800
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:3742 original size:29 final size:27
Alignment explanation
Indices: 3683--3742 Score: 66
Period size: 27 Copynumber: 2.1 Consensus size: 27
3673 CTGTGTGTTT
* *
3683 GAGATTGATATCTCAGCTCATTAAAGG
1 GAGATTGAAATCTCAGCTCATTAAAGA
* *
3710 GAGATTGAAATCTTAGGACTCATTAGAGA
1 GAGATTGAAATCTCA-G-CTCATTAAAGA
3739 GAGA
1 GAGA
3743 GAGACCTAGA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
27 13 0.48
28 1 0.04
29 13 0.48
ACGTcount: A:0.37, C:0.12, G:0.25, T:0.27
Consensus pattern (27 bp):
GAGATTGAAATCTCAGCTCATTAAAGA
Found at i:6322 original size:30 final size:30
Alignment explanation
Indices: 6286--6345 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
6276 TGGACAAAGT
6286 CAGTGGAGGTTCAAGTTGACAAAGGAAAAA
1 CAGTGGAGGTTCAAGTTGACAAAGGAAAAA
*
6316 CAGTGGAGGTTCAAGTTGACGAAGGAAAAA
1 CAGTGGAGGTTCAAGTTGACAAAGGAAAAA
6346 TATTTTGTCA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.42, C:0.10, G:0.32, T:0.17
Consensus pattern (30 bp):
CAGTGGAGGTTCAAGTTGACAAAGGAAAAA
Found at i:13724 original size:31 final size:31
Alignment explanation
Indices: 13665--13737 Score: 83
Period size: 31 Copynumber: 2.4 Consensus size: 31
13655 TTGATCTGAA
* * **
13665 CCGAAACCAATTGATCCGATATTGATCCGAC
1 CCGAAACCAACTGATCCGAGATCAATCCGAC
* *
13696 TCGAAACCAACTGATTCGAGATCAATCCGAC
1 CCGAAACCAACTGATCCGAGATCAATCCGAC
*
13727 CCGAAATCAAC
1 CCGAAACCAAC
13738 CCGATTTTGA
Statistics
Matches: 34, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.36, C:0.30, G:0.15, T:0.19
Consensus pattern (31 bp):
CCGAAACCAACTGATCCGAGATCAATCCGAC
Found at i:31950 original size:36 final size:36
Alignment explanation
Indices: 31882--31989 Score: 166
Period size: 36 Copynumber: 3.0 Consensus size: 36
31872 CCAATTTAAT
*
31882 TTTCATAAAAAATTTGGGTATTTTTTCTTATT-AAAG
1 TTTCATAAGAAATTTGGGTA-TTTTTCTTATTAAAAG
*
31918 ATTTCATAAGAAATTTGAGTATTTTTCTTATTAAAAG
1 -TTTCATAAGAAATTTGGGTATTTTTCTTATTAAAAG
31955 TTTCATAAGAAATTTGGGTA-TTTTCTTATTAAAAG
1 TTTCATAAGAAATTTGGGTATTTTTCTTATTAAAAG
31990 GATTTTGAGG
Statistics
Matches: 67, Mismatches: 3, Indels: 4
0.91 0.04 0.05
Matches are distributed among these distances:
35 15 0.22
36 30 0.45
37 22 0.33
ACGTcount: A:0.35, C:0.06, G:0.12, T:0.47
Consensus pattern (36 bp):
TTTCATAAGAAATTTGGGTATTTTTCTTATTAAAAG
Found at i:32486 original size:65 final size:63
Alignment explanation
Indices: 32383--32543 Score: 180
Period size: 65 Copynumber: 2.5 Consensus size: 63
32373 AATTAAATTG
* * * *
32383 AACATCGAATGCATTTCATGCATCGATGCACTTACCATGAACCAATGCACTGAGAATTTTATGAA
1 AACATCGAATGCATTTGATGCATCGATGCACTCACCATGAACCAATGCACTCAGAATATT-TG-A
* * * * **
32448 AACATCGAATGCATTTGATGCATCGATGCAC-CAGCCATGCATCGATGCACTCTGGCTATTTGA
1 AACATCGAATGCATTTGATGCATCGATGCACTCA-CCATGAACCAATGCACTCAGAATATTTGA
* *
32511 AACATCGAATGCACTTGATGCATCGTTGCACTC
1 AACATCGAATGCATTTGATGCATCGATGCACTC
32544 TTAGTGCACC
Statistics
Matches: 82, Mismatches: 12, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
63 30 0.37
64 4 0.05
65 48 0.59
ACGTcount: A:0.30, C:0.24, G:0.18, T:0.27
Consensus pattern (63 bp):
AACATCGAATGCATTTGATGCATCGATGCACTCACCATGAACCAATGCACTCAGAATATTTGA
Found at i:38076 original size:20 final size:20
Alignment explanation
Indices: 38040--38077 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
38030 ATCCTATTCC
**
38040 CTGGTAATCTTTTATTCCCA
1 CTGGTAATCTTACATTCCCA
38060 CTGGTAATCTTACATTCC
1 CTGGTAATCTTACATTCC
38078 GTGAACCAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.21, C:0.26, G:0.11, T:0.42
Consensus pattern (20 bp):
CTGGTAATCTTACATTCCCA
Found at i:38930 original size:24 final size:24
Alignment explanation
Indices: 38898--38977 Score: 73
Period size: 24 Copynumber: 3.5 Consensus size: 24
38888 CACTTAACAT
38898 TGCATCGATGCATCCCTTTGAATG
1 TGCATCGATGCATCCCTTTGAATG
* *
38922 TGCATCGATTCAT-CGTGTTG-A--
1 TGCATCGATGCATCCCT-TTGAATG
*
38943 TGCATCGATG-AACGCC-TTGAATG
1 TGCATCGATGCATC-CCTTTGAATG
38966 TGCATCGATGCA
1 TGCATCGATGCA
38978 CGAGGTCATG
Statistics
Matches: 44, Mismatches: 5, Indels: 14
0.70 0.08 0.22
Matches are distributed among these distances:
20 4 0.09
21 10 0.23
22 1 0.02
23 13 0.30
24 16 0.36
ACGTcount: A:0.23, C:0.23, G:0.24, T:0.31
Consensus pattern (24 bp):
TGCATCGATGCATCCCTTTGAATG
Found at i:38963 original size:44 final size:43
Alignment explanation
Indices: 38898--38997 Score: 121
Period size: 44 Copynumber: 2.3 Consensus size: 43
38888 CACTTAACAT
* * * * *
38898 TGCATCGATGCATCCCTTTGAATGTGCATCGATTCATCGTGTTGA
1 TGCATCGATG-AACCCTTTGAATGTGCATCGATGCA-CGAGGTCA
38943 TGCATCGATGAACGCC-TTGAATGTGCATCGATGCACGAGGTCA
1 TGCATCGATGAAC-CCTTTGAATGTGCATCGATGCACGAGGTCA
38986 TGCATCGATGAA
1 TGCATCGATGAA
38998 TCCATCGGGG
Statistics
Matches: 49, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
43 17 0.35
44 20 0.41
45 12 0.24
ACGTcount: A:0.24, C:0.22, G:0.25, T:0.29
Consensus pattern (43 bp):
TGCATCGATGAACCCTTTGAATGTGCATCGATGCACGAGGTCA
Found at i:40591 original size:65 final size:65
Alignment explanation
Indices: 40472--40683 Score: 202
Period size: 65 Copynumber: 3.3 Consensus size: 65
40462 TTTTTCAGAG
* * * * * **
40472 TGATGCACCGATGCAC-CAATCCATGCATCGATGCACCATGAATTAAATTG-AACATCGAATGCA
1 TGATGCATCGATGCACTC-AGCCATGCACCGATGCACTATGGA-TATTTTGAAACATCGAATGCA
40535 TT
64 TT
* *
40537 TCATGCATCGATGCACTTA-CCATGCACCGATGCACTGA-GGAT-TTTATGAAAACATCGAATGC
1 TGATGCATCGATGCACTCAGCCATGCACCGATGCACT-ATGGATATTT-TG-AAACATCGAATGC
40599 ATT
63 ATT
* * * * * *
40602 TGATGTATCGATACAC-CAGCCATGCATCGATGCACTATGGCTATTTTGAAACATCGAATGTACT
1 TGATGCATCGATGCACTCAGCCATGCACCGATGCACTATGGATATTTTGAAACATCGAATGCATT
40666 TGATGCATCGATGCACTC
1 TGATGCATCGATGCACTC
40684 TTAGTGCACC
Statistics
Matches: 120, Mismatches: 18, Indels: 18
0.77 0.12 0.12
Matches are distributed among these distances:
62 1 0.01
63 3 0.03
64 47 0.39
65 66 0.55
66 3 0.03
ACGTcount: A:0.31, C:0.24, G:0.18, T:0.27
Consensus pattern (65 bp):
TGATGCATCGATGCACTCAGCCATGCACCGATGCACTATGGATATTTTGAAACATCGAATGCATT
Found at i:42558 original size:14 final size:15
Alignment explanation
Indices: 42530--42558 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
42520 ATCTATGAAT
42530 CATATTTTAGTTATG
1 CATATTTTAGTTATG
42545 CATATTTT-GTTATG
1 CATATTTTAGTTATG
42559 ATTATAGATG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.24, C:0.07, G:0.14, T:0.55
Consensus pattern (15 bp):
CATATTTTAGTTATG
Found at i:44445 original size:24 final size:25
Alignment explanation
Indices: 44418--44475 Score: 82
Period size: 24 Copynumber: 2.4 Consensus size: 25
44408 TTTAACAATC
* * *
44418 ATATAATAATTCTATTTTTTTTAA-
1 ATATAATAATTATAATTTTTGTAAG
44442 ATATAATAATTATAATTTTTGTAAG
1 ATATAATAATTATAATTTTTGTAAG
44467 ATATAATAA
1 ATATAATAA
44476 CAAGAAAATA
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
24 21 0.70
25 9 0.30
ACGTcount: A:0.45, C:0.02, G:0.03, T:0.50
Consensus pattern (25 bp):
ATATAATAATTATAATTTTTGTAAG
Found at i:50609 original size:20 final size:20
Alignment explanation
Indices: 50544--50773 Score: 246
Period size: 20 Copynumber: 11.5 Consensus size: 20
50534 CGATTTTCCA
** *
50544 AAATCGCAACGCGAATATGA
1 AAATCGCAACGCGAATCCGT
*
50564 AAATCGCAACGCGAA-CACAT
1 AAATCGCAACGCGAATC-CGT
* *
50584 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGAATCCGT
* *
50604 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGAATCCGT
* *
50624 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGAATCCGT
* *
50644 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGAATCCGT
**
50664 AAATCGCAACGATAATCCGT
1 AAATCGCAACGCGAATCCGT
* *
50684 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGCGAATCCGT
**
50704 AAATCGCAACGATAATCCGT
1 AAATCGCAACGCGAATCCGT
*
50724 AAATCGCAACGAGAATCCGT
1 AAATCGCAACGCGAATCCGT
* *
50744 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGCGAATCCGT
*
50764 AAATCACAAC
1 AAATCGCAAC
50774 ACTGAAATTT
Statistics
Matches: 184, Mismatches: 24, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
20 183 0.99
21 1 0.01
ACGTcount: A:0.37, C:0.25, G:0.18, T:0.20
Consensus pattern (20 bp):
AAATCGCAACGCGAATCCGT
Found at i:51471 original size:24 final size:24
Alignment explanation
Indices: 51435--51489 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 24
51425 GTGAGTACTA
* * * *
51435 GTCAGTATTCGAAATTTGGTCTTG
1 GTCAATATCCGAAATTTGATATTG
*
51459 GTCAATATCCGAACTTTGATATTG
1 GTCAATATCCGAAATTTGATATTG
51483 GTCAATA
1 GTCAATA
51490 CACGGATTTT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.27, C:0.15, G:0.20, T:0.38
Consensus pattern (24 bp):
GTCAATATCCGAAATTTGATATTG
Found at i:51694 original size:12 final size:12
Alignment explanation
Indices: 51677--51701 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
51667 ATATAATCCT
51677 GAAGAAGAAAAA
1 GAAGAAGAAAAA
51689 GAAGAAGAAAAA
1 GAAGAAGAAAAA
51701 G
1 G
51702 TCCCCGAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:53987 original size:19 final size:19
Alignment explanation
Indices: 53947--54097 Score: 196
Period size: 19 Copynumber: 8.4 Consensus size: 19
53937 GATTCTCTCG
53947 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
53967 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
53986 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
54000 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
54020 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
54039 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
54053 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
54072 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
54091 TTGCGAT
1 TTGCGAT
54098 AGTCAATTTG
Statistics
Matches: 116, Mismatches: 4, Indels: 23
0.81 0.03 0.16
Matches are distributed among these distances:
14 12 0.10
16 14 0.12
17 12 0.10
18 2 0.02
19 46 0.40
20 30 0.26
ACGTcount: A:0.14, C:0.23, G:0.17, T:0.46
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:53995 original size:53 final size:53
Alignment explanation
Indices: 53928--54097 Score: 333
Period size: 53 Copynumber: 3.2 Consensus size: 53
53918 GAAATGAAAA
53928 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATT
1 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATT
53981 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATT
1 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATT
54034 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTT-CGCATTGCGATTTTCATT
1 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATT
54086 TCGCATTGCGAT
1 TCGCATTGCGAT
54098 AGTCAATTTG
Statistics
Matches: 117, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
52 30 0.26
53 87 0.74
ACGTcount: A:0.14, C:0.24, G:0.18, T:0.45
Consensus pattern (53 bp):
TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATT
Found at i:54062 original size:33 final size:34
Alignment explanation
Indices: 53928--54079 Score: 145
Period size: 33 Copynumber: 4.4 Consensus size: 34
53918 GAAATGAAAA
53928 TCGCATTGCGATTCTCTCG-TTGCGATTTTCATT
1 TCGCATTGCGATTCTCTCGATTGCGATTTTCATT
* *
53961 TCCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTT
1 T-CGCATTGCGA--TTC-TCTCG-ATTGCGATT-T-TCATT
* *
54002 GCG-ATTTTC-ATT-TC-CGCATTGCGATTTTCATT
1 TCGCA-TTGCGATTCTCTCG-ATTGCGATTTTCATT
54034 TCGCATTGCGATTCTCTCG-TTGCGATTTTCATT
1 TCGCATTGCGATTCTCTCGATTGCGATTTTCATT
54067 TCGCATTGCGATT
1 TCGCATTGCGATT
54080 TTCATTTCGC
Statistics
Matches: 98, Mismatches: 8, Indels: 26
0.74 0.06 0.20
Matches are distributed among these distances:
32 9 0.09
33 33 0.34
34 24 0.24
35 3 0.03
36 3 0.03
37 6 0.06
39 10 0.10
40 6 0.06
41 4 0.04
ACGTcount: A:0.13, C:0.24, G:0.18, T:0.45
Consensus pattern (34 bp):
TCGCATTGCGATTCTCTCGATTGCGATTTTCATT
Found at i:54207 original size:33 final size:33
Alignment explanation
Indices: 54155--54317 Score: 161
Period size: 33 Copynumber: 4.7 Consensus size: 33
54145 CCATTACATT
54155 TCGCAATGCGGAAATGAAAATCGCAACGAGAGAA
1 TCGCAATGC-GAAATGAAAATCGCAACGAGAGAA
* *
54189 TCGCAATGCGAAATGAAAATCGCAATGCGA-AA
1 TCGCAATGCGAAATGAAAATCGCAACGAGAGAA
* * * *
54221 T-GAAAAT-CGCAACGAGAGAATCGCAATGCGAAATGAAAA
1 TCG-CAATGCGAAATGA-A-AATCGCAA--CG--A-GAGAA
54260 TCGCAATGCGGAAATGAAAATCGCAACGAGAGAA
1 TCGCAATGC-GAAATGAAAATCGCAACGAGAGAA
54294 TCGCAATGCGAAATGAAAATCGCA
1 TCGCAATGCGAAATGAAAATCGCA
54318 TTGCGATTCT
Statistics
Matches: 106, Mismatches: 11, Indels: 25
0.75 0.08 0.18
Matches are distributed among these distances:
31 7 0.07
32 7 0.07
33 42 0.40
34 22 0.21
35 2 0.02
37 2 0.02
38 2 0.02
39 14 0.13
40 3 0.03
41 5 0.05
ACGTcount: A:0.45, C:0.18, G:0.24, T:0.13
Consensus pattern (33 bp):
TCGCAATGCGAAATGAAAATCGCAACGAGAGAA
Found at i:54297 original size:53 final size:53
Alignment explanation
Indices: 54155--54322 Score: 320
Period size: 53 Copynumber: 3.2 Consensus size: 53
54145 CCATTACATT
54155 TCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAA
1 TCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAA
54208 TCGCAATGC-GAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAA
1 TCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAA
54260 TCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAA
1 TCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAA
*
54313 TCGCATTGCG
1 TCGCAATGCG
54323 ATTCTCCCAT
Statistics
Matches: 113, Mismatches: 1, Indels: 2
0.97 0.01 0.02
Matches are distributed among these distances:
52 52 0.46
53 61 0.54
ACGTcount: A:0.43, C:0.18, G:0.24, T:0.14
Consensus pattern (53 bp):
TCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAA
Found at i:54357 original size:53 final size:52
Alignment explanation
Indices: 54294--54409 Score: 142
Period size: 53 Copynumber: 2.2 Consensus size: 52
54284 AACGAGAGAA
*
54294 TCGCAATGCGAAATGAAAATCGCATTGCGATTCTCCCATTGCGATTTTCATT
1 TCGCATTGCGAAATGAAAATCGCATTGCGATTCTCCCATTGCGATTTTCATT
** ** ** * *
54346 TCCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
1 T-CGCATTGCGAAATGAAAATCGCATTGCGATTCTCCCATTGCGATTTTCATT
54399 TCGCATTGCGA
1 TCGCATTGCGA
54410 TTTTCATTTC
Statistics
Matches: 54, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
52 11 0.20
53 43 0.80
ACGTcount: A:0.20, C:0.24, G:0.18, T:0.38
Consensus pattern (52 bp):
TCGCATTGCGAAATGAAAATCGCATTGCGATTCTCCCATTGCGATTTTCATT
Found at i:54372 original size:19 final size:19
Alignment explanation
Indices: 54330--54429 Score: 147
Period size: 19 Copynumber: 5.5 Consensus size: 19
54320 GCGATTCTCC
54330 CATTGCGATTTTCATTTCCG
1 CATTGCGATTTTCATTT-CG
54350 CATTGCGATTTTCATTTCG
1 CATTGCGATTTTCATTTCG
*
54369 CATTGCGA--TTC-TCTCG
1 CATTGCGATTTTCATTTCG
54385 --TTGCGATTTTCATTTCG
1 CATTGCGATTTTCATTTCG
54402 CATTGCGATTTTCATTTCG
1 CATTGCGATTTTCATTTCG
54421 CATTGCGAT
1 CATTGCGAT
54430 AGTCAATTTT
Statistics
Matches: 73, Mismatches: 2, Indels: 11
0.85 0.02 0.13
Matches are distributed among these distances:
14 6 0.08
16 7 0.10
17 7 0.10
19 36 0.49
20 17 0.23
ACGTcount: A:0.15, C:0.23, G:0.17, T:0.45
Consensus pattern (19 bp):
CATTGCGATTTTCATTTCG
Found at i:54426 original size:52 final size:53
Alignment explanation
Indices: 54313--54429 Score: 209
Period size: 53 Copynumber: 2.2 Consensus size: 53
54303 GAAATGAAAA
54313 TCGCATTGCGATTCTCCCATTGCGATTTTCATTTCCGCATTGCGATTTTCATT
1 TCGCATTGCGATTCTCCCATTGCGATTTTCATTTCCGCATTGCGATTTTCATT
* *
54366 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTT-CGCATTGCGATTTTCATT
1 TCGCATTGCGATTCTCCCATTGCGATTTTCATTTCCGCATTGCGATTTTCATT
54418 TCGCATTGCGAT
1 TCGCATTGCGAT
54430 AGTCAATTTT
Statistics
Matches: 62, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
52 30 0.48
53 32 0.52
ACGTcount: A:0.15, C:0.25, G:0.17, T:0.44
Consensus pattern (53 bp):
TCGCATTGCGATTCTCCCATTGCGATTTTCATTTCCGCATTGCGATTTTCATT
Found at i:56557 original size:14 final size:14
Alignment explanation
Indices: 56538--56594 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
56528 GCGAAATGAA
*
56538 AATCGCAACGACAG
1 AATCGCAACGAAAG
56552 AATCGCAATGCGAAATG
1 AATCGCAA--CGAAA-G
56569 AAAATCGCAACGAAAG
1 --AATCGCAACGAAAG
56585 AATCGCAACG
1 AATCGCAACG
56595 CGAAATGAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 18 0.49
16 5 0.14
17 6 0.16
19 8 0.22
ACGTcount: A:0.46, C:0.23, G:0.21, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAAAG
Found at i:56565 original size:33 final size:33
Alignment explanation
Indices: 56519--56611 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
56509 GCGAAACCAA
*
56519 AATCGCAACGCGAAATGAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
*
56552 AATCGCAATGCGAAATGAAAATCGCAACGAAAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
56585 AATCGCAACGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
56612 TGCGATTTTG
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.47, C:0.22, G:0.20, T:0.11
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAAAG
Found at i:56576 original size:19 final size:19
Alignment explanation
Indices: 56482--56616 Score: 128
Period size: 19 Copynumber: 7.6 Consensus size: 19
56472 TAGTTTACTT
* *
56482 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
**
56502 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
56521 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
56540 TCGCAA--CGACA-G--AA
1 TCGCAACGCGAAATGAAAA
*
56554 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
56573 TCGCAA--CGAAA-G--AA
1 TCGCAACGCGAAATGAAAA
56587 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
56606 TCGCAATGCGA
1 TCGCAACGCGA
56617 TTTTGGTTTC
Statistics
Matches: 97, Mismatches: 8, Indels: 21
0.77 0.06 0.17
Matches are distributed among these distances:
14 16 0.16
16 11 0.11
17 11 0.11
19 47 0.48
20 12 0.12
ACGTcount: A:0.46, C:0.24, G:0.19, T:0.11
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:56634 original size:19 final size:19
Alignment explanation
Indices: 56612--56740 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
56602 AAAATCGCAA
56612 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
56631 TGCGATCTT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
56645 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
56664 TGCGATTCT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
**
56678 TGCGATTTTCATTTCGCGT
1 TGCGATTTTGGTTTCGCGT
56697 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
* *
56716 TGCGATTTTAAGTTTCGTGT
1 TGCGATTTT-GGTTTCGCGT
56736 TGCGA
1 TGCGA
56741 AGTAAACTAT
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 22 0.24
15 1 0.01
16 2 0.02
17 2 0.02
18 2 0.02
19 48 0.53
20 13 0.14
ACGTcount: A:0.09, C:0.17, G:0.29, T:0.46
Consensus pattern (19 bp):
TGCGATTTTGGTTTCGCGT
Found at i:56654 original size:33 final size:33
Alignment explanation
Indices: 56612--56703 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 33
56602 AAAATCGCAA
56612 TGCGATTTTGGTTTCGCGTTGCGA-TCTTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTC-TGTCGT
56645 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
**
56678 TGCGATTTTCATTTCGCGTTGCGATT
1 TGCGATTTTGGTTTCGCGTTGCGATT
56704 TTGGTTTCGC
Statistics
Matches: 56, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
33 54 0.96
34 2 0.04
ACGTcount: A:0.08, C:0.18, G:0.28, T:0.46
Consensus pattern (33 bp):
TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
Found at i:56903 original size:93 final size:93
Alignment explanation
Indices: 56783--57255 Score: 894
Period size: 93 Copynumber: 5.1 Consensus size: 93
56773 TTGAATGGAT
56783 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
*
56848 AGTTTAGCAGAATTGGCAGCAACGGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
*
56876 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTATAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
56941 AG-TTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
* *
56968 AAATTTACTTTCAACCAAAAGAAAAAACAAAGACAAATACTATTTCACAGTGTTATAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
57033 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
57061 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
57126 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
57154 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
*
57219 AGTTTAGCAGAATTGGCAGCAACCGAAT
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
57247 AAATTTACT
1 AAATTTACT
57256 AAGCAATCTA
Statistics
Matches: 373, Mismatches: 6, Indels: 2
0.98 0.02 0.01
Matches are distributed among these distances:
92 90 0.24
93 283 0.76
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (93 bp):
AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
AGTTTAGCAGAATTGGCAGCAACCGAAC
Found at i:57095 original size:185 final size:186
Alignment explanation
Indices: 56783--57255 Score: 894
Period size: 185 Copynumber: 2.5 Consensus size: 186
56773 TTGAATGGAT
56783 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
*
56848 AGTTTAGCAGAATTGGCAGCAACGGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
66 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
*
56913 TACTATTTCACAGTGTTATAGAATACACAG-TTAGCAGAATTGGCAGCAACCGAAC
131 TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
* *
56968 AAATTTACTTTCAACCAAAAGAAAAAACAAAGACAAATACTATTTCACAGTGTTATAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
57033 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
66 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
57098 TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
131 TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
57154 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
*
57219 AGTTTAGCAGAATTGGCAGCAACCGAATAAATTTACT
66 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACT
57256 AAGCAATCTA
Statistics
Matches: 280, Mismatches: 7, Indels: 1
0.97 0.02 0.00
Matches are distributed among these distances:
185 156 0.56
186 124 0.44
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (186 bp):
AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
Found at i:58979 original size:14 final size:14
Alignment explanation
Indices: 58960--59049 Score: 81
Period size: 14 Copynumber: 5.7 Consensus size: 14
58950 TTGAAATGAA
58960 AATCGCAACGAGAG
1 AATCGCAACGAGAG
58974 AATCGCAACGCAAGATG
1 AATCGCAACG--AGA-G
58991 ACAATCGCAACGAGAG
1 --AATCGCAACGAGAG
*
59007 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
59026 AATCGCAACGAGAG
1 AATCGCAACGAGAG
59040 AATCGCAACG
1 AATCGCAACG
59050 CGAAATGAAA
Statistics
Matches: 64, Mismatches: 2, Indels: 20
0.74 0.02 0.23
Matches are distributed among these distances:
14 30 0.47
15 1 0.02
16 6 0.09
17 6 0.09
18 1 0.02
19 20 0.31
ACGTcount: A:0.43, C:0.23, G:0.24, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:58996 original size:19 final size:18
Alignment explanation
Indices: 58959--59065 Score: 80
Period size: 14 Copynumber: 6.5 Consensus size: 18
58949 GTTGAAATGA
58959 AAATCGCAACG--AGA-G
1 AAATCGCAACGCAAGATG
58974 -AATCGCAACGCAAGATG
1 AAATCGCAACGCAAGATG
58991 ACAATCGCAACG--AGA-G
1 A-AATCGCAACGCAAGATG
59007 -AATCGCAACGCGAA-ATG
1 AAATCGCAACGC-AAGATG
59024 AAAATCGCAACG--AGA-G
1 -AAATCGCAACGCAAGATG
59040 -AATCGCAACGCGAA-ATG
1 AAATCGCAACGC-AAGATG
59057 AAATCGCAA
1 AAATCGCAA
59066 TGCGATTTTG
Statistics
Matches: 75, Mismatches: 0, Indels: 31
0.71 0.00 0.29
Matches are distributed among these distances:
14 30 0.40
16 8 0.11
17 9 0.12
18 8 0.11
19 20 0.27
ACGTcount: A:0.45, C:0.22, G:0.23, T:0.09
Consensus pattern (18 bp):
AAATCGCAACGCAAGATG
Found at i:58997 original size:33 final size:33
Alignment explanation
Indices: 58952--59065 Score: 196
Period size: 33 Copynumber: 3.5 Consensus size: 33
58942 TCTTTTGGTT
58952 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
*
58985 -AAGATGACAATCGCAACGAGAGAATCGCAACGC
1 GAA-ATGAAAATCGCAACGAGAGAATCGCAACGC
59018 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
59051 GAAATG-AAATCGCAA
1 GAAATGAAAATCGCAA
59066 TGCGATTTTG
Statistics
Matches: 77, Mismatches: 2, Indels: 5
0.92 0.02 0.06
Matches are distributed among these distances:
32 11 0.14
33 64 0.83
34 2 0.03
ACGTcount: A:0.46, C:0.21, G:0.24, T:0.10
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:59101 original size:14 final size:14
Alignment explanation
Indices: 59082--59138 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
59072 TTTGGTTTCG
59082 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
59096 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
59115 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
59129 CGTTGCGATT
1 CGTTGCGATT
59139 TTCATTTCTC
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
16 3 0.08
17 3 0.08
19 10 0.28
ACGTcount: A:0.09, C:0.25, G:0.23, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:59114 original size:33 final size:33
Alignment explanation
Indices: 59066--59146 Score: 144
Period size: 33 Copynumber: 2.5 Consensus size: 33
59056 GAAATCGCAA
**
59066 TGCGATTTTGGTTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
59099 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
59132 TGCGATTTTCATTTC
1 TGCGATTTTCATTTC
59147 TCTCGTTGCG
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 46 1.00
ACGTcount: A:0.09, C:0.22, G:0.22, T:0.47
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
Found at i:59149 original size:21 final size:21
Alignment explanation
Indices: 59123--59198 Score: 109
Period size: 21 Copynumber: 3.7 Consensus size: 21
59113 CGCGTTGCGA
59123 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
***
59144 TTCTCTCGTTGCGACAGTCA-
1 TTCTCTCGTTGCGATTTTCAT
59164 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
*
59185 TTATCTCGTTGCGA
1 TTCTCTCGTTGCGA
59199 CTCTTCTGCA
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
20 17 0.36
21 30 0.64
ACGTcount: A:0.12, C:0.25, G:0.17, T:0.46
Consensus pattern (21 bp):
TTCTCTCGTTGCGATTTTCAT
Found at i:59179 original size:41 final size:41
Alignment explanation
Indices: 59122--59199 Score: 147
Period size: 41 Copynumber: 1.9 Consensus size: 41
59112 TCGCGTTGCG
*
59122 ATTCTCTCGTTGCGATTTTCATTTCTCTCGTTGCGACAGTC
1 ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGACAGTC
59163 ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGAC
1 ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGAC
59200 TCTTCTGCAA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
41 36 1.00
ACGTcount: A:0.13, C:0.26, G:0.17, T:0.45
Consensus pattern (41 bp):
ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGACAGTC
Found at i:59325 original size:33 final size:33
Alignment explanation
Indices: 59278--59348 Score: 106
Period size: 33 Copynumber: 2.2 Consensus size: 33
59268 AATACTAAAT
* *
59278 TGAAAATCGGAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
* *
59311 TGAAAATCGCAACGACAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
59344 TGAAA
1 TGAAA
59349 TCTAAGTGAA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.48, C:0.17, G:0.24, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGACAGAATAGCAACGCGAAA
Found at i:59580 original size:22 final size:22
Alignment explanation
Indices: 59528--59582 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
59518 TGGTTGTGAG
**
59528 GGATTTCGCCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
**
59550 GGAAATCTTCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
59572 GGATTTCTTCG
1 GGATTTCTTCG
59583 CCGTAGAGAG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.20, C:0.16, G:0.40, T:0.24
Consensus pattern (22 bp):
GGATTTCTTCGGAGATGGGGAC
Found at i:59753 original size:20 final size:20
Alignment explanation
Indices: 59728--59921 Score: 212
Period size: 20 Copynumber: 9.7 Consensus size: 20
59718 CTTTAAATAT
59728 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
59748 CGCGTTGCGATTTTATGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
*
59770 -TCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
59789 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
* **
59809 CGCATTGCGATTTACCCATA
1 CGCGTTGCGATTTACGGATA
59829 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
59849 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* * *
59869 CGCGTTGCAATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
59889 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
59909 CGCGTTGCGATTT
1 CGCGTTGCGATTT
59922 TGGAAAATCG
Statistics
Matches: 145, Mismatches: 24, Indels: 10
0.81 0.13 0.06
Matches are distributed among these distances:
19 2 0.01
20 126 0.87
21 15 0.10
22 2 0.01
ACGTcount: A:0.20, C:0.20, G:0.25, T:0.36
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:59915 original size:60 final size:60
Alignment explanation
Indices: 59728--59921 Score: 235
Period size: 60 Copynumber: 3.2 Consensus size: 60
59718 CTTTAAATAT
* **
59728 CGCGTTGCGATTTACGGATACGCGTTGCGATTTTATGTATTATCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGC-AATTTATGTATTCGCGTTGCGATTTACGGATA
* * * *** *
59789 CGCGTTGCGATATACGGATACGCATTGCGATTTACCCATACGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCAATTTATGTATTCGCGTTGCGATTTACGGATA
* * * ** *
59849 CACGTTGCGATTTACGGATACGCGTTGCAATTTATGTGTTCGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATACGCGTTGCAATTTATGTATTCGCGTTGCGATTTACGGATA
59909 CGCGTTGCGATTT
1 CGCGTTGCGATTT
59922 TGGAAAATCG
Statistics
Matches: 109, Mismatches: 24, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
60 83 0.76
61 26 0.24
ACGTcount: A:0.20, C:0.20, G:0.25, T:0.36
Consensus pattern (60 bp):
CGCGTTGCGATTTACGGATACGCGTTGCAATTTATGTATTCGCGTTGCGATTTACGGATA
Found at i:59938 original size:21 final size:21
Alignment explanation
Indices: 59908--59990 Score: 78
Period size: 21 Copynumber: 4.0 Consensus size: 21
59898 ATTTTCATAT
*
59908 TCGCGTTGCGATTTTGGAAAA
1 TCGCATTGCGATTTTGGAAAA
* * * **
59929 TCGCAATGCGAATTTGTACTA
1 TCGCATTGCGATTTTGGAAAA
*
59950 TCGCATTGCGATTTT-CAAGAA
1 TCGCATTGCGATTTTGGAA-AA
*
59971 TCGCGTTGCGATTTTGGAAA
1 TCGCATTGCGATTTTGGAAA
59991 CTGATTTGCG
Statistics
Matches: 47, Mismatches: 13, Indels: 4
0.73 0.20 0.06
Matches are distributed among these distances:
20 1 0.02
21 44 0.94
22 2 0.04
ACGTcount: A:0.25, C:0.17, G:0.24, T:0.34
Consensus pattern (21 bp):
TCGCATTGCGATTTTGGAAAA
Found at i:59981 original size:42 final size:43
Alignment explanation
Indices: 59888--59986 Score: 100
Period size: 42 Copynumber: 2.4 Consensus size: 43
59878 ATTTATGTGT
* *
59888 TCGCGTTGCG-ATTT-TCATATTCGCGTTGCGATTTTGGAAAA
1 TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
**
59929 TCGCAATGCGAATTTGT-ACTA-TCGCATTGCGATTTT-CAAGAA
1 TCGCGTTGCGAATTTGTCA-TATTCGCATTGCGATTTTGCAA-AA
*
59971 TCGCGTTGCGATTTTG
1 TCGCGTTGCGAATTTG
59987 GAAACTGATT
Statistics
Matches: 47, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
41 10 0.21
42 34 0.72
43 3 0.06
ACGTcount: A:0.21, C:0.18, G:0.23, T:0.37
Consensus pattern (43 bp):
TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
Found at i:60907 original size:46 final size:45
Alignment explanation
Indices: 60846--60940 Score: 154
Period size: 46 Copynumber: 2.1 Consensus size: 45
60836 CTTTTTATTT
* *
60846 AATTAAGATGTGATCACTTTTATTTAGTTTCCTCACTAACGTCAA
1 AATTAAGATGCGATCACTTTTATTTAGTTTCCTCACTAACATCAA
*
60891 AATTCAAGATGCGATCACTTTTATTTAGTTTCCTCGCTAACATCAA
1 AATT-AAGATGCGATCACTTTTATTTAGTTTCCTCACTAACATCAA
60937 AATT
1 AATT
60941 TAAGTGAATA
Statistics
Matches: 46, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
45 4 0.09
46 42 0.91
ACGTcount: A:0.32, C:0.19, G:0.11, T:0.39
Consensus pattern (45 bp):
AATTAAGATGCGATCACTTTTATTTAGTTTCCTCACTAACATCAA
Found at i:62213 original size:21 final size:21
Alignment explanation
Indices: 62189--62232 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
62179 GCCGCCACTT
*
62189 CCTCCACCTCCTCCACCCCCG
1 CCTCCACCACCTCCACCCCCG
*
62210 CCTCCACCACCTCCACCGCCG
1 CCTCCACCACCTCCACCCCCG
62231 CC
1 CC
62233 GCAACCATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.11, C:0.70, G:0.07, T:0.11
Consensus pattern (21 bp):
CCTCCACCACCTCCACCCCCG
Found at i:62239 original size:21 final size:21
Alignment explanation
Indices: 62198--62239 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
62188 TCCTCCACCT
* *
62198 CCTCCACCCCCGCCTCCACCA
1 CCTCCACCCCCGCCGCAACCA
*
62219 CCTCCACCGCCGCCGCAACCA
1 CCTCCACCCCCGCCGCAACCA
62240 TATCGCTATC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.17, C:0.67, G:0.10, T:0.07
Consensus pattern (21 bp):
CCTCCACCCCCGCCGCAACCA
Found at i:63418 original size:21 final size:21
Alignment explanation
Indices: 63392--63434 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
63382 ATCGGAAATA
*
63392 TTAAAA-AATTAATGTTTTAAG
1 TTAAAATAA-TAATATTTTAAG
63413 TTAAAATAATAATATTTTAAG
1 TTAAAATAATAATATTTTAAG
63434 T
1 T
63435 AATTATTTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 18 0.90
22 2 0.10
ACGTcount: A:0.49, C:0.00, G:0.07, T:0.44
Consensus pattern (21 bp):
TTAAAATAATAATATTTTAAG
Found at i:69615 original size:16 final size:16
Alignment explanation
Indices: 69592--69629 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
69582 TTTGATTTTC
69592 ATTTATA-TATTAATT
1 ATTTATATTATTAATT
*
69607 ATGTTATATTATTATTT
1 AT-TTATATTATTAATT
69624 ATTTAT
1 ATTTAT
69630 CGATAGTATT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
15 2 0.10
16 9 0.45
17 9 0.45
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.63
Consensus pattern (16 bp):
ATTTATATTATTAATT
Found at i:85881 original size:20 final size:20
Alignment explanation
Indices: 85834--86123 Score: 254
Period size: 20 Copynumber: 14.2 Consensus size: 20
85824 AATGACCAAC
85834 AAAATCGCAACGCGATATC--
1 AAAATCGCAACGCGAT-TCAG
* *
85853 AAAACCGCAACGCGATTTAG
1 AAAATCGCAACGCGATTCAG
* * **
85873 AAAAGCGCAACGTTGA-AAAG
1 AAAATCGCAACG-CGATTCAG
* *
85893 AAGATCGCAACACGATCTTCCA-
1 AAAATCGCAACGCGA--TT-CAG
* * *
85915 AGAATCGCAATGCGATTCAT
1 AAAATCGCAACGCGATTCAG
85935 AAAATCGCAACGCGATCTTCCA-
1 AAAATCGCAACGCGA--TT-CAG
*
85957 AGAATCGCAACGCGATTCAG
1 AAAATCGCAACGCGATTCAG
85977 AAAATCGCAACGCGATTCAG
1 AAAATCGCAACGCGATTCAG
85997 AAAATCGCAACGCGATCTTCCA-
1 AAAATCGCAACGCGA--TT-CAG
* *
86019 AGAATCGCAACGCGATTAAG
1 AAAATCGCAACGCGATTCAG
86039 AAAATCGCAACGCGATTCCA-
1 AAAATCGCAACGCGATT-CAG
*
86059 AGAATCGCAACGCGATTCAG
1 AAAATCGCAACGCGATTCAG
86079 AAAATCGCAACGCGATTCCA-
1 AAAATCGCAACGCGATT-CAG
* *
86099 AGAATCGCAACGCGATTAAG
1 AAAATCGCAACGCGATTCAG
86119 AAAAT
1 AAAAT
86124 GAGTAAATTC
Statistics
Matches: 222, Mismatches: 29, Indels: 39
0.77 0.10 0.13
Matches are distributed among these distances:
18 1 0.00
19 25 0.11
20 143 0.64
21 5 0.02
22 43 0.19
23 5 0.02
ACGTcount: A:0.40, C:0.25, G:0.19, T:0.16
Consensus pattern (20 bp):
AAAATCGCAACGCGATTCAG
Found at i:85983 original size:62 final size:61
Alignment explanation
Indices: 85917--86115 Score: 280
Period size: 62 Copynumber: 3.2 Consensus size: 61
85907 ATCTTCCAAG
*
85917 AATCGCAATGCGATTCATAAAATCGCAACGCGATCTTCCAAGAATCGCAACGCGATTCAGAA
1 AATCGCAACGCGATTCA-AAAATCGCAACGCGATCTTCCAAGAATCGCAACGCGATTCAGAA
*
85979 AATCGCAACGCGATTCAGAAAATCGCAACGCGATCTTCCAAGAATCGCAACGCGATTAAGAA
1 AATCGCAACGCGATTCA-AAAATCGCAACGCGATCTTCCAAGAATCGCAACGCGATTCAGAA
* * *
86041 AATCGCAACGCGATTCCAAGAATCGCAACGCGA--TT-CAGAAAATCGCAACGCGATTCCA-AG
1 AATCGCAACGCGATT-CAAAAATCGCAACGCGATCTTCCA-AGAATCGCAACGCGATT-CAGAA
86101 AATCGCAACGCGATT
1 AATCGCAACGCGATT
86116 AAGAAAATGA
Statistics
Matches: 127, Mismatches: 7, Indels: 8
0.89 0.05 0.06
Matches are distributed among these distances:
59 2 0.02
60 34 0.27
61 1 0.01
62 88 0.69
63 2 0.02
ACGTcount: A:0.37, C:0.27, G:0.19, T:0.17
Consensus pattern (61 bp):
AATCGCAACGCGATTCAAAAATCGCAACGCGATCTTCCAAGAATCGCAACGCGATTCAGAA
Found at i:86069 original size:40 final size:39
Alignment explanation
Indices: 85834--86123 Score: 280
Period size: 42 Copynumber: 7.1 Consensus size: 39
85824 AATGACCAAC
*
85834 AAAATCGCAACGCGATATCAA-AACCGCAACGCGATTTAG
1 AAAATCGCAACGCGAT-TCAAGAATCGCAACGCGATTTAG
* * * * **
85873 AAAAGCGCAACGTTGA--AAAGAAGATCGCAACACGATCTTCC
1 AAAATCGCAACG-CGATTCAAG-A-ATCGCAACGCGAT-TTAG
* * **
85914 AAGAATCGCAATGCGATTCATAAAATCGCAACGCGATCTTCC
1 AA-AATCGCAACGCGATTCA-AGAATCGCAACGCGAT-TTAG
* *
85956 AAGAATCGCAACGCGATTCAGAAAATCGCAACGCGATTCAG
1 AA-AATCGCAACGCGATTCA-AGAATCGCAACGCGATTTAG
*
85997 AAAATCGCAACGCGATCTTCCAAGAATCGCAACGCGATTAAG
1 AAAATCGCAACGCGA--TT-CAAGAATCGCAACGCGATTTAG
*
86039 AAAATCGCAACGCGATTCCAAGAATCGCAACGCGATTCAG
1 AAAATCGCAACGCGATT-CAAGAATCGCAACGCGATTTAG
*
86079 AAAATCGCAACGCGATTCCAAGAATCGCAACGCGATTAAG
1 AAAATCGCAACGCGATT-CAAGAATCGCAACGCGATTTAG
86119 AAAAT
1 AAAAT
86124 GAGTAAATTC
Statistics
Matches: 217, Mismatches: 22, Indels: 23
0.83 0.08 0.09
Matches are distributed among these distances:
37 2 0.01
39 12 0.06
40 94 0.43
41 9 0.04
42 95 0.44
43 4 0.02
44 1 0.00
ACGTcount: A:0.40, C:0.25, G:0.19, T:0.16
Consensus pattern (39 bp):
AAAATCGCAACGCGATTCAAGAATCGCAACGCGATTTAG
Found at i:86227 original size:6 final size:6
Alignment explanation
Indices: 86216--86296 Score: 141
Period size: 6 Copynumber: 14.0 Consensus size: 6
86206 GAAGACACGT
86216 ACGACC ACGACC ACGACC ACGACC ACGACC ACGACC ACGACC ACGACC
1 ACGACC ACGACC ACGACC ACGACC ACGACC ACGACC ACGACC ACGACC
86264 ACGACC ACGACC ACGACC -CGACC -CGACC -CGACC
1 ACGACC ACGACC ACGACC ACGACC ACGACC ACGACC
86297 CGAGACGAGA
Statistics
Matches: 75, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
5 15 0.20
6 60 0.80
ACGTcount: A:0.31, C:0.52, G:0.17, T:0.00
Consensus pattern (6 bp):
ACGACC
Found at i:86857 original size:20 final size:20
Alignment explanation
Indices: 86829--87581 Score: 906
Period size: 20 Copynumber: 37.0 Consensus size: 20
86819 GGTCGAATTA
86829 CTGAATCGCGTTGCGATTTT
1 CTGAATCGCGTTGCGATTTT
*
86849 CTTAATCGCGTTGCGATTCTT
1 CTGAATCGCGTTGCGATT-TT
*
86870 -GGAAGATCGCGTTGCGATTTT
1 CTG-A-ATCGCGTTGCGATTTT
*
86891 CTTAATCGCGTTGCGATTCTT
1 CTGAATCGCGTTGCGATT-TT
*
86912 -GGAATCGCGTTGCGATTTT
1 CTGAATCGCGTTGCGATTTT
86931 CTGAATCGCGTTGCGATTCTT
1 CTGAATCGCGTTGCGATT-TT
*
86952 -GGAATCGCGTTGCGATTTT
1 CTGAATCGCGTTGCGATTTT
*
86971 CTTAATCGCGTTGCGATTCTT
1 CTGAATCGCGTTGCGATT-TT
*
86992 -GGAAGATCGCGTTGCGATTTT
1 CTG-A-ATCGCGTTGCGATTTT
*
87013 CTAAATCGCGTTGCGATTTT
1 CTGAATCGCGTTGCGATTTT
87033 CTGAATCGCGTTGCGATTTT
1 CTGAATCGCGTTGCGATTTT
87053 CTGAATCGCGTTGCGATTCTT
1 CTGAATCGCGTTGCGATT-TT
*
87074 -GGAAGATCGCGTTGCGATTTT
1 CTG-A-ATCGCGTTGCGATTTT
* *
87095 ATGAATCGCATTGCGATTCTT
1 CTGAATCGCGTTGCGATT-TT
*
87116 -GGAAGATCGCGTTGCGATTCTT
1 CTG-A-ATCGCGTTGCGATT-TT
*
87138 -GGAATCGCGTTGCGATTTT
1 CTGAATCGCGTTGCGATTTT
87157 CTGAATCGCGTTGCGATTCTT
1 CTGAATCGCGTTGCGATT-TT
*
87178 -GGAATCGCGTTGCGATTTT
1 CTGAATCGCGTTGCGATTTT
*
87197 CTTAATCGCGTTGCGATTCTT
1 CTGAATCGCGTTGCGATT-TT
*
87218 -GGAAGATCGCGTTGCGATTTT
1 CTG-A-ATCGCGTTGCGATTTT
87239 CTGAATCGCGTTGCGATTTT
1 CTGAATCGCGTTGCGATTTT
87259 CTGAATCGCGTTGCGATTTT
1 CTGAATCGCGTTGCGATTTT
87279 CTGAATCGCGTTGCGATTTT
1 CTGAATCGCGTTGCGATTTT
87299 CTGAATCGCGTTGCGATTTT
1 CTGAATCGCGTTGCGATTTT
87319 CTGAATCGCGTTGCGATTTT
1 CTGAATCGCGTTGCGATTTT
87339 CTGAATCGCGTTGCGATTTT
1 CTGAATCGCGTTGCGATTTT
87359 CTGAATCGCGTTGCGATTTT
1 CTGAATCGCGTTGCGATTTT
87379 CTGAATCGCGTTGCGATTTT
1 CTGAATCGCGTTGCGATTTT
87399 CTGAATCGCGTTGCGATTTT
1 CTGAATCGCGTTGCGATTTT
87419 CTGAATCGCGTTGCGATTTT
1 CTGAATCGCGTTGCGATTTT
87439 CTGAATCGCGTTGCGATTCTT
1 CTGAATCGCGTTGCGATT-TT
*
87460 -GGAAGATCGCGTTGCGATTTT
1 CTG-A-ATCGCGTTGCGATTTT
* *
87481 ATG-ATTGCGATTGCGATTCTT
1 CTGAATCGCG-TTGCGATT-TT
* *
87502 -GGAAGATCGCGTTGCGATCTT
1 CTG-A-ATCGCGTTGCGATTTT
** * *
87523 CT-TTTCAACGTTGCGCTTTT
1 CTGAATC-GCGTTGCGATTTT
* *
87543 CTAAATCGCGTTGCG-GTTT
1 CTGAATCGCGTTGCGATTTT
87562 -TGATATCGCGTTGCGATTTT
1 CTGA-ATCGCGTTGCGATTTT
87582 GTTGGTCATT
Statistics
Matches: 647, Mismatches: 46, Indels: 80
0.84 0.06 0.10
Matches are distributed among these distances:
18 2 0.00
19 29 0.04
20 468 0.72
21 45 0.07
22 98 0.15
23 5 0.01
ACGTcount: A:0.16, C:0.19, G:0.26, T:0.39
Consensus pattern (20 bp):
CTGAATCGCGTTGCGATTTT
Found at i:88870 original size:128 final size:128
Alignment explanation
Indices: 88632--88897 Score: 311
Period size: 128 Copynumber: 2.1 Consensus size: 128
88622 TCAACCGTCC
* * *
88632 GTTTATTTAGTAAACGGACGAATATGAACAAGATTTTATGTTCGTTTTATTAAATGAACGAGCAC
1 GTTTATTTATTAAACGGACGAACATGAACAAGATTTTATGTTCGTTTAATTAAATGAACGAGCAC
* * * * * *
88697 AAAGAAAGGACTCGTTCATTCATTTACGTTCATGAACATTTGGTAA-TCTGTTCGTTTATGCTT
66 AAACAAAGGACCCGTCCATTCATTTACGTTCATAAACATTCGGTAATTC-GTTCATTTATGCTT
* * **
88760 GTTTATTTATTAAATGGGCGAACATGAATGAGATTTTATG-TCTGTTTAATTAAATGAACGAGCA
1 GTTTATTTATTAAACGGACGAACATGAACAAGATTTTATGTTC-GTTTAATTAAATGAACGAGCA
* * * * * * *
88824 CGAACAAAGGGCCCGTCCGTTCATTTGCGTTCGTAAACGTTCGGTAATTCGTTCATTTATGTTT
65 CAAACAAAGGACCCGTCCATTCATTTACGTTCATAAACATTCGGTAATTCGTTCATTTATGCTT
*
88888 ATTTATTTAT
1 GTTTATTTAT
88898 GTTCATTTTT
Statistics
Matches: 115, Mismatches: 21, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
127 2 0.02
128 111 0.97
129 2 0.02
ACGTcount: A:0.29, C:0.14, G:0.19, T:0.38
Consensus pattern (128 bp):
GTTTATTTATTAAACGGACGAACATGAACAAGATTTTATGTTCGTTTAATTAAATGAACGAGCAC
AAACAAAGGACCCGTCCATTCATTTACGTTCATAAACATTCGGTAATTCGTTCATTTATGCTT
Found at i:91583 original size:2 final size:2
Alignment explanation
Indices: 91540--91571 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
91530 TACTTTTTTG
91540 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
91572 TAAAAGCTCT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:93330 original size:2 final size:2
Alignment explanation
Indices: 93323--93350 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
93313 CGACCCAAAG
93323 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
93351 CCTCCACTCG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:97439 original size:2 final size:2
Alignment explanation
Indices: 97432--97464 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
97422 GATTTTGATA
97432 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
97465 AAACTAAATT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:97720 original size:20 final size:20
Alignment explanation
Indices: 97679--97723 Score: 54
Period size: 21 Copynumber: 2.2 Consensus size: 20
97669 TTCAACATTC
* *
97679 AAATCAGAAAAAATAACTAA
1 AAATCAGAAAAAAGAACAAA
*
97699 AAATCAGAAGAAAAGAAAAAA
1 AAATCAGAA-AAAAGAACAAA
97720 AAAT
1 AAAT
97724 GTAGCTCATC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 9 0.43
21 12 0.57
ACGTcount: A:0.73, C:0.07, G:0.09, T:0.11
Consensus pattern (20 bp):
AAATCAGAAAAAAGAACAAA
Found at i:98322 original size:2 final size:2
Alignment explanation
Indices: 98315--98355 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
98305 AAGCAACGGT
98315 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
98356 GTATGCATGA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:98528 original size:2 final size:2
Alignment explanation
Indices: 98523--98591 Score: 138
Period size: 2 Copynumber: 34.5 Consensus size: 2
98513 TCACACACAA
98523 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
98565 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
98592 CTATGTCTGG
Statistics
Matches: 67, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 67 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:100476 original size:2 final size:2
Alignment explanation
Indices: 100469--100510 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
100459 CTTTCCCCTA
100469 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
100511 GATTAAAATA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:103173 original size:21 final size:21
Alignment explanation
Indices: 103149--103205 Score: 98
Period size: 21 Copynumber: 2.8 Consensus size: 21
103139 AGTGCTACGA
*
103149 ACTTCTGCTAGCAACTTGAAC
1 ACTTCTGGTAGCAACTTGAAC
103170 ACTTCTGGTAGCAACTTGAAC
1 ACTTCTGGTAGCAACTTGAAC
103191 ACTTCTGGTAG-AACT
1 ACTTCTGGTAGCAACT
103206 AGCAACCCTA
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
20 4 0.11
21 31 0.89
ACGTcount: A:0.28, C:0.25, G:0.18, T:0.30
Consensus pattern (21 bp):
ACTTCTGGTAGCAACTTGAAC
Found at i:104974 original size:32 final size:32
Alignment explanation
Indices: 104938--105014 Score: 138
Period size: 32 Copynumber: 2.4 Consensus size: 32
104928 CTTTCCTCTG
104938 CCTCCCATCCC-CCATTCCCTTAGCCCCTTAGC
1 CCTCCC-TCCCTCCATTCCCTTAGCCCCTTAGC
104970 CCTCCCTCCCTCCATTCCCTTAGCCCCTTAGC
1 CCTCCCTCCCTCCATTCCCTTAGCCCCTTAGC
105002 CCTCCCTCCCTCC
1 CCTCCCTCCCTCC
105015 CTCCATTCCC
Statistics
Matches: 44, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
31 4 0.09
32 40 0.91
ACGTcount: A:0.09, C:0.60, G:0.05, T:0.26
Consensus pattern (32 bp):
CCTCCCTCCCTCCATTCCCTTAGCCCCTTAGC
Found at i:106469 original size:32 final size:32
Alignment explanation
Indices: 106433--106495 Score: 83
Period size: 32 Copynumber: 2.0 Consensus size: 32
106423 AACTCCAAGG
* *
106433 TAAGAACCTCAATCTATTCCTTT-CAAGCTCCT
1 TAAGAACATCAATCTACT-CTTTCCAAGCTCCT
*
106465 TAAGAACATTAATCTACTCTTTCCAAGCTCC
1 TAAGAACATCAATCTACTCTTTCCAAGCTCC
106496 ATTTCAAGCC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
31 4 0.15
32 23 0.85
ACGTcount: A:0.30, C:0.30, G:0.06, T:0.33
Consensus pattern (32 bp):
TAAGAACATCAATCTACTCTTTCCAAGCTCCT
Found at i:107627 original size:12 final size:13
Alignment explanation
Indices: 107597--107649 Score: 56
Period size: 13 Copynumber: 4.2 Consensus size: 13
107587 GTACTCATAG
107597 AAATTATTTTTAT
1 AAATTATTTTTAT
107610 AAATTATTTTT-T
1 AAATTATTTTTAT
* *
107622 ACATTACTTTTA-
1 AAATTATTTTTAT
*
107634 AAAGTTCTTTTTAT
1 AAA-TTATTTTTAT
107648 AA
1 AA
107650 TACGTTTTTT
Statistics
Matches: 32, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
12 12 0.38
13 18 0.56
14 2 0.06
ACGTcount: A:0.36, C:0.06, G:0.02, T:0.57
Consensus pattern (13 bp):
AAATTATTTTTAT
Done.