Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008180.1 Hibiscus syriacus cultivar Beakdansim tig00110777_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: 2670214
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 14
Found at i:335 original size:20 final size:19
Alignment explanation
Indices: 307--345 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
297 TTCATTAGTA
*
307 CACTCTTTCTTTTCTTTTTT
1 CACTCTTTC-CTTCTTTTTT
*
327 CACTTTTTCCTTCTTTTTT
1 CACTCTTTCCTTCTTTTTT
346 TTAAGCTGCT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.05, C:0.26, G:0.00, T:0.69
Consensus pattern (19 bp):
CACTCTTTCCTTCTTTTTT
Found at i:4653 original size:24 final size:24
Alignment explanation
Indices: 4622--4671 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
4612 ATAAAGAACC
4622 AAAATAAA-CTTAAACATACCATTA
1 AAAATAAAGCTTAAACAT-CCATTA
*
4646 AAAATAAAGTTTAAACATCCATTA
1 AAAATAAAGCTTAAACATCCATTA
4670 AA
1 AA
4672 CCAACCACCA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
24 16 0.67
25 8 0.33
ACGTcount: A:0.58, C:0.14, G:0.02, T:0.26
Consensus pattern (24 bp):
AAAATAAAGCTTAAACATCCATTA
Found at i:10872 original size:14 final size:13
Alignment explanation
Indices: 10763--10881 Score: 61
Period size: 13 Copynumber: 8.9 Consensus size: 13
10753 CCATGTTATC
* *
10763 TTTTATCTTATAA
1 TTTTATTTTATTA
10776 TTATTA-TTTATT-
1 TT-TTATTTTATTA
10788 TATTTATTTTATTA
1 T-TTTATTTTATTA
*
10802 TTTTATCCTTA-TA
1 TTTTAT-TTTATTA
** *
10815 TTCCATTTTA-AA
1 TTTTATTTTATTA
10827 TGATTTATATTTATTA
1 T--TTTAT-TTTATTA
10843 -TTTATTTTATTA
1 TTTTATTTTATTA
10855 TTTTATTCTTATCT-
1 TTTTATT-TTAT-TA
10869 TTTTATCTTTATT
1 TTTTAT-TTTATT
10882 TGAAATATCT
Statistics
Matches: 83, Mismatches: 10, Indels: 26
0.70 0.08 0.22
Matches are distributed among these distances:
12 16 0.19
13 36 0.43
14 24 0.29
15 6 0.07
16 1 0.01
ACGTcount: A:0.25, C:0.07, G:0.01, T:0.67
Consensus pattern (13 bp):
TTTTATTTTATTA
Found at i:11438 original size:20 final size:20
Alignment explanation
Indices: 11413--11451 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
11403 AAGATGGTAC
11413 ATGTGATTAGCATGAGTATT
1 ATGTGATTAGCATGAGTATT
*
11433 ATGTGATTGGCATGAGTAT
1 ATGTGATTAGCATGAGTAT
11452 AATATATTGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.28, C:0.05, G:0.28, T:0.38
Consensus pattern (20 bp):
ATGTGATTAGCATGAGTATT
Found at i:15469 original size:13 final size:13
Alignment explanation
Indices: 15451--15477 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
15441 ATTGCTCGTG
15451 GTGAAACATTTGT
1 GTGAAACATTTGT
15464 GTGAAACATTTGT
1 GTGAAACATTTGT
15477 G
1 G
15478 AGCAAAATTG
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:0.07, G:0.26, T:0.37
Consensus pattern (13 bp):
GTGAAACATTTGT
Found at i:22543 original size:14 final size:14
Alignment explanation
Indices: 22526--22552 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
22516 AAATCAAGTT
22526 TTGAAATTAGAAAA
1 TTGAAATTAGAAAA
22540 TTGAAATTAGAAA
1 TTGAAATTAGAAA
22553 TTACTCCCCC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.56, C:0.00, G:0.15, T:0.30
Consensus pattern (14 bp):
TTGAAATTAGAAAA
Found at i:24878 original size:20 final size:20
Alignment explanation
Indices: 24802--24886 Score: 64
Period size: 20 Copynumber: 4.0 Consensus size: 20
24792 AGCAGAACCC
*
24802 CAGGGGGGTATCGATTCCC-
1 CAGGGGGGAATCGATTCCCT
* *
24821 CTGTGGGGTGAATCGGTTCCCCTT
1 CAG-GGGG-GAATCGATT-CCC-T
* *
24845 CAAAGGGGGAATCGGTTCCCT
1 C-AGGGGGGAATCGATTCCCT
*
24866 CAGGGGGGGATCGATTCCCT
1 CAGGGGGGAATCGATTCCCT
24886 C
1 C
24887 TGCACCAAAA
Statistics
Matches: 52, Mismatches: 8, Indels: 11
0.73 0.11 0.15
Matches are distributed among these distances:
19 2 0.04
20 21 0.40
21 9 0.17
22 6 0.12
23 9 0.17
24 5 0.10
ACGTcount: A:0.15, C:0.26, G:0.35, T:0.24
Consensus pattern (20 bp):
CAGGGGGGAATCGATTCCCT
Found at i:28730 original size:22 final size:21
Alignment explanation
Indices: 28688--28727 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
28678 GAGTTTGTTT
*
28688 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
28709 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
28728 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:37735 original size:25 final size:25
Alignment explanation
Indices: 37707--37796 Score: 108
Period size: 25 Copynumber: 3.4 Consensus size: 25
37697 GTTTTTGGTT
*
37707 AGATGAAAGGAGTTTGTTGTGTAAGAG
1 AGATGAAAGGAGTGTGTTGTGT-A-AG
*
37734 ATTGAAGTGAAAAGAGTGTGTTGTGTAAG
1 A--G-A-TGAAAGGAGTGTGTTGTGTAAG
37763 AGATGAAAGGAGTGTGTTGTGTAAG
1 AGATGAAAGGAGTGTGTTGTGTAAG
37788 AGATGAAAG
1 AGATGAAAG
37797 ATGATGTTTA
Statistics
Matches: 56, Mismatches: 3, Indels: 10
0.81 0.04 0.14
Matches are distributed among these distances:
25 30 0.54
26 1 0.02
27 2 0.04
29 4 0.07
30 2 0.04
31 17 0.30
ACGTcount: A:0.36, C:0.00, G:0.37, T:0.28
Consensus pattern (25 bp):
AGATGAAAGGAGTGTGTTGTGTAAG
Found at i:38130 original size:159 final size:161
Alignment explanation
Indices: 37839--38151 Score: 558
Period size: 159 Copynumber: 2.0 Consensus size: 161
37829 TTTTTCGTTG
* *
37839 CGAGTTCCATGGACATTAAAATATTATTTTTTTTACATTTCTTTTAAAATTTTCATAAAAGAATA
1 CGAGTTCCACGGACATTAAAATATTATTTTTTTTACATTTCTTTTAAAATTTTCAAAAAAGAATA
37904 TTTATTTATTAGAACTCATCACGCAGTTATGACGAGTCCCGGAAGATATATTAAAATTATTCGGA
66 TTTATTTATTAGAACTCATCACGCAGTTATGACGAGTCCCGGAAGATATATTAAAATTATTCGGA
* *
37969 CTGTGGGACCCACCTAACACGGCCGGCGTGA
131 CTGCGAGACCCACCTAACACGGCCGGCGTGA
*
38000 CGAGTTCCACGGACATTAAAATATTA-TTTTTTTACATTTCTTTTAAAATTTTCAAAAAATAATA
1 CGAGTTCCACGGACATTAAAATATTATTTTTTTTACATTTCTTTTAAAATTTTCAAAAAAGAATA
*
38064 TTT-TTTATTGGAACTCATCACGCAGTTATGACGAGTCCCGGAAGATATATTAAAATTATTCGGA
66 TTTATTTATTAGAACTCATCACGCAGTTATGACGAGTCCCGGAAGATATATTAAAATTATTCGGA
38128 CTGCGAGACCCACCTAACACGGCC
131 CTGCGAGACCCACCTAACACGGCC
38152 CATTAAAAAT
Statistics
Matches: 146, Mismatches: 6, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
159 82 0.56
160 39 0.27
161 25 0.17
ACGTcount: A:0.33, C:0.18, G:0.15, T:0.34
Consensus pattern (161 bp):
CGAGTTCCACGGACATTAAAATATTATTTTTTTTACATTTCTTTTAAAATTTTCAAAAAAGAATA
TTTATTTATTAGAACTCATCACGCAGTTATGACGAGTCCCGGAAGATATATTAAAATTATTCGGA
CTGCGAGACCCACCTAACACGGCCGGCGTGA
Found at i:39513 original size:3 final size:3
Alignment explanation
Indices: 39505--39546 Score: 66
Period size: 3 Copynumber: 13.3 Consensus size: 3
39495 TTCTTGACAC
39505 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAAG AAG AAAG AAG A
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG -AAG AAG -AAG AAG A
39547 GGAGATTGCT
Statistics
Matches: 37, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
3 31 0.84
4 6 0.16
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:43957 original size:52 final size:52
Alignment explanation
Indices: 43879--43983 Score: 174
Period size: 52 Copynumber: 2.0 Consensus size: 52
43869 AAGTTGTTCG
*
43879 ACTTTGACTTGTAGGTTTTCATTGGTCTTTCAATAACTTAATCCACTTTTGT
1 ACTTTGACTTGTAGGTTTTCAGTGGTCTTTCAATAACTTAATCCACTTTTGT
* * *
43931 ACTTTGATTTGTGGGTTTTCAGTGGTCTTTCAATAACTTAATCGACTTTTGT
1 ACTTTGACTTGTAGGTTTTCAGTGGTCTTTCAATAACTTAATCCACTTTTGT
43983 A
1 A
43984 TTTCGTTTGT
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
52 49 1.00
ACGTcount: A:0.21, C:0.15, G:0.16, T:0.48
Consensus pattern (52 bp):
ACTTTGACTTGTAGGTTTTCAGTGGTCTTTCAATAACTTAATCCACTTTTGT
Found at i:51328 original size:31 final size:31
Alignment explanation
Indices: 51290--51349 Score: 111
Period size: 31 Copynumber: 1.9 Consensus size: 31
51280 CTTAAATGAC
*
51290 AACAATTAAATAGTTAGGTGGTTTGATTGAA
1 AACAATTAAATAGTTAAGTGGTTTGATTGAA
51321 AACAATTAAATAGTTAAGTGGTTTGATTG
1 AACAATTAAATAGTTAAGTGGTTTGATTG
51350 TTAAAATTGT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.38, C:0.03, G:0.22, T:0.37
Consensus pattern (31 bp):
AACAATTAAATAGTTAAGTGGTTTGATTGAA
Found at i:56061 original size:34 final size:34
Alignment explanation
Indices: 56022--56109 Score: 106
Period size: 34 Copynumber: 2.6 Consensus size: 34
56012 GTAAATAATA
* *
56022 AACAAAATTATCAAAATAAATTGAGAAAAAATCC
1 AACAAAATTAACAAAATAAATTGAAAAAAAATCC
* * *
56056 AACAAAATAAACAAAA-AATTTTTAAAAAAAATCC
1 AACAAAATTAACAAAATAA-ATTGAAAAAAAATCC
*
56090 AACCAAATTAACAAAATAAA
1 AACAAAATTAACAAAATAAA
56110 GTAAGTATTT
Statistics
Matches: 44, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
33 2 0.05
34 40 0.91
35 2 0.05
ACGTcount: A:0.66, C:0.12, G:0.02, T:0.19
Consensus pattern (34 bp):
AACAAAATTAACAAAATAAATTGAAAAAAAATCC
Found at i:56681 original size:27 final size:27
Alignment explanation
Indices: 56651--56702 Score: 104
Period size: 27 Copynumber: 1.9 Consensus size: 27
56641 CGATGGTGGC
56651 ATCTGGTAAGGGAAAGGCGGTGGCGGT
1 ATCTGGTAAGGGAAAGGCGGTGGCGGT
56678 ATCTGGTAAGGGAAAGGCGGTGGCG
1 ATCTGGTAAGGGAAAGGCGGTGGCG
56703 ACATTATATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.23, C:0.12, G:0.48, T:0.17
Consensus pattern (27 bp):
ATCTGGTAAGGGAAAGGCGGTGGCGGT
Found at i:59238 original size:20 final size:20
Alignment explanation
Indices: 59202--59239 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
59192 TTTTCAAATT
*
59202 ATAAATTTCATATATTTTTG
1 ATAAATTTCATAAATTTTTG
*
59222 ATAAATTTCTTAAATTTT
1 ATAAATTTCATAAATTTT
59240 AAAATTAATT
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:0.37, C:0.05, G:0.03, T:0.55
Consensus pattern (20 bp):
ATAAATTTCATAAATTTTTG
Found at i:60765 original size:20 final size:20
Alignment explanation
Indices: 60714--60765 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
60704 TAGTTGAAAA
*
60714 TCGCGTTGCAATTTTCCATT
1 TCGCGTTGCGATTTTCCATT
* *
60734 TCGCGTTACGATTTTTCATT
1 TCGCGTTGCGATTTTCCATT
60754 TCGCGTTGCGAT
1 TCGCGTTGCGAT
60766 AGTCTACAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.13, C:0.23, G:0.19, T:0.44
Consensus pattern (20 bp):
TCGCGTTGCGATTTTCCATT
Found at i:60820 original size:19 final size:20
Alignment explanation
Indices: 60758--60840 Score: 62
Period size: 19 Copynumber: 4.1 Consensus size: 20
60748 TTCATTTCGC
*
60758 GTTGCGATAGTCTACAATGTC
1 GTTGCGATAGTCTAC-ATGTT
** * * *
60779 GTTGCGATTTTCCAAAT-TC
1 GTTGCGATAGTCTACATGTT
60798 GTTGCGATAGTCTACAGTTGTT
1 GTTGCGATAGTCTACA--TGTT
*
60820 GTTGCGAAAGTCTACA-GTT
1 GTTGCGATAGTCTACATGTT
60839 GT
1 GT
60841 CGTTGCGATT
Statistics
Matches: 49, Mismatches: 10, Indels: 8
0.73 0.15 0.12
Matches are distributed among these distances:
19 19 0.39
20 2 0.04
21 12 0.24
22 16 0.33
ACGTcount: A:0.22, C:0.17, G:0.24, T:0.37
Consensus pattern (20 bp):
GTTGCGATAGTCTACATGTT
Found at i:60825 original size:22 final size:22
Alignment explanation
Indices: 60757--60849 Score: 95
Period size: 22 Copynumber: 4.4 Consensus size: 22
60747 TTTCATTTCG
*
60757 CGTTGCGATAGTCTACA-ATGT
1 CGTTGCGATAGTCTACAGTTGT
* * **
60778 CGTTGCGAT--TTTCCAAAT-T
1 CGTTGCGATAGTCTACAGTTGT
60797 CGTTGCGATAGTCTACAGTTGT
1 CGTTGCGATAGTCTACAGTTGT
* *
60819 TGTTGCGAAAGTCTACAGTTGT
1 CGTTGCGATAGTCTACAGTTGT
60841 CGTTGCGAT
1 CGTTGCGAT
60850 TTTCCAAATT
Statistics
Matches: 58, Mismatches: 10, Indels: 7
0.77 0.13 0.09
Matches are distributed among these distances:
19 14 0.24
20 2 0.03
21 14 0.24
22 28 0.48
ACGTcount: A:0.20, C:0.18, G:0.25, T:0.37
Consensus pattern (22 bp):
CGTTGCGATAGTCTACAGTTGT
Found at i:60963 original size:6 final size:6
Alignment explanation
Indices: 60954--60995 Score: 63
Period size: 6 Copynumber: 7.5 Consensus size: 6
60944 TATTACCATT
60954 ACCACG ACCACG ACCACG ACCACG ACC-CG ACC-CG ACC-CG ACC
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACC
60996 CGAGACGAGA
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 15 0.42
6 21 0.58
ACGTcount: A:0.29, C:0.55, G:0.17, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:60986 original size:5 final size:5
Alignment explanation
Indices: 60958--60998 Score: 55
Period size: 5 Copynumber: 7.6 Consensus size: 5
60948 ACCATTACCA
60958 CGACC ACGACC ACGACC ACGACC CGACC CGACC CGACC CGA
1 CGACC -CGACC -CGACC -CGACC CGACC CGACC CGACC CGA
60999 GACGAGACGG
Statistics
Matches: 35, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 18 0.51
6 17 0.49
ACGTcount: A:0.27, C:0.54, G:0.20, T:0.00
Consensus pattern (5 bp):
CGACC
Found at i:61638 original size:22 final size:22
Alignment explanation
Indices: 61609--61701 Score: 95
Period size: 22 Copynumber: 4.4 Consensus size: 22
61599 AATTTGGAAA
61609 ATCGCAACGACAACTGTAGACT
1 ATCGCAACGACAACTGTAGACT
* *
61631 TTCGCAACAACAACTGTAGACT
1 ATCGCAACGACAACTGTAGACT
* * **
61653 ATCGCAACG--AA-TTTGGAAA
1 ATCGCAACGACAACTGTAGACT
*
61672 ATCGCAACGAC-ATTGTAGACT
1 ATCGCAACGACAACTGTAGACT
61693 ATCGCAACG
1 ATCGCAACG
61702 CGAAATGAAA
Statistics
Matches: 56, Mismatches: 12, Indels: 7
0.75 0.16 0.09
Matches are distributed among these distances:
19 13 0.23
20 3 0.05
21 13 0.23
22 27 0.48
ACGTcount: A:0.37, C:0.25, G:0.18, T:0.20
Consensus pattern (22 bp):
ATCGCAACGACAACTGTAGACT
Found at i:61660 original size:19 final size:20
Alignment explanation
Indices: 61587--61701 Score: 72
Period size: 22 Copynumber: 5.6 Consensus size: 20
61577 TTTTTTTTTA
* *
61587 ACTATCGCAACGAA-TTTGG
1 ACTATCGCAACGAACTGTAG
**
61606 AAAATCGCAACGACAACTGTAG
1 ACTATCGCAACG--AACTGTAG
* *
61628 ACTTTCGCAACAACAACTGTAG
1 ACTATCGCAAC--GAACTGTAG
* *
61650 ACTATCGCAACGAA-TTTGG
1 ACTATCGCAACGAACTGTAG
** *
61669 AAAATCGCAACGACATTGTAG
1 ACTATCGCAACGA-ACTGTAG
61690 ACTATCGCAACG
1 ACTATCGCAACG
61702 CGAAATGAAA
Statistics
Matches: 71, Mismatches: 18, Indels: 12
0.70 0.18 0.12
Matches are distributed among these distances:
19 24 0.34
20 3 0.04
21 15 0.21
22 29 0.41
ACGTcount: A:0.37, C:0.23, G:0.18, T:0.21
Consensus pattern (20 bp):
ACTATCGCAACGAACTGTAG
Found at i:61714 original size:41 final size:40
Alignment explanation
Indices: 61645--61721 Score: 111
Period size: 40 Copynumber: 1.9 Consensus size: 40
61635 CAACAACAAC
* *
61645 TGTAGACTATCGCAACGAATTTGGAAAATCGCAACGACAT
1 TGTAGACTATCGCAACGAATATGAAAAATCGCAACGACAT
61685 TGTAGACTATCGCAACGCGAA-ATGAAAAATCGCAACG
1 TGTAGACTATCGCAA--CGAATATGAAAAATCGCAACG
61722 CGAAATGGAA
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
40 15 0.45
41 14 0.42
42 4 0.12
ACGTcount: A:0.39, C:0.21, G:0.21, T:0.19
Consensus pattern (40 bp):
TGTAGACTATCGCAACGAATATGAAAAATCGCAACGACAT
Found at i:61718 original size:20 final size:20
Alignment explanation
Indices: 61693--61783 Score: 121
Period size: 20 Copynumber: 4.6 Consensus size: 20
61683 ATTGTAGACT
61693 ATCGCAACGCGAAATGAAAA
1 ATCGCAACGCGAAATGAAAA
*
61713 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGAAAA
*
61733 ATCGCAACGAG-AATGAAAA
1 ATCGCAACGCGAAATGAAAA
* * *
61752 ATCGAAACGCGAACTGGAAA
1 ATCGCAACGCGAAATGAAAA
*
61772 ATCGAAACGCGA
1 ATCGCAACGCGA
61784 TTTTCAACTA
Statistics
Matches: 63, Mismatches: 7, Indels: 2
0.88 0.10 0.03
Matches are distributed among these distances:
19 16 0.25
20 47 0.75
ACGTcount: A:0.47, C:0.20, G:0.23, T:0.10
Consensus pattern (20 bp):
ATCGCAACGCGAAATGAAAA
Found at i:61755 original size:39 final size:40
Alignment explanation
Indices: 61693--61780 Score: 133
Period size: 39 Copynumber: 2.2 Consensus size: 40
61683 ATTGTAGACT
* *
61693 ATCGCAACGCGAAATGAAAAATCGCAACGCGAAATGGAAA
1 ATCGCAACGAGAAATGAAAAATCGAAACGCGAAATGGAAA
*
61733 ATCGCAACGAG-AATGAAAAATCGAAACGCGAACTGGAAA
1 ATCGCAACGAGAAATGAAAAATCGAAACGCGAAATGGAAA
*
61772 ATCGAAACG
1 ATCGCAACG
61781 CGATTTTCAA
Statistics
Matches: 44, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
39 34 0.77
40 10 0.23
ACGTcount: A:0.48, C:0.19, G:0.23, T:0.10
Consensus pattern (40 bp):
ATCGCAACGAGAAATGAAAAATCGAAACGCGAAATGGAAA
Found at i:61781 original size:59 final size:61
Alignment explanation
Indices: 61666--61783 Score: 150
Period size: 59 Copynumber: 2.0 Consensus size: 61
61656 GCAACGAATT
* ** * *
61666 TGGAAAATCGCAACGACATTGTAGACTATCGCAACGCGAAATGAAAAATCGCAACGCGAAA
1 TGGAAAATCGCAACGACAATGTAGAAAATCGAAACGCGAAATGAAAAATCGAAACGCGAAA
* * *
61727 TGGAAAATCGCAACGAGAATG-A-AAAATCGAAACGCGAACTGGAAAATCGAAACGCGA
1 TGGAAAATCGCAACGACAATGTAGAAAATCGAAACGCGAAATGAAAAATCGAAACGCGA
61784 TTTTCAACTA
Statistics
Matches: 49, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
59 29 0.59
60 1 0.02
61 19 0.39
ACGTcount: A:0.45, C:0.19, G:0.23, T:0.13
Consensus pattern (61 bp):
TGGAAAATCGCAACGACAATGTAGAAAATCGAAACGCGAAATGAAAAATCGAAACGCGAAA
Found at i:62525 original size:2 final size:2
Alignment explanation
Indices: 62518--62548 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
62508 CAGATCGGTC
62518 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 T
62549 CAATGTATGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:77765 original size:24 final size:24
Alignment explanation
Indices: 77738--77794 Score: 96
Period size: 24 Copynumber: 2.3 Consensus size: 24
77728 ATAATATTGT
77738 CGCACTTTTAAACTCTAAGAATGA
1 CGCACTTTTAAACTCTAAGAATGA
*
77762 CGCACTTTTAAACTCTAAGAATGG
1 CGCACTTTTAAACTCTAAGAATGA
77786 CGCGACTTT
1 CGC-ACTTT
77795 CAGCTATTGT
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
24 26 0.84
25 5 0.16
ACGTcount: A:0.32, C:0.23, G:0.16, T:0.30
Consensus pattern (24 bp):
CGCACTTTTAAACTCTAAGAATGA
Found at i:80996 original size:35 final size:34
Alignment explanation
Indices: 80957--81045 Score: 99
Period size: 34 Copynumber: 2.6 Consensus size: 34
80947 AATGGTAATA
* *
80957 AACAAAATTAACCAAAATACATTAACAAA-AAGTCC
1 AACAAAATTAA-CAAAATAAATTAA-AAATAAATCC
*
80992 AACAAATTTAACAAAATAAATTAAAAATAAATCC
1 AACAAAATTAACAAAATAAATTAAAAATAAATCC
* **
81026 AACCAAATTAATGAAATAAA
1 AACAAAATTAACAAAATAAA
81046 GTAAGTATTA
Statistics
Matches: 46, Mismatches: 7, Indels: 3
0.82 0.12 0.05
Matches are distributed among these distances:
33 3 0.07
34 33 0.72
35 10 0.22
ACGTcount: A:0.63, C:0.15, G:0.02, T:0.20
Consensus pattern (34 bp):
AACAAAATTAACAAAATAAATTAAAAATAAATCC
Found at i:84643 original size:22 final size:23
Alignment explanation
Indices: 84611--84656 Score: 85
Period size: 22 Copynumber: 2.0 Consensus size: 23
84601 TGATCATATG
84611 TACGTTTGCTGTTTAGCCTGAAT
1 TACGTTTGCTGTTTAGCCTGAAT
84634 TACG-TTGCTGTTTAGCCTGAAT
1 TACGTTTGCTGTTTAGCCTGAAT
84656 T
1 T
84657 GTTCCATACA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
22 19 0.83
23 4 0.17
ACGTcount: A:0.17, C:0.17, G:0.22, T:0.43
Consensus pattern (23 bp):
TACGTTTGCTGTTTAGCCTGAAT
Found at i:86677 original size:19 final size:20
Alignment explanation
Indices: 86650--86693 Score: 63
Period size: 19 Copynumber: 2.2 Consensus size: 20
86640 CTCCAATTTT
*
86650 GCAATGCGAATCTAT-AATC
1 GCAACGCGAATCTATAAATC
*
86669 GCAACGCGAATCTGTAAATC
1 GCAACGCGAATCTATAAATC
86689 GCAAC
1 GCAAC
86694 ACAAAGTCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 13 0.59
20 9 0.41
ACGTcount: A:0.36, C:0.25, G:0.18, T:0.20
Consensus pattern (20 bp):
GCAACGCGAATCTATAAATC
Found at i:86690 original size:20 final size:19
Alignment explanation
Indices: 86665--86793 Score: 77
Period size: 20 Copynumber: 6.5 Consensus size: 19
86655 GCGAATCTAT
86665 AATCGCAACGCGAATCTGTA
1 AATCGCAACGCGAAT-TGTA
* *
86685 AATCGCAACAC-AA-AGTCA
1 AATCGCAACGCGAATTGT-A
* *
86703 AATTCGCAACGTG-ATAGTCA
1 AA-TCGCAACGCGAATTGT-A
* **
86723 AATTCGCAACAC-AAAAGTCA
1 AA-TCGCAACGCGAATTGT-A
86743 AATTCGCAACGCGAATTTTGTA
1 AA-TCGCAACGCGAA--TTGTA
86765 AATCGCAACGCGAATTTGTA
1 AATCGCAACGCGAA-TTGTA
86785 AATCGCAAC
1 AATCGCAAC
86794 ACAAAAGTCA
Statistics
Matches: 91, Mismatches: 10, Indels: 16
0.78 0.09 0.14
Matches are distributed among these distances:
17 2 0.02
18 3 0.03
19 10 0.11
20 57 0.63
21 14 0.15
22 3 0.03
23 2 0.02
ACGTcount: A:0.40, C:0.23, G:0.16, T:0.21
Consensus pattern (19 bp):
AATCGCAACGCGAATTGTA
Found at i:86710 original size:39 final size:39
Alignment explanation
Indices: 86667--86773 Score: 137
Period size: 40 Copynumber: 2.7 Consensus size: 39
86657 GAATCTATAA
86667 TCGCAACGCGAATCTGTAAATCGCAACAC-AAAGTCAAAT
1 TCGCAACGCGAAT-TGTAAATCGCAACACAAAAGTCAAAT
* *
86706 TCGCAACGTG-ATAGTCAAATTCGCAACACAAAAGTCAAAT
1 TCGCAACGCGAATTGT-AAA-TCGCAACACAAAAGTCAAAT
86746 TCGCAACGCGAATTTTGTAAATCGCAAC
1 TCGCAACGCGAA--TTGTAAATCGCAAC
86774 GCGAATTTGT
Statistics
Matches: 58, Mismatches: 4, Indels: 10
0.81 0.06 0.14
Matches are distributed among these distances:
37 2 0.03
38 5 0.09
39 18 0.31
40 19 0.33
41 8 0.14
42 3 0.05
43 3 0.05
ACGTcount: A:0.39, C:0.24, G:0.16, T:0.21
Consensus pattern (39 bp):
TCGCAACGCGAATTGTAAATCGCAACACAAAAGTCAAAT
Found at i:86772 original size:21 final size:20
Alignment explanation
Indices: 86746--86793 Score: 87
Period size: 20 Copynumber: 2.4 Consensus size: 20
86736 AAAGTCAAAT
86746 TCGCAACGCGAATTTTGTAAA
1 TCGCAACGCGAA-TTTGTAAA
86767 TCGCAACGCGAATTTGTAAA
1 TCGCAACGCGAATTTGTAAA
86787 TCGCAAC
1 TCGCAAC
86794 ACAAAAGTCA
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
20 15 0.56
21 12 0.44
ACGTcount: A:0.33, C:0.23, G:0.19, T:0.25
Consensus pattern (20 bp):
TCGCAACGCGAATTTGTAAA
Found at i:86824 original size:20 final size:20
Alignment explanation
Indices: 86797--86846 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
86787 TCGCAACACA
* *
86797 AAAGTCAAATTTACAATGCG
1 AAAGTCAAATTCACAACGCG
* *
86817 ATAGTCAAATTCGCAACGCG
1 AAAGTCAAATTCACAACGCG
86837 AAAGTCAAAT
1 AAAGTCAAAT
86847 GTTTTTACGC
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.44, C:0.18, G:0.16, T:0.22
Consensus pattern (20 bp):
AAAGTCAAATTCACAACGCG
Found at i:86841 original size:101 final size:98
Alignment explanation
Indices: 86623--86846 Score: 288
Period size: 101 Copynumber: 2.3 Consensus size: 98
86613 AAATGACCAA
* * * *
86623 CAAATTCGCAACGCG-AACTCCAATTTTGCAATGCGAATCTATAATCGCAACGCGAATCTGTAAA
1 CAAATTCGCAACGCGAAAGT-CAAATTCGCAACGCGAATCTATAATCGCAACGCGAATCTGTAAA
* *
86687 TCGCAACACAAAGTCAAATTCGCAACGTGATAGT
65 TCGCAACACAAAGTCAAATTCACAACGCGATAGT
* * * * *
86721 CAAATTCGCAACACAAAAGTCAAATTCGCAACGCGAATTTTGTAAATCGCAACGCGAATTTGTAA
1 CAAATTCGCAACGCGAAAGTCAAATTCGCAACGCGAA-TCTAT-AATCGCAACGCGAATCTGTAA
* *
86786 ATCGCAACACAAAAGTCAAATTTACAATGCGATAGT
64 ATCGCAACAC-AAAGTCAAATTCACAACGCGATAGT
86822 CAAATTCGCAACGCGAAAGTCAAAT
1 CAAATTCGCAACGCGAAAGTCAAAT
86847 GTTTTTACGC
Statistics
Matches: 107, Mismatches: 15, Indels: 5
0.84 0.12 0.04
Matches are distributed among these distances:
98 27 0.25
99 6 0.06
100 30 0.28
101 44 0.41
ACGTcount: A:0.40, C:0.23, G:0.16, T:0.22
Consensus pattern (98 bp):
CAAATTCGCAACGCGAAAGTCAAATTCGCAACGCGAATCTATAATCGCAACGCGAATCTGTAAAT
CGCAACACAAAGTCAAATTCACAACGCGATAGT
Found at i:87336 original size:158 final size:156
Alignment explanation
Indices: 87035--87348 Score: 585
Period size: 158 Copynumber: 2.0 Consensus size: 156
87025 CATTCACTGT
87035 CAGAAATGGAAAATCAACCACCGAGGGTTAGTTTTTTTTAATCTCTTATTTTTATTTTGAATTTT
1 CAGAAATGGAAAATCAACCACCGAGGGTTAGTTTTTTTTAATCTCTTATTTTTATTTTGAATTTT
87100 GTATCATTATTAGATTTTTCTTATATTGATAATAATTTACTGGTAATTTCAATATATATAGATTA
66 GTATCATTATTAGATTTTTCTTATATTGATAATAATTTACTGGTAATTTCAATATATATAGATTA
87165 ACCATTTCATTGAGATTGCTTAGTAA
131 ACCATTTCATTGAGATTGCTTAGTAA
87191 CAGAAATGGAAAATCAACCACCGAGGGTTAG-TTTTTTTAATCTCTTATTTTTATTTTGAAATTT
1 CAGAAATGGAAAATCAACCACCGAGGGTTAGTTTTTTTTAATCTCTTATTTTTATTTTG-AA-TT
*
87255 TTGTATTATTATTAGATTTTTCTTATATTGATAATAAATTTACTGGTAATTTCAATATATATAGA
64 TTGTATCATTATTAGATTTTTCTTATATTGATAAT-AATTTACTGGTAATTTCAATATATATAGA
87320 TTAACCATTTCATTGAGATTGCTTAGTAA
128 TTAACCATTTCATTGAGATTGCTTAGTAA
87349 ATTCATTCGG
Statistics
Matches: 154, Mismatches: 1, Indels: 4
0.97 0.01 0.03
Matches are distributed among these distances:
155 27 0.18
156 33 0.21
157 36 0.23
158 58 0.38
ACGTcount: A:0.32, C:0.10, G:0.12, T:0.46
Consensus pattern (156 bp):
CAGAAATGGAAAATCAACCACCGAGGGTTAGTTTTTTTTAATCTCTTATTTTTATTTTGAATTTT
GTATCATTATTAGATTTTTCTTATATTGATAATAATTTACTGGTAATTTCAATATATATAGATTA
ACCATTTCATTGAGATTGCTTAGTAA
Found at i:87503 original size:20 final size:20
Alignment explanation
Indices: 87468--87550 Score: 132
Period size: 20 Copynumber: 4.2 Consensus size: 20
87458 AAATCGCAAC
*
87468 GCGATTTT-AGTTTCGCGTT
1 GCGATTTTCATTTTCGCGTT
87487 GCGATTTTCATTTTCGCGTT
1 GCGATTTTCATTTTCGCGTT
*
87507 GCGATTTTCATTTTTGCGTT
1 GCGATTTTCATTTTCGCGTT
*
87527 GCGATTTTCATTTTTGCGTT
1 GCGATTTTCATTTTCGCGTT
87547 GCGA
1 GCGA
87551 ATTTAAGTTT
Statistics
Matches: 61, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
19 8 0.13
20 53 0.87
ACGTcount: A:0.11, C:0.17, G:0.23, T:0.49
Consensus pattern (20 bp):
GCGATTTTCATTTTCGCGTT
Found at i:87529 original size:40 final size:39
Alignment explanation
Indices: 87468--87561 Score: 134
Period size: 40 Copynumber: 2.4 Consensus size: 39
87458 AAATCGCAAC
87468 GCGATTTTAGTTTCGCGTTGCGATTTTCATTTTCGCGTT
1 GCGATTTTAGTTTCGCGTTGCGATTTTCATTTTCGCGTT
* * *
87507 GCGATTTTCATTTTTGCGTTGCGATTTTCATTTTTGCGTT
1 GCGATTTT-AGTTTCGCGTTGCGATTTTCATTTTCGCGTT
*
87547 GCGAATTTAAGTTTC
1 GCG-ATTTTAGTTTC
87562 AGAAACTTCT
Statistics
Matches: 47, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
39 8 0.17
40 35 0.74
41 4 0.09
ACGTcount: A:0.13, C:0.16, G:0.21, T:0.50
Consensus pattern (39 bp):
GCGATTTTAGTTTCGCGTTGCGATTTTCATTTTCGCGTT
Found at i:89504 original size:4 final size:4
Alignment explanation
Indices: 89495--89540 Score: 56
Period size: 4 Copynumber: 11.5 Consensus size: 4
89485 TTTTTCGGCA
* * * *
89495 TTAT TTAT TTAT TTAT TTAT TTAC TGAT TTAT GTAT TAAT TTAT TT
1 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TT
89541 TCAGCGGCCC
Statistics
Matches: 34, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
4 34 1.00
ACGTcount: A:0.26, C:0.02, G:0.04, T:0.67
Consensus pattern (4 bp):
TTAT
Found at i:91269 original size:62 final size:60
Alignment explanation
Indices: 91148--91284 Score: 197
Period size: 62 Copynumber: 2.2 Consensus size: 60
91138 TTTTACATTG
91148 AAAGTTGATTTGTTTAATTGATGAGGAAATAAGATTTATTTTTTTGATTAATTGATTTGTA
1 AAAGTTGATTTGTTTAATTGAT-AGGAAATAAGATTTATTTTTTTGATTAATTGATTTGTA
* *
91209 AAAGTTGATTTGTTTAATTTGAT-GTAAATAAGA-TTATTTTTTGCTTGTTTAATTGATTTGTA
1 AAAGTTGATTTGTTTAA-TTGATAGGAAATAAGATTTA-TTTTT--TTGATTAATTGATTTGTA
91271 AAAGTTGATTTGTT
1 AAAGTTGATTTGTT
91285 GTTTCTAAAA
Statistics
Matches: 70, Mismatches: 2, Indels: 7
0.89 0.03 0.09
Matches are distributed among these distances:
59 3 0.04
60 14 0.20
61 17 0.24
62 36 0.51
ACGTcount: A:0.31, C:0.01, G:0.18, T:0.51
Consensus pattern (60 bp):
AAAGTTGATTTGTTTAATTGATAGGAAATAAGATTTATTTTTTTGATTAATTGATTTGTA
Found at i:91438 original size:34 final size:34
Alignment explanation
Indices: 91400--91493 Score: 170
Period size: 34 Copynumber: 2.8 Consensus size: 34
91390 TGAATTTGAC
91400 TTTCGCGTTGCGAATTTGACTATCGCAACGCTTA
1 TTTCGCGTTGCGAATTTGACTATCGCAACGCTTA
91434 TTTCGCGTTGCGAATTTGACTATCGCAACGCTTA
1 TTTCGCGTTGCGAATTTGACTATCGCAACGCTTA
* *
91468 TTTCGCGTTGCAAATTTGACTTTCGC
1 TTTCGCGTTGCGAATTTGACTATCGC
91494 GTTGATCGCA
Statistics
Matches: 58, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 58 1.00
ACGTcount: A:0.19, C:0.23, G:0.20, T:0.37
Consensus pattern (34 bp):
TTTCGCGTTGCGAATTTGACTATCGCAACGCTTA
Found at i:92564 original size:20 final size:20
Alignment explanation
Indices: 92515--92578 Score: 67
Period size: 20 Copynumber: 3.2 Consensus size: 20
92505 AAATAATGTA
* *
92515 CAACTTGAAAGTTAAATTCG
1 CAACATGAAAGTCAAATTCG
*
92535 CAACACGAAAGTCAAATTCG
1 CAACATGAAAGTCAAATTCG
**
92555 CAATGTGAAA-TCCAAATTCG
1 CAACATGAAAGT-CAAATTCG
92575 CAAC
1 CAAC
92579 GCGATTTTCG
Statistics
Matches: 36, Mismatches: 7, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
19 1 0.03
20 35 0.97
ACGTcount: A:0.42, C:0.22, G:0.14, T:0.22
Consensus pattern (20 bp):
CAACATGAAAGTCAAATTCG
Found at i:92663 original size:20 final size:20
Alignment explanation
Indices: 92638--92707 Score: 122
Period size: 20 Copynumber: 3.5 Consensus size: 20
92628 GTAATGCTTA
92638 TTTCGCGTTGCGAATTTGAC
1 TTTCGCGTTGCGAATTTGAC
92658 TTTCGCGTTGCGAATTTGAC
1 TTTCGCGTTGCGAATTTGAC
*
92678 TTTCGCGTTGCGAATTTAAC
1 TTTCGCGTTGCGAATTTGAC
*
92698 TTTCACGTTG
1 TTTCGCGTTG
92708 ATCGCAACAT
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 48 1.00
ACGTcount: A:0.16, C:0.20, G:0.23, T:0.41
Consensus pattern (20 bp):
TTTCGCGTTGCGAATTTGAC
Found at i:93003 original size:17 final size:18
Alignment explanation
Indices: 92981--93015 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
92971 GAAGCCGTTG
*
92981 TGATTGGGA-TTTGATTT
1 TGATTGCGAGTTTGATTT
92998 TGATTGCGAGTTTGATTT
1 TGATTGCGAGTTTGATTT
93016 CCTTTTGCTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.17, C:0.03, G:0.29, T:0.51
Consensus pattern (18 bp):
TGATTGCGAGTTTGATTT
Found at i:94747 original size:12 final size:12
Alignment explanation
Indices: 94726--94759 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
94716 GGTTGTGGGT
*
94726 TTTGAGATTGTG
1 TTTGATATTGTG
94738 TTTGATATTGTG
1 TTTGATATTGTG
*
94750 TTTGGTATTG
1 TTTGATATTG
94760 GAAATGTGGC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.15, C:0.00, G:0.29, T:0.56
Consensus pattern (12 bp):
TTTGATATTGTG
Found at i:101098 original size:20 final size:20
Alignment explanation
Indices: 101020--101098 Score: 54
Period size: 21 Copynumber: 3.9 Consensus size: 20
101010 TTGGTGCAGA
* *
101020 GGGAATCGATACCCTCAT-G
1 GGGAATCGATACCCCCTTAG
* *
101039 AGGGAA-CGATTCCCCTTTGAAG
1 -GGGAATCGATACCCCCTT--AG
* *
101061 GGGAACCGATTCCCCCCTTAG
1 GGGAATCGA-TACCCCCTTAG
101082 GGGAATCGATACCCCCT
1 GGGAATCGATACCCCCT
101099 GGGGTTCTGG
Statistics
Matches: 46, Mismatches: 8, Indels: 10
0.72 0.12 0.16
Matches are distributed among these distances:
19 8 0.17
20 12 0.26
21 15 0.33
22 4 0.09
23 7 0.15
ACGTcount: A:0.24, C:0.30, G:0.25, T:0.20
Consensus pattern (20 bp):
GGGAATCGATACCCCCTTAG
Found at i:104808 original size:19 final size:21
Alignment explanation
Indices: 104784--104836 Score: 83
Period size: 19 Copynumber: 2.6 Consensus size: 21
104774 ACTAAAACAT
104784 GTTGCGAATTTGAAATT-C-A
1 GTTGCGAATTTGAAATTCCGA
*
104803 GTTGCGAATTTGAAATTCCGT
1 GTTGCGAATTTGAAATTCCGA
104824 GTTGCGAATTTGA
1 GTTGCGAATTTGA
104837 CTATCGTGTT
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 17 0.55
20 1 0.03
21 13 0.42
ACGTcount: A:0.26, C:0.11, G:0.25, T:0.38
Consensus pattern (21 bp):
GTTGCGAATTTGAAATTCCGA
Found at i:104846 original size:20 final size:20
Alignment explanation
Indices: 104824--104919 Score: 138
Period size: 20 Copynumber: 4.8 Consensus size: 20
104814 GAAATTCCGT
*
104824 GTTGCGAATTTGACTATCGT
1 GTTGCGAATTTGACTATCGC
*
104844 GTTGCGTATTTGACTATCGC
1 GTTGCGAATTTGACTATCGC
* *
104864 GTTACGAATTTTGATTATCGC
1 GTTGCGAA-TTTGACTATCGC
*
104885 GTTGCGAATTTGGCTATCGC
1 GTTGCGAATTTGACTATCGC
104905 GTTGCGAATTTGACT
1 GTTGCGAATTTGACT
104920 TCTGTATTTC
Statistics
Matches: 66, Mismatches: 9, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
20 48 0.73
21 18 0.27
ACGTcount: A:0.19, C:0.17, G:0.25, T:0.40
Consensus pattern (20 bp):
GTTGCGAATTTGACTATCGC
Found at i:104877 original size:41 final size:40
Alignment explanation
Indices: 104828--104919 Score: 130
Period size: 41 Copynumber: 2.3 Consensus size: 40
104818 TTCCGTGTTG
* *
104828 CGAATTTGACTATCGTGTTGCGTATTTGACTATCGCGTTA
1 CGAATTTGACTATCGCGTTGCGAATTTGACTATCGCGTTA
* * *
104868 CGAATTTTGATTATCGCGTTGCGAATTTGGCTATCGCGTTG
1 CGAA-TTTGACTATCGCGTTGCGAATTTGACTATCGCGTTA
104909 CGAATTTGACT
1 CGAATTTGACT
104920 TCTGTATTTC
Statistics
Matches: 45, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
40 10 0.22
41 35 0.78
ACGTcount: A:0.20, C:0.17, G:0.24, T:0.39
Consensus pattern (40 bp):
CGAATTTGACTATCGCGTTGCGAATTTGACTATCGCGTTA
Found at i:108711 original size:18 final size:19
Alignment explanation
Indices: 108677--108712 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
108667 CATAGAATGT
*
108677 AAGATTATCATGGGAATAA
1 AAGATTACCATGGGAATAA
108696 AAGATTACCA-GGGAATA
1 AAGATTACCATGGGAATA
108713 GGATTACTGG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.47, C:0.08, G:0.22, T:0.22
Consensus pattern (19 bp):
AAGATTACCATGGGAATAA
Found at i:108765 original size:49 final size:49
Alignment explanation
Indices: 108709--108805 Score: 176
Period size: 49 Copynumber: 2.0 Consensus size: 49
108699 ATTACCAGGG
*
108709 AATAGGATTACTGGGAATGTTACATTACTGTGTTTGGTTGGTTTGGCAT
1 AATAGGATTACTAGGAATGTTACATTACTGTGTTTGGTTGGTTTGGCAT
*
108758 AATAGGATTACTAGGAATGTTATATTACTGTGTTTGGTTGGTTTGGCA
1 AATAGGATTACTAGGAATGTTACATTACTGTGTTTGGTTGGTTTGGCA
108806 GGAATGTAAT
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
49 46 1.00
ACGTcount: A:0.24, C:0.07, G:0.28, T:0.41
Consensus pattern (49 bp):
AATAGGATTACTAGGAATGTTACATTACTGTGTTTGGTTGGTTTGGCAT
Found at i:115759 original size:2 final size:2
Alignment explanation
Indices: 115744--115777 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
115734 TTAATAATTA
* *
115744 AT AT AT AA AC 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
115778 TTGAATTTGT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (2 bp):
AT
Found at i:116610 original size:18 final size:17
Alignment explanation
Indices: 116578--116624 Score: 60
Period size: 18 Copynumber: 2.6 Consensus size: 17
116568 TAAAAGTTAG
116578 ATATTATTTTA-AATAATT
1 ATATT-TTTTACAATAA-T
116596 ATATTTTTTACAATAAT
1 ATATTTTTTACAATAAT
116613 ATCATTTTTTAC
1 AT-ATTTTTTAC
116625 CTCATAAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
17 8 0.30
18 19 0.70
ACGTcount: A:0.38, C:0.06, G:0.00, T:0.55
Consensus pattern (17 bp):
ATATTTTTTACAATAAT
Found at i:117560 original size:3 final size:3
Alignment explanation
Indices: 117548--117633 Score: 165
Period size: 3 Copynumber: 29.0 Consensus size: 3
117538 ACTAGTAACT
117548 TAA T-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
117595 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
117634 ACAAGTTATA
Statistics
Matches: 82, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
2 2 0.02
3 80 0.98
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:118350 original size:22 final size:20
Alignment explanation
Indices: 118324--118380 Score: 60
Period size: 21 Copynumber: 2.6 Consensus size: 20
118314 ACAATATGAT
*
118324 AATTTTAAAAAAATATATATA
1 AATTTTAAAAAAAAAT-TATA
*
118345 AAATTTAATCAAAAAAATTATA
1 AATTTTAA--AAAAAAATTATA
118367 AATTTTATAAAAAA
1 AATTTTA-AAAAAA
118381 GAAAACACAA
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
21 12 0.40
22 10 0.33
23 8 0.27
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (20 bp):
AATTTTAAAAAAAAATTATA
Found at i:125664 original size:22 final size:22
Alignment explanation
Indices: 125638--125680 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
125628 TAATAAATTA
125638 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
125660 TTTAAAATAAATCAATCCATA
1 TTTAAAATAAATCAATCCATA
125681 CTAATAAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.51, C:0.14, G:0.00, T:0.35
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:125689 original size:22 final size:22
Alignment explanation
Indices: 125640--125688 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
125630 ATAAATTATT
**
125640 TAAAATAAATCAATCCATATTT
1 TAAAATAAATCAATCCATATAA
125662 TAAAATAAATCAATCCATACTAA
1 TAAAATAAATCAATCCATA-TAA
125685 TAAA
1 TAAA
125689 TTATTTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 19 0.79
23 5 0.21
ACGTcount: A:0.55, C:0.14, G:0.00, T:0.31
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:125779 original size:32 final size:32
Alignment explanation
Indices: 125740--125869 Score: 172
Period size: 32 Copynumber: 4.4 Consensus size: 32
125730 CAATCCATAT
* *
125740 TTTAAAATAAATTAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATTCATACTAATAAATTA
125772 TTTAAAATAAATCAA-TC---C--AT--A-T-
1 TTTAAAATAAATCAATTCATACTAATAAATTA
125794 TTTAAAATAAATCAATTCATACTAATAAATTA
1 TTTAAAATAAATCAATTCATACTAATAAATTA
125826 TTTAAAATAAATCAATTCATACTAATAAATTA
1 TTTAAAATAAATCAATTCATACTAATAAATTA
125858 TTTAAAATAAAT
1 TTTAAAATAAAT
125870 TATTTTAAAA
Statistics
Matches: 86, Mismatches: 2, Indels: 20
0.80 0.02 0.19
Matches are distributed among these distances:
22 15 0.17
23 3 0.03
24 1 0.01
26 3 0.03
28 3 0.03
30 1 0.01
31 2 0.02
32 58 0.67
ACGTcount: A:0.53, C:0.09, G:0.00, T:0.38
Consensus pattern (32 bp):
TTTAAAATAAATCAATTCATACTAATAAATTA
Found at i:125792 original size:54 final size:54
Alignment explanation
Indices: 125723--125846 Score: 221
Period size: 54 Copynumber: 2.3 Consensus size: 54
125713 CAACTACAAT
*
125723 AATAAATCAATCCATATTTTAAAATAAATTAATCCATACTAATAAATTATTTAA
1 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
*
125777 AATAAATCAATCCATATTTTAAAATAAATCAATTCATACTAATAAATTATTTAA
1 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
*
125831 AATAAATCAATTCATA
1 AATAAATCAATCCATA
125847 CTAATAAATT
Statistics
Matches: 67, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
54 67 1.00
ACGTcount: A:0.52, C:0.11, G:0.00, T:0.36
Consensus pattern (54 bp):
AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
Found at i:125797 original size:22 final size:22
Alignment explanation
Indices: 125772--125814 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
125762 TAATAAATTA
125772 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
*
125794 TTTAAAATAAATCAATTCATA
1 TTTAAAATAAATCAATCCATA
125815 CTAATAAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.51, C:0.12, G:0.00, T:0.37
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:125820 original size:18 final size:18
Alignment explanation
Indices: 125799--125855 Score: 68
Period size: 18 Copynumber: 3.4 Consensus size: 18
125789 CATATTTTAA
125799 AATAAATCAATTCATACT
1 AATAAATCAATTCATACT
* *
125817 AATAAAT-TATT--TA-A
1 AATAAATCAATTCATACT
125831 AATAAATCAATTCATACT
1 AATAAATCAATTCATACT
125849 AATAAAT
1 AATAAAT
125856 TATTTAAAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 8
0.72 0.09 0.19
Matches are distributed among these distances:
14 7 0.23
15 5 0.16
17 5 0.16
18 14 0.45
ACGTcount: A:0.54, C:0.11, G:0.00, T:0.35
Consensus pattern (18 bp):
AATAAATCAATTCATACT
Found at i:125823 original size:22 final size:22
Alignment explanation
Indices: 125774--125822 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
125764 ATAAATTATT
**
125774 TAAAATAAATCAATCCATATTT
1 TAAAATAAATCAATCCATATAA
*
125796 TAAAATAAATCAATTCATACTAA
1 TAAAATAAATCAATCCATA-TAA
125819 TAAA
1 TAAA
125823 TTATTTAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 18 0.78
23 5 0.22
ACGTcount: A:0.55, C:0.12, G:0.00, T:0.33
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:125878 original size:15 final size:15
Alignment explanation
Indices: 125817--125966 Score: 133
Period size: 15 Copynumber: 9.5 Consensus size: 15
125807 AATTCATACT
125817 AATAAATTA-TTTAA
1 AATAAATTATTTTAA
* * *
125831 AATAAATCAATTCATACT
1 AATAAAT-TATT-TTA-A
125849 AATAAATTA-TTTAA
1 AATAAATTATTTTAA
125863 AATAAATTATTTTAAAATA
1 AATAAATTATTTT---A-A
*
125882 AATAAATCCATATTTTAT
1 AATAAAT---TATTTTAA
*
125900 AATAATTTATTTTAA
1 AATAAATTATTTTAA
* *
125915 AATAATTTATTTTAT
1 AATAAATTATTTTAA
125930 AATAAATTATTTTAA
1 AATAAATTATTTTAA
125945 AATAAATTATTTTAA
1 AATAAATTATTTTAA
125960 AATAAAT
1 AATAAAT
125967 AACCTTATTA
Statistics
Matches: 112, Mismatches: 12, Indels: 23
0.76 0.08 0.16
Matches are distributed among these distances:
14 16 0.14
15 62 0.55
16 2 0.02
17 3 0.03
18 14 0.12
19 9 0.08
22 6 0.05
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (15 bp):
AATAAATTATTTTAA
Found at i:128577 original size:36 final size:36
Alignment explanation
Indices: 128537--128629 Score: 168
Period size: 36 Copynumber: 2.6 Consensus size: 36
128527 CAGTAGAAAA
128537 CCCGGAGGCATGCCTGGTGGGTTCCAGGGTGGAATG
1 CCCGGAGGCATGCCTGGTGGGTTCCAGGGTGGAATG
*
128573 CCCGGAGGCATGCCTGGTGGGTTCCCGGGTGGAATG
1 CCCGGAGGCATGCCTGGTGGGTTCCAGGGTGGAATG
*
128609 CCCGGAGGCATGCCGGGTGGG
1 CCCGGAGGCATGCCTGGTGGG
128630 ATGCCCGGAG
Statistics
Matches: 55, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
36 55 1.00
ACGTcount: A:0.12, C:0.25, G:0.46, T:0.17
Consensus pattern (36 bp):
CCCGGAGGCATGCCTGGTGGGTTCCAGGGTGGAATG
Found at i:128585 original size:12 final size:12
Alignment explanation
Indices: 128570--128646 Score: 57
Period size: 12 Copynumber: 6.4 Consensus size: 12
128560 CCAGGGTGGA
128570 ATGCCCGGAGGC
1 ATGCCCGGAGGC
* *
128582 ATGCCTGGTGG-
1 ATGCCCGGAGGC
* * * *
128593 GTTCCCGGGTGGA
1 ATGCCC-GGAGGC
128606 ATGCCCGGAGGC
1 ATGCCCGGAGGC
* * *
128618 ATGCCGGGTGGG
1 ATGCCCGGAGGC
128630 ATGCCCGGAGGC
1 ATGCCCGGAGGC
128642 ATGCC
1 ATGCC
128647 AGGAAATGTT
Statistics
Matches: 48, Mismatches: 15, Indels: 4
0.72 0.22 0.06
Matches are distributed among these distances:
11 3 0.06
12 41 0.85
13 4 0.08
ACGTcount: A:0.13, C:0.27, G:0.44, T:0.16
Consensus pattern (12 bp):
ATGCCCGGAGGC
Found at i:128624 original size:24 final size:24
Alignment explanation
Indices: 128597--128646 Score: 91
Period size: 24 Copynumber: 2.1 Consensus size: 24
128587 TGGTGGGTTC
128597 CCGGGTGGAATGCCCGGAGGCATG
1 CCGGGTGGAATGCCCGGAGGCATG
*
128621 CCGGGTGGGATGCCCGGAGGCATG
1 CCGGGTGGAATGCCCGGAGGCATG
128645 CC
1 CC
128647 AGGAAATGTT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.14, C:0.28, G:0.46, T:0.12
Consensus pattern (24 bp):
CCGGGTGGAATGCCCGGAGGCATG
Found at i:135748 original size:24 final size:24
Alignment explanation
Indices: 135716--135766 Score: 93
Period size: 24 Copynumber: 2.1 Consensus size: 24
135706 TAACTTCAAT
*
135716 CTTCTCCTTGTCCACCTCAATACC
1 CTTCGCCTTGTCCACCTCAATACC
135740 CTTCGCCTTGTCCACCTCAATACC
1 CTTCGCCTTGTCCACCTCAATACC
135764 CTT
1 CTT
135767 GTGAGAAATT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.16, C:0.45, G:0.06, T:0.33
Consensus pattern (24 bp):
CTTCGCCTTGTCCACCTCAATACC
Found at i:137924 original size:21 final size:21
Alignment explanation
Indices: 137884--137926 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
137874 GAGCTATGGA
* *
137884 TTTGAAGTAAGGCGCCTTGAT
1 TTTGAAGTAAAGCGCATTGAT
*
137905 TTTGAAGTAAAGCTCATTGAT
1 TTTGAAGTAAAGCGCATTGAT
137926 T
1 T
137927 CTTAATTGAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.28, C:0.12, G:0.23, T:0.37
Consensus pattern (21 bp):
TTTGAAGTAAAGCGCATTGAT
Found at i:139619 original size:25 final size:25
Alignment explanation
Indices: 139590--139645 Score: 94
Period size: 25 Copynumber: 2.2 Consensus size: 25
139580 AAAGTGTATG
*
139590 ATGGTGGATGTGGATGAATGGTCTA
1 ATGGTGAATGTGGATGAATGGTCTA
*
139615 ATGGTGAATGTGGATGAATGGTCTG
1 ATGGTGAATGTGGATGAATGGTCTA
139640 ATGGTG
1 ATGGTG
139646 TAGCAAATGG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.23, C:0.04, G:0.41, T:0.32
Consensus pattern (25 bp):
ATGGTGAATGTGGATGAATGGTCTA
Found at i:139740 original size:11 final size:11
Alignment explanation
Indices: 139724--139748 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
139714 AAAATGGTAA
139724 AAACAGTAAAT
1 AAACAGTAAAT
139735 AAACAGTAAAT
1 AAACAGTAAAT
139746 AAA
1 AAA
139749 ATGATAAGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.68, C:0.08, G:0.08, T:0.16
Consensus pattern (11 bp):
AAACAGTAAAT
Found at i:140097 original size:24 final size:24
Alignment explanation
Indices: 140070--140125 Score: 103
Period size: 24 Copynumber: 2.3 Consensus size: 24
140060 GAACGTTTGA
*
140070 TTATGTTTGTTCGGTTATGTTCGT
1 TTATGTTCGTTCGGTTATGTTCGT
140094 TTATGTTCGTTCGGTTATGTTCGT
1 TTATGTTCGTTCGGTTATGTTCGT
140118 TTATGTTC
1 TTATGTTC
140126 ATTCATTTAC
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.09, C:0.11, G:0.23, T:0.57
Consensus pattern (24 bp):
TTATGTTCGTTCGGTTATGTTCGT
Found at i:140115 original size:14 final size:14
Alignment explanation
Indices: 140070--140118 Score: 61
Period size: 14 Copynumber: 3.8 Consensus size: 14
140060 GAACGTTTGA
*
140070 TTATGTTTGTTCGG
1 TTATGTTCGTTCGG
140084 TTATGTTCG-T---
1 TTATGTTCGTTCGG
140094 TTATGTTCGTTCGG
1 TTATGTTCGTTCGG
140108 TTATGTTCGTT
1 TTATGTTCGTT
140119 TATGTTCATT
Statistics
Matches: 30, Mismatches: 1, Indels: 8
0.77 0.03 0.21
Matches are distributed among these distances:
10 9 0.30
11 1 0.03
13 1 0.03
14 19 0.63
ACGTcount: A:0.08, C:0.10, G:0.24, T:0.57
Consensus pattern (14 bp):
TTATGTTCGTTCGG
Found at i:140139 original size:24 final size:24
Alignment explanation
Indices: 140083--140141 Score: 73
Period size: 24 Copynumber: 2.5 Consensus size: 24
140073 TGTTTGTTCG
* * *
140083 GTTATGTTCGTTTATGTTCGTTCG
1 GTTACGTTCGTTTATGTTCATTCA
*
140107 GTTATGTTCGTTTATGTTCATTCA
1 GTTACGTTCGTTTATGTTCATTCA
*
140131 TTTACGTTCGT
1 GTTACGTTCGT
140142 GACCAATTTG
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.12, C:0.14, G:0.20, T:0.54
Consensus pattern (24 bp):
GTTACGTTCGTTTATGTTCATTCA
Found at i:141070 original size:16 final size:16
Alignment explanation
Indices: 141018--141072 Score: 83
Period size: 16 Copynumber: 3.4 Consensus size: 16
141008 GGGTCTCCAA
141018 CGTTTATGTTCATGTT
1 CGTTTATGTTCATGTT
* *
141034 CATTTATGTTCGTGTT
1 CGTTTATGTTCATGTT
141050 CGTTTATGTTCATGTT
1 CGTTTATGTTCATGTT
*
141066 TGTTTAT
1 CGTTTAT
141073 ATTTGTTTAT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 34 1.00
ACGTcount: A:0.13, C:0.11, G:0.18, T:0.58
Consensus pattern (16 bp):
CGTTTATGTTCATGTT
Found at i:141858 original size:24 final size:24
Alignment explanation
Indices: 141822--141903 Score: 137
Period size: 24 Copynumber: 3.4 Consensus size: 24
141812 CACAAACCAC
*
141822 CTTAGCTCGCTAGCTCCTCTCGAA
1 CTTAGCTCGCTAGCTCCTCTCGGA
*
141846 CTTGGCTCGCTAGCTCCTCTCGGA
1 CTTAGCTCGCTAGCTCCTCTCGGA
*
141870 CTTAGCTCACTAGCTCCTCTCGGA
1 CTTAGCTCGCTAGCTCCTCTCGGA
141894 CTTAGCTCGC
1 CTTAGCTCGC
141904 AACTCCTTGA
Statistics
Matches: 53, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 53 1.00
ACGTcount: A:0.13, C:0.38, G:0.20, T:0.29
Consensus pattern (24 bp):
CTTAGCTCGCTAGCTCCTCTCGGA
Found at i:153639 original size:221 final size:222
Alignment explanation
Indices: 153276--153807 Score: 759
Period size: 221 Copynumber: 2.4 Consensus size: 222
153266 GCTGTCACTC
* * *
153276 AGGGAATAT-TAGATAT-GGGGATGTTGATCCAATGAATCGGGGCAGACTTGTTCCGTTGTCACT
1 AGGGAATATCT-GATCTGGGGGA-GTTGATCCATTGAATCGGGGCAGACTTGTTCCGCTGTCACT
* * * * *
153339 CAGGGAATATCAAATCTTGGAAGATAGTGATTTGTTTCATTTCTTCTAAGGGAATATAAGATCTG
64 CAGGGAATATCAAATCTTGGAAGAGAGTGATTTGTTCCACTTCATCTAAAGGAATATAAGATCTG
* * *
153404 ACGGAGCTGATCCATTGAATCGGGGCAGACTTGTTCCCCTGTCACTCAGGGAA-ATCAAATCTTG
129 ACGGAGCTGATCCATTGAATCGAGACAGACTTGTTCCACTGTCACTCAGGGAATATCAAATCTTG
* *
153468 GAAGAGAGTGATCTGTTTCGCTTCTTCTA
194 GAAGAGAGTGATATGTTTCGCTTCTTCCA
*
153497 AGGGAATATCTGATCTGGGGGAGTTGATCCATTGAATCGGGGCAGACTTGTTTCGCTGTCACTCA
1 AGGGAATATCTGATCTGGGGGAGTTGATCCATTGAATCGGGGCAGACTTGTTCCGCTGTCACTCA
*
153562 GGGAATATCAAATATTGGAAGAGAGTGATTTGTTCCACTTCATCTAAAGGAATATCAA-ATCTG-
66 GGGAATATCAAATCTTGGAAGAGAGTGATTTGTTCCACTTCATCTAAAGGAATAT-AAGATCTGA
* * * *
153625 GGCGAGTTGATCCATTGAATCGAGACAGACTTGTTCCATTGTCACTGAGGGAATATCAAATCTTG
130 CG-GAGCTGATCCATTGAATCGAGACAGACTTGTTCCACTGTCACTCAGGGAATATCAAATCTTG
*
153690 GAAGAGAGTGATATGTTTCGCTTTTTCCA
194 GAAGAGAGTGATATGTTTCGCTTCTTCCA
* ** *
153719 AGGGAATATCCGATCTGGGGGAGTTGATTTATTGAATCGGGGCAGACTTGTTCCACTGTCACTCA
1 AGGGAATATCTGATCTGGGGGAGTTGATCCATTGAATCGGGGCAGACTTGTTCCGCTGTCACTCA
* *
153784 GGGAATATTAAATCTTGGAGGAGA
66 GGGAATATCAAATCTTGGAAGAGA
153808 AGGACATGTT
Statistics
Matches: 278, Mismatches: 28, Indels: 9
0.88 0.09 0.03
Matches are distributed among these distances:
220 1 0.00
221 151 0.54
222 126 0.45
ACGTcount: A:0.27, C:0.16, G:0.26, T:0.30
Consensus pattern (222 bp):
AGGGAATATCTGATCTGGGGGAGTTGATCCATTGAATCGGGGCAGACTTGTTCCGCTGTCACTCA
GGGAATATCAAATCTTGGAAGAGAGTGATTTGTTCCACTTCATCTAAAGGAATATAAGATCTGAC
GGAGCTGATCCATTGAATCGAGACAGACTTGTTCCACTGTCACTCAGGGAATATCAAATCTTGGA
AGAGAGTGATATGTTTCGCTTCTTCCA
Found at i:153817 original size:111 final size:111
Alignment explanation
Indices: 153276--153807 Score: 708
Period size: 111 Copynumber: 4.8 Consensus size: 111
153266 GCTGTCACTC
* * * **
153276 AGGGAATATTAGATAT-GGGGATGTTGATCCAATGAATCGGGGCAGACTTGTTCCGTTGTCACTC
1 AGGGAATATCAGATCTGGGGGA-GTTGATCCATTGAATCGGGGCAGACTTGTTCCACTGTCACTC
* * **
153340 AGGGAATATCAAATCTTGGAAGATAGTGATTTGTTTCATTTCTTCTA
65 AGGGAATATCAAATCTTGGAAGAGAGTGATATGTTTCGCTTCTTCTA
* ** * *
153387 AGGGAATATAAGATCTGACGGAGCTGATCCATTGAATCGGGGCAGACTTGTTCCCCTGTCACTCA
1 AGGGAATATCAGATCTGGGGGAGTTGATCCATTGAATCGGGGCAGACTTGTTCCACTGTCACTCA
*
153452 GGGAA-ATCAAATCTTGGAAGAGAGTGATCTGTTTCGCTTCTTCTA
66 GGGAATATCAAATCTTGGAAGAGAGTGATATGTTTCGCTTCTTCTA
* * *
153497 AGGGAATATCTGATCTGGGGGAGTTGATCCATTGAATCGGGGCAGACTTGTTTCGCTGTCACTCA
1 AGGGAATATCAGATCTGGGGGAGTTGATCCATTGAATCGGGGCAGACTTGTTCCACTGTCACTCA
* * * * *
153562 GGGAATATCAAATATTGGAAGAGAGTGATTTGTTCCACTTCATCTA
66 GGGAATATCAAATCTTGGAAGAGAGTGATATGTTTCGCTTCTTCTA
* * * * * * *
153608 AAGGAATATCAAATCTGGGCGAGTTGATCCATTGAATCGAGACAGACTTGTTCCATTGTCACTGA
1 AGGGAATATCAGATCTGGGGGAGTTGATCCATTGAATCGGGGCAGACTTGTTCCACTGTCACTCA
* *
153673 GGGAATATCAAATCTTGGAAGAGAGTGATATGTTTCGCTTTTTCCA
66 GGGAATATCAAATCTTGGAAGAGAGTGATATGTTTCGCTTCTTCTA
* **
153719 AGGGAATATCCGATCTGGGGGAGTTGATTTATTGAATCGGGGCAGACTTGTTCCACTGTCACTCA
1 AGGGAATATCAGATCTGGGGGAGTTGATCCATTGAATCGGGGCAGACTTGTTCCACTGTCACTCA
* *
153784 GGGAATATTAAATCTTGGAGGAGA
66 GGGAATATCAAATCTTGGAAGAGA
153808 AGGACATGTT
Statistics
Matches: 366, Mismatches: 53, Indels: 4
0.87 0.13 0.01
Matches are distributed among these distances:
110 99 0.27
111 264 0.72
112 3 0.01
ACGTcount: A:0.27, C:0.16, G:0.26, T:0.30
Consensus pattern (111 bp):
AGGGAATATCAGATCTGGGGGAGTTGATCCATTGAATCGGGGCAGACTTGTTCCACTGTCACTCA
GGGAATATCAAATCTTGGAAGAGAGTGATATGTTTCGCTTCTTCTA
Found at i:162082 original size:19 final size:21
Alignment explanation
Indices: 162045--162087 Score: 63
Period size: 20 Copynumber: 2.1 Consensus size: 21
162035 TAACTTTTTC
162045 TTTTATCTTTCATTATTAA-T
1 TTTTATCTTTCATTATTAACT
*
162065 TTTTCTCTTTCATT-TTAACT
1 TTTTATCTTTCATTATTAACT
162085 TTT
1 TTT
162088 ACCTTTTCTC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 4 0.19
20 17 0.81
ACGTcount: A:0.19, C:0.14, G:0.00, T:0.67
Consensus pattern (21 bp):
TTTTATCTTTCATTATTAACT
Found at i:162093 original size:19 final size:20
Alignment explanation
Indices: 162044--162093 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
162034 TTAACTTTTT
*
162044 CTTTTATCTTTCATTATTAA
1 CTTTTACCTTTCATTATTAA
*
162064 -TTTTTCTCTTTCATT-TTAA
1 CTTTTAC-CTTTCATTATTAA
162083 CTTTTACCTTT
1 CTTTTACCTTT
162094 TCTCTTTCTT
Statistics
Matches: 25, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
19 12 0.48
20 13 0.52
ACGTcount: A:0.18, C:0.18, G:0.00, T:0.64
Consensus pattern (20 bp):
CTTTTACCTTTCATTATTAA
Found at i:167425 original size:99 final size:98
Alignment explanation
Indices: 167274--167467 Score: 307
Period size: 99 Copynumber: 2.0 Consensus size: 98
167264 TAGCTGAATT
167274 ACCTTTATCAGGCTACCTAAATCTTATCCATAAAGTCGGGGCATTTAACCAATTGCTCTAGAGGG
1 ACCTTTATCAGGCTACCTAAATCTTATCCATAAAGTCGGGGCATTTAACCAATTGCTCTAGAGGG
*** *
167339 ACCGTTCAAGCTTTATTGTATATATAATATAGTC
66 ACAACTCAAGCTTTATTGTATACAT-ATATAGTC
* ** *
167373 ACCTTTATCAGGTTAGTTGAATCTTATCCATAAAGTCGGGGCATTTAACCAATTGCTCTAGAGGG
1 ACCTTTATCAGGCTACCTAAATCTTATCCATAAAGTCGGGGCATTTAACCAATTGCTCTAGAGGG
167438 ACAACTCAAGCTTTATTGTATACATATATA
66 ACAACTCAAGCTTTATTGTATACATATATA
167468 ATTACATTCT
Statistics
Matches: 87, Mismatches: 8, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
98 5 0.06
99 82 0.94
ACGTcount: A:0.31, C:0.19, G:0.16, T:0.34
Consensus pattern (98 bp):
ACCTTTATCAGGCTACCTAAATCTTATCCATAAAGTCGGGGCATTTAACCAATTGCTCTAGAGGG
ACAACTCAAGCTTTATTGTATACATATATAGTC
Found at i:173706 original size:5 final size:6
Alignment explanation
Indices: 173691--173715 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
173681 ATTGGGTCTG
173691 AAAAAT AAAAAT AAAAAT AAAAAT A
1 AAAAAT AAAAAT AAAAAT AAAAAT A
173716 TTAATTAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (6 bp):
AAAAAT
Found at i:173738 original size:3 final size:3
Alignment explanation
Indices: 173694--173758 Score: 51
Period size: 3 Copynumber: 21.3 Consensus size: 3
173684 GGGTCTGAAA
* * * * *
173694 AAT AAA AAT AAA AAT AAA AAT ATT AATT AAT AAT TAT AAAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AA-T AAT AAT AAT -AAT AAT AAT
*
173741 AAT -AT AAT GAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT A
173759 TATTAAAAAA
Statistics
Matches: 47, Mismatches: 12, Indels: 6
0.72 0.18 0.09
Matches are distributed among these distances:
2 2 0.04
3 40 0.85
4 5 0.11
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:173755 original size:14 final size:14
Alignment explanation
Indices: 173701--173760 Score: 59
Period size: 14 Copynumber: 4.2 Consensus size: 14
173691 AAAAATAAAA
* *
173701 ATAAAAATAAAAAT
1 ATAATAATAATAAT
*
173715 ATTAATTAATAATTAT
1 A-TAA-TAATAATAAT
173731 A-AATAATAATAAT
1 ATAATAATAATAAT
*
173744 ATAATGATAATAAT
1 ATAATAATAATAAT
173758 ATA
1 ATA
173761 TTAAAAAACA
Statistics
Matches: 38, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
13 10 0.26
14 17 0.45
15 3 0.08
16 8 0.21
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (14 bp):
ATAATAATAATAAT
Found at i:174484 original size:109 final size:109
Alignment explanation
Indices: 174293--174510 Score: 436
Period size: 109 Copynumber: 2.0 Consensus size: 109
174283 AAAAACAACT
174293 CAATAAGAAATTACATGTCGAGAGGGGATGAAAAAGGTGTTTAATAAAATGTGTGAGAGACATAA
1 CAATAAGAAATTACATGTCGAGAGGGGATGAAAAAGGTGTTTAATAAAATGTGTGAGAGACATAA
174358 CGTATATGTTAAATATTTTGTGTTGCAAAAGATATACAAATGAA
66 CGTATATGTTAAATATTTTGTGTTGCAAAAGATATACAAATGAA
174402 CAATAAGAAATTACATGTCGAGAGGGGATGAAAAAGGTGTTTAATAAAATGTGTGAGAGACATAA
1 CAATAAGAAATTACATGTCGAGAGGGGATGAAAAAGGTGTTTAATAAAATGTGTGAGAGACATAA
174467 CGTATATGTTAAATATTTTGTGTTGCAAAAGATATACAAATGAA
66 CGTATATGTTAAATATTTTGTGTTGCAAAAGATATACAAATGAA
174511 AGATTTGGCT
Statistics
Matches: 109, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
109 109 1.00
ACGTcount: A:0.43, C:0.06, G:0.22, T:0.28
Consensus pattern (109 bp):
CAATAAGAAATTACATGTCGAGAGGGGATGAAAAAGGTGTTTAATAAAATGTGTGAGAGACATAA
CGTATATGTTAAATATTTTGTGTTGCAAAAGATATACAAATGAA
Found at i:176226 original size:43 final size:43
Alignment explanation
Indices: 176121--176271 Score: 169
Period size: 43 Copynumber: 3.5 Consensus size: 43
176111 CTATTATACA
* ** ** * *
176121 TTTTTGGAACAAACGCTACAAAAAATCAGATCTATAGTGGTG-
1 TTTTTGAAACAAACGCCGCAAAATGTCAGATCTATAGAGGAGT
* *
176163 TTTTTGAAACAAACGTCGCAAAATGTCAGATCTATAGAGGCGT
1 TTTTTGAAACAAACGCCGCAAAATGTCAGATCTATAGAGGAGT
* * *
176206 TTTTTGAAACAAATGCCGCAAAATGTCATATCTATAGCGGAGT
1 TTTTTGAAACAAACGCCGCAAAATGTCAGATCTATAGAGGAGT
* *
176249 TTTTGGATACAAACGCCGCAAAA
1 TTTTTGAAACAAACGCCGCAAAA
176272 GGGCTCATGA
Statistics
Matches: 92, Mismatches: 16, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
42 34 0.37
43 58 0.63
ACGTcount: A:0.36, C:0.17, G:0.19, T:0.28
Consensus pattern (43 bp):
TTTTTGAAACAAACGCCGCAAAATGTCAGATCTATAGAGGAGT
Found at i:189032 original size:19 final size:19
Alignment explanation
Indices: 189008--189044 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
188998 ATGACCAACA
*
189008 AAATCGCAATGCGATCTCT
1 AAATCGCAACGCGATCTCT
189027 AAATCGCAACGCGATCTC
1 AAATCGCAACGCGATCTC
189045 CATTATCGCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.32, C:0.30, G:0.16, T:0.22
Consensus pattern (19 bp):
AAATCGCAACGCGATCTCT
Found at i:189157 original size:20 final size:20
Alignment explanation
Indices: 189130--189182 Score: 79
Period size: 20 Copynumber: 2.6 Consensus size: 20
189120 GATTTTAGAT
189130 AATCGCAATGCGAATATGTA
1 AATCGCAATGCGAATATGTA
* *
189150 AGTCGCAATGCAAATATGTA
1 AATCGCAATGCGAATATGTA
*
189170 AATCGCAACGCGA
1 AATCGCAATGCGA
189183 TAACACTTGA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.40, C:0.19, G:0.21, T:0.21
Consensus pattern (20 bp):
AATCGCAATGCGAATATGTA
Found at i:189197 original size:21 final size:20
Alignment explanation
Indices: 189171--189245 Score: 73
Period size: 21 Copynumber: 3.6 Consensus size: 20
189161 AAATATGTAA
189171 ATCGCAACGCGATAACACTTG
1 ATCGCAACGCGATAACAC-TG
*
189192 ATCGCAACGCGAT-TCTGACT-
1 ATCGCAACGCGATAAC--ACTG
* *
189212 ATCGCAACACGATAATACGTG
1 ATCGCAACGCGATAACAC-TG
189233 ATCGCAACGCGAT
1 ATCGCAACGCGAT
189246 TCTGACTATC
Statistics
Matches: 44, Mismatches: 5, Indels: 10
0.75 0.08 0.17
Matches are distributed among these distances:
19 2 0.05
20 14 0.32
21 26 0.59
22 2 0.05
ACGTcount: A:0.32, C:0.28, G:0.20, T:0.20
Consensus pattern (20 bp):
ATCGCAACGCGATAACACTG
Found at i:189216 original size:41 final size:41
Alignment explanation
Indices: 189171--189261 Score: 155
Period size: 41 Copynumber: 2.2 Consensus size: 41
189161 AAATATGTAA
*
189171 ATCGCAACGCGATAACACTTGATCGCAACGCGATTCTGACT
1 ATCGCAACGCGATAACACGTGATCGCAACGCGATTCTGACT
* *
189212 ATCGCAACACGATAATACGTGATCGCAACGCGATTCTGACT
1 ATCGCAACGCGATAACACGTGATCGCAACGCGATTCTGACT
189253 ATCGCAACG
1 ATCGCAACG
189262 AGATTCTGAC
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 46 1.00
ACGTcount: A:0.31, C:0.29, G:0.20, T:0.21
Consensus pattern (41 bp):
ATCGCAACGCGATAACACGTGATCGCAACGCGATTCTGACT
Found at i:189217 original size:20 final size:20
Alignment explanation
Indices: 189192--189277 Score: 111
Period size: 20 Copynumber: 4.2 Consensus size: 20
189182 ATAACACTTG
189192 ATCGCAACGCGATTCTGACT
1 ATCGCAACGCGATTCTGACT
* **
189212 ATCGCAACACGATAAT-ACGT
1 ATCGCAACGCGATTCTGAC-T
189232 GATCGCAACGCGATTCTGACT
1 -ATCGCAACGCGATTCTGACT
*
189253 ATCGCAACGAGATTCTGACT
1 ATCGCAACGCGATTCTGACT
189273 ATCGC
1 ATCGC
189278 GTTGCGATAA
Statistics
Matches: 56, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
19 2 0.04
20 38 0.68
21 14 0.25
22 2 0.04
ACGTcount: A:0.29, C:0.28, G:0.20, T:0.23
Consensus pattern (20 bp):
ATCGCAACGCGATTCTGACT
Found at i:189501 original size:21 final size:22
Alignment explanation
Indices: 189440--189518 Score: 133
Period size: 22 Copynumber: 3.6 Consensus size: 22
189430 TCACTCTCTA
*
189440 CGGCGACATCCGTCCCCATCTC
1 CGGCGAAATCCGTCCCCATCTC
*
189462 CGGCGAAATCCGTCCCCATTTC
1 CGGCGAAATCCGTCCCCATCTC
189484 CGGCGAAATCCG-CCCCATCTC
1 CGGCGAAATCCGTCCCCATCTC
189505 CGGCGAAATCCGTC
1 CGGCGAAATCCGTC
189519 TATCTCTATC
Statistics
Matches: 53, Mismatches: 3, Indels: 2
0.91 0.05 0.03
Matches are distributed among these distances:
21 20 0.38
22 33 0.62
ACGTcount: A:0.18, C:0.44, G:0.20, T:0.18
Consensus pattern (22 bp):
CGGCGAAATCCGTCCCCATCTC
Found at i:189956 original size:20 final size:19
Alignment explanation
Indices: 189918--189967 Score: 73
Period size: 20 Copynumber: 2.6 Consensus size: 19
189908 TCAAATTTGA
**
189918 GTTGCGATAATCATTTCGT
1 GTTGCGATTTTCATTTCGT
189937 GTTGCGATTTTCATTTTCGT
1 GTTGCGATTTTCA-TTTCGT
189957 GTTGCGATTTT
1 GTTGCGATTTT
189968 AAGTTTCAGA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
19 11 0.39
20 17 0.61
ACGTcount: A:0.14, C:0.14, G:0.22, T:0.50
Consensus pattern (19 bp):
GTTGCGATTTTCATTTCGT
Found at i:189974 original size:20 final size:20
Alignment explanation
Indices: 189931--189974 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
189921 GCGATAATCA
* *
189931 TTTCGTGTTGCGATTTTCAT
1 TTTCGTGTTGCGATTTTAAG
189951 TTTCGTGTTGCGATTTTAAG
1 TTTCGTGTTGCGATTTTAAG
189971 TTTC
1 TTTC
189975 AGAAACTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.11, C:0.14, G:0.20, T:0.55
Consensus pattern (20 bp):
TTTCGTGTTGCGATTTTAAG
Found at i:191584 original size:21 final size:21
Alignment explanation
Indices: 191560--191599 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
191550 ATGGCGTGAG
* *
191560 GAGGTAGCTACTTTACGTGGT
1 GAGGTAGCGACTCTACGTGGT
191581 GAGGTAGCGACTCTACGTG
1 GAGGTAGCGACTCTACGTG
191600 AGATGGTAGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.20, C:0.17, G:0.35, T:0.28
Consensus pattern (21 bp):
GAGGTAGCGACTCTACGTGGT
Found at i:191845 original size:31 final size:31
Alignment explanation
Indices: 191789--191850 Score: 90
Period size: 31 Copynumber: 2.0 Consensus size: 31
191779 TTGTCTTTGT
*
191789 TTTGTCTTTTGGTTGAAGTTAGTAAATTCATA
1 TTTGTCTTTTGGTTG-ACTTAGTAAATTCATA
191821 TTTGTCTTTTGGATTG-CTTAGTAAATTCAT
1 TTTGTCTTTTGG-TTGACTTAGTAAATTCAT
191851 TCGGTAGTAG
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
31 13 0.46
32 12 0.43
33 3 0.11
ACGTcount: A:0.23, C:0.08, G:0.18, T:0.52
Consensus pattern (31 bp):
TTTGTCTTTTGGTTGACTTAGTAAATTCATA
Found at i:192013 original size:20 final size:19
Alignment explanation
Indices: 191969--192128 Score: 97
Period size: 20 Copynumber: 8.6 Consensus size: 19
191959 AGAAGAATAG
* *
191969 TCGCAACACGAAAATGATTA
1 TCGCAACGCG-AAATGACTA
* *
191989 CCGCAACGCGAATTTGACTA
1 TCGCAACGCGAA-ATGACTA
*
192009 TCGCAACG-G-GAT-A--A
1 TCGCAACGCGAAATGACTA
* *
192023 TCGCAATGCGAAAACGACTA
1 TCGCAACGCG-AAATGACTA
192043 TCGCAACGCGGAAATGACTA
1 TCGCAACGC-GAAATGACTA
*
192063 TCGCAACGCGAATTTGACTA
1 TCGCAACGCGAA-ATGACTA
* *
192083 TTGCAACG-G-GAT-A--A
1 TCGCAACGCGAAATGACTA
*
192097 TCGCAATGCGAAAATGACTA
1 TCGCAACGCG-AAATGACTA
192117 TCGCAACGCGAA
1 TCGCAACGCGAA
192129 TTTAGTTTCG
Statistics
Matches: 105, Mismatches: 20, Indels: 31
0.67 0.13 0.20
Matches are distributed among these distances:
14 15 0.14
15 2 0.02
16 2 0.02
17 5 0.05
18 2 0.02
19 9 0.09
20 69 0.66
21 1 0.01
ACGTcount: A:0.36, C:0.24, G:0.22, T:0.18
Consensus pattern (19 bp):
TCGCAACGCGAAATGACTA
Found at i:192090 original size:74 final size:74
Alignment explanation
Indices: 191969--192128 Score: 266
Period size: 74 Copynumber: 2.2 Consensus size: 74
191959 AGAAGAATAG
* *
191969 TCGCAACACGAAAATGATTACCGCAACGCGAATTTGACTATCGCAACGGGATAATCGCAATGCGA
1 TCGCAACGCGAAAATGACTACCGCAACGCGAATTTGACTATCGCAACGGGATAATCGCAATGCGA
192034 AAACGACTA
66 AAACGACTA
* * *
192043 TCGCAACGCGGAAATGACTATCGCAACGCGAATTTGACTATTGCAACGGGATAATCGCAATGCGA
1 TCGCAACGCGAAAATGACTACCGCAACGCGAATTTGACTATCGCAACGGGATAATCGCAATGCGA
*
192108 AAATGACTA
66 AAACGACTA
192117 TCGCAACGCGAA
1 TCGCAACGCGAA
192129 TTTAGTTTCG
Statistics
Matches: 79, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
74 79 1.00
ACGTcount: A:0.36, C:0.24, G:0.22, T:0.18
Consensus pattern (74 bp):
TCGCAACGCGAAAATGACTACCGCAACGCGAATTTGACTATCGCAACGGGATAATCGCAATGCGA
AAACGACTA
Found at i:192167 original size:19 final size:19
Alignment explanation
Indices: 192133--192169 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
192123 CGCGAATTTA
*
192133 GTTTCGCGTTGCGATTTTG
1 GTTTCGCATTGCGATTTTG
*
192152 GTTTCGCATTGTGATTTT
1 GTTTCGCATTGCGATTTT
192170 CTCGTTGCGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.08, C:0.14, G:0.27, T:0.51
Consensus pattern (19 bp):
GTTTCGCATTGCGATTTTG
Found at i:192190 original size:33 final size:33
Alignment explanation
Indices: 192153--192233 Score: 108
Period size: 33 Copynumber: 2.4 Consensus size: 33
192143 GCGATTTTGG
* *
192153 TTTCGCATTGTGATTTTCTCGTTGCGATAGTCA
1 TTTCGCATTGCGATTATCTCGTTGCGATAGTCA
*
192186 TTTCGCGTTGCGATTATCTCGTTGCGATAGTCAA
1 TTTCGCATTGCGATTATCTCGTTGCGATAGTC-A
* *
192220 ATTCGCGTTGCGAT
1 TTTCGCATTGCGAT
192234 AATCATTTTC
Statistics
Matches: 43, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
33 29 0.67
34 14 0.33
ACGTcount: A:0.16, C:0.20, G:0.23, T:0.41
Consensus pattern (33 bp):
TTTCGCATTGCGATTATCTCGTTGCGATAGTCA
Found at i:192244 original size:20 final size:19
Alignment explanation
Indices: 192167--192241 Score: 70
Period size: 19 Copynumber: 4.2 Consensus size: 19
192157 GCATTGTGAT
*
192167 TTTCTCGTTGCGATAGTCA
1 TTTCGCGTTGCGATAGTCA
192186 TTTCGCGTTGCGAT--T-A
1 TTTCGCGTTGCGATAGTCA
*
192202 --TCTCGTTGCGATAGTCAA
1 TTTCGCGTTGCGATAGTC-A
* *
192220 ATTCGCGTTGCGATAATCA
1 TTTCGCGTTGCGATAGTCA
192239 TTT
1 TTT
192242 TCGTGTTGCA
Statistics
Matches: 45, Mismatches: 5, Indels: 12
0.73 0.08 0.19
Matches are distributed among these distances:
14 11 0.24
16 2 0.04
17 1 0.02
18 1 0.02
19 16 0.36
20 14 0.31
ACGTcount: A:0.19, C:0.20, G:0.21, T:0.40
Consensus pattern (19 bp):
TTTCGCGTTGCGATAGTCA
Found at i:192249 original size:20 final size:20
Alignment explanation
Indices: 192206--192273 Score: 57
Period size: 20 Copynumber: 3.4 Consensus size: 20
192196 CGATTATCTC
* * *
192206 GTTGCGATAGTCAAATTCGC
1 GTTGCGATAATCAATTTCGT
*
192226 GTTGCGATAATCATTTTCGT
1 GTTGCGATAATCAATTTCGT
* * *
192246 GTTGCAAT-TTTAAGTTTCGT
1 GTTGCGATAATCAA-TTTCGT
192266 GTTGCGAT
1 GTTGCGAT
192274 TTTAAGTTTC
Statistics
Matches: 38, Mismatches: 9, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
19 2 0.05
20 36 0.95
ACGTcount: A:0.21, C:0.15, G:0.24, T:0.41
Consensus pattern (20 bp):
GTTGCGATAATCAATTTCGT
Found at i:192275 original size:20 final size:20
Alignment explanation
Indices: 192240--192283 Score: 79
Period size: 20 Copynumber: 2.2 Consensus size: 20
192230 CGATAATCAT
192240 TTTCGTGTTGCAATTTTAAG
1 TTTCGTGTTGCAATTTTAAG
*
192260 TTTCGTGTTGCGATTTTAAG
1 TTTCGTGTTGCAATTTTAAG
192280 TTTC
1 TTTC
192284 AGAAACTATT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.16, C:0.11, G:0.20, T:0.52
Consensus pattern (20 bp):
TTTCGTGTTGCAATTTTAAG
Found at i:192855 original size:21 final size:21
Alignment explanation
Indices: 192760--192867 Score: 94
Period size: 21 Copynumber: 5.1 Consensus size: 21
192750 GCCCGACTCA
192760 CCTGTCATCGTTCAAGAGG--
1 CCTGTCATCGTTCAAGAGGCC
*
192779 CCTTTCCTATCGTTCAAGAGGCC
1 CCTGT-C-ATCGTTCAAGAGGCC
* ** *
192802 CCTATCATCCCTCAAGAGTCC
1 CCTGTCATCGTTCAAGAGGCC
** *
192823 CCTCCCACCGTTCAAGAGGCC
1 CCTGTCATCGTTCAAGAGGCC
* *
192844 CCTGTCATCGTTGAAGAGGTC
1 CCTGTCATCGTTCAAGAGGCC
192865 CCT
1 CCT
192868 CCCAACATTC
Statistics
Matches: 69, Mismatches: 16, Indels: 6
0.76 0.18 0.07
Matches are distributed among these distances:
19 4 0.06
20 1 0.01
21 59 0.86
22 1 0.01
23 4 0.06
ACGTcount: A:0.19, C:0.36, G:0.19, T:0.25
Consensus pattern (21 bp):
CCTGTCATCGTTCAAGAGGCC
Found at i:192861 original size:42 final size:42
Alignment explanation
Indices: 192760--192871 Score: 127
Period size: 42 Copynumber: 2.7 Consensus size: 42
192750 GCCCGACTCA
* ** * *
192760 CCTGTCATCGTTCAAGAGGCCTTTCCTATCGTTCAAGAGGCC
1 CCTGTCATCGTTCAAGAGTCCCCTCCCACCGTTCAAGAGGCC
* **
192802 CCTATCATCCCTCAAGAGTCCCCTCCCACCGTTCAAGAGGCC
1 CCTGTCATCGTTCAAGAGTCCCCTCCCACCGTTCAAGAGGCC
*
192844 CCTGTCATCGTTGAAGAGGT-CCCTCCCA
1 CCTGTCATCGTTCAAGA-GTCCCCTCCCA
192872 ACATTCTAGA
Statistics
Matches: 57, Mismatches: 12, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
42 55 0.96
43 2 0.04
ACGTcount: A:0.20, C:0.38, G:0.19, T:0.24
Consensus pattern (42 bp):
CCTGTCATCGTTCAAGAGTCCCCTCCCACCGTTCAAGAGGCC
Found at i:194327 original size:36 final size:30
Alignment explanation
Indices: 194247--194312 Score: 132
Period size: 30 Copynumber: 2.2 Consensus size: 30
194237 ATAAGAGTTG
194247 ATTTGTTTAATTGATGTGTAAATAATTCTT
1 ATTTGTTTAATTGATGTGTAAATAATTCTT
194277 ATTTGTTTAATTGATGTGTAAATAATTCTT
1 ATTTGTTTAATTGATGTGTAAATAATTCTT
194307 ATTTGT
1 ATTTGT
194313 GCTTGTTTAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 36 1.00
ACGTcount: A:0.29, C:0.03, G:0.14, T:0.55
Consensus pattern (30 bp):
ATTTGTTTAATTGATGTGTAAATAATTCTT
Found at i:194489 original size:20 final size:20
Alignment explanation
Indices: 194464--194719 Score: 217
Period size: 20 Copynumber: 13.8 Consensus size: 20
194454 GATTTTCTCA
*
194464 TTGCGATAGTCAAATTCCCG
1 TTGCGATAGTCAAATTCGCG
*
194484 TTGCGATAATCAAATTCGCG
1 TTGCGATAGTCAAATTCGCG
* *
194504 TTGCGATAGTC-ATTTCGCA
1 TTGCGATAGTCAAATTCGCG
*
194523 TTGCGAT--T---A-TCTCG
1 TTGCGATAGTCAAATTCGCG
194537 TTGCGATAGTCAAATTCGCG
1 TTGCGATAGTCAAATTCGCG
*
194557 TTGCGATAGTTAAATTCGCG
1 TTGCGATAGTCAAATTCGCG
* ** *
194577 CTGCGATAGTCATTTTCGCA
1 TTGCGATAGTCAAATTCGCG
*
194597 TTGCGAT--T---A-TCCCG
1 TTGCGATAGTCAAATTCGCG
194611 TTGCGATAGTCAAATTCGCG
1 TTGCGATAGTCAAATTCGCG
** *
194631 TTGCGATAGTCATTTTCGCA
1 TTGCGATAGTCAAATTCGCG
*
194651 TTGCGAT--T---A-TCCCG
1 TTGCGATAGTCAAATTCGCG
* *
194665 TTGCGATATTCAAATTCACG
1 TTGCGATAGTCAAATTCGCG
*
194685 TTGCGATAGTCATATTCGCG
1 TTGCGATAGTCAAATTCGCG
194705 TTGCGATAGTCAAAT
1 TTGCGATAGTCAAAT
194720 GAATGTGTAA
Statistics
Matches: 187, Mismatches: 31, Indels: 36
0.74 0.12 0.14
Matches are distributed among these distances:
14 30 0.16
16 3 0.02
17 1 0.01
18 2 0.01
19 16 0.09
20 135 0.72
ACGTcount: A:0.23, C:0.21, G:0.21, T:0.34
Consensus pattern (20 bp):
TTGCGATAGTCAAATTCGCG
Found at i:194613 original size:54 final size:54
Alignment explanation
Indices: 194555--194711 Score: 253
Period size: 54 Copynumber: 2.9 Consensus size: 54
194545 GTCAAATTCG
*
194555 CGTTGCGATAGTTAAATTCGCGCTGCGATAGTCATTTTCGCATTGCGATTATCC
1 CGTTGCGATAGTTAAATTCGCGTTGCGATAGTCATTTTCGCATTGCGATTATCC
*
194609 CGTTGCGATAGTCAAATTCGCGTTGCGATAGTCATTTTCGCATTGCGATTATCC
1 CGTTGCGATAGTTAAATTCGCGTTGCGATAGTCATTTTCGCATTGCGATTATCC
* * *
194663 CGTTGCGATA-TTCAAATTCACGTTGCGATAGTCATATTCGCGTTGCGAT
1 CGTTGCGATAGTT-AAATTCGCGTTGCGATAGTCATTTTCGCATTGCGAT
194712 AGTCAAATGA
Statistics
Matches: 96, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
53 1 0.01
54 95 0.99
ACGTcount: A:0.21, C:0.22, G:0.22, T:0.35
Consensus pattern (54 bp):
CGTTGCGATAGTTAAATTCGCGTTGCGATAGTCATTTTCGCATTGCGATTATCC
Found at i:194626 original size:74 final size:73
Alignment explanation
Indices: 194450--194642 Score: 314
Period size: 73 Copynumber: 2.6 Consensus size: 73
194440 CTAATACACT
* * * * *
194450 TTGCGATTTTCTCATTGCGATAGTCAAATTCCCGTTGCGATAATCAAATTCGCGTTGCGATAGTC
1 TTGCGATTATCTCGTTGCGATAGTCAAATTCGCGTTGCGATAGTCAAATTCGCGCTGCGATAGTC
194515 ATTTCGCA
66 ATTTCGCA
*
194523 TTGCGATTATCTCGTTGCGATAGTCAAATTCGCGTTGCGATAGTTAAATTCGCGCTGCGATAGTC
1 TTGCGATTATCTCGTTGCGATAGTCAAATTCGCGTTGCGATAGTCAAATTCGCGCTGCGATAGTC
194588 ATTTTCGCA
66 A-TTTCGCA
*
194597 TTGCGATTATCCCGTTGCGATAGTCAAATTCGCGTTGCGATAGTCA
1 TTGCGATTATCTCGTTGCGATAGTCAAATTCGCGTTGCGATAGTCA
194643 TTTTCGCATT
Statistics
Matches: 111, Mismatches: 8, Indels: 1
0.93 0.07 0.01
Matches are distributed among these distances:
73 60 0.54
74 51 0.46
ACGTcount: A:0.22, C:0.21, G:0.22, T:0.35
Consensus pattern (73 bp):
TTGCGATTATCTCGTTGCGATAGTCAAATTCGCGTTGCGATAGTCAAATTCGCGCTGCGATAGTC
ATTTCGCA
Found at i:194656 original size:74 final size:73
Alignment explanation
Indices: 194450--194719 Score: 321
Period size: 74 Copynumber: 3.7 Consensus size: 73
194440 CTAATACACT
* * * *
194450 TTGCGATTTTCTCATTGCGATAGTCAAATTCCCGTTGCGATAATCAAATTCGCGTTGCGATAGTC
1 TTGCGATTATCTCGTTGCGATAGTCAAATTCGCGTTGCGATAGTCAAATTCGCGTTGCGATAGTC
194515 ATTTCGCA
66 ATTTCGCA
* *
194523 TTGCGATTATCTCGTTGCGATAGTCAAATTCGCGTTGCGATAGTTAAATTCGCGCTGCGATAGTC
1 TTGCGATTATCTCGTTGCGATAGTCAAATTCGCGTTGCGATAGTCAAATTCGCGTTGCGATAGTC
194588 ATTTTCGCA
66 A-TTTCGCA
* ** *
194597 TTGCGATTATCCCGTTGCGATAGTCAAATTCGCGTTGCGATAGTCATTTTCGCATTGCGATTA-T
1 TTGCGATTATCTCGTTGCGATAGTCAAATTCGCGTTGCGATAGTCAAATTCGCGTTGCGA-TAGT
**
194661 CCCGTT-GCGA
65 -CATTTCGC-A
* * * * *
194671 TATTCAAAT-TCACGTTGCGATAGTCATATTCGCGTTGCGATAGTCAAAT
1 T-TGCGATTATCTCGTTGCGATAGTCAAATTCGCGTTGCGATAGTCAAAT
194720 GAATGTGTAA
Statistics
Matches: 171, Mismatches: 21, Indels: 9
0.85 0.10 0.04
Matches are distributed among these distances:
73 62 0.36
74 102 0.60
75 7 0.04
ACGTcount: A:0.23, C:0.21, G:0.21, T:0.35
Consensus pattern (73 bp):
TTGCGATTATCTCGTTGCGATAGTCAAATTCGCGTTGCGATAGTCAAATTCGCGTTGCGATAGTC
ATTTCGCA
Found at i:196984 original size:14 final size:14
Alignment explanation
Indices: 196965--197001 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
196955 TCCCGTGGCA
196965 TTTTCTTCGGGGAC
1 TTTTCTTCGGGGAC
*
196979 TTTTCTTCGGGGAT
1 TTTTCTTCGGGGAC
196993 TTCTTCTTC
1 TT-TTCTTC
197002 TTCTTTTTCT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
14 15 0.71
15 6 0.29
ACGTcount: A:0.05, C:0.22, G:0.22, T:0.51
Consensus pattern (14 bp):
TTTTCTTCGGGGAC
Found at i:198095 original size:20 final size:20
Alignment explanation
Indices: 198070--198211 Score: 164
Period size: 20 Copynumber: 7.0 Consensus size: 20
198060 AGTGATATGT
*
198070 TAGTCAGAATCGCGTTGTGA
1 TAGTCAGAATCGCGTTGCGA
198090 TAGTCAGAATCGCGTTGCGA
1 TAGTCAGAATCGCGTTGCGA
*
198110 TAGTCAGAATCTCGTTGCGA
1 TAGTCAGAATCGCGTTGCGA
* *
198130 TAGTCAGAATCTCGTTGTGA
1 TAGTCAGAATCGCGTTGCGA
*
198150 TAGTCAGAATCACGTTGCGA
1 TAGTCAGAATCGCGTTGCGA
*
198170 TCA--CATATTATCGCGTTGCGA
1 T-AGTCAGA--ATCGCGTTGCGA
*
198191 TAGTTC-GAATAGCGTTGCGA
1 TAG-TCAGAATCGCGTTGCGA
198211 T
1 T
198212 CACGTGTTAT
Statistics
Matches: 107, Mismatches: 9, Indels: 12
0.84 0.07 0.09
Matches are distributed among these distances:
19 3 0.03
20 89 0.83
21 13 0.12
22 1 0.01
23 1 0.01
ACGTcount: A:0.25, C:0.18, G:0.26, T:0.30
Consensus pattern (20 bp):
TAGTCAGAATCGCGTTGCGA
Found at i:198188 original size:21 final size:21
Alignment explanation
Indices: 198162--198241 Score: 63
Period size: 21 Copynumber: 3.8 Consensus size: 21
198152 GTCAGAATCA
198162 CGTTGCGATCACATATTATCG
1 CGTTGCGATCACATATTATCG
** *** *
198183 CGTTGCGAT-AGTTCGAATAG
1 CGTTGCGATCACATATTATCG
* *
198203 CGTTGCGATCACGTGTTATCG
1 CGTTGCGATCACATATTATCG
*
198224 CGTTGCGATTTACATATT
1 CGTTGCGA-TCACATATT
198242 CGCATTGCGA
Statistics
Matches: 42, Mismatches: 15, Indels: 3
0.70 0.25 0.05
Matches are distributed among these distances:
20 14 0.33
21 22 0.52
22 6 0.14
ACGTcount: A:0.21, C:0.20, G:0.24, T:0.35
Consensus pattern (21 bp):
CGTTGCGATCACATATTATCG
Found at i:198249 original size:20 final size:20
Alignment explanation
Indices: 198221--198293 Score: 137
Period size: 20 Copynumber: 3.6 Consensus size: 20
198211 TCACGTGTTA
*
198221 TCGCGTTGCGATTTACATAT
1 TCGCATTGCGATTTACATAT
198241 TCGCATTGCGATTTACATAT
1 TCGCATTGCGATTTACATAT
198261 TCGCATTGCGATTTACATAT
1 TCGCATTGCGATTTACATAT
198281 TCGCATTGCGATT
1 TCGCATTGCGATT
198294 ATCTAAAATC
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
20 52 1.00
ACGTcount: A:0.22, C:0.21, G:0.18, T:0.40
Consensus pattern (20 bp):
TCGCATTGCGATTTACATAT
Found at i:198363 original size:20 final size:19
Alignment explanation
Indices: 198340--198413 Score: 67
Period size: 20 Copynumber: 3.8 Consensus size: 19
198330 GCGATGGTCA
*
198340 AAATCGCATTGCGAATCTGG
1 AAATCGCATTGCG-ATATGG
* *
198360 AAATTGAATTGCGATAATGG
1 AAATCGCATTGCGAT-ATGG
* * *
198380 AGATCGCATTGCGATTTAG
1 AAATCGCATTGCGATATGG
*
198399 AGATCGCATTGCGAT
1 AAATCGCATTGCGAT
198414 TTTATTGGTC
Statistics
Matches: 45, Mismatches: 8, Indels: 3
0.80 0.14 0.05
Matches are distributed among these distances:
19 19 0.42
20 26 0.58
ACGTcount: A:0.31, C:0.15, G:0.26, T:0.28
Consensus pattern (19 bp):
AAATCGCATTGCGATATGG
Found at i:198403 original size:19 final size:19
Alignment explanation
Indices: 198379--198415 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
198369 TGCGATAATG
198379 GAGATCGCATTGCGATTTA
1 GAGATCGCATTGCGATTTA
198398 GAGATCGCATTGCGATTT
1 GAGATCGCATTGCGATTT
198416 TATTGGTCAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.24, C:0.16, G:0.27, T:0.32
Consensus pattern (19 bp):
GAGATCGCATTGCGATTTA
Found at i:202990 original size:20 final size:20
Alignment explanation
Indices: 202965--203057 Score: 96
Period size: 21 Copynumber: 4.5 Consensus size: 20
202955 TTTTCCCAAT
202965 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATAAGTAAA
* ** *
202985 TCGCAACGCGAATTGGGAAA
1 TCGCAATGCGAATAAGTAAA
203005 TTCGCAATGCGAATAAGTAAA
1 -TCGCAATGCGAATAAGTAAA
* ** *
203026 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAA-TAAGTAAA
203047 TCGCAATGCGA
1 TCGCAATGCGA
203058 TACTGACTAT
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 27 0.47
21 31 0.53
ACGTcount: A:0.39, C:0.18, G:0.25, T:0.18
Consensus pattern (20 bp):
TCGCAATGCGAATAAGTAAA
Found at i:203007 original size:41 final size:41
Alignment explanation
Indices: 202962--203057 Score: 183
Period size: 41 Copynumber: 2.3 Consensus size: 41
202952 CGATTTTCCC
202962 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
1 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
203003 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
1 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
*
203044 AAATCGCAATGCGA
1 AATTCGCAATGCGA
203058 TACTGACTAT
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 54 1.00
ACGTcount: A:0.40, C:0.18, G:0.24, T:0.19
Consensus pattern (41 bp):
AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
Found at i:203011 original size:21 final size:20
Alignment explanation
Indices: 202965--203057 Score: 96
Period size: 20 Copynumber: 4.5 Consensus size: 20
202955 TTTTCCCAAT
*
202965 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATAAGGAAA
* **
202985 TCGCAACGCGAATTGGGAAA
1 TCGCAATGCGAATAAGGAAA
*
203005 TTCGCAATGCGAATAAGTAAA
1 -TCGCAATGCGAATAAGGAAA
* **
203026 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGG-AAA
203047 TCGCAATGCGA
1 TCGCAATGCGA
203058 TACTGACTAT
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 29 0.50
21 29 0.50
ACGTcount: A:0.39, C:0.18, G:0.25, T:0.18
Consensus pattern (20 bp):
TCGCAATGCGAATAAGGAAA
Done.