Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold466
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: 253436
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Found at i:6221 original size:43 final size:43
Alignment explanation
Indices: 6157--6259 Score: 154
Period size: 43 Copynumber: 2.4 Consensus size: 43
6147 TCATAATTGA
* *
6157 ATTGTATCGAT-CTATTAAGCCCAACGGCTATAATTTCAACTAC
1 ATTGTATCGATAC-ATTAAGCCCAACGGCTAAAATTTCAAATAC
* *
6200 ATTGTATCGATACATTGAGCCCAACGGCTAAAATTTCAAATGC
1 ATTGTATCGATACATTAAGCCCAACGGCTAAAATTTCAAATAC
6243 ATTGTATCGATACATTA
1 ATTGTATCGATACATTA
6260 TGAATTGTAT
Statistics
Matches: 54, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
43 53 0.98
44 1 0.02
ACGTcount: A:0.34, C:0.20, G:0.14, T:0.32
Consensus pattern (43 bp):
ATTGTATCGATACATTAAGCCCAACGGCTAAAATTTCAAATAC
Found at i:6715 original size:25 final size:26
Alignment explanation
Indices: 6687--6736 Score: 75
Period size: 27 Copynumber: 1.9 Consensus size: 26
6677 TAAGTTATTG
*
6687 TCTTCGA-GGATACTCTAACCCCACT
1 TCTTCGAGGGATACTCCAACCCCACT
6712 TCTTCGAGGGGATACTCCAACCCCA
1 TCTTCGA-GGGATACTCCAACCCCA
6737 TTTTTCAACC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 7 0.32
27 15 0.68
ACGTcount: A:0.24, C:0.36, G:0.16, T:0.24
Consensus pattern (26 bp):
TCTTCGAGGGATACTCCAACCCCACT
Found at i:14015 original size:13 final size:14
Alignment explanation
Indices: 13982--14012 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
13972 AAAACACAAA
*
13982 TTTTAAAATTAATT
1 TTTTAAAAATAATT
13996 TTTTAAAAATAATT
1 TTTTAAAAATAATT
14010 TTT
1 TTT
14013 AAATTTTGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (14 bp):
TTTTAAAAATAATT
Found at i:16354 original size:53 final size:54
Alignment explanation
Indices: 16297--16401 Score: 185
Period size: 53 Copynumber: 2.0 Consensus size: 54
16287 GTGCATGATG
*
16297 ATGTTACCAGTATGAACTACAAAAATCACTTGAAAAAGAAA-TTAAAAAAAAGA
1 ATGTTACCAATATGAACTACAAAAATCACTTGAAAAAGAAATTTAAAAAAAAGA
*
16350 ATGTTACCAATATGAACTACAGAAATCACTTGAAAAAGAAATTTAAAAAAAA
1 ATGTTACCAATATGAACTACAAAAATCACTTGAAAAAGAAATTTAAAAAAAA
16402 AAAAAAAGAA
Statistics
Matches: 49, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
53 39 0.80
54 10 0.20
ACGTcount: A:0.56, C:0.11, G:0.10, T:0.22
Consensus pattern (54 bp):
ATGTTACCAATATGAACTACAAAAATCACTTGAAAAAGAAATTTAAAAAAAAGA
Found at i:17196 original size:45 final size:45
Alignment explanation
Indices: 17143--17247 Score: 124
Period size: 45 Copynumber: 2.3 Consensus size: 45
17133 ATTTTTATTA
* *
17143 ATTTTA-TTTTATATATTTTATTCCTTTTA-TTTATTAAATTCATAT
1 ATTTTATTTTTA-AAATTTTAATCCTTTTATTTTATTAAATTC-TAT
* * *
17188 TTTTTATTTTTAAAATTTTAATCTTTTTATTTTATTTAATTCTAT
1 ATTTTATTTTTAAAATTTTAATCCTTTTATTTTATTAAATTCTAT
*
17233 AATTTATTTTTAAAA
1 ATTTTATTTTTAAAA
17248 AATTTTAAAA
Statistics
Matches: 51, Mismatches: 7, Indels: 4
0.82 0.11 0.06
Matches are distributed among these distances:
45 35 0.69
46 16 0.31
ACGTcount: A:0.30, C:0.05, G:0.00, T:0.65
Consensus pattern (45 bp):
ATTTTATTTTTAAAATTTTAATCCTTTTATTTTATTAAATTCTAT
Found at i:17203 original size:22 final size:21
Alignment explanation
Indices: 17167--17247 Score: 65
Period size: 22 Copynumber: 3.7 Consensus size: 21
17157 ATTTTATTCC
17167 TTTTATTTATT-AAATTCATATT
1 TTTTATTT-TTAAAATTC-TATT
*
17189 TTTTATTTTTAAAATTTTAATCT
1 TTTTATTTTTAAAATTCT-AT-T
** *
17212 TTTTATTTTATTTAATTCTATA
1 TTTTATTTT-TAAAATTCTATT
*
17234 ATTTATTTTTAAAA
1 TTTTATTTTTAAAA
17248 AATTTTAAAA
Statistics
Matches: 47, Mismatches: 8, Indels: 9
0.73 0.12 0.14
Matches are distributed among these distances:
21 6 0.13
22 23 0.49
23 12 0.26
24 6 0.13
ACGTcount: A:0.32, C:0.04, G:0.00, T:0.64
Consensus pattern (21 bp):
TTTTATTTTTAAAATTCTATT
Found at i:18016 original size:27 final size:27
Alignment explanation
Indices: 17986--18040 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
17976 AATTTTTGTT
17986 ACTTTGGTTCAGTCGCCAAATGACGCA
1 ACTTTGGTTCAGTCGCCAAATGACGCA
18013 ACTTTGGTTCAGTCGCCAAATGACGCA
1 ACTTTGGTTCAGTCGCCAAATGACGCA
18040 A
1 A
18041 GTTGTCTGCA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.27, C:0.25, G:0.22, T:0.25
Consensus pattern (27 bp):
ACTTTGGTTCAGTCGCCAAATGACGCA
Found at i:18992 original size:20 final size:20
Alignment explanation
Indices: 18969--19021 Score: 106
Period size: 20 Copynumber: 2.6 Consensus size: 20
18959 CACACCCAGA
18969 TGTATCGATACATTATGCTT
1 TGTATCGATACATTATGCTT
18989 TGTATCGATACATTATGCTT
1 TGTATCGATACATTATGCTT
19009 TGTATCGATACAT
1 TGTATCGATACAT
19022 GGACAATTGT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.26, C:0.15, G:0.15, T:0.43
Consensus pattern (20 bp):
TGTATCGATACATTATGCTT
Found at i:27872 original size:20 final size:19
Alignment explanation
Indices: 27826--27882 Score: 87
Period size: 19 Copynumber: 2.9 Consensus size: 19
27816 TTGAATCGAT
*
27826 ACATTGTATCGATACATGT
1 ACATTGTATCGATACATGG
*
27845 TCATTGTATCGATACATGG
1 ACATTGTATCGATACATGG
27864 ACAATTGTATCGATACATG
1 AC-ATTGTATCGATACATG
27883 AAACTGGCAG
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
19 18 0.53
20 16 0.47
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.35
Consensus pattern (19 bp):
ACATTGTATCGATACATGG
Found at i:29850 original size:13 final size:13
Alignment explanation
Indices: 29832--29857 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
29822 CAATTTTTTG
29832 TGTATCGATACAT
1 TGTATCGATACAT
29845 TGTATCGATACAT
1 TGTATCGATACAT
29858 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:31403 original size:40 final size:40
Alignment explanation
Indices: 31352--31429 Score: 111
Period size: 40 Copynumber: 1.9 Consensus size: 40
31342 ATTCTGGAAG
* * * *
31352 GAAATTGTATCGATACATTTTTTAATGTATTGATACATAA
1 GAAATTGTATCGAGACATTTCTCAATGTATTAATACATAA
*
31392 GAAATTGTATCGAGACATTTCTCATTGTATTAATACAT
1 GAAATTGTATCGAGACATTTCTCAATGTATTAATACAT
31430 TCTGGATTTT
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
40 33 1.00
ACGTcount: A:0.36, C:0.10, G:0.13, T:0.41
Consensus pattern (40 bp):
GAAATTGTATCGAGACATTTCTCAATGTATTAATACATAA
Found at i:32254 original size:19 final size:19
Alignment explanation
Indices: 32230--32266 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
32220 TTATAGTGAG
32230 CCTAGTATGCTTCCATGAA
1 CCTAGTATGCTTCCATGAA
32249 CCTAGTATGCTTCCATGA
1 CCTAGTATGCTTCCATGA
32267 CCCTCTTAAG
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:0.27, G:0.16, T:0.32
Consensus pattern (19 bp):
CCTAGTATGCTTCCATGAA
Found at i:36841 original size:20 final size:20
Alignment explanation
Indices: 36816--36867 Score: 104
Period size: 20 Copynumber: 2.6 Consensus size: 20
36806 TCATGTTATT
36816 ATGTATCGATACTTTTCATA
1 ATGTATCGATACTTTTCATA
36836 ATGTATCGATACTTTTCATA
1 ATGTATCGATACTTTTCATA
36856 ATGTATCGATAC
1 ATGTATCGATAC
36868 ATGCATTTAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.31, C:0.15, G:0.12, T:0.42
Consensus pattern (20 bp):
ATGTATCGATACTTTTCATA
Found at i:37053 original size:13 final size:13
Alignment explanation
Indices: 37035--37059 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
37025 ACCAAGATCA
37035 TGTATCGATACAG
1 TGTATCGATACAG
37048 TGTATCGATACA
1 TGTATCGATACA
37060 AAGTAATATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.20, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAG
Found at i:40816 original size:84 final size:80
Alignment explanation
Indices: 40670--40829 Score: 198
Period size: 83 Copynumber: 1.9 Consensus size: 80
40660 AAATGTGTAA
* * * *
40670 TTGATAAATAGTGGGATTATTGAATGTTTGTCCATTCCAGAAAGGCCTTTGGTGGCAGTAATTAG
1 TTGATAAATAGTGGGATTATGGAATATATGTCCATTCCAGAAAGGCCTTTGGCGGCA-TAATTAG
40735 GATTTGTTGCCACGTAG
65 GA-TTGTTGCCACGTAG
*
40752 TTGATAAAATAGTGGGATTATGGAATATATGTCTTATTCCA-AAATGGCCTTTGGCGATGC-TAA
1 TTGAT-AAATAGTGGGATTATGGAATATATGTC-CATTCCAGAAA-GGCCTTTGGCG--GCATAA
40815 TTAGGATTGTTGCCA
61 TTAGGATTGTTGCCA
40830 TAACTTATCC
Statistics
Matches: 68, Mismatches: 5, Indels: 9
0.83 0.06 0.11
Matches are distributed among these distances:
82 5 0.07
83 36 0.53
84 25 0.37
86 2 0.03
ACGTcount: A:0.28, C:0.12, G:0.25, T:0.36
Consensus pattern (80 bp):
TTGATAAATAGTGGGATTATGGAATATATGTCCATTCCAGAAAGGCCTTTGGCGGCATAATTAGG
ATTGTTGCCACGTAG
Found at i:47217 original size:33 final size:33
Alignment explanation
Indices: 47180--47281 Score: 97
Period size: 33 Copynumber: 3.2 Consensus size: 33
47170 TGATTGCTGC
47180 ATCAGCAACTAAATTTGTGGATTACTGTTGCTA
1 ATCAGCAACTAAATTTGTGGATTACTGTTGCTA
* * * * *
47213 ATCAG-GA-TTACTCTT-TAGA-TA-TGATTGCTGC
1 ATCAGCAACTAAAT-TTGTGGATTACTG-TTGCT-A
47244 ATCAGCAACTAAATTTGTGGATTACTGTTGCTA
1 ATCAGCAACTAAATTTGTGGATTACTGTTGCTA
47277 ATCAG
1 ATCAG
47282 GATTACTTTT
Statistics
Matches: 51, Mismatches: 10, Indels: 16
0.66 0.13 0.21
Matches are distributed among these distances:
29 2 0.04
30 7 0.14
31 11 0.22
32 6 0.12
33 16 0.31
34 7 0.14
35 2 0.04
ACGTcount: A:0.29, C:0.16, G:0.19, T:0.36
Consensus pattern (33 bp):
ATCAGCAACTAAATTTGTGGATTACTGTTGCTA
Found at i:47261 original size:64 final size:64
Alignment explanation
Indices: 47160--47288 Score: 258
Period size: 64 Copynumber: 2.0 Consensus size: 64
47150 AATGTGATAG
47160 TCTTTAGATATGATTGCTGCATCAGCAACTAAATTTGTGGATTACTGTTGCTAATCAGGATTAC
1 TCTTTAGATATGATTGCTGCATCAGCAACTAAATTTGTGGATTACTGTTGCTAATCAGGATTAC
47224 TCTTTAGATATGATTGCTGCATCAGCAACTAAATTTGTGGATTACTGTTGCTAATCAGGATTAC
1 TCTTTAGATATGATTGCTGCATCAGCAACTAAATTTGTGGATTACTGTTGCTAATCAGGATTAC
47288 T
1 T
47289 TTTCTTCCTC
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
64 65 1.00
ACGTcount: A:0.28, C:0.16, G:0.19, T:0.38
Consensus pattern (64 bp):
TCTTTAGATATGATTGCTGCATCAGCAACTAAATTTGTGGATTACTGTTGCTAATCAGGATTAC
Found at i:49847 original size:224 final size:224
Alignment explanation
Indices: 49457--49904 Score: 896
Period size: 224 Copynumber: 2.0 Consensus size: 224
49447 GATTTTGGGG
49457 GAAGCTGCCCTCACTGTAAGTCTGTGGGGATACACATGCATTATTTTTTATACCTTTTAAAGTTC
1 GAAGCTGCCCTCACTGTAAGTCTGTGGGGATACACATGCATTATTTTTTATACCTTTTAAAGTTC
49522 AAATAGACAAGAATGTGTAAAGCAAGTTGTTTTCTTAGCGTTGAGTTGGTGAGAGACTAATATGG
66 AAATAGACAAGAATGTGTAAAGCAAGTTGTTTTCTTAGCGTTGAGTTGGTGAGAGACTAATATGG
49587 ACTCTCCCATCCTACATTAGTATGTGTTGTTCTGCTTCTGCTTTATATATATATATATAATAGTC
131 ACTCTCCCATCCTACATTAGTATGTGTTGTTCTGCTTCTGCTTTATATATATATATATAATAGTC
49652 AAAGTTGGTTGTCAGCTGTCTAAATCAGA
196 AAAGTTGGTTGTCAGCTGTCTAAATCAGA
49681 GAAGCTGCCCTCACTGTAAGTCTGTGGGGATACACATGCATTATTTTTTATACCTTTTAAAGTTC
1 GAAGCTGCCCTCACTGTAAGTCTGTGGGGATACACATGCATTATTTTTTATACCTTTTAAAGTTC
49746 AAATAGACAAGAATGTGTAAAGCAAGTTGTTTTCTTAGCGTTGAGTTGGTGAGAGACTAATATGG
66 AAATAGACAAGAATGTGTAAAGCAAGTTGTTTTCTTAGCGTTGAGTTGGTGAGAGACTAATATGG
49811 ACTCTCCCATCCTACATTAGTATGTGTTGTTCTGCTTCTGCTTTATATATATATATATAATAGTC
131 ACTCTCCCATCCTACATTAGTATGTGTTGTTCTGCTTCTGCTTTATATATATATATATAATAGTC
49876 AAAGTTGGTTGTCAGCTGTCTAAATCAGA
196 AAAGTTGGTTGTCAGCTGTCTAAATCAGA
49905 AACTAATTCA
Statistics
Matches: 224, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
224 224 1.00
ACGTcount: A:0.28, C:0.16, G:0.20, T:0.37
Consensus pattern (224 bp):
GAAGCTGCCCTCACTGTAAGTCTGTGGGGATACACATGCATTATTTTTTATACCTTTTAAAGTTC
AAATAGACAAGAATGTGTAAAGCAAGTTGTTTTCTTAGCGTTGAGTTGGTGAGAGACTAATATGG
ACTCTCCCATCCTACATTAGTATGTGTTGTTCTGCTTCTGCTTTATATATATATATATAATAGTC
AAAGTTGGTTGTCAGCTGTCTAAATCAGA
Found at i:50575 original size:13 final size:13
Alignment explanation
Indices: 50557--50583 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
50547 AAATGATGAT
50557 TGTTGCTGTTATA
1 TGTTGCTGTTATA
50570 TGTTGCTGTTATA
1 TGTTGCTGTTATA
50583 T
1 T
50584 ATTCCTTCTT
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:0.15, C:0.07, G:0.22, T:0.56
Consensus pattern (13 bp):
TGTTGCTGTTATA
Found at i:56284 original size:27 final size:28
Alignment explanation
Indices: 56232--56284 Score: 90
Period size: 27 Copynumber: 1.9 Consensus size: 28
56222 ATTTTAATCA
56232 CATATTTCTTTCTCCCCCTTAATCATCC
1 CATATTTCTTTCTCCCCCTTAATCATCC
*
56260 CATATTTCTTT-TTCCCCTTAATCAT
1 CATATTTCTTTCTCCCCCTTAATCAT
56285 AAAATTTATT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
27 13 0.54
28 11 0.46
ACGTcount: A:0.19, C:0.34, G:0.00, T:0.47
Consensus pattern (28 bp):
CATATTTCTTTCTCCCCCTTAATCATCC
Found at i:60169 original size:15 final size:15
Alignment explanation
Indices: 60149--60189 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
60139 GTTCATCAAT
60149 TTCATTTGGAGCTTC
1 TTCATTTGGAGCTTC
*
60164 TTCATTTTGAGCTTC
1 TTCATTTGGAGCTTC
*
60179 CTCAATTTGGA
1 TTC-ATTTGGA
60190 CGTTTTTATC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
15 16 0.73
16 6 0.27
ACGTcount: A:0.17, C:0.20, G:0.17, T:0.46
Consensus pattern (15 bp):
TTCATTTGGAGCTTC
Found at i:61759 original size:20 final size:20
Alignment explanation
Indices: 61714--61765 Score: 79
Period size: 19 Copynumber: 2.6 Consensus size: 20
61704 GTAGCCAAAC
**
61714 TTGTATCGATACACCAAGTA
1 TTGTATCGATACACCAAAAA
61734 -TGTATCGATACACCAAAAA
1 TTGTATCGATACACCAAAAA
61753 TTGTATCGATACA
1 TTGTATCGATACA
61766 TTGGCTTGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 17 0.59
20 12 0.41
ACGTcount: A:0.38, C:0.19, G:0.13, T:0.29
Consensus pattern (20 bp):
TTGTATCGATACACCAAAAA
Found at i:61830 original size:20 final size:21
Alignment explanation
Indices: 61800--61838 Score: 71
Period size: 20 Copynumber: 1.9 Consensus size: 21
61790 CTATATTTTC
61800 AAATATGTATCGATACATTAA
1 AAATATGTATCGATACATTAA
61821 AAAT-TGTATCGATACATT
1 AAATATGTATCGATACATT
61839 TACACGGGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.44, C:0.10, G:0.10, T:0.36
Consensus pattern (21 bp):
AAATATGTATCGATACATTAA
Found at i:63956 original size:84 final size:84
Alignment explanation
Indices: 63796--63956 Score: 186
Period size: 84 Copynumber: 1.9 Consensus size: 84
63786 ACTCAAAGAA
* * * *
63796 GAAAATAAATCAATAAGTGTAGAGAATCATATTCTTGAAAAGAAATTAAGTGAATTAGAGAAGAG
1 GAAAATAAATCAATAAGTGTAGAGAAACATATTCTTAAAAAGAAAATAAATGAATTAGAGAAGAG
* *
63861 TATGAAAGAGTTACAAAAT
66 AAAGAAAGAGTTACAAAAT
* *
63880 GAAAATAAATCAATGAGTTTAGA-AAACA-ATTCTTTTAAAAAGAAAATAAATGAATT--AGAAG
1 GAAAATAAATCAATAAGTGTAGAGAAACATATTC--TTAAAAAGAAAATAAATGAATTAGAGAAG
63941 AGAAAAGAAATGAGTT
64 AG-AAAGAAA-GAGTT
63957 GCAAGTGGAA
Statistics
Matches: 65, Mismatches: 8, Indels: 8
0.80 0.10 0.10
Matches are distributed among these distances:
82 11 0.17
83 9 0.14
84 45 0.69
ACGTcount: A:0.53, C:0.04, G:0.17, T:0.25
Consensus pattern (84 bp):
GAAAATAAATCAATAAGTGTAGAGAAACATATTCTTAAAAAGAAAATAAATGAATTAGAGAAGAG
AAAGAAAGAGTTACAAAAT
Found at i:65488 original size:13 final size:13
Alignment explanation
Indices: 65470--65494 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
65460 TTTTCCAGAT
65470 TGTATCGATACAA
1 TGTATCGATACAA
65483 TGTATCGATACA
1 TGTATCGATACA
65495 TTGCTTCAGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:67452 original size:13 final size:13
Alignment explanation
Indices: 67434--67459 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
67424 TACACCAAGT
67434 ATGTATCGATACA
1 ATGTATCGATACA
67447 ATGTATCGATACA
1 ATGTATCGATACA
67460 CCAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:67457 original size:32 final size:33
Alignment explanation
Indices: 67416--67479 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 33
67406 TAGCCAAACT
**
67416 TGTATCGATACACCAAGTA-TGTATCGATACAA
1 TGTATCGATACACCAAAAATTGTATCGATACAA
67448 TGTATCGATACACCAAAAATTGTATCGATACA
1 TGTATCGATACACCAAAAATTGTATCGATACA
67480 TTGGCTTGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 17 0.59
33 12 0.41
ACGTcount: A:0.39, C:0.19, G:0.14, T:0.28
Consensus pattern (33 bp):
TGTATCGATACACCAAAAATTGTATCGATACAA
Found at i:67544 original size:20 final size:21
Alignment explanation
Indices: 67514--67552 Score: 71
Period size: 20 Copynumber: 1.9 Consensus size: 21
67504 CTATATTTTC
67514 AAATATGTATCGATACATTAA
1 AAATATGTATCGATACATTAA
67535 AAAT-TGTATCGATACATT
1 AAATATGTATCGATACATT
67553 TACACGGGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.44, C:0.10, G:0.10, T:0.36
Consensus pattern (21 bp):
AAATATGTATCGATACATTAA
Found at i:70533 original size:3 final size:3
Alignment explanation
Indices: 70515--70548 Score: 50
Period size: 3 Copynumber: 11.3 Consensus size: 3
70505 AACCATTAAG
* *
70515 GAT GAT GAA GAC GAT GAT GAT GAT GAT GAT GAT G
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT G
70549 GTAATTCAGA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.35, C:0.03, G:0.35, T:0.26
Consensus pattern (3 bp):
GAT
Found at i:77680 original size:13 final size:13
Alignment explanation
Indices: 77662--77687 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
77652 CACACAAATA
77662 TGTATCGATACAT
1 TGTATCGATACAT
77675 TGTATCGATACAT
1 TGTATCGATACAT
77688 CCCAAAATGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:77683 original size:33 final size:33
Alignment explanation
Indices: 77641--77709 Score: 104
Period size: 33 Copynumber: 2.1 Consensus size: 33
77631 CCTTAACTGT
77641 TTGTATCGATACA-CACAAATATGTATCGATACA
1 TTGTATCGATACATCACAAA-ATGTATCGATACA
* *
77674 TTGTATCGATACATCCCAAAATGTGTCGATACA
1 TTGTATCGATACATCACAAAATGTATCGATACA
77707 TTG
1 TTG
77710 GCTTGTAACG
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
33 28 0.85
34 5 0.15
ACGTcount: A:0.35, C:0.19, G:0.14, T:0.32
Consensus pattern (33 bp):
TTGTATCGATACATCACAAAATGTATCGATACA
Found at i:81497 original size:19 final size:20
Alignment explanation
Indices: 81457--81499 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
81447 TAATCTCATC
**
81457 TATCGATACAATTGTCCATG
1 TATCGATACAATTGAACATG
81477 TATCGATACAA-TGAACATG
1 TATCGATACAATTGAACATG
81496 TATC
1 TATC
81500 TTTACAATGT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 10 0.48
20 11 0.52
ACGTcount: A:0.35, C:0.19, G:0.14, T:0.33
Consensus pattern (20 bp):
TATCGATACAATTGAACATG
Found at i:81696 original size:22 final size:21
Alignment explanation
Indices: 81669--81719 Score: 93
Period size: 21 Copynumber: 2.4 Consensus size: 21
81659 AAATTAAGGT
81669 TCAAAAACATTTGTTTATAAC
1 TCAAAAACATTTGTTTATAAC
81690 TCAAAAACATTTGTTTATAAC
1 TCAAAAACATTTGTTTATAAC
81711 TCTAAAAAC
1 TC-AAAAAC
81720 TTCCATTGAT
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
21 23 0.79
22 6 0.21
ACGTcount: A:0.45, C:0.16, G:0.04, T:0.35
Consensus pattern (21 bp):
TCAAAAACATTTGTTTATAAC
Found at i:82151 original size:22 final size:21
Alignment explanation
Indices: 82085--82157 Score: 73
Period size: 22 Copynumber: 3.6 Consensus size: 21
82075 AGTTTTTGTT
82085 TTTCTCCCCCTTAATTAAAGAA
1 TTTCTCCCCCTTAATTAAAG-A
* * *
82107 TTTCTTCTCTTTAA--AAA-A
1 TTTCTCCCCCTTAATTAAAGA
82125 -TTCTCCCCCTTAATTAAAGCA
1 TTTCTCCCCCTTAATTAAAG-A
82146 TTTCTCCCCCTT
1 TTTCTCCCCCTT
82158 TGTCAAATAA
Statistics
Matches: 40, Mismatches: 6, Indels: 10
0.71 0.11 0.18
Matches are distributed among these distances:
17 10 0.25
18 1 0.03
19 3 0.08
20 3 0.08
21 1 0.03
22 22 0.55
ACGTcount: A:0.26, C:0.30, G:0.03, T:0.41
Consensus pattern (21 bp):
TTTCTCCCCCTTAATTAAAGA
Found at i:84009 original size:13 final size:13
Alignment explanation
Indices: 83991--84021 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
83981 AAATAGTACC
83991 CAATGTATCGATA
1 CAATGTATCGATA
84004 CAATGTATCGATA
1 CAATGTATCGATA
*
84017 TAATG
1 CAATG
84022 AATGTTGTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.39, C:0.13, G:0.16, T:0.32
Consensus pattern (13 bp):
CAATGTATCGATA
Found at i:90193 original size:33 final size:32
Alignment explanation
Indices: 90153--90221 Score: 95
Period size: 33 Copynumber: 2.1 Consensus size: 32
90143 CCGTTACAAG
90153 CAATGTATCAATACAATTCAT-CATGTATCGATA
1 CAATGTATCAATAC-ATT-ATACATGTATCGATA
*
90186 CAATGTATCGATACATTATACCATGTATCGATA
1 CAATGTATCAATACATTATA-CATGTATCGATA
90219 CAA
1 CAA
90222 ACAGTGGTAG
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
31 2 0.06
32 3 0.09
33 28 0.85
ACGTcount: A:0.39, C:0.19, G:0.10, T:0.32
Consensus pattern (32 bp):
CAATGTATCAATACATTATACATGTATCGATA
Found at i:90206 original size:20 final size:20
Alignment explanation
Indices: 90183--90220 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
90173 TCATGTATCG
90183 ATACAATGTATCGATACATT
1 ATACAATGTATCGATACATT
*
90203 ATACCATGTATCGATACA
1 ATACAATGTATCGATACA
90221 AACAGTGGTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.39, C:0.18, G:0.11, T:0.32
Consensus pattern (20 bp):
ATACAATGTATCGATACATT
Found at i:90219 original size:13 final size:13
Alignment explanation
Indices: 90175--90200 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
90165 ACAATTCATC
90175 ATGTATCGATACA
1 ATGTATCGATACA
90188 ATGTATCGATACA
1 ATGTATCGATACA
90201 TTATACCATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:91103 original size:10 final size:10
Alignment explanation
Indices: 91088--91113 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
91078 TCTCTTCTTT
91088 TTTTTTTGTA
1 TTTTTTTGTA
91098 TTTTTTTGTA
1 TTTTTTTGTA
91108 TTTTTT
1 TTTTTT
91114 CGAATAAGTC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.08, C:0.00, G:0.08, T:0.85
Consensus pattern (10 bp):
TTTTTTTGTA
Found at i:94571 original size:148 final size:147
Alignment explanation
Indices: 94310--94575 Score: 345
Period size: 148 Copynumber: 1.8 Consensus size: 147
94300 TCTGAAAAGT
* * ** * ** *
94310 TTCATTTCGTGCCTTAATGGAGGACCGAAAAGATAAGAAAAGTTTTTAAAATTTTCATACTTCTA
1 TTCATTTCGTACCTCAATGGACAACCGAAAAGATAAGAAAAGTTTTAAAAATTTTCATACCCCCA
* * * * *
94375 CAGATGCTCATAGGAATATTGGAAATTCTGAAAAATTGGGATCATAATTTTTATTTAATTTAATT
66 CAGATACCCATAGGAATATTAGAAATTCTAAAAAATTAGGATCATAATTTTTATTTAATTTAATT
94440 TTTTATTTCCCAAAAAC
131 TTTTATTTCCCAAAAAC
* *
94457 TTCATTTCGTACCTCAATGGACAACCGAAAAGATACGAAAAAGTTTTAAAAATTTTTATACCCCC
1 TTCATTTCGTACCTCAATGGACAACCGAAAAGATAAG-AAAAGTTTTAAAAATTTTCATACCCCC
* * *
94522 ATAGATACCCATGGGAATATTAGAAATTCTAAAAAATTCAGG-TGATAATTTTTA
65 ACAGATACCCATAGGAATATTAGAAATTCTAAAAAATT-AGGATCATAATTTTTA
94576 GTGGATGAAA
Statistics
Matches: 99, Mismatches: 18, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
147 32 0.32
148 65 0.66
149 2 0.02
ACGTcount: A:0.38, C:0.14, G:0.13, T:0.35
Consensus pattern (147 bp):
TTCATTTCGTACCTCAATGGACAACCGAAAAGATAAGAAAAGTTTTAAAAATTTTCATACCCCCA
CAGATACCCATAGGAATATTAGAAATTCTAAAAAATTAGGATCATAATTTTTATTTAATTTAATT
TTTTATTTCCCAAAAAC
Found at i:95345 original size:2 final size:2
Alignment explanation
Indices: 95333--95365 Score: 57
Period size: 2 Copynumber: 16.0 Consensus size: 2
95323 ATTAAGAAAC
95333 AT AT CAT 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
95366 GTAAAAATAG
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 28 0.93
3 2 0.07
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:96270 original size:166 final size:166
Alignment explanation
Indices: 96084--96591 Score: 527
Period size: 164 Copynumber: 3.1 Consensus size: 166
96074 TATTAGGTAC
* ** * *
96084 ATTTTAAAAGTTTTAAACCAA-AGAAAATCTCCCCGAAAATATCTATGGAATAGAAAA-TTCGAT
1 ATTTTAAAAATTAAAAACCAAGA-AAAATC-CCCCGAAAAAATCTATGGAGTAGAAAACTTCG-T
* * *
96147 TTTTCAGGAAA-AGGGAAATTTCAAGAAAAAAATTAAAAACTCATGAATATAAATGAATTATTGA
63 TTTTCAGGAAACAGGGAAATTTCAAGAAAAAAATTAAAAACTCATGAAAATGAATGAATTTTTGA
* * *
96211 AAATGGATTTAATTTGAAATAAATAATAATATTTTATGG
128 AAATGGATTTAATATGAAATAAATAATAATATTTAATGA
* * *
96250 ATTTTAAAAATTAAAAACCAAGAAAAATCCCCCCAAAAAATCTACGGAGTAGAAAACTCCGTATT
1 ATTTTAAAAATTAAAAACCAAGAAAAATCCCCCGAAAAAATCTATGGAGTAGAAAACTTCGT-TT
* *
96315 TTC--GAAACATGGG-AATTTCCA-AAAAAATTTAAAAACTCATGAAAATGAATGAATTTTTGAA
65 TTCAGGAAACA-GGGAAATTTCAAGAAAAAAATTAAAAACTCATGAAAATGAATGAATTTTTGAA
* * *
96376 AACT-AATTTAATATAAAATAAATGATAATATTTAATGA
129 AA-TGGATTTAATATGAAATAAATAATAATATTTAATGA
* * * ** *
96414 ATTTTGAAATTTAAAAACCAAGAAAAATCCCTCTGAAAAAAAATTTGGAGTA-AAAAGC-TCTGT
1 ATTTTAAAAATTAAAAACCAAGAAAAATCCC-CCGAAAAAATCTATGGAGTAGAAAA-CTTC-GT
* * * * * *
96477 ATTT-AGAAAATAAGGAAATTTCAAGAAAAAAATAAAAAACTAATGAAAATGAA-GTAATTTTTG
63 TTTTCAGGAAACAGGGAAATTTCAAGAAAAAAATTAAAAACTCATGAAAATGAATG-AATTTTTG
* * * *
96540 AAAATGGATTTACTATGAAATAAATAATAGTATGTGATGA
127 AAAATGGATTTAATATGAAATAAATAATAATATTTAATGA
96580 ATTTTAAAAATT
1 ATTTTAAAAATT
96592 TTAAACCTAT
Statistics
Matches: 282, Mismatches: 45, Indels: 30
0.79 0.13 0.08
Matches are distributed among these distances:
164 109 0.39
165 63 0.22
166 109 0.39
167 1 0.00
ACGTcount: A:0.50, C:0.09, G:0.12, T:0.30
Consensus pattern (166 bp):
ATTTTAAAAATTAAAAACCAAGAAAAATCCCCCGAAAAAATCTATGGAGTAGAAAACTTCGTTTT
TCAGGAAACAGGGAAATTTCAAGAAAAAAATTAAAAACTCATGAAAATGAATGAATTTTTGAAAA
TGGATTTAATATGAAATAAATAATAATATTTAATGA
Found at i:96654 original size:166 final size:164
Alignment explanation
Indices: 96160--96685 Score: 485
Period size: 166 Copynumber: 3.2 Consensus size: 164
96150 TCAGGAAAAG
* * * *
96160 GGAAATTTCAAGAAAAAAATTAAAAACTCATGAATATAAATGAATTATTGAAAATGGATTTAATT
1 GGAAATTTCAA-AAAAAAATTAAAAACTCATGAAAATGAATGAATTTTTGAAAATGGATTTAATA
* * * ***
96225 TGAAATAAATAATAATATTTTATGGATTTTAAAAATTAAAAACCAAGAAAAATCCCCCCAAAAAA
65 TGAAATAAATAATAATATTTAATGAATTTTAAAAATTTAAAACCAAGAAAAATCCCTTGAAAAAA
* * ** * *
96290 TCTACGGAGTAGAAAACTCCGTATTTTCGAAACAT-
130 TTTACGAAAAAGAAAACTCCGTAATTTAGAAA-ATA
* * * *
96325 GGGAATTTCCAAAAAAATTTAAAAACTCATGAAAATGAATGAATTTTTGAAAACT-AATTTAATA
1 GGAAATTTCAAAAAAAAATTAAAAACTCATGAAAATGAATGAATTTTTGAAAA-TGGATTTAATA
* * *
96389 TAAAATAAATGATAATATTTAATGAATTTT-GAAATTTAAAAACCAAGAAAAATCCCTCTGAAAA
65 TGAAATAAATAATAATATTTAATGAATTTTAAAAATTT-AAAACCAAGAAAAATCCCT-TG--AA
* ** * *
96453 AAAATTT-GGAGTAA-AAAGCTCTGT-ATTTAGAAAATAA
126 AAAATTTACGAAAAAGAAAACTCCGTAATTTAGAAAAT-A
* * *
96490 GGAAATTTCAAGAAAAAAATAAAAAACTAATGAAAATGAA-GTAATTTTTGAAAATGGATTTACT
1 GGAAATTTCAA-AAAAAAATTAAAAACTCATGAAAATGAATG-AATTTTTGAAAATGGATTTAAT
* * * * * *
96554 ATGAAATAAATAATAGTATGTGATGAATTTTAAAAATTTTAAACCTATG-AAAATCGTCTTGAAA
64 ATGAAATAAATAATAATATTTAATGAATTTTAAAAATTTAAAACC-AAGAAAAATC-CCTTGAAA
* *
96618 AAATTTACGAAAAAGAAAACACCATAATTT-GAAAATA
127 AAATTTACGAAAAAGAAAACTCCGTAATTTAGAAAATA
* * *
96655 GGAGGAATTTCAAAAGAAAATCAATAACTCA
1 GGA--AATTTCAAAAAAAAATTAAAAACTCA
96686 AAAAATAAAA
Statistics
Matches: 289, Mismatches: 54, Indels: 35
0.76 0.14 0.09
Matches are distributed among these distances:
163 7 0.02
164 105 0.36
165 37 0.13
166 110 0.38
167 30 0.10
ACGTcount: A:0.51, C:0.09, G:0.12, T:0.29
Consensus pattern (164 bp):
GGAAATTTCAAAAAAAAATTAAAAACTCATGAAAATGAATGAATTTTTGAAAATGGATTTAATAT
GAAATAAATAATAATATTTAATGAATTTTAAAAATTTAAAACCAAGAAAAATCCCTTGAAAAAAT
TTACGAAAAAGAAAACTCCGTAATTTAGAAAATA
Found at i:99461 original size:154 final size:152
Alignment explanation
Indices: 99284--99702 Score: 458
Period size: 154 Copynumber: 2.7 Consensus size: 152
99274 TAAATTTATC
* *
99284 CGGTAGGA-TTTTCTAAATTTATAATTTTCAAAATTCTTTAAATATTATTGCTTAATTCATATTA
1 CGGTAAGATTTTTCTAAGTTTATAATTTTCAAAATTCTTTAAATATTATTG-TTAATTCATATTA
* * * *
99348 AATCAGTTTTGAAAAATTCAATTTATTTTATGAGTTTAAGAGTTTTTTCTGTTAGT-AAGATGC-
65 AATCAGTTTTGAAAAATTCAATTTATTTTATGAGTTTTAGAATTTTTCCTGCTA-TCAA-ATGCA
99411 GAAGCTTTCTACACCATAAATTTCTTT
128 G-AGCTTTCTACACCAT-AATTTCTTT
* **
99438 -GGTAATATTTTTCTAAGTTTATAATTTTCAAAATTCTTTAAATATTATTGTTTAATTTGTATTA
1 CGGTAAGATTTTTCTAAGTTTATAATTTTCAAAATTCTTTAAATATTATTG-TTAATTCATATTA
* *
99502 AATTAGTTTTAAAAAAATT-AATTTATTTTATGAGTTTTAGAATTTTTCCTGCTATCGAAATGCA
65 AATCAGTTTT-GAAAAATTCAATTTATTTTATGAGTTTTAGAATTTTTCCTGCTATC-AAATGCA
* **** *
99566 GAGCTTTCTTCTTTGTAATTTTTTT
128 GAGCTTTCTACACCATAATTTCTTT
* * * * ***
99591 CGGTAGGATTTTTCCT-AGTTCATAATTTTAAAAATTC-TTAAAAATTATTAGTTAGCCCATATT
1 CGGTAAGATTTTT-CTAAGTTTATAATTTTCAAAATTCTTTAAATATTATT-GTTAATTCATATT
*
99654 AAATCAGTTTTGAAAATTTCAATTT-TTTTGATGAGTTTTAGAATTTTTC
64 AAATCAGTTTTGAAAAATTCAATTTATTTT-ATGAGTTTTAGAATTTTTC
99703 TTATACCAAG
Statistics
Matches: 224, Mismatches: 31, Indels: 21
0.81 0.11 0.08
Matches are distributed among these distances:
152 10 0.04
153 66 0.29
154 136 0.61
155 12 0.05
ACGTcount: A:0.32, C:0.09, G:0.11, T:0.48
Consensus pattern (152 bp):
CGGTAAGATTTTTCTAAGTTTATAATTTTCAAAATTCTTTAAATATTATTGTTAATTCATATTAA
ATCAGTTTTGAAAAATTCAATTTATTTTATGAGTTTTAGAATTTTTCCTGCTATCAAATGCAGAG
CTTTCTACACCATAATTTCTTT
Found at i:100360 original size:7 final size:7
Alignment explanation
Indices: 100348--100379 Score: 64
Period size: 7 Copynumber: 4.6 Consensus size: 7
100338 GGCATTTTTG
100348 AAAAAGA
1 AAAAAGA
100355 AAAAAGA
1 AAAAAGA
100362 AAAAAGA
1 AAAAAGA
100369 AAAAAGA
1 AAAAAGA
100376 AAAA
1 AAAA
100380 CAAAAGATTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (7 bp):
AAAAAGA
Found at i:100473 original size:23 final size:24
Alignment explanation
Indices: 100429--100473 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 24
100419 TAAATACATC
* *
100429 ATTCTTTTTGTTTTTCTTATTTTG
1 ATTCTTTTTGTTTATCTCATTTTG
100453 ATTCTTTTT-TTTATCTCATTT
1 ATTCTTTTTGTTTATCTCATTT
100474 ATGAGTTAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 10 0.53
24 9 0.47
ACGTcount: A:0.11, C:0.11, G:0.04, T:0.73
Consensus pattern (24 bp):
ATTCTTTTTGTTTATCTCATTTTG
Found at i:101327 original size:2 final size:2
Alignment explanation
Indices: 101322--101346 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
101312 TTTGCTGTAT
101322 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 T
101347 GTACATTTTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:103761 original size:30 final size:32
Alignment explanation
Indices: 103708--103784 Score: 95
Period size: 31 Copynumber: 2.5 Consensus size: 32
103698 ATGCCTTAAG
** * *
103708 AGATCTAAGCTTGATTAAATATGATTCT-ACA
1 AGATCTAAGCTTGGCTGAATATGATCCTAACA
*
103739 AGATTTAA-CTTGGCTGAATATGATCCTAACA
1 AGATCTAAGCTTGGCTGAATATGATCCTAACA
103770 AGATCTAAGCTTGGC
1 AGATCTAAGCTTGGC
103785 CTATTGTTAT
Statistics
Matches: 38, Mismatches: 6, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
30 15 0.39
31 17 0.45
32 6 0.16
ACGTcount: A:0.35, C:0.16, G:0.17, T:0.32
Consensus pattern (32 bp):
AGATCTAAGCTTGGCTGAATATGATCCTAACA
Found at i:107581 original size:20 final size:19
Alignment explanation
Indices: 107538--107588 Score: 66
Period size: 20 Copynumber: 2.6 Consensus size: 19
107528 TAGCCAAACT
**
107538 TGTATCGATACACAAAGTA
1 TGTATCGATACACAAAAAA
107557 TGTATCGATACACAAAAAAA
1 TGTATCGATACAC-AAAAAA
*
107577 TGTATTGATACA
1 TGTATCGATACA
107589 TTGGCTTGTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 13 0.46
20 15 0.54
ACGTcount: A:0.45, C:0.14, G:0.14, T:0.27
Consensus pattern (19 bp):
TGTATCGATACACAAAAAA
Found at i:111672 original size:15 final size:15
Alignment explanation
Indices: 111654--111683 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
111644 CCAAATTGAG
111654 GAAGCTCAAAATGAA
1 GAAGCTCAAAATGAA
*
111669 GAAGCTCCAAATGAA
1 GAAGCTCAAAATGAA
111684 ATTGATCAAC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.50, C:0.17, G:0.20, T:0.13
Consensus pattern (15 bp):
GAAGCTCAAAATGAA
Found at i:111679 original size:16 final size:16
Alignment explanation
Indices: 111643--111683 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 16
111633 GATAAAAATG
* *
111643 TCCAAATTGAGGAAGC
1 TCCAAAATGAAGAAGC
111659 T-CAAAATGAAGAAGC
1 TCCAAAATGAAGAAGC
111674 TCC-AAATGAA
1 TCCAAAATGAA
111684 ATTGATCAAC
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
15 20 0.91
16 2 0.09
ACGTcount: A:0.46, C:0.17, G:0.20, T:0.17
Consensus pattern (16 bp):
TCCAAAATGAAGAAGC
Found at i:113916 original size:21 final size:20
Alignment explanation
Indices: 113892--113938 Score: 51
Period size: 22 Copynumber: 2.3 Consensus size: 20
113882 AAATCTTTTG
*
113892 CAAAATAC-TTGTTTTTCACTT
1 CAAAATACATCGTTTTTCA--T
*
113913 CAAATTACATCGTTTTTCAT
1 CAAAATACATCGTTTTTCAT
113933 CAAAAT
1 CAAAAT
113939 CAGCTTCAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
20 6 0.27
21 7 0.32
22 9 0.41
ACGTcount: A:0.34, C:0.19, G:0.04, T:0.43
Consensus pattern (20 bp):
CAAAATACATCGTTTTTCAT
Found at i:116315 original size:19 final size:19
Alignment explanation
Indices: 116291--116340 Score: 73
Period size: 19 Copynumber: 2.6 Consensus size: 19
116281 TAGCCAAACT
*
116291 TGTATCGATACACAAAGAA
1 TGTATCGATACACAAAAAA
*
116310 TGTATCCATACACAAAAAA
1 TGTATCGATACACAAAAAA
*
116329 TGTATTGATACA
1 TGTATCGATACA
116341 TTGGCTTGTA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.46, C:0.16, G:0.12, T:0.26
Consensus pattern (19 bp):
TGTATCGATACACAAAAAA
Found at i:125043 original size:19 final size:19
Alignment explanation
Indices: 125019--125066 Score: 87
Period size: 19 Copynumber: 2.5 Consensus size: 19
125009 GCCAAACTTT
*
125019 TATCGATACACAAAGAATG
1 TATCGATACACAAAAAATG
125038 TATCGATACACAAAAAATG
1 TATCGATACACAAAAAATG
125057 TATCGATACA
1 TATCGATACA
125067 TTGGCTTGTA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.48, C:0.17, G:0.12, T:0.23
Consensus pattern (19 bp):
TATCGATACACAAAAAATG
Found at i:131344 original size:21 final size:20
Alignment explanation
Indices: 131320--131366 Score: 51
Period size: 22 Copynumber: 2.3 Consensus size: 20
131310 AAATCTTTTG
*
131320 CAAAATAC-TTGTTTTTCACTT
1 CAAAATACATCGTTTTTCA--T
*
131341 CAAATTACATCGTTTTTCAT
1 CAAAATACATCGTTTTTCAT
131361 CAAAAT
1 CAAAAT
131367 CAGCTTCAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
20 6 0.27
21 7 0.32
22 9 0.41
ACGTcount: A:0.34, C:0.19, G:0.04, T:0.43
Consensus pattern (20 bp):
CAAAATACATCGTTTTTCAT
Found at i:133745 original size:19 final size:19
Alignment explanation
Indices: 133721--133770 Score: 73
Period size: 19 Copynumber: 2.6 Consensus size: 19
133711 TAGCCAAACT
* **
133721 TGTATCGATGCACAAAGTA
1 TGTATCGATACACAAAAAA
133740 TGTATCGATACACAAAAAA
1 TGTATCGATACACAAAAAA
133759 TGTATCGATACA
1 TGTATCGATACA
133771 TTGGCTTGTA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.42, C:0.16, G:0.16, T:0.26
Consensus pattern (19 bp):
TGTATCGATACACAAAAAA
Found at i:135952 original size:21 final size:21
Alignment explanation
Indices: 135926--135965 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
135916 AAGAAAAGCC
135926 AAAAA-GAAAAAAGAGGAGAAT
1 AAAAAGGAAAAAA-AGGAGAAT
*
135947 AAAAAGGGAAAAAAGGAGA
1 AAAAAGGAAAAAAAGGAGA
135966 TTACGAGGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 11 0.65
22 6 0.35
ACGTcount: A:0.70, C:0.00, G:0.28, T:0.03
Consensus pattern (21 bp):
AAAAAGGAAAAAAAGGAGAAT
Found at i:138157 original size:30 final size:30
Alignment explanation
Indices: 138075--138159 Score: 109
Period size: 30 Copynumber: 2.8 Consensus size: 30
138065 AATATATTGT
* *
138075 AATTCATTTTCTTGCAATTTAAATTCATGC
1 AATTTATTTTATTGCAATTTAAATTCATGC
* *
138105 AATTTATTTTATTGTAGTTTAAATTCATGC
1 AATTTATTTTATTGCAATTTAAATTCATGC
*
138135 ACATTTATTTT-TTGCAACTTAAATT
1 A-ATTTATTTTATTGCAATTTAAATT
138160 TTATACTTTA
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
30 38 0.81
31 9 0.19
ACGTcount: A:0.31, C:0.12, G:0.07, T:0.51
Consensus pattern (30 bp):
AATTTATTTTATTGCAATTTAAATTCATGC
Found at i:138630 original size:79 final size:79
Alignment explanation
Indices: 138522--138669 Score: 210
Period size: 79 Copynumber: 1.9 Consensus size: 79
138512 GACAATTAGC
* *
138522 TCATTTTGAGTCTATTTCATTAAAATTGAGTCTTTTAGGTCATGTTAGTATTTGCATATCAAAAC
1 TCATTTTGAGGCTATTTCATTAAAATTGAGTCTTTTAGGTCATGTTAGCATTTGCATATCAAAAC
138587 ATGTCCCTTTATGG
66 ATGTCCCTTTATGG
* * **
138601 TCATTTT-AGGCT-TTTCATATCAAAATTGAGTCTTTTAGGTCTTGTTGGCATTTTTATATCAAA
1 TCATTTTGAGGCTATTTCAT-T-AAAATTGAGTCTTTTAGGTCATGTTAGCATTTGCATATCAAA
138664 ACATGT
64 ACATGT
138670 TTATTAAGGT
Statistics
Matches: 61, Mismatches: 6, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
77 6 0.10
78 5 0.08
79 50 0.82
ACGTcount: A:0.26, C:0.14, G:0.15, T:0.45
Consensus pattern (79 bp):
TCATTTTGAGGCTATTTCATTAAAATTGAGTCTTTTAGGTCATGTTAGCATTTGCATATCAAAAC
ATGTCCCTTTATGG
Found at i:144203 original size:13 final size:13
Alignment explanation
Indices: 144185--144214 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
144175 ACATTTTACT
144185 ATGTATCGATACA
1 ATGTATCGATACA
144198 ATGTATCGATACA
1 ATGTATCGATACA
144211 ATGT
1 ATGT
144215 CCCATGTATC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.37, C:0.13, G:0.17, T:0.33
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:144222 original size:33 final size:33
Alignment explanation
Indices: 144162--144226 Score: 85
Period size: 33 Copynumber: 2.0 Consensus size: 33
144152 GTCGTTGGGC
* * * *
144162 ACAATGTATTGATACATTTTACTATGTATCGAT
1 ACAATGTATCGATACAATGTACCATGTATCGAT
*
144195 ACAATGTATCGATACAATGTCCCATGTATCGA
1 ACAATGTATCGATACAATGTACCATGTATCGA
144227 CACATTTCAC
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
33 27 1.00
ACGTcount: A:0.34, C:0.17, G:0.14, T:0.35
Consensus pattern (33 bp):
ACAATGTATCGATACAATGTACCATGTATCGAT
Found at i:144284 original size:20 final size:20
Alignment explanation
Indices: 144259--144313 Score: 76
Period size: 19 Copynumber: 2.8 Consensus size: 20
144249 CTGCCAGTTT
*
144259 TATGTATTGATACAATTAAG
1 TATGTATCGATACAATTAAG
*
144279 TATGTATCGATACAA-TGAG
1 TATGTATCGATACAATTAAG
*
144298 CATGTATCGATACAAT
1 TATGTATCGATACAAT
144314 GTATCGATAC
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
19 17 0.55
20 14 0.45
ACGTcount: A:0.38, C:0.11, G:0.16, T:0.35
Consensus pattern (20 bp):
TATGTATCGATACAATTAAG
Found at i:144317 original size:13 final size:13
Alignment explanation
Indices: 144299--144324 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
144289 TACAATGAGC
144299 ATGTATCGATACA
1 ATGTATCGATACA
144312 ATGTATCGATACA
1 ATGTATCGATACA
144325 TCTAGATGTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:146342 original size:33 final size:33
Alignment explanation
Indices: 146305--146371 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
146295 TTCAACGATT
146305 TGTATCGATACATAAAATGTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
*** *
146338 TGTATCGATACATATTTTTTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
146371 T
1 T
146372 TTAAGCTACT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.34, C:0.12, G:0.13, T:0.40
Consensus pattern (33 bp):
TGTATCGATACATAAAATGTTGTATCGATACAA
Found at i:146343 original size:13 final size:13
Alignment explanation
Indices: 146325--146349 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
146315 CATAAAATGT
146325 TGTATCGATACAA
1 TGTATCGATACAA
146338 TGTATCGATACA
1 TGTATCGATACA
146350 TATTTTTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:146432 original size:13 final size:13
Alignment explanation
Indices: 146414--146438 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
146404 ATTACTCACA
146414 TGTATCGATACAT
1 TGTATCGATACAT
146427 TGTATCGATACA
1 TGTATCGATACA
146439 CTGATCTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:146575 original size:52 final size:52
Alignment explanation
Indices: 146447--146567 Score: 224
Period size: 52 Copynumber: 2.3 Consensus size: 52
146437 CACTGATCTT
*
146447 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACATTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
*
146499 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
146551 TGTATCGATACATGCAG
1 TGTATCGATACATGCAG
146568 ATAAATTTTC
Statistics
Matches: 67, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
52 67 1.00
ACGTcount: A:0.35, C:0.18, G:0.18, T:0.29
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
Found at i:150072 original size:20 final size:20
Alignment explanation
Indices: 150049--150093 Score: 90
Period size: 20 Copynumber: 2.2 Consensus size: 20
150039 CTGGCCGGTT
150049 GCGACTTGGGTGTGCCGATC
1 GCGACTTGGGTGTGCCGATC
150069 GCGACTTGGGTGTGCCGATC
1 GCGACTTGGGTGTGCCGATC
150089 GCGAC
1 GCGAC
150094 CTGGAAGGGC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.11, C:0.27, G:0.40, T:0.22
Consensus pattern (20 bp):
GCGACTTGGGTGTGCCGATC
Found at i:155836 original size:49 final size:48
Alignment explanation
Indices: 155756--155848 Score: 132
Period size: 49 Copynumber: 1.9 Consensus size: 48
155746 ATAAGCTCCC
** * *
155756 ACCAAACAAGCTAGCAAAATATGAACCAAAAAAATAAAAAAGAAAGAAT
1 ACCAAACAAGCTAAAAAAATAT-AAACAAAAAAAAAAAAAAGAAAGAAT
*
155805 ACCAAACAAGCTAAAAAAATATAAACAAAAAAAAAGAAAAGAAA
1 ACCAAACAAGCTAAAAAAATATAAACAAAAAAAAAAAAAAGAAA
155849 AAAGGAATGG
Statistics
Matches: 39, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
48 19 0.49
49 20 0.51
ACGTcount: A:0.70, C:0.13, G:0.09, T:0.09
Consensus pattern (48 bp):
ACCAAACAAGCTAAAAAAATATAAACAAAAAAAAAAAAAAGAAAGAAT
Found at i:156344 original size:30 final size:30
Alignment explanation
Indices: 156307--156398 Score: 91
Period size: 30 Copynumber: 3.0 Consensus size: 30
156297 TTTTTTTTAG
156307 TCTTGGTTTCATCCAAGTCATTATTTAGGTT
1 TCTTGGTTTCATCCAAGTCATT-TTTAGGTT
**
156338 TC-TGG-TTCTATCCAAGTCATTTCTT-GGAG
1 TCTTGGTTTC-ATCCAAGTCATTT-TTAGGTT
* *
156367 TCTTGGTTCCGTCCAAGTCATTGTTTAGGTT
1 TCTTGGTTTCATCCAAGTCATT-TTTAGGTT
156398 T
1 T
156399 TTGATTTTGT
Statistics
Matches: 49, Mismatches: 6, Indels: 12
0.73 0.09 0.18
Matches are distributed among these distances:
29 8 0.16
30 33 0.67
31 8 0.16
ACGTcount: A:0.16, C:0.18, G:0.20, T:0.46
Consensus pattern (30 bp):
TCTTGGTTTCATCCAAGTCATTTTTAGGTT
Found at i:156419 original size:60 final size:60
Alignment explanation
Indices: 156305--156519 Score: 172
Period size: 60 Copynumber: 3.6 Consensus size: 60
156295 CATTTTTTTT
* * * * * *
156305 AGTCTTGGTTTCATCCAAGTCATTATTTAGGTTTCTGGTTCTATCCAAGTCATTTCTTGG
1 AGTCTTGGTTTCGTCCAAGTCATTGTTTAGGTTTTTGATTCTATACAAGCCATTTCTTGG
* * * * * *
156365 AGTCTTGGTTCCGTCCAAGTCATTGTTTAGGTTTTTGATTTTGTATATGCCATTTCTTTG
1 AGTCTTGGTTTCGTCCAAGTCATTGTTTAGGTTTTTGATTCTATACAAGCCATTTCTTGG
* * * * * *
156425 AGTCTTAGTTTTG-CCTAAGTCATTG-CTAGGTTTTTGGTTCCA-ACTAAGCCATTTCTTTG
1 AGTCTTGGTTTCGTCC-AAGTCATTGTTTAGGTTTTTGATTCTATAC-AAGCCATTTCTTGG
*
156484 ATTCTTGGTTTCACGT--AAGTCATT-TTGTAGGTTTTT
1 AGTCTTGGTTT--CGTCCAAGTCATTGTT-TAGGTTTTT
156520 AGTTTACCTT
Statistics
Matches: 122, Mismatches: 26, Indels: 14
0.75 0.16 0.09
Matches are distributed among these distances:
58 1 0.01
59 44 0.36
60 76 0.62
61 1 0.01
ACGTcount: A:0.17, C:0.16, G:0.19, T:0.47
Consensus pattern (60 bp):
AGTCTTGGTTTCGTCCAAGTCATTGTTTAGGTTTTTGATTCTATACAAGCCATTTCTTGG
Found at i:156716 original size:58 final size:59
Alignment explanation
Indices: 156582--156717 Score: 134
Period size: 58 Copynumber: 2.3 Consensus size: 59
156572 TTGCTTTCAC
** * * *
156582 CCAAGTCATTTTTAGAATTCTGGTTTTACCTAGGCCATTTCTTTGAGTCTTGGTTCCGT
1 CCAAGTCATTTTTAGGTTTATGGTTTTACCTAAGCCATTTCTTTGAATCTTGGTTCCGT
* * * ** *
156641 CCAAGTTAGTTTCAGGTTTATGG-TTTGGCTAAGCCATTTCTTTGAAT-TTGGACTT-TGT
1 CCAAGTCATTTTTAGGTTTATGGTTTTACCTAAGCCATTTCTTTGAATCTTGG--TTCCGT
156699 CCAAGTCATTTTTAGGTTT
1 CCAAGTCATTTTTAGGTTT
156718 TTTTTTTTAA
Statistics
Matches: 61, Mismatches: 14, Indels: 5
0.76 0.17 0.06
Matches are distributed among these distances:
57 4 0.07
58 38 0.62
59 19 0.31
ACGTcount: A:0.18, C:0.17, G:0.20, T:0.45
Consensus pattern (59 bp):
CCAAGTCATTTTTAGGTTTATGGTTTTACCTAAGCCATTTCTTTGAATCTTGGTTCCGT
Found at i:158120 original size:13 final size:13
Alignment explanation
Indices: 158101--158139 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
158091 TCTTTCTTAA
158101 ATATTTATTTTAT
1 ATATTTATTTTAT
*
158114 TTATTTATTTTAT
1 ATATTTATTTTAT
158127 ATATTTATTTTAT
1 ATATTTATTTTAT
158140 GTGAATTTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (13 bp):
ATATTTATTTTAT
Found at i:161418 original size:13 final size:13
Alignment explanation
Indices: 161400--161425 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
161390 ACAATTCTTC
161400 TTGTATCGATACA
1 TTGTATCGATACA
161413 TTGTATCGATACA
1 TTGTATCGATACA
161426 ATGTGCTATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:161438 original size:33 final size:33
Alignment explanation
Indices: 161381--161443 Score: 92
Period size: 33 Copynumber: 1.9 Consensus size: 33
161371 TTTGGGACAA
*
161381 TGTATCGATACAATTCTTCTTGTATCGATACAT
1 TGTATCGATACAATTCTGCTTGTATCGATACAT
*
161414 TGTATCGATACAA-TGTGCTATGTATCGATA
1 TGTATCGATACAATTCTGCT-TGTATCGATA
161444 TAAATAGTGG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
32 4 0.15
33 23 0.85
ACGTcount: A:0.29, C:0.16, G:0.16, T:0.40
Consensus pattern (33 bp):
TGTATCGATACAATTCTGCTTGTATCGATACAT
Found at i:162506 original size:33 final size:33
Alignment explanation
Indices: 162459--162531 Score: 119
Period size: 33 Copynumber: 2.2 Consensus size: 33
162449 TACGTCGATT
*
162459 AAGTGAACTAAAGTGCTCATCCATGCACTGTGA
1 AAGTGAACTAAAGTGCTCATCCATGCACTGCGA
* *
162492 AAGTGAACTTAAGTGCTCATCCATGCGCTGCGA
1 AAGTGAACTAAAGTGCTCATCCATGCACTGCGA
162525 AAGTGAA
1 AAGTGAA
162532 GTGATCAACT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
33 37 1.00
ACGTcount: A:0.33, C:0.21, G:0.23, T:0.23
Consensus pattern (33 bp):
AAGTGAACTAAAGTGCTCATCCATGCACTGCGA
Found at i:164030 original size:13 final size:13
Alignment explanation
Indices: 164007--164046 Score: 62
Period size: 13 Copynumber: 3.1 Consensus size: 13
163997 ATAGTAACCC
164007 ATGTATCGATACA
1 ATGTATCGATACA
* *
164020 TTGTATTGATACA
1 ATGTATCGATACA
164033 ATGTATCGATACA
1 ATGTATCGATACA
164046 A
1 A
164047 AGAACATTGT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.38, C:0.12, G:0.15, T:0.35
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:165461 original size:15 final size:16
Alignment explanation
Indices: 165436--165466 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
165426 CCACATTTCC
165436 TCAATTAAAAACTTTT
1 TCAATTAAAAACTTTT
165452 TCAA-TAAAAACTTTT
1 TCAATTAAAAACTTTT
165467 AAAAGCCTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 11 0.73
16 4 0.27
ACGTcount: A:0.45, C:0.13, G:0.00, T:0.42
Consensus pattern (16 bp):
TCAATTAAAAACTTTT
Found at i:175069 original size:20 final size:20
Alignment explanation
Indices: 175041--175112 Score: 81
Period size: 20 Copynumber: 3.6 Consensus size: 20
175031 ACCCAGAATA
*
175041 TATCAATACAATGAGAAATG
1 TATCGATACAATGAGAAATG
*****
175061 TATCGATACAATTTCTTATG
1 TATCGATACAATGAGAAATG
*
175081 TATCGATACATTGAGAAATG
1 TATCGATACAATGAGAAATG
175101 TATCGATACAAT
1 TATCGATACAAT
175113 TTCCATTCAG
Statistics
Matches: 39, Mismatches: 13, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
20 39 1.00
ACGTcount: A:0.40, C:0.12, G:0.14, T:0.33
Consensus pattern (20 bp):
TATCGATACAATGAGAAATG
Found at i:175181 original size:20 final size:20
Alignment explanation
Indices: 175138--175192 Score: 67
Period size: 20 Copynumber: 2.7 Consensus size: 20
175128 CACATGGTCC
175138 TGTATCGATACATTTCATGCA
1 TGTATCGATACA-TTCATGCA
*
175159 TGTATCGATACATTCACT-TA
1 TGTATCGATACATTCA-TGCA
*
175179 TGTATCAATACATT
1 TGTATCGATACATT
175193 GTGAAAGCTC
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
20 18 0.58
21 13 0.42
ACGTcount: A:0.31, C:0.18, G:0.11, T:0.40
Consensus pattern (20 bp):
TGTATCGATACATTCATGCA
Found at i:178047 original size:20 final size:21
Alignment explanation
Indices: 178018--178059 Score: 68
Period size: 20 Copynumber: 2.0 Consensus size: 21
178008 TGGGGGCTGC
*
178018 CCGGTTGCGACCTGG-GAGTG
1 CCGGTCGCGACCTGGTGAGTG
178038 CCGGTCGCGACCTGGTGAGTG
1 CCGGTCGCGACCTGGTGAGTG
178059 C
1 C
178060 TGCCTAGAGA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 14 0.70
21 6 0.30
ACGTcount: A:0.10, C:0.29, G:0.43, T:0.19
Consensus pattern (21 bp):
CCGGTCGCGACCTGGTGAGTG
Found at i:178498 original size:13 final size:13
Alignment explanation
Indices: 178476--178513 Score: 58
Period size: 13 Copynumber: 2.9 Consensus size: 13
178466 ATAAACCCTT
* *
178476 TGTATTGATACAC
1 TGTATCGATACAA
178489 TGTATCGATACAA
1 TGTATCGATACAA
178502 TGTATCGATACA
1 TGTATCGATACA
178514 GAGAATGCTG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:184768 original size:13 final size:13
Alignment explanation
Indices: 184750--184774 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
184740 TACAATGGTC
184750 ATGTATCGATACA
1 ATGTATCGATACA
184763 ATGTATCGATAC
1 ATGTATCGATAC
184775 TGTGCATTAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:190656 original size:20 final size:20
Alignment explanation
Indices: 190598--190662 Score: 69
Period size: 20 Copynumber: 3.1 Consensus size: 20
190588 CATGGTGCTA
* *
190598 TATCGATACATTTCATGCATG
1 TATCGATACATTTCCT-TATG
*
190619 TAACGATACA-TTCACTTATG
1 TATCGATACATTTC-CTTATG
190639 TATCGATACATTTCCTTATTG
1 TATCGATACATTTCCTTA-TG
190660 TAT
1 TAT
190663 TAATATAAAT
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
20 19 0.51
21 18 0.49
ACGTcount: A:0.29, C:0.18, G:0.11, T:0.42
Consensus pattern (20 bp):
TATCGATACATTTCCTTATG
Found at i:195572 original size:33 final size:32
Alignment explanation
Indices: 195508--195575 Score: 100
Period size: 33 Copynumber: 2.1 Consensus size: 32
195498 GTAGCTAAAC
** *
195508 TTGTATCGATACACATAGTATTTATCGATACA
1 TTGTATCGATACACATAAAATGTATCGATACA
195540 TTGTATCGATACACCATAAAATGTATCGATACA
1 TTGTATCGATACA-CATAAAATGTATCGATACA
195573 TTG
1 TTG
195576 GCTTGTAACG
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
32 13 0.41
33 19 0.59
ACGTcount: A:0.35, C:0.16, G:0.13, T:0.35
Consensus pattern (32 bp):
TTGTATCGATACACATAAAATGTATCGATACA
Found at i:197182 original size:18 final size:18
Alignment explanation
Indices: 197155--197190 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
197145 GTTAACCATC
197155 AAAGACGATGAAGATGAT
1 AAAGACGATGAAGATGAT
* *
197173 AAAGATGATGATGATGAT
1 AAAGACGATGAAGATGAT
197191 GGTGACTCAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.47, C:0.03, G:0.28, T:0.22
Consensus pattern (18 bp):
AAAGACGATGAAGATGAT
Found at i:201698 original size:13 final size:13
Alignment explanation
Indices: 201680--201718 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
201670 ACAGCATTCT
*
201680 TTGTATTGATACA
1 TTGTATCGATACA
201693 TTGTATCGATACA
1 TTGTATCGATACA
* *
201706 CTGTATCAATACA
1 TTGTATCGATACA
201719 AGGGGATTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.33, C:0.15, G:0.13, T:0.38
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:203558 original size:27 final size:27
Alignment explanation
Indices: 203528--203585 Score: 107
Period size: 27 Copynumber: 2.1 Consensus size: 27
203518 GTGCTTATGA
203528 TTAATTAAGGGGGAGAATGCGAATTTG
1 TTAATTAAGGGGGAGAATGCGAATTTG
*
203555 TTAATTAAGGGGGTGAATGCGAATTTG
1 TTAATTAAGGGGGAGAATGCGAATTTG
203582 TTAA
1 TTAA
203586 AATGACCTTA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.33, C:0.03, G:0.31, T:0.33
Consensus pattern (27 bp):
TTAATTAAGGGGGAGAATGCGAATTTG
Found at i:204287 original size:13 final size:13
Alignment explanation
Indices: 204269--204293 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
204259 ACACATAGTA
204269 TGTATCGATACAT
1 TGTATCGATACAT
204282 TGTATCGATACA
1 TGTATCGATACA
204294 CCATAAAATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:204290 original size:32 final size:33
Alignment explanation
Indices: 204249--204316 Score: 111
Period size: 33 Copynumber: 2.1 Consensus size: 33
204239 GTAGCTAAAC
**
204249 TTGTATCGATACA-CATAGTATGTATCGATACA
1 TTGTATCGATACACCATAAAATGTATCGATACA
204281 TTGTATCGATACACCATAAAATGTATCGATACA
1 TTGTATCGATACACCATAAAATGTATCGATACA
204314 TTG
1 TTG
204317 GCTTGTAATG
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
32 13 0.39
33 20 0.61
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.34
Consensus pattern (33 bp):
TTGTATCGATACACCATAAAATGTATCGATACA
Found at i:210603 original size:32 final size:34
Alignment explanation
Indices: 210564--210648 Score: 104
Period size: 32 Copynumber: 2.5 Consensus size: 34
210554 ATCTTTCAAG
*
210564 GCTAAGATAGAAACCTCCCT-ATCTTTTT-ACAA
1 GCTAAGATAGAAACCTCCCTAATCTTTTTCAAAA
*
210596 GCTAAGATAGAACCTCTTTCCCTAATCTTTTTCAAAA
1 GCTAAGATAGAAAC-C--TCCCTAATCTTTTTCAAAA
210633 GCTAAGATA-AAACCTC
1 GCTAAGATAGAAACCTC
210649 TCAATCACTT
Statistics
Matches: 45, Mismatches: 3, Indels: 9
0.79 0.05 0.16
Matches are distributed among these distances:
32 13 0.29
33 3 0.07
35 6 0.13
36 11 0.24
37 12 0.27
ACGTcount: A:0.35, C:0.25, G:0.09, T:0.31
Consensus pattern (34 bp):
GCTAAGATAGAAACCTCCCTAATCTTTTTCAAAA
Found at i:210638 original size:37 final size:34
Alignment explanation
Indices: 210564--210649 Score: 104
Period size: 37 Copynumber: 2.5 Consensus size: 34
210554 ATCTTTCAAG
* *
210564 GCTAAGATAGAAAC-C-TCCCTATCTTTTTACAA
1 GCTAAGATAGAACCTCTTCCCTATCTTTTTAAAA
210596 GCTAAGATAGAACCTCTTTCCCTAATCTTTTTCAAAA
1 GCTAAGATAGAACCTC-TTCCCT-ATCTTTTT-AAAA
*
210633 GCTAAGATAAAACCTCT
1 GCTAAGATAGAACCTCT
210650 CAATCACTTA
Statistics
Matches: 46, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
32 13 0.28
33 1 0.02
35 5 0.11
36 9 0.20
37 18 0.39
ACGTcount: A:0.35, C:0.24, G:0.09, T:0.31
Consensus pattern (34 bp):
GCTAAGATAGAACCTCTTCCCTATCTTTTTAAAA
Found at i:211780 original size:13 final size:13
Alignment explanation
Indices: 211735--211783 Score: 54
Period size: 13 Copynumber: 4.2 Consensus size: 13
211725 CCGTTACAAG
211735 CAATGTATCGATA
1 CAATGTATCGATA
211748 CAAT-T-TC-AT-
1 CAATGTATCGATA
*
211757 C-ATGCATCGATA
1 CAATGTATCGATA
211769 CAATGTATCGATA
1 CAATGTATCGATA
211782 CA
1 CA
211784 TTGTCCTATG
Statistics
Matches: 29, Mismatches: 2, Indels: 10
0.71 0.05 0.24
Matches are distributed among these distances:
8 2 0.07
9 1 0.03
10 4 0.14
11 4 0.14
12 2 0.07
13 16 0.55
ACGTcount: A:0.37, C:0.20, G:0.12, T:0.31
Consensus pattern (13 bp):
CAATGTATCGATA
Found at i:211857 original size:19 final size:19
Alignment explanation
Indices: 211833--211887 Score: 67
Period size: 19 Copynumber: 2.9 Consensus size: 19
211823 CTGCCAATCT
*
211833 CATGTATCGATA-AATTGTC
1 CATGTATCGATACAA-TGAC
*
211852 CATGTATCGATACAATGAG
1 CATGTATCGATACAATGAC
*
211871 CATGTATCGATGCAATG
1 CATGTATCGATACAATG
211888 TATCGATACA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
19 30 0.94
20 2 0.06
ACGTcount: A:0.33, C:0.16, G:0.20, T:0.31
Consensus pattern (19 bp):
CATGTATCGATACAATGAC
Found at i:213418 original size:13 final size:13
Alignment explanation
Indices: 213400--213425 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
213390 CAATTTTTTG
213400 TGTATCGATACAT
1 TGTATCGATACAT
213413 TGTATCGATACAT
1 TGTATCGATACAT
213426 ATTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:213441 original size:32 final size:33
Alignment explanation
Indices: 213380--213443 Score: 96
Period size: 32 Copynumber: 2.0 Consensus size: 33
213370 TACAAGCCAA
*
213380 TGTATCGATACAATTTTTTGTGTATCGATACAT
1 TGTATCGATACAATTATTTGTGTATCGATACAT
213413 TGTATCGATAC-A-TATTTGCTGTATCGATACA
1 TGTATCGATACAATTATTTG-TGTATCGATACA
213444 AGTTTGGCTA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
31 5 0.17
32 13 0.45
33 11 0.38
ACGTcount: A:0.28, C:0.14, G:0.16, T:0.42
Consensus pattern (33 bp):
TGTATCGATACAATTATTTGTGTATCGATACAT
Found at i:214167 original size:21 final size:21
Alignment explanation
Indices: 214126--214169 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
214116 CTCTCTTTTA
* *
214126 TCTCCCCCATTTATTAATAAT
1 TCTCCCCCATTAATCAATAAT
214147 TCTCCCCC-TTAATCAAGTAAT
1 TCTCCCCCATTAATCAA-TAAT
214168 TC
1 TC
214170 ATATTAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 6 0.30
21 14 0.70
ACGTcount: A:0.27, C:0.32, G:0.02, T:0.39
Consensus pattern (21 bp):
TCTCCCCCATTAATCAATAAT
Found at i:215807 original size:21 final size:21
Alignment explanation
Indices: 215783--215829 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
215773 TTTGATGCTG
215783 ATTTTG-A-TGAAAAACGAAGT
1 ATTTTGAAGTGAAAAAC-AAGT
215803 -TATTTGAAGTGAAAAACAAGT
1 AT-TTTGAAGTGAAAAACAAGT
215824 ATTTTG
1 ATTTTG
215830 CAAAAGATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 7
0.77 0.00 0.23
Matches are distributed among these distances:
19 1 0.04
20 4 0.17
21 9 0.39
22 9 0.39
ACGTcount: A:0.43, C:0.04, G:0.19, T:0.34
Consensus pattern (21 bp):
ATTTTGAAGTGAAAAACAAGT
Found at i:215968 original size:13 final size:13
Alignment explanation
Indices: 215950--215974 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
215940 ATAATCACCC
215950 TGTATCGATACAG
1 TGTATCGATACAG
215963 TGTATCGATACA
1 TGTATCGATACA
215975 AAGAAAAATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.20, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAG
Found at i:218072 original size:15 final size:15
Alignment explanation
Indices: 218052--218082 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
218042 ATTTCGTTTG
*
218052 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
218067 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
218082 G
1 G
218083 GACATTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:219915 original size:21 final size:21
Alignment explanation
Indices: 219886--219930 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
219876 AAGTTTTCAT
*
219886 TTTTCTTAGCTAAC-TCATTA
1 TTTTCTTAGCCAACTTCATTA
*
219906 TTTTCATTAGCCAACTTCTTTA
1 TTTTC-TTAGCCAACTTCATTA
219928 TTT
1 TTT
219931 CAACTTGCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 8 0.38
22 8 0.38
ACGTcount: A:0.22, C:0.20, G:0.04, T:0.53
Consensus pattern (21 bp):
TTTTCTTAGCCAACTTCATTA
Found at i:222162 original size:13 final size:13
Alignment explanation
Indices: 222144--222169 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
222134 CAATTTTTTG
222144 TGTATCGATACAT
1 TGTATCGATACAT
222157 TGTATCGATACAT
1 TGTATCGATACAT
222170 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:230445 original size:13 final size:13
Alignment explanation
Indices: 230427--230454 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
230417 CCGTTACAAG
230427 CAATGTATCGATA
1 CAATGTATCGATA
230440 CAATGTATCGATA
1 CAATGTATCGATA
230453 CA
1 CA
230455 TTGTCCTATG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.39, C:0.18, G:0.14, T:0.29
Consensus pattern (13 bp):
CAATGTATCGATA
Found at i:230548 original size:19 final size:19
Alignment explanation
Indices: 230504--230559 Score: 85
Period size: 19 Copynumber: 2.9 Consensus size: 19
230494 CTGCCAATCT
*
230504 CATGTATCGATACAATTGTC
1 CATGTATCGATACAA-TGAC
*
230524 CATGTATCGATACAATGAG
1 CATGTATCGATACAATGAC
230543 CATGTATCGATACAATG
1 CATGTATCGATACAATG
230560 TATCGATGCA
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
19 19 0.56
20 15 0.44
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.30
Consensus pattern (19 bp):
CATGTATCGATACAATGAC
Found at i:230965 original size:19 final size:20
Alignment explanation
Indices: 230941--230994 Score: 67
Period size: 19 Copynumber: 2.7 Consensus size: 20
230931 GTTTGGCTCA
230941 ATGTATCGATACAATGT-A-T
1 ATGTATCGATACAAT-TAAGT
*
230960 ATGTATTGATACAATTCAAGT
1 ATGTATCGATACAATT-AAGT
230981 ATGTATCGATACAA
1 ATGTATCGATACAA
230995 AATGAGTTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
18 1 0.03
19 14 0.47
20 1 0.03
21 14 0.47
ACGTcount: A:0.39, C:0.11, G:0.15, T:0.35
Consensus pattern (20 bp):
ATGTATCGATACAATTAAGT
Found at i:232652 original size:674 final size:673
Alignment explanation
Indices: 231451--232673 Score: 2087
Period size: 674 Copynumber: 1.8 Consensus size: 673
231441 AGAACCACTC
* * *
231451 ATATCAAAGCCAAAAGCTTAACAATCTCCCCTTTTTGATATAACAAAACTCAAAAATAAATTTGG
1 ATATCAAAACCAAAAGCTTAACAATCGCCCCTTTTTAATATAACAAAACTCAAAAATAAATTTGG
* *
231516 TTGACTTACTCACTTCACATGTTATAAGGAATTTCAAATATGCATTTTCGGAAACGTATATAACC
66 TTAACTTACTCACTTCACATGTTATAAGGAATTTCAAAGATGCATTTTCGGAAACGTATATAACC
231581 TTACAATTATTTCAAGGTCATTGAACAATCATACTCTCCATTTAATCAAAGATCGTAACCTGTAA
131 TTACAATTATTTCAAGGTCATTGAACAATCATACTCTCCATTTAATCAAAGATCGTAACCTGTAA
* *
231646 TTTGACATTCACAACTCAAGAAAATTATTAGAAAAGTTCATATATATTCAATGAAGTCCCAAAAT
196 TTTGACATTCACAACTCAAGAAAATTATTAGAAAAGTTCATAGATATTCAATAAAGTCCCAAAAT
*
231711 GTTTCTTAATACCAATTTTTAATTTTATAACCCGAAACATTTCTTTTATGAACTCTCCCCCTATT
261 GTTTCTTAATACCAATTTTTAATTTTATAACCCGAAACATTTCTTTTATAAACTCTCCCCCTATT
*
231776 TATAAACTTTTAGTGAATTCTCCCCTTTTTGTTATAAAGAAAGTTTTTACCAATTTTTTTCAATT
326 TATAAACTTTTAGTGAATTCTCCCCTTTTTGTTATAAAGAAAGTTTTTACCAATTTTCTTCAATT
231841 TTTCCAATTTCTTCCTTTATAACAAATAATCAATTCTATTTCTCTACGAATTCTCCCCCTCTGTG
391 TTTCCAATTTCTTCCTTTATAACAAATAATCAATTCTATTTCTCTACGAATTCTCCCCCTCTGTG
* *
231906 AAACATCTCTTTTCTCCCCCTTTCTATTAGGCCAAATCTATTTCTCCCTTTTTGTTATTCTTGTA
456 AAACATCTCTTTTCTCCCCATTTCTAGTAGGCCAAATCTATTTCTCCCTTTTTGTTATTCTTGTA
231971 ACTAATACCAAAAGTTTATGCAAGCTCTCCCACTTAATACATTCTCACCCTTAAACCAATAAACA
521 ACTAATACCAAAAGTTTATGCAAGCTCTCCCACTTAATACATTCTCACCCTTAAACCAATAAACA
232036 ATAATCTCTCCCCCTTTTTTGTTATAAGCTAAGTTGATAAGACCAAATTTATGGACAACAATCTA
586 ATAATCTCTCCCCCTTTTTTGTTATAAGCTAAGTTGATAAGACCAAATTTATGGACAACAATCTA
232101 AATTTATTTTTAGTTAATTTGTT
651 AATTTATTTTTAGTTAATTTGTT
*
232124 ATATCAAAACCAAAAGCTTAACAATCGCTCCCTTTTTAATATAACAAAACTCAAAAATAAATTTT
1 ATATCAAAACCAAAAGCTTAACAATCGC-CCCTTTTTAATATAACAAAACTCAAAAATAAATTTG
* *
232189 GTTAACTTACTCACTTCATATGTTATAAGGAATTTCAAAGATGCATTTTTGGAAACGTATATAAC
65 GTTAACTTACTCACTTCACATGTTATAAGGAATTTCAAAGATGCATTTTCGGAAACGTATATAAC
* ** * * *
232254 CTTACCTATTATTTCAAGGTCATTGAACAATCATACTCTCTGTTTCATCAAAGATCGTCACTTGT
130 CTTA-CAATTATTTCAAGGTCATTGAACAATCATACTCTCCATTTAATCAAAGATCGTAACCTGT
* *
232319 AATTTGACATTCACAACTCATGAAAATCT-TTAGAAAAGTTCGTAGATATTCAATAAAGTCCCAA
194 AATTTGACATTCACAACTCAAGAAAAT-TATTAGAAAAGTTCATAGATATTCAATAAAGTCCCAA
*
232383 AATGTTTCTTAATACCAATTTTTAATTTTATAACTCGAAAC-TTTCTTTTATAAACTCTCCCCCT
258 AATGTTTCTTAATACCAATTTTTAATTTTATAACCCGAAACATTTCTTTTATAAACTCTCCCCCT
* *
232447 ATTTGTAAACTTTTAGTGAATTCTTCCCTCTTTT-TTATAAAGAAA-TTTTATACCAATTTTCTT
323 ATTTATAAACTTTTAGTGAATTCTCCCCT-TTTTGTTATAAAGAAAGTTTT-TACCAATTTTCTT
* * *
232510 CAA-TTTTCTAATTTCTTCCTTTATAACAAATAATCAATTCTATTTCTCTACGAATTCTCTCCTT
386 CAATTTTTCCAATTTCTTCCTTTATAACAAATAATCAATTCTATTTCTCTACGAATTCTCCCCCT
*
232574 TTGTGAAACATCTCTTTTCTCCCCATTTCTAGTAGGCCAAATCTATTCTCTCCCTTTTTGTTATT
451 CTGTGAAACATCTCTTTTCTCCCCATTTCTAGTAGGCCAAATCTATT-TCTCCCTTTTTGTTATT
*
232639 CTTGTAACTAATACCAAAAGTTTATGTAAGCTCTC
515 CTTGTAACTAATACCAAAAGTTTATGCAAGCTCTC
232674 TACGAATTCT
Statistics
Matches: 514, Mismatches: 30, Indels: 11
0.93 0.05 0.02
Matches are distributed among these distances:
673 132 0.26
674 225 0.44
675 156 0.30
676 1 0.00
ACGTcount: A:0.33, C:0.20, G:0.08, T:0.39
Consensus pattern (673 bp):
ATATCAAAACCAAAAGCTTAACAATCGCCCCTTTTTAATATAACAAAACTCAAAAATAAATTTGG
TTAACTTACTCACTTCACATGTTATAAGGAATTTCAAAGATGCATTTTCGGAAACGTATATAACC
TTACAATTATTTCAAGGTCATTGAACAATCATACTCTCCATTTAATCAAAGATCGTAACCTGTAA
TTTGACATTCACAACTCAAGAAAATTATTAGAAAAGTTCATAGATATTCAATAAAGTCCCAAAAT
GTTTCTTAATACCAATTTTTAATTTTATAACCCGAAACATTTCTTTTATAAACTCTCCCCCTATT
TATAAACTTTTAGTGAATTCTCCCCTTTTTGTTATAAAGAAAGTTTTTACCAATTTTCTTCAATT
TTTCCAATTTCTTCCTTTATAACAAATAATCAATTCTATTTCTCTACGAATTCTCCCCCTCTGTG
AAACATCTCTTTTCTCCCCATTTCTAGTAGGCCAAATCTATTTCTCCCTTTTTGTTATTCTTGTA
ACTAATACCAAAAGTTTATGCAAGCTCTCCCACTTAATACATTCTCACCCTTAAACCAATAAACA
ATAATCTCTCCCCCTTTTTTGTTATAAGCTAAGTTGATAAGACCAAATTTATGGACAACAATCTA
AATTTATTTTTAGTTAATTTGTT
Found at i:232758 original size:116 final size:116
Alignment explanation
Indices: 232554--232789 Score: 472
Period size: 116 Copynumber: 2.0 Consensus size: 116
232544 CAATTCTATT
232554 TCTCTACGAATTCTCTCCTTTTGTGAAACATCTCTTTTCTCCCCATTTCTAGTAGGCCAAATCTA
1 TCTCTACGAATTCTCTCCTTTTGTGAAACATCTCTTTTCTCCCCATTTCTAGTAGGCCAAATCTA
232619 TTCTCTCCCTTTTTGTTATTCTTGTAACTAATACCAAAAGTTTATGTAAGC
66 TTCTCTCCCTTTTTGTTATTCTTGTAACTAATACCAAAAGTTTATGTAAGC
232670 TCTCTACGAATTCTCTCCTTTTGTGAAACATCTCTTTTCTCCCCATTTCTAGTAGGCCAAATCTA
1 TCTCTACGAATTCTCTCCTTTTGTGAAACATCTCTTTTCTCCCCATTTCTAGTAGGCCAAATCTA
232735 TTCTCTCCCTTTTTGTTATTCTTGTAACTAATACCAAAAGTTTATGTAAGC
66 TTCTCTCCCTTTTTGTTATTCTTGTAACTAATACCAAAAGTTTATGTAAGC
232786 TCTC
1 TCTC
232790 CCACTTAATA
Statistics
Matches: 120, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
116 120 1.00
ACGTcount: A:0.23, C:0.25, G:0.09, T:0.42
Consensus pattern (116 bp):
TCTCTACGAATTCTCTCCTTTTGTGAAACATCTCTTTTCTCCCCATTTCTAGTAGGCCAAATCTA
TTCTCTCCCTTTTTGTTATTCTTGTAACTAATACCAAAAGTTTATGTAAGC
Found at i:235139 original size:21 final size:20
Alignment explanation
Indices: 235115--235164 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 20
235105 TTTTATTAGT
*
235115 TAACTCATCATTTTCATTTTG
1 TAACTCATCATTTTC-TTTTC
*
235136 TAACTCACTTATTTTCTTTTC
1 TAACTCA-TCATTTTCTTTTC
*
235157 CAACTCAT
1 TAACTCAT
235165 TTACTTTCTT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
20 1 0.04
21 17 0.68
22 7 0.28
ACGTcount: A:0.24, C:0.24, G:0.02, T:0.50
Consensus pattern (20 bp):
TAACTCATCATTTTCTTTTC
Found at i:235172 original size:21 final size:21
Alignment explanation
Indices: 235137--235177 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
235127 TTCATTTTGT
*
235137 AACTCACTTATTTTCTTTTCC
1 AACTCACTTACTTTCTTTTCC
*
235158 AACTCATTTACTTTCTTTTC
1 AACTCACTTACTTTCTTTTC
235178 AAGAGTATTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.20, C:0.27, G:0.00, T:0.54
Consensus pattern (21 bp):
AACTCACTTACTTTCTTTTCC
Found at i:237270 original size:21 final size:20
Alignment explanation
Indices: 237225--237283 Score: 75
Period size: 20 Copynumber: 2.9 Consensus size: 20
237215 GTTGGGCTCA
237225 ATGTATCGATACAATGTACT
1 ATGTATCGATACAATGTACT
*
237245 ATGTATCGATACAAT-TCAAGT
1 ATGTATCGATACAATGT--ACT
*
237266 ATGTATCAATACAATGTA
1 ATGTATCGATACAATGTA
237284 TTGATACAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
19 1 0.03
20 16 0.47
21 16 0.47
22 1 0.03
ACGTcount: A:0.39, C:0.14, G:0.14, T:0.34
Consensus pattern (20 bp):
ATGTATCGATACAATGTACT
Found at i:243777 original size:16 final size:16
Alignment explanation
Indices: 243758--243788 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
243748 TTAATTTTTT
243758 ATAATTAAAATTAAAA
1 ATAATTAAAATTAAAA
*
243774 ATAATTATAATTAAA
1 ATAATTAAAATTAAA
243789 TTAAATTTAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (16 bp):
ATAATTAAAATTAAAA
Found at i:245288 original size:47 final size:51
Alignment explanation
Indices: 245223--245318 Score: 137
Period size: 47 Copynumber: 2.0 Consensus size: 51
245213 AAAGTTTTTA
* *
245223 TAAATTTAATTATTAAATA-ATAATTAAT-A-ATAAAAATAAT-TTTTATT
1 TAAATTTAATTATAAAATATATAAATAATAATATAAAAATAATATTTTATT
*
245270 TAAATTTATTTATAAAATATATAAATAATAATATAAAAATAATATTTTA
1 TAAATTTAATTATAAAATATATAAATAATAATATAAAAATAATATTTTA
245319 AATAATAAAA
Statistics
Matches: 42, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
47 17 0.40
48 8 0.19
49 1 0.02
50 11 0.26
51 5 0.12
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (51 bp):
TAAATTTAATTATAAAATATATAAATAATAATATAAAAATAATATTTTATT
Found at i:245322 original size:23 final size:23
Alignment explanation
Indices: 245296--245358 Score: 66
Period size: 23 Copynumber: 2.9 Consensus size: 23
245286 ATATATAAAT
245296 AATAATATAAA-AA-TAATATTTTA
1 AATAATA-AAATAATTAAT-TTTTA
245319 AATAATAAAATAATTAATTTTT-
1 AATAATAAAATAATTAATTTTTA
245341 AA-AA-AAAA-AATTAATTTT
1 AATAATAAAATAATTAATTTT
245359 GAACCATAAT
Statistics
Matches: 38, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
19 10 0.26
20 4 0.11
21 2 0.05
22 5 0.13
23 13 0.34
24 4 0.11
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (23 bp):
AATAATAAAATAATTAATTTTTA
Found at i:246214 original size:8 final size:8
Alignment explanation
Indices: 246201--246233 Score: 66
Period size: 8 Copynumber: 4.1 Consensus size: 8
246191 TATTTACTTA
246201 TAAAAATT
1 TAAAAATT
246209 TAAAAATT
1 TAAAAATT
246217 TAAAAATT
1 TAAAAATT
246225 TAAAAATT
1 TAAAAATT
246233 T
1 T
246234 TATATTTATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 25 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (8 bp):
TAAAAATT
Found at i:247005 original size:19 final size:19
Alignment explanation
Indices: 246977--247033 Score: 69
Period size: 19 Copynumber: 2.9 Consensus size: 19
246967 TTGTATCGAT
* * *
246977 ACATTATATCAATACATGT
1 ACATTGTATCGATACATGC
*
246996 TCATTGTATCGATACATGC
1 ACATTGTATCGATACATGC
247015 ACAATTGTATCGATACATG
1 AC-ATTGTATCGATACATG
247034 AAACTGGCAG
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
19 16 0.50
20 16 0.50
ACGTcount: A:0.35, C:0.18, G:0.12, T:0.35
Consensus pattern (19 bp):
ACATTGTATCGATACATGC
Found at i:247087 original size:20 final size:20
Alignment explanation
Indices: 247062--247112 Score: 75
Period size: 20 Copynumber: 2.5 Consensus size: 20
247052 ATACCACTGT
* *
247062 TTGTATCGATACATGGCACA
1 TTGTATCGATACATGACAAA
*
247082 TTGTATCGATACATGATAAA
1 TTGTATCGATACATGACAAA
247102 TTGTATCGATA
1 TTGTATCGATA
247113 TATTACTTCA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.33, C:0.14, G:0.18, T:0.35
Consensus pattern (20 bp):
TTGTATCGATACATGACAAA
Found at i:251532 original size:21 final size:21
Alignment explanation
Indices: 251508--251553 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
251498 AGACTTTATT
251508 AAATGAATTTATTGGATAATA
1 AAATGAATTTATTGGATAATA
**
251529 AAATTTATTTATTGGATAATA
1 AAATGAATTTATTGGATAATA
251550 AAAT
1 AAAT
251554 CTATCACATT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.11, T:0.41
Consensus pattern (21 bp):
AAATGAATTTATTGGATAATA
Found at i:252833 original size:18 final size:17
Alignment explanation
Indices: 252805--252839 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
252795 ATCGTTTGGT
*
252805 AGCAGAAAAAAGTCCCC
1 AGCAGAAAAAAATCCCC
252822 AGCAGCAAAAAAATCCCC
1 AGCAG-AAAAAAATCCCC
252840 TTGATACTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.49, C:0.31, G:0.14, T:0.06
Consensus pattern (17 bp):
AGCAGAAAAAAATCCCC
Done.