Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D01
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: 62811768
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 736185 characters in sequence are not A, C, G, or T
File 77 of 211
Found at i:20750033 original size:41 final size:41
Alignment explanation
Indices: 20749976--20750161 Score: 336
Period size: 41 Copynumber: 4.5 Consensus size: 41
20749966 GACTATACGT
*
20749976 CTAGCAGGCTAAGTGCCGGTGATCTAAATCAGGTTATAAAC
1 CTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGTTATAAAC
20750017 CTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGTTATAAAC
1 CTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGTTATAAAC
20750058 CTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGTTATAAAC
1 CTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGTTATAAAC
* * *
20750099 CTAGCAGGCTAAGTTCCGGTGATCTGAATCAGGCTATAAGC
1 CTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGTTATAAAC
20750140 CTAGCAGGCTAAGTGCCGGTGA
1 CTAGCAGGCTAAGTGCCGGTGA
20750162 ATCTATTAAA
Statistics
Matches: 140, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
41 140 1.00
ACGTcount: A:0.28, C:0.20, G:0.27, T:0.24
Consensus pattern (41 bp):
CTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGTTATAAAC
Found at i:20753740 original size:40 final size:40
Alignment explanation
Indices: 20753695--20753886 Score: 226
Period size: 40 Copynumber: 4.8 Consensus size: 40
20753685 ATAACCACAA
* * *
20753695 GCACAATTGCCTTCGGGTCTTAACCCGGGTATAGCAACTC
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATATAGCAACTC
*
20753735 GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATATAGCAACTC
* * *
20753775 GCACAAATGCCTTCGGGTCTTAGCCCGGATAAAATC-ACTA
1 GCACAAATGCCTTCGGGTCTTAGCCCGGAT-ATAGCAACTC
* * * * *
20753815 GCATAAATGCCTTCGGGACTTAGCCCGGATAAAATC-ACTA
1 GCACAAATGCCTTCGGGTCTTAGCCCGGAT-ATAGCAACTC
* *
20753855 GCATAAATGCCTTCGGGACTTAGCCCGGATAT
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATAT
20753887 CATTCAAATG
Statistics
Matches: 142, Mismatches: 9, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
39 1 0.01
40 137 0.96
41 4 0.03
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (40 bp):
GCACAAATGCCTTCGGGTCTTAGCCCGGATATAGCAACTC
Found at i:20753779 original size:80 final size:80
Alignment explanation
Indices: 20753666--20753885 Score: 248
Period size: 80 Copynumber: 2.8 Consensus size: 80
20753656 ACCCAAGTTT
* * * * * * * * *
20753666 CTTCGGAATTTAG-CCGGATATAACCACAAGCACAATTGCCTTCGGGTCTTAACCCGGGT-ATAG
1 CTTCGGGACTTAGCCCGGATAAAATCACTAGCACAAATGCCTTCGGGTCTTAGCCCGGATAAAAG
*
20753729 CAACTCGCACAAATGC
66 C-ACTAGCACAAATGC
* * *
20753745 CTTCGGGTCTTAGCCCGGAT-ATATCAACTCGCACAAATGCCTTCGGGTCTTAGCCCGGATAAAA
1 CTTCGGGACTTAGCCCGGATAAAATC-ACTAGCACAAATGCCTTCGGGTCTTAGCCCGGATAAAA
* *
20753809 TCACTAGCATAAATGC
65 GCACTAGCACAAATGC
* *
20753825 CTTCGGGACTTAGCCCGGATAAAATCACTAGCATAAATGCCTTCGGGACTTAGCCCGGATA
1 CTTCGGGACTTAGCCCGGATAAAATCACTAGCACAAATGCCTTCGGGTCTTAGCCCGGATA
20753886 TCATTCAAAT
Statistics
Matches: 117, Mismatches: 20, Indels: 7
0.81 0.14 0.05
Matches are distributed among these distances:
79 12 0.10
80 98 0.84
81 7 0.06
ACGTcount: A:0.28, C:0.27, G:0.21, T:0.24
Consensus pattern (80 bp):
CTTCGGGACTTAGCCCGGATAAAATCACTAGCACAAATGCCTTCGGGTCTTAGCCCGGATAAAAG
CACTAGCACAAATGC
Found at i:20760228 original size:7 final size:7
Alignment explanation
Indices: 20760218--20760243 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
20760208 GAATGAGAGT
20760218 GTGAGGG
1 GTGAGGG
20760225 GTGAGGG
1 GTGAGGG
20760232 GTGAGGG
1 GTGAGGG
20760239 GTGAG
1 GTGAG
20760244 TTGAATGATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.15, C:0.00, G:0.69, T:0.15
Consensus pattern (7 bp):
GTGAGGG
Found at i:20763920 original size:5 final size:5
Alignment explanation
Indices: 20763910--20763946 Score: 51
Period size: 5 Copynumber: 7.6 Consensus size: 5
20763900 AATGCATATG
20763910 ATGCA ATGCA ATGCA ATGCTA ATGC- ATG-A ATGCA ATG
1 ATGCA ATGCA ATGCA ATGC-A ATGCA ATGCA ATGCA ATG
20763947 GATGCAAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
4 6 0.21
5 18 0.62
6 5 0.17
ACGTcount: A:0.38, C:0.16, G:0.22, T:0.24
Consensus pattern (5 bp):
ATGCA
Found at i:20769581 original size:16 final size:17
Alignment explanation
Indices: 20769525--20769580 Score: 76
Period size: 17 Copynumber: 3.2 Consensus size: 17
20769515 TCAAACGTCC
* *
20769525 AAAAAAAATTTCCTAGT
1 AAAAAACATTTCCTAAT
*
20769542 AAAAAACATTTCGTAAT
1 AAAAAACATTTCCTAAT
20769559 AAAAAACATTTCCTAAT
1 AAAAAACATTTCCTAAT
20769576 CAAAA
1 -AAAA
20769581 CTCTATGAAC
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
17 30 0.88
18 4 0.12
ACGTcount: A:0.55, C:0.14, G:0.04, T:0.27
Consensus pattern (17 bp):
AAAAAACATTTCCTAAT
Found at i:20771559 original size:18 final size:18
Alignment explanation
Indices: 20771536--20771570 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
20771526 ATACATACTT
20771536 ATTAAATTAATCAATCTC
1 ATTAAATTAATCAATCTC
20771554 ATTAAATTAATCAATCT
1 ATTAAATTAATCAATCT
20771571 ATTGAACATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.46, C:0.14, G:0.00, T:0.40
Consensus pattern (18 bp):
ATTAAATTAATCAATCTC
Found at i:20774914 original size:44 final size:44
Alignment explanation
Indices: 20774848--20774935 Score: 158
Period size: 44 Copynumber: 2.0 Consensus size: 44
20774838 CATTTATTCA
* *
20774848 AAAAGAAAAATGAAAAATTAAGTATCTGATAAAATGAACGGGAT
1 AAAAGAAAAATGAAAAAATAAGTATCCGATAAAATGAACGGGAT
20774892 AAAAGAAAAATGAAAAAATAAGTATCCGATAAAATGAACGGGAT
1 AAAAGAAAAATGAAAAAATAAGTATCCGATAAAATGAACGGGAT
20774936 TTAATCTCGT
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
44 42 1.00
ACGTcount: A:0.58, C:0.06, G:0.18, T:0.18
Consensus pattern (44 bp):
AAAAGAAAAATGAAAAAATAAGTATCCGATAAAATGAACGGGAT
Found at i:20775869 original size:17 final size:17
Alignment explanation
Indices: 20775847--20775880 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
20775837 TTTTTGTTGG
20775847 TGACATTTCCAACCCTT
1 TGACATTTCCAACCCTT
20775864 TGACATTTCCAACCCTT
1 TGACATTTCCAACCCTT
20775881 GAATAATATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.24, C:0.35, G:0.06, T:0.35
Consensus pattern (17 bp):
TGACATTTCCAACCCTT
Found at i:20788058 original size:101 final size:101
Alignment explanation
Indices: 20787919--20788136 Score: 298
Period size: 101 Copynumber: 2.2 Consensus size: 101
20787909 ACAATTATTC
* * * *
20787919 AAACGTAAGACCATGGTTGGAGCATGGCAGTTTATATATGTAAGACCATAG-TCGGGCTATGGCA
1 AAACGTAAGACCATGGTTGGAGCACGACAATTTATATATGTAAGACCATAGCT-GGGCTATGACA
*
20787983 TTCTGATGATAAGACCATAACTAGGTTATGGCACTAT
65 TTCTAATGATAAGACCATAACTAGGTTATGGCACTAT
*
20788020 AAACATAAGACCATGGTTGGA-CTACGACAATGTT-TATATGTAAGACCATAGCTGGGCTATGAC
1 AAACGTAAGACCATGGTTGGAGC-ACGACAAT-TTATATATGTAAGACCATAGCTGGGCTATGAC
* * *
20788083 ATTCTAATGATAAGACCATAAGTGGGTTATGGTACTAT
64 ATTCTAATGATAAGACCATAACTAGGTTATGGCACTAT
*
20788121 GAACGTAAGACCATGG
1 AAACGTAAGACCATGG
20788137 CAGGGCCATG
Statistics
Matches: 103, Mismatches: 11, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
100 1 0.01
101 99 0.96
102 3 0.03
ACGTcount: A:0.33, C:0.16, G:0.24, T:0.27
Consensus pattern (101 bp):
AAACGTAAGACCATGGTTGGAGCACGACAATTTATATATGTAAGACCATAGCTGGGCTATGACAT
TCTAATGATAAGACCATAACTAGGTTATGGCACTAT
Found at i:20788101 original size:33 final size:33
Alignment explanation
Indices: 20787959--20788102 Score: 103
Period size: 33 Copynumber: 4.3 Consensus size: 33
20787949 TTTATATATG
* *
20787959 TAAGACCATAG-TCGGGCTATGGCATTCTGATGA
1 TAAGACCATAGCT-GGGCTATGACATTCTAATGA
* * * * * * **
20787992 TAAGACCATAACTAGGTTATGGCACTATAAACA
1 TAAGACCATAGCTGGGCTATGACATTCTAATGA
* * * * *
20788025 TAAGACCATGGTTGGACTACGACAATGTTTATATG-
1 TAAGACCATAGCTGGGCTATGAC-AT-TCTA-ATGA
20788060 TAAGACCATAGCTGGGCTATGACATTCTAATGA
1 TAAGACCATAGCTGGGCTATGACATTCTAATGA
20788093 TAAGACCATA
1 TAAGACCATA
20788103 AGTGGGTTAT
Statistics
Matches: 81, Mismatches: 25, Indels: 10
0.70 0.22 0.09
Matches are distributed among these distances:
32 3 0.04
33 51 0.63
34 4 0.05
35 22 0.27
36 1 0.01
ACGTcount: A:0.35, C:0.17, G:0.21, T:0.27
Consensus pattern (33 bp):
TAAGACCATAGCTGGGCTATGACATTCTAATGA
Found at i:20793568 original size:30 final size:30
Alignment explanation
Indices: 20793532--20793698 Score: 147
Period size: 30 Copynumber: 5.5 Consensus size: 30
20793522 GGTTGATACC
*
20793532 ATCCCTTTCCATAATTCAATAACCGAAGCT
1 ATCCCTTTCCATAATTCAATAGCCGAAGCT
*
20793562 ATCCCTTTCCATTATTCAATAGCCGAAGCT
1 ATCCCTTTCCATAATTCAATAGCCGAAGCT
** * *** * * * *
20793592 ATCTTTTTTCATAATTTTGGTGGTCGTCA-CC
1 ATCCCTTTCCATAA-TTCAATAGCCG-AAGCT
**
20793623 ATCCCTTTCCATAATTTGATAGCCGAAGCT
1 ATCCCTTTCCATAATTCAATAGCCGAAGCT
* * *
20793653 ATCCCTTTTCATGACTCAATAGCCGAAGCT
1 ATCCCTTTCCATAATTCAATAGCCGAAGCT
*
20793683 ATCCCTTTTCATAATT
1 ATCCCTTTCCATAATT
20793699 TTGATAGTCG
Statistics
Matches: 106, Mismatches: 28, Indels: 6
0.76 0.20 0.04
Matches are distributed among these distances:
29 1 0.01
30 86 0.81
31 18 0.17
32 1 0.01
ACGTcount: A:0.26, C:0.27, G:0.11, T:0.37
Consensus pattern (30 bp):
ATCCCTTTCCATAATTCAATAGCCGAAGCT
Found at i:20793684 original size:91 final size:91
Alignment explanation
Indices: 20793529--20793755 Score: 319
Period size: 91 Copynumber: 2.5 Consensus size: 91
20793519 GAGGGTTGAT
** * * *
20793529 ACCATCCCTTTCCATAATTCAATAACCGAAGCTATCCCTTTCCATTATTCAATAGCCGAAGCTAT
1 ACCATCCCTTTCCATAATTTGATAACCGAAGCTATCCCTTTTCATGACTCAATAGCCGAAGCTAT
** * *
20793594 CTTTTTTCATAATTTTGGTGGTCGTC
66 CCCTTTTCATAATTTTGATAGTCGTC
*
20793620 ACCATCCCTTTCCATAATTTGATAGCCGAAGCTATCCCTTTTCATGACTCAATAGCCGAAGCTAT
1 ACCATCCCTTTCCATAATTTGATAACCGAAGCTATCCCTTTTCATGACTCAATAGCCGAAGCTAT
20793685 CCCTTTTCATAATTTTGATAGTCGTC
66 CCCTTTTCATAATTTTGATAGTCGTC
* * * * *
20793711 ACAATCCCTTTTCATAGTTTGATAATCGAAACTATCCCTTTTCAT
1 ACCATCCCTTTCCATAATTTGATAACCGAAGCTATCCCTTTTCAT
20793756 TGGTCGATGA
Statistics
Matches: 120, Mismatches: 16, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
91 120 1.00
ACGTcount: A:0.26, C:0.26, G:0.11, T:0.37
Consensus pattern (91 bp):
ACCATCCCTTTCCATAATTTGATAACCGAAGCTATCCCTTTTCATGACTCAATAGCCGAAGCTAT
CCCTTTTCATAATTTTGATAGTCGTC
Found at i:20793734 original size:30 final size:31
Alignment explanation
Indices: 20793683--20793755 Score: 94
Period size: 30 Copynumber: 2.4 Consensus size: 31
20793673 AGCCGAAGCT
* * **
20793683 ATCCCTTTTCATAATTTTGATAGTCGTCACA
1 ATCCCTTTTCATAAGTTTGATAATCGAAACA
*
20793714 ATCCCTTTTCAT-AGTTTGATAATCGAAACT
1 ATCCCTTTTCATAAGTTTGATAATCGAAACA
20793744 ATCCCTTTTCAT
1 ATCCCTTTTCAT
20793756 TGGTCGATGA
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
30 25 0.68
31 12 0.32
ACGTcount: A:0.26, C:0.23, G:0.08, T:0.42
Consensus pattern (31 bp):
ATCCCTTTTCATAAGTTTGATAATCGAAACA
Found at i:20800046 original size:22 final size:19
Alignment explanation
Indices: 20799996--20800047 Score: 50
Period size: 22 Copynumber: 2.5 Consensus size: 19
20799986 TTTAAGATTT
*
20799996 ATGTTTAATTTGAGTATTA
1 ATGTTTATTTTGAGTATTA
*
20800015 ATTGTGTATTTATGAAGTATTA
1 A-TGTTTATTT-TG-AGTATTA
20800037 CATGTTTATTT
1 -ATGTTTATTT
20800048 GAAATAATTG
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
19 1 0.04
20 7 0.27
21 2 0.08
22 15 0.58
23 1 0.04
ACGTcount: A:0.29, C:0.02, G:0.15, T:0.54
Consensus pattern (19 bp):
ATGTTTATTTTGAGTATTA
Found at i:20803286 original size:16 final size:16
Alignment explanation
Indices: 20803265--20803297 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
20803255 TTTATGTTTT
20803265 TCAGCCATTTTTAATA
1 TCAGCCATTTTTAATA
20803281 TCAGCCATTTTTAATA
1 TCAGCCATTTTTAATA
20803297 T
1 T
20803298 TCTTTAGATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.30, C:0.18, G:0.06, T:0.45
Consensus pattern (16 bp):
TCAGCCATTTTTAATA
Found at i:20806808 original size:15 final size:15
Alignment explanation
Indices: 20806784--20806822 Score: 60
Period size: 15 Copynumber: 2.6 Consensus size: 15
20806774 GGTTATCATC
*
20806784 ATTATCATTAGAATT
1 ATTATTATTAGAATT
*
20806799 ATTATTATTAGTATT
1 ATTATTATTAGAATT
20806814 ATTATTATT
1 ATTATTATT
20806823 TATATTAGTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.36, C:0.03, G:0.05, T:0.56
Consensus pattern (15 bp):
ATTATTATTAGAATT
Found at i:20806813 original size:12 final size:11
Alignment explanation
Indices: 20806800--20806840 Score: 50
Period size: 12 Copynumber: 3.7 Consensus size: 11
20806790 ATTAGAATTA
20806800 TTATTATTAGT
1 TTATTATTAGT
20806811 ATTATTATTA-T
1 -TTATTATTAGT
20806822 TTA-TATTAGT
1 TTATTATTAGT
20806832 TTATATATT
1 TTAT-TATT
20806841 TATCCACATA
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
9 5 0.19
10 7 0.27
11 1 0.04
12 13 0.50
ACGTcount: A:0.32, C:0.00, G:0.05, T:0.63
Consensus pattern (11 bp):
TTATTATTAGT
Found at i:20808502 original size:17 final size:16
Alignment explanation
Indices: 20808477--20808512 Score: 54
Period size: 17 Copynumber: 2.2 Consensus size: 16
20808467 TCAAAACCAC
20808477 AAAATTTAAAAAATTT
1 AAAATTTAAAAAATTT
*
20808493 AAAATATTAATAAATTT
1 AAAAT-TTAAAAAATTT
20808510 AAA
1 AAA
20808513 TACGCTTTCA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 5 0.28
17 13 0.72
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (16 bp):
AAAATTTAAAAAATTT
Found at i:20810642 original size:19 final size:18
Alignment explanation
Indices: 20810607--20810644 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
20810597 TTCTTAATGG
20810607 GGTTTTGTTCGTTTTTTT
1 GGTTTTGTTCGTTTTTTT
20810625 GGTTTATGTTC-TTGTTTTT
1 GGTTT-TGTTCGTT-TTTTT
20810644 G
1 G
20810645 ATAAACTATT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 7 0.39
19 11 0.61
ACGTcount: A:0.03, C:0.05, G:0.24, T:0.68
Consensus pattern (18 bp):
GGTTTTGTTCGTTTTTTT
Found at i:20810927 original size:24 final size:22
Alignment explanation
Indices: 20810895--20810950 Score: 58
Period size: 24 Copynumber: 2.4 Consensus size: 22
20810885 AAATAAAAGT
* *
20810895 TAAATGTTTTTTAAAGTGCTTAAA
1 TAAAAGTTTTTCAAA-TG-TTAAA
*
20810919 TAAAAGTTTTTCAAATGTTACA
1 TAAAAGTTTTTCAAATGTTAAA
20810941 TATAAAGTTT
1 TA-AAAGTTT
20810951 CAAATTATGT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
22 6 0.21
23 9 0.32
24 13 0.46
ACGTcount: A:0.39, C:0.05, G:0.11, T:0.45
Consensus pattern (22 bp):
TAAAAGTTTTTCAAATGTTAAA
Found at i:20810947 original size:23 final size:25
Alignment explanation
Indices: 20810895--20810950 Score: 64
Period size: 23 Copynumber: 2.3 Consensus size: 25
20810885 AAATAAAAGT
*
20810895 TAAATGTTTTTTAAAGTGCTTAAATA
1 TAAA-GTTTTTCAAAGTGCTTAAATA
*
20810921 -AAAGTTTTTCAAA-TG-TTACATA
1 TAAAGTTTTTCAAAGTGCTTAAATA
20810943 TAAAGTTT
1 TAAAGTTT
20810951 CAAATTATGT
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
22 6 0.22
23 9 0.33
24 9 0.33
25 3 0.11
ACGTcount: A:0.39, C:0.05, G:0.11, T:0.45
Consensus pattern (25 bp):
TAAAGTTTTTCAAAGTGCTTAAATA
Found at i:20811145 original size:29 final size:30
Alignment explanation
Indices: 20811095--20811158 Score: 69
Period size: 29 Copynumber: 2.2 Consensus size: 30
20811085 AACACTCTTA
* * *
20811095 TAAATGTTAGACCCTTATAT-AATCAAT-TC
1 TAAAAGTTAGACCCTCACATAAAT-AATCTC
*
20811124 TAAAAGTTTGACCCTCACATAAATAATCTC
1 TAAAAGTTAGACCCTCACATAAATAATCTC
20811154 TAAAA
1 TAAAA
20811159 AGTTGAATTT
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
29 19 0.66
30 10 0.34
ACGTcount: A:0.42, C:0.19, G:0.06, T:0.33
Consensus pattern (30 bp):
TAAAAGTTAGACCCTCACATAAATAATCTC
Found at i:20816130 original size:56 final size:50
Alignment explanation
Indices: 20816035--20816331 Score: 249
Period size: 50 Copynumber: 5.8 Consensus size: 50
20816025 ATTTGGGTAA
* * * *
20816035 AGAGATCCCATGTAAAACCATGTTTGGGACATGACATTGGCATCATTGAGATTATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA-CA--GAG---ATG
* *
20816091 AGAGGTCCTATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACAGAGATG
* *
20816141 AGAGGTCCCATGTAAGACCATTTCTGGGACATGGCGTTGGCACCA-AGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA-CAGAGATG
** * * ** *
20816191 AGAGGTCCCCCGTAAGACCATGTTTGGGACATGGCATGGGCACCTATATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACAGAGATG
** * * * * *
20816241 AGAACTCTCATGTAAGACCATATCTGGGATATGGCATTGG--CAGTACAAG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACAG-AGATG
* ** * * *
20816290 AAACATCCCATGTAAGACTATGTCTGGGACATAGCTTTGGCA
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
20816332 TGTTATATTC
Statistics
Matches: 196, Mismatches: 40, Indels: 15
0.78 0.16 0.06
Matches are distributed among these distances:
48 1 0.01
49 35 0.18
50 118 0.60
51 1 0.01
53 3 0.02
55 1 0.01
56 37 0.19
ACGTcount: A:0.29, C:0.20, G:0.27, T:0.24
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACAGAGATG
Found at i:20822505 original size:50 final size:50
Alignment explanation
Indices: 20822430--20822613 Score: 178
Period size: 50 Copynumber: 3.7 Consensus size: 50
20822420 CATTGAGATT
* * *
20822430 ATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCAAG
1 ATGAGAAGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCAAG
** * *
20822480 ATGAGAAGTCCCCCGTAAGACCATGTCTGGGACATGGCATGGGCACCTAT
1 ATGAGAAGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCAAG
* * * * * * *
20822530 ATGAGAACTCTCATGTAAGACCATATCTGGGATATGACATTGGCAGTACAAG
1 ATGAGAAGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCA--CCAAG
*
20822582 A--A-ACA-TCCCATGTAAGACTATGTCTGGGACAT
1 ATGAGA-AGTCCCATGTAAGACCATGTCTGGGACAT
20822614 AGCTTTGGCA
Statistics
Matches: 109, Mismatches: 22, Indels: 7
0.79 0.16 0.05
Matches are distributed among these distances:
49 24 0.22
50 82 0.75
52 3 0.03
ACGTcount: A:0.30, C:0.22, G:0.26, T:0.22
Consensus pattern (50 bp):
ATGAGAAGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCAAG
Found at i:20827426 original size:21 final size:20
Alignment explanation
Indices: 20827389--20827432 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 20
20827379 ATAGAAATCT
*
20827389 ATAGAATTCTTATTTAGACAA
1 ATAGAATTCTTAGTTAGA-AA
20827410 ATAGAATT-TGTAGTTAGAAA
1 ATAGAATTCT-TAGTTAGAAA
20827430 ATA
1 ATA
20827433 ATTCTCACTA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 6 0.29
21 15 0.71
ACGTcount: A:0.45, C:0.05, G:0.14, T:0.36
Consensus pattern (20 bp):
ATAGAATTCTTAGTTAGAAA
Found at i:20830861 original size:3 final size:3
Alignment explanation
Indices: 20830853--20830934 Score: 137
Period size: 3 Copynumber: 27.3 Consensus size: 3
20830843 TATCAAGTTT
*
20830853 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA AAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
* *
20830901 AAA GAA GAA GAA AAA GAA GAA GAA GAA GAA GAA G
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA G
20830935 GTAGAAAACT
Statistics
Matches: 73, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
3 73 1.00
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:20831951 original size:43 final size:42
Alignment explanation
Indices: 20831889--20832084 Score: 225
Period size: 43 Copynumber: 4.6 Consensus size: 42
20831879 TTTTAGAAAT
*
20831889 AAACGCCGCTAAAAGTCATGACCTTTAGCGGCGCGTCTACCAC
1 AAACGCCGCTAAAA-TCATGACCTTTAGCGGCGCTTCTACCAC
20831932 AAACGCCGCTAAAGATCATGACCTTTAGCGGCGCTTCTACCAC
1 AAACGCCGCTAAA-ATCATGACCTTTAGCGGCGCTTCTACCAC
* * *
20831975 AAACGCCGCTAAAGATCTTAACCTTTAGCGGCGCTTATACCAC
1 AAACGCCGCTAAA-ATCATGACCTTTAGCGGCGCTTCTACCAC
* * ** ***
20832018 AAACGCCACTATAAAT-ATGACTTTTAGCGATGCTT-TTTGAC
1 AAACGCCGCTA-AAATCATGACCTTTAGCGGCGCTTCTACCAC
* *
20832059 AAACGCCGCTAAAAACATGACTTTTA
1 AAACGCCGCTAAAATCATGACCTTTA
20832085 AAAAAAATAT
Statistics
Matches: 135, Mismatches: 15, Indels: 8
0.85 0.09 0.05
Matches are distributed among these distances:
40 3 0.02
41 23 0.17
42 14 0.10
43 92 0.68
44 3 0.02
ACGTcount: A:0.31, C:0.28, G:0.17, T:0.24
Consensus pattern (42 bp):
AAACGCCGCTAAAATCATGACCTTTAGCGGCGCTTCTACCAC
Found at i:20836649 original size:16 final size:16
Alignment explanation
Indices: 20836628--20836658 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
20836618 ATTTAAACCC
20836628 AGAAAAGAACCCCAAA
1 AGAAAAGAACCCCAAA
20836644 AGAAAAGAACCCCAA
1 AGAAAAGAACCCCAA
20836659 TTAGAAATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.61, C:0.26, G:0.13, T:0.00
Consensus pattern (16 bp):
AGAAAAGAACCCCAAA
Found at i:20837999 original size:14 final size:14
Alignment explanation
Indices: 20837960--20838027 Score: 59
Period size: 14 Copynumber: 4.9 Consensus size: 14
20837950 CCCTAAATCA
* *
20837960 CTAACTCTTAACCT
1 CTAACCCTTAACCC
*
20837974 CTAA-GCTCTAACCC
1 CTAACCCT-TAACCC
20837988 CTAACCCTTAACCC
1 CTAACCCTTAACCC
*
20838002 CTAACCAC-AAACCC
1 CTAACC-CTTAACCC
*
20838016 CTAACCCCTAAC
1 CTAACCCTTAAC
20838028 TATTAACCCT
Statistics
Matches: 45, Mismatches: 5, Indels: 8
0.78 0.09 0.14
Matches are distributed among these distances:
13 3 0.07
14 39 0.87
15 3 0.07
ACGTcount: A:0.32, C:0.46, G:0.01, T:0.21
Consensus pattern (14 bp):
CTAACCCTTAACCC
Found at i:20838035 original size:21 final size:21
Alignment explanation
Indices: 20837981--20838036 Score: 67
Period size: 21 Copynumber: 2.7 Consensus size: 21
20837971 CCTCTAAGCT
* *
20837981 CTAACCCCTAACCCTTAACCC
1 CTAACCACTAACCCCTAACCC
*
20838002 CTAACCACAAACCCCTAACCC
1 CTAACCACTAACCCCTAACCC
* *
20838023 CTAACTATTAACCC
1 CTAACCACTAACCC
20838037 TTAAACCTTA
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.34, C:0.48, G:0.00, T:0.18
Consensus pattern (21 bp):
CTAACCACTAACCCCTAACCC
Found at i:20838040 original size:7 final size:7
Alignment explanation
Indices: 20837981--20838027 Score: 67
Period size: 7 Copynumber: 6.7 Consensus size: 7
20837971 CCTCTAAGCT
20837981 CTAACCC
1 CTAACCC
20837988 CTAACCC
1 CTAACCC
*
20837995 TTAACCC
1 CTAACCC
*
20838002 CTAACCA
1 CTAACCC
*
20838009 CAAACCC
1 CTAACCC
20838016 CTAACCC
1 CTAACCC
20838023 CTAAC
1 CTAAC
20838028 TATTAACCCT
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
7 34 1.00
ACGTcount: A:0.34, C:0.51, G:0.00, T:0.15
Consensus pattern (7 bp):
CTAACCC
Found at i:20838761 original size:42 final size:42
Alignment explanation
Indices: 20838690--20838790 Score: 159
Period size: 42 Copynumber: 2.4 Consensus size: 42
20838680 AAATGTTTTT
* *
20838690 GCGGCGCTTTTTC-AAAAACGCCGCTAAAGCCCTGAGCATTA
1 GCGGCGCTTTTCCAAAAAACGCCGCTAAAGCCCAGAGCATTA
20838731 GCGGCGCTTTTCCAAAAAACGCCGCTAAAGCCCAGAGCATTA
1 GCGGCGCTTTTCCAAAAAACGCCGCTAAAGCCCAGAGCATTA
* *
20838773 GTGGCGCTTCTCCAAAAA
1 GCGGCGCTTTTCCAAAAA
20838791 CAGCATTAGC
Statistics
Matches: 55, Mismatches: 4, Indels: 1
0.92 0.07 0.02
Matches are distributed among these distances:
41 12 0.22
42 43 0.78
ACGTcount: A:0.29, C:0.30, G:0.22, T:0.20
Consensus pattern (42 bp):
GCGGCGCTTTTCCAAAAAACGCCGCTAAAGCCCAGAGCATTA
Found at i:20838795 original size:26 final size:26
Alignment explanation
Indices: 20838766--20838816 Score: 93
Period size: 26 Copynumber: 2.0 Consensus size: 26
20838756 TAAAGCCCAG
*
20838766 AGCATTAGTGGCGCTTCTCCAAAAAC
1 AGCATTAGCGGCGCTTCTCCAAAAAC
20838792 AGCATTAGCGGCGCTTCTCCAAAAA
1 AGCATTAGCGGCGCTTCTCCAAAAA
20838817 TGCCGCTAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.31, C:0.27, G:0.20, T:0.22
Consensus pattern (26 bp):
AGCATTAGCGGCGCTTCTCCAAAAAC
Found at i:20838836 original size:67 final size:68
Alignment explanation
Indices: 20838724--20838858 Score: 218
Period size: 67 Copynumber: 2.0 Consensus size: 68
20838714 TAAAGCCCTG
* **
20838724 AGCATTAGCGGCGCTTTTCCAAAAAACGCCGCTAAAGCCCAGAGCATTAGTGGCGCTTCTCCAAA
1 AGCATTAGCGGCGCTTCTCCAAAAAACGCCGCTAAAGCCCAGAGCATTAGCAGCGCTTCTCCAAA
20838789 AAC
66 AAC
* *
20838792 AGCATTAGCGGCGCTTCTCC-AAAAATGCCGCTAAAGCCCAGAGCATTAGCAGCGCTTTTCCAAA
1 AGCATTAGCGGCGCTTCTCCAAAAAACGCCGCTAAAGCCCAGAGCATTAGCAGCGCTTCTCCAAA
20838856 AAC
66 AAC
20838859 GCCGCTAAAG
Statistics
Matches: 62, Mismatches: 5, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
67 43 0.69
68 19 0.31
ACGTcount: A:0.31, C:0.30, G:0.20, T:0.19
Consensus pattern (68 bp):
AGCATTAGCGGCGCTTCTCCAAAAAACGCCGCTAAAGCCCAGAGCATTAGCAGCGCTTCTCCAAA
AAC
Found at i:20838854 original size:41 final size:41
Alignment explanation
Indices: 20838792--20838871 Score: 133
Period size: 41 Copynumber: 2.0 Consensus size: 41
20838782 CTCCAAAAAC
* *
20838792 AGCATTAGCGGCGCTTCTCCAAAAATGCCGCTAAAGCCCAG
1 AGCATTAGCAGCGCTTCTCCAAAAACGCCGCTAAAGCCCAG
*
20838833 AGCATTAGCAGCGCTTTTCCAAAAACGCCGCTAAAGCCC
1 AGCATTAGCAGCGCTTCTCCAAAAACGCCGCTAAAGCCC
20838872 CGAAAGGTCA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 36 1.00
ACGTcount: A:0.30, C:0.33, G:0.20, T:0.17
Consensus pattern (41 bp):
AGCATTAGCAGCGCTTCTCCAAAAACGCCGCTAAAGCCCAG
Found at i:20846726 original size:17 final size:17
Alignment explanation
Indices: 20846677--20846728 Score: 68
Period size: 17 Copynumber: 3.1 Consensus size: 17
20846667 AGTATAGGAA
*
20846677 GTAATCTTAGAAGATAT
1 GTAATCTTAGAAGATTT
* *
20846694 GCAATCTTGGAAGATTT
1 GTAATCTTAGAAGATTT
*
20846711 GTAATATTAGAAGATTT
1 GTAATCTTAGAAGATTT
20846728 G
1 G
20846729 ATTCTATAAA
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
17 29 1.00
ACGTcount: A:0.37, C:0.06, G:0.21, T:0.37
Consensus pattern (17 bp):
GTAATCTTAGAAGATTT
Found at i:20855856 original size:9 final size:9
Alignment explanation
Indices: 20855842--20855885 Score: 56
Period size: 9 Copynumber: 5.1 Consensus size: 9
20855832 GGGTATTTAA
20855842 TAATATAAT
1 TAATATAAT
20855851 TAATATAAT
1 TAATATAAT
*
20855860 T-A-ATCAT
1 TAATATAAT
*
20855867 CAATATAAT
1 TAATATAAT
20855876 TAATATAAT
1 TAATATAAT
20855885 T
1 T
20855886 TATTGTTTTA
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
7 4 0.14
8 2 0.07
9 23 0.79
ACGTcount: A:0.52, C:0.05, G:0.00, T:0.43
Consensus pattern (9 bp):
TAATATAAT
Found at i:20855925 original size:19 final size:18
Alignment explanation
Indices: 20855903--20855938 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
20855893 TTAATAATTA
*
20855903 TTTAATATTAAAATTTTAT
1 TTTAATAAT-AAATTTTAT
20855922 TTTAATAATAAATTTTA
1 TTTAATAATAAATTTTA
20855939 GAAATTATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (18 bp):
TTTAATAATAAATTTTAT
Found at i:20860661 original size:21 final size:22
Alignment explanation
Indices: 20860605--20860661 Score: 80
Period size: 22 Copynumber: 2.6 Consensus size: 22
20860595 TTTTTCTGGG
*
20860605 TCACATGGGCGTATGCCTCCTT
1 TCACATGGGCGTGTGCCTCCTT
*
20860627 TCACACGGGCGTGTGCCTCCTT
1 TCACATGGGCGTGTGCCTCCTT
*
20860649 T-ACATGAGCGTGT
1 TCACATGGGCGTGT
20860662 TGACCCCCAC
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
21 10 0.32
22 21 0.68
ACGTcount: A:0.14, C:0.30, G:0.26, T:0.30
Consensus pattern (22 bp):
TCACATGGGCGTGTGCCTCCTT
Found at i:20862428 original size:14 final size:14
Alignment explanation
Indices: 20862379--20862429 Score: 50
Period size: 14 Copynumber: 3.6 Consensus size: 14
20862369 ATATGTTAAC
*
20862379 TTATTATATATATG
1 TTATAATATATATG
*
20862393 TTATAATATATA-A
1 TTATAATATATATG
* *
20862406 TAAGAAATATATATG
1 TTA-TAATATATATG
20862421 TTATAATAT
1 TTATAATAT
20862430 TAATAAAATA
Statistics
Matches: 28, Mismatches: 7, Indels: 4
0.72 0.18 0.10
Matches are distributed among these distances:
13 2 0.07
14 24 0.86
15 2 0.07
ACGTcount: A:0.47, C:0.00, G:0.06, T:0.47
Consensus pattern (14 bp):
TTATAATATATATG
Found at i:20872256 original size:17 final size:17
Alignment explanation
Indices: 20872234--20872269 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
20872224 AAAAAAGTTC
20872234 TCATGTTTTTTAATCAA
1 TCATGTTTTTTAATCAA
20872251 TCATGTTTTTTAATCAA
1 TCATGTTTTTTAATCAA
20872268 TC
1 TC
20872270 TTGGATTTTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.28, C:0.14, G:0.06, T:0.53
Consensus pattern (17 bp):
TCATGTTTTTTAATCAA
Found at i:20872911 original size:32 final size:32
Alignment explanation
Indices: 20872827--20872912 Score: 93
Period size: 33 Copynumber: 2.6 Consensus size: 32
20872817 TTTATAAAAT
* * **
20872827 GATTTACTGGAAAATATTTTCTGGTGTTTGATT
1 GATTT-CTTGAAAATATTTTCTGCTGTTTGACA
*
20872860 GA-ATCTGTGTAAAATATTTTCTGCTGTTTGACA
1 GATTTCT-TG-AAAATATTTTCTGCTGTTTGACA
20872893 GATTTCTTGAAAATATTTTC
1 GATTTCTTGAAAATATTTTC
20872913 CGAAAAAATT
Statistics
Matches: 44, Mismatches: 6, Indels: 7
0.77 0.11 0.12
Matches are distributed among these distances:
31 2 0.05
32 13 0.30
33 26 0.59
34 3 0.07
ACGTcount: A:0.27, C:0.09, G:0.17, T:0.47
Consensus pattern (32 bp):
GATTTCTTGAAAATATTTTCTGCTGTTTGACA
Found at i:20872975 original size:18 final size:18
Alignment explanation
Indices: 20872940--20872982 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
20872930 CATATATTAA
20872940 TATATATTAATAATTTTT
1 TATATATTAATAATTTTT
*
20872958 TATATTTTAAT-ATGTTTT
1 TATATATTAATAAT-TTTT
*
20872976 TACATAT
1 TATATAT
20872983 ATTGCAATGA
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
17 2 0.10
18 19 0.90
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.60
Consensus pattern (18 bp):
TATATATTAATAATTTTT
Found at i:20875474 original size:1 final size:1
Alignment explanation
Indices: 20875468--20875492 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
20875458 CGTTTTACGT
20875468 AAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAA
20875493 GACCTTTTCC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:20878194 original size:25 final size:28
Alignment explanation
Indices: 20878165--20878216 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 28
20878155 TTATGTTATT
*
20878165 TAAAT-AA-ATTTTAAATATA-ATAATC
1 TAAATAAATATTTTAAAAATACATAATC
20878190 TAAATAAATATTTTAAAAATACATAAT
1 TAAATAAATATTTTAAAAATACATAAT
20878217 TTCACTCAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
25 5 0.22
26 2 0.09
27 11 0.48
28 5 0.22
ACGTcount: A:0.58, C:0.04, G:0.00, T:0.38
Consensus pattern (28 bp):
TAAATAAATATTTTAAAAATACATAATC
Found at i:20878583 original size:2 final size:2
Alignment explanation
Indices: 20878576--20878600 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
20878566 GATTTCAACT
20878576 TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC T
20878601 TCGGTATTTA
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:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:20879639 original size:26 final size:28
Alignment explanation
Indices: 20879603--20879655 Score: 83
Period size: 26 Copynumber: 2.0 Consensus size: 28
20879593 ATGTAAATAG
*
20879603 AAAATGATAATTAT-TAT-AATTATTTT
1 AAAATAATAATTATATATAAATTATTTT
20879629 AAAATAATAATTATATATAAATTATTT
1 AAAATAATAATTATATATAAATTATTT
20879656 GTACTAACAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
26 13 0.54
27 3 0.12
28 8 0.33
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (28 bp):
AAAATAATAATTATATATAAATTATTTT
Found at i:20892843 original size:27 final size:26
Alignment explanation
Indices: 20892829--20892895 Score: 89
Period size: 27 Copynumber: 2.5 Consensus size: 26
20892819 TTAAGTCCGG
20892829 ACACTCAGTGCTATATAATCAACTCGC
1 ACACTCAGTGCTATAT-ATCAACTCGC
*
20892856 ACACTTAGTGCTATATAATCAAACTCGC
1 ACACTCAGTGCTATAT-ATC-AACTCGC
*
20892884 ACACTTAGTGCT
1 ACACTCAGTGCT
20892896 GTACAATTTA
Statistics
Matches: 38, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
27 19 0.50
28 19 0.50
ACGTcount: A:0.33, C:0.27, G:0.12, T:0.28
Consensus pattern (26 bp):
ACACTCAGTGCTATATATCAACTCGC
Found at i:20892889 original size:28 final size:28
Alignment explanation
Indices: 20892829--20892923 Score: 129
Period size: 28 Copynumber: 3.4 Consensus size: 28
20892819 TTAAGTCCGG
*
20892829 ACACTCAGTGCTATATAATC-AACTCGC
1 ACACTTAGTGCTATATAATCAAACTCGC
20892856 ACACTTAGTGCTATATAATCAAACTCGC
1 ACACTTAGTGCTATATAATCAAACTCGC
* * * *
20892884 ACACTTAGTGCTGTACAATTTAAACCCGC
1 ACACTTAGTGCTATATAA-TCAAACTCGC
20892913 ACACTTAGTGC
1 ACACTTAGTGC
20892924 CAATCTCATG
Statistics
Matches: 61, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
27 19 0.31
28 23 0.38
29 19 0.31
ACGTcount: A:0.33, C:0.27, G:0.13, T:0.27
Consensus pattern (28 bp):
ACACTTAGTGCTATATAATCAAACTCGC
Found at i:20900690 original size:9 final size:9
Alignment explanation
Indices: 20900676--20900707 Score: 55
Period size: 9 Copynumber: 3.6 Consensus size: 9
20900666 TTCGCATCAT
20900676 TTTCTCTTA
1 TTTCTCTTA
20900685 TTTCTCTTA
1 TTTCTCTTA
*
20900694 TTTATCTTA
1 TTTCTCTTA
20900703 TTTCT
1 TTTCT
20900708 TAATAGCAAG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.12, C:0.19, G:0.00, T:0.69
Consensus pattern (9 bp):
TTTCTCTTA
Found at i:20905005 original size:18 final size:18
Alignment explanation
Indices: 20904982--20905024 Score: 77
Period size: 18 Copynumber: 2.4 Consensus size: 18
20904972 GAATGCACAA
*
20904982 AGTAAGCTTTGGGAGCTT
1 AGTAAGCTTTAGGAGCTT
20905000 AGTAAGCTTTAGGAGCTT
1 AGTAAGCTTTAGGAGCTT
20905018 AGTAAGC
1 AGTAAGC
20905025 CTTAAGCAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.28, C:0.12, G:0.30, T:0.30
Consensus pattern (18 bp):
AGTAAGCTTTAGGAGCTT
Found at i:20905673 original size:31 final size:30
Alignment explanation
Indices: 20905631--20906282 Score: 246
Period size: 31 Copynumber: 21.3 Consensus size: 30
20905621 ACCATTAATG
20905631 AATCAAGTTCGGCAATATATAATCATATACA
1 AATCAA-TTCGGCAATATATAATCATATACA
* * *
20905662 AATCCAATTCGGC-ATCCTATATTCATAAAC-
1 AAT-CAATTCGGCAAT-ATATAATCATATACA
* * *
20905692 AATCTAATATCGACAATATATAACCATGTACA
1 AATC-AAT-TCGGCAATATATAATCATATACA
* ** ** * * *
20905724 AATTAATTTCAACAAGGTACAA-CATTTACG
1 AATCAA-TTCGGCAATATATAATCATATACA
*
20905754 AATCAATTCGACAACT-TAT-ATCCATATACCA
1 AATCAATTCGGCAA-TATATAAT-CATATA-CA
* ** *
20905785 AA-CAATTTGGCAAGGTATAACCAT-TCACA
1 AATCAATTCGGCAATATATAATCATAT-ACA
*
20905814 AATCAAGTTTGGCAATATATAATCATATACA
1 AATCAA-TTCGGCAATATATAATCATATACA
* * * *
20905845 AATCCAATTTGGC-ATCCTATATTCATAAACA
1 AAT-CAATTCGGCAAT-ATATAATCATATACA
* ** * *
20905876 ATTCAATATCGATAATATATAACCATGTACA
1 AATCAAT-TCGGCAATATATAATCATATACA
* * ** *
20905907 AATTAATTTCAGCAAGGTACAAT-ATATACA
1 AATCAA-TTCGGCAATATATAATCATATACA
*
20905937 AATCAATTCGACAACT-TAT-ATCCATATACCA
1 AATCAATTCGGCAA-TATATAAT-CATATA-CA
* ** * *
20905968 AA-CAATTCGACAAGGTATAACCAT-TCACG
1 AATCAATTCGGCAATATATAATCATAT-ACA
20905997 AATCAAGTTCGGCAATATATAATCATATACA
1 AATCAA-TTCGGCAATATATAATCATATACA
* * * *
20906028 AATCCAATTCAGC-ATCCTATATTCATAAACA
1 AAT-CAATTCGGCAAT-ATATAATCATATACA
* * * *
20906059 ATTCAATATCGACAATATATAACCATGTACA
1 AATCAAT-TCGGCAATATATAATCATATACA
* ** *
20906090 AATTAATTTTAGCAATGTATATAA-CATATACG
1 AATCAA-TTCGGCAA--TATATAATCATATACA
*
20906122 AATCAATTCGACAACT-TAT-ATCCATATACCA
1 AATCAATTCGGCAA-TATATAAT-CATATA-CA
** * *
20906153 AA-CAATTCGGCAAGGTATAACCAT-TCACG
1 AATCAATTCGGCAATATATAATCATAT-ACA
* *
20906182 AATTAAGTTCGGCAATATATAATCATATCCA
1 AATCAA-TTCGGCAATATATAATCATATACA
* * *
20906213 AATCCAATTCGGC-ATCCTATATTCATAAACA
1 AAT-CAATTCGGCAAT-ATATAATCATATACA
* * * * *
20906244 ATTCAATATTGACAATATATAACCATGTACA
1 AATCAAT-TCGGCAATATATAATCATATACA
*
20906275 AATTAATT
1 AATCAATT
20906283 TTAGCAATGT
Statistics
Matches: 455, Mismatches: 114, Indels: 105
0.68 0.17 0.16
Matches are distributed among these distances:
28 4 0.01
29 34 0.07
30 125 0.27
31 246 0.54
32 39 0.09
33 7 0.02
ACGTcount: A:0.43, C:0.20, G:0.08, T:0.30
Consensus pattern (30 bp):
AATCAATTCGGCAATATATAATCATATACA
Found at i:20905902 original size:183 final size:183
Alignment explanation
Indices: 20905588--20906289 Score: 1154
Period size: 183 Copynumber: 3.8 Consensus size: 183
20905578 TTAGCAATGA
* * * * * *
20905588 ATATCGATATACCCAACAATTCAGCAATGTATAACCATTAATGAATCAAGTTCGGCAATATATAA
1 ATATCCATATACCAAACAATTCGGCAAGGTATAACCATTCACGAATCAAGTTCGGCAATATATAA
20905653 TCATATACAAATCCAATTCGGCATCCTATATTCATAAACAA-TCTAATATCGACAATATATAACC
66 TCATATACAAATCCAATTCGGCATCCTATATTCATAAACAATTC-AATATCGACAATATATAACC
* *
20905717 ATGTACAAATTAATTTCAACAAGGTACAACATTTACGAATCAATTCGACAACTT
130 ATGTACAAATTAATTTCAGCAAGGTACAACATATACGAATCAATTCGACAACTT
* * *
20905771 ATATCCATATACCAAACAATTTGGCAAGGTATAACCATTCACAAATCAAGTTTGGCAATATATAA
1 ATATCCATATACCAAACAATTCGGCAAGGTATAACCATTCACGAATCAAGTTCGGCAATATATAA
* *
20905836 TCATATACAAATCCAATTTGGCATCCTATATTCATAAACAATTCAATATCGATAATATATAACCA
66 TCATATACAAATCCAATTCGGCATCCTATATTCATAAACAATTCAATATCGACAATATATAACCA
* *
20905901 TGTACAAATTAATTTCAGCAAGGTACAATATATACAAATCAATTCGACAACTT
131 TGTACAAATTAATTTCAGCAAGGTACAACATATACGAATCAATTCGACAACTT
*
20905954 ATATCCATATACCAAACAATTCGACAAGGTATAACCATTCACGAATCAAGTTCGGCAATATATAA
1 ATATCCATATACCAAACAATTCGGCAAGGTATAACCATTCACGAATCAAGTTCGGCAATATATAA
*
20906019 TCATATACAAATCCAATTCAGCATCCTATATTCATAAACAATTCAATATCGACAATATATAACCA
66 TCATATACAAATCCAATTCGGCATCCTATATTCATAAACAATTCAATATCGACAATATATAACCA
* * *
20906084 TGTACAAATTAATTTTAGCAATGTATATAACATATACGAATCAATTCGACAACTT
131 TGTACAAATTAATTTCAGCAA-G-GTACAACATATACGAATCAATTCGACAACTT
*
20906139 ATATCCATATACCAAACAATTCGGCAAGGTATAACCATTCACGAATTAAGTTCGGCAATATATAA
1 ATATCCATATACCAAACAATTCGGCAAGGTATAACCATTCACGAATCAAGTTCGGCAATATATAA
* *
20906204 TCATATCCAAATCCAATTCGGCATCCTATATTCATAAACAATTCAATATTGACAATATATAACCA
66 TCATATACAAATCCAATTCGGCATCCTATATTCATAAACAATTCAATATCGACAATATATAACCA
*
20906269 TGTACAAATTAATTTTAGCAA
131 TGTACAAATTAATTTCAGCAA
20906290 TGTATAAAAC
Statistics
Matches: 484, Mismatches: 32, Indels: 4
0.93 0.06 0.01
Matches are distributed among these distances:
183 308 0.64
184 3 0.01
185 173 0.36
ACGTcount: A:0.43, C:0.20, G:0.08, T:0.29
Consensus pattern (183 bp):
ATATCCATATACCAAACAATTCGGCAAGGTATAACCATTCACGAATCAAGTTCGGCAATATATAA
TCATATACAAATCCAATTCGGCATCCTATATTCATAAACAATTCAATATCGACAATATATAACCA
TGTACAAATTAATTTCAGCAAGGTACAACATATACGAATCAATTCGACAACTT
Found at i:20909291 original size:26 final size:26
Alignment explanation
Indices: 20909254--20909315 Score: 88
Period size: 26 Copynumber: 2.4 Consensus size: 26
20909244 TACCTACAGT
*
20909254 AGTTTCAGAATATCATAATATATATC
1 AGTTTTAGAATATCATAATATATATC
* *
20909280 TGTTTTAGAATATCATAATATGTATC
1 AGTTTTAGAATATCATAATATATATC
*
20909306 AATTTTAGAA
1 AGTTTTAGAA
20909316 CACTTCTAGG
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 31 1.00
ACGTcount: A:0.40, C:0.08, G:0.10, T:0.42
Consensus pattern (26 bp):
AGTTTTAGAATATCATAATATATATC
Found at i:20913726 original size:41 final size:41
Alignment explanation
Indices: 20913669--20913858 Score: 229
Period size: 41 Copynumber: 4.6 Consensus size: 41
20913659 TGAGTCCAAC
*
20913669 AGGCTTCGTGACGGTGTATTATACCAGGCTTTGTGCCTAGA
1 AGGCTTCGTGACGGTGTATTATATCAGGCTTTGTGCCTAGA
* * *
20913710 AGGCTTCGTGACGGTGTATTATATCAGGCTTTGTACTTAGC
1 AGGCTTCGTGACGGTGTATTATATCAGGCTTTGTGCCTAGA
* * * *
20913751 AGGCTTCGTGCCGGTGTATTATATCAAGCATTGTGCCTAGT
1 AGGCTTCGTGACGGTGTATTATATCAGGCTTTGTGCCTAGA
* * * * *
20913792 AGGCTTCATGTCGGTGTGTTATATTAGGCTTTGAGCCTAGCA
1 AGGCTTCGTGACGGTGTATTATATCAGGCTTTGTGCCTAG-A
* *
20913834 A-GCTTCGTGACAGTGTATTGTATCA
1 AGGCTTCGTGACGGTGTATTATATCA
20913859 TGTAGGTTGT
Statistics
Matches: 124, Mismatches: 24, Indels: 2
0.83 0.16 0.01
Matches are distributed among these distances:
41 123 0.99
42 1 0.01
ACGTcount: A:0.20, C:0.18, G:0.27, T:0.35
Consensus pattern (41 bp):
AGGCTTCGTGACGGTGTATTATATCAGGCTTTGTGCCTAGA
Found at i:20920534 original size:28 final size:28
Alignment explanation
Indices: 20920517--20920571 Score: 78
Period size: 27 Copynumber: 2.0 Consensus size: 28
20920507 TGATTAAATT
20920517 TTAATAAAAAT-ATAAAAATATTTAAAAA
1 TTAA-AAAAATCATAAAAATATTTAAAAA
*
20920545 TTAAAAAAATCATAAAAAT-TGTAAAAA
1 TTAAAAAAATCATAAAAATATTTAAAAA
20920572 AAATTATAAG
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
27 13 0.52
28 12 0.48
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.29
Consensus pattern (28 bp):
TTAAAAAAATCATAAAAATATTTAAAAA
Found at i:20920560 original size:18 final size:17
Alignment explanation
Indices: 20920520--20920564 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 17
20920510 TTAAATTTTA
*
20920520 ATAAAAATATAAAAATAT
1 ATAAAAAT-TAAAAAAAT
*
20920538 TTAAAAATTAAAAAAAT
1 ATAAAAATTAAAAAAAT
20920555 CATAAAAATT
1 -ATAAAAATT
20920565 GTAAAAAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
17 8 0.35
18 15 0.65
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (17 bp):
ATAAAAATTAAAAAAAT
Found at i:20920572 original size:28 final size:28
Alignment explanation
Indices: 20920517--20920572 Score: 71
Period size: 28 Copynumber: 2.0 Consensus size: 28
20920507 TGATTAAATT
*
20920517 TTAATAAAAATATAAAAATATTTAAAAA
1 TTAATAAAAATATAAAAATATTAAAAAA
20920545 TTAA-AAAAATCATAAAAAT-TGTAAAAAA
1 TTAATAAAAAT-ATAAAAATAT-TAAAAAA
20920573 AATTATAAGA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
27 7 0.28
28 18 0.72
ACGTcount: A:0.68, C:0.02, G:0.02, T:0.29
Consensus pattern (28 bp):
TTAATAAAAATATAAAAATATTAAAAAA
Found at i:20920620 original size:30 final size:30
Alignment explanation
Indices: 20920540--20920621 Score: 80
Period size: 30 Copynumber: 2.8 Consensus size: 30
20920530 AAAAATATTT
* *
20920540 AAAAATTA-AAAAAATCATAAAAATTGTAAA
1 AAAAATTATAAAAAAT-TTAAAAATCGTAAA
* *
20920570 AAAAATTAT-AAGATTTTAAAAAGTCGT-AA
1 AAAAATTATAAAAAATTTAAAAA-TCGTAAA
*
20920599 GAAAATTATAAAAAATTTAAAAA
1 AAAAATTATAAAAAATTTAAAAA
20920622 AAATGTAAAA
Statistics
Matches: 42, Mismatches: 7, Indels: 6
0.76 0.13 0.11
Matches are distributed among these distances:
29 16 0.38
30 26 0.62
ACGTcount: A:0.65, C:0.02, G:0.06, T:0.27
Consensus pattern (30 bp):
AAAAATTATAAAAAATTTAAAAATCGTAAA
Found at i:20920623 original size:20 final size:22
Alignment explanation
Indices: 20920600--20920653 Score: 69
Period size: 20 Copynumber: 2.6 Consensus size: 22
20920590 AAGTCGTAAG
20920600 AAAATTATAAAAAAT-TTAAAA
1 AAAATTATAAAAAATCTTAAAA
* *
20920621 AAAA-TGT-AAAATTCTTAAAA
1 AAAATTATAAAAAATCTTAAAA
20920641 AAAATTATAAAAA
1 AAAATTATAAAAA
20920654 TTATTGTAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
19 5 0.19
20 12 0.44
21 6 0.22
22 4 0.15
ACGTcount: A:0.69, C:0.02, G:0.02, T:0.28
Consensus pattern (22 bp):
AAAATTATAAAAAATCTTAAAA
Found at i:20920653 original size:10 final size:10
Alignment explanation
Indices: 20920512--20920622 Score: 54
Period size: 10 Copynumber: 11.3 Consensus size: 10
20920502 TAAAATGATT
*
20920512 AAATTTTAATA
1 AAATTATAA-A
*
20920523 AAAATATAAA
1 AAATTATAAA
20920533 AATATT-T-AA
1 AA-ATTATAAA
20920542 AAATTA-AAA
1 AAATTATAAA
*
20920551 AAATCATAAA
1 AAATTATAAA
* *
20920561 AATTGTAAAAA
1 AAAT-TATAAA
20920572 AAATTAT--A
1 AAATTATAAA
* *
20920580 AGATTTTAAA
1 AAATTATAAA
* **
20920590 AAGTCGTAAGA
1 AAATTATAA-A
20920601 AAATTATAAA
1 AAATTATAAA
20920611 AAATT-TAAA
1 AAATTATAAA
20920620 AAA
1 AAA
20920623 AATGTAAAAT
Statistics
Matches: 74, Mismatches: 18, Indels: 18
0.67 0.16 0.16
Matches are distributed among these distances:
8 9 0.12
9 18 0.24
10 24 0.32
11 23 0.31
ACGTcount: A:0.64, C:0.02, G:0.05, T:0.30
Consensus pattern (10 bp):
AAATTATAAA
Found at i:20920654 original size:50 final size:49
Alignment explanation
Indices: 20920540--20920657 Score: 116
Period size: 50 Copynumber: 2.3 Consensus size: 49
20920530 AAAAATATTT
*
20920540 AAAAATTAAAAAAATCATAAAAATTGTAAAAAAAATTATAAGATTTTAAA
1 AAAAATT-AAAAAATTATAAAAATTGTAAAAAAAATTATAAGATTTTAAA
****
20920590 AAGTCGTAAGAAAATTATAAAAAATT-TAAAAAAAATGTA-AA-ATTCTTAAA
1 AAAAATTAA-AAAATTAT-AAAAATTGTAAAAAAAAT-TATAAGATT-TTAAA
20920640 AAAAATTATAAAAATTAT
1 AAAAATTA-AAAAATTAT
20920658 TGTAATAAAA
Statistics
Matches: 54, Mismatches: 9, Indels: 10
0.74 0.12 0.14
Matches are distributed among these distances:
49 5 0.09
50 39 0.72
51 10 0.19
ACGTcount: A:0.64, C:0.03, G:0.05, T:0.29
Consensus pattern (49 bp):
AAAAATTAAAAAATTATAAAAATTGTAAAAAAAATTATAAGATTTTAAA
Found at i:20920904 original size:29 final size:29
Alignment explanation
Indices: 20920849--20920947 Score: 89
Period size: 29 Copynumber: 3.4 Consensus size: 29
20920839 TTTGTAATTT
* *
20920849 TTTTTATGATTTTTATAATAAATTTTAATATA
1 TTTTTATAATTTTTAT--TAAAATTTAATA-A
20920881 TTTTTAT-ATTTTTATTAAAATTTAATAA
1 TTTTTATAATTTTTATTAAAATTTAATAA
* * * *
20920909 TTTGTATAACTTTTATT--AATTT-TTAT
1 TTTTTATAATTTTTATTAAAATTTAATAA
20920935 TTTTTATAATTTT
1 TTTTTATAATTTT
20920948 GTTTGCCACA
Statistics
Matches: 59, Mismatches: 7, Indels: 8
0.80 0.09 0.11
Matches are distributed among these distances:
26 13 0.22
27 5 0.08
28 7 0.12
29 19 0.32
31 8 0.14
32 7 0.12
ACGTcount: A:0.33, C:0.01, G:0.02, T:0.64
Consensus pattern (29 bp):
TTTTTATAATTTTTATTAAAATTTAATAA
Found at i:20921333 original size:6 final size:7
Alignment explanation
Indices: 20921308--20921332 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
20921298 AGTGGCTTAA
20921308 TTTTTAT
1 TTTTTAT
20921315 TTTTTAT
1 TTTTTAT
20921322 TTTTTAT
1 TTTTTAT
20921329 TTTT
1 TTTT
20921333 AAGTTTAAGG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (7 bp):
TTTTTAT
Found at i:20926718 original size:43 final size:42
Alignment explanation
Indices: 20926647--20926749 Score: 152
Period size: 43 Copynumber: 2.4 Consensus size: 42
20926637 ATTAGGATAT
*
20926647 TATTATGGGATATTATCTTTTAGCAATTTGATTCCTAATGGGA
1 TATTATAGGATATTAT-TTTTAGCAATTTGATTCCTAATGGGA
* * *
20926690 TGTTATAGGTTATTATTTCTTAGCAATTTGATTCCTAATTGGA
1 TATTATAGGATATTATTT-TTAGCAATTTGATTCCTAATGGGA
20926733 TATTATAGGATATTATT
1 TATTATAGGATATTATT
20926750 ATGGGATATT
Statistics
Matches: 53, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
42 2 0.04
43 51 0.96
ACGTcount: A:0.28, C:0.08, G:0.17, T:0.48
Consensus pattern (42 bp):
TATTATAGGATATTATTTTTAGCAATTTGATTCCTAATGGGA
Found at i:20942408 original size:16 final size:16
Alignment explanation
Indices: 20942396--20942426 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
20942386 TTCTTTTGTG
20942396 TATTTACTCTTTTATA
1 TATTTACTCTTTTATA
20942412 TATTTACTCTTTTAT
1 TATTTACTCTTTTAT
20942427 GTTGATGACA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.23, C:0.13, G:0.00, T:0.65
Consensus pattern (16 bp):
TATTTACTCTTTTATA
Found at i:20947065 original size:16 final size:16
Alignment explanation
Indices: 20947040--20947112 Score: 58
Period size: 16 Copynumber: 4.4 Consensus size: 16
20947030 TAAAAAATAT
*
20947040 AAAATATAAAATTTTAG
1 AAAAT-TAAAATTTTAA
**
20947057 AAAATTAAAAAATTAA
1 AAAATTAAAATTTTAA
*
20947073 AAAATTAAAA-TTCAA
1 AAAATTAAAATTTTAA
*
20947088 AAAATGTATAAATTTGAGA
1 AAAAT-TA-AAATTTTA-A
20947107 AAAATT
1 AAAATT
20947113 CTAACAATAC
Statistics
Matches: 46, Mismatches: 6, Indels: 7
0.78 0.10 0.12
Matches are distributed among these distances:
15 8 0.17
16 20 0.43
17 8 0.17
18 4 0.09
19 6 0.13
ACGTcount: A:0.63, C:0.01, G:0.05, T:0.30
Consensus pattern (16 bp):
AAAATTAAAATTTTAA
Found at i:20947090 original size:8 final size:8
Alignment explanation
Indices: 20947030--20947082 Score: 54
Period size: 8 Copynumber: 6.6 Consensus size: 8
20947020 GAAAAACTTA
20947030 TAAAAAA-
1 TAAAAAAT
*
20947037 TATAAAAT
1 TAAAAAAT
**
20947045 ATAAAATTT
1 -TAAAAAAT
*
20947054 TAGAAAAT
1 TAAAAAAT
20947062 TAAAAAAT
1 TAAAAAAT
20947070 TAAAAAAT
1 TAAAAAAT
20947078 TAAAA
1 TAAAA
20947083 TTCAAAAAAT
Statistics
Matches: 36, Mismatches: 8, Indels: 3
0.77 0.17 0.06
Matches are distributed among these distances:
7 6 0.17
8 25 0.69
9 5 0.14
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.28
Consensus pattern (8 bp):
TAAAAAAT
Found at i:20948604 original size:14 final size:14
Alignment explanation
Indices: 20948585--20948629 Score: 72
Period size: 14 Copynumber: 3.2 Consensus size: 14
20948575 GGATCTGTCG
*
20948585 TAAACCTTAAACCT
1 TAAACCTTAAACCC
20948599 TAAACCTTAAACCC
1 TAAACCTTAAACCC
*
20948613 TAAACCCTAAACCC
1 TAAACCTTAAACCC
20948627 TAA
1 TAA
20948630 TCCCTTATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 29 1.00
ACGTcount: A:0.44, C:0.33, G:0.00, T:0.22
Consensus pattern (14 bp):
TAAACCTTAAACCC
Found at i:20948626 original size:7 final size:7
Alignment explanation
Indices: 20948585--20948634 Score: 64
Period size: 7 Copynumber: 7.1 Consensus size: 7
20948575 GGATCTGTCG
*
20948585 TAAACCT
1 TAAACCC
*
20948592 TAAACCT
1 TAAACCC
*
20948599 TAAACCT
1 TAAACCC
20948606 TAAACCC
1 TAAACCC
20948613 TAAACCC
1 TAAACCC
20948620 TAAACCC
1 TAAACCC
*
20948627 TAATCCC
1 TAAACCC
20948634 T
1 T
20948635 TATTTATTTA
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
7 41 1.00
ACGTcount: A:0.40, C:0.36, G:0.00, T:0.24
Consensus pattern (7 bp):
TAAACCC
Found at i:20948699 original size:22 final size:21
Alignment explanation
Indices: 20948659--20948704 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 21
20948649 TTTTCTTTAA
* *
20948659 AACCCTAAAAACCTTAAACCCT
1 AACCCTAAAAACC-CAAAACCT
20948681 AACCCTAAAAACCCAAAACCT
1 AACCCTAAAAACCCAAAACCT
20948702 AAC
1 AAC
20948705 GGTGGAGAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 9 0.41
22 13 0.59
ACGTcount: A:0.50, C:0.37, G:0.00, T:0.13
Consensus pattern (21 bp):
AACCCTAAAAACCCAAAACCT
Found at i:20949133 original size:18 final size:18
Alignment explanation
Indices: 20949098--20949137 Score: 64
Period size: 18 Copynumber: 2.2 Consensus size: 18
20949088 AAATTTTGAT
20949098 TTTTTATATATTTTTTAA
1 TTTTTATATATTTTTTAA
20949116 TTTTTAT-TATTTTCTTAA
1 TTTTTATATATTTT-TTAA
20949134 TTTT
1 TTTT
20949138 GTAGAACTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 6 0.29
18 15 0.71
ACGTcount: A:0.23, C:0.03, G:0.00, T:0.75
Consensus pattern (18 bp):
TTTTTATATATTTTTTAA
Found at i:20950704 original size:33 final size:32
Alignment explanation
Indices: 20950606--20950700 Score: 77
Period size: 33 Copynumber: 2.9 Consensus size: 32
20950596 TATTTGAATC
*
20950606 TAATTTAATAT-AAAATAATTA-ATTTCAAAATA
1 TAATTTAAAATAAAAATAATTATA-TT-AAAATA
* * * ** **
20950638 CAATTTAAAGTAAAACTAAAAAATATTTTAATA
1 TAATTTAAAATAAAAAT-AATTATATTAAAATA
20950671 TAATTTAAAATAAAAATAATTATATTAAAA
1 TAATTTAAAATAAAAATAATTATATTAAAA
20950701 ATATTATTAA
Statistics
Matches: 45, Mismatches: 15, Indels: 6
0.68 0.23 0.09
Matches are distributed among these distances:
32 17 0.38
33 22 0.49
34 5 0.11
35 1 0.02
ACGTcount: A:0.59, C:0.03, G:0.01, T:0.37
Consensus pattern (32 bp):
TAATTTAAAATAAAAATAATTATATTAAAATA
Found at i:20950745 original size:56 final size:58
Alignment explanation
Indices: 20950685--20950806 Score: 178
Period size: 59 Copynumber: 2.1 Consensus size: 58
20950675 TTAAAATAAA
* *
20950685 AATAATTATATTAAAAATATTATTAAATTA-TA-TATTT-TTATTAAATTATATTTAAT
1 AATAATCATATT-AAAATATGATTAAATTATTATTATTTATTATTAAATTATATTTAAT
*
20950741 AATAATCATATTAAAATATGATTAAATTATTTATTATTTATTATTAAATTATTTTTAAT
1 AATAATCATATTAAAATATGATTAAATTA-TTATTATTTATTATTAAATTATATTTAAT
20950800 AATAATC
1 AATAATC
20950807 CGTTTAAAAT
Statistics
Matches: 59, Mismatches: 3, Indels: 5
0.88 0.04 0.07
Matches are distributed among these distances:
55 16 0.27
56 11 0.19
57 2 0.03
58 5 0.08
59 25 0.42
ACGTcount: A:0.47, C:0.02, G:0.01, T:0.51
Consensus pattern (58 bp):
AATAATCATATTAAAATATGATTAAATTATTATTATTTATTATTAAATTATATTTAAT
Found at i:20952545 original size:22 final size:24
Alignment explanation
Indices: 20952502--20952545 Score: 65
Period size: 22 Copynumber: 1.9 Consensus size: 24
20952492 TGATAATATG
20952502 TTTTGATATAACAAATTAAAGTGT
1 TTTTGATATAACAAATTAAAGTGT
*
20952526 TTTTGA-ATAA-AAGTTAAAGT
1 TTTTGATATAACAAATTAAAGT
20952546 TGAACAAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 9 0.47
23 4 0.21
24 6 0.32
ACGTcount: A:0.43, C:0.02, G:0.14, T:0.41
Consensus pattern (24 bp):
TTTTGATATAACAAATTAAAGTGT
Found at i:20952785 original size:21 final size:21
Alignment explanation
Indices: 20952759--20952815 Score: 96
Period size: 21 Copynumber: 2.7 Consensus size: 21
20952749 AATTTTCACA
20952759 AAAAAGTATTGATACATTTAC
1 AAAAAGTATTGATACATTTAC
*
20952780 AAAAAGTATTGATACCTTTAC
1 AAAAAGTATTGATACATTTAC
*
20952801 AAAAAGTATCGATAC
1 AAAAAGTATTGATAC
20952816 CTTCTACCAA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.47, C:0.12, G:0.11, T:0.30
Consensus pattern (21 bp):
AAAAAGTATTGATACATTTAC
Found at i:20952816 original size:21 final size:21
Alignment explanation
Indices: 20952759--20952834 Score: 93
Period size: 21 Copynumber: 3.7 Consensus size: 21
20952749 AATTTTCACA
* *
20952759 AAAAAGTATTGATACATTTAC
1 AAAAAGTATCGATACCTTTAC
*
20952780 AAAAAGTATTGATACCTTTAC
1 AAAAAGTATCGATACCTTTAC
20952801 AAAAAGTATCGATACCTTCTAC
1 AAAAAGTATCGATACCTT-TAC
*
20952823 -CAAA-TATCGATA
1 AAAAAGTATCGATA
20952835 AATTGCCTTT
Statistics
Matches: 51, Mismatches: 3, Indels: 3
0.89 0.05 0.05
Matches are distributed among these distances:
20 8 0.16
21 40 0.78
22 3 0.06
ACGTcount: A:0.45, C:0.16, G:0.09, T:0.30
Consensus pattern (21 bp):
AAAAAGTATCGATACCTTTAC
Found at i:20953838 original size:52 final size:52
Alignment explanation
Indices: 20953749--20953850 Score: 145
Period size: 52 Copynumber: 2.0 Consensus size: 52
20953739 GAGTTGGGAC
* * *
20953749 ACACGGCTGTGTCCTAGCCCGTGTTTCTACCCTTGTAACTCACTGACTTGAG
1 ACACGGCTGTGTCCCAGCCCGTGTCTCCACCCTTGTAACTCACTGACTTGAG
20953801 ACACGG-TCGTGTCCCAGCCCGTGTCTCCA-CCTGTGTAACTCACTGACTTG
1 ACACGGCT-GTGTCCCAGCCCGTGTCTCCACCCT-TGTAACTCACTGACTTG
20953851 GGTCACACGG
Statistics
Matches: 45, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
51 4 0.09
52 41 0.91
ACGTcount: A:0.17, C:0.33, G:0.22, T:0.28
Consensus pattern (52 bp):
ACACGGCTGTGTCCCAGCCCGTGTCTCCACCCTTGTAACTCACTGACTTGAG
Found at i:20954169 original size:23 final size:23
Alignment explanation
Indices: 20954143--20954221 Score: 113
Period size: 23 Copynumber: 3.3 Consensus size: 23
20954133 CTACTTAGGT
**
20954143 TACCAAACTTTAAGCTAAATGCA
1 TACCAAACTTTAAGCTAAACACA
20954166 TACCAAACTTTAAGCTAAACACA
1 TACCAAACTTTAAGCTAAACACA
*
20954189 TACCAAACTTTAAGCTAAGCTATCA
1 TACCAAACTTTAAGCTAAAC-A-CA
20954214 TACCAAAC
1 TACCAAAC
20954222 ATAACCTTAA
Statistics
Matches: 51, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
23 40 0.78
24 1 0.02
25 10 0.20
ACGTcount: A:0.44, C:0.25, G:0.06, T:0.24
Consensus pattern (23 bp):
TACCAAACTTTAAGCTAAACACA
Found at i:20974736 original size:33 final size:33
Alignment explanation
Indices: 20974694--20974759 Score: 116
Period size: 33 Copynumber: 2.0 Consensus size: 33
20974684 TTTTTTAAGC
20974694 CTTAAATTGAAAATGAATTTTA-TATAGGGGGAG
1 CTTAAATTGAAAATGAATTTTATTA-AGGGGGAG
20974727 CTTAAATTGAAAATGAATTTTATTAAGGGGGAG
1 CTTAAATTGAAAATGAATTTTATTAAGGGGGAG
20974760 AAATTATTCA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
33 30 0.94
34 2 0.06
ACGTcount: A:0.39, C:0.03, G:0.24, T:0.33
Consensus pattern (33 bp):
CTTAAATTGAAAATGAATTTTATTAAGGGGGAG
Found at i:20974887 original size:22 final size:24
Alignment explanation
Indices: 20974844--20974887 Score: 65
Period size: 22 Copynumber: 1.9 Consensus size: 24
20974834 TGATAATATG
20974844 TTTTGATATAACAAATTAAAGTAT
1 TTTTGATATAACAAATTAAAGTAT
*
20974868 TTTTGA-ATAA-AAGTTAAAGT
1 TTTTGATATAACAAATTAAAGT
20974888 TGAACATAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 9 0.47
23 4 0.21
24 6 0.32
ACGTcount: A:0.45, C:0.02, G:0.11, T:0.41
Consensus pattern (24 bp):
TTTTGATATAACAAATTAAAGTAT
Found at i:20975648 original size:38 final size:38
Alignment explanation
Indices: 20975574--20975648 Score: 87
Period size: 38 Copynumber: 2.0 Consensus size: 38
20975564 GAGTATTAAG
* * *
20975574 GTTTGGGTAGAAACCTTAAGGTAGTTGCAATATTAAAA
1 GTTTGGGTAGAAACATTAAGGGAGTTGCAAGATTAAAA
* * * *
20975612 GTTTGGGTATAAATATTAAGGGAGTTGTAAGGTTAAA
1 GTTTGGGTAGAAACATTAAGGGAGTTGCAAGATTAAA
20975649 CCTTGTCCTC
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
38 30 1.00
ACGTcount: A:0.36, C:0.04, G:0.27, T:0.33
Consensus pattern (38 bp):
GTTTGGGTAGAAACATTAAGGGAGTTGCAAGATTAAAA
Found at i:20977466 original size:20 final size:21
Alignment explanation
Indices: 20977441--20977505 Score: 87
Period size: 20 Copynumber: 3.1 Consensus size: 21
20977431 ATAATAAATC
*
20977441 AAAATAAAATTTAGAAATTT-
1 AAAATAAAATTTAAAAATTTA
20977461 AAAATAAAATTTAAAAATTTA
1 AAAATAAAATTTAAAAATTTA
* *
20977482 AAAATAAAAATAAAAAATATTA
1 AAAATAAAATTTAAAAAT-TTA
20977504 AA
1 AA
20977506 TTAATAGAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
20 19 0.47
21 16 0.40
22 5 0.12
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (21 bp):
AAAATAAAATTTAAAAATTTA
Found at i:20979950 original size:49 final size:45
Alignment explanation
Indices: 20979897--20979992 Score: 111
Period size: 45 Copynumber: 2.0 Consensus size: 45
20979887 AAATTTGAAG
*
20979897 AAGAGAAGAAGAAGAAGAAGAGACCGGGAAGGGGAAAAAGAAAGAAAAA
1 AAGAGAAGAAG-AGAAG-AGAGA--GGGAAGGAGAAAAAGAAAGAAAAA
* * * *
20979946 AAGAGAAGCAGAGTAGAGAGAGGGAAGGAGAAAGAGAAGGAAAAA
1 AAGAGAAGAAGAGAAGAGAGAGGGAAGGAGAAAAAGAAAGAAAAA
20979991 AA
1 AA
20979993 ATAAATAGAA
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
45 23 0.55
47 5 0.12
48 4 0.10
49 10 0.24
ACGTcount: A:0.59, C:0.03, G:0.36, T:0.01
Consensus pattern (45 bp):
AAGAGAAGAAGAGAAGAGAGAGGGAAGGAGAAAAAGAAAGAAAAA
Found at i:20980015 original size:13 final size:13
Alignment explanation
Indices: 20979999--20980028 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
20979989 AAAAATAAAT
20979999 AGAAAAGGGAAGG
1 AGAAAAGGGAAGG
20980012 AG-AAAGGGAAGG
1 AGAAAAGGGAAGG
20980024 AGAAA
1 AGAAA
20980029 TTGTGTTTAG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
12 12 0.75
13 4 0.25
ACGTcount: A:0.57, C:0.00, G:0.43, T:0.00
Consensus pattern (13 bp):
AGAAAAGGGAAGG
Found at i:20980683 original size:15 final size:17
Alignment explanation
Indices: 20980657--20980700 Score: 53
Period size: 15 Copynumber: 2.9 Consensus size: 17
20980647 TGTTAATATA
20980657 TATTAT-ATTTTAAACT
1 TATTATCATTTTAAACT
20980673 TA-TA-CATTTT--ACT
1 TATTATCATTTTAAACT
20980686 TATTATCATTTTAAA
1 TATTATCATTTTAAA
20980701 TTAATAATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 9
0.72 0.00 0.28
Matches are distributed among these distances:
13 5 0.22
14 2 0.09
15 13 0.57
16 2 0.09
17 1 0.04
ACGTcount: A:0.36, C:0.09, G:0.00, T:0.55
Consensus pattern (17 bp):
TATTATCATTTTAAACT
Found at i:20984299 original size:40 final size:40
Alignment explanation
Indices: 20984262--20984447 Score: 225
Period size: 40 Copynumber: 4.7 Consensus size: 40
20984252 GCTACTCGTT
** * *
20984262 CAAATGCCTTCGGGAAATAGCTCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATT-TAGTAACTCGCA
20984302 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
20984342 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
** * * * *
20984382 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAACCCGGATTTAGTAAC-TCGCA
*
20984423 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAACCCGGA
20984448 CATCGTTCAA
Statistics
Matches: 131, Mismatches: 11, Indels: 8
0.87 0.07 0.05
Matches are distributed among these distances:
39 3 0.02
40 115 0.88
41 13 0.10
ACGTcount: A:0.27, C:0.26, G:0.22, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
Found at i:20991232 original size:40 final size:39
Alignment explanation
Indices: 20991107--20991308 Score: 212
Period size: 39 Copynumber: 5.1 Consensus size: 39
20991097 TCAGAATTTA
** **
20991107 CGGATATAGCT-ACTCGTTCAAATGCCTTCGGGAAATAGCC
1 CGGATATAG-TAACTCGCACAAATGCCTTC-GGACTTAGCC
* *
20991147 CGTTATATAGTAACTCGCACAAATGCCTTCGGACTTAACC
1 CG-GATATAGTAACTCGCACAAATGCCTTCGGACTTAGCC
* *
20991187 CGGATTTAGTAACTCGCACAAATGCCTTCGGGACTTAACC
1 CGGATATAGTAACTCGCACAAATGCCTTC-GGACTTAGCC
* *
20991227 CGGATTTAGT-ACTCGCACAAATGCCTTCGGATCTTAGTC
1 CGGATATAGTAACTCGCACAAATGCCTTCGGA-CTTAGCC
* * *
20991266 CGGATATGGTCACTTAGCACAAA-GCCTTCGGACTTAGCC
1 CGGATATAGTAAC-TCGCACAAATGCCTTCGGACTTAGCC
20991305 CGGA
1 CGGA
20991309 CATCGTTCAA
Statistics
Matches: 142, Mismatches: 14, Indels: 13
0.84 0.08 0.08
Matches are distributed among these distances:
38 3 0.02
39 66 0.46
40 43 0.30
41 30 0.21
ACGTcount: A:0.27, C:0.27, G:0.21, T:0.26
Consensus pattern (39 bp):
CGGATATAGTAACTCGCACAAATGCCTTCGGACTTAGCC
Found at i:20993148 original size:49 final size:48
Alignment explanation
Indices: 20993095--20993338 Score: 296
Period size: 49 Copynumber: 5.0 Consensus size: 48
20993085 GTATTTATTT
**
20993095 AATTAGATTAATTGCAACATTAAAACTTGGAACAAACTTTGTGGTCATA
1 AATTAGATTAATTGCAACATTAAAACTTGGAACAAACTTTGTAAT-ATA
* *
20993144 AATTAGATTAATTGCAACATTAAAACTTGGAACAAACTTTATGATCATA
1 AATTAGATTAATTGCAACATTAAAACTTGGAACAAACTTTGTAAT-ATA
* *
20993193 AATTAGATTAATTGCAACATTAAAACTTGGAGCAAACTTTGTAGTATA
1 AATTAGATTAATTGCAACATTAAAACTTGGAACAAACTTTGTAATATA
* * * * *
20993241 ATTTA-AATACACTACAACATTAAAACTTGGAACAAAATTTGTAATATA
1 AATTAGATTA-ATTGCAACATTAAAACTTGGAACAAACTTTGTAATATA
* * *
20993289 AATTA-AATATATTACAACATTAAAACTT-GATACAAACTTAGTAATATA
1 AATTAGATTA-ATTGCAACATTAAAACTTGGA-ACAAACTTTGTAATATA
20993337 AA
1 AA
20993339 ATAGGTACAT
Statistics
Matches: 175, Mismatches: 18, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
47 5 0.03
48 82 0.47
49 88 0.50
ACGTcount: A:0.46, C:0.11, G:0.10, T:0.32
Consensus pattern (48 bp):
AATTAGATTAATTGCAACATTAAAACTTGGAACAAACTTTGTAATATA
Found at i:20993198 original size:98 final size:96
Alignment explanation
Indices: 20993095--20993338 Score: 305
Period size: 96 Copynumber: 2.5 Consensus size: 96
20993085 GTATTTATTT
* * * *
20993095 AATTAGATTAATTGCAACATTAAAACTTGGAACAAACTTTGTGGTCATAAATTAGATTA-ATTGC
1 AATTAGATTAATTGCAACATTAAAACTTGGAACAAACTTTGTAGT-ATAAATTA-AATACACTAC
* *
20993159 AACATTAAAACTTGGAACAAACTTTATGATCATA
64 AACATTAAAACTTGGAACAAAATTTATAAT-ATA
* *
20993193 AATTAGATTAATTGCAACATTAAAACTTGGAGCAAACTTTGTAGTATAATTTAAATACACTACAA
1 AATTAGATTAATTGCAACATTAAAACTTGGAACAAACTTTGTAGTATAAATTAAATACACTACAA
*
20993258 CATTAAAACTTGGAACAAAATTTGTAATATA
66 CATTAAAACTTGGAACAAAATTTATAATATA
* * * *
20993289 AATTA-AATATATTACAACATTAAAACTT-GATACAAACTTAGTAATATAAA
1 AATTAGATTA-ATTGCAACATTAAAACTTGGA-ACAAACTTTGTAGTATAAA
20993339 ATAGGTACAT
Statistics
Matches: 128, Mismatches: 15, Indels: 8
0.85 0.10 0.05
Matches are distributed among these distances:
95 5 0.04
96 43 0.34
97 37 0.29
98 43 0.34
ACGTcount: A:0.46, C:0.11, G:0.10, T:0.32
Consensus pattern (96 bp):
AATTAGATTAATTGCAACATTAAAACTTGGAACAAACTTTGTAGTATAAATTAAATACACTACAA
CATTAAAACTTGGAACAAAATTTATAATATA
Found at i:20997396 original size:114 final size:114
Alignment explanation
Indices: 20997220--20997624 Score: 442
Period size: 114 Copynumber: 3.6 Consensus size: 114
20997210 AAGCTCTTTT
* * * * *
20997220 CCAAAACGCAGCGCTTTGGTCTTGATGTATAGTAGCCTTAGTGGCGCTTATATTCAAACGCCGCT
1 CCAAAACGCAGAGCTTTGGTCTTGAGGTATATTAGCATTAGTGGCGCTTATATTAAAACGCCGCT
*
20997285 AAAGTATAGTATTAGCGGCGAGTACTGAAAAGCGCCGCAATATTTCTTAA
66 AAAGAATAGTATTAGCGGCGAGTACTGAAAAGCGCCGCAA-ATTTCTTAA
* * *
20997335 CCGAAACGCAGAG-TTTGGTCTTGAGGTACATTAGGATTAGTGGCGCTTAT-TTAAAAACGCCGC
1 CCAAAACGCAGAGCTTTGGTCTTGAGGTATATTAGCATTAGTGGCGCTTATATT-AAAACGCCGC
* * * ** * * * * *
20997398 TAACGCATAGTAGTAGCGGCGCTTATTGTAAAGCGTCGCAAA-ATATTAA
65 TAAAGAATAGTATTAGCGGCGAGTACTGAAAAGCGCCGCAAATTTCTTAA
* * * * * * **
20997447 CCAAAACGCAGCGCTTTGGTCTTGATGTATACTACCAGTAGTGGCACTTATATTAAAACGCTACT
1 CCAAAACGCAGAGCTTTGGTCTTGAGGTATATTAGCATTAGTGGCGCTTATATTAAAACGCCGCT
* * *
20997512 AAAGAATAGTATTAGCAGCGAGTAGTGAAAAGCGCCGTAAGATTTCTTAA
66 AAAGAATAGTATTAGCGGCGAGTACTGAAAAGCGCCGCAA-ATTTCTTAA
* * *
20997562 CCAAAACGCAGAG-TTTGGTCTTGCGGTATATTAGGATTAGTGGCGCTTAT-TGGAAAACGCCGC
1 CCAAAACGCAGAGCTTTGGTCTTGAGGTATATTAGCATTAGTGGCGCTTATAT-TAAAACGCCGC
20997625 AAAATATTAA
Statistics
Matches: 232, Mismatches: 52, Indels: 13
0.78 0.18 0.04
Matches are distributed among these distances:
112 16 0.07
113 73 0.31
114 115 0.50
115 28 0.12
ACGTcount: A:0.30, C:0.19, G:0.24, T:0.27
Consensus pattern (114 bp):
CCAAAACGCAGAGCTTTGGTCTTGAGGTATATTAGCATTAGTGGCGCTTATATTAAAACGCCGCT
AAAGAATAGTATTAGCGGCGAGTACTGAAAAGCGCCGCAAATTTCTTAA
Found at i:20997732 original size:188 final size:188
Alignment explanation
Indices: 20997415--20997817 Score: 671
Period size: 188 Copynumber: 2.1 Consensus size: 188
20997405 TAGTAGTAGC
* * *
20997415 GGCGCTTATTGTAAAGCGTCGCAAAATATTAACCAAAACGCAGCGCTTTGGTCTTGATGTATACT
1 GGCGCTTATTGGAAAACGCCGCAAAATATTAACCAAAACGCAGCGCTTTGGTCTTGATGTATACT
20997480 ACCAGTAGTGGCACTTATATTAAAACGCTACTAAAGAATAGTATTAGCAGCGAGTAGTGAAAAGC
66 ACCAGTAGTGGCACTTATATTAAAACGCTACTAAAGAATAGTATTAGCAGCGAGTAGTGAAAAGC
* * * *
20997545 GCCGTAAGATTTCTTAACCAAAACGCAGAGTTTGGTCTTGCGGTATATTAGGATTAGT
131 GCCGCAAGATTTCTTAACCAAAACGCAGAGTTTGGTCTTGAGGTACATTACGATTAGT
20997603 GGCGCTTATTGGAAAACGCCGCAAAATATTAACCAAAACGCAGCGCTTTGGTCTTGATGTATACT
1 GGCGCTTATTGGAAAACGCCGCAAAATATTAACCAAAACGCAGCGCTTTGGTCTTGATGTATACT
* * * * *
20997668 AGCAGTAGTGGCGCTTATATTAAAACGCTGCTAAAGAATAGTATTAGCGGTGAGTAGTGAAAAGC
66 ACCAGTAGTGGCACTTATATTAAAACGCTACTAAAGAATAGTATTAGCAGCGAGTAGTGAAAAGC
*
20997733 GCCGCAATATTTCTTAACCAAAACGCAGAGTTTGGTCTTGAGGTACATTACGATTAGT
131 GCCGCAAGATTTCTTAACCAAAACGCAGAGTTTGGTCTTGAGGTACATTACGATTAGT
* *
20997791 GGCGCTTATTTGAAAACGCCGCTAAAT
1 GGCGCTTATTGGAAAACGCCGCAAAAT
20997818 CATAGTATTA
Statistics
Matches: 200, Mismatches: 15, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
188 200 1.00
ACGTcount: A:0.32, C:0.18, G:0.23, T:0.28
Consensus pattern (188 bp):
GGCGCTTATTGGAAAACGCCGCAAAATATTAACCAAAACGCAGCGCTTTGGTCTTGATGTATACT
ACCAGTAGTGGCACTTATATTAAAACGCTACTAAAGAATAGTATTAGCAGCGAGTAGTGAAAAGC
GCCGCAAGATTTCTTAACCAAAACGCAGAGTTTGGTCTTGAGGTACATTACGATTAGT
Found at i:20997924 original size:113 final size:112
Alignment explanation
Indices: 20997597--20997947 Score: 406
Period size: 113 Copynumber: 3.1 Consensus size: 112
20997587 GTATATTAGG
* *
20997597 ATTAGTGGCGCTTATTGGAAAA-CGCCGCAAAATATTAACCAAAACGCAGCGCTTTGGTCTTGAT
1 ATTAGCGGCGCTTATT-GAAAAGCGCCGCAAAACATTAACCAAAACGCAGCGCTTTGGTCTTGAT
* * *
20997661 GTATACTAGCAGTAGTGGCGCTTATATTAAAACGCTGCTAAAGA-ATAGT
65 GTATACTACCAGTTGTGGCGCTTAT-TTAAAACGCCGCTAAA-ACATAGT
* ** * * *
20997710 ATTAGCGGTGAGTAGTGAAAAGCGCCGCAATATTTC-TTAACCAAAACGCAGAG-TTTGGTCTTG
1 ATTAGCGGCGCTTATTGAAAAGCGCCGCAA-A--ACATTAACCAAAACGCAGCGCTTTGGTCTTG
* * * * *
20997773 AGGTACATTACGA-TTAGTGGCGCTTATTTGAAAACGCCGCTAAATCATAGT
63 ATGTATACTACCAGTT-GTGGCGCTTATTT-AAAACGCCGCTAAAACATAGT
*
20997824 ATTAGCGGCGCTTATTGTAAAGCGCCGCAAAACATTAACCAAAACGCAGCGCTTTGGTCTTGATG
1 ATTAGCGGCGCTTATTGAAAAGCGCCGCAAAACATTAACCAAAACGCAGCGCTTTGGTCTTGATG
* * *
20997889 TATACTACCAGTTGTGGCGCTTATGGTAAAACGCCGGTAAAACATATT
66 TATACTACCAGTTGTGGCGCTTAT-TTAAAACGCCGCTAAAACATAGT
20997937 ATTAGCGGCGC
1 ATTAGCGGCGC
20997948 GTTGTGGGAA
Statistics
Matches: 196, Mismatches: 31, Indels: 22
0.79 0.12 0.09
Matches are distributed among these distances:
111 1 0.01
112 21 0.11
113 82 0.42
114 76 0.39
115 16 0.08
ACGTcount: A:0.31, C:0.19, G:0.23, T:0.27
Consensus pattern (112 bp):
ATTAGCGGCGCTTATTGAAAAGCGCCGCAAAACATTAACCAAAACGCAGCGCTTTGGTCTTGATG
TATACTACCAGTTGTGGCGCTTATTTAAAACGCCGCTAAAACATAGT
Found at i:20998000 original size:17 final size:17
Alignment explanation
Indices: 20997969--20998018 Score: 84
Period size: 17 Copynumber: 3.0 Consensus size: 17
20997959 CGCCGCTAGA
*
20997969 TTATTATAT-ATGTAGT
1 TTATTATATAATGTAGG
20997985 TTATTATATAATGTAGG
1 TTATTATATAATGTAGG
20998002 TTATTATATAATGTAGG
1 TTATTATATAATGTAGG
20998019 AAATAGGATA
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
16 9 0.28
17 23 0.72
ACGTcount: A:0.34, C:0.00, G:0.16, T:0.50
Consensus pattern (17 bp):
TTATTATATAATGTAGG
Found at i:20998070 original size:7 final size:7
Alignment explanation
Indices: 20998058--20998134 Score: 57
Period size: 7 Copynumber: 11.0 Consensus size: 7
20998048 TTTGAATTCT
20998058 GGTTTAG
1 GGTTTAG
20998065 GGTTTAG
1 GGTTTAG
*
20998072 AGTTTAG
1 GGTTTAG
*
20998079 GGTTTAA
1 GGTTTAG
*
20998086 GGTTTAC
1 GGTTTAG
* *
20998093 GATGTA-
1 GGTTTAG
20998099 GGTTTAG
1 GGTTTAG
* **
20998106 TGTTTTT
1 GGTTTAG
20998113 GGTTTAG
1 GGTTTAG
20998120 GGTTTGAG
1 GGTTT-AG
*
20998128 AGTTTAG
1 GGTTTAG
20998135 TGATTAAGGT
Statistics
Matches: 53, Mismatches: 15, Indels: 4
0.74 0.21 0.06
Matches are distributed among these distances:
6 4 0.08
7 43 0.81
8 6 0.11
ACGTcount: A:0.18, C:0.01, G:0.35, T:0.45
Consensus pattern (7 bp):
GGTTTAG
Found at i:21000096 original size:11 final size:11
Alignment explanation
Indices: 21000059--21000098 Score: 64
Period size: 11 Copynumber: 3.7 Consensus size: 11
21000049 GAATATCTCA
21000059 AACT-ATGGGT
1 AACTAATGGGT
*
21000069 AACTAGTGGGT
1 AACTAATGGGT
21000080 AACTAATGGGT
1 AACTAATGGGT
21000091 AACTAATG
1 AACTAATG
21000099 TATTATCATC
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
10 4 0.15
11 23 0.85
ACGTcount: A:0.35, C:0.10, G:0.28, T:0.28
Consensus pattern (11 bp):
AACTAATGGGT
Found at i:21001462 original size:17 final size:17
Alignment explanation
Indices: 21001440--21001738 Score: 161
Period size: 17 Copynumber: 16.6 Consensus size: 17
21001430 GTTAAATTTA
21001440 TTACTAAAATACATTAC
1 TTACTAAAATACATTAC
*
21001457 TTACTAAAATAAATTAC
1 TTACTAAAATACATTAC
*
21001474 TTACTAAAATTTGTTTAAATTTA-
1 TTACTAAAA------TACA-TTAC
21001497 TTACTAAAATACATTAC
1 TTACTAAAATACATTAC
21001514 TTACTAAAATACATTAC
1 TTACTAAAATACATTAC
* *
21001531 TTACATAAATTTGTTTAAATTTA-
1 TTAC-TAAA-----ATACA-TTAC
*
21001554 TTTCTAAAATACATTAC
1 TTACTAAAATACATTAC
*
21001571 TTACTAAAATTTGTTTAAATTTA-
1 TTACTAAAA------TACA-TTAC
21001594 TTACTAAAATACATTAC
1 TTACTAAAATACATTAC
21001611 TTACTAAAATACATTAC
1 TTACTAAAATACATTAC
*
21001628 TTACTAAAAT---TT-G
1 TTACTAAAATACATTAC
** *
21001641 TT--T-AAATTTATTAA
1 TTACTAAAATACATTAC
*
21001655 TTACTTAAATACATTAC
1 TTACTAAAATACATTAC
*
21001672 TTACTAAAATTTGTTTAAATTTA-
1 TTACTAAAA------TACA-TTAC
21001695 TTACTAAAATACATTAC
1 TTACTAAAATACATTAC
21001712 TTACTAAAATACATTAC
1 TTACTAAAATACATTAC
21001729 TTACTAAAAT
1 TTACTAAAAT
21001739 TTGTTTAAAT
Statistics
Matches: 225, Mismatches: 18, Indels: 78
0.70 0.06 0.24
Matches are distributed among these distances:
10 4 0.02
11 1 0.00
13 4 0.02
14 4 0.02
16 13 0.06
17 136 0.60
18 4 0.02
22 4 0.02
23 43 0.19
24 12 0.05
ACGTcount: A:0.44, C:0.12, G:0.02, T:0.43
Consensus pattern (17 bp):
TTACTAAAATACATTAC
Found at i:21001513 original size:40 final size:40
Alignment explanation
Indices: 21001457--21001620 Score: 157
Period size: 40 Copynumber: 3.7 Consensus size: 40
21001447 AATACATTAC
*
21001457 TTACTAAAATAAATTACTTACTAAAATTTGTTTAAATTTA
1 TTACTAAAATACATTACTTACTAAAATTTGTTTAAATTTA
*
21001497 TTACTAAAATACATTACTTACTAAAATACATTACTTACATAAATTTGTTTAAA
1 TTACTAAAATACATTACTTACTAAAAT---TT-GTT---TAAA----TTT--A
21001550 TTTATTTCTAAAATACATTACTTACTAAAATTTGTTTAAATTTA
1 -TTA---CTAAAATACATTACTTACTAAAATTTGTTTAAATTTA
21001594 TTACTAAAATACATTACTTACTAAAAT
1 TTACTAAAATACATTACTTACTAAAAT
21001621 ACATTACTTA
Statistics
Matches: 104, Mismatches: 3, Indels: 34
0.74 0.02 0.24
Matches are distributed among these distances:
40 50 0.48
43 5 0.05
44 3 0.03
46 3 0.03
47 4 0.04
50 4 0.04
51 3 0.03
53 3 0.03
54 5 0.05
57 24 0.23
ACGTcount: A:0.44, C:0.11, G:0.02, T:0.43
Consensus pattern (40 bp):
TTACTAAAATACATTACTTACTAAAATTTGTTTAAATTTA
Found at i:21001519 original size:57 final size:57
Alignment explanation
Indices: 21001431--21001580 Score: 266
Period size: 57 Copynumber: 2.6 Consensus size: 57
21001421 CGATTGAATG
21001431 TTAAATTTATTACTAAAATACATTACTTACTAAAATAAATTACTTAC-TAAAATTTGT
1 TTAAATTTATTACTAAAATACATTACTTACTAAAATAAATTACTTACAT-AAATTTGT
*
21001488 TTAAATTTATTACTAAAATACATTACTTACTAAAATACATTACTTACATAAATTTGT
1 TTAAATTTATTACTAAAATACATTACTTACTAAAATAAATTACTTACATAAATTTGT
*
21001545 TTAAATTTATTTCTAAAATACATTACTTACTAAAAT
1 TTAAATTTATTACTAAAATACATTACTTACTAAAAT
21001581 TTGTTTAAAT
Statistics
Matches: 90, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
57 89 0.99
58 1 0.01
ACGTcount: A:0.45, C:0.11, G:0.01, T:0.43
Consensus pattern (57 bp):
TTAAATTTATTACTAAAATACATTACTTACTAAAATAAATTACTTACATAAATTTGT
Found at i:21001576 original size:97 final size:97
Alignment explanation
Indices: 21001460--21001771 Score: 518
Period size: 97 Copynumber: 3.2 Consensus size: 97
21001450 ACATTACTTA
*
21001460 CTAAAATAAATTACTTACTAAAATTTGTTTAAATTTATTACTAAAATACATTACTTACTAAAATA
1 CTAAAATACATTACTTACTAAAATTTGTTTAAATTTATTACTAAAATACATTACTTACTAAAATA
21001525 CATTACTTAC-ATAAATTTGTTTAAATTTATTT
66 CATTACTTACTA-AAATTTGTTTAAATTTATTT
21001557 CTAAAATACATTACTTACTAAAATTTGTTTAAATTTATTACTAAAATACATTACTTACTAAAATA
1 CTAAAATACATTACTTACTAAAATTTGTTTAAATTTATTACTAAAATACATTACTTACTAAAATA
21001622 CATTACTTACTAAAATTTGTTTAAATTTATTAATT
66 CATTACTTACTAAAATTTGTTTAAATTTA-T--TT
*
21001657 ACTTAAATACATTACTTACTAAAATTTGTTTAAATTTATTACTAAAATACATTACTTACTAAAAT
1 -CTAAAATACATTACTTACTAAAATTTGTTTAAATTTATTACTAAAATACATTACTTACTAAAAT
*
21001722 ACATTACTTACTAAAATTTGTTTAAATTTATTA
65 ACATTACTTACTAAAATTTGTTTAAATTTATTT
* **
21001755 CTTAAATATGTTACTTA
1 CTAAAATACATTACTTA
21001772 AATTTATTAC
Statistics
Matches: 205, Mismatches: 5, Indels: 10
0.93 0.02 0.05
Matches are distributed among these distances:
97 106 0.52
98 3 0.01
100 3 0.01
101 93 0.45
ACGTcount: A:0.43, C:0.11, G:0.02, T:0.44
Consensus pattern (97 bp):
CTAAAATACATTACTTACTAAAATTTGTTTAAATTTATTACTAAAATACATTACTTACTAAAATA
CATTACTTACTAAAATTTGTTTAAATTTATTT
Found at i:21001618 original size:57 final size:60
Alignment explanation
Indices: 21001557--21001681 Score: 211
Period size: 57 Copynumber: 2.1 Consensus size: 60
21001547 AAATTTATTT
21001557 CTAAAATACATTACTTACTAAAATTTGTTTAAA-T-TT-ATTACTAAAATACATTACTTA
1 CTAAAATACATTACTTACTAAAATTTGTTTAAATTATTAATTACTAAAATACATTACTTA
*
21001614 CTAAAATACATTACTTACTAAAATTTGTTTAAATTTATTAATTACTTAAATACATTACTTA
1 CTAAAATACATTACTTACTAAAATTTGTTTAAA-TTATTAATTACTAAAATACATTACTTA
21001675 CTAAAAT
1 CTAAAAT
21001682 TTGTTTAAAT
Statistics
Matches: 63, Mismatches: 1, Indels: 4
0.93 0.01 0.06
Matches are distributed among these distances:
57 33 0.52
59 1 0.02
60 2 0.03
61 27 0.43
ACGTcount: A:0.44, C:0.12, G:0.02, T:0.42
Consensus pattern (60 bp):
CTAAAATACATTACTTACTAAAATTTGTTTAAATTATTAATTACTAAAATACATTACTTA
Found at i:21001689 original size:101 final size:100
Alignment explanation
Indices: 21001452--21001754 Score: 533
Period size: 101 Copynumber: 3.0 Consensus size: 100
21001442 ACTAAAATAC
*
21001452 ATTACTTACTAAAATAAATTACTTACTAAAATTTGTTTAAATTTATTACTAAAATACATTACTTA
1 ATTA-TTACTAAAATACATTACTTACTAAAATTTGTTTAAATTTATTACTAAAATACATTACTTA
21001517 CTAAAATACATTACTTAC-ATAAATTTGTTTAAATTT
65 CTAAAATACATTACTTACTA-AAATTTGTTTAAATTT
21001553 A-T-TT-CTAAAATACATTACTTACTAAAATTTGTTTAAATTTATTACTAAAATACATTACTTAC
1 ATTATTACTAAAATACATTACTTACTAAAATTTGTTTAAATTTATTACTAAAATACATTACTTAC
21001615 TAAAATACATTACTTACTAAAATTTGTTTAAATTT
66 TAAAATACATTACTTACTAAAATTTGTTTAAATTT
*
21001650 ATTAATTACTTAAATACATTACTTACTAAAATTTGTTTAAATTTATTACTAAAATACATTACTTA
1 ATT-ATTACTAAAATACATTACTTACTAAAATTTGTTTAAATTTATTACTAAAATACATTACTTA
21001715 CTAAAATACATTACTTACTAAAATTTGTTTAAATTT
65 CTAAAATACATTACTTACTAAAATTTGTTTAAATTT
21001751 ATTA
1 ATTA
21001755 CTTAAATATG
Statistics
Matches: 195, Mismatches: 2, Indels: 11
0.94 0.01 0.05
Matches are distributed among these distances:
97 91 0.47
98 4 0.02
100 4 0.02
101 96 0.49
ACGTcount: A:0.43, C:0.11, G:0.02, T:0.44
Consensus pattern (100 bp):
ATTATTACTAAAATACATTACTTACTAAAATTTGTTTAAATTTATTACTAAAATACATTACTTAC
TAAAATACATTACTTACTAAAATTTGTTTAAATTT
Found at i:21001698 original size:40 final size:43
Alignment explanation
Indices: 21001606--21001721 Score: 184
Period size: 44 Copynumber: 2.7 Consensus size: 43
21001596 ACTAAAATAC
*
21001606 ATTACTTACTAAAATACATTACTTACTAAAATTTGTTTAAATTT
1 ATTAATTACTAAAATACATTACTTACTAAAATTTGTTTAAA-TT
*
21001650 ATTAATTACTTAAATACATTACTTACTAAAATTTGTTTAAA-T
1 ATTAATTACTAAAATACATTACTTACTAAAATTTGTTTAAATT
21001692 -TT-ATTACTAAAATACATTACTTACTAAAAT
1 ATTAATTACTAAAATACATTACTTACTAAAAT
21001722 ACATTACTTA
Statistics
Matches: 69, Mismatches: 3, Indels: 4
0.91 0.04 0.05
Matches are distributed among these distances:
40 27 0.39
41 2 0.03
42 1 0.01
44 39 0.57
ACGTcount: A:0.43, C:0.11, G:0.02, T:0.44
Consensus pattern (43 bp):
ATTAATTACTAAAATACATTACTTACTAAAATTTGTTTAAATT
Found at i:21001725 original size:57 final size:57
Alignment explanation
Indices: 21001650--21001771 Score: 199
Period size: 57 Copynumber: 2.1 Consensus size: 57
21001640 GTTTAAATTT
* *
21001650 ATTAATTACTTAAATACATTACTTACTAAAATTTGTTTAAATTTATTACTAAAATAC
1 ATTACTTACTAAAATACATTACTTACTAAAATTTGTTTAAATTTATTACTAAAATAC
* *
21001707 ATTACTTACTAAAATACATTACTTACTAAAATTTGTTTAAATTTATTACTTAAATAT
1 ATTACTTACTAAAATACATTACTTACTAAAATTTGTTTAAATTTATTACTAAAATAC
*
21001764 GTTACTTA
1 ATTACTTA
21001772 AATTTATTAC
Statistics
Matches: 60, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
57 60 1.00
ACGTcount: A:0.42, C:0.11, G:0.02, T:0.45
Consensus pattern (57 bp):
ATTACTTACTAAAATACATTACTTACTAAAATTTGTTTAAATTTATTACTAAAATAC
Found at i:21001761 original size:13 final size:13
Alignment explanation
Indices: 21001743--21001813 Score: 106
Period size: 13 Copynumber: 5.5 Consensus size: 13
21001733 TAAAATTTGT
21001743 TTAAATTTATTAC
1 TTAAATTTATTAC
* *
21001756 TTAAATATGTTAC
1 TTAAATTTATTAC
21001769 TTAAATTTATTAC
1 TTAAATTTATTAC
* *
21001782 TTAAATATGTTAC
1 TTAAATTTATTAC
21001795 TTAAATTTATTAC
1 TTAAATTTATTAC
21001808 TTAAAT
1 TTAAAT
21001814 AATTATAAAT
Statistics
Matches: 50, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 50 1.00
ACGTcount: A:0.39, C:0.07, G:0.03, T:0.51
Consensus pattern (13 bp):
TTAAATTTATTAC
Found at i:21001779 original size:26 final size:26
Alignment explanation
Indices: 21001743--21001814 Score: 144
Period size: 26 Copynumber: 2.8 Consensus size: 26
21001733 TAAAATTTGT
21001743 TTAAATTTATTACTTAAATATGTTAC
1 TTAAATTTATTACTTAAATATGTTAC
21001769 TTAAATTTATTACTTAAATATGTTAC
1 TTAAATTTATTACTTAAATATGTTAC
21001795 TTAAATTTATTACTTAAATA
1 TTAAATTTATTACTTAAATA
21001815 ATTATAAATA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 46 1.00
ACGTcount: A:0.40, C:0.07, G:0.03, T:0.50
Consensus pattern (26 bp):
TTAAATTTATTACTTAAATATGTTAC
Found at i:21001998 original size:38 final size:38
Alignment explanation
Indices: 21001956--21002075 Score: 124
Period size: 38 Copynumber: 3.2 Consensus size: 38
21001946 AAGATAAAAA
21001956 AAAATAAAAAAATATGTGGAATATTAAAATTGACTATT
1 AAAATAAAAAAATATGTGGAATATTAAAATTGACTATT
*** * * *
21001994 AAAATAAAATGTTAT-T---TTATTAAATATT-ATTAAT
1 AAAATAAAAAAATATGTGGAATATTAAA-ATTGACTATT
*
21002028 AATTATAAAAAAATATGTGGAATATTAAAATTGACTATT
1 AA-AATAAAAAAATATGTGGAATATTAAAATTGACTATT
21002067 AAAATAAAA
1 AAAATAAAA
21002076 TGTTATTTTA
Statistics
Matches: 61, Mismatches: 14, Indels: 14
0.69 0.16 0.16
Matches are distributed among these distances:
34 13 0.21
35 12 0.20
36 1 0.02
37 1 0.02
38 21 0.34
39 13 0.21
ACGTcount: A:0.55, C:0.02, G:0.07, T:0.36
Consensus pattern (38 bp):
AAAATAAAAAAATATGTGGAATATTAAAATTGACTATT
Found at i:21002038 original size:73 final size:73
Alignment explanation
Indices: 21001959--21002107 Score: 298
Period size: 73 Copynumber: 2.0 Consensus size: 73
21001949 ATAAAAAAAA
21001959 ATAAAAAAATATGTGGAATATTAAAATTGACTATTAAAATAAAATGTTATTTTATTAAATATTAT
1 ATAAAAAAATATGTGGAATATTAAAATTGACTATTAAAATAAAATGTTATTTTATTAAATATTAT
21002024 TAATAATT
66 TAATAATT
21002032 ATAAAAAAATATGTGGAATATTAAAATTGACTATTAAAATAAAATGTTATTTTATTAAATATTAT
1 ATAAAAAAATATGTGGAATATTAAAATTGACTATTAAAATAAAATGTTATTTTATTAAATATTAT
21002097 TAATAATT
66 TAATAATT
21002105 ATA
1 ATA
21002108 TTAGTAATGT
Statistics
Matches: 76, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
73 76 1.00
ACGTcount: A:0.51, C:0.01, G:0.07, T:0.41
Consensus pattern (73 bp):
ATAAAAAAATATGTGGAATATTAAAATTGACTATTAAAATAAAATGTTATTTTATTAAATATTAT
TAATAATT
Found at i:21002172 original size:19 final size:19
Alignment explanation
Indices: 21002148--21002374 Score: 100
Period size: 19 Copynumber: 12.5 Consensus size: 19
21002138 TATTAAATAA
21002148 TACATAATAACTTACAACT
1 TACATAATAACTTACAACT
*
21002167 TACATAAT-ACATT-TAACT
1 TACATAATAAC-TTACAACT
*
21002185 TACAT--T-ACTTACATA-A
1 TACATAATAACTTACA-ACT
21002201 TACATAATAACTTACAACT
1 TACATAATAACTTACAACT
21002220 TACATAATACATTTAACTTACAACT
1 TAC---ATA-A--TAACTTACAACT
**
21002245 TACATAAT-ACATT-TGACT
1 TACATAATAAC-TTACAACT
* *
21002263 GACATAAT-ACATT-TAACT
1 TACATAATAAC-TTACAACT
* *
21002281 TACA-ACTTAC--ACAA--
1 TACATAATAACTTACAACT
21002295 TACATAATAACTTACAACT
1 TACATAATAACTTACAACT
* *
21002314 TACATAAT-ACATAATAACT
1 TACATAATAAC-TTACAACT
* *
21002333 TACA-ACTTAC--ACAA--
1 TACATAATAACTTACAACT
21002347 TACATAATAACTTACAACT
1 TACATAATAACTTACAACT
21002366 TACATAATA
1 TACATAATA
21002375 CATAATAACT
Statistics
Matches: 161, Mismatches: 19, Indels: 56
0.68 0.08 0.24
Matches are distributed among these distances:
14 8 0.05
15 10 0.06
16 14 0.09
17 11 0.07
18 43 0.27
19 52 0.32
21 1 0.01
22 6 0.04
23 1 0.01
25 15 0.09
ACGTcount: A:0.47, C:0.20, G:0.01, T:0.33
Consensus pattern (19 bp):
TACATAATAACTTACAACT
Found at i:21002186 original size:18 final size:18
Alignment explanation
Indices: 21002163--21002284 Score: 74
Period size: 18 Copynumber: 6.4 Consensus size: 18
21002153 AATAACTTAC
21002163 AACTTACATAATACATTT
1 AACTTACATAATACATTT
*
21002181 AACTTACATTACTTACA--T
1 AACTTACA-TA-ATACATTT
*
21002199 AA--TACATAATA-ACTTAC
1 AACTTACATAATACA-TT-T
21002216 AACTTACATAATACATTTAACTT
1 AACTTACATAATACA--T---TT
21002239 ACAACTTACATAATACATTT
1 --AACTTACATAATACATTT
* *
21002259 GACTGACATAATACATTT
1 AACTTACATAATACATTT
21002277 AACTTACA
1 AACTTACA
21002285 ACTTACACAA
Statistics
Matches: 80, Mismatches: 9, Indels: 30
0.67 0.08 0.25
Matches are distributed among these distances:
13 1 0.01
14 2 0.03
15 2 0.03
16 4 0.05
17 2 0.03
18 33 0.41
19 11 0.14
20 7 0.09
21 1 0.01
23 1 0.01
24 1 0.01
25 15 0.19
ACGTcount: A:0.44, C:0.19, G:0.02, T:0.35
Consensus pattern (18 bp):
AACTTACATAATACATTT
Found at i:21002227 original size:26 final size:26
Alignment explanation
Indices: 21002144--21002549 Score: 579
Period size: 26 Copynumber: 16.1 Consensus size: 26
21002134 ATTTTATTAA
21002144 ATAATACATAATAACTTACAACTTAC
1 ATAATACATAATAACTTACAACTTAC
*
21002170 ATAATACAT-TTAACTTACATTACTTAC
1 ATAATACATAATAACTTACA--ACTTAC
21002197 ATAATACATAATAACTTACAACTTAC
1 ATAATACATAATAACTTACAACTTAC
*
21002223 ATAATACAT-TTAACTTACAACTTAC
1 ATAATACATAATAACTTACAACTTAC
* *
21002248 ATAATAC---AT---TT--GACTGAC
1 ATAATACATAATAACTTACAACTTAC
*
21002266 ATAATACATT-TAACTTACAACTTAC
1 ATAATACATAATAACTTACAACTTAC
*
21002291 ACAATACATAATAACTTACAACTTAC
1 ATAATACATAATAACTTACAACTTAC
21002317 ATAATACATAATAACTTACAACTTAC
1 ATAATACATAATAACTTACAACTTAC
*
21002343 ACAATACATAATAACTTACAACTTAC
1 ATAATACATAATAACTTACAACTTAC
21002369 ATAATACATAATAACTTACAACTTAC
1 ATAATACATAATAACTTACAACTTAC
* *
21002395 ATAATACAT-TTAACTTGCAACTTAC
1 ATAATACATAATAACTTACAACTTAC
*
21002420 ACAATACATAATAACTTACAACTTAC
1 ATAATACATAATAACTTACAACTTAC
21002446 ATAATACATAATAACTTACAACTTAC
1 ATAATACATAATAACTTACAACTTAC
*
21002472 ATAATACAT-TTAACTTACAACTTAC
1 ATAATACATAATAACTTACAACTTAC
* *
21002497 ACAATACAT-TTAACTTACAACTTAC
1 ATAATACATAATAACTTACAACTTAC
21002522 ATAATACATAATAACTTACAACTTAC
1 ATAATACATAATAACTTACAACTTAC
21002548 AT
1 AT
21002550 TTAACTTACA
Statistics
Matches: 343, Mismatches: 23, Indels: 28
0.87 0.06 0.07
Matches are distributed among these distances:
18 12 0.03
20 3 0.01
23 3 0.01
25 113 0.33
26 188 0.55
27 15 0.04
28 9 0.03
ACGTcount: A:0.47, C:0.20, G:0.01, T:0.32
Consensus pattern (26 bp):
ATAATACATAATAACTTACAACTTAC
Found at i:21002395 original size:19 final size:19
Alignment explanation
Indices: 21002321--21002451 Score: 65
Period size: 19 Copynumber: 7.5 Consensus size: 19
21002311 ACTTACATAA
21002321 TACATAATAACTTACAACT
1 TACATAATAACTTACAACT
* * *
21002340 TACACAAT-ACATAATAACT
1 TACATAATAAC-TTACAACT
*
21002359 TAC-----AACTTACATA-A
1 TACATAATAACTTACA-ACT
21002373 TACATAATAACTTACAACT
1 TACATAATAACTTACAACT
*
21002392 TACATAAT-ACATT-TAACT
1 TACATAATAAC-TTACAACT
* * *
21002410 TGCA-ACTTAC--ACAA--
1 TACATAATAACTTACAACT
21002424 TACATAATAACTTACAACT
1 TACATAATAACTTACAACT
21002443 TACATAATA
1 TACATAATA
21002452 CATAATAACT
Statistics
Matches: 81, Mismatches: 14, Indels: 34
0.63 0.11 0.26
Matches are distributed among these distances:
14 9 0.11
15 7 0.09
16 2 0.02
17 6 0.07
18 14 0.17
19 43 0.53
ACGTcount: A:0.48, C:0.21, G:0.01, T:0.31
Consensus pattern (19 bp):
TACATAATAACTTACAACT
Found at i:21002425 original size:77 final size:76
Alignment explanation
Indices: 21002268--21002549 Score: 492
Period size: 77 Copynumber: 3.7 Consensus size: 76
21002258 TGACTGACAT
* * *
21002268 AATACATTTAACTTACAACTTACACAATACATAATAACTTACAACTTACATAATACATAATAACT
1 AATACATATAACTTACAACTTACATAATACATAATAACTTACAACTTACATAATACAT-TTAACT
21002333 TACAACTTACAC
65 TACAACTTACAC
21002345 AATACATAATAACTTACAACTTACATAATACATAATAACTTACAACTTACATAATACATTTAACT
1 AATACAT-ATAACTTACAACTTACATAATACATAATAACTTACAACTTACATAATACATTTAACT
*
21002410 TGCAACTTACAC
65 TACAACTTACAC
21002422 AATACATAATAACTTACAACTTACATAATACATAATAACTTACAACTTACATAATACATTTAACT
1 AATACAT-ATAACTTACAACTTACATAATACATAATAACTTACAACTTACATAATACATTTAACT
21002487 TACAACTTACAC
65 TACAACTTACAC
*
21002499 AATACATTTAACTTACAACTTACATAATACATAATAACTTACAACTTACAT
1 AATACATATAACTTACAACTTACATAATACATAATAACTTACAACTTACAT
21002550 TTAACTTACA
Statistics
Matches: 198, Mismatches: 6, Indels: 3
0.96 0.03 0.01
Matches are distributed among these distances:
76 43 0.22
77 106 0.54
78 49 0.25
ACGTcount: A:0.48, C:0.21, G:0.00, T:0.31
Consensus pattern (76 bp):
AATACATATAACTTACAACTTACATAATACATAATAACTTACAACTTACATAATACATTTAACTT
ACAACTTACAC
Found at i:21002557 original size:11 final size:10
Alignment explanation
Indices: 21002541--21002594 Score: 55
Period size: 9 Copynumber: 5.7 Consensus size: 10
21002531 AATAACTTAC
21002541 AACTTACATTT
1 AACTTACA-TT
21002552 AACTTACA-T
1 AACTTACATT
21002561 AA--TACATTT
1 AACTTACA-TT
21002570 AACTTACA-T
1 AACTTACATT
21002579 AACTTACA-T
1 AACTTACATT
21002588 AACTTAC
1 AACTTAC
21002595 CATTGCAATT
Statistics
Matches: 39, Mismatches: 0, Indels: 10
0.80 0.00 0.20
Matches are distributed among these distances:
7 4 0.10
9 23 0.59
11 12 0.31
ACGTcount: A:0.43, C:0.20, G:0.00, T:0.37
Consensus pattern (10 bp):
AACTTACATT
Found at i:21002578 original size:18 final size:18
Alignment explanation
Indices: 21002515--21002580 Score: 89
Period size: 18 Copynumber: 3.6 Consensus size: 18
21002505 TTTAACTTAC
*
21002515 AACTTACATAATACATAAT
1 AACTTACATAATACAT-TT
*
21002534 AACTTACA-ACTTACATTT
1 AACTTACATA-ATACATTT
21002552 AACTTACATAATACATTT
1 AACTTACATAATACATTT
21002570 AACTTACATAA
1 AACTTACATAA
21002581 CTTACATAAC
Statistics
Matches: 42, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
18 28 0.67
19 14 0.33
ACGTcount: A:0.47, C:0.18, G:0.00, T:0.35
Consensus pattern (18 bp):
AACTTACATAATACATTT
Found at i:21002590 original size:18 final size:18
Alignment explanation
Indices: 21002430--21002594 Score: 69
Period size: 18 Copynumber: 9.5 Consensus size: 18
21002420 ACAATACATA
21002430 ATAACTTAC--AACTTAC
1 ATAACTTACATAACTTAC
*
21002446 ATAATACATA-ATAACTTAC
1 AT-A-ACTTACATAACTTAC
21002465 --AACTTACATAA--TAC
1 ATAACTTACATAACTTAC
21002479 ATTTAACTTAC--AACTTAC
1 A--TAACTTACATAACTTAC
*
21002497 ACAA--TACATTTAACTTAC
1 ATAACTTACA--TAACTTAC
*
21002515 --AACTTACATAATACATA-
1 ATAACTTACAT-A-ACTTAC
21002532 ATAACTTAC--AACTTAC
1 ATAACTTACATAACTTAC
21002548 ATTTAACTTACATAA--TAC
1 A--TAACTTACATAACTTAC
21002566 ATTTAACTTACATAACTTAC
1 A--TAACTTACATAACTTAC
21002586 ATAACTTAC
1 ATAACTTAC
21002595 CATTGCAATT
Statistics
Matches: 116, Mismatches: 5, Indels: 54
0.66 0.03 0.31
Matches are distributed among these distances:
14 6 0.05
15 8 0.07
16 16 0.14
17 2 0.02
18 64 0.55
19 14 0.12
20 6 0.05
ACGTcount: A:0.45, C:0.21, G:0.00, T:0.34
Consensus pattern (18 bp):
ATAACTTACATAACTTAC
Found at i:21008069 original size:21 final size:21
Alignment explanation
Indices: 21008043--21008113 Score: 79
Period size: 21 Copynumber: 3.4 Consensus size: 21
21008033 CTACAACTTA
* *
21008043 AAGCAGAGGCGGAAGCGAGGG
1 AAGCAGAGGCTGCAGCGAGGG
* *
21008064 AAGCAGCGACTGCAGCGAGGG
1 AAGCAGAGGCTGCAGCGAGGG
* * *
21008085 AAGCGGAGGCTGCAGCAAGAG
1 AAGCAGAGGCTGCAGCGAGGG
21008106 AAGCAGAG
1 AAGCAGAG
21008114 CAGAGCAAAA
Statistics
Matches: 40, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
21 40 1.00
ACGTcount: A:0.34, C:0.18, G:0.45, T:0.03
Consensus pattern (21 bp):
AAGCAGAGGCTGCAGCGAGGG
Found at i:21008589 original size:42 final size:41
Alignment explanation
Indices: 21008438--21008810 Score: 381
Period size: 42 Copynumber: 8.9 Consensus size: 41
21008428 TTTTGTATAA
* * * **
21008438 AAGCGCCACTAAAGAACATGTTCTTTTGCGGCGTTTGTAAA
1 AAGCGCCGCTAAAGAACATGTTCTTTAGCGGCGTTTTTATT
** * *** **
21008479 AAATGCCACTAAAGAACATGTTCTTTAGCGGCGATTAGAAAAA
1 AAGCGCCGCTAAAGAACATGTTCTTTAGCGGCG-TT-TTTATT
* * *
21008522 AAACGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTCCATT
1 AAGCGCCGCTAAAGAACATGTTCTTTAGCGGCGTTTT-TATT
*
21008564 AAGCGCCGCTAAAGAACATGTTCTTTAGCGGCGTTTTT-TCCA
1 AAGCGCCGCTAAAGAACATGTTCTTTAGCGGCGTTTTTAT--T
* * * *
21008606 AAGCGCCGCTAAAGAACATGGTCTTTAGTGGCATTTTT-TAC
1 AAGCGCCGCTAAAGAACATGTTCTTTAGCGGCGTTTTTAT-T
* *
21008647 AAACGCCGCTAAAGAACATGTTCTTTAGCGGCGTTTTTTTCT
1 AAGCGCCGCTAAAGAACATGTTCTTTAGCGGCGTTTTTAT-T
* *
21008689 AAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTTCT
1 AAGCGCCGCTAAAGAACATGTTCTTTAGCGGCGTTTTTAT-T
* *
21008731 AAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTTCT
1 AAGCGCCGCTAAAGAACATGTTCTTTAGCGGCGTTTTTAT-T
* * *
21008773 AAGCGCCGCTAAAGAACATGGTCTTTAACGGCTTTTTT
1 AAGCGCCGCTAAAGAACATGTTCTTTAGCGGCGTTTTT
21008811 GTTTGTAAAC
Statistics
Matches: 292, Mismatches: 34, Indels: 11
0.87 0.10 0.03
Matches are distributed among these distances:
40 1 0.00
41 64 0.22
42 194 0.66
43 33 0.11
ACGTcount: A:0.28, C:0.21, G:0.21, T:0.31
Consensus pattern (41 bp):
AAGCGCCGCTAAAGAACATGTTCTTTAGCGGCGTTTTTATT
Found at i:21008613 original size:84 final size:83
Alignment explanation
Indices: 21008423--21008810 Score: 436
Period size: 84 Copynumber: 4.6 Consensus size: 83
21008413 CAAAAATAGT
* * * * * ** * *
21008423 GGCGTTTTTGTATAAAAGCGCCACTAAAGAACATGTTCTTTTGCGGCGTTTGTAAAAAATGCCAC
1 GGCGTTTTT-T-TCAAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTATTAAACGCCGC
21008488 TAAAGAACATGTTCTTTAGC
64 TAAAGAACATGTTCTTTAGC
****** * * *
21008508 GGCGATTAGAAAAAAAACGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTCCATTAAGCGCCGC
1 GGCG-TTTTTTTCAAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTT-TATTAAACGCCGC
21008573 TAAAGAACATGTTCTTTAGC
64 TAAAGAACATGTTCTTTAGC
* * * * *
21008593 GGCGTTTTTTCCAAAGCGCCGCTAAAGAACATGGTCTTTAGTGGCATTTTT-TACAAACGCCGCT
1 GGCGTTTTTTTCAAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTAT-TAAACGCCGCT
21008657 AAAGAACATGTTCTTTAGC
65 AAAGAACATGTTCTTTAGC
* * *
21008676 GGCGTTTTTTTCTAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTTCTAAGCGCCGCT
1 GGCGTTTTTTTCAAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTAT-TAAACGCCGCT
*
21008741 AAAGAACATGATCTTTAGC
65 AAAGAACATGTTCTTTAGC
* * * *
21008760 GGCGTTTTTTTCTAAGCGCCGCTAAAGAACATGGTCTTTAACGGCTTTTTT
1 GGCGTTTTTTTCAAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTT
21008811 GTTTGTAAAC
Statistics
Matches: 258, Mismatches: 41, Indels: 9
0.84 0.13 0.03
Matches are distributed among these distances:
82 1 0.00
83 74 0.29
84 146 0.57
85 35 0.14
86 2 0.01
ACGTcount: A:0.27, C:0.20, G:0.21, T:0.31
Consensus pattern (83 bp):
GGCGTTTTTTTCAAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTATTAAACGCCGCTA
AAGAACATGTTCTTTAGC
Done.