Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001921.1 Hibiscus syriacus cultivar Beakdansim tig00003885_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 71608
ACGTcount: A:0.34, C:0.16, G:0.18, T:0.32
Found at i:1633 original size:18 final size:17
Alignment explanation
Indices: 1606--1649 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
1596 GTAACGACAA
1606 AAATATATTTAACTTTATT
1 AAATA-ATTTAACTTTA-T
* *
1625 AAATAATTTTATTTTAT
1 AAATAATTTAACTTTAT
1642 AAATAATT
1 AAATAATT
1650 AAATACATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 9 0.39
18 9 0.39
19 5 0.22
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.52
Consensus pattern (17 bp):
AAATAATTTAACTTTAT
Found at i:1765 original size:22 final size:20
Alignment explanation
Indices: 1740--1789 Score: 57
Period size: 22 Copynumber: 2.4 Consensus size: 20
1730 TAATAAAAAT
1740 AAATTA-AATTAAAAAATATTGA
1 AAATTATAA-TAAAAAAT-TT-A
1762 AAATTATTAATAAAAAATTTA
1 AAATTA-TAATAAAAAATTTA
1783 AAATTAT
1 AAATTAT
1790 TATTTCTTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
20 1 0.04
21 7 0.27
22 8 0.31
23 8 0.31
24 2 0.08
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (20 bp):
AAATTATAATAAAAAATTTA
Found at i:1785 original size:21 final size:23
Alignment explanation
Indices: 1749--1791 Score: 72
Period size: 21 Copynumber: 2.0 Consensus size: 23
1739 TAAATTAAAT
1749 TAAAAAATATTGAAAATTATTAA
1 TAAAAAATATTGAAAATTATTAA
1772 TAAAAAAT-TT-AAAATTATTA
1 TAAAAAATATTGAAAATTATTA
1792 TTTCTTTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 10 0.50
22 2 0.10
23 8 0.40
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.37
Consensus pattern (23 bp):
TAAAAAATATTGAAAATTATTAA
Found at i:1901 original size:18 final size:18
Alignment explanation
Indices: 1869--1913 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 18
1859 ATATATATAT
* *
1869 AATTATTT-GTAAAATTA
1 AATTATTTAATAAAATAA
1886 AATTATTTAATAAAATAA
1 AATTATTTAATAAAATAA
1904 AATTAATTTA
1 AATT-ATTTA
1914 TTAATTAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
17 8 0.33
18 11 0.46
19 5 0.21
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.44
Consensus pattern (18 bp):
AATTATTTAATAAAATAA
Found at i:1904 original size:23 final size:22
Alignment explanation
Indices: 1878--1924 Score: 67
Period size: 23 Copynumber: 2.1 Consensus size: 22
1868 TAATTATTTG
1878 TAAAATTAAATTATTTAATAAAA
1 TAAAATTAAATTA-TTAATAAAA
* *
1901 TAAAATTAATTTATTAATTAAA
1 TAAAATTAAATTATTAATAAAA
1923 TA
1 TA
1925 TATTTTCCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 10 0.45
23 12 0.55
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (22 bp):
TAAAATTAAATTATTAATAAAA
Found at i:2891 original size:22 final size:23
Alignment explanation
Indices: 2857--2905 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
2847 AAAAATGTAA
2857 TTATTATTTTA-TTTTAAATAAT
1 TTATTATTTTATTTTTAAATAAT
*
2879 TTATT-TTTATATTTTTAACTAAT
1 TTATTATTT-TATTTTTAAATAAT
2902 TTAT
1 TTAT
2906 AATTATATGT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
21 3 0.12
22 7 0.29
23 14 0.58
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (23 bp):
TTATTATTTTATTTTTAAATAAT
Found at i:2911 original size:23 final size:23
Alignment explanation
Indices: 2868--2913 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
2858 TATTATTTTA
**
2868 TTTTAAATAATTTATTTTTATAT
1 TTTTAAATAATTTATAATTATAT
*
2891 TTTTAACTAATTTATAATTATAT
1 TTTTAAATAATTTATAATTATAT
2914 GTTGAGTTCT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (23 bp):
TTTTAAATAATTTATAATTATAT
Found at i:3888 original size:18 final size:21
Alignment explanation
Indices: 3844--3891 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
3834 CTCCTAACTA
*
3844 GAGTATCGATACTTTTATACT
1 GAGTATCGATACTTATATACT
*
3865 GGGTATCGATAC-TATAT-C-
1 GAGTATCGATACTTATATACT
3883 GAGTATCGA
1 GAGTATCGA
3892 GTATCAATAC
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
18 8 0.33
19 1 0.04
20 4 0.17
21 11 0.46
ACGTcount: A:0.29, C:0.15, G:0.21, T:0.35
Consensus pattern (21 bp):
GAGTATCGATACTTATATACT
Found at i:5749 original size:20 final size:19
Alignment explanation
Indices: 5724--5774 Score: 66
Period size: 20 Copynumber: 2.6 Consensus size: 19
5714 TGATTGAATC
*
5724 AGTATCGATACCGAAGGGGA
1 AGTATCGATACC-AAAGGGA
5744 AGTATCGATACCAAAGGGA
1 AGTATCGATACCAAAGGGA
*
5763 AGGTATTGATAC
1 A-GTATCGATAC
5775 TATTTTGAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 7 0.25
20 21 0.75
ACGTcount: A:0.37, C:0.14, G:0.29, T:0.20
Consensus pattern (19 bp):
AGTATCGATACCAAAGGGA
Found at i:5825 original size:19 final size:19
Alignment explanation
Indices: 5801--5871 Score: 81
Period size: 19 Copynumber: 3.5 Consensus size: 19
5791 GCAAAAAGGA
5801 TATCGATACCATAGGAGGG
1 TATCGATACCATAGGAGGG
*
5820 TATCGATACCATAGTATGGTAG
1 TATCGATACCATAGGA-GG--G
5842 TATCGATACCAT-GGTAAGGG
1 TATCGATACCATAGG--AGGG
5862 TATCGATACC
1 TATCGATACC
5872 CGGTAACATC
Statistics
Matches: 45, Mismatches: 2, Indels: 9
0.80 0.04 0.16
Matches are distributed among these distances:
19 15 0.33
20 13 0.29
21 1 0.02
22 15 0.33
23 1 0.02
ACGTcount: A:0.31, C:0.17, G:0.25, T:0.27
Consensus pattern (19 bp):
TATCGATACCATAGGAGGG
Found at i:5847 original size:22 final size:19
Alignment explanation
Indices: 5801--5871 Score: 88
Period size: 22 Copynumber: 3.5 Consensus size: 19
5791 GCAAAAAGGA
*
5801 TATCGATACCATAGGAGGG
1 TATCGATACCATAGTAGGG
5820 TATCGATACCATAGTATGGTAG
1 TATCGATACCATAGTA-GG--G
*
5842 TATCGATACCATGGTAAGGG
1 TATCGATACCATAGT-AGGG
5862 TATCGATACC
1 TATCGATACC
5872 CGGTAACATC
Statistics
Matches: 46, Mismatches: 2, Indels: 7
0.84 0.04 0.13
Matches are distributed among these distances:
19 15 0.33
20 13 0.28
22 17 0.37
23 1 0.02
ACGTcount: A:0.31, C:0.17, G:0.25, T:0.27
Consensus pattern (19 bp):
TATCGATACCATAGTAGGG
Found at i:5920 original size:53 final size:53
Alignment explanation
Indices: 5859--5977 Score: 220
Period size: 53 Copynumber: 2.2 Consensus size: 53
5849 ACCATGGTAA
* *
5859 GGGTATCGATACCCGGTAACATCAAATATAATATTGGTATCGATATCGGAAGG
1 GGGTATCGATACCCGGTAACATCAAATAAAATATTGGTATCGATACCGGAAGG
5912 GGGTATCGATACCCGGTAACATCAAATAAAATATTGGTATCGATACCGGAAGG
1 GGGTATCGATACCCGGTAACATCAAATAAAATATTGGTATCGATACCGGAAGG
5965 GGGTATCGATACC
1 GGGTATCGATACC
5978 ATAGTATAGT
Statistics
Matches: 64, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
53 64 1.00
ACGTcount: A:0.34, C:0.17, G:0.25, T:0.24
Consensus pattern (53 bp):
GGGTATCGATACCCGGTAACATCAAATAAAATATTGGTATCGATACCGGAAGG
Found at i:6697 original size:54 final size:54
Alignment explanation
Indices: 6348--6679 Score: 484
Period size: 54 Copynumber: 6.1 Consensus size: 54
6338 CAAATAGGCG
* *
6348 CTAAGTGTGCATTTCACGGAATTCATCCTATGCGGATGAATAACCGCTTCGGCA
1 CTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTCGGCA
*
6402 CTAAGTGTGCATTTTACGGAATTCATCCTATGTGGATGAATAACCGTTTCGGCA
1 CTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTCGGCA
* * *
6456 CTAAGTGTGCATTTCACAGAATTCATCCTATGTGGATGAATAACAGTTTCGGTA
1 CTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTCGGCA
* *
6510 CTAAGTGCGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTTGGCA
1 CTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTCGGCA
* * * * * ***
6564 CTACGTGTGCATTTCACAGAATTAATCCTATGTCGATGAATAACCATTTTAACA
1 CTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTCGGCA
* * * *
6618 CTGAGTGTTCATTTCACGGAATTCATCCTATGTGGATGAATAACTGTTTCGACA
1 CTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTCGGCA
6672 CTAAGTGT
1 CTAAGTGT
6680 CCAAAACACG
Statistics
Matches: 247, Mismatches: 31, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
54 247 1.00
ACGTcount: A:0.28, C:0.20, G:0.20, T:0.33
Consensus pattern (54 bp):
CTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTCGGCA
Found at i:6697 original size:162 final size:162
Alignment explanation
Indices: 6362--6738 Score: 459
Period size: 162 Copynumber: 2.3 Consensus size: 162
6352 GTGTGCATTT
* * * * * *
6362 CACGGAATTCATCCTATGCGGATGAATAACCGCTTCGGCACTAAGTGTGCATTTTACGGAATTCA
1 CACGGAATTCATCCTATGTGGATGAATAACCGTTTCGGCACTACGTGTGCATTTCACAGAATTAA
* * **
6427 TCCTATGTGGATGAATAACCGTTTCGGCACTAAGTGTGCATTTCACAGAATTCATCCTATGTGGA
66 TCCTATGTCGATGAATAACCATTTCAACACTAAGTGTGCATTTCACAGAATTCATCCTATGTGGA
** ***
6492 TGAATAACAGTTTCGGTACTAAGTGCGCATTT
131 TGAATAACAGTTTCGACACTAAGTGCGCAAAA
*
6524 CACGGAATTCATCCTATGTGGATGAATAACCGTTTTGGCACTACGTGTGCATTTCACAGAATTAA
1 CACGGAATTCATCCTATGTGGATGAATAACCGTTTCGGCACTACGTGTGCATTTCACAGAATTAA
* * * *
6589 TCCTATGTCGATGAATAACCATTTTAACACTGAGTGTTCATTTCACGGAATTCATCCTATGTGGA
66 TCCTATGTCGATGAATAACCATTTCAACACTAAGTGTGCATTTCACAGAATTCATCCTATGTGGA
*
6654 TGAATAACTGTTTCGACACTAAGTGTC-CAAAA
131 TGAATAACAGTTTCGACACTAAGTG-CGCAAAA
* ** * ** * * * *
6686 CACGAAATTCATAATACGTTTATGAATGACCGTATGGGCACTACGGGTGCATT
1 CACGGAATTCATCCTATGTGGATGAATAACCGTTTCGGCACTACGTGTGCATT
6739 ACAATGAAAT
Statistics
Matches: 183, Mismatches: 31, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
162 182 0.99
163 1 0.01
ACGTcount: A:0.29, C:0.20, G:0.20, T:0.31
Consensus pattern (162 bp):
CACGGAATTCATCCTATGTGGATGAATAACCGTTTCGGCACTACGTGTGCATTTCACAGAATTAA
TCCTATGTCGATGAATAACCATTTCAACACTAAGTGTGCATTTCACAGAATTCATCCTATGTGGA
TGAATAACAGTTTCGACACTAAGTGCGCAAAA
Found at i:12760 original size:20 final size:19
Alignment explanation
Indices: 12731--12782 Score: 68
Period size: 20 Copynumber: 2.6 Consensus size: 19
12721 TGATTCAATC
*
12731 AGTATCGATACCGAAGGGGA
1 AGTATAGATACCGAA-GGGA
*
12751 AGTATTGATACCGAAGGGA
1 AGTATAGATACCGAAGGGA
12770 AGGTATAGATACC
1 A-GTATAGATACC
12783 ATTTTGAAAC
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 5 0.17
20 24 0.83
ACGTcount: A:0.37, C:0.13, G:0.31, T:0.19
Consensus pattern (19 bp):
AGTATAGATACCGAAGGGA
Found at i:12847 original size:19 final size:19
Alignment explanation
Indices: 12804--12840 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
12794 GAATGCAAAA
12804 ATGGTATCGATACCATAGG
1 ATGGTATCGATACCATAGG
*
12823 AGGGTATCGATACCATAG
1 ATGGTATCGATACCATAG
12841 TGTGGTAGTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.32, C:0.16, G:0.27, T:0.24
Consensus pattern (19 bp):
ATGGTATCGATACCATAGG
Found at i:13357 original size:54 final size:54
Alignment explanation
Indices: 13300--13776 Score: 706
Period size: 54 Copynumber: 8.9 Consensus size: 54
13290 ACCAAATAGG
* ** * * * * * *
13300 CACTAATTGTGCATTTCATAGAATTTATCTTATGTTGACGAATAACCATTTTGG
1 CACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCATTTCGA
* *
13354 CACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTTGA
1 CACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCATTTCGA
*
13408 CACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAA-CAGTTTCAA
1 CACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCA-TTTCGA
*
13462 CACTAAGTGTGCATTTCATGGAATTCATCC-ATGTGGATGAATAACCATTTCGA
1 CACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCATTTCGA
* * * * *
13515 CATTAAGTGTGTATTTCACAGAATTCATCCTATGTGGATGAATAACCGTTTCGG
1 CACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCATTTCGA
*
13569 CACTAAGTGTGCATTTTACGGAATTCATCCTATGTGGATGAATAACCATTTCGA
1 CACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCATTTCGA
*
13623 CACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTCGA
1 CACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCATTTCGA
* *
13677 CACTAAGTGTGCATTTCACGGAATTTATCCTATGTGGATGAATAACCATTTCGG
1 CACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCATTTCGA
* * *
13731 CACTAAGTGTGTATTTAACGAAATTCATCCTATGTGGATGAATAAC
1 CACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAAC
13777 GTATGTGGAT
Statistics
Matches: 385, Mismatches: 35, Indels: 6
0.90 0.08 0.01
Matches are distributed among these distances:
53 46 0.12
54 339 0.88
ACGTcount: A:0.30, C:0.18, G:0.19, T:0.34
Consensus pattern (54 bp):
CACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCATTTCGA
Found at i:13604 original size:161 final size:162
Alignment explanation
Indices: 13300--14027 Score: 976
Period size: 161 Copynumber: 4.4 Consensus size: 162
13290 ACCAAATAGG
* ** * * * * * *
13300 CACTAATTGTGCATTTCATAGAATTTATCTTATGTTGACGAATAACCATTTTGGCACTAAGTGTG
1 CACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCATTTCGACACTAAGTGTG
* *
13365 CATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTTGACACTAAGTGTGCATTTCACGGA
66 CATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTCGGCACTAAGTGTGCATTTCACGGA
*
13430 ATTCATCCTATGTGGATGAATAACAGTTTCAA
131 ATTCATCCTATGTGGATGAATAACAGTTTCGA
* *
13462 CACTAAGTGTGCATTTCATGGAATTCATCC-ATGTGGATGAATAACCATTTCGACATTAAGTGTG
1 CACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCATTTCGACACTAAGTGTG
* * *
13526 TATTTCACAGAATTCATCCTATGTGGATGAATAACCGTTTCGGCACTAAGTGTGCATTTTACGGA
66 CATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTCGGCACTAAGTGTGCATTTCACGGA
13591 ATTCATCCTATGTGGATGAATAACCA-TTTCGA
131 ATTCATCCTATGTGGATGAATAA-CAGTTTCGA
*
13623 CACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTCGACACTAAGTGTG
1 CACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCATTTCGACACTAAGTGTG
* * * * *
13688 CATTTCACGGAATTTATCCTATGTGGATGAATAACCATTTCGGCACTAAGTGTGTATTTAACGAA
66 CATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTCGGCACTAAGTGTGCATTTCACGGA
13753 ATTCATCCTATGTGGATGAATAACGTATGTGGATGAATAACCGTTTTGA
131 ATTCATCCTATGTGGATGAATAAC--A-GT---T---T---C-----GA
* * * * * *
13802 CACTACGTGTGCATTTAACGGAATTAATCCTATATGGATGAATAACCATTTTGGCACTAAGTGTG
1 CACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCATTTCGACACTAAGTGTG
*
13867 CATTTCACGGAATTCATCCTATGTGGATGAAT-ACCGTTTCGGCACTAGGTGTGCATTTCACGGA
66 CATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTCGGCACTAAGTGTGCATTTCACGGA
* *
13931 ATTCATCCTCTGTGGATGAATAACTGTTTCGA
131 ATTCATCCTATGTGGATGAATAACAGTTTCGA
*
13963 CACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCATTTCGAAACTAAGTGTG
1 CACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCATTTCGACACTAAGTGTG
14028 AAAAACACAG
Statistics
Matches: 499, Mismatches: 47, Indels: 41
0.85 0.08 0.07
Matches are distributed among these distances:
161 207 0.41
162 141 0.28
163 1 0.00
165 1 0.00
166 1 0.00
168 1 0.00
169 1 0.00
171 1 0.00
172 1 0.00
174 1 0.00
175 2 0.00
178 50 0.10
179 91 0.18
ACGTcount: A:0.29, C:0.18, G:0.20, T:0.33
Consensus pattern (162 bp):
CACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCATTTCGACACTAAGTGTG
CATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTCGGCACTAAGTGTGCATTTCACGGA
ATTCATCCTATGTGGATGAATAACAGTTTCGA
Found at i:13783 original size:17 final size:17
Alignment explanation
Indices: 13761--13793 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
13751 AAATTCATCC
13761 TATGTGGATGAATAACG
1 TATGTGGATGAATAACG
13778 TATGTGGATGAATAAC
1 TATGTGGATGAATAAC
13794 CGTTTTGACA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.36, C:0.06, G:0.27, T:0.30
Consensus pattern (17 bp):
TATGTGGATGAATAACG
Found at i:13832 original size:71 final size:71
Alignment explanation
Indices: 13707--13847 Score: 210
Period size: 71 Copynumber: 2.0 Consensus size: 71
13697 GAATTTATCC
* * * *
13707 TATGTGGATGAATAACCATTTCGGCACTAAGTGTGTATTTAACGAAATTCATCCTATGTGGATGA
1 TATGTGGATGAATAACCATTTCGACACTAAGTGTGCATTTAACGAAATTAATCCTATATGGATGA
13772 ATAACG
66 ATAACG
* * * *
13778 TATGTGGATGAATAACCGTTTTGACACTACGTGTGCATTTAACGGAATTAATCCTATATGGATGA
1 TATGTGGATGAATAACCATTTCGACACTAAGTGTGCATTTAACGAAATTAATCCTATATGGATGA
13843 ATAAC
66 ATAAC
13848 CATTTTGGCA
Statistics
Matches: 62, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
71 62 1.00
ACGTcount: A:0.33, C:0.14, G:0.21, T:0.33
Consensus pattern (71 bp):
TATGTGGATGAATAACCATTTCGACACTAAGTGTGCATTTAACGAAATTAATCCTATATGGATGA
ATAACG
Found at i:13881 original size:125 final size:125
Alignment explanation
Indices: 13653--13899 Score: 413
Period size: 125 Copynumber: 2.0 Consensus size: 125
13643 GAATTCATCC
* * *
13653 TATGTGGATGAATAACCGTTTCGACACTAAGTGTGCATTTCACGGAATTTATCCTATGTGGATGA
1 TATGTGGATGAATAACCGTTTCGACACTAAGTGTGCATTTAACGGAATTAATCCTATATGGATGA
*
13718 ATAACCATTTCGGCACTAAGTGTGTATTTAACGAAATTCATCCTATGTGGATGAATAACG
66 ATAACCATTTCGGCACTAAGTGTGCATTTAACGAAATTCATCCTATGTGGATGAATAACG
* *
13778 TATGTGGATGAATAACCGTTTTGACACTACGTGTGCATTTAACGGAATTAATCCTATATGGATGA
1 TATGTGGATGAATAACCGTTTCGACACTAAGTGTGCATTTAACGGAATTAATCCTATATGGATGA
* * *
13843 ATAACCATTTTGGCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATA
66 ATAACCATTTCGGCACTAAGTGTGCATTTAACGAAATTCATCCTATGTGGATGAATA
13900 CCGTTTCGGC
Statistics
Matches: 113, Mismatches: 9, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
125 113 1.00
ACGTcount: A:0.30, C:0.16, G:0.21, T:0.33
Consensus pattern (125 bp):
TATGTGGATGAATAACCGTTTCGACACTAAGTGTGCATTTAACGGAATTAATCCTATATGGATGA
ATAACCATTTCGGCACTAAGTGTGCATTTAACGAAATTCATCCTATGTGGATGAATAACG
Found at i:13899 original size:179 final size:178
Alignment explanation
Indices: 13599--13954 Score: 559
Period size: 179 Copynumber: 2.0 Consensus size: 178
13589 GAATTCATCC
* * *
13599 TATGTGGATGAATAACCATTTCGACACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGA
1 TATGTGGATGAATAACCATTTCGACACTAAGTGTGCATTTAACGGAATTAATCCTATATGGATGA
* *
13664 ATAACCGTTTCGACACTAAGTGTGCATTTCACGGAATTTATCCTATGTGGATGAATAACCATTTC
66 ATAACCATTTCGACACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAAT-ACCATTTC
*
13729 GGCACTAAGTGTGTATTTAACGAAATTCATCCTATGTGGATGAATAACG
130 GGCACTAAGTGTGCATTTAACGAAATTCATCCTATGTGGATGAATAACG
* * *
13778 TATGTGGATGAATAACCGTTTTGACACTACGTGTGCATTTAACGGAATTAATCCTATATGGATGA
1 TATGTGGATGAATAACCATTTCGACACTAAGTGTGCATTTAACGGAATTAATCCTATATGGATGA
* * *
13843 ATAACCATTTTGGCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATACCGTTTCG
66 ATAACCATTTCGACACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATACCATTTCG
* * * *
13908 GCACTAGGTGTGCATTTCACGGAATTCATCCTCTGTGGATGAATAAC
131 GCACTAAGTGTGCATTTAACGAAATTCATCCTATGTGGATGAATAAC
13955 TGTTTCGACA
Statistics
Matches: 161, Mismatches: 16, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
178 50 0.31
179 111 0.69
ACGTcount: A:0.29, C:0.18, G:0.21, T:0.33
Consensus pattern (178 bp):
TATGTGGATGAATAACCATTTCGACACTAAGTGTGCATTTAACGGAATTAATCCTATATGGATGA
ATAACCATTTCGACACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATACCATTTCG
GCACTAAGTGTGCATTTAACGAAATTCATCCTATGTGGATGAATAACG
Found at i:13967 original size:107 final size:108
Alignment explanation
Indices: 13778--14027 Score: 367
Period size: 107 Copynumber: 2.3 Consensus size: 108
13768 ATGAATAACG
*
13778 TATGTGGATGAATAACCGTTTTGACACTACGTGTGCATTTAACGGAATTAATCCTATATGGATGA
1 TATGTGGATGAATAACCGTTTCGACACTACGTGTGCATTTAACGGAATTAATCCTATATGGATGA
* *
13843 ATAACCATTTTGGCACTAAGTGTGCATTTCACGGAATTCATCC
66 ATAACCATTTCGACACTAAGTGTGCATTTCACGGAATTCATCC
* * * * * *
13886 TATGTGGATGAAT-ACCGTTTCGGCACTAGGTGTGCATTTCACGGAATTCATCCTCTGTGGATGA
1 TATGTGGATGAATAACCGTTTCGACACTACGTGTGCATTTAACGGAATTAATCCTATATGGATGA
**
13950 ATAACTGTTTCGACACTAAGTGTGCATTTCACGGAATTCATCC
66 ATAACCATTTCGACACTAAGTGTGCATTTCACGGAATTCATCC
* * *
13993 TATGTGGATGAATAACCATTTCGAAACTAAGTGTG
1 TATGTGGATGAATAACCGTTTCGACACTACGTGTG
14028 AAAAACACAG
Statistics
Matches: 126, Mismatches: 15, Indels: 2
0.88 0.10 0.01
Matches are distributed among these distances:
107 96 0.76
108 30 0.24
ACGTcount: A:0.28, C:0.18, G:0.21, T:0.33
Consensus pattern (108 bp):
TATGTGGATGAATAACCGTTTCGACACTACGTGTGCATTTAACGGAATTAATCCTATATGGATGA
ATAACCATTTCGACACTAAGTGTGCATTTCACGGAATTCATCC
Found at i:14044 original size:54 final size:54
Alignment explanation
Indices: 13778--14027 Score: 367
Period size: 54 Copynumber: 4.6 Consensus size: 54
13768 ATGAATAACG
* * * *
13778 TATGTGGATGAATAACCGTTTTGACACTACGTGTGCATTTAACGGAATTAATCC
1 TATGTGGATGAATAACCGTTTCGACACTAAGTGTGCATTTCACGGAATTCATCC
* * * *
13832 TATATGGATGAATAACCATTTTGGCACTAAGTGTGCATTTCACGGAATTCATCC
1 TATGTGGATGAATAACCGTTTCGACACTAAGTGTGCATTTCACGGAATTCATCC
* *
13886 TATGTGGATGAAT-ACCGTTTCGGCACTAGGTGTGCATTTCACGGAATTCATCC
1 TATGTGGATGAATAACCGTTTCGACACTAAGTGTGCATTTCACGGAATTCATCC
* *
13939 TCTGTGGATGAATAACTGTTTCGACACTAAGTGTGCATTTCACGGAATTCATCC
1 TATGTGGATGAATAACCGTTTCGACACTAAGTGTGCATTTCACGGAATTCATCC
* *
13993 TATGTGGATGAATAACCATTTCGAAACTAAGTGTG
1 TATGTGGATGAATAACCGTTTCGACACTAAGTGTG
14028 AAAAACACAG
Statistics
Matches: 177, Mismatches: 18, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
53 49 0.28
54 128 0.72
ACGTcount: A:0.28, C:0.18, G:0.21, T:0.33
Consensus pattern (54 bp):
TATGTGGATGAATAACCGTTTCGACACTAAGTGTGCATTTCACGGAATTCATCC
Found at i:14059 original size:54 final size:54
Alignment explanation
Indices: 13836--14051 Score: 137
Period size: 54 Copynumber: 4.0 Consensus size: 54
13826 TAATCCTATA
* ** * *** * **
13836 TGGATGAATAACCATTTTGGCACTAAGTGTGCATTTCACGGAATTCATCCTATG
1 TGGATGAATAACCATTTCGAAACTAAGTGTGAAAAACACAGAATTCATAATATG
* ** * * *** * ** *
13890 TGGATGAAT-ACCGTTTCGGCACTAGGTGTGCATTTCACGGAATTCATCCTCTG
1 TGGATGAATAACCATTTCGAAACTAAGTGTGAAAAACACAGAATTCATAATATG
** * * *** * **
13943 TGGATGAATAACTGTTTCGACACTAAGTGTGCATTTCACGGAATTCATCCTATG
1 TGGATGAATAACCATTTCGAAACTAAGTGTGAAAAACACAGAATTCATAATATG
13997 TGGATGAATAACCATTTCGAAACTAAGTGTGAAAAACACAGAATTCATAATATG
1 TGGATGAATAACCATTTCGAAACTAAGTGTGAAAAACACAGAATTCATAATATG
14051 T
1 T
14052 TTATGAATGA
Statistics
Matches: 143, Mismatches: 18, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
53 49 0.34
54 94 0.66
ACGTcount: A:0.30, C:0.18, G:0.20, T:0.31
Consensus pattern (54 bp):
TGGATGAATAACCATTTCGAAACTAAGTGTGAAAAACACAGAATTCATAATATG
Found at i:14075 original size:340 final size:340
Alignment explanation
Indices: 13438--14075 Score: 954
Period size: 340 Copynumber: 1.9 Consensus size: 340
13428 GAATTCATCC
* * * *
13438 TATGTGGATGAATAACAGTTTCAACACTAAGTGTGCATTTCATGGAATTCATCCATGTGGATGAA
1 TATGTGGATGAATAACAGTTTCAACACTAAGTGTGCATTTAACGGAATTAATCCATATGGATGAA
* *
13503 TAACCATTTCGACATTAAGTGTGTATTTCACAGAATTCATCCTATGTGGATGAATAACCGTTTCG
66 TAACCATTTCGACACTAAGTGTGCATTTCACAGAATTCATCCTATGTGGATGAATAACCGTTTCG
*
13568 GCACTAAGTGTGCATTTTACGGAATTCATCCTATGTGGATGAATAACCATTTCGACACTAAGTGT
131 GCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCATTTCGACACTAAGTGT
* * * *** *
13633 GCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTCGACACTAAGTGTGCATTTCACGG
196 GCATTTCACGGAATTCATCCTATGTGGATGAATAACCATTTCGAAACTAAGTGTGAAAAACACAG
* ** *
13698 AATTTATCCTATGTGGATGAATAACCATTTCGGCACTAAGTGTGTATTTAACGAAATTCATCCTA
261 AATTCATAATATGTGGATGAATAACCATATCGGCACTAAGTGTGTATTTAACGAAATTCATCCTA
13763 TGTGGATGAATAACG
326 TGTGGATGAATAACG
* ** *
13778 TATGTGGATGAATAACCGTTTTGACACTACGTGTGCATTTAACGGAATTAATCCTATATGGATGA
1 TATGTGGATGAATAACAGTTTCAACACTAAGTGTGCATTTAACGGAATTAATCC-ATATGGATGA
* * *
13843 ATAACCATTTTGGCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAAT-ACCGTTTC
65 ATAACCATTTCGACACTAAGTGTGCATTTCACAGAATTCATCCTATGTGGATGAATAACCGTTTC
* * **
13907 GGCACTAGGTGTGCATTTCACGGAATTCATCCTCTGTGGATGAATAACTGTTTCGACACTAAGTG
130 GGCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCATTTCGACACTAAGTG
13972 TGCATTTCACGGAATTCATCCTATGTGGATGAATAACCATTTCGAAACTAAGTGTGAAAAACACA
195 TGCATTTCACGGAATTCATCCTATGTGGATGAATAACCATTTCGAAACTAAGTGTGAAAAACACA
** * * *
14037 GAATTCATAATATGTTTATGAATGACCGTATGGGCACTA
260 GAATTCATAATATGTGGATGAATAACCATATCGGCACTA
14076 CGGGTGCATT
Statistics
Matches: 263, Mismatches: 34, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
340 203 0.77
341 60 0.23
ACGTcount: A:0.30, C:0.17, G:0.20, T:0.32
Consensus pattern (340 bp):
TATGTGGATGAATAACAGTTTCAACACTAAGTGTGCATTTAACGGAATTAATCCATATGGATGAA
TAACCATTTCGACACTAAGTGTGCATTTCACAGAATTCATCCTATGTGGATGAATAACCGTTTCG
GCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCATTTCGACACTAAGTGT
GCATTTCACGGAATTCATCCTATGTGGATGAATAACCATTTCGAAACTAAGTGTGAAAAACACAG
AATTCATAATATGTGGATGAATAACCATATCGGCACTAAGTGTGTATTTAACGAAATTCATCCTA
TGTGGATGAATAACG
Found at i:19864 original size:17 final size:17
Alignment explanation
Indices: 19842--19879 Score: 67
Period size: 17 Copynumber: 2.2 Consensus size: 17
19832 TTTAAAGGAG
19842 CTAGTTTAATTAATGAA
1 CTAGTTTAATTAATGAA
*
19859 CTAGTTTAATTAGTGAA
1 CTAGTTTAATTAATGAA
19876 CTAG
1 CTAG
19880 ATTCATTGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.37, C:0.08, G:0.16, T:0.39
Consensus pattern (17 bp):
CTAGTTTAATTAATGAA
Found at i:28541 original size:20 final size:20
Alignment explanation
Indices: 28493--28547 Score: 65
Period size: 22 Copynumber: 2.6 Consensus size: 20
28483 ACTGGAAGGA
* *
28493 GGTATCGGTACCATAGTAGG
1 GGTATCGATACCATAGTAAG
*
28513 GTAGTATCGATACCATGGTAAG
1 G--GTATCGATACCATAGTAAG
28535 GGTATCGATACCA
1 GGTATCGATACCA
28548 GGCAACATCG
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
20 13 0.43
22 17 0.57
ACGTcount: A:0.29, C:0.16, G:0.29, T:0.25
Consensus pattern (20 bp):
GGTATCGATACCATAGTAAG
Found at i:28552 original size:95 final size:95
Alignment explanation
Indices: 28417--28600 Score: 278
Period size: 95 Copynumber: 1.9 Consensus size: 95
28407 ATACCGACGA
* * * * *
28417 GGTACTATCAATACCATAGTAAGGGTATCGATACCGGGCAATATCGAATCTAATATTGTTATCGA
1 GGTACTATCAATACCATAGTAAGGGTATCGATACCAGGCAACATCGAACCTAAAATTGGTATCGA
*
28482 TACTGGAAGGAGGTATCGGTACCATAGTAG
66 TACCGGAAGGAGGTATCGGTACCATAGTAG
* * *
28512 GGTAGTATCGATACCATGGTAAGGGTATCGATACCAGGCAACATCGAACCTAAAATTGGTATCGA
1 GGTACTATCAATACCATAGTAAGGGTATCGATACCAGGCAACATCGAACCTAAAATTGGTATCGA
*
28577 TACCGGAAGGGGGTATCGGTACCA
66 TACCGGAAGGAGGTATCGGTACCA
28601 AAATATAGAA
Statistics
Matches: 79, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
95 79 1.00
ACGTcount: A:0.32, C:0.17, G:0.26, T:0.24
Consensus pattern (95 bp):
GGTACTATCAATACCATAGTAAGGGTATCGATACCAGGCAACATCGAACCTAAAATTGGTATCGA
TACCGGAAGGAGGTATCGGTACCATAGTAG
Found at i:28635 original size:95 final size:95
Alignment explanation
Indices: 28435--28640 Score: 236
Period size: 95 Copynumber: 2.2 Consensus size: 95
28425 CAATACCATA
* * * * * * *
28435 GTAAGGGTATCGATACCGGGCAATATCGAATCTAATATTGTTATCGATACTGGAAGGAGGTATCG
1 GTAAGAGTATCGATACCAGGCAACATCGAACCTAAAATTGGTATCGATACCGGAAGGAGGTATCG
* * * * *
28500 GTACCATAGTAGGGTAGTATCGATACCATG
66 GTACCAAAATAGAGAAGTATCGATACCAGG
* *
28530 GTAAGGGTATCGATACCAGGCAACATCGAACCTAAAATTGGTATCGATACCGGAAGGGGGTATCG
1 GTAAGAGTATCGATACCAGGCAACATCGAACCTAAAATTGGTATCGATACCGGAAGGAGGTATCG
* *
28595 GTACCAAAATATAGAAGTATC-AGTACTAGG
66 GTACCAAAATAGAGAAGTATCGA-TACCAGG
28625 GT-AGTAGTATCGATAC
1 GTAAG-AGTATCGATAC
28641 TATAGAGTCA
Statistics
Matches: 94, Mismatches: 15, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
94 3 0.03
95 91 0.97
ACGTcount: A:0.33, C:0.16, G:0.27, T:0.25
Consensus pattern (95 bp):
GTAAGAGTATCGATACCAGGCAACATCGAACCTAAAATTGGTATCGATACCGGAAGGAGGTATCG
GTACCAAAATAGAGAAGTATCGATACCAGG
Found at i:29061 original size:27 final size:27
Alignment explanation
Indices: 29029--29178 Score: 121
Period size: 27 Copynumber: 6.1 Consensus size: 27
29019 CTAAACCGAA
29029 GCCATAACTAAAAATGCATGAAAGGAT
1 GCCATAACTAAAAATGCATGAAAGGAT
* * *
29056 GCCATAGCTAAAAATGCATGAACGAAT
1 GCCATAACTAAAAATGCATGAAAGGAT
*
29083 G-C--AA-T---AAGGCATGAAAGGAT
1 GCCATAACTAAAAATGCATGAAAGGAT
29103 GCCATAACTAAAAATGCATGAAAGGAT
1 GCCATAACTAAAAATGCATGAAAGGAT
* *
29130 G-CAT---T---AAGGCATGGAAGGAT
1 GCCATAACTAAAAATGCATGAAAGGAT
* * *
29150 GCTATAACGAAAATTGCATGAAAGGAT
1 GCCATAACTAAAAATGCATGAAAGGAT
29177 GC
1 GC
29179 ATTAAGGCAT
Statistics
Matches: 94, Mismatches: 15, Indels: 28
0.69 0.11 0.20
Matches are distributed among these distances:
20 27 0.29
21 3 0.03
23 4 0.04
24 2 0.02
26 4 0.04
27 54 0.57
ACGTcount: A:0.44, C:0.14, G:0.23, T:0.19
Consensus pattern (27 bp):
GCCATAACTAAAAATGCATGAAAGGAT
Found at i:29098 original size:47 final size:47
Alignment explanation
Indices: 29044--29380 Score: 449
Period size: 47 Copynumber: 7.2 Consensus size: 47
29034 AACTAAAAAT
* * * *
29044 GCATGAAAGGATGCCATAGCTAAAAATGCATGAACGAATGCAATAAG
1 GCATGAAAGGATGCCATAACTAAAAATGCATGAAAGGATGCATTAAG
29091 GCATGAAAGGATGCCATAACTAAAAATGCATGAAAGGATGCATTAAG
1 GCATGAAAGGATGCCATAACTAAAAATGCATGAAAGGATGCATTAAG
* * * *
29138 GCATGGAAGGATGCTATAACGAAAATTGCATGAAAGGATGCATTAAG
1 GCATGAAAGGATGCCATAACTAAAAATGCATGAAAGGATGCATTAAG
* ** * * *
29185 GCATGAGAGGATTTCATAGCTAAAAGTGCATGAAATGATGCATTAAG
1 GCATGAAAGGATGCCATAACTAAAAATGCATGAAAGGATGCATTAAG
* *
29232 GCATGAAAAGATGCCATAACTAAAAATGCATGAAATGATGCATTAAG
1 GCATGAAAGGATGCCATAACTAAAAATGCATGAAAGGATGCATTAAG
** * * *
29279 GCATGAAATTATACCATAACTAAAAATGCATTAAAGGATGTATTAAG
1 GCATGAAAGGATGCCATAACTAAAAATGCATGAAAGGATGCATTAAG
* * * *
29326 GCATGAAAGGATGCCATAGCTAAAAATACACGAACGGATGCATTAAG
1 GCATGAAAGGATGCCATAACTAAAAATGCATGAAAGGATGCATTAAG
29373 GCATGAAA
1 GCATGAAA
29381 ATTAACGAAT
Statistics
Matches: 252, Mismatches: 38, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
47 252 1.00
ACGTcount: A:0.44, C:0.13, G:0.23, T:0.21
Consensus pattern (47 bp):
GCATGAAAGGATGCCATAACTAAAAATGCATGAAAGGATGCATTAAG
Found at i:29104 original size:20 final size:20
Alignment explanation
Indices: 29071--29156 Score: 55
Period size: 20 Copynumber: 4.0 Consensus size: 20
29061 AGCTAAAAAT
* *
29071 GCATGAACGAATGCAATAAG
1 GCATGAAAGGATGCAATAAG
*
29091 GCATGAAAGGATGCCATAACTAAAAAT
1 GCATGAAAGGATG-C--AA-T---AAG
*
29118 GCATGAAAGGATGCATTAAG
1 GCATGAAAGGATGCAATAAG
* *
29138 GCATGGAAGGATGCTATAA
1 GCATGAAAGGATGCAATAA
29157 CGAAAATTGC
Statistics
Matches: 51, Mismatches: 8, Indels: 14
0.70 0.11 0.19
Matches are distributed among these distances:
20 29 0.57
21 1 0.02
23 3 0.06
24 2 0.04
26 1 0.02
27 15 0.29
ACGTcount: A:0.43, C:0.13, G:0.26, T:0.19
Consensus pattern (20 bp):
GCATGAAAGGATGCAATAAG
Found at i:29190 original size:20 final size:20
Alignment explanation
Indices: 29165--29286 Score: 64
Period size: 20 Copynumber: 5.4 Consensus size: 20
29155 AACGAAAATT
29165 GCATGAAAGGATGCATTAAG
1 GCATGAAAGGATGCATTAAG
* *
29185 GCATGAGAGGATTTCATAGCTAAAAG
1 GCATGAAAGGA-TGCAT---T--AAG
*
29211 TGCATGAAATGATGCATTAAG
1 -GCATGAAAGGATGCATTAAG
* *
29232 GCATGAAAAGATGCCATAACTAAAAAT
1 GCATGAAAGGATG-CAT---T---AAG
*
29259 GCATGAAATGATGCATTAAG
1 GCATGAAAGGATGCATTAAG
29279 GCATGAAA
1 GCATGAAA
29287 TTATACCATA
Statistics
Matches: 79, Mismatches: 9, Indels: 28
0.68 0.08 0.24
Matches are distributed among these distances:
20 32 0.41
21 10 0.13
23 2 0.03
24 2 0.03
26 10 0.13
27 23 0.29
ACGTcount: A:0.43, C:0.11, G:0.24, T:0.22
Consensus pattern (20 bp):
GCATGAAAGGATGCATTAAG
Found at i:29287 original size:20 final size:20
Alignment explanation
Indices: 29212--29287 Score: 71
Period size: 20 Copynumber: 3.5 Consensus size: 20
29202 AGCTAAAAGT
29212 GCATGAAATGATGCATTAAG
1 GCATGAAATGATGCATTAAG
* *
29232 GCATGAAAAGATGCCATAACTAAAAAT
1 GCATGAAATGATG-CAT---T---AAG
29259 GCATGAAATGATGCATTAAG
1 GCATGAAATGATGCATTAAG
29279 GCATGAAAT
1 GCATGAAAT
29288 TATACCATAA
Statistics
Matches: 45, Mismatches: 4, Indels: 14
0.71 0.06 0.22
Matches are distributed among these distances:
20 23 0.51
21 3 0.07
23 1 0.02
24 1 0.02
26 3 0.07
27 14 0.31
ACGTcount: A:0.45, C:0.12, G:0.21, T:0.22
Consensus pattern (20 bp):
GCATGAAATGATGCATTAAG
Found at i:29835 original size:68 final size:68
Alignment explanation
Indices: 29726--29927 Score: 280
Period size: 68 Copynumber: 3.0 Consensus size: 68
29716 GGTTAATGGA
* * *
29726 CTAACTGTGTATTTGACAGAAAGGTGTCAATCATGCCAGTTAGATGAATGACTAAGTGCCTTTGA
1 CTAACTGTGCATTTGACAGAAAGGTGTCAATCATGCCAGTTAGATGAAAGGCTAAGTGCCTTTGA
29791 GGC
66 GGC
* * *
29794 CTAACTGTGCATTTGACAGAAAGGTGTCAATCATGCCAGTTATATGAAAGGGTAAGTGCCTTTAA
1 CTAACTGTGCATTTGACAGAAAGGTGTCAATCATGCCAGTTAGATGAAAGGCTAAGTGCCTTTGA
29859 GGC
66 GGC
* * * * * *
29862 CTGACTGTGCACTTGACAGGAAA-GTGTCAATGATGCCATTTAGATGAAAGGTTAAATGCCTTTG
1 CTAACTGTGCATTTGACA-GAAAGGTGTCAATCATGCCAGTTAGATGAAAGGCTAAGTGCCTTTG
29926 AG
65 AG
29928 TAAAAGACTA
Statistics
Matches: 119, Mismatches: 14, Indels: 2
0.88 0.10 0.01
Matches are distributed among these distances:
68 115 0.97
69 4 0.03
ACGTcount: A:0.30, C:0.16, G:0.25, T:0.29
Consensus pattern (68 bp):
CTAACTGTGCATTTGACAGAAAGGTGTCAATCATGCCAGTTAGATGAAAGGCTAAGTGCCTTTGA
GGC
Found at i:30021 original size:45 final size:45
Alignment explanation
Indices: 29972--30084 Score: 163
Period size: 45 Copynumber: 2.5 Consensus size: 45
29962 TATAAAAGGC
* *
29972 ATGAAAGGATGCCATAATTGAAATGCATATATGTGCATTCTAGGT
1 ATGAAAGGATGCCATAATTGAAATGCATATAGGTGCATTATAGGT
* *
30017 ATGAAAGGATGCCATAATTGAAATGCATATGGGTGCATTATCGGT
1 ATGAAAGGATGCCATAATTGAAATGCATATAGGTGCATTATAGGT
* * *
30062 ATGAAAAGATGCTATAAATGAAA
1 ATGAAAGGATGCCATAATTGAAA
30085 AGTCTTAATG
Statistics
Matches: 61, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
45 61 1.00
ACGTcount: A:0.39, C:0.10, G:0.23, T:0.28
Consensus pattern (45 bp):
ATGAAAGGATGCCATAATTGAAATGCATATAGGTGCATTATAGGT
Found at i:30112 original size:46 final size:46
Alignment explanation
Indices: 30061--30177 Score: 180
Period size: 46 Copynumber: 2.5 Consensus size: 46
30051 GCATTATCGG
*
30061 TATGAAAAGATGCTATAAATGAAAAGTCTTAATGATGCATTATAAA
1 TATGAAAAGATGCTATAAATGAAAAGGCTTAATGATGCATTATAAA
*
30107 TATGAAAAGATACTATAAATGAAAAGGCTTAATGATGCATTATAAA
1 TATGAAAAGATGCTATAAATGAAAAGGCTTAATGATGCATTATAAA
** * *
30153 TATGAATGGATGATATCAATGAAAA
1 TATGAAAAGATGCTATAAATGAAAA
30178 TAAATAATAA
Statistics
Matches: 64, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
46 64 1.00
ACGTcount: A:0.49, C:0.06, G:0.16, T:0.29
Consensus pattern (46 bp):
TATGAAAAGATGCTATAAATGAAAAGGCTTAATGATGCATTATAAA
Found at i:30805 original size:13 final size:13
Alignment explanation
Indices: 30768--30810 Score: 59
Period size: 13 Copynumber: 3.3 Consensus size: 13
30758 CTATGACTCG
*
30768 CATTTATGACACT
1 CATTTATGACGCT
* *
30781 CATTTATTACGCA
1 CATTTATGACGCT
30794 CATTTATGACGCT
1 CATTTATGACGCT
30807 CATT
1 CATT
30811 GCGCGTCATT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.28, C:0.23, G:0.09, T:0.40
Consensus pattern (13 bp):
CATTTATGACGCT
Found at i:30934 original size:85 final size:84
Alignment explanation
Indices: 30782--30939 Score: 203
Period size: 85 Copynumber: 1.9 Consensus size: 84
30772 TATGACACTC
* * * *
30782 ATTTATTACGCACATTTATGACGCTCATTGCGCGTCATTGAAGCCCCCATCATAAATGAAGACGA
1 ATTTATGACACACATTTATGACGCTCATTGCGCGTCATTGAAGCACACATCATAAA-GAAGACGA
30847 CACACATTTGTGTGTCATAA
65 CACACATTTGTGTGTCATAA
* * *
30867 ATTTATGACACACATTTATGAC-TTACATTGCGTGTCATTGAAGCACACATCATTAGAA-AAGAT
1 ATTTATGACACACATTTATGACGCT-CATTGCGCGTCATTGAAGCACACATCA-TA-AAGAAGAC
30930 GACACACATT
63 GACACACATT
30940 CATGTGTCGT
Statistics
Matches: 63, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
84 1 0.02
85 58 0.92
86 2 0.03
87 2 0.03
ACGTcount: A:0.34, C:0.22, G:0.15, T:0.30
Consensus pattern (84 bp):
ATTTATGACACACATTTATGACGCTCATTGCGCGTCATTGAAGCACACATCATAAAGAAGACGAC
ACACATTTGTGTGTCATAA
Found at i:30974 original size:2 final size:2
Alignment explanation
Indices: 30967--30997 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
30957 TGTCGTAAAT
30967 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
30998 GTAGATTGAC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:38533 original size:94 final size:95
Alignment explanation
Indices: 38372--38560 Score: 301
Period size: 94 Copynumber: 2.0 Consensus size: 95
38362 ATACCGACGA
* * * *
38372 GGTAGTATCGATACCATAGTAAGGGTATCGATGCCAAGCAATATCGAATCTAAAATTGGCATCGA
1 GGTAGTATCGATACCATAGTAAGGGTATCGATACCAAGAAACATCGAACCTAAAATTGGCATCGA
38437 TACCGGAA-GGGGTATCGGTACCATAGTAT
66 TACCGGAAGGGGGTATCGGTACCATAGTAT
* *
38466 GGTAGTATCGATACCAT-GATAAGGGTATCGATACCAGGAAACATCGAACCTAAAATTGGTATCG
1 GGTAGTATCGATACCATAG-TAAGGGTATCGATACCAAGAAACATCGAACCTAAAATTGGCATCG
38530 ATACCGGAAGGGGGTATCGGTACCATAGTAT
65 ATACCGGAAGGGGGTATCGGTACCATAGTAT
38561 TGAAGTAATA
Statistics
Matches: 87, Mismatches: 6, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
93 1 0.01
94 65 0.75
95 21 0.24
ACGTcount: A:0.33, C:0.17, G:0.26, T:0.24
Consensus pattern (95 bp):
GGTAGTATCGATACCATAGTAAGGGTATCGATACCAAGAAACATCGAACCTAAAATTGGCATCGA
TACCGGAAGGGGGTATCGGTACCATAGTAT
Found at i:39073 original size:47 final size:47
Alignment explanation
Indices: 38999--39175 Score: 241
Period size: 47 Copynumber: 3.8 Consensus size: 47
38989 CTAAACCGAA
* * *
38999 GCCATAACT-AAAATGAATGAAAGGATGCATTATGGTATGAAAAGAT
1 GCCATAACTAAAAATGCATGAAAGGATGCATTAAGGCATGAAAAGAT
* * *
39045 ACCATAGCTAAAAATGCATGAACA-GATGCATTAAGGCATGAAATGAT
1 GCCATAACTAAAAATGCATGAA-AGGATGCATTAAGGCATGAAAAGAT
* * *
39092 GCCATAACTAAAAATGCATGAATGGATGTATTAAGGCATGAAAGGAT
1 GCCATAACTAAAAATGCATGAAAGGATGCATTAAGGCATGAAAAGAT
*
39139 GCCATAAATAAAAATGCATGAAAGGATGCATTAAGGC
1 GCCATAACTAAAAATGCATGAAAGGATGCATTAAGGC
39176 TAGGGATGGC
Statistics
Matches: 114, Mismatches: 14, Indels: 5
0.86 0.11 0.04
Matches are distributed among these distances:
46 7 0.06
47 106 0.93
48 1 0.01
ACGTcount: A:0.45, C:0.12, G:0.21, T:0.22
Consensus pattern (47 bp):
GCCATAACTAAAAATGCATGAAAGGATGCATTAAGGCATGAAAAGAT
Found at i:39119 original size:27 final size:26
Alignment explanation
Indices: 39080--39167 Score: 80
Period size: 27 Copynumber: 3.5 Consensus size: 26
39070 ATGCATTAAG
*
39080 GCATGAAATGATGCCATAACTAAAAAT
1 GCATGAAAGGATGCCATAA-TAAAAAT
* * *
39107 GCATGAATGGATG---T-AT--TAAG
1 GCATGAAAGGATGCCATAATAAAAAT
39127 GCATGAAAGGATGCCATAAATAAAAAT
1 GCATGAAAGGATGCCAT-AATAAAAAT
39154 GCATGAAAGGATGC
1 GCATGAAAGGATGC
39168 ATTAAGGCTA
Statistics
Matches: 47, Mismatches: 7, Indels: 14
0.69 0.10 0.21
Matches are distributed among these distances:
20 14 0.30
22 1 0.02
23 2 0.04
24 1 0.02
25 2 0.04
27 27 0.57
ACGTcount: A:0.44, C:0.11, G:0.23, T:0.22
Consensus pattern (26 bp):
GCATGAAAGGATGCCATAATAAAAAT
Found at i:39916 original size:27 final size:27
Alignment explanation
Indices: 39877--39937 Score: 104
Period size: 27 Copynumber: 2.3 Consensus size: 27
39867 ATGCATTAAG
*
39877 GCATGAAAGGATGCCATAACTAAAAAT
1 GCATGAAAAGATGCCATAACTAAAAAT
*
39904 GCATGAAAAGATGCCATAGCTAAAAAT
1 GCATGAAAAGATGCCATAACTAAAAAT
39931 GCATGAA
1 GCATGAA
39938 CGAATAAATT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.48, C:0.15, G:0.20, T:0.18
Consensus pattern (27 bp):
GCATGAAAAGATGCCATAACTAAAAAT
Found at i:39917 original size:47 final size:46
Alignment explanation
Indices: 39825--39917 Score: 150
Period size: 47 Copynumber: 2.0 Consensus size: 46
39815 GACATCCCTA
* **
39825 ATTAAGGCATGAAAGGATGCATAGCTAAAAATGCATGAACGGATGC
1 ATTAAGGCATGAAAGGATGCATAACTAAAAATGCATGAAAAGATGC
39871 ATTAAGGCATGAAAGGATGCCATAACTAAAAATGCATGAAAAGATGC
1 ATTAAGGCATGAAAGGATG-CATAACTAAAAATGCATGAAAAGATGC
39918 CATAGCTAAA
Statistics
Matches: 43, Mismatches: 3, Indels: 1
0.91 0.06 0.02
Matches are distributed among these distances:
46 19 0.44
47 24 0.56
ACGTcount: A:0.44, C:0.13, G:0.24, T:0.19
Consensus pattern (46 bp):
ATTAAGGCATGAAAGGATGCATAACTAAAAATGCATGAAAAGATGC
Found at i:39951 original size:74 final size:73
Alignment explanation
Indices: 39831--39969 Score: 233
Period size: 74 Copynumber: 1.9 Consensus size: 73
39821 CCTAATTAAG
* * **
39831 GCATGAAAGGATGCATAGCTAAAAATGCATGAACGGATGCATTAAGGCATGAAAGGATGCCATAA
1 GCATGAAAAGATGCATAGCTAAAAATGCATGAACGAATAAATTAAGGCATGAAAGGATGCCATAA
39896 CTAAAAAT
66 CTAAAAAT
39904 GCATGAAAAGATGCCATAGCTAAAAATGCATGAACGAATAAATTAAGGCATGAAAGGATGCCATA
1 GCATGAAAAGATG-CATAGCTAAAAATGCATGAACGAATAAATTAAGGCATGAAAGGATGCCATA
39969 A
65 A
39970 GTGAAATTAA
Statistics
Matches: 61, Mismatches: 4, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
73 12 0.20
74 49 0.80
ACGTcount: A:0.45, C:0.14, G:0.22, T:0.19
Consensus pattern (73 bp):
GCATGAAAAGATGCATAGCTAAAAATGCATGAACGAATAAATTAAGGCATGAAAGGATGCCATAA
CTAAAAAT
Found at i:40434 original size:68 final size:68
Alignment explanation
Indices: 40316--40520 Score: 268
Period size: 68 Copynumber: 3.0 Consensus size: 68
40306 CAAGGTTAAT
* *
40316 GGCCTAACTGTGGATTTGACAGAAAGGTGTCAATCATGCCAA-TTAGATGAAAGGCTAAATGCCT
1 GGCCTAACTGTGCATTTGACATAAAGGTGTCAATCATG-CAAGTTAGATGAAAGGCTAAATGCCT
40380 TTGA
65 TTGA
* ** * *
40384 GGCCTAACTGTGCATTTGACATAAATGAATCAATCATGCAAGTTAAATGAAAGGCTAAGTGCCTT
1 GGCCTAACTGTGCATTTGACATAAAGGTGTCAATCATGCAAGTTAGATGAAAGGCTAAATGCCTT
40449 TGA
66 TGA
* * * * * * *
40452 GGCCTGACTGTACATTTGACATGAAGGTGTCAATGATGCCAGTTAGATGAAAGGTTGAATGCCTT
1 GGCCTAACTGTGCATTTGACATAAAGGTGTCAATCATGCAAGTTAGATGAAAGGCTAAATGCCTT
40517 TGA
66 TGA
40520 G
1 G
40521 TAAAAGACTA
Statistics
Matches: 117, Mismatches: 19, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
67 3 0.03
68 114 0.97
ACGTcount: A:0.32, C:0.16, G:0.25, T:0.28
Consensus pattern (68 bp):
GGCCTAACTGTGCATTTGACATAAAGGTGTCAATCATGCAAGTTAGATGAAAGGCTAAATGCCTT
TGA
Found at i:40614 original size:45 final size:44
Alignment explanation
Indices: 40565--40705 Score: 140
Period size: 45 Copynumber: 3.1 Consensus size: 44
40555 TATAAAAGAC
* * *
40565 ATGAAAGGATGCCATAATTGAAATGCATATGTGTGTATTCT-AGGT
1 ATGAAAGGATGCCATAATTGAAAAGCATATG-GTGCATTATCA-GT
*
40610 ATGAAAGGATTCCATAATTGAAAAGCATATGGTGCATTATCAGT
1 ATGAAAGGATGCCATAATTGAAAAGCATATGGTGCATTATCAGT
* * * * * * *
40654 ATGAAAAGATGCTATAAATGAAAAGTCTTAATGATGCATTATAAAT
1 ATGAAAGGATGCCATAATTGAAAAG-CAT-ATGGTGCATTATCAGT
40700 ATGAAA
1 ATGAAA
40706 AAAAATACTA
Statistics
Matches: 81, Mismatches: 12, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
44 30 0.37
45 32 0.40
46 19 0.23
ACGTcount: A:0.41, C:0.09, G:0.20, T:0.30
Consensus pattern (44 bp):
ATGAAAGGATGCCATAATTGAAAAGCATATGGTGCATTATCAGT
Found at i:40703 original size:46 final size:46
Alignment explanation
Indices: 40642--40771 Score: 179
Period size: 48 Copynumber: 2.8 Consensus size: 46
40632 AAGCATATGG
* * *
40642 TGCATTATCAGTATGAAAAGATGCTATAAATGAAAAGTCTTAATGA
1 TGCATTATAAATATGAAAAGATGCTATAAATGAAAAGGCTTAATGA
* *
40688 TGCATTATAAATATGAAAAAAAATACTATAAATGAAAAGGCTTAATGA
1 TGCATTATAAATATG--AAAAGATGCTATAAATGAAAAGGCTTAATGA
**
40736 TGCATTATAAATATGAATGGATGCTATAAATGAAAA
1 TGCATTATAAATATGAAAAGATGCTATAAATGAAAA
40772 TAAAGAATAA
Statistics
Matches: 73, Mismatches: 9, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
46 30 0.41
48 43 0.59
ACGTcount: A:0.48, C:0.07, G:0.15, T:0.29
Consensus pattern (46 bp):
TGCATTATAAATATGAAAAGATGCTATAAATGAAAAGGCTTAATGA
Found at i:44671 original size:163 final size:163
Alignment explanation
Indices: 44398--44737 Score: 547
Period size: 163 Copynumber: 2.1 Consensus size: 163
44388 ACAGGGTTTT
* *
44398 ATATGACAAAACCGATAAAGCGCTACCGGATATGTTGAATGTATTAATTTCATTCAAATAAGTAT
1 ATATGACAAAACCGATAAAGCGCTACCGGATATGTTGAATGTATCAATTCCATTCAAATAAGTAT
*
44463 CGATACTTTTGAAATTTAAAAGAAAAGAAATAATAGCGCCTATAAAGTATCAATACTTTATAAAC
66 CGATACTTTTGAAATTTAAAAGAAAAGAAATAATAGCGACTATAAAGTATCAATACTTTATAAAC
* *
44528 ATGTATCGATAAATAACAATATAATAGGTAAAA
131 ATGTATCAATAAATAACAATATAACAGGTAAAA
* * *
44561 TTATGACAAAACC-AGTAAAGCGCTACCGGATATGTTGAATGTATCCATTCCATTTAAATAAGTA
1 ATATGACAAAACCGA-TAAAGCGCTACCGGATATGTTGAATGTATCAATTCCATTCAAATAAGTA
* * *
44625 TCGATACTTTTGGAATTTAAAAGAAAAGCAATAATAGCGACTATAAAGTATCGATACTTTATAAA
65 TCGATACTTTTGAAATTTAAAAGAAAAGAAATAATAGCGACTATAAAGTATCAATACTTTATAAA
* *
44690 CATGTATCAATACATAATAATATAACAGGTAAAA
130 CATGTATCAATAAATAACAATATAACAGGTAAAA
44724 ATATGACAAAACCG
1 ATATGACAAAACCG
44738 GTTTCATTAT
Statistics
Matches: 161, Mismatches: 14, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
162 1 0.01
163 160 0.99
ACGTcount: A:0.45, C:0.13, G:0.13, T:0.29
Consensus pattern (163 bp):
ATATGACAAAACCGATAAAGCGCTACCGGATATGTTGAATGTATCAATTCCATTCAAATAAGTAT
CGATACTTTTGAAATTTAAAAGAAAAGAAATAATAGCGACTATAAAGTATCAATACTTTATAAAC
ATGTATCAATAAATAACAATATAACAGGTAAAA
Found at i:47359 original size:65 final size:66
Alignment explanation
Indices: 47231--47359 Score: 163
Period size: 65 Copynumber: 2.0 Consensus size: 66
47221 GGGGGAAGTT
* * *
47231 GGTGGAAAAATAGATGGAGTGGTGAAAGAATTTGTGGAGTTGAGGGGTAAAGTTAAGATGGTGAT
1 GGTGGAAAAATAGATGGAGTGGTGAAAGAATTTGTGGAATTGAGGGGTAAACTTAAGAGGGTGAT
47296 G
66 G
* * * * *
47297 GGTGG-AAAATTGATGGAGTGGTGAAGGAAGTTT-TGGAATTGAGGGGTGAACTTACGGGGGTGA
1 GGTGGAAAAATAGATGGAGTGGTGAAAGAA-TTTGTGGAATTGAGGGGTAAACTTAAGAGGGTGA
47360 AGGGAGTGGT
Statistics
Matches: 54, Mismatches: 8, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
65 46 0.85
66 8 0.15
ACGTcount: A:0.30, C:0.02, G:0.43, T:0.26
Consensus pattern (66 bp):
GGTGGAAAAATAGATGGAGTGGTGAAAGAATTTGTGGAATTGAGGGGTAAACTTAAGAGGGTGAT
G
Found at i:49353 original size:59 final size:59
Alignment explanation
Indices: 49175--49567 Score: 566
Period size: 59 Copynumber: 6.7 Consensus size: 59
49165 TCTCATATGG
* * * *
49175 AAATTCATACATTTATTATGAATCTCTTAACGA-TTT-GCACACACAGTGCCCAATAC-A
1 AAATTCATACACTTAGTATGAATTTCTTAAC-ATTTTAGCACACAAAGTGCCCAATACGA
* *
49232 GAAATTCAAACACTTAGAATGAATTTCTTAAC-TTTT-GCACACAAAGTGCCCAATACGA
1 -AAATTCATACACTTAGTATGAATTTCTTAACATTTTAGCACACAAAGTGCCCAATACGA
*
49290 AAATTCATACACTTAGTATGAATTTCTTAACATTTTATCACACAAAGTGCCCAATACGA
1 AAATTCATACACTTAGTATGAATTTCTTAACATTTTAGCACACAAAGTGCCCAATACGA
* * *
49349 AAATTCATACACTTAGTATGAATTTCTTGACATTTTAGCACACAAAGTGTCCAATACGG
1 AAATTCATACACTTAGTATGAATTTCTTAACATTTTAGCACACAAAGTGCCCAATACGA
* * *
49408 AAATTCATACATTTAGTATGAATTTCTTAACATTTTAGCACACAAAGTGCCCGATACGG
1 AAATTCATACACTTAGTATGAATTTCTTAACATTTTAGCACACAAAGTGCCCAATACGA
*
49467 AAATTCATAGACTTAGTATGAATTTCTTAACATTTTAGCACACAAAGTG-CCAAGTACGA
1 AAATTCATACACTTAGTATGAATTTCTTAACATTTTAGCACACAAAGTGCCCAA-TACGA
* *
49526 AAATTCATAAACTTAGTAGGAATTTCTTAACATTTT-GCACAC
1 AAATTCATACACTTAGTATGAATTTCTTAACATTTTAGCACAC
49568 TTAGTGCCAT
Statistics
Matches: 307, Mismatches: 23, Indels: 10
0.90 0.07 0.03
Matches are distributed among these distances:
57 51 0.17
58 40 0.13
59 216 0.70
ACGTcount: A:0.38, C:0.19, G:0.11, T:0.32
Consensus pattern (59 bp):
AAATTCATACACTTAGTATGAATTTCTTAACATTTTAGCACACAAAGTGCCCAATACGA
Found at i:50016 original size:20 final size:20
Alignment explanation
Indices: 49991--50046 Score: 58
Period size: 22 Copynumber: 2.7 Consensus size: 20
49981 CGATGTTTCC
*
49991 TGGTATCGATACCCTTACCA
1 TGGTATCGATACCCATACCA
* *
50011 TGGTATTGATACTACCATACTA
1 TGGTATCGATAC--CCATACCA
*
50033 TGGTACCGATACCC
1 TGGTATCGATACCC
50047 CCTTCCAGTA
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
20 13 0.45
22 16 0.55
ACGTcount: A:0.27, C:0.27, G:0.16, T:0.30
Consensus pattern (20 bp):
TGGTATCGATACCCATACCA
Found at i:50090 original size:95 final size:95
Alignment explanation
Indices: 49932--50121 Score: 308
Period size: 95 Copynumber: 2.0 Consensus size: 95
49922 CTATACTTCT
* * * *
49932 ATACTATGGTACCGATACCCCCTTCCGGTATCAATACCAAGTTTAGGTTCGATGTTTCCTGGTAT
1 ATACTATGGTACCGATACCCCCTTCCAGTATCAATACCAAGTTTAGATTCGATATTGCCTGGTAT
**
49997 CGATACCCTTACCATGGTATTGATACTACC
66 CGATACCCTTACCATGGTATCAATACTACC
* *
50027 ATACTATGGTACCGATACCCCCTTCCAGTATCAATACCAATTTTAGATTCGATATTGCTTGGTAT
1 ATACTATGGTACCGATACCCCCTTCCAGTATCAATACCAAGTTTAGATTCGATATTGCCTGGTAT
50092 CGATACCCTTACCATGGTATCAATACTACC
66 CGATACCCTTACCATGGTATCAATACTACC
50122 TCGTCGGTAT
Statistics
Matches: 87, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
95 87 1.00
ACGTcount: A:0.26, C:0.26, G:0.15, T:0.33
Consensus pattern (95 bp):
ATACTATGGTACCGATACCCCCTTCCAGTATCAATACCAAGTTTAGATTCGATATTGCCTGGTAT
CGATACCCTTACCATGGTATCAATACTACC
Found at i:50158 original size:21 final size:21
Alignment explanation
Indices: 50128--50195 Score: 118
Period size: 21 Copynumber: 3.2 Consensus size: 21
50118 TACCTCGTCG
*
50128 GTATCGATATTGATTGAATCA
1 GTATCAATATTGATTGAATCA
*
50149 ATATCAATATTGATTGAATCA
1 GTATCAATATTGATTGAATCA
50170 GTATCAATATTGATTGAATCA
1 GTATCAATATTGATTGAATCA
50191 GTATC
1 GTATC
50196 GATACTACTA
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 44 1.00
ACGTcount: A:0.37, C:0.10, G:0.15, T:0.38
Consensus pattern (21 bp):
GTATCAATATTGATTGAATCA
Found at i:63471 original size:17 final size:17
Alignment explanation
Indices: 63435--63484 Score: 66
Period size: 18 Copynumber: 2.9 Consensus size: 17
63425 TAAATAAGGT
63435 TTTAATATTTATGTTATA
1 TTTAATATTTAT-TTATA
*
63453 TTTCAT-TTTATTTATTA
1 TTTAATATTTATTTA-TA
63470 TTTAATATTTATTTA
1 TTTAATATTTATTTA
63485 GTAGTTTAGG
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
16 3 0.11
17 12 0.43
18 13 0.46
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.66
Consensus pattern (17 bp):
TTTAATATTTATTTATA
Found at i:66700 original size:19 final size:20
Alignment explanation
Indices: 66678--66717 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
66668 TTAGTGAATC
66678 TATT-GTAAAAAGAATATTT
1 TATTCGTAAAAAGAATATTT
* *
66697 TATTCGTAAAGAGATTATTT
1 TATTCGTAAAAAGAATATTT
66717 T
1 T
66718 TGTTTAATAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 4 0.22
20 14 0.78
ACGTcount: A:0.40, C:0.03, G:0.12, T:0.45
Consensus pattern (20 bp):
TATTCGTAAAAAGAATATTT
Done.