Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2533
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: 45504
ACGTcount: A:0.33, C:0.19, G:0.16, T:0.32
Found at i:1800 original size:13 final size:13
Alignment explanation
Indices: 1782--1807 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1772 ACAAAGATCC
1782 ATGTATCGATACA
1 ATGTATCGATACA
1795 ATGTATCGATACA
1 ATGTATCGATACA
1808 CAGAAAAAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1872 original size:19 final size:18
Alignment explanation
Indices: 1848--1915 Score: 83
Period size: 19 Copynumber: 3.9 Consensus size: 18
1838 CAGTAGCTAA
1848 TTATGTATCGATACAATAC
1 TTATGTATCGATACAA-AC
1867 TTATGTATCGATAC--A-
1 TTATGTATCGATACAAAC
1882 -T-TGTATCGATACAAAAC
1 TTATGTATCGATAC-AAAC
1899 TTATGTATCGATACAAA
1 TTATGTATCGATACAAA
1916 TCGTTGAATT
Statistics
Matches: 43, Mismatches: 0, Indels: 13
0.77 0.00 0.23
Matches are distributed among these distances:
13 11 0.26
14 1 0.02
16 2 0.05
18 4 0.09
19 25 0.58
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (18 bp):
TTATGTATCGATACAAAC
Found at i:1888 original size:13 final size:13
Alignment explanation
Indices: 1870--1894 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1860 ACAATACTTA
1870 TGTATCGATACAT
1 TGTATCGATACAT
1883 TGTATCGATACA
1 TGTATCGATACA
1895 AAACTTATGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1892 original size:32 final size:32
Alignment explanation
Indices: 1851--1913 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
1841 TAGCTAATTA
*
1851 TGTATCGATACAATACTTATGTATCGATACAT
1 TGTATCGATACAAAACTTATGTATCGATACAT
1883 TGTATCGATACAAAACTTATGTATCGATACA
1 TGTATCGATACAAAACTTATGTATCGATACA
1914 AATCGTTGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.35
Consensus pattern (32 bp):
TGTATCGATACAAAACTTATGTATCGATACAT
Found at i:4719 original size:13 final size:13
Alignment explanation
Indices: 4694--4734 Score: 57
Period size: 12 Copynumber: 3.2 Consensus size: 13
4684 AGTTCGAATA
4694 TAAATAATTAAATT
1 TAAA-AATTAAATT
*
4708 TAAAATTTAAA-T
1 TAAAAATTAAATT
4720 TAAAAATTAAATT
1 TAAAAATTAAATT
4733 TA
1 TA
4735 TTTTTATTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
12 11 0.46
13 9 0.38
14 4 0.17
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (13 bp):
TAAAAATTAAATT
Found at i:4771 original size:28 final size:27
Alignment explanation
Indices: 4693--4771 Score: 67
Period size: 28 Copynumber: 3.0 Consensus size: 27
4683 GAGTTCGAAT
4693 ATAAAT-AATTAAA-T-TTAAAATTTAA
1 ATAAATAAATTAAATTATTAAAA-TTAA
* ***
4718 ATTAA-AAATTAAATTTATTTTTATTAA
1 ATAAATAAATTAAA-TTATTAAAATTAA
4745 ATAAATAAATTAAATTAATTAAAATTA
1 ATAAATAAATTAAATT-ATTAAAATTA
4772 TTTAATTTTA
Statistics
Matches: 40, Mismatches: 8, Indels: 9
0.70 0.14 0.16
Matches are distributed among these distances:
25 11 0.28
27 11 0.28
28 18 0.45
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (27 bp):
ATAAATAAATTAAATTATTAAAATTAA
Found at i:4969 original size:43 final size:43
Alignment explanation
Indices: 4908--4990 Score: 166
Period size: 43 Copynumber: 1.9 Consensus size: 43
4898 CCCTAAGACA
4908 GACCAATTGGATAAGGATGAAAGAACGAGAGGACAGAACAGCT
1 GACCAATTGGATAAGGATGAAAGAACGAGAGGACAGAACAGCT
4951 GACCAATTGGATAAGGATGAAAGAACGAGAGGACAGAACA
1 GACCAATTGGATAAGGATGAAAGAACGAGAGGACAGAACA
4991 ACTTCAATAT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 40 1.00
ACGTcount: A:0.46, C:0.13, G:0.30, T:0.11
Consensus pattern (43 bp):
GACCAATTGGATAAGGATGAAAGAACGAGAGGACAGAACAGCT
Found at i:5061 original size:31 final size:31
Alignment explanation
Indices: 5023--5084 Score: 106
Period size: 31 Copynumber: 2.0 Consensus size: 31
5013 TTCATCAGGT
5023 ACCTAAACCTACGAGCGCCACGACAAAGGCG
1 ACCTAAACCTACGAGCGCCACGACAAAGGCG
* *
5054 ACCTAAACCTACGAGTGTCACGACAAAGGCG
1 ACCTAAACCTACGAGCGCCACGACAAAGGCG
5085 GCGTCTGACA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.35, C:0.32, G:0.23, T:0.10
Consensus pattern (31 bp):
ACCTAAACCTACGAGCGCCACGACAAAGGCG
Found at i:6721 original size:20 final size:20
Alignment explanation
Indices: 6696--6841 Score: 103
Period size: 20 Copynumber: 6.8 Consensus size: 20
6686 TTTTCACCAT
* *
6696 TTGTATCGGTATATTTTTCA
1 TTGTATCGATACATTTTTCA
6716 TTGTATCGATACATTTTTCA
1 TTGTATCGATACATTTTTCA
6736 TTGTATCGATACATTCTGGGTTTTAACCCA
1 TTGTATCGATACA---T---TTTT----CA
* * *
6766 GATGTATTGATACATTTCTCA
1 -TTGTATCGATACATTTTTCA
* *
6787 ATGTATCGATACATTTCTCA
1 TTGTATCGATACATTTTTCA
* *
6807 ATATATCGATACATTTTTCA
1 TTGTATCGATACATTTTTCA
*
6827 ATGTATCGATACATT
1 TTGTATCGATACATT
6842 CAGACATTTT
Statistics
Matches: 106, Mismatches: 9, Indels: 22
0.77 0.07 0.16
Matches are distributed among these distances:
20 82 0.77
21 2 0.02
23 1 0.01
25 3 0.03
26 4 0.04
28 1 0.01
30 2 0.02
31 11 0.10
ACGTcount: A:0.27, C:0.16, G:0.12, T:0.45
Consensus pattern (20 bp):
TTGTATCGATACATTTTTCA
Found at i:8821 original size:19 final size:17
Alignment explanation
Indices: 8795--8848 Score: 69
Period size: 19 Copynumber: 3.2 Consensus size: 17
8785 AGGGTTAGGT
8795 AAAA-AAGAAAGAAAGA
1 AAAAGAAGAAAGAAAGA
8811 AGATAAGAAGAAAGAAAGA
1 A-A-AAGAAGAAAGAAAGA
8830 AAAAGAA-AAA-AAAGA
1 AAAAGAAGAAAGAAAGA
8845 AAAA
1 AAAA
8849 AAATATGAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
15 9 0.26
16 4 0.11
17 6 0.17
18 3 0.09
19 13 0.37
ACGTcount: A:0.80, C:0.00, G:0.19, T:0.02
Consensus pattern (17 bp):
AAAAGAAGAAAGAAAGA
Found at i:8847 original size:8 final size:8
Alignment explanation
Indices: 8795--8850 Score: 51
Period size: 8 Copynumber: 6.8 Consensus size: 8
8785 AGGGTTAGGT
8795 AAAAAAGA
1 AAAAAAGA
*
8803 AAGAAAGA
1 AAAAAAGA
8811 AGATAAGAAGA
1 A-A-AA-AAGA
*
8822 AAGAAAGA
1 AAAAAAGA
*
8830 AAAAGA-A
1 AAAAAAGA
8837 AAAAAAGA
1 AAAAAAGA
8845 AAAAAA
1 AAAAAA
8851 ATATGAAATG
Statistics
Matches: 38, Mismatches: 6, Indels: 8
0.73 0.12 0.15
Matches are distributed among these distances:
7 6 0.16
8 23 0.61
9 2 0.05
10 2 0.05
11 5 0.13
ACGTcount: A:0.80, C:0.00, G:0.18, T:0.02
Consensus pattern (8 bp):
AAAAAAGA
Found at i:8858 original size:12 final size:10
Alignment explanation
Indices: 8795--8851 Score: 53
Period size: 10 Copynumber: 5.5 Consensus size: 10
8785 AGGGTTAGGT
8795 AAAAAAGAAA
1 AAAAAAGAAA
*
8805 GAAAGAAGATAA
1 -AAAAAAGA-AA
*
8817 GAAGAAAGAAA
1 -AAAAAAGAAA
*
8828 GAAAAAG-AA
1 AAAAAAGAAA
8837 AAAAAAGAAA
1 AAAAAAGAAA
8847 AAAAA
1 AAAAA
8852 TATGAAATGG
Statistics
Matches: 38, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
9 8 0.21
10 12 0.32
11 9 0.24
12 9 0.24
ACGTcount: A:0.81, C:0.00, G:0.18, T:0.02
Consensus pattern (10 bp):
AAAAAAGAAA
Found at i:9238 original size:2 final size:2
Alignment explanation
Indices: 9225--9265 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
9215 TTGTTTTATT
*
9225 TA TA TG TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
9266 TTTGAAAATC
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.51
Consensus pattern (2 bp):
TA
Found at i:15636 original size:12 final size:12
Alignment explanation
Indices: 15605--15636 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
15595 ACCTAATCCT
15605 AAAAAAAA-CAA
1 AAAAAAAACCAA
15616 AAAAAAAACCAA
1 AAAAAAAACCAA
15628 AAAAAAAAC
1 AAAAAAAAC
15637 TTTTCACCCT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 8 0.40
12 12 0.60
ACGTcount: A:0.88, C:0.12, G:0.00, T:0.00
Consensus pattern (12 bp):
AAAAAAAACCAA
Found at i:16805 original size:27 final size:27
Alignment explanation
Indices: 16655--17197 Score: 791
Period size: 27 Copynumber: 19.8 Consensus size: 27
16645 GACCTCTCTA
16655 AAGTCCACAACTCCGTGGCACCCTTTT
1 AAGTCCACAACTCCGTGGCACCCTTTT
* * *
16682 AGAGTCCACAACTTCGTGGTATCCTTTT
1 A-AGTCCACAACTCCGTGGCACCCTTTT
16710 AAAGTCCACAACTCCGTGGCACCCTTTT
1 -AAGTCCACAACTCCGTGGCACCCTTTT
* * *
16738 AGAGTCCACAACTTCGTGGTATCCTTTT
1 A-AGTCCACAACTCCGTGGCACCCTTTT
**
16766 AAAGTCCACAACTCCGTGGCATTCTTTT
1 -AAGTCCACAACTCCGTGGCACCCTTTT
* **
16794 AAGTCCATAACTCTATGGCA-CCTTTT
1 AAGTCCACAACTCCGTGGCACCCTTTT
16820 AAAGTCCACAACTCCGTGGCACCCTTTT
1 -AAGTCCACAACTCCGTGGCACCCTTTT
16848 AAAGTCCACAACTCCGTGGCACCCTTTT
1 -AAGTCCACAACTCCGTGGCACCCTTTT
*
16876 AAATCCACAACTCCGTGGCACCCTTTT
1 AAGTCCACAACTCCGTGGCACCCTTTT
*
16903 AAGTCCACAACTCCGTGGCACCTTTTT
1 AAGTCCACAACTCCGTGGCACCCTTTT
16930 AAGTCCACAACTCCGTGGCACCCTTTT
1 AAGTCCACAACTCCGTGGCACCCTTTT
*
16957 AAAGTCCACAACTCCGTGGCACCTTTTT
1 -AAGTCCACAACTCCGTGGCACCCTTTT
*
16985 AAGTCCACAACTCCGTGGCACTCTTTT
1 AAGTCCACAACTCCGTGGCACCCTTTT
17012 AAGTCCACAACTCCGTGGCACCCTTTT
1 AAGTCCACAACTCCGTGGCACCCTTTT
17039 AAGTCCACAACTCCGTGGCACCCTTTT
1 AAGTCCACAACTCCGTGGCACCCTTTT
* *
17066 AAGTCCACAACTCCATGGCATTCCTTTT
1 AAGTCCACAACTCCGTGGCA-CCCTTTT
**
17094 AAGTCCACAACTCCGTGATACCCTTTT
1 AAGTCCACAACTCCGTGGCACCCTTTT
17121 AAGTCCACAACTCCGTGGCATCCCTTTT
1 AAGTCCACAACTCCGTGGCA-CCCTTTT
*
17149 AAGTCCACAACTTCGTGGCACCCTTTTT
1 AAGTCCACAACTCCGTGGCACCC-TTTT
* *
17177 AAGTCCACAAGTCGGTGGCAC
1 AAGTCCACAACTCCGTGGCAC
17198 TATTTCAAAG
Statistics
Matches: 467, Mismatches: 39, Indels: 19
0.89 0.07 0.04
Matches are distributed among these distances:
26 5 0.01
27 237 0.51
28 223 0.48
29 2 0.00
ACGTcount: A:0.24, C:0.33, G:0.15, T:0.29
Consensus pattern (27 bp):
AAGTCCACAACTCCGTGGCACCCTTTT
Found at i:16848 original size:82 final size:82
Alignment explanation
Indices: 16655--17197 Score: 788
Period size: 82 Copynumber: 6.6 Consensus size: 82
16645 GACCTCTCTA
* * * *
16655 AAGTCCACAACTCCGTGGCACCCTTTTAGAGTCCACAACTTCGTGGTATCCTTTTAAAGTCCACA
1 AAGTCCACAACTCCGTGGCACCCTTTTAAAGTCCACAACTCCGTGGCACCCTTTT-AAGTCCACA
16720 ACTCCGTGGCACCCTTTT
65 ACTCCGTGGCACCCTTTT
* * * ** *
16738 AGAGTCCACAACTTCGTGGTATCCTTTTAAAGTCCACAACTCCGTGGCATTCTTTTAAGTCCATA
1 A-AGTCCACAACTCCGTGGCACCCTTTTAAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACA
**
16803 ACTCTATGGCA-CCTTTT
65 ACTCCGTGGCACCCTTTT
*
16820 AAAGTCCACAACTCCGTGGCACCCTTTTAAAGTCCACAACTCCGTGGCACCCTTTTAAATCCACA
1 -AAGTCCACAACTCCGTGGCACCCTTTTAAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACA
16885 ACTCCGTGGCACCCTTTT
65 ACTCCGTGGCACCCTTTT
*
16903 AAGTCCACAACTCCGTGGCA-CCTTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAAGTCCACA
1 AAGTCCACAACTCCGTGGCACCCTTTTAAAGTCCACAACTCCGTGGCACCCTTTT-AAGTCCACA
*
16967 ACTCCGTGGCACCTTTTT
65 ACTCCGTGGCACCCTTTT
*
16985 AAGTCCACAACTCCGTGGCACTCTTTT-AAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAA
1 AAGTCCACAACTCCGTGGCACCCTTTTAAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAA
17049 CTCCGTGGCACCCTTTT
66 CTCCGTGGCACCCTTTT
* * **
17066 AAGTCCACAACTCCATGGCATTCCTTTT-AAGTCCACAACTCCGTGATACCCTTTTAAGTCCACA
1 AAGTCCACAACTCCGTGGCA-CCCTTTTAAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACA
17130 ACTCCGTGGCATCCCTTTT
65 ACTCCGTGGCA-CCCTTTT
* * * *
17149 AAGTCCACAACTTCGTGGCACCCTTTTTAAGTCCACAAGTCGGTGGCAC
1 AAGTCCACAACTCCGTGGCACCCTTTTAAAGTCCACAACTCCGTGGCAC
17198 TATTTCAAAG
Statistics
Matches: 416, Mismatches: 36, Indels: 16
0.89 0.08 0.03
Matches are distributed among these distances:
81 78 0.19
82 219 0.53
83 72 0.17
84 47 0.11
ACGTcount: A:0.24, C:0.33, G:0.15, T:0.29
Consensus pattern (82 bp):
AAGTCCACAACTCCGTGGCACCCTTTTAAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAA
CTCCGTGGCACCCTTTT
Found at i:16950 original size:109 final size:109
Alignment explanation
Indices: 16653--17197 Score: 786
Period size: 109 Copynumber: 5.0 Consensus size: 109
16643 GTGACCTCTC
* * *
16653 TAAAGTCCACAACTCCGTGGCACCCTTTTAGAGTCCACAACTTCGTGGTATCCTTTTAAAGTCCA
1 TAAA-TCCACAACTCCGTGGCACCCTTTTA-AGTCCACAACTCCGTGGCA-CCTTTTTAAGTCCA
* * * *
16718 CAACTCCGTGGCACCCTTTTAGAGTCCACAACTTCGTGGTATCCTTT
63 CAACTCCGTGGCACCCTTTTAAAGTCCACAACTCCGTGGCACCCTTT
** * ** *
16765 TAAAGTCCACAACTCCGTGGCATTCTTTTAAGTCCATAACTCTATGGCACCTTTTAAAGTCCACA
1 TAAA-TCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCTTTTTAAGTCCACA
16830 ACTCCGTGGCACCCTTTTAAAGTCCACAACTCCGTGGCACCCTTT
65 ACTCCGTGGCACCCTTTTAAAGTCCACAACTCCGTGGCACCCTTT
16875 TAAATCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCTTTTTAAGTCCACAA
1 TAAATCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCTTTTTAAGTCCACAA
*
16940 CTCCGTGGCACCCTTTTAAAGTCCACAACTCCGTGGCACCTTTT
66 CTCCGTGGCACCCTTTTAAAGTCCACAACTCCGTGGCACCCTTT
* * *
16984 TAAGTCCACAACTCCGTGGCACTCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAA
1 TAAATCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCTTTTTAAGTCCACAA
* *
17049 CTCCGTGGCACCCTTTT-AAGTCCACAACTCCATGGCATTCCTTT
66 CTCCGTGGCACCCTTTTAAAGTCCACAACTCCGTGGCA-CCCTTT
* ** *
17093 TAAGTCCACAACTCCGTGATACCCTTTTAAGTCCACAACTCCGTGGCATCCCTTTTAAGTCCACA
1 TAAATCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCA-CCTTTTTAAGTCCACA
* * * *
17158 ACTTCGTGGCACCCTTTTTAAGTCCACAAGTCGGTGGCAC
65 ACTCCGTGGCACCCTTTTAAAGTCCACAACTCCGTGGCAC
17198 TATTTCAAAG
Statistics
Matches: 398, Mismatches: 32, Indels: 8
0.91 0.07 0.02
Matches are distributed among these distances:
108 19 0.05
109 226 0.57
110 94 0.24
111 31 0.08
112 28 0.07
ACGTcount: A:0.24, C:0.33, G:0.15, T:0.29
Consensus pattern (109 bp):
TAAATCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCTTTTTAAGTCCACAA
CTCCGTGGCACCCTTTTAAAGTCCACAACTCCGTGGCACCCTTT
Found at i:17241 original size:32 final size:31
Alignment explanation
Indices: 17182--17386 Score: 331
Period size: 32 Copynumber: 6.5 Consensus size: 31
17172 TTTTTAAGTC
*
17182 CACAAGTCGGTGGC-ACTATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCATTTCAAAGCCCA
17212 CACAAGTCGGTGGCAACCATTTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCA-TTTCAAAGCCCA
*
17244 CACAAGTCGGTGGCAACCCTTTTCAAAGCCCA
1 CACAAGTCGGTGGCAA-CCATTTCAAAGCCCA
17276 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAA-CCATTTCAAAGCCCA
17308 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAA-CCATTTCAAAGCCCA
*
17340 CACAAGTCGGTGGCAACCCTTTTCAAAGCCCA
1 CACAAGTCGGTGGCAA-CCATTTCAAAGCCCA
17372 CACAAGTCGGTGGCA
1 CACAAGTCGGTGGCA
17387 TAAGTCGGTG
Statistics
Matches: 168, Mismatches: 4, Indels: 4
0.95 0.02 0.02
Matches are distributed among these distances:
30 14 0.08
31 3 0.02
32 149 0.89
33 2 0.01
ACGTcount: A:0.30, C:0.33, G:0.20, T:0.18
Consensus pattern (31 bp):
CACAAGTCGGTGGCAACCATTTCAAAGCCCA
Found at i:17313 original size:96 final size:96
Alignment explanation
Indices: 17182--17667 Score: 663
Period size: 96 Copynumber: 4.9 Consensus size: 96
17172 TTTTTAAGTC
*
17182 CACAAGTCGGTGGC-A-CTATTTCAAAGCCCACACAAGTCGGTGGCAA-CCATTTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCACACAAGTCGGTGGCAACCCA-TTTCAAAGCCCA
17244 CACAAGTCGGTGGCAACCCTTTTCAAAGCCCA
65 CACAAGTCGGTGGCAACCCTTTTCAAAGCCCA
17276 CACAAGTCGGTGGCAACCCATTTCAAAGCCCACACAAGTCGGTGGCAACCCATTTCAAAGCCCAC
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCACACAAGTCGGTGGCAACCCATTTCAAAGCCCAC
17341 ACAAGTCGGTGGCAACCCTTTTCAAAGCCCA
66 ACAAGTCGGTGGCAACCCTTTTCAAAGCCCA
* *
17372 CACAAGTCGGTGGCATAAGTCGGTGGCAACTCATTTCAAAGCCCACACAAGTCGGTGGCGACCCT
1 CACAAGTCGGTGGC--AA--------C--C-CATTTCAAAGCCCACACAAGTCGGTGGCAACCCA
*
17437 TTTCAAAGCCCACACAAGTCGGTGGCAACCCATTTCAAAGCCCA
53 TTTCAAAGCCCACACAAGTCGGTGGCAACCCTTTTCAAAGCCCA
* *
17481 CACAAGTCGGTGGCAACCCATTTCAAAGCCCACACAAGTCAGTGGCAACCCATTCCAAAGCCCAC
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCACACAAGTCGGTGGCAACCCATTTCAAAGCCCAC
* * *
17546 ATAAGTCGGTGGCAACTCATTTCAAAGCCCA
66 ACAAGTCGGTGGCAACCCTTTTCAAAGCCCA
* * ** * *
17577 CACAAGTCGGTGGCGACCCTTTTCAAAGCCCACACAAGTCATTGGCAACCCATTTAAAAGCCCAT
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCACACAAGTCGGTGGCAACCCATTTCAAAGCCCAC
* **
17642 GCAAGTTAGTGGCAACCCTTTTCAAA
66 ACAAGTCGGTGGCAACCCTTTTCAAA
17668 TCACCATTTT
Statistics
Matches: 354, Mismatches: 22, Indels: 30
0.87 0.05 0.07
Matches are distributed among these distances:
94 14 0.04
95 1 0.00
96 239 0.68
97 4 0.01
98 2 0.01
99 1 0.00
106 1 0.00
107 2 0.01
108 1 0.00
109 89 0.25
ACGTcount: A:0.30, C:0.32, G:0.19, T:0.19
Consensus pattern (96 bp):
CACAAGTCGGTGGCAACCCATTTCAAAGCCCACACAAGTCGGTGGCAACCCATTTCAAAGCCCAC
ACAAGTCGGTGGCAACCCTTTTCAAAGCCCA
Found at i:17393 original size:13 final size:13
Alignment explanation
Indices: 17375--17399 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
17365 AAGCCCACAC
17375 AAGTCGGTGGCAT
1 AAGTCGGTGGCAT
17388 AAGTCGGTGGCA
1 AAGTCGGTGGCA
17400 ACTCATTTCA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.16, G:0.40, T:0.20
Consensus pattern (13 bp):
AAGTCGGTGGCAT
Found at i:17409 original size:45 final size:45
Alignment explanation
Indices: 17343--17430 Score: 158
Period size: 45 Copynumber: 2.0 Consensus size: 45
17333 AAGCCCACAC
*
17343 AAGTCGGTGGCAACCCTTTTCAAAGCCCACACAAGTCGGTGGCAT
1 AAGTCGGTGGCAACCCATTTCAAAGCCCACACAAGTCGGTGGCAT
*
17388 AAGTCGGTGGCAACTCATTTCAAAGCCCACACAAGTCGGTGGC
1 AAGTCGGTGGCAACCCATTTCAAAGCCCACACAAGTCGGTGGC
17431 GACCCTTTTC
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
45 41 1.00
ACGTcount: A:0.27, C:0.28, G:0.25, T:0.19
Consensus pattern (45 bp):
AAGTCGGTGGCAACCCATTTCAAAGCCCACACAAGTCGGTGGCAT
Found at i:17429 original size:32 final size:32
Alignment explanation
Indices: 17388--17667 Score: 407
Period size: 32 Copynumber: 8.8 Consensus size: 32
17378 TCGGTGGCAT
*
17388 AAGTCGGTGGCAACTCATTTCAAAGCCCACAC
1 AAGTCGGTGGCAACCCATTTCAAAGCCCACAC
* *
17420 AAGTCGGTGGCGACCCTTTTCAAAGCCCACAC
1 AAGTCGGTGGCAACCCATTTCAAAGCCCACAC
17452 AAGTCGGTGGCAACCCATTTCAAAGCCCACAC
1 AAGTCGGTGGCAACCCATTTCAAAGCCCACAC
17484 AAGTCGGTGGCAACCCATTTCAAAGCCCACAC
1 AAGTCGGTGGCAACCCATTTCAAAGCCCACAC
* * *
17516 AAGTCAGTGGCAACCCATTCCAAAGCCCACAT
1 AAGTCGGTGGCAACCCATTTCAAAGCCCACAC
*
17548 AAGTCGGTGGCAACTCATTTCAAAGCCCACAC
1 AAGTCGGTGGCAACCCATTTCAAAGCCCACAC
* *
17580 AAGTCGGTGGCGACCCTTTTCAAAGCCCACAC
1 AAGTCGGTGGCAACCCATTTCAAAGCCCACAC
** * **
17612 AAGTCATTGGCAACCCATTTAAAAGCCCATGC
1 AAGTCGGTGGCAACCCATTTCAAAGCCCACAC
** *
17644 AAGTTAGTGGCAACCCTTTTCAAA
1 AAGTCGGTGGCAACCCATTTCAAA
17668 TCACCATTTT
Statistics
Matches: 222, Mismatches: 26, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 222 1.00
ACGTcount: A:0.31, C:0.32, G:0.19, T:0.19
Consensus pattern (32 bp):
AAGTCGGTGGCAACCCATTTCAAAGCCCACAC
Found at i:17438 original size:77 final size:77
Alignment explanation
Indices: 17311--17463 Score: 288
Period size: 77 Copynumber: 2.0 Consensus size: 77
17301 AAGCCCACAC
17311 AAGTCGGTGGCAACCCATTTCAAAGCCCACACAAGTCGGTGGCAACCCTTTTCAAAGCCCACACA
1 AAGTCGGTGGCAACCCATTTCAAAGCCCACACAAGTCGGTGGCAACCCTTTTCAAAGCCCACACA
17376 AGTCGGTGGCAT
66 AGTCGGTGGCAT
* *
17388 AAGTCGGTGGCAACTCATTTCAAAGCCCACACAAGTCGGTGGCGACCCTTTTCAAAGCCCACACA
1 AAGTCGGTGGCAACCCATTTCAAAGCCCACACAAGTCGGTGGCAACCCTTTTCAAAGCCCACACA
17453 AGTCGGTGGCA
66 AGTCGGTGGCA
17464 ACCCATTTCA
Statistics
Matches: 74, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
77 74 1.00
ACGTcount: A:0.28, C:0.31, G:0.23, T:0.18
Consensus pattern (77 bp):
AAGTCGGTGGCAACCCATTTCAAAGCCCACACAAGTCGGTGGCAACCCTTTTCAAAGCCCACACA
AGTCGGTGGCAT
Found at i:18949 original size:8 final size:8
Alignment explanation
Indices: 18895--18952 Score: 53
Period size: 8 Copynumber: 6.8 Consensus size: 8
18885 AGGGTTAGGT
18895 AAAAAAGA
1 AAAAAAGA
*
18903 AAGAAAGA
1 AAAAAAGA
18911 AGATAAGAAGA
1 A-A-AA-AAGA
*
18922 AAGAAAGA
1 AAAAAAGA
*
18930 AAAAGAAAA
1 AAAA-AAGA
18939 AAAAAAGA
1 AAAAAAGA
18947 AAAAAA
1 AAAAAA
18953 ATATGAAATG
Statistics
Matches: 40, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
8 24 0.60
9 9 0.22
10 2 0.05
11 5 0.12
ACGTcount: A:0.81, C:0.00, G:0.17, T:0.02
Consensus pattern (8 bp):
AAAAAAGA
Found at i:18960 original size:12 final size:11
Alignment explanation
Indices: 18895--18953 Score: 57
Period size: 11 Copynumber: 5.4 Consensus size: 11
18885 AGGGTTAGGT
*
18895 AAAAAAGAAAG
1 AAAAAAGAAAA
* *
18906 AAAGAAGATAAG
1 AAAAAAGA-AAA
*
18918 AAGAAAG-AAA
1 AAAAAAGAAAA
*
18928 GAAAAAGAAAA
1 AAAAAAGAAAA
18939 AAAAAAGAAAA
1 AAAAAAGAAAA
18950 AAAA
1 AAAA
18954 TATGAAATGG
Statistics
Matches: 39, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
10 7 0.18
11 24 0.62
12 8 0.21
ACGTcount: A:0.81, C:0.00, G:0.17, T:0.02
Consensus pattern (11 bp):
AAAAAAGAAAA
Found at i:26830 original size:27 final size:27
Alignment explanation
Indices: 26736--27193 Score: 675
Period size: 27 Copynumber: 16.7 Consensus size: 27
26726 GACCTCTCTA
26736 AAGTCCACAACTCCGTGGCACCCTTTT
1 AAGTCCACAACTCCGTGGCACCCTTTT
* * *
26763 AGAGTCCACAACTTCGTGGTATCCTTTT
1 A-AGTCCACAACTCCGTGGCACCCTTTT
**
26791 AAAGTCCACAACTCCGTGGCATTCTTTT
1 -AAGTCCACAACTCCGTGGCACCCTTTT
* **
26819 AAGTCCATAACTCTATGGCA-CCTTTT
1 AAGTCCACAACTCCGTGGCACCCTTTT
26845 AAAGTCCACAACTCCGTGGCACCCTTTT
1 -AAGTCCACAACTCCGTGGCACCCTTTT
*
26873 AAAATCCACAACTCCGTGGCACCCTTTT
1 -AAGTCCACAACTCCGTGGCACCCTTTT
* * *
26901 AAATCCACAACTTCGTGGCACCCTTTC
1 AAGTCCACAACTCCGTGGCACCCTTTT
26928 AAGTCCACAACTCCGTGGCACCCTTTT
1 AAGTCCACAACTCCGTGGCACCCTTTT
26955 AAGTCCACAACTCCGTGGCACCCTTTT
1 AAGTCCACAACTCCGTGGCACCCTTTT
*
26982 AAAGTCCACAACTCCGTGGCACCTTTTT
1 -AAGTCCACAACTCCGTGGCACCCTTTT
*
27010 AAGTCCACAACTCCGTGGCACTCTTTT
1 AAGTCCACAACTCCGTGGCACCCTTTT
27037 AAGTCCACAACTCCGTGGCACCCTTTT
1 AAGTCCACAACTCCGTGGCACCCTTTT
27064 AAGTCCACAACTCCGTGGCACCCTTTT
1 AAGTCCACAACTCCGTGGCACCCTTTT
* *
27091 AAGTCCACAACTCCATGGCATTCCTTTT
1 AAGTCCACAACTCCGTGGCA-CCCTTTT
**
27119 AAGTCCACAACTCCGTGATACCCTTTT
1 AAGTCCACAACTCCGTGGCACCCTTTT
27146 AAGTCCACAACTCCGTGGCATCCCTTTT
1 AAGTCCACAACTCCGTGGCA-CCCTTTT
*
27174 AAGTCCACAACTTCGTGGCA
1 AAGTCCACAACTCCGTGGCA
27194 ACCCATTTCA
Statistics
Matches: 392, Mismatches: 32, Indels: 13
0.90 0.07 0.03
Matches are distributed among these distances:
26 5 0.01
27 232 0.59
28 154 0.39
29 1 0.00
ACGTcount: A:0.24, C:0.34, G:0.14, T:0.28
Consensus pattern (27 bp):
AAGTCCACAACTCCGTGGCACCCTTTT
Found at i:26874 original size:82 final size:81
Alignment explanation
Indices: 26736--27193 Score: 675
Period size: 82 Copynumber: 5.6 Consensus size: 81
26726 GACCTCTCTA
* * *
26736 AAGTCCACAACTCCGTGGCACCCTTTTAGAGTCCACAACTTCGTGGTATCCTTTTAAAGTCCACA
1 AAGTCCACAACTCCGTGGCACCCTTTTA-AGTCCACAACTCCGTGGCACCCTTTT-AAGTCCACA
**
26801 ACTCCGTGGCATTCTTTT
64 ACTCCGTGGCACCCTTTT
* ** *
26819 AAGTCCATAACTCTATGGCA-CCTTTTAAAGTCCACAACTCCGTGGCACCCTTTTAAAATCCACA
1 AAGTCCACAACTCCGTGGCACCCTTTT-AAGTCCACAACTCCGTGGCACCCTTTT-AAGTCCACA
26883 ACTCCGTGGCACCCTTTT
64 ACTCCGTGGCACCCTTTT
* * *
26901 AAATCCACAACTTCGTGGCACCCTTTCAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAAC
1 AAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAAC
26966 TCCGTGGCACCCTTTT
66 TCCGTGGCACCCTTTT
* *
26982 AAAGTCCACAACTCCGTGGCACCTTTTTAAGTCCACAACTCCGTGGCACTCTTTTAAGTCCACAA
1 -AAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAA
27047 CTCCGTGGCACCCTTTT
65 CTCCGTGGCACCCTTTT
* *
27064 AAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCATGGCATTCCTTTTAAGTCCACAA
1 AAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCA-CCCTTTTAAGTCCACAA
**
27129 CTCCGTGATACCCTTTT
65 CTCCGTGGCACCCTTTT
*
27146 AAGTCCACAACTCCGTGGCATCCCTTTTAAGTCCACAACTTCGTGGCA
1 AAGTCCACAACTCCGTGGCA-CCCTTTTAAGTCCACAACTCCGTGGCA
27194 ACCCATTTCA
Statistics
Matches: 341, Mismatches: 29, Indels: 10
0.90 0.08 0.03
Matches are distributed among these distances:
81 71 0.21
82 222 0.65
83 48 0.14
ACGTcount: A:0.24, C:0.34, G:0.14, T:0.28
Consensus pattern (81 bp):
AAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAAC
TCCGTGGCACCCTTTT
Found at i:26980 original size:109 final size:109
Alignment explanation
Indices: 26736--27212 Score: 679
Period size: 109 Copynumber: 4.3 Consensus size: 109
26726 GACCTCTCTA
* * * *
26736 AAGTCCACAACTCCGTGGCACCCTTTTAGAGTCCACAACTTCGTGGTATCCTTTTAAAGTCCACA
1 AAGTCCACAACTCCGTGGCACCCTTTTAAAGTCCACAACTCCGTGGCACCCTTTTAAA-TCCACA
** * **
26801 ACTCCGTGGCATTCTTTTAAGTCCATAACTCTATGGCA-CCTTTT
65 ACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTT
*
26845 AAAGTCCACAACTCCGTGGCACCCTTTTAAAATCCACAACTCCGTGGCACCCTTTTAAATCCACA
1 -AAGTCCACAACTCCGTGGCACCCTTTTAAAGTCCACAACTCCGTGGCACCCTTTTAAATCCACA
* *
26910 ACTTCGTGGCACCCTTTCAAGTCCACAACTCCGTGGCACCCTTTT
65 ACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTT
* *
26955 AAGTCCACAACTCCGTGGCACCCTTTTAAAGTCCACAACTCCGTGGCACCTTTTTAAGTCCACAA
1 AAGTCCACAACTCCGTGGCACCCTTTTAAAGTCCACAACTCCGTGGCACCCTTTTAAATCCACAA
*
27020 CTCCGTGGCACTCTTTTAAGTCCACAACTCCGTGGCACCCTTTT
66 CTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTT
* * *
27064 AAGTCCACAACTCCGTGGCACCCTTTT-AAGTCCACAACTCCATGGCATTCCTTTTAAGTCCACA
1 AAGTCCACAACTCCGTGGCACCCTTTTAAAGTCCACAACTCCGTGGCA-CCCTTTTAAATCCACA
**
27128 ACTCCGTGATACCCTTTTAAGTCCACAACTCCGTGGCATCCCTTTT
65 ACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCA-CCCTTTT
* * *
27174 AAGTCCACAACTTCGTGGCAACCCATTTCAAAGCCCACA
1 AAGTCCACAACTCCGTGGC-ACCC-TTTTAAAGTCCACA
27213 CAAGTCGGTG
Statistics
Matches: 334, Mismatches: 27, Indels: 9
0.90 0.07 0.02
Matches are distributed among these distances:
108 19 0.06
109 216 0.65
110 84 0.25
111 4 0.01
112 3 0.01
113 8 0.02
ACGTcount: A:0.25, C:0.34, G:0.14, T:0.28
Consensus pattern (109 bp):
AAGTCCACAACTCCGTGGCACCCTTTTAAAGTCCACAACTCCGTGGCACCCTTTTAAATCCACAA
CTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTT
Found at i:27224 original size:32 final size:32
Alignment explanation
Indices: 27188--27383 Score: 335
Period size: 32 Copynumber: 6.2 Consensus size: 32
27178 CCACAACTTC
27188 GTGGCAACCCATTTCAAAGCCCACACAAGTCG
1 GTGGCAACCCATTTCAAAGCCCACACAAGTCG
*
27220 GTGGC-A-CTATTTCAAAGCCCACACAAGTCG
1 GTGGCAACCCATTTCAAAGCCCACACAAGTCG
27250 GTGGCAA-CCATTTTCAAAGCCCACACAAGTCG
1 GTGGCAACCCA-TTTCAAAGCCCACACAAGTCG
*
27282 GTGGCAACCCTTTTCAAAGCCCACACAAGTCG
1 GTGGCAACCCATTTCAAAGCCCACACAAGTCG
27314 GTGGCAACCCATTTCAAAGCCCACACAAGTCG
1 GTGGCAACCCATTTCAAAGCCCACACAAGTCG
*
27346 GTGGCAACCCTTTTCAAAGCCCACACAAGTCG
1 GTGGCAACCCATTTCAAAGCCCACACAAGTCG
27378 GTGGCA
1 GTGGCA
27384 TAAGTCGGTG
Statistics
Matches: 156, Mismatches: 5, Indels: 6
0.93 0.03 0.04
Matches are distributed among these distances:
30 28 0.18
31 4 0.03
32 122 0.78
33 2 0.01
ACGTcount: A:0.30, C:0.33, G:0.20, T:0.18
Consensus pattern (32 bp):
GTGGCAACCCATTTCAAAGCCCACACAAGTCG
Found at i:27320 original size:64 final size:64
Alignment explanation
Indices: 27188--27824 Score: 692
Period size: 64 Copynumber: 9.8 Consensus size: 64
27178 CCACAACTTC
27188 GTGGCAACCCATTTCAAAGCCCACACAAGTCGGTGGC-A--CTATTTCAAAGCCCACACAAGTCG
1 GTGGCAACCCATTTCAAAGCCCACACAAGTCGGTGGCAACCCT-TTTCAAAGCCCACACAAGTCG
27250 GTGGCAA-CCATTTTCAAAGCCCACACAAGTCGGTGGCAACCCTTTTCAAAGCCCACACAAGTCG
1 GTGGCAACCCA-TTTCAAAGCCCACACAAGTCGGTGGCAACCCTTTTCAAAGCCCACACAAGTCG
27314 GTGGCAACCCATTTCAAAGCCCACACAAGTCGGTGGCAACCCTTTTCAAAGCCCACACAAGTCG
1 GTGGCAACCCATTTCAAAGCCCACACAAGTCGGTGGCAACCCTTTTCAAAGCCCACACAAGTCG
* ** ** **** ** **** * ** **
27378 GTGGCATAAGTCGGTGGCAACTCATTTCAAAGCC-CACACAAGTCGATGGCGACCCTTTTCAAAG
1 GTGGC--AA--C-----CCA-T--TTCAAAGCCCACACA-AGTCGGTGGCAACCCTTTTCAAAGC
*
27442 CC-CACACAAGTCT
53 CCACAC--AAGTCG
* *
27455 GTGGCAACCCATTTCAAAGCCCACACAAGTCGGTGGCAACTCATTTCAAAGCCCACACAAGTCG
1 GTGGCAACCCATTTCAAAGCCCACACAAGTCGGTGGCAACCCTTTTCAAAGCCCACACAAGTCG
* * * * * *
27519 GTGGCAACCTATTCCAAAGCCCACATAAGTCGATGGCAACTCATTTCAAAGCCCACACAAGTCG
1 GTGGCAACCCATTTCAAAGCCCACACAAGTCGGTGGCAACCCTTTTCAAAGCCCACACAAGTCG
* * *
27583 GTGGCGACCCTTTTCAAAGCCCACACAAGTCGGTGGCAACCCATTTCAAAGCCCACACAAGTCG
1 GTGGCAACCCATTTCAAAGCCCACACAAGTCGGTGGCAACCCTTTTCAAAGCCCACACAAGTCG
* * *
27647 GTGGCAACCCATTTCAAAGCCCACACAAGTCGGTGGCAACCCATTCCAAAGCCCACATAAGTCG
1 GTGGCAACCCATTTCAAAGCCCACACAAGTCGGTGGCAACCCTTTTCAAAGCCCACACAAGTCG
* *
27711 GTGGCAACTCATTTCAAAGCCCACACAAGTCGGTGGCGACCCTTTTCAAAGCCCACACAAGTCG
1 GTGGCAACCCATTTCAAAGCCCACACAAGTCGGTGGCAACCCTTTTCAAAGCCCACACAAGTCG
* * ** **
27775 ATGGCAACCCATTTAAAAGCCCATGCAAGTTAGTGGCAACCCTTTTCAAA
1 GTGGCAACCCATTTCAAAGCCCACACAAGTCGGTGGCAACCCTTTTCAAA
27825 TCACCATTTT
Statistics
Matches: 482, Mismatches: 71, Indels: 42
0.81 0.12 0.07
Matches are distributed among these distances:
61 3 0.01
62 33 0.07
63 1 0.00
64 369 0.77
65 22 0.05
66 9 0.02
67 1 0.00
68 3 0.01
73 3 0.01
74 1 0.00
75 9 0.02
76 18 0.04
77 10 0.02
ACGTcount: A:0.30, C:0.32, G:0.19, T:0.19
Consensus pattern (64 bp):
GTGGCAACCCATTTCAAAGCCCACACAAGTCGGTGGCAACCCTTTTCAAAGCCCACACAAGTCG
Found at i:27366 original size:96 final size:96
Alignment explanation
Indices: 27188--27824 Score: 884
Period size: 96 Copynumber: 6.5 Consensus size: 96
27178 CCACAACTTC
*
27188 GTGGCAACCCATTTCAAAGCCCACACAAGTCGGTGGC-A-CTATTTCAAAGCCCACACAAGTCGG
1 GTGGCAACCCATTTCAAAGCCCACACAAGTCGGTGGCAACCCATTTCAAAGCCCACACAAGTCGG
27251 TGGCAA-CCATTTTCAAAGCCCACACAAGTCG
66 TGGCAACCCA-TTTCAAAGCCCACACAAGTCG
*
27282 GTGGCAACCCTTTTCAAAGCCCACACAAGTCGGTGGCAACCCATTTCAAAGCCCACACAAGTCGG
1 GTGGCAACCCATTTCAAAGCCCACACAAGTCGGTGGCAACCCATTTCAAAGCCCACACAAGTCGG
*
27347 TGGCAACCCTTTTCAAAGCCCACACAAGTCG
66 TGGCAACCCATTTCAAAGCCCACACAAGTCG
* * *
27378 GTGGCATAAGTCGGTGGCAACTCATTTCAAAGCCCACACAAGTCGATGGCGACCCTTTTCAAAGC
1 GTGGC--AA--------C--C-CATTTCAAAGCCCACACAAGTCGGTGGCAACCCATTTCAAAGC
*
27443 CCACACAAGTCTGTGGCAACCCATTTCAAAGCCCACACAAGTCG
53 CCACACAAGTCGGTGGCAACCCATTTCAAAGCCCACACAAGTCG
* * * * *
27487 GTGGCAACTCATTTCAAAGCCCACACAAGTCGGTGGCAACCTATTCCAAAGCCCACATAAGTCGA
1 GTGGCAACCCATTTCAAAGCCCACACAAGTCGGTGGCAACCCATTTCAAAGCCCACACAAGTCGG
*
27552 TGGCAACTCATTTCAAAGCCCACACAAGTCG
66 TGGCAACCCATTTCAAAGCCCACACAAGTCG
* *
27583 GTGGCGACCCTTTTCAAAGCCCACACAAGTCGGTGGCAACCCATTTCAAAGCCCACACAAGTCGG
1 GTGGCAACCCATTTCAAAGCCCACACAAGTCGGTGGCAACCCATTTCAAAGCCCACACAAGTCGG
27648 TGGCAACCCATTTCAAAGCCCACACAAGTCG
66 TGGCAACCCATTTCAAAGCCCACACAAGTCG
* * *
27679 GTGGCAACCCATTCCAAAGCCCACATAAGTCGGTGGCAACTCATTTCAAAGCCCACACAAGTCGG
1 GTGGCAACCCATTTCAAAGCCCACACAAGTCGGTGGCAACCCATTTCAAAGCCCACACAAGTCGG
* *
27744 TGGCGACCCTTTTCAAAGCCCACACAAGTCG
66 TGGCAACCCATTTCAAAGCCCACACAAGTCG
* * ** ** *
27775 ATGGCAACCCATTTAAAAGCCCATGCAAGTTAGTGGCAACCCTTTTCAAA
1 GTGGCAACCCATTTCAAAGCCCACACAAGTCGGTGGCAACCCATTTCAAA
27825 TCACCATTTT
Statistics
Matches: 483, Mismatches: 44, Indels: 30
0.87 0.08 0.05
Matches are distributed among these distances:
94 36 0.07
95 1 0.00
96 351 0.73
97 2 0.00
98 2 0.00
99 1 0.00
106 1 0.00
107 2 0.00
108 1 0.00
109 86 0.18
ACGTcount: A:0.30, C:0.32, G:0.19, T:0.19
Consensus pattern (96 bp):
GTGGCAACCCATTTCAAAGCCCACACAAGTCGGTGGCAACCCATTTCAAAGCCCACACAAGTCGG
TGGCAACCCATTTCAAAGCCCACACAAGTCG
Found at i:27390 original size:13 final size:13
Alignment explanation
Indices: 27372--27396 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
27362 AAGCCCACAC
27372 AAGTCGGTGGCAT
1 AAGTCGGTGGCAT
27385 AAGTCGGTGGCA
1 AAGTCGGTGGCA
27397 ACTCATTTCA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.16, G:0.40, T:0.20
Consensus pattern (13 bp):
AAGTCGGTGGCAT
Found at i:27406 original size:45 final size:45
Alignment explanation
Indices: 27340--27427 Score: 149
Period size: 45 Copynumber: 2.0 Consensus size: 45
27330 AAGCCCACAC
* *
27340 AAGTCGGTGGCAACCCTTTTCAAAGCCCACACAAGTCGGTGGCAT
1 AAGTCGGTGGCAACCCATTTCAAAGCCCACACAAGTCGATGGCAT
*
27385 AAGTCGGTGGCAACTCATTTCAAAGCCCACACAAGTCGATGGC
1 AAGTCGGTGGCAACCCATTTCAAAGCCCACACAAGTCGATGGC
27428 GACCCTTTTC
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 40 1.00
ACGTcount: A:0.28, C:0.28, G:0.24, T:0.19
Consensus pattern (45 bp):
AAGTCGGTGGCAACCCATTTCAAAGCCCACACAAGTCGATGGCAT
Found at i:27435 original size:77 final size:77
Alignment explanation
Indices: 27308--27460 Score: 270
Period size: 77 Copynumber: 2.0 Consensus size: 77
27298 AAGCCCACAC
*
27308 AAGTCGGTGGCAACCCATTTCAAAGCCCACACAAGTCGGTGGCAACCCTTTTCAAAGCCCACACA
1 AAGTCGGTGGCAACCCATTTCAAAGCCCACACAAGTCGATGGCAACCCTTTTCAAAGCCCACACA
27373 AGTCGGTGGCAT
66 AGTCGGTGGCAT
* *
27385 AAGTCGGTGGCAACTCATTTCAAAGCCCACACAAGTCGATGGCGACCCTTTTCAAAGCCCACACA
1 AAGTCGGTGGCAACCCATTTCAAAGCCCACACAAGTCGATGGCAACCCTTTTCAAAGCCCACACA
*
27450 AGTCTGTGGCA
66 AGTCGGTGGCA
27461 ACCCATTTCA
Statistics
Matches: 72, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
77 72 1.00
ACGTcount: A:0.29, C:0.31, G:0.22, T:0.19
Consensus pattern (77 bp):
AAGTCGGTGGCAACCCATTTCAAAGCCCACACAAGTCGATGGCAACCCTTTTCAAAGCCCACACA
AGTCGGTGGCAT
Found at i:27438 original size:32 final size:32
Alignment explanation
Indices: 27385--27824 Score: 655
Period size: 32 Copynumber: 13.8 Consensus size: 32
27375 TCGGTGGCAT
*
27385 AAGTCGGTGGCAACTCATTTCAAAGCCCACAC
1 AAGTCGGTGGCAACCCATTTCAAAGCCCACAC
* * *
27417 AAGTCGATGGCGACCCTTTTCAAAGCCCACAC
1 AAGTCGGTGGCAACCCATTTCAAAGCCCACAC
*
27449 AAGTCTGTGGCAACCCATTTCAAAGCCCACAC
1 AAGTCGGTGGCAACCCATTTCAAAGCCCACAC
*
27481 AAGTCGGTGGCAACTCATTTCAAAGCCCACAC
1 AAGTCGGTGGCAACCCATTTCAAAGCCCACAC
* * *
27513 AAGTCGGTGGCAACCTATTCCAAAGCCCACAT
1 AAGTCGGTGGCAACCCATTTCAAAGCCCACAC
* *
27545 AAGTCGATGGCAACTCATTTCAAAGCCCACAC
1 AAGTCGGTGGCAACCCATTTCAAAGCCCACAC
* *
27577 AAGTCGGTGGCGACCCTTTTCAAAGCCCACAC
1 AAGTCGGTGGCAACCCATTTCAAAGCCCACAC
27609 AAGTCGGTGGCAACCCATTTCAAAGCCCACAC
1 AAGTCGGTGGCAACCCATTTCAAAGCCCACAC
27641 AAGTCGGTGGCAACCCATTTCAAAGCCCACAC
1 AAGTCGGTGGCAACCCATTTCAAAGCCCACAC
* *
27673 AAGTCGGTGGCAACCCATTCCAAAGCCCACAT
1 AAGTCGGTGGCAACCCATTTCAAAGCCCACAC
*
27705 AAGTCGGTGGCAACTCATTTCAAAGCCCACAC
1 AAGTCGGTGGCAACCCATTTCAAAGCCCACAC
* *
27737 AAGTCGGTGGCGACCCTTTTCAAAGCCCACAC
1 AAGTCGGTGGCAACCCATTTCAAAGCCCACAC
* * **
27769 AAGTCGATGGCAACCCATTTAAAAGCCCATGC
1 AAGTCGGTGGCAACCCATTTCAAAGCCCACAC
** *
27801 AAGTTAGTGGCAACCCTTTTCAAA
1 AAGTCGGTGGCAACCCATTTCAAA
27825 TCACCATTTT
Statistics
Matches: 364, Mismatches: 44, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
32 364 1.00
ACGTcount: A:0.31, C:0.32, G:0.19, T:0.19
Consensus pattern (32 bp):
AAGTCGGTGGCAACCCATTTCAAAGCCCACAC
Found at i:29482 original size:2 final size:2
Alignment explanation
Indices: 29469--29515 Score: 85
Period size: 2 Copynumber: 23.5 Consensus size: 2
29459 TTGTCTTATT
*
29469 TA TA TG TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
29511 TA TA T
1 TA TA T
29516 TTTGAAAATC
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (2 bp):
TA
Found at i:32246 original size:183 final size:183
Alignment explanation
Indices: 31938--32295 Score: 563
Period size: 183 Copynumber: 2.0 Consensus size: 183
31928 AACTACTTCG
* *
31938 GGATTGTGGAATGAACATGTGATGACCATGTCACTTCCCCATCTCGATTATGGACATTCGAATGT
1 GGATTGTGGAACGAACACGTGATGACCATGTCACTTCCCCATCTCGATTATGGACATTCGAATGT
* **
32003 CCGTGGCATGAGTTCAACCCAATGGAAAAACCAAAAACGCTAAATACCTCATTTGTTTTGGTCTG
66 CCATGGCACAAGTTCAACCCAATGGAAAAACCAAAAACGCTAAATACCTCATTTGTTTTGGTCTG
* * * *
32068 GCAACACTGTAGTATGAGTTTGAAAATTATGTAAAAAATATGAAATTACTCCA
131 ACAACACTATAATATGAGATTGAAAATTATGTAAAAAATATGAAATTACTCCA
* * *
32121 GGATTGTGGAACGAACACGTGATGCCCATGTCACTTTCCCATCTCGATTATGGATATTCGAATGT
1 GGATTGTGGAACGAACACGTGATGACCATGTCACTTCCCCATCTCGATTATGGACATTCGAATGT
* * * *
32186 CTATGGCACAAGTTCAACCCAATGGAAAAACCAAAAATGCTAAATACCTCCTTTGTTTTGGTTTG
66 CCATGGCACAAGTTCAACCCAATGGAAAAACCAAAAACGCTAAATACCTCATTTGTTTTGGTCTG
*
32251 ACAGCACTATAATATGAGATTGAAAATTATGTAAAAAATATGAAA
131 ACAACACTATAATATGAGATTGAAAATTATGTAAAAAATATGAAA
32296 CAATTTTTTT
Statistics
Matches: 158, Mismatches: 17, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
183 158 1.00
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.29
Consensus pattern (183 bp):
GGATTGTGGAACGAACACGTGATGACCATGTCACTTCCCCATCTCGATTATGGACATTCGAATGT
CCATGGCACAAGTTCAACCCAATGGAAAAACCAAAAACGCTAAATACCTCATTTGTTTTGGTCTG
ACAACACTATAATATGAGATTGAAAATTATGTAAAAAATATGAAATTACTCCA
Found at i:33170 original size:79 final size:79
Alignment explanation
Indices: 33000--33556 Score: 579
Period size: 78 Copynumber: 7.1 Consensus size: 79
32990 TCATTCATAT
* * **
33000 TTTTATTTTTAAAATACTAATTTTTCACAATCGGGGATACTCCAA-CCCATTATTTTCGAGGGGA
1 TTTTATTTCTAAAACACCGATTTTTCACAATCGGGGATACTCCAACCCCATTATTTTCGAGGGGA
* * *
33064 TACTCTAACCCCAG
66 TACTCCAACCCTAA
* *
33078 TTTTATTTCTAAAACACCAATTTTTCACAATCGGGGATACTCCAACCCCATTATTTCCGAGGGGA
1 TTTTATTTCTAAAACACCGATTTTTCACAATCGGGGATACTCCAACCCCATTATTTTCGAGGGGA
*
33143 TACTCCAACCATAA
66 TACTCCAACCCTAA
* * * * **
33157 TTTTATTTTTAAAACATCGATTTTTCACAATC-AGGATACTCCAACCCCGTTATTTTTTAGGGGA
1 TTTTATTTCTAAAACACCGATTTTTCACAATCGGGGATACTCCAACCCCATTATTTTCGAGGGGA
* * * *
33221 TATTCTAA-TCTCGA
66 TACTCCAACCCT-AA
* * * * * *
33235 TTTTATTTCCACAGCACCGATTTTTCACCATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGA
1 TTTTATTTCTAAAACACCGATTTTTCACAATCGGGGATACTCCAACCCCATTATTTTCGAGGGGA
* **
33300 TACTCCAACCTTGG
66 TACTCCAACCCTAA
* * * *
33314 TTTTATTTCCAAAAACACTGATTTTTCACAATCGAGAATACTCCAACCCCATTATTTTCGAGGGG
1 TTTTATTT-CTAAAACACCGATTTTTCACAATCGGGGATACTCCAACCCCATTATTTTCGAGGGG
**
33379 ATACTCCAACTCC-GG
65 ATACTCCAAC-CCTAA
* * * * *
33394 TTTTATTTCTAAAACATCGATTTTTCACAATCGGGGTTACTCCAA-CCTATTATTTTTGAGGGAA
1 TTTTATTTCTAAAACACCGATTTTTCACAATCGGGGATACTCCAACCCCATTATTTTCGAGGGGA
*
33458 TACTCCAACCCTGA
66 TACTCCAACCCTAA
* * * ** *
33472 TTTTATTT-TCAAAACATCAATTTTTCACCATCGGGGATACTCCAACCCTGTCA-TTTCTGAGGG
1 TTTTATTTCT-AAAACACCGATTTTTCACAATCGGGGATACTCCAACCCCATTATTTTC-GAGGG
* *
33535 GATACTCTAACCCTAT
64 GATACTCCAACCCTAA
33551 TTTTAT
1 TTTTAT
33557 CTCCAAAATA
Statistics
Matches: 403, Mismatches: 66, Indels: 19
0.83 0.14 0.04
Matches are distributed among these distances:
77 4 0.01
78 171 0.42
79 159 0.39
80 68 0.17
81 1 0.00
ACGTcount: A:0.28, C:0.24, G:0.13, T:0.35
Consensus pattern (79 bp):
TTTTATTTCTAAAACACCGATTTTTCACAATCGGGGATACTCCAACCCCATTATTTTCGAGGGGA
TACTCCAACCCTAA
Found at i:33194 original size:78 final size:79
Alignment explanation
Indices: 33019--33556 Score: 579
Period size: 79 Copynumber: 6.8 Consensus size: 79
33009 TAAAATACTA
* * *
33019 ATTTTTCACAATCGGGGATACTCCAA-CCCATTATTTTCGAGGGGATACTCTAACCCCAGTTTTA
1 ATTTTTCACAATCGGGGATACTCCAACCCCATTATTTTCGAGGGGATACTCCAACCCTAATTTTA
* *
33083 TTTCTAAAACACCA
66 TTTCTAAAACATCG
* *
33097 ATTTTTCACAATCGGGGATACTCCAACCCCATTATTTCCGAGGGGATACTCCAACCATAATTTTA
1 ATTTTTCACAATCGGGGATACTCCAACCCCATTATTTTCGAGGGGATACTCCAACCCTAATTTTA
*
33162 TTTTTAAAACATCG
66 TTTCTAAAACATCG
* * ** * * * *
33176 ATTTTTCACAATC-AGGATACTCCAACCCCGTTATTTTTTAGGGGATATTCTAA-TCTCGATTTT
1 ATTTTTCACAATCGGGGATACTCCAACCCCATTATTTTCGAGGGGATACTCCAACCCT-AATTTT
* * * *
33239 ATTTCCACAGCACCG
65 ATTTCTAAAACATCG
* * * * **
33254 ATTTTTCACCATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCTTGGTTTTA
1 ATTTTTCACAATCGGGGATACTCCAACCCCATTATTTTCGAGGGGATACTCCAACCCTAATTTTA
*
33319 TTTCCAAAAACA-CTG
66 TTT-CTAAAACATC-G
* * **
33334 ATTTTTCACAATCGAGAATACTCCAACCCCATTATTTTCGAGGGGATACTCCAACTCC-GGTTTT
1 ATTTTTCACAATCGGGGATACTCCAACCCCATTATTTTCGAGGGGATACTCCAAC-CCTAATTTT
33398 ATTTCTAAAACATCG
65 ATTTCTAAAACATCG
* * * * *
33413 ATTTTTCACAATCGGGGTTACTCCAA-CCTATTATTTTTGAGGGAATACTCCAACCCTGATTTTA
1 ATTTTTCACAATCGGGGATACTCCAACCCCATTATTTTCGAGGGGATACTCCAACCCTAATTTTA
*
33477 TTT-TCAAAACATCA
66 TTTCT-AAAACATCG
* ** * * *
33491 ATTTTTCACCATCGGGGATACTCCAACCCTGTCA-TTTCTGAGGGGATACTCTAACCCTATTTTT
1 ATTTTTCACAATCGGGGATACTCCAACCCCATTATTTTC-GAGGGGATACTCCAACCCTAATTTT
33555 AT
65 AT
33557 CTCCAAAATA
Statistics
Matches: 388, Mismatches: 60, Indels: 23
0.82 0.13 0.05
Matches are distributed among these distances:
77 4 0.01
78 155 0.40
79 160 0.41
80 68 0.18
81 1 0.00
ACGTcount: A:0.28, C:0.25, G:0.13, T:0.34
Consensus pattern (79 bp):
ATTTTTCACAATCGGGGATACTCCAACCCCATTATTTTCGAGGGGATACTCCAACCCTAATTTTA
TTTCTAAAACATCG
Found at i:33413 original size:237 final size:237
Alignment explanation
Indices: 33000--33564 Score: 708
Period size: 237 Copynumber: 2.4 Consensus size: 237
32990 TCATTCATAT
** * * * * *
33000 TTTTATTTTTAAAATACTAATTTTTCACAATCGGGGATACTCCAA-CCCATTATTTTCGAGGGGA
1 TTTTATTTCCAAAACACCAATTTTTCACCATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGA
* * * *
33064 TACTCTAACCCCAGTTTTATTT-CTAAAACACCAATTTTTCACAATCGGGGATACTCCAACCCCA
66 TACTCTAACCCTAGTTTTATTTCCAAAAACACCAATTTTTCACAATCGAGAATACTCCAACCCCA
* *
33128 TTATTTCCGAGGGGATACTCCAACCATAATTTTATTTTTAAAACATCGATTTTTCACAATC-AGG
131 TTATTTCCGAGGGGATACTCCAACCACAATTTTATTTCTAAAACATCGATTTTTCACAATCGAGG
* * * * * *
33192 ATACTCCAACCCCGTTATTTTTTAGGGGATATTCTAA-TCTCGA
196 ATACTCCAA-CCCATTATTTTTGAGGGAATACTCCAACCCT-GA
* * *
33235 TTTTATTTCCACAGCACCGATTTTTCACCATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGA
1 TTTTATTTCCAAAACACCAATTTTTCACCATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGA
* * * **
33300 TACTCCAACCTTGGTTTTATTTCCAAAAACACTGATTTTTCACAATCGAGAATACTCCAACCCCA
66 TACTCTAACCCTAGTTTTATTTCCAAAAACACCAATTTTTCACAATCGAGAATACTCCAACCCCA
* ** *
33365 TTATTTTCGAGGGGATACTCCAACTC-CGGTTTTATTTCTAAAACATCGATTTTTCACAATCGGG
131 TTATTTCCGAGGGGATACTCCAAC-CACAATTTTATTTCTAAAACATCGATTTTTCACAATCGAG
* *
33429 GTTACTCCAACCTATTATTTTTGAGGGAATACTCCAACCCTGA
195 GATACTCCAACCCATTATTTTTGAGGGAATACTCCAACCCTGA
* * * * *
33472 TTTTATTTTCAAAACATCAATTTTTCACCATCGGGGATACTCCAACCCTGTCATTTCTGAGGGGA
1 TTTTATTTCCAAAACACCAATTTTTCACCATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGA
* *
33537 TACTCTAACCCTATTTTTATCTCCAAAA
66 TACTCTAACCCTAGTTTTATTTCCAAAA
33565 TATTAAATTT
Statistics
Matches: 279, Mismatches: 46, Indels: 8
0.84 0.14 0.02
Matches are distributed among these distances:
235 37 0.13
236 35 0.13
237 194 0.70
238 13 0.05
ACGTcount: A:0.28, C:0.24, G:0.13, T:0.35
Consensus pattern (237 bp):
TTTTATTTCCAAAACACCAATTTTTCACCATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGA
TACTCTAACCCTAGTTTTATTTCCAAAAACACCAATTTTTCACAATCGAGAATACTCCAACCCCA
TTATTTCCGAGGGGATACTCCAACCACAATTTTATTTCTAAAACATCGATTTTTCACAATCGAGG
ATACTCCAACCCATTATTTTTGAGGGAATACTCCAACCCTGA
Found at i:33555 original size:157 final size:157
Alignment explanation
Indices: 33000--33556 Score: 651
Period size: 157 Copynumber: 3.5 Consensus size: 157
32990 TCATTCATAT
* * * *
33000 TTTTATTTTTAAAATACTAATTTTTCACAATCGGGGATACTCCAA-CCCATTATTTTCGAGGGGA
1 TTTTATTTTCAAAACACTAATTTTTCACAATCGAGGATACTCCAACCCCGTTATTTTCGAGGGGA
*
33064 TACTCTAACCCCAGTTTTATTTCTAAAACACCAATTTTTCACAATCGGGGATACTCCAACCCCAT
66 TACTCTAA-CCCAGTTTTATTTCTAAAACACCGATTTTTCACAATCGGGGATACTCCAACCCCAT
*
33129 TATTTCCGAGGGGATACTCCAACCATAA
130 TATTTCCGAGGGGATACTCCAACCATGA
* * **
33157 TTTTATTTTTAAAACA-TCGATTTTTCACAATC-AGGATACTCCAACCCCGTTATTTTTTAGGGG
1 TTTTATTTTCAAAACACT-AATTTTTCACAATCGAGGATACTCCAACCCCGTTATTTTCGAGGGG
* * * * * *
33220 ATATTCTAATCTC-GATTTTATTTCCACAGCACCGATTTTTCACCATCGGGGATACTCCAACCCC
65 ATACTCTAA-CCCAG-TTTTATTTCTAAAACACCGATTTTTCACAATCGGGGATACTCCAACCCC
* * *
33284 GTTATTTCCGAGGGGATACTCCAACCTTGG
128 ATTATTTCCGAGGGGATACTCCAACCATGA
* * * *
33314 TTTTATTTCCAAAAACACTGATTTTTCACAATCGAGAATACTCCAACCCCATTATTTTCGAGGGG
1 TTTTATTTTC-AAAACACTAATTTTTCACAATCGAGGATACTCCAACCCCGTTATTTTCGAGGGG
* * * * *
33379 ATACTCCAACTCCGGTTTTATTTCTAAAACATCGATTTTTCACAATCGGGGTTACTCCAA-CCTA
65 ATACTCTAAC-CCAGTTTTATTTCTAAAACACCGATTTTTCACAATCGGGGATACTCCAACCCCA
** * *
33443 TTATTTTTGAGGGAATACTCCAACCCTGA
129 TTATTTCCGAGGGGATACTCCAACCATGA
* * * *
33472 TTTTATTTTCAAAACA-TCAATTTTTCACCATCGGGGATACTCCAACCCTGTCA-TTTCTGAGGG
1 TTTTATTTTCAAAACACT-AATTTTTCACAATCGAGGATACTCCAACCCCGTTATTTTC-GAGGG
*
33535 GATACTCTAACCCTATTTTTAT
64 GATACTCTAACCC-AGTTTTAT
33557 CTCCAAAATA
Statistics
Matches: 338, Mismatches: 51, Indels: 22
0.82 0.12 0.05
Matches are distributed among these distances:
156 20 0.06
157 186 0.55
158 56 0.17
159 75 0.22
160 1 0.00
ACGTcount: A:0.28, C:0.24, G:0.13, T:0.35
Consensus pattern (157 bp):
TTTTATTTTCAAAACACTAATTTTTCACAATCGAGGATACTCCAACCCCGTTATTTTCGAGGGGA
TACTCTAACCCAGTTTTATTTCTAAAACACCGATTTTTCACAATCGGGGATACTCCAACCCCATT
ATTTCCGAGGGGATACTCCAACCATGA
Found at i:35962 original size:11 final size:11
Alignment explanation
Indices: 35946--35983 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
35936 ATATAAATAT
*
35946 TAATATATTAA
1 TAATATTTTAA
35957 TAATATTTTAA
1 TAATATTTTAA
35968 T-ATATTTTACA
1 TAATATTTTA-A
35979 TAATA
1 TAATA
35984 AAATAAAATT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
10 8 0.33
11 13 0.54
12 3 0.12
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (11 bp):
TAATATTTTAA
Found at i:38983 original size:25 final size:24
Alignment explanation
Indices: 38951--39001 Score: 75
Period size: 25 Copynumber: 2.1 Consensus size: 24
38941 AATATTATAT
*
38951 ATTTATATGATATAAATTATATAAA
1 ATTTATATGATATAAA-TATAAAAA
*
38976 ATTTATATTATATAAATATAAAAA
1 ATTTATATGATATAAATATAAAAA
39000 AT
1 AT
39002 AATATATAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
24 9 0.38
25 15 0.62
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (24 bp):
ATTTATATGATATAAATATAAAAA
Found at i:39007 original size:25 final size:25
Alignment explanation
Indices: 38954--39008 Score: 67
Period size: 25 Copynumber: 2.2 Consensus size: 25
38944 ATTATATATT
* *
38954 TATATGATATAAATTATATAAAATT
1 TATATGATATAAATTATAAAAAATA
*
38979 TATATTATATAAA-TATAAAAAATAA
1 TATATGATATAAATTATAAAAAAT-A
39004 TATAT
1 TATAT
39009 AATTAAAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
24 9 0.35
25 17 0.65
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (25 bp):
TATATGATATAAATTATAAAAAATA
Found at i:39009 original size:20 final size:18
Alignment explanation
Indices: 38984--39021 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 18
38974 AAATTTATAT
38984 TATATAAATATAAAAAATAA
1 TATAT-AAT-TAAAAAATAA
39004 TATATAATTAAAAAATAA
1 TATATAATTAAAAAATAA
39022 ATCAAATTGA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 10 0.56
19 3 0.17
20 5 0.28
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (18 bp):
TATATAATTAAAAAATAA
Found at i:40363 original size:23 final size:24
Alignment explanation
Indices: 40336--40381 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 24
40326 TAAAATATTA
*
40336 ATTTATTAATTA-ATAATAATTTT
1 ATTTATAAATTAGATAATAATTTT
40359 ATTTATAAATTAGATAATAATTT
1 ATTTATAAATTAGATAATAATTT
40382 AAATTTTTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
23 11 0.52
24 10 0.48
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (24 bp):
ATTTATAAATTAGATAATAATTTT
Found at i:41189 original size:16 final size:18
Alignment explanation
Indices: 41157--41189 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
41147 GAAATTTTAA
41157 TTTTAATATTTATAATTT
1 TTTTAATATTTATAATTT
41175 TTTTAAT-TTTA-AATT
1 TTTTAATATTTATAATT
41190 ACGATCTATA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.27
17 4 0.27
18 7 0.47
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (18 bp):
TTTTAATATTTATAATTT
Done.