Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009620.1 Hibiscus syriacus cultivar Beakdansim tig00117009_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: 1051670
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 4
Found at i:1657 original size:16 final size:17
Alignment explanation
Indices: 1636--1669 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
1626 TGAATTTTAC
1636 TTCAAA-ATTACTTTCT
1 TTCAAATATTACTTTCT
*
1652 TTCAAATTTTACTTTCT
1 TTCAAATATTACTTTCT
1669 T
1 T
1670 CGAACACAAC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.26, C:0.18, G:0.00, T:0.56
Consensus pattern (17 bp):
TTCAAATATTACTTTCT
Found at i:1759 original size:28 final size:29
Alignment explanation
Indices: 1712--1769 Score: 93
Period size: 28 Copynumber: 2.0 Consensus size: 29
1702 CAATTTCCGC
1712 CTAGCCCAGACACAAGACCAATTCATCGA
1 CTAGCCCAGACACAAGACCAATTCATCGA
1741 CTAGCCCAGA-AGCAA-ACCAATTCATCGA
1 CTAGCCCAGACA-CAAGACCAATTCATCGA
1769 C
1 C
1770 AATTTCAATA
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
28 15 0.54
29 13 0.46
ACGTcount: A:0.38, C:0.34, G:0.14, T:0.14
Consensus pattern (29 bp):
CTAGCCCAGACACAAGACCAATTCATCGA
Found at i:5967 original size:37 final size:36
Alignment explanation
Indices: 5917--5990 Score: 112
Period size: 37 Copynumber: 2.0 Consensus size: 36
5907 ATTATATCTT
*
5917 ATATAAAGTGATGAGGGTCACCTAAAAACTAAAATG
1 ATATAAAATGATGAGGGTCACCTAAAAACTAAAATG
* *
5953 ATATAATAATGATGAGGTTCACCTAAAAATTAAAATG
1 ATATAA-AATGATGAGGGTCACCTAAAAACTAAAATG
5990 A
1 A
5991 GAATTAAAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
36 6 0.18
37 28 0.82
ACGTcount: A:0.49, C:0.09, G:0.16, T:0.26
Consensus pattern (36 bp):
ATATAAAATGATGAGGGTCACCTAAAAACTAAAATG
Found at i:6274 original size:20 final size:20
Alignment explanation
Indices: 6249--6362 Score: 88
Period size: 20 Copynumber: 5.7 Consensus size: 20
6239 AATTGGGAAA
6249 ATCGCAATGCGATACTGACT
1 ATCGCAATGCGATACTGACT
* * **
6269 ATCGCAATGCGATAATAAAA
1 ATCGCAATGCGATACTGACT
* * *
6289 ATCGCAACGAGATACTTACT
1 ATCGCAATGCGATACTGACT
*
6309 TTCGCAACT-CGATACTGACT
1 ATCGCAA-TGCGATACTGACT
* * *
6329 TTCGCAACGCGATAAT-ACAT
1 ATCGCAATGCGATACTGAC-T
6349 AATCGCAATGCGAT
1 -ATCGCAATGCGAT
6363 TTTCAAAGCG
Statistics
Matches: 72, Mismatches: 18, Indels: 7
0.74 0.19 0.07
Matches are distributed among these distances:
19 2 0.03
20 59 0.82
21 11 0.15
ACGTcount: A:0.35, C:0.24, G:0.17, T:0.25
Consensus pattern (20 bp):
ATCGCAATGCGATACTGACT
Found at i:6557 original size:22 final size:22
Alignment explanation
Indices: 6529--6572 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
6519 CACTCTCTCA
6529 CCCATCTCCGACGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
* *
6551 CCCATCTCTGGCGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
6573 TATCTCCATC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.20, C:0.43, G:0.16, T:0.20
Consensus pattern (22 bp):
CCCATCTCCGACGAAATCCGTC
Found at i:6861 original size:20 final size:20
Alignment explanation
Indices: 6836--6873 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
6826 CGATTCTCTC
6836 GTTGCGATAGTCATTTTCGT
1 GTTGCGATAGTCATTTTCGT
**
6856 GTTGCGATTTTCATTTTC
1 GTTGCGATAGTCATTTTC
6874 AGAAACTATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.13, C:0.16, G:0.21, T:0.50
Consensus pattern (20 bp):
GTTGCGATAGTCATTTTCGT
Found at i:8209 original size:18 final size:18
Alignment explanation
Indices: 8188--8232 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
8178 TTCACTTCGG
*
8188 GAGCCATCACCTCGCCCA
1 GAGCCATCACCTCACCCA
*
8206 GAGCTATCACCTCACCCA
1 GAGCCATCACCTCACCCA
8224 GAGCCATCA
1 GAGCCATCA
8233 TCTGATCGAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.27, C:0.44, G:0.16, T:0.13
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:8717 original size:19 final size:20
Alignment explanation
Indices: 8664--8718 Score: 58
Period size: 20 Copynumber: 2.8 Consensus size: 20
8654 AGTTTACTTT
* * *
8664 CGCAACACGAAAATGACTAT
1 CGCAACGCGGAAATGACTAA
*
8684 CGCAACGCGGAAATGGCTAA
1 CGCAACGCGGAAATGACTAA
*
8704 CGCAATGC-GAAATGA
1 CGCAACGCGGAAATGA
8719 AAATCGCAAC
Statistics
Matches: 29, Mismatches: 6, Indels: 1
0.81 0.17 0.03
Matches are distributed among these distances:
19 6 0.21
20 23 0.79
ACGTcount: A:0.40, C:0.24, G:0.24, T:0.13
Consensus pattern (20 bp):
CGCAACGCGGAAATGACTAA
Found at i:8737 original size:14 final size:14
Alignment explanation
Indices: 8718--8807 Score: 81
Period size: 14 Copynumber: 5.9 Consensus size: 14
8708 ATGCGAAATG
8718 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
8732 AAAATCGCAATGCGAA
1 AAAATCGCAA--CGAC
*
8748 ATGAAATCACAACGAC
1 A--AAATCGCAACGAC
*
8764 AAAATCGCAATGCGAA
1 AAAATCGCAA--CGAC
8780 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
8796 AAAATCGCAACG
1 AAAATCGCAACG
8808 CGAAATGAAA
Statistics
Matches: 62, Mismatches: 6, Indels: 16
0.74 0.07 0.19
Matches are distributed among these distances:
14 29 0.47
16 16 0.26
18 17 0.27
ACGTcount: A:0.49, C:0.23, G:0.17, T:0.11
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:8761 original size:32 final size:32
Alignment explanation
Indices: 8704--8824 Score: 206
Period size: 32 Copynumber: 3.7 Consensus size: 32
8694 AAATGGCTAA
8704 CGCAATGCGAAATGAAAATCGCAACGACAAAAT
1 CGCAATGCGAAATG-AAATCGCAACGACAAAAT
*
8737 CGCAATGCGAAATGAAATCACAACGACAAAAT
1 CGCAATGCGAAATGAAATCGCAACGACAAAAT
8769 CGCAATGCGAAATGAAATCGCAACGACAAAAT
1 CGCAATGCGAAATGAAATCGCAACGACAAAAT
*
8801 CGCAACGCGAAATGAAAATCGCAA
1 CGCAATGCGAAATG-AAATCGCAA
8825 TGCGATTTGT
Statistics
Matches: 84, Mismatches: 3, Indels: 2
0.94 0.03 0.02
Matches are distributed among these distances:
32 61 0.73
33 23 0.27
ACGTcount: A:0.48, C:0.22, G:0.18, T:0.12
Consensus pattern (32 bp):
CGCAATGCGAAATGAAATCGCAACGACAAAAT
Found at i:8860 original size:14 final size:14
Alignment explanation
Indices: 8841--8898 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
8831 TTGTGTTTCG
8841 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
8855 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
8871 CGCGTTGCGATTTTGT
1 --CGTTGCGATTTTGT
8887 CGTTGCGATTTT
1 CGTTGCGATTTT
8899 CATTTCGCAT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 23 0.61
16 4 0.11
18 11 0.29
ACGTcount: A:0.09, C:0.17, G:0.26, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:8875 original size:32 final size:33
Alignment explanation
Indices: 8836--8914 Score: 142
Period size: 32 Copynumber: 2.4 Consensus size: 33
8826 GCGATTTGTG
8836 TTTCGCGTTGCGATTTTGTCGTTGCGA-TTTCA
1 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
8868 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
*
8901 TTTCGCATTGCGAT
1 TTTCGCGTTGCGAT
8915 AGCCATTTCC
Statistics
Matches: 45, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
32 27 0.60
33 18 0.40
ACGTcount: A:0.10, C:0.19, G:0.24, T:0.47
Consensus pattern (33 bp):
TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
Found at i:8913 original size:19 final size:19
Alignment explanation
Indices: 8855--8972 Score: 86
Period size: 20 Copynumber: 6.4 Consensus size: 19
8845 GCGATTTTGT
8855 CGTTGCGA-TTTCATTTCG
1 CGTTGCGATTTTCATTTCG
*
8873 CGTTGCGA-TTT--TGT--
1 CGTTGCGATTTTCATTTCG
8887 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
* ***
8906 CATTGCGATAGCCATTTCCG
1 CGTTGCGATTTTCATTT-CG
**
8926 CGTTGCGATAGTCATTTCG
1 CGTTGCGATTTTCATTTCG
* *
8945 TGTTGCGATTTTAAGTTTCG
1 CGTTGCGATTTTCA-TTTCG
*
8965 TGTTGCGA
1 CGTTGCGA
8973 AAGTAAACTA
Statistics
Matches: 81, Mismatches: 12, Indels: 12
0.77 0.11 0.11
Matches are distributed among these distances:
14 8 0.10
15 3 0.04
16 2 0.02
17 2 0.02
18 11 0.14
19 25 0.31
20 30 0.37
ACGTcount: A:0.14, C:0.19, G:0.25, T:0.42
Consensus pattern (19 bp):
CGTTGCGATTTTCATTTCG
Found at i:10830 original size:14 final size:14
Alignment explanation
Indices: 10811--10846 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
10801 ATTGTTTAAT
10811 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
10825 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
10839 TGATTTGT
1 TGATTTGT
10847 TAATTGATGT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:11016 original size:19 final size:19
Alignment explanation
Indices: 10962--11008 Score: 94
Period size: 19 Copynumber: 2.5 Consensus size: 19
10952 TCGCAACGAG
10962 AAATCGCAATGCGAAATGA
1 AAATCGCAATGCGAAATGA
10981 AAATCGCAATGCGAAATGA
1 AAATCGCAATGCGAAATGA
11000 AAATCGCAA
1 AAATCGCAA
11009 CGAGAAATCG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.49, C:0.17, G:0.19, T:0.15
Consensus pattern (19 bp):
AAATCGCAATGCGAAATGA
Found at i:11102 original size:20 final size:20
Alignment explanation
Indices: 11045--11102 Score: 89
Period size: 20 Copynumber: 2.9 Consensus size: 20
11035 TCGCATTGCG
* *
11045 ATTTTCTCGTTGCGATAACC
1 ATTTTCACGTTGCGATAGCC
*
11065 ATTTTCGCGTTGCGATAGCC
1 ATTTTCACGTTGCGATAGCC
11085 ATTTTCACGTTGCGATAG
1 ATTTTCACGTTGCGATAG
11103 TCAAATGAAT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.19, C:0.22, G:0.21, T:0.38
Consensus pattern (20 bp):
ATTTTCACGTTGCGATAGCC
Found at i:12189 original size:24 final size:24
Alignment explanation
Indices: 12162--12215 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
12152 GTATTCGAAA
* *
12162 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATATTGGTCAATACACGGAC
*
12186 TTTGATATTGGTCAATACACGGAT
1 TTTGATATTGGTCAATACACGGAC
12210 TTTGAT
1 TTTGAT
12216 GATGTTTCAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.24, C:0.17, G:0.20, T:0.39
Consensus pattern (24 bp):
TTTGATATTGGTCAATACACGGAC
Found at i:12404 original size:12 final size:12
Alignment explanation
Indices: 12387--12411 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
12377 ATATAATCCT
12387 GAAGAAGAAAAA
1 GAAGAAGAAAAA
12399 GAAGAAGAAAAA
1 GAAGAAGAAAAA
12411 G
1 G
12412 TCCCCGAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:14726 original size:19 final size:18
Alignment explanation
Indices: 14704--14834 Score: 70
Period size: 19 Copynumber: 7.7 Consensus size: 18
14694 GGAAATTACT
14704 ATCGCAATGCGAAATGAAA
1 ATCGCAA-GCGAAATGAAA
*
14723 ATCGCAA-CG--A-GAGA
1 ATCGCAAGCGAAATGAAA
14737 ATCGCAATGCGAAATGAAA
1 ATCGCAA-GCGAAATGAAA
* *
14756 ATCGCAA-CG--CT-AAT
1 ATCGCAAGCGAAATGAAA
*
14770 TTCGCAACGCGAAATGAAA
1 ATCGCAA-GCGAAATGAAA
**
14789 ATCGCAA-CG--A-GGGA
1 ATCGCAAGCGAAATGAAA
*
14803 ATCGTAATGCGAAATGAAA
1 ATCGCAA-GCGAAATGAAA
14822 ATCGCAACGCGAA
1 ATCGCAA-GCGAA
14835 TTTAATTTCG
Statistics
Matches: 82, Mismatches: 15, Indels: 30
0.65 0.12 0.24
Matches are distributed among these distances:
14 26 0.32
15 3 0.04
16 6 0.07
17 6 0.07
18 3 0.04
19 38 0.46
ACGTcount: A:0.43, C:0.20, G:0.23, T:0.15
Consensus pattern (18 bp):
ATCGCAAGCGAAATGAAA
Found at i:14746 original size:33 final size:33
Alignment explanation
Indices: 14704--14830 Score: 184
Period size: 33 Copynumber: 3.8 Consensus size: 33
14694 GGAAATTACT
14704 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
**
14737 ATCGCAATGCGAAATGAAAATCGCAACGCTA-A
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* * *
14769 TTTCGCAACGCGAAATGAAAATCGCAACGAGGGA
1 -ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
14803 ATCGTAATGCGAAATGAAAATCGCAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
14831 CGAATTTAAT
Statistics
Matches: 82, Mismatches: 10, Indels: 4
0.85 0.10 0.04
Matches are distributed among these distances:
32 1 0.01
33 80 0.98
34 1 0.01
ACGTcount: A:0.43, C:0.20, G:0.23, T:0.15
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:14812 original size:66 final size:66
Alignment explanation
Indices: 14705--14837 Score: 230
Period size: 66 Copynumber: 2.0 Consensus size: 66
14695 GAAATTACTA
* *
14705 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCTAAT
1 TCGCAACGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
14770 T
66 T
* *
14771 TCGCAACGCGAAATGAAAATCGCAACGAGGGAATCGTAATGCGAAATGAAAATCGCAACGCGAAT
1 TCGCAACGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
14836 T
66 T
14837 T
1 T
14838 AATTTCGCGT
Statistics
Matches: 63, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
66 63 1.00
ACGTcount: A:0.41, C:0.20, G:0.23, T:0.17
Consensus pattern (66 bp):
TCGCAACGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
T
Found at i:14852 original size:19 final size:20
Alignment explanation
Indices: 14830--14872 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
14820 AAATCGCAAC
14830 GCGAATTT-AATTTCGCGTT
1 GCGAATTTCAATTTCGCGTT
* *
14849 GCGATTTTCATTTTCGCGTT
1 GCGAATTTCAATTTCGCGTT
14869 GCGA
1 GCGA
14873 TTCTCTCGTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 7 0.33
20 14 0.67
ACGTcount: A:0.16, C:0.19, G:0.23, T:0.42
Consensus pattern (20 bp):
GCGAATTTCAATTTCGCGTT
Found at i:14857 original size:14 final size:14
Alignment explanation
Indices: 14858--14891 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
14848 TGCGATTTTC
14858 ATTTTCGCGTTGCG
1 ATTTTCGCGTTGCG
* *
14872 ATTCTCTCGTTGCG
1 ATTTTCGCGTTGCG
14886 ATTTTC
1 ATTTTC
14892 ATTTCGCATT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.09, C:0.24, G:0.21, T:0.47
Consensus pattern (14 bp):
ATTTTCGCGTTGCG
Found at i:15032 original size:14 final size:14
Alignment explanation
Indices: 15013--15049 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
15003 CATCAATTAA
15013 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
15027 ACAAATCACCTTTT
1 ACAAATCAACTTTT
15041 ACAAATCAA
1 ACAAATCAA
15050 TTAAACAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.24, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:16466 original size:21 final size:21
Alignment explanation
Indices: 16400--16466 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
16390 GTGAATCGGG
*
16400 CTCTTGAATGGTGGGA-GGGA
1 CTCTTGAACGGTGGGAGGGGA
* * ** * *
16420 CCTCTTCAACGATGACAGTGGC
1 -CTCTTGAACGGTGGGAGGGGA
16442 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGGGAGGGGA
16463 CTCT
1 CTCT
16467 CGAGGAATGA
Statistics
Matches: 32, Mismatches: 13, Indels: 2
0.68 0.28 0.04
Matches are distributed among these distances:
21 30 0.94
22 2 0.06
ACGTcount: A:0.19, C:0.21, G:0.36, T:0.24
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGGGGA
Found at i:16485 original size:42 final size:41
Alignment explanation
Indices: 16400--16522 Score: 113
Period size: 42 Copynumber: 2.9 Consensus size: 41
16390 GTGAATCGGG
* * * * *
16400 CTCTTGAATGGTGGGA-GGGACCTCTTCAACGATGACAGTGGC
1 CTCTTGAACGGTGGGAGGGGA-CTC-TCGAGGATGATAGGGGC
16442 CTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGC
1 CTCTTGAACGGTGGGAGGGGACTCTCGAGG-ATGATAGGGGC
* * * * *
16484 CTCTTCAACGATAGGAGTGGACTCTTGAGGGATGATAGG
1 CTCTTGAACGGTGGGAGGGGACTCTCGA-GGATGATAGG
16523 CGAGTCGGGC
Statistics
Matches: 68, Mismatches: 10, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
41 4 0.06
42 58 0.85
43 6 0.09
ACGTcount: A:0.23, C:0.18, G:0.37, T:0.23
Consensus pattern (41 bp):
CTCTTGAACGGTGGGAGGGGACTCTCGAGGATGATAGGGGC
Found at i:18600 original size:33 final size:33
Alignment explanation
Indices: 18543--18641 Score: 144
Period size: 33 Copynumber: 3.0 Consensus size: 33
18533 ACGAGATAAT
*
18543 GAGAATCGCAACGCGGAAATGACTATCGCAACGA
1 GAGAATCGCAACGC-GAAATGACTATCGCAACCA
*
18577 GAGAATCGCAACGCGAAATGACTATCGCGACCA
1 GAGAATCGCAACGCGAAATGACTATCGCAACCA
* **
18610 GACAATCGCAACGCGAAATGAAAATCGCAACC
1 GAGAATCGCAACGCGAAATGACTATCGCAACC
18642 GCAAAATAAA
Statistics
Matches: 59, Mismatches: 6, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
33 45 0.76
34 14 0.24
ACGTcount: A:0.39, C:0.26, G:0.23, T:0.11
Consensus pattern (33 bp):
GAGAATCGCAACGCGAAATGACTATCGCAACCA
Found at i:18635 original size:19 final size:19
Alignment explanation
Indices: 18518--18721 Score: 194
Period size: 19 Copynumber: 11.1 Consensus size: 19
18508 TCTTTTGGTT
*
18518 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGC
*
18537 GATAATGAGAATCGCAACGC
1 GA-AATGAAAATCGCAACGC
**
18557 GGAAATGACTATCGCAA--C
1 -GAAATGAAAATCGCAACGC
*
18575 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
** *
18591 GAAATGACTATCGCGAC-C
1 GAAATGAAAATCGCAACGC
*
18609 ---A-GACAATCGCAACGC
1 GAAATGAAAATCGCAACGC
18624 GAAATGAAAATCGCAACCGC
1 GAAATGAAAATCGCAA-CGC
* *
18644 AAAATAAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
18663 GAAATGAAAATCGCTACGC
1 GAAATGAAAATCGCAACGC
18682 GAAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
18701 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGC
18720 GA
1 GA
18722 TTTTGGTTTC
Statistics
Matches: 153, Mismatches: 19, Indels: 26
0.77 0.10 0.13
Matches are distributed among these distances:
14 19 0.12
15 3 0.02
16 2 0.01
17 1 0.01
18 4 0.03
19 78 0.51
20 44 0.29
21 2 0.01
ACGTcount: A:0.44, C:0.22, G:0.22, T:0.12
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:18733 original size:19 final size:19
Alignment explanation
Indices: 18711--18761 Score: 66
Period size: 19 Copynumber: 2.7 Consensus size: 19
18701 GAAATGAAAA
* *
18711 TCGCAATGCGATTTTGGTT
1 TCGCATTGCGATTTTGATT
* *
18730 TCGCGTTGCGATTTTTATT
1 TCGCATTGCGATTTTGATT
18749 TCGCATTGCGATT
1 TCGCATTGCGATT
18762 ATCTCGTTGC
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.14, C:0.18, G:0.24, T:0.45
Consensus pattern (19 bp):
TCGCATTGCGATTTTGATT
Found at i:19407 original size:41 final size:41
Alignment explanation
Indices: 19315--19409 Score: 102
Period size: 41 Copynumber: 2.3 Consensus size: 41
19305 CGCTATGTAA
* * * * ** *
19315 ATCGCGTTGCGAAAGTCAGTATCTCGTTGCGATTTTGTATT
1 ATCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCAAT
*
19356 ATCGCATTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
1 ATCGCGTTGCGATAGTAAGTATCGCATTGCGATTTT-CCAAT
19398 -TCGCGTTGCGAT
1 ATCGCGTTGCGAT
19410 TTACTTATTC
Statistics
Matches: 44, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
41 42 0.95
42 2 0.05
ACGTcount: A:0.21, C:0.20, G:0.23, T:0.36
Consensus pattern (41 bp):
ATCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCAAT
Found at i:19775 original size:50 final size:50
Alignment explanation
Indices: 19715--19816 Score: 186
Period size: 50 Copynumber: 2.0 Consensus size: 50
19705 GTTCCCACTA
* *
19715 TTGGCATAGAAAATAAAGTGGTCATTGTCAAATTTCAAGTAGAAATATCT
1 TTGGCATAGAAAATAAAGGGGTCATTGTCAAATTTCAAATAGAAATATCT
19765 TTGGCATAGAAAATAAAGGGGTCATTGTCAAATTTCAAATAGAAATATCT
1 TTGGCATAGAAAATAAAGGGGTCATTGTCAAATTTCAAATAGAAATATCT
19815 TT
1 TT
19817 AATATGTGCA
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
50 50 1.00
ACGTcount: A:0.40, C:0.10, G:0.18, T:0.32
Consensus pattern (50 bp):
TTGGCATAGAAAATAAAGGGGTCATTGTCAAATTTCAAATAGAAATATCT
Found at i:28416 original size:33 final size:32
Alignment explanation
Indices: 28343--28420 Score: 84
Period size: 33 Copynumber: 2.4 Consensus size: 32
28333 TGACACTACA
* * * *
28343 TCTATCTGAGTCACCAAATTCATAACATTACC
1 TCTATTTGAGGCACCAAAATCATAACATTAAC
* * *
28375 TCTCTTTGAGGCACTCAAAATCATACCCTTAAC
1 TCTATTTGAGGCAC-CAAAATCATAACATTAAC
28408 TCTATTTGAGGCA
1 TCTATTTGAGGCA
28421 ATAGGGTCAC
Statistics
Matches: 37, Mismatches: 8, Indels: 1
0.80 0.17 0.02
Matches are distributed among these distances:
32 11 0.30
33 26 0.70
ACGTcount: A:0.31, C:0.27, G:0.10, T:0.32
Consensus pattern (32 bp):
TCTATTTGAGGCACCAAAATCATAACATTAAC
Found at i:31700 original size:261 final size:258
Alignment explanation
Indices: 31200--32017 Score: 1115
Period size: 261 Copynumber: 3.2 Consensus size: 258
31190 TTATATAATT
* * *
31200 TGAAAAATGAGAAAGCGATTTTTAAAGTTTCTCATTTAATATTTTTAGAAAATGAAATTTTTGAA
1 TGAAAAATGAGAAAGCAATTTTCAAAGTTTCTCATTTAATATTTTCAGAAAATGAAATTTTTGAA
* * * *
31265 GAGTAAGAAAGTGATTTCCAAAGTTTCTTACCTAGTAAGCTATTTCCAAAATTTGTAAGTCCTTC
66 AAGTAAGAAAGTGATTTCCAAAGTTTCTTACCTAGTAAACTATTTCCAAAA-TAGTAAGTCCTTT
* * * * * * *
31330 GGGCTATCAATAAGTCTTTCGAGCATGATGATTAATTCCTTCGGGTCATCTGTCACTCTTTTGAG
130 GGGCCATCAGTAAGCCTTTCGAGCATGATGATTAATTCATTCGGGTCATCTTTCAATCTTTCGAG
* *
31395 CAGGATGATAAGTCCTTCGGGCCATCTATAAGACCTTTGGGCAAGATGCTTTCATATGATGTTTG
195 CAAGATGATAAGT-CTTCGGGCCATCTATAAGACCTTTGGGCAAGATGCTTTCATATGATATTTG
* *
31460 TGAAAAATGAGAAAAACAATTTTCAAAGTTTCTCATTTAATATTTTCAGAAAATGAAATATTTGA
1 TGAAAAATGAG-AAAGCAATTTTCAAAGTTTCTCATTTAATATTTTCAGAAAATGAAATTTTTGA
* * * * *
31525 AAAGTAAGAAAGCGATTTCCAAAGTTTCTTACCCAATAAAATATTTCCAAAACTAGTAAGTCATT
65 AAAGTAAGAAAGTGATTTCCAAAGTTTCTTACCTAGTAAACTATTTCCAAAA-TAGTAAGTCCTT
* * *
31590 TAGGCCATCAGTAAGCCTTTCGATCATGATGATTAAATCATTCGGGTCATCTTTCAATCTTTCGA
129 TGGGCCATCAGTAAGCCTTTCGAGCATGATGATTAATTCATTCGGGTCATCTTTCAATCTTTCGA
* *
31655 GCAAGATGATAAGTCTTCGGGCCATCTATGAGACCTTTGGGGCAAGATACTTTCATAT-A-ATTT
194 GCAAGATGATAAGTCTTCGGGCCATCTATAAGACCTTT-GGGCAAGATGCTTTCATATGATATTT
31718 -
258 G
* * ** *
31718 TAAAAAATGAGAAAGTAATTTTCAAAGTTTCTCATTTGGTATTTTCAAAAAATGAAATTTTTGAA
1 TGAAAAATGAGAAAGCAATTTTCAAAGTTTCTCATTTAATATTTTCAGAAAATGAAATTTTTGAA
* * * *
31783 AAGTAA-AAAATTATTTTCAAAGTTTCTTACCTAGTAAACTATTTCCAAAATCGGTAAGTCCTTT
66 AAGTAAGAAAGTGATTTCCAAAGTTTCTTACCTAGTAAACTATTTCCAAAAT-AGTAAGTCCTTT
* * *
31847 GGGCCATCAGTAAGCCTTTCAAGCATGATGATTAATTCTTTCGGGTCATCTTTCATTCTTTCGAG
130 GGGCCATCAGTAAGCCTTTCGAGCATGATGATTAATTCATTCGGGTCATCTTTCAATCTTTCGAG
* * * *
31912 CAAGGTGATAAGTCATTCAGGCCATCTATAAGACGTTTGGGCAAGATGCTTTCATATGGTATTTG
195 CAAGATGATAAGTC-TTCGGGCCATCTATAAGACCTTTGGGCAAGATGCTTTCATATGATATTTG
*
31977 T-AAGAGAATGAGAAAGCGATTTTCAAAGTTTCTCATTTAAT
1 TGAA-A-AATGAGAAAGCAATTTTCAAAGTTTCTCATTTAAT
32018 TAAAAAAAGA
Statistics
Matches: 488, Mismatches: 61, Indels: 18
0.86 0.11 0.03
Matches are distributed among these distances:
255 1 0.00
256 137 0.28
257 74 0.15
258 16 0.03
259 5 0.01
260 66 0.14
261 189 0.39
ACGTcount: A:0.33, C:0.15, G:0.17, T:0.35
Consensus pattern (258 bp):
TGAAAAATGAGAAAGCAATTTTCAAAGTTTCTCATTTAATATTTTCAGAAAATGAAATTTTTGAA
AAGTAAGAAAGTGATTTCCAAAGTTTCTTACCTAGTAAACTATTTCCAAAATAGTAAGTCCTTTG
GGCCATCAGTAAGCCTTTCGAGCATGATGATTAATTCATTCGGGTCATCTTTCAATCTTTCGAGC
AAGATGATAAGTCTTCGGGCCATCTATAAGACCTTTGGGCAAGATGCTTTCATATGATATTTG
Found at i:32081 original size:26 final size:26
Alignment explanation
Indices: 32032--32096 Score: 78
Period size: 27 Copynumber: 2.5 Consensus size: 26
32022 AAAAGAGAAA
*
32032 AGAAAAGAAAAATGGAGAGAAAAAAG
1 AGAAAAGAAAAATGAAGAGAAAAAAG
*
32058 AGAGAAAGAAAAATGAAGTGAAAAATAG
1 AGA-AAAGAAAAATGAAGAGAAAAA-AG
*
32086 A-AAGAGAAAAA
1 AGAAAAGAAAAA
32097 AGAGAAGGAA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
26 11 0.32
27 20 0.59
28 3 0.09
ACGTcount: A:0.69, C:0.00, G:0.25, T:0.06
Consensus pattern (26 bp):
AGAAAAGAAAAATGAAGAGAAAAAAG
Found at i:32096 original size:27 final size:26
Alignment explanation
Indices: 32029--32114 Score: 70
Period size: 27 Copynumber: 3.3 Consensus size: 26
32019 AAAAAAAGAG
*
32029 AAAAGAAA-AG-AAAAATGGAGAGAA
1 AAAAGAAAGAGAAAAAATGAAGAGAA
* * *
32053 AAAAGAGAGAAAGAAAAATGAAGTGAA
1 AAAAGAAAGAGA-AAAAATGAAGAGAA
*
32080 AAATAGAAAGAGAAAAAAGAGAAG-GAA
1 AAA-AGAAAGAGAAAAAA-TGAAGAGAA
*
32107 GAAAGAAA
1 AAAAGAAA
32115 TTAAATAAAA
Statistics
Matches: 49, Mismatches: 8, Indels: 8
0.75 0.12 0.12
Matches are distributed among these distances:
24 7 0.14
25 1 0.02
26 5 0.10
27 25 0.51
28 11 0.22
ACGTcount: A:0.70, C:0.00, G:0.26, T:0.05
Consensus pattern (26 bp):
AAAAGAAAGAGAAAAAATGAAGAGAA
Found at i:40227 original size:13 final size:13
Alignment explanation
Indices: 40209--40242 Score: 59
Period size: 13 Copynumber: 2.6 Consensus size: 13
40199 ACCCATTTTT
*
40209 TTTATTTTCTAAA
1 TTTATTTTCAAAA
40222 TTTATTTTCAAAA
1 TTTATTTTCAAAA
40235 TTTATTTT
1 TTTATTTT
40243 AATTCATGTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.29, C:0.06, G:0.00, T:0.65
Consensus pattern (13 bp):
TTTATTTTCAAAA
Found at i:43000 original size:18 final size:17
Alignment explanation
Indices: 42979--43016 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
42969 ATTTTTGAAA
42979 AATTTCCTTTGGATTTTT
1 AATTT-CTTTGGATTTTT
*
42997 AATTTTTTTGGATTTTT
1 AATTTCTTTGGATTTTT
43014 AAT
1 AAT
43017 CATGCAGTGA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 14 0.74
18 5 0.26
ACGTcount: A:0.21, C:0.05, G:0.11, T:0.63
Consensus pattern (17 bp):
AATTTCTTTGGATTTTT
Found at i:44823 original size:22 final size:22
Alignment explanation
Indices: 44798--44840 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
44788 CTGGTTATTA
*
44798 TATACATGATTTTTATCATGAT
1 TATACATGATGTTTATCATGAT
* *
44820 TATATATGATGTTTATTATGA
1 TATACATGATGTTTATCATGA
44841 ATGTTAATTC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.33, C:0.05, G:0.12, T:0.51
Consensus pattern (22 bp):
TATACATGATGTTTATCATGAT
Found at i:45146 original size:61 final size:61
Alignment explanation
Indices: 45022--45147 Score: 162
Period size: 61 Copynumber: 2.1 Consensus size: 61
45012 CACTAAGTGC
* * ** *
45022 AGGTGATGGGCACGACCTTATGTGTCTTATCCGAATTAGCACTATAGTGGAAACCTAGTGT
1 AGGTGATGGGCACGACCTTATGTGTCATATCCGAATTAGCACTAGAGCAGAAACCTAGAGT
* * * * *
45083 AGGTGGTGGGCACGACCTTATGTGTCATATCCGGATTAGCACTAGAGCATAAGCTTAGAGT
1 AGGTGATGGGCACGACCTTATGTGTCATATCCGAATTAGCACTAGAGCAGAAACCTAGAGT
45144 AGGT
1 AGGT
45148 TTAGCACTAC
Statistics
Matches: 55, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
61 55 1.00
ACGTcount: A:0.26, C:0.17, G:0.29, T:0.28
Consensus pattern (61 bp):
AGGTGATGGGCACGACCTTATGTGTCATATCCGAATTAGCACTAGAGCAGAAACCTAGAGT
Found at i:47265 original size:2 final size:2
Alignment explanation
Indices: 47258--47291 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
47248 GGGGATAAGA
47258 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
47292 CAAGGCAGCA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:50548 original size:18 final size:18
Alignment explanation
Indices: 50525--50564 Score: 80
Period size: 18 Copynumber: 2.2 Consensus size: 18
50515 GTCGGTCACC
50525 TTCGTAATTAGTTTTAAT
1 TTCGTAATTAGTTTTAAT
50543 TTCGTAATTAGTTTTAAT
1 TTCGTAATTAGTTTTAAT
50561 TTCG
1 TTCG
50565 ATTTTGGCCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.25, C:0.07, G:0.12, T:0.55
Consensus pattern (18 bp):
TTCGTAATTAGTTTTAAT
Found at i:50697 original size:14 final size:14
Alignment explanation
Indices: 50663--50712 Score: 55
Period size: 14 Copynumber: 3.5 Consensus size: 14
50653 TCCAGTCACT
* *
50663 GAGTCAACTCAGTC
1 GAGTCAACCCATTC
50677 TGAGTCAACCCATTC
1 -GAGTCAACCCATTC
* *
50692 GAGTCAACCCGTCC
1 GAGTCAACCCATTC
50706 GAGTCAA
1 GAGTCAA
50713 TTCGTTGACT
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
14 19 0.61
15 12 0.39
ACGTcount: A:0.28, C:0.32, G:0.20, T:0.20
Consensus pattern (14 bp):
GAGTCAACCCATTC
Found at i:56960 original size:113 final size:114
Alignment explanation
Indices: 56752--57182 Score: 661
Period size: 114 Copynumber: 3.8 Consensus size: 114
56742 TAATTCTCAG
56752 GTTTGACCCCGATTCAATGGATCAACTCCCTCCAGATCTGATATTCCCTTCAGAGTAAGCGGAAC
1 GTTTG-CCCCGATTCAATGGATCAACTCCCTCCAGATCTGATATTCCCTTCAGAGTAAGCGGAAC
* *
56817 AGGTCTCTCTTTTCCAATATTTGATATTCCCTTCAGAGTAAGTGGAACAA
65 ATGTCTCTCTTTTCCAAGATTTGATATTCCCTTCAGAGTAAGTGGAACAA
* *
56867 GTTTGCCTCGATTCAATGGATCAACTCCC-CCAAAATC-GATATTCCCTTCAGAGTAAGCGGAAC
1 GTTTGCCCCGATTCAATGGATCAACTCCCTCC-AGATCTGATATTCCCTTCAGAGTAAGCGGAAC
* * *
56930 AAGTATATCTTTTCCAAGATTTGATATTCCCTTCAGAGTAAGTGGAACAA
65 ATGTCTCTCTTTTCCAAGATTTGATATTCCCTTCAGAGTAAGTGGAACAA
* *
56980 GTCTACCCCGATTCAATGGATCAACTCCCTCCAGATCTGATATTCCCTTCAGAGTAAGCGGAACA
1 GTTTGCCCCGATTCAATGGATCAACTCCCTCCAGATCTGATATTCCCTTCAGAGTAAGCGGAACA
* *
57045 TGTCTCTCTTTTCCAAGATTTGATATTCCCTTCAGAATAAAG-CGAACAA
66 TGTCTCTCTTTTCCAAGATTTGATATTCCCTTCAGAGT-AAGTGGAACAA
* * *
57094 GTATGCCCCGATTCAATGGATCAACTCCCTCCAGATCTGATATTCCCTTAAGAGTAAGCGGGACA
1 GTTTGCCCCGATTCAATGGATCAACTCCCTCCAGATCTGATATTCCCTTCAGAGTAAGCGGAACA
* * *
57159 TGTCTTTCCTCTCCAAGATTTGAT
66 TGTCTCTCTTTTCCAAGATTTGAT
57183 TTCAGAAAGA
Statistics
Matches: 290, Mismatches: 22, Indels: 9
0.90 0.07 0.03
Matches are distributed among these distances:
113 104 0.36
114 178 0.61
115 8 0.03
ACGTcount: A:0.28, C:0.26, G:0.17, T:0.30
Consensus pattern (114 bp):
GTTTGCCCCGATTCAATGGATCAACTCCCTCCAGATCTGATATTCCCTTCAGAGTAAGCGGAACA
TGTCTCTCTTTTCCAAGATTTGATATTCCCTTCAGAGTAAGTGGAACAA
Found at i:69517 original size:14 final size:13
Alignment explanation
Indices: 69496--69534 Score: 55
Period size: 14 Copynumber: 3.1 Consensus size: 13
69486 TTTCAAGAGG
69496 TATTCTATTTATT
1 TATTCTATTTATT
69509 TATTTCTATTTA-T
1 TA-TTCTATTTATT
69522 TATT-TATTTATT
1 TATTCTATTTATT
69534 T
1 T
69535 TCGAAGCAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
11 6 0.25
12 4 0.17
13 5 0.21
14 9 0.38
ACGTcount: A:0.23, C:0.05, G:0.00, T:0.72
Consensus pattern (13 bp):
TATTCTATTTATT
Found at i:70453 original size:18 final size:18
Alignment explanation
Indices: 70426--70463 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
70416 TTAAGTCATA
70426 TTTTCATGTT-TTTAAAT
1 TTTTCATGTTGTTTAAAT
*
70443 TTTTGCATGTTGTTTACAT
1 TTTT-CATGTTGTTTAAAT
70462 TT
1 TT
70464 AGTTCATTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 4 0.22
18 6 0.33
19 8 0.44
ACGTcount: A:0.18, C:0.08, G:0.11, T:0.63
Consensus pattern (18 bp):
TTTTCATGTTGTTTAAAT
Found at i:77986 original size:20 final size:20
Alignment explanation
Indices: 77961--77998 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
77951 GGATCATATA
77961 TTTTGAATT-TTTGAAAGATC
1 TTTTG-ATTCTTTGAAAGATC
77981 TTTTGATTCTTTGAAAGA
1 TTTTGATTCTTTGAAAGA
77999 AAATTTAGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 3 0.18
20 14 0.82
ACGTcount: A:0.29, C:0.05, G:0.16, T:0.50
Consensus pattern (20 bp):
TTTTGATTCTTTGAAAGATC
Found at i:78298 original size:15 final size:15
Alignment explanation
Indices: 78280--78308 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
78270 TGATAAAAAA
78280 TAAAAATCTAAAATC
1 TAAAAATCTAAAATC
78295 TAAAAATCTAAAAT
1 TAAAAATCTAAAAT
78309 ATATAATAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.62, C:0.10, G:0.00, T:0.28
Consensus pattern (15 bp):
TAAAAATCTAAAATC
Found at i:80009 original size:20 final size:21
Alignment explanation
Indices: 79971--80010 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
79961 CACTATAACT
79971 GACCTAAAATTACTATTTTTG
1 GACCTAAAATTACTATTTTTG
*
79992 GACCTAAAA-TATTATTTTT
1 GACCTAAAATTACTATTTTT
80011 CTACAAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 9 0.50
21 9 0.50
ACGTcount: A:0.35, C:0.12, G:0.07, T:0.45
Consensus pattern (21 bp):
GACCTAAAATTACTATTTTTG
Found at i:80115 original size:45 final size:45
Alignment explanation
Indices: 80056--80161 Score: 117
Period size: 45 Copynumber: 2.4 Consensus size: 45
80046 AAATTGATTG
*
80056 AAAAAAT-ATCATTTTTGATAGCGACAAATATTAATATTTT-GAGTA
1 AAAAAATAAT-ATTTTAGATAGCGACAAATATTAATATTTTCGA-TA
* * *** *
80101 GAAAAATAATATTTTAGGTAGCGTTTAATATTTATATTTTCGATA
1 AAAAAATAATATTTTAGATAGCGACAAATATTAATATTTTCGATA
80146 AAAAAATAATATTTTA
1 AAAAAATAATATTTTA
80162 ATTAATATTT
Statistics
Matches: 51, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
45 47 0.92
46 4 0.08
ACGTcount: A:0.44, C:0.05, G:0.10, T:0.41
Consensus pattern (45 bp):
AAAAAATAATATTTTAGATAGCGACAAATATTAATATTTTCGATA
Found at i:82522 original size:41 final size:41
Alignment explanation
Indices: 82471--82551 Score: 108
Period size: 41 Copynumber: 2.0 Consensus size: 41
82461 CAACAAACGT
* * *
82471 CGCAATAGAGTAGTACGTTAGCGACGTTTATATACAAATGC
1 CGCAACAGAGTAATACGTTAGCGACATTTATATACAAATGC
* * *
82512 CGCAACAGAGTAATACTTTAGCGGCATTTTTATACAAATG
1 CGCAACAGAGTAATACGTTAGCGACATTTATATACAAATG
82552 TCGTAAGATG
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
41 34 1.00
ACGTcount: A:0.35, C:0.17, G:0.20, T:0.28
Consensus pattern (41 bp):
CGCAACAGAGTAATACGTTAGCGACATTTATATACAAATGC
Found at i:85883 original size:59 final size:57
Alignment explanation
Indices: 85820--86034 Score: 175
Period size: 59 Copynumber: 3.6 Consensus size: 57
85810 ATATTGAAAA
* *
85820 TATGGATTTCTAGATAGGGCATTTTATGTGCTAAAATGGTAAGAGAATCATACTGAGTG
1 TATGGATTT-TAGATAGGGCATTTCATGTGCTAAAATGGTAAGAGAATCATACT-AATG
** * * * * * *
85879 TATGGATTTCTAGATAAAGCA-CTAAGGGTACTACAA-GGATAAG-GAAATCACACTAATGG
1 TATGGATTT-TAGATAGGGCATTTCA-TGTGCTAAAATGG-TAAGAG-AATCATACTAAT-G
* * *
85938 TATGGATTTTCACATAGGGCATTTCATGTGCTAAAATGGTAACAGAAGCATACTAATG
1 TATGGATTTT-AGATAGGGCATTTCATGTGCTAAAATGGTAAGAGAATCATACTAATG
* * *
85996 ATATGGATTTTCGAATAGGGCACTTCGTGTGCTAAAATG
1 -TATGGATTTTAG-ATAGGGCATTTCATGTGCTAAAATG
86035 AAAGGGGAAG
Statistics
Matches: 122, Mismatches: 24, Indels: 20
0.73 0.14 0.12
Matches are distributed among these distances:
58 9 0.07
59 108 0.89
60 5 0.04
ACGTcount: A:0.34, C:0.12, G:0.23, T:0.30
Consensus pattern (57 bp):
TATGGATTTTAGATAGGGCATTTCATGTGCTAAAATGGTAAGAGAATCATACTAATG
Found at i:86222 original size:17 final size:18
Alignment explanation
Indices: 86197--86230 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
86187 ATTATAATAT
86197 ATTCATTGGA-ATTAAAG
1 ATTCATTGGAGATTAAAG
*
86214 ATTCCTTGGAGATTAAA
1 ATTCATTGGAGATTAAA
86231 TATCATAATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.38, C:0.09, G:0.18, T:0.35
Consensus pattern (18 bp):
ATTCATTGGAGATTAAAG
Found at i:93070 original size:59 final size:58
Alignment explanation
Indices: 92830--93106 Score: 204
Period size: 59 Copynumber: 4.7 Consensus size: 58
92820 TGTCACTTTG
* * ** * * *
92830 TGTGCTAAAATGATAAGGAAATCATACTGAGTGTATATATTTCCATAT-GGAGCA-CTGA
1 TGTGCTAAAATGGTAAGGAAATCATACTAAG-GTATGGATTTCCAAATAGG-GCATTTTA
* * **
92888 GTGTGCT-AAATGATAAGGAAATCATATTGAAAATATGGATTTCCAAATAGGGCATTTTA
1 -TGTGCTAAAATGGTAAGGAAATCATACT-AAGGTATGGATTTCCAAATAGGGCATTTTA
* * * * ** * *
92947 TGTGCTAAAATGGTAAGGGAATCATACTGAGTGTATGAATTTCCATATAAAGCA-CTAA
1 TGTGCTAAAATGGTAAGGAAATCATACTAAG-GTATGGATTTCCAAATAGGGCATTTTA
* * * * *
93005 GGGTGCTATAA-GGATAAGGAAATCATAATAATGGTATGGATTTTCACATAGGGCATTTTA
1 -TGTGCTAAAATGG-TAAGGAAATCATACTAA-GGTATGGATTTCCAAATAGGGCATTTTA
**
93065 TGTGCTAAAATGGTAACAAAATCATACTAATGGTATGGATTT
1 TGTGCTAAAATGGTAAGGAAATCATACTAA-GGTATGGATTT
93107 TTGAATAGGG
Statistics
Matches: 170, Mismatches: 38, Indels: 20
0.75 0.17 0.09
Matches are distributed among these distances:
58 46 0.27
59 119 0.70
60 5 0.03
ACGTcount: A:0.37, C:0.10, G:0.21, T:0.31
Consensus pattern (58 bp):
TGTGCTAAAATGGTAAGGAAATCATACTAAGGTATGGATTTCCAAATAGGGCATTTTA
Found at i:93101 original size:118 final size:117
Alignment explanation
Indices: 92830--93092 Score: 359
Period size: 118 Copynumber: 2.2 Consensus size: 117
92820 TGTCACTTTG
* ** * *
92830 TGTGCTAAAATGATAAGGAAATCATACTGAGTGTAT-ATATTTCCATATGGAGCACTGAGTGTGC
1 TGTGCTAAAATGGTAAGGAAATCATACTGAGTGTATGA-ATTTCCATATAAAGCACTAAGGGTGC
* *
92894 TAAATGATAAGGAAATCATATTGAAAATATGGATTTCCAAATAGGGCATTTTA
65 TAAAGGATAAGGAAATCATAATGAAAATATGGATTTCCAAATAGGGCATTTTA
*
92947 TGTGCTAAAATGGTAAGGGAATCATACTGAGTGTATGAATTTCCATATAAAGCACTAAGGGTGCT
1 TGTGCTAAAATGGTAAGGAAATCATACTGAGTGTATGAATTTCCATATAAAGCACTAAGGGTGCT
** * *
93012 ATAAGGATAAGGAAATCATAAT-AATGGTATGGATTTTCACATAGGGCATTTTA
66 A-AAGGATAAGGAAATCATAATGAA-AATATGGATTTCCAAATAGGGCATTTTA
**
93065 TGTGCTAAAATGGTAACAAAATCATACT
1 TGTGCTAAAATGGTAAGGAAATCATACT
93093 AATGGTATGG
Statistics
Matches: 128, Mismatches: 15, Indels: 5
0.86 0.10 0.03
Matches are distributed among these distances:
117 60 0.47
118 68 0.53
ACGTcount: A:0.38, C:0.11, G:0.21, T:0.31
Consensus pattern (117 bp):
TGTGCTAAAATGGTAAGGAAATCATACTGAGTGTATGAATTTCCATATAAAGCACTAAGGGTGCT
AAAGGATAAGGAAATCATAATGAAAATATGGATTTCCAAATAGGGCATTTTA
Found at i:93115 original size:59 final size:59
Alignment explanation
Indices: 93024--93135 Score: 154
Period size: 59 Copynumber: 1.9 Consensus size: 59
93014 AAGGATAAGG
* *
93024 AAATCATAATAATGGTATGGATTTTCACATAGGGCATTTTATGTGCTAAAATGGTAACA
1 AAATCATAATAATGGTATGGATTTTCACATAGGGCACTTCATGTGCTAAAATGGTAACA
* * * *
93083 AAATCATACTAATGGTATGGATTTTTGA-ATAGGGTACTTCGTGTGCTAAAATG
1 AAATCATAATAATGGTATGGA-TTTTCACATAGGGCACTTCATGTGCTAAAATG
93136 AAAGAGTAAG
Statistics
Matches: 46, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
59 41 0.89
60 5 0.11
ACGTcount: A:0.35, C:0.10, G:0.21, T:0.35
Consensus pattern (59 bp):
AAATCATAATAATGGTATGGATTTTCACATAGGGCACTTCATGTGCTAAAATGGTAACA
Found at i:93323 original size:17 final size:18
Alignment explanation
Indices: 93298--93331 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
93288 ATTATAGTAT
93298 ATTCATTGGA-ATTAAAG
1 ATTCATTGGAGATTAAAG
*
93315 ATTCCTTGGAGATTAAA
1 ATTCATTGGAGATTAAA
93332 TATAAGAATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.38, C:0.09, G:0.18, T:0.35
Consensus pattern (18 bp):
ATTCATTGGAGATTAAAG
Found at i:94776 original size:43 final size:43
Alignment explanation
Indices: 94688--94908 Score: 176
Period size: 43 Copynumber: 5.1 Consensus size: 43
94678 GTTTGTATAA
* * *
94688 AAAAACGCCGCTATAGATCT-GACCTTTTGCGGTTTTTGTGTCC
1 AAAAACGCCGCTATAGATATCAACCTTTTGCGGTGTTTGT-TCC
* * * *
94731 AAAAACGCCGCTATATATATCAACCTTTTGTGGTGTTTATCCC
1 AAAAACGCCGCTATAGATATCAACCTTTTGCGGTGTTTGTTCC
* * * *
94774 AAAAACACCTCTATAGATATCAACCTTTTGCAGCGTTTGTTCC
1 AAAAACGCCGCTATAGATATCAACCTTTTGCGGTGTTTGTTCC
* * * * ** * *
94817 AGAAATGCCGCTATATATAT-ATCCCTTTTGCGACGTTTATTCA
1 AAAAACGCCGCTATAGATATCA-ACCTTTTGCGGTGTTTGTTCC
* * * * ***
94860 AAAAATGTCGCTATAGATATCGATCTTTTGCGACATTTGTTCC
1 AAAAACGCCGCTATAGATATCAACCTTTTGCGGTGTTTGTTCC
94903 AAAAAC
1 AAAAAC
94909 TCTGCTAACT
Statistics
Matches: 140, Mismatches: 35, Indels: 6
0.77 0.19 0.03
Matches are distributed among these distances:
42 1 0.01
43 124 0.89
44 15 0.11
ACGTcount: A:0.29, C:0.22, G:0.15, T:0.34
Consensus pattern (43 bp):
AAAAACGCCGCTATAGATATCAACCTTTTGCGGTGTTTGTTCC
Found at i:96867 original size:15 final size:15
Alignment explanation
Indices: 96847--96880 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
96837 TTTTAATTAA
*
96847 GAAAAACATATAAAG
1 GAAAAACAAATAAAG
96862 GAAAAACAAATAAAG
1 GAAAAACAAATAAAG
96877 GAAA
1 GAAA
96881 GTATCACACC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.71, C:0.06, G:0.15, T:0.09
Consensus pattern (15 bp):
GAAAAACAAATAAAG
Found at i:104721 original size:21 final size:18
Alignment explanation
Indices: 104681--104721 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 18
104671 TAGTTGCAAT
104681 ATTCTAAATTTATATCAA
1 ATTCTAAATTTATATCAA
104699 ATTCTCAAGATTTATAGTCAA
1 ATTCT-AA-ATTTATA-TCAA
104720 AT
1 AT
104722 CAAACTAAAC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
18 5 0.25
19 2 0.10
20 7 0.35
21 6 0.30
ACGTcount: A:0.41, C:0.12, G:0.05, T:0.41
Consensus pattern (18 bp):
ATTCTAAATTTATATCAA
Found at i:105061 original size:27 final size:27
Alignment explanation
Indices: 105031--105090 Score: 84
Period size: 27 Copynumber: 2.2 Consensus size: 27
105021 GTATTTAGGC
*
105031 CATTTTAGTACTCGAGGTTATTTTAGT
1 CATTTTAGTACTAGAGGTTATTTTAGT
* *
105058 CATTTTGGTGCTAGAGGTTATTTTAGT
1 CATTTTAGTACTAGAGGTTATTTTAGT
*
105085 TATTTT
1 CATTTT
105091 GGGTCTAAGG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.20, C:0.08, G:0.20, T:0.52
Consensus pattern (27 bp):
CATTTTAGTACTAGAGGTTATTTTAGT
Found at i:108809 original size:42 final size:42
Alignment explanation
Indices: 108750--108834 Score: 152
Period size: 42 Copynumber: 2.0 Consensus size: 42
108740 TATGTGTAAG
*
108750 TATACACAATCACACAAATAATAAAGAGTGTGTGAGTATCGT
1 TATACACAATCACACAAATAATAAAGAGTGAGTGAGTATCGT
*
108792 TATACACAATCGCACAAATAATAAAGAGTGAGTGAGTATCGT
1 TATACACAATCACACAAATAATAAAGAGTGAGTGAGTATCGT
108834 T
1 T
108835 CTCACGAGGA
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.42, C:0.14, G:0.18, T:0.26
Consensus pattern (42 bp):
TATACACAATCACACAAATAATAAAGAGTGAGTGAGTATCGT
Found at i:110426 original size:10 final size:10
Alignment explanation
Indices: 110411--110451 Score: 82
Period size: 10 Copynumber: 4.1 Consensus size: 10
110401 TGGATCAAAT
110411 AGAAAATTTG
1 AGAAAATTTG
110421 AGAAAATTTG
1 AGAAAATTTG
110431 AGAAAATTTG
1 AGAAAATTTG
110441 AGAAAATTTG
1 AGAAAATTTG
110451 A
1 A
110452 AGGATGATAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 31 1.00
ACGTcount: A:0.51, C:0.00, G:0.20, T:0.29
Consensus pattern (10 bp):
AGAAAATTTG
Found at i:130344 original size:16 final size:16
Alignment explanation
Indices: 130319--130350 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
130309 AATTATCTAC
130319 AAAATAAAATAAAATA
1 AAAATAAAATAAAATA
*
130335 AAAATTAAATAAAATA
1 AAAATAAAATAAAATA
130351 TTAAATTTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (16 bp):
AAAATAAAATAAAATA
Found at i:130353 original size:12 final size:12
Alignment explanation
Indices: 130320--130356 Score: 53
Period size: 10 Copynumber: 3.3 Consensus size: 12
130310 ATTATCTACA
130320 AAATAAAATA--
1 AAATAAAATATT
130330 AAATAAAA-ATT
1 AAATAAAATATT
130341 AAATAAAATATT
1 AAATAAAATATT
130353 AAAT
1 AAAT
130357 TTAAAATTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
9 1 0.04
10 8 0.33
11 8 0.33
12 7 0.29
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (12 bp):
AAATAAAATATT
Found at i:135929 original size:46 final size:45
Alignment explanation
Indices: 135828--135934 Score: 146
Period size: 45 Copynumber: 2.4 Consensus size: 45
135818 GTTGTACTAA
* *
135828 GAGTGCATCGATGCATGAAGTGCATTCGATGTTTCAAAATAGCCT
1 GAGTGCATCGATGCATCAAATGCATTCGATGTTTCAAAATAGCCT
135873 GAGTGCATCGATGCATCAAATGCATTCGATGTTTTCATTAAA-A-CCT
1 GAGTGCATCGATGCATCAAATGCATTCGATG-TTTCA--AAATAGCCT
*
135919 GAGTGAATCGATGCAT
1 GAGTGCATCGATGCAT
135935 GGAGAGTGAA
Statistics
Matches: 56, Mismatches: 3, Indels: 5
0.88 0.05 0.08
Matches are distributed among these distances:
45 29 0.52
46 23 0.41
47 1 0.02
48 3 0.05
ACGTcount: A:0.30, C:0.18, G:0.22, T:0.30
Consensus pattern (45 bp):
GAGTGCATCGATGCATCAAATGCATTCGATGTTTCAAAATAGCCT
Found at i:142195 original size:116 final size:117
Alignment explanation
Indices: 141978--142198 Score: 315
Period size: 116 Copynumber: 1.9 Consensus size: 117
141968 CTTTCAAATC
*
141978 GAAATTTTCTTTTTCAATATTTTCAAATTTCATTTTTGAAAGCTCTAAATCATTCTTGAAGATTT
1 GAAATTTTCTTTTTCAATATTTTCAAATTTCATTTTTGAAAGCTCTAAATCATTCTTGAAAATTT
*
142043 CATTTTGATTTTCAAAATCCATTTTCGTTTCTAAAAGAAGTTTGTTTAATTT
66 CATTTTGATTTTCAAAATCCAGTTTCGTTTCTAAAAGAAGTTTGTTTAATTT
* * *
142095 GAAATTTT-TTTTTCAA-AGTTTTCAGATTTTATTTTTGAAAGCTCTAACTCATTTCTT-AAAAT
1 GAAATTTTCTTTTTCAATA-TTTTCAAATTTCATTTTTGAAAGCTCTAAATCA-TTCTTGAAAAT
* * *
142157 TTCATTTTGATTTTCTAAATCTAGTTTGGCTTTC-AAAAGAAG
64 TTCATTTTGATTTTCAAAATCCAGTTTCG-TTTCTAAAAGAAG
142199 ATCATTTTTA
Statistics
Matches: 93, Mismatches: 8, Indels: 7
0.86 0.07 0.06
Matches are distributed among these distances:
115 1 0.01
116 75 0.81
117 17 0.18
ACGTcount: A:0.30, C:0.12, G:0.10, T:0.49
Consensus pattern (117 bp):
GAAATTTTCTTTTTCAATATTTTCAAATTTCATTTTTGAAAGCTCTAAATCATTCTTGAAAATTT
CATTTTGATTTTCAAAATCCAGTTTCGTTTCTAAAAGAAGTTTGTTTAATTT
Found at i:143574 original size:65 final size:66
Alignment explanation
Indices: 143485--143628 Score: 161
Period size: 65 Copynumber: 2.2 Consensus size: 66
143475 GGGCCCTTAA
* * * *
143485 TGCATCGATGCAT-GAAGTGCATTCGATGTTTCAAAATA-GC-CTGAGTGCATCGATGCATGGAT
1 TGCATCGATGCATCAAACTACATTCGATG-TTCAAAATATGCACTG-GTGCATCGATGCATAGAT
143547 T-G
64 TGG
** *
143549 TGCATCGATGCATCAAACTACATTCGATGTTCAATTTATTCACTGGTGCATCGATGCATAGATTG
1 TGCATCGATGCATCAAACTACATTCGATGTTCAAAATATGCACTGGTGCATCGATGCATAGATTG
143614 G
66 G
* *
143615 TGCATTGGTGCATC
1 TGCATCGATGCATC
143629 CCTTTGAAAA
Statistics
Matches: 67, Mismatches: 9, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
64 20 0.30
65 31 0.46
66 16 0.24
ACGTcount: A:0.26, C:0.19, G:0.24, T:0.32
Consensus pattern (66 bp):
TGCATCGATGCATCAAACTACATTCGATGTTCAAAATATGCACTGGTGCATCGATGCATAGATTG
G
Found at i:146919 original size:20 final size:20
Alignment explanation
Indices: 146886--146930 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
146876 TTGATGGTAC
* *
146886 TGATATTGACCCTTCAGTAT
1 TGATATTAAACCTTCAGTAT
*
146906 TGATATTAAACCTTGAGTAT
1 TGATATTAAACCTTCAGTAT
*
146926 CGATA
1 TGATA
146931 CCTACCTTTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.38
Consensus pattern (20 bp):
TGATATTAAACCTTCAGTAT
Found at i:156587 original size:16 final size:16
Alignment explanation
Indices: 156562--156600 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 16
156552 AATGACCTAA
156562 AAATAATAATATAATT
1 AAATAATAATATAATT
*
156578 AAATATTAATATAA-T
1 AAATAATAATATAATT
156593 -AATAATAA
1 AAATAATAA
156601 AAAACTAAAC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
14 7 0.33
15 1 0.05
16 13 0.62
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (16 bp):
AAATAATAATATAATT
Found at i:163124 original size:24 final size:24
Alignment explanation
Indices: 163092--163171 Score: 151
Period size: 24 Copynumber: 3.3 Consensus size: 24
163082 CTATTCTTTC
163092 GCTTCAATTGAGCTCAAATTTTAG
1 GCTTCAATTGAGCTCAAATTTTAG
163116 GCTTCAATTGAGCTCAAATTTTAG
1 GCTTCAATTGAGCTCAAATTTTAG
*
163140 GCTTCAATTGAACTCAAATTTTAG
1 GCTTCAATTGAGCTCAAATTTTAG
163164 GCTTCAAT
1 GCTTCAAT
163172 CGAACTTCTA
Statistics
Matches: 55, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
24 55 1.00
ACGTcount: A:0.30, C:0.17, G:0.15, T:0.38
Consensus pattern (24 bp):
GCTTCAATTGAGCTCAAATTTTAG
Found at i:163176 original size:24 final size:24
Alignment explanation
Indices: 163092--163186 Score: 145
Period size: 24 Copynumber: 3.9 Consensus size: 24
163082 CTATTCTTTC
*
163092 GCTTCAATTGAGCTCAAATTTTAG
1 GCTTCAATTGAACTCAAATTTTAG
*
163116 GCTTCAATTGAGCTCAAATTTTAG
1 GCTTCAATTGAACTCAAATTTTAG
163140 GCTTCAATTGAACTCAAATTTTAG
1 GCTTCAATTGAACTCAAATTTTAG
* *
163164 GCTTCAATCGAACTTCTAATTTT
1 GCTTCAATTGAAC-TCAAATTTT
163187 TTTTTAGTTC
Statistics
Matches: 67, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
24 59 0.88
25 8 0.12
ACGTcount: A:0.29, C:0.18, G:0.14, T:0.39
Consensus pattern (24 bp):
GCTTCAATTGAACTCAAATTTTAG
Found at i:164976 original size:15 final size:13
Alignment explanation
Indices: 164930--164978 Score: 53
Period size: 14 Copynumber: 3.5 Consensus size: 13
164920 CAATTCACGT
*
164930 TAAACATATAAAA
1 TAAAAATATAAAA
164943 TAAAAATATAAAAA
1 TAAAAATAT-AAAA
*
164957 AAAAAATAGTAAACA
1 TAAAAATA-TAAA-A
164972 TAAAAAT
1 TAAAAAT
164979 GATCATTTGA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
13 8 0.27
14 14 0.47
15 8 0.27
ACGTcount: A:0.73, C:0.04, G:0.02, T:0.20
Consensus pattern (13 bp):
TAAAAATATAAAA
Found at i:167078 original size:21 final size:21
Alignment explanation
Indices: 167054--167093 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
167044 CATTTCCCTC
167054 ACTTTATGTTTTGTCAACAAA
1 ACTTTATGTTTTGTCAACAAA
167075 ACTTTATGTTTTGTCAACA
1 ACTTTATGTTTTGTCAACA
167094 TTGGACATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.30, C:0.15, G:0.10, T:0.45
Consensus pattern (21 bp):
ACTTTATGTTTTGTCAACAAA
Found at i:169803 original size:31 final size:31
Alignment explanation
Indices: 169746--169804 Score: 77
Period size: 31 Copynumber: 1.9 Consensus size: 31
169736 AAAATGTTAG
169746 TAATAACAGTAAAAATGAAAAATTAGTACAA
1 TAATAACAGTAAAAATGAAAAATTAGTACAA
*
169777 TAATAA-AGTGAATAAAT-AAAAGTTAGTA
1 TAATAACAGT-AA-AAATGAAAAATTAGTA
169805 AGTTAGTTTG
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
30 3 0.12
31 18 0.72
32 4 0.16
ACGTcount: A:0.59, C:0.03, G:0.12, T:0.25
Consensus pattern (31 bp):
TAATAACAGTAAAAATGAAAAATTAGTACAA
Found at i:178424 original size:18 final size:20
Alignment explanation
Indices: 178394--178434 Score: 52
Period size: 18 Copynumber: 2.1 Consensus size: 20
178384 CAAAAGTAAC
178394 CATTCTTAGAAAA-AGTT-T
1 CATTCTTAGAAAAGAGTTCT
178412 CATTCTT-GTAAAAGAGTTCT
1 CATTCTTAG-AAAAGAGTTCT
178432 CAT
1 CAT
178435 CATTACAAGA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
17 1 0.05
18 11 0.55
19 4 0.20
20 4 0.20
ACGTcount: A:0.34, C:0.15, G:0.12, T:0.39
Consensus pattern (20 bp):
CATTCTTAGAAAAGAGTTCT
Found at i:182832 original size:16 final size:18
Alignment explanation
Indices: 182811--182843 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
182801 TTAATTTGTA
182811 TAGTAAA-A-TAAAATGT
1 TAGTAAACAGTAAAATGT
182827 TAGTAAACAGTAAAATG
1 TAGTAAACAGTAAAATG
182844 AAAATTAGTA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
17 1 0.07
18 7 0.47
ACGTcount: A:0.55, C:0.03, G:0.15, T:0.27
Consensus pattern (18 bp):
TAGTAAACAGTAAAATGT
Found at i:206469 original size:2 final size:2
Alignment explanation
Indices: 206457--206488 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
206447 ATATGCCTAT
206457 TA TA T- TA TA TA TA T- 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
206489 ACAAATAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 2 0.07
2 26 0.93
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:206471 original size:9 final size:9
Alignment explanation
Indices: 206457--206487 Score: 55
Period size: 9 Copynumber: 3.6 Consensus size: 9
206447 ATATGCCTAT
206457 TATATTATA
1 TATATTATA
206466 TATATTATA
1 TATATTATA
206475 TATA-TATA
1 TATATTATA
206483 TATAT
1 TATAT
206488 AACAAATAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
8 8 0.38
9 13 0.62
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (9 bp):
TATATTATA
Found at i:207737 original size:13 final size:14
Alignment explanation
Indices: 207706--207739 Score: 52
Period size: 13 Copynumber: 2.5 Consensus size: 14
207696 TAAAATACAC
*
207706 ATTATTTACTATTT
1 ATTATTTACTATAT
207720 ATTATTTA-TATAT
1 ATTATTTACTATAT
207733 ATTATTT
1 ATTATTT
207740 TATTTTTTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 11 0.58
14 8 0.42
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (14 bp):
ATTATTTACTATAT
Found at i:224502 original size:24 final size:24
Alignment explanation
Indices: 224470--224557 Score: 167
Period size: 24 Copynumber: 3.7 Consensus size: 24
224460 AACAATAACA
224470 AAGCCTAAGGGAAATGGTAAGCCT
1 AAGCCTAAGGGAAATGGTAAGCCT
224494 AAGCCTAAGGGAAATGGTAAGCCT
1 AAGCCTAAGGGAAATGGTAAGCCT
224518 AAGCCTAAGGGAAATGGTAAGCCT
1 AAGCCTAAGGGAAATGGTAAGCCT
*
224542 AAGCCTAAAGGAAATG
1 AAGCCTAAGGGAAATG
224558 ATGCATTGAA
Statistics
Matches: 63, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
24 63 1.00
ACGTcount: A:0.40, C:0.16, G:0.28, T:0.16
Consensus pattern (24 bp):
AAGCCTAAGGGAAATGGTAAGCCT
Found at i:232021 original size:88 final size:91
Alignment explanation
Indices: 231908--232077 Score: 274
Period size: 89 Copynumber: 1.9 Consensus size: 91
231898 AATTTCAATT
*
231908 AATTAAATATAGATTTAATTAATTTGAAATAAT-AAAATCCCTAATATGATTAGGGTAACTTGGA
1 AATTAAATATA-ATTTAATTAATTTGAAATAATAAAAAACCCTAATATGATTAGGGTAACTTGGA
*
231972 TATAAAAG-GTTTGTTAAATTCTAATC
65 TATAAAAGAGTGTGTTAAATTCTAATC
* *
231998 AATTAAATAT-ATTTAATTAATTTGAAATAATAAAAAACCCTAATATGATTAGGGTAACTTTGCT
1 AATTAAATATAATTTAATTAATTTGAAATAATAAAAAACCCTAATATGATTAGGGTAACTTGGAT
232062 ATAAAAGAGTGTGTTA
66 ATAAAAGAGTGTGTTA
232078 GGTCTAGCAG
Statistics
Matches: 74, Mismatches: 4, Indels: 4
0.90 0.05 0.05
Matches are distributed among these distances:
88 21 0.28
89 36 0.49
90 17 0.23
ACGTcount: A:0.44, C:0.06, G:0.12, T:0.37
Consensus pattern (91 bp):
AATTAAATATAATTTAATTAATTTGAAATAATAAAAAACCCTAATATGATTAGGGTAACTTGGAT
ATAAAAGAGTGTGTTAAATTCTAATC
Found at i:232569 original size:20 final size:21
Alignment explanation
Indices: 232539--232578 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 21
232529 AGCCGTTGGG
232539 GCCTGATGGTATCGATACTAT
1 GCCTGATGGTATCGATACTAT
232560 GCCT-ATGGTATCGATACTA
1 GCCTGATGGTATCGATACTA
232579 CTATTCAAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 15 0.79
21 4 0.21
ACGTcount: A:0.25, C:0.20, G:0.23, T:0.33
Consensus pattern (21 bp):
GCCTGATGGTATCGATACTAT
Found at i:239962 original size:47 final size:45
Alignment explanation
Indices: 239869--239993 Score: 173
Period size: 47 Copynumber: 2.8 Consensus size: 45
239859 GTAAGTATGC
*
239869 AAATAAGCTTACGAGCTTAT-GAAT-AATGGCAAGTATATTGATA
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGATA
* *
239912 AAATAAGCTTACGAGCTTATGGAATTTAAATGGTAAGTATTTTGGTA
1 AAATAAGCTTACGAGCTTATGGAA--TAAATGGTAAGTATATTGATA
* *
239959 AAATAAGCCTACGAGCTTATGGGATAAATGGTAAG
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAG
239994 AGATTTTATA
Statistics
Matches: 73, Mismatches: 5, Indels: 6
0.87 0.06 0.07
Matches are distributed among these distances:
43 20 0.27
44 3 0.04
45 11 0.15
46 1 0.01
47 38 0.52
ACGTcount: A:0.39, C:0.09, G:0.22, T:0.30
Consensus pattern (45 bp):
AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGATA
Found at i:242692 original size:17 final size:18
Alignment explanation
Indices: 242670--242720 Score: 68
Period size: 17 Copynumber: 2.8 Consensus size: 18
242660 TATATATTAT
242670 AAGAAGAAGAAAAATAG-
1 AAGAAGAAGAAAAATAGA
*
242687 AAGAAGAAAAAAAATAGAA
1 AAGAAGAAGAAAAATAG-A
242706 AACGAAGAAGAAAAA
1 AA-GAAGAAGAAAAA
242721 AAATGAAAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
17 16 0.55
19 2 0.07
20 11 0.38
ACGTcount: A:0.75, C:0.02, G:0.20, T:0.04
Consensus pattern (18 bp):
AAGAAGAAGAAAAATAGA
Found at i:242721 original size:14 final size:13
Alignment explanation
Indices: 242670--242721 Score: 56
Period size: 14 Copynumber: 4.2 Consensus size: 13
242660 TATATATTAT
242670 AAGAAGAAGAAAA
1 AAGAAGAAGAAAA
242683 ATAGAAGAAGAAAA
1 A-AGAAGAAGAAAA
*
242697 AA-AA-TAG-AAA
1 AAGAAGAAGAAAA
*
242707 ACGAAGAAGAAAA
1 AAGAAGAAGAAAA
242720 AA
1 AA
242722 AATGAAAATG
Statistics
Matches: 31, Mismatches: 4, Indels: 8
0.72 0.09 0.19
Matches are distributed among these distances:
10 4 0.13
11 4 0.13
12 4 0.13
13 6 0.19
14 13 0.42
ACGTcount: A:0.75, C:0.02, G:0.19, T:0.04
Consensus pattern (13 bp):
AAGAAGAAGAAAA
Found at i:242728 original size:22 final size:23
Alignment explanation
Indices: 242686--242746 Score: 81
Period size: 23 Copynumber: 2.7 Consensus size: 23
242676 AAGAAAAATA
242686 GAAGAAGAAAAAAAATAGAAAAC
1 GAAGAAGAAAAAAAATAGAAAAC
*
242709 GAAGAAGAAAAAAAAT-GAAAAT
1 GAAGAAGAAAAAAAATAGAAAAC
242731 G-AGAAAGAAAAGAAAA
1 GAAG-AAGAAAA-AAAA
242747 AGAGAAAAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
21 2 0.06
22 13 0.37
23 20 0.57
ACGTcount: A:0.74, C:0.02, G:0.20, T:0.05
Consensus pattern (23 bp):
GAAGAAGAAAAAAAATAGAAAAC
Found at i:242753 original size:17 final size:17
Alignment explanation
Indices: 242692--242749 Score: 50
Period size: 17 Copynumber: 3.5 Consensus size: 17
242682 AATAGAAGAA
242692 GAAAAA-AAATAGAAAAC
1 GAAAAAGAAA-AGAAAAC
* *
242709 GAAGAAGAAAA-AAAAT
1 GAAAAAGAAAAGAAAAC
*
242725 GAAAATGAGAAAGAAAA-
1 GAAAAAGA-AAAGAAAAC
242742 GAAAAAGA
1 GAAAAAGA
242750 GAAAAAAATG
Statistics
Matches: 33, Mismatches: 5, Indels: 6
0.75 0.11 0.14
Matches are distributed among these distances:
16 10 0.30
17 16 0.48
18 7 0.21
ACGTcount: A:0.74, C:0.02, G:0.19, T:0.05
Consensus pattern (17 bp):
GAAAAAGAAAAGAAAAC
Found at i:246697 original size:47 final size:45
Alignment explanation
Indices: 246594--246718 Score: 164
Period size: 47 Copynumber: 2.8 Consensus size: 45
246584 GTAAGTATGC
**
246594 AAATAAGCTTACGAGCTTAT-GAAT-AATGACAAGTATATTGATA
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGATA
* *
246637 AAATAAGCTTACGAGCTTATGGAATTTAAATGGTAAGTATTTTGGTA
1 AAATAAGCTTACGAGCTTATGGAA--TAAATGGTAAGTATATTGATA
* *
246684 AAATAAGCCTACGAGCTTATGGGATAAATGGTAAG
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAG
246719 GGATTTTATA
Statistics
Matches: 72, Mismatches: 6, Indels: 6
0.86 0.07 0.07
Matches are distributed among these distances:
43 20 0.28
44 3 0.04
45 11 0.15
46 1 0.01
47 37 0.51
ACGTcount: A:0.40, C:0.09, G:0.21, T:0.30
Consensus pattern (45 bp):
AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGATA
Found at i:250582 original size:29 final size:29
Alignment explanation
Indices: 250550--250637 Score: 106
Period size: 29 Copynumber: 3.0 Consensus size: 29
250540 CCCCACACCA
250550 CTACAAGGTCGCCAAGCACTCCCAGCGAC
1 CTACAAGGTCGCCAAGCACTCCCAGCGAC
* *
250579 CTACAAGGTCGTCATGCACTCCCAGCGAC
1 CTACAAGGTCGCCAAGCACTCCCAGCGAC
** * *
250608 CTTGTAA-GTCGCCAAGCAGTCCCGGCGAC
1 C-TACAAGGTCGCCAAGCACTCCCAGCGAC
250637 C
1 C
250638 AAGCTTCACG
Statistics
Matches: 50, Mismatches: 8, Indels: 2
0.83 0.13 0.03
Matches are distributed among these distances:
29 47 0.94
30 3 0.06
ACGTcount: A:0.24, C:0.39, G:0.23, T:0.15
Consensus pattern (29 bp):
CTACAAGGTCGCCAAGCACTCCCAGCGAC
Found at i:250669 original size:18 final size:19
Alignment explanation
Indices: 250646--250684 Score: 71
Period size: 18 Copynumber: 2.1 Consensus size: 19
250636 CCAAGCTTCA
250646 CGTGCTCCCCT-CTGCTCC
1 CGTGCTCCCCTCCTGCTCC
250664 CGTGCTCCCCTCCTGCTCC
1 CGTGCTCCCCTCCTGCTCC
250683 CG
1 CG
250685 CTGCATGTCT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 11 0.55
19 9 0.45
ACGTcount: A:0.00, C:0.56, G:0.18, T:0.26
Consensus pattern (19 bp):
CGTGCTCCCCTCCTGCTCC
Found at i:250841 original size:33 final size:33
Alignment explanation
Indices: 250804--250870 Score: 125
Period size: 33 Copynumber: 2.0 Consensus size: 33
250794 CAATTGCACA
*
250804 ATTATTGGTGAAATAATTGAGGTAGCCGGTGAC
1 ATTATTGGTGAAATAATTGAGGCAGCCGGTGAC
250837 ATTATTGGTGAAATAATTGAGGCAGCCGGTGAC
1 ATTATTGGTGAAATAATTGAGGCAGCCGGTGAC
250870 A
1 A
250871 CCTAAATTAT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.31, C:0.10, G:0.30, T:0.28
Consensus pattern (33 bp):
ATTATTGGTGAAATAATTGAGGCAGCCGGTGAC
Found at i:250949 original size:26 final size:26
Alignment explanation
Indices: 250916--250973 Score: 82
Period size: 26 Copynumber: 2.3 Consensus size: 26
250906 ACATAAAAGA
* *
250916 AAGAAAGGGAGAAGAGATTGCAGCAG
1 AAGAAAGGGAGAAGAAATTACAGCAG
*
250942 AAGAAAGGGAGAAGAAATTACAGCCG
1 AAGAAAGGGAGAAGAAATTACAGCAG
250968 -AGAAAG
1 AAGAAAG
250974 AAAGAAAGGG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
25 6 0.21
26 23 0.79
ACGTcount: A:0.50, C:0.09, G:0.34, T:0.07
Consensus pattern (26 bp):
AAGAAAGGGAGAAGAAATTACAGCAG
Found at i:251278 original size:43 final size:42
Alignment explanation
Indices: 251170--251278 Score: 98
Period size: 43 Copynumber: 2.6 Consensus size: 42
251160 ATACATAAAT
* * *
251170 AAAAAATTATTTAATTAGTATGT-TTGATAGTTATATAGTTAA
1 AAAAAATTATTTAATTAGTTTTTGTTAATAGTTATATAG-TAA
* * * *
251212 AAAATAATTAATTAGTTTG-TTTTGTTAATCGTTAGTTATA-TAA
1 AAAA-AATTATTTAATTAGTTTTTGTTAATAGTTA--TATAGTAA
251255 AAAAAATTATTTAATTAGTTTTTG
1 AAAAAATTATTTAATTAGTTTTTG
251279 GTAGTTAAAT
Statistics
Matches: 52, Mismatches: 10, Indels: 9
0.73 0.14 0.13
Matches are distributed among these distances:
42 17 0.33
43 31 0.60
45 4 0.08
ACGTcount: A:0.40, C:0.01, G:0.11, T:0.48
Consensus pattern (42 bp):
AAAAAATTATTTAATTAGTTTTTGTTAATAGTTATATAGTAA
Found at i:251492 original size:16 final size:16
Alignment explanation
Indices: 251460--251506 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 16
251450 TTTAAAAAGT
*
251460 TTAGTTTGTTAGT-TTA
1 TTAGTTTATTA-TATTA
251476 TTAGTTTATTATATTA
1 TTAGTTTATTATATTA
*
251492 TAAG-TTATTATATTA
1 TTAGTTTATTATATTA
251507 AAGTTTAGTG
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
15 12 0.43
16 16 0.57
ACGTcount: A:0.30, C:0.00, G:0.11, T:0.60
Consensus pattern (16 bp):
TTAGTTTATTATATTA
Found at i:251501 original size:15 final size:14
Alignment explanation
Indices: 251481--251511 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
251471 GTTTATTAGT
251481 TTATTATATTATAAG
1 TTATTATATTA-AAG
251496 TTATTATATTAAAG
1 TTATTATATTAAAG
251510 TT
1 TT
251512 TAGTGTTGTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.31
15 11 0.69
ACGTcount: A:0.39, C:0.00, G:0.06, T:0.55
Consensus pattern (14 bp):
TTATTATATTAAAG
Found at i:253742 original size:14 final size:14
Alignment explanation
Indices: 253725--253766 Score: 54
Period size: 14 Copynumber: 3.2 Consensus size: 14
253715 TGGAAAATAG
253725 TTACTATCAAATCA
1 TTACTATCAAATCA
253739 TTAC--T-AAATCA
1 TTACTATCAAATCA
*
253750 TTAATATCAAATCA
1 TTACTATCAAATCA
253764 TTA
1 TTA
253767 AATATTAATA
Statistics
Matches: 24, Mismatches: 1, Indels: 6
0.77 0.03 0.19
Matches are distributed among these distances:
11 9 0.38
12 1 0.04
13 1 0.04
14 13 0.54
ACGTcount: A:0.45, C:0.17, G:0.00, T:0.38
Consensus pattern (14 bp):
TTACTATCAAATCA
Found at i:253791 original size:49 final size:48
Alignment explanation
Indices: 253738--253852 Score: 185
Period size: 48 Copynumber: 2.4 Consensus size: 48
253728 CTATCAAATC
*
253738 ATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAAATTATT
1 ATTACT-AATCATTACTATCAAATCATTAAATATTAATAATAAATTATT
* *
253787 ATTACTAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATT
1 ATTACTAATCATTACTATCAAATCATTAAATATTAATAATAAATT-ATT
253836 ATTACTAATCATTACTA
1 ATTACTAATCATTACTA
253853 AATCATTACT
Statistics
Matches: 62, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
48 36 0.58
49 26 0.42
ACGTcount: A:0.48, C:0.11, G:0.00, T:0.41
Consensus pattern (48 bp):
ATTACTAATCATTACTATCAAATCATTAAATATTAATAATAAATTATT
Found at i:253942 original size:120 final size:120
Alignment explanation
Indices: 253787--254387 Score: 1023
Period size: 120 Copynumber: 5.1 Consensus size: 120
253777 ATAAATTATT
* *
253787 ATTACT-AATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCATTAC
1 ATTACTAAATCATTACTATCAAATCATTAAATATTAATAACAATTTCATTATTACTAATCATTAC
* * *
253851 TAAATCATTACTATCAAATCATTAAATATAAATAACAATTTCATTATTACTAATC
66 TAAATCATTAATATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATC
253906 ATTACTAAATCATTACTATCAAATCATTAAATATTAATAACAATTTC------A-T--T-ATTAC
1 ATTACTAAATCATTACTATCAAATCATTAAATATTAATAACAATTTCATTATTACTAATCATTAC
253961 T-AATCATTAATATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATC
66 TAAATCATTAATATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATC
* * *
254015 ATTACT-AATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATAATTAC
1 ATTACTAAATCATTACTATCAAATCATTAAATATTAATAACAATTTCATTATTACTAATCATTAC
254079 TAAATCATTAATATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATC
66 TAAATCATTAATATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATC
254134 ATTACTAAATCATTACTATCAAATCATTAAATATTAATAACAATTTCATTATTACTAATCATTAC
1 ATTACTAAATCATTACTATCAAATCATTAAATATTAATAACAATTTCATTATTACTAATCATTAC
*
254199 TAAATCATTACTATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATC
66 TAAATCATTAATATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATC
254254 ATTACTAAATCATTACTATCAAATCATTAAATATTAATAACAATTTCATTATTACTAAT-ATTAC
1 ATTACTAAATCATTACTATCAAATCATTAAATATTAATAACAATTTCATTATTACTAATCATTAC
254318 TAAATCATTAATATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATC
66 TAAATCATTAATATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATC
254373 ATTACTAAATCATTA
1 ATTACTAAATCATTA
254388 TTATAAGTTC
Statistics
Matches: 457, Mismatches: 12, Indels: 26
0.92 0.02 0.05
Matches are distributed among these distances:
108 38 0.08
109 56 0.12
110 6 0.01
111 1 0.00
113 1 0.00
114 2 0.00
115 1 0.00
117 1 0.00
118 6 0.01
119 139 0.30
120 206 0.45
ACGTcount: A:0.46, C:0.13, G:0.00, T:0.41
Consensus pattern (120 bp):
ATTACTAAATCATTACTATCAAATCATTAAATATTAATAACAATTTCATTATTACTAATCATTAC
TAAATCATTAATATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATC
Found at i:253954 original size:22 final size:22
Alignment explanation
Indices: 253929--254005 Score: 66
Period size: 22 Copynumber: 3.3 Consensus size: 22
253919 TACTATCAAA
253929 TCATTAAATATTAATAACAATT
1 TCATTAAATATTAATAACAATT
* *
253951 TCATTATTACTAATCATTAATATCAA-A
1 TC---ATTA--AAT-ATTAATAACAATT
*
253978 TCATTAAATATTAATAATAATT
1 TCATTAAATATTAATAACAATT
254000 TCATTA
1 TCATTA
254006 TTACTAATCA
Statistics
Matches: 43, Mismatches: 5, Indels: 14
0.69 0.08 0.23
Matches are distributed among these distances:
21 9 0.21
22 11 0.26
24 4 0.09
25 4 0.09
27 5 0.12
28 10 0.23
ACGTcount: A:0.47, C:0.10, G:0.00, T:0.43
Consensus pattern (22 bp):
TCATTAAATATTAATAACAATT
Found at i:253969 original size:49 final size:53
Alignment explanation
Indices: 253735--254319 Score: 425
Period size: 60 Copynumber: 10.4 Consensus size: 53
253725 TTACTATCAA
* *
253735 ATCATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAA-AT-TA-T
1 ATCATTACT-AATCATTACTATCAAATCATTAAATATTAATAATAATTTCTACT
*
253786 -T-ATTACTAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACT
1 ATCATTACTAATCATTACTATCAAATCATTAAATATTAATAATAATTTC-----TACT
* *
253842 AATCATTACTAAATCATTACTATCAAATCATTAAATATAAATAACAATTTCATTATTACT
1 -ATCATTACT-AATCATTACTATCAAATCATTAAATATTAATAATAATTTC-----TACT
*
253902 AATCATTACTAAATCATTACTATCAAATCATTAAATATTAATAACAATTTC-A-T
1 -ATCATTACT-AATCATTACTATCAAATCATTAAATATTAATAATAATTTCTACT
*
253955 -T-ATTACTAATCATTAATATCAAATCATTAAATATTAATAATAATTTCATTATTACT
1 ATCATTACTAATCATTACTATCAAATCATTAAATATTAATAATAATTTC-----TACT
*
254011 AATCATTACTAATCATTACTATCAAATCATTAAAAATTAATAATAATTTC-A-T
1 -ATCATTACTAATCATTACTATCAAATCATTAAATATTAATAATAATTTCTACT
* *
254063 -T-ATTACTAATAATTACTAAATCATTAAT-ATCAAATCATTAAATATTAATAATAATTTCATTA
1 ATCATTACTAATCATTACT--ATCA--AATCATTAAAT-ATT--A-A-TAA---TAATTTC--TA
*
254125 TT
52 CT
* *
254127 ACTAATCATTACTAAATCATTACTATCAAATCATTAAATATTAATAACAATTTCATTATTACT
1 A-TCA---TTACT-AATCATTACTATCAAATCATTAAATATTAATAATAATTTC-----TACT
254190 AATCATTACTAAATCATTACTATCAAATCATTAAATATTAATAATAATTTCATTATTACT
1 -ATCATTACT-AATCATTACTATCAAATCATTAAATATTAATAATAATTTC-----TACT
*
254250 AATCATTACTAAATCATTACTATCAAATCATTAAATATTAATAACAATTTC-A-T
1 -ATCATTACT-AATCATTACTATCAAATCATTAAATATTAATAATAATTTCTACT
254303 -T-ATTACTAAT-ATTACTA
1 ATCATTACTAATCATTACTA
254320 AATCATTAAT
Statistics
Matches: 463, Mismatches: 21, Indels: 103
0.79 0.04 0.18
Matches are distributed among these distances:
48 41 0.09
49 63 0.14
50 14 0.03
51 6 0.01
52 6 0.01
53 9 0.02
54 2 0.00
55 4 0.01
56 3 0.01
57 3 0.01
58 2 0.00
59 50 0.11
60 213 0.46
63 11 0.02
64 3 0.01
65 1 0.00
66 1 0.00
67 7 0.02
68 6 0.01
69 4 0.01
70 5 0.01
71 9 0.02
ACGTcount: A:0.46, C:0.13, G:0.00, T:0.41
Consensus pattern (53 bp):
ATCATTACTAATCATTACTATCAAATCATTAAATATTAATAATAATTTCTACT
Found at i:254020 original size:10 final size:10
Alignment explanation
Indices: 254005--254031 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
253995 TAATTTCATT
254005 ATTACTAATC
1 ATTACTAATC
254015 ATTACTAATC
1 ATTACTAATC
254025 ATTACTA
1 ATTACTA
254032 TCAAATCATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.41, C:0.19, G:0.00, T:0.41
Consensus pattern (10 bp):
ATTACTAATC
Found at i:254401 original size:60 final size:60
Alignment explanation
Indices: 253956--254387 Score: 780
Period size: 60 Copynumber: 7.2 Consensus size: 60
253946 CAATTTCATT
*
253956 ATTACT-AATCATTAATATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATC
1 ATTACTAAATCATTACTATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATC
* *
254015 ATTACT-AATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATA
1 ATTACTAAATCATTACTATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATC
*
254074 ATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATC
1 ATTACTAAATCATTACTATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATC
*
254134 ATTACTAAATCATTACTATCAAATCATTAAATATTAATAACAATTTCATTATTACTAATC
1 ATTACTAAATCATTACTATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATC
254194 ATTACTAAATCATTACTATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATC
1 ATTACTAAATCATTACTATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATC
*
254254 ATTACTAAATCATTACTATCAAATCATTAAATATTAATAACAATTTCATTATTACTAAT-
1 ATTACTAAATCATTACTATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATC
*
254313 ATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATC
1 ATTACTAAATCATTACTATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATC
254373 ATTACTAAATCATTA
1 ATTACTAAATCATTA
254388 TTATAAGTTC
Statistics
Matches: 359, Mismatches: 12, Indels: 3
0.96 0.03 0.01
Matches are distributed among these distances:
59 119 0.33
60 240 0.67
ACGTcount: A:0.46, C:0.13, G:0.00, T:0.41
Consensus pattern (60 bp):
ATTACTAAATCATTACTATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATC
Found at i:254480 original size:14 final size:14
Alignment explanation
Indices: 254461--254508 Score: 66
Period size: 14 Copynumber: 3.6 Consensus size: 14
254451 TTCAAGTCGT
254461 AAATCATTACTATC
1 AAATCATTACTATC
254475 AAATCATTAC--T-
1 AAATCATTACTATC
*
254486 AAATCATTAATATC
1 AAATCATTACTATC
254500 AAATCATTA
1 AAATCATTA
254509 AATATTAATA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
11 9 0.30
12 1 0.03
13 1 0.03
14 19 0.63
ACGTcount: A:0.48, C:0.17, G:0.00, T:0.35
Consensus pattern (14 bp):
AAATCATTACTATC
Found at i:254533 original size:49 final size:49
Alignment explanation
Indices: 254480--254640 Score: 270
Period size: 49 Copynumber: 3.3 Consensus size: 49
254470 CTATCAAATC
*
254480 ATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAAATT-ATT
1 ATTACT-AATCATTAATATCAAATCATTAAATATTAATAATAATTTCATT
* *
254529 ATTACTAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATT
1 ATTACTAATCATTAATATCAAATCATTAAATATTAATAATAATTTCATT
*
254578 ATTACTAATCATTAATATCAAATCATTAAATATTAATAATAATTTCATC
1 ATTACTAATCATTAATATCAAATCATTAAATATTAATAATAATTTCATT
254627 ATTACTAATCATTA
1 ATTACTAATCATTA
254641 CTAAATCTTA
Statistics
Matches: 105, Mismatches: 6, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
48 36 0.34
49 69 0.66
ACGTcount: A:0.48, C:0.11, G:0.00, T:0.41
Consensus pattern (49 bp):
ATTACTAATCATTAATATCAAATCATTAAATATTAATAATAATTTCATT
Found at i:254554 original size:348 final size:345
Alignment explanation
Indices: 253787--254640 Score: 983
Period size: 348 Copynumber: 2.5 Consensus size: 345
253777 ATAAATTATT
*
253787 ATTACT-AATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCATTAC
1 ATTACTAAATCATTACTATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATCATTAC
253851 TAAATCATTACTATCAAATCATTAAATATAAATAACAATTTCATTATTACTAATCATTACTAAAT
66 TAAATCATTACTATCAAATCATTAAATATAAATAACAATTTCATTATTACTAATCATTACTAAAT
253916 CATTACTATCAAATCATTAAATATTAATAACAATTTCATTATTACTAATCATTAATATCAAATCA
131 CATTACTATCAAATCATTAAATATTAATAACAATTTCATTATTACTAATCATTAATATCAAATCA
253981 TTAAATATTAATAATAATTTCATTATTACTAATCATTACTAATCATTACTATCAAATCATTAAAA
196 TTAAATATTAATAATAATTTCATTATTACTAATCATTACTAATCATTACTATCAAATCATTAAAA
* ** * * *
254046 ATTAATAATAATTTCATTATTACTAATAATTACTAAATCATTAATATCAAATCATTAAATATTAA
261 ATTAATAAGAAAATCATGATTAC-AATAA-TACCAAATCATTAATATC-AATCATTAAATAGTAA
* *
254111 TAATAATTTCATTATTACTAATC
323 TAATAATTTCACTATTACAAATC
*
254134 ATTACTAAATCATTACTATCAAATCATTAAATATTAATAACAATTTCATTATTACTAATCATTAC
1 ATTACTAAATCATTACTATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATCATTAC
* *
254199 TAAATCATTACTATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATCATTACTAAAT
66 TAAATCATTACTATCAAATCATTAAATATAAATAACAATTTCATTATTACTAATCATTACTAAAT
254264 CATTACTATCAAATCATTAAATATTAATAACAATTTCATTATTACTAATATTACTAAATCATTAA
131 CATTACTATCAAATCATTAAATATTAATAACAATTTC------A-T--TATTACT-AATCATTAA
*
254329 TATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATCATTACTAAATCATTATTAT-A
186 TATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATCATTACT-AATCATTACTATCA
* ** * * * * * * **
254393 AGTTCATTACTAGTTATGTAACGAAAAT-ATGGTTA-ATTGA-ACCAAA-CATT-GT-TC-ATTG
250 A-ATCATTAAAAATTA-ATAA-GAAAATCATGATTACAATAATACCAAATCATTAATATCAATCA
* * *
254451 TTCAAGTCGT-A-AATCA-TT-ACTA-T-CAAATC
312 TT-AAATAGTAATAATAATTTCACTATTACAAATC
*
254480 ATTACTAAATCATTAATATCAAATCATTAAATATTAATAAT-A----A--ATTA-T--T-ATTAC
1 ATTACTAAATCATTACTATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATCATTAC
* * *
254534 T-AATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATC---A-T---T
66 TAAATCATTACTATCAAATCATTAAATATAAATAACAATTTCATTATTACTAATCATTACTAAAT
* *
254591 -A--A-TATCAAATCATTAAATATTAATAATAATTTCATCATTACTAATCATTA
131 CATTACTATCAAATCATTAAATATTAATAACAATTTCATTATTACTAATCATTA
254641 CTAAATCTTA
Statistics
Matches: 459, Mismatches: 32, Indels: 66
0.82 0.06 0.12
Matches are distributed among these distances:
313 8 0.02
314 6 0.01
316 1 0.00
317 1 0.00
323 30 0.07
324 1 0.00
326 1 0.00
327 1 0.00
330 1 0.00
331 1 0.00
334 52 0.11
335 6 0.01
336 1 0.00
338 1 0.00
339 4 0.01
341 1 0.00
345 1 0.00
346 44 0.10
347 7 0.02
348 159 0.35
349 2 0.00
350 4 0.01
351 5 0.01
352 4 0.01
353 2 0.00
354 2 0.00
355 5 0.01
356 5 0.01
357 7 0.02
358 64 0.14
359 21 0.05
360 8 0.02
361 3 0.01
ACGTcount: A:0.45, C:0.13, G:0.01, T:0.40
Consensus pattern (345 bp):
ATTACTAAATCATTACTATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATCATTAC
TAAATCATTACTATCAAATCATTAAATATAAATAACAATTTCATTATTACTAATCATTACTAAAT
CATTACTATCAAATCATTAAATATTAATAACAATTTCATTATTACTAATCATTAATATCAAATCA
TTAAATATTAATAATAATTTCATTATTACTAATCATTACTAATCATTACTATCAAATCATTAAAA
ATTAATAAGAAAATCATGATTACAATAATACCAAATCATTAATATCAATCATTAAATAGTAATAA
TAATTTCACTATTACAAATC
Found at i:258175 original size:28 final size:30
Alignment explanation
Indices: 258127--258188 Score: 101
Period size: 28 Copynumber: 2.1 Consensus size: 30
258117 ATTTTTTATA
258127 TAATATAATATATAACTTAAACTAAAAAAC
1 TAATATAATATATAACTTAAACTAAAAAAC
*
258157 TAATAT-A-ATATAACTTAAACTAACAAAC
1 TAATATAATATATAACTTAAACTAAAAAAC
258185 TAAT
1 TAAT
258189 TAACTAAATT
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
28 24 0.77
29 1 0.03
30 6 0.19
ACGTcount: A:0.58, C:0.11, G:0.00, T:0.31
Consensus pattern (30 bp):
TAATATAATATATAACTTAAACTAAAAAAC
Found at i:258689 original size:45 final size:45
Alignment explanation
Indices: 258622--258711 Score: 162
Period size: 45 Copynumber: 2.0 Consensus size: 45
258612 AATCTCCCAG
*
258622 CTATGGATGCAACCCATGCACGAGGGAGAAGGGTTAAGTTTGGTC
1 CTATGGATGCAACCCATACACGAGGGAGAAGGGTTAAGTTTGGTC
*
258667 CTATGGATGCAACCCATACACGAGGGAGCAGGGTTAAGTTTGGTC
1 CTATGGATGCAACCCATACACGAGGGAGAAGGGTTAAGTTTGGTC
258712 GCCAGTAGGG
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
45 43 1.00
ACGTcount: A:0.27, C:0.19, G:0.32, T:0.22
Consensus pattern (45 bp):
CTATGGATGCAACCCATACACGAGGGAGAAGGGTTAAGTTTGGTC
Found at i:258801 original size:29 final size:27
Alignment explanation
Indices: 258769--258849 Score: 119
Period size: 26 Copynumber: 2.9 Consensus size: 27
258759 GCGACCTACA
258769 AGGTCGCTGGGAGTGCATGGCGACCTTGT
1 AGGTCGCTGGGA-T-CATGGCGACCTTGT
258798 AGGTCGCTGGGA-CATGGCGACCTTGT
1 AGGTCGCTGGGATCATGGCGACCTTGT
258824 AGGTCGCTGGGACTACATGGCGACCT
1 AGGTCGCTGGGA-T-CATGGCGACCT
258850 GTGTTGGGTG
Statistics
Matches: 49, Mismatches: 0, Indels: 6
0.89 0.00 0.11
Matches are distributed among these distances:
26 26 0.53
29 23 0.47
ACGTcount: A:0.16, C:0.23, G:0.38, T:0.22
Consensus pattern (27 bp):
AGGTCGCTGGGATCATGGCGACCTTGT
Found at i:258880 original size:16 final size:16
Alignment explanation
Indices: 258859--258892 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
258849 TGTGTTGGGT
258859 GTTGGGTGCTGGGGAC
1 GTTGGGTGCTGGGGAC
258875 GTTGGGTGCTGGGGAC
1 GTTGGGTGCTGGGGAC
258891 GT
1 GT
258893 GCATGGCGAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.06, C:0.12, G:0.56, T:0.26
Consensus pattern (16 bp):
GTTGGGTGCTGGGGAC
Found at i:260807 original size:14 final size:14
Alignment explanation
Indices: 260788--260815 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
260778 AAGTGAAAGA
260788 ATAGTTATATAATT
1 ATAGTTATATAATT
260802 ATAGTTATATAATT
1 ATAGTTATATAATT
260816 TTGTTATGAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (14 bp):
ATAGTTATATAATT
Found at i:262360 original size:13 final size:13
Alignment explanation
Indices: 262342--262372 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
262332 GAATAATAAT
262342 AATATTTTTTGTA
1 AATATTTTTTGTA
*
262355 AATATTTTTTTTA
1 AATATTTTTTGTA
262368 AATAT
1 AATAT
262373 AAACATGACA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.61
Consensus pattern (13 bp):
AATATTTTTTGTA
Found at i:268638 original size:42 final size:41
Alignment explanation
Indices: 268572--268683 Score: 118
Period size: 42 Copynumber: 2.6 Consensus size: 41
268562 ATCCTGCCCG
* *
268572 AAGATCTTATGGATGGCCCAAAGGACTT-ATCATCTTGCTTCAA
1 AAGA-CTTAT-GATGGCCCAAAGGACTTAAACATCATGC-TCAA
* * * *
268615 AAGACTTATAGATGACCCGAAGGATTTAAACATCATGCTCGA
1 AAGACTTAT-GATGGCCCAAAGGACTTAAACATCATGCTCAA
268657 AAGACTTACTGATGGCCCAAAGGACTT
1 AAGACTTA-TGATGGCCCAAAGGACTT
268684 TTGCTAATTT
Statistics
Matches: 57, Mismatches: 10, Indels: 5
0.79 0.14 0.07
Matches are distributed among these distances:
42 44 0.77
43 13 0.23
ACGTcount: A:0.34, C:0.21, G:0.20, T:0.26
Consensus pattern (41 bp):
AAGACTTATGATGGCCCAAAGGACTTAAACATCATGCTCAA
Found at i:268795 original size:59 final size:59
Alignment explanation
Indices: 268702--268845 Score: 162
Period size: 59 Copynumber: 2.4 Consensus size: 59
268692 TTGAAATGTC
* * * * *
268702 GTGAATTGAGCAATAGGAAACGTTAATACCTCAAGTGGGGCGTTAATGATTCGAAGTGTT
1 GTGAATCGAGCAA-AGGAAAAGTTGATACCTCAAGTGAGGCATTAATGATTCGAAGTGTT
* * * ** *
268762 GTGAATCGAGCAAAGGAAATGTTGATCCCTCAAGTGAGGTATTGCTGATTGGAAGTGTT
1 GTGAATCGAGCAAAGGAAAAGTTGATACCTCAAGTGAGGCATTAATGATTCGAAGTGTT
* *
268821 GTGAATCAAGAAAAGGAAAAGTTGA
1 GTGAATCGAGCAAAGGAAAAGTTGA
268846 GAACATCACA
Statistics
Matches: 71, Mismatches: 13, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
59 59 0.83
60 12 0.17
ACGTcount: A:0.34, C:0.10, G:0.29, T:0.26
Consensus pattern (59 bp):
GTGAATCGAGCAAAGGAAAAGTTGATACCTCAAGTGAGGCATTAATGATTCGAAGTGTT
Found at i:268966 original size:42 final size:41
Alignment explanation
Indices: 268871--268971 Score: 114
Period size: 42 Copynumber: 2.4 Consensus size: 41
268861 AGGTCTTTTG
* * *
268871 GATGGTCCGAAGGACTTATCATCTTGCTCGAAAGACTTATA
1 GATGGCCCGAAGGACTTAGCATCATGCTCGAAAGACTTATA
* * * *
268912 AATGACCAGAAGGATTTAAGCATCATGCTCGAAAGACTTACT-
1 GATGGCCCGAAGGACTT-AGCATCATGCTCGAAAGACTTA-TA
268954 GATGGCCCGAAGGACTTA
1 GATGGCCCGAAGGACTTA
268972 CTAATCAAGA
Statistics
Matches: 47, Mismatches: 11, Indels: 4
0.76 0.18 0.06
Matches are distributed among these distances:
41 13 0.28
42 33 0.70
43 1 0.02
ACGTcount: A:0.33, C:0.20, G:0.23, T:0.25
Consensus pattern (41 bp):
GATGGCCCGAAGGACTTAGCATCATGCTCGAAAGACTTATA
Found at i:269107 original size:57 final size:56
Alignment explanation
Indices: 269030--269335 Score: 187
Period size: 57 Copynumber: 5.4 Consensus size: 56
269020 GTTTACAGTT
* * * * *
269030 ATCATCAAGGAACCCCTAAAAGTTACGCTTAACTTATTTAAAAATTCTTTGGAAATA
1 ATCATCAAGAAACACATAAAA-TCACGCTTAACTTCTTTAAAAATTCTTTGGAAATA
* * *
269087 ATCATCAAGAAACACATAAAAATCAGGCTTAGCTTCTTTAAAAATTCTTTGAAAATA
1 ATCATCAAGAAACACAT-AAAATCACGCTTAACTTCTTTAAAAATTCTTTGGAAATA
* **** * * * *
269144 ATCAT-AAAAAATTGTTGAAAACCATGCTTAAATTCTTTAAAAATTCTTGGGAAATA
1 ATCATCAAGAAACACAT-AAAATCACGCTTAACTTCTTTAAAAATTCTTTGGAAATA
* * * * * * * *
269200 ATCATCAAGAAACCCCTGAAAATTAGGCTT-AGTT-TCTAAAAACTCATCCT-G-AA-A
1 ATCATCAAGAAACACAT-AAAATCACGCTTAACTTCTTTAAAAATTC-T-TTGGAAATA
* * * * *
269254 A-CATCAAGAAAC-CTCTAAAAACTAGGCTTAGCTTCTTTTAAAATTCATTTGGAAATA
1 ATCATCAAGAAACAC-ATAAAATC-ACGCTTAACTTCTTTAAAAATTC-TTTGGAAATA
*
269311 ATCATCAAGAAACACCTGAAAATCA
1 ATCATCAAGAAACACAT-AAAATCA
269336 GGATTAGTTT
Statistics
Matches: 193, Mismatches: 42, Indels: 27
0.74 0.16 0.10
Matches are distributed among these distances:
52 5 0.03
53 19 0.10
54 5 0.03
55 22 0.11
56 51 0.26
57 67 0.35
58 18 0.09
59 6 0.03
ACGTcount: A:0.43, C:0.17, G:0.10, T:0.29
Consensus pattern (56 bp):
ATCATCAAGAAACACATAAAATCACGCTTAACTTCTTTAAAAATTCTTTGGAAATA
Found at i:269199 original size:56 final size:57
Alignment explanation
Indices: 269056--269352 Score: 187
Period size: 56 Copynumber: 5.3 Consensus size: 57
269046 TAAAAGTTAC
* * *
269056 GCTTAACTTATTTAAAAATTCTTTGGAAATAATCATCAAGAAACACATAAAAATCAG
1 GCTTAACTTCTTTAAAAATTCTTTGGAAATAATCATCAAAAAACACATAAAAACCAG
* * **** * *
269113 GCTTAGCTTCTTTAAAAATTCTTTGAAAATAATCAT-AAAAAATTGTTGAAAACCAT
1 GCTTAACTTCTTTAAAAATTCTTTGGAAATAATCATCAAAAAACACATAAAAACCAG
* * * * * * **
269169 GCTTAAATTCTTTAAAAATTCTTGGGAAATAATCATCAAGAAACCCCTGAAAATTAG
1 GCTTAACTTCTTTAAAAATTCTTTGGAAATAATCATCAAAAAACACATAAAAACCAG
* * * * * * *
269226 GCTT-AGTT-TCTAAAAACTCATCCT-G-AA-AA-CATCAAGAAAC-CTCTAAAAACTAG
1 GCTTAACTTCTTTAAAAATTC-T-TTGGAAATAATCATCAAAAAACAC-ATAAAAACCAG
* * * * * *
269279 GCTTAGCTTCTTTTAAAATTCATTTGGAAATAATCATCAAGAAACACCTGAAAATCAG
1 GCTTAACTTCTTTAAAAATTC-TTTGGAAATAATCATCAAAAAACACATAAAAACCAG
* **
269337 GATTAGTTTCTTTAAA
1 GCTTAACTTCTTTAAA
269353 CTATTTTTGA
Statistics
Matches: 187, Mismatches: 42, Indels: 21
0.75 0.17 0.08
Matches are distributed among these distances:
52 1 0.01
53 24 0.13
54 5 0.03
55 22 0.12
56 51 0.27
57 51 0.27
58 32 0.17
59 1 0.01
ACGTcount: A:0.42, C:0.16, G:0.10, T:0.31
Consensus pattern (57 bp):
GCTTAACTTCTTTAAAAATTCTTTGGAAATAATCATCAAAAAACACATAAAAACCAG
Found at i:269265 original size:53 final size:52
Alignment explanation
Indices: 269202--269475 Score: 262
Period size: 53 Copynumber: 5.1 Consensus size: 52
269192 GGGAAATAAT
* *
269202 CATCAAGAAACCCCTGAAAATTAGGCTTAGTTTCTAAAAACTCATCCTGAAAA
1 CATCAAGAAACCCCTGAAAATTAGGCTTAGTTTCTTAAAACTCAT-TTGAAAA
* * * * *
269255 CATCAAGAAACCTCTAAAAACTAGGCTTAGCTTCTTTTAAAATTCATTTGGAAATAA
1 CATCAAGAAACCCCTGAAAATTAGGCTTAG-TT-TCTTAAAACTCATTT-G-AA-AA
* * * *
269312 TCATCAAGAAACACCTGAAAATCAGGATTAGTTTCTTTAAACT-ATTTTTGAAAA
1 -CATCAAGAAACCCCTGAAAATTAGGCTTAGTTTCTTAAAACTCA--TTTGAAAA
* * *
269366 CATCAAGAAACCCCTAAAAATTAGGCTTAGTTTCTTTCAAAATTCATTTAAAAA
1 CATCAAGAAACCCCTGAAAATTAGGCTTAGTTTC-TT-AAAACTCATTTGAAAA
* * * * *
269420 CATCAAGAAACCCCTGAAAATCAGGCTTAGCTTCTTTCAAATTCGTTTGAAAA
1 CATCAAGAAACCCCTGAAAATTAGGCTTAGTTTC-TTAAAACTCATTTGAAAA
269473 CAT
1 CAT
269476 TATATCAAGA
Statistics
Matches: 181, Mismatches: 29, Indels: 22
0.78 0.12 0.09
Matches are distributed among these distances:
53 73 0.40
54 48 0.27
55 18 0.10
56 11 0.06
57 7 0.04
58 24 0.13
ACGTcount: A:0.40, C:0.19, G:0.11, T:0.30
Consensus pattern (52 bp):
CATCAAGAAACCCCTGAAAATTAGGCTTAGTTTCTTAAAACTCATTTGAAAA
Found at i:269329 original size:111 final size:109
Alignment explanation
Indices: 269032--269454 Score: 399
Period size: 111 Copynumber: 3.8 Consensus size: 109
269022 TTACAGTTAT
* ** * *
269032 CATCAAGGAACCCCTAAAAGTTACGCTTAACTTATTTAAAAATTCTTTGGAAATAATCATCAAGA
1 CATCAAGAAACCCCTAAAAACTAGGCTTAACTTCTTTAAAAATTCTTTGGAAATAATCATCAAGA
* * * *
269097 AACACATAAAAATCAGGCTTAGCTTCTTTAAAAATTC-TTTGAAAA
66 AACACCTGAAAATCAGGCTTAG-TT-TCTAAAAACTCATTTGAAAA
* * **** * * * * *
269142 TAATCATAAAAAATTGTTGAAAACCATGCTTAAATTCTTTAAAAATTCTTGGGAAATAATCATCA
1 -CATC--AAGAAACCCCTAAAAACTAGGCTTAACTTCTTTAAAAATTCTTTGGAAATAATCATCA
* * *
269207 AGAAACCCCTGAAAATTAGGCTTAGTTTCTAAAAACTCATCCTGAAAA
63 AGAAACACCTGAAAATCAGGCTTAGTTTCTAAAAACTCAT-TTGAAAA
* * *
269255 CATCAAGAAACCTCTAAAAACTAGGCTTAGCTTCTTTTAAAATTCATTTGGAAATAATCATCAAG
1 CATCAAGAAACCCCTAAAAACTAGGCTTAACTTCTTTAAAAATTC-TTTGGAAATAATCATCAAG
* **
269320 AAACACCTGAAAATCAGGATTAGTTTCTTTAAACT-ATTTTTGAAAA
65 AAACACCTGAAAATCAGGCTTAGTTTCTAAAAACTCA--TTTGAAAA
* ** *
269366 CATCAAGAAACCCCTAAAAATTAGGCTTAGTTTCTTTCAAAATTCATTT--AAA-AA-CATCAAG
1 CATCAAGAAACCCCTAAAAACTAGGCTTAACTTCTTTAAAAATTC-TTTGGAAATAATCATCAAG
* *
269427 AAACCCCTGAAAATCAGGCTTAGCTTCT
65 AAACACCTGAAAATCAGGCTTAGTTTCT
269455 TTCAAATTCG
Statistics
Matches: 257, Mismatches: 48, Indels: 18
0.80 0.15 0.06
Matches are distributed among these distances:
107 32 0.12
108 2 0.01
109 3 0.01
110 31 0.12
111 111 0.43
112 7 0.03
113 71 0.28
ACGTcount: A:0.42, C:0.18, G:0.10, T:0.30
Consensus pattern (109 bp):
CATCAAGAAACCCCTAAAAACTAGGCTTAACTTCTTTAAAAATTCTTTGGAAATAATCATCAAGA
AACACCTGAAAATCAGGCTTAGTTTCTAAAAACTCATTTGAAAA
Found at i:269485 original size:165 final size:164
Alignment explanation
Indices: 269089--269500 Score: 421
Period size: 165 Copynumber: 2.5 Consensus size: 164
269079 TGGAAATAAT
* * *
269089 CATCAAGAAACACATAAAAA-TCAGGCTTAGCTTCTTTAAAAATTC-TTTGAAAATAATCAT-AA
1 CATCAAGAAACCCCTAAAAACT-AGGCTTAGCTTCTTTTAAAATTCATTTGAAAATAATCATCAA
** * * * * ** * *
269151 -AAAATTGTTGAAAACCATGCTTAAATTCTTTAAA-AATTCTTGGGAAATAATCATCAAGAAACC
65 GAAACCT-CTGAAAATCAGGATTAGTTTCTTTAAACTATT-TT-TG-AA-AA-CATCAAGAAACC
* *
269214 CCTGAAAATTAGGCTTAGTTTCTAAAAACTCATCCTGAAAA
124 CCTAAAAATTAGGCTTAGTTTCTAAAAACTCATCCTAAAAA
* *
269255 CATCAAGAAACCTCTAAAAACTAGGCTTAGCTTCTTTTAAAATTCATTTGGAAATAATCATCAAG
1 CATCAAGAAACCCCTAAAAACTAGGCTTAGCTTCTTTTAAAATTCATTTGAAAATAATCATCAAG
269320 AAACAC-CTGAAAATCAGGATTAGTTTCTTTAAACTATTTTTGAAAACATCAAGAAACCCCTAAA
66 AAAC-CTCTGAAAATCAGGATTAGTTTCTTTAAACTATTTTTGAAAACATCAAGAAACCCCTAAA
* * *
269384 AATTAGGCTTAGTTTCTTTCAAAATTCAT-TTAAAAA
130 AATTAGGCTTAGTTTC--TAAAAACTCATCCTAAAAA
* * * *
269420 CATCAAGAAACCCCTGAAAA-TCAGGCTTAGCTTC-TTTCAAATTCGTTTGAAAACATTAT-ATC
1 CATCAAGAAACCCCTAAAAACT-AGGCTTAGCTTCTTTTAAAATTCATTTG-AAA-ATAATCATC
269482 AAGAAACCTCTGAAAATCA
63 AAGAAACCTCTGAAAATCA
269501 AGCCTAGATT
Statistics
Matches: 208, Mismatches: 26, Indels: 25
0.80 0.10 0.10
Matches are distributed among these distances:
164 48 0.23
165 59 0.28
166 54 0.26
167 16 0.08
168 25 0.12
169 6 0.03
ACGTcount: A:0.42, C:0.18, G:0.10, T:0.30
Consensus pattern (164 bp):
CATCAAGAAACCCCTAAAAACTAGGCTTAGCTTCTTTTAAAATTCATTTGAAAATAATCATCAAG
AAACCTCTGAAAATCAGGATTAGTTTCTTTAAACTATTTTTGAAAACATCAAGAAACCCCTAAAA
ATTAGGCTTAGTTTCTAAAAACTCATCCTAAAAA
Found at i:278430 original size:15 final size:15
Alignment explanation
Indices: 278410--278445 Score: 72
Period size: 15 Copynumber: 2.4 Consensus size: 15
278400 CCCTTTCCCC
278410 CGACCGACAGTAGGT
1 CGACCGACAGTAGGT
278425 CGACCGACAGTAGGT
1 CGACCGACAGTAGGT
278440 CGACCG
1 CGACCG
278446 TCTCGACCCC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.25, C:0.31, G:0.33, T:0.11
Consensus pattern (15 bp):
CGACCGACAGTAGGT
Done.