Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008954.1 Hibiscus syriacus cultivar Beakdansim tig00112282_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: 488355
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
File 1 of 3
Found at i:4940 original size:21 final size:21
Alignment explanation
Indices: 4898--4940 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
4888 TTTTCGGGCT
* * *
4898 AGGGGAATCGGTACCCATTCA
1 AGGGGAACCGATACCCACTCA
*
4919 AGGGGAACCGATACCCCCTCA
1 AGGGGAACCGATACCCACTCA
4940 A
1 A
4941 CGAATATGAT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.30, G:0.26, T:0.14
Consensus pattern (21 bp):
AGGGGAACCGATACCCACTCA
Found at i:4998 original size:64 final size:65
Alignment explanation
Indices: 4920--5066 Score: 251
Period size: 64 Copynumber: 2.3 Consensus size: 65
4910 ACCCATTCAA
*
4920 GGGGAACCGATACCCCCTCAACGAATATGATTTCCAGAATGCTAGAGGGGAATCGATACCCCA-G
1 GGGGAACCGATACCCCCTCAACGAATATGAATTCCAGAATGCTAGAGGGGAATCGATACCCCAGG
*
4984 GGGGAACCGATACCCCCTCAACGAATATGAATTCCAGAATGCTAGTGGGGAATCGATACCCCAGG
1 GGGGAACCGATACCCCCTCAACGAATATGAATTCCAGAATGCTAGAGGGGAATCGATACCCCA-G
5049 G
65 G
*
5050 GGGGAACCGATTCCCCC
1 GGGGAACCGATACCCCC
5067 ATGAAAAAAA
Statistics
Matches: 78, Mismatches: 3, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
64 61 0.78
66 17 0.22
ACGTcount: A:0.29, C:0.28, G:0.27, T:0.16
Consensus pattern (65 bp):
GGGGAACCGATACCCCCTCAACGAATATGAATTCCAGAATGCTAGAGGGGAATCGATACCCCAGG
Found at i:5705 original size:22 final size:23
Alignment explanation
Indices: 5673--5731 Score: 93
Period size: 22 Copynumber: 2.6 Consensus size: 23
5663 ATCATTATAT
* *
5673 GGCACTACGGTGTAATTCTAC-G
1 GGCACTTCGGTGCAATTCTACGG
5695 GGCACTTCGGTGCAATTCTACGG
1 GGCACTTCGGTGCAATTCTACGG
5718 GGCACTTCGGTGCA
1 GGCACTTCGGTGCA
5732 TTTATACGAG
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
22 19 0.56
23 15 0.44
ACGTcount: A:0.19, C:0.25, G:0.31, T:0.25
Consensus pattern (23 bp):
GGCACTTCGGTGCAATTCTACGG
Found at i:5739 original size:23 final size:23
Alignment explanation
Indices: 5673--5739 Score: 82
Period size: 23 Copynumber: 3.0 Consensus size: 23
5663 ATCATTATAT
* * *
5673 GGCACTACGGTGTAATTCTAC-G
1 GGCACTTCGGTGCAATTATACGG
*
5695 GGCACTTCGGTGCAATTCTACGG
1 GGCACTTCGGTGCAATTATACGG
*
5718 GGCACTTCGGTGCATTTATACG
1 GGCACTTCGGTGCAATTATACG
5740 AGCTGTGGTG
Statistics
Matches: 40, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
22 19 0.47
23 21 0.52
ACGTcount: A:0.19, C:0.24, G:0.28, T:0.28
Consensus pattern (23 bp):
GGCACTTCGGTGCAATTATACGG
Found at i:6569 original size:84 final size:83
Alignment explanation
Indices: 6309--6626 Score: 376
Period size: 84 Copynumber: 3.8 Consensus size: 83
6299 GGGGTGTTAC
* * * * *
6309 ATGATGTGTCTTTGAGCTAAGTGTAATCGAACTCGAAGGTC--T-TTGGAAGATAGCCCTTCTTG
1 ATGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTGTTGGCAGATAACCCTTATTG
* * * *
6371 CCTTAAGCTATGTTGCAA
66 CCTTGAGTTATGATGAAA
* * * * * * *
6389 ATGATGTGCCTTTGAGCTGAGCGTAATCGAACTCGAAGGTATTTGTTGACAAATAACCATTCTAG
1 ATGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTGTTGGCAGATAACCCTTATTG
* *
6454 CCTTGGGTTAT-ACTGTAA
66 CCTTGAGTTATGA-TGAAA
*
6472 ATGATGTGCCTTTGAGCTGAGTGTAATCGAACTTGAAGGTCTTGTGTTGGCAGATAACCCTT-TT
1 ATGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTT-TGTTGGCAGATAACCCTTATT
6536 AGCCTTGAGTTATGATGAAA
65 -GCCTTGAGTTATGATGAAA
* *
6556 ATGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAATGTCTTTTGGTGGCAGATAACCCTTATT
1 ATGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTC-TTTGTTGGCAGATAACCCTTATT
6621 GCCTTG
65 GCCTTG
6627 GGCTATGTTG
Statistics
Matches: 202, Mismatches: 27, Indels: 14
0.83 0.11 0.06
Matches are distributed among these distances:
80 37 0.18
82 1 0.00
83 67 0.33
84 92 0.46
85 5 0.02
ACGTcount: A:0.25, C:0.17, G:0.25, T:0.34
Consensus pattern (83 bp):
ATGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTGTTGGCAGATAACCCTTATTG
CCTTGAGTTATGATGAAA
Found at i:8012 original size:99 final size:100
Alignment explanation
Indices: 7841--8033 Score: 334
Period size: 99 Copynumber: 1.9 Consensus size: 100
7831 TACAAACACA
* * *
7841 TTTATCAGGTTAGTTGAATCTTATCCATAAAGTCGGGGCGTTTAACCAATTGCCTTAGAGGGACA
1 TTTATCAGGTTAGTTGAATCTTATCCATAAAGCCGAGGCGTTTAACAAATTGCCTTAGAGGGACA
7906 ACTCAAGCTTTATTGTATAGATAT-TATAATCACC
66 ACTCAAGCTTTATTGTATAGATATATATAATCACC
7940 TTTATCAGGTTAGTTGAATCTTATCCATAAAGCCGAGGCGTTTAACAAATTGCCTTAGAGGGACA
1 TTTATCAGGTTAGTTGAATCTTATCCATAAAGCCGAGGCGTTTAACAAATTGCCTTAGAGGGACA
* *
8005 TCTCAAGCTTTATTGTATATATATATATA
66 ACTCAAGCTTTATTGTATAGATATATATA
8034 TAATCTGGGT
Statistics
Matches: 88, Mismatches: 5, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
99 84 0.95
100 4 0.05
ACGTcount: A:0.31, C:0.16, G:0.18, T:0.35
Consensus pattern (100 bp):
TTTATCAGGTTAGTTGAATCTTATCCATAAAGCCGAGGCGTTTAACAAATTGCCTTAGAGGGACA
ACTCAAGCTTTATTGTATAGATATATATAATCACC
Found at i:10592 original size:3 final size:3
Alignment explanation
Indices: 10586--10661 Score: 50
Period size: 3 Copynumber: 25.3 Consensus size: 3
10576 TAAGCATTAA
* * *
10586 AAT AAT AAT AAT AAT AAT AA- ACAA AAC AAT -AG AAT AAT AA- AAT
1 AAT AAT AAT AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT AAT
* * *
10629 AAT AAAT CAAG ATT AAT AAA AAT AAT AAT AAT A
1 AAT -AAT -AAT AAT AAT AAT AAT AAT AAT AAT A
10662 GAAAACAAAA
Statistics
Matches: 57, Mismatches: 11, Indels: 10
0.73 0.14 0.13
Matches are distributed among these distances:
2 4 0.07
3 47 0.82
4 6 0.11
ACGTcount: A:0.68, C:0.04, G:0.03, T:0.25
Consensus pattern (3 bp):
AAT
Found at i:11805 original size:21 final size:21
Alignment explanation
Indices: 11775--11829 Score: 60
Period size: 21 Copynumber: 2.7 Consensus size: 21
11765 AACGAAAAGG
* *
11775 AAAAAGAAAT-TAGTAATAAAT
1 AAAAATAAATATAATAAT-AAT
11796 AAAAATAAATATAATAATAAT
1 AAAAATAAATATAATAATAAT
*
11817 AATAAT-AATATAA
1 AAAAATAAATATAA
11830 CATAAACTAT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
20 7 0.23
21 17 0.57
22 6 0.20
ACGTcount: A:0.69, C:0.00, G:0.04, T:0.27
Consensus pattern (21 bp):
AAAAATAAATATAATAATAAT
Found at i:11886 original size:38 final size:36
Alignment explanation
Indices: 11844--12224 Score: 294
Period size: 36 Copynumber: 10.5 Consensus size: 36
11834 AACTATAATA
*
11844 TATATATATATATATATATTTCAAAAATATTTTTAAAC
1 TATATAT-TATATATAT-TTTCAAAAATATTTTAAAAC
* * *
11882 TATATA-T-TATAT-TTTT-AATATTTTTTTCAAAAC
1 TATATATTATATATATTTTCAAAAATATTTT-AAAAC
11915 TATATATTATATA-ATTTTCAAAAATGA-TTT-AAA-
1 TATATATTATATATATTTTCAAAAAT-ATTTTAAAAC
*
11948 -A-ATATTATATA-AGTTTTCAAAAAATGTTTTTAAAAC
1 TATATATTATATATA-TTTTC-AAAAAT-ATTTTAAAAC
11984 TATATATTATATA-ATTTTTCAAAAATATTTTAAAAC
1 TATATATTATATATA-TTTTCAAAAATATTTTAAAAC
* *
12020 TATATATTATAGAAGTTTTTTTTCAAAAATATTTTAAAAAC
1 TATATATTAT---A-TATATTTTCAAAAATATTTT-AAAAC
*
12061 TATATATTATATATATATTTTC-AAAATGATTTCAAAAC
1 TATATA-T-TATATATATTTTCAAAAAT-ATTTTAAAAC
* * * *
12099 TTTATGTTATATATATTTTTAAAAGTATTTTCAAAAAC
1 TATATATTATATATATTTTCAAAAATATTTT--AAAAC
* *
12137 TATATATTATATATGTTTTC-AAAAT-TTTTCAAAAT
1 TATATATTATATATATTTTCAAAAATATTTT-AAAAC
* * * *
12172 TATATAATATATATATTTTC-GAAATGTTTTCGAAAC
1 TATATATTATATATATTTTCAAAAATATTTT-AAAAC
12208 TATATA--ATATATATTTT
1 TATATATTATATATATTTT
12225 AGAAAACTGT
Statistics
Matches: 285, Mismatches: 32, Indels: 56
0.76 0.09 0.15
Matches are distributed among these distances:
31 11 0.04
32 14 0.05
33 20 0.07
34 19 0.07
35 42 0.15
36 61 0.21
37 16 0.06
38 57 0.20
39 12 0.04
40 18 0.06
41 11 0.04
42 1 0.00
43 3 0.01
ACGTcount: A:0.43, C:0.06, G:0.03, T:0.48
Consensus pattern (36 bp):
TATATATTATATATATTTTCAAAAATATTTTAAAAC
Found at i:18365 original size:30 final size:30
Alignment explanation
Indices: 18329--18386 Score: 107
Period size: 30 Copynumber: 1.9 Consensus size: 30
18319 CCACCTTACT
*
18329 TCTCGATCTTACATATTTAAAAAAGATACC
1 TCTCGATCCTACATATTTAAAAAAGATACC
18359 TCTCGATCCTACATATTTAAAAAAGATA
1 TCTCGATCCTACATATTTAAAAAAGATA
18387 ATTACGAAAG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.41, C:0.19, G:0.07, T:0.33
Consensus pattern (30 bp):
TCTCGATCCTACATATTTAAAAAAGATACC
Found at i:24040 original size:17 final size:18
Alignment explanation
Indices: 24020--24060 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 18
24010 TACATTTTCA
* *
24020 ATTTTAT-TTGATTATTT
1 ATTTTATATTGAGTACTT
24037 ATTTT-TATTGAGTACTT
1 ATTTTATATTGAGTACTT
24054 ATTTTAT
1 ATTTTAT
24061 GTTTTTTTTG
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
16 1 0.05
17 18 0.90
18 1 0.05
ACGTcount: A:0.24, C:0.02, G:0.07, T:0.66
Consensus pattern (18 bp):
ATTTTATATTGAGTACTT
Found at i:26101 original size:17 final size:18
Alignment explanation
Indices: 26068--26105 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
26058 AGGATTATCC
*
26068 TTAGGTGTTTTATTTCCT
1 TTAGGTATTTTATTTCCT
26086 TTAGGTATTTTA-TTCCT
1 TTAGGTATTTTATTTCCT
26103 TTA
1 TTA
26106 TTCAATTTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 8 0.42
18 11 0.58
ACGTcount: A:0.16, C:0.11, G:0.13, T:0.61
Consensus pattern (18 bp):
TTAGGTATTTTATTTCCT
Found at i:26223 original size:4 final size:4
Alignment explanation
Indices: 26214--26260 Score: 94
Period size: 4 Copynumber: 11.8 Consensus size: 4
26204 TATTCTTTAT
26214 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTT
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTT
26261 TATATGCTAA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 43 1.00
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (4 bp):
TTTC
Found at i:26870 original size:6 final size:7
Alignment explanation
Indices: 26855--26879 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
26845 AATCATCTAC
26855 TTTTCTT
1 TTTTCTT
26862 TTTTCTT
1 TTTTCTT
26869 TTTTCTT
1 TTTTCTT
26876 TTTT
1 TTTT
26880 ATTCAATTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (7 bp):
TTTTCTT
Found at i:29496 original size:18 final size:18
Alignment explanation
Indices: 29473--29520 Score: 69
Period size: 18 Copynumber: 2.7 Consensus size: 18
29463 ATTGGATACT
**
29473 TCATCTTCATCATTGGAG
1 TCATCTTCATCATTAAAG
*
29491 TCATCTTCATTATTAAAG
1 TCATCTTCATCATTAAAG
29509 TCATCTTCATCA
1 TCATCTTCATCA
29521 CTCCAAGCCA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.27, C:0.23, G:0.08, T:0.42
Consensus pattern (18 bp):
TCATCTTCATCATTAAAG
Found at i:29826 original size:20 final size:20
Alignment explanation
Indices: 29788--29828 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
29778 ACCTACCTCA
* * *
29788 TTCTTCTTCTTGTTTTTCTT
1 TTCTTCTTCATCTTCTTCTT
29808 TTCTTCTTCATCTTCTTCTT
1 TTCTTCTTCATCTTCTTCTT
29828 T
1 T
29829 CTCCTTTACC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.02, C:0.24, G:0.02, T:0.71
Consensus pattern (20 bp):
TTCTTCTTCATCTTCTTCTT
Found at i:32004 original size:26 final size:26
Alignment explanation
Indices: 31975--32028 Score: 74
Period size: 26 Copynumber: 2.1 Consensus size: 26
31965 ACTTAGTGCA
*
31975 TATGGT-GGGAAGAACCTTATGTGTAT
1 TATGGTAGGCAAG-ACCTTATGTGTAT
*
32001 TATGGTAGGCATGACCTTATGTGTAT
1 TATGGTAGGCAAGACCTTATGTGTAT
32027 TA
1 TA
32029 GCACTTCTGT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 21 0.84
27 4 0.16
ACGTcount: A:0.26, C:0.09, G:0.28, T:0.37
Consensus pattern (26 bp):
TATGGTAGGCAAGACCTTATGTGTAT
Found at i:34103 original size:25 final size:26
Alignment explanation
Indices: 34066--34122 Score: 71
Period size: 26 Copynumber: 2.2 Consensus size: 26
34056 TGTTTTCCTT
*
34066 TTTTTGTCTTTTTTCTTTCGAACATC
1 TTTTTATCTTTTTTCTTTCGAACATC
* *
34092 TTTTTATCTTTTTT-TTTTGAACTTC
1 TTTTTATCTTTTTTCTTTCGAACATC
34117 TATTTT
1 T-TTTT
34123 TTTTATGGAG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
25 10 0.37
26 17 0.63
ACGTcount: A:0.12, C:0.14, G:0.05, T:0.68
Consensus pattern (26 bp):
TTTTTATCTTTTTTCTTTCGAACATC
Found at i:47529 original size:13 final size:13
Alignment explanation
Indices: 47511--47535 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
47501 TAAAGAAAAC
47511 AAAGTAAAAACGT
1 AAAGTAAAAACGT
47524 AAAGTAAAAACG
1 AAAGTAAAAACG
47536 GAGATGAAAA
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:0.64, C:0.08, G:0.16, T:0.12
Consensus pattern (13 bp):
AAAGTAAAAACGT
Found at i:60647 original size:7 final size:7
Alignment explanation
Indices: 60635--60669 Score: 70
Period size: 7 Copynumber: 5.0 Consensus size: 7
60625 GGATTGGGTG
60635 TTTAAAA
1 TTTAAAA
60642 TTTAAAA
1 TTTAAAA
60649 TTTAAAA
1 TTTAAAA
60656 TTTAAAA
1 TTTAAAA
60663 TTTAAAA
1 TTTAAAA
60670 AGGTGGGGGC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 28 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (7 bp):
TTTAAAA
Found at i:61010 original size:13 final size:14
Alignment explanation
Indices: 60988--61030 Score: 56
Period size: 13 Copynumber: 3.2 Consensus size: 14
60978 TACTCAATAA
60988 AAAT-AAATAAAAT
1 AAATGAAATAAAAT
61001 AAA-GAAATAAAA-
1 AAATGAAATAAAAT
61013 AAATGAAATGAAAAT
1 AAATGAAAT-AAAAT
61028 AAA
1 AAA
61031 AATGAGTTGT
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
12 3 0.12
13 16 0.62
14 4 0.15
15 3 0.12
ACGTcount: A:0.77, C:0.00, G:0.07, T:0.16
Consensus pattern (14 bp):
AAATGAAATAAAAT
Found at i:64877 original size:14 final size:14
Alignment explanation
Indices: 64858--64886 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
64848 AAAGATAATT
64858 TAAATGTTTTCAAA
1 TAAATGTTTTCAAA
64872 TAAATGTTTTCAAA
1 TAAATGTTTTCAAA
64886 T
1 T
64887 TCAAACTTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.41, C:0.07, G:0.07, T:0.45
Consensus pattern (14 bp):
TAAATGTTTTCAAA
Found at i:66957 original size:15 final size:17
Alignment explanation
Indices: 66928--66959 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
66918 CTTTTATTCA
66928 CTATATTATTCTTATTT
1 CTATATTATTCTTATTT
66945 CTAT-TTATT-TTATTT
1 CTATATTATTCTTATTT
66960 TGAAGAGGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 6 0.40
16 5 0.33
17 4 0.27
ACGTcount: A:0.22, C:0.09, G:0.00, T:0.69
Consensus pattern (17 bp):
CTATATTATTCTTATTT
Found at i:70872 original size:21 final size:21
Alignment explanation
Indices: 70846--70890 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
70836 ATTTATCATG
* *
70846 ATTCCGGCCGCCGCGTACGCT
1 ATTCCGGCCACCGCGGACGCT
*
70867 ATTCCGGCCATCGCGGACGCT
1 ATTCCGGCCACCGCGGACGCT
70888 ATT
1 ATT
70891 ACGACCATCG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.13, C:0.38, G:0.27, T:0.22
Consensus pattern (21 bp):
ATTCCGGCCACCGCGGACGCT
Found at i:70898 original size:21 final size:21
Alignment explanation
Indices: 70857--70901 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
70847 TTCCGGCCGC
* * *
70857 CGCGTACGCTATTCCGGCCAT
1 CGCGGACGCTATTACGACCAT
70878 CGCGGACGCTATTACGACCAT
1 CGCGGACGCTATTACGACCAT
70899 CGC
1 CGC
70902 TGGTAACTCA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.18, C:0.38, G:0.24, T:0.20
Consensus pattern (21 bp):
CGCGGACGCTATTACGACCAT
Found at i:76051 original size:52 final size:52
Alignment explanation
Indices: 75973--76071 Score: 189
Period size: 52 Copynumber: 1.9 Consensus size: 52
75963 GCTAAGTAAG
75973 AATTTAAATTTGAAGCCTTATCAATCTAATTTTTTCCATCTATTTTGCAAGC
1 AATTTAAATTTGAAGCCTTATCAATCTAATTTTTTCCATCTATTTTGCAAGC
*
76025 AATTTAAATTTGATGCCTTATCAATCTAATTTTTTCCATCTATTTTG
1 AATTTAAATTTGAAGCCTTATCAATCTAATTTTTTCCATCTATTTTG
76072 TAGGCATTGA
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
52 46 1.00
ACGTcount: A:0.29, C:0.16, G:0.07, T:0.47
Consensus pattern (52 bp):
AATTTAAATTTGAAGCCTTATCAATCTAATTTTTTCCATCTATTTTGCAAGC
Found at i:79082 original size:18 final size:18
Alignment explanation
Indices: 79050--79090 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
79040 AGGATTTTTA
79050 TTAGG-ATTCTATTTTCT
1 TTAGGTATTCTATTTTCT
*
79067 TTAGGTATTTTATTTTCT
1 TTAGGTATTCTATTTTCT
79085 TTAGGT
1 TTAGGT
79091 TTTCAAGATA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 5 0.23
18 17 0.77
ACGTcount: A:0.17, C:0.07, G:0.15, T:0.61
Consensus pattern (18 bp):
TTAGGTATTCTATTTTCT
Found at i:83319 original size:21 final size:22
Alignment explanation
Indices: 83276--83320 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
83266 TTCTTTAAAT
*
83276 TTAATTTTTATTCTTCGATTAA
1 TTAATTTTTATTCTACGATTAA
83298 TTAATTCTTTATT-TAC-ATTAA
1 TTAATT-TTTATTCTACGATTAA
83319 TT
1 TT
83321 TTTGTTTAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 7 0.33
22 8 0.38
23 6 0.29
ACGTcount: A:0.29, C:0.09, G:0.02, T:0.60
Consensus pattern (22 bp):
TTAATTTTTATTCTACGATTAA
Found at i:84842 original size:59 final size:52
Alignment explanation
Indices: 84740--84850 Score: 159
Period size: 59 Copynumber: 2.0 Consensus size: 52
84730 TCTTACCGCC
84740 GTGTTGCTATTTTCGATTATGGCTTTACTTATTTTCTATGGATGCCTAGATG
1 GTGTTGCTATTTTCGATTATGGCTTTACTTATTTTCTATGGATGCCTAGATG
84792 GTGTTGCTATTTTCGATATTATGGACTTTACTTATGCATTTTCTATGGATGCCTAGATG
1 GTGTTGCTATTTTCG--ATTATGG-CTTTAC-T-T--ATTTTCTATGGATGCCTAGATG
84851 AGCTTGCTTG
Statistics
Matches: 52, Mismatches: 0, Indels: 7
0.88 0.00 0.12
Matches are distributed among these distances:
52 15 0.29
54 7 0.13
55 6 0.12
56 1 0.02
57 1 0.02
59 22 0.42
ACGTcount: A:0.19, C:0.14, G:0.21, T:0.47
Consensus pattern (52 bp):
GTGTTGCTATTTTCGATTATGGCTTTACTTATTTTCTATGGATGCCTAGATG
Found at i:85326 original size:106 final size:104
Alignment explanation
Indices: 85179--85390 Score: 365
Period size: 107 Copynumber: 2.0 Consensus size: 104
85169 AGTTAAGTGA
85179 GGGATAGAGATTTCATCGAATTTCTTACTTTTCTTGTGATTTGTTTG-TTGTATATGTGGTTGAC
1 GGGATAGAGATTTCATCGAATTTCTTACTTTTCTTGTGATTTGTTTGATTGTATAT-TGGTTGAC
85243 -TGGAGGTAACTTGATTAAAATTCTTCGCTTTCGTTGATT
65 TTGGAGGTAACTTGATTAAAATTCTTCGCTTTCGTTGATT
*
85282 GGGATAGAGATTTCATCGAATTTCTTCTTACTTTTCTTGTGATTTGTTTGATTGTATGTTGGTTG
1 GGGATAGAGATTTCATCGAA--T-TTCTTACTTTTCTTGTGATTTGTTTGATTGTATATTGGTTG
85347 ACTTGGAGGTAACTTGATTAAAATTCTTCGCTTTCGTTGATT
63 ACTTGGAGGTAACTTGATTAAAATTCTTCGCTTTCGTTGATT
85389 GG
1 GG
85391 TTTTAATATG
Statistics
Matches: 103, Mismatches: 1, Indels: 6
0.94 0.01 0.05
Matches are distributed among these distances:
103 20 0.19
105 1 0.01
106 34 0.33
107 48 0.47
ACGTcount: A:0.20, C:0.11, G:0.23, T:0.47
Consensus pattern (104 bp):
GGGATAGAGATTTCATCGAATTTCTTACTTTTCTTGTGATTTGTTTGATTGTATATTGGTTGACT
TGGAGGTAACTTGATTAAAATTCTTCGCTTTCGTTGATT
Found at i:85996 original size:22 final size:24
Alignment explanation
Indices: 85944--86009 Score: 84
Period size: 22 Copynumber: 2.9 Consensus size: 24
85934 TTTTTTTGGG
*
85944 AAGAAA-AAAAAGGAAAAAATCGA
1 AAGAAAGAAAAAGAAAAAAATCGA
*
85967 AAGAAAGAGAAAGAAAAAAATCG-
1 AAGAAAGAAAAAGAAAAAAATCGA
*
85990 AA-TAAGAAAAAGAAAAAAAT
1 AAGAAAGAAAAAGAAAAAAAT
86010 GTTGTTTCAT
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
22 16 0.42
23 8 0.21
24 14 0.37
ACGTcount: A:0.74, C:0.03, G:0.17, T:0.06
Consensus pattern (24 bp):
AAGAAAGAAAAAGAAAAAAATCGA
Found at i:89418 original size:42 final size:42
Alignment explanation
Indices: 89339--89424 Score: 120
Period size: 42 Copynumber: 2.0 Consensus size: 42
89329 ACACAAACAA
* *
89339 CGCAATAGGTATGTTCTTTAACGGCATTTATTCAACAAATGC
1 CGCAATAGGTATGTTCTTTAACGGCATTTATTAAACAAACGC
* *
89381 CGCAATAGTTATGTTCTTTAACGGCGTTT-TTAAAACAAACGC
1 CGCAATAGGTATGTTCTTTAACGGCATTTATT-AAACAAACGC
89423 CG
1 CG
89425 TAAAATGCTT
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
41 2 0.05
42 37 0.95
ACGTcount: A:0.30, C:0.20, G:0.17, T:0.33
Consensus pattern (42 bp):
CGCAATAGGTATGTTCTTTAACGGCATTTATTAAACAAACGC
Found at i:90255 original size:63 final size:64
Alignment explanation
Indices: 90170--90297 Score: 249
Period size: 63 Copynumber: 2.0 Consensus size: 64
90160 AATAATTAAT
90170 TCAAATAAAAAATGTTATGGTACTGATATAAATAAAGTCAGGAAAAATTAAAACCTCTATCCAA
1 TCAAATAAAAAATGTTATGGTACTGATATAAATAAAGTCAGGAAAAATTAAAACCTCTATCCAA
90234 TCAAAT-AAAAATGTTATGGTACTGATATAAATAAAGTCAGGAAAAATTAAAACCTCTATCCAA
1 TCAAATAAAAAATGTTATGGTACTGATATAAATAAAGTCAGGAAAAATTAAAACCTCTATCCAA
90297 T
1 T
90298 AAACGTACCA
Statistics
Matches: 64, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
63 58 0.91
64 6 0.09
ACGTcount: A:0.49, C:0.12, G:0.11, T:0.27
Consensus pattern (64 bp):
TCAAATAAAAAATGTTATGGTACTGATATAAATAAAGTCAGGAAAAATTAAAACCTCTATCCAA
Found at i:97037 original size:82 final size:83
Alignment explanation
Indices: 96900--97165 Score: 268
Period size: 82 Copynumber: 3.2 Consensus size: 83
96890 ATTTTTGTAC
* * * ** * * *
96900 AAATATTTTGCGACGTTTGTTA-AAAAAAACCACTATATATTACACATATTGCGGCGTTTGTACA
1 AAATATTTTGCGGCGTTTGGTATCAAAACGCCACTATAGATTACACCTATTGCGGCGTTTGTATA
96964 AAAACGCAGCTAAAGTAT
66 AAAACGCAGCTAAAGTAT
* * * * *
96982 AAATATTTTGCGGCGTTT-TTATCCAAACGCCACTCTTGATTACACCTATTGCGGCGTTTTTATA
1 AAATATTTTGCGGCGTTTGGTATCAAAACGCCACTATAGATTACACCTATTGCGGCGTTTGTATA
* * ***
97046 AAAATGCCGCTTTTGTAT
66 AAAACGCAGCTAAAGTAT
* * * * *
97064 ACATATTTTACGGTGTTTGGTATTAAAACGCCACTATAGATTACACCTATTGCGGCATTTGTATA
1 AAATATTTTGCGGCGTTTGGTATCAAAACGCCACTATAGATTACACCTATTGCGGCGTTTGTATA
*
97129 AAAACGCCA-CTAAAGTAC
66 AAAACG-CAGCTAAAGTAT
*
97147 AAATATTTTTGCGACGTTT
1 AAATA-TTTTGCGGCGTTT
97166 CTTGAAAAAC
Statistics
Matches: 144, Mismatches: 36, Indels: 6
0.77 0.19 0.03
Matches are distributed among these distances:
81 3 0.02
82 77 0.53
83 53 0.37
84 11 0.08
ACGTcount: A:0.32, C:0.18, G:0.15, T:0.35
Consensus pattern (83 bp):
AAATATTTTGCGGCGTTTGGTATCAAAACGCCACTATAGATTACACCTATTGCGGCGTTTGTATA
AAAACGCAGCTAAAGTAT
Found at i:97133 original size:41 final size:41
Alignment explanation
Indices: 96907--97140 Score: 152
Period size: 41 Copynumber: 5.7 Consensus size: 41
96897 TACAAATATT
* ** *
96907 TTGCGACGTTTGT-TAAAAAAAACCACTATATATTACACATA
1 TTGCGGCGTTTGTAT-AAAAACGCCACTATAGATTACACATA
* * * * *
96948 TTGCGGCGTTTGTACAAAAACG-CAGCTAAAG-TATAAATATT
1 TTGCGGCGTTTGTATAAAAACGCCA-CTATAGAT-TACACATA
* ** * * *
96989 TTGCGGCGTTTTTATCCAAACGCCACTCTTGATTACACCTA
1 TTGCGGCGTTTGTATAAAAACGCCACTATAGATTACACATA
* * * * * * *
97030 TTGCGGCGTTTTTATAAAAATGCCGCTTTTG-TATACATATT
1 TTGCGGCGTTTGTATAAAAACGCCACTATAGAT-TACACATA
* * * *
97071 TTACGGTGTTTGGTATTAAAACGCCACTATAGATTACACCTA
1 TTGCGGCGTTT-GTATAAAAACGCCACTATAGATTACACATA
*
97113 TTGCGGCATTTGTATAAAAACGCCACTA
1 TTGCGGCGTTTGTATAAAAACGCCACTA
97141 AAGTACAAAT
Statistics
Matches: 142, Mismatches: 43, Indels: 16
0.71 0.21 0.08
Matches are distributed among these distances:
40 4 0.03
41 107 0.75
42 30 0.21
43 1 0.01
ACGTcount: A:0.31, C:0.19, G:0.16, T:0.34
Consensus pattern (41 bp):
TTGCGGCGTTTGTATAAAAACGCCACTATAGATTACACATA
Found at i:97175 original size:83 final size:81
Alignment explanation
Indices: 96896--97211 Score: 267
Period size: 83 Copynumber: 3.8 Consensus size: 81
96886 AGGTATTTTT
* * *
96896 GTACAAATATTTTGCGACGTTTGTTAAAAAAAACCACTATATATTACACATATTGCGGCGTTTGT
1 GTACAAATATTTTGCGACGTTTGTT-AAAAACACCACTATAGATTACACCTATTGCGGCGTTTGT
*
96961 ACAAAAACG-CAGCTAAA
65 ATAAAAACGCCA-CTAAA
* * * * * * *
96978 GTATAAATATTTTGCGGCGTTT-TTATCCAAACGCCACTCTTGATTACACCTATTGCGGCGTTTT
1 GTACAAATATTTTGCGACGTTTGTTA--AAAACACCACTATAGATTACACCTATTGCGGCGTTTG
* * ***
97042 TATAAAAATGCCGCTTTT
64 TATAAAAACGCCACTAAA
* * * ** * * *
97060 GTATACATATTTTACGGTGTTTGGTATTAAAACGCCACTATAGATTACACCTATTGCGGCATTTG
1 GTACAAATATTTTGCGACGTTT-GT-TAAAAACACCACTATAGATTACACCTATTGCGGCGTTTG
97125 TATAAAAACGCCACTAAA
64 TATAAAAACGCCACTAAA
* * * * * * *
97143 GTACAAATATTTTTGCGACGTTTCTTGAAAAACACAACTATATAGTAAACCTATTGCGACGTTTT
1 GTACAAATA-TTTTGCGACGTTTGTT-AAAAACACCACTATAGATTACACCTATTGCGGCGTTTG
97208 TATA
64 TATA
97212 TAAATACCGC
Statistics
Matches: 181, Mismatches: 45, Indels: 15
0.75 0.19 0.06
Matches are distributed among these distances:
80 1 0.01
81 2 0.01
82 79 0.44
83 87 0.48
84 11 0.06
85 1 0.01
ACGTcount: A:0.33, C:0.18, G:0.15, T:0.34
Consensus pattern (81 bp):
GTACAAATATTTTGCGACGTTTGTTAAAAACACCACTATAGATTACACCTATTGCGGCGTTTGTA
TAAAAACGCCACTAAA
Found at i:97448 original size:15 final size:17
Alignment explanation
Indices: 97417--97449 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 17
97407 ACTTAACAAC
97417 AGAATACATTAAAATTT
1 AGAATACATTAAAATTT
97434 AGAA-ACATT-AAATTT
1 AGAATACATTAAAATTT
97449 A
1 A
97450 TGTATAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.44
16 5 0.31
17 4 0.25
ACGTcount: A:0.55, C:0.06, G:0.06, T:0.33
Consensus pattern (17 bp):
AGAATACATTAAAATTT
Found at i:98253 original size:22 final size:22
Alignment explanation
Indices: 98226--98274 Score: 80
Period size: 22 Copynumber: 2.2 Consensus size: 22
98216 CACGTTTTGA
98226 AAAGCTATTATTATCATATTCG
1 AAAGCTATTATTATCATATTCG
* *
98248 AAAGCTATTATTTTTATATTCG
1 AAAGCTATTATTATCATATTCG
98270 AAAGC
1 AAAGC
98275 AGAAAAACGC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.37, C:0.12, G:0.10, T:0.41
Consensus pattern (22 bp):
AAAGCTATTATTATCATATTCG
Found at i:99450 original size:45 final size:45
Alignment explanation
Indices: 99401--99573 Score: 210
Period size: 45 Copynumber: 3.9 Consensus size: 45
99391 ATGGTGCTGG
* *
99401 TGGTGCAGGTGGTGCTGGAGGAGGCTGGAAGGGGTTTGGAAATAG
1 TGGTGCAGGTGGTGCTGGAGGAGGCTGGAAGGGGTTTGGAATTAA
* *
99446 TGGTGCAGGAGGTGCTGGAGGAGGCTGGAAGGGGTTCGGAATTAA
1 TGGTGCAGGTGGTGCTGGAGGAGGCTGGAAGGGGTTTGGAATTAA
* * * *
99491 TGGAGCTGGCGGTGCCGGAGGAGGCTGGAAGGGGTTTGGAATTAA
1 TGGTGCAGGTGGTGCTGGAGGAGGCTGGAAGGGGTTTGGAATTAA
* * * *
99536 T-G-G-AGCTGGTGCTGGAGGA-GCTGAAATGGATTTGGAAT
1 TGGTGCAGGTGGTGCTGGAGGAGGCTGGAAGGGGTTTGGAAT
99574 AAGTGGAGCT
Statistics
Matches: 112, Mismatches: 16, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
41 16 0.14
42 12 0.11
43 1 0.01
44 1 0.01
45 82 0.73
ACGTcount: A:0.21, C:0.09, G:0.48, T:0.22
Consensus pattern (45 bp):
TGGTGCAGGTGGTGCTGGAGGAGGCTGGAAGGGGTTTGGAATTAA
Found at i:99582 original size:41 final size:42
Alignment explanation
Indices: 99410--99621 Score: 183
Period size: 45 Copynumber: 5.1 Consensus size: 42
99400 GTGGTGCAGG
* * * *
99410 TGGTGCTGGAGGAGGCTGGAAGGGGTTTGGAAATAGTGGTGCAGG
1 TGGTGCTGGAGGAGGCTGAAAGGGGTTTGGAATTAAT-G-G-AGC
* * *
99455 AGGTGCTGGAGGAGGCTGGAAGGGGTTCGGAATTAATGGAGC
1 TGGTGCTGGAGGAGGCTGAAAGGGGTTTGGAATTAATGGAGC
* *
99497 TGGCGGTGCCGGAGGAGGCTGGAAGGGGTTTGGAATTAATGGAGC
1 T---GGTGCTGGAGGAGGCTGAAAGGGGTTTGGAATTAATGGAGC
* *
99542 TGGTGCTGGAGGA-GCTGAAATGGATTTGGAA-TAAGTGGAGC
1 TGGTGCTGGAGGAGGCTGAAAGGGGTTTGGAATTAA-TGGAGC
*
99583 T-G-G-T---GGAGGCTGAAA-GGG-TTGGAATTAGTGGAGC
1 TGGTGCTGGAGGAGGCTGAAAGGGGTTTGGAATTAATGGAGC
99617 TGGTG
1 TGGTG
99622 GAGGTTGAAA
Statistics
Matches: 145, Mismatches: 14, Indels: 25
0.79 0.08 0.14
Matches are distributed among these distances:
34 13 0.09
35 8 0.06
36 8 0.06
38 1 0.01
39 1 0.01
40 4 0.03
41 22 0.15
42 13 0.09
43 1 0.01
44 1 0.01
45 73 0.50
ACGTcount: A:0.22, C:0.08, G:0.48, T:0.22
Consensus pattern (42 bp):
TGGTGCTGGAGGAGGCTGAAAGGGGTTTGGAATTAATGGAGC
Found at i:99606 original size:34 final size:34
Alignment explanation
Indices: 99567--99631 Score: 112
Period size: 34 Copynumber: 1.9 Consensus size: 34
99557 TGAAATGGAT
99567 TTGGAATAAGTGGAGCTGGTGGAGGCTGAAAGGG
1 TTGGAATAAGTGGAGCTGGTGGAGGCTGAAAGGG
* *
99601 TTGGAATTAGTGGAGCTGGTGGAGGTTGAAA
1 TTGGAATAAGTGGAGCTGGTGGAGGCTGAAA
99632 AGGATTTGGA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 29 1.00
ACGTcount: A:0.26, C:0.05, G:0.45, T:0.25
Consensus pattern (34 bp):
TTGGAATAAGTGGAGCTGGTGGAGGCTGAAAGGG
Found at i:99652 original size:70 final size:77
Alignment explanation
Indices: 99510--99658 Score: 179
Period size: 70 Copynumber: 2.0 Consensus size: 77
99500 CGGTGCCGGA
* *
99510 GGAGGCTGGAAGGGGTTTGGAATTAATGGAGCTGGTGCTGGAGGAGCTGAAATGGATTTGGAATA
1 GGAGGCTGGAAAGGGTTTGGAATTAATGGAGCTGGTGCTGGAGGAGCTGAAAAGGATTTGGAATA
* *
99575 AGTGGAGCTGGT
66 AGCGGAGCGGGT
* *
99587 GGAGGCT-GAAAGGG-TTGGAATTAGTGGAGCT-G-G-TGGA-G-GTTGAAAAGGATTTGGAATC
1 GGAGGCTGGAAAGGGTTTGGAATTAATGGAGCTGGTGCTGGAGGAGCTGAAAAGGATTTGGAAT-
99645 AA-CGGAGCGGGT
65 AAGCGGAGCGGGT
99657 GG
1 GG
99659 CGGCAGTATA
Statistics
Matches: 65, Mismatches: 6, Indels: 9
0.81 0.08 0.11
Matches are distributed among these distances:
70 27 0.42
71 3 0.05
72 4 0.06
73 1 0.02
74 1 0.02
75 16 0.25
76 6 0.09
77 7 0.11
ACGTcount: A:0.26, C:0.07, G:0.45, T:0.23
Consensus pattern (77 bp):
GGAGGCTGGAAAGGGTTTGGAATTAATGGAGCTGGTGCTGGAGGAGCTGAAAAGGATTTGGAATA
AGCGGAGCGGGT
Found at i:108671 original size:21 final size:21
Alignment explanation
Indices: 108634--108687 Score: 62
Period size: 21 Copynumber: 2.7 Consensus size: 21
108624 ATGCCAAAAT
*
108634 GTATCGATACC---GAAATAG
1 GTATCGATACCATAGAAATAA
108652 GTATCGATACCATAGAAATAA
1 GTATCGATACCATAGAAATAA
108673 GTATC-AGTACCATAG
1 GTATCGA-TACCATAG
108688 TAGGAGTACT
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
18 11 0.35
20 1 0.03
21 19 0.61
ACGTcount: A:0.41, C:0.17, G:0.19, T:0.24
Consensus pattern (21 bp):
GTATCGATACCATAGAAATAA
Found at i:109327 original size:22 final size:23
Alignment explanation
Indices: 109251--109356 Score: 148
Period size: 24 Copynumber: 4.7 Consensus size: 23
109241 GTCGAGGTTT
109251 CTATGTGGTCCTTCGAGACAAAAC
1 CTATGTGGTCCTTCG-GACAAAAC
*
109275 CTATGTGGCCCTTCGGGACAAAAC
1 CTATGTGGTCCTTC-GGACAAAAC
*
109299 CTATGTGGCCCTTCGGACAAAA-
1 CTATGTGGTCCTTCGGACAAAAC
109321 CTATGTGGTCCTTCGGAC-AAA-
1 CTATGTGGTCCTTCGGACAAAAC
109342 -TATGTGGTCCTTCGG
1 CTATGTGGTCCTTCGG
109357 GATAAATATG
Statistics
Matches: 79, Mismatches: 2, Indels: 6
0.91 0.02 0.07
Matches are distributed among these distances:
20 15 0.19
21 3 0.04
22 17 0.22
23 8 0.10
24 35 0.44
25 1 0.01
ACGTcount: A:0.24, C:0.25, G:0.25, T:0.26
Consensus pattern (23 bp):
CTATGTGGTCCTTCGGACAAAAC
Found at i:109335 original size:46 final size:44
Alignment explanation
Indices: 109251--109356 Score: 144
Period size: 42 Copynumber: 2.4 Consensus size: 44
109241 GTCGAGGTTT
109251 CTATGTGGTCCTTCGAGACAAAACCTATGTGGCCCTTCGGGACAAAA
1 CTATGTGGTCCTTCG-GACAAAACCTATGTGGCCCTTC-GGAC-AAA
* *
109298 CCTATGTGGCCCTTCGGACAAAA-CTATGTGGTCCTTCGGACAAA
1 -CTATGTGGTCCTTCGGACAAAACCTATGTGGCCCTTCGGACAAA
109342 -TATGTGGTCCTTCGG
1 CTATGTGGTCCTTCGG
109357 GATAAATATG
Statistics
Matches: 55, Mismatches: 3, Indels: 6
0.86 0.05 0.09
Matches are distributed among these distances:
42 14 0.25
44 3 0.05
45 4 0.07
46 13 0.24
47 7 0.13
48 14 0.25
ACGTcount: A:0.24, C:0.25, G:0.25, T:0.26
Consensus pattern (44 bp):
CTATGTGGTCCTTCGGACAAAACCTATGTGGCCCTTCGGACAAA
Found at i:110788 original size:22 final size:21
Alignment explanation
Indices: 110745--110788 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 21
110735 AGACGCTTGG
* *
110745 CTTTGTACGCATAACTCTAAA
1 CTTTGTACGCATAACCCCAAA
*
110766 CTTTGTGCGCAATAACCCCAAA
1 CTTTGTACGC-ATAACCCCAAA
110788 C
1 C
110789 ATAAAGGGAT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
21 9 0.47
22 10 0.53
ACGTcount: A:0.32, C:0.30, G:0.11, T:0.27
Consensus pattern (21 bp):
CTTTGTACGCATAACCCCAAA
Found at i:110998 original size:3 final size:3
Alignment explanation
Indices: 110986--111023 Score: 62
Period size: 3 Copynumber: 13.3 Consensus size: 3
110976 TTAATCCGAG
110986 ATA A-A ATA ATA ATA ATA ATA ATA ATA AT- ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
111024 ATATTATTAT
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
2 4 0.12
3 29 0.88
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:111483 original size:21 final size:21
Alignment explanation
Indices: 111459--111547 Score: 67
Period size: 21 Copynumber: 4.2 Consensus size: 21
111449 GGGTTAAGAC
*
111459 CTTTCGATGAAATGACTTAAT
1 CTTTCGATGAAAGGACTTAAT
* *
111480 CTTTCAATTAAAGGACTT-AT
1 CTTTCGATGAAAGGACTTAAT
* *
111500 CCTTTTGATGAAAAGTG-CTTAAC
1 -CTTTCGATG-AAAG-GACTTAAT
*
111523 CTTTTC-ATGAAAGGATTTAAT
1 C-TTTCGATGAAAGGACTTAAT
111544 CTTT
1 CTTT
111548 ACATGAAGAG
Statistics
Matches: 52, Mismatches: 10, Indels: 13
0.69 0.13 0.17
Matches are distributed among these distances:
20 6 0.12
21 30 0.58
22 11 0.21
23 5 0.10
ACGTcount: A:0.31, C:0.15, G:0.13, T:0.40
Consensus pattern (21 bp):
CTTTCGATGAAAGGACTTAAT
Found at i:125520 original size:89 final size:90
Alignment explanation
Indices: 125367--125538 Score: 276
Period size: 89 Copynumber: 1.9 Consensus size: 90
125357 AACTTTTTCC
* * * *
125367 TTAAATCACCAAAAGTAAATATGGATAACTCAAACAATTTAGGTGTTTAATTGAAAAAATAAAAC
1 TTAAATCACCAAAAGTAAACATGGATAACTAAAAAAATTTAGGTGTTTAATTGAAAAAAGAAAAC
125432 TTAAATATC-AAC-ACATATCATCT
66 TTAAATATCTAACTACATATCATCT
*
125455 TTAAATCAATCAAAAGTAAACATGGATAACTAAAAAAATTTAGGTGTTTAATTGAAAAAAGAAAA
1 TTAAATC-ACCAAAAGTAAACATGGATAACTAAAAAAATTTAGGTGTTTAATTGAAAAAAGAAAA
125520 CTTAAATATCTAACTACAT
65 CTTAAATATCTAACTACAT
125539 CATTAAAAAG
Statistics
Matches: 76, Mismatches: 5, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
88 7 0.09
89 62 0.82
90 3 0.04
91 4 0.05
ACGTcount: A:0.51, C:0.12, G:0.09, T:0.29
Consensus pattern (90 bp):
TTAAATCACCAAAAGTAAACATGGATAACTAAAAAAATTTAGGTGTTTAATTGAAAAAAGAAAAC
TTAAATATCTAACTACATATCATCT
Found at i:126471 original size:24 final size:25
Alignment explanation
Indices: 126413--126474 Score: 72
Period size: 25 Copynumber: 2.5 Consensus size: 25
126403 TAGGATATTA
* ** *
126413 TTTTAAATATTTTAGTTTATCTTTG
1 TTTTAAGTATTTTAGTTTATAATAG
*
126438 TTTTAGGTATTTTAGTTTA-AATAG
1 TTTTAAGTATTTTAGTTTATAATAG
126462 TTTTAAGTATTTT
1 TTTTAAGTATTTT
126475 TATTAGGATA
Statistics
Matches: 31, Mismatches: 6, Indels: 1
0.82 0.16 0.03
Matches are distributed among these distances:
24 14 0.45
25 17 0.55
ACGTcount: A:0.26, C:0.02, G:0.11, T:0.61
Consensus pattern (25 bp):
TTTTAAGTATTTTAGTTTATAATAG
Found at i:127144 original size:17 final size:18
Alignment explanation
Indices: 127122--127163 Score: 68
Period size: 17 Copynumber: 2.4 Consensus size: 18
127112 CTTTAAATTA
127122 TTTATTTAATTATT-TCT
1 TTTATTTAATTATTATCT
*
127139 TTTATTTAATTCTTATCT
1 TTTATTTAATTATTATCT
127157 TTTATTT
1 TTTATTT
127164 TAAAAATAAC
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 13 0.57
18 10 0.43
ACGTcount: A:0.21, C:0.07, G:0.00, T:0.71
Consensus pattern (18 bp):
TTTATTTAATTATTATCT
Found at i:131898 original size:32 final size:32
Alignment explanation
Indices: 131862--131926 Score: 130
Period size: 32 Copynumber: 2.0 Consensus size: 32
131852 TGATAAGTCG
131862 AGTATCGTCTCCACAGGGAATTGGGGAAATCA
1 AGTATCGTCTCCACAGGGAATTGGGGAAATCA
131894 AGTATCGTCTCCACAGGGAATTGGGGAAATCA
1 AGTATCGTCTCCACAGGGAATTGGGGAAATCA
131926 A
1 A
131927 ATAGGTTTGT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.32, C:0.18, G:0.28, T:0.22
Consensus pattern (32 bp):
AGTATCGTCTCCACAGGGAATTGGGGAAATCA
Found at i:141464 original size:10 final size:10
Alignment explanation
Indices: 141449--141488 Score: 62
Period size: 10 Copynumber: 3.9 Consensus size: 10
141439 TATTTTTTTT
*
141449 AAAAAAACAAA
1 AAAAAAA-AAC
141460 AAAAAAAAAC
1 AAAAAAAAAC
141470 AAAAAAAAAC
1 AAAAAAAAAC
141480 AAAAAAAAA
1 AAAAAAAAA
141489 GCCAAAATTT
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
10 21 0.75
11 7 0.25
ACGTcount: A:0.93, C:0.07, G:0.00, T:0.00
Consensus pattern (10 bp):
AAAAAAAAAC
Found at i:141467 original size:13 final size:13
Alignment explanation
Indices: 141449--141488 Score: 64
Period size: 13 Copynumber: 3.1 Consensus size: 13
141439 TATTTTTTTT
141449 AAAAAAACAAAAA
1 AAAAAAACAAAAA
141462 AAAAAAACAAAAA
1 AAAAAAACAAAAA
141475 AAAACAAA-AAAAA
1 AAAA-AAACAAAAA
141488 A
1 A
141489 GCCAAAATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
13 23 0.88
14 3 0.12
ACGTcount: A:0.93, C:0.07, G:0.00, T:0.00
Consensus pattern (13 bp):
AAAAAAACAAAAA
Found at i:141495 original size:11 final size:11
Alignment explanation
Indices: 141449--141495 Score: 51
Period size: 12 Copynumber: 4.2 Consensus size: 11
141439 TATTTTTTTT
*
141449 AAAAAAACAAAA
1 AAAAAAAC-CAA
*
141461 AAAAAAAACAA
1 AAAAAAACCAA
141472 AAAAAAA-CAA
1 AAAAAAACCAA
141482 AAAAAAAGCCAA
1 AAAAAAA-CCAA
141494 AA
1 AA
141496 TTTCAAAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
10 10 0.32
11 9 0.29
12 12 0.39
ACGTcount: A:0.87, C:0.11, G:0.02, T:0.00
Consensus pattern (11 bp):
AAAAAAACCAA
Found at i:141508 original size:1 final size:1
Alignment explanation
Indices: 141449--141488 Score: 53
Period size: 1 Copynumber: 40.0 Consensus size: 1
141439 TATTTTTTTT
* * *
141449 AAAAAAACAAAAAAAAAAAACAAAAAAAAACAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
141489 GCCAAAATTT
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
1 33 1.00
ACGTcount: A:0.93, C:0.07, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:156756 original size:3 final size:3
Alignment explanation
Indices: 156748--156775 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
156738 TGGAAGTTAG
156748 CTT CTT CTT CTT CTT CTT CTT CTT CTT C
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT C
156776 CACCGTAAGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (3 bp):
CTT
Found at i:160341 original size:20 final size:18
Alignment explanation
Indices: 160319--160359 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
160309 CTTTAAATTA
160319 TTTATTT-ATTATT-TCT
1 TTTATTTAATTATTATCT
*
160335 TTTATTTAATTCTTATCT
1 TTTATTTAATTATTATCT
160353 TTTATTT
1 TTTATTT
160360 TTAAAAAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 7 0.32
17 5 0.23
18 10 0.45
ACGTcount: A:0.20, C:0.07, G:0.00, T:0.73
Consensus pattern (18 bp):
TTTATTTAATTATTATCT
Found at i:166786 original size:16 final size:15
Alignment explanation
Indices: 166766--166825 Score: 68
Period size: 16 Copynumber: 3.9 Consensus size: 15
166756 ATTATTTGGA
*
166766 ATTTTTATATTATTCT
1 ATTTTTATATT-TTAT
*
166782 -TTTTTCGTATTTTAT
1 ATTTTT-ATATTTTAT
166797 ATTTTTATATTTTTAT
1 ATTTTTATA-TTTTAT
166813 ATTTTTATATTTT
1 ATTTTTATATTTT
166826 TAATTATTTG
Statistics
Matches: 38, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
15 14 0.37
16 24 0.63
ACGTcount: A:0.22, C:0.03, G:0.02, T:0.73
Consensus pattern (15 bp):
ATTTTTATATTTTAT
Found at i:166802 original size:8 final size:8
Alignment explanation
Indices: 166791--166827 Score: 74
Period size: 8 Copynumber: 4.6 Consensus size: 8
166781 TTTTTTCGTA
166791 TTTTATAT
1 TTTTATAT
166799 TTTTATAT
1 TTTTATAT
166807 TTTTATAT
1 TTTTATAT
166815 TTTTATAT
1 TTTTATAT
166823 TTTTA
1 TTTTA
166828 ATTATTTGGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 29 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (8 bp):
TTTTATAT
Found at i:166809 original size:23 final size:24
Alignment explanation
Indices: 166766--166827 Score: 72
Period size: 23 Copynumber: 2.6 Consensus size: 24
166756 ATTATTTGGA
* * * *
166766 ATTTTTATATTATTCTTTTTTCGT
1 ATTTTTATATTTTTATATTTTCAT
*
166790 A-TTTTATATTTTTATATTTTTAT
1 ATTTTTATATTTTTATATTTTCAT
166813 ATTTTTATATTTTTA
1 ATTTTTATATTTTTA
166828 ATTATTTGGA
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
23 18 0.56
24 14 0.44
ACGTcount: A:0.23, C:0.03, G:0.02, T:0.73
Consensus pattern (24 bp):
ATTTTTATATTTTTATATTTTCAT
Found at i:166824 original size:31 final size:31
Alignment explanation
Indices: 166766--166825 Score: 77
Period size: 31 Copynumber: 1.9 Consensus size: 31
166756 ATTATTTGGA
* *
166766 ATTTTTATATTATTCTTTTTTCGTATTTTAT
1 ATTTTTATATTATTATTTTTTCATATTTTAT
*
166797 ATTTTTATATTTTTATATTTTT-ATATTTT
1 ATTTTTATATTATTAT-TTTTTCATATTTT
166826 TAATTATTTG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
31 20 0.80
32 5 0.20
ACGTcount: A:0.22, C:0.03, G:0.02, T:0.73
Consensus pattern (31 bp):
ATTTTTATATTATTATTTTTTCATATTTTAT
Found at i:168128 original size:3 final size:3
Alignment explanation
Indices: 168120--168220 Score: 105
Period size: 3 Copynumber: 33.0 Consensus size: 3
168110 TTTTACTTAA
* ** *
168120 ATT ATT ATT TTT AAA ATT ACT ATT ATT ATT ATT AATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT -ATT ATT ATT ATT
* * *
168166 ATT ACT ATA ACT ATT ATT ATT ATT ATT ATT ATT ATAT ATT A-T ATAT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT-T ATT ATT AT-T
168212 ATT ATT ATT
1 ATT ATT ATT
168221 TAATAATATT
Statistics
Matches: 80, Mismatches: 14, Indels: 8
0.78 0.14 0.08
Matches are distributed among these distances:
2 2 0.03
3 69 0.86
4 9 0.11
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (3 bp):
ATT
Found at i:171884 original size:9 final size:9
Alignment explanation
Indices: 171870--171913 Score: 63
Period size: 9 Copynumber: 4.9 Consensus size: 9
171860 TTGAAGAAGA
171870 AGAAAAAAG
1 AGAAAAAAG
171879 AGAAAAAAAG
1 AG-AAAAAAG
*
171889 AGAAAAAAA
1 AGAAAAAAG
171898 AGAAAAAAG
1 AGAAAAAAG
171907 -GAAAAAA
1 AGAAAAAA
171914 TTGAATCAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
8 7 0.22
9 16 0.50
10 9 0.28
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (9 bp):
AGAAAAAAG
Found at i:171885 original size:10 final size:10
Alignment explanation
Indices: 171872--171913 Score: 63
Period size: 10 Copynumber: 4.5 Consensus size: 10
171862 GAAGAAGAAG
171872 AAAAAAGAGA
1 AAAAAAGAGA
171882 AAAAAAGAGA
1 AAAAAAGAGA
171892 AAAAAA-AG-
1 AAAAAAGAGA
171900 AAAAAAG-GA
1 AAAAAAGAGA
171909 AAAAA
1 AAAAA
171914 TTGAATCAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
8 7 0.23
9 7 0.23
10 16 0.53
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (10 bp):
AAAAAAGAGA
Found at i:171894 original size:19 final size:18
Alignment explanation
Indices: 171870--171913 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 18
171860 TTGAAGAAGA
*
171870 AGAAAAAAGAGAAAAAAAG
1 AGAAAAAAAAG-AAAAAAG
171889 AGAAAAAAAAGAAAAAAG
1 AGAAAAAAAAGAAAAAAG
171907 -GAAAAAA
1 AGAAAAAA
171914 TTGAATCAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
17 7 0.29
18 7 0.29
19 10 0.42
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (18 bp):
AGAAAAAAAAGAAAAAAG
Found at i:175225 original size:74 final size:75
Alignment explanation
Indices: 175093--175275 Score: 183
Period size: 74 Copynumber: 2.5 Consensus size: 75
175083 CAACAAAAAG
* * * * * *
175093 CAAATGCTGGGGCAT-ACTGAAAGCTCATTTCAATCAGAATCAGGAATATTGACGCATTTTGAAT
1 CAAATGATGGGGCATGA-TGAAAGCCCATTTCAATCAAAATCAGAAATATTGACACATTTTGAAC
*
175157 GTTCACGTCAA
65 GTTCACATCAA
* *
175168 CAAATGAT-GGGCATGATGAAAGCCCATTTCAATCAAAAAT-TGAAATATTGGCACATTTTGAAC
1 CAAATGATGGGGCATGATGAAAGCCCATTTCAATC-AAAATCAGAAATATTGACACATTTTGAAC
*** * *
175231 GTTTGTATTAG
65 GTTCACATCAA
* *
175242 CAAATGTTGGGGCATGCTGAAAGCCCATTTCAAT
1 CAAATGATGGGGCATGATGAAAGCCCATTTCAAT
175276 ATGAAATTGG
Statistics
Matches: 89, Mismatches: 16, Indels: 6
0.80 0.14 0.05
Matches are distributed among these distances:
74 53 0.60
75 36 0.40
ACGTcount: A:0.34, C:0.17, G:0.20, T:0.29
Consensus pattern (75 bp):
CAAATGATGGGGCATGATGAAAGCCCATTTCAATCAAAATCAGAAATATTGACACATTTTGAACG
TTCACATCAA
Found at i:175283 original size:75 final size:70
Alignment explanation
Indices: 175147--175329 Score: 190
Period size: 70 Copynumber: 2.6 Consensus size: 70
175137 AATATTGACG
* ** * *
175147 CATTTTGAATGTTCACGTCAACAAATGAT-GGGCATGATGAAAGCCCATTTCAATCAAAAATTGA
1 CATTTTGAACGTTCATATCAGCAAATGATGGGGCATGCTGAAAGCCCATTTCAATCAAAAATTGA
175211 AATATTGGCA
66 AATA-----A
** * * *
175221 CATTTTGAACGTTTGTATTAGCAAATGTTGGGGCATGCTGAAAGCCCATTTCAAT-ATGAAATTG
1 CATTTTGAACGTTCATATCAGCAAATGATGGGGCATGCTGAAAGCCCATTTCAATCA-AAAATTG
*
175285 GAATAA
65 AAATAA
*
175291 CATTTTGAACGTTCATATCAGTAAATGATGGGGCATGCT
1 CATTTTGAACGTTCATATCAGCAAATGATGGGGCATGCT
175330 AATGGCCCAC
Statistics
Matches: 91, Mismatches: 16, Indels: 8
0.79 0.14 0.07
Matches are distributed among these distances:
70 35 0.38
74 22 0.24
75 34 0.37
ACGTcount: A:0.34, C:0.15, G:0.20, T:0.31
Consensus pattern (70 bp):
CATTTTGAACGTTCATATCAGCAAATGATGGGGCATGCTGAAAGCCCATTTCAATCAAAAATTGA
AATAA
Found at i:175329 original size:70 final size:71
Alignment explanation
Indices: 175091--175329 Score: 198
Period size: 75 Copynumber: 3.3 Consensus size: 71
175081 ATCAACAAAA
* * * * * *
175091 AGCAAATGCTGGGGCATACTGAAAGCTCATTTCAATC-AGAATCAGGAATATTGACGCATTTTGA
1 AGCAAATGATGGGGCATGCTGAAAGCCCATTTCAATCAAAAAT--TGAA-ATAGA--CATTTTGA
* **
175155 ATGTTCACGTC
61 ACGTTCATATC
* *
175166 AACAAATGAT-GGGCATGATGAAAGCCCATTTCAATCAAAAATTGAAATATTGGCACATTTTGAA
1 AGCAAATGATGGGGCATGCTGAAAGCCCATTTCAATCAAAAATTGAAATA---G-ACATTTTGAA
** *
175230 CGTTTGTATT
62 CGTTCATATC
* * *
175240 AGCAAATGTTGGGGCATGCTGAAAGCCCATTTCAAT-ATGAAATTGGAATA-ACATTTTGAACGT
1 AGCAAATGATGGGGCATGCTGAAAGCCCATTTCAATCA-AAAATTGAAATAGACATTTTGAACGT
175303 TCATATC
65 TCATATC
*
175310 AGTAAATGATGGGGCATGCT
1 AGCAAATGATGGGGCATGCT
175330 AATGGCCCAC
Statistics
Matches: 133, Mismatches: 24, Indels: 19
0.76 0.14 0.11
Matches are distributed among these distances:
70 35 0.26
72 2 0.02
73 3 0.02
74 45 0.34
75 47 0.35
76 1 0.01
ACGTcount: A:0.34, C:0.15, G:0.21, T:0.29
Consensus pattern (71 bp):
AGCAAATGATGGGGCATGCTGAAAGCCCATTTCAATCAAAAATTGAAATAGACATTTTGAACGTT
CATATC
Found at i:176597 original size:73 final size:73
Alignment explanation
Indices: 176471--177083 Score: 904
Period size: 73 Copynumber: 8.4 Consensus size: 73
176461 TTATTTCCCA
* * *
176471 CATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAACCCTTCGGGAGGTTTTTGATTTTAAAGC
1 CATCTGTAAGACCTACAGTGCAGGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATTTTAAAGC
176536 CTCAGGGT
66 CTCAGGGT
* * *
176544 CCTCTGTAAGACCTACAATGCCGGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATTTTAAAGC
1 CATCTGTAAGACCTACAGTGCAGGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATTTTAAAGC
176609 CTCAGGGT
66 CTCAGGGT
* *
176617 CATCTGTAAGACCTATAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATATTTAAAG
1 CATCTGTAAGACCTACAGTGCAGGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGAT-TTTAAAG
*
176682 CCTCGGGGT
65 CCTCAGGGT
* * *
176691 CATCTGTAAGACCTACAGTGCCGGATGTTTTCAAAAAGCTTTCAGGAGCTTTTTGATTTTAAAGC
1 CATCTGTAAGACCTACAGTGCAGGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATTTTAAAGC
176756 CTCAGGGT
66 CTCAGGGT
* * *
176764 CATCTGTAAGACCTACAGGGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTTATTTTAAAGC
1 CATCTGTAAGACCTACAGTGCAGGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATTTTAAAGC
*
176829 CTCGGGGT
66 CTCAGGGT
* * * *
176837 CATCTGTAAGACCTACAGTGCCGGATTTTTTCAAAAAGCCTTTGGGAACTTTTTGATTTTAAAGC
1 CATCTGTAAGACCTACAGTGCAGGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATTTTAAAGC
*
176902 CTCAGTGT
66 CTCAGGGT
* * *
176910 CATCTGTAAGACTTACAGTGAATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATTTTAAAGC
1 CATCTGTAAGACCTACAGTGCAGGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATTTTAAAGC
176975 CTCAGGGT
66 CTCAGGGT
* * * *
176983 CATCTGTAAGACCTACAGAGTAGGATGTTTTCAAAAAGCCTTCGGGAGATTTTTTATATTTAAAG
1 CATCTGTAAGACCTACAGTGCAGGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGAT-TTTAAAG
*
177048 CCTTTA-GGT
65 CC-TCAGGGT
* * *
177057 CATCTGTAATACTTACAGTGCAAGATG
1 CATCTGTAAGACCTACAGTGCAGGATG
177084 ATAAGACCTC
Statistics
Matches: 483, Mismatches: 54, Indels: 5
0.89 0.10 0.01
Matches are distributed among these distances:
73 380 0.79
74 101 0.21
75 2 0.00
ACGTcount: A:0.27, C:0.18, G:0.22, T:0.33
Consensus pattern (73 bp):
CATCTGTAAGACCTACAGTGCAGGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATTTTAAAGC
CTCAGGGT
Found at i:176870 original size:220 final size:219
Alignment explanation
Indices: 176471--177083 Score: 924
Period size: 220 Copynumber: 2.8 Consensus size: 219
176461 TTATTTCCCA
* *
176471 CATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAACCCTTCGGGAGGTTTTTGATTTTAAAGC
1 CATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATTTTAAAGC
* * *
176536 CTCAGGGTCCTCTGTAAGACCTACA-ATGCCGGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGA
66 CTCAGGGTCATCTGTAAGACCTACAGA-GCAGGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTTA
* * *
176600 TTTTAAAGCCTCAGGGTCATCTGTAAGACCTATAGTGCATGATGTTTTCAAAAAGCCTTCGGGAG
130 TTTTAAAGCCTCAGGGTCATCTGTAAGACCTACAGTGCAGGATGTTTTCAAAAAGCCTTCGGGAA
*
176665 CTTTTTGATATTTAAAGCCTCGGGGT
195 CTTTTTGAT-TTTAAAGCCTCAGGGT
** * *
176691 CATCTGTAAGACCTACAGTGCCGGATGTTTTCAAAAAGCTTTCAGGAGCTTTTTGATTTTAAAGC
1 CATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATTTTAAAGC
* *
176756 CTCAGGGTCATCTGTAAGACCTACAGGGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTTAT
66 CTCAGGGTCATCTGTAAGACCTACAGAGCAGGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTTAT
* * * *
176821 TTTAAAGCCTCGGGGTCATCTGTAAGACCTACAGTGCCGGATTTTTTCAAAAAGCCTTTGGGAAC
131 TTTAAAGCCTCAGGGTCATCTGTAAGACCTACAGTGCAGGATGTTTTCAAAAAGCCTTCGGGAAC
*
176886 TTTTTGATTTTAAAGCCTCAGTGT
196 TTTTTGATTTTAAAGCCTCAGGGT
* *
176910 CATCTGTAAGACTTACAGTGAATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATTTTAAAGC
1 CATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATTTTAAAGC
* *
176975 CTCAGGGTCATCTGTAAGACCTACAGAGTAGGATGTTTTCAAAAAGCCTTCGGGAGATTTTTTAT
66 CTCAGGGTCATCTGTAAGACCTACAGAGCAGGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTTAT
* * * *
177040 ATTTAAAGCCTTTA-GGTCATCTGTAATACTTACAGTGCAAGATG
131 -TTTAAAGCC-TCAGGGTCATCTGTAAGACCTACAGTGCAGGATG
177084 ATAAGACCTC
Statistics
Matches: 353, Mismatches: 37, Indels: 6
0.89 0.09 0.02
Matches are distributed among these distances:
219 134 0.38
220 218 0.62
221 1 0.00
ACGTcount: A:0.27, C:0.18, G:0.22, T:0.33
Consensus pattern (219 bp):
CATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATTTTAAAGC
CTCAGGGTCATCTGTAAGACCTACAGAGCAGGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTTAT
TTTAAAGCCTCAGGGTCATCTGTAAGACCTACAGTGCAGGATGTTTTCAAAAAGCCTTCGGGAAC
TTTTTGATTTTAAAGCCTCAGGGT
Found at i:177047 original size:293 final size:293
Alignment explanation
Indices: 176471--177083 Score: 960
Period size: 293 Copynumber: 2.1 Consensus size: 293
176461 TTATTTCCCA
*
176471 CATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAACCCTTCGGGAGGTTTTTGATTTTAAAGC
1 CATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAACCCTTCGGGAGCTTTTTGATTTTAAAGC
* *
176536 CTCAGGGTCCTCTGTAAGACCTACAATGCCGGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGAT
66 CTCAGGGTCATCTGTAAGACCTACAATGCCGGATGTTTTCAAAAAGCCTTCGGGAACTTTTTGAT
* *
176601 TTTAAAGCCTCAGGGTCATCTGTAAGACCTATAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGC
131 TTTAAAGCCTCAGGGTCATCTGTAAGACCTACAGTGAATGATGTTTTCAAAAAGCCTTCGGGAGC
* * * *
176666 TTTTTGATATTTAAAGCCTCGGGGTCATCTGTAAGACCTACAGTGCCGGATGTTTTCAAAAAGCT
196 TTTTTGATATTTAAAGCCTCAGGGTCATCTGTAAGACCTACAGAGCAGGATGTTTTCAAAAAGCC
*
176731 TTCAGGAGCTTTTTGATTTTAAAGCC-TCAGGGT
261 TTCAGGAGATTTTTGATTTTAAAGCCTTCA-GGT
* * *
176764 CATCTGTAAGACCTACAGGGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTTATTTTAAAGC
1 CATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAACCCTTCGGGAGCTTTTTGATTTTAAAGC
* * * *
176829 CTCGGGGTCATCTGTAAGACCTACAGTGCCGGATTTTTTCAAAAAGCCTTTGGGAACTTTTTGAT
66 CTCAGGGTCATCTGTAAGACCTACAATGCCGGATGTTTTCAAAAAGCCTTCGGGAACTTTTTGAT
* *
176894 TTTAAAGCCTCAGTGTCATCTGTAAGACTTACAGTGAATGATGTTTTCAAAAAGCCTTCGGGAGC
131 TTTAAAGCCTCAGGGTCATCTGTAAGACCTACAGTGAATGATGTTTTCAAAAAGCCTTCGGGAGC
*
176959 TTTTTGAT-TTTAAAGCCTCAGGGTCATCTGTAAGACCTACAGAGTAGGATGTTTTCAAAAAGCC
196 TTTTTGATATTTAAAGCCTCAGGGTCATCTGTAAGACCTACAGAGCAGGATGTTTTCAAAAAGCC
* * *
177023 TTCGGGAGATTTTTTATATTTAAAGCCTTTAGGT
261 TTCAGGAGATTTTTGAT-TTTAAAGCCTTCAGGT
* * *
177057 CATCTGTAATACTTACAGTGCAAGATG
1 CATCTGTAAGACCTACAGTGCATGATG
177084 ATAAGACCTC
Statistics
Matches: 291, Mismatches: 27, Indels: 4
0.90 0.08 0.01
Matches are distributed among these distances:
292 65 0.22
293 224 0.77
294 2 0.01
ACGTcount: A:0.27, C:0.18, G:0.22, T:0.33
Consensus pattern (293 bp):
CATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAACCCTTCGGGAGCTTTTTGATTTTAAAGC
CTCAGGGTCATCTGTAAGACCTACAATGCCGGATGTTTTCAAAAAGCCTTCGGGAACTTTTTGAT
TTTAAAGCCTCAGGGTCATCTGTAAGACCTACAGTGAATGATGTTTTCAAAAAGCCTTCGGGAGC
TTTTTGATATTTAAAGCCTCAGGGTCATCTGTAAGACCTACAGAGCAGGATGTTTTCAAAAAGCC
TTCAGGAGATTTTTGATTTTAAAGCCTTCAGGT
Found at i:177323 original size:2 final size:2
Alignment explanation
Indices: 177311--177343 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
177301 TTATTATTAC
*
177311 TA TA AA 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 T
177344 TATTTAATAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:178750 original size:11 final size:11
Alignment explanation
Indices: 178721--178755 Score: 52
Period size: 11 Copynumber: 3.1 Consensus size: 11
178711 AATAAGTTTA
178721 AATTATTACTTT
1 AATTATTA-TTT
178733 AATTATTATTT
1 AATTATTATTT
*
178744 TATTATTATTT
1 AATTATTATTT
178755 A
1 A
178756 GTCATATAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
11 13 0.62
12 8 0.38
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.63
Consensus pattern (11 bp):
AATTATTATTT
Found at i:178964 original size:21 final size:22
Alignment explanation
Indices: 178940--179005 Score: 64
Period size: 22 Copynumber: 3.0 Consensus size: 22
178930 TTTTTTGATA
178940 TTTTTTAAATAAATATTTTA-C
1 TTTTTTAAATAAATATTTTATC
* * *
178961 TTTTATAAATTATATATATTAATC
1 TTTTTTAAA-TAAATAT-TTTATC
178985 TATTTTT-AATAAATATTTTAT
1 T-TTTTTAAATAAATATTTTAT
179006 TATTATTTAT
Statistics
Matches: 35, Mismatches: 6, Indels: 7
0.73 0.12 0.15
Matches are distributed among these distances:
21 8 0.23
22 10 0.29
23 9 0.26
24 4 0.11
25 4 0.11
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (22 bp):
TTTTTTAAATAAATATTTTATC
Found at i:179009 original size:21 final size:21
Alignment explanation
Indices: 178941--179014 Score: 51
Period size: 22 Copynumber: 3.3 Consensus size: 21
178931 TTTTTGATAT
178941 TTTTTAAATAAATATTTTACTT-
1 TTTTT-AATAAATATTTTA-TTA
* * * *
178963 TTATAAATTATATATATTAATCTA
1 TTTTTAA-TAAATAT-TTTAT-TA
178987 TTTTTAATAAATATTTTATTA
1 TTTTTAATAAATATTTTATTA
179008 TTATTTA
1 TT-TTTA
179015 TTTATTTTTT
Statistics
Matches: 39, Mismatches: 8, Indels: 10
0.68 0.14 0.18
Matches are distributed among these distances:
21 6 0.15
22 18 0.46
23 10 0.26
24 5 0.13
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (21 bp):
TTTTTAATAAATATTTTATTA
Found at i:180620 original size:21 final size:22
Alignment explanation
Indices: 180579--180623 Score: 67
Period size: 21 Copynumber: 2.1 Consensus size: 22
180569 ATATGCTGTA
180579 TAAATTTATAAAATATTAAATT
1 TAAATTTATAAAATATTAAATT
180601 TAAATTT-TAAAA-ATTAAAATT
1 TAAATTTATAAAATATT-AAATT
180622 TA
1 TA
180624 TATTCGGATC
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 3 0.14
21 12 0.55
22 7 0.32
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (22 bp):
TAAATTTATAAAATATTAAATT
Found at i:181136 original size:37 final size:37
Alignment explanation
Indices: 181086--181158 Score: 137
Period size: 37 Copynumber: 2.0 Consensus size: 37
181076 TCAAACATAC
*
181086 ATTTCAATTTACAAGACACTACATTTGTGGTCTATAT
1 ATTTCAATTTACAAAACACTACATTTGTGGTCTATAT
181123 ATTTCAATTTACAAAACACTACATTTGTGGTCTATA
1 ATTTCAATTTACAAAACACTACATTTGTGGTCTATA
181159 CAAGGTATAT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 35 1.00
ACGTcount: A:0.34, C:0.16, G:0.10, T:0.40
Consensus pattern (37 bp):
ATTTCAATTTACAAAACACTACATTTGTGGTCTATAT
Found at i:181660 original size:12 final size:12
Alignment explanation
Indices: 181639--181684 Score: 58
Period size: 12 Copynumber: 3.8 Consensus size: 12
181629 GAATAAGTTG
181639 ATAAAAGAGCAT
1 ATAAAAGAGCAT
*
181651 ATAAACGAGC-T
1 ATAAAAGAGCAT
181662 CATAAAAGAGCAT
1 -ATAAAAGAGCAT
*
181675 ATAAACGAGC
1 ATAAAAGAGC
181685 TTGTTCGTTA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
11 1 0.03
12 27 0.93
13 1 0.03
ACGTcount: A:0.52, C:0.15, G:0.17, T:0.15
Consensus pattern (12 bp):
ATAAAAGAGCAT
Found at i:181666 original size:24 final size:24
Alignment explanation
Indices: 181639--181685 Score: 94
Period size: 24 Copynumber: 2.0 Consensus size: 24
181629 GAATAAGTTG
181639 ATAAAAGAGCATATAAACGAGCTC
1 ATAAAAGAGCATATAAACGAGCTC
181663 ATAAAAGAGCATATAAACGAGCT
1 ATAAAAGAGCATATAAACGAGCT
181686 TGTTCGTTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.51, C:0.15, G:0.17, T:0.17
Consensus pattern (24 bp):
ATAAAAGAGCATATAAACGAGCTC
Found at i:184738 original size:25 final size:23
Alignment explanation
Indices: 184684--184740 Score: 62
Period size: 25 Copynumber: 2.3 Consensus size: 23
184674 ATTTTTTTTG
*
184684 TATTTTCTTTTTTTTATAATCTT
1 TATTTTATTTTTTTTATAATCTT
184707 TATTTTTATTTGTTTTCTGATAAT-TT
1 TA-TTTTATTT-TTTT-T-ATAATCTT
184733 TATTTTAT
1 TATTTTAT
184741 GACACGCTAT
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
23 2 0.07
24 7 0.24
25 10 0.34
26 5 0.17
27 5 0.17
ACGTcount: A:0.19, C:0.05, G:0.04, T:0.72
Consensus pattern (23 bp):
TATTTTATTTTTTTTATAATCTT
Found at i:189989 original size:14 final size:14
Alignment explanation
Indices: 189967--190017 Score: 77
Period size: 14 Copynumber: 3.7 Consensus size: 14
189957 TTTTTCACTC
189967 TTTTT-CTTAGTTA
1 TTTTTACTTAGTTA
189980 TTTTTACTTAGTTA
1 TTTTTACTTAGTTA
189994 TTTTTACTTAGTTA
1 TTTTTACTTAGTTA
* *
190008 ATTTCACTTA
1 TTTTTACTTA
190018 ATCTTTATTT
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
13 5 0.14
14 30 0.86
ACGTcount: A:0.22, C:0.10, G:0.06, T:0.63
Consensus pattern (14 bp):
TTTTTACTTAGTTA
Found at i:191887 original size:60 final size:60
Alignment explanation
Indices: 191807--191919 Score: 163
Period size: 60 Copynumber: 1.9 Consensus size: 60
191797 TATAGGATAC
* * * * *
191807 TGCTTTATTAAGGCTTTCGACTATTAAAAGTTATAAAATAGTTATCCGACTATAAAATGT
1 TGCTCTATTAAGGCTCTCGACTATTAAAAGTTACAAAATAGTTACCCAACTATAAAATGT
* *
191867 TGCTCTATTAAGTCTCTCGACTATTAAAAGTTACAAAATGGTTACCCAACTAT
1 TGCTCTATTAAGGCTCTCGACTATTAAAAGTTACAAAATAGTTACCCAACTAT
191920 TAATTATGTT
Statistics
Matches: 46, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
60 46 1.00
ACGTcount: A:0.35, C:0.16, G:0.12, T:0.36
Consensus pattern (60 bp):
TGCTCTATTAAGGCTCTCGACTATTAAAAGTTACAAAATAGTTACCCAACTATAAAATGT
Found at i:196126 original size:3 final size:3
Alignment explanation
Indices: 196118--196173 Score: 78
Period size: 3 Copynumber: 19.0 Consensus size: 3
196108 ATTTGTAAAT
* **
196118 TAA TAA TAA TAG TAA TAA TAA TAA T-A TAA CGA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
196165 TAA TAA TAA
1 TAA TAA TAA
196174 CGATAAAAAA
Statistics
Matches: 46, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
2 2 0.04
3 44 0.96
ACGTcount: A:0.62, C:0.02, G:0.04, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:196389 original size:43 final size:42
Alignment explanation
Indices: 196328--196675 Score: 206
Period size: 43 Copynumber: 8.0 Consensus size: 42
196318 TGTTGGGGAC
* * *
196328 GACACTGCTCATACGTGATGAAGAGTTTGGGTCGTCTAAAGGT
1 GACACGGCTCCTACGTGATGAAGAGTTT-GGTCATCTAAAGGT
*
196371 GACACGGCTCCTACGTGATGAAGAGTTCTTGGCCATCTAAAGGT
1 GACACGGCTCCTACGTGATGAAGAG-T-TTGGTCATCTAAAGGT
* * * ** * *
196415 GATAACACAGTTCCTACGTGATGAGGACGGCTGGTTATCTAAGGGT
1 G---ACACGGCTCCTACGTGATGAAGA-GTTTGGTCATCTAAAGGT
* ****
196461 GACACGGCTCCTACGTGATGAAGAGATCTGGTC-GGGGAA--T
1 GACACGGCTCCTACGTGATGAAGAG-TTTGGTCATCTAAAGGT
* *
196501 GACACGGCTCATACGTGATGAAGAGTTCTGGCCATCTAAAGGT
1 GACACGGCTCCTACGTGATGAAGAGTT-TGGTCATCTAAAGGT
* * ** * *
196544 GATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCT-ATGGTT
1 G---ACACGGCTCCTACGTGATGAAGA-GTTTGGTCATCTAAAGG-T
* * ***
196590 GACACGGCTCATACGTGATGAAGAGATCTGGTC-TGGGGAA--T
1 GACACGGCTCCTACGTGATGAAGAG-TTTGGTCAT-CTAAAGGT
* * *
196631 GACACAGCTCATACGTGATGAAGAGTTCTGGCCATCTAAAGGT
1 GACACGGCTCCTACGTGATGAAGAGTT-TGGTCATCTAAAGGT
196674 GA
1 GA
196676 TAACACGATT
Statistics
Matches: 231, Mismatches: 51, Indels: 46
0.70 0.16 0.14
Matches are distributed among these distances:
39 1 0.00
40 30 0.13
41 33 0.14
42 5 0.02
43 78 0.34
44 15 0.06
45 5 0.02
46 42 0.18
47 21 0.09
48 1 0.00
ACGTcount: A:0.26, C:0.19, G:0.30, T:0.25
Consensus pattern (42 bp):
GACACGGCTCCTACGTGATGAAGAGTTTGGTCATCTAAAGGT
Found at i:196562 original size:129 final size:130
Alignment explanation
Indices: 196370--196707 Score: 597
Period size: 130 Copynumber: 2.6 Consensus size: 130
196360 CGTCTAAAGG
* *
196370 TGACACGGCTCCTACGTGATGAAGAGTTCTTGGCCATCTAAAGGTGATAACACAGTTCCTACGTG
1 TGACACGGCTCATACGTGATGAAGAGTTC-TGGCCATCTAAAGGTGATAACACGGTTCCTACGTG
*
196435 ATGAGGACGGCTGGTTATCTAAGGGTGACACGGCTCCTACGTGATGAAGAGATCTGGTC-GGGGA
65 ATGAGGACGGCTGGTTATCTAAGGGTGACACGGCTCATACGTGATGAAGAGATCTGGTCTGGGGA
196499 A
130 A
196500 TGACACGGCTCATACGTGATGAAGAGTTCTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGA
1 TGACACGGCTCATACGTGATGAAGAGTTCTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGA
* *
196565 TGAGGACGGCTGGTTATCTATGGTTGACACGGCTCATACGTGATGAAGAGATCTGGTCTGGGGAA
66 TGAGGACGGCTGGTTATCTAAGGGTGACACGGCTCATACGTGATGAAGAGATCTGGTCTGGGGAA
* *
196630 TGACACAGCTCATACGTGATGAAGAGTTCTGGCCATCTAAAGGTGATAACACGATTCCTACGTGA
1 TGACACGGCTCATACGTGATGAAGAGTTCTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGA
196695 TGAGGACGGCTGG
66 TGAGGACGGCTGG
196708 CCATCTTTAG
Statistics
Matches: 200, Mismatches: 7, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
129 90 0.45
130 110 0.55
ACGTcount: A:0.26, C:0.20, G:0.30, T:0.24
Consensus pattern (130 bp):
TGACACGGCTCATACGTGATGAAGAGTTCTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGA
TGAGGACGGCTGGTTATCTAAGGGTGACACGGCTCATACGTGATGAAGAGATCTGGTCTGGGGAA
Found at i:196777 original size:28 final size:28
Alignment explanation
Indices: 196746--196822 Score: 93
Period size: 28 Copynumber: 2.6 Consensus size: 28
196736 AAACCAAATT
196746 AAAGATTTGTTTCAAAAGAAACAAACCC
1 AAAGATTTGTTTCAAAAGAAACAAACCC
* *
196774 AAAGATTCGTTTCAAGAA-AAACAAACTC
1 AAAGATTTGTTTCAA-AAGAAACAAACCC
196802 AAAGATGATGTGTTTCAAAAG
1 AAAGAT--T-TGTTTCAAAAG
196823 CAACTGTCTC
Statistics
Matches: 41, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
28 29 0.71
29 2 0.05
30 3 0.07
31 7 0.17
ACGTcount: A:0.48, C:0.14, G:0.14, T:0.23
Consensus pattern (28 bp):
AAAGATTTGTTTCAAAAGAAACAAACCC
Found at i:197346 original size:30 final size:30
Alignment explanation
Indices: 197312--197375 Score: 101
Period size: 30 Copynumber: 2.1 Consensus size: 30
197302 AGAGACAAAA
* *
197312 TTTTGTTTCCAAAGAAACAAACTTAAAGAT
1 TTTTGTTTCAAAAGAAACAAACTCAAAGAT
*
197342 TTTTGTTTCAAAAGAAACAATCTCAAAGAT
1 TTTTGTTTCAAAAGAAACAAACTCAAAGAT
197372 TTTT
1 TTTT
197376 TTCACAAAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.41, C:0.12, G:0.09, T:0.38
Consensus pattern (30 bp):
TTTTGTTTCAAAAGAAACAAACTCAAAGAT
Found at i:197384 original size:30 final size:29
Alignment explanation
Indices: 197307--197384 Score: 88
Period size: 30 Copynumber: 2.7 Consensus size: 29
197297 TTAAGAGAGA
197307 CAAA-ATTTTGTTTCC-AAAGAAACAAACT
1 CAAAGATTTT-TTTCCAAAAGAAACAAACT
* * *
197335 TAAAGATTTTTGTTTCAAAAGAAACAATCT
1 CAAAGATTTTT-TTCCAAAAGAAACAAACT
197365 CAAAGATTTTTTTCACAAAA
1 CAAAGATTTTTTTC-CAAAA
197385 TTGTCTCAAG
Statistics
Matches: 41, Mismatches: 5, Indels: 6
0.79 0.10 0.12
Matches are distributed among these distances:
28 4 0.10
29 10 0.24
30 27 0.66
ACGTcount: A:0.45, C:0.14, G:0.08, T:0.33
Consensus pattern (29 bp):
CAAAGATTTTTTTCCAAAAGAAACAAACT
Found at i:197443 original size:52 final size:53
Alignment explanation
Indices: 197363--197466 Score: 174
Period size: 52 Copynumber: 2.0 Consensus size: 53
197353 AAGAAACAAT
*
197363 CTCAAAGATTTTTTTCACAAAATTGTCTCAAGAGAGACAACACTTTGTTTCAGA
1 CTCAAAGA-TTTTTTCACAAAATTGTCTCAAGAGAGACAAAACTTTGTTTCAGA
*
197417 CTCAAAGA-TTTTTCACGAAATTGTCTCAAGAGAGACAAAACTTTGTTTCA
1 CTCAAAGATTTTTTCACAAAATTGTCTCAAGAGAGACAAAACTTTGTTTCA
197467 AAATAAATAG
Statistics
Matches: 48, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
52 40 0.83
54 8 0.17
ACGTcount: A:0.36, C:0.18, G:0.13, T:0.33
Consensus pattern (53 bp):
CTCAAAGATTTTTTCACAAAATTGTCTCAAGAGAGACAAAACTTTGTTTCAGA
Found at i:197492 original size:27 final size:27
Alignment explanation
Indices: 197462--197641 Score: 132
Period size: 29 Copynumber: 6.4 Consensus size: 27
197452 CAAAACTTTG
* *
197462 TTTCAAAATAAATAGACTCAAAGAT-TT
1 TTTCAAAAGAAACA-ACTCAAAGATATT
197489 TTTCAAAAGAAACAACTCAAAGATATT
1 TTTCAAAAGAAACAACTCAAAGATATT
* * *
197516 TATTCAAAAGGAACAAACTCCAAGATTTT
1 T-TTCAAAAGAAAC-AACTCAAAGATATT
* * *
197545 TATTTAAAAGGAACAAACTCAAAGATTTT
1 T-TTCAAAAGAAAC-AACTCAAAGATATT
* * *
197574 TATTTAAAAGGAACAAACTCAAAGATTTT
1 T-TTCAAAAGAAAC-AACTCAAAGATATT
* *
197603 TATTTAAAAGGAACCAACTCAAAGAT-TT
1 T-TTCAAAA-GAAACAACTCAAAGATATT
*
197631 TTT-AAGAGAAA
1 TTTCAAAAGAAA
197642 TTATCTCAAG
Statistics
Matches: 138, Mismatches: 11, Indels: 10
0.87 0.07 0.06
Matches are distributed among these distances:
25 3 0.02
26 13 0.09
27 17 0.12
28 14 0.10
29 88 0.64
30 3 0.02
ACGTcount: A:0.48, C:0.12, G:0.10, T:0.29
Consensus pattern (27 bp):
TTTCAAAAGAAACAACTCAAAGATATT
Found at i:197546 original size:29 final size:29
Alignment explanation
Indices: 197477--197632 Score: 237
Period size: 29 Copynumber: 5.5 Consensus size: 29
197467 AAATAAATAG
* *
197477 ACTCAAAGA-TTTT-TTCAAAAGAAAC-A
1 ACTCAAAGATTTTTATTTAAAAGGAACAA
* *
197503 ACTCAAAGATATTTATTCAAAAGGAACAA
1 ACTCAAAGATTTTTATTTAAAAGGAACAA
*
197532 ACTCCAAGATTTTTATTTAAAAGGAACAA
1 ACTCAAAGATTTTTATTTAAAAGGAACAA
197561 ACTCAAAGATTTTTATTTAAAAGGAACAA
1 ACTCAAAGATTTTTATTTAAAAGGAACAA
*
197590 ACTCAAAGATTTTTATTTAAAAGGAACCA
1 ACTCAAAGATTTTTATTTAAAAGGAACAA
197619 ACTCAAAGATTTTT
1 ACTCAAAGATTTTT
197633 TAAGAGAAAT
Statistics
Matches: 120, Mismatches: 7, Indels: 3
0.92 0.05 0.02
Matches are distributed among these distances:
26 9 0.08
27 3 0.03
28 11 0.09
29 97 0.81
ACGTcount: A:0.47, C:0.13, G:0.10, T:0.30
Consensus pattern (29 bp):
ACTCAAAGATTTTTATTTAAAAGGAACAA
Found at i:198304 original size:4 final size:4
Alignment explanation
Indices: 198288--198333 Score: 62
Period size: 4 Copynumber: 12.2 Consensus size: 4
198278 ATACAAATTT
*
198288 TATG TAT- TATG TATG TATG --TG TATT TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
198333 T
1 T
198334 TTTCTCGATC
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
2 2 0.05
3 3 0.08
4 32 0.86
ACGTcount: A:0.24, C:0.00, G:0.22, T:0.54
Consensus pattern (4 bp):
TATG
Found at i:198317 original size:18 final size:17
Alignment explanation
Indices: 198290--198325 Score: 63
Period size: 18 Copynumber: 2.1 Consensus size: 17
198280 ACAAATTTTA
198290 TGTATTATGTATGTATG
1 TGTATTATGTATGTATG
198307 TGTATTTATGTATGTATG
1 TGTA-TTATGTATGTATG
198325 T
1 T
198326 ATGTATGTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 4 0.22
18 14 0.78
ACGTcount: A:0.22, C:0.00, G:0.22, T:0.56
Consensus pattern (17 bp):
TGTATTATGTATGTATG
Found at i:206261 original size:3 final size:3
Alignment explanation
Indices: 206253--206311 Score: 84
Period size: 3 Copynumber: 20.0 Consensus size: 3
206243 ATTTGTAAAT
* **
206253 TAA TAA TAA TAA TAG TAA TAA TAA TAA T-A TAA CGA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
206300 TAA TAA TAA TAA
1 TAA TAA TAA TAA
206312 CGATAAAAAA
Statistics
Matches: 49, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
2 2 0.04
3 47 0.96
ACGTcount: A:0.63, C:0.02, G:0.03, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:209365 original size:24 final size:24
Alignment explanation
Indices: 209294--209357 Score: 110
Period size: 24 Copynumber: 2.7 Consensus size: 24
209284 GACCGCTATG
209294 GCAATAACTAATCGGAGGCAGATA
1 GCAATAACTAATCGGAGGCAGATA
209318 GCAATAACTAATCGGAGGCAGATA
1 GCAATAACTAATCGGAGGCAGATA
* *
209342 GCAATACCTGATCGGA
1 GCAATAACTAATCGGA
209358 ATCAGATACA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 38 1.00
ACGTcount: A:0.39, C:0.19, G:0.25, T:0.17
Consensus pattern (24 bp):
GCAATAACTAATCGGAGGCAGATA
Found at i:212853 original size:53 final size:53
Alignment explanation
Indices: 212773--212885 Score: 217
Period size: 53 Copynumber: 2.1 Consensus size: 53
212763 TTTGAATTAT
212773 ATAATTGAAGATCAAAGAGCCACAGCGATAGAAGTTTGCTGCAGATGAAATAC
1 ATAATTGAAGATCAAAGAGCCACAGCGATAGAAGTTTGCTGCAGATGAAATAC
*
212826 ATAATTGATGATCAAAGAGCCACAGCGATAGAAGTTTGCTGCAGATGAAATAC
1 ATAATTGAAGATCAAAGAGCCACAGCGATAGAAGTTTGCTGCAGATGAAATAC
212879 ATAATTG
1 ATAATTG
212886 TTTCTCTCTG
Statistics
Matches: 59, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
53 59 1.00
ACGTcount: A:0.41, C:0.14, G:0.22, T:0.23
Consensus pattern (53 bp):
ATAATTGAAGATCAAAGAGCCACAGCGATAGAAGTTTGCTGCAGATGAAATAC
Found at i:217217 original size:19 final size:19
Alignment explanation
Indices: 217185--217239 Score: 67
Period size: 19 Copynumber: 2.9 Consensus size: 19
217175 TTAGTTTTTC
*
217185 TTTATCTTAATTATTTTAAA
1 TTTAT-TTATTTATTTTAAA
*
217205 TTTATTTATTTATTTTATA
1 TTTATTTATTTATTTTAAA
*
217224 TTTATCT-TTTATTTTA
1 TTTATTTATTTATTTTA
217240 TCCTTATCTT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
18 9 0.28
19 18 0.56
20 5 0.16
ACGTcount: A:0.27, C:0.04, G:0.00, T:0.69
Consensus pattern (19 bp):
TTTATTTATTTATTTTAAA
Found at i:217236 original size:18 final size:18
Alignment explanation
Indices: 217185--217250 Score: 69
Period size: 18 Copynumber: 3.5 Consensus size: 18
217175 TTAGTTTTTC
*
217185 TTTATCTTAATTATTTTAAA
1 TTTATCTT--TTATTTTATA
*
217205 TTTATTTATTTATTTTATA
1 TTTATCT-TTTATTTTATA
*
217224 TTTATCTTTTATTTTATC
1 TTTATCTTTTATTTTATA
*
217242 CTTATCTTT
1 TTTATCTTT
217251 ATCGCAATCA
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
18 18 0.45
19 15 0.38
20 6 0.15
21 1 0.03
ACGTcount: A:0.24, C:0.08, G:0.00, T:0.68
Consensus pattern (18 bp):
TTTATCTTTTATTTTATA
Found at i:225381 original size:31 final size:31
Alignment explanation
Indices: 225345--225403 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
225335 AACTTAAAAG
* *
225345 AGTTTTGCAATACTGAGATTTAAATAATTTT
1 AGTTTTACAATACTGAAATTTAAATAATTTT
225376 AGTTTTACAATACTGAAATTTAAATAAT
1 AGTTTTACAATACTGAAATTTAAATAAT
225404 CCATACAACT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.41, C:0.07, G:0.10, T:0.42
Consensus pattern (31 bp):
AGTTTTACAATACTGAAATTTAAATAATTTT
Found at i:225454 original size:22 final size:22
Alignment explanation
Indices: 225429--225470 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
225419 AATAAATTAC
225429 TTAAAATAAATCAATCCATATT
1 TTAAAATAAATCAATCCATATT
*
225451 TTAAAATAAATCAATTCATA
1 TTAAAATAAATCAATCCATA
225471 CTAATAAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.52, C:0.12, G:0.00, T:0.36
Consensus pattern (22 bp):
TTAAAATAAATCAATCCATATT
Found at i:225479 original size:22 final size:22
Alignment explanation
Indices: 225430--225478 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
225420 ATAAATTACT
**
225430 TAAAATAAATCAATCCATATTT
1 TAAAATAAATCAATCCATATAA
*
225452 TAAAATAAATCAATTCATACTAA
1 TAAAATAAATCAATCCATA-TAA
225475 TAAA
1 TAAA
225479 TTATTTAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 18 0.78
23 5 0.22
ACGTcount: A:0.55, C:0.12, G:0.00, T:0.33
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:225487 original size:54 final size:54
Alignment explanation
Indices: 225418--225951 Score: 597
Period size: 54 Copynumber: 9.6 Consensus size: 54
225408 ACAACTACAA
* *
225418 TAATAAATTACTTAAAATAAATCAATCCATATTTTAAAATAAATCAATTCATAC
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
* ** *
225472 TAATAAATTATTTAAAATAAATCAATCCATACAACTACAATAATAAATCAATTCATA-
1 TAATAAATTATTTAAAATAAATCAATCCAT---ATTTTAA-AATAAATCAATCCATAC
** * ** * ** ** *
225529 TTTTAAAATAAAT-CAATCCATACAAATAAATTTTTTAAAATAAATCAATCCATAC
1 TAATAAATTATTTAAAATAAAT-C-AATCCATATTTTAAAATAAATCAATCCATAC
* *
225584 TAATAAATTATTTAAAATAAATCAATTCATATTTTAAAATAAATCAATCGATAC
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
225638 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
* ** *
225692 TAATAAATTATTTAAAATAAATCAATCCATACAACTACAATAATAAATCAATCCATATTT
1 TAATAAATTATTTAAAATAAATCAATCCAT---ATTTTAA-AATAAATCAATCCATA--C
* * * ** * *
225752 TAAAATAAATCAATCAATCAATCCATACAA-ACAAATTATTTAAAATAAATCAATCCATAC
1 T--AATAAATTATTTAA--AATAAAT-CAATCCATA-T-TTTAAAATAAATCAATCCATAC
225812 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
*
225866 TAATAAATTATTTAAAATAAATCAATCTATATTTTAAAATAAATCAATCCATAC
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
225920 TAATAAATTATTTAAAATAAATCAATCCATAT
1 TAATAAATTATTTAAAATAAATCAATCCATAT
225952 AACTACAATA
Statistics
Matches: 401, Mismatches: 57, Indels: 44
0.80 0.11 0.09
Matches are distributed among these distances:
54 259 0.65
55 16 0.04
56 18 0.04
57 17 0.04
58 48 0.12
60 2 0.00
61 1 0.00
62 27 0.07
63 3 0.01
64 7 0.02
65 3 0.01
ACGTcount: A:0.52, C:0.13, G:0.00, T:0.34
Consensus pattern (54 bp):
TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
Found at i:225488 original size:32 final size:32
Alignment explanation
Indices: 225450--226026 Score: 366
Period size: 32 Copynumber: 20.5 Consensus size: 32
225440 CAATCCATAT
*
225450 TTTAAAATAAATCAATTCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
*
225482 TTTAAAATAAATCAATCCATAC-AACTACA--A
1 TTTAAAATAAATCAATCCATACTAA-TAAATTA
* **
225512 --T--AATAAATCAATTCATA-TTTTAAA--A
1 TTTAAAATAAATCAATCCATACTAATAAATTA
* *
225537 -------TAAATCAATCCATACAAATAAATTT
1 TTTAAAATAAATCAATCCATACTAATAAATTA
225562 TTTAAAATAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
225594 TTTAAAATAAATCAAT---T-C--AT--A-T-
1 TTTAAAATAAATCAATCCATACTAATAAATTA
*
225616 TTTAAAATAAATCAATCGATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
225648 TTTAAAATAAATCAAT-C---C--AT--A-T-
1 TTTAAAATAAATCAATCCATACTAATAAATTA
225670 TTTAAAATAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
*
225702 TTTAAAATAAATCAATCCATAC-AACTACA--A
1 TTTAAAATAAATCAATCCATACTAA-TAAATTA
** *
225732 --T--AATAAATCAATCCATA-TTTTAAAATA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
** * * * *
225759 AAT-CAATCAATCAATCCATACAAACAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
225790 TTTAAAATAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
225822 TTTAAAATAAATCAAT-C---C--AT--A-T-
1 TTTAAAATAAATCAATCCATACTAATAAATTA
225844 TTTAAAATAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
225876 TTTAAAATAAATC-A---AT-CT-AT--A-T-
1 TTTAAAATAAATCAATCCATACTAATAAATTA
225898 TTTAAAATAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
*
225930 TTTAAAATAAATCAATCCATA-TAACTACA--A
1 TTTAAAATAAATCAATCCATACTAA-TAAATTA
225960 --T--AATAAATCAATCC--A-T-AT------
1 TTTAAAATAAATCAATCCATACTAATAAATTA
225978 TTTAAAATAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
*
226010 TTTAAGATAAATCAATC
1 TTTAAAATAAATCAATC
226027 GATATTTTAA
Statistics
Matches: 437, Mismatches: 32, Indels: 152
0.70 0.05 0.24
Matches are distributed among these distances:
20 1 0.00
22 88 0.20
23 12 0.03
24 7 0.02
25 9 0.02
26 59 0.14
27 5 0.01
28 16 0.04
29 2 0.00
30 22 0.05
31 19 0.04
32 197 0.45
ACGTcount: A:0.52, C:0.14, G:0.00, T:0.34
Consensus pattern (32 bp):
TTTAAAATAAATCAATCCATACTAATAAATTA
Found at i:225674 original size:22 final size:22
Alignment explanation
Indices: 225648--225690 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
225638 TAATAAATTA
225648 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
225670 TTTAAAATAAATCAATCCATA
1 TTTAAAATAAATCAATCCATA
225691 CTAATAAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.51, C:0.14, G:0.00, T:0.35
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:225699 original size:22 final size:22
Alignment explanation
Indices: 225650--225698 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
225640 ATAAATTATT
**
225650 TAAAATAAATCAATCCATATTT
1 TAAAATAAATCAATCCATATAA
225672 TAAAATAAATCAATCCATACTAA
1 TAAAATAAATCAATCCATA-TAA
225695 TAAA
1 TAAA
225699 TTATTTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 19 0.79
23 5 0.21
ACGTcount: A:0.55, C:0.14, G:0.00, T:0.31
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:225848 original size:22 final size:22
Alignment explanation
Indices: 225822--225864 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
225812 TAATAAATTA
225822 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
225844 TTTAAAATAAATCAATCCATA
1 TTTAAAATAAATCAATCCATA
225865 CTAATAAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.51, C:0.14, G:0.00, T:0.35
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:225873 original size:22 final size:22
Alignment explanation
Indices: 225824--225872 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
225814 ATAAATTATT
**
225824 TAAAATAAATCAATCCATATTT
1 TAAAATAAATCAATCCATATAA
225846 TAAAATAAATCAATCCATACTAA
1 TAAAATAAATCAATCCATA-TAA
225869 TAAA
1 TAAA
225873 TTATTTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 19 0.79
23 5 0.21
ACGTcount: A:0.55, C:0.14, G:0.00, T:0.31
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:225927 original size:22 final size:22
Alignment explanation
Indices: 225878--225926 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
225868 ATAAATTATT
* **
225878 TAAAATAAATCAATCTATATTT
1 TAAAATAAATCAATCCATATAA
225900 TAAAATAAATCAATCCATACTAA
1 TAAAATAAATCAATCCATA-TAA
225923 TAAA
1 TAAA
225927 TTATTTAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 18 0.78
23 5 0.22
ACGTcount: A:0.55, C:0.12, G:0.00, T:0.33
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:225982 original size:80 final size:80
Alignment explanation
Indices: 225881--226031 Score: 275
Period size: 80 Copynumber: 1.9 Consensus size: 80
225871 AATTATTTAA
*
225881 AATAAATCAATCTATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAAT
1 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAAT
225946 CCATATAACTACAAT
66 CCATATAACTACAAT
*
225961 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAGATAAATCAAT
1 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAAT
*
226026 CGATAT
66 CCATAT
226032 TTTAAAATAA
Statistics
Matches: 68, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
80 68 1.00
ACGTcount: A:0.52, C:0.13, G:0.01, T:0.34
Consensus pattern (80 bp):
AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAAT
CCATATAACTACAAT
Found at i:225986 original size:22 final size:23
Alignment explanation
Indices: 225928--225998 Score: 90
Period size: 26 Copynumber: 3.0 Consensus size: 23
225918 ACTAATAAAT
225928 TATTTAAAATAAATCAATCCATA
1 TATTTAAAATAAATCAATCCATA
**
225951 TAACTACAATAATAAATCAATCCATA
1 T-A-TTTAA-AATAAATCAATCCATA
225977 T-TTTAAAATAAATCAATCCATA
1 TATTTAAAATAAATCAATCCATA
225999 CTAATAAATT
Statistics
Matches: 41, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
22 16 0.39
23 4 0.10
24 1 0.02
25 3 0.07
26 17 0.41
ACGTcount: A:0.52, C:0.15, G:0.00, T:0.32
Consensus pattern (23 bp):
TATTTAAAATAAATCAATCCATA
Found at i:226001 original size:188 final size:188
Alignment explanation
Indices: 225790--226129 Score: 644
Period size: 188 Copynumber: 1.8 Consensus size: 188
225780 AAACAAATTA
225790 TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAA
1 TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAA
225855 TCAATCCATACTAATAAATTATTTAAAATAAATCAATCTATATTTTAAAATAAATCAATCCATAC
66 TCAATCCATACTAATAAATTATTTAAAATAAATCAATCTATATTTTAAAATAAATCAATCCATAC
225920 TAATAAATTATTTAAAATAAATCAATCCATATAACTACAATAATAAATCAATCCATAT
131 TAATAAATTATTTAAAATAAATCAATCCATATAACTACAATAATAAATCAATCCATAT
* *
225978 TTTAAAATAAATCAATCCATACTAATAAATTATTTAAGATAAATCAATCGATATTTTAAAATAAA
1 TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAA
* *
226043 TTAATCCATACTAATAAATTATTTAAAATAAATCAATCTATATTTTAAAATAAATCAATTCATAC
66 TCAATCCATACTAATAAATTATTTAAAATAAATCAATCTATATTTTAAAATAAATCAATCCATAC
226108 TAATAAATTATTTAAAATAAAT
131 TAATAAATTATTTAAAATAAAT
226130 TATTTTAAAA
Statistics
Matches: 148, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
188 148 1.00
ACGTcount: A:0.52, C:0.11, G:0.01, T:0.36
Consensus pattern (188 bp):
TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAA
TCAATCCATACTAATAAATTATTTAAAATAAATCAATCTATATTTTAAAATAAATCAATCCATAC
TAATAAATTATTTAAAATAAATCAATCCATATAACTACAATAATAAATCAATCCATAT
Found at i:226004 original size:18 final size:19
Alignment explanation
Indices: 225960--226007 Score: 53
Period size: 22 Copynumber: 2.4 Consensus size: 19
225950 ATAACTACAA
*
225960 TAATAAATCAATCCATATTT
1 TAATAAATCAATCCATA-TC
225980 TAAAATAAATCAATCCATA-C
1 T--AATAAATCAATCCATATC
226000 TAATAAAT
1 TAATAAAT
226008 TATTTAAGAT
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
18 7 0.28
20 2 0.08
22 16 0.64
ACGTcount: A:0.52, C:0.15, G:0.00, T:0.33
Consensus pattern (19 bp):
TAATAAATCAATCCATATC
Found at i:226007 original size:22 final size:22
Alignment explanation
Indices: 225932--226006 Score: 87
Period size: 26 Copynumber: 3.2 Consensus size: 22
225922 ATAAATTATT
225932 TAAAATAAATCAATCCATATAA
1 TAAAATAAATCAATCCATATAA
**
225954 CTACAATAATAAATCAATCCATATTT
1 -T--AA-AATAAATCAATCCATATAA
225980 TAAAATAAATCAATCCATACTAA
1 TAAAATAAATCAATCCATA-TAA
226003 TAAA
1 TAAA
226007 TTATTTAAGA
Statistics
Matches: 44, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
22 16 0.36
23 8 0.18
25 3 0.07
26 17 0.39
ACGTcount: A:0.55, C:0.16, G:0.00, T:0.29
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:226032 original size:54 final size:54
Alignment explanation
Indices: 225961--226129 Score: 293
Period size: 54 Copynumber: 3.1 Consensus size: 54
225951 TAACTACAAT
225961 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
1 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
* * *
226015 GATAAATCAATCGATATTTTAAAATAAATTAATCCATACTAATAAATTATTTAA
1 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
* *
226069 AATAAATCAATCTATATTTTAAAATAAATCAATTCATACTAATAAATTATTTAA
1 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
226123 AATAAAT
1 AATAAAT
226130 TATTTTAAAA
Statistics
Matches: 108, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
54 108 1.00
ACGTcount: A:0.52, C:0.10, G:0.01, T:0.37
Consensus pattern (54 bp):
AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
Found at i:226061 original size:228 final size:220
Alignment explanation
Indices: 225418--226026 Score: 1047
Period size: 228 Copynumber: 2.7 Consensus size: 220
225408 ACAACTACAA
* *
225418 TAATAAATTACTTAAAATAAATCAATCCATATTTTAAAATAAATCAATTCATACTAATAAATTAT
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTAT
*
225483 TTAAAATAAATCAATCCATACAACTACAATAATAAATCAATTCATATTTTAAAATAAATCAATCC
66 TTAAAATAAATCAATCCATACAACTACAATAATAAATCAATCCATATTTTAAAATAAATCAATCC
* *
225548 ATACAAATAAATTTTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATTCA
131 ATACAAATAAATTATTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCA
*
225613 TATTTTAAAATAAATCAATCGATAC
196 TATTTTAAAATAAATCAATCCATAC
225638 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTAT
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTAT
225703 TTAAAATAAATCAATCCATACAACTACAATAATAAATCAATCCATATTTTAAAATAAATCAATCA
66 TTAAAATAAATCAATCCATACAACTACAATAATAAATCAATCCATATTTT---A-AAAT--A--A
*
225768 ATCAATCCATACAAACAAATTATTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAA
123 ATCAATCCATACAAATAAATTATTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAA
225833 TCAATCCATATTTTAAAATAAATCAATCCATAC
188 TCAATCCATATTTTAAAATAAATCAATCCATAC
*
225866 TAATAAATTATTTAAAATAAATCAATCTATATTTTAAAATAAATCAATCCATACTAATAAATTAT
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTAT
*
225931 TTAAAATAAATCAATCCATATAACTACAATAATAAATCAATCCATATTTTAAAATAAATCAATCC
66 TTAAAATAAATCAATCCATACAACTACAATAATAAATCAATCCATATTTTAAAATAAATCAATCC
* *
225996 ATACTAATAAATTATTTAAGATAAATCAATC
131 ATACAAATAAATTATTTAAAATAAATCAATC
226027 GATATTTTAA
Statistics
Matches: 369, Mismatches: 12, Indels: 16
0.93 0.03 0.04
Matches are distributed among these distances:
220 149 0.40
222 1 0.00
223 1 0.00
224 8 0.02
225 1 0.00
226 1 0.00
228 208 0.56
ACGTcount: A:0.52, C:0.13, G:0.00, T:0.34
Consensus pattern (220 bp):
TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTAT
TTAAAATAAATCAATCCATACAACTACAATAATAAATCAATCCATATTTTAAAATAAATCAATCC
ATACAAATAAATTATTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCA
TATTTTAAAATAAATCAATCCATAC
Found at i:226072 original size:32 final size:32
Alignment explanation
Indices: 226032--226131 Score: 103
Period size: 32 Copynumber: 3.4 Consensus size: 32
226022 CAATCGATAT
226032 TTTAAAATAAATTAATCCATACTAATAAATTA
1 TTTAAAATAAATTAATCCATACTAATAAATTA
*
226064 TTTAAAAT--A--AATCAAT-CT-AT--A-T-
1 TTTAAAATAAATTAATCCATACTAATAAATTA
* *
226086 TTTAAAATAAATCAATTCATACTAATAAATTA
1 TTTAAAATAAATTAATCCATACTAATAAATTA
226118 TTTAAAATAAATTA
1 TTTAAAATAAATTA
226132 TTTTAAAATA
Statistics
Matches: 54, Mismatches: 4, Indels: 20
0.69 0.05 0.26
Matches are distributed among these distances:
22 8 0.15
23 1 0.02
24 2 0.04
26 7 0.13
27 4 0.07
28 8 0.15
30 2 0.04
31 1 0.02
32 21 0.39
ACGTcount: A:0.53, C:0.08, G:0.00, T:0.39
Consensus pattern (32 bp):
TTTAAAATAAATTAATCCATACTAATAAATTA
Found at i:226138 original size:15 final size:15
Alignment explanation
Indices: 226109--226300 Score: 235
Period size: 15 Copynumber: 12.5 Consensus size: 15
226099 AATTCATACT
226109 AATAAATTA-TTTAA
1 AATAAATTATTTTAA
226123 AATAAATTATTTTAA
1 AATAAATTATTTTAA
*
226138 AATAAATCAATCCATATTTTAT
1 AAT--A--AAT---TATTTTAA
226160 AATAAATTA-TTTAA
1 AATAAATTATTTTAA
* *
226174 AAAAAATTATTTTAT
1 AATAAATTATTTTAA
*
226189 AATAAATTATTTTAT
1 AATAAATTATTTTAA
*
226204 AATAAATTATTTTAT
1 AATAAATTATTTTAA
* *
226219 AATAAATCATTTTAT
1 AATAAATTATTTTAA
226234 AATAAATTATTTTAA
1 AATAAATTATTTTAA
*
226249 AATAAATTATTTTAT
1 AATAAATTATTTTAA
226264 AATAAATTATTTTAA
1 AATAAATTATTTTAA
226279 AATAAATTATTTTAA
1 AATAAATTATTTTAA
226294 AATAAAT
1 AATAAAT
226301 AACCTTATTA
Statistics
Matches: 159, Mismatches: 10, Indels: 17
0.85 0.05 0.09
Matches are distributed among these distances:
14 21 0.13
15 120 0.75
17 1 0.01
18 3 0.02
19 3 0.02
20 1 0.01
22 10 0.06
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (15 bp):
AATAAATTATTTTAA
Found at i:228015 original size:28 final size:27
Alignment explanation
Indices: 227976--228030 Score: 65
Period size: 28 Copynumber: 2.0 Consensus size: 27
227966 TTACAGGGAT
* * * *
227976 TAAAATAGATGTTTTAAATTTTTATAA
1 TAAAATACATGTGTCAAATTCTTATAA
228003 TAAAATTACATGTGTCAAATTCTTATAA
1 TAAAA-TACATGTGTCAAATTCTTATAA
228031 ATAATATTTT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
27 5 0.22
28 18 0.78
ACGTcount: A:0.44, C:0.05, G:0.07, T:0.44
Consensus pattern (27 bp):
TAAAATACATGTGTCAAATTCTTATAA
Found at i:248555 original size:44 final size:44
Alignment explanation
Indices: 248507--248596 Score: 137
Period size: 44 Copynumber: 2.0 Consensus size: 44
248497 TTTTCTAATC
* * *
248507 TACTGTGAAGGTTTTTATGGCAGGTGG-TGTTTTTAAGTTTTATG
1 TACTGTAAAGGCTTTTATGCCAGG-GGATGTTTTTAAGTTTTATG
248551 TACTGTAAAGGCTTTTATGCCAGGGGATGTTTTTAAGTTTTATG
1 TACTGTAAAGGCTTTTATGCCAGGGGATGTTTTTAAGTTTTATG
248595 TA
1 TA
248597 TTTGTTATTG
Statistics
Matches: 42, Mismatches: 3, Indels: 2
0.89 0.06 0.04
Matches are distributed among these distances:
43 2 0.05
44 40 0.95
ACGTcount: A:0.21, C:0.07, G:0.27, T:0.46
Consensus pattern (44 bp):
TACTGTAAAGGCTTTTATGCCAGGGGATGTTTTTAAGTTTTATG
Done.