Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009086.1 Hibiscus syriacus cultivar Beakdansim tig00112530_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: 1596699
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 7
Found at i:4368 original size:21 final size:21
Alignment explanation
Indices: 4342--4383 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
4332 TGGGTCAGTG
4342 ACTTAAATGC-AAATTTTGAAA
1 ACTT-AATGCTAAATTTTGAAA
*
4363 ACTTAATGCTCAATTTTGAAA
1 ACTTAATGCTAAATTTTGAAA
4384 TAAGTTAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 5 0.26
21 14 0.74
ACGTcount: A:0.43, C:0.12, G:0.10, T:0.36
Consensus pattern (21 bp):
ACTTAATGCTAAATTTTGAAA
Found at i:6006 original size:18 final size:18
Alignment explanation
Indices: 5974--6026 Score: 81
Period size: 18 Copynumber: 2.9 Consensus size: 18
5964 AGGGATTTAC
*
5974 AGTGGTCCTTAGGGACAT
1 AGTGGTCCTTCGGGACAT
5992 AGTGG-CCATTCGGGACAT
1 AGTGGTCC-TTCGGGACAT
6010 AGTGGTCCTTCGGGACA
1 AGTGGTCCTTCGGGACA
6027 AACATTCAGT
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
17 2 0.06
18 28 0.88
19 2 0.06
ACGTcount: A:0.21, C:0.21, G:0.34, T:0.25
Consensus pattern (18 bp):
AGTGGTCCTTCGGGACAT
Found at i:12168 original size:23 final size:21
Alignment explanation
Indices: 12129--12173 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 21
12119 CATAAATATT
*
12129 TAAAAAATTAAATAAAATTAA
1 TAAAAAATTAAATAAAAATAA
*
12150 TAAAAATATTTAATAAAAAATAA
1 TAAAAA-ATTAAAT-AAAAATAA
12173 T
1 T
12174 TTTTTATACC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 6 0.30
22 6 0.30
23 8 0.40
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (21 bp):
TAAAAAATTAAATAAAAATAA
Found at i:12173 original size:10 final size:11
Alignment explanation
Indices: 12129--12170 Score: 50
Period size: 13 Copynumber: 3.7 Consensus size: 11
12119 CATAAATATT
12129 TAAAAAATTAA
1 TAAAAAATTAA
*
12140 -ATAAAATTAA
1 TAAAAAATTAA
12150 TAAAAATATTTAA
1 TAAAAA-A-TTAA
12163 TAAAAAAT
1 TAAAAAAT
12171 AATTTTTTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
10 9 0.35
11 5 0.19
12 2 0.08
13 10 0.38
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (11 bp):
TAAAAAATTAA
Found at i:16220 original size:6 final size:6
Alignment explanation
Indices: 16209--16240 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
16199 CTCATAGCCG
16209 TCTCCC TCTCCC TCTCCC TCTCCC TCTCCC TC
1 TCTCCC TCTCCC TCTCCC TCTCCC TCTCCC TC
16241 CCTCTCTCGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.00, C:0.66, G:0.00, T:0.34
Consensus pattern (6 bp):
TCTCCC
Found at i:16243 original size:10 final size:11
Alignment explanation
Indices: 16213--16246 Score: 52
Period size: 12 Copynumber: 3.1 Consensus size: 11
16203 TAGCCGTCTC
16213 CCTCTCCCTCT
1 CCTCTCCCTCT
16224 CCCTCTCCCTCT
1 -CCTCTCCCTCT
16236 CC-CTCCCTCT
1 CCTCTCCCTCT
16246 C
1 C
16247 TCGTTTTCAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 9 0.41
11 2 0.09
12 11 0.50
ACGTcount: A:0.00, C:0.68, G:0.00, T:0.32
Consensus pattern (11 bp):
CCTCTCCCTCT
Found at i:23735 original size:12 final size:12
Alignment explanation
Indices: 23718--23742 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
23708 AAGAGTCGAC
23718 AAGTTAAATTTG
1 AAGTTAAATTTG
23730 AAGTTAAATTTG
1 AAGTTAAATTTG
23742 A
1 A
23743 CTTGTCATCA
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:0.44, C:0.00, G:0.16, T:0.40
Consensus pattern (12 bp):
AAGTTAAATTTG
Found at i:24092 original size:36 final size:37
Alignment explanation
Indices: 24052--24121 Score: 115
Period size: 36 Copynumber: 1.9 Consensus size: 37
24042 TATGTGCAGG
24052 GGGAACAGATTCCCCCCT-GAGGAGTATCGATTCCCC
1 GGGAACAGATTCCCCCCTGGAGGAGTATCGATTCCCC
* *
24088 GGGAACAGATTCCCCCCTGGGGGGGTATCGATTC
1 GGGAACAGATTCCCCCCTGGAGGAGTATCGATTC
24122 TCCCCTAAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
36 18 0.58
37 13 0.42
ACGTcount: A:0.20, C:0.30, G:0.30, T:0.20
Consensus pattern (37 bp):
GGGAACAGATTCCCCCCTGGAGGAGTATCGATTCCCC
Found at i:30982 original size:21 final size:23
Alignment explanation
Indices: 30958--31009 Score: 72
Period size: 23 Copynumber: 2.3 Consensus size: 23
30948 AGAAAATCGA
30958 TCCCCCCATG-A-GGGAACCGAT
1 TCCCCCCATGAAGGGGAACCGAT
**
30979 TCCCCCTTTGAAGGGGAACCGAT
1 TCCCCCCATGAAGGGGAACCGAT
31002 TCCCCCCA
1 TCCCCCCA
31010 CAGGGGAATC
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
21 8 0.32
22 1 0.04
23 16 0.64
ACGTcount: A:0.21, C:0.40, G:0.21, T:0.17
Consensus pattern (23 bp):
TCCCCCCATGAAGGGGAACCGAT
Found at i:34790 original size:23 final size:23
Alignment explanation
Indices: 34764--34851 Score: 90
Period size: 23 Copynumber: 3.8 Consensus size: 23
34754 CAATCTTATA
*
34764 TGGCACTACGGTGCAATTCTACG
1 TGGCACTTCGGTGCAATTCTACG
* *
34787 TGGCACTTCGGTGCATTTCTACA
1 TGGCACTTCGGTGCAATTCTACG
34810 TGGTC-CTTCGG-GACAAATTCTACG
1 TGG-CACTTCGGTG-C-AATTCTACG
* *
34834 TGGCACATCAGTGCAATT
1 TGGCACTTCGGTGCAATT
34852 TATATGAGCT
Statistics
Matches: 53, Mismatches: 7, Indels: 10
0.76 0.10 0.14
Matches are distributed among these distances:
22 1 0.02
23 35 0.66
24 16 0.30
25 1 0.02
ACGTcount: A:0.22, C:0.25, G:0.24, T:0.30
Consensus pattern (23 bp):
TGGCACTTCGGTGCAATTCTACG
Found at i:47480 original size:21 final size:22
Alignment explanation
Indices: 47412--47481 Score: 65
Period size: 23 Copynumber: 3.3 Consensus size: 22
47402 TATTTGGCAG
* *
47412 AGGGAATCGATACCCCCA-T-A
1 AGGGAAACGATTCCCCCATTGA
* *
47432 AGGGAACCGATTCCCCCTTTGA
1 AGGGAAACGATTCCCCCATTGA
*
47454 ATGGGAAACGATTCCCTCATTG-
1 A-GGGAAACGATTCCCCCATTGA
47476 AGGGAA
1 AGGGAA
47482 TCAATACCCC
Statistics
Matches: 41, Mismatches: 6, Indels: 5
0.79 0.12 0.10
Matches are distributed among these distances:
20 15 0.37
21 6 0.15
22 3 0.07
23 17 0.41
ACGTcount: A:0.30, C:0.26, G:0.24, T:0.20
Consensus pattern (22 bp):
AGGGAAACGATTCCCCCATTGA
Found at i:53488 original size:35 final size:35
Alignment explanation
Indices: 53412--53490 Score: 104
Period size: 35 Copynumber: 2.3 Consensus size: 35
53402 AACACAATCA
**
53412 TCAATTACACTCTAAACCACAAATTCCAAAATGCT
1 TCAATTACACTCTAAACCACAAATTCCAAAATAAT
* * * *
53447 TTAATTATATTCTAAACCTCAAATTCCAAAATAAT
1 TCAATTACACTCTAAACCACAAATTCCAAAATAAT
53482 TCAATTACA
1 TCAATTACA
53491 TACCCAACCC
Statistics
Matches: 36, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.44, C:0.23, G:0.01, T:0.32
Consensus pattern (35 bp):
TCAATTACACTCTAAACCACAAATTCCAAAATAAT
Found at i:54494 original size:35 final size:35
Alignment explanation
Indices: 54448--54527 Score: 126
Period size: 35 Copynumber: 2.3 Consensus size: 35
54438 GGGGTTGGGC
54448 ATGTAATTGAAG-TATTTTGGAATACGAGGTTTAGA
1 ATGTAATTGAAGAT-TTTTGGAATACGAGGTTTAGA
**
54483 ATGTAATTGAAGATTTTTGGAATTTGAGGTTTAGA
1 ATGTAATTGAAGATTTTTGGAATACGAGGTTTAGA
54518 ATGTAATTGA
1 ATGTAATTGA
54528 TTATTGTGTT
Statistics
Matches: 42, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
35 41 0.98
36 1 0.02
ACGTcount: A:0.34, C:0.01, G:0.25, T:0.40
Consensus pattern (35 bp):
ATGTAATTGAAGATTTTTGGAATACGAGGTTTAGA
Found at i:62156 original size:44 final size:44
Alignment explanation
Indices: 62104--62196 Score: 170
Period size: 44 Copynumber: 2.1 Consensus size: 44
62094 TGCGTTGTGG
62104 GATT-GTTTCTATTATGTTATTTTAATTCTTTTTTATAAATTAA
1 GATTCGTTTCTATTATGTTATTTTAATTCTTTTTTATAAATTAA
*
62147 GATTCGTTTCTATTATGTTATTTTAATTCTTTTTTATAAGTTAA
1 GATTCGTTTCTATTATGTTATTTTAATTCTTTTTTATAAATTAA
62191 GATTCG
1 GATTCG
62197 GTATTTCTGT
Statistics
Matches: 48, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
43 4 0.08
44 44 0.92
ACGTcount: A:0.26, C:0.06, G:0.10, T:0.58
Consensus pattern (44 bp):
GATTCGTTTCTATTATGTTATTTTAATTCTTTTTTATAAATTAA
Found at i:65106 original size:13 final size:14
Alignment explanation
Indices: 65083--65111 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
65073 TTTTCAACTG
65083 AATTTTATTTTTAT
1 AATTTTATTTTTAT
65097 AATTTT-TTTTTAT
1 AATTTTATTTTTAT
65110 AA
1 AA
65112 AAAAAATCAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.60
14 6 0.40
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (14 bp):
AATTTTATTTTTAT
Found at i:70267 original size:29 final size:28
Alignment explanation
Indices: 70225--70289 Score: 85
Period size: 28 Copynumber: 2.3 Consensus size: 28
70215 ATCGATTAAT
** *
70225 TAAAAAAACGTATTTGTAGACTTCTTTTA
1 TAAAAAAAAATATTT-TAAACTTCTTTTA
*
70254 TAAAAAAAAATATTTTAAATTTCTTTTA
1 TAAAAAAAAATATTTTAAACTTCTTTTA
70282 TAAAAAAA
1 TAAAAAAA
70290 TTAATAAATT
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
28 19 0.59
29 13 0.41
ACGTcount: A:0.49, C:0.06, G:0.05, T:0.40
Consensus pattern (28 bp):
TAAAAAAAAATATTTTAAACTTCTTTTA
Found at i:70316 original size:26 final size:25
Alignment explanation
Indices: 70246--70325 Score: 63
Period size: 28 Copynumber: 3.0 Consensus size: 25
70236 ATTTGTAGAC
70246 TTCTTTTATAAAAAAA-AATATTTTAAAT
1 TTCTTTTATAAAAAAATAA-A---TAAAT
*
70274 TTCTTTTATAAAAAAATTAATAAAT
1 TTCTTTTATAAAAAAATAAATAAAT
* * *
70299 TTGTTTGTATATATAAATAAATCAAAT
1 TTCTTT-TATAAAAAAATAAAT-AAAT
70326 ATATTTATAT
Statistics
Matches: 44, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
25 10 0.23
26 12 0.27
27 4 0.09
28 17 0.39
29 1 0.02
ACGTcount: A:0.49, C:0.04, G:0.03, T:0.45
Consensus pattern (25 bp):
TTCTTTTATAAAAAAATAAATAAAT
Found at i:71411 original size:39 final size:39
Alignment explanation
Indices: 71368--71463 Score: 131
Period size: 39 Copynumber: 2.5 Consensus size: 39
71358 CAAATCTAAG
*
71368 AATTCAAATATA-AATTTAAGTTACGATCATATTATTCCA
1 AATTCAAACATACAATTTAA-TTACGATCATATTATTCCA
* * *
71407 AATTCCACCATACAATTTTATTACGATCATATTATTCCA
1 AATTCAAACATACAATTTAATTACGATCATATTATTCCA
*
71446 AATTCAATCATACAATTT
1 AATTCAAACATACAATTT
71464 TTATTTAACA
Statistics
Matches: 50, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
39 44 0.88
40 6 0.12
ACGTcount: A:0.41, C:0.18, G:0.03, T:0.39
Consensus pattern (39 bp):
AATTCAAACATACAATTTAATTACGATCATATTATTCCA
Found at i:71464 original size:39 final size:39
Alignment explanation
Indices: 71388--71464 Score: 136
Period size: 39 Copynumber: 2.0 Consensus size: 39
71378 TAAATTTAAG
*
71388 TTACGATCATATTATTCCAAATTCCACCATACAATTTTA
1 TTACGATCATATTATTCCAAATTCAACCATACAATTTTA
*
71427 TTACGATCATATTATTCCAAATTCAATCATACAATTTT
1 TTACGATCATATTATTCCAAATTCAACCATACAATTTT
71465 TATTTAACAA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 36 1.00
ACGTcount: A:0.36, C:0.21, G:0.03, T:0.40
Consensus pattern (39 bp):
TTACGATCATATTATTCCAAATTCAACCATACAATTTTA
Found at i:73792 original size:99 final size:99
Alignment explanation
Indices: 73621--73817 Score: 385
Period size: 99 Copynumber: 2.0 Consensus size: 99
73611 CCGGGTCTTC
*
73621 TCTAAATGTTTATGATGAATATTGATATAATTTCTTTGAGAAGTAGTTTCATTTGACTTATCTGC
1 TCTAAATGTTTACGATGAATATTGATATAATTTCTTTGAGAAGTAGTTTCATTTGACTTATCTGC
73686 TATATTATTTTGGATGGTTATTTTCACCCTTTGT
66 TATATTATTTTGGATGGTTATTTTCACCCTTTGT
73720 TCTAAATGTTTACGATGAATATTGATATAATTTCTTTGAGAAGTAGTTTCATTTGACTTATCTGC
1 TCTAAATGTTTACGATGAATATTGATATAATTTCTTTGAGAAGTAGTTTCATTTGACTTATCTGC
73785 TATATTATTTTGGATGGTTATTTTCACCCTTTG
66 TATATTATTTTGGATGGTTATTTTCACCCTTTG
73818 CGGCATAACC
Statistics
Matches: 97, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
99 97 1.00
ACGTcount: A:0.25, C:0.11, G:0.15, T:0.49
Consensus pattern (99 bp):
TCTAAATGTTTACGATGAATATTGATATAATTTCTTTGAGAAGTAGTTTCATTTGACTTATCTGC
TATATTATTTTGGATGGTTATTTTCACCCTTTGT
Found at i:83910 original size:25 final size:22
Alignment explanation
Indices: 83881--83926 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
83871 TTTTTAACCC
83881 AATCTTAATTCCTAATAAAATAATA
1 AATC-TAA-TCCTAA-AAAATAATA
*
83906 AATCTAATCCTAAAAGATAAT
1 AATCTAATCCTAAAAAATAAT
83927 GCATCATCCT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 7 0.35
23 6 0.30
24 3 0.15
25 4 0.20
ACGTcount: A:0.52, C:0.13, G:0.02, T:0.33
Consensus pattern (22 bp):
AATCTAATCCTAAAAAATAATA
Found at i:87705 original size:11 final size:11
Alignment explanation
Indices: 87691--87736 Score: 51
Period size: 11 Copynumber: 4.4 Consensus size: 11
87681 TTTTTTGAAA
87691 TTTTGGCTTTT
1 TTTTGGCTTTT
*
87702 TTTTGCCTTTT
1 TTTTGGCTTTT
* *
87713 TTTTTGCCTTT
1 TTTTGGCTTTT
87724 TTTT-G-TTTT
1 TTTTGGCTTTT
87733 TTTT
1 TTTT
87737 TTTGAAAAAA
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
9 7 0.23
10 1 0.03
11 22 0.73
ACGTcount: A:0.00, C:0.11, G:0.11, T:0.78
Consensus pattern (11 bp):
TTTTGGCTTTT
Found at i:87713 original size:12 final size:12
Alignment explanation
Indices: 87698--87727 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
87688 AAATTTTGGC
87698 TTTTTTTTGCCT
1 TTTTTTTTGCCT
87710 TTTTTTTTGCCT
1 TTTTTTTTGCCT
87722 TTTTTT
1 TTTTTT
87728 GTTTTTTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.00, C:0.13, G:0.07, T:0.80
Consensus pattern (12 bp):
TTTTTTTTGCCT
Found at i:87728 original size:10 final size:11
Alignment explanation
Indices: 87691--87727 Score: 56
Period size: 11 Copynumber: 3.3 Consensus size: 11
87681 TTTTTTGAAA
*
87691 TTTTGGCTTTT
1 TTTTGCCTTTT
87702 TTTTGCCTTTTT
1 TTTTGCC-TTTT
87714 TTTTGCCTTTT
1 TTTTGCCTTTT
87725 TTT
1 TTT
87728 GTTTTTTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
11 13 0.54
12 11 0.46
ACGTcount: A:0.00, C:0.14, G:0.11, T:0.76
Consensus pattern (11 bp):
TTTTGCCTTTT
Found at i:87739 original size:22 final size:22
Alignment explanation
Indices: 87699--87740 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
87689 AATTTTGGCT
87699 TTTTTTTGCCTTTTTTTTTGCC
1 TTTTTTTGCCTTTTTTTTTGCC
**
87721 TTTTTTTGTTTTTTTTTTTG
1 TTTTTTTGCCTTTTTTTTTG
87741 AAAAAATAGC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.00, C:0.10, G:0.10, T:0.81
Consensus pattern (22 bp):
TTTTTTTGCCTTTTTTTTTGCC
Found at i:88618 original size:25 final size:22
Alignment explanation
Indices: 88589--88634 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
88579 TTTTTAACCC
88589 AATCTTAATTCCTAATAAAATAATA
1 AATC-TAA-TCCTAA-AAAATAATA
*
88614 AATCTAATCCTAAAAGATAAT
1 AATCTAATCCTAAAAAATAAT
88635 GCATCATCCT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 7 0.35
23 6 0.30
24 3 0.15
25 4 0.20
ACGTcount: A:0.52, C:0.13, G:0.02, T:0.33
Consensus pattern (22 bp):
AATCTAATCCTAAAAAATAATA
Found at i:93104 original size:21 final size:21
Alignment explanation
Indices: 93080--93120 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
93070 TATGTGTTTA
93080 GTATCTAAACTATCAATTTTG
1 GTATCTAAACTATCAATTTTG
* * *
93101 GTATGTGAACTTTCAATTTT
1 GTATCTAAACTATCAATTTT
93121 TTTAAAAAAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.29, C:0.12, G:0.12, T:0.46
Consensus pattern (21 bp):
GTATCTAAACTATCAATTTTG
Found at i:96281 original size:19 final size:19
Alignment explanation
Indices: 96257--96295 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
96247 CTAAACTATA
96257 TGTATATAAGTTGAAAGGG
1 TGTATATAAGTTGAAAGGG
96276 TGTATATAAGTTGAAAGGG
1 TGTATATAAGTTGAAAGGG
96295 T
1 T
96296 CAAAAAGACA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.36, C:0.00, G:0.31, T:0.33
Consensus pattern (19 bp):
TGTATATAAGTTGAAAGGG
Found at i:106542 original size:375 final size:383
Alignment explanation
Indices: 105851--106921 Score: 1279
Period size: 375 Copynumber: 2.8 Consensus size: 383
105841 GAGGTTTACG
* * * * * *
105851 AAAATGTAAAGGAAGCGAAGATGAAGAGCTCACGTGC-TGCAGTCGGTGTTCTTGGAGAT-GGGA
1 AAAATGTAAAAGAAGCGAAGATGATGAACTCAC-TTCTTGCAATCGGTGTTCCTGGAGATGGGGA
* * * * *
105914 AAATTAAATTGAACGTTGCACTTGGTCGGGAGAGATGCAGCAGCCTCTTCCTTGATGCAGGGCAT
65 AAA-TAAATTGAACGTTGCACTTGGCCGGGAGAGATGCAGCGGCATCTTCCTTGATGGACGGCAT
* * * *
105979 ACTAGCGGCGGTCTCTTTGACGCAGTTGCAGGCCGCCTGCTTGTCCGCGGTGGTTGAGGCGATGG
129 ACTAGCGGCGGTGTCTTTAACGCAGTTGCAAGCCGCCTGCTTGTCCGCGGTGGTTGTGGCGATGG
*
106044 TTTGGAGTCTCGACACGCTGCTACAACAGTCAGCCGTAGGAACCGCTTG-GTTACCGGTAAGGAA
194 TTTGGAGTCTCGACACGCCGCTACAACAGTCAGCCGTAGGAACCGCTTGAG-TACCGGTAAGGAA
* * * * *
106108 AGGAATGCAGTGCACCAATGTGCCTCTAACTTGGTCGCAACTCACAGTGGCCGGCTCTTGGATAC
258 AGGAACGCAGTGCACCAATGTACCTCTAACTTGGTCACAACTTACGGTGGCCGGCTCTTGGATAC
* *** * * * **
106173 TGACAAG-GAAAC-A-TTTA-G-TCATTAG-CCGT-TC-TAT-TATAATGTTAAGGTTTATA
323 TGACAAGTCAAACAAGCCAAGGAACATTAGTCAGTATCGT-TCTATAATGTTAAGATCAATA
* * *
106226 CAAATGTAAAAGAAGCGAAGATGATGAACTCACTTTTTGCAATCGGTCTTCCTGGAGATGGGGAA
1 AAAATGTAAAAGAAGCGAAGATGATGAACTCACTTCTTGCAATCGGTGTTCCTGGAGATGGGGAA
* * * * * *
106291 ACTAACTTGAACGTTGCACTTGGCCGGCAGAGATGCCGCGGCATCTTCCTTGATGGATGGCATAG
66 AATAAATTGAACGTTGCACTTGGCCGGGAGAGATGCAGCGGCATCTTCCTTGATGGACGGCATAC
* * *
106356 TAGCGGCGGTGTCCTTAACACAGTTGCAAGCCGCCTGCTTGTCCGCGGTGGTTGTGGCAATGGTT
131 TAGCGGCGGTGTCTTTAACGCAGTTGCAAGCCGCCTGCTTGTCCGCGGTGGTTGTGGCGATGGTT
* *
106421 TGGAGTCTCGACACGCCGCTGCAACAGTCAGCCGTAGGAACCGCTTGAGTGCCGGTAAGGAAAGG
196 TGGAGTCTCGACACGCCGCTACAACAGTCAGCCGTAGGAACCGCTTGAGTACCGGTAAGGAAAGG
** * *
106486 AACGCAGTGCACCAATGTACCTCTAACTTGGTCACAGTTTACGGTGGTCTGCTCTTGGATACTGA
261 AACGCAGTGCACCAATGTACCTCTAACTTGGTCACAACTTACGGTGGCCGGCTCTTGGATACTGA
* *
106551 CAAGTTACAAACAAAGCCAAGGAAACATTAGTTATTAATCGTTCTATAATGTTAAGATCAATA
326 CAAG-T-CAAAC-AAGCCAAGG-AACATTAGTCAGT-ATCGTTCTATAATGTTAAGATCAATA
** *
106614 AAAATACAAAAGAAGCGAAGATGATGAACTCACTTCTTGCAATCGGTGTTTCTGGAGATGGGGAA
1 AAAATGTAAAAGAAGCGAAGATGATGAACTCACTTCTTGCAATCGGTGTTCCTGGAGATGGGGAA
* *
106679 AATAAATTGAACGTTGCATTTGGCCGGGAGAGATGCGGCGGCATCTTCCTTGATGGACGGCATAC
66 AATAAATTGAACGTTGCACTTGGCCGGGAGAGATGCAGCGGCATCTTCCTTGATGGACGGCATAC
* * * ** * *
106744 TGGCGGCGGCGTCTTTAACGCAGTTGCAAGCCGCCTGTTTGTCCGCGGTTATAGTGGCGATGGTC
131 TAGCGGCGGTGTCTTTAACGCAGTTGCAAGCCGCCTGCTTGTCCGCGGTGGTTGTGGCGATGGTT
* * * * ** ** *
106809 CGGAGTTTCAACACGCCACTACAACAACCAGCCGCGGGAACCGCTTGAGCACCGGTAAGGAAAGG
196 TGGAGTCTCGACACGCCGCTACAACAGTCAGCCGTAGGAACCGCTTGAGTACCGGTAAGGAAAGG
* * *
106874 AACGCACTTG-GCCAATG-AGCTTCTAACTTGGTCACAACTTACGGTGGC
261 AACGCA-GTGCACCAATGTA-CCTCTAACTTGGTCACAACTTACGGTGGC
106922 GTCTCCTTGC
Statistics
Matches: 588, Mismatches: 89, Indels: 25
0.84 0.13 0.04
Matches are distributed among these distances:
374 1 0.00
375 280 0.48
376 7 0.01
378 4 0.01
380 1 0.00
381 1 0.00
382 1 0.00
384 6 0.01
385 1 0.00
387 4 0.01
388 280 0.48
389 2 0.00
ACGTcount: A:0.26, C:0.22, G:0.28, T:0.24
Consensus pattern (383 bp):
AAAATGTAAAAGAAGCGAAGATGATGAACTCACTTCTTGCAATCGGTGTTCCTGGAGATGGGGAA
AATAAATTGAACGTTGCACTTGGCCGGGAGAGATGCAGCGGCATCTTCCTTGATGGACGGCATAC
TAGCGGCGGTGTCTTTAACGCAGTTGCAAGCCGCCTGCTTGTCCGCGGTGGTTGTGGCGATGGTT
TGGAGTCTCGACACGCCGCTACAACAGTCAGCCGTAGGAACCGCTTGAGTACCGGTAAGGAAAGG
AACGCAGTGCACCAATGTACCTCTAACTTGGTCACAACTTACGGTGGCCGGCTCTTGGATACTGA
CAAGTCAAACAAGCCAAGGAACATTAGTCAGTATCGTTCTATAATGTTAAGATCAATA
Found at i:109392 original size:219 final size:219
Alignment explanation
Indices: 109011--109448 Score: 840
Period size: 219 Copynumber: 2.0 Consensus size: 219
109001 CCAACTGTGC
109011 AGTGACTCCTAGGGCGACCACTGCGATCCACAAGCAGCCGAAGAAGCTGCGTTATAAGGGTGTAA
1 AGTGACTCCTAGGGCGACCACTGCGATCCACAAGCAGCCGAAGAAGCTGCGTTATAAGGGTGTAA
109076 GGAGAAGGCCATGGGGGACGTACGCAGCAGAGATAAAGGATCCTAAGAGAAATGGTGCCTGGATC
66 GGAGAAGGCCATGGGGGACGTACGCAGCAGAGATAAAGGATCCTAAGAGAAATGGTGCCTGGATC
109141 TGGCTTGGCACTTACGAGACGCCGGAAGATGCTGCACTGGCTTATGACAAAGCAGCTTTTAAAAT
131 TGGCTTGGCACTTACGAGACGCCGGAAGATGCTGCACTGGCTTATGACAAAGCAGCTTTTAAAAT
*
109206 GTGCGGCGCAAAAGCCAAGCTGAA
196 GTGCAGCGCAAAAGCCAAGCTGAA
*
109230 AGTGACTCCTAGGGCGACCACTGCGATTCACAAGCAGCCGAAGAAGCTGCGTTATAAGGGTGTAA
1 AGTGACTCCTAGGGCGACCACTGCGATCCACAAGCAGCCGAAGAAGCTGCGTTATAAGGGTGTAA
109295 GGAGAAGGCCATGGGGGACGTACGCAGCAGAGATAAAGGATCCTAAGAGAAATGGTGCCTGGATC
66 GGAGAAGGCCATGGGGGACGTACGCAGCAGAGATAAAGGATCCTAAGAGAAATGGTGCCTGGATC
* *
109360 TGGCTTGGTACTTACGAGACGCCGGCAGATGCTGCACTGGCTTATGACAAAGCAGCTTTTAAAAT
131 TGGCTTGGCACTTACGAGACGCCGGAAGATGCTGCACTGGCTTATGACAAAGCAGCTTTTAAAAT
109425 GTGCAGCGCAAAAGCCAAGCTGAA
196 GTGCAGCGCAAAAGCCAAGCTGAA
109449 TTTTCCTCAT
Statistics
Matches: 215, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
219 215 1.00
ACGTcount: A:0.30, C:0.21, G:0.31, T:0.18
Consensus pattern (219 bp):
AGTGACTCCTAGGGCGACCACTGCGATCCACAAGCAGCCGAAGAAGCTGCGTTATAAGGGTGTAA
GGAGAAGGCCATGGGGGACGTACGCAGCAGAGATAAAGGATCCTAAGAGAAATGGTGCCTGGATC
TGGCTTGGCACTTACGAGACGCCGGAAGATGCTGCACTGGCTTATGACAAAGCAGCTTTTAAAAT
GTGCAGCGCAAAAGCCAAGCTGAA
Found at i:110272 original size:2 final size:2
Alignment explanation
Indices: 110265--110299 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
110255 TTCAGTAAAC
*
110265 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG CG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
110300 AGGAGAACAT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.49, C:0.03, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:115030 original size:7 final size:7
Alignment explanation
Indices: 115018--115076 Score: 90
Period size: 7 Copynumber: 9.0 Consensus size: 7
115008 TAAGATTTCT
115018 CCAACTC
1 CCAACTC
115025 CCAACTC
1 CCAACTC
115032 CCAACTC
1 CCAACTC
115039 CCAACTC
1 CCAACTC
115046 CCAACT-
1 CCAACTC
115052 CCAACT-
1 CCAACTC
115058 CCAACT-
1 CCAACTC
115064 CCAACT-
1 CCAACTC
115070 CCAACTC
1 CCAACTC
115077 GTAAAGCCTT
Statistics
Matches: 51, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
6 24 0.47
7 27 0.53
ACGTcount: A:0.31, C:0.54, G:0.00, T:0.15
Consensus pattern (7 bp):
CCAACTC
Found at i:115057 original size:6 final size:6
Alignment explanation
Indices: 115016--115076 Score: 86
Period size: 6 Copynumber: 9.5 Consensus size: 6
115006 AATAAGATTT
115016 CTCCAA CTCCCAA CTCCCAA CTCCCAA CTCCCAA CTCCAA CTCCAA CTCCAA
1 CTCCAA CT-CCAA CT-CCAA CT-CCAA CT-CCAA CTCCAA CTCCAA CTCCAA
115068 CTCCAA CTC
1 CTCCAA CTC
115077 GTAAAGCCTT
Statistics
Matches: 54, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
6 27 0.50
7 27 0.50
ACGTcount: A:0.30, C:0.54, G:0.00, T:0.16
Consensus pattern (6 bp):
CTCCAA
Found at i:115882 original size:34 final size:33
Alignment explanation
Indices: 115806--115912 Score: 85
Period size: 34 Copynumber: 3.1 Consensus size: 33
115796 GTGGTAAGAA
* *
115806 ATTTATTTTTATGTTAGTAT-TTT-TTTAAATAGTT
1 ATTT-TTTTTAT-TTAATATATTTATATAAATA-TT
*
115840 ATTATTTTTTATATTAATATATTTATGTAAATATT
1 ATT-TTTTTTAT-TTAATATATTTATATAAATATT
* *
115875 A-TTTTTTTATTAAAATAATATTTATATAATTATT
1 ATTTTTTTTATT-TAAT-ATATTTATATAAATATT
115909 ATTT
1 ATTT
115913 ATTTAGAATT
Statistics
Matches: 61, Mismatches: 6, Indels: 11
0.78 0.08 0.14
Matches are distributed among these distances:
32 1 0.02
33 11 0.18
34 33 0.54
35 9 0.15
36 7 0.11
ACGTcount: A:0.35, C:0.00, G:0.04, T:0.62
Consensus pattern (33 bp):
ATTTTTTTTATTTAATATATTTATATAAATATT
Found at i:115894 original size:36 final size:34
Alignment explanation
Indices: 115839--115917 Score: 101
Period size: 34 Copynumber: 2.4 Consensus size: 34
115829 TTTAAATAGT
*
115839 TATTATTTTTTATATT--AAT-ATATTTATGTAAA
1 TATTATTTTTT-TATTAAAATAATATTTATATAAA
*
115871 TATTATTTTTTTATTAAAATAATATTTATATAAT
1 TATTATTTTTTTATTAAAATAATATTTATATAAA
*
115905 TATTATTTATTTA
1 TATTATTTTTTTA
115918 GAATTATTAA
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
31 4 0.10
32 11 0.27
33 3 0.07
34 23 0.56
ACGTcount: A:0.38, C:0.00, G:0.01, T:0.61
Consensus pattern (34 bp):
TATTATTTTTTTATTAAAATAATATTTATATAAA
Found at i:116079 original size:17 final size:17
Alignment explanation
Indices: 116057--116110 Score: 54
Period size: 17 Copynumber: 3.2 Consensus size: 17
116047 AATGTTAATA
116057 TTTAAATTTATTTTTAT
1 TTTAAATTTATTTTTAT
* * * *
116074 TTTAAAGTTATTATGAA
1 TTTAAATTTATTTTTAT
* *
116091 TTTATATTAATTTTTAT
1 TTTAAATTTATTTTTAT
116108 TTT
1 TTT
116111 TTATAATGTA
Statistics
Matches: 27, Mismatches: 10, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
17 27 1.00
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.65
Consensus pattern (17 bp):
TTTAAATTTATTTTTAT
Found at i:117670 original size:21 final size:21
Alignment explanation
Indices: 117640--117687 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
117630 GCAGGGGTAC
* *
117640 ATGCCCAGCCCTCCACTTCAT
1 ATGCCAAGCCCACCACTTCAT
* *
117661 ATGCCAAGCCCACCAGTTTAT
1 ATGCCAAGCCCACCACTTCAT
117682 ATGCCA
1 ATGCCA
117688 TCTCCGCAGG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.25, C:0.40, G:0.12, T:0.23
Consensus pattern (21 bp):
ATGCCAAGCCCACCACTTCAT
Found at i:117742 original size:21 final size:21
Alignment explanation
Indices: 117691--117742 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
117681 TATGCCATCT
*
117691 CCGCAGGGTTACATTCCTAGC
1 CCGCAGGGTTACATGCCTAGC
117712 CCGCCA-GGTTACATGCCTAGC
1 CCG-CAGGGTTACATGCCTAGC
117733 CCGCAGGGTT
1 CCGCAGGGTT
117743 TTATACCATA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
20 2 0.07
21 24 0.86
22 2 0.07
ACGTcount: A:0.17, C:0.35, G:0.27, T:0.21
Consensus pattern (21 bp):
CCGCAGGGTTACATGCCTAGC
Found at i:118324 original size:33 final size:34
Alignment explanation
Indices: 118265--118361 Score: 124
Period size: 33 Copynumber: 2.9 Consensus size: 34
118255 AAATGTTTTT
*
118265 AAAATACAAATTATATTATTCAAAATTTAAAATA
1 AAAATAAAAATTATATTATTCAAAATTTAAAATA
* * *
118299 AAAATAAAAATAATATTATTC-AAATTTAAATTT
1 AAAATAAAAATTATATTATTCAAAATTTAAAATA
* * *
118332 AAAATATAAATTATAGTATTCGAAATTTAA
1 AAAATAAAAATTATATTATTCAAAATTTAA
118362 CATTAAATTT
Statistics
Matches: 55, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
33 28 0.51
34 27 0.49
ACGTcount: A:0.57, C:0.04, G:0.02, T:0.37
Consensus pattern (34 bp):
AAAATAAAAATTATATTATTCAAAATTTAAAATA
Found at i:118368 original size:34 final size:32
Alignment explanation
Indices: 118263--118368 Score: 122
Period size: 34 Copynumber: 3.2 Consensus size: 32
118253 ATAAATGTTT
*
118263 TTAAAATACAAATTATATTATTCAAAATTTAAAA
1 TTAAAATAAAAATTATATTATTC-AAATTT-AAA
* *
118297 TAAAAATAAAAATAATATTATTCAAATTTAAA
1 TTAAAATAAAAATTATATTATTCAAATTTAAA
* *
118329 TTTAAAATATAAATTATAGTATTCGAAATTTAACA
1 -TTAAAATAAAAATTATATTATTC-AAATTTAA-A
118364 TTAAA
1 TTAAA
118369 TTTCAACTTA
Statistics
Matches: 62, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
32 3 0.05
33 25 0.40
34 33 0.53
35 1 0.02
ACGTcount: A:0.56, C:0.05, G:0.02, T:0.38
Consensus pattern (32 bp):
TTAAAATAAAAATTATATTATTCAAATTTAAA
Found at i:118995 original size:128 final size:128
Alignment explanation
Indices: 118762--119389 Score: 1107
Period size: 128 Copynumber: 4.9 Consensus size: 128
118752 TTACCTGATT
* *
118762 TACTGATATATCTAGTGTCCCCGATGGACATGAGTGACATAATAGGGCAATGATAACATATTCTA
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
* * * *** *
118827 TGACAAAATAATAGAAGGCGCGCCCCCGGGAACGCTCCTTCATGTCCCCT-GAGAAATAATAGG
66 TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGT-GAATAGTGAAATAATAGG
118890 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
*
118955 TAACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
66 TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
*
119018 TACTGATATATCTATTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
*
119083 TTACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
66 TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
*
119146 TACTGATATATCTAGTGTCCCCAAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
119211 TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
66 TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
119274 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
*
119339 TGACGAAATAATGGAAGGCGCG-CCCCGGGAATGCGCCTTCATGTGAATAGT
66 TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGT
119390 ACTTCGATTA
Statistics
Matches: 482, Mismatches: 17, Indels: 3
0.96 0.03 0.01
Matches are distributed among these distances:
127 29 0.06
128 453 0.94
ACGTcount: A:0.32, C:0.20, G:0.24, T:0.23
Consensus pattern (128 bp):
TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
Found at i:119473 original size:8 final size:8
Alignment explanation
Indices: 119460--119500 Score: 57
Period size: 8 Copynumber: 5.2 Consensus size: 8
119450 TCACAATCTT
119460 TCAAATTC
1 TCAAATTC
119468 TCAAATTC
1 TCAAATTC
* *
119476 CCAAACTC
1 TCAAATTC
119484 T-AAATTC
1 TCAAATTC
119491 TCAAATTC
1 TCAAATTC
119499 TC
1 TC
119501 TGAAAATGAG
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
7 6 0.21
8 22 0.79
ACGTcount: A:0.37, C:0.29, G:0.00, T:0.34
Consensus pattern (8 bp):
TCAAATTC
Found at i:123710 original size:86 final size:86
Alignment explanation
Indices: 123605--123801 Score: 292
Period size: 86 Copynumber: 2.3 Consensus size: 86
123595 AAAAAGCTGC
* * * *
123605 TATTGACTATGTATATAGTGGCGTTTTCTATATAAGCGCCGCAAAAGATCTCGAACTTTAGTGGT
1 TATTGACTATGTATTTAGTGGCGTTTTCTATATAAGCGACGCAAAAGATCTCAAACTTTAGTGGC
*
123670 GTTTTGTTTTACAAACGCCT-G
66 GTTTTGTTTTACAAAC-ACTAG
* *
123691 TATTGACTATGTATTTAGTGACGTTTTCTATATAAGCGATGCAAAAGATCTCAAACTTTAGTGGC
1 TATTGACTATGTATTTAGTGGCGTTTTCTATATAAGCGACGCAAAAGATCTCAAACTTTAGTGGC
123756 GTTTTGTTTTACAAACACTAG
66 GTTTTGTTTTACAAACACTAG
*
123777 TATTGA-T-TGTATTTAGTGGTGTTTT
1 TATTGACTATGTATTTAGTGGCGTTTT
123802 ATTATACAAA
Statistics
Matches: 101, Mismatches: 9, Indels: 4
0.89 0.08 0.04
Matches are distributed among these distances:
84 16 0.16
85 3 0.03
86 82 0.81
ACGTcount: A:0.26, C:0.13, G:0.20, T:0.41
Consensus pattern (86 bp):
TATTGACTATGTATTTAGTGGCGTTTTCTATATAAGCGACGCAAAAGATCTCAAACTTTAGTGGC
GTTTTGTTTTACAAACACTAG
Found at i:125917 original size:43 final size:43
Alignment explanation
Indices: 125829--125917 Score: 115
Period size: 43 Copynumber: 2.1 Consensus size: 43
125819 GACTCAAAAC
* *** *
125829 TTGCAACGTTTCTATTTAAAAACGCCACTAATGCATTGACTTA
1 TTGCAACGTTTCTATATAAAAACGCCACTAATGCACCAACATA
* *
125872 TTGCAGCGTTTGTATATAAAAACGCCACTAATGCACCAACATA
1 TTGCAACGTTTCTATATAAAAACGCCACTAATGCACCAACATA
125915 TTG
1 TTG
125918 TGACATTTGT
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
43 39 1.00
ACGTcount: A:0.34, C:0.21, G:0.13, T:0.31
Consensus pattern (43 bp):
TTGCAACGTTTCTATATAAAAACGCCACTAATGCACCAACATA
Found at i:125927 original size:43 final size:43
Alignment explanation
Indices: 125845--125935 Score: 103
Period size: 43 Copynumber: 2.1 Consensus size: 43
125835 CGTTTCTATT
*** * *
125845 TAAAAACGCCACTAATGCATTGACTTATTGCAGCGTTTGTATA
1 TAAAAACGCCACTAATGCACCAACATATTGCAGCATTTGTATA
* *
125888 TAAAAACGCCACTAATGCACCAACATATTG-TGACATTTGTTTA
1 TAAAAACGCCACTAATGCACCAACATATTGCAG-CATTTGTATA
125931 TAAAA
1 TAAAA
125936 TGCCCAAAAG
Statistics
Matches: 40, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
42 1 0.03
43 39 0.98
ACGTcount: A:0.37, C:0.19, G:0.13, T:0.31
Consensus pattern (43 bp):
TAAAAACGCCACTAATGCACCAACATATTGCAGCATTTGTATA
Found at i:126096 original size:122 final size:123
Alignment explanation
Indices: 125877--126137 Score: 321
Period size: 123 Copynumber: 2.1 Consensus size: 123
125867 ACTTATTGCA
* * * *
125877 GCGTTTGTATATAAAAACGCCACTAATGCACCAACATATTGTGACATTTGTTTATAAAATGCCCA
1 GCGTTTGTATTTAAAAACGCCACTAATGCACCAACATATTGCGACATTTGTTTAAAAAATGCACA
* * * *
125942 AAAGATGAGTATATAGAGGTGTTACTG-GGAAAATGCAGCTAATGTTACTATTTTGTG
66 AAAGATGAGGATATAGAGGCGTTACTGAGAAAAATGCAGCTAATGTTACCATTTTGTG
* * * *
125999 GCGTTTGTATTTAAAAACGTCAGTAATGCACTC-ACCTATTGCGGCATTTGTTTAAAAAATGTCA
1 GCGTTTGTATTTAAAAACGCCACTAATGCAC-CAACATATTGCGACATTTGTTTAAAAAATG-CA
* * * *
126063 CAAAAGATGAGGCTATAGCGGCGTTTCT-AGAAAAATGCCGCTAATGTTACCATTTTGTG
64 CAAAAGATGAGGATATAGAGGCGTTACTGAGAAAAATGCAGCTAATGTTACCATTTTGTG
*
126122 GCGTTTGGGATTTAAA
1 GCGTTT-GTATTTAAA
126138 TGCTGTTATA
Statistics
Matches: 118, Mismatches: 17, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
122 52 0.44
123 58 0.49
124 8 0.07
ACGTcount: A:0.32, C:0.15, G:0.21, T:0.32
Consensus pattern (123 bp):
GCGTTTGTATTTAAAAACGCCACTAATGCACCAACATATTGCGACATTTGTTTAAAAAATGCACA
AAAGATGAGGATATAGAGGCGTTACTGAGAAAAATGCAGCTAATGTTACCATTTTGTG
Found at i:128008 original size:74 final size:74
Alignment explanation
Indices: 127887--128037 Score: 293
Period size: 74 Copynumber: 2.0 Consensus size: 74
127877 TAATACTTAA
*
127887 GTTATGAGTCGTTTGAGGCCCGTATTATTAGGGTGGATGAGATAATTTATGGTGAACATACCTGC
1 GTTATGAGTCGTTTGAGGCCCGTATTATTAGGGTGGATGAGATAATTTATGGGGAACATACCTGC
127952 AAGCTTTAT
66 AAGCTTTAT
127961 GTTATGAGTCGTTTGAGGCCCGTATTATTAGGGTGGATGAGATAATTTATGGGGAACATACCTGC
1 GTTATGAGTCGTTTGAGGCCCGTATTATTAGGGTGGATGAGATAATTTATGGGGAACATACCTGC
128026 AAGCTTTAT
66 AAGCTTTAT
128035 GTT
1 GTT
128038 GGTGCTTGTA
Statistics
Matches: 76, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
74 76 1.00
ACGTcount: A:0.25, C:0.12, G:0.28, T:0.35
Consensus pattern (74 bp):
GTTATGAGTCGTTTGAGGCCCGTATTATTAGGGTGGATGAGATAATTTATGGGGAACATACCTGC
AAGCTTTAT
Found at i:130153 original size:21 final size:21
Alignment explanation
Indices: 130125--130200 Score: 93
Period size: 21 Copynumber: 3.6 Consensus size: 21
130115 ATTCCAAATT
130125 CGTTGCGATAGTCGAAGTTCG
1 CGTTGCGATAGTCGAAGTTCG
* * *
130146 CGTCGCGATTTATTCCAAGTT--
1 CGTTGCGA--TAGTCGAAGTTCG
130167 CGTTGCGATAGTCGAAGTTCG
1 CGTTGCGATAGTCGAAGTTCG
130188 CGTTGCGATAGTC
1 CGTTGCGATAGTC
130201 TAAAATCGCA
Statistics
Matches: 45, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
19 9 0.20
21 27 0.60
23 9 0.20
ACGTcount: A:0.18, C:0.21, G:0.29, T:0.32
Consensus pattern (21 bp):
CGTTGCGATAGTCGAAGTTCG
Found at i:130169 original size:42 final size:42
Alignment explanation
Indices: 130109--130196 Score: 158
Period size: 42 Copynumber: 2.1 Consensus size: 42
130099 TTATAATATA
130109 CGATTTATTCCAAATTCGTTGCGATAGTCGAAGTTCGCGTCG
1 CGATTTATTCCAAATTCGTTGCGATAGTCGAAGTTCGCGTCG
* *
130151 CGATTTATTCCAAGTTCGTTGCGATAGTCGAAGTTCGCGTTG
1 CGATTTATTCCAAATTCGTTGCGATAGTCGAAGTTCGCGTCG
130193 CGAT
1 CGAT
130197 AGTCTAAAAT
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
42 44 1.00
ACGTcount: A:0.20, C:0.20, G:0.25, T:0.34
Consensus pattern (42 bp):
CGATTTATTCCAAATTCGTTGCGATAGTCGAAGTTCGCGTCG
Found at i:130209 original size:21 final size:21
Alignment explanation
Indices: 130167--130209 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
130157 ATTCCAAGTT
**
130167 CGTTGCGATAGTCGAAGTTCG
1 CGTTGCGATAGTCGAAAATCG
*
130188 CGTTGCGATAGTCTAAAATCG
1 CGTTGCGATAGTCGAAAATCG
130209 C
1 C
130210 AACGACTGGT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.23, C:0.21, G:0.28, T:0.28
Consensus pattern (21 bp):
CGTTGCGATAGTCGAAAATCG
Found at i:130304 original size:6 final size:6
Alignment explanation
Indices: 130293--130317 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
130283 GACACGTATT
130293 ACCACG ACCACG ACCACG ACCACG A
1 ACCACG ACCACG ACCACG ACCACG A
130318 GACGAGACGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.36, C:0.48, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:130324 original size:5 final size:5
Alignment explanation
Indices: 130314--130342 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
130304 GACCACGACC
130314 ACGAG ACGAG ACGAG ACGAG ACGAG ACGA
1 ACGAG ACGAG ACGAG ACGAG ACGAG ACGA
130343 CGGCGCGCGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.41, C:0.21, G:0.38, T:0.00
Consensus pattern (5 bp):
ACGAG
Found at i:130954 original size:21 final size:21
Alignment explanation
Indices: 130928--131039 Score: 74
Period size: 19 Copynumber: 5.4 Consensus size: 21
130918 ATTTTGGACT
130928 ATCGCAACGAATTTGGAATAA
1 ATCGCAACGAATTTGGAATAA
* ** *
130949 ATCGCAACACAAACATGGACT--
1 ATCGC-A-ACGAATTTGGAATAA
*
130970 ATCGCAACGAATTTAGAATAA
1 ATCGCAACGAATTTGGAATAA
* * *
130991 ATCGCAACGCGAACTTCGACT--
1 ATCGCAA--CGAATTTGGAATAA
131012 ATCGCAACGAATTTGG-A-AA
1 ATCGCAACGAATTTGGAATAA
131031 ATCGCAACG
1 ATCGCAACG
131040 CGAACTTGGA
Statistics
Matches: 68, Mismatches: 15, Indels: 18
0.67 0.15 0.18
Matches are distributed among these distances:
19 24 0.35
20 1 0.01
21 24 0.35
22 1 0.01
23 18 0.26
ACGTcount: A:0.40, C:0.22, G:0.18, T:0.20
Consensus pattern (21 bp):
ATCGCAACGAATTTGGAATAA
Found at i:130981 original size:42 final size:42
Alignment explanation
Indices: 130921--131100 Score: 242
Period size: 42 Copynumber: 4.3 Consensus size: 42
130911 CGTTGCGATT
* *
130921 TTGGACTATCGCAACGAATTTGGAATAAATCGCAACACAAAC
1 TTGGACTATCGCAACGAATTTGGAATAAATCGCAACGCGAAC
* *
130963 ATGGACTATCGCAACGAATTTAGAATAAATCGCAACGCGAAC
1 TTGGACTATCGCAACGAATTTGGAATAAATCGCAACGCGAAC
*
131005 TTCGACTATCGCAACGAATTTGG-A-AAATCGCAACGCGAAC
1 TTGGACTATCGCAACGAATTTGGAATAAATCGCAACGCGAAC
* * *
131045 TTGGACTATCGCAACGCGAACTTAGACT--ATCGCAACGCGAAC
1 TTGGACTATCGCAA--CGAATTTGGAATAAATCGCAACGCGAAC
131087 TTGGACTATCGCAA
1 TTGGACTATCGCAA
131101 TGCGAATATG
Statistics
Matches: 123, Mismatches: 11, Indels: 8
0.87 0.08 0.06
Matches are distributed among these distances:
40 29 0.24
41 1 0.01
42 93 0.76
ACGTcount: A:0.36, C:0.24, G:0.19, T:0.21
Consensus pattern (42 bp):
TTGGACTATCGCAACGAATTTGGAATAAATCGCAACGCGAAC
Found at i:131048 original size:21 final size:21
Alignment explanation
Indices: 130921--131106 Score: 168
Period size: 21 Copynumber: 9.0 Consensus size: 21
130911 CGTTGCGATT
*
130921 TTGGACTATCGCAA--CGAAT
1 TTGGACTATCGCAACGCGAAC
* * *
130940 TTGGAATAAATCGCAACACAAAC
1 TTGGACT--ATCGCAACGCGAAC
* *
130963 ATGGACTATCGCAA--CGAAT
1 TTGGACTATCGCAACGCGAAC
* *
130982 TTAGAATAAATCGCAACGCGAAC
1 TTGGACT--ATCGCAACGCGAAC
* *
131005 TTCGACTATCGCAA--CGAAT
1 TTGGACTATCGCAACGCGAAC
**
131024 TTGGAAAATCGCAACGCGAAC
1 TTGGACTATCGCAACGCGAAC
131045 TTGGACTATCGCAACGCGAAC
1 TTGGACTATCGCAACGCGAAC
*
131066 TTAGACTATCGCAACGCGAAC
1 TTGGACTATCGCAACGCGAAC
*
131087 TTGGACTATCGCAATGCGAA
1 TTGGACTATCGCAACGCGAA
131107 TATGTAAATC
Statistics
Matches: 134, Mismatches: 23, Indels: 18
0.77 0.13 0.10
Matches are distributed among these distances:
19 28 0.21
21 89 0.66
23 17 0.13
ACGTcount: A:0.36, C:0.24, G:0.20, T:0.20
Consensus pattern (21 bp):
TTGGACTATCGCAACGCGAAC
Found at i:131077 original size:82 final size:83
Alignment explanation
Indices: 130924--131100 Score: 252
Period size: 82 Copynumber: 2.1 Consensus size: 83
130914 TGCGATTTTG
*
130924 GACTATCGCAACGAATTTGGAATAAATCGCAACACAAACATGGACTATCGCAACGAATTTAGAAT
1 GACTATCGCAACGAATTTGGAATAAATCGCAACACAAACATGGACTATCGCAACGAACTTAGAAT
130989 AAATCGCAACGCGAACTTC
66 -AATCGCAACGCGAACTTC
* * *
131008 GACTATCGCAACGAATTTGG-A-AAATCGCAACGCGAACTTGGACTATCGCAACGCGAACTTAGA
1 GACTATCGCAACGAATTTGGAATAAATCGCAACACAAACATGGACTATCGCAA--CGAACTTAGA
* *
131071 CT-ATCGCAACGCGAACTTG
64 ATAATCGCAACGCGAACTTC
131090 GACTATCGCAA
1 GACTATCGCAA
131101 TGCGAATATG
Statistics
Matches: 85, Mismatches: 6, Indels: 6
0.88 0.06 0.06
Matches are distributed among these distances:
82 54 0.64
83 1 0.01
84 30 0.35
ACGTcount: A:0.37, C:0.24, G:0.19, T:0.20
Consensus pattern (83 bp):
GACTATCGCAACGAATTTGGAATAAATCGCAACACAAACATGGACTATCGCAACGAACTTAGAAT
AATCGCAACGCGAACTTC
Found at i:131146 original size:21 final size:21
Alignment explanation
Indices: 131115--131167 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
131105 AATATGTAAA
131115 TCGCATTGCGATAGTCCAAGT
1 TCGCATTGCGATAGTCCAAGT
* * *
131136 TTGCGTTGCGATAGTCTAAGT
1 TCGCATTGCGATAGTCCAAGT
131157 TCGCATTGCGA
1 TCGCATTGCGA
131168 ATCTGGAAAC
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.21, C:0.21, G:0.26, T:0.32
Consensus pattern (21 bp):
TCGCATTGCGATAGTCCAAGT
Found at i:135856 original size:6 final size:6
Alignment explanation
Indices: 135842--135879 Score: 67
Period size: 6 Copynumber: 6.3 Consensus size: 6
135832 TGGCAGGCTA
*
135842 GCTTTT GCTTCT GCTTCT GCTTCT GCTTCT GCTTCT GC
1 GCTTCT GCTTCT GCTTCT GCTTCT GCTTCT GCTTCT GC
135880 ATTTTTCTTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 31 1.00
ACGTcount: A:0.00, C:0.32, G:0.18, T:0.50
Consensus pattern (6 bp):
GCTTCT
Found at i:138639 original size:19 final size:20
Alignment explanation
Indices: 138617--138655 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
138607 AGAAAAATCA
138617 TGAATAT-TTTTGAAAATTT
1 TGAATATATTTTGAAAATTT
*
138636 TGAATATATTTTTAAAATTT
1 TGAATATATTTTGAAAATTT
138656 AATATTTACA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 7 0.39
20 11 0.61
ACGTcount: A:0.38, C:0.00, G:0.08, T:0.54
Consensus pattern (20 bp):
TGAATATATTTTGAAAATTT
Found at i:143148 original size:266 final size:258
Alignment explanation
Indices: 142602--143156 Score: 839
Period size: 266 Copynumber: 2.1 Consensus size: 258
142592 TCATTTATTG
* * *
142602 AATAATTTTTTT-TTATTTCGGGTTGGGTCGGGTTTCTAATTCATATATTCGGGTTGTGTCGGGT
1 AATAATTTTTTTATTATTTCGGGTCGGGTCGGATTTCTAATTCATATATTCGGGTCGTGTCGGGT
142666 GAAACTTTATTTTGGTCGGGTCGGGTCGGTTTTTTTAAGTGTGATATTCGGGTCGGGTCGAGTTC
66 GAAACTTTATTTTGGTCGGGTCGGGTCGGTTTTTTTAAGTGTGATATTCGGGTCGGGTCGAGTTC
* * * * *
142731 GGGTTTAGGGTGAAAAATACCTGACCTGAAAATATATATAATTTTACCTTGTATATTTAGGAACA
131 GGGTTTAGGGTGAAAAATACCCGACCCGAAAAAATATAGAATTTTACCTTATATATTTAGGAACA
* * *
142796 ATTACAATAATACCCCTCTATATATAATTTTTTTCAATTAAGTCATTGTTTTTATTGAATAAA
196 ATTACAATAATACACCTCTATATATAATTTTTTCCAATTAAGTCATTATTTTTATTGAATAAA
142859 AATAATTTTTTTATTATTTCGGGTCGGGTCGGATTTCTAATTCATATATTCGGGTCG-GCTC-GG
1 AATAATTTTTTTATTATTTCGGGTCGGGTCGGATTTCTAATTCATATATTCGGGTCGTG-TCGGG
*
142922 TGAAACTTTATTTTGGTCGGGTCGGTTCAGGTTTTTTTAAGTGTGATATTCGGGTCGATCGGGTC
65 TGAAACTTTATTTTGGTCGGGTCGGGTC-GGTTTTTTTAAGTGTGATATTC-GG--G-TCGGGTC
*
142987 GGGTTCGGGTTTAGGGTGAAAAATACCCGACCCGACCCAAAAAATATAGAATTTTACCTTATATA
125 GAGTTCGGGTTTAGGGTGAAAAATACCCGACCCG----AAAAAATATAGAATTTTACCTTATATA
* *
143052 TTTAGGAATAATTACAATAATACACCTCTCTATAT-ATTTTTTCCAATTAAGTCATTATTTTTAT
186 TTTAGGAACAATTACAATAATACACCTCTATATATAATTTTTTCCAATTAAGTCATTATTTTTAT
143116 TGAATAAA
251 TGAATAAA
*
143124 AATAGTTTTTTTTATTATTTCGGGTCGGGTCGG
1 AATA-ATTTTTTTATTATTTCGGGTCGGGTCGG
143157 GTCTCGGATG
Statistics
Matches: 270, Mismatches: 16, Indels: 15
0.90 0.05 0.05
Matches are distributed among these distances:
257 42 0.16
258 65 0.24
259 2 0.01
261 1 0.00
262 38 0.14
265 39 0.14
266 83 0.31
ACGTcount: A:0.26, C:0.13, G:0.21, T:0.41
Consensus pattern (258 bp):
AATAATTTTTTTATTATTTCGGGTCGGGTCGGATTTCTAATTCATATATTCGGGTCGTGTCGGGT
GAAACTTTATTTTGGTCGGGTCGGGTCGGTTTTTTTAAGTGTGATATTCGGGTCGGGTCGAGTTC
GGGTTTAGGGTGAAAAATACCCGACCCGAAAAAATATAGAATTTTACCTTATATATTTAGGAACA
ATTACAATAATACACCTCTATATATAATTTTTTCCAATTAAGTCATTATTTTTATTGAATAAA
Found at i:143559 original size:18 final size:18
Alignment explanation
Indices: 143522--143572 Score: 86
Period size: 18 Copynumber: 2.9 Consensus size: 18
143512 TATAGAATTG
143522 GATTTCAATTCCTT-ACA
1 GATTTCAATTCCTTCACA
143539 GATTTCAATTCCTTCACA
1 GATTTCAATTCCTTCACA
*
143557 GATTCCAATTCCTTCA
1 GATTTCAATTCCTTCA
143573 GAAATATTCC
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
17 14 0.44
18 18 0.56
ACGTcount: A:0.27, C:0.27, G:0.06, T:0.39
Consensus pattern (18 bp):
GATTTCAATTCCTTCACA
Found at i:148706 original size:17 final size:17
Alignment explanation
Indices: 148686--148756 Score: 63
Period size: 17 Copynumber: 4.0 Consensus size: 17
148676 AATCTTATAT
148686 AATTTTAAATATTTTTA
1 AATTTTAAATATTTTTA
* *
148703 AATTTTAATAAAATTTTA
1 AATTTTAA-ATATTTTTA
*
148721 ATATTTTTAAAT-TTTAATA
1 A-A-TTTTAAATATTT-TTA
*
148740 AAATTTAAATATTTTTA
1 AATTTTAAATATTTTTA
148757 TCATATTTTA
Statistics
Matches: 42, Mismatches: 7, Indels: 10
0.71 0.12 0.17
Matches are distributed among these distances:
17 17 0.40
18 14 0.33
19 5 0.12
20 6 0.14
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (17 bp):
AATTTTAAATATTTTTA
Found at i:148768 original size:27 final size:26
Alignment explanation
Indices: 148675--148756 Score: 110
Period size: 27 Copynumber: 3.0 Consensus size: 26
148665 TATCATCTGA
* *
148675 AAATCTTATATAATTTTAAATATTTTT
1 AAATTTTATA-AAATTTAAATATTTTT
*
148702 AAATTTTAATAAAATTTTAATATTTTT
1 AAATTTT-ATAAAATTTAAATATTTTT
148729 AAATTTTAATAAAATTTAAATATTTTT
1 AAATTTT-ATAAAATTTAAATATTTTT
148756 A
1 A
148757 TCATATTTTA
Statistics
Matches: 50, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
27 47 0.94
28 3 0.06
ACGTcount: A:0.45, C:0.01, G:0.00, T:0.54
Consensus pattern (26 bp):
AAATTTTATAAAATTTAAATATTTTT
Found at i:149067 original size:24 final size:25
Alignment explanation
Indices: 149035--149081 Score: 62
Period size: 24 Copynumber: 1.9 Consensus size: 25
149025 TTAAGATATT
149035 ATTATAAATA-ATAATAAAAATTAGA
1 ATTATAAATATA-AATAAAAATTAGA
*
149060 ATTA-AAATATAAATATAAATTA
1 ATTATAAATATAAATAAAAATTA
149082 ATTTTGTATA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
24 15 0.75
25 5 0.25
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (25 bp):
ATTATAAATATAAATAAAAATTAGA
Found at i:149073 original size:18 final size:18
Alignment explanation
Indices: 149037--149082 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 18
149027 AAGATATTAT
149037 TATAAA-TAATAATAAAAA
1 TATAAATTAA-AATAAAAA
*
149055 T-TAGAATTAAAATATAAA
1 TATA-AATTAAAATAAAAA
149073 TATAAATTAA
1 TATAAATTAA
149083 TTTTGTATAA
Statistics
Matches: 24, Mismatches: 1, Indels: 6
0.77 0.03 0.19
Matches are distributed among these distances:
17 2 0.08
18 17 0.71
19 5 0.21
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (18 bp):
TATAAATTAAAATAAAAA
Found at i:149493 original size:41 final size:41
Alignment explanation
Indices: 149436--149522 Score: 165
Period size: 41 Copynumber: 2.1 Consensus size: 41
149426 CTCTATTCGT
*
149436 ATTTATAGTAATATTTTTATTTGGTATGCTGTGTTATTATG
1 ATTTATAGTAATATTTTTATTTGGAATGCTGTGTTATTATG
149477 ATTTATAGTAATATTTTTATTTGGAATGCTGTGTTATTATG
1 ATTTATAGTAATATTTTTATTTGGAATGCTGTGTTATTATG
149518 ATTTA
1 ATTTA
149523 ACCTGTATTT
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 45 1.00
ACGTcount: A:0.26, C:0.02, G:0.16, T:0.55
Consensus pattern (41 bp):
ATTTATAGTAATATTTTTATTTGGAATGCTGTGTTATTATG
Found at i:149902 original size:3 final size:3
Alignment explanation
Indices: 149896--149963 Score: 64
Period size: 3 Copynumber: 22.7 Consensus size: 3
149886 TTTATTTATT
* * * * * *
149896 ATA ATA ATA ATA ATA ATA ATT ATT ATT ATT ATT ATT ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* *
149944 ATA ATT ATT ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA AT
149964 TATTATTATA
Statistics
Matches: 61, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 61 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (3 bp):
ATA
Found at i:150766 original size:13 final size:13
Alignment explanation
Indices: 150766--150823 Score: 71
Period size: 13 Copynumber: 4.3 Consensus size: 13
150756 CCGTTGACCC
*
150766 GACCCGACCTGTT
1 GACCCGACCCGTT
*
150779 TACCCGACCCGTT
1 GACCCGACCCGTT
150792 GACCCGACCCGTT
1 GACCCGACCCGTT
*
150805 GACCGTTGACCCGTT
1 GACC--CGACCCGTT
150820 GACC
1 GACC
150824 GTTAACCGGA
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
13 27 0.69
15 12 0.31
ACGTcount: A:0.16, C:0.41, G:0.22, T:0.21
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:150797 original size:8 final size:8
Alignment explanation
Indices: 150784--150823 Score: 52
Period size: 8 Copynumber: 5.5 Consensus size: 8
150774 CTGTTTACCC
150784 GACCCGTT
1 GACCCGTT
150792 GACCC---
1 GACCCGTT
150797 GACCCGTT
1 GACCCGTT
150805 GA-CCGTT
1 GACCCGTT
150812 GACCCGTT
1 GACCCGTT
150820 GACC
1 GACC
150824 GTTAACCGGA
Statistics
Matches: 28, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
5 5 0.18
7 7 0.25
8 16 0.57
ACGTcount: A:0.15, C:0.40, G:0.25, T:0.20
Consensus pattern (8 bp):
GACCCGTT
Found at i:150802 original size:18 final size:18
Alignment explanation
Indices: 150744--150789 Score: 74
Period size: 18 Copynumber: 2.6 Consensus size: 18
150734 ACCGGTCACA
150744 ACCCGACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
* *
150762 ACCCGACCCGACCTGTTT
1 ACCCGACCCGACCCGTTG
150780 ACCCGACCCG
1 ACCCGACCCG
150790 TTGACCCGAC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.17, C:0.50, G:0.20, T:0.13
Consensus pattern (18 bp):
ACCCGACCCGACCCGTTG
Found at i:150817 original size:15 final size:15
Alignment explanation
Indices: 150784--150826 Score: 63
Period size: 15 Copynumber: 3.0 Consensus size: 15
150774 CTGTTTACCC
*
150784 GACCCGTTGACC--C
1 GACCCGTTGACCGTT
150797 GACCCGTTGACCGTT
1 GACCCGTTGACCGTT
150812 GACCCGTTGACCGTT
1 GACCCGTTGACCGTT
150827 AACCGGAGTT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
13 12 0.44
15 15 0.56
ACGTcount: A:0.14, C:0.37, G:0.26, T:0.23
Consensus pattern (15 bp):
GACCCGTTGACCGTT
Found at i:152166 original size:18 final size:18
Alignment explanation
Indices: 152140--152175 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
152130 TCGAAAGGAC
*
152140 TGAAGTAAATGATAAGAT
1 TGAAGTAAATAATAAGAT
*
152158 TGAATTAAATAATAAGAT
1 TGAAGTAAATAATAAGAT
152176 CGGATGGAAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.53, C:0.00, G:0.17, T:0.31
Consensus pattern (18 bp):
TGAAGTAAATAATAAGAT
Found at i:153382 original size:24 final size:24
Alignment explanation
Indices: 153293--153394 Score: 98
Period size: 24 Copynumber: 4.2 Consensus size: 24
153283 TTATCTGGTT
* * *
153293 TCTGATTTGAATTCTGTTTTGACA
1 TCTGATCTGAATTCTGTTCTGATA
*
153317 TCTGATCTGAAATCTGTTCTGAT-
1 TCTGATCTGAATTCTGTTCTGATA
* * *
153340 TCCTAACCTGGATTCTGTTCTGATA
1 T-CTGATCTGAATTCTGTTCTGATA
* * *
153365 TCTGATCTGAATTATGTTTTGATT
1 TCTGATCTGAATTCTGTTCTGATA
153389 TCTGAT
1 TCTGAT
153395 ATCTCCATTT
Statistics
Matches: 62, Mismatches: 14, Indels: 4
0.77 0.17 0.05
Matches are distributed among these distances:
23 1 0.02
24 60 0.97
25 1 0.02
ACGTcount: A:0.21, C:0.16, G:0.17, T:0.47
Consensus pattern (24 bp):
TCTGATCTGAATTCTGTTCTGATA
Found at i:155400 original size:3 final size:3
Alignment explanation
Indices: 155387--155445 Score: 50
Period size: 3 Copynumber: 19.0 Consensus size: 3
155377 TTATTTGCAA
*
155387 TAT TAT T-T TAT TAT TAT TAT TGCT T-T TAAT TAT TAT TGCAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT T-AT TAT T-AT TAT TAT T--AT TAT TAT
*
155434 TAT TTT TAT TAT
1 TAT TAT TAT TAT
155446 ATATATATAT
Statistics
Matches: 47, Mismatches: 3, Indels: 12
0.76 0.05 0.19
Matches are distributed among these distances:
2 4 0.09
3 36 0.77
4 4 0.09
5 3 0.06
ACGTcount: A:0.27, C:0.03, G:0.03, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:155420 original size:16 final size:14
Alignment explanation
Indices: 155376--155437 Score: 58
Period size: 16 Copynumber: 4.4 Consensus size: 14
155366 TATTTTAATC
*
155376 ATTATTTGCAATATT
1 ATTA-TTGCATTATT
155391 ATT-TT--ATTATT
1 ATTATTGCATTATT
*
155402 ATTATTGCTTTTAATT
1 ATTATTGC-ATT-ATT
155418 ATTATTGCATTATT
1 ATTATTGCATTATT
155432 ATTATT
1 ATTATT
155438 TTTATTATAT
Statistics
Matches: 39, Mismatches: 3, Indels: 11
0.74 0.06 0.21
Matches are distributed among these distances:
11 8 0.21
12 2 0.05
13 2 0.05
14 9 0.23
15 7 0.18
16 11 0.28
ACGTcount: A:0.29, C:0.05, G:0.05, T:0.61
Consensus pattern (14 bp):
ATTATTGCATTATT
Found at i:155450 original size:2 final size:2
Alignment explanation
Indices: 155443--155476 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
155433 TTATTTTTAT
155443 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
155477 ATAAATAATA
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):
TA
Found at i:157824 original size:8 final size:7
Alignment explanation
Indices: 157800--157841 Score: 50
Period size: 7 Copynumber: 6.0 Consensus size: 7
157790 TTTTCATACA
157800 TGCA-TT
1 TGCATTT
157806 TGCATTT
1 TGCATTT
157813 TGCATCTT
1 TGCAT-TT
157821 TGCATTT
1 TGCATTT
* *
157828 TTCATTG
1 TGCATTT
157835 TGCATTT
1 TGCATTT
157842 ATACTTTTAT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
6 4 0.13
7 19 0.63
8 7 0.23
ACGTcount: A:0.14, C:0.17, G:0.14, T:0.55
Consensus pattern (7 bp):
TGCATTT
Found at i:157824 original size:15 final size:14
Alignment explanation
Indices: 157800--157841 Score: 50
Period size: 15 Copynumber: 3.0 Consensus size: 14
157790 TTTTCATACA
157800 TGCA-TTTGCATTT
1 TGCATTTTGCATTT
157813 TGCATCTTTGCATTT
1 TGCAT-TTTGCATTT
* *
157828 TTCATTGTGCATTT
1 TGCATTTTGCATTT
157842 ATACTTTTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 4 0.16
14 8 0.32
15 13 0.52
ACGTcount: A:0.14, C:0.17, G:0.14, T:0.55
Consensus pattern (14 bp):
TGCATTTTGCATTT
Found at i:157937 original size:27 final size:27
Alignment explanation
Indices: 157901--157960 Score: 86
Period size: 27 Copynumber: 2.3 Consensus size: 27
157891 CATTCACATA
157901 TTTACATTTGCATTTACATTTGCATTT
1 TTTACATTTGCATTTACATTTGCATTT
* * *
157928 TTTACGTTTGTATTTACATTTTCA-TT
1 TTTACATTTGCATTTACATTTGCATTT
157954 TTTACAT
1 TTTACAT
157961 AATTACATTT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
26 8 0.28
27 21 0.72
ACGTcount: A:0.22, C:0.13, G:0.07, T:0.58
Consensus pattern (27 bp):
TTTACATTTGCATTTACATTTGCATTT
Found at i:157954 original size:12 final size:12
Alignment explanation
Indices: 157900--157927 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
157890 ACATTCACAT
157900 ATTTACATTTGC
1 ATTTACATTTGC
157912 ATTTACATTTGC
1 ATTTACATTTGC
157924 ATTT
1 ATTT
157928 TTTACGTTTG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.25, C:0.14, G:0.07, T:0.54
Consensus pattern (12 bp):
ATTTACATTTGC
Found at i:159915 original size:16 final size:16
Alignment explanation
Indices: 159891--159962 Score: 72
Period size: 16 Copynumber: 4.4 Consensus size: 16
159881 TCCAGCAAAG
159891 AAAGAAGAAGAAAAAA
1 AAAGAAGAAGAAAAAA
*
159907 AAAGTAGAAGAAAAAAA
1 AAAGAAGAAG-AAAAAA
* * *
159924 AAACAAAAATAAAAAA
1 AAAGAAGAAGAAAAAA
* * *
159940 AAACAAAAAGGAAAAA
1 AAAGAAGAAGAAAAAA
159956 AAAGAAG
1 AAAGAAG
159963 GAAAATTGAA
Statistics
Matches: 46, Mismatches: 9, Indels: 2
0.81 0.16 0.04
Matches are distributed among these distances:
16 34 0.74
17 12 0.26
ACGTcount: A:0.81, C:0.03, G:0.14, T:0.03
Consensus pattern (16 bp):
AAAGAAGAAGAAAAAA
Found at i:159926 original size:22 final size:20
Alignment explanation
Indices: 159891--159948 Score: 55
Period size: 21 Copynumber: 2.8 Consensus size: 20
159881 TCCAGCAAAG
* *
159891 AAAGAAGAAGAAAAAAAAAGT
1 AAAGAA-AAAAAAAAAAAAAT
159912 AGAAGAAAAAAAAAACAAAAAT
1 A-AAGAAAAAAAAAA-AAAAAT
159934 AAA-AAAAAACAAAAA
1 AAAGAAAAAA-AAAAA
159949 GGAAAAAAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
20 7 0.22
21 14 0.44
22 11 0.34
ACGTcount: A:0.83, C:0.03, G:0.10, T:0.03
Consensus pattern (20 bp):
AAAGAAAAAAAAAAAAAAAT
Found at i:162439 original size:114 final size:114
Alignment explanation
Indices: 162239--162458 Score: 359
Period size: 114 Copynumber: 1.9 Consensus size: 114
162229 CATGTTCTTG
* * * *
162239 TAGTAGAAATAAGGAGCCCCAATAGTATCTTTTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTT
1 TAGTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTC
*
162304 GGTATGAACCCCAAAACCAATCATTAGATTTAAAAGATGAATTTGCTCA
66 GGTAGGAACCCCAAAACCAATCATTAGATTTAAAAGATGAATTTGCTCA
* *
162353 TAGTAGAAATAAGGAGATCCAATTGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTC
1 TAGTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTC
* *
162418 GGTAGGAACCCCAAAACCAATCATTGGATTTGAAAGATGAA
66 GGTAGGAACCCCAAAACCAATCATTAGATTTAAAAGATGAA
162459 CATGATCGTC
Statistics
Matches: 97, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
114 97 1.00
ACGTcount: A:0.32, C:0.15, G:0.21, T:0.32
Consensus pattern (114 bp):
TAGTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTC
GGTAGGAACCCCAAAACCAATCATTAGATTTAAAAGATGAATTTGCTCA
Found at i:165087 original size:22 final size:22
Alignment explanation
Indices: 165056--165110 Score: 83
Period size: 22 Copynumber: 2.5 Consensus size: 22
165046 ATCTACACTC
* *
165056 TTCAAAGATGATAGATTCTTTT
1 TTCAAAGATGACAGATTCTCTT
*
165078 TTTAAAGATGACAGATTCTCTT
1 TTCAAAGATGACAGATTCTCTT
165100 TTCAAAGATGA
1 TTCAAAGATGA
165111 AAGCTTTATG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.35, C:0.11, G:0.15, T:0.40
Consensus pattern (22 bp):
TTCAAAGATGACAGATTCTCTT
Found at i:165856 original size:113 final size:113
Alignment explanation
Indices: 165510--165905 Score: 693
Period size: 113 Copynumber: 3.5 Consensus size: 113
165500 TAGCAAAGAT
* *
165510 TCAAATCCATCACTTGATGGATCAGCTTTTCTAGAAAAAGTTCATAATGAGAAGAACTCATCTGA
1 TCAAATCCATCACTTGATGGATCAACTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGA
165575 AGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
66 AGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
* *
165623 TCAAATCCATCATTTGATGGATCAACTTTTCCAGAAAAAAGTTAATAATGAGAAGAACTCATCTG
1 TCAAATCCATCACTTGATGGATCAACTTTTCCAG-AAAAAGTTCATAATGAGAAGAACTCATCTG
165688 AAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
65 AAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
* *
165737 TCAAATCCATCATTTGATGGATCAACTTTTCCATAAAAAGTTCATAATGAGAAGAACTCATCTGA
1 TCAAATCCATCACTTGATGGATCAACTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGA
165802 AGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
66 AGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
** * *
165850 TCAAATCCATCACTTGATAAATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAA
1 TCAAATCCATCACTTGATGGATCAACTTTTCCAGAAAAAGTTCATAATGAGAAGAA
165906 TTTGTTCAAT
Statistics
Matches: 270, Mismatches: 12, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
113 159 0.59
114 111 0.41
ACGTcount: A:0.40, C:0.15, G:0.16, T:0.28
Consensus pattern (113 bp):
TCAAATCCATCACTTGATGGATCAACTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGA
AGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
Found at i:165940 original size:73 final size:73
Alignment explanation
Indices: 165812--165978 Score: 203
Period size: 73 Copynumber: 2.3 Consensus size: 73
165802 AGAAGGAAGA
165812 AGAAA-TTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATCCATCACTTGATAAATCAGC
1 AGAAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATCCATCACTTGATAAATCAGC
* *
165876 TTTTCCAG
66 ATTGCCAG
* * ** * * ** *
165884 AGAAAGTTCATAATGAGAAGAATTTGTTCAATCTTTTGTTTGAATTCATCATTTGATGGATCATC
1 AGAAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATCCATCACTTGATAAATCAGC
165949 ATTGCCAG
66 ATTGCCAG
*
165957 -GTAGAGTTCATAATGAGAAGAA
1 AG-AAAGTTCATAATGAGAAGAA
165979 CTCATCTGAA
Statistics
Matches: 81, Mismatches: 12, Indels: 3
0.84 0.12 0.03
Matches are distributed among these distances:
72 6 0.07
73 75 0.93
ACGTcount: A:0.35, C:0.14, G:0.17, T:0.34
Consensus pattern (73 bp):
AGAAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATCCATCACTTGATAAATCAGC
ATTGCCAG
Found at i:166047 original size:39 final size:40
Alignment explanation
Indices: 165961--166054 Score: 163
Period size: 40 Copynumber: 2.4 Consensus size: 40
165951 TGCCAGGTAG
165961 AGTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGAAGA
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGAAGA
* *
166001 AGTTCATAATGAGAAGAACTTATCTGAAG-AGGAAGAAGA
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGAAGA
166040 AGTTCATAATGAGAA
1 AGTTCATAATGAGAA
166055 AATTTTGTTC
Statistics
Matches: 52, Mismatches: 2, Indels: 1
0.95 0.04 0.02
Matches are distributed among these distances:
39 24 0.46
40 28 0.54
ACGTcount: A:0.48, C:0.09, G:0.23, T:0.20
Consensus pattern (40 bp):
AGTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGAAGA
Found at i:166219 original size:124 final size:123
Alignment explanation
Indices: 165995--166344 Score: 453
Period size: 124 Copynumber: 2.9 Consensus size: 123
165985 TGAAGAAAGA
* * * **
165995 AGAAGAAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAAATTT
1 AGAAGAAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAGAAGAAGTTCATAATGAGAAGAGCT
* * * *
166060 TGTTCAACCTTTTTCATGACTCTATCATAAAAGGAGATAAATCAGCATCAACTTTTCC
66 TGTTCAACCTTTTGCATGACTCTATCACAGAAGGAGATAAATCAGCATCAACATTTCC
166118 AG-AGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGAAGAAGTTCATAATGAGAAGAG
1 AGAAG-AAGTTCATAATGAGAAGAACTCATCTGAAG-AAGAAGAAGAAGTTCATAATGAGAAGAG
* * ** *
166182 CTTGTTCGACCTTTTGCATGACTCTATCACAGAAGGAGATATATCATTATCAGCATTTCC
64 CTTGTTCAACCTTTTGCATGACTCTATCACAGAAGGAGATAAATCAGCATCAACATTTCC
* *
166242 AGAAGAAGTTCACAATGAGAAGAACTCATCT---GAAGAAGAAGAAGTTCACAATGAGAAGAGCT
1 AGAAGAAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAGAAGAAGTTCATAATGAGAAGAGCT
* *
166304 TGTTCAACC-TTTGC-TAGATTAC-ATCACAGAATGAGATAAAT
66 TGTTCAACCTTTTGCAT-GACT-CTATCACAGAAGGAGATAAAT
166345 TGTCATCCCC
Statistics
Matches: 202, Mismatches: 20, Indels: 14
0.86 0.08 0.06
Matches are distributed among these distances:
118 1 0.00
119 25 0.12
120 38 0.19
121 1 0.00
122 2 0.01
123 31 0.15
124 102 0.50
125 2 0.01
ACGTcount: A:0.41, C:0.15, G:0.19, T:0.26
Consensus pattern (123 bp):
AGAAGAAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAGAAGAAGTTCATAATGAGAAGAGCT
TGTTCAACCTTTTGCATGACTCTATCACAGAAGGAGATAAATCAGCATCAACATTTCC
Found at i:166264 original size:17 final size:17
Alignment explanation
Indices: 166242--166300 Score: 59
Period size: 17 Copynumber: 3.4 Consensus size: 17
166232 CAGCATTTCC
166242 AGAAGAAGTTCACAATG
1 AGAAGAAGTTCACAATG
*
166259 AGAAGAA-CTCATCTGAA-G
1 AGAAGAAGTTCA-C--AATG
166277 AAGAAGAAGTTCACAATG
1 -AGAAGAAGTTCACAATG
166295 AGAAGA
1 AGAAGA
166301 GCTTGTTCAA
Statistics
Matches: 34, Mismatches: 2, Indels: 12
0.71 0.04 0.25
Matches are distributed among these distances:
16 3 0.09
17 16 0.47
18 2 0.06
19 10 0.29
20 3 0.09
ACGTcount: A:0.49, C:0.12, G:0.24, T:0.15
Consensus pattern (17 bp):
AGAAGAAGTTCACAATG
Found at i:166559 original size:3 final size:3
Alignment explanation
Indices: 166551--166592 Score: 68
Period size: 3 Copynumber: 14.0 Consensus size: 3
166541 ATTTATTTAT
166551 TTA TTA TTA TTA TTA TTA TTA -TA TATA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA TTA
166593 AAAAAATAAT
Statistics
Matches: 37, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
2 2 0.05
3 32 0.86
4 3 0.08
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:166566 original size:24 final size:25
Alignment explanation
Indices: 166539--166591 Score: 83
Period size: 24 Copynumber: 2.2 Consensus size: 25
166529 CCCATTTTAT
*
166539 TTATTTATT-TATTTATTATTATTA
1 TTATTTATTATATATATTATTATTA
166563 TTA-TTATTATATATATTATTATTA
1 TTATTTATTATATATATTATTATTA
166587 TTATT
1 TTATT
166592 AAAAAAATAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
23 5 0.19
24 20 0.77
25 1 0.04
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (25 bp):
TTATTTATTATATATATTATTATTA
Found at i:166604 original size:21 final size:21
Alignment explanation
Indices: 166559--166604 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
166549 ATTTATTATT
* * * *
166559 ATTATTATTATTATATATATT
1 ATTATTATTATTAAAAAAATA
166580 ATTATTATTATTAAAAAAATA
1 ATTATTATTATTAAAAAAATA
166601 ATTA
1 ATTA
166605 CAAACCGGCC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (21 bp):
ATTATTATTATTAAAAAAATA
Found at i:167855 original size:16 final size:14
Alignment explanation
Indices: 167822--167873 Score: 59
Period size: 14 Copynumber: 3.6 Consensus size: 14
167812 TTATTTGCAA
167822 TATTATTTTATTAT
1 TATTATTTTATTAT
*
167836 TATTATTGTTTTTAAT
1 TATTATT-TTATT-AT
*
167852 TATTATTTCATTAT
1 TATTATTTTATTAT
*
167866 TTTTATTT
1 TATTATTT
167874 ATATAAATAT
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
14 16 0.50
15 7 0.22
16 9 0.28
ACGTcount: A:0.25, C:0.02, G:0.02, T:0.71
Consensus pattern (14 bp):
TATTATTTTATTAT
Found at i:167885 original size:2 final size:2
Alignment explanation
Indices: 167873--167908 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
167863 TATTTTTATT
*
167873 TA TA TA AA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
167909 ATAAATAACA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:172145 original size:19 final size:19
Alignment explanation
Indices: 172121--172160 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
172111 ACTCTAGGCG
172121 ATACACTCTGTAAGTTGCT
1 ATACACTCTGTAAGTTGCT
172140 ATACACTCTGTAAGTTGCT
1 ATACACTCTGTAAGTTGCT
172159 AT
1 AT
172161 TAATTACCAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.28, C:0.20, G:0.15, T:0.38
Consensus pattern (19 bp):
ATACACTCTGTAAGTTGCT
Found at i:175748 original size:2 final size:2
Alignment explanation
Indices: 175741--175774 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
175731 ACTACCTGTA
175741 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
175775 TGACAGCACA
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:180574 original size:41 final size:41
Alignment explanation
Indices: 180517--180599 Score: 166
Period size: 41 Copynumber: 2.0 Consensus size: 41
180507 CCATGTTCTT
180517 ACTGCTTCCTTTGTCCATGTCCTGCATATGTTACCCAGAAA
1 ACTGCTTCCTTTGTCCATGTCCTGCATATGTTACCCAGAAA
180558 ACTGCTTCCTTTGTCCATGTCCTGCATATGTTACCCAGAAA
1 ACTGCTTCCTTTGTCCATGTCCTGCATATGTTACCCAGAAA
180599 A
1 A
180600 AGGGCGTCTT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 42 1.00
ACGTcount: A:0.23, C:0.29, G:0.14, T:0.34
Consensus pattern (41 bp):
ACTGCTTCCTTTGTCCATGTCCTGCATATGTTACCCAGAAA
Found at i:180611 original size:41 final size:41
Alignment explanation
Indices: 180523--180613 Score: 139
Period size: 41 Copynumber: 2.2 Consensus size: 41
180513 TCTTACTGCT
* *
180523 TCCTTTGTCCATGTCCTGCATATGTTACCCAGAAAACTGCT
1 TCCTTTGTCCATGTCCTGCATATGTTACCCAGAAAACGGCG
*
180564 TCCTTTGTCCATGTCCTGCATATGTTACCCAGAAAAAGGGCG
1 TCCTTTGTCCATGTCCTGCATATGTTACCCAG-AAAACGGCG
180606 T-CTTTGTC
1 TCCTTTGTC
180614 TTGACTAGGG
Statistics
Matches: 46, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
41 39 0.85
42 7 0.15
ACGTcount: A:0.21, C:0.27, G:0.18, T:0.34
Consensus pattern (41 bp):
TCCTTTGTCCATGTCCTGCATATGTTACCCAGAAAACGGCG
Found at i:183181 original size:21 final size:20
Alignment explanation
Indices: 183143--183186 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 20
183133 AAGTTAAGGT
* *
183143 TTTTTTATAAACATAATAATA
1 TTTTTTATAAAAAAAATAA-A
183164 TTTTTTATAAAAAAAATAAA
1 TTTTTTATAAAAAAAATAAA
183184 TTT
1 TTT
183187 CAAAATTATC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 4 0.19
21 17 0.81
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (20 bp):
TTTTTTATAAAAAAAATAAA
Found at i:186532 original size:27 final size:27
Alignment explanation
Indices: 186452--186532 Score: 76
Period size: 27 Copynumber: 3.0 Consensus size: 27
186442 TATTTCCTTA
*
186452 AAAAATACTAATTTATTAA-TAGATAAT
1 AAAAGTACTAATTTATTAATTA-ATAAT
* * **
186479 AAATG-ATTAATTTATTAAATTTCTAAT
1 AAAAGTACTAATTTATT-AATTAATAAT
*
186506 AAAAGTACTAAATTATTAATTAATAAT
1 AAAAGTACTAATTTATTAATTAATAAT
186533 TATTATTTCA
Statistics
Matches: 41, Mismatches: 10, Indels: 6
0.72 0.18 0.11
Matches are distributed among these distances:
26 10 0.24
27 21 0.51
28 10 0.24
ACGTcount: A:0.52, C:0.04, G:0.04, T:0.41
Consensus pattern (27 bp):
AAAAGTACTAATTTATTAATTAATAAT
Found at i:186776 original size:28 final size:28
Alignment explanation
Indices: 186736--186808 Score: 146
Period size: 28 Copynumber: 2.6 Consensus size: 28
186726 AAATTTTGCG
186736 AGCTTAATGAGCAACGAAACGAGTAACA
1 AGCTTAATGAGCAACGAAACGAGTAACA
186764 AGCTTAATGAGCAACGAAACGAGTAACA
1 AGCTTAATGAGCAACGAAACGAGTAACA
186792 AGCTTAATGAGCAACGA
1 AGCTTAATGAGCAACGA
186809 GTTTAAAAAA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 45 1.00
ACGTcount: A:0.45, C:0.18, G:0.22, T:0.15
Consensus pattern (28 bp):
AGCTTAATGAGCAACGAAACGAGTAACA
Found at i:189333 original size:21 final size:21
Alignment explanation
Indices: 189307--189356 Score: 73
Period size: 21 Copynumber: 2.4 Consensus size: 21
189297 CCGTAGGGGT
* *
189307 ATATGCCCAGCCCTCCACTTC
1 ATATGCCAAGCCCACCACTTC
*
189328 ATATGCCAAGCCCACCAGTTC
1 ATATGCCAAGCCCACCACTTC
189349 ATATGCCA
1 ATATGCCA
189357 TCTTCACAGG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.26, C:0.40, G:0.12, T:0.22
Consensus pattern (21 bp):
ATATGCCAAGCCCACCACTTC
Found at i:189390 original size:21 final size:21
Alignment explanation
Indices: 189363--189447 Score: 127
Period size: 21 Copynumber: 4.0 Consensus size: 21
189353 GCCATCTTCA
189363 CAGGGTTACATTCCGAGCCCG
1 CAGGGTTACATTCCGAGCCCG
* *
189384 TAGGGTTACATTCCTAGCCCG
1 CAGGGTTACATTCCGAGCCCG
189405 CCA-GGTTACATTCCGAGCCCG
1 -CAGGGTTACATTCCGAGCCCG
*
189426 CAGGGTTACATTCCTAGCCCG
1 CAGGGTTACATTCCGAGCCCG
189447 C
1 C
189448 TGTCAACACA
Statistics
Matches: 57, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
20 2 0.04
21 54 0.95
22 1 0.02
ACGTcount: A:0.19, C:0.34, G:0.25, T:0.22
Consensus pattern (21 bp):
CAGGGTTACATTCCGAGCCCG
Found at i:189413 original size:42 final size:42
Alignment explanation
Indices: 189366--189447 Score: 155
Period size: 42 Copynumber: 2.0 Consensus size: 42
189356 ATCTTCACAG
*
189366 GGTTACATTCCGAGCCCGTAGGGTTACATTCCTAGCCCGCCA
1 GGTTACATTCCGAGCCCGCAGGGTTACATTCCTAGCCCGCCA
189408 GGTTACATTCCGAGCCCGCAGGGTTACATTCCTAGCCCGC
1 GGTTACATTCCGAGCCCGCAGGGTTACATTCCTAGCCCGC
189448 TGTCAACACA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
42 39 1.00
ACGTcount: A:0.18, C:0.34, G:0.24, T:0.23
Consensus pattern (42 bp):
GGTTACATTCCGAGCCCGCAGGGTTACATTCCTAGCCCGCCA
Found at i:189516 original size:34 final size:36
Alignment explanation
Indices: 189472--189573 Score: 172
Period size: 34 Copynumber: 2.9 Consensus size: 36
189462 TTTCGTCCTA
189472 CTAGGATTCAAACTCCTAAAAATAGGATAGAA-TTT
1 CTAGGATTCAAACTCCTAAAAATAGGATAGAATTTT
*
189507 -TAGGATTCAAACTCCTAAAAATAGGATAAAATTTT
1 CTAGGATTCAAACTCCTAAAAATAGGATAGAATTTT
189542 GCTAGGATTCAAACTCCTAAAAATAGGATAGA
1 -CTAGGATTCAAACTCCTAAAAATAGGATAGA
189574 GTTCTACTAT
Statistics
Matches: 62, Mismatches: 2, Indels: 4
0.91 0.03 0.06
Matches are distributed among these distances:
34 30 0.48
35 3 0.05
37 29 0.47
ACGTcount: A:0.44, C:0.14, G:0.15, T:0.27
Consensus pattern (36 bp):
CTAGGATTCAAACTCCTAAAAATAGGATAGAATTTT
Found at i:190154 original size:28 final size:28
Alignment explanation
Indices: 190122--190193 Score: 69
Period size: 28 Copynumber: 2.6 Consensus size: 28
190112 ATATATATGC
*
190122 TTTTACGTTTTTATATATTTACTCATTTA
1 TTTTACGTTTTTATATATTTA-TCATATA
*
190151 -TTTATC-TATTTT-TATATTTATCCTATA
1 TTTTA-CGT-TTTTATATATTTATCATATA
*
190178 TTTTATGTTTTTATAT
1 TTTTACGTTTTTATAT
190194 TCTTTTACTT
Statistics
Matches: 35, Mismatches: 3, Indels: 11
0.71 0.06 0.22
Matches are distributed among these distances:
27 9 0.26
28 21 0.60
29 5 0.14
ACGTcount: A:0.24, C:0.08, G:0.03, T:0.65
Consensus pattern (28 bp):
TTTTACGTTTTTATATATTTATCATATA
Found at i:190168 original size:16 final size:18
Alignment explanation
Indices: 190149--190183 Score: 56
Period size: 16 Copynumber: 2.1 Consensus size: 18
190139 TTTACTCATT
190149 TATTTAT-CTAT-TTTTA
1 TATTTATCCTATATTTTA
190165 TATTTATCCTATATTTTA
1 TATTTATCCTATATTTTA
190183 T
1 T
190184 GTTTTTATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.41
17 4 0.24
18 6 0.35
ACGTcount: A:0.26, C:0.09, G:0.00, T:0.66
Consensus pattern (18 bp):
TATTTATCCTATATTTTA
Found at i:193438 original size:21 final size:20
Alignment explanation
Indices: 193393--193461 Score: 66
Period size: 20 Copynumber: 3.2 Consensus size: 20
193383 CAAAAAGGGC
*
193393 AAAAAGAAAAAAGAAAATAAGCA
1 AAAAAGAAAAAA-CAAA-AA-CA
*
193416 AAAAAGGAAAAAACAAGAACA
1 AAAAA-GAAAAAACAAAAACA
* *
193437 AAAAAGAAAGAACAAAAATA
1 AAAAAGAAAAAACAAAAACA
193457 AAAAA
1 AAAAA
193462 AAGGGGACAA
Statistics
Matches: 40, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
20 17 0.43
21 7 0.17
22 2 0.05
23 7 0.17
24 7 0.17
ACGTcount: A:0.80, C:0.06, G:0.12, T:0.03
Consensus pattern (20 bp):
AAAAAGAAAAAACAAAAACA
Found at i:194121 original size:22 final size:22
Alignment explanation
Indices: 194096--194144 Score: 89
Period size: 22 Copynumber: 2.2 Consensus size: 22
194086 CCATCAATCT
*
194096 TTTGAGCATCCAATGTCAAACC
1 TTTGAGCATCAAATGTCAAACC
194118 TTTGAGCATCAAATGTCAAACC
1 TTTGAGCATCAAATGTCAAACC
194140 TTTGA
1 TTTGA
194145 CCAAACACAA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.33, C:0.22, G:0.14, T:0.31
Consensus pattern (22 bp):
TTTGAGCATCAAATGTCAAACC
Found at i:194582 original size:18 final size:18
Alignment explanation
Indices: 194559--194594 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
194549 TCAACATCAA
* *
194559 ATATTGGGGCATTTTTGG
1 ATATTGAGGCATCTTTGG
194577 ATATTGAGGCATCTTTGG
1 ATATTGAGGCATCTTTGG
194595 GGATTCAACA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.19, C:0.08, G:0.31, T:0.42
Consensus pattern (18 bp):
ATATTGAGGCATCTTTGG
Found at i:195117 original size:36 final size:36
Alignment explanation
Indices: 195074--195355 Score: 303
Period size: 36 Copynumber: 8.0 Consensus size: 36
195064 ACTATAAGAG
195074 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
1 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
*
195110 TTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAAA
1 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
* * *
195146 TTTCGTCTATCTTGAGACAGTTTCCCTTGAAATAAA
1 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
195182 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
1 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
* * * * *
195218 ------ATAT-TTGA-ATATGTTTTCTTTGAAACAAA
1 TTTTGTCTCTCTTGAGACA-GTTTCCCTTGAAACAAA
** * ** * *
195247 TTCCGTCTCCCTTGAGACAGTTTCTTTTGGAACTAAG
1 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAAC-AAA
*
195284 TTTTGTCTCTCTTGAGACAGTTTCTCTTGAAAC-AA
1 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
* *
195319 TTTTCGTTTATCTTGAGACAGTTTCCCTTGAAACAAA
1 TTTT-GTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
195356 ACCTTTGAAT
Statistics
Matches: 204, Mismatches: 30, Indels: 23
0.79 0.12 0.09
Matches are distributed among these distances:
28 2 0.01
29 19 0.09
30 2 0.01
35 6 0.03
36 141 0.69
37 34 0.17
ACGTcount: A:0.26, C:0.20, G:0.14, T:0.40
Consensus pattern (36 bp):
TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
Found at i:195117 original size:71 final size:72
Alignment explanation
Indices: 195032--195355 Score: 221
Period size: 72 Copynumber: 4.6 Consensus size: 72
195022 GTTTTTCTTA
* * * * * *
195032 AAACAAGA-TTTGTCTCGCTTGAGACCGTTTTCAC-TATAA-GAGTTTTGTCTCTCTTGAGACAG
1 AAACAA-ATTTTGTCTCTCTTGAGACAGTTTTCACTTA-AACAAATTTCGTCTATCTTGAGACAG
195094 TTTCCCTTG
64 TTTCCCTTG
*
195103 AAACAAATTTTGTCTCTCTTGAGACAG-TTTCTCTTGAAACAAATTTCGTCTATCTTGAGACAGT
1 AAACAAATTTTGTCTCTCTTGAGACAGTTTTCACTT-AAACAAATTTCGTCTATCTTGAGACAGT
195167 TTCCCTTG
65 TTCCCTTG
* * * *
195175 AAATAAATTTTGTCTCTCTTGAGACAG-TTTCCCTTGAAACAAA------ATAT-TTGA-ATATG
1 AAACAAATTTTGTCTCTCTTGAGACAGTTTTCACTT-AAACAAATTTCGTCTATCTTGAGACA-G
* *
195231 TTTTCTTTG
64 TTTCCCTTG
** * ** * * * *
195240 AAACAAATTCCGTCTCCCTTGAGACAG-TTTCTTTTGGAACTAAGTTTTGTCTCTCTTGAGACAG
1 AAACAAATTTTGTCTCTCTTGAGACAGTTTTCACTT-AAAC-AAATTTCGTCTATCTTGAGACAG
*
195304 TTTCTCTTG
64 TTTCCCTTG
* * *
195313 AAAC-AATTTTCGTTTATCTTGAGACAG-TTTCCCTTGAAACAAA
1 AAACAAATTTT-GTCTCTCTTGAGACAGTTTTCACTT-AAACAAA
195356 ACCTTTGAAT
Statistics
Matches: 202, Mismatches: 36, Indels: 29
0.76 0.13 0.11
Matches are distributed among these distances:
64 2 0.01
65 45 0.22
66 5 0.02
70 6 0.03
71 26 0.13
72 78 0.39
73 38 0.19
74 2 0.01
ACGTcount: A:0.27, C:0.19, G:0.15, T:0.39
Consensus pattern (72 bp):
AAACAAATTTTGTCTCTCTTGAGACAGTTTTCACTTAAACAAATTTCGTCTATCTTGAGACAGTT
TCCCTTG
Found at i:195315 original size:102 final size:102
Alignment explanation
Indices: 195130--195318 Score: 290
Period size: 102 Copynumber: 1.9 Consensus size: 102
195120 CTTGAGACAG
* *
195130 TTTCTCTTGAAACAAATTTCGTCTATCTTGAGACAGTTTCCCTTGAAATAAATTTTGTCTCTCTT
1 TTTCTCTTGAAACAAATTCCGTCTACCTTGAGACAGTTTCCCTTGAAATAAATTTTGTCTCTCTT
195195 GAGACAGTTTCCCTTGAAACAAAATATTTGAATATGT
66 GAGACAGTTTCCCTTGAAACAAAATATTTGAATATGT
* ** * *
195232 TTTCT-TTGAAACAAATTCCGTCTCCCTTGAGACAGTTTCTTTTGGAACTAAGTTTTGTCTCTCT
1 TTTCTCTTGAAACAAATTCCGTCTACCTTGAGACAGTTTCCCTT-GAAATAAATTTTGTCTCTCT
*
195296 TGAGACAGTTTCTCTTGAAACAA
65 TGAGACAGTTTCCCTTGAAACAA
195319 TTTTCGTTTA
Statistics
Matches: 78, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
101 33 0.42
102 45 0.58
ACGTcount: A:0.27, C:0.19, G:0.14, T:0.40
Consensus pattern (102 bp):
TTTCTCTTGAAACAAATTCCGTCTACCTTGAGACAGTTTCCCTTGAAATAAATTTTGTCTCTCTT
GAGACAGTTTCCCTTGAAACAAAATATTTGAATATGT
Found at i:195347 original size:138 final size:137
Alignment explanation
Indices: 195094--195418 Score: 436
Period size: 138 Copynumber: 2.4 Consensus size: 137
195084 CTTGAGACAG
*
195094 TTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAAATTTCGTCTATCTT
1 TTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACAAATTTCGTCTATCTT
* *
195159 GAGACAGTTTCCCTTGAAATAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATATTT
66 GAGACAGTTTCCCTTGAAATAAATTTTGTCTATCTTGAGACAGTTTCCCTTGAAACAAAACATTT
*
195224 GAATATG
131 GAATATA
* * ** * * * * *
195231 TTTTCTTTGAAACAAATTCCGTCTCCCTTGAGACAGTTTCTTTTGGAACTAAGTTTTGTCTCTCT
1 TTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAAC-AAATTTCGTCTATCT
* * * *
195296 TGAGACAGTTTCTCTTGAAA-CAATTTTCGTTTATCTTGAGACAGTTTCCCTTGAAACAAAACCT
65 TGAGACAGTTTCCCTTGAAATAAATTTT-GTCTATCTTGAGACAGTTTCCCTTGAAACAAAACAT
*
195360 TTGAATTTA
129 TTGAATATA
* * *
195369 TTTCCCCTAAAACAAATTTTGTCTCCCTTGAGACAGTTACTCTTGAAACA
1 TTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACA
195419 CAAAATCTTC
Statistics
Matches: 159, Mismatches: 27, Indels: 4
0.84 0.14 0.02
Matches are distributed among these distances:
137 49 0.31
138 110 0.69
ACGTcount: A:0.27, C:0.20, G:0.13, T:0.39
Consensus pattern (137 bp):
TTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACAAATTTCGTCTATCTT
GAGACAGTTTCCCTTGAAATAAATTTTGTCTATCTTGAGACAGTTTCCCTTGAAACAAAACATTT
GAATATA
Found at i:195448 original size:67 final size:68
Alignment explanation
Indices: 195330--195486 Score: 212
Period size: 68 Copynumber: 2.4 Consensus size: 68
195320 TTTCGTTTAT
* **
195330 CTTGAGACAGTTTCCCTTG-AA-ACAAAACCTTTGAATTTATTTCCCCTAAAACA-AATTTTGTC
1 CTTGAGACAGTTTCTCTTGAAACACAAAACCTTCAAATTTATTTCCCCTAAAACATAATTTTGTC
195392 TCC
66 TCC
* * * *
195395 CTTGAGACAGTTACTCTTGAAACACAAAATCTTCAAATTTATTTCCCTTAAAACATAATTTTGTT
1 CTTGAGACAGTTTCTCTTGAAACACAAAACCTTCAAATTTATTTCCCCTAAAACATAATTTTGTC
195460 TCC
66 TCC
* *
195463 CTTGAGACCGTTTCTCATGAAACA
1 CTTGAGACAGTTTCTCTTGAAACA
195487 ACATATATCT
Statistics
Matches: 79, Mismatches: 10, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
65 17 0.22
66 2 0.03
67 28 0.35
68 32 0.41
ACGTcount: A:0.32, C:0.23, G:0.10, T:0.36
Consensus pattern (68 bp):
CTTGAGACAGTTTCTCTTGAAACACAAAACCTTCAAATTTATTTCCCCTAAAACATAATTTTGTC
TCC
Found at i:196197 original size:105 final size:105
Alignment explanation
Indices: 196011--197160 Score: 1806
Period size: 105 Copynumber: 11.0 Consensus size: 105
196001 GCACTCGAGG
* * * *
196011 CAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAACTTCTCAATTTCAG
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAAC-AACAACTTCTCAATTTCAG
*
196076 AGTCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
65 AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
* *
196117 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCCTGTCAACAACAAATTCTCAATTTCAGA
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGA
* * *
196182 GCCAATTTCAACTTCACAATGAAGGATATTGGACTTCAAA
66 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
*
196222 CAACGCAAGTTCAACTTCATGACGAAGGGACCGCTGCTGCTTGTCAACAACAACTTCTCAATTTC
1 CAACGCAAGTTCAACTTCACGACGAAGGGA-C-C-GCTGCTTGTCAACAACAACTTCTCAATTTC
*
196287 AGAGCCAATTTCAACTTCAAAACGAAGGATATTGGACTCCAGA
63 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
* * *
196330 CAACGCAAGTTCAACTTCATGACGAAGGGACCGCTGCTTGTCAACAACTACTTCTCAATTTCATA
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGA
*
196395 GCCAATTTCAACTTCACAACGAAGGATATTGGACTTCAGA
66 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
* *
196435 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCAATCTCAGA
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGA
*
196500 GCCAATTTCAACTTCACAACGAAGAATATTGGACTCCAGA
66 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
* * *
196540 CAACGCAAGTTCAACTTCATGGCGAAGGGACCGCTGCCTGTCAACAACAACTTCTCAATTTCAGA
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGA
196605 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
66 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
* *
196645 CAACGCAAGTTCAACTTCACGACGAAGGAACCGCTGCTTGTCAACAACAACTTCTCAATTTCATA
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGA
*
196710 GCCAATTTCAACTTCACAACGAAGGATATTGGACTTCAGA
66 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
* *
196750 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCAATCTCAGA
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGA
*
196815 GCTAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
66 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
* * * *
196855 CAATGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCAATCTAAGA
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGA
196920 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
66 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
196960 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAAC-ACAA-TT-TC-A-TTCAGA
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGA
** *
197020 TTCAATTTCAACTTCACAACGAAGGATATTGGACTCGAGA
66 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
* * * * * * ** *
197060 CAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCCGGTTCCAG
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAAC-AACAACTTCTCAATTTCAG
* *
197125 AGCCAATTTCAACTTCACGACGGAGGATATTGGACT
65 AGCCAATTTCAACTTCACAACGAAGGATATTGGACT
197161 TGGAACAATG
Statistics
Matches: 968, Mismatches: 67, Indels: 18
0.92 0.06 0.02
Matches are distributed among these distances:
100 82 0.08
101 1 0.00
102 5 0.01
103 4 0.00
104 5 0.01
105 694 0.72
106 78 0.08
107 2 0.00
108 97 0.10
ACGTcount: A:0.34, C:0.27, G:0.17, T:0.23
Consensus pattern (105 bp):
CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGA
GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
Found at i:197752 original size:34 final size:36
Alignment explanation
Indices: 197708--197808 Score: 154
Period size: 34 Copynumber: 2.9 Consensus size: 36
197698 TTTCGTCCTA
197708 CTAGGATTCAAACTCCTAAAAATAGGATAGAA-TTT
1 CTAGGATTCAAACTCCTAAAAATAGGATAGAATTTT
*
197743 -TAGGATTCAAACTCCT-AAAATAGGATAAAATTTT
1 CTAGGATTCAAACTCCTAAAAATAGGATAGAATTTT
*
197777 GCTAGGATTCAAACTCCTAAAAATAAGATAGA
1 -CTAGGATTCAAACTCCTAAAAATAGGATAGA
197809 GTTCTACTAT
Statistics
Matches: 59, Mismatches: 3, Indels: 6
0.87 0.04 0.09
Matches are distributed among these distances:
33 13 0.22
34 19 0.32
36 16 0.27
37 11 0.19
ACGTcount: A:0.45, C:0.14, G:0.14, T:0.28
Consensus pattern (36 bp):
CTAGGATTCAAACTCCTAAAAATAGGATAGAATTTT
Found at i:197790 original size:36 final size:34
Alignment explanation
Indices: 197708--197798 Score: 139
Period size: 36 Copynumber: 2.6 Consensus size: 34
197698 TTTCGTCCTA
*
197708 CTAGGATTCAAACTCCTAAAAATAGGATAGAATTT
1 CTAGGATTCAAACTCCT-AAAATAGGATAAAATTT
197743 -TAGGATTCAAACTCCTAAAATAGGATAAAATTTT
1 CTAGGATTCAAACTCCTAAAATAGGATAAAA-TTT
197777 GCTAGGATTCAAACTCCTAAAA
1 -CTAGGATTCAAACTCCTAAAA
197799 ATAAGATAGA
Statistics
Matches: 52, Mismatches: 1, Indels: 5
0.90 0.02 0.09
Matches are distributed among these distances:
33 13 0.25
34 19 0.37
36 20 0.38
ACGTcount: A:0.43, C:0.15, G:0.13, T:0.29
Consensus pattern (34 bp):
CTAGGATTCAAACTCCTAAAATAGGATAAAATTT
Found at i:198408 original size:57 final size:59
Alignment explanation
Indices: 198347--198461 Score: 128
Period size: 57 Copynumber: 2.0 Consensus size: 59
198337 ATTTTACTTA
*
198347 TATATATAT-ATATGCTTTTACGTTTTTATA-TATTTTAC-TCATTTATTTATCTATTTT
1 TATATATATCATAT-ATTTTACGTTTTTATATTATTTTACTTCATTTATTTATCTATTTT
* * * * ** *
198404 TATATTTATCCTATATTTTATGTTTTTATATTCTTTTACTTGTTTTATTTATTTATTT
1 TATATATATCATATATTTTACGTTTTTATATTATTTTACTTCATTTATTTATCTATTT
198462 GCATTATCAT
Statistics
Matches: 47, Mismatches: 8, Indels: 4
0.80 0.14 0.07
Matches are distributed among these distances:
57 22 0.47
58 10 0.21
59 15 0.32
ACGTcount: A:0.23, C:0.08, G:0.03, T:0.65
Consensus pattern (59 bp):
TATATATATCATATATTTTACGTTTTTATATTATTTTACTTCATTTATTTATCTATTTT
Found at i:198411 original size:16 final size:18
Alignment explanation
Indices: 198390--198424 Score: 56
Period size: 16 Copynumber: 2.1 Consensus size: 18
198380 TTTACTCATT
198390 TATTTAT-CTAT-TTTTA
1 TATTTATCCTATATTTTA
198406 TATTTATCCTATATTTTA
1 TATTTATCCTATATTTTA
198424 T
1 T
198425 GTTTTTATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.41
17 4 0.24
18 6 0.35
ACGTcount: A:0.26, C:0.09, G:0.00, T:0.66
Consensus pattern (18 bp):
TATTTATCCTATATTTTA
Done.