Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012003.1 Kokia drynarioides strain JFW-HI SEQ_127001, 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: 291786
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Warning! 113 characters in sequence are not A, C, G, or T
File 1 of 2
Found at i:1516 original size:194 final size:194
Alignment explanation
Indices: 1180--1799 Score: 857
Period size: 194 Copynumber: 3.2 Consensus size: 194
1170 AAATGGTTAG
* * * * *
1180 CTTCCTAATGAGGTACAGAGAAGTATACCAACTAAATACGAACAAATCTTCGAACCCCAGCTTGC
1 CTTCCTGATGAGATACAGAGAAGTATACCAACTCAATATGAACAAATCTTCGAACCCCAGCTTCC
*
1245 TGATGAGATACTGAGAAGCAGGTCGAAGAAATAAAAAGGTTAGCTTCCTGATGAGAC-CTTGAGA
66 TGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAAAGGTTAGCTTCCTGATGAGACAC-TGAGA
* * * * * *
1309 AGTGGACCAAATTCATCTTCTTAATGAGGTACAGAGAAGCGGATTGAAACAAATGAGGCGGTCAT
130 AGTGAACCAAATTCGTCTTCCTGATGAGGTACAGAGAAGCGGATTGAAACAAACGAGGCAGTCAT
*
1374 CTTCCTGATGAGGTACAGAGAAGTATACCAACTCAATATGAACAAATCTTCGAACCCCAGCTTCC
1 CTTCCTGATGAGATACAGAGAAGTATACCAACTCAATATGAACAAATCTTCGAACCCCAGCTTCC
* * *
1439 TGATAAGATACTGAGAAGTAGGTCGAAGCAATAAAAGGGTTAGCTTCCTGATGAGACACTGAGAA
66 TGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAAAGGTTAGCTTCCTGATGAGACACTGAGAA
*
1504 GTGAACCAAATTCGTCTTCCTGATGAGGTACAGAGAAGCGGATTGAAACAAACGAGGCAGTTAT
131 GTGAACCAAATTCGTCTTCCTGATGAGGTACAGAGAAGCGGATTGAAACAAACGAGGCAGTCAT
* * * *
1568 CTTCCTGATGAGATACATAGAAGTATACCAACTCAGGGCTTGATGTGAGCAAATCTTCGAATCCC
1 CTTCCTGATGAGATACAGAGAAGTATACCAACTCA-------ATATGAACAAATCTTCGAACCCC
* * * * *
1633 AGCTTCCTGATGAGATACTGAAAAGCAGGTCGAAGCAATAAAATGGTTAGCTTCGTGATGAAATA
59 AGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAAAGGTTAGCTTCCTGATGAGACA
* * * *
1698 CTGAGAAGTAAAACAAATTCGTCTTCCTGATGAGGTACAGAGAAGCGGATTGAAACAAGCGATGC
124 CTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGGTACAGAGAAGCGGATTGAAACAAACGAGGC
1763 AGTCAT
189 AGTCAT
* *
1769 CTTCCTGATAAGATACTA-AGAAGTAGACCAA
1 CTTCCTGATGAGATAC-AGAGAAGTATACCAA
1800 ATTAACGACA
Statistics
Matches: 383, Mismatches: 34, Indels: 11
0.89 0.08 0.03
Matches are distributed among these distances:
194 210 0.55
195 1 0.00
201 171 0.45
202 1 0.00
ACGTcount: A:0.36, C:0.18, G:0.23, T:0.23
Consensus pattern (194 bp):
CTTCCTGATGAGATACAGAGAAGTATACCAACTCAATATGAACAAATCTTCGAACCCCAGCTTCC
TGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAAAGGTTAGCTTCCTGATGAGACACTGAGAA
GTGAACCAAATTCGTCTTCCTGATGAGGTACAGAGAAGCGGATTGAAACAAACGAGGCAGTCAT
Found at i:2111 original size:11 final size:11
Alignment explanation
Indices: 2096--2178 Score: 69
Period size: 11 Copynumber: 7.4 Consensus size: 11
2086 CCAGGCCCCT
* *
2096 TTTAAGTTTAT
1 TTTAAATTTAA
*
2107 TTTAAATTT-G
1 TTTAAATTTAA
*
2117 TTTTAATTTAGA
1 TTTAAATTTA-A
**
2129 TTTATTTTTAA
1 TTTAAATTTAA
2140 TTTAAATTTAAA
1 TTTAAATTT-AA
2152 TTTAAATTTAA
1 TTTAAATTTAA
*
2163 TTTAAGTTTAAA
1 TTTAAATTT-AA
2175 TTTA
1 TTTA
2179 TTTTCAAATT
Statistics
Matches: 58, Mismatches: 10, Indels: 7
0.77 0.13 0.09
Matches are distributed among these distances:
10 8 0.14
11 26 0.45
12 24 0.41
ACGTcount: A:0.36, C:0.00, G:0.05, T:0.59
Consensus pattern (11 bp):
TTTAAATTTAA
Found at i:2137 original size:17 final size:17
Alignment explanation
Indices: 2102--2197 Score: 71
Period size: 17 Copynumber: 5.9 Consensus size: 17
2092 CCCTTTTAAG
* *
2102 TTTATTTTAAATTT-GT
1 TTTAATTTAAATTTATT
*
2118 TTTAATTTAGATTTATT
1 TTTAATTTAAATTTATT
2135 TTTAATTTAAATTTA--
1 TTTAATTTAAATTTATT
*
2150 ---AATTTAAATTTA-A
1 TTTAATTTAAATTTATT
2163 TTTAAGTTTAAATTTATT
1 TTTAA-TTTAAATTTATT
* *
2181 TTCAAATTTAAAATTAT
1 TT-TAATTTAAATTTAT
2198 GTCCCAATAC
Statistics
Matches: 65, Mismatches: 7, Indels: 14
0.76 0.08 0.16
Matches are distributed among these distances:
12 12 0.18
16 14 0.22
17 25 0.38
18 12 0.18
19 2 0.03
ACGTcount: A:0.38, C:0.01, G:0.03, T:0.58
Consensus pattern (17 bp):
TTTAATTTAAATTTATT
Found at i:2147 original size:6 final size:6
Alignment explanation
Indices: 2138--2192 Score: 69
Period size: 6 Copynumber: 9.3 Consensus size: 6
2128 ATTTATTTTT
* *
2138 AATTTA AATTTA AATTTA AATTT- AATTTA AGTTTA AATTT- ATTTTCA
1 AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTT-A
2185 AATTTA AA
1 AATTTA AA
2193 ATTATGTCCC
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
5 9 0.21
6 29 0.69
7 4 0.10
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.51
Consensus pattern (6 bp):
AATTTA
Found at i:2147 original size:23 final size:23
Alignment explanation
Indices: 2121--2192 Score: 90
Period size: 23 Copynumber: 3.1 Consensus size: 23
2111 AATTTGTTTT
*
2121 AATTTAGATTTATTTTTAATTTA
1 AATTTAAATTTATTTTTAATTTA
**
2144 AATTTAAATTTAAATTTAATTTA
1 AATTTAAATTTATTTTTAATTTA
* *
2167 AGTTTAAATTTATTTTCAAATTTA
1 AATTTAAATTTATTTT-TAATTTA
2191 AA
1 AA
2193 ATTATGTCCC
Statistics
Matches: 40, Mismatches: 8, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
23 33 0.82
24 7 0.17
ACGTcount: A:0.42, C:0.01, G:0.03, T:0.54
Consensus pattern (23 bp):
AATTTAAATTTATTTTTAATTTA
Found at i:2966 original size:21 final size:21
Alignment explanation
Indices: 2940--2996 Score: 62
Period size: 21 Copynumber: 2.8 Consensus size: 21
2930 ATTATTAATG
* *
2940 ATAATATTATTAATAACAGTA
1 ATAATATAATTAATAACAATA
* * *
2961 ATAATAGATTTAATAATAATA
1 ATAATATAATTAATAACAATA
2982 ATAA-ATAATTAATAA
1 ATAATATAATTAATAA
2997 AAAAAGGAAG
Statistics
Matches: 29, Mismatches: 7, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
20 9 0.31
21 20 0.69
ACGTcount: A:0.58, C:0.02, G:0.04, T:0.37
Consensus pattern (21 bp):
ATAATATAATTAATAACAATA
Found at i:4078 original size:30 final size:30
Alignment explanation
Indices: 4042--4103 Score: 90
Period size: 30 Copynumber: 2.1 Consensus size: 30
4032 CCTTAAAGGT
4042 CCCTAAACTATCT-AAAAATTATATTTTAAC
1 CCCTAAACT-TCTCAAAAATTATATTTTAAC
* *
4072 CCCTAAACTTCTCCAAAATTATATTTTGAC
1 CCCTAAACTTCTCAAAAATTATATTTTAAC
4102 CC
1 CC
4104 TCGAACTTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 3 0.10
30 26 0.90
ACGTcount: A:0.37, C:0.26, G:0.02, T:0.35
Consensus pattern (30 bp):
CCCTAAACTTCTCAAAAATTATATTTTAAC
Found at i:4111 original size:30 final size:29
Alignment explanation
Indices: 4056--4142 Score: 95
Period size: 30 Copynumber: 2.9 Consensus size: 29
4046 AAACTATCTA
*
4056 AAAATTATATTTTAACCC-CTAAACTTCTCC
1 AAAATTATATTTTAACCCTC-GAACTT-TCC
* *
4086 AAAATTATATTTTGACCCTCGAACTTTCT
1 AAAATTATATTTTAACCCTCGAACTTTCC
* *
4115 AAAGATTACATTTTTACCCTCGAACTTT
1 AAA-ATTATATTTTAACCCTCGAACTTT
4143 TTAAAATTCC
Statistics
Matches: 50, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
29 5 0.10
30 44 0.88
31 1 0.02
ACGTcount: A:0.33, C:0.23, G:0.05, T:0.39
Consensus pattern (29 bp):
AAAATTATATTTTAACCCTCGAACTTTCC
Found at i:4190 original size:58 final size:58
Alignment explanation
Indices: 4126--4253 Score: 177
Period size: 58 Copynumber: 2.2 Consensus size: 58
4116 AAGATTACAT
** *
4126 TTTTACCCTCGAACTTTTTAAAATTCCATTTTTGA-CTCGATTTCACCAAAAATTACCA
1 TTTTACCCTCGAACTTCCTAAAATTCCATTTTTGACCCCGATTTCACC-AAAATTACCA
* * **
4184 TTTTACCCTCGATCTTCCTAAAATTCCGTTTTTGACCCCGATTTTTCCAAAATTACCA
1 TTTTACCCTCGAACTTCCTAAAATTCCATTTTTGACCCCGATTTCACCAAAATTACCA
4242 TTTTACCCTCGA
1 TTTTACCCTCGA
4254 GTGTCTAGAA
Statistics
Matches: 62, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
58 53 0.85
59 9 0.15
ACGTcount: A:0.27, C:0.27, G:0.06, T:0.40
Consensus pattern (58 bp):
TTTTACCCTCGAACTTCCTAAAATTCCATTTTTGACCCCGATTTCACCAAAATTACCA
Found at i:4206 original size:29 final size:29
Alignment explanation
Indices: 4086--4277 Score: 114
Period size: 30 Copynumber: 6.6 Consensus size: 29
4076 AAACTTCTCC
* * *
4086 AAAATTA-TATTTTGACCCTCGAACTTTCT
1 AAAATTACCATTTT-ACCCTCGATCTTCCT
* **
4115 AAAGATTA-CATTTTTACCCTCGAACTTTTT
1 AAA-ATTACCA-TTTTACCCTCGATCTTCCT
*** *
4145 AAAATT-CCATTTTTGACTCGAT-TTCACCA
1 AAAATTACCATTTTACCCTCGATCTT--CCT
4174 AAAATTACCATTTTACCCTCGATCTTCCT
1 AAAATTACCATTTTACCCTCGATCTTCCT
* *
4203 AAAATT-CCGTTTTTGACCC-CGATTTTTCC-
1 AAAATTACC-ATTTT-ACCCTCGA-TCTTCCT
*
4232 AAAATTACCATTTTACCCTCGAGT-GT-CT
1 AAAATTACCATTTTACCCTCGA-TCTTCCT
*
4260 AGAATTACCATTTTACCC
1 AAAATTACCATTTTACCC
4278 CCGGGTACTT
Statistics
Matches: 131, Mismatches: 19, Indels: 27
0.74 0.11 0.15
Matches are distributed among these distances:
27 3 0.02
28 33 0.25
29 43 0.33
30 46 0.35
31 6 0.05
ACGTcount: A:0.29, C:0.25, G:0.07, T:0.39
Consensus pattern (29 bp):
AAAATTACCATTTTACCCTCGATCTTCCT
Found at i:12345 original size:56 final size:56
Alignment explanation
Indices: 12240--12347 Score: 128
Period size: 56 Copynumber: 1.9 Consensus size: 56
12230 CTCTATTCGT
* * * *
12240 TGTTGTTATCTTCTTTTGTTTACCCACTTCTTTCTCTTCTATCTCCTCTACTAAGC
1 TGTTGTTATCTCCTTTTGTTTACCCACTCCATTCTCTTCTATATCCTCTACTAAGC
** * *
12296 TGTTGTTATCTCCTTCTT-TTTACCTTCTCCATTCTCTTCTTTATTCTCTACT
1 TGTTGTTATCTCCTT-TTGTTTACCCACTCCATTCTCTTCTATATCCTCTACT
12348 CTTTTTTTTT
Statistics
Matches: 43, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
56 41 0.95
57 2 0.05
ACGTcount: A:0.11, C:0.29, G:0.06, T:0.55
Consensus pattern (56 bp):
TGTTGTTATCTCCTTTTGTTTACCCACTCCATTCTCTTCTATATCCTCTACTAAGC
Found at i:24785 original size:29 final size:29
Alignment explanation
Indices: 24753--24876 Score: 95
Period size: 29 Copynumber: 4.3 Consensus size: 29
24743 TTCACACACA
* * * *
24753 ATTAGTTCCCTTATAATAGTTCCCATATG
1 ATTAGCTCCCATATAATAATTCACATATG
* *
24782 ATTAGCTCGCATATAATAATTCACATATA
1 ATTAGCTCCCATATAATAATTCACATATG
* * * * *
24811 ATCAACTCGCATACAATAATTCACATATA
1 ATTAGCTCCCATATAATAATTCACATATG
* ** * * *
24840 ATCAGCTTGCATACAATAATTTACATATA
1 ATTAGCTCCCATATAATAATTCACATATG
24869 ATTAGCTC
1 ATTAGCTC
24877 AATCTAGTGA
Statistics
Matches: 81, Mismatches: 14, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 81 1.00
ACGTcount: A:0.38, C:0.20, G:0.07, T:0.35
Consensus pattern (29 bp):
ATTAGCTCCCATATAATAATTCACATATG
Found at i:24810 original size:14 final size:14
Alignment explanation
Indices: 24791--24841 Score: 66
Period size: 14 Copynumber: 3.6 Consensus size: 14
24781 GATTAGCTCG
24791 CATATAATAATTCA
1 CATATAATAATTCA
* *
24805 CATATAATCAACTCG
1 CATATAAT-AATTCA
*
24820 CATACAATAATTCA
1 CATATAATAATTCA
24834 CATATAAT
1 CATATAAT
24842 CAGCTTGCAT
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
14 19 0.63
15 11 0.37
ACGTcount: A:0.47, C:0.20, G:0.02, T:0.31
Consensus pattern (14 bp):
CATATAATAATTCA
Found at i:25676 original size:21 final size:21
Alignment explanation
Indices: 25652--25693 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
25642 CATCAAGTAG
25652 AAGAG-TCCGCAAAACATATAA
1 AAGAGTTCC-CAAAACATATAA
*
25673 AAGAGTTCCCATAACATATAA
1 AAGAGTTCCCAAAACATATAA
25694 CTTGCTCGTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 16 0.84
22 3 0.16
ACGTcount: A:0.50, C:0.19, G:0.12, T:0.19
Consensus pattern (21 bp):
AAGAGTTCCCAAAACATATAA
Found at i:36449 original size:17 final size:17
Alignment explanation
Indices: 36423--36461 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
36413 TTAGCATTCT
36423 TGCA-TTTTATTGTGC-C
1 TGCATTTTTATTGT-CAC
36439 TGCATTTTTATTGTCAC
1 TGCATTTTTATTGTCAC
36456 TGCATT
1 TGCATT
36462 CATTTTGATA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.24
17 16 0.76
ACGTcount: A:0.15, C:0.18, G:0.15, T:0.51
Consensus pattern (17 bp):
TGCATTTTTATTGTCAC
Found at i:43024 original size:15 final size:15
Alignment explanation
Indices: 43006--43049 Score: 52
Period size: 16 Copynumber: 2.9 Consensus size: 15
42996 AAAAATTATG
43006 TTTTCCATCCTTCAA
1 TTTTCCATCCTTCAA
* *
43021 TTTTCTACCCCTTCAA
1 TTTTCCA-TCCTTCAA
*
43037 TTTTTCATCCTTC
1 TTTTCCATCCTTC
43050 CACTTTTTTT
Statistics
Matches: 23, Mismatches: 5, Indels: 2
0.77 0.17 0.07
Matches are distributed among these distances:
15 11 0.48
16 12 0.52
ACGTcount: A:0.16, C:0.34, G:0.00, T:0.50
Consensus pattern (15 bp):
TTTTCCATCCTTCAA
Found at i:43707 original size:91 final size:90
Alignment explanation
Indices: 43552--43763 Score: 266
Period size: 91 Copynumber: 2.3 Consensus size: 90
43542 CTATACCATC
* * * * *
43552 TTTTCCCAAGTTGGTAACTAAACTTTTTTTGGTCATAGGTGGCACATAAACTATACTTCGTTACC
1 TTTTCCAAAGTTAGTAACTAAACTTTTTTTGGTCATAAGTAGCACATAAACTATACTTCATTACC
* *
43617 CAAAGTGTTACCTCACCTACACCCT
66 CAAAGTGATACCTCAACTACACCCT
* * *
43642 TTTTCCAAAGTTAGTATCTAGACTTCTTTTTGGTCATAAGTAGTACCA-AAACTATACTTCATTA
1 TTTTCCAAAGTTAGTAACTAAACTT-TTTTTGGTCATAAGTAGCA-CATAAACTATACTTCATTA
*
43706 CCCAAAGTGATACCTCAACTATACCCT
64 CCCAAAGTGATACCTCAACTACACCCT
*
43733 TTTTCCCAAA-TTAGTACCTAAACGTTTTTTT
1 TTTT-CCAAAGTTAGTAACTAAAC-TTTTTTT
43764 TTTTATAAAT
Statistics
Matches: 105, Mismatches: 13, Indels: 7
0.84 0.10 0.06
Matches are distributed among these distances:
90 21 0.20
91 75 0.71
92 9 0.09
ACGTcount: A:0.29, C:0.24, G:0.11, T:0.37
Consensus pattern (90 bp):
TTTTCCAAAGTTAGTAACTAAACTTTTTTTGGTCATAAGTAGCACATAAACTATACTTCATTACC
CAAAGTGATACCTCAACTACACCCT
Found at i:43779 original size:91 final size:91
Alignment explanation
Indices: 43552--43798 Score: 250
Period size: 91 Copynumber: 2.7 Consensus size: 91
43542 CTATACCATC
* * * ** * * *
43552 TTTTCCCAAGTTGGTAACTAAACTT-TTTTTGGTCATAGGTGGCA-CATAAACTATACTTCGTTA
1 TTTTCCAAAGTTAGTACCTAAACTTCTTTTTGGTCATAAATAGTACCA-AAACTATACTTCATTA
* *
43615 CCCAAAGTGTTACCTCACCTACACCCT
65 CCCAAAGTGATACCTCAACTACACCCT
* * *
43642 TTTTCCAAAGTTAGTATCTAGACTTCTTTTTGGTCATAAGTAGTACCAAAACTATACTTCATTAC
1 TTTTCCAAAGTTAGTACCTAAACTTCTTTTTGGTCATAAATAGTACCAAAACTATACTTCATTAC
*
43707 CCAAAGTGATACCTCAACTATACCCT
66 CCAAAGTGATACCTCAACTACACCCT
** * * * * *
43733 TTTTCCCAAA-TTAGTACCTAAACGTT-TTTTTTTTTATAAATGGTACCTAAACTACACTTTATT
1 TTTT-CCAAAGTTAGTACCTAAAC-TTCTTTTTGGTCATAAATAGTACCAAAACTATACTTCATT
43796 ACC
64 ACC
43799 AAAAATGGTA
Statistics
Matches: 132, Mismatches: 21, Indels: 7
0.82 0.13 0.04
Matches are distributed among these distances:
90 21 0.16
91 102 0.77
92 9 0.07
ACGTcount: A:0.30, C:0.23, G:0.10, T:0.37
Consensus pattern (91 bp):
TTTTCCAAAGTTAGTACCTAAACTTCTTTTTGGTCATAAATAGTACCAAAACTATACTTCATTAC
CCAAAGTGATACCTCAACTACACCCT
Found at i:43808 original size:31 final size:31
Alignment explanation
Indices: 43770--43829 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
43760 TTTTTTTTAT
*
43770 AAATGGTACCTAAACTACACTTTATTACCAA
1 AAATGGTACCTAAACTACACTTCATTACCAA
** *
43801 AAATGGTATTTAAACTATACTTCATTACC
1 AAATGGTACCTAAACTACACTTCATTACC
43830 CAAATTACTC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.40, C:0.20, G:0.07, T:0.33
Consensus pattern (31 bp):
AAATGGTACCTAAACTACACTTCATTACCAA
Found at i:53442 original size:25 final size:26
Alignment explanation
Indices: 53410--53470 Score: 79
Period size: 25 Copynumber: 2.4 Consensus size: 26
53400 TACTCCTAAC
*
53410 AAAATTTTGACAATTTTACCCTTGGT
1 AAAATTTTGACAATTTTACCCATGGT
** *
53436 -AAATTTTGAGGATTTTGCCCATGGT
1 AAAATTTTGACAATTTTACCCATGGT
53461 AAAATTTTGA
1 AAAATTTTGA
53471 GAAAATATAT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
25 21 0.70
26 9 0.30
ACGTcount: A:0.31, C:0.11, G:0.16, T:0.41
Consensus pattern (26 bp):
AAAATTTTGACAATTTTACCCATGGT
Found at i:56121 original size:6 final size:6
Alignment explanation
Indices: 56110--56153 Score: 56
Period size: 6 Copynumber: 7.3 Consensus size: 6
56100 TTTCAACAAA
56110 TTCTTT TTCTTT TTC-TT TTCTTT CTTCTTT TT-TTT TTCATTT TT
1 TTCTTT TTCTTT TTCTTT TTCTTT -TTCTTT TTCTTT TTC-TTT TT
56154 TTTGTTTTTC
Statistics
Matches: 34, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
5 10 0.29
6 13 0.38
7 11 0.32
ACGTcount: A:0.02, C:0.16, G:0.00, T:0.82
Consensus pattern (6 bp):
TTCTTT
Found at i:56130 original size:11 final size:11
Alignment explanation
Indices: 56114--56161 Score: 53
Period size: 11 Copynumber: 4.4 Consensus size: 11
56104 AACAAATTCT
56114 TTTTCTTTTTC
1 TTTTCTTTTTC
56125 TTTTCTTTCTTC
1 TTTTCTTT-TTC
*
56137 TTTTTTTTTTC
1 TTTTCTTTTTC
* *
56148 ATTT-TTTTTG
1 TTTTCTTTTTC
56158 TTTT
1 TTTT
56162 TCAAGTGACT
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
10 8 0.25
11 14 0.44
12 10 0.31
ACGTcount: A:0.02, C:0.12, G:0.02, T:0.83
Consensus pattern (11 bp):
TTTTCTTTTTC
Found at i:67801 original size:27 final size:26
Alignment explanation
Indices: 67778--67835 Score: 71
Period size: 26 Copynumber: 2.2 Consensus size: 26
67768 ATTTATGGTG
*
67778 AACTCTAAAGGAATAGTATGTATGGCA
1 AACTCTAAA-GAATAATATGTATGGCA
* *
67805 AATTCTTAAGAATAATATGTATGGCGA
1 AACTCTAAAGAATAATATGTATGGC-A
67832 AACT
1 AACT
67836 TTGAAGGAAT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
26 15 0.58
27 11 0.42
ACGTcount: A:0.41, C:0.10, G:0.19, T:0.29
Consensus pattern (26 bp):
AACTCTAAAGAATAATATGTATGGCA
Found at i:71318 original size:33 final size:32
Alignment explanation
Indices: 71245--71321 Score: 84
Period size: 32 Copynumber: 2.4 Consensus size: 32
71235 TTAGTCAAAG
* ** *
71245 TTATTTATTTTATTAATTTTGTTTTGATTAAA
1 TTATTTATTTTACTAATTTCATTTTGATAAAA
*
71277 TT-TGTTATTTTCCTAATTTCATTTTGACTAAAA
1 TTAT-TTATTTTACTAATTTCATTTTGA-TAAAA
71310 TTATTTATTTTA
1 TTATTTATTTTA
71322 AGTAAATAGG
Statistics
Matches: 36, Mismatches: 6, Indels: 5
0.77 0.13 0.11
Matches are distributed among these distances:
31 1 0.03
32 21 0.58
33 13 0.36
34 1 0.03
ACGTcount: A:0.27, C:0.05, G:0.05, T:0.62
Consensus pattern (32 bp):
TTATTTATTTTACTAATTTCATTTTGATAAAA
Found at i:78097 original size:17 final size:17
Alignment explanation
Indices: 78051--78086 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 17
78041 TATAAAAGAA
78051 AAAAATGTTT-ATTTATT
1 AAAAAT-TTTAATTTATT
78068 AAAAATTTTAATTTATT
1 AAAAATTTTAATTTATT
78085 AA
1 AA
78087 GTAATTTAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 3 0.17
17 15 0.83
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (17 bp):
AAAAATTTTAATTTATT
Found at i:87295 original size:58 final size:57
Alignment explanation
Indices: 87220--87362 Score: 153
Period size: 58 Copynumber: 2.5 Consensus size: 57
87210 AGAACTCTGG
* * * * **
87220 TTAAGAAGTGCTTTTGTGGAAATCTTTGTAAAGGAAACACCTTTGTTG-TGAACTCTAT
1 TTAAGAAATGC-TTTGTGGAAATCTCTATAAAGAAAACACCTTTG-TGACCAACTCTAT
* * *
87278 TTAATAAATGACTTTGTGGCAATCTCTATGAAGAAAACACCTTTGTGACCAACTCTAT
1 TTAAGAAATG-CTTTGTGGAAATCTCTATAAAGAAAACACCTTTGTGACCAACTCTAT
*
87336 TTAAGAAATGTTTCTGTGGAAATCTCT
1 TTAAGAAATGCTT-TGTGGAAATCTCT
87363 GAAATGAAAG
Statistics
Matches: 70, Mismatches: 12, Indels: 6
0.80 0.14 0.07
Matches are distributed among these distances:
57 4 0.06
58 65 0.93
59 1 0.01
ACGTcount: A:0.31, C:0.15, G:0.17, T:0.36
Consensus pattern (57 bp):
TTAAGAAATGCTTTGTGGAAATCTCTATAAAGAAAACACCTTTGTGACCAACTCTAT
Found at i:87566 original size:31 final size:29
Alignment explanation
Indices: 87529--87594 Score: 91
Period size: 27 Copynumber: 2.3 Consensus size: 29
87519 AAACCCCGAA
87529 TGAAGGAAACAATGACATGTAACACGAACTC
1 TGAAGG-AA-AATGACATGTAACACGAACTC
*
87560 TGAAGG--AATGACATGTAAGACGAACTC
1 TGAAGGAAAATGACATGTAACACGAACTC
87587 TGAAGGAA
1 TGAAGGAA
87595 CAACTCAGTA
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
27 26 0.81
31 6 0.19
ACGTcount: A:0.44, C:0.15, G:0.24, T:0.17
Consensus pattern (29 bp):
TGAAGGAAAATGACATGTAACACGAACTC
Found at i:87569 original size:27 final size:27
Alignment explanation
Indices: 87539--87594 Score: 103
Period size: 27 Copynumber: 2.1 Consensus size: 27
87529 TGAAGGAAAC
87539 AATGACATGTAACACGAACTCTGAAGG
1 AATGACATGTAACACGAACTCTGAAGG
*
87566 AATGACATGTAAGACGAACTCTGAAGG
1 AATGACATGTAACACGAACTCTGAAGG
87593 AA
1 AA
87595 CAACTCAGTA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.43, C:0.16, G:0.23, T:0.18
Consensus pattern (27 bp):
AATGACATGTAACACGAACTCTGAAGG
Found at i:89423 original size:14 final size:15
Alignment explanation
Indices: 89395--89432 Score: 53
Period size: 14 Copynumber: 2.6 Consensus size: 15
89385 TCGTTTGGCG
89395 CAAAATAAAGCAAA-
1 CAAAATAAAGCAAAC
89409 CAAAA-AAAGCAAAAC
1 CAAAATAAAGC-AAAC
89424 CAAAATAAA
1 CAAAATAAA
89433 AAAAAACCAA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
13 5 0.24
14 8 0.38
15 5 0.24
16 3 0.14
ACGTcount: A:0.74, C:0.16, G:0.05, T:0.05
Consensus pattern (15 bp):
CAAAATAAAGCAAAC
Found at i:89440 original size:16 final size:16
Alignment explanation
Indices: 89419--89450 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
89409 CAAAAAAAGC
89419 AAAACCAAAATAAAAA
1 AAAACCAAAATAAAAA
*
89435 AAAACCAAATTAAAAA
1 AAAACCAAAATAAAAA
89451 TCCATTTACA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.78, C:0.12, G:0.00, T:0.09
Consensus pattern (16 bp):
AAAACCAAAATAAAAA
Found at i:92509 original size:21 final size:23
Alignment explanation
Indices: 92479--92524 Score: 69
Period size: 21 Copynumber: 2.1 Consensus size: 23
92469 TTTCTTTTAT
*
92479 AAATGGTGTTTGG-AAGA-AGAA
1 AAATGATGTTTGGCAAGAGAGAA
92500 AAATGATGTTTGGCAAGAGAGAA
1 AAATGATGTTTGGCAAGAGAGAA
92523 AA
1 AA
92525 TGAAAGAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 12 0.55
22 4 0.18
23 6 0.27
ACGTcount: A:0.46, C:0.02, G:0.30, T:0.22
Consensus pattern (23 bp):
AAATGATGTTTGGCAAGAGAGAA
Found at i:95244 original size:41 final size:38
Alignment explanation
Indices: 95144--95247 Score: 93
Period size: 37 Copynumber: 2.7 Consensus size: 38
95134 TTTGAAGCAA
* *
95144 TAAAGTGACACCCAGTGTCTCATCG-GCCTAGCCGAAG
1 TAAAATGACACCCAGTGTCTCATCGAACCTAGCCGAAG
* ** ** * *
95181 TAAAGTGGTACCCAGTACCTCATCGAATCTATCCGAAG
1 TAAAATGACACCCAGTGTCTCATCGAACCTAGCCGAAG
95219 TAAAATAATGACACCCAGTGTCTCATCGA
1 T--AA-AATGACACCCAGTGTCTCATCGA
95248 CTCAAGGTCG
Statistics
Matches: 51, Mismatches: 12, Indels: 4
0.76 0.18 0.06
Matches are distributed among these distances:
37 21 0.41
38 10 0.20
40 2 0.04
41 18 0.35
ACGTcount: A:0.32, C:0.27, G:0.19, T:0.22
Consensus pattern (38 bp):
TAAAATGACACCCAGTGTCTCATCGAACCTAGCCGAAG
Found at i:95373 original size:18 final size:18
Alignment explanation
Indices: 95350--95386 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
95340 ACAATTCATA
95350 TCACTTTCAATTCCAATT
1 TCACTTTCAATTCCAATT
* *
95368 TCACTTTCACTTTCAATT
1 TCACTTTCAATTCCAATT
95386 T
1 T
95387 TGATCACAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.24, C:0.27, G:0.00, T:0.49
Consensus pattern (18 bp):
TCACTTTCAATTCCAATT
Found at i:99032 original size:97 final size:97
Alignment explanation
Indices: 98847--99040 Score: 250
Period size: 97 Copynumber: 2.0 Consensus size: 97
98837 AACTTTGGAA
* * *
98847 AAGGATATTCGATTATCTTGATTTGAAGAAAAGTCGCACCTAGTAAGTTAAGACACGAATTTTCA
1 AAGGATATTCGATTATCTTAATTTGAAGAAAAATCGCACCTAGTAAGTTAAGACACAAATTTTCA
* * *
98912 GAATCAGAGATAAAGGAACATTGCCTTGATTT
66 AAATCAGAAATAAAGGAACATTGCCTCGATTT
* * *
98944 AAGGGTATTCGATTAT-TTCAATTTGAGGAAAAATCGCACCTAGTAAGTTAAGGCACAAATTTTC
1 AAGGATATTCGATTATCTT-AATTTGAAGAAAAATCGCACCTAGTAAGTTAAGACACAAATTTTC
*
99008 AAAACTCA-AAATAGAA-GAATATTGCCTCGATTT
65 AAAA-TCAGAAATA-AAGGAACATTGCCTCGATTT
99041 TAAAGTTTTC
Statistics
Matches: 84, Mismatches: 10, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
96 2 0.02
97 77 0.92
98 5 0.06
ACGTcount: A:0.38, C:0.14, G:0.18, T:0.30
Consensus pattern (97 bp):
AAGGATATTCGATTATCTTAATTTGAAGAAAAATCGCACCTAGTAAGTTAAGACACAAATTTTCA
AAATCAGAAATAAAGGAACATTGCCTCGATTT
Found at i:99301 original size:29 final size:29
Alignment explanation
Indices: 99269--99491 Score: 90
Period size: 29 Copynumber: 7.7 Consensus size: 29
99259 TAGGTATCTG
* *
99269 GGGGAAAAATGGTAATTTTGGGAAATTTT
1 GGGGTAAAATGGTAATTTTGGGAAATTTA
* * *
99298 GGGGTTAAATTGG-AATTTTTGGAAGTTTA
1 GGGG-TAAAATGGTAATTTTGGGAAATTTA
** **
99327 GGGGTAAAATAATAATTTTTGGAGAAATCGA
1 GGGGTAAAATGGTAA-TTTTGG-GAAATTTA
* * * *
99358 -GGTTAAAAAT-GAAATTTT-GG-AAGTTC
1 GGGGT-AAAATGGTAATTTTGGGAAATTTA
**
99384 GAGGGTAAAATGGTAATTTTTGGAGAAATCGA
1 G-GGGTAAAATGGTAA-TTTTGG-GAAATTTA
***
99416 GGTCAAAAATGG-AATTTT-GGAAAGTTTA
1 GGGGTAAAATGGTAATTTTGGGAAA-TTTA
*
99444 GAGGTAAAAAT-GTAATTTTTGGAGAAA-TT-
1 GGGGT-AAAATGGTAA-TTTTGG-GAAATTTA
99473 GGGGTCAAAATGG-AATTTT
1 GGGGT-AAAATGGTAATTTT
99492 TTTTCAAGGG
Statistics
Matches: 139, Mismatches: 36, Indels: 39
0.65 0.17 0.18
Matches are distributed among these distances:
26 2 0.01
27 10 0.07
28 21 0.15
29 53 0.38
30 26 0.19
31 20 0.14
32 7 0.05
ACGTcount: A:0.37, C:0.02, G:0.28, T:0.33
Consensus pattern (29 bp):
GGGGTAAAATGGTAATTTTGGGAAATTTA
Found at i:99362 original size:58 final size:60
Alignment explanation
Indices: 99308--99637 Score: 357
Period size: 59 Copynumber: 5.7 Consensus size: 60
99298 GGGGTTAAAT
* *
99308 TGGAATTTTTGG-AAGTTTAGGGGT-AAAATAATAATTTTTGGAGAAATCGAGGTTAAAAA
1 TGGAATTTTTGGAAAGTTTAGGGGTAAAAAT-GTAATTTTTGGAGAAATCGAGGTCAAAAA
* *
99367 T-GAAATTTTGG-AAG-TTCGAGGGT-AAAATGGTAATTTTTGGAGAAATCGAGGTCAAAAA
1 TGGAATTTTTGGAAAGTTTAG-GGGTAAAAAT-GTAATTTTTGGAGAAATCGAGGTCAAAAA
* * *
99425 TGGAA-TTTTGGAAAGTTTAGAGGTAAAAATGTAATTTTTGGAGAAATTGGGGTC-AAAA
1 TGGAATTTTTGGAAAGTTTAGGGGTAAAAATGTAATTTTTGGAGAAATCGAGGTCAAAAA
* * * *
99483 TGGAATTTTT------TTTCAAGGGTAAAAATGTGATTTTTGGATAAATCGGGGTCAAAAA
1 TGGAATTTTTGGAAAGTTT-AGGGGTAAAAATGTAATTTTTGGAGAAATCGAGGTCAAAAA
* * * *
99538 TGGAATTTTTGGAAAGCTTAGGGGTAAAAATGTAATTTTTAGAAAAAACGAGGTCAAAAA
1 TGGAATTTTTGGAAAGTTTAGGGGTAAAAATGTAATTTTTGGAGAAATCGAGGTCAAAAA
* * *
99598 TGGAA-TTTTGGAAAGTTTAAGGGTAAATATGTGATTTTTG
1 TGGAATTTTTGGAAAGTTTAGGGGTAAAAATGTAATTTTTG
99638 CACAGTTTAA
Statistics
Matches: 231, Mismatches: 26, Indels: 28
0.81 0.09 0.10
Matches are distributed among these distances:
53 3 0.01
54 31 0.13
55 14 0.06
57 3 0.01
58 64 0.28
59 66 0.29
60 48 0.21
61 2 0.01
ACGTcount: A:0.38, C:0.03, G:0.26, T:0.33
Consensus pattern (60 bp):
TGGAATTTTTGGAAAGTTTAGGGGTAAAAATGTAATTTTTGGAGAAATCGAGGTCAAAAA
Found at i:99470 original size:59 final size:59
Alignment explanation
Indices: 99308--99637 Score: 353
Period size: 58 Copynumber: 5.7 Consensus size: 59
99298 GGGGTTAAAT
* *
99308 TGGAATTTTTGGAAGTTTAG-GGGT-AAAATAATAATTTTTGGAGAAATCGAGGTTAAAAA
1 TGGAA-TTTTGGAAGTTTAGAGGGTAAAAAT-GTAATTTTTGGAGAAATCGAGGTCAAAAA
* *
99367 TGAAATTTTGGAAG-TTCGAGGGT-AAAATGGTAATTTTTGGAGAAATCGAGGTCAAAAA
1 TGGAATTTTGGAAGTTTAGAGGGTAAAAAT-GTAATTTTTGGAGAAATCGAGGTCAAAAA
* *
99425 TGGAATTTTGGAAAGTTTAGA-GGTAAAAATGTAATTTTTGGAGAAATTGGGGTC-AAAA
1 TGGAATTTTGG-AAGTTTAGAGGGTAAAAATGTAATTTTTGGAGAAATCGAGGTCAAAAA
* * * *
99483 TGGAATTTT----TTTTCA-AGGGTAAAAATGTGATTTTTGGATAAATCGGGGTCAAAAA
1 TGGAATTTTGGAAGTTT-AGAGGGTAAAAATGTAATTTTTGGAGAAATCGAGGTCAAAAA
* * * *
99538 TGGAATTTTTGGAAAGCTTAG-GGGTAAAAATGTAATTTTTAGAAAAAACGAGGTCAAAAA
1 TGGAA-TTTTGG-AAGTTTAGAGGGTAAAAATGTAATTTTTGGAGAAATCGAGGTCAAAAA
* *
99598 TGGAATTTTGGAAAGTTTA-AGGGTAAATATGTGATTTTTG
1 TGGAATTTTGG-AAGTTTAGAGGGTAAAAATGTAATTTTTG
99638 CACAGTTTAA
Statistics
Matches: 232, Mismatches: 24, Indels: 30
0.81 0.08 0.10
Matches are distributed among these distances:
53 4 0.02
54 31 0.13
55 9 0.04
56 4 0.02
57 3 0.01
58 68 0.29
59 62 0.27
60 49 0.21
61 2 0.01
ACGTcount: A:0.38, C:0.03, G:0.26, T:0.33
Consensus pattern (59 bp):
TGGAATTTTGGAAGTTTAGAGGGTAAAAATGTAATTTTTGGAGAAATCGAGGTCAAAAA
Found at i:99492 original size:29 final size:29
Alignment explanation
Indices: 99267--99606 Score: 147
Period size: 30 Copynumber: 11.7 Consensus size: 29
99257 TTTAGGTATC
*
99267 TGGGGGAAAAATGGTAA-TTTTGG-GAAATTT
1 TGGGGTAAAAATGG-AATTTTTGGAGAAA--T
* * **
99297 TGGGGTTAAATTGGAATTTTTGGA-AGTT
1 TGGGGTAAAAATGGAATTTTTGGAGAAAT
99325 TAGGGGTAAAATAAT--AATTTTTGGAGAAAT
1 T-GGGGT-AAA-AATGGAATTTTTGGAGAAAT
* * * *
99355 CGAGGTTAAAAAT-GAAATTTT-G-GAAGT
1 TG-GGGTAAAAATGGAATTTTTGGAGAAAT
99382 TCGAGGGT-AAAATGGTAATTTTTGGAGAAAT
1 T-G-GGGTAAAAATGG-AATTTTTGGAGAAAT
* * *
99413 CGAGGTCAAAAATGGAA-TTTTGGA-AAGTT
1 TGGGGT-AAAAATGGAATTTTTGGAGAA-AT
* *
99442 TAGAGGTAAAAATGTAATTTTTGGAGAAAT
1 T-GGGGTAAAAATGGAATTTTTGGAGAAAT
* ****
99472 TGGGGTCAAAATGGAATTTTT-TTTCAA-
1 TGGGGTAAAAATGGAATTTTTGGAGAAAT
*
99499 --GGGTAAAAATGTG-ATTTTTGGATAAAT
1 TGGGGTAAAAATG-GAATTTTTGGAGAAAT
* *
99526 CGGGGTCAAAAATGGAATTTTTGGA-AAGCT
1 TGGGGT-AAAAATGGAATTTTTGGAGAA-AT
* * * *
99556 TAGGGGTAAAAATGTAATTTTTAGAAAAAA
1 T-GGGGTAAAAATGGAATTTTTGGAGAAAT
* *
99586 CGAGGTCAAAAATGGAATTTT
1 TGGGGT-AAAAATGGAATTTT
99607 GGAAAGTTTA
Statistics
Matches: 237, Mismatches: 43, Indels: 60
0.70 0.13 0.18
Matches are distributed among these distances:
25 16 0.07
26 4 0.02
27 9 0.04
28 16 0.07
29 81 0.34
30 89 0.38
31 22 0.09
ACGTcount: A:0.37, C:0.03, G:0.26, T:0.33
Consensus pattern (29 bp):
TGGGGTAAAAATGGAATTTTTGGAGAAAT
Found at i:99611 original size:29 final size:28
Alignment explanation
Indices: 99343--99611 Score: 134
Period size: 29 Copynumber: 9.3 Consensus size: 28
99333 AAATAATAAT
* *
99343 TTTTGGAGAAATCGAGGTTAAAAATGAAA
1 TTTTGGAAAAATCGAGG-TAAAAATGGAA
**
99372 TTTTGG-AAGTTCGAGGGT-AAAATGGTAA
1 TTTTGGAAAAATCGA-GGTAAAAATGG-AA
*
99400 TTTTTGGAGAAATCGAGGTCAAAAATGGAA
1 -TTTTGGAAAAATCGAGGT-AAAAATGGAA
** * *
99430 TTTTGGAAAGTTTAGAGGTAAAAATGTAA
1 TTTTGGAAA-AATCGAGGTAAAAATGGAA
* * * *
99459 TTTTTGGAGAAATTGGGGTCAAAATGGAA
1 -TTTTGGAAAAATCGAGGTAAAAATGGAA
***** *
99488 TTTTTTTTCAA--G-GGTAAAAATGTGAT
1 TTTTGGAAAAATCGAGGTAAAAATG-GAA
* *
99514 TTTTGGATAAATCGGGGTCAAAAATGGAA
1 TTTTGGAAAAATCGAGGT-AAAAATGGAA
** * * *
99543 TTTTTGGAAAGCTTAGGGGTAAAAATGTAA
1 -TTTTGGAAA-AATCGAGGTAAAAATGGAA
* *
99573 TTTTTAGAAAAAACGAGGTCAAAAATGGAA
1 -TTTTGGAAAAATCGAGGT-AAAAATGGAA
99603 TTTTGGAAA
1 TTTTGGAAA
99612 GTTTAAGGGT
Statistics
Matches: 180, Mismatches: 44, Indels: 32
0.70 0.17 0.12
Matches are distributed among these distances:
25 9 0.05
26 10 0.06
27 6 0.03
28 15 0.08
29 64 0.36
30 63 0.35
31 13 0.07
ACGTcount: A:0.39, C:0.04, G:0.26, T:0.32
Consensus pattern (28 bp):
TTTTGGAAAAATCGAGGTAAAAATGGAA
Found at i:100798 original size:3 final size:3
Alignment explanation
Indices: 100792--100865 Score: 94
Period size: 3 Copynumber: 24.3 Consensus size: 3
100782 ACTATCATCA
* * * *
100792 ATT ATT ATT AATT ACT ATT ATT GTT ATT GTT ATT GTT ATT ATT ATT
1 ATT ATT ATT -ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
*
100838 ATT ATT ATT ATT ATT ACT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT A
100866 ATGCTATTAA
Statistics
Matches: 60, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
3 57 0.95
4 3 0.05
ACGTcount: A:0.31, C:0.03, G:0.04, T:0.62
Consensus pattern (3 bp):
ATT
Found at i:101578 original size:18 final size:19
Alignment explanation
Indices: 101555--101592 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
101545 TTTGGGCTTG
101555 AATTAGACATTT-TTTTGT
1 AATTAGACATTTATTTTGT
*
101573 AATTAGACTTTTATTTTGT
1 AATTAGACATTTATTTTGT
101592 A
1 A
101593 TTTTATTTTG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 11 0.61
19 7 0.39
ACGTcount: A:0.29, C:0.05, G:0.11, T:0.55
Consensus pattern (19 bp):
AATTAGACATTTATTTTGT
Found at i:101675 original size:31 final size:29
Alignment explanation
Indices: 101638--101718 Score: 99
Period size: 31 Copynumber: 2.7 Consensus size: 29
101628 AAATCAATTC
101638 AAATTTAAAGCAAATTTAAATTTAAAAAGAT
1 AAATTTAAA-CAAATTTAAATTTAAAAA-AT
* *
101669 AAATTTAAATTTAAGTTTAAATTTAAAAAAT
1 AAATTTAAA--CAAATTTAAATTTAAAAAAT
*
101700 AAATTTAAACCAATTTAAA
1 AAATTTAAACAAATTTAAA
101719 CCTAATTTAA
Statistics
Matches: 43, Mismatches: 6, Indels: 4
0.81 0.11 0.08
Matches are distributed among these distances:
29 7 0.16
31 20 0.47
32 16 0.37
ACGTcount: A:0.57, C:0.04, G:0.04, T:0.36
Consensus pattern (29 bp):
AAATTTAAACAAATTTAAATTTAAAAAAT
Found at i:101716 original size:10 final size:11
Alignment explanation
Indices: 101701--101729 Score: 51
Period size: 10 Copynumber: 2.7 Consensus size: 11
101691 TTAAAAAATA
101701 AATTTAAACC-
1 AATTTAAACCT
101711 AATTTAAACCT
1 AATTTAAACCT
101722 AATTTAAA
1 AATTTAAA
101730 ATCAAAAGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 10 0.56
11 8 0.44
ACGTcount: A:0.52, C:0.14, G:0.00, T:0.34
Consensus pattern (11 bp):
AATTTAAACCT
Found at i:104743 original size:194 final size:194
Alignment explanation
Indices: 104414--104803 Score: 762
Period size: 194 Copynumber: 2.0 Consensus size: 194
104404 GATGAGCATA
104414 GACACTTACGCAAGCAACCAATAATATCCTCATTAAGTATAGTCGAAATAGCATTTGAAAGAATC
1 GACACTTACGCAAGCAACCAATAATATCCTCATTAAGTATAGTCGAAATAGCATTTGAAAGAATC
*
104479 TCTCCCAAAAAGTAAAGATGAAAATGAGCATCAGAACTCATATGAGCTAGAAAATCTGCAACAAA
66 TCTCCCAAAAAGTAAAGATCAAAATGAGCATCAGAACTCATATGAGCTAGAAAATCTGCAACAAA
*
104544 CCTTCTCTGTACGCGTGCTTGATTTGTACTTCCCAAGCTCGGTCGCAAAGTTCCCTGATGCTTC
131 CCTTCTCTGTACGCGTGCTTGATTTGCACTTCCCAAGCTCGGTCGCAAAGTTCCCTGATGCTTC
104608 GACACTTACGCAAGCAACCAATAATATCCTCATTAAGTATAGTCGAAATAGCATTTGAAAGAATC
1 GACACTTACGCAAGCAACCAATAATATCCTCATTAAGTATAGTCGAAATAGCATTTGAAAGAATC
104673 TCTCCCAAAAAGTAAAGATCAAAATGAGCATCAGAACTCATATGAGCTAGAAAATCTGCAACAAA
66 TCTCCCAAAAAGTAAAGATCAAAATGAGCATCAGAACTCATATGAGCTAGAAAATCTGCAACAAA
104738 CCTTCTCTGTACGCGTGCTTGATTTGCACTTCCCAAGCTCGGTCGCAAAGTTCCCTGATGCTTC
131 CCTTCTCTGTACGCGTGCTTGATTTGCACTTCCCAAGCTCGGTCGCAAAGTTCCCTGATGCTTC
104802 GA
1 GA
104804 ACTAATGCAA
Statistics
Matches: 194, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
194 194 1.00
ACGTcount: A:0.35, C:0.24, G:0.16, T:0.25
Consensus pattern (194 bp):
GACACTTACGCAAGCAACCAATAATATCCTCATTAAGTATAGTCGAAATAGCATTTGAAAGAATC
TCTCCCAAAAAGTAAAGATCAAAATGAGCATCAGAACTCATATGAGCTAGAAAATCTGCAACAAA
CCTTCTCTGTACGCGTGCTTGATTTGCACTTCCCAAGCTCGGTCGCAAAGTTCCCTGATGCTTC
Found at i:117251 original size:18 final size:18
Alignment explanation
Indices: 117228--117267 Score: 71
Period size: 18 Copynumber: 2.2 Consensus size: 18
117218 CGGAAGGAAT
*
117228 AGCATACTGGCTCATTTG
1 AGCATACTGGCTCATATG
117246 AGCATACTGGCTCATATG
1 AGCATACTGGCTCATATG
117264 AGCA
1 AGCA
117268 ATATTGGATC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.28, C:0.23, G:0.23, T:0.28
Consensus pattern (18 bp):
AGCATACTGGCTCATATG
Found at i:120540 original size:79 final size:79
Alignment explanation
Indices: 120456--120611 Score: 197
Period size: 79 Copynumber: 2.0 Consensus size: 79
120446 CCATATCTAC
* * * * *
120456 ATTTTCAAAGTTGTTTTTATTGTTACGTGAATACATATACTTTTAAAATTTTAAAATGTCA-CAT
1 ATTTTCAAAGTTATTTTTATTATTACATGAATACATAAACTTTT-AAATTTTAAAATATCACCAT
*
120520 TGTGAATTTAACAAA
65 AGTGAATTTAACAAA
* * * * *
120535 ATTTTCAATGTTATTTTTATTATTACATGAATACCTAAAGTTTTTAATTTTAAAATATCACCCTA
1 ATTTTCAAAGTTATTTTTATTATTACATGAATACATAAACTTTTAAATTTTAAAATATCACCATA
120600 GTGAATTTAACA
66 GTGAATTTAACA
120612 GAAGAATTTT
Statistics
Matches: 65, Mismatches: 11, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
78 14 0.22
79 51 0.78
ACGTcount: A:0.37, C:0.10, G:0.08, T:0.45
Consensus pattern (79 bp):
ATTTTCAAAGTTATTTTTATTATTACATGAATACATAAACTTTTAAATTTTAAAATATCACCATA
GTGAATTTAACAAA
Found at i:135478 original size:31 final size:31
Alignment explanation
Indices: 135441--135499 Score: 109
Period size: 31 Copynumber: 1.9 Consensus size: 31
135431 TTAGACACTG
135441 TTATTATATACTTTTATCATTTTAATCATTA
1 TTATTATATACTTTTATCATTTTAATCATTA
*
135472 TTATTATATACTTTTATTATTTTAATCA
1 TTATTATATACTTTTATCATTTTAATCA
135500 CTCACCATTA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.32, C:0.08, G:0.00, T:0.59
Consensus pattern (31 bp):
TTATTATATACTTTTATCATTTTAATCATTA
Found at i:136946 original size:13 final size:13
Alignment explanation
Indices: 136928--136952 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
136918 CTTTTGAAAA
136928 TATGTTTATGAGG
1 TATGTTTATGAGG
136941 TATGTTTATGAG
1 TATGTTTATGAG
136953 CAGATTTATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.00, G:0.28, T:0.48
Consensus pattern (13 bp):
TATGTTTATGAGG
Found at i:137150 original size:20 final size:19
Alignment explanation
Indices: 137117--137175 Score: 55
Period size: 20 Copynumber: 3.0 Consensus size: 19
137107 GAAACAATAA
* *
137117 AAAAATGTTCCAATCTATTT
1 AAAAAGGTTTCAATC-ATTT
*
137137 GAAAAGGTTTCAATCGATTT
1 AAAAAGGTTTCAATC-ATTT
* *
137157 AAAAATGTTTGAATCATTT
1 AAAAAGGTTTCAATCATTT
137176 TTGAATTTTG
Statistics
Matches: 32, Mismatches: 7, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
19 4 0.12
20 28 0.88
ACGTcount: A:0.39, C:0.10, G:0.12, T:0.39
Consensus pattern (19 bp):
AAAAAGGTTTCAATCATTT
Found at i:137236 original size:20 final size:19
Alignment explanation
Indices: 137188--137237 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 19
137178 GAATTTTGAC
137188 CAAAATTTTTCTAAGTGTT
1 CAAAATTTTTCTAAGTGTT
*
137207 CAAAATATTTTTTAAGATGTTT
1 CAAAAT-TTTTCTAAG-TG-TT
137229 CAAAATTTT
1 CAAAATTTT
137238 GAAATGATTT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
19 6 0.22
20 8 0.30
21 5 0.19
22 8 0.30
ACGTcount: A:0.36, C:0.08, G:0.08, T:0.48
Consensus pattern (19 bp):
CAAAATTTTTCTAAGTGTT
Found at i:139733 original size:22 final size:22
Alignment explanation
Indices: 139707--139748 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
139697 AAAATTGCCC
139707 AAATTACTCAGAATCCAAATTT
1 AAATTACTCAGAATCCAAATTT
* * *
139729 AAATTATTCATAATTCAAAT
1 AAATTACTCAGAATCCAAAT
139749 ATTCATCTAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.48, C:0.14, G:0.02, T:0.36
Consensus pattern (22 bp):
AAATTACTCAGAATCCAAATTT
Found at i:140185 original size:22 final size:22
Alignment explanation
Indices: 140155--140199 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
140145 ATATTTGAGA
*
140155 TTTAATCTT-TCTTATTTTTATT
1 TTTAATCTTCACTT-TTTTTATT
*
140177 TTTAGTCTTCACTTTTTTTATT
1 TTTAATCTTCACTTTTTTTATT
140199 T
1 T
140200 AGTGGGAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 17 0.85
23 3 0.15
ACGTcount: A:0.16, C:0.11, G:0.02, T:0.71
Consensus pattern (22 bp):
TTTAATCTTCACTTTTTTTATT
Found at i:140433 original size:44 final size:45
Alignment explanation
Indices: 140365--140461 Score: 178
Period size: 44 Copynumber: 2.2 Consensus size: 45
140355 GTACCTTTTG
140365 TATATGAATTTGTGGCGTTGTGGTTGGAATACACTTAAAGAGCAA
1 TATATGAATTTGTGGCGTTGTGGTTGGAATACACTTAAAGAGCAA
*
140410 TATA-GAATTTGTGGCGTTGTGGTTGGAATGCACTTAAAGAGCAA
1 TATATGAATTTGTGGCGTTGTGGTTGGAATACACTTAAAGAGCAA
140454 TATATGAA
1 TATATGAA
140462 ATCTAACAAC
Statistics
Matches: 50, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
44 43 0.86
45 7 0.14
ACGTcount: A:0.32, C:0.08, G:0.27, T:0.33
Consensus pattern (45 bp):
TATATGAATTTGTGGCGTTGTGGTTGGAATACACTTAAAGAGCAA
Found at i:141584 original size:18 final size:18
Alignment explanation
Indices: 141561--141596 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
141551 ACTATCGAAG
141561 TAAGCTTATAATTTGTCT
1 TAAGCTTATAATTTGTCT
141579 TAAGCTTATAATTTGTCT
1 TAAGCTTATAATTTGTCT
141597 CATAACTTGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.28, C:0.11, G:0.11, T:0.50
Consensus pattern (18 bp):
TAAGCTTATAATTTGTCT
Found at i:150787 original size:10 final size:10
Alignment explanation
Indices: 150772--150800 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
150762 CTAAGTGTTC
150772 TAAACTAAAT
1 TAAACTAAAT
150782 TAAACTAAAT
1 TAAACTAAAT
150792 TAAACTAAA
1 TAAACTAAA
150801 ACTAAATTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.62, C:0.10, G:0.00, T:0.28
Consensus pattern (10 bp):
TAAACTAAAT
Found at i:151518 original size:12 final size:12
Alignment explanation
Indices: 151501--151525 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
151491 ATTAAATAAT
151501 TAATAGCATTCA
1 TAATAGCATTCA
151513 TAATAGCATTCA
1 TAATAGCATTCA
151525 T
1 T
151526 CATAATAACA
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:0.40, C:0.16, G:0.08, T:0.36
Consensus pattern (12 bp):
TAATAGCATTCA
Found at i:153603 original size:2 final size:2
Alignment explanation
Indices: 153596--153625 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
153586 CATGCACCCC
153596 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
153626 CACACTCCAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:159650 original size:23 final size:23
Alignment explanation
Indices: 159620--159695 Score: 75
Period size: 23 Copynumber: 3.3 Consensus size: 23
159610 GATTTACAGC
159620 TCACATGTAAAATTGAATAATCA
1 TCACATGTAAAATTGAATAATCA
** * * *
159643 TCACATGT-TTATTACAACAGTC-
1 TCACATGTAAAATT-GAATAATCA
*
159665 TCACATGTAAAACTGAATAATCA
1 TCACATGTAAAATTGAATAATCA
159688 TCACATGT
1 TCACATGT
159696 TTATTACAAC
Statistics
Matches: 39, Mismatches: 11, Indels: 6
0.70 0.20 0.11
Matches are distributed among these distances:
22 16 0.41
23 23 0.59
ACGTcount: A:0.41, C:0.18, G:0.09, T:0.32
Consensus pattern (23 bp):
TCACATGTAAAATTGAATAATCA
Found at i:159668 original size:45 final size:45
Alignment explanation
Indices: 159615--159719 Score: 178
Period size: 45 Copynumber: 2.4 Consensus size: 45
159605 AGGCCGATTT
*
159615 ACAG-CTCACATGTAAAATTGAATAATCATCACATGTTTATTACA
1 ACAGTCTCACATGTAAAACTGAATAATCATCACATGTTTATTACA
159659 ACAGTCTCACATGTAAAACTGAATAATCATCACATGTTTATTACA
1 ACAGTCTCACATGTAAAACTGAATAATCATCACATGTTTATTACA
159704 ACAGT-TGCACATGTAA
1 ACAGTCT-CACATGTAA
159720 TATTATTAAC
Statistics
Matches: 58, Mismatches: 1, Indels: 3
0.94 0.02 0.05
Matches are distributed among these distances:
44 5 0.09
45 53 0.91
ACGTcount: A:0.40, C:0.19, G:0.10, T:0.30
Consensus pattern (45 bp):
ACAGTCTCACATGTAAAACTGAATAATCATCACATGTTTATTACA
Found at i:165426 original size:13 final size:13
Alignment explanation
Indices: 165408--165437 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
165398 ACCTATCAAG
165408 ATTTATTAAAAAA
1 ATTTATTAAAAAA
*
165421 ATTTATTAAAAGA
1 ATTTATTAAAAAA
165434 ATTT
1 ATTT
165438 TGGTCATTGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.43
Consensus pattern (13 bp):
ATTTATTAAAAAA
Found at i:165983 original size:31 final size:31
Alignment explanation
Indices: 165945--166042 Score: 100
Period size: 31 Copynumber: 3.3 Consensus size: 31
165935 TACATAATAA
165945 AAAATAATACATATACCAAATACAATAAAAT
1 AAAATAATACATATACCAAATACAATAAAAT
* *
165976 --AA-AATA-ATATA-CATATGCACATAATAA-
1 AAAATAATACATATACCAAATACA-ATAA-AAT
*
166003 AAAATAATACATATACAAAATACAATAAAAT
1 AAAATAATACATATACCAAATACAATAAAAT
*
166034 AACATAATA
1 AAAATAATA
166043 TACATATGCA
Statistics
Matches: 53, Mismatches: 6, Indels: 16
0.71 0.08 0.21
Matches are distributed among these distances:
26 6 0.11
27 9 0.17
28 6 0.11
29 4 0.08
30 6 0.11
31 17 0.32
32 5 0.09
ACGTcount: A:0.64, C:0.11, G:0.01, T:0.23
Consensus pattern (31 bp):
AAAATAATACATATACCAAATACAATAAAAT
Found at i:165985 original size:27 final size:28
Alignment explanation
Indices: 165940--166032 Score: 102
Period size: 28 Copynumber: 3.2 Consensus size: 28
165930 AAGTATACAT
165940 AATAAAAAATAATACATATACCAAATAC
1 AATAAAAAATAATACATATACCAAATAC
*
165968 AATAAAATAA-AATA-ATATA-CATATGCAC
1 AATAAAA-AATAATACATATACCAAAT--AC
*
165996 ATAATAAAAAATAATACATATACAAAATAC
1 --AATAAAAAATAATACATATACCAAATAC
166026 AATAAAA
1 AATAAAA
166033 TAACATAATA
Statistics
Matches: 54, Mismatches: 3, Indels: 16
0.74 0.04 0.22
Matches are distributed among these distances:
26 4 0.07
27 5 0.09
28 20 0.37
29 4 0.07
30 13 0.24
31 5 0.09
32 3 0.06
ACGTcount: A:0.66, C:0.11, G:0.01, T:0.23
Consensus pattern (28 bp):
AATAAAAAATAATACATATACCAAATAC
Found at i:166000 original size:58 final size:58
Alignment explanation
Indices: 165936--166057 Score: 217
Period size: 58 Copynumber: 2.1 Consensus size: 58
165926 TTACAAGTAT
*
165936 ACATAATAAAAAATAATACATATACCAAATACAATAAAATAAAATAATATACATATGC
1 ACATAATAAAAAATAATACATATACAAAATACAATAAAATAAAATAATATACATATGC
*
165994 ACATAATAAAAAATAATACATATACAAAATACAATAAAATAACATAATATACATATGC
1 ACATAATAAAAAATAATACATATACAAAATACAATAAAATAAAATAATATACATATGC
*
166052 ATATAA
1 ACATAA
166058 AAATGTGTTA
Statistics
Matches: 61, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
58 61 1.00
ACGTcount: A:0.62, C:0.11, G:0.02, T:0.25
Consensus pattern (58 bp):
ACATAATAAAAAATAATACATATACAAAATACAATAAAATAAAATAATATACATATGC
Found at i:166043 original size:27 final size:27
Alignment explanation
Indices: 165940--166046 Score: 94
Period size: 28 Copynumber: 3.8 Consensus size: 27
165930 AAGTATACAT
*
165940 AATAAAA-AATAATACATATACCAAATAC
1 AATAAAATAA-AATA-ATATACAAAATAC
*
165968 AATAAAATAAAATAATATAC-ATATGCAC
1 AATAAAATAAAATAATATACAAAAT--AC
165996 ATAATAAAA-AATAATACATATACAAAATAC
1 --AATAAAATAA-AATA-ATATACAAAATAC
*
166026 AATAAAATAACATAATATACA
1 AATAAAATAAAATAATATACA
166047 TATGCATATA
Statistics
Matches: 67, Mismatches: 3, Indels: 19
0.75 0.03 0.21
Matches are distributed among these distances:
26 3 0.04
27 13 0.19
28 23 0.34
29 6 0.09
30 13 0.19
31 6 0.09
32 3 0.04
ACGTcount: A:0.64, C:0.11, G:0.01, T:0.23
Consensus pattern (27 bp):
AATAAAATAAAATAATATACAAAATAC
Found at i:166057 original size:27 final size:27
Alignment explanation
Indices: 165969--166059 Score: 87
Period size: 27 Copynumber: 3.2 Consensus size: 27
165959 ACCAAATACA
165969 ATAAAATAAAATAATATACATATGCACAT
1 ATAAAATAAAATAATATACATATG--CAT
* *
165998 AATAAAA-AATAATACATATACAAAATACA-
1 -ATAAAATAA-AATA-ATATAC-ATATGCAT
*
166027 ATAAAATAACATAATATACATATGCAT
1 ATAAAATAAAATAATATACATATGCAT
166054 ATAAAA
1 ATAAAA
166060 ATGTGTTAAA
Statistics
Matches: 51, Mismatches: 5, Indels: 13
0.74 0.07 0.19
Matches are distributed among these distances:
26 5 0.10
27 12 0.24
28 9 0.18
29 4 0.08
30 12 0.24
31 6 0.12
32 3 0.06
ACGTcount: A:0.63, C:0.10, G:0.02, T:0.25
Consensus pattern (27 bp):
ATAAAATAAAATAATATACATATGCAT
Found at i:166125 original size:30 final size:30
Alignment explanation
Indices: 166091--166268 Score: 171
Period size: 30 Copynumber: 5.9 Consensus size: 30
166081 CATTAAAATT
* *
166091 GGGTCAAATTTAAATTTTT-GAAAACCTAAG
1 GGGTCAAATTTAAATTTTTGGAAAA-TTTAG
** * * *
166121 GGGTCAAATCAAAATTTTTGGAAAGTGTGG
1 GGGTCAAATTTAAATTTTTGGAAAATTTAG
* * *
166151 GGGCCAAATTTAAATTTTTAGAAAATTTGG
1 GGGTCAAATTTAAATTTTTGGAAAATTTAG
* *
166181 GGGCCAAATTTGAATTTTTGGAAAATTTAG
1 GGGTCAAATTTAAATTTTTGGAAAATTTAG
* *
166211 GGGTCAAATTCAAATTTTTGGAAAATTTAA
1 GGGTCAAATTTAAATTTTTGGAAAATTTAG
* * *
166241 AGGTCAAA-ATATAATTTTTAGAAAATTT
1 GGGTCAAATTTA-AATTTTTGGAAAATTT
166269 GGGATCACAA
Statistics
Matches: 122, Mismatches: 24, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
29 1 0.01
30 117 0.96
31 4 0.03
ACGTcount: A:0.38, C:0.07, G:0.20, T:0.35
Consensus pattern (30 bp):
GGGTCAAATTTAAATTTTTGGAAAATTTAG
Found at i:166281 original size:30 final size:30
Alignment explanation
Indices: 166163--166286 Score: 112
Period size: 30 Copynumber: 4.2 Consensus size: 30
166153 GCCAAATTTA
* * *
166163 AATTTTTAGAAAATTT-GGGGGCCAAATTT
1 AATTTTTAGAAAATTTAGGGGTCAAAATAT
* *
166192 GAATTTTTGGAAAATTTAGGGGTCAAATTCA-
1 -AATTTTTAGAAAATTTAGGGGTCAAAAT-AT
* **
166223 AATTTTTGGAAAATTTAAAGGTCAAAATAT
1 AATTTTTAGAAAATTTAGGGGTCAAAATAT
* *
166253 AATTTTTAGAAAATTT-GGGATCACAA-AT
1 AATTTTTAGAAAATTTAGGGGTCAAAATAT
166281 AATTTT
1 AATTTT
166287 AAATAAAGTA
Statistics
Matches: 78, Mismatches: 13, Indels: 8
0.79 0.13 0.08
Matches are distributed among these distances:
28 8 0.10
29 7 0.09
30 55 0.71
31 8 0.10
ACGTcount: A:0.40, C:0.06, G:0.17, T:0.38
Consensus pattern (30 bp):
AATTTTTAGAAAATTTAGGGGTCAAAATAT
Found at i:168111 original size:40 final size:38
Alignment explanation
Indices: 167988--168166 Score: 134
Period size: 39 Copynumber: 4.6 Consensus size: 38
167978 ATATCTTTAG
* *
167988 GGGTAAAAGA-TGATAGTCTTCAAACTGCCCTCTAGTTA
1 GGGTAAAAGATTGAT-GTCTTCAATCTGCCCTCTGGTTA
* * *
168026 GGGTAAAAGATTGGAT-TACTTCAATCTATCCC-ATGGTCA
1 GGGTAAAAGATT-GATGT-CTTCAATCT-GCCCTCTGGTTA
168065 GGGTAAAAGATCTGATGGTCTTCAATCTGCCCTCTGGTTA
1 GGGTAAAAGAT-TGAT-GTCTTCAATCTGCCCTCTGGTTA
* * **
168105 GAGTAAAAGATTGGAT-TGCTTTAATCTGCCC-CATGGTCG
1 GGGTAAAAGATT-GATGT-CTTCAATCTGCCCTC-TGGTTA
*
168144 GGGTAAGAGATTGAATTGTCTTC
1 GGGTAAAAGATTG-A-TGTCTTC
168167 GTTCCATTTC
Statistics
Matches: 112, Mismatches: 15, Indels: 26
0.73 0.10 0.17
Matches are distributed among these distances:
38 14 0.12
39 58 0.52
40 38 0.34
41 2 0.02
ACGTcount: A:0.27, C:0.17, G:0.24, T:0.31
Consensus pattern (38 bp):
GGGTAAAAGATTGATGTCTTCAATCTGCCCTCTGGTTA
Found at i:168117 original size:79 final size:78
Alignment explanation
Indices: 167988--168166 Score: 234
Period size: 79 Copynumber: 2.3 Consensus size: 78
167978 ATATCTTTAG
*
167988 GGGTAAAAGA-TGATAGTCTTCAAACTGCCCTCTAGTTAGGGTAAAAGATTGGATTACTTCAATC
1 GGGTAAAAGATTGATAGTCTTCAAACTGCCCTCTAGTTAGAGTAAAAGATTGGATTACTTCAATC
*
168052 TATCCCATGGTCA
66 TACCCCATGGTCA
* * * * *
168065 GGGTAAAAGATCTGATGGTCTTCAATCTGCCCTCTGGTTAGAGTAAAAGATTGGATTGCTTTAAT
1 GGGTAAAAGAT-TGATAGTCTTCAAACTGCCCTCTAGTTAGAGTAAAAGATTGGATTACTTCAAT
* *
168130 CTGCCCCATGGTCG
65 CTACCCCATGGTCA
* *
168144 GGGTAAGAGATTGAATTGTCTTC
1 GGGTAAAAGATTG-ATAGTCTTC
168167 GTTCCATTTC
Statistics
Matches: 88, Mismatches: 11, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
77 10 0.11
78 2 0.02
79 76 0.86
ACGTcount: A:0.27, C:0.17, G:0.24, T:0.31
Consensus pattern (78 bp):
GGGTAAAAGATTGATAGTCTTCAAACTGCCCTCTAGTTAGAGTAAAAGATTGGATTACTTCAATC
TACCCCATGGTCA
Found at i:168155 original size:39 final size:39
Alignment explanation
Indices: 168025--168166 Score: 144
Period size: 39 Copynumber: 3.6 Consensus size: 39
168015 CCCTCTAGTT
* **
168025 AGGGTAAAAGATTGGATTACTTCAATCTATCCCATGGTC
1 AGGGTAAAAGATTGGATTGCTTCAATCTGCCCCATGGTC
* *
168064 AGGGTAAAAGATCT-GATGGTCTTCAATCTGCCCTC-TGGTT
1 AGGGTAAAAGAT-TGGATTG-CTTCAATCTGCCC-CATGGTC
* *
168104 AGAGTAAAAGATTGGATTGCTTTAATCTGCCCCATGGTC
1 AGGGTAAAAGATTGGATTGCTTCAATCTGCCCCATGGTC
* * *
168143 GGGGTAAGAGATTGAATTGTCTTC
1 AGGGTAAAAGATTGGATTG-CTTC
168167 GTTCCATTTC
Statistics
Matches: 83, Mismatches: 14, Indels: 11
0.77 0.13 0.10
Matches are distributed among these distances:
38 1 0.01
39 47 0.57
40 34 0.41
41 1 0.01
ACGTcount: A:0.27, C:0.17, G:0.25, T:0.32
Consensus pattern (39 bp):
AGGGTAAAAGATTGGATTGCTTCAATCTGCCCCATGGTC
Found at i:168256 original size:50 final size:50
Alignment explanation
Indices: 168189--168296 Score: 146
Period size: 50 Copynumber: 2.2 Consensus size: 50
168179 CTTTAGGAAT
*
168189 ATAAGATTCATCCTTGCGACTTCAATCTGCCCCTATACAGCTTTAGGTGA
1 ATAAGATTCATCCTTGCGACTTCAATCTACCCCTATACAGCTTTAGGTGA
* * * * *
168239 ATGAGATTCA-CCATTGCGATTTCAATCTACCCCTCTATAGCTTTAGGTGC
1 ATAAGATTCATCC-TTGCGACTTCAATCTACCCCTATACAGCTTTAGGTGA
168289 ATAAGATT
1 ATAAGATT
168297 TTCCATTACA
Statistics
Matches: 50, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
49 2 0.04
50 48 0.96
ACGTcount: A:0.27, C:0.24, G:0.16, T:0.33
Consensus pattern (50 bp):
ATAAGATTCATCCTTGCGACTTCAATCTACCCCTATACAGCTTTAGGTGA
Found at i:168313 original size:50 final size:50
Alignment explanation
Indices: 168189--168315 Score: 132
Period size: 50 Copynumber: 2.5 Consensus size: 50
168179 CTTTAGGAAT
* *
168189 ATAAGATTCATCC-TTGCGACTTCAATCTGCCCCTATACAGCTTTAGGTGA
1 ATAAGATTCA-CCATTACGACTTCAATCTACCCCTATACAGCTTTAGGTGA
* * * * * *
168239 ATGAGATTCACCATTGCGATTTCAATCTACCCCTCTATAGCTTTAGGTGC
1 ATAAGATTCACCATTACGACTTCAATCTACCCCTATACAGCTTTAGGTGA
**
168289 ATAAGATTTTCCATTAC-AGCTTCAATC
1 ATAAGATTCACCATTACGA-CTTCAATC
168316 CGTTCCTTTA
Statistics
Matches: 64, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
49 3 0.05
50 61 0.95
ACGTcount: A:0.27, C:0.25, G:0.14, T:0.34
Consensus pattern (50 bp):
ATAAGATTCACCATTACGACTTCAATCTACCCCTATACAGCTTTAGGTGA
Found at i:175483 original size:31 final size:31
Alignment explanation
Indices: 175448--175506 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
175438 ATTTTAATGC
175448 ATGAAAATGCGATGCAAAACTTTATGAATAT
1 ATGAAAATGCGATGCAAAACTTTATGAATAT
* *
175479 ATGAAAATGCGATGCGAAATTTTATGAA
1 ATGAAAATGCGATGCAAAACTTTATGAA
175507 CGCATGAATG
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:0.44, C:0.08, G:0.19, T:0.29
Consensus pattern (31 bp):
ATGAAAATGCGATGCAAAACTTTATGAATAT
Found at i:175514 original size:31 final size:31
Alignment explanation
Indices: 175446--175514 Score: 93
Period size: 31 Copynumber: 2.2 Consensus size: 31
175436 AAATTTTAAT
*
175446 GCATGAAAATGCGATGCAAAACTTTATGAAT
1 GCATGAAAATGCGATGCAAAACTTTATGAAC
** * *
175477 ATATGAAAATGCGATGCGAAATTTTATGAAC
1 GCATGAAAATGCGATGCAAAACTTTATGAAC
175508 GCATGAA
1 GCATGAA
175515 TGCATATGCA
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.42, C:0.12, G:0.20, T:0.26
Consensus pattern (31 bp):
GCATGAAAATGCGATGCAAAACTTTATGAAC
Found at i:177488 original size:31 final size:30
Alignment explanation
Indices: 177439--177547 Score: 84
Period size: 31 Copynumber: 3.7 Consensus size: 30
177429 ATTTATAAAT
177439 ATACATAATAA-AAAATAATACATACACAAA
1 ATACATAA-AATAAAATAATACATACACAAA
* *
177469 ATACATTAAAATAAAATAAT--ATACA-TAT
1 ATACA-TAAAATAAAATAATACATACACAAA
** **
177497 GCACATAATAA-AAAATAATACATATGCAAA
1 ATACATAA-AATAAAATAATACATACACAAA
*
177527 ATACAATAAAATAACATAATA
1 ATAC-ATAAAATAAAATAATA
177548 TACATATGCA
Statistics
Matches: 60, Mismatches: 11, Indels: 15
0.70 0.13 0.17
Matches are distributed among these distances:
27 11 0.18
28 6 0.10
29 8 0.13
30 12 0.20
31 23 0.38
ACGTcount: A:0.63, C:0.11, G:0.02, T:0.24
Consensus pattern (30 bp):
ATACATAAAATAAAATAATACATACACAAA
Found at i:177510 original size:58 final size:58
Alignment explanation
Indices: 177441--177566 Score: 200
Period size: 58 Copynumber: 2.2 Consensus size: 58
177431 TTATAAATAT
*
177441 ACATAATAAAAAATAATACATACACAAAATACATTAAAATAAAATAATATACATATGC
1 ACATAATAAAAAATAATACATACACAAAATACAATAAAATAAAATAATATACATATGC
** *
177499 ACATAATAAAAAATAATACATATGCAAAATACAATAAAATAACATAATATACATATGC
1 ACATAATAAAAAATAATACATACACAAAATACAATAAAATAAAATAATATACATATGC
*
177557 ATATAA-AAAA
1 ACATAATAAAA
177567 GATATTAAAT
Statistics
Matches: 63, Mismatches: 5, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
57 4 0.06
58 59 0.94
ACGTcount: A:0.63, C:0.11, G:0.02, T:0.24
Consensus pattern (58 bp):
ACATAATAAAAAATAATACATACACAAAATACAATAAAATAAAATAATATACATATGC
Found at i:177514 original size:27 final size:27
Alignment explanation
Indices: 177481--177566 Score: 79
Period size: 25 Copynumber: 3.1 Consensus size: 27
177471 ACATTAAAAT
*
177481 AAAATAATATACATATGCACATAATAA
1 AAAATAATATACATATGCAAATAATAA
177508 AAAAT-A-ATACATATGCAAAATACAATAAA
1 AAAATAATATACATATGC-AAAT--AAT-AA
*
177537 ATAACATAATATACATATGCATATAA-AA
1 A-AA-ATAATATACATATGCAAATAATAA
177565 AA
1 AA
177567 GATATTAAAT
Statistics
Matches: 49, Mismatches: 2, Indels: 16
0.73 0.03 0.24
Matches are distributed among these distances:
25 10 0.20
26 4 0.08
27 6 0.12
28 6 0.12
29 3 0.06
30 4 0.08
31 2 0.04
32 4 0.08
33 10 0.20
ACGTcount: A:0.62, C:0.10, G:0.03, T:0.24
Consensus pattern (27 bp):
AAAATAATATACATATGCAAATAATAA
Found at i:177695 original size:30 final size:30
Alignment explanation
Indices: 177608--177695 Score: 90
Period size: 30 Copynumber: 2.9 Consensus size: 30
177598 ATCAAATTTG
* * *
177608 AATTTTTGAAAACTTCAAGTGTCAAA-TCAA
1 AATTTTGGAAAACTT-GAGGGTCAAATTCAA
*
177638 AATTTTTGGAAAA-TGTGGGGGTCAAATTCAA
1 AA-TTTTGGAAAACT-TGAGGGTCAAATTCAA
*
177669 AATTTTGGAAAACTTGAGGGTTAAATT
1 AATTTTGGAAAACTTGAGGGTCAAATT
177696 TGAATTTTTA
Statistics
Matches: 48, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
30 31 0.65
31 17 0.35
ACGTcount: A:0.39, C:0.08, G:0.19, T:0.34
Consensus pattern (30 bp):
AATTTTGGAAAACTTGAGGGTCAAATTCAA
Found at i:184494 original size:20 final size:18
Alignment explanation
Indices: 184447--184531 Score: 61
Period size: 18 Copynumber: 4.7 Consensus size: 18
184437 CAAGATAAAC
184447 ATTAAATT-ATATTTAAT
1 ATTAAATTAATATTTAAT
184464 ATT-AATATAATCACTTTAAT
1 ATTAAAT-TAAT-A-TTTAAT
** *
184484 ATTAAATTAATAAATACT
1 ATTAAATTAATATTTAAT
*
184502 ATTAAAATAAGTA-TTAA-
1 ATTAAATTAA-TATTTAAT
184519 ATTAAATTTAATA
1 ATTAAA-TTAATA
184532 CTATTTTTGG
Statistics
Matches: 54, Mismatches: 7, Indels: 14
0.72 0.09 0.19
Matches are distributed among these distances:
16 3 0.06
17 12 0.22
18 19 0.35
19 4 0.07
20 13 0.24
21 3 0.06
ACGTcount: A:0.52, C:0.04, G:0.01, T:0.44
Consensus pattern (18 bp):
ATTAAATTAATATTTAAT
Found at i:188783 original size:183 final size:183
Alignment explanation
Indices: 188510--188870 Score: 481
Period size: 183 Copynumber: 2.0 Consensus size: 183
188500 ACACGGGTGA
* * * * * *
188510 ACTAAACCACACTAGATAGCTCGTATGAGCTTAAACTACACCAGACCAAGACACCAAAGTGCAAA
1 ACTAAACCACACCAAATAGCTCGTATGAGCCTAAAATACACCACAACAAGACACCAAAGTGCAAA
* * *
188575 GCCCGTAGATATCAAATGATTAAACATTTTCAATTACATCCTTCCACCACATCAAAGTCTCCATA
66 GCCCGTAGATATCAAATGATTAAACATTTTCAATTACATCCCTCCACAACACCAAAGTCTCCATA
* * *
188640 GAGACAAAGAGCACTCGACGATCCATAACAAATGCTAGATCTTGATATTCTTC
131 GAAACAAAGAACACTCGACGATCCACAACAAATGCTAGATCTTGATATTCTTC
* * *
188693 ACTACACCACACCAAATAGCTCGTATGAGCCTAAAATACATCACAACAAGGCACCAAAGTGCAAA
1 ACTAAACCACACCAAATAGCTCGTATGAGCCTAAAATACACCACAACAAGACACCAAAGTGCAAA
* * * **
188758 GCCTGTAG-TCATTAAATGTTTAAACATTTTCAATTATGTCCCTCCACAACACCAAAGTCTCCAT
66 GCCCGTAGAT-ATCAAATGATTAAACATTTTCAATTACATCCCTCCACAACACCAAAGTCTCCAT
* * * * *
188822 AGAAACAAATAATACTTGATGATCCGCAACAAATGCTAGATCTTGATAT
130 AGAAACAAAGAACACTCGACGATCCACAACAAATGCTAGATCTTGATAT
188871 AACCTATCAT
Statistics
Matches: 152, Mismatches: 25, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
182 1 0.01
183 151 0.99
ACGTcount: A:0.39, C:0.25, G:0.12, T:0.24
Consensus pattern (183 bp):
ACTAAACCACACCAAATAGCTCGTATGAGCCTAAAATACACCACAACAAGACACCAAAGTGCAAA
GCCCGTAGATATCAAATGATTAAACATTTTCAATTACATCCCTCCACAACACCAAAGTCTCCATA
GAAACAAAGAACACTCGACGATCCACAACAAATGCTAGATCTTGATATTCTTC
Found at i:191483 original size:21 final size:21
Alignment explanation
Indices: 191459--191500 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
191449 TTGGTGGTTC
*
191459 CTTAAAAGCTCCTTCTATATA
1 CTTAAAAGCTCATTCTATATA
191480 CTTAAAAGCTCATTCTATATA
1 CTTAAAAGCTCATTCTATATA
191501 TGTATACTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.36, C:0.21, G:0.05, T:0.38
Consensus pattern (21 bp):
CTTAAAAGCTCATTCTATATA
Found at i:192697 original size:29 final size:29
Alignment explanation
Indices: 192637--192826 Score: 108
Period size: 29 Copynumber: 6.6 Consensus size: 29
192627 CAAATGGAGT
* *
192637 TAAAAT-ATGATTTTTGGATGC-CGAGGG
1 TAAAATGATAATTTTTGGATGCTTGAGGG
* *
192664 CAAAATGATAATTTTTGGAGGCTTGAGGG
1 TAAAATGATAATTTTTGGATGCTTGAGGG
* * ** ** **
192693 TAAAACGGTAATTTTCAGACACCCGAGGG
1 TAAAATGATAATTTTTGGATGCTTGAGGG
* *
192722 TAAAAT-AGTAATTTTTGGAAAGTTTG-GGG
1 TAAAATGA-TAATTTTTGG-ATGCTTGAGGG
*
192751 TTAAAATGGTAATTTTTGGA--CATTCGAGGG
1 -TAAAATGATAATTTTTGGATGC-TT-GAGGG
* *
192781 TAAAACGGTAATTTTTGGATG-TTCG-GGG
1 TAAAATGATAATTTTTGGATGCTT-GAGGG
192809 ATAAAATGATAATTTTTG
1 -TAAAATGATAATTTTTG
192827 AAAAGTTTGA
Statistics
Matches: 124, Mismatches: 27, Indels: 22
0.72 0.16 0.13
Matches are distributed among these distances:
27 5 0.04
28 18 0.15
29 80 0.65
30 21 0.17
ACGTcount: A:0.32, C:0.07, G:0.27, T:0.34
Consensus pattern (29 bp):
TAAAATGATAATTTTTGGATGCTTGAGGG
Found at i:192763 original size:30 final size:30
Alignment explanation
Indices: 192722--193095 Score: 228
Period size: 29 Copynumber: 12.8 Consensus size: 30
192712 CACCCGAGGG
*
192722 TAAAATAGTAATTTTTGGAAAGTTTGGGGT
1 TAAAATGGTAATTTTTGGAAAGTTTGGGGT
* *
192752 TAAAATGGTAATTTTTGGACA-TTCGAGGG-
1 TAAAATGGTAATTTTTGGAAAGTTTG-GGGT
* * * *
192781 TAAAACGGTAATTTTTGG-ATGTTCGGGGA
1 TAAAATGGTAATTTTTGGAAAGTTTGGGGT
* * *
192810 TAAAATGATAATTTTTGAAAAGTTTGAGGT
1 TAAAATGGTAATTTTTGGAAAGTTTGGGGT
* * * * **
192840 CAAAAAT-GTATTTTTTTGACA-TTCAAGGG-
1 -TAAAATGGTAATTTTTGGAAAGTT-TGGGGT
* * *
192869 TAAAATGGTAA-TTTTGG-ATGTTCGGGGA
1 TAAAATGGTAATTTTTGGAAAGTTTGGGGT
192897 TAAAATGGTAATTTTTGGAAA-TTTGGGGT
1 TAAAATGGTAATTTTTGGAAAGTTTGGGGT
* * * *
192926 AAAAATATGT--TTTTTGG-AAGTTCGAGGGC
1 TAAAAT-GGTAATTTTTGGAAAGTTTG-GGGT
* *
192955 AAAAATGG-AATTTTTGG-AAGTTTGGGGGC
1 TAAAATGGTAATTTTTGGAAAGTTT-GGGGT
* * *
192984 AAAAAT-GTGATTTTTGAAAAGTTTAGGGG-
1 TAAAATGGTAATTTTTGGAAAGTTT-GGGGT
* *
193013 TCAAAT-GTAATTTTTGGAAAGTTTTAGGGT
1 TAAAATGGTAATTTTTGGAAAG-TTTGGGGT
* *
193043 TAAAAT-ATAATTTTTGGAAAGTTTAAGGGT
1 TAAAATGGTAATTTTTGGAAAGTTT-GGGGT
* *
193073 CAAAAT-GTAATTTTTGGATAGTT
1 TAAAATGGTAATTTTTGGAAAGTT
193096 CAAGAACCTT
Statistics
Matches: 271, Mismatches: 51, Indels: 44
0.74 0.14 0.12
Matches are distributed among these distances:
27 5 0.02
28 38 0.14
29 122 0.45
30 101 0.37
31 5 0.02
ACGTcount: A:0.33, C:0.03, G:0.26, T:0.38
Consensus pattern (30 bp):
TAAAATGGTAATTTTTGGAAAGTTTGGGGT
Found at i:192779 original size:59 final size:59
Alignment explanation
Indices: 192716--193095 Score: 270
Period size: 59 Copynumber: 6.5 Consensus size: 59
192706 TTCAGACACC
*
192716 CGAGGGTAAAATAGTAATTTTTGGAAAGTTTGGGGTTAAAATGGTAATTTTTGGACA-TT
1 CGAGGGTAAAAT-GTAATTTTTGGAAAGTTTGGGGTTAAAATGGTAATTTTTGGAAAGTT
* * * * * *
192775 CGAGGGTAAAACGGTAATTTTTGG-ATGTTCGGGGATAAAATGATAATTTTTGAAAAGTT
1 CGAGGGTAAAA-TGTAATTTTTGGAAAGTTTGGGGTTAAAATGGTAATTTTTGGAAAGTT
* * * * ** *
192834 TGA-GGTCAAAAATGTATTTTTTTGACA-TTCAAGGG-TAAAATGGTAA-TTTTGG-ATGTT
1 CGAGGGT--AAAATGTAATTTTTGGAAAGTT-TGGGGTTAAAATGGTAATTTTTGGAAAGTT
* *
192891 CG-GGGATAAAATGGTAATTTTTGGAAA-TTTGGGGTAAAAATATGT--TTTTTGG-AAGTT
1 CGAGGG-TAAAAT-GTAATTTTTGGAAAGTTTGGGGTTAAAAT-GGTAATTTTTGGAAAGTT
* * ** * *
192948 CGAGGGCAAAAATGGAATTTTTGG-AAGTTTGGGGGCAAAAAT-GTGATTTTTGAAAAGTT
1 CGAGGG-TAAAATGTAATTTTTGGAAAGTTT-GGGGTTAAAATGGTAATTTTTGGAAAGTT
* * * *
193007 -TAGGGGTCAAATGTAATTTTTGGAAAGTTTTAGGGTTAAAAT-ATAATTTTTGGAAAGTT
1 CGA-GGGTAAAATGTAATTTTTGGAAAG-TTTGGGGTTAAAATGGTAATTTTTGGAAAGTT
** *
193066 TAAGGGTCAAAATGTAATTTTTGGATAGTT
1 CGAGGGT-AAAATGTAATTTTTGGAAAGTT
193096 CAAGAACCTT
Statistics
Matches: 253, Mismatches: 45, Indels: 46
0.74 0.13 0.13
Matches are distributed among these distances:
56 12 0.05
57 50 0.20
58 76 0.30
59 86 0.34
60 29 0.11
ACGTcount: A:0.33, C:0.04, G:0.26, T:0.37
Consensus pattern (59 bp):
CGAGGGTAAAATGTAATTTTTGGAAAGTTTGGGGTTAAAATGGTAATTTTTGGAAAGTT
Found at i:192814 original size:88 final size:86
Alignment explanation
Indices: 192665--193030 Score: 336
Period size: 88 Copynumber: 4.2 Consensus size: 86
192655 TGCCGAGGGC
** ****
192665 AAAATGATAATTTTTGGAGGC-TT-GAGGGTAAAACGGTAATTTTCAGACACCCGAGGG-TAAAA
1 AAAATG-TAATTTTTGGA--CATTCGAGGGTAAAACGGTAATTTTTGGATGTTCG-GGGATAAAA
* *
192727 TAGTAATTTTTGGAAAGTTTGGGGTT
62 T-GTAATTTTTGAAAAGTTTGGGGTA
192753 AAAATGGTAATTTTTGGACATTCGAGGGTAAAACGGTAATTTTTGGATGTTCGGGGATAAAATGA
1 AAAAT-GTAATTTTTGGACATTCGAGGGTAAAACGGTAATTTTTGGATGTTCGGGGATAAAATG-
*
192818 TAATTTTTGAAAAGTTTGAGGTCA
64 TAATTTTTGAAAAGTTTGGGGT-A
* * * *
192842 AAAATGTATTTTTTTGACATTCAAGGGTAAAATGGTAA-TTTTGGATGTTCGGGGATAAAATGGT
1 AAAATGTAATTTTTGGACATTCGAGGGTAAAACGGTAATTTTTGGATGTTCGGGGATAAAAT-GT
*
192906 AATTTTTGGAAA-TTTGGGGTA
65 AATTTTTGAAAAGTTTGGGGTA
* ** * * * *
192927 AAAATATGTTTTTTGGA-AGTTCGAGGGCAAAAATGG-AATTTTTGGAAGTTTGGGGGCA-AAAA
1 AAAATGTAATTTTTGGACA-TTCGAGGG-TAAAACGGTAATTTTTGGATG-TTCGGGG-ATAAAA
*
192989 TGTGATTTTTGAAAAGTTTAGGGGT-
62 TGTAATTTTTGAAAAGTTT-GGGGTA
*
193014 CAAATGTAATTTTTGGA
1 AAAATGTAATTTTTGGA
193031 AAGTTTTAGG
Statistics
Matches: 236, Mismatches: 28, Indels: 29
0.81 0.10 0.10
Matches are distributed among these distances:
84 1 0.00
85 24 0.10
86 35 0.15
87 68 0.29
88 102 0.43
89 6 0.03
ACGTcount: A:0.33, C:0.05, G:0.27, T:0.35
Consensus pattern (86 bp):
AAAATGTAATTTTTGGACATTCGAGGGTAAAACGGTAATTTTTGGATGTTCGGGGATAAAATGTA
ATTTTTGAAAAGTTTGGGGTA
Found at i:192909 original size:87 final size:87
Alignment explanation
Indices: 192722--193030 Score: 344
Period size: 87 Copynumber: 3.6 Consensus size: 87
192712 CACCCGAGGG
* * * * *
192722 TAAAATAGTAATTTTTGGAAAGTTTGGGGTTAAAATGGTAATTTTTGGACATTCGAGGGTAAAAC
1 TAAAATGGTAATTTTTGAAAAGTTTGGGGTAAAAAT-GTATTTTTTGGACATTCGAGGGTAAAAT
192787 GGTAATTTTTGGATGTTCGGGGA
65 GGTAATTTTTGGATGTTCGGGGA
* * * *
192810 TAAAATGATAATTTTTGAAAAGTTTGAGGTCAAAAATGTATTTTTTTGACATTCAAGGGTAAAAT
1 TAAAATGGTAATTTTTGAAAAGTTTGGGGT-AAAAATGTATTTTTTGGACATTCGAGGGTAAAAT
192875 GGTAA-TTTTGGATGTTCGGGGA
65 GGTAATTTTTGGATGTTCGGGGA
* * * *
192897 TAAAATGGTAATTTTTGGAAA-TTTGGGGTAAAAATATGTTTTTTGGA-AGTTCGAGGGCAAAAA
1 TAAAATGGTAATTTTTGAAAAGTTTGGGGTAAAAATGTATTTTTTGGACA-TTCGAGGG-TAAAA
* *
192960 TGG-AATTTTTGGAAGTTTGGGGGCA
64 TGGTAATTTTTGGATG-TTCGGGG-A
* * *
192985 -AAAAT-GTGATTTTTGAAAAGTTTAGGGGT-CAAATGTAATTTTTGGA
1 TAAAATGGTAATTTTTGAAAAGTTT-GGGGTAAAAATGTATTTTTTGGA
193031 AAGTTTTAGG
Statistics
Matches: 188, Mismatches: 25, Indels: 17
0.82 0.11 0.07
Matches are distributed among these distances:
84 1 0.01
85 24 0.13
86 34 0.18
87 63 0.34
88 61 0.32
89 5 0.03
ACGTcount: A:0.33, C:0.04, G:0.27, T:0.37
Consensus pattern (87 bp):
TAAAATGGTAATTTTTGAAAAGTTTGGGGTAAAAATGTATTTTTTGGACATTCGAGGGTAAAATG
GTAATTTTTGGATGTTCGGGGA
Found at i:193406 original size:162 final size:162
Alignment explanation
Indices: 193132--193433 Score: 380
Period size: 162 Copynumber: 1.9 Consensus size: 162
193122 AAAAAGAGGT
* * * * * *
193132 GACACGTGGCAACTTCTCATGCCTTTAGAAGTCAAAGGACCAATTTGAAAATCATTTAAAATTAC
1 GACACGTCGCAACTTCTCATGCCTTCAGAAGTCAAAGGACCAAATTGAAAAACAATCAAAATTAC
* *
193197 TGGGCAAATTTATAATTAAAACAAAACTTGATTTAAGGACGAAATTAAAACAAATCAAAAATAAA
66 TGGGCAAATTTAAAATTAAAACAAAACTAGATTTAAGGACGAAATTAAAACAAAT-AAAAATAAA
193262 -AAGGACCAAATGCATAAATAAACCAAAAATGG
130 GAAGGACCAAATGCATAAATAAACCAAAAATGG
* **
193294 GACACGTCGCAGCTTCTCATG-CTTACAGAGAGTTTAAGGACCAAATTGAAAAACAATCAAAATT
1 GACACGTCGCAACTTCTCATGCCTT-CAGA-AGTCAAAGGACCAAATTGAAAAACAATCAAAATT
* * * *
193358 ATTGGGTAAATTTAAAATTAATTA-AAAA-TAGCA-TTAAGGACTAAATTAAAACAAATAAAAAT
64 ACTGGGCAAATTTAAAATTAA-AACAAAACTAG-ATTTAAGGACGAAATTAAAACAAATAAAAAT
*
193420 AAAGAAGGATCAAA
127 AAAGAAGGACCAAA
193434 GGAGAAAATA
Statistics
Matches: 119, Mismatches: 16, Indels: 10
0.82 0.11 0.07
Matches are distributed among these distances:
161 12 0.10
162 55 0.46
163 51 0.43
164 1 0.01
ACGTcount: A:0.49, C:0.14, G:0.14, T:0.24
Consensus pattern (162 bp):
GACACGTCGCAACTTCTCATGCCTTCAGAAGTCAAAGGACCAAATTGAAAAACAATCAAAATTAC
TGGGCAAATTTAAAATTAAAACAAAACTAGATTTAAGGACGAAATTAAAACAAATAAAAATAAAG
AAGGACCAAATGCATAAATAAACCAAAAATGG
Found at i:194941 original size:17 final size:17
Alignment explanation
Indices: 194890--194967 Score: 66
Period size: 17 Copynumber: 4.5 Consensus size: 17
194880 TTAAAATTTT
194890 ATTTCAAAATAAATTTAA
1 ATTT-AAAATAAATTTAA
* ** **
194908 ACTCCAAATAAGCTTAA
1 ATTTAAAATAAATTTAA
*
194925 ATTTACAATAAATTTAA
1 ATTTAAAATAAATTTAA
* * *
194942 ACTTAAAATGAATTAAA
1 ATTTAAAATAAATTTAA
194959 ATTTAAAAT
1 ATTTAAAAT
194968 CTAAAATTGG
Statistics
Matches: 44, Mismatches: 16, Indels: 1
0.72 0.26 0.02
Matches are distributed among these distances:
17 42 0.95
18 2 0.05
ACGTcount: A:0.54, C:0.09, G:0.03, T:0.35
Consensus pattern (17 bp):
ATTTAAAATAAATTTAA
Found at i:194961 original size:34 final size:33
Alignment explanation
Indices: 194897--194963 Score: 82
Period size: 34 Copynumber: 2.0 Consensus size: 33
194887 TTTATTTCAA
*
194897 AATAAATTTAAACTCCAAATAAGCTTAAATTTAC
1 AATAAATTTAAACTCAAAATAA-CTTAAATTTAC
*
194931 AATAAATTTAAACTTAAAATGAA-TTAAAATTTA
1 AATAAATTTAAACTCAAAAT-AACTT-AAATTTA
194964 AAATCTAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
33 2 0.07
34 25 0.86
35 2 0.07
ACGTcount: A:0.54, C:0.09, G:0.03, T:0.34
Consensus pattern (33 bp):
AATAAATTTAAACTCAAAATAACTTAAATTTAC
Found at i:197695 original size:42 final size:42
Alignment explanation
Indices: 197648--197732 Score: 161
Period size: 42 Copynumber: 2.0 Consensus size: 42
197638 TATTACTTAA
*
197648 CTTTAATGTCACTTGTAAATAAATATGTTATATTATTAATGT
1 CTTTAATGTCACTTGTAAATAAATATATTATATTATTAATGT
197690 CTTTAATGTCACTTGTAAATAAATATATTATATTATTAATGT
1 CTTTAATGTCACTTGTAAATAAATATATTATATTATTAATGT
197732 C
1 C
197733 ACAAGTCAAC
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.36, C:0.08, G:0.08, T:0.47
Consensus pattern (42 bp):
CTTTAATGTCACTTGTAAATAAATATATTATATTATTAATGT
Found at i:200718 original size:82 final size:82
Alignment explanation
Indices: 200581--200735 Score: 238
Period size: 82 Copynumber: 1.9 Consensus size: 82
200571 GGCGCAAAAC
* * * * *
200581 CGTTGGTTAATCTAACTAGAGCTGGGCTGACTTATTGCGGTTTATCCACTAGGCACTGGGTGCCA
1 CGTTGGTTAATCCAACTAGAGCCGAGCTCACTTATTGCGGTTTATCCACTAGGCACCGGGTGCCA
200646 GGAATTGATTGAATTAT
66 GGAATTGATTGAATTAT
* *
200663 CGTTGGTTAATCCAACTAGAGCCGAGTTCACTTATTGCGGTTTATCCGCTAGGCACCGGGTGCCA
1 CGTTGGTTAATCCAACTAGAGCCGAGCTCACTTATTGCGGTTTATCCACTAGGCACCGGGTGCCA
*
200728 TGAATTGA
66 GGAATTGA
200736 CGGATTTATA
Statistics
Matches: 65, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
82 65 1.00
ACGTcount: A:0.23, C:0.20, G:0.26, T:0.31
Consensus pattern (82 bp):
CGTTGGTTAATCCAACTAGAGCCGAGCTCACTTATTGCGGTTTATCCACTAGGCACCGGGTGCCA
GGAATTGATTGAATTAT
Found at i:206154 original size:56 final size:56
Alignment explanation
Indices: 206087--206199 Score: 208
Period size: 56 Copynumber: 2.0 Consensus size: 56
206077 CACTATCAAC
* *
206087 ATTATAGAAACTGGGTGCAATGGACGATTATTACTATATGTGGTCAGATGAGGGAA
1 ATTATAGAAACTGGGTGCAACGGACAATTATTACTATATGTGGTCAGATGAGGGAA
206143 ATTATAGAAACTGGGTGCAACGGACAATTATTACTATATGTGGTCAGATGAGGGAA
1 ATTATAGAAACTGGGTGCAACGGACAATTATTACTATATGTGGTCAGATGAGGGAA
206199 A
1 A
206200 AATTATGATG
Statistics
Matches: 55, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
56 55 1.00
ACGTcount: A:0.35, C:0.10, G:0.27, T:0.27
Consensus pattern (56 bp):
ATTATAGAAACTGGGTGCAACGGACAATTATTACTATATGTGGTCAGATGAGGGAA
Found at i:219302 original size:13 final size:13
Alignment explanation
Indices: 219284--219308 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
219274 GAAAATTCAA
219284 TTACTTTTTAATT
1 TTACTTTTTAATT
219297 TTACTTTTTAAT
1 TTACTTTTTAAT
219309 ATTTTTGAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.08, G:0.00, T:0.68
Consensus pattern (13 bp):
TTACTTTTTAATT
Found at i:219405 original size:11 final size:12
Alignment explanation
Indices: 219382--219414 Score: 59
Period size: 11 Copynumber: 2.8 Consensus size: 12
219372 TTTGATTCGA
219382 ATAAAATAAATT
1 ATAAAATAAATT
219394 ATAAAA-AAATT
1 ATAAAATAAATT
219405 ATAAAATAAA
1 ATAAAATAAA
219415 AAAATTCTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 11 0.55
12 9 0.45
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (12 bp):
ATAAAATAAATT
Found at i:222498 original size:12 final size:14
Alignment explanation
Indices: 222481--222512 Score: 50
Period size: 12 Copynumber: 2.4 Consensus size: 14
222471 GAATATATTT
222481 TATTATT-AATT-A
1 TATTATTAAATTGA
222493 TATTATTAAATTGA
1 TATTATTAAATTGA
222507 TATTAT
1 TATTAT
222513 ACTAATATGA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 7 0.39
13 4 0.22
14 7 0.39
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (14 bp):
TATTATTAAATTGA
Found at i:227272 original size:10 final size:11
Alignment explanation
Indices: 227237--227274 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
227227 ATTAAAAATG
227237 TTTTTATATAT
1 TTTTTATATAT
*
227248 TTTTTA-ATAA
1 TTTTTATATAT
*
227258 TTTTTATATTT
1 TTTTTATATAT
227269 TTTTTA
1 TTTTTA
227275 AATTTTAAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
10 9 0.39
11 14 0.61
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (11 bp):
TTTTTATATAT
Found at i:229721 original size:96 final size:96
Alignment explanation
Indices: 229573--229761 Score: 265
Period size: 96 Copynumber: 2.0 Consensus size: 96
229563 TTTGAATGGC
* *
229573 CGAAATTAAGAGGCAACAAATTTCAAATTGCAATAAAAGAAAAGATTGAATATTGATCCCTC-AA
1 CGAAATTAAGAGGCAACAAATTTCAAATTCCAATAAAAGAAAAGATTAAATATTGA-CCCTCGAA
*
229637 T-AAAGAGAGAAAGTAAAGAGAGTTTAAATTGT
65 TAAAAG-GAGAAAGTAAAAAGAGTTTAAATTGT
* * * *
229669 CGAAATTATGAGGCAATATATTTCAAATTCCAATCAAAGAAAAGATTAAATATTGACCCTCGAAT
1 CGAAATTAAGAGGCAACAAATTTCAAATTCCAATAAAAGAAAAGATTAAATATTGACCCTCGAAT
* *
229734 AAAAGGAGAAATTAAAAAGGGTTTAAAT
66 AAAAGGAGAAAGTAAAAAGAGTTTAAAT
229762 AATTGAAATT
Statistics
Matches: 82, Mismatches: 9, Indels: 4
0.86 0.09 0.04
Matches are distributed among these distances:
95 5 0.06
96 73 0.89
97 4 0.05
ACGTcount: A:0.49, C:0.10, G:0.16, T:0.25
Consensus pattern (96 bp):
CGAAATTAAGAGGCAACAAATTTCAAATTCCAATAAAAGAAAAGATTAAATATTGACCCTCGAAT
AAAAGGAGAAAGTAAAAAGAGTTTAAATTGT
Found at i:230671 original size:29 final size:29
Alignment explanation
Indices: 230639--230874 Score: 264
Period size: 30 Copynumber: 8.0 Consensus size: 29
230629 CGGATACCCG
* *
230639 GGGGT-AAAATGGTAATTTTTGGAAGTTTT
1 GGGGTAAAAATGG-GATTTTTGGAAGTTTC
**
230668 GGGGTAAAAAATGATATTTTTGGAAG-TTC
1 GGGGT-AAAAATGGGATTTTTGGAAGTTTC
230697 GGGGATAAAAATGGGATTTTTGGAAG-TTC
1 GGGG-TAAAAATGGGATTTTTGGAAGTTTC
230726 GGGGATAAAAATGGGATTTTTGGAAGTTTC
1 GGGG-TAAAAATGGGATTTTTGGAAGTTTC
** **
230756 TAGGTCAAAAATGGGATTTTTAAAAG-TTC
1 GGGGT-AAAAATGGGATTTTTGGAAGTTTC
*
230785 GAGGGTAAAAATGGGATTTTTGGAAGTTTT
1 G-GGGTAAAAATGGGATTTTTGGAAGTTTC
*
230815 GGGGTCAAAAATAGGATTTTTGGAAGTTTC
1 GGGGT-AAAAATGGGATTTTTGGAAGTTTC
*
230845 GAGGTCAAAAATGGGATTTTTGGATAGTTT
1 GGGGT-AAAAATGGGATTTTTGGA-AGTTT
230875 AGGGACCTCC
Statistics
Matches: 180, Mismatches: 18, Indels: 16
0.84 0.08 0.07
Matches are distributed among these distances:
29 84 0.47
30 85 0.47
31 11 0.06
ACGTcount: A:0.31, C:0.03, G:0.30, T:0.35
Consensus pattern (29 bp):
GGGGTAAAAATGGGATTTTTGGAAGTTTC
Found at i:230716 original size:59 final size:59
Alignment explanation
Indices: 230644--230874 Score: 263
Period size: 59 Copynumber: 3.9 Consensus size: 59
230634 ACCCGGGGGT
* * **
230644 AAAATGGTAATTTTTGGAAGTTTTGGGGTAAAAAATGATATTTTTGGAAG-TTCGGGGAT-A
1 AAAATGG-GATTTTTGGAAG-TTCGGGGTAAAAAATGGGATTTTTGGAAGTTTCGGGG-TCA
**
230704 AAAATGGGATTTTTGGAAGTTCGGGG-ATAAAAATGGGATTTTTGGAAGTTTCTAGGTCA
1 AAAATGGGATTTTTGGAAGTTCGGGGTA-AAAAATGGGATTTTTGGAAGTTTCGGGGTCA
** *
230763 AAAATGGGATTTTTAAAAGTTCGAGGGT-AAAAATGGGATTTTTGGAAGTTTTGGGGTCA
1 AAAATGGGATTTTTGGAAGTTCG-GGGTAAAAAATGGGATTTTTGGAAGTTTCGGGGTCA
* * *
230822 AAAATAGGATTTTTGGAAGTTTCGAGGTCAAAAATGGGATTTTTGGATAGTTT
1 AAAATGGGATTTTTGGAAG-TTCGGGGTAAAAAATGGGATTTTTGGA-AGTTT
230875 AGGGACCTCC
Statistics
Matches: 148, Mismatches: 15, Indels: 15
0.83 0.08 0.08
Matches are distributed among these distances:
57 1 0.01
58 25 0.17
59 85 0.57
60 32 0.22
61 5 0.03
ACGTcount: A:0.32, C:0.03, G:0.29, T:0.35
Consensus pattern (59 bp):
AAAATGGGATTTTTGGAAGTTCGGGGTAAAAAATGGGATTTTTGGAAGTTTCGGGGTCA
Found at i:231871 original size:18 final size:18
Alignment explanation
Indices: 231848--231900 Score: 63
Period size: 18 Copynumber: 2.9 Consensus size: 18
231838 CTTTTTTTAT
231848 TTATTATTATTATTAATA
1 TTATTATTATTATTAATA
*
231866 TTATTATTATTATCAA-A
1 TTATTATTATTATTAATA
**
231883 ACATTTATTATTATTAAT
1 TTA-TTATTATTATTAAT
231901 GACTATTAAG
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
17 2 0.07
18 27 0.93
ACGTcount: A:0.40, C:0.04, G:0.00, T:0.57
Consensus pattern (18 bp):
TTATTATTATTATTAATA
Found at i:231898 original size:3 final size:3
Alignment explanation
Indices: 231848--231878 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
231838 CTTTTTTTAT
*
231848 TTA TTA TTA TTA TTA ATA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
231879 CAAAACATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:232692 original size:17 final size:17
Alignment explanation
Indices: 232654--232722 Score: 84
Period size: 17 Copynumber: 4.0 Consensus size: 17
232644 TTTGAACTTT
* *
232654 TTTAATTTTAAAGTTAAA
1 TTTAAATTTAAAATT-AA
*
232672 TTTAAATTTAAGATTAA
1 TTTAAATTTAAAATTAA
*
232689 TTTAAATTTAAAATAAA
1 TTTAAATTTAAAATTAA
*
232706 TCTAAATTTAAAATTAA
1 TTTAAATTTAAAATTAA
232723 AAAGGGGCTC
Statistics
Matches: 44, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
17 32 0.73
18 12 0.27
ACGTcount: A:0.51, C:0.01, G:0.03, T:0.45
Consensus pattern (17 bp):
TTTAAATTTAAAATTAA
Found at i:232713 original size:23 final size:23
Alignment explanation
Indices: 232661--232724 Score: 69
Period size: 23 Copynumber: 2.8 Consensus size: 23
232651 TTTTTTAATT
* *
232661 TTAAAGTTAAATTTAAATTTAAGA
1 TTAAATTTAAATTTAAA-ATAAGA
232685 TT-AATTTAAATTTAAAATAA-A
1 TTAAATTTAAATTTAAAATAAGA
*
232706 TCTAAATTTAAAATTAAAA
1 T-TAAATTTAAATTTAAAA
232725 AGGGGCTCGA
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
21 2 0.06
22 4 0.11
23 27 0.77
24 2 0.06
ACGTcount: A:0.55, C:0.02, G:0.03, T:0.41
Consensus pattern (23 bp):
TTAAATTTAAATTTAAAATAAGA
Found at i:232719 original size:7 final size:6
Alignment explanation
Indices: 232654--232723 Score: 65
Period size: 6 Copynumber: 12.0 Consensus size: 6
232644 TTTGAACTTT
* *
232654 TTTAAT TTTAAA GTTAAA TTTAAA TTTAAGA -TT-AA TTTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAA-A TTTAAA TTTAAA TTTAAA
* * *
232701 -ATAAA TCTAAA TTTAAA ATTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA
232724 AAGGGGCTCG
Statistics
Matches: 53, Mismatches: 7, Indels: 8
0.78 0.10 0.12
Matches are distributed among these distances:
4 1 0.02
5 7 0.13
6 44 0.83
7 1 0.02
ACGTcount: A:0.51, C:0.01, G:0.03, T:0.44
Consensus pattern (6 bp):
TTTAAA
Found at i:233435 original size:205 final size:206
Alignment explanation
Indices: 233185--233631 Score: 711
Period size: 205 Copynumber: 2.2 Consensus size: 206
233175 CTTCTTAGTG
* *
233185 TCTCATCATGAAGCTGGGGTTCGAAGATTTGCTCACATCAGGCGTGTGTTTGATTTGGTCTTCTT
1 TCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCACATCAGGCGTGAGTTTGATTTGGTCTTCTT
* * *
233250 CTCAGTATCTTATCAGGAAGATGACT-GTGTCGTTTGTTTCAATTCGCTTCTCTGTATCTCATCA
66 CTCAGTATCTCATCAGGAAGATGACTGGT-TCGTTTGTTTCAATTCACTTCTCTATATCTCATCA
* * *
233314 GGAAGACGAATTTGGTCTACTTCTCAG-TATCTCATCAGGAAGCTAACCCTTTATTGCTTTACCC
130 GGAAGACGAATTTGGTCCACTTCTCAGCTATCTCATCAGGAAGCTAACCCTTTATTGCTTCACAC
233378 TGCTTT-TCCGTA
195 TG-TTTCTCCGTA
*
233390 TCTCATCAGGAAGCTGGGGTTCGAGGATTTGCTCACATCAGGCGTGAGTTTGATTTGGTCTTCTT
1 TCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCACATCAGGCGTGAGTTTGATTTGGTCTTCTT
*
233455 CTCAGTATCTCATCAGGAAGATGACTGGTTCGTTTGTTTCAATTCACTTCTCTATATCTCATTAG
66 CTCAGTATCTCATCAGGAAGATGACTGGTTCGTTTGTTTCAATTCACTTCTCTATATCTCATCAG
* * *
233520 GAAGGCGAATTTGGTCCATTTCTCAGCTATCTCATCAGGAAGCTAACCTTTTATTGCTTCACACT
131 GAAGACGAATTTGGTCCACTTCTCAGCTATCTCATCAGGAAGCTAACCCTTTATTGCTTCACACT
*
233585 GTTTCTTCGTA
196 GTTTCTCCGTA
* *
233596 TCTCATCAGTAAGCTAGGGTTCGAAGATTTGCTCAC
1 TCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCAC
233632 TTTGAGCCTC
Statistics
Matches: 222, Mismatches: 17, Indels: 5
0.91 0.07 0.02
Matches are distributed among these distances:
205 146 0.66
206 76 0.34
ACGTcount: A:0.21, C:0.22, G:0.20, T:0.37
Consensus pattern (206 bp):
TCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCACATCAGGCGTGAGTTTGATTTGGTCTTCTT
CTCAGTATCTCATCAGGAAGATGACTGGTTCGTTTGTTTCAATTCACTTCTCTATATCTCATCAG
GAAGACGAATTTGGTCCACTTCTCAGCTATCTCATCAGGAAGCTAACCCTTTATTGCTTCACACT
GTTTCTCCGTA
Found at i:237504 original size:6 final size:6
Alignment explanation
Indices: 237495--237564 Score: 56
Period size: 6 Copynumber: 12.0 Consensus size: 6
237485 TTTTTTAATT
* * * * *
237495 TTAAAA TTAAAA TTAAAT TTAAAT TTAAGA TT-AAT TTAAAT TTAAAA
1 TTAAAA TTAAAA TTAAAA TTAAAA TTAAAA TTAAAA TTAAAA TTAAAA
*
237542 -T-AAA TCTAAAT TTAAAA TTAAAA
1 TTAAAA T-TAAAA TTAAAA TTAAAA
237565 AGGGGCCCGG
Statistics
Matches: 52, Mismatches: 8, Indels: 8
0.76 0.12 0.12
Matches are distributed among these distances:
4 3 0.06
5 4 0.08
6 42 0.81
7 3 0.06
ACGTcount: A:0.57, C:0.01, G:0.01, T:0.40
Consensus pattern (6 bp):
TTAAAA
Found at i:237518 original size:11 final size:11
Alignment explanation
Indices: 237498--237563 Score: 55
Period size: 11 Copynumber: 5.7 Consensus size: 11
237488 TTTAATTTTA
*
237498 AAATTAAAATT
1 AAATTAAATTT
237509 AAATTTAAATTT
1 AAA-TTAAATTT
237521 AAGATT-AATTT
1 AA-ATTAAATTT
*
237532 AAATTTAAA-AT
1 AAA-TTAAATTT
237543 AAATCTAAATTT
1 AAAT-TAAATTT
237555 AAAATTAAA
1 -AAATTAAA
237564 AAGGGGCCCG
Statistics
Matches: 45, Mismatches: 3, Indels: 13
0.74 0.05 0.21
Matches are distributed among these distances:
10 2 0.04
11 20 0.44
12 18 0.40
13 5 0.11
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.39
Consensus pattern (11 bp):
AAATTAAATTT
Found at i:237530 original size:17 final size:17
Alignment explanation
Indices: 237489--237562 Score: 94
Period size: 17 Copynumber: 4.2 Consensus size: 17
237479 TTGAACTTTT
*
237489 TTAATTTTAAAATTAAAA
1 TTAA-TTTAAATTTAAAA
*
237507 TTAAATTTAAATTTAAGA
1 TT-AATTTAAATTTAAAA
237525 TTAATTTAAATTTAAAA
1 TTAATTTAAATTTAAAA
* *
237542 TAAATCTAAATTTAAAA
1 TTAATTTAAATTTAAAA
237559 TTAA
1 TTAA
237563 AAAGGGGCCC
Statistics
Matches: 49, Mismatches: 6, Indels: 3
0.84 0.10 0.05
Matches are distributed among these distances:
17 32 0.65
18 15 0.31
19 2 0.04
ACGTcount: A:0.54, C:0.01, G:0.01, T:0.43
Consensus pattern (17 bp):
TTAATTTAAATTTAAAA
Found at i:237546 original size:34 final size:36
Alignment explanation
Indices: 237489--237562 Score: 107
Period size: 34 Copynumber: 2.1 Consensus size: 36
237479 TTGAACTTTT
* *
237489 TTAATTTTAAAATTAAAATTAAATTTAAATTTAAGA
1 TTAATTTTAAAATTAAAATTAAATCTAAATTTAAAA
*
237525 TTAA-TTTAAATTTAAAA-TAAATCTAAATTTAAAA
1 TTAATTTTAAAATTAAAATTAAATCTAAATTTAAAA
237559 TTAA
1 TTAA
237563 AAAGGGGCCC
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
34 19 0.54
35 12 0.34
36 4 0.11
ACGTcount: A:0.54, C:0.01, G:0.01, T:0.43
Consensus pattern (36 bp):
TTAATTTTAAAATTAAAATTAAATCTAAATTTAAAA
Found at i:237553 original size:23 final size:22
Alignment explanation
Indices: 237498--237564 Score: 73
Period size: 23 Copynumber: 3.0 Consensus size: 22
237488 TTTAATTTTA
* *
237498 AAATTAAAATTAAATTTAAATTT
1 AAATTAAATTTAAATTTAAA-AT
237521 AAGATT-AATTTAAATTTAAAAT
1 AA-ATTAAATTTAAATTTAAAAT
*
237543 AAATCTAAATTTAAAATTAAAA
1 AAAT-TAAATTTAAATTTAAAA
237565 AGGGGCCCGG
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
21 2 0.05
22 4 0.11
23 29 0.76
24 3 0.08
ACGTcount: A:0.58, C:0.01, G:0.01, T:0.39
Consensus pattern (22 bp):
AAATTAAATTTAAATTTAAAAT
Found at i:247388 original size:42 final size:43
Alignment explanation
Indices: 247303--247398 Score: 151
Period size: 42 Copynumber: 2.3 Consensus size: 43
247293 TTATAAGAAA
*
247303 AAACGCCGCTAAAGAACATGGTCTTTAGCGGCCCTTTACCCAC
1 AAACGCCGCTAAAGAACACGGTCTTTAGCGGCCCTTTACCCAC
*
247346 AAACGCCGCTAAAG-ACACGGTCTTTAGCGGCGC-TTACTCCAC
1 AAACGCCGCTAAAGAACACGGTCTTTAGCGGCCCTTTAC-CCAC
247388 AAACGCCGCTA
1 AAACGCCGCTA
247399 TAAATAGTGT
Statistics
Matches: 50, Mismatches: 2, Indels: 3
0.91 0.04 0.05
Matches are distributed among these distances:
41 4 0.08
42 32 0.64
43 14 0.28
ACGTcount: A:0.28, C:0.33, G:0.20, T:0.19
Consensus pattern (43 bp):
AAACGCCGCTAAAGAACACGGTCTTTAGCGGCCCTTTACCCAC
Found at i:253854 original size:8 final size:8
Alignment explanation
Indices: 253852--253897 Score: 64
Period size: 8 Copynumber: 6.2 Consensus size: 8
253842 ATTAAATATT
253852 TAATTAAA
1 TAATTAAA
253860 TAATTAAA
1 TAATTAAA
253868 T-ATT---
1 TAATTAAA
253872 TAATTAAA
1 TAATTAAA
253880 TAATTAAA
1 TAATTAAA
253888 TAATTAAA
1 TAATTAAA
253896 TA
1 TA
253898 TTTTGAATTA
Statistics
Matches: 34, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
4 1 0.03
5 3 0.09
7 3 0.09
8 27 0.79
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (8 bp):
TAATTAAA
Found at i:253857 original size:12 final size:12
Alignment explanation
Indices: 253840--253914 Score: 68
Period size: 12 Copynumber: 6.1 Consensus size: 12
253830 TTGTTTTTAA
253840 TAATTAAATATT
1 TAATTAAATATT
253852 TAATT-AA-A--
1 TAATTAAATATT
253860 TAATTAAATATT
1 TAATTAAATATT
253872 TAATTAAATAATT
1 TAATTAAAT-ATT
253885 AAATAATTAAATATTT
1 ---TAATTAAATA-TT
253901 TGAATTAAATATT
1 T-AATTAAATATT
253914 T
1 T
253915 GGGTTGTTTT
Statistics
Matches: 53, Mismatches: 0, Indels: 19
0.74 0.00 0.26
Matches are distributed among these distances:
8 5 0.09
9 2 0.04
10 2 0.04
11 2 0.04
12 14 0.26
13 7 0.13
14 9 0.17
15 1 0.02
16 11 0.21
ACGTcount: A:0.52, C:0.00, G:0.01, T:0.47
Consensus pattern (12 bp):
TAATTAAATATT
Found at i:253863 original size:20 final size:20
Alignment explanation
Indices: 253838--253894 Score: 105
Period size: 20 Copynumber: 2.9 Consensus size: 20
253828 AGTTGTTTTT
253838 AATAATTAAATATTTAATTA
1 AATAATTAAATATTTAATTA
253858 AATAATTAAATATTTAATTA
1 AATAATTAAATATTTAATTA
*
253878 AATAATTAAATAATTAA
1 AATAATTAAATATTTAA
253895 ATATTTTGAA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (20 bp):
AATAATTAAATATTTAATTA
Found at i:253968 original size:34 final size:34
Alignment explanation
Indices: 253929--254022 Score: 125
Period size: 34 Copynumber: 2.8 Consensus size: 34
253919 TGTTTTAAAT
* *
253929 ATTTAAATAAATAATTAATTAATTAATTGGGTTG
1 ATTTAAATAATTAAATAATTAATTAATTGGGTTG
* *
253963 ATTTAAATAATTAAATAATTAAGTATTTGGGTTG
1 ATTTAAATAATTAAATAATTAATTAATTGGGTTG
* * *
253997 TTTTTAATAATTAAATATTTAATTAA
1 ATTTAAATAATTAAATAATTAATTAA
254023 ATAGTTAAAT
Statistics
Matches: 51, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
34 51 1.00
ACGTcount: A:0.44, C:0.00, G:0.10, T:0.47
Consensus pattern (34 bp):
ATTTAAATAATTAAATAATTAATTAATTGGGTTG
Found at i:254025 original size:114 final size:113
Alignment explanation
Indices: 253886--254322 Score: 466
Period size: 114 Copynumber: 3.8 Consensus size: 113
253876 TAAATAATTA
*
253886 AATAATTAAATATTTTGAATTAAATATTTGGGTTGTTTTAAATATTTAAATAAATAATTAATTAA
1 AATAATTAAATA-TTT-AATTAAATATTTGGATTGTTTTAAATATTT-AATAAATAATTAATTAA
253951 TTAATTGGGTTGATTTAAATAATTAAATAATTAAGTATTTGGGTTGTTTTT
63 TTAATTGGGTTGATTTAAATAATTAAATAATTAAGTATTTGGGTTGTTTTT
* ** ** ** * * *
254002 AATAATTAAATATTTAATTAAATAGTTAAATAT-TTGGATTGTTTTTAATAAATAAATAAATAAT
1 AATAATTAAATATTTAATTAAATATTTGGAT-TGTTTTA-AATATTTAATAAATAATTAATTAAT
*
254066 TAATTGGGTTGATTTAAATAATTAAATAATTAATTATTTGGGTTGTTTTT
64 TAATTGGGTTGATTTAAATAATTAAATAATTAAGTATTTGGGTTGTTTTT
* *
254116 AATAATTAAATATTTAATTAAATAATTAAATATTTGGATTGTTTTTAATAATTAAT---TAATTA
1 AATAATT-AA-A--T-ATT---TAATTAAATATTTGGATTGTTTTAAATATTTAATAAATAATTA
*
254178 ATTAATTAATTGGGTTGATTTAAATAATTAAATAATTAAGTATTTGAGTTGTTTTT
58 ATTAATTAATTGGGTTGATTTAAATAATTAAATAATTAAGTATTTGGGTTGTTTTT
* * * * * * *
254234 AATAATTAAATATTTAATTAAATAATT-AAATATTTGAATTGTTT--T---TAA-TAATTAATTA
1 AATAATTAAATATTTAATTAAATATTTGGATTGTTTTAAATATTTAATAAATAATTAATTAATTA
254292 ATTGGGTT-ATTTTAAATAATTAAATAATTAA
66 ATTGGGTTGA-TTTAAATAATTAAATAATTAA
254323 ATAGAAAAAA
Statistics
Matches: 274, Mismatches: 35, Indels: 34
0.80 0.10 0.10
Matches are distributed among these distances:
105 1 0.00
106 39 0.14
107 4 0.01
109 9 0.03
110 12 0.04
113 3 0.01
114 88 0.32
115 10 0.04
116 14 0.05
117 2 0.01
118 66 0.24
119 3 0.01
121 7 0.03
122 16 0.06
ACGTcount: A:0.42, C:0.00, G:0.10, T:0.48
Consensus pattern (113 bp):
AATAATTAAATATTTAATTAAATATTTGGATTGTTTTAAATATTTAATAAATAATTAATTAATTA
ATTGGGTTGATTTAAATAATTAAATAATTAAGTATTTGGGTTGTTTTT
Found at i:254036 original size:46 final size:45
Alignment explanation
Indices: 253970--254288 Score: 214
Period size: 46 Copynumber: 7.9 Consensus size: 45
253960 TTGATTTAAA
*
253970 TAATTAAATAATTAAGTATTTGGGTTGTTTTTAATAATTAAATATT
1 TAATTAAATAATTAAATATTTGGGTTGTTTTTAATAATTAAATA-T
* *
254016 TAATTAAATAGTTAAATATTTGGATTG-TTTT--TAA-TAAATA-
1 TAATTAAATAATTAAATATTTGGGTTGTTTTTAATAATTAAATAT
* *
254056 -AA-TAAATAATT--A-A-TTGGGTTGATTTAAATAATT-AA-A-
1 TAATTAAATAATTAAATATTTGGGTTGTTTTTAATAATTAAATAT
254092 TAA-T---TAA-T---TATTTGGGTTGTTTTTAATAATTAAATATT
1 TAATTAAATAATTAAATATTTGGGTTGTTTTTAATAATTAAATA-T
*
254130 TAATTAAATAATTAAATATTTGGATTGTTTTTAATAATT--A-AT
1 TAATTAAATAATTAAATATTTGGGTTGTTTTTAATAATTAAATAT
* * *
254172 TAATTAATTAATT--A-A-TTGGGTTG-ATTT-A-AA-TAAT---
1 TAATTAAATAATTAAATATTTGGGTTGTTTTTAATAATTAAATAT
* *
254206 ----TAAATAATTAAGTATTTGAGTTGTTTTTAATAATTAAATATT
1 TAATTAAATAATTAAATATTTGGGTTGTTTTTAATAATTAAATA-T
**
254248 TAATTAAATAATTAAATATTTGAATTGTTTTTAATAATTAA
1 TAATTAAATAATTAAATATTTGGGTTGTTTTTAATAATTAA
254289 TTAATTGGGT
Statistics
Matches: 216, Mismatches: 20, Indels: 74
0.70 0.06 0.24
Matches are distributed among these distances:
30 8 0.04
33 3 0.01
34 36 0.17
35 11 0.05
36 5 0.02
37 13 0.06
38 22 0.10
39 4 0.02
40 1 0.00
42 22 0.10
43 5 0.02
44 1 0.00
45 4 0.02
46 81 0.38
ACGTcount: A:0.42, C:0.00, G:0.09, T:0.49
Consensus pattern (45 bp):
TAATTAAATAATTAAATATTTGGGTTGTTTTTAATAATTAAATAT
Found at i:254055 original size:118 final size:118
Alignment explanation
Indices: 253903--254294 Score: 630
Period size: 118 Copynumber: 3.3 Consensus size: 118
253893 AAATATTTTG
* *
253903 AATTAAATATTTGGGTTGTTTTAAATATTTAAATAAATAATTAATTAATTAATTGGGTTGATTTA
1 AATTAAATATTTGGATTGTTTT---TA-ATAAATAAATAATTAATTAATTAATTGGGTTGATTTA
253968 AATAATTAAATAATTAAGTATTTGGGTTGTTTTTAATAATTAAATATTTAATTAAAT
62 AATAATTAAATAATTAAGTATTTGGGTTGTTTTTAATAATTAAATATTTAATTAAAT
*
254025 AGTTAAATATTTGGATTGTTTTTAATAAATAAAT-A--AA-TAATTAATTGGGTTGATTTAAATA
1 AATTAAATATTTGGATTGTTTTTAATAAATAAATAATTAATTAATTAATTGGGTTGATTTAAATA
*
254086 ATTAAATAATTAATTATTTGGGTTGTTTTTAATAATTAAATATTTAATTAAAT
66 ATTAAATAATTAAGTATTTGGGTTGTTTTTAATAATTAAATATTTAATTAAAT
* *
254139 AATTAAATATTTGGATTGTTTTTAATAATTAATTAATTAATTAATTAATTGGGTTGATTTAAATA
1 AATTAAATATTTGGATTGTTTTTAATAAATAAATAATTAATTAATTAATTGGGTTGATTTAAATA
*
254204 ATTAAATAATTAAGTATTTGAGTTGTTTTTAATAATTAAATATTTAATTAAAT
66 ATTAAATAATTAAGTATTTGGGTTGTTTTTAATAATTAAATATTTAATTAAAT
* * *
254257 AATTAAATATTTGAATTGTTTTTAATAATTAATTAATT
1 AATTAAATATTTGGATTGTTTTTAATAAATAAATAATT
254295 GGGTTATTTT
Statistics
Matches: 256, Mismatches: 10, Indels: 12
0.92 0.04 0.04
Matches are distributed among these distances:
114 107 0.42
115 3 0.01
117 3 0.01
118 121 0.47
119 2 0.01
122 20 0.08
ACGTcount: A:0.42, C:0.00, G:0.10, T:0.48
Consensus pattern (118 bp):
AATTAAATATTTGGATTGTTTTTAATAAATAAATAATTAATTAATTAATTGGGTTGATTTAAATA
ATTAAATAATTAAGTATTTGGGTTGTTTTTAATAATTAAATATTTAATTAAAT
Found at i:254086 original size:34 final size:34
Alignment explanation
Indices: 254016--254136 Score: 134
Period size: 34 Copynumber: 3.6 Consensus size: 34
254006 ATTAAATATT
* * * * * *
254016 TAATTAAATAGTTAAATATTTGGATTGTTTTTAA
1 TAATTAAATAATTAATTAATTGGGTTGATTTAAA
* *
254050 TAAATAAATAAATAATTAATTGGGTTGATTTAAA
1 TAATTAAATAATTAATTAATTGGGTTGATTTAAA
* * *
254084 TAATTAAATAATTAATTATTTGGGTTGTTTTTAA
1 TAATTAAATAATTAATTAATTGGGTTGATTTAAA
*
254118 TAATTAAATATTTAATTAA
1 TAATTAAATAATTAATTAA
254137 ATAATTAAAT
Statistics
Matches: 72, Mismatches: 15, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
34 72 1.00
ACGTcount: A:0.43, C:0.00, G:0.10, T:0.47
Consensus pattern (34 bp):
TAATTAAATAATTAATTAATTGGGTTGATTTAAA
Found at i:254099 original size:80 final size:77
Alignment explanation
Indices: 253913--254322 Score: 233
Period size: 80 Copynumber: 5.4 Consensus size: 77
253903 AATTAAATAT
* * * * *
253913 TTGGGTTGTTTTAAATATTTAAATAAATAATT-AATTAATTAATTGGGTTGATTTAAATAATTAA
1 TTGGGTTGTTTTAAATAATTAAATAATTAATTAAATTAAATAATTGGATTGATTTAAATAAATAA
* *
253977 ATAATTAAGTAT
66 ATAAATAAGTAA
* * * * *
253989 TTGGGTTGTTTTTAATAATTAAATATTTAATTAAATAGTTAAATATTTGGATTGTTTTTAATAAA
1 TTGGGTTGTTTTAAATAATTAAATAATTAATT-AA-A-TTAAATAATTGGATTGATTTAAATAAA
*
254054 TAAATAAATAATTAA
63 TAAATAAATAAGTAA
* * *** ** * *
254069 TTGGGTTGATTTAAATAATTAAATAATTAATT-ATTTGGGTTGTT--TTTAATAATTAAATATTT
1 TTGGGTTGTTTTAAATAATTAAATAATTAATTAAATTAAATAATTGGATTGAT--TTAAATA---
* * *
254131 AATTAAATAATTAAATAT
61 AA-TAAATAAATAAGTAA
* * * * *
254149 TTGGATTGTTTT---TAA-TAATTAATTAATT-AATTAATTAATTGGGTTGATTTAAATAATTAA
1 TTGGGTTGTTTTAAATAATTAAATAATTAATTAAATTAAATAATTGGATTGATTTAAATAAATAA
* *
254209 ATAATTAAGTAT
66 ATAAATAAGTAA
* * * * *
254221 TTGAGTTGTTTTTAATAATTAAATATTTAATTAAATAATTAAATATTTGAATTG-TTT---T---
1 TTGGGTTGTTTTAAATAATTAAATAATTAATT--A-AATTAAATAATTGGATTGATTTAAATAAA
* *
254279 T-AATAATTAATTAA
63 TAAATAAATAAGTAA
*
254293 TTGGGTTATTTTAAATAATTAAATAATTAA
1 TTGGGTTGTTTTAAATAATTAAATAATTAA
254323 ATAGAAAAAA
Statistics
Matches: 258, Mismatches: 56, Indels: 44
0.72 0.16 0.12
Matches are distributed among these distances:
72 61 0.24
73 2 0.01
74 3 0.01
75 3 0.01
76 76 0.29
77 3 0.01
78 6 0.02
79 6 0.02
80 98 0.38
ACGTcount: A:0.42, C:0.00, G:0.10, T:0.48
Consensus pattern (77 bp):
TTGGGTTGTTTTAAATAATTAAATAATTAATTAAATTAAATAATTGGATTGATTTAAATAAATAA
ATAAATAAGTAA
Done.