Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009234.1 Hibiscus syriacus cultivar Beakdansim tig00112856_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 912649
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 5
Found at i:4857 original size:7 final size:7
Alignment explanation
Indices: 4845--4875 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
4835 GGTCAAAGAA
4845 GTCAACG
1 GTCAACG
4852 GTCAACG
1 GTCAACG
4859 GTCAACG
1 GTCAACG
4866 GTCAACG
1 GTCAACG
4873 GTC
1 GTC
4876 GGGTCGGGTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.26, C:0.29, G:0.29, T:0.16
Consensus pattern (7 bp):
GTCAACG
Found at i:4888 original size:21 final size:21
Alignment explanation
Indices: 4864--4926 Score: 119
Period size: 21 Copynumber: 3.0 Consensus size: 21
4854 CAACGGTCAA
4864 CGGTCAACGGTCGGGTCGGGT
1 CGGTCAACGGTCGGGTCGGGT
4885 CGGTCAACGGTCGGGTC-GGT
1 CGGTCAACGGTCGGGTCGGGT
4905 CGGTCAACGGTCGGGTCGGGT
1 CGGTCAACGGTCGGGTCGGGT
4926 C
1 C
4927 AGACCGGTCA
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
20 20 0.49
21 21 0.51
ACGTcount: A:0.10, C:0.25, G:0.46, T:0.19
Consensus pattern (21 bp):
CGGTCAACGGTCGGGTCGGGT
Found at i:4907 original size:20 final size:20
Alignment explanation
Indices: 4864--4923 Score: 111
Period size: 20 Copynumber: 3.0 Consensus size: 20
4854 CAACGGTCAA
4864 CGGTCAACGGTCGGGTCGGGT
1 CGGTCAACGGTCGGGTC-GGT
4885 CGGTCAACGGTCGGGTCGGT
1 CGGTCAACGGTCGGGTCGGT
4905 CGGTCAACGGTCGGGTCGG
1 CGGTCAACGGTCGGGTCGG
4924 GTCAGACCGG
Statistics
Matches: 39, Mismatches: 0, Indels: 1
0.98 0.00 0.03
Matches are distributed among these distances:
20 22 0.56
21 17 0.44
ACGTcount: A:0.10, C:0.25, G:0.47, T:0.18
Consensus pattern (20 bp):
CGGTCAACGGTCGGGTCGGT
Found at i:4941 original size:9 final size:9
Alignment explanation
Indices: 4923--5020 Score: 88
Period size: 9 Copynumber: 10.3 Consensus size: 9
4913 GGTCGGGTCG
*
4923 GGTCAGACC
1 GGTCAAACC
4932 GGTCAAACC
1 GGTCAAACC
* *
4941 GTTCAGACC
1 GGTCAAACC
4950 GGTCAAACC
1 GGTCAAACC
*
4959 GGTTCGAACC
1 GG-TCAAACC
*
4969 GGTTGAAACC
1 GG-TCAAACC
4979 GGTCAAACC
1 GGTCAAACC
4988 GGTCAGAACC
1 GGTCA-AACC
*
4998 GGTTGAAAACC
1 GG-T-CAAACC
*
5009 GGTTAAACC
1 GGTCAAACC
5018 GGT
1 GGT
5021 TTCCAGCAGC
Statistics
Matches: 74, Mismatches: 11, Indels: 8
0.80 0.12 0.09
Matches are distributed among these distances:
9 43 0.58
10 23 0.31
11 7 0.09
12 1 0.01
ACGTcount: A:0.29, C:0.28, G:0.28, T:0.16
Consensus pattern (9 bp):
GGTCAAACC
Found at i:4969 original size:19 final size:19
Alignment explanation
Indices: 4929--5021 Score: 86
Period size: 19 Copynumber: 4.8 Consensus size: 19
4919 GTCGGGTCAG
4929 ACCGGTCAAACC-GTTC-A
1 ACCGGTCAAACCGGTTCGA
4946 GACCGGTCAAACCGGTTCGA
1 -ACCGGTCAAACCGGTTCGA
* *
4966 ACCGGTTGAAACCGG-TCAA
1 ACCGG-TCAAACCGGTTCGA
4985 ACCGGTCAGAACCGGTT-GAAA
1 ACCGGTCA-AACCGGTTCG--A
*
5006 ACCGGTTAAACCGGTT
1 ACCGGTCAAACCGGTT
5022 TCCAGCAGCC
Statistics
Matches: 63, Mismatches: 5, Indels: 12
0.79 0.06 0.15
Matches are distributed among these distances:
18 14 0.22
19 23 0.37
20 18 0.29
21 8 0.13
ACGTcount: A:0.29, C:0.28, G:0.26, T:0.17
Consensus pattern (19 bp):
ACCGGTCAAACCGGTTCGA
Found at i:4981 original size:29 final size:31
Alignment explanation
Indices: 4947--5021 Score: 120
Period size: 29 Copynumber: 2.5 Consensus size: 31
4937 AACCGTTCAG
4947 ACCGGTCAAACCGGTTC-GAACCGGTTG-AA
1 ACCGGTCAAACCGGTTCAGAACCGGTTGAAA
4976 ACCGGTCAAACCGG-TCAGAACCGGTTGAAA
1 ACCGGTCAAACCGGTTCAGAACCGGTTGAAA
*
5006 ACCGGTTAAACCGGTT
1 ACCGGTCAAACCGGTT
5022 TCCAGCAGCC
Statistics
Matches: 42, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
28 2 0.05
29 24 0.57
30 15 0.36
31 1 0.02
ACGTcount: A:0.29, C:0.27, G:0.27, T:0.17
Consensus pattern (31 bp):
ACCGGTCAAACCGGTTCAGAACCGGTTGAAA
Found at i:6583 original size:2 final size:2
Alignment explanation
Indices: 6576--6605 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
6566 ACTTGCTATG
6576 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
6606 TAATAAAATA
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):
AT
Found at i:18082 original size:18 final size:18
Alignment explanation
Indices: 18056--18103 Score: 53
Period size: 17 Copynumber: 2.7 Consensus size: 18
18046 CAGAGTCAAT
*
18056 TCATACAGAGCTTTTGAA
1 TCATTCAGAGCTTTTGAA
**
18074 TCATTCAGA-CGATTGAA
1 TCATTCAGAGCTTTTGAA
*
18091 TCATTCAGCGCTT
1 TCATTCAGAGCTT
18104 AATCATTTTA
Statistics
Matches: 23, Mismatches: 6, Indels: 2
0.74 0.19 0.06
Matches are distributed among these distances:
17 14 0.61
18 9 0.39
ACGTcount: A:0.29, C:0.21, G:0.17, T:0.33
Consensus pattern (18 bp):
TCATTCAGAGCTTTTGAA
Found at i:18109 original size:15 final size:17
Alignment explanation
Indices: 18069--18110 Score: 61
Period size: 17 Copynumber: 2.6 Consensus size: 17
18059 TACAGAGCTT
18069 TTGAATCATTCAGACGA
1 TTGAATCATTCAGACGA
*
18086 TTGAATCATTCAG-CGC
1 TTGAATCATTCAGACGA
18102 TT-AATCATT
1 TTGAATCATT
18111 TTATTTTATC
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
15 7 0.29
16 4 0.17
17 13 0.54
ACGTcount: A:0.31, C:0.19, G:0.14, T:0.36
Consensus pattern (17 bp):
TTGAATCATTCAGACGA
Found at i:28238 original size:2 final size:2
Alignment explanation
Indices: 28231--28270 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
28221 TCTCCAGGTA
28231 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
28271 GTCGAAATTC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:33486 original size:35 final size:35
Alignment explanation
Indices: 33439--33518 Score: 133
Period size: 35 Copynumber: 2.3 Consensus size: 35
33429 AACACAGTCA
*
33439 TCAATTATATTCTAAACCCCAAAATCCAAAATACT
1 TCAATTACATTCTAAACCCCAAAATCCAAAATACT
* *
33474 TCAATTACATTCTAAACCTCAAATTCCAAAATACT
1 TCAATTACATTCTAAACCCCAAAATCCAAAATACT
33509 TCAATTACAT
1 TCAATTACAT
33519 GCCCAACCCC
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
35 42 1.00
ACGTcount: A:0.44, C:0.25, G:0.00, T:0.31
Consensus pattern (35 bp):
TCAATTACATTCTAAACCCCAAAATCCAAAATACT
Found at i:33532 original size:35 final size:35
Alignment explanation
Indices: 33452--33534 Score: 121
Period size: 35 Copynumber: 2.4 Consensus size: 35
33442 ATTATATTCT
* * *
33452 AAACCCCAAAATCCAAAATACTTCAATTACATTCT
1 AAACCCCAAATTCCAAAATACTTCAATTACATGCC
*
33487 AAACCTCAAATTCCAAAATACTTCAATTACATGCC
1 AAACCCCAAATTCCAAAATACTTCAATTACATGCC
*
33522 CAACCCCAAATTC
1 AAACCCCAAATTC
33535 ATATCCATTA
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
35 42 1.00
ACGTcount: A:0.43, C:0.31, G:0.01, T:0.24
Consensus pattern (35 bp):
AAACCCCAAATTCCAAAATACTTCAATTACATGCC
Found at i:34164 original size:19 final size:20
Alignment explanation
Indices: 34126--34166 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
34116 CAATTTTTTA
34126 TTTGATTGTATAATATAATG
1 TTTGATTGTATAATATAATG
34146 TTTGATT-T-TAATCATAATG
1 TTTGATTGTATAAT-ATAATG
34165 TT
1 TT
34167 ATGCTCAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
18 4 0.20
19 9 0.45
20 7 0.35
ACGTcount: A:0.32, C:0.02, G:0.12, T:0.54
Consensus pattern (20 bp):
TTTGATTGTATAATATAATG
Found at i:34957 original size:16 final size:16
Alignment explanation
Indices: 34933--34964 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
34923 ATATCAATTA
34933 AATTATATTAAATATT
1 AATTATATTAAATATT
*
34949 AATTTTATTAAATATT
1 AATTATATTAAATATT
34965 TTTTCAAAAT
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:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
AATTATATTAAATATT
Found at i:35543 original size:255 final size:255
Alignment explanation
Indices: 35096--35833 Score: 1166
Period size: 255 Copynumber: 2.9 Consensus size: 255
35086 TTTTTAACTT
* * * * * *
35096 TTGTTGAGAGTTGAACTCAAGACCTCCCGCTTACTAAACAAGTACTCTAACCAACTAAGCTGCAA
1 TTGTTGAGAGTTGAACTCAAGACCTCCCGCTTACTAAACAGGTGCTCTAGCCAGCTGAGCTACAA
* * * * * * * * *
35161 GAGTTAATTCATAAACTTATCATGAGTTAGATTGTCA-AAATATATTTAAGATGAGAGGTG-GAG
66 GAGCTAATTCATAAATTTAACACGTGTTAGAGTCTAAGAAATATATTTAAGATGAGAGATGAG-G
** *
35224 TAGCTATTTTATGG---ATTCAAATAAATTTATTCTTTGAATTTCTTTATCTAAAATACTTTTTA
130 TATTTATTTCATGGATTATTCAAATAAATTTATTCTTTGAATTTCTTTATCTAAAATACTTTTTA
*
35286 AAATTTGTTGTGTGGTATATCGTTTGAAAGATGTTTAAGTTAACGAAGTACCGATTTGCTC
195 AAATTTGTTGTGTGGTATATCGTTTGAAAGATGTTTAAGTTAACGAAGTACCAATTTGCTC
35347 TTGTTGAGAGTTGAACTCAAGACCTCCCGCTTACTAAACAGGTGCTCTAGCCAGCTGAGCTACAA
1 TTGTTGAGAGTTGAACTCAAGACCTCCCGCTTACTAAACAGGTGCTCTAGCCAGCTGAGCTACAA
35412 GAGCTAATTCATAAATTTAACACGTGTTAGAGTCTAAGAAATATATTTAAGATGAGAGATGAGGT
66 GAGCTAATTCATAAATTTAACACGTGTTAGAGTCTAAGAAATATATTTAAGATGAGAGATGAGGT
35477 ATTTATTTCATGGATTATTCAAATAAATTTATTCTTTGAATTTCTTTATCTAAAATACTTTTTAA
131 ATTTATTTCATGGATTATTCAAATAAATTTATTCTTTGAATTTCTTTATCTAAAATACTTTTTAA
35542 AATTTGTTGTGTGGTATATCGTTTGAAAGATGTTTAAGTTAACGAAGTACCAATTTGCTC
196 AATTTGTTGTGTGGTATATCGTTTGAAAGATGTTTAAGTTAACGAAGTACCAATTTGCTC
35602 TTGTTGAGAGTTGAACTCAAGACCTCCCGCTTACTAAACAGGTGCTCTAGCCAGCTGAGCTACAA
1 TTGTTGAGAGTTGAACTCAAGACCTCCCGCTTACTAAACAGGTGCTCTAGCCAGCTGAGCTACAA
35667 GAGCTAATTCATAAATTTAACACGTGTTAGAGTCTAAGAAATATATTTAAGATGAGAGATGAGGT
66 GAGCTAATTCATAAATTTAACACGTGTTAGAGTCTAAGAAATATATTTAAGATGAGAGATGAGGT
* * * *
35732 ATTTATTTCATGGATTATTCAAATAAATTAATTCTTTGAAAATT-TTCATCTAAAATACTCTTTA
131 ATTTATTTCATGGATTATTCAAATAAATTTATTCTTTG-AATTTCTTTATCTAAAATACTTTTTA
* ** *
35796 AAA-ATACTGTGTGGTATATTGTTTGAAAGATGTTTAAG
195 AAATTTGTTGTGTGGTATATCGTTTGAAAGATGTTTAAG
35834 ATAAAAGAGT
Statistics
Matches: 454, Mismatches: 27, Indels: 9
0.93 0.06 0.02
Matches are distributed among these distances:
251 88 0.19
252 34 0.07
253 1 0.00
254 31 0.07
255 296 0.65
256 4 0.01
ACGTcount: A:0.33, C:0.13, G:0.17, T:0.36
Consensus pattern (255 bp):
TTGTTGAGAGTTGAACTCAAGACCTCCCGCTTACTAAACAGGTGCTCTAGCCAGCTGAGCTACAA
GAGCTAATTCATAAATTTAACACGTGTTAGAGTCTAAGAAATATATTTAAGATGAGAGATGAGGT
ATTTATTTCATGGATTATTCAAATAAATTTATTCTTTGAATTTCTTTATCTAAAATACTTTTTAA
AATTTGTTGTGTGGTATATCGTTTGAAAGATGTTTAAGTTAACGAAGTACCAATTTGCTC
Found at i:35882 original size:23 final size:23
Alignment explanation
Indices: 35838--35888 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
35828 TTTAAGATAA
* *
35838 AAGAGTAACACTTTGATTTTGTT
1 AAGAGTAACACCTTGATCTTGTT
*
35861 AAGAGTAACACCTTGCTCTTGTT
1 AAGAGTAACACCTTGATCTTGTT
*
35884 GAGAG
1 AAGAG
35889 CTGAACTCAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.29, C:0.14, G:0.22, T:0.35
Consensus pattern (23 bp):
AAGAGTAACACCTTGATCTTGTT
Found at i:37479 original size:182 final size:183
Alignment explanation
Indices: 37157--37535 Score: 535
Period size: 182 Copynumber: 2.1 Consensus size: 183
37147 GGTAGACTTA
* * * *
37157 TATCATAGAGTGTTCCTTTTTTTATATTAAGGTAAGATGATTATAAAGTAGTATTTGTTCTAAAT
1 TATCATAAAGTGTTCCTTTTTTTATATTAAGCTAAGATGATTATAAAGTAATATTTGTACTAAAT
* * * * *
37222 ACTCTTAACCATTTGACAATTAACTCTTAATCACCCTGCTACAGTTATTGGTGCTTGAACGAATG
66 ACTCTTAACCATTTGACAACTAACACTCAATCACCCTGCTACAGTTATTGATGCTTGAACCAATG
* *
37287 ACCTCTAAGAACAACACCAATTCTTTTAACCACTAAGATAAGTTGATTCGTGC
131 ACCTCTAAGAACAACACCAATTCTTTTAACCACTAAGATAAATTAATTCGTGC
* * *
37340 TATCATAAATTGTT-CTTTTTTTATATTAAGCTAAGGTGATTATTAAGTAATATTTGTACTAAAT
1 TATCATAAAGTGTTCCTTTTTTTATATTAAGCTAAGATGATTATAAAGTAATATTTGTACTAAAT
* * * * * *
37404 ACTCTTCATCATTTGATAACTGACACTCAATCACCCTGCTATAGTTGTTGATGCTTGAACCAATG
66 ACTCTTAACCATTTGACAACTAACACTCAATCACCCTGCTACAGTTATTGATGCTTGAACCAATG
* * *
37469 ACCTCTAAGAATAACATCAATTCTTTTAACCACTAAGGTAAATTAATTCGTGC
131 ACCTCTAAGAACAACACCAATTCTTTTAACCACTAAGATAAATTAATTCGTGC
*
37522 TATCATATAGTGTT
1 TATCATAAAGTGTT
37536 ATTATGTACT
Statistics
Matches: 171, Mismatches: 25, Indels: 1
0.87 0.13 0.01
Matches are distributed among these distances:
182 159 0.93
183 12 0.07
ACGTcount: A:0.32, C:0.17, G:0.13, T:0.38
Consensus pattern (183 bp):
TATCATAAAGTGTTCCTTTTTTTATATTAAGCTAAGATGATTATAAAGTAATATTTGTACTAAAT
ACTCTTAACCATTTGACAACTAACACTCAATCACCCTGCTACAGTTATTGATGCTTGAACCAATG
ACCTCTAAGAACAACACCAATTCTTTTAACCACTAAGATAAATTAATTCGTGC
Found at i:39544 original size:2 final size:2
Alignment explanation
Indices: 39537--39603 Score: 134
Period size: 2 Copynumber: 33.5 Consensus size: 2
39527 CACCATTCAC
39537 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
39579 CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT C
39604 AACGTCTTCA
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 65 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:39714 original size:2 final size:2
Alignment explanation
Indices: 39707--39732 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
39697 ACATACATAA
39707 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
39733 TAATTTAGGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:41688 original size:142 final size:142
Alignment explanation
Indices: 41432--41723 Score: 575
Period size: 142 Copynumber: 2.1 Consensus size: 142
41422 TTCATTTATG
41432 TTCGAACAGAGGGCAAGTTGAATATGTTACGAAGATTATTGAAGTTGTTTGAATTTCAAGAAGAT
1 TTCGAACAGAGGGCAAGTTGAATATGTTACGAAGATTATTGAAGTTGTTTGAATTTCAAGAAGAT
41497 TGTTTTGTTGAACAAATTAACTTTAATACTTTATTATGTTCATATAGCTTATTTATGATTTATAT
66 TGTTTTGTTGAACAAATTAACTTTAATACTTTATTATGTTCATATAGCTTATTTATGATTTATAT
41562 ATGTTTGTCGTA
131 ATGTTTGTCGTA
*
41574 TTCGAACAGAGGGCAAGTTGAATATGTTACGAAGATTATTGAAGTTGTTTGGATTTCAAGAAGAT
1 TTCGAACAGAGGGCAAGTTGAATATGTTACGAAGATTATTGAAGTTGTTTGAATTTCAAGAAGAT
41639 TGTTTTGTTGAACAAATTAACTTTAATACTTTATTATGTTCATATAGCTTATTTATGATTTATAT
66 TGTTTTGTTGAACAAATTAACTTTAATACTTTATTATGTTCATATAGCTTATTTATGATTTATAT
41704 ATGTTTGTCGTA
131 ATGTTTGTCGTA
41716 TTCGAACA
1 TTCGAACA
41724 AATTAACTCT
Statistics
Matches: 149, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
142 149 1.00
ACGTcount: A:0.32, C:0.08, G:0.18, T:0.42
Consensus pattern (142 bp):
TTCGAACAGAGGGCAAGTTGAATATGTTACGAAGATTATTGAAGTTGTTTGAATTTCAAGAAGAT
TGTTTTGTTGAACAAATTAACTTTAATACTTTATTATGTTCATATAGCTTATTTATGATTTATAT
ATGTTTGTCGTA
Found at i:41845 original size:13 final size:13
Alignment explanation
Indices: 41829--41881 Score: 51
Period size: 13 Copynumber: 4.2 Consensus size: 13
41819 TTTTTTGTGT
*
41829 GTTTGTGTTGTTC
1 GTTTATGTTGTTC
41842 GTTTA---TGTTC
1 GTTTATGTTGTTC
41852 GTTTAT-TGTGTTC
1 GTTTATGT-TGTTC
41865 GTTTATGTTCGTTC
1 GTTTATGTT-GTTC
41879 GTT
1 GTT
41882 CGTGTTCGTT
Statistics
Matches: 34, Mismatches: 1, Indels: 9
0.77 0.02 0.20
Matches are distributed among these distances:
10 10 0.29
13 16 0.47
14 8 0.24
ACGTcount: A:0.06, C:0.09, G:0.25, T:0.60
Consensus pattern (13 bp):
GTTTATGTTGTTC
Found at i:41852 original size:10 final size:10
Alignment explanation
Indices: 41837--41877 Score: 55
Period size: 10 Copynumber: 3.8 Consensus size: 10
41827 GTGTTTGTGT
41837 TGTTCGTTTA
1 TGTTCGTTTA
41847 TGTTCGTTTA
1 TGTTCGTTTA
41857 TTGTGTTCGTTTA
1 ---TGTTCGTTTA
41870 TGTTCGTT
1 TGTTCGTT
41878 CGTTCGTGTT
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
10 18 0.64
13 10 0.36
ACGTcount: A:0.07, C:0.10, G:0.22, T:0.61
Consensus pattern (10 bp):
TGTTCGTTTA
Found at i:41855 original size:23 final size:23
Alignment explanation
Indices: 41829--41894 Score: 89
Period size: 23 Copynumber: 2.8 Consensus size: 23
41819 TTTTTTGTGT
41829 GTTTG-TGTTGTTCGTTTATGTTC
1 GTTTGTTG-TGTTCGTTTATGTTC
*
41852 GTTTATTGTGTTCGTTTATGTTC
1 GTTTGTTGTGTTCGTTTATGTTC
*
41875 GTTCGTTCGTGTTCGTTTAT
1 GTTTGTT-GTGTTCGTTTAT
41895 TTATTAAATG
Statistics
Matches: 38, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
23 24 0.63
24 14 0.37
ACGTcount: A:0.06, C:0.11, G:0.24, T:0.59
Consensus pattern (23 bp):
GTTTGTTGTGTTCGTTTATGTTC
Found at i:46303 original size:17 final size:18
Alignment explanation
Indices: 46260--46306 Score: 53
Period size: 17 Copynumber: 2.7 Consensus size: 18
46250 ATTATTACGT
46260 TATA-AAAATATATATAA
1 TATATAAAATATATATAA
* * *
46277 TATCTTAAATAT-TATCA
1 TATATAAAATATATATAA
46294 TATATAAAATATA
1 TATATAAAATATA
46307 CTAATACAAA
Statistics
Matches: 23, Mismatches: 5, Indels: 3
0.74 0.16 0.10
Matches are distributed among these distances:
17 17 0.74
18 6 0.26
ACGTcount: A:0.55, C:0.04, G:0.00, T:0.40
Consensus pattern (18 bp):
TATATAAAATATATATAA
Found at i:46578 original size:8 final size:9
Alignment explanation
Indices: 46560--46589 Score: 60
Period size: 9 Copynumber: 3.3 Consensus size: 9
46550 TCTTTTATAA
46560 TTTATTTTT
1 TTTATTTTT
46569 TTTATTTTT
1 TTTATTTTT
46578 TTTATTTTT
1 TTTATTTTT
46587 TTT
1 TTT
46590 CATTGGTGAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.10, C:0.00, G:0.00, T:0.90
Consensus pattern (9 bp):
TTTATTTTT
Found at i:47896 original size:20 final size:20
Alignment explanation
Indices: 47867--47919 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 20
47857 TCGGTTTGAA
* *
47867 TCAACTCGAACC-GACCTGAT
1 TCAACCCGAACCAG-CCTGAG
47887 TCAACCCGAACCAGCCTGAG
1 TCAACCCGAACCAGCCTGAG
*
47907 TCAACCTGAACCA
1 TCAACCCGAACCA
47920 ATCTAACCCA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
20 28 0.97
21 1 0.03
ACGTcount: A:0.32, C:0.38, G:0.15, T:0.15
Consensus pattern (20 bp):
TCAACCCGAACCAGCCTGAG
Found at i:55420 original size:35 final size:33
Alignment explanation
Indices: 55376--55483 Score: 144
Period size: 35 Copynumber: 3.1 Consensus size: 33
55366 CAATTCTCAT
55376 TTTCATTCTAAACCACAAATTCCAAAGTAATTCAA
1 TTTCATTCTAAACC-CAAATTCCAAA-TAATTCAA
55411 TTTCATTCTAAACCCTAAATTCCAAAATAATTCAA
1 TTTCATTCTAAACCC-AAATTCC-AAATAATTCAA
* * *
55446 TTACATTCTAAAACCCAAATTCTAAATACTTCAA
1 TTTCATTCT-AAACCCAAATTCCAAATAATTCAA
55480 TTTC
1 TTTC
55484 TGTCTTTTTA
Statistics
Matches: 66, Mismatches: 4, Indels: 7
0.86 0.05 0.09
Matches are distributed among these distances:
34 14 0.21
35 43 0.65
36 9 0.14
ACGTcount: A:0.42, C:0.23, G:0.01, T:0.34
Consensus pattern (33 bp):
TTTCATTCTAAACCCAAATTCCAAATAATTCAA
Found at i:55553 original size:31 final size:30
Alignment explanation
Indices: 55518--55583 Score: 71
Period size: 30 Copynumber: 2.2 Consensus size: 30
55508 CCTAAATTAT
55518 TAATTAATTACTT-TTATATTTAAAAACATGA
1 TAATTAATTA-TTATTA-ATTTAAAAACATGA
** *
55549 TAATTTTTTATTATTAATTTAAAGACATGA
1 TAATTAATTATTATTAATTTAAAAACATGA
*
55579 AAATT
1 TAATT
55584 TTTTCAATAG
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
30 19 0.63
31 11 0.37
ACGTcount: A:0.44, C:0.05, G:0.05, T:0.47
Consensus pattern (30 bp):
TAATTAATTATTATTAATTTAAAAACATGA
Found at i:56327 original size:35 final size:34
Alignment explanation
Indices: 56279--56390 Score: 145
Period size: 35 Copynumber: 3.2 Consensus size: 34
56269 ATTTCTCCTT
*
56279 AAATTGAAGTATTTTAGAATTTAGGGTTTAGAATG
1 AAATTGAATTATTTT-GAATTTAGGGTTTAGAATG
*
56314 TAATTGAATTATTTTGGAATTTAGGGTTTAGAATG
1 AAATTGAATTATTTT-GAATTTAGGGTTTAGAATG
* *
56349 AAATTGAATTACTTTGAAATTT-GGGATTTATAATG
1 AAATTGAATTATTTTG-AATTTAGGG-TTTAGAATG
56384 AAATTGA
1 AAATTGA
56391 GGAATGTTTT
Statistics
Matches: 69, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
34 4 0.06
35 65 0.94
ACGTcount: A:0.37, C:0.01, G:0.21, T:0.42
Consensus pattern (34 bp):
AAATTGAATTATTTTGAATTTAGGGTTTAGAATG
Found at i:57556 original size:3 final size:3
Alignment explanation
Indices: 57550--57581 Score: 55
Period size: 3 Copynumber: 10.3 Consensus size: 3
57540 CACCCCCAGG
57550 TCT TCT TCT TCCT TCT TCT TCT TCT TCT TCT T
1 TCT TCT TCT T-CT TCT TCT TCT TCT TCT TCT T
57582 GGAAAACGGT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 25 0.89
4 3 0.11
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (3 bp):
TCT
Found at i:63457 original size:18 final size:19
Alignment explanation
Indices: 63434--63472 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
63424 TTTAAATATT
*
63434 AATAAAAACGATTAAA-TA
1 AATAAAAACAATTAAAGTA
*
63452 AATAAAAGCAATTAAAGTA
1 AATAAAAACAATTAAAGTA
63471 AA
1 AA
63473 AATAAGAGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 14 0.78
19 4 0.22
ACGTcount: A:0.67, C:0.05, G:0.08, T:0.21
Consensus pattern (19 bp):
AATAAAAACAATTAAAGTA
Found at i:64687 original size:17 final size:17
Alignment explanation
Indices: 64667--64699 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
64657 ATATTTATTT
64667 ATATAAAATATAATATA
1 ATATAAAATATAATATA
64684 ATATAAAATATAATAT
1 ATATAAAATATAATAT
64700 CGTGATCTCG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (17 bp):
ATATAAAATATAATATA
Found at i:69817 original size:24 final size:25
Alignment explanation
Indices: 69757--69817 Score: 90
Period size: 24 Copynumber: 2.5 Consensus size: 25
69747 TAAAATAATT
69757 CAGGTCAAGTA-TCAGATCAAAATC
1 CAGGTCAAGTATTCAGATCAAAATC
*
69781 CAGGTCAAGTATTCA-ATCAGAATC
1 CAGGTCAAGTATTCAGATCAAAATC
*
69805 CAGGTCAGGTATT
1 CAGGTCAAGTATT
69818 ATAATAGAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
24 31 0.91
25 3 0.09
ACGTcount: A:0.36, C:0.20, G:0.20, T:0.25
Consensus pattern (25 bp):
CAGGTCAAGTATTCAGATCAAAATC
Found at i:76344 original size:20 final size:20
Alignment explanation
Indices: 76319--76356 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
76309 TTTGGTTCAC
76319 GGAATGTAAGATTACCAGTG
1 GGAATGTAAGATTACCAGTG
76339 GGAATGTAAGATTACCAG
1 GGAATGTAAGATTACCAG
76357 GGAATAGGAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.37, C:0.11, G:0.29, T:0.24
Consensus pattern (20 bp):
GGAATGTAAGATTACCAGTG
Found at i:79922 original size:2 final size:2
Alignment explanation
Indices: 79915--79958 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
79905 TTTAAGTTAG
79915 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
79957 AT
1 AT
79959 GTAACTAAAT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:81764 original size:45 final size:45
Alignment explanation
Indices: 81699--81784 Score: 118
Period size: 45 Copynumber: 1.9 Consensus size: 45
81689 TGTATTTCTT
*
81699 ATATTAACATTTCCGGTAAAAAAAATAACATTTTAGGTAGTGCTA
1 ATATTAACATTTCCGATAAAAAAAATAACATTTTAGGTAGTGCTA
* * * * *
81744 ATATTAATATTTTCGATAAAAATAATAATATTTTATGTAGT
1 ATATTAACATTTCCGATAAAAAAAATAACATTTTAGGTAGT
81785 ACTTTATCGA
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
45 35 1.00
ACGTcount: A:0.43, C:0.07, G:0.10, T:0.40
Consensus pattern (45 bp):
ATATTAACATTTCCGATAAAAAAAATAACATTTTAGGTAGTGCTA
Found at i:87452 original size:41 final size:41
Alignment explanation
Indices: 87400--87519 Score: 159
Period size: 41 Copynumber: 2.9 Consensus size: 41
87390 AAAATACCGC
* * *
87400 TAAAGATTCGTACTTTAGTGGCGTTTGTATACAAACGCCGT
1 TAAAGACTCGTACTTTAGTGGCGTTTTTATACAAACGCCAT
*
87441 TAAAGACTCGTACTTTAGTGGCGTTTTTATACAAACACCAT
1 TAAAGACTCGTACTTTAGTGGCGTTTTTATACAAACGCCAT
* * * * *
87482 TAAATACTCATACATTAGTGGTGTTTTTATATAAACGC
1 TAAAGACTCGTACTTTAGTGGCGTTTTTATACAAACGC
87520 TGTAATAGGA
Statistics
Matches: 69, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
41 69 1.00
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.36
Consensus pattern (41 bp):
TAAAGACTCGTACTTTAGTGGCGTTTTTATACAAACGCCAT
Found at i:89847 original size:25 final size:26
Alignment explanation
Indices: 89805--89853 Score: 64
Period size: 25 Copynumber: 1.9 Consensus size: 26
89795 TTCACCAAAA
*
89805 AAATATTTTAAATAAAAAT-AAATTT
1 AAATAATTTAAATAAAAATCAAATTT
* *
89830 AAATAATTTAACTCAAAATCAAAT
1 AAATAATTTAAATAAAAATCAAAT
89854 ATAATCATAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 16 0.80
26 4 0.20
ACGTcount: A:0.59, C:0.06, G:0.00, T:0.35
Consensus pattern (26 bp):
AAATAATTTAAATAAAAATCAAATTT
Found at i:93104 original size:21 final size:21
Alignment explanation
Indices: 93074--93114 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
93064 AAATATTAAA
*
93074 AAATATTAATGTTTTAGGTAG
1 AAATAATAATGTTTTAGGTAG
93095 AAATAATAATGTTTTAGGTA
1 AAATAATAATGTTTTAGGTA
93115 ATTTTTACTG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.41, C:0.00, G:0.17, T:0.41
Consensus pattern (21 bp):
AAATAATAATGTTTTAGGTAG
Found at i:98004 original size:49 final size:49
Alignment explanation
Indices: 97932--98031 Score: 200
Period size: 49 Copynumber: 2.0 Consensus size: 49
97922 TGTTCTTAGT
97932 CTTGATGTACTTGATTCTAGTGATGATCATTTTCACTAAAAAAGTTTTA
1 CTTGATGTACTTGATTCTAGTGATGATCATTTTCACTAAAAAAGTTTTA
97981 CTTGATGTACTTGATTCTAGTGATGATCATTTTCACTAAAAAAGTTTTA
1 CTTGATGTACTTGATTCTAGTGATGATCATTTTCACTAAAAAAGTTTTA
98030 CT
1 CT
98032 GTCTAAAAGT
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 51 1.00
ACGTcount: A:0.30, C:0.13, G:0.14, T:0.43
Consensus pattern (49 bp):
CTTGATGTACTTGATTCTAGTGATGATCATTTTCACTAAAAAAGTTTTA
Found at i:100544 original size:99 final size:99
Alignment explanation
Indices: 100361--100566 Score: 234
Period size: 99 Copynumber: 2.1 Consensus size: 99
100351 AGGACCGACA
* *
100361 CAAAGATCTGCAGCTTTAGCAGCTTTAATGACTGCATTAAATCCATCAGCAGAACCCAAAACCTC
1 CAAAGAGCTGCAGCTTTAGCAGCTTTAATGACTGCATTAAATCCATCAGCAGAAACCAAAACCTC
* * * * *
100426 ATCTCCAAAGCCTCCCAGTTCTAGTCAGGGATCG
66 AGCTCCAAAGCATACCAGTTCTAGTCAAGCATCG
* * ** * * * *
100460 CAAAGAGCTTCAGCTTTGGCAGCTTTAGA-GTTTGCATTCAATCCTTCATCGGAAACCAAAACCT
1 CAAAGAGCTGCAGCTTTAGCAGCTTTA-ATGACTGCATTAAATCCATCAGCAGAAACCAAAACCT
* * *
100524 CAGCTCCAAAGCATATCAGTTTTCGTCAAGCATCG
65 CAGCTCCAAAGCATACCAGTTCTAGTCAAGCATCG
100559 CAAAGAGC
1 CAAAGAGC
100567 GGCCGCAATA
Statistics
Matches: 88, Mismatches: 18, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
99 87 0.99
100 1 0.01
ACGTcount: A:0.31, C:0.28, G:0.17, T:0.24
Consensus pattern (99 bp):
CAAAGAGCTGCAGCTTTAGCAGCTTTAATGACTGCATTAAATCCATCAGCAGAAACCAAAACCTC
AGCTCCAAAGCATACCAGTTCTAGTCAAGCATCG
Found at i:105092 original size:55 final size:54
Alignment explanation
Indices: 105020--105472 Score: 368
Period size: 55 Copynumber: 8.2 Consensus size: 54
105010 CAGGATAAGC
* * * *
105020 AAGACTTGAAAAATCTTCGAATGACGGGTCTGCTCCCTATTCTTTCAGGGAGTAT
1 AAGACTCGAACAATCTTC-AATAACGGGTCTGCTCCCTATTCTTTCAGAGAGTAT
* * * ** * *
105075 AAGACTCAAACAATCTTCGGCA-AACGTGTCTGCTCCCTATTCAGTCGGGGAGTAT
1 AAGACTCGAACAATCTTC--AATAACGGGTCTGCTCCCTATTCTTTCAGAGAGTAT
* * *
105130 AAGACTCGAATAATCTTCAATAAACGAGT-TCGCTCTCTATT-TCTTCAGAGAGTAT
1 AAGACTCGAACAATCTTCAAT-AACGGGTCT-GCTCCCTATTCT-TTCAGAGAGTAT
* * * * *
105185 -AGAACACGAACAATTTTCATAAAATGGGT-TCGCTCTCTATTCTTTCAGAGAGTAT
1 AAG-ACTCGAACAATCTTCA-ATAACGGGTCT-GCTCCCTATTCTTTCAGAGAGTAT
** * ** * *
105240 GTGACTCGAATAATCTTCTGTAATCAGGTTTGCTCCCTATTGC-TTCAGAGAGTAT
1 AAGACTCGAACAATCTTCAATAA-CGGGTCTGCTCCCTATT-CTTTCAGAGAGTAT
* *
105295 GAGACTCGAACAATCTTCAATAATCGTGTCTGCTCCCTATTTCTTT-AGAGAGTAT
1 AAGACTCGAACAATCTTCAATAA-CGGGTCTGCTCCCTA-TTCTTTCAGAGAGTAT
*
105350 AAGACTCGAACAATCTTCAATAAACGGGT-TCGCTCCCTCTTTCTTTCAG-GAAGTAT
1 AAGACTCGAACAATCTTCAAT-AACGGGTCT-GCTCCCT-ATTCTTTCAGAG-AGTAT
* * * *
105406 -AGAACTCGAATAATCTTCAACAATCGTGTCTGCTCCCTATTCCTTCAGAGAGTAT
1 AAG-ACTCGAACAATCTTCAATAA-CGGGTCTGCTCCCTATTCTTTCAGAGAGTAT
105461 AAGACTCGAACA
1 AAGACTCGAACA
105473 TATTCTCTTA
Statistics
Matches: 324, Mismatches: 50, Indels: 48
0.77 0.12 0.11
Matches are distributed among these distances:
53 1 0.00
54 6 0.02
55 266 0.82
56 50 0.15
57 1 0.00
ACGTcount: A:0.29, C:0.22, G:0.18, T:0.31
Consensus pattern (54 bp):
AAGACTCGAACAATCTTCAATAACGGGTCTGCTCCCTATTCTTTCAGAGAGTAT
Found at i:105225 original size:110 final size:109
Alignment explanation
Indices: 105051--105470 Score: 433
Period size: 110 Copynumber: 3.8 Consensus size: 109
105041 TGACGGGTCT
* * **
105051 GCTCCCTA-TTCTTTCAGGGAGTATA-AGACTCAAACAATCTTCGGCAAA-CGTGTCTGCTCCCT
1 GCTCCCTATTTC-TTCAGAGAGTATAGA-ACTCGAACAATCTTC-AAAAATCGTGTCTGCTCCCT
* * *
105113 ATTCAGTCGGGGAGTATAAGACTCGAATAATCTTCAATAAACGAGTTC
63 ATTC-TTCAGAGAGTATAAGACTCGAATAATCTTCAATAAACGAGTTC
* * * * *
105161 GCTCTCTATTTCTTCAGAGAGTATAGAACACGAACAATTTTCATAAAAT-GGGT-TCGCTCTCTA
1 GCTCCCTATTTCTTCAGAGAGTATAGAACTCGAACAATCTTCA-AAAATCGTGTCT-GCTCCCTA
** ** * *
105224 TTCTTTCAGAGAGTATGTGACTCGAATAATCTTCTGTAATC-AGGTTT
64 TTC-TTCAGAGAGTATAAGACTCGAATAATCTTCAATAAACGA-GTTC
* *
105271 GCTCCCTATTGCTTCAGAGAGTAT-GAGACTCGAACAATCTTCAATAATCGTGTCTGCTCCCTAT
1 GCTCCCTATTTCTTCAGAGAGTATAGA-ACTCGAACAATCTTCAAAAATCGTGTCTGCTCCCTA-
* * *
105335 TTCTTTAGAGAGTATAAGACTCGAACAATCTTCAATAAACGGGTTC
64 TTCTTCAGAGAGTATAAGACTCGAATAATCTTCAATAAACGAGTTC
* * *
105381 GCTCCCTCTTTCTTTCAG-GAAGTATAGAACTCGAATAATCTTCAACAATCGTGTCTGCTCCCTA
1 GCTCCCTATTTC-TTCAGAG-AGTATAGAACTCGAACAATCTTCAAAAATCGTGTCTGCTCCCTA
105445 TTCCTTCAGAGAGTATAAGACTCGAA
64 TT-CTTCAGAGAGTATAAGACTCGAA
105471 CATATTCTCT
Statistics
Matches: 255, Mismatches: 40, Indels: 29
0.79 0.12 0.09
Matches are distributed among these distances:
109 8 0.03
110 171 0.67
111 74 0.29
112 2 0.01
ACGTcount: A:0.29, C:0.22, G:0.17, T:0.32
Consensus pattern (109 bp):
GCTCCCTATTTCTTCAGAGAGTATAGAACTCGAACAATCTTCAAAAATCGTGTCTGCTCCCTATT
CTTCAGAGAGTATAAGACTCGAATAATCTTCAATAAACGAGTTC
Found at i:105553 original size:54 final size:54
Alignment explanation
Indices: 105464--105966 Score: 909
Period size: 54 Copynumber: 9.3 Consensus size: 54
105454 AGAGTATAAG
* * *
105464 ACTCGAACATATTC-TCTTACAGGTTCGCTCACTCTTTCTCTAGGGAGTATGGA
1 ACTCGAACATCTTCTTCTTACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGA
*
105517 ACTCGAACATCTTCTTCTTACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATGTA
1 ACTCGAACATCTTCTTCTTACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGA
105571 ACTCGAACATCTTCTTCTTACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGA
1 ACTCGAACATCTTCTTCTTACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGA
105625 ACTCGAACATCTTCTTCTTACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGA
1 ACTCGAACATCTTCTTCTTACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGA
*
105679 ACTCGAACATCTTCTTCTTACGGGTTCGCTCCCTCTTTCTCTAAGGAGTATGGA
1 ACTCGAACATCTTCTTCTTACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGA
105733 ACTCGAACATCTTCTTCTTACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGA
1 ACTCGAACATCTTCTTCTTACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGA
* *
105787 ACTCGAACATCTTCTTCTTACGGGTTCGCTCTCTCTTTCTCTAGGAAGTATGGA
1 ACTCGAACATCTTCTTCTTACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGA
* *
105841 ACTCGAACATCTTCTTCTTACGGGTTCGCTCTCTCTTTCTCTAGGGAGTATGAA
1 ACTCGAACATCTTCTTCTTACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGA
105895 ACTCGAACATCTTCTTCTTACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGA
1 ACTCGAACATCTTCTTCTTACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGA
*
105949 ACTCGAACATTTTCTTCT
1 ACTCGAACATCTTCTTCT
105967 GCTTTACTAC
Statistics
Matches: 435, Mismatches: 14, Indels: 1
0.97 0.03 0.00
Matches are distributed among these distances:
53 13 0.03
54 422 0.97
ACGTcount: A:0.18, C:0.27, G:0.19, T:0.36
Consensus pattern (54 bp):
ACTCGAACATCTTCTTCTTACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGA
Found at i:106024 original size:37 final size:37
Alignment explanation
Indices: 105966--106045 Score: 108
Period size: 37 Copynumber: 2.2 Consensus size: 37
105956 CATTTTCTTC
* * *
105966 TGCTTTACTACTTTCTTGTGAAGACTTCAAGATT-ATT
1 TGCTTCACTACTCTCTCGTGAAGACTT-AAGATTGATT
*
106003 TGCTTCACTACTCTCTCGTGAAGACTTAAGTTTGATT
1 TGCTTCACTACTCTCTCGTGAAGACTTAAGATTGATT
106040 TGCTTC
1 TGCTTC
106046 GAAGGTCGAA
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
36 5 0.13
37 33 0.87
ACGTcount: A:0.21, C:0.20, G:0.15, T:0.44
Consensus pattern (37 bp):
TGCTTCACTACTCTCTCGTGAAGACTTAAGATTGATT
Found at i:106416 original size:36 final size:37
Alignment explanation
Indices: 106341--106464 Score: 142
Period size: 37 Copynumber: 3.4 Consensus size: 37
106331 TTGCTCAAAC
* * * *
106341 ACTCTTCCGAGAAGGCTTAAAAAGGATATGCTTCACT
1 ACTCTTCGGTGAAGGCTTAAAATGGATTTGCTTCACT
*
106378 ACTCTTCGGTGAAGGCTTAAGATGG-TTTGCTTCACT
1 ACTCTTCGGTGAAGGCTTAAAATGGATTTGCTTCACT
* * * *
106414 ACTATTTGGTGAAGGCTCAAAATGGATTTGTTTCACT
1 ACTCTTCGGTGAAGGCTTAAAATGGATTTGCTTCACT
* *
106451 GCTCTTTGGTGAAG
1 ACTCTTCGGTGAAG
106465 ACTTGACTTT
Statistics
Matches: 74, Mismatches: 12, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
36 31 0.42
37 43 0.58
ACGTcount: A:0.25, C:0.18, G:0.23, T:0.34
Consensus pattern (37 bp):
ACTCTTCGGTGAAGGCTTAAAATGGATTTGCTTCACT
Found at i:107826 original size:125 final size:125
Alignment explanation
Indices: 107617--107849 Score: 335
Period size: 125 Copynumber: 1.9 Consensus size: 125
107607 TCTTATTCAG
** *
107617 GTACGAGTCTTCAAAATGCCCCAACACCTCAAATTATAAGGCTCATTTTCAATGCCTTCTTGGTC
1 GTACGAGTCTTCAAAATGCCCCAACACCTCAAATTATAAGGCTCATTTTCAATGAATCCTTGGTC
* *
107682 TAAATCTTATCATCTCAACATGATGTGGGTTCAGTCGTGCCCCGACTTTATCTCATACTA
66 CAAATCTTATCATCTCAACATGATGTGGGTTCAGTCATGCCCCGACTTTATCTCATACTA
* * *
107742 GTACG-GTCCTTCAAAATGCCCCATCACCTCAATTTGTAAGGCTCATTCTTC-ATGAATCCTTGG
1 GTACGAGT-CTTCAAAATGCCCCAACACCTCAAATTATAAGGCTCATT-TTCAATGAATCCTTGG
* * *
107805 TCCAAATCTTGTCATCTCAACATTATGTGGGTTTAGTCATGCCCC
64 TCCAAATCTTATCATCTCAACATGATGTGGGTTCAGTCATGCCCC
107850 AATATGGGTA
Statistics
Matches: 95, Mismatches: 11, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
124 2 0.02
125 90 0.95
126 3 0.03
ACGTcount: A:0.25, C:0.27, G:0.15, T:0.33
Consensus pattern (125 bp):
GTACGAGTCTTCAAAATGCCCCAACACCTCAAATTATAAGGCTCATTTTCAATGAATCCTTGGTC
CAAATCTTATCATCTCAACATGATGTGGGTTCAGTCATGCCCCGACTTTATCTCATACTA
Found at i:109652 original size:13 final size:13
Alignment explanation
Indices: 109634--109659 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
109624 AAAGTAACAT
109634 GAATTTTTTTAAA
1 GAATTTTTTTAAA
109647 GAATTTTTTTAAA
1 GAATTTTTTTAAA
109660 TATCATTATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.00, G:0.08, T:0.54
Consensus pattern (13 bp):
GAATTTTTTTAAA
Found at i:116658 original size:20 final size:20
Alignment explanation
Indices: 116620--116658 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
116610 TGTGCACGTG
* *
116620 GTGTGAATGGTTGCTAGCTA
1 GTGTGAATGGCTGCAAGCTA
116640 GTGTGAATGGCTGCAAGCT
1 GTGTGAATGGCTGCAAGCT
116659 GTTAGCACGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.21, C:0.13, G:0.36, T:0.31
Consensus pattern (20 bp):
GTGTGAATGGCTGCAAGCTA
Found at i:118593 original size:20 final size:20
Alignment explanation
Indices: 118565--118628 Score: 67
Period size: 20 Copynumber: 3.2 Consensus size: 20
118555 TTTATGAATT
118565 TTATTGTTTTAGACTTAATA
1 TTATTGTTTTAGACTTAATA
* * * *
118585 TTATAG-TTTATACATATATT
1 TTATTGTTTTAGACTTA-ATA
*
118605 TTATTGTTTTAGAGTTAATA
1 TTATTGTTTTAGACTTAATA
118625 TTAT
1 TTAT
118629 GATCGAATCT
Statistics
Matches: 33, Mismatches: 9, Indels: 4
0.72 0.20 0.09
Matches are distributed among these distances:
19 8 0.24
20 18 0.55
21 7 0.21
ACGTcount: A:0.31, C:0.03, G:0.09, T:0.56
Consensus pattern (20 bp):
TTATTGTTTTAGACTTAATA
Found at i:118595 original size:40 final size:40
Alignment explanation
Indices: 118539--118631 Score: 127
Period size: 40 Copynumber: 2.3 Consensus size: 40
118529 ATTTGATACT
**
118539 TTAATATTATGATTTATTTATGA-ATTTTATTGTTTTAGAC
1 TTAATATTATGATTTATACAT-ATATTTTATTGTTTTAGAC
*
118579 TTAATATTAT-AGTTTATACATATATTTTATTGTTTTAGAG
1 TTAATATTATGA-TTTATACATATATTTTATTGTTTTAGAC
118619 TTAATATTATGAT
1 TTAATATTATGAT
118632 CGAATCTTGA
Statistics
Matches: 47, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
39 2 0.04
40 44 0.94
41 1 0.02
ACGTcount: A:0.32, C:0.02, G:0.10, T:0.56
Consensus pattern (40 bp):
TTAATATTATGATTTATACATATATTTTATTGTTTTAGAC
Found at i:136524 original size:2 final size:2
Alignment explanation
Indices: 136517--136542 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
136507 CCTTCAATTA
136517 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
136543 TATTCAAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:144214 original size:23 final size:22
Alignment explanation
Indices: 144161--144216 Score: 58
Period size: 24 Copynumber: 2.4 Consensus size: 22
144151 TATGAGGATC
*
144161 ATGCCACAAAAGCAAAGGAAAT
1 ATGCCACAAAAGCAAAGAAAAT
* *
144183 ACGTACCACAAGAGCAAAGAAAAAT
1 A--TGCCACAAAAGCAAAG-AAAAT
144208 ATGCCACAA
1 ATGCCACAA
144217 TGACATATAT
Statistics
Matches: 27, Mismatches: 4, Indels: 5
0.75 0.11 0.14
Matches are distributed among these distances:
22 1 0.04
23 7 0.26
24 14 0.52
25 5 0.19
ACGTcount: A:0.54, C:0.21, G:0.16, T:0.09
Consensus pattern (22 bp):
ATGCCACAAAAGCAAAGAAAAT
Found at i:148570 original size:32 final size:32
Alignment explanation
Indices: 148534--148610 Score: 91
Period size: 32 Copynumber: 2.4 Consensus size: 32
148524 TTGGGCGTAG
* * *
148534 GAGCCAATCTAAGACAGTACCTTGGGGCCATA
1 GAGCCAACCCAAGACAGTACCTTGGGGACATA
** *
148566 GAGCCAACCCAAGGGAGTACCTTGGGGACTTA
1 GAGCCAACCCAAGACAGTACCTTGGGGACATA
*
148598 GAGCCTACCCAAG
1 GAGCCAACCCAAG
148611 GGTCACCATA
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
32 38 1.00
ACGTcount: A:0.30, C:0.27, G:0.27, T:0.16
Consensus pattern (32 bp):
GAGCCAACCCAAGACAGTACCTTGGGGACATA
Found at i:148611 original size:32 final size:32
Alignment explanation
Indices: 148549--148612 Score: 101
Period size: 32 Copynumber: 2.0 Consensus size: 32
148539 AATCTAAGAC
*
148549 AGTACCTTGGGGCCATAGAGCCAACCCAAGGG
1 AGTACCTTGGGGACATAGAGCCAACCCAAGGG
* *
148581 AGTACCTTGGGGACTTAGAGCCTACCCAAGGG
1 AGTACCTTGGGGACATAGAGCCAACCCAAGGG
148613 TCACCATATG
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.27, C:0.27, G:0.31, T:0.16
Consensus pattern (32 bp):
AGTACCTTGGGGACATAGAGCCAACCCAAGGG
Found at i:151053 original size:16 final size:17
Alignment explanation
Indices: 151013--151060 Score: 62
Period size: 16 Copynumber: 2.8 Consensus size: 17
151003 TGTTTCTGAG
*
151013 GGAATTGAAATCTGTAAA
1 GGAATTGGAATCTGT-AA
*
151031 TGAATTGGAATCTGT-A
1 GGAATTGGAATCTGTAA
151047 GGAATTGGAATCTG
1 GGAATTGGAATCTG
151061 AATCTGAAAC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
16 14 0.52
18 13 0.48
ACGTcount: A:0.35, C:0.06, G:0.27, T:0.31
Consensus pattern (17 bp):
GGAATTGGAATCTGTAA
Found at i:153037 original size:323 final size:318
Alignment explanation
Indices: 152376--153051 Score: 858
Period size: 323 Copynumber: 2.1 Consensus size: 318
152366 TGTTTCTTAT
* * * *
152376 GTTCATTGGTTTGGAATGTTAAGAATGGAACAGTTAGGTGTGGTTTGGTAAATGATAATTGATTG
1 GTTCATTGGTTTTGAATGTTAAGAATGGAACAGATAGGTGTGGTTTCGTAAATGATAAGTGATTG
* *
152441 TCAATCTCATATAGGAGATTAGCCTTAAATTGGTTATTTTCAATAACACGTGATACTTAAAGCAT
66 TCAATCCCATATAGGAGATTAGCCTTAAATTGGTTATTTTCAACAACACGTGATACTTAAAGCAT
* * * * *
152506 TCAAGCAATGTTATTTTTATTCATCATTTGACCACCTTACCTCACCATTTATCGCGTTTGACTAC
131 TCAAGCAATGCTATTTTTATTCATCATTTGACCACATTACCTCACCATTTATCACATTTAACTAC
* * * *
152571 TATTCGTTCAGTTCTTGTTTGGTTACCAATAAAGTAACAAAAATTGGAGGAAAGGGAAACTTGAA
196 TATTCATTCACTTCATGTTTGGTTACCAATAAAGTAACAAAAATGGGAGGAAAGGGAAACTTGAA
* * ** * *
152636 ACAATTGTTTCACTGTGCTAAAGAACCTGCGACACCTGAGTTTAGTAAAGGGTAGTGTTTTAT
261 ACAATTGTTTCACTGTGCTAAACAACCTGCGACACCTGAGTTCAGT--A---TAGCATTTCAA
* *
152699 GTTCATTGATTTTGAATGCTAAGAATGGAACAGATAGGTGCT-GTTTCGTAAATGATAAGTGATT
1 GTTCATTGGTTTTGAATGTTAAGAATGGAACAGATAGGTG-TGGTTTCGTAAATGATAAGTGATT
*
152763 GTCAATCCCATAT-GGAAGATTAGCCTTAAATTGGTTATTTTCAACAACACGTGATACTTAATGC
65 GTCAATCCCATATAGG-AGATTAGCCTTAAATTGGTTATTTTCAACAACACGTGATACTTAAAGC
* * * *
152827 ATTC-GGACAATGCTATTTTTATTCATCATTTGACTACATTACCTCATCATTTCTCACATTTAAC
129 ATTCAAG-CAATGCTATTTTTATTCATCATTTGACCACATTACCTCACCATTTATCACATTTAAC
* * *
152891 TAC-AGTTTATTCACTTCATGTTTGGTTACCAATAAAGTAAACAAAAGTGGGAGGAAAATGGAAA
193 TACTA-TTCATTCACTTCATGTTTGGTTACCAATAAAGT-AACAAAAATGGGAGG-AAAGGGAAA
* * *
152955 CTTGAAACAATTGTTTCGCTGTGCTAAACAACCTGCTTTTGTCATCTGAGTTCAGT-TAGCATTT
255 CTTGAAACAATTGTTTCACTGTGCTAAACAACCTGC----GACACCTGAGTTCAGTATAGCATTT
153019 CAA
316 CAA
* *
153022 GTTCTTTGGTTTTGAATGTTAAAAATGGAA
1 GTTCATTGGTTTTGAATGTTAAGAATGGAA
153052 TAATTAAGTG
Statistics
Matches: 305, Mismatches: 38, Indels: 20
0.84 0.10 0.06
Matches are distributed among these distances:
322 4 0.01
323 232 0.76
324 14 0.05
325 42 0.14
329 13 0.04
ACGTcount: A:0.31, C:0.15, G:0.18, T:0.36
Consensus pattern (318 bp):
GTTCATTGGTTTTGAATGTTAAGAATGGAACAGATAGGTGTGGTTTCGTAAATGATAAGTGATTG
TCAATCCCATATAGGAGATTAGCCTTAAATTGGTTATTTTCAACAACACGTGATACTTAAAGCAT
TCAAGCAATGCTATTTTTATTCATCATTTGACCACATTACCTCACCATTTATCACATTTAACTAC
TATTCATTCACTTCATGTTTGGTTACCAATAAAGTAACAAAAATGGGAGGAAAGGGAAACTTGAA
ACAATTGTTTCACTGTGCTAAACAACCTGCGACACCTGAGTTCAGTATAGCATTTCAA
Found at i:153276 original size:330 final size:335
Alignment explanation
Indices: 152779--153493 Score: 761
Period size: 330 Copynumber: 2.1 Consensus size: 335
152769 CCCATATGGA
* * *
152779 AGATTAGCCTTAAATTGGTTATTTTCAACAACACGTGATACTTAATGCATTCGGACAATGCTATT
1 AGATTACCCTT-AATTGGTTATTTTCAATAACA--TG-TAGTTAATGCATTCGGACAATGCTATT
* *
152844 TTTATTCATCATTTGACTACATTACCTCATCATTTCTCACATTTAACTACAGTTTATTCACTTCA
62 TTTATTCATCATTTGACTACATTACCTCAACATTACTCACATTTAACTACAGTTTATTCACTTCA
* * ** * *
152909 TGTTTGGTTACCAATAAAGTAAACAAAAGTGGGAGGAAAATGGAAACTTGAAACAATTGTTTCGC
127 TGTTTGGTAACCAAGAAAACAAACAAAAGTGGGAGGAAAATGCAAACTTGAAACAATTGTTTCAC
* * * *
152974 TGTGCTAAACAACCTGCTTTTGTCATCTGAGTTCAG-T-TA-G-CA-TTTCA-AGTT-CTTTGGT
192 TGTGCAAAACAACCTGCTTTTGTCACCTGACTTCAGATATAGGTCATTTTCATAGTTCCATTGGT
* * * * *
153032 TTTGAATGTTAAAAATGGAATAATTAAGTGCTGTTTGGT-GTGATAAGTAATTGCTCAATGCGAT
257 TATGAACGTTAAAAATGAAATAATTAAGTGCTGTTTGGTAATGATAAATAATT-CTCAATGCGAT
*
153096 TGGTTTCTTATTTTGG
321 TGGTTT-TCATTTTGG
* *
153112 AGATTACCCTTAATTGGTTATTTTCAATAACATGTAGTTAATGCATTCAGG-GAATGGTATTTGT
1 AGATTACCCTTAATTGGTTATTTTCAATAACATGTAGTTAATGCATTC-GGACAATGCTATTT-T
* * * * * * *
153176 TTTTCATCATTTGGAC-ATATTATCTTAACATTACTCTCATTTGACTACAG-TTAGTTCACTTCC
64 TATTCATCATTT-GACTACATTACCTCAACATTACTCACATTTAACTACAGTTTA-TTCACTTCA
* * * *
153239 TGTTTGGTAACCGAGAAAACAAAGGAAAA-TTGGAGGAAAATGCAAACTTGAAACAATTTTTTCA
127 TGTTTGGTAACCAAGAAAACAAA-CAAAAGTGGGAGGAAAATGCAAACTTGAAACAATTGTTTCA
* * * * *
153303 CTTTGCAAAAGAACTTGCTTTTGTCACCTGACTTCAGTAAATAATAGTGTTTTATTTTCATATTT
191 CTGTGCAAAACAACCTGCTTTTGTCACCTGACTTCAG---AT-ATAG-G--TCATTTTCATAGTT
* * * *
153368 CCATTGGTTATGAACGTTAAAAATGAAATAGTTAGGTGTTTTTTGGTAAATGATAAATAATTCTC
249 CCATTGGTTATGAACGTTAAAAATGAAATAATTAAGTGCTGTTTGGT-AATGATAAATAATTCTC
*
153433 AATGCGTTTGGTTTTCATTTTGG
313 AATGCGATTGGTTTTCATTTTGG
* *
153456 AGGTTACCCTTAATTGGTTATTTTCAATAACTTGTAGT
1 AGATTACCCTTAATTGGTTATTTTCAATAACATGTAGT
153494 ACTTAATGCA
Statistics
Matches: 315, Mismatches: 46, Indels: 31
0.80 0.12 0.08
Matches are distributed among these distances:
329 25 0.08
330 131 0.42
331 7 0.02
332 20 0.06
333 10 0.03
334 1 0.00
336 2 0.01
338 1 0.00
341 1 0.00
342 5 0.02
343 3 0.01
344 82 0.26
345 16 0.05
346 11 0.03
ACGTcount: A:0.30, C:0.14, G:0.17, T:0.39
Consensus pattern (335 bp):
AGATTACCCTTAATTGGTTATTTTCAATAACATGTAGTTAATGCATTCGGACAATGCTATTTTTA
TTCATCATTTGACTACATTACCTCAACATTACTCACATTTAACTACAGTTTATTCACTTCATGTT
TGGTAACCAAGAAAACAAACAAAAGTGGGAGGAAAATGCAAACTTGAAACAATTGTTTCACTGTG
CAAAACAACCTGCTTTTGTCACCTGACTTCAGATATAGGTCATTTTCATAGTTCCATTGGTTATG
AACGTTAAAAATGAAATAATTAAGTGCTGTTTGGTAATGATAAATAATTCTCAATGCGATTGGTT
TTCATTTTGG
Found at i:161350 original size:20 final size:21
Alignment explanation
Indices: 161305--161361 Score: 66
Period size: 20 Copynumber: 2.8 Consensus size: 21
161295 AAACCGATTT
* *
161305 AACCGGTTTTCAACCGGTTATG
1 AACCGG-TTTCGACCGGTTACG
161327 -ACCGGTTTCGACCGGTT-CG
1 AACCGGTTTCGACCGGTTACG
161346 AACCGGTTT-GACCGGT
1 AACCGGTTTCGACCGGT
161362 CTGACCCGAT
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
19 8 0.25
20 19 0.59
21 5 0.16
ACGTcount: A:0.18, C:0.26, G:0.28, T:0.28
Consensus pattern (21 bp):
AACCGGTTTCGACCGGTTACG
Found at i:161359 original size:9 final size:9
Alignment explanation
Indices: 161317--161367 Score: 57
Period size: 10 Copynumber: 5.3 Consensus size: 9
161307 CCGGTTTTCA
161317 ACCGGTTATG
1 ACCGGTT-TG
161327 ACCGGTTTCG
1 ACCGGTTT-G
*
161337 ACCGGTTCG
1 ACCGGTTTG
161346 AACCGGTTTG
1 -ACCGGTTTG
*
161356 ACCGGTCTG
1 ACCGGTTTG
161365 ACC
1 ACC
161368 CGATCGACCG
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
9 13 0.36
10 23 0.64
ACGTcount: A:0.16, C:0.29, G:0.29, T:0.25
Consensus pattern (9 bp):
ACCGGTTTG
Found at i:161399 original size:17 final size:17
Alignment explanation
Indices: 161377--161414 Score: 76
Period size: 17 Copynumber: 2.2 Consensus size: 17
161367 CCGATCGACC
161377 GACCCGACCCGACCGTT
1 GACCCGACCCGACCGTT
161394 GACCCGACCCGACCGTT
1 GACCCGACCCGACCGTT
161411 GACC
1 GACC
161415 GTTGACTTTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.18, C:0.47, G:0.24, T:0.11
Consensus pattern (17 bp):
GACCCGACCCGACCGTT
Found at i:168606 original size:10 final size:9
Alignment explanation
Indices: 168591--168650 Score: 57
Period size: 10 Copynumber: 6.3 Consensus size: 9
168581 GCTGCTGGAA
168591 ACCGGTTCTG
1 ACCGGTT-TG
168601 ACCGGTTTG
1 ACCGGTTTG
168610 ACCGGTTTCG
1 ACCGGTTT-G
*
168620 ACCGGTTCG
1 ACCGGTTTG
*
168629 AACCGATTTG
1 -ACCGGTTTG
* *
168639 ACTGGTCTG
1 ACCGGTTTG
168648 ACC
1 ACC
168651 CGACCGACCG
Statistics
Matches: 41, Mismatches: 7, Indels: 5
0.77 0.13 0.09
Matches are distributed among these distances:
9 19 0.46
10 22 0.54
ACGTcount: A:0.15, C:0.28, G:0.28, T:0.28
Consensus pattern (9 bp):
ACCGGTTTG
Found at i:168666 original size:5 final size:5
Alignment explanation
Indices: 168647--168718 Score: 67
Period size: 5 Copynumber: 13.8 Consensus size: 5
168637 TGACTGGTCT
*
168647 GACCC GA-CC GA-CC GACCC GACCCC GACCGTT GACCC GACCC GACCC
1 GACCC GACCC GACCC GACCC GA-CCC GACC--C GACCC GACCC GACCC
*
168693 GACCGTT GACCC GACCC GACCC GACC
1 GACC--C GACCC GACCC GACCC GACC
168719 GTTGACCGTT
Statistics
Matches: 57, Mismatches: 4, Indels: 12
0.78 0.05 0.16
Matches are distributed among these distances:
4 8 0.14
5 36 0.63
6 5 0.09
7 8 0.14
ACGTcount: A:0.19, C:0.53, G:0.22, T:0.06
Consensus pattern (5 bp):
GACCC
Found at i:168693 original size:22 final size:22
Alignment explanation
Indices: 168658--168725 Score: 127
Period size: 22 Copynumber: 3.0 Consensus size: 22
168648 ACCCGACCGA
168658 CCGACCCGACCCCGACCGTTGAC
1 CCGACCCGA-CCCGACCGTTGAC
168681 CCGACCCGACCCGACCGTTGAC
1 CCGACCCGACCCGACCGTTGAC
168703 CCGACCCGACCCGACCGTTGAC
1 CCGACCCGACCCGACCGTTGAC
168725 C
1 C
168726 GTTGCTTTCT
Statistics
Matches: 45, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
22 36 0.80
23 9 0.20
ACGTcount: A:0.18, C:0.51, G:0.22, T:0.09
Consensus pattern (22 bp):
CCGACCCGACCCGACCGTTGAC
Found at i:170691 original size:34 final size:35
Alignment explanation
Indices: 170636--170710 Score: 134
Period size: 34 Copynumber: 2.2 Consensus size: 35
170626 CGATTATATA
*
170636 TATATATATTATTATTTTATATTTTTTATATTAAT
1 TATATATATTAATATTTTATATTTTTTATATTAAT
170671 TATATATA-TAATATTTTATATTTTTTATATTAAT
1 TATATATATTAATATTTTATATTTTTTATATTAAT
170705 TATATA
1 TATATA
170711 AAAAAATATT
Statistics
Matches: 39, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
34 31 0.79
35 8 0.21
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (35 bp):
TATATATATTAATATTTTATATTTTTTATATTAAT
Found at i:178489 original size:20 final size:21
Alignment explanation
Indices: 178461--178505 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 21
178451 TTGTTCTTCG
178461 CTTTCTCTTTATA-TTTT-TTT
1 CTTTCTCTTT-TACTTTTGTTT
*
178481 CTTTTTCTTTTACTTTTGTTT
1 CTTTCTCTTTTACTTTTGTTT
178502 CTTT
1 CTTT
178506 ATTTTATTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
19 2 0.09
20 13 0.59
21 7 0.32
ACGTcount: A:0.07, C:0.16, G:0.02, T:0.76
Consensus pattern (21 bp):
CTTTCTCTTTTACTTTTGTTT
Found at i:192574 original size:7 final size:7
Alignment explanation
Indices: 192552--192602 Score: 50
Period size: 7 Copynumber: 7.4 Consensus size: 7
192542 GTAGTTTTTT
192552 TTTAGGG
1 TTTAGGG
*
192559 -TTAGAG
1 TTTAGGG
192565 TTTAGGG
1 TTTAGGG
*
192572 TTTAGAG
1 TTTAGGG
*
192579 TTTAAGG
1 TTTAGGG
* *
192586 TTTATGA
1 TTTAGGG
192593 TTTAGGG
1 TTTAGGG
192600 TTT
1 TTT
192603 TAAGGTTTAT
Statistics
Matches: 34, Mismatches: 9, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
6 5 0.15
7 29 0.85
ACGTcount: A:0.22, C:0.00, G:0.31, T:0.47
Consensus pattern (7 bp):
TTTAGGG
Found at i:192578 original size:14 final size:14
Alignment explanation
Indices: 192552--192602 Score: 70
Period size: 14 Copynumber: 3.7 Consensus size: 14
192542 GTAGTTTTTT
192552 TTTAGGG-TTAGAG
1 TTTAGGGTTTAGAG
192565 TTTAGGGTTTAGAG
1 TTTAGGGTTTAGAG
*
192579 TTTAAGGTTTATGA-
1 TTTAGGGTTTA-GAG
192593 TTTAGGGTTT
1 TTTAGGGTTT
192603 TAAGGTTTAT
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
13 7 0.21
14 25 0.74
15 2 0.06
ACGTcount: A:0.22, C:0.00, G:0.31, T:0.47
Consensus pattern (14 bp):
TTTAGGGTTTAGAG
Found at i:192839 original size:16 final size:16
Alignment explanation
Indices: 192820--192851 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
192810 CTTTAGTTTT
192820 ATATAGATTTAAAACC
1 ATATAGATTTAAAACC
192836 ATATAGATTTAAAACC
1 ATATAGATTTAAAACC
192852 GTTTGATGAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.12, G:0.06, T:0.31
Consensus pattern (16 bp):
ATATAGATTTAAAACC
Found at i:193111 original size:2 final size:2
Alignment explanation
Indices: 193104--193129 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
193094 ATCGTAAACT
193104 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
193130 ATTAATTAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:195494 original size:22 final size:22
Alignment explanation
Indices: 195414--195509 Score: 60
Period size: 22 Copynumber: 4.5 Consensus size: 22
195404 TATCATTGAC
*
195414 ATAAATATATATATAT-ATATA
1 ATAAATATATAAATATGATATA
* *
195435 TATAAAT-T-TAAAAATCAT-TA
1 -ATAAATATATAAATATGATATA
* * *
195455 A-AAGTAAATTAATTATGATATA
1 ATAAATATA-TAAATATGATATA
195477 ATAAATATATAAATATGATAATA
1 ATAAATATATAAATATGAT-ATA
*
195500 CTAAA-ATATA
1 ATAAATATATA
195510 GCTGGATTAT
Statistics
Matches: 56, Mismatches: 11, Indels: 14
0.69 0.14 0.17
Matches are distributed among these distances:
18 3 0.05
19 1 0.02
20 7 0.12
21 10 0.18
22 23 0.41
23 12 0.21
ACGTcount: A:0.57, C:0.02, G:0.03, T:0.38
Consensus pattern (22 bp):
ATAAATATATAAATATGATATA
Found at i:199797 original size:21 final size:21
Alignment explanation
Indices: 199759--199798 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
199749 TTCCTTCAAA
*
199759 TTTCCTTTATGCTTAATTTTT
1 TTTCCTTTATGCTCAATTTTT
* *
199780 TTTCCTTTCTTCTCAATTT
1 TTTCCTTTATGCTCAATTT
199799 CCTGGAAACT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.12, C:0.20, G:0.03, T:0.65
Consensus pattern (21 bp):
TTTCCTTTATGCTCAATTTTT
Found at i:201775 original size:18 final size:18
Alignment explanation
Indices: 201752--201787 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
201742 GATGGCTCAT
201752 AAATTCCCTTTCATATTG
1 AAATTCCCTTTCATATTG
201770 AAATTCCCTTTCATATTG
1 AAATTCCCTTTCATATTG
201788 TTGGATATTG
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:0.22, G:0.06, T:0.44
Consensus pattern (18 bp):
AAATTCCCTTTCATATTG
Found at i:204928 original size:21 final size:21
Alignment explanation
Indices: 204902--204950 Score: 82
Period size: 20 Copynumber: 2.4 Consensus size: 21
204892 TTTATCCGGG
*
204902 AAAAAATTCGGTCTGGGGTTT
1 AAAAAATTCGGTCTGAGGTTT
204923 AAAAAA-TCGGTCTGAGGTTT
1 AAAAAATTCGGTCTGAGGTTT
204943 AAAAAATT
1 AAAAAATT
204951 GGATGACCAG
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
20 19 0.73
21 7 0.27
ACGTcount: A:0.39, C:0.08, G:0.22, T:0.31
Consensus pattern (21 bp):
AAAAAATTCGGTCTGAGGTTT
Found at i:209033 original size:7 final size:7
Alignment explanation
Indices: 209023--209051 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
209013 TATTTATTTC
209023 ATTTAAA
1 ATTTAAA
209030 ATTTAAA
1 ATTTAAA
209037 ATTTAAA
1 ATTTAAA
209044 ATTTAAA
1 ATTTAAA
209051 A
1 A
209052 CTTCTAAAGG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (7 bp):
ATTTAAA
Found at i:212555 original size:9 final size:10
Alignment explanation
Indices: 212536--212592 Score: 53
Period size: 10 Copynumber: 5.4 Consensus size: 10
212526 TATATATATA
212536 TATAATATTT
1 TATAATATTT
*
212546 TATAATTTTT
1 TATAATATTT
*
212556 ATATTAATTATATA
1 -TA-TAA-TAT-TT
212570 TATAATATTT
1 TATAATATTT
212580 TAT-ATATTT
1 TATAATATTT
212589 TATA
1 TATA
212593 TTAATTATAT
Statistics
Matches: 38, Mismatches: 4, Indels: 10
0.73 0.08 0.19
Matches are distributed among these distances:
9 9 0.24
10 13 0.34
11 5 0.13
12 6 0.16
13 4 0.11
14 1 0.03
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (10 bp):
TATAATATTT
Found at i:212569 original size:34 final size:34
Alignment explanation
Indices: 212530--212614 Score: 145
Period size: 34 Copynumber: 2.5 Consensus size: 34
212520 TATATATATA
212530 TATATATATAATATTTTATA-ATTTTTATATTAAT
1 TATATATATAATATTTTATATA-TTTTATATTAAT
212564 TATATATATAATATTTTATATATTTTATATTAAT
1 TATATATATAATATTTTATATATTTTATATTAAT
*
212598 TATATATAGAATATTTT
1 TATATATATAATATTTT
212615 CGGGTTCGGG
Statistics
Matches: 49, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
34 48 0.98
35 1 0.02
ACGTcount: A:0.41, C:0.00, G:0.01, T:0.58
Consensus pattern (34 bp):
TATATATATAATATTTTATATATTTTATATTAAT
Found at i:212593 original size:9 final size:9
Alignment explanation
Indices: 212526--212593 Score: 54
Period size: 8 Copynumber: 7.6 Consensus size: 9
212516 CGATTATATA
*
212526 TATATATATA
1 TATATAT-TT
212536 TATAATATTT
1 TAT-ATATTT
212546 TATA-ATTT
1 TATATATTT
212554 T-TATATTAAT
1 TATATATT--T
*
212564 TATATA-TA
1 TATATATTT
212572 TA-ATATTT
1 TATATATTT
212580 TATATATTT
1 TATATATTT
212589 TATAT
1 TATAT
212594 TAATTATATA
Statistics
Matches: 48, Mismatches: 3, Indels: 15
0.73 0.05 0.23
Matches are distributed among these distances:
7 5 0.10
8 13 0.27
9 12 0.25
10 10 0.21
11 8 0.17
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (9 bp):
TATATATTT
Found at i:212611 original size:18 final size:18
Alignment explanation
Indices: 212530--212612 Score: 77
Period size: 16 Copynumber: 4.8 Consensus size: 18
212520 TATATATATA
212530 TATATATATAATATT--T
1 TATATATATAATATTAAT
* *
212546 TATA-ATTTTTATATTAAT
1 TATATA-TATAATATTAAT
212564 TATATATATAATATT--T
1 TATATATATAATATTAAT
* *
212580 TATATATTTTATATTAAT
1 TATATATATAATATTAAT
*
212598 TATATATAGAATATT
1 TATATATATAATATT
212613 TTCGGGTTCG
Statistics
Matches: 52, Mismatches: 9, Indels: 10
0.73 0.13 0.14
Matches are distributed among these distances:
15 1 0.02
16 25 0.48
18 25 0.48
19 1 0.02
ACGTcount: A:0.42, C:0.00, G:0.01, T:0.57
Consensus pattern (18 bp):
TATATATATAATATTAAT
Found at i:212624 original size:6 final size:6
Alignment explanation
Indices: 212613--212637 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
212603 ATAGAATATT
212613 TTCGGG TTCGGG TTCGGG TTCGGG T
1 TTCGGG TTCGGG TTCGGG TTCGGG T
212638 ATAATATTTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.00, C:0.16, G:0.48, T:0.36
Consensus pattern (6 bp):
TTCGGG
Found at i:218323 original size:3 final size:3
Alignment explanation
Indices: 218310--218359 Score: 91
Period size: 3 Copynumber: 16.3 Consensus size: 3
218300 TAGAGAGATT
218310 TAA TAAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
218356 TAA T
1 TAA T
218360 TGTTAAAGAA
Statistics
Matches: 46, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
3 43 0.93
4 3 0.07
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:220889 original size:2 final size:2
Alignment explanation
Indices: 220882--220945 Score: 121
Period size: 2 Copynumber: 32.5 Consensus size: 2
220872 TGTTTATACT
220882 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
220924 -A TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA T
220946 GTATGTCGAT
Statistics
Matches: 61, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.02
2 60 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:229325 original size:25 final size:26
Alignment explanation
Indices: 229285--229333 Score: 66
Period size: 25 Copynumber: 1.9 Consensus size: 26
229275 CTTAATTAAT
229285 TTCTAATCAAATAACTTAAA-CTAAGG
1 TTCTAATCAAATAAC-TAAAGCTAAGG
*
229311 TTCTAA-CTAATAACTAAAGCTAA
1 TTCTAATCAAATAACTAAAGCTAA
229334 AATTTAAAGA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 4 0.19
25 11 0.52
26 6 0.29
ACGTcount: A:0.47, C:0.16, G:0.06, T:0.31
Consensus pattern (26 bp):
TTCTAATCAAATAACTAAAGCTAAGG
Found at i:230128 original size:21 final size:21
Alignment explanation
Indices: 230099--230145 Score: 85
Period size: 21 Copynumber: 2.2 Consensus size: 21
230089 GGGATAGCGA
*
230099 GTCGCATTGAAAATAATGGAG
1 GTCGTATTGAAAATAATGGAG
230120 GTCGTATTGAAAATAATGGAG
1 GTCGTATTGAAAATAATGGAG
230141 GTCGT
1 GTCGT
230146 GACATTACTC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.34, C:0.09, G:0.30, T:0.28
Consensus pattern (21 bp):
GTCGTATTGAAAATAATGGAG
Found at i:231713 original size:20 final size:19
Alignment explanation
Indices: 231688--231729 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
231678 TTAAAATGTA
231688 AAATTTAAAAAAATGATATT
1 AAATTT-AAAAAATGATATT
* *
231708 AAATTTTAAAAGTGATATT
1 AAATTTAAAAAATGATATT
231727 AAA
1 AAA
231730 AAAATATAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 14 0.70
20 6 0.30
ACGTcount: A:0.57, C:0.00, G:0.07, T:0.36
Consensus pattern (19 bp):
AAATTTAAAAAATGATATT
Found at i:232972 original size:15 final size:15
Alignment explanation
Indices: 232952--232981 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
232942 AGCAAAACAA
232952 TGCTGAATGATTCAG
1 TGCTGAATGATTCAG
*
232967 TGCTGACTGATTCAG
1 TGCTGAATGATTCAG
232982 CACAGAAGTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.23, C:0.17, G:0.27, T:0.33
Consensus pattern (15 bp):
TGCTGAATGATTCAG
Found at i:239764 original size:18 final size:18
Alignment explanation
Indices: 239743--239806 Score: 56
Period size: 18 Copynumber: 3.3 Consensus size: 18
239733 AAATAAATAA
239743 ATTATTTAAAATATTTAC
1 ATTATTTAAAATATTTAC
* *
239761 ATTATAATATATACATATATTAA
1 ATTAT--T-TA-AAATAT-TTAC
*
239784 ATTAATTAAAATATTTAC
1 ATTATTTAAAATATTTAC
239802 ATTAT
1 ATTAT
239807 AATATAGTAT
Statistics
Matches: 35, Mismatches: 6, Indels: 10
0.69 0.12 0.20
Matches are distributed among these distances:
18 12 0.34
19 5 0.14
20 3 0.09
21 3 0.09
22 5 0.14
23 7 0.20
ACGTcount: A:0.48, C:0.05, G:0.00, T:0.47
Consensus pattern (18 bp):
ATTATTTAAAATATTTAC
Found at i:239769 original size:14 final size:14
Alignment explanation
Indices: 239752--239811 Score: 63
Period size: 14 Copynumber: 4.4 Consensus size: 14
239742 AATTATTTAA
239752 AATATTTACATTAT
1 AATATTTACATTAT
*
239766 AATATATACATATATT
1 AATATTTACAT-TA-T
*
239782 AA-A-TTA-ATTAA
1 AATATTTACATTAT
239793 AATATTTACATTAT
1 AATATTTACATTAT
239807 AATAT
1 AATAT
239812 AGTATAATAT
Statistics
Matches: 37, Mismatches: 4, Indels: 10
0.73 0.08 0.20
Matches are distributed among these distances:
11 2 0.05
12 3 0.08
13 5 0.14
14 21 0.57
15 3 0.08
16 3 0.08
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (14 bp):
AATATTTACATTAT
Found at i:239837 original size:41 final size:41
Alignment explanation
Indices: 239740--239823 Score: 114
Period size: 41 Copynumber: 2.0 Consensus size: 41
239730 ATAAAATAAA
* * *
239740 TAAATTATTTAAAATATTTACATTATAATATATACATATAT
1 TAAATTAATCAAAATATTTACATTATAATATATAAATATAT
*
239781 TAAATTAATTAAAATATTTACATTATAATATAGTATAATATAT
1 TAAATTAATCAAAATATTTACATTATAATATA-TA-AATATAT
239824 ATATAACAGA
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
41 31 0.79
42 2 0.05
43 6 0.15
ACGTcount: A:0.50, C:0.04, G:0.01, T:0.45
Consensus pattern (41 bp):
TAAATTAATCAAAATATTTACATTATAATATATAAATATAT
Found at i:240227 original size:2 final size:2
Alignment explanation
Indices: 240220--240262 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
240210 ATTTAAGTTC
240220 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
240262 A
1 A
240263 GGGTTAGGAT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:240489 original size:2 final size:2
Alignment explanation
Indices: 240482--240509 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
240472 ATCCTGCCTC
240482 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
240510 TCCATTAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:255439 original size:3 final size:3
Alignment explanation
Indices: 255431--255516 Score: 172
Period size: 3 Copynumber: 28.7 Consensus size: 3
255421 GAAACTGAGT
255431 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA
255479 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TC
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TC
255517 CCGCCTCGTA
Statistics
Matches: 83, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 83 1.00
ACGTcount: A:0.33, C:0.34, G:0.00, T:0.34
Consensus pattern (3 bp):
TCA
Found at i:259318 original size:22 final size:23
Alignment explanation
Indices: 259293--259345 Score: 74
Period size: 23 Copynumber: 2.3 Consensus size: 23
259283 TATCCTTTAC
*
259293 AATTATCTTTTGTAA-TTTTAGG
1 AATTATCTTTTGCAACTTTTAGG
259315 AATTATC-TTTGCAACTTTTTAGG
1 AATTATCTTTTGCAAC-TTTTAGG
259338 AATTATCT
1 AATTATCT
259346 CTTAAGATTT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
21 6 0.22
22 7 0.26
23 14 0.52
ACGTcount: A:0.28, C:0.09, G:0.11, T:0.51
Consensus pattern (23 bp):
AATTATCTTTTGCAACTTTTAGG
Found at i:270524 original size:18 final size:19
Alignment explanation
Indices: 270501--270552 Score: 63
Period size: 18 Copynumber: 2.8 Consensus size: 19
270491 AATGCTCATC
*
270501 TATATAACTAT-ATATTAT
1 TATATAAATATAATATTAT
*
270519 TATATAAATATAATATTTT
1 TATATAAATATAATATTAT
*
270538 TAT-TATATATAATAT
1 TATATAAATATAATAT
270553 ATACCTATAA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
18 21 0.70
19 9 0.30
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (19 bp):
TATATAAATATAATATTAT
Found at i:276044 original size:11 final size:11
Alignment explanation
Indices: 276030--276074 Score: 74
Period size: 11 Copynumber: 4.1 Consensus size: 11
276020 AATCAAAGAA
276030 ATTAAATTAAA-
1 ATTAAA-TAAAT
276041 ATTAAATAAAT
1 ATTAAATAAAT
276052 ATTAAATAAAT
1 ATTAAATAAAT
276063 ATTAAATAAAT
1 ATTAAATAAAT
276074 A
1 A
276075 AGAAAAATAT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
10 4 0.12
11 29 0.88
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (11 bp):
ATTAAATAAAT
Found at i:277338 original size:3 final size:3
Alignment explanation
Indices: 277330--277392 Score: 65
Period size: 3 Copynumber: 20.3 Consensus size: 3
277320 TTAAATAAGA
* * *
277330 AAT AAT AAT AAT AAAT AA- AAT AAT TAC AAT AAT AAT AAAT GAT AAT
1 AAT AAT AAT AAT -AAT AAT AAT AAT AAT AAT AAT AAT -AAT AAT AAT
277376 AAT AAT AAT ATAT AAT A
1 AAT AAT AAT A-AT AAT A
277393 TATATAAATA
Statistics
Matches: 50, Mismatches: 6, Indels: 8
0.78 0.09 0.12
Matches are distributed among these distances:
2 2 0.04
3 39 0.78
4 9 0.18
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:277345 original size:13 final size:13
Alignment explanation
Indices: 277323--277392 Score: 74
Period size: 13 Copynumber: 5.5 Consensus size: 13
277313 AAAATAATTA
*
277323 AATAAGAAATAAT
1 AATAATAAATAAT
277336 AATAATAAATAA-
1 AATAATAAATAAT
* *
277348 AATAAT-TACAAT
1 AATAATAAATAAT
*
277360 AATAATAAATGAT
1 AATAATAAATAAT
277373 AATAAT-AATAAT
1 AATAATAAATAAT
277385 ATATAATA
1 A-ATAATA
277393 TATATAAATA
Statistics
Matches: 46, Mismatches: 7, Indels: 7
0.77 0.12 0.12
Matches are distributed among these distances:
11 3 0.07
12 18 0.39
13 25 0.54
ACGTcount: A:0.66, C:0.01, G:0.03, T:0.30
Consensus pattern (13 bp):
AATAATAAATAAT
Found at i:277525 original size:38 final size:38
Alignment explanation
Indices: 277403--277541 Score: 120
Period size: 38 Copynumber: 3.6 Consensus size: 38
277393 TATATAAATA
* ** *
277403 TTTTAAAAA-CATATAATATATAATTTCCAAAATGTTTT
1 TTTTAAAAATTATATAATATAT-ATTTTTAAAATATTTT
* * * **
277441 TTTT-TAAATTATATAATATATATATTTTAAAAAAATGC
1 TTTTAAAAATTATATAATATATAT-TTTTAAAATATTTT
* *
277479 TTTAAAAAATTATATATTATATATTTTTAAAATATTTT
1 TTTTAAAAATTATATAATATATATTTTTAAAATATTTT
*
277517 TTTTAAAAAAACTATATAATATATA
1 TTTT--AAAAATTATATAATATATA
277542 AATGTTTTCA
Statistics
Matches: 77, Mismatches: 19, Indels: 8
0.74 0.18 0.08
Matches are distributed among these distances:
37 5 0.06
38 38 0.49
39 17 0.22
40 17 0.22
ACGTcount: A:0.47, C:0.04, G:0.01, T:0.47
Consensus pattern (38 bp):
TTTTAAAAATTATATAATATATATTTTTAAAATATTTT
Found at i:277557 original size:11 final size:11
Alignment explanation
Indices: 277541--277565 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
277531 TATAATATAT
277541 AAATGTTTTCA
1 AAATGTTTTCA
277552 AAATGTTTTCA
1 AAATGTTTTCA
277563 AAA
1 AAA
277566 CTATATATCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.44, C:0.08, G:0.08, T:0.40
Consensus pattern (11 bp):
AAATGTTTTCA
Found at i:277566 original size:38 final size:37
Alignment explanation
Indices: 277524--277726 Score: 155
Period size: 38 Copynumber: 5.1 Consensus size: 37
277514 TTTTTTTAAA
277524 AAAACTATATAATATATAAATGTTTTCAAAATGTTTTC
1 AAAACTATATAATATATAAAT-TTTTCAAAATGTTTTC
277562 AAAACTATAT-ATCATATAAA-TTTTCAAAAATGTTTTTC
1 AAAACTATATAAT-ATATAAATTTTTC-AAAATG-TTTTC
**
277600 AAAACTATAT-ATATTATATACGTTTTCAAAAATGCTTTT-
1 AAAACTATATAATA-TATA-AATTTTTC-AAAATG-TTTTC
*
277639 AAATATATATATATATATATATTATATACATTTTCAAAATGTTTTC
1 AAA-A-CTATATA-ATATATA--A-AT---TTTTCAAAATGTTTTC
* *
277685 AAAGACTATATATTATATATATTTTT-AAAATGTTTTC
1 AAA-ACTATATAATATATAAATTTTTCAAAATGTTTTC
277722 GAAAA
1 -AAAA
277727 AAAAACATAT
Statistics
Matches: 139, Mismatches: 9, Indels: 35
0.76 0.05 0.19
Matches are distributed among these distances:
36 5 0.04
37 21 0.15
38 45 0.32
39 4 0.03
40 17 0.12
41 7 0.05
42 4 0.03
43 5 0.04
44 6 0.04
45 10 0.07
46 10 0.07
47 5 0.04
ACGTcount: A:0.44, C:0.08, G:0.04, T:0.44
Consensus pattern (37 bp):
AAAACTATATAATATATAAATTTTTCAAAATGTTTTC
Found at i:277658 original size:47 final size:46
Alignment explanation
Indices: 277605--277707 Score: 147
Period size: 47 Copynumber: 2.2 Consensus size: 46
277595 TTTTCAAAAC
* *
277605 TATATATATTATATACGTTTTCAAAAATGCTTTT-AAATA-TATATAT
1 TATATATATTATATACATTTTC-AAAATG-TTTTCAAAGACTATATAT
277651 ATATATATATTATATACATTTTCAAAATGTTTTCAAAGACTATATAT
1 -TATATATATTATATACATTTTCAAAATGTTTTCAAAGACTATATAT
277698 TATATATATT
1 TATATATATT
277708 TTTAAAATGT
Statistics
Matches: 52, Mismatches: 2, Indels: 5
0.88 0.03 0.08
Matches are distributed among these distances:
45 4 0.08
46 20 0.38
47 28 0.54
ACGTcount: A:0.42, C:0.07, G:0.04, T:0.48
Consensus pattern (46 bp):
TATATATATTATATACATTTTCAAAATGTTTTCAAAGACTATATAT
Found at i:277737 original size:86 final size:85
Alignment explanation
Indices: 277567--277796 Score: 209
Period size: 86 Copynumber: 2.6 Consensus size: 85
277557 TTTTCAAAAC
*
277567 TATATATCATATAAATTTTCAAAAATGTTTTTCAAAACTATATATATTATATACGTTTTCAAAAA
1 TATATATTATATAAATTTTC-AAAATGTTTTTCAAAACTATATATATTATATAC-TTTTCAAAAA
* * *
277632 TGCTTTTAAATATATATATATA
64 TGCTTTTAAAAAAACATATATA
* *
277654 TATATATTATATACATTTTCAAAATG-TTTTCAAAGACTATATAT-TATATATA-TTTT-TAAAA
1 TATATATTATATAAATTTTCAAAATGTTTTTCAAA-ACTATATATAT-TATATACTTTTCAAAAA
277715 TG-TTTTCGAAAAAAAAACATATATA
64 TGCTTTT----AAAAAAACATATATA
* * * *
277740 TATATCATATAATATATACTTTTCAAAAAGCTATTCTCAAAATTATATATATTATAT
1 TATAT-AT-T-ATATA-AATTTTCAAAATG-T-TTTTCAAAACTATATATATTATAT
277797 GTATTTTAAA
Statistics
Matches: 118, Mismatches: 11, Indels: 23
0.78 0.07 0.15
Matches are distributed among these distances:
82 4 0.03
83 6 0.05
84 4 0.03
85 9 0.08
86 38 0.32
87 20 0.17
88 1 0.01
89 5 0.04
90 10 0.08
92 13 0.11
93 8 0.07
ACGTcount: A:0.44, C:0.08, G:0.03, T:0.44
Consensus pattern (85 bp):
TATATATTATATAAATTTTCAAAATGTTTTTCAAAACTATATATATTATATACTTTTCAAAAATG
CTTTTAAAAAAACATATATA
Found at i:278594 original size:84 final size:81
Alignment explanation
Indices: 278454--279207 Score: 758
Period size: 84 Copynumber: 9.2 Consensus size: 81
278444 TTGAATATAA
* * * * *
278454 TCGAACTCAAAGGTCTTTAG-CAGATAACCCTTCTTGACTTAAGCTATGCTACAAATGATGTGCC
1 TCGAACTCGAAGGTCTTTGGTCAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGTGCC
*
278518 TTGGAGCTGAGCGGAG
66 TTGGAGCTGAGCGTAG
* * *
278534 TCGAACTCGAAGGTCTTTTGGTCACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGT
1 TCGAACTCGAAGGTC-TTTGGT--CAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGT
278599 GCCGTT-GAGCTGAGCGTAG
63 GCC-TTGGAGCTGAGCGTAG
* * * * * *
278618 TCGAACTCAAAGGTCTTTTGTTGGCAGACAACCCTTGTAGACTTAAGTTGTGCTGCAAATGATAT
1 TCGAACTCGAAGGTC-TTTG--GTCAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGT
*
278683 GCCTTGGAGCTTAGCGTAG
63 GCCTTGGAGCTGAGCGTAG
*
278702 TCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGT
1 TCGAACTCGAAGGTCTTTGG-T--CAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGT
* * * *
278767 GCCCTCGAAGCTGAGTGTAA
63 G-CCTTGGAGCTGAGCGTAG
* ** * * * *
278787 TCGAACTTGGGGGTCTTTGG-CAGATAGCCCTTCTCGACTTAAGCTATTCTGCAAATGATGTGCC
1 TCGAACTCGAAGGTCTTTGGTCAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGTGCC
278851 TTGGAGCTGAGCGTAG
66 TTGGAGCTGAGCGTAG
* * *
278867 TCGAACTCGAAGGTCTTTTGGTCACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGT
1 TCGAACTCGAAGGTC-TTTGGT--CAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGT
* * *
278932 GCCCTCGAAGCTGAGCGTAA
63 G-CCTTGGAGCTGAGCGTAG
* * * *
278952 TCGAACTC-AGGGGTCTTTGG-CAGATAGCCC-T-T---CTTAAGCTATTCTGCAAATGATGTGC
1 TCGAACTCGA-AGGTCTTTGGTCAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGTGC
279010 CTTGGAGCTGAGCGTAG
65 CTTGGAGCTGAGCGTAG
* * * * * * *
279027 TCGAACTCAAAGGTCTTTGCTAACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGTTATG
1 TCGAACTCGAAGGTCTTTGGT--CAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGTG
* * *
279092 CCCTTGAAGCTGAGTGTAA
64 -CCTTGGAGCTGAGCGTAG
* * * * * *
279111 TCGAACT-TAAGGGTCTTTGG-CAGATAGCCCTTCTCGACTTAAGCTATTCTGTAAATGATGTGC
1 TCGAACTCGAA-GGTCTTTGGTCAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGTGC
279174 CTTGGAGCTGAGCGTAG
65 CTTGGAGCTGAGCGTAG
279191 TCGAACTCGAAGGTCTT
1 TCGAACTCGAAGGTCTT
279208 GGTGGCAGGT
Statistics
Matches: 555, Mismatches: 89, Indels: 60
0.79 0.13 0.09
Matches are distributed among these distances:
75 31 0.06
76 22 0.04
78 9 0.02
79 2 0.00
80 70 0.13
81 94 0.17
83 27 0.05
84 240 0.43
85 59 0.11
86 1 0.00
ACGTcount: A:0.24, C:0.21, G:0.25, T:0.30
Consensus pattern (81 bp):
TCGAACTCGAAGGTCTTTGGTCAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGTGCC
TTGGAGCTGAGCGTAG
Found at i:278876 original size:165 final size:164
Alignment explanation
Indices: 278391--279207 Score: 1054
Period size: 165 Copynumber: 5.0 Consensus size: 164
278381 AATTTTATTG
* * * * * * * ***
278391 ACAGATAACCCTTCTTGCCTTGAGCTATTCTGTAAGCTTGATTTG-CCTCTAAGTTGAATATAAT
1 ACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAA--ATGATGTGCCCTCGAAGCTGAGCGTAAT
* * * * * *
278455 CGAACTCAAAGGTCTTTAGCAGATAACCCTTCTTGACTTAAGCTATGCTACAAATGATGTGCCTT
64 CGAACTCAAGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATTCTGCAAATGATGTGCCTT
*
278520 GGAGCTGAGCGGAGTCGAACTCGAAGGTCTTTTGGTC
129 GGAGCTGAGCGTAGTCGAACTCGAAGGTC-TTTGGTC
* * *
278557 ACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCGTTG-AGCTGAGCGTAGTCG
1 ACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGCGTAATCG
* * * * * * * * *
278621 AACTCAAAGGTCTTTTGTTGGCAGACAACCCTTGTAGACTTAAGTTGTGCTGCAAATGATATGCC
66 AACTCAAGGGTC---T-TTGGCAGATAGCCCTTCTCGACTTAAGCTATTCTGCAAATGATGTGCC
* *
278686 TTGGAGCTTAGCGTAGTCGAACTCGAAGGTCTTTGGTTG
127 TTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGG-TC
* * * * * *
278725 GCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCCTCGAAGCTGAGTGTAATCG
1 ACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGCGTAATCG
***
278790 AACTTGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATTCTGCAAATGATGTGCCTTGG
66 AACTCAAGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATTCTGCAAATGATGTGCCTTGG
278855 AGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTC
131 AGCTGAGCGTAGTCGAACTCGAAGGTC-TTTGGTC
278890 ACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGCGTAATCG
1 ACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGCGTAATCG
*
278955 AACTCAGGGGTCTTTGGCAGATAGCCC-T-T---CTTAAGCTATTCTGCAAATGATGTGCCTTGG
66 AACTCAAGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATTCTGCAAATGATGTGCCTTGG
* * *
279015 AGCTGAGCGTAGTCGAACTCAAAGGTCTTTGCTA
131 AGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTC
* * * *
279049 ACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGTTATGCCCTTGAAGCTGAGTGTAATCG
1 ACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGCGTAATCG
* *
279114 AACTTAAGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATTCTGTAAATGATGTGCCTTGG
66 AACTCAAGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATTCTGCAAATGATGTGCCTTGG
279179 AGCTGAGCGTAGTCGAACTCGAAGGTCTT
131 AGCTGAGCGTAGTCGAACTCGAAGGTCTT
279208 GGTGGCAGGT
Statistics
Matches: 572, Mismatches: 66, Indels: 28
0.86 0.10 0.04
Matches are distributed among these distances:
159 91 0.16
160 58 0.10
161 1 0.00
163 1 0.00
164 87 0.15
165 157 0.27
166 38 0.07
167 6 0.01
168 112 0.20
169 21 0.04
ACGTcount: A:0.24, C:0.21, G:0.24, T:0.31
Consensus pattern (164 bp):
ACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGCGTAATCG
AACTCAAGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATTCTGCAAATGATGTGCCTTGG
AGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTC
Found at i:282648 original size:18 final size:19
Alignment explanation
Indices: 282607--282651 Score: 74
Period size: 19 Copynumber: 2.4 Consensus size: 19
282597 AGTTAATGTG
282607 AATGCAAAGAAAATAACAA
1 AATGCAAAGAAAATAACAA
*
282626 AATGCAAAGAAAATAA-GA
1 AATGCAAAGAAAATAACAA
282644 AATGCAAA
1 AATGCAAA
282652 ATGTCTAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
18 9 0.36
19 16 0.64
ACGTcount: A:0.67, C:0.09, G:0.13, T:0.11
Consensus pattern (19 bp):
AATGCAAAGAAAATAACAA
Found at i:283296 original size:17 final size:17
Alignment explanation
Indices: 283270--283302 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
283260 TGCAAACGAT
*
283270 GAACACAAAATAAAAGA
1 GAACAAAAAATAAAAGA
283287 GAACAAAAAATAAAAG
1 GAACAAAAAATAAAAG
283303 GGTTAGTGAG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.73, C:0.09, G:0.12, T:0.06
Consensus pattern (17 bp):
GAACAAAAAATAAAAGA
Found at i:284269 original size:6 final size:6
Alignment explanation
Indices: 284251--284284 Score: 59
Period size: 6 Copynumber: 5.5 Consensus size: 6
284241 TTAGTTGCGA
284251 AAATTT AAAATTT AAATTT AAATTT AAATTT AAA
1 AAATTT -AAATTT AAATTT AAATTT AAATTT AAA
284285 AACTCGATGC
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 21 0.78
7 6 0.22
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (6 bp):
AAATTT
Found at i:284453 original size:11 final size:11
Alignment explanation
Indices: 284439--284483 Score: 65
Period size: 11 Copynumber: 4.1 Consensus size: 11
284429 AATCAAAGAA
284439 ATTAAATTAAA-
1 ATTAAA-TAAAT
284450 ATTAAATAAAT
1 ATTAAATAAAT
*
284461 AATAAATAAAT
1 ATTAAATAAAT
284472 ATTAAATAAAT
1 ATTAAATAAAT
284483 A
1 A
284484 AGAAAAATAT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
10 4 0.13
11 27 0.87
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (11 bp):
ATTAAATAAAT
Found at i:284461 original size:4 final size:4
Alignment explanation
Indices: 284418--284484 Score: 50
Period size: 4 Copynumber: 17.0 Consensus size: 4
284408 AAGTAGTAAT
* * * *
284418 ATAA AAAA ATAA ATCAA AGAA ATTAA ATTA A-AA TTAA ATAA AT-A ATAA
1 ATAA ATAA ATAA AT-AA ATAA A-TAA ATAA ATAA ATAA ATAA ATAA ATAA
*
284466 ATAA AT-A TTAA ATAA ATAA
1 ATAA ATAA ATAA ATAA ATAA
284485 GAAAAATATT
Statistics
Matches: 48, Mismatches: 10, Indels: 10
0.71 0.15 0.15
Matches are distributed among these distances:
3 6 0.12
4 36 0.75
5 6 0.12
ACGTcount: A:0.70, C:0.01, G:0.01, T:0.27
Consensus pattern (4 bp):
ATAA
Found at i:284475 original size:22 final size:22
Alignment explanation
Indices: 284441--284484 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
284431 TCAAAGAAAT
284441 TAAATTAAAATTAAATAAATAA
1 TAAATTAAAATTAAATAAATAA
284463 TAAA-TAAATATTAAATAAATAA
1 TAAATTAAA-ATTAAATAAATAA
284485 GAAAAATATT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 4 0.19
22 17 0.81
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (22 bp):
TAAATTAAAATTAAATAAATAA
Found at i:285747 original size:3 final size:3
Alignment explanation
Indices: 285739--285804 Score: 71
Period size: 3 Copynumber: 21.3 Consensus size: 3
285729 TTAAATAAGA
* * *
285739 AAT AAT AAT AAT AAAT AA- AAT AAT TAC AAT AAT AAT AAAT GAT AAT
1 AAT AAT AAT AAT -AAT AAT AAT AAT AAT AAT AAT AAT -AAT AAT AAT
285785 AAT AAAT AAT AAT AAT AAT A
1 AAT -AAT AAT AAT AAT AAT A
285805 GTATAATATA
Statistics
Matches: 53, Mismatches: 6, Indels: 8
0.79 0.09 0.12
Matches are distributed among these distances:
2 2 0.04
3 42 0.79
4 9 0.17
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:285754 original size:13 final size:13
Alignment explanation
Indices: 285732--285802 Score: 92
Period size: 13 Copynumber: 5.6 Consensus size: 13
285722 AAAATAATTA
*
285732 AATAAGAAATAAT
1 AATAATAAATAAT
285745 AATAATAAATAA-
1 AATAATAAATAAT
* *
285757 AATAAT-TACAAT
1 AATAATAAATAAT
*
285769 AATAATAAATGAT
1 AATAATAAATAAT
285782 AATAATAAATAAT
1 AATAATAAATAAT
285795 AATAATAA
1 AATAATAA
285803 TAGTATAATA
Statistics
Matches: 49, Mismatches: 7, Indels: 4
0.82 0.12 0.07
Matches are distributed among these distances:
11 3 0.06
12 12 0.24
13 34 0.69
ACGTcount: A:0.68, C:0.01, G:0.03, T:0.28
Consensus pattern (13 bp):
AATAATAAATAAT
Found at i:285811 original size:37 final size:36
Alignment explanation
Indices: 285732--285828 Score: 99
Period size: 37 Copynumber: 2.6 Consensus size: 36
285722 AAAATAATTA
* *
285732 AATAAGAAATAATAATAATAAATAAAATAATTACAAT
1 AATAATAAAT-ATAATAATAAATAAAATAATAACAAT
* *
285769 AATAATAAATGATAATAATAAATAATAATAATAATAGT
1 AATAATAAAT-ATAATAATAAATAA-AATAATAACAAT
*
285807 -ATAATATATAT-ATATATAAATA
1 AATAATAAATATAATA-ATAAATA
285829 TTTTAAAAAA
Statistics
Matches: 52, Mismatches: 6, Indels: 5
0.83 0.10 0.08
Matches are distributed among these distances:
35 3 0.06
36 9 0.17
37 31 0.60
38 9 0.17
ACGTcount: A:0.64, C:0.01, G:0.03, T:0.32
Consensus pattern (36 bp):
AATAATAAATATAATAATAAATAAAATAATAACAAT
Found at i:285812 original size:8 final size:7
Alignment explanation
Indices: 285740--285853 Score: 53
Period size: 7 Copynumber: 16.7 Consensus size: 7
285730 TAAATAAGAA
285740 ATAATA-
1 ATAATAT
*
285746 ATAATAA
1 ATAATAT
285753 ATAA-A-
1 ATAATAT
285758 ATAAT-T
1 ATAATAT
*
285764 ACAATA-
1 ATAATAT
*
285770 ATAATAA
1 ATAATAT
*
285777 ATGATA-
1 ATAATAT
*
285783 ATAATAA
1 ATAATAT
285790 ATAATAAT
1 ATAAT-AT
285798 AATAATAGT
1 -ATAATA-T
285807 ATAATAT
1 ATAATAT
285814 ATATATAT
1 ATA-ATAT
285822 ATAA-AT
1 ATAATAT
** *
285828 ATTTTAA
1 ATAATAT
* *
285835 AAAACAT
1 ATAATAT
285842 ATAATAT
1 ATAATAT
285849 ATAAT
1 ATAAT
285854 TTCCAAAATG
Statistics
Matches: 82, Mismatches: 15, Indels: 21
0.69 0.13 0.18
Matches are distributed among these distances:
5 4 0.05
6 25 0.30
7 32 0.39
8 15 0.18
9 6 0.07
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.35
Consensus pattern (7 bp):
ATAATAT
Found at i:285901 original size:39 final size:38
Alignment explanation
Indices: 285872--285965 Score: 116
Period size: 39 Copynumber: 2.4 Consensus size: 38
285862 TGTTTTTTTT
285872 AATTATATAATATATATATTTTAAAAAAATGCTTTAAAA
1 AATTATATAATATATAT-TTTTAAAAAAATGCTTTAAAA
* * ** *
285911 AATTATATATTATATATTTTTAAAATATATTTTTTTAAA
1 AATTATATAATATATATTTTTAAAA-AAATGCTTTAAAA
*
285950 AACTATATAATATATA
1 AATTATATAATATATA
285966 AATGTTTTCA
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
38 8 0.17
39 39 0.83
ACGTcount: A:0.50, C:0.02, G:0.01, T:0.47
Consensus pattern (38 bp):
AATTATATAATATATATTTTTAAAAAAATGCTTTAAAA
Found at i:285945 original size:15 final size:15
Alignment explanation
Indices: 285921--285950 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
285911 AATTATATAT
285921 TATATATTTTTAAAA
1 TATATATTTTTAAAA
*
285936 TATATTTTTTTAAAA
1 TATATATTTTTAAAA
285951 ACTATATAAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (15 bp):
TATATATTTTTAAAA
Found at i:285981 original size:11 final size:11
Alignment explanation
Indices: 285965--285989 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
285955 TATAATATAT
285965 AAATGTTTTCA
1 AAATGTTTTCA
285976 AAATGTTTTCA
1 AAATGTTTTCA
285987 AAA
1 AAA
285990 CTATATCATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.44, C:0.08, G:0.08, T:0.40
Consensus pattern (11 bp):
AAATGTTTTCA
Found at i:286021 original size:36 final size:35
Alignment explanation
Indices: 285959--286073 Score: 121
Period size: 36 Copynumber: 3.2 Consensus size: 35
285949 AAACTATATA
285959 ATATATAAATGTTTTC-AAAATG-TTTTCAAAACTAT
1 ATATATAAA--TTTTCAAAAATGTTTTTCAAAACTAT
285994 ATCATATAAATTTTCAAAAATGTTTTTCAAAACTAT
1 AT-ATATAAATTTTCAAAAATGTTTTTCAAAACTAT
* *
286030 ATATATTATACGTTTTCAAAAATGCTTTT-AAATA-TAT
1 ATATA-TA-A-ATTTTCAAAAATGTTTTTCAAA-ACTAT
286067 ATATATA
1 ATATATA
286074 TATATATATA
Statistics
Matches: 71, Mismatches: 2, Indels: 13
0.83 0.02 0.15
Matches are distributed among these distances:
34 5 0.07
35 11 0.15
36 26 0.37
37 12 0.17
38 17 0.24
ACGTcount: A:0.43, C:0.09, G:0.04, T:0.43
Consensus pattern (35 bp):
ATATATAAATTTTCAAAAATGTTTTTCAAAACTAT
Found at i:286068 original size:2 final size:2
Alignment explanation
Indices: 286061--286113 Score: 106
Period size: 2 Copynumber: 26.5 Consensus size: 2
286051 ATGCTTTTAA
286061 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
286103 AT AT AT AT AT A
1 AT AT AT AT AT A
286114 CATTTTCAAA
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:286142 original size:36 final size:35
Alignment explanation
Indices: 286102--286173 Score: 99
Period size: 37 Copynumber: 2.0 Consensus size: 35
286092 TATATATATA
286102 TATATATATATACATTTTCAAAATGTTTTCAAAGAC
1 TATATATATATACATTTTCAAAATGTTTTCAAA-AC
* *
286138 TATATATTATATATATTTTTAAAATGTTTTCGAAAA
1 TATATA-TATATACATTTTCAAAATGTTTTC-AAAA
286174 AAAAACATAT
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
36 6 0.19
37 23 0.72
38 3 0.09
ACGTcount: A:0.42, C:0.07, G:0.06, T:0.46
Consensus pattern (35 bp):
TATATATATATACATTTTCAAAATGTTTTCAAAAC
Done.