Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009387.1 Hibiscus syriacus cultivar Beakdansim tig00113279_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: 929501
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 5
Found at i:167969 original size:12 final size:12
Alignment explanation
Indices: 167948--168014 Score: 55
Period size: 12 Copynumber: 5.6 Consensus size: 12
167938 ATGACCTGGA
*
167948 TTCTGTTCTGAT
1 TTCTGATCTGAT
167960 TTCTGATCTGGA-
1 TTCTGATCT-GAT
*
167972 TTCTGTTCTGAT
1 TTCTGATCTGAT
* * *
167984 ATCTGATTTGAA
1 TTCTGATCTGAT
* *
167996 TTCTGTTTTGAT
1 TTCTGATCTGAT
168008 TTCTGAT
1 TTCTGAT
168015 ATCTCCGTTT
Statistics
Matches: 43, Mismatches: 10, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
11 2 0.05
12 39 0.91
13 2 0.05
ACGTcount: A:0.15, C:0.13, G:0.18, T:0.54
Consensus pattern (12 bp):
TTCTGATCTGAT
Found at i:167984 original size:48 final size:49
Alignment explanation
Indices: 167906--168014 Score: 116
Period size: 48 Copynumber: 2.3 Consensus size: 49
167896 AAATATTTTA
* * *
167906 TCTGATTTCCGA-CTTGAATTCTATTTTGATA-CATGACCTGGATTCTGT
1 TCTGATTTCTGATCTTGAATTCTATTCTGATATC-TGACCTGAATTCTGT
* * **
167954 TCTGATTTCTGATC-TGGATTCTGTTCTGATATCTGATTTGAATTCTGT
1 TCTGATTTCTGATCTTGAATTCTATTCTGATATCTGACCTGAATTCTGT
*
168002 TTTGATTTCTGAT
1 TCTGATTTCTGAT
168015 ATCTCCGTTT
Statistics
Matches: 51, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
48 49 0.96
49 2 0.04
ACGTcount: A:0.18, C:0.16, G:0.17, T:0.49
Consensus pattern (49 bp):
TCTGATTTCTGATCTTGAATTCTATTCTGATATCTGACCTGAATTCTGT
Found at i:168012 original size:24 final size:24
Alignment explanation
Indices: 167947--168014 Score: 100
Period size: 24 Copynumber: 2.8 Consensus size: 24
167937 CATGACCTGG
*
167947 ATTCTGTTCTGATTTCTGATCTGG
1 ATTCTGTTCTGATTTCTGATCTGA
* *
167971 ATTCTGTTCTGATATCTGATTTGA
1 ATTCTGTTCTGATTTCTGATCTGA
*
167995 ATTCTGTTTTGATTTCTGAT
1 ATTCTGTTCTGATTTCTGAT
168015 ATCTCCGTTT
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 39 1.00
ACGTcount: A:0.16, C:0.13, G:0.18, T:0.53
Consensus pattern (24 bp):
ATTCTGTTCTGATTTCTGATCTGA
Found at i:169812 original size:17 final size:17
Alignment explanation
Indices: 169790--169830 Score: 66
Period size: 17 Copynumber: 2.4 Consensus size: 17
169780 ACGGTCAACT
169790 GTTGACCGTTGACCTG-C
1 GTTGACCGTTGACC-GAC
169807 GTTGACCGTTGACCGAC
1 GTTGACCGTTGACCGAC
169824 GTTGACC
1 GTTGACC
169831 ACTGTTGACC
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
16 1 0.04
17 22 0.96
ACGTcount: A:0.15, C:0.29, G:0.29, T:0.27
Consensus pattern (17 bp):
GTTGACCGTTGACCGAC
Found at i:169826 original size:10 final size:9
Alignment explanation
Indices: 169796--169866 Score: 51
Period size: 10 Copynumber: 7.8 Consensus size: 9
169786 AACTGTTGAC
*
169796 CGTTGACCTG
1 CGTTGACC-A
169806 CGTTGA-C-
1 CGTTGACCA
169813 CGTTGACCGA
1 CGTTGACC-A
169823 CGTTGACCA
1 CGTTGACCA
169832 CTGTTGA-C-
1 C-GTTGACCA
169840 CGTTGACCGA
1 CGTTGACC-A
*
169850 CGTTGATCA
1 CGTTGACCA
169859 CTGTTGAC
1 C-GTTGAC
169867 TAGAACTTTG
Statistics
Matches: 51, Mismatches: 2, Indels: 16
0.74 0.03 0.23
Matches are distributed among these distances:
7 11 0.22
8 3 0.06
9 6 0.12
10 31 0.61
ACGTcount: A:0.17, C:0.28, G:0.27, T:0.28
Consensus pattern (9 bp):
CGTTGACCA
Found at i:169830 original size:27 final size:27
Alignment explanation
Indices: 169807--169866 Score: 111
Period size: 27 Copynumber: 2.2 Consensus size: 27
169797 GTTGACCTGC
169807 GTTGACCGTTGACCGACGTTGACCACT
1 GTTGACCGTTGACCGACGTTGACCACT
*
169834 GTTGACCGTTGACCGACGTTGATCACT
1 GTTGACCGTTGACCGACGTTGACCACT
169861 GTTGAC
1 GTTGAC
169867 TAGAACTTTG
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.18, C:0.27, G:0.27, T:0.28
Consensus pattern (27 bp):
GTTGACCGTTGACCGACGTTGACCACT
Found at i:190440 original size:22 final size:21
Alignment explanation
Indices: 190398--190437 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
190388 GAGTTTATTT
*
190398 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
190419 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
190438 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:193793 original size:44 final size:43
Alignment explanation
Indices: 193741--193841 Score: 123
Period size: 43 Copynumber: 2.3 Consensus size: 43
193731 TACCATCAGG
* *
193741 GGGGTATCGATACCAATTCAAGGGGGGTATCGATACTTATT-GCA
1 GGGGTATCGATACCAATTCAA-AGGGGTATCGATAC-CATTCGCA
* * * *
193785 TGGGTATCGATAACTATTCAAAGGGGTATCGATACCATTCTCA
1 GGGGTATCGATACCAATTCAAAGGGGTATCGATACCATTCGCA
193828 GGGGTATCGATACC
1 GGGGTATCGATACC
193842 TTATGCAGAA
Statistics
Matches: 48, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
42 3 0.06
43 27 0.56
44 18 0.38
ACGTcount: A:0.28, C:0.18, G:0.27, T:0.28
Consensus pattern (43 bp):
GGGGTATCGATACCAATTCAAAGGGGTATCGATACCATTCGCA
Found at i:193830 original size:21 final size:20
Alignment explanation
Indices: 193722--193841 Score: 91
Period size: 21 Copynumber: 5.7 Consensus size: 20
193712 AACCCGAAGA
* *
193722 GGGTATCGGTACCA-TCAGGG
1 GGGTATCGATACCATTCA-AG
193742 GGGTATCGATACCAATTCAAGGG
1 GGGTATCGATACC-ATTCAA--G
* *
193765 GGGTATCGATACTTATTGC-AT
1 GGGTATCGATAC-CATT-CAAG
*
193786 GGGTATCGATAACTATTCAAAG
1 GGGTATCGAT-ACCATTC-AAG
*
193808 GGGTATCGATACCATTCTCAG
1 GGGTATCGATACCATTC-AAG
193829 GGGTATCGATACC
1 GGGTATCGATACC
193842 TTATGCAGAA
Statistics
Matches: 83, Mismatches: 8, Indels: 17
0.77 0.07 0.16
Matches are distributed among these distances:
20 13 0.16
21 36 0.43
22 16 0.19
23 17 0.20
24 1 0.01
ACGTcount: A:0.27, C:0.18, G:0.28, T:0.27
Consensus pattern (20 bp):
GGGTATCGATACCATTCAAG
Found at i:199168 original size:13 final size:13
Alignment explanation
Indices: 199162--199205 Score: 61
Period size: 13 Copynumber: 3.4 Consensus size: 13
199152 CCCGTTGACC
**
199162 TGACCCGACATGT
1 TGACCCGACCCGT
*
199175 TGACCCGACCTGT
1 TGACCCGACCCGT
199188 TGACCCGACCCGT
1 TGACCCGACCCGT
199201 TGACC
1 TGACC
199206 GGCATTGACC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 29 1.00
ACGTcount: A:0.18, C:0.39, G:0.23, T:0.20
Consensus pattern (13 bp):
TGACCCGACCCGT
Found at i:199199 original size:18 final size:18
Alignment explanation
Indices: 199141--199184 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
199131 ACCGGTCATA
* *
199141 ACCCAACCCGACCCGTTG
1 ACCCGACCCGACACGTTG
* *
199159 ACCTGACCCGACATGTTG
1 ACCCGACCCGACACGTTG
199177 ACCCGACC
1 ACCCGACC
199185 TGTTGACCCG
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.23, C:0.45, G:0.18, T:0.14
Consensus pattern (18 bp):
ACCCGACCCGACACGTTG
Found at i:200956 original size:21 final size:22
Alignment explanation
Indices: 200885--200967 Score: 111
Period size: 22 Copynumber: 4.0 Consensus size: 22
200875 AGTACCCCTT
*
200885 CATA-GGGTATCGGTACCA-T-
1 CATAGGGGTATCGATACCATTG
200904 CATAGGGGTATCGATACCATTG
1 CATAGGGGTATCGATACCATTG
200926 CATAGGGGTATCGATACCATTG
1 CATAGGGGTATCGATACCATTG
* *
200948 -GTGGGGGTATCGATACCATT
1 CATAGGGGTATCGATACCATT
200968 CGAGCATTCT
Statistics
Matches: 58, Mismatches: 3, Indels: 4
0.89 0.05 0.06
Matches are distributed among these distances:
19 4 0.07
20 13 0.22
21 19 0.33
22 22 0.38
ACGTcount: A:0.25, C:0.18, G:0.29, T:0.28
Consensus pattern (22 bp):
CATAGGGGTATCGATACCATTG
Found at i:201054 original size:20 final size:20
Alignment explanation
Indices: 201007--201059 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
200997 ATGTTCACAT
*
201007 GGGTATCAGTACCCTGTAGG
1 GGGTATCGGTACCCTGTAGG
201027 GGGTATCGGTACCCTGTAGG
1 GGGTATCGGTACCCTGTAGG
*
201047 GGGTATCGATACC
1 GGGTATCGGTACC
201060 ATACTTAATC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.19, C:0.21, G:0.36, T:0.25
Consensus pattern (20 bp):
GGGTATCGGTACCCTGTAGG
Found at i:202576 original size:13 final size:15
Alignment explanation
Indices: 202557--202593 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
202547 TATTTATTAT
202557 ATAATAAAAG-AATA
1 ATAATAAAAGTAATA
202571 AT-ATAAAAAGTAATA
1 ATAAT-AAAAGTAATA
202586 ATAATAAA
1 ATAATAAA
202594 TAATATTGCA
Statistics
Matches: 20, Mismatches: 0, Indels: 5
0.80 0.00 0.20
Matches are distributed among these distances:
13 2 0.10
14 7 0.35
15 9 0.45
16 2 0.10
ACGTcount: A:0.70, C:0.00, G:0.05, T:0.24
Consensus pattern (15 bp):
ATAATAAAAGTAATA
Found at i:202587 original size:15 final size:15
Alignment explanation
Indices: 202557--202593 Score: 51
Period size: 14 Copynumber: 2.5 Consensus size: 15
202547 TATTTATTAT
202557 ATAAT-AAAAGAATA
1 ATAATAAAAAGAATA
202571 AT-ATAAAAAGTAATA
1 ATAATAAAAAG-AATA
202586 ATAATAAA
1 ATAATAAA
202594 TAATATTGCA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
13 2 0.10
14 7 0.35
15 6 0.30
16 5 0.25
ACGTcount: A:0.70, C:0.00, G:0.05, T:0.24
Consensus pattern (15 bp):
ATAATAAAAAGAATA
Found at i:202597 original size:13 final size:12
Alignment explanation
Indices: 202557--202661 Score: 52
Period size: 13 Copynumber: 8.2 Consensus size: 12
202547 TATTTATTAT
*
202557 ATAATAA-AAGA
1 ATAATAATAAAA
202568 ATAAT-ATAAAA
1 ATAATAATAAAA
202579 AGTAATAATAATAA
1 A-TAATAATAA-AA
* **
202593 ATAATATTGCAA
1 ATAATAATAAAA
202605 ATAATAATTAAAA
1 ATAATAA-TAAAA
*
202618 ATATAGTATTAAAA
1 ATA-A-TAATAAAA
*
202632 TATAAAATATTAAAA
1 -AT--AATAATAAAA
*
202647 AAAATAATCAAAA
1 ATAATAAT-AAAA
202660 AT
1 AT
202662 GAAATTTGAA
Statistics
Matches: 72, Mismatches: 11, Indels: 20
0.70 0.11 0.19
Matches are distributed among these distances:
10 1 0.01
11 9 0.12
12 17 0.24
13 21 0.29
14 10 0.14
15 12 0.17
16 1 0.01
17 1 0.01
ACGTcount: A:0.66, C:0.02, G:0.04, T:0.29
Consensus pattern (12 bp):
ATAATAATAAAA
Found at i:203843 original size:3 final size:3
Alignment explanation
Indices: 203835--203928 Score: 104
Period size: 3 Copynumber: 30.0 Consensus size: 3
203825 AATTATTTTT
203835 TAA TAA TAA TAA T-A TATA TAA TAA TATA TATA TAA TAA T-A TATA TATA
1 TAA TAA TAA TAA TAA TA-A TAA TAA TA-A TA-A TAA TAA TAA TA-A TA-A
203883 TATA TATA TAA TAA TAA -AA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TA-A TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
203929 ATAAATAAAT
Statistics
Matches: 85, Mismatches: 0, Indels: 12
0.88 0.00 0.12
Matches are distributed among these distances:
2 6 0.07
3 54 0.64
4 25 0.29
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:203851 original size:2 final size:2
Alignment explanation
Indices: 203846--203892 Score: 66
Period size: 2 Copynumber: 25.5 Consensus size: 2
203836 AATAATAATA
203846 AT AT AT AT A- AT A- AT AT AT AT AT A- AT A- 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
203884 AT AT AT AT A
1 AT AT AT AT A
203893 ATAATAAAAT
Statistics
Matches: 41, Mismatches: 0, Indels: 8
0.84 0.00 0.16
Matches are distributed among these distances:
1 4 0.10
2 37 0.90
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:203947 original size:9 final size:8
Alignment explanation
Indices: 203836--203947 Score: 55
Period size: 9 Copynumber: 12.4 Consensus size: 8
203826 ATTATTTTTT
203836 AATAATAA
1 AATAATAA
*
203844 TAATATATAT
1 -AATA-ATAA
203854 AATAATATA
1 AATAATA-A
203863 TATATAATAA
1 -A-ATAATAA
*
203873 TATATATATA
1 AATA-ATA-A
* *
203883 TATATATAT
1 AATA-ATAA
203892 AATAATAA
1 AATAATAA
203900 AATAATAA
1 AATAATAA
203908 TAATAATAA
1 -AATAATAA
203917 TAATAATAATA
1 -AATAAT-A-A
203928 AATAA-ATA
1 AATAATA-A
203936 AATAAATAA
1 AAT-AATAA
203945 AAT
1 AAT
203948 GGGTAAAAAA
Statistics
Matches: 86, Mismatches: 6, Indels: 22
0.75 0.05 0.19
Matches are distributed among these distances:
8 23 0.27
9 35 0.41
10 21 0.24
11 7 0.08
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (8 bp):
AATAATAA
Found at i:204318 original size:120 final size:121
Alignment explanation
Indices: 204139--204471 Score: 315
Period size: 113 Copynumber: 2.8 Consensus size: 121
204129 GATGACAATT
* *
204139 TATCTCCTTCTGTGATGTAATCTAGCAAAGGTTGAACAAGCTCTTCTCATTGTGAA-CTTCTT-A
1 TATCTCCTTCTGTGATGTAATCTAGCAAAGGTCGAACAAGCTCTTCTCATTATGAATCTTCTTCA
* *
204202 TTCTTCATATGAGTTCTTCTCATTGTGAACT-TCTTCTGGAAATGCCGATGATGATA
66 TTCTTCAGATGAGTTCTTCTCATTATGAACTCTC-TCTGGAAATGCCGATGATGATA
*
204258 TATCTCCTTCTGTGATAG-AGTC-ATGCAAAAGGTCGAACAAGCTCTTCTCATTATGAACTTCTT
1 TATCTCCTTCTGTGAT-GTAATCTA-GC-AAAGGTCGAACAAGCTCTTCTCATTATGAA--TCTT
*
204321 CTTCTTTCTTCAGATGAGTTCTTCTCATTATGAACTCTCTCTGGAAA-----A-G-T--T-
61 CTTCATTCTTCAGATGAGTTCTTCTCATTATGAACTCTCTCTGGAAATGCCGATGATGATA
* * * * * * *
204372 GA--TCCATCGAGTGATG-AATTCGAGCAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTT
1 TATCTCCTTC-TGTGATGTAA-TCTAGC-AAAGGTCGAACAAGCTCTTCTCATTATGAA--TCTT
*
204434 CTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCT
61 CTTCATTCTTCAGATGAGTTCTTCTCATTATGAACTCT
204472 TTCACTGGGG
Statistics
Matches: 189, Mismatches: 14, Indels: 28
0.82 0.06 0.12
Matches are distributed among these distances:
112 7 0.04
113 80 0.42
114 2 0.01
115 1 0.01
117 1 0.01
118 2 0.01
119 22 0.12
120 29 0.15
123 6 0.03
124 37 0.20
125 2 0.01
ACGTcount: A:0.25, C:0.21, G:0.16, T:0.38
Consensus pattern (121 bp):
TATCTCCTTCTGTGATGTAATCTAGCAAAGGTCGAACAAGCTCTTCTCATTATGAATCTTCTTCA
TTCTTCAGATGAGTTCTTCTCATTATGAACTCTCTCTGGAAATGCCGATGATGATA
Found at i:204427 original size:113 final size:113
Alignment explanation
Indices: 204282--204955 Score: 1024
Period size: 113 Copynumber: 5.9 Consensus size: 113
204272 ATAGAGTCAT
* ** *
204282 GCAAAAGGTCGAACAAGCTCTTCTCATTATGAACTTCTTCTTCTTTCTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
* * * * *
204347 ATTATGAACTCTCTCTGGAAAAGTTGATCCATCGAGTGATGAATTCGA
66 ATTATGAACTTTTTCTGGAAAAGCTGATCCATCAAATGATGAATTCGA
* *
204395 GCAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
* ** * * *
204460 ATTATGAACTCTTTCACTGGGGATGCTGATTCATCAAATGATGAATTCAA
66 ATTATGAACT-TTT-TCTGGAAAAGCTGATCCATCAAATGATGAATTCGA
* *
204510 ACAAAAGGTTGAACAAATTATTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
* * * *
204575 ATTATGAACTTTTTCTGGAAAAGCTAATCTATCAAGTGATGAATTTGA
66 ATTATGAACTTTTTCTGGAAAAGCTGATCCATCAAATGATGAATTCGA
*
204623 GCAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
* *
204688 ATTATGAACTTTTTTCTGGAAAAGCTGATCCATCAAATGATGGATTTGA
66 ATTATGAAC-TTTTTCTGGAAAAGCTGATCCATCAAATGATGAATTCGA
* *
204737 GCAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTATTCTC
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
* * *
204802 ATTATGAACTTTTTCTAGAAAAGCTGATCCATCAAATGATGGATTAGA
66 ATTATGAACTTTTTCTGGAAAAGCTGATCCATCAAATGATGAATTCGA
*
204850 GCAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
*
204915 ATTATGAACTTTTTCTGGAAAAGCTGATCCATCAAGTGATG
66 ATTATGAACTTTTTCTGGAAAAGCTGATCCATCAAATGATG
204956 GATTTGAATC
Statistics
Matches: 516, Mismatches: 42, Indels: 6
0.91 0.07 0.01
Matches are distributed among these distances:
113 307 0.59
114 112 0.22
115 97 0.19
ACGTcount: A:0.29, C:0.19, G:0.15, T:0.38
Consensus pattern (113 bp):
GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
ATTATGAACTTTTTCTGGAAAAGCTGATCCATCAAATGATGAATTCGA
Found at i:204825 original size:227 final size:227
Alignment explanation
Indices: 204282--204962 Score: 1058
Period size: 227 Copynumber: 3.0 Consensus size: 227
204272 ATAGAGTCAT
* ** *
204282 GCAAAAGGTCGAACAAGCTCTTCTCATTATGAACTTCTTCTTCTTTCTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
* * * * * * *
204347 ATTATGAACTCTCTCTGGAAAAGTTGATCCATCGAGTGATGAATTCGAGCAAAAAGTTGAACAAG
66 ATTATGAACTTTTTCTGGAAAAGCTGATCCATCAAGTGATGAATTAGAGCAAAAGGTTGAACAAA
* **
204412 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTTTCAC
131 TTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACT-TTTTTC
** * * * **
204477 TGGGGATGCTGATTCATCAAATGATGAATTCAA
195 TGGAAAAGCTGATCCATCAAATGATGGATTTGA
* *
204510 ACAAAAGGTTGAACAAATTATTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
* * *
204575 ATTATGAACTTTTTCTGGAAAAGCTAATCTATCAAGTGATGAATTTGAGCAAAAGGTTGAACAAA
66 ATTATGAACTTTTTCTGGAAAAGCTGATCCATCAAGTGATGAATTAGAGCAAAAGGTTGAACAAA
204640 TTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTTTTCT
131 TTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTTTTCT
204705 GGAAAAGCTGATCCATCAAATGATGGATTTGA
196 GGAAAAGCTGATCCATCAAATGATGGATTTGA
* *
204737 GCAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTATTCTC
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
* * *
204802 ATTATGAACTTTTTCTAGAAAAGCTGATCCATCAAATGATGGATTAGAGCAAAAGGTTGAACAAA
66 ATTATGAACTTTTTCTGGAAAAGCTGATCCATCAAGTGATGAATTAGAGCAAAAGGTTGAACAAA
204867 TTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAAC-TTTTTCT
131 TTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTTTTCT
*
204931 GGAAAAGCTGATCCATCAAGTGATGGATTTGA
196 GGAAAAGCTGATCCATCAAATGATGGATTTGA
204963 ATCTTTGCTA
Statistics
Matches: 417, Mismatches: 36, Indels: 2
0.92 0.08 0.00
Matches are distributed among these distances:
226 38 0.09
227 207 0.50
228 172 0.41
ACGTcount: A:0.29, C:0.18, G:0.15, T:0.38
Consensus pattern (227 bp):
GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
ATTATGAACTTTTTCTGGAAAAGCTGATCCATCAAGTGATGAATTAGAGCAAAAGGTTGAACAAA
TTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTTTTCT
GGAAAAGCTGATCCATCAAATGATGGATTTGA
Found at i:205811 original size:54 final size:54
Alignment explanation
Indices: 205717--205852 Score: 154
Period size: 54 Copynumber: 2.6 Consensus size: 54
205707 AGAATAGCAG
* * * * * *
205717 GTTCGTAAAACATTTGACAGCGCATTCATCCTTTCCTGTGGCTTCTGCTCAGAT
1 GTTCGTAAAACATTTGACAACACATTCATCATCTCATGTGGCTTCAGCTCAGAT
* * *
205771 GTTCGTAAACCATTTGACAACACATTCTTCATCTCATGTGGTTTCAGCTCAGA-
1 GTTCGTAAAACATTTGACAACACATTCATCATCTCATGTGGCTTCAGCTCAGAT
*
205824 --T-GTAAAACACTTGACAACACATTCATCAT
1 GTTCGTAAAACATTTGACAACACATTCATCAT
205853 TTTCTGTGGG
Statistics
Matches: 70, Mismatches: 12, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
50 25 0.36
51 1 0.01
54 44 0.63
ACGTcount: A:0.27, C:0.25, G:0.15, T:0.33
Consensus pattern (54 bp):
GTTCGTAAAACATTTGACAACACATTCATCATCTCATGTGGCTTCAGCTCAGAT
Found at i:205866 original size:40 final size:40
Alignment explanation
Indices: 205822--205901 Score: 151
Period size: 40 Copynumber: 2.0 Consensus size: 40
205812 TTTCAGCTCA
205822 GATGTAAAACACTTGACAACACATTCATCATTTTCTGTGG
1 GATGTAAAACACTTGACAACACATTCATCATTTTCTGTGG
*
205862 GATGTAAAACACTTGACAACACATTCATCCTTTTCTGTGG
1 GATGTAAAACACTTGACAACACATTCATCATTTTCTGTGG
205902 CTTCTGCTCA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
40 39 1.00
ACGTcount: A:0.31, C:0.21, G:0.15, T:0.33
Consensus pattern (40 bp):
GATGTAAAACACTTGACAACACATTCATCATTTTCTGTGG
Found at i:208203 original size:115 final size:115
Alignment explanation
Indices: 208035--208491 Score: 781
Period size: 115 Copynumber: 4.0 Consensus size: 115
208025 GATCATGCAG
* * * * * * *
208035 TTCATCTTTTAATTCCAATGATTGG-TTCTGTGGTTCCTACCGAACCAGGTCAGATAACTCAAAG
1 TTCATCTTTCAAATCCAATGATTGGTTTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAAG
* * * *
208099 AACACTTCTAGAAGATGCTATTGGGCCTCCTTATTTCTACCATGAGCAAA
66 AACACTTCCAGAAGATGCTATTGGGTCTTCTTATTTCTACTATGAGCAAA
* *
208149 TTCATCTTTCAAATCTAATGATTGGTTTTTGGGGTTCATACCAAACCAGCTCAGATAACTCAAAG
1 TTCATCTTTCAAATCCAATGATTGGTTTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAAG
208214 AACACTTCCAGAAGATGCTATTGGGTCTTCTTATTTCTACTATGAGCAAA
66 AACACTTCCAGAAGATGCTATTGGGTCTTCTTATTTCTACTATGAGCAAA
*
208264 TTCATCTTTCAAATCCAATGATTAGTTTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAAG
1 TTCATCTTTCAAATCCAATGATTGGTTTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAAG
208329 AACACTTCCAGAAGATGCTATTGGGTCTTCTTATTTCTACTATGAGCAAA
66 AACACTTCCAGAAGATGCTATTGGGTCTTCTTATTTCTACTATGAGCAAA
208379 TTCATCTTTCAAATCCAATGATTGGTTTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAAG
1 TTCATCTTTCAAATCCAATGATTGGTTTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAAG
208444 AACACTTCCAGAAGATGCTATTGGGTCTTCTTATTTCTACTATGAGCA
66 AACACTTCCAGAAGATGCTATTGGGTCTTCTTATTTCTACTATGAGCA
208492 CATGTCACTT
Statistics
Matches: 326, Mismatches: 16, Indels: 1
0.95 0.05 0.00
Matches are distributed among these distances:
114 22 0.07
115 304 0.93
ACGTcount: A:0.30, C:0.21, G:0.16, T:0.33
Consensus pattern (115 bp):
TTCATCTTTCAAATCCAATGATTGGTTTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAAG
AACACTTCCAGAAGATGCTATTGGGTCTTCTTATTTCTACTATGAGCAAA
Found at i:211255 original size:115 final size:115
Alignment explanation
Indices: 211095--211551 Score: 781
Period size: 115 Copynumber: 4.0 Consensus size: 115
211085 AAGTGACATG
211095 TGCTCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
1 TGCTCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
211160 TGGTTTGGTATGAACCCCAAAAACCAATCATTGGATTTGAAAGATGAATT
66 TGGTTTGGTATGAACCCCAAAAACCAATCATTGGATTTGAAAGATGAATT
211210 TGCTCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
1 TGCTCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
*
211275 TGGTTTGGTATGAACCCCAAAAACTAATCATTGGATTTGAAAGATGAATT
66 TGGTTTGGTATGAACCCCAAAAACCAATCATTGGATTTGAAAGATGAATT
*
211325 TGCTCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGAGC
1 TGCTCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
*
211390 TGGTTTGGTATGAACCCCAAAAACCAATCATTAGATTTGAAAGATGAATT
66 TGGTTTGGTATGAACCCCAAAAACCAATCATTGGATTTGAAAGATGAATT
* * * * *
211440 TGCTCATGGTAGAAATAAGGAGGCCCAATAGCATCTTCTAGAAGTGTTCTTTGAGTTATCTGACC
1 TGCTCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
* * * * * *
211505 TGGTTCGGTAGGAACCAC-AGAACCAATCATTGGAATTAAAAGATGAA
66 TGGTTTGGTATGAACCCCAAAAACCAATCATTGGATTTGAAAGATGAA
211552 CTGCATGATC
Statistics
Matches: 326, Mismatches: 16, Indels: 1
0.95 0.05 0.00
Matches are distributed among these distances:
114 25 0.08
115 301 0.92
ACGTcount: A:0.33, C:0.16, G:0.21, T:0.30
Consensus pattern (115 bp):
TGCTCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
TGGTTTGGTATGAACCCCAAAAACCAATCATTGGATTTGAAAGATGAATT
Found at i:213749 original size:40 final size:40
Alignment explanation
Indices: 213691--213770 Score: 142
Period size: 40 Copynumber: 2.0 Consensus size: 40
213681 TGAGCAGAAG
*
213691 CCACATAAAAGGAAGAATGTGTTGTCAAGTGTTTTACATC
1 CCACAAAAAAGGAAGAATGTGTTGTCAAGTGTTTTACATC
*
213731 CCACAAAAAAGGATGAATGTGTTGTCAAGTGTTTTACATC
1 CCACAAAAAAGGAAGAATGTGTTGTCAAGTGTTTTACATC
213771 TGAGCTGAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 38 1.00
ACGTcount: A:0.35, C:0.15, G:0.20, T:0.30
Consensus pattern (40 bp):
CCACAAAAAAGGAAGAATGTGTTGTCAAGTGTTTTACATC
Found at i:213806 original size:90 final size:92
Alignment explanation
Indices: 213637--213817 Score: 240
Period size: 90 Copynumber: 2.0 Consensus size: 92
213627 TGAGCAGAAG
* *
213637 CCACAGAAAAGGATGAATGTATTGTCAAATGCTTTACGAACATCTGAGCAGAAGCCACATAAAAG
1 CCACAAAAAAGGATGAATGTATTGTCAAATGCTTTA--AACATCTGAGCAGAAACCACATAAAAG
*
213702 GAAGAATGTGTTGTCAAGTGTTTTACATC
64 GAAGAATGTGTTGTCAAATGTTTTACATC
* * * * * * *
213731 CCACAAAAAAGGATGAATGTGTTGTCAAGTG-TTT-TACATCTGAGCTGAAACCACATGAGATGA
1 CCACAAAAAAGGATGAATGTATTGTCAAATGCTTTAAACATCTGAGCAGAAACCACATAAAAGGA
213794 AGAATGTGTTGTCAAATGTTTTAC
66 AGAATGTGTTGTCAAATGTTTTAC
213818 GAACATCTGA
Statistics
Matches: 77, Mismatches: 10, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
90 46 0.60
93 3 0.04
94 28 0.36
ACGTcount: A:0.36, C:0.15, G:0.22, T:0.28
Consensus pattern (92 bp):
CCACAAAAAAGGATGAATGTATTGTCAAATGCTTTAAACATCTGAGCAGAAACCACATAAAAGGA
AGAATGTGTTGTCAAATGTTTTACATC
Found at i:213853 original size:54 final size:54
Alignment explanation
Indices: 213738--213875 Score: 167
Period size: 54 Copynumber: 2.6 Consensus size: 54
213728 ATCCCACAAA
* * *
213738 AAAGGATGAATGTGTTGTCAAGTGTTTT----ACATCTGAGCTGAAACCACATG
1 AAAGGATGAATGTGTTGTCAAATGTTTTACGAACATCTGAGCAGAAACCACAGG
* * * *
213788 AGATGAAGAATGTGTTGTCAAATGTTTTACGAACATCTGAGCAGAAGCCACAGG
1 AAAGGATGAATGTGTTGTCAAATGTTTTACGAACATCTGAGCAGAAACCACAGG
* *
213842 AAAGGATGAATGCGCTGTCAAATGTTTTACGAAC
1 AAAGGATGAATGTGTTGTCAAATGTTTTACGAAC
213876 CTGCTATTCT
Statistics
Matches: 72, Mismatches: 12, Indels: 4
0.82 0.14 0.05
Matches are distributed among these distances:
50 24 0.33
54 48 0.67
ACGTcount: A:0.34, C:0.14, G:0.25, T:0.27
Consensus pattern (54 bp):
AAAGGATGAATGTGTTGTCAAATGTTTTACGAACATCTGAGCAGAAACCACAGG
Found at i:215025 original size:227 final size:226
Alignment explanation
Indices: 214631--215311 Score: 1040
Period size: 227 Copynumber: 3.0 Consensus size: 226
214621 TAGCAAAGAT
* *
214631 TCAAATCCATCACTTGATGGATCAACTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGA
1 TCAAATCCATCATTTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGA
* * * *
214696 AGAAGGAAGAAGAAATTCATAATAAGAAGAATTTGTTTAACCTTTTGCTCAAATCCATCATTTGA
66 AGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATTCATCACTTGA
*
214761 TGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATT
131 TGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTT
214826 CATAATGAGAAGAATTTGTTCAACCTTTTGC
196 CATAATGAGAAGAATTTGTTCAACCTTTTGC
*
214857 TCAAATCCATCATTTGATGGATCAGTTTTTCCAGAAAAAAGTTCATAATGAGAAGAACTCATCTG
1 TCAAATCCATCATTTGATGGATCAGCTTTTCCAG-AAAAAGTTCATAATGAGAAGAACTCATCTG
*
214922 AAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTATTCAACCTTTTGCTCAAATTCATCACTTG
65 AAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATTCATCACTTG
* *
214987 ATAGATCAGCTTTTCAAGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGT
130 ATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGT
*
215052 TCATAATGAGAAGAATTTGTTCAACCTTTTGT
195 TCATAATGAGAAGAATTTGTTCAACCTTTTGC
** * * ** *
215084 TTGAATTCATCATTTGATGGATCAGCATCCCCAGTGAAAGAGTTCATAATGAGAAGAACTCATCT
1 TCAAATCCATCATTTGATGGATCAGCTTTTCCA--GAAAAAGTTCATAATGAGAAGAACTCATCT
* * * *
215149 GAAGAAGGAATAAGAAGTTCATAATGAGAAGAACTTGTTCAA-CTTTTCGCTCGAATTCATCACT
64 GAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTT-GCTCAAATTCATCACT
* * * * *
215213 CGATGGATCAACTTTTCCAGAGAGAGTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGAAGAA
128 TGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAA
** *
215278 GTTCATAATGAGAAGAGCTTGTTCGACCTTTTGC
193 GTTCATAATGAGAAGAATTTGTTCAACCTTTTGC
215312 ATGACTCTAT
Statistics
Matches: 415, Mismatches: 36, Indels: 6
0.91 0.08 0.01
Matches are distributed among these distances:
226 31 0.07
227 214 0.52
228 169 0.41
229 1 0.00
ACGTcount: A:0.39, C:0.15, G:0.18, T:0.28
Consensus pattern (226 bp):
TCAAATCCATCATTTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGA
AGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATTCATCACTTGA
TGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTT
CATAATGAGAAGAATTTGTTCAACCTTTTGC
Found at i:215324 original size:113 final size:113
Alignment explanation
Indices: 214631--215311 Score: 1013
Period size: 113 Copynumber: 6.0 Consensus size: 113
214621 TAGCAAAGAT
* *
214631 TCAAATCCATCACTTGATGGATCAACTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGA
1 TCAAATTCATCACTTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGA
* *
214696 AGAAGGAAGAAGAAATTCATAATAAGAAGAATTTGTTTAACCTTTTGC
66 AGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
* *
214744 TCAAATCCATCATTTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGA
1 TCAAATTCATCACTTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGA
214809 AGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
66 AGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
* * *
214857 TCAAATCCATCATTTGATGGATCAGTTTTTCCAGAAAAAAGTTCATAATGAGAAGAACTCATCTG
1 TCAAATTCATCACTTGATGGATCAGCTTTTCCAG-AAAAAGTTCATAATGAGAAGAACTCATCTG
*
214922 AAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTATTCAACCTTTTGC
65 AAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
* *
214971 TCAAATTCATCACTTGATAGATCAGCTTTTCAAGAAAAAGTTCATAATGAGAAGAACTCATCTGA
1 TCAAATTCATCACTTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGA
* *
215036 AGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGT
66 AGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
** * * ** *
215084 TTGAATTCATCATTTGATGGATCAGCATCCCCAGTGAAAGAGTTCATAATGAGAAGAACTCATCT
1 TCAAATTCATCACTTGATGGATCAGCTTTTCCA--GAAAAAGTTCATAATGAGAAGAACTCATCT
* * *
215149 GAAGAAGGAATAAGAAGTTCATAATGAGAAGAACTTGTTCAA-CTTTTCGC
64 GAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTT-GC
* * * * *
215199 TCGAATTCATCACTCGATGGATCAACTTTTCCAGAGAGAGTTCATAATGAGAAGAACTCATCTGA
1 TCAAATTCATCACTTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGA
* * ** *
215264 AGAAAGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCGACCTTTTGC
66 AGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
215312 ATGACTCTAT
Statistics
Matches: 525, Mismatches: 38, Indels: 10
0.92 0.07 0.02
Matches are distributed among these distances:
113 312 0.59
114 117 0.22
115 96 0.18
ACGTcount: A:0.39, C:0.15, G:0.18, T:0.28
Consensus pattern (113 bp):
TCAAATTCATCACTTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGA
AGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
Found at i:215391 original size:124 final size:119
Alignment explanation
Indices: 215226--215454 Score: 311
Period size: 120 Copynumber: 1.9 Consensus size: 119
215216 TGGATCAACT
* * * *
215226 TTTCCAGAGAGAGTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGAAGAAGTTCATAATGAGA
1 TTTCCAGAGAGAGTTCACAATGAGAACAACTCA--T-ATG-AAGAAGAAGAAGTTCACAATGAGA
*
215291 AGAGCTTGTTCGACCTTTTGC-ATGACT-CTATCACAGAAGGAGATATATCATCATCAGCA
62 AGAGCTTGTTCAACC-TTTGCTA-GACTAC-ATCACAGAAGGAGATATATCATCATCAGCA
215350 TTTCCAGA-AGAAGTTCACAATGAGAACAACTCATATGAAGAAGAAGAAGTTCACAATGAGAAGA
1 TTTCCAGAGAG-AGTTCACAATGAGAACAACTCATATGAAGAAGAAGAAGTTCACAATGAGAAGA
*
215414 GCTTGTTCAACCTTTGCTAGATTACATCACAGAAGGAGATA
65 GCTTGTTCAACCTTTGCTAGACTACATCACAGAAGGAGATA
215455 AATTGTCATC
Statistics
Matches: 96, Mismatches: 6, Indels: 11
0.85 0.05 0.10
Matches are distributed among these distances:
119 24 0.25
120 39 0.41
121 2 0.02
122 1 0.01
123 2 0.02
124 28 0.29
ACGTcount: A:0.39, C:0.16, G:0.21, T:0.24
Consensus pattern (119 bp):
TTTCCAGAGAGAGTTCACAATGAGAACAACTCATATGAAGAAGAAGAAGTTCACAATGAGAAGAG
CTTGTTCAACCTTTGCTAGACTACATCACAGAAGGAGATATATCATCATCAGCA
Found at i:215669 original size:3 final size:3
Alignment explanation
Indices: 215661--215726 Score: 82
Period size: 3 Copynumber: 22.0 Consensus size: 3
215651 ATTTATTTAT
* *
215661 TTA TTA TTA TTA TTA TTA TAA TAA TTA TTA TTA TTA -TA TATA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA
215706 TTA -TA TATA TTA TTA TTA TTA
1 TTA TTA T-TA TTA TTA TTA TTA
215727 AAAAATAATT
Statistics
Matches: 57, Mismatches: 2, Indels: 8
0.85 0.03 0.12
Matches are distributed among these distances:
2 4 0.07
3 47 0.82
4 6 0.11
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (3 bp):
TTA
Found at i:215687 original size:18 final size:16
Alignment explanation
Indices: 215661--215726 Score: 95
Period size: 15 Copynumber: 4.4 Consensus size: 16
215651 ATTTATTTAT
215661 TTATTAT-TATTATTA
1 TTATTATATATTATTA
*
215676 TTATAATA-ATTATTA
1 TTATTATATATTATTA
215691 TTATTATATA-TATTA
1 TTATTATATATTATTA
215706 TTA-TATATATTATTA
1 TTATTATATATTATTA
215721 TTATTA
1 TTATTA
215727 AAAAATAATT
Statistics
Matches: 45, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
14 6 0.13
15 36 0.80
16 3 0.07
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (16 bp):
TTATTATATATTATTA
Found at i:216951 original size:3 final size:3
Alignment explanation
Indices: 216945--216987 Score: 52
Period size: 3 Copynumber: 14.3 Consensus size: 3
216935 TTATTTGCAA
* *
216945 TAT TAT T-T TAT TAT TAT TACT TTT TAT TAT TAT TCT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT TAT T
216988 TATATAAATA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
2 2 0.06
3 30 0.88
4 2 0.06
ACGTcount: A:0.26, C:0.05, G:0.00, T:0.70
Consensus pattern (3 bp):
TAT
Found at i:216971 original size:16 final size:15
Alignment explanation
Indices: 216950--216987 Score: 58
Period size: 16 Copynumber: 2.5 Consensus size: 15
216940 TGCAATATTA
216950 TTTTATTATTATTACT
1 TTTTATTATTATT-CT
216966 TTTTATTATTATTCT
1 TTTTATTATTATTCT
*
216981 TATTATT
1 TTTTATT
216988 TATATAAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
15 8 0.38
16 13 0.62
ACGTcount: A:0.24, C:0.05, G:0.00, T:0.71
Consensus pattern (15 bp):
TTTTATTATTATTCT
Found at i:216990 original size:16 final size:15
Alignment explanation
Indices: 216945--216987 Score: 56
Period size: 13 Copynumber: 3.1 Consensus size: 15
216935 TTATTTGCAA
216945 TATTATT-TTATTAT
1 TATTATTCTTATTAT
*
216959 TATTA--CTTTTTAT
1 TATTATTCTTATTAT
216972 TATTATTCTTATTAT
1 TATTATTCTTATTAT
216987 T
1 T
216988 TATATAAATA
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
13 11 0.46
14 5 0.21
15 8 0.33
ACGTcount: A:0.26, C:0.05, G:0.00, T:0.70
Consensus pattern (15 bp):
TATTATTCTTATTAT
Found at i:217200 original size:115 final size:116
Alignment explanation
Indices: 217068--217294 Score: 248
Period size: 116 Copynumber: 2.0 Consensus size: 116
217058 CATAAATTAC
* * * *
217068 TTTTTTAATAATCATATT--TTAATATATATTTATTTATTTTTCAATAT-TAAG-AAAGGGCAGT
1 TTTTTTAATAATCATATTAATT-AT-TATAATTATATATTTTTCAATATCGAAGAAAAGAGCAGT
* * *
217129 CTTAAAACAACTGGATGTCCATTTTCTGATATTTTTAAATAAATAAATATCCTA
64 CTTAAAACAACTAGAAG-CCATTTTCTGATATTTCTAAATAAATAAATATCCTA
* * * *
217183 TTTTTTAAATCAT-ATATTAATTATTTTAATTATATATTTTTTAATATCGAAGAAAAGAGCTGTC
1 TTTTTT-AATAATCATATTAATTATTATAATTATATATTTTTCAATATCGAAGAAAAGAGCAGTC
** * *
217247 TTAAGGCACCTAGAAGCCCTTTTCTGATATTTCTAAATAAATAAATAT
65 TTAAAACAACTAGAAGCCATTTTCTGATATTTCTAAATAAATAAATAT
217295 TTTATTTATA
Statistics
Matches: 92, Mismatches: 15, Indels: 9
0.79 0.13 0.08
Matches are distributed among these distances:
115 30 0.33
116 40 0.43
117 22 0.24
ACGTcount: A:0.37, C:0.10, G:0.08, T:0.44
Consensus pattern (116 bp):
TTTTTTAATAATCATATTAATTATTATAATTATATATTTTTCAATATCGAAGAAAAGAGCAGTCT
TAAAACAACTAGAAGCCATTTTCTGATATTTCTAAATAAATAAATATCCTA
Found at i:219834 original size:18 final size:18
Alignment explanation
Indices: 219811--219848 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
219801 TTTCGTACAT
*
219811 TATATAT-TAGTGTGTGTA
1 TATATATATA-TGTATGTA
219829 TATATATATATGTATGTA
1 TATATATATATGTATGTA
219847 TA
1 TA
219849 AGTCATAATG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 16 0.89
19 2 0.11
ACGTcount: A:0.34, C:0.00, G:0.16, T:0.50
Consensus pattern (18 bp):
TATATATATATGTATGTA
Found at i:221416 original size:45 final size:48
Alignment explanation
Indices: 221341--221446 Score: 128
Period size: 45 Copynumber: 2.2 Consensus size: 48
221331 TATTTTCATT
* * *
221341 TTTTTCGAATAAATGCATGCGAACTAGATATCATGTGGTTAGG-TTT-A
1 TTTTGCGAAT-AATGCATACGAACTAGATATCATGCGGTTAGGATTTCA
* *
221388 TTTTGCGAATAA-GCATACGAATTAGATATCATGCGGTTAGGATTTCT
1 TTTTGCGAATAATGCATACGAACTAGATATCATGCGGTTAGGATTTCA
*
221435 TTTTGTGAATAA
1 TTTTGCGAATAA
221447 CAAAGCATGG
Statistics
Matches: 51, Mismatches: 6, Indels: 4
0.84 0.10 0.07
Matches are distributed among these distances:
45 26 0.51
46 5 0.10
47 20 0.39
ACGTcount: A:0.30, C:0.10, G:0.21, T:0.39
Consensus pattern (48 bp):
TTTTGCGAATAATGCATACGAACTAGATATCATGCGGTTAGGATTTCA
Found at i:231087 original size:8 final size:7
Alignment explanation
Indices: 231074--231278 Score: 64
Period size: 7 Copynumber: 27.1 Consensus size: 7
231064 AAGAAGAAAT
231074 AAAAGAGA
1 AAAAGA-A
231082 AAAAGAA
1 AAAAGAA
*
231089 AAATGAAA
1 AAAAG-AA
231097 AAAATGAA
1 AAAA-GAA
*
231105 AATAATAA
1 AA-AAGAA
*
231113 TAATAATAA
1 -AA-AAGAA
*
231122 AAATGAGA
1 AAAAGA-A
*
231130 AGAAG-A
1 AAAAGAA
231136 AAAAGAA
1 AAAAGAA
231143 GAAAAGAA
1 -AAAAGAA
231151 AAATGAGAA
1 AAA--AGAA
231160 AAAAGAA
1 AAAAGAA
231167 AAATGATGGAA
1 AAA--A--GAA
231178 AAAACGAA
1 AAAA-GAA
231186 AAGAA-AA
1 AA-AAGAA
231193 AAAAG-A
1 AAAAGAA
231199 AAAA-AA
1 AAAAGAA
*
231205 AGAAGAA
1 AAAAGAA
*
231212 AAATGGAA
1 AAA-AGAA
231220 AATGGAAGAA
1 AA---AAGAA
231230 AAAATG-A
1 AAAA-GAA
*
231237 AAGAGAA
1 AAAAGAA
231244 AAACA-AA
1 AAA-AGAA
*
231251 AAGAGAA
1 AAAAGAA
*
231258 AAATGAA
1 AAAAGAA
231265 AAAA-AA
1 AAAAGAA
*
231271 AAGAGAA
1 AAAAGAA
231278 A
1 A
231279 TAAAAGGAGG
Statistics
Matches: 151, Mismatches: 20, Indels: 53
0.67 0.09 0.24
Matches are distributed among these distances:
6 23 0.15
7 52 0.34
8 42 0.28
9 22 0.15
10 5 0.03
11 7 0.05
ACGTcount: A:0.74, C:0.01, G:0.18, T:0.07
Consensus pattern (7 bp):
AAAAGAA
Found at i:231143 original size:9 final size:9
Alignment explanation
Indices: 231129--231214 Score: 53
Period size: 9 Copynumber: 10.2 Consensus size: 9
231119 TAAAAATGAG
231129 AAGAAGAAA
1 AAGAAGAAA
231138 AAGAAG-AA
1 AAGAAGAAA
231146 AAG-A-AAA
1 AAGAAGAAA
*
231153 ATG-AG-AA
1 AAGAAGAAA
231160 AA-AAGAAA
1 AAGAAGAAA
*
231168 AATGATGGAAA
1 AA-GA-AGAAA
*
231179 AA-ACG-AA
1 AAGAAGAAA
*
231186 AAGAAAAAA
1 AAGAAGAAA
*
231195 AAGAAAAAA
1 AAGAAGAAA
231204 AAGAAGAAA
1 AAGAAGAAA
231213 AA
1 AA
231215 TGGAAAATGG
Statistics
Matches: 61, Mismatches: 7, Indels: 18
0.71 0.08 0.21
Matches are distributed among these distances:
7 15 0.25
8 11 0.18
9 28 0.46
10 1 0.02
11 6 0.10
ACGTcount: A:0.77, C:0.01, G:0.19, T:0.03
Consensus pattern (9 bp):
AAGAAGAAA
Found at i:231186 original size:19 final size:16
Alignment explanation
Indices: 231081--231202 Score: 87
Period size: 15 Copynumber: 7.7 Consensus size: 16
231071 AATAAAAGAG
231081 AAAAAGAAAAATGA-A
1 AAAAAGAAAAATGAGA
* *
231096 AAAAATG-AAAATAATA
1 AAAAA-GAAAAATGAGA
*
231112 ATAATAATAAAAATGAG-
1 A-AA-AAGAAAAATGAGA
*
231129 AAGAAGAAAAA-GA-A
1 AAAAAGAAAAATGAGA
*
231143 GAAAAGAAAAATGAGA
1 AAAAAGAAAAATGAGA
231159 AAAAAGAAAAATGATGGA
1 AAAAAGAAAAATGA--GA
*
231177 AAAAACG-AAAA-GAAA
1 AAAAA-GAAAAATGAGA
231192 AAAAAGAAAAA
1 AAAAAGAAAAA
231203 AAAGAAGAAA
Statistics
Matches: 85, Mismatches: 10, Indels: 24
0.71 0.08 0.20
Matches are distributed among these distances:
14 12 0.14
15 30 0.35
16 18 0.21
17 5 0.06
18 19 0.22
19 1 0.01
ACGTcount: A:0.75, C:0.01, G:0.16, T:0.09
Consensus pattern (16 bp):
AAAAAGAAAAATGAGA
Found at i:231221 original size:18 final size:19
Alignment explanation
Indices: 231146--231269 Score: 55
Period size: 19 Copynumber: 6.4 Consensus size: 19
231136 AAAAGAAGAA
231146 AAGAAAAATGAGAAAAAAG
1 AAGAAAAATGAGAAAAAAG
*
231165 AA-AAATGATG-GAAAAAACG
1 AAGAAA-AATGAGAAAAAA-G
* *
231184 AAAAGAAAAAAAAGAAAAAAAAG
1 --AAG--AAAAATGAGAAAAAAG
**
231207 AAGAAAAATG-GAAAATGG
1 AAGAAAAATGAGAAAAAAG
231225 AAGAAAAAATGA-AAGAGAAA-
1 AAG-AAAAATGAGAA-A-AAAG
* *
231245 AACAAAAA-GAGAAAAATG
1 AAGAAAAATGAGAAAAAAG
231263 AA-AAAAA
1 AAGAAAAA
231270 AAAGAGAAAT
Statistics
Matches: 79, Mismatches: 12, Indels: 30
0.65 0.10 0.25
Matches are distributed among these distances:
17 7 0.09
18 23 0.29
19 28 0.35
20 3 0.04
21 6 0.08
23 3 0.04
24 9 0.11
ACGTcount: A:0.74, C:0.02, G:0.19, T:0.06
Consensus pattern (19 bp):
AAGAAAAATGAGAAAAAAG
Found at i:231270 original size:18 final size:17
Alignment explanation
Indices: 231189--231283 Score: 50
Period size: 19 Copynumber: 5.1 Consensus size: 17
231179 AAACGAAAAG
231189 AAAAAAAAGAAAAA-AA
1 AAAAAAAAGAAAAATAA
*
231205 AGAAGAAAAATGGAAAATGGAA
1 A-AA-AAAAA-GAAAAAT--AA
* *
231227 GAAAAAATGAAAGAGA-AA
1 AAAAAAAAGAAA-A-ATAA
231245 AACAAAAAGAGAAAAATGAA
1 AA-AAAAA-AGAAAAAT-AA
*
231265 AAAAAAAAGAGAAATAA
1 AAAAAAAAGAAAAATAA
231282 AA
1 AA
231284 GGAGGGTTCA
Statistics
Matches: 60, Mismatches: 7, Indels: 23
0.67 0.08 0.26
Matches are distributed among these distances:
16 1 0.02
17 6 0.10
18 16 0.27
19 19 0.32
20 13 0.22
21 3 0.05
22 2 0.03
ACGTcount: A:0.77, C:0.01, G:0.17, T:0.05
Consensus pattern (17 bp):
AAAAAAAAGAAAAATAA
Found at i:232620 original size:37 final size:36
Alignment explanation
Indices: 232563--232634 Score: 108
Period size: 37 Copynumber: 2.0 Consensus size: 36
232553 AAACAGGTTA
* *
232563 ATCTTAAGCCTTCACGGAAGAGTAGTGAAGCAAACC
1 ATCTTAAGCATTCACAGAAGAGTAGTGAAGCAAACC
*
232599 ATCTGTAAGCATTCACAGAAGATTAGTGAAGCAAAC
1 ATCT-TAAGCATTCACAGAAGAGTAGTGAAGCAAAC
232635 TCATTTTATG
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
36 4 0.12
37 28 0.88
ACGTcount: A:0.39, C:0.19, G:0.21, T:0.21
Consensus pattern (36 bp):
ATCTTAAGCATTCACAGAAGAGTAGTGAAGCAAACC
Found at i:232718 original size:55 final size:55
Alignment explanation
Indices: 232649--233008 Score: 452
Period size: 55 Copynumber: 6.5 Consensus size: 55
232639 TTTATGAAGA
* * * * *
232649 TCGAGTCCTATACTCTCTGAAGGAATAGGGAGCAGACATGTTTATTGAAGATTTT
1 TCGAGTCTTATACTCTCTGAATGAATAGGGAGCAGACACGTTTGTTGAAGATTGT
* ** * ** *
232704 TCGAGT-TCTATACTCTCTGAAGGAATATAGAGCGGACTTGTTTTATTGAAGATTGT
1 TCGAGTCT-TATACTCTCTGAATGAATAGGGAGCAGACACG-TTTGTTGAAGATTGT
* * * * * *
232760 TCAAGTCTTATACTCCCTAAACGAATAGGGAGCAGACACGTTTGCTGAAAATTGT
1 TCGAGTCTTATACTCTCTGAATGAATAGGGAGCAGACACGTTTGTTGAAGATTGT
*
232815 TCGAGTCTTATACTCTCTGAATGAATAGAGAGCAGACACGTTTGTTGAAGATTGT
1 TCGAGTCTTATACTCTCTGAATGAATAGGGAGCAGACACGTTTGTTGAAGATTGT
* *
232870 TCGAGTCTTATACTCTCTGAATGAATAGAGAGCAGACACGTTTGTTGAAGATTGA
1 TCGAGTCTTATACTCTCTGAATGAATAGGGAGCAGACACGTTTGTTGAAGATTGT
* * *
232925 TCGAGTCTTATACTCCCTGAATGAATAGGGAGCAGACACATTTGTTAAAGATTGT
1 TCGAGTCTTATACTCTCTGAATGAATAGGGAGCAGACACGTTTGTTGAAGATTGT
* * *
232980 TCGAGTCTTATGCTCCCTGAAAGAATAGG
1 TCGAGTCTTATACTCTCTGAATGAATAGG
233009 AAACAGACTC
Statistics
Matches: 269, Mismatches: 33, Indels: 6
0.87 0.11 0.02
Matches are distributed among these distances:
55 225 0.84
56 43 0.16
57 1 0.00
ACGTcount: A:0.30, C:0.16, G:0.23, T:0.32
Consensus pattern (55 bp):
TCGAGTCTTATACTCTCTGAATGAATAGGGAGCAGACACGTTTGTTGAAGATTGT
Found at i:234940 original size:18 final size:18
Alignment explanation
Indices: 234917--234954 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
234907 TTTCGTACAT
*
234917 TATATAT-TAGTGTGTGTA
1 TATATATATA-TGTATGTA
234935 TATATATATATGTATGTA
1 TATATATATATGTATGTA
234953 TA
1 TA
234955 AGTCATAATG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 16 0.89
19 2 0.11
ACGTcount: A:0.34, C:0.00, G:0.16, T:0.50
Consensus pattern (18 bp):
TATATATATATGTATGTA
Found at i:238589 original size:12 final size:12
Alignment explanation
Indices: 238560--238651 Score: 64
Period size: 12 Copynumber: 7.3 Consensus size: 12
238550 AATTATTAAC
238560 ATATTTAA-AAT
1 ATATTTAATAAT
*
238571 ATATTTATTAAT
1 ATATTTAATAAT
*
238583 ATTTTTAATAAT
1 ATATTTAATAAT
238595 ATAATATAATAATAAT
1 AT-AT-T--TAATAAT
*
238611 ATTATTACAATAAT
1 A-TATT-TAATAAT
*
238625 ATATTCAAT--T
1 ATATTTAATAAT
238635 ATATTATAATAAT
1 ATATT-TAATAAT
238648 ATAT
1 ATAT
238652 GATACTATTA
Statistics
Matches: 66, Mismatches: 6, Indels: 16
0.75 0.07 0.18
Matches are distributed among these distances:
10 6 0.09
11 10 0.15
12 19 0.29
13 10 0.15
14 9 0.14
15 1 0.02
16 10 0.15
17 1 0.02
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (12 bp):
ATATTTAATAAT
Found at i:238589 original size:23 final size:23
Alignment explanation
Indices: 238542--238599 Score: 71
Period size: 23 Copynumber: 2.4 Consensus size: 23
238532 CATTTTAATA
238542 AAAATATTAATTATTAACATATTT
1 AAAATA-TAATTATTAACATATTT
* * *
238566 AAAATATATTTATTAATATTTTT
1 AAAATATAATTATTAACATATTT
238589 AATAATATAAT
1 AA-AATATAAT
238600 ATAATAATAA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
23 16 0.55
24 13 0.45
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (23 bp):
AAAATATAATTATTAACATATTT
Found at i:243045 original size:184 final size:186
Alignment explanation
Indices: 242719--243117 Score: 644
Period size: 184 Copynumber: 2.1 Consensus size: 186
242709 ACCGAAATAA
* *
242719 AATTTAAAATTTTAAATATATATTATATATAACATATGGGCTCAGCCCAAACCATTTAAAACCCA
1 AATTTAAAATATT-AA-ATATATTATATATAACATATGAGCTCAGCCCAAACCATTTAAAACCCA
242784 ATTAATAATTTAAGATCCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAAATTATA
64 ATTAATAATTTAAGATCCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAAATTATA
* *
242849 TAAAATTTTTA-TTTTATAATTATATATTATTTAAATTAATTGTAAACTGTTTTTTTG
129 TAAAATTTTTATTTTTATAATTATATATTATTTAAATTAATTATAAACTGCTTTTTTG
*
242906 AA-TTAAAATATTAAATATATTATATATAACATATGAGCTCAGCCCAAACCATTTAAAACCTAAT
1 AATTTAAAATATTAAATATATTATATATAACATATGAGCTCAGCCCAAACCATTTAAAACCCAAT
* * *
242970 TAATAATTTAAGATCCAATAACTTTTAAACTTAAAT-AATTGTTAATTAATTAAAAAATTTATAT
66 TAATAATTTAAGATCCAATAACTTTTAAACCTAAATCAA-TATTAATTAATTAAAAAAATTATAT
243034 AAAATTTTTATTTTTATAATTATATATTATTTAAATTAATTATAAACTGCTTTTTTG
130 AAAATTTTTATTTTTATAATTATATATTATTTAAATTAATTATAAACTGCTTTTTTG
* *
243091 AATTATAAAATATTTAAT-TTTTATATA
1 AATT-TAAAATATTAAATATATTATATA
243118 AATTAAAAAA
Statistics
Matches: 198, Mismatches: 10, Indels: 9
0.91 0.05 0.04
Matches are distributed among these distances:
183 2 0.01
184 116 0.59
185 48 0.24
186 18 0.09
187 14 0.07
ACGTcount: A:0.45, C:0.09, G:0.04, T:0.43
Consensus pattern (186 bp):
AATTTAAAATATTAAATATATTATATATAACATATGAGCTCAGCCCAAACCATTTAAAACCCAAT
TAATAATTTAAGATCCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAAATTATATA
AAATTTTTATTTTTATAATTATATATTATTTAAATTAATTATAAACTGCTTTTTTG
Found at i:246590 original size:16 final size:14
Alignment explanation
Indices: 246574--246616 Score: 61
Period size: 13 Copynumber: 3.1 Consensus size: 14
246564 TATTTATATA
246574 AATAATAAGAATAAT
1 AATAATAA-AATAAT
*
246589 AATAA-AAAGTAAT
1 AATAATAAAATAAT
246602 AATAATAAAATAAT
1 AATAATAAAATAAT
246616 A
1 A
246617 TTGCAAATAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 10 0.40
14 10 0.40
15 5 0.20
ACGTcount: A:0.70, C:0.00, G:0.05, T:0.26
Consensus pattern (14 bp):
AATAATAAAATAAT
Found at i:246630 original size:3 final size:3
Alignment explanation
Indices: 246574--246616 Score: 52
Period size: 3 Copynumber: 14.3 Consensus size: 3
246564 TATTTATATA
* *
246574 AAT AAT AAG AAT AAT AAT AAA AAGT AAT AAT AAT AA- AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AA-T AAT AAT AAT AAT AAT AAT A
246617 TTGCAAATAA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
2 2 0.06
3 30 0.88
4 2 0.06
ACGTcount: A:0.70, C:0.00, G:0.05, T:0.26
Consensus pattern (3 bp):
AAT
Found at i:247809 original size:3 final size:3
Alignment explanation
Indices: 247801--247847 Score: 60
Period size: 3 Copynumber: 15.0 Consensus size: 3
247791 AATTATTTTT
247801 TAA TAA TAA TAA T-A TATA TAA TAA TAA TATA TATA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TA-A TAA TAA TAA TA-A TA-A TAA TAA TAA TAA
247848 ATAAATAAAT
Statistics
Matches: 41, Mismatches: 0, Indels: 6
0.87 0.00 0.13
Matches are distributed among these distances:
2 2 0.05
3 29 0.71
4 10 0.24
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:247823 original size:15 final size:15
Alignment explanation
Indices: 247803--247851 Score: 77
Period size: 15 Copynumber: 3.5 Consensus size: 15
247793 TTATTTTTTA
247803 ATAATAATAATATAT
1 ATAATAATAATATAT
247818 ATAATAATAATATAT
1 ATAATAATAATATAT
247833 AT-ATAATAATA-AT
1 ATAATAATAATATAT
247846 A-AATAA
1 ATAATAA
247852 ATAAATAAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
13 7 0.21
14 9 0.27
15 17 0.52
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (15 bp):
ATAATAATAATATAT
Found at i:247855 original size:17 final size:17
Alignment explanation
Indices: 247801--247855 Score: 83
Period size: 17 Copynumber: 3.2 Consensus size: 17
247791 AATTATTTTT
247801 TAATAATAATAATATATA
1 TAATAATAATAA-ATATA
*
247819 TAATAATAATATATATA
1 TAATAATAATAAATATA
*
247836 TAATAATAATAAATAAA
1 TAATAATAATAAATATA
247853 TAA
1 TAA
247856 ATAAATAAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
17 23 0.68
18 11 0.32
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (17 bp):
TAATAATAATAAATATA
Found at i:247866 original size:17 final size:18
Alignment explanation
Indices: 247801--247859 Score: 66
Period size: 20 Copynumber: 3.2 Consensus size: 18
247791 AATTATTTTT
*
247801 TAATAAT-AATAATATATA
1 TAATAATAAATAA-ATAAA
*
247819 TAATAATAATATATATATAA
1 TAATAATAA-ATAAATA-AA
247839 TAATAATAAATAAATAAA
1 TAATAATAAATAAATAAA
247857 TAA
1 TAA
247860 ATAAAATGGG
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
18 12 0.34
19 10 0.29
20 13 0.37
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (18 bp):
TAATAATAAATAAATAAA
Found at i:248101 original size:103 final size:103
Alignment explanation
Indices: 247970--248180 Score: 413
Period size: 103 Copynumber: 2.0 Consensus size: 103
247960 GATTTATTTT
247970 GACTCCTTATGAATTGAACTTACTATCAAATAAGAAATCCAAAGAAATGATAATTGGACAGAGAA
1 GACTCCTTATGAATTGAACTTACTATCAAATAAGAAATCCAAAGAAATGATAATTGGACAGAGAA
*
248035 GAAGGCAGTGGAGCTTCGACATCACCAGAAACTTAATG
66 GAAGGCAGTCGAGCTTCGACATCACCAGAAACTTAATG
248073 GACTCCTTATGAATTGAACTTACTATCAAATAAGAAATCCAAAGAAATGATAATTGGACAGAGAA
1 GACTCCTTATGAATTGAACTTACTATCAAATAAGAAATCCAAAGAAATGATAATTGGACAGAGAA
248138 GAAGGCAGTCGAGCTTCGACATCACCAGAAACTTAATG
66 GAAGGCAGTCGAGCTTCGACATCACCAGAAACTTAATG
248176 GACTC
1 GACTC
248181 AGCATTTGAA
Statistics
Matches: 107, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
103 107 1.00
ACGTcount: A:0.41, C:0.18, G:0.19, T:0.22
Consensus pattern (103 bp):
GACTCCTTATGAATTGAACTTACTATCAAATAAGAAATCCAAAGAAATGATAATTGGACAGAGAA
GAAGGCAGTCGAGCTTCGACATCACCAGAAACTTAATG
Found at i:248959 original size:20 final size:20
Alignment explanation
Indices: 248934--248971 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
248924 TATGCTCGGA
248934 GGGTATCGATTCCCCCCAGG
1 GGGTATCGATTCCCCCCAGG
*
248954 GGGTATCGATTCGCCCCA
1 GGGTATCGATTCCCCCCA
248972 CTGTTCAATG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.16, C:0.34, G:0.29, T:0.21
Consensus pattern (20 bp):
GGGTATCGATTCCCCCCAGG
Found at i:254783 original size:23 final size:23
Alignment explanation
Indices: 254752--254824 Score: 130
Period size: 23 Copynumber: 3.2 Consensus size: 23
254742 GGAATTGATA
254752 CCCCC-TTGAAGGGGAACCGATT
1 CCCCCTTTGAAGGGGAACCGATT
254774 CCCCCTTTGAAGGGGAACCGATT
1 CCCCCTTTGAAGGGGAACCGATT
*
254797 CCCCATTTGAAGGGGAACCGATT
1 CCCCCTTTGAAGGGGAACCGATT
254820 CCCCC
1 CCCCC
254825 CTAGGGGAAT
Statistics
Matches: 48, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
22 5 0.10
23 43 0.90
ACGTcount: A:0.22, C:0.34, G:0.25, T:0.19
Consensus pattern (23 bp):
CCCCCTTTGAAGGGGAACCGATT
Found at i:254862 original size:18 final size:19
Alignment explanation
Indices: 254807--254868 Score: 90
Period size: 19 Copynumber: 3.3 Consensus size: 19
254797 CCCCATTTGA
* *
254807 AGGGGAACCGATTCCCCCCT
1 AGGGGAATCGA-TACCCCCT
254827 AGGGGAATCGATACCCCCT
1 AGGGGAATCGATACCCCCT
254846 AGGGGAATCGATACCCCCT
1 AGGGGAATCGATACCCCCT
254865 -GGGG
1 AGGGG
254869 TTCTGGTTTT
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
18 4 0.10
19 26 0.65
20 10 0.25
ACGTcount: A:0.23, C:0.32, G:0.31, T:0.15
Consensus pattern (19 bp):
AGGGGAATCGATACCCCCT
Found at i:255227 original size:29 final size:29
Alignment explanation
Indices: 255187--255248 Score: 99
Period size: 29 Copynumber: 2.2 Consensus size: 29
255177 TAGTGATTAG
*
255187 AAAA-TAGATTTTATAACTAATTTTATCA
1 AAAACTAGATTTTACAACTAATTTTATCA
*
255215 AAAACTAGATTTTGCAACTAATTTTATCA
1 AAAACTAGATTTTACAACTAATTTTATCA
255244 AAAAC
1 AAAAC
255249 ACAAGAATTT
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
28 4 0.13
29 27 0.87
ACGTcount: A:0.47, C:0.11, G:0.05, T:0.37
Consensus pattern (29 bp):
AAAACTAGATTTTACAACTAATTTTATCA
Found at i:259858 original size:35 final size:35
Alignment explanation
Indices: 259811--259887 Score: 145
Period size: 35 Copynumber: 2.2 Consensus size: 35
259801 AACAACATAG
259811 AAGAACAAGAGGAAACTTTGGCTCAACTCTCGATTA
1 AAGAA-AAGAGGAAACTTTGGCTCAACTCTCGATTA
259847 AAGAAAAGAGGAAACTTTGGCTCAACTCTCGATTA
1 AAGAAAAGAGGAAACTTTGGCTCAACTCTCGATTA
259882 AAGAAA
1 AAGAAA
259888 GGTATAATTC
Statistics
Matches: 41, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
35 36 0.88
36 5 0.12
ACGTcount: A:0.43, C:0.17, G:0.19, T:0.21
Consensus pattern (35 bp):
AAGAAAAGAGGAAACTTTGGCTCAACTCTCGATTA
Found at i:260443 original size:16 final size:16
Alignment explanation
Indices: 260422--260455 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
260412 TCGACATATT
260422 TCTTCCTTATCGTTTA
1 TCTTCCTTATCGTTTA
260438 TCTTCCTTATCGTTTA
1 TCTTCCTTATCGTTTA
260454 TC
1 TC
260456 CCCTCATCAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.12, C:0.26, G:0.06, T:0.56
Consensus pattern (16 bp):
TCTTCCTTATCGTTTA
Found at i:261788 original size:18 final size:17
Alignment explanation
Indices: 261748--261800 Score: 54
Period size: 18 Copynumber: 3.1 Consensus size: 17
261738 TAATTTCTTT
* *
261748 TTTTATTTCATATTATT
1 TTTTATTTAATATTATA
261765 TATTTATTTAAATATTATA
1 T-TTTATTT-AATATTATA
*
261784 TTTTA-TTATTATTATA
1 TTTTATTTAATATTATA
261800 T
1 T
261801 ATGTTTGTTT
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
16 9 0.29
17 3 0.10
18 11 0.35
19 8 0.26
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (17 bp):
TTTTATTTAATATTATA
Found at i:262062 original size:19 final size:20
Alignment explanation
Indices: 262038--262075 Score: 69
Period size: 19 Copynumber: 1.9 Consensus size: 20
262028 TATATATTAT
262038 TTTTTCTCTTTTTG-TTTTC
1 TTTTTCTCTTTTTGCTTTTC
262057 TTTTTCTCTTTTTGCTTTT
1 TTTTTCTCTTTTTGCTTTT
262076 TTTCTATTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 14 0.78
20 4 0.22
ACGTcount: A:0.00, C:0.16, G:0.05, T:0.79
Consensus pattern (20 bp):
TTTTTCTCTTTTTGCTTTTC
Found at i:263073 original size:25 final size:25
Alignment explanation
Indices: 263045--263097 Score: 63
Period size: 27 Copynumber: 2.0 Consensus size: 25
263035 ATTAGTATGA
*
263045 TTATTTATC-TAATTTAAATATATTT
1 TTATCTATCTTAATTT-AATATATTT
263070 TTATCTATCTTATAATTTAATATATTT
1 TTATCTATC-T-TAATTTAATATATTT
263097 T
1 T
263098 AATTAAAAAG
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
25 8 0.33
27 10 0.42
28 6 0.25
ACGTcount: A:0.34, C:0.06, G:0.00, T:0.60
Consensus pattern (25 bp):
TTATCTATCTTAATTTAATATATTT
Found at i:263735 original size:29 final size:29
Alignment explanation
Indices: 263693--263781 Score: 124
Period size: 29 Copynumber: 3.1 Consensus size: 29
263683 TACCGGGGGT
*
263693 AGGTCGCCATGCACGCCCGGCGACCTACC
1 AGGTCGCCATGCACGCCCAGCGACCTACC
***
263722 AGGTCGCCATGCACGCCCAGCGACCTGGT
1 AGGTCGCCATGCACGCCCAGCGACCTACC
* *
263751 AGGTCGCCATGCATGCCCTGCGACCTACC
1 AGGTCGCCATGCACGCCCAGCGACCTACC
263780 AG
1 AG
263782 CCAACGACCT
Statistics
Matches: 51, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 51 1.00
ACGTcount: A:0.18, C:0.40, G:0.28, T:0.13
Consensus pattern (29 bp):
AGGTCGCCATGCACGCCCAGCGACCTACC
Found at i:264033 original size:27 final size:28
Alignment explanation
Indices: 263979--264035 Score: 89
Period size: 27 Copynumber: 2.0 Consensus size: 28
263969 TCCCCATGAA
263979 TCCTTGGTCGCCCCGAGTGCATGGCGACC
1 TCCTTGGTCG-CCCGAGTGCATGGCGACC
*
264008 TCCTTGGTCG-CCGGGTGCATGGCGACC
1 TCCTTGGTCGCCCGAGTGCATGGCGACC
264035 T
1 T
264036 AGGAGGTCGC
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
27 17 0.63
29 10 0.37
ACGTcount: A:0.09, C:0.35, G:0.33, T:0.23
Consensus pattern (28 bp):
TCCTTGGTCGCCCGAGTGCATGGCGACC
Found at i:264043 original size:27 final size:29
Alignment explanation
Indices: 263984--264065 Score: 87
Period size: 29 Copynumber: 2.9 Consensus size: 29
263974 ATGAATCCTT
* * * **
263984 GGTCGCCCCGAGTGCATGGCGACCTCCTT
1 GGTCGCTCGGAGTGCATGGCGACCTACGA
*
264013 GGTCGC-CGG-GTGCATGGCGACCTAGGA
1 GGTCGCTCGGAGTGCATGGCGACCTACGA
*
264040 GGTCGCTGGGAGTGCATGGCGACCTA
1 GGTCGCTCGGAGTGCATGGCGACCTA
264066 TGGTTGGGTT
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
27 20 0.44
28 4 0.09
29 21 0.47
ACGTcount: A:0.13, C:0.29, G:0.39, T:0.18
Consensus pattern (29 bp):
GGTCGCTCGGAGTGCATGGCGACCTACGA
Found at i:266773 original size:17 final size:17
Alignment explanation
Indices: 266753--266788 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
266743 CCGACCCGAC
266753 CCGTTGACCAGCATTGA
1 CCGTTGACCAGCATTGA
* *
266770 CCGTTGACCGGCGTTGA
1 CCGTTGACCAGCATTGA
266787 CC
1 CC
266789 ACTGTTGACC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.17, C:0.33, G:0.28, T:0.22
Consensus pattern (17 bp):
CCGTTGACCAGCATTGA
Found at i:269019 original size:12 final size:12
Alignment explanation
Indices: 269004--269096 Score: 71
Period size: 12 Copynumber: 7.8 Consensus size: 12
268994 ATTTTCGATT
269004 TGATTTCTGTTC
1 TGATTTCTGTTC
*
269016 TGATTTCTGATC
1 TGATTTCTGTTC
* *
269028 TGAATTCTATTC
1 TGATTTCTGTTC
*
269040 TGATTTCTGATC
1 TGATTTCTGTTC
*
269052 TGGA-TTCTGTTA
1 T-GATTTCTGTTC
* * *
269064 TGATATCTGATG
1 TGATTTCTGTTC
* * *
269076 TGAATTCTATTT
1 TGATTTCTGTTC
269088 TGATTTCTG
1 TGATTTCTG
269097 ATATCTCCAT
Statistics
Matches: 60, Mismatches: 19, Indels: 4
0.72 0.23 0.05
Matches are distributed among these distances:
11 2 0.03
12 56 0.93
13 2 0.03
ACGTcount: A:0.18, C:0.13, G:0.17, T:0.52
Consensus pattern (12 bp):
TGATTTCTGTTC
Found at i:269035 original size:24 final size:24
Alignment explanation
Indices: 268990--269098 Score: 121
Period size: 24 Copynumber: 4.5 Consensus size: 24
268980 GAATGTTTTA
* * *
268990 TCTGATTT-TCGATTTGATTTCTGT
1 TCTGATTTCT-GATCTGAATTCTAT
269014 TCTGATTTCTGATCTGAATTCTAT
1 TCTGATTTCTGATCTGAATTCTAT
* *
269038 TCTGATTTCTGATCTGGATTCTGT
1 TCTGATTTCTGATCTGAATTCTAT
* * *
269062 TATGATATCTGATGTGAATTCTAT
1 TCTGATTTCTGATCTGAATTCTAT
*
269086 TTTGATTTCTGAT
1 TCTGATTTCTGAT
269099 ATCTCCATTT
Statistics
Matches: 72, Mismatches: 12, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
24 71 0.99
25 1 0.01
ACGTcount: A:0.18, C:0.13, G:0.17, T:0.52
Consensus pattern (24 bp):
TCTGATTTCTGATCTGAATTCTAT
Found at i:269042 original size:48 final size:49
Alignment explanation
Indices: 268990--269098 Score: 136
Period size: 48 Copynumber: 2.3 Consensus size: 49
268980 GAATGTTTTA
* * *
268990 TCTGATTTTC-GAT-TTGATTTCTGTTCTGATTTCTGATCTGAATTCTAT
1 TCTGATTTTCTGATCTGGA-TTCTGTTATGATATCTGATCTGAATTCTAT
*
269038 TCTGA-TTTCTGATCTGGATTCTGTTATGATATCTGATGTGAATTCTAT
1 TCTGATTTTCTGATCTGGATTCTGTTATGATATCTGATCTGAATTCTAT
*
269086 TTTGA-TTTCTGAT
1 TCTGATTTTCTGAT
269099 ATCTCCATTT
Statistics
Matches: 54, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
47 4 0.07
48 47 0.87
49 3 0.06
ACGTcount: A:0.18, C:0.13, G:0.17, T:0.52
Consensus pattern (49 bp):
TCTGATTTTCTGATCTGGATTCTGTTATGATATCTGATCTGAATTCTAT
Found at i:271293 original size:22 final size:22
Alignment explanation
Indices: 271245--271303 Score: 75
Period size: 22 Copynumber: 2.6 Consensus size: 22
271235 TTTGGTCAGA
271245 GTTGACTGTTGACCGTCCAGACC
1 GTTGACT-TTGACCGTCCAGACC
* *
271268 GTTGACTTTGACCAGT-CTGACT
1 GTTGACTTTGACC-GTCCAGACC
271290 GTTGACTTTGACCG
1 GTTGACTTTGACCG
271304 AAAAAGTCAA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
21 1 0.03
22 23 0.70
23 9 0.27
ACGTcount: A:0.17, C:0.25, G:0.25, T:0.32
Consensus pattern (22 bp):
GTTGACTTTGACCGTCCAGACC
Found at i:273903 original size:20 final size:21
Alignment explanation
Indices: 273878--273923 Score: 69
Period size: 20 Copynumber: 2.2 Consensus size: 21
273868 TATATTGGGA
273878 TATTGTCTATTG-TTTATGG-T
1 TATTGTCTA-TGATTTATGGTT
273898 TATTGTCTATGATTTATGGTT
1 TATTGTCTATGATTTATGGTT
273919 TATTG
1 TATTG
273924 GTTAATAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
19 2 0.08
20 16 0.67
21 6 0.25
ACGTcount: A:0.17, C:0.04, G:0.20, T:0.59
Consensus pattern (21 bp):
TATTGTCTATGATTTATGGTT
Found at i:274096 original size:91 final size:90
Alignment explanation
Indices: 273942--274116 Score: 242
Period size: 91 Copynumber: 1.9 Consensus size: 90
273932 ATGATAAACT
* * * *
273942 GGTAAAATAAGCTTACGAGCTTATGGAATAAATGATATGTGTATTGATAAAATAAGCTTACGAGC
1 GGTAAAATAAGATTACGAGCTTATGGAATAAATGATAAGTATATTGATAAAAGAAGCTTACGAGC
*
274007 TTTTGGAATAAATGGTAAGTATATA
66 TTATGGAATAAATGGTAAGTATATA
* * * * *
274032 GGTAAAATATGATTACGAGCTTATGTGATTAAATGGTAAGTATTTTGGTAAAAGAAGCTTACGAG
1 GGTAAAATAAGATTACGAGCTTATG-GAATAAATGATAAGTATATTGATAAAAGAAGCTTACGAG
*
274097 CTTATGGGATAAATGGTAAG
65 CTTATGGAATAAATGGTAAG
274117 AAATTTTATA
Statistics
Matches: 73, Mismatches: 11, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
90 23 0.32
91 50 0.68
ACGTcount: A:0.38, C:0.06, G:0.23, T:0.32
Consensus pattern (90 bp):
GGTAAAATAAGATTACGAGCTTATGGAATAAATGATAAGTATATTGATAAAAGAAGCTTACGAGC
TTATGGAATAAATGGTAAGTATATA
Found at i:274123 original size:46 final size:45
Alignment explanation
Indices: 273941--274116 Score: 235
Period size: 45 Copynumber: 3.9 Consensus size: 45
273931 AATGATAAAC
* * *
273941 TGGTAAAATAAGCTTACGAGCTTATGGAATAAATGATATGTGTAT
1 TGGTAAAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATAT
* *
273986 TGATAAAATAAGCTTACGAGCTTTTGGAATAAATGGTAAGTATAT
1 TGGTAAAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATAT
* * * * *
274031 AGGTAAAATATGATTACGAGCTTATGTGATTAAATGGTAAGTATTT
1 TGGTAAAATAAGCTTACGAGCTTATG-GAATAAATGGTAAGTATAT
* *
274077 TGGTAAAAGAAGCTTACGAGCTTATGGGATAAATGGTAAG
1 TGGTAAAATAAGCTTACGAGCTTATGGAATAAATGGTAAG
274117 AAATTTTATA
Statistics
Matches: 112, Mismatches: 18, Indels: 2
0.85 0.14 0.02
Matches are distributed among these distances:
45 73 0.65
46 39 0.35
ACGTcount: A:0.38, C:0.06, G:0.23, T:0.32
Consensus pattern (45 bp):
TGGTAAAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATAT
Found at i:276977 original size:21 final size:21
Alignment explanation
Indices: 276937--277006 Score: 81
Period size: 21 Copynumber: 3.3 Consensus size: 21
276927 AATATTATAT
276937 AAGAAAAAAGAAACATAAAAA
1 AAGAAAAAAGAAACATAAAAA
*
276958 AAGAAGAAA-AAACATAAAAA
1 AAGAAAAAAGAAACATAAAAA
* *
276978 ACATAAAAAAGAAA-AGGAAAAA
1 A-AGAAAAAAGAAACA-TAAAAA
277000 AAGAAAA
1 AAGAAAA
277007 TGAAAATGAA
Statistics
Matches: 41, Mismatches: 5, Indels: 6
0.79 0.10 0.12
Matches are distributed among these distances:
20 12 0.29
21 20 0.49
22 9 0.22
ACGTcount: A:0.80, C:0.04, G:0.11, T:0.04
Consensus pattern (21 bp):
AAGAAAAAAGAAACATAAAAA
Found at i:276997 original size:6 final size:6
Alignment explanation
Indices: 276983--277059 Score: 59
Period size: 6 Copynumber: 12.8 Consensus size: 6
276973 AAAAAACATA
* * * * *
276983 AAAAAG AAAAGGAA AAAAAG AAAATG AAAATG AAAATG AAGAAG -AAAA-
1 AAAAAG AAAA--AG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG
* *
277031 AAATAG AAAATG AAAAAG AAAAAG AAAAA
1 AAAAAG AAAAAG AAAAAG AAAAAG AAAAA
277060 AAATGAATGA
Statistics
Matches: 57, Mismatches: 10, Indels: 8
0.76 0.13 0.11
Matches are distributed among these distances:
5 6 0.11
6 46 0.81
8 5 0.09
ACGTcount: A:0.77, C:0.00, G:0.17, T:0.06
Consensus pattern (6 bp):
AAAAAG
Found at i:277042 original size:22 final size:22
Alignment explanation
Indices: 277009--277066 Score: 75
Period size: 22 Copynumber: 2.7 Consensus size: 22
276999 AAAGAAAATG
*
277009 AAAAT-GAAAATGAAGAAGAAA
1 AAAATAGAAAATGAAAAAGAAA
277030 AAAATAGAAAATGAAAAAGAAA
1 AAAATAGAAAATGAAAAAGAAA
*
277052 AAGAA-AAAAAATGAA
1 AA-AATAGAAAATGAA
277067 TGAGATATAA
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
21 5 0.15
22 26 0.79
23 2 0.06
ACGTcount: A:0.76, C:0.00, G:0.16, T:0.09
Consensus pattern (22 bp):
AAAATAGAAAATGAAAAAGAAA
Found at i:281048 original size:20 final size:20
Alignment explanation
Indices: 281023--281063 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 20
281013 TATATTTGGC
281023 TATTGTCTATTG-TTTATGGT
1 TATTGTCTA-TGATTTATGGT
281043 TATTGTCTATGATTTATGGT
1 TATTGTCTATGATTTATGGT
281063 T
1 T
281064 TGTTGGTTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 2 0.10
20 18 0.90
ACGTcount: A:0.17, C:0.05, G:0.20, T:0.59
Consensus pattern (20 bp):
TATTGTCTATGATTTATGGT
Found at i:281138 original size:45 final size:45
Alignment explanation
Indices: 281086--281305 Score: 343
Period size: 45 Copynumber: 4.9 Consensus size: 45
281076 AATGATAAAC
*
281086 TGGTAAAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTGTAT
1 TGGTAAAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATAT
* * *
281131 TGGTAAAATAAGCTTACGATCTTAGGGAATAAATGGTAAGTGTAT
1 TGGTAAAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATAT
*
281176 TGGTAAAATAAGCTTACGAGCTTATAGAATAAATGGTAAGTATAT
1 TGGTAAAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATAT
* * *
281221 GGGTAAAATAAGCTTACGAGCTTATGTGATTAAATGGTAAGTATTT
1 TGGTAAAATAAGCTTACGAGCTTATG-GAATAAATGGTAAGTATAT
*
281267 TGGTAAAATAAGCTTACGAGCTTATGGGATAAAT-GTAAG
1 TGGTAAAATAAGCTTACGAGCTTATGGAATAAATGGTAAG
281306 AAATTTTATA
Statistics
Matches: 161, Mismatches: 13, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
44 5 0.03
45 114 0.71
46 42 0.26
ACGTcount: A:0.38, C:0.07, G:0.24, T:0.31
Consensus pattern (45 bp):
TGGTAAAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATAT
Found at i:284190 original size:6 final size:6
Alignment explanation
Indices: 284153--284254 Score: 79
Period size: 6 Copynumber: 17.3 Consensus size: 6
284143 ATTATATAAG
* * *
284153 AAAA-A AAAAGA AACATA AAAAGA AAGAAGA AAAAGA AAATAAA AAACAGA
1 AAAAGA AAAAGA AAAAGA AAAAGA AA-AAGA AAAAGA AAA-AGA AAA-AGA
* * * *
284203 AAAAG- AAAATA AAATGA AGAAG- AAAA-A AATAGA AAAAG- AAAAGA
1 AAAAGA AAAAGA AAAAGA AAAAGA AAAAGA AAAAGA AAAAGA AAAAGA
284247 AAAAGA AA
1 AAAAGA AA
284255 CAAATGAATG
Statistics
Matches: 75, Mismatches: 15, Indels: 13
0.73 0.15 0.13
Matches are distributed among these distances:
5 19 0.25
6 40 0.53
7 16 0.21
ACGTcount: A:0.79, C:0.02, G:0.14, T:0.05
Consensus pattern (6 bp):
AAAAGA
Found at i:284205 original size:20 final size:19
Alignment explanation
Indices: 284155--284249 Score: 88
Period size: 20 Copynumber: 4.9 Consensus size: 19
284145 TATATAAGAA
* *
284155 AAAAAAAGAAACATAAAA-
1 AAAAAAAGAAAAAGAAAAT
*
284173 AGAAAGAAGAAAAAGAAAAT
1 A-AAAAAAGAAAAAGAAAAT
284193 AAAAAACAGAAAAAGAAAAT
1 AAAAAA-AGAAAAAGAAAAT
*
284213 AAAATGAAGAAGAAA-AAAAT
1 AAAA-AAAGAA-AAAGAAAAT
*
284233 AGAAAAAG-AAAAGAAAA
1 AAAAAAAGAAAAAGAAAA
284250 AGAAACAAAT
Statistics
Matches: 64, Mismatches: 7, Indels: 12
0.77 0.08 0.14
Matches are distributed among these distances:
17 3 0.05
18 6 0.09
19 21 0.33
20 30 0.47
21 4 0.06
ACGTcount: A:0.79, C:0.02, G:0.14, T:0.05
Consensus pattern (19 bp):
AAAAAAAGAAAAAGAAAAT
Found at i:288263 original size:45 final size:45
Alignment explanation
Indices: 288212--288428 Score: 317
Period size: 45 Copynumber: 4.8 Consensus size: 45
288202 AATGATAAAC
* * * *
288212 TGGTAAAATAAGCTTACAATCTTATGGAATAAATAGTAAGTGTAT
1 TGGTAAAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATAT
* * *
288257 TGGTAAAATAAGTTTACGAGCTTAGGGAATAAATGGTAAGTGTAT
1 TGGTAAAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATAT
*
288302 TGGTAATATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATAT
1 TGGTAAAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATAT
* * *
288347 GGGTAAAATAAGCTTACGAGCTTATGTGATTAAATGGTAAGTATTT
1 TGGTAAAATAAGCTTACGAGCTTATG-GAATAAATGGTAAGTATAT
*
288393 TGGTAAAATAAGCTTACGAGCTTATGGGATAAATGG
1 TGGTAAAATAAGCTTACGAGCTTATGGAATAAATGG
288429 CAAGAAATTT
Statistics
Matches: 155, Mismatches: 16, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
45 113 0.73
46 42 0.27
ACGTcount: A:0.38, C:0.06, G:0.24, T:0.32
Consensus pattern (45 bp):
TGGTAAAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATAT
Found at i:292070 original size:2 final size:2
Alignment explanation
Indices: 292063--292099 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
292053 TATGTGTTAT
292063 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
292100 TTTATTTTTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:292484 original size:24 final size:24
Alignment explanation
Indices: 292444--292500 Score: 71
Period size: 24 Copynumber: 2.4 Consensus size: 24
292434 ATGTTAGTTT
*
292444 TATCAC-TATTTTGATTATCAATC
1 TATCACTTTTTTTGATTATCAATC
* *
292467 TATCACTTTTTTTTATTATCATTC
1 TATCACTTTTTTTGATTATCAATC
*
292491 TTTCACTTTT
1 TATCACTTTT
292501 AATTCAAAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
23 6 0.21
24 23 0.79
ACGTcount: A:0.23, C:0.18, G:0.02, T:0.58
Consensus pattern (24 bp):
TATCACTTTTTTTGATTATCAATC
Found at i:292846 original size:16 final size:16
Alignment explanation
Indices: 292827--292860 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
292817 AAATAACTAT
292827 TTATAATAATAT-AAAA
1 TTATAA-AATATCAAAA
292843 TTATAAAATATCAAAA
1 TTATAAAATATCAAAA
292859 TT
1 TT
292861 TATCATATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 5 0.29
16 12 0.71
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (16 bp):
TTATAAAATATCAAAA
Found at i:297695 original size:13 final size:13
Alignment explanation
Indices: 297677--297708 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
297667 GGCAGCTTGG
297677 TGAGCCACTGAGC
1 TGAGCCACTGAGC
297690 TGAGCCACTGAGC
1 TGAGCCACTGAGC
*
297703 CGAGCC
1 TGAGCC
297709 GTTGAGTCGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.22, C:0.34, G:0.31, T:0.12
Consensus pattern (13 bp):
TGAGCCACTGAGC
Found at i:299239 original size:24 final size:24
Alignment explanation
Indices: 299212--299260 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
299202 TTTTGCTTTA
*
299212 AATTATGTTGAGATTTCTGCTCTG
1 AATTATGTTGAGATTTCTACTCTG
* **
299236 AATTTTGTTTTGATTTCTACTCTG
1 AATTATGTTGAGATTTCTACTCTG
299260 A
1 A
299261 TTTCTACTTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.20, C:0.12, G:0.16, T:0.51
Consensus pattern (24 bp):
AATTATGTTGAGATTTCTACTCTG
Found at i:299263 original size:12 final size:12
Alignment explanation
Indices: 299246--299277 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
299236 AATTTTGTTT
299246 TGATTTCTACTC
1 TGATTTCTACTC
*
299258 TGATTTCTACTT
1 TGATTTCTACTC
299270 TGATTTCT
1 TGATTTCT
299278 GATATCTCTG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.16, C:0.19, G:0.09, T:0.56
Consensus pattern (12 bp):
TGATTTCTACTC
Found at i:301268 original size:26 final size:28
Alignment explanation
Indices: 301238--301300 Score: 85
Period size: 31 Copynumber: 2.2 Consensus size: 28
301228 GAAAATTTTA
301238 AGCTCA-C-GAGTTTTCGAGTCGAGTCG
1 AGCTCATCAGAGTTTTCGAGTCGAGTCG
301264 AGCTCCATTTCAGAGTTTTCGAGTCGAGTCG
1 AGCT-CA--TCAGAGTTTTCGAGTCGAGTCG
301295 AGCTCA
1 AGCTCA
301301 GCAATACTAA
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
26 4 0.12
27 2 0.06
30 3 0.09
31 23 0.72
ACGTcount: A:0.21, C:0.24, G:0.27, T:0.29
Consensus pattern (28 bp):
AGCTCATCAGAGTTTTCGAGTCGAGTCG
Found at i:302368 original size:3 final size:3
Alignment explanation
Indices: 302360--302410 Score: 50
Period size: 3 Copynumber: 17.0 Consensus size: 3
302350 GGATTCTCAT
* ** *
302360 TTA TTA TTA AT- TTA TTA TTAA CAA TTA TTA TTA TTA TTA ATA TTA
1 TTA TTA TTA TTA TTA TTA TT-A TTA TTA TTA TTA TTA TTA TTA TTA
302405 TTA TTA
1 TTA TTA
302411 ATATATTTTA
Statistics
Matches: 38, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
2 1 0.03
3 36 0.95
4 1 0.03
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (3 bp):
TTA
Found at i:302403 original size:12 final size:12
Alignment explanation
Indices: 302360--302414 Score: 59
Period size: 12 Copynumber: 5.1 Consensus size: 12
302350 GGATTCTCAT
302360 TTATTATTAAT-
1 TTATTATTAATA
*
302371 TTATTATTAACA
1 TTATTATTAATA
302383 --ATTA-T--TA
1 TTATTATTAATA
302390 TTATTATTAATA
1 TTATTATTAATA
302402 TTATTATTAATA
1 TTATTATTAATA
302414 T
1 T
302415 ATTTTACATT
Statistics
Matches: 36, Mismatches: 2, Indels: 11
0.73 0.04 0.22
Matches are distributed among these distances:
7 1 0.03
9 5 0.14
10 5 0.14
11 10 0.28
12 15 0.42
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (12 bp):
TTATTATTAATA
Found at i:305124 original size:29 final size:30
Alignment explanation
Indices: 305092--305150 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
305082 AAAAGCTTTC
305092 CTGC-AATATGCATGAAGTAAAGAGCTGTA
1 CTGCAAATATGCATGAAGTAAAGAGCTGTA
305121 CTGCAAATATGCATGAAGTAAAGAGCTGTA
1 CTGCAAATATGCATGAAGTAAAGAGCTGTA
305151 GGAAAATTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
29 4 0.14
30 25 0.86
ACGTcount: A:0.39, C:0.14, G:0.24, T:0.24
Consensus pattern (30 bp):
CTGCAAATATGCATGAAGTAAAGAGCTGTA
Found at i:306389 original size:85 final size:86
Alignment explanation
Indices: 306242--306406 Score: 244
Period size: 85 Copynumber: 1.9 Consensus size: 86
306232 ACAATCACGA
* * * *
306242 CACACGAATGTGTGTCATCTTCATTTATGACGGGGGCTTCAATGACACGCAATATAACTCATT-T
1 CACACAAATGTGTGTCATCTTAATTTATGACGGGGGCTTCAATGACACGCAATAGAACTCATTAA
306306 ATGCGTGTCATAAATTTATGC
66 ATGCGTGTCATAAATTTATGC
**
306327 CACACAAATGTGTGTCATCTTAATTTATGACGGGGGCTTCAATGACACTTAAT-GAACGTCATTA
1 CACACAAATGTGTGTCATCTTAATTTATGACGGGGGCTTCAATGACACGCAATAGAAC-TCATTA
*
306391 AATGTGTGTCATAAAT
65 AATGCGTGTCATAAAT
306407 GCGCGTCATA
Statistics
Matches: 71, Mismatches: 7, Indels: 3
0.88 0.09 0.04
Matches are distributed among these distances:
84 3 0.04
85 54 0.76
86 14 0.20
ACGTcount: A:0.30, C:0.18, G:0.19, T:0.33
Consensus pattern (86 bp):
CACACAAATGTGTGTCATCTTAATTTATGACGGGGGCTTCAATGACACGCAATAGAACTCATTAA
ATGCGTGTCATAAATTTATGC
Found at i:306712 original size:86 final size:83
Alignment explanation
Indices: 306573--306744 Score: 292
Period size: 86 Copynumber: 2.0 Consensus size: 83
306563 CCATTCAAAC
306573 CCACAGGTTTTGGCCCAAGACTGGATAACCAGAAGCTGACCCGATTACAAACATCCAAGCTAACC
1 CCACAGGTTTTGGCCCAAGACTGGATAACCAGAAGCTGACCCGATTACAAACATCCAAGCTAACC
306638 CAAAGCCCAATTATAGGA
66 CAAAGCCCAATTATAGGA
*
306656 CCACACGG-TTTGGCCCAAGACTGGAGTCCACCAGAAAGCTGACCCGATTACAAACATCCAAGCT
1 CCACA-GGTTTTGGCCCAAGACTGGA-T-AACCAG-AAGCTGACCCGATTACAAACATCCAAGCT
306720 AACCCAAAGCCCAATTATAGGA
62 AACCCAAAGCCCAATTATAGGA
306742 CCA
1 CCA
306745 AAAAAAGGGG
Statistics
Matches: 84, Mismatches: 1, Indels: 5
0.93 0.01 0.06
Matches are distributed among these distances:
83 22 0.26
84 3 0.04
85 5 0.06
86 54 0.64
ACGTcount: A:0.35, C:0.31, G:0.18, T:0.16
Consensus pattern (83 bp):
CCACAGGTTTTGGCCCAAGACTGGATAACCAGAAGCTGACCCGATTACAAACATCCAAGCTAACC
CAAAGCCCAATTATAGGA
Found at i:311345 original size:16 final size:16
Alignment explanation
Indices: 311324--311358 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
311314 TAGCAAGTCT
*
311324 TAACTAATGAAATAAA
1 TAACTAAGGAAATAAA
311340 TAACTAAGGAAATAAA
1 TAACTAAGGAAATAAA
311356 TAA
1 TAA
311359 TTTACCATGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.63, C:0.06, G:0.09, T:0.23
Consensus pattern (16 bp):
TAACTAAGGAAATAAA
Found at i:320367 original size:38 final size:34
Alignment explanation
Indices: 320291--320390 Score: 101
Period size: 36 Copynumber: 2.8 Consensus size: 34
320281 TCTTAAAAAT
* * *
320291 AAATTTTGTCTAGCTTGACACAATTTCTATTGAA
1 AAATTTTGTCTCGCTTGAGACAATTTCTATCGAA
* *
320325 AAATTTTTTGTCTCGCTTGAGACAATTTTTCTCGAAA
1 AAA--TTTTGTCTCGCTTGAGACAATTTCTATCG-AA
* *
320362 CAAATTTAGTCTCGCTTGAGAAAATTTCT
1 -AAATTTTGTCTCGCTTGAGACAATTTCT
320391 CTTGAGATGC
Statistics
Matches: 54, Mismatches: 8, Indels: 6
0.79 0.12 0.09
Matches are distributed among these distances:
34 3 0.06
36 46 0.85
37 2 0.04
38 3 0.06
ACGTcount: A:0.30, C:0.16, G:0.13, T:0.41
Consensus pattern (34 bp):
AAATTTTGTCTCGCTTGAGACAATTTCTATCGAA
Found at i:320626 original size:103 final size:103
Alignment explanation
Indices: 320503--320774 Score: 318
Period size: 103 Copynumber: 2.6 Consensus size: 103
320493 TTAAGACACG
*
320503 AACATTTGAGATTATTTTTCTTAAAAACAAATTTTGTCTCACTTGAGACATTTTGCCC-TAGAAA
1 AACATTTGAGATT-TTTTTCTTAAAAACAAATTTTGTCTCGCTTGAGACATTTT-CCCTTA-AAA
*
320567 CACAAATTCT-GAAATTGTTTCACTTGAAA-AACAATTAAT-
63 CACAAATTCTGGAAATGGTTTCACTTGAAACAA-AATTAATA
** * *
320606 AACATTTGAGATTGTTTTTCTTAAAAACAAATTTCATCCCGGTTGAGACAATTTTCCCTTAAAAC
1 AACATTTGAGATT-TTTTTCTTAAAAACAAATTTTGTCTCGCTTGAGAC-ATTTTCCCTTAAAAC
* *
320671 ACAAATTTTGGAAATGGTTTCACTTGAAACAAAATTGATA
64 ACAAATTCTGGAAATGGTTTCACTTGAAACAAAATTAATA
* * ** * * * *
320711 AACCTTTGAGATTATTTTCTTTGAAACAAATTTTGTCTTGCTTGAGACAGTTTCTCTTGAAACA
1 AACATTTGAGATTTTTTTCTTAAAAACAAATTTTGTCTCGCTTGAGACATTTTCCCTTAAAACA
320775 AAGTTTTGTC
Statistics
Matches: 143, Mismatches: 21, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
103 71 0.50
104 58 0.41
105 14 0.10
ACGTcount: A:0.35, C:0.15, G:0.12, T:0.38
Consensus pattern (103 bp):
AACATTTGAGATTTTTTTCTTAAAAACAAATTTTGTCTCGCTTGAGACATTTTCCCTTAAAACAC
AAATTCTGGAAATGGTTTCACTTGAAACAAAATTAATA
Found at i:320756 original size:36 final size:37
Alignment explanation
Indices: 320726--320811 Score: 142
Period size: 37 Copynumber: 2.4 Consensus size: 37
320716 TTGAGATTAT
320726 TTTCT-TTGAAACAAA-TTTTGTCT-TGCTTGAGACAG
1 TTTCTCTTGAAACAAAGTTTTGTCTCT-CTTGAGACAG
320761 TTTCTCTTGAAACAAAGTTTTGTCTCTCTTGAGACAG
1 TTTCTCTTGAAACAAAGTTTTGTCTCTCTTGAGACAG
320798 TTTCTCTTGAAACA
1 TTTCTCTTGAAACA
320812 TAAACAATTG
Statistics
Matches: 48, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
35 5 0.10
36 10 0.21
37 32 0.67
38 1 0.02
ACGTcount: A:0.26, C:0.17, G:0.15, T:0.42
Consensus pattern (37 bp):
TTTCTCTTGAAACAAAGTTTTGTCTCTCTTGAGACAG
Found at i:320756 original size:104 final size:103
Alignment explanation
Indices: 320503--320759 Score: 315
Period size: 104 Copynumber: 2.5 Consensus size: 103
320493 TTAAGACACG
*
320503 AACATTTGAGATTATTTTTCTTAAAAACAAATTTTGTCTCACTTGAGAC-ATTTTGCCCTAGAAA
1 AACATTTGAGATTA-TTTTCTTAAAAACAAATTTTGTCTCGCTTGAGACAATTTTGCCCTAGAAA
*
320567 CACAAATTCTGAAATTGTTTCACTTGAAAAACAATTAAT
65 CACAAATTCTGAAATGGTTTCACTTGAAAAACAATTAAT
* ** * *
320606 AACATTTGAGATTGTTTTTCTTAAAAACAAATTTCATCCCGGTTGAGACAATTTT-CCCTTA-AA
1 AACATTTGAGATT-ATTTTCTTAAAAACAAATTTTGTCTCGCTTGAGACAATTTTGCCC-TAGAA
* *
320669 ACACAAATTTTGGAAATGGTTTCACTTGAAACAA-AATTGAT
64 ACACAAATTCT-GAAATGGTTTCACTTGAAA-AACAATTAAT
* ** *
320710 AAACCTTTGAGATTATTTTCTTTGAAACAAATTTTGTCTTGCTTGAGACA
1 -AACATTTGAGATTATTTTCTTAAAAACAAATTTTGTCTCGCTTGAGACA
320760 GTTTCTCTTG
Statistics
Matches: 130, Mismatches: 18, Indels: 11
0.82 0.11 0.07
Matches are distributed among these distances:
103 57 0.44
104 59 0.45
105 14 0.11
ACGTcount: A:0.36, C:0.15, G:0.12, T:0.37
Consensus pattern (103 bp):
AACATTTGAGATTATTTTCTTAAAAACAAATTTTGTCTCGCTTGAGACAATTTTGCCCTAGAAAC
ACAAATTCTGAAATGGTTTCACTTGAAAAACAATTAAT
Found at i:321149 original size:140 final size:138
Alignment explanation
Indices: 320876--321167 Score: 381
Period size: 140 Copynumber: 2.1 Consensus size: 138
320866 TCTCTTGAAA
* * *
320876 CAAATTATCCTTAAGACAGCTAGACATCCTCATCACGTAGGAACAATGTTGTCCACCAACCAGAT
1 CAAATTATCCTAAAGACAGCTAGACATCCTCATCACGTAGGAAAAATGTTATCCACCAACCAGAT
*
320941 CTCCTCATCACGTAGGAGCAACATCACCCTCAGATAACCAGACTTCCTCATCACGTAGGAACCGT
66 CTCCTCATCACGTAGGAGCAACATCACCCTCAGATAACCAGACTTCCTCATCACGTAGGAACCAT
*
321006 GTTGTTTCC
131 GTTGTCT-C
* * *
321015 CAAATTATCCCTAAAGA-AGGCTAGACGTCCTCATCACGTAGGAAAAATGTTATCCACCGACCAT
1 CAAATTAT-CCTAAAGACA-GCTAGACATCCTCATCACGTAGGAAAAATGTTATCCACCAACCAG
* * * * * * * * *
321079 ATCTCTTCATCACGTATGAGCAACGTCACCTTTAGATAATCATATTTCCTCATCATGTAGGAACC
64 ATCTCCTCATCACGTAGGAGCAACATCACCCTCAGATAACCAGACTTCCTCATCACGTAGGAACC
321144 ATGTTGTCTC
129 ATGTTGTCTC
321154 CAAATT-TACCTAAA
1 CAAATTAT-CCTAAA
321168 AATGACCAGA
Statistics
Matches: 133, Mismatches: 18, Indels: 5
0.85 0.12 0.03
Matches are distributed among these distances:
138 7 0.05
139 16 0.12
140 110 0.83
ACGTcount: A:0.32, C:0.28, G:0.14, T:0.26
Consensus pattern (138 bp):
CAAATTATCCTAAAGACAGCTAGACATCCTCATCACGTAGGAAAAATGTTATCCACCAACCAGAT
CTCCTCATCACGTAGGAGCAACATCACCCTCAGATAACCAGACTTCCTCATCACGTAGGAACCAT
GTTGTCTC
Found at i:324578 original size:5 final size:5
Alignment explanation
Indices: 324548--324642 Score: 53
Period size: 5 Copynumber: 20.4 Consensus size: 5
324538 CCTTCCCTTC
* * * * *
324548 ATTTT GTTTT GTTTT ATTTT -TATTT ATTTT A--TT ATTTC GTTTT GTTTT
1 ATTTT ATTTT ATTTT ATTTT AT-TTT ATTTT ATTTT ATTTT ATTTT ATTTT
* * *
324596 A--TT ATTTT A-TTT ATTTT AATTT GTTTT CTTTT A--TT ATTTT ATTTT
1 ATTTT ATTTT ATTTT ATTTT ATTTT ATTTT ATTTT ATTTT ATTTT ATTTT
324641 AT
1 AT
324643 GTCATAGCCA
Statistics
Matches: 70, Mismatches: 11, Indels: 18
0.71 0.11 0.18
Matches are distributed among these distances:
3 9 0.13
4 5 0.07
5 55 0.79
6 1 0.01
ACGTcount: A:0.17, C:0.02, G:0.05, T:0.76
Consensus pattern (5 bp):
ATTTT
Found at i:324584 original size:18 final size:18
Alignment explanation
Indices: 324561--324639 Score: 71
Period size: 18 Copynumber: 4.7 Consensus size: 18
324551 TTGTTTTGTT
324561 TTATTTTTATTTATTTTA
1 TTATTTTTATTTATTTTA
* *
324579 TTATTTCGT-TTTGTTTTA
1 TTATTT-TTATTTATTTTA
324597 TTA-TTTTATTTATTTTA
1 TTATTTTTATTTATTTTA
* *
324614 --ATTTGT-TTTCTTTTA
1 TTATTTTTATTTATTTTA
324629 TTA-TTTTATTT
1 TTATTTTTATTT
324640 TATGTCATAG
Statistics
Matches: 48, Mismatches: 7, Indels: 13
0.71 0.10 0.19
Matches are distributed among these distances:
15 9 0.19
16 7 0.15
17 14 0.29
18 17 0.35
19 1 0.02
ACGTcount: A:0.18, C:0.03, G:0.04, T:0.76
Consensus pattern (18 bp):
TTATTTTTATTTATTTTA
Found at i:324618 original size:27 final size:27
Alignment explanation
Indices: 324565--324641 Score: 77
Period size: 27 Copynumber: 2.8 Consensus size: 27
324555 TTTGTTTTAT
***
324565 TTTTATTTATTTTA-TTATTTCGTTTTG
1 TTTTA-TTATTTTATTTATTTTAATTTG
324592 TTTTATTATTTTATTTATTTTAATTTG
1 TTTTATTATTTTATTTATTTTAATTTG
*
324619 TTTTCTT-TTATTATTTTATTTTA
1 TTTTATTATT-TTA-TTTATTTTA
324642 TGTCATAGCC
Statistics
Matches: 43, Mismatches: 4, Indels: 5
0.83 0.08 0.10
Matches are distributed among these distances:
26 10 0.23
27 24 0.56
28 9 0.21
ACGTcount: A:0.18, C:0.03, G:0.04, T:0.75
Consensus pattern (27 bp):
TTTTATTATTTTATTTATTTTAATTTG
Found at i:324628 original size:32 final size:33
Alignment explanation
Indices: 324550--324639 Score: 132
Period size: 32 Copynumber: 2.8 Consensus size: 33
324540 TTCCCTTCAT
324550 TTTGTTTTGTTTTA-T-TTTTATTTATTTTATTA
1 TTTGTTTTGTTTTATTATTTTATTTATTTTA-TA
324582 TTTCGTTTTGTTTTATTATTTTATTTATTTTA-A
1 TTT-GTTTTGTTTTATTATTTTATTTATTTTATA
*
324615 TTTGTTTTCTTTTATTATTTTATTT
1 TTTGTTTTGTTTTATTATTTTATTT
324640 TATGTCATAG
Statistics
Matches: 54, Mismatches: 1, Indels: 6
0.89 0.02 0.10
Matches are distributed among these distances:
32 24 0.44
33 15 0.28
34 1 0.02
35 14 0.26
ACGTcount: A:0.16, C:0.02, G:0.06, T:0.77
Consensus pattern (33 bp):
TTTGTTTTGTTTTATTATTTTATTTATTTTATA
Found at i:335240 original size:15 final size:15
Alignment explanation
Indices: 335222--335263 Score: 61
Period size: 14 Copynumber: 2.9 Consensus size: 15
335212 GAAAAAGAGA
335222 AAAAAAGAACAAAAG
1 AAAAAAGAACAAAAG
335237 AAAAAAGAA-AAAAG
1 AAAAAAGAACAAAAG
*
335251 -AGAAAGAACAAAA
1 AAAAAAGAACAAAA
335264 ATAAAGTGGG
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
13 7 0.28
14 9 0.36
15 9 0.36
ACGTcount: A:0.81, C:0.05, G:0.14, T:0.00
Consensus pattern (15 bp):
AAAAAAGAACAAAAG
Found at i:335247 original size:6 final size:7
Alignment explanation
Indices: 335212--335251 Score: 53
Period size: 7 Copynumber: 5.3 Consensus size: 7
335202 TGAAAAAATT
335212 GAAAAAGA
1 GAAAAA-A
335220 GAAAAAAA
1 G-AAAAAA
335228 GAACAAAA
1 GAA-AAAA
335236 GAAAAAA
1 GAAAAAA
335243 GAAAAAA
1 GAAAAAA
335250 GA
1 GA
335252 GAAAGAACAA
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
7 15 0.50
8 10 0.33
9 5 0.17
ACGTcount: A:0.80, C:0.03, G:0.17, T:0.00
Consensus pattern (7 bp):
GAAAAAA
Found at i:335881 original size:14 final size:14
Alignment explanation
Indices: 335862--335888 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
335852 GATCGAAACT
335862 TCAAGATTCCAGAA
1 TCAAGATTCCAGAA
335876 TCAAGATTCCAGA
1 TCAAGATTCCAGA
335889 CAGGCAACTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.41, C:0.22, G:0.15, T:0.22
Consensus pattern (14 bp):
TCAAGATTCCAGAA
Found at i:337796 original size:3 final size:3
Alignment explanation
Indices: 337788--337842 Score: 74
Period size: 3 Copynumber: 17.7 Consensus size: 3
337778 ATTATATTTT
**
337788 TAA TAA TAA TAA TATA TAA TTAA TAA TAA TAA TTT TAA TAA TAA TAA
1 TAA TAA TAA TAA TA-A TAA -TAA TAA TAA TAA TAA TAA TAA TAA TAA
337835 TAA TAA TA
1 TAA TAA TA
337843 TGAAAAAATT
Statistics
Matches: 46, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
3 40 0.87
4 6 0.13
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (3 bp):
TAA
Found at i:344353 original size:2 final size:2
Alignment explanation
Indices: 344346--344391 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
344336 TAATAACAAT
344346 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
344388 TA TA
1 TA TA
344392 ATAAATACAA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:359423 original size:25 final size:25
Alignment explanation
Indices: 359386--359434 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
359376 CGTCCAGCTA
* *
359386 CCAGCCTCTTAGGAAGTGACCACTT
1 CCAGCCTCCTAGGAAGGGACCACTT
*
359411 CCAGCCTCCTAGGAGGGGACCACT
1 CCAGCCTCCTAGGAAGGGACCACT
359435 GCCACCTTTG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.22, C:0.35, G:0.24, T:0.18
Consensus pattern (25 bp):
CCAGCCTCCTAGGAAGGGACCACTT
Found at i:365346 original size:25 final size:25
Alignment explanation
Indices: 365318--365378 Score: 122
Period size: 25 Copynumber: 2.4 Consensus size: 25
365308 GCCTTCTAGG
365318 AAGGGACCACTTCTAGCCACACAGA
1 AAGGGACCACTTCTAGCCACACAGA
365343 AAGGGACCACTTCTAGCCACACAGA
1 AAGGGACCACTTCTAGCCACACAGA
365368 AAGGGACCACT
1 AAGGGACCACT
365379 GCCACCCTTG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 36 1.00
ACGTcount: A:0.36, C:0.31, G:0.21, T:0.11
Consensus pattern (25 bp):
AAGGGACCACTTCTAGCCACACAGA
Found at i:368908 original size:18 final size:18
Alignment explanation
Indices: 368864--368909 Score: 65
Period size: 18 Copynumber: 2.6 Consensus size: 18
368854 ATATATCATC
*
368864 ATTATCATCATCAACATT
1 ATTATCATTATCAACATT
* *
368882 CTTATCATTATCAATATT
1 ATTATCATTATCAACATT
368900 ATTATCATTA
1 ATTATCATTA
368910 ATCCGTTTAT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.37, C:0.17, G:0.00, T:0.46
Consensus pattern (18 bp):
ATTATCATTATCAACATT
Found at i:369171 original size:23 final size:23
Alignment explanation
Indices: 369145--369189 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
369135 ACCATATACT
*
369145 TTTGCATCGAAGTGCCACATAGG
1 TTTGCACCGAAGTGCCACATAGG
*
369168 TTTGCACCGAAGTGTCACATAG
1 TTTGCACCGAAGTGCCACATAG
369190 AAACCTCGAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.27, C:0.22, G:0.24, T:0.27
Consensus pattern (23 bp):
TTTGCACCGAAGTGCCACATAGG
Found at i:375086 original size:18 final size:18
Alignment explanation
Indices: 375042--375087 Score: 65
Period size: 18 Copynumber: 2.6 Consensus size: 18
375032 ATATATCATC
*
375042 ATTATCATCATCAACATT
1 ATTATCATTATCAACATT
* *
375060 CTTATCATTATCAATATT
1 ATTATCATTATCAACATT
375078 ATTATCATTA
1 ATTATCATTA
375088 ATACCTTTAT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.37, C:0.17, G:0.00, T:0.46
Consensus pattern (18 bp):
ATTATCATTATCAACATT
Found at i:375364 original size:23 final size:23
Alignment explanation
Indices: 375333--375377 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
375323 TTTGCACTGA
*
375333 AGGTATGCACCGAAGTGCCACAT
1 AGGTATGCAACGAAGTGCCACAT
* *
375356 AGGTTTGCAATGAAGTGCCACA
1 AGGTATGCAACGAAGTGCCACA
375378 CAGAACCCTC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.31, C:0.22, G:0.27, T:0.20
Consensus pattern (23 bp):
AGGTATGCAACGAAGTGCCACAT
Found at i:377982 original size:27 final size:27
Alignment explanation
Indices: 377928--377984 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 27
377918 CTAATAAATC
* *
377928 AATATAAGTTCAACAACCAAATATATA
1 AATATAAGTCCAACAACCAAATACATA
*
377955 AATATAAGTCCAAGCATCCAAA-ACATA
1 AATATAAGTCCAA-CAACCAAATACATA
377982 AAT
1 AAT
377985 CCAAACAAAG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
27 19 0.73
28 7 0.27
ACGTcount: A:0.54, C:0.18, G:0.05, T:0.23
Consensus pattern (27 bp):
AATATAAGTCCAACAACCAAATACATA
Done.