Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008016.1 Hibiscus syriacus cultivar Beakdansim tig00110482_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: 5469637
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 25 of 25
Found at i:5322146 original size:21 final size:21
Alignment explanation
Indices: 5322121--5322225 Score: 64
Period size: 22 Copynumber: 5.0 Consensus size: 21
5322111 ATTATAAACT
5322121 ATATTATATTAATATAATTTA
1 ATATTATATTAATATAATTTA
5322142 ATATTA-A--AAT-TAA-TT-
1 ATATTATATTAATATAATTTA
*
5322157 ATATTAATATTAATTATAATAT-
1 ATATT-ATATTAA-TATAATTTA
*
5322179 ATAATTATTTTAATATTAATTATA
1 AT-ATTATATTAATA-TAATT-TA
5322203 AGTAGTT-TATTAATATAAATTTA
1 A-TA-TTATATTAATAT-AATTTA
5322226 TAGAGATGAA
Statistics
Matches: 66, Mismatches: 4, Indels: 26
0.69 0.04 0.27
Matches are distributed among these distances:
15 5 0.08
16 3 0.05
17 4 0.06
18 3 0.05
19 2 0.03
20 2 0.03
21 11 0.17
22 13 0.20
23 7 0.11
24 13 0.20
25 3 0.05
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (21 bp):
ATATTATATTAATATAATTTA
Found at i:5322148 original size:6 final size:6
Alignment explanation
Indices: 5322121--5322198 Score: 53
Period size: 6 Copynumber: 13.3 Consensus size: 6
5322111 ATTATAAACT
*
5322121 ATATT- ATATTA ATA-TA AT-TTA ATATTA AAATT- A-ATT- ATATTA
1 ATATTA ATATTA ATATTA ATATTA ATATTA ATATTA ATATTA ATATTA
5322163 ATATTA AT-TATA ATATATA ATTATTTTA ATATTA AT
1 ATATTA ATAT-TA ATAT-TA A-TA--TTA ATATTA AT
5322199 TATAAGTAGT
Statistics
Matches: 62, Mismatches: 1, Indels: 19
0.76 0.01 0.23
Matches are distributed among these distances:
4 4 0.06
5 18 0.29
6 27 0.44
7 5 0.08
8 4 0.06
9 3 0.05
10 1 0.02
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (6 bp):
ATATTA
Found at i:5322185 original size:13 final size:12
Alignment explanation
Indices: 5322126--5322203 Score: 54
Period size: 15 Copynumber: 6.1 Consensus size: 12
5322116 AAACTATATT
5322126 ATATTAA-TATA
1 ATATTAATTATA
5322137 AT-TTAA-TATTA
1 ATATTAATTA-TA
*
5322148 AAATTAATTATATTA
1 ATATTAA-T-TA-TA
5322163 ATATTAATTATA
1 ATATTAATTATA
5322175 ATATATAATTATTTTA
1 ATAT-TAATTA---TA
5322191 ATATTAATTATA
1 ATATTAATTATA
5322203 A
1 A
5322204 GTAGTTTATT
Statistics
Matches: 56, Mismatches: 2, Indels: 17
0.75 0.03 0.23
Matches are distributed among these distances:
10 6 0.11
11 5 0.09
12 13 0.23
13 8 0.14
14 1 0.02
15 17 0.30
16 6 0.11
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (12 bp):
ATATTAATTATA
Found at i:5324644 original size:16 final size:16
Alignment explanation
Indices: 5324623--5324711 Score: 61
Period size: 16 Copynumber: 5.4 Consensus size: 16
5324613 CAAAAAAGTA
5324623 ATCATATTAATTAATT
1 ATCATATTAATTAATT
* * *
5324639 ATCATAATAATTTATG
1 ATCATATTAATTAATT
* * ** *
5324655 ATAAAATTTCAAAAAATA
1 ATCATA-TT-AATTAATT
5324673 ATCATATTAATTTAATT
1 ATCATATTAA-TTAATT
* *
5324690 ATCATAATAAGTAATT
1 ATCATATTAATTAATT
5324706 ATCATA
1 ATCATA
5324712 AGTTTATTAT
Statistics
Matches: 53, Mismatches: 17, Indels: 6
0.70 0.22 0.08
Matches are distributed among these distances:
16 30 0.57
17 15 0.28
18 8 0.15
ACGTcount: A:0.49, C:0.07, G:0.02, T:0.42
Consensus pattern (16 bp):
ATCATATTAATTAATT
Found at i:5334495 original size:37 final size:37
Alignment explanation
Indices: 5334453--5334536 Score: 132
Period size: 37 Copynumber: 2.3 Consensus size: 37
5334443 AATGGTTTAG
*
5334453 ATTTGAGATAAAATCAAATAAATATTGATTTAGTGAA
1 ATTTGAGATAAAATCAAATAAATATTGACTTAGTGAA
* * *
5334490 ATTTGAGATAAAATGAAATAATTATTGGCTTAGTGAA
1 ATTTGAGATAAAATCAAATAAATATTGACTTAGTGAA
5334527 ATTTGAGATA
1 ATTTGAGATA
5334537 GTTTATTAAT
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
37 43 1.00
ACGTcount: A:0.45, C:0.02, G:0.17, T:0.36
Consensus pattern (37 bp):
ATTTGAGATAAAATCAAATAAATATTGACTTAGTGAA
Found at i:5337349 original size:31 final size:31
Alignment explanation
Indices: 5337314--5337376 Score: 126
Period size: 31 Copynumber: 2.0 Consensus size: 31
5337304 ACCCCAATAA
5337314 TTTGCATTTCCTGGATTTTGGATCCAATTTT
1 TTTGCATTTCCTGGATTTTGGATCCAATTTT
5337345 TTTGCATTTCCTGGATTTTGGATCCAATTTT
1 TTTGCATTTCCTGGATTTTGGATCCAATTTT
5337376 T
1 T
5337377 GAAATTTCTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.16, C:0.16, G:0.16, T:0.52
Consensus pattern (31 bp):
TTTGCATTTCCTGGATTTTGGATCCAATTTT
Found at i:5337384 original size:30 final size:30
Alignment explanation
Indices: 5337314--5337384 Score: 99
Period size: 31 Copynumber: 2.3 Consensus size: 30
5337304 ACCCCAATAA
*
5337314 TTTGCATTTCCTGGATTTTGGATCCAATTTT
1 TTTGAATTTCCTGGATTTTGGATCCAA-TTT
*
5337345 TTTGCATTTCCTGGATTTTGGATCCAA-TT
1 TTTGAATTTCCTGGATTTTGGATCCAATTT
5337374 TTTGAAATTTC
1 TTTG-AATTTC
5337385 TTGAGAGTTG
Statistics
Matches: 38, Mismatches: 1, Indels: 3
0.90 0.02 0.07
Matches are distributed among these distances:
29 6 0.16
30 5 0.13
31 27 0.71
ACGTcount: A:0.18, C:0.15, G:0.15, T:0.51
Consensus pattern (30 bp):
TTTGAATTTCCTGGATTTTGGATCCAATTT
Found at i:5337838 original size:25 final size:25
Alignment explanation
Indices: 5337810--5337861 Score: 95
Period size: 25 Copynumber: 2.1 Consensus size: 25
5337800 CTGACTTCTT
5337810 CTTAATAGGGTACACCCAACATCTC
1 CTTAATAGGGTACACCCAACATCTC
*
5337835 CTTAATAGGGTACACCCATCATCTC
1 CTTAATAGGGTACACCCAACATCTC
5337860 CT
1 CT
5337862 AGAGTAGTCA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.29, C:0.33, G:0.12, T:0.27
Consensus pattern (25 bp):
CTTAATAGGGTACACCCAACATCTC
Found at i:5340551 original size:123 final size:121
Alignment explanation
Indices: 5340333--5340621 Score: 435
Period size: 123 Copynumber: 2.3 Consensus size: 121
5340323 GCAATAATTA
5340333 GTGAAGTGT-AAAGATTTAAGTGT-TCATTGTGCTTTTTTTTGGCATGCTCATTGGTGTGTGTGT
1 GTGAAGTGTCAAAGATTTAAGTGTAT--TTGTGCTTTTTTTT-GCATGCTCATTGGTGTGTGTGT
5340396 GTGTGTTTTTTTTTTTGTTATTGTGATCTTAGTAAGTATGAAATTATTTGTTTAAATGG
63 GTGTGTTTTTTTTTTTGTTATTGTGATCTTAGTAAGTATGAAATTATTTGTTTAAATGG
5340455 GTGAAGTGTCAAAGATTTAAG-GTATTTGTGCTTTTTTTTGCATG-TCATTGGTGTGTGTGTGTG
1 GTGAAGTGTCAAAGATTTAAGTGTATTTGTGCTTTTTTTTGCATGCTCA-T--TG-GTGTGTGTG
*
5340518 TGTGTGTTTTTTTTTTTTGTTATTGTGAT-TTAGTAAGTATGAAATTATTTGTTTAAATTG
62 TGTGTG-TTTTTTTTTTTGTTATTGTGATCTTAGTAAGTATGAAATTATTTGTTTAAATGG
5340578 GTGAAGTGTCAAAGATTTAAGTGTTCATTTGTGTCTTTTTTTTG
1 GTGAAGTGTCAAAGATTTAAGTG-T-ATTTGTG-CTTTTTTTTG
5340622 TTATTATGAT
Statistics
Matches: 155, Mismatches: 1, Indels: 17
0.90 0.01 0.10
Matches are distributed among these distances:
119 3 0.02
120 6 0.04
121 14 0.09
122 13 0.08
123 78 0.50
124 23 0.15
125 1 0.01
126 7 0.05
127 10 0.06
ACGTcount: A:0.20, C:0.04, G:0.24, T:0.52
Consensus pattern (121 bp):
GTGAAGTGTCAAAGATTTAAGTGTATTTGTGCTTTTTTTTGCATGCTCATTGGTGTGTGTGTGTG
TGTTTTTTTTTTTGTTATTGTGATCTTAGTAAGTATGAAATTATTTGTTTAAATGG
Found at i:5342196 original size:16 final size:16
Alignment explanation
Indices: 5342143--5342218 Score: 73
Period size: 16 Copynumber: 4.6 Consensus size: 16
5342133 TTTTAAGAAC
*
5342143 AATAAATTAATCTAAA
1 AATAATTTAATCTAAA
* *
5342159 TATTAATTTAATC-AAG
1 -AATAATTTAATCTAAA
5342175 AATAATTTAATCTAAA
1 AATAATTTAATCTAAA
* *
5342191 AATAATCTAAACTAAA
1 AATAATTTAATCTAAA
5342207 ATATTAATTTAA
1 A-A-TAATTTAA
5342219 ACAACAACTA
Statistics
Matches: 48, Mismatches: 8, Indels: 5
0.79 0.13 0.08
Matches are distributed among these distances:
15 11 0.23
16 19 0.40
17 11 0.23
18 7 0.15
ACGTcount: A:0.55, C:0.07, G:0.01, T:0.37
Consensus pattern (16 bp):
AATAATTTAATCTAAA
Found at i:5342574 original size:54 final size:55
Alignment explanation
Indices: 5342515--5342618 Score: 156
Period size: 54 Copynumber: 1.9 Consensus size: 55
5342505 ATGCATGCAA
* * *
5342515 GAGTTAATGTTTTTTTCAGCATCATTACTATC-AAGGTTGCAGCATTCACAGCAC
1 GAGTTAATGCTTTTTACAGCATCATTACTATCAAAGGCTGCAGCATTCACAGCAC
* *
5342569 GAGTTAATGCTTTTTACAGGATCATTACTATCAAAGGCTGCAGTATTCAC
1 GAGTTAATGCTTTTTACAGCATCATTACTATCAAAGGCTGCAGCATTCAC
5342619 GGGGGCATCC
Statistics
Matches: 44, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
54 29 0.66
55 15 0.34
ACGTcount: A:0.29, C:0.19, G:0.17, T:0.35
Consensus pattern (55 bp):
GAGTTAATGCTTTTTACAGCATCATTACTATCAAAGGCTGCAGCATTCACAGCAC
Found at i:5344897 original size:38 final size:39
Alignment explanation
Indices: 5344844--5344938 Score: 117
Period size: 38 Copynumber: 2.5 Consensus size: 39
5344834 CCGATTTTTA
5344844 AAAAAAAACCG-ACCGAACCCGAAC-GAATATCACAC-TT
1 AAAAAAAACCGAACCGAACCCGAACTGAATATCA-ACTTT
* *
5344881 AAAAAAACCCGAACCG-ACCCGACCTGAATATCAACTTT
1 AAAAAAAACCGAACCGAACCCGAACTGAATATCAACTTT
* *
5344919 AAAAAAATCCGACCCGAACC
1 AAAAAAAACCGAACCGAACC
5344939 GACTTTTTTA
Statistics
Matches: 50, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
37 19 0.38
38 28 0.56
39 3 0.06
ACGTcount: A:0.46, C:0.32, G:0.11, T:0.12
Consensus pattern (39 bp):
AAAAAAAACCGAACCGAACCCGAACTGAATATCAACTTT
Found at i:5344975 original size:29 final size:30
Alignment explanation
Indices: 5344919--5344995 Score: 75
Period size: 29 Copynumber: 2.6 Consensus size: 30
5344909 TATCAACTTT
* **
5344919 AAAAAAATCCGACCCGAACCGACTTTTTTA
1 AAAAAAATCCAACCCGAACCGAAATTTTTA
* *
5344949 AAAAAAATCCAACCCGATCC-AAATTTTTT
1 AAAAAAATCCAACCCGAACCGAAATTTTTA
** *
5344978 TTAAAAATCTAACCCGAA
1 AAAAAAATCCAACCCGAA
5344996 TACCAAAAGA
Statistics
Matches: 38, Mismatches: 9, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
29 20 0.53
30 18 0.47
ACGTcount: A:0.44, C:0.25, G:0.06, T:0.25
Consensus pattern (30 bp):
AAAAAAATCCAACCCGAACCGAAATTTTTA
Found at i:5344976 original size:30 final size:29
Alignment explanation
Indices: 5344916--5344995 Score: 88
Period size: 30 Copynumber: 2.7 Consensus size: 29
5344906 GAATATCAAC
* * *
5344916 TTTAAAAAAATCCGACCCGAACCGACTTT
1 TTTAAAAAAATCCAACCCGAACCAAATTT
*
5344945 TTTAAAAAAAATCCAACCCGATCCAAATTT
1 TTT-AAAAAAATCCAACCCGAACCAAATTT
** *
5344975 TTTTTAAAAATCTAACCCGAA
1 TTTAAAAAAATCCAACCCGAA
5344996 TACCAAAAGA
Statistics
Matches: 42, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
29 17 0.40
30 25 0.60
ACGTcount: A:0.42, C:0.24, G:0.06, T:0.28
Consensus pattern (29 bp):
TTTAAAAAAATCCAACCCGAACCAAATTT
Found at i:5347490 original size:2 final size:2
Alignment explanation
Indices: 5347483--5347518 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
5347473 TATCCTTGTA
5347483 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
5347519 TTTAACAAGT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5347552 original size:21 final size:23
Alignment explanation
Indices: 5347528--5347581 Score: 62
Period size: 21 Copynumber: 2.4 Consensus size: 23
5347518 TTTTAACAAG
5347528 TAAAAT-TTTAATATT-AAA-TTA
1 TAAAATATTTAA-ATTAAAATTTA
5347549 T-AAATATTTAAATTAAAATTTA
1 TAAAATATTTAAATTAAAATTTA
5347571 TAAAAATATTT
1 T-AAAATATTT
5347582 TAGTATTACA
Statistics
Matches: 28, Mismatches: 0, Indels: 7
0.80 0.00 0.20
Matches are distributed among these distances:
20 7 0.25
21 9 0.32
22 4 0.14
24 8 0.29
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (23 bp):
TAAAATATTTAAATTAAAATTTA
Found at i:5349951 original size:105 final size:105
Alignment explanation
Indices: 5349615--5350036 Score: 453
Period size: 105 Copynumber: 4.1 Consensus size: 105
5349605 TCACCAAATA
*** * * * ** *
5349615 TTGTCACATATAGTATATTGGTTGATGCGTTTTGCAAGGAGGGGCTTATTT-TGAAGCTGTAGAT
1 TTGTCACATATAGTATATTGGTTGATGCACATTGCAAGAAAGGGATGGTTTCTGAAGCTGAAGAT
* * * * *
5349679 ACTGTTCACAC-ATGAGAAAGCAAGGCCTTAAGCCTAATG
66 ATTGTTGACACAATGAGAAAGGAAGGCATTGAGCCTAATG
* * * * *
5349718 TTGT--CATATACTATATTGGTTGATGCTCTTTGCAAG-AAGGGAATGGTTTTTGAAGCTAAAGA
1 TTGTCACATATAGTATATTGGTTGATGCACATTGCAAGAAAGGG-ATGGTTTCTGAAGCTGAAGA
* * *
5349780 TATTGTTGATAAAATGAG-AAGGAAGGCATTGAGCCTGATG
65 TATTGTTGACACAATGAGAAAGGAAGGCATTGAGCCTAATG
* * **
5349820 TTGTCACATACAATACGTTGGTTGATGCACATTGCAAGAAAGGGATGGTTTCTGAAGCTGAAGAT
1 TTGTCACATATAGTATATTGGTTGATGCACATTGCAAGAAAGGGATGGTTTCTGAAGCTGAAGAT
*
5349885 ATTGTTGACACGATGAGAAAGGAAGGCATTGAGCCTAATG
66 ATTGTTGACACAATGAGAAAGGAAGGCATTGAGCCTAATG
* * * * *
5349925 TTGTAACGTATAGTATATTGGTTGATGCAAATTGCAAGAAAGGAATGGTTTCT-ATAGCCGAAGA
1 TTGTCACATATAGTATATTGGTTGATGCACATTGCAAGAAAGGGATGGTTTCTGA-AGCTGAAGA
* * * *
5349989 TATTGTCGAGACAATGAGAAAGGAGGGCATTGAGCCCAATG
65 TATTGTTGACACAATGAGAAAGGAAGGCATTGAGCCTAATG
5350030 TTGTCAC
1 TTGTCAC
5350037 GTACAACACT
Statistics
Matches: 267, Mismatches: 44, Indels: 14
0.82 0.14 0.04
Matches are distributed among these distances:
100 4 0.01
101 33 0.12
102 40 0.15
103 9 0.03
104 60 0.22
105 121 0.45
ACGTcount: A:0.31, C:0.12, G:0.27, T:0.30
Consensus pattern (105 bp):
TTGTCACATATAGTATATTGGTTGATGCACATTGCAAGAAAGGGATGGTTTCTGAAGCTGAAGAT
ATTGTTGACACAATGAGAAAGGAAGGCATTGAGCCTAATG
Found at i:5349972 original size:209 final size:207
Alignment explanation
Indices: 5349666--5350042 Score: 506
Period size: 209 Copynumber: 1.8 Consensus size: 207
5349656 GGGCTTATTT
* *
5349666 TGAAGCTGTAGATACTGTTCACACATGAGAAAGCAAGGCCTTAAGCCTAATGTTGTCATATACTA
1 TGAAGCTGAAGATACTGTTCACACATGAGAAAGCAAGGCATTAAGCCTAATGTTGTCATATACTA
*** * * * * *
5349731 TATTGGTTGATGCTCTTTGCAAGAAGGGAATGGTTTTTGA-AGCTAAAGATATTGTTGATAAAAT
66 TATTGGTTGATGCAAATTGCAAGAAAGGAATGGTTTCT-ATAGCCAAAGATATTGTCGAGAAAAT
**
5349795 GAG-AAGGAAGGCATTGAGCCTGATGTTGTCACATACAATACGTTGGTTGATGCACATTGCAAGA
130 GAGAAAGGAAGGCATTGAGCCCAATGTTGTCACATACAATACGTTGGTTGATGCACATTGCAAGA
5349859 AAGGGATGGTTTC
195 AAGGGATGGTTTC
* * * * *
5349872 TGAAGCTGAAGATATTGTTGACACGATGAGAAAGGAAGGCATTGAGCCTAATGTTGTAACGTATA
1 TGAAGCTGAAGATACTGTTCACAC-ATGAGAAAGCAAGGCATTAAGCCTAATGTTGT--CATATA
* * *
5349937 GTATATTGGTTGATGCAAATTGCAAGAAAGGAATGGTTTCTATAGCCGAAGATATTGTCGAGACA
63 CTATATTGGTTGATGCAAATTGCAAGAAAGGAATGGTTTCTATAGCCAAAGATATTGTCGAGAAA
* *
5350002 ATGAGAAAGGAGGGCATTGAGCCCAATGTTGTCACGTACAA
128 ATGAGAAAGGAAGGCATTGAGCCCAATGTTGTCACATACAA
5350043 CACTCTTATG
Statistics
Matches: 144, Mismatches: 22, Indels: 6
0.84 0.13 0.03
Matches are distributed among these distances:
206 21 0.15
207 29 0.20
208 1 0.01
209 62 0.43
210 31 0.22
ACGTcount: A:0.33, C:0.13, G:0.26, T:0.28
Consensus pattern (207 bp):
TGAAGCTGAAGATACTGTTCACACATGAGAAAGCAAGGCATTAAGCCTAATGTTGTCATATACTA
TATTGGTTGATGCAAATTGCAAGAAAGGAATGGTTTCTATAGCCAAAGATATTGTCGAGAAAATG
AGAAAGGAAGGCATTGAGCCCAATGTTGTCACATACAATACGTTGGTTGATGCACATTGCAAGAA
AGGGATGGTTTC
Found at i:5353262 original size:168 final size:166
Alignment explanation
Indices: 5352888--5353223 Score: 638
Period size: 168 Copynumber: 2.0 Consensus size: 166
5352878 ATGTGAATGA
5352888 AATTGGCTCCAGCCTCATTAGCTACAGACTTTGCAATCAACGTTTTACCCCAGCCTGGTGGTCCA
1 AATTGGCTCCAGCCTCATTAGCTACAGACTTTGCAATCAACGTTTTACCCCAGCCTGGTGGTCCA
5352953 TAAAGCAAAATCCTGTCTCAAGTCCACTCCAAATTCCTGAAATTGTGAACAACACAAGAATTTGA
66 TAAAGCAAAATCCTGTCTCAAGTCCACTCCAAATTCCTGAAATTGTGAACAACACAAGAATTTGA
5353018 AAATCATACTAATAATAGCAAGTTGACTAACAAAGT
131 AAATCATACTAATAATAGCAAGTTGACTAACAAAGT
5353054 AATTGGCTCCAGCCTCATTAGCTACAGACTTTGCAATCAACGTTTTACCCCAGCCTGGTGGTCCA
1 AATTGGCTCCAGCCTCATTAGCTACAGACTTTGCAATCAACGTTTTACCCCAGCCTGGTGGTCCA
5353119 TAAAGCAAAAATCCTGTCTCCAAGTCCACTCCAAATTCCTGAAATTGTGAACAACACAAGAATTT
66 TAAAGC-AAAATCCTGTCT-CAAGTCCACTCCAAATTCCTGAAATTGTGAACAACACAAGAATTT
5353184 GAAAATCAATACT-ATAATAGCAAGTTGACTAACAAAGT
129 GAAAATC-ATACTAATAATAGCAAGTTGACTAACAAAGT
5353222 AA
1 AA
5353224 ATATGCTTCG
Statistics
Matches: 167, Mismatches: 0, Indels: 4
0.98 0.00 0.02
Matches are distributed among these distances:
166 71 0.43
167 12 0.07
168 79 0.47
169 5 0.03
ACGTcount: A:0.36, C:0.24, G:0.14, T:0.26
Consensus pattern (166 bp):
AATTGGCTCCAGCCTCATTAGCTACAGACTTTGCAATCAACGTTTTACCCCAGCCTGGTGGTCCA
TAAAGCAAAATCCTGTCTCAAGTCCACTCCAAATTCCTGAAATTGTGAACAACACAAGAATTTGA
AAATCATACTAATAATAGCAAGTTGACTAACAAAGT
Found at i:5353966 original size:105 final size:103
Alignment explanation
Indices: 5353777--5354185 Score: 387
Period size: 105 Copynumber: 3.9 Consensus size: 103
5353767 GGCATTTAAT
** * ** * * * *
5353777 ATTGGTTGATGCTTATTGCAAGGAAGGGCTTATTTTTGAAGCTGTAGATACTGTTCATACAATGA
1 ATTGGTTGATGCACATTGCAA-GAAGGGATGGTTTTTGAAGCTGAAGATATTGTTGACACAATGA
* * **
5353842 GAAAGCAAGGCCTTAAGCCTGATGTTGTCCCGTATACTAC
65 GAAAGCAAGGCATTGAGCCTGATGTTGTCATGTATAC-AC
** * * *
5353882 ATTGGTTGATGCGTATTGCAAGAAGGGAATGGTTTATGAAGCTGAAGTTATTGTTGATACAATGA
1 ATTGGTTGATGCACATTGCAAGAAGGG-ATGGTTTTTGAAGCTGAAGATATTGTTGACACAATGA
* * *
5353947 GAAGGCAAGGTATTGAGCCTGATGTTGTCATGTACAGCAC
65 GAAAGCAAGGCATTGAGCCTGATGTTGTCATGTATA-CAC
* * * * *
5353987 ATTGGTTGATGCACGTTGCAAGAAAGGGATGGTTTCTAAAACTAAAGATATT-TTCGACACAATG
1 ATTGGTTGATGCACATTGCAAG-AAGGGATGGTTTTTGAAGCTGAAGATATTGTT-GACACAATG
*
5354051 AGAAAGCAAGGCATTGAGCCAGATGTTGTCATGTATAACAC
64 AGAAAGCAAGGCATTGAGCCTGATGTTGTCATGTAT-ACAC
* * * * *
5354092 ATTGG-TGATGCACATTGTAAGAAAGCAGTGGTTTTTTTTGAAGCTGAAGATGTTGTCGACACAA
1 ATTGGTTGATGCACATTGCAAGAAGGGA-TGG---TTTTTGAAGCTGAAGATATTGTTGACACAA
*
5354156 T--GAAAGCAAGG-ATTGAGCCTAATGTTGTCA
62 TGAGAAAGCAAGGCATTGAGCCTGATGTTGTCA
5354186 CACACCACTC
Statistics
Matches: 253, Mismatches: 41, Indels: 21
0.80 0.13 0.07
Matches are distributed among these distances:
103 4 0.02
104 42 0.17
105 176 0.70
106 7 0.03
107 23 0.09
108 1 0.00
ACGTcount: A:0.31, C:0.13, G:0.26, T:0.30
Consensus pattern (103 bp):
ATTGGTTGATGCACATTGCAAGAAGGGATGGTTTTTGAAGCTGAAGATATTGTTGACACAATGAG
AAAGCAAGGCATTGAGCCTGATGTTGTCATGTATACAC
Found at i:5360430 original size:22 final size:22
Alignment explanation
Indices: 5360398--5360453 Score: 69
Period size: 22 Copynumber: 2.5 Consensus size: 22
5360388 GTAAAAATTC
5360398 AATAAGTTTAATGA-TCAGTTTAT
1 AATAA-TTTAATGACT-AGTTTAT
*
5360421 AATAATTTAATGACTATTTTAT
1 AATAATTTAATGACTAGTTTAT
*
5360443 AATATTTTAAT
1 AATAATTTAAT
5360454 AAGTTAATAA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
22 24 0.80
23 6 0.20
ACGTcount: A:0.41, C:0.04, G:0.07, T:0.48
Consensus pattern (22 bp):
AATAATTTAATGACTAGTTTAT
Found at i:5360513 original size:24 final size:24
Alignment explanation
Indices: 5360465--5360514 Score: 66
Period size: 25 Copynumber: 2.1 Consensus size: 24
5360455 AGTTAATAAA
*
5360465 TTTTATAACTTTTAAATGATTATTT
1 TTTTATAAATTTTAAAT-ATTATTT
*
5360490 TTTTATAAATTTTAAAT-TTAATT
1 TTTTATAAATTTTAAATATTATTT
5360513 TT
1 TT
5360515 AACCTTAATC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 7 0.30
25 16 0.70
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.62
Consensus pattern (24 bp):
TTTTATAAATTTTAAATATTATTT
Found at i:5362143 original size:2 final size:2
Alignment explanation
Indices: 5362138--5362176 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
5362128 GTTTATAAGT
5362138 TA 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 TA T
5362177 TTCCCTTCTT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:5362386 original size:6 final size:6
Alignment explanation
Indices: 5362371--5362460 Score: 128
Period size: 6 Copynumber: 14.8 Consensus size: 6
5362361 TATACATATG
*
5362371 TTATTT TTATTA TTATTT TTATTT TTA-TT TTATTCAT TTATTT TTATTT
1 TTATTT TTATTT TTATTT TTATTT TTATTT TTATT--T TTATTT TTATTT
* *
5362420 TTATTT TTATTT TTATTT TTATTT TTAATT TTAATT TTATT
1 TTATTT TTATTT TTATTT TTATTT TTATTT TTATTT TTATT
5362461 GTTTCCTTTA
Statistics
Matches: 77, Mismatches: 4, Indels: 6
0.89 0.05 0.07
Matches are distributed among these distances:
5 5 0.06
6 66 0.86
8 6 0.08
ACGTcount: A:0.21, C:0.01, G:0.00, T:0.78
Consensus pattern (6 bp):
TTATTT
Found at i:5362451 original size:37 final size:36
Alignment explanation
Indices: 5362372--5362460 Score: 103
Period size: 37 Copynumber: 2.4 Consensus size: 36
5362362 ATACATATGT
5362372 TATTTTTATTATTATT-TTTATTTTTA-TTTTATTCATT
1 TATTTTTATT-TTATTATTTATTTTTATTTTTATT--TT
5362409 TATTTTTATTTTTATT-TTTATTTTTATTTTTATTTT
1 TATTTTTA-TTTTATTATTTATTTTTATTTTTATTTT
*
5362445 TAATTTTAATTTTATT
1 T-ATTTTTATTTTATT
5362461 GTTTCCTTTA
Statistics
Matches: 48, Mismatches: 1, Indels: 7
0.86 0.02 0.12
Matches are distributed among these distances:
36 10 0.21
37 29 0.60
38 9 0.19
ACGTcount: A:0.21, C:0.01, G:0.00, T:0.78
Consensus pattern (36 bp):
TATTTTTATTTTATTATTTATTTTTATTTTTATTTT
Found at i:5366810 original size:96 final size:95
Alignment explanation
Indices: 5366676--5366932 Score: 293
Period size: 96 Copynumber: 2.7 Consensus size: 95
5366666 AATATTACAT
* * * * * * *
5366676 ATATACAATAAAGCTTGAGTTGTCCCTCAAAAGTAATTGGTTAAACGCCCCGACTTTATGGATAA
1 ATATATAATAAAACTTGAGTTGTTCCTCTAGAGTAATTGGTTAAACGCCCTGGCTTTATGGATAA
**
5366741 GATTCAGCTAAGCCTGATAAAGGTGATTATA
66 GATTCAG-TAAGCCTGATAAAGACGATTATA
* **
5366772 ATATATAATAAAACTTGAGTTGTTCCTCTAGAGCAATTGGTTAAACATCCTGGCTTTATGGATAA
1 ATATATAATAAAACTTGAGTTGTTCCTCTAGAGTAATTGGTTAAACGCCCTGGCTTTATGGATAA
* *
5366837 TATTCAGTTAGCCTGATAAAGACGATTATA
66 GATTCAGTAAGCCTGATAAAGACGATTATA
* * *
5366867 ATATCT-ATACAATGATATTAAGTT-TTCCCTCTAGAGTAATTGGTTAAACGCCCTGGCTTTATG
1 ATATATAATA-AA--A-CTTGAGTTGTT-CCTCTAGAGTAATTGGTTAAACGCCCTGGCTTTATG
5366930 GAT
61 GAT
5366933 CCATCTAGCC
Statistics
Matches: 136, Mismatches: 20, Indels: 8
0.83 0.12 0.05
Matches are distributed among these distances:
94 3 0.02
95 27 0.20
96 61 0.45
97 3 0.02
98 42 0.31
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Consensus pattern (95 bp):
ATATATAATAAAACTTGAGTTGTTCCTCTAGAGTAATTGGTTAAACGCCCTGGCTTTATGGATAA
GATTCAGTAAGCCTGATAAAGACGATTATA
Found at i:5368275 original size:36 final size:36
Alignment explanation
Indices: 5368222--5368302 Score: 117
Period size: 36 Copynumber: 2.2 Consensus size: 36
5368212 AATTTACTCA
*
5368222 AAACAAAGTTTTGTCTCTCTTGAGACAATTTCCCTTG
1 AAACAAA-TTTTATCTCTCTTGAGACAATTTCCCTTG
* * *
5368259 AAATAAATTTTATCTCTTTTGAGACAGTTTCCCTTG
1 AAACAAATTTTATCTCTCTTGAGACAATTTCCCTTG
5368295 AAACAAAT
1 AAACAAAT
5368303 CTTTGAATAT
Statistics
Matches: 39, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
36 33 0.85
37 6 0.15
ACGTcount: A:0.32, C:0.19, G:0.11, T:0.38
Consensus pattern (36 bp):
AAACAAATTTTATCTCTCTTGAGACAATTTCCCTTG
Found at i:5368397 original size:101 final size:100
Alignment explanation
Indices: 5368222--5368407 Score: 266
Period size: 101 Copynumber: 1.9 Consensus size: 100
5368212 AATTTACTCA
* * *
5368222 AAACAAAGTTTTGTCTCTCTTGAGACAATTTCCCTTGAAATAAATTTTATCTCTTTTGAGACAGT
1 AAACAAAGTTTCGTCTCCCTTGAGACAATTTCCCTTGAAATAAATTTTATCTCTCTTGAGACAGT
5368287 TTCCCTTGAAACAAATCTTTGAATATGTTTTCCTTG
66 TTCCCTTGAAACAAAT-TTTGAATATGTTTTCCTTG
** * * *
5368323 AAACAAA-TTTCGTCTCCCTTGAGACAATTTCTTTTGGAACTAAGTTTTTTCTCTCTTGAGACAG
1 AAACAAAGTTTCGTCTCCCTTGAGACAATTTCCCTT-GAAATAAATTTTATCTCTCTTGAGACAG
*
5368387 TTTCTCTTGAAACAAATTTTG
65 TTTCCCTTGAAACAAATTTTG
5368408 TCTCACTTGA
Statistics
Matches: 75, Mismatches: 9, Indels: 3
0.86 0.10 0.03
Matches are distributed among these distances:
100 28 0.37
101 47 0.63
ACGTcount: A:0.28, C:0.18, G:0.12, T:0.41
Consensus pattern (100 bp):
AAACAAAGTTTCGTCTCCCTTGAGACAATTTCCCTTGAAATAAATTTTATCTCTCTTGAGACAGT
TTCCCTTGAAACAAATTTTGAATATGTTTTCCTTG
Found at i:5368411 original size:73 final size:73
Alignment explanation
Indices: 5368315--5368473 Score: 221
Period size: 73 Copynumber: 2.2 Consensus size: 73
5368305 TTGAATATGT
* ** * * **
5368315 TTTC-CTTGAAACAAATTTCGTCTCCCTTGAGACAATTTCTTTTGGAACTAAGTTTTTTCTCTCT
1 TTTCTCTTGAAACAAATTTCGTCTCACTTGAGACAATTTCCCTTGAAACAAAGTTTTGCCTCTCT
*
5368379 TGAGACAG
66 TGAGACAA
* *
5368387 TTTCTCTTGAAACAAATTTTGTCTCACTTGAGACAGTTTCCCTTGAAACAAAGTTTTGCCTCTCT
1 TTTCTCTTGAAACAAATTTCGTCTCACTTGAGACAATTTCCCTTGAAACAAAGTTTTGCCTCTCT
5368452 TGAGACAA
66 TGAGACAA
5368460 TTTCTCTTGAAACA
1 TTTCTCTTGAAACA
5368474 CCAATCTTTG
Statistics
Matches: 76, Mismatches: 10, Indels: 1
0.87 0.11 0.01
Matches are distributed among these distances:
72 4 0.05
73 72 0.95
ACGTcount: A:0.26, C:0.21, G:0.13, T:0.40
Consensus pattern (73 bp):
TTTCTCTTGAAACAAATTTCGTCTCACTTGAGACAATTTCCCTTGAAACAAAGTTTTGCCTCTCT
TGAGACAA
Found at i:5368422 original size:36 final size:36
Alignment explanation
Indices: 5368315--5368473 Score: 194
Period size: 37 Copynumber: 4.4 Consensus size: 36
5368305 TTGAATATGT
* *
5368315 TTTC-CTTGAAACAAATTTCGTCTCCCTTGAGACAA
1 TTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAA
* * * * *
5368350 TTTCTTTTGGAACTAAGTTTTTTCTCTCTTGAGACAG
1 TTTCTCTTGAAAC-AAATTTTGTCTCTCTTGAGACAA
* *
5368387 TTTCTCTTGAAACAAATTTTGTCTCACTTGAGACAG
1 TTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAA
* *
5368423 TTTCCCTTGAAACAAAGTTTTGCCTCTCTTGAGACAA
1 TTTCTCTTGAAACAAA-TTTTGTCTCTCTTGAGACAA
5368460 TTTCTCTTGAAACA
1 TTTCTCTTGAAACA
5368474 CCAATCTTTG
Statistics
Matches: 104, Mismatches: 17, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
35 4 0.04
36 41 0.39
37 59 0.57
ACGTcount: A:0.26, C:0.21, G:0.13, T:0.40
Consensus pattern (36 bp):
TTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAA
Found at i:5368568 original size:33 final size:33
Alignment explanation
Indices: 5368526--5368646 Score: 154
Period size: 33 Copynumber: 3.6 Consensus size: 33
5368516 CCTGAAGACA
5368526 GTTTCTCTTGAAACACAAAAAACTTTTGAAATC
1 GTTTCTCTTGAAACACAAAAAACTTTTGAAATC
* *
5368559 ATTTCTCTTGAAACACAAAAAACCTTTGAAATC
1 GTTTCTCTTGAAACACAAAAAACTTTTGAAATC
* **
5368592 GTTTCTCCTGAAACACACAAAAAACCCTTTAAAAAT-
1 GTTTCTCTTG-AA-ACACAAAAAA--CTTTTGAAATC
5368628 GTTTCTCTTGAAACACAAA
1 GTTTCTCTTGAAACACAAA
5368647 GTTGATCGTA
Statistics
Matches: 76, Mismatches: 8, Indels: 7
0.84 0.09 0.08
Matches are distributed among these distances:
33 39 0.51
34 9 0.12
35 12 0.16
36 9 0.12
37 7 0.09
ACGTcount: A:0.41, C:0.21, G:0.07, T:0.30
Consensus pattern (33 bp):
GTTTCTCTTGAAACACAAAAAACTTTTGAAATC
Found at i:5371512 original size:165 final size:164
Alignment explanation
Indices: 5371096--5371652 Score: 726
Period size: 162 Copynumber: 3.4 Consensus size: 164
5371086 AAACATGCGC
* * ** *
5371096 CTTTAATTTAGGATGGGATGGAACACTATGACATGATAGACATTCTCTGAATAATAATGGAAAAC
1 CTTTCATTTCGGATGGGATGGAACACTATGACATGGCAGAGATTCTCTGAATAATAATGGAAAAC
** * * *
5371161 GCTTCCCAAGGAACGCGTCTTTCATTTTGGATGGGATGAAACACTATGACATGACAAAAAGTCTC
66 GCTTCCCCTGGAACGCGTCTTTCATTTTGGATGGGATGGAACACTATGACATGACAAAGATTCTC
* * *
5371226 TGAATAATAATGGAAAACACTTCCCCTGCA--GC
131 TTAATAATAATGGAAAACACTTCCCCTGAATGGT
* * *
5371258 CTTTCATTTCGGATGGGATGGAACACTATGACATGGTAGAGATTCTCTGAATAATAACGGAATAC
1 CTTTCATTTCGGATGGGATGGAACACTATGACATGGCAGAGATTCTCTGAATAATAATGGAAAAC
** * * *
5371323 GCTTCCCCTGGAACGCGTCTTTCATTTCAGAAGAGTTGGAACACTATGACATGACAAAGATTCTC
66 GCTTCCCCTGGAACGCGTCTTTCATTTTGGATGGGATGGAACACTATGACATGACAAAGATTCTC
5371388 TTAATAATAATGGAAAACACTTCCCCTGAATGTGT
131 TTAATAATAATGGAAAACACTTCCCCTGAATG-GT
* * * * * *
5371423 CTTTCATTTTGTATGGGATGGAACACTATAACATGGCATAGATTTTCTGAATAATAATAGAAAAC
1 CTTTCATTTCGGATGGGATGGAACACTATGACATGGCAGAGATTCTCTGAATAATAATGGAAAAC
* * *
5371488 GCTTCCCCTGAAACGCGCCTTTCATTTTGGATGGGATGGAACACTATGACATGACAGAGATTCT-
66 GCTTCCCCTGGAACGCGTCTTTCATTTTGGATGGGATGGAACACTATGACATGACAAAGATTCTC
* *
5371552 TTGAATAATAATGGAAAATGA-TTCCCTTGAAATGCGT
131 TT-AATAATAATGGAAAA-CACTTCCCCTG-AATG-GT
* * *
5371589 CTTTCATTTCGGATGGGATGAAACACTATGACATGACAGAGATTCTCTGAATAAAAATGGAAAA
1 CTTTCATTTCGGATGGGATGGAACACTATGACATGGCAGAGATTCTCTGAATAATAATGGAAAA
5371653 TGCTATGACA
Statistics
Matches: 341, Mismatches: 48, Indels: 8
0.86 0.12 0.02
Matches are distributed among these distances:
162 142 0.42
164 2 0.01
165 135 0.40
166 62 0.18
ACGTcount: A:0.34, C:0.18, G:0.20, T:0.29
Consensus pattern (164 bp):
CTTTCATTTCGGATGGGATGGAACACTATGACATGGCAGAGATTCTCTGAATAATAATGGAAAAC
GCTTCCCCTGGAACGCGTCTTTCATTTTGGATGGGATGGAACACTATGACATGACAAAGATTCTC
TTAATAATAATGGAAAACACTTCCCCTGAATGGT
Found at i:5371559 original size:248 final size:245
Alignment explanation
Indices: 5371112--5371652 Score: 706
Period size: 248 Copynumber: 2.2 Consensus size: 245
5371102 TTTAGGATGG
* * *
5371112 GATGGAACACTATGACATGATAGACATTCTCTGAATAATAATGGAAAACGCTTCCCAAGGAACGC
1 GATGGAACACTATGACATGACAGAGATTCTCTGAATAATAATGGAAAACACTTCCCAAGGAACGC
* *
5371177 GTCTTTCATTTTGGATGGGATGAAACACTATGACATGACAAAAAGTCTCTGAATAATAATGGAAA
66 GTCTTTCATTTTGGATGGGATGAAACACTATAACATGACAAAAAGTCTCTGAATAATAATAGAAA
**
5371242 ACACTTCCCCTGCAGCCTTTCATTTCGGATGGGATGGAACACTATGACATGGTAGAGATTCTCTG
131 ACACTTCCCCTGCAGCCTTTCATTTCGGATGGGATGGAACACTATGACATGACAGAGATTCTCTG
* * *
5371307 AATAATAACGGAATACGCTTCCCCTGGAACGCGTCTTTCATTTCAGAAGA
196 AATAATAACGGAAAACGATTCCCCTGAAACGCGTCTTTCATTTCAGAAGA
* * * ** * *
5371357 GTTGGAACACTATGACATGACAAAGATTCTCTTAATAATAATGGAAAACACTTCCC-CTGAATGT
1 GATGGAACACTATGACATGACAGAGATTCTCTGAATAATAATGGAAAACACTTCCCAAGGAACGC
* * * * * * *
5371421 GTCTTTCATTTTGTATGGGATGGAACACTATAACATGGCATAGATTTTCTGAATAATAATAGAAA
66 GTCTTTCATTTTGGATGGGATGAAACACTATAACATGACAAAAAGTCTCTGAATAATAATAGAAA
* * *
5371486 ACGCTTCCCCTGAAACGCGCCTTTCATTTTGGATGGGATGGAACACTATGACATGACAGAGATTC
131 ACACTTCCCCTG---C-AGCCTTTCATTTCGGATGGGATGGAACACTATGACATGACAGAGATTC
* * * * * * * *
5371551 TTTGAATAATAATGGAAAATGATTCCCTTGAAATGCGTCTTTCATTTCGGATGG
192 TCTGAATAATAACGGAAAACGATTCCCCTGAAACGCGTCTTTCATTTCAGAAGA
* *
5371605 GATGAAACACTATGACATGACAGAGATTCTCTGAATAAAAATGGAAAA
1 GATGGAACACTATGACATGACAGAGATTCTCTGAATAATAATGGAAAA
5371653 TGCTATGACA
Statistics
Matches: 252, Mismatches: 40, Indels: 5
0.85 0.13 0.02
Matches are distributed among these distances:
244 71 0.28
245 50 0.20
247 1 0.00
248 130 0.52
ACGTcount: A:0.34, C:0.18, G:0.20, T:0.28
Consensus pattern (245 bp):
GATGGAACACTATGACATGACAGAGATTCTCTGAATAATAATGGAAAACACTTCCCAAGGAACGC
GTCTTTCATTTTGGATGGGATGAAACACTATAACATGACAAAAAGTCTCTGAATAATAATAGAAA
ACACTTCCCCTGCAGCCTTTCATTTCGGATGGGATGGAACACTATGACATGACAGAGATTCTCTG
AATAATAACGGAAAACGATTCCCCTGAAACGCGTCTTTCATTTCAGAAGA
Found at i:5371654 original size:83 final size:82
Alignment explanation
Indices: 5371096--5371652 Score: 647
Period size: 83 Copynumber: 6.8 Consensus size: 82
5371086 AAACATGCGC
* * * *
5371096 CTTTAATTTAGGATGGGATGGAACACTATGACATGATAGACATTCTCTGAATAATAATGGAAAAC
1 CTTTCATTTCGGATGGGATGGAACACTATGACATGACAGAGATTCTCTGAATAATAATGGAAAAC
* **
5371161 GCTTCCCAAGGAACGCGT
66 GATTCCC-CTGAACGCGT
* * * * *
5371179 CTTTCATTTTGGATGGGATGAAACACTATGACATGACAAAAAGTCTCTGAATAATAATGGAAAAC
1 CTTTCATTTCGGATGGGATGGAACACTATGACATGACAGAGATTCTCTGAATAATAATGGAAAAC
*
5371244 -ACTTCCCCTGCA-GC--
66 GA-TTCCCCTGAACGCGT
** * *
5371258 CTTTCATTTCGGATGGGATGGAACACTATGACATGGTAGAGATTCTCTGAATAATAACGGAATAC
1 CTTTCATTTCGGATGGGATGGAACACTATGACATGACAGAGATTCTCTGAATAATAATGGAAAAC
*
5371323 GCTTCCCCTGGAACGCGT
66 GATTCCCCT-GAACGCGT
* * * * * *
5371341 CTTTCATTTCAGAAGAGTTGGAACACTATGACATGACAAAGATTCTCTTAATAATAATGGAAAAC
1 CTTTCATTTCGGATGGGATGGAACACTATGACATGACAGAGATTCTCTGAATAATAATGGAAAAC
* *
5371406 -ACTTCCCCTGAATGTGT
66 GA-TTCCCCTGAACGCGT
* * * * * * *
5371423 CTTTCATTTTGTATGGGATGGAACACTATAACATGGCATAGATTTTCTGAATAATAATAGAAAAC
1 CTTTCATTTCGGATGGGATGGAACACTATGACATGACAGAGATTCTCTGAATAATAATGGAAAAC
* *
5371488 GCTTCCCCTGAAACGCGC
66 GATTCCCCTG-AACGCGT
* * *
5371506 CTTTCATTTTGGATGGGATGGAACACTATGACATGACAGAGATTCTTTGAATAATAATGGAAAAT
1 CTTTCATTTCGGATGGGATGGAACACTATGACATGACAGAGATTCTCTGAATAATAATGGAAAAC
* *
5371571 GATTCCCTTGAAATGCGT
66 GATTCCCCTG-AACGCGT
* *
5371589 CTTTCATTTCGGATGGGATGAAACACTATGACATGACAGAGATTCTCTGAATAAAAATGGAAAA
1 CTTTCATTTCGGATGGGATGGAACACTATGACATGACAGAGATTCTCTGAATAATAATGGAAAA
5371653 TGCTATGACA
Statistics
Matches: 398, Mismatches: 67, Indels: 18
0.82 0.14 0.04
Matches are distributed among these distances:
79 63 0.16
80 2 0.01
81 4 0.01
82 69 0.17
83 260 0.65
ACGTcount: A:0.34, C:0.18, G:0.20, T:0.29
Consensus pattern (82 bp):
CTTTCATTTCGGATGGGATGGAACACTATGACATGACAGAGATTCTCTGAATAATAATGGAAAAC
GATTCCCCTGAACGCGT
Found at i:5372659 original size:30 final size:31
Alignment explanation
Indices: 5372620--5372689 Score: 97
Period size: 30 Copynumber: 2.3 Consensus size: 31
5372610 TCTTTCACAT
* *
5372620 ACCTTAAACAATAAATAAAAGC-ACGCATAC
1 ACCTAAAACAACAAATAAAAGCAACGCATAC
*
5372650 ACCTAAAACAACAAATAAAAGCATACGCGTAC
1 ACCTAAAACAACAAATAAAAGCA-ACGCATAC
5372682 ACCTAAAA
1 ACCTAAAA
5372690 TTCATTTTGT
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
30 20 0.57
32 15 0.43
ACGTcount: A:0.54, C:0.24, G:0.07, T:0.14
Consensus pattern (31 bp):
ACCTAAAACAACAAATAAAAGCAACGCATAC
Found at i:5377154 original size:21 final size:21
Alignment explanation
Indices: 5377121--5377173 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
5377111 ATTCTGACTA
5377121 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTCCAAAT
* * *
5377142 TCGCGTTGTGATTTTCCTAAT
1 TCGCATTGCGATTTTCCAAAT
*
5377163 TCGCAATGCGA
1 TCGCATTGCGA
5377174 ATACGTAAAT
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.21, C:0.23, G:0.19, T:0.38
Consensus pattern (21 bp):
TCGCATTGCGATTTTCCAAAT
Found at i:5377188 original size:20 final size:20
Alignment explanation
Indices: 5377163--5377276 Score: 174
Period size: 20 Copynumber: 5.7 Consensus size: 20
5377153 TTTTCCTAAT
5377163 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
* ** *
5377183 TCGCAACGCGAATTTGGAAAA
1 TCGCAATGCGAA-TACGTAAA
*
5377204 TCGCAATGCGATTACGTAAA
1 TCGCAATGCGAATACGTAAA
5377224 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
5377244 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
5377264 TCGCAATGCGAAT
1 TCGCAATGCGAAT
5377277 CTGACTATCG
Statistics
Matches: 83, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
20 68 0.82
21 15 0.18
ACGTcount: A:0.38, C:0.20, G:0.21, T:0.21
Consensus pattern (20 bp):
TCGCAATGCGAATACGTAAA
Found at i:5377260 original size:40 final size:40
Alignment explanation
Indices: 5377163--5377294 Score: 176
Period size: 40 Copynumber: 3.3 Consensus size: 40
5377153 TTTTCCTAAT
* **
5377163 TCGCAATGCGAATACGTAAATCGCAACGCGAATTTGGAAAA
1 TCGCAATGCGAATACGTAAATCGCAATGCGAA-TACGAAAA
* *
5377204 TCGCAATGCGATTACGTAAATCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAATCGCAATGCGAATACGAAAA
**
5377244 TCGCAATGCGAATACGTAAATCGCAATGCGAAT-CTGACTA
1 TCGCAATGCGAATACGTAAATCGCAATGCGAATAC-GAAAA
5377284 TCGCAATGCGA
1 TCGCAATGCGA
5377295 TTTACATAGT
Statistics
Matches: 81, Mismatches: 9, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
39 1 0.01
40 50 0.62
41 30 0.37
ACGTcount: A:0.36, C:0.21, G:0.21, T:0.21
Consensus pattern (40 bp):
TCGCAATGCGAATACGTAAATCGCAATGCGAATACGAAAA
Found at i:5377486 original size:22 final size:22
Alignment explanation
Indices: 5377461--5377536 Score: 116
Period size: 22 Copynumber: 3.5 Consensus size: 22
5377451 CACTCCCTAA
* *
5377461 GACGACATCCGTCCCCATCTCC
1 GACGAAATCAGTCCCCATCTCC
5377483 GACGAAATCAGTCCCCATCTCC
1 GACGAAATCAGTCCCCATCTCC
* *
5377505 GACGATATCAGTCTCCATCTCC
1 GACGAAATCAGTCCCCATCTCC
5377527 GACGAAATCA
1 GACGAAATCA
5377537 TTCACGGTCA
Statistics
Matches: 49, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 49 1.00
ACGTcount: A:0.26, C:0.39, G:0.14, T:0.20
Consensus pattern (22 bp):
GACGAAATCAGTCCCCATCTCC
Found at i:5377941 original size:20 final size:21
Alignment explanation
Indices: 5377874--5377941 Score: 72
Period size: 20 Copynumber: 3.4 Consensus size: 21
5377864 CGATTCTGTC
* *
5377874 GTTGCGATT-TTCA-TTTCGC
1 GTTGCGATTAGTCATTTTCGT
5377893 GTTGCGA-TAGTCATTTTCGT
1 GTTGCGATTAGTCATTTTCGT
**
5377913 GTTGCGATTA-TCATTTTTTT
1 GTTGCGATTAGTCATTTTCGT
5377933 GTTGCGATT
1 GTTGCGATT
5377942 TAAAGTTTCA
Statistics
Matches: 42, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
18 1 0.02
19 10 0.24
20 29 0.69
21 2 0.05
ACGTcount: A:0.13, C:0.15, G:0.22, T:0.50
Consensus pattern (21 bp):
GTTGCGATTAGTCATTTTCGT
Found at i:5379831 original size:20 final size:20
Alignment explanation
Indices: 5379806--5379947 Score: 123
Period size: 20 Copynumber: 7.8 Consensus size: 20
5379796 AATAGTTTAT
5379806 TATCGCAATGCGAAAATGAC
1 TATCGCAATGCGAAAATGAC
*
5379826 TATCGCAACGCGAAAATGAC
1 TATCGCAATGCGAAAATGAC
*
5379846 TATCGCAA--CG-AGA-GA-
1 TATCGCAATGCGAAAATGAC
*
5379861 -ATCGCAATGCG-AAATGAA
1 TATCGCAATGCGAAAATGAC
*
5379879 AATCGCAA--C-AACAA--A-
1 TATCGCAATGCGAA-AATGAC
*
5379894 -ATCGCAACGCGAAAATGAC
1 TATCGCAATGCGAAAATGAC
*
5379913 TATCGCAATGCGAAAATAAC
1 TATCGCAATGCGAAAATGAC
5379933 TATCGCAATGCGAAA
1 TATCGCAATGCGAAA
5379948 TGAAAATCGC
Statistics
Matches: 103, Mismatches: 5, Indels: 28
0.76 0.04 0.21
Matches are distributed among these distances:
14 14 0.14
16 10 0.10
17 8 0.08
18 5 0.05
19 7 0.07
20 59 0.57
ACGTcount: A:0.44, C:0.22, G:0.19, T:0.15
Consensus pattern (20 bp):
TATCGCAATGCGAAAATGAC
Found at i:5379884 original size:19 final size:19
Alignment explanation
Indices: 5379860--5379964 Score: 87
Period size: 20 Copynumber: 5.7 Consensus size: 19
5379850 GCAACGAGAG
5379860 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
5379879 AATCGCAA--C--AA-CAA
1 AATCGCAATGCGAAATGAA
* *
5379893 AATCGCAACGCGAAAATGAC
1 AATCGCAATGCG-AAATGAA
*
5379913 TATCGCAATGCGAAAAT-AA
1 AATCGCAATGCG-AAATGAA
*
5379932 CTATCGCAATGCGAAATGAA
1 -AATCGCAATGCGAAATGAA
*
5379952 AATCGCATTGCGA
1 AATCGCAATGCGA
5379965 TTCTCTCGTT
Statistics
Matches: 70, Mismatches: 8, Indels: 16
0.74 0.09 0.17
Matches are distributed among these distances:
14 10 0.14
15 2 0.03
16 1 0.01
17 1 0.01
19 26 0.37
20 30 0.43
ACGTcount: A:0.45, C:0.21, G:0.18, T:0.16
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:5379946 original size:73 final size:67
Alignment explanation
Indices: 5379827--5379958 Score: 192
Period size: 67 Copynumber: 1.9 Consensus size: 67
5379817 GAAAATGACT
* *
5379827 ATCGCAACGCGAAAATGACTATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACAACA
1 ATCGCAACGCGAAAATGACTATCGCAACGAAAAAATCGCAATGCGAAATGAAAATCGCAACAACA
5379892 AA
66 AA
5379894 ATCGCAACGCGAAAATGACTATCGCAATGCGAAAATAACTATCGCAATGCGAAATGAAAATCGCA
1 ATCGCAACGCGAAAATGACTATCGCAA--CG-AAA-AA--ATCGCAATGCGAAATGAAAATCGCA
5379959 TTGCGATTCT
Statistics
Matches: 57, Mismatches: 2, Indels: 6
0.88 0.03 0.09
Matches are distributed among these distances:
67 27 0.47
69 2 0.04
70 2 0.04
71 1 0.02
73 25 0.44
ACGTcount: A:0.45, C:0.22, G:0.19, T:0.14
Consensus pattern (67 bp):
ATCGCAACGCGAAAATGACTATCGCAACGAAAAAATCGCAATGCGAAATGAAAATCGCAACAACA
AA
Found at i:5380030 original size:20 final size:20
Alignment explanation
Indices: 5379976--5380059 Score: 87
Period size: 20 Copynumber: 4.2 Consensus size: 20
5379966 TCTCTCGTTA
* *
5379976 CGATAGTTAAATTCGCATTA
1 CGATAGTCAAATTCGCATTG
5379996 CGATAGTCAAATTCGCATTG
1 CGATAGTCAAATTCGCATTG
* ** *
5380016 CGATAGTTATTTTCGCGTTG
1 CGATAGTCAAATTCGCATTG
** *
5380036 CGATAGTCATTTTCGCGTTG
1 CGATAGTCAAATTCGCATTG
5380056 CGAT
1 CGAT
5380060 TTTAAGTTTC
Statistics
Matches: 57, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 57 1.00
ACGTcount: A:0.24, C:0.18, G:0.21, T:0.37
Consensus pattern (20 bp):
CGATAGTCAAATTCGCATTG
Found at i:5380031 original size:40 final size:40
Alignment explanation
Indices: 5379976--5380059 Score: 105
Period size: 40 Copynumber: 2.1 Consensus size: 40
5379966 TCTCTCGTTA
5379976 CGATAGTTAAATTCGCATTACGATAGTCAAATTCGCATTG
1 CGATAGTTAAATTCGCATTACGATAGTCAAATTCGCATTG
** * * ** *
5380016 CGATAGTTATTTTCGCGTTGCGATAGTCATTTTCGCGTTG
1 CGATAGTTAAATTCGCATTACGATAGTCAAATTCGCATTG
5380056 CGAT
1 CGAT
5380060 TTTAAGTTTC
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
40 37 1.00
ACGTcount: A:0.24, C:0.18, G:0.21, T:0.37
Consensus pattern (40 bp):
CGATAGTTAAATTCGCATTACGATAGTCAAATTCGCATTG
Found at i:5380069 original size:20 final size:20
Alignment explanation
Indices: 5380007--5380069 Score: 63
Period size: 20 Copynumber: 3.1 Consensus size: 20
5379997 GATAGTCAAA
* * *
5380007 TTCGCATTGCGATAGTTATT
1 TTCGCGTTGCGATAGTAAGT
* *
5380027 TTCGCGTTGCGATAGTCATT
1 TTCGCGTTGCGATAGTAAGT
**
5380047 TTCGCGTTGCGATTTTAAGT
1 TTCGCGTTGCGATAGTAAGT
5380067 TTC
1 TTC
5380070 AGATTCTATT
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 37 1.00
ACGTcount: A:0.16, C:0.17, G:0.22, T:0.44
Consensus pattern (20 bp):
TTCGCGTTGCGATAGTAAGT
Found at i:5380640 original size:42 final size:42
Alignment explanation
Indices: 5380540--5380650 Score: 118
Period size: 42 Copynumber: 2.6 Consensus size: 42
5380530 CCCGACTCAC
* * * *
5380540 CTGTCATCATTCAAGAGGCCTCC-CCTATCGTTCAAGAGGCCC
1 CTGTCATCATTCAAGAGTCC-CCTCCCACCGTTCAAGAGGCCA
* **
5380582 CTATCATCCCTCAAGAGTCCCCTCCCACCGTTCAAGAGGCCA
1 CTGTCATCATTCAAGAGTCCCCTCCCACCGTTCAAGAGGCCA
*
5380624 CTGTCATCATTGAAGAGGT-CCCTCCCA
1 CTGTCATCATTCAAGA-GTCCCCTCCCA
5380651 ACATTCTAGA
Statistics
Matches: 56, Mismatches: 11, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
41 2 0.04
42 52 0.93
43 2 0.04
ACGTcount: A:0.23, C:0.38, G:0.17, T:0.23
Consensus pattern (42 bp):
CTGTCATCATTCAAGAGTCCCCTCCCACCGTTCAAGAGGCCA
Found at i:5382239 original size:33 final size:33
Alignment explanation
Indices: 5382196--5382315 Score: 123
Period size: 33 Copynumber: 3.4 Consensus size: 33
5382186 ACAAGATAAA
**
5382196 TTCGCGTTGCGATTCACTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTCACTCGTTGCGATAGTCAT
* *
5382229 TTCGCATTGCGATTCTCTCGTTGCGATAGTCAT
1 TTCGCGTTGCGATTCACTCGTTGCGATAGTCAT
5382262 TTCCGCGTTGCGATAGTCAATTCTGCGTTGCGATAGTCAT
1 TT-CGCGTTGCGAT--TC-A--CT-CGTTGCGATAGTCAT
*
5382302 TTCCGTGTTGCGAT
1 TT-CGCGTTGCGAT
5382316 AGTCATATTT
Statistics
Matches: 73, Mismatches: 7, Indels: 7
0.84 0.08 0.08
Matches are distributed among these distances:
33 31 0.42
34 10 0.14
36 2 0.03
39 2 0.03
40 28 0.38
ACGTcount: A:0.14, C:0.23, G:0.23, T:0.39
Consensus pattern (33 bp):
TTCGCGTTGCGATTCACTCGTTGCGATAGTCAT
Found at i:5382296 original size:40 final size:40
Alignment explanation
Indices: 5382247--5382331 Score: 145
Period size: 40 Copynumber: 2.1 Consensus size: 40
5382237 GCGATTCTCT
5382247 CGTTGCGATAGTCATTTCCGCGTTGCGATAGTCA-ATTCTG
1 CGTTGCGATAGTCATTTCCGCGTTGCGATAGTCATATT-TG
*
5382287 CGTTGCGATAGTCATTTCCGTGTTGCGATAGTCATATTTG
1 CGTTGCGATAGTCATTTCCGCGTTGCGATAGTCATATTTG
5382327 CGTTG
1 CGTTG
5382332 TGATTTCCGC
Statistics
Matches: 43, Mismatches: 1, Indels: 2
0.93 0.02 0.04
Matches are distributed among these distances:
40 40 0.93
41 3 0.07
ACGTcount: A:0.16, C:0.20, G:0.26, T:0.38
Consensus pattern (40 bp):
CGTTGCGATAGTCATTTCCGCGTTGCGATAGTCATATTTG
Found at i:5382331 original size:20 final size:20
Alignment explanation
Indices: 5382247--5382321 Score: 123
Period size: 20 Copynumber: 3.8 Consensus size: 20
5382237 GCGATTCTCT
5382247 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATAGTCATTTCCG
* *
5382267 CGTTGCGATAGTCAATTCTG
1 CGTTGCGATAGTCATTTCCG
5382287 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATAGTCATTTCCG
*
5382307 TGTTGCGATAGTCAT
1 CGTTGCGATAGTCAT
5382322 ATTTGCGTTG
Statistics
Matches: 50, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 50 1.00
ACGTcount: A:0.17, C:0.21, G:0.25, T:0.36
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTCCG
Found at i:5385512 original size:3 final size:3
Alignment explanation
Indices: 5385504--5385580 Score: 145
Period size: 3 Copynumber: 25.7 Consensus size: 3
5385494 ATTATATATT
*
5385504 TAA TAA TAA TAA TAA TAA TAA TGA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
5385552 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
5385581 TGGATAAAAA
Statistics
Matches: 72, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
3 72 1.00
ACGTcount: A:0.65, C:0.00, G:0.01, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:5386145 original size:113 final size:113
Alignment explanation
Indices: 5385898--5386458 Score: 905
Period size: 113 Copynumber: 5.0 Consensus size: 113
5385888 ATAGAATTAT
* * * *
5385898 GCAAAAAGTTGAACAAGTTCTTCTTATTATGAACTTCTTCTTTCTTCTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
* *
5385963 ATTATGAAC-TTCTCTGGAAAAGATAATCCATCAATTGATGAATTCAG
66 ATTATGAACTTTCTCTGGAAAAGATAATCCATCAAATGATGGATTCAG
*
5386010 GTAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
* *
5386075 ATTATGAACTTTCTCTGGAAAAGATGACCCATCAAATGATGGATTCAG
66 ATTATGAACTTTCTCTGGAAAAGATAATCCATCAAATGATGGATTCAG
*
5386123 GTAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
* *
5386188 ATTATGAACTTTCTCTGGAAAAGATGATCCATCAAATGATGGATT-TG
66 ATTATGAACTTTCTCTGGAAAAGATAATCCATCAAATGATGGATTCAG
*
5386235 AGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCT
1 -GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCT
* * *
5386300 CATTATGAACCTTCTCTGGCAAAA-ATAATCCATCAAGTGATGAATTCAG
65 CATTATGAACTTTCTCTGG-AAAAGATAATCCATCAAATGATGGATTCAG
*
5386349 ACAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
*
5386414 ATTATGAACTTTCTCTGGCAAAA-ATAATCCATCAAATGATAGATT
66 ATTATGAACTTTCTCTGG-AAAAGATAATCCATCAAATGATGGATT
5386459 TGAATCTTTG
Statistics
Matches: 421, Mismatches: 24, Indels: 7
0.93 0.05 0.02
Matches are distributed among these distances:
112 70 0.17
113 346 0.82
114 5 0.01
ACGTcount: A:0.30, C:0.19, G:0.14, T:0.37
Consensus pattern (113 bp):
GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
ATTATGAACTTTCTCTGGAAAAGATAATCCATCAAATGATGGATTCAG
Found at i:5387266 original size:82 final size:82
Alignment explanation
Indices: 5387110--5388031 Score: 1492
Period size: 82 Copynumber: 11.2 Consensus size: 82
5387100 TTTACTATGA
* * * * *
5387110 GCAAATTCATCTTCCAAATTCAATGATTGGTTTTTTGGGTTCATACCAAACCAGATAACTCAAAG
1 GCAAATTCATCTTCTAAATTCAATGATT-G--TTCT--GTCCA-ACCAGATCAGATAACTCAAAG
5387175 AACACTTCCAGAAGATGCTATTG
60 AACACTTCCAGAAGATGCTATTG
*
5387198 GCAAATTCATCTTCTAAACTCAATGATTGTTCTGTCCAACCAGATCAGATAACTCAAAGAACACT
1 GCAAATTCATCTTCTAAATTCAATGATTGTTCTGTCCAACCAGATCAGATAACTCAAAGAACACT
5387263 TCCAGAAGATGCTA-TG
66 TCCAGAAGATGCTATTG
* * * *
5387279 AACACATTCTTCTTCCAAATTCAATGATTGTTCTGTCCAACCAGATCAGATAACTCAAAGAACAC
1 -GCAAATTCATCTTCTAAATTCAATGATTGTTCTGTCCAACCAGATCAGATAACTCAAAGAACAC
5387344 TTCCAGAAGATGCTATTG
65 TTCCAGAAGATGCTATTG
5387362 GCAAATTCATCTTCTAAATTCAATGATTGTTCTGTCCAACCAGATCAGATAACTCAAAGAACACT
1 GCAAATTCATCTTCTAAATTCAATGATTGTTCTGTCCAACCAGATCAGATAACTCAAAGAACACT
5387427 TCCAGAAGATGCTATTG
66 TCCAGAAGATGCTATTG
* *
5387444 GCAAATTCATCTTCTAAACTCAATGATTGTTCTGTCCAACCAGATCAGATAACTCAAAGAACGCT
1 GCAAATTCATCTTCTAAATTCAATGATTGTTCTGTCCAACCAGATCAGATAACTCAAAGAACACT
5387509 TCCAGAAGATGCTATTG
66 TCCAGAAGATGCTATTG
* *
5387526 GCAAATTCATCTTCTAAACTCAATGATTATTCTGTCCAACCAGATCAGATAACTCAAAGAACACT
1 GCAAATTCATCTTCTAAATTCAATGATTGTTCTGTCCAACCAGATCAGATAACTCAAAGAACACT
5387591 TCCAGAAGATGC-ATTTG
66 TCCAGAAGATGCTA-TTG
5387608 GCAAATTCATCTTCTAAATTCAATGATTGTTCTGTCCAACCAGATCAGATAACTCAAAGAACACT
1 GCAAATTCATCTTCTAAATTCAATGATTGTTCTGTCCAACCAGATCAGATAACTCAAAGAACACT
5387673 TCCAGAAGATGCTATTG
66 TCCAGAAGATGCTATTG
* *
5387690 GCAAATTCATCTTCTAAACTCAATGATTATTCTGTCCAACCAGATCAGATAACTCAAAGAACACT
1 GCAAATTCATCTTCTAAATTCAATGATTGTTCTGTCCAACCAGATCAGATAACTCAAAGAACACT
5387755 TCCAGAAGATGCTATTG
66 TCCAGAAGATGCTATTG
5387772 GCAAATTCATCTTCTAAATTCAATGATTGTTCTGTCCAACCAGATCAGATAACTCAAAGAACACT
1 GCAAATTCATCTTCTAAATTCAATGATTGTTCTGTCCAACCAGATCAGATAACTCAAAGAACACT
5387837 TCCAGAAGATGCTATTG
66 TCCAGAAGATGCTATTG
* *
5387854 GCAAATTCATATTCTAAATTCAATGATTTTTCTGTCCAACCAGATCAGATAACTCAAAGAACACT
1 GCAAATTCATCTTCTAAATTCAATGATTGTTCTGTCCAACCAGATCAGATAACTCAAAGAACACT
*
5387919 TCCAGAAGATGCTATTA
66 TCCAGAAGATGCTATTG
* * * * *
5387936 ACACATTCTTCTTCCAAATTTAATGATTGTTTCTG-CCAAACCAGATCAGATAACTCAAAGAACA
1 GCAAATTCATCTTCTAAATTCAATGATTG-TTCTGTCC-AACCAGATCAGATAACTCAAAGAACA
5388000 CTTCCAGAAGATGCTA-TG
64 CTTCCAGAAGATGCTATTG
*
5388018 AGCACATTCATCTT
1 -GCAAATTCATCTT
5388032 TCATTTAATT
Statistics
Matches: 789, Mismatches: 38, Indels: 19
0.93 0.04 0.02
Matches are distributed among these distances:
81 3 0.00
82 691 0.88
83 65 0.08
85 3 0.00
87 1 0.00
88 26 0.03
ACGTcount: A:0.35, C:0.23, G:0.13, T:0.29
Consensus pattern (82 bp):
GCAAATTCATCTTCTAAATTCAATGATTGTTCTGTCCAACCAGATCAGATAACTCAAAGAACACT
TCCAGAAGATGCTATTG
Found at i:5389192 original size:17 final size:15
Alignment explanation
Indices: 5389170--5389235 Score: 78
Period size: 16 Copynumber: 4.1 Consensus size: 15
5389160 CTTGACCCCC
5389170 TTTCTTTCTCTTTTTTT
1 TTTCTTT-T-TTTTTTT
*
5389187 TTTCTTTTTTCTTTT
1 TTTCTTTTTTTTTTT
5389202 TTTCTATTTTTATTTTT
1 TTTCT-TTTTT-TTTTT
5389219 TTTCTTTTTTCTTTTT
1 TTTCTTTTTT-TTTTT
5389235 T
1 T
5389236 CTTCAAGCAT
Statistics
Matches: 44, Mismatches: 3, Indels: 5
0.85 0.06 0.10
Matches are distributed among these distances:
15 11 0.25
16 17 0.39
17 16 0.36
ACGTcount: A:0.03, C:0.12, G:0.00, T:0.85
Consensus pattern (15 bp):
TTTCTTTTTTTTTTT
Found at i:5389196 original size:7 final size:7
Alignment explanation
Indices: 5389169--5389238 Score: 70
Period size: 7 Copynumber: 9.4 Consensus size: 7
5389159 CCTTGACCCC
5389169 CTTTCTTT
1 CTTT-TTT
*
5389177 CTCTTTT
1 CTTTTTT
5389184 -TTTTTT
1 CTTTTTT
5389190 CTTTTTT
1 CTTTTTT
5389197 CTTTTTTT
1 C-TTTTTT
5389205 CTATTTTTAT
1 C--TTTTT-T
*
5389215 TTTTTTT
1 CTTTTTT
5389222 CTTTTTT
1 CTTTTTT
5389229 CTTTTTT
1 CTTTTTT
5389236 CTT
1 CTT
5389239 CAAGCATAAT
Statistics
Matches: 53, Mismatches: 5, Indels: 9
0.79 0.07 0.13
Matches are distributed among these distances:
6 5 0.09
7 27 0.51
8 15 0.28
9 5 0.09
10 1 0.02
ACGTcount: A:0.03, C:0.14, G:0.00, T:0.83
Consensus pattern (7 bp):
CTTTTTT
Found at i:5400134 original size:15 final size:14
Alignment explanation
Indices: 5400092--5400136 Score: 56
Period size: 15 Copynumber: 3.1 Consensus size: 14
5400082 CAGAAAGAAC
5400092 TTAATTTAATAAT-
1 TTAATTTAATAATA
*
5400105 TTAAATTAATAAATA
1 TTAATTTAAT-AATA
5400120 TTAATTTAAATAATA
1 TTAATTT-AATAATA
5400135 TT
1 TT
5400137 GTTTAATTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
13 9 0.33
14 3 0.11
15 12 0.44
16 3 0.11
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (14 bp):
TTAATTTAATAATA
Found at i:5400759 original size:151 final size:154
Alignment explanation
Indices: 5400580--5400884 Score: 523
Period size: 155 Copynumber: 2.0 Consensus size: 154
5400570 TAAAATAAAA
5400580 AAATTAAAATTAAAGATTTGAATTAAAAGTATTATAAAATCGATTTTAGTGACTAAAATGT-AAA
1 AAATTAAAATTAAAGATTTGAATTAAAAGTATTAT-AAATCGA-TTTAGTGACTAAAATGTAAAA
5400644 C-AT-AA-AGAGGGATTACAGAAAGGGTTTAACATTTA-AAAATTACACAAAATAGCCCTCCGCA
64 CAATAAACAGAGGGATTACAGAAAGGGTTTAACATTTATAAAATTACAC-AAATAGCCCTCCGCA
5400705 AAACGGCGTCGTTGGGAAGGGCTATAG
128 AAACGGCGTCGTTGGGAAGGGCTATAG
5400732 AAATTAAAATT-AAGATTTGAATTAAAAGTATTATAAATCGATTTAGTGACTAAAATGTAAAACA
1 AAATTAAAATTAAAGATTTGAATTAAAAGTATTATAAATCGATTTAGTGACTAAAATGTAAAACA
5400796 TATAAAACAGAGGGATTACAGAAAGGGTTTAACATTTATAAAATTACACAAATAGCCCTCCGCAA
66 -AT-AAACAGAGGGATTACAGAAAGGGTTTAACATTTATAAAATTACACAAATAGCCCTCCGCAA
5400861 AACGGCGTCGTTGGGAAGGGCTAT
129 AACGGCGTCGTTGGGAAGGGCTAT
5400885 TTAATGCCCA
Statistics
Matches: 146, Mismatches: 0, Indels: 11
0.93 0.00 0.07
Matches are distributed among these distances:
149 17 0.12
150 11 0.08
151 23 0.16
152 13 0.09
154 2 0.01
155 70 0.48
156 10 0.07
ACGTcount: A:0.44, C:0.11, G:0.18, T:0.27
Consensus pattern (154 bp):
AAATTAAAATTAAAGATTTGAATTAAAAGTATTATAAATCGATTTAGTGACTAAAATGTAAAACA
ATAAACAGAGGGATTACAGAAAGGGTTTAACATTTATAAAATTACACAAATAGCCCTCCGCAAAA
CGGCGTCGTTGGGAAGGGCTATAG
Found at i:5401797 original size:11 final size:11
Alignment explanation
Indices: 5401776--5401805 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
5401766 TGTAATTAAT
5401776 TATTT-ATATA
1 TATTTAATATA
5401786 TATTTAATATA
1 TATTTAATATA
5401797 TATTTAATA
1 TATTTAATA
5401806 ATAATAATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 5 0.26
11 14 0.74
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (11 bp):
TATTTAATATA
Found at i:5401809 original size:3 final size:3
Alignment explanation
Indices: 5401801--5401864 Score: 112
Period size: 3 Copynumber: 21.7 Consensus size: 3
5401791 AATATATATT
*
5401801 TAA TAA TAA TAA TAA TAA TGA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
5401849 TAA TAA TAA T-A TAA TA
1 TAA TAA TAA TAA TAA TA
5401865 TGGATAAAAA
Statistics
Matches: 58, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
2 2 0.03
3 56 0.97
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:5403704 original size:79 final size:80
Alignment explanation
Indices: 5403572--5403731 Score: 313
Period size: 79 Copynumber: 2.0 Consensus size: 80
5403562 AACGTAACAT
5403572 TAGAGGTTTCATAAGTTAACTTTTTTAATGACAGTTTTAGTTGAAGATTCATGGGTAAAGGCATA
1 TAGAGGTTTCATAAGTTAACTTTTTTAATGACAGTTTTAGTTGAAGATTCATGGGTAAAGGCATA
5403637 TATTGTAAAACACCA
66 TATTGTAAAACACCA
5403652 TAGA-GTTTCATAAGTTAACTTTTTTAATGACAGTTTTAGTTGAAGATTCATGGGTAAAGGCATA
1 TAGAGGTTTCATAAGTTAACTTTTTTAATGACAGTTTTAGTTGAAGATTCATGGGTAAAGGCATA
5403716 TATTGTAAAACACCA
66 TATTGTAAAACACCA
5403731 T
1 T
5403732 GAACATTCTC
Statistics
Matches: 80, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
79 76 0.95
80 4 0.05
ACGTcount: A:0.35, C:0.10, G:0.18, T:0.37
Consensus pattern (80 bp):
TAGAGGTTTCATAAGTTAACTTTTTTAATGACAGTTTTAGTTGAAGATTCATGGGTAAAGGCATA
TATTGTAAAACACCA
Found at i:5404101 original size:20 final size:20
Alignment explanation
Indices: 5404028--5404113 Score: 104
Period size: 20 Copynumber: 4.4 Consensus size: 20
5404018 GAAATTCAGT
5404028 ATTGCGATAGTCAGAAT--C
1 ATTGCGATAGTCAGAATCGC
* * *
5404046 TTTGCGATAGTCAAAATCTC
1 ATTGCGATAGTCAGAATCGC
* *
5404066 GTTGCGATAGTCAGATTCGC
1 ATTGCGATAGTCAGAATCGC
*
5404086 ATTGCGATAGTCAGATTCGC
1 ATTGCGATAGTCAGAATCGC
5404106 ATTGCGAT
1 ATTGCGAT
5404114 TTACGTAATC
Statistics
Matches: 59, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
18 15 0.25
20 44 0.75
ACGTcount: A:0.27, C:0.19, G:0.23, T:0.31
Consensus pattern (20 bp):
ATTGCGATAGTCAGAATCGC
Found at i:5404125 original size:20 final size:20
Alignment explanation
Indices: 5404102--5404173 Score: 83
Period size: 20 Copynumber: 3.5 Consensus size: 20
5404092 ATAGTCAGAT
5404102 TCGCATTGCGATTTACGTAA
1 TCGCATTGCGATTTACGTAA
* *
5404122 TCGCATTGCGATTTTTC-AAA
1 TCGCATTGCGA-TTTACGTAA
* *
5404142 TTCGCGTTGCGATTTACGTAT
1 -TCGCATTGCGATTTACGTAA
5404163 TCGCATTGCGA
1 TCGCATTGCGA
5404174 ATTAGGAAAA
Statistics
Matches: 42, Mismatches: 7, Indels: 6
0.76 0.13 0.11
Matches are distributed among these distances:
20 27 0.64
21 15 0.36
ACGTcount: A:0.21, C:0.21, G:0.21, T:0.38
Consensus pattern (20 bp):
TCGCATTGCGATTTACGTAA
Found at i:5404153 original size:41 final size:40
Alignment explanation
Indices: 5404082--5404173 Score: 130
Period size: 41 Copynumber: 2.3 Consensus size: 40
5404072 ATAGTCAGAT
*
5404082 TCGCATTGCGATAGTCAGATTCGCATTGCGATTTACGTAA
1 TCGCATTGCGATAGTCAAATTCGCATTGCGATTTACGTAA
** * *
5404122 TCGCATTGCGATTTTTCAAATTCGCGTTGCGATTTACGTAT
1 TCGCATTGCGA-TAGTCAAATTCGCATTGCGATTTACGTAA
5404163 TCGCATTGCGA
1 TCGCATTGCGA
5404174 ATTAGGAAAA
Statistics
Matches: 46, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
40 11 0.24
41 35 0.76
ACGTcount: A:0.22, C:0.21, G:0.22, T:0.36
Consensus pattern (40 bp):
TCGCATTGCGATAGTCAAATTCGCATTGCGATTTACGTAA
Found at i:5408624 original size:13 final size:13
Alignment explanation
Indices: 5408606--5408632 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
5408596 AGTCTATCGG
5408606 ATTCGTATGATCA
1 ATTCGTATGATCA
5408619 ATTCGTATGATCA
1 ATTCGTATGATCA
5408632 A
1 A
5408633 CTCATCATCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.37
Consensus pattern (13 bp):
ATTCGTATGATCA
Found at i:5417977 original size:106 final size:106
Alignment explanation
Indices: 5417792--5418006 Score: 430
Period size: 106 Copynumber: 2.0 Consensus size: 106
5417782 CTATAATGGT
5417792 ATTATGTTAGCAAGTCTTAACCTGATGGTGGGATCAGGGATGGATCAAGGCAGAGGCGGATGAGG
1 ATTATGTTAGCAAGTCTTAACCTGATGGTGGGATCAGGGATGGATCAAGGCAGAGGCGGATGAGG
5417857 ATGGTCGCCCCTAAAATATATAAAATTATCATATATCTTAG
66 ATGGTCGCCCCTAAAATATATAAAATTATCATATATCTTAG
5417898 ATTATGTTAGCAAGTCTTAACCTGATGGTGGGATCAGGGATGGATCAAGGCAGAGGCGGATGAGG
1 ATTATGTTAGCAAGTCTTAACCTGATGGTGGGATCAGGGATGGATCAAGGCAGAGGCGGATGAGG
5417963 ATGGTCGCCCCTAAAATATATAAAATTATCATATATCTTAG
66 ATGGTCGCCCCTAAAATATATAAAATTATCATATATCTTAG
5418004 ATT
1 ATT
5418007 TTTTTATTTA
Statistics
Matches: 109, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
106 109 1.00
ACGTcount: A:0.32, C:0.14, G:0.26, T:0.28
Consensus pattern (106 bp):
ATTATGTTAGCAAGTCTTAACCTGATGGTGGGATCAGGGATGGATCAAGGCAGAGGCGGATGAGG
ATGGTCGCCCCTAAAATATATAAAATTATCATATATCTTAG
Found at i:5418042 original size:17 final size:19
Alignment explanation
Indices: 5418013--5418053 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 19
5418003 GATTTTTTTA
*
5418013 TTTATTTTCTA-TTGAAAT
1 TTTATTTTCTATTTAAAAT
5418031 TTTATTTT-TATTTAAAAT
1 TTTATTTTCTATTTAAAAT
5418049 TTTAT
1 TTTAT
5418054 AAATTTAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 2 0.10
18 19 0.90
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.66
Consensus pattern (19 bp):
TTTATTTTCTATTTAAAAT
Found at i:5421218 original size:17 final size:17
Alignment explanation
Indices: 5421174--5421218 Score: 72
Period size: 17 Copynumber: 2.6 Consensus size: 17
5421164 TTCTTTACTT
* *
5421174 GTATTTTGTTCCTTGTA
1 GTATTTTGTTTCTTATA
5421191 GTATTTTGTTTCTTATA
1 GTATTTTGTTTCTTATA
5421208 GTATTTTGTTT
1 GTATTTTGTTT
5421219 TTAATCATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
17 26 1.00
ACGTcount: A:0.13, C:0.07, G:0.16, T:0.64
Consensus pattern (17 bp):
GTATTTTGTTTCTTATA
Found at i:5424308 original size:21 final size:21
Alignment explanation
Indices: 5424282--5424398 Score: 180
Period size: 21 Copynumber: 5.6 Consensus size: 21
5424272 GTTTCCAGAT
* *
5424282 TCGCAACGCGAACTTCGACTA
1 TCGCAATGCGAACTTGGACTA
5424303 TCGCAATGCGAACTTGGACTA
1 TCGCAATGCGAACTTGGACTA
* *
5424324 TCGCAACGCGAACTTGGATTA
1 TCGCAATGCGAACTTGGACTA
*
5424345 TCGCAATGCAAACTTGGACTA
1 TCGCAATGCGAACTTGGACTA
5424366 TCGCAATGCGAACTTGGACTA
1 TCGCAATGCGAACTTGGACTA
*
5424387 TCGCAATACGAA
1 TCGCAATGCGAA
5424399 TATGTAAATT
Statistics
Matches: 87, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 87 1.00
ACGTcount: A:0.31, C:0.26, G:0.21, T:0.22
Consensus pattern (21 bp):
TCGCAATGCGAACTTGGACTA
Found at i:5424558 original size:6 final size:6
Alignment explanation
Indices: 5424547--5424593 Score: 87
Period size: 6 Copynumber: 8.0 Consensus size: 6
5424537 GAAGACACGT
5424547 ACGACC ACGACC ACGACC ACGACC ACGACC ACGACC ACGACC -CGACC
1 ACGACC ACGACC ACGACC ACGACC ACGACC ACGACC ACGACC ACGACC
5424594 CGAGACGAGA
Statistics
Matches: 41, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
5 5 0.12
6 36 0.88
ACGTcount: A:0.32, C:0.51, G:0.17, T:0.00
Consensus pattern (6 bp):
ACGACC
Found at i:5425127 original size:12 final size:11
Alignment explanation
Indices: 5425095--5425130 Score: 56
Period size: 10 Copynumber: 3.3 Consensus size: 11
5425085 TCTCGTCTCG
5425095 GGTCGGGTCG-
1 GGTCGGGTCGT
5425105 GGTCGGGTCGT
1 GGTCGGGTCGT
5425116 GGTCGTGGTCGT
1 GGTCG-GGTCGT
5425128 GGT
1 GGT
5425131 AATGGTAATA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 10 0.42
11 5 0.21
12 9 0.38
ACGTcount: A:0.00, C:0.17, G:0.56, T:0.28
Consensus pattern (11 bp):
GGTCGGGTCGT
Found at i:5425130 original size:6 final size:5
Alignment explanation
Indices: 5425092--5425126 Score: 52
Period size: 5 Copynumber: 6.6 Consensus size: 5
5425082 CCGTCTCGTC
5425092 TCGGG TCGGG TCGGG TCGGG TCGTGG TCGTGG TCG
1 TCGGG TCGGG TCGGG TCGGG TCG-GG TCG-GG TCG
5425127 TGGTAATGGT
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 18 0.62
6 11 0.38
ACGTcount: A:0.00, C:0.20, G:0.54, T:0.26
Consensus pattern (5 bp):
TCGGG
Found at i:5425278 original size:21 final size:20
Alignment explanation
Indices: 5425254--5425342 Score: 92
Period size: 21 Copynumber: 4.3 Consensus size: 20
5425244 TTTGGAATAA
5425254 ATCGCAATGCGAACTTCGACT
1 ATCGCAATGCGAA-TTCGACT
*
5425275 ATCGCAATGCGAATAT-GTA-A
1 ATCGCAATGCGAAT-TCG-ACT
5425295 ATCGCAATGCGAACTTCGACT
1 ATCGCAATGCGAA-TTCGACT
* *
5425316 ATCGCATTGCGATAGTCGACT
1 ATCGCAATGCGA-ATTCGACT
5425337 ATCGCA
1 ATCGCA
5425343 TTACGATTTA
Statistics
Matches: 58, Mismatches: 4, Indels: 12
0.78 0.05 0.16
Matches are distributed among these distances:
20 17 0.29
21 40 0.69
22 1 0.02
ACGTcount: A:0.30, C:0.25, G:0.20, T:0.25
Consensus pattern (20 bp):
ATCGCAATGCGAATTCGACT
Found at i:5425343 original size:21 final size:21
Alignment explanation
Indices: 5425310--5425373 Score: 71
Period size: 21 Copynumber: 3.1 Consensus size: 21
5425300 AATGCGAACT
5425310 TCGACTATCGCATTGCGATAG
1 TCGACTATCGCATTGCGATAG
*
5425331 TCGACTATCGCATTACGAT--
1 TCGACTATCGCATTGCGATAG
*
5425350 T-TACATATTCGCATTGCGATAG
1 TCGAC-TA-TCGCATTGCGATAG
5425372 TC
1 TC
5425374 CAAGTTCCCA
Statistics
Matches: 35, Mismatches: 3, Indels: 8
0.76 0.07 0.17
Matches are distributed among these distances:
18 2 0.06
19 3 0.09
20 11 0.31
21 18 0.51
22 1 0.03
ACGTcount: A:0.25, C:0.23, G:0.19, T:0.33
Consensus pattern (21 bp):
TCGACTATCGCATTGCGATAG
Found at i:5425409 original size:21 final size:21
Alignment explanation
Indices: 5425381--5425543 Score: 206
Period size: 21 Copynumber: 7.8 Consensus size: 21
5425371 GTCCAAGTTC
5425381 CCAAGTTCGCATTGCGATAGT
1 CCAAGTTCGCATTGCGATAGT
* *
5425402 CGAAGTTCGCGTTGCGATAGT
1 CCAAGTTCGCATTGCGATAGT
5425423 CCAAGTTCGCATTGCGATAGT
1 CCAAGTTCGCATTGCGATAGT
* * *
5425444 -CGACTATCGCATTGCGAT-TT
1 CCAAGT-TCGCATTGCGATAGT
*
5425464 ACATA-TTCGCATTGCGATAGT
1 CCA-AGTTCGCATTGCGATAGT
*
5425485 CCAAGTTCGCATTGTGATAGT
1 CCAAGTTCGCATTGCGATAGT
5425506 CCAAGTTCGCATTGCGATAGT
1 CCAAGTTCGCATTGCGATAGT
* *
5425527 CGAAGTTCGCGTTGCGA
1 CCAAGTTCGCATTGCGA
5425544 ATCTAGAAAC
Statistics
Matches: 123, Mismatches: 14, Indels: 10
0.84 0.10 0.07
Matches are distributed among these distances:
20 17 0.14
21 105 0.85
22 1 0.01
ACGTcount: A:0.23, C:0.22, G:0.25, T:0.30
Consensus pattern (21 bp):
CCAAGTTCGCATTGCGATAGT
Found at i:5425485 original size:62 final size:62
Alignment explanation
Indices: 5425407--5425523 Score: 182
Period size: 62 Copynumber: 1.9 Consensus size: 62
5425397 ATAGTCGAAG
* *
5425407 TTCGCGTTGCGATAGTCCAAGTTCGCATTGCGATAGT-CGACTATCGCATTGCGATTTACATA
1 TTCGCATTGCGATAGTCCAAGTTCGCATTGCGATAGTCCAACT-TCGCATTGCGATTTACATA
* *
5425469 TTCGCATTGCGATAGTCCAAGTTCGCATTGTGATAGTCCAAGTTCGCATTGCGAT
1 TTCGCATTGCGATAGTCCAAGTTCGCATTGCGATAGTCCAACTTCGCATTGCGAT
5425524 AGTCGAAGTT
Statistics
Matches: 50, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
62 47 0.94
63 3 0.06
ACGTcount: A:0.22, C:0.22, G:0.23, T:0.32
Consensus pattern (62 bp):
TTCGCATTGCGATAGTCCAAGTTCGCATTGCGATAGTCCAACTTCGCATTGCGATTTACATA
Found at i:5426060 original size:29 final size:30
Alignment explanation
Indices: 5426003--5426062 Score: 79
Period size: 29 Copynumber: 2.0 Consensus size: 30
5425993 TATATTGTTA
5426003 TTTAATATTTAATGATAAAATATTTATTTAT
1 TTTAATATTTAAT-ATAAAATATTTATTTAT
*
5426034 TTTAATATTTTAAT-TAAATTA-TTATTTAT
1 TTTAATA-TTTAATATAAAATATTTATTTAT
5426063 AACTTTTAGA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
29 8 0.30
30 6 0.22
31 7 0.26
32 6 0.22
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (30 bp):
TTTAATATTTAATATAAAATATTTATTTAT
Found at i:5426701 original size:4 final size:4
Alignment explanation
Indices: 5426692--5426773 Score: 69
Period size: 4 Copynumber: 20.0 Consensus size: 4
5426682 GGAGGTAACC
** * *
5426692 TTTA TTTA TTTA TTTA TTT- TGAA TTT- TTTG TTTA TTTA TTTCAA ATTA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT--A TTTA
*
5426740 TTTA TTTA TTTTGA ATTA TTTA TTTA TTTA TTTA
1 TTTA TTTA -TTT-A TTTA TTTA TTTA TTTA TTTA
5426774 ATTGAATGGG
Statistics
Matches: 63, Mismatches: 9, Indels: 12
0.75 0.11 0.14
Matches are distributed among these distances:
3 4 0.06
4 50 0.79
5 5 0.08
6 4 0.06
ACGTcount: A:0.26, C:0.01, G:0.04, T:0.70
Consensus pattern (4 bp):
TTTA
Found at i:5426725 original size:22 final size:21
Alignment explanation
Indices: 5426696--5426772 Score: 88
Period size: 22 Copynumber: 3.7 Consensus size: 21
5426686 GTAACCTTTA
5426696 TTTATTTATTTATTTTGAATTT
1 TTTATTTATTTATTTTGAA-TT
* *
5426718 TTTGTTTATTTA-TTTCAA--
1 TTTATTTATTTATTTTGAATT
*
5426736 ATTATTTATTTATTTTGAATT
1 TTTATTTATTTATTTTGAATT
5426757 ATTTATTTATTTATTT
1 -TTTATTTATTTATTT
5426773 AATTGAATGG
Statistics
Matches: 45, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
18 10 0.22
19 5 0.11
21 5 0.11
22 25 0.56
ACGTcount: A:0.25, C:0.01, G:0.04, T:0.70
Consensus pattern (21 bp):
TTTATTTATTTATTTTGAATT
Found at i:5426741 original size:40 final size:40
Alignment explanation
Indices: 5426697--5426772 Score: 134
Period size: 40 Copynumber: 1.9 Consensus size: 40
5426687 TAACCTTTAT
* *
5426697 TTATTTATTTATTTTGAATTTTTTGTTTATTTATTTCAAA
1 TTATTTATTTATTTTGAATTATTTATTTATTTATTTCAAA
5426737 TTATTTATTTATTTTGAATTATTTATTTATTTATTT
1 TTATTTATTTATTTTGAATTATTTATTTATTTATTT
5426773 AATTGAATGG
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
40 34 1.00
ACGTcount: A:0.25, C:0.01, G:0.04, T:0.70
Consensus pattern (40 bp):
TTATTTATTTATTTTGAATTATTTATTTATTTATTTCAAA
Found at i:5426743 original size:18 final size:18
Alignment explanation
Indices: 5426722--5426768 Score: 76
Period size: 18 Copynumber: 2.6 Consensus size: 18
5426712 GAATTTTTTG
5426722 TTTATTTATTTCAAATTA
1 TTTATTTATTTCAAATTA
**
5426740 TTTATTTATTTTGAATTA
1 TTTATTTATTTCAAATTA
5426758 TTTATTTATTT
1 TTTATTTATTT
5426769 ATTTAATTGA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.28, C:0.02, G:0.02, T:0.68
Consensus pattern (18 bp):
TTTATTTATTTCAAATTA
Found at i:5429028 original size:17 final size:17
Alignment explanation
Indices: 5429006--5429051 Score: 92
Period size: 17 Copynumber: 2.7 Consensus size: 17
5428996 GATTGAATGG
5429006 ACTCGACTCGAGCTCAA
1 ACTCGACTCGAGCTCAA
5429023 ACTCGACTCGAGCTCAA
1 ACTCGACTCGAGCTCAA
5429040 ACTCGACTCGAG
1 ACTCGACTCGAG
5429052 TTCTTAATGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 29 1.00
ACGTcount: A:0.28, C:0.35, G:0.20, T:0.17
Consensus pattern (17 bp):
ACTCGACTCGAGCTCAA
Found at i:5434465 original size:200 final size:197
Alignment explanation
Indices: 5433908--5434465 Score: 564
Period size: 200 Copynumber: 2.8 Consensus size: 197
5433898 TTTTTGTTTT
** * * * * *
5433908 GAACCATTTTGAACGCGATTTTTACACTGCTTAGAATGTCTCGCATGTGTTGTTACTAGCCTCAA
1 GAACCATTTTGAACGCGATTTTTAC-CCACTTACAATGTCTCGTATGTGTCGATATTAGCCTCAA
* * * * *
5433973 TTGAAACATAAATATCAATATTAAGCCTCTAATCTTATAAATGACAAAAACTTTTAACTAACTTC
65 TTGAAAGATAAAT-TCAATATTAAGCCTATAATCTTATAAATTACAAAAACTTTTAAATAACTAC
* ** * ** * *
5434038 CCGAAAATACTCCCCGAACATGCCTATCAATCCATGCTAGTTTTTTCTTCATGTAGAAAATCAAG
129 CCGAAAA-AATCTTCGAACATGCCTATCAAACCATGCTAGCATTTTCTTCATGCACAAAATCAAG
5434103 CTTTG
193 CTTTG
* * * * * *
5434108 GAACAATTTTGAACGCGATTTTTACCCTACTTACAATGTCTCATATATGTCAATATTACCCTGAA
1 GAACCATTTTGAACGCGATTTTTACCC-ACTTACAATGTCTCGTATGTGTCGATATTAGCCTCAA
* * * * * *
5434173 TTGAAAGAAAAATTACAATATTATGTCTTTAATCTTATAAATTACAAAAACATTTAGATGAACTA
65 TTGAAAGATAAATT-CAATATTAAGCCTATAATCTTATAAATTACAAAAACTTTTAAAT-AACTA
** * * **
5434238 CCAAAAAAAAAACCTT-GAATATGCCTATCAAACCATTTTAGCATTTTCTTCATGCACAAAA-CA
128 CC--CGAAAAAATCTTCGAACATGCCTATCAAACCATGCTAGCATTTTCTTCATGCACAAAATCA
5434301 AGCTTTG
191 AGCTTTG
* * * *
5434308 GAACCATTTTCAACGCAATTTTTAACCCACTTACAATATCTCGTATGTGTCGATATTGGCCTCAA
1 GAACCATTTTGAACGCGATTTTT-ACCCACTTACAATGTCTCGTATGTGTCGATATTAGCCTCAA
* * *
5434373 CTGAAAGATAAATTCCAATACTAAGCCTATAATCTTATAAATTATGAAAAA-TTTTATAATAACT
65 TTGAAAGATAAATT-CAATATTAAGCCTATAATCTTATAAATTA-CAAAAACTTTTA-AATAACT
*
5434437 ACCCGAAAAAATCGTTCGAACGTGCCTAT
127 ACCCGAAAAAATC-TTCGAACATGCCTAT
5434466 AAAAGCTTGT
Statistics
Matches: 286, Mismatches: 62, Indels: 20
0.78 0.17 0.05
Matches are distributed among these distances:
198 7 0.02
199 4 0.01
200 215 0.75
201 54 0.19
202 2 0.01
203 4 0.01
ACGTcount: A:0.37, C:0.20, G:0.11, T:0.33
Consensus pattern (197 bp):
GAACCATTTTGAACGCGATTTTTACCCACTTACAATGTCTCGTATGTGTCGATATTAGCCTCAAT
TGAAAGATAAATTCAATATTAAGCCTATAATCTTATAAATTACAAAAACTTTTAAATAACTACCC
GAAAAAATCTTCGAACATGCCTATCAAACCATGCTAGCATTTTCTTCATGCACAAAATCAAGCTT
TG
Found at i:5436718 original size:16 final size:16
Alignment explanation
Indices: 5436697--5436727 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
5436687 TCAACTGAGC
5436697 AGAAATCTCAATTGAA
1 AGAAATCTCAATTGAA
*
5436713 AGAAATCTCAGTTGA
1 AGAAATCTCAATTGA
5436728 GAGCCCTGCT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.45, C:0.13, G:0.16, T:0.26
Consensus pattern (16 bp):
AGAAATCTCAATTGAA
Found at i:5439835 original size:11 final size:11
Alignment explanation
Indices: 5439819--5439845 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
5439809 GGATCCTACA
5439819 GTTCAACCTTC
1 GTTCAACCTTC
5439830 GTTCAACCTTC
1 GTTCAACCTTC
5439841 GTTCA
1 GTTCA
5439846 CGTGTCTCAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.19, C:0.33, G:0.11, T:0.37
Consensus pattern (11 bp):
GTTCAACCTTC
Found at i:5446938 original size:3 final size:3
Alignment explanation
Indices: 5446886--5446926 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
5446876 ATAAAAATAC
5446886 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
5446927 GCTAATTATT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:5450315 original size:3 final size:3
Alignment explanation
Indices: 5450300--5450365 Score: 62
Period size: 3 Copynumber: 21.0 Consensus size: 3
5450290 TTTTACTTAA
* * *
5450300 ATT ATT ATA ATT ATT ATA ATA ATT ATT ATT ATT ATT -TAT ATTT ATAT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT-T A-TT AT-T
5450347 ATAT ATT ATT ATT ATT ATT
1 AT-T ATT ATT ATT ATT ATT
5450366 TAATAAATAT
Statistics
Matches: 55, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
2 1 0.02
3 44 0.80
4 9 0.16
5 1 0.02
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (3 bp):
ATT
Found at i:5450353 original size:24 final size:23
Alignment explanation
Indices: 5450300--5450377 Score: 84
Period size: 27 Copynumber: 3.2 Consensus size: 23
5450290 TTTTACTTAA
* *
5450300 ATTATTATAATTATTATAATAATT
1 ATTATTATTATTATT-TAATAAAT
*
5450324 ATTATTATTATTTATATTTATATATAT
1 ATTATTATTA--T-TATTTA-ATAAAT
5450351 ATTATTATTATTATTTAATAAAT
1 ATTATTATTATTATTTAATAAAT
5450374 ATTA
1 ATTA
5450378 CAAACCCAAA
Statistics
Matches: 46, Mismatches: 4, Indels: 9
0.78 0.07 0.15
Matches are distributed among these distances:
23 9 0.20
24 15 0.33
25 1 0.02
26 3 0.07
27 18 0.39
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (23 bp):
ATTATTATTATTATTTAATAAAT
Found at i:5451750 original size:3 final size:3
Alignment explanation
Indices: 5451732--5451794 Score: 60
Period size: 3 Copynumber: 21.0 Consensus size: 3
5451722 TATTTTAATC
*
5451732 ATT ATTT ATT -TT ATT ATT ATT ATT ATTT ATT GTT -TT AATT ATT ATT
1 ATT A-TT ATT ATT ATT ATT ATT ATT A-TT ATT ATT ATT -ATT ATT ATT
*
5451778 -TC ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT
5451795 TATAAAAATA
Statistics
Matches: 51, Mismatches: 3, Indels: 12
0.77 0.05 0.18
Matches are distributed among these distances:
2 5 0.10
3 38 0.75
4 8 0.16
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.68
Consensus pattern (3 bp):
ATT
Found at i:5452484 original size:23 final size:24
Alignment explanation
Indices: 5452448--5452494 Score: 87
Period size: 23 Copynumber: 2.0 Consensus size: 24
5452438 TATTCATGAG
5452448 AATGACATCGGTATATCTAATCGA
1 AATGACATCGGTATATCTAATCGA
5452472 AATGACATC-GTATATCTAATCGA
1 AATGACATCGGTATATCTAATCGA
5452495 CATTCATTAC
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 14 0.61
24 9 0.39
ACGTcount: A:0.38, C:0.17, G:0.15, T:0.30
Consensus pattern (24 bp):
AATGACATCGGTATATCTAATCGA
Found at i:5464060 original size:2 final size:2
Alignment explanation
Indices: 5464053--5464081 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
5464043 CATCCTTCTT
5464053 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
5464082 ATATATATAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:5464307 original size:2 final size:2
Alignment explanation
Indices: 5464302--5464343 Score: 66
Period size: 2 Copynumber: 21.0 Consensus size: 2
5464292 TCTCTCTCTC
**
5464302 TA TA TA TA TA TA TA TA CC 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
5464344 CACACATACA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.48, C:0.05, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Done.