Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008936.1 Hibiscus syriacus cultivar Beakdansim tig00112254_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: 973811
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 5
Found at i:356 original size:68 final size:68
Alignment explanation
Indices: 245--546 Score: 412
Period size: 68 Copynumber: 4.4 Consensus size: 68
235 AAAAGATTAA
* *
245 AGGCCTAACTGTGCATTTGATAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGATTAAGTGCCT
1 AGGCCTAACTGTGCATTTGATAGAAAGGTGTCAATTATTCCAGTTAGATGAAAGACTAAGTGCCT
310 TTG
66 TTG
*
313 AGGCCTAACTGTGCATTTGATAGAAAGGTGTCAATTATTCCAGTTAGATGAAAGGCTAAGTGCCT
1 AGGCCTAACTGTGCATTTGATAGAAAGGTGTCAATTATTCCAGTTAGATGAAAGACTAAGTGCCT
378 TTG
66 TTG
* * * * *
381 AGGCCTAACTGTG-ACTTTGATAGAAAGGTGTCAATTAATCTAGTTAGATGAAAGGCTAAATACC
1 AGGCCTAACTGTGCA-TTTGATAGAAAGGTGTCAATTATTCCAGTTAGATGAAAGACTAAGTGCC
445 TTTG
65 TTTG
* * * * *
449 ATGCTTAACTGTGCATATGACAGAAAGGTGT-ACATTATTCCAGTTAGATGAAA-AGCTAAGTGT
1 AGGCCTAACTGTGCATTTGATAGAAAGGTGTCA-ATTATTCCAGTTAGATGAAAGA-CTAAGTGC
*
512 CTTTC
64 CTTTG
* *
517 AGGCCTAGCTGTGCATTTGAGAGAAAGGTG
1 AGGCCTAACTGTGCATTTGATAGAAAGGTG
547 CAGTTAGATG
Statistics
Matches: 207, Mismatches: 23, Indels: 8
0.87 0.10 0.03
Matches are distributed among these distances:
67 2 0.01
68 204 0.99
69 1 0.00
ACGTcount: A:0.31, C:0.14, G:0.25, T:0.30
Consensus pattern (68 bp):
AGGCCTAACTGTGCATTTGATAGAAAGGTGTCAATTATTCCAGTTAGATGAAAGACTAAGTGCCT
TTG
Found at i:684 original size:81 final size:81
Alignment explanation
Indices: 547--905 Score: 488
Period size: 81 Copynumber: 4.5 Consensus size: 81
537 GAGAAAGGTG
* * * *
547 CAGTTAGATGAACGGTTAAGTATCGTTGAGTAAAAGAATAATAGCCTAGCTATGCATTTGACAAA
1 CAGTTAGATGAACGGTTAAGTACCGTTGAGTAAAAGAATAATAGCCTAGTTGTGCATTTGACAGA
612 AAGGTGTCAATTATGC
66 AAGGTGTCAATTATGC
* * *
628 CTGTTAGATGAATGGTTAAGTACCGTTGAGTAAAAGAATAATAGCCTAGTTGTGCATTTGATAGA
1 CAGTTAGATGAACGGTTAAGTACCGTTGAGTAAAAGAATAATAGCCTAGTTGTGCATTTGACAGA
693 AA-G-GTCAATTATGC
66 AAGGTGTCAATTATGC
* * * *
707 CAGTTAGATGAACAGATAAGTACCATTGAGTAAAAGAATAATAGCCTAATTGTGCATTTGACAGA
1 CAGTTAGATGAACGGTTAAGTACCGTTGAGTAAAAGAATAATAGCCTAGTTGTGCATTTGACAGA
* *
772 AATGTGTCAATTATGT
66 AAGGTGTCAATTATGC
* * * * *
788 TATTTAGATGAACGGTTAAGTACCGTTGAGTAAAAGAATAATAGCCTAGATGTGTATTTGATAGA
1 CAGTTAGATGAACGGTTAAGTACCGTTGAGTAAAAGAATAATAGCCTAGTTGTGCATTTGACAGA
*
853 AAGGTGTCAATTATGT
66 AAGGTGTCAATTATGC
* * ** *
869 CAGTTAGAGGAACAGTTAAACACGGTTGAGTAAAAGA
1 CAGTTAGATGAACGGTTAAGTACCGTTGAGTAAAAGA
906 TGAACGGTTA
Statistics
Matches: 244, Mismatches: 32, Indels: 4
0.87 0.11 0.01
Matches are distributed among these distances:
79 71 0.29
80 2 0.01
81 171 0.70
ACGTcount: A:0.37, C:0.10, G:0.23, T:0.30
Consensus pattern (81 bp):
CAGTTAGATGAACGGTTAAGTACCGTTGAGTAAAAGAATAATAGCCTAGTTGTGCATTTGACAGA
AAGGTGTCAATTATGC
Found at i:781 original size:160 final size:162
Alignment explanation
Indices: 547--883 Score: 500
Period size: 160 Copynumber: 2.1 Consensus size: 162
537 GAGAAAGGTG
* * * * *
547 CAGTTAGATGAACGGTTAAGTATCGTTGAGTAAAAGAATAATAGCCTAGCTATGCATTTGACAAA
1 CAGTTAGATGAACAGATAAGTACCATTGAGTAAAAGAATAATAGCCTAACTATGCATTTGACAAA
*
612 AAGGTGTCAATTATGCCT-GTTAGATGAATGGTTAAGTACCGTTGAGTAAAAGAATAATAGCCTA
66 AAGGTGTCAATTATG-CTAGTTAGATGAACGGTTAAGTACCGTTGAGTAAAAGAATAATAGCCTA
*
676 GTTGTGCATTTGATAGAAA-G-GTCAATTATGC
130 GATGTGCATTTGATAGAAAGGTGTCAATTATGC
* * *
707 CAGTTAGATGAACAGATAAGTACCATTGAGTAAAAGAATAATAGCCTAATTGTGCATTTGACAGA
1 CAGTTAGATGAACAGATAAGTACCATTGAGTAAAAGAATAATAGCCTAACTATGCATTTGACAAA
* * *
772 AATGTGTCAATTATGTTATTTAGATGAACGGTTAAGTACCGTTGAGTAAAAGAATAATAGCCTAG
66 AAGGTGTCAATTATGCTAGTTAGATGAACGGTTAAGTACCGTTGAGTAAAAGAATAATAGCCTAG
* *
837 ATGTGTATTTGATAGAAAGGTGTCAATTATGT
131 ATGTGCATTTGATAGAAAGGTGTCAATTATGC
*
869 CAGTTAGAGGAACAG
1 CAGTTAGATGAACAG
884 TTAAACACGG
Statistics
Matches: 158, Mismatches: 16, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
159 1 0.01
160 132 0.84
161 1 0.01
162 24 0.15
ACGTcount: A:0.37, C:0.10, G:0.23, T:0.30
Consensus pattern (162 bp):
CAGTTAGATGAACAGATAAGTACCATTGAGTAAAAGAATAATAGCCTAACTATGCATTTGACAAA
AAGGTGTCAATTATGCTAGTTAGATGAACGGTTAAGTACCGTTGAGTAAAAGAATAATAGCCTAG
ATGTGCATTTGATAGAAAGGTGTCAATTATGC
Found at i:15907 original size:9 final size:9
Alignment explanation
Indices: 15875--15899 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
15865 CTCCTTCATT
15875 TTTTATTTG
1 TTTTATTTG
15884 TTTTATTTG
1 TTTTATTTG
15893 TTTTATT
1 TTTTATT
15900 ATTTTTATCT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.12, C:0.00, G:0.08, T:0.80
Consensus pattern (9 bp):
TTTTATTTG
Found at i:26317 original size:1 final size:1
Alignment explanation
Indices: 26307--26371 Score: 67
Period size: 1 Copynumber: 65.0 Consensus size: 1
26297 TCAAAGGAAG
* * * * * * *
26307 AAAAAGAAAAAAAAAAAAACAAAAAAAACAAAAAACAAAAAAACAAAAAACAAAAAATAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
26372 CGTTTAGAGT
Statistics
Matches: 50, Mismatches: 14, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
1 50 1.00
ACGTcount: A:0.89, C:0.08, G:0.02, T:0.02
Consensus pattern (1 bp):
A
Found at i:26331 original size:15 final size:15
Alignment explanation
Indices: 26313--26372 Score: 93
Period size: 15 Copynumber: 3.9 Consensus size: 15
26303 GAAGAAAAAG
26313 AAAAAAAAAAAAACA
1 AAAAAAAAAAAAACA
26328 AAAAAAACAAAAAACA
1 AAAAAAA-AAAAAACA
*
26344 AAAAAACAAAAAACA
1 AAAAAAAAAAAAACA
*
26359 AAAAATAAAAAAAC
1 AAAAAAAAAAAAAC
26373 GTTTAGAGTG
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
15 27 0.66
16 14 0.34
ACGTcount: A:0.88, C:0.10, G:0.00, T:0.02
Consensus pattern (15 bp):
AAAAAAAAAAAAACA
Found at i:26333 original size:22 final size:22
Alignment explanation
Indices: 26307--26372 Score: 87
Period size: 24 Copynumber: 2.9 Consensus size: 22
26297 TCAAAGGAAG
*
26307 AAAAAGAAAAAAAAAAAAACAA
1 AAAAAAAAAAAAAAAAAAACAA
26329 AAAAAACAAAAAACAAAAAAACAA
1 AAAAAA-AAAAAA-AAAAAAACAA
* *
26353 AAAACAAAAAATAAAAAAAC
1 AAAAAAAAAAAAAAAAAAAC
26373 GTTTAGAGTG
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
22 13 0.33
23 11 0.28
24 15 0.38
ACGTcount: A:0.88, C:0.09, G:0.02, T:0.02
Consensus pattern (22 bp):
AAAAAAAAAAAAAAAAAAACAA
Found at i:28303 original size:45 final size:46
Alignment explanation
Indices: 28215--28305 Score: 130
Period size: 45 Copynumber: 2.0 Consensus size: 46
28205 TTGAAAAAGC
* * *
28215 CTGAGTGCGTCGATACATGGTCTTGTGCATCGATGAATCAAATGCA
1 CTGAGTGCATCGATACATGGTCATGTGCATCGATGAATAAAATGCA
* *
28261 CTGAGTGCATCGATGCATGGT-ATGTGCATCGATGCATAAAATGCA
1 CTGAGTGCATCGATACATGGTCATGTGCATCGATGAATAAAATGCA
28306 TTCGATGTTC
Statistics
Matches: 40, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
45 21 0.52
46 19 0.47
ACGTcount: A:0.27, C:0.19, G:0.26, T:0.27
Consensus pattern (46 bp):
CTGAGTGCATCGATACATGGTCATGTGCATCGATGAATAAAATGCA
Found at i:28353 original size:20 final size:20
Alignment explanation
Indices: 28325--28363 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
28315 CAAGAAATTA
28325 ATTGATGCATCGATGCATGG
1 ATTGATGCATCGATGCATGG
* *
28345 ATTGGTGCATCGGTGCATG
1 ATTGATGCATCGATGCATG
28364 CCCTTGAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.21, C:0.15, G:0.33, T:0.31
Consensus pattern (20 bp):
ATTGATGCATCGATGCATGG
Found at i:29045 original size:19 final size:19
Alignment explanation
Indices: 29003--29046 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
28993 AGATCAAACC
29003 AAACAGTTCAAACATCCAA
1 AAACAGTTCAAACATCCAA
* *
29022 CAACAGTT-AAACAATTCAA
1 AAACAGTTCAAAC-ATCCAA
29041 AAACAG
1 AAACAG
29047 CAAAATGTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
18 4 0.19
19 17 0.81
ACGTcount: A:0.55, C:0.23, G:0.07, T:0.16
Consensus pattern (19 bp):
AAACAGTTCAAACATCCAA
Found at i:31065 original size:23 final size:22
Alignment explanation
Indices: 31039--31118 Score: 99
Period size: 22 Copynumber: 3.6 Consensus size: 22
31029 ACATGGCCTT
31039 GTGCATCGATGCACATTCAAGG
1 GTGCATCGATGCACATTCAAGG
* * *
31061 CGTGCATCGGTGCACCTTC-ATG
1 -GTGCATCGATGCACATTCAAGG
*
31083 GTGTATCGATGCACATTCAAGG
1 GTGCATCGATGCACATTCAAGG
*
31105 ATGCATCGATGCAC
1 GTGCATCGATGCAC
31119 TGTTAGGTGT
Statistics
Matches: 47, Mismatches: 9, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
21 15 0.32
22 16 0.34
23 16 0.34
ACGTcount: A:0.24, C:0.25, G:0.26, T:0.25
Consensus pattern (22 bp):
GTGCATCGATGCACATTCAAGG
Found at i:31092 original size:44 final size:42
Alignment explanation
Indices: 31043--31137 Score: 129
Period size: 44 Copynumber: 2.2 Consensus size: 42
31033 GGCCTTGTGC
* *
31043 ATCGATGCACATTCAAGGCGTGCATCGGTGCACCT-TCATGGTGT
1 ATCGATGCACATTCAAGG-ATGCATCGATGCA-CTGTCA-GGTGT
*
31087 ATCGATGCACATTCAAGGATGCATCGATGCACTGTTAGGTGT
1 ATCGATGCACATTCAAGGATGCATCGATGCACTGTCAGGTGT
31129 ATCGATGCA
1 ATCGATGCA
31138 TGAAGCACAA
Statistics
Matches: 47, Mismatches: 3, Indels: 4
0.87 0.06 0.07
Matches are distributed among these distances:
42 16 0.34
43 13 0.28
44 18 0.38
ACGTcount: A:0.24, C:0.22, G:0.26, T:0.27
Consensus pattern (42 bp):
ATCGATGCACATTCAAGGATGCATCGATGCACTGTCAGGTGT
Found at i:31134 original size:20 final size:21
Alignment explanation
Indices: 31043--31137 Score: 86
Period size: 21 Copynumber: 4.4 Consensus size: 21
31033 GGCCTTGTGC
*
31043 ATCGATGCACATTCAAGGCGTGC
1 ATCGATGCACATTCAA-G-GTGT
* * *
31066 ATCGGTGCACCTTCATGGTGT
1 ATCGATGCACATTCAAGGTGT
*
31087 ATCGATGCACATTCAAGGATGC
1 ATCGATGCACATTCAAGG-TGT
*
31109 ATCGATGCAC-TGT-TAGGTGT
1 ATCGATGCACAT-TCAAGGTGT
31129 ATCGATGCA
1 ATCGATGCA
31138 TGAAGCACAA
Statistics
Matches: 60, Mismatches: 10, Indels: 7
0.78 0.13 0.09
Matches are distributed among these distances:
20 11 0.18
21 22 0.37
22 14 0.23
23 13 0.22
ACGTcount: A:0.24, C:0.22, G:0.26, T:0.27
Consensus pattern (21 bp):
ATCGATGCACATTCAAGGTGT
Found at i:35785 original size:45 final size:46
Alignment explanation
Indices: 35697--35787 Score: 139
Period size: 45 Copynumber: 2.0 Consensus size: 46
35687 TTGAAAAAGC
* * *
35697 CTGAGTGCGTAGATGCATGGTCTTGTGCATCGATGCATCAAATGCA
1 CTGAGTGCATAGATGCATGGTCATGTGCATCGATGCATAAAATGCA
*
35743 CTGAGTGCATCGATGCATGGT-ATGTGCATCGATGCATAAAATGCA
1 CTGAGTGCATAGATGCATGGTCATGTGCATCGATGCATAAAATGCA
35788 TTCGATGTTC
Statistics
Matches: 41, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
45 22 0.54
46 19 0.46
ACGTcount: A:0.26, C:0.19, G:0.27, T:0.27
Consensus pattern (46 bp):
CTGAGTGCATAGATGCATGGTCATGTGCATCGATGCATAAAATGCA
Found at i:35835 original size:20 final size:20
Alignment explanation
Indices: 35807--35845 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
35797 CAAGAAATTA
35807 ATTGATGCATCGATGCATGG
1 ATTGATGCATCGATGCATGG
* *
35827 ATTGGTGCATCGGTGCATG
1 ATTGATGCATCGATGCATG
35846 CCCTTGAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.21, C:0.15, G:0.33, T:0.31
Consensus pattern (20 bp):
ATTGATGCATCGATGCATGG
Found at i:36302 original size:109 final size:106
Alignment explanation
Indices: 36108--36359 Score: 326
Period size: 109 Copynumber: 2.3 Consensus size: 106
36098 CCAATTTCAA
* *
36108 AGCCAATTTCAACTTCACAGCGAATGATATTGGACTCAAGACAACACAAGCTCAACTTCACAACG
1 AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCAAGACAACACAAGCTCAACTTCACAACG
* * * * *
36173 AAGGGGCTGCTGATTGTCAACAAACAATTT-TCAGTTTCATTTGG
66 AAGGGGCGGCAGACTGTCAACAAACAATTTCCCAGTTCCA----G
* * * * *
36217 AGTCAATTTCAACTTCACAACGAAGGATATTAGACTCGAGACATCACAAGCTCAACTTCACAGCG
1 AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCAAGACAACACAAGCTCAACTTCACAACG
*
36282 AGGGGGCGGCAGACTGTCAACAAACAATTTCCCAGTTCCAG
66 AAGGGGCGGCAGACTGTCAACAAACAATTTCCCAGTTCCAG
* *
36323 AGCCAATTTCAACTTCACGACGGAGGATATTGGACTC
1 AGCCAATTTCAACTTCACAACGAAGGATATTGGACTC
36360 TGAGCAATAC
Statistics
Matches: 125, Mismatches: 17, Indels: 5
0.85 0.12 0.03
Matches are distributed among these distances:
106 34 0.27
109 84 0.67
110 7 0.06
ACGTcount: A:0.33, C:0.25, G:0.19, T:0.23
Consensus pattern (106 bp):
AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCAAGACAACACAAGCTCAACTTCACAACG
AAGGGGCGGCAGACTGTCAACAAACAATTTCCCAGTTCCAG
Found at i:38455 original size:3 final size:3
Alignment explanation
Indices: 38436--38484 Score: 82
Period size: 3 Copynumber: 16.7 Consensus size: 3
38426 ACTTTTTTCC
*
38436 TTA TTG TTA TT- TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
38483 TT
1 TT
38485 TTTTTACTTT
Statistics
Matches: 43, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
2 2 0.05
3 41 0.95
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:39106 original size:2 final size:2
Alignment explanation
Indices: 39099--39152 Score: 108
Period size: 2 Copynumber: 27.0 Consensus size: 2
39089 CGGTTCCGAC
39099 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
39141 AT AT AT AT AT AT
1 AT AT AT AT AT AT
39153 TTTTAGAAAA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:41270 original size:38 final size:37
Alignment explanation
Indices: 41228--41301 Score: 103
Period size: 37 Copynumber: 2.0 Consensus size: 37
41218 ATATAAATTG
* * *
41228 TATAAAATCATTTTTAATAAATTTATATCATGATTAAT
1 TATAAAATC-TATTTAAAAAAATTATATCATGATTAAT
*
41266 TATAAACTCTATTTAAAAAAATTATATCATGATTAA
1 TATAAAATCTATTTAAAAAAATTATATCATGATTAA
41302 ACATTTTGAT
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
37 24 0.75
38 8 0.25
ACGTcount: A:0.47, C:0.07, G:0.03, T:0.43
Consensus pattern (37 bp):
TATAAAATCTATTTAAAAAAATTATATCATGATTAAT
Found at i:44832 original size:81 final size:79
Alignment explanation
Indices: 44668--44990 Score: 335
Period size: 81 Copynumber: 4.0 Consensus size: 79
44658 ATTTTGTTGA
* * ** * * *
44668 CAGATAGCCCTTCTT-GCCTTGAGTTATGCTGTGAATGATGTGCCTTGAGATGAATGGAATCGAA
1 CAGATAACCCTT-TTAGCCTTGAGCTATGCTGCAAATGATGTGCCTTGAGTTGAGTGTAATCGAA
44732 CTCGAAGGTCTTTGG
65 CTCGAAGGTCTTTGG
* * *
44747 CAGATAACCCTTTTAGCCTTGAGCTATGCTGCAAATGATAGTGCCTTTGAGCTGAGTGAAATCAA
1 CAGATAACCCTTTTAGCCTTGAGCTATGCTGCAAATGAT-GTGCC-TTGAGTTGAGTGTAATCGA
*
44812 ACTCTAAGGTCTTTGG
64 ACTCGAAGGTCTTTGG
* * * * *
44828 CAGATAACCCTTTTTGCCTTAAGCTATTG-TGCAAATGATGTGTCGTTGAGTTGAGCGTAGTCGA
1 CAGATAACCCTTTTAGCCTTGAGCTA-TGCTGCAAATGATGTG-CCTTGAGTTGAGTGTAATCGA
* *
44892 ACTCAAAGGTCTTTTTTGA
64 ACTCGAAGGTC---TTTGG
* * * * *
44911 TAGATAATCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCCTTGAAGTTGAGTGTAGTCGA
1 CAGATAACCCTTTTAGCCTTGAGCTATGCTGCAAATGATGTG-CCTTG-AGTTGAGTGTAATCGA
44976 ACTCGAAGGTCTTTG
64 ACTCGAAGGTCTTTG
44991 TGTTTCAAGA
Statistics
Matches: 205, Mismatches: 29, Indels: 18
0.81 0.12 0.07
Matches are distributed among these distances:
78 2 0.01
79 32 0.16
80 32 0.16
81 69 0.34
82 4 0.02
83 41 0.20
84 25 0.12
ACGTcount: A:0.24, C:0.18, G:0.24, T:0.33
Consensus pattern (79 bp):
CAGATAACCCTTTTAGCCTTGAGCTATGCTGCAAATGATGTGCCTTGAGTTGAGTGTAATCGAAC
TCGAAGGTCTTTGG
Found at i:45033 original size:33 final size:32
Alignment explanation
Indices: 44991--45104 Score: 147
Period size: 33 Copynumber: 3.5 Consensus size: 32
44981 AAGGTCTTTG
* *
44991 TGTTTCAAGATAAACATTTTCAAAGTTTTTTTA
1 TGTTTCAAGAGAAACA-TTTCAAAGGTTTTTTA
*
45024 TGTTTCAAGAGAAACGATTTCAAAGGTTTTTTC
1 TGTTTCAAGAGAAAC-ATTTCAAAGGTTTTTTA
* * *
45057 TGTTGCAAGAAAAACAGTTTCAAAGGTTTTTTG
1 TGTTTCAAGAGAAACA-TTTCAAAGGTTTTTTA
45090 TGTTTCAAGAGAAAC
1 TGTTTCAAGAGAAAC
45105 TGTCTCCAGG
Statistics
Matches: 71, Mismatches: 8, Indels: 4
0.86 0.10 0.05
Matches are distributed among these distances:
32 1 0.01
33 69 0.97
34 1 0.01
ACGTcount: A:0.33, C:0.11, G:0.17, T:0.39
Consensus pattern (32 bp):
TGTTTCAAGAGAAACATTTCAAAGGTTTTTTA
Found at i:45154 original size:70 final size:67
Alignment explanation
Indices: 45052--45265 Score: 177
Period size: 72 Copynumber: 3.0 Consensus size: 67
45042 TTCAAAGGTT
* * * *
45052 TTTTCTGTTGCAAGAAAAACAGTTTCAAAGGTTTTTTGTGTTTCAAGAGAAACTGTCTCCAGGGA
1 TTTTCT-TT-CAAGAGAAACAGTTTCAAAGG---TTGGTGTTTCAAGAGAAACTGTCTCAAGAGA
45117 GGA-AAAA
61 -GACAAAA
45124 TTTTCTTTCAAGAGAAACA-TATTCAAAGGTTGGTGTTTCAAGAGAAACTGTCTCAAGAGAGACA
1 TTTTCTTTCAAGAGAAACAGT-TTCAAAGGTTGGTGTTTCAAGAGAAACTGTCTCAAGAGAGACA
45188 AAA
65 AAA
* * * * *
45191 -TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATT--TGTTTCAAGGGAAACTGTCTCAAG
1 TTTTCTTTCAAGAGAAACAGTTTCAA-AG-G------TTGGTGTTTCAAGAGAAACTGTCTCAAG
45253 AGAGACAAAA
58 AGAGACAAAA
45263 TTT
1 TTT
45266 GTCTCAAGAG
Statistics
Matches: 121, Mismatches: 9, Indels: 23
0.79 0.06 0.15
Matches are distributed among these distances:
66 21 0.17
67 35 0.29
68 1 0.01
69 1 0.01
70 18 0.15
71 2 0.02
72 39 0.32
73 2 0.02
74 2 0.02
ACGTcount: A:0.36, C:0.13, G:0.21, T:0.29
Consensus pattern (67 bp):
TTTTCTTTCAAGAGAAACAGTTTCAAAGGTTGGTGTTTCAAGAGAAACTGTCTCAAGAGAGACAA
AA
Found at i:45207 original size:36 final size:36
Alignment explanation
Indices: 45157--45273 Score: 216
Period size: 36 Copynumber: 3.2 Consensus size: 36
45147 CAAAGGTTGG
*
45157 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATT
45193 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATT
45229 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATT
*
45265 TGTCTCAAG
1 TGTTTCAAG
45274 AGAGACAAAA
Statistics
Matches: 79, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
36 79 1.00
ACGTcount: A:0.38, C:0.15, G:0.21, T:0.26
Consensus pattern (36 bp):
TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATT
Found at i:45270 original size:21 final size:21
Alignment explanation
Indices: 45172--45288 Score: 105
Period size: 21 Copynumber: 6.1 Consensus size: 21
45162 CAAGAGAAAC
45172 TGTCTCAAGAGAGACAAAATT
1 TGTCTCAAGAGAGACAAAATT
* *
45193 TGTTTCAAG-G-G---AAA-C
1 TGTCTCAAGAGAGACAAAATT
45208 TGTCTCAAGAGAGACAAAATT
1 TGTCTCAAGAGAGACAAAATT
* *
45229 TGTTTCAAG-G-G---AAA-C
1 TGTCTCAAGAGAGACAAAATT
45244 TGTCTCAAGAGAGACAAAATT
1 TGTCTCAAGAGAGACAAAATT
45265 TGTCTCAAGAGAGACAAAACTT
1 TGTCTCAAGAGAGACAAAA-TT
45287 TG
1 TG
45289 GTTTTAGTAA
Statistics
Matches: 75, Mismatches: 8, Indels: 25
0.69 0.07 0.23
Matches are distributed among these distances:
15 16 0.21
16 8 0.11
17 2 0.03
19 2 0.03
20 8 0.11
21 35 0.47
22 4 0.05
ACGTcount: A:0.39, C:0.15, G:0.21, T:0.25
Consensus pattern (21 bp):
TGTCTCAAGAGAGACAAAATT
Found at i:47065 original size:12 final size:12
Alignment explanation
Indices: 47050--47103 Score: 54
Period size: 12 Copynumber: 4.3 Consensus size: 12
47040 TTCTTCTTGT
*
47050 TTTTTTTCTTTA
1 TTTTTTTCTTTG
*
47062 TTTTTTCCTTTG
1 TTTTTTTCTTTG
* *
47074 TTTTTGCTTTTTTC
1 TTTTT--TTCTTTG
47088 TTTTTTTCTTTG
1 TTTTTTTCTTTG
47100 TTTT
1 TTTT
47104 CTCTTTTTTC
Statistics
Matches: 33, Mismatches: 7, Indels: 4
0.75 0.16 0.09
Matches are distributed among these distances:
12 24 0.73
14 9 0.27
ACGTcount: A:0.02, C:0.11, G:0.06, T:0.81
Consensus pattern (12 bp):
TTTTTTTCTTTG
Found at i:47103 original size:19 final size:19
Alignment explanation
Indices: 47050--47112 Score: 74
Period size: 19 Copynumber: 3.3 Consensus size: 19
47040 TTCTTCTTGT
*
47050 TTTTTTTCTTTATTTTTTC
1 TTTTTTTCTTTGTTTTTTC
* *
47069 CTTTGTT-TTTGCTTTTTTC
1 TTTTTTTCTTTG-TTTTTTC
*
47088 TTTTTTTCTTTGTTTTCTC
1 TTTTTTTCTTTGTTTTTTC
47107 TTTTTT
1 TTTTTT
47113 CTTCTTCTCT
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
18 3 0.08
19 29 0.81
20 4 0.11
ACGTcount: A:0.02, C:0.13, G:0.05, T:0.81
Consensus pattern (19 bp):
TTTTTTTCTTTGTTTTTTC
Found at i:47113 original size:26 final size:25
Alignment explanation
Indices: 47046--47132 Score: 88
Period size: 26 Copynumber: 3.4 Consensus size: 25
47036 CATATTCTTC
* *
47046 TTGTTTTT-TTTCTTTATTTTTTCCT
1 TTGTTTTTCTTT-TTTCTTTTTTTCT
47071 TTGTTTTTGCTTTTTTCTTTTTTTCT
1 TTGTTTTT-CTTTTTTCTTTTTTTCT
* *
47097 TTGTTTTCTCTTTTTTCTTCTTCTCT
1 TTGTTTT-TCTTTTTTCTTTTTTTCT
*
47123 TT-TTATTCTT
1 TTGTTTTTCTT
47133 GATTGGATCT
Statistics
Matches: 54, Mismatches: 5, Indels: 7
0.82 0.08 0.11
Matches are distributed among these distances:
24 4 0.07
25 11 0.20
26 35 0.65
27 4 0.07
ACGTcount: A:0.02, C:0.15, G:0.05, T:0.78
Consensus pattern (25 bp):
TTGTTTTTCTTTTTTCTTTTTTTCT
Found at i:47132 original size:9 final size:8
Alignment explanation
Indices: 47081--47132 Score: 59
Period size: 8 Copynumber: 6.1 Consensus size: 8
47071 TTGTTTTTGC
47081 TTTTTTCT
1 TTTTTTCT
47089 TTTTTTCT
1 TTTTTTCT
47097 TTGTTTTCT
1 TT-TTTTCT
47106 CTTTTTTCT
1 -TTTTTTCT
* *
47115 TCTTCTCT
1 TTTTTTCT
47123 TTTTATTCT
1 TTTT-TTCT
47132 T
1 T
47133 GATTGGATCT
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
8 19 0.51
9 16 0.43
10 2 0.05
ACGTcount: A:0.02, C:0.17, G:0.02, T:0.79
Consensus pattern (8 bp):
TTTTTTCT
Found at i:60363 original size:19 final size:19
Alignment explanation
Indices: 60339--60375 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
60329 ATTGAATTTA
60339 TTCAAAA-AATTTCAAAGTT
1 TTCAAAATAA-TTCAAAGTT
60358 TTCAAAATAATTCAAAGT
1 TTCAAAATAATTCAAAGT
60376 CCTTAAAAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 15 0.88
20 2 0.12
ACGTcount: A:0.49, C:0.11, G:0.05, T:0.35
Consensus pattern (19 bp):
TTCAAAATAATTCAAAGTT
Found at i:64897 original size:7 final size:6
Alignment explanation
Indices: 64883--64978 Score: 77
Period size: 5 Copynumber: 17.2 Consensus size: 6
64873 ACACATTTAG
* *
64883 TATATA TAGTATA TAT-TA TAT-TA TATAGTA TAT-TA TGGTATA T-TTTA
1 TATATA TA-TATA TATATA TATATA TATA-TA TATATA T-ATATA TATATA
64930 TATATA TAT-TA TATAT- TATAT- TATATA T-TATA TAT-TA TA-ATA
1 TATATA TATATA TATATA TATATA TATATA TATATA TATATA TATATA
64972 TATATA T
1 TATATA T
64979 TTTGTGTTAT
Statistics
Matches: 76, Mismatches: 3, Indels: 22
0.75 0.03 0.22
Matches are distributed among these distances:
5 45 0.59
6 17 0.22
7 14 0.18
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.54
Consensus pattern (6 bp):
TATATA
Found at i:64902 original size:5 final size:5
Alignment explanation
Indices: 64894--65056 Score: 78
Period size: 5 Copynumber: 33.0 Consensus size: 5
64884 ATATATAGTA
** *
64894 TATAT TATAT TATAT AGTATAT TATGG TATAT TTTA- TATA- TATATT
1 TATAT TATAT TATAT --TATAT TATAT TATAT TATAT TATAT TATA-T
* * *
64940 ATATAT TATAT TATA- TAT-T ATATAT TATAA TATA- TATAT TTTGT GT-TA-
1 -TATAT TATAT TATAT TATAT -TATAT TATAT TATAT TATAT TATAT -TATAT
* * *
64988 TATAT TATA- TAT-T TATAT TTTA- TATGAG TATTAT TATAT TACAT TATTAT
1 TATAT TATAT TATAT TATAT TATAT TAT-AT TA-TAT TATAT TATAT TA-TAT
*
65038 TAT-T TATTT TATAT TATAT
1 TATAT TATAT TATAT TATAT
65057 ATTGATTTAT
Statistics
Matches: 123, Mismatches: 16, Indels: 38
0.69 0.09 0.21
Matches are distributed among these distances:
3 1 0.01
4 28 0.23
5 72 0.59
6 12 0.10
7 10 0.08
ACGTcount: A:0.37, C:0.01, G:0.04, T:0.58
Consensus pattern (5 bp):
TATAT
Found at i:64997 original size:7 final size:7
Alignment explanation
Indices: 64885--65059 Score: 123
Period size: 7 Copynumber: 25.1 Consensus size: 7
64875 ACATTTAGTA
*
64885 TATATAG
1 TATATAT
64892 TATATA-
1 TATATAT
64898 T-TATAT
1 TATATAT
*
64904 TATATAG
1 TATATAT
64911 TATATTAT
1 TATA-TAT
**
64919 GGTATAT
1 TATATAT
*
64926 TTTATA-
1 TATATAT
64932 TATATAT
1 TATATAT
64939 TATATA-
1 TATATAT
64945 T-TATAT
1 TATATAT
64951 TATATAT
1 TATATAT
64958 TATATAT
1 TATATAT
64965 TATA-AT
1 TATATAT
64971 ATATATAT
1 -TATATAT
* * *
64979 TTTGTGT
1 TATATAT
64986 TATATAT
1 TATATAT
64993 TATATAT
1 TATATAT
65000 T-TATAT
1 TATATAT
*
65006 TTTATAT
1 TATATAT
*
65013 GAGTATTAT
1 TA-TA-TAT
65022 TATATTACAT
1 TATA-T--AT
65032 TAT-TAT
1 TATATAT
*
65038 TATTTAT
1 TATATAT
*
65045 TTTATAT
1 TATATAT
65052 TATATAT
1 TATATAT
65059 T
1 T
65060 GATTTATTTA
Statistics
Matches: 135, Mismatches: 19, Indels: 28
0.74 0.10 0.15
Matches are distributed among these distances:
5 8 0.06
6 22 0.16
7 83 0.61
8 13 0.10
9 4 0.03
10 5 0.04
ACGTcount: A:0.37, C:0.01, G:0.05, T:0.58
Consensus pattern (7 bp):
TATATAT
Found at i:64998 original size:2 final size:2
Alignment explanation
Indices: 64883--64978 Score: 77
Period size: 2 Copynumber: 51.5 Consensus size: 2
64873 ACACATTTAG
*
64883 TA TA TA TA GTA TA TA T- TA TA T- TA TA TA GTA TA T- TA TGG TA
1 TA TA TA TA -TA TA TA TA TA TA TA TA TA TA -TA TA TA TA T-A TA
*
64923 TA T- TT TA TA TA TA TA T- TA TA TA T- TA TA T- TA TA TA T- TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
64960 TA TA T- TA TA -A TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA T
64979 TTTGTGTTAT
Statistics
Matches: 78, Mismatches: 3, Indels: 26
0.73 0.03 0.24
Matches are distributed among these distances:
1 10 0.13
2 63 0.81
3 5 0.06
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.54
Consensus pattern (2 bp):
TA
Found at i:65046 original size:4 final size:4
Alignment explanation
Indices: 65037--65084 Score: 51
Period size: 4 Copynumber: 11.5 Consensus size: 4
65027 TACATTATTA
* * *
65037 TTAT TTATT TTAT ATTAT ATAT TGAT TTAT TTAT TTAT TTAA TTAT TT
1 TTAT TTA-T TTAT -TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TT
65085 TCAAGTTCAA
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
4 28 0.78
5 8 0.22
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (4 bp):
TTAT
Found at i:65073 original size:25 final size:24
Alignment explanation
Indices: 64991--65074 Score: 77
Period size: 25 Copynumber: 3.5 Consensus size: 24
64981 TGTGTTATAT
* *
64991 ATTATATATTTATATTTTATA-TG
1 ATTATTTATTTATATTATATATTG
* *
65014 AGTA-TTA-TTATATTACATTATT-
1 ATTATTTATTTATATTATA-TATTG
65036 ATTATTTATTTTATATTATATATTG
1 ATTATTTA-TTTATATTATATATTG
65061 ATTTATTTATTTAT
1 A-TTATTTATTTAT
65075 TTAATTATTT
Statistics
Matches: 48, Mismatches: 6, Indels: 12
0.73 0.09 0.18
Matches are distributed among these distances:
21 8 0.17
22 7 0.15
23 7 0.15
24 4 0.08
25 15 0.31
26 7 0.15
ACGTcount: A:0.33, C:0.01, G:0.04, T:0.62
Consensus pattern (24 bp):
ATTATTTATTTATATTATATATTG
Found at i:65409 original size:22 final size:22
Alignment explanation
Indices: 65355--65411 Score: 87
Period size: 22 Copynumber: 2.6 Consensus size: 22
65345 ACTATACGGT
** *
65355 ATGAACAATAATGTGAACATTA
1 ATGAACAATACCGTGAACAGTA
65377 ATGAACAATACCGTGAACAGTA
1 ATGAACAATACCGTGAACAGTA
65399 ATGAACAATACCG
1 ATGAACAATACCG
65412 AATGCTAAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.47, C:0.16, G:0.16, T:0.21
Consensus pattern (22 bp):
ATGAACAATACCGTGAACAGTA
Found at i:65482 original size:20 final size:21
Alignment explanation
Indices: 65442--65483 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
65432 TTGCTTCAGG
* *
65442 GGTATCGATACCCCTGTTACA
1 GGTACCGATACCCCTGCTACA
65463 GGTACCGATA-CCCTGCTACA
1 GGTACCGATACCCCTGCTACA
65483 G
1 G
65484 TACTTTCATA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 10 0.53
21 9 0.47
ACGTcount: A:0.24, C:0.31, G:0.21, T:0.24
Consensus pattern (21 bp):
GGTACCGATACCCCTGCTACA
Found at i:66296 original size:31 final size:31
Alignment explanation
Indices: 66253--66315 Score: 90
Period size: 31 Copynumber: 2.0 Consensus size: 31
66243 TGACCTATGT
* *
66253 AACTATCCATATGTTTCGAAGAACATTGGTA
1 AACTATCCATATGTTCCGAAGAACATAGGTA
* *
66284 AACTGTCCATATGTTCCGTAGAACATAGGTA
1 AACTATCCATATGTTCCGAAGAACATAGGTA
66315 A
1 A
66316 CCATCGACTC
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.30
Consensus pattern (31 bp):
AACTATCCATATGTTCCGAAGAACATAGGTA
Found at i:67625 original size:22 final size:22
Alignment explanation
Indices: 67584--67625 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
67574 TCCCCCATGC
67584 TTATCTCTTAATAAAGAGATAA
1 TTATCTCTTAATAAAGAGATAA
*
67606 TTATCTTTTAGATAAA-AGAT
1 TTATCTCTTA-ATAAAGAGAT
67626 CATTTCACCC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 13 0.72
23 5 0.28
ACGTcount: A:0.43, C:0.07, G:0.10, T:0.40
Consensus pattern (22 bp):
TTATCTCTTAATAAAGAGATAA
Found at i:68945 original size:43 final size:41
Alignment explanation
Indices: 68895--68974 Score: 115
Period size: 43 Copynumber: 1.9 Consensus size: 41
68885 AGTTTAATAT
*
68895 TTTTATTTTAACCCTAGTATTAATTCTTTTCACTTTTATTTTA
1 TTTTATTTTAACCCTAATATTAA-T-TTTTCACTTTTATTTTA
* *
68938 TTTTATTTTAACCCTAATTTTAATTTTTCCCTTTTAT
1 TTTTATTTTAACCCTAATATTAATTTTTCACTTTTAT
68975 AAAATTTTTG
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
41 12 0.35
42 1 0.03
43 21 0.62
ACGTcount: A:0.23, C:0.15, G:0.01, T:0.61
Consensus pattern (41 bp):
TTTTATTTTAACCCTAATATTAATTTTTCACTTTTATTTTA
Found at i:69373 original size:2 final size:2
Alignment explanation
Indices: 69366--69421 Score: 112
Period size: 2 Copynumber: 28.0 Consensus size: 2
69356 AATTACGACA
69366 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
69408 AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT
69422 TCACAGGTTA
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 54 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:71948 original size:12 final size:12
Alignment explanation
Indices: 71931--71956 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
71921 CTCGCTGTCA
71931 TCATCGTCGTCG
1 TCATCGTCGTCG
71943 TCATCGTCGTCG
1 TCATCGTCGTCG
71955 TC
1 TC
71957 CTGAGCAGGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.08, C:0.35, G:0.23, T:0.35
Consensus pattern (12 bp):
TCATCGTCGTCG
Found at i:74050 original size:17 final size:18
Alignment explanation
Indices: 74007--74047 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
73997 GAATTATATT
74007 AGTAAAATA-TTAAATAA
1 AGTAAAATACTTAAATAA
74024 AGTAAAATACTTAAATAA
1 AGTAAAATACTTAAATAA
*
74042 ATTAAA
1 AGTAAA
74048 TACATAATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 9 0.41
18 13 0.59
ACGTcount: A:0.63, C:0.02, G:0.05, T:0.29
Consensus pattern (18 bp):
AGTAAAATACTTAAATAA
Found at i:74387 original size:51 final size:52
Alignment explanation
Indices: 74280--74393 Score: 130
Period size: 51 Copynumber: 2.2 Consensus size: 52
74270 CCTACGTGAC
* **
74280 GTATAGCGCGG-ATCAGGGGGCGCGTTATACCCACGTGTAATCTATGTCAGA
1 GTATAGCGCGGTATCAGGGGGCGCGCTATACCCACGTGTAATCTAAATCAGA
*
74331 GTATAGCGCGGTA-CAGGGGGCGCGCTATACCCCACGTG-ACGT-TAAATCAGCA
1 GTATAGCGCGGTATCAGGGGGCGCGCTATA-CCCACGTGTA-ATCTAAATCAG-A
74383 -TATAGCGCGGT
1 GTATAGCGCGGT
74394 TCAAGAGGCG
Statistics
Matches: 55, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
51 44 0.80
52 11 0.20
ACGTcount: A:0.24, C:0.24, G:0.32, T:0.21
Consensus pattern (52 bp):
GTATAGCGCGGTATCAGGGGGCGCGCTATACCCACGTGTAATCTAAATCAGA
Found at i:74463 original size:29 final size:29
Alignment explanation
Indices: 74421--74497 Score: 109
Period size: 29 Copynumber: 2.7 Consensus size: 29
74411 CTGCTACGGG
*
74421 TGTTAGATCGAGAAATATAATCTGACCGA
1 TGTTAGATCGAGAAATATAATCTAACCGA
* *
74450 TGTTATATCGAGAAATATAATTTAACCGA
1 TGTTAGATCGAGAAATATAATCTAACCGA
* *
74479 TGTTAGATCAATAAATATA
1 TGTTAGATCGAGAAATATA
74498 CGATCACCGA
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
29 42 1.00
ACGTcount: A:0.42, C:0.10, G:0.16, T:0.32
Consensus pattern (29 bp):
TGTTAGATCGAGAAATATAATCTAACCGA
Found at i:76682 original size:21 final size:23
Alignment explanation
Indices: 76648--76692 Score: 60
Period size: 21 Copynumber: 2.0 Consensus size: 23
76638 GTGACTAGTG
76648 ATAACTTGATAAAC-A-ATATAA
1 ATAACTTGATAAACGACATATAA
76669 ATAA-TTGATGAAACGACATATAA
1 ATAACTTGAT-AAACGACATATAA
76692 A
1 A
76693 GACGGATTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
20 5 0.24
21 8 0.38
22 1 0.05
23 7 0.33
ACGTcount: A:0.56, C:0.09, G:0.09, T:0.27
Consensus pattern (23 bp):
ATAACTTGATAAACGACATATAA
Found at i:77046 original size:13 final size:14
Alignment explanation
Indices: 77023--77053 Score: 55
Period size: 13 Copynumber: 2.3 Consensus size: 14
77013 TAATTCAGTT
77023 ATTTGATTTTCTAA
1 ATTTGATTTTCTAA
77037 ATTT-ATTTTCTAA
1 ATTTGATTTTCTAA
77050 ATTT
1 ATTT
77054 TTTAAAATTC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 13 0.76
14 4 0.24
ACGTcount: A:0.29, C:0.06, G:0.03, T:0.61
Consensus pattern (14 bp):
ATTTGATTTTCTAA
Found at i:78255 original size:20 final size:20
Alignment explanation
Indices: 78222--78261 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
78212 CAATCCAATC
*
78222 AAGTCATTGTGAAGGGCATA
1 AAGTCATTGAGAAGGGCATA
*
78242 AAGTCCTTGAGAAGGGCATA
1 AAGTCATTGAGAAGGGCATA
78262 TCTGTCTTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.35, C:0.12, G:0.30, T:0.23
Consensus pattern (20 bp):
AAGTCATTGAGAAGGGCATA
Found at i:82841 original size:29 final size:30
Alignment explanation
Indices: 82808--82870 Score: 74
Period size: 30 Copynumber: 2.1 Consensus size: 30
82798 CCTAATTTTT
* *
82808 TTTTAA-AAAATTTAATGACTAAATTGAAA
1 TTTTAATAAAATTTAAGGACTAAAGTGAAA
* * *
82837 TTTTAATTAAATTTAGGGACTAAGGTGAAA
1 TTTTAATAAAATTTAAGGACTAAAGTGAAA
82867 TTTT
1 TTTT
82871 GATTAATTCG
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
29 6 0.21
30 22 0.79
ACGTcount: A:0.43, C:0.03, G:0.13, T:0.41
Consensus pattern (30 bp):
TTTTAATAAAATTTAAGGACTAAAGTGAAA
Found at i:82850 original size:30 final size:30
Alignment explanation
Indices: 82815--82876 Score: 79
Period size: 30 Copynumber: 2.1 Consensus size: 30
82805 TTTTTTTAAA
* *
82815 AAATTTAATGACTAAATTGAAATTTTAATT
1 AAATTTAAGGACTAAAGTGAAATTTTAATT
* * *
82845 AAATTTAGGGACTAAGGTGAAATTTTGATT
1 AAATTTAAGGACTAAAGTGAAATTTTAATT
82875 AA
1 AA
82877 TTCGGATTCA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.44, C:0.03, G:0.15, T:0.39
Consensus pattern (30 bp):
AAATTTAAGGACTAAAGTGAAATTTTAATT
Found at i:85341 original size:24 final size:27
Alignment explanation
Indices: 85294--85346 Score: 67
Period size: 25 Copynumber: 2.1 Consensus size: 27
85284 TCTTTAGCCC
* *
85294 TATCTCTTTTATTTATTTTTAAT-ATT
1 TATCTCTTTTATTTACTTTAAATAATT
85320 TATCT-TTTTATTT-CTTTAAATAATT
1 TATCTCTTTTATTTACTTTAAATAATT
85345 TA
1 TA
85347 AAAACCCCTT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
24 6 0.25
25 13 0.54
26 5 0.21
ACGTcount: A:0.26, C:0.08, G:0.00, T:0.66
Consensus pattern (27 bp):
TATCTCTTTTATTTACTTTAAATAATT
Found at i:85380 original size:16 final size:16
Alignment explanation
Indices: 85359--85389 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
85349 AACCCCTTTT
85359 ATATTTATTACTATTA
1 ATATTTATTACTATTA
*
85375 ATATTTATTATTATT
1 ATATTTATTACTATT
85390 TTTTTAATTT
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:0.35, C:0.03, G:0.00, T:0.61
Consensus pattern (16 bp):
ATATTTATTACTATTA
Found at i:85399 original size:19 final size:20
Alignment explanation
Indices: 85377--85415 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
85367 TACTATTAAT
*
85377 ATTTATTATTATTT-TTTTA
1 ATTTATAATTATTTATTTTA
85396 ATTTATAATTATTTATTTTA
1 ATTTATAATTATTTATTTTA
85416 TTATATCTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 13 0.72
20 5 0.28
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (20 bp):
ATTTATAATTATTTATTTTA
Found at i:90399 original size:14 final size:14
Alignment explanation
Indices: 90368--90412 Score: 54
Period size: 14 Copynumber: 3.1 Consensus size: 14
90358 TTTTACCTAG
**
90368 ATTTATTTCATTCC
1 ATTTATTTCATTTT
90382 ATTTATTTCATTTT
1 ATTTATTTCATTTT
*
90396 ATTTTATTTTATTTT
1 A-TTTATTTCATTTT
90411 AT
1 AT
90413 CATATGCTTA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
14 14 0.52
15 13 0.48
ACGTcount: A:0.22, C:0.09, G:0.00, T:0.69
Consensus pattern (14 bp):
ATTTATTTCATTTT
Found at i:90431 original size:5 final size:5
Alignment explanation
Indices: 90383--90412 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
90373 TTTCATTCCA
*
90383 TTTAT TTCAT TTTAT TTTAT TTTAT TTTAT
1 TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT
90413 CATATGCTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.20, C:0.03, G:0.00, T:0.77
Consensus pattern (5 bp):
TTTAT
Found at i:92645 original size:15 final size:16
Alignment explanation
Indices: 92620--92649 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
92610 TGCTATTTTT
92620 AAAACAAAACAAAAAC
1 AAAACAAAACAAAAAC
92636 AAAA-AAAACAAAAA
1 AAAACAAAACAAAAA
92650 AAGCCAAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.87, C:0.13, G:0.00, T:0.00
Consensus pattern (16 bp):
AAAACAAAACAAAAAC
Found at i:98155 original size:84 final size:85
Alignment explanation
Indices: 98015--98169 Score: 249
Period size: 84 Copynumber: 1.8 Consensus size: 85
98005 ATTTTAAACA
* * *
98015 TTATATTTGTTTTAAGTATTTTAGTTTAAATAGGTTTTAGTATTTTAATTAGGATTTAGGATATT
1 TTATATTTGTTTTAAGTATTTTAGTTAAAATAGGTTTAAGTATTTTAATTAGGATTTAAGATATT
98080 ATTTTAAATATTATTTTATT
66 ATTTTAAATATTATTTTATT
* * *
98100 TTATCTTTGTTTTAGGTATTTTAGTTAAAATA-GTTTAAGTGTTTTAATTAGGATTTAAGATATT
1 TTATATTTGTTTTAAGTATTTTAGTTAAAATAGGTTTAAGTATTTTAATTAGGATTTAAGATATT
98164 ATTTTA
66 ATTTTA
98170 GGAATTATCT
Statistics
Matches: 64, Mismatches: 6, Indels: 1
0.90 0.08 0.01
Matches are distributed among these distances:
84 35 0.55
85 29 0.45
ACGTcount: A:0.30, C:0.01, G:0.13, T:0.56
Consensus pattern (85 bp):
TTATATTTGTTTTAAGTATTTTAGTTAAAATAGGTTTAAGTATTTTAATTAGGATTTAAGATATT
ATTTTAAATATTATTTTATT
Found at i:109006 original size:29 final size:29
Alignment explanation
Indices: 108964--109037 Score: 141
Period size: 29 Copynumber: 2.6 Consensus size: 29
108954 TGATATGAAG
108964 TGACATGAGCTACATGATCACAAGAGAAA
1 TGACATGAGCTACATGATCACAAGAGAAA
108993 TGACATGAGCTACATGATCACAAGAGAAA
1 TGACATGAGCTACATGATCACAAGAGAAA
109022 TGACATGAG-TACATGA
1 TGACATGAGCTACATGA
109038 ACATATGAAA
Statistics
Matches: 45, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
28 7 0.16
29 38 0.84
ACGTcount: A:0.43, C:0.16, G:0.22, T:0.19
Consensus pattern (29 bp):
TGACATGAGCTACATGATCACAAGAGAAA
Found at i:110905 original size:32 final size:34
Alignment explanation
Indices: 110854--110921 Score: 113
Period size: 32 Copynumber: 2.1 Consensus size: 34
110844 ACTCAACTCA
*
110854 AACTCACAAGCTCGAAATATAATATTGAAACTTG
1 AACTCACAAGCTCAAAATATAATATTGAAACTTG
110888 AACTCA-AA-CTCAAAATATAATATTGAAACTTG
1 AACTCACAAGCTCAAAATATAATATTGAAACTTG
110920 AA
1 AA
110922 ATATAATATT
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
32 25 0.76
33 2 0.06
34 6 0.18
ACGTcount: A:0.49, C:0.16, G:0.09, T:0.26
Consensus pattern (34 bp):
AACTCACAAGCTCAAAATATAATATTGAAACTTG
Found at i:110923 original size:20 final size:20
Alignment explanation
Indices: 110900--110941 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
110890 CTCAAACTCA
110900 AAATATAATATTGAAACTTG
1 AAATATAATATTGAAACTTG
110920 AAATATAATATTGAAACTTG
1 AAATATAATATTGAAACTTG
110940 AA
1 AA
110942 CTCAAAAAGG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.52, C:0.05, G:0.10, T:0.33
Consensus pattern (20 bp):
AAATATAATATTGAAACTTG
Found at i:111437 original size:28 final size:29
Alignment explanation
Indices: 111386--111445 Score: 113
Period size: 29 Copynumber: 2.1 Consensus size: 29
111376 CCAAATTTAT
111386 TTTTTAATTATAGTTATATAATTATATTA
1 TTTTTAATTATAGTTATATAATTATATTA
111415 TTTTTAATTATAGTTATA-AATTATATTA
1 TTTTTAATTATAGTTATATAATTATATTA
111443 TTT
1 TTT
111446 AATATGTTTA
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
28 13 0.42
29 18 0.58
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.60
Consensus pattern (29 bp):
TTTTTAATTATAGTTATATAATTATATTA
Found at i:125096 original size:16 final size:16
Alignment explanation
Indices: 125077--125107 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
125067 GATGTTTCAA
125077 AATAAACACAGTTAAC
1 AATAAACACAGTTAAC
*
125093 AATAAACACCGTTAA
1 AATAAACACAGTTAA
125108 GCACATTAAT
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:0.55, C:0.19, G:0.06, T:0.19
Consensus pattern (16 bp):
AATAAACACAGTTAAC
Found at i:125920 original size:2 final size:2
Alignment explanation
Indices: 125913--125968 Score: 105
Period size: 2 Copynumber: 28.5 Consensus size: 2
125903 ATTCTCTTGA
125913 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
125955 AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT A
125969 ATTTTGATCA
Statistics
Matches: 53, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 52 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:135277 original size:34 final size:34
Alignment explanation
Indices: 135239--135311 Score: 83
Period size: 34 Copynumber: 2.1 Consensus size: 34
135229 TTCACAAACA
* *
135239 TGTTCATTTAATATTTGTGAAAATGTTCATTTAG
1 TGTTCATTTAACATTAGTGAAAATGTTCATTTAG
* * * *
135273 TGTTCGTTTAACGTTAGTGAACATGTTCGTTTAG
1 TGTTCATTTAACATTAGTGAAAATGTTCATTTAG
*
135307 CGTTC
1 TGTTC
135312 GTGTTCATTT
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
34 32 1.00
ACGTcount: A:0.23, C:0.11, G:0.19, T:0.47
Consensus pattern (34 bp):
TGTTCATTTAACATTAGTGAAAATGTTCATTTAG
Found at i:138352 original size:14 final size:16
Alignment explanation
Indices: 138335--138366 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
138325 TCGATTCAAA
138335 TAATT-GGTTAA-AAT
1 TAATTAGGTTAATAAT
138349 TAATTAGGTTAATAAT
1 TAATTAGGTTAATAAT
138365 TA
1 TA
138367 GAGCCTCCAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 5 0.31
15 6 0.38
16 5 0.31
ACGTcount: A:0.44, C:0.00, G:0.12, T:0.44
Consensus pattern (16 bp):
TAATTAGGTTAATAAT
Found at i:145920 original size:20 final size:20
Alignment explanation
Indices: 145895--145964 Score: 88
Period size: 20 Copynumber: 3.5 Consensus size: 20
145885 TACTGTTCAT
*
145895 TACTATTCACATAGTATAAG
1 TACTATTCATATAGTATAAG
* **
145915 TACTATTCATACAGTATCGG
1 TACTATTCATATAGTATAAG
*
145935 TACTATTCATATAATATAA-
1 TACTATTCATATAGTATAAG
145954 TACTATTCATA
1 TACTATTCATA
145965 AAAACATTTT
Statistics
Matches: 42, Mismatches: 8, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
19 11 0.26
20 31 0.74
ACGTcount: A:0.39, C:0.16, G:0.07, T:0.39
Consensus pattern (20 bp):
TACTATTCATATAGTATAAG
Found at i:148952 original size:20 final size:20
Alignment explanation
Indices: 148927--148966 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
148917 GGCTTGAAAT
*
148927 TACTGTAGCATTATCGATAC
1 TACTGTAGCAGTATCGATAC
148947 TACTGTAGCAGTATCGATAC
1 TACTGTAGCAGTATCGATAC
148967 CCATTTTTCA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.30, C:0.20, G:0.17, T:0.33
Consensus pattern (20 bp):
TACTGTAGCAGTATCGATAC
Found at i:149037 original size:20 final size:19
Alignment explanation
Indices: 149012--149078 Score: 73
Period size: 20 Copynumber: 3.4 Consensus size: 19
149002 TGTTTATTAC
* *
149012 TATTCACACAGTATCGATAT
1 TATTCATACAATATC-ATAT
*
149032 TATTCATACAATATCAGTAC
1 TATTCATACAATATCA-TAT
149052 TATTCATACAATA-CAATAT
1 TATTCATACAATATC-ATAT
149071 TATTCATA
1 TATTCATA
149079 AAAACATTTT
Statistics
Matches: 41, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
19 12 0.29
20 29 0.71
ACGTcount: A:0.40, C:0.18, G:0.04, T:0.37
Consensus pattern (19 bp):
TATTCATACAATATCATAT
Found at i:154073 original size:26 final size:25
Alignment explanation
Indices: 154042--154358 Score: 184
Period size: 20 Copynumber: 13.9 Consensus size: 25
154032 ATGCATTAAG
154042 GCATGAAAGGATGCCATAAATAAAAT
1 GCATGAAAGGATGCCATAAAT-AAAT
*
154068 GCATGAAAGGATG-CAT---T-AAG
1 GCATGAAAGGATGCCATAAATAAAT
*
154088 GCATGAAAGGATG-CAT---T-AAG
1 GCATGAAAGGATGCCATAAATAAAT
* *
154108 GCATGAAAGGATTCCATAAAAGAAAT
1 GCATGAAAGGATGCCAT-AAATAAAT
*
154134 GCATGAAAGGATGCCATAAAAGAAAT
1 GCATGAAAGGATGCCAT-AAATAAAT
* *
154160 GCATGAAAGTATG-CAT---T-AAG
1 GCATGAAAGGATGCCATAAATAAAT
154180 GCATGAAAGGATGCCATAAATGAAAT
1 GCATGAAAGGATGCCATAAAT-AAAT
* *
154206 GCATGAAATGATG-CAT---T-AAG
1 GCATGAAAGGATGCCATAAATAAAT
154226 GCATGAAAGGATGCCATAAATAAAAT
1 GCATGAAAGGATGCCATAAAT-AAAT
* *
154252 GCATGAAAGG-T-ACAT---T-AAG
1 GCATGAAAGGATGCCATAAATAAAT
*
154271 GCATGAAAGGAT-ACAT---T-AAT
1 GCATGAAAGGATGCCATAAATAAAT
*
154291 GCATGAAATGATGCCATAAATTAAAT
1 GCATGAAAGGATGCCATAAA-TAAAT
* *
154317 GCATGAAATGATG-CAT---T-AAG
1 GCATGAAAGGATGCCATAAATAAAT
*
154337 GCATGAAAGGATTCCATAAATA
1 GCATGAAAGGATGCCATAAATA
154359 GAATTAACAA
Statistics
Matches: 239, Mismatches: 22, Indels: 61
0.74 0.07 0.19
Matches are distributed among these distances:
19 12 0.05
20 94 0.39
21 17 0.07
22 2 0.01
24 6 0.03
25 14 0.06
26 94 0.39
ACGTcount: A:0.45, C:0.11, G:0.22, T:0.21
Consensus pattern (25 bp):
GCATGAAAGGATGCCATAAATAAAT
Found at i:154082 original size:46 final size:46
Alignment explanation
Indices: 154010--154282 Score: 337
Period size: 46 Copynumber: 6.0 Consensus size: 46
154000 AAAACAAATT
* **
154010 CATAAATGAAATGCATGAAATAATGCATTAAGGCATGAAAGGATGC
1 CATAAATAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGC
154056 CATAAATAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATG-
1 CATAAATAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGC
* * *
154101 CAT---T--AAGGCATGAAAGGATTCCATAAAAGAAATGCATGAAAGGATGC
1 CATAAATAAAATGCATGAAAGGA-TGCAT-TAAG----GCATGAAAGGATGC
*
154148 CATAAA-AGAAATGCATGAAAGTATGCATTAAGGCATGAAAGGATGC
1 CATAAATA-AAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGC
* *
154194 CATAAATGAAATGCATGAAATGATGCATTAAGGCATGAAAGGATGC
1 CATAAATAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGC
*
154240 CATAAATAAAATGCATGAAAGG-TACATTAAGGCATGAAAGGAT
1 CATAAATAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGAT
154283 ACATTAATGC
Statistics
Matches: 197, Mismatches: 16, Indels: 29
0.81 0.07 0.12
Matches are distributed among these distances:
40 13 0.07
41 4 0.02
42 4 0.02
45 23 0.12
46 131 0.66
47 3 0.02
50 3 0.02
51 4 0.02
52 12 0.06
ACGTcount: A:0.46, C:0.11, G:0.23, T:0.21
Consensus pattern (46 bp):
CATAAATAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGC
Found at i:154142 original size:13 final size:13
Alignment explanation
Indices: 154126--154168 Score: 52
Period size: 13 Copynumber: 3.3 Consensus size: 13
154116 GGATTCCATA
154126 AAAGAAATGCATG
1 AAAGAAATGCATG
* *
154139 AAAG-GATGCCATA
1 AAAGAAATG-CATG
154152 AAAGAAATGCATG
1 AAAGAAATGCATG
154165 AAAG
1 AAAG
154169 TATGCATTAA
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
12 3 0.12
13 18 0.75
14 3 0.12
ACGTcount: A:0.53, C:0.09, G:0.23, T:0.14
Consensus pattern (13 bp):
AAAGAAATGCATG
Found at i:154288 original size:65 final size:66
Alignment explanation
Indices: 154206--154348 Score: 216
Period size: 65 Copynumber: 2.2 Consensus size: 66
154196 TAAATGAAAT
* * *
154206 GCATGAAATGATGCATTAAGGCATGAAAGGATGCCATAAATAAAATGCATGAAA-GGTACATTAA
1 GCATGAAAGGATACATTAAGGCATGAAAGGATGCCATAAATAAAATGCATGAAATGATACATTAA
154270 G
66 G
* * * *
154271 GCATGAAAGGATACATTAATGCATGAAATGATGCCATAAATTAAATGCATGAAATGATGCATTAA
1 GCATGAAAGGATACATTAAGGCATGAAAGGATGCCATAAATAAAATGCATGAAATGATACATTAA
154336 G
66 G
154337 GCATGAAAGGAT
1 GCATGAAAGGAT
154349 TCCATAAATA
Statistics
Matches: 70, Mismatches: 7, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
65 49 0.70
66 21 0.30
ACGTcount: A:0.44, C:0.10, G:0.22, T:0.23
Consensus pattern (66 bp):
GCATGAAAGGATACATTAAGGCATGAAAGGATGCCATAAATAAAATGCATGAAATGATACATTAA
G
Found at i:154329 original size:111 final size:116
Alignment explanation
Indices: 154088--154361 Score: 398
Period size: 111 Copynumber: 2.4 Consensus size: 116
154078 ATGCATTAAG
* *
154088 GCATGAAAGGATGCATTAAGGCATGAAAGGATTCCATAAA-AGAAATGCATGAAAGGATGCCATA
1 GCATGAAATGATGCATTAAGGCATGAAAGGATTCCATAAATAGAAATGCATGAAAGGATGACATA
* *
154152 AAAGAAATGCATGAAAGTATGCATTAAGGCATGAAAGGATGCCATAAATGAAAT
66 AAAG--A-GCATGAAAGGATACATTAAGGCATGAAAGGATGCCATAAATGAAAT
*
154206 GCATGAAATGATGCATTAAGGCATGAAAGGATGCCATAAATA-AAATGCATGAAAGG-T-ACAT-
1 GCATGAAATGATGCATTAAGGCATGAAAGGATTCCATAAATAGAAATGCATGAAAGGATGACATA
* * * *
154267 TAAG-GCATGAAAGGATACATTAATGCATGAAATGATGCCATAAATTAAAT
66 AAAGAGCATGAAAGGATACATTAAGGCATGAAAGGATGCCATAAATGAAAT
154317 GCATGAAATGATGCATTAAGGCATGAAAGGATTCCATAAATAGAA
1 GCATGAAATGATGCATTAAGGCATGAAAGGATTCCATAAATAGAA
154362 TTAACAAATA
Statistics
Matches: 144, Mismatches: 10, Indels: 10
0.88 0.06 0.06
Matches are distributed among these distances:
111 82 0.57
112 2 0.01
115 3 0.02
116 3 0.02
117 1 0.01
118 52 0.36
119 1 0.01
ACGTcount: A:0.45, C:0.11, G:0.22, T:0.22
Consensus pattern (116 bp):
GCATGAAATGATGCATTAAGGCATGAAAGGATTCCATAAATAGAAATGCATGAAAGGATGACATA
AAAGAGCATGAAAGGATACATTAAGGCATGAAAGGATGCCATAAATGAAAT
Found at i:158521 original size:35 final size:35
Alignment explanation
Indices: 158429--158500 Score: 126
Period size: 35 Copynumber: 2.1 Consensus size: 35
158419 CCAAAAAAGA
*
158429 AGAGTTGGATTAGGAATCAAATACTAGTCTAAAAT
1 AGAGTTGGATTAGGACTCAAATACTAGTCTAAAAT
*
158464 AGAGTTGGATTAGGACTCAAATATTAGTCTAAAAT
1 AGAGTTGGATTAGGACTCAAATACTAGTCTAAAAT
158499 AG
1 AG
158501 GGTTTTTTAG
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.42, C:0.08, G:0.21, T:0.29
Consensus pattern (35 bp):
AGAGTTGGATTAGGACTCAAATACTAGTCTAAAAT
Found at i:158901 original size:17 final size:18
Alignment explanation
Indices: 158875--158914 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
158865 ATTATATGGA
158875 TATT-TTATTCAT-TTAT
1 TATTATTATTCATGTTAT
*
158891 TTTTATTATTCATGTTAT
1 TATTATTATTCATGTTAT
158909 TATTAT
1 TATTAT
158915 ACGTATATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
16 3 0.15
17 8 0.40
18 9 0.45
ACGTcount: A:0.25, C:0.05, G:0.03, T:0.68
Consensus pattern (18 bp):
TATTATTATTCATGTTAT
Found at i:158974 original size:2 final size:2
Alignment explanation
Indices: 158969--158993 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
158959 TATATTTTAT
158969 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 T
158994 CTTTAATATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:159225 original size:16 final size:16
Alignment explanation
Indices: 159185--159228 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 16
159175 TATATATATA
159185 TATTGTTTTTTATTAT
1 TATTGTTTTTTATTAT
159201 T-TTCGTTTTTTATTCAT
1 TATT-GTTTTTTATT-AT
159218 TATT-TTTTTTA
1 TATTGTTTTTTA
159229 AATCTTGTGT
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
15 2 0.08
16 18 0.72
17 3 0.12
18 2 0.08
ACGTcount: A:0.16, C:0.05, G:0.05, T:0.75
Consensus pattern (16 bp):
TATTGTTTTTTATTAT
Found at i:159439 original size:38 final size:40
Alignment explanation
Indices: 159388--159466 Score: 110
Period size: 40 Copynumber: 2.0 Consensus size: 40
159378 AGTGAGAGGG
*
159388 TAGCTTTTCTATTTT-TAAATA-TTTGTTGTATATATATA
1 TAGCTTTTCTATTTTATAAATACTTTGATGTATATATATA
*
159426 TAGCTTATT-TATTTTATTAATACTTTGATGTATATATATA
1 TAGCTT-TTCTATTTTATAAATACTTTGATGTATATATATA
159466 T
1 T
159467 GTATATATTT
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
38 12 0.33
39 7 0.19
40 17 0.47
ACGTcount: A:0.30, C:0.05, G:0.08, T:0.57
Consensus pattern (40 bp):
TAGCTTTTCTATTTTATAAATACTTTGATGTATATATATA
Found at i:160517 original size:15 final size:14
Alignment explanation
Indices: 160495--160524 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
160485 TTTTCTTGCC
160495 ATTTTTTTTATTTT
1 ATTTTTTTTATTTT
160509 ATTTGTTTTTATTTT
1 ATTT-TTTTTATTTT
160524 A
1 A
160525 CTAACTATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.27
15 11 0.73
ACGTcount: A:0.17, C:0.00, G:0.03, T:0.80
Consensus pattern (14 bp):
ATTTTTTTTATTTT
Found at i:162803 original size:17 final size:19
Alignment explanation
Indices: 162781--162818 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
162771 ATACTTTGCA
162781 TTTTATA-TTT-CATGTTT
1 TTTTATATTTTCCATGTTT
162798 TTTTATATTTTCCATGTTT
1 TTTTATATTTTCCATGTTT
162817 TT
1 TT
162819 ACATTCATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 7 0.37
18 3 0.16
19 9 0.47
ACGTcount: A:0.16, C:0.08, G:0.05, T:0.71
Consensus pattern (19 bp):
TTTTATATTTTCCATGTTT
Found at i:169940 original size:51 final size:51
Alignment explanation
Indices: 169860--169958 Score: 126
Period size: 51 Copynumber: 1.9 Consensus size: 51
169850 AATACTTCGC
* * *
169860 TTAGGATGAAAACCTGAAAGGGCATCCTAAGTCAAAAAAAAGGAAAAACGT
1 TTAGGATGAAAACCCGAAAGGGCACCCTAAATCAAAAAAAAGGAAAAACGT
* * ** *
169911 TTAGGGTGAAAACCCGAAAGGGCGCCCTAAATTGAAAAAAATGAAAAA
1 TTAGGATGAAAACCCGAAAGGGCACCCTAAATCAAAAAAAAGGAAAAA
169959 GAGAAAAAAG
Statistics
Matches: 40, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
51 40 1.00
ACGTcount: A:0.48, C:0.14, G:0.22, T:0.15
Consensus pattern (51 bp):
TTAGGATGAAAACCCGAAAGGGCACCCTAAATCAAAAAAAAGGAAAAACGT
Found at i:171219 original size:106 final size:105
Alignment explanation
Indices: 170976--171584 Score: 757
Period size: 106 Copynumber: 5.9 Consensus size: 105
170966 ATATCGTGCC
* *
170976 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGACTGGTTGTCAACAAACCAATTT-T
1 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAA-CAATTTCC
* * * * *
171040 CAGTTTCATTCAGAGCCAATTTCAACTTAAAACCGAAGAATATTGG
65 CA--AT--TTCAGAG-CAATTTCAACTTCACAGCGAAGGATATTGG
* **
171086 ACTC-AGGATAACACAAGTTCAACTTCACAACGAAGGGACAACTGGTTGTCAACAAACAATTTCC
1 ACTCGA-GACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCC
* *
171150 CAATTTCAGAGCCAATTTCAACTTCACATCGAAGGATGTTGG
65 CAATTTCAGAG-CAATTTCAACTTCACAGCGAAGGATATTGG
* *
171192 ACTCGGGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAATAATTTCCC
1 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCC
171257 AATTTCAGAGTCAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAG-CAATTTCAACTTCACAGCGAAGGATATTGG
* * *
171298 ACTCAAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAAAAAACAATCTCCC
1 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCC
*
171363 AATTTCAGAGC-----CAA--T---AGCGAATGATA-TGG
66 AATTTCAGAGCAATTTCAACTTCACAGCGAAGGATATTGG
* **
171392 ACTCGAGACGACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCAT
1 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCC
* *
171457 AATTTCAG-GGAATTTCAACTTCACATCGAAGGATATTGG
66 AATTTCAGAGCAATTTCAACTTCACAGCGAAGGATATTGG
* * *
171496 ACTCGAGAC--CACAAGTTCAATTTCACAACGAAGGGAC-GCTGGTTGTCAATAAATAATTTCCC
1 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCC
* *
171558 AATTTCAGGGTCAATTACAACTTCACA
66 AATTTCAGAG-CAATTTCAACTTCACA
171585 ATGAAGGGTA
Statistics
Matches: 444, Mismatches: 39, Indels: 39
0.85 0.07 0.07
Matches are distributed among these distances:
93 1 0.00
94 70 0.16
95 10 0.02
98 4 0.01
100 4 0.01
101 29 0.07
102 28 0.06
103 23 0.05
104 12 0.03
105 1 0.00
106 200 0.45
108 1 0.00
109 7 0.02
110 54 0.12
ACGTcount: A:0.36, C:0.23, G:0.18, T:0.23
Consensus pattern (105 bp):
ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCC
AATTTCAGAGCAATTTCAACTTCACAGCGAAGGATATTGG
Found at i:172013 original size:35 final size:35
Alignment explanation
Indices: 171967--172038 Score: 126
Period size: 35 Copynumber: 2.1 Consensus size: 35
171957 CCAAAAAACA
*
171967 AGAGTTGGATTAGGACTCAAATACTAGTCTAAAAT
1 AGAGTTGGATTAGGACTAAAATACTAGTCTAAAAT
*
172002 AGAGTTGGATTAGGACTAAAATATTAGTCTAAAAT
1 AGAGTTGGATTAGGACTAAAATACTAGTCTAAAAT
172037 AG
1 AG
172039 GATTTTTTAT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.42, C:0.08, G:0.21, T:0.29
Consensus pattern (35 bp):
AGAGTTGGATTAGGACTAAAATACTAGTCTAAAAT
Found at i:172439 original size:17 final size:18
Alignment explanation
Indices: 172413--172452 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
172403 ATTATATGAA
172413 TATT-TTATTCAT-TTAT
1 TATTATTATTCATGTTAT
*
172429 TTTTATTATTCATGTTAT
1 TATTATTATTCATGTTAT
172447 TATTAT
1 TATTAT
172453 ACATATATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
16 3 0.15
17 8 0.40
18 9 0.45
ACGTcount: A:0.25, C:0.05, G:0.03, T:0.68
Consensus pattern (18 bp):
TATTATTATTCATGTTAT
Found at i:172638 original size:86 final size:82
Alignment explanation
Indices: 172503--172660 Score: 194
Period size: 86 Copynumber: 1.9 Consensus size: 82
172493 TTTACTATAT
* * *
172503 TTTATTATTATATATATATATATATATATTTCTTTAATATTTTACTTATA-AGTCTATTATTACT
1 TTTATTATTATATATATATATATATATATTTCTTTAATAGTTTACTTATATA-CCTATTATTAAT
172567 ATATATATTGTAATTATC
65 ATATATATTGTAATTATC
* * *
172585 TTTATCTAGTTATATATATATATAT-TTTTTTATACTTTTAATAGTTTATTTATATACCTATTAT
1 TTTAT-TA-TTATATATATATATATATATATT-T-C-TTTAATAGTTTACTTATATACCTATTAT
172649 TAATATATATAT
61 TAATATATATAT
172661 ATTCTTAATT
Statistics
Matches: 64, Mismatches: 6, Indels: 8
0.82 0.08 0.10
Matches are distributed among these distances:
82 5 0.08
83 6 0.09
84 17 0.27
85 1 0.02
86 34 0.53
87 1 0.02
ACGTcount: A:0.35, C:0.06, G:0.03, T:0.57
Consensus pattern (82 bp):
TTTATTATTATATATATATATATATATATTTCTTTAATAGTTTACTTATATACCTATTATTAATA
TATATATTGTAATTATC
Found at i:172723 original size:2 final size:2
Alignment explanation
Indices: 172718--172746 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
172708 CTTATAACTT
172718 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 T
172747 TATTTTTTAT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:176342 original size:46 final size:46
Alignment explanation
Indices: 176275--176654 Score: 493
Period size: 46 Copynumber: 8.3 Consensus size: 46
176265 AAAATGAATT
* *
176275 CATAAATGAAATCCATGAAATGATGCATTAAGGCATGAAAGGATGC
1 CATAAATGAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGC
* * * * *
176321 CATAAATAAAATGCATTAAATGATGCATTAAGGAATGAAAGGATTC
1 CATAAATGAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGC
* *
176367 CATAAAAGAAATGCATGAAAGGATACATTAAGGCATGAAAGGATG-
1 CATAAATGAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGC
* *
176412 CATTAA-G--A--CATGAAAGGATGCCATAAATAAAATGCATGAAAGGATGC
1 CATAAATGAAATGCATGAAAGGATG-CAT---T--AAGGCATGAAAGGATGC
* * * *
176459 CATAAAAGAAATGCATGAAAGGATGAATTAAGGCATGAAATGATGT
1 CATAAATGAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGC
*
176505 CATAAATGAAATGCATGAAATGATGCATTAAGGCATGAAAGGATGC
1 CATAAATGAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGC
*
176551 CATAATTGAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGC
1 CATAAATGAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGC
* *
176597 CATAATTGAAATGCATGAAAGGATGCATTAAGGCATGAAATGATGC
1 CATAAATGAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGC
176643 CATAAATGAAAT
1 CATAAATGAAAT
176655 TAACAAATAA
Statistics
Matches: 293, Mismatches: 29, Indels: 24
0.85 0.08 0.07
Matches are distributed among these distances:
40 11 0.04
41 3 0.01
42 1 0.00
44 2 0.01
45 5 0.02
46 249 0.85
47 5 0.02
48 2 0.01
50 1 0.00
51 2 0.01
52 12 0.04
ACGTcount: A:0.46, C:0.10, G:0.22, T:0.22
Consensus pattern (46 bp):
CATAAATGAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGC
Found at i:176530 original size:12 final size:12
Alignment explanation
Indices: 176491--176532 Score: 50
Period size: 12 Copynumber: 3.3 Consensus size: 12
176481 ATGAATTAAG
176491 GCATGAAATGAT
1 GCATGAAATGAT
176503 GTCAT-AAATGAAAT
1 G-CATGAAATG--AT
176517 GCATGAAATGAT
1 GCATGAAATGAT
176529 GCAT
1 GCAT
176533 TAAGGCATGA
Statistics
Matches: 26, Mismatches: 0, Indels: 8
0.76 0.00 0.24
Matches are distributed among these distances:
12 12 0.46
13 6 0.23
14 8 0.31
ACGTcount: A:0.43, C:0.10, G:0.21, T:0.26
Consensus pattern (12 bp):
GCATGAAATGAT
Found at i:176567 original size:72 final size:66
Alignment explanation
Indices: 176333--176654 Score: 250
Period size: 66 Copynumber: 4.7 Consensus size: 66
176323 TAAATAAAAT
* * * * * *
176333 GCATTAAATGATGC-ATTAAGGAATGAAAGGATTCCATAAAAGAAATGCATGAAAGGATACATTA
1 GCATGAAAGGATGCAATTAA-GCATGAAAGGATGCCATAAATGAAATGCATGAAAGGATGCATTA
176397 AG
65 AG
*
176399 GCATGAAAGGATGC-ATTAAGACATGAAAGGATGCCATAAATAAAATGCATGAAAGGATGCCATA
1 GCATGAAAGGATGCAATTAAG-CATGAAAGGATGCCATAAATGAAATGCATGAAAGGATG-CAT-
*
176463 AAAG
63 TAAG
* * *
176467 AAATGCATGAAAGGATG-AATTAAGGCATGAAATGATGTCATAAATGAAATGCATGAAATGATGC
1 ----GCATGAAAGGATGCAATTAA-GCATGAAAGGATGCCATAAATGAAATGCATGAAAGGATGC
176531 ATTAAG
61 ATTAAG
*
176537 GCATGAAAGGATGCCATAATTGAAATGCATGAAAGGATG-CAT---T--AAGGCATGAAAGGATG
1 GCATGAAAGGATG-C--AATT--AA-GCATGAAAGGATGCCATAAATGAAATGCATGAAAGGATG
*
176596 CCATAATTGAAAT
60 -C---ATT--AAG
*
176609 GCATGAAAGGATGC-ATTAAGGCATGAAATGATGCCATAAATGAAAT
1 GCATGAAAGGATGCAATTAA-GCATGAAAGGATGCCATAAATGAAAT
176655 TAACAAATAA
Statistics
Matches: 208, Mismatches: 21, Indels: 48
0.75 0.08 0.17
Matches are distributed among these distances:
65 1 0.00
66 91 0.44
67 7 0.03
68 7 0.03
70 11 0.05
71 7 0.03
72 83 0.40
73 1 0.00
ACGTcount: A:0.45, C:0.10, G:0.23, T:0.22
Consensus pattern (66 bp):
GCATGAAAGGATGCAATTAAGCATGAAAGGATGCCATAAATGAAATGCATGAAAGGATGCATTAA
G
Found at i:177929 original size:15 final size:15
Alignment explanation
Indices: 177906--177936 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
177896 TGGAATCAAC
*
177906 TAAATAATAATTATA
1 TAAAAAATAATTATA
177921 TAAAAAATAATTATA
1 TAAAAAATAATTATA
177936 T
1 T
177937 CTAATACATA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (15 bp):
TAAAAAATAATTATA
Found at i:182340 original size:23 final size:23
Alignment explanation
Indices: 182314--182407 Score: 80
Period size: 23 Copynumber: 4.0 Consensus size: 23
182304 AGTCGAGGGT
*
182314 TCTATGCAGTCATTCGGGACAAA
1 TCTATGCGGTCATTCGGGACAAA
* * * * *
182337 TCTATGTGATCCTTCGGGATAAT
1 TCTATGCGGTCATTCGGGACAAA
* * * *
182360 TCTATGTGGTCCTTCAGAACAAA
1 TCTATGCGGTCATTCGGGACAAA
*
182383 TTCTAAGCGGTCATTCGGGACAAA
1 -TCTATGCGGTCATTCGGGACAAA
182407 T
1 T
182408 TCTACGTGGC
Statistics
Matches: 54, Mismatches: 16, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
23 36 0.67
24 18 0.33
ACGTcount: A:0.28, C:0.20, G:0.21, T:0.31
Consensus pattern (23 bp):
TCTATGCGGTCATTCGGGACAAA
Found at i:182423 original size:24 final size:24
Alignment explanation
Indices: 182326--182437 Score: 97
Period size: 24 Copynumber: 4.8 Consensus size: 24
182316 TATGCAGTCA
*
182326 TTCGGGACAAA-TCTATGTGATCC
1 TTCGGGACAAATTCTATGTGGTCC
*
182349 TTCGGGA-TAATTCTATGTGGTCC
1 TTCGGGACAAATTCTATGTGGTCC
* * * * *
182372 TTCAGAACAAATTCTAAGCGGTCA
1 TTCGGGACAAATTCTATGTGGTCC
*
182396 TTCGGGACAAATTCTACGTGG-CAC
1 TTCGGGACAAATTCTATGTGGTC-C
*
182420 TTCGGTG-CAAATTATATG
1 TTCGG-GACAAATTCTATG
182438 AGCAATAGTA
Statistics
Matches: 70, Mismatches: 15, Indels: 7
0.76 0.16 0.08
Matches are distributed among these distances:
22 2 0.03
23 24 0.34
24 43 0.61
25 1 0.01
ACGTcount: A:0.27, C:0.20, G:0.22, T:0.31
Consensus pattern (24 bp):
TTCGGGACAAATTCTATGTGGTCC
Found at i:184150 original size:7 final size:8
Alignment explanation
Indices: 184132--184172 Score: 57
Period size: 8 Copynumber: 5.1 Consensus size: 8
184122 TGATATATAA
184132 AAAAAATG
1 AAAAAATG
*
184140 AAAAAATA
1 AAAAAATG
184148 AAAAAATG
1 AAAAAATG
184156 AAAAAGA-G
1 AAAAA-ATG
184164 AAAAAATG
1 AAAAAATG
184172 A
1 A
184173 TTTTTTAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
7 1 0.03
8 27 0.93
9 1 0.03
ACGTcount: A:0.78, C:0.00, G:0.12, T:0.10
Consensus pattern (8 bp):
AAAAAATG
Found at i:186251 original size:19 final size:19
Alignment explanation
Indices: 186227--186268 Score: 84
Period size: 19 Copynumber: 2.2 Consensus size: 19
186217 TAAGTAAACT
186227 AATCTAAATTTAAAACACA
1 AATCTAAATTTAAAACACA
186246 AATCTAAATTTAAAACACA
1 AATCTAAATTTAAAACACA
186265 AATC
1 AATC
186269 ATTAAACAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.57, C:0.17, G:0.00, T:0.26
Consensus pattern (19 bp):
AATCTAAATTTAAAACACA
Found at i:187543 original size:139 final size:139
Alignment explanation
Indices: 187382--187891 Score: 700
Period size: 139 Copynumber: 3.7 Consensus size: 139
187372 GTGACAAAAA
* * * *
187382 CGAGCTAAGGTTGAACAAGTTCTTCTCATTATAAACTTTTTCTCCCTCGTCGGATGAGTTCTTCT
1 CGAGCTAAGGTTGAACAAGTTCTTGTCATTATGAACTTTTTCTCCCTCATCGAATGAGTTCTTCT
* *
187447 CGTTATGAACTCTCCACTAGAAATGTTGATCCCTCGAGTGAGGTGTTGCTGATTGAACTCCATAT
66 CATTATGAACTCTCCACTAGAAATGTTGATCCCTCGAGTGAGGTGTTGCTGATTCAACTCCATAT
187512 GTGATGAAT
131 GTGATGAAT
* * *
187521 CGAGCTAAGGTTGAACAAGTTCTTGTCATTATGAACTTCTTCTCCCTCATCGGACGAGTTCTTCT
1 CGAGCTAAGGTTGAACAAGTTCTTGTCATTATGAACTTTTTCTCCCTCATCGAATGAGTTCTTCT
*
187586 CATTATGAACTCTCCACTGGAAATGTTGATCCCTCGAGTGAGGTGTTGCTGATTCAACTCCATAT
66 CATTATGAACTCTCCACTAGAAATGTTGATCCCTCGAGTGAGGTGTTGCTGATTCAACTCCATAT
187651 GTGATGAAT
131 GTGATGAAT
** *
187660 CGAGCTAATATTGAACAAGTT-TTGTCATTATGAACTTCTTT-TCCCTCATCGAATGAGTTCTTA
1 CGAGCTAAGGTTGAACAAGTTCTTGTCATTATGAACTT-TTTCTCCCTCATCGAATGAGTTCTTC
* * ** * * * * * *
187723 TCATTACGAACCCTTAATTGGAAATATTGATCCATCGAGTGAGGTCTTGCTGATTCAACTCTATA
65 TCATTATGAACTCTCCACTAGAAATGTTGATCCCTCGAGTGAGGTGTTGCTGATTCAACTCCATA
* *
187788 TGCGACGAAT
130 TGTGATGAAT
* * * * * *
187798 CGAGCTAAAGTTGAACAAGTTCTTATTATTATGAACTTATTCTCCCTCATCAAATGAGTTCATCT
1 CGAGCTAAGGTTGAACAAGTTCTTGTCATTATGAACTTTTTCTCCCTCATCGAATGAGTTCTTCT
* *
187863 CATTATAAACTCTCCACTAGAAGTGTTGA
66 CATTATGAACTCTCCACTAGAAATGTTGA
187892 CTAGTTTATC
Statistics
Matches: 326, Mismatches: 42, Indels: 6
0.87 0.11 0.02
Matches are distributed among these distances:
138 120 0.37
139 206 0.63
ACGTcount: A:0.26, C:0.21, G:0.18, T:0.35
Consensus pattern (139 bp):
CGAGCTAAGGTTGAACAAGTTCTTGTCATTATGAACTTTTTCTCCCTCATCGAATGAGTTCTTCT
CATTATGAACTCTCCACTAGAAATGTTGATCCCTCGAGTGAGGTGTTGCTGATTCAACTCCATAT
GTGATGAAT
Found at i:188534 original size:42 final size:42
Alignment explanation
Indices: 188445--188534 Score: 101
Period size: 42 Copynumber: 2.1 Consensus size: 42
188435 AAAAGACTTA
* *
188445 TCATCTTGCTCGAAAGACTTACAGATGACTCGAAGGATTTAG
1 TCATCATGCTCGAAAGACTTACAGATGACTCGAAGGATTTAC
* * * * *
188487 GCATCATGCTCGAAAGCCTTACTGGTGGC-CTGAAGGATTTAC
1 TCATCATGCTCGAAAGACTTACAGATGACTC-GAAGGATTTAC
188529 TCATCA
1 TCATCA
188535 ATAAACCCTT
Statistics
Matches: 39, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
41 1 0.03
42 38 0.97
ACGTcount: A:0.28, C:0.22, G:0.22, T:0.28
Consensus pattern (42 bp):
TCATCATGCTCGAAAGACTTACAGATGACTCGAAGGATTTAC
Found at i:188711 original size:53 final size:53
Alignment explanation
Indices: 188627--188773 Score: 197
Period size: 53 Copynumber: 2.8 Consensus size: 53
188617 GCTTCTATAA
*
188627 AAAATTCATTTGAAAATATTAAGAAAA-CCCTAAAAATCAGGAGCAGCTTCTTT
1 AAAATTCATTTGAAAATATCAA-AAAACCCCTAAAAATCAGGAGCAGCTTCTTT
* * * ***
188680 CAAATTCATTTGAAAACATCAAAAAACCCCTAAAAATTAGGCTTAGCTTCTTT
1 AAAATTCATTTGAAAATATCAAAAAACCCCTAAAAATCAGGAGCAGCTTCTTT
* *
188733 AAAATTCATTTGAAAATATCAAGAAACCCCTGAAAATCAGG
1 AAAATTCATTTGAAAATATCAAAAAACCCCTAAAAATCAGG
188774 CCTAGATTAT
Statistics
Matches: 81, Mismatches: 12, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
52 4 0.05
53 77 0.95
ACGTcount: A:0.45, C:0.18, G:0.10, T:0.27
Consensus pattern (53 bp):
AAAATTCATTTGAAAATATCAAAAAACCCCTAAAAATCAGGAGCAGCTTCTTT
Found at i:188829 original size:99 final size:103
Alignment explanation
Indices: 188588--188840 Score: 298
Period size: 99 Copynumber: 2.4 Consensus size: 103
188578 TTACAGTTAT
* *
188588 CATCAAGAAACCCATAAAAATTAGGCTTAGCTTCTATAAAAAATTCATTTGAAAATATTAAGAAA
1 CATCAAGAAACCCATAAAAATTAGGCTTAGCTTCT-T-TAAAATTCATTTGAAAATATCAAGAAA
* *
188653 ACCCTAAAAATCAGGAGCAGCTTCTTTCAAATTCATTTGAAAA
64 ACCCTAAAAATCAGGAGCA-CTACATT--AATTCATTTGAAAA
* * *
188696 CATCAAAAAACCCCTAAAAATTAGGCTTAGCTTCTTTAAAATTCATTTGAAAATATCAAGAAACC
1 CATCAAGAAACCCATAAAAATTAGGCTTAGCTTCTTTAAAATTCATTTGAAAATATCAAGAAAAC
* * *
188761 CCTGAAAATCA-G-GC-CTAGATT-ATTCCTTTGAAAA
66 CCTAAAAATCAGGAGCACTACATTAATTCATTTGAAAA
* * * * *
188795 CATCAAGAAACCCTTGAAAATCAGGCTTAACTTCTTTCAAATTCAT
1 CATCAAGAAACCCATAAAAATTAGGCTTAGCTTCTTTAAAATTCAT
188841 CATGTCAAAA
Statistics
Matches: 129, Mismatches: 16, Indels: 9
0.84 0.10 0.06
Matches are distributed among these distances:
99 52 0.40
102 4 0.03
104 2 0.02
105 1 0.01
106 36 0.28
107 1 0.01
108 33 0.26
ACGTcount: A:0.42, C:0.19, G:0.10, T:0.28
Consensus pattern (103 bp):
CATCAAGAAACCCATAAAAATTAGGCTTAGCTTCTTTAAAATTCATTTGAAAATATCAAGAAAAC
CCTAAAAATCAGGAGCACTACATTAATTCATTTGAAAA
Found at i:188932 original size:55 final size:55
Alignment explanation
Indices: 188858--189151 Score: 365
Period size: 55 Copynumber: 5.4 Consensus size: 55
188848 AAAAACCTTT
* * * * * * **
188858 GAAAATAAGACTTAATTTCTTTGAAAGCTCATTTAAAAATCATCAAGAAACTTTT
1 GAAAATCAGACTTAGTTTCTTTAAAAACTCATTTAAAAATAATTAAGAAACTTCC
* * * *
188913 GAAAATCAGAGTTAGTTTCTTTAAAAACTCATTTGAAAATCATTAAGAAACTTCT
1 GAAAATCAGACTTAGTTTCTTTAAAAACTCATTTAAAAATAATTAAGAAACTTCC
* * *
188968 GAAAATCAAACTTAGTTTTTTTAAAAACTCATTTCAAAAT-ATTAAGAAACTTCC
1 GAAAATCAGACTTAGTTTCTTTAAAAACTCATTTAAAAATAATTAAGAAACTTCC
* * * *
189022 AAAAATCAGAATTAGTTTCTTTAAAAGCTCATTGAAAAATAATTAAGAAACTTCC
1 GAAAATCAGACTTAGTTTCTTTAAAAACTCATTTAAAAATAATTAAGAAACTTCC
* * * *
189077 AAAAACCAGACTTAGTTTCTTTAAAAATTCATTTAAAAATAATTAAGAAACTTTC
1 GAAAATCAGACTTAGTTTCTTTAAAAACTCATTTAAAAATAATTAAGAAACTTCC
*
189132 GAAAATCGGACTTAGTTTCT
1 GAAAATCAGACTTAGTTTCT
189152 AAAAAAATCG
Statistics
Matches: 209, Mismatches: 29, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
54 46 0.22
55 163 0.78
ACGTcount: A:0.44, C:0.13, G:0.09, T:0.34
Consensus pattern (55 bp):
GAAAATCAGACTTAGTTTCTTTAAAAACTCATTTAAAAATAATTAAGAAACTTCC
Found at i:189053 original size:109 final size:110
Alignment explanation
Indices: 188857--189151 Score: 371
Period size: 109 Copynumber: 2.7 Consensus size: 110
188847 AAAAAACCTT
* * * * * *
188857 TGAAAAT-AAGACTTAATTTCTTTGAAAGCTCATTTAAAAATCATCAAGAAACTTTTGAAAATCA
1 TGAAAATCAA-ACTTAGTTTCTTTAAAAACTCATTTAAAAATAATTAAGAAACTTTCGAAAATCA
* *
188921 GAGTTAGTTTCTTTAAAAACTCATTTG-AAAATCATTAAGAAACTTC
65 GAATTAGTTTCTTTAAAAACTCA-TTGAAAAATAATTAAGAAACTTC
* * * *
188967 TGAAAATCAAACTTAGTTTTTTTAAAAACTCATTTCAAAAT-ATTAAGAAACTTCCAAAAATCAG
1 TGAAAATCAAACTTAGTTTCTTTAAAAACTCATTTAAAAATAATTAAGAAACTTTCGAAAATCAG
*
189031 AATTAGTTTCTTTAAAAGCTCATTGAAAAATAATTAAGAAACTTC
66 AATTAGTTTCTTTAAAAACTCATTGAAAAATAATTAAGAAACTTC
** * * * *
189076 CAAAAACCAGACTTAGTTTCTTTAAAAATTCATTTAAAAATAATTAAGAAACTTTCGAAAATCGG
1 TGAAAATCAAACTTAGTTTCTTTAAAAACTCATTTAAAAATAATTAAGAAACTTTCGAAAATCAG
*
189141 ACTTAGTTTCT
66 AATTAGTTTCT
189152 AAAAAAATCG
Statistics
Matches: 159, Mismatches: 23, Indels: 6
0.85 0.12 0.03
Matches are distributed among these distances:
108 3 0.02
109 91 0.57
110 63 0.40
111 2 0.01
ACGTcount: A:0.44, C:0.13, G:0.09, T:0.34
Consensus pattern (110 bp):
TGAAAATCAAACTTAGTTTCTTTAAAAACTCATTTAAAAATAATTAAGAAACTTTCGAAAATCAG
AATTAGTTTCTTTAAAAACTCATTGAAAAATAATTAAGAAACTTC
Found at i:190458 original size:28 final size:28
Alignment explanation
Indices: 190426--190481 Score: 67
Period size: 28 Copynumber: 2.0 Consensus size: 28
190416 AAAAGTAGAC
* *
190426 CGTTTCAAATTAATTTGGGGAGGTAATG
1 CGTTTCAAATCAATTTGGGGAGGCAATG
* **
190454 CGTTTTAGGTCAATTTGGGGAGGCAATG
1 CGTTTCAAATCAATTTGGGGAGGCAATG
190482 TGTTCCTGGT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.25, C:0.09, G:0.32, T:0.34
Consensus pattern (28 bp):
CGTTTCAAATCAATTTGGGGAGGCAATG
Found at i:191201 original size:7 final size:7
Alignment explanation
Indices: 191185--191268 Score: 97
Period size: 7 Copynumber: 12.4 Consensus size: 7
191175 ATCGATTTTC
191185 TTTCTTT
1 TTTCTTT
191192 TTTCTCTT
1 TTTCT-TT
191200 TTTC--T
1 TTTCTTT
191205 TTTCTTT
1 TTTCTTT
191212 TTT-TTT
1 TTTCTTT
191218 TTT-TTT
1 TTTCTTT
191224 TTT-TTT
1 TTTCTTT
*
191230 TTTTTTT
1 TTTCTTT
191237 TTTCTTT
1 TTTCTTT
*
191244 TTTTTTT
1 TTTCTTT
191251 TTTCTTT
1 TTTCTTT
191258 TTTCTCTT
1 TTTCT-TT
191266 TTT
1 TTT
191269 TCGCTTCTTT
Statistics
Matches: 69, Mismatches: 3, Indels: 9
0.85 0.04 0.11
Matches are distributed among these distances:
5 5 0.07
6 18 0.26
7 35 0.51
8 11 0.16
ACGTcount: A:0.00, C:0.11, G:0.00, T:0.89
Consensus pattern (7 bp):
TTTCTTT
Found at i:191210 original size:20 final size:20
Alignment explanation
Indices: 191180--191259 Score: 105
Period size: 20 Copynumber: 4.2 Consensus size: 20
191170 ACTTAATCGA
*
191180 TTTTC-TTTCTTTTTTCTCT
1 TTTTCTTTTCTTTTTTTTCT
191199 TTTTCTTTTCTTTTTTTT-T
1 TTTTCTTTTCTTTTTTTTCT
*
191218 TTTT-TTTT-TTTTTTTTTT
1 TTTTCTTTTCTTTTTTTTCT
*
191236 TTTTCTTTTTTTTTTTTTCT
1 TTTTCTTTTCTTTTTTTTCT
191256 TTTT
1 TTTT
191260 TCTCTTTTTT
Statistics
Matches: 55, Mismatches: 2, Indels: 7
0.86 0.03 0.11
Matches are distributed among these distances:
17 8 0.15
18 9 0.16
19 14 0.25
20 24 0.44
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (20 bp):
TTTTCTTTTCTTTTTTTTCT
Found at i:191280 original size:1 final size:1
Alignment explanation
Indices: 191198--191260 Score: 90
Period size: 1 Copynumber: 63.0 Consensus size: 1
191188 CTTTTTTCTC
* * * *
191198 TTTTTCTTTTCTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTCTTTTTTTTTTTTTCTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
191261 CTCTTTTTTC
Statistics
Matches: 54, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
1 54 1.00
ACGTcount: A:0.00, C:0.06, G:0.00, T:0.94
Consensus pattern (1 bp):
T
Found at i:191280 original size:32 final size:32
Alignment explanation
Indices: 191180--191269 Score: 126
Period size: 32 Copynumber: 2.8 Consensus size: 32
191170 ACTTAATCGA
*
191180 TTTTCTTTCTTTTTTCTCTTTTTCTTTTCTTTTT
1 TTTTTTTTCTTTTTTCTC-TTTT-TTTTCTTTTT
* * *
191214 TTTTTTTTTTTTTTTTTTTTTTTTTTCTTTTT
1 TTTTTTTTCTTTTTTCTCTTTTTTTTCTTTTT
191246 TTTTTTTTCTTTTTTCTCTTTTTT
1 TTTTTTTTCTTTTTTCTCTTTTTT
191270 CGCTTCTTTT
Statistics
Matches: 49, Mismatches: 7, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
32 31 0.63
33 4 0.08
34 14 0.29
ACGTcount: A:0.00, C:0.11, G:0.00, T:0.89
Consensus pattern (32 bp):
TTTTTTTTCTTTTTTCTCTTTTTTTTCTTTTT
Found at i:192623 original size:8 final size:7
Alignment explanation
Indices: 192609--192687 Score: 67
Period size: 6 Copynumber: 11.3 Consensus size: 7
192599 TATATATGCT
192609 AATGCAA
1 AATGCAA
192616 AGATGCAA
1 A-ATGCAA
192624 AGATGC-A
1 A-ATGCAA
*
192631 CATGC-A
1 AATGCAA
192637 AATGCAA
1 AATGCAA
*
192644 AGATGTAAA
1 A-ATG-CAA
*
192653 AATG-AG
1 AATGCAA
192659 AATGCAA
1 AATGCAA
192666 AATGCAA
1 AATGCAA
192673 AATG-AA
1 AATGCAA
192679 AATGCAA
1 AATGCAA
192686 AA
1 AA
192688 AAGGAATTGA
Statistics
Matches: 61, Mismatches: 5, Indels: 12
0.78 0.06 0.15
Matches are distributed among these distances:
6 20 0.33
7 20 0.33
8 18 0.30
9 3 0.05
ACGTcount: A:0.54, C:0.11, G:0.19, T:0.15
Consensus pattern (7 bp):
AATGCAA
Found at i:192663 original size:28 final size:27
Alignment explanation
Indices: 192604--192686 Score: 82
Period size: 28 Copynumber: 3.0 Consensus size: 27
192594 AAATGTATAT
* * *
192604 ATGCTAATGCAAAGATGCAAAGATGCAC
1 ATGCAAATGCAAAGATG-AAAAATGCAA
192632 ATGCAAATGCAAAGATGTAAAAATG-AGA
1 ATGCAAATGCAAAGATG-AAAAATGCA-A
192660 ATGCAAAATGCAAA-ATG-AAAATGCAA
1 ATGC-AAATGCAAAGATGAAAAATGCAA
192686 A
1 A
192687 AAAGGAATTG
Statistics
Matches: 48, Mismatches: 4, Indels: 8
0.80 0.07 0.13
Matches are distributed among these distances:
26 8 0.17
27 2 0.04
28 29 0.60
29 9 0.19
ACGTcount: A:0.52, C:0.12, G:0.19, T:0.17
Consensus pattern (27 bp):
ATGCAAATGCAAAGATGAAAAATGCAA
Found at i:192676 original size:20 final size:21
Alignment explanation
Indices: 192636--192687 Score: 70
Period size: 20 Copynumber: 2.5 Consensus size: 21
192626 ATGCACATGC
192636 AAATGCAAAGATGTAAAAATGA
1 AAATGCAAA-ATGTAAAAATGA
* *
192658 GAATGCAAAATG-CAAAATGA
1 AAATGCAAAATGTAAAAATGA
192678 AAATGCAAAA
1 AAATGCAAAA
192688 AAGGAATTGA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
20 16 0.59
21 3 0.11
22 8 0.30
ACGTcount: A:0.60, C:0.08, G:0.17, T:0.15
Consensus pattern (21 bp):
AAATGCAAAATGTAAAAATGA
Found at i:197162 original size:2 final size:2
Alignment explanation
Indices: 197155--197184 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
197145 TTTTATTTGA
197155 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
197185 TGTAATAATT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:197460 original size:63 final size:63
Alignment explanation
Indices: 197361--197506 Score: 283
Period size: 63 Copynumber: 2.3 Consensus size: 63
197351 ATTTAATTAG
*
197361 GCGTATTTCAGCTATTGTTTTTGTAAAAATAAGACTATCAATCTTTCAAACTCTCAGAATGAA
1 GCGTATTTCAGCTATTGTTTTTGTAAAAATAAGACTATCAATCTTCCAAACTCTCAGAATGAA
197424 GCGTATTTCAGCTATTGTTTTTGTAAAAATAAGACTATCAATCTTCCAAACTCTCAGAATGAA
1 GCGTATTTCAGCTATTGTTTTTGTAAAAATAAGACTATCAATCTTCCAAACTCTCAGAATGAA
197487 GCGTATTTCAGCTATTGTTT
1 GCGTATTTCAGCTATTGTTT
197507 ACTATGATGG
Statistics
Matches: 82, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
63 82 1.00
ACGTcount: A:0.32, C:0.16, G:0.14, T:0.38
Consensus pattern (63 bp):
GCGTATTTCAGCTATTGTTTTTGTAAAAATAAGACTATCAATCTTCCAAACTCTCAGAATGAA
Found at i:198227 original size:60 final size:60
Alignment explanation
Indices: 198131--198245 Score: 158
Period size: 60 Copynumber: 1.9 Consensus size: 60
198121 GACACACTGT
* * * * * *
198131 CTTCAAGCTCCAGGGGGAGGCATTCAACTGCGAGCTTCTTCGACCTTAATGTCGAGATTC
1 CTTCAAGCTCAAGGGGAAGGCATGCAACTACCAGCTTCTTCGACCTAAATGTCGAGATTC
* *
198191 CTTCAAGTTCAAGGGGAAGGCATGCAACTACCAGCTTGTTCGACCTAAATGTCGA
1 CTTCAAGCTCAAGGGGAAGGCATGCAACTACCAGCTTCTTCGACCTAAATGTCGA
198246 TAGCGTTGAG
Statistics
Matches: 47, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
60 47 1.00
ACGTcount: A:0.25, C:0.25, G:0.24, T:0.25
Consensus pattern (60 bp):
CTTCAAGCTCAAGGGGAAGGCATGCAACTACCAGCTTCTTCGACCTAAATGTCGAGATTC
Found at i:199527 original size:66 final size:66
Alignment explanation
Indices: 199439--199664 Score: 302
Period size: 66 Copynumber: 3.4 Consensus size: 66
199429 GAATACCATG
*
199439 AGTGGCACCTTTTATG-CAGATAATGCACCGTTATGAATTAAAT-AAAATTGATCGATAATTTTC
1 AGTGACACCTTTTATGTC-GATAATGCACCGTTATGAATT-AATCAAAATTGATCGATAATTTTC
199502 ATT
64 ATT
* *
199505 AGTGACACCTTTTATGTCGATAACGCACCGTTATGCATTAATCAAAA-TGTATCGATAATTTTCA
1 AGTGACACCTTTTATGTCGATAATGCACCGTTATGAATTAATCAAAATTG-ATCGATAATTTTCA
199569 TT
65 TT
* * *
199571 AGTTG-CACCTTTTATGCCGATAATGCACCGTTATGAATTAATGAAAATTGATCGATAATTTTAA
1 AG-TGACACCTTTTATGTCGATAATGCACCGTTATGAATTAATCAAAATTGATCGATAATTTTCA
199635 TT
65 TT
*
199637 AAT-ATCACCTTTTATGTCGAT-ATGCACC
1 AGTGA-CACCTTTTATGTCGATAATGCACC
199665 TATGACTCTC
Statistics
Matches: 143, Mismatches: 10, Indels: 15
0.85 0.06 0.09
Matches are distributed among these distances:
65 13 0.09
66 125 0.87
67 5 0.03
ACGTcount: A:0.33, C:0.16, G:0.14, T:0.37
Consensus pattern (66 bp):
AGTGACACCTTTTATGTCGATAATGCACCGTTATGAATTAATCAAAATTGATCGATAATTTTCAT
T
Found at i:200212 original size:22 final size:21
Alignment explanation
Indices: 200170--200222 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 21
200160 AGACTCAATA
200170 GTATCGATAC-CCCTACCATG
1 GTATCGATACTCCCTACCATG
* *
200190 GTATCGATACTTCTCTACTATG
1 GTATCGATAC-TCCCTACCATG
200212 GTA-CTGATACT
1 GTATC-GATACT
200223 GTATTTCAGT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
20 10 0.36
21 2 0.07
22 16 0.57
ACGTcount: A:0.25, C:0.26, G:0.15, T:0.34
Consensus pattern (21 bp):
GTATCGATACTCCCTACCATG
Found at i:205255 original size:9 final size:9
Alignment explanation
Indices: 205241--205271 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
205231 GTGTTTCTTT
205241 CTTTATTTG
1 CTTTATTTG
205250 CTTTATTTG
1 CTTTATTTG
*
205259 CTTTATTTA
1 CTTTATTTG
205268 CTTT
1 CTTT
205272 TAATATTAGT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.13, C:0.13, G:0.06, T:0.68
Consensus pattern (9 bp):
CTTTATTTG
Found at i:206817 original size:21 final size:20
Alignment explanation
Indices: 206793--206832 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
206783 TGAAGACGTT
*
206793 GAGGAATAGATTTGTCTTGCC
1 GAGGAA-AGATTTATCTTGCC
*
206814 GAGGCAAGATTTATCTTGC
1 GAGGAAAGATTTATCTTGC
206833 AAATCTGACG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.25, C:0.15, G:0.28, T:0.33
Consensus pattern (20 bp):
GAGGAAAGATTTATCTTGCC
Found at i:211080 original size:64 final size:65
Alignment explanation
Indices: 210879--211090 Score: 318
Period size: 66 Copynumber: 3.2 Consensus size: 65
210869 GAATACCATG
** * *
210879 AGTGGCACCTTTTATGCCGTTAATGCACCGTTATGCATTAAATAAAATTGATCGATAATTTTCAT
1 AGTGGCACCTTTTATGCCAATAATGCACCGTTATGCATT-AATCAAATCGATCGATAATTTTCAT
210944 T
65 T
* * *
210945 AGTGTCACCTTTTATGTCAATAATGCACCATTATGCATTAATCAAAATCGATCGATAATTTTCAT
1 AGTGGCACCTTTTATGCCAATAATGCACCGTTATGCATTAATC-AAATCGATCGATAATTTTCAT
211010 T
65 T
*
211011 AGTGGCACCTTTTATGCCAATAATGCA-CGTTATGTATTAATCAAATCGATCGATAATTTTCATT
1 AGTGGCACCTTTTATGCCAATAATGCACCGTTATGCATTAATCAAATCGATCGATAATTTTCATT
*
211075 AGTGGCACATTTTATG
1 AGTGGCACCTTTTATG
211091 TCGATATGAA
Statistics
Matches: 133, Mismatches: 12, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
64 37 0.28
65 16 0.12
66 80 0.60
ACGTcount: A:0.31, C:0.17, G:0.14, T:0.38
Consensus pattern (65 bp):
AGTGGCACCTTTTATGCCAATAATGCACCGTTATGCATTAATCAAATCGATCGATAATTTTCATT
Found at i:214391 original size:3 final size:3
Alignment explanation
Indices: 214383--214439 Score: 78
Period size: 3 Copynumber: 19.0 Consensus size: 3
214373 CTCCTCACTC
* * *
214383 TCA TCA TCA TCA TCA TCA TCA TCA CCA CCA TCA TCA TCA TCA TCA TCG
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA
*
214431 TCA TTA TCA
1 TCA TCA TCA
214440 AGAGCAGATA
Statistics
Matches: 48, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 48 1.00
ACGTcount: A:0.32, C:0.35, G:0.02, T:0.32
Consensus pattern (3 bp):
TCA
Found at i:215368 original size:25 final size:22
Alignment explanation
Indices: 215340--215385 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 22
215330 CATTCAAACT
215340 AAAACAAATATATATAATTCTTATC
1 AAAA-AAATA-ATATAATT-TTATC
*
215365 AAAATAATAATATAATTTTAT
1 AAAAAAATAATATAATTTTAT
215386 AACGATAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 4 0.20
23 8 0.40
24 4 0.20
25 4 0.20
ACGTcount: A:0.54, C:0.07, G:0.00, T:0.39
Consensus pattern (22 bp):
AAAAAAATAATATAATTTTATC
Found at i:218496 original size:15 final size:15
Alignment explanation
Indices: 218475--218524 Score: 55
Period size: 15 Copynumber: 3.3 Consensus size: 15
218465 TTGATTGATT
*
218475 AATTTCTGTTATTTG
1 AATTTCTGTTATTTA
* **
218490 CATTTCTGTCCTTTA
1 AATTTCTGTTATTTA
*
218505 AATTTCTGTTATTTT
1 AATTTCTGTTATTTA
218520 AATTT
1 AATTT
218525 ATTCTTTACT
Statistics
Matches: 27, Mismatches: 8, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
15 27 1.00
ACGTcount: A:0.20, C:0.12, G:0.08, T:0.60
Consensus pattern (15 bp):
AATTTCTGTTATTTA
Found at i:219973 original size:20 final size:22
Alignment explanation
Indices: 219930--219987 Score: 57
Period size: 22 Copynumber: 2.6 Consensus size: 22
219920 TATATTTTAA
219930 ATTATAATAATATATTTAAGGAAT
1 ATTAT-ATAATAT-TTTAAGGAAT
* *
219954 -TTTTATAATATTTTTA-GAAT
1 ATTATATAATATTTTAAGGAAT
219974 ATTATATTAATATT
1 ATTATA-TAATATT
219988 AAATACATAA
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
20 4 0.14
21 8 0.28
22 14 0.48
23 3 0.10
ACGTcount: A:0.43, C:0.00, G:0.05, T:0.52
Consensus pattern (22 bp):
ATTATATAATATTTTAAGGAAT
Done.