Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167938.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_20, 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: 19866354
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 74000 characters in sequence are not A, C, G, or T
File 2 of 100
Found at i:107397 original size:27 final size:28
Alignment explanation
Indices: 107356--107409 Score: 92
Period size: 27 Copynumber: 2.0 Consensus size: 28
107346 AACTCTATTT
*
107356 AATAAGTTATTTAAATTTAATATGTTTG
1 AATAAGTTATATAAATTTAATATGTTTG
107384 AATAA-TTATATAAATTTAATATGTTT
1 AATAAGTTATATAAATTTAATATGTTT
107410 AGATAACTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
27 20 0.80
28 5 0.20
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (28 bp):
AATAAGTTATATAAATTTAATATGTTTG
Found at i:107415 original size:27 final size:28
Alignment explanation
Indices: 107353--107415 Score: 87
Period size: 27 Copynumber: 2.3 Consensus size: 28
107343 AGTAACTCTA
*
107353 TTTA-ATAAGTTATTTAAATTTAATATG
1 TTTAGATAAGTTATATAAATTTAATATG
107380 TTT-GAATAA-TTATATAAATTTAATATG
1 TTTAG-ATAAGTTATATAAATTTAATATG
107407 TTTAGATAA
1 TTTAGATAA
107416 CTATTTTAAT
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
27 27 0.84
28 5 0.16
ACGTcount: A:0.43, C:0.00, G:0.08, T:0.49
Consensus pattern (28 bp):
TTTAGATAAGTTATATAAATTTAATATG
Found at i:107426 original size:27 final size:27
Alignment explanation
Indices: 107363--107426 Score: 85
Period size: 27 Copynumber: 2.4 Consensus size: 27
107353 TTTAATAAGT
*
107363 TATTTAAATTTAATATGTTTGAATAAT
1 TATTTAAATTTAATATGTTTGAATAAC
*
107390 TATATAAATTTAATATGTTT-AGATAAC
1 TATTTAAATTTAATATGTTTGA-ATAAC
*
107417 TATTTTAATT
1 TATTTAAATT
107427 CAAATAAAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
26 1 0.03
27 31 0.97
ACGTcount: A:0.41, C:0.02, G:0.06, T:0.52
Consensus pattern (27 bp):
TATTTAAATTTAATATGTTTGAATAAC
Found at i:108331 original size:16 final size:16
Alignment explanation
Indices: 108307--108339 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
108297 AAATCGGTTC
*
108307 ATATGTTTATATATAT
1 ATATATTTATATATAT
108323 ATATATTTATATATAT
1 ATATATTTATATATAT
108339 A
1 A
108340 AACAGGATAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (16 bp):
ATATATTTATATATAT
Found at i:110433 original size:18 final size:18
Alignment explanation
Indices: 110412--110476 Score: 64
Period size: 18 Copynumber: 3.7 Consensus size: 18
110402 TTAATTATTA
110412 TAATAATAAAATTAAAAT
1 TAATAATAAAATTAAAAT
*
110430 TAATAATAAAA-TATATAT
1 TAATAATAAAATTA-AAAT
* *
110448 T-TTAATAAAAATAACAA-
1 TAATAATAAAATTAA-AAT
110465 TAATAATAAAAT
1 TAATAATAAAAT
110477 AAATTACAAT
Statistics
Matches: 38, Mismatches: 5, Indels: 8
0.75 0.10 0.16
Matches are distributed among these distances:
17 12 0.32
18 26 0.68
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.34
Consensus pattern (18 bp):
TAATAATAAAATTAAAAT
Found at i:110571 original size:27 final size:25
Alignment explanation
Indices: 110511--110571 Score: 68
Period size: 25 Copynumber: 2.4 Consensus size: 25
110501 ACTTTAAAGG
*
110511 AAAAATTAAAAAATTAAAAAAATTT
1 AAAAATTATAAAATTAAAAAAATTT
***
110536 AATGTTTATAAAATTAACAAATAATTT
1 AAAAATTATAAAATTAA-AAA-AATTT
110563 AAAAATTAT
1 AAAAATTAT
110572 TAAACTATTT
Statistics
Matches: 27, Mismatches: 7, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
25 13 0.48
26 3 0.11
27 11 0.41
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.34
Consensus pattern (25 bp):
AAAAATTATAAAATTAAAAAAATTT
Found at i:110608 original size:11 final size:11
Alignment explanation
Indices: 110592--110628 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
110582 TTATATCAAA
110592 TAATAAATAAT
1 TAATAAATAAT
110603 TAATAAATAAT
1 TAATAAATAAT
110614 TAA-AATATAA-
1 TAATAA-ATAAT
110624 TAATA
1 TAATA
110629 TATTAAATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
10 5 0.21
11 19 0.79
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (11 bp):
TAATAAATAAT
Found at i:110612 original size:18 final size:19
Alignment explanation
Indices: 110589--110641 Score: 65
Period size: 18 Copynumber: 2.8 Consensus size: 19
110579 TTTTTATATC
110589 AAATAATAAATAAT-TAAT
1 AAATAATAAATAATATAAT
*
110607 AAATAATTAA-AATATAAT
1 AAATAATAAATAATATAAT
*
110625 AATATATTAAATAATAT
1 AA-ATAATAAATAATAT
110642 TTTCTACTAT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
17 3 0.10
18 15 0.52
19 6 0.21
20 5 0.17
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (19 bp):
AAATAATAAATAATATAAT
Found at i:112016 original size:2 final size:2
Alignment explanation
Indices: 112009--112039 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
111999 CACCGTCATC
*
112009 TA TA TA TA TA TA TA TA TA TA TA CA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
112040 TAATAAAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:112864 original size:26 final size:26
Alignment explanation
Indices: 112809--112876 Score: 104
Period size: 26 Copynumber: 2.7 Consensus size: 26
112799 TATTAATATA
*
112809 ATTATTAAAATAT-TAAAAATTATTT
1 ATTATTAAAATATATTAAAATTATTT
*
112834 ATTATTAAAATATATTAAATTTATTT
1 ATTATTAAAATATATTAAAATTATTT
112860 ATTATTAAAAT-TATTAA
1 ATTATTAAAATATATTAA
112877 TATTCAAAAA
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
25 19 0.47
26 21 0.52
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (26 bp):
ATTATTAAAATATATTAAAATTATTT
Found at i:112921 original size:19 final size:20
Alignment explanation
Indices: 112899--112940 Score: 52
Period size: 19 Copynumber: 2.2 Consensus size: 20
112889 ATAATATTTT
112899 AATAAAAAT-TTAATATAAA
1 AATAAAAATGTTAATATAAA
**
112918 AAT-ATTATGTTAATATAAA
1 AATAAAAATGTTAATATAAA
112937 AATA
1 AATA
112941 CTTAAAATAA
Statistics
Matches: 19, Mismatches: 2, Indels: 3
0.79 0.08 0.12
Matches are distributed among these distances:
18 3 0.16
19 16 0.84
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (20 bp):
AATAAAAATGTTAATATAAA
Found at i:112995 original size:10 final size:12
Alignment explanation
Indices: 112973--113009 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
112963 TTCTTTTTAT
112973 TATTTATTAATA
1 TATTTATTAATA
112985 TA-TTA-TAATA
1 TATTTATTAATA
112995 TTATTTATTAATA
1 -TATTTATTAATA
113008 TA
1 TA
113010 ATATTATTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
10 5 0.23
11 5 0.23
12 7 0.32
13 5 0.23
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (12 bp):
TATTTATTAATA
Found at i:113009 original size:18 final size:18
Alignment explanation
Indices: 112988--113038 Score: 93
Period size: 18 Copynumber: 2.8 Consensus size: 18
112978 ATTAATATAT
112988 TATAATATTATTTATTAA
1 TATAATATTATTTATTAA
113006 TATAATATTATTTATTAA
1 TATAATATTATTTATTAA
*
113024 TATGATATTATTTAT
1 TATAATATTATTTAT
113039 AAGTAAAATT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 32 1.00
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (18 bp):
TATAATATTATTTATTAA
Found at i:113031 original size:23 final size:22
Alignment explanation
Indices: 112970--113031 Score: 78
Period size: 18 Copynumber: 2.9 Consensus size: 22
112960 TTATTCTTTT
112970 TATTATTTATTAATATATTATAA
1 TATTATTTATTAATATA-TATAA
112993 TATTATTTA-T--TA-ATATAA
1 TATTATTTATTAATATATATAA
113011 TATTATTTATTAATATGATAT
1 TATTATTTATTAATAT-ATAT
113032 TATTTATAAG
Statistics
Matches: 34, Mismatches: 0, Indels: 10
0.77 0.00 0.23
Matches are distributed among these distances:
18 14 0.41
19 2 0.06
20 2 0.06
21 2 0.06
22 1 0.03
23 13 0.38
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (22 bp):
TATTATTTATTAATATATATAA
Found at i:113217 original size:13 final size:14
Alignment explanation
Indices: 113192--113219 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
113182 TAAAAAATGT
113192 AAAAATTATTTTTC
1 AAAAATTATTTTTC
113206 AAAAATTATTTTTC
1 AAAAATTATTTTTC
113220 GCTAAACAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.07, G:0.00, T:0.50
Consensus pattern (14 bp):
AAAAATTATTTTTC
Found at i:117107 original size:201 final size:199
Alignment explanation
Indices: 116802--117190 Score: 481
Period size: 200 Copynumber: 1.9 Consensus size: 199
116792 TAATTTAATA
** * *
116802 AAAATAAAAAATAATAATAAATTTTGGGAATAAATATTAATTATCCAATGATGAAATTTATAGAA
1 AAAATAAAAAATAATAATAAATTTTGGGAATAAATACAAATTACCCAAGGATGAAATTTATAGAA
*
116867 ATTTCAAAGGTAAATTTCTATAAAATTTCTAGGTGAGAAATTTTGTT-TAAATTTGTCCCAAATG
66 ATTTCAAAGGTAAATTTCTATAAAATTTCTAGGTGAGAAATTTT-TTCTAAATTTGACCCAAATG
*
116931 GTGAAATAATTTAGATAAAATTTCAATAACAA-TAATTAATATTTATTTTCAAACAAAAAAAATT
130 GTGAAATAATTTAGATAAAATTTAAAT-ACAAGTAATT-ATATTTATTTTCAAACAAAAAAAATT
116995 ATAAAAT
193 ATAAAAT
117002 AAAATATAAAAAT-ATAA-AAATCTTT-GGAATTAAATACAAATTACCCAAGGAT-AAGATTCT-
1 AAAATA-AAAAATAATAATAAAT-TTTGGGAA-TAAATACAAATTACCCAAGGATGAA-ATT-TA
* *
117062 TAGAAATTTCAAATGGT-AAGTTCT-TAAGAAATTTTTAGGTGAGAAATTTTTTCTAAATTTGAC
61 TAGAAATTTCAAA-GGTAAATTTCTAT-A-AAATTTCTAGGTGAGAAATTTTTTCTAAATTTGAC
* * * * * * *
117125 TCAAATTGTGAAATAATTTAGATGAAATTTAAATACAAGTAATTGTATTTTTTTTGAAATAAAAA
123 CCAAATGGTGAAATAATTTAGATAAAATTTAAATACAAGTAATTATATTTATTTTCAAACAAAAA
117190 A
188 A
117191 TTTTGGTTGA
Statistics
Matches: 164, Mismatches: 15, Indels: 20
0.82 0.08 0.10
Matches are distributed among these distances:
199 11 0.07
200 78 0.48
201 75 0.46
ACGTcount: A:0.47, C:0.06, G:0.10, T:0.36
Consensus pattern (199 bp):
AAAATAAAAAATAATAATAAATTTTGGGAATAAATACAAATTACCCAAGGATGAAATTTATAGAA
ATTTCAAAGGTAAATTTCTATAAAATTTCTAGGTGAGAAATTTTTTCTAAATTTGACCCAAATGG
TGAAATAATTTAGATAAAATTTAAATACAAGTAATTATATTTATTTTCAAACAAAAAAAATTATA
AAAT
Found at i:118492 original size:16 final size:16
Alignment explanation
Indices: 118471--118514 Score: 79
Period size: 16 Copynumber: 2.7 Consensus size: 16
118461 TAACATTTTA
118471 TATCATTTCATTCTAT
1 TATCATTTCATTCTAT
118487 TATCATTTCATTCTAT
1 TATCATTTCATTCTAT
118503 TATCATTCTCAT
1 TATCATT-TCAT
118515 GTTCATATTT
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 23 0.85
17 4 0.15
ACGTcount: A:0.25, C:0.20, G:0.00, T:0.55
Consensus pattern (16 bp):
TATCATTTCATTCTAT
Found at i:129025 original size:43 final size:43
Alignment explanation
Indices: 128906--129182 Score: 344
Period size: 42 Copynumber: 6.4 Consensus size: 43
128896 GTCAATGAGT
* * *
128906 AATTTATTTTT-TCAAAGTTCTGTTGTCTTTATTTAGAGGAGT
1 AATTTATTTTTCTCAAAGTTCTGTTGCCTCTATTTAGAGGAGC
*
128948 AATTTATTTTT-TCAAAGTTCTGTTGTCTCTATTTAGAGGAGC
1 AATTTATTTTTCTCAAAGTTCTGTTGCCTCTATTTAGAGGAGC
* * * * *
128990 AATTTATTTTTCTCAAAGTTTTGTTACCTCCATTTAAAAGAGC
1 AATTTATTTTTCTCAAAGTTCTGTTGCCTCTATTTAGAGGAGC
* *
129033 AATTTA-TTTTCCCAAAGTTCTGTTGCCTCTATTTAAAGGAGC
1 AATTTATTTTTCTCAAAGTTCTGTTGCCTCTATTTAGAGGAGC
* * * *
129075 AATTTATTTATTTTTTTAAAGTTCTATTGCCTCTATTTATAGGAGC
1 AATTTA--T-TTTTCTCAAAGTTCTGTTGCCTCTATTTAGAGGAGC
* *
129121 AATTTATTTTTCCCAAAGTTCTGTCGCCTCTATTTAGAGGAGC
1 AATTTATTTTTCTCAAAGTTCTGTTGCCTCTATTTAGAGGAGC
*
129164 AATTTGTTTTTCTCAAAGT
1 AATTTATTTTTCTCAAAGT
129183 CGTTAAACCT
Statistics
Matches: 204, Mismatches: 26, Indels: 9
0.85 0.11 0.04
Matches are distributed among these distances:
42 88 0.43
43 78 0.38
44 1 0.00
46 37 0.18
ACGTcount: A:0.26, C:0.14, G:0.14, T:0.47
Consensus pattern (43 bp):
AATTTATTTTTCTCAAAGTTCTGTTGCCTCTATTTAGAGGAGC
Found at i:129138 original size:131 final size:127
Alignment explanation
Indices: 128906--129182 Score: 347
Period size: 131 Copynumber: 2.1 Consensus size: 127
128896 GTCAATGAGT
* * * * *
128906 AATTTATTTTTTCAAAGTTCTGTTGTCTTTATTTAGAGGAGTAATTTATTTTTTCAAAGTTCTGT
1 AATTTATTTTCTCAAAGTTCTGTTGCCTCTATTTAAAGGAGTAATTTATTTTTTCAAAGTTCTAT
* * * *
128971 TGTCTCTATTTAGAGGAGCAATTTATTTTTCTCAAAGTTTTGTTACCTCCATTTAAAAGAGC
66 TGCCTCTATTTAGAGGAGCAATTTATTTTTCCCAAAGTTCTGTCACCTCCATTTAAAAGAGC
* * *
129033 AATTTATTTTCCCAAAGTTCTGTTGCCTCTATTTAAAGGAGCAATTTATTTATTTTTTTAAAGTT
1 AATTTATTTTCTCAAAGTTCTGTTGCCTCTATTTAAAGGAG----TAATTTATTTTTTCAAAGTT
* * * * *
129098 CTATTGCCTCTATTTATAGGAGCAATTTATTTTTCCCAAAGTTCTGTCGCCTCTATTTAGAGGAG
62 CTATTGCCTCTATTTAGAGGAGCAATTTATTTTTCCCAAAGTTCTGTCACCTCCATTTAAAAGAG
129163 C
127 C
*
129164 AATTTGTTTTTCTCAAAGT
1 AATTT-ATTTTCTCAAAGT
129183 CGTTAAACCT
Statistics
Matches: 126, Mismatches: 19, Indels: 5
0.84 0.13 0.03
Matches are distributed among these distances:
127 36 0.29
131 79 0.63
132 11 0.09
ACGTcount: A:0.26, C:0.14, G:0.14, T:0.47
Consensus pattern (127 bp):
AATTTATTTTCTCAAAGTTCTGTTGCCTCTATTTAAAGGAGTAATTTATTTTTTCAAAGTTCTAT
TGCCTCTATTTAGAGGAGCAATTTATTTTTCCCAAAGTTCTGTCACCTCCATTTAAAAGAGC
Found at i:129194 original size:43 final size:42
Alignment explanation
Indices: 128906--129206 Score: 295
Period size: 43 Copynumber: 7.0 Consensus size: 42
128896 GTCAATGAGT
* * *
128906 AATTTATTTTT-TCAAAGTTCTGTTGTCTTTATTTAGAGGAGT
1 AATTTATTTTTCTCAAAGTTC-GTTGCCTCTATTTAGAGGAGC
*
128948 AATTTATTTTT-TCAAAGTTCTGTTGTCTCTATTTAGAGGAGC
1 AATTTATTTTTCTCAAAGTTC-GTTGCCTCTATTTAGAGGAGC
* * * * *
128990 AATTTATTTTTCTCAAAGTTTTGTTACCTCCATTTAAAAGAGC
1 AATTTATTTTTCTCAAAG-TTCGTTGCCTCTATTTAGAGGAGC
* *
129033 AATTTA-TTTTCCCAAAGTTCTGTTGCCTCTATTTAAAGGAGC
1 AATTTATTTTTCTCAAAGTTC-GTTGCCTCTATTTAGAGGAGC
* * * *
129075 AATTTATTTATTTTTTTAAAGTTCTATTGCCTCTATTTATAGGAGC
1 AATTTA--T-TTTTCTCAAAGTTC-GTTGCCTCTATTTAGAGGAGC
* *
129121 AATTTATTTTTCCCAAAGTTCTGTCGCCTCTATTTAGAGGAGC
1 AATTTATTTTTCTCAAAGTTC-GTTGCCTCTATTTAGAGGAGC
* * *
129164 AATTTGTTTTTCTCAAAG-TCGTTAAACCTCTGTTTAGAGGAGC
1 AATTTATTTTTCTCAAAGTTCGTT--GCCTCTATTTAGAGGAGC
129207 TTTGTTTACT
Statistics
Matches: 221, Mismatches: 29, Indels: 17
0.83 0.11 0.06
Matches are distributed among these distances:
41 4 0.02
42 87 0.39
43 90 0.41
44 3 0.01
46 37 0.17
ACGTcount: A:0.26, C:0.15, G:0.15, T:0.45
Consensus pattern (42 bp):
AATTTATTTTTCTCAAAGTTCGTTGCCTCTATTTAGAGGAGC
Found at i:129220 original size:131 final size:130
Alignment explanation
Indices: 128906--129224 Score: 335
Period size: 131 Copynumber: 2.5 Consensus size: 130
128896 GTCAATGAGT
** ** * * *
128906 AATTTATTTTTTCAAAGTTCTGTTGTCTTTATTTAGAGGAG---TAATTTATTTTTTCAAAGTTC
1 AATTTATTTTCCCAAAGTTCTGTTACCTCTATTTAAAGGAGCATTTATTTATTTTTTCAAAGTTC
* * * * *
128968 TGTTGTCTCTATTTAGAGGAGCAATTTATTTTTCTCAAAGTTTTGTTACCTCCATTTAAAAGAGC
66 TATTGCCTCTATTTAGAGGAGCAATTTATTTTTCCCAAAGTTCTGTCACCTCCATTTAAAAGAGC
* *
129033 AATTTATTTTCCCAAAGTTCTGTTGCCTCTATTTAAAGGAGCAATTTATTTATTTTTTTAAAGTT
1 AATTTATTTTCCCAAAGTTCTGTTACCTCTATTTAAAGGAGC-ATTTATTTATTTTTTCAAAGTT
* * * * *
129098 CTATTGCCTCTATTTATAGGAGCAATTTATTTTTCCCAAAGTTCTGTCGCCTCTATTTAGAGGAG
65 CTATTGCCTCTATTTAGAGGAGCAATTTATTTTTCCCAAAGTTCTGTCACCTCCATTTAAAAGAG
129163 C
130 C
* * * * * *
129164 AATTTGTTTTTCTCAAAG-TC-GTTAAACCTCTGTTTAGAGGAGC-TTTGTTTACTTTTTCAAA
1 AATTT-ATTTTCCCAAAGTTCTGTT--ACCTCTATTTAAAGGAGCATTTATTTATTTTTTCAAA
129225 AAAAAAGCAT
Statistics
Matches: 160, Mismatches: 25, Indels: 11
0.82 0.13 0.06
Matches are distributed among these distances:
127 36 0.22
130 18 0.11
131 81 0.51
132 25 0.16
ACGTcount: A:0.25, C:0.14, G:0.14, T:0.46
Consensus pattern (130 bp):
AATTTATTTTCCCAAAGTTCTGTTACCTCTATTTAAAGGAGCATTTATTTATTTTTTCAAAGTTC
TATTGCCTCTATTTAGAGGAGCAATTTATTTTTCCCAAAGTTCTGTCACCTCCATTTAAAAGAGC
Found at i:130557 original size:202 final size:201
Alignment explanation
Indices: 130195--130567 Score: 472
Period size: 201 Copynumber: 1.9 Consensus size: 201
130185 GATTTAATTT
** * *
130195 AATAAAAATAAAAAATAATAATAAATTTTGGGAATAAATATTAATTATCCAATGATGAAATTTAT
1 AATAAAAATAAAAAATAATAATAAATTTTGGGAATAAATACAAATTACCCAAGGATGAAATTTAT
* * * *
130260 AGAAATTTCAAACGGTAAATTTCTATAAAATTCATAGGTGAGAAATTTTCTCTAAATTTATCTTC
66 AGAAATTTCAAACGGTAAATTCCTATAAAATTCATAGGTAAGAAATTTTCTCTAAATTTAGCTCC
*
130325 AATGGTGGAATAATTTAGATAAAGTTTCAATAAAAATAATTAATATTTATTTTTAAACAAAAAAA
131 AATGATGGAATAATTTAGATAAAGTTTCAATAAAAATAATTAATATTTATTTTTAAACAAAAAAA
130390 TTATAA
196 TTATAA
*
130396 AATAAAAATATAAAAAT-ATAA-AAATCTTT-GGAATTAAATACAAATTACCCAAGGATGAGATT
1 AATAAAAATA-AAAAATAATAATAAAT-TTTGGGAA-TAAATACAAATTACCCAAGGATGAAATT
* * * * *
130458 TTTAGAAATTTCAAATGGTAAGTTCCTA-AGAAATCTC-TAGGTAAGAAATTTTTTTTTAAATTT
63 TATAGAAATTTCAAACGGTAAATTCCTATA-AAAT-TCATAGGTAAGAAA-TTTTCTCTAAATTT
* *
130521 AGC-CCAAATGATGGAATAATTTAGATGAAA-TTTCAATACAAGTAATT
125 AGCTCC-AATGATGGAATAATTTAGAT-AAAGTTTCAATAAAAATAATT
130568 GTATTTTTTT
Statistics
Matches: 147, Mismatches: 17, Indels: 15
0.82 0.09 0.08
Matches are distributed among these distances:
200 9 0.06
201 79 0.54
202 56 0.38
203 3 0.02
ACGTcount: A:0.47, C:0.07, G:0.10, T:0.35
Consensus pattern (201 bp):
AATAAAAATAAAAAATAATAATAAATTTTGGGAATAAATACAAATTACCCAAGGATGAAATTTAT
AGAAATTTCAAACGGTAAATTCCTATAAAATTCATAGGTAAGAAATTTTCTCTAAATTTAGCTCC
AATGATGGAATAATTTAGATAAAGTTTCAATAAAAATAATTAATATTTATTTTTAAACAAAAAAA
TTATAA
Found at i:130775 original size:173 final size:169
Alignment explanation
Indices: 130438--130751 Score: 441
Period size: 173 Copynumber: 1.8 Consensus size: 169
130428 ATTAAATACA
* *
130438 AATTACCCAAGGATGAGATTTTTAGAAATTTCAAATGGTAAGTTCCTAAGAAATCTCTAGGTAAG
1 AATTACCCAAGGATGAGATTTTTAGAAATTTCAAATGGTAAATTCCTAAGAAATCTCTAAGTAAG
* * * *
130503 AAATTTTTTTTTAAATTTAGCCCAAATGATGGAATAATTTAGATGAAATTTCAATACAAGTAATT
66 AAATTTTTATGTAAATTTAGCCCAAATGATGGAATAATTTAGATGAAATTTCAATAAAAATAATT
* *
130568 GTATTTTTTTCCAAATAAAAAATTTTGGTTAAAAATATGTGAC
131 GTATTTTTTTCCAAAGAAAAAA---T-ATTAAAAATATGTGAC
* * *
130611 AATTATCCAAGGATGAGATTTTTAGGAATTTCAAATGGTAAATTCCTAAGAAATCTCTAAGTGAG
1 AATTACCCAAGGATGAGATTTTTAGAAATTTCAAATGGTAAATTCCTAAGAAATCTCTAAGTAAG
* * *
130676 AAA-TTTTATGTAAATTTGGTCCAAATGGTGGAATAATTTAGATGAAATTTCAATAAAAATAATT
66 AAATTTTTATGTAAATTTAGCCCAAATGATGGAATAATTTAGATGAAATTTCAATAAAAATAATT
130740 GTCATATTTTTT
131 GT-AT-TTTTTT
130752 TCTTTCTAAG
Statistics
Matches: 127, Mismatches: 12, Indels: 3
0.89 0.08 0.02
Matches are distributed among these distances:
172 56 0.44
173 65 0.51
174 6 0.05
ACGTcount: A:0.39, C:0.09, G:0.15, T:0.37
Consensus pattern (169 bp):
AATTACCCAAGGATGAGATTTTTAGAAATTTCAAATGGTAAATTCCTAAGAAATCTCTAAGTAAG
AAATTTTTATGTAAATTTAGCCCAAATGATGGAATAATTTAGATGAAATTTCAATAAAAATAATT
GTATTTTTTTCCAAAGAAAAAATATTAAAAATATGTGAC
Found at i:135698 original size:23 final size:23
Alignment explanation
Indices: 135649--135698 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
135639 TTACCATTTA
* *
135649 AAAAAAAAAAAAGCGAAATTTTG
1 AAAAAAAAAAAAGCGAAATATTC
*
135672 AAAAACAAAAAA-CGAAAATATTC
1 AAAAAAAAAAAAGCG-AAATATTC
135695 AAAA
1 AAAA
135699 TAGGAGGTGA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
22 2 0.09
23 21 0.91
ACGTcount: A:0.70, C:0.08, G:0.08, T:0.14
Consensus pattern (23 bp):
AAAAAAAAAAAAGCGAAATATTC
Found at i:139699 original size:56 final size:56
Alignment explanation
Indices: 139638--139747 Score: 166
Period size: 56 Copynumber: 2.0 Consensus size: 56
139628 CTTCTCGATA
** *
139638 TATATGATTGTAATTTTTCATTTTGTTTTATTAATAATAAAACGATCATTTAAGGT
1 TATATGATTACAACTTTTCATTTTGTTTTATTAATAATAAAACGATCATTTAAGGT
* * *
139694 TATATGATTACAACTTTTCATTTTGTTTTATTGATAATAAAAGGATTATTTAAG
1 TATATGATTACAACTTTTCATTTTGTTTTATTAATAATAAAACGATCATTTAAG
139748 ATGTTTTTGT
Statistics
Matches: 48, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
56 48 1.00
ACGTcount: A:0.35, C:0.05, G:0.11, T:0.49
Consensus pattern (56 bp):
TATATGATTACAACTTTTCATTTTGTTTTATTAATAATAAAACGATCATTTAAGGT
Found at i:139883 original size:27 final size:27
Alignment explanation
Indices: 139851--139919 Score: 70
Period size: 27 Copynumber: 2.6 Consensus size: 27
139841 AATAATCATT
139851 TAATTTATTTATAAAAAATTAT-TTAAA
1 TAATTTATTTATAAAAAA-TATCTTAAA
* * *
139878 -ATATTTCTATACAAAAAATATCTTAAA
1 TA-ATTTATTTATAAAAAATATCTTAAA
*
139905 TAATTTTTTTATAAA
1 TAATTTATTTATAAA
139920 TAAAATAAAA
Statistics
Matches: 33, Mismatches: 6, Indels: 6
0.73 0.13 0.13
Matches are distributed among these distances:
26 4 0.12
27 28 0.85
28 1 0.03
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.46
Consensus pattern (27 bp):
TAATTTATTTATAAAAAATATCTTAAA
Found at i:139925 original size:29 final size:26
Alignment explanation
Indices: 139851--139926 Score: 73
Period size: 29 Copynumber: 2.8 Consensus size: 26
139841 AATAATCATT
* *
139851 TAATTTATTTATAAAAAATTATTTAA
1 TAATTTTTTTATAAAAAAATATTTAA
* *
139877 -AATATTTCTATACAAAAAATATCTTAAA
1 TAATTTTTTTATA-AAAAAATAT-TT-AA
139905 TAATTTTTTTATAAATAAAATA
1 TAATTTTTTTATAAA-AAAATA
139927 AAATCTTTTA
Statistics
Matches: 39, Mismatches: 6, Indels: 7
0.75 0.12 0.13
Matches are distributed among these distances:
25 9 0.23
26 8 0.21
27 2 0.05
28 4 0.10
29 16 0.41
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (26 bp):
TAATTTTTTTATAAAAAAATATTTAA
Found at i:142270 original size:12 final size:12
Alignment explanation
Indices: 142241--142271 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
142231 TCATTATTAT
*
142241 AGTGACTGCTAC
1 AGTGATTGCTAC
142253 AGTGATTGCTAC
1 AGTGATTGCTAC
142265 AGTGATT
1 AGTGATT
142272 ACTGTTTGAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.26, C:0.16, G:0.26, T:0.32
Consensus pattern (12 bp):
AGTGATTGCTAC
Found at i:144174 original size:72 final size:72
Alignment explanation
Indices: 144084--144227 Score: 243
Period size: 72 Copynumber: 2.0 Consensus size: 72
144074 AATTCTCAGG
* *
144084 GGCAAAATAAATACGAAAAAGAGTTATTACATGTTTTATAGCAAGTAATTCTTTTTAAAAAATAA
1 GGCAAAATAAATACGAAAAACAGTTATTACATATTTTATAGCAAGTAATTCTTTTTAAAAAATAA
144149 TATATTT
66 TATATTT
* * *
144156 GGCAAAATAAATATGAAAACCAGTTATTACATATTTTATAGCAAGTAATTCTTTTTCAAAAATAA
1 GGCAAAATAAATACGAAAAACAGTTATTACATATTTTATAGCAAGTAATTCTTTTTAAAAAATAA
144221 TATATTT
66 TATATTT
144228 TATTTTTTTC
Statistics
Matches: 67, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
72 67 1.00
ACGTcount: A:0.45, C:0.08, G:0.10, T:0.37
Consensus pattern (72 bp):
GGCAAAATAAATACGAAAAACAGTTATTACATATTTTATAGCAAGTAATTCTTTTTAAAAAATAA
TATATTT
Found at i:144375 original size:15 final size:15
Alignment explanation
Indices: 144355--144384 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
144345 AATCTCCTCA
144355 TTTAGGAAGATAAAC
1 TTTAGGAAGATAAAC
*
144370 TTTAGGAATATAAAC
1 TTTAGGAAGATAAAC
144385 AATATTTGAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.47, C:0.07, G:0.17, T:0.30
Consensus pattern (15 bp):
TTTAGGAAGATAAAC
Found at i:153750 original size:38 final size:41
Alignment explanation
Indices: 153670--153754 Score: 122
Period size: 42 Copynumber: 2.1 Consensus size: 41
153660 GGGGGGAGAC
* *
153670 ATGGTATGAAAAATTTTTATTTGATTGATGATCTTGATATTG
1 ATGGTATGAAAAATTCTTATTTGATTGATGA-CTTGACATTG
153712 ATGGTATGAAAAATTCTTATTTGA-TGAT-A-TTGACATTG
1 ATGGTATGAAAAATTCTTATTTGATTGATGACTTGACATTG
153750 ATGGT
1 ATGGT
153755 TATATCCTTG
Statistics
Matches: 41, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
38 13 0.32
40 1 0.02
41 4 0.10
42 23 0.56
ACGTcount: A:0.32, C:0.04, G:0.20, T:0.45
Consensus pattern (41 bp):
ATGGTATGAAAAATTCTTATTTGATTGATGACTTGACATTG
Found at i:164018 original size:16 final size:14
Alignment explanation
Indices: 163988--164015 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
163978 GCCCATAGCA
163988 ATTATAATATATTT
1 ATTATAATATATTT
164002 ATTATAATATATTT
1 ATTATAATATATTT
164016 TTAACTTTAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (14 bp):
ATTATAATATATTT
Found at i:165450 original size:20 final size:20
Alignment explanation
Indices: 165425--165496 Score: 54
Period size: 20 Copynumber: 3.3 Consensus size: 20
165415 ATGCCAAAAT
165425 ATAAACTAAATATAACAATA
1 ATAAACTAAATATAACAATA
*
165445 ATAAACAAAGCCTAAATAGAACAATA
1 AT----AAA--CTAAATATAACAATA
** *
165471 ACCATCTAAATATAACAATA
1 ATAAACTAAATATAACAATA
165491 ATAAAC
1 ATAAAC
165497 AAAGCCTAAA
Statistics
Matches: 38, Mismatches: 8, Indels: 12
0.66 0.14 0.21
Matches are distributed among these distances:
20 19 0.50
22 1 0.03
24 3 0.08
26 15 0.39
ACGTcount: A:0.61, C:0.15, G:0.03, T:0.21
Consensus pattern (20 bp):
ATAAACTAAATATAACAATA
Found at i:165467 original size:26 final size:26
Alignment explanation
Indices: 165430--165508 Score: 89
Period size: 26 Copynumber: 3.3 Consensus size: 26
165420 AAAATATAAA
165430 CTAAATATAACAATAATAAACAAAGC
1 CTAAATATAACAATAATAAACAAAGC
* * *
165456 CTAAATAGAAC---AAT-AAC-CA-T
1 CTAAATATAACAATAATAAACAAAGC
165476 CTAAATATAACAATAATAAACAAAGC
1 CTAAATATAACAATAATAAACAAAGC
165502 CTAAATA
1 CTAAATA
165509 AAGCCTAAAT
Statistics
Matches: 41, Mismatches: 6, Indels: 12
0.69 0.10 0.20
Matches are distributed among these distances:
20 10 0.24
21 1 0.02
22 3 0.07
23 6 0.15
24 3 0.07
25 1 0.02
26 17 0.41
ACGTcount: A:0.59, C:0.16, G:0.04, T:0.20
Consensus pattern (26 bp):
CTAAATATAACAATAATAAACAAAGC
Found at i:165506 original size:11 final size:11
Alignment explanation
Indices: 165492--165522 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
165482 ATAACAATAA
*
165492 TAAACAAAGCC
1 TAAATAAAGCC
165503 TAAATAAAGCC
1 TAAATAAAGCC
165514 TAAATAAAG
1 TAAATAAAG
165523 TGATTAAAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.58, C:0.16, G:0.10, T:0.16
Consensus pattern (11 bp):
TAAATAAAGCC
Found at i:166545 original size:59 final size:60
Alignment explanation
Indices: 166459--166699 Score: 330
Period size: 59 Copynumber: 4.1 Consensus size: 60
166449 CCTTAAAGCA
* *
166459 TTTTAAAATTTTTATTTTCAA-AGAAAATTGATACTTTCAACTTTTCCTTAAAAATATC-T
1 TTTTAAAATTTTTATTTTCAAGA-AAAATTAATACTTTCAACTTTTCCTTAAAAATACCTT
* * * *
166518 TTTTAAAATATTTATTTTCAAGAAAAATTGATACTTTTAACTTTTCCTTAGAAATACCTT
1 TTTTAAAATTTTTATTTTCAAGAAAAATTAATACTTTCAACTTTTCCTTAAAAATACCTT
*
166578 TTTTGAAATTTTTATTTTCAAGAAAAATTAATACTTTCAACTTTT-CTTCAAAAAT--CTT
1 TTTTAAAATTTTTATTTTCAAGAAAAATTAATACTTTCAACTTTTCCTT-AAAAATACCTT
* * * *
166636 TTTTGAAATTTTTATTTTTAAGAAAAATTAATACTTTCAATTTTTTCTTAAAAATACCTT
1 TTTTAAAATTTTTATTTTCAAGAAAAATTAATACTTTCAACTTTTCCTTAAAAATACCTT
166696 TTTT
1 TTTT
166700 TGAAATATTT
Statistics
Matches: 165, Mismatches: 11, Indels: 11
0.88 0.06 0.06
Matches are distributed among these distances:
58 52 0.32
59 58 0.35
60 55 0.33
ACGTcount: A:0.36, C:0.11, G:0.04, T:0.49
Consensus pattern (60 bp):
TTTTAAAATTTTTATTTTCAAGAAAAATTAATACTTTCAACTTTTCCTTAAAAATACCTT
Found at i:166665 original size:58 final size:58
Alignment explanation
Indices: 166422--166710 Score: 320
Period size: 59 Copynumber: 4.9 Consensus size: 58
166412 TGCTTTTATA
* * * *
166422 CAAGGAAAATTAATACCTTT-AACTTTTCCTT--AAAGC-ATTTTAAAATTTTTATTTT
1 CAAGAAAAATTAATA-CTTTCAACTTTTCCTTAAAAATCTTTTTTGAAATTTTTATTTT
* * * *
166477 CAA-AGAAAATTGATACTTTCAACTTTTCCTTAAAAATATCTTTTTAAAATATTTATTTT
1 CAAGA-AAAATTAATACTTTCAACTTTTCCTTAAAAATCT-TTTTTGAAATTTTTATTTT
* * *
166536 CAAGAAAAATTGATACTTTTAACTTTTCCTTAGAAATACCTTTTTTGAAATTTTTATTTT
1 CAAGAAAAATTAATACTTTCAACTTTTCCTTA-AAA-ATCTTTTTTGAAATTTTTATTTT
166596 CAAGAAAAATTAATACTTTCAACTTTT-CTTCAAAAATCTTTTTTGAAATTTTTATTTT
1 CAAGAAAAATTAATACTTTCAACTTTTCCTT-AAAAATCTTTTTTGAAATTTTTATTTT
* * *
166654 TAAGAAAAATTAATACTTTCAATTTTTTCTTAAAAATACCTTTTTTTGAAATATTTT
1 CAAGAAAAATTAATACTTTCAACTTTTCCTTAAAAAT--C-TTTTTTGAAAT-TTTT
166711 TGTATTTATT
Statistics
Matches: 203, Mismatches: 16, Indels: 23
0.84 0.07 0.10
Matches are distributed among these distances:
54 4 0.02
55 23 0.11
57 3 0.01
58 53 0.26
59 55 0.27
60 48 0.24
61 13 0.06
62 4 0.02
ACGTcount: A:0.37, C:0.11, G:0.04, T:0.47
Consensus pattern (58 bp):
CAAGAAAAATTAATACTTTCAACTTTTCCTTAAAAATCTTTTTTGAAATTTTTATTTT
Found at i:169234 original size:17 final size:17
Alignment explanation
Indices: 169194--169336 Score: 60
Period size: 17 Copynumber: 8.4 Consensus size: 17
169184 AAAAATTCGT
* * *
169194 AAGAATTTCATATTCAT
1 AAGAATTTTAGATTCAC
*
169211 AAAAATTTTAGATTCAC
1 AAGAATTTTAGATTCAC
** **
169228 AAGAATTGGAGATTCGT
1 AAGAATTTTAGATTCAC
*
169245 AAG-ATTTTCAGAGTCAC
1 AAGAATTTT-AGATTCAC
**
169262 AAGAATTAGAGATTCGA-
1 AAGAATTTTAGATTC-AC
* *
169279 AA-AACTTTCAGATTCAT
1 AAGAA-TTTTAGATTCAC
**
169296 AAGAATTAAAGATTCAC
1 AAGAATTTTAGATTCAC
* * *
169313 AA-AGTTTTCATATTCGC
1 AAGAATTTT-AGATTCAC
169330 AAGAATT
1 AAGAATT
169337 AGAGATTTGT
Statistics
Matches: 90, Mismatches: 28, Indels: 15
0.68 0.21 0.11
Matches are distributed among these distances:
16 9 0.10
17 72 0.80
18 9 0.10
ACGTcount: A:0.42, C:0.12, G:0.14, T:0.32
Consensus pattern (17 bp):
AAGAATTTTAGATTCAC
Found at i:169262 original size:34 final size:34
Alignment explanation
Indices: 169215--169356 Score: 144
Period size: 34 Copynumber: 4.2 Consensus size: 34
169205 ATTCATAAAA
*
169215 ATTTT-AGATTCACAAGAATTGGAGATTCGTAAG
1 ATTTTCAGATTCACAAGAATTAGAGATTCGTAAG
* * *
169248 ATTTTCAGAGTCACAAGAATTAGAGATTCGAAAA
1 ATTTTCAGATTCACAAGAATTAGAGATTCGTAAG
* * * **
169282 ACTTTCAGATTCATAAGAATTAAAGATTCACAA-
1 ATTTTCAGATTCACAAGAATTAGAGATTCGTAAG
* * *
169315 AGTTTTCATATTCGCAAGAATTAGAGATTTGTAAG
1 A-TTTTCAGATTCACAAGAATTAGAGATTCGTAAG
*
169350 ACTTTCA
1 ATTTTCA
169357 AATTGGAGAT
Statistics
Matches: 87, Mismatches: 19, Indels: 5
0.78 0.17 0.05
Matches are distributed among these distances:
33 6 0.07
34 80 0.92
35 1 0.01
ACGTcount: A:0.39, C:0.12, G:0.16, T:0.32
Consensus pattern (34 bp):
ATTTTCAGATTCACAAGAATTAGAGATTCGTAAG
Found at i:169292 original size:68 final size:67
Alignment explanation
Indices: 169211--169343 Score: 160
Period size: 68 Copynumber: 2.0 Consensus size: 67
169201 TCATATTCAT
* ** **
169211 AAAAATTTTAGATTCACAAGAATTGGAGATTC-GTAAGATTTTCAGAGTCACAAGAATTAGAGAT
1 AAAAATTTCAGATTCACAAGAATTAAAGATTCACAAAG-TTTTCAGAGTCACAAGAATTAGAGAT
169275 TCG
65 TCG
* * * *
169278 AAAAACTTTCAGATTCATAAGAATTAAAGATTCACAAAGTTTTCATATTCGCAAGAATTAGAGAT
1 AAAAA-TTTCAGATTCACAAGAATTAAAGATTCACAAAGTTTTCAGAGTCACAAGAATTAGAGAT
169343 T
65 T
169344 TGTAAGACTT
Statistics
Matches: 55, Mismatches: 9, Indels: 3
0.82 0.13 0.04
Matches are distributed among these distances:
67 5 0.09
68 47 0.85
69 3 0.05
ACGTcount: A:0.42, C:0.11, G:0.16, T:0.31
Consensus pattern (67 bp):
AAAAATTTCAGATTCACAAGAATTAAAGATTCACAAAGTTTTCAGAGTCACAAGAATTAGAGATT
CG
Found at i:170435 original size:62 final size:62
Alignment explanation
Indices: 170364--170488 Score: 223
Period size: 62 Copynumber: 2.0 Consensus size: 62
170354 GTCACTAGGG
*
170364 TAAGTATTTGAATGGTATAACAATATCCAAATAATGGACATTCAGACAATTTTTAACATTAA
1 TAAGTATTTGAATGGTATAACAATATCCAAATAATGAACATTCAGACAATTTTTAACATTAA
* *
170426 TAAGTATTTGAATGGTATAACAATATCCAAATAATGAATATTTAGACAATTTTTAACATTAA
1 TAAGTATTTGAATGGTATAACAATATCCAAATAATGAACATTCAGACAATTTTTAACATTAA
170488 T
1 T
170489 CTAGAATCTT
Statistics
Matches: 60, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
62 60 1.00
ACGTcount: A:0.44, C:0.10, G:0.10, T:0.36
Consensus pattern (62 bp):
TAAGTATTTGAATGGTATAACAATATCCAAATAATGAACATTCAGACAATTTTTAACATTAA
Found at i:170715 original size:19 final size:20
Alignment explanation
Indices: 170691--170765 Score: 62
Period size: 23 Copynumber: 3.5 Consensus size: 20
170681 TTCTCTTTCA
170691 TTTTCTTAT-TTTCTTTTTT
1 TTTTCTTATCTTTCTTTTTT
170710 TTTTCTACTATTCTTTCATTTTTCAT
1 TTTTCT--TA-TCTTTC-TTTTT--T
* *
170736 TTTTTTTATCTTTCTTTCTT
1 TTTTCTTATCTTTCTTTTTT
170756 TTTTCATTAT
1 TTTTC-TTAT
170766 TGATATCTCC
Statistics
Matches: 45, Mismatches: 3, Indels: 14
0.73 0.05 0.23
Matches are distributed among these distances:
19 6 0.13
20 5 0.11
21 6 0.13
22 5 0.11
23 10 0.22
24 7 0.16
26 6 0.13
ACGTcount: A:0.11, C:0.15, G:0.00, T:0.75
Consensus pattern (20 bp):
TTTTCTTATCTTTCTTTTTT
Found at i:170750 original size:27 final size:29
Alignment explanation
Indices: 170706--170763 Score: 84
Period size: 27 Copynumber: 2.1 Consensus size: 29
170696 TTATTTTCTT
*
170706 TTTTTTTTCTACTATTCTTTCATTTTTCA
1 TTTTTTTTATACTATTCTTTCATTTTTCA
*
170735 TTTTTTTTAT-CT-TTCTTTCTTTTTTCA
1 TTTTTTTTATACTATTCTTTCATTTTTCA
170762 TT
1 TT
170764 ATTGATATCT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
27 16 0.59
28 2 0.07
29 9 0.33
ACGTcount: A:0.10, C:0.16, G:0.00, T:0.74
Consensus pattern (29 bp):
TTTTTTTTATACTATTCTTTCATTTTTCA
Found at i:170772 original size:27 final size:27
Alignment explanation
Indices: 170720--170773 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
170710 TTTTCTACTA
* **
170720 TTCTTTCATTTTTCATTTTTTTTATCT
1 TTCTTTCATTTTTCATTATTGATATCT
*
170747 TTCTTTCTTTTTTCATTATTGATATCT
1 TTCTTTCATTTTTCATTATTGATATCT
170774 CCTACACATC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.13, C:0.15, G:0.02, T:0.70
Consensus pattern (27 bp):
TTCTTTCATTTTTCATTATTGATATCT
Found at i:174765 original size:16 final size:16
Alignment explanation
Indices: 174735--174764 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
174725 GACACTTTCA
174735 ACTTTTCTTTAAAAAT
1 ACTTTTCTTTAAAAAT
174751 ACTTTT-TTTAAAAA
1 ACTTTTCTTTAAAAA
174765 AATATTTTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.40, C:0.10, G:0.00, T:0.50
Consensus pattern (16 bp):
ACTTTTCTTTAAAAAT
Found at i:174765 original size:17 final size:17
Alignment explanation
Indices: 174745--174777 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
174735 ACTTTTCTTT
174745 AAAAATACTTTT-TTTAA
1 AAAAATA-TTTTATTTAA
174762 AAAAATATTTTATTTA
1 AAAAATATTTTATTTA
174778 TTTATTTATT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (17 bp):
AAAAATATTTTATTTAA
Found at i:177333 original size:37 final size:41
Alignment explanation
Indices: 177248--177333 Score: 108
Period size: 41 Copynumber: 2.2 Consensus size: 41
177238 GGGGGAAAAT
* *
177248 TAATAGCGTTTATTTAAAAAATGCCACTAATTTTCTCTTTT
1 TAATAGCATTTATTTAAAAAATGCCACTAATTTTCTCTTTC
* *
177289 TAGTAGCATTTATTTATAAAATGCCACT-A-TTT-T-TTTC
1 TAATAGCATTTATTTAAAAAATGCCACTAATTTTCTCTTTC
177326 TAATAGCA
1 TAATAGCA
177334 GCGTTTCTTA
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
37 10 0.25
38 1 0.03
39 3 0.08
40 1 0.03
41 25 0.62
ACGTcount: A:0.33, C:0.14, G:0.08, T:0.45
Consensus pattern (41 bp):
TAATAGCATTTATTTAAAAAATGCCACTAATTTTCTCTTTC
Found at i:178915 original size:50 final size:50
Alignment explanation
Indices: 178783--178928 Score: 175
Period size: 52 Copynumber: 2.9 Consensus size: 50
178773 AACCATTATT
* * ** *
178783 GAGAGATTTTTGAGATTTAATTTCAGAATCAACTGGCATTAAAAATGATGTG
1 GAGAGA-TTTTGGGATTTAATTTCAGAATCAATTCACATT-AAAATGATGAG
* * *
178835 GAGAGATTGTTGGGATTTAATTCCATAATCAATTCACATTAAATTGATGAG
1 GAGAGATT-TTGGGATTTAATTTCAGAATCAATTCACATTAAAATGATGAG
* *
178886 GAGAGATTTTGGGATTTGATTTCAGAATCAATTCTCATTAAAA
1 GAGAGATTTTGGGATTTAATTTCAGAATCAATTCACATTAAAA
178929 AAAAAATCAA
Statistics
Matches: 80, Mismatches: 13, Indels: 4
0.82 0.13 0.04
Matches are distributed among these distances:
50 30 0.38
51 19 0.24
52 31 0.39
ACGTcount: A:0.36, C:0.09, G:0.20, T:0.36
Consensus pattern (50 bp):
GAGAGATTTTGGGATTTAATTTCAGAATCAATTCACATTAAAATGATGAG
Found at i:183570 original size:26 final size:28
Alignment explanation
Indices: 183519--183570 Score: 72
Period size: 28 Copynumber: 1.9 Consensus size: 28
183509 AAAAAAGTGT
*
183519 AAAAAAAAAAAAGATAAGAAGGAAAAGC
1 AAAAAAAAAAAAGATAAGAAGCAAAAGC
*
183547 AAAAAAAAAAAA-TTAA-AAGCAAAA
1 AAAAAAAAAAAAGATAAGAAGCAAAA
183571 AAATTAAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 7 0.32
27 3 0.14
28 12 0.55
ACGTcount: A:0.79, C:0.04, G:0.12, T:0.06
Consensus pattern (28 bp):
AAAAAAAAAAAAGATAAGAAGCAAAAGC
Found at i:183571 original size:27 final size:28
Alignment explanation
Indices: 183498--183558 Score: 72
Period size: 28 Copynumber: 2.2 Consensus size: 28
183488 AAAATATGAG
* *
183498 AAAAAA-ATAAGAA-AAAAGTGTAAAAAA
1 AAAAAAGATAAGAAGAAAA-AGCAAAAAA
*
183525 AAAAAAGATAAGAAGGAAAAGCAAAAAA
1 AAAAAAGATAAGAAGAAAAAGCAAAAAA
183553 AAAAAA
1 AAAAAA
183559 TTAAAAGCAA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
27 6 0.21
28 20 0.69
29 3 0.10
ACGTcount: A:0.79, C:0.02, G:0.13, T:0.07
Consensus pattern (28 bp):
AAAAAAGATAAGAAGAAAAAGCAAAAAA
Found at i:183587 original size:15 final size:14
Alignment explanation
Indices: 183547--183588 Score: 57
Period size: 15 Copynumber: 2.9 Consensus size: 14
183537 AAGGAAAAGC
183547 AAAAAAAAAAAATT
1 AAAAAAAAAAAATT
*
183561 AAAAGCAAAAAAATT
1 AAAA-AAAAAAAATT
183576 AAAAAAATAAAAA
1 AAAAAAA-AAAAA
183589 AAAAGACAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
14 6 0.25
15 18 0.75
ACGTcount: A:0.83, C:0.02, G:0.02, T:0.12
Consensus pattern (14 bp):
AAAAAAAAAAAATT
Found at i:184623 original size:86 final size:86
Alignment explanation
Indices: 184465--184850 Score: 434
Period size: 86 Copynumber: 4.5 Consensus size: 86
184455 TTTTGTTATG
* * * ** *
184465 ACATCTTTGCGAATATAGAACCCTTGCGAAACTTGGAGTCTTGAAAATCTTTTTTTCTTGTGAAC
1 ACATCTTTGTGAATCTAGAACCTTTGCGAAACTTGGAGTCTTGCGAATCTTTCTTTCTTGTGAAC
* * *
184530 TTGAAAATCTTTGCAAAGCTT
66 CTAAAAATCTTTGCGAAGCTT
* * *
184551 ACATCTTTGTGAATCTAGAACCTTTACGAAGCTTGGAGTCTTGCGAATCTTTCTTTCTTAG-AAA
1 ACATCTTTGTGAATCTAGAACCTTTGCGAAACTTGGAGTCTTGCGAATCTTTCTTTCTT-GTGAA
* *
184615 CCTAAAAATCATTGTGAAGCTT
65 CCTAAAAATCTTTGCGAAGCTT
** ** * * * * *
184637 TTATCTTTGCCAATCTAAAACCTTTGCAAAACTTAGAGTCTTGTGAATTTTTCTTTCTTGTGAAC
1 ACATCTTTGTGAATCTAGAACCTTTGCGAAACTTGGAGTCTTGCGAATCTTTCTTTCTTGTGAAC
* * *
184702 CTAAAAATTTTTGTGAATCTT
66 CTAAAAATCTTTGCGAAGCTT
* * * *
184723 GCATCTTTGTGAATCTACAACCTTTGCGAAACTTGGAGTCTTACGAATCTTTCTTTCTTATGAAC
1 ACATCTTTGTGAATCTAGAACCTTTGCGAAACTTGGAGTCTTGCGAATCTTTCTTTCTTGTGAAC
*
184788 CTAAAAAT-TCTTGCGAATCTT
66 CTAAAAATCT-TTGCGAAGCTT
* **
184809 ACATCTTTGTGAATCTAGAACCTTTGTGAAACTCAGAGTCTT
1 ACATCTTTGTGAATCTAGAACCTTTGCGAAACTTGGAGTCTT
184851 ACAAATTTGA
Statistics
Matches: 251, Mismatches: 46, Indels: 6
0.83 0.15 0.02
Matches are distributed among these distances:
85 2 0.01
86 248 0.99
87 1 0.00
ACGTcount: A:0.28, C:0.18, G:0.15, T:0.39
Consensus pattern (86 bp):
ACATCTTTGTGAATCTAGAACCTTTGCGAAACTTGGAGTCTTGCGAATCTTTCTTTCTTGTGAAC
CTAAAAATCTTTGCGAAGCTT
Found at i:184760 original size:172 final size:172
Alignment explanation
Indices: 184465--184850 Score: 490
Period size: 172 Copynumber: 2.2 Consensus size: 172
184455 TTTTGTTATG
* * *
184465 ACATCTTTGCGAATATAGAACCCTTGCGAAACTTGGAGTCTTGAAAATCTTTTTTTCTTGTGAAC
1 ACATCTTTGCGAATCTAGAACCTTTGCGAAACTTAGAGTCTTGAAAATCTTTTTTTCTTGTGAAC
* * * * *
184530 TTGAAAATCTTTGCAAAGCTTACATCTTTGTGAATCTAGAACCTTTACGAAGCTTGGAGTCTTGC
66 CTAAAAATCTTTGCAAAGCTTACATCTTTGTGAATCTACAACCTTTACGAAACTTGGAGTCTTAC
*
184595 GAATCTTTCTTTCTTA-GAAACCTAAAAA-TCATTGTGAAGCTT
131 GAATCTTTCTTTCTTATG-AACCTAAAAATTC-TTGCGAAGCTT
** * * * **
184637 TTATCTTTGCCAATCTAAAACCTTTGCAAAACTTAGAGTCTTGTGAAT-TTTTCTTTCTTGTGAA
1 ACATCTTTGCGAATCTAGAACCTTTGCGAAACTTAGAGTCTTGAAAATCTTTT-TTTCTTGTGAA
* ** * * *
184701 CCTAAAAATTTTTGTGAATCTTGCATCTTTGTGAATCTACAACCTTTGCGAAACTTGGAGTCTTA
65 CCTAAAAATCTTTGCAAAGCTTACATCTTTGTGAATCTACAACCTTTACGAAACTTGGAGTCTTA
*
184766 CGAATCTTTCTTTCTTATGAACCTAAAAATTCTTGCGAATCTT
130 CGAATCTTTCTTTCTTATGAACCTAAAAATTCTTGCGAAGCTT
* * *
184809 ACATCTTTGTGAATCTAGAACCTTTGTGAAACTCAGAGTCTT
1 ACATCTTTGCGAATCTAGAACCTTTGCGAAACTTAGAGTCTT
184851 ACAAATTTGA
Statistics
Matches: 180, Mismatches: 31, Indels: 6
0.83 0.14 0.03
Matches are distributed among these distances:
171 4 0.02
172 173 0.96
173 3 0.02
ACGTcount: A:0.28, C:0.18, G:0.15, T:0.39
Consensus pattern (172 bp):
ACATCTTTGCGAATCTAGAACCTTTGCGAAACTTAGAGTCTTGAAAATCTTTTTTTCTTGTGAAC
CTAAAAATCTTTGCAAAGCTTACATCTTTGTGAATCTACAACCTTTACGAAACTTGGAGTCTTAC
GAATCTTTCTTTCTTATGAACCTAAAAATTCTTGCGAAGCTT
Found at i:187014 original size:5 final size:5
Alignment explanation
Indices: 187006--187057 Score: 86
Period size: 5 Copynumber: 10.4 Consensus size: 5
186996 GTATATTGCC
**
187006 ATATT ATATT ATGCT ATATT ATATT ATATT ATATT ATATT ATATT ATATT
1 ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT
187056 AT
1 AT
187058 TACTATTTAT
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
5 43 1.00
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.58
Consensus pattern (5 bp):
ATATT
Found at i:187967 original size:17 final size:17
Alignment explanation
Indices: 187945--187992 Score: 53
Period size: 16 Copynumber: 2.9 Consensus size: 17
187935 TCTATTTTTA
*
187945 TTTTATTTTATTTTATT
1 TTTTATTTTATTTTAGT
* *
187962 TTTTATTTT-CTTAAGT
1 TTTTATTTTATTTTAGT
*
187978 TTTTATTTCATTTTA
1 TTTTATTTTATTTTA
187993 ATCTTTTTTT
Statistics
Matches: 24, Mismatches: 6, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
16 12 0.50
17 12 0.50
ACGTcount: A:0.19, C:0.04, G:0.02, T:0.75
Consensus pattern (17 bp):
TTTTATTTTATTTTAGT
Found at i:189316 original size:15 final size:15
Alignment explanation
Indices: 189296--189326 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
189286 ACTAATCGAT
*
189296 TTTCTTTTTTTTTTA
1 TTTCTTTTTTTCTTA
189311 TTTCTTTTTTTCTTA
1 TTTCTTTTTTTCTTA
189326 T
1 T
189327 GCATATTTAT
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:0.06, C:0.10, G:0.00, T:0.84
Consensus pattern (15 bp):
TTTCTTTTTTTCTTA
Found at i:192125 original size:7 final size:6
Alignment explanation
Indices: 192097--192197 Score: 54
Period size: 5 Copynumber: 16.7 Consensus size: 6
192087 AAATGTTGAA
* *
192097 AAAACAG AAAGAG AAAAAG AAATAAG AAAAAGGTG TACAAA- AAAAAG
1 AAAA-AG AAAAAG AAAAAG AAA-AAG AAAAA---G -AAAAAG AAAAAG
*
192144 -AAAAG -AAAA- AAAAAG CAAAAA- AAAAAG AAAAA- AAAACAT AAAAAG
1 AAAAAG AAAAAG AAAAAG -AAAAAG AAAAAG AAAAAG AAAA-AG AAAAAG
192189 AAAAA- AAAA
1 AAAAAG AAAA
192198 CAAAGAAAAT
Statistics
Matches: 77, Mismatches: 5, Indels: 26
0.71 0.05 0.24
Matches are distributed among these distances:
5 30 0.39
6 24 0.31
7 18 0.23
9 1 0.01
10 4 0.05
ACGTcount: A:0.79, C:0.04, G:0.13, T:0.04
Consensus pattern (6 bp):
AAAAAG
Found at i:192139 original size:1 final size:1
Alignment explanation
Indices: 192135--192197 Score: 54
Period size: 1 Copynumber: 63.0 Consensus size: 1
192125 AAAGGTGTAC
* * ** * * * *
192135 AAAAAAAAGAAAAGAAAAAAAAAGCAAAAAAAAAAGAAAAAAAAACATAAAAAGAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
192198 CAAAGAAAAT
Statistics
Matches: 47, Mismatches: 15, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
1 47 1.00
ACGTcount: A:0.87, C:0.03, G:0.08, T:0.02
Consensus pattern (1 bp):
A
Found at i:192152 original size:12 final size:11
Alignment explanation
Indices: 192137--192206 Score: 65
Period size: 11 Copynumber: 6.4 Consensus size: 11
192127 AGGTGTACAA
192137 AAAAAAGAAAAG
1 AAAAAA-AAAAG
192149 -AAAAAAAAAG
1 AAAAAAAAAAG
192159 CAAAAAAAAAAG
1 -AAAAAAAAAAG
192171 AAAAAAAAACA-
1 AAAAAAAAA-AG
* *
192182 TAAAAAGAAA-
1 AAAAAAAAAAG
*
192192 AAAAAACAAAG
1 AAAAAAAAAAG
192203 AAAA
1 AAAA
192207 TGAGACAAAA
Statistics
Matches: 50, Mismatches: 4, Indels: 9
0.79 0.06 0.14
Matches are distributed among these distances:
10 14 0.28
11 25 0.50
12 11 0.22
ACGTcount: A:0.86, C:0.04, G:0.09, T:0.01
Consensus pattern (11 bp):
AAAAAAAAAAG
Found at i:192157 original size:10 final size:10
Alignment explanation
Indices: 192138--192206 Score: 68
Period size: 10 Copynumber: 6.4 Consensus size: 10
192128 GGTGTACAAA
192138 AAAAAGAAAAG
1 AAAAA-AAAAG
192149 AAAAAAAAAG
1 AAAAAAAAAG
192159 CAAAAAAAAAAG
1 --AAAAAAAAAG
*
192171 AAAAAAAAAC
1 AAAAAAAAAG
192181 ATAAAAAGAAA-
1 A-AAAAA-AAAG
192192 AAAAAACAAAG
1 AAAAAA-AAAG
192203 AAAA
1 AAAA
192207 TGAGACAAAA
Statistics
Matches: 51, Mismatches: 2, Indels: 10
0.81 0.03 0.16
Matches are distributed among these distances:
10 23 0.45
11 15 0.29
12 13 0.25
ACGTcount: A:0.86, C:0.04, G:0.09, T:0.01
Consensus pattern (10 bp):
AAAAAAAAAG
Found at i:192169 original size:22 final size:23
Alignment explanation
Indices: 192137--192206 Score: 94
Period size: 22 Copynumber: 3.2 Consensus size: 23
192127 AGGTGTACAA
192137 AAAAAAGAAAAGAAAAAAAAAGC
1 AAAAAAGAAAAGAAAAAAAAAGC
192160 AAAAAA-AAAAGAAAAAAAAA-C
1 AAAAAAGAAAAGAAAAAAAAAGC
*
192181 ATAAAAAGAAAA-AAAAACAAAG-
1 A-AAAAAGAAAAGAAAAAAAAAGC
192203 AAAA
1 AAAA
192207 TGAGACAAAA
Statistics
Matches: 43, Mismatches: 1, Indels: 8
0.83 0.02 0.15
Matches are distributed among these distances:
21 5 0.12
22 28 0.65
23 10 0.23
ACGTcount: A:0.86, C:0.04, G:0.09, T:0.01
Consensus pattern (23 bp):
AAAAAAGAAAAGAAAAAAAAAGC
Found at i:192218 original size:22 final size:18
Alignment explanation
Indices: 192135--192206 Score: 76
Period size: 18 Copynumber: 3.9 Consensus size: 18
192125 AAAGGTGTAC
*
192135 AAAAAAAAGAAAAGAAA-A
1 AAAAAAAACAAAA-AAAGA
192153 AAAAAGCAAA-AAAAAAAGA
1 AAAAA--AAACAAAAAAAGA
*
192172 AAAAAAAACATAAAAAGA
1 AAAAAAAACAAAAAAAGA
192190 AAAAAAAACAAAGAAAA
1 AAAAAAAACAAA-AAAA
192207 TGAGACAAAA
Statistics
Matches: 47, Mismatches: 2, Indels: 9
0.81 0.03 0.16
Matches are distributed among these distances:
17 3 0.06
18 27 0.57
19 14 0.30
20 3 0.06
ACGTcount: A:0.86, C:0.04, G:0.08, T:0.01
Consensus pattern (18 bp):
AAAAAAAACAAAAAAAGA
Found at i:192225 original size:32 final size:31
Alignment explanation
Indices: 192135--192206 Score: 89
Period size: 27 Copynumber: 2.4 Consensus size: 31
192125 AAAGGTGTAC
* *
192135 AAAAAAAAG-AAAAGAAA-A-AAAAAG-CAA
1 AAAAAAAAGAAAAAAAAACATAAAAAGAAAA
192162 AAAAAAAAGAAAAAAAAACATAAAAAGAAAA
1 AAAAAAAAGAAAAAAAAACATAAAAAGAAAA
192193 AAAAACAAAGAAAA
1 AAAAA-AAAGAAAA
192207 TGAGACAAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
27 9 0.24
28 7 0.18
29 1 0.03
30 6 0.16
31 7 0.18
32 8 0.21
ACGTcount: A:0.86, C:0.04, G:0.08, T:0.01
Consensus pattern (31 bp):
AAAAAAAAGAAAAAAAAACATAAAAAGAAAA
Found at i:193413 original size:86 final size:85
Alignment explanation
Indices: 193246--193422 Score: 192
Period size: 86 Copynumber: 2.1 Consensus size: 85
193236 AAATCCTTGC
** * * * *
193246 GAATCTAGAACCTTTGCAAAACTTGGAGTCTTGCAAATCTTTTTTTCTTGCAAACCTGAAAATCC
1 GAATCTAGAACCTTTGCAAAACTTAAAATCATGCAAATATTTCTTTCTTGCAAACCTGAAAATCC
* * * *
193311 TTGTAAATTTTGCATCTTTGT
66 TTATAAATCTTACATC-TTAT
** * ** *
193332 GAATCTAGAACCTTTGTGAAACTTAAAATCATGTAAATATTTCTTTCTTGTGAACTTGAAAATCC
1 GAATCTAGAACCTTTGCAAAACTTAAAATCATGCAAATATTTCTTTCTTGCAAACCTGAAAATCC
*
193397 TTATGAATCTTACATCTTAT
66 TTATAAATCTTACATCTTAT
193417 GAATCT
1 GAATCT
193423 TTCTTTCTTG
Statistics
Matches: 74, Mismatches: 17, Indels: 1
0.80 0.18 0.01
Matches are distributed among these distances:
85 9 0.12
86 65 0.88
ACGTcount: A:0.31, C:0.17, G:0.12, T:0.40
Consensus pattern (85 bp):
GAATCTAGAACCTTTGCAAAACTTAAAATCATGCAAATATTTCTTTCTTGCAAACCTGAAAATCC
TTATAAATCTTACATCTTAT
Found at i:193461 original size:51 final size:51
Alignment explanation
Indices: 193371--193471 Score: 130
Period size: 51 Copynumber: 2.0 Consensus size: 51
193361 CATGTAAATA
* * * **
193371 TTTCTTTCTTGTGAACTTGAAAATCCTTATGAATCTTACATCTTATGAATC
1 TTTCTTTCTTGCGAACCTAAAAATCCTTACAAATCTTACATCTTATGAATC
* * *
193422 TTTCTTTCTTGCGAACCTAAAAATCCTTGCAAATTTTACATCTTGTGAAT
1 TTTCTTTCTTGCGAACCTAAAAATCCTTACAAATCTTACATCTTATGAAT
193472 ATTCCATTCC
Statistics
Matches: 42, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
51 42 1.00
ACGTcount: A:0.28, C:0.19, G:0.10, T:0.44
Consensus pattern (51 bp):
TTTCTTTCTTGCGAACCTAAAAATCCTTACAAATCTTACATCTTATGAATC
Found at i:194248 original size:121 final size:121
Alignment explanation
Indices: 194089--194313 Score: 283
Period size: 121 Copynumber: 1.9 Consensus size: 121
194079 TTCATTTCGG
* * ** * *
194089 TCATTTATCTTCGACCTAGACTCAATTTTGGTTGTTTTATCTTCTAAACTCATGGTTTT-CTCCT
1 TCATTTACCTTCGACCTAGACTCAATCTTGGTCATTTTATCTTCTAAACTCATGGTTTTACCCCA
*
194153 GATCATCCGATCTTGGCTCAGT-TCAGATCATCATTCATGATTGTGGTTTCGTCTTGA
66 G-TCATCCGATCCTGGCTCAGTCT-AGATCATCATTCATGATTGTGGTTTCGTCTTGA
* * * * *
194210 TCATTTACCTTTGACCTCGACTCGATCTTGGTCATTTTATCTTTTAAACTCGTGGTTTTACCCCA
1 TCATTTACCTTCGACCTAGACTCAATCTTGGTCATTTTATCTTCTAAACTCATGGTTTTACCCCA
* * *
194275 GTTATCCGATCCTGGCTCAGTCTATATCATCTTTCATGA
66 GTCATCCGATCCTGGCTCAGTCTAGATCATCATTCATGA
194314 CTCGTGATTT
Statistics
Matches: 87, Mismatches: 15, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
121 82 0.94
122 5 0.06
ACGTcount: A:0.19, C:0.24, G:0.15, T:0.43
Consensus pattern (121 bp):
TCATTTACCTTCGACCTAGACTCAATCTTGGTCATTTTATCTTCTAAACTCATGGTTTTACCCCA
GTCATCCGATCCTGGCTCAGTCTAGATCATCATTCATGATTGTGGTTTCGTCTTGA
Found at i:194324 original size:304 final size:305
Alignment explanation
Indices: 193769--194324 Score: 677
Period size: 304 Copynumber: 1.8 Consensus size: 305
193759 CATATGACCA
* * * * *
193769 GTGATTTCATCTCGGTCATTTACCTTCAACTTCGACTCAGTCATGGTTGCTTTATCTTTTAGACT
1 GTGATTTCATCTCGGTCATTTACCTTCAACCTAGACTCAATCATGGTTGCTTTATCTTCTAAACT
** ** *
193834 TTTGATTTTATCGCAGTCATCCAATCTTGGCTCAGTCTAGATCATTTTTAATGACTTATGGTTTT
66 CATGATTTTATCGCAGTCATCCAATCTTGGCTCAGTCTAGATCATCATTAATGACTTATGGTTTC
* * * * *
193899 ATCCTGATTATTTACCATCGATCTCGACTTGGTCCTAGTCACTTTATCTTTTAGACTCATGGTTT
131 ATCCTGATCATTTACCATCGACCTCGACTCGATCCTAGTCACTTTATCTTTTAAACTCATGGTTT
*** * *
193964 TACCTTGGTCATCCGATCTTGGCTTAGTCCAGATCATCTTTCATGACTCATGATTTTCGTCATGT
196 TACCCCAGTCATCCGATCCTGGCTCAGTCCAGATCATCTTTCATGACTCATGATTTTCGTCATGT
194029 TCATTTGTCATCAACCTCGACTCAATCCCAATCACCTCCTAACCT
261 TCATTTGTCATCAACCTCGACTCAATCCCAATCACCTCCTAACCT
* * * ** *
194074 GTGATTTCATTTCGGTCATTTATCTTCGACCTAGACTCAATTTTGGTTGTTTTATCTTCTAAACT
1 GTGATTTCATCTCGGTCATTTACCTTCAACCTAGACTCAATCATGGTTGCTTTATCTTCTAAACT
* * * * * *
194139 CATGGTTTTCTC-CTGATCATCCGATCTTGGCTCAGT-TCAGATCATCATTCATGA-TTGTGGTT
66 CATGATTTTATCGCAG-TCATCCAATCTTGGCTCAGTCT-AGATCATCATTAATGACTTATGGTT
* * * * * * * *
194201 TCGTCTTGATCATTTACCTTTGACCTCGACTCGATCTTGGTCATTTTATCTTTTAAACTCGTGGT
129 TCATCCTGATCATTTACCATCGACCTCGACTCGATCCTAGTCACTTTATCTTTTAAACTCATGGT
* * * *
194266 TTTACCCCAGTTATCCGATCCTGGCTCAGTCTATATCATCTTTCATGACTCGTGATTTT
194 TTTACCCCAGTCATCCGATCCTGGCTCAGTCCAGATCATCTTTCATGACTCATGATTTT
194325 ATCCCAATCA
Statistics
Matches: 205, Mismatches: 44, Indels: 5
0.81 0.17 0.02
Matches are distributed among these distances:
304 111 0.54
305 94 0.46
ACGTcount: A:0.20, C:0.24, G:0.15, T:0.42
Consensus pattern (305 bp):
GTGATTTCATCTCGGTCATTTACCTTCAACCTAGACTCAATCATGGTTGCTTTATCTTCTAAACT
CATGATTTTATCGCAGTCATCCAATCTTGGCTCAGTCTAGATCATCATTAATGACTTATGGTTTC
ATCCTGATCATTTACCATCGACCTCGACTCGATCCTAGTCACTTTATCTTTTAAACTCATGGTTT
TACCCCAGTCATCCGATCCTGGCTCAGTCCAGATCATCTTTCATGACTCATGATTTTCGTCATGT
TCATTTGTCATCAACCTCGACTCAATCCCAATCACCTCCTAACCT
Found at i:195091 original size:19 final size:19
Alignment explanation
Indices: 195058--195105 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 19
195048 GGAAAATTTT
*
195058 TGAAAAAATTAGGAA-ATC
1 TGAAAAATTTAGGAATATC
* *
195076 TGGAAAAATTTTGGAATTTC
1 T-GAAAAATTTAGGAATATC
195096 TGAAAAATTT
1 TGAAAAATTT
195106 CTAGATTTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
18 1 0.04
19 21 0.84
20 3 0.12
ACGTcount: A:0.46, C:0.04, G:0.17, T:0.33
Consensus pattern (19 bp):
TGAAAAATTTAGGAATATC
Found at i:195537 original size:12 final size:13
Alignment explanation
Indices: 195510--195543 Score: 52
Period size: 12 Copynumber: 2.7 Consensus size: 13
195500 CATTTTTCCA
195510 TTTTTATTTAATT
1 TTTTTATTTAATT
*
195523 TTTTTATTTGA-T
1 TTTTTATTTAATT
195535 TTTTTATTT
1 TTTTTATTT
195544 TCTTAAGTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
12 10 0.50
13 10 0.50
ACGTcount: A:0.18, C:0.00, G:0.03, T:0.79
Consensus pattern (13 bp):
TTTTTATTTAATT
Found at i:196531 original size:28 final size:29
Alignment explanation
Indices: 196496--196551 Score: 87
Period size: 28 Copynumber: 2.0 Consensus size: 29
196486 ATCTTTCAAA
*
196496 ATTTTTATTTGAAAATATT-TTTTTATTT
1 ATTTTTATTTGAAAAGATTGTTTTTATTT
*
196524 ATTTTTATTTGCAAAGATTGTTTTTATT
1 ATTTTTATTTGAAAAGATTGTTTTTATT
196552 GAATAATTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 17 0.68
29 8 0.32
ACGTcount: A:0.27, C:0.02, G:0.07, T:0.64
Consensus pattern (29 bp):
ATTTTTATTTGAAAAGATTGTTTTTATTT
Found at i:197017 original size:31 final size:32
Alignment explanation
Indices: 196976--197037 Score: 83
Period size: 32 Copynumber: 2.0 Consensus size: 32
196966 AATAGCATTA
196976 AAAACTTCAAAC-TTCA-CTGAAAAAATCATCG
1 AAAACTTCAAACTTTCATC-GAAAAAATCATCG
* *
197007 AAAATTTCAAACTTTCATCGAAAAATTCATC
1 AAAACTTCAAACTTTCATCGAAAAAATCATC
197038 CCAAACCTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
31 11 0.41
32 15 0.56
33 1 0.04
ACGTcount: A:0.47, C:0.21, G:0.05, T:0.27
Consensus pattern (32 bp):
AAAACTTCAAACTTTCATCGAAAAAATCATCG
Found at i:197524 original size:3 final size:3
Alignment explanation
Indices: 197518--197564 Score: 57
Period size: 3 Copynumber: 17.0 Consensus size: 3
197508 AAAAAACAAA
*
197518 AAT AAT AAT AAT -AT AAT AAT -AT AAT -AT AAT -AC AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
197562 AAT
1 AAT
197565 GGCATTAATA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
2 7 0.18
3 31 0.82
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:197533 original size:8 final size:8
Alignment explanation
Indices: 197522--197564 Score: 50
Period size: 8 Copynumber: 5.0 Consensus size: 8
197512 AACAAAAATA
197522 ATAATAAT
1 ATAATAAT
197530 ATAATAAT
1 ATAATAAT
197538 ATAATATAAT
1 AT-A-ATAAT
*
197548 ACAATAAT
1 ATAATAAT
197556 AATAATAAT
1 -ATAATAAT
197565 GGCATTAATA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
8 15 0.50
9 9 0.30
10 6 0.20
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (8 bp):
ATAATAAT
Found at i:197665 original size:25 final size:23
Alignment explanation
Indices: 197626--197675 Score: 75
Period size: 22 Copynumber: 2.2 Consensus size: 23
197616 AAGGAAAATA
197626 AATAATAATAATAATAATAATAAT
1 AATAATAAT-ATAATAATAATAAT
*
197650 -ATAATAATATAGTAATAATAAT
1 AATAATAATATAATAATAATAAT
197672 AATA
1 AATA
197676 GTGACATTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
22 13 0.54
23 11 0.46
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (23 bp):
AATAATAATATAATAATAATAAT
Found at i:197689 original size:3 final size:3
Alignment explanation
Indices: 197626--197675 Score: 77
Period size: 3 Copynumber: 17.3 Consensus size: 3
197616 AAGGAAAATA
*
197626 AAT AAT AAT AAT AAT AAT AAT AAT -AT AAT AAT -AT AGT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
197672 AAT A
1 AAT A
197676 GTGACATTAA
Statistics
Matches: 43, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
2 4 0.09
3 39 0.91
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:198047 original size:114 final size:113
Alignment explanation
Indices: 197900--198338 Score: 382
Period size: 114 Copynumber: 3.9 Consensus size: 113
197890 AAAACCATAG
* * * ** *
197900 GTCAAAATGAAA-CAACCAGGACCAAATCGAGGTCGAAAATGATCAGGATAAAACCATGAATCAT
1 GTCAAAAT-AAAGCGACCAGGACCAAGTCAAGGTAAAAAATGA-CAGGATAAAACCACGAATCAT
* * * *
197964 ATGAACTGATCTAGATTGAGCCAAGATCAAGTAATTGGGATGAAAC-CAAA
64 ATGAAATGATCTAGACTGAGCCAAGATCAAGTGATTGGGATGAAACAC-GA
* * * * *
198014 GTCAAAATAAAGTGACCAGGACCAAGTCAAGGTCAAAAATGACCAGGA-GAAGCCACAAATCATA
1 GTCAAAATAAAGCGACCAGGACCAAGTCAAGGTAAAAAATGA-CAGGATAAAACCACGAATCATA
* * * * * * * *
198078 TAAAATGATATAGACTAAGCCAATATCAAGTGACTAGGATAAAATTACGA
65 TGAAATGATCTAGACTGAGCCAAGATCAAGTGATTGGGATGAAA-CACGA
* * * ** * * *
198128 GTCAAAATAAAACGATCAAGACCAAGTCAAAATAAAAAATGACTAGGATGAAATCATGAATCATA
1 GTCAAAATAAAGCGACCAGGACCAAGTCAAGGTAAAAAATGAC-AGGATAAAACCACGAATCATA
* * * *
198193 TGAAATGATTTGGACTGAACCAAGATCAAGTGATCGGGATGAAACACGA
65 TGAAATGATCTAGACTGAGCCAAGATCAAGTGATTGGGATGAAACACGA
* * ** * * *
198242 GTTAAAAAAAAGCGACCAGGATTAAGTCAAGGTAAAAAATGACTGG-GACAACCACGAATCATAT
1 GTCAAAATAAAGCGACCAGGACCAAGTCAAGGTAAAAAATGACAGGATAAAACCACGAATCATAT
* * * *
198306 GAAATGATCTGGATTGAGCTAAGATAAAGTGAT
66 GAAATGATCTAGACTGAGCCAAGATCAAGTGAT
198339 CGAGACGAAA
Statistics
Matches: 256, Mismatches: 64, Indels: 12
0.77 0.19 0.04
Matches are distributed among these distances:
112 41 0.16
113 52 0.20
114 116 0.45
115 47 0.18
ACGTcount: A:0.46, C:0.15, G:0.20, T:0.19
Consensus pattern (113 bp):
GTCAAAATAAAGCGACCAGGACCAAGTCAAGGTAAAAAATGACAGGATAAAACCACGAATCATAT
GAAATGATCTAGACTGAGCCAAGATCAAGTGATTGGGATGAAACACGA
Found at i:198556 original size:115 final size:115
Alignment explanation
Indices: 198335--198602 Score: 313
Period size: 115 Copynumber: 2.3 Consensus size: 115
198325 TAAGATAAAG
* * * * *
198335 TGATCGAGACGAAATCATGAATCATATGAAATGATTTGGACTGAACCAAGATCAAGCAACTGGAA
1 TGATCAAGACGAAACCACGAATCATATGAAATGATCTGGACTGAACCAAAATCAAGCAACTGGAA
* * * *
198400 TGAAATCGTGAGTTAAAAATAAAGCGACCAGGCCCAATCAAGGTAAAAAA
66 TGAAATCATAAGTTAAAAATAAAGCGACCAAGACCAATCAAGGTAAAAAA
* * * * ** *
198450 TGATCAAGATGAAACTACGAATCATATGAAATGATCTGGACTGAGCTAAAATCAAGTGACTGGGA
1 TGATCAAGACGAAACCACGAATCATATGAAATGATCTGGACTGAACCAAAATCAAGCAACTGGAA
** *
198515 TGAAATCATAAG-TCCAAATAAAGCGACCAAGATCAAGTCAAGGTAAAAAA
66 TGAAATCATAAGTTAAAAATAAAGCGACCAAGACCAA-TCAAGGTAAAAAA
* * **
198565 TGATCGAGACGAGACCATAAATCATATGAAATGATCTG
1 TGATCAAGACGAAACCACGAATCATATGAAATGATCTG
198603 AATTGAGTCA
Statistics
Matches: 127, Mismatches: 25, Indels: 2
0.82 0.16 0.01
Matches are distributed among these distances:
114 19 0.15
115 108 0.85
ACGTcount: A:0.44, C:0.15, G:0.21, T:0.20
Consensus pattern (115 bp):
TGATCAAGACGAAACCACGAATCATATGAAATGATCTGGACTGAACCAAAATCAAGCAACTGGAA
TGAAATCATAAGTTAAAAATAAAGCGACCAAGACCAATCAAGGTAAAAAA
Found at i:206621 original size:27 final size:28
Alignment explanation
Indices: 206583--206637 Score: 85
Period size: 27 Copynumber: 2.0 Consensus size: 28
206573 CTCTATAACG
*
206583 TGTACAAAAAAAGA-AATAAGAAAAAAA
1 TGTACAAAAAAAGAGAAAAAGAAAAAAA
*
206610 TGTACAAAAAAAGAGAAAAAGCAAAAAA
1 TGTACAAAAAAAGAGAAAAAGAAAAAAA
206638 CAAAAAAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
27 14 0.56
28 11 0.44
ACGTcount: A:0.73, C:0.05, G:0.13, T:0.09
Consensus pattern (28 bp):
TGTACAAAAAAAGAGAAAAAGAAAAAAA
Found at i:206635 original size:28 final size:28
Alignment explanation
Indices: 206583--206664 Score: 89
Period size: 28 Copynumber: 3.0 Consensus size: 28
206573 CTCTATAACG
* *
206583 TGTACAAAAAAAGA-AATAAGAAAAAAA
1 TGTACAAAAAAAGAGAAAAAGCAAAAAA
206610 TGTACAAAAAAAGAGAAAAAGCAAAAAA
1 TGTACAAAAAAAGAGAAAAAGCAAAAAA
* *
206638 --CAAAAAAAAAGAAGTAAAAAGCAAAAA
1 TGTACAAAAAAAG-AG-AAAAAGCAAAAA
206665 GTAACAAAAA
Statistics
Matches: 48, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
26 9 0.19
27 16 0.33
28 23 0.48
ACGTcount: A:0.74, C:0.06, G:0.12, T:0.07
Consensus pattern (28 bp):
TGTACAAAAAAAGAGAAAAAGCAAAAAA
Found at i:207716 original size:86 final size:86
Alignment explanation
Indices: 207559--207777 Score: 224
Period size: 86 Copynumber: 2.5 Consensus size: 86
207549 TTTGTTATGA
* * * * ** * *
207559 CATCTTTGCGAATCTAGAACCTTTACGAAACTTGGAGTCCTACAAATTTTTCTTTTTTGATAACT
1 CATCTTTGCGAATCTAGAACCTTTGCGAAACTTGGAGTCTTACGAATTTTTATTTCATGAGAACC
* * *
207624 TGAAAATCCTTGCTAAGCTTG
66 TAAAAATCCTTACAAAGCTTG
* ** *
207645 CATCTTTGAGAATCTAGAATGTTTGCAAAACTTGGAGTCTTACGAATTTTTATTTCAT-ACGAAC
1 CATCTTTGCGAATCTAGAACCTTTGCGAAACTTGGAGTCTTACGAATTTTTATTTCATGA-GAAC
** *
207709 CTAAAAATTTTTACAAATCTTG
65 CTAAAAATCCTTACAAAGCTTG
* * * *
207731 CATCTTTTCGAATCTAGAACCTTTGCGACACTTAGAGTCTTGCGAAT
1 CATCTTTGCGAATCTAGAACCTTTGCGAAACTTGGAGTCTTACGAAT
207778 CTGAAAATCC
Statistics
Matches: 106, Mismatches: 26, Indels: 2
0.79 0.19 0.01
Matches are distributed among these distances:
85 1 0.01
86 105 0.99
ACGTcount: A:0.30, C:0.19, G:0.14, T:0.37
Consensus pattern (86 bp):
CATCTTTGCGAATCTAGAACCTTTGCGAAACTTGGAGTCTTACGAATTTTTATTTCATGAGAACC
TAAAAATCCTTACAAAGCTTG
Found at i:224201 original size:10 final size:10
Alignment explanation
Indices: 224186--224210 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
224176 AAATCACGCC
224186 AAAAAGAAAG
1 AAAAAGAAAG
224196 AAAAAGAAAG
1 AAAAAGAAAG
224206 AAAAA
1 AAAAA
224211 ATCACATCCC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (10 bp):
AAAAAGAAAG
Found at i:226793 original size:2 final size:2
Alignment explanation
Indices: 226788--226815 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
226778 GCCTTTCTCA
226788 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
226816 GACTGAATGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:227059 original size:53 final size:51
Alignment explanation
Indices: 226960--227066 Score: 119
Period size: 50 Copynumber: 2.1 Consensus size: 51
226950 CATAATAACA
*
226960 AAATTACAATAATAAAATATATCTTGAAAAAAAGTTATAAAC-AAAAAAAT
1 AAATTACAATAATAAAATATATCTTGAAAAAAAGTTACAAACAAAAAAAAT
* * * *
227010 AAATTACAATAGTAATATGATATATCTTG-GAAAAAGTTGCAAATTAAAAAAAAT
1 AAATTACAATAATAA-A--ATATATCTTGAAAAAAAGTTACAAA-CAAAAAAAAT
227064 AAA
1 AAA
227067 AAACTGATAT
Statistics
Matches: 47, Mismatches: 5, Indels: 6
0.81 0.09 0.10
Matches are distributed among these distances:
50 14 0.30
51 1 0.02
52 11 0.23
53 10 0.21
54 11 0.23
ACGTcount: A:0.60, C:0.06, G:0.07, T:0.27
Consensus pattern (51 bp):
AAATTACAATAATAAAATATATCTTGAAAAAAAGTTACAAACAAAAAAAAT
Found at i:227344 original size:30 final size:30
Alignment explanation
Indices: 227294--227354 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
227284 AAAGATTTAA
* *
227294 TATGAAAATTTGTTTCAATTTTCAATATCT
1 TATGAAAAGTTGTTTAAATTTTCAATATCT
* *
227324 TATGCAAAGTTGTTTAAATTTTCACTATCT
1 TATGAAAAGTTGTTTAAATTTTCAATATCT
227354 T
1 T
227355 GCGTAAATTT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.31, C:0.11, G:0.08, T:0.49
Consensus pattern (30 bp):
TATGAAAAGTTGTTTAAATTTTCAATATCT
Found at i:227554 original size:14 final size:14
Alignment explanation
Indices: 227535--227568 Score: 52
Period size: 14 Copynumber: 2.4 Consensus size: 14
227525 ATTAAGAAGA
227535 TAAAA-TTTATATTT
1 TAAAATTTTA-ATTT
227549 TAAAATTTTAATTT
1 TAAAATTTTAATTT
227563 TAAAAT
1 TAAAAT
227569 ATACATCTCT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 15 0.79
15 4 0.21
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (14 bp):
TAAAATTTTAATTT
Found at i:227656 original size:27 final size:27
Alignment explanation
Indices: 227585--227656 Score: 62
Period size: 27 Copynumber: 2.7 Consensus size: 27
227575 CTCTAGATTG
*
227585 ATTTAATTTCTAATTATAATTAACTAATT
1 ATTTAATTTATAATTA-AATTAAC-AATT
*
227614 -TTGATATTTA-AA-TAAATTTAA-AATT
1 ATTTA-ATTTATAATTAAA-TTAACAATT
227639 ATTTAATTTATAATTAAA
1 ATTTAATTTATAATTAAA
227657 AGAAACTACC
Statistics
Matches: 35, Mismatches: 3, Indels: 12
0.70 0.06 0.24
Matches are distributed among these distances:
25 9 0.26
26 7 0.20
27 10 0.29
28 5 0.14
29 4 0.11
ACGTcount: A:0.46, C:0.03, G:0.01, T:0.50
Consensus pattern (27 bp):
ATTTAATTTATAATTAAATTAACAATT
Found at i:227750 original size:5 final size:5
Alignment explanation
Indices: 227740--227768 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
227730 TGCTTAAACC
227740 TTTTA TTTTA TTTTA TTTTA TTTTA TTTT
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTT
227769 TGCCCTTGCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (5 bp):
TTTTA
Found at i:229751 original size:13 final size:13
Alignment explanation
Indices: 229713--229751 Score: 51
Period size: 15 Copynumber: 2.8 Consensus size: 13
229703 TATCAGGGGG
*
229713 TTTCTGGTTTTTT
1 TTTCTGTTTTTTT
229726 TTTCTCGTCTTTTTT
1 TTTCT-GT-TTTTTT
229741 TTTCTGTTTTT
1 TTTCTGTTTTT
229752 GATATCTTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
13 9 0.39
14 3 0.13
15 11 0.48
ACGTcount: A:0.00, C:0.13, G:0.10, T:0.77
Consensus pattern (13 bp):
TTTCTGTTTTTTT
Found at i:230887 original size:43 final size:43
Alignment explanation
Indices: 230801--231344 Score: 514
Period size: 43 Copynumber: 12.7 Consensus size: 43
230791 CTCCCTTAAG
* * *
230801 TAGAGGCTTACCAACTTTTGAAAAAATAAAATAAAGCTCCTCTAAA
1 TAGAGGCTCAACAAC-TTTG-AAAAAT-AAATAATGCTCCTCTAAA
* * * *
230847 TAGAGGCTCAACAACTTTGGAAAGTCAATAAAGCTCCTCTAAA
1 TAGAGGCTCAACAACTTTGAAAAATAAATAATGCTCCTCTAAA
* * * *
230890 TAAAGGTTCAACAAC-TTCATAAAATAAATAATGTTCCTCT-AA
1 TAGAGGCTCAACAACTTTGA-AAAATAAATAATGCTCCTCTAAA
* * * *
230932 TCAGAGGCTCCATAACTTTGGAAAATAAATAATGCTCTTCTAAA
1 T-AGAGGCTCAACAACTTTGAAAAATAAATAATGCTCCTCTAAA
* * * *
230976 CAGAGGCTCAACAACTTTAAAAAAAATAAATAAGGCTCCTCTAAT
1 TAGAGGCTCAACAACTTT--GAAAAATAAATAATGCTCCTCTAAA
231021 TAGAGG-TCAACAACTTTGAAAAATAAATAATGCTCCTCTAAA
1 TAGAGGCTCAACAACTTTGAAAAATAAATAATGCTCCTCTAAA
* ** *
231063 TAAAGGCTCAATGACTTTGAAAAATAAATAATGCTCTTCT-AA
1 TAGAGGCTCAACAACTTTGAAAAATAAATAATGCTCCTCTAAA
** * *
231105 TCAGAGATTCAACAACTTTGAAAAATAAATGATGCTCTTCT-AA
1 T-AGAGGCTCAACAACTTTGAAAAATAAATAATGCTCCTCTAAA
* *
231148 TAAAAGGCTCAACAACTTTGAAAAATAAATAATGCTCCTCTAAG
1 T-AGAGGCTCAACAACTTTGAAAAATAAATAATGCTCCTCTAAA
* * * *
231192 CAGAAGCTCAACAACTTTGAAAAATAAAATAAGGCTCATCTAAA
1 TAGAGGCTCAACAACTTTGAAAAAT-AAATAATGCTCCTCTAAA
* * ** * * *
231236 CAGAGGTTCAATGATTTTGAAAAAT--ATAAGGCTCCTCTAAG
1 TAGAGGCTCAACAACTTTGAAAAATAAATAATGCTCCTCTAAA
* * * * * *
231277 CAGAAGCTCAATAACTTTGAAAAAT--A-AAGGCTCATCTAAG
1 TAGAGGCTCAACAACTTTGAAAAATAAATAATGCTCCTCTAAA
231317 TAGAGGCTCAACAACTTTGAAAAATAAA
1 TAGAGGCTCAACAACTTTGAAAAATAAA
231345 GCTCCTCAAC
Statistics
Matches: 415, Mismatches: 71, Indels: 28
0.81 0.14 0.05
Matches are distributed among these distances:
40 35 0.08
41 36 0.09
42 36 0.09
43 211 0.51
44 55 0.13
45 29 0.07
46 13 0.03
ACGTcount: A:0.44, C:0.17, G:0.13, T:0.26
Consensus pattern (43 bp):
TAGAGGCTCAACAACTTTGAAAAATAAATAATGCTCCTCTAAA
Found at i:231093 original size:173 final size:171
Alignment explanation
Indices: 230802--231344 Score: 580
Period size: 173 Copynumber: 3.2 Consensus size: 171
230792 TCCCTTAAGT
* * * *
230802 AGAGGCTTACCAACTTTTGAAAAAATAAAATAAAGCTCCTCTAAATAGAGGCTCAACAACTTTGG
1 AGAGGCTCAACAAC-TTTAAAAAAAT-AAATAAAGCTCCTCTAAATAGAGG-TCAACAACTTTGA
* * ** * *
230867 AAAGTCAATAAAGCTCCTCTAAATAAAGGTTCAACAAC-TTCATAAAATAAATAATGTTCCTCTA
63 AAAATAAATAAAGCTCCTCTAAATAAAGGTTCAATGACTTTGA-AAAATAAATAATGCTCCTCTA
*
230931 ATCAGAGGCTCCATAACTTTGGAAAATAAATAATGCTCTTCTAAA
127 ATCAGAGGCTCAATAACTTTGGAAAATAAATAATGCTCTTCTAAA
* *
230976 CAGAGGCTCAACAACTTTAAAAAAAATAAATAAGGCTCCTCTAATTAGAGGTCAACAACTTTGAA
1 -AGAGGCTCAACAACTTT-AAAAAAATAAATAAAGCTCCTCTAAATAGAGGTCAACAACTTTGAA
* * *
231041 AAATAAATAATGCTCCTCTAAATAAAGGCTCAATGACTTTGAAAAATAAATAATGCTCTTCTAAT
64 AAATAAATAAAGCTCCTCTAAATAAAGGTTCAATGACTTTGAAAAATAAATAATGCTCCTCTAAT
** * * *
231106 CAGAGATTCAACAACTTTGAAAAATAAATGATGCTCTTCTAATA
129 CAGAGGCTCAATAACTTTGGAAAATAAATAATGCTCTTCTAA-A
* * * ** *
231150 AAAGGCTCAACAACTTT-GAAAAATAAATAATGCTCCTCTAAGCAGAAGCTCAACAACTTTGAAA
1 AGAGGCTCAACAACTTTAAAAAAATAAATAAAGCTCCTCTAAATAG-AGGTCAACAACTTTGAAA
* * * * * * *
231214 AATAAAATAAGGCTCATCTAAACAGAGGTTCAATGATTTTGAAAAAT--ATAAGGCTCCTCTAAG
65 AAT-AAATAAAGCTCCTCTAAATAAAGGTTCAATGACTTTGAAAAATAAATAATGCTCCTCTAAT
* * * * *
231277 CAGAAGCTCAATAACTTT-GAAAA-ATA-AAGGCTCATCTAAGT
129 CAGAGGCTCAATAACTTTGGAAAATAAATAATGCTCTTCTAA-A
*
231318 AGAGGCTCAACAACTTT-GAAAAATAAA
1 AGAGGCTCAACAACTTTAAAAAAATAAA
231345 GCTCCTCAAC
Statistics
Matches: 315, Mismatches: 48, Indels: 17
0.83 0.13 0.04
Matches are distributed among these distances:
168 36 0.11
169 2 0.01
170 4 0.01
171 51 0.16
172 20 0.06
173 154 0.49
174 29 0.09
175 19 0.06
ACGTcount: A:0.44, C:0.17, G:0.13, T:0.26
Consensus pattern (171 bp):
AGAGGCTCAACAACTTTAAAAAAATAAATAAAGCTCCTCTAAATAGAGGTCAACAACTTTGAAAA
ATAAATAAAGCTCCTCTAAATAAAGGTTCAATGACTTTGAAAAATAAATAATGCTCCTCTAATCA
GAGGCTCAATAACTTTGGAAAATAAATAATGCTCTTCTAAA
Found at i:231815 original size:23 final size:23
Alignment explanation
Indices: 231784--231882 Score: 103
Period size: 23 Copynumber: 4.3 Consensus size: 23
231774 TTTTTTTAAT
*
231784 GATTTTCATTTGAAAAACTCAAA
1 GATTCTCATTTGAAAAACTCAAA
*
231807 GATTCTCATTCGAAAAACTCAAA
1 GATTCTCATTTGAAAAACTCAAA
* * *
231830 GATTCTTATTTTAAAAAACTAAAA
1 GATTCTCA-TTTGAAAAACTCAAA
* * *
231854 AATTCTTATTT--AAGACTCAAA
1 GATTCTCATTTGAAAAACTCAAA
231875 GATTCTCA
1 GATTCTCA
231883 AGGATTCTCA
Statistics
Matches: 64, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
21 14 0.22
23 31 0.48
24 19 0.30
ACGTcount: A:0.43, C:0.15, G:0.07, T:0.34
Consensus pattern (23 bp):
GATTCTCATTTGAAAAACTCAAA
Found at i:231896 original size:31 final size:31
Alignment explanation
Indices: 231855--231913 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
231845 AAACTAAAAA
* *
231855 ATTCTTATTTAAGACTCAAAGATTCTCAAGG
1 ATTCTCATTTAAAACTCAAAGATTCTCAAGG
*
231886 ATTCTCATTTAAAACTCAAAGGTTCTCA
1 ATTCTCATTTAAAACTCAAAGATTCTCA
231914 TTTGAAAATA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.36, C:0.19, G:0.10, T:0.36
Consensus pattern (31 bp):
ATTCTCATTTAAAACTCAAAGATTCTCAAGG
Found at i:231903 original size:21 final size:22
Alignment explanation
Indices: 231882--231963 Score: 71
Period size: 21 Copynumber: 3.7 Consensus size: 22
231872 AAAGATTCTC
231882 AAGGATTCTCATTT-AAAACTCA
1 AAGG-TTCTCATTTGAAAACTCA
* *
231904 AAGGTTCTCATTTGAAAATATTTTA
1 AAGGTTCTCATTTG-AAA-A-CTCA
* *
231929 AAGATTC-CATTT-AAGACTCA
1 AAGGTTCTCATTTGAAAACTCA
231949 AAGGTTCTCATTTGA
1 AAGGTTCTCATTTGA
231964 GGACTCAATT
Statistics
Matches: 47, Mismatches: 7, Indels: 12
0.71 0.11 0.18
Matches are distributed among these distances:
20 8 0.17
21 15 0.32
22 7 0.15
23 3 0.06
24 6 0.13
25 8 0.17
ACGTcount: A:0.37, C:0.15, G:0.12, T:0.37
Consensus pattern (22 bp):
AAGGTTCTCATTTGAAAACTCA
Found at i:233596 original size:20 final size:20
Alignment explanation
Indices: 233542--233603 Score: 54
Period size: 20 Copynumber: 3.1 Consensus size: 20
233532 GTGGCATTTA
* *
233542 TTTCTCTTTTCTCTCTTTC-
1 TTTCTTTTTTCTTTCTTTCT
* * *
233561 CTTCATTTTGCTTTTCTTTCT
1 TTTCTTTTTTC-TTTCTTTCT
*
233582 TTTCTTTTTTCTTTCTATCT
1 TTTCTTTTTTCTTTCTTTCT
233602 TT
1 TT
233604 GAGACCTTTT
Statistics
Matches: 32, Mismatches: 9, Indels: 3
0.73 0.20 0.07
Matches are distributed among these distances:
19 7 0.22
20 17 0.53
21 8 0.25
ACGTcount: A:0.03, C:0.24, G:0.02, T:0.71
Consensus pattern (20 bp):
TTTCTTTTTTCTTTCTTTCT
Found at i:237486 original size:7 final size:6
Alignment explanation
Indices: 237459--237518 Score: 50
Period size: 6 Copynumber: 9.7 Consensus size: 6
237449 AAATACTAAA
* * * *
237459 AAAAAT AAACAC ATAAAT AAATAAT AAATAA- ATAAAT ACAAAAT AAAAAT
1 AAAAAT AAAAAT AAAAAT AAA-AAT AAA-AAT AAAAAT A-AAAAT AAAAAT
237509 AAAAAT AAAA
1 AAAAAT AAAA
237519 TGGCTTGGCT
Statistics
Matches: 43, Mismatches: 8, Indels: 6
0.75 0.14 0.11
Matches are distributed among these distances:
5 2 0.05
6 27 0.63
7 14 0.33
ACGTcount: A:0.77, C:0.05, G:0.00, T:0.18
Consensus pattern (6 bp):
AAAAAT
Found at i:237487 original size:11 final size:11
Alignment explanation
Indices: 237461--237517 Score: 57
Period size: 11 Copynumber: 5.3 Consensus size: 11
237451 ATACTAAAAA
*
237461 AAATAAACACAT
1 AAATAAATA-AT
237473 AAATAAATAAT
1 AAATAAATAAT
237484 AAATAAATAAAT
1 AAATAAAT-AAT
*
237496 ACA-AAATAA-
1 AAATAAATAAT
237505 AAATAAA-AAT
1 AAATAAATAAT
237515 AAA
1 AAA
237518 ATGGCTTGGC
Statistics
Matches: 39, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
9 4 0.10
10 8 0.21
11 14 0.36
12 13 0.33
ACGTcount: A:0.75, C:0.05, G:0.00, T:0.19
Consensus pattern (11 bp):
AAATAAATAAT
Found at i:237491 original size:15 final size:14
Alignment explanation
Indices: 237461--237517 Score: 64
Period size: 15 Copynumber: 3.9 Consensus size: 14
237451 ATACTAAAAA
237461 AAATAAACACATAAAT
1 AAATAAA-A-ATAAAT
237477 AAATAATAAATAAAT
1 AAATAA-AAATAAAT
237492 AAATACAAAAT-AA-
1 AAATA-AAAATAAAT
237505 AAATAAAAATAAA
1 AAATAAAAATAAA
237518 ATGGCTTGGC
Statistics
Matches: 38, Mismatches: 0, Indels: 9
0.81 0.00 0.19
Matches are distributed among these distances:
12 5 0.13
13 7 0.18
14 2 0.05
15 15 0.39
16 8 0.21
17 1 0.03
ACGTcount: A:0.75, C:0.05, G:0.00, T:0.19
Consensus pattern (14 bp):
AAATAAAAATAAAT
Found at i:237514 original size:19 final size:19
Alignment explanation
Indices: 237447--237515 Score: 59
Period size: 22 Copynumber: 3.4 Consensus size: 19
237437 TTAATCATGC
*
237447 AAAAATACTAAA-AAAAAT
1 AAAAATACAAAATAAAAAT
*
237465 AAACACATAAATAAATAATAAAT
1 AAA-A-ATACA-AAATAA-AAAT
237488 AAATAAATACAAAATAAAAAT
1 -AA-AAATACAAAATAAAAAT
237509 AAAAATA
1 AAAAATA
237516 AAATGGCTTG
Statistics
Matches: 41, Mismatches: 3, Indels: 13
0.72 0.05 0.23
Matches are distributed among these distances:
18 3 0.07
19 6 0.15
20 5 0.12
21 7 0.17
22 8 0.20
23 8 0.20
24 3 0.07
25 1 0.02
ACGTcount: A:0.75, C:0.06, G:0.00, T:0.19
Consensus pattern (19 bp):
AAAAATACAAAATAAAAAT
Found at i:239941 original size:3 final size:3
Alignment explanation
Indices: 239933--239957 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
239923 CTTACTAAAC
239933 TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA T
239958 AAAGTTTTCC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:244387 original size:17 final size:17
Alignment explanation
Indices: 244365--244405 Score: 75
Period size: 17 Copynumber: 2.5 Consensus size: 17
244355 TCATATCATG
244365 AGCAGCAGTGCCCAGCA
1 AGCAGCAGTGCCCAGCA
244382 AGCAGCAGTGCCCAGCA
1 AGCAGCAGTGCCCAGCA
244399 A-CAGCAG
1 AGCAGCAG
244406 CAGTGATTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 6 0.25
17 18 0.75
ACGTcount: A:0.32, C:0.34, G:0.29, T:0.05
Consensus pattern (17 bp):
AGCAGCAGTGCCCAGCA
Found at i:253800 original size:34 final size:34
Alignment explanation
Indices: 253757--253822 Score: 114
Period size: 34 Copynumber: 1.9 Consensus size: 34
253747 GCAGAAATGC
253757 AACAAATCAGACAGAAAATTTAGGGATTTGACCT
1 AACAAATCAGACAGAAAATTTAGGGATTTGACCT
* *
253791 AACAAATCAGACTGAAAGTTTAGGGATTTGAC
1 AACAAATCAGACAGAAAATTTAGGGATTTGAC
253823 TAAAATTACA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 30 1.00
ACGTcount: A:0.42, C:0.14, G:0.20, T:0.24
Consensus pattern (34 bp):
AACAAATCAGACAGAAAATTTAGGGATTTGACCT
Found at i:254631 original size:62 final size:62
Alignment explanation
Indices: 254549--254722 Score: 195
Period size: 64 Copynumber: 2.8 Consensus size: 62
254539 ATTTTTTATG
** * * *
254549 AGAGAATTATTGAAAATATTTTAGGCCAAAAACGCATTTAATAATCCTCTTAAATTTTGATAA
1 AGAG-ATTATTGAAGGTATTTTTGGCCAAAAACGCCTTAAATAATCCTCTTAAATTTTGATAA
** * *
254612 AGAGATTATTGAAGGTATTTTTTTTACCAAAAATGCCTTAAATAATTCTCTTAAATTTTGATAA
1 AGAGATTATTGAAGGTA--TTTTTGGCCAAAAACGCCTTAAATAATCCTCTTAAATTTTGATAA
* * * * *
254676 GGAGATTATTGAAGGCATTTTTGGTCAAAAACCCCTTCAATAATCCT
1 AGAGATTATTGAAGGTATTTTTGGCCAAAAACGCCTTAAATAATCCT
254723 TTTCATTTTT
Statistics
Matches: 91, Mismatches: 18, Indels: 5
0.80 0.16 0.04
Matches are distributed among these distances:
62 34 0.37
63 4 0.04
64 53 0.58
ACGTcount: A:0.38, C:0.13, G:0.13, T:0.37
Consensus pattern (62 bp):
AGAGATTATTGAAGGTATTTTTGGCCAAAAACGCCTTAAATAATCCTCTTAAATTTTGATAA
Found at i:254859 original size:63 final size:63
Alignment explanation
Indices: 254791--254988 Score: 183
Period size: 63 Copynumber: 3.2 Consensus size: 63
254781 CAAAAACGCT
* *
254791 TTCAATAATCCCCTTAAATTTTTATAAGGAGATTATTGAAGGTATTTTTTAGCAAAACATACC
1 TTCAATAATCCCCTTAAATTTTTATAAGGAGATTATTGAAAGTATTTTTTAGCAAAAAATACC
* * *
254854 TTCAATAAT-CCCTTCCAATTTTT-TAGAGGGGATTATTGAAAGTATTTTCTGTA--AAAAAATG
1 TTCAATAATCCCCTT-AAATTTTTATA-AGGAGATTATTGAAAGTATTTT-T-TAGCAAAAAATA
*
254915 CT
62 CC
* * * * * * * *
254917 TTCAATAATCCTCTTAAATTTTGATGAGAAAAATATTGAATG-CTTTTTT-GACAAAAAATACC
1 TTCAATAATCCCCTTAAATTTTTATAAGGAGATTATTGAAAGTATTTTTTAG-CAAAAAATACC
254979 TTCAATAATC
1 TTCAATAATC
254989 TATTTTTTAT
Statistics
Matches: 108, Mismatches: 18, Indels: 19
0.74 0.12 0.13
Matches are distributed among these distances:
60 1 0.01
61 1 0.01
62 29 0.27
63 69 0.64
64 6 0.06
65 2 0.02
ACGTcount: A:0.37, C:0.14, G:0.11, T:0.38
Consensus pattern (63 bp):
TTCAATAATCCCCTTAAATTTTTATAAGGAGATTATTGAAAGTATTTTTTAGCAAAAAATACC
Found at i:254967 original size:206 final size:205
Alignment explanation
Indices: 254574--254985 Score: 467
Period size: 206 Copynumber: 2.0 Consensus size: 205
254564 ATATTTTAGG
*
254574 CCAAAAACGCATTTAATAATCCTCTTAAATTTTGATAAAGAGATTATTGAAGGTATTTTTTTTAC
1 CCAAAAACGCATTTAATAATCCCCTTAAATTTTGATAAAGAGATTATTGAAGGTA-TTTTTTTAC
* * * *
254639 CAAAAATGCCTTAAATAATTCTCTTAAATTTTGATAAGGAGATTATTGAAGGCATTTTTGGTCAA
65 CAAAAATACCTTAAATAATTCCCTTAAATTTTGATAAGGAGATTATTGAAAGCATTTTTGGTAAA
* * * * * * *
254704 AAACCCCTTCAATAATCCTTTTCATTTTTTACGAAGAAATTATTAAAGGCGTTTTTGATAAAAAT
130 AAACCCCTTCAATAATCCTCTTAAATTTTGACGAAGAAAATATTAAAGGCGTTTTTGACAAAAAA
254769 TACCTTCAATA
195 TACCTTCAATA
* * *
254780 CCAAAAACGC-TTTCAATAATCCCCTTAAATTTTTATAAGGAGATTATTGAAGGTA-TTTTTTAG
1 CCAAAAACGCATTT-AATAATCCCCTTAAATTTTGATAAAGAGATTATTGAAGGTATTTTTTTAC
* * * * *
254843 CAAAACATACCTTCAATAA-TCCCTTCCAATTTT-TTAGAGGGGATTATTGAAAGTATTTTCT-G
65 CAAAA-ATACCTTAAATAATTCCCTT-AAATTTTGATA-AGGAGATTATTGAAAGCATTTT-TGG
** * * * * *
254905 TAAAAAAATGCTTTCAATAATCCTCTTAAATTTTGATG-AGAAAAATATTGAATGCTTTTTTGAC
126 T-AAAAAACCCCTTCAATAATCCTCTTAAATTTTGACGAAG-AAAATATTAAAGGCGTTTTTGAC
254969 AAAAAATACCTTCAATA
189 AAAAAATACCTTCAATA
254986 ATCTATTTTT
Statistics
Matches: 172, Mismatches: 27, Indels: 14
0.81 0.13 0.07
Matches are distributed among these distances:
204 19 0.11
205 43 0.25
206 110 0.64
ACGTcount: A:0.37, C:0.14, G:0.11, T:0.38
Consensus pattern (205 bp):
CCAAAAACGCATTTAATAATCCCCTTAAATTTTGATAAAGAGATTATTGAAGGTATTTTTTTACC
AAAAATACCTTAAATAATTCCCTTAAATTTTGATAAGGAGATTATTGAAAGCATTTTTGGTAAAA
AACCCCTTCAATAATCCTCTTAAATTTTGACGAAGAAAATATTAAAGGCGTTTTTGACAAAAAAT
ACCTTCAATA
Found at i:255194 original size:63 final size:62
Alignment explanation
Indices: 255126--255496 Score: 236
Period size: 62 Copynumber: 6.0 Consensus size: 62
255116 CGTTTTGGCT
* *
255126 AAAAATGTCTTTAATAATCCTTTTCAATTTTTTTA-AAAGGATTATTGAAGGCATTTTTTGCC
1 AAAAATGCCTTCAATAATCCTTTTCAA-TTTTTTAGAAAGGATTATTGAAGGCATTTTTTGCC
* * * * * * *** *
255188 AAAAAATACATTTAATAATTCATTTC-ATTTTTTACGAAGGGATTATTGAAGGCATTTCAAGCA
1 -AAAAATGCCTTCAATAATCCTTTTCAATTTTTTA-GAAAGGATTATTGAAGGCATTTTTTGCC
* * * * * * *
255251 AAAAATACATTCAATAATTCTCTTAAATTTTGATAAGAAA--ATTATTGAAAG--TGTTTTTGAC
1 AAAAATGCCTTCAATAATCCTTTTCAATTTT--TTAGAAAGGATTATTGAAGGCAT-TTTTTG-C
255312 C
62 C
** * * ** * * *
255313 AAAAATGCCTTCAATAATCAATTCCAAATTTTTAGAGGGGATTATTGAAGGTATTTTCTACC
1 AAAAATGCCTTCAATAATCCTTTTCAATTTTTTAGAAAGGATTATTGAAGGCATTTTTTGCC
** * * * * * **
255375 AAAAATGCCTTCAATAATCCCCTT-AAATTTTTATAAAGAGAATATTAAATGTG-TTTTTTTATC
1 AAAAATGCCTTCAATAATCCTTTTCAATTTTTTAGAAAG-GATTATTGAA-G-GCATTTTTTGCC
* * *
255438 AAAAACGCCTTTAATAATCCTTTTCAATTTTTTAGAAGGGATTATTGAAGGCATTTTTT
1 AAAAATGCCTTCAATAATCCTTTTCAATTTTTTAGAAAGGATTATTGAAGGCATTTTTT
255497 ATATACAAAA
Statistics
Matches: 234, Mismatches: 58, Indels: 33
0.72 0.18 0.10
Matches are distributed among these distances:
60 5 0.02
61 22 0.09
62 102 0.44
63 87 0.37
64 16 0.07
65 2 0.01
ACGTcount: A:0.37, C:0.12, G:0.12, T:0.40
Consensus pattern (62 bp):
AAAAATGCCTTCAATAATCCTTTTCAATTTTTTAGAAAGGATTATTGAAGGCATTTTTTGCC
Found at i:255280 original size:125 final size:121
Alignment explanation
Indices: 255151--255493 Score: 316
Period size: 124 Copynumber: 2.8 Consensus size: 121
255141 AATCCTTTTC
* * *
255151 AATTTTTTTAAAAGGATTATTGAAGGCATTTTTTGCCAAAAAATACATTTAATAATTCATTTC-A
1 AATTTTTATAAAAGGATTATTGAAGG--TTTTTTGCC-AAAAATGCCTTTAATAATTCATTTCAA
* *
255215 TTTTTTACGAAGGGATTATTGAAGGCATTTCAAGCAAAAAATACATTCAATAATTCTCTTA
63 TTTTTTA-GAAGGGATTATTGAAGGCATTTCAA-CAAAAAATACATTCAATAATCCCCTTA
* * * * *
255276 AATTTTGATAAGAA-AATTATTGAAAGTGTTTTTGACCAAAAATGCCTTCAATAA-TCAATTCCA
1 AATTTTTATAA-AAGGATTATTGAAGGT-TTTTTG-CCAAAAATGCCTTTAATAATTC-ATTTCA
* * * * * * *
255339 AATTTTTAGAGGGGATTATTGAAGGTATTTTCTACCAAAAATGCCTTCAATAATCCCCTTA
62 ATTTTTTAGAAGGGATTATTGAAGGCA-TTTCAACAAAAAATACATTCAATAATCCCCTTA
* * ** * * *
255400 AATTTTTAT-AAAGAGAATATTAAATGTGTTTTTTTATCAAAAACGCCTTTAATAATCCTTTTCA
1 AATTTTTATAAAAG-GATTATTGAA-G-G-TTTTTTGCCAAAAATGCCTTTAATAATTCATTTCA
255464 ATTTTTTAGAAGGGATTATTGAAGGCATTT
62 ATTTTTTAGAAGGGATTATTGAAGGCATTT
255494 TTTATATACA
Statistics
Matches: 174, Mismatches: 32, Indels: 25
0.75 0.14 0.11
Matches are distributed among these distances:
122 2 0.01
123 4 0.02
124 81 0.47
125 77 0.44
126 9 0.05
127 1 0.01
ACGTcount: A:0.37, C:0.12, G:0.12, T:0.39
Consensus pattern (121 bp):
AATTTTTATAAAAGGATTATTGAAGGTTTTTTGCCAAAAATGCCTTTAATAATTCATTTCAATTT
TTTAGAAGGGATTATTGAAGGCATTTCAACAAAAAATACATTCAATAATCCCCTTA
Found at i:255494 original size:125 final size:125
Alignment explanation
Indices: 255198--255494 Score: 352
Period size: 125 Copynumber: 2.4 Consensus size: 125
255188 AAAAAATACA
*
255198 TTTAATAATTCATTTC-ATTTTTTACGAAGGGATTATTGAAGGCA-TTTCAAGCAAAAAATACAT
1 TTTAATAATCCATTTCAATTTTTTA-GAAGGGATTATTGAAGGCATTTTCAAGCAAAAAATACAT
* * *
255261 TCAATAATTCTCTTAAATTTTGATAAGAAAATTATTGAAAGTGTTTTTGACCAAAAATGCC
65 TCAATAATCCCCTTAAATTTTGATAAGAAAATTATTGAAAGTGTTTTTGACCAAAAACGCC
* * * * * * * * * *
255322 TTCAATAATCAATTCCAAATTTTTAGAGGGGATTATTGAAGGTATTTTCTA-CCAAAAATGCCTT
1 TTTAATAATCCATTTCAATTTTTTAGAAGGGATTATTGAAGGCATTTTCAAGCAAAAAATACATT
* * * *
255386 CAATAATCCCCTTAAATTTTTATAAAGAGAA-TATT-AAATGTGTTTTTTTATCAAAAACGCC
66 CAATAATCCCCTTAAATTTTGAT-AAGAAAATTATTGAAA-GTG-TTTTTGACCAAAAACGCC
*
255447 TTTAATAATCCTTTTCAATTTTTTAGAAGGGATTATTGAAGGCATTTT
1 TTTAATAATCCATTTCAATTTTTTAGAAGGGATTATTGAAGGCATTTT
255495 TTATATACAA
Statistics
Matches: 143, Mismatches: 25, Indels: 9
0.81 0.14 0.05
Matches are distributed among these distances:
123 3 0.02
124 66 0.46
125 74 0.52
ACGTcount: A:0.36, C:0.12, G:0.12, T:0.39
Consensus pattern (125 bp):
TTTAATAATCCATTTCAATTTTTTAGAAGGGATTATTGAAGGCATTTTCAAGCAAAAAATACATT
CAATAATCCCCTTAAATTTTGATAAGAAAATTATTGAAAGTGTTTTTGACCAAAAACGCC
Found at i:255714 original size:124 final size:124
Alignment explanation
Indices: 255572--255827 Score: 284
Period size: 124 Copynumber: 2.1 Consensus size: 124
255562 TCAATAATTC
* ** * *
255572 ATTTTTTATGAAGAGATTATTGAAGGTATTTTTGATC-AAAAACGCATTCAATAATCCCCTTAAA
1 ATTTTTTATGAAGAGATTATTGAAGGCATTTCAG-GCAAAAAACGCATTAAATAATCCCCTTAAA
* * * * * * *
255636 TTTTGATTAGGAGATTATTGAAGGTATTTTTGGCCAAAAACACCTTCAATAATCCACTCTA
65 TTTTAATGAAGAGATTATTGAAGGCATTTTT-ACCAAAAACACCTTCAACAATCCACTCCA
* * * *
255697 ATTTTTTAT--AGAGGATTATTGAAGGCGTTTCAGGCAAAAAATGCCTTAAATAATCCTCTTAAA
1 ATTTTTTATGAAGA-GATTATTGAAGGCATTTCAGGCAAAAAACGCATTAAATAATCCCCTTAAA
* * * *
255760 TTTTAATGAAGAGATTATTGAAGGCATTTTTACTAAAAATATCTTCAACAATCCCCTCCA
65 TTTTAATGAAGAGATTATTGAAGGCATTTTTACCAAAAACACCTTCAACAATCCACTCCA
255820 ATTTTTTA
1 ATTTTTTA
255828 AATGAGATTT
Statistics
Matches: 109, Mismatches: 20, Indels: 6
0.81 0.15 0.04
Matches are distributed among these distances:
123 34 0.31
124 66 0.61
125 9 0.08
ACGTcount: A:0.36, C:0.14, G:0.13, T:0.37
Consensus pattern (124 bp):
ATTTTTTATGAAGAGATTATTGAAGGCATTTCAGGCAAAAAACGCATTAAATAATCCCCTTAAAT
TTTAATGAAGAGATTATTGAAGGCATTTTTACCAAAAACACCTTCAACAATCCACTCCA
Found at i:255798 original size:62 final size:62
Alignment explanation
Indices: 255574--255798 Score: 201
Period size: 62 Copynumber: 3.6 Consensus size: 62
255564 AATAATTCAT
* * * *
255574 TTTTTATGAAGAGATTATTGAAGGTATTTTTGA-TCAAAAACGCATTCAATAATCCCCTTAAA
1 TTTTTATGAAGAGATTATTGAAGGCATTTTTGACT-AAAAAAGCCTTCAATAATCCACTTAAA
* * * * * * *
255636 TTTTGATTAGGAGATTATTGAAGGTATTTTTGGCCAAAAACA-CCTTCAATAATCCACTCTAAT
1 TTTTTATGAAGAGATTATTGAAGGCATTTTTGACTAAAAA-AGCCTTCAATAATCCACT-TAAA
* ** * * *
255699 TTTTTAT--AGAGGATTATTGAAGGCGTTTCAGGC-AAAAAATGCCTTAAATAATCCTCTTAAA
1 TTTTTATGAAGA-GATTATTGAAGGCATTTTTGACTAAAAAA-GCCTTCAATAATCCACTTAAA
*
255760 TTTTAATGAAGAGATTATTGAAGGCATTTTT-ACTAAAAA
1 TTTTTATGAAGAGATTATTGAAGGCATTTTTGACTAAAAA
255799 TATCTTCAAC
Statistics
Matches: 131, Mismatches: 23, Indels: 18
0.76 0.13 0.10
Matches are distributed among these distances:
60 1 0.01
61 17 0.13
62 101 0.77
63 12 0.09
ACGTcount: A:0.36, C:0.12, G:0.15, T:0.36
Consensus pattern (62 bp):
TTTTTATGAAGAGATTATTGAAGGCATTTTTGACTAAAAAAGCCTTCAATAATCCACTTAAA
Found at i:256766 original size:2 final size:2
Alignment explanation
Indices: 256759--256787 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
256749 GCATTTCTTG
256759 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
256788 GTATGTATGT
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:257071 original size:20 final size:20
Alignment explanation
Indices: 257046--257091 Score: 92
Period size: 20 Copynumber: 2.3 Consensus size: 20
257036 AATGTGGATA
257046 GCTGCATGTCCATCAGCATT
1 GCTGCATGTCCATCAGCATT
257066 GCTGCATGTCCATCAGCATT
1 GCTGCATGTCCATCAGCATT
257086 GCTGCA
1 GCTGCA
257092 ATAGTTCCTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.20, C:0.30, G:0.22, T:0.28
Consensus pattern (20 bp):
GCTGCATGTCCATCAGCATT
Found at i:258825 original size:39 final size:40
Alignment explanation
Indices: 258746--258838 Score: 129
Period size: 39 Copynumber: 2.4 Consensus size: 40
258736 GATTGGATGG
*
258746 GGTGGGGA-GGATTGGGTGTGGTAGGGCGTTGGGGGGGAA
1 GGTGGGGAGGGATTGGGTGTGGTAGGGCGTTGGGGGAGAA
*
258785 GGTGGGGAGGGATTGGGTGTGGT-GGGATGTT-GGGGAGAA
1 GGTGGGGAGGGATTGGGTGTGGTAGGG-CGTTGGGGGAGAA
*
258824 GGTGGAGAGGGATTG
1 GGTGGGGAGGGATTG
258839 ATGGGGGTGG
Statistics
Matches: 49, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
39 32 0.65
40 17 0.35
ACGTcount: A:0.15, C:0.01, G:0.62, T:0.22
Consensus pattern (40 bp):
GGTGGGGAGGGATTGGGTGTGGTAGGGCGTTGGGGGAGAA
Found at i:262790 original size:27 final size:27
Alignment explanation
Indices: 262760--262811 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
262750 GTCCAACACC
*
262760 AAGT-CAGAGTGATGATAGTGGTGGTTT
1 AAGTCCAGA-TGATGATAGTGATGGTTT
*
262787 AAGTCCAGATGATGATGGTGATGGT
1 AAGTCCAGATGATGATAGTGATGGT
262812 GCGAATTTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
27 18 0.82
28 4 0.18
ACGTcount: A:0.27, C:0.06, G:0.37, T:0.31
Consensus pattern (27 bp):
AAGTCCAGATGATGATAGTGATGGTTT
Found at i:263185 original size:21 final size:21
Alignment explanation
Indices: 263160--263202 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
263150 TTATTATCTA
*
263160 CCTCAAATGTATCCTCCACCT
1 CCTCAAATATATCCTCCACCT
263181 CCTCAAATATATCCTCCACCT
1 CCTCAAATATATCCTCCACCT
263202 C
1 C
263203 AAATGTATCA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.26, C:0.44, G:0.02, T:0.28
Consensus pattern (21 bp):
CCTCAAATATATCCTCCACCT
Found at i:263204 original size:18 final size:18
Alignment explanation
Indices: 263159--263280 Score: 108
Period size: 18 Copynumber: 6.8 Consensus size: 18
263149 ATTATTATCT
263159 ACCTCAAATGTATCCTCC
1 ACCTCAAATGTATCCTCC
*
263177 ACCTCCTCAAATATATCCTCC
1 A---CCTCAAATGTATCCTCC
* *
263198 ACCTCAAATGTATCAGT-T
1 ACCTCAAATGTATC-CTCC
* *
263216 ACCACAAATGTACCCTCC
1 ACCTCAAATGTATCCTCC
* *
263234 ACCACAAATGTATCAT--
1 ACCTCAAATGTATCCTCC
*
263250 -CCTCAAATATATCCTCC
1 ACCTCAAATGTATCCTCC
263267 ACCTCAAATGTATC
1 ACCTCAAATGTATC
263281 AAGAACAAAG
Statistics
Matches: 82, Mismatches: 14, Indels: 16
0.73 0.12 0.14
Matches are distributed among these distances:
15 12 0.15
17 1 0.01
18 51 0.62
19 1 0.01
21 17 0.21
ACGTcount: A:0.33, C:0.35, G:0.05, T:0.27
Consensus pattern (18 bp):
ACCTCAAATGTATCCTCC
Found at i:264558 original size:50 final size:50
Alignment explanation
Indices: 264483--264579 Score: 158
Period size: 50 Copynumber: 1.9 Consensus size: 50
264473 CTCTTTCTTA
* *
264483 CATTGTCTTAGCTGTGCGCGGAAGAAAGGAATGCCCATTAGCTAAATGCC
1 CATTGTCTTAGATGTGCACGGAAGAAAGGAATGCCCATTAGCTAAATGCC
* *
264533 CATTGTCTTTGATGTGCACGGAAGAAGGGAATGCCCATTAGCTAAAT
1 CATTGTCTTAGATGTGCACGGAAGAAAGGAATGCCCATTAGCTAAAT
264580 TCCTAATGGG
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
50 43 1.00
ACGTcount: A:0.29, C:0.20, G:0.26, T:0.26
Consensus pattern (50 bp):
CATTGTCTTAGATGTGCACGGAAGAAAGGAATGCCCATTAGCTAAATGCC
Found at i:265075 original size:16 final size:17
Alignment explanation
Indices: 265035--265081 Score: 53
Period size: 17 Copynumber: 2.8 Consensus size: 17
265025 AAGAAAATAA
265035 TTTATTATAATAATTTT
1 TTTATTATAATAATTTT
* *
265052 TTCAATTATAAT-CTTTT
1 TT-TATTATAATAATTTT
265069 TTTATTA-AATAAT
1 TTTATTATAATAAT
265082 ATATACTATA
Statistics
Matches: 24, Mismatches: 4, Indels: 5
0.73 0.12 0.15
Matches are distributed among these distances:
15 3 0.12
16 5 0.21
17 8 0.33
18 8 0.33
ACGTcount: A:0.36, C:0.04, G:0.00, T:0.60
Consensus pattern (17 bp):
TTTATTATAATAATTTT
Found at i:270130 original size:17 final size:17
Alignment explanation
Indices: 270108--270173 Score: 62
Period size: 17 Copynumber: 3.8 Consensus size: 17
270098 ATTATTTATT
270108 ATTTTATTATATAATAA
1 ATTTTATTATATAATAA
*
270125 ATTTTATT-TATTAATTA
1 ATTTTATTATA-TAATAA
*
270142 ATTTATAATATAATAATAA
1 ATTT-TATTAT-ATAATAA
* *
270161 AATTTATTTTATA
1 ATTTTATTATATA
270174 TCAAATTAAC
Statistics
Matches: 39, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
16 2 0.05
17 20 0.51
18 7 0.18
19 9 0.23
20 1 0.03
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (17 bp):
ATTTTATTATATAATAA
Found at i:272422 original size:17 final size:17
Alignment explanation
Indices: 272400--272432 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
272390 TTTTTTCCTT
272400 ATATTAATCTTTCTGGG
1 ATATTAATCTTTCTGGG
272417 ATATTAATCTTTCTGG
1 ATATTAATCTTTCTGG
272433 TTCAGCTATC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.24, C:0.12, G:0.15, T:0.48
Consensus pattern (17 bp):
ATATTAATCTTTCTGGG
Found at i:281163 original size:15 final size:16
Alignment explanation
Indices: 281143--281173 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
281133 AAAAATTAAT
281143 ATTACTCTTAA-AATA
1 ATTACTCTTAAGAATA
281158 ATTACTCTTAAGAATA
1 ATTACTCTTAAGAATA
281174 GATTGATATC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 11 0.73
16 4 0.27
ACGTcount: A:0.45, C:0.13, G:0.03, T:0.39
Consensus pattern (16 bp):
ATTACTCTTAAGAATA
Done.