Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168048.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_3, 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: 33276047
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 139000 characters in sequence are not A, C, G, or T
File 155 of 190
Found at i:25114085 original size:19 final size:19
Alignment explanation
Indices: 25113765--25114090 Score: 278
Period size: 19 Copynumber: 16.9 Consensus size: 19
25113755 TATGAAACTA
*
25113765 TAAACCACCATTCTAAA-CC
1 TAAACCACCA-TCCAAACCC
* *
25113784 TAAACCACTATCCAAACTC
1 TAAACCACCATCCAAACCC
* *
25113803 TAAACCACCATCTAAACCT
1 TAAACCACCATCCAAACCC
* * *
25113822 TAAACTATCATTCCTAACCC
1 TAAACCACCA-TCCAAACCC
* * *
25113842 CACACCACCATCTAAACCC
1 TAAACCACCATCCAAACCC
* * *
25113861 TATACCATCATTCCTAACCC
1 TAAACCACCA-TCCAAACCC
* *
25113881 CAGACCACCATTCCAAACCC
1 TAAACCACCA-TCCAAACCC
* *
25113901 CAAACCACCATTCTAAACCC
1 TAAACCACCA-TCCAAACCC
* * *
25113921 AAAACCACCATTCTAAACCT
1 TAAACCACCA-TCCAAACCC
* * *
25113941 TAAACCATCATCCAAGCTC
1 TAAACCACCATCCAAACCC
*
25113960 TAAACCACCATCTAAACCC
1 TAAACCACCATCCAAACCC
*
25113979 TAAATCACCATCCAAACCC
1 TAAACCACCATCCAAACCC
* * *
25113998 TAAACCATCA-ACTAACCC
1 TAAACCACCATCCAAACCC
*
25114016 TAAACCACCATCTAAACCC
1 TAAACCACCATCCAAACCC
* *
25114035 TAAACTACCATCCAAACCT
1 TAAACCACCATCCAAACCC
25114054 TAAACCACCATCCAAACCC
1 TAAACCACCATCCAAACCC
**
25114073 TAAACCATTATCCAAACC
1 TAAACCACCATCCAAACC
25114091 TTGAATCCTA
Statistics
Matches: 245, Mismatches: 58, Indels: 8
0.79 0.19 0.03
Matches are distributed among these distances:
18 20 0.08
19 146 0.60
20 79 0.32
ACGTcount: A:0.40, C:0.40, G:0.01, T:0.19
Consensus pattern (19 bp):
TAAACCACCATCCAAACCC
Found at i:25114149 original size:20 final size:20
Alignment explanation
Indices: 25114121--25114192 Score: 72
Period size: 20 Copynumber: 3.6 Consensus size: 20
25114111 AAACCCATCC
* *
25114121 AAACTCTAAACCTTGAACCA
1 AAACCCTAAACCTTAAACCA
* *
25114141 AAACCCTAAACCGTAAATCA
1 AAACCCTAAACCTTAAACCA
* * *
25114161 AAACCTTAATCCTTAAACCC
1 AAACCCTAAACCTTAAACCA
*
25114181 AAACCTTAAACC
1 AAACCCTAAACC
25114193 AACCTAAACC
Statistics
Matches: 42, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 42 1.00
ACGTcount: A:0.46, C:0.32, G:0.03, T:0.19
Consensus pattern (20 bp):
AAACCCTAAACCTTAAACCA
Found at i:25115496 original size:178 final size:177
Alignment explanation
Indices: 25115198--25115550 Score: 616
Period size: 178 Copynumber: 2.0 Consensus size: 177
25115188 AAACATATCG
* * * *
25115198 AAGAGTTTTTGGTCAGAAGGTAAAAAAAAGATGGCTACAACTTTTTAAGGTAGGTAAGAAATGGT
1 AAGAGTTTTTAGTCAGAAGGTAAAAAAAAAATGGCTACAACATTTTAAGATAGGTAAGAAATGGT
* *
25115263 AGACTAGAAAGCTTCGAAGTGAGAAACTAGGACCTTAAAGGGCCCTTTATATAGCCAAGTCCCAA
66 AGACTAGAAAGCTTCAAAATGAGAAACTAGGACCTTAAAGGGCCCTTTATATAGCCAAGTCCCAA
25115328 ATCAATTGGATGTCTTAAATTAAGCCATGTCACTACAACGGTTATTA
131 ATCAATTGGATGTCTTAAATTAAGCCATGTCACTACAACGGTTATTA
25115375 AAGAGTTTTTAGTCAGAAGGTCAAAAAAAAAATGGCTACAACATTTTAAGATAGGTAAGAAATGG
1 AAGAGTTTTTAGTCAGAAGGT-AAAAAAAAAATGGCTACAACATTTTAAGATAGGTAAGAAATGG
*
25115440 TAGACTAGAAAGCTTTAAAATGAGAAACTAGGACCTTAAAGGGCCCTTTATATAGCCAAGTCCCA
65 TAGACTAGAAAGCTTCAAAATGAGAAACTAGGACCTTAAAGGGCCCTTTATATAGCCAAGTCCCA
* *
25115505 AATCAGTTGGATGTCTTAAATTAAGCCATGTCACTACAATGGTTAT
130 AATCAATTGGATGTCTTAAATTAAGCCATGTCACTACAACGGTTAT
25115551 CGAGGATGAC
Statistics
Matches: 166, Mismatches: 9, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
177 20 0.12
178 146 0.88
ACGTcount: A:0.39, C:0.14, G:0.20, T:0.27
Consensus pattern (177 bp):
AAGAGTTTTTAGTCAGAAGGTAAAAAAAAAATGGCTACAACATTTTAAGATAGGTAAGAAATGGT
AGACTAGAAAGCTTCAAAATGAGAAACTAGGACCTTAAAGGGCCCTTTATATAGCCAAGTCCCAA
ATCAATTGGATGTCTTAAATTAAGCCATGTCACTACAACGGTTATTA
Found at i:25116913 original size:5 final size:5
Alignment explanation
Indices: 25116903--25116937 Score: 61
Period size: 5 Copynumber: 6.8 Consensus size: 5
25116893 TTATTTAACA
25116903 AATAT AATAT AATAT AATAT AATAT AAGTAT AATA
1 AATAT AATAT AATAT AATAT AATAT AA-TAT AATA
25116938 CAAATTAAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
5 24 0.83
6 5 0.17
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.37
Consensus pattern (5 bp):
AATAT
Found at i:25118800 original size:3 final size:3
Alignment explanation
Indices: 25118792--25118819 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
25118782 GTAGAAAGAA
25118792 AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT A
25118820 GTGATATAGG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:25129019 original size:86 final size:84
Alignment explanation
Indices: 25128922--25129290 Score: 248
Period size: 86 Copynumber: 4.2 Consensus size: 84
25128912 CTCAAAGACT
* *
25128922 TTTGAAAAATATAAAAGGCTCATTTAAATAAGGGCTTAATGATTTTAGAAAATTTAAAAAGCTCT
1 TTTGAAAAATATAAAAGGCTCATTT-AATAAGGGCTTAATAACTTTAGAAAATTTAAAAAGCTCT
25128987 TTTCATCAAAAGCTCAACAAC
65 TTT-ATCAAAAGCTCAACAAC
* * * * * * * *
25129008 TTTGAGAAATAT-AAAGGCTCATCTCATTAAAGGTTTAACAACTTTTTGAAACATATAAAAAGCT
1 TTTGAAAAATATAAAAGGCTCAT-TTAATAAGGGCTTAATAAC-TTTAGAAA-ATTTAAAAAGCT
* * *
25129072 CATCTTATCAGAGGCTC-ACTAAC
63 C-TTTTATCAAAAGCTCAAC-AAC
* * * * * *
25129095 TTTTTGATACATATAAAAAAGCTAATCTT-ATCAGAGG-TT-ATGCAACTTTAAAAAATTTAAAA
1 --TTTGAAAAATAT-AAAAGGCTCAT-TTAATAAG-GGCTTAAT--AACTTTAGAAAATTTAAAA
* * * *
25129157 GGCTCTTCTTATCAGAAGCTTAATAAC
59 AGCTCTT-TTATCAAAAGCTCAACAAC
* * * *
25129184 TTTGAAAAATATAAAAGACTCATTTTATCATA-GGCTCAATAACTTT-GAAAAATTTAAAAGGCT
1 TTTGAAAAATATAAAAGGCTCATTTAAT-A-AGGGCTTAATAACTTTAG-AAAATTTAAAAAGCT
* *
25129247 CTTTTCATCAAAGGCTCAACAATT
63 CTTTT-ATCAAAAGCTCAACAA-C
25129271 TTTGAAAAATATAAAAGGCT
1 TTTGAAAAATATAAAAGGCT
25129291 TTCCTTAAAC
Statistics
Matches: 217, Mismatches: 44, Indels: 43
0.71 0.14 0.14
Matches are distributed among these distances:
85 25 0.12
86 69 0.32
87 54 0.25
88 7 0.03
89 36 0.17
90 11 0.05
91 15 0.07
ACGTcount: A:0.42, C:0.14, G:0.12, T:0.33
Consensus pattern (84 bp):
TTTGAAAAATATAAAAGGCTCATTTAATAAGGGCTTAATAACTTTAGAAAATTTAAAAAGCTCTT
TTATCAAAAGCTCAACAAC
Found at i:25129143 original size:46 final size:44
Alignment explanation
Indices: 25129045--25129131 Score: 138
Period size: 46 Copynumber: 1.9 Consensus size: 44
25129035 TAAAGGTTTA
*
25129045 ACAACTTTTTGAAACATATAAAAAGCTCATCTTATCAGAGGCTC
1 ACAACTTTTTGAAACATATAAAAAGCTAATCTTATCAGAGGCTC
*
25129089 ACTAACTTTTTGATACATATAAAAAAGCTAATCTTATCAGAGG
1 AC-AACTTTTTGAAACATAT-AAAAAGCTAATCTTATCAGAGG
25129132 TTATGCAACT
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
44 2 0.05
45 16 0.41
46 21 0.54
ACGTcount: A:0.40, C:0.17, G:0.11, T:0.31
Consensus pattern (44 bp):
ACAACTTTTTGAAACATATAAAAAGCTAATCTTATCAGAGGCTC
Found at i:25129185 original size:43 final size:42
Alignment explanation
Indices: 25129138--25129290 Score: 173
Period size: 43 Copynumber: 3.5 Consensus size: 42
25129128 GAGGTTATGC
* *
25129138 AACTTTAAAAAATTTAAAAGGCTCTTCTTATCAGAAGCTTAAT
1 AACTTTGAAAAATTTAAAAGGCTCTT-TTATCAGAAGCTCAAT
* * * *
25129181 AACTTTGAAAAATATAAAAGACTCATTTTATCATAGGCTCAAT
1 AACTTTGAAAAATTTAAAAGGCTC-TTTTATCAGAAGCTCAAT
*
25129224 AACTTTGAAAAATTTAAAAGGCTCTTTTCATCA-AAGGCTCAAC
1 AACTTTGAAAAATTTAAAAGGCTCTTTT-ATCAGAA-GCTCAAT
* *
25129267 AATTTTTGAAAAATATAAAAGGCT
1 AA-CTTTGAAAAATTTAAAAGGCT
25129291 TTCCTTAAAC
Statistics
Matches: 94, Mismatches: 12, Indels: 7
0.83 0.11 0.06
Matches are distributed among these distances:
42 5 0.05
43 68 0.72
44 21 0.22
ACGTcount: A:0.43, C:0.14, G:0.10, T:0.33
Consensus pattern (42 bp):
AACTTTGAAAAATTTAAAAGGCTCTTTTATCAGAAGCTCAAT
Found at i:25130310 original size:18 final size:18
Alignment explanation
Indices: 25130289--25130330 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 18
25130279 TTTTATTTTT
25130289 TCATCATTTTT-CTTTCAC
1 TCATCATTTTTAC-TTCAC
*
25130307 TCATCATTTTTACTTCAT
1 TCATCATTTTTACTTCAC
25130325 TCATCA
1 TCATCA
25130331 CGGTCATTCT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 21 0.95
19 1 0.05
ACGTcount: A:0.21, C:0.26, G:0.00, T:0.52
Consensus pattern (18 bp):
TCATCATTTTTACTTCAC
Found at i:25141293 original size:19 final size:19
Alignment explanation
Indices: 25141269--25141367 Score: 58
Period size: 19 Copynumber: 5.2 Consensus size: 19
25141259 AGGTTTCGAA
25141269 GTTTCACTTAGGGTTTAGG
1 GTTTCACTTAGGGTTTAGG
* * **
25141288 GTTTCATTTAAGGTTTTTG
1 GTTTCACTTAGGGTTTAGG
* * *
25141307 ATTTCA-TTTGGGATTTAGA
1 GTTTCACTTAGGG-TTTAGG
** *
25141326 GTTTCACTTATAGTTTCGAG
1 GTTTCACTTAGGGTTTAG-G
* *
25141346 G-TTCACCTAGGATTTAGG
1 GTTTCACTTAGGGTTTAGG
25141364 GTTT
1 GTTT
25141368 TACCTAGGTT
Statistics
Matches: 55, Mismatches: 21, Indels: 8
0.65 0.25 0.10
Matches are distributed among these distances:
18 6 0.11
19 45 0.82
20 4 0.07
ACGTcount: A:0.19, C:0.10, G:0.24, T:0.46
Consensus pattern (19 bp):
GTTTCACTTAGGGTTTAGG
Found at i:25143600 original size:20 final size:19
Alignment explanation
Indices: 25143568--25143618 Score: 50
Period size: 20 Copynumber: 2.7 Consensus size: 19
25143558 TTGGCCAAGC
* **
25143568 TTTTTCTTATATTTTTATT
1 TTTTTATTATATTAGTATT
25143587 TTTTTATTATTATTAGTATT
1 TTTTTATTA-TATTAGTATT
*
25143607 TATTTATT-TATT
1 TTTTTATTATATT
25143619 TTTGTTTAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
18 4 0.15
19 8 0.30
20 15 0.56
ACGTcount: A:0.22, C:0.02, G:0.02, T:0.75
Consensus pattern (19 bp):
TTTTTATTATATTAGTATT
Found at i:25149610 original size:27 final size:26
Alignment explanation
Indices: 25149555--25149610 Score: 60
Period size: 27 Copynumber: 2.1 Consensus size: 26
25149545 TGTTAAAAAT
* *
25149555 AAAATAAAATCAAATCAAATCAAATAA
1 AAAATAAAATAAAATCAAA-CAAAGAA
25149582 AAAATAAAAATAAAATCGAAA-AAAGAA
1 AAAAT-AAAATAAAATC-AAACAAAGAA
25149609 AA
1 AA
25149611 GCTACAATCA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
27 12 0.48
28 10 0.40
29 3 0.12
ACGTcount: A:0.75, C:0.07, G:0.04, T:0.14
Consensus pattern (26 bp):
AAAATAAAATAAAATCAAACAAAGAA
Found at i:25150458 original size:3 final size:3
Alignment explanation
Indices: 25150452--25150516 Score: 84
Period size: 3 Copynumber: 23.0 Consensus size: 3
25150442 AAAAAACAAA
*
25150452 AAT AAT AGT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
*
25150499 GAT -AT AAT -AT AAT -AT AAT
1 AAT AAT AAT AAT AAT AAT AAT
25150517 CAACTTAAAA
Statistics
Matches: 56, Mismatches: 2, Indels: 8
0.85 0.03 0.12
Matches are distributed among these distances:
2 8 0.14
3 48 0.86
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (3 bp):
AAT
Found at i:25150633 original size:26 final size:26
Alignment explanation
Indices: 25150578--25150662 Score: 66
Period size: 26 Copynumber: 3.3 Consensus size: 26
25150568 CCTAAATGCT
* *
25150578 AATGGGCTTGATCGAGCCCAAACATT
1 AATGGGCTTAATCGAGCCCAAACATC
* *
25150604 AATGGGCTTAATC-AGGCCCAGACGTC
1 AATGGGCTTAATCGA-GCCCAAACATC
* ** *
25150630 AATGTGCCCAATCGAGCCAAAACA-C
1 AATGGGCTTAATCGAGCCCAAACATC
25150655 AAATGGGC
1 -AATGGGC
25150663 CTAGTTAGGC
Statistics
Matches: 45, Mismatches: 11, Indels: 6
0.73 0.18 0.10
Matches are distributed among these distances:
25 2 0.04
26 42 0.93
27 1 0.02
ACGTcount: A:0.33, C:0.26, G:0.24, T:0.18
Consensus pattern (26 bp):
AATGGGCTTAATCGAGCCCAAACATC
Found at i:25150707 original size:52 final size:52
Alignment explanation
Indices: 25150651--25150750 Score: 130
Period size: 52 Copynumber: 1.9 Consensus size: 52
25150641 TCGAGCCAAA
* * *
25150651 ACACAAATGGGCCTAGTTAGGCTTAGACGTCAATAGGT-CTACTTGGGCTCAG
1 ACACAAATGGGCCCAGTTAGGCCTAAACGTCAAT-GGTCCTACTTGGGCTCAG
* * *
25150703 ACACAAGTGGGCCCAGTTGGGCCTAAACGTTAATGGTCCTACTTGGGC
1 ACACAAATGGGCCCAGTTAGGCCTAAACGTCAATGGTCCTACTTGGGC
25150751 CTAGATAAAA
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
51 3 0.07
52 38 0.93
ACGTcount: A:0.25, C:0.23, G:0.28, T:0.24
Consensus pattern (52 bp):
ACACAAATGGGCCCAGTTAGGCCTAAACGTCAATGGTCCTACTTGGGCTCAG
Found at i:25151253 original size:109 final size:108
Alignment explanation
Indices: 25151065--25151471 Score: 312
Period size: 109 Copynumber: 3.5 Consensus size: 108
25151055 AAGGACCCAG
* * ** * * * *
25151065 TCAAGGTCAAAAATAAATGATCGTGACAAAATCACGAATGATAAGAAATGATCTAAACTGAACCA
1 TCAAGGTAAAAAATAAATGATCGAGATGAAACCACGAATCATAAGAAATGATCTAGACTGAGCCA
*
25151130 AGATCGGGTTACCGAGACAAAACAATGAAACAACTAGGACTAAA
66 AGATC-GGTGACCGAGACAAAACAATGAAACAACTAGGACTAAA
* *
25151174 TCAAGGTAAAAAATAAATGATCGAGATGAAACCACGAATAATAAGAAATGATCTAGATTGAGCCA
1 TCAAGGTAAAAAATAAATGATCGAGATGAAACCACGAATCATAAGAAATGATCTAGACTGAGCCA
* ** * * * *
25151239 AGATTGAGTGACCGAGATGAAACCATGAGATAGAAAATGGAGTGACCAAGATTGAA
66 AGATCG-GTGACCGAGACAAAACAATGA-A-A-CAACT--AG-GA-C-----TAAA
* * * *
25151295 TCAAGGTTAAAAATAAATGA-CGAGATGAAACCACGAATCATAAGAAATGATCTGGACTAAGTCA
1 TCAAGGTAAAAAATAAATGATCGAGATGAAACCACGAATCATAAGAAATGATCTAGACTGAGCCA
* * *
25151359 AGATCGGATGACCGAGACGAAATCACGAGTCAAAAAATGGAGCAACTAGGACCAAA
66 AGATCGG-TGACCGAGAC--AA--A--A--C----AATGAAACAACTAGGACTAAA
* **
25151415 TCAAGGTAAAAAATAAATGATCGAGATGAAATCATAAATCATAAGAAATGATCTAGA
1 TCAAGGTAAAAAATAAATGATCGAGATGAAACCACGAATCATAAGAAATGATCTAGA
25151472 TTGACTTATG
Statistics
Matches: 233, Mismatches: 38, Indels: 42
0.74 0.12 0.13
Matches are distributed among these distances:
108 1 0.00
109 77 0.33
110 1 0.00
111 1 0.00
112 3 0.01
114 2 0.01
115 2 0.01
116 1 0.00
119 1 0.00
120 74 0.32
121 54 0.23
122 1 0.00
124 1 0.00
125 1 0.00
126 3 0.01
127 2 0.01
128 1 0.00
129 3 0.01
131 1 0.00
132 3 0.01
ACGTcount: A:0.48, C:0.14, G:0.20, T:0.18
Consensus pattern (108 bp):
TCAAGGTAAAAAATAAATGATCGAGATGAAACCACGAATCATAAGAAATGATCTAGACTGAGCCA
AGATCGGTGACCGAGACAAAACAATGAAACAACTAGGACTAAA
Found at i:25151396 original size:120 final size:121
Alignment explanation
Indices: 25151171--25151471 Score: 374
Period size: 120 Copynumber: 2.5 Consensus size: 121
25151161 AACTAGGACT
* * *
25151171 AAATCAAGGTAAAAAATAAATGATCGAGATGAAACCACGAATAATAAGAAATGATCTAGATTGAG
1 AAATCAAGGTAAAAAATAAATGATCGAGATGAAACCACGAATCATAAGAAATGATCTAGACTAAG
* * * * ** **
25151236 CCAAGATTGAGTGACCGAGATGAAACCATGAGATAGAAAATGGAGTGACCAAGATT
66 CCAAGATGGAGTGACCGAGACGAAACCACGAGATAAAAAATGGAGCAACCAAGACC
* * *
25151292 GAATCAAGGTTAAAAATAAATGA-CGAGATGAAACCACGAATCATAAGAAATGATCTGGACTAAG
1 AAATCAAGGTAAAAAATAAATGATCGAGATGAAACCACGAATCATAAGAAATGATCTAGACTAAG
* * * *
25151356 TCAAGATCGGA-TGACCGAGACGAAATCACGAG-TCAAAAAATGGAGCAACTAGGACC
66 CCAAGAT-GGAGTGACCGAGACGAAACCACGAGAT-AAAAAATGGAGCAACCAAGACC
* **
25151412 AAATCAAGGTAAAAAATAAATGATCGAGATGAAATCATAAATCATAAGAAATGATCTAGA
1 AAATCAAGGTAAAAAATAAATGATCGAGATGAAACCACGAATCATAAGAAATGATCTAGA
25151472 TTGACTTATG
Statistics
Matches: 153, Mismatches: 24, Indels: 6
0.84 0.13 0.03
Matches are distributed among these distances:
119 1 0.01
120 97 0.63
121 55 0.36
ACGTcount: A:0.48, C:0.13, G:0.21, T:0.18
Consensus pattern (121 bp):
AAATCAAGGTAAAAAATAAATGATCGAGATGAAACCACGAATCATAAGAAATGATCTAGACTAAG
CCAAGATGGAGTGACCGAGACGAAACCACGAGATAAAAAATGGAGCAACCAAGACC
Found at i:25169375 original size:12 final size:14
Alignment explanation
Indices: 25169356--25169430 Score: 109
Period size: 15 Copynumber: 5.4 Consensus size: 14
25169346 AAAAAAGCAA
*
25169356 AATAAAAAAATAA-
1 AATAAAATAATAAT
25169369 AATAAAA-AATAAT
1 AATAAAATAATAAT
25169382 AATAAAATAATAAT
1 AATAAAATAATAAT
25169396 AATAATAATAATAAT
1 AATAA-AATAATAAT
25169411 AATAATAATAATAAT
1 AATAA-AATAATAAT
25169426 AATAA
1 AATAA
25169431 TAACATGATA
Statistics
Matches: 59, Mismatches: 0, Indels: 4
0.94 0.00 0.06
Matches are distributed among these distances:
12 5 0.08
13 14 0.24
14 11 0.19
15 29 0.49
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (14 bp):
AATAAAATAATAAT
Found at i:25169382 original size:3 final size:3
Alignment explanation
Indices: 25169364--25169433 Score: 112
Period size: 3 Copynumber: 24.7 Consensus size: 3
25169354 AAAATAAAAA
25169364 AAT AA- AAT AA- AA- AAT AAT AAT AA- AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
25169408 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
25169434 CATGATATAA
Statistics
Matches: 64, Mismatches: 0, Indels: 6
0.91 0.00 0.09
Matches are distributed among these distances:
2 8 0.12
3 56 0.88
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:25169608 original size:26 final size:26
Alignment explanation
Indices: 25169555--25169618 Score: 71
Period size: 26 Copynumber: 2.5 Consensus size: 26
25169545 ATCAGGCTCG
* *
25169555 AACATT-ATGGGCCTAATCAGACCTA
1 AACATTAATGGGCCCAATCAGACCCA
25169580 AACATTAATGGGCCCAATCA-AGCCCA
1 AACATTAATGGGCCCAATCAGA-CCCA
*
25169606 AACA-AAATGGGCC
1 AACATTAATGGGCC
25169619 TAGTTGGGTT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
25 15 0.44
26 19 0.56
ACGTcount: A:0.39, C:0.27, G:0.17, T:0.17
Consensus pattern (26 bp):
AACATTAATGGGCCCAATCAGACCCA
Found at i:25171674 original size:49 final size:50
Alignment explanation
Indices: 25171577--25171709 Score: 139
Period size: 49 Copynumber: 2.7 Consensus size: 50
25171567 TTCGCCCTAG
* *
25171577 TCAAAGATGAGATTTTTAAAGTTTCAAAGTCTCTATTCAAGAAAAGTTTT
1 TCAAAGATCAGATTTTTAAAGTTTCAAAGACTCTATTCAAGAAAAGTTTT
* * * *
25171627 TC-AGGATCAGATTTTTAAAGTTTCAAA-ACATTTGTTTAA-AAAGAGTTTT
1 TCAAAGATCAGATTTTTAAAGTTTCAAAGAC-TCTATTCAAGAAA-AGTTTT
* *
25171676 TCAAAGATGAGATTTTTAAAGCTTT-AAAGCCTCT
1 TCAAAGATCAGATTTTTAAAG-TTTCAAAGACTCT
25171710 GCTCAAGATA
Statistics
Matches: 68, Mismatches: 10, Indels: 10
0.77 0.11 0.11
Matches are distributed among these distances:
48 4 0.06
49 37 0.54
50 23 0.34
51 4 0.06
ACGTcount: A:0.37, C:0.11, G:0.14, T:0.38
Consensus pattern (50 bp):
TCAAAGATCAGATTTTTAAAGTTTCAAAGACTCTATTCAAGAAAAGTTTT
Found at i:25173061 original size:19 final size:19
Alignment explanation
Indices: 25173037--25173082 Score: 62
Period size: 18 Copynumber: 2.6 Consensus size: 19
25173027 GAATCATAAT
25173037 ATGAAATAAAAAAATGAAA
1 ATGAAATAAAAAAATGAAA
*
25173056 ATGAAAT-TAAAAATGAAA
1 ATGAAATAAAAAAATGAAA
25173074 A--AAATAAAA
1 ATGAAATAAAA
25173083 GAAACAAAAG
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
16 4 0.17
17 2 0.08
18 11 0.46
19 7 0.29
ACGTcount: A:0.74, C:0.00, G:0.09, T:0.17
Consensus pattern (19 bp):
ATGAAATAAAAAAATGAAA
Found at i:25173527 original size:50 final size:50
Alignment explanation
Indices: 25173428--25173559 Score: 142
Period size: 50 Copynumber: 2.7 Consensus size: 50
25173418 TATCATAGTA
* * *
25173428 AAAGATGAGATTTTTAAAGTTTCAAAACCATTGTTCAAGAGAAAATTTTC
1 AAAGATGAGATTTTTAAAGTTTTAAAGCCTTTGTTCAAGAGAAAATTTTC
* * * **
25173478 AAAGATGACATTTTTAAAGTTTTAAAGCCTTTGTTCAGGAGGAGCTTTTC
1 AAAGATGAGATTTTTAAAGTTTTAAAGCCTTTGTTCAAGAGAAAATTTTC
* * *
25173528 -AGGATGAGAGTTTTAAA-TTTGTTAAGCCTTTG
1 AAAGATGAGATTTTTAAAGTTT-TAAAGCCTTTG
25173560 GTTAAATGGG
Statistics
Matches: 69, Mismatches: 12, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
48 3 0.04
49 24 0.35
50 42 0.61
ACGTcount: A:0.34, C:0.10, G:0.19, T:0.37
Consensus pattern (50 bp):
AAAGATGAGATTTTTAAAGTTTTAAAGCCTTTGTTCAAGAGAAAATTTTC
Found at i:25174013 original size:20 final size:20
Alignment explanation
Indices: 25173990--25174061 Score: 76
Period size: 20 Copynumber: 3.5 Consensus size: 20
25173980 TATTATGCCT
25173990 AAAGAAAAAA-AAAGCAAAAA
1 AAAGAAAAAAGAAAG-AAAAA
*
25174010 AAAGAAAAAAGAAAG-AAGA
1 AAAGAAAAAAGAAAGAAAAA
*
25174029 AGAGAAAAAATGAAAGAAATGAA
1 AAAGAAAAAA-GAAAGAAA--AA
25174052 AAAGAAAAAA
1 AAAGAAAAAA
25174062 AGATCGAGAT
Statistics
Matches: 43, Mismatches: 4, Indels: 7
0.80 0.07 0.13
Matches are distributed among these distances:
19 12 0.28
20 15 0.35
21 6 0.14
23 10 0.23
ACGTcount: A:0.79, C:0.01, G:0.17, T:0.03
Consensus pattern (20 bp):
AAAGAAAAAAGAAAGAAAAA
Found at i:25174044 original size:24 final size:24
Alignment explanation
Indices: 25174017--25174062 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
25174007 AAAAAAGAAA
*
25174017 AAAGAAA-GAAGAAGAGAAAAAATG
1 AAAGAAATGAAAAAGA-AAAAAATG
25174041 AAAGAAATGAAAAAGAAAAAAA
1 AAAGAAATGAAAAAGAAAAAAA
25174063 GATCGAGATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
24 13 0.65
25 7 0.35
ACGTcount: A:0.76, C:0.00, G:0.20, T:0.04
Consensus pattern (24 bp):
AAAGAAATGAAAAAGAAAAAAATG
Found at i:25174046 original size:12 final size:11
Alignment explanation
Indices: 25173990--25174061 Score: 57
Period size: 10 Copynumber: 6.9 Consensus size: 11
25173980 TATTATGCCT
25173990 AAAGAAAAAA-
1 AAAGAAAAAAG
*
25174000 AAAGCAAAAA-
1 AAAGAAAAAAG
25174010 AAAGAAAAAAG
1 AAAGAAAAAAG
*
25174021 AAAG-AAGAAG
1 AAAGAAAAAAG
25174031 --AGAAAAAATG
1 AAAGAAAAAA-G
*
25174041 AAAGAAATGAA-
1 AAAGAAA-AAAG
25174052 AAAGAAAAAA
1 AAAGAAAAAA
25174062 AGATCGAGAT
Statistics
Matches: 50, Mismatches: 6, Indels: 12
0.74 0.09 0.18
Matches are distributed among these distances:
8 2 0.04
9 4 0.08
10 26 0.52
11 11 0.22
12 5 0.10
13 2 0.04
ACGTcount: A:0.79, C:0.01, G:0.17, T:0.03
Consensus pattern (11 bp):
AAAGAAAAAAG
Found at i:25174056 original size:25 final size:23
Alignment explanation
Indices: 25173990--25174062 Score: 65
Period size: 27 Copynumber: 2.9 Consensus size: 23
25173980 TATTATGCCT
* *
25173990 AAAGAAAAAAAAAGCAAAAAAAAG
1 AAAGAAAGAAAAAG-AAAAAAATG
*
25174014 AAAAAAGAAAGAAGAAGAGAAAAAATG
1 ---AAAGAAAGAAAAAGA-AAAAAATG
25174041 AAAGAAATGAAAAAGAAAAAAA
1 AAAGAAA-GAAAAAGAAAAAAA
25174063 GATCGAGATT
Statistics
Matches: 40, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
24 13 0.32
25 7 0.17
26 1 0.03
27 19 0.47
ACGTcount: A:0.79, C:0.01, G:0.16, T:0.03
Consensus pattern (23 bp):
AAAGAAAGAAAAAGAAAAAAATG
Found at i:25174780 original size:14 final size:16
Alignment explanation
Indices: 25174751--25174784 Score: 54
Period size: 14 Copynumber: 2.2 Consensus size: 16
25174741 AAGGAAAGAT
25174751 AAATGAAAAATGAAAA
1 AAATGAAAAATGAAAA
25174767 AAAT-AAAAAT-AAAA
1 AAATGAAAAATGAAAA
25174781 AAAT
1 AAAT
25174785 CTAATAGAGG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 8 0.44
15 6 0.33
16 4 0.22
ACGTcount: A:0.79, C:0.00, G:0.06, T:0.15
Consensus pattern (16 bp):
AAATGAAAAATGAAAA
Found at i:25175449 original size:46 final size:46
Alignment explanation
Indices: 25175380--25175762 Score: 281
Period size: 47 Copynumber: 8.2 Consensus size: 46
25175370 GATGACCTTT
* * *
25175380 ATTAAGTCTTTGCCTAAATGAGCTTTCAAATTTATTTTCAAAAGTC
1 ATTAAGCCTTTGCTTAAAGGAGCTTTCAAATTTATTTTCAAAAGTC
* *
25175426 ATTAAGCCTTTGGTTAAAGGAGCTTTCAAATTTATTTTGAAAAAGTC
1 ATTAAGCCTTTGCTTAAAGGAGCTTTCAAATTTATTTT-CAAAAGTC
* ** **
25175473 A-TAGAGCCTTT-ATCTAAAGGAGCACTCAAATTTGCTTTCAAAAAGT-
1 ATTA-AGCCTTTGCT-TAAAGGAGCTTTCAAATTTATTTTC-AAAAGTC
* * * * * *
25175519 TTTGAAGCTTTTGCTTAAAAGAG-TTTTAAATTTACTTTCAAAAGTT
1 ATT-AAGCCTTTGCTTAAAGGAGCTTTCAAATTTATTTTCAAAAGTC
* * ** * * * * * *
25175565 GTTGAGTTTTTGTTTAAAGAAGTTTTTAAATTTATTTTCAAAAATTT
1 ATTAAGCCTTTGCTTAAAGGAGCTTTCAAATTTATTTTC-AAAAGTC
* *
25175612 ATTAAACCTTTACTTAAAGGAGCTTTCAAATTTATTTTCAAAAAGTC
1 ATTAAGCCTTTGCTTAAAGGAGCTTTCAAATTTATTTTC-AAAAGTC
* * *
25175659 ATTGAGCCTTTGCTTAAAGGAACTTTCAAATTTATTTTTAAAAAG-C
1 ATTAAGCCTTTGCTTAAAGGAGCTTTCAAATTTA-TTTTCAAAAGTC
* * * ** * * * *
25175705 TGTTAAACCTTTACTTAAATAAGTTTTCAATTTTATCTTCAAAAGTT
1 -ATTAAGCCTTTGCTTAAAGGAGCTTTCAAATTTATTTTCAAAAGTC
*
25175752 ATTGAGCCTTT
1 ATTAAGCCTTT
25175763 ACCTAAAAGA
Statistics
Matches: 265, Mismatches: 59, Indels: 26
0.76 0.17 0.07
Matches are distributed among these distances:
45 20 0.08
46 83 0.31
47 156 0.59
48 6 0.02
ACGTcount: A:0.34, C:0.12, G:0.12, T:0.42
Consensus pattern (46 bp):
ATTAAGCCTTTGCTTAAAGGAGCTTTCAAATTTATTTTCAAAAGTC
Found at i:25175583 original size:139 final size:140
Alignment explanation
Indices: 25175387--25175701 Score: 332
Period size: 139 Copynumber: 2.3 Consensus size: 140
25175377 TTTATTAAGT
* * * *
25175387 CTTTGCCTAAATGAGCTTTCAAATTTATTTTCAAAAGTCATTAAGCCTTTGGTTAAAGGAGCTTT
1 CTTTGCTTAAAAGAGCTTTCAAATTTACTTTCAAAAGTCATTAAGCCTTTGGTTAAAGAAGCTTT
* * *
25175452 CAAATTTATTTTGAAAAAGTCA-TAGAGCCTTTA-TCTAAAGGAGCACTCAAATTTGCTTTCAAA
66 CAAATTTATTTTCAAAAAGTCATTA-AACCTTTACT-TAAAGGAGCACTCAAATTTACTTTCAAA
*
25175515 AAGT-TTTGAAGC
129 AAGTCATTG-AGC
* * ** * ** * *
25175527 TTTTGCTTAAAAGAG-TTTTAAATTTACTTTCAAAAGTTGTTGAGTTTTTGTTTAAAGAAGTTTT
1 CTTTGCTTAAAAGAGCTTTCAAATTTACTTTCAAAAGTCATTAAGCCTTTGGTTAAAGAAGCTTT
* * * ** *
25175591 TAAATTTATTTTCAAAAATTTATTAAACCTTTACTTAAAGGAGCTTTCAAATTTATTTTCAAAAA
66 CAAATTTATTTTCAAAAAGTCATTAAACCTTTACTTAAAGGAGCACTCAAATTTACTTTCAAAAA
25175656 GTCATTGAGC
131 GTCATTGAGC
* * * *
25175666 CTTTGCTTAAAGGAACTTTCAAATTTATTTTTAAAA
1 CTTTGCTTAAAAGAGCTTTCAAATTTACTTTCAAAA
25175702 AGCTGTTAAA
Statistics
Matches: 142, Mismatches: 29, Indels: 8
0.79 0.16 0.04
Matches are distributed among these distances:
139 107 0.75
140 35 0.25
ACGTcount: A:0.34, C:0.12, G:0.13, T:0.41
Consensus pattern (140 bp):
CTTTGCTTAAAAGAGCTTTCAAATTTACTTTCAAAAGTCATTAAGCCTTTGGTTAAAGAAGCTTT
CAAATTTATTTTCAAAAAGTCATTAAACCTTTACTTAAAGGAGCACTCAAATTTACTTTCAAAAA
GTCATTGAGC
Found at i:25175860 original size:17 final size:16
Alignment explanation
Indices: 25175830--25175893 Score: 74
Period size: 17 Copynumber: 3.8 Consensus size: 16
25175820 TAAAATTTGC
* *
25175830 AAAAACATAGAAAACA
1 AAAAACAAAAAAAACA
25175846 AAAAACAAACAAAAACA
1 AAAAACAAA-AAAAACA
*
25175863 ACAAAACAAAATAAACA
1 A-AAAACAAAAAAAACA
25175880 AACAAACAAAAAAA
1 AA-AAACAAAAAAA
25175894 GATCTCTCTC
Statistics
Matches: 41, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
16 9 0.22
17 24 0.59
18 8 0.20
ACGTcount: A:0.80, C:0.16, G:0.02, T:0.03
Consensus pattern (16 bp):
AAAAACAAAAAAAACA
Found at i:25175867 original size:13 final size:12
Alignment explanation
Indices: 25175841--25175890 Score: 57
Period size: 13 Copynumber: 3.9 Consensus size: 12
25175831 AAAACATAGA
25175841 AAAC-AAAAAAC
1 AAACAAAAAAAC
25175852 AAACAAAAACAAC
1 AAACAAAAA-AAC
25175865 AAAACAAAATAAAC
1 -AAACAAAA-AAAC
25175879 AAACAAACAAAA
1 AAACAAA-AAAA
25175891 AAAGATCTCT
Statistics
Matches: 34, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
11 4 0.12
12 4 0.12
13 13 0.38
14 12 0.35
15 1 0.03
ACGTcount: A:0.80, C:0.18, G:0.00, T:0.02
Consensus pattern (12 bp):
AAACAAAAAAAC
Found at i:25176746 original size:27 final size:25
Alignment explanation
Indices: 25176704--25176762 Score: 66
Period size: 27 Copynumber: 2.3 Consensus size: 25
25176694 TAAAAAAACT
*
25176704 AAAAAAAAAAAGAGAAAG-CTTGTAG
1 AAAAAAAAAAAAAGAAAGACTT-TAG
*
25176729 AAAAAAAATGAAAAAGAAAGACTTTAT
1 AAAAAAAA--AAAAAGAAAGACTTTAG
25176756 AAAAAAA
1 AAAAAAA
25176763 GCTTGTGAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
25 8 0.28
27 18 0.62
28 3 0.10
ACGTcount: A:0.69, C:0.03, G:0.14, T:0.14
Consensus pattern (25 bp):
AAAAAAAAAAAAAGAAAGACTTTAG
Found at i:25183376 original size:18 final size:19
Alignment explanation
Indices: 25183349--25183402 Score: 58
Period size: 18 Copynumber: 2.9 Consensus size: 19
25183339 AAAAAAAATT
25183349 TAAACATTAAACCAAATAAA
1 TAAA-ATTAAACCAAATAAA
* * *
25183369 T-AACTTAATCAAAATAAA
1 TAAAATTAAACCAAATAAA
25183387 TAAAATT-AACCAAATA
1 TAAAATTAAACCAAATA
25183403 TAAATAAATA
Statistics
Matches: 27, Mismatches: 6, Indels: 4
0.73 0.16 0.11
Matches are distributed among these distances:
18 20 0.74
19 6 0.22
20 1 0.04
ACGTcount: A:0.63, C:0.13, G:0.00, T:0.24
Consensus pattern (19 bp):
TAAAATTAAACCAAATAAA
Found at i:25183418 original size:18 final size:17
Alignment explanation
Indices: 25183362--25183418 Score: 60
Period size: 18 Copynumber: 3.1 Consensus size: 17
25183352 ACATTAAACC
*
25183362 AAATAAATAACTTAATCA
1 AAATAAATAA-ATAATCA
*
25183380 AAATAAATAAAATTAACCA
1 AAATAAAT-AAA-TAATCA
25183399 AATATAAATAAATAATCA
1 AA-ATAAATAAATAATCA
25183417 AA
1 AA
25183419 GTAATAAAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
18 15 0.45
19 12 0.36
20 6 0.18
ACGTcount: A:0.67, C:0.09, G:0.00, T:0.25
Consensus pattern (17 bp):
AAATAAATAAATAATCA
Found at i:25183425 original size:20 final size:21
Alignment explanation
Indices: 25183381--25183436 Score: 55
Period size: 20 Copynumber: 2.7 Consensus size: 21
25183371 ACTTAATCAA
25183381 AATAAATAAAATTAACCAAAT
1 AATAAATAAAATTAACCAAAT
*
25183402 -ATAAAT-AAA-TAATCAAAGT
1 AATAAATAAAATTAACCAAA-T
*
25183421 AATAAAATAACATTAA
1 AAT-AAATAAAATTAA
25183437 TAAAAAAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
18 7 0.25
19 4 0.14
20 8 0.29
21 4 0.14
22 2 0.07
23 3 0.11
ACGTcount: A:0.66, C:0.07, G:0.02, T:0.25
Consensus pattern (21 bp):
AATAAATAAAATTAACCAAAT
Found at i:25183623 original size:20 final size:22
Alignment explanation
Indices: 25183600--25183645 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 22
25183590 TATTTAAAGC
25183600 CTTTTT-CATTT-ATTTTCTCA
1 CTTTTTCCATTTCATTTTCTCA
* *
25183620 CTTTTTCCTTTTCATTTTCTCT
1 CTTTTTCCATTTCATTTTCTCA
25183642 CTTT
1 CTTT
25183646 AATCGATTCT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 6 0.27
21 4 0.18
22 12 0.55
ACGTcount: A:0.09, C:0.24, G:0.00, T:0.67
Consensus pattern (22 bp):
CTTTTTCCATTTCATTTTCTCA
Found at i:25185174 original size:24 final size:23
Alignment explanation
Indices: 25185111--25185176 Score: 60
Period size: 25 Copynumber: 2.7 Consensus size: 23
25185101 AATTTTAACC
*
25185111 TTTTTTATTCTTTTCTACTTCTTTT
1 TTTTTTATT-TTTT-AACTTCTTTT
* *
25185136 TTTTTTAAATATTTTAATTTCTTTT
1 TTTTTT--ATTTTTTAACTTCTTTT
25185161 ATTTTTTATTTTTTAA
1 -TTTTTTATTTTTTAA
25185177 AATTTTATTT
Statistics
Matches: 34, Mismatches: 4, Indels: 7
0.76 0.09 0.16
Matches are distributed among these distances:
24 8 0.24
25 14 0.41
26 10 0.29
27 2 0.06
ACGTcount: A:0.18, C:0.08, G:0.00, T:0.74
Consensus pattern (23 bp):
TTTTTTATTTTTTAACTTCTTTT
Found at i:25185182 original size:15 final size:15
Alignment explanation
Indices: 25185132--25185188 Score: 53
Period size: 15 Copynumber: 3.7 Consensus size: 15
25185122 TTTCTACTTC
25185132 TTTT-TTTTTTAAATA
1 TTTTATTTTTTAAA-A
* **
25185147 TTTTAATTTCTTTTATT
1 TTTT-ATTT-TTTAAAA
25185164 TTTTATTTTTTAAAA
1 TTTTATTTTTTAAAA
25185179 TTTTATTTTT
1 TTTTATTTTT
25185189 CCCTTTCTTT
Statistics
Matches: 33, Mismatches: 6, Indels: 6
0.73 0.13 0.13
Matches are distributed among these distances:
15 18 0.55
16 4 0.12
17 7 0.21
18 4 0.12
ACGTcount: A:0.23, C:0.02, G:0.00, T:0.75
Consensus pattern (15 bp):
TTTTATTTTTTAAAA
Found at i:25187104 original size:7 final size:7
Alignment explanation
Indices: 25187094--25187297 Score: 50
Period size: 7 Copynumber: 31.6 Consensus size: 7
25187084 AACTAAACTA
25187094 TAAACCC
1 TAAACCC
*
25187101 TAAAGCC
1 TAAACCC
*
25187108 T--AGCC
1 TAAACCC
25187113 TAAACCC
1 TAAACCC
*
25187120 TAAACTC
1 TAAACCC
25187127 T-AA-CC
1 TAAACCC
*
25187132 TAAA-TC
1 TAAACCC
*
25187138 TCAAAACC
1 T-AAACCC
*
25187146 TAAAGCC
1 TAAACCC
25187153 T-AA-CC
1 TAAACCC
**
25187158 TAAACAT
1 TAAACCC
*
25187165 TAAA-TC
1 TAAACCC
25187171 T-AACCC
1 TAAACCC
*
25187177 TAAACTC
1 TAAACCC
25187184 T-AA-CC
1 TAAACCC
*
25187189 TAAATCC
1 TAAACCC
*
25187196 TAAACAC
1 TAAACCC
25187203 T-AACCC
1 TAAACCC
*
25187209 -AAA-TC
1 TAAACCC
*
25187214 TCATACCC
1 T-AAACCC
25187222 TAAACCC
1 TAAACCC
*
25187229 TAAATCC
1 TAAACCC
25187236 T-AACCC
1 TAAACCC
*
25187242 TAAACTC
1 TAAACCC
*
25187249 T-AA-CT
1 TAAACCC
25187254 TAAACCC
1 TAAACCC
* * *
25187261 CAAATCT
1 TAAACCC
*
25187268 TAAACTC
1 TAAACCC
*
25187275 TAAA-TC
1 TAAACCC
*
25187281 -AAACTC
1 TAAACCC
25187287 TAAACCC
1 TAAACCC
25187294 TAAA
1 TAAA
25187298 TTTAATCTTA
Statistics
Matches: 142, Mismatches: 35, Indels: 40
0.65 0.16 0.18
Matches are distributed among these distances:
5 19 0.13
6 36 0.25
7 83 0.58
8 4 0.03
ACGTcount: A:0.44, C:0.33, G:0.01, T:0.22
Consensus pattern (7 bp):
TAAACCC
Found at i:25187133 original size:19 final size:19
Alignment explanation
Indices: 25187094--25187207 Score: 78
Period size: 19 Copynumber: 6.0 Consensus size: 19
25187084 AACTAAACTA
*
25187094 TAAACCCTAAAGC-CTAGCC
1 TAAACCCTAAA-CTCTAACC
25187113 TAAACCCTAAACTCTAACC
1 TAAACCCTAAACTCTAACC
* *
25187132 TAAATCTCAAAAC-CTAAAGCC
1 TAAA-CCCTAAACTCT-AA-CC
*
25187153 T-AA-CCTAAACAT-TAAATC
1 TAAACCCTAAAC-TCT-AACC
25187171 T-AACCCTAAACTCTAACC
1 TAAACCCTAAACTCTAACC
* *
25187189 TAAATCCTAAACACTAACC
1 TAAACCCTAAACTCTAACC
25187208 CAAATCTCAT
Statistics
Matches: 77, Mismatches: 9, Indels: 18
0.74 0.09 0.17
Matches are distributed among these distances:
18 15 0.19
19 49 0.64
20 10 0.13
21 3 0.04
ACGTcount: A:0.44, C:0.32, G:0.03, T:0.21
Consensus pattern (19 bp):
TAAACCCTAAACTCTAACC
Found at i:25187241 original size:20 final size:21
Alignment explanation
Indices: 25187175--25187251 Score: 67
Period size: 19 Copynumber: 3.9 Consensus size: 21
25187165 TAAATCTAAC
*
25187175 CCTAAACTCT-AA-CCTAAAT
1 CCTAAACCCTAAACCCTAAAT
*
25187194 CCTAAACACT-AACCC-AAAT
1 CCTAAACCCTAAACCCTAAAT
*
25187213 -CTCATACCCTAAACCCTAAAT
1 CCT-AAACCCTAAACCCTAAAT
*
25187234 CCT-AACCCTAAACTCTAA
1 CCTAAACCCTAAACCCTAA
25187252 CTTAAACCCC
Statistics
Matches: 48, Mismatches: 5, Indels: 9
0.77 0.08 0.15
Matches are distributed among these distances:
18 2 0.04
19 20 0.42
20 20 0.42
21 4 0.08
22 2 0.04
ACGTcount: A:0.42, C:0.36, G:0.00, T:0.22
Consensus pattern (21 bp):
CCTAAACCCTAAACCCTAAAT
Found at i:25187297 original size:26 final size:26
Alignment explanation
Indices: 25187237--25187297 Score: 68
Period size: 26 Copynumber: 2.3 Consensus size: 26
25187227 CCTAAATCCT
* *
25187237 AACCCTAAACTCTAACTTAAACCCCA
1 AACCCTAAACTCTAAATCAAACCCCA
* * * *
25187263 AATCTTAAACTCTAAATCAAACTCTA
1 AACCCTAAACTCTAAATCAAACCCCA
25187289 AACCCTAAA
1 AACCCTAAA
25187298 TTTAATCTTA
Statistics
Matches: 27, Mismatches: 8, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.46, C:0.31, G:0.00, T:0.23
Consensus pattern (26 bp):
AACCCTAAACTCTAAATCAAACCCCA
Found at i:25187309 original size:19 final size:19
Alignment explanation
Indices: 25187263--25187355 Score: 64
Period size: 19 Copynumber: 4.8 Consensus size: 19
25187253 TTAAACCCCA
*
25187263 AATCTTAAACTCTAAA-TC
1 AATCTTAAACCCTAAATTC
* *
25187281 AAACTCTAAACCCTAAATTT
1 AATCT-TAAACCCTAAATTC
* *
25187301 AATCTTAAACCTTAAATCC
1 AATCTTAAACCCTAAATTC
* *
25187320 TAATCCTAATCCCT-AATTC
1 -AATCTTAAACCCTAAATTC
* *
25187339 AAACCTTACACCCTAAA
1 -AATCTTAAACCCTAAA
25187356 CCAAATCCTA
Statistics
Matches: 55, Mismatches: 16, Indels: 6
0.71 0.21 0.08
Matches are distributed among these distances:
18 4 0.07
19 34 0.62
20 17 0.31
ACGTcount: A:0.42, C:0.28, G:0.00, T:0.30
Consensus pattern (19 bp):
AATCTTAAACCCTAAATTC
Found at i:25190482 original size:2 final size:2
Alignment explanation
Indices: 25190475--25190504 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
25190465 TTTGGCTTTG
25190475 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
25190505 TAGTATTATA
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:25191193 original size:101 final size:101
Alignment explanation
Indices: 25191018--25191219 Score: 386
Period size: 101 Copynumber: 2.0 Consensus size: 101
25191008 TATCAACAAT
*
25191018 GAAAAGTTTGGCTTACTCAACCAAATTTAACTCCATAAACATTCAACAACACTTCTTAATCGAGA
1 GAAAAGTTTGGCTTACTCAACCAAATTTAACTCCATAAACACTCAACAACACTTCTTAATCGAGA
25191083 TACGAGCAGCTGCACAAATTGCTGATCGACAACTAC
66 TACGAGCAGCTGCACAAATTGCTGATCGACAACTAC
*
25191119 GAAAAGTTTGGCTTACTCAACCAAATTTAACTTCATAAACACTCAACAACACTTCTTAATCGAGA
1 GAAAAGTTTGGCTTACTCAACCAAATTTAACTCCATAAACACTCAACAACACTTCTTAATCGAGA
25191184 TACGAGCAGCTGCACAAATTGCTGATCGACAACTAC
66 TACGAGCAGCTGCACAAATTGCTGATCGACAACTAC
25191220 TAGATTTTAA
Statistics
Matches: 99, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
101 99 1.00
ACGTcount: A:0.38, C:0.25, G:0.13, T:0.25
Consensus pattern (101 bp):
GAAAAGTTTGGCTTACTCAACCAAATTTAACTCCATAAACACTCAACAACACTTCTTAATCGAGA
TACGAGCAGCTGCACAAATTGCTGATCGACAACTAC
Found at i:25193761 original size:29 final size:29
Alignment explanation
Indices: 25193693--25193762 Score: 77
Period size: 29 Copynumber: 2.4 Consensus size: 29
25193683 CTTATTTATC
* * * *
25193693 AATGACTAAATTATAAATTTTCAAAGTTA
1 AATGACTAAAATAAAAATTTTAAAAATTA
* *
25193722 AGTGATTAAAATAAAAATTTTAAAAATTA
1 AATGACTAAAATAAAAATTTTAAAAATTA
*
25193751 AATGACCAAAAT
1 AATGACTAAAAT
25193763 TTATTTATTT
Statistics
Matches: 32, Mismatches: 9, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.54, C:0.06, G:0.07, T:0.33
Consensus pattern (29 bp):
AATGACTAAAATAAAAATTTTAAAAATTA
Found at i:25196323 original size:3 final size:3
Alignment explanation
Indices: 25196315--25196366 Score: 104
Period size: 3 Copynumber: 17.3 Consensus size: 3
25196305 CTTAAATAAA
25196315 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
25196363 ATT A
1 ATT A
25196367 ATTCTGACTT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 49 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:25196989 original size:20 final size:20
Alignment explanation
Indices: 25196951--25196989 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
25196941 TTAGAAAAGT
**
25196951 TTAAATTTTTCAATGATCGG
1 TTAAATTTTTCAACCATCGG
25196971 TTAAATTTTTCAACCATCG
1 TTAAATTTTTCAACCATCG
25196990 AAATATAAAA
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:0.31, C:0.15, G:0.10, T:0.44
Consensus pattern (20 bp):
TTAAATTTTTCAACCATCGG
Found at i:25197382 original size:3 final size:3
Alignment explanation
Indices: 25197374--25197407 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
25197364 TTTTCTATGA
25197374 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
25197408 CATTCTTTCA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:25199501 original size:30 final size:28
Alignment explanation
Indices: 25199408--25199497 Score: 119
Period size: 29 Copynumber: 3.1 Consensus size: 28
25199398 ATGATTTTTA
* *
25199408 AAATTAAAAAATTTAAATTTAAATTATT
1 AAATTAAAAAATATATATTTAAATTATT
25199436 AAATTAAAAAAATAATATATTTGAAAATT-TT
1 AAATT-AAAAAAT-ATATATTT--AAATTATT
25199467 AAATTAAAAAATATATATTTAAATTATT
1 AAATTAAAAAATATATATTTAAATTATT
25199495 AAA
1 AAA
25199498 AATTTTATTT
Statistics
Matches: 55, Mismatches: 2, Indels: 10
0.82 0.03 0.15
Matches are distributed among these distances:
27 5 0.09
28 10 0.18
29 15 0.27
30 13 0.24
31 7 0.13
32 5 0.09
ACGTcount: A:0.59, C:0.00, G:0.01, T:0.40
Consensus pattern (28 bp):
AAATTAAAAAATATATATTTAAATTATT
Found at i:25199504 original size:37 final size:40
Alignment explanation
Indices: 25199459--25199532 Score: 102
Period size: 37 Copynumber: 1.9 Consensus size: 40
25199449 AATATATTTG
25199459 AAAATTTTAAATTAAAAA-ATAT-ATAT-T-TAAATTATTA
1 AAAATTTT-AATTAAAAAGATATAATATATGTAAATTATTA
*
25199496 AAAATTTTATTTAAAAAGATATAATATATGTAAATTA
1 AAAATTTTAATTAAAAAGATATAATATATGTAAATTA
25199533 GATTATATTG
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
36 8 0.25
37 12 0.38
38 4 0.12
39 1 0.03
40 7 0.22
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (40 bp):
AAAATTTTAATTAAAAAGATATAATATATGTAAATTATTA
Found at i:25199506 original size:21 final size:20
Alignment explanation
Indices: 25199464--25199510 Score: 60
Period size: 20 Copynumber: 2.3 Consensus size: 20
25199454 ATTTGAAAAT
25199464 TTTAAATTAAAAAATATATA
1 TTTAAATTAAAAAATATATA
*
25199484 TTTAAATTATTAAAAAT-TTTA
1 TTTAAATTA--AAAAATATATA
25199505 TTTAAA
1 TTTAAA
25199511 AAGATATAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
20 9 0.38
21 9 0.38
22 6 0.25
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (20 bp):
TTTAAATTAAAAAATATATA
Found at i:25202014 original size:10 final size:10
Alignment explanation
Indices: 25202001--25202030 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
25201991 TTTTTACATA
*
25202001 TTAATCGAGT
1 TTAATCGAGC
25202011 TTAATCGAGC
1 TTAATCGAGC
25202021 TTAATCGAGC
1 TTAATCGAGC
25202031 GAGCTCGAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.30, C:0.17, G:0.20, T:0.33
Consensus pattern (10 bp):
TTAATCGAGC
Found at i:25206354 original size:11 final size:11
Alignment explanation
Indices: 25206338--25206379 Score: 52
Period size: 11 Copynumber: 4.0 Consensus size: 11
25206328 AAATTTTATC
25206338 ATATATATATA
1 ATATATATATA
25206349 ATATATATATA
1 ATATATATATA
* *
25206360 TTATA-ATATG
1 ATATATATATA
25206370 ATAT-TATATA
1 ATATATATATA
25206380 CGATTCAAAC
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
10 11 0.42
11 15 0.58
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (11 bp):
ATATATATATA
Found at i:25206356 original size:13 final size:13
Alignment explanation
Indices: 25206333--25206379 Score: 60
Period size: 13 Copynumber: 3.5 Consensus size: 13
25206323 TAAATAAATT
25206333 TTATCATATATATA
1 TTAT-ATATATATA
*
25206347 TAATATATATATA
1 TTATATATATATA
25206360 TTATA-ATATGATA
1 TTATATATAT-ATA
25206373 TTATATA
1 TTATATA
25206380 CGATTCAAAC
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
12 4 0.14
13 21 0.72
14 4 0.14
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (13 bp):
TTATATATATATA
Found at i:25208874 original size:6 final size:6
Alignment explanation
Indices: 25208822--25208873 Score: 77
Period size: 6 Copynumber: 8.7 Consensus size: 6
25208812 ATTTGTATTA
* * *
25208822 ATATGT ATATGT ATATGT ATATGT ATATGT ATATAT ATATAT ATATAT
1 ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT
25208870 ATAT
1 ATAT
25208874 AAATCCATAT
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
6 45 1.00
ACGTcount: A:0.40, C:0.00, G:0.10, T:0.50
Consensus pattern (6 bp):
ATATGT
Found at i:25209269 original size:2 final size:2
Alignment explanation
Indices: 25209262--25209288 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
25209252 AGGATTAGTT
25209262 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 T
25209289 TTTGGGTGGG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:25217720 original size:22 final size:21
Alignment explanation
Indices: 25217678--25217725 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 21
25217668 TCTATTTAAA
25217678 AAAAACAAAAAAAGCAAAAAG
1 AAAAACAAAAAAAGCAAAAAG
* *
25217699 CAAAACTAAAAAAATG-ACAAAG
1 AAAAAC-AAAAAAA-GCAAAAAG
25217721 AAAAA
1 AAAAA
25217726 TATTTTTAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
21 5 0.23
22 16 0.73
23 1 0.05
ACGTcount: A:0.77, C:0.10, G:0.08, T:0.04
Consensus pattern (21 bp):
AAAAACAAAAAAAGCAAAAAG
Found at i:25217869 original size:20 final size:20
Alignment explanation
Indices: 25217846--25217891 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
25217836 AGAAAATAAG
* * *
25217846 AAAAAGATAACGAATGAAAA
1 AAAAAGAAAACAAAAGAAAA
25217866 AAAAAGAAAACAAAAGAAAA
1 AAAAAGAAAACAAAAGAAAA
25217886 AAAAAG
1 AAAAAG
25217892 TTAAAAGGGA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.78, C:0.04, G:0.13, T:0.04
Consensus pattern (20 bp):
AAAAAGAAAACAAAAGAAAA
Found at i:25217880 original size:10 final size:10
Alignment explanation
Indices: 25217861--25217891 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
25217851 GATAACGAAT
25217861 GAAAAAAAAA
1 GAAAAAAAAA
*
25217871 GAAAACAAAA
1 GAAAAAAAAA
25217881 GAAAAAAAAA
1 GAAAAAAAAA
25217891 G
1 G
25217892 TTAAAAGGGA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.84, C:0.03, G:0.13, T:0.00
Consensus pattern (10 bp):
GAAAAAAAAA
Found at i:25218694 original size:16 final size:16
Alignment explanation
Indices: 25218684--25218739 Score: 58
Period size: 20 Copynumber: 3.2 Consensus size: 16
25218674 AAAGATGAAC
25218684 AAAGAAAAAGAAAAAA
1 AAAGAAAAAGAAAAAA
25218700 AAAGAAAAAAGAAAACACGA
1 AAAG-AAAAAGAAAA-A--A
*
25218720 AACGCAAAAAGAAAAAA
1 AAAG-AAAAAGAAAAAA
25218737 AAA
1 AAA
25218740 TTAAGTTGCA
Statistics
Matches: 33, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
16 4 0.12
17 13 0.39
18 1 0.03
19 1 0.03
20 14 0.42
ACGTcount: A:0.80, C:0.07, G:0.12, T:0.00
Consensus pattern (16 bp):
AAAGAAAAAGAAAAAA
Found at i:25218857 original size:14 final size:16
Alignment explanation
Indices: 25218840--25218873 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
25218830 CCTATAAAAG
25218840 AAAA-TTATTAAATA-
1 AAAATTTATTAAATAT
25218854 AAAATTTATTAAATAT
1 AAAATTTATTAAATAT
25218870 AAAA
1 AAAA
25218874 ATAGAAAAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 4 0.22
15 10 0.56
16 4 0.22
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (16 bp):
AAAATTTATTAAATAT
Found at i:25219031 original size:18 final size:18
Alignment explanation
Indices: 25219004--25219038 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
25218994 AAACACAAAT
*
25219004 AAAAAGCAAATAAAAAAG
1 AAAAAACAAATAAAAAAG
25219022 AAAAAACAAATAAAAAA
1 AAAAAACAAATAAAAAA
25219039 AAAGATTAAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.83, C:0.06, G:0.06, T:0.06
Consensus pattern (18 bp):
AAAAAACAAATAAAAAAG
Found at i:25220688 original size:12 final size:12
Alignment explanation
Indices: 25220666--25220699 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
25220656 GCATAAAAGT
25220666 AAAAATAAAACAA
1 AAAAAT-AAACAA
*
25220679 ATAAATAAACAA
1 AAAAATAAACAA
25220691 AAAAATAAA
1 AAAAATAAA
25220700 TATAAATAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
12 14 0.74
13 5 0.26
ACGTcount: A:0.82, C:0.06, G:0.00, T:0.12
Consensus pattern (12 bp):
AAAAATAAACAA
Found at i:25221476 original size:3 final size:3
Alignment explanation
Indices: 25221468--25221506 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
25221458 AAAATTTTCT
25221468 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
25221507 TAAACGGTAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:25225171 original size:3 final size:3
Alignment explanation
Indices: 25225165--25225203 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
25225155 ATAATAATAA
25225165 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
25225204 GCATAATTTT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:25227116 original size:145 final size:144
Alignment explanation
Indices: 25226791--25227127 Score: 356
Period size: 145 Copynumber: 2.3 Consensus size: 144
25226781 ATATCCCAAG
* * * * * * * *
25226791 AAATGTGAAATTACCAAAATACCCTTATAAGGGTATTTTGGTAATTTCACATTTCTTGGGATATT
1 AAATGTTAAATTACAAAAATATCCTTATAAGGATATTTTGATAATTTCACATTTCTCGGGAGACT
* * * * ** * **
25226856 GCTAGGATTCTAATTGCACTAAAAATCATGAAATATTATGAAATTAAGATTTGAAAAGTTTCATG
66 GCTAGGATTCTAAATGCACCAAAAATCAAGAAATATTATAAAATTAAGATTACAAAAATTTCACA
*
25226921 AAAATCTGAGCTTA
131 AAAATCTAAGCTTA
* * * *
25226935 AGAAGGCTAAATTACAAAAATATCCCTACAAGGATATTTTGATAATTTCACACTTT-TCGAGG-G
1 A-AATGTTAAATTACAAAAATATCCTTATAAGGATATTTTGATAATTTCACA-TTTCTCG-GGAG
** * * *
25226998 ACTGCTCTGATTTTAAATGCACCAAAAATTAAGAAATATTATAAAATTGAGA-TACAAAAATTTC
63 ACTGCTAGGATTCTAAATGCACCAAAAATCAAGAAATATTATAAAATTAAGATTACAAAAATTTC
25227062 ACAAAAATCTAAGCTTGA
128 ACAAAAATCTAAGCTT-A
*
25227080 AAATGTTAAATTACAAAAATATTCCTTATAAAGATATTTTGATAATTT
1 AAATGTTAAATTACAAAAATA-TCCTTATAAGGATATTTTGATAATTT
25227128 TTTCTTTCCC
Statistics
Matches: 156, Mismatches: 32, Indels: 9
0.79 0.16 0.05
Matches are distributed among these distances:
144 41 0.26
145 110 0.71
146 5 0.03
ACGTcount: A:0.42, C:0.12, G:0.13, T:0.34
Consensus pattern (144 bp):
AAATGTTAAATTACAAAAATATCCTTATAAGGATATTTTGATAATTTCACATTTCTCGGGAGACT
GCTAGGATTCTAAATGCACCAAAAATCAAGAAATATTATAAAATTAAGATTACAAAAATTTCACA
AAAATCTAAGCTTA
Found at i:25227552 original size:8 final size:8
Alignment explanation
Indices: 25227539--25227593 Score: 56
Period size: 8 Copynumber: 6.5 Consensus size: 8
25227529 AAACCATTGC
25227539 TTTTTTAT
1 TTTTTTAT
25227547 TTTTTTATTT
1 TTTTTTA--T
25227557 TTTTTTAT
1 TTTTTTAT
*
25227565 ATTTTTTGT
1 -TTTTTTAT
*
25227574 TTTTTCAT
1 TTTTTTAT
*
25227582 TTTTTTGT
1 TTTTTTAT
25227590 TTTT
1 TTTT
25227594 GTTTTCATTT
Statistics
Matches: 39, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
8 24 0.62
9 7 0.18
10 8 0.21
ACGTcount: A:0.09, C:0.02, G:0.04, T:0.85
Consensus pattern (8 bp):
TTTTTTAT
Found at i:25227567 original size:12 final size:11
Alignment explanation
Indices: 25227546--25227608 Score: 56
Period size: 12 Copynumber: 5.5 Consensus size: 11
25227536 TGCTTTTTTA
25227546 TTTTTTTATTT
1 TTTTTTTATTT
25227557 TTTTTTATATTT
1 TTTTTT-TATTT
*
25227569 TTTGTTTT-TTCA
1 TTT-TTTTATT-T
*
25227581 TTTTTTTGTTT
1 TTTTTTTATTT
*
25227592 TTGTTTTCATTT
1 TT-TTTTTATTT
25227604 TTTTT
1 TTTTT
25227609 ATGTTTTTGT
Statistics
Matches: 43, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
11 17 0.40
12 23 0.53
13 3 0.07
ACGTcount: A:0.08, C:0.03, G:0.05, T:0.84
Consensus pattern (11 bp):
TTTTTTTATTT
Found at i:25227584 original size:35 final size:36
Alignment explanation
Indices: 25227539--25227608 Score: 99
Period size: 35 Copynumber: 2.0 Consensus size: 36
25227529 AAACCATTGC
25227539 TTTTTTATTTTTTTATTTTT-TTTT-ATATTTTTTG
1 TTTTTTATTTTTTTATTTTTGTTTTCATATTTTTTG
* *
25227573 TTTTTTCATTTTTTTGTTTTTGTTTTCATTTTTTTT
1 TTTTTT-ATTTTTTTATTTTTGTTTTCATATTTTTT
25227609 ATGTTTTTGT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
34 6 0.19
35 13 0.42
36 4 0.13
37 8 0.26
ACGTcount: A:0.09, C:0.03, G:0.04, T:0.84
Consensus pattern (36 bp):
TTTTTTATTTTTTTATTTTTGTTTTCATATTTTTTG
Found at i:25227615 original size:8 final size:8
Alignment explanation
Indices: 25227558--25227637 Score: 53
Period size: 8 Copynumber: 10.2 Consensus size: 8
25227548 TTTTTATTTT
*
25227558 TTTTTATA
1 TTTTTATG
25227566 TTTTT-TG
1 TTTTTATG
25227573 TTTTTTCAT-
1 -TTTTT-ATG
25227582 TTTTT-TG
1 TTTTTATG
25227589 -TTTT-TG
1 TTTTTATG
* *
25227595 TTTTCATTT
1 TTTTTA-TG
25227604 TTTTTATG
1 TTTTTATG
*
25227612 TTTTTGTG
1 TTTTTATG
*
25227620 TTTTTGTG
1 TTTTTATG
25227628 TTTTTATG
1 TTTTTATG
25227636 TT
1 TT
25227638 GTTGTTTTTT
Statistics
Matches: 58, Mismatches: 7, Indels: 14
0.73 0.09 0.18
Matches are distributed among these distances:
6 7 0.12
7 4 0.07
8 40 0.69
9 6 0.10
10 1 0.02
ACGTcount: A:0.07, C:0.03, G:0.11, T:0.79
Consensus pattern (8 bp):
TTTTTATG
Found at i:25227623 original size:7 final size:8
Alignment explanation
Indices: 25227604--25227647 Score: 54
Period size: 8 Copynumber: 5.6 Consensus size: 8
25227594 GTTTTCATTT
*
25227604 TTTTTATG
1 TTTTTGTG
25227612 TTTTTGTG
1 TTTTTGTG
25227620 TTTTTGTG
1 TTTTTGTG
*
25227628 TTTTTATG
1 TTTTTGTG
*
25227636 TTGTTGT-
1 TTTTTGTG
25227643 TTTTT
1 TTTTT
25227648 TTTTAATTAT
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
7 4 0.13
8 27 0.87
ACGTcount: A:0.05, C:0.00, G:0.18, T:0.77
Consensus pattern (8 bp):
TTTTTGTG
Found at i:25227632 original size:47 final size:46
Alignment explanation
Indices: 25227555--25227645 Score: 121
Period size: 47 Copynumber: 2.0 Consensus size: 46
25227545 ATTTTTTTAT
* *
25227555 TTTTTTTTATATTTTTTGTTTTTTCATTTTTTTGTTTTTGTTTTCA
1 TTTTTTTTATATTTTTTGTTTTTTCATTTTTATGTTGTTGTTTTCA
* *
25227601 TTTTTTTTATGTTTTTGTGTTTTTGT-GTTTTTATGTTGTTGTTTT
1 TTTTTTTTATATTTTT-TGTTTTT-TCATTTTTATGTTGTTGTTTT
25227646 TTTTTTAATT
Statistics
Matches: 39, Mismatches: 4, Indels: 3
0.85 0.09 0.07
Matches are distributed among these distances:
46 15 0.38
47 23 0.59
48 1 0.03
ACGTcount: A:0.07, C:0.02, G:0.12, T:0.79
Consensus pattern (46 bp):
TTTTTTTTATATTTTTTGTTTTTTCATTTTTATGTTGTTGTTTTCA
Found at i:25228064 original size:70 final size:70
Alignment explanation
Indices: 25227990--25228171 Score: 193
Period size: 70 Copynumber: 2.6 Consensus size: 70
25227980 TCGGACTGCG
* * * * **
25227990 AGTCAGAAGACAAAGATGACCAAGATTGAACCGCAAGTGAAATAATAATGACCACTGGGACCAAG
1 AGTCAGAAGATAAAGATGATCAAGATTGAACCGCAAGTCAAAGAATAACAACCACTGGGACCAAG
25228055 CTATA
66 CTATA
* * * ** * ***
25228060 AGTCAAAAGATAAAGATGATTAGGATTGAACCGTGAGTCAAAGAATAACAACTACTGGGATTGAG
1 AGTCAGAAGATAAAGATGATCAAGATTGAACCGCAAGTCAAAGAATAACAACCACTGGGACCAAG
*
25228125 CTGTA
66 CTATA
* * *
25228130 AGTCAGAAGATAAAGATGATCGAGATTGAACCACGAGTCAAA
1 AGTCAGAAGATAAAGATGATCAAGATTGAACCGCAAGTCAAA
25228172 AAAATAAATA
Statistics
Matches: 90, Mismatches: 22, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
70 90 1.00
ACGTcount: A:0.43, C:0.15, G:0.23, T:0.19
Consensus pattern (70 bp):
AGTCAGAAGATAAAGATGATCAAGATTGAACCGCAAGTCAAAGAATAACAACCACTGGGACCAAG
CTATA
Found at i:25228169 original size:35 final size:34
Alignment explanation
Indices: 25228129--25228230 Score: 98
Period size: 36 Copynumber: 2.9 Consensus size: 34
25228119 ATTGAGCTGT
* *
25228129 AAGTCAGAAGATAAAGATGATCGAGATTGAACCAC
1 AAGTCAAAAAATAAA-ATGATCGAGATTGAACCAC
* * *
25228164 GAGTCAAAAAAATAAATATGATTG-GTATTGAACTAC
1 AAGTC-AAAAAATAAA-ATGATCGAG-ATTGAACCAC
*
25228200 AAGTAAAAAAATGAAAATGATCGAGATTGAA
1 AAGTCAAAAAAT-AAAATGATCGAGATTGAA
25228231 TCGTAAGTTG
Statistics
Matches: 54, Mismatches: 9, Indels: 8
0.76 0.13 0.11
Matches are distributed among these distances:
35 24 0.44
36 30 0.56
ACGTcount: A:0.50, C:0.09, G:0.20, T:0.22
Consensus pattern (34 bp):
AAGTCAAAAAATAAAATGATCGAGATTGAACCAC
Found at i:25228301 original size:211 final size:211
Alignment explanation
Indices: 25228080--25228592 Score: 527
Period size: 211 Copynumber: 2.4 Consensus size: 211
25228070 TAAAGATGAT
* * ** *** * *
25228080 TAGGATTGAACCGTGAGTCAAAGAATAACAACTACTGGGATTGAGCTGTAAGTCAGAAGATA-AA
1 TAGGATTGAACCATGAGTCAAAGAATAACAACGACTAAGACCAAGCCGTAAGTCAAAAGATAGAA
***
25228144 GATGA-TCGAGATTGAACCACGAGTCAAAAAAATAAATATGA-TTGGTATTGAA-CTACAAGTAA
66 -ATGACT-GAGATTGAACCACGAGTCAAAAAAATAAATATGACCAAG-ATTGAATC-ACAAGTAA
* ** * *
25228206 AAAAATGAAAATGATC-GAGATTGAA-TCGTAAGTTGAAAAATAAATATGACTGGGACTGAGCTA
127 AAAAATGAAAATGACCAG-GATTGAACT-GTAAGTTGAAAAATAAATATGACCAGGACTAAGCCA
25228269 TAAGTTAGAAGATAGATAAAAC
190 TAAGTTAGAAGATAGATAAAAC
*
25228291 TAGGATTGAACCATGAGTCAAATAATAACAACGACTAAGACCAAGCCGTAAGTCAAAAGATAGAA
1 TAGGATTGAACCATGAGTCAAAGAATAACAACGACTAAGACCAAGCCGTAAGTCAAAAGATAGAA
* * * *
25228356 ATGACTGAGATTGAACCATGAGTCAAAGAAATAAATATGACCAAGATTGAATCGCAAGTCAAAAA
66 ATGACTGAGATTGAACCACGAGTCAAAAAAATAAATATGACCAAGATTGAATCACAAGTAAAAAA
* *
25228421 ATGAAAATGACCAGGATTGAACTGTGAGTTGAGAAATAAATATGACCAGGACTAAGCCATAAGTT
131 ATGAAAATGACCAGGATTGAACTGTAAGTTGAAAAATAAATATGACCAGGACTAAGCCATAAGTT
* * ** *
25228486 AGAAGATAAAGATGAT
196 AGAAGATAGATAAAAC
* * * ** * ** * * * *
25228502 TGGGATTGAACCATAAGTCAAATAATAATGACAACTGGGACCAAGCCGCAAGTTAGAAGATACAA
1 TAGGATTGAACCATGAGTCAAAGAATAACAACGACTAAGACCAAGCCGTAAGTCAAAAGATAGAA
* *
25228567 ATGA-TGGAGATTAAACCATGAGTCAA
66 ATGACT-GAGATTGAACCACGAGTCAA
25228593 TGAATAACGA
Statistics
Matches: 254, Mismatches: 41, Indels: 14
0.82 0.13 0.05
Matches are distributed among these distances:
210 1 0.00
211 246 0.97
212 7 0.03
ACGTcount: A:0.45, C:0.12, G:0.21, T:0.21
Consensus pattern (211 bp):
TAGGATTGAACCATGAGTCAAAGAATAACAACGACTAAGACCAAGCCGTAAGTCAAAAGATAGAA
ATGACTGAGATTGAACCACGAGTCAAAAAAATAAATATGACCAAGATTGAATCACAAGTAAAAAA
ATGAAAATGACCAGGATTGAACTGTAAGTTGAAAAATAAATATGACCAGGACTAAGCCATAAGTT
AGAAGATAGATAAAAC
Found at i:25228318 original size:70 final size:71
Alignment explanation
Indices: 25228243--25228401 Score: 155
Period size: 70 Copynumber: 2.3 Consensus size: 71
25228233 GTAAGTTGAA
** ** * * *
25228243 AAATAAATATGACTGGGACTGAGCTATAAGTTAGAAGATAGATAA-AACT-AGGATTGAACCATG
1 AAATAAATATGACTAAGACCAAGCCATAAGTCAAAAGATAGA-AATAACTGA-GATTGAACCATG
25228306 AGTCAAA-
64 AGTCAAAG
* * * *
25228313 TAATAACA-ACGACTAAGACCAAGCCGTAAGTCAAAAGATAGAAATGACTGAGATTGAACCATGA
1 AAATAA-ATATGACTAAGACCAAGCCATAAGTCAAAAGATAGAAATAACTGAGATTGAACCATGA
25228377 GTCAAAG
65 GTCAAAG
*
25228384 AAATAAATATGACCAAGA
1 AAATAAATATGACTAAGA
25228402 TTGAATCGCA
Statistics
Matches: 70, Mismatches: 14, Indels: 9
0.75 0.15 0.10
Matches are distributed among these distances:
69 2 0.03
70 53 0.76
71 15 0.21
ACGTcount: A:0.48, C:0.13, G:0.19, T:0.19
Consensus pattern (71 bp):
AAATAAATATGACTAAGACCAAGCCATAAGTCAAAAGATAGAAATAACTGAGATTGAACCATGAG
TCAAAG
Found at i:25228403 original size:36 final size:36
Alignment explanation
Indices: 25228363--25228468 Score: 105
Period size: 35 Copynumber: 3.0 Consensus size: 36
25228353 GAAATGACTG
25228363 AGATTGAACCATGAGTCAAAGAAATAAATATGACCA
1 AGATTGAACCATGAGTCAAAGAAATAAATATGACCA
25228399 AGATTGAATCGCA--AGTCAAA-AAATGAAA-ATGACCA
1 AGATTGAA-C-CATGAGTCAAAGAAAT-AAATATGACCA
* ** **
25228434 GGATTGAACTGTGAGT-TGAGAAATAAATATGACCA
1 AGATTGAACCATGAGTCAAAGAAATAAATATGACCA
25228469 GGACTAAGCC
Statistics
Matches: 58, Mismatches: 5, Indels: 15
0.74 0.06 0.19
Matches are distributed among these distances:
34 5 0.09
35 32 0.55
36 18 0.31
37 1 0.02
38 2 0.03
ACGTcount: A:0.47, C:0.12, G:0.20, T:0.21
Consensus pattern (36 bp):
AGATTGAACCATGAGTCAAAGAAATAAATATGACCA
Found at i:25228669 original size:211 final size:211
Alignment explanation
Indices: 25228198--25228676 Score: 484
Period size: 211 Copynumber: 2.3 Consensus size: 211
25228188 GTATTGAACT
* * * **
25228198 ACAAGTAAAAAAATGAAAATGATCGAGATTGAA-T-CGTAAGTTGAA-AAATAAATATGACTGGG
1 ACAAGTCAAAAAATGAAAATGACCAAGATTGAACTACG--AGTT-AAGAAATAAATATGACCAGG
* * * * * *
25228260 ACTGAGCTATAAGTTAGAAGATAGATAAAACTAGGATTGAACCATGAGTCAAATAATAACAACGA
63 ACTAAGCCATAAGTTAGAAGATAAAGAAAACTAGGATTGAACCATAAGTCAAATAATAACAACAA
* * *
25228325 CTAAGACCAAGCCGTAAGTCAAAAGATAGAAATGACTGAGATTGAACCATGAGTCAAAGAAATAA
128 CTAAGACCAAGCCGCAAGTCAAAAGATACAAATGACTGAGATTAAACCATGAGTCAAAGAAATAA
* *
25228390 ATATGACCAAGATTGAATC
193 AGATGACCAAGACTGAATC
* * ** *
25228409 GCAAGTCAAAAAATGAAAATGACCAGGATTGAACTGTGAGTTGAGAAATAAATATGACCAGGACT
1 ACAAGTCAAAAAATGAAAATGACCAAGATTGAACTACGAGTTAAGAAATAAATATGACCAGGACT
** * * ** *
25228474 AAGCCATAAGTTAGAAGATAAAGATGATTGGGATTGAACCATAAGTCAAATAATAATGACAACTG
66 AAGCCATAAGTTAGAAGATAAAGAAAACTAGGATTGAACCATAAGTCAAATAATAACAACAACTA
* * * * *
25228539 GGACCAAGCCGCAAGTTAGAAGATACAAATGA-TGGAGATTAAACCATGAGTCAATG-AATAACG
131 AGACCAAGCCGCAAGTCAAAAGATACAAATGACT-GAGATTAAACCATGAGTCAAAGAAATAAAG
*** *
25228602 ATGATTGAGACTGAGTC
195 ATGACCAAGACTGAATC
* * * * *
25228619 ACAAGTCAGAAGAT-ACAGATGACTAAGATTGATCTACGAGTTAAAGAAATAAATATGA
1 ACAAGTCAAAAAATGA-AAATGACCAAGATTGAACTACGAGTT-AAGAAATAAATATGA
25228677 TCGAGATTGA
Statistics
Matches: 216, Mismatches: 46, Indels: 12
0.79 0.17 0.04
Matches are distributed among these distances:
209 1 0.00
210 50 0.23
211 163 0.75
212 1 0.00
213 1 0.00
ACGTcount: A:0.46, C:0.12, G:0.21, T:0.21
Consensus pattern (211 bp):
ACAAGTCAAAAAATGAAAATGACCAAGATTGAACTACGAGTTAAGAAATAAATATGACCAGGACT
AAGCCATAAGTTAGAAGATAAAGAAAACTAGGATTGAACCATAAGTCAAATAATAACAACAACTA
AGACCAAGCCGCAAGTCAAAAGATACAAATGACTGAGATTAAACCATGAGTCAAAGAAATAAAGA
TGACCAAGACTGAATC
Found at i:25228790 original size:70 final size:71
Alignment explanation
Indices: 25228708--25228863 Score: 187
Period size: 70 Copynumber: 2.2 Consensus size: 71
25228698 AATAATGAAA
* * *
25228708 ATGATC-GAGATTGAATTGTGAGTC-AATAAATAAATATGACTAGCACTGAA-CCAC-AGTCAAA
1 ATGATCAGAGATTGAACTGTGAGTCGAAT-AATAAAGATGACTAGCA-TCAAGCCACAAGTCAAA
25228769 AGATAGAG
64 AGATAGAG
* * * * *
25228777 ATGATCAGGGATTGAACTGTGAGTCGAATAATAACGATGATTGGGATCAAGCCACAAGTCAAAAG
1 ATGATCAGAGATTGAACTGTGAGTCGAATAATAAAGATGACTAGCATCAAGCCACAAGTCAAAAG
25228842 ATAGAG
66 ATAGAG
25228848 ATGATCA-AGATTGAAC
1 ATGATCAGAGATTGAAC
25228864 CAAGAGTCAA
Statistics
Matches: 74, Mismatches: 9, Indels: 7
0.82 0.10 0.08
Matches are distributed among these distances:
69 9 0.12
70 40 0.54
71 25 0.34
ACGTcount: A:0.42, C:0.13, G:0.23, T:0.22
Consensus pattern (71 bp):
ATGATCAGAGATTGAACTGTGAGTCGAATAATAAAGATGACTAGCATCAAGCCACAAGTCAAAAG
ATAGAG
Found at i:25228790 original size:281 final size:281
Alignment explanation
Indices: 25228340--25228880 Score: 622
Period size: 281 Copynumber: 1.9 Consensus size: 281
25228330 ACCAAGCCGT
* * *
25228340 AAGTCAAAAGATAGAAATGACTGAGATTGAACCATGAGTCAAAGAAATAAATATGACCAAGATTG
1 AAGTCAAAAGATACAAATGACTAAGATTGAACCACGAGTCAAAGAAATAAATATGACCAAGATTG
**
25228405 AATCGCAAGTCAAAAAATGAAAATGACCAGGATTGAACTGTGAGTTGAGAAATAAATATGACCAG
66 AATCGCAAGTCAAAAAATGAAAATGACCAGGATTGAACTGTGAGTCAAGAAATAAATATGACCAG
* * * * *
25228470 GACTAAGCCATAAGTTAGAAGATAAAGATGATTGGGATTGAACCATAAGTCAAATAATAATGACA
131 CACTAAGCCATAAGTCAAAAGATAAAGATGATAGGGATTGAACCATAAGTCAAATAATAACGACA
* * * ** * *
25228535 ACTGGGACCAAGCCGCAAGTTAGAAGATACAAATGATGGAGATTAAACCATGAGTCAATGAATAA
196 ACTGGGACCAAGCCACAAGTCAAAAGATACAAATGATCAAGATTAAACCAAGAGTCAAAGAATAA
25228600 CGATGATTGAGACTGAGTCAC
261 CGATGATTGAGACTGAGTCAC
* * * * * * *
25228621 AAGTCAGAAGATACAGATGACTAAGATTGATCTACGAGTTAAAGAAATAAATATGATCGAGATTG
1 AAGTCAAAAGATACAAATGACTAAGATTGAACCACGAGTCAAAGAAATAAATATGACCAAGATTG
** * * * * *
25228686 AA-CTGCAAGTTGAATAATGAAAATGATC-GAGATTGAATTGTGAGTCAATAAATAAATATGACT
66 AATC-GCAAGTCAAAAAATGAAAATGACCAG-GATTGAACTGTGAGTCAAGAAATAAATATGACC
* * ** * *
25228749 AGCACTGAA-CCA-CAGTCAAAAGATAGAGATGATCAGGGATTGAACTGTGAGTCGAATAATAAC
129 AGCACT-AAGCCATAAGTCAAAAGATAAAGATGAT-AGGGATTGAACCATAAGTCAAATAATAAC
** * * * * *
25228812 GATGATTGGGATCAAGCCACAAGTCAAAAGATAGAGATGATCAAGATTGAACCAAGAGTCAAAGA
192 GACAACTGGGACCAAGCCACAAGTCAAAAGATACAAATGATCAAGATTAAACCAAGAGTCAAAGA
25228877 ATAA
257 ATAA
25228881 TGAAACCAAG
Statistics
Matches: 212, Mismatches: 44, Indels: 8
0.80 0.17 0.03
Matches are distributed among these distances:
280 19 0.09
281 191 0.90
282 2 0.01
ACGTcount: A:0.45, C:0.12, G:0.22, T:0.21
Consensus pattern (281 bp):
AAGTCAAAAGATACAAATGACTAAGATTGAACCACGAGTCAAAGAAATAAATATGACCAAGATTG
AATCGCAAGTCAAAAAATGAAAATGACCAGGATTGAACTGTGAGTCAAGAAATAAATATGACCAG
CACTAAGCCATAAGTCAAAAGATAAAGATGATAGGGATTGAACCATAAGTCAAATAATAACGACA
ACTGGGACCAAGCCACAAGTCAAAAGATACAAATGATCAAGATTAAACCAAGAGTCAAAGAATAA
CGATGATTGAGACTGAGTCAC
Found at i:25228943 original size:34 final size:35
Alignment explanation
Indices: 25228832--25228986 Score: 91
Period size: 34 Copynumber: 4.5 Consensus size: 35
25228822 ATCAAGCCAC
* * **
25228832 AAGTCAAAAGATAGAGATGATCAAGATTGAACCA-
1 AAGTCAAAAAATAAAGACAATCAAGATTGAACCAT
* * * *
25228866 AGAGTCAAAGAATAATGA-AACCAAGATTGAACCAC
1 A-AGTCAAAAAATAAAGACAATCAAGATTGAACCAT
** * * *
25228901 GGGCCAAAAAATAAAGA-GATTAAGATTGAACCAT
1 AAGTCAAAAAATAAAGACAATCAAGATTGAACCAT
* * *** *
25228935 AAGTCAAAAATTAAAAACAATTGGGATTGAATCAT
1 AAGTCAAAAAATAAAGACAATCAAGATTGAACCAT
* *
25228970 GAGTTAAAAAATAAAGA
1 AAGTCAAAAAATAAAGA
25228987 TGATCGAGAT
Statistics
Matches: 90, Mismatches: 28, Indels: 5
0.73 0.23 0.04
Matches are distributed among these distances:
34 52 0.58
35 38 0.42
ACGTcount: A:0.52, C:0.11, G:0.18, T:0.19
Consensus pattern (35 bp):
AAGTCAAAAAATAAAGACAATCAAGATTGAACCAT
Found at i:25229103 original size:36 final size:37
Alignment explanation
Indices: 25229063--25229134 Score: 101
Period size: 36 Copynumber: 2.0 Consensus size: 37
25229053 AAGAACAATA
** **
25229063 AGGATGACATTGTAAGTTGAAAAAT-AAAAAATGACT
1 AGGATGACATCATAAGTCAAAAAATAAAAAAATGACT
25229099 AGGATGACATCATAAGTCAAAAAATAAAAAAATGAC
1 AGGATGACATCATAAGTCAAAAAATAAAAAAATGAC
25229135 CAAACAAAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
36 21 0.68
37 10 0.32
ACGTcount: A:0.54, C:0.08, G:0.17, T:0.21
Consensus pattern (37 bp):
AGGATGACATCATAAGTCAAAAAATAAAAAAATGACT
Found at i:25229275 original size:37 final size:37
Alignment explanation
Indices: 25229215--25229305 Score: 125
Period size: 37 Copynumber: 2.5 Consensus size: 37
25229205 CAAGATAACA
* ** *
25229215 ACTA-AAGTCAAAAAAT-AATGGGCAATTGGGACAAC
1 ACTATAAGTCAAAAAATAAAAGGGCAACCGAGACAAC
25229250 ACTATAAGTCAAAAAATAAAAGGGCAACCGAGACAAC
1 ACTATAAGTCAAAAAATAAAAGGGCAACCGAGACAAC
25229287 ACTATAAGT-AAAAAATAAA
1 ACTATAAGTCAAAAAATAAA
25229306 GAACAATCGG
Statistics
Matches: 50, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
35 4 0.08
36 22 0.44
37 24 0.48
ACGTcount: A:0.55, C:0.14, G:0.15, T:0.15
Consensus pattern (37 bp):
ACTATAAGTCAAAAAATAAAAGGGCAACCGAGACAAC
Found at i:25229410 original size:109 final size:110
Alignment explanation
Indices: 25229290--25229565 Score: 307
Period size: 109 Copynumber: 2.5 Consensus size: 110
25229280 AGACAACACT
* * * **
25229290 ATAAGT-AAAAAATAAAGAACAATCGGGATGACACT-GTAAGC-CAAAAA-TAAAGAATGTGATC
1 ATAAGTCAAAAAATGAAGAACAATCGGGATGACACTCATAAGCAAAAAAAGTAAA-AA-AAGATC
* * *
25229351 GGGATAACATCGTAAGTCAAAAAATAAAGAACGATTGA-AGTGACATC
64 GAGACAACATCGCAAGTCAAAAAATAAAGAACGATTGAGA-TGACATC
*
25229398 ATAAGTCAAAAAATGAAGAACAA-CTGGGATGAC-GTCATAAGCAAAAAAAGTAAAAAAAGATCG
1 ATAAGTCAAAAAATGAAGAACAATC-GGGATGACACTCATAAGCAAAAAAAGTAAAAAAAGATCG
*
25229461 AGACAACATTGCAAGTCAAAAAATAAAGAACGATTGAGATGACATC
65 AGACAACATCGCAAGTCAAAAAATAAAGAACGATTGAGATGACATC
* * * * * *
25229507 ATAACTCAAAAAATGAAGAACGATTGGGATGACAC-CACAAGTCAAAAAATGAAAAAAAA
1 ATAAGTCAAAAAATGAAGAACAATCGGGATGACACTCATAAG-CAAAAAAAGTAAAAAAA
25229566 CTAAGATGAC
Statistics
Matches: 142, Mismatches: 17, Indels: 16
0.81 0.10 0.09
Matches are distributed among these distances:
108 8 0.06
109 107 0.75
110 23 0.16
111 4 0.03
ACGTcount: A:0.53, C:0.13, G:0.18, T:0.16
Consensus pattern (110 bp):
ATAAGTCAAAAAATGAAGAACAATCGGGATGACACTCATAAGCAAAAAAAGTAAAAAAAGATCGA
GACAACATCGCAAGTCAAAAAATAAAGAACGATTGAGATGACATC
Found at i:25229446 original size:73 final size:71
Alignment explanation
Indices: 25229369--25229576 Score: 177
Period size: 73 Copynumber: 2.9 Consensus size: 71
25229359 ATCGTAAGTC
* * *
25229369 AAAAAATAAAGAACGATTGAAGTGACATCATAAGTCAAAAAATGAAGAACAACTGGGATGACGTC
1 AAAAAATAAAGAACGATTG-AGTGACAACATAAGTCAAAAAATGAAGAACAACTGAGATGACATC
25229434 ATAAGCAA
65 ATAA-CAA
* * * * * * *
25229442 AAAAAGTAAAAAAAGATCGA--GACAACATTGCAAGTCAAAAAATAAAGAACGATTGAGATGACA
1 AAAAAATAAAGAACGATTGAGTGACAACA-T--AAGTCAAAAAATGAAGAACAACTGAGATGACA
**
25229505 TCATAACTC
63 TCATAACAA
* * * * * * *
25229514 AAAAAATGAAGAACGATTGGGATGACACCACAAGTCAAAAAATGAAAAAAAACTAAGATGACA
1 AAAAAATAAAGAACGATTGAG-TGACAACATAAGTCAAAAAATGAAGAACAACTGAGATGACA
25229577 CTGCAAGTTG
Statistics
Matches: 103, Mismatches: 26, Indels: 13
0.73 0.18 0.09
Matches are distributed among these distances:
70 6 0.06
71 1 0.01
72 42 0.41
73 48 0.47
75 6 0.06
ACGTcount: A:0.54, C:0.13, G:0.17, T:0.15
Consensus pattern (71 bp):
AAAAAATAAAGAACGATTGAGTGACAACATAAGTCAAAAAATGAAGAACAACTGAGATGACATCA
TAACAA
Found at i:25229559 original size:36 final size:36
Alignment explanation
Indices: 25229290--25229556 Score: 202
Period size: 36 Copynumber: 7.4 Consensus size: 36
25229280 AGACAACACT
* *
25229290 ATAAGT-AAAAAATAAAGAACAATCGGGATGACA-C
1 ATAAGTCAAAAAATAAAGAACGATTGGGATGACATC
* * * * *
25229324 TGTAAG-CCAAAAATAAAGAATGTGATCGGGATAACATC
1 -ATAAGTCAAAAAATAAAGAA--CGATTGGGATGACATC
* *
25229362 GTAAGTCAAAAAATAAAGAACGATT-GAAGTGACATC
1 ATAAGTCAAAAAATAAAGAACGATTGGGA-TGACATC
* * * *
25229398 ATAAGTCAAAAAATGAAGAACAACTGGGATGACGTC
1 ATAAGTCAAAAAATAAAGAACGATTGGGATGACATC
* * * * ** *
25229434 ATAAG-CAAAAAAAGTAAAAAAAGATCGAGACAACATT
1 ATAAGTC-AAAAAA-TAAAGAACGATTGGGATGACATC
** *
25229471 GCAAGTCAAAAAATAAAGAACGATTGAGATGACATC
1 ATAAGTCAAAAAATAAAGAACGATTGGGATGACATC
* * *
25229507 ATAACTCAAAAAATGAAGAACGATTGGGATGACACC
1 ATAAGTCAAAAAATAAAGAACGATTGGGATGACATC
*
25229543 ACAAGTCAAAAAAT
1 ATAAGTCAAAAAAT
25229557 GAAAAAAAAC
Statistics
Matches: 179, Mismatches: 43, Indels: 19
0.74 0.18 0.08
Matches are distributed among these distances:
35 19 0.11
36 106 0.59
37 39 0.22
38 15 0.08
ACGTcount: A:0.52, C:0.13, G:0.18, T:0.17
Consensus pattern (36 bp):
ATAAGTCAAAAAATAAAGAACGATTGGGATGACATC
Found at i:25229574 original size:36 final size:37
Alignment explanation
Indices: 25229534--25229632 Score: 103
Period size: 37 Copynumber: 2.7 Consensus size: 37
25229524 GAACGATTGG
*
25229534 GATGACACCACAAGTCAAAAAATGAAAAAAA-ACTAA
1 GATGACACCGCAAGTCAAAAAATGAAAAAAAGACTAA
* **
25229570 GATGACACTGCAAGTTGAAAAAT-AAAAAAATGACTAA
1 GATGACACCGCAAGTCAAAAAATGAAAAAAA-GACTAA
** * *
25229607 GACAATATCGCAAGTCAAAAAATGAA
1 GATGACACCGCAAGTCAAAAAATGAA
25229633 GAATGATCAA
Statistics
Matches: 49, Mismatches: 11, Indels: 4
0.77 0.17 0.06
Matches are distributed among these distances:
35 7 0.14
36 19 0.39
37 21 0.43
38 2 0.04
ACGTcount: A:0.57, C:0.14, G:0.14, T:0.15
Consensus pattern (37 bp):
GATGACACCGCAAGTCAAAAAATGAAAAAAAGACTAA
Found at i:25229591 original size:109 final size:109
Alignment explanation
Indices: 25229364--25229595 Score: 292
Period size: 109 Copynumber: 2.1 Consensus size: 109
25229354 ATAACATCGT
*
25229364 AAGTCAAAAAATAAAGAACGATTGAAGTGACATCATAAGTCAAAAAATGAAGAACAACTGGGATG
1 AAGTCAAAAAATAAAGAACGATTGAAGTGACATCATAACTCAAAAAATGAAGAACAACTGGGATG
** * * *
25229429 ACGTCATAAGCAAAAAAAGTAAAAAAAGATCGAGACAACATTGC
66 ACACCACAAGCAAAAAAAGTAAAAAAAGATCAAGACAACACTGC
* *
25229473 AAGTCAAAAAATAAAGAACGATTG-AGATGACATCATAACTCAAAAAATGAAGAACGATTGGGAT
1 AAGTCAAAAAATAAAGAACGATTGAAG-TGACATCATAACTCAAAAAATGAAGAACAACTGGGAT
* **
25229537 GACACCACAAGTCAAAAAATG-AAAAAAA-A-CTAAGATGACACTGC
65 GACACCACAAG-CAAAAAAAGTAAAAAAAGATC-AAGACAACACTGC
**
25229581 AAGTTGAAAAATAAA
1 AAGTCAAAAAATAAA
25229596 AAAATGACTA
Statistics
Matches: 107, Mismatches: 13, Indels: 7
0.84 0.10 0.06
Matches are distributed among these distances:
107 1 0.01
108 25 0.23
109 73 0.68
110 8 0.07
ACGTcount: A:0.54, C:0.13, G:0.17, T:0.16
Consensus pattern (109 bp):
AAGTCAAAAAATAAAGAACGATTGAAGTGACATCATAACTCAAAAAATGAAGAACAACTGGGATG
ACACCACAAGCAAAAAAAGTAAAAAAAGATCAAGACAACACTGC
Found at i:25229810 original size:37 final size:36
Alignment explanation
Indices: 25229713--25229808 Score: 95
Period size: 37 Copynumber: 2.6 Consensus size: 36
25229703 AAAATGATTG
* *
25229713 AGACGATACCATAAGTCAAAAATAAAGAACATGATCA
1 AGACAATACCATAAGTAAAAAATAAAGAACA-GATCA
* * *
25229750 AGACAATACCACAAGTTAGAAAATAAAGAAC-GATCGG
1 AGACAATACCATAAG-TAAAAAATAAAGAACAGATC-A
* *
25229787 GGACATTACCATAAGTAAAAAA
1 AGACAATACCATAAGTAAAAAA
25229809 ATGAAGAATG
Statistics
Matches: 48, Mismatches: 9, Indels: 5
0.77 0.15 0.08
Matches are distributed among these distances:
36 10 0.21
37 25 0.52
38 13 0.27
ACGTcount: A:0.53, C:0.16, G:0.16, T:0.16
Consensus pattern (36 bp):
AGACAATACCATAAGTAAAAAATAAAGAACAGATCA
Found at i:25230086 original size:36 final size:36
Alignment explanation
Indices: 25230041--25230200 Score: 112
Period size: 36 Copynumber: 4.5 Consensus size: 36
25230031 ACGAAACCAT
* *** *
25230041 AAGTAAAAAAATAAAGAACAATTGGGATGACATTGC
1 AAGTCAAAAAATAAAGAACAATCAAGATGACATCGC
* ** * *
25230077 AAGTCAAAAAATGAAGAATGACCAAGATGACATCAC
1 AAGTCAAAAAATAAAGAACAATCAAGATGACATCGC
** * *
25230113 AAG-CTAAAAAATAAA-AA-AATCAAGACAACACCGT
1 AAGTC-AAAAAATAAAGAACAATCAAGATGACATCGC
** **
25230147 AAGTCAAAAAATAAAGAACAATCGGGATGACA-CTTT
1 AAGTCAAAAAATAAAGAACAATCAAGATGACATC-GC
25230183 AAGTCAAAAAATAAAGAA
1 AAGTCAAAAAATAAAGAA
25230201 TGATTAGGAC
Statistics
Matches: 96, Mismatches: 23, Indels: 10
0.74 0.18 0.08
Matches are distributed among these distances:
34 23 0.24
35 7 0.07
36 66 0.69
ACGTcount: A:0.56, C:0.13, G:0.15, T:0.16
Consensus pattern (36 bp):
AAGTCAAAAAATAAAGAACAATCAAGATGACATCGC
Found at i:25230543 original size:38 final size:38
Alignment explanation
Indices: 25230426--25230559 Score: 130
Period size: 38 Copynumber: 3.6 Consensus size: 38
25230416 TAAACGACAT
* ** ** *
25230426 CATAAGTTAATAAAATAATGAACATGACCGGGATAGCAC
1 CATAAGTGAA-AAAATAAAAAACATGATTGGGATAACAC
* * *
25230465 CACAAGTCAAAAAAT-AAAAA-ATGATTGGGATGACAC
1 CATAAGTGAAAAAATAAAAAACATGATTGGGATAACAC
* *
25230501 CATAAGTGAAAAAATAAAAAACATGATTGGGACAACAT
1 CATAAGTGAAAAAATAAAAAACATGATTGGGATAACAC
25230539 CATAAGTTG-AAAAATAAAAAA
1 CATAAG-TGAAAAAATAAAAAA
25230560 TGACTAAGAC
Statistics
Matches: 79, Mismatches: 13, Indels: 7
0.80 0.13 0.07
Matches are distributed among these distances:
36 25 0.32
37 8 0.10
38 36 0.46
39 10 0.13
ACGTcount: A:0.54, C:0.12, G:0.16, T:0.19
Consensus pattern (38 bp):
CATAAGTGAAAAAATAAAAAACATGATTGGGATAACAC
Found at i:25242571 original size:146 final size:144
Alignment explanation
Indices: 25242372--25242784 Score: 496
Period size: 146 Copynumber: 2.8 Consensus size: 144
25242362 TCAATTTTTG
* * * *
25242372 GATTTTAAAT-CACCAAAATTCATGAAGTATTATGAAATTAAGATCT-GAAAAGTTTCATGAAAA
1 GATTTAAAATGCACCAAAAATCATGAAATATTATGAAATTAAGATCTAG-AAAGTTTCATAAAAA
*
25242435 TTCAAGCTCGGAAAGGCTAAATTATGAAAATACCCCTATAAGGGTATTTTGATAATTTCACACTT
65 TCCAAGCTCGGAAAGGCTAAATTAT-AAAATACCCCTATAAGGGTATTTTGATAATTTCACACTT
25242500 CTTG-GGGTATTGCTGT
129 CTTGAGGG-ATTGCTGT
* *
25242516 GATTTAAAATGCATCAAAAATCATGAAATATTATGAAAGTTAAGATCTAGGAAGTTTCATAAAAA
1 GATTTAAAATGCACCAAAAATCATGAAATATTATGAAA-TTAAGATCTAGAAAGTTTCATAAAAA
* * * * * *
25242581 TCCAAGCTCGGGAAGGCCAAACTATAAAATTACCCCTACAAGGGTATTTTGATAATTTCATATTT
65 TCCAAGCTCGGAAAGGCTAAATTATAAAA-TACCCCTATAAGGGTATTTTGATAATTTCACACTT
*
25242646 TTTGAGGGATTGCTGT
129 CTTGAGGGATTGCTGT
* * * * * *
25242662 GATTTCAAATGCACCACAAATCATGAAATGTTATAAAATTGAA-ATCTAAAAAGTTTCACAAAAA
1 GATTTAAAATGCACCAAAAATCATGAAATATTATGAAATT-AAGATCTAGAAAGTTTCATAAAAA
* *
25242726 TCCAAGCTC-GAGAAGG-TCAAATTACAAAAATAACCCTTATAAGGGTATTTTGATAATTT
65 TCCAAGCTCGGA-AAGGCT-AAATTA-TAAAAT-ACCCCTATAAGGGTATTTTGATAATTT
25242785 TATTTTTTTC
Statistics
Matches: 231, Mismatches: 28, Indels: 18
0.83 0.10 0.06
Matches are distributed among these distances:
144 10 0.04
145 67 0.29
146 150 0.65
147 4 0.02
ACGTcount: A:0.40, C:0.14, G:0.15, T:0.31
Consensus pattern (144 bp):
GATTTAAAATGCACCAAAAATCATGAAATATTATGAAATTAAGATCTAGAAAGTTTCATAAAAAT
CCAAGCTCGGAAAGGCTAAATTATAAAATACCCCTATAAGGGTATTTTGATAATTTCACACTTCT
TGAGGGATTGCTGT
Found at i:25245502 original size:12 final size:12
Alignment explanation
Indices: 25245487--25245511 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
25245477 TTTCGTTTCT
25245487 TATTTCTTTTTG
1 TATTTCTTTTTG
25245499 TATTTCTTTTTG
1 TATTTCTTTTTG
25245511 T
1 T
25245512 TTAAGTGAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.08, C:0.08, G:0.08, T:0.76
Consensus pattern (12 bp):
TATTTCTTTTTG
Found at i:25253107 original size:29 final size:28
Alignment explanation
Indices: 25253058--25253127 Score: 77
Period size: 29 Copynumber: 2.4 Consensus size: 28
25253048 ATTTAAAGGC
* *
25253058 AAATTCTATGGCTGCCCTTTGACCAAAA
1 AAATTCTATGGCCGCCATTTGACCAAAA
* *
25253086 AAATGTCTCTGGCCGCCATTTGAGCAAAAA
1 AAAT-TCTATGGCCGCCATTTGA-CCAAAA
*
25253116 AAATTTTATGGC
1 AAATTCTATGGC
25253128 TGCCGTAGAC
Statistics
Matches: 34, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
28 4 0.12
29 21 0.62
30 9 0.26
ACGTcount: A:0.33, C:0.21, G:0.17, T:0.29
Consensus pattern (28 bp):
AAATTCTATGGCCGCCATTTGACCAAAA
Found at i:25255483 original size:30 final size:30
Alignment explanation
Indices: 25255449--25255528 Score: 76
Period size: 29 Copynumber: 2.7 Consensus size: 30
25255439 AAAGGAAGGG
* *
25255449 TTAATGTCATCTTTAAATTATTACGAAA-TT
1 TTAATGTAATCTTTAAATTATTA-AAAATTT
* *
25255479 TTAATATAATATTTAAATT-TTAAAAATTT
1 TTAATGTAATCTTTAAATTATTAAAAATTT
*
25255508 TTAATGTGA-CATTTAAATTAT
1 TTAATGTAATC-TTTAAATTAT
25255529 AAATCTACTA
Statistics
Matches: 40, Mismatches: 7, Indels: 6
0.75 0.13 0.11
Matches are distributed among these distances:
28 3 0.08
29 20 0.50
30 17 0.43
ACGTcount: A:0.41, C:0.05, G:0.05, T:0.49
Consensus pattern (30 bp):
TTAATGTAATCTTTAAATTATTAAAAATTT
Found at i:25256535 original size:17 final size:17
Alignment explanation
Indices: 25256509--25256567 Score: 52
Period size: 17 Copynumber: 3.6 Consensus size: 17
25256499 AATATTTTAT
*
25256509 TTTATAAAAAAATATTA
1 TTTATCAAAAAATATTA
*
25256526 TTTATCAAAAATAAATT-
1 TTTATCAAAAA-ATATTA
* *
25256543 TTTATC-ATATATATTA
1 TTTATCAAAAAATATTA
25256559 TTT-TCAAAA
1 TTTATCAAAA
25256568 TTTTAATATA
Statistics
Matches: 33, Mismatches: 6, Indels: 7
0.72 0.13 0.15
Matches are distributed among these distances:
15 6 0.18
16 7 0.21
17 16 0.48
18 4 0.12
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (17 bp):
TTTATCAAAAAATATTA
Found at i:25264240 original size:13 final size:13
Alignment explanation
Indices: 25264222--25264247 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
25264212 AACCATGTTT
25264222 AATAACTACTACC
1 AATAACTACTACC
25264235 AATAACTACTACC
1 AATAACTACTACC
25264248 CACTAATCTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.31, G:0.00, T:0.23
Consensus pattern (13 bp):
AATAACTACTACC
Found at i:25271013 original size:5 final size:5
Alignment explanation
Indices: 25270998--25271028 Score: 53
Period size: 5 Copynumber: 6.2 Consensus size: 5
25270988 ATTATGGGTA
*
25270998 AGATT AAATT AGATT AGATT AGATT AGATT A
1 AGATT AGATT AGATT AGATT AGATT AGATT A
25271029 AATGATGTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.45, C:0.00, G:0.16, T:0.39
Consensus pattern (5 bp):
AGATT
Found at i:25271827 original size:8 final size:8
Alignment explanation
Indices: 25271814--25271889 Score: 64
Period size: 8 Copynumber: 9.0 Consensus size: 8
25271804 AAAAATTTTC
25271814 GAAAAAAA
1 GAAAAAAA
25271822 GAAAAAGAGA
1 GAAAAA-A-A
25271832 GAAAGAAAA
1 GAAA-AAAA
25271841 GAGAAAAAA
1 GA-AAAAAA
**
25271850 GAAATGAA
1 GAAAAAAA
*
25271858 -AAAAATA
1 GAAAAAAA
25271865 GAAAAAAA
1 GAAAAAAA
*
25271873 GGAAAAAAG
1 -GAAAAAAA
25271882 GAAAAAAA
1 GAAAAAAA
25271890 ATAAAAAAAT
Statistics
Matches: 54, Mismatches: 8, Indels: 12
0.73 0.11 0.16
Matches are distributed among these distances:
7 4 0.07
8 23 0.43
9 17 0.31
10 8 0.15
11 2 0.04
ACGTcount: A:0.78, C:0.00, G:0.20, T:0.03
Consensus pattern (8 bp):
GAAAAAAA
Found at i:25271827 original size:9 final size:9
Alignment explanation
Indices: 25271815--25271898 Score: 62
Period size: 9 Copynumber: 8.7 Consensus size: 9
25271805 AAAATTTTCG
25271815 AAAAAAAGA
1 AAAAAAAGA
*
25271824 AAAAGAGAGA
1 AAAA-AAAGA
25271834 AAGAAAAGAGAA
1 AA-AAAA-AG-A
25271846 AAAAGAAATGA
1 AAAA-AAA-GA
25271857 AAAAAATAG-
1 AAAAAA-AGA
*
25271866 AAAAAAAGG
1 AAAAAAAGA
*
25271875 AAAAAAGGA
1 AAAAAAAGA
*
25271884 AAAAAAATA
1 AAAAAAAGA
25271893 AAAAAA
1 AAAAAA
25271899 TTGTTTGAGT
Statistics
Matches: 61, Mismatches: 6, Indels: 16
0.73 0.07 0.19
Matches are distributed among these distances:
8 2 0.03
9 30 0.49
10 10 0.16
11 13 0.21
12 6 0.10
ACGTcount: A:0.80, C:0.00, G:0.17, T:0.04
Consensus pattern (9 bp):
AAAAAAAGA
Found at i:25271840 original size:19 final size:18
Alignment explanation
Indices: 25271814--25271859 Score: 51
Period size: 19 Copynumber: 2.5 Consensus size: 18
25271804 AAAAATTTTC
25271814 GAAA-AAAAGA-AAAAGAGA
1 GAAAGAAAAGAGAAAA-A-A
25271832 GAAAGAAAAGAGAAAAAA
1 GAAAGAAAAGAGAAAAAA
25271850 GAAATGAAAA
1 GAAA-GAAAA
25271860 AAATAGAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
18 9 0.36
19 12 0.48
20 4 0.16
ACGTcount: A:0.76, C:0.00, G:0.22, T:0.02
Consensus pattern (18 bp):
GAAAGAAAAGAGAAAAAA
Found at i:25271848 original size:22 final size:22
Alignment explanation
Indices: 25271815--25271871 Score: 66
Period size: 22 Copynumber: 2.7 Consensus size: 22
25271805 AAAATTTTCG
*
25271815 AAAAAA-AG-AAAAAGAGA-GA
1 AAAAAAGAGAAAAAAGAAATGA
25271834 AAGAAAAGAGAAAAAAGAAATGA
1 AA-AAAAGAGAAAAAAGAAATGA
*
25271857 AAAAAATAGAAAAAA
1 AAAAAAGAGAAAAAA
25271872 AGGAAAAAAG
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
19 2 0.06
20 4 0.12
21 2 0.06
22 20 0.62
23 4 0.12
ACGTcount: A:0.79, C:0.00, G:0.18, T:0.04
Consensus pattern (22 bp):
AAAAAAGAGAAAAAAGAAATGA
Found at i:25271850 original size:14 final size:14
Alignment explanation
Indices: 25271816--25271869 Score: 56
Period size: 14 Copynumber: 3.8 Consensus size: 14
25271806 AAATTTTCGA
25271816 AAAAAAGAAAA-AG
1 AAAAAAGAAAAGAG
*
25271829 AGAGAAAGAAAAGAG
1 A-AAAAAGAAAAGAG
* *
25271844 AAAAAAGAAATGAA
1 AAAAAAGAAAAGAG
25271858 AAAAATAGAAAA
1 AAAAA-AGAAAA
25271870 AAAGGAAAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
13 1 0.03
14 24 0.73
15 8 0.24
ACGTcount: A:0.78, C:0.00, G:0.19, T:0.04
Consensus pattern (14 bp):
AAAAAAGAAAAGAG
Found at i:25271895 original size:17 final size:17
Alignment explanation
Indices: 25271815--25271897 Score: 64
Period size: 17 Copynumber: 4.8 Consensus size: 17
25271805 AAAATTTTCG
25271815 AAAAAAAGAAAAAGAGAGA
1 AAAAAAAGAAAAA-AG-GA
25271834 AAGAAAAGAGAAAAAA-GA
1 AA-AAAA-AGAAAAAAGGA
** *
25271852 AATGAAA-AAAATA-GA
1 AAAAAAAGAAAAAAGGA
*
25271867 AAAAAAGGAAAAAAGGA
1 AAAAAAAGAAAAAAGGA
*
25271884 AAAAAAATAAAAAA
1 AAAAAAAGAAAAAA
25271898 ATTGTTTGAG
Statistics
Matches: 51, Mismatches: 9, Indels: 10
0.73 0.13 0.14
Matches are distributed among these distances:
15 11 0.22
16 6 0.12
17 16 0.31
18 4 0.08
19 2 0.04
20 5 0.10
21 7 0.14
ACGTcount: A:0.80, C:0.00, G:0.17, T:0.04
Consensus pattern (17 bp):
AAAAAAAGAAAAAAGGA
Found at i:25272636 original size:19 final size:21
Alignment explanation
Indices: 25272612--25272650 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 21
25272602 TATTATTATT
25272612 TAAAAATTAA-AAA-TAAAAA
1 TAAAAATTAATAAACTAAAAA
25272631 TAAAAATTAATAAACTAAAA
1 TAAAAATTAATAAACTAAAA
25272651 GATCTCATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 10 0.56
20 3 0.17
21 5 0.28
ACGTcount: A:0.74, C:0.03, G:0.00, T:0.23
Consensus pattern (21 bp):
TAAAAATTAATAAACTAAAAA
Found at i:25272803 original size:19 final size:18
Alignment explanation
Indices: 25272779--25272817 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
25272769 ATCAATCAAA
*
25272779 TTTAAATTTTAAATAATTT
1 TTTAAATATT-AATAATTT
*
25272798 TTTAAATATTATTAATTT
1 TTTAAATATTAATAATTT
25272816 TT
1 TT
25272818 ACATTAAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 9 0.50
19 9 0.50
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (18 bp):
TTTAAATATTAATAATTT
Found at i:25274174 original size:6 final size:6
Alignment explanation
Indices: 25274163--25274215 Score: 79
Period size: 6 Copynumber: 8.8 Consensus size: 6
25274153 TCATTGAAGG
* *
25274163 ATTTTC ATTTTC ATTTTC ATTTTC ATTTTT ATTTTT ATTTTC ATTTTC
1 ATTTTC ATTTTC ATTTTC ATTTTC ATTTTC ATTTTC ATTTTC ATTTTC
*
25274211 GTTTT
1 ATTTT
25274216 TGTTTTCGTT
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 44 1.00
ACGTcount: A:0.15, C:0.11, G:0.02, T:0.72
Consensus pattern (6 bp):
ATTTTC
Found at i:25274216 original size:18 final size:18
Alignment explanation
Indices: 25274163--25274227 Score: 85
Period size: 18 Copynumber: 3.6 Consensus size: 18
25274153 TCATTGAAGG
*
25274163 ATTTTCATTTTCATTTTC
1 ATTTTCATTTTCATTTTT
*
25274181 ATTTTCATTTTTATTTTT
1 ATTTTCATTTTCATTTTT
*
25274199 ATTTTCATTTTCGTTTTT
1 ATTTTCATTTTCATTTTT
* *
25274217 GTTTTCGTTTT
1 ATTTTCATTTT
25274228 GTTTTCGTTT
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 41 1.00
ACGTcount: A:0.12, C:0.11, G:0.05, T:0.72
Consensus pattern (18 bp):
ATTTTCATTTTCATTTTT
Found at i:25274221 original size:5 final size:6
Alignment explanation
Indices: 25274200--25274244 Score: 56
Period size: 6 Copynumber: 7.7 Consensus size: 6
25274190 TTTATTTTTA
* * *
25274200 TTTTCA TTTTCG TTTTTG TTTTCG TTTT-G TTTTCG TTTTCC TTTT
1 TTTTCG TTTTCG TTTTCG TTTTCG TTTTCG TTTTCG TTTTCG TTTT
25274245 TTTAACACTT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
5 5 0.15
6 29 0.85
ACGTcount: A:0.02, C:0.13, G:0.11, T:0.73
Consensus pattern (6 bp):
TTTTCG
Found at i:25274221 original size:12 final size:12
Alignment explanation
Indices: 25274206--25274238 Score: 59
Period size: 11 Copynumber: 2.8 Consensus size: 12
25274196 TTTATTTTCA
25274206 TTTTCGTTTTTG
1 TTTTCGTTTTTG
25274218 TTTTCG-TTTTG
1 TTTTCGTTTTTG
25274229 TTTTCGTTTT
1 TTTTCGTTTT
25274239 CCTTTTTTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 11 0.55
12 9 0.45
ACGTcount: A:0.00, C:0.09, G:0.15, T:0.76
Consensus pattern (12 bp):
TTTTCGTTTTTG
Found at i:25276136 original size:12 final size:12
Alignment explanation
Indices: 25276119--25276143 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
25276109 TACAGATACC
25276119 AAACAATATATA
1 AAACAATATATA
25276131 AAACAATATATA
1 AAACAATATATA
25276143 A
1 A
25276144 TTATCTCTCG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.68, C:0.08, G:0.00, T:0.24
Consensus pattern (12 bp):
AAACAATATATA
Found at i:25283714 original size:24 final size:24
Alignment explanation
Indices: 25283686--25283765 Score: 73
Period size: 24 Copynumber: 3.5 Consensus size: 24
25283676 TATCATTCAA
25283686 ATATAATATTAATCATGCAATAAC
1 ATATAATATTAATCATGCAATAAC
* **
25283710 ATATAATATCATATCATGTGATAA-
1 ATATAATATTA-ATCATGCAATAAC
25283734 ATAT-A-A--AATCATGCAATAAC
1 ATATAATATTAATCATGCAATAAC
*
25283754 A-ATAATAATAAT
1 ATATAATATTAAT
25283766 AATAATAATA
Statistics
Matches: 45, Mismatches: 5, Indels: 13
0.71 0.08 0.21
Matches are distributed among these distances:
19 12 0.27
20 3 0.07
21 1 0.02
22 1 0.02
23 4 0.09
24 14 0.31
25 10 0.22
ACGTcount: A:0.53, C:0.10, G:0.05, T:0.33
Consensus pattern (24 bp):
ATATAATATTAATCATGCAATAAC
Found at i:25283762 original size:3 final size:3
Alignment explanation
Indices: 25283748--25283788 Score: 64
Period size: 3 Copynumber: 13.7 Consensus size: 3
25283738 AAAATCATGC
* *
25283748 AAT AAC AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT CAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
25283789 CCATGAAAAT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.66, C:0.05, G:0.00, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:25283870 original size:32 final size:31
Alignment explanation
Indices: 25283834--25284195 Score: 128
Period size: 32 Copynumber: 11.6 Consensus size: 31
25283824 CACAAATAAA
*
25283834 TAAATTAATAATCATGCAAATAAACATACAAT
1 TAAA-TAATAATCATGCAAATAAACATGCAAT
* *
25283866 TAAATATATAATCATATAATTAACAATGTAAAACATGCAAT
1 TAAATA-ATAATC-----A-T-GCAA-ATAA-ACATGCAAT
25283907 TAAAT-ATAATCATGCAAATAAACATGCAAT
1 TAAATAATAATCATGCAAATAAACATGCAAT
*
25283937 TAAATATATAATCATGCAATTAACAATGTAAAATATGCAAT
1 TAAATA-ATAATCATGC-----A-AA--T-AAACATGCAAT
*
25283978 TAAAT-ATAATCATGCAAATAAAAAT---AT
1 TAAATAATAATCATGCAAATAAACATGCAAT
* * *
25284005 T-AATAATAA--A-GC-AATCACACA-ACTAAA
1 TAAATAATAATCATGCAAAT-AAACATGC-AAT
* * *
25284032 TAAATTAATAATCATGCTATTAAATATGCAAT
1 TAAA-TAATAATCATGCAAATAAACATGCAAT
*
25284064 CAAATATATAATCATGCAAAT--A-AT--AA-
1 TAAATA-ATAATCATGCAAATAAACATGCAAT
* *
25284090 T-ATTAATAATCACGCAAATAAACATGCAAT
1 TAAATAATAATCATGCAAATAAACATGCAAT
*
25284120 TAAATATATAATCATGTAAAT-AA-A---AA-
1 TAAATA-ATAATCATGCAAATAAACATGCAAT
* *
25284146 TATATAA-ACT-ATGCAAATAAACATGCAAT
1 TAAATAATAATCATGCAAATAAACATGCAAT
* *
25284175 TAAAAATATAATTATGCAAAT
1 TAAATA-ATAATCATGCAAAT
25284196 CATAATATAT
Statistics
Matches: 248, Mismatches: 30, Indels: 104
0.65 0.08 0.27
Matches are distributed among these distances:
23 10 0.04
24 22 0.09
25 6 0.02
26 9 0.04
27 15 0.06
28 4 0.02
29 14 0.06
30 23 0.09
31 16 0.06
32 65 0.26
33 6 0.02
34 2 0.01
37 2 0.01
38 3 0.01
39 19 0.08
40 4 0.02
41 28 0.11
ACGTcount: A:0.54, C:0.11, G:0.05, T:0.29
Consensus pattern (31 bp):
TAAATAATAATCATGCAAATAAACATGCAAT
Found at i:25283876 original size:20 final size:20
Alignment explanation
Indices: 25283853--25283914 Score: 63
Period size: 20 Copynumber: 3.0 Consensus size: 20
25283843 AATCATGCAA
25283853 ATAAACATACAATTAAATAT
1 ATAAACATACAATTAAATAT
* *
25283873 ATAATCATATAATTAACA-AT
1 ATAAACATACAATTAA-ATAT
* *
25283893 GTAAAACATGCAATTAAATAT
1 AT-AAACATACAATTAAATAT
25283914 A
1 A
25283915 ATCATGCAAA
Statistics
Matches: 32, Mismatches: 7, Indels: 5
0.73 0.16 0.11
Matches are distributed among these distances:
20 18 0.56
21 14 0.44
ACGTcount: A:0.56, C:0.10, G:0.03, T:0.31
Consensus pattern (20 bp):
ATAAACATACAATTAAATAT
Found at i:25283922 original size:71 final size:71
Alignment explanation
Indices: 25283841--25283999 Score: 282
Period size: 71 Copynumber: 2.2 Consensus size: 71
25283831 AAATAAATTA
*
25283841 ATAATCATGCAAATAAACATACAATTAAATATATAATCATATAATTAACAATGTAAAACATGCAA
1 ATAATCATGCAAATAAACATACAATTAAATATATAATCATACAATTAACAATGTAAAACATGCAA
25283906 TTAAAT
66 TTAAAT
* * *
25283912 ATAATCATGCAAATAAACATGCAATTAAATATATAATCATGCAATTAACAATGTAAAATATGCAA
1 ATAATCATGCAAATAAACATACAATTAAATATATAATCATACAATTAACAATGTAAAACATGCAA
25283977 TTAAAT
66 TTAAAT
25283983 ATAATCATGCAAATAAA
1 ATAATCATGCAAATAAA
25284000 AATATTAATA
Statistics
Matches: 84, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
71 84 1.00
ACGTcount: A:0.54, C:0.11, G:0.06, T:0.29
Consensus pattern (71 bp):
ATAATCATGCAAATAAACATACAATTAAATATATAATCATACAATTAACAATGTAAAACATGCAA
TTAAAT
Found at i:25284021 original size:71 final size:69
Alignment explanation
Indices: 25283841--25284021 Score: 211
Period size: 71 Copynumber: 2.5 Consensus size: 69
25283831 AAATAAATTA
* * * **
25283841 ATAATCATGCAAATAAACATACAATTAAATATATAATCATATAATTAACAATGTAAAACATGCAA
1 ATAATCATGCAAATAAA-A-ATAATTAAATAAACAATCATGCAATTAACAATGTAAAACATGCAA
25283906 TTAAAT
64 TTAAAT
* * * *
25283912 ATAATCATGCAAATAAACATGCAATTAAATATATAATCATGCAATTAACAATGTAAAATATGCAA
1 ATAATCATGCAAATAAAAAT--AATTAAATAAACAATCATGCAATTAACAATGTAAAACATGCAA
25283977 TTAAAT
64 TTAAAT
25283983 ATAATCATGCAAATAAAAAT-ATTAATAATAAAGCAATCA
1 ATAATCATGCAAATAAAAATAATT-A-AATAAA-CAATCA
25284022 CACAACTAAA
Statistics
Matches: 97, Mismatches: 8, Indels: 10
0.84 0.07 0.09
Matches are distributed among these distances:
68 3 0.03
69 2 0.02
70 5 0.05
71 87 0.90
ACGTcount: A:0.55, C:0.11, G:0.06, T:0.29
Consensus pattern (69 bp):
ATAATCATGCAAATAAAAATAATTAAATAAACAATCATGCAATTAACAATGTAAAACATGCAATT
AAAT
Found at i:25284077 original size:56 final size:56
Alignment explanation
Indices: 25284017--25284186 Score: 157
Period size: 56 Copynumber: 3.1 Consensus size: 56
25284007 ATAATAAAGC
* * * * *
25284017 AATCACACAACTAAATAA-ATTAATAATCATGCTATTAAATATGCAATCAAATATAT
1 AATCACACAAAT-AATAATATTAATAATCACGCAAATAAACATGCAATCAAATATAT
** *
25284073 AATCATGCAAATAATAATATTAATAATCACGCAAATAAACATGCAATTAAATATAT
1 AATCACACAAATAATAATATTAATAATCACGCAAATAAACATGCAATCAAATATAT
*** * * * * *
25284129 AATCATGTAAATAAAAATA-T-ATAAACTATGCAAATAAACATGCAATTAAAAATAT
1 AATCACACAAATAATAATATTAATAATC-ACGCAAATAAACATGCAATCAAATATAT
25284184 AAT
1 AAT
25284187 TATGCAAATC
Statistics
Matches: 99, Mismatches: 13, Indels: 5
0.85 0.11 0.04
Matches are distributed among these distances:
54 5 0.05
55 35 0.35
56 59 0.60
ACGTcount: A:0.55, C:0.12, G:0.05, T:0.29
Consensus pattern (56 bp):
AATCACACAAATAATAATATTAATAATCACGCAAATAAACATGCAATCAAATATAT
Done.