Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D12
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: 63843421
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1690000 characters in sequence are not A, C, G, or T
File 56 of 214
Found at i:15723161 original size:15 final size:16
Alignment explanation
Indices: 15723141--15723172 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
15723131 AGAAAATGAA
15723141 AAAGAAAAAGAA-ATG
1 AAAGAAAAAGAAGATG
15723156 AAAGAAAAAGAAGATG
1 AAAGAAAAAGAAGATG
15723172 A
1 A
15723173 GTGTGAGATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.72, C:0.00, G:0.22, T:0.06
Consensus pattern (16 bp):
AAAGAAAAAGAAGATG
Found at i:15723287 original size:17 final size:18
Alignment explanation
Indices: 15723255--15723288 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
15723245 AAAAGAGAGT
*
15723255 GAGATTGAAGGAAGAAAC
1 GAGAGTGAAGGAAGAAAC
15723273 GAGAGTGAA-GAAGAAA
1 GAGAGTGAAGGAAGAAA
15723289 GGAGTGTTGT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.53, C:0.03, G:0.35, T:0.09
Consensus pattern (18 bp):
GAGAGTGAAGGAAGAAAC
Found at i:15724576 original size:20 final size:20
Alignment explanation
Indices: 15724553--15724606 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
15724543 AGTTTTTCCC
*
15724553 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTCACATG
* ***
15724573 AGCTTAATTTAGCTCGTTTG
1 AGCTCAATTTAGCTCACATG
15724593 AGCTCAATTTAGCT
1 AGCTCAATTTAGCT
15724607 TACTTTAGCT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.24, C:0.20, G:0.19, T:0.37
Consensus pattern (20 bp):
AGCTCAATTTAGCTCACATG
Found at i:15724588 original size:30 final size:30
Alignment explanation
Indices: 15724553--15724626 Score: 98
Period size: 30 Copynumber: 2.5 Consensus size: 30
15724543 AGTTTTTCCC
15724553 AGCTCGATTT-AGCTCACA-TGAGCTTAATTT
1 AGCTCG-TTTGAGCTCA-ATTGAGCTTAATTT
* *
15724583 AGCTCGTTTGAGCTCAATTTAGCTTACTTT
1 AGCTCGTTTGAGCTCAATTGAGCTTAATTT
15724613 AGCTCGTTTGAGCT
1 AGCTCGTTTGAGCT
15724627 TGGCTTAAGT
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
29 4 0.10
30 36 0.90
ACGTcount: A:0.22, C:0.20, G:0.19, T:0.39
Consensus pattern (30 bp):
AGCTCGTTTGAGCTCAATTGAGCTTAATTT
Found at i:15724616 original size:20 final size:20
Alignment explanation
Indices: 15724553--15724617 Score: 53
Period size: 20 Copynumber: 3.2 Consensus size: 20
15724543 AGTTTTTCCC
* * * *
15724553 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTTACTTT
*
15724573 AGCTTAATTTAGC-T-CGTTT
1 AGCTCAATTTAGCTTAC-TTT
15724592 GAGCTCAATTTAGCTTACTTT
1 -AGCTCAATTTAGCTTACTTT
15724613 AGCTC
1 AGCTC
15724618 GTTTGAGCTT
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 28 0.80
21 4 0.11
22 1 0.03
ACGTcount: A:0.23, C:0.22, G:0.17, T:0.38
Consensus pattern (20 bp):
AGCTCAATTTAGCTTACTTT
Found at i:15726367 original size:11 final size:11
Alignment explanation
Indices: 15726351--15726401 Score: 54
Period size: 11 Copynumber: 4.9 Consensus size: 11
15726341 AGCTGAATTA
*
15726351 AGCTCAATTTC
1 AGCTCAATATC
*
15726362 AGCTC-A-ATG
1 AGCTCAATATC
*
15726371 AGCTCAA-ACC
1 AGCTCAATATC
15726381 AGCTCAATATC
1 AGCTCAATATC
15726392 AGCTCAATAT
1 AGCTCAATAT
15726402 AATTTAGTCA
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
9 6 0.18
10 10 0.30
11 17 0.52
ACGTcount: A:0.35, C:0.27, G:0.12, T:0.25
Consensus pattern (11 bp):
AGCTCAATATC
Found at i:15729290 original size:21 final size:21
Alignment explanation
Indices: 15729245--15729307 Score: 81
Period size: 21 Copynumber: 3.0 Consensus size: 21
15729235 TTTGAACCAT
* *
15729245 TACCAATTCGTACCAAATACCA
1 TACCATTTCGTACC-AATTCCA
15729267 TACCATTTCGTACCAATTCCA
1 TACCATTTCGTACCAATTCCA
* *
15729288 TACTATTTCGAACCAATTCC
1 TACCATTTCGTACCAATTCC
15729308 CAAATACCAA
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
21 24 0.65
22 13 0.35
ACGTcount: A:0.33, C:0.32, G:0.05, T:0.30
Consensus pattern (21 bp):
TACCATTTCGTACCAATTCCA
Found at i:15731162 original size:17 final size:17
Alignment explanation
Indices: 15731142--15731187 Score: 76
Period size: 17 Copynumber: 2.8 Consensus size: 17
15731132 AGTCAAAATC
15731142 GAAAAAAAAATTG-AAA
1 GAAAAAAAAATTGAAAA
*
15731158 GGAAAAAAAATTGAAAA
1 GAAAAAAAAATTGAAAA
15731175 GAAAAAAAAATTG
1 GAAAAAAAAATTG
15731188 CATACGGTCT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
16 12 0.44
17 15 0.56
ACGTcount: A:0.72, C:0.00, G:0.15, T:0.13
Consensus pattern (17 bp):
GAAAAAAAAATTGAAAA
Found at i:15731163 original size:16 final size:16
Alignment explanation
Indices: 15731144--15731183 Score: 71
Period size: 16 Copynumber: 2.5 Consensus size: 16
15731134 TCAAAATCGA
*
15731144 AAAAAAAATTGAAAGG
1 AAAAAAAATTGAAAAG
15731160 AAAAAAAATTGAAAAG
1 AAAAAAAATTGAAAAG
15731176 AAAAAAAA
1 AAAAAAAA
15731184 ATTGCATACG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.78, C:0.00, G:0.12, T:0.10
Consensus pattern (16 bp):
AAAAAAAATTGAAAAG
Found at i:15733972 original size:22 final size:22
Alignment explanation
Indices: 15733944--15733987 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
15733934 TTTTGAACCA
15733944 TTACCATTTCGTACCAAATCCC
1 TTACCATTTCGTACCAAATCCC
*
15733966 TTACCATTTCGTACCAATTCCC
1 TTACCATTTCGTACCAAATCCC
15733988 AAATACCAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.25, C:0.36, G:0.05, T:0.34
Consensus pattern (22 bp):
TTACCATTTCGTACCAAATCCC
Found at i:15734320 original size:13 final size:13
Alignment explanation
Indices: 15734304--15734339 Score: 65
Period size: 12 Copynumber: 2.8 Consensus size: 13
15734294 AGGAGTTCGA
15734304 AAAAAAAAATTTG
1 AAAAAAAAATTTG
15734317 AAAAAAAAA-TTG
1 AAAAAAAAATTTG
15734329 AAAAAAAAATT
1 AAAAAAAAATT
15734340 GCATACGGTT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
12 12 0.55
13 10 0.45
ACGTcount: A:0.75, C:0.00, G:0.06, T:0.19
Consensus pattern (13 bp):
AAAAAAAAATTTG
Found at i:15737647 original size:40 final size:40
Alignment explanation
Indices: 15737603--15737863 Score: 244
Period size: 40 Copynumber: 6.5 Consensus size: 40
15737593 AGCATGATTA
* * * *
15737603 CTCTTCGGGACCTAGCCTGGATATAACACCAGCACGAATG
1 CTCTTCGGGACTTAGCCCGGATATATCACTAGCACGAATG
* ** *
15737643 CTCTTTGGGGTTTAGCACGGATATATCACTAGCACGAATG
1 CTCTTCGGGACTTAGCCCGGATATATCACTAGCACGAATG
* * *
15737683 TTCTTCGGAACTTAGCCCGGATACATCACTAGCACGAATG
1 CTCTTCGGGACTTAGCCCGGATATATCACTAGCACGAATG
* * *
15737723 CTCCTT-GGGACTTAGCCCAGATATATCAGTAGCATGAATG
1 CT-CTTCGGGACTTAGCCCGGATATATCACTAGCACGAATG
* * * * *
15737763 CTCTTCGGGACTTAGCCTGGATTTAGTAACTTGCACCAATG
1 CTCTTCGGGACTTAGCCCGGATATA-TCACTAGCACGAATG
* * *
15737804 C-CTTC-GGATCTTAGTCCGGATATGGTCACTTAGCAC-AAAG
1 CTCTTCGGGA-CTTAGCCCGGATAT-ATCAC-TAGCACGAATG
15737844 C-CTTCGGGACTTAGCCCGGA
1 CTCTTCGGGACTTAGCCCGGA
15737864 CATCATTCGA
Statistics
Matches: 177, Mismatches: 37, Indels: 14
0.78 0.16 0.06
Matches are distributed among these distances:
39 6 0.03
40 149 0.84
41 22 0.12
ACGTcount: A:0.25, C:0.26, G:0.23, T:0.26
Consensus pattern (40 bp):
CTCTTCGGGACTTAGCCCGGATATATCACTAGCACGAATG
Found at i:15738208 original size:29 final size:29
Alignment explanation
Indices: 15738169--15738247 Score: 106
Period size: 29 Copynumber: 2.7 Consensus size: 29
15738159 CTTAATAATC
*
15738169 AACCACGCACACTTAGTGCCATGTACTTT-A
1 AACC-CGCACACTTAGTGCCATGCA-TTTCA
*
15738199 AACTCGCACACTTAGTGCCATGCATTTCA
1 AACCCGCACACTTAGTGCCATGCATTTCA
*
15738228 AGCCCGCACACTTAGTGCCA
1 AACCCGCACACTTAGTGCCA
15738248 ATCTCACAAC
Statistics
Matches: 44, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
28 3 0.07
29 38 0.86
30 3 0.07
ACGTcount: A:0.28, C:0.33, G:0.15, T:0.24
Consensus pattern (29 bp):
AACCCGCACACTTAGTGCCATGCATTTCA
Found at i:15740215 original size:37 final size:37
Alignment explanation
Indices: 15740154--15740232 Score: 106
Period size: 37 Copynumber: 2.1 Consensus size: 37
15740144 TTATTACGAA
* *
15740154 GTCTTACCCAGACATAATCTCCACACGAAGTTATCGG
1 GTCTTACCCAGACAAAATCTCCACACGAAGTCATCGG
* *
15740191 GTCTTACCCGGACAAAAT-TCCCACACGTAGTCATCGG
1 GTCTTACCCAGACAAAATCT-CCACACGAAGTCATCGG
15740228 GTCTT
1 GTCTT
15740233 TAGAGCTCGA
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
36 1 0.03
37 36 0.97
ACGTcount: A:0.27, C:0.30, G:0.18, T:0.25
Consensus pattern (37 bp):
GTCTTACCCAGACAAAATCTCCACACGAAGTCATCGG
Found at i:15740429 original size:47 final size:47
Alignment explanation
Indices: 15740351--15740875 Score: 816
Period size: 47 Copynumber: 11.1 Consensus size: 47
15740341 CCCTTCGGGA
* * * * * * *
15740351 CTTATCACATTTATGCACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*** *
15740398 CCCGTCACATATATACACTTTCACGTTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
15740445 CTTATCACATATATACACTTTCACATTCATCAAATCAGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
15740492 CTTATTACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
15740539 CTTATCACACATATACACTTTCACATTCATCACATCGGCCATTGGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
15740586 CTTATCACATATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
15740635 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
15740682 CTTATCACACATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
15740729 CTTATCACACATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
15740776 CTTATCACATGTATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACA--TATATACACTTTCACATTCATCACATCGGCCATTAGGC
15740825 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
15740872 CTTA
1 CTTA
15740876 CTATCATTTC
Statistics
Matches: 443, Mismatches: 31, Indels: 8
0.92 0.06 0.02
Matches are distributed among these distances:
47 353 0.80
49 90 0.20
ACGTcount: A:0.29, C:0.30, G:0.09, T:0.32
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:15740661 original size:143 final size:141
Alignment explanation
Indices: 15740351--15740875 Score: 816
Period size: 143 Copynumber: 3.7 Consensus size: 141
15740341 CCCTTCGGGA
* * * * * * * *** *
15740351 CTTATCACATTTATGCACTTTCACATCCATCACGTTGGCCACTCGGCCCCGTCACATATATACAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACACATATACAC
* *
15740416 TTTCACGTTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCAAATC
66 TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATC
*
15740481 AGCCATTAGGC
131 GGCCATTAGGC
* *
15740492 CTTATTACATATATACACTTTCACATTCATCACATCGGCTATTAGGCCTTATCACACATATACAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACACATATACAC
*
15740557 TTTCACATTCATCACATCGGCCATTGGGCCTTATCACATATATATACACTTTCACATTCATCACA
66 TTTCACATTCATCACATCGGCCATTAGGCCTTATCAC--ATATATACACTTTCACATTCATCACA
*
15740622 TCGGCTATTAGGC
129 TCGGCCATTAGGC
*
15740635 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGCCTTATCACACATATACAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACACATATACAC
* *
15740700 TTTCACATTCATCACATCGGCTATTAGGCCTTATCACACATATACACTTTCACATTCATCACATC
66 TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATC
15740765 GGCCATTAGGC
131 GGCCATTAGGC
*
15740776 CTTATCACATGTATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC
1 CTTATCACA--TATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACACATATAC
15740841 ACTTTCACATTCATCACATCGGCCATTAGGCCTTA
64 ACTTTCACATTCATCACATCGGCCATTAGGCCTTA
15740876 CTATCATTTC
Statistics
Matches: 354, Mismatches: 26, Indels: 6
0.92 0.07 0.02
Matches are distributed among these distances:
141 133 0.38
143 221 0.62
ACGTcount: A:0.29, C:0.30, G:0.09, T:0.32
Consensus pattern (141 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACACATATACAC
TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATC
GGCCATTAGGC
Found at i:15740681 original size:190 final size:190
Alignment explanation
Indices: 15740406--15740875 Score: 859
Period size: 190 Copynumber: 2.5 Consensus size: 190
15740396 GCCCCGTCAC
*
15740406 ATATATACACTTTCACGTTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACAT
1 ATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACAT
* * * *
15740471 TCATCAAATCAGCCATTAGGCCTTATTACATATATACACTTTCACATTCATCACATCGGCTATTA
66 TCATCACATCGGCCATTAGGCCTTATCACACATATACACTTTCACATTCATCACATCGGCTATTA
*
15740536 GGCCTTATCACACATATACACTTTCACATTCATCACATCGGCCATTGGGCCTTATCACAT
131 GGCCTTATCACACATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACAT
*
15740596 ATATATACACTTTCACATTCATCACATCGGCTATTAGGCCTTATCACATATATACACTTTCACAT
1 ATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACAT
*
15740661 TCATCACATCGGCTATTAGGCCTTATCACACATATACACTTTCACATTCATCACATCGGCTATTA
66 TCATCACATCGGCCATTAGGCCTTATCACACATATACACTTTCACATTCATCACATCGGCTATTA
15740726 GGCCTTATCACACATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACAT
131 GGCCTTATCACACATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACAT
*
15740786 GTATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACAT
1 ATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACAT
15740851 TCATCACATCGGCCATTAGGCCTTA
66 TCATCACATCGGCCATTAGGCCTTA
15740876 CTATCATTTC
Statistics
Matches: 269, Mismatches: 11, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
190 269 1.00
ACGTcount: A:0.30, C:0.29, G:0.09, T:0.33
Consensus pattern (190 bp):
ATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACAT
TCATCACATCGGCCATTAGGCCTTATCACACATATACACTTTCACATTCATCACATCGGCTATTA
GGCCTTATCACACATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACAT
Found at i:15745647 original size:21 final size:21
Alignment explanation
Indices: 15745602--15745664 Score: 81
Period size: 21 Copynumber: 3.0 Consensus size: 21
15745592 TTTGAACCAT
* *
15745602 TACCAATTCGTACCAAATACCA
1 TACCATTTCGTACC-AATTCCA
15745624 TACCATTTCGTACCAATTCCA
1 TACCATTTCGTACCAATTCCA
* *
15745645 TACTATTTCGAACCAATTCC
1 TACCATTTCGTACCAATTCC
15745665 CAAATACCAA
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
21 24 0.65
22 13 0.35
ACGTcount: A:0.33, C:0.32, G:0.05, T:0.30
Consensus pattern (21 bp):
TACCATTTCGTACCAATTCCA
Found at i:15746015 original size:15 final size:15
Alignment explanation
Indices: 15745997--15746033 Score: 65
Period size: 15 Copynumber: 2.5 Consensus size: 15
15745987 CAAAATCAAA
*
15745997 AAAAAAATTGAAAGG
1 AAAAAAATTGAAAAG
15746012 AAAAAAATTGAAAAG
1 AAAAAAATTGAAAAG
15746027 AAAAAAA
1 AAAAAAA
15746034 AATGCATACG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.76, C:0.00, G:0.14, T:0.11
Consensus pattern (15 bp):
AAAAAAATTGAAAAG
Found at i:15746015 original size:16 final size:16
Alignment explanation
Indices: 15745996--15746034 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
15745986 TCAAAATCAA
15745996 AAAAAAAATTG-AAAG
1 AAAAAAAATTGAAAAG
*
15746011 GAAAAAAATTGAAAAG
1 AAAAAAAATTGAAAAG
15746027 AAAAAAAA
1 AAAAAAAA
15746035 ATGCATACGG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 10 0.48
16 11 0.52
ACGTcount: A:0.77, C:0.00, G:0.13, T:0.10
Consensus pattern (16 bp):
AAAAAAAATTGAAAAG
Found at i:15747036 original size:17 final size:17
Alignment explanation
Indices: 15746996--15747037 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 17
15746986 AATGAAAACG
*
15746996 CAAAAGAAAAGAAAAAT
1 CAAAAAAAAAGAAAAAT
* *
15747013 GAGAAAAAAAGAAAAAT
1 CAAAAAAAAAGAAAAAT
15747030 CAAAAAAA
1 CAAAAAAA
15747038 GGGAGAGAAA
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.79, C:0.05, G:0.12, T:0.05
Consensus pattern (17 bp):
CAAAAAAAAAGAAAAAT
Found at i:15749265 original size:26 final size:25
Alignment explanation
Indices: 15749237--15749286 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 25
15749227 AAAAAGTAGA
*
15749237 AAAAGTCAA-AAAAATTGAAAAATAC
1 AAAA-TCAACAAAAATTAAAAAATAC
15749262 AAAATCAATCAAAAATTAAAAAATA
1 AAAATCAA-CAAAAATTAAAAAATA
15749287 TTCAGCGGGT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
24 4 0.18
25 4 0.18
26 14 0.64
ACGTcount: A:0.70, C:0.08, G:0.04, T:0.18
Consensus pattern (25 bp):
AAAATCAACAAAAATTAAAAAATAC
Found at i:15750201 original size:22 final size:22
Alignment explanation
Indices: 15750171--15750214 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
15750161 TTTGGTATTT
15750171 GGGAATTGGTACGAAATGGTAA
1 GGGAATTGGTACGAAATGGTAA
*
15750193 GGGATTTGGTACGAAATGGTAA
1 GGGAATTGGTACGAAATGGTAA
15750215 TGGTTCAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.34, C:0.05, G:0.36, T:0.25
Consensus pattern (22 bp):
GGGAATTGGTACGAAATGGTAA
Found at i:15751799 original size:10 final size:10
Alignment explanation
Indices: 15751783--15751840 Score: 64
Period size: 10 Copynumber: 5.7 Consensus size: 10
15751773 CAACTCCGAC
15751783 CAGCTCAATT
1 CAGCTCAATT
* *
15751793 GAGCTCATTT
1 CAGCTCAATT
15751803 CAGCTCAA-T
1 CAGCTCAATT
15751812 CGAGCTCAATT
1 C-AGCTCAATT
*
15751823 TAGCTACAATT
1 CAGCT-CAATT
15751834 CAGCTCA
1 CAGCTCA
15751841 TTTATTTTAT
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
9 2 0.05
10 27 0.69
11 10 0.26
ACGTcount: A:0.29, C:0.28, G:0.14, T:0.29
Consensus pattern (10 bp):
CAGCTCAATT
Found at i:15751806 original size:20 final size:20
Alignment explanation
Indices: 15751783--15751843 Score: 79
Period size: 20 Copynumber: 3.0 Consensus size: 20
15751773 CAACTCCGAC
15751783 CAGCTCAATTGAGCTCATTT
1 CAGCTCAATTGAGCTCATTT
*
15751803 CAGCTCAATCGAGCTCAATTT
1 CAGCTCAATTGAGCTC-ATTT
*
15751824 -AGCTACAATTCAGCTCATTT
1 CAGCT-CAATTGAGCTCATTT
15751844 ATTTTATTGG
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
20 23 0.64
21 13 0.36
ACGTcount: A:0.28, C:0.26, G:0.13, T:0.33
Consensus pattern (20 bp):
CAGCTCAATTGAGCTCATTT
Found at i:15753134 original size:12 final size:11
Alignment explanation
Indices: 15753103--15753131 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
15753093 AAAAAAAAGG
15753103 AAAAAAATTCA
1 AAAAAAATTCA
15753114 AAAAAAATTCA
1 AAAAAAATTCA
15753125 AAAAAAA
1 AAAAAAA
15753132 ATTTGTATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.79, C:0.07, G:0.00, T:0.14
Consensus pattern (11 bp):
AAAAAAATTCA
Found at i:15753221 original size:17 final size:17
Alignment explanation
Indices: 15753185--15753222 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
15753175 TCAGTATTGG
*
15753185 AAAAAAAAGAGAAATTA
1 AAAAAAAAGAGAAATAA
15753202 AAAAAAAAGAAGAAA-AA
1 AAAAAAAAG-AGAAATAA
15753219 AAAA
1 AAAA
15753223 TGTTTCAGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 14 0.74
18 5 0.26
ACGTcount: A:0.84, C:0.00, G:0.11, T:0.05
Consensus pattern (17 bp):
AAAAAAAAGAGAAATAA
Found at i:15754153 original size:17 final size:15
Alignment explanation
Indices: 15754133--15754171 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 15
15754123 GCGAGCGAGA
15754133 AAATGAACATGAAAAAG
1 AAATGAA-A-GAAAAAG
15754150 AAATGAAAGAAAAAG
1 AAATGAAAGAAAAAG
15754165 AAGATGA
1 AA-ATGA
15754172 GTGGGAGATA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 9 0.43
16 5 0.24
17 7 0.33
ACGTcount: A:0.67, C:0.03, G:0.21, T:0.10
Consensus pattern (15 bp):
AAATGAAAGAAAAAG
Found at i:15755678 original size:20 final size:20
Alignment explanation
Indices: 15755653--15755707 Score: 74
Period size: 20 Copynumber: 2.8 Consensus size: 20
15755643 TGCGGTTCAA
* *
15755653 CTCATTCGAGCTTAAGTTAG
1 CTCATTCGAGCTCAAGTCAG
*
15755673 CTCATTCGTGCTCAAGTCAG
1 CTCATTCGAGCTCAAGTCAG
*
15755693 CTCATTCAAGCTCAA
1 CTCATTCGAGCTCAA
15755708 TTTAACTCGT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.25, C:0.27, G:0.16, T:0.31
Consensus pattern (20 bp):
CTCATTCGAGCTCAAGTCAG
Found at i:15757810 original size:13 final size:13
Alignment explanation
Indices: 15757794--15757841 Score: 53
Period size: 13 Copynumber: 3.6 Consensus size: 13
15757784 CAAAAAAATC
15757794 AAAAAAAATTCGA
1 AAAAAAAATTCGA
*
15757807 AAAAAAAATTTGA
1 AAAAAAAATTCGA
*
15757820 TTGAAAAAAATTC-A
1 --AAAAAAAATTCGA
15757834 AAAAAAAA
1 AAAAAAAA
15757842 AGTTAAAAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
12 7 0.24
13 12 0.41
14 1 0.03
15 9 0.31
ACGTcount: A:0.71, C:0.04, G:0.06, T:0.19
Consensus pattern (13 bp):
AAAAAAAATTCGA
Found at i:15757864 original size:28 final size:27
Alignment explanation
Indices: 15757833--15757908 Score: 73
Period size: 28 Copynumber: 2.7 Consensus size: 27
15757823 AAAAAAATTC
15757833 AAAAAAAAAAGTTAAAAAAA-TCGAGCAA
1 AAAAAAAAAAGTTAAAAAAAGT-GAG-AA
* **
15757861 AAAAAGAAAAGAAAAAAAAAGTGAGAA
1 AAAAAAAAAAGTTAAAAAAAGTGAGAA
**
15757888 AAAAAATCAAGTTTAAAAAAA
1 AAAAAAAAAAG-TTAAAAAAA
15757909 AAGTGAAAAG
Statistics
Matches: 38, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
27 10 0.26
28 27 0.71
29 1 0.03
ACGTcount: A:0.74, C:0.04, G:0.12, T:0.11
Consensus pattern (27 bp):
AAAAAAAAAAGTTAAAAAAAGTGAGAA
Found at i:15758459 original size:22 final size:23
Alignment explanation
Indices: 15758434--15758476 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
15758424 GCTAATTTTT
*
15758434 AGCTC-ATTTGAATTTCTTTTCA
1 AGCTCTATTTCAATTTCTTTTCA
*
15758456 AGCTCTCTTTCAATTTCTTTT
1 AGCTCTATTTCAATTTCTTTT
15758477 TTCGCTTTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 5 0.28
23 13 0.72
ACGTcount: A:0.19, C:0.21, G:0.07, T:0.53
Consensus pattern (23 bp):
AGCTCTATTTCAATTTCTTTTCA
Found at i:15758493 original size:21 final size:21
Alignment explanation
Indices: 15758464--15758519 Score: 51
Period size: 21 Copynumber: 2.7 Consensus size: 21
15758454 CAAGCTCTCT
*
15758464 TTCAATTTCTTTTTTCGCTTT-
1 TTCATTTTCTTTTTTC-CTTTC
* ** *
15758485 TTCTTTTTCAATTTTCTTTTC
1 TTCATTTTCTTTTTTCCTTTC
15758506 TTCATTTTCTTTTT
1 TTCATTTTCTTTTT
15758520 CTCTCACTTT
Statistics
Matches: 26, Mismatches: 8, Indels: 2
0.72 0.22 0.06
Matches are distributed among these distances:
20 3 0.12
21 23 0.88
ACGTcount: A:0.09, C:0.18, G:0.02, T:0.71
Consensus pattern (21 bp):
TTCATTTTCTTTTTTCCTTTC
Found at i:15758512 original size:14 final size:14
Alignment explanation
Indices: 15758463--15758519 Score: 57
Period size: 14 Copynumber: 4.1 Consensus size: 14
15758453 TCAAGCTCTC
15758463 TTTCAA-TTTCTTT
1 TTTCAATTTTCTTT
**
15758476 TTTCGCTTTT-TCTT
1 TTTCAATTTTCT-TT
15758490 TTTCAATTTTCTTT
1 TTTCAATTTTCTTT
15758504 TCTTC-ATTTTCTTT
1 T-TTCAATTTTCTTT
15758518 TT
1 TT
15758520 CTCTCACTTT
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
13 6 0.17
14 26 0.72
15 4 0.11
ACGTcount: A:0.09, C:0.18, G:0.02, T:0.72
Consensus pattern (14 bp):
TTTCAATTTTCTTT
Found at i:15758601 original size:6 final size:6
Alignment explanation
Indices: 15758481--15758588 Score: 67
Period size: 6 Copynumber: 17.7 Consensus size: 6
15758471 TCTTTTTTCG
* * * **
15758481 CTTTTT CTTTTT CAATTTT CTTTTCTT CATTTT CTTTTT CTCTCA CTTTTT
1 CTTTTT CTTTTT C-TTTTT C-TTT-TT CTTTTT CTTTTT CTTTTT CTTTTT
* * ** *
15758532 -TGATTT CTTTTT CTTTTG CAATTT CTTTTT CTTTTT CGTTTT CTTTTT
1 CT-TTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT
*
15758580 -GTTTT CTTT
1 CTTTTT CTTT
15758589 CAATTTCTTT
Statistics
Matches: 74, Mismatches: 23, Indels: 10
0.69 0.21 0.09
Matches are distributed among these distances:
5 5 0.07
6 56 0.76
7 10 0.14
8 3 0.04
ACGTcount: A:0.06, C:0.18, G:0.04, T:0.72
Consensus pattern (6 bp):
CTTTTT
Found at i:15759548 original size:13 final size:13
Alignment explanation
Indices: 15759530--15759556 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
15759520 GTAAAAGCCA
15759530 TATTGTTCAAGTT
1 TATTGTTCAAGTT
15759543 TATTGTTCAAGTT
1 TATTGTTCAAGTT
15759556 T
1 T
15759557 CATGAACTTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.22, C:0.07, G:0.15, T:0.56
Consensus pattern (13 bp):
TATTGTTCAAGTT
Found at i:15759729 original size:10 final size:10
Alignment explanation
Indices: 15759713--15759770 Score: 64
Period size: 10 Copynumber: 5.7 Consensus size: 10
15759703 CAACTCCGAC
15759713 CAGCTCAATT
1 CAGCTCAATT
* *
15759723 GAGCTCATTT
1 CAGCTCAATT
15759733 CAGCTCAA-T
1 CAGCTCAATT
15759742 CGAGCTCAATT
1 C-AGCTCAATT
*
15759753 TAGCTACAATT
1 CAGCT-CAATT
15759764 CAGCTCA
1 CAGCTCA
15759771 TTTATTTTAT
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
9 2 0.05
10 27 0.69
11 10 0.26
ACGTcount: A:0.29, C:0.28, G:0.14, T:0.29
Consensus pattern (10 bp):
CAGCTCAATT
Found at i:15759736 original size:20 final size:20
Alignment explanation
Indices: 15759713--15759773 Score: 79
Period size: 20 Copynumber: 3.0 Consensus size: 20
15759703 CAACTCCGAC
15759713 CAGCTCAATTGAGCTCATTT
1 CAGCTCAATTGAGCTCATTT
*
15759733 CAGCTCAATCGAGCTCAATTT
1 CAGCTCAATTGAGCTC-ATTT
*
15759754 -AGCTACAATTCAGCTCATTT
1 CAGCT-CAATTGAGCTCATTT
15759774 ATTTTATTGG
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
20 23 0.64
21 13 0.36
ACGTcount: A:0.28, C:0.26, G:0.13, T:0.33
Consensus pattern (20 bp):
CAGCTCAATTGAGCTCATTT
Found at i:15767974 original size:6 final size:6
Alignment explanation
Indices: 15767961--15767996 Score: 54
Period size: 6 Copynumber: 6.0 Consensus size: 6
15767951 TCAATTTTTT
* *
15767961 TCTCAA TATCAA TATCAA TCTCAA TCTCAA TCTCAA
1 TCTCAA TCTCAA TCTCAA TCTCAA TCTCAA TCTCAA
15767997 ATTCTTTTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.39, C:0.28, G:0.00, T:0.33
Consensus pattern (6 bp):
TCTCAA
Found at i:15768048 original size:21 final size:20
Alignment explanation
Indices: 15768004--15768048 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
15767994 CAAATTCTTT
*
15768004 TTTCTTTTTCTCACTCTCAT
1 TTTCTTTTTCTCACTCTCAA
* *
15768024 TTTCTTTTTTTCTTCTCTCAA
1 TTTCTTTTTCTC-ACTCTCAA
15768045 TTTC
1 TTTC
15768049 ATTCAAGATT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 11 0.52
21 10 0.48
ACGTcount: A:0.09, C:0.27, G:0.00, T:0.64
Consensus pattern (20 bp):
TTTCTTTTTCTCACTCTCAA
Found at i:15768897 original size:27 final size:29
Alignment explanation
Indices: 15768854--15768922 Score: 97
Period size: 28 Copynumber: 2.4 Consensus size: 29
15768844 TTTCAATCAC
**
15768854 TCTTTTTTTTTTCAATTTTG-ATTTTTTT
1 TCTTTTTTTTTTCAATTCCGAATTTTTTT
15768882 TCTTTTTTTTTT-AATTCCGAATTTTTTT
1 TCTTTTTTTTTTCAATTCCGAATTTTTTT
15768910 TCTTCTTTTTTTT
1 TCTT-TTTTTTTT
15768923 TTCTTCAATA
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
27 5 0.14
28 24 0.65
29 8 0.22
ACGTcount: A:0.10, C:0.10, G:0.03, T:0.77
Consensus pattern (29 bp):
TCTTTTTTTTTTCAATTCCGAATTTTTTT
Found at i:15768987 original size:13 final size:13
Alignment explanation
Indices: 15768969--15769013 Score: 56
Period size: 14 Copynumber: 3.5 Consensus size: 13
15768959 GAATACAAAC
*
15768969 TTTTTTTT-GAAT
1 TTTTTTTTAAAAT
15768981 TTTTTTTTCAAAAT
1 TTTTTTTT-AAAAT
*
15768995 TTTTTTTTCAAAT
1 TTTTTTTTAAAAT
15769008 TTTTTT
1 TTTTTT
15769014 ATATTTTTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
12 8 0.28
13 10 0.34
14 11 0.38
ACGTcount: A:0.20, C:0.04, G:0.02, T:0.73
Consensus pattern (13 bp):
TTTTTTTTAAAAT
Found at i:15768988 original size:14 final size:14
Alignment explanation
Indices: 15768978--15769013 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
15768968 CTTTTTTTTG
15768978 AATTTTTTTTTCAA
1 AATTTTTTTTTCAA
15768992 AATTTTTTTTTC-A
1 AATTTTTTTTTCAA
15769005 AATTTTTTT
1 AATTTTTTT
15769014 ATATTTTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
13 10 0.45
14 12 0.55
ACGTcount: A:0.25, C:0.06, G:0.00, T:0.69
Consensus pattern (14 bp):
AATTTTTTTTTCAA
Found at i:15769010 original size:23 final size:23
Alignment explanation
Indices: 15768984--15769029 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
15768974 TTTGAATTTT
*
15768984 TTTTTCAAAATTTTTTTTTCAAA
1 TTTTTCAAAATTTTTTTTACAAA
** *
15769007 TTTTTTTATATTTTTTTTACAAA
1 TTTTTCAAAATTTTTTTTACAAA
15769030 ACCGTAATAC
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.28, C:0.07, G:0.00, T:0.65
Consensus pattern (23 bp):
TTTTTCAAAATTTTTTTTACAAA
Found at i:15780143 original size:20 final size:20
Alignment explanation
Indices: 15780097--15780143 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
15780087 AGCTTGTTTC
*
15780097 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* * *
15780117 CAACTCATTCAAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
15780137 CAGCTCA
1 CAGCTCA
15780144 ATCTTAACCT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.30, C:0.34, G:0.13, T:0.23
Consensus pattern (20 bp):
CAGCTCACTCAAGCTCAAGT
Found at i:15782776 original size:48 final size:47
Alignment explanation
Indices: 15782697--15782802 Score: 135
Period size: 48 Copynumber: 2.2 Consensus size: 47
15782687 GAGTGTCATG
*
15782697 GAAAAAGAAATTGAGATTGAAAAAGGATGTGA-AAAAGAGAAAGAAATC
1 GAAAAAGAAATTGAGATTGAAAAAAGATGTGAGAAAA-AGAAA-AAATC
* *
15782745 GAAAAAGAAATTGAGATTGAACAAAAG-TGTGAGGAAAAAGAGAAAATT
1 GAAAAAGAAATTGAGATTGAA-AAAAGATGTGA-GAAAAAGAAAAAATC
15782793 GAAAAAGAAA
1 GAAAAAGAAA
15782803 GAAAAGACAA
Statistics
Matches: 52, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
48 40 0.77
49 8 0.15
50 4 0.08
ACGTcount: A:0.59, C:0.02, G:0.25, T:0.14
Consensus pattern (47 bp):
GAAAAAGAAATTGAGATTGAAAAAAGATGTGAGAAAAAGAAAAAATC
Found at i:15784518 original size:20 final size:20
Alignment explanation
Indices: 15784472--15784518 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
15784462 AGCTTGTTTC
*
15784472 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* * *
15784492 CAACTCATTCAAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
15784512 CAGCTCA
1 CAGCTCA
15784519 ATCTTAACCT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.30, C:0.34, G:0.13, T:0.23
Consensus pattern (20 bp):
CAGCTCACTCAAGCTCAAGT
Found at i:15791785 original size:17 final size:16
Alignment explanation
Indices: 15791763--15791805 Score: 50
Period size: 17 Copynumber: 2.6 Consensus size: 16
15791753 TGGACTGAAT
*
15791763 ATAAAAATTTAAACTAA
1 ATAAAAATATAAA-TAA
*
15791780 ATAAAATAAATAAATAA
1 ATAAAA-ATATAAATAA
15791797 ATAAAAATA
1 ATAAAAATA
15791806 AAACTTTACA
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
16 2 0.09
17 15 0.68
18 5 0.23
ACGTcount: A:0.72, C:0.02, G:0.00, T:0.26
Consensus pattern (16 bp):
ATAAAAATATAAATAA
Found at i:15791803 original size:18 final size:18
Alignment explanation
Indices: 15791772--15791807 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
15791762 TATAAAAATT
15791772 TAAACTAAATAAAATAAA
1 TAAACTAAATAAAATAAA
15791790 TAAA-TAAATAAAAATAAA
1 TAAACTAAAT-AAAATAAA
15791808 ACTTTACAAC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 5 0.29
18 12 0.71
ACGTcount: A:0.75, C:0.03, G:0.00, T:0.22
Consensus pattern (18 bp):
TAAACTAAATAAAATAAA
Found at i:15795542 original size:20 final size:20
Alignment explanation
Indices: 15795519--15795572 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
15795509 AGTTTTTCCC
*
15795519 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTCACATG
* ***
15795539 AGCTTAATTTAGCTCGTTTG
1 AGCTCAATTTAGCTCACATG
15795559 AGCTCAATTTAGCT
1 AGCTCAATTTAGCT
15795573 TACTTTAGCT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.24, C:0.20, G:0.19, T:0.37
Consensus pattern (20 bp):
AGCTCAATTTAGCTCACATG
Found at i:15795554 original size:30 final size:30
Alignment explanation
Indices: 15795519--15795592 Score: 98
Period size: 30 Copynumber: 2.5 Consensus size: 30
15795509 AGTTTTTCCC
15795519 AGCTCGATTT-AGCTCACA-TGAGCTTAATTT
1 AGCTCG-TTTGAGCTCA-ATTGAGCTTAATTT
* *
15795549 AGCTCGTTTGAGCTCAATTTAGCTTACTTT
1 AGCTCGTTTGAGCTCAATTGAGCTTAATTT
15795579 AGCTCGTTTGAGCT
1 AGCTCGTTTGAGCT
15795593 TGGCTTAAGT
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
29 4 0.10
30 36 0.90
ACGTcount: A:0.22, C:0.20, G:0.19, T:0.39
Consensus pattern (30 bp):
AGCTCGTTTGAGCTCAATTGAGCTTAATTT
Found at i:15795582 original size:20 final size:20
Alignment explanation
Indices: 15795519--15795583 Score: 53
Period size: 20 Copynumber: 3.2 Consensus size: 20
15795509 AGTTTTTCCC
* * * *
15795519 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTTACTTT
*
15795539 AGCTTAATTTAGC-T-CGTTT
1 AGCTCAATTTAGCTTAC-TTT
15795558 GAGCTCAATTTAGCTTACTTT
1 -AGCTCAATTTAGCTTACTTT
15795579 AGCTC
1 AGCTC
15795584 GTTTGAGCTT
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 28 0.80
21 4 0.11
22 1 0.03
ACGTcount: A:0.23, C:0.22, G:0.17, T:0.38
Consensus pattern (20 bp):
AGCTCAATTTAGCTTACTTT
Found at i:15797202 original size:11 final size:12
Alignment explanation
Indices: 15797186--15797219 Score: 52
Period size: 11 Copynumber: 2.8 Consensus size: 12
15797176 ATTGGAGTAA
15797186 CAAAAAAAAA-T
1 CAAAAAAAAATT
15797197 CAAAAAAAAATT
1 CAAAAAAAAATT
15797209 CGAAAAAAAAA
1 C-AAAAAAAAA
15797220 ATTGATTGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 10 0.48
12 2 0.10
13 9 0.43
ACGTcount: A:0.79, C:0.09, G:0.03, T:0.09
Consensus pattern (12 bp):
CAAAAAAAAATT
Found at i:15797204 original size:12 final size:13
Alignment explanation
Indices: 15797187--15797221 Score: 54
Period size: 12 Copynumber: 2.8 Consensus size: 13
15797177 TTGGAGTAAC
15797187 AAAAAAAAATC-A
1 AAAAAAAAATCGA
*
15797199 AAAAAAAATTCGA
1 AAAAAAAAATCGA
15797212 AAAAAAAAAT
1 AAAAAAAAAT
15797222 TGATTGAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
12 10 0.50
13 10 0.50
ACGTcount: A:0.80, C:0.06, G:0.03, T:0.11
Consensus pattern (13 bp):
AAAAAAAAATCGA
Found at i:15797215 original size:14 final size:14
Alignment explanation
Indices: 15797187--15797263 Score: 56
Period size: 14 Copynumber: 5.5 Consensus size: 14
15797177 TTGGAGTAAC
15797187 AAAAAAAAA-TC--
1 AAAAAAAAATTCGA
15797198 AAAAAAAAATTCGA
1 AAAAAAAAATTCGA
*
15797212 AAAAAAAAATTGATTGAA
1 AAAAAAAAA-T--TCG-A
15797230 AAAAAAAATATTC-A
1 AAAAAAAA-ATTCGA
*
15797244 AAAAAAAAAGT-GA
1 AAAAAAAAATTCGA
15797257 AAAAAAA
1 AAAAAAA
15797264 TTGAGCAAAA
Statistics
Matches: 54, Mismatches: 3, Indels: 16
0.74 0.04 0.22
Matches are distributed among these distances:
11 9 0.17
12 2 0.04
13 10 0.19
14 18 0.33
15 1 0.02
16 1 0.02
17 2 0.04
18 10 0.19
19 1 0.02
ACGTcount: A:0.75, C:0.04, G:0.06, T:0.14
Consensus pattern (14 bp):
AAAAAAAAATTCGA
Found at i:15797216 original size:15 final size:16
Alignment explanation
Indices: 15797198--15797252 Score: 71
Period size: 15 Copynumber: 3.5 Consensus size: 16
15797188 AAAAAAAATC
15797198 AAAAAAAA-ATTCGAA
1 AAAAAAAATATTCGAA
15797213 AAAAAAAATTGATT-GAA
1 AAAAAAAA-T-ATTCGAA
15797230 AAAAAAAATATTC-AA
1 AAAAAAAATATTCGAA
15797245 AAAAAAAA
1 AAAAAAAA
15797253 GTGAAAAAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 8
0.82 0.00 0.18
Matches are distributed among these distances:
15 21 0.58
16 1 0.03
17 11 0.31
18 3 0.08
ACGTcount: A:0.75, C:0.04, G:0.05, T:0.16
Consensus pattern (16 bp):
AAAAAAAATATTCGAA
Found at i:15797220 original size:17 final size:17
Alignment explanation
Indices: 15797198--15797252 Score: 53
Period size: 16 Copynumber: 3.4 Consensus size: 17
15797188 AAAAAAAATC
15797198 AAAAAAAAATTCGAAAA
1 AAAAAAAAATTCGAAAA
**
15797215 AAAAAATTGATT-G-AAA
1 AAAAAA-AAATTCGAAAA
*
15797231 AAAAAAATATTC-AAAA
1 AAAAAAAAATTCGAAAA
15797247 AAAAAA
1 AAAAAA
15797253 GTGAAAAAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 7
0.74 0.10 0.17
Matches are distributed among these distances:
15 3 0.10
16 18 0.58
17 7 0.23
18 3 0.10
ACGTcount: A:0.75, C:0.04, G:0.05, T:0.16
Consensus pattern (17 bp):
AAAAAAAAATTCGAAAA
Found at i:15798368 original size:17 final size:18
Alignment explanation
Indices: 15798336--15798369 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
15798326 AAAAGAGAGT
*
15798336 GAGATTGAAGGAAGAAAC
1 GAGAGTGAAGGAAGAAAC
15798354 GAGAGTGAA-GAAGAAA
1 GAGAGTGAAGGAAGAAA
15798370 GGAGTGTTGT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.53, C:0.03, G:0.35, T:0.09
Consensus pattern (18 bp):
GAGAGTGAAGGAAGAAAC
Found at i:15799658 original size:20 final size:20
Alignment explanation
Indices: 15799635--15799688 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
15799625 AGTTTTTCCC
*
15799635 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTCACATG
* ***
15799655 AGCTTAATTTAGCTCGTTTG
1 AGCTCAATTTAGCTCACATG
15799675 AGCTCAATTTAGCT
1 AGCTCAATTTAGCT
15799689 TACTTTAGCT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.24, C:0.20, G:0.19, T:0.37
Consensus pattern (20 bp):
AGCTCAATTTAGCTCACATG
Found at i:15799670 original size:30 final size:30
Alignment explanation
Indices: 15799635--15799708 Score: 98
Period size: 30 Copynumber: 2.5 Consensus size: 30
15799625 AGTTTTTCCC
15799635 AGCTCGATTT-AGCTCACA-TGAGCTTAATTT
1 AGCTCG-TTTGAGCTCA-ATTGAGCTTAATTT
* *
15799665 AGCTCGTTTGAGCTCAATTTAGCTTACTTT
1 AGCTCGTTTGAGCTCAATTGAGCTTAATTT
15799695 AGCTCGTTTGAGCT
1 AGCTCGTTTGAGCT
15799709 TGGCTTAAGT
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
29 4 0.10
30 36 0.90
ACGTcount: A:0.22, C:0.20, G:0.19, T:0.39
Consensus pattern (30 bp):
AGCTCGTTTGAGCTCAATTGAGCTTAATTT
Found at i:15799698 original size:20 final size:20
Alignment explanation
Indices: 15799635--15799699 Score: 53
Period size: 20 Copynumber: 3.2 Consensus size: 20
15799625 AGTTTTTCCC
* * * *
15799635 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTTACTTT
*
15799655 AGCTTAATTTAGC-T-CGTTT
1 AGCTCAATTTAGCTTAC-TTT
15799674 GAGCTCAATTTAGCTTACTTT
1 -AGCTCAATTTAGCTTACTTT
15799695 AGCTC
1 AGCTC
15799700 GTTTGAGCTT
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 28 0.80
21 4 0.11
22 1 0.03
ACGTcount: A:0.23, C:0.22, G:0.17, T:0.38
Consensus pattern (20 bp):
AGCTCAATTTAGCTTACTTT
Found at i:15803921 original size:22 final size:23
Alignment explanation
Indices: 15803896--15803955 Score: 63
Period size: 22 Copynumber: 2.7 Consensus size: 23
15803886 TGGACTGAAT
15803896 ATAAAAATTTAAACTAAAT-AAA
1 ATAAAAATTTAAACTAAATAAAA
*
15803918 ATAAATAA-ATAAA-TAAATAAAA
1 ATAAA-AATTTAAACTAAATAAAA
*
15803940 ATAAAACTTTACAACT
1 ATAAAAATTTA-AACT
15803956 TGGGCCACTT
Statistics
Matches: 30, Mismatches: 3, Indels: 8
0.73 0.07 0.20
Matches are distributed among these distances:
21 6 0.20
22 19 0.63
23 4 0.13
24 1 0.03
ACGTcount: A:0.67, C:0.07, G:0.00, T:0.27
Consensus pattern (23 bp):
ATAAAAATTTAAACTAAATAAAA
Found at i:15803923 original size:4 final size:4
Alignment explanation
Indices: 15803905--15803938 Score: 50
Period size: 4 Copynumber: 8.0 Consensus size: 4
15803895 TATAAAAATT
15803905 TAAA CTAAA TAAAA TAAA TAAA TAAA TAAA TAAA
1 TAAA -TAAA T-AAA TAAA TAAA TAAA TAAA TAAA
15803939 AATAAAACTT
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
4 20 0.71
5 8 0.29
ACGTcount: A:0.74, C:0.03, G:0.00, T:0.24
Consensus pattern (4 bp):
TAAA
Found at i:15804699 original size:19 final size:19
Alignment explanation
Indices: 15804675--15804716 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
15804665 TTCATTCTCT
*
15804675 TTTTTTGAATTTTCTTTTC
1 TTTTTTCAATTTTCTTTTC
*
15804694 TTTTTTCATTTTTCTTTTC
1 TTTTTTCAATTTTCTTTTC
15804713 TTTT
1 TTTT
15804717 GTATTTTCAC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.07, C:0.12, G:0.02, T:0.79
Consensus pattern (19 bp):
TTTTTTCAATTTTCTTTTC
Found at i:15804716 original size:24 final size:26
Alignment explanation
Indices: 15804684--15804737 Score: 76
Period size: 24 Copynumber: 2.2 Consensus size: 26
15804674 TTTTTTTGAA
*
15804684 TTTTCTTTTCTTTTTTCA-T-TTTTC
1 TTTTCTTTTCTATTTTCACTCTTTTC
*
15804708 TTTTCTTTTGTATTTTCACTCTTTTC
1 TTTTCTTTTCTATTTTCACTCTTTTC
15804734 TTTT
1 TTTT
15804738 TCTCTCATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
24 16 0.62
25 1 0.04
26 9 0.35
ACGTcount: A:0.06, C:0.17, G:0.02, T:0.76
Consensus pattern (26 bp):
TTTTCTTTTCTATTTTCACTCTTTTC
Found at i:15806782 original size:21 final size:20
Alignment explanation
Indices: 15806756--15806794 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
15806746 ACTTACAAAC
15806756 TCGAAACACTTTTTTTTTATA
1 TCGAAA-ACTTTTTTTTTATA
15806777 TCGAAAACTTTTTTTTTA
1 TCGAAAACTTTTTTTTTA
15806795 ATTGCGTGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.28, C:0.13, G:0.05, T:0.54
Consensus pattern (20 bp):
TCGAAAACTTTTTTTTTATA
Found at i:15806951 original size:13 final size:13
Alignment explanation
Indices: 15806933--15806957 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
15806923 AAACCGTATG
15806933 CAATTTTTTTTTT
1 CAATTTTTTTTTT
15806946 CAATTTTTTTTT
1 CAATTTTTTTTT
15806958 CGAACTCTTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.16, C:0.08, G:0.00, T:0.76
Consensus pattern (13 bp):
CAATTTTTTTTTT
Found at i:15807152 original size:24 final size:24
Alignment explanation
Indices: 15807121--15807169 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
15807111 CAAGAAGAAG
15807121 ATAGAATATATTTGAGTTCAAAGA
1 ATAGAATATATTTGAGTTCAAAGA
15807145 ATAGAATATATTTGAGTTCAAAGA
1 ATAGAATATATTTGAGTTCAAAGA
15807169 A
1 A
15807170 GTAAAGTAAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.47, C:0.04, G:0.16, T:0.33
Consensus pattern (24 bp):
ATAGAATATATTTGAGTTCAAAGA
Found at i:15807326 original size:22 final size:22
Alignment explanation
Indices: 15807296--15807339 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
15807286 TTTGGTATTT
15807296 GGGAATTGGTACGAAATGGTAA
1 GGGAATTGGTACGAAATGGTAA
*
15807318 GGGATTTGGTACGAAATGGTAA
1 GGGAATTGGTACGAAATGGTAA
15807340 TGGTTCAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.34, C:0.05, G:0.36, T:0.25
Consensus pattern (22 bp):
GGGAATTGGTACGAAATGGTAA
Found at i:15813197 original size:28 final size:27
Alignment explanation
Indices: 15813140--15813197 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 27
15813130 TTGTATGAGT
* *
15813140 TTAGGACATATTTAAGACACTAAATAA
1 TTAGGACATATCTAAAACACTAAATAA
* *
15813167 TTAGGACATATCTAATAACACTCAATTA
1 TTAGGACATATCTAA-AACACTAAATAA
15813195 TTA
1 TTA
15813198 TTTGACCAGA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
27 14 0.54
28 12 0.46
ACGTcount: A:0.45, C:0.14, G:0.09, T:0.33
Consensus pattern (27 bp):
TTAGGACATATCTAAAACACTAAATAA
Found at i:15818104 original size:22 final size:23
Alignment explanation
Indices: 15818076--15818118 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
15818066 TATTTGGGAA
15818076 TTGGTACGAAATGGT-ATGGTAT
1 TTGGTACGAAATGGTAATGGTAT
*
15818098 TTGGTACGAATTGGTAATGGT
1 TTGGTACGAAATGGTAATGGT
15818119 TCAAAGAGGT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.26, C:0.05, G:0.33, T:0.37
Consensus pattern (23 bp):
TTGGTACGAAATGGTAATGGTAT
Found at i:15819748 original size:20 final size:20
Alignment explanation
Indices: 15819725--15819771 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
15819715 GGGTTAAGAT
*
15819725 TGAGCTGAATTGAGCTTGAA
1 TGAGCTGAATTGAGCTCGAA
* * *
15819745 TGAGTTGACTTGAGCTCGAG
1 TGAGCTGAATTGAGCTCGAA
15819765 TGAGCTG
1 TGAGCTG
15819772 GAAACAAGCT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.23, C:0.13, G:0.34, T:0.30
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCGAA
Found at i:15820628 original size:20 final size:20
Alignment explanation
Indices: 15820582--15820628 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
15820572 AGCTCGTTTC
*
15820582 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* *
15820602 CAACTCACTCAAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
15820622 CAGCTCA
1 CAGCTCA
15820629 ATCTTAACCC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.30, C:0.36, G:0.13, T:0.21
Consensus pattern (20 bp):
CAGCTCACTCAAGCTCAAGT
Found at i:15833781 original size:8 final size:8
Alignment explanation
Indices: 15833770--15833799 Score: 60
Period size: 8 Copynumber: 3.8 Consensus size: 8
15833760 TGCGGTTTTC
15833770 GGGGTATA
1 GGGGTATA
15833778 GGGGTATA
1 GGGGTATA
15833786 GGGGTATA
1 GGGGTATA
15833794 GGGGTA
1 GGGGTA
15833800 AAATTGGAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.23, C:0.00, G:0.53, T:0.23
Consensus pattern (8 bp):
GGGGTATA
Found at i:15833943 original size:24 final size:23
Alignment explanation
Indices: 15833911--15833984 Score: 130
Period size: 23 Copynumber: 3.2 Consensus size: 23
15833901 GTCTCCAGAC
15833911 TTTTTTTTGCTTTCAAATTTCTCT
1 TTTTTTTTGCTTTCAAATTTCT-T
*
15833935 TTTTTTTTGCTTTCGAATTTCTT
1 TTTTTTTTGCTTTCAAATTTCTT
15833958 TTTTTTTTGCTTTCAAATTTCTT
1 TTTTTTTTGCTTTCAAATTTCTT
15833981 TTTT
1 TTTT
15833985 GAAATCCCGA
Statistics
Matches: 48, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
23 27 0.56
24 21 0.44
ACGTcount: A:0.11, C:0.14, G:0.05, T:0.70
Consensus pattern (23 bp):
TTTTTTTTGCTTTCAAATTTCTT
Found at i:15837594 original size:16 final size:16
Alignment explanation
Indices: 15837573--15837615 Score: 86
Period size: 16 Copynumber: 2.7 Consensus size: 16
15837563 CAAAAAAATC
15837573 AAAAAAAAATTGATTG
1 AAAAAAAAATTGATTG
15837589 AAAAAAAAATTGATTG
1 AAAAAAAAATTGATTG
15837605 AAAAAAAAATT
1 AAAAAAAAATT
15837616 CAAAAAAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.09, T:0.23
Consensus pattern (16 bp):
AAAAAAAAATTGATTG
Found at i:15837600 original size:12 final size:12
Alignment explanation
Indices: 15837601--15837639 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
15837591 AAAAAAATTG
15837601 ATTGAAAAAAAA
1 ATTGAAAAAAAA
*
15837613 ATTCAAAAAAAAA
1 ATT-GAAAAAAAA
*
15837626 AGTGAAAAAAAA
1 ATTGAAAAAAAA
15837638 AT
1 AT
15837640 CGAGCAAAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
12 12 0.55
13 10 0.45
ACGTcount: A:0.74, C:0.03, G:0.08, T:0.15
Consensus pattern (12 bp):
ATTGAAAAAAAA
Found at i:15837621 original size:13 final size:13
Alignment explanation
Indices: 15837605--15837638 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
15837595 AAATTGATTG
*
15837605 AAAAAAAAATTCA
1 AAAAAAAAAGTCA
*
15837618 AAAAAAAAAGTGA
1 AAAAAAAAAGTCA
15837631 AAAAAAAA
1 AAAAAAAA
15837639 TCGAGCAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.82, C:0.03, G:0.06, T:0.09
Consensus pattern (13 bp):
AAAAAAAAAGTCA
Found at i:15837647 original size:28 final size:28
Alignment explanation
Indices: 15837616--15837689 Score: 87
Period size: 28 Copynumber: 2.6 Consensus size: 28
15837606 AAAAAAAATT
*
15837616 CAAAAAAAAAAGTGAAAAAAAAATCGAG
1 CAAAAAAAAAAGTGAAAAAAAAATCAAG
* *
15837644 CAAAAAAAAAGGTGACCAAAAAAATCAAG
1 CAAAAAAAAAAGTGA-AAAAAAAATCAAG
**
15837673 -TTAAAAAAAAGTGAAAA
1 CAAAAAAAAAAGTGAAAA
15837690 GTCTTGCGAG
Statistics
Matches: 38, Mismatches: 7, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
27 2 0.05
28 25 0.66
29 11 0.29
ACGTcount: A:0.69, C:0.08, G:0.14, T:0.09
Consensus pattern (28 bp):
CAAAAAAAAAAGTGAAAAAAAAATCAAG
Found at i:15837664 original size:29 final size:28
Alignment explanation
Indices: 15837616--15837689 Score: 87
Period size: 29 Copynumber: 2.6 Consensus size: 28
15837606 AAAAAAAATT
* *
15837616 CAAAAAAAAAAGTGAAAAAAAAATCGAG
1 CAAAAAAAAAGGTGAAAAAAAAATCAAG
*
15837644 CAAAAAAAAAGGTGACCAAAAAAATCAAG
1 CAAAAAAAAAGGTGA-AAAAAAAATCAAG
**
15837673 TTAAAAAAAA-GTGAAAA
1 CAAAAAAAAAGGTGAAAA
15837690 GTCTTGCGAG
Statistics
Matches: 39, Mismatches: 6, Indels: 3
0.81 0.12 0.06
Matches are distributed among these distances:
27 2 0.05
28 18 0.46
29 19 0.49
ACGTcount: A:0.69, C:0.08, G:0.14, T:0.09
Consensus pattern (28 bp):
CAAAAAAAAAGGTGAAAAAAAAATCAAG
Found at i:15838579 original size:18 final size:18
Alignment explanation
Indices: 15838558--15838592 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
15838548 AGAAAAGAAA
15838558 ATTGA-AAAAGAAATTGAG
1 ATTGAGAAAA-AAATTGAG
15838576 ATTGAGAAAAAAATTGA
1 ATTGAGAAAAAAATTGA
15838593 AAAAGAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.57, C:0.00, G:0.20, T:0.23
Consensus pattern (18 bp):
ATTGAGAAAAAAATTGAG
Found at i:15848407 original size:17 final size:18
Alignment explanation
Indices: 15848387--15848422 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
15848377 CACACTCATT
15848387 TTCTCAATGTTTTT-TTC
1 TTCTCAATGTTTTTCTTC
*
15848404 TTCTCCATGTTTTTCTTC
1 TTCTCAATGTTTTTCTTC
15848422 T
1 T
15848423 ATTGCTGCCT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 13 0.76
18 4 0.24
ACGTcount: A:0.08, C:0.22, G:0.06, T:0.64
Consensus pattern (18 bp):
TTCTCAATGTTTTTCTTC
Found at i:15851432 original size:12 final size:12
Alignment explanation
Indices: 15851415--15851460 Score: 65
Period size: 12 Copynumber: 3.8 Consensus size: 12
15851405 TTGTAGATTC
*
15851415 AAAAAAAATAAA
1 AAAAAAAATGAA
15851427 AAAAAAAATCGAA
1 AAAAAAAAT-GAA
*
15851440 AAAAAAATTGAA
1 AAAAAAAATGAA
15851452 AAAAAAAAT
1 AAAAAAAAT
15851461 TTGCATACGG
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
12 20 0.67
13 10 0.33
ACGTcount: A:0.83, C:0.02, G:0.04, T:0.11
Consensus pattern (12 bp):
AAAAAAAATGAA
Found at i:15853160 original size:21 final size:21
Alignment explanation
Indices: 15853111--15853177 Score: 71
Period size: 21 Copynumber: 3.1 Consensus size: 21
15853101 CCTCTTTGAA
* * *
15853111 CCATAACCAATTCGTACCAAATA
1 CCAT-ACCATTTCATACC-AATT
*
15853134 CCATACTATTTCATACCAATT
1 CCATACCATTTCATACCAATT
*
15853155 CCATACCATTTCGTACCAATT
1 CCATACCATTTCATACCAATT
15853176 CC
1 CC
15853178 CAAATACCAA
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
21 24 0.63
22 10 0.26
23 4 0.11
ACGTcount: A:0.34, C:0.33, G:0.03, T:0.30
Consensus pattern (21 bp):
CCATACCATTTCATACCAATT
Found at i:15853521 original size:12 final size:12
Alignment explanation
Indices: 15853476--15853523 Score: 71
Period size: 12 Copynumber: 3.9 Consensus size: 12
15853466 ATAGGTGCGT
15853476 AAAAAAAAAGTTCG
1 AAAAAAAAA-TT-G
15853490 -AAAAAAAATTG
1 AAAAAAAAATTG
15853501 AAAAAAAAATTG
1 AAAAAAAAATTG
15853513 AAAAAAAAATT
1 AAAAAAAAATT
15853524 TTCGATATAA
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
11 1 0.03
12 24 0.73
13 8 0.24
ACGTcount: A:0.73, C:0.02, G:0.08, T:0.17
Consensus pattern (12 bp):
AAAAAAAAATTG
Found at i:15855616 original size:21 final size:21
Alignment explanation
Indices: 15855570--15855616 Score: 51
Period size: 21 Copynumber: 2.2 Consensus size: 21
15855560 CAAATGAGAG
*
15855570 AAAAAGAAAAGAGCGAAAATA
1 AAAAAGAAAAGAGAGAAAATA
* *
15855591 CAAAAGAAAAGA-AGAATGATA
1 AAAAAGAAAAGAGAGAA-AATA
15855612 AAAAA
1 AAAAA
15855617 AAAGAAAATT
Statistics
Matches: 21, Mismatches: 4, Indels: 2
0.78 0.15 0.07
Matches are distributed among these distances:
20 3 0.14
21 18 0.86
ACGTcount: A:0.72, C:0.04, G:0.17, T:0.06
Consensus pattern (21 bp):
AAAAAGAAAAGAGAGAAAATA
Found at i:15855631 original size:17 final size:17
Alignment explanation
Indices: 15855584--15855639 Score: 51
Period size: 17 Copynumber: 3.2 Consensus size: 17
15855574 AGAAAAGAGC
* *
15855584 GAAAATACAAAAGAAAA
1 GAAAATTCAAAAAAAAA
15855601 GAAGAATGAT-AAAAAAAAA
1 GAA-AAT--TCAAAAAAAAA
*
15855620 GAAAATTCAAAAAAAGA
1 GAAAATTCAAAAAAAAA
15855637 GAA
1 GAA
15855640 TGAAAAGAGA
Statistics
Matches: 32, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
16 1 0.03
17 14 0.44
18 6 0.19
19 11 0.34
ACGTcount: A:0.73, C:0.04, G:0.14, T:0.09
Consensus pattern (17 bp):
GAAAATTCAAAAAAAAA
Found at i:15859930 original size:21 final size:21
Alignment explanation
Indices: 15859881--15859947 Score: 71
Period size: 21 Copynumber: 3.1 Consensus size: 21
15859871 CCTCTTTGAA
* * *
15859881 CCATAACCAATTCGTACCAAATA
1 CCAT-ACCATTTCATACC-AATT
*
15859904 CCATACTATTTCATACCAATT
1 CCATACCATTTCATACCAATT
*
15859925 CCATACCATTTCGTACCAATT
1 CCATACCATTTCATACCAATT
15859946 CC
1 CC
15859948 CAAATACCAA
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
21 24 0.63
22 10 0.26
23 4 0.11
ACGTcount: A:0.34, C:0.33, G:0.03, T:0.30
Consensus pattern (21 bp):
CCATACCATTTCATACCAATT
Found at i:15869064 original size:18 final size:18
Alignment explanation
Indices: 15869043--15869077 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
15869033 AGAAAAGAAA
15869043 ATTGA-AAAAGAAATTGAG
1 ATTGAGAAAA-AAATTGAG
15869061 ATTGAGAAAAAAATTGA
1 ATTGAGAAAAAAATTGA
15869078 AAAAGAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.57, C:0.00, G:0.20, T:0.23
Consensus pattern (18 bp):
ATTGAGAAAAAAATTGAG
Found at i:15875328 original size:23 final size:24
Alignment explanation
Indices: 15875295--15875346 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
15875285 ACAAATTCTT
* *
15875295 TTTTTCATTTT-CATCACTCATTTC
1 TTTTTCATTTTGAATCACTC-TCTC
15875319 TTTTTC-TTTTGAATCACTCTCTC
1 TTTTTCATTTTGAATCACTCTCTC
15875342 TTTTT
1 TTTTT
15875347 TTATCACTCA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
23 12 0.48
24 13 0.52
ACGTcount: A:0.13, C:0.23, G:0.02, T:0.62
Consensus pattern (24 bp):
TTTTTCATTTTGAATCACTCTCTC
Found at i:15878774 original size:23 final size:22
Alignment explanation
Indices: 15878722--15878774 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
15878712 TCCACGTCTT
*
15878722 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
15878744 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
15878767 TTTCTTTT
1 TTTCTTTT
15878775 TCACTCTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 3 0.12
22 5 0.19
23 12 0.46
24 6 0.23
ACGTcount: A:0.09, C:0.19, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTCTTTTCTTTCTTTTTCTAA
Found at i:15881963 original size:847 final size:846
Alignment explanation
Indices: 15880310--15882002 Score: 3350
Period size: 847 Copynumber: 2.0 Consensus size: 846
15880300 TCTGATACCA
*
15880310 AATGATACGGGGTTGCGCGCGGGCCAAGATCGAGTTGCCAAGTCACGGGAAACTCCCTCAAGGAG
1 AATGATACGGGGTTGCGCGCGGACCAAGATCGAGTTGCCAAGTCACGGGAAACTCCCTCAAGGAG
15880375 ATTGTGATTCTGCCCAATTGAACACCAAGATAGTTTTCCCCAAATTTCGACAATCTAATTTCACC
66 ATTGTGATTCTGCCCAATTGAACACCAAGATAGTTTTCCCCAAATTTCGACAATCTAATTTCACC
15880440 CAAAAAGAGTATGGAAAAACCCTAGAAATTGGGGATTTTTGGGCTGATTCCTTAAGATAGAAAAA
131 CAAAAAGAGTATGGAAAAACCCTAGAAATTGGGGATTTTTGGGCTGATTCCTTAAGATAGAAAAA
15880505 GGCTGAAAACACAATAAGAACAGAAAATAGATTAGATAATGATTCAGCACAAGTAGAAATAAAGA
196 GGCTGAAAACACAATAAGAACAGAAAATAGATTAGATAATGATTCAGCACAAGTAGAAATAAAGA
15880570 AAGAATTGACAGTAAGAAATTAAAAGATAAGTCCTAAGAAGCCTTGAAATCTCGAAAGATCTCAC
261 AAGAATTGACAGTAAGAAATTAAAAGATAAGTCCTAAGAAGCCTTGAAATCTCGAAAGATCTCAC
15880635 AACTCCCTTCAAACGGCTCTAATCTCCCCTCCAAAGAATATCAATGGCAAGAAGAAGGTTGAAGA
326 AACTCCCTTCAAACGGCTCTAATCTCCCCTCCAAAGAATATCAATGGCAAGAAGAAGGTTGAAGA
15880700 TGGCTCCCACAATCAAAAGATTGTTAAAACAACTTCTAAAGAAAACTCAAGAGAAAATCCTTGAA
391 TGGCTCCCACAATCAAAAGATTGTTAAAACAACTTCTAAAGAAAACTCAAGAGAAAATCCTTGAA
15880765 GAACTCAAAGAAAATTCTGCTCTCAACAAATCTGAAATTTTCAATGTAATTGTAATGTAATGTAG
456 GAACTCAAAGAAAATTCTGCTCTCAACAAATCTGAAATTTTCAATGTAATTGTAATGTAATGTAG
15880830 GGTGGCTGGCCAAGCCATATAAATAGGCCTTTCAAATGTTTTCCTAATTTAATTAGAACACTAAA
521 GGTGGCTGGCCAAGCCATATAAATAGGCCTTTCAAATGTTTTCCTAATTTAATTAGAACACTAAA
15880895 ACTAAAACTAAAAAAACTCCTAATTATTTTAATATGGAAATTCGGCCAAGGGTCTTTTATTTGGG
586 ACTAAAACTAAAAAAACTCCTAATTATTTTAATATGGAAATTCGGCCAAGGGTCTTTTATTTGGG
15880960 ACTCTTGGACTGAATATAAAAATTTAAACTAAGTAAAATAAATAAATAAATAAATAAAAATAAAA
651 ACTCTTGGACTGAATATAAAAATTTAAACTAAGTAAAATAAATAAATAAATAAATAAAAATAAAA
15881025 CTTTACAACTTGGGCCACTTTGACAATTTGGCCTGATTTTCAACTAAGTATGGATGGATTTCTTG
716 CTTTACAACTTGGGCCACTTTGACAATTTGGCCTGATTTTCAACTAAGTATGGATGGATTTCTTG
15881090 ATTGGGCTGGGAATTTGCTTATTGGGCCTCGCCTTCAAGAATTTGGGCTTTTGTGACTCGTATCA
781 ATTGGGCTGGGAATTTGCTTATTGGGCCTCGCCTTCAAGAATTTGGGCTTTTGTGACTCGTATCA
15881155 T
846 T
*
15881156 AATGATACGGGGTTGCGCGTGGACCAAGATCGAGTTGCCAAGTCACGGGAAACTCCCTCAAGGAG
1 AATGATACGGGGTTGCGCGCGGACCAAGATCGAGTTGCCAAGTCACGGGAAACTCCCTCAAGGAG
15881221 ATTGTGATTCTGCCCAATTGAACACCAAGATAGTTTTCCCCAAATTTCGACAATCTAATTTCACC
66 ATTGTGATTCTGCCCAATTGAACACCAAGATAGTTTTCCCCAAATTTCGACAATCTAATTTCACC
15881286 CAAAAAGAGTATGGAAAAACCCTAGAAATTGGGGATTTTTGGGCTGATTCCTTAAGATAGAAAAA
131 CAAAAAGAGTATGGAAAAACCCTAGAAATTGGGGATTTTTGGGCTGATTCCTTAAGATAGAAAAA
15881351 GGCTGAAAACACAATAAGAACAGAAAATAGATTAGATAATGATTCAGCACAAGTAGAAATAAAGA
196 GGCTGAAAACACAATAAGAACAGAAAATAGATTAGATAATGATTCAGCACAAGTAGAAATAAAGA
15881416 AAGAATTGACAGTAAGAAATTAAAAGATAAGTCCTAAGAAGCCTTGAAATCTCGAAAGATCTCAC
261 AAGAATTGACAGTAAGAAATTAAAAGATAAGTCCTAAGAAGCCTTGAAATCTCGAAAGATCTCAC
*
15881481 AACTCCCTTCAAATGGCTCTAATCTCCCCTCCAAAGAATATCAATGGCAAGAAGAAGGTTGAAGA
326 AACTCCCTTCAAACGGCTCTAATCTCCCCTCCAAAGAATATCAATGGCAAGAAGAAGGTTGAAGA
15881546 TGGCTCCCACAATCAAAAAGATTGTTAAAACAACTTCTAAAGAAAACTCAAGAGAAAATCCTTGA
391 TGGCTCCCACAATC-AAAAGATTGTTAAAACAACTTCTAAAGAAAACTCAAGAGAAAATCCTTGA
15881611 AGAACTCAAAGAAAATTCTGCTCTCAACAAATCTGAAATTTTCAATGTAATTGTAATGTAATGTA
455 AGAACTCAAAGAAAATTCTGCTCTCAACAAATCTGAAATTTTCAATGTAATTGTAATGTAATGTA
15881676 GGGTGGCTGGCCAAGCCATATAAATAGGCCTTTCAAATGTTTTCCTAATTTAATTAGAACACTAA
520 GGGTGGCTGGCCAAGCCATATAAATAGGCCTTTCAAATGTTTTCCTAATTTAATTAGAACACTAA
15881741 AACTAAAACTAAAAAAACTCCTAATTATTTTAATATGGAAATTCGGCCAAGGGTCTTTTATTTGG
585 AACTAAAACTAAAAAAACTCCTAATTATTTTAATATGGAAATTCGGCCAAGGGTCTTTTATTTGG
15881806 GACTCTTGGACTGAATATAAAAATTTAAACTAAGTAAAATAAATAAATAAATAAATAAAAATAAA
650 GACTCTTGGACTGAATATAAAAATTTAAACTAAGTAAAATAAATAAATAAATAAATAAAAATAAA
15881871 ACTTTACAACTTGGGCCACTTTGACAATTTGGCCTGATTTTCAACTAAGTATGGATGGATTTCTT
715 ACTTTACAACTTGGGCCACTTTGACAATTTGGCCTGATTTTCAACTAAGTATGGATGGATTTCTT
15881936 GATTGGGCTGGGAATTTGCTTATTGGGCCTCGCCTTCAAGAATTTGGGCTTTTGTGACTCGTATC
780 GATTGGGCTGGGAATTTGCTTATTGGGCCTCGCCTTCAAGAATTTGGGCTTTTGTGACTCGTATC
15882001 AT
845 AT
15882003 TTTTGCTTTC
Statistics
Matches: 843, Mismatches: 3, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
846 401 0.48
847 442 0.52
ACGTcount: A:0.38, C:0.17, G:0.18, T:0.27
Consensus pattern (846 bp):
AATGATACGGGGTTGCGCGCGGACCAAGATCGAGTTGCCAAGTCACGGGAAACTCCCTCAAGGAG
ATTGTGATTCTGCCCAATTGAACACCAAGATAGTTTTCCCCAAATTTCGACAATCTAATTTCACC
CAAAAAGAGTATGGAAAAACCCTAGAAATTGGGGATTTTTGGGCTGATTCCTTAAGATAGAAAAA
GGCTGAAAACACAATAAGAACAGAAAATAGATTAGATAATGATTCAGCACAAGTAGAAATAAAGA
AAGAATTGACAGTAAGAAATTAAAAGATAAGTCCTAAGAAGCCTTGAAATCTCGAAAGATCTCAC
AACTCCCTTCAAACGGCTCTAATCTCCCCTCCAAAGAATATCAATGGCAAGAAGAAGGTTGAAGA
TGGCTCCCACAATCAAAAGATTGTTAAAACAACTTCTAAAGAAAACTCAAGAGAAAATCCTTGAA
GAACTCAAAGAAAATTCTGCTCTCAACAAATCTGAAATTTTCAATGTAATTGTAATGTAATGTAG
GGTGGCTGGCCAAGCCATATAAATAGGCCTTTCAAATGTTTTCCTAATTTAATTAGAACACTAAA
ACTAAAACTAAAAAAACTCCTAATTATTTTAATATGGAAATTCGGCCAAGGGTCTTTTATTTGGG
ACTCTTGGACTGAATATAAAAATTTAAACTAAGTAAAATAAATAAATAAATAAATAAAAATAAAA
CTTTACAACTTGGGCCACTTTGACAATTTGGCCTGATTTTCAACTAAGTATGGATGGATTTCTTG
ATTGGGCTGGGAATTTGCTTATTGGGCCTCGCCTTCAAGAATTTGGGCTTTTGTGACTCGTATCA
T
Found at i:15882962 original size:14 final size:14
Alignment explanation
Indices: 15882943--15882969 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
15882933 CTAGACCGTA
15882943 TGCAATTTTTTTTT
1 TGCAATTTTTTTTT
15882957 TGCAATTTTTTTT
1 TGCAATTTTTTTT
15882970 CCTTCTTTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.15, C:0.07, G:0.07, T:0.70
Consensus pattern (14 bp):
TGCAATTTTTTTTT
Found at i:15888288 original size:20 final size:19
Alignment explanation
Indices: 15888265--15888329 Score: 51
Period size: 20 Copynumber: 3.3 Consensus size: 19
15888255 AAGCTCAAAC
15888265 GAGCTAAAGTAAGCTAAATT
1 GAGCTAAAGT-AGCTAAATT
15888285 GAGCTCAAACG-AGCTAAATT
1 GAGCT-AAA-GTAGCTAAATT
* * * *
15888305 AAGCTCATGTGAGCTAAATC
1 GAGCTAAAGT-AGCTAAATT
15888325 GAGCT
1 GAGCT
15888330 GGGAAAAACT
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 30 0.83
21 3 0.08
22 1 0.03
ACGTcount: A:0.38, C:0.17, G:0.22, T:0.23
Consensus pattern (19 bp):
GAGCTAAAGTAGCTAAATT
Found at i:15890147 original size:33 final size:33
Alignment explanation
Indices: 15890109--15890171 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
15890099 GATTACTCAC
15890109 TTCACTCG-TTTCTTTT-ACAGACTCTCTTTCTTT
1 TTCACTCGATTTCTTTTCA-AG-CTCTCTTTCTTT
*
15890142 TTCACTTGATTTCTTTTCAAGCTCTCTTTC
1 TTCACTCGATTTCTTTTCAAGCTCTCTTTC
15890172 AATTTCTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
33 16 0.59
34 10 0.37
35 1 0.04
ACGTcount: A:0.13, C:0.27, G:0.06, T:0.54
Consensus pattern (33 bp):
TTCACTCGATTTCTTTTCAAGCTCTCTTTCTTT
Found at i:15890239 original size:18 final size:18
Alignment explanation
Indices: 15890218--15890289 Score: 81
Period size: 18 Copynumber: 3.9 Consensus size: 18
15890208 TTTTCTCTCA
*
15890218 CTTTTTCGATTTCTTTTG
1 CTTTTTCAATTTCTTTTG
* *
15890236 CTTTTGCAATTTCTTTTT
1 CTTTTTCAATTTCTTTTG
**
15890254 CTTTTTCGTTTTCTTTTG
1 CTTTTTCAATTTCTTTTG
*
15890272 TTTCTTTCAATTTCTTTT
1 CTT-TTTCAATTTCTTTT
15890290 TCAATCTCTT
Statistics
Matches: 43, Mismatches: 10, Indels: 1
0.80 0.19 0.02
Matches are distributed among these distances:
18 31 0.72
19 12 0.28
ACGTcount: A:0.07, C:0.17, G:0.07, T:0.69
Consensus pattern (18 bp):
CTTTTTCAATTTCTTTTG
Found at i:15890258 original size:36 final size:37
Alignment explanation
Indices: 15890218--15890291 Score: 114
Period size: 36 Copynumber: 2.0 Consensus size: 37
15890208 TTTTCTCTCA
15890218 CTTTTTCGATTTCTTTTGCTT-TTGCAATTTCTTTTT
1 CTTTTTCGATTTCTTTTGCTTCTTGCAATTTCTTTTT
* * *
15890254 CTTTTTCGTTTTCTTTTGTTTCTTTCAATTTCTTTTT
1 CTTTTTCGATTTCTTTTGCTTCTTGCAATTTCTTTTT
15890291 C
1 C
15890292 AATCTCTTTC
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
36 19 0.56
37 15 0.44
ACGTcount: A:0.07, C:0.18, G:0.07, T:0.69
Consensus pattern (37 bp):
CTTTTTCGATTTCTTTTGCTTCTTGCAATTTCTTTTT
Found at i:15890265 original size:7 final size:6
Alignment explanation
Indices: 15890186--15890270 Score: 53
Period size: 6 Copynumber: 13.8 Consensus size: 6
15890176 TCTTTTTTCG
* * ** ** *
15890186 CTTTTT CTTTTCTT CATTTT CTTTTT CTCTCA CTTTTT CGATTT CTTTTG
1 CTTTTT C-TTT-TT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT
* ** *
15890236 CTTTTG CAATTT CTTTTT CTTTTT CGTTTT CTTTT
1 CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTT
15890271 GTTTCTTTCA
Statistics
Matches: 57, Mismatches: 20, Indels: 4
0.70 0.25 0.05
Matches are distributed among these distances:
6 49 0.86
7 5 0.09
8 3 0.05
ACGTcount: A:0.06, C:0.20, G:0.05, T:0.69
Consensus pattern (6 bp):
CTTTTT
Found at i:15894993 original size:10 final size:10
Alignment explanation
Indices: 15894980--15895069 Score: 58
Period size: 10 Copynumber: 8.9 Consensus size: 10
15894970 TTCTCGTGCA
15894980 AGCTCATTTC
1 AGCTCATTTC
15894990 AGCTCCATTTC
1 AGCT-CATTTC
* *
15895001 AGCTCCTCT-
1 AGCTCATTTC
*
15895010 AGCTCGTTTC
1 AGCTCATTTC
****
15895020 AGCTCCGACC
1 AGCTCATTTC
*
15895030 AGCTC-TATTG
1 AGCTCAT-TTC
15895040 AGCTCATTTC
1 AGCTCATTTC
15895050 AGCTACATTTC
1 AGCT-CATTTC
*
15895061 AGCTTATTT
1 AGCTCATTT
15895070 ATTTTATTGG
Statistics
Matches: 61, Mismatches: 14, Indels: 10
0.72 0.16 0.12
Matches are distributed among these distances:
9 7 0.11
10 33 0.54
11 21 0.34
ACGTcount: A:0.19, C:0.31, G:0.13, T:0.37
Consensus pattern (10 bp):
AGCTCATTTC
Found at i:15895014 original size:30 final size:31
Alignment explanation
Indices: 15894980--15895064 Score: 88
Period size: 30 Copynumber: 2.8 Consensus size: 31
15894970 TTCTCGTGCA
15894980 AGCTCATTTCAGCTCCATTTCAGCTCCT-CT-
1 AGCTCATTTCAGCTCCATTTCAGCT-CTACTG
* * *
15895010 AGCTCGTTTCAGCTCCGA--CCAGCTCTATTG
1 AGCTCATTTCAGCTCC-ATTTCAGCTCTACTG
*
15895040 AGCTCATTTCAGCTACATTTCAGCT
1 AGCTCATTTCAGCTCCATTTCAGCT
15895065 TATTTATTTT
Statistics
Matches: 44, Mismatches: 6, Indels: 9
0.75 0.10 0.15
Matches are distributed among these distances:
28 2 0.05
29 7 0.16
30 29 0.66
31 6 0.14
ACGTcount: A:0.19, C:0.33, G:0.14, T:0.34
Consensus pattern (31 bp):
AGCTCATTTCAGCTCCATTTCAGCTCTACTG
Found at i:15895878 original size:22 final size:22
Alignment explanation
Indices: 15895824--15895889 Score: 71
Period size: 21 Copynumber: 3.0 Consensus size: 22
15895814 GGTATTTGGG
* *
15895824 AATTGGTTCGAAATAGTATGG-
1 AATTGGTACGAAATGGTATGGT
*
15895845 AATTAGTACGAAATGGTATGGT
1 AATTGGTACGAAATGGTATGGT
* *
15895867 ATTTGGTACGAATTGGTAATGGT
1 AATTGGTACGAAATGGT-ATGGT
15895890 TCAAAGAGGT
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
21 18 0.49
22 14 0.38
23 5 0.14
ACGTcount: A:0.32, C:0.05, G:0.29, T:0.35
Consensus pattern (22 bp):
AATTGGTACGAAATGGTATGGT
Found at i:15898231 original size:46 final size:46
Alignment explanation
Indices: 15898179--15898268 Score: 155
Period size: 46 Copynumber: 2.0 Consensus size: 46
15898169 TGTGGCGTTC
*
15898179 ATCATATACCAAGGTTCTTATCA-TCATTGATAGTGGGTCGAGGTTT
1 ATCATATACCAAGGTTCCTATCATTC-TTGATAGTGGGTCGAGGTTT
15898225 ATCATATACCAAGGTTCCTATCATTCTTGATAGTGGGTCGAGGT
1 ATCATATACCAAGGTTCCTATCATTCTTGATAGTGGGTCGAGGT
15898269 CTTTTCTTTG
Statistics
Matches: 42, Mismatches: 1, Indels: 2
0.93 0.02 0.04
Matches are distributed among these distances:
46 40 0.95
47 2 0.05
ACGTcount: A:0.26, C:0.17, G:0.22, T:0.36
Consensus pattern (46 bp):
ATCATATACCAAGGTTCCTATCATTCTTGATAGTGGGTCGAGGTTT
Found at i:15898602 original size:11 final size:11
Alignment explanation
Indices: 15898586--15898629 Score: 52
Period size: 11 Copynumber: 3.9 Consensus size: 11
15898576 TAGTTTCTCG
15898586 AAAAAAAACTC
1 AAAAAAAACTC
* *
15898597 AAAAAAAATTTA
1 AAAAAAAA-CTC
*
15898609 AAAAAAAATTC
1 AAAAAAAACTC
15898620 AAAAAAAACT
1 AAAAAAAACT
15898630 AGTTTCCATT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
11 19 0.68
12 9 0.32
ACGTcount: A:0.75, C:0.09, G:0.00, T:0.16
Consensus pattern (11 bp):
AAAAAAAACTC
Found at i:15898603 original size:12 final size:12
Alignment explanation
Indices: 15898586--15898627 Score: 59
Period size: 12 Copynumber: 3.6 Consensus size: 12
15898576 TAGTTTCTCG
*
15898586 AAAAAAAACTC-
1 AAAAAAAATTCA
*
15898597 AAAAAAAATTTA
1 AAAAAAAATTCA
15898609 AAAAAAAATTCA
1 AAAAAAAATTCA
15898621 AAAAAAA
1 AAAAAAA
15898628 CTAGTTTCCA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
11 9 0.33
12 18 0.67
ACGTcount: A:0.79, C:0.07, G:0.00, T:0.14
Consensus pattern (12 bp):
AAAAAAAATTCA
Found at i:15898689 original size:14 final size:14
Alignment explanation
Indices: 15898670--15898716 Score: 64
Period size: 14 Copynumber: 3.6 Consensus size: 14
15898660 TCAAGTTGTG
15898670 AAAAAAAATTTTGA
1 AAAAAAAATTTTGA
*
15898684 AAAAAAAATTGTG-
1 AAAAAAAATTTTGA
15898697 AAAAAAAA--TTGA
1 AAAAAAAATTTTGA
15898709 AAAAAAAA
1 AAAAAAAA
15898717 GAGAGCTAGT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
11 2 0.07
12 8 0.27
13 8 0.27
14 12 0.40
ACGTcount: A:0.72, C:0.00, G:0.09, T:0.19
Consensus pattern (14 bp):
AAAAAAAATTTTGA
Found at i:15898695 original size:27 final size:25
Alignment explanation
Indices: 15898665--15898716 Score: 86
Period size: 27 Copynumber: 2.0 Consensus size: 25
15898655 GGATATCAAG
15898665 TTGTGAAAAAAAATTTTGAAAAAAAAA
1 TTGTGAAAAAAAA--TTGAAAAAAAAA
15898692 TTGTGAAAAAAAATTGAAAAAAAAA
1 TTGTGAAAAAAAATTGAAAAAAAAA
15898717 GAGAGCTAGT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
25 12 0.48
27 13 0.52
ACGTcount: A:0.65, C:0.00, G:0.12, T:0.23
Consensus pattern (25 bp):
TTGTGAAAAAAAATTGAAAAAAAAA
Found at i:15898716 original size:13 final size:13
Alignment explanation
Indices: 15898668--15898716 Score: 55
Period size: 13 Copynumber: 3.8 Consensus size: 13
15898658 TATCAAGTTG
**
15898668 TGAAAAAAAATTT
1 TGAAAAAAAAAAT
15898681 TG-AAAAAAAAAT
1 TGAAAAAAAAAAT
**
15898693 TGTGAAAAAAAAT
1 TGAAAAAAAAAAT
15898706 TGAAAAAAAAA
1 TGAAAAAAAAA
15898717 GAGAGCTAGT
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
12 10 0.33
13 20 0.67
ACGTcount: A:0.69, C:0.00, G:0.10, T:0.20
Consensus pattern (13 bp):
TGAAAAAAAAAAT
Found at i:15900528 original size:22 final size:22
Alignment explanation
Indices: 15900498--15900541 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
15900488 TTTGGTATTT
15900498 GGGAATTGGTACGAAATGGTAA
1 GGGAATTGGTACGAAATGGTAA
*
15900520 GGGATTTGGTACGAAATGGTAA
1 GGGAATTGGTACGAAATGGTAA
15900542 TGGTTCAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.34, C:0.05, G:0.36, T:0.25
Consensus pattern (22 bp):
GGGAATTGGTACGAAATGGTAA
Found at i:15904268 original size:10 final size:10
Alignment explanation
Indices: 15904253--15904290 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
15904243 TTGGGTTAAG
15904253 ATTGAGCTGA
1 ATTGAGCTGA
15904263 ATTGAGCTCGA
1 ATTGAGCT-GA
15904274 A-TGAGCTGA
1 ATTGAGCTGA
*
15904283 CTTGAGCT
1 ATTGAGCT
15904291 CGAGTGAGCT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
9 2 0.08
10 20 0.80
11 3 0.12
ACGTcount: A:0.26, C:0.16, G:0.29, T:0.29
Consensus pattern (10 bp):
ATTGAGCTGA
Found at i:15904278 original size:20 final size:20
Alignment explanation
Indices: 15904255--15904301 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
15904245 GGGTTAAGAT
15904255 TGAGCTGAATTGAGCTCGAA
1 TGAGCTGAATTGAGCTCGAA
* *
15904275 TGAGCTGACTTGAGCTCGAG
1 TGAGCTGAATTGAGCTCGAA
15904295 TGAGCTG
1 TGAGCTG
15904302 GAAACGAGCT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.23, C:0.17, G:0.34, T:0.26
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCGAA
Found at i:15905218 original size:119 final size:119
Alignment explanation
Indices: 15905007--15905244 Score: 476
Period size: 119 Copynumber: 2.0 Consensus size: 119
15904997 CATTTAATTA
15905007 AGTGGCTGTTCAAGTTCTTTTGAGTTACAATTAAAGGGGCTGTTATAAAGGGAGCTTAAAAATCA
1 AGTGGCTGTTCAAGTTCTTTTGAGTTACAATTAAAGGGGCTGTTATAAAGGGAGCTTAAAAATCA
15905072 TTAAAGGAGTTTTTAAAGAGCATTTTATGCCCTTTAAAATTCAGCAGCAACTCT
66 TTAAAGGAGTTTTTAAAGAGCATTTTATGCCCTTTAAAATTCAGCAGCAACTCT
15905126 AGTGGCTGTTCAAGTTCTTTTGAGTTACAATTAAAGGGGCTGTTATAAAGGGAGCTTAAAAATCA
1 AGTGGCTGTTCAAGTTCTTTTGAGTTACAATTAAAGGGGCTGTTATAAAGGGAGCTTAAAAATCA
15905191 TTAAAGGAGTTTTTAAAGAGCATTTTATGCCCTTTAAAATTCAGCAGCAACTCT
66 TTAAAGGAGTTTTTAAAGAGCATTTTATGCCCTTTAAAATTCAGCAGCAACTCT
15905245 TCCACTTCCA
Statistics
Matches: 119, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
119 119 1.00
ACGTcount: A:0.33, C:0.13, G:0.20, T:0.34
Consensus pattern (119 bp):
AGTGGCTGTTCAAGTTCTTTTGAGTTACAATTAAAGGGGCTGTTATAAAGGGAGCTTAAAAATCA
TTAAAGGAGTTTTTAAAGAGCATTTTATGCCCTTTAAAATTCAGCAGCAACTCT
Found at i:15905741 original size:46 final size:46
Alignment explanation
Indices: 15905687--15905780 Score: 154
Period size: 46 Copynumber: 2.0 Consensus size: 46
15905677 ATAGTGTGGC
* *
15905687 GTTCATCATATACCAAGGTTCTTATCA-TCATTGATAGTGGGTTGAG
1 GTTCATCATATACCAAGGTTCCTATCATTC-TTGATAGTGGGTCGAG
15905733 GTTCATCATATACCAAGGTTCCTATCATTCTTGATAGTGGGTCGAG
1 GTTCATCATATACCAAGGTTCCTATCATTCTTGATAGTGGGTCGAG
15905779 GT
1 GT
15905781 CTTTTCTTTG
Statistics
Matches: 45, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
46 43 0.96
47 2 0.04
ACGTcount: A:0.24, C:0.17, G:0.22, T:0.36
Consensus pattern (46 bp):
GTTCATCATATACCAAGGTTCCTATCATTCTTGATAGTGGGTCGAG
Found at i:15907618 original size:8 final size:7
Alignment explanation
Indices: 15907588--15907614 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
15907578 ATTCAAATGA
15907588 TCAAAAG
1 TCAAAAG
15907595 TCAAAAG
1 TCAAAAG
15907602 TCAAAAG
1 TCAAAAG
15907609 TCAAAA
1 TCAAAA
15907615 AGTCCTTTAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.59, C:0.15, G:0.11, T:0.15
Consensus pattern (7 bp):
TCAAAAG
Found at i:15912303 original size:19 final size:20
Alignment explanation
Indices: 15912279--15912323 Score: 65
Period size: 19 Copynumber: 2.3 Consensus size: 20
15912269 CTTTTCATTC
*
15912279 TCTTTTTTTGAATTTTC-TT
1 TCTTTTTTTCAATTTTCTTT
*
15912298 TCTTTTTTTCATTTTTCTTT
1 TCTTTTTTTCAATTTTCTTT
15912318 TCTTTT
1 TCTTTT
15912324 GTATTTTCGC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 15 0.65
20 8 0.35
ACGTcount: A:0.07, C:0.13, G:0.02, T:0.78
Consensus pattern (20 bp):
TCTTTTTTTCAATTTTCTTT
Found at i:15915229 original size:13 final size:13
Alignment explanation
Indices: 15915213--15915260 Score: 78
Period size: 13 Copynumber: 3.6 Consensus size: 13
15915203 AAAAAATTCA
*
15915213 AAAAAAAATTTTG
1 AAAAAAAATTGTG
15915226 AAAAAAAATTGTG
1 AAAAAAAATTGTG
15915239 AAAAAAAAATTGTG
1 -AAAAAAAATTGTG
15915253 AAAAAAAA
1 AAAAAAAA
15915261 GAGAGCTAGT
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
13 20 0.61
14 13 0.39
ACGTcount: A:0.69, C:0.00, G:0.10, T:0.21
Consensus pattern (13 bp):
AAAAAAAATTGTG
Found at i:15915229 original size:14 final size:14
Alignment explanation
Indices: 15915212--15915260 Score: 82
Period size: 14 Copynumber: 3.6 Consensus size: 14
15915202 AAAAAAATTC
*
15915212 AAAAAAAAATTTTG
1 AAAAAAAAATTGTG
15915226 -AAAAAAAATTGTG
1 AAAAAAAAATTGTG
15915239 AAAAAAAAATTGTG
1 AAAAAAAAATTGTG
15915253 AAAAAAAA
1 AAAAAAAA
15915261 GAGAGCTAGT
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
13 12 0.36
14 21 0.64
ACGTcount: A:0.69, C:0.00, G:0.10, T:0.20
Consensus pattern (14 bp):
AAAAAAAAATTGTG
Found at i:15916693 original size:20 final size:20
Alignment explanation
Indices: 15916647--15916693 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
15916637 AGCTCGTTTC
*
15916647 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* * *
15916667 CAACTCATTCAAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
15916687 CAGCTCA
1 CAGCTCA
15916694 ATCTTAACCC
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.30, C:0.34, G:0.13, T:0.23
Consensus pattern (20 bp):
CAGCTCACTCAAGCTCAAGT
Found at i:15922446 original size:15 final size:14
Alignment explanation
Indices: 15922426--15922473 Score: 60
Period size: 15 Copynumber: 3.3 Consensus size: 14
15922416 CTCATTTTCA
15922426 TCTTTTTCTTTTATT
1 TCTTTTTCTTTT-TT
*
15922441 TCTTTTTCTTTTTC
1 TCTTTTTCTTTTTT
*
15922455 TCTCATTTCTTTTTT
1 TCT-TTTTCTTTTTT
15922470 TCTT
1 TCTT
15922474 CTCTCAATTT
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
14 4 0.14
15 24 0.86
ACGTcount: A:0.04, C:0.19, G:0.00, T:0.77
Consensus pattern (14 bp):
TCTTTTTCTTTTTT
Found at i:15922478 original size:22 final size:21
Alignment explanation
Indices: 15922426--15922484 Score: 75
Period size: 21 Copynumber: 2.8 Consensus size: 21
15922416 CTCATTTTCA
* *
15922426 TCTTTTTCTTTTATTTCTTTT
1 TCTTTTTCTCTCATTTCTTTT
15922447 TCTTTTTCTCTCATTTCTTTT
1 TCTTTTTCTCTCATTTCTTTT
*
15922468 T-TTCTTCTCTCAATTTC
1 TCTTTTTCTCTC-ATTTC
15922485 ATTCAAGATT
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
20 9 0.26
21 25 0.74
ACGTcount: A:0.07, C:0.22, G:0.00, T:0.71
Consensus pattern (21 bp):
TCTTTTTCTCTCATTTCTTTT
Found at i:15923406 original size:31 final size:32
Alignment explanation
Indices: 15923371--15923444 Score: 116
Period size: 31 Copynumber: 2.4 Consensus size: 32
15923361 TTTCAATCAC
**
15923371 TCTTTTTTTTTCAATTTTG-ATTTTTTTTTCT
1 TCTTTTTTTTTCAATTCCGAATTTTTTTTTCT
15923402 TCTTTTTTTTT-AATTCCGAATTTTTTTTTCT
1 TCTTTTTTTTTCAATTCCGAATTTTTTTTTCT
15923433 TCTTTTTTTTTC
1 TCTTTTTTTTTC
15923445 TTCAATACTA
Statistics
Matches: 39, Mismatches: 2, Indels: 3
0.89 0.05 0.07
Matches are distributed among these distances:
30 5 0.13
31 34 0.87
ACGTcount: A:0.09, C:0.12, G:0.03, T:0.76
Consensus pattern (32 bp):
TCTTTTTTTTTCAATTCCGAATTTTTTTTTCT
Done.