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 173 of 190
Found at i:28659009 original size:53 final size:53
Alignment explanation
Indices: 28658895--28659082 Score: 139
Period size: 53 Copynumber: 3.4 Consensus size: 53
28658885 CAAAAACAAA
* * *
28658895 AAAAAAAGAAAAAGAATTTCTAAATAGGCCCAAAT-AGTGAAAAATTTAGAAATTTC
1 AAAAAAAG-AAAA-TATTTTTAAATAGACCCAAATGA-TGAAAAATTTAGAAA-TTC
* * * *
28658951 -GAAAAAGAAAATATTTTTAAATTGACCCAAATGATGAAAAATTTATAAATCC
1 AAAAAAAGAAAATATTTTTAAATAGACCCAAATGATGAAAAATTTAGAAATTC
* * * * *
28659003 AAAAAAATACATAAATAAAATTTTTAAATAGGCTCAAATGGT-AGAGAATTTAGAAATTC
1 -AAAAAA-AGA-AAAT---ATTTTTAAATAGACCCAAATGATGA-AAAATTTAGAAATTC
*
28659062 AAAACAAGAAAATATTTTTAA
1 AAAAAAAGAAAATATTTTTAA
28659083 TTTGACTCAA
Statistics
Matches: 105, Mismatches: 18, Indels: 21
0.73 0.12 0.15
Matches are distributed among these distances:
52 2 0.02
53 39 0.37
54 9 0.09
55 8 0.08
56 8 0.08
57 2 0.02
58 6 0.06
59 31 0.30
ACGTcount: A:0.54, C:0.08, G:0.11, T:0.27
Consensus pattern (53 bp):
AAAAAAAGAAAATATTTTTAAATAGACCCAAATGATGAAAAATTTAGAAATTC
Found at i:28660380 original size:46 final size:46
Alignment explanation
Indices: 28660311--28660511 Score: 264
Period size: 46 Copynumber: 4.4 Consensus size: 46
28660301 TTGAATCTTT
* * *
28660311 AAATGAGAATTTTTTAGTTTTAAATGAAAATCTTTAAGATATTTTC
1 AAATGAGAATCTTTGAGTCTTAAATGAAAATCTTTAAGATATTTTC
* *
28660357 AAATGAGAATCTTTGAATCTTAAATGAAAAT-TTTAAGATGTTTTC
1 AAATGAGAATCTTTGAGTCTTAAATGAAAATCTTTAAGATATTTTC
* * *
28660402 AAATGAGAACCTTTGAGTTTTAAAT-AAGAATCTTTAAGACATTTTC
1 AAATGAGAATCTTTGAGTCTTAAATGAA-AATCTTTAAGATATTTTC
*
28660448 AAATGAGAA-CATTTGAGTCTTAAATGAGAATCTTTAAGATATTTTC
1 AAATGAGAATC-TTTGAGTCTTAAATGAAAATCTTTAAGATATTTTC
* *
28660494 AAATCAGAATATTTGAGT
1 AAATGAGAATCTTTGAGT
28660512 TTTGAGTTTC
Statistics
Matches: 135, Mismatches: 15, Indels: 10
0.84 0.09 0.06
Matches are distributed among these distances:
44 2 0.01
45 39 0.29
46 93 0.69
47 1 0.01
ACGTcount: A:0.40, C:0.07, G:0.13, T:0.39
Consensus pattern (46 bp):
AAATGAGAATCTTTGAGTCTTAAATGAAAATCTTTAAGATATTTTC
Found at i:28660469 original size:91 final size:92
Alignment explanation
Indices: 28660311--28660514 Score: 288
Period size: 91 Copynumber: 2.2 Consensus size: 92
28660301 TTGAATCTTT
* * *
28660311 AAATGAGAATTTTTTAGTTTTAAATGAAAATCTTTAAGATATTTTCAAATGAGAATCTTTGAATC
1 AAATGAGAATATTTGAGTTTTAAATGAAAATCTTTAAGACATTTTCAAATGAGAATCTTTGAATC
*
28660376 TTAAATGAAAAT-TTTAAGATGTTTTC
66 TTAAATGAAAATCTTTAAGATATTTTC
** *
28660402 AAATGAGAACCTTTGAGTTTTAAAT-AAGAATCTTTAAGACATTTTCAAATGAGAA-CATTTGAG
1 AAATGAGAATATTTGAGTTTTAAATGAA-AATCTTTAAGACATTTTCAAATGAGAATC-TTTGAA
*
28660465 TCTTAAATGAGAATCTTTAAGATATTTTC
64 TCTTAAATGAAAATCTTTAAGATATTTTC
*
28660494 AAATCAGAATATTTGAGTTTT
1 AAATGAGAATATTTGAGTTTT
28660515 GAGTTTCAAA
Statistics
Matches: 100, Mismatches: 10, Indels: 5
0.87 0.09 0.04
Matches are distributed among these distances:
90 3 0.03
91 66 0.66
92 31 0.31
ACGTcount: A:0.39, C:0.07, G:0.13, T:0.40
Consensus pattern (92 bp):
AAATGAGAATATTTGAGTTTTAAATGAAAATCTTTAAGACATTTTCAAATGAGAATCTTTGAATC
TTAAATGAAAATCTTTAAGATATTTTC
Found at i:28661002 original size:41 final size:41
Alignment explanation
Indices: 28660899--28661242 Score: 331
Period size: 41 Copynumber: 8.4 Consensus size: 41
28660889 ATGATTGTCT
* * * *
28660899 AGGAGCTTTTTATTTTTCAAAGTCATTGTGTCTCTGTTTAG
1 AGGAGCCTTTTATTTTTCAAAGTCGTTATGCCTCTGTTTAG
28660940 AGG-GCCTTTTATTTTTCAAAGTCGTTATGCCTCTGTTTAG
1 AGGAGCCTTTTATTTTTCAAAGTCGTTATGCCTCTGTTTAG
** * *
28660980 AGGAGTGTTTTATTTTTCAAAGTGGTTGTGCCTCTGTTTAG
1 AGGAGCCTTTTATTTTTCAAAGTCGTTATGCCTCTGTTTAG
* * *
28661021 AGGAGCCTTTTATTTTTCAAAGTCATTGTGCTTCTGTTTAG
1 AGGAGCCTTTTATTTTTCAAAGTCGTTATGCCTCTGTTTAG
* * * *
28661062 ATGG-GCATTTTATTTTTCAAAGTCGTTCTGCTTCTGTTTAA
1 A-GGAGCCTTTTATTTTTCAAAGTCGTTATGCCTCTGTTTAG
** * *
28661103 AGGAGATTTTTATTTTTTTAAAGTCGTTGA-ACCTCTGTTTAG
1 AGGAGCCTTTTA-TTTTTCAAAGTCGTT-ATGCCTCTGTTTAG
* ***
28661145 AGAAG-CTTTTATTTTTCAAAGTCGTTGA-GCCTCTACCTAG
1 AGGAGCCTTTTATTTTTCAAAGTCGTT-ATGCCTCTGTTTAG
* * * * *
28661185 ATGAGCATTTTATTTTTCAAAGTTGTTGA-GCCTTTGCTTAG
1 AGGAGCCTTTTATTTTTCAAAGTCGTT-ATGCCTCTGTTTAG
* *
28661226 AGGAGCTTTTTTTTTTT
1 AGGAGCCTTTTATTTTT
28661243 ATTTTTTCAA
Statistics
Matches: 256, Mismatches: 41, Indels: 12
0.83 0.13 0.04
Matches are distributed among these distances:
40 65 0.25
41 162 0.63
42 29 0.11
ACGTcount: A:0.20, C:0.13, G:0.20, T:0.47
Consensus pattern (41 bp):
AGGAGCCTTTTATTTTTCAAAGTCGTTATGCCTCTGTTTAG
Found at i:28661117 original size:123 final size:124
Alignment explanation
Indices: 28660899--28661207 Score: 412
Period size: 123 Copynumber: 2.5 Consensus size: 124
28660889 ATGATTGTCT
* *
28660899 AGGAGCTTTTTATTTTTCAAAGTCATTGTG-TCTCTGTTTAGA-GGGCCTTTTATTTTTCAAAGT
1 AGGAGCCTTTTATTTTTCAAAGTCATTGTGCT-TCTGTTTAGATGGGCATTTTATTTTTCAAAGT
* * **
28660962 CGTTATGCCTCTGTTTAGAGGAGTGTTTTA-TTTTTCAAAGTGGTTGTGCCTCTGTTTAG
65 CGTTATGCCTCTGTTTAAAGGAGTGTTTTATTTTTTCAAAGTCGTTGAACCTCTGTTTAG
28661021 AGGAGCCTTTTATTTTTCAAAGTCATTGTGCTTCTGTTTAGATGGGCATTTTATTTTTCAAAGTC
1 AGGAGCCTTTTATTTTTCAAAGTCATTGTGCTTCTGTTTAGATGGGCATTTTATTTTTCAAAGTC
* * *
28661086 GTTCTGCTTCTGTTTAAAGGAGAT-TTTTATTTTTTTAAAGTCGTTGAACCTCTGTTTAG
66 GTTATGCCTCTGTTTAAAGGAG-TGTTTTATTTTTTCAAAGTCGTTGAACCTCTGTTTAG
* * * * *** *
28661145 AGAAG-CTTTTATTTTTCAAAGTCGTTGAGCCTCTACCTAGATGAGCATTTTATTTTTCAAAGT
1 AGGAGCCTTTTATTTTTCAAAGTCATTGTGCTTCTGTTTAGATGGGCATTTTATTTTTCAAAGT
28661208 TGTTGAGCCT
Statistics
Matches: 166, Mismatches: 17, Indels: 7
0.87 0.09 0.04
Matches are distributed among these distances:
122 39 0.23
123 97 0.58
124 30 0.18
ACGTcount: A:0.21, C:0.14, G:0.19, T:0.46
Consensus pattern (124 bp):
AGGAGCCTTTTATTTTTCAAAGTCATTGTGCTTCTGTTTAGATGGGCATTTTATTTTTCAAAGTC
GTTATGCCTCTGTTTAAAGGAGTGTTTTATTTTTTCAAAGTCGTTGAACCTCTGTTTAG
Found at i:28661230 original size:123 final size:122
Alignment explanation
Indices: 28660906--28661242 Score: 405
Period size: 123 Copynumber: 2.7 Consensus size: 122
28660896 TCTAGGAGCT
* *
28660906 TTTTATTTTTCAAAGTCATTGTGTCTCTGTTTAGA-GGGCCTTTTATTTTTCAAAGTCGTTATGC
1 TTTTATTTTTCAAAGTCATTGTGCCTCTGTTTAGATGGGCATTTTATTTTTCAAAGTCGTTA-GC
* * ** *
28660970 CTCTGTTTAGAGGAGTGTTTTA-TTTTTCAAAGTGGTTGTGCCTCTGTTTAGAGGAGCC
65 CTTTGTTTAGAGGAGT-TTTTATTTTTTCAAAGTCGTTGAACCTCTGTTTAGAGAAGCC
* *
28661028 TTTTATTTTTCAAAGTCATTGTGCTTCTGTTTAGATGGGCATTTTATTTTTCAAAGTCGTTCTG-
1 TTTTATTTTTCAAAGTCATTGTGCCTCTGTTTAGATGGGCATTTTATTTTTCAAAGTCGTT-AGC
* *
28661092 CTTCTGTTTAAAGGAGATTTTTATTTTTTTAAAGTCGTTGAACCTCTGTTTAGAGAAG-C
65 CTT-TGTTTAGAGGAG-TTTTTATTTTTTCAAAGTCGTTGAACCTCTGTTTAGAGAAGCC
* * *** * *
28661151 TTTTATTTTTCAAAGTCGTTGAGCCTCTACCTAGATGAGCATTTTATTTTTCAAAGTTGTTGAGC
1 TTTTATTTTTCAAAGTCATTGTGCCTCTGTTTAGATGGGCATTTTATTTTTCAAAGTCGTT-AGC
*
28661216 CTTTGCTTAGAGGAGCTTTTT-TTTTTT
65 CTTTGTTTAGAGGAG-TTTTTATTTTTT
28661243 ATTTTTTCAA
Statistics
Matches: 185, Mismatches: 24, Indels: 12
0.84 0.11 0.05
Matches are distributed among these distances:
122 41 0.22
123 111 0.60
124 33 0.18
ACGTcount: A:0.20, C:0.13, G:0.19, T:0.47
Consensus pattern (122 bp):
TTTTATTTTTCAAAGTCATTGTGCCTCTGTTTAGATGGGCATTTTATTTTTCAAAGTCGTTAGCC
TTTGTTTAGAGGAGTTTTTATTTTTTCAAAGTCGTTGAACCTCTGTTTAGAGAAGCC
Found at i:28661242 original size:82 final size:82
Alignment explanation
Indices: 28660899--28661242 Score: 385
Period size: 82 Copynumber: 4.2 Consensus size: 82
28660889 ATGATTGTCT
* * *
28660899 AGGAGCTTTTTATTTTTCAAAGTCATTGTGTCTCTGTTTAGAGG-GCCTTTTATTTTTCAAAGTC
1 AGGAGCTTTTTATTTTTCAAAGTCGTTGTGCCTCTGTTTAGAGGAGCATTTTATTTTTCAAAGTC
28660963 GTT-ATGCCTCTGTTTAG
66 GTTGA-GCCTCTGTTTAG
* *
28660980 AGGAG-TGTTTTATTTTTCAAAGTGGTTGTGCCTCTGTTTAGAGGAGCCTTTTATTTTTCAAAGT
1 AGGAGCT-TTTTATTTTTCAAAGTCGTTGTGCCTCTGTTTAGAGGAGCATTTTATTTTTCAAAGT
* * *
28661044 CATTGTGCTTCTGTTTAG
65 CGTTGAGCCTCTGTTTAG
* * * * *
28661062 ATGG-GCATTTTATTTTTCAAAGTCGTTCTGCTTCTGTTTAAAGGAG-ATTTTTATTTTTTTAAA
1 A-GGAGCTTTTTATTTTTCAAAGTCGTTGTGCCTCTGTTTAGAGGAGCA-TTTTA-TTTTTCAAA
*
28661125 GTCGTTGAACCTCTGTTTAG
63 GTCGTTGAGCCTCTGTTTAG
* * *** * *
28661145 AGAAGC-TTTTATTTTTCAAAGTCGTTGAGCCTCTACCTAGATGAGCATTTTATTTTTCAAAGTT
1 AGGAGCTTTTTATTTTTCAAAGTCGTTGTGCCTCTGTTTAGAGGAGCATTTTATTTTTCAAAGTC
* *
28661209 GTTGAGCCTTTGCTTAG
66 GTTGAGCCTCTGTTTAG
*
28661226 AGGAGCTTTTTTTTTTT
1 AGGAGCTTTTTATTTTT
28661243 ATTTTTTCAA
Statistics
Matches: 220, Mismatches: 33, Indels: 19
0.81 0.12 0.07
Matches are distributed among these distances:
80 1 0.00
81 68 0.31
82 121 0.55
83 30 0.14
ACGTcount: A:0.20, C:0.13, G:0.20, T:0.47
Consensus pattern (82 bp):
AGGAGCTTTTTATTTTTCAAAGTCGTTGTGCCTCTGTTTAGAGGAGCATTTTATTTTTCAAAGTC
GTTGAGCCTCTGTTTAG
Found at i:28661261 original size:89 final size:89
Alignment explanation
Indices: 28661151--28661314 Score: 224
Period size: 89 Copynumber: 1.8 Consensus size: 89
28661141 TTAGAGAAGC
*
28661151 TTTTATTTTTCAAAGTCGTTGAGCCTCTACCTAGATGAGC-AT-TTTATTTTTCAAAGTTGTTGA
1 TTTTATTTTTCAAAGTCGTTGAGCCTCTACCTAGATGAGCTATATTTATTTTCCAAAGTTG-TGA
* *
28661214 GCCTTTGCTTAGAGGAGCTTTTTTT
65 ACCTGTGCTTAGAGGAGCTTTTTTT
* * * * *
28661239 TTTTATTTTTTCAAAGTTGTTGAGCCTTTGCTTAGATGAGCTTTATTTATTTTCCAAAGTTGTGA
1 TTTTA-TTTTTCAAAGTCGTTGAGCCTCTACCTAGATGAGCTATATTTATTTTCCAAAGTTGTGA
28661304 ACCTGTGCTTA
65 ACCTGTGCTTA
28661315 AAGAAGTTTT
Statistics
Matches: 65, Mismatches: 8, Indels: 4
0.84 0.10 0.05
Matches are distributed among these distances:
88 5 0.08
89 31 0.48
90 13 0.20
91 16 0.25
ACGTcount: A:0.21, C:0.14, G:0.18, T:0.48
Consensus pattern (89 bp):
TTTTATTTTTCAAAGTCGTTGAGCCTCTACCTAGATGAGCTATATTTATTTTCCAAAGTTGTGAA
CCTGTGCTTAGAGGAGCTTTTTTT
Found at i:28661262 original size:48 final size:48
Alignment explanation
Indices: 28661191--28661291 Score: 168
Period size: 48 Copynumber: 2.1 Consensus size: 48
28661181 CTAGATGAGC
28661191 ATTTTATTTTTCAAAGTTGTTGAGCCTTTGCTTAGAGGAGCTTT-TTT
1 ATTTTATTTTTCAAAGTTGTTGAGCCTTTGCTTAGAGGAGCTTTATTT
* *
28661238 TTTTTATTTTTTCAAAGTTGTTGAGCCTTTGCTTAGATGAGCTTTATTT
1 ATTTTA-TTTTTCAAAGTTGTTGAGCCTTTGCTTAGAGGAGCTTTATTT
28661287 ATTTT
1 ATTTT
28661292 CCAAAGTTGT
Statistics
Matches: 49, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
47 5 0.10
48 37 0.76
49 7 0.14
ACGTcount: A:0.19, C:0.10, G:0.17, T:0.54
Consensus pattern (48 bp):
ATTTTATTTTTCAAAGTTGTTGAGCCTTTGCTTAGAGGAGCTTTATTT
Found at i:28661326 original size:42 final size:44
Alignment explanation
Indices: 28661193--28661326 Score: 114
Period size: 48 Copynumber: 3.0 Consensus size: 44
28661183 AGATGAGCAT
* * * *
28661193 TTTATTTTT-CAAAGTTGTTGAGCCTTTGCTTAGAGGAGCTTTTTTTT
1 TTTATTTTTCCAAAGTTGTTGAACCTGTGCTTAGAAGAG----TTTTA
* * * * *
28661240 TTTATTTTTTCAAAGTTGTTGAGCCTTTGCTTAGATGAGCTTTA
1 TTTATTTTTCCAAAGTTGTTGAACCTGTGCTTAGAAGAGTTTTA
28661284 TTTA-TTTTCCAAAGTTG-TGAACCTGTGCTTA-AAGAAGTTTTA
1 TTTATTTTTCCAAAGTTGTTGAACCTGTGCTTAGAAG-AGTTTTA
28661326 T
1 T
28661327 GTCATTTAGC
Statistics
Matches: 77, Mismatches: 8, Indels: 9
0.82 0.09 0.10
Matches are distributed among these distances:
41 2 0.03
42 19 0.25
43 12 0.16
44 7 0.09
47 9 0.12
48 28 0.36
ACGTcount: A:0.22, C:0.11, G:0.18, T:0.49
Consensus pattern (44 bp):
TTTATTTTTCCAAAGTTGTTGAACCTGTGCTTAGAAGAGTTTTA
Found at i:28661607 original size:3 final size:3
Alignment explanation
Indices: 28661599--28661624 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
28661589 ATTATTTATC
28661599 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
28661625 TTAAGAGATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:28661610 original size:18 final size:17
Alignment explanation
Indices: 28661532--28661624 Score: 59
Period size: 18 Copynumber: 5.3 Consensus size: 17
28661522 GTCCAATGAT
28661532 TTATTGATTTATTTA-TA
1 TTATT-ATTTATTTATTA
28661549 TTATTTATTTTATTTTATTA
1 TTA-TTA-TTTA-TTTATTA
* **
28661569 TTATTCTAAATTTTATCT-
1 TTATTATTTA-TTTAT-TA
*
28661587 TGATTATTTATCTTATTA
1 TTATTATTTAT-TTATTA
28661605 TTATTA-TTA-TTATTA
1 TTATTATTTATTTATTA
28661620 TTATT
1 TTATT
28661625 TTAAGAGATA
Statistics
Matches: 61, Mismatches: 8, Indels: 16
0.72 0.09 0.19
Matches are distributed among these distances:
15 11 0.18
17 9 0.15
18 29 0.48
19 7 0.11
20 5 0.08
ACGTcount: A:0.28, C:0.03, G:0.02, T:0.67
Consensus pattern (17 bp):
TTATTATTTATTTATTA
Found at i:28661947 original size:13 final size:13
Alignment explanation
Indices: 28661928--28661957 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
28661918 GAAAAAGAGG
28661928 ATTTTTTTG-AAA
1 ATTTTTTTGAAAA
28661940 ATTTTTTTGAAAA
1 ATTTTTTTGAAAA
28661953 ATTTT
1 ATTTT
28661958 CCAAATTCAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 9 0.53
13 8 0.47
ACGTcount: A:0.33, C:0.00, G:0.07, T:0.60
Consensus pattern (13 bp):
ATTTTTTTGAAAA
Found at i:28662658 original size:7 final size:8
Alignment explanation
Indices: 28662630--28662660 Score: 53
Period size: 8 Copynumber: 3.8 Consensus size: 8
28662620 TTCAATCCAA
28662630 AAAAATTAT
1 AAAAA-TAT
28662639 AAAAATAT
1 AAAAATAT
28662647 AAAAATAT
1 AAAAATAT
28662655 AAAAAT
1 AAAAAT
28662661 TTTTGGTTGA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 17 0.77
9 5 0.23
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (8 bp):
AAAAATAT
Found at i:28666009 original size:28 final size:28
Alignment explanation
Indices: 28665969--28666023 Score: 110
Period size: 28 Copynumber: 2.0 Consensus size: 28
28665959 TAGTTACTAA
28665969 ATTAAAAAATTTAATAGTTTGATAATCG
1 ATTAAAAAATTTAATAGTTTGATAATCG
28665997 ATTAAAAAATTTAATAGTTTGATAATC
1 ATTAAAAAATTTAATAGTTTGATAATC
28666024 AATCATTTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.47, C:0.04, G:0.09, T:0.40
Consensus pattern (28 bp):
ATTAAAAAATTTAATAGTTTGATAATCG
Found at i:28676267 original size:24 final size:24
Alignment explanation
Indices: 28676220--28676268 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
28676210 AAAAGTTTTT
*
28676220 ATTTGATATATTATCAATATATAA
1 ATTTGATATATTATCAATAAATAA
* * *
28676244 ATTTTATATATTGTCAGTAAATAA
1 ATTTGATATATTATCAATAAATAA
28676268 A
1 A
28676269 ATGATATTAT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.45, C:0.04, G:0.06, T:0.45
Consensus pattern (24 bp):
ATTTGATATATTATCAATAAATAA
Found at i:28679962 original size:39 final size:39
Alignment explanation
Indices: 28679889--28679963 Score: 91
Period size: 39 Copynumber: 1.9 Consensus size: 39
28679879 ATATATTTTT
* *
28679889 ATTATTTTTTAAATATAATTTAAATTTTTATAAAATAAA
1 ATTATTTTTTAAATATAATTTAAATATATATAAAATAAA
*
28679928 ATTATTTTATATAAAT-TTATTTAAATATAT-TAAAAT
1 ATTATTTT-T-TAAATATAATTTAAATATATATAAAAT
28679964 TTTTATTAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
39 14 0.45
40 12 0.39
41 5 0.16
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (39 bp):
ATTATTTTTTAAATATAATTTAAATATATATAAAATAAA
Found at i:28679975 original size:22 final size:24
Alignment explanation
Indices: 28679943--28679986 Score: 65
Period size: 22 Copynumber: 1.9 Consensus size: 24
28679933 TTTATATAAA
*
28679943 TTTATTTAAAT-ATAT-TAAAATT
1 TTTATTAAAATAATATATAAAATT
28679965 TTTATTAAAATAATATATAAAA
1 TTTATTAAAATAATATATAAAA
28679987 AGCAAAAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 10 0.53
23 4 0.21
24 5 0.26
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (24 bp):
TTTATTAAAATAATATATAAAATT
Found at i:28680191 original size:2 final size:2
Alignment explanation
Indices: 28680172--28680208 Score: 51
Period size: 2 Copynumber: 19.5 Consensus size: 2
28680162 TTTAATTTCT
*
28680172 TA TA T- TA TA T- TT TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
28680209 CCTCGTTCAA
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
1 2 0.06
2 30 0.94
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (2 bp):
TA
Found at i:28680962 original size:147 final size:147
Alignment explanation
Indices: 28680695--28680989 Score: 554
Period size: 147 Copynumber: 2.0 Consensus size: 147
28680685 TCCCAATGGA
28680695 TACGTTGGAGTTGACGGAATGATCATTAACTTGGCTACCCTTTTGGTAACACTGTTACCGATCCG
1 TACGTTGGAGTTGACGGAATGATCATTAACTTGGCTACCCTTTTGGTAACACTGTTACCGATCCG
* *
28680760 TTTTAATAACGGGTATCTGCAGGGGCCTGCCAACGCTCCTTTAGAGGCGGTTTCAGAATGCACGG
66 TTTTAATAACGGGTATCTGCAGAGGCCTGCCAACGCTCCCTTAGAGGCGGTTTCAGAATGCACGG
*
28680825 GGATGTTCGGGTCGGGT
131 GGATGTTCGCGTCGGGT
28680842 TACGTTGGAGTTGACGGAATGATCATTAACTTGGCTACCCTTTTGGTAACACTGTTACCGATCCG
1 TACGTTGGAGTTGACGGAATGATCATTAACTTGGCTACCCTTTTGGTAACACTGTTACCGATCCG
*
28680907 TTTTAATAACGGGTATTTGCAGAGGCCTGCCAACGCTCCCTTAGAGGCGGTTTCAGAATGCACGG
66 TTTTAATAACGGGTATCTGCAGAGGCCTGCCAACGCTCCCTTAGAGGCGGTTTCAGAATGCACGG
28680972 GGATGTTCGCGTCGGGT
131 GGATGTTCGCGTCGGGT
28680989 T
1 T
28680990 CGTAGCCGGG
Statistics
Matches: 144, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
147 144 1.00
ACGTcount: A:0.21, C:0.21, G:0.28, T:0.29
Consensus pattern (147 bp):
TACGTTGGAGTTGACGGAATGATCATTAACTTGGCTACCCTTTTGGTAACACTGTTACCGATCCG
TTTTAATAACGGGTATCTGCAGAGGCCTGCCAACGCTCCCTTAGAGGCGGTTTCAGAATGCACGG
GGATGTTCGCGTCGGGT
Found at i:28681790 original size:21 final size:22
Alignment explanation
Indices: 28681749--28681790 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
28681739 AATTTAAAAT
* *
28681749 TTTAATAAAAATTATATATAAG
1 TTTAATAAAAATTAAAAATAAG
28681771 TTTAAT-AAAATTAAAAATAA
1 TTTAATAAAAATTAAAAATAA
28681791 ATATTTTATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 12 0.67
22 6 0.33
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (22 bp):
TTTAATAAAAATTAAAAATAAG
Found at i:28686426 original size:21 final size:21
Alignment explanation
Indices: 28686402--28686447 Score: 51
Period size: 21 Copynumber: 2.2 Consensus size: 21
28686392 TAGCTTTGTA
28686402 TATT-AAATATTTCTATTGT-GT
1 TATTGAAA-ATTT-TATTGTAGT
*
28686423 TATTGAAAATTTTATTTTAGT
1 TATTGAAAATTTTATTGTAGT
28686444 TATT
1 TATT
28686448 TCTTTAAGTG
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
20 5 0.23
21 14 0.64
22 3 0.14
ACGTcount: A:0.30, C:0.02, G:0.09, T:0.59
Consensus pattern (21 bp):
TATTGAAAATTTTATTGTAGT
Found at i:28687335 original size:2 final size:2
Alignment explanation
Indices: 28687328--28687363 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
28687318 TCCATCTCTG
* *
28687328 TA TA TA TA TA TA TA TA TA TA TG TA TA TA TA TT TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
28687364 ATGAATTTCT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (2 bp):
TA
Found at i:28689046 original size:13 final size:13
Alignment explanation
Indices: 28689028--28689059 Score: 64
Period size: 13 Copynumber: 2.5 Consensus size: 13
28689018 GAATTATAAA
28689028 ATCTGAAATAATT
1 ATCTGAAATAATT
28689041 ATCTGAAATAATT
1 ATCTGAAATAATT
28689054 ATCTGA
1 ATCTGA
28689060 TCCAGTTTGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.44, C:0.09, G:0.09, T:0.38
Consensus pattern (13 bp):
ATCTGAAATAATT
Found at i:28693651 original size:12 final size:12
Alignment explanation
Indices: 28693634--28693659 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
28693624 ATTCTAGAGG
28693634 ACGAGCAGAACA
1 ACGAGCAGAACA
28693646 ACGAGCAGAACA
1 ACGAGCAGAACA
28693658 AC
1 AC
28693660 ATATATAGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.50, C:0.27, G:0.23, T:0.00
Consensus pattern (12 bp):
ACGAGCAGAACA
Found at i:28698050 original size:16 final size:16
Alignment explanation
Indices: 28698031--28698066 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
28698021 ATCGTCATTA
*
28698031 AAGCAATAATTATTGT
1 AAGCAATAATCATTGT
*
28698047 AAGCATTAATCATTGT
1 AAGCAATAATCATTGT
28698063 AAGC
1 AAGC
28698067 TAAAATCAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.42, C:0.11, G:0.14, T:0.33
Consensus pattern (16 bp):
AAGCAATAATCATTGT
Found at i:28698689 original size:21 final size:21
Alignment explanation
Indices: 28698660--28698722 Score: 92
Period size: 21 Copynumber: 3.0 Consensus size: 21
28698650 GAAAATAATG
* *
28698660 ATAAAAATAAAATTAATTATT
1 ATAATAATAAAATTAAATATT
28698681 ATAATAATAAAATTAAATATT
1 ATAATAATAAAATTAAATATT
*
28698702 ATAATATTAAAATTAAA-ATT
1 ATAATAATAAAATTAAATATT
28698722 A
1 A
28698723 ATGATGAGAT
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
20 4 0.10
21 35 0.90
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (21 bp):
ATAATAATAAAATTAAATATT
Found at i:28698964 original size:25 final size:25
Alignment explanation
Indices: 28698887--28698970 Score: 93
Period size: 24 Copynumber: 3.4 Consensus size: 25
28698877 TCAATAAAAC
* * *
28698887 AATAAACATATTATTTGTTATATAAT
1 AATAAA-ATTTTATTTATCATATAAT
28698913 AATAAAA-TTTATTTATCATATAAT
1 AATAAAATTTTATTTATCATATAAT
28698937 AATAAAATTTTATTTAT-AT-TAAATT
1 AATAAAATTTTATTTATCATAT-AA-T
28698962 AATAAAATT
1 AATAAAATT
28698971 ATTTTAAAAA
Statistics
Matches: 52, Mismatches: 3, Indels: 7
0.84 0.05 0.11
Matches are distributed among these distances:
23 1 0.02
24 25 0.48
25 20 0.38
26 6 0.12
ACGTcount: A:0.50, C:0.02, G:0.01, T:0.46
Consensus pattern (25 bp):
AATAAAATTTTATTTATCATATAAT
Found at i:28699459 original size:30 final size:30
Alignment explanation
Indices: 28699423--28699488 Score: 114
Period size: 30 Copynumber: 2.2 Consensus size: 30
28699413 CAGTGGTAAG
*
28699423 GGAGACTTCCATCTATTTGTCCGTATGACA
1 GGAGACTTCCATCTATTTGTCCATATGACA
28699453 GGAGACTTCCATCTATTTGTCCATATGACA
1 GGAGACTTCCATCTATTTGTCCATATGACA
*
28699483 CGAGAC
1 GGAGAC
28699489 ATCTTTCCTT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 34 1.00
ACGTcount: A:0.26, C:0.24, G:0.20, T:0.30
Consensus pattern (30 bp):
GGAGACTTCCATCTATTTGTCCATATGACA
Found at i:28703881 original size:24 final size:24
Alignment explanation
Indices: 28703802--28703879 Score: 115
Period size: 24 Copynumber: 3.2 Consensus size: 24
28703792 AATGAACATG
28703802 TTATTTATTATATAATAATAAAAT
1 TTATTTATTATATAATAATAAAAT
*
28703826 TTATTTATCATATAATAATAAAATT
1 TTATTTATTATATAATAATAAAA-T
28703851 TTATTTATTAT-TAATTAATAAAA-
1 TTATTTATTATATAA-TAATAAAAT
28703874 TTATTT
1 TTATTT
28703880 TAAAATTTAT
Statistics
Matches: 50, Mismatches: 2, Indels: 5
0.88 0.04 0.09
Matches are distributed among these distances:
23 6 0.12
24 25 0.50
25 19 0.38
ACGTcount: A:0.46, C:0.01, G:0.00, T:0.53
Consensus pattern (24 bp):
TTATTTATTATATAATAATAAAAT
Found at i:28703895 original size:52 final size:49
Alignment explanation
Indices: 28703802--28703901 Score: 114
Period size: 49 Copynumber: 2.0 Consensus size: 49
28703792 AATGAACATG
** *
28703802 TTATTTATTATATAATAATAAAATTTATTTATCATATAATAATAAAATT
1 TTATTTATTATATAATAATAAAATTTATTTAAAATATAATAAAAAAATT
28703851 TTATTTATTAT-TAATTAATAAAA-TTATTTTAAAATTTATAAATAAAAAAAT
1 TTATTTATTATATAA-TAATAAAATTTA-TTTAAAA--TAT-AATAAAAAAAT
28703902 CAAAATAAAA
Statistics
Matches: 43, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
48 6 0.14
49 24 0.56
51 3 0.07
52 10 0.23
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.48
Consensus pattern (49 bp):
TTATTTATTATATAATAATAAAATTTATTTAAAATATAATAAAAAAATT
Found at i:28708240 original size:16 final size:16
Alignment explanation
Indices: 28708215--28708245 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
28708205 TGATTAATGT
*
28708215 TTAATTATTGTAAGCA
1 TTAATCATTGTAAGCA
28708231 TTAATCATTGTAAGC
1 TTAATCATTGTAAGC
28708246 TACAAGCAAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.10, G:0.13, T:0.42
Consensus pattern (16 bp):
TTAATCATTGTAAGCA
Found at i:28708857 original size:21 final size:20
Alignment explanation
Indices: 28708833--28708895 Score: 63
Period size: 21 Copynumber: 3.0 Consensus size: 20
28708823 AAAAATTACG
28708833 ATAAAAATAAAATTAATTATT
1 ATAAAAATAAAATTAA-TATT
**
28708854 ATAACGATAAAATTTAATATT
1 ATAAAAATAAAA-TTAATATT
* * *
28708875 ATAATATTAAAATTAAAATT
1 ATAAAAATAAAATTAATATT
28708895 A
1 A
28708896 ATAGTAAAAT
Statistics
Matches: 35, Mismatches: 6, Indels: 3
0.80 0.14 0.07
Matches are distributed among these distances:
20 8 0.23
21 23 0.66
22 4 0.11
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.38
Consensus pattern (20 bp):
ATAAAAATAAAATTAATATT
Found at i:28709153 original size:25 final size:24
Alignment explanation
Indices: 28709076--28709163 Score: 83
Period size: 24 Copynumber: 3.6 Consensus size: 24
28709066 CAATATGAAC
* *
28709076 AATAAACATATTATTTATTGTATAAT
1 AATAAA-AT-TTATTTATTCTACAAT
28709102 AATAAAATTTATTTATTCTACAAT
1 AATAAAATTTATTTATTCTACAAT
*
28709126 AATAAATTTTTATTTATAT-TA-AATT
1 AATAAA-ATTTATTTAT-TCTACAA-T
28709151 AATAAAA-TTATTT
1 AATAAAATTTATTT
28709164 TAAAATTTAT
Statistics
Matches: 55, Mismatches: 4, Indels: 9
0.81 0.06 0.13
Matches are distributed among these distances:
23 6 0.11
24 22 0.40
25 20 0.36
26 7 0.13
ACGTcount: A:0.47, C:0.03, G:0.01, T:0.49
Consensus pattern (24 bp):
AATAAAATTTATTTATTCTACAAT
Found at i:28715833 original size:16 final size:15
Alignment explanation
Indices: 28715801--28715840 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 15
28715791 GCAGGTTGGT
*
28715801 AAAATTTTGTTTTAA
1 AAAATTTTGTTTGAA
28715816 AAAATTTATGTTTGAA
1 AAAATTT-TGTTTGAA
28715832 AAATATTTT
1 AAA-ATTTT
28715841 TTAAAAATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
15 7 0.32
16 11 0.50
17 4 0.18
ACGTcount: A:0.42, C:0.00, G:0.07, T:0.50
Consensus pattern (15 bp):
AAAATTTTGTTTGAA
Found at i:28716220 original size:13 final size:13
Alignment explanation
Indices: 28716190--28716235 Score: 53
Period size: 12 Copynumber: 3.8 Consensus size: 13
28716180 TATATGTTTG
*
28716190 ATAATTTAA-AAT
1 ATAATATAATAAT
28716202 ATAATATAATAAT
1 ATAATATAATAAT
*
28716215 ACAATAT-A-AAT
1 ATAATATAATAAT
28716226 ATAATATAAT
1 ATAATATAAT
28716236 TTAAAATTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
11 9 0.32
12 10 0.36
13 9 0.32
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (13 bp):
ATAATATAATAAT
Found at i:28716320 original size:12 final size:12
Alignment explanation
Indices: 28716303--28716354 Score: 52
Period size: 12 Copynumber: 4.2 Consensus size: 12
28716293 ATTTTTATAT
*
28716303 TAATATTAATTA
1 TAATATAAATTA
28716315 TAATATATAATT-
1 TAATATA-AATTA
* *
28716327 TTATATAAAATA
1 TAATATAAATTA
28716339 TAATATAAATATA
1 TAATATAAAT-TA
28716352 TAA
1 TAA
28716355 ATTTTAGTAT
Statistics
Matches: 32, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
11 3 0.09
12 20 0.62
13 9 0.28
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (12 bp):
TAATATAAATTA
Found at i:28716329 original size:30 final size:31
Alignment explanation
Indices: 28716290--28716380 Score: 91
Period size: 30 Copynumber: 3.0 Consensus size: 31
28716280 AAATATATTT
* *
28716290 TATATTTTTATATTAATAT-TAAT-TATAATA
1 TATAATTTTATATTAAAATATAATATA-AATA
28716320 TATAATTTTATA-TAAAATATAATATAAATA
1 TATAATTTTATATTAAAATATAATATAAATA
* *
28716350 TATAAATTTTAGTATT-ATATACAATATAAAT
1 TAT-AATTTTA-TATTAAAATATAATATAAAT
28716381 CGTCAAGTCT
Statistics
Matches: 52, Mismatches: 4, Indels: 8
0.81 0.06 0.12
Matches are distributed among these distances:
29 5 0.10
30 22 0.42
31 9 0.17
32 15 0.29
33 1 0.02
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.48
Consensus pattern (31 bp):
TATAATTTTATATTAAAATATAATATAAATA
Found at i:28716369 original size:67 final size:58
Alignment explanation
Indices: 28716244--28716369 Score: 128
Period size: 58 Copynumber: 2.0 Consensus size: 58
28716234 ATTTAAAATT
* *
28716244 TTAATAATAATTATATATAAATTTAATAAAATTAAAAAATATATTTTATATTTTTATA
1 TTAATAATAATTATATATAAATTTAATAAAATTAAAAAATATATTTTATAGTATTATA
*
28716302 TTAATATTAATTATAATATATAATTTTATATAAAATATAATATAAATATATAAATTT-TAGTATT
1 TTAATAATAATTAT-ATATA-AA-TTTA-ATAAAAT-TAA-A-AAATATAT---TTTATAGTATT
28716366 ATA
56 ATA
28716369 T
1 T
28716370 ACAATATAAA
Statistics
Matches: 55, Mismatches: 3, Indels: 11
0.80 0.04 0.16
Matches are distributed among these distances:
58 13 0.24
59 5 0.09
60 2 0.04
61 4 0.07
62 7 0.13
63 3 0.05
64 1 0.02
65 8 0.15
67 9 0.16
68 3 0.05
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.48
Consensus pattern (58 bp):
TTAATAATAATTATATATAAATTTAATAAAATTAAAAAATATATTTTATAGTATTATA
Found at i:28716376 original size:32 final size:30
Alignment explanation
Indices: 28716316--28716380 Score: 85
Period size: 32 Copynumber: 2.1 Consensus size: 30
28716306 TATTAATTAT
*
28716316 AATATATAATTTTATATAAAATATAATATA
1 AATATATAATTTTATATAAAATACAATATA
* *
28716346 AATATATAAATTTTAGTATTATATACAATATA
1 AATATAT-AATTTTA-TATAAAATACAATATA
28716378 AAT
1 AAT
28716381 CGTCAAGTCT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
30 7 0.23
31 7 0.23
32 16 0.53
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.43
Consensus pattern (30 bp):
AATATATAATTTTATATAAAATACAATATA
Found at i:28716580 original size:18 final size:21
Alignment explanation
Indices: 28716509--28716582 Score: 66
Period size: 21 Copynumber: 3.6 Consensus size: 21
28716499 TGTGATTAAA
* *
28716509 AATAATAATGATAATGAGATT-
1 AATAAT-ATAATAATGAAATTG
*
28716530 AATTATTATAATAATGAAATTG
1 AA-TAATATAATAATGAAATTG
*
28716552 AATATTATAATAATGAAATT-
1 AATAATATAATAATGAAATTG
28716572 AA-AAT-TAATAA
1 AATAATATAATAA
28716583 CAAATTATGA
Statistics
Matches: 47, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
18 6 0.13
19 2 0.04
20 2 0.04
21 32 0.68
22 5 0.11
ACGTcount: A:0.55, C:0.00, G:0.08, T:0.36
Consensus pattern (21 bp):
AATAATATAATAATGAAATTG
Found at i:28716582 original size:21 final size:20
Alignment explanation
Indices: 28716519--28716578 Score: 84
Period size: 21 Copynumber: 2.9 Consensus size: 20
28716509 AATAATAATG
*
28716519 ATAATGAGATTAATTATTATA
1 ATAATGAAATTAA-TATTATA
28716540 ATAATGAAATTGAATATTATA
1 ATAATGAAATT-AATATTATA
*
28716561 ATAATGAAATTAAAATTA
1 ATAATGAAATTAATATTA
28716579 ATAACAAATT
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
20 6 0.17
21 28 0.78
22 2 0.06
ACGTcount: A:0.53, C:0.00, G:0.08, T:0.38
Consensus pattern (20 bp):
ATAATGAAATTAATATTATA
Found at i:28716803 original size:36 final size:35
Alignment explanation
Indices: 28716758--28716844 Score: 129
Period size: 36 Copynumber: 2.4 Consensus size: 35
28716748 TTAATATATA
*
28716758 TTATTTATTTATTAATTTATTATATAATAAAAGAAC
1 TTATTTATTTATTAATTTATCATATAATAAAA-AAC
**
28716794 TTATTTATTTATTAATTTATCATATAATAAAAATT
1 TTATTTATTTATTAATTTATCATATAATAAAAAAC
28716829 TTATTTATTATATTAA
1 TTATTTATT-TATTAA
28716845 ATCAATAAAG
Statistics
Matches: 47, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
35 10 0.21
36 37 0.79
ACGTcount: A:0.43, C:0.02, G:0.01, T:0.54
Consensus pattern (35 bp):
TTATTTATTTATTAATTTATCATATAATAAAAAAC
Found at i:28717648 original size:19 final size:18
Alignment explanation
Indices: 28717602--28717648 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 18
28717592 AACTCTGGAT
*
28717602 ATCAT-ATTTTTTTTAAA
1 ATCATAATTTCTTTTAAA
* *
28717619 ATCATACTTTCTTTTGAA
1 ATCATAATTTCTTTTAAA
28717637 ATCTATAATTTC
1 ATC-ATAATTTC
28717649 ACGAACTAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
17 5 0.21
18 12 0.50
19 7 0.29
ACGTcount: A:0.32, C:0.13, G:0.02, T:0.53
Consensus pattern (18 bp):
ATCATAATTTCTTTTAAA
Found at i:28717693 original size:16 final size:15
Alignment explanation
Indices: 28717672--28717701 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
28717662 TCTTTAAGGT
28717672 TAAAAAAGATAAAAAC
1 TAAAAAAGA-AAAAAC
28717688 TAAAAAAGAAAAAA
1 TAAAAAAGAAAAAA
28717702 GGAAGGAAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.80, C:0.03, G:0.07, T:0.10
Consensus pattern (15 bp):
TAAAAAAGAAAAAAC
Found at i:28718112 original size:112 final size:110
Alignment explanation
Indices: 28717889--28718117 Score: 293
Period size: 111 Copynumber: 2.1 Consensus size: 110
28717879 TTGAAAAGTG
* *
28717889 TTAAAAGTGAAAGTTTATGAAAAATTACAAAGGAAAAAAAGAAATTTTGTTAAAAATTTTGATGA
1 TTAAAAGTGAAAGTTTATGAAAAATTACAAAGG-AAAAAAGAAATTGTGTTAAAAATATTGATGA
* *
28717954 ATTACTGTAAAGAAAAATGTTATTATTAGAAAAAAATTTATTAATT
65 ATTACTATAAAGAAAAATGTTATTATTAGAAAAAAATTTATAAATT
* *
28718000 TTAAGAGTGAAAGTTTATGAAAAATTAGAAAGG-AAAAA-AAATTGTGTTAAAAATATTGATGAA
1 TTAAAAGTGAAAGTTTATGAAAAATTACAAAGGAAAAAAGAAATTGTGTTAAAAATATTGATGAA
*** *
28718063 TTACTTACTATAA-AGAAAATAGTTATTATTAGAAAATTCTTTCTAAATT
66 TTAC-TA-TA-AAGA-AAAAT-GTTATTATTAGAAAAAAATTTATAAATT
28718112 TTAAAA
1 TTAAAA
28718118 TTAATAAAAA
Statistics
Matches: 102, Mismatches: 11, Indels: 9
0.84 0.09 0.07
Matches are distributed among these distances:
108 27 0.26
109 6 0.06
110 3 0.03
111 38 0.37
112 28 0.27
ACGTcount: A:0.50, C:0.03, G:0.13, T:0.34
Consensus pattern (110 bp):
TTAAAAGTGAAAGTTTATGAAAAATTACAAAGGAAAAAAGAAATTGTGTTAAAAATATTGATGAA
TTACTATAAAGAAAAATGTTATTATTAGAAAAAAATTTATAAATT
Found at i:28719427 original size:22 final size:22
Alignment explanation
Indices: 28719402--28719461 Score: 63
Period size: 22 Copynumber: 2.7 Consensus size: 22
28719392 TTTTATATTA
28719402 ATATAAATTATAATATATAATTAT
1 ATATAAATTATAATATATAA--AT
28719426 ATATAAA--AT-ATGATATAAAT
1 ATATAAATTATAAT-ATATAAAT
*
28719446 ATATAAATTTTAATAT
1 ATATAAATTATAATAT
28719462 TTTATATAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 10
0.74 0.02 0.24
Matches are distributed among these distances:
20 9 0.29
21 2 0.06
22 11 0.35
23 2 0.06
24 7 0.23
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (22 bp):
ATATAAATTATAATATATAAAT
Found at i:28719461 original size:12 final size:12
Alignment explanation
Indices: 28719400--28719451 Score: 61
Period size: 12 Copynumber: 4.2 Consensus size: 12
28719390 ATTTTTATAT
28719400 TAATATAAATTA
1 TAATATAAATTA
28719412 TAATATATAATTA
1 TAATATA-AATTA
*
28719425 T-ATATAAAATA
1 TAATATAAATTA
*
28719436 TGATATAAATATA
1 TAATATAAAT-TA
28719449 TAA
1 TAA
28719452 ATTTTAATAT
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
11 5 0.15
12 19 0.56
13 10 0.29
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (12 bp):
TAATATAAATTA
Found at i:28719461 original size:20 final size:20
Alignment explanation
Indices: 28719400--28719452 Score: 60
Period size: 17 Copynumber: 2.9 Consensus size: 20
28719390 ATTTTTATAT
*
28719400 TAATATAAAT-TATAATATA
1 TAATATAAATATATAAAATA
28719419 TAAT-T--ATATATAAAATA
1 TAATATAAATATATAAAATA
*
28719436 TGATATAAATATATAAA
1 TAATATAAATATATAAA
28719453 TTTTAATATT
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
16 2 0.07
17 11 0.39
18 2 0.07
19 4 0.14
20 9 0.32
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (20 bp):
TAATATAAATATATAAAATA
Found at i:28724659 original size:20 final size:21
Alignment explanation
Indices: 28724618--28724674 Score: 80
Period size: 21 Copynumber: 2.7 Consensus size: 21
28724608 ATTCGATCCG
28724618 AAATAATAAAATATTATTTTTTA
1 AAAT-ATAAAATATTA-TTTTTA
*
28724641 AAATATAAAATATTATTTTTT
1 AAATATAAAATATTATTTTTA
28724662 AAATAT-AAATATT
1 AAATATAAAATATT
28724675 TAAAAATATC
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
20 7 0.21
21 11 0.33
22 11 0.33
23 4 0.12
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (21 bp):
AAATATAAAATATTATTTTTA
Found at i:28724665 original size:21 final size:22
Alignment explanation
Indices: 28724618--28724674 Score: 91
Period size: 22 Copynumber: 2.6 Consensus size: 22
28724608 ATTCGATCCG
28724618 AAATAATAAAATATTATTTTTTA
1 AAAT-ATAAAATATTATTTTTTA
28724641 AAATATAAAATATTATTTTTT-
1 AAATATAAAATATTATTTTTTA
28724662 AAATAT-AAATATT
1 AAATATAAAATATT
28724675 TAAAAATATC
Statistics
Matches: 34, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
20 7 0.21
21 6 0.18
22 17 0.50
23 4 0.12
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (22 bp):
AAATATAAAATATTATTTTTTA
Found at i:28724681 original size:30 final size:30
Alignment explanation
Indices: 28724647--28724703 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 30
28724637 TTTAAAATAT
* * *
28724647 AAAATATTATTTTTTAAATATAAATATTTA
1 AAAATATCATTATATAAATATAAATATTTA
*
28724677 AAAATATCATTATATAAATATATATAT
1 AAAATATCATTATATAAATATAAATAT
28724704 AAATAAAAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 23 1.00
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.46
Consensus pattern (30 bp):
AAAATATCATTATATAAATATAAATATTTA
Found at i:28726446 original size:17 final size:18
Alignment explanation
Indices: 28726415--28726453 Score: 62
Period size: 17 Copynumber: 2.2 Consensus size: 18
28726405 ATTAAATTAT
28726415 TTTTAAATAAATTAATAG
1 TTTTAAATAAATTAATAG
*
28726433 TTTT-AATAATTTAATAG
1 TTTTAAATAAATTAATAG
28726450 TTTT
1 TTTT
28726454 GCTAATAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 16 0.80
18 4 0.20
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.54
Consensus pattern (18 bp):
TTTTAAATAAATTAATAG
Found at i:28731329 original size:29 final size:29
Alignment explanation
Indices: 28731278--28731350 Score: 92
Period size: 29 Copynumber: 2.4 Consensus size: 29
28731268 GTAAATAATT
*
28731278 TTTAAATTATAATGAAATATTTAATGTGATA
1 TTTAAATTATAA--AAATATTTAATATGATA
* *
28731309 TTTAAATTTTAAAAATTTTTAATATGATA
1 TTTAAATTATAAAAATATTTAATATGATA
*
28731338 TTTGAATTATAAA
1 TTTAAATTATAAA
28731351 TTTATTAATT
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
29 26 0.70
31 11 0.30
ACGTcount: A:0.45, C:0.00, G:0.07, T:0.48
Consensus pattern (29 bp):
TTTAAATTATAAAAATATTTAATATGATA
Found at i:28738844 original size:27 final size:27
Alignment explanation
Indices: 28738814--28738872 Score: 102
Period size: 27 Copynumber: 2.2 Consensus size: 27
28738804 AATTAATCAC
28738814 TAGATTTCATATG-CTGTTCAAGATTTA
1 TAGATTTCAT-TGTCTGTTCAAGATTTA
28738841 TAGATTTCATTGTCTGTTCAAGATTTA
1 TAGATTTCATTGTCTGTTCAAGATTTA
28738868 TAGAT
1 TAGAT
28738873 AAATCTTTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
26 2 0.06
27 29 0.94
ACGTcount: A:0.29, C:0.10, G:0.15, T:0.46
Consensus pattern (27 bp):
TAGATTTCATTGTCTGTTCAAGATTTA
Found at i:28745055 original size:6 final size:7
Alignment explanation
Indices: 28745029--28745058 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
28745019 AATGGATATT
28745029 TTAAAAA
1 TTAAAAA
28745036 TTAAAAA
1 TTAAAAA
28745043 TTAAAAA
1 TTAAAAA
*
28745050 TAAAAAA
1 TTAAAAA
28745057 TT
1 TT
28745059 CTAAACATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (7 bp):
TTAAAAA
Found at i:28745438 original size:29 final size:29
Alignment explanation
Indices: 28745406--28745482 Score: 84
Period size: 32 Copynumber: 2.6 Consensus size: 29
28745396 ACTTACTGTA
* *
28745406 AAATAAATGTTATTATATAATAAATTAAT
1 AAATAAATATTATTATATAATAAACTAAT
28745435 AAATAAAATTTATTATTATATAATAAACTAAT
1 AAAT-AAA--TATTATTATATAATAAACTAAT
*
28745467 -AATAAATTTTAATTAT
1 AAATAAATATT-ATTAT
28745483 TTATTAACAA
Statistics
Matches: 41, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
28 3 0.07
29 9 0.22
30 6 0.15
31 3 0.07
32 20 0.49
ACGTcount: A:0.55, C:0.01, G:0.01, T:0.43
Consensus pattern (29 bp):
AAATAAATATTATTATATAATAAACTAAT
Found at i:28745456 original size:32 final size:32
Alignment explanation
Indices: 28745415--28745483 Score: 104
Period size: 32 Copynumber: 2.2 Consensus size: 32
28745405 AAAATAAATG
*
28745415 TTATTATATAATAAATTAATAAATAAAATTT-A
1 TTATTATATAATAAACTAAT-AATAAAATTTAA
*
28745447 TTATTATATAATAAACTAATAATAAATTTTAA
1 TTATTATATAATAAACTAATAATAAAATTTAA
28745479 TTATT
1 TTATT
28745484 TATTAACAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
31 9 0.26
32 25 0.74
ACGTcount: A:0.52, C:0.01, G:0.00, T:0.46
Consensus pattern (32 bp):
TTATTATATAATAAACTAATAATAAAATTTAA
Found at i:28745907 original size:18 final size:18
Alignment explanation
Indices: 28745886--28745923 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
28745876 GATATTAGTT
*
28745886 ATGATAAAATTAAAAATA
1 ATGATAAAAATAAAAATA
*
28745904 ATGATAAAAATAAAATTA
1 ATGATAAAAATAAAAATA
28745922 AT
1 AT
28745924 TATTGTAATA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.66, C:0.00, G:0.05, T:0.29
Consensus pattern (18 bp):
ATGATAAAAATAAAAATA
Found at i:28747463 original size:24 final size:23
Alignment explanation
Indices: 28747423--28747468 Score: 65
Period size: 24 Copynumber: 2.0 Consensus size: 23
28747413 AGATGATATT
28747423 ATTTTATTAATGATTAAATATAAA
1 ATTTTATTAATGATTAAA-ATAAA
**
28747447 ATTTTATTAATTTTTAAAATAA
1 ATTTTATTAATGATTAAAATAA
28747469 TTATACAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 4 0.20
24 16 0.80
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (23 bp):
ATTTTATTAATGATTAAAATAAA
Found at i:28748288 original size:29 final size:30
Alignment explanation
Indices: 28748226--28748288 Score: 71
Period size: 29 Copynumber: 2.2 Consensus size: 30
28748216 ATTTTTTTTG
*
28748226 TTTTTGATATTAAAAATTATAAATTATAAA
1 TTTTTAATATTAAAAATTATAAATTATAAA
28748256 -TTTTAATATTAAATAAATTA-AAA-TA-AAA
1 TTTTTAATATT-AA-AAATTATAAATTATAAA
28748284 TTTTT
1 TTTTT
28748289 GTTCTAAATT
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
28 3 0.10
29 15 0.52
30 5 0.17
31 6 0.21
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.48
Consensus pattern (30 bp):
TTTTTAATATTAAAAATTATAAATTATAAA
Found at i:28753519 original size:38 final size:38
Alignment explanation
Indices: 28753468--28753542 Score: 114
Period size: 38 Copynumber: 2.0 Consensus size: 38
28753458 ATTCAGACAG
* *
28753468 TTAACTACCAATAATTTTGTCAAGCAGATACAAGGATA
1 TTAACTACCAATAATTTTATCAAGCAGAGACAAGGATA
* *
28753506 TTAACTACCAATAATTTTATCATGCAGAGATAAGGAT
1 TTAACTACCAATAATTTTATCAAGCAGAGACAAGGAT
28753543 GTGGTGCACT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
38 33 1.00
ACGTcount: A:0.41, C:0.15, G:0.13, T:0.31
Consensus pattern (38 bp):
TTAACTACCAATAATTTTATCAAGCAGAGACAAGGATA
Found at i:28759491 original size:20 final size:20
Alignment explanation
Indices: 28759466--28759504 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
28759456 GTGCTATTCA
28759466 CTCATTAACAATCTAATCCG
1 CTCATTAACAATCTAATCCG
*
28759486 CTCATTAGCAATCTAATCC
1 CTCATTAACAATCTAATCC
28759505 AAAGGCAACC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.33, C:0.31, G:0.05, T:0.31
Consensus pattern (20 bp):
CTCATTAACAATCTAATCCG
Found at i:28762753 original size:156 final size:156
Alignment explanation
Indices: 28762576--28762891 Score: 587
Period size: 156 Copynumber: 2.0 Consensus size: 156
28762566 TCTTTAATAA
*
28762576 AAAAAATACCATCAAAACTTGTAGGATATTGGTATGGGATTCAACAAAGTAGAGACTAGAGACCA
1 AAAAAATACCATCAAAACTTGTAGGATATTGGTATGGAATTCAACAAAGTAGAGACTAGAGACCA
*
28762641 AAAAGCAAGCAATTAAAATTTTGCTACCTTTTATGACATAACCCTTGCCAATTTGGAAAGAGAAA
66 AAAAGCAAGCAATTAAAATTTTGCTACCTTTAATGACATAACCCTTGCCAATTTGGAAAGAGAAA
*
28762706 GGTTGCAGTTCTTTATCCTTGGTGCT
131 GGTTGCAGTCCTTTATCCTTGGTGCT
*
28762732 AAAAAATACCATCAAAACTTGTAGGATATTGGTATGGAATTCAACAAGGTAGAGACTAGAGACCA
1 AAAAAATACCATCAAAACTTGTAGGATATTGGTATGGAATTCAACAAAGTAGAGACTAGAGACCA
*
28762797 AAAAGCAAGCAATTAAAATTTTGCTACCTTTAATGACATAACCCTTGCCGATTTGGAAAGAGAAA
66 AAAAGCAAGCAATTAAAATTTTGCTACCTTTAATGACATAACCCTTGCCAATTTGGAAAGAGAAA
28762862 GGTTGCAGTCCTTTATCCTTGGTGCT
131 GGTTGCAGTCCTTTATCCTTGGTGCT
28762888 AAAA
1 AAAA
28762892 TGACACAAAC
Statistics
Matches: 155, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
156 155 1.00
ACGTcount: A:0.38, C:0.16, G:0.19, T:0.27
Consensus pattern (156 bp):
AAAAAATACCATCAAAACTTGTAGGATATTGGTATGGAATTCAACAAAGTAGAGACTAGAGACCA
AAAAGCAAGCAATTAAAATTTTGCTACCTTTAATGACATAACCCTTGCCAATTTGGAAAGAGAAA
GGTTGCAGTCCTTTATCCTTGGTGCT
Found at i:28763472 original size:2 final size:2
Alignment explanation
Indices: 28763440--28763489 Score: 64
Period size: 2 Copynumber: 25.0 Consensus size: 2
28763430 GTCAAATGTA
* * * *
28763440 AT AT AT CT AT AT CT AT AT CT AT AT CT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
28763482 AT AT AT AT
1 AT AT AT AT
28763490 TATTCCATGT
Statistics
Matches: 40, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.42, C:0.08, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:28763833 original size:34 final size:34
Alignment explanation
Indices: 28763795--28763862 Score: 93
Period size: 34 Copynumber: 2.0 Consensus size: 34
28763785 TTAATTATAT
* **
28763795 CAAAAAT-TCATTTTCGAAAAGTATTACAATTATC
1 CAAAAATAT-ATTTTCAAAAAACATTACAATTATC
28763829 CAAAAATATATTTTCAAAAAACATTACAATTATC
1 CAAAAATATATTTTCAAAAAACATTACAATTATC
28763863 TTAAAAAGCA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
34 29 0.97
35 1 0.03
ACGTcount: A:0.49, C:0.15, G:0.03, T:0.34
Consensus pattern (34 bp):
CAAAAATATATTTTCAAAAAACATTACAATTATC
Found at i:28765291 original size:19 final size:19
Alignment explanation
Indices: 28765269--28765311 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 19
28765259 AAAAAATCTT
28765269 AAAAATTTAATAAAAATTC
1 AAAAATTTAATAAAAATTC
** *
28765288 AAAAATTTTCTTAAAATTC
1 AAAAATTTAATAAAAATTC
28765307 AAAAA
1 AAAAA
28765312 AAAATTTCTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.60, C:0.07, G:0.00, T:0.33
Consensus pattern (19 bp):
AAAAATTTAATAAAAATTC
Found at i:28765319 original size:22 final size:21
Alignment explanation
Indices: 28765288--28765331 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 21
28765278 ATAAAAATTC
*
28765288 AAAAATTTTCTTAAAATTCAAA
1 AAAAAATTTCTTAAAATT-AAA
28765310 AAAAAATTTCTTAAAATTAAA
1 AAAAAATTTCTTAAAATTAAA
28765331 A
1 A
28765332 GCATTCATAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
21 4 0.19
22 17 0.81
ACGTcount: A:0.59, C:0.07, G:0.00, T:0.34
Consensus pattern (21 bp):
AAAAAATTTCTTAAAATTAAA
Found at i:28766909 original size:30 final size:30
Alignment explanation
Indices: 28766873--28766935 Score: 108
Period size: 30 Copynumber: 2.1 Consensus size: 30
28766863 TTGGTAACAC
*
28766873 TTAATTTAGAGATGTAAATCCTTCAATAAT
1 TTAATTTAGAGATGTAAATCCTCCAATAAT
*
28766903 TTAATTTAGAGATTTAAATCCTCCAATAAT
1 TTAATTTAGAGATGTAAATCCTCCAATAAT
28766933 TTA
1 TTA
28766936 GTAGGATTAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.40, C:0.11, G:0.08, T:0.41
Consensus pattern (30 bp):
TTAATTTAGAGATGTAAATCCTCCAATAAT
Found at i:28768061 original size:14 final size:15
Alignment explanation
Indices: 28768041--28768075 Score: 54
Period size: 14 Copynumber: 2.4 Consensus size: 15
28768031 AAATCATAAT
28768041 CAAATAAATT-TAAA
1 CAAATAAATTCTAAA
*
28768055 TAAATAAATTCTAAA
1 CAAATAAATTCTAAA
28768070 CAAATA
1 CAAATA
28768076 TAAACGAACC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
14 9 0.50
15 9 0.50
ACGTcount: A:0.63, C:0.09, G:0.00, T:0.29
Consensus pattern (15 bp):
CAAATAAATTCTAAA
Found at i:28768092 original size:20 final size:20
Alignment explanation
Indices: 28768067--28768105 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
28768057 AATAAATTCT
28768067 AAACAAATATAAACGAACCC
1 AAACAAATATAAACGAACCC
28768087 AAACAAATATAAACGAACC
1 AAACAAATATAAACGAACC
28768106 TTAAAATAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.62, C:0.23, G:0.05, T:0.10
Consensus pattern (20 bp):
AAACAAATATAAACGAACCC
Found at i:28768501 original size:21 final size:21
Alignment explanation
Indices: 28768477--28768518 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
28768467 TAAAAAAAAA
28768477 AAAGATA-ATTAAGAAATAAAT
1 AAAGATATA-TAAGAAATAAAT
28768498 AAAGATATATAAGAAATAAAT
1 AAAGATATATAAGAAATAAAT
28768519 TAGTAAATAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 19 0.95
22 1 0.05
ACGTcount: A:0.67, C:0.00, G:0.10, T:0.24
Consensus pattern (21 bp):
AAAGATATATAAGAAATAAAT
Found at i:28773170 original size:14 final size:14
Alignment explanation
Indices: 28773153--28773179 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
28773143 TCATTCCAAG
28773153 TTTTTTTTTTTAAA
1 TTTTTTTTTTTAAA
28773167 TTTTTTTTTTTAA
1 TTTTTTTTTTTAA
28773180 GTTTAAGAAC
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:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (14 bp):
TTTTTTTTTTTAAA
Found at i:28774510 original size:34 final size:32
Alignment explanation
Indices: 28774471--28774583 Score: 97
Period size: 32 Copynumber: 3.4 Consensus size: 32
28774461 TTATCTAATA
28774471 ATATTAATATAACTATTAAAATATTAAAAATTATT
1 ATATTAATATAA-TATT--AATATTAAAAATTATT
* * *
28774506 -TATTATTAAAATTATTAATATTAAAAAATATT
1 ATATTAATATAA-TATTAATATTAAAAATTATT
28774538 ATATTTTAATAATAATATTTAATATT-AAAA-TATT
1 ATA--TTAAT-ATAATA-TTAATATTAAAAATTATT
*
28774572 ATGTTAATATAA
1 ATATTAATATAA
28774584 AAATACTTAA
Statistics
Matches: 66, Mismatches: 7, Indels: 14
0.76 0.08 0.16
Matches are distributed among these distances:
31 4 0.06
32 20 0.30
33 2 0.03
34 19 0.29
35 10 0.15
36 11 0.17
ACGTcount: A:0.52, C:0.01, G:0.01, T:0.46
Consensus pattern (32 bp):
ATATTAATATAATATTAATATTAAAAATTATT
Found at i:28774531 original size:32 final size:33
Alignment explanation
Indices: 28774490--28774612 Score: 112
Period size: 32 Copynumber: 3.7 Consensus size: 33
28774480 TAACTATTAA
28774490 AATATTAAAAATTATTTATTATTAAAATTA-TT
1 AATATTAAAAATTATTTATTATTAAAATTACTT
* *
28774522 AATATTAAAAAATATTATATT-TTAATAATAATATTT
1 AATATTAAAAATTATT-TATTATTAA-AAT--TACTT
* *
28774558 AATATTAAAATATTATGTTAATA-TAAAAATACTT
1 AATATTAAAA-ATTAT-TTATTATTAAAATTACTT
*
28774592 AA-AAT-AAAATTATTTATTATT
1 AATATTAAAAATTATTTATTATT
28774613 CTTTATATTA
Statistics
Matches: 75, Mismatches: 7, Indels: 19
0.74 0.07 0.19
Matches are distributed among these distances:
30 5 0.07
31 6 0.08
32 22 0.29
33 9 0.12
34 6 0.08
35 2 0.03
36 14 0.19
37 10 0.13
38 1 0.01
ACGTcount: A:0.52, C:0.01, G:0.01, T:0.46
Consensus pattern (33 bp):
AATATTAAAAATTATTTATTATTAAAATTACTT
Found at i:28774578 original size:19 final size:17
Alignment explanation
Indices: 28774490--28774612 Score: 89
Period size: 16 Copynumber: 7.4 Consensus size: 17
28774480 TAACTATTAA
28774490 AATATTAAAAATTATTT
1 AATATTAAAAATTATTT
*
28774507 ATTATT-AAAATTA-TT
1 AATATTAAAAATTATTT
*
28774522 AATATTAAAAAATA-TT
1 AATATTAAAAATTATTT
* *
28774538 ATATTTTAATAATAATATTT
1 A-ATATTAA-AA-ATTATTT
28774558 AATATTAAAATATTATGTT
1 AATATTAAAA-ATTAT-TT
*
28774577 AATA-TAAAAA-TACTT
1 AATATTAAAAATTATTT
*
28774592 AA-AAT-AAAATTATTT
1 AATATTAAAAATTATTT
*
28774607 ATTATT
1 AATATT
28774613 CTTTATATTA
Statistics
Matches: 87, Mismatches: 10, Indels: 19
0.75 0.09 0.16
Matches are distributed among these distances:
14 5 0.06
15 17 0.20
16 20 0.23
17 12 0.14
18 14 0.16
19 16 0.18
20 3 0.03
ACGTcount: A:0.52, C:0.01, G:0.01, T:0.46
Consensus pattern (17 bp):
AATATTAAAAATTATTT
Found at i:28774634 original size:15 final size:15
Alignment explanation
Indices: 28774616--28774730 Score: 83
Period size: 15 Copynumber: 7.4 Consensus size: 15
28774606 TATTATTCTT
28774616 TATATTATTTATTAA
1 TATATTATTTATTAA
*
28774631 TATATTATAATATT-A
1 TATATTAT-TTATTAA
* * *
28774646 TTTACTA-ATATATAA
1 TATATTATTTAT-TAA
28774661 TAATATTATTTATTAA
1 T-ATATTATTTATTAA
* *
28774677 TATATTTATTAATT-G
1 TATA-TTATTTATTAA
28774692 TATATTATTTATTCATA
1 TATATTATTTATT-A-A
*
28774709 TAATATTAATTATTAA
1 T-ATATTATTTATTAA
28774725 TATATT
1 TATATT
28774731 GTAACATTAT
Statistics
Matches: 79, Mismatches: 11, Indels: 20
0.72 0.10 0.18
Matches are distributed among these distances:
13 4 0.05
14 9 0.11
15 28 0.35
16 22 0.28
17 5 0.06
18 11 0.14
ACGTcount: A:0.42, C:0.02, G:0.01, T:0.56
Consensus pattern (15 bp):
TATATTATTTATTAA
Found at i:28774643 original size:23 final size:23
Alignment explanation
Indices: 28774617--28774770 Score: 134
Period size: 23 Copynumber: 6.4 Consensus size: 23
28774607 ATTATTCTTT
28774617 ATATTATTTATTAATATATTATA
1 ATATTATTTATTAATATATTATA
* *
28774640 ATATTATTTACTAATATATAATA
1 ATATTATTTATTAATATATTATA
28774663 ATATTATTTATTAATATATTTATTA
1 ATATTATTTATTAATATA-TTA-TA
*
28774688 AT-TGTATATTATTTAT-TCA-TATA
1 ATAT-TAT-TTATTAATAT-ATTATA
* *
28774711 ATATTAATTATTAATATATTGTA
1 ATATTATTTATTAATATATTATA
* * *
28774734 ACATTATATTATTTATTTATCAATATA
1 ATATTAT-TTA-TTA-ATAT-ATTATA
28774761 ATATTATTTA
1 ATATTATTTA
28774771 GAAGTAAAAT
Statistics
Matches: 105, Mismatches: 14, Indels: 21
0.75 0.10 0.15
Matches are distributed among these distances:
22 8 0.08
23 53 0.50
24 9 0.09
25 11 0.10
26 14 0.13
27 10 0.10
ACGTcount: A:0.42, C:0.03, G:0.01, T:0.55
Consensus pattern (23 bp):
ATATTATTTATTAATATATTATA
Found at i:28774714 original size:18 final size:18
Alignment explanation
Indices: 28774636--28774770 Score: 81
Period size: 18 Copynumber: 7.8 Consensus size: 18
28774626 ATTAATATAT
*
28774636 TATAATATTATTTACTAA
1 TATAATATTATTTATTAA
* *
28774654 TAT-ATAATAATATTATTTA
1 TATAAT-ATTAT-TTATTAA
28774673 T-TAATA-TATTTATTAA
1 TATAATATTATTTATTAA
* *
28774689 T-TGTATATTATTTATTCA
1 TAT-AATATTATTTATTAA
*
28774707 TATAATATTAATTATTAA
1 TATAATATTATTTATTAA
**
28774725 TAT-AT-TGTA-ACATT-A
1 TATAATAT-TATTTATTAA
* *
28774740 TATTAT-TTATTTATCAA
1 TATAATATTATTTATTAA
28774757 TATAATATTATTTA
1 TATAATATTATTTA
28774771 GAAGTAAAAT
Statistics
Matches: 90, Mismatches: 16, Indels: 22
0.70 0.12 0.17
Matches are distributed among these distances:
15 6 0.07
16 17 0.19
17 17 0.19
18 41 0.46
19 9 0.10
ACGTcount: A:0.41, C:0.03, G:0.01, T:0.54
Consensus pattern (18 bp):
TATAATATTATTTATTAA
Found at i:28774729 original size:33 final size:31
Alignment explanation
Indices: 28774616--28774730 Score: 96
Period size: 30 Copynumber: 3.7 Consensus size: 31
28774606 TATTATTCTT
* *
28774616 TATATTATTTATTAATATATTATAATATTAT-
1 TATATTAATTATTAATATATTAT-TTATTATA
*
28774647 T-TACTAA-TATATAATAATATTATTTATTA-A
1 TATATTAATTAT-TAAT-ATATTATTTATTATA
* *
28774677 TATATTTATTAATT-GTATATTATTTATTCATA
1 TATATTAATT-ATTAATATATTATTTATT-ATA
28774709 TAATATTAATTATTAATATATT
1 T-ATATTAATTATTAATATATT
28774731 GTAACATTAT
Statistics
Matches: 66, Mismatches: 8, Indels: 18
0.72 0.09 0.20
Matches are distributed among these distances:
29 3 0.05
30 26 0.39
31 14 0.21
32 7 0.11
33 16 0.24
ACGTcount: A:0.42, C:0.02, G:0.01, T:0.56
Consensus pattern (31 bp):
TATATTAATTATTAATATATTATTTATTATA
Found at i:28780177 original size:99 final size:99
Alignment explanation
Indices: 28780002--28780386 Score: 366
Period size: 99 Copynumber: 3.9 Consensus size: 99
28779992 ATGCTTCTTT
* * * * * *
28780002 GATTTAGGTAACTTAGGATACTCGGGCACTTCCGGCTTTGATAACTATGGTTC-TTTT-GGCAAT
1 GATTTGGGTAACTCAGGATACTCGGGAACTTCCGGCTTTGACAACTCTGG--CATTTTGGGAAAT
* * * *
28780065 T-AGTGTTTATGTTTCTTAGGGACTTCTGGTTTTTCC
64 TCAG-GTTTTTGTTTCTTAGGCACTTCAGGCTTTTCC
* * * * *
28780101 GATTTGGGTAACTCGGGATATTCGGGAACTTCTGGCTTTGACAACTGTGGGATTTTGGGAAATTC
1 GATTTGGGTAACTCAGGATACTCGGGAACTTCCGGCTTTGACAACTCTGGCATTTTGGGAAATTC
28780166 AGGTTTTTGTTTCTTAGGCACTTCAGGCTTTTCC
66 AGGTTTTTGTTTCTTAGGCACTTCAGGCTTTTCC
* * * * ** * *
28780200 CATTCGGGTAACTCGGGATACTCAGGCGCTTCTC-GCTTCGAAAACTCTGGCATTTTGGGAAATT
1 GATTTGGGTAACTCAGGATACTCGGGAACTTC-CGGCTTTGACAACTCTGGCATTTTGGGAAATT
* * ** * *
28780264 TAGGTTTTTGTTTCTCATACGCTTCAGGCTTTTCT
65 CAGGTTTTTGTTTCTTAGGCACTTCAGGCTTTTCC
* * * * *
28780299 GATTTGGGTAACTCAGAACACTTGGAAACTTCCGGTTTTGACAACTCTGGCATTTT-GGACAATT
1 GATTTGGGTAACTCAGGATACTCGGGAACTTCCGGCTTTGACAACTCTGGCATTTTGGGA-AATT
* *
28780363 CAGGTTTTTGCTTCTCAGGCACTT
65 CAGGTTTTTGTTTCTTAGGCACTT
28780387 TGGGCATCTC
Statistics
Matches: 231, Mismatches: 49, Indels: 12
0.79 0.17 0.04
Matches are distributed among these distances:
98 8 0.03
99 221 0.96
100 2 0.01
ACGTcount: A:0.19, C:0.19, G:0.24, T:0.38
Consensus pattern (99 bp):
GATTTGGGTAACTCAGGATACTCGGGAACTTCCGGCTTTGACAACTCTGGCATTTTGGGAAATTC
AGGTTTTTGTTTCTTAGGCACTTCAGGCTTTTCC
Found at i:28783676 original size:18 final size:18
Alignment explanation
Indices: 28783620--28783678 Score: 52
Period size: 18 Copynumber: 3.4 Consensus size: 18
28783610 ATGGTAAGCG
28783620 ATTCAGGCAACTTGGGCA
1 ATTCAGGCAACTTGGGCA
* ** *
28783638 CTTC-TTC--CTTCGGCA
1 ATTCAGGCAACTTGGGCA
*
28783653 AGTCAGGCAACTTGGGCA
1 ATTCAGGCAACTTGGGCA
28783671 ATTCAGGC
1 ATTCAGGC
28783679 TTTGGCAACT
Statistics
Matches: 28, Mismatches: 10, Indels: 6
0.64 0.23 0.14
Matches are distributed among these distances:
15 9 0.32
16 1 0.04
17 1 0.04
18 17 0.61
ACGTcount: A:0.22, C:0.27, G:0.25, T:0.25
Consensus pattern (18 bp):
ATTCAGGCAACTTGGGCA
Found at i:28783686 original size:33 final size:33
Alignment explanation
Indices: 28783622--28783686 Score: 85
Period size: 33 Copynumber: 2.0 Consensus size: 33
28783612 GGTAAGCGAT
* **
28783622 TCAGGCAACTTGGGCACTTCTTCCTTCGGCAAG
1 TCAGGCAACTTGGGCAATTCAGCCTTCGGCAAG
* *
28783655 TCAGGCAACTTGGGCAATTCAGGCTTTGGCAA
1 TCAGGCAACTTGGGCAATTCAGCCTTCGGCAA
28783687 CTCCGAAAAT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
33 27 1.00
ACGTcount: A:0.22, C:0.26, G:0.26, T:0.26
Consensus pattern (33 bp):
TCAGGCAACTTGGGCAATTCAGCCTTCGGCAAG
Found at i:28783760 original size:33 final size:34
Alignment explanation
Indices: 28783670--28783760 Score: 78
Period size: 33 Copynumber: 2.7 Consensus size: 34
28783660 CAACTTGGGC
* *
28783670 AATTCAGGCTTTGGCAACTC-CGAAAATTTGGTT
1 AATTCAGGCTTTGGCAACTCAGGAAAATTTGGAT
** * ** * * *
28783703 TCTTCAGGTTTTGTTAAGTTAGGAAACTTT-GAT
1 AATTCAGGCTTTGGCAACTCAGGAAAATTTGGAT
28783736 AATTCAGGCTTTGGCAACTCAGGAA
1 AATTCAGGCTTTGGCAACTCAGGAA
28783761 CCTTGGGCTC
Statistics
Matches: 40, Mismatches: 17, Indels: 2
0.68 0.29 0.03
Matches are distributed among these distances:
33 33 0.82
34 7 0.17
ACGTcount: A:0.27, C:0.15, G:0.22, T:0.35
Consensus pattern (34 bp):
AATTCAGGCTTTGGCAACTCAGGAAAATTTGGAT
Found at i:28783814 original size:33 final size:33
Alignment explanation
Indices: 28783777--28784002 Score: 107
Period size: 33 Copynumber: 6.8 Consensus size: 33
28783767 GCTCCTCAGG
* * *
28783777 TTTTGGCCATTCAGGCTTTGGTAAGTCGGGAAC
1 TTTTGGCAATTCAGGCTTTGGTAACTCAGGAAC
* * * *
28783810 TTTTGGCGATTCAAGTTTTGGCAACTCAGGAAC
1 TTTTGGCAATTCAGGCTTTGGTAACTCAGGAAC
* * * * *
28783843 TTTAGGTAATTCTGGCTTTTGTAACTCTGGAAC
1 TTTTGGCAATTCAGGCTTTGGTAACTCAGGAAC
** * * * * *
28783876 -TTTGGCTTCTTCAGGTTTTTGCAAGTCAGGCGAC
1 TTTTGGC-AATTCAGGCTTTGGTAACTCAGG-AAC
* * * * *
28783910 -TTGGGCAACTCTGGCACTTTTGGAAACTCAGGAGC
1 TTTTGGCAATTCAGG--C-TTTGGTAACTCAGGAAC
* * * *
28783945 TTTGGGCAATTCAGGCTTTGGCAACTCAGGCAT
1 TTTTGGCAATTCAGGCTTTGGTAACTCAGGAAC
* * *
28783978 TTTTGGTATTTCTGGCTTTGG-AACT
1 TTTTGGCAATTCAGGCTTTGGTAACT
28784003 TCTGGCAACT
Statistics
Matches: 141, Mismatches: 46, Indels: 13
0.70 0.23 0.06
Matches are distributed among these distances:
32 8 0.06
33 101 0.72
34 8 0.06
35 1 0.01
36 23 0.16
ACGTcount: A:0.19, C:0.19, G:0.26, T:0.36
Consensus pattern (33 bp):
TTTTGGCAATTCAGGCTTTGGTAACTCAGGAAC
Found at i:28783973 original size:15 final size:15
Alignment explanation
Indices: 28783928--28783975 Score: 51
Period size: 15 Copynumber: 3.0 Consensus size: 15
28783918 CTCTGGCACT
*
28783928 TTTGGAAACTCAGGAGC
1 TTTGGCAACTCA-G-GC
*
28783945 TTTGGGCAATTCAGGC
1 TTT-GGCAACTCAGGC
28783961 TTTGGCAACTCAGGC
1 TTTGGCAACTCAGGC
28783976 ATTTTTGGTA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
15 11 0.41
16 5 0.19
17 4 0.15
18 7 0.26
ACGTcount: A:0.23, C:0.21, G:0.29, T:0.27
Consensus pattern (15 bp):
TTTGGCAACTCAGGC
Found at i:28793826 original size:3 final size:3
Alignment explanation
Indices: 28793820--28793846 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
28793810 AAAAAAAAAT
28793820 TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA
28793847 ATTCATTTCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:28795391 original size:33 final size:33
Alignment explanation
Indices: 28795354--28795418 Score: 85
Period size: 33 Copynumber: 2.0 Consensus size: 33
28795344 ATTCCTATCT
28795354 GATTAACCCGACTCGTCCGGATAGGCTCGGGCC
1 GATTAACCCGACTCGTCCGGATAGGCTCGGGCC
* * * **
28795387 GATTAACCTGGCTCGTCTGTTTAGGCTCGGGC
1 GATTAACCCGACTCGTCCGGATAGGCTCGGGC
28795419 TCAGGCCGAT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
33 27 1.00
ACGTcount: A:0.15, C:0.29, G:0.31, T:0.25
Consensus pattern (33 bp):
GATTAACCCGACTCGTCCGGATAGGCTCGGGCC
Found at i:28798797 original size:57 final size:59
Alignment explanation
Indices: 28798703--28798840 Score: 146
Period size: 58 Copynumber: 2.4 Consensus size: 59
28798693 AAATTTCTTC
* ** * *
28798703 TAAAT-AAAAAAT-TTTAAAAAAATTTTTTGAGAGAAAGTT-GAAGTATCAATTTTCCT
1 TAAATAAAAAAATATTTCAAAAAATTTTAAGAGAGAAAGTTAAAAATATCAATTTTCCT
*
28798759 TAAATAAAAAAATATTTCAAAAAATGTTTAAG-GA-AAAGTTAAAAATATCAATTTTTCT
1 TAAATAAAAAAATATTTCAAAAAAT-TTTAAGAGAGAAAGTTAAAAATATCAATTTTCCT
*
28798817 TAAA-AATAAAAA-AATTCAAAAAAT
1 TAAATAA-AAAAATATTTCAAAAAAT
28798841 ATATTTCAAA
Statistics
Matches: 70, Mismatches: 7, Indels: 9
0.81 0.08 0.10
Matches are distributed among these distances:
56 5 0.07
57 26 0.37
58 35 0.50
59 4 0.06
ACGTcount: A:0.54, C:0.05, G:0.07, T:0.33
Consensus pattern (59 bp):
TAAATAAAAAAATATTTCAAAAAATTTTAAGAGAGAAAGTTAAAAATATCAATTTTCCT
Found at i:28798878 original size:74 final size:66
Alignment explanation
Indices: 28798763--28798909 Score: 195
Period size: 74 Copynumber: 2.1 Consensus size: 66
28798753 TTTCCTTAAA
* *
28798763 TAAAAAAATATTTCAAAAAATGTTTAAGGAAAAGTTAAAAATATCAATTTTTCTTAAAAATAAAA
1 TAAAAAAATATTTCAAAAAATGTTTAAGGAAAAGTTAAAAATATCAACTTTCCTT--AAAT-AAA
28798828 AAAT
63 AAAT
*
28798832 TCAAAAAATATATTTCAAAATAAATGTTTTAAGGAAAAGTTGAAAATATCAACTTTCCTTAAATA
1 T-AAAAAA-ATATTTC-AAA-AAATG-TTTAAGGAAAAGTTAAAAATATCAACTTTCCTTAAATA
28798897 AAAAAT
61 AAAAAT
28798903 TAAAAAA
1 TAAAAAA
28798910 GAAGCTTTAA
Statistics
Matches: 70, Mismatches: 3, Indels: 9
0.85 0.04 0.11
Matches are distributed among these distances:
69 1 0.01
70 12 0.17
71 15 0.21
72 7 0.10
73 5 0.07
74 30 0.43
ACGTcount: A:0.56, C:0.06, G:0.06, T:0.31
Consensus pattern (66 bp):
TAAAAAAATATTTCAAAAAATGTTTAAGGAAAAGTTAAAAATATCAACTTTCCTTAAATAAAAAA
T
Found at i:28802605 original size:21 final size:21
Alignment explanation
Indices: 28802581--28802629 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
28802571 TATTTTCTAC
*
28802581 ATTTTTATTAGTATTTTA-TTT
1 ATTTTTATCA-TATTTTATTTT
* *
28802602 ATTTTTGTCATTTTTTATTTT
1 ATTTTTATCATATTTTATTTT
28802623 ATTTTTA
1 ATTTTTA
28802630 AAGAAAATTT
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
20 6 0.26
21 17 0.74
ACGTcount: A:0.20, C:0.02, G:0.04, T:0.73
Consensus pattern (21 bp):
ATTTTTATCATATTTTATTTT
Found at i:28807698 original size:199 final size:199
Alignment explanation
Indices: 28807207--28807720 Score: 499
Period size: 199 Copynumber: 2.6 Consensus size: 199
28807197 TAAAACCTGT
** * * * * *
28807207 TAAAGTGATGTTATCCCACATTTAATAAATATCTAAGTTCTTATAATCTTATATTCAAGTTGGGT
1 TAAAGTG-TGTTATCTTACATATAATAAATATCTAATTTCTTATAATCTTATATTTAAGATAGGT
* *
28807272 CTCTTCATTTACTATCAATT-AGTTTTAAGTTGATACATAATATGGTATCAAAACTAGAATTTTT
65 CCCTTCATTTACTATCAATTGA-TTTTAAGTTGATACTTAATATGGTATCAAAACTAGAATTTTT
* * * * * * *
28807336 TTCTGTTAACTTTTCCTAATTTGTCACATGGAAAGCTTCTTTCAACTTTGCCTACACGTGATGGG
129 TTCTATTAACTTTTCCAAATCTCTCAAATGGAAAGCTTCTTTCAACTTTACCTACACGTGATGAG
28807401 GGTTGA
194 GGTTGA
* * * *
28807407 TAAAGTGTGTTATCTTACATATGATAAATAT-TAAATTTCTTATAATCTTATA-TTCAGGTTGAG
1 TAAAGTGTGTTATCTTACATATAATAAATATCT-AATTTCTTATAATCTTATATTTAAGATAG-G
* * * * * **
28807470 TCCTTTCACTTAC-AGTCAATTGGTTTTAAGTTAGATGCTTAATATGGTATCAAAGCTA-TTTTT
64 TCCCTTCATTTACTA-TCAATTGATTTTAAGTT-GATACTTAATATGGTATCAAAACTAGAATTT
* * * *
28807533 TTTTCTATTATCATTTT-CAAATCTCTCAAAT-GATAGGCTTTTTTCATCTTTACCTACACGTGA
127 TTTTCTATTAAC-TTTTCCAAATCTCTCAAATGGA-AAGCTTCTTTCAACTTTACCTACACGTGA
* *
28807596 T-AGGTTCTGT
190 TGAGGGT-TGA
* * * *
28807606 TAAAGTAGTGTTTTC-TACATATAATAAATATCTAATTTCTTATAGTGTTATATTTAAGATAGGC
1 TAAAGT-GTGTTATCTTACATATAATAAATATCTAATTTCTTATAATCTTATATTTAAGATAGGT
* *
28807670 CCCTCCATTTACTA-CTAATTGATTTTAAGTTTGATACTTAACATGGTATCA
65 CCCTTCATTTACTATC-AATTGATTTTAAG-TTGATACTTAATATGGTATCA
28807721 GAGTCAAGAT
Statistics
Matches: 255, Mismatches: 45, Indels: 29
0.78 0.14 0.09
Matches are distributed among these distances:
198 13 0.05
199 192 0.75
200 50 0.20
ACGTcount: A:0.30, C:0.14, G:0.13, T:0.43
Consensus pattern (199 bp):
TAAAGTGTGTTATCTTACATATAATAAATATCTAATTTCTTATAATCTTATATTTAAGATAGGTC
CCTTCATTTACTATCAATTGATTTTAAGTTGATACTTAATATGGTATCAAAACTAGAATTTTTTT
CTATTAACTTTTCCAAATCTCTCAAATGGAAAGCTTCTTTCAACTTTACCTACACGTGATGAGGG
TTGA
Found at i:28809996 original size:27 final size:28
Alignment explanation
Indices: 28809926--28809984 Score: 84
Period size: 28 Copynumber: 2.1 Consensus size: 28
28809916 TACTCCTCTA
* *
28809926 ATGTTACCATTTTGTTGAACAACTTTTG
1 ATGTTATCATTTTGTTGAACAACTGTTG
*
28809954 ATGTTATCATTTTGTTTAACAAC-GTTG
1 ATGTTATCATTTTGTTGAACAACTGTTG
28809981 ATGT
1 ATGT
28809985 CTTTATTTTG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
27 7 0.25
28 21 0.75
ACGTcount: A:0.25, C:0.12, G:0.15, T:0.47
Consensus pattern (28 bp):
ATGTTATCATTTTGTTGAACAACTGTTG
Found at i:28811282 original size:22 final size:23
Alignment explanation
Indices: 28811232--28811291 Score: 68
Period size: 22 Copynumber: 2.7 Consensus size: 23
28811222 TCAGTAAAAA
* *
28811232 AAGGTCTAACTTATGCTGGAATT
1 AAGGTCTAGCTTATGATGGAATT
* *
28811255 AGGGTCTAGTTTATGAT-GAATT
1 AAGGTCTAGCTTATGATGGAATT
*
28811277 AAGGTCAAGCTTATG
1 AAGGTCTAGCTTATG
28811292 GTGCATTTTG
Statistics
Matches: 30, Mismatches: 7, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
22 17 0.57
23 13 0.43
ACGTcount: A:0.30, C:0.10, G:0.25, T:0.35
Consensus pattern (23 bp):
AAGGTCTAGCTTATGATGGAATT
Found at i:28813427 original size:11 final size:12
Alignment explanation
Indices: 28813413--28813447 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
28813403 GTATAAGAGA
*
28813413 TTTTAAGATTTT
1 TTTTAAAATTTT
28813425 TTTTAAAATTTT
1 TTTTAAAATTTT
28813437 TTTT-AAATTTT
1 TTTTAAAATTTT
28813448 GGTGGGATCA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
11 7 0.32
12 15 0.68
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.69
Consensus pattern (12 bp):
TTTTAAAATTTT
Found at i:28816054 original size:12 final size:12
Alignment explanation
Indices: 28816040--28816074 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
28816030 TCAAAAATGT
* *
28816040 TATATATATATT
1 TATATATTTATA
28816052 TATATATTTATA
1 TATATATTTATA
28816064 TATATATTTAT
1 TATATATTTAT
28816075 GGATGGAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (12 bp):
TATATATTTATA
Found at i:28821422 original size:24 final size:23
Alignment explanation
Indices: 28821394--28821442 Score: 64
Period size: 22 Copynumber: 2.1 Consensus size: 23
28821384 AGAATTAATC
28821394 ATCCTCTTGATATAGAATGATTCA
1 ATCC-CTTGATATAGAATGATTCA
* *
28821418 AT-CCTTGGTGTAGAATGATTCA
1 ATCCCTTGATATAGAATGATTCA
28821440 ATC
1 ATC
28821443 TTCTCAAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
22 19 0.86
23 1 0.05
24 2 0.09
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.37
Consensus pattern (23 bp):
ATCCCTTGATATAGAATGATTCA
Found at i:28822933 original size:40 final size:40
Alignment explanation
Indices: 28822869--28822945 Score: 118
Period size: 40 Copynumber: 1.9 Consensus size: 40
28822859 ACTGACAGTA
* * *
28822869 TATAGAATTTATACATTAATAGTGTATTAAATATAAATTC
1 TATAAAATATATACATTAATAGTGTATCAAATATAAATTC
*
28822909 TATAAAATATATACATTAGTAGTGTATCAAATATAAA
1 TATAAAATATATACATTAATAGTGTATCAAATATAAA
28822946 CTCATTTTTT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
40 33 1.00
ACGTcount: A:0.48, C:0.05, G:0.08, T:0.39
Consensus pattern (40 bp):
TATAAAATATATACATTAATAGTGTATCAAATATAAATTC
Found at i:28823651 original size:26 final size:26
Alignment explanation
Indices: 28823621--28823696 Score: 89
Period size: 30 Copynumber: 2.8 Consensus size: 26
28823611 TTTAAGTGTG
28823621 AATATGAGACTATAAAATGGCCAACC
1 AATATGAGACTATAAAATGGCCAACC
* * *
28823647 AATATGAAATTAAAAATTAAATGGCCAACC
1 AATATGAGACT----ATAAAATGGCCAACC
28823677 AATATGAGACTATAAAATGG
1 AATATGAGACTATAAAATGG
28823697 GACATGGATA
Statistics
Matches: 40, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
26 17 0.43
30 23 0.57
ACGTcount: A:0.50, C:0.13, G:0.14, T:0.22
Consensus pattern (26 bp):
AATATGAGACTATAAAATGGCCAACC
Found at i:28834813 original size:3 final size:3
Alignment explanation
Indices: 28834807--28834846 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
28834797 TTTTTTTTGT
28834807 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
28834847 ATTTGAGGAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:28835760 original size:5 final size:5
Alignment explanation
Indices: 28835750--28835789 Score: 53
Period size: 5 Copynumber: 7.8 Consensus size: 5
28835740 GGAGGAGCAA
* *
28835750 TGGGG TGGGG TGGGG TGGGG TTGGG TGAGG TGGGGG TGGG
1 TGGGG TGGGG TGGGG TGGGG TGGGG TGGGG T-GGGG TGGG
28835790 ATTGGAATTA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
5 26 0.87
6 4 0.13
ACGTcount: A:0.03, C:0.00, G:0.75, T:0.23
Consensus pattern (5 bp):
TGGGG
Found at i:28837530 original size:172 final size:172
Alignment explanation
Indices: 28837244--28837582 Score: 574
Period size: 172 Copynumber: 2.0 Consensus size: 172
28837234 GTGGATTAAG
* *
28837244 ATTGTATTATTTTACATTTGTTTACAAGAATTAGCTGTTGACTTGTTTACACTTTACAAATTGTC
1 ATTGTATTATTTTACATTCGTTTACAAGAATCAGCTGTTGACTTGTTTACACTTTACAAATTGTC
*
28837309 TCTATGAATTTTTTTTCTTTCATATTGTTTACCAGAATGGCAGAATCAGTTGTTTTAAAAAAAAT
66 TCTACGAATTTTTTTTCTTTCATATTGTTTACCAGAATGGCAGAATCAGTTGTTTTAAAAAAAAT
*
28837374 TTCTTATTGCACATTGTGTTTATCTTTTATGGTAATAATATC
131 TTCTTATTGCACATTGTGTTTATCTTTTATGCTAATAATATC
* *
28837416 ATTGTATTATTTTACATTCGTTTAGC-AGAATCAGTTGTTGACTTGTTTACACTTTACATATTGT
1 ATTGTATTATTTTACATTCGTTTA-CAAGAATCAGCTGTTGACTTGTTTACACTTTACAAATTGT
*
28837480 CTCTACGAATTTTTTTTCTTTCATATTGTTTATCC-GAATGGCAGAATCAGTTGTTTTAAAAAAT
65 CTCTACGAATTTTTTTTCTTTCATATTGTTTA-CCAGAATGGCAGAATCAGTTGTTTTAAAAAAA
*
28837544 TTTTCTTATTGCACATTGTGTTTATCTTTTATGCTAATA
129 ATTTCTTATTGCACATTGTGTTTATCTTTTATGCTAATA
28837583 TCGCTTTTCA
Statistics
Matches: 157, Mismatches: 8, Indels: 4
0.93 0.05 0.02
Matches are distributed among these distances:
172 154 0.98
173 3 0.02
ACGTcount: A:0.27, C:0.12, G:0.12, T:0.48
Consensus pattern (172 bp):
ATTGTATTATTTTACATTCGTTTACAAGAATCAGCTGTTGACTTGTTTACACTTTACAAATTGTC
TCTACGAATTTTTTTTCTTTCATATTGTTTACCAGAATGGCAGAATCAGTTGTTTTAAAAAAAAT
TTCTTATTGCACATTGTGTTTATCTTTTATGCTAATAATATC
Found at i:28842462 original size:30 final size:30
Alignment explanation
Indices: 28842426--28842485 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
28842416 ATCATTCCTC
28842426 AAATTCCAACATTATGGAGGGGTCTAACAA
1 AAATTCCAACATTATGGAGGGGTCTAACAA
28842456 AAATTCCAACATTATGGAGGGGTCTAACAA
1 AAATTCCAACATTATGGAGGGGTCTAACAA
28842486 TTTTGCATTC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.40, C:0.17, G:0.20, T:0.23
Consensus pattern (30 bp):
AAATTCCAACATTATGGAGGGGTCTAACAA
Found at i:28850055 original size:10 final size:10
Alignment explanation
Indices: 28850040--28850069 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
28850030 ATCAAGCTTT
28850040 TATATTTTAA
1 TATATTTTAA
28850050 TATATTTTAA
1 TATATTTTAA
28850060 T-TATTTTAA
1 TATATTTTAA
28850069 T
1 T
28850070 TGATAAAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 9 0.45
10 11 0.55
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (10 bp):
TATATTTTAA
Found at i:28851200 original size:157 final size:157
Alignment explanation
Indices: 28850914--28851231 Score: 609
Period size: 157 Copynumber: 2.0 Consensus size: 157
28850904 TGATTGCTGA
*
28850914 ATATATGATCGATGCGTTCGGTATAATGTAGATAGGCAAAAAAAAATCACGTGAAATTTGATTCT
1 ATATATGATCGATGCGTTCGGTATAATATAGATAGGCAAAAAAAAATCACGTGAAATTTGATTCT
28850979 TCAAAGTTGACGTCATAGAGGGGGATCAATATTAAGGGACAACTAGATTTGAGCCACGGTCTGAC
66 TCAAAGTTGACGTCATAGAGGGGGATCAATATTAAGGGACAACTAGATTTGAGCCACGGTCTGAC
28851044 CTTGTGATTGTCTAATCTTGCGTGTAT
131 CTTGTGATTGTCTAATCTTGCGTGTAT
*
28851071 ATATATGATCGATGCGTTCGGTATAGTATAGATAGGCAAAAAAAAATCACGTGAAATTTGATTCT
1 ATATATGATCGATGCGTTCGGTATAATATAGATAGGCAAAAAAAAATCACGTGAAATTTGATTCT
*
28851136 TCAAAGTTGACGTTATAGAGGGGGATCAATATTAAGGGACAACTAGATTTGAGCCACGGTCTGAC
66 TCAAAGTTGACGTCATAGAGGGGGATCAATATTAAGGGACAACTAGATTTGAGCCACGGTCTGAC
28851201 CTTGTGATTGTCTAATCTTGCGTGTAT
131 CTTGTGATTGTCTAATCTTGCGTGTAT
28851228 ATAT
1 ATAT
28851232 TGGGTTGAGT
Statistics
Matches: 158, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
157 158 1.00
ACGTcount: A:0.32, C:0.14, G:0.23, T:0.31
Consensus pattern (157 bp):
ATATATGATCGATGCGTTCGGTATAATATAGATAGGCAAAAAAAAATCACGTGAAATTTGATTCT
TCAAAGTTGACGTCATAGAGGGGGATCAATATTAAGGGACAACTAGATTTGAGCCACGGTCTGAC
CTTGTGATTGTCTAATCTTGCGTGTAT
Found at i:28854234 original size:8 final size:8
Alignment explanation
Indices: 28854221--28854245 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
28854211 AATCGACCTA
28854221 AAAAAAAG
1 AAAAAAAG
28854229 AAAAAAAG
1 AAAAAAAG
28854237 AAAAAAAG
1 AAAAAAAG
28854245 A
1 A
28854246 TGATGATAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (8 bp):
AAAAAAAG
Found at i:28868094 original size:12 final size:12
Alignment explanation
Indices: 28868077--28868111 Score: 61
Period size: 12 Copynumber: 2.9 Consensus size: 12
28868067 AAGATGGTGC
*
28868077 TGATAAAGATGA
1 TGATAATGATGA
28868089 TGATAATGATGA
1 TGATAATGATGA
28868101 TGATAATGATG
1 TGATAATGATG
28868112 CAGATGATGG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.43, C:0.00, G:0.26, T:0.31
Consensus pattern (12 bp):
TGATAATGATGA
Found at i:28872014 original size:12 final size:12
Alignment explanation
Indices: 28871997--28872048 Score: 72
Period size: 12 Copynumber: 4.3 Consensus size: 12
28871987 TTTTTTAATA
28871997 TAAATATAAAAT
1 TAAATATAAAAT
28872009 TAAATATATAAA-
1 TAAATATA-AAAT
28872021 TAAATATAAAAT
1 TAAATATAAAAT
28872033 TAAATA-AATAAT
1 TAAATATAA-AAT
28872045 TAAA
1 TAAA
28872049 AAATAATTTA
Statistics
Matches: 37, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
11 5 0.14
12 29 0.78
13 3 0.08
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (12 bp):
TAAATATAAAAT
Found at i:28872017 original size:20 final size:21
Alignment explanation
Indices: 28871994--28872075 Score: 69
Period size: 24 Copynumber: 3.9 Consensus size: 21
28871984 TTATTTTTTA
28871994 ATATAAATATAAAATTAAATAT
1 ATATAAATATAAAATT-AATAT
28872016 ATAAATAAATATAAAATTAA-AT
1 AT--ATAAATATAAAATTAATAT
* * * *
28872038 AAATAATTA-AAAAATAATTT
1 ATATAAATATAAAATTAATAT
* *
28872058 ATATATATATTAAATTAA
1 ATATAAATATAAAATTAA
28872076 AAATTCCGAT
Statistics
Matches: 47, Mismatches: 9, Indels: 9
0.72 0.14 0.14
Matches are distributed among these distances:
19 7 0.15
20 13 0.28
21 6 0.13
22 5 0.11
23 2 0.04
24 14 0.30
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (21 bp):
ATATAAATATAAAATTAATAT
Found at i:28872023 original size:24 final size:24
Alignment explanation
Indices: 28871996--28872048 Score: 88
Period size: 24 Copynumber: 2.2 Consensus size: 24
28871986 ATTTTTTAAT
*
28871996 ATAAATATAAAATTAAATATATAA
1 ATAAATATAAAATTAAATAAATAA
28872020 ATAAATATAAAATTAAATAAATAA
1 ATAAATATAAAATTAAATAAATAA
*
28872044 TTAAA
1 ATAAA
28872049 AAATAATTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (24 bp):
ATAAATATAAAATTAAATAAATAA
Found at i:28872054 original size:11 final size:12
Alignment explanation
Indices: 28871992--28872056 Score: 64
Period size: 12 Copynumber: 5.4 Consensus size: 12
28871982 TATTATTTTT
28871992 TAATATAAATATAA
1 TAAT-TAAATA-AA
*
28872006 -AATTAAATATA
1 TAATTAAATAAA
*
28872017 TAAATAAATATAA
1 TAATTAAATA-AA
28872030 -AATTAAATAAA
1 TAATTAAATAAA
28872041 TAATTAAA-AAA
1 TAATTAAATAAA
28872052 TAATT
1 TAATT
28872057 TATATATATA
Statistics
Matches: 44, Mismatches: 4, Indels: 9
0.77 0.07 0.16
Matches are distributed among these distances:
11 11 0.25
12 29 0.66
13 4 0.09
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (12 bp):
TAATTAAATAAA
Found at i:28873873 original size:36 final size:36
Alignment explanation
Indices: 28873799--28873873 Score: 87
Period size: 36 Copynumber: 2.1 Consensus size: 36
28873789 CAGTTCTGCC
* * * *
28873799 GGAGACTTTACGCAGACCTATTGAGGTACTTCCTCA
1 GGAGACTTTACACAGACCTATAGAGGCACTTCCCCA
* **
28873835 GGAGACTTTGCACAGACCTATAGAGGCGGTTCCCCA
1 GGAGACTTTACACAGACCTATAGAGGCACTTCCCCA
28873871 GGA
1 GGA
28873874 CCCATTGAAC
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.25, C:0.25, G:0.27, T:0.23
Consensus pattern (36 bp):
GGAGACTTTACACAGACCTATAGAGGCACTTCCCCA
Found at i:28877281 original size:26 final size:26
Alignment explanation
Indices: 28877252--28877380 Score: 99
Period size: 24 Copynumber: 4.9 Consensus size: 26
28877242 ATCTGTTTTT
28877252 TATAATATTAATATATTATTTGA-TAA
1 TATAATATTAATATATTATTT-ATTAA
* *
28877278 TAT-ATATTATGTATGTTATTTATTAA
1 TATAATATTA-ATATATTATTTATTAA
28877304 TATATTATATTAATAGTATATTATTTATTAA
1 TATA--ATATT-A-A-TATATTATTTATTAA
* *
28877335 -AT-ATATTATTATAATATTTATTAA
1 TATAATATTAATATATTATTTATTAA
* *
28877359 TATATTA-TAATAT-TTTTTTATT
1 TATAATATTAATATATTATTTATT
28877381 CATGTATTAT
Statistics
Matches: 84, Mismatches: 10, Indels: 20
0.74 0.09 0.18
Matches are distributed among these distances:
24 21 0.25
25 14 0.17
26 21 0.25
27 5 0.06
29 5 0.06
30 4 0.05
31 14 0.17
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (26 bp):
TATAATATTAATATATTATTTATTAA
Found at i:28877337 original size:19 final size:19
Alignment explanation
Indices: 28877251--28877366 Score: 66
Period size: 19 Copynumber: 6.1 Consensus size: 19
28877241 AATCTGTTTT
*
28877251 TTATAATATTAATATATTA
1 TTATTATATTAATATATTA
* *
28877270 TT-TGATAAT-ATATATTA
1 TTATTATATTAATATATTA
* *
28877287 TGTATGT-TATTTAT-TAATA
1 T-TAT-TATATTAATATATTA
28877306 -TATTATATTAATAGTA-TA
1 TTATTATATTAATA-TATTA
28877324 TTATT-TATTAAATATATTA
1 TTATTATATT-AATATATTA
28877343 TTATAATATTTATTAATATATTA
1 TTAT--TA--TATTAATATATTA
28877366 T
1 T
28877367 AATATTTTTT
Statistics
Matches: 76, Mismatches: 6, Indels: 26
0.70 0.06 0.24
Matches are distributed among these distances:
16 1 0.01
17 18 0.24
18 14 0.18
19 26 0.34
20 2 0.03
21 1 0.01
23 10 0.13
24 4 0.05
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.55
Consensus pattern (19 bp):
TTATTATATTAATATATTA
Found at i:28877345 original size:35 final size:29
Alignment explanation
Indices: 28877280--28877367 Score: 105
Period size: 31 Copynumber: 3.1 Consensus size: 29
28877270 TTTGATAATA
*
28877280 TATATTATGTATGTTATTTATTAATATAT
1 TATATTATGTATATTATTTATTAATATAT
28877309 TATATTAATAGTATATTATTTATT-A-A-A-
1 TATATT-AT-GTATATTATTTATTAATATAT
*
28877336 TATATTAT-TATAATATTTATTAATATAT
1 TATATTATGTATATTATTTATTAATATAT
28877364 TATA
1 TATA
28877368 ATATTTTTTT
Statistics
Matches: 51, Mismatches: 2, Indels: 13
0.77 0.03 0.20
Matches are distributed among these distances:
24 12 0.24
25 1 0.02
26 3 0.06
27 7 0.14
28 5 0.10
29 7 0.14
30 3 0.06
31 13 0.25
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (29 bp):
TATATTATGTATATTATTTATTAATATAT
Found at i:28877378 original size:24 final size:24
Alignment explanation
Indices: 28877294--28877390 Score: 79
Period size: 24 Copynumber: 3.9 Consensus size: 24
28877284 TTATGTATGT
* * *
28877294 TATTTATTAATATATTATATTAATAG
1 TATTTATTTAT-TAATATATT-ATAA
*
28877320 TATATTATTTATTAAATATATTATTA
1 TAT-TTATTTATT-AATATATTATAA
*
28877346 TA-ATATTTATTAATATATTATAA
1 TATTTATTTATTAATATATTATAA
* * *
28877369 TATTTTTTTATTCATGTATTAT
1 TATTTATTTATTAATATATTAT
28877391 TTATTAATAT
Statistics
Matches: 58, Mismatches: 10, Indels: 8
0.76 0.13 0.11
Matches are distributed among these distances:
23 13 0.22
24 23 0.40
26 8 0.14
27 14 0.24
ACGTcount: A:0.39, C:0.01, G:0.02, T:0.58
Consensus pattern (24 bp):
TATTTATTTATTAATATATTATAA
Found at i:28877407 original size:47 final size:50
Alignment explanation
Indices: 28877293--28877413 Score: 114
Period size: 47 Copynumber: 2.5 Consensus size: 50
28877283 ATTATGTATG
*
28877293 TTATTTATTAATAT-AT--TATATTAATAGTATATTATTTATTAAATATA
1 TTATTTATTAATATAATAATATATTAATAATATATTATTTATTAAATATA
* * * *
28877340 TTA-TTA-TAATATTTATTAATATATT-ATAATAT-TTTTTTATT-CATGTA
1 TTATTTATTAATA--TAATAATATATTAATAATATATTATTTATTAAATATA
*
28877387 TTATTTATTAATATAATAATATTTTAA
1 TTATTTATTAATATAATAATATATTAA
28877414 GTAAAATTAT
Statistics
Matches: 59, Mismatches: 7, Indels: 15
0.73 0.09 0.19
Matches are distributed among these distances:
45 5 0.08
46 3 0.05
47 21 0.36
48 13 0.22
49 11 0.19
50 6 0.10
ACGTcount: A:0.40, C:0.01, G:0.02, T:0.57
Consensus pattern (50 bp):
TTATTTATTAATATAATAATATATTAATAATATATTATTTATTAAATATA
Found at i:28878196 original size:2 final size:2
Alignment explanation
Indices: 28878189--28878214 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
28878179 TATTTGCCGT
28878189 TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC
28878215 ATTGTTTTCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:28881879 original size:2 final size:2
Alignment explanation
Indices: 28881872--28881906 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
28881862 CAGCAATAGT
28881872 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
28881907 TACAAAAGAG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:28882612 original size:22 final size:22
Alignment explanation
Indices: 28882568--28882613 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
28882558 GTAGTTTTTT
* *
28882568 TTTTTAATTTAAAATTATCAAA
1 TTTTAAATTTAAAATTATAAAA
28882590 TTTTAAATTT-AAATTATTAAAA
1 TTTTAAATTTAAAATTA-TAAAA
28882612 TT
1 TT
28882614 AAAAATTGAG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 6 0.29
22 15 0.71
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (22 bp):
TTTTAAATTTAAAATTATAAAA
Done.