Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr12
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: 39383930
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.32
Warning! 780790 characters in sequence are not A, C, G, or T
File 19 of 126
Found at i:5587840 original size:24 final size:24
Alignment explanation
Indices: 5587813--5587859 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
5587803 ATTGAAATGG
5587813 ATTG-ATTTAATATGTGA-TGAATTT
1 ATTGAATTT-ATAT-TGATTGAATTT
5587837 ATTGAATTTATATTGATTGAATT
1 ATTGAATTTATATTGATTGAATT
5587860 GGTATATATA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
23 3 0.14
24 14 0.67
25 4 0.19
ACGTcount: A:0.34, C:0.00, G:0.15, T:0.51
Consensus pattern (24 bp):
ATTGAATTTATATTGATTGAATTT
Found at i:5620403 original size:23 final size:24
Alignment explanation
Indices: 5620377--5620427 Score: 70
Period size: 23 Copynumber: 2.2 Consensus size: 24
5620367 TAATTTTTAA
*
5620377 ATTTTA-AATTATTTAGTGATAAT
1 ATTTTAGAATTATTTAATGATAAT
*
5620400 A-TTTAGGATTATTTAATGATAAT
1 ATTTTAGAATTATTTAATGATAAT
5620423 ATTTT
1 ATTTT
5620428 TAAAAAATCT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
22 4 0.17
23 17 0.71
24 3 0.12
ACGTcount: A:0.37, C:0.00, G:0.10, T:0.53
Consensus pattern (24 bp):
ATTTTAGAATTATTTAATGATAAT
Found at i:5620404 original size:13 final size:13
Alignment explanation
Indices: 5620386--5620426 Score: 52
Period size: 13 Copynumber: 3.4 Consensus size: 13
5620376 AATTTTAAAT
5620386 TATTTAGTGATAA
1 TATTTAGTGATAA
5620399 TATTTAG-GAT--
1 TATTTAGTGATAA
*
5620409 TATTTAATGATAA
1 TATTTAGTGATAA
5620422 TATTT
1 TATTT
5620427 TTAAAAAATC
Statistics
Matches: 24, Mismatches: 1, Indels: 6
0.77 0.03 0.19
Matches are distributed among these distances:
10 6 0.25
11 3 0.12
12 3 0.12
13 12 0.50
ACGTcount: A:0.37, C:0.00, G:0.12, T:0.51
Consensus pattern (13 bp):
TATTTAGTGATAA
Found at i:5642045 original size:21 final size:21
Alignment explanation
Indices: 5642021--5642062 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
5642011 TCATACTCAA
*
5642021 ATTTATTTATTC-TCTTCTCTT
1 ATTT-TTTATTCTTCCTCTCTT
*
5642042 ATTTTTTCTTCTTCCTCTCTT
1 ATTTTTTATTCTTCCTCTCTT
5642063 TGTTAATGGA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.10, C:0.24, G:0.00, T:0.67
Consensus pattern (21 bp):
ATTTTTTATTCTTCCTCTCTT
Found at i:5643181 original size:22 final size:24
Alignment explanation
Indices: 5643155--5643198 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
5643145 GAAAAATATT
5643155 AAATAT-ATA-TTTTTTATTTTTA
1 AAATATAATAGTTTTTTATTTTTA
5643177 AAATATAATAGTTTTTTATTTT
1 AAATATAATAGTTTTTTATTTT
5643199 AAGTTTATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 6 0.30
23 3 0.15
24 11 0.55
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.61
Consensus pattern (24 bp):
AAATATAATAGTTTTTTATTTTTA
Found at i:5643309 original size:9 final size:9
Alignment explanation
Indices: 5643295--5643322 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
5643285 TTTTGTTACA
5643295 ACAATTAAT
1 ACAATTAAT
5643304 ACAATTAAT
1 ACAATTAAT
5643313 ACAATTAAT
1 ACAATTAAT
5643322 A
1 A
5643323 ATTTGATAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.57, C:0.11, G:0.00, T:0.32
Consensus pattern (9 bp):
ACAATTAAT
Found at i:5643344 original size:68 final size:66
Alignment explanation
Indices: 5643265--5643406 Score: 248
Period size: 68 Copynumber: 2.1 Consensus size: 66
5643255 TCAAGTTTAT
*
5643265 TTTACTAATCAAATGTTAGATTTTGTTACAACAATTAATACAATTAATACAATTAATAATTTGAT
1 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATT-A-ACAATTAATAATTTGAT
5643330 AAA
64 AAA
5643333 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAACAATTAATAATTTGATAA
1 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAACAATTAATAATTTGATAA
*
5643398 T
66 A
5643399 TTTACTAA
1 TTTACTAA
5643407 CAATTAATTT
Statistics
Matches: 72, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
66 27 0.38
67 1 0.01
68 44 0.61
ACGTcount: A:0.45, C:0.09, G:0.05, T:0.41
Consensus pattern (66 bp):
TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAACAATTAATAATTTGATAA
A
Found at i:5643416 original size:16 final size:16
Alignment explanation
Indices: 5643395--5643436 Score: 66
Period size: 16 Copynumber: 2.6 Consensus size: 16
5643385 AATAATTTGA
*
5643395 TAATTTTACTAACAAT
1 TAATTTTAATAACAAT
5643411 TAATTTTAATAACAAT
1 TAATTTTAATAACAAT
*
5643427 TAGTTTTAAT
1 TAATTTTAAT
5643437 TTTATTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.43, C:0.07, G:0.02, T:0.48
Consensus pattern (16 bp):
TAATTTTAATAACAAT
Found at i:5643425 original size:59 final size:66
Alignment explanation
Indices: 5643265--5643428 Score: 216
Period size: 68 Copynumber: 2.5 Consensus size: 66
5643255 TCAAGTTTAT
*
5643265 TTTACTAATCAAATGTTAGATTTTGTTACAACAATTAATACAATTAATACAATTAATAATTTGAT
1 TTTACTAATCAAA-GTTAGATTTT-ATACAACAATTAATACAATTAATACAATTAATAATTTGAT
5643330 AAA
64 AAA
5643333 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATT-A-ACAATTAATAATTTGAT
1 TTTACTAATCAAA-GTTAGATTTTA-TACAACAATTAATACAATTAATACAATTAATAATTTGAT
*
5643396 AAT
64 AAA
*
5643399 TTTACTAA-C-AA-TTA-ATTTTA-ATAACAATTA
1 TTTACTAATCAAAGTTAGATTTTATACAACAATTA
5643429 GTTTTAATTT
Statistics
Matches: 92, Mismatches: 3, Indels: 11
0.87 0.03 0.10
Matches are distributed among these distances:
59 9 0.10
61 6 0.07
62 3 0.03
64 2 0.02
65 1 0.01
66 27 0.29
67 1 0.01
68 43 0.47
ACGTcount: A:0.46, C:0.09, G:0.04, T:0.41
Consensus pattern (66 bp):
TTTACTAATCAAAGTTAGATTTTATACAACAATTAATACAATTAATACAATTAATAATTTGATAA
A
Found at i:5646077 original size:13 final size:13
Alignment explanation
Indices: 5646059--5646210 Score: 67
Period size: 13 Copynumber: 11.2 Consensus size: 13
5646049 ATTTTGAATA
5646059 TAATATACTGTTT
1 TAATATACTGTTT
5646072 TAATATACTGATTACT
1 TAATATACTG-TT--T
* * * *
5646088 GTTATAAAAT-TTG
1 -TAATATACTGTTT
*
5646101 TAATATATTGTTT
1 TAATATACTGTTT
*
5646114 TAACTTTTAACT-TTT
1 TAA--TAT-ACTGTTT
*
5646129 -AATATACTATTAT
1 TAATATACTGTT-T
* *
5646142 AAATATACTTTTT
1 TAATATACTGTTT
* *
5646155 TAATATATTATTT
1 TAATATACTGTTT
*
5646168 TAATATATTGTTAT
1 TAATATACTGTT-T
* *
5646182 AAATATATTGTTT
1 TAATATACTGTTT
*
5646195 TAATATAATGTTT
1 TAATATACTGTTT
5646208 TAA
1 TAA
5646211 CTTTTAATAT
Statistics
Matches: 108, Mismatches: 19, Indels: 24
0.72 0.13 0.16
Matches are distributed among these distances:
11 3 0.03
12 10 0.09
13 53 0.49
14 26 0.24
15 7 0.06
16 3 0.03
17 6 0.06
ACGTcount: A:0.37, C:0.05, G:0.05, T:0.53
Consensus pattern (13 bp):
TAATATACTGTTT
Found at i:5646168 original size:15 final size:13
Alignment explanation
Indices: 5646125--5646201 Score: 75
Period size: 13 Copynumber: 5.8 Consensus size: 13
5646115 AACTTTTAAC
*
5646125 TTTTAATATACTA
1 TTTTAATATATTA
*
5646138 TTATAAATATACTT-
1 TT-TTAATATA-TTA
5646152 TTTTAATATATTA
1 TTTTAATATATTA
*
5646165 TTTTAATATATTG
1 TTTTAATATATTA
* *
5646178 TTATAAATATATTG
1 TT-TTAATATATTA
5646192 TTTTAATATA
1 TTTTAATATA
5646202 ATGTTTTAAC
Statistics
Matches: 54, Mismatches: 6, Indels: 8
0.79 0.09 0.12
Matches are distributed among these distances:
12 2 0.04
13 30 0.56
14 21 0.39
15 1 0.02
ACGTcount: A:0.39, C:0.03, G:0.03, T:0.56
Consensus pattern (13 bp):
TTTTAATATATTA
Found at i:5646182 original size:40 final size:40
Alignment explanation
Indices: 5646102--5646210 Score: 123
Period size: 40 Copynumber: 2.7 Consensus size: 40
5646092 TAAAATTTGT
* *
5646102 AATATATTGTTTTAACTTTTAA-CTTTTAATATACTATTATA
1 AATATATTGTTTTAA--TATAATATTTTAATATACTATTATA
* * *
5646143 AATATACTT-TTTTAATATATTATTTTAATATATTGTTATA
1 AATATA-TTGTTTTAATATAATATTTTAATATACTATTATA
*
5646183 AATATATTGTTTTAATATAATGTTTTAA
1 AATATATTGTTTTAATATAATATTTTAA
5646211 CTTTTAATAT
Statistics
Matches: 58, Mismatches: 7, Indels: 7
0.81 0.10 0.10
Matches are distributed among these distances:
39 5 0.09
40 39 0.67
41 12 0.21
42 2 0.03
ACGTcount: A:0.38, C:0.04, G:0.04, T:0.55
Consensus pattern (40 bp):
AATATATTGTTTTAATATAATATTTTAATATACTATTATA
Found at i:5648838 original size:10 final size:10
Alignment explanation
Indices: 5648823--5648847 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
5648813 TGGGGTTTAA
5648823 CTTATGTTTT
1 CTTATGTTTT
5648833 CTTATGTTTT
1 CTTATGTTTT
5648843 CTTAT
1 CTTAT
5648848 CTCAAAGATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.12, C:0.12, G:0.08, T:0.68
Consensus pattern (10 bp):
CTTATGTTTT
Found at i:5648897 original size:30 final size:30
Alignment explanation
Indices: 5648861--5648919 Score: 109
Period size: 30 Copynumber: 2.0 Consensus size: 30
5648851 AAAGATAGTT
5648861 TGAAGCAAAATTACAGATTGGGATTTTCAG
1 TGAAGCAAAATTACAGATTGGGATTTTCAG
*
5648891 TGAAGCAAAATTATAGATTGGGATTTTCA
1 TGAAGCAAAATTACAGATTGGGATTTTCA
5648920 ATGCTTGATT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.37, C:0.08, G:0.22, T:0.32
Consensus pattern (30 bp):
TGAAGCAAAATTACAGATTGGGATTTTCAG
Found at i:5654540 original size:5 final size:5
Alignment explanation
Indices: 5654530--5654573 Score: 58
Period size: 5 Copynumber: 9.2 Consensus size: 5
5654520 GATTATGTTT
5654530 TTATA TTATA TTATTA TTA-A -TATA TTATA TTATA TTATA -TATA T
1 TTATA TTATA TTA-TA TTATA TTATA TTATA TTATA TTATA TTATA T
5654574 AACAAAAGAG
Statistics
Matches: 35, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
3 2 0.06
4 6 0.17
5 22 0.63
6 5 0.14
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (5 bp):
TTATA
Found at i:5654555 original size:19 final size:19
Alignment explanation
Indices: 5654531--5654573 Score: 70
Period size: 19 Copynumber: 2.3 Consensus size: 19
5654521 ATTATGTTTT
5654531 TATATTATATTATTATTA-A
1 TATATTATATTA-TATTATA
5654550 TATATTATATTATATTATA
1 TATATTATATTATATTATA
5654569 TATAT
1 TATAT
5654574 AACAAAAGAG
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
18 5 0.22
19 18 0.78
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (19 bp):
TATATTATATTATATTATA
Found at i:5655749 original size:41 final size:37
Alignment explanation
Indices: 5655701--5655800 Score: 92
Period size: 41 Copynumber: 2.6 Consensus size: 37
5655691 TCGACCTTGA
5655701 GTCGATGAGACACTGGGTGTCATACTGTTACTTCGGATAG
1 GTCGATGAGACACTGGGTGTCA-AC--TTACTTCGGATAG
* ** ** * *
5655741 ATTCGATGAGGTACTGGGTACCAACTTACTTCGGCTTG
1 -GTCGATGAGACACTGGGTGTCAACTTACTTCGGATAG
*
5655779 GCCGATGAGACACTGGGTGTCA
1 GTCGATGAGACACTGGGTGTCA
5655801 CTTTATTGCT
Statistics
Matches: 46, Mismatches: 13, Indels: 4
0.73 0.21 0.06
Matches are distributed among these distances:
37 16 0.35
38 11 0.24
40 2 0.04
41 17 0.37
ACGTcount: A:0.22, C:0.20, G:0.30, T:0.28
Consensus pattern (37 bp):
GTCGATGAGACACTGGGTGTCAACTTACTTCGGATAG
Found at i:5658707 original size:32 final size:32
Alignment explanation
Indices: 5658671--5658737 Score: 116
Period size: 32 Copynumber: 2.1 Consensus size: 32
5658661 TATATAGCCT
*
5658671 CTTATTCAAGCAGAACTTATCTCTCCTTGATC
1 CTTATTCAAGCAAAACTTATCTCTCCTTGATC
*
5658703 CTTATTCAAGCAAAACTTATCTCTCTTTGATC
1 CTTATTCAAGCAAAACTTATCTCTCCTTGATC
5658735 CTT
1 CTT
5658738 CCTCTATGTG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.25, C:0.27, G:0.07, T:0.40
Consensus pattern (32 bp):
CTTATTCAAGCAAAACTTATCTCTCCTTGATC
Found at i:5660409 original size:46 final size:46
Alignment explanation
Indices: 5660348--5660438 Score: 173
Period size: 46 Copynumber: 2.0 Consensus size: 46
5660338 TTTTTCCACG
5660348 TTAAATTTGTCTGTTCATCTTCTCAATTTCTTCTACTATTTTTACA
1 TTAAATTTGTCTGTTCATCTTCTCAATTTCTTCTACTATTTTTACA
*
5660394 TTAAATTTGTGTGTTCATCTTCTCAATTTCTTCTACTATTTTTAC
1 TTAAATTTGTCTGTTCATCTTCTCAATTTCTTCTACTATTTTTAC
5660439 TTGTTCGTTG
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 44 1.00
ACGTcount: A:0.21, C:0.19, G:0.05, T:0.55
Consensus pattern (46 bp):
TTAAATTTGTCTGTTCATCTTCTCAATTTCTTCTACTATTTTTACA
Found at i:5663062 original size:8 final size:7
Alignment explanation
Indices: 5663042--5663074 Score: 57
Period size: 7 Copynumber: 4.6 Consensus size: 7
5663032 TTAACAAGTC
5663042 TTAAAAA
1 TTAAAAA
5663049 TTAAAAA
1 TTAAAAA
5663056 TTAAAAA
1 TTAAAAA
5663063 TTACAAAA
1 TTA-AAAA
5663071 TTAA
1 TTAA
5663075 TTAGCCAAAG
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
7 18 0.72
8 7 0.28
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.30
Consensus pattern (7 bp):
TTAAAAA
Found at i:5668547 original size:30 final size:30
Alignment explanation
Indices: 5668511--5668569 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
5668501 TTGGGTATTT
*
5668511 CCACACGGGCTGGCCACACG-CTCGTGTGCG
1 CCACACGAGCTGGCCACACGCCTC-TGTGCG
5668541 CCACACGAGCTGGCCACACGCCTCTGTGC
1 CCACACGAGCTGGCCACACGCCTCTGTGC
5668570 CAGCCCGTGA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
30 24 0.89
31 3 0.11
ACGTcount: A:0.15, C:0.42, G:0.29, T:0.14
Consensus pattern (30 bp):
CCACACGAGCTGGCCACACGCCTCTGTGCG
Found at i:5673043 original size:188 final size:188
Alignment explanation
Indices: 5672669--5673046 Score: 639
Period size: 189 Copynumber: 2.0 Consensus size: 188
5672659 AAGAAATAGG
*
5672669 TTTAAATTTATGAGTAAAATCATCCAAAATCCCTTCTTAATTCCTGTTTATAACAAAGGTAGTTT
1 TTTAAATTTATGAGTAAAATCATCCAAAATCCCTTCTTAATTCCTGTTTATAAAAAAGGTAGTTT
*
5672734 GTAATTGTATGTTTCTAATCTGTGTATTTAGGTCTGACACAATTTCTAGACGATTTGGTGCTAAT
66 GTAATTGTATGTTTCTAATCTGTGTATTTAGGTCTGACACAATTTCTAGACGATTTGGTGCCAAT
* * *
5672799 GAATCAGAATGGAGCAGGTAAATCTCTCATCTTTTTCTATAGATTAGGTAAAAAAAAT
131 GAATCAGAATAGAGCAGGTAAACCTCTCATCTTTTTCTATAGATTAGATAAAAAAAAT
* *
5672857 TTTAAATTTATTAGTAAAATCATCCAAAATTCCTTCTTAATTCCTGTTTATAAAAAAAGGTAGTT
1 TTTAAATTTATGAGTAAAATCATCCAAAATCCCTTCTTAATTCCTGTTTAT-AAAAAAGGTAGTT
* * *
5672922 TGTAATTGTATGTTTCTAATCTGTGTGTTTAGGTTTGACACAATTTCTAGATGATTTGGTGCCAA
65 TGTAATTGTATGTTTCTAATCTGTGTATTTAGGTCTGACACAATTTCTAGACGATTTGGTGCCAA
* *
5672987 TGAATCAGAATAGAGCAGGTAAACCTCTCATCTTTTTCTGTAGATTTGATAAAAAAAAT
130 TGAATCAGAATAGAGCAGGTAAACCTCTCATCTTTTTCTATAGATTAGATAAAAAAAAT
5673046 T
1 T
5673047 GGATTTACAT
Statistics
Matches: 177, Mismatches: 12, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
188 49 0.28
189 128 0.72
ACGTcount: A:0.33, C:0.13, G:0.15, T:0.39
Consensus pattern (188 bp):
TTTAAATTTATGAGTAAAATCATCCAAAATCCCTTCTTAATTCCTGTTTATAAAAAAGGTAGTTT
GTAATTGTATGTTTCTAATCTGTGTATTTAGGTCTGACACAATTTCTAGACGATTTGGTGCCAAT
GAATCAGAATAGAGCAGGTAAACCTCTCATCTTTTTCTATAGATTAGATAAAAAAAAT
Found at i:5675358 original size:14 final size:15
Alignment explanation
Indices: 5675339--5675372 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
5675329 TCAACATGTC
5675339 TAAAAAAT-TATAAA
1 TAAAAAATATATAAA
*
5675353 TAAAAAATATTTAAA
1 TAAAAAATATATAAA
5675368 TAAAA
1 TAAAA
5675373 GTACGAGAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 8 0.44
15 10 0.56
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (15 bp):
TAAAAAATATATAAA
Found at i:5687051 original size:27 final size:27
Alignment explanation
Indices: 5686961--5687423 Score: 362
Period size: 27 Copynumber: 17.1 Consensus size: 27
5686951 GGTATAACAA
* * *
5686961 TCATTTTACCCTATGGGGGTATTTCGA
1 TCATTTTACCTTATAGGGGTATTTCGG
* * * *
5686988 CCAGTCTACCTTAT-GGCGGTATTTCAG
1 TCATTTTACCTTATAGG-GGTATTTCGG
*
5687015 TCATTCTACCTTATAGGGGTATTTCGG
1 TCATTTTACCTTATAGGGGTATTTCGG
* * ** *
5687042 TTATTTTACCCTAT-GAGATTAATTCGG
1 TCATTTTACCTTATAG-GGGTATTTCGG
** * * *
5687069 TCAACTTACCCTATGGGGGTATTTCAG
1 TCATTTTACCTTATAGGGGTATTTCGG
* * *
5687096 TTATTTTACCTTATGGGGGTATTTTGG
1 TCATTTTACCTTATAGGGGTATTTCGG
* * * *
5687123 TCATTATACCCTATAGGTGTACTTCGG
1 TCATTTTACCTTATAGGGGTATTTCGG
* *
5687150 TCATTCTACCTTATAGGGGTATTTTGG
1 TCATTTTACCTTATAGGGGTATTTCGG
* * * **
5687177 TCATTTTACCCTAGAGGGGGTAATTCTA
1 TCATTTTACCTTATA-GGGGTATTTCGG
* * *
5687205 ACATTTTACGTTAT-GGGGATATTTCGA
1 TCATTTTACCTTATAGGGG-TATTTCGG
* * * *
5687232 TCATTCTACCCTATGGGGGTATTTCGA
1 TCATTTTACCTTATAGGGGTATTTCGG
*
5687259 TCA-TTTACCTTATAGGGGTATTTCAG
1 TCATTTTACCTTATAGGGGTATTTCGG
* *
5687285 TCATTTTACCCTAT-GTGGGTATTTTGG
1 TCATTTTACCTTATAG-GGGTATTTCGG
* * * *
5687312 TTATTTTAGCTTATGGGGGTATTTTGG
1 TCATTTTACCTTATAGGGGTATTTCGG
*
5687339 TCATTTTACCTTAT-GAGGGTATTTCAG
1 TCATTTTACCTTATAG-GGGTATTTCGG
*
5687366 TCATTTTACCTTATAGGGGTATTTCGA
1 TCATTTTACCTTATAGGGGTATTTCGG
* * * *
5687393 TCAATCTACCCTATAGGGGTATTTTGG
1 TCATTTTACCTTATAGGGGTATTTCGG
5687420 TCAT
1 TCAT
5687424 AACAGTGTAG
Statistics
Matches: 344, Mismatches: 80, Indels: 24
0.77 0.18 0.05
Matches are distributed among these distances:
26 30 0.09
27 287 0.83
28 27 0.08
ACGTcount: A:0.21, C:0.16, G:0.21, T:0.42
Consensus pattern (27 bp):
TCATTTTACCTTATAGGGGTATTTCGG
Found at i:5687417 original size:81 final size:81
Alignment explanation
Indices: 5686961--5687423 Score: 420
Period size: 81 Copynumber: 5.7 Consensus size: 81
5686951 GGTATAACAA
* * * * * *
5686961 TCATTTTACCCTATGGGGGTATTTCGACCAGTCTACCTTATGGCGGTATTTCAGTCATTCTACCT
1 TCATTTTACCCTAT-GGGGTATTTCGATCATTCTACCCTATGGGGGTATTTCGGTCATTTTACCT
*
5687026 TAT-AGGGGTATTTCGG
65 TATGAGGGGTATTTCAG
* ** * * * * *
5687042 TTATTTTACCCTATGAGATTAATTCGGTCA-ACTTACCCTATGGGGGTATTTCAGTTATTTTACC
1 TCATTTTACCCTATG-GGGTATTTCGATCATTC-TACCCTATGGGGGTATTTCGGTCATTTTACC
**
5687106 TTATG-GGGGTATTTTGG
64 TTATGAGGGGTATTTCAG
* * * * * * * *
5687123 TCATTATACCCTATAGGTGTACTTCGGTCATTCTACCTTATAGGGGTATTTTGGTCATTTTACCC
1 TCATTTTACCCTAT-GGGGTATTTCGATCATTCTACCCTATGGGGGTATTTCGGTCATTTTACCT
*
5687188 TA-GAGGGGGTAATTCTA-
65 TATGA-GGGGTATTTC-AG
* ** *
5687205 ACATTTTACGTTATGGGGATATTTCGATCATTCTACCCTATGGGGGTATTTCGATCA-TTTACCT
1 TCATTTTACCCTATGGGG-TATTTCGATCATTCTACCCTATGGGGGTATTTCGGTCATTTTACCT
5687269 TAT-AGGGGTATTTCAG
65 TATGAGGGGTATTTCAG
* * * * * * *
5687285 TCATTTTACCCTATGTGGGTATTTTGGTTATTTTAGCTTATGGGGGTATTTTGGTCATTTTACCT
1 TCATTTTACCCTATG-GGGTATTTCGATCATTCTACCCTATGGGGGTATTTCGGTCATTTTACCT
5687350 TATGA-GGGTATTTCAG
65 TATGAGGGGTATTTCAG
* * * *
5687366 TCATTTTACCTTATAGGGGTATTTCGATCAATCTACCCTATAGGGGTATTTTGGTCAT
1 TCATTTTACCCTAT-GGGGTATTTCGATCATTCTACCCTATGGGGGTATTTCGGTCAT
5687424 AACAGTGTAG
Statistics
Matches: 307, Mismatches: 60, Indels: 30
0.77 0.15 0.08
Matches are distributed among these distances:
79 1 0.00
80 54 0.18
81 198 0.64
82 54 0.18
ACGTcount: A:0.21, C:0.16, G:0.21, T:0.42
Consensus pattern (81 bp):
TCATTTTACCCTATGGGGTATTTCGATCATTCTACCCTATGGGGGTATTTCGGTCATTTTACCTT
ATGAGGGGTATTTCAG
Found at i:5700591 original size:2 final size:2
Alignment explanation
Indices: 5700586--5700611 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
5700576 TTTTAGAGGG
5700586 GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA
5700612 TTTTTTTCAC
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:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:5707900 original size:27 final size:27
Alignment explanation
Indices: 5707872--5708362 Score: 572
Period size: 27 Copynumber: 18.2 Consensus size: 27
5707862 GGATATAACA
*
5707872 GTCATTTTACCCTATGGGGGTATTTCA
1 GTCATTTTACCCTATGGGGGTATTTCG
5707899 GTCATTTTACCCTAT-GGGGTATTTCG
1 GTCATTTTACCCTATGGGGGTATTTCG
* * *
5707925 ATCATTCTACCCTATGGGGGTATTTTG
1 GTCATTTTACCCTATGGGGGTATTTCG
*
5707952 GTCATTCTACCCTATGGGGGTATTTCG
1 GTCATTTTACCCTATGGGGGTATTTCG
*
5707979 ATCATTTTACCCTATGGGGGTATTTCG
1 GTCATTTTACCCTATGGGGGTATTTCG
* * * *
5708006 ATCAATTTACCCTATAGGGGTATTTTG
1 GTCATTTTACCCTATGGGGGTATTTCG
* * * *
5708033 ATCAATTTACCCTATAGGGGTATTTCA
1 GTCATTTTACCCTATGGGGGTATTTCG
* *
5708060 GTCATTTTACCTTATGGGGGTATTTCA
1 GTCATTTTACCCTATGGGGGTATTTCG
*
5708087 GTCATTATACCCTATGGGGGTACTTT-G
1 GTCATTTTACCCTATGGGGGTA-TTTCG
* * *
5708114 GTCATTCTACCCTATAGGGGTATTTTG
1 GTCATTTTACCCTATGGGGGTATTTCG
*
5708141 GTCATTTTACCCTATGGAGGCTATTTCG
1 GTCATTTTACCCTATGG-GGGTATTTCG
* * *
5708169 ATCATTTTACCCTATAGGGATATTTCG
1 GTCATTTTACCCTATGGGGGTATTTCG
* * * **
5708196 GTCATTCTATCTTATAAGGGTATTTCG
1 GTCATTTTACCCTATGGGGGTATTTCG
* *
5708223 GTCATTTTACCCTATGAGGGTATTTTG
1 GTCATTTTACCCTATGGGGGTATTTCG
* * *
5708250 GTTATTTTACCTTATGGGGATATTTCG
1 GTCATTTTACCCTATGGGGGTATTTCG
*
5708277 GTCATTTTACCCTATAGGGGTATTTCG
1 GTCATTTTACCCTATGGGGGTATTTCG
* ** *
5708304 GTTATTTTACCCTATAAGGGTATTTCT
1 GTCATTTTACCCTATGGGGGTATTTCG
* * *
5708331 ATCATTCTACCCTATAGGGGTATTTCG
1 GTCATTTTACCCTATGGGGGTATTTCG
5708358 GTCAT
1 GTCAT
5708363 AACAATATAA
Statistics
Matches: 402, Mismatches: 58, Indels: 8
0.86 0.12 0.02
Matches are distributed among these distances:
26 26 0.06
27 350 0.87
28 26 0.06
ACGTcount: A:0.20, C:0.18, G:0.21, T:0.41
Consensus pattern (27 bp):
GTCATTTTACCCTATGGGGGTATTTCG
Found at i:5725787 original size:41 final size:41
Alignment explanation
Indices: 5725640--5725863 Score: 357
Period size: 41 Copynumber: 5.5 Consensus size: 41
5725630 AACTTTATGT
5725640 CTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGTTATAAAC
1 CTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGTTATAAAC
5725681 CTAGCA-GCT-AGTGCCGGTGATCTGAATCAGGTTATAAAC
1 CTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGTTATAAAC
**
5725720 CTAGCAAACT-AGTGCCGGTGATCTGAATCAGGTTATAAAC
1 CTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGTTATAAAC
5725760 CTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGTTATAAAC
1 CTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGTTATAAAC
* * *
5725801 CTAGTAGGCTAAGTGCCGGTGATCTGAATTA-GTCTATAAGC
1 CTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGT-TATAAAC
*
5725842 CTAGCAAGCTAAGTGCCGGTGA
1 CTAGCAGGCTAAGTGCCGGTGA
5725864 ATATGTTAAA
Statistics
Matches: 172, Mismatches: 8, Indels: 6
0.92 0.04 0.03
Matches are distributed among these distances:
39 36 0.21
40 45 0.26
41 91 0.53
ACGTcount: A:0.29, C:0.20, G:0.26, T:0.25
Consensus pattern (41 bp):
CTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGTTATAAAC
Found at i:5727149 original size:196 final size:196
Alignment explanation
Indices: 5726813--5727211 Score: 746
Period size: 196 Copynumber: 2.0 Consensus size: 196
5726803 ATTATGATCT
*
5726813 TTTATTTGATTTGTTGAATTAGTTATTATTGTAAAAAAATAAAAAGAAAAAAGAAAACCGAAAGA
1 TTTATTTGATTTGTTGAATTAGTTATTATTGTAAAAAAATAAAAAGAAAAAAGAAAACCAAAAGA
5726878 AAAAAAGATATATATTGATTATTTAGTTCTATGATTGAGCTTGAACAGTTAAATTAATATTATGA
66 AAAAAAGATATATATTGATTATTTAGTTCTATGATTGAGCTTGAACAGTTAAATTAATATTATGA
5726943 GATGAAGCTCGTTTTTATTCTTGATTAGTTTTAGATCGATGTAATTTTTTTAAAATTCAGCATTA
131 GATGAAGCTCGTTTTTATTCTTGATTAGTTTTAGATCGATGTAATTTTTTTAAAATTCAGCATTA
5727008 G
196 G
5727009 TTTATTTGATTTGTTGAATTAGTTATTATTGT-AAAAAATAAAAAGAAAAAAGAAAACCAAAAGA
1 TTTATTTGATTTGTTGAATTAGTTATTATTGTAAAAAAATAAAAAGAAAAAAGAAAACCAAAAG-
*
5727073 AAAAAAAGATATATATTGATTATTTAGTTCTATGATTGAGCTTGAATAGTTAAATTAATATTATG
65 AAAAAAAGATATATATTGATTATTTAGTTCTATGATTGAGCTTGAACAGTTAAATTAATATTATG
* *
5727138 AGATTAAGCTCGTTTTTATTCTTGATTAGTTTTAGATTGATGTAATTTTTTTAAAATTCAGCATT
130 AGATGAAGCTCGTTTTTATTCTTGATTAGTTTTAGATCGATGTAATTTTTTTAAAATTCAGCATT
5727203 AG
195 AG
5727205 TTTATTT
1 TTTATTT
5727212 TTCTAGTTTG
Statistics
Matches: 198, Mismatches: 4, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
195 30 0.15
196 168 0.85
ACGTcount: A:0.40, C:0.05, G:0.14, T:0.41
Consensus pattern (196 bp):
TTTATTTGATTTGTTGAATTAGTTATTATTGTAAAAAAATAAAAAGAAAAAAGAAAACCAAAAGA
AAAAAAGATATATATTGATTATTTAGTTCTATGATTGAGCTTGAACAGTTAAATTAATATTATGA
GATGAAGCTCGTTTTTATTCTTGATTAGTTTTAGATCGATGTAATTTTTTTAAAATTCAGCATTA
G
Found at i:5730800 original size:13 final size:13
Alignment explanation
Indices: 5730782--5730807 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
5730772 AATGAAATTA
5730782 AAAAAGAATTTTC
1 AAAAAGAATTTTC
5730795 AAAAAGAATTTTC
1 AAAAAGAATTTTC
5730808 TTGAAATAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.08, G:0.08, T:0.31
Consensus pattern (13 bp):
AAAAAGAATTTTC
Found at i:5732502 original size:2 final size:2
Alignment explanation
Indices: 5732495--5732519 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
5732485 TTTTTCAGAT
5732495 AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG A
5732520 ACAATAAAAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:5733027 original size:16 final size:17
Alignment explanation
Indices: 5733006--5733038 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
5732996 GATGTAGTTG
5733006 CCTTTATAT-TGTTTTT
1 CCTTTATATGTGTTTTT
*
5733022 CCTTTATGTGTGTTTTT
1 CCTTTATATGTGTTTTT
5733039 TAGTCAGGGT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.09, C:0.12, G:0.12, T:0.67
Consensus pattern (17 bp):
CCTTTATATGTGTTTTT
Found at i:5734122 original size:16 final size:16
Alignment explanation
Indices: 5734098--5734132 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
5734088 ATACATAGGT
*
5734098 ATATAAAAATTATGAA
1 ATATAAAAATAATGAA
*
5734114 ATATGAAAATAATGAA
1 ATATAAAAATAATGAA
5734130 ATA
1 ATA
5734133 CATGTAAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.63, C:0.00, G:0.09, T:0.29
Consensus pattern (16 bp):
ATATAAAAATAATGAA
Found at i:5736144 original size:50 final size:50
Alignment explanation
Indices: 5736090--5736625 Score: 382
Period size: 50 Copynumber: 10.8 Consensus size: 50
5736080 CTAAGAAGTA
* *
5736090 AGATTCGCCGTTGTGGCTTCAATCTTTTTAATTGCATTGTC-GGAGAAGCG
1 AGATTCGCCGTTGTGGCTTCAATCTTTTTAATTGCAATGCCAGG-GAAGCG
* * * * ** * ** * **
5736140 AGATTTGCCATTGTAGCTTCAATCTGTTCCACTGCACCGCCTGGGAAGTA
1 AGATTCGCCGTTGTGGCTTCAATCTTTTTAATTGCAATGCCAGGGAAGCG
* * *
5736190 AGATTCGTCGTTTTGGCTTCAATC-TTTTAATTGCAATGTCAGGGAAGCG
1 AGATTCGCCGTTGTGGCTTCAATCTTTTTAATTGCAATGCCAGGGAAGCG
* * * ** * ** **
5736239 AGATTCACCGTTGTAGCTTCAATCTGTTCCACTGC-ATCGCCAGATAAGTA
1 AGATTCGCCGTTGTGGCTTCAATCTTTTTAATTGCAAT-GCCAGGGAAGCG
* * * *
5736289 AGATTCTCTGTTGTGGCTTCAATCTTTTAAATTGCAATGTCAGGGAAGCG
1 AGATTCGCCGTTGTGGCTTCAATCTTTTTAATTGCAATGCCAGGGAAGCG
* * * ** * ** *
5736339 AGATTCTCCGTTGTAGCTTCAATCTGTTCCACTGCACCGCCAGGGAAG-T
1 AGATTCGCCGTTGTGGCTTCAATCTTTTTAATTGCAATGCCAGGGAAGCG
* * *
5736388 ACGATTCGCCGTTGTGGCTTCAATCTTTTTAATTGTAATGTCGGGGAAGCG
1 A-GATTCGCCGTTGTGGCTTCAATCTTTTTAATTGCAATGCCAGGGAAGCG
* * ** * * ** * **
5736439 AGATTCGCCGTTGTAGCTTCAATCTGTTCCACTACACCGCCTGGGAAGTA
1 AGATTCGCCGTTGTGGCTTCAATCTTTTTAATTGCAATGCCAGGGAAGCG
* * * *
5736489 AGATTCGCCGTTATGGCTTTAATC-TTTTAATTGTAATGCCGGGGAAGCG
1 AGATTCGCCGTTGTGGCTTCAATCTTTTTAATTGCAATGCCAGGGAAGCG
* * * * * * * * * *
5736538 AGATTCACCGTCGTAGCTTTAATC-TTCTCACTGTACTGCCAGGGAAGTG
1 AGATTCGCCGTTGTGGCTTCAATCTTTTTAATTGCAATGCCAGGGAAGCG
*
5736587 AGATTCGCCGTTGTGGCTTCAATCTTTTTAATTACAATG
1 AGATTCGCCGTTGTGGCTTCAATCTTTTTAATTGCAATG
5736626 TCGGGGAACA
Statistics
Matches: 358, Mismatches: 121, Indels: 14
0.73 0.25 0.03
Matches are distributed among these distances:
49 111 0.31
50 242 0.68
51 5 0.01
ACGTcount: A:0.22, C:0.21, G:0.23, T:0.33
Consensus pattern (50 bp):
AGATTCGCCGTTGTGGCTTCAATCTTTTTAATTGCAATGCCAGGGAAGCG
Found at i:5736157 original size:100 final size:100
Alignment explanation
Indices: 5735977--5736683 Score: 904
Period size: 100 Copynumber: 7.1 Consensus size: 100
5735967 TCAATCTGTT
* * ** *
5735977 CGCCAGGGAAGTAAGATTTGCCGTTGCGGCTTTGATCTTTTTAATTGCAATGTCGGGGAAACGAG
1 CGCCAGGGAAGTAAGATTCGCCGTTGTGGCTTCAATCTTTTTAATTGCAATGTCGGGGAAGCGAG
* * * *
5736042 ATTCACCATCGTAGCTTTAATTTGTTCCACTGCAC
66 ATTCACCGTTGTAGCTTCAATCTGTTCCACTGCAC
* * *
5736077 CGCCTA-AGAAGTAAGATTCGCCGTTGTGGCTTCAATCTTTTTAATTGCATTGTCGGAGAAGCGA
1 CGCC-AGGGAAGTAAGATTCGCCGTTGTGGCTTCAATCTTTTTAATTGCAATGTCGGGGAAGCGA
** *
5736141 GATTTGCCATTGTAGCTTCAATCTGTTCCACTGCAC
65 GATTCACCGTTGTAGCTTCAATCTGTTCCACTGCAC
* * * *
5736177 CGCCTGGGAAGTAAGATTCGTCGTTTTGGCTTCAATC-TTTTAATTGCAATGTCAGGGAAGCGAG
1 CGCCAGGGAAGTAAGATTCGCCGTTGTGGCTTCAATCTTTTTAATTGCAATGTCGGGGAAGCGAG
*
5736241 ATTCACCGTTGTAGCTTCAATCTGTTCCACTGCAT
66 ATTCACCGTTGTAGCTTCAATCTGTTCCACTGCAC
** * * * *
5736276 CGCCAGATAAGTAAGATTCTCTGTTGTGGCTTCAATCTTTTAAATTGCAATGTCAGGGAAGCGAG
1 CGCCAGGGAAGTAAGATTCGCCGTTGTGGCTTCAATCTTTTTAATTGCAATGTCGGGGAAGCGAG
*
5736341 ATTCTCCGTTGTAGCTTCAATCTGTTCCACTGCAC
66 ATTCACCGTTGTAGCTTCAATCTGTTCCACTGCAC
* *
5736376 CGCCAGGGAAGTACGATTCGCCGTTGTGGCTTCAATCTTTTTAATTGTAATGTCGGGGAAGCGAG
1 CGCCAGGGAAGTAAGATTCGCCGTTGTGGCTTCAATCTTTTTAATTGCAATGTCGGGGAAGCGAG
* *
5736441 ATTCGCCGTTGTAGCTTCAATCTGTTCCACTACAC
66 ATTCACCGTTGTAGCTTCAATCTGTTCCACTGCAC
* * * * *
5736476 CGCCTGGGAAGTAAGATTCGCCGTTATGGCTTTAATC-TTTTAATTGTAATGCCGGGGAAGCGAG
1 CGCCAGGGAAGTAAGATTCGCCGTTGTGGCTTCAATCTTTTTAATTGCAATGTCGGGGAAGCGAG
* * *
5736540 ATTCACCGTCGTAGCTTTAATC--TTCTCACTGTAC
66 ATTCACCGTTGTAGCTTCAATCTGTTC-CACTGCAC
* * * *
5736574 TGCCAGGGAAGTGAGATTCGCCGTTGTGGCTTCAATCTTTTTAATTACAATGTCGGGGAA-CAAG
1 CGCCAGGGAAGTAAGATTCGCCGTTGTGGCTTCAATCTTTTTAATTGCAATGTCGGGGAAGCGAG
* * * ** *
5736638 ATTCACCATCGTAGCTTTAATCTACTCCATTGCAC
66 ATTCACCGTTGTAGCTTCAATCTGTTCCACTGCAC
*
5736673 TGCCAGGGAAG
1 CGCCAGGGAAG
5736684 GTAACTTCAT
Statistics
Matches: 533, Mismatches: 67, Indels: 15
0.87 0.11 0.02
Matches are distributed among these distances:
97 3 0.01
98 62 0.12
99 166 0.31
100 301 0.56
101 1 0.00
ACGTcount: A:0.23, C:0.22, G:0.23, T:0.32
Consensus pattern (100 bp):
CGCCAGGGAAGTAAGATTCGCCGTTGTGGCTTCAATCTTTTTAATTGCAATGTCGGGGAAGCGAG
ATTCACCGTTGTAGCTTCAATCTGTTCCACTGCAC
Found at i:5736515 original size:299 final size:297
Alignment explanation
Indices: 5735976--5736683 Score: 983
Period size: 299 Copynumber: 2.4 Consensus size: 297
5735966 TTCAATCTGT
* **
5735976 TCGCCAGGGAAGTAAGATT-TGCCGTTGCGGCTTTGATCTTTTTAATTGCAATGTCGGGGAAACG
1 TCGCCAGGGAAGTAAGATTCT-CCGTTGTGGCTTCAATCTTTTTAATTGCAATGTCGGGG-AACG
* *
5736040 AGATTCACCATCGTAGCTTTAATTTGTTCCACTGCACCGCCTA-AGAAGTAAGATTCGCCGTTGT
64 AGATTCACCATCGTAGCTTTAATCTGTTCCACTGCACCGCC-AGGGAAGTAAGATTCGCCGTTGT
* *
5736104 GGCTTCAATCTTTTTAATTGCATTGTCGGAGAAGCGAGATTTGCCATTGTAGCTTCAATCTGTTC
128 GGCTTCAATCTTTTTAATTGCAATGTCGGAGAAGCGAGATTCGCCATTGTAGCTTCAATCTGTTC
* * * *
5736169 CACTGCACCGCCTGGGAAGTAAGATTCGTCGTTTTGGCTTCAATCTTTTAATTGCAATGTCAGGG
193 CACTACACCGCCTGGGAAGTAAGATTCGCCGTTATGGCTTCAATCTTTTAATTGCAATGCCAGGG
*
5736234 AAGCGAGATTCACCGTTGTAGCTTCAATCTGT-TCCACTGCA
258 AAGCGAGATTCACCGTCGTAGCTTCAATCT-TCT-CACTGCA
** * * *
5736275 TCGCCAGATAAGTAAGATTCTCTGTTGTGGCTTCAATCTTTTAAATTGCAATGTCAGGGAAGCGA
1 TCGCCAGGGAAGTAAGATTCTCCGTTGTGGCTTCAATCTTTTTAATTGCAATGTCGGGGAA-CGA
* * * * *
5736340 GATTCTCCGTTGTAGCTTCAATCTGTTCCACTGCACCGCCAGGGAAGTACGATTCGCCGTTGTGG
65 GATTCACCATCGTAGCTTTAATCTGTTCCACTGCACCGCCAGGGAAGTAAGATTCGCCGTTGTGG
* * *
5736405 CTTCAATCTTTTTAATTGTAATGTCGGGGAAGCGAGATTCGCCGTTGTAGCTTCAATCTGTTCCA
130 CTTCAATCTTTTTAATTGCAATGTCGGAGAAGCGAGATTCGCCATTGTAGCTTCAATCTGTTCCA
* * *
5736470 CTACACCGCCTGGGAAGTAAGATTCGCCGTTATGGCTTTAATCTTTTAATTGTAATGCCGGGGAA
195 CTACACCGCCTGGGAAGTAAGATTCGCCGTTATGGCTTCAATCTTTTAATTGCAATGCCAGGGAA
* *
5736535 GCGAGATTCACCGTCGTAGCTTTAATCTTCTCACTGTA
260 GCGAGATTCACCGTCGTAGCTTCAATCTTCTCACTGCA
* * * *
5736573 -CTGCCAGGGAAGTGAGATTCGCCGTTGTGGCTTCAATCTTTTTAATTACAATGTCGGGGAACAA
1 TC-GCCAGGGAAGTAAGATTCTCCGTTGTGGCTTCAATCTTTTTAATTGCAATGTCGGGGAACGA
** * *
5736637 GATTCACCATCGTAGCTTTAATCTACTCCATTGCACTGCCAGGGAAG
65 GATTCACCATCGTAGCTTTAATCTGTTCCACTGCACCGCCAGGGAAG
5736684 GTAACTTCAT
Statistics
Matches: 357, Mismatches: 47, Indels: 12
0.86 0.11 0.03
Matches are distributed among these distances:
297 42 0.12
298 61 0.17
299 253 0.71
300 1 0.00
ACGTcount: A:0.23, C:0.22, G:0.23, T:0.32
Consensus pattern (297 bp):
TCGCCAGGGAAGTAAGATTCTCCGTTGTGGCTTCAATCTTTTTAATTGCAATGTCGGGGAACGAG
ATTCACCATCGTAGCTTTAATCTGTTCCACTGCACCGCCAGGGAAGTAAGATTCGCCGTTGTGGC
TTCAATCTTTTTAATTGCAATGTCGGAGAAGCGAGATTCGCCATTGTAGCTTCAATCTGTTCCAC
TACACCGCCTGGGAAGTAAGATTCGCCGTTATGGCTTCAATCTTTTAATTGCAATGCCAGGGAAG
CGAGATTCACCGTCGTAGCTTCAATCTTCTCACTGCA
Found at i:5737984 original size:6 final size:7
Alignment explanation
Indices: 5737933--5737976 Score: 54
Period size: 7 Copynumber: 6.0 Consensus size: 7
5737923 TTAGCCTCTC
5737933 CATTTTT
1 CATTTTT
5737940 -ACTTTTT
1 CA-TTTTT
5737947 CATTTTTT
1 CA-TTTTT
5737955 CATTTTTT
1 CA-TTTTT
5737963 CATTTTT
1 CATTTTT
5737970 CATTTTT
1 CATTTTT
5737977 TTCATTTTTT
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
6 1 0.03
7 17 0.50
8 16 0.47
ACGTcount: A:0.14, C:0.14, G:0.00, T:0.73
Consensus pattern (7 bp):
CATTTTT
Found at i:5737987 original size:9 final size:8
Alignment explanation
Indices: 5737942--5737986 Score: 74
Period size: 8 Copynumber: 5.6 Consensus size: 8
5737932 CCATTTTTAC
5737942 TTTTTCAT
1 TTTTTCAT
5737950 TTTTTCAT
1 TTTTTCAT
5737958 TTTTTCA-
1 TTTTTCAT
5737965 TTTTTCATT
1 TTTTTCA-T
5737974 TTTTTCAT
1 TTTTTCAT
5737982 TTTTT
1 TTTTT
5737987 TGTTTCACTC
Statistics
Matches: 35, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
7 7 0.20
8 21 0.60
9 7 0.20
ACGTcount: A:0.11, C:0.11, G:0.00, T:0.78
Consensus pattern (8 bp):
TTTTTCAT
Found at i:5738797 original size:6 final size:6
Alignment explanation
Indices: 5738786--5738825 Score: 62
Period size: 6 Copynumber: 6.3 Consensus size: 6
5738776 TTGACCTCTC
5738786 CTTTTT CTTTTT CTTTTT CTTTTTT CTTCTTT CTTTTT CT
1 CTTTTT CTTTTT CTTTTT C-TTTTT CTT-TTT CTTTTT CT
5738826 CCTATTTTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
6 20 0.62
7 12 0.38
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (6 bp):
CTTTTT
Found at i:5738803 original size:7 final size:7
Alignment explanation
Indices: 5738787--5738823 Score: 51
Period size: 7 Copynumber: 5.6 Consensus size: 7
5738777 TGACCTCTCC
5738787 TTTTTC-
1 TTTTTCT
5738793 TTTTTC-
1 TTTTTCT
5738799 TTTTTCT
1 TTTTTCT
5738806 TTTTTCT
1 TTTTTCT
*
5738813 TCTTTCT
1 TTTTTCT
5738820 TTTT
1 TTTT
5738824 CTCCTATTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
6 12 0.43
7 16 0.57
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (7 bp):
TTTTTCT
Found at i:5738809 original size:13 final size:13
Alignment explanation
Indices: 5738786--5738823 Score: 60
Period size: 14 Copynumber: 2.9 Consensus size: 13
5738776 TTGACCTCTC
5738786 CTTTTTC-TTTTT
1 CTTTTTCTTTTTT
5738798 CTTTTTCTTTTTT
1 CTTTTTCTTTTTT
5738811 CTTCTTTCTTTTT
1 CTT-TTTCTTTTT
5738824 CTCCTATTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
12 7 0.29
13 8 0.33
14 9 0.38
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (13 bp):
CTTTTTCTTTTTT
Found at i:5738824 original size:13 final size:12
Alignment explanation
Indices: 5738786--5738825 Score: 62
Period size: 13 Copynumber: 3.2 Consensus size: 12
5738776 TTGACCTCTC
5738786 CTTTTTCTTTTT
1 CTTTTTCTTTTT
5738798 CTTTTTCTTTTTT
1 CTTTTTC-TTTTT
5738811 CTTCTTTCTTTTT
1 CTT-TTTCTTTTT
5738824 CT
1 CT
5738826 CCTATTTTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
12 7 0.27
13 15 0.58
14 4 0.15
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (12 bp):
CTTTTTCTTTTT
Found at i:5742677 original size:9 final size:9
Alignment explanation
Indices: 5742660--5742721 Score: 54
Period size: 9 Copynumber: 6.7 Consensus size: 9
5742650 ATACGTGAAT
*
5742660 TATAAAATA
1 TATATAATA
5742669 TATATAATA
1 TATATAATA
5742678 TATATAATA
1 TATATAATA
* *
5742687 TATTTTAAAA
1 TA-TATAATA
*
5742697 TATA-AAGAA
1 TATATAA-TA
5742706 TATATAAATA
1 TATAT-AATA
5742716 TATATA
1 TATATA
5742722 TCTATAAAAA
Statistics
Matches: 44, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
8 2 0.05
9 27 0.61
10 13 0.30
11 2 0.05
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (9 bp):
TATATAATA
Found at i:5742696 original size:30 final size:29
Alignment explanation
Indices: 5742662--5742718 Score: 87
Period size: 30 Copynumber: 1.9 Consensus size: 29
5742652 ACGTGAATTA
* *
5742662 TAAAATATATATAATATATATAATATATTT
1 TAAAATATAAAGAATATATA-AATATATTT
5742692 TAAAATATAAAGAATATATAAATATAT
1 TAAAATATAAAGAATATATAAATATAT
5742719 ATATCTATAA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
29 7 0.28
30 18 0.72
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (29 bp):
TAAAATATAAAGAATATATAAATATATTT
Found at i:5742754 original size:27 final size:27
Alignment explanation
Indices: 5742697--5742771 Score: 71
Period size: 27 Copynumber: 2.7 Consensus size: 27
5742687 TATTTTAAAA
* * *
5742697 TATAAAGAATATATAAATATATATATC
1 TATAAAAAATATATAAATATACATAGC
* * *
5742724 TATAAAAAATATGTACATATACATAGG
1 TATAAAAAATATATAAATATACATAGC
5742751 TATATAAAAAT-TATGAAATAT
1 TATA-AAAAATATAT-AAATAT
5742772 GAAAATAATG
Statistics
Matches: 38, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
27 27 0.71
28 11 0.29
ACGTcount: A:0.55, C:0.04, G:0.07, T:0.35
Consensus pattern (27 bp):
TATAAAAAATATATAAATATACATAGC
Found at i:5742776 original size:16 final size:16
Alignment explanation
Indices: 5742752--5742786 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
5742742 ATACATAGGT
*
5742752 ATATAAAAATTATGAA
1 ATATAAAAATAATGAA
*
5742768 ATATGAAAATAATGAA
1 ATATAAAAATAATGAA
5742784 ATA
1 ATA
5742787 CATGTAAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.63, C:0.00, G:0.09, T:0.29
Consensus pattern (16 bp):
ATATAAAAATAATGAA
Found at i:5754612 original size:18 final size:18
Alignment explanation
Indices: 5754573--5754606 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
5754563 AATGATGTTT
5754573 GCCCGTGTAGGCCCACAC
1 GCCCGTGTAGGCCCACAC
5754591 GCCCGTGT-GGCCCACA
1 GCCCGTGTAGGCCCACA
5754607 TGGCCCAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.15, C:0.44, G:0.29, T:0.12
Consensus pattern (18 bp):
GCCCGTGTAGGCCCACAC
Found at i:5757487 original size:27 final size:25
Alignment explanation
Indices: 5757432--5757495 Score: 65
Period size: 25 Copynumber: 2.5 Consensus size: 25
5757422 CAGCTCGTAC
* *
5757432 GAGCTTCCCATTATACACCTCAAAT
1 GAGCTTCCCGTTATACACCTCAAAA
* *
5757457 GAGCTTCCCGTTATATAGCTCAAGAGA
1 GAGCTTCCCGTTATACACCTCAA-A-A
*
5757484 GAGCTTCTCGTT
1 GAGCTTCCCGTT
5757496 TATGTGCTCC
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
25 20 0.62
26 1 0.03
27 11 0.34
ACGTcount: A:0.27, C:0.27, G:0.17, T:0.30
Consensus pattern (25 bp):
GAGCTTCCCGTTATACACCTCAAAA
Found at i:5769277 original size:18 final size:17
Alignment explanation
Indices: 5769247--5769280 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
5769237 ATTTTGATCT
*
5769247 AATTTTTACTTTTTTAG
1 AATTTTTAATTTTTTAG
5769264 AATTTTCTAATTTTTTA
1 AATTTT-TAATTTTTTA
5769281 AAAAGAATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.26, C:0.06, G:0.03, T:0.65
Consensus pattern (17 bp):
AATTTTTAATTTTTTAG
Found at i:5771234 original size:34 final size:35
Alignment explanation
Indices: 5771191--5771263 Score: 139
Period size: 34 Copynumber: 2.1 Consensus size: 35
5771181 ATTCTCTCCC
5771191 TCTTGCCATTGTAAGTTATGCTGCCTCTCTTTGTT
1 TCTTGCCATTGTAAGTTATGCTGCCTCTCTTTGTT
5771226 TCTT-CCATTGTAAGTTATGCTGCCTCTCTTTGTT
1 TCTTGCCATTGTAAGTTATGCTGCCTCTCTTTGTT
5771260 TCTT
1 TCTT
5771264 TCTCTCATTC
Statistics
Matches: 38, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
34 34 0.89
35 4 0.11
ACGTcount: A:0.11, C:0.23, G:0.15, T:0.51
Consensus pattern (35 bp):
TCTTGCCATTGTAAGTTATGCTGCCTCTCTTTGTT
Found at i:5775160 original size:23 final size:23
Alignment explanation
Indices: 5775127--5775170 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
5775117 TGGGTAGGAA
*
5775127 GTTTTCTAAAAATTCTGCATTAT
1 GTTTTCCAAAAATTCTGCATTAT
*
5775150 GTTTTCCAAAAATTTTGCATT
1 GTTTTCCAAAAATTCTGCATT
5775171 TACATAACCA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.30, C:0.14, G:0.09, T:0.48
Consensus pattern (23 bp):
GTTTTCCAAAAATTCTGCATTAT
Found at i:5778928 original size:16 final size:15
Alignment explanation
Indices: 5778903--5778933 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
5778893 TTGAGGAGAG
5778903 AAAAATAAAATAAAT
1 AAAAATAAAATAAAT
5778918 AAAAATAAAAATAAAT
1 AAAAAT-AAAATAAAT
5778934 TAAACTCAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.40
16 9 0.60
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (15 bp):
AAAAATAAAATAAAT
Found at i:5778929 original size:21 final size:22
Alignment explanation
Indices: 5778903--5778951 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 22
5778893 TTGAGGAGAG
5778903 AAAAATAAAATAAA-TAAAAAT
1 AAAAATAAAATAAACTAAAAAT
* * *
5778924 AAAAATAAATTAAACTCAAACT
1 AAAAATAAAATAAACTAAAAAT
5778946 AAAAAT
1 AAAAAT
5778952 CCCATTATAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
21 13 0.54
22 11 0.46
ACGTcount: A:0.73, C:0.06, G:0.00, T:0.20
Consensus pattern (22 bp):
AAAAATAAAATAAACTAAAAAT
Found at i:5793924 original size:89 final size:88
Alignment explanation
Indices: 5793779--5794200 Score: 389
Period size: 88 Copynumber: 4.8 Consensus size: 88
5793769 GTGGTGAATT
* * * * * * * * *
5793779 TTATCTCCATGAAAGTTGCAGTGGAGCAGATTAAAGCCAAAAATCTTGTCTTCCTAAAGTTGCAG
1 TTATCTCCCTG-AAGTTACAGTAGAGTAGATTGAAGCTACAAATCTTATCTCCCTAAAGTTGCAG
*
5793844 TGGAGCAGATTGAAGATAGCAAATC
65 TGGAGCAGATTAAAGATA-CAAATC
* * * * * * * *
5793869 TTATCTCTCTAAAGTTATAGTAGAGCAAATTAAAGCTACAAACCTTATCTCCCTAAAGTTGCAAT
1 TTATCTCCCTGAAGTTACAGTAGAGTAGATTGAAGCTACAAATCTTATCTCCCTAAAGTTGCAGT
* * *
5793934 AGAGCAGATTAAAAATAGTAAATC
66 GGAGCAGATTAAAGATA-CAAATC
* * * * *
5793958 TTATCTCCCTGAAGCT-CTAGTGGAGTAGATTGAAGTTACAAAACTTATCTCCCTGAAGTTGCAG
1 TTATCTCCCTGAAGTTAC-AGTAGAGTAGATTGAAGCTACAAATCTTATCTCCCTAAAGTTGCAG
* * *
5794022 TGGAGCGGATTGAAGTTACAAATC
65 TGGAGCAGATTAAAGATACAAATC
* * * * * * * *
5794046 TCATCTCCCTGAAGTTGCAATAGAGTAGATTGAAGATACGAGTCTCATCTCCCTAAAGTTGTAGT
1 TTATCTCCCTGAAGTTACAGTAGAGTAGATTGAAGCTACAAATCTTATCTCCCTAAAGTTGCAGT
* *
5794111 GGAGCAGATTAAAGCTACAAGTC
66 GGAGCAGATTAAAGATACAAATC
* * * * *
5794134 TAATCTCCCTGAAGTTACAGTGGAGTAGATTGAAGCAACAAATCTTATAC-CTCTAAAGTTGTAG
1 TTATCTCCCTGAAGTTACAGTAGAGTAGATTGAAGCTACAAATCTTAT-CTCCCTAAAGTTGCAG
5794198 TGG
65 TGG
5794201 GTTAGAATGA
Statistics
Matches: 269, Mismatches: 60, Indels: 8
0.80 0.18 0.02
Matches are distributed among these distances:
88 131 0.49
89 130 0.48
90 8 0.03
ACGTcount: A:0.34, C:0.18, G:0.20, T:0.28
Consensus pattern (88 bp):
TTATCTCCCTGAAGTTACAGTAGAGTAGATTGAAGCTACAAATCTTATCTCCCTAAAGTTGCAGT
GGAGCAGATTAAAGATACAAATC
Found at i:5794200 original size:44 final size:44
Alignment explanation
Indices: 5793779--5794200 Score: 316
Period size: 44 Copynumber: 9.5 Consensus size: 44
5793769 GTGGTGAATT
* *
5793779 TTATCTCCATGAAAGTTGCAGTGGAGCAGATTAAAGCCAA-AAATC
1 TTATCTCCCT-AAAGTTGCAGTGGAGCAGATTGAAG-CAACAAATC
* *
5793824 TTGTCTTCCTAAAGTTGCAGTGGAGCAGATTGAAG-ATAGCAAATC
1 TTATCTCCCTAAAGTTGCAGTGGAGCAGATTGAAGCA-A-CAAATC
* ** * * * * *
5793869 TTATCTCTCTAAAGTTATAGTAGAGCAAATTAAAGCTACAAACC
1 TTATCTCCCTAAAGTTGCAGTGGAGCAGATTGAAGCAACAAATC
* * ** *
5793913 TTATCTCCCTAAAGTTGCAATAGAGCAGATT-AAAAATAGTAAATC
1 TTATCTCCCTAAAGTTGCAGTGGAGCAGATTGAAGCA-A-CAAATC
* * * ** *
5793958 TTATCTCCCTGAAGCT-CTAGTGGAGTAGATTGAAGTTACAAAAC
1 TTATCTCCCTAAAGTTGC-AGTGGAGCAGATTGAAGCAACAAATC
* * **
5794002 TTATCTCCCTGAAGTTGCAGTGGAGCGGATTGAAGTTACAAATC
1 TTATCTCCCTAAAGTTGCAGTGGAGCAGATTGAAGCAACAAATC
* * * * * * *
5794046 TCATCTCCCTGAAGTTGCAATAGAGTAGATTGAAG-ATACGAGTC
1 TTATCTCCCTAAAGTTGCAGTGGAGCAGATTGAAGCA-ACAAATC
* * * * *
5794090 TCATCTCCCTAAAGTTGTAGTGGAGCAGATTAAAGCTACAAGTC
1 TTATCTCCCTAAAGTTGCAGTGGAGCAGATTGAAGCAACAAATC
* * * *
5794134 TAATCTCCCTGAAGTTACAGTGGAGTAGATTGAAGCAACAAATC
1 TTATCTCCCTAAAGTTGCAGTGGAGCAGATTGAAGCAACAAATC
* *
5794178 TTATAC-CTCTAAAGTTGTAGTGG
1 TTAT-CTCCCTAAAGTTGCAGTGG
5794201 GTTAGAATGA
Statistics
Matches: 298, Mismatches: 67, Indels: 25
0.76 0.17 0.06
Matches are distributed among these distances:
42 1 0.00
43 3 0.01
44 221 0.74
45 71 0.24
46 2 0.01
ACGTcount: A:0.34, C:0.18, G:0.20, T:0.28
Consensus pattern (44 bp):
TTATCTCCCTAAAGTTGCAGTGGAGCAGATTGAAGCAACAAATC
Found at i:5795766 original size:12 final size:12
Alignment explanation
Indices: 5795749--5795773 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
5795739 GTTCCTTTAT
5795749 TTTATTTTATTA
1 TTTATTTTATTA
5795761 TTTATTTTATTA
1 TTTATTTTATTA
5795773 T
1 T
5795774 GATTTATACT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (12 bp):
TTTATTTTATTA
Found at i:5795992 original size:28 final size:28
Alignment explanation
Indices: 5795960--5796017 Score: 107
Period size: 28 Copynumber: 2.1 Consensus size: 28
5795950 ATTTATGTTG
5795960 TTCATATTTGTACATTTTTCGCTCATTA
1 TTCATATTTGTACATTTTTCGCTCATTA
*
5795988 TTCATATTTGTACATTTTTTGCTCATTA
1 TTCATATTTGTACATTTTTCGCTCATTA
5796016 TT
1 TT
5796018 TATTTATATT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.21, C:0.16, G:0.07, T:0.57
Consensus pattern (28 bp):
TTCATATTTGTACATTTTTCGCTCATTA
Found at i:5798380 original size:17 final size:17
Alignment explanation
Indices: 5798357--5798390 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
5798347 AGTTCAATTG
*
5798357 ATTTTTAAT-ATTTTTT
1 ATTTTTTATAATTTTTT
5798373 ATTTTTTATAATTTTTT
1 ATTTTTTATAATTTTTT
5798390 A
1 A
5798391 ATAATTTATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (17 bp):
ATTTTTTATAATTTTTT
Found at i:5801440 original size:46 final size:47
Alignment explanation
Indices: 5801328--5801442 Score: 114
Period size: 46 Copynumber: 2.5 Consensus size: 47
5801318 CTGCACTATC
* * * *
5801328 TAGTGGTTTAACCACAT-T-TCTGTTCTGGCAGCTTGACTACATTTA
1 TAGTGGCTTCACCACATATATCTGTTATGGCAGCTTGACTACATATA
* * *
5801373 TGGTGGC-TCGACCACAGATATCTGTTATGGCAGCTT-AGCTGCA-ATA
1 TAGTGGCTTC-ACCACATATATCTGTTATGGCAGCTTGA-CTACATATA
5801419 TAGTGGCTTCACCACATATATCTG
1 TAGTGGCTTCACCACATATATCTG
5801443 ATCTAGCAAT
Statistics
Matches: 56, Mismatches: 9, Indels: 9
0.76 0.12 0.12
Matches are distributed among these distances:
44 1 0.02
45 11 0.20
46 23 0.41
47 21 0.38
ACGTcount: A:0.23, C:0.22, G:0.21, T:0.34
Consensus pattern (47 bp):
TAGTGGCTTCACCACATATATCTGTTATGGCAGCTTGACTACATATA
Found at i:5801586 original size:23 final size:23
Alignment explanation
Indices: 5801556--5801599 Score: 72
Period size: 23 Copynumber: 1.9 Consensus size: 23
5801546 TGGGTAGGAA
5801556 GTTTTCTGAAAA-ATCTGCATTTT
1 GTTTTCTGAAAATAT-TGCATTTT
5801579 GTTTTCTGAAAATATTGCATT
1 GTTTTCTGAAAATATTGCATT
5801600 CACGTAATCA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
23 18 0.90
24 2 0.10
ACGTcount: A:0.27, C:0.11, G:0.14, T:0.48
Consensus pattern (23 bp):
GTTTTCTGAAAATATTGCATTTT
Found at i:5805750 original size:34 final size:34
Alignment explanation
Indices: 5805682--5805748 Score: 100
Period size: 34 Copynumber: 1.9 Consensus size: 34
5805672 CAGTAAAATA
5805682 TTTTCCGTAAAATGATTTTAGGAAAATATTTTTC
1 TTTTCCGTAAAATGATTTTAGGAAAATATTTTTC
*
5805716 TTTTCTGTAAAATGA-TTTACTGGAAAATATTTT
1 TTTTCCGTAAAATGATTTTA--GGAAAATATTTT
5805749 CTGGTGTTTG
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
33 4 0.13
34 14 0.47
35 12 0.40
ACGTcount: A:0.33, C:0.07, G:0.12, T:0.48
Consensus pattern (34 bp):
TTTTCCGTAAAATGATTTTAGGAAAATATTTTTC
Found at i:5810226 original size:60 final size:59
Alignment explanation
Indices: 5810152--5810283 Score: 183
Period size: 60 Copynumber: 2.2 Consensus size: 59
5810142 CAATCTCAAT
* * * * *
5810152 TAGTTGAGTGACCAAATTTAATAAATTGATAGTTAGGTGACCAAAAGAGAAAAGGGGCAA
1 TAGTTGGGTGACCAAATTAAAAAAATTGATAGTTAGGTGACCAAAAAAGAAAA-GGACAA
* *
5810212 TAGTTGGGTGACCAAATTAAAAAAATTGGTAGTTGGGTGACCAAAAAAGAAAAGGACAA
1 TAGTTGGGTGACCAAATTAAAAAAATTGATAGTTAGGTGACCAAAAAAGAAAAGGACAA
*
5810271 TAGTTGGCTGACC
1 TAGTTGGGTGACC
5810284 TATGTTGTAG
Statistics
Matches: 64, Mismatches: 8, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
59 17 0.27
60 47 0.73
ACGTcount: A:0.42, C:0.10, G:0.26, T:0.23
Consensus pattern (59 bp):
TAGTTGGGTGACCAAATTAAAAAAATTGATAGTTAGGTGACCAAAAAAGAAAAGGACAA
Found at i:5819388 original size:17 final size:17
Alignment explanation
Indices: 5819368--5819414 Score: 62
Period size: 17 Copynumber: 2.8 Consensus size: 17
5819358 CACATTTTAT
5819368 ATTATTTATATTATTGA
1 ATTATTTATATTATTGA
5819385 ATTATTTAGTCA-TATTGA
1 ATTATTTA-T-ATTATTGA
5819403 A-TATTTATATTA
1 ATTATTTATATTA
5819415 AAATTGAATT
Statistics
Matches: 27, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
15 1 0.04
16 3 0.11
17 14 0.52
18 8 0.30
19 1 0.04
ACGTcount: A:0.36, C:0.02, G:0.06, T:0.55
Consensus pattern (17 bp):
ATTATTTATATTATTGA
Found at i:5820031 original size:61 final size:61
Alignment explanation
Indices: 5819904--5820030 Score: 186
Period size: 61 Copynumber: 2.1 Consensus size: 61
5819894 GTCACTCTTA
* ** * *
5819904 TTTTTTGGTCATCCAACTATGAAAAGTTACAAAATGGTCACTTAATTATGTTTTTTTTTTC
1 TTTTTTGGTCATCCAACCATGAAAAGTTACAAAATAATCACTCAACTATGTTTTTTTTTTC
5819965 TTTTTTGGTCA-CCAAACCATGAAAAGTTACAAAATAATCACTCAACTATG-TTTTTTTTTC
1 TTTTTTGGTCATCC-AACCATGAAAAGTTACAAAATAATCACTCAACTATGTTTTTTTTTTC
5820025 TTTTTT
1 TTTTTT
5820031 TATCATGAGT
Statistics
Matches: 60, Mismatches: 5, Indels: 3
0.88 0.07 0.04
Matches are distributed among these distances:
60 18 0.30
61 42 0.70
ACGTcount: A:0.29, C:0.15, G:0.09, T:0.46
Consensus pattern (61 bp):
TTTTTTGGTCATCCAACCATGAAAAGTTACAAAATAATCACTCAACTATGTTTTTTTTTTC
Found at i:5820392 original size:16 final size:16
Alignment explanation
Indices: 5820371--5820412 Score: 66
Period size: 16 Copynumber: 2.6 Consensus size: 16
5820361 AATAATTTGA
*
5820371 TAATTTTACTAACAAT
1 TAATTTTAATAACAAT
5820387 TAATTTTAATAACAAT
1 TAATTTTAATAACAAT
*
5820403 TAGTTTTAAT
1 TAATTTTAAT
5820413 TTTATTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.43, C:0.07, G:0.02, T:0.48
Consensus pattern (16 bp):
TAATTTTAATAACAAT
Found at i:5820396 original size:22 final size:23
Alignment explanation
Indices: 5820386--5820447 Score: 72
Period size: 23 Copynumber: 2.7 Consensus size: 23
5820376 TTACTAACAA
* * *
5820386 TTAATTTTAAT-AACAATTAGTT
1 TTAATTTTAATAAAAAAATAATT
*
5820408 TTAATTTTATTAAAAAAATAATT
1 TTAATTTTAATAAAAAAATAATT
*
5820431 TTAATTTTAATTAAAAA
1 TTAATTTTAATAAAAAA
5820448 CGGGTCGGGC
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
22 10 0.30
23 23 0.70
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (23 bp):
TTAATTTTAATAAAAAAATAATT
Found at i:5821243 original size:10 final size:11
Alignment explanation
Indices: 5821198--5821254 Score: 64
Period size: 11 Copynumber: 5.3 Consensus size: 11
5821188 CGGCCTATTT
5821198 TTATTTTAAAA
1 TTATTTTAAAA
*
5821209 -AATTTTAAAAA
1 TTATTTT-AAAA
* *
5821220 GTATTTTTAAA
1 TTATTTTAAAA
5821231 TTA-TTTAAAA
1 TTATTTTAAAA
5821241 TTATTTTAAAA
1 TTATTTTAAAA
5821252 TTA
1 TTA
5821255 AAAAAATTTA
Statistics
Matches: 38, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
10 14 0.37
11 19 0.50
12 5 0.13
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (11 bp):
TTATTTTAAAA
Found at i:5821245 original size:21 final size:21
Alignment explanation
Indices: 5821207--5821254 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
5821197 TTTATTTTAA
5821207 AAAATT-TTAAAAAGTATTTT
1 AAAATTATTAAAAAGTATTTT
* * *
5821227 TAAATTATTTAAAATTATTTT
1 AAAATTATTAAAAAGTATTTT
5821248 AAAATTA
1 AAAATTA
5821255 AAAAAATTTA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
20 5 0.22
21 18 0.78
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (21 bp):
AAAATTATTAAAAAGTATTTT
Found at i:5821281 original size:43 final size:40
Alignment explanation
Indices: 5821232--5821345 Score: 156
Period size: 43 Copynumber: 2.8 Consensus size: 40
5821222 ATTTTTAAAT
*
5821232 TATTTAAAATTATTTTAAAATTAAAAAAATTTAAAAAAAAAG
1 TATTTAAAAATATTTTAAAATTAAAAAAATTT--AAAAAAAG
*
5821274 TATTTTAAAAATATTTTAAAATTAAAAAAAAATTAAAAAAAG
1 TA-TTTAAAAATATTTTAAAATT-AAAAAAATTTAAAAAAAG
* *
5821316 TATGTAAAAATATTTTAAAGTTAAAAAAAT
1 TATTTAAAAATATTTTAAAATTAAAAAAAT
5821346 AAATATATTT
Statistics
Matches: 65, Mismatches: 5, Indels: 6
0.86 0.07 0.08
Matches are distributed among these distances:
40 7 0.11
41 18 0.28
42 12 0.18
43 19 0.29
44 9 0.14
ACGTcount: A:0.61, C:0.00, G:0.04, T:0.35
Consensus pattern (40 bp):
TATTTAAAAATATTTTAAAATTAAAAAAATTTAAAAAAAG
Found at i:5821325 original size:53 final size:53
Alignment explanation
Indices: 5821214--5821334 Score: 129
Period size: 53 Copynumber: 2.3 Consensus size: 53
5821204 TAAAAAATTT
* * **** *
5821214 TAAAAAGTATTTTTAAATTATTTAAAATTATTTTAAAATTAAAAAAATTTAAA
1 TAAAAAGTATTTTAAAAATATTTAAAATTAAAAAAAAATTAAAAAAATGTAAA
* **
5821267 AAAAAAGTATTTTAAAAATATTTTAAAATTAAAAAAAAATTAAAAAAA-GTATG
1 TAAAAAGTATTTTAAAAATA-TTTAAAATTAAAAAAAAATTAAAAAAATGTAAA
5821320 TAAAAA-TATTTTAAA
1 TAAAAAGTATTTTAAA
5821335 GTTAAAAAAA
Statistics
Matches: 56, Mismatches: 11, Indels: 3
0.80 0.16 0.04
Matches are distributed among these distances:
52 9 0.16
53 24 0.43
54 23 0.41
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.37
Consensus pattern (53 bp):
TAAAAAGTATTTTAAAAATATTTAAAATTAAAAAAAAATTAAAAAAATGTAAA
Found at i:5827638 original size:14 final size:15
Alignment explanation
Indices: 5827619--5827651 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
5827609 ATATAATTAC
*
5827619 TTAATT-AATTTATT
1 TTAATTAAACTTATT
5827633 TTAATTAAACTTATT
1 TTAATTAAACTTATT
5827648 TTAA
1 TTAA
5827652 ATTTTTTATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 6 0.35
15 11 0.65
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (15 bp):
TTAATTAAACTTATT
Found at i:5833725 original size:14 final size:14
Alignment explanation
Indices: 5833703--5833736 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
5833693 CAATCAATTC
*
5833703 TTTTGAGTTTAATA
1 TTTTTAGTTTAATA
5833717 TTTTTAGTTTAATA
1 TTTTTAGTTTAATA
*
5833731 TATTTA
1 TTTTTA
5833737 AAAATATTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.29, C:0.00, G:0.09, T:0.62
Consensus pattern (14 bp):
TTTTTAGTTTAATA
Found at i:5840455 original size:20 final size:21
Alignment explanation
Indices: 5840427--5840467 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
5840417 TTCTAATTAG
* *
5840427 AAAATTCTAA-TAATTAAAAT
1 AAAAATCTAAGTAAATAAAAT
5840447 AAAAATCTAAGTAAATAAAAT
1 AAAAATCTAAGTAAATAAAAT
5840468 TTTCTAAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 9 0.50
21 9 0.50
ACGTcount: A:0.63, C:0.05, G:0.02, T:0.29
Consensus pattern (21 bp):
AAAAATCTAAGTAAATAAAAT
Found at i:5855275 original size:26 final size:26
Alignment explanation
Indices: 5855223--5855273 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 26
5855213 TATATTAATA
* **
5855223 ATTAATAATTTCATATATTTTTATTT
1 ATTAAAAATTTCATATATAATTATTT
5855249 ATTAAAAATTT-ATATATAATTATTT
1 ATTAAAAATTTCATATATAATTATTT
5855274 TAATATTTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
25 12 0.55
26 10 0.45
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (26 bp):
ATTAAAAATTTCATATATAATTATTT
Found at i:5855323 original size:22 final size:23
Alignment explanation
Indices: 5855288--5855331 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
5855278 ATTTTTTAAT
5855288 ATTTAAATTATTATATACTATAG
1 ATTTAAATTATTATATACTATAG
* *
5855311 ATTT-AATTTTTATATATTATA
1 ATTTAAATTATTATATACTATA
5855332 AATTACGTGA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.55
Consensus pattern (23 bp):
ATTTAAATTATTATATACTATAG
Found at i:5856252 original size:25 final size:25
Alignment explanation
Indices: 5856202--5856252 Score: 59
Period size: 25 Copynumber: 2.0 Consensus size: 25
5856192 AAACCGAGCC
* *
5856202 AAGCTCAAGCTCAACTCAAAATTCG
1 AAGCTCAAACTCAACTCAAAACTCG
*
5856227 AAGCTCAATACTCAACTC-GAACTCG
1 AAGCTCAA-ACTCAACTCAAAACTCG
5856252 A
1 A
5856253 TCGAATGTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
25 14 0.64
26 8 0.36
ACGTcount: A:0.39, C:0.29, G:0.12, T:0.20
Consensus pattern (25 bp):
AAGCTCAAACTCAACTCAAAACTCG
Found at i:5858988 original size:24 final size:22
Alignment explanation
Indices: 5858952--5858997 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
5858942 TATTCCTCAA
5858952 AATACCATCATATATAAAAACT
1 AATACCATCATATATAAAAACT
5858974 AATACCATCATATATAAAAACT
1 AATACCATCATATATAAAAACT
5858996 AA
1 AA
5858998 GCTAAGTCAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.57, C:0.17, G:0.00, T:0.26
Consensus pattern (22 bp):
AATACCATCATATATAAAAACT
Found at i:5859205 original size:18 final size:18
Alignment explanation
Indices: 5859182--5859216 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
5859172 GAAACTTGTC
* *
5859182 CAACAGGGTTAGAGTTTT
1 CAACAGAGTCAGAGTTTT
5859200 CAACAGAGTCAGAGTTT
1 CAACAGAGTCAGAGTTT
5859217 CGAATGGAAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.31, C:0.14, G:0.26, T:0.29
Consensus pattern (18 bp):
CAACAGAGTCAGAGTTTT
Found at i:5861319 original size:3 final size:3
Alignment explanation
Indices: 5861311--5861337 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
5861301 CAGTACCATT
5861311 ATC ATC ATC ATC ATC ATC ATC ATC ATC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC
5861338 CAAATTCAGA
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:0.33, C:0.33, G:0.00, T:0.33
Consensus pattern (3 bp):
ATC
Found at i:5864619 original size:34 final size:34
Alignment explanation
Indices: 5864576--5864650 Score: 141
Period size: 34 Copynumber: 2.2 Consensus size: 34
5864566 TCGATTCAGT
5864576 TCGAAAAGTAAGAGGATTAGAATAAAAATATAGG
1 TCGAAAAGTAAGAGGATTAGAATAAAAATATAGG
*
5864610 TCGAAAAGTAAGAGGGTTAGAATAAAAATATAGG
1 TCGAAAAGTAAGAGGATTAGAATAAAAATATAGG
5864644 TCGAAAA
1 TCGAAAA
5864651 ATAGGATTGG
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
34 40 1.00
ACGTcount: A:0.52, C:0.04, G:0.24, T:0.20
Consensus pattern (34 bp):
TCGAAAAGTAAGAGGATTAGAATAAAAATATAGG
Found at i:5865657 original size:28 final size:31
Alignment explanation
Indices: 5865625--5865687 Score: 87
Period size: 30 Copynumber: 2.1 Consensus size: 31
5865615 TATATAAAAA
*
5865625 ATAATT-T-TTTTATAAAATTAAAA-AATAT
1 ATAATTATATTTTATAAAATCAAAATAATAT
*
5865653 ATAATTATATTTTTTAAAATCAAAATAATAT
1 ATAATTATATTTTATAAAATCAAAATAATAT
5865684 ATAA
1 ATAA
5865688 AAATTTATTT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
28 6 0.20
29 1 0.03
30 14 0.47
31 9 0.30
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (31 bp):
ATAATTATATTTTATAAAATCAAAATAATAT
Found at i:5865720 original size:22 final size:24
Alignment explanation
Indices: 5865686--5865730 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 24
5865676 AATAATATAT
*
5865686 AAAAATTTATTTTTA-AACTTTTA
1 AAAAATATATTTTTACAACTTTTA
5865709 AAAAATAT-TTTTTACAACTTTT
1 AAAAATATATTTTTACAACTTTT
5865731 TACATTTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 6 0.30
23 14 0.70
ACGTcount: A:0.42, C:0.07, G:0.00, T:0.51
Consensus pattern (24 bp):
AAAAATATATTTTTACAACTTTTA
Found at i:5866308 original size:29 final size:29
Alignment explanation
Indices: 5866250--5866308 Score: 66
Period size: 29 Copynumber: 2.0 Consensus size: 29
5866240 GAATTTGATC
*
5866250 AAATCAAAATTTCATGCATAAAATTACACA
1 AAATCAAAATTTCAT-CATAAAAGTACACA
* *
5866280 AAATCAAAATTCTTAT-ATAAAAGTGCACA
1 AAATCAAAATT-TCATCATAAAAGTACACA
5866309 TTAAACTAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
29 11 0.44
30 11 0.44
31 3 0.12
ACGTcount: A:0.53, C:0.15, G:0.05, T:0.27
Consensus pattern (29 bp):
AAATCAAAATTTCATCATAAAAGTACACA
Found at i:5875216 original size:12 final size:11
Alignment explanation
Indices: 5875186--5875216 Score: 53
Period size: 11 Copynumber: 2.7 Consensus size: 11
5875176 TTATTTAAAA
5875186 TATTAATTTTT
1 TATTAATTTTT
5875197 TATTAATTTTT
1 TATTAATTTTT
5875208 TATTGAATT
1 TATT-AATT
5875217 AATGTCGGAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 15 0.79
12 4 0.21
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.68
Consensus pattern (11 bp):
TATTAATTTTT
Found at i:5878027 original size:16 final size:16
Alignment explanation
Indices: 5878006--5878061 Score: 69
Period size: 16 Copynumber: 3.4 Consensus size: 16
5877996 CAAATAGTTT
5878006 TAAAATATTTTCTTTC
1 TAAAATATTTTCTTTC
* *
5878022 TAAAATA-ATTCAATTTT
1 TAAAATATTTTC--TTTC
5878039 TAAAATATTTTCTTTC
1 TAAAATATTTTCTTTC
5878055 TAAAATA
1 TAAAATA
5878062 ATTCAATTTC
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
15 3 0.09
16 17 0.52
17 10 0.30
18 3 0.09
ACGTcount: A:0.41, C:0.09, G:0.00, T:0.50
Consensus pattern (16 bp):
TAAAATATTTTCTTTC
Found at i:5878044 original size:17 final size:17
Alignment explanation
Indices: 5878018--5878071 Score: 67
Period size: 17 Copynumber: 3.2 Consensus size: 17
5878008 AAATATTTTC
5878018 TTTCTAAAATAATTCAA
1 TTTCTAAAATAATTCAA
* *
5878035 TTTTTAAAATATTTTC--
1 TTTCTAAAATA-ATTCAA
5878051 TTTCTAAAATAATTCAA
1 TTTCTAAAATAATTCAA
5878068 TTTC
1 TTTC
5878072 ATCATGTAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 6
0.75 0.10 0.15
Matches are distributed among these distances:
15 3 0.10
16 10 0.33
17 14 0.47
18 3 0.10
ACGTcount: A:0.39, C:0.11, G:0.00, T:0.50
Consensus pattern (17 bp):
TTTCTAAAATAATTCAA
Found at i:5878045 original size:33 final size:33
Alignment explanation
Indices: 5878003--5878070 Score: 136
Period size: 33 Copynumber: 2.1 Consensus size: 33
5877993 AAACAAATAG
5878003 TTTTAAAATATTTTCTTTCTAAAATAATTCAAT
1 TTTTAAAATATTTTCTTTCTAAAATAATTCAAT
5878036 TTTTAAAATATTTTCTTTCTAAAATAATTCAAT
1 TTTTAAAATATTTTCTTTCTAAAATAATTCAAT
5878069 TT
1 TT
5878071 CATCATGTAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.38, C:0.09, G:0.00, T:0.53
Consensus pattern (33 bp):
TTTTAAAATATTTTCTTTCTAAAATAATTCAAT
Found at i:5881334 original size:30 final size:30
Alignment explanation
Indices: 5881295--5881351 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 30
5881285 TTTTATAAAT
5881295 AATTAATATTT-AT-TACTTAAAAATATTTAA
1 AATTAATATTTCATATA-TT-AAAATATTTAA
*
5881325 AATTTATATTTCATATATTAAAATATT
1 AATTAATATTTCATATATTAAAATATT
5881352 AATAACAAGT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
30 18 0.75
31 4 0.17
32 2 0.08
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (30 bp):
AATTAATATTTCATATATTAAAATATTTAA
Found at i:5881558 original size:26 final size:26
Alignment explanation
Indices: 5881529--5881578 Score: 75
Period size: 26 Copynumber: 1.9 Consensus size: 26
5881519 CTTAAACCAA
5881529 ACTTTT-CAGAAATATTTCTCAAAATC
1 ACTTTTCCA-AAATATTTCTCAAAATC
*
5881555 ACTTTTCCAAACTATTTCTCAAAA
1 ACTTTTCCAAAATATTTCTCAAAA
5881579 AAATGCTAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
26 20 0.91
27 2 0.09
ACGTcount: A:0.38, C:0.22, G:0.02, T:0.38
Consensus pattern (26 bp):
ACTTTTCCAAAATATTTCTCAAAATC
Found at i:5884760 original size:31 final size:29
Alignment explanation
Indices: 5884725--5884787 Score: 85
Period size: 27 Copynumber: 2.2 Consensus size: 29
5884715 GTAAATTTAA
*
5884725 AAAATATATATATATACAGGGGTGAAGCCAG
1 AAAATAT-T-TATATACAGGGGCGAAGCCAG
5884756 -AAA-ATTTATATACAGGGGCGAAGCCAG
1 AAAATATTTATATACAGGGGCGAAGCCAG
5884783 AAAAT
1 AAAAT
5884788 TTTTCTTTAG
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
27 20 0.69
28 4 0.14
29 2 0.07
30 3 0.10
ACGTcount: A:0.46, C:0.11, G:0.22, T:0.21
Consensus pattern (29 bp):
AAAATATTTATATACAGGGGCGAAGCCAG
Found at i:5884801 original size:27 final size:27
Alignment explanation
Indices: 5884735--5884789 Score: 101
Period size: 27 Copynumber: 2.0 Consensus size: 27
5884725 AAAATATATA
*
5884735 TATATACAGGGGTGAAGCCAGAAAATT
1 TATATACAGGGGCGAAGCCAGAAAATT
5884762 TATATACAGGGGCGAAGCCAGAAAATT
1 TATATACAGGGGCGAAGCCAGAAAATT
5884789 T
1 T
5884790 TTCTTTAGGG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.40, C:0.13, G:0.25, T:0.22
Consensus pattern (27 bp):
TATATACAGGGGCGAAGCCAGAAAATT
Found at i:5885995 original size:106 final size:106
Alignment explanation
Indices: 5885810--5886013 Score: 345
Period size: 106 Copynumber: 1.9 Consensus size: 106
5885800 TGGGTTGAGA
* * *
5885810 TTTAAGAGGATATTTGGCTATTTGGTCGAACGAGAAATTGAAACCCAGCACGTTAGGGCACGTTT
1 TTTAAAAGGATATTTGGCTATTTGGTCAAACGAGAAATCGAAACCCAGCACGTTAGGGCACGTTT
* *
5885875 TCTTGAATTTCCAAACGTAAAATATTACCTTATTTTGAAAT
66 TCTCGAATTTCCAAACGCAAAATATTACCTTATTTTGAAAT
*
5885916 TTTAAAAGGATATTTGGCTGTTTGGTCAAACGAGAAATCGAAACCCAGCACGTTAGGGCACGTTT
1 TTTAAAAGGATATTTGGCTATTTGGTCAAACGAGAAATCGAAACCCAGCACGTTAGGGCACGTTT
*
5885981 TCTCGAATTTCCAAACGCAAAATATTGCCTTAT
66 TCTCGAATTTCCAAACGCAAAATATTACCTTAT
5886014 CTTAAAACAT
Statistics
Matches: 91, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
106 91 1.00
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Consensus pattern (106 bp):
TTTAAAAGGATATTTGGCTATTTGGTCAAACGAGAAATCGAAACCCAGCACGTTAGGGCACGTTT
TCTCGAATTTCCAAACGCAAAATATTACCTTATTTTGAAAT
Found at i:5886438 original size:18 final size:19
Alignment explanation
Indices: 5886415--5886450 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
5886405 AAACCAATGT
5886415 ATAAAAAATGAA-TAATAA
1 ATAAAAAATGAACTAATAA
*
5886433 ATAAAATATGAACTAATA
1 ATAAAAAATGAACTAATA
5886451 TAAGTTGACC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 11 0.69
19 5 0.31
ACGTcount: A:0.67, C:0.03, G:0.06, T:0.25
Consensus pattern (19 bp):
ATAAAAAATGAACTAATAA
Found at i:5894580 original size:16 final size:16
Alignment explanation
Indices: 5894560--5894612 Score: 88
Period size: 16 Copynumber: 3.3 Consensus size: 16
5894550 TTGGTTCGCT
*
5894560 GTAATGGAATAGAGGT
1 GTAATGGAATAGAGGC
*
5894576 GTAATGGAATAGATGC
1 GTAATGGAATAGAGGC
5894592 GTAATGGAATAGAGGC
1 GTAATGGAATAGAGGC
5894608 GTAAT
1 GTAAT
5894613 AGATAATTCT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 34 1.00
ACGTcount: A:0.38, C:0.04, G:0.34, T:0.25
Consensus pattern (16 bp):
GTAATGGAATAGAGGC
Found at i:5894853 original size:18 final size:17
Alignment explanation
Indices: 5894801--5894846 Score: 74
Period size: 18 Copynumber: 2.6 Consensus size: 17
5894791 TTATTATTAA
5894801 ATATAATTTAATAAAAAT
1 ATATAATTTAAT-AAAAT
5894819 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
5894836 ATATGAATTTA
1 ATAT-AATTTA
5894847 CTTAAATCAT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
17 9 0.33
18 18 0.67
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:5894874 original size:41 final size:41
Alignment explanation
Indices: 5894816--5894999 Score: 95
Period size: 41 Copynumber: 4.6 Consensus size: 41
5894806 ATTTAATAAA
* *
5894816 AATATATAAT-TTAATAAAATATATGAATTT-ACTTAAATCAT
1 AATATATAATACT-ATAAAATATAT-AATTTAACTAAAATCAT
* * *
5894857 AATATATAATACTATAAAA-A-ATAATTTAAAATAATTATTATT
1 AATATATAATACTATAAAATATATAATTT-AACTAA-AATCA-T
* * *
5894899 AA-ATATAAT-TTAATAAAAATATATAATTTGA-TAAAATTCTT
1 AATATATAATACT-AT-AAAATATATAATTTAACTAAAA-TCAT
* ***
5894940 AGTAT-TAA-A-TAT-TCTTATATGAATTT-ACTAAAATCAT
1 AATATATAATACTATAAAATATAT-AATTTAACTAAAATCAT
5894977 AATATATAATACTATAAAATATA
1 AATATATAATACTATAAAATATA
5895000 ATTTAAAATA
Statistics
Matches: 106, Mismatches: 19, Indels: 36
0.66 0.12 0.22
Matches are distributed among these distances:
37 13 0.12
38 18 0.17
39 5 0.05
40 9 0.08
41 38 0.36
42 14 0.13
43 2 0.02
44 7 0.07
ACGTcount: A:0.53, C:0.04, G:0.02, T:0.41
Consensus pattern (41 bp):
AATATATAATACTATAAAATATATAATTTAACTAAAATCAT
Found at i:5894994 original size:61 final size:61
Alignment explanation
Indices: 5894835--5895017 Score: 189
Period size: 59 Copynumber: 3.0 Consensus size: 61
5894825 TTTAATAAAA
5894835 TATATGAATTTACTTAAATCATAATATATAATACTATAAAA-AATAATTTAAAATAATTAT
1 TATATGAATTTACTTAAATCATAATATATAATACTATAAAATAATAATTTAAAATAATTAT
* * * * * * * ** * *
5894895 TAT-TAAATATAATTTAATAAAAATATATAAT-TTGATAAAATTCTTAGTATT-AAAT-ATTCT
1 TATATGAATTTACTTAAATCATAATATATAATACT-ATAAAA-TAATAAT-TTAAAATAATTAT
*
5894955 TATATGAATTTACTAAAATCATAATATATAATACTATAAAAT-ATAATTTAAAATAATTAT
1 TATATGAATTTACTTAAATCATAATATATAATACTATAAAATAATAATTTAAAATAATTAT
5895015 TAT
1 TAT
5895018 TAAATATAAT
Statistics
Matches: 93, Mismatches: 22, Indels: 16
0.71 0.17 0.12
Matches are distributed among these distances:
58 3 0.03
59 35 0.38
60 18 0.19
61 34 0.37
62 3 0.03
ACGTcount: A:0.51, C:0.04, G:0.02, T:0.42
Consensus pattern (61 bp):
TATATGAATTTACTTAAATCATAATATATAATACTATAAAATAATAATTTAAAATAATTAT
Found at i:5901822 original size:17 final size:17
Alignment explanation
Indices: 5901801--5901837 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
5901791 ATTTGATAAG
5901801 TAAAAATATTTT--AAAA
1 TAAAAA-ATTTTAAAAAA
5901817 TAAAAAATTTTAAAAAA
1 TAAAAAATTTTAAAAAA
5901834 TAAA
1 TAAA
5901838 GTAAATTTAG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 5 0.26
16 6 0.32
17 8 0.42
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (17 bp):
TAAAAAATTTTAAAAAA
Found at i:5901826 original size:15 final size:16
Alignment explanation
Indices: 5901801--5901831 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
5901791 ATTTGATAAG
5901801 TAAAAATATTTTAAAA
1 TAAAAATATTTTAAAA
5901817 TAAAAA-ATTTTAAAA
1 TAAAAATATTTTAAAA
5901832 AATAAAGTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.60
16 6 0.40
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (16 bp):
TAAAAATATTTTAAAA
Found at i:5901951 original size:23 final size:24
Alignment explanation
Indices: 5901920--5901969 Score: 68
Period size: 23 Copynumber: 2.1 Consensus size: 24
5901910 ATTAATTTTT
*
5901920 TTTATAAATCTATTATA-ATTAATA
1 TTTATAAATATA-TATAGATTAATA
5901944 TTTA-AAATATATATAGATTAATA
1 TTTATAAATATATATAGATTAATA
5901967 TTT
1 TTT
5901970 GAAACTGCAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
22 4 0.17
23 16 0.67
24 4 0.17
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.50
Consensus pattern (24 bp):
TTTATAAATATATATAGATTAATA
Found at i:5916507 original size:68 final size:69
Alignment explanation
Indices: 5916407--5916630 Score: 261
Period size: 68 Copynumber: 3.0 Consensus size: 69
5916397 TTTTTTAATT
*
5916407 TTTAAATATTAATTAGAATATTTGTCAGGTTTTAAATTCCT-CGAAAAAAATGAGATGTGTTTTT
1 TTTAAATATTAATTAGAATATTTGTCAGGTTTTAAATTCCTCCAAAAAAAATGAGATGTGTTTTT
5916471 TTTA
66 TTTA
5916475 TTTAAATATTAATTAGAATATTTGTCAGGTTTTAAATTCCTCCAAAAAAAATGAGATGTGTTTTA
1 TTTAAATATTAATTAGAATATTTGTCAGGTTTTAAATTCCTCCAAAAAAAATGAGATGTG-----
5916540 ATTTTAATTTTTTA
61 ---TT--TTTTTTA
* * *
5916554 TTTTTTAAATATTAATTAGAATATTTGTCGGGTTTTAAATTCCTCCCAAAAAAACTAAGATGTGT
1 ---TTTAAATATTAATTAGAATATTTGTCAGGTTTTAAATTCCT-CCAAAAAAAATGAGATGTGT
*
5916619 TTAATTTTA
62 TT-TTTTTA
5916628 TTT
1 TTT
5916631 TTTTTAAATT
Statistics
Matches: 135, Mismatches: 5, Indels: 29
0.80 0.03 0.17
Matches are distributed among these distances:
68 41 0.30
69 17 0.13
71 3 0.02
73 1 0.01
74 5 0.04
75 2 0.01
77 2 0.01
79 7 0.05
82 40 0.30
83 17 0.13
ACGTcount: A:0.35, C:0.07, G:0.11, T:0.46
Consensus pattern (69 bp):
TTTAAATATTAATTAGAATATTTGTCAGGTTTTAAATTCCTCCAAAAAAAATGAGATGTGTTTTT
TTTA
Found at i:5916561 original size:82 final size:83
Alignment explanation
Indices: 5916466--5916665 Score: 307
Period size: 82 Copynumber: 2.4 Consensus size: 83
5916456 ATGAGATGTG
* *
5916466 TTTTTT-TTATTTAAATATTAATTAGAATATTTGTCAGGTTTTAAATTCCT-CCAAAAAAAATGA
1 TTTTTTATTTTTTAAATATTAATTAGAATATTTGTCAGGTTTTAAATTCCTCCCAAAAAAAATAA
5916529 GATGTGTTTTAATTTTA-A
66 GATGTG-TTTAATTTTATA
* *
5916547 TTTTTTATTTTTTAAATATTAATTAGAATATTTGTCGGGTTTTAAATTCCTCCCAAAAAAACTAA
1 TTTTTTATTTTTTAAATATTAATTAGAATATTTGTCAGGTTTTAAATTCCTCCCAAAAAAAATAA
*
5916612 GATGTGTTTAATTTTATT
66 GATGTGTTTAATTTTATA
**
5916630 TTTTTTAAATTTTAAATATTAATTAGAATATTTGTC
1 TTTTTTATTTTTTAAATATTAATTAGAATATTTGTC
5916666 CGATCTAAAA
Statistics
Matches: 109, Mismatches: 7, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
81 6 0.06
82 52 0.48
83 51 0.47
ACGTcount: A:0.34, C:0.07, G:0.09, T:0.50
Consensus pattern (83 bp):
TTTTTTATTTTTTAAATATTAATTAGAATATTTGTCAGGTTTTAAATTCCTCCCAAAAAAAATAA
GATGTGTTTAATTTTATA
Found at i:5916655 original size:83 final size:82
Alignment explanation
Indices: 5916475--5916665 Score: 303
Period size: 83 Copynumber: 2.3 Consensus size: 82
5916465 GTTTTTTTTA
*
5916475 TTTAAATATTAATTAGAATATTTGTCAGGTTTTAAATTCCTCCAAAAAAAATGAGATGTGTTTTA
1 TTTAAATATTAATTAGAATATTTGTCAGGTTTTAAATTCCTCCAAAAAAAATAAGATGTGTTTTA
**
5916540 ATTTTAATTTTTTATTT
66 ATTTTAATTTTTTAAAT
* *
5916557 TTTAAATATTAATTAGAATATTTGTCGGGTTTTAAATTCCTCCCAAAAAAACTAAGATGTG-TTT
1 TTTAAATATTAATTAGAATATTTGTCAGGTTTTAAATTCCT-CCAAAAAAAATAAGATGTGTTTT
*
5916621 AATTTTATTTTTTTTAAAT
65 AATTTTA-ATTTTTTAAAT
5916640 TTTAAATATTAATTAGAATATTTGTC
1 TTTAAATATTAATTAGAATATTTGTC
5916666 CGATCTAAAA
Statistics
Matches: 101, Mismatches: 6, Indels: 3
0.92 0.05 0.03
Matches are distributed among these distances:
82 50 0.50
83 51 0.50
ACGTcount: A:0.36, C:0.07, G:0.09, T:0.48
Consensus pattern (82 bp):
TTTAAATATTAATTAGAATATTTGTCAGGTTTTAAATTCCTCCAAAAAAAATAAGATGTGTTTTA
ATTTTAATTTTTTAAAT
Found at i:5923977 original size:28 final size:28
Alignment explanation
Indices: 5923937--5923993 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
5923927 CTCTGCCATG
5923937 ATATTTCTTTTTTGGGTCAACTCTAACT
1 ATATTTCTTTTTTGGGTCAACTCTAACT
5923965 ATATTTCTTTTTTGGGTCAACTCTAACT
1 ATATTTCTTTTTTGGGTCAACTCTAACT
5923993 A
1 A
5923994 ACATCCTCAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.23, C:0.18, G:0.11, T:0.49
Consensus pattern (28 bp):
ATATTTCTTTTTTGGGTCAACTCTAACT
Found at i:5925206 original size:21 final size:24
Alignment explanation
Indices: 5925180--5925232 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 24
5925170 TTTAAAATAC
5925180 TTTTAAAAT-AATTTTT-TGTTT-
1 TTTTAAAATAAATTTTTATGTTTA
5925201 TTTT-AAATAAATTTTTAATGTTTA
1 TTTTAAAATAAATTTTT-ATGTTTA
5925225 TTTTAAAA
1 TTTTAAAA
5925233 ATGGGCCGGG
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
20 4 0.15
21 11 0.41
23 5 0.19
24 4 0.15
25 3 0.11
ACGTcount: A:0.36, C:0.00, G:0.04, T:0.60
Consensus pattern (24 bp):
TTTTAAAATAAATTTTTATGTTTA
Found at i:5925208 original size:20 final size:22
Alignment explanation
Indices: 5925180--5925231 Score: 63
Period size: 20 Copynumber: 2.4 Consensus size: 22
5925170 TTTAAAATAC
*
5925180 TTTTAAAAT-AATTTTT-TGTT
1 TTTTTAAATAAATTTTTATGTT
5925200 TTTTTAAATAAATTTTTAATGTT
1 TTTTTAAATAAATTTTT-ATGTT
5925223 TATTTTAAA
1 T-TTTTAAA
5925232 AATGGGCCGG
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
20 8 0.30
21 7 0.26
23 5 0.19
24 7 0.26
ACGTcount: A:0.35, C:0.00, G:0.04, T:0.62
Consensus pattern (22 bp):
TTTTTAAATAAATTTTTATGTT
Found at i:5925799 original size:24 final size:24
Alignment explanation
Indices: 5925771--5925818 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
5925761 AAGATTGAGT
* *
5925771 ATTTATTTGTATAATATATTTAAC
1 ATTTATTAGCATAATATATTTAAC
*
5925795 ATTTATTAGCATAATTTATTTAAC
1 ATTTATTAGCATAATATATTTAAC
5925819 TTACTAATTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.38, C:0.06, G:0.04, T:0.52
Consensus pattern (24 bp):
ATTTATTAGCATAATATATTTAAC
Found at i:5927082 original size:3 final size:3
Alignment explanation
Indices: 5927071--5927101 Score: 53
Period size: 3 Copynumber: 10.0 Consensus size: 3
5927061 CTTTTTTTTC
5927071 TAA TAAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA
5927102 ACTACGGCAT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 24 0.89
4 3 0.11
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:5927527 original size:20 final size:20
Alignment explanation
Indices: 5927502--5927541 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
5927492 CGTAAAATGA
*
5927502 TTTCTGAAAAATGTTTTACT
1 TTTCTGAAAAATGATTTACT
*
5927522 TTTCTGTAAAATGATTTACT
1 TTTCTGAAAAATGATTTACT
5927542 GAAAAATATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.30, C:0.10, G:0.10, T:0.50
Consensus pattern (20 bp):
TTTCTGAAAAATGATTTACT
Found at i:5927531 original size:34 final size:35
Alignment explanation
Indices: 5927487--5927553 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
5927477 CAGTAAAATA
*
5927487 TTTTCCGTAAAATGATTT-CTGAAAAATGTTTTAC
1 TTTTCCGTAAAATGATTTACTGAAAAATATTTTAC
*
5927521 TTTTCTGTAAAATGATTTACTGAAAAATATTTT
1 TTTTCCGTAAAATGATTTACTGAAAAATATTTT
5927554 CTGATGTTTA
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 17 0.57
35 13 0.43
ACGTcount: A:0.34, C:0.09, G:0.10, T:0.46
Consensus pattern (35 bp):
TTTTCCGTAAAATGATTTACTGAAAAATATTTTAC
Found at i:5936831 original size:19 final size:19
Alignment explanation
Indices: 5936783--5936862 Score: 56
Period size: 19 Copynumber: 4.2 Consensus size: 19
5936773 GTACGATAAC
* * *
5936783 TTTTATAATTTTTTTACGAA
1 TTTTATAATTTCTTTA-TAT
5936803 TTTTAT-ATTTCTTTATAT
1 TTTTATAATTTCTTTATAT
* *
5936821 TTTTATAATTT-TATAAAAT
1 TTTTATAATTTCT-TTATAT
* *
5936840 TTTTCTATATTTCTATATAT
1 TTTTATA-ATTTCTTTATAT
5936860 TTT
1 TTT
5936863 ATATTTTTTT
Statistics
Matches: 47, Mismatches: 9, Indels: 8
0.73 0.14 0.12
Matches are distributed among these distances:
18 8 0.17
19 22 0.47
20 16 0.34
21 1 0.02
ACGTcount: A:0.29, C:0.05, G:0.01, T:0.65
Consensus pattern (19 bp):
TTTTATAATTTCTTTATAT
Found at i:5936835 original size:46 final size:47
Alignment explanation
Indices: 5936778--5936870 Score: 111
Period size: 46 Copynumber: 2.0 Consensus size: 47
5936768 TTTTTGTACG
** *
5936778 ATAACTTTTATAATTTTTTTACGA-ATTT-TATATTTCTTTATATTTTT
1 ATAACTTTTATAAAATTTTT-CGATATTTCTATATAT-TTTATATTTTT
*
5936825 ATAA-TTTTATAAAATTTTTCTATATTTCTATATATTTTATATTTTT
1 ATAACTTTTATAAAATTTTTCGATATTTCTATATATTTTATATTTTT
5936871 TTCTAATTCT
Statistics
Matches: 40, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
45 2 0.05
46 28 0.70
47 10 0.25
ACGTcount: A:0.30, C:0.05, G:0.01, T:0.63
Consensus pattern (47 bp):
ATAACTTTTATAAAATTTTTCGATATTTCTATATATTTTATATTTTT
Found at i:5936871 original size:29 final size:28
Alignment explanation
Indices: 5936801--5936900 Score: 84
Period size: 29 Copynumber: 3.6 Consensus size: 28
5936791 TTTTTTTACG
* *
5936801 AATTTTATA-TTTCTT-TATATTTTTAT
1 AATTTTATATTTTTTTCTATATTTCTAT
**
5936827 AATTTTATAAAATTTTTCTATATTTCTAT
1 AATTTTAT-ATTTTTTTCTATATTTCTAT
5936856 ATATTTTATATTTTTTTCTA-A-TTCTTAAT
1 A-ATTTTATATTTTTTTCTATATTTC-T-AT
5936885 AAATTTTA-ATTTTTTT
1 -AATTTTATATTTTTTT
5936901 ATATTTTTTA
Statistics
Matches: 62, Mismatches: 5, Indels: 12
0.78 0.06 0.15
Matches are distributed among these distances:
26 8 0.13
27 4 0.06
28 14 0.23
29 28 0.45
30 8 0.13
ACGTcount: A:0.30, C:0.05, G:0.00, T:0.65
Consensus pattern (28 bp):
AATTTTATATTTTTTTCTATATTTCTAT
Found at i:5937575 original size:16 final size:16
Alignment explanation
Indices: 5937554--5937593 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
5937544 GCCTACTCCT
5937554 CCCAATTTAAACCCAG
1 CCCAATTTAAACCCAG
* *
5937570 CCCAATTTAAATCTAG
1 CCCAATTTAAACCCAG
5937586 CCCAATTT
1 CCCAATTT
5937594 TCACAACACC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.35, C:0.33, G:0.05, T:0.28
Consensus pattern (16 bp):
CCCAATTTAAACCCAG
Found at i:5938303 original size:9 final size:9
Alignment explanation
Indices: 5938289--5938337 Score: 71
Period size: 9 Copynumber: 5.2 Consensus size: 9
5938279 CTTAAATATT
5938289 TTCGGGTAA
1 TTCGGGTAA
*
5938298 TTCGGGTCATT
1 TTCGGGT-A-A
5938309 TTCGGGTAA
1 TTCGGGTAA
5938318 TTCGGGTAA
1 TTCGGGTAA
5938327 TTCGGGTAA
1 TTCGGGTAA
5938336 TT
1 TT
5938338 TTTAACCAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
9 27 0.75
10 2 0.06
11 7 0.19
ACGTcount: A:0.18, C:0.12, G:0.31, T:0.39
Consensus pattern (9 bp):
TTCGGGTAA
Found at i:5938311 original size:20 final size:19
Alignment explanation
Indices: 5938285--5938337 Score: 81
Period size: 20 Copynumber: 2.8 Consensus size: 19
5938275 TAGGCTTAAA
5938285 TATTTTCGGGTAATTCGGG
1 TATTTTCGGGTAATTCGGG
5938304 TCATTTTCGGGTAATTCGGG
1 T-ATTTTCGGGTAATTCGGG
*
5938324 TA-ATTCGGGTAATT
1 TATTTTCGGGTAATT
5938338 TTTAACCAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
18 11 0.34
19 2 0.06
20 19 0.59
ACGTcount: A:0.19, C:0.11, G:0.28, T:0.42
Consensus pattern (19 bp):
TATTTTCGGGTAATTCGGG
Found at i:5938411 original size:12 final size:12
Alignment explanation
Indices: 5938394--5938418 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
5938384 AAGAATTTCG
5938394 GGTCGGTTAACC
1 GGTCGGTTAACC
5938406 GGTCGGTTAACC
1 GGTCGGTTAACC
5938418 G
1 G
5938419 ACTGAACACC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.24, G:0.36, T:0.24
Consensus pattern (12 bp):
GGTCGGTTAACC
Found at i:5938625 original size:86 final size:84
Alignment explanation
Indices: 5938471--5938807 Score: 394
Period size: 84 Copynumber: 4.0 Consensus size: 84
5938461 CCGCCTCTGG
* * *
5938471 CTTTTTTGATGCATTTTGACAATTCAAGTACCCAATTGAGTGAAAAAAAAAACATAGGCTTAATT
1 CTTTTTTGATACATTTTGACAGTTCAAGTACCCAATTAAGTG-AAAAAAAAACATAGGCTTAATT
*
5938536 TTTTTTTTAAGTTTGAGGGT
65 TTTTTTTTAAGTTTGAAGGT
* *
5938556 CTTTTTTTTATACATTTTGACAGTTCAAGTGCCCAATTAAGT-AAAAAAAAACATAGGCTTAATT
1 C-TTTTTTGATACATTTTGACAGTTCAAGTACCCAATTAAGTGAAAAAAAAACATAGGCTTAATT
* * *
5938620 GTTTTTTTTTAGTTTGAATGC
65 -TTTTTTTTAAGTTTGAAGGT
* * * * *
5938641 CTTTTTTTATACATTTTTG-CAGTTAAAGTGCCCAATTAAGTGAAAAAAAAACAAAGGTTTAATT
1 CTTTTTTGATACA-TTTTGACAGTTCAAGTACCCAATTAAGTGAAAAAAAAACATAGGCTTAATT
5938705 TTTTTTTTAAGTTTGAAGGT
65 TTTTTTTTAAGTTTGAAGGT
* * * * *
5938725 C-TTTTTGATACATTTTGAAAGTTCAAATACCCAATTGAGTGCAAAAAAAATA-AGGGCTTAATT
1 CTTTTTTGATACATTTTGACAGTTCAAGTACCCAATTAAGTGAAAAAAAAACATA-GGCTTAA--
5938788 GCTTTTTTTTTTAAGTTTGA
63 --TTTTTTTTTTAAGTTTGA
5938808 GAGCTTTTCA
Statistics
Matches: 218, Mismatches: 24, Indels: 18
0.84 0.09 0.07
Matches are distributed among these distances:
82 6 0.03
83 43 0.20
84 73 0.33
85 43 0.20
86 35 0.16
87 18 0.08
ACGTcount: A:0.33, C:0.10, G:0.15, T:0.42
Consensus pattern (84 bp):
CTTTTTTGATACATTTTGACAGTTCAAGTACCCAATTAAGTGAAAAAAAAACATAGGCTTAATTT
TTTTTTTAAGTTTGAAGGT
Found at i:5939555 original size:29 final size:30
Alignment explanation
Indices: 5939488--5939556 Score: 90
Period size: 28 Copynumber: 2.4 Consensus size: 30
5939478 CGAATATAAT
*
5939488 AAAT-ATTTTTTTTCATTTTTTAATTTTTA
1 AAATAATTTTTTATCATTTTTTAATTTTTA
*
5939517 AAATACTTTTTTAT-ATTTTTT-ATTTTTA
1 AAATAATTTTTTATCATTTTTTAATTTTTA
*
5939545 AAATAAATTTTT
1 AAATAATTTTTT
5939557 GGTGTTTATT
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
28 17 0.49
29 11 0.31
30 7 0.20
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (30 bp):
AAATAATTTTTTATCATTTTTTAATTTTTA
Found at i:5940098 original size:23 final size:22
Alignment explanation
Indices: 5940060--5940119 Score: 65
Period size: 21 Copynumber: 2.8 Consensus size: 22
5940050 TAATTTTAAA
5940060 AATATATTTTAT-ATT-AATATT
1 AATATATTTTATAATTAAAT-TT
5940081 AATATATTTTTATAATTAAATTT
1 AATATA-TTTTATAATTAAATTT
5940104 AA-ATAATTTT-TAATTA
1 AATAT-ATTTTATAATTA
5940120 TTTAATTTGA
Statistics
Matches: 35, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
21 12 0.34
22 12 0.34
23 8 0.23
24 3 0.09
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (22 bp):
AATATATTTTATAATTAAATTT
Done.