Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr8
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: 56894857
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.32
Warning! 1173888 characters in sequence are not A, C, G, or T
File 175 of 185
Found at i:52837104 original size:47 final size:47
Alignment explanation
Indices: 52836822--52837114 Score: 338
Period size: 47 Copynumber: 6.3 Consensus size: 47
52836812 TTGATTTGGT
* **
52836822 TATGCTGTCCAATTTTGATGCTTAAATGCTGCCCAATTTGTTACATA
1 TATGCTGTCCAATTTTGATGCTAAAATGCTGCCCAAACTGTTACATA
* **
52836869 TATGCTGTCCAATTTTGATGCTTAAATGCTGCCCAATTTGTTACATA
1 TATGCTGTCCAATTTTGATGCTAAAATGCTGCCCAAACTGTTACATA
* * * * **
52836916 TATGCTGTCCAATTTCGATGCTTAAGTGCTGCCTAATTTGTTACATA
1 TATGCTGTCCAATTTTGATGCTAAAATGCTGCCCAAACTGTTACATA
* * **
52836963 TATGCTGTCTAATTTTGATGCTTAAATGCTG-CCAATTTGTTACATA
1 TATGCTGTCCAATTTTGATGCTAAAATGCTGCCCAAACTGTTACATA
* **
52837009 TATGCTGTCCAATTTTGATGCTTAAATGCTGCCCAATTTGTTACATA
1 TATGCTGTCCAATTTTGATGCTAAAATGCTGCCCAAACTGTTACATA
* * * **
52837056 TATGCTGTCCAGTTTTGGTG-TAAAAATGCTGCTCAAACTGTTGTATA
1 TATGCTGTCCAATTTTGATGCT-AAAATGCTGCCCAAACTGTTACATA
*
52837103 TATGCTGCCCAA
1 TATGCTGTCCAA
52837115 ATTGTTGTAT
Statistics
Matches: 226, Mismatches: 18, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
46 45 0.20
47 181 0.80
ACGTcount: A:0.25, C:0.18, G:0.16, T:0.40
Consensus pattern (47 bp):
TATGCTGTCCAATTTTGATGCTAAAATGCTGCCCAAACTGTTACATA
Found at i:52837104 original size:140 final size:141
Alignment explanation
Indices: 52836822--52837114 Score: 448
Period size: 140 Copynumber: 2.1 Consensus size: 141
52836812 TTGATTTGGT
52836822 TATGCTGTCCAATTTTGATGCTTAAATGCTGCCCAATTTGTTACATATATGCTGTCCAATTTTGA
1 TATGCTGTCCAATTTTGATGCTTAAATGCTGCCCAATTTGTTACATATATGCTGTCCAATTTTGA
* *
52836887 TGCTTAAATGCTGCCCAATTTGTTACATATATGCTGTCCAATTTCGATGCTTAAGTGCTGCCTAA
66 TGCTTAAATGCTGCCCAATTTGTTACATATATGCTGTCCAATTTCGATGCTAAAATGCTGCCTAA
**
52836952 TTTGTTACATA
131 ACTGTTACATA
*
52836963 TATGCTGTCTAATTTTGATGCTTAAATGCTG-CCAATTTGTTACATATATGCTGTCCAATTTTGA
1 TATGCTGTCCAATTTTGATGCTTAAATGCTGCCCAATTTGTTACATATATGCTGTCCAATTTTGA
* * *
52837027 TGCTTAAATGCTGCCCAATTTGTTACATATATGCTGTCCAGTTTTGGTG-TAAAAATGCTG-CTC
66 TGCTTAAATGCTGCCCAATTTGTTACATATATGCTGTCCAATTTCGATGCT-AAAATGCTGCCT-
**
52837090 AAACTGTTGTATA
129 AAACTGTTACATA
*
52837103 TATGCTGCCCAA
1 TATGCTGTCCAA
52837115 ATTGTTGTAT
Statistics
Matches: 138, Mismatches: 12, Indels: 5
0.89 0.08 0.03
Matches are distributed among these distances:
139 3 0.02
140 105 0.76
141 30 0.22
ACGTcount: A:0.25, C:0.18, G:0.16, T:0.40
Consensus pattern (141 bp):
TATGCTGTCCAATTTTGATGCTTAAATGCTGCCCAATTTGTTACATATATGCTGTCCAATTTTGA
TGCTTAAATGCTGCCCAATTTGTTACATATATGCTGTCCAATTTCGATGCTAAAATGCTGCCTAA
ACTGTTACATA
Found at i:52837155 original size:71 final size:69
Alignment explanation
Indices: 52837033--52837196 Score: 179
Period size: 71 Copynumber: 2.3 Consensus size: 69
52837023 TTGATGCTTA
* ** * *
52837033 AATGCTGCCCAATTTGTTACATATATGCTGTCCAGTTTTGGTGTAAAAATGCTGCTCAAACTGTT
1 AATGCTGCCCAAATTGTTGTATATATGCTATCCAATTTTGGTGTAAAAATGCTG-TCAAA-T-TT
52837098 -GTATAT
63 GGTATAT
* * *
52837104 -ATGCTGCCCAAATTGTTGTATTTATGCTATCCAAATTTTGGTGTGAAAATGCTGTCTAATTTGG
1 AATGCTGCCCAAATTGTTGTATATATGCTATCC-AATTTTGGTGTAAAAATGCTGTCAAATTTGG
52837168 TATAT
65 TATAT
* *
52837173 AAATGCTGTCCAAATTGATGTATA
1 -AATGCTGCCCAAATTGTTGTATA
52837197 AAAGCTGTCC
Statistics
Matches: 78, Mismatches: 11, Indels: 8
0.80 0.11 0.08
Matches are distributed among these distances:
68 2 0.03
69 7 0.09
70 31 0.40
71 38 0.49
ACGTcount: A:0.28, C:0.15, G:0.18, T:0.39
Consensus pattern (69 bp):
AATGCTGCCCAAATTGTTGTATATATGCTATCCAATTTTGGTGTAAAAATGCTGTCAAATTTGGT
ATAT
Found at i:52837178 original size:187 final size:187
Alignment explanation
Indices: 52836822--52837185 Score: 438
Period size: 187 Copynumber: 1.9 Consensus size: 187
52836812 TTGATTTGGT
52836822 TATGCTGTCCAATTTTGATGCTTAAATGCTGCCCAATTTGTTACATATATGCTGTCCAATTTTGA
1 TATGCTGTCCAATTTTGATGCTTAAATGCTGCCCAATTTGTTACATATATGCTGTCCAATTTTGA
* ** * * * *
52836887 TGCTTAAATGCTGCCCAATTTGTTACATATATGCTGTCCAATTTCGATGCTTAAGTGCTGCCTAA
66 TGCTAAAATGCTGCCCAAACTGTTACATATATGCTGCCCAAATTCGATGATTAAGTGCTGCCAAA
* *
52836952 TTTGTTACATATATGCTGTCTAATTTTGATGCTTAAATGCTG-CCAATTTGTTACATA
131 TTTGTTACATATATGCTGTCTAATTTGGAT-CATAAATGCTGTCCAATTTGTTACATA
* *
52837009 TATGCTGTCCAATTTTGATGCTTAAATGCTGCCCAATTTGTTACATATATGCTGTCCAGTTTTGG
1 TATGCTGTCCAATTTTGATGCTTAAATGCTGCCCAATTTGTTACATATATGCTGTCCAATTTTGA
* ** * * *
52837074 TG-TAAAAATGCTGCTCAAACTGTTGTATATATGCTGCCCAAATT-GTTGTATTTA-TGCTATCC
66 TGCT-AAAATGCTGCCCAAACTGTTACATATATGCTGCCCAAATTCGATG-ATTAAGTGCT-GCC
52837136 AAATTTTGGTGTGA-A-A-ATGCTGTCTAATTTGGTAT-ATAAATGCTGTCCAA
128 AAA-TTT-GT-T-ACATATATGCTGTCTAATTTGG-ATCATAAATGCTGTCCAA
52837186 ATTGATGTAT
Statistics
Matches: 151, Mismatches: 17, Indels: 17
0.82 0.09 0.09
Matches are distributed among these distances:
186 8 0.05
187 113 0.75
188 22 0.15
189 5 0.03
190 2 0.01
191 1 0.01
ACGTcount: A:0.26, C:0.17, G:0.17, T:0.40
Consensus pattern (187 bp):
TATGCTGTCCAATTTTGATGCTTAAATGCTGCCCAATTTGTTACATATATGCTGTCCAATTTTGA
TGCTAAAATGCTGCCCAAACTGTTACATATATGCTGCCCAAATTCGATGATTAAGTGCTGCCAAA
TTTGTTACATATATGCTGTCTAATTTGGATCATAAATGCTGTCCAATTTGTTACATA
Found at i:52837196 original size:23 final size:23
Alignment explanation
Indices: 52837070--52837210 Score: 106
Period size: 23 Copynumber: 6.0 Consensus size: 23
52837060 CTGTCCAGTT
*
52837070 TTGGTGTAAAAATGCTG-CTCAAA
1 TTGGTGTATAAATGCTGTC-CAAA
* * * *
52837093 CTGTTGTATATATGCTGCCCAAA
1 TTGGTGTATAAATGCTGTCCAAA
* ** *
52837116 TTGTTGTATTTATGCTATCCAAA
1 TTGGTGTATAAATGCTGTCCAAA
* *
52837139 TTTTGGTGTGA-AAATGCTGTCTAAT
1 --TTGGTGT-ATAAATGCTGTCCAAA
*
52837164 TTGGTATATAAATGCTGTCCAAA
1 TTGGTGTATAAATGCTGTCCAAA
* *
52837187 TTGATGTATAAAAGCTGTCCAAA
1 TTGGTGTATAAATGCTGTCCAAA
52837210 T
1 T
52837211 AGGGTAGATT
Statistics
Matches: 93, Mismatches: 20, Indels: 10
0.76 0.16 0.08
Matches are distributed among these distances:
22 1 0.01
23 75 0.81
24 1 0.01
25 15 0.16
26 1 0.01
ACGTcount: A:0.30, C:0.13, G:0.18, T:0.38
Consensus pattern (23 bp):
TTGGTGTATAAATGCTGTCCAAA
Found at i:52841709 original size:29 final size:30
Alignment explanation
Indices: 52841650--52841715 Score: 71
Period size: 29 Copynumber: 2.2 Consensus size: 30
52841640 TGTATTTCAA
* **
52841650 TGATGGACGGTTTAATTGATGGTTGTGTTT
1 TGATGGACGATTTAATTGATGGTTGAATTT
* *
52841680 TGATGGAC-ATTTTATTGATGTTTGAATTT
1 TGATGGACGATTTAATTGATGGTTGAATTT
*
52841709 TAATGGA
1 TGATGGA
52841716 TGGTTCAATT
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
29 22 0.73
30 8 0.27
ACGTcount: A:0.23, C:0.03, G:0.27, T:0.47
Consensus pattern (30 bp):
TGATGGACGATTTAATTGATGGTTGAATTT
Found at i:52843285 original size:18 final size:19
Alignment explanation
Indices: 52843257--52843295 Score: 71
Period size: 18 Copynumber: 2.1 Consensus size: 19
52843247 AAATCGCTCC
52843257 CCTAGGGGCGCGTTTTGCT
1 CCTAGGGGCGCGTTTTGCT
52843276 CCTA-GGGCGCGTTTTGCT
1 CCTAGGGGCGCGTTTTGCT
52843294 CC
1 CC
52843296 GTGTGTGTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 16 0.80
19 4 0.20
ACGTcount: A:0.05, C:0.31, G:0.33, T:0.31
Consensus pattern (19 bp):
CCTAGGGGCGCGTTTTGCT
Found at i:52843377 original size:17 final size:15
Alignment explanation
Indices: 52843339--52843377 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
52843329 GTTTAGTCCC
52843339 TAGGGTTTTTTGGTT
1 TAGGGTTTTTTGGTT
*
52843354 TAAGGTTTTTTAGGGTT
1 TAGGGTTTTTT--GGTT
52843371 TAGGGTT
1 TAGGGTT
52843378 AGGGTTTTGT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
15 10 0.50
17 10 0.50
ACGTcount: A:0.13, C:0.00, G:0.33, T:0.54
Consensus pattern (15 bp):
TAGGGTTTTTTGGTT
Found at i:52843530 original size:34 final size:32
Alignment explanation
Indices: 52843464--52843554 Score: 101
Period size: 34 Copynumber: 2.8 Consensus size: 32
52843454 TTTAAAAAAC
* *
52843464 AAATTATGGTTTAGTGTTTTTTAAAATCAATT
1 AAATTAGGGTTTAGAGTTTTTTAAAATCAATT
* * *
52843496 AATTTGGGGTTTAGAGTTTTTAATAAAATTAATT
1 AAATTAGGGTTTAGAGTTTTT--TAAAATCAATT
**
52843530 AAATTAGGGTTTAGCTTTTTTTAAA
1 AAATTAGGGTTTAGAGTTTTTTAAA
52843555 TAACTTTGTG
Statistics
Matches: 48, Mismatches: 9, Indels: 4
0.79 0.15 0.07
Matches are distributed among these distances:
32 21 0.44
34 27 0.56
ACGTcount: A:0.34, C:0.02, G:0.15, T:0.48
Consensus pattern (32 bp):
AAATTAGGGTTTAGAGTTTTTTAAAATCAATT
Found at i:52843833 original size:126 final size:125
Alignment explanation
Indices: 52843621--52843877 Score: 433
Period size: 126 Copynumber: 2.0 Consensus size: 125
52843611 TTTTCTATTT
* * *
52843621 TAGTTCTTGAAAAAATTATTTTGAGAAGACAGTTCTGAACAAATAGTGTCAAAAACGCTTCAAGC
1 TAGTTCTTGAAAAAATAATTTTGAGAAGACAGTTATGAACAAATAGTGTAAAAAACGCTTCAAGC
* *
52843686 AGGATGCACTGTCAACAAAATTGATGAAAAAAACTCCCACGTGGACGCTCTTTTTCTACAG
66 AGGATGCACTATCAACAAAATTGAT-AAAAAAACTCCCACGTGGACGCTCTTTTTCTACAA
*
52843747 TAGTTCTTGAAAAAATAATTTTGAGAAGACGGTTATGAACAAATAGTGTAAAAAACGCTTCAAGC
1 TAGTTCTTGAAAAAATAATTTTGAGAAGACAGTTATGAACAAATAGTGTAAAAAACGCTTCAAGC
* *
52843812 AGGATGCACTATCAGCAAAATTGATAAAAAAGCTCCCACGTGGACGCTCTTTTTCTACAA
66 AGGATGCACTATCAACAAAATTGATAAAAAAACTCCCACGTGGACGCTCTTTTTCTACAA
52843872 TAGTTC
1 TAGTTC
52843878 CTGTTTGATC
Statistics
Matches: 123, Mismatches: 8, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
125 39 0.32
126 84 0.68
ACGTcount: A:0.38, C:0.18, G:0.18, T:0.27
Consensus pattern (125 bp):
TAGTTCTTGAAAAAATAATTTTGAGAAGACAGTTATGAACAAATAGTGTAAAAAACGCTTCAAGC
AGGATGCACTATCAACAAAATTGATAAAAAAACTCCCACGTGGACGCTCTTTTTCTACAA
Found at i:52847153 original size:24 final size:24
Alignment explanation
Indices: 52847126--52847171 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
52847116 GTTGCTCCGA
*
52847126 TTGTGGGTGTTGGGAGGATGACGG
1 TTGTGGGTGTTAGGAGGATGACGG
52847150 TTGTGGGTGTTAGGAGGATGAC
1 TTGTGGGTGTTAGGAGGATGAC
52847172 CCACATTGAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.15, C:0.04, G:0.50, T:0.30
Consensus pattern (24 bp):
TTGTGGGTGTTAGGAGGATGACGG
Found at i:52849102 original size:18 final size:18
Alignment explanation
Indices: 52849064--52849103 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
52849054 TTTGATTAAA
**
52849064 AATTAACCGAATTACTTG
1 AATTAACCGAATTACCCG
*
52849082 AATTATCCGAATTACCCG
1 AATTAACCGAATTACCCG
52849100 AATT
1 AATT
52849104 GAATCACTAC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.38, C:0.20, G:0.10, T:0.33
Consensus pattern (18 bp):
AATTAACCGAATTACCCG
Found at i:52849148 original size:37 final size:37
Alignment explanation
Indices: 52849102--52849176 Score: 123
Period size: 37 Copynumber: 2.0 Consensus size: 37
52849092 ATTACCCGAA
* *
52849102 TTGAATCACTACATAATTAAAAATATTACATAAATCT
1 TTGAATCACTACATAATTAAAAACATTAAATAAATCT
*
52849139 TTGAATCACTACATAATTAAAAACATTAAATAATTCT
1 TTGAATCACTACATAATTAAAAACATTAAATAAATCT
52849176 T
1 T
52849177 GAAATTAACA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
37 35 1.00
ACGTcount: A:0.48, C:0.13, G:0.03, T:0.36
Consensus pattern (37 bp):
TTGAATCACTACATAATTAAAAACATTAAATAAATCT
Found at i:52849355 original size:38 final size:39
Alignment explanation
Indices: 52849304--52849381 Score: 124
Period size: 38 Copynumber: 2.0 Consensus size: 39
52849294 ACTTAAGAGT
*
52849304 TAGACTTTAGTTTTA-TTTCTATTGTGTT-GGTAATTGGG
1 TAGACTTTAGTTTTAGTTT-TATTGGGTTGGGTAATTGGG
52849342 TAGACTTTAGTTTTAGTTTTATTGGGTTGGGTAATTGGG
1 TAGACTTTAGTTTTAGTTTTATTGGGTTGGGTAATTGGG
52849381 T
1 T
52849382 TGGGTTCGTA
Statistics
Matches: 37, Mismatches: 1, Indels: 3
0.90 0.02 0.07
Matches are distributed among these distances:
38 23 0.62
39 14 0.38
ACGTcount: A:0.18, C:0.04, G:0.27, T:0.51
Consensus pattern (39 bp):
TAGACTTTAGTTTTAGTTTTATTGGGTTGGGTAATTGGG
Found at i:52849380 original size:13 final size:13
Alignment explanation
Indices: 52849362--52849386 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
52849352 TTTTAGTTTT
52849362 ATTGGGTTGGGTA
1 ATTGGGTTGGGTA
52849375 ATTGGGTTGGGT
1 ATTGGGTTGGGT
52849387 TCGTAATTGG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.12, C:0.00, G:0.48, T:0.40
Consensus pattern (13 bp):
ATTGGGTTGGGTA
Found at i:52849386 original size:18 final size:18
Alignment explanation
Indices: 52849363--52849412 Score: 66
Period size: 17 Copynumber: 2.8 Consensus size: 18
52849353 TTTAGTTTTA
52849363 TTGGGTTGGGTAATTGGG
1 TTGGGTTGGGTAATTGGG
*
52849381 TTGGGTT-CGTAATTGGG
1 TTGGGTTGGGTAATTGGG
* *
52849398 TTTGGTTGGATAATT
1 TTGGGTTGGGTAATT
52849413 TTATTTATTA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
17 15 0.56
18 12 0.44
ACGTcount: A:0.14, C:0.02, G:0.40, T:0.44
Consensus pattern (18 bp):
TTGGGTTGGGTAATTGGG
Found at i:52849902 original size:30 final size:30
Alignment explanation
Indices: 52849868--52849932 Score: 105
Period size: 30 Copynumber: 2.2 Consensus size: 30
52849858 ATTAATTAAA
52849868 GAGAGCTTTGAGAAATTTAAGGA-AAATTTT
1 GAGAGCTTTGAGAAATTTAAGGAGAAA-TTT
*
52849898 GAGAGCTTTGAGAAATTTAGGGAGAAATTT
1 GAGAGCTTTGAGAAATTTAAGGAGAAATTT
52849928 GAGAG
1 GAGAG
52849933 TTTTTTGCCA
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
30 30 0.91
31 3 0.09
ACGTcount: A:0.38, C:0.03, G:0.29, T:0.29
Consensus pattern (30 bp):
GAGAGCTTTGAGAAATTTAAGGAGAAATTT
Found at i:52850797 original size:29 final size:29
Alignment explanation
Indices: 52850736--52850798 Score: 72
Period size: 29 Copynumber: 2.2 Consensus size: 29
52850726 GTTTAATGTG
* * ** * *
52850736 CAATTTTATACATGAACTTTGATTTTGTG
1 CAATTTTATACATGAAATTTAAACTTATC
52850765 CAATTTTATACATGAAATTTAAACTTATC
1 CAATTTTATACATGAAATTTAAACTTATC
52850794 CAATT
1 CAATT
52850799 CTCACAAATT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.35, C:0.13, G:0.08, T:0.44
Consensus pattern (29 bp):
CAATTTTATACATGAAATTTAAACTTATC
Found at i:52863443 original size:9 final size:9
Alignment explanation
Indices: 52863429--52863454 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
52863419 AAAAAAACTT
52863429 CATCATCTA
1 CATCATCTA
52863438 CATCATCTA
1 CATCATCTA
52863447 CATCATCT
1 CATCATCT
52863455 TTTCCAAACA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.31, C:0.35, G:0.00, T:0.35
Consensus pattern (9 bp):
CATCATCTA
Found at i:52867469 original size:43 final size:43
Alignment explanation
Indices: 52867408--52867493 Score: 172
Period size: 43 Copynumber: 2.0 Consensus size: 43
52867398 TTTTCAAATT
52867408 AATTTATCTTGTTGGTTGTAAATTGTTACTGAGTTTCCAACTC
1 AATTTATCTTGTTGGTTGTAAATTGTTACTGAGTTTCCAACTC
52867451 AATTTATCTTGTTGGTTGTAAATTGTTACTGAGTTTCCAACTC
1 AATTTATCTTGTTGGTTGTAAATTGTTACTGAGTTTCCAACTC
52867494 TTGAACTCGG
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 43 1.00
ACGTcount: A:0.23, C:0.14, G:0.16, T:0.47
Consensus pattern (43 bp):
AATTTATCTTGTTGGTTGTAAATTGTTACTGAGTTTCCAACTC
Found at i:52873943 original size:53 final size:53
Alignment explanation
Indices: 52873886--52873988 Score: 138
Period size: 53 Copynumber: 1.9 Consensus size: 53
52873876 GATTTTCTTC
*
52873886 TCTATTGATTCATTATGGTATTC-TCCCATGATTCTTTGT-GTTTTTCTTTCTCT
1 TCTATTGATTCATTATGGT-TTCTTCCC-TGATTCTCTGTGGTTTTTCTTTCTCT
* * *
52873939 TCTATTGGTTCCTTCTGGTTTCTTCCCTGATTCTCTGTGGTTTTTCTTTC
1 TCTATTGATTCATTATGGTTTCTTCCCTGATTCTCTGTGGTTTTTCTTTC
52873989 CTATGTCTGT
Statistics
Matches: 44, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
52 13 0.30
53 31 0.70
ACGTcount: A:0.09, C:0.21, G:0.14, T:0.56
Consensus pattern (53 bp):
TCTATTGATTCATTATGGTTTCTTCCCTGATTCTCTGTGGTTTTTCTTTCTCT
Found at i:52884374 original size:46 final size:44
Alignment explanation
Indices: 52884322--52884409 Score: 140
Period size: 46 Copynumber: 2.0 Consensus size: 44
52884312 AGAACAGAAA
*
52884322 TGAGCCATGTAAGTCCATATTAGAAATATGGCTTTGGAGACAGGGT
1 TGAGCCATGTAAGTCCATATT--AAATATGGCATTGGAGACAGGGT
*
52884368 TGAGCCATGTAAGTCCATATTATATATGGCATTGGAGACAGG
1 TGAGCCATGTAAGTCCATATTAAATATGGCATTGGAGACAGG
52884410 AATAATTCAT
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
44 19 0.47
46 21 0.52
ACGTcount: A:0.31, C:0.14, G:0.27, T:0.28
Consensus pattern (44 bp):
TGAGCCATGTAAGTCCATATTAAATATGGCATTGGAGACAGGGT
Found at i:52884421 original size:44 final size:45
Alignment explanation
Indices: 52884315--52884448 Score: 135
Period size: 46 Copynumber: 3.0 Consensus size: 45
52884305 ACAGGACAGA
* * *
52884315 ACAGAAATGAGCCATGTAAGTCCATATTAGAAATATGGCTTTGGAG
1 ACAGGAATAAGCCATGTAAGTCCATATTA-AAATATGGCATTGGAG
** * *
52884361 ACAGGGTTGAGCCATGTAAGTCCATATT-ATATATGGCATTGGAG
1 ACAGGAATAAGCCATGTAAGTCCATATTAAAATATGGCATTGGAG
** * * *
52884405 ACAGGAATAATTCATGTAAGTCCATGTCAAAGACATGGCATTGG
1 ACAGGAATAAGCCATGTAAGTCCATATTAAA-ATATGGCATTGG
52884449 CAGGGTATTG
Statistics
Matches: 72, Mismatches: 14, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
44 35 0.49
45 1 0.01
46 36 0.50
ACGTcount: A:0.34, C:0.14, G:0.25, T:0.27
Consensus pattern (45 bp):
ACAGGAATAAGCCATGTAAGTCCATATTAAAATATGGCATTGGAG
Found at i:52887025 original size:7 final size:7
Alignment explanation
Indices: 52887002--52887035 Score: 50
Period size: 7 Copynumber: 4.6 Consensus size: 7
52886992 TTACACAATA
52887002 ATCACCAT
1 ATCA-CAT
52887010 ATCCACAT
1 AT-CACAT
52887018 ATCACAT
1 ATCACAT
52887025 ATCACAT
1 ATCACAT
52887032 ATCA
1 ATCA
52887036 TGCATATTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
7 16 0.64
8 7 0.28
9 2 0.08
ACGTcount: A:0.41, C:0.32, G:0.00, T:0.26
Consensus pattern (7 bp):
ATCACAT
Found at i:52898134 original size:78 final size:78
Alignment explanation
Indices: 52898005--52898173 Score: 275
Period size: 78 Copynumber: 2.2 Consensus size: 78
52897995 GTCTTTGAAG
* * *
52898005 AAATTAATTGATTAGCTTTAACATTTGGAGTTCCTGAACAGCCATTGGAGTGGACTTAGGAGTTG
1 AAATTAATTGATCAGCTTGAACATTTGGAGTTCCCGAACAGCCATTGGAGTGGACTTAGGAGTTG
*
52898070 AGCTAAATGAATC
66 AGCTAAATAAATC
*
52898083 AAATTAATTGATCAGCTTGGACATTTGGAGTTCCCGAACAGCCATTGGAGTGGACTTAGGAGTTG
1 AAATTAATTGATCAGCTTGAACATTTGGAGTTCCCGAACAGCCATTGGAGTGGACTTAGGAGTTG
*
52898148 AGCTGAATAAATC
66 AGCTAAATAAATC
*
52898161 AAATTACTTGATC
1 AAATTAATTGATC
52898174 GGTCAATGGT
Statistics
Matches: 84, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
78 84 1.00
ACGTcount: A:0.32, C:0.14, G:0.23, T:0.31
Consensus pattern (78 bp):
AAATTAATTGATCAGCTTGAACATTTGGAGTTCCCGAACAGCCATTGGAGTGGACTTAGGAGTTG
AGCTAAATAAATC
Found at i:52908969 original size:17 final size:17
Alignment explanation
Indices: 52908947--52908979 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
52908937 TGAGTCTCTG
52908947 TAAACTTCTAAATTCTT
1 TAAACTTCTAAATTCTT
52908964 TAAACTTCTAAATTCT
1 TAAACTTCTAAATTCT
52908980 CTCATAAACC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.36, C:0.18, G:0.00, T:0.45
Consensus pattern (17 bp):
TAAACTTCTAAATTCTT
Found at i:52914230 original size:42 final size:41
Alignment explanation
Indices: 52914161--52914292 Score: 178
Period size: 41 Copynumber: 3.2 Consensus size: 41
52914151 GGCCTATTTT
* *
52914161 TATTTTAAATTTTTTTAAAAATT-AAAAAAGTATTTAAAAAA
1 TATTTTAAA-ATTTTAAAAAATTAAAAAAAGTATTTAAAAAA
*
52914202 TATTTTAAAATTTTAAAAAATTAAAAAAAGTATTTTAAAAA
1 TATTTTAAAATTTTAAAAAATTAAAAAAAGTATTTAAAAAA
* *
52914243 TATTTTAAAATTTTAAAAAA-AAATTAAAAAGTATGTAAAAAA
1 TATTTTAAAATTTTAAAAAATTAA--AAAAAGTATTTAAAAAA
52914285 TATTTTAA
1 TATTTTAA
52914293 CATTAAAAAT
Statistics
Matches: 82, Mismatches: 6, Indels: 5
0.88 0.06 0.05
Matches are distributed among these distances:
40 13 0.16
41 46 0.56
42 23 0.28
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (41 bp):
TATTTTAAAATTTTAAAAAATTAAAAAAAGTATTTAAAAAA
Found at i:52919811 original size:33 final size:33
Alignment explanation
Indices: 52919746--52919812 Score: 84
Period size: 33 Copynumber: 2.0 Consensus size: 33
52919736 CATGCTAGTA
* *
52919746 TTTTGAATTTTTATGAATTATTTATATTTATAT
1 TTTTGAATTTTTATGAAATATTTAAATTTATAT
52919779 TTTTGAATATTTTAT-AAAT-TTTAAATTATATAT
1 TTTTGAAT-TTTTATGAAATATTTAAATT-TATAT
52919812 T
1 T
52919813 GACGTGTCAT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
32 7 0.23
33 17 0.57
34 6 0.20
ACGTcount: A:0.34, C:0.00, G:0.04, T:0.61
Consensus pattern (33 bp):
TTTTGAATTTTTATGAAATATTTAAATTTATAT
Found at i:52922740 original size:6 final size:7
Alignment explanation
Indices: 52922661--52922842 Score: 86
Period size: 7 Copynumber: 25.7 Consensus size: 7
52922651 ACTAATTAAT
52922661 CTAAACC
1 CTAAACC
52922668 CTAAACTC
1 CTAAAC-C
*
52922676 CTAACCC
1 CTAAACC
*
52922683 CT-ATCTC
1 CTAAAC-C
52922690 CTAAACC
1 CTAAACC
*
52922697 CTAAATC
1 CTAAACC
* *
52922704 ATAAAAC
1 CTAAACC
* *
52922711 ATAAAAC
1 CTAAACC
*
52922718 ATAAACC
1 CTAAACC
52922725 CTAAACCC
1 CTAAA-CC
52922733 CT-AACC
1 CTAAACC
52922739 CTAAACC
1 CTAAACC
*
52922746 C-CAACC
1 CTAAACC
52922752 CTTAAACC
1 C-TAAACC
*
52922760 ATAAACC
1 CTAAACC
* *
52922767 ATAAATC
1 CTAAACC
*
52922774 ATAAACC
1 CTAAACC
* *
52922781 ATAATCC
1 CTAAACC
*
52922788 TTAAACC
1 CTAAACC
*
52922795 TTAAA--
1 CTAAACC
*
52922800 ATAGTAACTC
1 CTA--AAC-C
52922810 CTAAACC
1 CTAAACC
*
52922817 TTAAACC
1 CTAAACC
52922824 CTAAACC
1 CTAAACC
*
52922831 ATAAACC
1 CTAAACC
52922838 CTAAA
1 CTAAA
52922843 TTATAATGAT
Statistics
Matches: 141, Mismatches: 22, Indels: 24
0.75 0.12 0.13
Matches are distributed among these distances:
5 2 0.01
6 11 0.08
7 107 0.76
8 19 0.13
10 2 0.01
ACGTcount: A:0.46, C:0.34, G:0.01, T:0.20
Consensus pattern (7 bp):
CTAAACC
Found at i:52922763 original size:49 final size:50
Alignment explanation
Indices: 52922669--52922780 Score: 120
Period size: 49 Copynumber: 2.3 Consensus size: 50
52922659 ATCTAAACCC
* * *
52922669 TAAACTCCT-AACCCCTATCTCCTAAACCCTAAATCATAAAACATAAAACA
1 TAAAC-CCTAAACCCCTAACTCCTAAACCCCAAACCATAAAACATAAAACA
* * * *
52922719 TAAACCCTAAACCCCTAAC-CCTAAACCCCAACCCTTAAACCATAAACCA
1 TAAACCCTAAACCCCTAACTCCTAAACCCCAAACCATAAAACATAAAACA
* *
52922768 TAAATCATAAACC
1 TAAACCCTAAACC
52922781 ATAATCCTTA
Statistics
Matches: 52, Mismatches: 9, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
49 38 0.73
50 14 0.27
ACGTcount: A:0.46, C:0.36, G:0.00, T:0.19
Consensus pattern (50 bp):
TAAACCCTAAACCCCTAACTCCTAAACCCCAAACCATAAAACATAAAACA
Found at i:52923331 original size:40 final size:40
Alignment explanation
Indices: 52923229--52923377 Score: 165
Period size: 40 Copynumber: 3.7 Consensus size: 40
52923219 TCGTTAATGG
*
52923229 TCGACCTATAGAGGCGTTTTTCAAGAAGCGCTGCCAAAGC
1 TCGACCTATAGCGGCGTTTTTCAAGAAGCGCTGCCAAAGC
* *
52923269 TCGACCTATAGCGGCGTCTTTCAAGAAGCGTTGCCAAAGC
1 TCGACCTATAGCGGCGTTTTTCAAGAAGCGCTGCCAAAGC
* * * * * * *
52923309 TCGACCTATAGCGTCATTTTTCATA-AGGTGCCGCTAATGC
1 TCGACCTATAGCGGCGTTTTTCA-AGAAGCGCTGCCAAAGC
* * *
52923349 TCGATCTATAGCGGCATTTTTCAAAAAGC
1 TCGACCTATAGCGGCGTTTTTCAAGAAGC
52923378 ACCACTAATG
Statistics
Matches: 91, Mismatches: 16, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
39 1 0.01
40 89 0.98
41 1 0.01
ACGTcount: A:0.26, C:0.25, G:0.22, T:0.27
Consensus pattern (40 bp):
TCGACCTATAGCGGCGTTTTTCAAGAAGCGCTGCCAAAGC
Found at i:52923386 original size:40 final size:40
Alignment explanation
Indices: 52923223--52923388 Score: 107
Period size: 40 Copynumber: 4.2 Consensus size: 40
52923213 AAGGTGTCGT
* * * * * **
52923223 TAATGGTCGACCTATAGAGGCGTTTTTCAAGAAGCGCTGC
1 TAATGCTCGACCTATAGCGGCATTTTTCAAAAAGCACCAC
* * * * * ****
52923263 CAAAGCTCGACCTATAGCGGCGTCTTTCAAGAAGCGTTGC
1 TAATGCTCGACCTATAGCGGCATTTTTCAAAAAGCACCAC
* * * * * ** *
52923303 CAAAGCTCGACCTATAGCGTCATTTTTCATAAGGTGCCGC
1 TAATGCTCGACCTATAGCGGCATTTTTCAAAAAGCACCAC
*
52923343 TAATGCTCGATCTATAGCGGCATTTTTCAAAAAGCACCAC
1 TAATGCTCGACCTATAGCGGCATTTTTCAAAAAGCACCAC
52923383 TAATGC
1 TAATGC
52923389 CACGGCATTG
Statistics
Matches: 102, Mismatches: 24, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
40 102 1.00
ACGTcount: A:0.27, C:0.25, G:0.22, T:0.27
Consensus pattern (40 bp):
TAATGCTCGACCTATAGCGGCATTTTTCAAAAAGCACCAC
Found at i:52923515 original size:40 final size:39
Alignment explanation
Indices: 52923416--52923544 Score: 114
Period size: 40 Copynumber: 3.2 Consensus size: 39
52923406 TTTTTTTGCG
* * * * *
52923416 GCGTTTTTCAAAAAGCACCGCTAATACTCGACCTAGAGC
1 GCGTTTTTAAAAAAGCGCCGCTAATGCTCGATCTATAGC
* * * *
52923455 GACATTTTTTTAAGAAGCGCCGCTAATGCTTGATCTATAGC
1 G-C-GTTTTTAAAAAAGCGCCGCTAATGCTCGATCTATAGC
* *
52923496 AGCGTTTTTAAAAAAGCGCCACTAAAGCTCGATCTATAGTC
1 -GCGTTTTTAAAAAAGCGCCGCTAATGCTCGATCTATAG-C
*
52923537 GTGTTTTT
1 GCGTTTTT
52923545 TATCTAAACG
Statistics
Matches: 71, Mismatches: 15, Indels: 7
0.76 0.16 0.08
Matches are distributed among these distances:
39 1 0.01
40 38 0.54
41 31 0.44
42 1 0.01
ACGTcount: A:0.29, C:0.22, G:0.19, T:0.31
Consensus pattern (39 bp):
GCGTTTTTAAAAAAGCGCCGCTAATGCTCGATCTATAGC
Found at i:52929142 original size:56 final size:56
Alignment explanation
Indices: 52929075--52929186 Score: 197
Period size: 56 Copynumber: 2.0 Consensus size: 56
52929065 TTCACATTTT
* *
52929075 TTATTGATAACAATATCGATACCGATTAAATTAATACTCAATCAACTACAACTCAA
1 TTATTGATAACAATATCAATACCGATTAAATTAAGACTCAATCAACTACAACTCAA
*
52929131 TTATTGATAACAATATCAATACCGATTAAATTAAGACTCAATCAACTACCACTCAA
1 TTATTGATAACAATATCAATACCGATTAAATTAAGACTCAATCAACTACAACTCAA
52929187 AGCAAACAAC
Statistics
Matches: 53, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
56 53 1.00
ACGTcount: A:0.45, C:0.21, G:0.05, T:0.29
Consensus pattern (56 bp):
TTATTGATAACAATATCAATACCGATTAAATTAAGACTCAATCAACTACAACTCAA
Found at i:52933459 original size:19 final size:18
Alignment explanation
Indices: 52933420--52933461 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 18
52933410 GTTTAAGAAC
52933420 TTTTAAATTATTTTTACTA
1 TTTTAAATTATTTTTA-TA
52933439 TTTTAAATATAATTTTT-TA
1 TTTTAAAT-T-ATTTTTATA
52933458 TTTT
1 TTTT
52933462 TATATAATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
19 14 0.67
20 1 0.05
21 6 0.29
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (18 bp):
TTTTAAATTATTTTTATA
Found at i:52938190 original size:25 final size:25
Alignment explanation
Indices: 52938131--52938193 Score: 65
Period size: 25 Copynumber: 2.5 Consensus size: 25
52938121 ATACATGTAT
* * *
52938131 GCTCATTCGAGCTATGAATCGGTAT
1 GCTCATACGAGTTATGAATCGGTAA
* *
52938156 GCTC-TCACGAGTTTTGAATTGGTAA
1 GCTCAT-ACGAGTTATGAATCGGTAA
52938181 GCTCATACGAGTT
1 GCTCATACGAGTT
52938194 GAGAATCAAT
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
24 1 0.03
25 29 0.94
26 1 0.03
ACGTcount: A:0.24, C:0.19, G:0.24, T:0.33
Consensus pattern (25 bp):
GCTCATACGAGTTATGAATCGGTAA
Found at i:52938206 original size:25 final size:25
Alignment explanation
Indices: 52938178--52938244 Score: 75
Period size: 25 Copynumber: 2.7 Consensus size: 25
52938168 TTTGAATTGG
*
52938178 TAAGCTCATACGAGTTG-AGAATCAA
1 TAAGCTCATACGAGCTGCA-AATCAA
* *
52938203 TAAGCTC-TCATGAGCTGCAAATCGA
1 TAAGCTCAT-ACGAGCTGCAAATCAA
52938228 TAAGCTCATACGAGCTG
1 TAAGCTCATACGAGCTG
52938245 TGGTGTGTCC
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
24 1 0.03
25 32 0.91
26 2 0.06
ACGTcount: A:0.34, C:0.21, G:0.21, T:0.24
Consensus pattern (25 bp):
TAAGCTCATACGAGCTGCAAATCAA
Found at i:52950767 original size:28 final size:28
Alignment explanation
Indices: 52950716--52950769 Score: 83
Period size: 28 Copynumber: 1.9 Consensus size: 28
52950706 GGGAAAAGAA
*
52950716 ATTCCAGGATACTCGGGCTCGAGAAGTC
1 ATTCCAGGATACTCAGGCTCGAGAAGTC
52950744 ATTCCAGGATACTCAGGCGT-GAGAAG
1 ATTCCAGGATACTCAGGC-TCGAGAAG
52950770 GCTCCTTGGA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
28 23 0.96
29 1 0.04
ACGTcount: A:0.28, C:0.22, G:0.30, T:0.20
Consensus pattern (28 bp):
ATTCCAGGATACTCAGGCTCGAGAAGTC
Found at i:52959845 original size:46 final size:45
Alignment explanation
Indices: 52959778--52960205 Score: 224
Period size: 44 Copynumber: 9.8 Consensus size: 45
52959768 ATTATACAGG
*
52959778 TCTTATCTCCCTGAGATTACAGTGGAACAGACCAAAGAATTTCAGA
1 TCTTATCTCCCTGAGATTACAGTGGAACAGATCAAAGAA-TTCAGA
* * * *
52959824 TCTTATCTCCCTGAGATTACAGCGGAGCAGATCAAGGATAGT-A-A
1 TCTTATCTCCCTGAGATTACAGTGGAACAGATCAAAGA-ATTCAGA
* * * * * *
52959868 TCCTATCTCCTTGAGATTACAATGGAGCGGATTAAAG------GA
1 TCTTATCTCCCTGAGATTACAGTGGAACAGATCAAAGAATTCAGA
* * * *
52959907 TCTTATCTCTCTGA-AGTTACAGTAGAGA-AGATC--A-CA-TCAGG
1 TCTTATCTCCCTGAGA-TTACAGTGGA-ACAGATCAAAGAATTCAGA
*
52959948 TCTTATCTCCCTGAGATTACAGTGGAACAGACCAAAGAATTTCAGA
1 TCTTATCTCCCTGAGATTACAGTGGAACAGATCAAAGAA-TTCAGA
* * * *
52959994 TCTTATCTCCCTGAGATTACAGCGGAGCAGATCGAAG-A--CACTA
1 TCTTATCTCCCTGAGATTACAGTGGAACAGATCAAAGAATTCA-GA
* * * * **
52960037 TCCTATCTCCCTGA-AGTTACAGTGGAGCGGAT-TAA-AATAAGAGA
1 TCTTATCTCCCTGAGA-TTACAGTGGAACAGATCAAAGAAT-TCAGA
* * * *
52960081 TCTTATCTCCCTGAGATTACAGCGGAGCAGATCGAAG-A--CACTA
1 TCTTATCTCCCTGAGATTACAGTGGAACAGATCAAAGAATTCA-GA
* * * * **
52960124 TCCTATCTCCCTGA-AGTTACAGTGGAGCGGAT-TAA-AATAAGAGA
1 TCTTATCTCCCTGAGA-TTACAGTGGAACAGATCAAAGAAT-TCAGA
* * *
52960168 TCTTATCTCCCTGAGATTACAGCGGAGCAGATCGAAGA
1 TCTTATCTCCCTGAGATTACAGTGGAACAGATCAAAGA
52960206 CACTATCTTA
Statistics
Matches: 295, Mismatches: 53, Indels: 68
0.71 0.13 0.16
Matches are distributed among these distances:
37 1 0.00
38 1 0.00
39 23 0.08
40 1 0.00
41 27 0.09
42 12 0.04
43 57 0.19
44 88 0.30
45 11 0.04
46 73 0.25
47 1 0.00
ACGTcount: A:0.32, C:0.21, G:0.21, T:0.25
Consensus pattern (45 bp):
TCTTATCTCCCTGAGATTACAGTGGAACAGATCAAAGAATTCAGA
Found at i:52960058 original size:43 final size:43
Alignment explanation
Indices: 52959948--52960238 Score: 234
Period size: 43 Copynumber: 6.7 Consensus size: 43
52959938 TCACATCAGG
* * * * *
52959948 TCTTATCTCCCTGAGATTACAGTGGAACAGACCAAAGA-ATTTCAGA
1 TCTTATCTCCCTGAGATTACAGCGGAGCAGATCGAAGACA---C-TA
52959994 TCTTATCTCCCTGAGATTACAGCGGAGCAGATCGAAGACACTA
1 TCTTATCTCCCTGAGATTACAGCGGAGCAGATCGAAGACACTA
* * * * * * **
52960037 TCCTATCTCCCTGA-AGTTACAGTGGAGCGGAT-TAAAATAAGAGA
1 TCTTATCTCCCTGAGA-TTACAGCGGAGCAGATCGAAGA-CA-CTA
52960081 TCTTATCTCCCTGAGATTACAGCGGAGCAGATCGAAGACACTA
1 TCTTATCTCCCTGAGATTACAGCGGAGCAGATCGAAGACACTA
* * * * * * **
52960124 TCCTATCTCCCTGA-AGTTACAGTGGAGCGGAT-TAAAATAAGAGA
1 TCTTATCTCCCTGAGA-TTACAGCGGAGCAGATCGAAGA-CA-CTA
52960168 TCTTATCTCCCTGAGATTACAGCGGAGCAGATCGAAGACACTA
1 TCTTATCTCCCTGAGATTACAGCGGAGCAGATCGAAGACACTA
* *
52960211 TCTTATCTCCCCGA-AGTTACAGTGGAGC
1 TCTTATCTCCCTGAGA-TTACAGCGGAGC
52960239 GGATTAAAGG
Statistics
Matches: 194, Mismatches: 39, Indels: 27
0.75 0.15 0.10
Matches are distributed among these distances:
42 9 0.05
43 83 0.43
44 59 0.30
45 8 0.04
46 34 0.18
47 1 0.01
ACGTcount: A:0.31, C:0.23, G:0.21, T:0.25
Consensus pattern (43 bp):
TCTTATCTCCCTGAGATTACAGCGGAGCAGATCGAAGACACTA
Found at i:52960082 original size:87 final size:87
Alignment explanation
Indices: 52959991--52960283 Score: 497
Period size: 87 Copynumber: 3.4 Consensus size: 87
52959981 AAAGAATTTC
52959991 AGATCTTATCTCCCTGAGATTACAGCGGAGCAGATCGAAGACACTATCCTATCTCCCTGAAGTTA
1 AGATCTTATCTCCCTGAGATTACAGCGGAGCAGATCGAAGACACTATCCTATCTCCCTGAAGTTA
52960056 CAGTGGAGCGGATTAAAATAAG
66 CAGTGGAGCGGATTAAAATAAG
52960078 AGATCTTATCTCCCTGAGATTACAGCGGAGCAGATCGAAGACACTATCCTATCTCCCTGAAGTTA
1 AGATCTTATCTCCCTGAGATTACAGCGGAGCAGATCGAAGACACTATCCTATCTCCCTGAAGTTA
52960143 CAGTGGAGCGGATTAAAATAAG
66 CAGTGGAGCGGATTAAAATAAG
* *
52960165 AGATCTTATCTCCCTGAGATTACAGCGGAGCAGATCGAAGACACTATCTTATCTCCCCGAAGTTA
1 AGATCTTATCTCCCTGAGATTACAGCGGAGCAGATCGAAGACACTATCCTATCTCCCTGAAGTTA
52960230 CAGTGGAGCGGATT---A-AAG
66 CAGTGGAGCGGATTAAAATAAG
* * * *
52960248 -GATCTTATCTCTCTGAGGTTACAGCAGAGTAGATCG
1 AGATCTTATCTCCCTGAGATTACAGCGGAGCAGATCG
52960284 CTTCAAGTCT
Statistics
Matches: 200, Mismatches: 6, Indels: 5
0.95 0.03 0.02
Matches are distributed among these distances:
82 32 0.16
83 3 0.01
84 1 0.00
87 164 0.82
ACGTcount: A:0.31, C:0.22, G:0.23, T:0.25
Consensus pattern (87 bp):
AGATCTTATCTCCCTGAGATTACAGCGGAGCAGATCGAAGACACTATCCTATCTCCCTGAAGTTA
CAGTGGAGCGGATTAAAATAAG
Found at i:52960094 original size:44 final size:42
Alignment explanation
Indices: 52959991--52960271 Score: 187
Period size: 43 Copynumber: 6.6 Consensus size: 42
52959981 AAAGAATTTC
* * * * *
52959991 AGATCTTATCTCCCTG-AGATTACAGCGGAGCAGATCGAAGACA
1 AGATCTTATCTCCCTGAAG-TTACAGTGGAGCGGAT-TAAAAAA
** *
52960034 CTATCCTATCTCCCTGAAGTTACAGTGGAGCGGATTAAAATAA
1 AGATCTTATCTCCCTGAAGTTACAGTGGAGCGGATTAAAA-AA
* * * * *
52960077 GAGATCTTATCTCCCTG-AGATTACAGCGGAGCAGATCGAAGACA
1 -AGATCTTATCTCCCTGAAG-TTACAGTGGAGCGGAT-TAAAAAA
** *
52960121 CTATCCTATCTCCCTGAAGTTACAGTGGAGCGGATTAAAATAA
1 AGATCTTATCTCCCTGAAGTTACAGTGGAGCGGATTAAAA-AA
* * * * *
52960164 GAGATCTTATCTCCCTG-AGATTACAGCGGAGCAGATCGAAGACA
1 -AGATCTTATCTCCCTGAAG-TTACAGTGGAGCGGAT-TAAAAAA
** *
52960208 CTATCTTATCTCCCCGAAGTTACAGTGGAGCGGATT---AAA
1 AGATCTTATCTCCCTGAAGTTACAGTGGAGCGGATTAAAAAA
* * *
52960247 GGATCTTATCTCTCTGAGGTTACAG
1 AGATCTTATCTCCCTGAAGTTACAG
52960272 CAGAGTAGAT
Statistics
Matches: 183, Mismatches: 44, Indels: 26
0.72 0.17 0.10
Matches are distributed among these distances:
39 22 0.12
42 6 0.03
43 87 0.48
44 62 0.34
45 6 0.03
ACGTcount: A:0.31, C:0.22, G:0.22, T:0.25
Consensus pattern (42 bp):
AGATCTTATCTCCCTGAAGTTACAGTGGAGCGGATTAAAAAA
Found at i:52960196 original size:174 final size:170
Alignment explanation
Indices: 52959781--52960283 Score: 617
Period size: 174 Copynumber: 2.9 Consensus size: 170
52959771 ATACAGGTCT
**
52959781 TATCTCCCTGAGATTACAGTGGAACAGACCAAAGAATTTCAGATCTTATCTCCCTGAGATTACAG
1 TATCTCCCTGAGATTACAGTGGAACAGACCAAAGAATAACAGATCTTATCTCCCTGAGATTACAG
* * * *
52959846 CGGAGCAGATC-AAGGATAGTAATCCTATCTCCTTG-AGATTACAATGGAGCGGATTAAAGGATC
66 CGGAGCAGATCGAA-GACACT-ATCCTATCTCCCTGAAG-TTACAGTGGAGCGGATTAAAGGATC
* * * *
52959909 TTATCTCTCTGA-AGTTACAGTAGAGAAGATC-ACATCAGGTCT
128 TTATCTCTCTGAGA-TTACAGCAGAGAAGATCGACAACAGATCC
**
52959951 TATCTCCCTGAGATTACAGTGGAACAGACCAAAGAATTTCAGATCTTATCTCCCTGAGATTACAG
1 TATCTCCCTGAGATTACAGTGGAACAGACCAAAGAATAACAGATCTTATCTCCCTGAGATTACAG
52960016 CGGAGCAGATCGAAGACACTATCCTATCTCCCTGAAGTTACAGTGGAGCGGATTAAAATAAGAGA
66 CGGAGCAGATCGAAGACACTATCCTATCTCCCTGAAGTTACAGTGGAGCGGATT---A-AAG-GA
* * * *
52960081 TCTTATCTCCCTGAGATTACAGCGGAGCAGATCGA-AGACACTATCC
126 TCTTATCTCTCTGAGATTACAGCAGAGAAGATCGACA-ACA-GATCC
* * ** *
52960127 TATCTCCCTGA-AGTTACAGTGGAGCGGA-TTAA-AATAAGAGATCTTATCTCCCTGAGATTACA
1 TATCTCCCTGAGA-TTACAGTGGAACAGACCAAAGAATAACAGATCTTATCTCCCTGAGATTACA
* *
52960189 GCGGAGCAGATCGAAGACACTATCTTATCTCCCCGAAGTTACAGTGGAGCGGATTAAAGGATCTT
65 GCGGAGCAGATCGAAGACACTATCCTATCTCCCTGAAGTTACAGTGGAGCGGATTAAAGGATCTT
* *
52960254 ATCTCTCTGAGGTTACAGCAGAGTAGATCG
130 ATCTCTCTGAGATTACAGCAGAGAAGATCG
52960284 CTTCAAGTCT
Statistics
Matches: 296, Mismatches: 25, Indels: 25
0.86 0.07 0.07
Matches are distributed among these distances:
169 61 0.21
170 85 0.29
171 3 0.01
172 1 0.00
173 3 0.01
174 110 0.37
175 7 0.02
176 26 0.09
ACGTcount: A:0.32, C:0.21, G:0.21, T:0.26
Consensus pattern (170 bp):
TATCTCCCTGAGATTACAGTGGAACAGACCAAAGAATAACAGATCTTATCTCCCTGAGATTACAG
CGGAGCAGATCGAAGACACTATCCTATCTCCCTGAAGTTACAGTGGAGCGGATTAAAGGATCTTA
TCTCTCTGAGATTACAGCAGAGAAGATCGACAACAGATCC
Found at i:52960872 original size:46 final size:45
Alignment explanation
Indices: 52960805--52960893 Score: 169
Period size: 46 Copynumber: 2.0 Consensus size: 45
52960795 GCAGCTGTAC
52960805 AAGCCCAATCTGAACCAGCCCAAACCCAAGACCCAAAACAGACCCA
1 AAGCCCAATCTGAACCAGCCCAAACCCAAGA-CCAAAACAGACCCA
52960851 AAGCCCAATCTGAACCAGCCCAAACCCAAGACCAAAACAGACC
1 AAGCCCAATCTGAACCAGCCCAAACCCAAGACCAAAACAGACC
52960894 TAACCCCTAA
Statistics
Matches: 43, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
45 12 0.28
46 31 0.72
ACGTcount: A:0.44, C:0.40, G:0.11, T:0.04
Consensus pattern (45 bp):
AAGCCCAATCTGAACCAGCCCAAACCCAAGACCAAAACAGACCCA
Found at i:52970747 original size:19 final size:19
Alignment explanation
Indices: 52970711--52970748 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
52970701 AATAAATTGA
*
52970711 TAAATTAGTTTCTTTACAT
1 TAAATTAGTTTCTATACAT
52970730 TAAATTAGTATT-TATACAT
1 TAAATTAGT-TTCTATACAT
52970749 AAGGTATAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 15 0.88
20 2 0.12
ACGTcount: A:0.37, C:0.08, G:0.05, T:0.50
Consensus pattern (19 bp):
TAAATTAGTTTCTATACAT
Found at i:52971913 original size:17 final size:16
Alignment explanation
Indices: 52971886--52971946 Score: 58
Period size: 16 Copynumber: 3.9 Consensus size: 16
52971876 ACTAAATTAA
52971886 AAGAGATGGAAAAAAG
1 AAGAGATGGAAAAAAG
*
52971902 AAGAGAATGG-AAAAAC
1 AAGAG-ATGGAAAAAAG
*
52971918 AA-AG--GGAGAAAAG
1 AAGAGATGGAAAAAAG
52971931 AAGAGAATGGAAAAAA
1 AAGAG-ATGGAAAAAA
52971947 AACGTTAAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 11
0.70 0.08 0.22
Matches are distributed among these distances:
12 2 0.06
13 6 0.17
14 2 0.06
15 2 0.06
16 12 0.34
17 11 0.31
ACGTcount: A:0.64, C:0.02, G:0.30, T:0.05
Consensus pattern (16 bp):
AAGAGATGGAAAAAAG
Found at i:52972565 original size:20 final size:20
Alignment explanation
Indices: 52972537--52972575 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
52972527 TTTAAACCCA
* *
52972537 ACTTTTCTCTCTAAATCCAC
1 ACTTCTCTCCCTAAATCCAC
*
52972557 ACTTCTCTCCCTAAGTCCA
1 ACTTCTCTCCCTAAATCCA
52972576 AAAAGGCCAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.23, C:0.38, G:0.03, T:0.36
Consensus pattern (20 bp):
ACTTCTCTCCCTAAATCCAC
Found at i:52982094 original size:16 final size:17
Alignment explanation
Indices: 52982073--52982106 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
52982063 CTCAGAGCTT
52982073 GGCTTG-TGTAGCTTAG
1 GGCTTGATGTAGCTTAG
52982089 GGCTTGACTGTAGCTTAG
1 GGCTTGA-TGTAGCTTAG
52982107 ATACGTGTCA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 6 0.38
18 10 0.62
ACGTcount: A:0.15, C:0.15, G:0.35, T:0.35
Consensus pattern (17 bp):
GGCTTGATGTAGCTTAG
Found at i:52987101 original size:41 final size:41
Alignment explanation
Indices: 52987052--52987179 Score: 229
Period size: 41 Copynumber: 3.1 Consensus size: 41
52987042 ATTAATCTCA
*
52987052 ATTTTTACTATATTCAAATGAAAAATTAGCACTTTAATATT
1 ATTTTTACTATATTCAAATAAAAAATTAGCACTTTAATATT
52987093 ATTTTTACTATATTCAAATAAAAAATTAGCACTTTAATATT
1 ATTTTTACTATATTCAAATAAAAAATTAGCACTTTAATATT
* *
52987134 AATTTTACTATATTCAAATAAAAAATTACCACTTTAATATT
1 ATTTTTACTATATTCAAATAAAAAATTAGCACTTTAATATT
52987175 ATTTT
1 ATTTT
52987180 GAATTTAGGG
Statistics
Matches: 83, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 83 1.00
ACGTcount: A:0.43, C:0.10, G:0.02, T:0.45
Consensus pattern (41 bp):
ATTTTTACTATATTCAAATAAAAAATTAGCACTTTAATATT
Found at i:52987162 original size:21 final size:21
Alignment explanation
Indices: 52987097--52987162 Score: 50
Period size: 21 Copynumber: 3.2 Consensus size: 21
52987087 AATATTATTT
52987097 TTACTATATTCAAATAAAAAA
1 TTACTATATTCAAATAAAAAA
* **
52987118 TTAGC-ACT-TT--AATATTAATT
1 TTA-CTA-TATTCAAATA-AAAAA
52987138 TTACTATATTCAAATAAAAAA
1 TTACTATATTCAAATAAAAAA
52987159 TTAC
1 TTAC
52987163 CACTTTAATA
Statistics
Matches: 32, Mismatches: 6, Indels: 14
0.62 0.12 0.27
Matches are distributed among these distances:
19 6 0.19
20 8 0.25
21 12 0.38
22 6 0.19
ACGTcount: A:0.48, C:0.11, G:0.02, T:0.39
Consensus pattern (21 bp):
TTACTATATTCAAATAAAAAA
Found at i:52987727 original size:19 final size:21
Alignment explanation
Indices: 52987691--52987729 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 21
52987681 GAGAGGGTTT
52987691 GGGTAAGATTTGTTTAGCCTG
1 GGGTAAGATTTGTTTAGCCTG
52987712 GGGTAAGA-TT-TTTAGCCT
1 GGGTAAGATTTGTTTAGCCT
52987730 ATGCCTGGCC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 8 0.44
20 2 0.11
21 8 0.44
ACGTcount: A:0.21, C:0.10, G:0.31, T:0.38
Consensus pattern (21 bp):
GGGTAAGATTTGTTTAGCCTG
Found at i:52988617 original size:2 final size:2
Alignment explanation
Indices: 52988610--52988634 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
52988600 CTATCACATT
52988610 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 T
52988635 GATTTGTGCT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:52988957 original size:52 final size:51
Alignment explanation
Indices: 52988866--52988963 Score: 117
Period size: 52 Copynumber: 1.9 Consensus size: 51
52988856 TGATTAATAT
*
52988866 TTTTATAATATTAAGTTAAAATTTTATTATTTATGAAAAATTAAAATGTAA
1 TTTTATAATATTAAGTTAAAATTTTATTATTTATGAAAAAATAAAATGTAA
* * * * *
52988917 TTTTATCATTATTAATTTATAATTTTA-TACTTTTTTAAAAAATAAAA
1 TTTTAT-AATATTAAGTTAAAATTTTATTA-TTTATGAAAAAATAAAA
52988964 AAATAAAATT
Statistics
Matches: 39, Mismatches: 6, Indels: 3
0.81 0.12 0.06
Matches are distributed among these distances:
51 8 0.21
52 31 0.79
ACGTcount: A:0.45, C:0.02, G:0.03, T:0.50
Consensus pattern (51 bp):
TTTTATAATATTAAGTTAAAATTTTATTATTTATGAAAAAATAAAATGTAA
Found at i:52992127 original size:27 final size:24
Alignment explanation
Indices: 52992097--52992145 Score: 71
Period size: 27 Copynumber: 1.9 Consensus size: 24
52992087 TAAATTATGC
52992097 TATTTATATTCTTAATTATATTATTTA
1 TATTTATATT-TT-ATT-TATTATTTA
52992124 TATTTATATTTTATTTATTATT
1 TATTTATATTTTATTTATTATT
52992146 GATTTAGGGA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
24 7 0.32
25 3 0.14
26 2 0.09
27 10 0.45
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (24 bp):
TATTTATATTTTATTTATTATTTA
Found at i:52992202 original size:21 final size:20
Alignment explanation
Indices: 52992176--52992215 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
52992166 AAAAATGAGG
*
52992176 TTATATTATAAACTAAGAGAA
1 TTATATAATAAAC-AAGAGAA
52992197 TTATATAATAAACAAGAGA
1 TTATATAATAAACAAGAGA
52992216 GAATAATAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.55, C:0.05, G:0.10, T:0.30
Consensus pattern (20 bp):
TTATATAATAAACAAGAGAA
Found at i:52996984 original size:3 final size:3
Alignment explanation
Indices: 52996976--52997003 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
52996966 CTTGGTACTT
52996976 TGA TGA TGA TGA TGA TGA TGA TGA TGA T
1 TGA TGA TGA TGA TGA TGA TGA TGA TGA T
52997004 AAAATTGAGC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.32, T:0.36
Consensus pattern (3 bp):
TGA
Found at i:53016806 original size:26 final size:26
Alignment explanation
Indices: 53016614--53016808 Score: 108
Period size: 26 Copynumber: 7.8 Consensus size: 26
53016604 TGGCTATCCG
*
53016614 GAGC-TCCTGATTA-ATGGCTCTTCGT
1 GAGCTTCCTG-TTATATGGCTCTTTGT
* * *
53016639 GAGTTTCCTGTT-TAAAGGCTCTTCGT
1 GAGCTTCCTGTTAT-ATGGCTCTTTGT
** * *
53016665 GAGCTTCCTGATTA-AAAGTTATTTGT
1 GAGCTTCCTG-TTATATGGCTCTTTGT
* * *
53016691 GAACTTCCTGAT-TATGGCTCTGTGT
1 GAGCTTCCTGTTATATGGCTCTTTGT
* **
53016716 GAG-TTCCTGTTATATAGC-C-CGGAT
1 GAGCTTCCTGTTATATGGCTCTTTG-T
* *
53016740 AAGCTTTCTG--ATA-GGCTCTTTGT
1 GAGCTTCCTGTTATATGGCTCTTTGT
*
53016763 GAGCTTCCCGATTA-ATGGCTCTTTGT
1 GAGCTTCCTG-TTATATGGCTCTTTGT
53016789 GAGCTTCCTGTTATATGGCT
1 GAGCTTCCTGTTATATGGCT
53016809 TGAGAGAGAA
Statistics
Matches: 126, Mismatches: 28, Indels: 31
0.68 0.15 0.17
Matches are distributed among these distances:
22 2 0.02
23 13 0.10
24 12 0.10
25 29 0.23
26 68 0.54
27 2 0.02
ACGTcount: A:0.18, C:0.19, G:0.23, T:0.39
Consensus pattern (26 bp):
GAGCTTCCTGTTATATGGCTCTTTGT
Found at i:53020856 original size:33 final size:34
Alignment explanation
Indices: 53020819--53020887 Score: 131
Period size: 33 Copynumber: 2.1 Consensus size: 34
53020809 ATCTTGATAT
53020819 GTCTGAACTGGAACTTGATA-TTTGATTTGATTA
1 GTCTGAACTGGAACTTGATATTTTGATTTGATTA
53020852 GTCTGAACTGGAACTTGATATTTTGATTTGATTA
1 GTCTGAACTGGAACTTGATATTTTGATTTGATTA
53020886 GT
1 GT
53020888 TCGACAAAGA
Statistics
Matches: 35, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
33 20 0.57
34 15 0.43
ACGTcount: A:0.26, C:0.09, G:0.22, T:0.43
Consensus pattern (34 bp):
GTCTGAACTGGAACTTGATATTTTGATTTGATTA
Found at i:53027724 original size:18 final size:18
Alignment explanation
Indices: 53027703--53027737 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
53027693 TTTAACTCCC
53027703 TATTTTAACTTAAATCCA
1 TATTTTAACTTAAATCCA
*
53027721 TATTTTCACTTAAATCC
1 TATTTTAACTTAAATCC
53027738 CTAAATTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.34, C:0.20, G:0.00, T:0.46
Consensus pattern (18 bp):
TATTTTAACTTAAATCCA
Found at i:53033018 original size:45 final size:45
Alignment explanation
Indices: 53032965--53033054 Score: 171
Period size: 45 Copynumber: 2.0 Consensus size: 45
53032955 TAACTGTGAA
*
53032965 GCGAATATTAAATTTAGCAACATTTATCCCAGGCTGCTAGATTTC
1 GCGAATATTAAATTTAGCAACATTTATCCCAGGCTGCTACATTTC
53033010 GCGAATATTAAATTTAGCAACATTTATCCCAGGCTGCTACATTTC
1 GCGAATATTAAATTTAGCAACATTTATCCCAGGCTGCTACATTTC
53033055 CAAGCTATAC
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 44 1.00
ACGTcount: A:0.31, C:0.21, G:0.14, T:0.33
Consensus pattern (45 bp):
GCGAATATTAAATTTAGCAACATTTATCCCAGGCTGCTACATTTC
Found at i:53033424 original size:38 final size:39
Alignment explanation
Indices: 53033381--53033459 Score: 142
Period size: 38 Copynumber: 2.1 Consensus size: 39
53033371 GAATCAGTTT
*
53033381 AATCATTTTTATATCATGAAAAG-CAAAAAAAAAAAAAA
1 AATCATTTTTATAACATGAAAAGCCAAAAAAAAAAAAAA
53033419 AATCATTTTTATAACATGAAAAGCCAAAAAAAAAAAAAA
1 AATCATTTTTATAACATGAAAAGCCAAAAAAAAAAAAAA
53033458 AA
1 AA
53033460 AGATACATAC
Statistics
Matches: 39, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
38 22 0.56
39 17 0.44
ACGTcount: A:0.65, C:0.09, G:0.05, T:0.22
Consensus pattern (39 bp):
AATCATTTTTATAACATGAAAAGCCAAAAAAAAAAAAAA
Found at i:53041662 original size:11 final size:11
Alignment explanation
Indices: 53041646--53041670 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
53041636 GTATCTACTA
53041646 AAACCTTCCTT
1 AAACCTTCCTT
53041657 AAACCTTCCTT
1 AAACCTTCCTT
53041668 AAA
1 AAA
53041671 TCTAAATGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.36, C:0.32, G:0.00, T:0.32
Consensus pattern (11 bp):
AAACCTTCCTT
Found at i:53042491 original size:27 final size:27
Alignment explanation
Indices: 53042460--53042512 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 27
53042450 CACAACAACT
*
53042460 AAAAATAGCATTTATGGCGAACTCTGA
1 AAAAATAACATTTATGGCGAACTCTGA
* *
53042487 AAAAATAACCTTTATGGCGTACTCTG
1 AAAAATAACATTTATGGCGAACTCTG
53042513 GATGAACAGA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.38, C:0.17, G:0.17, T:0.28
Consensus pattern (27 bp):
AAAAATAACATTTATGGCGAACTCTGA
Found at i:53045281 original size:18 final size:17
Alignment explanation
Indices: 53045258--53045296 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
53045248 TCTGTACAGT
*
53045258 ATGATTAGGAATGAATGA
1 ATGATTAGGAA-GAAAGA
*
53045276 ATGATTTGGAAGAAAGA
1 ATGATTAGGAAGAAAGA
53045293 ATGA
1 ATGA
53045297 AAGATTAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 9 0.47
18 10 0.53
ACGTcount: A:0.46, C:0.00, G:0.28, T:0.26
Consensus pattern (17 bp):
ATGATTAGGAAGAAAGA
Found at i:53047258 original size:19 final size:20
Alignment explanation
Indices: 53047234--53047277 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 20
53047224 CGTGAAAGTC
* *
53047234 TAATGCATATG-ATGCAATG
1 TAATGCAAATGCATGAAATG
53047253 TAATGCAAATGCATGAAATG
1 TAATGCAAATGCATGAAATG
53047273 -AATGC
1 TAATGC
53047278 CAAAAGAAAC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 15 0.68
20 7 0.32
ACGTcount: A:0.41, C:0.11, G:0.20, T:0.27
Consensus pattern (20 bp):
TAATGCAAATGCATGAAATG
Found at i:53053579 original size:16 final size:16
Alignment explanation
Indices: 53053537--53053579 Score: 68
Period size: 16 Copynumber: 2.7 Consensus size: 16
53053527 TTGTAATTGA
53053537 AGAGCTGTAATGGAAT
1 AGAGCTGTAATGGAAT
* *
53053553 AGCGCTATAATGGAAT
1 AGAGCTGTAATGGAAT
53053569 AGAGCTGTAAT
1 AGAGCTGTAAT
53053580 CAGTAATTCA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.37, C:0.09, G:0.28, T:0.26
Consensus pattern (16 bp):
AGAGCTGTAATGGAAT
Found at i:53066822 original size:3 final size:3
Alignment explanation
Indices: 53066811--53066877 Score: 82
Period size: 3 Copynumber: 22.3 Consensus size: 3
53066801 CAATAATACC
* * * *
53066811 AAT ACT AAT AAT AGT AA- AGAT GAT AAT AAT GAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT
53066856 AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT A
53066878 GCAAAGTACT
Statistics
Matches: 54, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
2 1 0.02
3 53 0.98
ACGTcount: A:0.61, C:0.01, G:0.06, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:53074049 original size:23 final size:21
Alignment explanation
Indices: 53073996--53074053 Score: 62
Period size: 23 Copynumber: 2.6 Consensus size: 21
53073986 ATATAATTAC
* *
53073996 TTAAAATTTTTAAATATTTTT
1 TTAATATTTTCAAATATTTTT
*
53074017 TTACTAATTTTCAATATATATTTT
1 TTAAT-ATTTTCAA-ATAT-TTTT
53074041 TTAATATTTTCAA
1 TTAATATTTTCAA
53074054 GTACTAACGT
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
21 3 0.10
22 7 0.23
23 12 0.40
24 8 0.27
ACGTcount: A:0.36, C:0.05, G:0.00, T:0.59
Consensus pattern (21 bp):
TTAATATTTTCAAATATTTTT
Found at i:53075672 original size:8 final size:8
Alignment explanation
Indices: 53075659--53075729 Score: 61
Period size: 7 Copynumber: 9.9 Consensus size: 8
53075649 GTCAAAAATA
53075659 ATTTTAAT
1 ATTTTAAT
53075667 ATTTTAAT
1 ATTTTAAT
53075675 A-TTTAAT
1 ATTTTAAT
53075682 -TTTATAAT
1 ATTT-TAAT
53075690 ATTTT-AT
1 ATTTTAAT
*
53075697 TTTTTAA-
1 ATTTTAAT
53075704 A-TTTAA-
1 ATTTTAAT
53075710 ATTTT-AT
1 ATTTTAAT
53075717 ATTTT--T
1 ATTTTAAT
53075723 ATTTTAA
1 ATTTTAA
53075730 ATAAACTTAA
Statistics
Matches: 53, Mismatches: 2, Indels: 16
0.75 0.03 0.23
Matches are distributed among these distances:
6 13 0.25
7 22 0.42
8 15 0.28
9 3 0.06
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (8 bp):
ATTTTAAT
Found at i:53075681 original size:15 final size:15
Alignment explanation
Indices: 53075657--53075729 Score: 68
Period size: 15 Copynumber: 5.2 Consensus size: 15
53075647 AAGTCAAAAA
53075657 TAAT-TTTAATATTT
1 TAATATTTAATATTT
53075671 TAATATTTAAT-TTT
1 TAATATTTAATATTT
* *
53075685 ATAATATTTTATTTTT
1 -TAATATTTAATATTT
53075701 TAA-ATTTAA-ATTT
1 TAATATTTAATATTT
*
53075714 T-ATATTT-TTATTT
1 TAATATTTAATATTT
53075727 TAA
1 TAA
53075730 ATAAACTTAA
Statistics
Matches: 49, Mismatches: 4, Indels: 12
0.75 0.06 0.18
Matches are distributed among these distances:
12 1 0.02
13 13 0.27
14 13 0.27
15 19 0.39
16 3 0.06
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (15 bp):
TAATATTTAATATTT
Found at i:53075702 original size:23 final size:23
Alignment explanation
Indices: 53075658--53075722 Score: 73
Period size: 23 Copynumber: 2.9 Consensus size: 23
53075648 AGTCAAAAAT
* *
53075658 AATTT-TAATATTTTAATATTTA
1 AATTTATAATATTTTATTTTTTA
*
53075680 ATTTTATAATATTTTATTTTTTA
1 AATTTATAATATTTTATTTTTTA
53075703 AATTTA-AAT-TTTATATTTTT
1 AATTTATAATATTT-TATTTTT
53075723 ATTTTAAATA
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
21 3 0.08
22 14 0.38
23 20 0.54
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (23 bp):
AATTTATAATATTTTATTTTTTA
Found at i:53079352 original size:34 final size:35
Alignment explanation
Indices: 53079308--53079374 Score: 100
Period size: 34 Copynumber: 1.9 Consensus size: 35
53079298 GAGTAAAATA
*
53079308 TTTTCCGTAAAATGATTT-CTAGAAAATGTTTTAC
1 TTTTCCGTAAAATGATTTACTAGAAAATATTTTAC
* *
53079342 TTTTCTGTAAAATGATTTACTGGAAAATATTTT
1 TTTTCCGTAAAATGATTTACTAGAAAATATTTT
53079375 CTGGTGTTTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 17 0.59
35 12 0.41
ACGTcount: A:0.33, C:0.09, G:0.12, T:0.46
Consensus pattern (35 bp):
TTTTCCGTAAAATGATTTACTAGAAAATATTTTAC
Found at i:53085831 original size:23 final size:24
Alignment explanation
Indices: 53085785--53085831 Score: 60
Period size: 25 Copynumber: 2.0 Consensus size: 24
53085775 ATTTGGATAC
*
53085785 ATATATATATTTAATAATTTTTAAA
1 ATATATATATTTAATAA-TGTTAAA
*
53085810 ATATATATATTTGATAA-GTTAA
1 ATATATATATTTAATAATGTTAA
53085832 TAGATAAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 4 0.20
25 16 0.80
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (24 bp):
ATATATATATTTAATAATGTTAAA
Found at i:53094699 original size:3 final size:3
Alignment explanation
Indices: 53094691--53094715 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
53094681 TTCCATCACC
53094691 TTG TTG TTG TTG TTG TTG TTG TTG T
1 TTG TTG TTG TTG TTG TTG TTG TTG T
53094716 AACTTAGAGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.00, C:0.00, G:0.32, T:0.68
Consensus pattern (3 bp):
TTG
Found at i:53108694 original size:20 final size:21
Alignment explanation
Indices: 53108665--53108738 Score: 57
Period size: 20 Copynumber: 3.7 Consensus size: 21
53108655 TTTATTTTAA
*
53108665 AAAAACTATT-AAAATATTAT
1 AAAAATTATTAAAAATATTAT
* * *
53108685 AAAAATTATTGAAACT-TGAT
1 AAAAATTATTAAAAATATTAT
* *
53108705 GAAAACTT-TTAAAAAAATTAT
1 -AAAAATTATTAAAAATATTAT
53108726 AAAAA-TATTAAAA
1 AAAAATTATTAAAA
53108739 CTTTTAAATA
Statistics
Matches: 41, Mismatches: 9, Indels: 8
0.71 0.16 0.14
Matches are distributed among these distances:
19 1 0.02
20 27 0.66
21 13 0.32
ACGTcount: A:0.59, C:0.04, G:0.04, T:0.32
Consensus pattern (21 bp):
AAAAATTATTAAAAATATTAT
Found at i:53108740 original size:40 final size:40
Alignment explanation
Indices: 53108666--53108741 Score: 109
Period size: 40 Copynumber: 1.9 Consensus size: 40
53108656 TTATTTTAAA
* *
53108666 AAAACTATTAAAATATTATAAAAATTATTGAAACTTGATG
1 AAAACTATTAAAAAATTATAAAAATTATTAAAACTTGATG
*
53108706 AAAACTTTTAAAAAAATTATAAAAA-TATTAAAACTT
1 AAAACTATT-AAAAAATTATAAAAATTATTAAAACTT
53108742 TTAAATAATT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
40 18 0.56
41 14 0.44
ACGTcount: A:0.57, C:0.05, G:0.04, T:0.34
Consensus pattern (40 bp):
AAAACTATTAAAAAATTATAAAAATTATTAAAACTTGATG
Found at i:53110156 original size:24 final size:23
Alignment explanation
Indices: 53110105--53110157 Score: 70
Period size: 23 Copynumber: 2.3 Consensus size: 23
53110095 TATAAATTTG
*
53110105 AAATTTAATCTTTGTATTTTTTA
1 AAATTTAATCTTTCTATTTTTTA
* *
53110128 GAATTTAATTTTTCTATTTTTTTA
1 AAATTTAATCTTTCTA-TTTTTTA
53110152 AAATTT
1 AAATTT
53110158 TAAAATTAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
23 13 0.52
24 12 0.48
ACGTcount: A:0.30, C:0.04, G:0.04, T:0.62
Consensus pattern (23 bp):
AAATTTAATCTTTCTATTTTTTA
Found at i:53110358 original size:7 final size:7
Alignment explanation
Indices: 53110346--53110380 Score: 61
Period size: 7 Copynumber: 4.9 Consensus size: 7
53110336 AAGTCAAGGT
53110346 TGGCAAA
1 TGGCAAA
53110353 TGGCAAA
1 TGGCAAA
53110360 TGGCAAA
1 TGGCAAA
53110367 TGGCAAA
1 TGGCAAA
53110374 CTGGCAA
1 -TGGCAA
53110381 TGATATATTA
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 21 0.78
8 6 0.22
ACGTcount: A:0.40, C:0.17, G:0.29, T:0.14
Consensus pattern (7 bp):
TGGCAAA
Found at i:53111157 original size:3 final size:3
Alignment explanation
Indices: 53111149--53111173 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
53111139 ATCAATACCT
53111149 TCA TCA TCA TCA TCA TCA TCA TCA T
1 TCA TCA TCA TCA TCA TCA TCA TCA T
53111174 AGTCAACCCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.32, G:0.00, T:0.36
Consensus pattern (3 bp):
TCA
Found at i:53130999 original size:16 final size:16
Alignment explanation
Indices: 53130978--53131046 Score: 129
Period size: 16 Copynumber: 4.2 Consensus size: 16
53130968 TTTGGTTCGC
53130978 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
53130994 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
53131010 TGTATTGGGATTAGAGG
1 TGTATT-GGATTAGAGG
53131027 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
53131043 TGTA
1 TGTA
53131047 ATAGCTAATC
Statistics
Matches: 52, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
16 36 0.69
17 16 0.31
ACGTcount: A:0.25, C:0.00, G:0.38, T:0.38
Consensus pattern (16 bp):
TGTATTGGATTAGAGG
Found at i:53131024 original size:33 final size:32
Alignment explanation
Indices: 53130978--53131046 Score: 129
Period size: 33 Copynumber: 2.1 Consensus size: 32
53130968 TTTGGTTCGC
53130978 TGTATTGGATTAGAGGTGTATTGGATTAGAGG
1 TGTATTGGATTAGAGGTGTATTGGATTAGAGG
53131010 TGTATTGGGATTAGAGGTGTATTGGATTAGAGG
1 TGTATT-GGATTAGAGGTGTATTGGATTAGAGG
53131043 TGTA
1 TGTA
53131047 ATAGCTAATC
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
32 6 0.17
33 30 0.83
ACGTcount: A:0.25, C:0.00, G:0.38, T:0.38
Consensus pattern (32 bp):
TGTATTGGATTAGAGGTGTATTGGATTAGAGG
Found at i:53131111 original size:44 final size:45
Alignment explanation
Indices: 53131027--53131117 Score: 121
Period size: 45 Copynumber: 2.0 Consensus size: 45
53131017 GGATTAGAGG
* * *
53131027 TGTATTGGATTAGAGGTGTAATAGCTAATCCACTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGCTAATCCACTGTTTGGTTGAA
***
53131072 TGTAATGGAATAGAGGCGTAATAG-TAATCTTGTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGCTAATCCACTGTTTGGTTGAA
53131116 TG
1 TG
53131118 AAATAGAGGT
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
44 19 0.47
45 21 0.52
ACGTcount: A:0.27, C:0.07, G:0.29, T:0.37
Consensus pattern (45 bp):
TGTAATGGAATAGAGGCGTAATAGCTAATCCACTGTTTGGTTGAA
Found at i:53131134 original size:39 final size:42
Alignment explanation
Indices: 53131037--53131140 Score: 115
Period size: 44 Copynumber: 2.5 Consensus size: 42
53131027 TGTATTGGAT
53131037 TAGAGGTGTAATAGCTAATCCACTGTTTGGTTGAATGTAATGGAA
1 TAGAGGTGTAATAGCTAATCCACTGTTTGGTTGAATG-AA--GAA
* ***
53131082 TAGAGGCGTAATAG-TAATCTTGTGTTTGGTTGAATG-A-AA
1 TAGAGGTGTAATAGCTAATCCACTGTTTGGTTGAATGAAGAA
53131121 TAGAGGTGTAATAGCATAAT
1 TAGAGGTGTAATAGC-TAAT
53131141 GGAAAAAACT
Statistics
Matches: 52, Mismatches: 5, Indels: 8
0.80 0.08 0.12
Matches are distributed among these distances:
39 15 0.29
41 4 0.08
42 1 0.02
44 19 0.37
45 13 0.25
ACGTcount: A:0.33, C:0.07, G:0.27, T:0.34
Consensus pattern (42 bp):
TAGAGGTGTAATAGCTAATCCACTGTTTGGTTGAATGAAGAA
Found at i:53131303 original size:18 final size:17
Alignment explanation
Indices: 53131282--53131316 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
53131272 TTATTATTAA
*
53131282 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
53131300 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
53131317 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:53131402 original size:120 final size:120
Alignment explanation
Indices: 53131265--53131706 Score: 866
Period size: 120 Copynumber: 3.7 Consensus size: 120
53131255 ATCATATTTA
53131265 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
53131330 TATTCTTATATTAATTTACTGAAATCATAATATATGATACTGTAAAATATAAATT
66 TATTCTTATATTAATTTACTGAAATCATAATATATGATACTGTAAAATATAAATT
*
53131385 AACATAATTATTATTAAATATATTTTAATTAAACTATATAATTTAATAAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
53131450 TATTCTTATATTAATTTACTGAAATCATAATATATGATACTGTAAAATATAAATT
66 TATTCTTATATTAATTTACTGAAATCATAATATATGATACTGTAAAATATAAATT
53131505 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
53131570 TATTCTTATATTAATTTACTGAAATCATAATATATGATACTGTAAAATATAAATT
66 TATTCTTATATTAATTTACTGAAATCATAATATATGATACTGTAAAATATAAATT
*
53131625 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATCAA
1 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
53131690 TATTCTTATATTAATTT
66 TATTCTTATATTAATTT
53131707 TTTCATTTAA
Statistics
Matches: 319, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
120 319 1.00
ACGTcount: A:0.48, C:0.05, G:0.02, T:0.45
Consensus pattern (120 bp):
AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
TATTCTTATATTAATTTACTGAAATCATAATATATGATACTGTAAAATATAAATT
Found at i:53131543 original size:18 final size:17
Alignment explanation
Indices: 53131522--53131556 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
53131512 TTATTATTAA
*
53131522 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
53131540 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
53131557 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:53131663 original size:18 final size:17
Alignment explanation
Indices: 53131642--53131676 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
53131632 TTATTATTAA
*
53131642 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
53131660 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
53131677 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:53136694 original size:7 final size:7
Alignment explanation
Indices: 53136684--53136713 Score: 60
Period size: 7 Copynumber: 4.3 Consensus size: 7
53136674 TTATTATTTA
53136684 ATTATAT
1 ATTATAT
53136691 ATTATAT
1 ATTATAT
53136698 ATTATAT
1 ATTATAT
53136705 ATTATAT
1 ATTATAT
53136712 AT
1 AT
53136714 GTTATTATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (7 bp):
ATTATAT
Found at i:53136710 original size:19 final size:20
Alignment explanation
Indices: 53136688--53136732 Score: 51
Period size: 19 Copynumber: 2.4 Consensus size: 20
53136678 TATTTAATTA
53136688 TATATTAT-ATATTATATAT
1 TATATTATGATATTATATAT
* *
53136707 TATA-TATGTTATTATTTAT
1 TATATTATGATATTATATAT
53136726 TAT-TTAT
1 TATATTAT
53136733 TTTAAATTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
18 3 0.14
19 19 0.86
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (20 bp):
TATATTATGATATTATATAT
Found at i:53136725 original size:7 final size:7
Alignment explanation
Indices: 53136673--53136733 Score: 56
Period size: 7 Copynumber: 8.9 Consensus size: 7
53136663 AAATAAAATT
53136673 TTTATTA
1 TTTATTA
53136680 TTTAATTA
1 TTT-ATTA
*
53136688 TATATTA
1 TTTATTA
*
53136695 TATATTA
1 TTTATTA
*
53136702 TATATTA
1 TTTATTA
53136709 --TA-TA
1 TTTATTA
53136713 TGTTATTA
1 T-TTATTA
53136721 TTTATTA
1 TTTATTA
53136728 TTTATT
1 TTTATT
53136734 TTAAATTTAA
Statistics
Matches: 48, Mismatches: 1, Indels: 10
0.81 0.02 0.17
Matches are distributed among these distances:
4 2 0.04
5 2 0.04
7 35 0.73
8 9 0.19
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (7 bp):
TTTATTA
Found at i:53145533 original size:160 final size:157
Alignment explanation
Indices: 53145269--53145585 Score: 571
Period size: 160 Copynumber: 2.0 Consensus size: 157
53145259 AGTTCCCAGT
*
53145269 GATTGATGTTATCAGGACTCTAGCTTTGCAGCTTAGCAAAATATTTTTGAGAGGTTTAGGAAGAG
1 GATTGATGTTATCAAGACTCTAGCTTTGCAGCTTAGCAAAATATTTTTGAGAGGTTTAGGAAGAG
*
53145334 ATTTTGAAGCTATGCTGTGAACGCCGAAATAGTTATTTCATCTTATATCTGTTTATATCCTGTAT
66 ATTTTGAAGCTATGCTGTGAACGCCAAAATAGTTATTTCATCTTATATCTGTTTATATCCTGTAT
53145399 ACAAAACTTGAATATAAATAATCACTATCG
131 ACAAAACTT---TATAAATAATCACTATCG
53145429 GATTGATGTTATCAAGACTCTAGCTTTGCAGCTTAGCAAAATATTTTTGAGAGGTTTAGGAAGAG
1 GATTGATGTTATCAAGACTCTAGCTTTGCAGCTTAGCAAAATATTTTTGAGAGGTTTAGGAAGAG
* *
53145494 GTTTTGAAGCTATGCTGTGAATGCCAAAATAGTTATTTCATCTTATATCTGTTTATATCCTGTAT
66 ATTTTGAAGCTATGCTGTGAACGCCAAAATAGTTATTTCATCTTATATCTGTTTATATCCTGTAT
53145559 ACAAAACTTTATAAATAATCACTATCG
131 ACAAAACTTTATAAATAATCACTATCG
53145586 CCTCCAAAAT
Statistics
Matches: 153, Mismatches: 4, Indels: 3
0.96 0.03 0.02
Matches are distributed among these distances:
157 18 0.12
160 135 0.88
ACGTcount: A:0.32, C:0.14, G:0.18, T:0.37
Consensus pattern (157 bp):
GATTGATGTTATCAAGACTCTAGCTTTGCAGCTTAGCAAAATATTTTTGAGAGGTTTAGGAAGAG
ATTTTGAAGCTATGCTGTGAACGCCAAAATAGTTATTTCATCTTATATCTGTTTATATCCTGTAT
ACAAAACTTTATAAATAATCACTATCG
Found at i:53151672 original size:30 final size:30
Alignment explanation
Indices: 53151650--53151706 Score: 82
Period size: 29 Copynumber: 1.9 Consensus size: 30
53151640 TTAATATTTT
*
53151650 TTTTATA-ATTCTTAATCATTTTAA-AATAA
1 TTTTATATATTCTTAA-AATTTTAATAATAA
53151679 TTTTATATATTCTTAAAATTTTAATAAT
1 TTTTATATATTCTTAAAATTTTAATAAT
53151707 TCTTTAAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
29 14 0.56
30 11 0.44
ACGTcount: A:0.40, C:0.05, G:0.00, T:0.54
Consensus pattern (30 bp):
TTTTATATATTCTTAAAATTTTAATAATAA
Found at i:53151678 original size:21 final size:21
Alignment explanation
Indices: 53151654--53151697 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
53151644 TATTTTTTTT
53151654 ATAATTCTTA-ATCATT-TTAAA
1 ATAATT-TTATAT-ATTCTTAAA
53151675 ATAATTTTATATATTCTTAAA
1 ATAATTTTATATATTCTTAAA
53151696 AT
1 AT
53151698 TTTAATAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
20 6 0.29
21 15 0.71
ACGTcount: A:0.43, C:0.07, G:0.00, T:0.50
Consensus pattern (21 bp):
ATAATTTTATATATTCTTAAA
Found at i:53151700 original size:18 final size:19
Alignment explanation
Indices: 53151677--53151715 Score: 55
Period size: 18 Copynumber: 2.1 Consensus size: 19
53151667 ATTTTAAAAT
53151677 AATTTT-ATATATTC-TTAA
1 AATTTTAATA-ATTCTTTAA
53151695 AATTTTAATAATTCTTTAA
1 AATTTTAATAATTCTTTAA
53151714 AA
1 AA
53151716 AATCGCATTC
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 10 0.53
19 9 0.47
ACGTcount: A:0.44, C:0.05, G:0.00, T:0.51
Consensus pattern (19 bp):
AATTTTAATAATTCTTTAA
Found at i:53151717 original size:21 final size:21
Alignment explanation
Indices: 53151669--53151718 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 21
53151659 TCTTAATCAT
53151669 TTTAAAATAATTTTATATATTC
1 TTTAAAA-AATTTTATATATTC
53151691 -TT--AAAATTTTA-ATAATTC
1 TTTAAAAAATTTTATAT-ATTC
53151709 TTTAAAAAAT
1 TTTAAAAAAT
53151719 CGCATTCAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 9
0.73 0.00 0.27
Matches are distributed among these distances:
17 2 0.08
18 11 0.46
19 4 0.17
21 7 0.29
ACGTcount: A:0.46, C:0.04, G:0.00, T:0.50
Consensus pattern (21 bp):
TTTAAAAAATTTTATATATTC
Found at i:53159089 original size:8 final size:8
Alignment explanation
Indices: 53159076--53159104 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
53159066 TTTTAAATAA
53159076 TATTTTAT
1 TATTTTAT
53159084 TATTTTAT
1 TATTTTAT
53159092 TATTTTAT
1 TATTTTAT
53159100 TATTT
1 TATTT
53159105 AGTATATATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (8 bp):
TATTTTAT
Found at i:53161820 original size:8 final size:8
Alignment explanation
Indices: 53161807--53161835 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
53161797 TTTTAAATAA
53161807 TATTTTAT
1 TATTTTAT
53161815 TATTTTAT
1 TATTTTAT
53161823 TATTTTAT
1 TATTTTAT
53161831 TATTT
1 TATTT
53161836 AGTATATATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (8 bp):
TATTTTAT
Found at i:53165573 original size:23 final size:21
Alignment explanation
Indices: 53165515--53165570 Score: 60
Period size: 20 Copynumber: 2.6 Consensus size: 21
53165505 ACTGATCAGT
* *
53165515 ATACGACACATAAGTGCTTGA
1 ATACGACACATAAGTACCTGA
*
53165536 A-ACGACACACGAAGTACCTGAA
1 ATACGACACA-TAAGTACCTG-A
53165558 ATACGACACATAA
1 ATACGACACATAA
53165571 AGTGACTGAT
Statistics
Matches: 28, Mismatches: 4, Indels: 5
0.76 0.11 0.14
Matches are distributed among these distances:
20 8 0.29
21 8 0.29
22 4 0.14
23 8 0.29
ACGTcount: A:0.45, C:0.23, G:0.16, T:0.16
Consensus pattern (21 bp):
ATACGACACATAAGTACCTGA
Found at i:53165579 original size:23 final size:22
Alignment explanation
Indices: 53165515--53165579 Score: 57
Period size: 23 Copynumber: 3.0 Consensus size: 22
53165505 ACTGATCAGT
53165515 ATACGACACATAAGTG-CTTG-A
1 ATACGACACATAAGTGAC-TGAA
*
53165536 A-ACGACACACGAAGT-ACCTGAA
1 ATACGACACA-TAAGTGA-CTGAA
53165558 ATACGACACATAAAGTGACTGA
1 ATACGACACAT-AAGTGACTGA
53165580 TCGACAAAGT
Statistics
Matches: 35, Mismatches: 2, Indels: 12
0.71 0.04 0.24
Matches are distributed among these distances:
20 8 0.23
21 7 0.20
22 3 0.09
23 16 0.46
24 1 0.03
ACGTcount: A:0.43, C:0.22, G:0.18, T:0.17
Consensus pattern (22 bp):
ATACGACACATAAGTGACTGAA
Found at i:53165751 original size:30 final size:30
Alignment explanation
Indices: 53165698--53165756 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
53165688 ACTTTCATAA
* * *
53165698 CAAATTTAAGATCACTATTCAATTTCAATTT
1 CAAATTCAAGATCAATATACAA-TTCAATTT
53165729 CAAATTCAA-ATCAATATACAATTCAATT
1 CAAATTCAAGATCAATATACAATTCAATT
53165757 ATACTTACAC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 7 0.28
30 10 0.40
31 8 0.32
ACGTcount: A:0.44, C:0.17, G:0.02, T:0.37
Consensus pattern (30 bp):
CAAATTCAAGATCAATATACAATTCAATTT
Found at i:53166783 original size:25 final size:25
Alignment explanation
Indices: 53166753--53166824 Score: 85
Period size: 25 Copynumber: 3.0 Consensus size: 25
53166743 AGCACTCTCT
* *
53166753 CGAGCCATATAACAGGATGCTCATG
1 CGAGCCATATAACAGGAAGCTCATC
* * *
53166778 TGAGCCATGTAACAGGAAGCTTATC
1 CGAGCCATATAACAGGAAGCTCATC
53166803 CGAG-C-TATAACAGGAAGCTCAT
1 CGAGCCATATAACAGGAAGCTCAT
53166825 TAAGCTTAAC
Statistics
Matches: 39, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
23 15 0.38
24 1 0.03
25 23 0.59
ACGTcount: A:0.33, C:0.22, G:0.24, T:0.21
Consensus pattern (25 bp):
CGAGCCATATAACAGGAAGCTCATC
Found at i:53167110 original size:24 final size:25
Alignment explanation
Indices: 53167054--53167121 Score: 77
Period size: 24 Copynumber: 2.8 Consensus size: 25
53167044 ATACCGATTG
* *
53167054 GGATGCTCGCAAGAACTATATAACG
1 GGATGCTCGCAAGAGCTATATAACA
*
53167079 GGAAGCTCG-AGAGAGCT-TATAACA
1 GGATGCTCGCA-AGAGCTATATAACA
*
53167103 GGATGCTCGTAAGAGCTAT
1 GGATGCTCGCAAGAGCTAT
53167122 GGTGTGTCCG
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
24 21 0.58
25 15 0.42
ACGTcount: A:0.34, C:0.18, G:0.28, T:0.21
Consensus pattern (25 bp):
GGATGCTCGCAAGAGCTATATAACA
Found at i:53167350 original size:25 final size:25
Alignment explanation
Indices: 53167311--53167358 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
53167301 TATACACAAA
53167311 TATATCAGGAAGCTCACAAATAGTC
1 TATATCAGGAAGCTCACAAATAGTC
* * *
53167336 TATATCATGACGCTCATAAATAG
1 TATATCAGGAAGCTCACAAATAG
53167359 CTGCGGTATG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.40, C:0.19, G:0.15, T:0.27
Consensus pattern (25 bp):
TATATCAGGAAGCTCACAAATAGTC
Found at i:53167667 original size:410 final size:410
Alignment explanation
Indices: 53166907--53167721 Score: 1364
Period size: 410 Copynumber: 2.0 Consensus size: 410
53166897 GAACCACATT
* *
53166907 AGGAAGCTCACAAGGAGCCTATATCATAACGCTCATAAATAGCTGTGGTATGTTCGCATTATATG
1 AGGAAGCTCACAAAGAGCCTATATCATAACGCTCATAAATAGCTGCGGTATGTTCGCATTATATG
* *
53166972 TAGGATCCATACTGATATTATAACATGACGCTCACAAAGAGCTGCGGTATGACTGCAACACATGC
66 TAGGATCCATACCGATATTATAACAGGACGCTCACAAAGAGCTGCGGTATGACTGCAACACATGC
* *
53167037 AGGGTCAATACCGATTGGGATGCTCGCAAGAACTATATAACGGGAAGCTCGAGAGAGCTTATAAC
131 AGGGTCAATACCGATTGGGATGCTCGCAAGAACCATATAACGGAAAGCTCGAGAGAGCTTATAAC
* * *
53167102 AGGATGCTCGTAAGAGCTATGGTGTGTCCGCAACATATGCAGAACCACAACCAATATGGGAAATC
196 AGGATGCTCGTAAGAGCTATGGTGTGTCCACAACATATGCAGAACCACAACCAATACGAGAAATC
* *
53167167 CTGTTCCCATCGAATTTCATTAATTCAAACAGGACATATTACTTATTAGGCATTATTGAACATGA
261 ATGTTCCCATCGAATTTCATTAATTCAAACAGGACATATTACTTATCAGGCATTATTGAACATGA
*
53167232 GATCAATTTCATATTTTCATAGCATTTATATAATTCACATATACACGACGTTCAATTCAAACATA
326 GATCAATTTCATATTTTCATAGCATTTATACAATTCACATATACACGACGTTCAATTCAAACATA
*
53167297 TAAATATACACAAATATATC
391 CAAATATACACAAATATATC
* * *
53167317 AGGAAGCTCACAAATAGTCTATATCATGACGCTCATAAATAGCTGCGGTATG-TCTGCATTATAT
1 AGGAAGCTCACAAAGAGCCTATATCATAACGCTCATAAATAGCTGCGGTATGTTC-GCATTATAT
* *
53167381 GTAGGATCCATACCGATCA-TATAACAGGACGCTCACAAAGAGCTGTGGTATGACTGCAACATAT
65 GTAGGATCCATACCGAT-ATTATAACAGGACGCTCACAAAGAGCTGCGGTATGACTGCAACACAT
* * *
53167445 GCAGGGTCAATACCGATTGGGATGCTTGCAATAACCATATAATGGAAAGCTCGAGAGAGCTTATA
129 GCAGGGTCAATACCGATTGGGATGCTCGCAAGAACCATATAACGGAAAGCTCGAGAGAGCTTATA
*
53167510 ACAGGATGCTCGTAAGAGCTATGGTGTGTTCACAACATATGCAGAACCACAACCAATACGAGAAA
194 ACAGGATGCTCGTAAGAGCTATGGTGTGTCCACAACATATGCAGAACCACAACCAATACGAGAAA
* * *
53167575 TCATGTTTCCATCGAATTTCATTAATTCAAACGGGACATATTACTTATCGGGCATTATTGAACAT
259 TCATGTTCCCATCGAATTTCATTAATTCAAACAGGACATATTACTTATCAGGCATTATTGAACAT
*
53167640 GTGATCAATTTCATATTTTCATAGCATTTATACAATTCACATATACACGACGTTCAATTCAAACA
324 GAGATCAATTTCATATTTTCATAGCATTTATACAATTCACATATACACGACGTTCAATTCAAACA
53167705 TACAAATATACACAAAT
389 TACAAATATACACAAAT
53167722 TAGTTACACA
Statistics
Matches: 377, Mismatches: 26, Indels: 4
0.93 0.06 0.01
Matches are distributed among these distances:
409 2 0.01
410 374 0.99
411 1 0.00
ACGTcount: A:0.35, C:0.20, G:0.18, T:0.27
Consensus pattern (410 bp):
AGGAAGCTCACAAAGAGCCTATATCATAACGCTCATAAATAGCTGCGGTATGTTCGCATTATATG
TAGGATCCATACCGATATTATAACAGGACGCTCACAAAGAGCTGCGGTATGACTGCAACACATGC
AGGGTCAATACCGATTGGGATGCTCGCAAGAACCATATAACGGAAAGCTCGAGAGAGCTTATAAC
AGGATGCTCGTAAGAGCTATGGTGTGTCCACAACATATGCAGAACCACAACCAATACGAGAAATC
ATGTTCCCATCGAATTTCATTAATTCAAACAGGACATATTACTTATCAGGCATTATTGAACATGA
GATCAATTTCATATTTTCATAGCATTTATACAATTCACATATACACGACGTTCAATTCAAACATA
CAAATATACACAAATATATC
Found at i:53173284 original size:52 final size:52
Alignment explanation
Indices: 53173227--53173331 Score: 183
Period size: 52 Copynumber: 2.0 Consensus size: 52
53173217 AAAACTTTGT
53173227 TAGGTGCTGGTAGATTGGATTGAGTTTTTAGATTATGGTTAGAATTGATTAG
1 TAGGTGCTGGTAGATTGGATTGAGTTTTTAGATTATGGTTAGAATTGATTAG
* * *
53173279 TAGGTGTTGGTAGATTGGATTGGGTTTTTAGGTTATGGTTAGAATTGATTAG
1 TAGGTGCTGGTAGATTGGATTGAGTTTTTAGATTATGGTTAGAATTGATTAG
53173331 T
1 T
53173332 CTAATTCAAA
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 50 1.00
ACGTcount: A:0.23, C:0.01, G:0.32, T:0.44
Consensus pattern (52 bp):
TAGGTGCTGGTAGATTGGATTGAGTTTTTAGATTATGGTTAGAATTGATTAG
Found at i:53173317 original size:28 final size:28
Alignment explanation
Indices: 53173234--53173317 Score: 74
Period size: 28 Copynumber: 3.1 Consensus size: 28
53173224 TGTTAGGTGC
*
53173234 TGGTAGATTGGATTGAGTTTTTAGATTA
1 TGGTAGATTGGATTGAGTTTTTAGGTTA
53173262 TGGTTAGAATT-GATT-AG----TAGGTGT-
1 TGG-TAG-ATTGGATTGAGTTTTTAGGT-TA
*
53173286 TGGTAGATTGGATTGGGTTTTTAGGTTA
1 TGGTAGATTGGATTGAGTTTTTAGGTTA
53173314 TGGT
1 TGGT
53173318 TAGAATTGAT
Statistics
Matches: 44, Mismatches: 2, Indels: 20
0.67 0.03 0.30
Matches are distributed among these distances:
22 3 0.07
23 7 0.16
24 8 0.18
25 1 0.02
27 1 0.02
28 14 0.32
29 7 0.16
30 3 0.07
ACGTcount: A:0.21, C:0.00, G:0.33, T:0.45
Consensus pattern (28 bp):
TGGTAGATTGGATTGAGTTTTTAGGTTA
Found at i:53191156 original size:23 final size:24
Alignment explanation
Indices: 53191100--53191157 Score: 61
Period size: 22 Copynumber: 2.6 Consensus size: 24
53191090 TAGTGAAAAT
53191100 AATTA-CTCTCAATTTGGAATCTA
1 AATTAGCTCTCAATTTGGAATCTA
* *
53191123 AATTAG-T-TCAATTTTGAAT-TC
1 AATTAGCTCTCAATTTGGAATCTA
*
53191144 AATTGGCTCTCAAT
1 AATTAGCTCTCAAT
53191158 AATACTACTA
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
21 6 0.21
22 12 0.41
23 11 0.38
ACGTcount: A:0.33, C:0.16, G:0.10, T:0.41
Consensus pattern (24 bp):
AATTAGCTCTCAATTTGGAATCTA
Found at i:53192292 original size:23 final size:24
Alignment explanation
Indices: 53192244--53192292 Score: 57
Period size: 23 Copynumber: 2.1 Consensus size: 24
53192234 AAAATCAGAT
*
53192244 AATTACTTAATTTTTTATTAATTA
1 AATTACTTAATTTTTTATTAAATA
*
53192268 AATTA-TTTATTTTTT-TCTAAATA
1 AATTACTTAATTTTTTAT-TAAATA
53192291 AA
1 AA
53192293 GTAAAATATA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
22 1 0.05
23 16 0.73
24 5 0.23
ACGTcount: A:0.39, C:0.04, G:0.00, T:0.57
Consensus pattern (24 bp):
AATTACTTAATTTTTTATTAAATA
Found at i:53210529 original size:27 final size:27
Alignment explanation
Indices: 53210478--53210532 Score: 69
Period size: 27 Copynumber: 2.0 Consensus size: 27
53210468 CATTCCTCTA
53210478 AAACCCTCGGTTTTCCATATATATTTT
1 AAACCCTCGGTTTTCCATATATATTTT
*
53210505 AAACCCT-GGATTGTTCCAT-TGTATTTT
1 AAACCCTCGG-TT-TTCCATATATATTTT
53210532 A
1 A
53210533 TACCATGCGG
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
26 2 0.08
27 17 0.68
28 6 0.24
ACGTcount: A:0.25, C:0.20, G:0.11, T:0.44
Consensus pattern (27 bp):
AAACCCTCGGTTTTCCATATATATTTT
Found at i:53213092 original size:20 final size:19
Alignment explanation
Indices: 53213058--53213096 Score: 60
Period size: 20 Copynumber: 2.0 Consensus size: 19
53213048 GAGTTTAGAG
*
53213058 TTTATGATTTTATTATTTA
1 TTTATAATTTTATTATTTA
53213077 TTTATAATTATTATTATTTA
1 TTTATAATT-TTATTATTTA
53213097 GTTGTGCTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 8 0.44
20 10 0.56
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.67
Consensus pattern (19 bp):
TTTATAATTTTATTATTTA
Found at i:53223441 original size:13 final size:12
Alignment explanation
Indices: 53223417--53223446 Score: 51
Period size: 13 Copynumber: 2.4 Consensus size: 12
53223407 AGAAAAGAAC
53223417 AAATATATATAT
1 AAATATATATAT
53223429 AAATATAATATAT
1 AAATAT-ATATAT
53223442 AAATA
1 AAATA
53223447 AACTATGGGA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 6 0.35
13 11 0.65
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (12 bp):
AAATATATATAT
Found at i:53225307 original size:100 final size:100
Alignment explanation
Indices: 53225203--53225790 Score: 899
Period size: 100 Copynumber: 5.9 Consensus size: 100
53225193 TGCAATGTTG
* * * * *
53225203 GGGAAACTAGATCCGCCGTCGTAGCTTCAATCTGTTCCACCGCACCG-TCAGGGAAGTAAGATCT
1 GGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCCGCTGCACTGCT-AAGGAAGTAAGATCT
53225267 GCCGTTGTGGCTTCAATCTTTTTAATTGCAATATCA
65 GCCGTTGTGGCTTCAATCTTTTTAATTGCAATATCA
* * * * *
53225303 GGGAAACCAGATCTGCCGTCGTAGGTTCAATGTGTTCCGCGGCACTGCTAAGGAAGTAAGATTTG
1 GGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCCGCTGCACTGCTAAGGAAGTAAGATCTG
*
53225368 CCGTTGTGGCTTCAATCTTTTTAATTGCAATGTCA
66 CCGTTGTGGCTTCAATCTTTTTAATTGCAATATCA
* * * * * ** * *
53225403 GGAAAACTAGATCCACCGTCGTAGTTTCAATCTATTCCATTGCGCTGCTAAGGAAGTAAGATTTG
1 GGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCCGCTGCACTGCTAAGGAAGTAAGATCTG
53225468 CCGTTGTGGCTTCAATCTTTTTAATTGCAATATCA
66 CCGTTGTGGCTTCAATCTTTTTAATTGCAATATCA
* * *
53225503 GGGAAACCAGATCCACCGTCGTAGCTTCAATCTATTCCGCTGCACTACTAAGGAAGTAAGATCTG
1 GGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCCGCTGCACTGCTAAGGAAGTAAGATCTG
53225568 CCGTTGTGGCTTCAATCTTTTTAATTGCAATATCA
66 CCGTTGTGGCTTCAATCTTTTTAATTGCAATATCA
* *
53225603 GGGAAACCAGATCTGCCGTCGTAGCTTCAATCTGTTCCGCTGCACTGCTAAGGAAGTAAGATCCG
1 GGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCCGCTGCACTGCTAAGGAAGTAAGATCTG
*
53225668 TCGTTGTGGCTTCAATCTTTTTAATTGCAATATCA
66 CCGTTGTGGCTTCAATCTTTTTAATTGCAATATCA
* *
53225703 GGGAAACCAGATCTGCCGTCGTAGCTTCAATCTGTTCCGCTGCACTGCTAAGGAAGTAAGATCCG
1 GGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCCGCTGCACTGCTAAGGAAGTAAGATCTG
*
53225768 CCGTTGTGGCTTTAATCTTTTTA
66 CCGTTGTGGCTTCAATCTTTTTA
53225791 CTTTTCAACC
Statistics
Matches: 449, Mismatches: 38, Indels: 2
0.92 0.08 0.00
Matches are distributed among these distances:
100 448 1.00
101 1 0.00
ACGTcount: A:0.24, C:0.23, G:0.22, T:0.31
Consensus pattern (100 bp):
GGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCCGCTGCACTGCTAAGGAAGTAAGATCTG
CCGTTGTGGCTTCAATCTTTTTAATTGCAATATCA
Found at i:53225765 original size:50 final size:50
Alignment explanation
Indices: 53225211--53225788 Score: 288
Period size: 50 Copynumber: 11.6 Consensus size: 50
53225201 TGGGGAAACT
* * ** * *
53225211 AGATCCGCCGTCGTAGCTTCAATCTGTTCCACCGCACCG-TCAGGGAAGTA
1 AGATCTGCCGTCGTAGCTTCAATCTTTTCCATTGCACTGCT-AAGGAAGTA
* * ** * * * ***
53225261 AGATCTGCCGTTGTGGCTTCAATCTTTTTAATTGCAAT-ATCAGGGAAACC
1 AGATCTGCCGTCGTAGCTTCAATCTTTTCCATTGCACTGCT-AAGGAAGTA
* * * ***
53225311 AGATCTGCCGTCGTAGGTTCAATGTGTTCCGCGGCACTGCTAAGGAAGTA
1 AGATCTGCCGTCGTAGCTTCAATCTTTTCCATTGCACTGCTAAGGAAGTA
* * * ** * * *
53225361 AGATTTGCCGTTGTGGCTTCAATCTTTTTAATTGCAATG-TCAGGAA-AA
1 AGATCTGCCGTCGTAGCTTCAATCTTTTCCATTGCACTGCTAAGGAAGTA
** * * *
53225409 CTAGATCCACCGTCGTAGTTTCAATCTATTCCATTGCGCTGCTAAGGAAGTA
1 --AGATCTGCCGTCGTAGCTTCAATCTTTTCCATTGCACTGCTAAGGAAGTA
* * * ** * * * ***
53225461 AGATTTGCCGTTGTGGCTTCAATCTTTTTAATTGCAAT-ATCAGGGAAACC
1 AGATCTGCCGTCGTAGCTTCAATCTTTTCCATTGCACTGCT-AAGGAAGTA
** * ** *
53225511 AGATCCACCGTCGTAGCTTCAATCTATTCCGCTGCACTACTAAGGAAGTA
1 AGATCTGCCGTCGTAGCTTCAATCTTTTCCATTGCACTGCTAAGGAAGTA
* * ** * * * ***
53225561 AGATCTGCCGTTGTGGCTTCAATCTTTTTAATTGCAAT-ATCAGGGAAACC
1 AGATCTGCCGTCGTAGCTTCAATCTTTTCCATTGCACTGCT-AAGGAAGTA
* **
53225611 AGATCTGCCGTCGTAGCTTCAATCTGTTCCGCTGCACTGCTAAGGAAGTA
1 AGATCTGCCGTCGTAGCTTCAATCTTTTCCATTGCACTGCTAAGGAAGTA
* * * * ** * * * ***
53225661 AGATCCGTCGTTGTGGCTTCAATCTTTTTAATTGCAAT-ATCAGGGAAACC
1 AGATCTGCCGTCGTAGCTTCAATCTTTTCCATTGCACTGCT-AAGGAAGTA
* **
53225711 AGATCTGCCGTCGTAGCTTCAATCTGTTCCGCTGCACTGCTAAGGAAGTA
1 AGATCTGCCGTCGTAGCTTCAATCTTTTCCATTGCACTGCTAAGGAAGTA
* * * *
53225761 AGATCCGCCGTTGTGGCTTTAATCTTTT
1 AGATCTGCCGTCGTAGCTTCAATCTTTT
53225789 TACTTTTCAA
Statistics
Matches: 365, Mismatches: 151, Indels: 24
0.68 0.28 0.04
Matches are distributed among these distances:
48 1 0.00
49 9 0.02
50 344 0.94
51 10 0.03
52 1 0.00
ACGTcount: A:0.24, C:0.23, G:0.22, T:0.31
Consensus pattern (50 bp):
AGATCTGCCGTCGTAGCTTCAATCTTTTCCATTGCACTGCTAAGGAAGTA
Found at i:53233859 original size:20 final size:20
Alignment explanation
Indices: 53233834--53233873 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
53233824 TAAAGGTCTT
53233834 TAATGCATATAATGCGATGC
1 TAATGCATATAATGCGATGC
*
53233854 TAATGCATATGATGCGATGC
1 TAATGCATATAATGCGATGC
53233874 ATGAGGTGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.33, C:0.15, G:0.23, T:0.30
Consensus pattern (20 bp):
TAATGCATATAATGCGATGC
Found at i:53243617 original size:22 final size:22
Alignment explanation
Indices: 53243583--53243627 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
53243573 GGCTTCAAAA
53243583 TTCAATTTCATACCTAAGTTTT
1 TTCAATTTCATACCTAAGTTTT
* * * *
53243605 TTCATTTTGATACTTGAGTTTT
1 TTCAATTTCATACCTAAGTTTT
53243627 T
1 T
53243628 ATTTTTTCTA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.22, C:0.13, G:0.09, T:0.56
Consensus pattern (22 bp):
TTCAATTTCATACCTAAGTTTT
Found at i:53250042 original size:40 final size:40
Alignment explanation
Indices: 53249991--53250077 Score: 115
Period size: 40 Copynumber: 2.2 Consensus size: 40
53249981 AATTATGGAA
* * *
53249991 TACTGAATATTGTTTTG-AGTACTG-AGTTGAATTGTGAAGT
1 TACTGAATATTGTTATGTA-TACTGCA-TTGAACTGTGAAAT
53250031 TACTGAATATTGTTATGTATACTGCATTGAACTGTGAAAT
1 TACTGAATATTGTTATGTATACTGCATTGAACTGTGAAAT
53250071 TACTGAA
1 TACTGAA
53250078 GTAATGAATT
Statistics
Matches: 42, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
40 40 0.95
41 2 0.05
ACGTcount: A:0.31, C:0.08, G:0.21, T:0.40
Consensus pattern (40 bp):
TACTGAATATTGTTATGTATACTGCATTGAACTGTGAAAT
Found at i:53250335 original size:33 final size:33
Alignment explanation
Indices: 53250283--53250359 Score: 118
Period size: 33 Copynumber: 2.3 Consensus size: 33
53250273 CGACTACTGT
* *
53250283 TACTGTTACCGATTTGGCACTTTGTGTGTCGAA
1 TACTGTTACTGATTCGGCACTTTGTGTGTCGAA
*
53250316 TACTGTTACTGATTCGGCACTTTGTTTGTCGAA
1 TACTGTTACTGATTCGGCACTTTGTGTGTCGAA
*
53250349 TACTATTACTG
1 TACTGTTACTG
53250360 TTACTGTTAC
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 40 1.00
ACGTcount: A:0.19, C:0.18, G:0.21, T:0.42
Consensus pattern (33 bp):
TACTGTTACTGATTCGGCACTTTGTGTGTCGAA
Found at i:53250367 original size:45 final size:46
Alignment explanation
Indices: 53250316--53250505 Score: 237
Period size: 45 Copynumber: 4.2 Consensus size: 46
53250306 GTGTGTCGAA
* * *
53250316 TACTGTTACT-GATTCGGCACTTTGTTTGTCGAATACTATTACTGT
1 TACTGTTACTAGATTCGACACTTTGTGTGTCGAATACTATTACCGT
* * *
53250361 TACTGTTAC-CGATTCGACACTTTGTGTATCGAATACTGTTACCGT
1 TACTGTTACTAGATTCGACACTTTGTGTGTCGAATACTATTACCGT
* * *
53250406 TACTGTTA-TCGATTCGACACTTTGTGTGCCGAATACTGTTACCG-
1 TACTGTTACTAGATTCGACACTTTGTGTGTCGAATACTATTACCGT
* * *
53250450 TACTGTTA-TAGATTCGACACTTTGTGCGTTGAATACTATTACTGT
1 TACTGTTACTAGATTCGACACTTTGTGTGTCGAATACTATTACCGT
53250495 TACTGTTACTA
1 TACTGTTACTA
53250506 CTACCGTTAC
Statistics
Matches: 128, Mismatches: 13, Indels: 7
0.86 0.09 0.05
Matches are distributed among these distances:
44 38 0.30
45 88 0.69
46 2 0.02
ACGTcount: A:0.22, C:0.19, G:0.18, T:0.41
Consensus pattern (46 bp):
TACTGTTACTAGATTCGACACTTTGTGTGTCGAATACTATTACCGT
Found at i:53250485 original size:89 final size:90
Alignment explanation
Indices: 53250316--53250504 Score: 247
Period size: 89 Copynumber: 2.1 Consensus size: 90
53250306 GTGTGTCGAA
* * * * *
53250316 TACTGTTACTGATTCGGCACTTTGTTTGTCGAATACTATTACTGTTACTGTTACCGATTCGACAC
1 TACTGTTACTGATTCGACACTTTGTGTGCCGAATACTATTACCGTTACTGTTACAGATTCGACAC
* *
53250381 TTTGTGTATCGAATACTGTTACCGT
66 TTTGTGCATCGAATACTATTACCGT
* *
53250406 TACTGTTA-TCGATTCGACACTTTGTGTGCCGAATACTGTTACCG-TACTGTTATAGATTCGACA
1 TACTGTTACT-GATTCGACACTTTGTGTGCCGAATACTATTACCGTTACTGTTACAGATTCGACA
* * *
53250469 CTTTGTGCGTTGAATACTATTACTGT
65 CTTTGTGCATCGAATACTATTACCGT
53250495 TACTGTTACT
1 TACTGTTACT
53250505 ACTACCGTTA
Statistics
Matches: 85, Mismatches: 12, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
89 47 0.55
90 38 0.45
ACGTcount: A:0.22, C:0.20, G:0.18, T:0.41
Consensus pattern (90 bp):
TACTGTTACTGATTCGACACTTTGTGTGCCGAATACTATTACCGTTACTGTTACAGATTCGACAC
TTTGTGCATCGAATACTATTACCGT
Found at i:53250514 original size:18 final size:19
Alignment explanation
Indices: 53250483--53250523 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 19
53250473 GTGCGTTGAA
* *
53250483 TACTATTACTGTTACTG-T
1 TACTACTACCGTTACTGAT
53250501 TACTACTACCGTTACTGAT
1 TACTACTACCGTTACTGAT
53250520 TACT
1 TACT
53250524 GTTTAGGTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 15 0.75
19 5 0.25
ACGTcount: A:0.24, C:0.22, G:0.10, T:0.44
Consensus pattern (19 bp):
TACTACTACCGTTACTGAT
Done.