Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A05
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: 100714657
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 3970000 characters in sequence are not A, C, G, or T
File 165 of 318
Found at i:52199178 original size:20 final size:20
Alignment explanation
Indices: 52199153--52199219 Score: 109
Period size: 20 Copynumber: 3.4 Consensus size: 20
52199143 GATATGATAT
*
52199153 ACATGAT-TGATATGATATGC
1 ACATGATATG-TATGAAATGC
52199173 ACATGATATGTATGAAATGC
1 ACATGATATGTATGAAATGC
52199193 ACATGATATGTATGAAATGC
1 ACATGATATGTATGAAATGC
52199213 ACATGAT
1 ACATGAT
52199220 GTATTCATAA
Statistics
Matches: 45, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
20 43 0.96
21 2 0.04
ACGTcount: A:0.39, C:0.10, G:0.19, T:0.31
Consensus pattern (20 bp):
ACATGATATGTATGAAATGC
Found at i:52199305 original size:26 final size:26
Alignment explanation
Indices: 52199269--52199429 Score: 233
Period size: 26 Copynumber: 6.3 Consensus size: 26
52199259 GAGGAAGTGC
*
52199269 AAAAGGGCTTACGCCCCAGTTTATTG
1 AAAAGGGCTTATGCCCCAGTTTATTG
52199295 AAAAGGGCTTATGCCCCAGTTTATTG
1 AAAAGGGCTTATGCCCCAGTTTATTG
**
52199321 AAAAGGGCTTATGCCCCAGTTTACCG
1 AAAAGGGCTTATGCCCCAGTTTATTG
52199347 AAAAGGGCTTATGCCCCAGTTTATTG
1 AAAAGGGCTTATGCCCCAGTTTATTG
**
52199373 AAAAGGGCTT-TGCCCCAGTTTACCG
1 AAAAGGGCTTATGCCCCAGTTTATTG
52199398 AAAA-GGCTT-TGCCCCAG-TTATT-
1 AAAAGGGCTTATGCCCCAGTTTATTG
52199420 AAAAGAGGCT
1 AAAAG-GGCT
52199430 AGGCCTCCAG
Statistics
Matches: 124, Mismatches: 9, Indels: 6
0.89 0.06 0.04
Matches are distributed among these distances:
22 4 0.03
23 3 0.02
24 17 0.14
25 17 0.14
26 83 0.67
ACGTcount: A:0.28, C:0.22, G:0.23, T:0.27
Consensus pattern (26 bp):
AAAAGGGCTTATGCCCCAGTTTATTG
Found at i:52199621 original size:42 final size:42
Alignment explanation
Indices: 52199562--52199653 Score: 139
Period size: 42 Copynumber: 2.2 Consensus size: 42
52199552 TAGTCTTCCC
* ** *
52199562 AAATGGGCTTGCATACATTCATTGGTATTTCATATGATATTG
1 AAATGGGCTTGCATACATCCATTGACATTACATATGATATTG
*
52199604 AAATGGGCTTGCATACATCCATTGACATTACATGTGATATTG
1 AAATGGGCTTGCATACATCCATTGACATTACATATGATATTG
52199646 AAATGGGC
1 AAATGGGC
52199654 CTATGGGCCA
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 45 1.00
ACGTcount: A:0.30, C:0.14, G:0.21, T:0.35
Consensus pattern (42 bp):
AAATGGGCTTGCATACATCCATTGACATTACATATGATATTG
Found at i:52202008 original size:27 final size:27
Alignment explanation
Indices: 52201988--52202079 Score: 112
Period size: 27 Copynumber: 3.4 Consensus size: 27
52201978 ATTACCAAAG
* *
52201988 TACCCCCGATTTATAAAATTACCGTTC
1 TACCCTCGATTTATAAAATTACCATTC
* * *
52202015 TACCATCGATTTATAGAATTACCATTT
1 TACCCTCGATTTATAAAATTACCATTC
* * *
52202042 TACCCTCGATTTACAAAATTACCGTTT
1 TACCCTCGATTTATAAAATTACCATTC
52202069 TACCCTCGATT
1 TACCCTCGATT
52202080 GTGAAATTAC
Statistics
Matches: 56, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 56 1.00
ACGTcount: A:0.29, C:0.26, G:0.08, T:0.37
Consensus pattern (27 bp):
TACCCTCGATTTATAAAATTACCATTC
Found at i:52202141 original size:27 final size:27
Alignment explanation
Indices: 52202111--52202224 Score: 102
Period size: 27 Copynumber: 4.2 Consensus size: 27
52202101 AATAGGGTAG
*
52202111 AATTACCAAAACACCCCTAGTTTGTAA
1 AATTACCAAAACACCCCTAATTTGTAA
* ** *** *
52202138 AATTACCAAAATACCATTGGCTTGTGA
1 AATTACCAAAACACCCCTAATTTGTAA
* * *
52202165 AATTACCGAAACATCCTTAATTTGTAA
1 AATTACCAAAACACCCCTAATTTGTAA
* **
52202192 AATTACCAAAATACCCCTAATTTACAA
1 AATTACCAAAACACCCCTAATTTGTAA
52202219 AATTAC
1 AATTAC
52202225 AGAAATATTC
Statistics
Matches: 67, Mismatches: 20, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
27 67 1.00
ACGTcount: A:0.42, C:0.22, G:0.07, T:0.29
Consensus pattern (27 bp):
AATTACCAAAACACCCCTAATTTGTAA
Found at i:52202150 original size:54 final size:54
Alignment explanation
Indices: 52202078--52202208 Score: 126
Period size: 54 Copynumber: 2.4 Consensus size: 54
52202068 TTACCCTCGA
* ** *
52202078 TTGTGAAATTACTGAAATACCCCAATAGG-GT-AGAATTACCAAAACACCCCTAGT
1 TTGTAAAATTACCAAAATACCCC-ATAGGTGTGA-AATTACCAAAACACCCCTAAT
* * * *
52202132 TTGTAAAATTACCAAAATA--CCATTGGCTTGTGAAATTACCGAAACATCCTTAAT
1 TTGTAAAATTACCAAAATACCCCATAGG--TGTGAAATTACCAAAACACCCCTAAT
52202186 TTGTAAAATTACCAAAATACCCC
1 TTGTAAAATTACCAAAATACCCC
52202209 TAATTTACAA
Statistics
Matches: 63, Mismatches: 8, Indels: 10
0.78 0.10 0.12
Matches are distributed among these distances:
51 4 0.06
52 2 0.03
54 54 0.86
55 1 0.02
56 2 0.03
ACGTcount: A:0.40, C:0.21, G:0.11, T:0.27
Consensus pattern (54 bp):
TTGTAAAATTACCAAAATACCCCATAGGTGTGAAATTACCAAAACACCCCTAAT
Found at i:52202325 original size:27 final size:26
Alignment explanation
Indices: 52202295--52202354 Score: 75
Period size: 27 Copynumber: 2.3 Consensus size: 26
52202285 ACCCCTAATA
52202295 GGTAAAAAGACCGTAAAGCCCCTGTAG
1 GGTAAAAAGACCGTAAA-CCCCTGTAG
** * *
52202322 GGTAAAGTGACCGTAAACCCTTGTAT
1 GGTAAAAAGACCGTAAACCCCTGTAG
52202348 GGTAAAA
1 GGTAAAA
52202355 TGATGAATAC
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
26 13 0.46
27 15 0.54
ACGTcount: A:0.37, C:0.18, G:0.25, T:0.20
Consensus pattern (26 bp):
GGTAAAAAGACCGTAAACCCCTGTAG
Found at i:52203089 original size:20 final size:21
Alignment explanation
Indices: 52203054--52203110 Score: 77
Period size: 20 Copynumber: 2.9 Consensus size: 21
52203044 TGATACGTGG
52203054 GATATGATAT--ACATGAT-T
1 GATATGATATGCACATGATAT
52203072 GATATGATATGCACATGATAT
1 GATATGATATGCACATGATAT
*
52203093 G-TATGAAATGCACATGAT
1 GATATGATATGCACATGAT
52203111 GTATTCATAA
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
18 10 0.29
20 23 0.66
21 2 0.06
ACGTcount: A:0.39, C:0.09, G:0.19, T:0.33
Consensus pattern (21 bp):
GATATGATATGCACATGATAT
Found at i:52203189 original size:26 final size:26
Alignment explanation
Indices: 52203160--52203320 Score: 233
Period size: 26 Copynumber: 6.3 Consensus size: 26
52203150 GAGGAAGTGC
52203160 AAAAGGGCTTATGCCCCAGTTTATTG
1 AAAAGGGCTTATGCCCCAGTTTATTG
52203186 AAAAGGGCTTATGCCCCAGTTTATTG
1 AAAAGGGCTTATGCCCCAGTTTATTG
**
52203212 AAAAGGGCTTATGCCCCAGTTTACCG
1 AAAAGGGCTTATGCCCCAGTTTATTG
52203238 AAAAGGGCTTATGCCCCAGTTTATTG
1 AAAAGGGCTTATGCCCCAGTTTATTG
* **
52203264 AAAAGGGATT-TGCCCCAGTTTACCG
1 AAAAGGGCTTATGCCCCAGTTTATTG
52203289 AAAA-GGCTT-TGCCCCAG-TTATT-
1 AAAAGGGCTTATGCCCCAGTTTATTG
52203311 AAAAGAGGCT
1 AAAAG-GGCT
52203321 AGGCCTGAGT
Statistics
Matches: 123, Mismatches: 10, Indels: 6
0.88 0.07 0.04
Matches are distributed among these distances:
22 4 0.03
23 3 0.02
24 16 0.13
25 17 0.14
26 83 0.67
ACGTcount: A:0.29, C:0.21, G:0.23, T:0.27
Consensus pattern (26 bp):
AAAAGGGCTTATGCCCCAGTTTATTG
Found at i:52209420 original size:39 final size:39
Alignment explanation
Indices: 52209377--52209574 Score: 234
Period size: 39 Copynumber: 5.1 Consensus size: 39
52209367 CCGTATACCA
** * *
52209377 TTCCAGCACGTAGCTTGCGGACTTCAAGTCTGGATATAT
1 TTCCAGCATATAGCCTGCGGACTTCATGTCTGGATATAT
* *
52209416 TTCCAGCATATAGCCTGCGGACCTCATGTCTGGATACAT
1 TTCCAGCATATAGCCTGCGGACTTCATGTCTGGATATAT
* *
52209455 TCCCAGCATATAGCCTGCGGACTTCATGTCCGGATATAT
1 TTCCAGCATATAGCCTGCGGACTTCATGTCTGGATATAT
* * * * *
52209494 TTCCAGCATATAGCCTACAGACCTCATGTCCGAATATAT
1 TTCCAGCATATAGCCTGCGGACTTCATGTCTGGATATAT
* * * * *
52209533 TTCCAGCATATAGCCTACAGTCCTCATGTCCGGATATAT
1 TTCCAGCATATAGCCTGCGGACTTCATGTCTGGATATAT
52209572 TTC
1 TTC
52209575 AAATACCATG
Statistics
Matches: 142, Mismatches: 17, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
39 142 1.00
ACGTcount: A:0.25, C:0.27, G:0.18, T:0.30
Consensus pattern (39 bp):
TTCCAGCATATAGCCTGCGGACTTCATGTCTGGATATAT
Found at i:52209508 original size:78 final size:78
Alignment explanation
Indices: 52209387--52209574 Score: 259
Period size: 78 Copynumber: 2.4 Consensus size: 78
52209377 TTCCAGCACG
* * * * * * *
52209387 TAGCTTGCGGACTTCAAGTCTGGATATATTTCCAGCATATAGCCTGCGGACCTCATGTCTGGATA
1 TAGCCTGCGGACTTCATGTCCGGATATATTTCCAGCATATAGCCTACAGACCTCATGTCCGAATA
52209452 CATTCCCAGCATA
66 CATTCCCAGCATA
52209465 TAGCCTGCGGACTTCATGTCCGGATATATTTCCAGCATATAGCCTACAGACCTCATGTCCGAATA
1 TAGCCTGCGGACTTCATGTCCGGATATATTTCCAGCATATAGCCTACAGACCTCATGTCCGAATA
* *
52209530 TATTTCCAGCATA
66 CATTCCCAGCATA
* * * *
52209543 TAGCCTACAGTCCTCATGTCCGGATATATTTC
1 TAGCCTGCGGACTTCATGTCCGGATATATTTC
52209575 AAATACCATG
Statistics
Matches: 97, Mismatches: 13, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
78 97 1.00
ACGTcount: A:0.25, C:0.27, G:0.18, T:0.30
Consensus pattern (78 bp):
TAGCCTGCGGACTTCATGTCCGGATATATTTCCAGCATATAGCCTACAGACCTCATGTCCGAATA
CATTCCCAGCATA
Found at i:52212031 original size:27 final size:27
Alignment explanation
Indices: 52211973--52212366 Score: 222
Period size: 27 Copynumber: 14.6 Consensus size: 27
52211963 TTAGTTTACC
** * * *
52211973 AAATTACTGAAATACCCTCAAATTGTA
1 AAATTACCAAAATACCCTCGATTTATA
*
52212000 AAATTACCAAAGTACCCTCGATTTATA
1 AAATTACCAAAATACCCTCGATTTATA
* **** *
52212027 GAATTACCGTTTTACCCTCGATTTACA
1 AAATTACCAAAATACCCTCGATTTATA
* * ****
52212054 GAATTATCGTTTTACCCTCGATTTATA
1 AAATTACCAAAATACCCTCGATTTATA
* * *** * *
52212081 GAATTACTATTTTACCCTTGATTTACA
1 AAATTACCAAAATACCCTCGATTTATA
* ***** *
52212108 GAATTACTGTTTTACCCTCGATTTACA
1 AAATTACCAAAATACCCTCGATTTATA
* *
52212135 AAATTACTAAAATACCCTC-AGTTTACA
1 AAATTACCAAAATACCCTCGA-TTTATA
* *
52212162 AAATTACCAAAATACCTTCGA-TCAGTA
1 AAATTACCAAAATACCCTCGATTTA-TA
* * *
52212189 AAATTACCAAAATACCCTAG-TCTGTA
1 AAATTACCAAAATACCCTCGATTTATA
* * * * *
52212215 AAATTGCTAAAATACCCTTGGTTTGTA
1 AAATTACCAAAATACCCTCGATTTATA
* * *
52212242 AAATTACCGAAATACCCTCAATTTGTA
1 AAATTACCAAAATACCCTCGATTTATA
* *
52212269 AAATTACCAAAATACCC-CTATTTTGTA
1 AAATTACCAAAATACCCTCGA-TTTATA
* * *
52212296 AAATTACCAAAATACCACT-GGTTTGTG
1 AAATTACCAAAATACC-CTCGATTTATA
* * *
52212323 AAATTACCGAAATACCCTCAATTTGTA
1 AAATTACCAAAATACCCTCGATTTATA
52212350 AAATTACCAAAATACCC
1 AAATTACCAAAATACCC
52212367 CTAATTTACA
Statistics
Matches: 303, Mismatches: 55, Indels: 18
0.81 0.15 0.05
Matches are distributed among these distances:
26 26 0.09
27 275 0.91
28 2 0.01
ACGTcount: A:0.38, C:0.21, G:0.08, T:0.33
Consensus pattern (27 bp):
AAATTACCAAAATACCCTCGATTTATA
Found at i:52212205 original size:81 final size:79
Alignment explanation
Indices: 52212120--52212394 Score: 284
Period size: 81 Copynumber: 3.4 Consensus size: 79
52212110 ATTACTGTTT
* ** * * * *
52212120 TACCCTCGATTTACAAAATTACTAAAATACCCTCAGTTTACAAAATTACCAAAATACCTTCGATC
1 TACCC-CGATTTACAAAATTACTAAAATACCCT-GGTTTGTAAAATTACCGAAATACCCTCAATT
*
52212185 AGTAAAATTACCAAAA
64 TGTAAAATTACCAAAA
* * ** *
52212201 TA-CCCTAGTCTGTAAAATTGCTAAAATACCCTTGGTTTGTAAAATTACCGAAATACCCTCAATT
1 TACCCCGA-TTTACAAAATTACTAAAATACCC-TGGTTTGTAAAATTACCGAAATACCCTCAATT
52212265 TGTAAAATTACCAAAA
64 TGTAAAATTACCAAAA
* ** * *
52212281 TACCCCTATTTTGTAAAATTACCAAAATACCACTGGTTTGTGAAATTACCGAAATACCCTCAATT
1 TACCCCGA-TTTACAAAATTACTAAAATACC-CTGGTTTGTAAAATTACCGAAATACCCTCAATT
52212346 TGTAAAATTACCAAAA
64 TGTAAAATTACCAAAA
* *
52212362 TACCCCTAATTTACAAAGTTAC-AGAAATACCCT
1 TACCCC-GATTTACAAAATTACTA-AAATACCCT
52212395 TGACTTTCTA
Statistics
Matches: 166, Mismatches: 22, Indels: 13
0.83 0.11 0.06
Matches are distributed among these distances:
79 2 0.01
80 65 0.39
81 97 0.58
82 2 0.01
ACGTcount: A:0.41, C:0.22, G:0.08, T:0.29
Consensus pattern (79 bp):
TACCCCGATTTACAAAATTACTAAAATACCCTGGTTTGTAAAATTACCGAAATACCCTCAATTTG
TAAAATTACCAAAA
Found at i:52212372 original size:27 final size:26
Alignment explanation
Indices: 52212134--52212373 Score: 228
Period size: 27 Copynumber: 8.9 Consensus size: 26
52212124 CTCGATTTAC
* * **
52212134 AAAATTACTAAAATACCCTCAGTTTAC
1 AAAATTACCAAAATACCCT-AATTTGT
* * **
52212161 AAAATTACCAAAATACCTTCGATCAGT
1 AAAATTACCAAAATACCCT-AATTTGT
* *
52212188 AAAATTACCAAAATACCCTAGTCTGT
1 AAAATTACCAAAATACCCTAATTTGT
* * **
52212214 AAAATTGCTAAAATACCCTTGGTTTGT
1 AAAATTACCAAAATACCC-TAATTTGT
*
52212241 AAAATTACCGAAATACCCTCAATTTGT
1 AAAATTACCAAAATACCCT-AATTTGT
*
52212268 AAAATTACCAAAATACCCCTATTTTGT
1 AAAATTACCAAAATA-CCCTAATTTGT
**
52212295 AAAATTACCAAAATACCACTGGTTTGT
1 AAAATTACCAAAATACC-CTAATTTGT
* *
52212322 GAAATTACCGAAATACCCTCAATTTGT
1 AAAATTACCAAAATACCCT-AATTTGT
52212349 AAAATTACCAAAATACCCCTAATTT
1 AAAATTACCAAAATA-CCCTAATTT
52212374 ACAAAGTTAC
Statistics
Matches: 176, Mismatches: 31, Indels: 12
0.80 0.14 0.05
Matches are distributed among these distances:
26 25 0.14
27 143 0.81
28 8 0.05
ACGTcount: A:0.41, C:0.21, G:0.07, T:0.30
Consensus pattern (26 bp):
AAAATTACCAAAATACCCTAATTTGT
Found at i:52212389 original size:54 final size:51
Alignment explanation
Indices: 52212120--52212477 Score: 218
Period size: 54 Copynumber: 6.6 Consensus size: 51
52212110 ATTACTGTTT
** *
52212120 TACCCTCGATTTACAAAATTACTAAAATACCCTCAGTTTACAAAATTACCAAAA
1 TACCCTCGATTTGTAAAATTACCAAAATACCCT-AGTTTAC-AAATTA-CAAAA
* ** *
52212174 TACCTTCGATCAGTAAAATTACCAAAATACCCTAGTCTGTA-AAATTGCTAAAA
1 TACCCTCGATTTGTAAAATTACCAAAATACCCTAGT-T-TACAAATTAC-AAAA
* * * *
52212227 TACCCTTGGTTTGTAAAATTACCGAAATACCCTCAATTTGTA-AAATTACCAAAA
1 TACCCTCGATTTGTAAAATTACCAAAATACCCT--AGTT-TACAAATTA-CAAAA
* * ** *
52212281 TACCC-CTATTTTGTAAAATTACCAAAATACCACTGGTTTGTGAAATTACCGAAA
1 TACCCTCGA-TTTGTAAAATTACCAAAATACC-CTAGTTT-ACAAATTA-CAAAA
* *
52212335 TACCCTCAATTTGTAAAATTACCAAAATACCCCTAATTTACAAAGTTACAGAAA
1 TACCCTCGATTTGTAAAATTACCAAAATA-CCCTAGTTTACAAA-TTACA-AAA
* * *** * *
52212389 TACCCTTGACTTTCTAAAAATTATGGAAATACCATTGGTTTACAAAATTACTAAAA
1 TACCCTCGA-TTTGT-AAAATTACCAAAATACC-CTAGTTTAC-AAATTAC-AAAA
* * * * * *
52212445 TACCTTTGGTTTGTAGATTTACCAAAACACCCT
1 TACCCTCGATTTGTAAAATTACCAAAATACCCT
52212478 TGTAGGATGA
Statistics
Matches: 237, Mismatches: 48, Indels: 39
0.73 0.15 0.12
Matches are distributed among these distances:
52 2 0.01
53 46 0.19
54 132 0.56
55 21 0.09
56 32 0.14
57 4 0.02
ACGTcount: A:0.40, C:0.21, G:0.08, T:0.31
Consensus pattern (51 bp):
TACCCTCGATTTGTAAAATTACCAAAATACCCTAGTTTACAAATTACAAAA
Found at i:52212547 original size:27 final size:27
Alignment explanation
Indices: 52212509--52212595 Score: 106
Period size: 27 Copynumber: 3.3 Consensus size: 27
52212499 TACCCCTATT
* *
52212509 AGGTAAAAAGACCGTAAAGCCCTTGTA
1 AGGTAAAGAGACCGTAAAGCCCCTGTA
*
52212536 GGGTAAAGAGACCGTAAAGCCCCTGTA
1 AGGTAAAGAGACCGTAAAGCCCCTGTA
*
52212563 AGGTAAAGTGACCGTAATA-CCCC-GTA
1 AGGTAAAGAGACCGTAA-AGCCCCTGTA
*
52212589 TGGTAAA
1 AGGTAAA
52212596 ATGACGAATA
Statistics
Matches: 53, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
26 9 0.17
27 43 0.81
28 1 0.02
ACGTcount: A:0.37, C:0.20, G:0.25, T:0.18
Consensus pattern (27 bp):
AGGTAAAGAGACCGTAAAGCCCCTGTA
Found at i:52213477 original size:52 final size:51
Alignment explanation
Indices: 52213397--52213545 Score: 228
Period size: 52 Copynumber: 2.9 Consensus size: 51
52213387 GAGGAAGTGC
* *
52213397 AAAAGGGCTTATGCCCTAGTTTACCGAAAAGGGCTTATGCCCTAGTTTATTG
1 AAAAGGGCTT-TGCCCCAGTTTACCGAAAAGGGCTTATGCCCCAGTTTATTG
* *
52213449 AAAAGGGCTTGTGCCCCAATTTATCGAAAAGGGCTTATGCCCCAGTTTATTG
1 AAAAGGGCTT-TGCCCCAGTTTACCGAAAAGGGCTTATGCCCCAGTTTATTG
*
52213501 AAAAGGGCTTTGCCCCAGTTTACCGAAAAGGGCTT-TGCCGCAGTT
1 AAAAGGGCTTTGCCCCAGTTTACCGAAAAGGGCTTATGCCCCAGTT
52213546 CTTAAAAGAG
Statistics
Matches: 89, Mismatches: 8, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
50 9 0.10
51 23 0.26
52 57 0.64
ACGTcount: A:0.26, C:0.21, G:0.24, T:0.28
Consensus pattern (51 bp):
AAAAGGGCTTTGCCCCAGTTTACCGAAAAGGGCTTATGCCCCAGTTTATTG
Found at i:52213520 original size:25 final size:26
Alignment explanation
Indices: 52213397--52213545 Score: 203
Period size: 26 Copynumber: 5.8 Consensus size: 26
52213387 GAGGAAGTGC
* *
52213397 AAAAGGGCTTATGCCCTAGTTTACCG
1 AAAAGGGCTTATGCCCCAGTTTATCG
* *
52213423 AAAAGGGCTTATGCCCTAGTTTATTG
1 AAAAGGGCTTATGCCCCAGTTTATCG
* *
52213449 AAAAGGGCTTGTGCCCCAATTTATCG
1 AAAAGGGCTTATGCCCCAGTTTATCG
*
52213475 AAAAGGGCTTATGCCCCAGTTTATTG
1 AAAAGGGCTTATGCCCCAGTTTATCG
*
52213501 AAAAGGGCTT-TGCCCCAGTTTACCG
1 AAAAGGGCTTATGCCCCAGTTTATCG
*
52213526 AAAAGGGCTT-TGCCGCAGTT
1 AAAAGGGCTTATGCCCCAGTT
52213546 CTTAAAAGAG
Statistics
Matches: 111, Mismatches: 12, Indels: 1
0.90 0.10 0.01
Matches are distributed among these distances:
25 32 0.29
26 79 0.71
ACGTcount: A:0.26, C:0.21, G:0.24, T:0.28
Consensus pattern (26 bp):
AAAAGGGCTTATGCCCCAGTTTATCG
Found at i:52213841 original size:31 final size:31
Alignment explanation
Indices: 52213764--52213842 Score: 122
Period size: 31 Copynumber: 2.5 Consensus size: 31
52213754 CGTTTATAGT
* *
52213764 AAAGGCTTCGGCCCAATGATATGATTTATGA
1 AAAGGCTTCGGCCCAGTGATATAATTTATGA
*
52213795 AAAGGCTTTGGCCCAGTGATATAATTTATGA
1 AAAGGCTTCGGCCCAGTGATATAATTTATGA
*
52213826 AAAGGCTTCAGCCCAGT
1 AAAGGCTTCGGCCCAGT
52213843 AACCGTTAAA
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 43 1.00
ACGTcount: A:0.32, C:0.18, G:0.23, T:0.28
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTGATATAATTTATGA
Found at i:52220774 original size:39 final size:39
Alignment explanation
Indices: 52220719--52220885 Score: 262
Period size: 39 Copynumber: 4.3 Consensus size: 39
52220709 CTTCAACTCT
* *
52220719 GGATATATTTCTAGCATATAGCCTGCAGACCTCATGTCC
1 GGATATATTTCCAGCATATAGCCTGCGGACCTCATGTCC
* * *
52220758 GGATATAATCCCAGCATATAGCCTGCGGACTTCATGTCC
1 GGATATATTTCCAGCATATAGCCTGCGGACCTCATGTCC
*
52220797 GGATATATTTCCAGCATATAGCCTGGGGACCTCATGTCC
1 GGATATATTTCCAGCATATAGCCTGCGGACCTCATGTCC
* *
52220836 GGATATATTTCCAGCATATAGCCTACGGTCCTCATGTCC
1 GGATATATTTCCAGCATATAGCCTGCGGACCTCATGTCC
52220875 GGATATATTTC
1 GGATATATTTC
52220886 AAATACCATG
Statistics
Matches: 116, Mismatches: 12, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
39 116 1.00
ACGTcount: A:0.25, C:0.26, G:0.20, T:0.30
Consensus pattern (39 bp):
GGATATATTTCCAGCATATAGCCTGCGGACCTCATGTCC
Found at i:52223695 original size:14 final size:14
Alignment explanation
Indices: 52223676--52223702 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
52223666 TCTATTTTTA
52223676 TTATGTGTGAAATT
1 TTATGTGTGAAATT
52223690 TTATGTGTGAAAT
1 TTATGTGTGAAAT
52223703 CTTCGTGATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.30, C:0.00, G:0.22, T:0.48
Consensus pattern (14 bp):
TTATGTGTGAAATT
Found at i:52224920 original size:54 final size:55
Alignment explanation
Indices: 52224859--52224965 Score: 135
Period size: 56 Copynumber: 1.9 Consensus size: 55
52224849 TGACTTCGAT
* ** *
52224859 ATATGTGTGT-GAGTAAGAGTACATTTAATACGTTGGCATCAATATGTGATTTCG
1 ATATGTGTGTCGAATAAGACCACATTTAATACATTGGCATCAATATGTGATTTCG
** *
52224913 ATATGTGTGTGCGAATAAGACCATGTTTAATACATTGGCATCGATATGTGATT
1 ATATGTGTGT-CGAATAAGACCACATTTAATACATTGGCATCAATATGTGATT
52224966 ACGAGTAAGA
Statistics
Matches: 44, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
54 10 0.23
56 34 0.77
ACGTcount: A:0.30, C:0.10, G:0.23, T:0.36
Consensus pattern (55 bp):
ATATGTGTGTCGAATAAGACCACATTTAATACATTGGCATCAATATGTGATTTCG
Found at i:52224975 original size:43 final size:43
Alignment explanation
Indices: 52224948--52225160 Score: 257
Period size: 43 Copynumber: 5.0 Consensus size: 43
52224938 TTTAATACAT
*
52224948 TGGCATCGATATGTGATTACGAGTAAGACCTTGTCTGGGACAA
1 TGGCATCGATATGTGATTACGAGTAAGACCATGTCTGGGACAA
* * *** *
52224991 TGGCATCGATATGTGATTATGAGTAAGACCATGTTTAATACAT
1 TGGCATCGATATGTGATTACGAGTAAGACCATGTCTGGGACAA
* *
52225034 TGGCATCAATATGTGATTACGAGTAAGACCTTGTCTGGGACAA
1 TGGCATCGATATGTGATTACGAGTAAGACCATGTCTGGGACAA
* * * * * *
52225077 TGGCATCGATATGGGATTATGAGTAAGACCCTGTCGGGGATAG
1 TGGCATCGATATGTGATTACGAGTAAGACCATGTCTGGGACAA
* *
52225120 TGGCATCGATATGTGATTAC-ATGTAAGACCACGTCAGGGAC
1 TGGCATCGATATGTGATTACGA-GTAAGACCATGTCTGGGAC
52225161 GTTGGCATTG
Statistics
Matches: 141, Mismatches: 28, Indels: 2
0.82 0.16 0.01
Matches are distributed among these distances:
42 1 0.01
43 140 0.99
ACGTcount: A:0.29, C:0.15, G:0.27, T:0.28
Consensus pattern (43 bp):
TGGCATCGATATGTGATTACGAGTAAGACCATGTCTGGGACAA
Found at i:52225055 original size:86 final size:86
Alignment explanation
Indices: 52224928--52225106 Score: 340
Period size: 86 Copynumber: 2.1 Consensus size: 86
52224918 TGTGTGCGAA
*
52224928 TAAGACCATGTTTAATACATTGGCATCGATATGTGATTACGAGTAAGACCTTGTCTGGGACAATG
1 TAAGACCATGTTTAATACATTGGCATCAATATGTGATTACGAGTAAGACCTTGTCTGGGACAATG
*
52224993 GCATCGATATGTGATTATGAG
66 GCATCGATATGGGATTATGAG
52225014 TAAGACCATGTTTAATACATTGGCATCAATATGTGATTACGAGTAAGACCTTGTCTGGGACAATG
1 TAAGACCATGTTTAATACATTGGCATCAATATGTGATTACGAGTAAGACCTTGTCTGGGACAATG
52225079 GCATCGATATGGGATTATGAG
66 GCATCGATATGGGATTATGAG
52225100 TAAGACC
1 TAAGACC
52225107 CTGTCGGGGA
Statistics
Matches: 91, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
86 91 1.00
ACGTcount: A:0.31, C:0.15, G:0.24, T:0.30
Consensus pattern (86 bp):
TAAGACCATGTTTAATACATTGGCATCAATATGTGATTACGAGTAAGACCTTGTCTGGGACAATG
GCATCGATATGGGATTATGAG
Found at i:52225168 original size:86 final size:86
Alignment explanation
Indices: 52224928--52225149 Score: 302
Period size: 86 Copynumber: 2.6 Consensus size: 86
52224918 TGTGTGCGAA
** * *
52224928 TAAGACCATGTTTAATACATTGGCATCGATATGTGATTACGAGTAAGACCTTGTCTGGGACAATG
1 TAAGACCATGTCGAAGACAGTGGCATCGATATGTGATTACGAGTAAGACCTTGTCTGGGACAATG
*
52224993 GCATCGATATGTGATTATGAG
66 GCATCGATATGGGATTATGAG
** * * *
52225014 TAAGACCATGTTTAATACATTGGCATCAATATGTGATTACGAGTAAGACCTTGTCTGGGACAATG
1 TAAGACCATGTCGAAGACAGTGGCATCGATATGTGATTACGAGTAAGACCTTGTCTGGGACAATG
52225079 GCATCGATATGGGATTATGAG
66 GCATCGATATGGGATTATGAG
* ** *
52225100 TAAGACCCTGTCGGGGATAGTGGCATCGATATGTGATTAC-ATGTAAGACC
1 TAAGACCATGTCGAAGACAGTGGCATCGATATGTGATTACGA-GTAAGACC
52225150 ACGTCAGGGA
Statistics
Matches: 124, Mismatches: 11, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
85 1 0.01
86 123 0.99
ACGTcount: A:0.30, C:0.15, G:0.25, T:0.30
Consensus pattern (86 bp):
TAAGACCATGTCGAAGACAGTGGCATCGATATGTGATTACGAGTAAGACCTTGTCTGGGACAATG
GCATCGATATGGGATTATGAG
Found at i:52226025 original size:26 final size:26
Alignment explanation
Indices: 52225989--52226066 Score: 156
Period size: 26 Copynumber: 3.0 Consensus size: 26
52225979 CCATGCGAAA
52225989 ATGGCTAATTTGATACCTAAATATTT
1 ATGGCTAATTTGATACCTAAATATTT
52226015 ATGGCTAATTTGATACCTAAATATTT
1 ATGGCTAATTTGATACCTAAATATTT
52226041 ATGGCTAATTTGATACCTAAATATTT
1 ATGGCTAATTTGATACCTAAATATTT
52226067 GCTATCTTGT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 52 1.00
ACGTcount: A:0.35, C:0.12, G:0.12, T:0.42
Consensus pattern (26 bp):
ATGGCTAATTTGATACCTAAATATTT
Found at i:52239209 original size:3 final size:3
Alignment explanation
Indices: 52239201--52239230 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
52239191 TCCTCATTCC
52239201 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
52239231 CTCTATTTAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:52240510 original size:27 final size:27
Alignment explanation
Indices: 52240419--52240557 Score: 126
Period size: 27 Copynumber: 5.2 Consensus size: 27
52240409 TTAGTTTACC
* * *
52240419 AAATTACTGAAATACCC-CCAGTTGTA
1 AAATTACCGAAATACCCTCGATTTGTA
* *
52240445 AAATTA-CGAAAGTACCC-CTGGTTTAT-
1 AAATTACCGAAA-TACCCTC-GATTTGTA
* *
52240471 AAATTACCCAAATATCCTCGATTTGTA
1 AAATTACCGAAATACCCTCGATTTGTA
*
52240498 AAATTACCGAAATACCCTC-AGTTTGCA
1 AAATTACCGAAATACCCTCGA-TTTGTA
* *
52240525 AAATTACTGAAATACCCTCGACTTGTA
1 AAATTACCGAAATACCCTCGATTTGTA
52240552 AAATTA
1 AAATTA
52240558 TCAAAGTACC
Statistics
Matches: 91, Mismatches: 15, Indels: 13
0.76 0.13 0.11
Matches are distributed among these distances:
25 4 0.04
26 28 0.31
27 58 0.64
28 1 0.01
ACGTcount: A:0.38, C:0.22, G:0.11, T:0.29
Consensus pattern (27 bp):
AAATTACCGAAATACCCTCGATTTGTA
Found at i:52240567 original size:27 final size:26
Alignment explanation
Indices: 52240479--52240569 Score: 94
Period size: 27 Copynumber: 3.4 Consensus size: 26
52240469 ATAAATTACC
* *
52240479 CAAATATCCTCGATTTGTAAAATTAC
1 CAAATACCCTCGATTTGTAAAATTAT
*
52240505 CGAAATACCCTC-AGTTTGCAAAATTACT
1 C-AAATACCCTCGA-TTTGTAAAATTA-T
* *
52240533 GAAATACCCTCGACTTGTAAAATTAT
1 CAAATACCCTCGATTTGTAAAATTAT
52240559 CAAAGTACCCT
1 CAAA-TACCCT
52240570 TAAATTTCAA
Statistics
Matches: 53, Mismatches: 7, Indels: 9
0.77 0.10 0.13
Matches are distributed among these distances:
26 6 0.11
27 46 0.87
28 1 0.02
ACGTcount: A:0.37, C:0.23, G:0.10, T:0.30
Consensus pattern (26 bp):
CAAATACCCTCGATTTGTAAAATTAT
Found at i:52240569 original size:54 final size:53
Alignment explanation
Indices: 52240419--52240586 Score: 166
Period size: 54 Copynumber: 3.2 Consensus size: 53
52240409 TTAGTTTACC
* * *
52240419 AAATTACTGAAATACCC-CCAGTTGTAAAATTACGAAAGTACCC-CTGGTTT-A
1 AAATTACTGAAATACCCTCGACTTGTAAAATTACGAAAGTACCCTC-AGTTTCA
** * *
52240470 TAAATTACCCAAATATCCTCGATTTGTAAAATTACCGAAA-TACCCTCAGTTTGCA
1 -AAATTACTGAAATACCCTCGACTTGTAAAATTA-CGAAAGTACCCTCAGTTT-CA
* *
52240525 AAATTACTGAAATACCCTCGACTTGTAAAATTATC-AAAGTACCCTTAAATTTCA
1 AAATTACTGAAATACCCTCGACTTGTAAAATTA-CGAAAGTACCC-TCAGTTTCA
52240579 AAATTACT
1 AAATTACT
52240587 ATTTTACCAT
Statistics
Matches: 96, Mismatches: 13, Indels: 12
0.79 0.11 0.10
Matches are distributed among these distances:
52 14 0.15
53 25 0.26
54 51 0.53
55 6 0.06
ACGTcount: A:0.39, C:0.21, G:0.10, T:0.30
Consensus pattern (53 bp):
AAATTACTGAAATACCCTCGACTTGTAAAATTACGAAAGTACCCTCAGTTTCA
Found at i:52240594 original size:27 final size:27
Alignment explanation
Indices: 52240573--52240919 Score: 396
Period size: 27 Copynumber: 12.9 Consensus size: 27
52240563 GTACCCTTAA
* *
52240573 ATTT-CAAAATTACTATTTTACCATCG
1 ATTTACAAAATTACTGTTTTACCCTCG
* * * *
52240599 ATTTACAGAATTATTATTTTACCCTCA
1 ATTTACAAAATTACTGTTTTACCCTCG
* *
52240626 ATTTACAAAATTACCGTTTTACCCTCA
1 ATTTACAAAATTACTGTTTTACCCTCG
*
52240653 ATTTACAAAATTACCGTTTTACCCTCG
1 ATTTACAAAATTACTGTTTTACCCTCG
* *
52240680 ATTTACAAAATTACTATTTTACCATCG
1 ATTTACAAAATTACTGTTTTACCCTCG
52240707 ATTTACAAAATTA-TCGTTTTACCCTCG
1 ATTTACAAAATTACT-GTTTTACCCTCG
*
52240734 ATTTACAAAATTACCGTTTTACCCTCG
1 ATTTACAAAATTACTGTTTTACCCTCG
*
52240761 ATTTACAGAATTA-TCGTTTTACCCTCG
1 ATTTACAAAATTACT-GTTTTACCCTCG
* **
52240788 ATTTATAGAAA-TACTGTTTTACCCTTA
1 ATTTACA-AAATTACTGTTTTACCCTCG
* *
52240815 ATTTACAAAATTACTATTTTACCCTAG
1 ATTTACAAAATTACTGTTTTACCCTCG
* *
52240842 ATTTAAAAAATTACTATTTTACCCTCG
1 ATTTACAAAATTACTGTTTTACCCTCG
* * **
52240869 ATTTATAGAATTACCATTTTACCCTCG
1 ATTTACAAAATTACTGTTTTACCCTCG
* **
52240896 ATTTATAAAATTACCATTTTACCC
1 ATTTACAAAATTACTGTTTTACCC
52240920 CTAGGTGTTA
Statistics
Matches: 283, Mismatches: 31, Indels: 13
0.87 0.09 0.04
Matches are distributed among these distances:
26 8 0.03
27 272 0.96
28 3 0.01
ACGTcount: A:0.33, C:0.21, G:0.05, T:0.41
Consensus pattern (27 bp):
ATTTACAAAATTACTGTTTTACCCTCG
Found at i:52241198 original size:27 final size:26
Alignment explanation
Indices: 52241154--52241205 Score: 68
Period size: 27 Copynumber: 2.0 Consensus size: 26
52241144 CTCGCTGCAA
*
52241154 TCTGGTGGCCTCGCCACATATATCTGT
1 TCTGGTGACCTCGCCACA-ATATCTGT
* *
52241181 TCTGGTGACTTCGTCACAATATCTG
1 TCTGGTGACCTCGCCACAATATCTG
52241206 GCAGCCTCGC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 7 0.32
27 15 0.68
ACGTcount: A:0.17, C:0.27, G:0.21, T:0.35
Consensus pattern (26 bp):
TCTGGTGACCTCGCCACAATATCTGT
Found at i:52241457 original size:31 final size:31
Alignment explanation
Indices: 52241422--52241498 Score: 91
Period size: 31 Copynumber: 2.5 Consensus size: 31
52241412 TTGCATTCAC
* * *
52241422 ATTCTGATTTTGATTATGTTACCTGATACTG
1 ATTCTGATTCTGATTATGTCACCTAATACTG
* * *
52241453 ATTCTGATTCTAATTCTGTCACCTAATTCTG
1 ATTCTGATTCTGATTATGTCACCTAATACTG
*
52241484 ATTCTAATTCTGATT
1 ATTCTGATTCTGATT
52241499 TTGATTCTAT
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 38 1.00
ACGTcount: A:0.23, C:0.17, G:0.12, T:0.48
Consensus pattern (31 bp):
ATTCTGATTCTGATTATGTCACCTAATACTG
Found at i:52241461 original size:6 final size:6
Alignment explanation
Indices: 52241422--52241552 Score: 63
Period size: 6 Copynumber: 21.3 Consensus size: 6
52241412 TTGCATTCAC
* * * *
52241422 ATTCTG ATTTTG ATTATG -TTACCTG ATACTG ATTCTG ATTCTA ATTCTG
1 ATTCTG ATTCTG ATTCTG ATT--CTG ATTCTG ATTCTG ATTCTG ATTCTG
* * * * *
52241471 -TCACCTA ATTCTG ATTCTA ATTCTG ATTTTG ATTCT- ATCACCTG ATTCTG
1 AT--TCTG ATTCTG ATTCTG ATTCTG ATTCTG ATTCTG AT--TCTG ATTCTG
* * *
52241521 ATTCTG ATTTTC ATTTTG ATTCT- AGTTCTG AT
1 ATTCTG ATTCTG ATTCTG ATTCTG A-TTCTG AT
52241553 AATGTTTCTT
Statistics
Matches: 93, Mismatches: 21, Indels: 22
0.68 0.15 0.16
Matches are distributed among these distances:
5 6 0.06
6 76 0.82
7 7 0.08
8 4 0.04
ACGTcount: A:0.21, C:0.17, G:0.12, T:0.50
Consensus pattern (6 bp):
ATTCTG
Found at i:52241485 original size:37 final size:37
Alignment explanation
Indices: 52241444--52241529 Score: 118
Period size: 37 Copynumber: 2.3 Consensus size: 37
52241434 ATTATGTTAC
* *
52241444 CTGATACTGATTCTGATTCTAATTCTGTCACCTAATT
1 CTGATTCTGATTCTGATTCTAATTCTATCACCTAATT
* * * *
52241481 CTGATTCTAATTCTGATTTTGATTCTATCACCTGATT
1 CTGATTCTGATTCTGATTCTAATTCTATCACCTAATT
52241518 CTGATTCTGATT
1 CTGATTCTGATT
52241530 TTCATTTTGA
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
37 42 1.00
ACGTcount: A:0.22, C:0.20, G:0.12, T:0.47
Consensus pattern (37 bp):
CTGATTCTGATTCTGATTCTAATTCTATCACCTAATT
Found at i:52241537 original size:37 final size:37
Alignment explanation
Indices: 52241465--52241544 Score: 115
Period size: 37 Copynumber: 2.2 Consensus size: 37
52241455 TCTGATTCTA
* *
52241465 ATTCTGTCACCTAATTCTGATTCTAATTCTGATTTTG
1 ATTCTATCACCTAATTCTGATTCTAATTCTCATTTTG
* * *
52241502 ATTCTATCACCTGATTCTGATTCTGATTTTCATTTTG
1 ATTCTATCACCTAATTCTGATTCTAATTCTCATTTTG
52241539 ATTCTA
1 ATTCTA
52241545 GTTCTGATAA
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.21, C:0.19, G:0.10, T:0.50
Consensus pattern (37 bp):
ATTCTATCACCTAATTCTGATTCTAATTCTCATTTTG
Found at i:52243610 original size:27 final size:27
Alignment explanation
Indices: 52243580--52243696 Score: 103
Period size: 27 Copynumber: 4.3 Consensus size: 27
52243570 CCTTGGTTTA
*
52243580 TAAAATTACCCAAATATCCTCAATTTG
1 TAAAATTACCCAAATACCCTCAATTTG
* * * *
52243607 TAAAATTATCGAAATACCCTCAGTTTA
1 TAAAATTACCCAAATACCCTCAATTTG
* ** * *
52243634 CAAAATTACTGAAATACCCTCGACTTG
1 TAAAATTACCCAAATACCCTCAATTTG
*
52243661 TAAAATTA-TCAAAGTACCCTCGAATTT-
1 TAAAATTACCCAAA-TACCCTC-AATTTG
52243688 TAAAATTAC
1 TAAAATTAC
52243697 TATTTTACCC
Statistics
Matches: 71, Mismatches: 16, Indels: 5
0.77 0.17 0.05
Matches are distributed among these distances:
26 4 0.06
27 64 0.90
28 3 0.04
ACGTcount: A:0.41, C:0.21, G:0.07, T:0.32
Consensus pattern (27 bp):
TAAAATTACCCAAATACCCTCAATTTG
Found at i:52243697 original size:54 final size:55
Alignment explanation
Indices: 52243529--52243698 Score: 170
Period size: 54 Copynumber: 3.2 Consensus size: 55
52243519 TTAGTTTACC
* * * * * *
52243529 AAATTACTAAAATACCC-CCAGTCGTAAAATTACCAAAGTGCCCTTG-GTTTATA
1 AAATTACTAAAATACCCTCAACTTGTAAAATTATCAAAGTACCCTCGAGTTTATA
** * * *
52243582 AAATTACCCAAATATCCTCAATTTGTAAAATTATCGAAA-TACCCTC-AGTTTACA
1 AAATTACTAAAATACCCTCAACTTGTAAAATTATC-AAAGTACCCTCGAGTTTATA
* * *
52243636 AAATTACTGAAATACCCTCGACTTGTAAAATTATCAAAGTACCCTCGAATTT-TA
1 AAATTACTAAAATACCCTCAACTTGTAAAATTATCAAAGTACCCTCGAGTTTATA
52243690 AAATTACTA
1 AAATTACTA
52243699 TTTTACCCTC
Statistics
Matches: 94, Mismatches: 18, Indels: 9
0.78 0.15 0.07
Matches are distributed among these distances:
53 17 0.18
54 70 0.74
55 7 0.07
ACGTcount: A:0.40, C:0.21, G:0.08, T:0.31
Consensus pattern (55 bp):
AAATTACTAAAATACCCTCAACTTGTAAAATTATCAAAGTACCCTCGAGTTTATA
Found at i:52243705 original size:27 final size:27
Alignment explanation
Indices: 52243675--52243868 Score: 264
Period size: 27 Copynumber: 7.2 Consensus size: 27
52243665 ATTATCAAAG
52243675 TACCCTCGAATTT-TAAAATTACTATTT
1 TACCCTCG-ATTTATAAAATTACTATTT
*
52243702 TACCCTCGATTTATAGAATTACTATTT
1 TACCCTCGATTTATAAAATTACTATTT
* **
52243729 TACCCCCGATTTATAAAATTACCGTTT
1 TACCCTCGATTTATAAAATTACTATTT
* *
52243756 TACCCTCGATTTACAAAATTACTGTTT
1 TACCCTCGATTTATAAAATTACTATTT
* * *
52243783 TACCCTCGATTTACAATATTACCATTT
1 TACCCTCGATTTATAAAATTACTATTT
52243810 TACCCTCGATTTATAAAATTACTATTT
1 TACCCTCGATTTATAAAATTACTATTT
* * *
52243837 TACCCTTGATTTACAAAATTACCATTT
1 TACCCTCGATTTATAAAATTACTATTT
52243864 TACCC
1 TACCC
52243869 CTAGGGTGTT
Statistics
Matches: 149, Mismatches: 17, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
26 4 0.03
27 145 0.97
ACGTcount: A:0.31, C:0.23, G:0.05, T:0.41
Consensus pattern (27 bp):
TACCCTCGATTTATAAAATTACTATTT
Found at i:52243722 original size:81 final size:81
Alignment explanation
Indices: 52243637--52243868 Score: 200
Period size: 81 Copynumber: 2.9 Consensus size: 81
52243627 CAGTTTACAA
* * * *
52243637 AATTACTGA-AATACCCTCGACTTGTAAAATTATCAAAGTACCCTCGAATTT-TAAAATTACTAT
1 AATTACT-ATAATACCCCCGACTTATAAAATTACCAAAGTACCCTCG-ATTTACAAAATTACTAT
52243700 TTTACCCTCGATTTATAG
64 TTTACCCTCGATTTATAG
** * **** *
52243718 AATTACTATTTTACCCCCGATTTATAAAATTACCGTTTTACCCTCGATTTACAAAATTACTGTTT
1 AATTACTATAATACCCCCGACTTATAAAATTACCAAAGTACCCTCGATTTACAAAATTACTATTT
*
52243783 TACCCTCGATTTACA-
66 TACCCTCGATTTATAG
* ** * * * *** * *
52243798 ATATTACCATTTTACCCTCGATTTATAAAATTACTATTTTACCCTTGATTTACAAAATTACCATT
1 A-ATTACTATAATACCCCCGACTTATAAAATTACCAAAGTACCCTCGATTTACAAAATTACTATT
52243863 TTACCC
65 TTACCC
52243869 CTAGGGTGTT
Statistics
Matches: 128, Mismatches: 20, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
80 6 0.05
81 122 0.95
ACGTcount: A:0.33, C:0.22, G:0.06, T:0.39
Consensus pattern (81 bp):
AATTACTATAATACCCCCGACTTATAAAATTACCAAAGTACCCTCGATTTACAAAATTACTATTT
TACCCTCGATTTATAG
Found at i:52244148 original size:27 final size:26
Alignment explanation
Indices: 52244104--52244155 Score: 68
Period size: 27 Copynumber: 2.0 Consensus size: 26
52244094 CTCGCTGCAA
*
52244104 TCTGGTGGCCTCGCCACATATATCTGT
1 TCTGGTGACCTCGCCACA-ATATCTGT
* *
52244131 TCTGGTGACTTCGTCACAATATCTG
1 TCTGGTGACCTCGCCACAATATCTG
52244156 GCAGCCTCAC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 7 0.32
27 15 0.68
ACGTcount: A:0.17, C:0.27, G:0.21, T:0.35
Consensus pattern (26 bp):
TCTGGTGACCTCGCCACAATATCTGT
Found at i:52244411 original size:6 final size:6
Alignment explanation
Indices: 52244372--52244493 Score: 70
Period size: 6 Copynumber: 19.8 Consensus size: 6
52244362 TTGCATTCAC
* * * *
52244372 ATTCTG ATTTTG ATTATG -TTACCTG ATACTG ATTCTG ATTCTA ATTCTG
1 ATTCTG ATTCTG ATTCTG ATT--CTG ATTCTG ATTCTG ATTCTG ATTCTG
* * * * *
52244421 -TCACCTA ATTCTG ATTTTG ATTCTG ATTTTG ATTCTG -TCACCTG ATTCTG
1 AT--TCTG ATTCTG ATTCTG ATTCTG ATTCTG ATTCTG AT--TCTG ATTCTG
* *
52244471 ATTCTG ATTCTC ATTTTG ATTCT
1 ATTCTG ATTCTG ATTCTG ATTCT
52244494 AGTTTTGATA
Statistics
Matches: 86, Mismatches: 21, Indels: 18
0.69 0.17 0.14
Matches are distributed among these distances:
5 4 0.05
6 72 0.84
7 7 0.08
8 3 0.03
ACGTcount: A:0.20, C:0.17, G:0.13, T:0.50
Consensus pattern (6 bp):
ATTCTG
Found at i:52244466 original size:31 final size:31
Alignment explanation
Indices: 52244372--52244479 Score: 108
Period size: 31 Copynumber: 3.3 Consensus size: 31
52244362 TTGCATTCAC
* * *
52244372 ATTCTGATTTTGATTATGTTACCTGATACTG
1 ATTCTGATTTTGATTCTGTCACCTGATTCTG
* * *
52244403 ATTCTGATTCTAATTCTGTCACCTAATTCTGATTTTG
1 ATTCTGATTTTGATTCTGTCA-C-----CTGATTCTG
52244440 ATTCTGATTTTGATTCTGTCACCTGATTCTG
1 ATTCTGATTTTGATTCTGTCACCTGATTCTG
52244471 ATTCTGATT
1 ATTCTGATT
52244480 CTCATTTTGA
Statistics
Matches: 62, Mismatches: 9, Indels: 12
0.75 0.11 0.14
Matches are distributed among these distances:
31 34 0.55
32 1 0.02
36 1 0.02
37 26 0.42
ACGTcount: A:0.20, C:0.17, G:0.14, T:0.49
Consensus pattern (31 bp):
ATTCTGATTTTGATTCTGTCACCTGATTCTG
Found at i:52244487 original size:37 final size:37
Alignment explanation
Indices: 52244372--52244493 Score: 148
Period size: 37 Copynumber: 3.5 Consensus size: 37
52244362 TTGCATTCAC
* * *
52244372 ATTCTGATTTTGATTATGTTACCTGATACTGATTCTG
1 ATTCTGATTTTGATTCTGTCACCTGATTCTGATTCTG
* *
52244409 ATTCT-A-----ATTCTGTCACCTAATTCTGATTTTG
1 ATTCTGATTTTGATTCTGTCACCTGATTCTGATTCTG
52244440 ATTCTGATTTTGATTCTGTCACCTGATTCTGATTCTG
1 ATTCTGATTTTGATTCTGTCACCTGATTCTGATTCTG
*
52244477 ATTCTCATTTTGATTCT
1 ATTCTGATTTTGATTCT
52244494 AGTTTTGATA
Statistics
Matches: 71, Mismatches: 8, Indels: 12
0.78 0.09 0.13
Matches are distributed among these distances:
31 25 0.35
32 1 0.01
36 1 0.01
37 44 0.62
ACGTcount: A:0.20, C:0.17, G:0.13, T:0.50
Consensus pattern (37 bp):
ATTCTGATTTTGATTCTGTCACCTGATTCTGATTCTG
Found at i:52244499 original size:12 final size:12
Alignment explanation
Indices: 52244428--52244502 Score: 55
Period size: 12 Copynumber: 6.2 Consensus size: 12
52244418 CTGTCACCTA
*
52244428 ATTCTGATTTTG
1 ATTCTCATTTTG
*
52244440 ATTCTGATTTTG
1 ATTCTCATTTTG
**
52244452 ATTCTGTCA-CCTG
1 ATTC--TCATTTTG
* *
52244465 ATTCTGATTCTG
1 ATTCTCATTTTG
52244477 ATTCTCATTTTG
1 ATTCTCATTTTG
52244489 ATTCT-AGTTTTG
1 ATTCTCA-TTTTG
52244501 AT
1 AT
52244503 AATGTTTCTT
Statistics
Matches: 52, Mismatches: 7, Indels: 8
0.78 0.10 0.12
Matches are distributed among these distances:
11 3 0.06
12 41 0.79
13 6 0.12
14 2 0.04
ACGTcount: A:0.17, C:0.15, G:0.15, T:0.53
Consensus pattern (12 bp):
ATTCTCATTTTG
Found at i:52246114 original size:31 final size:31
Alignment explanation
Indices: 52246079--52246139 Score: 88
Period size: 31 Copynumber: 2.0 Consensus size: 31
52246069 TCTGATTTAT
52246079 TTTTATGTT-TATGTTTATCTTTATTTTTACC
1 TTTTAT-TTCTATGTTTATCTTTATTTTTACC
* *
52246110 TTTTATTTCTATTTTTATTTTTATTTTTAC
1 TTTTATTTCTATGTTTATCTTTATTTTTAC
52246140 TCTTCTTGTT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
30 2 0.07
31 25 0.93
ACGTcount: A:0.16, C:0.08, G:0.03, T:0.72
Consensus pattern (31 bp):
TTTTATTTCTATGTTTATCTTTATTTTTACC
Found at i:52246122 original size:6 final size:6
Alignment explanation
Indices: 52246074--52246138 Score: 76
Period size: 6 Copynumber: 10.7 Consensus size: 6
52246064 TTGAGTCTGA
* * * * *
52246074 TTTATT TTTATG TTTATG TTTATC TTTATT TTTACCT TTTATT TCTATT
1 TTTATT TTTATT TTTATT TTTATT TTTATT TTTA-TT TTTATT TTTATT
52246123 TTTATT TTTATT TTTA
1 TTTATT TTTATT TTTA
52246139 CTCTTCTTGT
Statistics
Matches: 51, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
6 46 0.90
7 5 0.10
ACGTcount: A:0.17, C:0.06, G:0.03, T:0.74
Consensus pattern (6 bp):
TTTATT
Found at i:52246871 original size:16 final size:15
Alignment explanation
Indices: 52246835--52246877 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
52246825 ATCTATAACA
* *
52246835 ATTCAAATTCAATTT
1 ATTCAAACTCAATTC
52246850 ATTCAAACTCACATTC
1 ATTCAAACTCA-ATTC
52246866 ATTCAAA-TCAAT
1 ATTCAAACTCAAT
52246878 CCAAAAATAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
14 2 0.08
15 13 0.52
16 10 0.40
ACGTcount: A:0.42, C:0.21, G:0.00, T:0.37
Consensus pattern (15 bp):
ATTCAAACTCAATTC
Found at i:52249040 original size:22 final size:22
Alignment explanation
Indices: 52249014--52249065 Score: 86
Period size: 22 Copynumber: 2.4 Consensus size: 22
52249004 AAAATAGTAT
*
52249014 TTGTTGTGGAAGCTTTCAAAAG
1 TTGTTGCGGAAGCTTTCAAAAG
52249036 TTGTTGCGGAAGCTTTCAAAAG
1 TTGTTGCGGAAGCTTTCAAAAG
*
52249058 GTGTTGCG
1 TTGTTGCG
52249066 TAAACATTGT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.23, C:0.12, G:0.31, T:0.35
Consensus pattern (22 bp):
TTGTTGCGGAAGCTTTCAAAAG
Found at i:52256597 original size:25 final size:25
Alignment explanation
Indices: 52256551--52256601 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 25
52256541 CCATTATAAT
* *
52256551 GTGAAAATGACCTTTTTGCCCCTAG
1 GTGAAAATGACCTTTATACCCCTAG
52256576 GTGAAAATGA-CTATTATACCCCTAG
1 GTGAAAATGACCT-TTATACCCCTAG
52256601 G
1 G
52256602 GTTATGTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 2 0.09
25 21 0.91
ACGTcount: A:0.29, C:0.22, G:0.20, T:0.29
Consensus pattern (25 bp):
GTGAAAATGACCTTTATACCCCTAG
Found at i:52256660 original size:10 final size:10
Alignment explanation
Indices: 52256645--52256679 Score: 61
Period size: 10 Copynumber: 3.4 Consensus size: 10
52256635 TTTGTACATA
52256645 ATATGCCATG
1 ATATGCCATG
52256655 ATATGCACATG
1 ATATGC-CATG
52256666 ATATGCCATG
1 ATATGCCATG
52256676 ATAT
1 ATAT
52256680 ATACATATAT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 14 0.58
11 10 0.42
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.31
Consensus pattern (10 bp):
ATATGCCATG
Found at i:52256664 original size:21 final size:21
Alignment explanation
Indices: 52256640--52256679 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
52256630 ACTGATTTGT
52256640 ACATAATATGCCATGATATGC
1 ACATAATATGCCATGATATGC
*
52256661 ACATGATATGCCATGATAT
1 ACATAATATGCCATGATAT
52256680 ATACATATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.38, C:0.17, G:0.15, T:0.30
Consensus pattern (21 bp):
ACATAATATGCCATGATATGC
Found at i:52256685 original size:21 final size:20
Alignment explanation
Indices: 52256639--52256691 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 20
52256629 TACTGATTTG
*
52256639 TACATAATATGCCATGATATG
1 TACAT-ATATGCCATGATATA
*
52256660 CACATGATATGCCATGATATA
1 TACAT-ATATGCCATGATATA
52256681 TACATATATGC
1 TACATATATGC
52256692 ATGGGTTGGG
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
20 6 0.21
21 22 0.79
ACGTcount: A:0.38, C:0.17, G:0.13, T:0.32
Consensus pattern (20 bp):
TACATATATGCCATGATATA
Found at i:52256753 original size:25 final size:25
Alignment explanation
Indices: 52256725--52256791 Score: 116
Period size: 25 Copynumber: 2.7 Consensus size: 25
52256715 GAGGAAGTGC
*
52256725 AAAAGGGCTATGCCCCAATTTACCG
1 AAAAGGGCTTTGCCCCAATTTACCG
52256750 AAAAGGGCTTTGCCCCAATTTACCG
1 AAAAGGGCTTTGCCCCAATTTACCG
*
52256775 GAAAGGGCTTTGCCCCA
1 AAAAGGGCTTTGCCCCA
52256792 GTTACTATAA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
25 40 1.00
ACGTcount: A:0.28, C:0.28, G:0.22, T:0.21
Consensus pattern (25 bp):
AAAAGGGCTTTGCCCCAATTTACCG
Found at i:52257053 original size:31 final size:31
Alignment explanation
Indices: 52257015--52257098 Score: 125
Period size: 31 Copynumber: 2.7 Consensus size: 31
52257005 CATTTATAGT
*
52257015 AAAGGCTTCAGCCCAGTGATATGAATAATGA
1 AAAGGCTTCGGCCCAGTGATATGAATAATGA
* * *
52257046 AAAGGCTTCGGCCTAGTGGTATGAATAATGT
1 AAAGGCTTCGGCCCAGTGATATGAATAATGA
52257077 AAAGGCTTCGGCCCAGT-ATATG
1 AAAGGCTTCGGCCCAGTGATATG
52257099 CTGAGATTGA
Statistics
Matches: 47, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
30 4 0.09
31 43 0.91
ACGTcount: A:0.32, C:0.17, G:0.26, T:0.25
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTGATATGAATAATGA
Found at i:52264604 original size:10 final size:10
Alignment explanation
Indices: 52264589--52264623 Score: 61
Period size: 10 Copynumber: 3.4 Consensus size: 10
52264579 TTTGTACATA
52264589 ATATGCCATG
1 ATATGCCATG
52264599 ATATGCACATG
1 ATATGC-CATG
52264610 ATATGCCATG
1 ATATGCCATG
52264620 ATAT
1 ATAT
52264624 ATACATATAT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 14 0.58
11 10 0.42
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.31
Consensus pattern (10 bp):
ATATGCCATG
Found at i:52264608 original size:21 final size:21
Alignment explanation
Indices: 52264584--52264623 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
52264574 ACTGATTTGT
52264584 ACATAATATGCCATGATATGC
1 ACATAATATGCCATGATATGC
*
52264605 ACATGATATGCCATGATAT
1 ACATAATATGCCATGATAT
52264624 ATACATATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.38, C:0.17, G:0.15, T:0.30
Consensus pattern (21 bp):
ACATAATATGCCATGATATGC
Found at i:52264629 original size:21 final size:20
Alignment explanation
Indices: 52264583--52264635 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 20
52264573 TACTGATTTG
*
52264583 TACATAATATGCCATGATATG
1 TACAT-ATATGCCATGATATA
*
52264604 CACATGATATGCCATGATATA
1 TACAT-ATATGCCATGATATA
52264625 TACATATATGC
1 TACATATATGC
52264636 ATGGGTTGGG
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
20 6 0.21
21 22 0.79
ACGTcount: A:0.38, C:0.17, G:0.13, T:0.32
Consensus pattern (20 bp):
TACATATATGCCATGATATA
Found at i:52264707 original size:25 final size:25
Alignment explanation
Indices: 52264669--52264735 Score: 116
Period size: 25 Copynumber: 2.7 Consensus size: 25
52264659 GAGGAAGTGC
*
52264669 AAAAGGGCTATGCCCCAATTTACCG
1 AAAAGGGCTTTGCCCCAATTTACCG
52264694 AAAAGGGCTTTGCCCCAATTTACCG
1 AAAAGGGCTTTGCCCCAATTTACCG
*
52264719 GAAAGGGCTTTGCCCCA
1 AAAAGGGCTTTGCCCCA
52264736 GTTTTTAAAA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
25 40 1.00
ACGTcount: A:0.28, C:0.28, G:0.22, T:0.21
Consensus pattern (25 bp):
AAAAGGGCTTTGCCCCAATTTACCG
Found at i:52264997 original size:31 final size:31
Alignment explanation
Indices: 52264959--52265042 Score: 134
Period size: 31 Copynumber: 2.7 Consensus size: 31
52264949 TGTTTACAGT
*
52264959 AAAGGCTTCTGCCCAGTGATATGAATAATGA
1 AAAGGCTTCGGCCCAGTGATATGAATAATGA
* *
52264990 AAAGGCTTCGGCCCAGTGGTATGAATAATGT
1 AAAGGCTTCGGCCCAGTGATATGAATAATGA
52265021 AAAGGCTTCGGCCCAGT-ATATG
1 AAAGGCTTCGGCCCAGTGATATG
52265043 CTGAGATTGA
Statistics
Matches: 49, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
30 4 0.08
31 45 0.92
ACGTcount: A:0.31, C:0.18, G:0.26, T:0.25
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTGATATGAATAATGA
Found at i:52268292 original size:34 final size:34
Alignment explanation
Indices: 52268221--52268306 Score: 93
Period size: 34 Copynumber: 2.5 Consensus size: 34
52268211 GGGCCTTAGC
* * *
52268221 CCCACTTTTAGTAGCAGTAGCAGTCTGGGCCTGAG
1 CCCAC-TTCAGTAACAGTAGCAGTCTGAGCCTGAG
* * *
52268256 CCCGCTTCAGTAACAGTGGCAGTCTGAGCCTTAG
1 CCCACTTCAGTAACAGTAGCAGTCTGAGCCTGAG
*
52268290 CCCATTTCAGT-ACAGTA
1 CCCACTTCAGTAACAGTA
52268307 TGCAAACAAA
Statistics
Matches: 42, Mismatches: 9, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
33 5 0.12
34 33 0.79
35 4 0.10
ACGTcount: A:0.22, C:0.28, G:0.24, T:0.26
Consensus pattern (34 bp):
CCCACTTCAGTAACAGTAGCAGTCTGAGCCTGAG
Found at i:52271498 original size:30 final size:30
Alignment explanation
Indices: 52271463--52271536 Score: 98
Period size: 30 Copynumber: 2.5 Consensus size: 30
52271453 AGTTTTTCCC
52271463 AGCTCGATTT-AGCTCACATGT-GCTTAATTT
1 AGCTCG-TTTGAGCTCA-ATGTAGCTTAATTT
* *
52271493 AGCTCGTTTGAGCTCAATTTAGCTTACTTT
1 AGCTCGTTTGAGCTCAATGTAGCTTAATTT
52271523 AGCTCGTTTGAGCT
1 AGCTCGTTTGAGCT
52271537 TGGCTTAAGT
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
29 6 0.15
30 34 0.85
ACGTcount: A:0.20, C:0.20, G:0.19, T:0.41
Consensus pattern (30 bp):
AGCTCGTTTGAGCTCAATGTAGCTTAATTT
Found at i:52280903 original size:27 final size:27
Alignment explanation
Indices: 52280872--52281049 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
52280862 TAAATTGTAC
52280872 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** *
52280899 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
52280925 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
*
52280953 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* *
52280981 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
52281008 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
52281035 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
52281050 GACTCAATAT
Statistics
Matches: 129, Mismatches: 19, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 23 0.18
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:52280986 original size:82 final size:81
Alignment explanation
Indices: 52280873--52281028 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
52280863 AAATTGTACA
* *
52280873 GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTG
1 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTA-GCACTAAGTG
52280937 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
** *
52280954 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTG
1 GCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTG
*
52281019 TGCGAGTTGA
65 TGCGAATTGA
52281029 TTATATAGCA
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 15 0.22
82 51 0.76
83 1 0.01
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.29
Consensus pattern (81 bp):
GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:52281040 original size:82 final size:81
Alignment explanation
Indices: 52280869--52281049 Score: 229
Period size: 82 Copynumber: 2.2 Consensus size: 81
52280859 GATTAAATTG
* *
52280869 TACAGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
52280934 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * ** *
52280950 TGCGGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TAGCACT
1 TACAGCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACT
* **
52281014 AAGTGTGCGAGTTGATTA
64 AAGTGTGCGAATTGACCA
* *
52281032 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
52281050 GACTCAATAT
Statistics
Matches: 84, Mismatches: 14, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
81 18 0.21
82 66 0.79
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
GTGTGCGAATTGACCA
Found at i:52282794 original size:14 final size:14
Alignment explanation
Indices: 52282775--52282802 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
52282765 AAGTCATTCT
52282775 TTGTGAATTTTTGA
1 TTGTGAATTTTTGA
52282789 TTGTGAATTTTTGA
1 TTGTGAATTTTTGA
52282803 ATTTTGTAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.21, C:0.00, G:0.21, T:0.57
Consensus pattern (14 bp):
TTGTGAATTTTTGA
Found at i:52289347 original size:25 final size:26
Alignment explanation
Indices: 52289303--52289356 Score: 67
Period size: 25 Copynumber: 2.1 Consensus size: 26
52289293 TTCTCCTAAA
*
52289303 TTTCAATTTTATTTGATTATTTAAT-T
1 TTTCAATTTTATTGGATTA-TTAATAT
*
52289329 TTTCAA-TTTATTGGGTTATTAATAT
1 TTTCAATTTTATTGGATTATTAATAT
52289354 TTT
1 TTT
52289357 ATGCAAATTG
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
24 5 0.20
25 14 0.56
26 6 0.24
ACGTcount: A:0.26, C:0.04, G:0.07, T:0.63
Consensus pattern (26 bp):
TTTCAATTTTATTGGATTATTAATAT
Found at i:52297898 original size:38 final size:38
Alignment explanation
Indices: 52297856--52298045 Score: 290
Period size: 38 Copynumber: 4.9 Consensus size: 38
52297846 ATGCTAGAAA
52297856 TATATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGTAT
1 TATATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGTAT
*
52297894 TATATCCGGGTTAAATCCCACAGGCTTCGTGCTGGTAT
1 TATATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGTAT
*
52297932 TATATCCGGGTTAAATCCCGCAAGCTTCGTGCTGGTAT
1 TATATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGTAT
* *
52297970 TATATCCGGGTTAAATCCCGCAGGCCTAGTGCTGGTAT
1 TATATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGTAT
* * * *
52298008 TATATCTGAGCTTAAAGTCCCGCAGGTTTTGTGCTGGT
1 TATATCCG-GGTTAAA-TCCCGCAGGCTTCGTGCTGGT
52298046 GACTGGATTC
Statistics
Matches: 139, Mismatches: 11, Indels: 2
0.91 0.07 0.01
Matches are distributed among these distances:
38 115 0.83
39 6 0.04
40 18 0.13
ACGTcount: A:0.20, C:0.23, G:0.25, T:0.32
Consensus pattern (38 bp):
TATATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGTAT
Found at i:52303207 original size:49 final size:49
Alignment explanation
Indices: 52303138--52303574 Score: 638
Period size: 49 Copynumber: 9.1 Consensus size: 49
52303128 GAAATGATAG
*
52303138 TAAGGCCTAATGGTCGATGTGATGAATGTGAAAGTGTATATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGA
52303187 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG--TATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGA
*
52303234 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTGTATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGA
52303283 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGA
*
52303332 TAGGGCCTAATGGCCGATGTGATGAATGTGAAAGTG--TATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGA
*
52303379 TAAGGCCTAATGGCCGATGTGATGAATGTGGAAGTGTATATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGA
* * * * * * * *
52303428 CAGGGCCGAGTGGCCAACGTGATGAATGTGAGAGTG--TATATGTGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGA
*
52303475 TAAGGCCTAATGGCCGATGTGATGAATGTGGAAGTGTATATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGA
* * * * * * *
52303524 CAGGGCCGAGTGGCCAACGTGATGGATGTGAAAGTGTATA-A-ATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGA
52303571 TAAG
1 TAAG
52303575 TCCCGAAGGG
Statistics
Matches: 349, Mismatches: 33, Indels: 14
0.88 0.08 0.04
Matches are distributed among these distances:
47 138 0.40
48 1 0.00
49 210 0.60
ACGTcount: A:0.31, C:0.09, G:0.32, T:0.29
Consensus pattern (49 bp):
TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGA
Found at i:52303302 original size:96 final size:96
Alignment explanation
Indices: 52303141--52303574 Score: 624
Period size: 96 Copynumber: 4.5 Consensus size: 96
52303131 ATGATAGTAA
* *
52303141 GGCCTAATGGTCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATG
1 GGCCTAATGGCCGATGTGATGAATGTGAAAG-GTGTATATATGTGATAAGGCCTAATGGCCGATG
*
52303206 TGATGAATGTGAAAGTG-TATATATGTGATAA
65 TGATGAATGTGAAAGTGATATATATGTGATAG
52303237 GGCCTAATGGCCGATGTGATGAATGTGAAAGTGTGTATATATGTGATAAGGCCTAATGGCCGATG
1 GGCCTAATGGCCGATGTGATGAATGTGAAAG-GTGTATATATGTGATAAGGCCTAATGGCCGATG
52303302 TGATGAATGTGAAAGTGTATATATATGTGATAG
65 TGATGAATGTGAAAGTG-ATATATATGTGATAG
52303335 GGCCTAATGGCCGATGTGATGAATGTGAAA-GTGTATATATGTGATAAGGCCTAATGGCCGATGT
1 GGCCTAATGGCCGATGTGATGAATGTGAAAGGTGTATATATGTGATAAGGCCTAATGGCCGATGT
* *
52303399 GATGAATGTGGAAGTGTATATATATGTGACAG
66 GATGAATGTGAAAGTG-ATATATATGTGATAG
* * * * * *
52303431 GGCCGAGTGGCCAACGTGATGAATGTGAGA-GTGTATATGTGTGATAAGGCCTAATGGCCGATGT
1 GGCCTAATGGCCGATGTGATGAATGTGAAAGGTGTATATATGTGATAAGGCCTAATGGCCGATGT
* *
52303495 GATGAATGTGGAAGTGTATATATATGTGACAG
66 GATGAATGTGAAAGTG-ATATATATGTGATAG
* * * * * *
52303527 GGCCGAGTGGCCAACGTGATGGATGTGAAA-GTGTATAAATGTGATAAG
1 GGCCTAATGGCCGATGTGATGAATGTGAAAGGTGTATATATGTGATAAG
52303575 TCCCGAAGGG
Statistics
Matches: 321, Mismatches: 15, Indels: 4
0.94 0.04 0.01
Matches are distributed among these distances:
96 278 0.87
98 43 0.13
ACGTcount: A:0.30, C:0.09, G:0.32, T:0.29
Consensus pattern (96 bp):
GGCCTAATGGCCGATGTGATGAATGTGAAAGGTGTATATATGTGATAAGGCCTAATGGCCGATGT
GATGAATGTGAAAGTGATATATATGTGATAG
Found at i:52303401 original size:145 final size:145
Alignment explanation
Indices: 52303138--52303574 Score: 639
Period size: 145 Copynumber: 3.0 Consensus size: 145
52303128 GAAATGATAG
*
52303138 TAAGGCCTAATGGTCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCG
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCG
52303203 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAG
66 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAG
52303268 TGTGTATATATGTGA
131 TGTGTATATATGTGA
*
52303283 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAGGGCCTAATGGCCG
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCG
*
52303348 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGGAAG
66 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAG
*
52303413 TGTATATATATGTGA
131 TGTGTATATATGTGA
* * * * * * * *
52303428 CAGGGCCGAGTGGCCAACGTGATGAATGTGAGAGTG--TATATGTGTGATAAGGCCTAATGGCCG
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCG
* * * * * * * *
52303491 ATGTGATGAATGTGGAAGTGTATATATATGTGACAGGGCCGAGTGGCCAACGTGATGGATGTGAA
66 ATGTGATGAATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
*
52303556 A--GTGTATAAATGTGA
129 AGTGTGTATATATGTGA
52303571 TAAG
1 TAAG
52303575 TCCCGAAGGG
Statistics
Matches: 264, Mismatches: 26, Indels: 6
0.89 0.09 0.02
Matches are distributed among these distances:
143 58 0.22
145 206 0.78
ACGTcount: A:0.31, C:0.09, G:0.32, T:0.29
Consensus pattern (145 bp):
TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCG
ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAG
TGTGTATATATGTGA
Found at i:52306605 original size:40 final size:40
Alignment explanation
Indices: 52306546--52306699 Score: 238
Period size: 40 Copynumber: 3.9 Consensus size: 40
52306536 TATTCGGATG
* * *
52306546 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCTAATGACT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
*
52306586 A-ATTCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
1 ATA-ACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
*
52306626 ATAACCGGGCTAAGTCCCGAAGGCAATTGTGCGAGTTACT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
*
52306666 ATAACCGGGCTAAGTCCCGAAGGCATTTGAGCGA
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGA
52306700 ATAGCTATAT
Statistics
Matches: 104, Mismatches: 8, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
39 1 0.01
40 102 0.98
41 1 0.01
ACGTcount: A:0.27, C:0.23, G:0.27, T:0.23
Consensus pattern (40 bp):
ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
Found at i:52306708 original size:40 final size:40
Alignment explanation
Indices: 52306546--52306727 Score: 228
Period size: 40 Copynumber: 4.6 Consensus size: 40
52306536 TATTCGGATG
*
52306546 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCTA-ATGACT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGAT-ACT
* *
52306586 A-ATTCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
1 ATA-ACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACT
* *
52306626 ATAACCGGGCTAAGTCCCGAAGGCAATTGTGCGAGTTACT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACT
*
52306666 ATAACCGGGCTAAGTCCCGAAGGCATTTGAGCGA-ATAGCT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATA-CT
* **
52306706 ATATCC-GGCTAAACCCCGAAGG
1 ATAACCGGGCTAAGTCCCGAAGG
52306728 TACTTGGTTG
Statistics
Matches: 127, Mismatches: 11, Indels: 9
0.86 0.07 0.06
Matches are distributed among these distances:
39 17 0.13
40 108 0.85
41 2 0.02
ACGTcount: A:0.27, C:0.24, G:0.26, T:0.23
Consensus pattern (40 bp):
ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACT
Found at i:52313748 original size:40 final size:39
Alignment explanation
Indices: 52313664--52313848 Score: 212
Period size: 40 Copynumber: 4.6 Consensus size: 39
52313654 TTGAATGATG
* * * *
52313664 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGT-CCGAAGGCATTTGTGC-GAGTTACTAAA
* * *
52313704 TCCGGACTAAGATCCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAG-TCCGAAGGCATTTGTGCGAGTTACTAAA
*
52313744 TCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCGAAGGCATTTGTGCGAGTTACTAAA
*
52313783 TCCGGGTTAAGTCCTGAAGGCATTTGTGCGAGTTACTATAA
1 TCCGGGCTAAGTCC-GAAGGCATTTGTGCGAGTTACTA-AA
*
52313824 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGT-CCGAAGGCATTTG
52313849 AACGAGGAGC
Statistics
Matches: 125, Mismatches: 15, Indels: 10
0.83 0.10 0.07
Matches are distributed among these distances:
39 37 0.30
40 76 0.61
41 12 0.10
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.26
Consensus pattern (39 bp):
TCCGGGCTAAGTCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:52313802 original size:79 final size:81
Alignment explanation
Indices: 52313664--52313848 Score: 236
Period size: 79 Copynumber: 2.3 Consensus size: 81
52313654 TTGAATGATG
*
52313664 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATT
52313728 TGTGCGAGATACTA-A
66 TGTGCGAGATACTATA
* * * **
52313743 TTCCGGGCTAAG-CCCGAAGGCATTTGTGC-GAGTTACTAAATCCGGGTTAAG-TCCTGAAGGCA
1 -TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCC-GAAGGCA
*
52313805 TTTGTGCGAGTTACTATA
64 TTTGTGCGAGATACTATA
* *
52313823 ACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
52313849 AACGAGGAGC
Statistics
Matches: 92, Mismatches: 9, Indels: 8
0.84 0.08 0.07
Matches are distributed among these distances:
78 3 0.03
79 56 0.61
80 33 0.36
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.26
Consensus pattern (81 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATT
TGTGCGAGATACTATA
Found at i:52313870 original size:79 final size:78
Alignment explanation
Indices: 52313665--52313881 Score: 210
Period size: 79 Copynumber: 2.7 Consensus size: 78
52313655 TGAATGATGT
** * * *
52313665 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATTT
1 CCGGGCTAAG-CCCGAAGGCATTTGAAC-GAGTGACTATATCCGG-TTAAGATCCGAAGGCATTT
*
52313729 GTGCGAGATACTAATT
63 GTGCGAGATACTAATA
** * *
52313745 CCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAAATCCGGGTTAAG-TCCTGAAGGCATTTG
1 CCGGGCTAAGCCCGAAGGCATTTGAACGAGTGACTATATCC-GGTTAAGATCC-GAAGGCATTTG
*
52313809 TGCGAGTTACT-ATAA
64 TGCGAGATACTAAT-A
*
52313824 CCGGGCTATGTCCCGAAGGCATTTGAACGAG-GAGCTATATCCGGTTAA-ATTCCGAAGG
1 CCGGGCTAAG-CCCGAAGGCATTTGAACGAGTGA-CTATATCCGGTTAAGA-TCCGAAGG
52313882 TACGTGATTT
Statistics
Matches: 117, Mismatches: 12, Indels: 17
0.80 0.08 0.12
Matches are distributed among these distances:
78 5 0.04
79 65 0.56
80 47 0.40
ACGTcount: A:0.26, C:0.22, G:0.28, T:0.25
Consensus pattern (78 bp):
CCGGGCTAAGCCCGAAGGCATTTGAACGAGTGACTATATCCGGTTAAGATCCGAAGGCATTTGTG
CGAGATACTAATA
Found at i:52321685 original size:79 final size:81
Alignment explanation
Indices: 52321549--52321733 Score: 236
Period size: 79 Copynumber: 2.3 Consensus size: 81
52321539 TTGAATGATG
*
52321549 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATT
52321613 TGTGCGAGATACTA-A
66 TGTGCGAGATACTATA
* * * **
52321628 TTCCGGGCTAAG-CCCGAAGGCATTTGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCA
1 -TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCA
*
52321690 TTTGTGCGAGTTACTATA
64 TTTGTGCGAGATACTATA
* *
52321708 ACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
52321734 AACGAGGAGC
Statistics
Matches: 92, Mismatches: 9, Indels: 8
0.84 0.08 0.07
Matches are distributed among these distances:
78 1 0.01
79 58 0.63
80 33 0.36
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (81 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATT
TGTGCGAGATACTATA
Found at i:52321747 original size:40 final size:40
Alignment explanation
Indices: 52321550--52321733 Score: 216
Period size: 40 Copynumber: 4.6 Consensus size: 40
52321540 TGAATGATGT
* * * *
52321550 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTATAA
* * *
52321590 CCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTA-ATT
1 CCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTATA-A
52321630 CCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTA-AA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
*
52321668 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 -CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
*
52321709 CCGGGCTATGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTG
52321734 AACGAGGAGC
Statistics
Matches: 126, Mismatches: 11, Indels: 14
0.83 0.07 0.09
Matches are distributed among these distances:
39 35 0.28
40 81 0.64
41 10 0.08
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
Found at i:52321755 original size:79 final size:79
Alignment explanation
Indices: 52321550--52321756 Score: 199
Period size: 79 Copynumber: 2.6 Consensus size: 79
52321540 TGAATGATGT
** * * * **
52321550 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGAT-CCGAAGGCATT
1 CCGGGCTAAG-CCCGAAGGCATTTGAAC-GAGTGACTAAATCCGGGTTAAG-TCCCGAAGGCATT
*
52321613 TGTGCGAGATACTAATT
63 TGTGCGAGATACTAATA
** *
52321630 CCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAAATCCGGGTTAAGTCCCGAAGGCATTTGT
1 CCGGGCTAAGCCCGAAGGCATTTGAACGAGTGACTAAATCCGGGTTAAGTCCCGAAGGCATTTGT
*
52321695 GCGAGTTACT-ATAA
66 GCGAGATACTAAT-A
* *
52321709 CCGGGCTATGTCCCGAAGGCATTTGAACGAG-GAGCTATATCC-GGTTAA
1 CCGGGCTAAG-CCCGAAGGCATTTGAACGAGTGA-CTAAATCCGGGTTAA
52321757 ATTTCCGAAG
Statistics
Matches: 109, Mismatches: 13, Indels: 11
0.82 0.10 0.08
Matches are distributed among these distances:
78 3 0.03
79 64 0.59
80 42 0.39
ACGTcount: A:0.26, C:0.22, G:0.28, T:0.25
Consensus pattern (79 bp):
CCGGGCTAAGCCCGAAGGCATTTGAACGAGTGACTAAATCCGGGTTAAGTCCCGAAGGCATTTGT
GCGAGATACTAATA
Found at i:52324159 original size:38 final size:38
Alignment explanation
Indices: 52324098--52324198 Score: 123
Period size: 38 Copynumber: 2.6 Consensus size: 38
52324088 ATTTGATGTG
*
52324098 TATCCGGGCTTAAAGACCCACAGGCTAT-ATGCTGGAAATA
1 TATCCGGG-TTAAA-TCCCACAGGCT-TCATGCTGGAAATA
* * *
52324138 TATCCGGGTTAAATCCCACAGGCTTCGTGCTGGTATTA
1 TATCCGGGTTAAATCCCACAGGCTTCATGCTGGAAATA
*
52324176 TATCCGGGTTAAATCCCGCAGGC
1 TATCCGGGTTAAATCCCACAGGC
52324199 CTAGTGCTGG
Statistics
Matches: 55, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
37 1 0.02
38 41 0.75
39 5 0.09
40 8 0.15
ACGTcount: A:0.26, C:0.25, G:0.24, T:0.26
Consensus pattern (38 bp):
TATCCGGGTTAAATCCCACAGGCTTCATGCTGGAAATA
Found at i:52324206 original size:38 final size:38
Alignment explanation
Indices: 52324127--52324237 Score: 141
Period size: 38 Copynumber: 2.9 Consensus size: 38
52324117 ACAGGCTATA
* * * * *
52324127 TGCTGGAAATATATCCGGGTTAAATCCCACAGGCTTCG
1 TGCTGGTATTATATCCGGGTTAAATCCCGCAGGCCTAG
52324165 TGCTGGTATTATATCCGGGTTAAATCCCGCAGGCCTAG
1 TGCTGGTATTATATCCGGGTTAAATCCCGCAGGCCTAG
* *
52324203 TGCTGGTATTATATCTGAGCTTAAAGTCCCGCAGG
1 TGCTGGTATTATATCCG-GGTTAAA-TCCCGCAGG
52324238 TTTCGTGCCA
Statistics
Matches: 64, Mismatches: 7, Indels: 2
0.88 0.10 0.03
Matches are distributed among these distances:
38 49 0.77
39 6 0.09
40 9 0.14
ACGTcount: A:0.23, C:0.23, G:0.25, T:0.29
Consensus pattern (38 bp):
TGCTGGTATTATATCCGGGTTAAATCCCGCAGGCCTAG
Found at i:52331651 original size:31 final size:31
Alignment explanation
Indices: 52331608--52331693 Score: 129
Period size: 31 Copynumber: 2.8 Consensus size: 31
52331598 TCAATCTCAG
*
52331608 CATAT-ACTGGGCCGAGGCCTTTACATTACT
1 CATATCACTGGGCCGAAGCCTTTACATTACT
* * *
52331638 CATATCACTGGGCCAAAGCCTTTTCATTATT
1 CATATCACTGGGCCGAAGCCTTTACATTACT
52331669 CATATCACTGGGCCGAAGCCTTTAC
1 CATATCACTGGGCCGAAGCCTTTAC
52331694 TGTAACAATA
Statistics
Matches: 49, Mismatches: 6, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
30 5 0.10
31 44 0.90
ACGTcount: A:0.24, C:0.28, G:0.17, T:0.30
Consensus pattern (31 bp):
CATATCACTGGGCCGAAGCCTTTACATTACT
Found at i:52331925 original size:25 final size:25
Alignment explanation
Indices: 52331897--52331981 Score: 93
Period size: 26 Copynumber: 3.4 Consensus size: 25
52331887 CTAGAGGCCT
*
52331897 AGCCTCTTTTAAT-AATTGGGGCAAA
1 AGCC-CTTTTAATAAACTGGGGCAAA
*
52331922 AGCCCTTTTTGATAAACTGGGGCAAA
1 AGCCC-TTTTAATAAACTGGGGCAAA
**
52331948 AGCCCTTTTCGGTAAACTGGGGC-AA
1 AGCCCTTTT-AATAAACTGGGGCAAA
52331973 AGCCCTTTT
1 AGCCCTTTT
52331982 GCACTTCCTC
Statistics
Matches: 54, Mismatches: 3, Indels: 6
0.86 0.05 0.10
Matches are distributed among these distances:
24 1 0.02
25 25 0.46
26 28 0.52
ACGTcount: A:0.27, C:0.21, G:0.22, T:0.29
Consensus pattern (25 bp):
AGCCCTTTTAATAAACTGGGGCAAA
Found at i:52331949 original size:26 final size:26
Alignment explanation
Indices: 52331913--52331981 Score: 113
Period size: 26 Copynumber: 2.7 Consensus size: 26
52331903 TTTTAATAAT
*
52331913 TGGGGCAAAAGCCCTTTTTGATAAAC
1 TGGGGCAAAAGCCCTTTTCGATAAAC
*
52331939 TGGGGCAAAAGCCCTTTTCGGTAAAC
1 TGGGGCAAAAGCCCTTTTCGATAAAC
52331965 TGGGGC-AAAGCCCTTTT
1 TGGGGCAAAAGCCCTTTT
52331982 GCACTTCCTC
Statistics
Matches: 41, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
25 11 0.27
26 30 0.73
ACGTcount: A:0.26, C:0.22, G:0.26, T:0.26
Consensus pattern (26 bp):
TGGGGCAAAAGCCCTTTTCGATAAAC
Found at i:52334664 original size:27 final size:26
Alignment explanation
Indices: 52334620--52334670 Score: 66
Period size: 27 Copynumber: 1.9 Consensus size: 26
52334610 CTCGCTGAAA
*
52334620 TCTGGTGGCCTCGCCACATATATCTTT
1 TCTGGTGACCTCGCCACA-ATATCTTT
* *
52334647 TCTGGTGACTTCGTCACAATATCT
1 TCTGGTGACCTCGCCACAATATCT
52334671 GGCAGCCTCA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
26 6 0.29
27 15 0.71
ACGTcount: A:0.18, C:0.27, G:0.18, T:0.37
Consensus pattern (26 bp):
TCTGGTGACCTCGCCACAATATCTTT
Found at i:52338314 original size:47 final size:47
Alignment explanation
Indices: 52338197--52338491 Score: 392
Period size: 47 Copynumber: 6.2 Consensus size: 47
52338187 AATTCTAAAT
* *
52338197 TGTGATAAGGCCTAATAGCTGATGTGATGAATGTGAAAGTGTATATATA
1 TGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG--TATATA
* *
52338246 TGTGATAAGGCTTAATGGCCGATGTGATGAATGTGAAAGTGTATATG
1 TGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATA
* *
52338293 TGCGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATA
1 TGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG--TATATA
* *
52338342 TGTGATAAGGCTTAATGGCCGATGTGATGAATGTGAAAGTGTATATG
1 TGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATA
* *
52338389 CGTGATAAGGCTTAATGGCCGATGTGATGAATGTGAAAGTGTATATA
1 TGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATA
* * * * * * * *
52338436 TGTGACAGGGCCGAGTGGCCAATGTGATGGATGTGAAAGTGCATAAA
1 TGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATA
52338483 TGTGATAAG
1 TGTGATAAG
52338492 TCCCGAAGGG
Statistics
Matches: 218, Mismatches: 26, Indels: 6
0.87 0.10 0.02
Matches are distributed among these distances:
47 137 0.63
49 81 0.37
ACGTcount: A:0.32, C:0.08, G:0.31, T:0.29
Consensus pattern (47 bp):
TGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATA
Found at i:52338344 original size:96 final size:96
Alignment explanation
Indices: 52338200--52338476 Score: 432
Period size: 96 Copynumber: 2.9 Consensus size: 96
52338190 TCTAAATTGT
*
52338200 GATAAGGCCTAATAGCTGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCTTAATGGC
1 GATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCTTAATGGC
*
52338265 CGATGTGATGAATGTGAAAGTGTATATGTGC
66 CGATGTGATGAATGTGAAAGTGTATATGCGC
52338296 GATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCTTAATGGC
1 GATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCTTAATGGC
*
52338361 CGATGTGATGAATGTGAAAGTGTATATGCGT
66 CGATGTGATGAATGTGAAAGTGTATATGCGC
* * * * ** *
52338392 GATAAGGCTTAATGGCCGATGTGATGAATGTGAAAGTG--TATATATGTGACAGGGCCGAGTGGC
1 GATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCTTAATGGC
* *
52338455 CAATGTGATGGATGTGAAAGTG
66 CGATGTGATGAATGTGAAAGTG
52338477 CATAAATGTG
Statistics
Matches: 169, Mismatches: 12, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
94 40 0.24
96 129 0.76
ACGTcount: A:0.31, C:0.08, G:0.31, T:0.29
Consensus pattern (96 bp):
GATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCTTAATGGC
CGATGTGATGAATGTGAAAGTGTATATGCGC
Found at i:52338665 original size:37 final size:37
Alignment explanation
Indices: 52338609--52338687 Score: 122
Period size: 37 Copynumber: 2.1 Consensus size: 37
52338599 TCGAGCTCTA
* * *
52338609 AAGACCCGATGACTACGTGTGGGGATTTTGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
*
52338646 AAGACCCGATAACTTCGTGTGGAGATTATGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
52338683 AAGAC
1 AAGAC
52338688 TTCGTAATAA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.24, C:0.19, G:0.32, T:0.25
Consensus pattern (37 bp):
AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
Found at i:52340460 original size:18 final size:18
Alignment explanation
Indices: 52340439--52340477 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
52340429 TGTTTGAGTT
52340439 TTCGAGATTAGATTTGTG
1 TTCGAGATTAGATTTGTG
52340457 TTCGAGATTAGATTTGTG
1 TTCGAGATTAGATTTGTG
52340475 TTC
1 TTC
52340478 CGAAAAATCT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.21, C:0.08, G:0.26, T:0.46
Consensus pattern (18 bp):
TTCGAGATTAGATTTGTG
Found at i:52343087 original size:44 final size:42
Alignment explanation
Indices: 52343024--52343143 Score: 138
Period size: 42 Copynumber: 2.8 Consensus size: 42
52343014 TGAGTTATCG
* * *
52343024 TGTAAGACCACGTCTGGGACGTTGGCGTCGAT-T-TGAGATGTACA
1 TGTAAGACCATGTCTGGGACATTGGCATC-ATATATGA-AT-T-CA
52343068 TGTAAGACCATGTCTGGGACATTGGCATCATATATGAATTCA
1 TGTAAGACCATGTCTGGGACATTGGCATCATATATGAATTCA
* *
52343110 TGTAAGACCCTGTCTGGGACAGTGGCATCA-ATAT
1 TGTAAGACCATGTCTGGGACATTGGCATCATATAT
52343144 TTGATCACAT
Statistics
Matches: 69, Mismatches: 5, Indels: 7
0.85 0.06 0.09
Matches are distributed among these distances:
41 4 0.06
42 30 0.43
43 3 0.04
44 29 0.42
45 3 0.04
ACGTcount: A:0.27, C:0.18, G:0.27, T:0.28
Consensus pattern (42 bp):
TGTAAGACCATGTCTGGGACATTGGCATCATATATGAATTCA
Found at i:52343169 original size:43 final size:41
Alignment explanation
Indices: 52343064--52343171 Score: 110
Period size: 42 Copynumber: 2.5 Consensus size: 41
52343054 ATTTGAGATG
* *
52343064 TACATGTAAGACCATGTCTGGGACATTGGCATCATATATGAA
1 TACATGTAAGA-CACGTCTGGGACAGTGGCATCATATATGAA
* * *
52343106 TTCATGTAAGACCCTGTCTGGGACAGTGGCATCAATATTTG-A
1 TACATGTAAGACAC-GTCTGGGACAGTGGCATC-ATATATGAA
*
52343148 TCACATGTAAAACAACGTCTGGGA
1 T-ACATGTAAGAC-ACGTCTGGGA
52343172 TGTTGGCATT
Statistics
Matches: 54, Mismatches: 8, Indels: 7
0.78 0.12 0.10
Matches are distributed among these distances:
41 1 0.02
42 29 0.54
43 23 0.43
44 1 0.02
ACGTcount: A:0.31, C:0.19, G:0.22, T:0.28
Consensus pattern (41 bp):
TACATGTAAGACACGTCTGGGACAGTGGCATCATATATGAA
Found at i:52345300 original size:93 final size:93
Alignment explanation
Indices: 52345193--52345363 Score: 315
Period size: 93 Copynumber: 1.8 Consensus size: 93
52345183 GCCCCTAAGT
* *
52345193 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
52345258 CGAGTTCGGATGCCTAGTTACATCTCAC
66 CGAGTTCGGATGCCTAGTTACATCTCAC
*
52345286 GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
52345351 CGAGTTCGGATGC
66 CGAGTTCGGATGC
52345364 TCAACCATCC
Statistics
Matches: 75, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 75 1.00
ACGTcount: A:0.28, C:0.29, G:0.22, T:0.21
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATCTCAC
Found at i:52345360 original size:46 final size:46
Alignment explanation
Indices: 52345188--52345360 Score: 219
Period size: 46 Copynumber: 3.7 Consensus size: 46
52345178 AACCCGCCCC
* * *
52345188 TAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
*
52345234 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT-C-
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCATCCA
* *
52345282 TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
52345327 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
52345361 TGCTCAACCA
Statistics
Matches: 109, Mismatches: 9, Indels: 18
0.80 0.07 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 2 0.02
45 2 0.02
46 61 0.56
47 29 0.27
48 2 0.02
49 2 0.02
50 3 0.03
51 2 0.02
ACGTcount: A:0.29, C:0.28, G:0.21, T:0.21
Consensus pattern (46 bp):
TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
Found at i:52345815 original size:30 final size:30
Alignment explanation
Indices: 52345781--52345840 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
52345771 ATTTAATACG
*
52345781 AACTTTGGAAAAATTACACATTTGCCCCTA
1 AACTTTGGAAAAATTACACATTTACCCCTA
* * * *
52345811 AACTTTTGCATAATTACACTTTTACCCCTA
1 AACTTTGGAAAAATTACACATTTACCCCTA
52345841 GGCTCGGGAA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.33, C:0.25, G:0.07, T:0.35
Consensus pattern (30 bp):
AACTTTGGAAAAATTACACATTTACCCCTA
Found at i:52348289 original size:40 final size:40
Alignment explanation
Indices: 52348147--52348326 Score: 201
Period size: 40 Copynumber: 4.5 Consensus size: 40
52348137 ATGATGTCCA
* * *
52348147 GGCTAAGTCCCGAAGGC--TTGTGCTAAGTGAC-AATACCCG
1 GGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAA-ATCCG
* * *
52348186 GACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAATTCCG
1 GGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAATCCG
52348226 GGCTAAGT-CCGAAGGCATTTGTGCGAGTTACTAAATCCG
1 GGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAATCCG
* *
52348265 GGTTAAGTCCCGAAGGCATTTGTGCGAATTACTATAA-CCG
1 GGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AATCCG
*
52348305 GGCTATGTCCCGAAGGCATTTG
1 GGCTAAGTCCCGAAGGCATTTG
52348327 AACGAGGAGC
Statistics
Matches: 122, Mismatches: 13, Indels: 11
0.84 0.09 0.08
Matches are distributed among these distances:
39 51 0.42
40 61 0.50
41 10 0.08
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.25
Consensus pattern (40 bp):
GGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAATCCG
Found at i:52348348 original size:79 final size:79
Alignment explanation
Indices: 52348195--52348349 Score: 192
Period size: 79 Copynumber: 2.0 Consensus size: 79
52348185 GGACTAAGAT
* ** *
52348195 CCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGTCCGAAGGCATTTGTGCGAGTTACTAA
1 CCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGTCCGAAGGCATTTGAACGAGTGACTAA
52348260 ATCCGGGTTAAGTC
66 ATCCGGGTTAAGTC
*
52348274 CCGAAGGCATTTGTGCGA-ATTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG-GAG
1 CCGAAGGCATTTGTGCGAGA-TACTAAT-ACCGGGCTAAGT-CCGAAGGCATTTGAACGAGTGA-
*
52348336 CTATATCC-GGTTAA
62 CTAAATCCGGGTTAA
52348350 ATTCCAAAGG
Statistics
Matches: 66, Mismatches: 6, Indels: 8
0.82 0.08 0.10
Matches are distributed among these distances:
78 3 0.05
79 39 0.59
80 24 0.36
ACGTcount: A:0.26, C:0.21, G:0.27, T:0.26
Consensus pattern (79 bp):
CCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGTCCGAAGGCATTTGAACGAGTGACTAA
ATCCGGGTTAAGTC
Found at i:52356176 original size:39 final size:40
Alignment explanation
Indices: 52356081--52356303 Score: 259
Period size: 39 Copynumber: 5.7 Consensus size: 40
52356071 TTGAATGATG
*
52356081 TCCGGGCTAAGTCCCGAAGGC--TTGTGCTA-AGTGAC-AAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGA-T-ACTAAT
*
52356119 ATCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT
1 -TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGATACTAAT
52356160 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
*
52356199 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTAAAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACT-AAT
*
52356239 T-CGGGTTAAGTCCCGAAGGCATTTGTGCGA-ATTACT-AT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGA-TACTAAT
* *
52356277 AACCGGGCTATGTCCCGAAGGCATTTG
1 -TCCGGGCTAAGTCCCGAAGGCATTTG
52356304 AACGAGGAGC
Statistics
Matches: 164, Mismatches: 9, Indels: 21
0.85 0.05 0.11
Matches are distributed among these distances:
38 2 0.01
39 88 0.54
40 62 0.38
41 11 0.07
42 1 0.01
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.25
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
Found at i:52356259 original size:79 final size:81
Alignment explanation
Indices: 52356081--52356303 Score: 275
Period size: 79 Copynumber: 2.8 Consensus size: 81
52356071 TTGAATGATG
* * *
52356081 TCCGGGCTAAGTCCCGAAGGC--TTGTGCTAAGTGAC-AATATCCGGACTAAGATCCGAAGGCAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAAGT-ACTAATATCCGGGCTAAGACCCGAAGGCAT
52356143 TTGTGCGAGATACTAAT
65 TTGTGCGAGATACTAAT
52356160 TCCGGGCTAAG-CCCGAAGGCATTTGTGCG-AGATACTAAT-TCCGGGCTAAG-CCCGAAGGCAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAAG-TACTAATATCCGGGCTAAGACCCGAAGGCAT
*
52356221 TTGTGCGAGTTACTAAAT
65 TTGTGCGAGATACT-AAT
* * * * *
52356239 T-CGGGTTAAGTCCCGAAGGCATTTGTGCGAATTACT-ATAACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAAGTACTAATATCCGGGCTAAGACCCGAAGGCATT
52356302 TG
66 TG
52356304 AACGAGGAGC
Statistics
Matches: 127, Mismatches: 8, Indels: 17
0.84 0.05 0.11
Matches are distributed among these distances:
78 42 0.33
79 60 0.47
80 25 0.20
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.25
Consensus pattern (81 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAAGTACTAATATCCGGGCTAAGACCCGAAGGCATT
TGTGCGAGATACTAAT
Found at i:52356325 original size:79 final size:78
Alignment explanation
Indices: 52356133--52356326 Score: 193
Period size: 79 Copynumber: 2.5 Consensus size: 78
52356123 GGACTAAGAT
** *
52356133 CCGAAGGCATTTGTGCGAGAT-ACT-AATTCCGGGCTAAGCCCGAAGGCATTTGTGCGAGATACT
1 CCGAAGGCATTTGAACGAG-TGACTAAATTCC-GGTTAAGCCCGAAGGCATTTGTGCGAGATACT
*
52356196 AATTCCGGGCTAAGC
64 AATACCGGGCTAAGC
** * *
52356211 CCGAAGGCATTTGTGCGAGTTACTAAATTCGGGTTAAGTCCCGAAGGCATTTGTGCGA-ATTACT
1 CCGAAGGCATTTGAACGAGTGACTAAATTCCGGTTAAG-CCCGAAGGCATTTGTGCGAGA-TACT
*
52356275 -ATAACCGGGCTATGTC
64 AAT-ACCGGGCTAAG-C
*
52356291 CCGAAGGCATTTGAACGAG-GAGCTATA-TCCGGTTAA
1 CCGAAGGCATTTGAACGAGTGA-CTAAATTCCGGTTAA
52356327 ATTCTGAAGG
Statistics
Matches: 100, Mismatches: 9, Indels: 13
0.82 0.07 0.11
Matches are distributed among these distances:
77 1 0.01
78 31 0.31
79 46 0.46
80 22 0.22
ACGTcount: A:0.26, C:0.21, G:0.27, T:0.25
Consensus pattern (78 bp):
CCGAAGGCATTTGAACGAGTGACTAAATTCCGGTTAAGCCCGAAGGCATTTGTGCGAGATACTAA
TACCGGGCTAAGC
Found at i:52359450 original size:27 final size:27
Alignment explanation
Indices: 52359411--52359581 Score: 141
Period size: 27 Copynumber: 6.3 Consensus size: 27
52359401 TTAGTTTACC
** *
52359411 AAATTACTGAAATACCCTCGA-TTAGCA
1 AAATTACCAAAATACCCTCGACTT-GTA
* *
52359438 AAATTACCAAAATACCC-CTAGTTTGTA
1 AAATTACCAAAATACCCTCGA-CTTGTA
* * *
52359465 AAATTACCAAAATACCC-CTAATTTGTG
1 AAATTACCAAAATACCCTC-GACTTGTA
** *
52359492 AAATTACTGAAATACCCTCGACCTGTA
1 AAATTACCAAAATACCCTCGACTTGTA
*
52359519 AAATTACTAAAATACCCTCGACTTGTA
1 AAATTACCAAAATACCCTCGACTTGTA
** * *
52359546 AAATTACCAAAGCACCCTCGATTTATA
1 AAATTACCAAAATACCCTCGACTTGTA
*
52359573 GAATTACCA
1 AAATTACCA
52359582 TTTTACCCTC
Statistics
Matches: 120, Mismatches: 20, Indels: 8
0.81 0.14 0.05
Matches are distributed among these distances:
26 2 0.02
27 114 0.95
28 4 0.03
ACGTcount: A:0.40, C:0.23, G:0.09, T:0.27
Consensus pattern (27 bp):
AAATTACCAAAATACCCTCGACTTGTA
Found at i:52359579 original size:81 final size:81
Alignment explanation
Indices: 52359411--52359562 Score: 200
Period size: 81 Copynumber: 1.9 Consensus size: 81
52359401 TTAGTTTACC
* * *
52359411 AAATTACTGAAATACCCTCGATTAGCAAAATTACCAAAATACCCCTAGTTTGTAAAATTACCAAA
1 AAATTACTGAAATACCCTCGACTAGCAAAATTACCAAAATACCCCGAGCTTGTAAAATTACCAAA
* *
52359476 ATACCCCTAATTTGTG
66 ACACCCCTAATTTATG
* *
52359492 AAATTACTGAAATACCCTCGACCT-GTAAAATTACTAAAATACCCTCGA-CTTGTAAAATTACCA
1 AAATTACTGAAATACCCTCGA-CTAGCAAAATTACCAAAATACCC-CGAGCTTGTAAAATTACCA
*
52359555 AAGCACCC
64 AAACACCC
52359563 TCGATTTATA
Statistics
Matches: 62, Mismatches: 7, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
81 59 0.95
82 3 0.05
ACGTcount: A:0.41, C:0.24, G:0.09, T:0.26
Consensus pattern (81 bp):
AAATTACTGAAATACCCTCGACTAGCAAAATTACCAAAATACCCCGAGCTTGTAAAATTACCAAA
ACACCCCTAATTTATG
Found at i:52360767 original size:27 final size:27
Alignment explanation
Indices: 52359601--52360766 Score: 1516
Period size: 27 Copynumber: 43.2 Consensus size: 27
52359591 CGATTTACAA
* *
52359601 AATTATTGAAATACCCTTGTAGGGTAG
1 AATTACTGAAATACCCCTGTAGGGTAG
*
52359628 AATTATTGAAATACCCCTGTAGGGTAG
1 AATTACTGAAATACCCCTGTAGGGTAG
*
52359655 AATTACTGAAATACCCCTGTAAGGTAG
1 AATTACTGAAATACCCCTGTAGGGTAG
** * * *
52359682 AATTACCAAAATACCCTTGAAAGGTAG
1 AATTACTGAAATACCCCTGTAGGGTAG
*
52359709 AATTA-TCGAAACACCCCTGTAGGGTAG
1 AATTACT-GAAATACCCCTGTAGGGTAG
* *
52359736 AATTACTGAAATACCCCTATAAGGTAG
1 AATTACTGAAATACCCCTGTAGGGTAG
* *
52359763 AATTACCGAAATACCCCTATAGGGTAG
1 AATTACTGAAATACCCCTGTAGGGTAG
* *
52359790 AATTATTGAAATA-CCCTGTAAGGTAG
1 AATTACTGAAATACCCCTGTAGGGTAG
*
52359816 AATTATTGAAATACCCCTGTAGGGTAG
1 AATTACTGAAATACCCCTGTAGGGTAG
*
52359843 AATTACTGAAATACCCCTGTAAGGTAG
1 AATTACTGAAATACCCCTGTAGGGTAG
* *
52359870 AATTACCGAAATACCCCTTTAGGGTAG
1 AATTACTGAAATACCCCTGTAGGGTAG
*
52359897 AATTACTGAAATACCCCTGTAAGGTAG
1 AATTACTGAAATACCCCTGTAGGGTAG
* *
52359924 AATTACCGAAATACCCCTGTAAGGTAG
1 AATTACTGAAATACCCCTGTAGGGTAG
*
52359951 AATTACCGAAATACCCCTGTAGGGTAG
1 AATTACTGAAATACCCCTGTAGGGTAG
*
52359978 AATTACTGAAATACCCCTGTAAGGTAG
1 AATTACTGAAATACCCCTGTAGGGTAG
*
52360005 AATTA-TCGAAATACCCCTTTAGGGTAG
1 AATTACT-GAAATACCCCTGTAGGGTAG
* *
52360032 AATTACTGAAATACCCTTGTAAGGTAG
1 AATTACTGAAATACCCCTGTAGGGTAG
*
52360059 AATTACTAAAATACCCCTGTAGGGTAG
1 AATTACTGAAATACCCCTGTAGGGTAG
* * * *
52360086 AATTACTAAAATTCCCCTGTAAGATAG
1 AATTACTGAAATACCCCTGTAGGGTAG
* *
52360113 AATAACCGAAATACCCCTGTAGGGTAG
1 AATTACTGAAATACCCCTGTAGGGTAG
* *
52360140 AATTACTAAAATACCCCTGTAAGGTAG
1 AATTACTGAAATACCCCTGTAGGGTAG
*
52360167 AATTACCGAAATACCCCTGTAGGGTAG
1 AATTACTGAAATACCCCTGTAGGGTAG
* *
52360194 AATTACTGAAATACCCTTATAGGGTAG
1 AATTACTGAAATACCCCTGTAGGGTAG
* *
52360221 AATTACCGAAATACCCCTATAGGGTAG
1 AATTACTGAAATACCCCTGTAGGGTAG
* * *
52360248 AATTATTGATATACCCCTGTAAGGTAG
1 AATTACTGAAATACCCCTGTAGGGTAG
*
52360275 AATTATTGAAATACCCCTGTAGGGTAG
1 AATTACTGAAATACCCCTGTAGGGTAG
** *
52360302 AATTACCAAAATACCCCTGTAAGGTAG
1 AATTACTGAAATACCCCTGTAGGGTAG
* *
52360329 AATTACCGAAATACCCCTTTAGGGTAG
1 AATTACTGAAATACCCCTGTAGGGTAG
*
52360356 AATTACTGAAATACCCCTGTAAGGTAG
1 AATTACTGAAATACCCCTGTAGGGTAG
*
52360383 AATTA-TCGAAATACCCCTGTAAGGTAG
1 AATTACT-GAAATACCCCTGTAGGGTAG
*
52360410 AATTATTGAAATACCCCTGTAGGGTAG
1 AATTACTGAAATACCCCTGTAGGGTAG
* * *
52360437 AATTACTGAAATACCCCTCTAAGGTAC
1 AATTACTGAAATACCCCTGTAGGGTAG
* *
52360464 AATTA-TCGAAATACCTCTTTAGGGTAG
1 AATTACT-GAAATACCCCTGTAGGGTAG
*
52360491 AATTACTGAAATACCCCTGTATGGTAG
1 AATTACTGAAATACCCCTGTAGGGTAG
* *
52360518 AATTACTAAAATACCCTTGTAGGGTAG
1 AATTACTGAAATACCCCTGTAGGGTAG
* * *
52360545 AATTACTAAAATACCCCTGTAAGATAG
1 AATTACTGAAATACCCCTGTAGGGTAG
* *
52360572 AATAACCGAAATACCCCTGTAGGGTAG
1 AATTACTGAAATACCCCTGTAGGGTAG
* *
52360599 AATTACTAAAATACCCCTGTAAGGTAG
1 AATTACTGAAATACCCCTGTAGGGTAG
* *
52360626 AATTACCGAAATACCCCTATAGGGTAG
1 AATTACTGAAATACCCCTGTAGGGTAG
* *
52360653 AATTACTAAAATACCCCTATAGGGTAG
1 AATTACTGAAATACCCCTGTAGGGTAG
* * *
52360680 AATTACCGAAATACCCTTGTAGGGTAA
1 AATTACTGAAATACCCCTGTAGGGTAG
* *
52360707 AAATATTGAAATACCCCTGTAGGGTAG
1 AATTACTGAAATACCCCTGTAGGGTAG
* * *
52360734 AATTACCGAGATA-CCCTCGTAGGGTAA
1 AATTACTGAAATACCCCT-GTAGGGTAG
52360761 AATTAC
1 AATTAC
52360767 CATTTTGCCC
Statistics
Matches: 1000, Mismatches: 129, Indels: 20
0.87 0.11 0.02
Matches are distributed among these distances:
26 31 0.03
27 965 0.96
28 4 0.00
ACGTcount: A:0.37, C:0.19, G:0.18, T:0.26
Consensus pattern (27 bp):
AATTACTGAAATACCCCTGTAGGGTAG
Found at i:52361360 original size:27 final size:26
Alignment explanation
Indices: 52361337--52361437 Score: 112
Period size: 27 Copynumber: 3.8 Consensus size: 26
52361327 TAAGTGGCGT
*
52361337 TGCCACATTATCTGATTCTGGTGGCTA
1 TGCCACAATATCTG-TTCTGGTGGCTA
*
52361364 TGCCACAAATATCTGTTCTGGTGGCTC
1 TGCCAC-AATATCTGTTCTGGTGGCTA
* * *
52361391 TGCCACAATATATGTATCTGGTGACTC
1 TGCCACAATATCTGT-TCTGGTGGCTA
* *
52361418 TGTCACAATATCTATTCTGG
1 TGCCACAATATCTGTTCTGG
52361438 CAGCCATGCT
Statistics
Matches: 65, Mismatches: 7, Indels: 5
0.84 0.09 0.06
Matches are distributed among these distances:
26 13 0.20
27 45 0.69
28 7 0.11
ACGTcount: A:0.22, C:0.23, G:0.20, T:0.36
Consensus pattern (26 bp):
TGCCACAATATCTGTTCTGGTGGCTA
Found at i:52361585 original size:6 final size:6
Alignment explanation
Indices: 52361554--52361647 Score: 77
Period size: 6 Copynumber: 15.3 Consensus size: 6
52361544 TTGCATTCAC
* * *
52361554 ATTCTG ATTGTG ATTCT- ATTACCTG ATACTG ATTCTG ATTCTG -TCACCTG
1 ATTCTG ATTCTG ATTCTG ATT--CTG ATTCTG ATTCTG ATTCTG AT--TCTG
* *
52361604 ATTCTG ATTCTG ATTCTG ATTCTT ATTTTG ATTCT- AGTTCTG AT
1 ATTCTG ATTCTG ATTCTG ATTCTG ATTCTG ATTCTG A-TTCTG AT
52361648 AATGCTTCTT
Statistics
Matches: 70, Mismatches: 10, Indels: 16
0.73 0.10 0.17
Matches are distributed among these distances:
5 5 0.07
6 56 0.80
7 6 0.09
8 3 0.04
ACGTcount: A:0.19, C:0.17, G:0.15, T:0.49
Consensus pattern (6 bp):
ATTCTG
Found at i:52361621 original size:25 final size:25
Alignment explanation
Indices: 52361554--52361621 Score: 100
Period size: 25 Copynumber: 2.7 Consensus size: 25
52361544 TTGCATTCAC
* * *
52361554 ATTCTGATTGTGATTCTATTACCTG
1 ATTCTGATTCTGATTCTGTCACCTG
*
52361579 ATACTGATTCTGATTCTGTCACCTG
1 ATTCTGATTCTGATTCTGTCACCTG
52361604 ATTCTGATTCTGATTCTG
1 ATTCTGATTCTGATTCTG
52361622 ATTCTTATTT
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 38 1.00
ACGTcount: A:0.19, C:0.19, G:0.16, T:0.46
Consensus pattern (25 bp):
ATTCTGATTCTGATTCTGTCACCTG
Found at i:52364831 original size:34 final size:35
Alignment explanation
Indices: 52364758--52364843 Score: 129
Period size: 34 Copynumber: 2.5 Consensus size: 35
52364748 GGGCCTATGT
* *
52364758 CCATATCAGTAACAGTAGCAGTCTGGGGCCTTAGC
1 CCATTTCAGTAACAGTAGCAGTCTGGGACCTTAGC
*
52364793 CCATTTCAGTAACAGTAGCAGTCT-GGACTTTAGC
1 CCATTTCAGTAACAGTAGCAGTCTGGGACCTTAGC
*
52364827 CCATTTCAGTAATAGTA
1 CCATTTCAGTAACAGTA
52364844 ATTAGTGCAG
Statistics
Matches: 47, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
34 24 0.51
35 23 0.49
ACGTcount: A:0.28, C:0.23, G:0.21, T:0.28
Consensus pattern (35 bp):
CCATTTCAGTAACAGTAGCAGTCTGGGACCTTAGC
Found at i:52365264 original size:27 final size:27
Alignment explanation
Indices: 52365234--52365348 Score: 126
Period size: 27 Copynumber: 4.3 Consensus size: 27
52365224 AACAAATCTT
* * *
52365234 TCATTTTACCTTATCGGGGTATTACAG
1 TCATTTTACCCTATCAGGGTATTTCAG
* *
52365261 TCATTTTACCCTA-CAAGGTTATTTCGG
1 TCATTTTACCCTATC-AGGGTATTTCAG
* * *
52365288 TCATTCTACCCTATAAGGGTATTTCGG
1 TCATTTTACCCTATCAGGGTATTTCAG
*
52365315 TCA-TTTACCCTATGAGGGTATTTCAG
1 TCATTTTACCCTATCAGGGTATTTCAG
52365341 TCATTTTA
1 TCATTTTA
52365349 TCACATAAGG
Statistics
Matches: 74, Mismatches: 11, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
26 24 0.32
27 50 0.68
ACGTcount: A:0.23, C:0.20, G:0.17, T:0.41
Consensus pattern (27 bp):
TCATTTTACCCTATCAGGGTATTTCAG
Found at i:52365357 original size:53 final size:54
Alignment explanation
Indices: 52365250--52365361 Score: 129
Period size: 53 Copynumber: 2.1 Consensus size: 54
52365240 TACCTTATCG
* * *
52365250 GGGTATTACAGTCATTTTACCCTACAAGGTTATTTCGGTCATTCTACCCTATAA
1 GGGTATTACAGTCATTTTACCCTACAAGGGTATTTCAGTCATTCTACACTATAA
* * ** *
52365304 GGGTATTTCGGTCA-TTTACCCTATGAGGGTATTTCAGTCATTTTATCAC-ATAA
1 GGGTATTACAGTCATTTTACCCTACAAGGGTATTTCAGTCATTCTA-CACTATAA
52365357 GGGTA
1 GGGTA
52365362 AATCATCATT
Statistics
Matches: 49, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
53 35 0.71
54 14 0.29
ACGTcount: A:0.25, C:0.19, G:0.19, T:0.38
Consensus pattern (54 bp):
GGGTATTACAGTCATTTTACCCTACAAGGGTATTTCAGTCATTCTACACTATAA
Found at i:52365359 original size:27 final size:27
Alignment explanation
Indices: 52365250--52365385 Score: 118
Period size: 27 Copynumber: 5.1 Consensus size: 27
52365240 TACCTTATCG
* * *
52365250 GGGTATTACAGTCATTTTACCCTACAA
1 GGGTATTTCAGTCATTTTACACTATAA
* * * *
52365277 GGTTATTTCGGTCATTCTACCCTATAA
1 GGGTATTTCAGTCATTTTACACTATAA
* * *
52365304 GGGTATTTCGGTCA-TTTACCCTATGA
1 GGGTATTTCAGTCATTTTACACTATAA
52365330 GGGTATTTCAGTCATTTTATCAC-ATAA
1 GGGTATTTCAGTCATTTTA-CACTATAA
**
52365357 GGGTAAATCA-TCATTTTATCAC-ATAA
1 GGGTATTTCAGTCATTTTA-CACTATAA
52365383 GGG
1 GGG
52365386 CAAAATCGTC
Statistics
Matches: 94, Mismatches: 13, Indels: 5
0.84 0.12 0.04
Matches are distributed among these distances:
26 42 0.45
27 50 0.53
28 2 0.02
ACGTcount: A:0.27, C:0.18, G:0.18, T:0.37
Consensus pattern (27 bp):
GGGTATTTCAGTCATTTTACACTATAA
Found at i:52365370 original size:26 final size:27
Alignment explanation
Indices: 52365340--52365434 Score: 138
Period size: 27 Copynumber: 3.6 Consensus size: 27
52365330 GGGTATTTCA
*
52365340 GTCATTTTATCACATAAGGG-TAAATC
1 GTCATTTTATCACATAAGGGAAAAATC
* *
52365366 ATCATTTTATCACATAAGGGCAAAATC
1 GTCATTTTATCACATAAGGGAAAAATC
*
52365393 GTCGTTTTATCACATAAGGGAAAAATC
1 GTCATTTTATCACATAAGGGAAAAATC
*
52365420 GTCATCTTATCACAT
1 GTCATTTTATCACAT
52365435 TAGGATTCAG
Statistics
Matches: 61, Mismatches: 7, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
26 19 0.31
27 42 0.69
ACGTcount: A:0.36, C:0.18, G:0.14, T:0.33
Consensus pattern (27 bp):
GTCATTTTATCACATAAGGGAAAAATC
Found at i:52367082 original size:16 final size:16
Alignment explanation
Indices: 52367045--52367076 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
52367035 TCGACAAATC
*
52367045 CTGAAATGCCGAAAAG
1 CTGAAATACCGAAAAG
52367061 CTGAAATACCGAAAAG
1 CTGAAATACCGAAAAG
52367077 TCGAAAGTCT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.47, C:0.19, G:0.22, T:0.12
Consensus pattern (16 bp):
CTGAAATACCGAAAAG
Found at i:52367405 original size:28 final size:29
Alignment explanation
Indices: 52367315--52367412 Score: 153
Period size: 29 Copynumber: 3.4 Consensus size: 29
52367305 TTCGGGACAG
*
52367315 ATGGGCCATATGAACGTGATTTGGGCCTA
1 ATGGGCCATATGAATGTGATTTGGGCCTA
*
52367344 ATGGGCCATATTAATGTGATTTGGGCCTA
1 ATGGGCCATATGAATGTGATTTGGGCCTA
*
52367373 ATGGGCCATATGAATGAGA-TTGGGCCTA
1 ATGGGCCATATGAATGTGATTTGGGCCTA
*
52367401 GTGGGCCATATG
1 ATGGGCCATATG
52367413 CATATATGTA
Statistics
Matches: 64, Mismatches: 5, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
28 20 0.31
29 44 0.69
ACGTcount: A:0.24, C:0.15, G:0.32, T:0.29
Consensus pattern (29 bp):
ATGGGCCATATGAATGTGATTTGGGCCTA
Found at i:52372081 original size:46 final size:46
Alignment explanation
Indices: 52372013--52372195 Score: 294
Period size: 46 Copynumber: 4.0 Consensus size: 46
52372003 TATATATACA
* * * *
52372013 CATCTCATACATATCTCACATTAGCCATTTGGCTTTACCACATATC
1 CATCTCATACACATTTCGCATTAGCCATTCGGCTTTACCACATATC
* *
52372059 CATCTCATACACGTTTCGCATTAGCCATTCGGCTTTACCTCATATC
1 CATCTCATACACATTTCGCATTAGCCATTCGGCTTTACCACATATC
* *
52372105 CATCTCATACACGTTTCGCATTAGCCATTCGGCTTTACCTCATATC
1 CATCTCATACACATTTCGCATTAGCCATTCGGCTTTACCACATATC
52372151 CATCTCATACACATTTCGCATTAGCCATTCGGCTTTACCACATAT
1 CATCTCATACACATTTCGCATTAGCCATTCGGCTTTACCACATAT
52372196 ATACACTTCC
Statistics
Matches: 129, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
46 129 1.00
ACGTcount: A:0.25, C:0.32, G:0.09, T:0.34
Consensus pattern (46 bp):
CATCTCATACACATTTCGCATTAGCCATTCGGCTTTACCACATATC
Found at i:52372238 original size:22 final size:22
Alignment explanation
Indices: 52372212--52372287 Score: 59
Period size: 22 Copynumber: 3.3 Consensus size: 22
52372202 TTCCACGTTC
52372212 ATCACATTGGCCATTCTGCCTT
1 ATCACATTGGCCATTCTGCCTT
*
52372234 ATCACATATATG-CATGT-T-CACATT
1 ATCACAT-T-GGCCAT-TCTGC-C-TT
*
52372258 CATCACATTGGCCATTCGGCCTT
1 -ATCACATTGGCCATTCTGCCTT
52372281 ATCACAT
1 ATCACAT
52372288 ATATGCATAT
Statistics
Matches: 42, Mismatches: 3, Indels: 18
0.67 0.05 0.29
Matches are distributed among these distances:
22 15 0.36
23 10 0.24
24 9 0.21
25 8 0.19
ACGTcount: A:0.25, C:0.29, G:0.12, T:0.34
Consensus pattern (22 bp):
ATCACATTGGCCATTCTGCCTT
Found at i:52372240 original size:47 final size:47
Alignment explanation
Indices: 52372169--52372547 Score: 562
Period size: 47 Copynumber: 8.1 Consensus size: 47
52372159 ACACATTTCG
* * * * * *
52372169 CATTAGCCATTCGGCTTTACCACATATATACACT-TCCACGTTCATCA
1 CATTGGCCATTCGGCCTTATCACATATATGCA-TGTTCACATTCATCA
*
52372216 CATTGGCCATTCTGCCTTATCACATATATGCATGTTCACATTCATCA
1 CATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCATCA
*
52372263 CATTGGCCATTCGGCCTTATCACATATATGCATATTCACATTCATCA
1 CATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCATCA
* * *
52372310 CATTGGCCATTCGACCTTATTACACATATGCATGTTCACATTCATCA
1 CATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCATCA
*
52372357 CATTGGCCATTCGGCCTTATCACACATATGCATGTTCACATTCATCA
1 CATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCATCA
52372404 CATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCATCA
1 CATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCATCA
*
52372451 CATTGGCCATTCGGCCTTATCTCATATATGCATGTTCACATTCATCA
1 CATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCATCA
** * * * **
52372498 CATTTTCCATTCGACCTTATCTCATATATACACATTCACATTCATCA
1 CATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCATCA
52372545 CAT
1 CAT
52372548 AAAATCCTAA
Statistics
Matches: 308, Mismatches: 23, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
46 1 0.00
47 307 1.00
ACGTcount: A:0.27, C:0.29, G:0.10, T:0.35
Consensus pattern (47 bp):
CATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCATCA
Found at i:52378419 original size:31 final size:31
Alignment explanation
Indices: 52378381--52378440 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
52378371 TTCATATTTC
52378381 ATATTTCATAACACTGGGCCGAAGCCTTTTT
1 ATATTTCATAACACTGGGCCGAAGCCTTTTT
** *
52378412 ATATTTCATATTACTGGGCTGAAGCCTTT
1 ATATTTCATAACACTGGGCCGAAGCCTTT
52378441 ACTGTAAACG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.25, C:0.20, G:0.17, T:0.38
Consensus pattern (31 bp):
ATATTTCATAACACTGGGCCGAAGCCTTTTT
Found at i:52378677 original size:25 final size:24
Alignment explanation
Indices: 52378649--52378725 Score: 129
Period size: 23 Copynumber: 3.2 Consensus size: 24
52378639 GGCCTAGTCT
*
52378649 CTTTTAATAACTGGGGCAAAAAGCC
1 CTTTTAATAACTGGGGC-ATAAGCC
52378674 CTTTTAATAACTGGGGCATAAGCC
1 CTTTTAATAACTGGGGCATAAGCC
52378698 C-TTTAATAACTGGGGCATAAGCC
1 CTTTTAATAACTGGGGCATAAGCC
52378721 CTTTT
1 CTTTT
52378726 GCACTTCCTC
Statistics
Matches: 50, Mismatches: 1, Indels: 3
0.93 0.02 0.06
Matches are distributed among these distances:
23 23 0.46
24 10 0.20
25 17 0.34
ACGTcount: A:0.30, C:0.21, G:0.19, T:0.30
Consensus pattern (24 bp):
CTTTTAATAACTGGGGCATAAGCC
Found at i:52378800 original size:20 final size:20
Alignment explanation
Indices: 52378775--52378841 Score: 107
Period size: 20 Copynumber: 3.4 Consensus size: 20
52378765 TTATGAATAC
52378775 ATCATGTGCATATCATACAT
1 ATCATGTGCATATCATACAT
*
52378795 ATCATGTGCATAGCATACAT
1 ATCATGTGCATATCATACAT
*
52378815 GTCATGTGCATATCATACAT
1 ATCATGTGCATATCATACAT
*
52378835 ACCATGT
1 ATCATGT
52378842 TTACTAAAAT
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 42 1.00
ACGTcount: A:0.33, C:0.21, G:0.13, T:0.33
Consensus pattern (20 bp):
ATCATGTGCATATCATACAT
Found at i:52383807 original size:30 final size:30
Alignment explanation
Indices: 52383771--52384051 Score: 223
Period size: 30 Copynumber: 9.4 Consensus size: 30
52383761 AGTTGTCACC
* *
52383771 ATCCCTTTTCATAGTTCGATCGTCGAAGCT
1 ATCCCTTTTCATAATTCGATAGTCGAAGCT
* ** *
52383801 ATCCCTTTTCATAGTTTAATAGTCAAAGCT
1 ATCCCTTTTCATAATTCGATAGTCGAAGCT
*
52383831 ATCCCTTTTCATATTTCGATAG-CTGAAGCT
1 ATCCCTTTTCATAATTCGATAGTC-GAAGCT
* * * * *
52383861 ATCCATTTCCATAATTAGATAGCCAAAGCT
1 ATCCCTTTTCATAATTCGATAGTCGAAGCT
* * * *
52383891 ATCCATTTTCATAATTTGATAGCCGAAGTT
1 ATCCCTTTTCATAATTCGATAGTCGAAGCT
52383921 ATCCCTTTTCATAATTCGATAGAT-GAAGCT
1 ATCCCTTTTCATAATTCGATAG-TCGAAGCT
* * * * *
52383951 ATCCTTTTTCATAATTTGATGGTC-ATGACC
1 ATCCCTTTTCATAATTCGATAGTCGAAG-CT
* * * *
52383981 ATCCTTTTTCATTATT-GATGGTC-ATCA-CC
1 ATCCCTTTTCATAATTCGATAGTCGA--AGCT
* * *
52384010 ATTCCTTTTCATAATTCTATAGCCGAAGCT
1 ATCCCTTTTCATAATTCGATAGTCGAAGCT
52384040 ATCCCTTTTCAT
1 ATCCCTTTTCAT
52384052 TGGTCGATGA
Statistics
Matches: 205, Mismatches: 36, Indels: 20
0.79 0.14 0.08
Matches are distributed among these distances:
29 28 0.14
30 175 0.85
31 2 0.01
ACGTcount: A:0.26, C:0.22, G:0.12, T:0.40
Consensus pattern (30 bp):
ATCCCTTTTCATAATTCGATAGTCGAAGCT
Found at i:52383949 original size:90 final size:90
Alignment explanation
Indices: 52383796--52383966 Score: 252
Period size: 90 Copynumber: 1.9 Consensus size: 90
52383786 TCGATCGTCG
* * * * *
52383796 AAGCTATCCCTTTTCATAGTTTAATAGTCAAAGCTATCCCTTTTCATATTTCGATAGCTGAAGCT
1 AAGCTATCCATTTTCATAATTTAATAGCCAAAGCTATCCCTTTTCATAATTCGATAGATGAAGCT
52383861 ATCCATTTCCATAATTAGATAGCCA
66 ATCCATTTCCATAATTAGATAGCCA
* * *
52383886 AAGCTATCCATTTTCATAATTTGATAGCCGAAGTTATCCCTTTTCATAATTCGATAGATGAAGCT
1 AAGCTATCCATTTTCATAATTTAATAGCCAAAGCTATCCCTTTTCATAATTCGATAGATGAAGCT
* *
52383951 ATCCTTTTTCATAATT
66 ATCCATTTCCATAATT
52383967 TGATGGTCAT
Statistics
Matches: 71, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
90 71 1.00
ACGTcount: A:0.30, C:0.20, G:0.11, T:0.39
Consensus pattern (90 bp):
AAGCTATCCATTTTCATAATTTAATAGCCAAAGCTATCCCTTTTCATAATTCGATAGATGAAGCT
ATCCATTTCCATAATTAGATAGCCA
Done.