Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008527.1 Hibiscus syriacus cultivar Beakdansim tig00111402_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 9057482
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 22 of 37
Found at i:5222586 original size:14 final size:14
Alignment explanation
Indices: 5222567--5222623 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
5222557 TTTGGTTTCG
5222567 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
5222581 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
5222600 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
5222614 CGTTGCGATT
1 CGTTGCGATT
5222624 TTCATTTCTC
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
16 3 0.08
17 3 0.08
19 10 0.28
ACGTcount: A:0.09, C:0.25, G:0.23, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:5222599 original size:33 final size:33
Alignment explanation
Indices: 5222551--5222631 Score: 144
Period size: 33 Copynumber: 2.5 Consensus size: 33
5222541 AAAATCGCAA
**
5222551 TGCGATTTTGGTTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
5222584 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
5222617 TGCGATTTTCATTTC
1 TGCGATTTTCATTTC
5222632 TCTCGTTGCG
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 46 1.00
ACGTcount: A:0.09, C:0.22, G:0.22, T:0.47
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
Found at i:5222634 original size:21 final size:21
Alignment explanation
Indices: 5222608--5222683 Score: 109
Period size: 21 Copynumber: 3.7 Consensus size: 21
5222598 CGCGTTGCGA
5222608 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
***
5222629 TTCTCTCGTTGCGACAGTCA-
1 TTCTCTCGTTGCGATTTTCAT
5222649 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
*
5222670 TTATCTCGTTGCGA
1 TTCTCTCGTTGCGA
5222684 CTCTTCTGCA
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
20 17 0.36
21 30 0.64
ACGTcount: A:0.12, C:0.25, G:0.17, T:0.46
Consensus pattern (21 bp):
TTCTCTCGTTGCGATTTTCAT
Found at i:5222664 original size:41 final size:41
Alignment explanation
Indices: 5222607--5222684 Score: 147
Period size: 41 Copynumber: 1.9 Consensus size: 41
5222597 TCGCGTTGCG
*
5222607 ATTCTCTCGTTGCGATTTTCATTTCTCTCGTTGCGACAGTC
1 ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGACAGTC
5222648 ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGAC
1 ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGAC
5222685 TCTTCTGCAA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
41 36 1.00
ACGTcount: A:0.13, C:0.26, G:0.17, T:0.45
Consensus pattern (41 bp):
ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGACAGTC
Found at i:5222805 original size:33 final size:33
Alignment explanation
Indices: 5222763--5222833 Score: 106
Period size: 33 Copynumber: 2.2 Consensus size: 33
5222753 AATACTAACT
* *
5222763 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACACGAAA
* *
5222796 TGAAAATCGCAACGACAGAATCGTAACACGAAA
1 TGAAAATCGCAACGACAGAATAGCAACACGAAA
5222829 TGAAA
1 TGAAA
5222834 TCTAAGTGAA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.49, C:0.18, G:0.21, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGACAGAATAGCAACACGAAA
Found at i:5223066 original size:22 final size:22
Alignment explanation
Indices: 5223014--5223068 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
5223004 TGGTTGTGAG
**
5223014 GGATTTCGCCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
**
5223036 GGAAATCTTCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
5223058 GGATTTCTTCG
1 GGATTTCTTCG
5223069 CCGTAGAGAG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.20, C:0.16, G:0.40, T:0.24
Consensus pattern (22 bp):
GGATTTCTTCGGAGATGGGGAC
Found at i:5223240 original size:20 final size:20
Alignment explanation
Indices: 5223215--5223368 Score: 168
Period size: 20 Copynumber: 7.7 Consensus size: 20
5223205 CTTTAAATAT
5223215 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
5223235 CGCGTTGCGATTTTATGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
*
5223257 -TCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
5223276 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
*
5223296 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
5223316 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
5223336 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
5223356 CGCGTTGCGATTT
1 CGCGTTGCGATTT
5223369 TAGAAAATCG
Statistics
Matches: 113, Mismatches: 16, Indels: 10
0.81 0.12 0.07
Matches are distributed among these distances:
19 2 0.02
20 94 0.83
21 15 0.13
22 2 0.02
ACGTcount: A:0.18, C:0.18, G:0.27, T:0.37
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:5223342 original size:40 final size:40
Alignment explanation
Indices: 5223214--5223368 Score: 186
Period size: 40 Copynumber: 3.9 Consensus size: 40
5223204 GCTTTAAATA
*
5223214 TCGCGTTGCGATTTACGGATACGCGTTGCGATTTTATGTAT
1 TCGCGTTGCGATTTACGGATACGCGTTGCGA-TTTATGTGT
** * *
5223255 TATCGTTGCGATTTACGGATACGCGTTGCGATATACG-GAT
1 TCGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTG-T
* *
5223295 ACACGTTGCGATTTACGGATACGCGTTGCGATTTATGTGT
1 TCGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTGT
* ** *
5223335 TCGCGTTGCGATTTTCATATTCGCGTTGCGATTT
1 TCGCGTTGCGATTTACGGATACGCGTTGCGATTT
5223369 TAGAAAATCG
Statistics
Matches: 96, Mismatches: 16, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
40 66 0.69
41 30 0.31
ACGTcount: A:0.18, C:0.18, G:0.26, T:0.37
Consensus pattern (40 bp):
TCGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTGT
Found at i:5223420 original size:21 final size:21
Alignment explanation
Indices: 5223335--5223432 Score: 74
Period size: 21 Copynumber: 4.7 Consensus size: 21
5223325 ATTTATGTGT
* *
5223335 TCGCGTTGCGATTTTC-ATAT
1 TCGCGTTGCGATTTTCAAAAA
5223355 TCGCGTTGCGATTTT-AGAAAA
1 TCGCGTTGCGATTTTCA-AAAA
** * ** **
5223376 TCGCAATGCGAATTTGTACTA
1 TCGCGTTGCGATTTTCAAAAA
* *
5223397 TCGCATTGCGATTTTCAAGAA
1 TCGCGTTGCGATTTTCAAAAA
5223418 TCGCGTTGCGATTTT
1 TCGCGTTGCGATTTT
5223433 GGAAACTGAT
Statistics
Matches: 60, Mismatches: 15, Indels: 5
0.75 0.19 0.06
Matches are distributed among these distances:
20 15 0.25
21 45 0.75
ACGTcount: A:0.22, C:0.18, G:0.21, T:0.38
Consensus pattern (21 bp):
TCGCGTTGCGATTTTCAAAAA
Found at i:5223428 original size:42 final size:43
Alignment explanation
Indices: 5223335--5223433 Score: 100
Period size: 42 Copynumber: 2.4 Consensus size: 43
5223325 ATTTATGTGT
*
5223335 TCGCGTTGCG-ATTT-TCATATTCGCGTTGCGATTTTAGAAAA
1 TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTAGAAAA
** *
5223376 TCGCAATGCGAATTTGT-ACTA-TCGCATTGCGATTTTCA-AGAA
1 TCGCGTTGCGAATTTGTCA-TATTCGCATTGCGATTTT-AGAAAA
*
5223418 TCGCGTTGCGATTTTG
1 TCGCGTTGCGAATTTG
5223434 GAAACTGATT
Statistics
Matches: 47, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
41 8 0.17
42 35 0.74
43 4 0.09
ACGTcount: A:0.22, C:0.18, G:0.22, T:0.37
Consensus pattern (43 bp):
TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTAGAAAA
Found at i:5225672 original size:24 final size:24
Alignment explanation
Indices: 5225643--5225711 Score: 84
Period size: 24 Copynumber: 2.8 Consensus size: 24
5225633 TTTTGGTAGG
* *
5225643 GGTGTTCGTGTGTTTATTTTTTAA
1 GGTGTTCGTGTATTTATTTTTGAA
* *
5225667 TGTGTTCGTTTATTTATTTTTGAA
1 GGTGTTCGTGTATTTATTTTTGAA
5225691 GGTGTTCGTGTTTATTTATTT
1 GGTGTTCGTG--TATTTATTT
5225712 ATTGTTCGCG
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
24 28 0.76
26 9 0.24
ACGTcount: A:0.13, C:0.04, G:0.22, T:0.61
Consensus pattern (24 bp):
GGTGTTCGTGTATTTATTTTTGAA
Found at i:5225740 original size:23 final size:23
Alignment explanation
Indices: 5225708--5225802 Score: 91
Period size: 23 Copynumber: 4.1 Consensus size: 23
5225698 GTGTTTATTT
* *
5225708 ATTTATTGTTCGCGAACATGTTC
1 ATTTAATGTTCACGAACATGTTC
* **
5225731 GTTTAATGTTCGTGAACATGTTC
1 ATTTAATGTTCACGAACATGTTC
**
5225754 ATTTATATGTTCACGAATGTGTTC
1 ATTTA-ATGTTCACGAACATGTTC
* **
5225778 ATTTAGTGTTCACGAAGGTGTTC
1 ATTTAATGTTCACGAACATGTTC
5225801 AT
1 AT
5225803 CTAGCGTTCG
Statistics
Matches: 61, Mismatches: 10, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
23 42 0.69
24 19 0.31
ACGTcount: A:0.23, C:0.14, G:0.20, T:0.43
Consensus pattern (23 bp):
ATTTAATGTTCACGAACATGTTC
Found at i:5225811 original size:23 final size:23
Alignment explanation
Indices: 5225762--5225811 Score: 73
Period size: 23 Copynumber: 2.2 Consensus size: 23
5225752 TCATTTATAT
* * *
5225762 GTTCACGAATGTGTTCATTTAGT
1 GTTCACGAAGGTGTTCATCTAGC
5225785 GTTCACGAAGGTGTTCATCTAGC
1 GTTCACGAAGGTGTTCATCTAGC
5225808 GTTC
1 GTTC
5225812 GTTTAGTTAG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.20, C:0.18, G:0.24, T:0.38
Consensus pattern (23 bp):
GTTCACGAAGGTGTTCATCTAGC
Found at i:5230743 original size:24 final size:24
Alignment explanation
Indices: 5230683--5230750 Score: 66
Period size: 24 Copynumber: 2.8 Consensus size: 24
5230673 ATGTTTACAA
*
5230683 ATAAACTCGTTTATTGATTCATTT
1 ATAAGCTCGTTTATTGATTCATTT
* * * *
5230707 GTAAGTTCTTTTA-TGAGTTCGTTT
1 ATAAGCTCGTTTATTGA-TTCATTT
5230731 ATAAGCTCGTTTACTTGATT
1 ATAAGCTCGTTTA-TTGATT
5230751 TTTCTTTTTC
Statistics
Matches: 33, Mismatches: 8, Indels: 5
0.72 0.17 0.11
Matches are distributed among these distances:
23 3 0.09
24 25 0.76
25 2 0.06
26 3 0.09
ACGTcount: A:0.24, C:0.12, G:0.15, T:0.50
Consensus pattern (24 bp):
ATAAGCTCGTTTATTGATTCATTT
Found at i:5238265 original size:19 final size:19
Alignment explanation
Indices: 5238241--5238305 Score: 85
Period size: 19 Copynumber: 3.4 Consensus size: 19
5238231 CCACATCATA
5238241 CAAATTCGCAACACAAAGT
1 CAAATTCGCAACACAAAGT
** **
5238260 CAAATTCGCAACGGAATTT
1 CAAATTCGCAACACAAAGT
*
5238279 CCAATTCGCAACACAAAGT
1 CAAATTCGCAACACAAAGT
5238298 CAAATTCG
1 CAAATTCG
5238306 TAACTGAATT
Statistics
Matches: 36, Mismatches: 10, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
19 36 1.00
ACGTcount: A:0.42, C:0.26, G:0.12, T:0.20
Consensus pattern (19 bp):
CAAATTCGCAACACAAAGT
Found at i:5238319 original size:19 final size:19
Alignment explanation
Indices: 5238259--5238347 Score: 106
Period size: 19 Copynumber: 4.7 Consensus size: 19
5238249 CAACACAAAG
*
5238259 TCAAATTCGCAACGGAATT
1 TCAAATTCGCAACTGAATT
* ** **
5238278 TCCAATTCGCAACACAAAG
1 TCAAATTCGCAACTGAATT
*
5238297 TCAAATTCGTAACTGAATT
1 TCAAATTCGCAACTGAATT
*
5238316 TCAAATTCGCAATTGAATT
1 TCAAATTCGCAACTGAATT
5238335 TCAAATTCGCAAC
1 TCAAATTCGCAAC
5238348 AGGTTTTAGT
Statistics
Matches: 56, Mismatches: 14, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
19 56 1.00
ACGTcount: A:0.38, C:0.22, G:0.11, T:0.28
Consensus pattern (19 bp):
TCAAATTCGCAACTGAATT
Found at i:5238343 original size:38 final size:38
Alignment explanation
Indices: 5238241--5238327 Score: 147
Period size: 38 Copynumber: 2.3 Consensus size: 38
5238231 CCACATCATA
5238241 CAAATTCGCAACACAAAGTCAAATTCGCAACGGAATTT
1 CAAATTCGCAACACAAAGTCAAATTCGCAACGGAATTT
* * *
5238279 CCAATTCGCAACACAAAGTCAAATTCGTAACTGAATTT
1 CAAATTCGCAACACAAAGTCAAATTCGCAACGGAATTT
5238317 CAAATTCGCAA
1 CAAATTCGCAA
5238328 TTGAATTTCA
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
38 45 1.00
ACGTcount: A:0.41, C:0.24, G:0.11, T:0.23
Consensus pattern (38 bp):
CAAATTCGCAACACAAAGTCAAATTCGCAACGGAATTT
Found at i:5238539 original size:16 final size:15
Alignment explanation
Indices: 5238504--5238542 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
5238494 TCCCCATCTC
*
5238504 TAATTTTTTTTTACA
1 TAATTTTTTTCTACA
*
5238519 TAATTTTATTTCTATA
1 TAATTTT-TTTCTACA
5238535 TAATTTTT
1 TAATTTTT
5238543 CAATGATTTC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
15 8 0.38
16 13 0.62
ACGTcount: A:0.28, C:0.05, G:0.00, T:0.67
Consensus pattern (15 bp):
TAATTTTTTTCTACA
Found at i:5239302 original size:24 final size:24
Alignment explanation
Indices: 5239249--5239304 Score: 67
Period size: 24 Copynumber: 2.3 Consensus size: 24
5239239 CAGTATTCGA
*
5239249 ATTTTGATCTTGGTCAATACCCAG
1 ATTTTGATCTTGGGCAATACCCAG
* * * *
5239273 ACTTTGATCTTGGGGAATACTCGG
1 ATTTTGATCTTGGGCAATACCCAG
5239297 ATTTTGAT
1 ATTTTGAT
5239305 GATGTGATGG
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.23, C:0.16, G:0.21, T:0.39
Consensus pattern (24 bp):
ATTTTGATCTTGGGCAATACCCAG
Found at i:5241431 original size:17 final size:17
Alignment explanation
Indices: 5241409--5241442 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
5241399 AAGCAAATGG
5241409 AAATC-AAATCGCAATCA
1 AAATCAAAATC-CAATCA
5241426 AAATCAAAATCCAATCA
1 AAATCAAAATCCAATCA
5241443 CAACGGCTTC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.56, C:0.24, G:0.03, T:0.18
Consensus pattern (17 bp):
AAATCAAAATCCAATCA
Found at i:5241921 original size:28 final size:28
Alignment explanation
Indices: 5241890--5241943 Score: 72
Period size: 28 Copynumber: 1.9 Consensus size: 28
5241880 AAAATTCTTA
*
5241890 TTTACACATCAAATTAAACAAATCAACT
1 TTTACAAATCAAATTAAACAAATCAACT
* **
5241918 TTTACAAATCAACTTTTACAAATCAA
1 TTTACAAATCAAATTAAACAAATCAA
5241944 TTAATCAAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 22 1.00
ACGTcount: A:0.48, C:0.20, G:0.00, T:0.31
Consensus pattern (28 bp):
TTTACAAATCAAATTAAACAAATCAACT
Found at i:5241924 original size:14 final size:14
Alignment explanation
Indices: 5241907--5241943 Score: 74
Period size: 14 Copynumber: 2.6 Consensus size: 14
5241897 ATCAAATTAA
5241907 ACAAATCAACTTTT
1 ACAAATCAACTTTT
5241921 ACAAATCAACTTTT
1 ACAAATCAACTTTT
5241935 ACAAATCAA
1 ACAAATCAA
5241944 TTAATCAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:5242839 original size:20 final size:19
Alignment explanation
Indices: 5242814--5243001 Score: 91
Period size: 20 Copynumber: 9.5 Consensus size: 19
5242804 ATTGACTTTC
5242814 GCGTTGCGAATTTGATTTAT
1 GCGTTGCGAATTTGA-TTAT
* * *
5242834 GTGTTGCG-ATTTACAAATT-C
1 GCGTTGCGAATTT---GATTAT
* *
5242854 GCGTTACGAATTTGACTTTT
1 GCGTTGCGAATTTGA-TTAT
* *
5242874 GTGTTGCGAATTTGACTAT
1 GCGTTGCGAATTTGATTAT
*
5242893 -CAAGTTGCGAATTTGACTAT
1 GC--GTTGCGAATTTGATTAT
5242913 CGCGTTGCGAATTTGACTT-T
1 -GCGTTGCGAATTTGA-TTAT
*
5242933 AG-GTTGCGAATTTGACTAT
1 -GCGTTGCGAATTTGATTAT
*
5242952 -CAAGTTGCGAATTTGACTAT
1 GC--GTTGCGAATTTGATTAT
* *
5242972 CGCATTGCGAATTTGACTTCT
1 -GCGTTGCGAATTTGA-TTAT
*
5242993 GTGTTGCGA
1 GCGTTGCGA
5243002 TTTACAAATT
Statistics
Matches: 130, Mismatches: 20, Indels: 36
0.70 0.11 0.19
Matches are distributed among these distances:
18 2 0.02
19 22 0.17
20 94 0.72
21 9 0.07
22 3 0.02
ACGTcount: A:0.22, C:0.15, G:0.23, T:0.39
Consensus pattern (19 bp):
GCGTTGCGAATTTGATTAT
Found at i:5242880 original size:60 final size:59
Alignment explanation
Indices: 5242805--5242990 Score: 216
Period size: 59 Copynumber: 3.1 Consensus size: 59
5242795 GCGTAAAACA
* * **
5242805 TTGACTTTCGCGTTGCGAATTTGATTTAT-GTGTTGCG-ATTT-ACAAATTCGCGTTACGAAT
1 TTGACTTTAG-GTTGCGAATTTGA-CTATCAAGTTGCGAATTTGAC-AA-TCGCGTTACGAAT
* * *
5242865 TTGACTTTTGTGTTGCGAATTTGACTATCAAGTTGCGAATTTGACTATCGCGTTGCGAAT
1 TTGACTTTAG-GTTGCGAATTTGACTATCAAGTTGCGAATTTGACAATCGCGTTACGAAT
* * *
5242925 TTGACTTTAGGTTGCGAATTTGACTATCAAGTTGCGAATTTGACTATCGCATTGCGAAT
1 TTGACTTTAGGTTGCGAATTTGACTATCAAGTTGCGAATTTGACAATCGCGTTACGAAT
5242984 TTGACTT
1 TTGACTT
5242991 CTGTGTTGCG
Statistics
Matches: 114, Mismatches: 9, Indels: 7
0.88 0.07 0.05
Matches are distributed among these distances:
59 58 0.51
60 49 0.43
61 5 0.04
62 2 0.02
ACGTcount: A:0.23, C:0.15, G:0.22, T:0.40
Consensus pattern (59 bp):
TTGACTTTAGGTTGCGAATTTGACTATCAAGTTGCGAATTTGACAATCGCGTTACGAAT
Found at i:5242961 original size:59 final size:60
Alignment explanation
Indices: 5242852--5243001 Score: 250
Period size: 59 Copynumber: 2.5 Consensus size: 60
5242842 ATTTACAAAT
* *
5242852 TCGCGTTACGAATTTGACTTTTGTGTTGCGAATTTGACTATCAAGTTGCGAATTTGACTA
1 TCGCGTTGCGAATTTGACTTTAGTGTTGCGAATTTGACTATCAAGTTGCGAATTTGACTA
5242912 TCGCGTTGCGAATTTGACTTTAG-GTTGCGAATTTGACTATCAAGTTGCGAATTTGACTA
1 TCGCGTTGCGAATTTGACTTTAGTGTTGCGAATTTGACTATCAAGTTGCGAATTTGACTA
*
5242971 TCGCATTGCGAATTTGACTTCT-GTGTTGCGA
1 TCGCGTTGCGAATTTGACTT-TAGTGTTGCGA
5243002 TTTACAAATT
Statistics
Matches: 85, Mismatches: 3, Indels: 4
0.92 0.03 0.04
Matches are distributed among these distances:
59 56 0.66
60 29 0.34
ACGTcount: A:0.22, C:0.16, G:0.23, T:0.39
Consensus pattern (60 bp):
TCGCGTTGCGAATTTGACTTTAGTGTTGCGAATTTGACTATCAAGTTGCGAATTTGACTA
Found at i:5243015 original size:40 final size:41
Alignment explanation
Indices: 5242811--5243022 Score: 167
Period size: 40 Copynumber: 5.3 Consensus size: 41
5242801 AACATTGACT
* * *
5242811 TTCGCGTTGCGAATTTGATTTATGTGTTGCG-ATTT-ACAAA
1 TTCGCATTGCGAATTTGACTTCTGTGTTGCGAATTTGAC-AA
* * * *
5242851 TTCGCGTTACGAATTTGACTTTTGTGTTGCGAATTTGACTA
1 TTCGCATTGCGAATTTGACTTCTGTGTTGCGAATTTGACAA
* * *
5242892 -TC-AAGTTGCGAATTTGACTATC-GCGTTGCGAATTTGAC-T
1 TTCGCA-TTGCGAATTTGACT-TCTGTGTTGCGAATTTGACAA
* * ** *
5242931 TTAG-GTTGCGAATTTGACTATC-AAGTTGCGAATTTGACTA
1 TTCGCATTGCGAATTTGACT-TCTGTGTTGCGAATTTGACAA
5242971 -TCGCATTGCGAATTTGACTTCTGTGTTGCG-ATTT-ACAAA
1 TTCGCATTGCGAATTTGACTTCTGTGTTGCGAATTTGAC-AA
5243010 TTCGCATTGCGAA
1 TTCGCATTGCGAA
5243023 ATTGGAAACT
Statistics
Matches: 141, Mismatches: 20, Indels: 22
0.77 0.11 0.12
Matches are distributed among these distances:
38 2 0.01
39 40 0.28
40 91 0.65
41 6 0.04
42 2 0.01
ACGTcount: A:0.23, C:0.16, G:0.22, T:0.39
Consensus pattern (41 bp):
TTCGCATTGCGAATTTGACTTCTGTGTTGCGAATTTGACAA
Found at i:5246108 original size:27 final size:29
Alignment explanation
Indices: 5246077--5246134 Score: 75
Period size: 27 Copynumber: 2.1 Consensus size: 29
5246067 TATTTCAATA
* *
5246077 AAAATTAATTTTTAAAT-ATTTAAT-ATT
1 AAAATTAATTATAAAATAATTTAATGATT
*
5246104 AAAATTTATTATAAAATAATTTAATGATT
1 AAAATTAATTATAAAATAATTTAATGATT
5246133 AA
1 AA
5246135 TTTTAAATTA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
27 14 0.54
28 7 0.27
29 5 0.19
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.47
Consensus pattern (29 bp):
AAAATTAATTATAAAATAATTTAATGATT
Found at i:5248021 original size:15 final size:15
Alignment explanation
Indices: 5247998--5248027 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
5247988 ACAAGGCTGT
5247998 AATTACAACAACAAC
1 AATTACAACAACAAC
*
5248013 AATTCCAACAACAAC
1 AATTACAACAACAAC
5248028 TATGAGAAAG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.57, C:0.30, G:0.00, T:0.13
Consensus pattern (15 bp):
AATTACAACAACAAC
Found at i:5251433 original size:29 final size:29
Alignment explanation
Indices: 5251398--5251479 Score: 128
Period size: 29 Copynumber: 2.8 Consensus size: 29
5251388 AAACTAAATT
* *
5251398 GATGTCATTACTTACATCATTTAATTAAA
1 GATGTCATTGCTTACATCATTTAAGTAAA
*
5251427 GATGTCATTGCTTACATCATTTAAGTAAT
1 GATGTCATTGCTTACATCATTTAAGTAAA
5251456 GATGTCATTGCTTACATCAATTTA
1 GATGTCATTGCTTACATC-ATTTA
5251480 GTTAGGTGAG
Statistics
Matches: 49, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
29 44 0.90
30 5 0.10
ACGTcount: A:0.33, C:0.15, G:0.11, T:0.41
Consensus pattern (29 bp):
GATGTCATTGCTTACATCATTTAAGTAAA
Found at i:5258349 original size:24 final size:24
Alignment explanation
Indices: 5258306--5258368 Score: 63
Period size: 24 Copynumber: 2.6 Consensus size: 24
5258296 TTGCTTGTTT
* * *
5258306 ATAAGTTTGTTTATCAACTCGTTG
1 ATAAGCTTGTTTATCAACTCATTC
* **
5258330 ATAATCTTGTTTATTGACTCATTC
1 ATAAGCTTGTTTATCAACTCATTC
*
5258354 ATAAGCTCGTTTATC
1 ATAAGCTTGTTTATC
5258369 CGACTCTCTT
Statistics
Matches: 30, Mismatches: 9, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.25, C:0.16, G:0.13, T:0.46
Consensus pattern (24 bp):
ATAAGCTTGTTTATCAACTCATTC
Found at i:5275391 original size:136 final size:130
Alignment explanation
Indices: 5275150--5275397 Score: 354
Period size: 136 Copynumber: 1.9 Consensus size: 130
5275140 TGGTCTTTAC
*
5275150 CAATCTGTTCCTAATGAACTTCTAGAATGCACTGAAGAGCACTCTTCCTGAAAACGATGATAGAA
1 CAATCTGTTCCTAAAGAACTTCTAGAATGCACTGAAGAGCACTCTTCCTGAAAACGATGATAGAA
*
5275215 AAAGCCACTTCAAAGTTAGCAGTAGTTGCTTTGGTGAGGAAACAAACCATGCAACCAGTCTTCAT
66 AAAGCCACTTCAAAATTAGCAGTAGTTGCTTTGGTGAGGAAACAAACCATGCAACCAGTCTTCAT
* *
5275280 CAATCTGTTCCTAAAGGACTTCTAGAATGCATGAACCTGAAGAGCACTCTTCCTGAAAATGATGA
1 CAATCTGTTCCTAAAGAACTTCTAGAATGC----A-CTGAAGAGCACTCTTCCTGAAAACGATGA
* * * *
5275345 TTAGAAAAAGTCACCTT-AAAATTAGCTGTAGTTTCTTTGGTGAGGAATCAAAC
61 -TAGAAAAAGCCA-CTTCAAAATTAGCAGTAGTTGCTTTGGTGAGGAAACAAAC
5275398 TGTGCACTGC
Statistics
Matches: 103, Mismatches: 8, Indels: 8
0.87 0.07 0.07
Matches are distributed among these distances:
130 28 0.27
134 1 0.01
135 28 0.27
136 43 0.42
137 3 0.03
ACGTcount: A:0.35, C:0.20, G:0.19, T:0.27
Consensus pattern (130 bp):
CAATCTGTTCCTAAAGAACTTCTAGAATGCACTGAAGAGCACTCTTCCTGAAAACGATGATAGAA
AAAGCCACTTCAAAATTAGCAGTAGTTGCTTTGGTGAGGAAACAAACCATGCAACCAGTCTTCAT
Found at i:5277389 original size:24 final size:24
Alignment explanation
Indices: 5277357--5277408 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
5277347 CTTGCAAATG
**
5277357 AACATGTTCGTGAACATATAAACA
1 AACATGTTCACGAACATATAAACA
**
5277381 AACATGTTCACGAACATATTCACA
1 AACATGTTCACGAACATATAAACA
5277405 AACA
1 AACA
5277409 CATAAATGAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.46, C:0.21, G:0.10, T:0.23
Consensus pattern (24 bp):
AACATGTTCACGAACATATAAACA
Found at i:5282906 original size:35 final size:35
Alignment explanation
Indices: 5282860--5282940 Score: 153
Period size: 35 Copynumber: 2.3 Consensus size: 35
5282850 TTCATGAGGA
*
5282860 ACGCCTCATTTTGTGGTATTATATTTCTCAATCCT
1 ACGCCTCATTTTGTGGTATAATATTTCTCAATCCT
5282895 ACGCCTCATTTTGTGGTATAATATTTCTCAATCCT
1 ACGCCTCATTTTGTGGTATAATATTTCTCAATCCT
5282930 ACGCCTCATTT
1 ACGCCTCATTT
5282941 ATTTATTGGT
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
35 45 1.00
ACGTcount: A:0.21, C:0.25, G:0.11, T:0.43
Consensus pattern (35 bp):
ACGCCTCATTTTGTGGTATAATATTTCTCAATCCT
Found at i:5284299 original size:20 final size:21
Alignment explanation
Indices: 5284271--5284329 Score: 84
Period size: 20 Copynumber: 2.8 Consensus size: 21
5284261 ATTTATGGGT
5284271 AAGGGGAATCGGTACCCATTC
1 AAGGGGAATCGGTACCCATTC
*
5284292 AA-GGGAATCGGTAACCATTC
1 AAGGGGAATCGGTACCCATTC
*
5284312 AATGGGGAATCGATACCC
1 AA-GGGGAATCGGTACCC
5284330 CTCAAGCGAA
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
20 19 0.58
21 2 0.06
22 12 0.36
ACGTcount: A:0.32, C:0.22, G:0.27, T:0.19
Consensus pattern (21 bp):
AAGGGGAATCGGTACCCATTC
Found at i:5285914 original size:103 final size:103
Alignment explanation
Indices: 5285694--5285906 Score: 399
Period size: 103 Copynumber: 2.1 Consensus size: 103
5285684 GGGTCTGCGC
5285694 GGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGAT
1 GGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGAT
* *
5285759 CCTTGGCATATGTATATGATTCTTAAGGAATGATATGT
66 CCCTAGCATATGTATATGATTCTTAAGGAATGATATGT
5285797 GGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGAT
1 GGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGAT
*
5285862 CCCTAGTATATGTATATGATTCTTAAGGAATGATATGT
66 CCCTAGCATATGTATATGATTCTTAAGGAATGATATGT
5285900 GGTCCTT
1 GGTCCTT
5285907 ATGGACATTA
Statistics
Matches: 107, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
103 107 1.00
ACGTcount: A:0.26, C:0.14, G:0.24, T:0.36
Consensus pattern (103 bp):
GGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGAT
CCCTAGCATATGTATATGATTCTTAAGGAATGATATGT
Found at i:5285982 original size:23 final size:23
Alignment explanation
Indices: 5285931--5285985 Score: 65
Period size: 23 Copynumber: 2.4 Consensus size: 23
5285921 ATGGAACTAA
*
5285931 GGTGCAATTCTACGCGGCACTCC
1 GGTGCAATTCTAAGCGGCACTCC
* * * *
5285954 GATGCAATTCTAAGTGGCATTTC
1 GGTGCAATTCTAAGCGGCACTCC
5285977 GGTGCAATT
1 GGTGCAATT
5285986 ATACGAGCTG
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.22, C:0.24, G:0.25, T:0.29
Consensus pattern (23 bp):
GGTGCAATTCTAAGCGGCACTCC
Found at i:5288750 original size:16 final size:16
Alignment explanation
Indices: 5288729--5288771 Score: 50
Period size: 17 Copynumber: 2.6 Consensus size: 16
5288719 GGTAATTAAA
5288729 GATTGATAAGGAATTT
1 GATTGATAAGGAATTT
* *
5288745 GATTGATTAATGATTTT
1 GATTGA-TAAGGAATTT
*
5288762 GAGTGATAAG
1 GATTGATAAG
5288772 AACTGATGCT
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
16 9 0.41
17 13 0.59
ACGTcount: A:0.35, C:0.00, G:0.26, T:0.40
Consensus pattern (16 bp):
GATTGATAAGGAATTT
Found at i:5289685 original size:20 final size:21
Alignment explanation
Indices: 5289660--5289715 Score: 87
Period size: 20 Copynumber: 2.7 Consensus size: 21
5289650 TCTGGGTAAG
5289660 GGGAATCGGTACCCATTCAA-
1 GGGAATCGGTACCCATTCAAT
5289680 GGGAATCGGTACCCATTCAAT
1 GGGAATCGGTACCCATTCAAT
*
5289701 GAGGAATCGATACCC
1 G-GGAATCGGTACCC
5289716 CTCAAGCGAA
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
20 20 0.61
21 1 0.03
22 12 0.36
ACGTcount: A:0.30, C:0.25, G:0.25, T:0.20
Consensus pattern (21 bp):
GGGAATCGGTACCCATTCAAT
Found at i:5289793 original size:23 final size:22
Alignment explanation
Indices: 5289749--5289793 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
5289739 AATCTCATAG
*
5289749 GGGAACCGATTCCCCCACAGGA
1 GGGAACCGATTCCCCCAAAGGA
*
5289771 GGGAATCGATTCCCCCTAAAGGA
1 GGGAACCGATTCCCCC-AAAGGA
5289794 AAAATTTGAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 15 0.75
23 5 0.25
ACGTcount: A:0.29, C:0.31, G:0.27, T:0.13
Consensus pattern (22 bp):
GGGAACCGATTCCCCCAAAGGA
Found at i:5290956 original size:24 final size:24
Alignment explanation
Indices: 5290913--5290965 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 24
5290903 TAAGTGAATC
*
5290913 ATGTG-TTTATATGTATATGAGAT
1 ATGTGATTTATATGTAGATGAGAT
*
5290936 ATGTGATTTATATG-ACGATGAGCT
1 ATGTGATTTATATGTA-GATGAGAT
5290960 ATGTGA
1 ATGTGA
5290966 AAGAACTACA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
23 6 0.23
24 20 0.77
ACGTcount: A:0.30, C:0.04, G:0.25, T:0.42
Consensus pattern (24 bp):
ATGTGATTTATATGTAGATGAGAT
Found at i:5291303 original size:103 final size:103
Alignment explanation
Indices: 5291083--5291295 Score: 390
Period size: 103 Copynumber: 2.1 Consensus size: 103
5291073 GGGTCTACGC
5291083 GGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGAT
1 GGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGAT
* * *
5291148 CCTTGGCATATGTATATGATTCTTAAGGAATGATATGT
66 CCCTAGCATATGTATATGATTCTTAAGGAACGATATGT
5291186 GGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGAT
1 GGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGAT
*
5291251 CCCTAGTATATGTATATGATTCTTAAGGAACGATATGT
66 CCCTAGCATATGTATATGATTCTTAAGGAACGATATGT
5291289 GGTCCTT
1 GGTCCTT
5291296 ATGGACATTA
Statistics
Matches: 106, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
103 106 1.00
ACGTcount: A:0.26, C:0.15, G:0.24, T:0.36
Consensus pattern (103 bp):
GGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGAT
CCCTAGCATATGTATATGATTCTTAAGGAACGATATGT
Found at i:5291345 original size:23 final size:23
Alignment explanation
Indices: 5291312--5291379 Score: 82
Period size: 23 Copynumber: 3.0 Consensus size: 23
5291302 ATTATTATAT
5291312 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTCTACGC
* * *
5291335 GGCACTCCGGTGCAATTCTAAGT
1 GGCACTACGGTGCAATTCTACGC
* * *
5291358 GGCATTTCGGTGCAATTATACG
1 GGCACTACGGTGCAATTCTACG
5291380 AGTTGTGGTG
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.22, C:0.25, G:0.26, T:0.26
Consensus pattern (23 bp):
GGCACTACGGTGCAATTCTACGC
Found at i:5294966 original size:22 final size:21
Alignment explanation
Indices: 5294915--5294973 Score: 93
Period size: 20 Copynumber: 2.8 Consensus size: 21
5294905 ATTTATGGGT
5294915 AAGGGGAATCGGTACCCATTC
1 AAGGGGAATCGGTACCCATTC
5294936 AA-GGGAATCGGTACCCATTC
1 AAGGGGAATCGGTACCCATTC
*
5294956 AATGGGGAATCGATACCC
1 AA-GGGGAATCGGTACCC
5294974 CTCAAGCGAA
Statistics
Matches: 35, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
20 20 0.57
21 2 0.06
22 13 0.37
ACGTcount: A:0.31, C:0.24, G:0.27, T:0.19
Consensus pattern (21 bp):
AAGGGGAATCGGTACCCATTC
Found at i:5295051 original size:23 final size:22
Alignment explanation
Indices: 5295007--5295051 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
5294997 AATCTCATAG
*
5295007 GGGAACCGATTCCCCCACAGGA
1 GGGAACCGATTCCCCCAAAGGA
*
5295029 GGGAATCGATTCCCCCTAAAGGA
1 GGGAACCGATTCCCCC-AAAGGA
5295052 AAAATTTGAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 15 0.75
23 5 0.25
ACGTcount: A:0.29, C:0.31, G:0.27, T:0.13
Consensus pattern (22 bp):
GGGAACCGATTCCCCCAAAGGA
Found at i:5296567 original size:103 final size:103
Alignment explanation
Indices: 5296347--5296559 Score: 381
Period size: 103 Copynumber: 2.1 Consensus size: 103
5296337 GGGTCTACGC
5296347 GGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGAT
1 GGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGAT
* *
5296412 CCTTGGCATATGTATATGATTCTTAAGGAATGATATGT
66 CCCTAGCATATGTATATGATTCTTAAGGAATGATATGT
* *
5296450 GGTTCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTTGTGAGACACATACTTGAT
1 GGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGAT
*
5296515 CCCTAGTATATGTATATGATTCTTAAGGAATGATATGT
66 CCCTAGCATATGTATATGATTCTTAAGGAATGATATGT
5296553 GGTCCTT
1 GGTCCTT
5296560 ATGGACATTA
Statistics
Matches: 104, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
103 104 1.00
ACGTcount: A:0.26, C:0.14, G:0.23, T:0.37
Consensus pattern (103 bp):
GGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGAT
CCCTAGCATATGTATATGATTCTTAAGGAATGATATGT
Found at i:5296609 original size:23 final size:23
Alignment explanation
Indices: 5296576--5296643 Score: 82
Period size: 23 Copynumber: 3.0 Consensus size: 23
5296566 ATTATTATAT
5296576 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTCTACGC
* * *
5296599 GGCACTCCGGTGCAATTCTAAGT
1 GGCACTACGGTGCAATTCTACGC
* * *
5296622 GGCACTTCAGTGCAATTATACG
1 GGCACTACGGTGCAATTCTACG
5296644 AGTTGTGGTG
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.24, C:0.26, G:0.25, T:0.25
Consensus pattern (23 bp):
GGCACTACGGTGCAATTCTACGC
Found at i:5299347 original size:14 final size:15
Alignment explanation
Indices: 5299328--5299356 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
5299318 AAGTGTGAAA
5299328 TGATAT-AAGTTATG
1 TGATATGAAGTTATG
5299342 TGATATGAAGTTATG
1 TGATATGAAGTTATG
5299357 GGTATATGTG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.34, C:0.00, G:0.24, T:0.41
Consensus pattern (15 bp):
TGATATGAAGTTATG
Found at i:5299873 original size:30 final size:29
Alignment explanation
Indices: 5299828--5299899 Score: 81
Period size: 29 Copynumber: 2.4 Consensus size: 29
5299818 GGTTCTTCGG
* * * *
5299828 GACCTATAGACAGTTGTCGAGGTTCTTTAT
1 GACCTCTAGATAGTTGCCG-GGGTCTTTAT
* *
5299858 GACCTCTGGATAGTTGCCGGGGTCTTTGT
1 GACCTCTAGATAGTTGCCGGGGTCTTTAT
5299887 GACCTCTAGATAG
1 GACCTCTAGATAG
5299900 GTCCTTCGGG
Statistics
Matches: 35, Mismatches: 7, Indels: 1
0.81 0.16 0.02
Matches are distributed among these distances:
29 20 0.57
30 15 0.43
ACGTcount: A:0.19, C:0.19, G:0.28, T:0.33
Consensus pattern (29 bp):
GACCTCTAGATAGTTGCCGGGGTCTTTAT
Found at i:5304891 original size:28 final size:28
Alignment explanation
Indices: 5304837--5304891 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 28
5304827 ATCATCGTTG
* * **
5304837 GTTTCAAGCACTAGCTCAATGGTATAAT
1 GTTTAAAGCACTAGCTCAACGACATAAT
5304865 GTTTAAAGCACTAGCTCAACGACATAA
1 GTTTAAAGCACTAGCTCAACGACATAA
5304892 AATAAACGGA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.36, C:0.20, G:0.16, T:0.27
Consensus pattern (28 bp):
GTTTAAAGCACTAGCTCAACGACATAAT
Found at i:5307147 original size:19 final size:20
Alignment explanation
Indices: 5307099--5307152 Score: 71
Period size: 19 Copynumber: 2.9 Consensus size: 20
5307089 TTTGTTTCTC
5307099 TGTATTTCTCT-TCTCTCTT
1 TGTATTTCTCTGTCTCTCTT
5307118 TGTATTT-TCTGTCTCTCTT
1 TGTATTTCTCTGTCTCTCTT
5307137 T-T-TTGTCTCTGTCTCT
1 TGTATT-TCTCTGTCTCT
5307153 GTGTTCTTCT
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
17 2 0.06
18 5 0.16
19 25 0.78
ACGTcount: A:0.04, C:0.24, G:0.09, T:0.63
Consensus pattern (20 bp):
TGTATTTCTCTGTCTCTCTT
Found at i:5307358 original size:16 final size:16
Alignment explanation
Indices: 5307333--5307369 Score: 67
Period size: 16 Copynumber: 2.4 Consensus size: 16
5307323 GGACGTGGCA
5307333 GCGG-TGGAGGCAGAG
1 GCGGCTGGAGGCAGAG
5307348 GCGGCTGGAGGCAGAG
1 GCGGCTGGAGGCAGAG
5307364 GCGGCT
1 GCGGCT
5307370 AGGGATTAGG
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 4 0.19
16 17 0.81
ACGTcount: A:0.16, C:0.19, G:0.57, T:0.08
Consensus pattern (16 bp):
GCGGCTGGAGGCAGAG
Found at i:5307497 original size:3 final size:3
Alignment explanation
Indices: 5307489--5307575 Score: 120
Period size: 3 Copynumber: 29.0 Consensus size: 3
5307479 TATATATATT
* * *
5307489 TAA TAA TAA TAA TAA TAT TTA TAA TAA TAA TAA TAA TAA TTA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * *
5307537 TTA TAA TAA TAA TAA TAA TTA TAA TTA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
5307576 ATAAATTAAT
Statistics
Matches: 72, Mismatches: 12, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
3 72 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (3 bp):
TAA
Found at i:5307585 original size:18 final size:18
Alignment explanation
Indices: 5307488--5307586 Score: 78
Period size: 18 Copynumber: 5.3 Consensus size: 18
5307478 ATATATATAT
5307488 TTAATAATAAT-AATAATA
1 TTAATAATAATAAATAA-A
*
5307506 TTTATAATAAT-AATAATA
1 TTAATAATAATAAATAA-A
* * *
5307524 ATAATTATAATAATTATAA
1 TTAATAATAATAAATA-AA
*
5307543 -TAATAATAATAATTATAAT
1 TTAATAATAATAA--ATAAA
5307562 TATAATAATAATAAATAAA
1 T-TAATAATAATAAATAAA
5307581 TTAATA
1 TTAATA
5307587 TGGGTAAAAA
Statistics
Matches: 66, Mismatches: 9, Indels: 12
0.76 0.10 0.14
Matches are distributed among these distances:
18 41 0.62
19 10 0.15
20 3 0.05
21 12 0.18
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (18 bp):
TTAATAATAATAAATAAA
Found at i:5307990 original size:80 final size:77
Alignment explanation
Indices: 5307847--5307995 Score: 190
Period size: 80 Copynumber: 1.9 Consensus size: 77
5307837 ATGAACTTCC
* * * * * *
5307847 TCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTTTCTGTAAAAGTTGATCCATCGAGTGATGG
1 TCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTTCCTGGAAAAGTTAATCCATCAAGTGATGA
5307912 ATTTGAGCAAAT
66 ATTTGAGCAAAT
* * *
5307924 TCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTTCCTGGCAATGTTAATCCATCAATTGA
1 TCTTCTTCAGAT---GAGTTCTTCTCATTATGAACTCTTCCTGGAAAAGTTAATCCATCAAGTGA
5307989 TGAATTT
63 TGAATTT
5307996 AAACAAAAGG
Statistics
Matches: 60, Mismatches: 9, Indels: 3
0.83 0.12 0.04
Matches are distributed among these distances:
77 12 0.20
80 48 0.80
ACGTcount: A:0.26, C:0.18, G:0.16, T:0.40
Consensus pattern (77 bp):
TCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTTCCTGGAAAAGTTAATCCATCAAGTGATGA
ATTTGAGCAAAT
Found at i:5308071 original size:113 final size:114
Alignment explanation
Indices: 5307925--5308525 Score: 912
Period size: 113 Copynumber: 5.3 Consensus size: 114
5307915 TGAGCAAATT
* * * * *
5307925 CTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTTC-CTGGCAATGTTAATCCATCAATTGA
1 CTTCTTCAGAT---GAGTTCTTCTCATTATGAACTCTTCTCTGGAAAAGCTGATCCATCAAATGA
* * *
5307989 TGAATTTAAACAAAAGGTTGAACAAATTCTTCTCATTATGAACTTTTTCCTC
63 TGAATTTGAGCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTTTTCTTC
* *
5308041 CTTCTTCAGATGAATTCTTCTCATTATGAAC-CTTCTCTGGAAAAGCTGATCCATCAAGTGATGA
1 CTTCTTCAGATGAGTTCTTCTCATTATGAACTCTTCTCTGGAAAAGCTGATCCATCAAATGATGA
*
5308105 A-TTCAGGCAAAAGGTTGAACAAATTCTTCTCATTATGAA-TTTCTTCTTC
66 ATTTGA-GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTT-TTCTTC
*
5308154 CTTCTTCAGATGAGTTCTTCTCATTATGAACT-TTCTCTGGAAAAGCTGATCCATCAAATGATGG
1 CTTCTTCAGATGAGTTCTTCTCATTATGAACTCTTCTCTGGAAAAGCTGATCCATCAAATGATGA
5308218 ATTTGAGCAAAAGGTTGAACAAATTCTTCTCATTATGAA-TTTCTTCTTC
66 ATTTGAGCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTT-TTCTTC
*
5308267 CTTCTTCAGATGAGTTCTTCTCATTATGAACT-TTCTCTGGAAAAGCTGATCCATCAAATGATGG
1 CTTCTTCAGATGAGTTCTTCTCATTATGAACTCTTCTCTGGAAAAGCTGATCCATCAAATGATGA
**
5308331 ATTTGAGCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTTTTCTTC
66 ATTTGAGCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTTTTCTTC
* * *
5308380 CTTCTTCAAATGAGTTCTTCTCATTATGAAC-CTTCTCTGGAAAAGTTGATCCATCAAGTGATGA
1 CTTCTTCAGATGAGTTCTTCTCATTATGAACTCTTCTCTGGAAAAGCTGATCCATCAAATGATGA
* *
5308444 ATTCGAGCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTC
66 ATTTGAGCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTTTTCTTC
5308493 CTTCTTCAGATGAGTTCTTCTCATTATGAACTC
1 CTTCTTCAGATGAGTTCTTCTCATTATGAACTC
5308526 GAACTGGAAA
Statistics
Matches: 453, Mismatches: 24, Indels: 18
0.92 0.05 0.04
Matches are distributed among these distances:
112 10 0.02
113 425 0.94
114 7 0.02
116 11 0.02
ACGTcount: A:0.28, C:0.20, G:0.14, T:0.37
Consensus pattern (114 bp):
CTTCTTCAGATGAGTTCTTCTCATTATGAACTCTTCTCTGGAAAAGCTGATCCATCAAATGATGA
ATTTGAGCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTTTTCTTC
Found at i:5308559 original size:339 final size:340
Alignment explanation
Indices: 5307925--5308560 Score: 1008
Period size: 339 Copynumber: 1.9 Consensus size: 340
5307915 TGAGCAAATT
* * * *
5307925 CTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTTCCTGGCAATGTTAATCCATCAATTGAT
1 CTTCTTCAGAT-A-GAGTTCTTCTCATTATGAACTCTTCCTGGAAAAGCTAATCCATCAAATGAT
* *
5307990 GAATTTAAACAAAAGGTTGAACAAATTCTTCTCATTATGAACTTTTTCCTCCTTCTTCAGATGAA
64 GAATTTAAACAAAAGGTTGAACAAACTCTTCTCATTATGAACTTTTTCCTCCTTCTTCAAATGAA
5308055 TTCTTCTCATTATGAACCTTCTCTGGAAAAGCTGATCCATCAAGTGATGAATTCAGGCAAAAGGT
129 TTCTTCTCATTATGAACCTTCTCTGGAAAAGCTGATCCATCAAGTGATGAATTCAGGCAAAAGGT
*
5308120 TGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAAC
194 TGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAAC
**** * *
5308185 TTTCTCTGGAAAAGCTGATCCATCAAATGATGGATTTGAGCAAAAGGTTGAACAAATTCTTCTCA
259 TCGAACTGGAAAAGCTAATCCATCAAATAATGGATTTGAGCAAAAGGTTGAACAAATTCTTCTCA
5308250 TTATGAATTTCTTCTTC
324 TTATGAATTTCTTCTTC
*
5308267 CTTCTTCAGAT-GAGTTCTTCTCATTATGAACT-TTCTCTGGAAAAGCTGATCCATCAAATGATG
1 CTTCTTCAGATAGAGTTCTTCTCATTATGAACTCTTC-CTGGAAAAGCTAATCCATCAAATGATG
* * * * * *
5308330 GATTTGAGCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTTTTCTTCCTTCTTCAAATGAGT
65 AATTTAAACAAAAGGTTGAACAAACTCTTCTCATTATGAACTTTTTCCTCCTTCTTCAAATGAAT
*
5308395 TCTTCTCATTATGAACCTTCTCTGGAAAAGTTGATCCATCAAGTGATGAATTC-GAGCAAAAGGT
130 TCTTCTCATTATGAACCTTCTCTGGAAAAGCTGATCCATCAAGTGATGAATTCAG-GCAAAAGGT
5308459 TGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAAC
194 TGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAAC
* *
5308524 TCGAACTGGAAAATCTAATCCATCAAGTAATGGATTT
259 TCGAACTGGAAAAGCTAATCCATCAAATAATGGATTT
5308561 AAATCTTTGC
Statistics
Matches: 269, Mismatches: 23, Indels: 7
0.90 0.08 0.02
Matches are distributed among these distances:
338 4 0.01
339 254 0.94
342 11 0.04
ACGTcount: A:0.29, C:0.20, G:0.14, T:0.37
Consensus pattern (340 bp):
CTTCTTCAGATAGAGTTCTTCTCATTATGAACTCTTCCTGGAAAAGCTAATCCATCAAATGATGA
ATTTAAACAAAAGGTTGAACAAACTCTTCTCATTATGAACTTTTTCCTCCTTCTTCAAATGAATT
CTTCTCATTATGAACCTTCTCTGGAAAAGCTGATCCATCAAGTGATGAATTCAGGCAAAAGGTTG
AACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTC
GAACTGGAAAAGCTAATCCATCAAATAATGGATTTGAGCAAAAGGTTGAACAAATTCTTCTCATT
ATGAATTTCTTCTTC
Found at i:5309496 original size:83 final size:83
Alignment explanation
Indices: 5309352--5309705 Score: 672
Period size: 83 Copynumber: 4.3 Consensus size: 83
5309342 CTTATTTCTA
* *
5309352 CTATGAGCAAATTCATCTTCCAAATTCAATGATTGGTTCTGTCAAACCAGATCAGATAACTCAAA
1 CTATTAGCAAATTCATCTTCCAAATTCAATGATTGGTTCTGCCAAACCAGATCAGATAACTCAAA
5309417 GAACACTTCCAGAAGATG
66 GAACACTTCCAGAAGATG
*
5309435 CTATTAGCAAATTCATCTTCCAAATTCAATGATTGGTTCTGCCAAACAAGATCAGATAACTCAAA
1 CTATTAGCAAATTCATCTTCCAAATTCAATGATTGGTTCTGCCAAACCAGATCAGATAACTCAAA
*
5309500 GAACACTTCCAGAATATG
66 GAACACTTCCAGAAGATG
5309518 CTATTAGCAAATTCATCTTCCAAATTCAATGATTGGTTCTGCCAAACCAGATCAGATAACTCAAA
1 CTATTAGCAAATTCATCTTCCAAATTCAATGATTGGTTCTGCCAAACCAGATCAGATAACTCAAA
5309583 GAACACTTCCAGAAGATG
66 GAACACTTCCAGAAGATG
5309601 CTATTAGCAAATTCATCTTCCAAATTCAATGATTGGTTCTGCCAAACCAGATCAGATAACTCAAA
1 CTATTAGCAAATTCATCTTCCAAATTCAATGATTGGTTCTGCCAAACCAGATCAGATAACTCAAA
5309666 GAACACTTCCAGAAGATG
66 GAACACTTCCAGAAGATG
5309684 CTATTAGCAAATTCATCTTCCA
1 CTATTAGCAAATTCATCTTCCA
5309706 TTTAATGTTT
Statistics
Matches: 265, Mismatches: 6, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
83 265 1.00
ACGTcount: A:0.37, C:0.23, G:0.13, T:0.27
Consensus pattern (83 bp):
CTATTAGCAAATTCATCTTCCAAATTCAATGATTGGTTCTGCCAAACCAGATCAGATAACTCAAA
GAACACTTCCAGAAGATG
Found at i:5317971 original size:15 final size:15
Alignment explanation
Indices: 5317948--5317979 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
5317938 TGAAATGAAT
5317948 AATGAATGTATGCAA
1 AATGAATGTATGCAA
*
5317963 AATGCATGTATGCAA
1 AATGAATGTATGCAA
5317978 AA
1 AA
5317980 AGGTATTGAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.47, C:0.09, G:0.19, T:0.25
Consensus pattern (15 bp):
AATGAATGTATGCAA
Found at i:5321302 original size:24 final size:22
Alignment explanation
Indices: 5321275--5321332 Score: 61
Period size: 24 Copynumber: 2.7 Consensus size: 22
5321265 ATGAAATATT
5321275 AATAATATATATAAATACTATAAA
1 AATAATAT-TATAAATA-TATAAA
5321299 AATAATATGTAT--ATATATAAA
1 AATAATAT-TATAAATATATAAA
5321320 AA-AA-ATTATAAAT
1 AATAATATTATAAAT
5321333 TAAATATATG
Statistics
Matches: 31, Mismatches: 1, Indels: 8
0.77 0.03 0.20
Matches are distributed among these distances:
18 3 0.10
19 2 0.06
20 4 0.13
21 8 0.26
22 3 0.10
24 11 0.35
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.34
Consensus pattern (22 bp):
AATAATATTATAAATATATAAA
Found at i:5323004 original size:17 final size:19
Alignment explanation
Indices: 5322973--5323007 Score: 56
Period size: 17 Copynumber: 1.9 Consensus size: 19
5322963 TTTGTTTCTC
5322973 TGTATTTCTCTTGTCTCTT
1 TGTATTTCTCTTGTCTCTT
5322992 TGTATTT-TC-TGTCTCT
1 TGTATTTCTCTTGTCTCT
5323008 CTTTTTTGTC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.44
18 2 0.12
19 7 0.44
ACGTcount: A:0.06, C:0.20, G:0.11, T:0.63
Consensus pattern (19 bp):
TGTATTTCTCTTGTCTCTT
Found at i:5323008 original size:19 final size:19
Alignment explanation
Indices: 5322973--5323011 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
5322963 TTTGTTTCTC
*
5322973 TGTATTTCTCTTGTCTCTT
1 TGTATTTCTCTTCTCTCTT
5322992 TGTATTT-TCTGTCTCTCTT
1 TGTATTTCTCT-TCTCTCTT
5323011 T
1 T
5323012 TTTGTCTCTG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 3 0.17
19 15 0.83
ACGTcount: A:0.05, C:0.21, G:0.10, T:0.64
Consensus pattern (19 bp):
TGTATTTCTCTTCTCTCTT
Found at i:5323232 original size:16 final size:16
Alignment explanation
Indices: 5323207--5323243 Score: 67
Period size: 16 Copynumber: 2.4 Consensus size: 16
5323197 GGACGTGGCA
5323207 GCGG-TGGAGGCAGAG
1 GCGGCTGGAGGCAGAG
5323222 GCGGCTGGAGGCAGAG
1 GCGGCTGGAGGCAGAG
5323238 GCGGCT
1 GCGGCT
5323244 AGAGATTAGG
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 4 0.19
16 17 0.81
ACGTcount: A:0.16, C:0.19, G:0.57, T:0.08
Consensus pattern (16 bp):
GCGGCTGGAGGCAGAG
Found at i:5323352 original size:23 final size:19
Alignment explanation
Indices: 5323325--5323451 Score: 101
Period size: 18 Copynumber: 6.8 Consensus size: 19
5323315 TAATTTATTA
5323325 TTATTATATATATATATATATAT
1 TTATTA-ATA-ATA-ATA-ATAT
5323348 TTATTAATAATAATAATAT
1 TTATTAATAATAATAATAT
5323367 TTA-TAATAATAATAATA-
1 TTATTAATAATAATAATAT
5323384 --A-TAATAATAATAAT-T
1 TTATTAATAATAATAATAT
*
5323399 ATTATT-ATAATTATAATA-
1 -TTATTAATAATAATAATAT
* * *
5323417 ATAATAATAATAATAATAAA
1 TTATTAATAATAATAAT-AT
5323437 TTA-TAATAATAATAA
1 TTATTAATAATAATAA
5323452 ATAAATTAAT
Statistics
Matches: 90, Mismatches: 5, Indels: 22
0.77 0.04 0.19
Matches are distributed among these distances:
15 14 0.16
17 3 0.03
18 35 0.39
19 21 0.23
20 5 0.06
21 3 0.03
22 3 0.03
23 6 0.07
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (19 bp):
TTATTAATAATAATAATAT
Found at i:5323360 original size:3 final size:3
Alignment explanation
Indices: 5323352--5323451 Score: 128
Period size: 3 Copynumber: 33.0 Consensus size: 3
5323342 ATATATTTAT
* * *
5323352 TAA TAA TAA TAA TAT TTA TAA TAA TAA TAA TAA TAA TAA TAA TAA TTA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * * *
5323400 TTA TTA TAA TTA TAA TAA TAA TAA TAA TAA TAA TAAA TTA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA
5323446 TAA TAA
1 TAA TAA
5323452 ATAAATTAAT
Statistics
Matches: 86, Mismatches: 10, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
3 83 0.97
4 3 0.03
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (3 bp):
TAA
Found at i:5324293 original size:2 final size:2
Alignment explanation
Indices: 5324286--5324312 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
5324276 TAATAATTGG
5324286 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
5324313 TAATGATTCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:5324883 original size:2 final size:2
Alignment explanation
Indices: 5324876--5324932 Score: 107
Period size: 2 Copynumber: 29.0 Consensus size: 2
5324866 TAATATTTAA
5324876 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5324918 -T AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT
5324933 GGGTACTACT
Statistics
Matches: 54, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 53 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:5326488 original size:49 final size:49
Alignment explanation
Indices: 5326434--5326532 Score: 180
Period size: 49 Copynumber: 2.0 Consensus size: 49
5326424 TTGAGTTATA
5326434 ATAAGATCAATTGTCATTATGTTGTTATGGTTATAATCATTTGTATATT
1 ATAAGATCAATTGTCATTATGTTGTTATGGTTATAATCATTTGTATATT
* *
5326483 ATAAGATCAATTGTCATTGTGTTGTTATTGTTATAATCATTTGTATATT
1 ATAAGATCAATTGTCATTATGTTGTTATGGTTATAATCATTTGTATATT
5326532 A
1 A
5326533 GTATTGATGA
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
49 48 1.00
ACGTcount: A:0.30, C:0.06, G:0.14, T:0.49
Consensus pattern (49 bp):
ATAAGATCAATTGTCATTATGTTGTTATGGTTATAATCATTTGTATATT
Found at i:5326510 original size:26 final size:25
Alignment explanation
Indices: 5326434--5326510 Score: 61
Period size: 26 Copynumber: 3.1 Consensus size: 25
5326424 TTGAGTTATA
5326434 ATAAGATCAATTGTCATTATGTTGTT
1 ATAAGATCAATTGTCATT-TGTTGTT
* * ** *
5326460 AT--GGT-TATAATCATTTGTATATT
1 ATAAGATCAATTGTCATTTGT-TGTT
5326483 ATAAGATCAATTGTCATTGTGTTGTT
1 ATAAGATCAATTGTCATT-TGTTGTT
5326509 AT
1 AT
5326511 TGTTATAATC
Statistics
Matches: 36, Mismatches: 10, Indels: 10
0.64 0.18 0.18
Matches are distributed among these distances:
22 3 0.08
23 12 0.33
24 2 0.06
25 2 0.06
26 14 0.39
27 3 0.08
ACGTcount: A:0.30, C:0.06, G:0.16, T:0.48
Consensus pattern (25 bp):
ATAAGATCAATTGTCATTTGTTGTT
Found at i:5327321 original size:17 final size:17
Alignment explanation
Indices: 5327276--5327335 Score: 52
Period size: 17 Copynumber: 3.4 Consensus size: 17
5327266 CTTCCGTCTT
5327276 TTTCTTTCTTGTCAGTTTCCA
1 TTTCTTTCTTGTCAG--T--A
*
5327297 TTTTTTTCTT-TCATGTA
1 TTTCTTTCTTGTCA-GTA
5327314 TTTCTTTCTTGTCAGT-
1 TTTCTTTCTTGTCAGTA
5327330 TTTCTT
1 TTTCTT
5327336 CTTCTTCTTT
Statistics
Matches: 35, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
16 6 0.17
17 12 0.34
18 3 0.09
19 1 0.03
20 3 0.09
21 10 0.29
ACGTcount: A:0.08, C:0.18, G:0.08, T:0.65
Consensus pattern (17 bp):
TTTCTTTCTTGTCAGTA
Found at i:5330193 original size:2 final size:2
Alignment explanation
Indices: 5330182--5330221 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
5330172 ACAAAAGTTT
5330182 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
5330222 CCACTCTTAA
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 36 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:5332456 original size:21 final size:21
Alignment explanation
Indices: 5332405--5332457 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 21
5332395 ATTATGACTA
*
5332405 TCGCAATGCGATTTTTCAATT
1 TCGCAATGCGATTTTCCAATT
**
5332426 TCGCGTTGCGATTTTCCCAA-T
1 TCGCAATGCGATTTT-CCAATT
5332447 TCGCAATGCGA
1 TCGCAATGCGA
5332458 ATAAGTAAAT
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
21 23 0.88
22 3 0.12
ACGTcount: A:0.21, C:0.25, G:0.19, T:0.36
Consensus pattern (21 bp):
TCGCAATGCGATTTTCCAATT
Found at i:5343527 original size:28 final size:28
Alignment explanation
Indices: 5343495--5343549 Score: 92
Period size: 28 Copynumber: 2.0 Consensus size: 28
5343485 TTGTCCTTGC
* *
5343495 TTTCAAGCACTAGCTCAATGGTATAATG
1 TTTCAAGCACTAGCTCAACGGCATAATG
5343523 TTTCAAGCACTAGCTCAACGGCATAAT
1 TTTCAAGCACTAGCTCAACGGCATAAT
5343550 ATAAACGGAC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.33, C:0.22, G:0.16, T:0.29
Consensus pattern (28 bp):
TTTCAAGCACTAGCTCAACGGCATAATG
Found at i:5345547 original size:25 final size:25
Alignment explanation
Indices: 5345505--5345552 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 25
5345495 ACATCTCAAT
* *
5345505 ATTTAAATATATATATATATATTGA
1 ATTTAAATATAAAAATATATATTGA
* *
5345530 ATTTAAATCTAAAAATATTTATT
1 ATTTAAATATAAAAATATATATT
5345553 CAAGATTTAA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 19 1.00
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (25 bp):
ATTTAAATATAAAAATATATATTGA
Found at i:5345931 original size:16 final size:16
Alignment explanation
Indices: 5345907--5345943 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
5345897 TTGAGTTGAA
* *
5345907 CTCTAAAATTGATTAT
1 CTCTTAAATCGATTAT
5345923 CTCTTAAATCGATTAT
1 CTCTTAAATCGATTAT
5345939 CTCTT
1 CTCTT
5345944 GATGTTAGTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.30, C:0.19, G:0.05, T:0.46
Consensus pattern (16 bp):
CTCTTAAATCGATTAT
Found at i:5346062 original size:49 final size:49
Alignment explanation
Indices: 5345985--5346083 Score: 144
Period size: 49 Copynumber: 2.0 Consensus size: 49
5345975 TTGAGTTATA
* * *
5345985 ATAAGATCGGTTGTCATTATGTTATTATTGTTATAATCATTTGTATATT
1 ATAAGATCAGTTGCCATTATGTTATTATTGTTATAATCATTTATATATT
* * *
5346034 ATAAGATCATTTGCCATTGTGTTGTTATTGTTATAATCATTTATATATT
1 ATAAGATCAGTTGCCATTATGTTATTATTGTTATAATCATTTATATATT
5346083 A
1 A
5346084 GTATTGATGA
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
49 44 1.00
ACGTcount: A:0.29, C:0.07, G:0.13, T:0.51
Consensus pattern (49 bp):
ATAAGATCAGTTGCCATTATGTTATTATTGTTATAATCATTTATATATT
Found at i:5349276 original size:74 final size:74
Alignment explanation
Indices: 5349193--5349361 Score: 320
Period size: 74 Copynumber: 2.3 Consensus size: 74
5349183 TTTAGTGATT
5349193 TTTTTCTTTTAATTTGGGTGAAAGAGTTATAATTAATTTTACAATAGGAAGATAAAAGAGGATAA
1 TTTTTCTTTTAATTTGGGTGAAAGAGTTATAATTAATTTTACAATAGGAAGATAAAAGAGGATAA
5349258 AAGGGTTGA
66 AAGGGTTGA
* *
5349267 TTTTTCTTTTAATTTGGGTGAAAGAGTTATAATTGATTTTACAGTAGGAAGATAAAAGAGGATAA
1 TTTTTCTTTTAATTTGGGTGAAAGAGTTATAATTAATTTTACAATAGGAAGATAAAAGAGGATAA
5349332 AAGGGTTGA
66 AAGGGTTGA
5349341 TTTTTCTTTTAATTTGGGTGA
1 TTTTTCTTTTAATTTGGGTGA
5349362 GGATATCACG
Statistics
Matches: 93, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
74 93 1.00
ACGTcount: A:0.35, C:0.03, G:0.22, T:0.40
Consensus pattern (74 bp):
TTTTTCTTTTAATTTGGGTGAAAGAGTTATAATTAATTTTACAATAGGAAGATAAAAGAGGATAA
AAGGGTTGA
Found at i:5351678 original size:21 final size:21
Alignment explanation
Indices: 5351627--5351679 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 21
5351617 ATTATGACTA
*
5351627 TCGCAATGCGATTTTTCAATT
1 TCGCAATGCGATTTTCCAATT
**
5351648 TCGCGTTGCGATTTTCCCAA-T
1 TCGCAATGCGATTTT-CCAATT
5351669 TCGCAATGCGA
1 TCGCAATGCGA
5351680 ATAAGTAAAT
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
21 23 0.88
22 3 0.12
ACGTcount: A:0.21, C:0.25, G:0.19, T:0.36
Consensus pattern (21 bp):
TCGCAATGCGATTTTCCAATT
Found at i:5362694 original size:28 final size:28
Alignment explanation
Indices: 5362662--5362716 Score: 92
Period size: 28 Copynumber: 2.0 Consensus size: 28
5362652 TTGTCCTTGC
* *
5362662 TTTCAAGCACTAGCTCAATGGTATAATG
1 TTTCAAGCACTAGCTCAACGGCATAATG
5362690 TTTCAAGCACTAGCTCAACGGCATAAT
1 TTTCAAGCACTAGCTCAACGGCATAAT
5362717 ATAAACGGAC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.33, C:0.22, G:0.16, T:0.29
Consensus pattern (28 bp):
TTTCAAGCACTAGCTCAACGGCATAATG
Found at i:5364705 original size:25 final size:25
Alignment explanation
Indices: 5364663--5364710 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 25
5364653 ACATCTCAAT
* *
5364663 ATTTAAATATATATATATATATTGA
1 ATTTAAATATAAAAATATATATTGA
* *
5364688 ATTTAAATCTAAAAATATTTATT
1 ATTTAAATATAAAAATATATATT
5364711 CAAGATTTAA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 19 1.00
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (25 bp):
ATTTAAATATAAAAATATATATTGA
Found at i:5365077 original size:16 final size:16
Alignment explanation
Indices: 5365053--5365089 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
5365043 TTGAGTTGAA
* *
5365053 CTCTAAAATTGATTAT
1 CTCTTAAATCGATTAT
5365069 CTCTTAAATCGATTAT
1 CTCTTAAATCGATTAT
5365085 CTCTT
1 CTCTT
5365090 GATGTTAGTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.30, C:0.19, G:0.05, T:0.46
Consensus pattern (16 bp):
CTCTTAAATCGATTAT
Found at i:5365208 original size:49 final size:49
Alignment explanation
Indices: 5365131--5365229 Score: 144
Period size: 49 Copynumber: 2.0 Consensus size: 49
5365121 TTGAGTTATA
* * *
5365131 ATAAGATCGGTTGTCATTATGTTATTATTGTTATAATCATTTGTATATT
1 ATAAGATCAGTTGCCATTATGTTATTATTGTTATAATCATTTATATATT
* * *
5365180 ATAAGATCATTTGCCATTGTGTTGTTATTGTTATAATCATTTATATATT
1 ATAAGATCAGTTGCCATTATGTTATTATTGTTATAATCATTTATATATT
5365229 A
1 A
5365230 GTATTGATGA
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
49 44 1.00
ACGTcount: A:0.29, C:0.07, G:0.13, T:0.51
Consensus pattern (49 bp):
ATAAGATCAGTTGCCATTATGTTATTATTGTTATAATCATTTATATATT
Found at i:5368502 original size:2 final size:2
Alignment explanation
Indices: 5368491--5368520 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
5368481 ACAAAAGTTT
5368491 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
5368521 CCACTCTTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:5373861 original size:13 final size:14
Alignment explanation
Indices: 5373824--5373861 Score: 51
Period size: 15 Copynumber: 2.7 Consensus size: 14
5373814 GTGAAATTCT
*
5373824 AAATATTTAAATAA
1 AAATATTTATATAA
5373838 AAATTATTTATATAA
1 AAA-TATTTATATAA
5373853 AAA-ATTTAT
1 AAATATTTAT
5373862 CTGTTGATAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
13 6 0.27
14 3 0.14
15 13 0.59
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (14 bp):
AAATATTTATATAA
Found at i:5385926 original size:20 final size:20
Alignment explanation
Indices: 5385889--5385926 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
5385879 ATATAAATAT
*
5385889 ATAGTATTATTATTTATTGA
1 ATAGTATTATTATGTATTGA
5385909 ATAGTATATATTA-GTATT
1 ATAGTAT-TATTATGTATT
5385927 AGATAAACTG
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 11 0.69
21 5 0.31
ACGTcount: A:0.37, C:0.00, G:0.11, T:0.53
Consensus pattern (20 bp):
ATAGTATTATTATGTATTGA
Found at i:5386235 original size:31 final size:32
Alignment explanation
Indices: 5386200--5386275 Score: 93
Period size: 33 Copynumber: 2.4 Consensus size: 32
5386190 ACATTAAGGA
*
5386200 TTAATTTGACTTAAAAAACA-AGAGTTAAGAT
1 TTAATTTGACTTAAAAAACAGAGAGTTAAGAC
* * *
5386231 TTAATTTAATTTTAAAAAACAGAGAGTTGAGAC
1 TTAATTTGA-CTTAAAAAACAGAGAGTTAAGAC
5386264 TTAATTTG-CTTA
1 TTAATTTGACTTA
5386276 TTTTTATAAT
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
31 11 0.30
32 10 0.27
33 16 0.43
ACGTcount: A:0.43, C:0.07, G:0.13, T:0.37
Consensus pattern (32 bp):
TTAATTTGACTTAAAAAACAGAGAGTTAAGAC
Found at i:5396720 original size:22 final size:22
Alignment explanation
Indices: 5396695--5396745 Score: 84
Period size: 22 Copynumber: 2.3 Consensus size: 22
5396685 CACCACAGCT
*
5396695 CGTATAAATGCACCGAAGTGCC
1 CGTAGAAATGCACCGAAGTGCC
*
5396717 CGTAGAATTGCACCGAAGTGCC
1 CGTAGAAATGCACCGAAGTGCC
5396739 CGTAGAA
1 CGTAGAA
5396746 TTTTGTCCAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.31, C:0.25, G:0.25, T:0.18
Consensus pattern (22 bp):
CGTAGAAATGCACCGAAGTGCC
Found at i:5396746 original size:22 final size:22
Alignment explanation
Indices: 5396703--5396747 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
5396693 CTCGTATAAA
5396703 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
5396725 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
5396747 T
1 T
5396748 TTGTCCATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.27, C:0.27, G:0.27, T:0.20
Consensus pattern (22 bp):
TGCACCGAAGTGCCCGTAGAAT
Found at i:5397081 original size:29 final size:29
Alignment explanation
Indices: 5397039--5397110 Score: 108
Period size: 29 Copynumber: 2.5 Consensus size: 29
5397029 TTTTCTGCAT
**
5397039 ATTCATGTCATGTAATACATATAAGATGA
1 ATTCATGTCATGTAATACATATAAGACAA
* *
5397068 ATTCATGTCATGTAATACATTTAATACAA
1 ATTCATGTCATGTAATACATATAAGACAA
5397097 ATTCATGTCATGTA
1 ATTCATGTCATGTA
5397111 TCATAATATG
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 39 1.00
ACGTcount: A:0.39, C:0.12, G:0.11, T:0.38
Consensus pattern (29 bp):
ATTCATGTCATGTAATACATATAAGACAA
Found at i:5397532 original size:68 final size:67
Alignment explanation
Indices: 5397414--5397565 Score: 207
Period size: 68 Copynumber: 2.3 Consensus size: 67
5397404 TTTTTCTCAT
* * *
5397414 GGGGGAATCGGTTCCCCCCCCTGGGGTATCGATTCCCCTTAAGCAATCTGGAATTCATATACGAT
1 GGGGGTATCGGTTCCCCCCCCTGGGGTACCGATTCCCCTTAAGCAATCTGGAAATCATATACGAT
5397479 GA
66 GA
* * *
5397481 GGGGGTATCGGTTCCCCCCCCTGGGGGTACCGATTCCCCTCT-AGCATTCTGGAAATCATATTCT
1 GGGGGTATCGGTTCCCCCCCCT-GGGGTACCGATTCCCCT-TAAGCAATCTGGAAATCATATACG
*
5397545 TTGA
64 ATGA
*
5397549 AGGGGTATCGGTTCCCC
1 GGGGGTATCGGTTCCCC
5397566 TTGAATGGGT
Statistics
Matches: 75, Mismatches: 8, Indels: 3
0.87 0.09 0.03
Matches are distributed among these distances:
67 21 0.28
68 53 0.71
69 1 0.01
ACGTcount: A:0.18, C:0.28, G:0.26, T:0.27
Consensus pattern (67 bp):
GGGGGTATCGGTTCCCCCCCCTGGGGTACCGATTCCCCTTAAGCAATCTGGAAATCATATACGAT
GA
Found at i:5397575 original size:21 final size:21
Alignment explanation
Indices: 5397545--5397587 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
5397535 ATCATATTCT
* *
5397545 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
5397566 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
5397587 T
1 T
5397588 AACCCAGAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.16, C:0.26, G:0.28, T:0.30
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:5403630 original size:22 final size:22
Alignment explanation
Indices: 5403605--5403655 Score: 75
Period size: 22 Copynumber: 2.3 Consensus size: 22
5403595 CACCACAGCT
* *
5403605 CGTATAAATGCACCGAAGTGCC
1 CGTAGAAATACACCGAAGTGCC
*
5403627 CGTAGAATTACACCGAAGTGCC
1 CGTAGAAATACACCGAAGTGCC
5403649 CGTAGAA
1 CGTAGAA
5403656 TTTTGTCCAT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.33, C:0.25, G:0.24, T:0.18
Consensus pattern (22 bp):
CGTAGAAATACACCGAAGTGCC
Found at i:5403656 original size:22 final size:22
Alignment explanation
Indices: 5403615--5403657 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
5403605 CGTATAAATG
5403615 CACCGAAGTGCCCGTAGAATTA
1 CACCGAAGTGCCCGTAGAATTA
5403637 CACCGAAGTGCCCGTAGAATT
1 CACCGAAGTGCCCGTAGAATT
5403658 TTGTCCATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.30, C:0.28, G:0.23, T:0.19
Consensus pattern (22 bp):
CACCGAAGTGCCCGTAGAATTA
Found at i:5403991 original size:29 final size:29
Alignment explanation
Indices: 5403949--5404020 Score: 108
Period size: 29 Copynumber: 2.5 Consensus size: 29
5403939 TTTTCTGCAT
**
5403949 ATTCATGTCATGTAATACATATAAGATGA
1 ATTCATGTCATGTAATACATATAAGACAA
* *
5403978 ATTCATGTCATGTAATACATTTAATACAA
1 ATTCATGTCATGTAATACATATAAGACAA
5404007 ATTCATGTCATGTA
1 ATTCATGTCATGTA
5404021 TCATAATATG
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 39 1.00
ACGTcount: A:0.39, C:0.12, G:0.11, T:0.38
Consensus pattern (29 bp):
ATTCATGTCATGTAATACATATAAGACAA
Found at i:5404441 original size:67 final size:66
Alignment explanation
Indices: 5404325--5404474 Score: 212
Period size: 67 Copynumber: 2.3 Consensus size: 66
5404315 TTTTTCTCAT
* * *
5404325 GGGGGAATCGGTTCCCCCCCTGGGGTATCGATTCCCCTTAAGCAATCTGGAATTCATATACGATG
1 GGGGGTATCGGTTCCCCCCCTGGGGTACCGATTCCCCTTAAGCAATCTGGAAATCATATACGATG
5404390 A
66 A
* * *
5404391 GGGGGTATCGGTTCCCCCCCTGGGGGTACCGATTCCCCTCT-AGCATTCTGGAAATCATATTCGT
1 GGGGGTATCGGTTCCCCCCCT-GGGGTACCGATTCCCCT-TAAGCAATCTGGAAATCATATACGA
5404455 TGA
64 TGA
*
5404458 AGGGGTATCGGTTCCCC
1 GGGGGTATCGGTTCCCC
5404475 TTGAATGGGT
Statistics
Matches: 75, Mismatches: 7, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
66 20 0.27
67 54 0.72
68 1 0.01
ACGTcount: A:0.19, C:0.27, G:0.27, T:0.27
Consensus pattern (66 bp):
GGGGGTATCGGTTCCCCCCCTGGGGTACCGATTCCCCTTAAGCAATCTGGAAATCATATACGATG
A
Found at i:5407513 original size:16 final size:17
Alignment explanation
Indices: 5407480--5407514 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
5407470 TTATAAATAC
*
5407480 ATTTTAATAAATAATTA
1 ATTTTAATAAAAAATTA
5407497 ATTTTAA-AAAAAATTA
1 ATTTTAATAAAAAATTA
5407513 AT
1 AT
5407515 AAATAATTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 10 0.59
17 7 0.41
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (17 bp):
ATTTTAATAAAAAATTA
Found at i:5409742 original size:127 final size:127
Alignment explanation
Indices: 5409516--5409768 Score: 506
Period size: 127 Copynumber: 2.0 Consensus size: 127
5409506 GACTGAAAAA
5409516 TCAAACTAACTAAAATAATCTAGCACCGAAAGTTGCAAATCTAGCTTGTTTCCCTCGACAGCATT
1 TCAAACTAACTAAAATAATCTAGCACCGAAAGTTGCAAATCTAGCTTGTTTCCCTCGACAGCATT
5409581 AATCCCTGATAAGTTGACATTTGCAGCAATCTAGACGAGTACTAAAAAAAAGATAGACTAAG
66 AATCCCTGATAAGTTGACATTTGCAGCAATCTAGACGAGTACTAAAAAAAAGATAGACTAAG
5409643 TCAAACTAACTAAAATAATCTAGCACCGAAAGTTGCAAATCTAGCTTGTTTCCCTCGACAGCATT
1 TCAAACTAACTAAAATAATCTAGCACCGAAAGTTGCAAATCTAGCTTGTTTCCCTCGACAGCATT
5409708 AATCCCTGATAAGTTGACATTTGCAGCAATCTAGACGAGTACTAAAAAAAAGATAGACTAA
66 AATCCCTGATAAGTTGACATTTGCAGCAATCTAGACGAGTACTAAAAAAAAGATAGACTAA
5409769 ACTAAAGATT
Statistics
Matches: 126, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
127 126 1.00
ACGTcount: A:0.40, C:0.21, G:0.15, T:0.25
Consensus pattern (127 bp):
TCAAACTAACTAAAATAATCTAGCACCGAAAGTTGCAAATCTAGCTTGTTTCCCTCGACAGCATT
AATCCCTGATAAGTTGACATTTGCAGCAATCTAGACGAGTACTAAAAAAAAGATAGACTAAG
Found at i:5414459 original size:21 final size:22
Alignment explanation
Indices: 5414422--5414465 Score: 56
Period size: 21 Copynumber: 2.0 Consensus size: 22
5414412 TAATGATGTT
*
5414422 TAAATATTATTTATATAA-AAA
1 TAAATAATATTTATATAATAAA
5414443 TAAATAATA-TTATTATAATAAA
1 TAAATAATATTTA-TATAATAAA
5414465 T
1 T
5414466 TAACAAAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
20 3 0.15
21 13 0.65
22 4 0.20
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (22 bp):
TAAATAATATTTATATAATAAA
Found at i:5422734 original size:34 final size:35
Alignment explanation
Indices: 5422667--5422737 Score: 135
Period size: 35 Copynumber: 2.1 Consensus size: 35
5422657 GATCCAGTTA
5422667 ACATATACCAATAATTTAGAGATAAAATTATTAAC
1 ACATATACCAATAATTTAGAGATAAAATTATTAAC
5422702 ACATATACCAATAATTTAGAGAT-AAATTATTAAC
1 ACATATACCAATAATTTAGAGATAAAATTATTAAC
5422736 AC
1 AC
5422738 TCAAAATGTT
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
34 13 0.36
35 23 0.64
ACGTcount: A:0.51, C:0.13, G:0.06, T:0.31
Consensus pattern (35 bp):
ACATATACCAATAATTTAGAGATAAAATTATTAAC
Found at i:5423944 original size:3 final size:3
Alignment explanation
Indices: 5423930--5423964 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
5423920 AGAGCTTCTC
*
5423930 CAT CAT CCT CAT CAT CAT CAT CAT CAT CAT CAT CA
1 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CA
5423965 CTACGACAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.31, C:0.37, G:0.00, T:0.31
Consensus pattern (3 bp):
CAT
Found at i:5431800 original size:12 final size:12
Alignment explanation
Indices: 5431774--5431816 Score: 54
Period size: 12 Copynumber: 3.7 Consensus size: 12
5431764 AGAAAAAATG
5431774 TAATA-AATATA
1 TAATATAATATA
*
5431785 TAATATAATTTA
1 TAATATAATATA
5431797 TAATATAA-ATA
1 TAATATAATATA
5431808 TATATATAA
1 TA-ATATAA
5431817 GGACGAAATT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
11 9 0.32
12 19 0.68
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (12 bp):
TAATATAATATA
Found at i:5432051 original size:20 final size:20
Alignment explanation
Indices: 5432028--5432069 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
5432018 GAATCCTTCG
5432028 TCGTGAAATTGAAATCGAAC
1 TCGTGAAATTGAAATCGAAC
*
5432048 TCGTGAAGTTGAAATCGAAC
1 TCGTGAAATTGAAATCGAAC
5432068 TC
1 TC
5432070 AGAGTTCTGG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.36, C:0.17, G:0.21, T:0.26
Consensus pattern (20 bp):
TCGTGAAATTGAAATCGAAC
Found at i:5432324 original size:105 final size:105
Alignment explanation
Indices: 5432127--5432970 Score: 1535
Period size: 105 Copynumber: 8.0 Consensus size: 105
5432117 CGTTGTGAAG
* * * *
5432127 CTGAAATTGGGTAATTGTTTATTGACAACCAGCGGTCCCTTCGTCATGAAGTTGAACTTGCGTTG
1 CTGAAATTGAG-AAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTG
*
5432192 CCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCT
65 TCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCT
*
5432233 CTGAATTTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
1 CTGAAATTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
* *
5432298 CTGGAGTCCAATATCCTTCGTTGTGAAGTTGAGATTAGCT
66 CTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCT
* * *
5432338 CTGAATTTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCTTGAAGTTGAACTTGTGTTGT
1 CTGAAATTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
5432403 CTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCT
66 CTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCT
5432443 CTGAAATTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
1 CTGAAATTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
*
5432508 ATGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCT
66 CTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCT
*
5432548 CTGAAATTGAGAAATGTTTGTTGACAACTAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
1 CTGAAATTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
5432613 CTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCT
66 CTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCT
*
5432653 CTGAAATTGAGAAATGTTTGTTGACAACCAGTGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
1 CTGAAATTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
5432718 CTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCT
66 CTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCT
**
5432758 CTGGGATTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
1 CTGAAATTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
5432823 CTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCT
66 CTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCT
5432863 CTGAAATTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
1 CTGAAATTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
5432928 CTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCT
66 CTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCT
5432968 CTG
1 CTG
5432971 GGTAAAACCT
Statistics
Matches: 713, Mismatches: 25, Indels: 1
0.96 0.03 0.00
Matches are distributed among these distances:
105 704 0.99
106 9 0.01
ACGTcount: A:0.22, C:0.18, G:0.26, T:0.34
Consensus pattern (105 bp):
CTGAAATTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
CTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCT
Found at i:5433792 original size:23 final size:23
Alignment explanation
Indices: 5433762--5433811 Score: 82
Period size: 23 Copynumber: 2.2 Consensus size: 23
5433752 ACCCCAAACG
**
5433762 TTTTTTCTTTCTTTTTTTTTTTT
1 TTTTTTCTTTCTTTTTCATTTTT
5433785 TTTTTTCTTTCTTTTTCATTTTT
1 TTTTTTCTTTCTTTTTCATTTTT
5433808 TTTT
1 TTTT
5433812 CAACTTAGGA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.02, C:0.10, G:0.00, T:0.88
Consensus pattern (23 bp):
TTTTTTCTTTCTTTTTCATTTTT
Found at i:5433813 original size:11 final size:10
Alignment explanation
Indices: 5433762--5433812 Score: 68
Period size: 11 Copynumber: 5.0 Consensus size: 10
5433752 ACCCCAAACG
5433762 TTTTTTCTTTC
1 TTTTTT-TTTC
5433773 TTTTTTTTT-
1 TTTTTTTTTC
5433782 TTTTTTTTTC
1 TTTTTTTTTC
*
5433792 TTTCTTTTTC
1 TTTTTTTTTC
5433802 ATTTTTTTTTC
1 -TTTTTTTTTC
5433813 AACTTAGGAC
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
9 9 0.25
10 12 0.33
11 15 0.42
ACGTcount: A:0.02, C:0.12, G:0.00, T:0.86
Consensus pattern (10 bp):
TTTTTTTTTC
Found at i:5446127 original size:12 final size:12
Alignment explanation
Indices: 5446101--5446143 Score: 54
Period size: 12 Copynumber: 3.7 Consensus size: 12
5446091 AGAAAAAATG
5446101 TAATA-AATATA
1 TAATATAATATA
*
5446112 TAATATAATTTA
1 TAATATAATATA
5446124 TAATATAA-ATA
1 TAATATAATATA
5446135 TATATATAA
1 TA-ATATAA
5446144 GGACGAAATT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
11 9 0.32
12 19 0.68
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (12 bp):
TAATATAATATA
Found at i:5448593 original size:12 final size:12
Alignment explanation
Indices: 5448576--5448600 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
5448566 TGCAACTAAT
5448576 TGAAAATCTATC
1 TGAAAATCTATC
5448588 TGAAAATCTATC
1 TGAAAATCTATC
5448600 T
1 T
5448601 TTCAAATGAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.16, G:0.08, T:0.36
Consensus pattern (12 bp):
TGAAAATCTATC
Found at i:5448870 original size:15 final size:16
Alignment explanation
Indices: 5448843--5448873 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
5448833 ATAAATTAAA
5448843 ATATTTACAAAATAAT
1 ATATTTACAAAATAAT
5448859 ATATTT-CAAAATAAT
1 ATATTTACAAAATAAT
5448874 TTTAATTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.60
16 6 0.40
ACGTcount: A:0.55, C:0.06, G:0.00, T:0.39
Consensus pattern (16 bp):
ATATTTACAAAATAAT
Found at i:5449433 original size:21 final size:20
Alignment explanation
Indices: 5449409--5449447 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
5449399 TAATTTAAGA
5449409 TAATTATAAAATAATATATTT
1 TAATTAT-AAATAATATATTT
*
5449430 TAATTATTAATAATATAT
1 TAATTATAAATAATATAT
5449448 AAATTTTCTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (20 bp):
TAATTATAAATAATATATTT
Found at i:5449453 original size:24 final size:21
Alignment explanation
Indices: 5449409--5449454 Score: 56
Period size: 24 Copynumber: 2.0 Consensus size: 21
5449399 TAATTTAAGA
*
5449409 TAATTATAAAATAATATATTT
1 TAATTATAAAATAATAAATTT
5449430 TAATTATTAATAATATATAAATTT
1 TAATTA-TAA-AATA-ATAAATTT
5449454 T
1 T
5449455 CTATCTATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 6 0.29
22 3 0.14
23 4 0.19
24 8 0.38
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (21 bp):
TAATTATAAAATAATAAATTT
Found at i:5458935 original size:28 final size:29
Alignment explanation
Indices: 5458895--5458952 Score: 91
Period size: 29 Copynumber: 2.0 Consensus size: 29
5458885 TGCGATCTCT
5458895 AATTCGCATTGCGA-TCTCCACTATCGCA
1 AATTCGCATTGCGATTCTCCACTATCGCA
* *
5458923 AATTCGCGTTGCGATTTTCCACTATCGCA
1 AATTCGCATTGCGATTCTCCACTATCGCA
5458952 A
1 A
5458953 TGCGAAATGC
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
28 13 0.48
29 14 0.52
ACGTcount: A:0.24, C:0.29, G:0.16, T:0.31
Consensus pattern (29 bp):
AATTCGCATTGCGATTCTCCACTATCGCA
Found at i:5459244 original size:31 final size:31
Alignment explanation
Indices: 5459207--5459305 Score: 109
Period size: 31 Copynumber: 3.3 Consensus size: 31
5459197 ATAAGAATTG
5459207 AGTGACCAAAACATAAATTAAATAATATATA
1 AGTGACCAAAACATAAATTAAATAATATATA
* ** *
5459238 AATGACCAAATAGGT-AGTT-AAT-A-ATA-A
1 AGTGACCAAA-ACATAAATTAAATAATATATA
*
5459265 AGTGACCAAAACATAAATTAGATAATATATA
1 AGTGACCAAAACATAAATTAAATAATATATA
5459296 AGTGACCAAA
1 AGTGACCAAA
5459306 TAGGTAGTTT
Statistics
Matches: 53, Mismatches: 9, Indels: 12
0.72 0.12 0.16
Matches are distributed among these distances:
26 2 0.04
27 13 0.25
28 5 0.09
29 2 0.04
30 6 0.11
31 23 0.43
32 2 0.04
ACGTcount: A:0.55, C:0.10, G:0.11, T:0.24
Consensus pattern (31 bp):
AGTGACCAAAACATAAATTAAATAATATATA
Found at i:5460162 original size:15 final size:15
Alignment explanation
Indices: 5460127--5460156 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
5460117 AAGTTCGTGC
5460127 GATTTTTTGTTATAA
1 GATTTTTTGTTATAA
5460142 GATTTTTTGTTATAA
1 GATTTTTTGTTATAA
5460157 TTTTTTAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.27, C:0.00, G:0.13, T:0.60
Consensus pattern (15 bp):
GATTTTTTGTTATAA
Found at i:5462130 original size:18 final size:17
Alignment explanation
Indices: 5462099--5462143 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 17
5462089 AATTATATTT
5462099 GTAAAATATTAAATAAA
1 GTAAAATATTAAATAAA
5462116 GTAAAATACTTAAATAAA
1 GTAAAATA-TTAAATAAA
*
5462134 TTAAATATAT
1 GTAAA-ATAT
5462144 AATATTAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
17 8 0.32
18 14 0.56
19 3 0.12
ACGTcount: A:0.60, C:0.02, G:0.04, T:0.33
Consensus pattern (17 bp):
GTAAAATATTAAATAAA
Found at i:5462205 original size:12 final size:10
Alignment explanation
Indices: 5462188--5462216 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
5462178 TAGAGAGTAT
5462188 TTGAGAGAAA
1 TTGAGAGAAA
5462198 TTGAGAGAAA
1 TTGAGAGAAA
5462208 TTGAGAGAA
1 TTGAGAGAA
5462217 TTTGGTGTGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.48, C:0.00, G:0.31, T:0.21
Consensus pattern (10 bp):
TTGAGAGAAA
Found at i:5463695 original size:6 final size:6
Alignment explanation
Indices: 5463684--5463715 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
5463674 TGTATACTTC
5463684 CAGTGA CAGTGA CAGTGA CAGTGA CAGTGA CA
1 CAGTGA CAGTGA CAGTGA CAGTGA CAGTGA CA
5463716 AAGGTTCTAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.34, C:0.19, G:0.31, T:0.16
Consensus pattern (6 bp):
CAGTGA
Found at i:5467685 original size:15 final size:16
Alignment explanation
Indices: 5467667--5467700 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
5467657 TATGAACATC
*
5467667 AAATAAATTAACAA-A
1 AAATAAAATAACAATA
5467682 AAATAAAATAACAATA
1 AAATAAAATAACAATA
5467698 AAA
1 AAA
5467701 ATAATTTCTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 13 0.76
16 4 0.24
ACGTcount: A:0.76, C:0.06, G:0.00, T:0.18
Consensus pattern (16 bp):
AAATAAAATAACAATA
Found at i:5469329 original size:25 final size:25
Alignment explanation
Indices: 5469291--5469439 Score: 264
Period size: 25 Copynumber: 6.0 Consensus size: 25
5469281 TGGAAGGGGA
*
5469291 TTAGGG-TTGAAACCCTAAATTGAT
1 TTAGGGTTTGAAACCCTAAACTGAT
*
5469315 TTAGGGTTTGAAACCCTAAATTGAT
1 TTAGGGTTTGAAACCCTAAACTGAT
5469340 TTAGGGTTTGAAACCCTAAACTGAT
1 TTAGGGTTTGAAACCCTAAACTGAT
5469365 TTAGGGTTTGAAACCCTAAACTGAT
1 TTAGGGTTTGAAACCCTAAACTGAT
5469390 TTAGGGTTTGAAACCCTAAACTGAT
1 TTAGGGTTTGAAACCCTAAACTGAT
*
5469415 TTAGGGTTTGAAACCCTAATCTGAT
1 TTAGGGTTTGAAACCCTAAACTGAT
5469440 GGGTTATTGG
Statistics
Matches: 122, Mismatches: 2, Indels: 1
0.98 0.02 0.01
Matches are distributed among these distances:
24 6 0.05
25 116 0.95
ACGTcount: A:0.32, C:0.15, G:0.20, T:0.34
Consensus pattern (25 bp):
TTAGGGTTTGAAACCCTAAACTGAT
Found at i:5469577 original size:3 final size:3
Alignment explanation
Indices: 5469569--5469632 Score: 89
Period size: 3 Copynumber: 22.0 Consensus size: 3
5469559 GCAAAAATTG
*
5469569 TAA TAA TAAA TAA TAA TAA -AA TAA TAA T-A TAA TGA TAA TAA TAA
1 TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
5469613 TAA TAA TAA TAA TAA -AA TAA
1 TAA TAA TAA TAA TAA TAA TAA
5469633 CGGAAAAAAA
Statistics
Matches: 55, Mismatches: 2, Indels: 8
0.85 0.03 0.12
Matches are distributed among these distances:
2 6 0.11
3 46 0.84
4 3 0.05
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (3 bp):
TAA
Found at i:5469993 original size:87 final size:87
Alignment explanation
Indices: 5469834--5470126 Score: 370
Period size: 87 Copynumber: 3.3 Consensus size: 87
5469824 CGTCTAAGGG
* * * * * * *
5469834 TGACATGGCTCCTACGTGATGAGGAAATCTGGTCATTTTTAGGGATGATAACTCGGTTCCTACGT
1 TGACACGGCTCCTACGTGATGAAGAGATCTGGCCA-TCTAAAGG-TGATAACTCGGTTCCTACGT
* *
5469899 AATGAGGACGACTGGTTATCAGGT
64 GATGAGGACGGCTGGTTATCAGGT
* *
5469923 TGACACGGCTCTTACGTGATGAAGAGATCTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGA
1 TGACACGGCTCCTACGTGATGAAGAGATCTGGCCATCTAAAGGTGATAACTCGGTTCCTACGTGA
5469988 TGAGGACGGCTGGTTATCAGGT
66 TGAGGACGGCTGGTTATCAGGT
*
5470010 TGACACGGCTCTTACGTGATGAAGAGATCTGGCCATCTAAAGGTGAGGTGATAACTCGGTTCCTA
1 TGACACGGCTCCTACGTGATGAAGAGATCTGGCCATCT-AA----AGGTGATAACTCGGTTCCTA
* *
5470075 CGTGATAAGGACGGCTGGTTATCCTAATGT
61 CGTGATGAGGACGGCTGGTTAT-C--AGGT
5470105 TGACACGGCTCCTACGTGATGA
1 TGACACGGCTCCTACGTGATGA
5470127 GGAAGTCTGG
Statistics
Matches: 181, Mismatches: 15, Indels: 10
0.88 0.07 0.05
Matches are distributed among these distances:
87 79 0.44
88 7 0.04
89 30 0.17
92 40 0.22
93 1 0.01
95 24 0.13
ACGTcount: A:0.25, C:0.19, G:0.29, T:0.27
Consensus pattern (87 bp):
TGACACGGCTCCTACGTGATGAAGAGATCTGGCCATCTAAAGGTGATAACTCGGTTCCTACGTGA
TGAGGACGGCTGGTTATCAGGT
Found at i:5470028 original size:41 final size:41
Alignment explanation
Indices: 5469894--5470031 Score: 143
Period size: 41 Copynumber: 3.2 Consensus size: 41
5469884 ACTCGGTTCC
*
5469894 TACGTAATGAGGACGACTGGTTATCAGGTTGACACGGCTCT
1 TACGTGATGAGGACGACTGGTTATCAGGTTGACACGGCTCT
* ** * * *
5469935 TACGTGATGAAGA-GATCTGGCCATCTAAAGGTGATAACACGGTTCC
1 TACGTGATGAGGACGA-CTGGTTATC---AGGT--TGACACGGCTCT
*
5469981 TACGTGATGAGGACGGCTGGTTATCAGGTTGACACGGCTCT
1 TACGTGATGAGGACGACTGGTTATCAGGTTGACACGGCTCT
5470022 TACGTGATGA
1 TACGTGATGA
5470032 AGAGATCTGG
Statistics
Matches: 76, Mismatches: 14, Indels: 14
0.73 0.13 0.13
Matches are distributed among these distances:
40 2 0.03
41 37 0.49
43 4 0.05
44 4 0.05
46 28 0.37
47 1 0.01
ACGTcount: A:0.25, C:0.19, G:0.30, T:0.26
Consensus pattern (41 bp):
TACGTGATGAGGACGACTGGTTATCAGGTTGACACGGCTCT
Done.