Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr8
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 56894857
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.32
Warning! 1173888 characters in sequence are not A, C, G, or T
File 88 of 185
Found at i:27882733 original size:15 final size:15
Alignment explanation
Indices: 27882713--27882744 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
27882703 TTCGACTTGG
*
27882713 TTTTATTTTTTTATT
1 TTTTATTTTCTTATT
27882728 TTTTATTTTCTTATT
1 TTTTATTTTCTTATT
27882743 TT
1 TT
27882745 CTTGCGTTTT
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:0.12, C:0.03, G:0.00, T:0.84
Consensus pattern (15 bp):
TTTTATTTTCTTATT
Found at i:27882745 original size:8 final size:8
Alignment explanation
Indices: 27882715--27882747 Score: 50
Period size: 8 Copynumber: 4.2 Consensus size: 8
27882705 CGACTTGGTT
*
27882715 TTATTTTT
1 TTATTTTC
27882723 TTATTTT-
1 TTATTTTC
27882730 TTATTTTC
1 TTATTTTC
27882738 TTATTTTC
1 TTATTTTC
27882746 TT
1 TT
27882748 GCGTTTTCTT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
7 7 0.29
8 17 0.71
ACGTcount: A:0.12, C:0.06, G:0.00, T:0.82
Consensus pattern (8 bp):
TTATTTTC
Found at i:27884862 original size:3 final size:3
Alignment explanation
Indices: 27884850--27884888 Score: 71
Period size: 3 Copynumber: 13.3 Consensus size: 3
27884840 CTTGTATGTT
27884850 ATA A-A ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
27884889 ACAGTTAAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.06
3 33 0.94
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:27886472 original size:27 final size:26
Alignment explanation
Indices: 27886424--27886474 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 26
27886414 TAGAATTAAT
*
27886424 TTGTTATTCATCATTTGCTTTGTATA
1 TTGTTAATCATCATTTGCTTTGTATA
27886450 TTGTTAATCAATCATATTG-TTTGTA
1 TTGTTAATC-ATCAT-TTGCTTTGTA
27886475 AAAATTTCAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
26 8 0.36
27 11 0.50
28 3 0.14
ACGTcount: A:0.24, C:0.10, G:0.12, T:0.55
Consensus pattern (26 bp):
TTGTTAATCATCATTTGCTTTGTATA
Found at i:27887244 original size:9 final size:9
Alignment explanation
Indices: 27887232--27887261 Score: 60
Period size: 9 Copynumber: 3.3 Consensus size: 9
27887222 AATATATTTA
27887232 TTTTTTAAT
1 TTTTTTAAT
27887241 TTTTTTAAT
1 TTTTTTAAT
27887250 TTTTTTAAT
1 TTTTTTAAT
27887259 TTT
1 TTT
27887262 AAAATATTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (9 bp):
TTTTTTAAT
Found at i:27887295 original size:39 final size:40
Alignment explanation
Indices: 27887240--27887316 Score: 138
Period size: 39 Copynumber: 1.9 Consensus size: 40
27887230 TATTTTTTAA
27887240 TTTTTTTAATTTTTTTAATTTTAAAATATTTTTAAAATGC
1 TTTTTTTAATTTTTTTAATTTTAAAATATTTTTAAAATGC
*
27887280 TTTTTTTTA-TTTTTTAATTTTAAAATATTTTTAAAAT
1 TTTTTTTAATTTTTTTAATTTTAAAATATTTTTAAAAT
27887317 ATTTTTAATT
Statistics
Matches: 36, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
39 28 0.78
40 8 0.22
ACGTcount: A:0.32, C:0.01, G:0.01, T:0.65
Consensus pattern (40 bp):
TTTTTTTAATTTTTTTAATTTTAAAATATTTTTAAAATGC
Found at i:27887301 original size:28 final size:28
Alignment explanation
Indices: 27887290--27887364 Score: 98
Period size: 28 Copynumber: 2.6 Consensus size: 28
27887280 TTTTTTTTAT
*
27887290 TTTTTAATTTTAAAATATTTTTAAAATA
1 TTTTTAATTTTAAAATCTTTTTAAAATA
27887318 TTTTTAATTTTAAAATAC-TTTTAAAATA
1 TTTTTAATTTTAAAAT-CTTTTTAAAATA
27887346 CTTTTTTAATTTTTAAAAT
1 --TTTTTAA-TTTTAAAAT
27887365 AAATTTTTGG
Statistics
Matches: 42, Mismatches: 1, Indels: 5
0.88 0.02 0.10
Matches are distributed among these distances:
28 26 0.62
30 7 0.17
31 9 0.21
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (28 bp):
TTTTTAATTTTAAAATCTTTTTAAAATA
Found at i:27887310 original size:17 final size:17
Alignment explanation
Indices: 27887308--27887341 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
27887298 TTTAAAATAT
*
27887308 TTTTAAAATATTTTTAA
1 TTTTAAAATACTTTTAA
27887325 TTTTAAAATACTTTTAA
1 TTTTAAAATACTTTTAA
27887342 AATACTTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (17 bp):
TTTTAAAATACTTTTAA
Found at i:27887311 original size:11 final size:11
Alignment explanation
Indices: 27887297--27887351 Score: 57
Period size: 11 Copynumber: 5.4 Consensus size: 11
27887287 TATTTTTTAA
27887297 TTTTAAAATAT
1 TTTTAAAATAT
27887308 TTTTAAAATAT
1 TTTTAAAATAT
27887319 TTTT---A-A-
1 TTTTAAAATAT
*
27887325 TTTTAAAATAC
1 TTTTAAAATAT
27887336 TTTTAAAATACT
1 TTTTAAAATA-T
27887348 TTTT
1 TTTT
27887352 TAATTTTTAA
Statistics
Matches: 37, Mismatches: 1, Indels: 11
0.76 0.02 0.22
Matches are distributed among these distances:
6 4 0.11
7 1 0.03
8 1 0.03
9 1 0.03
10 1 0.03
11 25 0.68
12 4 0.11
ACGTcount: A:0.40, C:0.04, G:0.00, T:0.56
Consensus pattern (11 bp):
TTTTAAAATAT
Found at i:27894420 original size:23 final size:23
Alignment explanation
Indices: 27894372--27894422 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 23
27894362 ATTTGGAAGC
* *
27894372 ATAAAATAAAATAAAATATATGG
1 ATAAAATAAAATAAAATACATAG
*
27894395 ATAATATAAAAGTAAAATACA-AG
1 ATAAAATAAAA-TAAAATACATAG
27894418 ATAAA
1 ATAAA
27894423 GGATCGAAAG
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
23 15 0.65
24 8 0.35
ACGTcount: A:0.67, C:0.02, G:0.08, T:0.24
Consensus pattern (23 bp):
ATAAAATAAAATAAAATACATAG
Found at i:27898246 original size:8 final size:8
Alignment explanation
Indices: 27898233--27898298 Score: 52
Period size: 8 Copynumber: 8.6 Consensus size: 8
27898223 AGTTATTTTA
27898233 TATATATT
1 TATATATT
27898241 TATATATT
1 TATATATT
27898249 TATCAT-TT
1 TAT-ATATT
*
27898257 TAT-CATT
1 TATATATT
27898264 T-T-TATT
1 TATATATT
27898270 TATATA-T
1 TATATATT
27898277 TATATATT
1 TATATATT
* *
27898285 CTAAATTTT
1 -TATATATT
27898294 TATAT
1 TATAT
27898299 GTTTTTCAAA
Statistics
Matches: 47, Mismatches: 5, Indels: 12
0.73 0.08 0.19
Matches are distributed among these distances:
6 5 0.11
7 11 0.23
8 23 0.49
9 8 0.17
ACGTcount: A:0.33, C:0.05, G:0.00, T:0.62
Consensus pattern (8 bp):
TATATATT
Found at i:27898294 original size:29 final size:29
Alignment explanation
Indices: 27898237--27898296 Score: 79
Period size: 29 Copynumber: 2.1 Consensus size: 29
27898227 ATTTTATATA
* *
27898237 TATTTATATATTTATCATTTTATCATTTT
1 TATTTATATATTTATCATTCTATAATTTT
27898266 TATTTATATATTATAT-ATTCTA-AATTTT
1 TATTTATATATT-TATCATTCTATAATTTT
27898294 TAT
1 TAT
27898297 ATGTTTTTCA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
28 8 0.29
29 17 0.61
30 3 0.11
ACGTcount: A:0.32, C:0.05, G:0.00, T:0.63
Consensus pattern (29 bp):
TATTTATATATTTATCATTCTATAATTTT
Found at i:27907862 original size:25 final size:25
Alignment explanation
Indices: 27907829--27907898 Score: 113
Period size: 25 Copynumber: 2.8 Consensus size: 25
27907819 CAGGCCCATT
27907829 TTCACAGCTCATGTGAGCATTCTGA
1 TTCACAGCTCATGTGAGCATTCTGA
* *
27907854 TTCATAGCTCATGTGAGCATTTTGA
1 TTCACAGCTCATGTGAGCATTCTGA
*
27907879 TTCACAACTCATGTGAGCAT
1 TTCACAGCTCATGTGAGCAT
27907899 ACATGTACAG
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 41 1.00
ACGTcount: A:0.26, C:0.21, G:0.19, T:0.34
Consensus pattern (25 bp):
TTCACAGCTCATGTGAGCATTCTGA
Found at i:27909055 original size:15 final size:16
Alignment explanation
Indices: 27909035--27909064 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
27909025 TGGTGCCTTG
27909035 TTGAT-ATGTGTTAAT
1 TTGATAATGTGTTAAT
27909050 TTGATAATGTGTTAA
1 TTGATAATGTGTTAA
27909065 AGCATGTTTG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.30, C:0.00, G:0.20, T:0.50
Consensus pattern (16 bp):
TTGATAATGTGTTAAT
Found at i:27914847 original size:25 final size:25
Alignment explanation
Indices: 27914819--27914872 Score: 72
Period size: 25 Copynumber: 2.2 Consensus size: 25
27914809 TGTAGTGGCA
27914819 AGGTGGCAACACAGGTGTGGCAAGG
1 AGGTGGCAACACAGGTGTGGCAAGG
*** *
27914844 AGGTGGTGTCACAGGTGTGGTAAGG
1 AGGTGGCAACACAGGTGTGGCAAGG
27914869 AGGT
1 AGGT
27914873 CAGAGGTTCA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.24, C:0.11, G:0.46, T:0.19
Consensus pattern (25 bp):
AGGTGGCAACACAGGTGTGGCAAGG
Found at i:27915021 original size:24 final size:21
Alignment explanation
Indices: 27914988--27915034 Score: 58
Period size: 24 Copynumber: 2.1 Consensus size: 21
27914978 TCAAATGAGT
*
27914988 GATTTAAGGAGTGGATCATGGAG
1 GATTTAAGGAGAGGAT--TGGAG
27915011 GATTTCAAGGAGAGGATTGGAG
1 GATTT-AAGGAGAGGATTGGAG
27915033 GA
1 GA
27915035 GAGATTTTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
22 7 0.32
23 5 0.23
24 10 0.45
ACGTcount: A:0.32, C:0.04, G:0.40, T:0.23
Consensus pattern (21 bp):
GATTTAAGGAGAGGATTGGAG
Found at i:27915048 original size:25 final size:24
Alignment explanation
Indices: 27915007--27915058 Score: 61
Period size: 24 Copynumber: 2.1 Consensus size: 24
27914997 AGTGGATCAT
27915007 GGAGGATTTCAAGGAGAGGATTGGA
1 GGAGGATTTCAAGGAGA-GATTGGA
* *
27915032 GGAGAGATTTTAA-GAGAGATTTGA
1 GGAG-GATTTCAAGGAGAGATTGGA
27915056 GGA
1 GGA
27915059 ATTTGAGTAG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
24 9 0.38
25 8 0.33
26 7 0.29
ACGTcount: A:0.35, C:0.02, G:0.40, T:0.23
Consensus pattern (24 bp):
GGAGGATTTCAAGGAGAGATTGGA
Found at i:27916153 original size:27 final size:27
Alignment explanation
Indices: 27916119--27916228 Score: 148
Period size: 27 Copynumber: 4.1 Consensus size: 27
27916109 TTAACTTTAT
*
27916119 CGAAATACCCTCGATGGGTAAAATTAT
1 CGAAATACCCTCGATGGGTAAAATTAC
* **
27916146 TGAAATACCCTTAATGGGTAAAATTAC
1 CGAAATACCCTCGATGGGTAAAATTAC
*
27916173 TGAAATACCCTCGATGGGTAAAATTAC
1 CGAAATACCCTCGATGGGTAAAATTAC
* * *
27916200 CAAAATACCCTCGAAGAGTAAAATTAC
1 CGAAATACCCTCGATGGGTAAAATTAC
27916227 CG
1 CG
27916229 TAATGCCCCC
Statistics
Matches: 72, Mismatches: 11, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 72 1.00
ACGTcount: A:0.40, C:0.19, G:0.16, T:0.25
Consensus pattern (27 bp):
CGAAATACCCTCGATGGGTAAAATTAC
Found at i:27916472 original size:26 final size:26
Alignment explanation
Indices: 27916423--27916472 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 26
27916413 ACATATACTG
* **
27916423 TACTGGCAGCTCTGCTGCGTTATTAT
1 TACTGGCAGCTATGCTGCAATATTAT
*
27916449 TACTGGCAGCTATGTTGCAATATT
1 TACTGGCAGCTATGCTGCAATATT
27916473 GGTGTGTGGG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 20 1.00
ACGTcount: A:0.20, C:0.20, G:0.22, T:0.38
Consensus pattern (26 bp):
TACTGGCAGCTATGCTGCAATATTAT
Found at i:27921153 original size:50 final size:49
Alignment explanation
Indices: 27921048--27921154 Score: 126
Period size: 50 Copynumber: 2.1 Consensus size: 49
27921038 TTATTGAGGT
*
27921048 TATGAGAGGTCCCACGCAAGACCATGTCTGGGACATGGCGCTGGTACCAA
1 TATGAGAGGTCCCACGCAAGACCATGTCTGGGACAT-GCGCTGGAACCAA
* * * * *
27921098 GATGAGAGGTCCCTCGTAAGATCATGTCTGGGACAT-CGCATAGGAACCGA
1 TATGAGAGGTCCCACGCAAGACCATGTCTGGGACATGCGC-T-GGAACCAA
27921148 TATGAGA
1 TATGAGA
27921155 ACTCTCATGT
Statistics
Matches: 48, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
48 3 0.06
49 1 0.02
50 44 0.92
ACGTcount: A:0.28, C:0.22, G:0.30, T:0.20
Consensus pattern (49 bp):
TATGAGAGGTCCCACGCAAGACCATGTCTGGGACATGCGCTGGAACCAA
Found at i:27921470 original size:20 final size:20
Alignment explanation
Indices: 27921445--27921483 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
27921435 TGAGTTATTT
27921445 AAGTAAGCA-AGTAAGTAAAC
1 AAGTAA-CAGAGTAAGTAAAC
27921465 AAGTAACAGAGTAAGTAAA
1 AAGTAACAGAGTAAGTAAA
27921484 GAAGAAAGTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 2 0.11
20 16 0.89
ACGTcount: A:0.56, C:0.08, G:0.21, T:0.15
Consensus pattern (20 bp):
AAGTAACAGAGTAAGTAAAC
Found at i:27922954 original size:40 final size:39
Alignment explanation
Indices: 27922825--27922960 Score: 134
Period size: 40 Copynumber: 3.4 Consensus size: 39
27922815 GCGTTTGGAA
* *
27922825 AAAAATGCCGCTAAAAATCGAGCATTAGCGGCACTTTAC
1 AAAAACGCCGCTAAAAATCGAGCATTAGCGGCATTTTAC
* * * * *
27922864 ACAAAACACTGCTAAAGATCGAGCATTAGCAGCACTTT-C
1 A-AAAACGCCGCTAAAAATCGAGCATTAGCGGCATTTTAC
*
27922903 AGGAAATCGCCGCTAAAAAT-GAGCATTAGCGGCATTTTTACC
1 A--AAAACGCCGCTAAAAATCGAGCATTAGCGGCA-TTTTA-C
27922945 AAAAACGCCG-TAAAAA
1 AAAAACGCCGCTAAAAA
27922961 CCTAAGCCCA
Statistics
Matches: 79, Mismatches: 13, Indels: 10
0.77 0.13 0.10
Matches are distributed among these distances:
39 22 0.28
40 55 0.70
42 2 0.03
ACGTcount: A:0.40, C:0.23, G:0.18, T:0.20
Consensus pattern (39 bp):
AAAAACGCCGCTAAAAATCGAGCATTAGCGGCATTTTAC
Found at i:27923071 original size:41 final size:41
Alignment explanation
Indices: 27922995--27923272 Score: 358
Period size: 41 Copynumber: 6.8 Consensus size: 41
27922985 TGACCTTTCG
* * * * *
27922995 GGGCTTTAGTGGTGTTTTTAAAAAAGCACCGCTAATGCTTA
1 GGGCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTCA
* * * * * *
27923036 GGGATTTAGTGGCGTTTTTGGAGAAGCGCCACTAATGCTTA
1 GGGCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTCA
*
27923077 GGGCTTTAGCGACGTTTTTGAAAAAGCGCCGCTAATGCTCA
1 GGGCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTCA
* * *
27923118 GGGCTTGAGCGGCGTTTTTGGAGAAGCGCCGCTAATGCTCA
1 GGGCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTCA
* *
27923159 GGGCTTTAGCGGCGTTTTTGGAAAAGCGCCGCTAATACTCA
1 GGGCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTCA
* * *
27923200 GGACTTTAGTGGCGTTTTTGAAAAAGCGTCGCTAATGCTCA
1 GGGCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTCA
* *
27923241 GGGCTTTAGCGGCGTTTTTAAAAAAGTGCCGC
1 GGGCTTTAGCGGCGTTTTTGAAAAAGCGCCGC
27923273 AAAAACATTT
Statistics
Matches: 206, Mismatches: 31, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
41 206 1.00
ACGTcount: A:0.23, C:0.19, G:0.29, T:0.29
Consensus pattern (41 bp):
GGGCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTCA
Found at i:27923626 original size:14 final size:14
Alignment explanation
Indices: 27923601--27923634 Score: 68
Period size: 14 Copynumber: 2.4 Consensus size: 14
27923591 GGGTTTAATA
27923601 TATATGGTTTAGGG
1 TATATGGTTTAGGG
27923615 TATATGGTTTAGGG
1 TATATGGTTTAGGG
27923629 TATATG
1 TATATG
27923635 ATTAATTTAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.24, C:0.00, G:0.32, T:0.44
Consensus pattern (14 bp):
TATATGGTTTAGGG
Found at i:27923873 original size:68 final size:70
Alignment explanation
Indices: 27923800--27923934 Score: 229
Period size: 68 Copynumber: 2.0 Consensus size: 70
27923790 CAGTGTTAGG
* *
27923800 TTAAGGTTTAGGGTTTAGATTAATTAGTGTATTTTAA-TT-TATATTAAATAAGGTTTATGGGTT
1 TTAAGGTTTACGGTTTAGATTAATTAGTGTATTTTAATTTATATATTAAATAAGGTTTAGGGGTT
27923863 AGGGT
66 AGGGT
*
27923868 TTAAGGTTTACGGTTTAGATTAATTAGTGTTTTTTAATTTATATATTAAATAAGGTTTAGGGGTT
1 TTAAGGTTTACGGTTTAGATTAATTAGTGTATTTTAATTTATATATTAAATAAGGTTTAGGGGTT
27923933 AG
66 AG
27923935 TAGTTAGGGG
Statistics
Matches: 62, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
68 35 0.56
69 2 0.03
70 25 0.40
ACGTcount: A:0.30, C:0.01, G:0.22, T:0.47
Consensus pattern (70 bp):
TTAAGGTTTACGGTTTAGATTAATTAGTGTATTTTAATTTATATATTAAATAAGGTTTAGGGGTT
AGGGT
Found at i:27924102 original size:94 final size:93
Alignment explanation
Indices: 27923990--27924162 Score: 258
Period size: 94 Copynumber: 1.8 Consensus size: 93
27923980 ATTTGAGGTC
* *
27923990 GGGTTAGGGTTGAAGGTTTAAATTAACTAGTATTTTTT-AATTTATATATTAATTAAGTTCTTAT
1 GGGTTAGGGTTGAAGGTTTAAATTAACTAGT-TTTTTTAAATTTATATATTAAATAAGTTATTAT
27924054 ATAATTGTAAAAGAGGGGTTAAGGGTTAG
65 ATAATTGTAAAAGAGGGGTTAAGGGTTAG
* * * * *
27924083 GGGTTAGAGGTTTAAGGTTTAGATTAATTGGTTTTTTTAAATTTATATATTAAATAATTTATTAT
1 GGGTTAG-GGTTGAAGGTTTAAATTAACTAGTTTTTTTAAATTTATATATTAAATAAGTTATTAT
27924148 ATAATTGTAAAAGAG
65 ATAATTGTAAAAGAG
27924163 ATAATATTAA
Statistics
Matches: 71, Mismatches: 7, Indels: 3
0.88 0.09 0.04
Matches are distributed among these distances:
93 13 0.18
94 58 0.82
ACGTcount: A:0.35, C:0.01, G:0.20, T:0.44
Consensus pattern (93 bp):
GGGTTAGGGTTGAAGGTTTAAATTAACTAGTTTTTTTAAATTTATATATTAAATAAGTTATTATA
TAATTGTAAAAGAGGGGTTAAGGGTTAG
Found at i:27926430 original size:7 final size:7
Alignment explanation
Indices: 27926418--27926458 Score: 55
Period size: 7 Copynumber: 5.9 Consensus size: 7
27926408 GGGTTGTGAT
27926418 TTAGGGG
1 TTAGGGG
27926425 TTAGGGG
1 TTAGGGG
27926432 TTAGGGG
1 TTAGGGG
*
27926439 TTAGAGG
1 TTAGGGG
* *
27926446 TTAAGAG
1 TTAGGGG
27926453 TTAGGG
1 TTAGGG
27926459 ATTTAGGGTT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
7 28 1.00
ACGTcount: A:0.22, C:0.00, G:0.49, T:0.29
Consensus pattern (7 bp):
TTAGGGG
Found at i:27926559 original size:68 final size:70
Alignment explanation
Indices: 27926487--27926621 Score: 229
Period size: 68 Copynumber: 2.0 Consensus size: 70
27926477 CAGTGTTAGG
* *
27926487 TTAAGGTTTAGGGTTTAGATTAATTAGTGTATTTTAA-TT-TATATTAAATAAGGTTTATGGGTT
1 TTAAGGTTTACGGTTTAGATTAATTAGTGTATTTTAATTTATATATTAAATAAGGTTTAGGGGTT
27926550 AGGGT
66 AGGGT
*
27926555 TTAAGGTTTACGGTTTAGATTAATTAGTGTTTTTTAATTTATATATTAAATAAGGTTTAGGGGTT
1 TTAAGGTTTACGGTTTAGATTAATTAGTGTATTTTAATTTATATATTAAATAAGGTTTAGGGGTT
27926620 AG
66 AG
27926622 TAGTTAGGGG
Statistics
Matches: 62, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
68 35 0.56
69 2 0.03
70 25 0.40
ACGTcount: A:0.30, C:0.01, G:0.22, T:0.47
Consensus pattern (70 bp):
TTAAGGTTTACGGTTTAGATTAATTAGTGTATTTTAATTTATATATTAAATAAGGTTTAGGGGTT
AGGGT
Found at i:27926789 original size:94 final size:94
Alignment explanation
Indices: 27926677--27927131 Score: 824
Period size: 94 Copynumber: 4.9 Consensus size: 94
27926667 ATTTGAGGTC
* * * * * * *
27926677 GGGTTAG-GGTTGAAGGTTTAAATTAACTAGTATTTTTT-AATTTATATATTAATTAAGTTCTTA
1 GGGTTAGAGGTTTAAGGTTTAGATTAATTGGT-TTTTTTAAATTTATATATTAAATAATTTATTA
27926740 TATAATTGTAAAAGAGGGGTTAAGGGTTAG
65 TATAATTGTAAAAGAGGGGTTAAGGGTTAG
27926770 GGGTTAGAGGTTTAAGGTTTAGATTAATTGGTTTTTTTAAATTTATATATTAAATAATTTATTAT
1 GGGTTAGAGGTTTAAGGTTTAGATTAATTGGTTTTTTTAAATTTATATATTAAATAATTTATTAT
27926835 ATAATTGTAAAAGAGGGGTTAAGGGTTAG
66 ATAATTGTAAAAGAGGGGTTAAGGGTTAG
27926864 GGGTTAGAGGTTTAAGGTTTAGATTAATTGGTTTTTTTAAATTTATATATTAAATAATTTATTAT
1 GGGTTAGAGGTTTAAGGTTTAGATTAATTGGTTTTTTTAAATTTATATATTAAATAATTTATTAT
27926929 ATAATTGTAAAAGAGGGGTTAAGGGTTAG
66 ATAATTGTAAAAGAGGGGTTAAGGGTTAG
27926958 GGGTTAGAGGTTTAAGGTTTAGATTAATTGGTTTTTTTAAATTTATATATTAAATAATTTATTAT
1 GGGTTAGAGGTTTAAGGTTTAGATTAATTGGTTTTTTTAAATTTATATATTAAATAATTTATTAT
27927023 ATAATTGTAAAAGAGGGGTTAAGGGTTAG
66 ATAATTGTAAAAGAGGGGTTAAGGGTTAG
27927052 GGGTTAGAGGTTTAAGGTTTAGATTAATTGGTTTTTTTAAATTTATATATTAAATAATTTATTAT
1 GGGTTAGAGGTTTAAGGTTTAGATTAATTGGTTTTTTTAAATTTATATATTAAATAATTTATTAT
27927117 ATAATTGTAAAAGAG
66 ATAATTGTAAAAGAG
27927132 ATAATATTAA
Statistics
Matches: 353, Mismatches: 7, Indels: 3
0.97 0.02 0.01
Matches are distributed among these distances:
93 13 0.04
94 340 0.96
ACGTcount: A:0.34, C:0.00, G:0.22, T:0.44
Consensus pattern (94 bp):
GGGTTAGAGGTTTAAGGTTTAGATTAATTGGTTTTTTTAAATTTATATATTAAATAATTTATTAT
ATAATTGTAAAAGAGGGGTTAAGGGTTAG
Found at i:27931264 original size:22 final size:22
Alignment explanation
Indices: 27931236--27931284 Score: 98
Period size: 22 Copynumber: 2.2 Consensus size: 22
27931226 GGAAAACTGG
27931236 AAATAGGCATGGCAACATGCAA
1 AAATAGGCATGGCAACATGCAA
27931258 AAATAGGCATGGCAACATGCAA
1 AAATAGGCATGGCAACATGCAA
27931280 AAATA
1 AAATA
27931285 AAAAGAGGGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.49, C:0.16, G:0.20, T:0.14
Consensus pattern (22 bp):
AAATAGGCATGGCAACATGCAA
Found at i:27934021 original size:14 final size:15
Alignment explanation
Indices: 27934002--27934032 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
27933992 TTAATTTTGG
27934002 AAATT-AATAAATAA
1 AAATTAAATAAATAA
27934016 AAATTAAATAAATAA
1 AAATTAAATAAATAA
27934031 AA
1 AA
27934033 CAATTAAAGT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.31
15 11 0.69
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (15 bp):
AAATTAAATAAATAA
Found at i:27950369 original size:20 final size:20
Alignment explanation
Indices: 27950346--27950384 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
27950336 GGATTCAGAG
27950346 TTAATTCAGAAGATTTTGTT
1 TTAATTCAGAAGATTTTGTT
27950366 TTAATTCAGAAGATTTTGT
1 TTAATTCAGAAGATTTTGT
27950385 ATGAAGCTCA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.31, C:0.05, G:0.15, T:0.49
Consensus pattern (20 bp):
TTAATTCAGAAGATTTTGTT
Found at i:27953228 original size:25 final size:26
Alignment explanation
Indices: 27953186--27953239 Score: 76
Period size: 25 Copynumber: 2.1 Consensus size: 26
27953176 TTCTCCTAAA
*
27953186 TTTCAATTTTATTTAATTATTTAAT-T
1 TTTCAATTTTATTGAATTA-TTAATAT
27953212 TTTCAA-TTTATTGAATTATTAATAT
1 TTTCAATTTTATTGAATTATTAATAT
27953237 TTT
1 TTT
27953240 ATACTAATTA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
24 5 0.19
25 15 0.58
26 6 0.23
ACGTcount: A:0.31, C:0.04, G:0.02, T:0.63
Consensus pattern (26 bp):
TTTCAATTTTATTGAATTATTAATAT
Found at i:27957915 original size:30 final size:30
Alignment explanation
Indices: 27957881--27957940 Score: 102
Period size: 30 Copynumber: 2.0 Consensus size: 30
27957871 TTATTCTTAG
*
27957881 TCCATTTACTAATTAAGGCTATGTTAGCTA
1 TCCATTTACTAATTAAGGCTATATTAGCTA
*
27957911 TCCATTTTCTAATTAAGGCTATATTAGCTA
1 TCCATTTACTAATTAAGGCTATATTAGCTA
27957941 AATTTTATTA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.30, C:0.17, G:0.12, T:0.42
Consensus pattern (30 bp):
TCCATTTACTAATTAAGGCTATATTAGCTA
Found at i:27959877 original size:17 final size:17
Alignment explanation
Indices: 27959845--27959882 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
27959835 TTCAATTCTA
27959845 ATTTGACCCAAAATATTT
1 ATTTGACCCAAAATA-TT
*
27959863 ATTTTACCC-AAATATT
1 ATTTGACCCAAAATATT
27959879 ATTT
1 ATTT
27959883 AAAACTATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 6 0.32
17 5 0.26
18 8 0.42
ACGTcount: A:0.37, C:0.16, G:0.03, T:0.45
Consensus pattern (17 bp):
ATTTGACCCAAAATATT
Found at i:27970517 original size:23 final size:22
Alignment explanation
Indices: 27970485--27970531 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 22
27970475 TTTAACATTA
27970485 TCTTTTATTTCCTTT-TAGGTTT
1 TCTTTTATTTCCTTTCTA-GTTT
*
27970507 TCTTTTCATTTTCTTTCTAGTTT
1 TCTTTT-ATTTCCTTTCTAGTTT
27970530 TC
1 TC
27970532 ACTCAAAGTA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
22 6 0.27
23 14 0.64
24 2 0.09
ACGTcount: A:0.09, C:0.17, G:0.06, T:0.68
Consensus pattern (22 bp):
TCTTTTATTTCCTTTCTAGTTT
Found at i:27970692 original size:15 final size:14
Alignment explanation
Indices: 27970642--27970692 Score: 50
Period size: 13 Copynumber: 3.5 Consensus size: 14
27970632 CTCTTGTCAA
27970642 TTATTATTTTTATG
1 TTATTATTTTTATG
*
27970656 ATTATTTATTTTTGT-
1 -TTA-TTATTTTTATG
*
27970671 TTGTTATTTTTATG
1 TTATTATTTTTATG
27970685 TTCATTAT
1 TT-ATTAT
27970693 GAACTAATTG
Statistics
Matches: 29, Mismatches: 4, Indels: 6
0.74 0.10 0.15
Matches are distributed among these distances:
13 9 0.31
14 4 0.14
15 7 0.24
16 9 0.31
ACGTcount: A:0.20, C:0.02, G:0.08, T:0.71
Consensus pattern (14 bp):
TTATTATTTTTATG
Found at i:27971201 original size:13 final size:12
Alignment explanation
Indices: 27971182--27971211 Score: 51
Period size: 13 Copynumber: 2.4 Consensus size: 12
27971172 AAATTAGTTA
27971182 TTTTATTTTATT
1 TTTTATTTTATT
27971194 TGTTTATTTTATT
1 T-TTTATTTTATT
27971207 TTTTA
1 TTTTA
27971212 AATAATTATT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
12 5 0.29
13 12 0.71
ACGTcount: A:0.17, C:0.00, G:0.03, T:0.80
Consensus pattern (12 bp):
TTTTATTTTATT
Found at i:27972396 original size:14 final size:14
Alignment explanation
Indices: 27972377--27972403 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
27972367 ATTAAATTTG
27972377 AGAAATAATCTCCC
1 AGAAATAATCTCCC
27972391 AGAAATAATCTCC
1 AGAAATAATCTCC
27972404 TAGTTAAACT
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:0.44, C:0.26, G:0.07, T:0.22
Consensus pattern (14 bp):
AGAAATAATCTCCC
Found at i:27974193 original size:29 final size:29
Alignment explanation
Indices: 27974149--27974215 Score: 80
Period size: 29 Copynumber: 2.3 Consensus size: 29
27974139 TGCAGAAATT
* * *
27974149 TTGCCATATAATGAATACATGCCATAAAA
1 TTGCCAAATAACGAATAAATGCCATAAAA
**
27974178 TTGCCAAATAACGAATAAATGTGATAAAA
1 TTGCCAAATAACGAATAAATGCCATAAAA
*
27974207 TCGCCAAAT
1 TTGCCAAAT
27974216 CCCCTCGAAT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.46, C:0.16, G:0.12, T:0.25
Consensus pattern (29 bp):
TTGCCAAATAACGAATAAATGCCATAAAA
Found at i:27976675 original size:30 final size:30
Alignment explanation
Indices: 27976641--27976699 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 30
27976631 TACAAGCTTT
27976641 GGGGCAAAAGTGTAAATATGCAAAAGTTTA
1 GGGGCAAAAGTGTAAATATGCAAAAGTTTA
* * * *
27976671 GGGGCAAAATTGTAATTTTGCCAAAGTTT
1 GGGGCAAAAGTGTAAATATGCAAAAGTTT
27976700 GAGTCAAGGA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.37, C:0.08, G:0.25, T:0.29
Consensus pattern (30 bp):
GGGGCAAAAGTGTAAATATGCAAAAGTTTA
Found at i:27977184 original size:23 final size:23
Alignment explanation
Indices: 27977151--27977244 Score: 116
Period size: 23 Copynumber: 4.1 Consensus size: 23
27977141 AGTGTTATTG
*
27977151 ATCAGTGGTAGCTACGGCTACAT
1 ATCAATGGTAGCTACGGCTACAT
* * *
27977174 ATCATTTGTAGCTTCGGCTACAT
1 ATCAATGGTAGCTACGGCTACAT
* * *
27977197 TTTAGTGGTAGCTACGGCTACAT
1 ATCAATGGTAGCTACGGCTACAT
*
27977220 ATCAATGGTAGCTTCGGCTACAT
1 ATCAATGGTAGCTACGGCTACAT
27977243 AT
1 AT
27977245 TAGTGTGGCA
Statistics
Matches: 59, Mismatches: 12, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 59 1.00
ACGTcount: A:0.24, C:0.20, G:0.22, T:0.33
Consensus pattern (23 bp):
ATCAATGGTAGCTACGGCTACAT
Found at i:27977207 original size:46 final size:46
Alignment explanation
Indices: 27977154--27977249 Score: 165
Period size: 46 Copynumber: 2.1 Consensus size: 46
27977144 GTTATTGATC
* * *
27977154 AGTGGTAGCTACGGCTACATATCATTTGTAGCTTCGGCTACATTTT
1 AGTGGTAGCTACGGCTACATATCAATGGTAGCTTCGGCTACATATT
27977200 AGTGGTAGCTACGGCTACATATCAATGGTAGCTTCGGCTACATATT
1 AGTGGTAGCTACGGCTACATATCAATGGTAGCTTCGGCTACATATT
27977246 AGTG
1 AGTG
27977250 TGGCACTTAT
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
46 47 1.00
ACGTcount: A:0.24, C:0.19, G:0.24, T:0.33
Consensus pattern (46 bp):
AGTGGTAGCTACGGCTACATATCAATGGTAGCTTCGGCTACATATT
Found at i:27989991 original size:27 final size:27
Alignment explanation
Indices: 27989953--27990428 Score: 459
Period size: 27 Copynumber: 17.7 Consensus size: 27
27989943 GACTTATAGG
*
27989953 AAAATGACTGAAATACCCTCGAAGGGT
1 AAAATGACTGAAATACCCTTGAAGGGT
* * *
27989980 AAAACGACTGAAATACCTTTGAACGGT
1 AAAATGACTGAAATACCCTTGAAGGGT
** **
27990007 AAAATGACCAAAATACCCTCAAAGGGT
1 AAAATGACTGAAATACCCTTGAAGGGT
*
27990034 AAAATGACTGAAATACCCTTGAAGGAT
1 AAAATGACTGAAATACCCTTGAAGGGT
* *
27990061 AAAATGA-TCGAAATGCCCTCGAAGGGT
1 AAAATGACT-GAAATACCCTTGAAGGGT
27990088 AAAATGA-TCGAAATACCCTTGAAGGGT
1 AAAATGACT-GAAATACCCTTGAAGGGT
* * *
27990115 AAAATGA-TCGAAATGCCATCGAAGGGT
1 AAAATGACT-GAAATACCCTTGAAGGGT
*
27990142 AAAATGA-TCGAAATACCCTTAAAGGGT
1 AAAATGACT-GAAATACCCTTGAAGGGT
27990169 AAAATGACTGAAATACCCTTGAAGGGT
1 AAAATGACTGAAATACCCTTGAAGGGT
* *
27990196 AAAATGACCGAAATTCCCTTGAAGGGT
1 AAAATGACTGAAATACCCTTGAAGGGT
* *
27990223 AAAATAACTGAAATACCTTTGAAGGGT
1 AAAATGACTGAAATACCCTTGAAGGGT
** *
27990250 AAAATGACCAAAATACCCTTAAAGGGT
1 AAAATGACTGAAATACCCTTGAAGGGT
* * *
27990277 AAAATGACTGAAATGCCCTTGAAAGAT
1 AAAATGACTGAAATACCCTTGAAGGGT
* * *
27990304 AAAATGA-TCAAAACACCCCTGAAGGGT
1 AAAATGACT-GAAATACCCTTGAAGGGT
* * *
27990331 AAAATGA-TCAAAATACCCCTGAACGGT
1 AAAATGACT-GAAATACCCTTGAAGGGT
*
27990358 AAAATGA-TCGAAATACCC-TCATAGGGT
1 AAAATGACT-GAAATACCCTTGA-AGGGT
* * * *
27990385 AAAAGGAAC-GAAA-ACCCCTAAAGAGT
1 AAAATG-ACTGAAATACCCTTGAAGGGT
* *
27990411 GAAATGACCGAAATACCC
1 AAAATGACTGAAATACCC
27990429 CCATAAGGTA
Statistics
Matches: 378, Mismatches: 62, Indels: 18
0.83 0.14 0.04
Matches are distributed among these distances:
25 2 0.01
26 20 0.05
27 354 0.94
28 2 0.01
ACGTcount: A:0.43, C:0.18, G:0.20, T:0.19
Consensus pattern (27 bp):
AAAATGACTGAAATACCCTTGAAGGGT
Found at i:27990654 original size:26 final size:26
Alignment explanation
Indices: 27990625--27990695 Score: 124
Period size: 26 Copynumber: 2.7 Consensus size: 26
27990615 CATATACTGC
*
27990625 TACTGGCAGCTTTGCTGCGTTACTAT
1 TACTGGCAGCTTTGCTGCGTCACTAT
27990651 TACTGGCAGCTTTGCTGCGTCACTAT
1 TACTGGCAGCTTTGCTGCGTCACTAT
*
27990677 TACTGGCAGCTTGGCTGCG
1 TACTGGCAGCTTTGCTGCG
27990696 ATATTGGTGT
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 43 1.00
ACGTcount: A:0.14, C:0.25, G:0.27, T:0.34
Consensus pattern (26 bp):
TACTGGCAGCTTTGCTGCGTCACTAT
Found at i:27990828 original size:30 final size:28
Alignment explanation
Indices: 27990763--27990855 Score: 114
Period size: 28 Copynumber: 3.2 Consensus size: 28
27990753 TACTGCATTG
*
27990763 CACTGATTACTATATTGGGCTAAGGCCCC
1 CACTG-TTACTATATTGGGCTAAGGCCCA
* *
27990792 CACTGTTACTGTATTGGGTTAAGGCCTACA
1 CACTGTTACTATATTGGGCTAAGGCC--CA
* *
27990822 CACTGTTACTATAATGGGCTAAAGCCCA
1 CACTGTTACTATATTGGGCTAAGGCCCA
27990850 CACTGT
1 CACTGT
27990856 ACTGATACTA
Statistics
Matches: 55, Mismatches: 7, Indels: 5
0.82 0.10 0.07
Matches are distributed among these distances:
28 27 0.49
29 5 0.09
30 23 0.42
ACGTcount: A:0.26, C:0.25, G:0.20, T:0.29
Consensus pattern (28 bp):
CACTGTTACTATATTGGGCTAAGGCCCA
Found at i:28004406 original size:40 final size:40
Alignment explanation
Indices: 28004362--28004585 Score: 308
Period size: 40 Copynumber: 5.6 Consensus size: 40
28004352 AAGTGAATAT
* * * * **
28004362 ATCCGGATTAAGAT-CCGAAGGCCTTTGTGCGAGATACTAA
1 ATCCGGGTTAAG-TCCCGAAGGCATTCGTGCGAGTTGTTAA
28004402 ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAA
1 ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAA
28004442 ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAA
1 ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAA
28004482 ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAA
1 ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAA
* * **
28004522 ATCCGGGTTATGTCCCGAAGGCATT-GTGTGAGTTACTAA
1 ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAA
* * *
28004561 AACCGGGCTATGTCCCGAAGGCATT
1 ATCCGGGTTAAGTCCCGAAGGCATT
28004586 TGAACGAGGA
Statistics
Matches: 171, Mismatches: 12, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
39 35 0.20
40 136 0.80
ACGTcount: A:0.24, C:0.21, G:0.29, T:0.27
Consensus pattern (40 bp):
ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAA
Found at i:28004460 original size:80 final size:80
Alignment explanation
Indices: 28004323--28004585 Score: 318
Period size: 80 Copynumber: 3.3 Consensus size: 80
28004313 TTGAATGCTG
* * * * *
28004323 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAG-TGAATATATCCGGATTAAGAT-CCGAAGGCC
1 TCCGGGCTAAGTCCCGAAGGCATTCGTGC-GAGTTG-TTAAATCCGGGTTAAG-TCCCGAAGGCC
*
28004385 TTTGTGCGAGATACTAAA
63 TTTGTGCGAGTTACTAAA
* * *
28004403 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAAATCCGGGTTAAGTCCCGAAGGCATTC
1 TCCGGGCTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAAATCCGGGTTAAGTCCCGAAGGCCTTT
**
28004468 GTGCGAGTTGTTAAA
66 GTGCGAGTTACTAAA
* * *
28004483 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAAATCCGGGTTATGTCCCGAAGG-CATT
1 TCCGGGCTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAAATCCGGGTTAAGTCCCGAAGGCCTTT
*
28004547 GTGTGAGTTACTAAA
66 GTGCGAGTTACTAAA
* *
28004562 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATT
28004586 TGAACGAGGA
Statistics
Matches: 159, Mismatches: 21, Indels: 7
0.85 0.11 0.04
Matches are distributed among these distances:
79 35 0.22
80 116 0.73
81 8 0.05
ACGTcount: A:0.24, C:0.21, G:0.29, T:0.27
Consensus pattern (80 bp):
TCCGGGCTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAAATCCGGGTTAAGTCCCGAAGGCCTTT
GTGCGAGTTACTAAA
Found at i:28004537 original size:120 final size:120
Alignment explanation
Indices: 28004323--28004585 Score: 318
Period size: 120 Copynumber: 2.2 Consensus size: 120
28004313 TTGAATGCTG
* * *
28004323 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAATATATCCGGATTAAGATCCGAAGGCCTT
1 TCCGGGCTAAGTCCCGAAGGCATTCGTGCTAAGTGAATAAATCCGGATTAAGATCCGAAGGCATT
* **
28004387 TGTGCGAGATACTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAAA
66 CGTGCGAGATACTAAATCCGGGTTAAGTCCCGAAGGCATT-GTGCGAGTTACTAAA
* * * *
28004443 TCCGGGTTAAGTCCCGAAGGCATTCGTGC-GAGTTG-TTAAATCCGGGTTAAG-TCCCGAAGGCA
1 TCCGGGCTAAGTCCCGAAGGCATTCGTGCTAAG-TGAATAAATCCGGATTAAGAT-CCGAAGGCA
* ** * *
28004505 TTCGTGCGAGTTGTTAAATCCGGGTTATGTCCCGAAGGCATTGTGTGAGTTACTAAA
64 TTCGTGCGAGATACTAAATCCGGGTTAAGTCCCGAAGGCATTGTGCGAGTTACTAAA
* *
28004562 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATT
28004586 TGAACGAGGA
Statistics
Matches: 122, Mismatches: 18, Indels: 7
0.83 0.12 0.05
Matches are distributed among these distances:
119 34 0.28
120 80 0.66
121 8 0.07
ACGTcount: A:0.24, C:0.21, G:0.29, T:0.27
Consensus pattern (120 bp):
TCCGGGCTAAGTCCCGAAGGCATTCGTGCTAAGTGAATAAATCCGGATTAAGATCCGAAGGCATT
CGTGCGAGATACTAAATCCGGGTTAAGTCCCGAAGGCATTGTGCGAGTTACTAAA
Found at i:28009986 original size:27 final size:27
Alignment explanation
Indices: 28009940--28010331 Score: 339
Period size: 27 Copynumber: 14.6 Consensus size: 27
28009930 CATGGGCAAT
* *
28009940 TGATTGAAATA-CCTTCGAAGGATAAAA
1 TGATCGAAATACCCTT-GAAGGGTAAAA
*
28009967 TGACCGAAATACCCTTGAAGGGTAAAA
1 TGATCGAAATACCCTTGAAGGGTAAAA
28009994 TGATCGAAATACCCTTGAAGGGTAAAA
1 TGATCGAAATACCCTTGAAGGGTAAAA
* * * ** *
28010021 TGA-CCAAAAACTCTCAAAAGGTAAAA
1 TGATCGAAATACCCTTGAAGGGTAAAA
* ** * *
28010047 TTATTAAAATGCCCTCGAAGGGTAAAA
1 TGATCGAAATACCCTTGAAGGGTAAAA
*
28010074 TGA-CAGAAATACCCTTAAAGGGTAAAA
1 TGATC-GAAATACCCTTGAAGGGTAAAA
* * * *
28010101 TGATCGAAATGCCCTCGAAAGCTAAAA
1 TGATCGAAATACCCTTGAAGGGTAAAA
* * * **
28010128 TGATCAAAATTCCCTCGAAGAATAAAA
1 TGATCGAAATACCCTTGAAGGGTAAAA
* *
28010155 TGATCGAAATGCCCCTGAAGGGTAAAA
1 TGATCGAAATACCCTTGAAGGGTAAAA
*
28010182 TGA-CAAAAATACCCTT-AGAGGGTAAAA
1 TGATC-GAAATACCCTTGA-AGGGTAAAA
** *
28010209 TGATTAAAATGA-CCTCGAAGGGTAAAA
1 TGATCGAAAT-ACCCTTGAAGGGTAAAA
* * *
28010236 TGATTGAAATACCCCTGAAAGGTAAAA
1 TGATCGAAATACCCTTGAAGGGTAAAA
* *
28010263 TGACCGAAATACCCTTAAAGGGTAAAA
1 TGATCGAAATACCCTTGAAGGGTAAAA
* * *
28010290 TGATTGAAATGCCCTCGAAGGGTAAAA
1 TGATCGAAATACCCTTGAAGGGTAAAA
28010317 TGAAT-GAAATACCCT
1 TG-ATCGAAATACCCT
28010332 CATAAGATAA
Statistics
Matches: 294, Mismatches: 60, Indels: 22
0.78 0.16 0.06
Matches are distributed among these distances:
26 22 0.07
27 263 0.89
28 9 0.03
ACGTcount: A:0.44, C:0.16, G:0.19, T:0.21
Consensus pattern (27 bp):
TGATCGAAATACCCTTGAAGGGTAAAA
Found at i:28010772 original size:30 final size:30
Alignment explanation
Indices: 28010731--28010787 Score: 96
Period size: 30 Copynumber: 1.9 Consensus size: 30
28010721 AAGGGCCCCA
*
28010731 TGTTGCTGTATTGGGCAAAGGCCCACAGAC
1 TGTTACTGTATTGGGCAAAGGCCCACAGAC
*
28010761 TGTTACTGTATTGGGCTAAGGCCCACA
1 TGTTACTGTATTGGGCAAAGGCCCACA
28010788 CTGTATTGAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.23, C:0.23, G:0.28, T:0.26
Consensus pattern (30 bp):
TGTTACTGTATTGGGCAAAGGCCCACAGAC
Found at i:28014896 original size:29 final size:29
Alignment explanation
Indices: 28014845--28014960 Score: 155
Period size: 29 Copynumber: 4.0 Consensus size: 29
28014835 CGCAGTTTCC
* *
28014845 ATAAGAAA-TCCTTGTGGCGATCTCTATT
1 ATAAGAAATTCTTTCTGGCGATCTCTATT
28014873 ATAAGAAATTCTTTCTGGCGATCTCTATT
1 ATAAGAAATTCTTTCTGGCGATCTCTATT
* *
28014902 ATGAGAAATTCTTTCTGGCGATCTCTTTT
1 ATAAGAAATTCTTTCTGGCGATCTCTATT
* *
28014931 ATAAGAAAATT-TTTGTGGCTATCTCTATT
1 ATAAG-AAATTCTTTCTGGCGATCTCTATT
28014960 A
1 A
28014961 AAGGAATGTC
Statistics
Matches: 78, Mismatches: 8, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
28 8 0.10
29 65 0.83
30 5 0.06
ACGTcount: A:0.28, C:0.16, G:0.16, T:0.41
Consensus pattern (29 bp):
ATAAGAAATTCTTTCTGGCGATCTCTATT
Found at i:28022852 original size:266 final size:266
Alignment explanation
Indices: 28022378--28022911 Score: 811
Period size: 266 Copynumber: 2.0 Consensus size: 266
28022368 GTGATTCTTA
* * * *
28022378 TCATAAGAGAATGCTAGCTAATCATAATGTTAGACGGAAGTATTGTTGGTCTAGTTGATTCATGA
1 TCATAAGAGAATGCTAGCTAATCATAATGTTAAACAGAAGTATTGTTAGTCTAGTTGATTAATGA
** * * *
28022443 TCAGTTTTAATCTATCTTTCTTTGGCATTCTATTCTATTATGTTCTGTAGAAGAATCGATTATGT
66 TCAGCATTAATCTATCGTTCTTTGGCATTCTATTCCATTATGTTCAGTAGAAGAATCGATTATGT
* * * * *
28022508 TGTCTCTGTCACAATTGGTTCCAGTGTGTATGAGCGATATTCTTCTTCTATGTTTTCTCTAGGTT
131 TATCTCTATCACAACTGGTTCCAGTGCGTATGAGCGATATTCTTCTTCTATGTTTTCTCTAAGTT
* * *
28022573 ATCATCAATCTCTTTATCACTCAATATGGGTTGTATTCTTGGAGATTCAGTAGAGTTCCACATAT
196 ATCATCAATCTCTTTATCACTCAATATGGGTTGTATTCTTAGAGATTCAATAGAGTTCCACAGAT
28022638 TGGATT
261 TGGATT
* *
28022644 TCATAAGAGAATTCTAGCTAATCATAATGTTAAACAGAAGTATTGTTAGTCTGGTTGATTAATGA
1 TCATAAGAGAATGCTAGCTAATCATAATGTTAAACAGAAGTATTGTTAGTCTAGTTGATTAATGA
* * *
28022709 TCAGCATTGATCTATCGTTCTTTGGCATTCTATTCCATTATGTTCAGTAGAAGATTCTATTATGT
66 TCAGCATTAATCTATCGTTCTTTGGCATTCTATTCCATTATGTTCAGTAGAAGAATCGATTATGT
28022774 TATCTCTATCACAACTGGTTCCAGTGCGTATGAGCGATATTCTTCTT-T-TGGATTTTCTCTAAG
131 TATCTCTATCACAACTGGTTCCAGTGCGTATGAGCGATATTCTTCTTCTAT-G-TTTTCTCTAAG
* *
28022837 TTATCATCAATCTCTTTATCATTCAATATGGGTTGTATTCTTAGAGATTCAATAGAGTTCTACAG
194 TTATCATCAATCTCTTTATCACTCAATATGGGTTGTATTCTTAGAGATTCAATAGAGTTCCACAG
*
28022902 CTTGGATT
259 ATTGGATT
28022910 TC
1 TC
28022912 GTTATCTCAG
Statistics
Matches: 241, Mismatches: 25, Indels: 4
0.89 0.09 0.01
Matches are distributed among these distances:
264 1 0.00
265 2 0.01
266 238 0.99
ACGTcount: A:0.26, C:0.15, G:0.17, T:0.42
Consensus pattern (266 bp):
TCATAAGAGAATGCTAGCTAATCATAATGTTAAACAGAAGTATTGTTAGTCTAGTTGATTAATGA
TCAGCATTAATCTATCGTTCTTTGGCATTCTATTCCATTATGTTCAGTAGAAGAATCGATTATGT
TATCTCTATCACAACTGGTTCCAGTGCGTATGAGCGATATTCTTCTTCTATGTTTTCTCTAAGTT
ATCATCAATCTCTTTATCACTCAATATGGGTTGTATTCTTAGAGATTCAATAGAGTTCCACAGAT
TGGATT
Found at i:28024634 original size:5 final size:5
Alignment explanation
Indices: 28024624--28024648 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
28024614 GGTAATTTGG
28024624 TAAAA TAAAA TAAAA TAAAA TAAAA
1 TAAAA TAAAA TAAAA TAAAA TAAAA
28024649 ACAAAAGGTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
TAAAA
Found at i:28025793 original size:20 final size:20
Alignment explanation
Indices: 28025748--28025795 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
28025738 GTACGGGATT
* * *
28025748 TACACTTCGGTGCCCCTGTT
1 TACACTTCAGTGCCCCAGTA
*
28025768 TGCACTTCAGTGCCCCAGTA
1 TACACTTCAGTGCCCCAGTA
28025788 TACACTTC
1 TACACTTC
28025796 GATGTCTCTA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.17, C:0.35, G:0.17, T:0.31
Consensus pattern (20 bp):
TACACTTCAGTGCCCCAGTA
Found at i:28027433 original size:30 final size:30
Alignment explanation
Indices: 28027399--28027455 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 30
28027389 ACGACCTTAG
* *
28027399 ACACGGGCATGTGTCTCAGCCGTGTGTGAC
1 ACACGGGCATGCGTCACAGCCGTGTGTGAC
**
28027429 ACACGGTTATGCGTCACAGCCGTGTGT
1 ACACGGGCATGCGTCACAGCCGTGTGT
28027456 CCCCTGTAGG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 23 1.00
ACGTcount: A:0.18, C:0.26, G:0.32, T:0.25
Consensus pattern (30 bp):
ACACGGGCATGCGTCACAGCCGTGTGTGAC
Found at i:28031457 original size:20 final size:20
Alignment explanation
Indices: 28031391--28031477 Score: 77
Period size: 20 Copynumber: 4.3 Consensus size: 20
28031381 TTGTACGGGA
28031391 TTTGCACTTCGGTGCCCCTG
1 TTTGCACTTCGGTGCCCCTG
* * * * *
28031411 TATACACTTTGGTGCCTCTA
1 TTTGCACTTCGGTGCCCCTG
* *
28031431 TTCGCACTACGGTGCCCCTG
1 TTTGCACTTCGGTGCCCCTG
*
28031451 TTTGCACATT-TGTGCCCCTG
1 TTTGCAC-TTCGGTGCCCCTG
28031471 TTATGCA
1 TT-TGCA
28031478 TCTATGATGC
Statistics
Matches: 50, Mismatches: 15, Indels: 3
0.74 0.22 0.04
Matches are distributed among these distances:
20 45 0.90
21 5 0.10
ACGTcount: A:0.13, C:0.31, G:0.21, T:0.36
Consensus pattern (20 bp):
TTTGCACTTCGGTGCCCCTG
Found at i:28034327 original size:34 final size:36
Alignment explanation
Indices: 28034289--28034381 Score: 120
Period size: 36 Copynumber: 2.6 Consensus size: 36
28034279 TAGGTACGTG
28034289 TATATATAATATAAATATGTGTGCATGGTTTTATTA
1 TATATATAATATAAATATGTGTGCATGGTTTTATTA
* *
28034325 TATATATAATATAAATATGAGTGCAT--TTTT-TTGT
1 TATATATAATATAAATATGTGTGCATGGTTTTATT-A
* *
28034359 TATATATAATATATATAGGTGTG
1 TATATATAATATAAATATGTGTG
28034382 GCTTTGTCAT
Statistics
Matches: 51, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
33 2 0.04
34 24 0.47
36 25 0.49
ACGTcount: A:0.37, C:0.02, G:0.14, T:0.47
Consensus pattern (36 bp):
TATATATAATATAAATATGTGTGCATGGTTTTATTA
Found at i:28041508 original size:43 final size:43
Alignment explanation
Indices: 28041444--28041545 Score: 123
Period size: 43 Copynumber: 2.4 Consensus size: 43
28041434 ATGCTGCTAT
* * * * *
28041444 AGAACATGACATTTAACGGCGCTTTTTCCACGAACGCCATTAT
1 AGAACATGACATTTAACGGCGCTATTCCCACAAACGCCACTAA
* * *
28041487 CGAACATGACTTTTAATGGCGCTATTCCCACAAACGCCACTAA
1 AGAACATGACATTTAACGGCGCTATTCCCACAAACGCCACTAA
*
28041530 AGAACATGACCTTTAA
1 AGAACATGACATTTAA
28041546 AACAAATTTA
Statistics
Matches: 49, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
43 49 1.00
ACGTcount: A:0.33, C:0.26, G:0.15, T:0.25
Consensus pattern (43 bp):
AGAACATGACATTTAACGGCGCTATTCCCACAAACGCCACTAA
Found at i:28045042 original size:38 final size:37
Alignment explanation
Indices: 28044978--28045050 Score: 121
Period size: 38 Copynumber: 1.9 Consensus size: 37
28044968 GGGCAAGTCA
28044978 ATGTAAAAAAAAAAAAAAAAATCAGAGGTTACCATAG
1 ATGTAAAAAAAAAAAAAAAAATCAGAGGTTACCATAG
28045015 ATGTAAAAATAAAAAAATAAAAA-CAGAGGTTACCAT
1 ATGTAAAAA-AAAAAAA-AAAAATCAGAGGTTACCAT
28045051 TGCTGAACCA
Statistics
Matches: 34, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
37 9 0.26
38 20 0.59
39 5 0.15
ACGTcount: A:0.62, C:0.08, G:0.12, T:0.18
Consensus pattern (37 bp):
ATGTAAAAAAAAAAAAAAAAATCAGAGGTTACCATAG
Found at i:28046098 original size:13 final size:14
Alignment explanation
Indices: 28046077--28046117 Score: 50
Period size: 13 Copynumber: 3.1 Consensus size: 14
28046067 TTAATAAATT
28046077 ATTTAATTTT-ACA
1 ATTTAATTTTAACA
*
28046090 ATTTTATTTTAACA
1 ATTTAATTTTAACA
*
28046104 A-TAAATTTTAACA
1 ATTTAATTTTAACA
28046117 A
1 A
28046118 CAATAATTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
13 20 0.83
14 4 0.17
ACGTcount: A:0.44, C:0.07, G:0.00, T:0.49
Consensus pattern (14 bp):
ATTTAATTTTAACA
Found at i:28046127 original size:15 final size:16
Alignment explanation
Indices: 28046100--28046129 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
28046090 ATTTTATTTT
28046100 AACAATAAATTTTAAC
1 AACAATAAATTTTAAC
28046116 AACAAT-AATTTTAA
1 AACAATAAATTTTAA
28046130 ATTTTAAATA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.57, C:0.10, G:0.00, T:0.33
Consensus pattern (16 bp):
AACAATAAATTTTAAC
Found at i:28046476 original size:14 final size:14
Alignment explanation
Indices: 28046459--28046492 Score: 52
Period size: 14 Copynumber: 2.4 Consensus size: 14
28046449 TTGTTTTATT
28046459 AAAAATAAATTTTA-
1 AAAAAT-AATTTTAG
28046473 AAAAATAATTTTAG
1 AAAAATAATTTTAG
28046487 AAAAAT
1 AAAAAT
28046493 TTACTAAAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 7 0.37
14 12 0.63
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (14 bp):
AAAAATAATTTTAG
Found at i:28057050 original size:21 final size:21
Alignment explanation
Indices: 28057024--28057077 Score: 63
Period size: 21 Copynumber: 2.6 Consensus size: 21
28057014 AATTGATGGA
**
28057024 TGTGTCGTGACTTGGAACCCC
1 TGTGTCGTGACACGGAACCCC
* *
28057045 TGTGTCATGACACGGAACCCT
1 TGTGTCGTGACACGGAACCCC
*
28057066 TGTGTTGTGACA
1 TGTGTCGTGACA
28057078 TTGTTGCAAA
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.19, C:0.24, G:0.28, T:0.30
Consensus pattern (21 bp):
TGTGTCGTGACACGGAACCCC
Found at i:28060720 original size:20 final size:22
Alignment explanation
Indices: 28060694--28060744 Score: 63
Period size: 20 Copynumber: 2.4 Consensus size: 22
28060684 ATGCCATTAG
28060694 CTTAGATTAT-TTCTTTAG-TTT
1 CTTAGATT-TGTTCTTTAGCTTT
*
28060715 -TTAGATTTGTTCTTTTGCTTT
1 CTTAGATTTGTTCTTTAGCTTT
28060736 CTTAGATTT
1 CTTAGATTT
28060745 TTTGTTTATT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
19 1 0.04
20 14 0.54
21 3 0.12
22 8 0.31
ACGTcount: A:0.16, C:0.10, G:0.12, T:0.63
Consensus pattern (22 bp):
CTTAGATTTGTTCTTTAGCTTT
Found at i:28063770 original size:23 final size:22
Alignment explanation
Indices: 28063718--28063770 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
28063708 TCCACGTCTT
*
28063718 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
28063740 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
28063763 TTTCTTTT
1 TTTCTTTT
28063771 TCACTCTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 3 0.12
22 5 0.19
23 12 0.46
24 6 0.23
ACGTcount: A:0.09, C:0.19, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTCTTTTCTTTCTTTTTCTAA
Found at i:28066123 original size:22 final size:23
Alignment explanation
Indices: 28066098--28066157 Score: 63
Period size: 22 Copynumber: 2.7 Consensus size: 23
28066088 TGGACTGAAT
28066098 ATAAAAATTTAAACTAAAT-AAA
1 ATAAAAATTTAAACTAAATAAAA
*
28066120 ATAAATAA-ATAAA-TAAATAAAA
1 ATAAA-AATTTAAACTAAATAAAA
*
28066142 ATAAAACTTTACAACT
1 ATAAAAATTTA-AACT
28066158 TGGGCCACTT
Statistics
Matches: 30, Mismatches: 3, Indels: 8
0.73 0.07 0.20
Matches are distributed among these distances:
21 6 0.20
22 19 0.63
23 4 0.13
24 1 0.03
ACGTcount: A:0.67, C:0.07, G:0.00, T:0.27
Consensus pattern (23 bp):
ATAAAAATTTAAACTAAATAAAA
Found at i:28066125 original size:4 final size:4
Alignment explanation
Indices: 28066107--28066140 Score: 50
Period size: 4 Copynumber: 8.0 Consensus size: 4
28066097 TATAAAAATT
28066107 TAAA CTAAA TAAAA TAAA TAAA TAAA TAAA TAAA
1 TAAA -TAAA T-AAA TAAA TAAA TAAA TAAA TAAA
28066141 AATAAAACTT
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
4 20 0.71
5 8 0.29
ACGTcount: A:0.74, C:0.03, G:0.00, T:0.24
Consensus pattern (4 bp):
TAAA
Found at i:28081493 original size:17 final size:17
Alignment explanation
Indices: 28081471--28081505 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
28081461 TTAGGAGAGC
28081471 TAGACATGCATGAAAGT
1 TAGACATGCATGAAAGT
28081488 TAGACATGCATGAAAGT
1 TAGACATGCATGAAAGT
28081505 T
1 T
28081506 TAAGTCTCTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.40, C:0.11, G:0.23, T:0.26
Consensus pattern (17 bp):
TAGACATGCATGAAAGT
Found at i:28087633 original size:144 final size:144
Alignment explanation
Indices: 28087373--28087664 Score: 557
Period size: 144 Copynumber: 2.0 Consensus size: 144
28087363 TCCCTGTGGG
* *
28087373 TACAATAACTCGACACTTACTTGTCACTTTATTACTTGATATGATTGTGTTCATATTTCCATCTT
1 TACAATAACTCGACACTTACTTGTCACTTTATTACTTGATATGATTGTGTCCATATTTCCATCGT
28087438 TCTACTTGCTTACCTTATTTCTCCAAATTTTAAGAAGTTATTATGCGATATTGGCACTTACAAAA
66 TCTACTTGCTTACCTTATTTCTCCAAATTTTAAGAAGTTATTATGCGATATTGGCACTTACAAAA
28087503 CTAGTACACATGAA
131 CTAGTACACATGAA
*
28087517 TACAATAACTCGACATTTACTTGTCACTTTATTACTTGATATGATTGTGTCCATATTTCCATCGT
1 TACAATAACTCGACACTTACTTGTCACTTTATTACTTGATATGATTGTGTCCATATTTCCATCGT
28087582 TCTACTTGCTTACCTTATTTCTCCAAATTTTAAGAAGTTATTATGCGATATTGGCACTTACAAAA
66 TCTACTTGCTTACCTTATTTCTCCAAATTTTAAGAAGTTATTATGCGATATTGGCACTTACAAAA
28087647 CTAGTACACATGAA
131 CTAGTACACATGAA
28087661 TACA
1 TACA
28087665 TTGTAAATCA
Statistics
Matches: 145, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
144 145 1.00
ACGTcount: A:0.30, C:0.20, G:0.11, T:0.40
Consensus pattern (144 bp):
TACAATAACTCGACACTTACTTGTCACTTTATTACTTGATATGATTGTGTCCATATTTCCATCGT
TCTACTTGCTTACCTTATTTCTCCAAATTTTAAGAAGTTATTATGCGATATTGGCACTTACAAAA
CTAGTACACATGAA
Found at i:28088706 original size:18 final size:18
Alignment explanation
Indices: 28088658--28088706 Score: 50
Period size: 18 Copynumber: 2.8 Consensus size: 18
28088648 AAGAAAACTC
28088658 AAAT-AAAACAATAGCAA
1 AAATAAAAACAATAGCAA
*
28088675 ATAATAACAA-AATATG-AA
1 A-AATAAAAACAATA-GCAA
28088693 AAATAAAAACAATA
1 AAATAAAAACAATA
28088707 AAACAAATAT
Statistics
Matches: 26, Mismatches: 2, Indels: 7
0.74 0.06 0.20
Matches are distributed among these distances:
17 8 0.31
18 14 0.54
19 4 0.15
ACGTcount: A:0.71, C:0.08, G:0.04, T:0.16
Consensus pattern (18 bp):
AAATAAAAACAATAGCAA
Found at i:28100824 original size:50 final size:50
Alignment explanation
Indices: 28100712--28101053 Score: 404
Period size: 50 Copynumber: 6.7 Consensus size: 50
28100702 ATTTGGGTAA
* *
28100712 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTTGAGATCATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCA-CC--GAG---ATG
*
28100768 AGAGGTCCCCTGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGATG
* *
28100818 AGAGGTCCCATGTAATG-CCATGTCTGGGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAA-GACCATGTCTGGGACATGGCATGGGCACCGAGATG
* *
28100868 AGAGGTCCTC-CGTAAGACCATGTTTGGGACATGGCATGGGCACCGAGATG
1 AGAGGTCC-CATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGATG
* *
28100918 AGAGGTCCCATGTAATG-CCATGTCTGGGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAA-GACCATGTCTGGGACATGGCATGGGCACCGAGATG
* * *
28100968 AGAGGTCCTC-CGTAAGACCATGTTTGGGACATGGCATGGGCACCGACATG
1 AGAGGTCC-CATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGATG
** * * *
28101018 AGAACATCTCATGTAAGACCATTTTTGGGACATGGC
1 AG-AGGTCCCATGTAAGACCATGTCTGGGACATGGC
28101054 TTTGGCATGT
Statistics
Matches: 253, Mismatches: 24, Indels: 23
0.84 0.08 0.08
Matches are distributed among these distances:
49 3 0.01
50 176 0.70
51 30 0.12
53 3 0.01
55 2 0.01
56 39 0.15
ACGTcount: A:0.25, C:0.22, G:0.31, T:0.22
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGATG
Found at i:28100902 original size:100 final size:100
Alignment explanation
Indices: 28100712--28101060 Score: 497
Period size: 100 Copynumber: 3.4 Consensus size: 100
28100702 ATTTGGGTAA
*
28100712 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTTGAGATCATGAGAGGTCC-
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCA-CC--GAG---ATGAGAGGTCCT
*
28100776 CCTGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGATG
60 CC-GTAAGACCATGTTTGGGACATGGCATGGGCACCGAGATG
*
28100818 AGAGGTCCCATGTAATG-CCATGTCTGGGACATGGCGTTGGCACCGAGATGAGAGGTCCTCCGTA
1 AGAGATCCCATGTAA-GACCATGTCTGGGACATGGCGTTGGCACCGAGATGAGAGGTCCTCCGTA
28100882 AGACCATGTTTGGGACATGGCATGGGCACCGAGATG
65 AGACCATGTTTGGGACATGGCATGGGCACCGAGATG
*
28100918 AGAGGTCCCATGTAATG-CCATGTCTGGGACATGGCGTTGGCACCGAGATGAGAGGTCCTCCGTA
1 AGAGATCCCATGTAA-GACCATGTCTGGGACATGGCGTTGGCACCGAGATGAGAGGTCCTCCGTA
*
28100982 AGACCATGTTTGGGACATGGCATGGGCACCGACATG
65 AGACCATGTTTGGGACATGGCATGGGCACCGAGATG
* * * * *
28101018 AGAACATCTCATGTAAGACCATTTTTGGGACATGGCTTTGGCA
1 AG-AGATCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCA
28101061 TGTTTTTACC
Statistics
Matches: 229, Mismatches: 10, Indels: 13
0.91 0.04 0.05
Matches are distributed among these distances:
100 151 0.66
101 34 0.15
103 3 0.01
105 2 0.01
106 38 0.17
107 1 0.00
ACGTcount: A:0.24, C:0.22, G:0.31, T:0.22
Consensus pattern (100 bp):
AGAGATCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAGAGGTCCTCCGTAA
GACCATGTTTGGGACATGGCATGGGCACCGAGATG
Found at i:28107513 original size:38 final size:38
Alignment explanation
Indices: 28107397--28107513 Score: 110
Period size: 40 Copynumber: 3.0 Consensus size: 38
28107387 GGCGTTTGAA
* * * * * *
28107397 TAAAAAACGCCACTAAAAATCAAGCATTAGCGGCGCTTTT
1 TAAAAAATGCCGCTAAAAATCGAGCATTAG-AG-ACATTT
* * **
28107437 TAAAAAATGCCGCTAAAGATCGAGCATTAGCGTGATTT
1 TAAAAAATGCCGCTAAAAATCGAGCATTAGAGACATTT
28107475 TAAGAAAATGCCGCTAAAAAT-GAGCATTAGAGACATTT
1 TAA-AAAATGCCGCTAAAAATCGAGCATTAGAGACATTT
28107513 T
1 T
28107514 CCCGAAAATC
Statistics
Matches: 64, Mismatches: 12, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
38 21 0.33
39 17 0.27
40 26 0.41
ACGTcount: A:0.40, C:0.17, G:0.18, T:0.25
Consensus pattern (38 bp):
TAAAAAATGCCGCTAAAAATCGAGCATTAGAGACATTT
Found at i:28107522 original size:39 final size:39
Alignment explanation
Indices: 28107434--28107513 Score: 110
Period size: 38 Copynumber: 2.1 Consensus size: 39
28107424 TAGCGGCGCT
* * **
28107434 TTTTAA-AAAATGCCGCTAAAGATCGAGCATTAGCGTGA
1 TTTTAAGAAAATGCCGCTAAAAATCGAGCATTAGAGACA
28107472 TTTTAAGAAAATGCCGCTAAAAAT-GAGCATTAGAGACA
1 TTTTAAGAAAATGCCGCTAAAAATCGAGCATTAGAGACA
28107510 TTTT
1 TTTT
28107514 CCCGAAAATC
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
38 21 0.57
39 16 0.43
ACGTcount: A:0.39, C:0.14, G:0.19, T:0.29
Consensus pattern (39 bp):
TTTTAAGAAAATGCCGCTAAAAATCGAGCATTAGAGACA
Found at i:28107687 original size:41 final size:41
Alignment explanation
Indices: 28107572--28107729 Score: 156
Period size: 41 Copynumber: 3.9 Consensus size: 41
28107562 TTTTTAGGGC
* ** * *
28107572 TTTAGCGGCGTTTCAAAAAAAGCACCGCTAATGCTTGGGGA
1 TTTAGTGGCGTTTTTAAAAAAGCGCCGCTAATGCTCGGGGA
* * ** *
28107613 TTTAGTGGCGTTTTTGAAAAGGCGTTGCTAATGCTCGGGGG
1 TTTAGTGGCGTTTTTAAAAAAGCGCCGCTAATGCTCGGGGA
* ****
28107654 TTTAGTGGCGTTTTTAAAAAAGCGCCGCGAATGCTC-TATT
1 TTTAGTGGCGTTTTTAAAAAAGCGCCGCTAATGCTCGGGGA
* *
28107694 TTTAGTAGCGTTTTTAAAAAAGCGCCTCTAATGCTC
1 TTTAGTGGCGTTTTTAAAAAAGCGCCGCTAATGCTC
28107730 TATTTTTAGC
Statistics
Matches: 95, Mismatches: 22, Indels: 1
0.81 0.19 0.01
Matches are distributed among these distances:
40 33 0.35
41 62 0.65
ACGTcount: A:0.25, C:0.17, G:0.26, T:0.32
Consensus pattern (41 bp):
TTTAGTGGCGTTTTTAAAAAAGCGCCGCTAATGCTCGGGGA
Found at i:28107709 original size:40 final size:40
Alignment explanation
Indices: 28107654--28107738 Score: 143
Period size: 40 Copynumber: 2.1 Consensus size: 40
28107644 TGCTCGGGGG
*
28107654 TTTAGTGGCGTTTTTAAAAAAGCGCCGCGAATGCTCTATT
1 TTTAGTAGCGTTTTTAAAAAAGCGCCGCGAATGCTCTATT
* *
28107694 TTTAGTAGCGTTTTTAAAAAAGCGCCTCTAATGCTCTATT
1 TTTAGTAGCGTTTTTAAAAAAGCGCCGCGAATGCTCTATT
28107734 TTTAG
1 TTTAG
28107739 CAATTCTTTA
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
40 42 1.00
ACGTcount: A:0.26, C:0.16, G:0.19, T:0.39
Consensus pattern (40 bp):
TTTAGTAGCGTTTTTAAAAAAGCGCCGCGAATGCTCTATT
Found at i:28107814 original size:7 final size:7
Alignment explanation
Indices: 28107793--28107931 Score: 57
Period size: 7 Copynumber: 19.4 Consensus size: 7
28107783 TTAACTATCA
*
28107793 TTATAGT
1 TTATGGT
*
28107800 TTAGGGT
1 TTATGGT
28107807 TTATGGT
1 TTATGGT
*
28107814 TTAGGGT
1 TTATGGT
* *
28107821 TTAAGAT
1 TTATGGT
*
28107828 TTAAGAGT
1 TTATG-GT
* **
28107836 TTCTATT
1 TTATGGT
*
28107843 TTAAGGT
1 TTATGGT
* *
28107850 TTAGGGA
1 TTATGGT
*
28107857 TTATGTAT
1 TTATG-GT
28107865 TTA-GGT
1 TTATGGT
* *
28107871 ATTATAGA
1 -TTATGGT
28107879 TTATGGT
1 TTATGGT
28107886 TTATGGT
1 TTATGGT
28107893 TTATGGT
1 TTATGGT
* *
28107900 TTAAGGG
1 TTATGGT
28107907 TTATGGGT
1 TTAT-GGT
28107915 TTA-GTGT
1 TTATG-GT
*
28107922 TTAGGGT
1 TTATGGT
28107929 TTA
1 TTA
28107932 GATTAATTGA
Statistics
Matches: 96, Mismatches: 29, Indels: 14
0.69 0.21 0.10
Matches are distributed among these distances:
6 2 0.02
7 81 0.84
8 13 0.14
ACGTcount: A:0.23, C:0.01, G:0.27, T:0.49
Consensus pattern (7 bp):
TTATGGT
Found at i:28109683 original size:18 final size:18
Alignment explanation
Indices: 28109660--28109706 Score: 60
Period size: 18 Copynumber: 2.6 Consensus size: 18
28109650 TGTTTGGTTA
*
28109660 CCCTTCTTC-TCCTCTTTC
1 CCCTTCTCCTTCC-CTTTC
28109678 CCCTTCTCCTTCCCTTTC
1 CCCTTCTCCTTCCCTTTC
*
28109696 CCCTTCCCCTT
1 CCCTTCTCCTT
28109707 GGGTTGCAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
18 23 0.88
19 3 0.12
ACGTcount: A:0.00, C:0.55, G:0.00, T:0.45
Consensus pattern (18 bp):
CCCTTCTCCTTCCCTTTC
Found at i:28117165 original size:43 final size:43
Alignment explanation
Indices: 28117063--28117214 Score: 157
Period size: 43 Copynumber: 3.6 Consensus size: 43
28117053 AATATTTTTT
* *
28117063 AAGTCATG-TTTTTAGCAGCGTTTGT-GAAAAAGCGTCGCTAA
1 AAGTCATGATTTTTAGCGGCGTTTGTGGTAAAAGCGTCGCTAA
* * *
28117104 AAGTCAAT-TTTTTATAGTGGCGTTTGTGGTAGAAGCGTCGCTAA
1 AAGTC-ATGATTTT-TAGCGGCGTTTGTGGTAAAAGCGTCGCTAA
* * * *
28117148 ATGTCATGATTTTTAGTGGCGTTTGTGGTATAAGCGCCGCTAA
1 AAGTCATGATTTTTAGCGGCGTTTGTGGTAAAAGCGTCGCTAA
* * *
28117191 AGGTCATCATCTTTAGCGGCGTTT
1 AAGTCATGATTTTTAGCGGCGTTT
28117215 TTCTCACATA
Statistics
Matches: 94, Mismatches: 12, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
41 5 0.05
42 6 0.06
43 61 0.65
44 22 0.23
ACGTcount: A:0.24, C:0.14, G:0.26, T:0.36
Consensus pattern (43 bp):
AAGTCATGATTTTTAGCGGCGTTTGTGGTAAAAGCGTCGCTAA
Found at i:28130552 original size:20 final size:21
Alignment explanation
Indices: 28130521--28130559 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
28130511 TAATTGAATA
*
28130521 AATAATAATACATGATAAAGG
1 AATAATAATACATAATAAAGG
28130542 AATAA-AATACATAATAAA
1 AATAATAATACATAATAAA
28130560 ATAAAATAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.64, C:0.05, G:0.08, T:0.23
Consensus pattern (21 bp):
AATAATAATACATAATAAAGG
Found at i:28132296 original size:44 final size:43
Alignment explanation
Indices: 28132183--28132306 Score: 131
Period size: 44 Copynumber: 2.8 Consensus size: 43
28132173 AGACTTGATA
* * * *
28132183 CAATCTGCTCTACTGTAACTTCAGAGAGATAAGATCTATTACTT
1 CAATCTGCTCTACTGCAACTTCAGGGAGATAAGAT-TATGAATT
* ** * * *
28132227 TAATCCACTCCACTACAACTTCAGGGAGATAGGATTATCGAATT
1 CAATCTGCTCTACTGCAACTTCAGGGAGATAAGATTAT-GAATT
*
28132271 CAATCTGCTCTACTGCAACGTCAGGGAGATAAGATT
1 CAATCTGCTCTACTGCAACTTCAGGGAGATAAGATT
28132307 TGCTTCTTCA
Statistics
Matches: 62, Mismatches: 17, Indels: 2
0.77 0.21 0.02
Matches are distributed among these distances:
43 3 0.05
44 59 0.95
ACGTcount: A:0.32, C:0.22, G:0.17, T:0.29
Consensus pattern (43 bp):
CAATCTGCTCTACTGCAACTTCAGGGAGATAAGATTATGAATT
Found at i:28132322 original size:44 final size:43
Alignment explanation
Indices: 28132234--28132393 Score: 144
Period size: 44 Copynumber: 3.7 Consensus size: 43
28132224 CTTTAATCCA
* * * *
28132234 CTCCACTACAACTTCAGGGAGATAGGA-TT-ATCGAATTCAATCTG
1 CTCCACTGCAACTTCAGGGAGATAAGACTTGTTC---TTCAGTCTG
* * *
28132278 CTCTACTGCAACGTCAGGGAGATAAGATTTGCTTCTTCAGTCTG
1 CTCCACTGCAACTTCAGGGAGATAAGACTTG-TTCTTCAGTCTG
* ** * *
28132322 CCCCACTGTGACTTCAGGGGGATAAGACTTGTTTTCTCAGTCTG
1 CTCCACTGCAACTTCAGGGAGATAAGACTTGTTCT-TCAGTCTG
*
28132366 CTCCGCTGCAACTTCAGGGAGATAAGAC
1 CTCCACTGCAACTTCAGGGAGATAAGAC
28132394 CCGATGCGAT
Statistics
Matches: 93, Mismatches: 19, Indels: 8
0.77 0.16 0.07
Matches are distributed among these distances:
43 3 0.03
44 86 0.92
45 2 0.02
47 2 0.02
ACGTcount: A:0.25, C:0.24, G:0.23, T:0.28
Consensus pattern (43 bp):
CTCCACTGCAACTTCAGGGAGATAAGACTTGTTCTTCAGTCTG
Found at i:28132635 original size:128 final size:128
Alignment explanation
Indices: 28132503--28132747 Score: 312
Period size: 128 Copynumber: 1.9 Consensus size: 128
28132493 GCTCCACTAT
* * ** *
28132503 TGCTTAGGGAGATAAGA-CTTGTAATTTCCAACCTATTCCACTGCTGGTCAGGGACATAAGACTT
1 TGCTTAGGGAGACAAGATC-TGCAATTTCCAACCTATTCCACTGCTGACCAGGGACATAAGACTC
* * * * * *
28132567 ATGGCTTGACTCTATTTCCCTACTCTTGGAGATAATATTTGCCATCTTCGATCTGCTCCGCCAC
65 ATGGCTTGAATCTACTTCCCTACACTTGAAGATAAGATTCGCCATCTTCGATCTGCTCCGCCAC
* * * *
28132631 TGCTTAGGGAGACAAGATCTGCAATTTCCAACCTATTCCACTGTTGACCAGGGATATAGGACTCG
1 TGCTTAGGGAGACAAGATCTGCAATTTCCAACCTATTCCACTGCTGACCAGGGACATAAGACTCA
* * *
28132696 TGGCTTGAATCTGCTTCCTTACACTTGAAGATAAGATTCGCCGTCTTCGATC
66 TGGCTTGAATCTACTTCCCTACACTTGAAGATAAGATTCGCCATCTTCGATC
28132748 CGCTTCACTG
Statistics
Matches: 98, Mismatches: 18, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
128 97 0.99
129 1 0.01
ACGTcount: A:0.24, C:0.24, G:0.20, T:0.31
Consensus pattern (128 bp):
TGCTTAGGGAGACAAGATCTGCAATTTCCAACCTATTCCACTGCTGACCAGGGACATAAGACTCA
TGGCTTGAATCTACTTCCCTACACTTGAAGATAAGATTCGCCATCTTCGATCTGCTCCGCCAC
Found at i:28133019 original size:7 final size:7
Alignment explanation
Indices: 28133007--28133039 Score: 50
Period size: 7 Copynumber: 4.7 Consensus size: 7
28132997 CTCTTTCATT
28133007 TTTTTCA
1 TTTTTCA
28133014 TTTTTCA
1 TTTTTCA
28133021 -TTTTCA
1 TTTTTCA
28133027 TTTTTCA
1 TTTTTCA
28133034 TCTTTT
1 T-TTTT
28133040 TTTTTGAACT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
6 6 0.25
7 14 0.58
8 4 0.17
ACGTcount: A:0.12, C:0.15, G:0.00, T:0.73
Consensus pattern (7 bp):
TTTTTCA
Found at i:28133044 original size:13 final size:13
Alignment explanation
Indices: 28133008--28133034 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
28132998 TCTTTCATTT
28133008 TTTTCATTTTTCA
1 TTTTCATTTTTCA
28133021 TTTTCATTTTTCA
1 TTTTCATTTTTCA
28133034 T
1 T
28133035 CTTTTTTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.15, C:0.15, G:0.00, T:0.70
Consensus pattern (13 bp):
TTTTCATTTTTCA
Found at i:28133460 original size:30 final size:27
Alignment explanation
Indices: 28133420--28133488 Score: 84
Period size: 30 Copynumber: 2.4 Consensus size: 27
28133410 CTTTTTTATA
*
28133420 TTTTTATTTTGACTTTAATTGATTTCTCT
1 TTTTTGTTTTGACTTTAATT-ATTTCT-T
* *
28133449 TTTTTGCTTTTGACTTTGATTTTTTCTT
1 TTTTTG-TTTTGACTTTAATTATTTCTT
28133477 TTTTTGTTTTGA
1 TTTTTGTTTTGA
28133489 TTTTGATTTT
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
27 6 0.17
28 7 0.19
29 10 0.28
30 13 0.36
ACGTcount: A:0.12, C:0.09, G:0.10, T:0.70
Consensus pattern (27 bp):
TTTTTGTTTTGACTTTAATTATTTCTT
Found at i:28133476 original size:27 final size:28
Alignment explanation
Indices: 28133420--28133498 Score: 90
Period size: 27 Copynumber: 2.8 Consensus size: 28
28133410 CTTTTTTATA
* *
28133420 TTTTTATTTTGACTTTAATTGATTTCTC-T
1 TTTTTGTTTTGACTTTGATT--TTTCTCTT
28133449 TTTTTGCTTTTGACTTTGATTTTT-TCTT
1 TTTTTG-TTTTGACTTTGATTTTTCTCTT
*
28133477 TTTTTGTTTTGATTTTGATTTT
1 TTTTTGTTTTGACTTTGATTTT
28133499 GATTTTTTTC
Statistics
Matches: 45, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
27 17 0.38
28 10 0.22
29 5 0.11
30 13 0.29
ACGTcount: A:0.11, C:0.08, G:0.10, T:0.71
Consensus pattern (28 bp):
TTTTTGTTTTGACTTTGATTTTTCTCTT
Found at i:28133505 original size:27 final size:28
Alignment explanation
Indices: 28133426--28133507 Score: 80
Period size: 27 Copynumber: 2.9 Consensus size: 28
28133416 TATATTTTTA
*
28133426 TTTTGACTTTAATTGATT-TCTCTTTTTTGC
1 TTTTGACTTTGATT--TTATCT-TTTTTTGC
*
28133456 TTTTGACTTTGATTTTTTCTTTTTTTG-
1 TTTTGACTTTGATTTTATCTTTTTTTGC
*
28133483 TTTTGATTTTGATTTTGAT-TTTTTT
1 TTTTGACTTTGATTTT-ATCTTTTTT
28133508 CTCTCTTCTT
Statistics
Matches: 47, Mismatches: 3, Indels: 7
0.82 0.05 0.12
Matches are distributed among these distances:
27 21 0.45
28 10 0.21
29 3 0.06
30 13 0.28
ACGTcount: A:0.11, C:0.07, G:0.11, T:0.71
Consensus pattern (28 bp):
TTTTGACTTTGATTTTATCTTTTTTTGC
Found at i:28137795 original size:20 final size:21
Alignment explanation
Indices: 28137764--28137802 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
28137754 TAATTGAATA
*
28137764 AATAATAATACATGATAAAGG
1 AATAATAATACATAATAAAGG
28137785 AATAA-AATACATAATAAA
1 AATAATAATACATAATAAA
28137803 ATAAAATAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.64, C:0.05, G:0.08, T:0.23
Consensus pattern (21 bp):
AATAATAATACATAATAAAGG
Found at i:28141062 original size:50 final size:50
Alignment explanation
Indices: 28141001--28141637 Score: 321
Period size: 50 Copynumber: 12.7 Consensus size: 50
28140991 CGCAACTTTT
* *
28141001 GGGAAGTAAGATTCACCATTGTAGCTTCAATCTTTTTAACTGCACCGCCA
1 GGGAAGTAAGATTCACCATTGTAGCTTTAATCTTTTTAACTGCAACGCCA
** * * * * * * *
28141051 GGGAAGTAAGATTTGCCTTTATGGCAGCTTTAATCCTTTTAGCTACAATGCCG
1 GGGAAGTAAGATTCACC---ATTGTAGCTTTAATCTTTTTAACTGCAACGCCA
** * * * ** *
28141104 GGGAAGCGAGATTCACCAATGTGGCTTTAATCTGTTCCACTGCACCGCCA
1 GGGAAGTAAGATTCACCATTGTAGCTTTAATCTTTTTAACTGCAACGCCA
** ** * * * *
28141154 GGGAAGTAAGATTTGCTGTTGTAGCTTTAATCTCTTTAACTGCAATGTCG
1 GGGAAGTAAGATTCACCATTGTAGCTTTAATCTTTTTAACTGCAACGCCA
* * * ** * * *
28141204 GGGAAGCAAGATTCACGGA-TGTGGCTTTAAT-TTGTTCCACCGCATCGCCT
1 GGGAAGTAAGATTCAC-CATTGTAGCTTTAATCTT-TTTAACTGCAACGCCA
* * ** * * *
28141254 GTGAGGTAAGATTCACTGTTGTAGCTTTAATCTTTTTGAACTGCAATGTCG
1 GGGAAGTAAGATTCACCATTGTAGCTTTAATCTTTTT-AACTGCAACGCCA
* * ** ** * * *
28141305 GGGAAGCAAGATTCACCGA-TGTGGCTTTAATCTGCTCCACTGCACCACCT
1 GGGAAGTAAGATTCACC-ATTGTAGCTTTAATCTTTTTAACTGCAACGCCA
* * ** * * *
28141355 GGGAGGTAAGATTCGCTGTTGTAGCTTTAATCTCTTTAACTGCAATGTCA
1 GGGAAGTAAGATTCACCATTGTAGCTTTAATCTTTTTAACTGCAACGCCA
* * * ** *
28141405 GGGAAGCAAGATTCACCGA-TGTGGCTTTAATCTGTTCCACTGCATCGCCA
1 GGGAAGTAAGATTCACC-ATTGTAGCTTTAATCTTTTTAACTGCAACGCCA
* * * * * * *
28141455 GGGAAGTAACG-CTCGCCGTTGTGGCTTTAGTCTTTTTAACTGCAATGTCA
1 GGGAAGTAA-GATTCACCATTGTAGCTTTAATCTTTTTAACTGCAACGCCA
* * * * ** * * *
28141505 GGGAAGCAAGATTCACCGTTGTGGCTTTAATCTGTTTCGCTGCATCACCT
1 GGGAAGTAAGATTCACCATTGTAGCTTTAATCTTTTTAACTGCAACGCCA
** * ** * * * *
28141555 GGGGTGTAAGATTCGCTGTTGTAGCTTTAATCTTTCTAACTGCAATGTCG
1 GGGAAGTAAGATTCACCATTGTAGCTTTAATCTTTTTAACTGCAACGCCA
* * * *
28141605 GGGAAGCAAGATTCATCGTTGTGGCTTTAATCT
1 GGGAAGTAAGATTCACCATTGTAGCTTTAATCT
28141638 GTTCCATTAC
Statistics
Matches: 416, Mismatches: 157, Indels: 28
0.69 0.26 0.05
Matches are distributed among these distances:
49 2 0.00
50 340 0.82
51 37 0.09
53 37 0.09
ACGTcount: A:0.23, C:0.21, G:0.24, T:0.32
Consensus pattern (50 bp):
GGGAAGTAAGATTCACCATTGTAGCTTTAATCTTTTTAACTGCAACGCCA
Found at i:28141226 original size:100 final size:100
Alignment explanation
Indices: 28141001--28141643 Score: 772
Period size: 100 Copynumber: 6.4 Consensus size: 100
28140991 CGCAACTTTT
* * * * ** *
28141001 GGGAAGTAAGATTCACC-ATTGTAGCTTCAATCTTTTTAACTGCACCGCCAGGGAAGTAAGATTT
1 GGGAAGCAAGATTCACCGA-TGTGGCTTTAATCTGTTCCACTGCACCGCCAGGGAAGTAAGATTC
* * * * *
28141065 GCCTTTATGGCAGCTTTAATC-CTTTTAGCTACAATGCCG
65 G-CTGT-T-GTAGCTTTAATCTC-TTTAACTGCAATGTCG
* * *
28141104 GGGAAGCGAGATTCACCAATGTGGCTTTAATCTGTTCCACTGCACCGCCAGGGAAGTAAGATTTG
1 GGGAAGCAAGATTCACCGATGTGGCTTTAATCTGTTCCACTGCACCGCCAGGGAAGTAAGATTCG
28141169 CTGTTGTAGCTTTAATCTCTTTAACTGCAATGTCG
66 CTGTTGTAGCTTTAATCTCTTTAACTGCAATGTCG
* * * * * * * *
28141204 GGGAAGCAAGATTCACGGATGTGGCTTTAATTTGTTCCACCGCATCGCCTGTGAGGTAAGATTCA
1 GGGAAGCAAGATTCACCGATGTGGCTTTAATCTGTTCCACTGCACCGCCAGGGAAGTAAGATTCG
*
28141269 CTGTTGTAGCTTTAATCTTTTTGAACTGCAATGTCG
66 CTGTTGTAGCTTTAATCTCTTT-AACTGCAATGTCG
* * * *
28141305 GGGAAGCAAGATTCACCGATGTGGCTTTAATCTGCTCCACTGCACCACCTGGGAGGTAAGATTCG
1 GGGAAGCAAGATTCACCGATGTGGCTTTAATCTGTTCCACTGCACCGCCAGGGAAGTAAGATTCG
*
28141370 CTGTTGTAGCTTTAATCTCTTTAACTGCAATGTCA
66 CTGTTGTAGCTTTAATCTCTTTAACTGCAATGTCG
* *
28141405 GGGAAGCAAGATTCACCGATGTGGCTTTAATCTGTTCCACTGCATCGCCAGGGAAGTAACG-CTC
1 GGGAAGCAAGATTCACCGATGTGGCTTTAATCTGTTCCACTGCACCGCCAGGGAAGTAA-GATTC
* * * * *
28141469 GCCGTTGTGGCTTTAGTCTTTTTAACTGCAATGTCA
65 GCTGTTGTAGCTTTAATCTCTTTAACTGCAATGTCG
* * * * * * **
28141505 GGGAAGCAAGATTCACCGTTGTGGCTTTAATCTGTTTCGCTGCATCACCTGGGGTGTAAGATTCG
1 GGGAAGCAAGATTCACCGATGTGGCTTTAATCTGTTCCACTGCACCGCCAGGGAAGTAAGATTCG
28141570 CTGTTGTAGCTTTAATCT-TTCTAACTGCAATGTCG
66 CTGTTGTAGCTTTAATCTCTT-TAACTGCAATGTCG
* *
28141605 GGGAAGCAAGATTCATCGTTGTGGCTTTAATCTGTTCCA
1 GGGAAGCAAGATTCACCGATGTGGCTTTAATCTGTTCCA
28141644 TTACATCGCT
Statistics
Matches: 475, Mismatches: 59, Indels: 15
0.87 0.11 0.03
Matches are distributed among these distances:
99 3 0.01
100 318 0.67
101 94 0.20
102 3 0.01
103 56 0.12
104 1 0.00
ACGTcount: A:0.23, C:0.21, G:0.24, T:0.32
Consensus pattern (100 bp):
GGGAAGCAAGATTCACCGATGTGGCTTTAATCTGTTCCACTGCACCGCCAGGGAAGTAAGATTCG
CTGTTGTAGCTTTAATCTCTTTAACTGCAATGTCG
Found at i:28141742 original size:44 final size:44
Alignment explanation
Indices: 28141692--28141943 Score: 168
Period size: 44 Copynumber: 5.5 Consensus size: 44
28141682 GTATTCCACC
* * *
28141692 GTAATCTCAGGGAAATAGGATTACTGGCTTCAATCTGCTCCGCT
1 GTAATCTCAGGGAGATAAGATTACTGGCTTTAATCTGCTCCGCT
* *
28141736 GTAATCTCAGAGAGATAAGATTTCTGGCTTTAATCTGATGCGATCTATTCTGCT
1 GTAATCTCAGGGAGATAAGATTACTGGCTTTAATC---TGC--TC----C-GCT
* * *** * *
28141790 GTAA-CTTCAGAGAGATAAGA-TCCTTTATTTTAATCCGCTCCACT
1 GTAATC-TCAGGGAGATAAGATTAC-TGGCTTTAATCTGCTCCGCT
* * * * *
28141834 GTAGTCTTAGGGAGATAGGATTACTAGCTTTAATCTGCTTCGCT
1 GTAATCTCAGGGAGATAAGATTACTGGCTTTAATCTGCTCCGCT
* * *
28141878 GTAATCTCAGGGAGATAAGATTTCTGGCTTCAATCTGCTCCACT
1 GTAATCTCAGGGAGATAAGATTACTGGCTTTAATCTGCTCCGCT
* *
28141922 ATAA-CATCAGGGAAATAAGATT
1 GTAATC-TCAGGGAGATAAGATT
28141944 CACCGTTTCT
Statistics
Matches: 161, Mismatches: 32, Indels: 30
0.72 0.14 0.13
Matches are distributed among these distances:
43 1 0.01
44 114 0.71
45 4 0.02
47 3 0.02
49 4 0.02
51 2 0.01
53 4 0.02
54 29 0.18
ACGTcount: A:0.28, C:0.19, G:0.20, T:0.33
Consensus pattern (44 bp):
GTAATCTCAGGGAGATAAGATTACTGGCTTTAATCTGCTCCGCT
Found at i:28143319 original size:7 final size:7
Alignment explanation
Indices: 28143307--28143352 Score: 76
Period size: 7 Copynumber: 6.6 Consensus size: 7
28143297 CCGTCATTGC
28143307 TTTTCAT
1 TTTTCAT
28143314 TTTTCA-
1 TTTTCAT
28143320 TTTTCAT
1 TTTTCAT
28143327 TTTTCAT
1 TTTTCAT
28143334 TTTTCAT
1 TTTTCAT
28143341 TTTTCAT
1 TTTTCAT
28143348 ATTTT
1 -TTTT
28143353 TTTAGTTTGA
Statistics
Matches: 37, Mismatches: 0, Indels: 3
0.93 0.00 0.08
Matches are distributed among these distances:
6 6 0.16
7 27 0.73
8 4 0.11
ACGTcount: A:0.15, C:0.13, G:0.00, T:0.72
Consensus pattern (7 bp):
TTTTCAT
Found at i:28143325 original size:13 final size:13
Alignment explanation
Indices: 28143307--28143347 Score: 73
Period size: 13 Copynumber: 3.1 Consensus size: 13
28143297 CCGTCATTGC
28143307 TTTTCATTTTTCA
1 TTTTCATTTTTCA
28143320 TTTTCATTTTTCA
1 TTTTCATTTTTCA
28143333 TTTTTCATTTTTCA
1 -TTTTCATTTTTCA
28143347 T
1 T
28143348 ATTTTTTTAG
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
13 14 0.52
14 13 0.48
ACGTcount: A:0.15, C:0.15, G:0.00, T:0.71
Consensus pattern (13 bp):
TTTTCATTTTTCA
Found at i:28150570 original size:26 final size:26
Alignment explanation
Indices: 28150534--28150586 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
28150524 GGGTGAGTTT
28150534 TCTCTTTGATTTCAACAAAGAAACTG
1 TCTCTTTGATTTCAACAAAGAAACTG
28150560 TCTCTTTGATTTCAACAAAGAAACTG
1 TCTCTTTGATTTCAACAAAGAAACTG
28150586 T
1 T
28150587 GATTTTAGGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.34, C:0.19, G:0.11, T:0.36
Consensus pattern (26 bp):
TCTCTTTGATTTCAACAAAGAAACTG
Found at i:28151995 original size:18 final size:17
Alignment explanation
Indices: 28151972--28152006 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
28151962 TTTATATTAG
*
28151972 CAATTCATATCATCATTT
1 CAATTCAAAT-ATCATTT
28151990 CAATTCAAATATCATTT
1 CAATTCAAATATCATTT
28152007 ATCCAATTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.37, C:0.20, G:0.00, T:0.43
Consensus pattern (17 bp):
CAATTCAAATATCATTT
Found at i:28157487 original size:21 final size:21
Alignment explanation
Indices: 28157461--28157514 Score: 99
Period size: 21 Copynumber: 2.6 Consensus size: 21
28157451 ACTATAGGGT
*
28157461 GTGTCACGATATCGAACCCTA
1 GTGTCACGACATCGAACCCTA
28157482 GTGTCACGACATCGAACCCTA
1 GTGTCACGACATCGAACCCTA
28157503 GTGTCACGACAT
1 GTGTCACGACAT
28157515 AAGCAATCTG
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.28, C:0.30, G:0.20, T:0.22
Consensus pattern (21 bp):
GTGTCACGACATCGAACCCTA
Found at i:28159773 original size:18 final size:18
Alignment explanation
Indices: 28159743--28159790 Score: 55
Period size: 18 Copynumber: 2.7 Consensus size: 18
28159733 TGTCGTTCGT
28159743 TTTCAAAAT-ATTATTC-A
1 TTTC-AAATCATTATTCAA
28159760 TTTACAAATCATTATTCAA
1 TTT-CAAATCATTATTCAA
*
28159779 TTTCAAAACATT
1 TTTCAAATCATT
28159791 TTTTTATTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
17 7 0.26
18 16 0.59
19 4 0.15
ACGTcount: A:0.42, C:0.15, G:0.00, T:0.44
Consensus pattern (18 bp):
TTTCAAATCATTATTCAA
Found at i:28165295 original size:39 final size:40
Alignment explanation
Indices: 28165200--28165461 Score: 337
Period size: 39 Copynumber: 6.7 Consensus size: 40
28165190 TTGAATGATG
*
28165200 TCCGGGCTAAGTCCCGAAGGC--TTGTGCTA-AGTGAC-AAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGA-T-ACTAAT
*
28165238 ATCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT
1 -TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGATACTAAT
28165279 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
28165318 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
* *
28165357 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
*
28165396 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGA-ATTACT-AT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGA-TACTAAT
* *
28165435 AACCGGGCTATGTCCCGAAGGCATTTG
1 -TCCGGGCTAAGTCCCGAAGGCATTTG
28165462 AACGAGGAGC
Statistics
Matches: 203, Mismatches: 11, Indels: 17
0.88 0.05 0.07
Matches are distributed among these distances:
39 132 0.65
40 59 0.29
41 11 0.05
42 1 0.00
ACGTcount: A:0.26, C:0.23, G:0.27, T:0.24
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
Found at i:28178278 original size:16 final size:16
Alignment explanation
Indices: 28178257--28178290 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
28178247 GCTCTTTTGG
28178257 CACATGTTATGGACAC
1 CACATGTTATGGACAC
28178273 CACATGTTATGGACAC
1 CACATGTTATGGACAC
28178289 CA
1 CA
28178291 TTCCATTAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.32, C:0.26, G:0.18, T:0.24
Consensus pattern (16 bp):
CACATGTTATGGACAC
Found at i:28179701 original size:17 final size:17
Alignment explanation
Indices: 28179673--28179716 Score: 61
Period size: 17 Copynumber: 2.6 Consensus size: 17
28179663 ATCCGCAAGG
*
28179673 CAATACTATTCGCCAAA
1 CAATACTGTTCGCCAAA
* *
28179690 CGATACTGTTCGCCAAC
1 CAATACTGTTCGCCAAA
28179707 CAATACTGTT
1 CAATACTGTT
28179717 TCCCAAGTAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.32, C:0.30, G:0.11, T:0.27
Consensus pattern (17 bp):
CAATACTGTTCGCCAAA
Found at i:28179780 original size:17 final size:17
Alignment explanation
Indices: 28179723--28179787 Score: 51
Period size: 17 Copynumber: 3.8 Consensus size: 17
28179713 TGTTTCCCAA
* *
28179723 GTAATACTATTTGCTAG
1 GTAATACTATCTGCCAG
* * *
28179740 GCAATA-TAATTTGACAG
1 GTAATACT-ATCTGCCAG
*
28179757 GTGATACTATCTGCCAG
1 GTAATACTATCTGCCAG
*
28179774 GTAATACTGTCTGC
1 GTAATACTATCTGC
28179788 TAATGTTGTA
Statistics
Matches: 37, Mismatches: 9, Indels: 4
0.74 0.18 0.08
Matches are distributed among these distances:
16 1 0.03
17 35 0.95
18 1 0.03
ACGTcount: A:0.29, C:0.17, G:0.20, T:0.34
Consensus pattern (17 bp):
GTAATACTATCTGCCAG
Found at i:28184260 original size:27 final size:27
Alignment explanation
Indices: 28184229--28184285 Score: 105
Period size: 27 Copynumber: 2.1 Consensus size: 27
28184219 GACGGATTCA
28184229 AAAGATATTTTCAAATCTATTTTAACT
1 AAAGATATTTTCAAATCTATTTTAACT
*
28184256 AAAGATATTTTCGAATCTATTTTAACT
1 AAAGATATTTTCAAATCTATTTTAACT
28184283 AAA
1 AAA
28184286 TGTTTTTGTG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.42, C:0.11, G:0.05, T:0.42
Consensus pattern (27 bp):
AAAGATATTTTCAAATCTATTTTAACT
Found at i:28184663 original size:13 final size:13
Alignment explanation
Indices: 28184641--28184671 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
28184631 TTTAAATACC
28184641 AATT-TATAAAAA
1 AATTATATAAAAA
28184653 AATTATATAAAAA
1 AATTATATAAAAA
28184666 AATTAT
1 AATTAT
28184672 TTAATCAGGG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 4 0.22
13 14 0.78
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (13 bp):
AATTATATAAAAA
Found at i:28184859 original size:13 final size:15
Alignment explanation
Indices: 28184841--28184877 Score: 51
Period size: 13 Copynumber: 2.5 Consensus size: 15
28184831 TCATTAGGTG
28184841 AAAGATAA-TG-ATA
1 AAAGATAAGTGAATA
28184854 AAAGATAAGTGAATA
1 AAAGATAAGTGAATA
28184869 AACAGATAA
1 AA-AGATAA
28184878 CAAATAAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 8 0.38
14 2 0.10
15 5 0.24
16 6 0.29
ACGTcount: A:0.62, C:0.03, G:0.16, T:0.19
Consensus pattern (15 bp):
AAAGATAAGTGAATA
Found at i:28186185 original size:29 final size:29
Alignment explanation
Indices: 28186126--28186185 Score: 77
Period size: 29 Copynumber: 2.1 Consensus size: 29
28186116 TACGATTTAA
* *
28186126 TGTGTAATTATATATATAAATTTTAATTT
1 TGTGTAATTATATAAATAAATTTTAAGTT
*
28186155 TGTGTAATTTTATAAATAAAATTTT-AGTT
1 TGTGTAATTATATAAAT-AAATTTTAAGTT
28186184 TG
1 TG
28186186 ATCAAATTCT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
29 20 0.74
30 7 0.26
ACGTcount: A:0.37, C:0.00, G:0.10, T:0.53
Consensus pattern (29 bp):
TGTGTAATTATATAAATAAATTTTAAGTT
Found at i:28195075 original size:37 final size:37
Alignment explanation
Indices: 28195032--28195105 Score: 148
Period size: 37 Copynumber: 2.0 Consensus size: 37
28195022 GTAAGTCTGT
28195032 CTCTCATGGAGGTTAATTTTCCTATTTTTATAACACA
1 CTCTCATGGAGGTTAATTTTCCTATTTTTATAACACA
28195069 CTCTCATGGAGGTTAATTTTCCTATTTTTATAACACA
1 CTCTCATGGAGGTTAATTTTCCTATTTTTATAACACA
28195106 GTTCCTAGAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.27, C:0.19, G:0.11, T:0.43
Consensus pattern (37 bp):
CTCTCATGGAGGTTAATTTTCCTATTTTTATAACACA
Found at i:28208071 original size:16 final size:15
Alignment explanation
Indices: 28208045--28208074 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
28208035 TTTGTTGCTA
28208045 ATTTTACTTTTTCAT
1 ATTTTACTTTTTCAT
28208060 ATTTTCACTTTTTCA
1 ATTTT-ACTTTTTCA
28208075 CTTTCAATCA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.20, C:0.17, G:0.00, T:0.63
Consensus pattern (15 bp):
ATTTTACTTTTTCAT
Found at i:28208360 original size:51 final size:51
Alignment explanation
Indices: 28208298--28208491 Score: 236
Period size: 51 Copynumber: 3.8 Consensus size: 51
28208288 GATACCGGTT
* *
28208298 CACATAGTAGCCTGCACATAGTACTACACATGTGACCATCACTATCTGATA
1 CACATAGTAGCCTGCACATAGTACTACACACGTGACCATCACTATCTGGTA
* * *
28208349 CACGTAGTAGCCTGCACATAGTACTACACACGTGATCGA--AGCTATCCGGTA
1 CACATAGTAGCCTGCACATAGTACTACACACGTGA-CCATCA-CTATCTGGTA
* * * *
28208400 CGCATAATAGCCTGCACATAGTACTACACATGCGACCTATCA-T-TCTGGTA
1 CACATAGTAGCCTGCACATAGTACTACACACGTGACC-ATCACTATCTGGTA
*
28208450 -AAATAGTAGCCTGCACATAGTACTACACACGTGACCATCACT
1 CACATAGTAGCCTGCACATAGTACTACACACGTGACCATCACT
28208492 TTCACTTTCA
Statistics
Matches: 120, Mismatches: 17, Indels: 14
0.79 0.11 0.09
Matches are distributed among these distances:
48 4 0.03
49 32 0.27
50 8 0.07
51 73 0.61
52 2 0.02
53 1 0.01
ACGTcount: A:0.32, C:0.28, G:0.16, T:0.24
Consensus pattern (51 bp):
CACATAGTAGCCTGCACATAGTACTACACACGTGACCATCACTATCTGGTA
Found at i:28208482 original size:100 final size:102
Alignment explanation
Indices: 28208300--28208483 Score: 293
Period size: 102 Copynumber: 1.8 Consensus size: 102
28208290 TACCGGTTCA
* * **
28208300 CATAGTAGCCTGCACATAGTACTACACATGTGACCATCACTATCTGATACACGTAGTAGCCTGCA
1 CATAATAGCCTGCACATAGTACTACACATGCGACCATCACTATCTGATACAAATAGTAGCCTGCA
28208365 CATAGTACTACACACGTGATCGAAGCTATCCGGTACG
66 CATAGTACTACACACGTGATCGAAGCTATCCGGTACG
*
28208402 CATAATAGCCTGCACATAGTACTACACATGCGACCTATCA-T-TCTGGTA-AAATAGTAGCCTGC
1 CATAATAGCCTGCACATAGTACTACACATGCGACC-ATCACTATCTGATACAAATAGTAGCCTGC
28208464 ACATAGTACTACACACGTGA
65 ACATAGTACTACACACGTGA
28208484 CCATCACTTT
Statistics
Matches: 76, Mismatches: 5, Indels: 4
0.89 0.06 0.05
Matches are distributed among these distances:
100 32 0.42
101 6 0.08
102 34 0.45
103 4 0.05
ACGTcount: A:0.32, C:0.27, G:0.17, T:0.24
Consensus pattern (102 bp):
CATAATAGCCTGCACATAGTACTACACATGCGACCATCACTATCTGATACAAATAGTAGCCTGCA
CATAGTACTACACACGTGATCGAAGCTATCCGGTACG
Found at i:28215399 original size:25 final size:25
Alignment explanation
Indices: 28215371--28215420 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
28215361 CAGGTAAGGC
* * *
28215371 TCCTTCTCCTTTTTTCGTTCTTCAT
1 TCCTTCTCCTTCTTCCCTTCTTCAT
*
28215396 TCCTTTTCCTTCTTCCCTTCTTCAT
1 TCCTTCTCCTTCTTCCCTTCTTCAT
28215421 CTTCTCTTCC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.04, C:0.36, G:0.02, T:0.58
Consensus pattern (25 bp):
TCCTTCTCCTTCTTCCCTTCTTCAT
Found at i:28218080 original size:14 final size:14
Alignment explanation
Indices: 28218043--28218073 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
28218033 CCAGAAAAGT
28218043 AAATCATTTTCCAG
1 AAATCATTTTCCAG
28218057 AAATCATTTTCCAG
1 AAATCATTTTCCAG
28218071 AAA
1 AAA
28218074 ATATTTTACT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.42, C:0.19, G:0.06, T:0.32
Consensus pattern (14 bp):
AAATCATTTTCCAG
Found at i:28218218 original size:45 final size:45
Alignment explanation
Indices: 28218151--28218285 Score: 128
Period size: 45 Copynumber: 3.0 Consensus size: 45
28218141 TATATATATG
* *
28218151 GCATCACGAATCAAACGAGTAAGACCATAGCTGAAAGACGCTATA
1 GCATCATGAATCAAACGAGTAAGACCATAGCTGAAAGACACTATA
* * * * *
28218196 GCATCATGATTCAAACGTGTAAGATCATAGTTGAAAGACACTATG
1 GCATCATGAATCAAACGAGTAAGACCATAGCTGAAAGACACTATA
* * ** * *
28218241 GCAACATGACGA-AAAATAAATAAGACCATAGTTGAAAGACACTAT
1 GCATCATGA--ATCAAACGAGTAAGACCATAGCTGAAAGACACTAT
28218286 GGCACCAGGT
Statistics
Matches: 73, Mismatches: 15, Indels: 3
0.80 0.16 0.03
Matches are distributed among these distances:
45 46 0.63
46 27 0.37
ACGTcount: A:0.44, C:0.18, G:0.19, T:0.20
Consensus pattern (45 bp):
GCATCATGAATCAAACGAGTAAGACCATAGCTGAAAGACACTATA
Found at i:28218322 original size:45 final size:46
Alignment explanation
Indices: 28218215--28218324 Score: 123
Period size: 46 Copynumber: 2.4 Consensus size: 46
28218205 TTCAAACGTG
* * *
28218215 TAAGATCATAGTTGAAAGACACTATGGCAACATGACGAAAAATAAA
1 TAAGACCATAGCTGAAAGACACTATGGCAACAGGACGAAAAATAAA
* * * **
28218261 TAAGACCATAGTTGAAAGACACTATGGCACCAGGTCG-GGAATAAA
1 TAAGACCATAGCTGAAAGACACTATGGCAACAGGACGAAAAATAAA
* *
28218306 TAAGACCGTGGCTGAAAGA
1 TAAGACCATAGCTGAAAGA
28218325 TGCCATGGCA
Statistics
Matches: 55, Mismatches: 9, Indels: 1
0.85 0.14 0.02
Matches are distributed among these distances:
45 22 0.40
46 33 0.60
ACGTcount: A:0.44, C:0.15, G:0.23, T:0.18
Consensus pattern (46 bp):
TAAGACCATAGCTGAAAGACACTATGGCAACAGGACGAAAAATAAA
Found at i:28223974 original size:54 final size:54
Alignment explanation
Indices: 28223902--28224009 Score: 207
Period size: 54 Copynumber: 2.0 Consensus size: 54
28223892 TTAAAATACC
*
28223902 TCCTAACTCAGAAAGAACTTAATTTAAGGAAAAGGAGATGGATCAAGCTGCTCA
1 TCCTAACTCAGAAAGAACTTAATTTAAGGAAAAGGAGATGGATCAAGCTACTCA
28223956 TCCTAACTCAGAAAGAACTTAATTTAAGGAAAAGGAGATGGATCAAGCTACTCA
1 TCCTAACTCAGAAAGAACTTAATTTAAGGAAAAGGAGATGGATCAAGCTACTCA
28224010 AAGACTACAT
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
54 53 1.00
ACGTcount: A:0.42, C:0.17, G:0.19, T:0.22
Consensus pattern (54 bp):
TCCTAACTCAGAAAGAACTTAATTTAAGGAAAAGGAGATGGATCAAGCTACTCA
Found at i:28225996 original size:23 final size:22
Alignment explanation
Indices: 28225970--28226014 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 22
28225960 CAGTAAAAAA
28225970 AAGGTATGTTAATTAATCCAAAG
1 AAGGTATGTTAATTAAT-CAAAG
28225993 AAGGTATGTTAATTAATCAAAG
1 AAGGTATGTTAATTAATCAAAG
28226015 GTCCAACTGA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
22 5 0.23
23 17 0.77
ACGTcount: A:0.44, C:0.07, G:0.18, T:0.31
Consensus pattern (22 bp):
AAGGTATGTTAATTAATCAAAG
Found at i:28229033 original size:21 final size:22
Alignment explanation
Indices: 28228988--28229033 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
28228978 AGAGAAAAAT
*
28228988 AAAAGTGAAAAAGAAGAAAATG
1 AAAAGTGAAAAAGAAGAAAAGG
**
28229010 AAAA-TGAAAAAGGCGAAAAGG
1 AAAAGTGAAAAAGAAGAAAAGG
28229031 AAA
1 AAA
28229034 GCGAGAGAGA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 17 0.81
22 4 0.19
ACGTcount: A:0.67, C:0.02, G:0.24, T:0.07
Consensus pattern (22 bp):
AAAAGTGAAAAAGAAGAAAAGG
Found at i:28229132 original size:36 final size:33
Alignment explanation
Indices: 28229067--28229133 Score: 80
Period size: 33 Copynumber: 1.9 Consensus size: 33
28229057 GTGAATGAAG
*
28229067 TGAGTGAAAAAGAGAGAGAGCTTAAACAAGGAA
1 TGAGTGAAAAAGAGAGAGAGCTAAAACAAGGAA
* *
28229100 TGAGTGAAGAAGAAGAGAGTGCTCAAACACAAGG
1 TGAGTGAAAAAG-AGAGAGAGCT-AAA-ACAAGG
28229134 GAGGAATATT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
33 11 0.39
34 9 0.32
35 2 0.07
36 6 0.21
ACGTcount: A:0.48, C:0.09, G:0.31, T:0.12
Consensus pattern (33 bp):
TGAGTGAAAAAGAGAGAGAGCTAAAACAAGGAA
Found at i:28235707 original size:11 final size:12
Alignment explanation
Indices: 28235683--28235710 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
28235673 TGAGTTTAGT
28235683 AAAATATTTAAA
1 AAAATATTTAAA
28235695 AAAATATTTAAA
1 AAAATATTTAAA
28235707 AAAA
1 AAAA
28235711 GAGATATCAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (12 bp):
AAAATATTTAAA
Done.