Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr3
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: 42799318
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.32
Warning! 891409 characters in sequence are not A, C, G, or T
File 128 of 141
Found at i:38347746 original size:31 final size:31
Alignment explanation
Indices: 38347602--38347746 Score: 111
Period size: 31 Copynumber: 4.7 Consensus size: 31
38347592 TTAAATTATT
* * *
38347602 TATGAATATAGGA-TGCCGAATTTGATTTGTA
1 TATGAATATA-TATTGCTGAATTTGATTCGTA
* * **
38347633 TATGATTATACATTGCCAAATTTGATTCGTA
1 TATGAATATATATTGCTGAATTTGATTCGTA
** * *
38347664 TATGGTTATATATTG-TCGAA-TTGTTTGGTA
1 TATGAATATATATTGCT-GAATTTGATTCGTA
*
38347694 TATCAATAT-TCATTG-TCGAATTTGATTCGTA
1 TATGAATATAT-ATTGCT-GAATTTGATTCGTA
38347725 TATGAATATATATTGCTGAATT
1 TATGAATATATATTGCTGAATT
38347747 GAATTGAGCA
Statistics
Matches: 92, Mismatches: 16, Indels: 12
0.77 0.13 0.10
Matches are distributed among these distances:
29 1 0.01
30 24 0.26
31 65 0.71
32 2 0.02
ACGTcount: A:0.30, C:0.08, G:0.17, T:0.44
Consensus pattern (31 bp):
TATGAATATATATTGCTGAATTTGATTCGTA
Found at i:38349731 original size:41 final size:41
Alignment explanation
Indices: 38349544--38349723 Score: 279
Period size: 41 Copynumber: 4.4 Consensus size: 41
38349534 AGATTCACTA
* * * * * * *
38349544 GCACTTCGTCTGCTAGGTTTAAAGTCTAATTCAGTTCACTG
1 GCACTTAGCCTGCTAGGCTTATAGCCTGATTCAGTTCACCG
38349585 GCACTTAGCCTGCTAGGCTTATAGCCTGATTCAGTTCACCG
1 GCACTTAGCCTGCTAGGCTTATAGCCTGATTCAGTTCACCG
*
38349626 GCACTTAGCCTGCTAGGCTTATAGCCTGATTCAATTCACCG
1 GCACTTAGCCTGCTAGGCTTATAGCCTGATTCAGTTCACCG
*
38349667 GCACTTAGCCTGCTAGGCTTATAGCCTGATTCGGTTCACCG
1 GCACTTAGCCTGCTAGGCTTATAGCCTGATTCAGTTCACCG
38349708 GCACTTAGCCTGCTAG
1 GCACTTAGCCTGCTAG
38349724 ACATATAGTC
Statistics
Matches: 129, Mismatches: 10, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
41 129 1.00
ACGTcount: A:0.20, C:0.28, G:0.22, T:0.31
Consensus pattern (41 bp):
GCACTTAGCCTGCTAGGCTTATAGCCTGATTCAGTTCACCG
Found at i:38349746 original size:41 final size:41
Alignment explanation
Indices: 38349544--38349751 Score: 247
Period size: 41 Copynumber: 5.1 Consensus size: 41
38349534 AGATTCACTA
* * * * * * * *
38349544 GCACTTCGTCTGCTAGGTTTAAAGTCTAATTCAGTTCACTG
1 GCACTTAGCCTGCTAGGCTTATAGCCTGATTAAGTTCACCG
*
38349585 GCACTTAGCCTGCTAGGCTTATAGCCTGATTCAGTTCACCG
1 GCACTTAGCCTGCTAGGCTTATAGCCTGATTAAGTTCACCG
38349626 GCACTTAGCCTGCTAGGCTTATAGCCTGATTCAA-TTCACCG
1 GCACTTAGCCTGCTAGGCTTATAGCCTGATT-AAGTTCACCG
**
38349667 GCACTTAGCCTGCTAGGCTTATAGCCTGATTCGGTTCACCG
1 GCACTTAGCCTGCTAGGCTTATAGCCTGATTAAGTTCACCG
* * * * * *
38349708 GCACTTAGCCTGCTAGACATATAGTCTGAATAATTTCACTG
1 GCACTTAGCCTGCTAGGCTTATAGCCTGATTAAGTTCACCG
38349749 GCA
1 GCA
38349752 ATAAATCCGA
Statistics
Matches: 147, Mismatches: 18, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
41 146 0.99
42 1 0.01
ACGTcount: A:0.22, C:0.26, G:0.21, T:0.31
Consensus pattern (41 bp):
GCACTTAGCCTGCTAGGCTTATAGCCTGATTAAGTTCACCG
Found at i:38349746 original size:82 final size:82
Alignment explanation
Indices: 38349578--38349751 Score: 278
Period size: 82 Copynumber: 2.1 Consensus size: 82
38349568 TCTAATTCAG
*
38349578 TTCACTGGCACTTAGCCTGCTAGGCTTATAGCCTGATTCAGTTCACCGGCACTTAGCCTGCTAGG
1 TTCACTGGCACTTAGCCTGCTAGGCTTATAGCCTGATTCAGTTCACCGGCACTTAGCCTGCTAGA
* *
38349643 CTTATAGCCTGATTCAA
66 CATATAGCCTGAATCAA
* *
38349660 TTCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATTCGGTTCACCGGCACTTAGCCTGCTAGA
1 TTCACTGGCACTTAGCCTGCTAGGCTTATAGCCTGATTCAGTTCACCGGCACTTAGCCTGCTAGA
*
38349725 CATATAGTCTGAAT-AA
66 CATATAGCCTGAATCAA
38349741 TTTCACTGGCA
1 -TTCACTGGCA
38349752 ATAAATCCGA
Statistics
Matches: 84, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
81 2 0.02
82 82 0.98
ACGTcount: A:0.22, C:0.28, G:0.21, T:0.30
Consensus pattern (82 bp):
TTCACTGGCACTTAGCCTGCTAGGCTTATAGCCTGATTCAGTTCACCGGCACTTAGCCTGCTAGA
CATATAGCCTGAATCAA
Found at i:38357077 original size:41 final size:41
Alignment explanation
Indices: 38357032--38357202 Score: 252
Period size: 41 Copynumber: 4.2 Consensus size: 41
38357022 AGCACTTCAT
* * * * **
38357032 CTGCTAGGTTTAAAGTCTAATTCAATTCACTAGCACTTAGC
1 CTGCTAGGCTTATAGCCTGATTCAATTCACCGGCACTTAGC
*
38357073 CTGCTAGGCTTATAGCCTGATTCAGTTCACCGGCACTTAGC
1 CTGCTAGGCTTATAGCCTGATTCAATTCACCGGCACTTAGC
*
38357114 CTGCTAAGCTTATAGCCTGATTCAATTCACCGGCACTTAGC
1 CTGCTAGGCTTATAGCCTGATTCAATTCACCGGCACTTAGC
**
38357155 CTGCTAGGCTTATAGCCTGATTCGGTTCACCGGCACTTAGC
1 CTGCTAGGCTTATAGCCTGATTCAATTCACCGGCACTTAGC
38357196 CTGCTAG
1 CTGCTAG
38357203 ACATATAGTC
Statistics
Matches: 118, Mismatches: 12, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
41 118 1.00
ACGTcount: A:0.22, C:0.27, G:0.20, T:0.30
Consensus pattern (41 bp):
CTGCTAGGCTTATAGCCTGATTCAATTCACCGGCACTTAGC
Found at i:38357225 original size:41 final size:41
Alignment explanation
Indices: 38357064--38357230 Score: 212
Period size: 41 Copynumber: 4.1 Consensus size: 41
38357054 CAATTCACTA
* *
38357064 GCACTTAGCCTGCTAGGCTTATAGCCTGATTCAGTTCACCG
1 GCACTTAGCCTGCTAGACTTATAGCCTGATTAAGTTCACCG
38357105 GCACTTAGCCTGCTA-AGCTTATAGCCTGATTCAA-TTCACCG
1 GCACTTAGCCTGCTAGA-CTTATAGCCTGATT-AAGTTCACCG
* **
38357146 GCACTTAGCCTGCTAGGCTTATAGCCTGATTCGGTTCACCG
1 GCACTTAGCCTGCTAGACTTATAGCCTGATTAAGTTCACCG
* * * * *
38357187 GCACTTAGCCTGCTAGACATATAGTCTGAATAATTTCACTG
1 GCACTTAGCCTGCTAGACTTATAGCCTGATTAAGTTCACCG
38357228 GCA
1 GCA
38357231 ATAAATCCGA
Statistics
Matches: 109, Mismatches: 13, Indels: 8
0.84 0.10 0.06
Matches are distributed among these distances:
41 108 0.99
42 1 0.01
ACGTcount: A:0.23, C:0.28, G:0.20, T:0.29
Consensus pattern (41 bp):
GCACTTAGCCTGCTAGACTTATAGCCTGATTAAGTTCACCG
Found at i:38357225 original size:82 final size:82
Alignment explanation
Indices: 38357053--38357230 Score: 261
Period size: 82 Copynumber: 2.2 Consensus size: 82
38357043 AAAGTCTAAT
**
38357053 TCAATTCACTAGCACTTAGCCTGCTAGGCTTATAGCCTGATTCAGTTCACCGGCACTTAGCCTGC
1 TCAATTCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATTCAGTTCACCGGCACTTAGCCTGC
* *
38357118 TAAGCTTATAGCCTGAT
66 TAAGCATATAGCCTGAA
*
38357135 TCAATTCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATTCGGTTCACCGGCACTTAGCCTGC
1 TCAATTCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATTCAGTTCACCGGCACTTAGCCTGC
*
38357200 T-AGACATATAGTCTGAA
66 TAAG-CATATAGCCTGAA
*
38357217 T-AATTTCACTGGCA
1 TCAA-TTCACCGGCA
38357231 ATAAATCCGA
Statistics
Matches: 87, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
81 4 0.05
82 83 0.95
ACGTcount: A:0.24, C:0.28, G:0.19, T:0.30
Consensus pattern (82 bp):
TCAATTCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATTCAGTTCACCGGCACTTAGCCTGC
TAAGCATATAGCCTGAA
Found at i:38361290 original size:16 final size:16
Alignment explanation
Indices: 38361269--38361300 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
38361259 ATGCTAAGCT
38361269 ACCAAACTTTAAACTA
1 ACCAAACTTTAAACTA
38361285 ACCAAACTTTAAACTA
1 ACCAAACTTTAAACTA
38361301 TCACATACCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.25, G:0.00, T:0.25
Consensus pattern (16 bp):
ACCAAACTTTAAACTA
Found at i:38368072 original size:19 final size:19
Alignment explanation
Indices: 38368046--38368082 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
38368036 TAAAGTTTTA
38368046 AAATT-AAAAATTTTAAAT
1 AAATTAAAAAATTTTAAAT
38368064 AAATATAAAAAATTTTAAA
1 AAAT-TAAAAAATTTTAAA
38368083 AAACTAAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 4 0.24
19 1 0.06
20 12 0.71
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (19 bp):
AAATTAAAAAATTTTAAAT
Found at i:38370252 original size:282 final size:278
Alignment explanation
Indices: 38369740--38370259 Score: 618
Period size: 282 Copynumber: 1.9 Consensus size: 278
38369730 AAAAAATGGC
*
38369740 AATAGCATGATAAACAATTTGAGTGCATTTAATATTTTTTAAACGTGATGTATTTACCTATTTAA
1 AATACCATGATAAACAATTTGAGTGCATTTAATATTTTTTAAACGTGATGTATTTACCTATTTAA
* * *
38369805 TTTTTTTACTCACAATTTAAACTAATTTTTCATTTTAATTTCACACATATCACGTATGTGTTATT
66 TTTATTTACTCACAATTTAAACTAATTTTTAATTTTAATTTCACACATATCACATATGTGTTATT
* * * * * *
38369870 ATTTTTATTTTCAAATAATACATTTTTTATTTATTGTATGTTACTTTTAAAAGCATACATGTGTT
131 ATTATTAGTTTCAAATAATACATTTTTTATTTATTATATGTTACTTTTAAAAGCACACATATATT
* * * *
38369935 CTAAATATATGGTTTCTATACGCATGCGCGTGTGATAGAATTTTTAATATTGTTAATCTTGTTGG
196 CTAAATATATGGTTTCCACAAGCAT-CACGTGTGATAG-ATTTTTAATATTGTTAATCTTGTTGG
38370000 TTCAGTTGGTGTCACAAGTT
259 TTCAGTTGGTGTCACAAGTT
* ** *
38370020 AATACCATGATAAAC-ATTTAGATTGCATTTAATA-TTTTT-AATTTGATGTATTTACCTTTTTA
1 AATACCATGATAAACAATTT-GAGTGCATTTAATATTTTTTAAACGTGATGTATTTACCTATTT-
* * **** **
38370082 AATTTCGATTTACTCGCAATTTAACCTAATTTTTTAATTTTAATTTTGTGCATATTGCATATGTG
64 AATTT--ATTTACTCACAATTTAAACTAA-TTTTTAATTTTAATTTCACACATATCACATATGTG
* * * *
38370147 TTGTTATTATTAGTTTCAAACT-TTACATTTTAATTATTTATTATATGTTATTTTTAAACGCACA
126 TTATTATTATTAGTTTCAAA-TAATACATTTT--TTATTTATTATATGTTACTTTTAAAAGCACA
* * *
38370211 CCTATATTCTAAATATATTGTTTCCACAAGCAT-ATGTGTGATAGATTTT
188 CATATATTCTAAATATATGGTTTCCACAAGCATCACGTGTGATAGATTTT
38370260 CTAGTTGTAC
Statistics
Matches: 199, Mismatches: 33, Indels: 15
0.81 0.13 0.06
Matches are distributed among these distances:
278 19 0.10
279 14 0.07
280 27 0.14
281 24 0.12
282 61 0.31
283 1 0.01
284 53 0.27
ACGTcount: A:0.30, C:0.11, G:0.11, T:0.48
Consensus pattern (278 bp):
AATACCATGATAAACAATTTGAGTGCATTTAATATTTTTTAAACGTGATGTATTTACCTATTTAA
TTTATTTACTCACAATTTAAACTAATTTTTAATTTTAATTTCACACATATCACATATGTGTTATT
ATTATTAGTTTCAAATAATACATTTTTTATTTATTATATGTTACTTTTAAAAGCACACATATATT
CTAAATATATGGTTTCCACAAGCATCACGTGTGATAGATTTTTAATATTGTTAATCTTGTTGGTT
CAGTTGGTGTCACAAGTT
Found at i:38371762 original size:6 final size:6
Alignment explanation
Indices: 38371742--38371785 Score: 61
Period size: 6 Copynumber: 7.2 Consensus size: 6
38371732 ACCCTTCTTC
* *
38371742 TCCCCTT TCCTCT TCCCCT TCCCCT TCCCTT TCCCCT TCCCCT T
1 TCCCC-T TCCCCT TCCCCT TCCCCT TCCCCT TCCCCT TCCCCT T
38371786 GGGTTGCAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
6 29 0.88
7 4 0.12
ACGTcount: A:0.00, C:0.59, G:0.00, T:0.41
Consensus pattern (6 bp):
TCCCCT
Found at i:38371769 original size:18 final size:18
Alignment explanation
Indices: 38371742--38371785 Score: 70
Period size: 18 Copynumber: 2.4 Consensus size: 18
38371732 ACCCTTCTTC
*
38371742 TCCCCTTTCCTCTTCCCCT
1 TCCCCTTCCCT-TTCCCCT
38371761 TCCCCTTCCCTTTCCCCT
1 TCCCCTTCCCTTTCCCCT
38371779 TCCCCTT
1 TCCCCTT
38371786 GGGTTGCAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 14 0.58
19 10 0.42
ACGTcount: A:0.00, C:0.59, G:0.00, T:0.41
Consensus pattern (18 bp):
TCCCCTTCCCTTTCCCCT
Found at i:38371903 original size:25 final size:26
Alignment explanation
Indices: 38371845--38371903 Score: 65
Period size: 25 Copynumber: 2.4 Consensus size: 26
38371835 CAGGTAAGGC
*
38371845 TCTTCTC--CTTCTTCTGTTCTTCAT
1 TCTTCTCTTCTTCTTCCGTTCTTCAT
38371869 TCCTT-T-TTCTTCTTCCGTTCTTCA-
1 T-CTTCTCTTCTTCTTCCGTTCTTCAT
38371893 TCTTCTCTTCT
1 TCTTCTCTTCT
38371904 CAGCATATTC
Statistics
Matches: 29, Mismatches: 1, Indels: 9
0.74 0.03 0.23
Matches are distributed among these distances:
23 3 0.10
24 4 0.14
25 22 0.76
ACGTcount: A:0.03, C:0.34, G:0.03, T:0.59
Consensus pattern (26 bp):
TCTTCTCTTCTTCTTCCGTTCTTCAT
Found at i:38375296 original size:21 final size:21
Alignment explanation
Indices: 38375272--38375324 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
38375262 CGTTGTTTCT
* *
38375272 AATCTCACTGCTACAGTATCC
1 AATCTCACCGCTACAGTAACC
*
38375293 AATCTCACCGCTACAGTAACT
1 AATCTCACCGCTACAGTAACC
38375314 AATCTCACCGC
1 AATCTCACCGC
38375325 CACTGCTGTT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.30, C:0.36, G:0.09, T:0.25
Consensus pattern (21 bp):
AATCTCACCGCTACAGTAACC
Found at i:38376616 original size:17 final size:16
Alignment explanation
Indices: 38376591--38376629 Score: 60
Period size: 17 Copynumber: 2.4 Consensus size: 16
38376581 AAACTGTTCG
38376591 TTTAAAATAATTTAATA
1 TTTAAAATAATTTAA-A
*
38376608 TTTATAATAATTTAAA
1 TTTAAAATAATTTAAA
38376624 TTTAAA
1 TTTAAA
38376630 TTTAAATTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
16 6 0.30
17 14 0.70
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (16 bp):
TTTAAAATAATTTAAA
Found at i:38379895 original size:19 final size:19
Alignment explanation
Indices: 38379871--38379919 Score: 80
Period size: 19 Copynumber: 2.6 Consensus size: 19
38379861 TTTGGTACAA
*
38379871 AGACTAAATCGTAAAAATT
1 AGACTAAATCGTAAAAACT
38379890 AGACTAAATCGTAAAAACT
1 AGACTAAATCGTAAAAACT
*
38379909 GGACTAAATCG
1 AGACTAAATCG
38379920 AATAAAGTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.49, C:0.14, G:0.14, T:0.22
Consensus pattern (19 bp):
AGACTAAATCGTAAAAACT
Found at i:38393119 original size:18 final size:18
Alignment explanation
Indices: 38393096--38393136 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
38393086 ATCATGATTC
38393096 TAAAAATT-AAAAACTAT
1 TAAAAATTCAAAAACTAT
*
38393113 GTAAAAATTCAAAAATTAT
1 -TAAAAATTCAAAAACTAT
38393132 TAAAA
1 TAAAA
38393137 TTTATAAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 13 0.62
19 8 0.38
ACGTcount: A:0.63, C:0.05, G:0.02, T:0.29
Consensus pattern (18 bp):
TAAAAATTCAAAAACTAT
Found at i:38393655 original size:24 final size:24
Alignment explanation
Indices: 38393607--38393666 Score: 75
Period size: 25 Copynumber: 2.4 Consensus size: 24
38393597 TAAATTTTAA
* *
38393607 TAATTTTTTAATTTGTATGTGTTT
1 TAATTTTTTAATTTATATATGTTT
*
38393631 TAATTATTTTAATTTATATATTTTTT
1 TAATT-TTTTAATTTATATA-TGTTT
38393657 TAATTTTTTA
1 TAATTTTTTA
38393667 GAACCATGAT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
24 5 0.16
25 17 0.55
26 9 0.29
ACGTcount: A:0.27, C:0.00, G:0.05, T:0.68
Consensus pattern (24 bp):
TAATTTTTTAATTTATATATGTTT
Found at i:38395207 original size:14 final size:13
Alignment explanation
Indices: 38395173--38395213 Score: 55
Period size: 14 Copynumber: 3.0 Consensus size: 13
38395163 TAATTATTGA
38395173 ATATAATTAAAAT
1 ATATAATTAAAAT
*
38395186 ATATTAATTTAAAT
1 ATA-TAATTAAAAT
38395200 ATTATAATTAAAAT
1 A-TATAATTAAAAT
38395214 TTTTAAACTA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 3 0.12
14 19 0.79
15 2 0.08
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (13 bp):
ATATAATTAAAAT
Found at i:38395218 original size:22 final size:23
Alignment explanation
Indices: 38395193--38395247 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 23
38395183 AATATATTAA
38395193 TTTAAATATTATAATTAAA-ATT
1 TTTAAATATTATAATTAAACATT
*
38395215 TTT-AA-ACTATAATTAAAGCATT
1 TTTAAATATTATAATTAAA-CATT
38395237 TTTAATATATT
1 TTTAA-ATATT
38395248 CAAGAAAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 7
0.74 0.06 0.20
Matches are distributed among these distances:
20 11 0.42
21 2 0.08
22 9 0.35
23 1 0.04
24 1 0.04
25 2 0.08
ACGTcount: A:0.45, C:0.04, G:0.02, T:0.49
Consensus pattern (23 bp):
TTTAAATATTATAATTAAACATT
Found at i:38395225 original size:20 final size:21
Alignment explanation
Indices: 38395202--38395241 Score: 64
Period size: 20 Copynumber: 1.9 Consensus size: 21
38395192 ATTTAAATAT
38395202 TATAATTAAA-ATTTTTAAAC
1 TATAATTAAACATTTTTAAAC
38395222 TATAATTAAAGCATTTTTAA
1 TATAATTAAA-CATTTTTAA
38395242 TATATTCAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 10 0.56
22 8 0.44
ACGTcount: A:0.47, C:0.05, G:0.03, T:0.45
Consensus pattern (21 bp):
TATAATTAAACATTTTTAAAC
Found at i:38405592 original size:29 final size:30
Alignment explanation
Indices: 38405549--38405613 Score: 98
Period size: 29 Copynumber: 2.2 Consensus size: 30
38405539 TTTTTTAAAA
*
38405549 TTTAAAAATTAAAAAATAATTAAAACTATT
1 TTTAAAAATTAAAAAATAATTAAAAATATT
*
38405579 TTTAGAAATT-AAAAATAATTAAAAATA-T
1 TTTAAAAATTAAAAAATAATTAAAAATATT
38405607 TTTAAAA
1 TTTAAAA
38405614 TATAAAGATT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
28 7 0.22
29 16 0.50
30 9 0.28
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.37
Consensus pattern (30 bp):
TTTAAAAATTAAAAAATAATTAAAAATATT
Found at i:38408344 original size:31 final size:31
Alignment explanation
Indices: 38408218--38408346 Score: 77
Period size: 31 Copynumber: 4.2 Consensus size: 31
38408208 TGGTCAAAAG
* * *
38408218 AAGTTCAAGCCTCAATGTGGGAACAATTGCC
1 AAGTTCAGGCCCCAATGTGGGAAAAATTGCC
* * * * *
38408249 TAGTCCAGGCCCCAATATGGGAACAATTGTC
1 AAGTTCAGGCCCCAATGTGGGAAAAATTGCC
* ** * ***
38408280 AAGTTTAGGATCTAACT-T-GGATAAAA--AAA
1 AAGTTCAGGCCCCAA-TGTGGGA-AAAATTGCC
38408309 AAGTTCAGGCCCCAATGTGGGAAAAATTGCC
1 AAGTTCAGGCCCCAATGTGGGAAAAATTGCC
38408340 AAGTTCA
1 AAGTTCA
38408347 AGCTCCAAAT
Statistics
Matches: 69, Mismatches: 23, Indels: 12
0.66 0.22 0.12
Matches are distributed among these distances:
28 1 0.01
29 16 0.23
30 6 0.09
31 45 0.65
32 1 0.01
ACGTcount: A:0.36, C:0.19, G:0.22, T:0.23
Consensus pattern (31 bp):
AAGTTCAGGCCCCAATGTGGGAAAAATTGCC
Found at i:38411156 original size:5 final size:5
Alignment explanation
Indices: 38411148--38411200 Score: 52
Period size: 5 Copynumber: 10.2 Consensus size: 5
38411138 TATTTACCAA
* ** *
38411148 TTTAT TTTAT TTTCT TAAAT TTATTT TTTCAT TTTAT TTTAT TTTAT TTTAT
1 TTTAT TTTAT TTTAT TTTAT TT-TAT TTT-AT TTTAT TTTAT TTTAT TTTAT
38411200 T
1 T
38411201 ACACTTCATA
Statistics
Matches: 38, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
5 31 0.82
6 7 0.18
ACGTcount: A:0.21, C:0.04, G:0.00, T:0.75
Consensus pattern (5 bp):
TTTAT
Found at i:38413398 original size:25 final size:25
Alignment explanation
Indices: 38413382--38413468 Score: 131
Period size: 25 Copynumber: 3.5 Consensus size: 25
38413372 GCATATGAAC
38413382 GGGAAGCTCATGTGAGCCATGTAAA
1 GGGAAGCTCATGTGAGCCATGTAAA
38413407 GGGAAGCTCATGTGAGCCATGTAAA
1 GGGAAGCTCATGTGAGCCATGTAAA
**
38413432 GGGAAGCTCATCCGAGCCATGTAACA
1 GGGAAGCTCATGTGAGCCATGTAA-A
*
38413458 -GAAAGCTCATG
1 GGGAAGCTCATG
38413469 CAAGCCAATA
Statistics
Matches: 57, Mismatches: 4, Indels: 2
0.90 0.06 0.03
Matches are distributed among these distances:
25 56 0.98
26 1 0.02
ACGTcount: A:0.32, C:0.20, G:0.30, T:0.18
Consensus pattern (25 bp):
GGGAAGCTCATGTGAGCCATGTAAA
Found at i:38423393 original size:43 final size:43
Alignment explanation
Indices: 38423327--38423553 Score: 276
Period size: 43 Copynumber: 5.3 Consensus size: 43
38423317 TTTTAGAAAA
* * *
38423327 AAACACCGCTGAAGACCAAGACCTTTAGCGGCGCTTTTCCCAC
1 AAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTACCAC
* *
38423370 AAACGCCGCTAAAGACCACGACCTTTAGCGGCGCTTTTCCCAC
1 AAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTACCAC
* * * * *
38423413 AAACGCTGCTAAAGACCAAAACTTTTAGCGGCGCTTTTATCGC
1 AAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTACCAC
*
38423456 AAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTATCAC
1 AAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTACCAC
** * * * * * *
38423499 AATTGCCGCTAAAGAACGA-ACCTTTAGCGACGCTTCTAGCAA
1 AAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTACCAC
38423541 AAACGCCGCTAAA
1 AAACGCCGCTAAA
38423554 AATAGAATCT
Statistics
Matches: 160, Mismatches: 24, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
42 30 0.19
43 130 0.81
ACGTcount: A:0.30, C:0.31, G:0.19, T:0.20
Consensus pattern (43 bp):
AAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTACCAC
Found at i:38425220 original size:37 final size:37
Alignment explanation
Indices: 38425162--38425626 Score: 894
Period size: 37 Copynumber: 12.6 Consensus size: 37
38425152 GCTCAGACGA
* * *
38425162 AATCTCCACACGAAGTTATCGGGTCTTACCCGGACAA
1 AATCTCCACACGTAGTCATCGGGTCTTACCCGGACAT
*
38425199 AATCTCCATACGTAGTCATCGGGTCTTACCCGGACAT
1 AATCTCCACACGTAGTCATCGGGTCTTACCCGGACAT
38425236 AATCTCCACACGTAGTCATCGGGTCTTACCCGGACAT
1 AATCTCCACACGTAGTCATCGGGTCTTACCCGGACAT
38425273 AATCTCCACACGTAGTCATCGGGTCTTACCCGGACAT
1 AATCTCCACACGTAGTCATCGGGTCTTACCCGGACAT
38425310 AATCTCCACACGTAGTCATCGGGTCTTACCCGGACAT
1 AATCTCCACACGTAGTCATCGGGTCTTACCCGGACAT
38425347 AATCTCCACACGTAGTCATCGGGTCTTACCCGGACAT
1 AATCTCCACACGTAGTCATCGGGTCTTACCCGGACAT
38425384 AATCTCCACACGTAGTCATCGGGTCTTACCCGGACAT
1 AATCTCCACACGTAGTCATCGGGTCTTACCCGGACAT
38425421 AATCTCCACACGTAGTCATCGGGTCTTACCCGGACAT
1 AATCTCCACACGTAGTCATCGGGTCTTACCCGGACAT
38425458 AATCTCCACACGTAGTCATCGGGTCTTACCCGGACAT
1 AATCTCCACACGTAGTCATCGGGTCTTACCCGGACAT
38425495 AATCTCCACACGTAGTCATCGGGTCTTACCCGGACAT
1 AATCTCCACACGTAGTCATCGGGTCTTACCCGGACAT
38425532 AATCTCCACACGTAGTCATCGGGTCTTACCCGGACAT
1 AATCTCCACACGTAGTCATCGGGTCTTACCCGGACAT
38425569 AATCTCCACACGTAGTCATCGGGTCTTACCCGGACAT
1 AATCTCCACACGTAGTCATCGGGTCTTACCCGGACAT
38425606 AATCTCCACACGTAGTCATCG
1 AATCTCCACACGTAGTCATCG
38425627 CCATTCGGCC
Statistics
Matches: 423, Mismatches: 5, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
37 423 1.00
ACGTcount: A:0.25, C:0.32, G:0.19, T:0.24
Consensus pattern (37 bp):
AATCTCCACACGTAGTCATCGGGTCTTACCCGGACAT
Found at i:38425690 original size:47 final size:47
Alignment explanation
Indices: 38425622--38425944 Score: 612
Period size: 47 Copynumber: 6.9 Consensus size: 47
38425612 CACACGTAGT
*
38425622 CATC-GCCATTCGGCCTTATCACATATATACACTTTCACATTCATCA
1 CATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCA
38425668 CATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCA
1 CATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCA
38425715 CATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCA
1 CATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCA
38425762 CATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCA
1 CATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCA
38425809 CATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCA
1 CATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCA
38425856 CATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCA
1 CATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCA
* *
38425903 CATCGGCTATTAAGCCTTATCACATATATACACTTTCACATT
1 CATCGGCCATTAGGCCTTATCACATATATACACTTTCACATT
38425945 TATTCAAATA
Statistics
Matches: 273, Mismatches: 3, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
46 4 0.01
47 269 0.99
ACGTcount: A:0.30, C:0.30, G:0.08, T:0.33
Consensus pattern (47 bp):
CATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCA
Found at i:38428792 original size:12 final size:12
Alignment explanation
Indices: 38428775--38428799 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
38428765 ATTTGATCTG
38428775 TATACTAAATGA
1 TATACTAAATGA
38428787 TATACTAAATGA
1 TATACTAAATGA
38428799 T
1 T
38428800 GCCAGTATCA
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:0.48, C:0.08, G:0.08, T:0.36
Consensus pattern (12 bp):
TATACTAAATGA
Found at i:38429457 original size:15 final size:13
Alignment explanation
Indices: 38429428--38429467 Score: 62
Period size: 15 Copynumber: 2.9 Consensus size: 13
38429418 ACTAACCTGG
38429428 TTTAAAATAATTA
1 TTTAAAATAATTA
38429441 TTTAAAATACTATTA
1 TTTAAAATA--ATTA
38429456 TTTAAAATAATT
1 TTTAAAATAATT
38429468 TTAAAGCTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
13 12 0.48
15 13 0.52
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (13 bp):
TTTAAAATAATTA
Found at i:38433367 original size:126 final size:125
Alignment explanation
Indices: 38433132--38433360 Score: 325
Period size: 126 Copynumber: 1.8 Consensus size: 125
38433122 AAGAACTTAA
* * * *
38433132 TTAATATATAAATTAAAAAATACTAATTAATCTAAACCTTAAACCCTAACCCGACCCCGAATCTC
1 TTAATATATAAATTAAAAAACACTAATTAATCTAAACCATAAACCCTAACCCAACACCGAATCTC
* *
38433197 TAAATCCTAAATCACTAACTCTTAACCTCTAATCTCTAACCCCTAACCCTTAAACTTTAT
66 TAAATCCTAAATCACTAACTCTTAACCTCTAACCCCTAACCCCTAACCCTTAAACTTTAT
* * *
38433257 TTAATATATAAATTAAAAAAACACTAATTAATCTAAACCATAAACCGTGACCTAACACCGAATC-
1 TTAATATATAAATT-AAAAAACACTAATTAATCTAAACCATAAACCCTAACCCAACACCGAATCT
* * *
38433321 CATAAATCCTAAATCCCTAATTCTTAATCTCTAACCCCTA
65 C-TAAATCCTAAATCACTAACTCTTAACCTCTAACCCCTA
38433361 GGCCCTAGCC
Statistics
Matches: 90, Mismatches: 12, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
125 15 0.17
126 75 0.83
ACGTcount: A:0.42, C:0.27, G:0.02, T:0.29
Consensus pattern (125 bp):
TTAATATATAAATTAAAAAACACTAATTAATCTAAACCATAAACCCTAACCCAACACCGAATCTC
TAAATCCTAAATCACTAACTCTTAACCTCTAACCCCTAACCCCTAACCCTTAAACTTTAT
Found at i:38433425 original size:14 final size:15
Alignment explanation
Indices: 38433402--38433434 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
38433392 CTTAAACCAG
*
38433402 AATCCTTAA-TCCAT
1 AATCCCTAATTCCAT
38433416 AATCCCTAATTCCAT
1 AATCCCTAATTCCAT
38433431 AATC
1 AATC
38433435 TATAAACTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 8 0.47
15 9 0.53
ACGTcount: A:0.36, C:0.30, G:0.00, T:0.33
Consensus pattern (15 bp):
AATCCCTAATTCCAT
Found at i:38434138 original size:41 final size:41
Alignment explanation
Indices: 38433826--38434135 Score: 476
Period size: 41 Copynumber: 7.6 Consensus size: 41
38433816 ATATTTTTGT
* *
38433826 GGCGCATTCTCAAAAACGTCGCTAAAAGTCTGAGCATTAGC
1 GGCGCATTCTCAAAAACGCCGCTAAAAGCCTGAGCATTAGC
* *
38433867 GGCACTTTCTCAAAAACGCCGCTAAAAGCCTGAGCATTAGC
1 GGCGCATTCTCAAAAACGCCGCTAAAAGCCTGAGCATTAGC
* * *
38433908 GGCGCTTTCTCAAAAACACCGCTAAAAGCTTGAGCATTAGC
1 GGCGCATTCTCAAAAACGCCGCTAAAAGCCTGAGCATTAGC
*
38433949 GGCGCATTCCCAAAAACGCCGCTAAAAGCCTGAGCATTAGC
1 GGCGCATTCTCAAAAACGCCGCTAAAAGCCTGAGCATTAGC
* * *
38433990 GGCGCTTTCTCAAAAACACCGCTAAAAGCTTGAGCATTAGC
1 GGCGCATTCTCAAAAACGCCGCTAAAAGCCTGAGCATTAGC
*
38434031 GGCGCATTCCCAAAAACGCCGCTAAAAGCCTGAGCATTAGC
1 GGCGCATTCTCAAAAACGCCGCTAAAAGCCTGAGCATTAGC
* * *
38434072 GGCGCATTCCCAAAAACGCTGCTGAAAGCCTGAGCATTAGC
1 GGCGCATTCTCAAAAACGCCGCTAAAAGCCTGAGCATTAGC
*
38434113 GGCGCTTTCTCAAAAACGCCGCT
1 GGCGCATTCTCAAAAACGCCGCT
38434136 GAAGCCCTAA
Statistics
Matches: 245, Mismatches: 24, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
41 245 1.00
ACGTcount: A:0.31, C:0.29, G:0.21, T:0.19
Consensus pattern (41 bp):
GGCGCATTCTCAAAAACGCCGCTAAAAGCCTGAGCATTAGC
Found at i:38434227 original size:40 final size:38
Alignment explanation
Indices: 38434177--38434314 Score: 125
Period size: 40 Copynumber: 3.5 Consensus size: 38
38434167 TGGGCTTATG
* *
38434177 TTTTTTGCGGCGTTTTTCTAAAAAACGCCGCTAATGCTCA
1 TTTTTAGCGGCGTTTTT-T-AAAAGCGCCGCTAATGCTCA
* * * *
38434217 TTTTTAGCGGCGCTTTTTGAAAAGCACCGCGAATGCTGGA
1 TTTTTAGCGGCG-TTTTTTAAAAGCGCCGCTAATGCT-CA
* * *
38434257 TCTTTAGCGACGTTTTATGT-AAAGCGCTGCTAATGCTCGA
1 TTTTTAGCGGCGTTTT-T-TAAAAGCGCCGCTAATGCTC-A
38434297 TTTTTAGCGGCGTTTTTT
1 TTTTTAGCGGCGTTTTTT
38434315 GTCCAAACGC
Statistics
Matches: 78, Mismatches: 15, Indels: 12
0.74 0.14 0.11
Matches are distributed among these distances:
38 1 0.01
39 20 0.26
40 52 0.67
41 5 0.06
ACGTcount: A:0.20, C:0.20, G:0.22, T:0.38
Consensus pattern (38 bp):
TTTTTAGCGGCGTTTTTTAAAAGCGCCGCTAATGCTCA
Found at i:38434854 original size:50 final size:50
Alignment explanation
Indices: 38434750--38434885 Score: 132
Period size: 50 Copynumber: 2.7 Consensus size: 50
38434740 TACAGGTATG
* * * * *
38434750 CTCATACGAG-CATATAAACGGGAAGCTCTTTCGAGCCATATAACAGGAAA
1 CTCATGCGAGCCATGTAAA-GGGAAGCTCATGCGAGCCATATAACAGAAAA
* * *
38434800 CTCATGTGAGTCATGTAAAGGGAAGCTCATGCGAGCCATTTAAC-GAAAA
1 CTCATGCGAGCCATGTAAAGGGAAGCTCATGCGAGCCATATAACAGAAAA
* * **
38434849 GCTCATGCGAGCCATTTAACGAAAAGCTCATGCGAGC
1 -CTCATGCGAGCCATGTAAAGGGAAGCTCATGCGAGC
38434886 TAATATCGTG
Statistics
Matches: 71, Mismatches: 13, Indels: 4
0.81 0.15 0.05
Matches are distributed among these distances:
49 4 0.06
50 60 0.85
51 7 0.10
ACGTcount: A:0.35, C:0.22, G:0.23, T:0.21
Consensus pattern (50 bp):
CTCATGCGAGCCATGTAAAGGGAAGCTCATGCGAGCCATATAACAGAAAA
Found at i:38434910 original size:49 final size:50
Alignment explanation
Indices: 38434782--38434962 Score: 134
Period size: 50 Copynumber: 3.6 Consensus size: 50
38434772 AAGCTCTTTC
* * * * * * ** *
38434782 GAGCCATATAACAGGAAACTCATGTGAGTCATGTAAAGGGAAGCTCATGC
1 GAGCCAAATAACAGGAAGCTCATGAGAGCCATTTAACGAAAAGCTCATGA
** * * *
38434832 GAGCCATTTAAC-GAAAAGCTCATGCGAGCCATTTAACGAAAAGCTCATGC
1 GAGCCAAATAACAG-GAAGCTCATGAGAGCCATTTAACGAAAAGCTCATGA
* * * * * *
38434882 GAG-CTAATATC-GTGAAGCTCATGAGAGCCAATTATCGAGAAGCTCGTGA
1 GAGCCAAATAACAG-GAAGCTCATGAGAGCCATTTAACGAAAAGCTCATGA
*
38434931 GAGCCAAATAACAGGAAGCTCAAGAGAGCCAT
1 GAGCCAAATAACAGGAAGCTCATGAGAGCCAT
38434963 ATACTGGGAT
Statistics
Matches: 103, Mismatches: 25, Indels: 6
0.77 0.19 0.04
Matches are distributed among these distances:
49 38 0.37
50 64 0.62
51 1 0.01
ACGTcount: A:0.36, C:0.20, G:0.24, T:0.19
Consensus pattern (50 bp):
GAGCCAAATAACAGGAAGCTCATGAGAGCCATTTAACGAAAAGCTCATGA
Found at i:38434923 original size:25 final size:25
Alignment explanation
Indices: 38434821--38434961 Score: 133
Period size: 25 Copynumber: 5.7 Consensus size: 25
38434811 CATGTAAAGG
* *
38434821 GAAGCTCATGCGAGCCATTTAACGA
1 GAAGCTCATGAGAGCCAATTAACGA
* * *
38434846 AAAGCTCATGCGAGCCATTTAACGA
1 GAAGCTCATGAGAGCCAATTAACGA
* * * * *
38434871 AAAGCTCATGCGAGCTAA-TATCGT
1 GAAGCTCATGAGAGCCAATTAACGA
*
38434895 GAAGCTCATGAGAGCCAATTATCGA
1 GAAGCTCATGAGAGCCAATTAACGA
* *
38434920 GAAGCTCGTGAGAGCCAAATAAC-A
1 GAAGCTCATGAGAGCCAATTAACGA
*
38434944 GGAAGCTCAAGAGAGCCA
1 -GAAGCTCATGAGAGCCA
38434962 TATACTGGGA
Statistics
Matches: 100, Mismatches: 14, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
24 20 0.20
25 80 0.80
ACGTcount: A:0.36, C:0.22, G:0.24, T:0.18
Consensus pattern (25 bp):
GAAGCTCATGAGAGCCAATTAACGA
Found at i:38437400 original size:14 final size:14
Alignment explanation
Indices: 38437383--38437414 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
38437373 GAAAAAAAAT
38437383 AAAAATAAAAACAA
1 AAAAATAAAAACAA
*
38437397 AAAAATAAAAATAA
1 AAAAATAAAAACAA
38437411 AAAA
1 AAAA
38437415 TGTATATAGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.88, C:0.03, G:0.00, T:0.09
Consensus pattern (14 bp):
AAAAATAAAAACAA
Found at i:38437400 original size:20 final size:20
Alignment explanation
Indices: 38437375--38437413 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
38437365 CTATGTTTGA
38437375 AAAAAAATAAAAATAAAAAC
1 AAAAAAATAAAAATAAAAAC
38437395 AAAAAAATAAAAATAAAAA
1 AAAAAAATAAAAATAAAAA
38437414 ATGTATATAG
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:0.87, C:0.03, G:0.00, T:0.10
Consensus pattern (20 bp):
AAAAAAATAAAAATAAAAAC
Found at i:38439269 original size:29 final size:30
Alignment explanation
Indices: 38439213--38439275 Score: 76
Period size: 29 Copynumber: 2.1 Consensus size: 30
38439203 AATTTTTTAG
* *
38439213 AAATTATTATAAATTATAATAACATTATAA
1 AAATTATTAGAAATTATAAAAACATTATAA
*
38439243 AAATT-TTAGAAATTATAGAAAAC-TTATAT
1 AAATTATTAGAAATTATA-AAAACATTATAA
38439272 AAAT
1 AAAT
38439276 CATTCAAATA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
29 20 0.69
30 9 0.31
ACGTcount: A:0.56, C:0.03, G:0.03, T:0.38
Consensus pattern (30 bp):
AAATTATTAGAAATTATAAAAACATTATAA
Found at i:38439386 original size:20 final size:20
Alignment explanation
Indices: 38439363--38439414 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 20
38439353 TTTTAGTAAG
38439363 TTTTTAAAACATTTTTATAGT
1 TTTTTAAAAC-TTTTTATAGT
* *
38439384 TTTTTAATACTTTTTATTAAT
1 TTTTTAAAACTTTTTA-TAGT
38439405 ATTTTTAAAA
1 -TTTTTAAAA
38439415 ATTAATTAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
20 6 0.23
21 12 0.46
22 8 0.31
ACGTcount: A:0.35, C:0.04, G:0.02, T:0.60
Consensus pattern (20 bp):
TTTTTAAAACTTTTTATAGT
Found at i:38440692 original size:24 final size:24
Alignment explanation
Indices: 38440657--38440702 Score: 67
Period size: 25 Copynumber: 1.9 Consensus size: 24
38440647 TCCCCTTAAC
*
38440657 AAAT-AAACCCAATTTTATAAATAA
1 AAATAAAACCAAATTTTA-AAATAA
38440681 AAATAAAACCAAATTTTAAAAT
1 AAATAAAACCAAATTTTAAAAT
38440703 GTCCATAGTC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
24 8 0.40
25 12 0.60
ACGTcount: A:0.61, C:0.11, G:0.00, T:0.28
Consensus pattern (24 bp):
AAATAAAACCAAATTTTAAAATAA
Found at i:38441918 original size:21 final size:25
Alignment explanation
Indices: 38441894--38441980 Score: 92
Period size: 25 Copynumber: 3.6 Consensus size: 25
38441884 TGGAATGTAT
38441894 TTATTTATTTTAAA-C-TT-TA-TA
1 TTATTTATTTTAAATCTTTCTATTA
38441915 TTATTTATTTTAAATCTTTCTATTA
1 TTATTTATTTTAAATCTTTCTATTA
* * *
38441940 TTATTTATTTTAAGTTTTTTTTATATA
1 TTATTTATTTTAA-ATCTTTCTAT-TA
*
38441967 TTATGTATTTTAAA
1 TTATTTATTTTAAA
38441981 CTATGTTAAT
Statistics
Matches: 55, Mismatches: 5, Indels: 7
0.82 0.07 0.10
Matches are distributed among these distances:
21 14 0.25
22 1 0.02
23 2 0.04
24 2 0.04
25 15 0.27
26 7 0.13
27 14 0.25
ACGTcount: A:0.30, C:0.03, G:0.02, T:0.64
Consensus pattern (25 bp):
TTATTTATTTTAAATCTTTCTATTA
Found at i:38441976 original size:27 final size:26
Alignment explanation
Indices: 38441911--38442033 Score: 92
Period size: 27 Copynumber: 4.7 Consensus size: 26
38441901 TTTTAAACTT
38441911 TATATTATTTATTTTAAATCTTTCTA
1 TATATTATTTATTTTAAATCTTTCTA
* * *
38441937 T-TATTATTTATTTTAAGTTTTTTTTA
1 TATATTATTTATTTTAA-ATCTTTCTA
*
38441963 TATATTATGTATTTTAAA-CTATGT-TA
1 TATATTATTTATTTTAAATCT-T-TCTA
* * * *
38441989 -ATCAATTATTCATTTTAAATATATATA
1 TAT--ATTATTTATTTTAAATCTTTCTA
*
38442016 TATATTATTTATGTTAAA
1 TATATTATTTATTTTAAA
38442034 CTACATATGT
Statistics
Matches: 76, Mismatches: 12, Indels: 18
0.72 0.11 0.17
Matches are distributed among these distances:
25 18 0.24
26 25 0.33
27 30 0.39
28 3 0.04
ACGTcount: A:0.34, C:0.04, G:0.03, T:0.59
Consensus pattern (26 bp):
TATATTATTTATTTTAAATCTTTCTA
Found at i:38442049 original size:27 final size:26
Alignment explanation
Indices: 38441993--38442054 Score: 79
Period size: 27 Copynumber: 2.3 Consensus size: 26
38441983 ATGTTAATCA
* * *
38441993 ATTATTCATTTTAAATATATATATAT
1 ATTATTTATGTTAAATACATATATAT
*
38442019 ATTATTTATGTTAAACTACATATGTAT
1 ATTATTTATGTTAAA-TACATATATAT
38442046 ATTATTTAT
1 ATTATTTAT
38442055 TTGGAATTGT
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
26 13 0.42
27 18 0.58
ACGTcount: A:0.39, C:0.05, G:0.03, T:0.53
Consensus pattern (26 bp):
ATTATTTATGTTAAATACATATATAT
Found at i:38442195 original size:26 final size:26
Alignment explanation
Indices: 38442166--38442236 Score: 72
Period size: 28 Copynumber: 2.7 Consensus size: 26
38442156 ATTTTACATA
38442166 TTATTTTAAATTGTTTTCTATG-TTAT
1 TTATTTTAAATTGTTTTCTA-GATTAT
* *
38442192 TTATTTTTTAAATTGCTTTGTAGATTAT
1 TTA--TTTTAAATTGTTTTCTAGATTAT
* *
38442220 TCATTTTAACTTGTTTT
1 TTATTTTAAATTGTTTT
38442237 ACACATTATT
Statistics
Matches: 37, Mismatches: 5, Indels: 6
0.77 0.10 0.12
Matches are distributed among these distances:
26 15 0.41
27 1 0.03
28 21 0.57
ACGTcount: A:0.23, C:0.06, G:0.08, T:0.63
Consensus pattern (26 bp):
TTATTTTAAATTGTTTTCTAGATTAT
Found at i:38442225 original size:28 final size:28
Alignment explanation
Indices: 38442169--38442226 Score: 73
Period size: 28 Copynumber: 2.1 Consensus size: 28
38442159 TTACATATTA
* *
38442169 TTTTAAATTGTTTTCTATGTTATTTATT
1 TTTTAAATTGCTTTCTATGTTATTCATT
*
38442197 TTTTAAATTGCTTTGTA-GATTATTCATT
1 TTTTAAATTGCTTTCTATG-TTATTCATT
38442225 TT
1 TT
38442227 AACTTGTTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
27 1 0.04
28 25 0.96
ACGTcount: A:0.22, C:0.05, G:0.09, T:0.64
Consensus pattern (28 bp):
TTTTAAATTGCTTTCTATGTTATTCATT
Found at i:38443437 original size:16 final size:17
Alignment explanation
Indices: 38443416--38443447 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
38443406 AAAATTATTG
38443416 TAAAATATTAA-ATATA
1 TAAAATATTAACATATA
38443432 TAAAATATTAACATAT
1 TAAAATATTAACATAT
38443448 TTTCAAGAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (17 bp):
TAAAATATTAACATATA
Found at i:38445183 original size:12 final size:13
Alignment explanation
Indices: 38445166--38445202 Score: 51
Period size: 12 Copynumber: 3.0 Consensus size: 13
38445156 GGGTTTTTTG
38445166 ATGAAGATGAT-A
1 ATGAAGATGATGA
*
38445178 ATGAAGGTGATGA
1 ATGAAGATGATGA
38445191 A-GAAGATGATGA
1 ATGAAGATGATGA
38445203 TGGTCTTTTG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
12 20 0.91
13 2 0.09
ACGTcount: A:0.46, C:0.00, G:0.32, T:0.22
Consensus pattern (13 bp):
ATGAAGATGATGA
Found at i:38452448 original size:28 final size:28
Alignment explanation
Indices: 38452417--38452473 Score: 96
Period size: 28 Copynumber: 2.0 Consensus size: 28
38452407 AAAAGACTAA
*
38452417 AGTAACCTCAAATAATATAACATATTTT
1 AGTAACCTCAAATAACATAACATATTTT
*
38452445 AGTACCCTCAAATAACATAACATATTTT
1 AGTAACCTCAAATAACATAACATATTTT
38452473 A
1 A
38452474 ATTACGAAAG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.46, C:0.18, G:0.04, T:0.33
Consensus pattern (28 bp):
AGTAACCTCAAATAACATAACATATTTT
Found at i:38453104 original size:15 final size:15
Alignment explanation
Indices: 38453070--38453107 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
38453060 TATTAAAATC
*
38453070 AATTTTATTTTATTA
1 AATTTTATTTTATAA
38453085 AATTTTATTTT-TAA
1 AATTTTATTTTATAA
38453099 ATATTTTAT
1 A-ATTTTAT
38453108 ATATTAATTG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 3 0.14
15 18 0.86
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (15 bp):
AATTTTATTTTATAA
Found at i:38454651 original size:49 final size:49
Alignment explanation
Indices: 38454593--38454693 Score: 148
Period size: 49 Copynumber: 2.1 Consensus size: 49
38454583 ACAGTAATGA
**
38454593 GTTGAAGTATAACTAGAGCTCCTAGTTGACAGTGGTTATGCGATCACAG
1 GTTGAAGTATAACTAGAGAGCCTAGTTGACAGTGGTTATGCGATCACAG
* * * *
38454642 GTTGGAGTATAACTCGAGAGCCTAGTTGATAGTGGTTATGCGGTCACAG
1 GTTGAAGTATAACTAGAGAGCCTAGTTGACAGTGGTTATGCGATCACAG
38454691 GTT
1 GTT
38454694 CATGTTTCTT
Statistics
Matches: 46, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
49 46 1.00
ACGTcount: A:0.26, C:0.15, G:0.30, T:0.30
Consensus pattern (49 bp):
GTTGAAGTATAACTAGAGAGCCTAGTTGACAGTGGTTATGCGATCACAG
Found at i:38455339 original size:49 final size:48
Alignment explanation
Indices: 38455220--38455339 Score: 152
Period size: 48 Copynumber: 2.5 Consensus size: 48
38455210 GTGGCATTAA
* *
38455220 ACTTGAACCCATGATCGCATAACCACCGTCAATTGAGGCTCGAGCTAT
1 ACTTGAACCCATGATTGCATAACCACCGTCAATTGAGGCCCGAGCTAT
* *
38455268 ACTTGAACCCATGACTGCATAACCACCGTCAATTGAGAGCCCTAG-TCAT
1 ACTTGAACCCATGATTGCATAACCACCGTCAATTGAG-GCCCGAGCT-AT
* * *
38455317 ACTTCAACCCGTGATTGTATAAC
1 ACTTGAACCCATGATTGCATAAC
38455340 TACTGTGAAC
Statistics
Matches: 62, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
48 36 0.58
49 26 0.42
ACGTcount: A:0.30, C:0.29, G:0.17, T:0.24
Consensus pattern (48 bp):
ACTTGAACCCATGATTGCATAACCACCGTCAATTGAGGCCCGAGCTAT
Found at i:38457736 original size:15 final size:15
Alignment explanation
Indices: 38457713--38457742 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
38457703 GACATGCACG
*
38457713 TTCTTATTACCACAC
1 TTCTCATTACCACAC
38457728 TTCTCATTACCACAC
1 TTCTCATTACCACAC
38457743 ATGTATTTTC
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:0.27, C:0.37, G:0.00, T:0.37
Consensus pattern (15 bp):
TTCTCATTACCACAC
Found at i:38458687 original size:38 final size:38
Alignment explanation
Indices: 38458645--38458721 Score: 136
Period size: 38 Copynumber: 2.0 Consensus size: 38
38458635 TATATGTAAT
*
38458645 AGTTGAGAATAAATTCTCTCTATTTTTCGTCAGAAAAC
1 AGTTGAGAATAAATTCTCTCTATTTTTCGGCAGAAAAC
*
38458683 AGTTGAGAATAAATTCTCTCTATTTTTTGGCAGAAAAC
1 AGTTGAGAATAAATTCTCTCTATTTTTCGGCAGAAAAC
38458721 A
1 A
38458722 ATCTCTCAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.35, C:0.14, G:0.14, T:0.36
Consensus pattern (38 bp):
AGTTGAGAATAAATTCTCTCTATTTTTCGGCAGAAAAC
Found at i:38459117 original size:26 final size:25
Alignment explanation
Indices: 38459068--38459139 Score: 108
Period size: 26 Copynumber: 2.8 Consensus size: 25
38459058 TCTCATCCCT
**
38459068 ATTTTACCCCTAAAAAATTTTGACG
1 ATTTTACCCCTGTAAAATTTTGACG
38459093 ATTTTACCCCTGGTAAAATTTTGACG
1 ATTTTACCCCT-GTAAAATTTTGACG
38459119 ATTTTACCCCTAGTAAAATTT
1 ATTTTACCCCT-GTAAAATTT
38459140 CAAGGAAATA
Statistics
Matches: 43, Mismatches: 3, Indels: 1
0.91 0.06 0.02
Matches are distributed among these distances:
25 11 0.26
26 32 0.74
ACGTcount: A:0.32, C:0.19, G:0.10, T:0.39
Consensus pattern (25 bp):
ATTTTACCCCTGTAAAATTTTGACG
Found at i:38470314 original size:90 final size:90
Alignment explanation
Indices: 38470143--38470540 Score: 552
Period size: 90 Copynumber: 4.4 Consensus size: 90
38470133 ATTAAAAATT
* * *
38470143 AATTAATATAATAGTACAGCAGCATAAATTAAAC-AAAAAAAGTATGTTAAACTACATTTTAAAC
1 AATTAATATAATAGTACAACAGCATAAATTAAACAAAAAAAAGTATGTTAAACTACAGTTTAAAA
38470207 TTTAAAGTTAGTTAATTGAAGCCTA
66 TTTAAAGTTAGTTAATTGAAGCCTA
* * * *
38470232 AATTAATATAATAGTACAATAGCATAAATTAAACAGAAAAAAGTCTGTTAAGCTATC-GTTTAAA
1 AATTAATATAATAGTACAACAGCATAAATTAAACAAAAAAAAGTATGTTAAACTA-CAGTTTAAA
*
38470296 ATTTAAAGTTAGTTAATTGAGGCCTA
65 ATTTAAAGTTAGTTAATTGAAGCCTA
*
38470322 AATTAATATAATAGTATAAGTACAACAACATAAATTAAACCAAAAAAAAGTATGTTAAACTACAG
1 AATT-A-AT-ATA--AT-AGTACAACAGCATAAATTAAA-CAAAAAAAAGTATGTTAAACTACAG
38470387 -TTAAAATTTAAAGTTAGTTAATTGAAGCCTA
59 TTTAAAATTTAAAGTTAGTTAATTGAAGCCTA
* * *
38470418 AATTAATATAATAGTACAATAGCATAAATTAAACAAAAAAAATGTCTGTTAAAAC-ATAGTTTAA
1 AATTAATATAATAGTACAACAGCATAAATTAAACAAAAAAAA-GTATGTT-AAACTACAGTTTAA
* *
38470482 ACTTCAAAGTTAGTTAATTGAAGCCTA
64 AATTTAAAGTTAGTTAATTGAAGCCTA
38470509 AATTAATATAATAGTACAACAGCATAAATTAA
1 AATTAATATAATAGTACAACAGCATAAATTAA
38470541 GTAATTGAAG
Statistics
Matches: 275, Mismatches: 21, Indels: 24
0.86 0.07 0.08
Matches are distributed among these distances:
89 41 0.15
90 79 0.29
91 68 0.25
92 2 0.01
93 6 0.02
94 2 0.01
95 3 0.01
96 54 0.20
97 20 0.07
ACGTcount: A:0.49, C:0.10, G:0.10, T:0.31
Consensus pattern (90 bp):
AATTAATATAATAGTACAACAGCATAAATTAAACAAAAAAAAGTATGTTAAACTACAGTTTAAAA
TTTAAAGTTAGTTAATTGAAGCCTA
Found at i:38470417 original size:186 final size:186
Alignment explanation
Indices: 38470138--38470524 Score: 606
Period size: 187 Copynumber: 2.1 Consensus size: 186
38470128 AGTAAATTAA
* * *
38470138 AAATTAAT-TAATA-TAATAGTACAGCAGCATAAATTAAACAAAAAAAGTATGTTAAACTACATT
1 AAATTAATATAATAGTAATAGTACAACAACATAAATTAAACAAAAAAAGTATGTTAAACTACATG
*
38470201 TTAAACTTTAAAGTTAGTTAATTGAAGCCTAAATTAATATAATAGTACAATAGCATAAATTAAAC
66 TTAAAATTTAAAGTTAGTTAATTGAAGCCTAAATTAATATAATAGTACAATAGCATAAATTAAAC
* * * * *
38470266 AGAAAAAA-GTCTGTT-AAGCTATCGTTTAAAATTTAAAGTTAGTTAATTGAGGCCT
131 AAAAAAAATGTCTGTTAAAAC-ATAGTTTAAAATTCAAAGTTAGTTAATTGAAGCCT
38470321 AAATTAATATAATAGT-ATAAGTACAACAACATAAATTAAACCAAAAAAAAGTATGTTAAACTAC
1 AAATTAATATAATAGTAAT-AGTACAACAACATAAATTAAA-C-AAAAAAAGTATGTTAAACTAC
38470385 A-GTTAAAATTTAAAGTTAGTTAATTGAAGCCTAAATTAATATAATAGTACAATAGCATAAATTA
63 ATGTTAAAATTTAAAGTTAGTTAATTGAAGCCTAAATTAATATAATAGTACAATAGCATAAATTA
*
38470449 AACAAAAAAAATGTCTGTTAAAACATAGTTTAAACTTCAAAGTTAGTTAATTGAAGCCT
128 AACAAAAAAAATGTCTGTTAAAACATAGTTTAAAATTCAAAGTTAGTTAATTGAAGCCT
38470508 AAATTAATATAATAGTA
1 AAATTAATATAATAGTA
38470525 CAACAGCATA
Statistics
Matches: 186, Mismatches: 10, Indels: 11
0.90 0.05 0.05
Matches are distributed among these distances:
183 8 0.04
184 7 0.04
185 20 0.11
186 72 0.39
187 76 0.41
188 3 0.02
ACGTcount: A:0.49, C:0.09, G:0.10, T:0.31
Consensus pattern (186 bp):
AAATTAATATAATAGTAATAGTACAACAACATAAATTAAACAAAAAAAGTATGTTAAACTACATG
TTAAAATTTAAAGTTAGTTAATTGAAGCCTAAATTAATATAATAGTACAATAGCATAAATTAAAC
AAAAAAAATGTCTGTTAAAACATAGTTTAAAATTCAAAGTTAGTTAATTGAAGCCT
Found at i:38470727 original size:12 final size:13
Alignment explanation
Indices: 38470696--38470734 Score: 53
Period size: 12 Copynumber: 3.0 Consensus size: 13
38470686 TAAGGTCTTG
*
38470696 TATTTAATATTTAA
1 TATTTAAAATTT-A
38470710 TATTTAAAATTT-
1 TATTTAAAATTTA
38470722 TATTTAAAATTTA
1 TATTTAAAATTTA
38470735 AATATGATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
12 12 0.52
14 11 0.48
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (13 bp):
TATTTAAAATTTA
Found at i:38470868 original size:17 final size:17
Alignment explanation
Indices: 38470846--38470897 Score: 77
Period size: 17 Copynumber: 3.1 Consensus size: 17
38470836 TTTTCTCTAT
*
38470846 TAATATTACGTTATTAC
1 TAATATTACATTATTAC
*
38470863 TAATATTATATTATTAC
1 TAATATTACATTATTAC
*
38470880 TAATATTGCATTATTAC
1 TAATATTACATTATTAC
38470897 T
1 T
38470898 TTGGGAAATT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 31 1.00
ACGTcount: A:0.37, C:0.10, G:0.04, T:0.50
Consensus pattern (17 bp):
TAATATTACATTATTAC
Found at i:38471320 original size:19 final size:19
Alignment explanation
Indices: 38471293--38471355 Score: 56
Period size: 19 Copynumber: 3.3 Consensus size: 19
38471283 GGAGAAGGAA
*
38471293 AATAGAGCGAAAATCATTC
1 AATAAAGCGAAAATCATTC
* *
38471312 AATAAAGCGAAACA-GATGC
1 AATAAAGCGAAA-ATCATTC
* *
38471331 AAATAGAGCTAAAATCATTC
1 -AATAAAGCGAAAATCATTC
38471351 AATAA
1 AATAA
38471356 TTCAAAAATA
Statistics
Matches: 33, Mismatches: 8, Indels: 6
0.70 0.17 0.13
Matches are distributed among these distances:
19 19 0.58
20 14 0.42
ACGTcount: A:0.52, C:0.14, G:0.14, T:0.19
Consensus pattern (19 bp):
AATAAAGCGAAAATCATTC
Found at i:38472701 original size:14 final size:14
Alignment explanation
Indices: 38472682--38472708 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
38472672 GTGGTCCAGT
38472682 TGAACTGAACCGAG
1 TGAACTGAACCGAG
38472696 TGAACTGAACCGA
1 TGAACTGAACCGA
38472709 CCGAGAAATG
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:0.37, C:0.22, G:0.26, T:0.15
Consensus pattern (14 bp):
TGAACTGAACCGAG
Found at i:38475199 original size:104 final size:104
Alignment explanation
Indices: 38475012--38475578 Score: 978
Period size: 104 Copynumber: 5.5 Consensus size: 104
38475002 TGTATATAAA
** * * * * *
38475012 AGGGGTTGCTGTGTGCTGATTCCCCAATTCATTGGTGGTACTATGTGCG-TGATCCACCATATAT
1 AGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGAT-ATCCACCGTATCT
**
38475076 TTGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCCG
65 TTGAAATGAAAAAGGGGGTTGCTATGTGCTGATTCCCCCG
38475116 AGGGGTTGCTAAGTGCTGATTCCCCGATTTCATTGGTGGTGCTAAGTGCGATATCCACCGTATCT
1 AGGGGTTGCTAAGTGCTGATTCCCCGA-TTCATTGGTGGTGCTAAGTGCGATATCCACCGTATCT
38475181 TTGAAATG-AAAAGGGGGTTGCTATGTGCTGATTCCCCCG
65 TTGAAATGAAAAAGGGGGTTGCTATGTGCTGATTCCCCCG
38475220 AGGGGTTGCTAAGTGCTGATTCCCCGATTTCATTGGTGGTGCTAAGTGCGATATCCACCGTATCT
1 AGGGGTTGCTAAGTGCTGATTCCCCGA-TTCATTGGTGGTGCTAAGTGCGATATCCACCGTATCT
38475285 TTGAAATG-AAAAGGGGGTTGCTATGTGCTGATTCCCCCG
65 TTGAAATGAAAAAGGGGGTTGCTATGTGCTGATTCCCCCG
*
38475324 AGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGATGCTAAGTGCGATATCCACCGTATCTT
1 AGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGATATCCACCGTATCTT
38475389 TGAAATGAAAAAGGGGGTTGCTATGTGCTGATTCCCCCG
66 TGAAATGAAAAAGGGGGTTGCTATGTGCTGATTCCCCCG
*
38475428 AGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGATGCTAAGTGCGATATCCACCGTATCTT
1 AGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGATATCCACCGTATCTT
38475493 TGAAATGAAAAAGGGGGTTGCTATGTGCTGATTCCCCCG
66 TGAAATGAAAAAGGGGGTTGCTATGTGCTGATTCCCCCG
*
38475532 AGGGGTTGCTAAGTGCTGATTCCCCGATTCAGTGGTGGTGCTAAGTG
1 AGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTG
38475579 TGGGATCCAC
Statistics
Matches: 449, Mismatches: 11, Indels: 6
0.96 0.02 0.01
Matches are distributed among these distances:
103 44 0.10
104 365 0.81
105 39 0.09
106 1 0.00
ACGTcount: A:0.20, C:0.20, G:0.29, T:0.31
Consensus pattern (104 bp):
AGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGATATCCACCGTATCTT
TGAAATGAAAAAGGGGGTTGCTATGTGCTGATTCCCCCG
Found at i:38478673 original size:5 final size:5
Alignment explanation
Indices: 38478663--38478691 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
38478653 GCCAAAAAGC
38478663 GAATT GAATT GAATT GAATT GAATT GAAT
1 GAATT GAATT GAATT GAATT GAATT GAAT
38478692 ATAAATTTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.41, C:0.00, G:0.21, T:0.38
Consensus pattern (5 bp):
GAATT
Found at i:38479067 original size:24 final size:25
Alignment explanation
Indices: 38479035--38479087 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 25
38479025 CGTTATTAGA
*
38479035 TCTCCTGAGCATCCTAATGT-TGGC
1 TCTCCTGAGCATCCTAATATATGGC
* * *
38479059 TCTCTTGAGCTTCCTGATATATGGC
1 TCTCCTGAGCATCCTAATATATGGC
38479084 TCTC
1 TCTC
38479088 ACGAGCTTTC
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
24 16 0.67
25 8 0.33
ACGTcount: A:0.15, C:0.28, G:0.19, T:0.38
Consensus pattern (25 bp):
TCTCCTGAGCATCCTAATATATGGC
Found at i:38479214 original size:25 final size:27
Alignment explanation
Indices: 38479186--38479236 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 27
38479176 CTTGATATAT
38479186 GGCTC-TTC-GGAGCTTCCCGATTAAA
1 GGCTCTTTCAGGAGCTTCCCGATTAAA
* *
38479211 GGCTCTTTCATGAGCTTCCTGATTAA
1 GGCTCTTTCAGGAGCTTCCCGATTAA
38479237 TAGCTTTCTG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 5 0.23
26 3 0.14
27 14 0.64
ACGTcount: A:0.20, C:0.25, G:0.22, T:0.33
Consensus pattern (27 bp):
GGCTCTTTCAGGAGCTTCCCGATTAAA
Found at i:38485359 original size:22 final size:22
Alignment explanation
Indices: 38485334--38485383 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
38485324 TGTACTATGG
*
38485334 TGCCTACTAATTCT-CACTTTGA
1 TGCCTACT-ACTCTACACTTTGA
*
38485356 TGCCTACTACTCTACACTTTGG
1 TGCCTACTACTCTACACTTTGA
38485378 TGCCTA
1 TGCCTA
38485384 TTGTTAAAAC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 4 0.16
22 21 0.84
ACGTcount: A:0.20, C:0.30, G:0.12, T:0.38
Consensus pattern (22 bp):
TGCCTACTACTCTACACTTTGA
Found at i:38487645 original size:20 final size:20
Alignment explanation
Indices: 38487616--38487659 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
38487606 CCCTTTCCAA
38487616 ATTTTCTTACTTT-CATTTGC
1 ATTTTCTTACTTTCCA-TTGC
*
38487636 ATTTTGTTACTTTCCATTGC
1 ATTTTCTTACTTTCCATTGC
38487656 ATTT
1 ATTT
38487660 ACTTTCTTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 20 0.91
21 2 0.09
ACGTcount: A:0.16, C:0.18, G:0.07, T:0.59
Consensus pattern (20 bp):
ATTTTCTTACTTTCCATTGC
Found at i:38489629 original size:12 final size:12
Alignment explanation
Indices: 38489612--38489642 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
38489602 GAGAATCCAT
*
38489612 AAATATTTATAA
1 AAATATTCATAA
38489624 AAATATTCATAA
1 AAATATTCATAA
38489636 AAATATT
1 AAATATT
38489643 GACGGCTCGG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (12 bp):
AAATATTCATAA
Found at i:38490611 original size:8 final size:8
Alignment explanation
Indices: 38490598--38490623 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
38490588 CATGATTTGT
38490598 TTGATGAA
1 TTGATGAA
38490606 TTGATGAA
1 TTGATGAA
38490614 TTGATGAA
1 TTGATGAA
38490622 TT
1 TT
38490624 AAGATTATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.35, C:0.00, G:0.23, T:0.42
Consensus pattern (8 bp):
TTGATGAA
Found at i:38500592 original size:19 final size:19
Alignment explanation
Indices: 38500568--38500605 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
38500558 TAAGCGCGAT
38500568 GGGGAAAGTCACAAGGTGC
1 GGGGAAAGTCACAAGGTGC
*
38500587 GGGGAAAGTCGCAAGGTGC
1 GGGGAAAGTCACAAGGTGC
38500606 ATGTGAGGGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.29, C:0.16, G:0.45, T:0.11
Consensus pattern (19 bp):
GGGGAAAGTCACAAGGTGC
Found at i:38500941 original size:16 final size:15
Alignment explanation
Indices: 38500916--38500949 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
38500906 AAAGTTGATA
*
38500916 ATAATTAATATATATT
1 ATAATAAATATA-ATT
38500932 ATAATAAATATAATT
1 ATAATAAATATAATT
38500947 ATA
1 ATA
38500950 TACTAGCTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 6 0.35
16 11 0.65
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (15 bp):
ATAATAAATATAATT
Found at i:38516390 original size:25 final size:25
Alignment explanation
Indices: 38516271--38516396 Score: 117
Period size: 25 Copynumber: 5.0 Consensus size: 25
38516261 TCTTCTACAT
* * * *
38516271 GTATGGTCACACGATCTGTGAATCG
1 GTATGCTCTCACGAGCTGTGAATCA
* *
38516296 GTATGCTCTTACGAGCTGTAAATCA
1 GTATGCTCTCACGAGCTGTGAATCA
* * *
38516321 GTATGCTCTCATGATCTGTAAATCA
1 GTATGCTCTCACGAGCTGTGAATCA
* * * *
38516346 ATATGCTCTCGCGAACTGTGAATCG
1 GTATGCTCTCACGAGCTGTGAATCA
* *
38516371 GTATGCTCTTACGAGCTGTGAGTCA
1 GTATGCTCTCACGAGCTGTGAATCA
38516396 G
1 G
38516397 AACTTAACTA
Statistics
Matches: 80, Mismatches: 21, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
25 80 1.00
ACGTcount: A:0.25, C:0.21, G:0.24, T:0.31
Consensus pattern (25 bp):
GTATGCTCTCACGAGCTGTGAATCA
Found at i:38520717 original size:24 final size:24
Alignment explanation
Indices: 38520689--38520743 Score: 76
Period size: 23 Copynumber: 2.3 Consensus size: 24
38520679 AAAATCTACT
*
38520689 CTAAAAAGAAAAAAGAAAACTTAA-
1 CTAAAAA-AAAAAAGAAAACCTAAC
*
38520713 CTAAAAAAGAAAAGAAAACCTAAC
1 CTAAAAAAAAAAAGAAAACCTAAC
38520737 CTAAAAA
1 CTAAAAA
38520744 CTATAAGCCC
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
23 14 0.50
24 14 0.50
ACGTcount: A:0.69, C:0.13, G:0.07, T:0.11
Consensus pattern (24 bp):
CTAAAAAAAAAAAGAAAACCTAAC
Found at i:38523079 original size:19 final size:20
Alignment explanation
Indices: 38523037--38523081 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 20
38523027 CTCATAGTAT
*
38523037 CGATACTTAGCTTTGGGTAT
1 CGATACTTAGCTTTGGGTAC
* *
38523057 CGATACTT-TCTTTTGGTAC
1 CGATACTTAGCTTTGGGTAC
38523076 CGATAC
1 CGATAC
38523082 CATTTTAACA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
19 14 0.64
20 8 0.36
ACGTcount: A:0.20, C:0.20, G:0.20, T:0.40
Consensus pattern (20 bp):
CGATACTTAGCTTTGGGTAC
Found at i:38528845 original size:40 final size:40
Alignment explanation
Indices: 38528782--38528876 Score: 136
Period size: 40 Copynumber: 2.4 Consensus size: 40
38528772 GTAACAACCT
* * *
38528782 TTTTTAACCTTTTAATTGGATATCCATTTCGGATATATCC
1 TTTTCAACCTTTTCATTGGATATCCATTTCGGATATACCC
* * *
38528822 TTTTCAACATTTTCATTTGATATCTATTTCGGATATACCC
1 TTTTCAACCTTTTCATTGGATATCCATTTCGGATATACCC
38528862 TTTTCAACCTTTTCA
1 TTTTCAACCTTTTCA
38528877 AGAATTCAAA
Statistics
Matches: 48, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
40 48 1.00
ACGTcount: A:0.24, C:0.20, G:0.07, T:0.48
Consensus pattern (40 bp):
TTTTCAACCTTTTCATTGGATATCCATTTCGGATATACCC
Found at i:38532699 original size:69 final size:69
Alignment explanation
Indices: 38532588--38532725 Score: 276
Period size: 69 Copynumber: 2.0 Consensus size: 69
38532578 TTGCGATATT
38532588 AGATAAATTAGATTAGAAAATTTATATTAAAAACAATAACTCCAATTTGTCGGCTAAATAATAGA
1 AGATAAATTAGATTAGAAAATTTATATTAAAAACAATAACTCCAATTTGTCGGCTAAATAATAGA
38532653 ATAA
66 ATAA
38532657 AGATAAATTAGATTAGAAAATTTATATTAAAAACAATAACTCCAATTTGTCGGCTAAATAATAGA
1 AGATAAATTAGATTAGAAAATTTATATTAAAAACAATAACTCCAATTTGTCGGCTAAATAATAGA
38532722 ATAA
66 ATAA
38532726 TGGTAATTAC
Statistics
Matches: 69, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
69 69 1.00
ACGTcount: A:0.51, C:0.09, G:0.10, T:0.30
Consensus pattern (69 bp):
AGATAAATTAGATTAGAAAATTTATATTAAAAACAATAACTCCAATTTGTCGGCTAAATAATAGA
ATAA
Found at i:38532908 original size:10 final size:10
Alignment explanation
Indices: 38532895--38532936 Score: 50
Period size: 10 Copynumber: 4.1 Consensus size: 10
38532885 TAATTTAGCC
38532895 ATTTATTTTT
1 ATTTATTTTT
38532905 ATTTATTTTT
1 ATTTATTTTT
*
38532915 GTTT-TTTTT
1 ATTTATTTTT
38532924 AGTTTAATTTTT
1 A-TTT-ATTTTT
38532936 A
1 A
38532937 CATTCTAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
9 5 0.19
10 16 0.59
12 6 0.22
ACGTcount: A:0.19, C:0.00, G:0.05, T:0.76
Consensus pattern (10 bp):
ATTTATTTTT
Found at i:38538891 original size:42 final size:43
Alignment explanation
Indices: 38538806--38538910 Score: 108
Period size: 45 Copynumber: 2.4 Consensus size: 43
38538796 TTGCCCTATT
* *
38538806 TTATTTATTTATTTGTTTCTTATCTATTATTATTAGTTATATTATA
1 TTATTTATTTATTT-TTTATCATCTATTATTATTA-TTATATTA-A
*
38538852 TTATTTATTTATTTTTTATCATCTATTATT-TT-TCT-TATTAG
1 TTATTTATTTATTTTTTATCATCTATTATTATTAT-TATATTAA
38538893 TTATATTATTTTATTTTT
1 TTAT-TTA-TTTATTTTT
38538911 CTAATTCTAC
Statistics
Matches: 53, Mismatches: 3, Indels: 9
0.82 0.05 0.14
Matches are distributed among these distances:
41 4 0.08
42 9 0.17
43 10 0.19
44 2 0.04
45 14 0.26
46 14 0.26
ACGTcount: A:0.24, C:0.05, G:0.03, T:0.69
Consensus pattern (43 bp):
TTATTTATTTATTTTTTATCATCTATTATTATTATTATATTAA
Found at i:38538896 original size:26 final size:24
Alignment explanation
Indices: 38538835--38538912 Score: 68
Period size: 26 Copynumber: 3.0 Consensus size: 24
38538825 TTATCTATTA
*
38538835 TTATTAGTTATATTA-TATTATTTAT
1 TTATTAGTTATATTATTATT-TTT-C
**
38538860 TTATTTTTTATCATCTATTATTTTTC
1 TTATTAGTTAT-AT-TATTATTTTTC
38538886 TTATTAGTTATATTATTTTATTTTTC
1 TTATTAGTTATATTA--TTATTTTTC
38538912 T
1 T
38538913 AATTCTACTT
Statistics
Matches: 43, Mismatches: 5, Indels: 9
0.75 0.09 0.16
Matches are distributed among these distances:
24 2 0.05
25 11 0.26
26 21 0.49
27 5 0.12
28 4 0.09
ACGTcount: A:0.24, C:0.05, G:0.03, T:0.68
Consensus pattern (24 bp):
TTATTAGTTATATTATTATTTTTC
Found at i:38538897 original size:46 final size:46
Alignment explanation
Indices: 38538806--38538908 Score: 129
Period size: 46 Copynumber: 2.2 Consensus size: 46
38538796 TTGCCCTATT
* * *
38538806 TTATTTATTTATTTGTTTCTTATCTATTATTATTAGTTATATTATA
1 TTATTTATTTATTTGTTTATCATCTATTATTATTACTTATATTATA
*
38538852 TTATTTATTTATTT-TTTATCATCTATTATT-TTTCTTATTAGTTATA
1 TTATTTATTTATTTGTTTATCATCTATTATTATTACTTA-TA-TTATA
38538898 TTATTTTATTT
1 TTA-TTTATTT
38538909 TTCTAATTCT
Statistics
Matches: 50, Mismatches: 4, Indels: 5
0.85 0.07 0.08
Matches are distributed among these distances:
44 5 0.10
45 16 0.32
46 22 0.44
47 7 0.14
ACGTcount: A:0.24, C:0.05, G:0.03, T:0.68
Consensus pattern (46 bp):
TTATTTATTTATTTGTTTATCATCTATTATTATTACTTATATTATA
Found at i:38551884 original size:2 final size:2
Alignment explanation
Indices: 38551877--38551904 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
38551867 CATTCCGAAG
38551877 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
38551905 AGTATGCCAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:38552418 original size:27 final size:27
Alignment explanation
Indices: 38552387--38552564 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
38552377 TAAATTGTAC
38552387 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** *
38552414 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
38552440 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
*
38552468 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* *
38552496 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
38552523 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
38552550 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
38552565 GACTCAATAT
Statistics
Matches: 129, Mismatches: 19, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 23 0.18
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:38552501 original size:82 final size:81
Alignment explanation
Indices: 38552388--38552543 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
38552378 AAATTGTACA
* *
38552388 GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTG
1 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTA-GCACTAAGTG
38552452 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
** *
38552469 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTG
1 GCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTG
*
38552534 TGCGAGTTGA
65 TGCGAATTGA
38552544 TTATATAGCA
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 15 0.22
82 51 0.76
83 1 0.01
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.29
Consensus pattern (81 bp):
GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:38552555 original size:82 final size:81
Alignment explanation
Indices: 38552384--38552564 Score: 229
Period size: 82 Copynumber: 2.2 Consensus size: 81
38552374 GATTAAATTG
* *
38552384 TACAGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
38552449 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * ** *
38552465 TGCGGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TAGCACT
1 TACAGCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACT
* **
38552529 AAGTGTGCGAGTTGATTA
64 AAGTGTGCGAATTGACCA
* *
38552547 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
38552565 GACTCAATAT
Statistics
Matches: 84, Mismatches: 14, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
81 18 0.21
82 66 0.79
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
GTGTGCGAATTGACCA
Found at i:38563571 original size:20 final size:20
Alignment explanation
Indices: 38563543--38563588 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
38563533 ATAAACGTAT
*
38563543 ATATATTATATTTTCTATAC
1 ATATATTATAATTTCTATAC
* *
38563563 ATATTTTATAATTTCTATAT
1 ATATATTATAATTTCTATAC
38563583 ATATAT
1 ATATAT
38563589 ATTTCTTTAT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.37, C:0.07, G:0.00, T:0.57
Consensus pattern (20 bp):
ATATATTATAATTTCTATAC
Found at i:38563714 original size:10 final size:10
Alignment explanation
Indices: 38563694--38563729 Score: 56
Period size: 10 Copynumber: 3.6 Consensus size: 10
38563684 ACACGCCTTA
38563694 TATTCTTTATT
1 TATT-TTTATT
38563705 TATTTTTATT
1 TATTTTTATT
38563715 TATTTTTATT
1 TATTTTTATT
38563725 T-TTTT
1 TATTTT
38563730 ATAAGTTTGT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
9 4 0.16
10 17 0.68
11 4 0.16
ACGTcount: A:0.17, C:0.03, G:0.00, T:0.81
Consensus pattern (10 bp):
TATTTTTATT
Found at i:38576302 original size:44 final size:45
Alignment explanation
Indices: 38576247--38576367 Score: 131
Period size: 44 Copynumber: 2.8 Consensus size: 45
38576237 GAATAGGGCG
* *
38576247 AATCTTATCTCCCTAAAGTTGCAGTGGAGCATATTAAAGCCA-AT
1 AATCTTATCTCCCTAAAGTTGCAGTGGAGCAGATTAAAACCACAT
* * * ***
38576291 AATCCTATCTCCCTGAAGTTGAAGTGGATTGGATTAAAACCACAT
1 AATCTTATCTCCCTAAAGTTGCAGTGGAGCAGATTAAAACCACAT
* *
38576336 -ATCTTATCTCTCTAAAGTTGCAG-AGAGCAGAT
1 AATCTTATCTCCCTAAAGTTGCAGTGGAGCAGAT
38576368 CGCATCTAGT
Statistics
Matches: 60, Mismatches: 16, Indels: 3
0.76 0.20 0.04
Matches are distributed among these distances:
43 5 0.08
44 53 0.88
45 2 0.03
ACGTcount: A:0.33, C:0.20, G:0.17, T:0.30
Consensus pattern (45 bp):
AATCTTATCTCCCTAAAGTTGCAGTGGAGCAGATTAAAACCACAT
Found at i:38577623 original size:20 final size:20
Alignment explanation
Indices: 38577595--38577633 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
38577585 ATAAACGTAT
*
38577595 ATATATTATATTTTCTATAC
1 ATATATTATAATTTCTATAC
*
38577615 ATATTTTATAATTTCTATA
1 ATATATTATAATTTCTATA
38577634 TATACATATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.36, C:0.08, G:0.00, T:0.56
Consensus pattern (20 bp):
ATATATTATAATTTCTATAC
Found at i:38577636 original size:18 final size:18
Alignment explanation
Indices: 38577592--38577637 Score: 56
Period size: 20 Copynumber: 2.4 Consensus size: 18
38577582 TATATAAACG
*
38577592 TATATATATTATATTTTC
1 TATATATATTATAATTTC
*
38577610 TATACATATTTTATAATTTC
1 TAT--ATATATTATAATTTC
38577630 TATATATA
1 TATATATA
38577638 CATATTTTTC
Statistics
Matches: 23, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
18 7 0.30
20 16 0.70
ACGTcount: A:0.37, C:0.07, G:0.00, T:0.57
Consensus pattern (18 bp):
TATATATATTATAATTTC
Found at i:38577698 original size:7 final size:7
Alignment explanation
Indices: 38577671--38577709 Score: 51
Period size: 7 Copynumber: 5.1 Consensus size: 7
38577661 ATGCATTATA
38577671 TATATATT
1 TATA-ATT
38577679 TATAAATTT
1 TAT-AA-TT
38577688 TATAATT
1 TATAATT
38577695 TATAATT
1 TATAATT
38577702 TATAATT
1 TATAATT
38577709 T
1 T
38577710 TTTTATTTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
7 17 0.59
8 6 0.21
9 6 0.21
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (7 bp):
TATAATT
Found at i:38577922 original size:26 final size:25
Alignment explanation
Indices: 38577882--38577934 Score: 88
Period size: 26 Copynumber: 2.1 Consensus size: 25
38577872 TCGCATGTCA
38577882 TTGTTTTTTATTATTTATATTAATT
1 TTGTTTTTTATTATTTATATTAATT
*
38577907 TTGTTTATTTATTATTTATATTATTT
1 TTGTTT-TTTATTATTTATATTAATT
38577933 TT
1 TT
38577935 ATATCATTGT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
25 6 0.23
26 20 0.77
ACGTcount: A:0.23, C:0.00, G:0.04, T:0.74
Consensus pattern (25 bp):
TTGTTTTTTATTATTTATATTAATT
Found at i:38582266 original size:21 final size:23
Alignment explanation
Indices: 38582230--38582272 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
38582220 CCTGTCATCA
38582230 CTCAACCACCAATTAA-GCCACCC
1 CTCAACCA-CAATTAAGGCCACCC
38582253 CTCAACCA-AATTAAGGCCAC
1 CTCAACCACAATTAAGGCCAC
38582273 ATATATCCAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 6 0.32
22 5 0.26
23 8 0.42
ACGTcount: A:0.37, C:0.42, G:0.07, T:0.14
Consensus pattern (23 bp):
CTCAACCACAATTAAGGCCACCC
Found at i:38586618 original size:50 final size:50
Alignment explanation
Indices: 38586552--38586742 Score: 186
Period size: 50 Copynumber: 3.7 Consensus size: 50
38586542 TTTTGTACTA
* * **
38586552 CCAATGCCATATCCCAGATATGGTCTTACATGGGAGTTCTCATA-TCGGTG
1 CCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCA-ACTCGGTG
* * ** *
38586602 CCCATGCCATGTCCCAGACATGGCCTTACGGGGGACCTCTCAACTTGGTG
1 CCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCAACTCGGTG
* * *
38586652 CCAACGCCATGTCCCAGACATGGTCTTACATAGGACCTCTCATAACCTCAATGATG
1 CCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTC--AA-CTC---GGTG
* *
38586708 CCAATGCCATGTTCCAAACATGGTCTTACATGGGA
1 CCAATGCCATGTCCCAGACATGGTCTTACATGGGA
38586743 TCTCATCACC
Statistics
Matches: 113, Mismatches: 21, Indels: 8
0.80 0.15 0.06
Matches are distributed among these distances:
49 1 0.01
50 74 0.65
52 2 0.02
53 2 0.02
56 34 0.30
ACGTcount: A:0.25, C:0.29, G:0.21, T:0.25
Consensus pattern (50 bp):
CCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCAACTCGGTG
Found at i:38589963 original size:18 final size:18
Alignment explanation
Indices: 38589936--38589973 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
38589926 CAAATCAGAG
38589936 CAACAGCCTCAACAACCA
1 CAACAGCCTCAACAACCA
* *
38589954 CAACATCCTCCACAACCA
1 CAACAGCCTCAACAACCA
38589972 CA
1 CA
38589974 CCGAGAGGCA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.42, C:0.47, G:0.03, T:0.08
Consensus pattern (18 bp):
CAACAGCCTCAACAACCA
Found at i:38598024 original size:16 final size:17
Alignment explanation
Indices: 38597997--38598030 Score: 61
Period size: 16 Copynumber: 2.1 Consensus size: 17
38597987 AGATATAATA
38597997 AAATATTTTAAAAAAAT
1 AAATATTTTAAAAAAAT
38598014 AAATA-TTTAAAAAAAT
1 AAATATTTTAAAAAAAT
38598030 A
1 A
38598031 CATGAAAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 12 0.71
17 5 0.29
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (17 bp):
AAATATTTTAAAAAAAT
Found at i:38602333 original size:28 final size:28
Alignment explanation
Indices: 38602301--38602372 Score: 108
Period size: 28 Copynumber: 2.6 Consensus size: 28
38602291 TAATGAGATT
* *
38602301 AGCACTAAGTGTGCGAGTTTAATTGTAA
1 AGCACTAAGTGTGCGAGATTAATTATAA
* *
38602329 AGCACTAAGTGTGCGAGATTGATTATTA
1 AGCACTAAGTGTGCGAGATTAATTATAA
38602357 AGCACTAAGTGTGCGA
1 AGCACTAAGTGTGCGA
38602373 ACTTATTAAA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
28 40 1.00
ACGTcount: A:0.32, C:0.12, G:0.26, T:0.29
Consensus pattern (28 bp):
AGCACTAAGTGTGCGAGATTAATTATAA
Found at i:38602378 original size:24 final size:24
Alignment explanation
Indices: 38602301--38602381 Score: 63
Period size: 28 Copynumber: 3.0 Consensus size: 24
38602291 TAATGAGATT
* *
38602301 AGCACTAAGTGTGCGAGTTTAATTGTAA
1 AGCACTAAGTGTGCGA----AATTATTA
38602329 AGCACTAAGTGTGCGAGATTGATTATTA
1 AGCACTAAGTGTGCGA-A---ATTATTA
*
38602357 AGCACTAAGTGTGCGAACTTATTA
1 AGCACTAAGTGTGCGAAATTATTA
38602381 A
1 A
38602382 ATATTTTTGA
Statistics
Matches: 46, Mismatches: 4, Indels: 10
0.77 0.07 0.17
Matches are distributed among these distances:
24 7 0.15
25 1 0.02
27 1 0.02
28 37 0.80
ACGTcount: A:0.33, C:0.12, G:0.23, T:0.31
Consensus pattern (24 bp):
AGCACTAAGTGTGCGAAATTATTA
Found at i:38603173 original size:70 final size:70
Alignment explanation
Indices: 38603113--38603487 Score: 486
Period size: 70 Copynumber: 5.3 Consensus size: 70
38603103 TCGTTGTATT
38603113 TATGCTGCCTAAATTGTTGTATATATGCTGTCCAATTTTGATGTAAAAATGTTGCTCAATTTGGT
1 TATGCTGCCTAAATTGTTGTATATATGCTGTCCAATTTTGATGTAAAAATGTTGCTCAATTTGGT
38603178 ATATA
66 ATATA
* * *
38603183 AATTCTGCCTAAATTGTTGTATATATGCTTTCCAATTTTGATGTAAAAATGTTGCTCAATTTGGT
1 TATGCTGCCTAAATTGTTGTATATATGCTGTCCAATTTTGATGTAAAAATGTTGCTCAATTTGGT
38603248 ATATA
66 ATATA
* * * *
38603253 AATTCTGCCTAAATTGTTGTATATATGCTTTCCAATTTTGATGTAAAAATGTTGCTTAATTTGGT
1 TATGCTGCCTAAATTGTTGTATATATGCTGTCCAATTTTGATGTAAAAATGTTGCTCAATTTGGT
38603318 ATATA
66 ATATA
* * * * *
38603323 TATCCTGCCCAATTTGTTGTATATATGCTGTCCAATTTTTGGTGTAAAAATGCTGCTCAATTTTG
1 TATGCTGCCTAAATTGTTGTATATATGCTGTCCAA-TTTTGATGTAAAAATGTTGCTCAA-TTTG
* * *
38603388 TTGTGTA
64 GTATATA
* * * * *
38603395 TATGCTACCCAAATTGTTGTATATATGCTGTCCAAATTTTGGTGTGAAAATGTTG-TCTAGTTTG
1 TATGCTGCCTAAATTGTTGTATATATGCTGTCC-AATTTTGATGTAAAAATGTTGCTC-AATTTG
38603459 GTATATA
64 GTATATA
* *
38603466 AAT-CTGTCC-AAATTGATGTATA
1 TATGCTG-CCTAAATTGTTGTATA
38603488 AGGGCTGTCC
Statistics
Matches: 273, Mismatches: 27, Indels: 10
0.88 0.09 0.03
Matches are distributed among these distances:
70 180 0.66
71 35 0.13
72 56 0.21
73 2 0.01
ACGTcount: A:0.28, C:0.12, G:0.17, T:0.43
Consensus pattern (70 bp):
TATGCTGCCTAAATTGTTGTATATATGCTGTCCAATTTTGATGTAAAAATGTTGCTCAATTTGGT
ATATA
Found at i:38603363 original size:25 final size:24
Alignment explanation
Indices: 38603091--38603435 Score: 168
Period size: 23 Copynumber: 14.7 Consensus size: 24
38603081 TGATGCTTAA
* *
38603091 ATGCTGCCCAA-TTCGTTGTATTT
1 ATGCTGCCCAATTTTGTTGTATAT
* *
38603114 ATGCTGCCTAA-ATTGTTGTATAT
1 ATGCTGCCCAATTTTGTTGTATAT
* * * *
38603137 ATGCTGTCCAATTTTGATGTAAAA
1 ATGCTGCCCAATTTTGTTGTATAT
* * * * *
38603161 ATGTTGCTCAA-TTTGGTATATAA
1 ATGCTGCCCAATTTTGTTGTATAT
* * *
38603184 ATTCTGCCTAA-ATTGTTGTATAT
1 ATGCTGCCCAATTTTGTTGTATAT
** * * *
38603207 ATGCTTTCCAATTTTGATGTAAAA
1 ATGCTGCCCAATTTTGTTGTATAT
* * * * *
38603231 ATGTTGCTCAA-TTTGGTATATAA
1 ATGCTGCCCAATTTTGTTGTATAT
* * *
38603254 ATTCTGCCTAA-ATTGTTGTATAT
1 ATGCTGCCCAATTTTGTTGTATAT
** * * *
38603277 ATGCTTTCCAATTTTGATGTAAAA
1 ATGCTGCCCAATTTTGTTGTATAT
* ** * *
38603301 ATGTTGCTTAA-TTTGGTATATAT
1 ATGCTGCCCAATTTTGTTGTATAT
*
38603324 ATCCTGCCCAA-TTTGTTGTATAT
1 ATGCTGCCCAATTTTGTTGTATAT
* * * *
38603347 ATGCTGTCCAATTTTTGGTGTAAAA
1 ATGCTGCCCAA-TTTTGTTGTATAT
* *
38603372 ATGCTGCTCAATTTTGTTGTGTAT
1 ATGCTGCCCAATTTTGTTGTATAT
* *
38603396 ATGCTACCCAA-ATTGTTGTATAT
1 ATGCTGCCCAATTTTGTTGTATAT
*
38603419 ATGCTGTCCAAATTTTG
1 ATGCTG-CCCAATTTTG
38603436 GTGTGAAAAT
Statistics
Matches: 227, Mismatches: 88, Indels: 12
0.69 0.27 0.04
Matches are distributed among these distances:
23 139 0.61
24 67 0.30
25 21 0.09
ACGTcount: A:0.27, C:0.13, G:0.16, T:0.44
Consensus pattern (24 bp):
ATGCTGCCCAATTTTGTTGTATAT
Found at i:38609906 original size:28 final size:28
Alignment explanation
Indices: 38609874--38609945 Score: 108
Period size: 28 Copynumber: 2.6 Consensus size: 28
38609864 TAATGAGATT
* *
38609874 AGCACTAAGTGTGCGAGTTTAATTGTAA
1 AGCACTAAGTGTGCGAGATTAATTATAA
* *
38609902 AGCACTAAGTGTGCGAGATTGATTATTA
1 AGCACTAAGTGTGCGAGATTAATTATAA
38609930 AGCACTAAGTGTGCGA
1 AGCACTAAGTGTGCGA
38609946 ACTTATTAAA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
28 40 1.00
ACGTcount: A:0.32, C:0.12, G:0.26, T:0.29
Consensus pattern (28 bp):
AGCACTAAGTGTGCGAGATTAATTATAA
Found at i:38609951 original size:24 final size:24
Alignment explanation
Indices: 38609874--38609954 Score: 63
Period size: 28 Copynumber: 3.0 Consensus size: 24
38609864 TAATGAGATT
* *
38609874 AGCACTAAGTGTGCGAGTTTAATTGTAA
1 AGCACTAAGTGTGCGA----AATTATTA
38609902 AGCACTAAGTGTGCGAGATTGATTATTA
1 AGCACTAAGTGTGCGA-A---ATTATTA
*
38609930 AGCACTAAGTGTGCGAACTTATTA
1 AGCACTAAGTGTGCGAAATTATTA
38609954 A
1 A
38609955 ATATTTTTGA
Statistics
Matches: 46, Mismatches: 4, Indels: 10
0.77 0.07 0.17
Matches are distributed among these distances:
24 7 0.15
25 1 0.02
27 1 0.02
28 37 0.80
ACGTcount: A:0.33, C:0.12, G:0.23, T:0.31
Consensus pattern (24 bp):
AGCACTAAGTGTGCGAAATTATTA
Found at i:38610707 original size:23 final size:23
Alignment explanation
Indices: 38610676--38610788 Score: 88
Period size: 23 Copynumber: 4.8 Consensus size: 23
38610666 AATGCTATCC
*
38610676 AATTCGTTGTATTTATGCTGCCTA
1 AATT-GTTGTATATATGCTGCCTA
*
38610700 AATTGTTGTATATATGTTGTCC-A
1 AATTGTTGTATATATGCTG-CCTA
* * * * * *
38610723 ATTTTGATGTAAAAATGTTG-CTC
1 A-ATTGTTGTATATATGCTGCCTA
38610746 AATT-TTGTATATATATGCTGCCTA
1 AATTGTTG--TATATATGCTGCCTA
38610770 AATTGTTGTATATATGCTG
1 AATTGTTGTATATATGCTG
38610789 TCCAATCAGC
Statistics
Matches: 69, Mismatches: 13, Indels: 15
0.71 0.13 0.15
Matches are distributed among these distances:
21 2 0.03
22 3 0.04
23 35 0.51
24 26 0.38
25 3 0.04
ACGTcount: A:0.27, C:0.11, G:0.17, T:0.46
Consensus pattern (23 bp):
AATTGTTGTATATATGCTGCCTA
Found at i:38610983 original size:23 final size:24
Alignment explanation
Indices: 38610957--38611062 Score: 117
Period size: 23 Copynumber: 4.5 Consensus size: 24
38610947 TTGATATATA
38610957 TATATATGCTGCCCAA-TTTGTTG
1 TATATATGCTGCCCAATTTTGTTG
* ** *
38610980 TATATATGTTGTTCAATTTTTGGTG
1 TATATATGCTGCCCAA-TTTTGTTG
* *
38611005 TAAATATGCTGCTCAATTTTGTTG
1 TATATATGCTGCCCAATTTTGTTG
**
38611029 TATATATGCTGCCCAA-ACTGTTG
1 TATATATGCTGCCCAATTTTGTTG
38611052 TATATATGCTG
1 TATATATGCTG
38611063 TTCAAATTTT
Statistics
Matches: 69, Mismatches: 12, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
23 29 0.42
24 21 0.30
25 19 0.28
ACGTcount: A:0.24, C:0.13, G:0.18, T:0.45
Consensus pattern (24 bp):
TATATATGCTGCCCAATTTTGTTG
Found at i:38613482 original size:41 final size:41
Alignment explanation
Indices: 38613433--38613650 Score: 269
Period size: 41 Copynumber: 5.3 Consensus size: 41
38613423 TACCAATCAT
* *
38613433 ATAGCCGAAGCTATTATAATTCTGCACACTAAGTGCCTTAC
1 ATAGCCAAAGCTATTATAATTCCGCACACTAAGTGCCTTAC
* * * * *
38613474 CTAGCCGAAGCTATTATAATTCCACAAACTAAGTGCCTTCC
1 ATAGCCAAAGCTATTATAATTCCGCACACTAAGTGCCTTAC
38613515 ATAGCCAAAGCTATTATAATTCCGCACACTAAGTGCCTTAC
1 ATAGCCAAAGCTATTATAATTCCGCACACTAAGTGCCTTAC
** * *
38613556 ATAGCCAAAGCTATTATAATTATGCACACTAAGTGCCATAT
1 ATAGCCAAAGCTATTATAATTCCGCACACTAAGTGCCTTAC
** *
38613597 ATAGCCAAAGCTATTCCAAAT-CGCACACTAAGTGCCATTA-
1 ATAGCCAAAGCTATTATAATTCCGCACACTAAGTGCC-TTAC
* *
38613637 ATAACCGAAGCTAT
1 ATAGCCAAAGCTAT
38613651 CTCGAATTTC
Statistics
Matches: 155, Mismatches: 21, Indels: 3
0.87 0.12 0.02
Matches are distributed among these distances:
40 26 0.17
41 129 0.83
ACGTcount: A:0.35, C:0.25, G:0.13, T:0.27
Consensus pattern (41 bp):
ATAGCCAAAGCTATTATAATTCCGCACACTAAGTGCCTTAC
Found at i:38620881 original size:41 final size:41
Alignment explanation
Indices: 38620815--38621010 Score: 229
Period size: 41 Copynumber: 4.8 Consensus size: 41
38620805 CAATGTGTCA
* *
38620815 CACACTAATTGCCAATCATATAGCCGAAGCTATTATAATTCTG
1 CACACTAAGTGCC-TTC-TATAGCCGAAGCTATTATAATTCTG
38620858 CACACTAAGTGCCTTCTATAGCCGAAGCTATTATAATT-TCG
1 CACACTAAGTGCCTTCTATAGCCGAAGCTATTATAATTCT-G
38620899 CACACTAAGTGCCTTAC-ATAGCCGAAGCTATTATAATTCTG
1 CACACTAAGTGCCTT-CTATAGCCGAAGCTATTATAATTCTG
* * * ** *
38620940 CACACTAAGTGCCATATATAGCCAAAGCTATTCCAAATC-G
1 CACACTAAGTGCCTTCTATAGCCGAAGCTATTATAATTCTG
* *
38620980 CACACTAAGTGCCATT-AATAACCGAAGCTAT
1 CACACTAAGTGCC-TTCTATAGCCGAAGCTAT
38621011 CTCGACTTTC
Statistics
Matches: 136, Mismatches: 12, Indels: 13
0.84 0.07 0.08
Matches are distributed among these distances:
40 27 0.20
41 93 0.68
42 4 0.03
43 12 0.09
ACGTcount: A:0.34, C:0.25, G:0.13, T:0.28
Consensus pattern (41 bp):
CACACTAAGTGCCTTCTATAGCCGAAGCTATTATAATTCTG
Found at i:38620971 original size:82 final size:81
Alignment explanation
Indices: 38620815--38621010 Score: 268
Period size: 82 Copynumber: 2.4 Consensus size: 81
38620805 CAATGTGTCA
* * * *
38620815 CACACTAATTGCCAATCATATAGCCGAAGCTATTATAATTCTGCACACTAAGTGCCTTCTATAGC
1 CACACTAAGTGCC-ATTA-ATAGCCGAAGCTATTATAATTCTGCACACTAAGTGCCATATATAGC
* * *
38620880 CGAAGCTATTATAATTTCG
64 CAAAGCTATTACAA-ATCG
38620899 CACACTAAGTGCC-TTACATAGCCGAAGCTATTATAATTCTGCACACTAAGTGCCATATATAGCC
1 CACACTAAGTGCCATTA-ATAGCCGAAGCTATTATAATTCTGCACACTAAGTGCCATATATAGCC
*
38620963 AAAGCTATTCCAAATCG
65 AAAGCTATTACAAATCG
*
38620980 CACACTAAGTGCCATTAATAACCGAAGCTAT
1 CACACTAAGTGCCATTAATAGCCGAAGCTAT
38621011 CTCGACTTTC
Statistics
Matches: 101, Mismatches: 10, Indels: 5
0.87 0.09 0.04
Matches are distributed among these distances:
81 29 0.29
82 60 0.59
84 12 0.12
ACGTcount: A:0.34, C:0.25, G:0.13, T:0.28
Consensus pattern (81 bp):
CACACTAAGTGCCATTAATAGCCGAAGCTATTATAATTCTGCACACTAAGTGCCATATATAGCCA
AAGCTATTACAAATCG
Found at i:38625937 original size:25 final size:25
Alignment explanation
Indices: 38625891--38625938 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
38625881 CGTTATATGA
*
38625891 CTCTTTGTGAACTTCTCAATTAAAG
1 CTCTTTGTGAACTTCCCAATTAAAG
*
38625916 CTCTTTGTGATA-TTCCCGATTAA
1 CTCTTTGTGA-ACTTCCCAATTAA
38625939 TGGCTCTCCG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
25 19 0.95
26 1 0.05
ACGTcount: A:0.25, C:0.21, G:0.12, T:0.42
Consensus pattern (25 bp):
CTCTTTGTGAACTTCCCAATTAAAG
Found at i:38637755 original size:103 final size:105
Alignment explanation
Indices: 38637567--38637762 Score: 297
Period size: 103 Copynumber: 1.9 Consensus size: 105
38637557 CCTTGTGTCG
* * * *
38637567 TTTTCATTTTAGATGTAGGTTTCACACGGTCTGAGACACGGCCGTGTGTACCAAGTCAGTGACTT
1 TTTTCATTTTAGATGCAGGTTTCACACGATCTGAGACACGGACGTGTGTACCAAGTCAATGACTT
38637632 ACACGGTCTGGCACACGGCTTGCGACACAGTCGTGTGCCA
66 ACACGGTCTGGCACACGGCTTGCGACACAGTCGTGTGCCA
* * *
38637672 TTTTTATTTTAGGTGCAGGTTTCACACGATCTGAGACAC-GAC-TGTGTACCAAGTCAATGAGTT
1 TTTTCATTTTAGATGCAGGTTTCACACGATCTGAGACACGGACGTGTGTACCAAGTCAATGACTT
* *
38637735 ACACGGTCTGGCATATGGCTTGCGACAC
66 ACACGGTCTGGCACACGGCTTGCGACAC
38637763 GACCGTGTGA
Statistics
Matches: 82, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
103 45 0.55
104 2 0.02
105 35 0.43
ACGTcount: A:0.22, C:0.23, G:0.26, T:0.29
Consensus pattern (105 bp):
TTTTCATTTTAGATGCAGGTTTCACACGATCTGAGACACGGACGTGTGTACCAAGTCAATGACTT
ACACGGTCTGGCACACGGCTTGCGACACAGTCGTGTGCCA
Found at i:38643711 original size:13 final size:12
Alignment explanation
Indices: 38643667--38643718 Score: 52
Period size: 13 Copynumber: 4.2 Consensus size: 12
38643657 ATCAACAACC
*
38643667 AAAAA-AAAAAG
1 AAAAAGAAAAAA
38643678 AAAAAGAAAACAA
1 AAAAAGAAAA-AA
* *
38643691 CAAGAGAAAATAA
1 AAAAAGAAAA-AA
38643704 AAAAAGAAAAAA
1 AAAAAGAAAAAA
38643716 AAA
1 AAA
38643719 TCACCTTTTT
Statistics
Matches: 33, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
11 5 0.15
12 9 0.27
13 19 0.58
ACGTcount: A:0.85, C:0.04, G:0.10, T:0.02
Consensus pattern (12 bp):
AAAAAGAAAAAA
Found at i:38647062 original size:23 final size:22
Alignment explanation
Indices: 38647015--38647063 Score: 55
Period size: 23 Copynumber: 2.2 Consensus size: 22
38647005 TGTAAAATGT
* * *
38647015 AAAA-TTTAGTTTTTAATTTTT
1 AAAATTTTAGTTTTAAATTATA
38647036 AAAATTTTAAGTTTTAAATTATA
1 AAAATTTT-AGTTTTAAATTATA
38647059 AAAAT
1 AAAAT
38647064 ATATTTTCAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
21 4 0.17
22 3 0.13
23 16 0.70
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51
Consensus pattern (22 bp):
AAAATTTTAGTTTTAAATTATA
Found at i:38648636 original size:40 final size:42
Alignment explanation
Indices: 38648592--38648671 Score: 128
Period size: 43 Copynumber: 1.9 Consensus size: 42
38648582 TAAGAAAGTA
*
38648592 ATTGATAGATCTT-CCCAA-AAAAAAGAATAATAAATTTGTT
1 ATTGATAGATCTTCCCCAAGAAAAAAGAAAAATAAATTTGTT
38648632 ATTGATAGATCTTCCCCCAAGAAAAAAGAAAAATAAATTT
1 ATTGATAGATCTT-CCCCAAGAAAAAAGAAAAATAAATTT
38648672 ATATATACTA
Statistics
Matches: 36, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
40 13 0.36
42 5 0.14
43 18 0.50
ACGTcount: A:0.49, C:0.12, G:0.10, T:0.29
Consensus pattern (42 bp):
ATTGATAGATCTTCCCCAAGAAAAAAGAAAAATAAATTTGTT
Found at i:38658763 original size:23 final size:22
Alignment explanation
Indices: 38658720--38658763 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 22
38658710 TTCTAAGTCG
38658720 ATATTCAATTCAATTCCACACCT
1 ATATTCAATTCAATT-CACACCT
38658743 ATATTCATTATTCAATT-ACAC
1 ATATTCA--ATTCAATTCACAC
38658764 TTAGTCATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
23 11 0.58
25 8 0.42
ACGTcount: A:0.36, C:0.25, G:0.00, T:0.39
Consensus pattern (22 bp):
ATATTCAATTCAATTCACACCT
Found at i:38658873 original size:45 final size:45
Alignment explanation
Indices: 38658809--38658896 Score: 158
Period size: 45 Copynumber: 2.0 Consensus size: 45
38658799 ACAGATACTC
* *
38658809 GGTGGATTCAGCACATAGCAACCACCTTATTAATCAATGATGTCT
1 GGTGGAATCAGCACATAGCAACCACCTTACTAATCAATGATGTCT
38658854 GGTGGAATCAGCACATAGCAACCACCTTACTAATCAATGATGT
1 GGTGGAATCAGCACATAGCAACCACCTTACTAATCAATGATGT
38658897 TCGGTTCATA
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
45 41 1.00
ACGTcount: A:0.33, C:0.23, G:0.18, T:0.26
Consensus pattern (45 bp):
GGTGGAATCAGCACATAGCAACCACCTTACTAATCAATGATGTCT
Found at i:38659113 original size:101 final size:100
Alignment explanation
Indices: 38658906--38659089 Score: 253
Period size: 101 Copynumber: 1.8 Consensus size: 100
38658896 TTCGGTTCAT
* * *
38658906 ATAGTAGCCTGCACATAGTACTACACATGTAACAATTACCATCTGATATATGTAGTAGCCTGCAC
1 ATAGTAGCCTGCACATAGTACTACACATGCAAC-ATTACCATCCGATACATGTAGTAGCCTGCAC
* *
38658971 ATAGTACTACACACGTGATCGAAACTATCCAGTACGC
65 ATAGTACTACACACATGATCCAAACTATCCAGTAC-C
* * * *
38659008 ATAGTAGCCTGCATATAGTACTACACATGCGAC-TTATCATTCCGGTACATGTAGTAGCCTGCAC
1 ATAGTAGCCTGCACATAGTACTACACATGCAACATTACCA-TCCGATACATGTAGTAGCCTGCAC
38659072 ATAGTACTACACACATGA
65 ATAGTACTACACACATGA
38659090 CCATCACTTT
Statistics
Matches: 73, Mismatches: 8, Indels: 3
0.87 0.10 0.04
Matches are distributed among these distances:
100 5 0.07
101 38 0.52
102 30 0.41
ACGTcount: A:0.33, C:0.24, G:0.16, T:0.26
Consensus pattern (100 bp):
ATAGTAGCCTGCACATAGTACTACACATGCAACATTACCATCCGATACATGTAGTAGCCTGCACA
TAGTACTACACACATGATCCAAACTATCCAGTACC
Found at i:38660457 original size:36 final size:36
Alignment explanation
Indices: 38660406--38660479 Score: 121
Period size: 36 Copynumber: 2.1 Consensus size: 36
38660396 AGCAAGCTCT
* *
38660406 ATTCAATTCAGTAGCCTTTTGGATCTATTCTGACTG
1 ATTCAATTCAGTAGCCTTTCGGATCTATTCTAACTG
*
38660442 ATTCAATTCATTAGCCTTTCGGATCTATTCTAACTG
1 ATTCAATTCAGTAGCCTTTCGGATCTATTCTAACTG
38660478 AT
1 AT
38660480 GTGCTCCTCC
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.24, C:0.20, G:0.14, T:0.42
Consensus pattern (36 bp):
ATTCAATTCAGTAGCCTTTCGGATCTATTCTAACTG
Found at i:38662961 original size:68 final size:69
Alignment explanation
Indices: 38662830--38663289 Score: 260
Period size: 69 Copynumber: 6.8 Consensus size: 69
38662820 TTTCGTCTGC
* * * ** *
38662830 AAACCTTAATATGACAACTAGGAGTTTTGCTCTTACTAACTGTTTTGGAGGTTGTGATTCTTCAC
1 AAACCTTAATATGACAATTGGGAGCTTTGCTCTCGCTAACTATTTTGGAGGTTGTGATTCTTCAC
38662895 CTGT
66 CTGT
* * * * * *
38662899 AAACCTTATTATGATAGTTGGGAGCTTTGCTCTCGTTAA-TTTTTTGGAGGTTGTGGTTCTTCAC
1 AAACCTTAATATGACAATTGGGAGCTTTGCTCTCGCTAACTATTTTGGAGGTTGTGATTCTTCAC
38662963 CTGT
66 CTGT
* * * * * * **
38662967 GAACCTTAATATTACAATTGGGAGCTTTGTTGTCGCTAACTATTTTGGAGGTTG-CAGCTCTTTG
1 AAACCTTAATATGACAATTGGGAGCTTTGCTCTCGCTAACTATTTTGGAGGTTGTGA-TTCTTCA
*
38663031 CCTGCG
65 CCTG-T
* ** * * * * * * ** * *
38663037 AAA-TTTAATATGACAGCTGAGAGGTTTACTCTCACTAATTTTTTTGGAGGTT-ACAGCTCTTCG
1 AAACCTTAATATGACAATTGGGAGCTTTGCTCTCGCTAACTATTTTGGAGGTTGTGA-TTCTTCA
* *
38663100 CTTGC
65 CCTGT
* * * * * **
38663105 GAACATTAATATGACAGTTGGGAGCTTTGCTCTCACTAACTGTTTTGGAGGTTGT-AGTTCTTTT
1 AAACCTTAATATGACAATTGGGAGCTTTGCTCTCGCTAACTATTTTGGAGGTTGTGA-TTCTTCA
**
38663169 CCTAC
65 CCTGT
* * * ** * * *
38663174 GAACTTTAATATGACAACTGGGAGCTTTATTCTCGCTAACTGTTTTAGAGG-T-T-A--C-T-GC
1 AAACCTTAATATGACAATTGGGAGCTTTGCTCTCGCTAACTATTTTGGAGGTTGTGATTCTTCAC
38663232 CTGT
66 CTGT
* * * * * **
38663236 GAGCCTTGATATGACAGTTGTGAGCTTTGCTCTCGCTAACTGCTTTGGAGGTTG
1 AAACCTTAATATGACAATTGGGAGCTTTGCTCTCGCTAACTATTTTGGAGGTTG
38663290 CAACTCTTTA
Statistics
Matches: 307, Mismatches: 76, Indels: 21
0.76 0.19 0.05
Matches are distributed among these distances:
62 44 0.14
63 2 0.01
64 1 0.00
67 2 0.01
68 61 0.20
69 195 0.64
70 2 0.01
ACGTcount: A:0.22, C:0.17, G:0.22, T:0.39
Consensus pattern (69 bp):
AAACCTTAATATGACAATTGGGAGCTTTGCTCTCGCTAACTATTTTGGAGGTTGTGATTCTTCAC
CTGT
Found at i:38663133 original size:138 final size:131
Alignment explanation
Indices: 38662962--38663298 Score: 377
Period size: 138 Copynumber: 2.5 Consensus size: 131
38662952 TGGTTCTTCA
* * * * *
38662962 CCTGTGAACCTTAATATTACAATTGGGAGCTTTGTTGTCGCTAACTATTTTGGAGGTTGCAGCTC
1 CCTGTGAACCTTAATATGACAGTTGGGAGCTTTGCTCTCGCTAACTGTTTTGGAGGTTGCAGCTC
* * * * * *
38663027 TTTGCCTGCGAAATTTAATATGACAGCTGAGAGGTTTACTCTCACTAATTTTTTTGGAGGTTACA
66 TTTGCCTACGAAATTTAATATGACAACTGAGAGCTTTACTCTCACTAACTGTTTTAGAGGTTACA
38663092 G
131 G
* *
38663093 CTCTTCGCTTGCGAACATTAATATGACAGTTGGGAGCTTTGCTCTCACTAACTGTTTTGGAGGTT
1 C-C-T-G--T--GAACCTTAATATGACAGTTGGGAGCTTTGCTCTCGCTAACTGTTTTGGAGGTT
* * * * * * *
38663158 GTAGTTCTTTTCCTACGAACTTTAATATGACAACTGGGAGCTTTATTCTCGCTAACTGTTTTAGA
59 GCAGCTCTTTGCCTACGAAATTTAATATGACAACTGAGAGCTTTACTCTCACTAACTGTTTTAGA
*
38663223 GGTTACTG
124 GGTTACAG
* * * * *
38663231 CCTGTGAGCCTTGATATGACAGTTGTGAGCTTTGCTCTCGCTAACTGCTTTGGAGGTTGCAACTC
1 CCTGTGAACCTTAATATGACAGTTGGGAGCTTTGCTCTCGCTAACTGTTTTGGAGGTTGCAGCTC
38663296 TTT
66 TTT
38663299 ACCTTTAAAC
Statistics
Matches: 169, Mismatches: 30, Indels: 14
0.79 0.14 0.07
Matches are distributed among these distances:
131 55 0.33
132 1 0.01
133 2 0.01
134 1 0.01
135 1 0.01
136 2 0.01
137 1 0.01
138 106 0.63
ACGTcount: A:0.21, C:0.19, G:0.22, T:0.38
Consensus pattern (131 bp):
CCTGTGAACCTTAATATGACAGTTGGGAGCTTTGCTCTCGCTAACTGTTTTGGAGGTTGCAGCTC
TTTGCCTACGAAATTTAATATGACAACTGAGAGCTTTACTCTCACTAACTGTTTTAGAGGTTACA
G
Found at i:38679447 original size:262 final size:262
Alignment explanation
Indices: 38678988--38679459 Score: 591
Period size: 262 Copynumber: 1.8 Consensus size: 262
38678978 AAATAAGAAC
* * * * * * *
38678988 ATATCCCCAAAACTAAGATGGGAATTTTAAAGTCAAATTGTACAATTCTGAAACTTTAAATTTAG
1 ATATCCACAAAACTAAGATGGGAACTTTAAAGTCAAATTGCACAATTCTAAAAATTAAAATTCAG
* * *
38679053 GAGAAAATGAAAAAGTATGACATTAGCTTTCTCATAGATTTTATGACTACAAAGAGCTAAAGTTA
66 GAGAAAATGAAAAAGTATAACATTAGCTTTCTCATAGAATTTATGACTACAAAGAGCAAAAGTTA
*
38679118 TGCTACAAAATTTTCATCAGCCAATAATCATGCAACCCATATAACCAGAAACCGAGACTACATCT
131 TGCTACAAAATTTTCATCAACCAATAATCATGCAACCCATATAACCAGAAACCGAGACTACATCT
*
38679183 AGTCAGTAAAACTCTGATGTCCAAGAAACACACTGCTCAAAACCTGGACATTTTAAAATAACAAA
196 AGTCAGGAAAACTCTGATGTCCAAGAAACACACTGCTCAAAACCTGGACATTTTAAAATAACAAA
38679248 AT
261 AT
*
38679250 ATATCCACAAAACTAAGATGGGAACTTTAAAGTCAATTTGCACAATTCTAAAAATTCAAACATTC
1 ATATCCACAAAACTAAGATGGGAACTTTAAAGTCAAATTGCACAATTCTAAAAATT-AAA-ATTC
* * *
38679315 A-GAGAAAATGAAGAAGTATAACGTTAGCTTTCTGGCA-A-AATTTATG-TTAGCAGAA-AGTCA
64 AGGAGAAAATGAAAAAGTATAACATTAGCTTTCT--CATAGAATTTATGACTA-CA-AAGAG-CA
* * * * * * * *
38679375 AAATTTATGCTGCAAATTTTTCATCAACCGATAATTATGCCACCTATATAACCAGAAA-C-TGAC
124 AAAGTTATGCTACAAAATTTTCATCAACCAATAATCATGCAACCCATATAACCAGAAACCGAGAC
*
38679438 T-CTATCTAGTTAGGAAAACTCT
189 TAC-ATCTAGTCAGGAAAACTCT
38679460 CTAGTCCCAA
Statistics
Matches: 177, Mismatches: 25, Indels: 16
0.81 0.11 0.07
Matches are distributed among these distances:
261 1 0.01
262 73 0.41
263 43 0.24
264 58 0.33
265 2 0.01
ACGTcount: A:0.42, C:0.18, G:0.13, T:0.28
Consensus pattern (262 bp):
ATATCCACAAAACTAAGATGGGAACTTTAAAGTCAAATTGCACAATTCTAAAAATTAAAATTCAG
GAGAAAATGAAAAAGTATAACATTAGCTTTCTCATAGAATTTATGACTACAAAGAGCAAAAGTTA
TGCTACAAAATTTTCATCAACCAATAATCATGCAACCCATATAACCAGAAACCGAGACTACATCT
AGTCAGGAAAACTCTGATGTCCAAGAAACACACTGCTCAAAACCTGGACATTTTAAAATAACAAA
AT
Found at i:38684177 original size:26 final size:27
Alignment explanation
Indices: 38684132--38684200 Score: 77
Period size: 27 Copynumber: 2.6 Consensus size: 27
38684122 TGAATAAAAT
* **
38684132 TATAAAAATATAAAAGATATATATGTG
1 TATAAAATTATAAAAGATATATACATG
*
38684159 TATAAAATTATGAAA-ATATATACATG
1 TATAAAATTATAAAAGATATATACATG
*
38684185 TATACAAATTTTAAAA
1 TATA-AAATTATAAAA
38684201 TTATTATACA
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
26 13 0.37
27 22 0.63
ACGTcount: A:0.55, C:0.03, G:0.07, T:0.35
Consensus pattern (27 bp):
TATAAAATTATAAAAGATATATACATG
Done.