Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr03 135709677
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: 135709677
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 350 characters in sequence are not A, C, G, or T
File 133 of 438
Found at i:39526302 original size:30 final size:30
Alignment explanation
Indices: 39526267--39526324 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 30
39526257 TAGGCATTTC
*
39526267 CACACGGGTGAT-CCACACGCCCGTGTGTGA
1 CACACGGGT-ATACCACACGCCCATGTGTGA
*
39526297 CACACGGGTATACCACACTCCCATGTGT
1 CACACGGGTATACCACACGCCCATGTGT
39526325 CATGACCATG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 2 0.08
30 23 0.92
ACGTcount: A:0.22, C:0.34, G:0.24, T:0.19
Consensus pattern (30 bp):
CACACGGGTATACCACACGCCCATGTGTGA
Found at i:39536971 original size:28 final size:28
Alignment explanation
Indices: 39536930--39537006 Score: 84
Period size: 28 Copynumber: 2.8 Consensus size: 28
39536920 CGTTGCATCT
* * *
39536930 TCAATGTCTTGCACACTAGGTGT-CATAC
1 TCAATATCTCGCACACTAAGT-TCCATAC
* *
39536958 TCAATATCTCGCACACCAAGTTCCATTC
1 TCAATATCTCGCACACTAAGTTCCATAC
*
39536986 TCAATATTTCGCACACTAAGT
1 TCAATATCTCGCACACTAAGT
39537007 GCCACACATA
Statistics
Matches: 41, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
27 1 0.02
28 40 0.98
ACGTcount: A:0.29, C:0.29, G:0.12, T:0.31
Consensus pattern (28 bp):
TCAATATCTCGCACACTAAGTTCCATAC
Found at i:39542621 original size:23 final size:25
Alignment explanation
Indices: 39542565--39542621 Score: 59
Period size: 23 Copynumber: 2.4 Consensus size: 25
39542555 TCAATTATAT
*
39542565 TAATTTTATT-TAATATTAAAATAA
1 TAATATTATTATAATATTAAAATAA
**
39542589 T-ATAAAATTATAAT-TTAAAA-AA
1 TAATATTATTATAATATTAAAATAA
39542611 TAATATTATTA
1 TAATATTATTA
39542622 ATTTCAGGTT
Statistics
Matches: 26, Mismatches: 5, Indels: 5
0.72 0.14 0.14
Matches are distributed among these distances:
22 3 0.12
23 18 0.69
24 5 0.19
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (25 bp):
TAATATTATTATAATATTAAAATAA
Found at i:39544397 original size:19 final size:19
Alignment explanation
Indices: 39544362--39544421 Score: 77
Period size: 18 Copynumber: 3.2 Consensus size: 19
39544352 GTGTTGATAT
39544362 TGAGATGGGAAAT-GAATA
1 TGAGATGGGAAATGGAATA
39544380 TGAGATGGGAAATGGAATA
1 TGAGATGGGAAATGGAATA
* * *
39544399 TGAAATGATGAAATGAAATA
1 TGAGATG-GGAAATGGAATA
39544419 TGA
1 TGA
39544422 ATATTGAAAT
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
18 13 0.35
19 11 0.30
20 13 0.35
ACGTcount: A:0.47, C:0.00, G:0.30, T:0.23
Consensus pattern (19 bp):
TGAGATGGGAAATGGAATA
Found at i:39544431 original size:19 final size:19
Alignment explanation
Indices: 39544370--39544434 Score: 62
Period size: 19 Copynumber: 3.4 Consensus size: 19
39544360 ATTGAGATGG
* **
39544370 GAAATG-AATATGAGATGG
1 GAAATGAAATATGAAATAT
*
39544388 GAAATGGAATATGAAATGAT
1 GAAATGAAATATGAAAT-AT
39544408 GAAATGAAATATG-AATATT
1 GAAATGAAATATGAAATA-T
39544427 GAAATGAA
1 GAAATGAA
39544435 TTCATGTACT
Statistics
Matches: 40, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
18 7 0.17
19 21 0.52
20 12 0.30
ACGTcount: A:0.51, C:0.00, G:0.25, T:0.25
Consensus pattern (19 bp):
GAAATGAAATATGAAATAT
Found at i:39550117 original size:31 final size:27
Alignment explanation
Indices: 39550059--39550112 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
39550049 AGTTTCCACG
39550059 TAAAATCTGTATGTTCTATTTTTCTTT
1 TAAAATCTGTATGTTCTATTTTTCTTT
39550086 TAAAATCTGTATGTTCTATTTTTCTTT
1 TAAAATCTGTATGTTCTATTTTTCTTT
39550113 CTTTTCTTTG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.22, C:0.11, G:0.07, T:0.59
Consensus pattern (27 bp):
TAAAATCTGTATGTTCTATTTTTCTTT
Found at i:39566567 original size:29 final size:28
Alignment explanation
Indices: 39566535--39566637 Score: 116
Period size: 29 Copynumber: 3.6 Consensus size: 28
39566525 GTGACGAGAT
* *
39566535 TGGCACTGAGTGTGCGAGCTTGTAATGTA
1 TGGCACTAAGTGTGCGAGCTTG-AATATA
* *
39566564 TGGCACTAAGTGTGCGAGTTTGGACTATA
1 TGGCACTAAGTGTGCGAGCTT-GAATATA
* * *
39566593 TGGCACTATGTGTGCGGGCTTGAATCACA
1 TGGCACTAAGTGTGCGAGCTTGAAT-ATA
39566622 TGGCACTAAGTGTGCG
1 TGGCACTAAGTGTGCG
39566638 TGATTGAGTA
Statistics
Matches: 62, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
28 3 0.05
29 58 0.94
30 1 0.02
ACGTcount: A:0.21, C:0.17, G:0.33, T:0.29
Consensus pattern (28 bp):
TGGCACTAAGTGTGCGAGCTTGAATATA
Found at i:39573157 original size:17 final size:19
Alignment explanation
Indices: 39573115--39573160 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
39573105 ATGAAATTTT
*
39573115 AATTAGTATTATGAGATAA
1 AATTATTATTATGAGATAA
*
39573134 AATTATTATTATTAGA-AA
1 AATTATTATTATGAGATAA
39573152 AA-TATTATT
1 AATTATTATT
39573161 GTATGTATGT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
17 7 0.28
18 4 0.16
19 14 0.56
ACGTcount: A:0.48, C:0.00, G:0.09, T:0.43
Consensus pattern (19 bp):
AATTATTATTATGAGATAA
Found at i:39573271 original size:15 final size:15
Alignment explanation
Indices: 39573253--39573281 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
39573243 ATATTTATAA
39573253 AATTATTATTATTAT
1 AATTATTATTATTAT
39573268 AATTATTATTATTA
1 AATTATTATTATTA
39573282 GATAGGAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (15 bp):
AATTATTATTATTAT
Found at i:39575412 original size:40 final size:40
Alignment explanation
Indices: 39575346--39575496 Score: 155
Period size: 40 Copynumber: 3.8 Consensus size: 40
39575336 AAATTGAATG
* * *
39575346 ATATCCGGGCTAAG-CCCGAAGACAATTATGCTGGAAATT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
* * ***
39575385 ATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGCT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
* *
39575425 ACATCCGGGCTAAGACCCGAAGGC-ATTCGTGC-GAGTCATT
1 ATATCCGGGCTAAGACCCGAAGGCAATT-GTGCTG-GTAATT
* *
39575465 CTATCCGGGCTAAGACCCGAAGGCATTTGTGC
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGC
39575497 ACATGGTTAT
Statistics
Matches: 91, Mismatches: 17, Indels: 7
0.79 0.15 0.06
Matches are distributed among these distances:
39 16 0.18
40 73 0.80
41 2 0.02
ACGTcount: A:0.26, C:0.24, G:0.27, T:0.23
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
Found at i:39575510 original size:40 final size:40
Alignment explanation
Indices: 39575383--39575512 Score: 154
Period size: 40 Copynumber: 3.2 Consensus size: 40
39575373 ATGCTGGAAA
* * *
39575383 TTATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGG
1 TTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTGG
* * * **
39575423 CTACATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTCA
1 TTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTGG
* *
39575463 TTCTATCCGGGCTAAGACCCGAAGGCATTTGTGC-ACATGG
1 TTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGA-GTGG
39575503 TTATATCCGG
1 TTATATCCGG
39575513 TTATATTCCG
Statistics
Matches: 73, Mismatches: 16, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
39 1 0.01
40 72 0.99
ACGTcount: A:0.24, C:0.24, G:0.28, T:0.25
Consensus pattern (40 bp):
TTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTGG
Found at i:39583413 original size:40 final size:40
Alignment explanation
Indices: 39583347--39583497 Score: 155
Period size: 40 Copynumber: 3.8 Consensus size: 40
39583337 AAATTGAATG
* * *
39583347 ATATCCGGGCTAAG-CCCGAAGACAATTATGCTGGAAATT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
* * ***
39583386 ATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGCT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
* *
39583426 ACATCCGGGCTAAGACCCGAAGGC-ATTCGTGC-GAGTCATT
1 ATATCCGGGCTAAGACCCGAAGGCAATT-GTGCTG-GTAATT
* *
39583466 CTATCCGGGCTAAGACCCGAAGGCATTTGTGC
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGC
39583498 ACATGGTTAT
Statistics
Matches: 91, Mismatches: 17, Indels: 7
0.79 0.15 0.06
Matches are distributed among these distances:
39 16 0.18
40 73 0.80
41 2 0.02
ACGTcount: A:0.26, C:0.24, G:0.27, T:0.23
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
Found at i:39583511 original size:40 final size:40
Alignment explanation
Indices: 39583384--39583513 Score: 154
Period size: 40 Copynumber: 3.2 Consensus size: 40
39583374 ATGCTGGAAA
* * *
39583384 TTATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGG
1 TTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTGG
* * * **
39583424 CTACATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTCA
1 TTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTGG
* *
39583464 TTCTATCCGGGCTAAGACCCGAAGGCATTTGTGC-ACATGG
1 TTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGA-GTGG
39583504 TTATATCCGG
1 TTATATCCGG
39583514 TTATATTCCG
Statistics
Matches: 73, Mismatches: 16, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
39 1 0.01
40 72 0.99
ACGTcount: A:0.24, C:0.24, G:0.28, T:0.25
Consensus pattern (40 bp):
TTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTGG
Found at i:39591302 original size:3 final size:3
Alignment explanation
Indices: 39591294--39591340 Score: 94
Period size: 3 Copynumber: 15.7 Consensus size: 3
39591284 GATTTGTTCT
39591294 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
39591341 TCATTACATA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:39595890 original size:46 final size:46
Alignment explanation
Indices: 39595741--39595911 Score: 202
Period size: 46 Copynumber: 3.7 Consensus size: 46
39595731 TCATTTGTGT
* * *
39595741 GCTAGTGTAAGACATGTCTGGGACATGCATCAGCCAC-ATTATGAGA
1 GCTAGTGTAAGACATGTCTGGAACATGCATCAGCCTCGA-GATGAGA
* * * * * *
39595787 GCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCATTGAGACGAGA
1 GCTAGTGTAAGA-CATGTCTGGAACAT-GCATCAGCCTCGAGATGAGA
*
39595835 GCTAATGTAAGACATGTCTGGAACATGCATCAGCCTCGAGATGTA-A
1 GCTAGTGTAAGACATGTCTGGAACATGCATCAGCCTCGAGATG-AGA
39595881 GCTAGTGTAAGACATGTCTGGAACATGCATC
1 GCTAGTGTAAGACATGTCTGGAACATGCATC
39595912 GGCTACAAAA
Statistics
Matches: 106, Mismatches: 15, Indels: 8
0.82 0.12 0.06
Matches are distributed among these distances:
46 55 0.52
47 28 0.26
48 22 0.21
49 1 0.01
ACGTcount: A:0.30, C:0.20, G:0.27, T:0.23
Consensus pattern (46 bp):
GCTAGTGTAAGACATGTCTGGAACATGCATCAGCCTCGAGATGAGA
Found at i:39596076 original size:31 final size:31
Alignment explanation
Indices: 39596033--39596093 Score: 113
Period size: 31 Copynumber: 2.0 Consensus size: 31
39596023 CCAGTGTAAG
*
39596033 ACCATGTTTGGGACATGGCATCGGCATTATT
1 ACCATGTCTGGGACATGGCATCGGCATTATT
39596064 ACCATGTCTGGGACATGGCATCGGCATTAT
1 ACCATGTCTGGGACATGGCATCGGCATTAT
39596094 ACCTTGTGTT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.23, C:0.21, G:0.26, T:0.30
Consensus pattern (31 bp):
ACCATGTCTGGGACATGGCATCGGCATTATT
Found at i:39599416 original size:27 final size:27
Alignment explanation
Indices: 39599375--39599428 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
39599365 TGTCATGTGA
* *
39599375 AATTGAATGGCAAATTATTGTTACATG
1 AATTGAATGGCAAATTACTATTACATG
**
39599402 AATTGAATGTTAAATTACTATTACATG
1 AATTGAATGGCAAATTACTATTACATG
39599429 GGTTGTAGGA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.39, C:0.07, G:0.15, T:0.39
Consensus pattern (27 bp):
AATTGAATGGCAAATTACTATTACATG
Found at i:39599753 original size:49 final size:49
Alignment explanation
Indices: 39599674--39599855 Score: 256
Period size: 49 Copynumber: 3.7 Consensus size: 49
39599664 TCTATTGTGA
*
39599674 GGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATT
1 GGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATT
* * ** *
39599723 GGTCGCATGTGTAGTACTAAGTGCAGGCTACTATGCATACCCGATAACTTT
1 GGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAA--TT
* * * *
39599774 GATCACGTGTGTAGTACTAAGAGCAGGCTACTACGTGTACCGAATAATT
1 GGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATT
39599823 GGTCACATGTGTAGTACTAAGTGCAGGCTACTA
1 GGTCACATGTGTAGTACTAAGTGCAGGCTACTA
39599856 TGCATACCAG
Statistics
Matches: 113, Mismatches: 18, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
49 73 0.65
51 40 0.35
ACGTcount: A:0.27, C:0.19, G:0.26, T:0.28
Consensus pattern (49 bp):
GGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATT
Found at i:39599849 original size:100 final size:100
Alignment explanation
Indices: 39599676--39599868 Score: 350
Period size: 100 Copynumber: 1.9 Consensus size: 100
39599666 TATTGTGAGG
* * *
39599676 TCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATTGGTCGCATGTGTAGTACT
1 TCACGTGTGTAGTACTAAGAGCAGGCTACTACGTGTACCGAATAATTGGTCACATGTGTAGTACT
*
39599741 AAGTGCAGGCTACTATGCATACCCGATAACTTTGA
66 AAGTGCAGGCTACTATGCATACCAGATAACTTTGA
39599776 TCACGTGTGTAGTACTAAGAGCAGGCTACTACGTGTACCGAATAATTGGTCACATGTGTAGTACT
1 TCACGTGTGTAGTACTAAGAGCAGGCTACTACGTGTACCGAATAATTGGTCACATGTGTAGTACT
39599841 AAGTGCAGGCTACTATGCATACCAGATA
66 AAGTGCAGGCTACTATGCATACCAGATA
39599869 GCCTTGTCTA
Statistics
Matches: 89, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
100 89 1.00
ACGTcount: A:0.28, C:0.20, G:0.24, T:0.28
Consensus pattern (100 bp):
TCACGTGTGTAGTACTAAGAGCAGGCTACTACGTGTACCGAATAATTGGTCACATGTGTAGTACT
AAGTGCAGGCTACTATGCATACCAGATAACTTTGA
Found at i:39618110 original size:47 final size:47
Alignment explanation
Indices: 39618047--39618435 Score: 616
Period size: 47 Copynumber: 8.3 Consensus size: 47
39618037 CCCTTCGGGA
* *
39618047 CTTATCACATTTATACACTTTCACATCCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
* *
39618094 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTAGGT
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
*
39618141 CTTATCTCATATATACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
* * * * *
39618188 CTTATCACATATATACACTTTCACATTCATTACGTTGGTCACTCGAC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
* * *
39618235 CCTATCACATATATACACTTTCACATTCATCACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
* * *
39618282 CCTATCACATATATATACTTTCACATTCATCACATTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
* *
39618329 CTTATCACGTATATATACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
39618376 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
39618423 CTTATCACATATA
1 CTTATCACATATA
39618436 CATATCTTGT
Statistics
Matches: 318, Mismatches: 24, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
47 318 1.00
ACGTcount: A:0.27, C:0.30, G:0.09, T:0.34
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
Found at i:39618383 original size:22 final size:22
Alignment explanation
Indices: 39618357--39618432 Score: 64
Period size: 22 Copynumber: 3.3 Consensus size: 22
39618347 TTTCACATTC
39618357 ATCACATTGGCCATTCGGCCTT
1 ATCACATTGGCCATTCGGCCTT
** * * *
39618379 ATCACATATATACACTTTC-ACATT
1 ATCACAT-T-GGC-CATTCGGCCTT
39618403 CATCACATTGGCCATTCGGCCTT
1 -ATCACATTGGCCATTCGGCCTT
39618426 ATCACAT
1 ATCACAT
39618433 ATACATATCT
Statistics
Matches: 39, Mismatches: 10, Indels: 10
0.66 0.17 0.17
Matches are distributed among these distances:
22 18 0.46
23 5 0.13
24 5 0.13
25 11 0.28
ACGTcount: A:0.26, C:0.30, G:0.11, T:0.33
Consensus pattern (22 bp):
ATCACATTGGCCATTCGGCCTT
Found at i:39621897 original size:20 final size:20
Alignment explanation
Indices: 39621872--39621918 Score: 78
Period size: 20 Copynumber: 2.4 Consensus size: 20
39621862 ATTTTGATAT
39621872 ACATGAT-TGATATGATATGC
1 ACATGATATG-TATGATATGC
39621892 ACATGATATGTATGATATGC
1 ACATGATATGTATGATATGC
39621912 ACATGAT
1 ACATGAT
39621919 GTATTCATAA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
20 24 0.92
21 2 0.08
ACGTcount: A:0.36, C:0.11, G:0.19, T:0.34
Consensus pattern (20 bp):
ACATGATATGTATGATATGC
Found at i:39621997 original size:26 final size:27
Alignment explanation
Indices: 39621968--39622040 Score: 132
Period size: 27 Copynumber: 2.8 Consensus size: 27
39621958 GAGGAAGTAC
39621968 AAAAGGGCTTATGCCCCAGTTTATTGA
1 AAAAGGGCTTATGCCCCAGTTTATTGA
39621995 AAAAGGGCTTATGCCCCAGTTTATTG-
1 AAAAGGGCTTATGCCCCAGTTTATTGA
39622021 AAAAGGGCTT-TGCCCCAGTT
1 AAAAGGGCTTATGCCCCAGTT
39622041 ATTAAAGAGG
Statistics
Matches: 46, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
25 10 0.22
26 10 0.22
27 26 0.57
ACGTcount: A:0.27, C:0.21, G:0.23, T:0.29
Consensus pattern (27 bp):
AAAAGGGCTTATGCCCCAGTTTATTGA
Found at i:39629747 original size:6 final size:6
Alignment explanation
Indices: 39629724--39629905 Score: 303
Period size: 6 Copynumber: 30.5 Consensus size: 6
39629714 TTAAAATAAA
* *
39629724 TTTTA- TTTCAT TTCTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT
1 TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT
* *
39629771 TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAA TTTTAA
1 TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT
39629819 TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT
1 TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT
* *
39629867 TTTTAT TTTTAT TTTTAT TTCTAT TTTCAT TTTTAT TTT
1 TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTT
39629906 CCCTCATCTT
Statistics
Matches: 166, Mismatches: 10, Indels: 1
0.94 0.06 0.01
Matches are distributed among these distances:
5 4 0.02
6 162 0.98
ACGTcount: A:0.18, C:0.02, G:0.00, T:0.80
Consensus pattern (6 bp):
TTTTAT
Found at i:39629900 original size:1 final size:1
Alignment explanation
Indices: 39629740--39629882 Score: 61
Period size: 1 Copynumber: 143.0 Consensus size: 1
39629730 TTCATTTCTA
* * * * * * * * * *
39629740 TTTTTATTTTTATTTTTATTTTTATTTTTATTTTTATTTTTATTTTTATTTTTATTTTTATTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
* ** ** * * * * * * * *
39629805 ATTTTTAATTTTAATTTTATTTTTATTTTTATTTTTATTTTTATTTTTATTTTTATTTTTATTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
* *
39629870 TATTTTTATTTTT
1 TTTTTTTTTTTTT
39629883 ATTTCTATTT
Statistics
Matches: 96, Mismatches: 46, Indels: 0
0.68 0.32 0.00
Matches are distributed among these distances:
1 96 1.00
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (1 bp):
T
Found at i:39631075 original size:6 final size:6
Alignment explanation
Indices: 39631069--39631289 Score: 388
Period size: 6 Copynumber: 36.8 Consensus size: 6
39631059 TTTTGCATAT
* * * * *
39631069 CTGTAT CTGTAT CTGTAT CTGTAT CTGTAT CTGTAC CTGTAC CTGTAC
1 CTGTAC CTGTAC CTGTAC CTGTAC CTGTAC CTGTAC CTGTAC CTGTAC
39631117 CTGTAC CTGTAC CTGTAC CTGTAC CTGTAC CTGTAC CTGTAC CTGTAC
1 CTGTAC CTGTAC CTGTAC CTGTAC CTGTAC CTGTAC CTGTAC CTGTAC
39631165 CTGTAC CTGTAC CTGTAC CTGTAC CTGTAC CTGTAC CTGTAC CTGTAC
1 CTGTAC CTGTAC CTGTAC CTGTAC CTGTAC CTGTAC CTGTAC CTGTAC
39631213 CTGTAC CTGTAC CTGTAC CTGTAC CTGTAC CTGTAC CTGTAC CTGTAC
1 CTGTAC CTGTAC CTGTAC CTGTAC CTGTAC CTGTAC CTGTAC CTGTAC
*
39631261 CTGTAC CTATAC CTGTAC CTGTAC CTGTA
1 CTGTAC CTGTAC CTGTAC CTGTAC CTGTA
39631290 TCTATATCTG
Statistics
Matches: 212, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
6 212 1.00
ACGTcount: A:0.17, C:0.31, G:0.16, T:0.36
Consensus pattern (6 bp):
CTGTAC
Found at i:39635707 original size:15 final size:15
Alignment explanation
Indices: 39635684--39635718 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
39635674 TTATGCATCA
39635684 TATTACTGTATCTGT
1 TATTACTGTATCTGT
*
39635699 TATTTCTGTATCTGT
1 TATTACTGTATCTGT
*
39635714 GATTA
1 TATTA
39635719 GGGGGTCTTG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.20, C:0.11, G:0.14, T:0.54
Consensus pattern (15 bp):
TATTACTGTATCTGT
Found at i:39635953 original size:6 final size:6
Alignment explanation
Indices: 39635942--39636312 Score: 591
Period size: 6 Copynumber: 61.8 Consensus size: 6
39635932 GTATCTGCGC
* *
39635942 CTGTAT CTGTAT TTGTAT CTGTAT CTGTTT CTGTAT CTGTAT CTGTAT
1 CTGTAT CTGTAT CTGTAT CTGTAT CTGTAT CTGTAT CTGTAT CTGTAT
39635990 CTGTAT CTGTAT CTGTAT CTGTAT CTGTAT CTGTAT CTGTAT CTGTAT
1 CTGTAT CTGTAT CTGTAT CTGTAT CTGTAT CTGTAT CTGTAT CTGTAT
* ** * *
39636038 CCGTAT CCATAT CTGTAT CTGTAT -TCGTAT CTGTAT CCGTAT CCGTAT
1 CTGTAT CTGTAT CTGTAT CTGTAT CT-GTAT CTGTAT CTGTAT CTGTAT
* * * * *
39636086 CCGTAT CTGTAT CCGTAT CTGTAT CTATAT CTGTAT CTATAT TTGTAT
1 CTGTAT CTGTAT CTGTAT CTGTAT CTGTAT CTGTAT CTGTAT CTGTAT
* * *
39636134 CTGTAT CTATAC CTGTAC CTGTAT CTGTAT CTGTAT CTGTAT CTGTAT
1 CTGTAT CTGTAT CTGTAT CTGTAT CTGTAT CTGTAT CTGTAT CTGTAT
39636182 CTGTAT CTGTAT CTGTAT CTGTAT CTGTAT CTGTAT CTGTAT CTGTAT
1 CTGTAT CTGTAT CTGTAT CTGTAT CTGTAT CTGTAT CTGTAT CTGTAT
39636230 CTGTAT CTGTAT CTGTAT CTGTAT CTGTAT CTGTAT CTGTAT CTGTAT
1 CTGTAT CTGTAT CTGTAT CTGTAT CTGTAT CTGTAT CTGTAT CTGTAT
39636278 CTGTAT CTGTAT CTGTAT CTGTAT CTGTAT CTGTA
1 CTGTAT CTGTAT CTGTAT CTGTAT CTGTAT CTGTA
39636313 AAGGACTTAA
Statistics
Matches: 341, Mismatches: 22, Indels: 4
0.93 0.06 0.01
Matches are distributed among these distances:
5 1 0.00
6 339 0.99
7 1 0.00
ACGTcount: A:0.18, C:0.18, G:0.16, T:0.49
Consensus pattern (6 bp):
CTGTAT
Found at i:39638409 original size:10 final size:10
Alignment explanation
Indices: 39638390--39638431 Score: 50
Period size: 10 Copynumber: 4.1 Consensus size: 10
39638380 TCCTCAATTC
39638390 ATCA-ACCAA
1 ATCATACCAA
39638399 ATCATACCAA
1 ATCATACCAA
*
39638409 ATCTAAACCAAA
1 ATC-ATACC-AA
39638421 ATCATACCAA
1 ATCATACCAA
39638431 A
1 A
39638432 GTATATGTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
9 4 0.14
10 11 0.39
11 8 0.29
12 5 0.18
ACGTcount: A:0.55, C:0.29, G:0.00, T:0.17
Consensus pattern (10 bp):
ATCATACCAA
Found at i:39639211 original size:43 final size:42
Alignment explanation
Indices: 39639154--39639301 Score: 142
Period size: 42 Copynumber: 3.5 Consensus size: 42
39639144 AATGCCAACA
* * *
39639154 TCCCAGACGTGGTCTTACATGTAATCGAA-TATCGATGCCACTG
1 TCCCAGACGTGGTCTTACACGTAATC-AAGTA-CGATGCAAATG
* *
39639197 TCCCAGACAG-GGTCTTACACGAAATCAAGTACGATGGAAATG
1 TCCCAGAC-GTGGTCTTACACGTAATCAAGTACGATGCAAATG
* *
39639239 TCCCAGACGTGGTCTTACACGTAAATCATAAGT-CGATGCCAACG
1 TCCCAGACGTGGTCTTACACGT-AATC--AAGTACGATGCAAATG
39639283 TCCCTA-ACGTGGTCTTACA
1 TCCC-AGACGTGGTCTTACA
39639302 TGATAACACA
Statistics
Matches: 89, Mismatches: 9, Indels: 13
0.80 0.08 0.12
Matches are distributed among these distances:
41 1 0.01
42 29 0.33
43 28 0.31
44 26 0.29
45 5 0.06
ACGTcount: A:0.29, C:0.26, G:0.21, T:0.24
Consensus pattern (42 bp):
TCCCAGACGTGGTCTTACACGTAATCAAGTACGATGCAAATG
Found at i:39640798 original size:31 final size:31
Alignment explanation
Indices: 39640757--39640831 Score: 132
Period size: 31 Copynumber: 2.4 Consensus size: 31
39640747 CTCAAATGAT
*
39640757 TGCTCAATTAAGGACCAAACCTTTTCGAAAA
1 TGCTCGATTAAGGACCAAACCTTTTCGAAAA
*
39640788 TGCTTGATTAAGGACCAAACCTTTTCGAAAA
1 TGCTCGATTAAGGACCAAACCTTTTCGAAAA
39640819 TGCTCGATTAAGG
1 TGCTCGATTAAGG
39640832 GCTTTTCAAA
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 41 1.00
ACGTcount: A:0.35, C:0.20, G:0.17, T:0.28
Consensus pattern (31 bp):
TGCTCGATTAAGGACCAAACCTTTTCGAAAA
Found at i:39641815 original size:19 final size:19
Alignment explanation
Indices: 39641781--39641821 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
39641771 GCAAGGCAGT
* * *
39641781 AATAATAAATAGATAAATA
1 AATAATAAAAAAATAAAAA
39641800 AATAATAAAAAAATAAAAA
1 AATAATAAAAAAATAAAAA
39641819 AAT
1 AAT
39641822 CCATGAAAGG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.76, C:0.00, G:0.02, T:0.22
Consensus pattern (19 bp):
AATAATAAAAAAATAAAAA
Found at i:39643640 original size:44 final size:44
Alignment explanation
Indices: 39643570--39643875 Score: 161
Period size: 44 Copynumber: 6.7 Consensus size: 44
39643560 GATTCACAAC
* * *
39643570 TTGTAGCTTTAATCTGTTCCATTGCAACTTCAAGGAAATAAGAT
1 TTGTAGCTTAAATCTGCTCCACTGCAACTTCAAGGAAATAAGAT
* * * *
39643614 TTGTAGCTTAAATCTACTCCACTGCAACTTCAGGGAGATAATAT
1 TTGTAGCTTAAATCTGCTCCACTGCAACTTCAAGGAAATAAGAT
* * * * *
39643658 TTGTAACTTCAATCTGCTCCACTGCAAC-TCTAGGGAGATAAAACTTGTAAC
1 TTGTAGCTTAAATCTGCTCCACTGCAACTTC-AAGGA-A-ATAA---G--AT
* * * * * *
39643709 TTGTAGTTTTAATTTGTTCCACTACAACTTCAGGGAAATAAGAT
1 TTGTAGCTTAAATCTGCTCCACTGCAACTTCAAGGAAATAAGAT
* * * * *
39643753 TTATAGCTTCAATTTGCTCCACTGCAACTT-TAGAGAGATAAGAT
1 TTGTAGCTTAAATCTGCTCCACTGCAACTTCAAG-GAAATAAGAT
* * * * ** *
39643797 TCGCCA-CGATAAATTCAAT-CTAACCACTGCAACTTCAGGGGTATAGGAT
1 TTG-TAGC-TTAAA-TC--TGCT--CCACTGCAACTTCAAGGAAATAAGAT
*
39643846 TTGTAGCTTCAATCTGCTCCACTGCAACTT
1 TTGTAGCTTAAATCTGCTCCACTGCAACTT
39643876 TAGTAAGATA
Statistics
Matches: 197, Mismatches: 45, Indels: 40
0.70 0.16 0.14
Matches are distributed among these distances:
43 3 0.02
44 116 0.59
45 5 0.03
46 7 0.04
47 4 0.02
48 5 0.03
49 25 0.13
50 2 0.01
51 28 0.14
52 2 0.01
ACGTcount: A:0.31, C:0.21, G:0.16, T:0.33
Consensus pattern (44 bp):
TTGTAGCTTAAATCTGCTCCACTGCAACTTCAAGGAAATAAGAT
Found at i:39643713 original size:95 final size:94
Alignment explanation
Indices: 39643614--39643893 Score: 273
Period size: 95 Copynumber: 3.0 Consensus size: 94
39643604 GAAATAAGAT
* * *
39643614 TTGTAGCTTAAATCTACTCCACTGCAACTTCAGGGAGATAATATTTGTAACTTCAATCTGCTCCA
1 TTGTAGATTAAATCTA-TCCACTGCAACTTCAGGGAGATAAGATTTGTAGCTTCAATCTGCTCCA
* *
39643679 CTGCAACTCTAGGGAGATAAAACTT-GTAAC
65 CTGCAACTCTAGAGAGATAAAA-TTCGCAAC
* * * * * * * *
39643709 TTGTAGTTTTAATTTGTTCCACTACAACTTCAGGGAAATAAGATTTATAGCTTCAATTTGCTCCA
1 TTGTAGATTAAATCT-ATCCACTGCAACTTCAGGGAGATAAGATTTGTAGCTTCAATCTGCTCCA
* * *
39643774 CTGCAACTTTAGAGAGATAAGATTCGCCAC
65 CTGCAACTCTAGAGAGATAAAATTCGCAAC
* * * *
39643804 --GATAAATTCAATCTAACCACTGCAACTTCAGGG-GTATAGGATTTGTAGCTTCAATCTGCTCC
1 TTG-TAGATTAAATCTATCCACTGCAACTTCAGGGAG-ATAAGATTTGTAGCTTCAATCTGCTCC
* *
39643866 ACTGCAACTTTAGTA-AGATAAGATTCGC
64 ACTGCAACTCTAG-AGAGATAAAATTCGC
39643894 CATGATGACT
Statistics
Matches: 154, Mismatches: 26, Indels: 12
0.80 0.14 0.06
Matches are distributed among these distances:
93 67 0.44
94 11 0.07
95 76 0.49
ACGTcount: A:0.31, C:0.21, G:0.16, T:0.32
Consensus pattern (94 bp):
TTGTAGATTAAATCTATCCACTGCAACTTCAGGGAGATAAGATTTGTAGCTTCAATCTGCTCCAC
TGCAACTCTAGAGAGATAAAATTCGCAAC
Found at i:39643727 original size:139 final size:139
Alignment explanation
Indices: 39643493--39643793 Score: 363
Period size: 139 Copynumber: 2.2 Consensus size: 139
39643483 TCATTCTAAC
* ** ** * *
39643493 CCACTGCAACTTCAAAG-GTATAAGGTTTGTGGCTTCAATCTCCTCCACTGCTACTTTAAGGAGA
1 CCACTGCAACTTCAGAGAG-ATAATATTTGTAACTTCAATCTCCTCCACTGCAACTCTAAGGAGA
* * * *
39643557 TAAGATTCACAACTTGTAGCTTTAATCTGTTCCATTGCAACTTCAAGGAAATAAGATTTGTAGCT
65 TAAAATTCACAACTTGTAGCTTTAATCTGTTCCACTACAACTTCAAGGAAATAAGATTTATAGCT
39643622 TAAATCTACT
130 TAAATCTACT
* * *
39643632 CCACTGCAACTTCAGGGAGATAATATTTGTAACTTCAATCTGCTCCACTGCAACTCTAGGGAGAT
1 CCACTGCAACTTCAGAGAGATAATATTTGTAACTTCAATCTCCTCCACTGCAACTCTAAGGAGAT
** * * *
39643697 AAAACTT-GTAACTTGTAGTTTTAATTTGTTCCACTACAACTTCAGGGAAATAAGATTTATAGCT
66 AAAA-TTCACAACTTGTAGCTTTAATCTGTTCCACTACAACTTCAAGGAAATAAGATTTATAGCT
* * *
39643761 TCAATTTGCT
130 TAAATCTACT
*
39643771 CCACTGCAACTTTAGAGAGATAA
1 CCACTGCAACTTCAGAGAGATAA
39643794 GATTCGCCAC
Statistics
Matches: 136, Mismatches: 24, Indels: 4
0.83 0.15 0.02
Matches are distributed among these distances:
139 133 0.98
140 3 0.02
ACGTcount: A:0.31, C:0.20, G:0.16, T:0.33
Consensus pattern (139 bp):
CCACTGCAACTTCAGAGAGATAATATTTGTAACTTCAATCTCCTCCACTGCAACTCTAAGGAGAT
AAAATTCACAACTTGTAGCTTTAATCTGTTCCACTACAACTTCAAGGAAATAAGATTTATAGCTT
AAATCTACT
Found at i:39643856 original size:93 final size:93
Alignment explanation
Indices: 39643727--39643895 Score: 268
Period size: 93 Copynumber: 1.8 Consensus size: 93
39643717 TTAATTTGTT
*
39643727 CCACTACAACTTCAGGGAAATAAGATTTATAGCTTCAATTTGCTCCACTGCAACTTTAG-AGAGA
1 CCACTACAACTTCAGGGAAATAAGATTTATAGCTTCAATCTGCTCCACTGCAACTTTAGTA-AGA
39643791 TAAGATTCGCCACGATAAATTCAATCTAA
65 TAAGATTCGCCACGATAAATTCAATCTAA
* ** * *
39643820 CCACTGCAACTTCAGGGGTATAGGATTTGTAGCTTCAATCTGCTCCACTGCAACTTTAGTAAGAT
1 CCACTACAACTTCAGGGAAATAAGATTTATAGCTTCAATCTGCTCCACTGCAACTTTAGTAAGAT
39643885 AAGATTCGCCA
66 AAGATTCGCCA
39643896 TGATGACTTT
Statistics
Matches: 69, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
93 68 0.99
94 1 0.01
ACGTcount: A:0.33, C:0.22, G:0.17, T:0.28
Consensus pattern (93 bp):
CCACTACAACTTCAGGGAAATAAGATTTATAGCTTCAATCTGCTCCACTGCAACTTTAGTAAGAT
AAGATTCGCCACGATAAATTCAATCTAA
Found at i:39651295 original size:22 final size:23
Alignment explanation
Indices: 39651269--39651314 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
39651259 CAACCAAACC
39651269 AATTCA-ACATATTT-TCAAGATA
1 AATTCATACATATTTAT-AAGATA
*
39651291 AATTCATGCATATTTATAAGATA
1 AATTCATACATATTTATAAGATA
39651314 A
1 A
39651315 CGTCATCACA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 6 0.29
23 14 0.67
24 1 0.05
ACGTcount: A:0.46, C:0.11, G:0.07, T:0.37
Consensus pattern (23 bp):
AATTCATACATATTTATAAGATA
Found at i:39651320 original size:23 final size:23
Alignment explanation
Indices: 39651276--39651320 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
39651266 ACCAATTCAA
*
39651276 CATATTTTCAAGATAAATTCATG
1 CATATTTTCAAGATAAAGTCATG
*
39651299 CATATTTAT-AAGATAACGTCAT
1 CATATTT-TCAAGATAAAGTCAT
39651321 CACATACCCA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 18 0.95
24 1 0.05
ACGTcount: A:0.40, C:0.13, G:0.09, T:0.38
Consensus pattern (23 bp):
CATATTTTCAAGATAAAGTCATG
Found at i:39655518 original size:41 final size:41
Alignment explanation
Indices: 39655460--39655607 Score: 176
Period size: 41 Copynumber: 3.6 Consensus size: 41
39655450 AAGCTTGGTC
39655460 TCGAAGGGCTTTTGAGCCAGTGCTAATAACCGAACTTAGTT
1 TCGAAGGGCTTTTGAGCCAGTGCTAATAACCGAACTTAGTT
* * *
39655501 TCGAAGGGCTTTAGAGCCAGTG-TCATAACCGGACTTAGTT
1 TCGAAGGGCTTTTGAGCCAGTGCTAATAACCGAACTTAGTT
* * * * * *
39655541 CCGAAGGGCCTTCGAGCCAGTGGTCTAAT--CCGAGCTTGGTC
1 TCGAAGGGCTTTTGAGCCAGT-G-CTAATAACCGAACTTAGTT
39655582 TCGAAGGGCTTTTGAGCCAGTGCTAA
1 TCGAAGGGCTTTTGAGCCAGTGCTAA
39655608 GAATCGGGCT
Statistics
Matches: 90, Mismatches: 14, Indels: 8
0.80 0.12 0.07
Matches are distributed among these distances:
39 4 0.04
40 35 0.39
41 48 0.53
43 3 0.03
ACGTcount: A:0.23, C:0.22, G:0.28, T:0.26
Consensus pattern (41 bp):
TCGAAGGGCTTTTGAGCCAGTGCTAATAACCGAACTTAGTT
Found at i:39655629 original size:41 final size:41
Alignment explanation
Indices: 39655462--39655629 Score: 132
Period size: 41 Copynumber: 4.1 Consensus size: 41
39655452 GCTTGGTCTC
*
39655462 GAAGGGCTTTTGAGCCAGTGCTAATAACCGAACTTAGTTTC-
1 GAAGGGCTTTTGAGCCAGTGCTAATAACCGAACTT-GATTCT
* * * *
39655503 GAAGGGCTTTAGAGCCAGTG-TCATAACCGGACTT-AGTTCC
1 GAAGGGCTTTTGAGCCAGTGCTAATAACCGAACTTGA-TTCT
* * * *
39655543 GAAGGGCCTTCGAGCCAGTGGTCTAAT--CCGAGCTTG-GTCT
1 GAAGGGCTTTTGAGCCAGT-G-CTAATAACCGAACTTGATTCT
* * **
39655583 CGAAGGGCTTTTGAGCCAGTGCTAAGAATCGGGCTTGATTCT
1 -GAAGGGCTTTTGAGCCAGTGCTAATAACCGAACTTGATTCT
39655625 GAAGG
1 GAAGG
39655630 ATGTTTGTGC
Statistics
Matches: 100, Mismatches: 17, Indels: 20
0.73 0.12 0.15
Matches are distributed among these distances:
39 7 0.07
40 32 0.32
41 55 0.55
42 3 0.03
43 3 0.03
ACGTcount: A:0.23, C:0.21, G:0.30, T:0.26
Consensus pattern (41 bp):
GAAGGGCTTTTGAGCCAGTGCTAATAACCGAACTTGATTCT
Found at i:39659883 original size:40 final size:40
Alignment explanation
Indices: 39659785--39660002 Score: 284
Period size: 40 Copynumber: 5.5 Consensus size: 40
39659775 TGGATGATAA
*
39659785 CCGGGCTAAGTCCCGAAGGCATTT-TGCGCTAGTGACTAGT-T
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCG--AGTTACTA-TAT
* *
39659826 CTGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTATTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
39659866 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* *
39659906 CCGGGCTAAGTCCCGAAGGCATTGGTGTGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* *
39659946 CCGGGCTATGTCCCGAAGGCA-TTGAGCGAG-TAGCTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATAT
* *
39659985 CC-GGTTAAATCCCGAAGG
1 CCGGGCTAAGTCCCGAAGG
39660003 TACTTGGCTT
Statistics
Matches: 160, Mismatches: 14, Indels: 9
0.87 0.08 0.05
Matches are distributed among these distances:
38 15 0.09
39 15 0.09
40 103 0.64
41 23 0.14
42 4 0.03
ACGTcount: A:0.22, C:0.22, G:0.29, T:0.27
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
Found at i:39667282 original size:41 final size:41
Alignment explanation
Indices: 39667224--39667370 Score: 167
Period size: 41 Copynumber: 3.6 Consensus size: 41
39667214 AAGCTTGGTC
39667224 TCGAAGGGCTTTTGAGCCAGTGCTAATAACCGAACTTAGTT
1 TCGAAGGGCTTTTGAGCCAGTGCTAATAACCGAACTTAGTT
* * *
39667265 TCGAAGGGCTTTAGAGCCAGTG-TCATAACCGGACTTAGTT
1 TCGAAGGGCTTTTGAGCCAGTGCTAATAACCGAACTTAGTT
* * * * * *
39667305 CCGAAGGGCCTTCGAGCCAGTGGTCTAAT--CCGAGCTTGGTC
1 TCGAAGGGCTTTTGAGCCAGT-G-CTAATAACCGAACTTAGTT
39667346 TCGAAGGGCTTTTGAG-CAGTGCTAA
1 TCGAAGGGCTTTTGAGCCAGTGCTAA
39667371 GAATCGGGCT
Statistics
Matches: 89, Mismatches: 14, Indels: 9
0.79 0.12 0.08
Matches are distributed among these distances:
38 4 0.04
39 1 0.01
40 38 0.43
41 43 0.48
43 3 0.03
ACGTcount: A:0.23, C:0.22, G:0.29, T:0.27
Consensus pattern (41 bp):
TCGAAGGGCTTTTGAGCCAGTGCTAATAACCGAACTTAGTT
Found at i:39674492 original size:46 final size:46
Alignment explanation
Indices: 39674405--39674494 Score: 137
Period size: 46 Copynumber: 2.0 Consensus size: 46
39674395 AGAGTGAGTA
* *
39674405 TCATTGAGATAGCTCCGGTTATGTATTGGCACTTCATGTGCGAGAT
1 TCATTGAGATAGCTCCGGCTATGTATTGGCACTTCAGGTGCGAGAT
*
39674451 TCATTGAGATAGCTTCGGCTATGTATTGGCACTT-AGGGTGCGAG
1 TCATTGAGATAGCTCCGGCTATGTATTGGCACTTCA-GGTGCGAG
39674495 TTCTCAAGTA
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
45 1 0.03
46 39 0.98
ACGTcount: A:0.21, C:0.17, G:0.29, T:0.33
Consensus pattern (46 bp):
TCATTGAGATAGCTCCGGCTATGTATTGGCACTTCAGGTGCGAGAT
Found at i:39677576 original size:27 final size:27
Alignment explanation
Indices: 39677520--39677702 Score: 235
Period size: 27 Copynumber: 6.8 Consensus size: 27
39677510 TCGATTGTAG
* * *
39677520 AATTACC-ATTTACCCTCGATTTATAG
1 AATTACCGTTTTACCCTCGATTTACAA
* *
39677546 AATTACCGTTTCACCTTCGATTTACAA
1 AATTACCGTTTTACCCTCGATTTACAA
*
39677573 AATTACCGTTTTACCCTCGATTTATAA
1 AATTACCGTTTTACCCTCGATTTACAA
* *
39677600 AATTACCATTTTACCCTCGATTTACAG
1 AATTACCGTTTTACCCTCGATTTACAA
*
39677627 AATTACCGTTTTACCCTCTATTTACAA
1 AATTACCGTTTTACCCTCGATTTACAA
* *
39677654 AATTACCATTTTACCCTC-AGTTTAGAA
1 AATTACCGTTTTACCCTCGA-TTTACAA
*
39677681 AATTATCGTTTTACCCTCGATT
1 AATTACCGTTTTACCCTCGATT
39677703 GTGAAATTAC
Statistics
Matches: 136, Mismatches: 18, Indels: 5
0.86 0.11 0.03
Matches are distributed among these distances:
26 8 0.06
27 127 0.93
28 1 0.01
ACGTcount: A:0.30, C:0.24, G:0.07, T:0.39
Consensus pattern (27 bp):
AATTACCGTTTTACCCTCGATTTACAA
Found at i:39677633 original size:81 final size:81
Alignment explanation
Indices: 39677505--39677702 Score: 276
Period size: 81 Copynumber: 2.5 Consensus size: 81
39677495 ATTACTGAAA
* * * *
39677505 TACCCTCGA-TTGTAGAATTACCA-TTTACCCTCGATTTATAGAATTACCGTTTCACCTTCGATT
1 TACCCTCGATTTATAAAATTACCATTTTACCCTCGATTTACAGAATTACCGTTTCACCCTCGATT
*
39677568 TACAAAATTACCGTTT
66 TACAAAATTACCATTT
* *
39677584 TACCCTCGATTTATAAAATTACCATTTTACCCTCGATTTACAGAATTACCGTTTTACCCTCTATT
1 TACCCTCGATTTATAAAATTACCATTTTACCCTCGATTTACAGAATTACCGTTTCACCCTCGATT
39677649 TACAAAATTACCATTT
66 TACAAAATTACCATTT
* * *
39677665 TACCCTC-AGTTTAGAAAATTATCGTTTTACCCTCGATT
1 TACCCTCGA-TTTATAAAATTACCATTTTACCCTCGATT
39677703 GTGAAATTAC
Statistics
Matches: 106, Mismatches: 10, Indels: 4
0.88 0.08 0.03
Matches are distributed among these distances:
79 9 0.08
80 13 0.12
81 84 0.79
ACGTcount: A:0.29, C:0.24, G:0.08, T:0.39
Consensus pattern (81 bp):
TACCCTCGATTTATAAAATTACCATTTTACCCTCGATTTACAGAATTACCGTTTCACCCTCGATT
TACAAAATTACCATTT
Found at i:39677818 original size:54 final size:54
Alignment explanation
Indices: 39677734--39677884 Score: 157
Period size: 54 Copynumber: 2.8 Consensus size: 54
39677724 TATAGGATAG
* * *
39677734 AATTA-CAAAATACCCCTAGTTTGTAAAATTACCA-ACATACCC-CTAGTTTGTAA
1 AATTACCAAAATACCACTAGTTTGTAAAATTA-CAGAAATACCCTC-AATTTGTAA
* * *
39677787 AATTACCGAAATACCACTGGTTTGTGAAATTACAGAAATACCCTCAATTTGTAA
1 AATTACCAAAATACCACTAGTTTGTAAAATTACAGAAATACCCTCAATTTGTAA
* ** *
39677841 AATTACCAAAATACCCCT-GATTTACAAAATTATAGAAATACCCT
1 AATTACCAAAATACCACTAG-TTTGTAAAATTACAGAAATACCCT
39677885 TGACTTTCTA
Statistics
Matches: 82, Mismatches: 12, Indels: 7
0.81 0.12 0.07
Matches are distributed among these distances:
53 8 0.10
54 73 0.89
55 1 0.01
ACGTcount: A:0.41, C:0.21, G:0.09, T:0.29
Consensus pattern (54 bp):
AATTACCAAAATACCACTAGTTTGTAAAATTACAGAAATACCCTCAATTTGTAA
Found at i:39677863 original size:27 final size:26
Alignment explanation
Indices: 39677701--39677872 Score: 141
Period size: 27 Copynumber: 6.4 Consensus size: 26
39677691 TTACCCTCGA
* **
39677701 TTGTGAAATTACTGAAATACCCCTAT
1 TTGTAAAATTACCAAAATACCCCTAT
** *
39677727 AGGATAGAATTA-CAAAATACCCCTAGT
1 TTG-TAAAATTACCAAAATACCCCTA-T
*
39677754 TTGTAAAATTACCAACATACCCCTAGT
1 TTGTAAAATTACCAAAATACCCCTA-T
* * *
39677781 TTGTAAAATTACCGAAATACCACTGGT
1 TTGTAAAATTACCAAAATACCCCT-AT
* *
39677808 TTGTGAAATTA-CAGAAATACCCTCAAT
1 TTGTAAAATTACCA-AAATACCC-CTAT
39677835 TTGTAAAATTACCAAAATACCCCTGAT
1 TTGTAAAATTACCAAAATACCCCT-AT
**
39677862 TTACAAAATTA
1 TTGTAAAATTA
39677873 TAGAAATACC
Statistics
Matches: 115, Mismatches: 23, Indels: 15
0.75 0.15 0.10
Matches are distributed among these distances:
26 21 0.18
27 91 0.79
28 3 0.03
ACGTcount: A:0.40, C:0.20, G:0.10, T:0.30
Consensus pattern (26 bp):
TTGTAAAATTACCAAAATACCCCTAT
Found at i:39677870 original size:81 final size:80
Alignment explanation
Indices: 39677734--39677882 Score: 203
Period size: 81 Copynumber: 1.9 Consensus size: 80
39677724 TATAGGATAG
* * ** *
39677734 AATTACAAAATACCCCTAGTTTGTAAAATTACCAACATACCCCTAGTTTGTAAAATTACCGAAAT
1 AATTACAAAATACCCCTAATTTGTAAAATTACCAAAATACCCCTAGTTTACAAAATTACAGAAAT
39677799 ACCACTGGTTTGTGA
66 ACCACTGGTTTGTGA
*
39677814 AATTACAGAAATA-CCCTCAATTTGTAAAATTACCAAAATACCCCT-GATTTACAAAATTATAGA
1 AATTACA-AAATACCCCT-AATTTGTAAAATTACCAAAATACCCCTAG-TTTACAAAATTACAGA
39677877 AATACC
63 AATACC
39677883 CTTGACTTTC
Statistics
Matches: 60, Mismatches: 6, Indels: 5
0.85 0.08 0.07
Matches are distributed among these distances:
80 12 0.20
81 48 0.80
ACGTcount: A:0.42, C:0.21, G:0.09, T:0.29
Consensus pattern (80 bp):
AATTACAAAATACCCCTAATTTGTAAAATTACCAAAATACCCCTAGTTTACAAAATTACAGAAAT
ACCACTGGTTTGTGA
Found at i:39677879 original size:27 final size:27
Alignment explanation
Indices: 39677813--39677942 Score: 113
Period size: 27 Copynumber: 4.7 Consensus size: 27
39677803 CTGGTTTGTG
* ** **
39677813 AAATTACAGAAATACCCTCAATTTGTA
1 AAATTATAGAAATACCCTTGATTTACA
* *
39677840 AAATTACCA-AAATACCCCTGATTTACA
1 AAATTA-TAGAAATACCCTTGATTTACA
39677867 AAATTATAGAAATACCCTTGACTTT-CTAA
1 AAATTATAGAAATACCCTTGA-TTTAC--A
* *
39677896 AAATTATAGAAATACCATTGGTTTACA
1 AAATTATAGAAATACCCTTGATTTACA
39677923 AAATTACT-GAAATACCCTTG
1 AAATTA-TAGAAATACCCTTG
39677943 GTTTGTAGAT
Statistics
Matches: 86, Mismatches: 10, Indels: 14
0.78 0.09 0.13
Matches are distributed among these distances:
26 1 0.01
27 55 0.64
28 9 0.10
29 21 0.24
ACGTcount: A:0.43, C:0.18, G:0.08, T:0.31
Consensus pattern (27 bp):
AAATTATAGAAATACCCTTGATTTACA
Found at i:39677943 original size:27 final size:27
Alignment explanation
Indices: 39677785--39677946 Score: 98
Period size: 27 Copynumber: 5.9 Consensus size: 27
39677775 CCTAGTTTGT
* **
39677785 AAAATTACCGAAATACCAC-TGGTTTGT
1 AAAATTACTGAAATACC-CTTGGTTTAC
* * *** **
39677812 GAAATTACAGAAATACCCTCAATTTGT
1 AAAATTACTGAAATACCCTTGGTTTAC
** * *
39677839 AAAATTACCAAAATACCCCTGATTTAC
1 AAAATTACTGAAATACCCTTGGTTTAC
*
39677866 AAAATTA-TAGAAATACCCTTGACTTT-C
1 AAAATTACT-GAAATACCCTTG-GTTTAC
*
39677893 TAAAAATTA-TAGAAATACCATTGGTTTAC
1 --AAAATTACT-GAAATACCCTTGGTTTAC
39677922 AAAATTACTGAAATACCCTTGGTTT
1 AAAATTACTGAAATACCCTTGGTTT
39677947 GTAGATTTAC
Statistics
Matches: 108, Mismatches: 20, Indels: 14
0.76 0.14 0.10
Matches are distributed among these distances:
26 1 0.01
27 79 0.73
28 7 0.06
29 21 0.19
ACGTcount: A:0.41, C:0.18, G:0.10, T:0.31
Consensus pattern (27 bp):
AAAATTACTGAAATACCCTTGGTTTAC
Found at i:39678064 original size:27 final size:27
Alignment explanation
Indices: 39678002--39678064 Score: 74
Period size: 27 Copynumber: 2.3 Consensus size: 27
39677992 CCCTAATAGT
*
39678002 TAAAAAGACCGTAAAGCCCCTGTAGGG
1 TAAAATGACCGTAAAGCCCCTGTAGGG
* * *
39678029 TAAAGTGACCGTAATA-CCCTTGTATGG
1 TAAAATGACCGTAA-AGCCCCTGTAGGG
39678056 TAAAATGAC
1 TAAAATGAC
39678065 GAATATGCCC
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
27 29 0.97
28 1 0.03
ACGTcount: A:0.37, C:0.19, G:0.22, T:0.22
Consensus pattern (27 bp):
TAAAATGACCGTAAAGCCCCTGTAGGG
Found at i:39678911 original size:25 final size:25
Alignment explanation
Indices: 39678873--39678942 Score: 113
Period size: 25 Copynumber: 2.8 Consensus size: 25
39678863 AGGAAGTGCT
* *
39678873 AAAAGGGCTCTGCCCCAGTTTACCG
1 AAAAGGGCTTTGCCCCAGTTTACCA
*
39678898 AAAAGGGCTTTGCCCCAGTTTATCA
1 AAAAGGGCTTTGCCCCAGTTTACCA
39678923 AAAAGGGCTTTGCCCCAGTT
1 AAAAGGGCTTTGCCCCAGTT
39678943 ATTAAAAGAG
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 42 1.00
ACGTcount: A:0.26, C:0.27, G:0.23, T:0.24
Consensus pattern (25 bp):
AAAAGGGCTTTGCCCCAGTTTACCA
Found at i:39678955 original size:24 final size:24
Alignment explanation
Indices: 39678872--39678955 Score: 98
Period size: 25 Copynumber: 3.4 Consensus size: 24
39678862 GAGGAAGTGC
* *
39678872 TAAAAGGGCTCTGCCCCAGTTTACC
1 TAAAAGGGCTTTGCCCCAGTTTA-T
*
39678897 GAAAAGGGCTTTGCCCCAGTTTAT
1 TAAAAGGGCTTTGCCCCAGTTTAT
*
39678921 CAAAAAGGGCTTTGCCCCAG-TTAT
1 -TAAAAGGGCTTTGCCCCAGTTTAT
39678945 TAAAAGAGGCT
1 TAAAAG-GGCT
39678956 AGGCCTCTAG
Statistics
Matches: 52, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
23 5 0.10
24 8 0.15
25 39 0.75
ACGTcount: A:0.29, C:0.24, G:0.23, T:0.25
Consensus pattern (24 bp):
TAAAAGGGCTTTGCCCCAGTTTAT
Found at i:39679149 original size:42 final size:42
Alignment explanation
Indices: 39679090--39679223 Score: 250
Period size: 42 Copynumber: 3.2 Consensus size: 42
39679080 TAGTCTCCCC
39679090 AAATGGGCTTGCATACATTCATTGACATTACATGTGATATTG
1 AAATGGGCTTGCATACATTCATTGACATTACATGTGATATTG
39679132 AAATGGGCTTGCATACATTCATTGACATTACATGTGATATTG
1 AAATGGGCTTGCATACATTCATTGACATTACATGTGATATTG
* *
39679174 AAATGGGCTTGCATACATCCATTGACATTACATGTGATATTA
1 AAATGGGCTTGCATACATTCATTGACATTACATGTGATATTG
39679216 AAATGGGC
1 AAATGGGC
39679224 CTAAGGGCCA
Statistics
Matches: 90, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 90 1.00
ACGTcount: A:0.32, C:0.15, G:0.19, T:0.34
Consensus pattern (42 bp):
AAATGGGCTTGCATACATTCATTGACATTACATGTGATATTG
Found at i:39679283 original size:31 final size:31
Alignment explanation
Indices: 39679247--39679361 Score: 198
Period size: 31 Copynumber: 3.7 Consensus size: 31
39679237 CGTTTACAGT
*
39679247 AAAGGCTTCGGCCTAGTGATATGATTTATGA
1 AAAGGCTTCGGCCCAGTGATATGATTTATGA
39679278 AAAGGCTTCGGCCCAGTGATATGATTTATGA
1 AAAGGCTTCGGCCCAGTGATATGATTTATGA
39679309 AAAGGCTTCGGCCCAGTGATATGATTTATGGA
1 AAAGGCTTCGGCCCAGTGATATGATTTAT-GA
39679341 AAA-GCTTCGGCCCAGT-ATATG
1 AAAGGCTTCGGCCCAGTGATATG
39679362 TCAATACTAA
Statistics
Matches: 82, Mismatches: 1, Indels: 3
0.95 0.01 0.03
Matches are distributed among these distances:
30 5 0.06
31 72 0.88
32 5 0.06
ACGTcount: A:0.29, C:0.17, G:0.26, T:0.29
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTGATATGATTTATGA
Found at i:39681298 original size:40 final size:40
Alignment explanation
Indices: 39681224--39681369 Score: 175
Period size: 40 Copynumber: 3.6 Consensus size: 40
39681214 CCGCACCAAG
* * * * * *
39681224 GCCTACGGGACTTAACCCGGATATCACGATTTGCACAAAT
1 GCCTTCGGGTCTTAGCCCGGATATAACAACTTGCACAAAT
* *
39681264 GCCTTCGGGTCTTAGCCCGGATTTAACAACTTGCACGAAT
1 GCCTTCGGGTCTTAGCCCGGATATAACAACTTGCACAAAT
* * * *
39681304 GCCTTCGGGTCTTAGCCCGGATATAGCTACTAGCACAATT
1 GCCTTCGGGTCTTAGCCCGGATATAACAACTTGCACAAAT
*
39681344 GCCTTCGGGTCTTAACCCGGATATAA
1 GCCTTCGGGTCTTAGCCCGGATATAA
39681370 TTTTCAGCAT
Statistics
Matches: 90, Mismatches: 16, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
40 90 1.00
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.26
Consensus pattern (40 bp):
GCCTTCGGGTCTTAGCCCGGATATAACAACTTGCACAAAT
Found at i:39681384 original size:40 final size:40
Alignment explanation
Indices: 39681256--39681407 Score: 164
Period size: 40 Copynumber: 3.8 Consensus size: 40
39681246 ATCACGATTT
* * * * *
39681256 GCACAAATGCCTTCGGGTCTTAGCCCGGATTTAACAACTT
1 GCACAATTGCCTTCGGGTCTTAGCCCGGATATAGCTACTA
39681296 GCACGAA-TGCCTTCGGGTCTTAGCCCGGATATAGCTACTA
1 GCAC-AATTGCCTTCGGGTCTTAGCCCGGATATAGCTACTA
* * **
39681336 GCACAATTGCCTTCGGGTCTTAACCCGGATATA-ATTTTCA
1 GCACAATTGCCTTCGGGTCTTAGCCCGGATATAGCTACT-A
* * *
39681376 GCATAATTGTCTTCGGGGCTTAGCCCGGATAT
1 GCACAATTGCCTTCGGGTCTTAGCCCGGATAT
39681408 CATTCAATTT
Statistics
Matches: 97, Mismatches: 12, Indels: 6
0.84 0.10 0.05
Matches are distributed among these distances:
39 4 0.04
40 91 0.94
41 2 0.02
ACGTcount: A:0.23, C:0.26, G:0.22, T:0.29
Consensus pattern (40 bp):
GCACAATTGCCTTCGGGTCTTAGCCCGGATATAGCTACTA
Found at i:39683474 original size:16 final size:16
Alignment explanation
Indices: 39683453--39683483 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
39683443 ACAAATGTAA
39683453 TATTTAAAACAATAAG
1 TATTTAAAACAATAAG
*
39683469 TATTTAAAACGATAA
1 TATTTAAAACAATAA
39683484 AGTAACTTAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.55, C:0.06, G:0.06, T:0.32
Consensus pattern (16 bp):
TATTTAAAACAATAAG
Found at i:39684242 original size:13 final size:13
Alignment explanation
Indices: 39684224--39684249 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
39684214 AGTAGCGGCG
39684224 CCAGAAACCCTAA
1 CCAGAAACCCTAA
39684237 CCAGAAACCCTAA
1 CCAGAAACCCTAA
39684250 GGTTTCTGGC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.38, G:0.08, T:0.08
Consensus pattern (13 bp):
CCAGAAACCCTAA
Found at i:39684932 original size:2 final size:2
Alignment explanation
Indices: 39684915--39684952 Score: 60
Period size: 2 Copynumber: 19.0 Consensus size: 2
39684905 ACCTAATACA
39684915 AT AT A- AT AT GAT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT AT
39684953 TGTGTGGAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 1 0.03
2 31 0.91
3 2 0.06
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:39687327 original size:29 final size:29
Alignment explanation
Indices: 39687273--39687328 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
39687263 GAGTTACACT
* * *
39687273 GCCTACCACATGGTCGTGTGGCTCACATG
1 GCCTACCACATGGCCATGTAGCTCACATG
*
39687302 GCCTACCACATGGCCATGTAGTTCACA
1 GCCTACCACATGGCCATGTAGCTCACA
39687329 CAGTCGTGTG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.21, C:0.32, G:0.23, T:0.23
Consensus pattern (29 bp):
GCCTACCACATGGCCATGTAGCTCACATG
Found at i:39687750 original size:25 final size:26
Alignment explanation
Indices: 39687722--39687777 Score: 71
Period size: 25 Copynumber: 2.2 Consensus size: 26
39687712 GTAATGAAAG
39687722 GAAAAGAAAAGAAAGAA-AAAA-AATA
1 GAAAAGAAAAG-AAGAACAAAACAATA
*
39687747 GAAAAGGAAAGAAGAACAAAACAATA
1 GAAAAGAAAAGAAGAACAAAACAATA
*
39687773 AAAAA
1 GAAAA
39687778 ATGTTAAACA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
24 5 0.19
25 14 0.52
26 8 0.30
ACGTcount: A:0.77, C:0.04, G:0.16, T:0.04
Consensus pattern (26 bp):
GAAAAGAAAAGAAGAACAAAACAATA
Found at i:39698442 original size:42 final size:42
Alignment explanation
Indices: 39698395--39698501 Score: 187
Period size: 42 Copynumber: 2.5 Consensus size: 42
39698385 TATTGGTCTC
39698395 GGCACTAAGTGTGCGGGTATAAATGGACACGGTGACAAGATT
1 GGCACTAAGTGTGCGGGTATAAATGGACACGGTGACAAGATT
39698437 GGCACTAAGTGTGCGGGTATAAATGGACACGGTGACAAGATT
1 GGCACTAAGTGTGCGGGTATAAATGGACACGGTGACAAGATT
* * *
39698479 GGCACTACGTGTGTGGGTTTAAA
1 GGCACTAAGTGTGCGGGTATAAA
39698502 ATTGTACAGC
Statistics
Matches: 62, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 62 1.00
ACGTcount: A:0.29, C:0.14, G:0.34, T:0.23
Consensus pattern (42 bp):
GGCACTAAGTGTGCGGGTATAAATGGACACGGTGACAAGATT
Found at i:39698566 original size:27 final size:28
Alignment explanation
Indices: 39698509--39698578 Score: 97
Period size: 27 Copynumber: 2.5 Consensus size: 28
39698499 AAAATTGTAC
**
39698509 AGCACTAAGTGTGCGAATTTGATTATAT
1 AGCACTAAGTGTGCGAAGCTGATTATAT
* *
39698537 AGCACTATGTGTGCG-AGCTGATTTTAT
1 AGCACTAAGTGTGCGAAGCTGATTATAT
39698564 AGCACTAAGTGTGCG
1 AGCACTAAGTGTGCG
39698579 GATTCACTAT
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
27 23 0.62
28 14 0.38
ACGTcount: A:0.27, C:0.14, G:0.26, T:0.33
Consensus pattern (28 bp):
AGCACTAAGTGTGCGAAGCTGATTATAT
Found at i:39705673 original size:42 final size:42
Alignment explanation
Indices: 39705626--39705732 Score: 196
Period size: 42 Copynumber: 2.5 Consensus size: 42
39705616 TATTGGTCTC
39705626 GGCACTAAGTGTGCGGGTATAAATGGACACGGTGACAAGATT
1 GGCACTAAGTGTGCGGGTATAAATGGACACGGTGACAAGATT
39705668 GGCACTAAGTGTGCGGGTATAAATGGACACGGTGACAAGATT
1 GGCACTAAGTGTGCGGGTATAAATGGACACGGTGACAAGATT
* *
39705710 GGCACTACGTGTGCGGGTTTAAA
1 GGCACTAAGTGTGCGGGTATAAA
39705733 ATTGTACAGC
Statistics
Matches: 63, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
42 63 1.00
ACGTcount: A:0.29, C:0.15, G:0.34, T:0.22
Consensus pattern (42 bp):
GGCACTAAGTGTGCGGGTATAAATGGACACGGTGACAAGATT
Found at i:39705797 original size:27 final size:28
Alignment explanation
Indices: 39705740--39705809 Score: 97
Period size: 27 Copynumber: 2.5 Consensus size: 28
39705730 AAAATTGTAC
**
39705740 AGCACTAAGTGTGCGAATTTGATTATAT
1 AGCACTAAGTGTGCGAAGCTGATTATAT
* *
39705768 AGCACTATGTGTGCG-AGCTGATTTTAT
1 AGCACTAAGTGTGCGAAGCTGATTATAT
39705795 AGCACTAAGTGTGCG
1 AGCACTAAGTGTGCG
39705810 GATTCACTAT
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
27 23 0.62
28 14 0.38
ACGTcount: A:0.27, C:0.14, G:0.26, T:0.33
Consensus pattern (28 bp):
AGCACTAAGTGTGCGAAGCTGATTATAT
Found at i:39709019 original size:139 final size:139
Alignment explanation
Indices: 39708763--39709041 Score: 375
Period size: 139 Copynumber: 2.0 Consensus size: 139
39708753 GGAGAGTAAT
* ** * * *
39708763 AGGCTATAAATGGATTTTTAAGCTAAAACAGAATGCTAATGGGACTATATTCAAATATAAAGCCA
1 AGGCTATAAATGGATTTTTAAGCTAAAAAAGAATAATAATGGGAATATACTCAAATACAAAGCCA
* * *
39708828 AACTGGTGGTCAAAAGGTATCTCCAATAAGCTGGTATTGATTTCCAGAAAACTTTTAGCCCTTTG
66 AACTGGTGGTCAAAAGGTATCTCCAATAAACTGGTATTGATTTCCAGAAAACTGTTAGCCCTCTG
39708893 GTCAAACCA
131 GTCAAACCA
* * *
39708902 AGGCTA-AAAGTGGATTTTTAAGCTAAAAAAGAATAATGATGGGAATATAGCT-AGATACAAGGC
1 AGGCTATAAA-TGGATTTTTAAGCTAAAAAAGAATAATAATGGGAATATA-CTCAAATACAAAGC
* * *
39708965 TAAACTGGTGGTCAAAGGGTATCTCCAATAAACTGGTATTGATTTCCA-AGAAACTGTTAGTCCT
64 CAAACTGGTGGTCAAAAGGTATCTCCAATAAACTGGTATTGATTTCCAGA-AAACTGTTAGCCCT
39709029 CTGGTCAAACCA
128 CTGGTCAAACCA
39709041 A
1 A
39709042 CTACTATCTA
Statistics
Matches: 122, Mismatches: 15, Indels: 6
0.85 0.10 0.04
Matches are distributed among these distances:
138 4 0.03
139 117 0.96
140 1 0.01
ACGTcount: A:0.37, C:0.15, G:0.20, T:0.28
Consensus pattern (139 bp):
AGGCTATAAATGGATTTTTAAGCTAAAAAAGAATAATAATGGGAATATACTCAAATACAAAGCCA
AACTGGTGGTCAAAAGGTATCTCCAATAAACTGGTATTGATTTCCAGAAAACTGTTAGCCCTCTG
GTCAAACCA
Found at i:39709487 original size:28 final size:28
Alignment explanation
Indices: 39709452--39709505 Score: 99
Period size: 28 Copynumber: 1.9 Consensus size: 28
39709442 GACTTGGTGA
*
39709452 AGATACATTTTTTCTTAGACATGGAGGT
1 AGATACATTTTTTCCTAGACATGGAGGT
39709480 AGATACATTTTTTCCTAGACATGGAG
1 AGATACATTTTTTCCTAGACATGGAG
39709506 ACGTCTTACA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.30, C:0.13, G:0.20, T:0.37
Consensus pattern (28 bp):
AGATACATTTTTTCCTAGACATGGAGGT
Found at i:39713134 original size:5 final size:5
Alignment explanation
Indices: 39713124--39713148 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
39713114 AGTATAAATA
39713124 TATAT TATAT TATAT TATAT TATAT
1 TATAT TATAT TATAT TATAT TATAT
39713149 AAAACAAATA
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:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (5 bp):
TATAT
Found at i:39713379 original size:72 final size:72
Alignment explanation
Indices: 39713303--39713444 Score: 284
Period size: 72 Copynumber: 2.0 Consensus size: 72
39713293 AAAATTTTAG
39713303 AAATTATTGAGTTTTTTAAATGTTGTCTATGTTGAATAATTAGAGTATTAGGGACTAAATTGATA
1 AAATTATTGAGTTTTTTAAATGTTGTCTATGTTGAATAATTAGAGTATTAGGGACTAAATTGATA
39713368 GATTTTC
66 GATTTTC
39713375 AAATTATTGAGTTTTTTAAATGTTGTCTATGTTGAATAATTAGAGTATTAGGGACTAAATTGATA
1 AAATTATTGAGTTTTTTAAATGTTGTCTATGTTGAATAATTAGAGTATTAGGGACTAAATTGATA
39713440 GATTT
66 GATTT
39713445 CAAGTTAGAA
Statistics
Matches: 70, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
72 70 1.00
ACGTcount: A:0.34, C:0.04, G:0.18, T:0.44
Consensus pattern (72 bp):
AAATTATTGAGTTTTTTAAATGTTGTCTATGTTGAATAATTAGAGTATTAGGGACTAAATTGATA
GATTTTC
Found at i:39713468 original size:72 final size:72
Alignment explanation
Indices: 39713320--39713468 Score: 192
Period size: 72 Copynumber: 2.1 Consensus size: 72
39713310 TGAGTTTTTT
***
39713320 AAATGTTGTCTATGTTGAATAATTAGAGTATTAGGGACTAAATTGATAGATTTTCAAATTATTGA
1 AAATGTTGTCTATGTTGAATAATTAGAGTATTAGGGACTAAATTGATAGATTTTCAAATTAGAAA
******
39713385 GTTTTTT
66 GAAAAAG
*
39713392 AAATGTTGTCTATGTTGAATAATTAGAGTATTAGGGACTAAATTGATAGA-TTTCAAGTTAGAAA
1 AAATGTTGTCTATGTTGAATAATTAGAGTATTAGGGACTAAATTGATAGATTTTCAAATTAGAAA
39713456 TGAAAAAG
66 -GAAAAAG
39713464 AAATG
1 AAATG
39713469 AACTGTAGAA
Statistics
Matches: 66, Mismatches: 10, Indels: 2
0.85 0.13 0.03
Matches are distributed among these distances:
71 10 0.15
72 56 0.85
ACGTcount: A:0.38, C:0.04, G:0.19, T:0.38
Consensus pattern (72 bp):
AAATGTTGTCTATGTTGAATAATTAGAGTATTAGGGACTAAATTGATAGATTTTCAAATTAGAAA
GAAAAAG
Found at i:39715869 original size:12 final size:12
Alignment explanation
Indices: 39715854--39715882 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
39715844 AATATTTATA
39715854 TTTTAAAAATAT
1 TTTTAAAAATAT
39715866 TTTTAAAAATAT
1 TTTTAAAAATAT
39715878 TTTTA
1 TTTTA
39715883 TTTAAATTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (12 bp):
TTTTAAAAATAT
Found at i:39733059 original size:21 final size:21
Alignment explanation
Indices: 39733033--39733080 Score: 96
Period size: 21 Copynumber: 2.3 Consensus size: 21
39733023 ACCGTCCACC
39733033 ATCATTATATTAGGTATTTTT
1 ATCATTATATTAGGTATTTTT
39733054 ATCATTATATTAGGTATTTTT
1 ATCATTATATTAGGTATTTTT
39733075 ATCATT
1 ATCATT
39733081 TCAGGCCACC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.29, C:0.06, G:0.08, T:0.56
Consensus pattern (21 bp):
ATCATTATATTAGGTATTTTT
Found at i:39738827 original size:29 final size:29
Alignment explanation
Indices: 39738771--39738833 Score: 101
Period size: 29 Copynumber: 2.2 Consensus size: 29
39738761 ACTATGTGAA
39738771 ACACACAGCCGTGTCGCAGATCGTGTGGG
1 ACACACAGCCGTGTCGCAGATCGTGTGGG
*
39738800 ACACACGGCCGTGTCGCAG-TCCGTGTGGG
1 ACACACAGCCGTGTCGCAGAT-CGTGTGGG
39738829 ACACA
1 ACACA
39738834 TGGCTATGTG
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
28 1 0.03
29 31 0.97
ACGTcount: A:0.21, C:0.30, G:0.33, T:0.16
Consensus pattern (29 bp):
ACACACAGCCGTGTCGCAGATCGTGTGGG
Found at i:39741520 original size:35 final size:35
Alignment explanation
Indices: 39741474--39741543 Score: 131
Period size: 35 Copynumber: 2.0 Consensus size: 35
39741464 TTTGATAGTG
*
39741474 AAGATGCCATAGATGAAAACACTATCGAGTACCAA
1 AAGATGCCATAGACGAAAACACTATCGAGTACCAA
39741509 AAGATGCCATAGACGAAAACACTATCGAGTACCAA
1 AAGATGCCATAGACGAAAACACTATCGAGTACCAA
39741544 CCTTACGAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.46, C:0.21, G:0.17, T:0.16
Consensus pattern (35 bp):
AAGATGCCATAGACGAAAACACTATCGAGTACCAA
Found at i:39748583 original size:22 final size:22
Alignment explanation
Indices: 39748555--39748630 Score: 64
Period size: 22 Copynumber: 3.3 Consensus size: 22
39748545 AAGTGTGTAT
39748555 ATGTGATAAGGCCGAATGGCCA
1 ATGTGATAAGGCCGAATGGCCA
* * ***
39748577 ATGTGATGAATG-TGAAAGTGTATA
1 ATGTGAT-AAGGCCG-AA-TGGCCA
39748601 TATGTGATAAGGCCGAATGGCCA
1 -ATGTGATAAGGCCGAATGGCCA
39748624 ATGTGAT
1 ATGTGAT
39748631 GAATGTGAAA
Statistics
Matches: 39, Mismatches: 10, Indels: 10
0.66 0.17 0.17
Matches are distributed among these distances:
22 15 0.38
23 8 0.21
24 8 0.21
25 8 0.21
ACGTcount: A:0.33, C:0.11, G:0.30, T:0.26
Consensus pattern (22 bp):
ATGTGATAAGGCCGAATGGCCA
Found at i:39748589 original size:47 final size:47
Alignment explanation
Indices: 39748520--39748722 Score: 295
Period size: 47 Copynumber: 4.3 Consensus size: 47
39748510 AGCTTAAGAT
*
39748520 CGAATGGCCAATGTGATGAATGTGAAAGTGTGTATATGTGATAAGGC
1 CGAATGGCCAATGTGATGAATGTGAAAGTGTATATATGTGATAAGGC
39748567 CGAATGGCCAATGTGATGAATGTGAAAGTGTATATATGTGATAAGGC
1 CGAATGGCCAATGTGATGAATGTGAAAGTGTATATATGTGATAAGGC
* * *
39748614 CGAATGGCCAATGTGATGAATGTGAAAGTGCATACATGTGATAAGAC
1 CGAATGGCCAATGTGATGAATGTGAAAGTGTATATATGTGATAAGGC
** *
39748661 CGAATGGTTAATGTGAT-ATATGTGTAAGTG-A-ATATGTGATAAGGC
1 CGAATGGCCAATGTGATGA-ATGTGAAAGTGTATATATGTGATAAGGC
*
39748706 CGAATGACCAATTGTGA
1 CGAATGGCCAA-TGTGA
39748723 AAAGTGTGCA
Statistics
Matches: 142, Mismatches: 12, Indels: 5
0.89 0.08 0.03
Matches are distributed among these distances:
45 20 0.14
46 7 0.05
47 115 0.81
ACGTcount: A:0.34, C:0.09, G:0.29, T:0.28
Consensus pattern (47 bp):
CGAATGGCCAATGTGATGAATGTGAAAGTGTATATATGTGATAAGGC
Found at i:39748847 original size:39 final size:40
Alignment explanation
Indices: 39748793--39748877 Score: 118
Period size: 40 Copynumber: 2.1 Consensus size: 40
39748783 AAATGAATTG
* * * *
39748793 TGCTGAGATTGTATCCGGG-TTAGAGACCCGCTGGCTTCA
1 TGCTGGGATTGTATCCGGGTTTAAAGACCCGCAGGCTTAA
*
39748832 TGCTGGGATTGTATCCGGGTTTAAAGTCCCGCAGGCTTAA
1 TGCTGGGATTGTATCCGGGTTTAAAGACCCGCAGGCTTAA
39748872 TGCTGG
1 TGCTGG
39748878 TGAATTAAGT
Statistics
Matches: 40, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
39 18 0.45
40 22 0.55
ACGTcount: A:0.18, C:0.21, G:0.32, T:0.29
Consensus pattern (40 bp):
TGCTGGGATTGTATCCGGGTTTAAAGACCCGCAGGCTTAA
Found at i:39750976 original size:25 final size:25
Alignment explanation
Indices: 39750939--39750989 Score: 93
Period size: 25 Copynumber: 2.0 Consensus size: 25
39750929 TAGATGTCAC
39750939 CTCTAAAAACATGACTTATTCTCTG
1 CTCTAAAAACATGACTTATTCTCTG
*
39750964 CTCTAAAATCATGACTTATTCTCTG
1 CTCTAAAAACATGACTTATTCTCTG
39750989 C
1 C
39750990 ATCTTAGATA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.29, C:0.25, G:0.08, T:0.37
Consensus pattern (25 bp):
CTCTAAAAACATGACTTATTCTCTG
Found at i:39756040 original size:40 final size:39
Alignment explanation
Indices: 39755970--39756138 Score: 209
Period size: 39 Copynumber: 4.3 Consensus size: 39
39755960 GACTAGCTCA
*
39755970 AATGCCTTCGGGAC-AAACCCTGG-TTATAGTAACTCGCACG
1 AATGCCTTCGGG-CTTAACCC-GGATT-TAGTAACTCGCACG
39756010 AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC-
1 AATGCCTTCGGG-CTTAACCCGGATTTAGTAACTCGCACG
* * *
39756049 AAGTGCCTTCGGGCTTAACCCGGATTTATTAACTGGCACA
1 AA-TGCCTTCGGGCTTAACCCGGATTTAGTAACTCGCACG
* *
39756089 AATGCCTTCGGGCTTAACCCGAATTTATTAACTCGCACG
1 AATGCCTTCGGGCTTAACCCGGATTTAGTAACTCGCACG
*
39756128 AACGCCTTCGG
1 AATGCCTTCGG
39756139 ATCTTAGTTC
Statistics
Matches: 118, Mismatches: 7, Indels: 9
0.88 0.05 0.07
Matches are distributed among these distances:
39 70 0.59
40 41 0.35
41 7 0.06
ACGTcount: A:0.25, C:0.28, G:0.21, T:0.25
Consensus pattern (39 bp):
AATGCCTTCGGGCTTAACCCGGATTTAGTAACTCGCACG
Found at i:39763463 original size:17 final size:17
Alignment explanation
Indices: 39763441--39763473 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
39763431 TTATTTTATT
39763441 TAATTA-ATTTTACTAAA
1 TAATTATATTTT-CTAAA
39763458 TAATTATATTTTCTAA
1 TAATTATATTTTCTAA
39763474 TGTTGCATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.42, C:0.06, G:0.00, T:0.52
Consensus pattern (17 bp):
TAATTATATTTTCTAAA
Found at i:39764633 original size:30 final size:28
Alignment explanation
Indices: 39764584--39764646 Score: 74
Period size: 31 Copynumber: 2.2 Consensus size: 28
39764574 AAAATATTAA
* *
39764584 TTTTTACTTTTCTTTGTTTAATTTTTGTATT
1 TTTTTACCTTTCTTAGTTT-A-TTTT-TATT
39764615 TTTTTACCTTT-TTAGTTTATTTTTATT
1 TTTTTACCTTTCTTAGTTTATTTTTATT
39764642 TTTTT
1 TTTTT
39764647 CCCCAAATAT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
27 9 0.30
28 4 0.13
29 1 0.03
30 6 0.20
31 10 0.33
ACGTcount: A:0.13, C:0.06, G:0.05, T:0.76
Consensus pattern (28 bp):
TTTTTACCTTTCTTAGTTTATTTTTATT
Found at i:39771649 original size:49 final size:46
Alignment explanation
Indices: 39771482--39771651 Score: 123
Period size: 50 Copynumber: 3.5 Consensus size: 46
39771472 TTTGTGCGCT
* *
39771482 AGTGTAAGA-CATGTCTGGGACAT-GCACTGGCCAC-ATTATGAGAGCC
1 AGTGTAAGACCATGTCTGGGACATGGCTC-GGCC-CGATTATGAAAG-C
* * * * *
39771528 ATTGTAAAACCATGTCTAGGACATGGCATCGGCACAGATATGTGAAAGC
1 AGTGTAAGACCATGTCTGGGACATGGC-TCGGC-CCGAT-TATGAAAGC
* * *
39771577 TAGTGTAAGACCATATCCT-GGACATGGCGTCGGCCTCGATTTTGATAGTC
1 -AGTGTAAGACCATGT-CTGGGACATGGC-TCGGCC-CGATTATGAAAG-C
39771627 AGTGTAAGACCATGTCTGGGACATG
1 AGTGTAAGACCATGTCTGGGACATG
39771652 ACATCGGCAT
Statistics
Matches: 98, Mismatches: 15, Indels: 19
0.74 0.11 0.14
Matches are distributed among these distances:
46 7 0.07
47 13 0.13
48 7 0.07
49 33 0.34
50 36 0.37
51 2 0.02
ACGTcount: A:0.28, C:0.20, G:0.27, T:0.25
Consensus pattern (46 bp):
AGTGTAAGACCATGTCTGGGACATGGCTCGGCCCGATTATGAAAGC
Found at i:39771659 original size:49 final size:47
Alignment explanation
Indices: 39771482--39771659 Score: 141
Period size: 49 Copynumber: 3.7 Consensus size: 47
39771472 TTTGTGCGCT
*
39771482 AGTGTAAGA-CATGTCTGGGACAT-GCA-CTGGCCAC-ATTATGAGAGCC
1 AGTGTAAGACCATGTCTGGGACATGGCATC-GGCC-CGATTATGAAAG-C
* * * * *
39771528 ATTGTAAAACCATGTCTAGGACATGGCATCGGCACAGATATGTGAAAGC
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGC-CCGAT-TATGAAAGC
* * * *
39771577 TAGTGTAAGACCATATCCT-GGACATGGCGTCGGCCTCGATTTTGATAGTC
1 -AGTGTAAGACCATGT-CTGGGACATGGCATCGGCC-CGATTATGAAAG-C
*
39771627 AGTGTAAGACCATGTCTGGGACATGACATCGGC
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGC
39771660 ATTATACCTT
Statistics
Matches: 105, Mismatches: 16, Indels: 19
0.75 0.11 0.14
Matches are distributed among these distances:
46 7 0.07
47 13 0.12
48 8 0.08
49 39 0.37
50 36 0.34
51 2 0.02
ACGTcount: A:0.28, C:0.21, G:0.27, T:0.24
Consensus pattern (47 bp):
AGTGTAAGACCATGTCTGGGACATGGCATCGGCCCGATTATGAAAGC
Found at i:39779561 original size:21 final size:21
Alignment explanation
Indices: 39779537--39779577 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
39779527 TCATCAGATC
*
39779537 TACACCTTGAGGCATCGGGGG
1 TACACCTTGAGGAATCGGGGG
**
39779558 TACAGGTTGAGGAATCGGGG
1 TACACCTTGAGGAATCGGGG
39779578 AGGTGGGGGA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.22, C:0.17, G:0.41, T:0.20
Consensus pattern (21 bp):
TACACCTTGAGGAATCGGGGG
Found at i:39787528 original size:24 final size:24
Alignment explanation
Indices: 39787501--39787563 Score: 117
Period size: 24 Copynumber: 2.6 Consensus size: 24
39787491 CTTATTATGT
39787501 TCGCACACATAGTGCCATAGTAAA
1 TCGCACACATAGTGCCATAGTAAA
39787525 TCGCACACATAGTGCCATAGTAAA
1 TCGCACACATAGTGCCATAGTAAA
*
39787549 TTGCACACATAGTGC
1 TCGCACACATAGTGC
39787564 ATTTGAGATT
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 38 1.00
ACGTcount: A:0.35, C:0.25, G:0.17, T:0.22
Consensus pattern (24 bp):
TCGCACACATAGTGCCATAGTAAA
Found at i:39795370 original size:24 final size:24
Alignment explanation
Indices: 39795343--39795388 Score: 92
Period size: 24 Copynumber: 1.9 Consensus size: 24
39795333 ATTATGTTCG
39795343 CACACATAGTGCCATAGTAAATCA
1 CACACATAGTGCCATAGTAAATCA
39795367 CACACATAGTGCCATAGTAAAT
1 CACACATAGTGCCATAGTAAAT
39795389 ACATAGTGCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.41, C:0.24, G:0.13, T:0.22
Consensus pattern (24 bp):
CACACATAGTGCCATAGTAAATCA
Found at i:39802562 original size:39 final size:39
Alignment explanation
Indices: 39802519--39802629 Score: 170
Period size: 39 Copynumber: 2.8 Consensus size: 39
39802509 CAAAATTTCA
*
39802519 ATCAAAACTTTTAATTCTGTTTTTATTTTATTTTTCCAG
1 ATCAAAAATTTTAATTCTGTTTTTATTTTATTTTTCCAG
*
39802558 ATCAAAAATTTTAATTCTGTTTTTATTTTATGTTTCCAG
1 ATCAAAAATTTTAATTCTGTTTTTATTTTATTTTTCCAG
* *
39802597 ATCAAAATTTTTAATTTTGTTTTT-TTATTATTT
1 ATCAAAAATTTTAATTCTGTTTTTATT-TTATTT
39802630 CTTTTCCAAG
Statistics
Matches: 66, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
38 2 0.03
39 64 0.97
ACGTcount: A:0.27, C:0.09, G:0.05, T:0.59
Consensus pattern (39 bp):
ATCAAAAATTTTAATTCTGTTTTTATTTTATTTTTCCAG
Found at i:39805720 original size:20 final size:20
Alignment explanation
Indices: 39805691--39805747 Score: 105
Period size: 20 Copynumber: 2.9 Consensus size: 20
39805681 AAATAGGAGT
*
39805691 CACATAGCCGTGTGGCTTCA
1 CACATGGCCGTGTGGCTTCA
39805711 CACATGGCCGTGTGGCTTCA
1 CACATGGCCGTGTGGCTTCA
39805731 CACATGGCCGTGTGGCT
1 CACATGGCCGTGTGGCT
39805748 AGACCGTGTA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.16, C:0.30, G:0.30, T:0.25
Consensus pattern (20 bp):
CACATGGCCGTGTGGCTTCA
Found at i:39806390 original size:2 final size:2
Alignment explanation
Indices: 39806383--39806416 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
39806373 ATTTCAAAAC
39806383 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
39806417 GCAAGTATGT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:39808671 original size:40 final size:40
Alignment explanation
Indices: 39808626--39808755 Score: 172
Period size: 40 Copynumber: 3.2 Consensus size: 40
39808616 CGGAATATAA
39808626 CCGGATATAACCA-TGTGCACAAATGCCTTCGGGTCTTAGC
1 CCGGATATAACCACT-TGCACAAATGCCTTCGGGTCTTAGC
* ** * *
39808666 CCGGATAGAATGACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAACCACTTGCACAAATGCCTTCGGGTCTTAGC
* * *
39808706 CCGGATATAGCCACTTGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATATAACCACTTGCACAAATGCCTTCGGGTCTTAGC
39808746 CCGGATATAA
1 CCGGATATAA
39808756 TTTCCAGCAT
Statistics
Matches: 75, Mismatches: 14, Indels: 2
0.82 0.15 0.02
Matches are distributed among these distances:
40 74 0.99
41 1 0.01
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.25
Consensus pattern (40 bp):
CCGGATATAACCACTTGCACAAATGCCTTCGGGTCTTAGC
Found at i:39808776 original size:80 final size:79
Alignment explanation
Indices: 39808626--39808792 Score: 196
Period size: 80 Copynumber: 2.1 Consensus size: 79
39808616 CGGAATATAA
* *
39808626 CCGGATATAACCATGTGCACAAATGCCTTCGGGTCTTAGCCCGGATAGAATGACTCGCACGAATG
1 CCGGATATAACCATGTGCACAAATGCCTTCGGGTCTTAACCCGGATAGAATGACTCGCACGAATA
39808691 CCTTCGGGTCTTAGC
66 CCTTCGGG-CTTAGC
* * * ** *
39808706 CCGGATATAGCCACT-TGCACAATTGCCTTCGGGTCTTAACCCGGATATAATTTC-CAGCA-TAA
1 CCGGATATAACCA-TGTGCACAAATGCCTTCGGGTCTTAACCCGGATAGAATGACTC-GCACGAA
*
39808768 TTATCTTCGGGCTTAGC
64 -TACCTTCGGGCTTAGC
39808785 CCGGATAT
1 CCGGATAT
39808793 CATTCAATTT
Statistics
Matches: 75, Mismatches: 9, Indels: 7
0.82 0.10 0.08
Matches are distributed among these distances:
79 17 0.23
80 57 0.76
81 1 0.01
ACGTcount: A:0.24, C:0.27, G:0.22, T:0.27
Consensus pattern (79 bp):
CCGGATATAACCATGTGCACAAATGCCTTCGGGTCTTAACCCGGATAGAATGACTCGCACGAATA
CCTTCGGGCTTAGC
Found at i:39812768 original size:37 final size:37
Alignment explanation
Indices: 39812706--39812777 Score: 108
Period size: 37 Copynumber: 1.9 Consensus size: 37
39812696 AGCTCAGACG
*
39812706 AAATCTCCACACGAAGTTATCGGGTCTTACCCGGACA
1 AAATCTCCACACGAAGTCATCGGGTCTTACCCGGACA
* * *
39812743 AAATCTCCACATGTAGTCATTGGGTCTTACCCGGA
1 AAATCTCCACACGAAGTCATCGGGTCTTACCCGGA
39812778 ATATATTTCC
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
37 31 1.00
ACGTcount: A:0.28, C:0.28, G:0.19, T:0.25
Consensus pattern (37 bp):
AAATCTCCACACGAAGTCATCGGGTCTTACCCGGACA
Found at i:39813049 original size:48 final size:49
Alignment explanation
Indices: 39812924--39813060 Score: 197
Period size: 50 Copynumber: 2.8 Consensus size: 49
39812914 GCACATCGCC
* *
39812924 TACATATTTCACACTAGCCATTCGGCTTTATCACATATACATATCTCATA
1 TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCA-A
* *
39812974 TATATATTTCACATT-GACCATTCGGCTTTACCACATATGCATATCTC-A
1 TACATATTTCACATTAG-CCATTCGGCTTTACCACATATACATATCTCAA
*
39813022 TACATATTTCACATTAGCCATTTGGCTTTACCACATATA
1 TACATATTTCACATTAGCCATTCGGCTTTACCACATATA
39813061 TGCATGTTCA
Statistics
Matches: 78, Mismatches: 7, Indels: 6
0.86 0.08 0.07
Matches are distributed among these distances:
48 35 0.45
49 2 0.03
50 41 0.53
ACGTcount: A:0.31, C:0.25, G:0.07, T:0.37
Consensus pattern (49 bp):
TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCAA
Found at i:39813109 original size:47 final size:47
Alignment explanation
Indices: 39813030--39813223 Score: 280
Period size: 47 Copynumber: 4.1 Consensus size: 47
39813020 CATACATATT
* * * *
39813030 TCACATTAGCCATTTGGCTTTACCACATATATGCATGTTCACATTCA
1 TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCA
* * *
39813077 CCACATTGGCCATTCGGCCTTATCACACATATGCATGCTCACATTCA
1 TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCA
*
39813124 TCACATTGGCCATTCGACCTTATCACATATATGCATGTTCACATTCA
1 TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCA
* * **
39813171 TCACATTGGCCATTCGGCCTTATCTCATATATACACATTCACATTCA
1 TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCA
39813218 TCACAT
1 TCACAT
39813224 AAAATCCTAA
Statistics
Matches: 131, Mismatches: 16, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
47 131 1.00
ACGTcount: A:0.27, C:0.29, G:0.10, T:0.33
Consensus pattern (47 bp):
TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCA
Found at i:39813150 original size:22 final size:22
Alignment explanation
Indices: 39813123--39813194 Score: 58
Period size: 22 Copynumber: 3.1 Consensus size: 22
39813113 GCTCACATTC
39813123 ATCACATTGGCCATTCGACCTT
1 ATCACATTGGCCATTCGACCTT
* *
39813145 ATCACATATATG-CATGTTC-ACATT
1 ATCACAT-T-GGCCA--TTCGACCTT
*
39813169 CATCACATTGGCCATTCGGCCTT
1 -ATCACATTGGCCATTCGACCTT
39813192 ATC
1 ATC
39813195 TCATATATAC
Statistics
Matches: 38, Mismatches: 5, Indels: 14
0.67 0.09 0.25
Matches are distributed among these distances:
22 13 0.34
23 7 0.18
24 8 0.21
25 10 0.26
ACGTcount: A:0.25, C:0.29, G:0.12, T:0.33
Consensus pattern (22 bp):
ATCACATTGGCCATTCGACCTT
Found at i:39813151 original size:94 final size:93
Alignment explanation
Indices: 39812983--39813223 Score: 288
Period size: 94 Copynumber: 2.5 Consensus size: 93
39812973 ATATATATTT
* * * *
39812983 CACATTGACCATTCGGCTTTA-CCACATATGCATATCTCATACATAT-TTCACATTAGCCATTTG
1 CACATTGGCCATTCGGCCTTATCCACATATGCATA-CTC--ACAT-TCATCACATTAGCCATTCG
* *
39813046 GCTTTACCACATATATGCATGTTCACATTCAC
62 ACCTTACCACATATATGCATGTTCACATTCAC
* *
39813078 CACATTGGCCATTCGGCCTTATCACACATATGCATGCTCACATTCATCACATTGGCCATTCGACC
1 CACATTGGCCATTCGGCCTTATC-CACATATGCATACTCACATTCATCACATTAGCCATTCGACC
* *
39813143 TTATCACATATATGCATGTTCACATTCAT
65 TTACCACATATATGCATGTTCACATTCAC
* * * *
39813172 CACATTGGCCATTCGGCCTTATCTCATATATACACATTCACATTCATCACAT
1 CACATTGGCCATTCGGCCTTATC-CACATATGCATACTCACATTCATCACAT
39813224 AAAATCCTAA
Statistics
Matches: 127, Mismatches: 16, Indels: 7
0.85 0.11 0.05
Matches are distributed among these distances:
93 1 0.01
94 92 0.72
95 19 0.15
96 4 0.03
97 11 0.09
ACGTcount: A:0.28, C:0.29, G:0.10, T:0.33
Consensus pattern (93 bp):
CACATTGGCCATTCGGCCTTATCCACATATGCATACTCACATTCATCACATTAGCCATTCGACCT
TACCACATATATGCATGTTCACATTCAC
Found at i:39815081 original size:28 final size:28
Alignment explanation
Indices: 39815041--39815098 Score: 116
Period size: 28 Copynumber: 2.1 Consensus size: 28
39815031 CACACATGAT
39815041 CATTTGTTTGATTCAAGCACCTATCCAC
1 CATTTGTTTGATTCAAGCACCTATCCAC
39815069 CATTTGTTTGATTCAAGCACCTATCCAC
1 CATTTGTTTGATTCAAGCACCTATCCAC
39815097 CA
1 CA
39815099 AAAATTCATC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.26, C:0.29, G:0.10, T:0.34
Consensus pattern (28 bp):
CATTTGTTTGATTCAAGCACCTATCCAC
Found at i:39817069 original size:17 final size:17
Alignment explanation
Indices: 39817032--39817069 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
39817022 CTTGATATTA
*
39817032 AAAATGGAAGAAGAGGC
1 AAAATGGAAGAAAAGGC
39817049 AAAATGGAAAGAAAAGG-
1 AAAATGG-AAGAAAAGGC
39817066 AAAA
1 AAAA
39817070 AAAAATTTGT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 11 0.58
18 8 0.42
ACGTcount: A:0.63, C:0.03, G:0.29, T:0.05
Consensus pattern (17 bp):
AAAATGGAAGAAAAGGC
Found at i:39817070 original size:18 final size:17
Alignment explanation
Indices: 39817031--39817070 Score: 53
Period size: 18 Copynumber: 2.3 Consensus size: 17
39817021 TCTTGATATT
*
39817031 AAAAATGGAAGAAGAGG
1 AAAAATGGAAGAAAAGG
*
39817048 CAAAATGGAAAGAAAAGG
1 AAAAATGG-AAGAAAAGG
39817066 AAAAA
1 AAAAA
39817071 AAAATTTGTT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
17 7 0.37
18 12 0.63
ACGTcount: A:0.65, C:0.03, G:0.28, T:0.05
Consensus pattern (17 bp):
AAAAATGGAAGAAAAGG
Found at i:39819899 original size:13 final size:13
Alignment explanation
Indices: 39819881--39819906 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
39819871 TGAATTAGTA
39819881 TGTGTGAAAATTT
1 TGTGTGAAAATTT
39819894 TGTGTGAAAATTT
1 TGTGTGAAAATTT
39819907 AATCATTTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.00, G:0.23, T:0.46
Consensus pattern (13 bp):
TGTGTGAAAATTT
Found at i:39826542 original size:28 final size:28
Alignment explanation
Indices: 39826477--39826575 Score: 119
Period size: 28 Copynumber: 3.5 Consensus size: 28
39826467 CATGAGATTG
* * *
39826477 GCACTAAGTGTGCGGGTTCAAATTGTATA
1 GCACTAAGTGTGCGAGTT-AGATTATATA
*
39826506 GCACTAAGTGTGCGAGTTTGATTATATA
1 GCACTAAGTGTGCGAGTTAGATTATATA
* *
39826534 GCACTAAGTGTGCGAGTTCGACTAT-TAA
1 GCACTAAGTGTGCGAGTTAGATTATAT-A
39826562 GCACTAAGTGTGCG
1 GCACTAAGTGTGCG
39826576 GGCTTATTAT
Statistics
Matches: 63, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
27 1 0.02
28 45 0.71
29 17 0.27
ACGTcount: A:0.27, C:0.15, G:0.27, T:0.30
Consensus pattern (28 bp):
GCACTAAGTGTGCGAGTTAGATTATATA
Found at i:39831529 original size:28 final size:28
Alignment explanation
Indices: 39831489--39831545 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
39831479 CGACAATGAT
39831489 TGCTTGACGTTCAGAGGTCGATTATGTG
1 TGCTTGACGTTCAGAGGTCGATTATGTG
39831517 TGCTTGACGTTCAGAGGTCGATTATGTG
1 TGCTTGACGTTCAGAGGTCGATTATGTG
39831545 T
1 T
39831546 TCCAAGAAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.18, C:0.14, G:0.32, T:0.37
Consensus pattern (28 bp):
TGCTTGACGTTCAGAGGTCGATTATGTG
Found at i:39834570 original size:28 final size:28
Alignment explanation
Indices: 39834505--39834603 Score: 119
Period size: 28 Copynumber: 3.5 Consensus size: 28
39834495 CATGAGATTG
* * *
39834505 GCACTAAGTGTGCGGGTTCAAATTGTATA
1 GCACTAAGTGTGCGAGTT-AGATTATATA
*
39834534 GCACTAAGTGTGCGAGTTTGATTATATA
1 GCACTAAGTGTGCGAGTTAGATTATATA
* *
39834562 GCACTAAGTGTGCGAGTTCGACTAT-TAA
1 GCACTAAGTGTGCGAGTTAGATTATAT-A
39834590 GCACTAAGTGTGCG
1 GCACTAAGTGTGCG
39834604 GGCTTATTAT
Statistics
Matches: 63, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
27 1 0.02
28 45 0.71
29 17 0.27
ACGTcount: A:0.27, C:0.15, G:0.27, T:0.30
Consensus pattern (28 bp):
GCACTAAGTGTGCGAGTTAGATTATATA
Found at i:39845918 original size:94 final size:94
Alignment explanation
Indices: 39845757--39845942 Score: 273
Period size: 94 Copynumber: 2.0 Consensus size: 94
39845747 TTCCTAACAC
* * **
39845757 GGGCGTGTCACACAGTCGTGTCCATTTGGCAGGATTGAAGCATGACTTACACCGGTAGACTACAC
1 GGGCGTGTCACACAGCCGTGTCCATTTGGCAAGATTGAAGCACAACTTACACCGGTAGACTACAC
39845822 GCCCGTACCTATTCAACAGCCCTGACCGT
66 GCCCGTACCTATTCAACAGCCCTGACCGT
* * ** *
39845851 GGGCGTGTCACACGGCCGTGTCCATTTGGTAAGATTGAAGCACAACTTACATGGGTAGAGTACAC
1 GGGCGTGTCACACAGCCGTGTCCATTTGGCAAGATTGAAGCACAACTTACACCGGTAGACTACAC
* *
39845916 GCCCGTGCCTATTCAACAGCCTTGACC
66 GCCCGTACCTATTCAACAGCCCTGACC
39845943 ACAAGCGTGT
Statistics
Matches: 81, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
94 81 1.00
ACGTcount: A:0.24, C:0.28, G:0.25, T:0.23
Consensus pattern (94 bp):
GGGCGTGTCACACAGCCGTGTCCATTTGGCAAGATTGAAGCACAACTTACACCGGTAGACTACAC
GCCCGTACCTATTCAACAGCCCTGACCGT
Found at i:39849536 original size:13 final size:13
Alignment explanation
Indices: 39849518--39849542 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
39849508 GAATTAGTAT
39849518 GTGTGAAAATTTC
1 GTGTGAAAATTTC
39849531 GTGTGAAAATTT
1 GTGTGAAAATTT
39849543 AATCGTTTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.04, G:0.24, T:0.40
Consensus pattern (13 bp):
GTGTGAAAATTTC
Found at i:39850715 original size:42 final size:44
Alignment explanation
Indices: 39850614--39850749 Score: 120
Period size: 42 Copynumber: 3.2 Consensus size: 44
39850604 GTTTTTGTGA
* * * * *
39850614 AAGACCACATCTGGGACATTGGCATCGACT-TATGATTTACGTGT
1 AAGACCATATCTGGGATAGTGACATCGA-TATTTGATTTACGTGT
* *
39850658 TAGACCATGTCTGGGAT-GTTGACATCG-TATTTGATTT-CGTGT
1 AAGACCATATCTGGGATAG-TGACATCGATATTTGATTTACGTGT
* * * *
39850700 AAGACCTTATTTGGGATAGTGGCATCGATATTTG-TTTACATGT
1 AAGACCATATCTGGGATAGTGACATCGATATTTGATTTACGTGT
39850743 AAGACCA
1 AAGACCA
39850750 CGTCTGAGAC
Statistics
Matches: 73, Mismatches: 14, Indels: 11
0.74 0.14 0.11
Matches are distributed among these distances:
42 29 0.40
43 24 0.33
44 20 0.27
ACGTcount: A:0.26, C:0.16, G:0.24, T:0.35
Consensus pattern (44 bp):
AAGACCATATCTGGGATAGTGACATCGATATTTGATTTACGTGT
Found at i:39850911 original size:27 final size:27
Alignment explanation
Indices: 39850880--39850934 Score: 101
Period size: 27 Copynumber: 2.0 Consensus size: 27
39850870 TACGTTTGAA
39850880 TTGTATACCATGTTTGAGATTGAAAGG
1 TTGTATACCATGTTTGAGATTGAAAGG
*
39850907 TTGTATACCTTGTTTGAGATTGAAAGG
1 TTGTATACCATGTTTGAGATTGAAAGG
39850934 T
1 T
39850935 AAGTATATGT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.27, C:0.07, G:0.25, T:0.40
Consensus pattern (27 bp):
TTGTATACCATGTTTGAGATTGAAAGG
Found at i:39852549 original size:30 final size:30
Alignment explanation
Indices: 39852515--39852574 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
39852505 TAGGAGCATC
39852515 GAATTCACTTAAAACCAAGGAAAAATCATT
1 GAATTCACTTAAAACCAAGGAAAAATCATT
*
39852545 GAATTCACTTAAAACCAAGGAAATATCATT
1 GAATTCACTTAAAACCAAGGAAAAATCATT
39852575 CATAAATATG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.48, C:0.17, G:0.10, T:0.25
Consensus pattern (30 bp):
GAATTCACTTAAAACCAAGGAAAAATCATT
Found at i:39854260 original size:6 final size:6
Alignment explanation
Indices: 39854251--39854286 Score: 54
Period size: 6 Copynumber: 6.0 Consensus size: 6
39854241 AAGAAAATTT
* *
39854251 AAATAA AAATAA ATATAA AAGTAA AAATAA AAATAA
1 AAATAA AAATAA AAATAA AAATAA AAATAA AAATAA
39854287 TAGTAAAATA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.78, C:0.00, G:0.03, T:0.19
Consensus pattern (6 bp):
AAATAA
Found at i:39854268 original size:12 final size:12
Alignment explanation
Indices: 39854253--39854298 Score: 51
Period size: 12 Copynumber: 3.9 Consensus size: 12
39854243 GAAAATTTAA
39854253 ATAAAAATAAAT
1 ATAAAAATAAAT
* *
39854265 ATAAAAGTAAAA
1 ATAAAAATAAAT
39854277 ATAAAAAT-AAT
1 ATAAAAATAAAT
39854288 AGT-AAAATAAA
1 A-TAAAAATAAA
39854299 GGGACTCAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
11 8 0.29
12 20 0.71
ACGTcount: A:0.74, C:0.00, G:0.04, T:0.22
Consensus pattern (12 bp):
ATAAAAATAAAT
Found at i:39854277 original size:18 final size:18
Alignment explanation
Indices: 39854254--39854298 Score: 65
Period size: 18 Copynumber: 2.6 Consensus size: 18
39854244 AAAATTTAAA
*
39854254 TAAAAATAAATATAAAAG
1 TAAAAATAAAAATAAAAG
*
39854272 TAAAAATAAAAATAATAG
1 TAAAAATAAAAATAAAAG
39854290 T-AAAATAAA
1 TAAAAATAAA
39854299 GGGACTCAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
17 8 0.32
18 17 0.68
ACGTcount: A:0.73, C:0.00, G:0.04, T:0.22
Consensus pattern (18 bp):
TAAAAATAAAAATAAAAG
Found at i:39857809 original size:17 final size:18
Alignment explanation
Indices: 39857767--39857815 Score: 50
Period size: 17 Copynumber: 2.8 Consensus size: 18
39857757 AGTTGAAAAG
39857767 GAGCATGATTGTCATACTT
1 GAGCATGA-TGTCATACTT
*
39857786 G-GCCATGATG-CATTCTT
1 GAG-CATGATGTCATACTT
39857803 GAGCATGAT-TCAT
1 GAGCATGATGTCAT
39857816 GCTTCTTGCA
Statistics
Matches: 26, Mismatches: 1, Indels: 8
0.74 0.03 0.23
Matches are distributed among these distances:
17 16 0.62
18 4 0.15
19 6 0.23
ACGTcount: A:0.24, C:0.18, G:0.22, T:0.35
Consensus pattern (18 bp):
GAGCATGATGTCATACTT
Found at i:39858704 original size:40 final size:40
Alignment explanation
Indices: 39858638--39858804 Score: 169
Period size: 40 Copynumber: 4.2 Consensus size: 40
39858628 AAATTGAATG
* * *
39858638 ATATCCGGGCTAAG-CCCGAAGACAATTATGCTGGAAATT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
* * **
39858677 ATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGTT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
* *
39858717 ATATCCGGGCTAAGGCCCGAAGGC-ATTCGTGC-GAGTTATT
1 ATATCCGGGCTAAGACCCGAAGGCAATT-GTGCTG-GTAATT
* * ** *
39858757 CTATCCGGGCTAAGACCCGAAGGCATTTGTGCACGTGATT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
39858797 ATATCCGG
1 ATATCCGG
39858805 TTATATTCCG
Statistics
Matches: 105, Mismatches: 18, Indels: 9
0.80 0.14 0.07
Matches are distributed among these distances:
39 16 0.15
40 87 0.83
41 2 0.02
ACGTcount: A:0.26, C:0.22, G:0.28, T:0.25
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
Found at i:39865812 original size:17 final size:18
Alignment explanation
Indices: 39865770--39865818 Score: 50
Period size: 17 Copynumber: 2.8 Consensus size: 18
39865760 AGTTGAAAAG
39865770 GAGCATGATTGTCATACTT
1 GAGCATGA-TGTCATACTT
*
39865789 G-GCCATGATG-CATTCTT
1 GAG-CATGATGTCATACTT
39865806 GAGCATGAT-TCAT
1 GAGCATGATGTCAT
39865819 GCTTCTTGCA
Statistics
Matches: 26, Mismatches: 1, Indels: 8
0.74 0.03 0.23
Matches are distributed among these distances:
17 16 0.62
18 4 0.15
19 6 0.23
ACGTcount: A:0.24, C:0.18, G:0.22, T:0.35
Consensus pattern (18 bp):
GAGCATGATGTCATACTT
Found at i:39866705 original size:40 final size:39
Alignment explanation
Indices: 39866639--39866804 Score: 158
Period size: 40 Copynumber: 4.2 Consensus size: 39
39866629 AAATTGAATG
* * *
39866639 ATATCCGGGCTAAG-CCCGAAGACAATTATGCTGGAAATT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGG-TATT
* * **
39866678 ATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTATT
*
39866717 ATATCCGGGCTAAGGCCCGAAGGC-ATTCGTGC-GAGTTATT
1 ATATCCGGGCTAAGACCCGAAGGCAATT-GTGCTG-G-TATT
* * **
39866757 CTATCCGGGCTAAGACCCGAAGGCATTTGTGCACGTGATT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGT-ATT
39866797 ATATCCGG
1 ATATCCGG
39866805 TTATATTCCG
Statistics
Matches: 103, Mismatches: 17, Indels: 13
0.77 0.13 0.10
Matches are distributed among these distances:
38 3 0.03
39 42 0.41
40 56 0.54
41 2 0.02
ACGTcount: A:0.26, C:0.22, G:0.28, T:0.25
Consensus pattern (39 bp):
ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTATT
Found at i:39868442 original size:24 final size:25
Alignment explanation
Indices: 39868415--39868463 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
39868405 TACTTTTTAT
*
39868415 TAAATAAAAAAC-TTTAAAATATAA
1 TAAATAAAAAACATTTAAAACATAA
* *
39868439 TAAATCAAATACATTTAAAACATAA
1 TAAATAAAAAACATTTAAAACATAA
39868464 AAACAAATAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
24 10 0.48
25 11 0.52
ACGTcount: A:0.63, C:0.08, G:0.00, T:0.29
Consensus pattern (25 bp):
TAAATAAAAAACATTTAAAACATAA
Found at i:39868456 original size:25 final size:23
Alignment explanation
Indices: 39868427--39868491 Score: 66
Period size: 25 Copynumber: 2.9 Consensus size: 23
39868417 AATAAAAAAC
*
39868427 TTTAAAATATAATAAATCAAATACA
1 TTTAAAACATAA-AAA-CAAATACA
39868452 TTTAAAACATAAAAACAAAT--A
1 TTTAAAACATAAAAACAAATACA
*
39868473 -TTAAAACA-AAAAATAAATA
1 TTTAAAACATAAAAACAAATA
39868492 AATAATGGGA
Statistics
Matches: 37, Mismatches: 2, Indels: 7
0.80 0.04 0.15
Matches are distributed among these distances:
19 9 0.24
20 8 0.22
21 1 0.03
23 5 0.14
24 3 0.08
25 11 0.30
ACGTcount: A:0.66, C:0.08, G:0.00, T:0.26
Consensus pattern (23 bp):
TTTAAAACATAAAAACAAATACA
Found at i:39868490 original size:19 final size:20
Alignment explanation
Indices: 39868453--39868491 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
39868443 TCAAATACAT
39868453 TTAAAACATAAAAACAAATA
1 TTAAAACATAAAAACAAATA
*
39868473 TTAAAACA-AAAAATAAATA
1 TTAAAACATAAAAACAAATA
39868492 AATAATGGGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 10 0.56
20 8 0.44
ACGTcount: A:0.72, C:0.08, G:0.00, T:0.21
Consensus pattern (20 bp):
TTAAAACATAAAAACAAATA
Found at i:39873414 original size:16 final size:16
Alignment explanation
Indices: 39873395--39873425 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
39873385 CTTCTTCACT
39873395 TACTCACTTACTTAAA
1 TACTCACTTACTTAAA
*
39873411 TACTTACTTACTTAA
1 TACTCACTTACTTAA
39873426 CCAAATTTAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.23, G:0.00, T:0.42
Consensus pattern (16 bp):
TACTCACTTACTTAAA
Done.