Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr6
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: 47432654
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2298022 characters in sequence are not A, C, G, or T
File 115 of 136
Found at i:38945107 original size:40 final size:40
Alignment explanation
Indices: 38945052--38945133 Score: 146
Period size: 40 Copynumber: 2.0 Consensus size: 40
38945042 TTGAAGGACC
*
38945052 AATAGCGTAAATATTTTAAGGGTGGAATAATCTAGAAACT
1 AATAGCGTAAATATTTTAACGGTGGAATAATCTAGAAACT
*
38945092 AATAGTGTAAATATTTTAACGGTGGAATAATCTAGAAACT
1 AATAGCGTAAATATTTTAACGGTGGAATAATCTAGAAACT
38945132 AA
1 AA
38945134 GGAAAATGGA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.44, C:0.07, G:0.18, T:0.30
Consensus pattern (40 bp):
AATAGCGTAAATATTTTAACGGTGGAATAATCTAGAAACT
Found at i:38947420 original size:25 final size:22
Alignment explanation
Indices: 38947387--38947437 Score: 59
Period size: 25 Copynumber: 2.2 Consensus size: 22
38947377 TTTGTAATTG
38947387 AAAAAAAATATT-CGAAGTATATAA
1 AAAAAAAAT-TTACGAAGT-TA-AA
38947411 AAAAATAAATTTACGAAGTTAAA
1 AAAAA-AAATTTACGAAGTTAAA
38947434 AAAA
1 AAAA
38947438 GTATTGAAAG
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
23 6 0.24
24 9 0.36
25 10 0.40
ACGTcount: A:0.65, C:0.04, G:0.08, T:0.24
Consensus pattern (22 bp):
AAAAAAAATTTACGAAGTTAAA
Found at i:38948420 original size:30 final size:29
Alignment explanation
Indices: 38948376--38948479 Score: 95
Period size: 30 Copynumber: 3.4 Consensus size: 29
38948366 GATTGAGAGC
38948376 GAAAAAGA-ATGTGAGCAAGAAAAGAAAGTT
1 GAAAAAGAGA-GTGAGCAAGAAAAGAAA-TT
* * *
38948406 GAAAACGAGAGTGAGAGAAAGCAAAACGAGATT
1 GAAAAAGAGAGT--GAGCAAG-AAAA-GAAATT
38948439 GAAAAAGA-ATGTGAGCAAGAAAAGCAAATT
1 GAAAAAGAGA-GTGAGCAAGAAAAG-AAATT
38948469 GAAAAAGAGAG
1 GAAAAAGAGAG
38948480 CGAGAATGTG
Statistics
Matches: 60, Mismatches: 6, Indels: 16
0.73 0.07 0.20
Matches are distributed among these distances:
29 1 0.02
30 26 0.43
31 8 0.13
32 7 0.12
33 15 0.25
34 3 0.05
ACGTcount: A:0.56, C:0.06, G:0.28, T:0.11
Consensus pattern (29 bp):
GAAAAAGAGAGTGAGCAAGAAAAGAAATT
Found at i:38951057 original size:21 final size:20
Alignment explanation
Indices: 38951028--38951070 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
38951018 AGCTTGTTTG
38951028 AGCTCATTTTAATTTATTCCT
1 AGCTCA-TTTAATTTATTCCT
* * *
38951049 AGCTTATTTACTTTATTTCT
1 AGCTCATTTAATTTATTCCT
38951069 AG
1 AG
38951071 AATAAACTAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
20 14 0.74
21 5 0.26
ACGTcount: A:0.23, C:0.16, G:0.07, T:0.53
Consensus pattern (20 bp):
AGCTCATTTAATTTATTCCT
Found at i:38957122 original size:39 final size:39
Alignment explanation
Indices: 38957063--38957318 Score: 332
Period size: 39 Copynumber: 6.5 Consensus size: 39
38957053 TGTAATTATA
* *
38957063 CCTGACTGCACATACGTGCCCCTTTTGTACTTCGGTACC
1 CCTGAATGCACATACGTGCCCCTGTTGTACTTCGGTACC
* * * *
38957102 CCTGAATACACATACATGCCCCTATTGTACTTCGATACC
1 CCTGAATGCACATACGTGCCCCTGTTGTACTTCGGTACC
* * * *
38957141 CCTAAATGCACATACATGCCCCTGTTGTACTTCAGCACC
1 CCTGAATGCACATACGTGCCCCTGTTGTACTTCGGTACC
***
38957180 CCTGAATGCACATACGTGCATTTGTTGTACTTCGGTACC
1 CCTGAATGCACATACGTGCCCCTGTTGTACTTCGGTACC
* *
38957219 CCTGAATGCACATACGTTCCCCTGTTGTACTTCAGTACC
1 CCTGAATGCACATACGTGCCCCTGTTGTACTTCGGTACC
**
38957258 CCTGAATGCACATACGTGCCCCTGTTGTACTTCTATACC
1 CCTGAATGCACATACGTGCCCCTGTTGTACTTCGGTACC
* *
38957297 CCTGATTCGCACTTACGTGCCC
1 CCTGAAT-GCACATACGTGCCC
38957319 TTGATTATAT
Statistics
Matches: 188, Mismatches: 28, Indels: 1
0.87 0.13 0.00
Matches are distributed among these distances:
39 175 0.93
40 13 0.07
ACGTcount: A:0.21, C:0.34, G:0.16, T:0.30
Consensus pattern (39 bp):
CCTGAATGCACATACGTGCCCCTGTTGTACTTCGGTACC
Found at i:38957242 original size:20 final size:20
Alignment explanation
Indices: 38957214--38957281 Score: 68
Period size: 20 Copynumber: 3.5 Consensus size: 20
38957204 TTGTACTTCG
38957214 GTACCCCTGAATGCACATAC
1 GTACCCCTGAATGCACATAC
* * * *
38957234 GTTCCCCTG-TTGTAC-TTC
1 GTACCCCTGAATGCACATAC
38957252 AGTACCCCTGAATGCACATAC
1 -GTACCCCTGAATGCACATAC
*
38957273 GTGCCCCTG
1 GTACCCCTG
38957282 TTGTACTTCT
Statistics
Matches: 36, Mismatches: 9, Indels: 6
0.71 0.18 0.12
Matches are distributed among these distances:
18 2 0.06
19 12 0.33
20 20 0.56
21 2 0.06
ACGTcount: A:0.21, C:0.35, G:0.18, T:0.26
Consensus pattern (20 bp):
GTACCCCTGAATGCACATAC
Found at i:38957261 original size:19 final size:19
Alignment explanation
Indices: 38957237--38957300 Score: 51
Period size: 19 Copynumber: 3.3 Consensus size: 19
38957227 CACATACGTT
38957237 CCCCTGTTGTACTTCAGTA
1 CCCCTGTTGTACTTCAGTA
* * * *
38957256 CCCCTGAATGCACAT-ACGTG
1 CCCCTG-TTGTACTTCA-GTA
38957276 CCCCTGTTGTACTTCTA-TA
1 CCCCTGTTGTACTTC-AGTA
38957295 CCCCTG
1 CCCCTG
38957301 ATTCGCACTT
Statistics
Matches: 33, Mismatches: 8, Indels: 8
0.67 0.16 0.16
Matches are distributed among these distances:
19 19 0.58
20 13 0.39
21 1 0.03
ACGTcount: A:0.17, C:0.36, G:0.16, T:0.31
Consensus pattern (19 bp):
CCCCTGTTGTACTTCAGTA
Found at i:38972453 original size:10 final size:11
Alignment explanation
Indices: 38972428--38972453 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
38972418 ACTAAATAAT
38972428 AAAAAAGTTTC
1 AAAAAAGTTTC
38972439 AAAAAAGTTTC
1 AAAAAAGTTTC
38972450 AAAA
1 AAAA
38972454 CTAAAAATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.62, C:0.08, G:0.08, T:0.23
Consensus pattern (11 bp):
AAAAAAGTTTC
Found at i:38972962 original size:18 final size:17
Alignment explanation
Indices: 38972929--38972963 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
38972919 AATGAATGGG
*
38972929 AAATAAGAAATAAAATA
1 AAATAAAAAATAAAATA
38972946 AAATAAAAAAGTAAAATA
1 AAATAAAAAA-TAAAATA
38972964 CCTGCCATTC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.77, C:0.00, G:0.06, T:0.17
Consensus pattern (17 bp):
AAATAAAAAATAAAATA
Found at i:38974124 original size:20 final size:19
Alignment explanation
Indices: 38974087--38974149 Score: 56
Period size: 20 Copynumber: 3.3 Consensus size: 19
38974077 TTGATTTTTA
38974087 AAAAAATATAAAAATATTAT
1 AAAAAATATAAAAATATT-T
* * *
38974107 AAAAATTATTAAATTATTT
1 AAAAAATATAAAAATATTT
* * *
38974126 AAAAAGTATGAAAAT-TCT
1 AAAAAATATAAAAATATTT
38974144 AAAAAA
1 AAAAAA
38974150 ATATTTTTTA
Statistics
Matches: 35, Mismatches: 8, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
18 7 0.20
19 13 0.37
20 15 0.43
ACGTcount: A:0.63, C:0.02, G:0.03, T:0.32
Consensus pattern (19 bp):
AAAAAATATAAAAATATTT
Found at i:38974523 original size:24 final size:24
Alignment explanation
Indices: 38974496--38974553 Score: 107
Period size: 24 Copynumber: 2.4 Consensus size: 24
38974486 AGCTTCTTGA
38974496 TGGGCCCTATACTATGCTTCTAAG
1 TGGGCCCTATACTATGCTTCTAAG
*
38974520 TGGGCCCTATGCTATGCTTCTAAG
1 TGGGCCCTATACTATGCTTCTAAG
38974544 TGGGCCCTAT
1 TGGGCCCTAT
38974554 CGTTGGCTCA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.17, C:0.26, G:0.24, T:0.33
Consensus pattern (24 bp):
TGGGCCCTATACTATGCTTCTAAG
Found at i:38975115 original size:24 final size:25
Alignment explanation
Indices: 38975070--38975132 Score: 58
Period size: 24 Copynumber: 2.5 Consensus size: 25
38975060 GCGTTTAATT
38975070 TTTTAATTAATTTTTAAATAATATCTTA
1 TTTTAATTAA-TTTT--ATAATATCTTA
* *
38975098 TTTTAATTAATTTT-TAATTTGTTA
1 TTTTAATTAATTTTATAATATCTTA
*
38975122 TTCTAA-TAATT
1 TTTTAATTAATT
38975133 AAATATAATT
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
23 5 0.16
24 13 0.41
27 4 0.12
28 10 0.31
ACGTcount: A:0.35, C:0.03, G:0.02, T:0.60
Consensus pattern (25 bp):
TTTTAATTAATTTTATAATATCTTA
Found at i:38975589 original size:34 final size:32
Alignment explanation
Indices: 38975537--38975608 Score: 83
Period size: 32 Copynumber: 2.2 Consensus size: 32
38975527 ATTTCTGTTA
*
38975537 AATTATAATTACTTTTTTAATATATAAATATCAC
1 AATTATAATTAATTTTTTAA-AT-TAAATATCAC
* *
38975571 AATT-TAATTAATATTTTTAAATTAAATATTAT
1 AATTATAATTAAT-TTTTTAAATTAAATATCAC
38975603 AATTAT
1 AATTAT
38975609 TTTAAAATAT
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
32 12 0.36
33 10 0.30
34 11 0.33
ACGTcount: A:0.46, C:0.04, G:0.00, T:0.50
Consensus pattern (32 bp):
AATTATAATTAATTTTTTAAATTAAATATCAC
Found at i:38975616 original size:24 final size:25
Alignment explanation
Indices: 38975582--38975636 Score: 67
Period size: 25 Copynumber: 2.2 Consensus size: 25
38975572 ATTTAATTAA
* *
38975582 TATTTTTAAAT-TAAATATTATAAT
1 TATTTTAAAATATAAATATAATAAT
* *
38975606 TATTTTAAAATATTAATCTAATAAT
1 TATTTTAAAATATAAATATAATAAT
38975631 TATTTT
1 TATTTT
38975637 TACTAAATTA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
24 10 0.38
25 16 0.62
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.55
Consensus pattern (25 bp):
TATTTTAAAATATAAATATAATAAT
Found at i:38980907 original size:18 final size:18
Alignment explanation
Indices: 38980884--38980920 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
38980874 TAGAGATTGA
*
38980884 GCTTAAATAATTTTTTTT
1 GCTTAAATAATTTTCTTT
38980902 GCTTAAATAATTTTCTTT
1 GCTTAAATAATTTTCTTT
38980920 G
1 G
38980921 TATTATGATT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.27, C:0.08, G:0.08, T:0.57
Consensus pattern (18 bp):
GCTTAAATAATTTTCTTT
Found at i:38987433 original size:22 final size:22
Alignment explanation
Indices: 38987130--38987430 Score: 332
Period size: 22 Copynumber: 13.7 Consensus size: 22
38987120 AAGTAAAAAT
38987130 TGTTGATTAAATGCTGTCCAAA
1 TGTTGATTAAATGCTGTCCAAA
* * *
38987152 TATTGATTGAATGCTGTCCAAT
1 TGTTGATTAAATGCTGTCCAAA
* *
38987174 TGTTCATTAAATTCTGTCCAAA
1 TGTTGATTAAATGCTGTCCAAA
* * * *
38987196 TGTTAATTTAATGTTGTCCAAT
1 TGTTGATTAAATGCTGTCCAAA
*
38987218 TGTTGATTAAATGATGTCCAAA
1 TGTTGATTAAATGCTGTCCAAA
* * * * *
38987240 TATTGATTGAATGTTGTCTAAT
1 TGTTGATTAAATGCTGTCCAAA
*
38987262 TGTTGATTAAATGTTGTCCAAA
1 TGTTGATTAAATGCTGTCCAAA
* *
38987284 TGTTGATTTAATGCTGTCCAAT
1 TGTTGATTAAATGCTGTCCAAA
*
38987306 TGTTGACTAAATGCTGTCCAAA
1 TGTTGATTAAATGCTGTCCAAA
* * * * *
38987328 TATGGATTGAATGTTGTCCAAT
1 TGTTGATTAAATGCTGTCCAAA
*
38987350 TGTTGATTAAATGTTGTCCAAA
1 TGTTGATTAAATGCTGTCCAAA
* * *
38987372 TGTAGATTGAATGCTGTCCAAT
1 TGTTGATTAAATGCTGTCCAAA
*
38987394 TGTTGATTAAATGCTATCCAAA
1 TGTTGATTAAATGCTGTCCAAA
*
38987416 TGTTAATTAAATGCT
1 TGTTGATTAAATGCT
38987431 ATCTGAATGT
Statistics
Matches: 228, Mismatches: 51, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 228 1.00
ACGTcount: A:0.30, C:0.12, G:0.17, T:0.41
Consensus pattern (22 bp):
TGTTGATTAAATGCTGTCCAAA
Found at i:38987442 original size:44 final size:44
Alignment explanation
Indices: 38987127--38987430 Score: 419
Period size: 44 Copynumber: 6.9 Consensus size: 44
38987117 TTGAAGTAAA
*
38987127 AATTGTTGATTAAATGCTGTCCAAATATTGATTGAATGCTGTCC
1 AATTGTTGATTAAATGCTGTCCAAATGTTGATTGAATGCTGTCC
* * * * *
38987171 AATTGTTCATTAAATTCTGTCCAAATGTTAATTTAATGTTGTCC
1 AATTGTTGATTAAATGCTGTCCAAATGTTGATTGAATGCTGTCC
* * * *
38987215 AATTGTTGATTAAATGATGTCCAAATATTGATTGAATGTTGTCT
1 AATTGTTGATTAAATGCTGTCCAAATGTTGATTGAATGCTGTCC
* *
38987259 AATTGTTGATTAAATGTTGTCCAAATGTTGATTTAATGCTGTCC
1 AATTGTTGATTAAATGCTGTCCAAATGTTGATTGAATGCTGTCC
* * * *
38987303 AATTGTTGACTAAATGCTGTCCAAATATGGATTGAATGTTGTCC
1 AATTGTTGATTAAATGCTGTCCAAATGTTGATTGAATGCTGTCC
* *
38987347 AATTGTTGATTAAATGTTGTCCAAATGTAGATTGAATGCTGTCC
1 AATTGTTGATTAAATGCTGTCCAAATGTTGATTGAATGCTGTCC
* * *
38987391 AATTGTTGATTAAATGCTATCCAAATGTTAATTAAATGCT
1 AATTGTTGATTAAATGCTGTCCAAATGTTGATTGAATGCT
38987431 ATCTGAATGT
Statistics
Matches: 226, Mismatches: 34, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
44 226 1.00
ACGTcount: A:0.31, C:0.12, G:0.17, T:0.41
Consensus pattern (44 bp):
AATTGTTGATTAAATGCTGTCCAAATGTTGATTGAATGCTGTCC
Found at i:38995229 original size:22 final size:22
Alignment explanation
Indices: 38995201--38995443 Score: 247
Period size: 22 Copynumber: 11.0 Consensus size: 22
38995191 NNNNNNNNNN
*
38995201 TGTCCAATTGTTGATTAAATGC
1 TGTCCAAATGTTGATTAAATGC
*
38995223 TGTCCAAATGTTGAATTTAATG-
1 TGTCCAAATGTTG-ATTAAATGC
* *
38995245 TTTCCAATTGTTGATTAAATGC
1 TGTCCAAATGTTGATTAAATGC
* *
38995267 TGTCCAAATATTGATTGAATTG-
1 TGTCCAAATGTTGATT-AAATGC
*
38995289 TGTCCAATTGTTGATTAAATGC
1 TGTCCAAATGTTGATTAAATGC
* *
38995311 TGTCCAAATGTTGATTTAATGT
1 TGTCCAAATGTTGATTAAATGC
* *
38995333 TGTCCAATTGTTGATTAAATGA
1 TGTCCAAATGTTGATTAAATGC
* * * *
38995355 TGTCCGAATGTTGATTGAAGGT
1 TGTCCAAATGTTGATTAAATGC
* * *
38995377 TGTTCAATTGTTGATTAAATGT
1 TGTCCAAATGTTGATTAAATGC
* *
38995399 TGTCCAAATGTTAATTAAATGT
1 TGTCCAAATGTTGATTAAATGC
* * *
38995421 TGTCTAAATGTTGAATAATTGC
1 TGTCCAAATGTTGATTAAATGC
38995443 T
1 T
38995444 ATTCGTTTTT
Statistics
Matches: 181, Mismatches: 36, Indels: 8
0.80 0.16 0.04
Matches are distributed among these distances:
21 11 0.06
22 159 0.88
23 11 0.06
ACGTcount: A:0.29, C:0.10, G:0.19, T:0.42
Consensus pattern (22 bp):
TGTCCAAATGTTGATTAAATGC
Found at i:38995266 original size:44 final size:44
Alignment explanation
Indices: 38995201--38995443 Score: 328
Period size: 44 Copynumber: 5.5 Consensus size: 44
38995191 NNNNNNNNNN
*
38995201 TGTCCAATTGTTGATTAAATGCTGTCCAAATGTTGAATTTAATGT
1 TGTCCAATTGTTGATTAAATGCTGTCCAAATGTTG-ATTGAATGT
*
38995246 T-TCCAATTGTTGATTAAATGCTGTCCAAATATTGATTGAAT-T
1 TGTCCAATTGTTGATTAAATGCTGTCCAAATGTTGATTGAATGT
*
38995288 GTGTCCAATTGTTGATTAAATGCTGTCCAAATGTTGATTTAATGT
1 -TGTCCAATTGTTGATTAAATGCTGTCCAAATGTTGATTGAATGT
* * *
38995333 TGTCCAATTGTTGATTAAATGATGTCCGAATGTTGATTGAAGGT
1 TGTCCAATTGTTGATTAAATGCTGTCCAAATGTTGATTGAATGT
* * * *
38995377 TGTTCAATTGTTGATTAAATGTTGTCCAAATGTTAATTAAATGT
1 TGTCCAATTGTTGATTAAATGCTGTCCAAATGTTGATTGAATGT
* * * *
38995421 TGTCTAAATGTTGAATAATTGCT
1 TGTCCAATTGTTGATTAAATGCT
38995444 ATTCGTTTTT
Statistics
Matches: 175, Mismatches: 20, Indels: 7
0.87 0.10 0.03
Matches are distributed among these distances:
42 1 0.01
43 7 0.04
44 165 0.94
45 2 0.01
ACGTcount: A:0.29, C:0.10, G:0.19, T:0.42
Consensus pattern (44 bp):
TGTCCAATTGTTGATTAAATGCTGTCCAAATGTTGATTGAATGT
Found at i:38995399 original size:11 final size:11
Alignment explanation
Indices: 38995297--38995434 Score: 63
Period size: 11 Copynumber: 12.5 Consensus size: 11
38995287 TGTGTCCAAT
38995297 TGTTGATTAAA
1 TGTTGATTAAA
* *
38995308 TGCTG-TCCAAA
1 TGTTGAT-TAAA
*
38995319 TGTTGATTTAA
1 TGTTGATTAAA
* *
38995330 TGTTG-TCCAAT
1 TGTTGAT-TAAA
38995341 TGTTGATTAAA
1 TGTTGATTAAA
* **
38995352 TGATG-TCCGAA
1 TGTTGAT-TAAA
*
38995363 TGTTGATTGAA
1 TGTTGATTAAA
* *
38995374 GGTTG-TTCAAT
1 TGTTGATT-AAA
38995385 TGTTGATTAAA
1 TGTTGATTAAA
*
38995396 TGTTG-TCCAAA
1 TGTTGAT-TAAA
*
38995407 TGTTAATTAAA
1 TGTTGATTAAA
38995418 TGTTG-TCTAAA
1 TGTTGAT-TAAA
38995429 TGTTGA
1 TGTTGA
38995435 ATAATTGCTA
Statistics
Matches: 91, Mismatches: 24, Indels: 23
0.66 0.17 0.17
Matches are distributed among these distances:
10 7 0.08
11 78 0.86
12 6 0.07
ACGTcount: A:0.29, C:0.08, G:0.20, T:0.43
Consensus pattern (11 bp):
TGTTGATTAAA
Found at i:39006822 original size:20 final size:20
Alignment explanation
Indices: 39006775--39006841 Score: 71
Period size: 20 Copynumber: 3.4 Consensus size: 20
39006765 TTGTACGGGA
*
39006775 TTTGCACTTCGGTGCCCCTA
1 TTTGCACTTCGGTGCCCCTG
* * * *
39006795 TATACACTTCGGTGTCCTTG
1 TTTGCACTTCGGTGCCCCTG
* *
39006815 TTTGCACTACAGTGCCCCTG
1 TTTGCACTTCGGTGCCCCTG
39006835 TTTGCAC
1 TTTGCAC
39006842 ATTTCTGTCC
Statistics
Matches: 36, Mismatches: 11, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.13, C:0.31, G:0.19, T:0.36
Consensus pattern (20 bp):
TTTGCACTTCGGTGCCCCTG
Found at i:39007922 original size:24 final size:24
Alignment explanation
Indices: 39007895--39007941 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
39007885 TAGGTTGTTG
39007895 AAATGACATATTTATGCATGTTTT
1 AAATGACATATTTATGCATGTTTT
*
39007919 AAATGGCATATTTATGCATGTTT
1 AAATGACATATTTATGCATGTTT
39007942 GAATGATGCT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.32, C:0.09, G:0.15, T:0.45
Consensus pattern (24 bp):
AAATGACATATTTATGCATGTTTT
Found at i:39009935 original size:20 final size:21
Alignment explanation
Indices: 39009883--39009938 Score: 64
Period size: 19 Copynumber: 2.8 Consensus size: 21
39009873 TAAAACTAAA
*
39009883 AGTGTGGATAAAAACATTGGTG
1 AGTGT-GATAAAAGCATTGGTG
*
39009905 AG-G-GTTAAAAGCATT-GTG
1 AGTGTGATAAAAGCATTGGTG
39009923 AGTGTGATAAAAGCAT
1 AGTGTGATAAAAGCAT
39009939 AGAACGAATA
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
18 5 0.17
19 11 0.38
20 10 0.34
21 1 0.03
22 2 0.07
ACGTcount: A:0.38, C:0.05, G:0.30, T:0.27
Consensus pattern (21 bp):
AGTGTGATAAAAGCATTGGTG
Found at i:39011068 original size:30 final size:30
Alignment explanation
Indices: 39011034--39011093 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
39011024 TTAATTAAAG
*
39011034 TTATTCAATTTATTTTCCTTTGGAAGCGAA
1 TTATTCAATTTATTTTCCTTTGCAAGCGAA
39011064 TTATTCAATTTATTTTCCTTTGCAAGCGAA
1 TTATTCAATTTATTTTCCTTTGCAAGCGAA
39011094 GAGATTCGTT
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:0.27, C:0.15, G:0.12, T:0.47
Consensus pattern (30 bp):
TTATTCAATTTATTTTCCTTTGCAAGCGAA
Found at i:39011996 original size:22 final size:22
Alignment explanation
Indices: 39011968--39012009 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
39011958 CCGCTACACA
39011968 CCATAATAACTTTCGTAGAACT
1 CCATAATAACTTTCGTAGAACT
* *
39011990 CCATAATGAGTTTCGTAGAA
1 CCATAATAACTTTCGTAGAA
39012010 TTCGTTCATC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.36, C:0.19, G:0.14, T:0.31
Consensus pattern (22 bp):
CCATAATAACTTTCGTAGAACT
Found at i:39016126 original size:30 final size:31
Alignment explanation
Indices: 39016092--39016159 Score: 84
Period size: 30 Copynumber: 2.2 Consensus size: 31
39016082 TTGCCCAAGA
** * **
39016092 GTAAATACTCAAAATTTGAGGGGTTAA-AGT
1 GTAAATACGAAAAATTTGAAGGACTAATAGT
39016122 GTAAATACGAAAAATTTGAAGGACTAATAGT
1 GTAAATACGAAAAATTTGAAGGACTAATAGT
39016153 GTAAATA
1 GTAAATA
39016160 TTTAAGGGTG
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
30 22 0.69
31 10 0.31
ACGTcount: A:0.46, C:0.06, G:0.21, T:0.28
Consensus pattern (31 bp):
GTAAATACGAAAAATTTGAAGGACTAATAGT
Found at i:39019633 original size:23 final size:22
Alignment explanation
Indices: 39019596--39019638 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
39019586 TAAATACCAC
*
39019596 CCCTCATTCGCTCATTTCATCAT
1 CCCTCATTCACTCA-TTCATCAT
*
39019619 CCCTCATTCATTCATTCATC
1 CCCTCATTCACTCATTCATC
39019639 TCTCTCTCTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 6 0.33
23 12 0.67
ACGTcount: A:0.19, C:0.40, G:0.02, T:0.40
Consensus pattern (22 bp):
CCCTCATTCACTCATTCATCAT
Found at i:39021416 original size:14 final size:14
Alignment explanation
Indices: 39021397--39021424 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
39021387 TAAAGTTATA
39021397 TTTAATAATTCATT
1 TTTAATAATTCATT
39021411 TTTAATAATTCATT
1 TTTAATAATTCATT
39021425 AATAAATTGG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.07, G:0.00, T:0.57
Consensus pattern (14 bp):
TTTAATAATTCATT
Found at i:39029069 original size:14 final size:14
Alignment explanation
Indices: 39029050--39029077 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
39029040 TAAAGTTATA
39029050 TTTAATAATTCATT
1 TTTAATAATTCATT
39029064 TTTAATAATTCATT
1 TTTAATAATTCATT
39029078 AATAAATTGG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.07, G:0.00, T:0.57
Consensus pattern (14 bp):
TTTAATAATTCATT
Found at i:39037619 original size:43 final size:41
Alignment explanation
Indices: 39037565--39037713 Score: 131
Period size: 43 Copynumber: 3.5 Consensus size: 41
39037555 AAAAAACTAG
*
39037565 TAAAGGTCATGTTTTATAGTGACAATTTTAGTAAAAGCGTCGC
1 TAAAGGTCATGTTTTATAGTGACATTTTTAGTAAAAG-G-CGC
* * * * *
39037608 TAAAGGTCATGTTCTT-TAGCGGCGTTTTTGGGAAAAGTGCGGC
1 TAAAGGTCATGTT-TTATAGTGACATTTTTAGTAAAAG-GC-GC
* * *
39037651 TAAAAGTCATGTTCTATAGT-AGCTTTTTTAGTAAAAGGCCGC
1 TAAAGGTCATGTTTTATAGTGA-CATTTTTAGTAAAAGG-CGC
*
39037693 TAAAGGTCATGTTTTTTAGTG
1 TAAAGGTCATGTTTTATAGTG
39037714 GCGTTTGTGG
Statistics
Matches: 83, Mismatches: 17, Indels: 12
0.74 0.15 0.11
Matches are distributed among these distances:
42 22 0.27
43 59 0.71
44 2 0.02
ACGTcount: A:0.28, C:0.12, G:0.24, T:0.36
Consensus pattern (41 bp):
TAAAGGTCATGTTTTATAGTGACATTTTTAGTAAAAGGCGC
Found at i:39037696 original size:42 final size:43
Alignment explanation
Indices: 39037590--39037705 Score: 135
Period size: 43 Copynumber: 2.7 Consensus size: 43
39037580 ATAGTGACAA
* * *
39037590 TTTTAGTAAAAGCGTCGCTAAAGGTCATGTTCTTTAGCGGCGT
1 TTTTAGTAAAAGCGCCGCTAAAGGTCATGTTCTATAGCAGCGT
* * * * * * *
39037633 TTTTGGGAAAAGTGCGGCTAAAAGTCATGTTCTATAGTAGCTT
1 TTTTAGTAAAAGCGCCGCTAAAGGTCATGTTCTATAGCAGCGT
39037676 TTTTAGTAAAAG-GCCGCTAAAGGTCATGTT
1 TTTTAGTAAAAGCGCCGCTAAAGGTCATGTT
39037706 TTTTAGTGGC
Statistics
Matches: 59, Mismatches: 14, Indels: 1
0.80 0.19 0.01
Matches are distributed among these distances:
42 16 0.27
43 43 0.73
ACGTcount: A:0.27, C:0.14, G:0.25, T:0.34
Consensus pattern (43 bp):
TTTTAGTAAAAGCGCCGCTAAAGGTCATGTTCTATAGCAGCGT
Found at i:39043118 original size:35 final size:35
Alignment explanation
Indices: 39043072--39043138 Score: 116
Period size: 35 Copynumber: 1.9 Consensus size: 35
39043062 TTTTTCTATT
39043072 CTTTAAATGTTTATGTAAGTTATGATAATCATAAA
1 CTTTAAATGTTTATGTAAGTTATGATAATCATAAA
* *
39043107 CTTTAAATGTTTGTGTAAGTTATGATTATCAT
1 CTTTAAATGTTTATGTAAGTTATGATAATCAT
39043139 CTTTAAATAT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 30 1.00
ACGTcount: A:0.34, C:0.06, G:0.13, T:0.46
Consensus pattern (35 bp):
CTTTAAATGTTTATGTAAGTTATGATAATCATAAA
Found at i:39045405 original size:15 final size:16
Alignment explanation
Indices: 39045382--39045412 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
39045372 AAAAATTGAG
39045382 AAAGAAAAGTGCAGAA
1 AAAGAAAAGTGCAGAA
39045398 AAAG-AAAGTGCAGAA
1 AAAGAAAAGTGCAGAA
39045413 TAAATCTCAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 11 0.73
16 4 0.27
ACGTcount: A:0.61, C:0.06, G:0.26, T:0.06
Consensus pattern (16 bp):
AAAGAAAAGTGCAGAA
Found at i:39046802 original size:41 final size:41
Alignment explanation
Indices: 39046753--39046869 Score: 164
Period size: 42 Copynumber: 2.8 Consensus size: 41
39046743 GATTTTGCTT
* *
39046753 ACCTTTTGC-GACGTTTGTGAGAAAACGCCGCTATAGTTCTA
1 ACCTTTTGCAG-CGTTTATGAGAAAATGCCGCTATAGTTCTA
* *
39046794 ACCTTTTGCAGCATTTATGAGAAAAATGACGCTATAGTTCTA
1 ACCTTTTGCAGCGTTTATGAG-AAAATGCCGCTATAGTTCTA
*
39046836 ACCTTTTGCAGTGTTTATGAGAAAATGCCGCTAT
1 ACCTTTTGCAGCGTTTATGAGAAAATGCCGCTAT
39046870 TGCTTTACTT
Statistics
Matches: 67, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
41 29 0.43
42 38 0.57
ACGTcount: A:0.28, C:0.19, G:0.20, T:0.33
Consensus pattern (41 bp):
ACCTTTTGCAGCGTTTATGAGAAAATGCCGCTATAGTTCTA
Found at i:39059431 original size:25 final size:25
Alignment explanation
Indices: 39059402--39059508 Score: 144
Period size: 25 Copynumber: 4.3 Consensus size: 25
39059392 ATTCCCACTC
39059402 ACAGCTCGTGAGAGCATACCGATCT
1 ACAGCTCGTGAGAGCATACCGATCT
* *
39059427 ACAGCTCGTGTGAGCATACCGATTT
1 ACAGCTCGTGAGAGCATACCGATCT
* *
39059452 ATAGCTCGTGAAAGCATACCGATCT
1 ACAGCTCGTGAGAGCATACCGATCT
* *
39059477 ACAGCTCATGTGAGCATACCGAT-T
1 ACAGCTCGTGAGAGCATACCGATCT
39059501 CACAGCTC
1 -ACAGCTC
39059509 TATGAGCATA
Statistics
Matches: 71, Mismatches: 10, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
24 1 0.01
25 70 0.99
ACGTcount: A:0.28, C:0.27, G:0.21, T:0.23
Consensus pattern (25 bp):
ACAGCTCGTGAGAGCATACCGATCT
Found at i:39059508 original size:50 final size:50
Alignment explanation
Indices: 39059400--39059508 Score: 182
Period size: 50 Copynumber: 2.2 Consensus size: 50
39059390 ACATTCCCAC
* *
39059400 TCACAGCTCGTGAGAGCATACCGATCTACAGCTCGTGTGAGCATACCGAT
1 TCACAGCTCGTGAAAGCATACCGATCTACAGCTCATGTGAGCATACCGAT
* *
39059450 TTATAGCTCGTGAAAGCATACCGATCTACAGCTCATGTGAGCATACCGAT
1 TCACAGCTCGTGAAAGCATACCGATCTACAGCTCATGTGAGCATACCGAT
39059500 TCACAGCTC
1 TCACAGCTC
39059509 TATGAGCATA
Statistics
Matches: 53, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
50 53 1.00
ACGTcount: A:0.28, C:0.28, G:0.21, T:0.24
Consensus pattern (50 bp):
TCACAGCTCGTGAAAGCATACCGATCTACAGCTCATGTGAGCATACCGAT
Found at i:39087501 original size:20 final size:20
Alignment explanation
Indices: 39087476--39087513 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
39087466 ACCAATCGAA
39087476 GATAATTA-ATTATTTAATTT
1 GATAATTAGA-TATTTAATTT
39087496 GATAATTAGATATTTAAT
1 GATAATTAGATATTTAAT
39087514 CGATCATAGG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 16 0.94
21 1 0.06
ACGTcount: A:0.42, C:0.00, G:0.08, T:0.50
Consensus pattern (20 bp):
GATAATTAGATATTTAATTT
Found at i:39089259 original size:16 final size:16
Alignment explanation
Indices: 39089221--39089259 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
39089211 ATTTAACTTA
*
39089221 AAAATTTGTTATTAAT
1 AAAATTTCTTATTAAT
* *
39089237 TACATTTCTTATTAAT
1 AAAATTTCTTATTAAT
39089253 AAAATTT
1 AAAATTT
39089260 TAATATAAAT
Statistics
Matches: 18, Mismatches: 5, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.41, C:0.05, G:0.03, T:0.51
Consensus pattern (16 bp):
AAAATTTCTTATTAAT
Found at i:39094393 original size:34 final size:34
Alignment explanation
Indices: 39094288--39094401 Score: 104
Period size: 34 Copynumber: 3.4 Consensus size: 34
39094278 TGCACTGATT
* * * *
39094288 TGTTATAAGCATATTAATTGCCATCGTATTGATC
1 TGTTATAAGCATATTAATTGCTACCATATTAATC
* * * * * * *
39094322 CGTTAAAACCATATTATTTGTTACCACATCGAA-C
1 TGTTATAAGCATATTAATTGCTACCATAT-TAATC
*
39094356 TGTTATGAGCATATTAATTGCTACCATATTAATC
1 TGTTATAAGCATATTAATTGCTACCATATTAATC
39094390 TGTTATAAGCAT
1 TGTTATAAGCAT
39094402 GTCATATCGC
Statistics
Matches: 58, Mismatches: 20, Indels: 4
0.71 0.24 0.05
Matches are distributed among these distances:
33 2 0.03
34 55 0.95
35 1 0.02
ACGTcount: A:0.32, C:0.17, G:0.12, T:0.39
Consensus pattern (34 bp):
TGTTATAAGCATATTAATTGCTACCATATTAATC
Found at i:39095816 original size:50 final size:50
Alignment explanation
Indices: 39095721--39095858 Score: 150
Period size: 50 Copynumber: 2.8 Consensus size: 50
39095711 TATTAACGTT
* *
39095721 ATGAGAGGTCCCACGTAAGACCATGTCTAGGACATGGCGTTGGCACCGAA
1 ATGAGAGGTCCCACGTAAGACCATGTCTAGGACATGGCCTGGGCACCGAA
* * * ** *
39095771 ATGAGAGGTCCCCCGTAAGACCATGTTTGGGACATGGCCTGGGCACTTAT
1 ATGAGAGGTCCCACGTAAGACCATGTCTAGGACATGGCCTGGGCACCGAA
** * * * *
39095821 ATGAGAACTCCCATGTAAGACCATATCTGGGATATGGC
1 ATGAGAGGTCCCACGTAAGACCATGTCTAGGACATGGC
39095859 ATTGGCAGTA
Statistics
Matches: 73, Mismatches: 15, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
50 73 1.00
ACGTcount: A:0.27, C:0.23, G:0.28, T:0.22
Consensus pattern (50 bp):
ATGAGAGGTCCCACGTAAGACCATGTCTAGGACATGGCCTGGGCACCGAA
Found at i:39099125 original size:27 final size:27
Alignment explanation
Indices: 39098823--39099123 Score: 363
Period size: 27 Copynumber: 11.2 Consensus size: 27
39098813 TTACACTGTT
*
39098823 ATGACCAAAATACCCCCATAGGGTAAA
1 ATGACCGAAATACCCCCATAGGGTAAA
* *
39098850 ATGATCGAAATACCCCCATAGGGTAGA
1 ATGACCGAAATACCCCCATAGGGTAAA
*
39098877 ATGACCGAAATA-CCCTATAGGGTAAA
1 ATGACCGAAATACCCCCATAGGGTAAA
39098903 ATGACCGAAATACCCCCATAGGGTAAA
1 ATGACCGAAATACCCCCATAGGGTAAA
*
39098930 ATGACC-AAAAACCCCTCATAGGGTAAA
1 ATGACCGAAATACCCC-CATAGGGTAAA
* *
39098957 ATGACCGAAATACCCACATAGGGTAGA
1 ATGACCGAAATACCCCCATAGGGTAAA
* * * * *
39098984 ATAACTGAAATATCCCTATAGGGTAGA
1 ATGACCGAAATACCCCCATAGGGTAAA
* * *
39099011 ATGATCAAAATACCCCCATAGGGTAGA
1 ATGACCGAAATACCCCCATAGGGTAAA
* * *
39099038 ATCACCAAAATACCCCCATAGGGTAGA
1 ATGACCGAAATACCCCCATAGGGTAAA
* * * *
39099065 ATCACCAAAATAACCTCATAGGGTAAA
1 ATGACCGAAATACCCCCATAGGGTAAA
* *
39099092 ATGACTGAAATACCCTCATAGGGTAAA
1 ATGACCGAAATACCCCCATAGGGTAAA
39099119 ATGAC
1 ATGAC
39099124 TGTTATACCC
Statistics
Matches: 240, Mismatches: 31, Indels: 6
0.87 0.11 0.02
Matches are distributed among these distances:
26 32 0.13
27 201 0.84
28 7 0.03
ACGTcount: A:0.42, C:0.23, G:0.18, T:0.18
Consensus pattern (27 bp):
ATGACCGAAATACCCCCATAGGGTAAA
Found at i:39111493 original size:26 final size:26
Alignment explanation
Indices: 39111463--39111515 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 26
39111453 CACCAATATC
* *
39111463 GCAGCATAGCTGCCAGTAGTAATAAT
1 GCAGCAGAGCTGCCAGTAGTAAGAAT
*
39111489 GCAGCAGAGTTGCCAGTAGTAAGAAT
1 GCAGCAGAGCTGCCAGTAGTAAGAAT
39111515 G
1 G
39111516 GCTAAGAGCT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.34, C:0.17, G:0.28, T:0.21
Consensus pattern (26 bp):
GCAGCAGAGCTGCCAGTAGTAAGAAT
Found at i:39111667 original size:32 final size:32
Alignment explanation
Indices: 39111585--39111799 Score: 206
Period size: 32 Copynumber: 6.7 Consensus size: 32
39111575 TACAATAATG
* * * * *
39111585 TGATTGGCAGAAAGCCATCAGTAGCAGTGATA
1 TGATCGGCATAAAGCCATCAGTAACAGTAACA
* *
39111617 TGA-CTGGCACATAA-CCATCAGTAACGGTAACA
1 TGATC-GGCATA-AAGCCATCAGTAACAGTAACA
*
39111649 TGATCGACATAAAGCCATCAGTAAC-GATAACA
1 TGATCGGCATAAAGCCATCAGTAACAG-TAACA
39111681 TGATCGGCATAAAGCCATCAGTAACAGTGAA-A
1 TGATCGGCATAAAGCCATCAGTAACAGT-AACA
* * * *
39111713 TGATCGGCACACAGCCATCGGTAACAGTAATA
1 TGATCGGCATAAAGCCATCAGTAACAGTAACA
* *
39111745 TGATCGGCACAAAGCTATCAGTAACAGT-ACTA
1 TGATCGGCATAAAGCCATCAGTAACAGTAAC-A
**
39111777 TGATCAACATAAAGCCATCAGTA
1 TGATCGGCATAAAGCCATCAGTA
39111800 CTATAAACAG
Statistics
Matches: 154, Mismatches: 20, Indels: 18
0.80 0.10 0.09
Matches are distributed among these distances:
31 6 0.04
32 142 0.92
33 6 0.04
ACGTcount: A:0.39, C:0.21, G:0.20, T:0.20
Consensus pattern (32 bp):
TGATCGGCATAAAGCCATCAGTAACAGTAACA
Found at i:39111759 original size:96 final size:96
Alignment explanation
Indices: 39111585--39111866 Score: 256
Period size: 96 Copynumber: 3.0 Consensus size: 96
39111575 TACAATAATG
* * * * * *
39111585 TGATTGGCAGAAAGCCATCAGTAGCAGTGATATGACTGGCACATAACCATCAGTAACGGTAACAT
1 TGATCGGCATAAAGCCATCAGTAACAGTGAAATGACTGGCACACAACCATCAGTAACAGTAACAT
*
39111650 GATCGACATAAAGCCATCAGTAAC-GATAAC-A
66 GATCGACACAAAGCCATCAGTAACAG-T-ACTA
* * *
39111681 TGATCGGCATAAAGCCATCAGTAACAGTGAAATGA-TCGGCACACAGCCATCGGTAACAGTAATA
1 TGATCGGCATAAAGCCATCAGTAACAGTGAAATGACT-GGCACACAACCATCAGTAACAGTAACA
* *
39111745 TGATCGGCACAAAGCTATCAGTAACAGTACTA
65 TGATCGACACAAAGCCATCAGTAACAGTACTA
** * * * * * *
39111777 TGATCAACATAAAGCCATCAGT-ACTA-T-AAACAGAATGGC-TACAACCATAAGT-ACAATAAT
1 TGATCGGCATAAAGCCATCAGTAAC-AGTGAAA-TGACTGGCACACAACCATCAGTAACAGTAAC
* * *
39111837 GTGATTGGCACAAAGCCATCAGTAACAGTA
64 ATGATCGACACAAAGCCATCAGTAACAGTA
39111867 ATACCTTGAA
Statistics
Matches: 157, Mismatches: 23, Indels: 15
0.81 0.12 0.08
Matches are distributed among these distances:
93 34 0.22
94 12 0.08
95 11 0.07
96 99 0.63
97 1 0.01
ACGTcount: A:0.40, C:0.21, G:0.19, T:0.20
Consensus pattern (96 bp):
TGATCGGCATAAAGCCATCAGTAACAGTGAAATGACTGGCACACAACCATCAGTAACAGTAACAT
GATCGACACAAAGCCATCAGTAACAGTACTA
Found at i:39119550 original size:17 final size:16
Alignment explanation
Indices: 39119526--39119577 Score: 61
Period size: 17 Copynumber: 3.2 Consensus size: 16
39119516 AGGCAGTTCG
39119526 CATA-AAATAACAGTT
1 CATACAAATAACAGTT
*
39119541 CATACGAAATAATAGTT
1 CATAC-AAATAACAGTT
*
39119558 CATTCAATATAACAGTT
1 CATACAA-ATAACAGTT
39119575 CAT
1 CAT
39119578 TCAATATAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
15 4 0.13
16 2 0.06
17 25 0.81
ACGTcount: A:0.46, C:0.15, G:0.08, T:0.31
Consensus pattern (16 bp):
CATACAAATAACAGTT
Found at i:39119578 original size:17 final size:17
Alignment explanation
Indices: 39119532--39119586 Score: 76
Period size: 17 Copynumber: 3.2 Consensus size: 17
39119522 TTCGCATAAA
*
39119532 ATAACAGTTCATACGAA-
1 ATAACAGTTCATTC-AAT
*
39119549 ATAATAGTTCATTCAAT
1 ATAACAGTTCATTCAAT
39119566 ATAACAGTTCATTCAAT
1 ATAACAGTTCATTCAAT
39119583 ATAA
1 ATAA
39119587 TAATTCATCC
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
16 2 0.06
17 32 0.94
ACGTcount: A:0.45, C:0.15, G:0.07, T:0.33
Consensus pattern (17 bp):
ATAACAGTTCATTCAAT
Found at i:39119593 original size:17 final size:17
Alignment explanation
Indices: 39119549--39119594 Score: 74
Period size: 17 Copynumber: 2.7 Consensus size: 17
39119539 TTCATACGAA
39119549 ATAATAGTTCATTCAAT
1 ATAATAGTTCATTCAAT
*
39119566 ATAACAGTTCATTCAAT
1 ATAATAGTTCATTCAAT
*
39119583 ATAATAATTCAT
1 ATAATAGTTCAT
39119595 CCATACAACA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 26 1.00
ACGTcount: A:0.43, C:0.13, G:0.04, T:0.39
Consensus pattern (17 bp):
ATAATAGTTCATTCAAT
Found at i:39120304 original size:18 final size:18
Alignment explanation
Indices: 39120262--39120310 Score: 53
Period size: 18 Copynumber: 2.7 Consensus size: 18
39120252 CACAATTTCG
**
39120262 CAAATTAATACAGTTCAC
1 CAAATTAATACAAATCAC
*
39120280 CATATTAATACAAATCAC
1 CAAATTAATACAAATCAC
* *
39120298 TAAATTAACACAA
1 CAAATTAATACAA
39120311 TTGGCGATAA
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.51, C:0.20, G:0.02, T:0.27
Consensus pattern (18 bp):
CAAATTAATACAAATCAC
Found at i:39120650 original size:32 final size:31
Alignment explanation
Indices: 39120565--39120693 Score: 127
Period size: 31 Copynumber: 4.0 Consensus size: 31
39120555 CGCAAGCATT
*
39120565 ACAAAACCCGTATACATATATATTATATA-A-A
1 ACAAAACCC--ATGCATATATATTATATATATA
39120596 ACAAAACCCATATATGCATATATATTATATATATA
1 ACAAAACCC----ATGCATATATATTATATATATA
* *
39120631 ATCAAGACCCATGCATATATATTATGTATATA
1 A-CAAAACCCATGCATATATATTATATATATA
* * *
39120663 ACAAAACCCAAGAATATATATTGTATATATA
1 ACAAAACCCATGCATATATATTATATATATA
39120694 CACATACCTT
Statistics
Matches: 84, Mismatches: 9, Indels: 10
0.82 0.09 0.10
Matches are distributed among these distances:
31 34 0.40
32 22 0.26
33 18 0.21
34 1 0.01
35 2 0.02
36 7 0.08
ACGTcount: A:0.48, C:0.15, G:0.05, T:0.32
Consensus pattern (31 bp):
ACAAAACCCATGCATATATATTATATATATA
Found at i:39123793 original size:21 final size:21
Alignment explanation
Indices: 39123767--39123811 Score: 90
Period size: 21 Copynumber: 2.1 Consensus size: 21
39123757 TTTTGGACTA
39123767 AATTGAATGAAATTATGTTTG
1 AATTGAATGAAATTATGTTTG
39123788 AATTGAATGAAATTATGTTTG
1 AATTGAATGAAATTATGTTTG
39123809 AAT
1 AAT
39123812 GAGTTCAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.40, C:0.00, G:0.18, T:0.42
Consensus pattern (21 bp):
AATTGAATGAAATTATGTTTG
Found at i:39124165 original size:42 final size:41
Alignment explanation
Indices: 39124117--39124198 Score: 119
Period size: 42 Copynumber: 2.0 Consensus size: 41
39124107 CTATATGAAT
* * * *
39124117 GGCACTAAGTGTGTGAAATTAAAATGATGATGTTGAATAACA
1 GGCACTAAGTGTGCGAAACTAAAATGACGATG-GGAATAACA
39124159 GGCACTAAGTGTGCGAAACTAAAATGACGATGGGAATAAC
1 GGCACTAAGTGTGCGAAACTAAAATGACGATGGGAATAAC
39124199 TTCATTATGG
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
41 7 0.19
42 29 0.81
ACGTcount: A:0.40, C:0.11, G:0.26, T:0.23
Consensus pattern (41 bp):
GGCACTAAGTGTGCGAAACTAAAATGACGATGGGAATAACA
Found at i:39130852 original size:23 final size:24
Alignment explanation
Indices: 39130809--39130858 Score: 59
Period size: 23 Copynumber: 2.1 Consensus size: 24
39130799 TTAAGTAAAT
*
39130809 ATTTAAAAATAATAATTAAA-TTC
1 ATTTAAAAATAATAATGAAATTTC
*
39130832 ATTTAAACATAA-AATAGAAATTTC
1 ATTTAAAAATAATAAT-GAAATTTC
39130856 ATT
1 ATT
39130859 CAGTCGAGAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
22 3 0.13
23 14 0.61
24 6 0.26
ACGTcount: A:0.54, C:0.06, G:0.02, T:0.38
Consensus pattern (24 bp):
ATTTAAAAATAATAATGAAATTTC
Found at i:39133771 original size:23 final size:25
Alignment explanation
Indices: 39133727--39133772 Score: 69
Period size: 23 Copynumber: 1.9 Consensus size: 25
39133717 AAGCTTTCTC
39133727 ATACCTATGTTATATTGTGAATAAA
1 ATACCTATGTTATATTGTGAATAAA
*
39133752 ATACTTATG-TAT-TTGTGAATA
1 ATACCTATGTTATATTGTGAATA
39133773 TGTTAATTCA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 9 0.45
24 3 0.15
25 8 0.40
ACGTcount: A:0.37, C:0.07, G:0.13, T:0.43
Consensus pattern (25 bp):
ATACCTATGTTATATTGTGAATAAA
Found at i:39135495 original size:27 final size:27
Alignment explanation
Indices: 39135464--39136014 Score: 485
Period size: 27 Copynumber: 20.4 Consensus size: 27
39135454 AAAAATTATT
* * *
39135464 GAAATACCCTCGAATGGTAAAATTACC
1 GAAATACCCCCGAAAGGTAAAATGACC
* * *
39135491 AAAATACCCCCGAAGGGTAAAATGATC
1 GAAATACCCCCGAAAGGTAAAATGACC
*
39135518 GAAATACCCCCGAATGGGTAAAATGACC
1 GAAATACCCCCGAA-AGGTAAAATGACC
* *
39135546 GAAATACCCCTGAAGGGTAAAATGACC
1 GAAATACCCCCGAAAGGTAAAATGACC
**
39135573 GAAATACCCCCGATGGGTAAAATGACC
1 GAAATACCCCCGAAAGGTAAAATGACC
** * *
39135600 GAAATACCCCTAAAAGATAAAATGACT
1 GAAATACCCCCGAAAGGTAAAATGACC
* * *
39135627 GAATTACCCCCGAACGGTAAAATGACT
1 GAAATACCCCCGAAAGGTAAAATGACC
* * * *
39135654 GAATTACCCCCAAAAGGTAAAACGACT
1 GAAATACCCCCGAAAGGTAAAATGACC
* * *
39135681 GAATTACCCCTGAAGGGTAAAATGACC
1 GAAATACCCCCGAAAGGTAAAATGACC
* **
39135708 GAATTACCCCTAAAAGGTAAAATGACC
1 GAAATACCCCCGAAAGGTAAAATGACC
* * * *
39135735 GAATTACCCCTGAAGGGTAAAATTACC
1 GAAATACCCCCGAAAGGTAAAATGACC
* * * *
39135762 GAATTACCCCCAAAAGGTAGAATGACT
1 GAAATACCCCCGAAAGGTAAAATGACC
* ** * *
39135789 GAATTACCATCGAAGGGTAAAATGACT
1 GAAATACCCCCGAAAGGTAAAATGACC
* *
39135816 GAATTACCCCCTAAAGGTAAAATGACC
1 GAAATACCCCCGAAAGGTAAAATGACC
** *
39135843 GAAATACCCTTGAAAGGTAAAATGACT
1 GAAATACCCCCGAAAGGTAAAATGACC
* ** * *
39135870 GAAATAGCCCTAAAAGGTAAAATAACT
1 GAAATACCCCCGAAAGGTAAAATGACC
* * **
39135897 GAAATACCCTCGAAGGGTAAAATGATT
1 GAAATACCCCCGAAAGGTAAAATGACC
* * *
39135924 GAAATACCCTCGAAGGGTAAAATTACC
1 GAAATACCCCCGAAAGGTAAAATGACC
* *
39135951 AAAATACCCCTG-AAGGATAAAATGACC
1 GAAATACCCCCGAAAGG-TAAAATGACC
* * *
39135978 GAAACACCCCC-ATAGGGTAAAATGACT
1 GAAATACCCCCGA-AAGGTAAAATGACC
*
39136005 GATATACCCC
1 GAAATACCCC
39136015 TAGGAGTAGA
Statistics
Matches: 439, Mismatches: 81, Indels: 8
0.83 0.15 0.02
Matches are distributed among these distances:
26 3 0.01
27 408 0.93
28 28 0.06
ACGTcount: A:0.42, C:0.22, G:0.18, T:0.18
Consensus pattern (27 bp):
GAAATACCCCCGAAAGGTAAAATGACC
Found at i:39136014 original size:54 final size:54
Alignment explanation
Indices: 39135463--39136015 Score: 556
Period size: 54 Copynumber: 10.2 Consensus size: 54
39135453 GAAAAATTAT
* * * * *
39135463 TGAAATA-CCCTCGAATGGTAAAATTACCAAAATACCCCCGAAGGGTAAAATGA-
1 TGAAATACCCCT-GAAGGGTAAAATGACCGAAATACCCCCAAAAGGTAAAATGAC
* ** *
39135516 TCGAAATACCCCCGAATGGGTAAAATGACCGAAATACCCCTGAAGGGTAAAATGAC
1 T-GAAATACCCCTGAA-GGGTAAAATGACCGAAATACCCCCAAAAGGTAAAATGAC
* * * * *
39135572 CGAAATACCCCCGATGGGTAAAATGACCGAAATACCCCTAAAAGATAAAATGAC
1 TGAAATACCCCTGAAGGGTAAAATGACCGAAATACCCCCAAAAGGTAAAATGAC
* * * * * *
39135626 TGAATTACCCCCGAACGGTAAAATGACTGAATTACCCCCAAAAGGTAAAACGAC
1 TGAAATACCCCTGAAGGGTAAAATGACCGAAATACCCCCAAAAGGTAAAATGAC
* * *
39135680 TGAATTACCCCTGAAGGGTAAAATGACCGAATTACCCCTAAAAGGTAAAATGAC
1 TGAAATACCCCTGAAGGGTAAAATGACCGAAATACCCCCAAAAGGTAAAATGAC
* * * * *
39135734 CGAATTACCCCTGAAGGGTAAAATTACCGAATTACCCCCAAAAGGTAGAATGAC
1 TGAAATACCCCTGAAGGGTAAAATGACCGAAATACCCCCAAAAGGTAAAATGAC
* * * * *
39135788 TGAATTA-CCATCGAAGGGTAAAATGACTGAATTACCCCCTAAAGGTAAAATGAC
1 TGAAATACCCCT-GAAGGGTAAAATGACCGAAATACCCCCAAAAGGTAAAATGAC
* * * * * * *
39135842 CGAAATACCCTTGAAAGGTAAAATGACTGAAATAGCCCTAAAAGGTAAAATAAC
1 TGAAATACCCCTGAAGGGTAAAATGACCGAAATACCCCCAAAAGGTAAAATGAC
** * * * *
39135896 TGAAATA-CCCTCGAAGGGTAAAATGATTGAAATACCCTCGAAGGGTAAAATTAC
1 TGAAATACCCCT-GAAGGGTAAAATGACCGAAATACCCCCAAAAGGTAAAATGAC
** * * * *
39135950 CAAAATACCCCTGAAGGATAAAATGACCGAAACACCCCCATAGGGTAAAATGAC
1 TGAAATACCCCTGAAGGGTAAAATGACCGAAATACCCCCAAAAGGTAAAATGAC
*
39136004 TGATATACCCCT
1 TGAAATACCCCT
39136016 AGGAGTAGAA
Statistics
Matches: 426, Mismatches: 66, Indels: 15
0.84 0.13 0.03
Matches are distributed among these distances:
53 7 0.02
54 362 0.85
55 57 0.13
ACGTcount: A:0.42, C:0.22, G:0.18, T:0.18
Consensus pattern (54 bp):
TGAAATACCCCTGAAGGGTAAAATGACCGAAATACCCCCAAAAGGTAAAATGAC
Found at i:39136422 original size:28 final size:28
Alignment explanation
Indices: 39136378--39136460 Score: 148
Period size: 28 Copynumber: 3.0 Consensus size: 28
39136368 TGCAATGTAT
*
39136378 TGTTACTGTATTAGGCTAAGGCCCACAC
1 TGTTACTGTATTGGGCTAAGGCCCACAC
39136406 TGTTACTGTATTGGGCTAAGGCCCACAC
1 TGTTACTGTATTGGGCTAAGGCCCACAC
*
39136434 TGTTACTATATTGGGCTAAGGCCCACA
1 TGTTACTGTATTGGGCTAAGGCCCACA
39136461 TTCCACTGTT
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 53 1.00
ACGTcount: A:0.24, C:0.24, G:0.23, T:0.29
Consensus pattern (28 bp):
TGTTACTGTATTGGGCTAAGGCCCACAC
Found at i:39144022 original size:30 final size:29
Alignment explanation
Indices: 39143961--39144066 Score: 106
Period size: 30 Copynumber: 3.6 Consensus size: 29
39143951 TTGTTGACAC
* * *
39143961 ATCCCTTTCCTTTATTCGATAATCGAGGCT
1 ATCCCTTTCCATAATTCGAT-ATCGAAGCT
39143991 ATCCCTTTCCATAATTCGATATCTGAAGCT
1 ATCCCTTTCCATAATTCGATATC-GAAGCT
* * *
39144021 ATCACTATT-CATAATTCGATAGCCAAGGCT
1 ATCCCT-TTCCATAATTCGATATCGAA-GCT
*
39144051 ATCCCTTTTCATAATT
1 ATCCCTTTCCATAATT
39144067 TAGTGGTCGT
Statistics
Matches: 65, Mismatches: 7, Indels: 8
0.81 0.09 0.10
Matches are distributed among these distances:
29 7 0.11
30 56 0.86
31 2 0.03
ACGTcount: A:0.26, C:0.25, G:0.10, T:0.38
Consensus pattern (29 bp):
ATCCCTTTCCATAATTCGATATCGAAGCT
Found at i:39144090 original size:30 final size:30
Alignment explanation
Indices: 39144051--39144124 Score: 103
Period size: 30 Copynumber: 2.5 Consensus size: 30
39144041 AGCCAAGGCT
* *
39144051 ATCCCTTTTCATAATTTAGTGGTCGTCACC
1 ATCCCTTTTCATAATTCAATGGTCGTCACC
* * *
39144081 ATCCGTTTTCATTATTCAATGGTCGTCATC
1 ATCCCTTTTCATAATTCAATGGTCGTCACC
39144111 ATCCCTTTTCATAA
1 ATCCCTTTTCATAA
39144125 CCAATAGCCG
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 37 1.00
ACGTcount: A:0.22, C:0.26, G:0.11, T:0.42
Consensus pattern (30 bp):
ATCCCTTTTCATAATTCAATGGTCGTCACC
Found at i:39147179 original size:147 final size:147
Alignment explanation
Indices: 39146967--39147312 Score: 514
Period size: 147 Copynumber: 2.4 Consensus size: 147
39146957 TTACCATTAT
* * * * ** * *
39146967 GGATGGCTCAACAATGATGGT-TTGCACTATTTCAATGTTCTACCATCCCGAATGACTCAACAAT
1 GGATAGCTCGACAATGATGGTATT-CAATATCTCAACATTCTACCATCTCGGATGACTCAACAAT
* *
39147031 GATGCCTTTCATTATTCCTACATTTTACCATCTTGGGTGGTCCGACAACGATGGTTCTCATAGTT
65 GATGCCTTTCATTATTCCTACATTTTACCATCTTGGGTGGTCCAACAACGATGGTTCTCACAGTT
39147096 TACTTATTCTACCATCCC
130 TACTTATTCTACCATCCC
*
39147114 GGATAGCTCGACAATGATGGTATTCAATATCTCAACATTCTACCATCTCGGATGACTCAGCAATG
1 GGATAGCTCGACAATGATGGTATTCAATATCTCAACATTCTACCATCTCGGATGACTCAACAATG
* *
39147179 ATGCCTTTCATTATTCCTACATTTTACCATCTTGGGTGGTCCAACAATGATTGTTCTCACAGTTT
66 ATGCCTTTCATTATTCCTACATTTTACCATCTTGGGTGGTCCAACAACGATGGTTCTCACAGTTT
39147244 ACTTATTCTACCATCCC
131 ACTTATTCTACCATCCC
* * * * *
39147261 GAATAGCTTGACAATGATGGCATTCAATATCTGAACATTATACCATCTCGGA
1 GGATAGCTCGACAATGATGGTATTCAATATCTCAACATTCTACCATCTCGGA
39147313 AGGCCCGAAA
Statistics
Matches: 180, Mismatches: 18, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
147 178 0.99
148 2 0.01
ACGTcount: A:0.27, C:0.24, G:0.15, T:0.34
Consensus pattern (147 bp):
GGATAGCTCGACAATGATGGTATTCAATATCTCAACATTCTACCATCTCGGATGACTCAACAATG
ATGCCTTTCATTATTCCTACATTTTACCATCTTGGGTGGTCCAACAACGATGGTTCTCACAGTTT
ACTTATTCTACCATCCC
Found at i:39147210 original size:49 final size:49
Alignment explanation
Indices: 39147004--39147210 Score: 144
Period size: 49 Copynumber: 4.2 Consensus size: 49
39146994 TATTTCAATG
* *
39147004 TTCTACCATCCCGAATGACTCA-ACAATGATGCCTTTCATTATTCCTACA
1 TTCTACCATCTCGGATGACTCAGACAATGATG-CTTTCATTATTCCTACA
* * * * * * *
39147053 TTTTACCATCTTGGGTG-GTCCGACAACGATGGTTCTCA-TAGTT--TACTTA
1 TTCTACCATCTCGGATGACTCAGACAATGATGCTT-TCATTA-TTCCTAC--A
* * * *
39147102 TTCTACCATCCCGGAT-AGCTC-GACAATGATGGTATTCAATA-TCTCAACA
1 TTCTACCATCTCGGATGA-CTCAGACAATGATGCT-TTCATTATTC-CTACA
39147151 TTCTACCATCTCGGATGACTCAG-CAATGATGCCTTTCATTATTCCTACA
1 TTCTACCATCTCGGATGACTCAGACAATGATG-CTTTCATTATTCCTACA
*
39147200 TTTTACCATCT
1 TTCTACCATCT
39147211 TGGGTGGTCC
Statistics
Matches: 121, Mismatches: 21, Indels: 32
0.70 0.12 0.18
Matches are distributed among these distances:
47 3 0.02
48 7 0.06
49 99 0.82
50 10 0.08
51 2 0.02
ACGTcount: A:0.26, C:0.27, G:0.13, T:0.35
Consensus pattern (49 bp):
TTCTACCATCTCGGATGACTCAGACAATGATGCTTTCATTATTCCTACA
Found at i:39147227 original size:49 final size:49
Alignment explanation
Indices: 39146967--39147229 Score: 141
Period size: 49 Copynumber: 5.4 Consensus size: 49
39146957 TTACCATTAT
* * * * ** *
39146967 GGATGG-CTCAACAATGATGGTTTGCACTATTTCAATGTTCTACCATCCC
1 GGATGGTCTCAACAATGATGCTTT-CATTATTCCTACATTCTACCATCTC
* * * *
39147016 GAAT-GACTCAACAATGATGCCTTTCATTATTCCTACATTTTACCATCTT
1 GGATGGTCTCAACAATGATG-CTTTCATTATTCCTACATTCTACCATCTC
* * * * *
39147065 GGGTGGTC-CGACAACGATGGTTCTCA-TAGTT--TACTTATTCTACCATCCC
1 GGATGGTCTCAACAATGATGCTT-TCATTA-TTCCTAC--ATTCTACCATCTC
* * * * *
39147114 GGATAG-CTCGACAATGATGGTATTCAATA-TCTCAACATTCTACCATCTC
1 GGATGGTCTCAACAATGATGCT-TTCATTATTC-CTACATTCTACCATCTC
* * * *
39147163 GGAT-GACTCAGCAATGATGCCTTTCATTATTCCTACATTTTACCATCTT
1 GGATGGTCTCAACAATGATG-CTTTCATTATTCCTACATTCTACCATCTC
*
39147212 GGGTGGTC-CAACAATGAT
1 GGATGGTCTCAACAATGAT
39147230 TGTTCTCACA
Statistics
Matches: 163, Mismatches: 34, Indels: 34
0.71 0.15 0.15
Matches are distributed among these distances:
47 3 0.02
48 8 0.05
49 137 0.84
50 13 0.08
51 2 0.01
ACGTcount: A:0.26, C:0.24, G:0.16, T:0.34
Consensus pattern (49 bp):
GGATGGTCTCAACAATGATGCTTTCATTATTCCTACATTCTACCATCTC
Found at i:39147373 original size:147 final size:147
Alignment explanation
Indices: 39147031--39147377 Score: 385
Period size: 147 Copynumber: 2.4 Consensus size: 147
39147021 ACTCAACAAT
* * * ** * *
39147031 GATGCCTTTCATTATTCCTACATTTTACCATCTTGGGTGGTCCGACAACGATGGTTCTCATAGTT
1 GATGACTTTCACTATTACTACATTCAACCATCTTGGGTGGTCCGACAATGATGGTTCTCACAGTT
* * *
39147096 TACTTATTCTACCATCCCGGATAGCTCGACAATGATGGTATTCAATATCTCAACATTCTACCATC
66 TACTTATTCTACCATCCCGAATAGCTCGACAATGATGGCATTCAATATCTCAACATTATACCATC
* * * *
39147161 TCGGATGACTCAGCAAT
131 TCGGAAGACCCAGAAAC
* * * ** * *
39147178 GATGCCTTTCATTATTCCTACATTTTACCATCTTGGGTGGTCCAACAATGATTGTTCTCACAGTT
1 GATGACTTTCACTATTACTACATTCAACCATCTTGGGTGGTCCGACAATGATGGTTCTCACAGTT
* *
39147243 TACTTATTCTACCATCCCGAATAGCTTGACAATGATGGCATTCAATATCTGAACATTATACCATC
66 TACTTATTCTACCATCCCGAATAGCTCGACAATGATGGCATTCAATATCTCAACATTATACCATC
*
39147308 TCGGAAGGCCC-GAAAAC
131 TCGGAAGACCCAG-AAAC
* ** * *
39147325 GATGATTTTTGCTATATAC-ACATTCAACCATCCTGGATGG-CCTGACAATGATG
1 GATGACTTTCACTAT-TACTACATTCAACCATCTTGGGTGGTCC-GACAATGATG
39147378 ATTTTCAACC
Statistics
Matches: 171, Mismatches: 26, Indels: 6
0.84 0.13 0.03
Matches are distributed among these distances:
146 3 0.02
147 166 0.97
148 2 0.01
ACGTcount: A:0.27, C:0.24, G:0.16, T:0.33
Consensus pattern (147 bp):
GATGACTTTCACTATTACTACATTCAACCATCTTGGGTGGTCCGACAATGATGGTTCTCACAGTT
TACTTATTCTACCATCCCGAATAGCTCGACAATGATGGCATTCAATATCTCAACATTATACCATC
TCGGAAGACCCAGAAAC
Found at i:39150084 original size:57 final size:58
Alignment explanation
Indices: 39150016--39150135 Score: 154
Period size: 57 Copynumber: 2.1 Consensus size: 58
39150006 AGGGCATTTT
* * *
39150016 CATTTTCATTTTCATTTTGGAGAAAACCACATTCATTTCCAAATGATTT-C-ATTTCTC
1 CATTTTCATTTTAATTTTGGAAAAAACCACAATCATTTCCAAATG-TTTCCTATTTCTC
* * *
39150073 CATTTTTATTTTAATTTTGGAAAAAACCATAATCATTTCTAAATGTTTCCTATTTCTC
1 CATTTTCATTTTAATTTTGGAAAAAACCACAATCATTTCCAAATGTTTCCTATTTCTC
*
39150131 TATTT
1 CATTT
39150136 CACCATTTCT
Statistics
Matches: 54, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
56 3 0.06
57 40 0.74
58 11 0.20
ACGTcount: A:0.29, C:0.17, G:0.06, T:0.47
Consensus pattern (58 bp):
CATTTTCATTTTAATTTTGGAAAAAACCACAATCATTTCCAAATGTTTCCTATTTCTC
Found at i:39153978 original size:30 final size:30
Alignment explanation
Indices: 39153914--39153979 Score: 89
Period size: 30 Copynumber: 2.2 Consensus size: 30
39153904 TTCACTACTG
* *
39153914 AATTTAACTTATACACTATCTTTATAAATA
1 AATTTAACTTATACACAAACTTTATAAATA
*
39153944 AATTTAACTTATACACAAACTTTTATCAAT-
1 AATTTAACTTATACACAAAC-TTTATAAATA
39153974 AATTTA
1 AATTTA
39153980 TACATTTTAT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
30 24 0.75
31 8 0.25
ACGTcount: A:0.44, C:0.14, G:0.00, T:0.42
Consensus pattern (30 bp):
AATTTAACTTATACACAAACTTTATAAATA
Found at i:39155055 original size:22 final size:22
Alignment explanation
Indices: 39155009--39155053 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 22
39154999 CACTTTCAAA
*
39155009 TTAAAATTTAAAATAATTATTT
1 TTAAAATTAAAAATAATTATTT
*
39155031 TTAAAATTAAAAAT-TTTATTT
1 TTAAAATTAAAAATAATTATTT
39155052 TT
1 TT
39155054 TATTTTTTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 8 0.38
22 13 0.62
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (22 bp):
TTAAAATTAAAAATAATTATTT
Found at i:39159960 original size:18 final size:18
Alignment explanation
Indices: 39159919--39159953 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
39159909 AAATATCTCT
*
39159919 AATATTTTAATCAAATAA
1 AATAATTTAATCAAATAA
*
39159937 AATAATTTAATCTAATA
1 AATAATTTAATCAAATA
39159954 TTATAATAAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.54, C:0.06, G:0.00, T:0.40
Consensus pattern (18 bp):
AATAATTTAATCAAATAA
Found at i:39180417 original size:28 final size:28
Alignment explanation
Indices: 39180386--39180442 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
39180376 AGAAACAAAT
39180386 AAAAATGTTTGTTTATCTACATTATAAA
1 AAAAATGTTTGTTTATCTACATTATAAA
39180414 AAAAATGTTTGTTTATCTACATTATAAA
1 AAAAATGTTTGTTTATCTACATTATAAA
39180442 A
1 A
39180443 TTGGAAAATG
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:0.44, C:0.07, G:0.07, T:0.42
Consensus pattern (28 bp):
AAAAATGTTTGTTTATCTACATTATAAA
Found at i:39181011 original size:4 final size:4
Alignment explanation
Indices: 39181002--39181052 Score: 102
Period size: 4 Copynumber: 12.8 Consensus size: 4
39180992 TTACCAAACT
39181002 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
39181050 ATA
1 ATA
39181053 TGTTACCTGA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 47 1.00
ACGTcount: A:0.51, C:0.24, G:0.00, T:0.25
Consensus pattern (4 bp):
ATAC
Found at i:39198637 original size:67 final size:67
Alignment explanation
Indices: 39198471--39198637 Score: 190
Period size: 67 Copynumber: 2.5 Consensus size: 67
39198461 GTCTTCTGGT
* * * *** * *
39198471 TTACACATGTCACCCCATGTTTAATGTCTTGGTGGACTCCTCATGTGGTCATAATCGAACTAAGG
1 TTACACATGTAACCCTATGTTTAATGTCCTGGCAAACACCTCATGTGGCCATAATCGAACTAAGG
39198536 TC
66 TC
* * * * * * * *
39198538 TTAAATATGTAACCCTATGTTTAATATTCTGGCAAACACCTCATGTTGCCATAGTTGAGCTAAGG
1 TTACACATGTAACCCTATGTTTAATGTCCTGGCAAACACCTCATGTGGCCATAATCGAACTAAGG
39198603 TC
66 TC
39198605 TTACACATGTAACCCTATGTTTAATGTCCTGGC
1 TTACACATGTAACCCTATGTTTAATGTCCTGGC
39198638 GGACTACCCC
Statistics
Matches: 80, Mismatches: 20, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
67 80 1.00
ACGTcount: A:0.26, C:0.22, G:0.17, T:0.34
Consensus pattern (67 bp):
TTACACATGTAACCCTATGTTTAATGTCCTGGCAAACACCTCATGTGGCCATAATCGAACTAAGG
TC
Found at i:39198735 original size:14 final size:14
Alignment explanation
Indices: 39198716--39198742 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
39198706 TGTGACCCCA
39198716 TGCTTAATGTCTTT
1 TGCTTAATGTCTTT
39198730 TGCTTAATGTCTT
1 TGCTTAATGTCTT
39198743 GATGATCTCC
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:0.15, C:0.15, G:0.15, T:0.56
Consensus pattern (14 bp):
TGCTTAATGTCTTT
Found at i:39204041 original size:43 final size:43
Alignment explanation
Indices: 39203973--39204055 Score: 112
Period size: 43 Copynumber: 1.9 Consensus size: 43
39203963 AGGAAGGTTA
** * *
39203973 TTTCCTAATTGTGGTTCTCTGTGTGTCCTAGGATGATGAGGGG
1 TTTCCTAATTACGGTTCTCTATGTGTCCTAGGACGATGAGGGG
* *
39204016 TTTCCTAATTACGGTTTTCTATGTGTTCTAGGACGATGAG
1 TTTCCTAATTACGGTTCTCTATGTGTCCTAGGACGATGAG
39204056 AGGCATCACT
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
43 34 1.00
ACGTcount: A:0.17, C:0.14, G:0.28, T:0.41
Consensus pattern (43 bp):
TTTCCTAATTACGGTTCTCTATGTGTCCTAGGACGATGAGGGG
Found at i:39204182 original size:32 final size:28
Alignment explanation
Indices: 39204113--39204196 Score: 98
Period size: 29 Copynumber: 2.8 Consensus size: 28
39204103 CCAGGAGAAT
39204113 GAAAGCCTTTGTGGTAATACTTTAAACTG
1 GAAAGCCTTTGTGGTAATACTTTAAAC-G
39204142 GAAAGCCTTTGTGGTGAATACTAGATGTAAA-G
1 GAAAGCCTTTGTGGT-AATACT---T-TAAACG
*
39204174 GAAAGCCTTTGTGGCAATACTTT
1 GAAAGCCTTTGTGGTAATACTTT
39204197 GGACAAGAAA
Statistics
Matches: 49, Mismatches: 1, Indels: 12
0.79 0.02 0.19
Matches are distributed among these distances:
27 1 0.02
28 1 0.02
29 15 0.31
30 6 0.12
31 6 0.12
32 15 0.31
33 1 0.02
34 4 0.08
ACGTcount: A:0.31, C:0.13, G:0.24, T:0.32
Consensus pattern (28 bp):
GAAAGCCTTTGTGGTAATACTTTAAACG
Found at i:39204283 original size:61 final size:60
Alignment explanation
Indices: 39204110--39204316 Score: 186
Period size: 61 Copynumber: 3.4 Consensus size: 60
39204100 TCACCAGGAG
* * * ** *
39204110 AATGA-AAGCCTTTGTGGTAATACTTTAAACTGGAAAGCCTTTGTGGTGAATACTAGATGTA
1 AATGACAA-CCTTTGTGGCAATACTCTAGACAAGAAAGCCTTT-TGGTGAGTACTAGATGTA
* * * *
39204171 AAGGA-AAGCCTTTGTGGCAATACTTTGGACAAGAAAGACCTTTTGGCGAGTACTAGATGTA
1 AATGACAA-CCTTTGTGGCAATACTCTAGACAAGAAAG-CCTTTTGGTGAGTACTAGATGTA
* * ** *
39204232 AATGACAACCTTTGTGGCAATACTCTAGATACGAAAGCCTTTATATTGAGTA-TAGGATATA
1 AATGACAACCTTTGTGGCAATACTCTAGACAAGAAAGCCTTT-TGGTGAGTACTA-GATGTA
* *
39204293 AATGACAACCTTTTTGGTAATACT
1 AATGACAACCTTTGTGGCAATACT
39204317 GGATGTAAAG
Statistics
Matches: 123, Mismatches: 19, Indels: 8
0.82 0.13 0.05
Matches are distributed among these distances:
60 7 0.06
61 109 0.89
62 7 0.06
ACGTcount: A:0.34, C:0.14, G:0.21, T:0.31
Consensus pattern (60 bp):
AATGACAACCTTTGTGGCAATACTCTAGACAAGAAAGCCTTTTGGTGAGTACTAGATGTA
Found at i:39216454 original size:28 final size:28
Alignment explanation
Indices: 39216353--39216460 Score: 126
Period size: 30 Copynumber: 3.7 Consensus size: 28
39216343 CATGCAGAAT
* * * *
39216353 CAGTCTGGGCCTGAGCCCTATACAGTAG
1 CAGTGTGGGCCTTAGCCCAATACAGTAA
*
39216381 CAGTGTGTGGGCCATAGCCCAATACAGTAA
1 CA--GTGTGGGCCTTAGCCCAATACAGTAA
*
39216411 CAGAGTGTGGGCCTTAGCCCAATTCAGTAA
1 C--AGTGTGGGCCTTAGCCCAATACAGTAA
39216441 CAGTGTGGGCCTTAGCCCAA
1 CAGTGTGGGCCTTAGCCCAA
39216461 AATAGTAATC
Statistics
Matches: 69, Mismatches: 7, Indels: 8
0.82 0.08 0.10
Matches are distributed among these distances:
28 21 0.30
30 47 0.68
32 1 0.01
ACGTcount: A:0.25, C:0.26, G:0.28, T:0.21
Consensus pattern (28 bp):
CAGTGTGGGCCTTAGCCCAATACAGTAA
Found at i:39216467 original size:28 final size:29
Alignment explanation
Indices: 39216385--39216468 Score: 100
Period size: 28 Copynumber: 2.9 Consensus size: 29
39216375 CAGTAGCAGT
* * *
39216385 GTGTGGGCCATAGCCCAATACAGTAACAGA
1 GTGTGGGCCTTAGCCCAAAATAGTAACA-A
*
39216415 GTGTGGGCCTTAGCCC-AATTCAGTAAC-A
1 GTGTGGGCCTTAGCCCAAAAT-AGTAACAA
39216443 GTGTGGGCCTTAGCCCAAAATAGTAA
1 GTGTGGGCCTTAGCCCAAAATAGTAA
39216469 TCACTACAAC
Statistics
Matches: 47, Mismatches: 5, Indels: 6
0.81 0.09 0.10
Matches are distributed among these distances:
28 22 0.47
29 4 0.09
30 21 0.45
ACGTcount: A:0.30, C:0.23, G:0.26, T:0.21
Consensus pattern (29 bp):
GTGTGGGCCTTAGCCCAAAATAGTAACAA
Found at i:39216610 original size:26 final size:27
Alignment explanation
Indices: 39216581--39216656 Score: 93
Period size: 26 Copynumber: 2.9 Consensus size: 27
39216571 CACCAATATC
*
39216581 GCAGTAAAGCTGCCAGTAACAGTAA-A
1 GCAGCAAAGCTGCCAGTAACAGTAACA
* * * *
39216607 GCAGCAGAGCTACCAGTATCAATAACA
1 GCAGCAAAGCTGCCAGTAACAGTAACA
39216634 -CAGCAAAGCTGCCAGTAACAGTA
1 GCAGCAAAGCTGCCAGTAACAGTA
39216657 TTTGTGGCAA
Statistics
Matches: 40, Mismatches: 9, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
26 39 0.98
27 1 0.03
ACGTcount: A:0.41, C:0.24, G:0.21, T:0.14
Consensus pattern (27 bp):
GCAGCAAAGCTGCCAGTAACAGTAACA
Found at i:39216887 original size:27 final size:26
Alignment explanation
Indices: 39216840--39217033 Score: 194
Period size: 27 Copynumber: 7.2 Consensus size: 26
39216830 TATAACAGTT
*
39216840 ATTTTACCCTTCGAGGGTATTTCAGTA
1 ATTTTACCCTTTGAGGGTATTTC-GTA
39216867 ATTTTACCCTTT-AGGGTTATTTCGATA
1 ATTTTACCCTTTGAGGG-TATTTCG-TA
* *
39216894 ATTTTA-CCTTTCGAAGGTATTTTGGTA
1 ATTTTACCCTTT-GAGGGTA-TTTCGTA
*
39216921 ATTTTACCCTTTGAGGGTATTTTAGTA
1 ATTTTACCCTTTGAGGGTA-TTTCGTA
* *
39216948 ATTTTACCATTCGAGGGTATTTCGATA
1 ATTTTACCCTTTGAGGGTATTTCG-TA
*
39216975 ATTTTACCATTTGAGGGTATTTCGATA
1 ATTTTACCCTTTGAGGGTATTTCG-TA
* * * *
39217002 ATTTTACACTTCGAGAGTATTTCAATA
1 ATTTTACCCTTTGAGGGTATTTC-GTA
39217029 ATTTT
1 ATTTT
39217034 CTGGCCTAAG
Statistics
Matches: 145, Mismatches: 14, Indels: 16
0.83 0.08 0.09
Matches are distributed among these distances:
26 14 0.10
27 119 0.82
28 12 0.08
ACGTcount: A:0.25, C:0.13, G:0.16, T:0.45
Consensus pattern (26 bp):
ATTTTACCCTTTGAGGGTATTTCGTA
Found at i:39216907 original size:54 final size:53
Alignment explanation
Indices: 39216840--39217033 Score: 241
Period size: 54 Copynumber: 3.6 Consensus size: 53
39216830 TATAACAGTT
39216840 ATTTTACCCTTCGAGGGTATTTCAGTAATTTTACCCTTT-AGGGTTATTTCGATA
1 ATTTTA-CCTTCGAGGGTATTTCAGTAATTTTACCCTTTGAGGG-TATTTCGATA
* ** *
39216894 ATTTTACCTTTCGAAGGTATTTTGGTAATTTTACCCTTTGAGGGTATTT-TAGTA
1 ATTTTACC-TTCGAGGGTATTTCAGTAATTTTACCCTTTGAGGGTATTTCGA-TA
*
39216948 ATTTTACCATTCGAGGGTATTTC-GATAATTTTACCATTTGAGGGTATTTCGATA
1 ATTTTACC-TTCGAGGGTATTTCAG-TAATTTTACCCTTTGAGGGTATTTCGATA
* *
39217002 ATTTTACACTTCGAGAGTATTTCAATAATTTT
1 ATTTTAC-CTTCGAGGGTATTTCAGTAATTTT
39217034 CTGGCCTAAG
Statistics
Matches: 122, Mismatches: 11, Indels: 14
0.83 0.07 0.10
Matches are distributed among these distances:
53 4 0.03
54 112 0.92
55 6 0.05
ACGTcount: A:0.25, C:0.13, G:0.16, T:0.45
Consensus pattern (53 bp):
ATTTTACCTTCGAGGGTATTTCAGTAATTTTACCCTTTGAGGGTATTTCGATA
Found at i:39216969 original size:81 final size:81
Alignment explanation
Indices: 39216840--39217033 Score: 266
Period size: 81 Copynumber: 2.4 Consensus size: 81
39216830 TATAACAGTT
* *
39216840 ATTTTACCCTTCGAGGGTATTTCAGTAATTTTACCCTTTAGGGTTATTTCGATAATTTTACC-TT
1 ATTTTACCCTTCGAGGGTATTTCAGTAATTTTACCATTGAGGGTTATTTCGATAATTTTACCATT
* *
39216904 TCGAAGGTATTTTGGTA
66 T-GAAGGTATTTCGATA
* *
39216921 ATTTTACCCTTTGAGGGTATTTTAGTAATTTTACCATTCGAGGG-TATTTCGATAATTTTACCAT
1 ATTTTACCCTTCGAGGGTATTTCAGTAATTTTACCATT-GAGGGTTATTTCGATAATTTTACCAT
*
39216985 TTGAGGGTATTTCGATA
65 TTGAAGGTATTTCGATA
* * *
39217002 ATTTTACACTTCGAGAGTATTTCAATAATTTT
1 ATTTTACCCTTCGAGGGTATTTCAGTAATTTT
39217034 CTGGCCTAAG
Statistics
Matches: 99, Mismatches: 12, Indels: 4
0.86 0.10 0.03
Matches are distributed among these distances:
81 92 0.93
82 7 0.07
ACGTcount: A:0.25, C:0.13, G:0.16, T:0.45
Consensus pattern (81 bp):
ATTTTACCCTTCGAGGGTATTTCAGTAATTTTACCATTGAGGGTTATTTCGATAATTTTACCATT
TGAAGGTATTTCGATA
Found at i:39220862 original size:63 final size:63
Alignment explanation
Indices: 39220784--39220958 Score: 210
Period size: 63 Copynumber: 2.8 Consensus size: 63
39220774 CATGCCCATT
* * * *
39220784 TCTCTAGCTCGTGTGAACCTAATTCCAAAATAGTGAGTTATATGACCT-GAAAACACGCCCGTG
1 TCTCTAGCCCGTGTGAACCTAATTCCAAAACAGTGAGTTACACGACCTAG-AAACACGCCCGTG
* * * **
39220847 TCTCTAGCCCTTGTG-ACTCTAATTCCAAAACAGTGAGTTACACGACCTAGACATACGTTCGTG
1 TCTCTAGCCCGTGTGAAC-CTAATTCCAAAACAGTGAGTTACACGACCTAGAAACACGCCCGTG
* * *
39220910 TCTCTGGCCCGTGTGAACCTAATTCTAAAACAATGAGTTACACGACCTA
1 TCTCTAGCCCGTGTGAACCTAATTCCAAAACAGTGAGTTACACGACCTA
39220959 ACACACGGCC
Statistics
Matches: 96, Mismatches: 13, Indels: 6
0.83 0.11 0.05
Matches are distributed among these distances:
62 2 0.02
63 91 0.95
64 3 0.03
ACGTcount: A:0.29, C:0.26, G:0.18, T:0.27
Consensus pattern (63 bp):
TCTCTAGCCCGTGTGAACCTAATTCCAAAACAGTGAGTTACACGACCTAGAAACACGCCCGTG
Found at i:39222484 original size:2 final size:2
Alignment explanation
Indices: 39222477--39222525 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
39222467 CAGAGAATAG
39222477 TA TA TA TA TA TA TA 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 TA TA TA TA TA TA TA
39222519 TA TA TA T
1 TA TA TA T
39222526 GAAATCTAAT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:39240412 original size:18 final size:18
Alignment explanation
Indices: 39240389--39240436 Score: 62
Period size: 18 Copynumber: 2.7 Consensus size: 18
39240379 TGTTTTTTTA
39240389 GTTTATTTTTATTATATT
1 GTTTATTTTTATTATATT
*
39240407 GTTTATATTGT-TTATATT
1 GTTTAT-TTTTATTATATT
*
39240425 GTTTATTATTAT
1 GTTTATTTTTAT
39240437 AATTATTATA
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
17 2 0.08
18 20 0.80
19 3 0.12
ACGTcount: A:0.23, C:0.00, G:0.08, T:0.69
Consensus pattern (18 bp):
GTTTATTTTTATTATATT
Found at i:39240441 original size:9 final size:8
Alignment explanation
Indices: 39240397--39240453 Score: 53
Period size: 9 Copynumber: 6.9 Consensus size: 8
39240387 TAGTTTATTT
39240397 TTATTATA
1 TTATTATA
*
39240405 TTGTTTATA
1 TT-ATTATA
*
39240414 TTGTTTATA
1 TT-ATTATA
*
39240423 TTGTT-TA
1 TTATTATA
39240430 TTATTATAA
1 TTATTAT-A
39240439 TTATTATA
1 TTATTATA
39240447 TTATTAT
1 TTATTAT
39240454 TATTGTATTT
Statistics
Matches: 43, Mismatches: 3, Indels: 6
0.83 0.06 0.12
Matches are distributed among these distances:
7 6 0.14
8 13 0.30
9 24 0.56
ACGTcount: A:0.30, C:0.00, G:0.05, T:0.65
Consensus pattern (8 bp):
TTATTATA
Found at i:39246799 original size:17 final size:17
Alignment explanation
Indices: 39246758--39246792 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
39246748 CTAGTTTTCG
* *
39246758 TATAAAGTAATTTATTT
1 TATAAAATAATTCATTT
39246775 TATAAAATAATTCATTT
1 TATAAAATAATTCATTT
39246792 T
1 T
39246793 CAAAAATTTC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.43, C:0.03, G:0.03, T:0.51
Consensus pattern (17 bp):
TATAAAATAATTCATTT
Found at i:39252732 original size:13 final size:13
Alignment explanation
Indices: 39252714--39252738 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
39252704 ACTTCTGTCT
39252714 AAAATAATAACAC
1 AAAATAATAACAC
39252727 AAAATAATAACA
1 AAAATAATAACA
39252739 GTGTTCACTG
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:0.72, C:0.12, G:0.00, T:0.16
Consensus pattern (13 bp):
AAAATAATAACAC
Found at i:39256712 original size:15 final size:15
Alignment explanation
Indices: 39256692--39256722 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
39256682 ATGAGGTATG
*
39256692 ACGAAAGTGATGGTT
1 ACGAAAGGGATGGTT
39256707 ACGAAAGGGATGGTT
1 ACGAAAGGGATGGTT
39256722 A
1 A
39256723 TGAGGTATGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.35, C:0.06, G:0.35, T:0.23
Consensus pattern (15 bp):
ACGAAAGGGATGGTT
Found at i:39259873 original size:43 final size:43
Alignment explanation
Indices: 39259823--39259908 Score: 109
Period size: 43 Copynumber: 2.0 Consensus size: 43
39259813 TCATATCTCA
*
39259823 TTTCTCATATTATAATCATTTATCATATTTGCCATTTCAATAT
1 TTTCTCATATCATAATCATTTATCATATTTGCCATTTCAATAT
* * * * **
39259866 TTTCTCATCTCATATTCATTTCTCATCTTTTTCATTTCAATAT
1 TTTCTCATATCATAATCATTTATCATATTTGCCATTTCAATAT
39259909 CAATCACATA
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
43 36 1.00
ACGTcount: A:0.26, C:0.20, G:0.01, T:0.53
Consensus pattern (43 bp):
TTTCTCATATCATAATCATTTATCATATTTGCCATTTCAATAT
Found at i:39259901 original size:16 final size:17
Alignment explanation
Indices: 39259866--39259903 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
39259856 ATTTCAATAT
39259866 TTTCTCATCTCATATTCA
1 TTTCTCATCT-ATATTCA
*
39259884 TTTCTCATCT-TTTTCA
1 TTTCTCATCTATATTCA
39259900 TTTC
1 TTTC
39259904 AATATCAATC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 9 0.47
18 10 0.53
ACGTcount: A:0.16, C:0.26, G:0.00, T:0.58
Consensus pattern (17 bp):
TTTCTCATCTATATTCA
Found at i:39262557 original size:12 final size:11
Alignment explanation
Indices: 39262528--39262558 Score: 62
Period size: 11 Copynumber: 2.8 Consensus size: 11
39262518 CACAAAATAC
39262528 AAGAAAAATCA
1 AAGAAAAATCA
39262539 AAGAAAAATCA
1 AAGAAAAATCA
39262550 AAGAAAAAT
1 AAGAAAAAT
39262559 GTAGAAACAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.74, C:0.06, G:0.10, T:0.10
Consensus pattern (11 bp):
AAGAAAAATCA
Found at i:39275386 original size:21 final size:21
Alignment explanation
Indices: 39275357--39275404 Score: 87
Period size: 21 Copynumber: 2.3 Consensus size: 21
39275347 TCCTTCTGTT
*
39275357 GCAATAAGCTACTTGGATGTC
1 GCAACAAGCTACTTGGATGTC
39275378 GCAACAAGCTACTTGGATGTC
1 GCAACAAGCTACTTGGATGTC
39275399 GCAACA
1 GCAACA
39275405 CGACTTCTAG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.31, C:0.23, G:0.23, T:0.23
Consensus pattern (21 bp):
GCAACAAGCTACTTGGATGTC
Found at i:39287111 original size:27 final size:28
Alignment explanation
Indices: 39287071--39287124 Score: 83
Period size: 27 Copynumber: 2.0 Consensus size: 28
39287061 ACTGAATATA
*
39287071 AAGGTGGTTACTAAGTGTTGATTCCCCC
1 AAGGTGGTTACTAAGTGCTGATTCCCCC
*
39287099 AAGG-GGTTGCTAAGTGCTGATTCCCC
1 AAGGTGGTTACTAAGTGCTGATTCCCC
39287125 GAATCATTAG
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
27 20 0.83
28 4 0.17
ACGTcount: A:0.20, C:0.22, G:0.28, T:0.30
Consensus pattern (28 bp):
AAGGTGGTTACTAAGTGCTGATTCCCCC
Found at i:39287145 original size:33 final size:33
Alignment explanation
Indices: 39287103--39287227 Score: 117
Period size: 33 Copynumber: 3.5 Consensus size: 33
39287093 TCCCCCAAGG
39287103 GGTTGCTAAGTGCTGATTCCCCGAATCATTAGT
1 GGTTGCTAAGTGCTGATTCCCCGAATCATTAGT
*
39287136 GGTTGCTAAGTGCTGATTCCACC-ATATCTTAAATGTGAAAGG
1 GGTTGCTAAGTGCTGATTCC-CCGA-ATC----AT-T---AGT
* *
39287178 GGTTGCTAAGTGCTGATTCCTCGAATCATTGGT
1 GGTTGCTAAGTGCTGATTCCCCGAATCATTAGT
*
39287211 GCTTGCTAAGTGCTGAT
1 GGTTGCTAAGTGCTGAT
39287228 CCCACCGTAT
Statistics
Matches: 76, Mismatches: 5, Indels: 22
0.74 0.05 0.21
Matches are distributed among these distances:
33 38 0.50
34 5 0.07
36 1 0.01
37 2 0.03
38 2 0.03
39 1 0.01
41 4 0.05
42 23 0.30
ACGTcount: A:0.22, C:0.18, G:0.26, T:0.34
Consensus pattern (33 bp):
GGTTGCTAAGTGCTGATTCCCCGAATCATTAGT
Found at i:39287195 original size:42 final size:42
Alignment explanation
Indices: 39287136--39287272 Score: 157
Period size: 42 Copynumber: 3.5 Consensus size: 42
39287126 AATCATTAGT
39287136 GGTTGCTAAGTGCTGATTCCACCATATCTTAAATGTGAAAGG
1 GGTTGCTAAGTGCTGATTCCACCATATCTTAAATGTGAAAGG
* * *
39287178 GGTTGCTAAGTGCTGATTCCTCGA-ATC----AT-TG---GT
1 GGTTGCTAAGTGCTGATTCCACCATATCTTAAATGTGAAAGG
* * *
39287211 GCTTGCTAAGTGCTGATCCCACCGTATCTTAAATGTGAAAGG
1 GGTTGCTAAGTGCTGATTCCACCATATCTTAAATGTGAAAGG
39287253 GGTTGCTAAGTGCTGATTCC
1 GGTTGCTAAGTGCTGATTCC
39287273 NNNNNNNNNN
Statistics
Matches: 75, Mismatches: 11, Indels: 18
0.72 0.11 0.17
Matches are distributed among these distances:
33 20 0.27
34 3 0.04
36 2 0.03
37 2 0.03
38 2 0.03
39 2 0.03
41 3 0.04
42 41 0.55
ACGTcount: A:0.23, C:0.19, G:0.26, T:0.32
Consensus pattern (42 bp):
GGTTGCTAAGTGCTGATTCCACCATATCTTAAATGTGAAAGG
Found at i:39287222 original size:75 final size:75
Alignment explanation
Indices: 39287099--39287272 Score: 303
Period size: 75 Copynumber: 2.3 Consensus size: 75
39287089 TGATTCCCCC
* *
39287099 AAGGGGTTGCTAAGTGCTGATTCCCCGAATCATTAGTGGTTGCTAAGTGCTGATTCCACCATATC
1 AAGGGGTTGCTAAGTGCTGATTCCCCGAATCATTAGTGCTTGCTAAGTGCTGATCCCACCATATC
39287164 TTAAATGTGA
66 TTAAATGTGA
* * *
39287174 AAGGGGTTGCTAAGTGCTGATTCCTCGAATCATTGGTGCTTGCTAAGTGCTGATCCCACCGTATC
1 AAGGGGTTGCTAAGTGCTGATTCCCCGAATCATTAGTGCTTGCTAAGTGCTGATCCCACCATATC
39287239 TTAAATGTGA
66 TTAAATGTGA
39287249 AAGGGGTTGCTAAGTGCTGATTCC
1 AAGGGGTTGCTAAGTGCTGATTCC
39287273 NNNNNNNNNN
Statistics
Matches: 94, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
75 94 1.00
ACGTcount: A:0.24, C:0.19, G:0.26, T:0.32
Consensus pattern (75 bp):
AAGGGGTTGCTAAGTGCTGATTCCCCGAATCATTAGTGCTTGCTAAGTGCTGATCCCACCATATC
TTAAATGTGA
Found at i:39288973 original size:13 final size:13
Alignment explanation
Indices: 39288955--39288980 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
39288945 ACCTTCAAAG
39288955 GATATAAATGAAC
1 GATATAAATGAAC
39288968 GATATAAATGAAC
1 GATATAAATGAAC
39288981 TACCCGATGA
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:0.54, C:0.08, G:0.15, T:0.23
Consensus pattern (13 bp):
GATATAAATGAAC
Found at i:39289218 original size:42 final size:42
Alignment explanation
Indices: 39289159--39289335 Score: 336
Period size: 42 Copynumber: 4.2 Consensus size: 42
39289149 AAGATAGTCC
39289159 GCAACAAATGCTAGACTTTGTTATATTCAGTGAATAGAAACA
1 GCAACAAATGCTAGACTTTGTTATATTCAGTGAATAGAAACA
39289201 GCAACAAATGCTAGACTTTGTTATATTCAGTGAATAGAAACA
1 GCAACAAATGCTAGACTTTGTTATATTCAGTGAATAGAAACA
39289243 GCAACAAATGCTAGACTTTGTTATATTCAGTGAATAGAAACA
1 GCAACAAATGCTAGACTTTGTTATATTCAGTGAATAGAAACA
39289285 GCAACAAATGCTAGACTTTGTTATATTCAGTGAATAGAAACA
1 GCAACAAATGCTAGACTTTGTTATATTCAGTGAATAGAAACA
39289327 TGTCAACAA
1 -G-CAACAA
39289336 TCATCATCTC
Statistics
Matches: 133, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
42 126 0.95
43 1 0.01
44 6 0.05
ACGTcount: A:0.41, C:0.15, G:0.16, T:0.28
Consensus pattern (42 bp):
GCAACAAATGCTAGACTTTGTTATATTCAGTGAATAGAAACA
Found at i:39299324 original size:41 final size:42
Alignment explanation
Indices: 39299259--39299365 Score: 135
Period size: 41 Copynumber: 2.6 Consensus size: 42
39299249 ATGGCCTAGC
* ** * * *
39299259 ACACGGCCTGGTACATAGGTGTGTGAGGCCATTT-TAGAGGT
1 ACACGGCCTGGCACACGGGCGTGTGAGGCCATTTCGAAAGGT
39299300 ACACGGCCTGGCACACGGGCGTGTGAGGCCATTTCGAAAGGT
1 ACACGGCCTGGCACACGGGCGTGTGAGGCCATTTCGAAAGGT
* *
39299342 ACACGGCCTGGCTCACGAGCGTGT
1 ACACGGCCTGGCACACGGGCGTGT
39299366 ATCTTGGCTG
Statistics
Matches: 57, Mismatches: 8, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
41 30 0.53
42 27 0.47
ACGTcount: A:0.21, C:0.24, G:0.35, T:0.21
Consensus pattern (42 bp):
ACACGGCCTGGCACACGGGCGTGTGAGGCCATTTCGAAAGGT
Found at i:39303217 original size:18 final size:18
Alignment explanation
Indices: 39303196--39303233 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
39303186 CTTTCTCATT
**
39303196 TTCAGCAACTTCTTCTTC
1 TTCAGCAACAACTTCTTC
39303214 TTCAGCAACAACTTCTTC
1 TTCAGCAACAACTTCTTC
39303232 TT
1 TT
39303234 TTGTAACATC
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:0.21, C:0.32, G:0.05, T:0.42
Consensus pattern (18 bp):
TTCAGCAACAACTTCTTC
Found at i:39304022 original size:130 final size:130
Alignment explanation
Indices: 39303784--39304048 Score: 503
Period size: 130 Copynumber: 2.0 Consensus size: 130
39303774 GACTTCAGTG
39303784 GTTGAGCCTTTATTTTCTAGGATTTCCTCACCAGCACGGGGCATGATTCCTCTTTGCTGGCATAA
1 GTTGAGCCTTTATTTTCTAGGATTTCCTCACCAGCACGGGGCATGATTCCTCTTTGCTGGCATAA
39303849 TAACATCACTAGGGATGGGAAAACTAAGATCCCAGACTGCTTTGCAGCGTAGTCAACTATTTTTT
66 TAACATCACTAGGGATGGGAAAACTAAGATCCCAGACTGCTTTGCAGCGTAGTCAACTATTTTTT
39303914 GTTGAGCCTTTATTTTCTAGGATTTCCTCACCAGCACGGGGCATGATTCCTCTTTGCTGGCATAA
1 GTTGAGCCTTTATTTTCTAGGATTTCCTCACCAGCACGGGGCATGATTCCTCTTTGCTGGCATAA
* * *
39303979 TAACATCACTAGGGATGGGAAAACTAAGATCCCAGTCTTCTTTGTAGCGTAGTCAACTATTTTTT
66 TAACATCACTAGGGATGGGAAAACTAAGATCCCAGACTGCTTTGCAGCGTAGTCAACTATTTTTT
39304044 GTTGA
1 GTTGA
39304049 AGAATTATGC
Statistics
Matches: 132, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
130 132 1.00
ACGTcount: A:0.24, C:0.22, G:0.21, T:0.34
Consensus pattern (130 bp):
GTTGAGCCTTTATTTTCTAGGATTTCCTCACCAGCACGGGGCATGATTCCTCTTTGCTGGCATAA
TAACATCACTAGGGATGGGAAAACTAAGATCCCAGACTGCTTTGCAGCGTAGTCAACTATTTTTT
Found at i:39309921 original size:18 final size:19
Alignment explanation
Indices: 39309894--39309929 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
39309884 AATAAAATGT
39309894 AAAAAAAAACA-CAAACAC
1 AAAAAAAAACATCAAACAC
*
39309912 AAAAATAAACATCAAACA
1 AAAAAAAAACATCAAACA
39309930 AACGCCATCC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 10 0.62
19 6 0.38
ACGTcount: A:0.75, C:0.19, G:0.00, T:0.06
Consensus pattern (19 bp):
AAAAAAAAACATCAAACAC
Found at i:39314183 original size:30 final size:27
Alignment explanation
Indices: 39314124--39314209 Score: 72
Period size: 26 Copynumber: 3.3 Consensus size: 27
39314114 TTTTATTTTC
* * *
39314124 ATTTATTTTAAGTTTTTTATATATATT
1 ATTTATTTGAAGTGTTTTACATATATT
39314151 ATTTATTTGAAGCTGTTTTAC--ATATT
1 ATTTATTTGAAG-TGTTTTACATATATT
* **
39314177 ATTTATTT-AAAT-TTCTTTTATATATT
1 ATTTATTTGAAGTGTT-TTACATATATT
39314203 ATTTATT
1 ATTTATT
39314210 GTAAACTATT
Statistics
Matches: 49, Mismatches: 6, Indels: 9
0.77 0.09 0.14
Matches are distributed among these distances:
23 2 0.04
24 3 0.06
25 2 0.04
26 25 0.51
27 11 0.22
28 6 0.12
ACGTcount: A:0.29, C:0.03, G:0.05, T:0.63
Consensus pattern (27 bp):
ATTTATTTGAAGTGTTTTACATATATT
Found at i:39314224 original size:26 final size:25
Alignment explanation
Indices: 39314140--39314226 Score: 84
Period size: 26 Copynumber: 3.4 Consensus size: 25
39314130 TTTAAGTTTT
* *
39314140 TTATATATATTATTTATTTGAAGCTG
1 TTATATATATTATTTATTT-AAACTA
* * * *
39314166 TTTTACATATTATTTATTTAAATTTC
1 TTATATATATTATTTATTTAAA-CTA
*
39314192 TTTTATATATTATTTATTGTAAACTA
1 TTATATATATTATTTATT-TAAACTA
39314218 TTATATATA
1 TTATATATA
39314227 ACTTTCAAAT
Statistics
Matches: 50, Mismatches: 9, Indels: 4
0.79 0.14 0.06
Matches are distributed among these distances:
25 2 0.04
26 44 0.88
27 4 0.08
ACGTcount: A:0.33, C:0.05, G:0.05, T:0.57
Consensus pattern (25 bp):
TTATATATATTATTTATTTAAACTA
Found at i:39314292 original size:15 final size:15
Alignment explanation
Indices: 39314272--39314317 Score: 51
Period size: 14 Copynumber: 3.1 Consensus size: 15
39314262 GTTTTATATG
39314272 TTATTTTTATATTAT
1 TTATTTTTATATTAT
*
39314287 TTA-TTTTAAATTATT
1 TTATTTTTATATTA-T
*
39314302 TTATTGTTAT-TTAT
1 TTATTTTTATATTAT
39314316 TT
1 TT
39314318 TAAGTTTTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
14 12 0.46
15 10 0.38
16 4 0.15
ACGTcount: A:0.26, C:0.00, G:0.02, T:0.72
Consensus pattern (15 bp):
TTATTTTTATATTAT
Found at i:39314300 original size:25 final size:24
Alignment explanation
Indices: 39314276--39314369 Score: 86
Period size: 25 Copynumber: 4.0 Consensus size: 24
39314266 TATATGTTAT
39314276 TTTTATATTATTTATTTTAAATTA
1 TTTTATATTATTTATTTTAAATTA
* * *
39314300 TTTTATTGTTATTTATTTTAAGTTTT
1 TTTTA-TATTATTTATTTTAA-ATTA
* * *
39314326 TTTTATTTTGTTTATTTGAAA--A
1 TTTTATATTATTTATTTTAAATTA
*
39314348 TTTT-TATTATTTATTTTGAATT
1 TTTTATATTATTTATTTTAAATT
39314370 GTCATTATAA
Statistics
Matches: 54, Mismatches: 12, Indels: 9
0.72 0.16 0.12
Matches are distributed among these distances:
21 12 0.22
22 4 0.07
24 5 0.09
25 26 0.48
26 7 0.13
ACGTcount: A:0.26, C:0.00, G:0.05, T:0.69
Consensus pattern (24 bp):
TTTTATATTATTTATTTTAAATTA
Found at i:39318983 original size:41 final size:41
Alignment explanation
Indices: 39318925--39319022 Score: 153
Period size: 41 Copynumber: 2.4 Consensus size: 41
39318915 GGATACTTGA
39318925 CAGCTTGTGTGAGCAGCACCGTGTAACTACATTACGACCAAT
1 CAGCTTGTGTGAGCAGCACCGTGTAACTACATTACGACC-AT
* * *
39318967 -AGCTTATGTGAGCAGCACCGTGTAACTACATTACTACCGT
1 CAGCTTGTGTGAGCAGCACCGTGTAACTACATTACGACCAT
39319007 CAGCTTGTGTGAGCAG
1 CAGCTTGTGTGAGCAG
39319023 ACCCACTTGT
Statistics
Matches: 51, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
40 1 0.02
41 50 0.98
ACGTcount: A:0.27, C:0.24, G:0.23, T:0.26
Consensus pattern (41 bp):
CAGCTTGTGTGAGCAGCACCGTGTAACTACATTACGACCAT
Found at i:39321278 original size:11 final size:11
Alignment explanation
Indices: 39321262--39321297 Score: 54
Period size: 11 Copynumber: 3.3 Consensus size: 11
39321252 ATTAACCAAA
39321262 TAATTCAAACT
1 TAATTCAAACT
39321273 TAATTCAAACT
1 TAATTCAAACT
* *
39321284 TGATTCAAGCT
1 TAATTCAAACT
39321295 TAA
1 TAA
39321298 CTTAATATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.42, C:0.17, G:0.06, T:0.36
Consensus pattern (11 bp):
TAATTCAAACT
Found at i:39322436 original size:51 final size:51
Alignment explanation
Indices: 39322360--39322499 Score: 126
Period size: 51 Copynumber: 2.7 Consensus size: 51
39322350 ATTGATATAA
* *
39322360 TAATAAATTTAGCTCATAAAATTTACACATATC-ATCAATTTAGTCTTAATT
1 TAATAAATTTAGCTCAGAAAATTTACACAT-TCTATCAATTTAGTCATAATT
* * * *
39322411 TAATAAATTTAG-TCCGAAATATTTACACGTTCTGTCAATTTAGTCATGATT
1 TAATAAATTTAGCTCAGAAA-ATTTACACATTCTATCAATTTAGTCATAATT
* * * *
39322462 T-ATCAAATTTAACT-TGCAAAATTTTCACAATCTATCAA
1 TAAT-AAATTTAGCTCAG-AAAATTTACACATTCTATCAA
39322500 CATTCACACA
Statistics
Matches: 72, Mismatches: 12, Indels: 10
0.77 0.13 0.11
Matches are distributed among these distances:
50 9 0.12
51 59 0.82
52 4 0.06
ACGTcount: A:0.39, C:0.15, G:0.06, T:0.40
Consensus pattern (51 bp):
TAATAAATTTAGCTCAGAAAATTTACACATTCTATCAATTTAGTCATAATT
Found at i:39325310 original size:2 final size:2
Alignment explanation
Indices: 39325303--39325329 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
39325293 TCATAATGTA
39325303 AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG A
39325330 AATGCAAAGG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:39334969 original size:25 final size:25
Alignment explanation
Indices: 39334934--39335005 Score: 83
Period size: 25 Copynumber: 2.8 Consensus size: 25
39334924 AGGGTTACCG
39334934 ATTTCAGCTCG-AGAGAGCTTACCGTT
1 ATTT-AGCTCGCA-AGAGCTTACCGTT
* *
39334960 ATTTAGCTCGCATGAGCTTACTGTT
1 ATTTAGCTCGCAAGAGCTTACCGTT
* *
39334985 ATTCAGCTCGCACGAGCTTAC
1 ATTTAGCTCGCAAGAGCTTAC
39335006 TGATTACAGC
Statistics
Matches: 41, Mismatches: 4, Indels: 3
0.85 0.08 0.06
Matches are distributed among these distances:
25 36 0.88
26 5 0.12
ACGTcount: A:0.22, C:0.25, G:0.21, T:0.32
Consensus pattern (25 bp):
ATTTAGCTCGCAAGAGCTTACCGTT
Found at i:39335006 original size:25 final size:25
Alignment explanation
Indices: 39334948--39335025 Score: 97
Period size: 25 Copynumber: 3.2 Consensus size: 25
39334938 CAGCTCGAGA
* * *
39334948 GAGCTTACCGTTATTTAGCTCGCAT
1 GAGCTTACTGTTATTCAGCTCGCAC
39334973 GAGCTTACTGTTATTCAGCTCGCAC
1 GAGCTTACTGTTATTCAGCTCGCAC
*
39334998 GAGCTTACTG--ATTACAGCTCGTAC
1 GAGCTTACTGTTATT-CAGCTCGCAC
39335022 GAGC
1 GAGC
39335026 ATACAGATTC
Statistics
Matches: 48, Mismatches: 4, Indels: 3
0.87 0.07 0.05
Matches are distributed among these distances:
23 3 0.06
24 13 0.27
25 32 0.67
ACGTcount: A:0.22, C:0.26, G:0.22, T:0.31
Consensus pattern (25 bp):
GAGCTTACTGTTATTCAGCTCGCAC
Found at i:39335023 original size:24 final size:25
Alignment explanation
Indices: 39334964--39335043 Score: 83
Period size: 25 Copynumber: 3.2 Consensus size: 25
39334954 ACCGTTATTT
*
39334964 AGCTCGCATGAGCTTACTG-TTATTC
1 AGCTCGCACGAGCTTACTGATTA-TC
39334989 AGCTCGCACGAGCTTACTGATTA-C
1 AGCTCGCACGAGCTTACTGATTATC
* * * * *
39335013 AGCTCGTACGAGCATACAGATTCTT
1 AGCTCGCACGAGCTTACTGATTATC
39335038 AGCTCG
1 AGCTCG
39335044 TATGAGCATA
Statistics
Matches: 47, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
24 20 0.43
25 24 0.51
26 3 0.06
ACGTcount: A:0.24, C:0.26, G:0.21, T:0.29
Consensus pattern (25 bp):
AGCTCGCACGAGCTTACTGATTATC
Found at i:39337245 original size:2 final size:2
Alignment explanation
Indices: 39337238--39337267 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
39337228 AATGCCTCTT
*
39337238 GA GA GA GA GA GA GA AA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
39337268 ATTTTCGATT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.53, C:0.00, G:0.47, T:0.00
Consensus pattern (2 bp):
GA
Found at i:39352301 original size:35 final size:35
Alignment explanation
Indices: 39352255--39352325 Score: 133
Period size: 35 Copynumber: 2.0 Consensus size: 35
39352245 ATTAATCATC
39352255 ATGTTAATCATTTATGAAGCACTTATTAGTACTGA
1 ATGTTAATCATTTATGAAGCACTTATTAGTACTGA
*
39352290 ATGTTAATCATTTTTGAAGCACTTATTAGTACTGA
1 ATGTTAATCATTTATGAAGCACTTATTAGTACTGA
39352325 A
1 A
39352326 AATCATTCAT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.34, C:0.11, G:0.14, T:0.41
Consensus pattern (35 bp):
ATGTTAATCATTTATGAAGCACTTATTAGTACTGA
Found at i:39352719 original size:20 final size:20
Alignment explanation
Indices: 39352696--39352737 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
39352686 TAAAGTGTAT
*
39352696 ACAAAGGCACCGAAGTGCAA
1 ACAAAGGCACCGAAGTGAAA
*
39352716 ACAAAGGCACTGAAGTGAAA
1 ACAAAGGCACCGAAGTGAAA
39352736 AC
1 AC
39352738 CCCGTACAAG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.48, C:0.21, G:0.24, T:0.07
Consensus pattern (20 bp):
ACAAAGGCACCGAAGTGAAA
Found at i:39357517 original size:83 final size:82
Alignment explanation
Indices: 39357427--39357588 Score: 270
Period size: 83 Copynumber: 2.0 Consensus size: 82
39357417 TGAGATGATA
* * *
39357427 GAGAATCAGTGTTAAAAATTCTCGTTGAAACATTAGGAATGTATCAGATACAAATGTCATGACAT
1 GAGAATCAGTGTTAAAAAGTCCCGTTGAAACATTAAGAATGTATCAGATACAAATGTCATGACAT
*
39357492 TAAGGGGATGAGATCGTT
66 T-AGGAGATGAGATCGTT
*
39357510 GAGAATCAGTGTTAAAAAGTCCCGTTGAAACATTAAGAATGTATCGGATACAAATGTCATGACAT
1 GAGAATCAGTGTTAAAAAGTCCCGTTGAAACATTAAGAATGTATCAGATACAAATGTCATGACAT
39357575 TAGGAGATGAGATC
66 TAGGAGATGAGATC
39357589 CCGTGTAAGA
Statistics
Matches: 74, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
82 12 0.16
83 62 0.84
ACGTcount: A:0.38, C:0.12, G:0.23, T:0.27
Consensus pattern (82 bp):
GAGAATCAGTGTTAAAAAGTCCCGTTGAAACATTAAGAATGTATCAGATACAAATGTCATGACAT
TAGGAGATGAGATCGTT
Found at i:39357693 original size:50 final size:50
Alignment explanation
Indices: 39357635--39357740 Score: 142
Period size: 50 Copynumber: 2.1 Consensus size: 50
39357625 TTTTGAGGAT
* *
39357635 ATGAGAGGTCCCCCGTAAGA-TCATGTCTAGGACATGGCGTTGGCACCGAG
1 ATGAGAGGTCCCCCGTAAGACT-ATGTCTAGGACATGGCATGGGCACCGAG
* * * *
39357685 ATGAGAGGTCCCCCGTAAGACTATGTTTGGGACATGGCATGGGCTCCGAT
1 ATGAGAGGTCCCCCGTAAGACTATGTCTAGGACATGGCATGGGCACCGAG
39357735 ATGAGA
1 ATGAGA
39357741 ATCTCTCATG
Statistics
Matches: 49, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
50 48 0.98
51 1 0.02
ACGTcount: A:0.25, C:0.22, G:0.32, T:0.22
Consensus pattern (50 bp):
ATGAGAGGTCCCCCGTAAGACTATGTCTAGGACATGGCATGGGCACCGAG
Found at i:39358029 original size:20 final size:20
Alignment explanation
Indices: 39358004--39358042 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
39357994 TGAGTTATTT
39358004 AAGTAAGCA-AGTAAGTAAAC
1 AAGTAAG-AGAGTAAGTAAAC
39358024 AAGTAAGAGAGTAAGTAAA
1 AAGTAAGAGAGTAAGTAAA
39358043 GAAGAAGTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 1 0.06
20 17 0.94
ACGTcount: A:0.56, C:0.05, G:0.23, T:0.15
Consensus pattern (20 bp):
AAGTAAGAGAGTAAGTAAAC
Found at i:39359994 original size:17 final size:17
Alignment explanation
Indices: 39359942--39359996 Score: 65
Period size: 17 Copynumber: 3.2 Consensus size: 17
39359932 GTAAGGGATT
* * *
39359942 TTGCGGCGGTGATAGGC
1 TTGCGACGGCGATAGGG
*
39359959 TCGCGACGGCGATAGGG
1 TTGCGACGGCGATAGGG
*
39359976 TTGCGACGGCGATATGG
1 TTGCGACGGCGATAGGG
39359993 TTGC
1 TTGC
39359997 TCCGAAAAAA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
17 32 1.00
ACGTcount: A:0.15, C:0.20, G:0.44, T:0.22
Consensus pattern (17 bp):
TTGCGACGGCGATAGGG
Found at i:39360673 original size:130 final size:134
Alignment explanation
Indices: 39360412--39360673 Score: 397
Period size: 130 Copynumber: 2.0 Consensus size: 134
39360402 GACCCCCTTA
39360412 TAAATCATAAACAATTAAAGTTAACATTAAAAACAGAAATTAAAGTGAAAAATAAAAATTTTAAA
1 TAAATCATAAACAATTAAAGTTAACATTAAAAACAGAAATTAAAGTG--AAATAAAAATTTTAAA
* * * *
39360477 ATTAATCAGAAAATTTCTTCTCAAAAGATTACATTAAATTAATGCCCAGGAACGGTTGGAGGGGT
64 ATTAATCAAAAAATTTCTTCTCAAAAGATTACATTAAATTAATGCCCAGAAAAGGTTGGAGAGGT
39360542 CAATAT
129 CAATAT
* * *
39360548 TAAA-CATAAACAATTAAAGTTAACATTAAATATAGAAGTTAAAGTG-AA-AAAAA-TTTAAAAT
1 TAAATCATAAACAATTAAAGTTAACATTAAAAACAGAAATTAAAGTGAAATAAAAATTTTAAAAT
* *
39360609 TAATCAAAAAATTTCTTCTCAAAAGATTACATTAAATTAATGCCTAGAAAAGGTTTGAGAGGTCA
66 TAATCAAAAAATTTCTTCTCAAAAGATTACATTAAATTAATGCCCAGAAAAGGTTGGAGAGGTCA
39360674 CAATGGTCCC
Statistics
Matches: 117, Mismatches: 9, Indels: 6
0.89 0.07 0.05
Matches are distributed among these distances:
130 67 0.57
131 5 0.04
132 2 0.02
135 39 0.33
136 4 0.03
ACGTcount: A:0.50, C:0.10, G:0.12, T:0.29
Consensus pattern (134 bp):
TAAATCATAAACAATTAAAGTTAACATTAAAAACAGAAATTAAAGTGAAATAAAAATTTTAAAAT
TAATCAAAAAATTTCTTCTCAAAAGATTACATTAAATTAATGCCCAGAAAAGGTTGGAGAGGTCA
ATAT
Found at i:39365892 original size:14 final size:14
Alignment explanation
Indices: 39365873--39365899 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
39365863 GTGGTCCAGT
39365873 TGAACTGAACCGAG
1 TGAACTGAACCGAG
39365887 TGAACTGAACCGA
1 TGAACTGAACCGA
39365900 CCAAGAAATG
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
Done.