Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr13 ID=Chr13-JGI_221_v2.0
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: 58321163
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 747533 characters in sequence are not A, C, G, or T
File 56 of 199
Found at i:16458618 original size:20 final size:21
Alignment explanation
Indices: 16458595--16458633 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
16458585 TCGTTTTATT
16458595 TTTATTTTATTTT-ATTTTTA
1 TTTATTTTATTTTAATTTTTA
16458615 TTTATCTTT-TTTTAATTTT
1 TTTAT-TTTATTTTAATTTT
16458634 GTTTTAGTTG
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.18, C:0.03, G:0.00, T:0.79
Consensus pattern (21 bp):
TTTATTTTATTTTAATTTTTA
Found at i:16458618 original size:26 final size:27
Alignment explanation
Indices: 16458567--16458638 Score: 69
Period size: 26 Copynumber: 2.6 Consensus size: 27
16458557 ATTGAGTTTA
16458567 TTATTATTATTATTATTTTCGTTTTAT-TT
1 TTATT-TTATT-TTATTTTC-TTTTATCTT
16458596 TTATTTTATTTTATTTT-TATTTATCTT
1 TTATTTTATTTTATTTTCT-TTTATCTT
* *
16458623 TT-TTTAATTTTGTTTT
1 TTATTTTATTTTATTTT
16458639 AGTTGCTTTA
Statistics
Matches: 39, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
25 1 0.03
26 17 0.44
27 11 0.28
28 5 0.13
29 5 0.13
ACGTcount: A:0.18, C:0.03, G:0.03, T:0.76
Consensus pattern (27 bp):
TTATTTTATTTTATTTTCTTTTATCTT
Found at i:16458624 original size:17 final size:16
Alignment explanation
Indices: 16458573--16458624 Score: 68
Period size: 17 Copynumber: 3.1 Consensus size: 16
16458563 TTTATTATTA
*
16458573 TTATTATTATTTTCGTT
1 TTATTTTTATTTTC-TT
*
16458590 TTATTTTTATTTTATT
1 TTATTTTTATTTTCTT
16458606 TTATTTTTATTTATCTT
1 TTATTTTTATTT-TCTT
16458623 TT
1 TT
16458625 TTTAATTTTG
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
16 14 0.45
17 17 0.55
ACGTcount: A:0.17, C:0.04, G:0.02, T:0.77
Consensus pattern (16 bp):
TTATTTTTATTTTCTT
Found at i:16460501 original size:30 final size:30
Alignment explanation
Indices: 16460467--16460524 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
16460457 CTGGGCACTT
* *
16460467 CCACACGGGCTGGCCACATGCCCGTGTGAG
1 CCACACGAGCTGGCCACATGCCCATGTGAG
*
16460497 CCACACGAGCTGGGCACATGCCCATGTG
1 CCACACGAGCTGGCCACATGCCCATGTG
16460525 CCAGCCCGTG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.19, C:0.36, G:0.31, T:0.14
Consensus pattern (30 bp):
CCACACGAGCTGGCCACATGCCCATGTGAG
Found at i:16471890 original size:50 final size:50
Alignment explanation
Indices: 16471775--16472024 Score: 252
Period size: 50 Copynumber: 4.9 Consensus size: 50
16471765 ACATTAAGAG
* * *
16471775 GATGAGA--TCCCATGTAAGACCATGTCTGGGACATGGCATTGGAATCGTTGA
1 GATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCA-C--CGA
* * *
16471826 GATTATGAGTGGTCCCATGTGAGACCATGTTTGGGACATGGCGTTGGCACCGA
1 G---ATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGA
16471879 GATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGA
1 GATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGA
** * * * *
16471929 GATGAGAGGTCCCCCGTAAGACCATGTCTGGGACATGGCATGGGTACCTA
1 GATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGA
* * ** * * * *
16471979 TATGAAAACTCTCATGTAAGACCATATCTGGGATATGGCATTGGCA
1 GATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCA
16472025 GTACAAGAAA
Statistics
Matches: 168, Mismatches: 26, Indels: 11
0.82 0.13 0.05
Matches are distributed among these distances:
50 125 0.74
51 1 0.01
53 3 0.02
54 5 0.03
55 1 0.01
56 33 0.20
ACGTcount: A:0.26, C:0.20, G:0.30, T:0.24
Consensus pattern (50 bp):
GATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGA
Found at i:16478674 original size:16 final size:16
Alignment explanation
Indices: 16478653--16478696 Score: 81
Period size: 16 Copynumber: 2.8 Consensus size: 16
16478643 AAAATTAACT
16478653 AAGTAATAAAAATAAA
1 AAGTAATAAAAATAAA
16478669 AAGTAATAAAAATAAA
1 AAGTAATAAAAATAAA
16478685 AAGTAA-AAAAAT
1 AAGTAATAAAAAT
16478697 TCCAATGCAC
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
15 6 0.21
16 22 0.79
ACGTcount: A:0.75, C:0.00, G:0.07, T:0.18
Consensus pattern (16 bp):
AAGTAATAAAAATAAA
Found at i:16485114 original size:21 final size:20
Alignment explanation
Indices: 16485072--16485110 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
16485062 GATATTTATA
16485072 TTATTTTTAATTTAATAAAT
1 TTATTTTTAATTTAATAAAT
*
16485092 TTATTCTTT-ATTTATTAAA
1 TTATT-TTTAATTTAATAAA
16485111 ATTTTATATA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 14 0.82
21 3 0.18
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.62
Consensus pattern (20 bp):
TTATTTTTAATTTAATAAAT
Found at i:16488285 original size:6 final size:6
Alignment explanation
Indices: 16488274--16488327 Score: 81
Period size: 6 Copynumber: 9.0 Consensus size: 6
16488264 AGTCAAAATG
* *
16488274 ATATAT ATATAT ATATAT ATATAT ATATAT ATATGT ATATAT GTATAT
1 ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT
*
16488322 GTATAT
1 ATATAT
16488328 TCTTTGTATT
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 45 1.00
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (6 bp):
ATATAT
Found at i:16488287 original size:8 final size:8
Alignment explanation
Indices: 16488274--16488327 Score: 81
Period size: 8 Copynumber: 6.8 Consensus size: 8
16488264 AGTCAAAATG
16488274 ATATATAT
1 ATATATAT
16488282 ATATATAT
1 ATATATAT
16488290 ATATATAT
1 ATATATAT
16488298 ATATATAT
1 ATATATAT
*
16488306 ATGTATAT
1 ATATATAT
*
16488314 ATGTATAT
1 ATATATAT
*
16488322 GTATAT
1 ATATAT
16488328 TCTTTGTATT
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
8 43 1.00
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (8 bp):
ATATATAT
Found at i:16488293 original size:14 final size:14
Alignment explanation
Indices: 16488274--16488327 Score: 81
Period size: 14 Copynumber: 3.9 Consensus size: 14
16488264 AGTCAAAATG
16488274 ATATATATATATAT
1 ATATATATATATAT
16488288 ATATATATATATAT
1 ATATATATATATAT
*
16488302 ATATATGTATATAT
1 ATATATATATATAT
* *
16488316 GTATATGTATAT
1 ATATATATATAT
16488328 TCTTTGTATT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 38 1.00
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (14 bp):
ATATATATATATAT
Found at i:16488520 original size:24 final size:25
Alignment explanation
Indices: 16488470--16488524 Score: 76
Period size: 25 Copynumber: 2.2 Consensus size: 25
16488460 TCGGTTTATT
*
16488470 TTTAATTATATTTAAAATATTTTAA
1 TTTATTTATATTTAAAATATTTTAA
**
16488495 TTTATTTATATTTTCAA-ATTTTAA
1 TTTATTTATATTTAAAATATTTTAA
16488519 TTTATT
1 TTTATT
16488525 AACATTATCT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
24 13 0.48
25 14 0.52
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (25 bp):
TTTATTTATATTTAAAATATTTTAA
Found at i:16489421 original size:21 final size:21
Alignment explanation
Indices: 16489397--16489439 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
16489387 ATTGGATAAA
*
16489397 TTTAAAAAATAAATCTAATTT
1 TTTAAAAAATAAATATAATTT
**
16489418 TTTATTAAATAAATATAATTT
1 TTTAAAAAATAAATATAATTT
16489439 T
1 T
16489440 ATATATAAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (21 bp):
TTTAAAAAATAAATATAATTT
Found at i:16489467 original size:17 final size:18
Alignment explanation
Indices: 16489426--16489470 Score: 65
Period size: 18 Copynumber: 2.6 Consensus size: 18
16489416 TTTTTATTAA
*
16489426 ATAAATATAATTTTATAT
1 ATAAATATGATTTTATAT
16489444 ATAAATATGATTTTAT-T
1 ATAAATATGATTTTATAT
*
16489461 TTAAATATGA
1 ATAAATATGA
16489471 AAATAATTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
17 10 0.40
18 15 0.60
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (18 bp):
ATAAATATGATTTTATAT
Found at i:16491458 original size:62 final size:62
Alignment explanation
Indices: 16491361--16491510 Score: 264
Period size: 62 Copynumber: 2.4 Consensus size: 62
16491351 TCATGTTTCC
* *
16491361 AGGCCGTGTAACTCACTGTTTGTGAAATAGGGTCTCACGGCTAGGGGCACGAGCGTGTGCTT
1 AGGCCGTGTAACTCACTGTTTGTGAAATAGGGTCTCACGGCTAAGGGCACGAGCGTGTGCCT
*
16491423 AGGCCGTGTAACTCACTGTTTGTGAAATAGTGTCTCACGGCTAAGGGCACGAGCGTGTGCCT
1 AGGCCGTGTAACTCACTGTTTGTGAAATAGGGTCTCACGGCTAAGGGCACGAGCGTGTGCCT
*
16491485 AGGCCGTGTAACTCACTGTTCGTGAA
1 AGGCCGTGTAACTCACTGTTTGTGAA
16491511 TTAAAGTCAC
Statistics
Matches: 84, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
62 84 1.00
ACGTcount: A:0.21, C:0.22, G:0.31, T:0.26
Consensus pattern (62 bp):
AGGCCGTGTAACTCACTGTTTGTGAAATAGGGTCTCACGGCTAAGGGCACGAGCGTGTGCCT
Found at i:16496371 original size:47 final size:47
Alignment explanation
Indices: 16496317--16496433 Score: 141
Period size: 47 Copynumber: 2.5 Consensus size: 47
16496307 ACCGGATAGG
* *
16496317 TGATGCTTAAATGCTG-CCTAATTTGTTGCATATATGTTGTCCAATTT
1 TGATGCTTAAATGCTGTCC-AATTTGTTGCATATATGCTGCCCAATTT
* *
16496364 TGATGCTTAAATGCTGTCCAATTTTTTGTATATATGCTGCCCAA-TT
1 TGATGCTTAAATGCTGTCCAATTTGTTGCATATATGCTGCCCAATTT
* *
16496410 TGTTG-TATATATGCTGTCCAATTT
1 TGATGCT-TAAATGCTGTCCAATTT
16496434 TGGTGTACAA
Statistics
Matches: 62, Mismatches: 6, Indels: 5
0.85 0.08 0.07
Matches are distributed among these distances:
45 1 0.02
46 22 0.35
47 37 0.60
48 2 0.03
ACGTcount: A:0.23, C:0.15, G:0.16, T:0.45
Consensus pattern (47 bp):
TGATGCTTAAATGCTGTCCAATTTGTTGCATATATGCTGCCCAATTT
Found at i:16496407 original size:23 final size:23
Alignment explanation
Indices: 16496327--16496434 Score: 112
Period size: 23 Copynumber: 4.7 Consensus size: 23
16496317 TGATGCTTAA
* *
16496327 ATGCTG-CCTAATTTGTTGCATAT
1 ATGCTGTCC-AATTTTTTGTATAT
* * *
16496350 ATGTTGTCCAATTTTGATGCT-TAA
1 ATGCTGTCCAATTTT-TTG-TATAT
16496374 ATGCTGTCCAATTTTTTGTATAT
1 ATGCTGTCCAATTTTTTGTATAT
* *
16496397 ATGCTGCCCAATTTGTTGTATAT
1 ATGCTGTCCAATTTTTTGTATAT
16496420 ATGCTGTCCAATTTT
1 ATGCTGTCCAATTTT
16496435 GGTGTACAAT
Statistics
Matches: 69, Mismatches: 12, Indels: 8
0.78 0.13 0.09
Matches are distributed among these distances:
22 1 0.01
23 48 0.70
24 20 0.29
ACGTcount: A:0.22, C:0.16, G:0.16, T:0.46
Consensus pattern (23 bp):
ATGCTGTCCAATTTTTTGTATAT
Found at i:16496446 original size:13 final size:13
Alignment explanation
Indices: 16496428--16496453 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
16496418 ATATGCTGTC
16496428 CAATTTTGGTGTA
1 CAATTTTGGTGTA
16496441 CAATTTTGGTGTA
1 CAATTTTGGTGTA
16496454 AAAATGCTGC
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:0.23, C:0.08, G:0.23, T:0.46
Consensus pattern (13 bp):
CAATTTTGGTGTA
Found at i:16496558 original size:70 final size:70
Alignment explanation
Indices: 16496441--16496619 Score: 281
Period size: 70 Copynumber: 2.6 Consensus size: 70
16496431 TTTTGGTGTA
16496441 CAATTTTGGTGTAAAAATGCTGCTCAAATTGTTGTATATATGCTGCCCAAATTGTTGAATTTATG
1 CAATTTTGGTGTAAAAATGCTGCTCAAATTGTTGTATATATGCTGCCCAAATTGTTGAATTTATG
16496506 CTGTC
66 CTGTC
* *
16496511 CAATTTTGGTGTAAAAATGCTGCTCAAATTGTTGTATATATGTTGCCCAAATTGTTGTATTTATG
1 CAATTTTGGTGTAAAAATGCTGCTCAAATTGTTGTATATATGCTGCCCAAATTGTTGAATTTATG
16496576 CTGTC
66 CTGTC
* * * *
16496581 CAATTTTTGGTGTGAGAATGCTG-TCTAATT-TGGTATATA
1 CAA-TTTTGGTGTAAAAATGCTGCTCAAATTGTTGTATATA
16496620 AATGCTGTCC
Statistics
Matches: 102, Mismatches: 6, Indels: 3
0.92 0.05 0.03
Matches are distributed among these distances:
69 8 0.08
70 77 0.75
71 17 0.17
ACGTcount: A:0.26, C:0.12, G:0.20, T:0.42
Consensus pattern (70 bp):
CAATTTTGGTGTAAAAATGCTGCTCAAATTGTTGTATATATGCTGCCCAAATTGTTGAATTTATG
CTGTC
Found at i:16496583 original size:23 final size:22
Alignment explanation
Indices: 16496457--16496583 Score: 119
Period size: 23 Copynumber: 5.5 Consensus size: 22
16496447 TGGTGTAAAA
16496457 ATGCTGCTCAAATTGTTGTATAT
1 ATGCTGC-CAAATTGTTGTATAT
* *
16496480 ATGCTGCCCAAATTGTTGAATTT
1 ATGCTG-CCAAATTGTTGTATAT
* * * *
16496503 ATGCTGTCCAATTTTGGTGTAAAA
1 ATGCTG-CCAA-ATTGTTGTATAT
16496527 ATGCTGCTCAAATTGTTGTATAT
1 ATGCTGC-CAAATTGTTGTATAT
* *
16496550 ATGTTGCCCAAATTGTTGTATTT
1 ATGCTG-CCAAATTGTTGTATAT
16496573 ATGCTGTCCAA
1 ATGCTG-CCAA
16496584 TTTTTGGTGT
Statistics
Matches: 83, Mismatches: 17, Indels: 8
0.77 0.16 0.07
Matches are distributed among these distances:
23 66 0.80
24 17 0.20
ACGTcount: A:0.26, C:0.15, G:0.18, T:0.41
Consensus pattern (22 bp):
ATGCTGCCAAATTGTTGTATAT
Found at i:16501293 original size:126 final size:126
Alignment explanation
Indices: 16501068--16501296 Score: 323
Period size: 126 Copynumber: 1.8 Consensus size: 126
16501058 GTGTCAAGCT
* * * *
16501068 GTGTGTCCAAGTCGTGTAACTCACTATTTGTGAATTAAGGTCACACGAGCTAGGGGCATGGGCGT
1 GTGTGTCCAAGCCGTGTAACTCACTATTTGTGAATTAAGGTCACACGAGCTAGGGACACGGGCAT
*
16501133 GTGTCTAAGCCATGTAAGTCACTATTTGTAAATTAGAGCCACATGGGTTAGGGACATGGGA
66 GTGTCTAAGCCATGTAACTCACTATTTGTAAATTAGAGCCACATGGGTTAGGGACATGGGA
* * * *
16501194 GTGTGTCCAAGCCGTGTAACTCACTGTTTGTGAATTAGGGTCACATGGGCTAGGGACACGGGCAT
1 GTGTGTCCAAGCCGTGTAACTCACTATTTGTGAATTAAGGTCACACGAGCTAGGGACACGGGCAT
* * * * * *
16501259 GTGTCTAGGTCGTGTAACTCATTGTTTGTGAATTAGAG
66 GTGTCTAAGCCATGTAACTCACTATTTGTAAATTAGAG
16501297 TCACGCGGAC
Statistics
Matches: 88, Mismatches: 15, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
126 88 1.00
ACGTcount: A:0.24, C:0.17, G:0.30, T:0.29
Consensus pattern (126 bp):
GTGTGTCCAAGCCGTGTAACTCACTATTTGTGAATTAAGGTCACACGAGCTAGGGACACGGGCAT
GTGTCTAAGCCATGTAACTCACTATTTGTAAATTAGAGCCACATGGGTTAGGGACATGGGA
Found at i:16501294 original size:63 final size:63
Alignment explanation
Indices: 16501069--16501300 Score: 261
Period size: 63 Copynumber: 3.7 Consensus size: 63
16501059 TGTCAAGCTG
* * * * *
16501069 TGTGTCCAAGTCGTGTAACTCACTATTTGTGAATTA-AGGTCACACGAGCTAGGGGCATGGGCG
1 TGTGTCCAAGCCGTGTAACTCACTATTTGTGAATTAGA-GTCACATGGGCTAGGGACATGGGCA
* * * * * *
16501132 TGTGTCTAAGCCATGTAAGTCACTATTTGTAAATTAGAGCCACATGGGTTAGGGACATGGG-A
1 TGTGTCCAAGCCGTGTAACTCACTATTTGTGAATTAGAGTCACATGGGCTAGGGACATGGGCA
* * *
16501194 GTGTGTCCAAGCCGTGTAACTCACTGTTTGTGAATTAGGGTCACATGGGCTAGGGACACGGGCA
1 -TGTGTCCAAGCCGTGTAACTCACTATTTGTGAATTAGAGTCACATGGGCTAGGGACATGGGCA
* * * * *
16501258 TGTGTCTAGGTCGTGTAACTCATTGTTTGTGAATTAGAGTCAC
1 TGTGTCCAAGCCGTGTAACTCACTATTTGTGAATTAGAGTCAC
16501301 GCGGACGTGT
Statistics
Matches: 141, Mismatches: 25, Indels: 6
0.82 0.15 0.03
Matches are distributed among these distances:
63 139 0.99
64 2 0.01
ACGTcount: A:0.24, C:0.17, G:0.29, T:0.29
Consensus pattern (63 bp):
TGTGTCCAAGCCGTGTAACTCACTATTTGTGAATTAGAGTCACATGGGCTAGGGACATGGGCA
Found at i:16502750 original size:37 final size:37
Alignment explanation
Indices: 16502649--16502754 Score: 142
Period size: 37 Copynumber: 2.9 Consensus size: 37
16502639 AAATCTTATT
* * *
16502649 ATTATACTGAATGAATCTCAATCAAGCAAATTATACC
1 ATTATACTGAATGAAGCTCAATCGAGCAAATCATACC
* *
16502686 GTTATATTGAATGAAGCTCAATCGAGCAAATCATACC
1 ATTATACTGAATGAAGCTCAATCGAGCAAATCATACC
*
16502723 ATTATACTGAATGGAGCTCAA-CTGAGCAAATC
1 ATTATACTGAATGAAGCTCAATC-GAGCAAATC
16502755 TTACTGTTAT
Statistics
Matches: 60, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
36 1 0.02
37 59 0.98
ACGTcount: A:0.40, C:0.19, G:0.14, T:0.27
Consensus pattern (37 bp):
ATTATACTGAATGAAGCTCAATCGAGCAAATCATACC
Found at i:16502765 original size:37 final size:37
Alignment explanation
Indices: 16502638--16502767 Score: 138
Period size: 37 Copynumber: 3.5 Consensus size: 37
16502628 TCTATCAAGC
** * *
16502638 CAAATCTTATTATTATACTGAATGAATCTCAATCAAG
1 CAAATCTTACCATTATACTGAATGAAGCTCAATCGAG
* *
16502675 CAAAT-TATACCGTTATATTGAATGAAGCTCAATCGAG
1 CAAATCT-TACCATTATACTGAATGAAGCTCAATCGAG
* *
16502712 CAAATCATACCATTATACTGAATGGAGCTCAA-CTGAG
1 CAAATCTTACCATTATACTGAATGAAGCTCAATC-GAG
**
16502749 CAAATCTTACTGTTATACT
1 CAAATCTTACCATTATACT
16502768 AACTGATGTT
Statistics
Matches: 77, Mismatches: 13, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
36 2 0.03
37 75 0.97
ACGTcount: A:0.38, C:0.18, G:0.12, T:0.32
Consensus pattern (37 bp):
CAAATCTTACCATTATACTGAATGAAGCTCAATCGAG
Found at i:16504394 original size:25 final size:25
Alignment explanation
Indices: 16504357--16504411 Score: 76
Period size: 25 Copynumber: 2.2 Consensus size: 25
16504347 TGAGCATCTT
*
16504357 GATA-TTGGCTCTCTTGAGCTACCC
1 GATAGTTGGCTCTCTCGAGCTACCC
*
16504381 GATAGTTGGCTCTCTCGAGCTTCCC
1 GATAGTTGGCTCTCTCGAGCTACCC
*
16504406 GTTAGT
1 GATAGT
16504412 AGCTCTTTTA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
24 4 0.15
25 23 0.85
ACGTcount: A:0.15, C:0.27, G:0.24, T:0.35
Consensus pattern (25 bp):
GATAGTTGGCTCTCTCGAGCTACCC
Found at i:16507018 original size:33 final size:33
Alignment explanation
Indices: 16506976--16507046 Score: 142
Period size: 33 Copynumber: 2.2 Consensus size: 33
16506966 GCAAACTCTG
16506976 TGTGAGAAACAACTGTATGCTAAATTTAGCAAA
1 TGTGAGAAACAACTGTATGCTAAATTTAGCAAA
16507009 TGTGAGAAACAACTGTATGCTAAATTTAGCAAA
1 TGTGAGAAACAACTGTATGCTAAATTTAGCAAA
16507042 TGTGA
1 TGTGA
16507047 ATTTTGGCTT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 38 1.00
ACGTcount: A:0.41, C:0.11, G:0.20, T:0.28
Consensus pattern (33 bp):
TGTGAGAAACAACTGTATGCTAAATTTAGCAAA
Found at i:16510529 original size:24 final size:24
Alignment explanation
Indices: 16510467--16510523 Score: 62
Period size: 24 Copynumber: 2.3 Consensus size: 24
16510457 CAACTTGAAA
* *
16510467 GAGCATCATGTTATT-AGCTCTCAT
1 GAGCATCCTGATATTGA-CTCTCAT
*
16510491 GAGCATCCTGATATTGACTCTCTT
1 GAGCATCCTGATATTGACTCTCAT
16510515 GAGCTATCC
1 GAGC-ATCC
16510524 GGTATTTGGC
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
24 23 0.82
25 5 0.18
ACGTcount: A:0.23, C:0.25, G:0.18, T:0.35
Consensus pattern (24 bp):
GAGCATCCTGATATTGACTCTCAT
Found at i:16510536 original size:25 final size:24
Alignment explanation
Indices: 16510478--16510543 Score: 62
Period size: 25 Copynumber: 2.7 Consensus size: 24
16510468 AGCATCATGT
* *
16510478 TATTAGCTCTCATGAGCATCCTGA
1 TATTGGCTCTCATGAGCATCCGGA
* *
16510502 TATTGACTCTCTTGAGCTATCCGG-
1 TATTGGCTCTCATGAGC-ATCCGGA
*
16510526 TATTTGGCTCTCAAGAGC
1 TA-TTGGCTCTCATGAGC
16510544 TTCATGTTAT
Statistics
Matches: 33, Mismatches: 7, Indels: 3
0.77 0.16 0.07
Matches are distributed among these distances:
24 16 0.48
25 17 0.52
ACGTcount: A:0.21, C:0.24, G:0.20, T:0.35
Consensus pattern (24 bp):
TATTGGCTCTCATGAGCATCCGGA
Found at i:16512211 original size:10 final size:10
Alignment explanation
Indices: 16512196--16512226 Score: 62
Period size: 10 Copynumber: 3.1 Consensus size: 10
16512186 TATAAGGGAC
16512196 AATATGATTG
1 AATATGATTG
16512206 AATATGATTG
1 AATATGATTG
16512216 AATATGATTG
1 AATATGATTG
16512226 A
1 A
16512227 TTTCTAATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.42, C:0.00, G:0.19, T:0.39
Consensus pattern (10 bp):
AATATGATTG
Found at i:16512494 original size:32 final size:32
Alignment explanation
Indices: 16512453--16512516 Score: 119
Period size: 32 Copynumber: 2.0 Consensus size: 32
16512443 TGTTTTGACT
16512453 TGTTGTGCACTTGATCAACTTGTGATTTCCTA
1 TGTTGTGCACTTGATCAACTTGTGATTTCCTA
*
16512485 TGTTGTGCACTTTATCAACTTGTGATTTCCTA
1 TGTTGTGCACTTGATCAACTTGTGATTTCCTA
16512517 CTTGTTACCT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.19, C:0.19, G:0.17, T:0.45
Consensus pattern (32 bp):
TGTTGTGCACTTGATCAACTTGTGATTTCCTA
Found at i:16512834 original size:43 final size:43
Alignment explanation
Indices: 16512785--16512866 Score: 137
Period size: 43 Copynumber: 1.9 Consensus size: 43
16512775 GAGACACTGG
*
16512785 CGTGTGACTCGACCATGCGAGGCACACGGCCTTGCAACATGGC
1 CGTGTGACTCGACCATGCGAGGCACACGGCCTTACAACATGGC
* *
16512828 CGTGTGACTCGACCGTGTGAGGCACACGGCCTTACAACA
1 CGTGTGACTCGACCATGCGAGGCACACGGCCTTACAACA
16512867 CTTCCATGTG
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
43 36 1.00
ACGTcount: A:0.22, C:0.32, G:0.29, T:0.17
Consensus pattern (43 bp):
CGTGTGACTCGACCATGCGAGGCACACGGCCTTACAACATGGC
Found at i:16516270 original size:5 final size:5
Alignment explanation
Indices: 16516260--16516285 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
16516250 TATAAAATCA
16516260 ATAAT ATAAT ATAAT ATAAT ATAAT A
1 ATAAT ATAAT ATAAT ATAAT ATAAT A
16516286 AAAAATAGTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (5 bp):
ATAAT
Found at i:16521464 original size:58 final size:57
Alignment explanation
Indices: 16521285--16521464 Score: 152
Period size: 57 Copynumber: 3.2 Consensus size: 57
16521275 TGTAAAATCA
* * * * ** * *
16521285 CGAGCTATTTTGAACTTAAG--TATATTTAAAATAATCAGCTGGGGATGTAAATCCGT
1 CGAGCTGTTTTGAACTTAGGCATATTTTTTAAATAATCAAATGAGAATGTAAATCC-T
* * *
16521341 -GAGCTATTTTTAACTTAGGCATATTTTTTATATAATCAAATGAGAATGTAAATCCT
1 CGAGCTGTTTTGAACTTAGGCATATTTTTTAAATAATCAAATGAGAATGTAAATCCT
* * * * * *
16521397 CGAGTTGTTTTGAACTTAGGCATATTTTTTGAAATACTTAATTGGGAATGTAAAT-TT
1 CGAGCTGTTTTGAACTTAGGCATATTTTTT-AAATAATCAAATGAGAATGTAAATCCT
16521454 ACGAGCTGTTT
1 -CGAGCTGTTT
16521465 GGAGGTTGCG
Statistics
Matches: 100, Mismatches: 19, Indels: 8
0.79 0.15 0.06
Matches are distributed among these distances:
55 17 0.17
56 1 0.01
57 54 0.54
58 28 0.28
ACGTcount: A:0.32, C:0.11, G:0.18, T:0.39
Consensus pattern (57 bp):
CGAGCTGTTTTGAACTTAGGCATATTTTTTAAATAATCAAATGAGAATGTAAATCCT
Found at i:16521723 original size:71 final size:71
Alignment explanation
Indices: 16521462--16522193 Score: 594
Period size: 71 Copynumber: 10.4 Consensus size: 71
16521452 TTACGAGCTG
* * * * ** ** * * *
16521462 TTTGGAGGTTGCGGTGTTAAA-CTGCGAGCCTTAAAATGACAGTTAAGCGCTTTTAACTATTGCT
1 TTTGGAGGCTGCGGTATTAAACCTGCAAGCCTTAGAATGACAACTGGGAGCTTTTAACTCTCGCT
16521526 AA-T-T
66 AACTAT
* * ** * * **
16521530 GTTTGGAGGTTGCAGTATTAAACCTGTGAGCCTTAAAACGACAGTTGGGAGCTTTTAACTCTCGC
1 -TTTGGAGGCTGCGGTATTAAACCTGCAAGCCTTAGAATGACAACTGGGAGCTTTTAACTCTCGC
*
16521595 TAACT-G
65 TAACTAT
* * * * ** * *
16521601 TTTGGAGGCAGCGATATTACACTTGTGAGCCTTAGAATGACAAATGGGAGCTTTCAACTCTCGCT
1 TTTGGAGGCTGCGGTATTAAACCTGCAAGCCTTAGAATGACAACTGGGAGCTTTTAACTCTCGCT
16521666 AACTAT
66 AACTAT
* * * * * *
16521672 TTGGGAGGCTACGGTTTTAAACCTACAAGCCTTAGAATGACAGCTGAGAGCTTTTAACTCTCGCT
1 TTTGGAGGCTGCGGTATTAAACCTGCAAGCCTTAGAATGACAACTGGGAGCTTTTAACTCTCGCT
16521737 AACTAT
66 AACTAT
* * * * * * * **
16521743 TTGGGAGGCTGCGGTTTTAAACCTGCAATG-CTTAAAATGATAGCTAGGAGCTTTTTACTCTCTT
1 TTTGGAGGCTGCGGTATTAAACCTGCAA-GCCTTAGAATGACAACTGGGAGCTTTTAACTCTCGC
16521807 TAACTAT
65 TAACTAT
* ** * * ** * * ** *
16521814 TTTTGATACTGCGATATTAAACTTGGGAGCCTTACAATGAGAACTGGGAGCTTTTAGGTCTCGTT
1 TTTGGAGGCTGCGGTATTAAACCTGCAAGCCTTAGAATGACAACTGGGAGCTTTTAACTCTCGCT
16521879 AACTAT
66 AACTAT
* * ** * *
16521885 TTTGGAGTCTGCAGTGCTAAACATGCAAGCCTTAGAATGA-AACCTGGGAGCTTTTAACTCTCAC
1 TTTGGAGGCTGCGGTATTAAACCTGCAAGCCTTAGAATGACAA-CTGGGAGCTTTTAACTCTCGC
*
16521949 TAGCTAT
65 TAACTAT
* * * * ** * *
16521956 ATTAGAGGCTGTGGTATTAAACTTGTGAGCCTTAGAATGACAACTGAGAGCTTTTAACTCTCGTT
1 TTTGGAGGCTGCGGTATTAAACCTGCAAGCCTTAGAATGACAACTGGGAGCTTTTAACTCTCGCT
*
16522021 AACTGT
66 AACTAT
* ** * ** * * * *
16522027 TTTGAAGGCTGCAATATTAAATCTGTGAGCCTTGGAATGACAACTAGGAGCTTTTAACTTTTGCT
1 TTTGGAGGCTGCGGTATTAAACCTGCAAGCCTTAGAATGACAACTGGGAGCTTTTAACTCTCGCT
16522092 AACTAT
66 AACTAT
* * * * ** *
16522098 TTTGGAGGCTGCGATATTAAACCTACAAGCCTTCGAATGATAGTTGGGAGCTTTTAACTCTCGTT
1 TTTGGAGGCTGCGGTATTAAACCTGCAAGCCTTAGAATGACAACTGGGAGCTTTTAACTCTCGCT
16522163 AACTAT
66 AACTAT
*
16522169 TTTTGAGGCTGCGGTATTAAACCTG
1 TTTGGAGGCTGCGGTATTAAACCTG
16522194 TGAGACTTGC
Statistics
Matches: 531, Mismatches: 125, Indels: 12
0.79 0.19 0.02
Matches are distributed among these distances:
69 19 0.04
70 99 0.19
71 410 0.77
72 3 0.01
ACGTcount: A:0.27, C:0.18, G:0.22, T:0.33
Consensus pattern (71 bp):
TTTGGAGGCTGCGGTATTAAACCTGCAAGCCTTAGAATGACAACTGGGAGCTTTTAACTCTCGCT
AACTAT
Found at i:16522222 original size:213 final size:210
Alignment explanation
Indices: 16521510--16522265 Score: 693
Period size: 213 Copynumber: 3.6 Consensus size: 210
16521500 ACAGTTAAGC
* * * * * * * *
16521510 GCTTTTAACTATTGCTAA-T-TGTTTGGAGGTTGCAGTATTAAACCTGTGAGCCTTAAAACGACA
1 GCTTTTAACTCTCGCTAACTAT-TTTAGAGGCTGCGGTATTAAACCTGTGAG-CTT-GAATGATA
* * *
16521573 GTTGGGAGCTTTTAACTCTCGCTAACTG-TTTGGAGGCAGCGATATTACACTTGTGAGCCTTAGA
63 GTT-GGAGCTTTTAACTCTCGCTAACTGTTTTGAAGGCTGCGATATTAAACTTGTGAGCCTTAGA
* * * * * *
16521637 ATGACAAATGGGAGCTTTCAACTCTCGCTAACTATTTGGGAGGCTACGGTTTTAAACCTACAAGC
127 ATGACAACTGGGAGCTTTTAACTCTCGCTAACTATTTTGGAGGCTGCGATATTAAACCTACAAGC
* *
16521702 CTTAGAATGACAGCTGAGA
192 CTTAGAATGAAAGCTGGGA
** * ** *
16521721 GCTTTTAACTCTCGCTAACTATTTGGGAGGCTGCGGTTTTAAACCTGCAATGCTTAAAATGATAG
1 GCTTTTAACTCTCGCTAACTATTTTAGAGGCTGCGGTATTAAACCTGTGA-GCTT-GAATGATAG
* * ** * * *
16521786 CTAGGAGCTTTTTACTCTCTTTAACTATTTTTGATA--CTGCGATATTAAACTTGGGAGCCTTAC
64 -TTGGAGCTTTTAACTCTCGCTAACT-GTTTTGA-AGGCTGCGATATTAAACTTGTGAGCCTTAG
* ** * * ** * *
16521849 AATGAGAACTGGGAGCTTTTAGGTCTCGTTAACTATTTTGGAGTCTGC-AGTGCTAAACATGCAA
126 AATGACAACTGGGAGCTTTTAACTCTCGCTAACTATTTTGGAGGCTGCGA-TATTAAACCTACAA
*
16521913 GCCTTAGAATGAAACCTGGGA
190 GCCTTAGAATGAAAGCTGGGA
* * * * * * *
16521934 GCTTTTAACTCTCACTAGCTATATTAGAGGCTGTGGTATTAAACTTGTGAGCCTTAGAATGACAA
1 GCTTTTAACTCTCGCTAACTATTTTAGAGGCTGCGGTATTAAACCTGTGAG-CTT-GAATGATAG
* * * *
16521999 CTGAGAGCTTTTAACTCTCGTTAACTGTTTTGAAGGCTGCAATATTAAA-TCTGTGAGCCTTGGA
64 TTG-GAGCTTTTAACTCTCGCTAACTGTTTTGAAGGCTGCGATATTAAACT-TGTGAGCCTTAGA
* * *
16522063 ATGACAACTAGGAGCTTTTAACTTTTGCTAACTATTTTGGAGGCTGCGATATTAAACCTACAAGC
127 ATGACAACTGGGAGCTTTTAACTCTCGCTAACTATTTTGGAGGCTGCGATATTAAACCTACAAGC
* * *
16522128 CTTCGAATGATAGTTGGGA
192 CTTAGAATGAAAGCTGGGA
* *
16522147 GCTTTTAACTCTCGTTAACTATTTTTGAGGCTGCGGTATTAAACCTGTGAGACTTGCAAT-AGTA
1 GCTTTTAACTCTCGCTAACTATTTTAGAGGCTGCGGTATTAAACCTGTGAG-CTTG-AATGA-TA
* * * *
16522211 GTTGTGAGCTTTTCACTTTTGCTAACTGTTTTGAAGG-TCGTGATATTAAACTTGT
63 GTTG-GAGCTTTTAACTCTCGCTAACTGTTTTGAAGGCT-GCGATATTAAACTTGT
16522266 ATTGGAATTG
Statistics
Matches: 434, Mismatches: 93, Indels: 34
0.77 0.17 0.06
Matches are distributed among these distances:
211 17 0.04
212 66 0.15
213 344 0.79
214 6 0.01
215 1 0.00
ACGTcount: A:0.27, C:0.17, G:0.22, T:0.34
Consensus pattern (210 bp):
GCTTTTAACTCTCGCTAACTATTTTAGAGGCTGCGGTATTAAACCTGTGAGCTTGAATGATAGTT
GGAGCTTTTAACTCTCGCTAACTGTTTTGAAGGCTGCGATATTAAACTTGTGAGCCTTAGAATGA
CAACTGGGAGCTTTTAACTCTCGCTAACTATTTTGGAGGCTGCGATATTAAACCTACAAGCCTTA
GAATGAAAGCTGGGA
Found at i:16531169 original size:27 final size:29
Alignment explanation
Indices: 16531139--16531192 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
16531129 ATTTTCTTAC
*
16531139 TATT-CAATA-ATTTGATTATAAAAAATG
1 TATTGCAATAGATTAGATTATAAAAAATG
*
16531166 TATTGCATTAGATTAGATTATAAAAAA
1 TATTGCAATAGATTAGATTATAAAAAA
16531193 ATATTTATAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 4 0.17
28 4 0.17
29 15 0.65
ACGTcount: A:0.48, C:0.04, G:0.09, T:0.39
Consensus pattern (29 bp):
TATTGCAATAGATTAGATTATAAAAAATG
Found at i:16539541 original size:5 final size:5
Alignment explanation
Indices: 16539531--16539556 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
16539521 AATTATTTAT
16539531 ATAAA ATAAA ATAAA ATAAA ATAAA A
1 ATAAA ATAAA ATAAA ATAAA ATAAA A
16539557 AATTTGTATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
ATAAA
Found at i:16541273 original size:43 final size:43
Alignment explanation
Indices: 16541203--16541401 Score: 251
Period size: 43 Copynumber: 4.6 Consensus size: 43
16541193 TTATGTGAAA
* *
16541203 AAACGCCGCTAAAGAACGTGA-CATTTAGCGACGC-TTTACCCAC
1 AAACGCCGCTAAAGAACATGATC-TTTAGCGGCGCTTTTA-CCAC
* *
16541246 AAACGCCGCTAAAGAACATGATCTTTAGCTGCGCTTTTATCAC
1 AAACGCCGCTAAAGAACATGATCTTTAGCGGCGCTTTTACCAC
* * *
16541289 AAACGCAGCTAAAGAACATGATCTTTAGTGGCGC-CTTACCTAC
1 AAACGCCGCTAAAGAACATGATCTTTAGCGGCGCTTTTACC-AC
* * * *
16541332 AAACGCCACTAAAGATCATGTTCTTTAGCGGCGCTTTTATCAC
1 AAACGCCGCTAAAGAACATGATCTTTAGCGGCGCTTTTACCAC
16541375 AAACGCCGCTAAAGAACATGATCTTTA
1 AAACGCCGCTAAAGAACATGATCTTTA
16541402 ACATGTTCTT
Statistics
Matches: 133, Mismatches: 19, Indels: 8
0.83 0.12 0.05
Matches are distributed among these distances:
42 4 0.03
43 120 0.90
44 9 0.07
ACGTcount: A:0.32, C:0.26, G:0.17, T:0.25
Consensus pattern (43 bp):
AAACGCCGCTAAAGAACATGATCTTTAGCGGCGCTTTTACCAC
Found at i:16541316 original size:86 final size:86
Alignment explanation
Indices: 16541203--16541401 Score: 292
Period size: 86 Copynumber: 2.3 Consensus size: 86
16541193 TTATGTGAAA
* * *
16541203 AAACGCCGCTAAAGAACGTGA-CATTTAGCGACGCTTTACCCACAAACGCCGCTAAAGAACATGA
1 AAACGCCGCTAAAGAACATGATC-TTTAGCGACGCCTTACCCACAAACGCCACTAAAGAACATGA
*
16541267 TCTTTAGCTGCGCTTTTATCAC
65 TCTTTAGCGGCGCTTTTATCAC
* * * * * *
16541289 AAACGCAGCTAAAGAACATGATCTTTAGTGGCGCCTTACCTACAAACGCCACTAAAGATCATGTT
1 AAACGCCGCTAAAGAACATGATCTTTAGCGACGCCTTACCCACAAACGCCACTAAAGAACATGAT
16541354 CTTTAGCGGCGCTTTTATCAC
66 CTTTAGCGGCGCTTTTATCAC
16541375 AAACGCCGCTAAAGAACATGATCTTTA
1 AAACGCCGCTAAAGAACATGATCTTTA
16541402 ACATGTTCTT
Statistics
Matches: 101, Mismatches: 11, Indels: 2
0.89 0.10 0.02
Matches are distributed among these distances:
86 100 0.99
87 1 0.01
ACGTcount: A:0.32, C:0.26, G:0.17, T:0.25
Consensus pattern (86 bp):
AAACGCCGCTAAAGAACATGATCTTTAGCGACGCCTTACCCACAAACGCCACTAAAGAACATGAT
CTTTAGCGGCGCTTTTATCAC
Found at i:16549651 original size:42 final size:41
Alignment explanation
Indices: 16549559--16549682 Score: 114
Period size: 42 Copynumber: 3.1 Consensus size: 41
16549549 ACGACACCGT
**
16549559 TTTGC-AC-AAAACGCCACTATTGCTTGACTTTTAGCGGCG
1 TTTGCAACAAAAACGCCACTATTGCTCAACTTTTAGCGGCG
* * *
16549598 TTTAG-ACCAAAAACGCTACTATTGCTCAACTTTTTTGCGGCG
1 TTT-GCAACAAAAACGCCACTATTGCTCAAC-TTTTAGCGGCG
* * *
16549640 TTTGCAACAAAAACGACGCTATTGCT-TACTGTTT-GCGGCG
1 TTTGCAACAAAAACGCCACTATTGCTCAACT-TTTAGCGGCG
16549680 TTT
1 TTT
16549683 TTTTCATGAA
Statistics
Matches: 69, Mismatches: 10, Indels: 11
0.77 0.11 0.12
Matches are distributed among these distances:
39 3 0.04
40 12 0.17
41 24 0.35
42 30 0.43
ACGTcount: A:0.24, C:0.23, G:0.19, T:0.33
Consensus pattern (41 bp):
TTTGCAACAAAAACGCCACTATTGCTCAACTTTTAGCGGCG
Found at i:16549838 original size:19 final size:19
Alignment explanation
Indices: 16549814--16549862 Score: 71
Period size: 19 Copynumber: 2.5 Consensus size: 19
16549804 TAAAATTATA
* *
16549814 ATTTTTAGTTTTTGTGTTTT
1 ATTTTTA-TTTTTGTATTTC
16549834 ATTTTTATTTTTGTATTTC
1 ATTTTTATTTTTGTATTTC
16549853 ATTTTTATTT
1 ATTTTTATTT
16549863 GTTATAATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
19 20 0.74
20 7 0.26
ACGTcount: A:0.14, C:0.02, G:0.08, T:0.76
Consensus pattern (19 bp):
ATTTTTATTTTTGTATTTC
Found at i:16550214 original size:7 final size:7
Alignment explanation
Indices: 16550202--16550436 Score: 68
Period size: 7 Copynumber: 33.0 Consensus size: 7
16550192 AACTAATTAA
16550202 CCTAAAC
1 CCTAAAC
16550209 CCTAAAC
1 CCTAAAC
16550216 CCTAAAC
1 CCTAAAC
16550223 TCCT-AAC
1 -CCTAAAC
* *
16550230 CCTCATC
1 CCTAAAC
16550237 TCCTAAAC
1 -CCTAAAC
* *
16550245 CCTGAAT
1 CCTAAAC
* *
16550252 CATAAAA
1 CCTAAAC
*
16550259 CATAAAC
1 CCTAAAC
*
16550266 CATGAAA-
1 CCT-AAAC
16550273 CCTAAAC
1 CCTAAAC
*
16550280 CCTCAAC
1 CCTAAAC
* *
16550287 TCTTAACC
1 -CCTAAAC
16550295 CCT-AAC
1 CCTAAAC
*
16550301 CCTTAAAT
1 CC-TAAAC
*
16550309 CTTAAA-
1 CCTAAAC
*
16550315 CCTCAAC
1 CCTAAAC
16550322 CCTTAAAC
1 CC-TAAAC
* *
16550330 CATAAAT
1 CCTAAAC
*
16550337 CATAAAC
1 CCTAAAC
* *
16550344 CATAATC
1 CCTAAAC
*
16550351 CATAAAC
1 CCTAAAC
*
16550358 CCATAATC
1 CC-TAAAC
*
16550366 CATAAAC
1 CCTAAAC
*
16550373 CTTAAA-
1 CCTAAAC
*
16550379 -ATAGTAAC
1 CCTA--AAC
*
16550387 TCTTAAAC
1 -CCTAAAC
*
16550395 CTTAAAC
1 CCTAAAC
16550402 CCTAAAC
1 CCTAAAC
* *
16550409 CATATAC
1 CCTAAAC
16550416 CCTAAAC
1 CCTAAAC
*
16550423 CATAAAC
1 CCTAAAC
*
16550430 CTTAAAC
1 CCTAAAC
16550437 TATAATGATA
Statistics
Matches: 172, Mismatches: 40, Indels: 32
0.70 0.16 0.13
Matches are distributed among these distances:
5 2 0.01
6 14 0.08
7 123 0.72
8 31 0.18
10 2 0.01
ACGTcount: A:0.43, C:0.33, G:0.01, T:0.23
Consensus pattern (7 bp):
CCTAAAC
Found at i:16550219 original size:14 final size:14
Alignment explanation
Indices: 16550202--16550441 Score: 87
Period size: 14 Copynumber: 16.9 Consensus size: 14
16550192 AACTAATTAA
*
16550202 CCTAAACCCTAAAC
1 CCTAAACCATAAAC
*
16550216 CCTAAACTCCT-AAC
1 CCTAAAC-CATAAAC
* * *
16550230 CCTCATCTCCTAAAC
1 CCTAAAC-CATAAAC
* * *
16550245 CCTGAATCATAAAA
1 CCTAAACCATAAAC
*
16550259 CATAAACCATGAAA-
1 CCTAAACCAT-AAAC
* *
16550273 CCTAAACCCTCAAC
1 CCTAAACCATAAAC
* * *
16550287 TCTTAACCCCT-AAC
1 -CCTAAACCATAAAC
* *
16550301 CCTTAAATCTTAAA-
1 CC-TAAACCATAAAC
* *
16550315 CCTCAACCCTTAAAC
1 CCT-AAACCATAAAC
* *
16550330 CATAAATCATAAAC
1 CCTAAACCATAAAC
* *
16550344 CATAATCCATAAAC
1 CCTAAACCATAAAC
*
16550358 CCATAATCCATAAAC
1 CC-TAAACCATAAAC
*
16550373 CTTAAA--ATAGTAAC
1 CCTAAACCATA--AAC
* *
16550387 TCTTAAACCTTAAAC
1 -CCTAAACCATAAAC
*
16550402 CCTAAACCATATAC
1 CCTAAACCATAAAC
16550416 CCTAAACCATAAAC
1 CCTAAACCATAAAC
* *
16550430 CTTAAACTATAA
1 CCTAAACCATAA
16550442 TGATAAATAA
Statistics
Matches: 174, Mismatches: 37, Indels: 30
0.72 0.15 0.12
Matches are distributed among these distances:
12 3 0.02
13 4 0.02
14 118 0.68
15 47 0.27
17 2 0.01
ACGTcount: A:0.43, C:0.33, G:0.01, T:0.23
Consensus pattern (14 bp):
CCTAAACCATAAAC
Found at i:16550378 original size:22 final size:22
Alignment explanation
Indices: 16550326--16550430 Score: 58
Period size: 22 Copynumber: 4.9 Consensus size: 22
16550316 CTCAACCCTT
*
16550326 AAACCATAAATCATAAA-CCAT
1 AAACCATAAACCATAAACCCAT
* *
16550347 AATCCATAAACCCAT-AATCCAT
1 AAACCATAAA-CCATAAACCCAT
* * *
16550369 AAACCTTAAA--ATAGTAACTCTT
1 AAACCATAAACCATA--AACCCAT
* *
16550391 AAACCTTAAACCCTAAA-CCAT
1 AAACCATAAACCATAAACCCAT
* *
16550412 ATACCCTAAACCATAAACC
1 AAACCATAAACCATAAACC
16550431 TTAAACTATA
Statistics
Matches: 63, Mismatches: 13, Indels: 15
0.69 0.14 0.16
Matches are distributed among these distances:
19 2 0.03
21 27 0.43
22 32 0.51
24 2 0.03
ACGTcount: A:0.49, C:0.29, G:0.01, T:0.22
Consensus pattern (22 bp):
AAACCATAAACCATAAACCCAT
Found at i:16550923 original size:40 final size:40
Alignment explanation
Indices: 16550864--16551294 Score: 339
Period size: 40 Copynumber: 10.9 Consensus size: 40
16550854 TTTTTTGCGA
* * *
16550864 CGTTTTGCAAAAAGCGCCGCTAATGCTGGATCTATAGCGG
1 CGTTTTTCAAAAAGCGCCGCTAATGCTCGATCTATAGAGG
* * *
16550904 CGATTTTT-GAAAAGTGCCGCTAATGCTCGATCTATAGAAG
1 CG-TTTTTCAAAAAGCGCCGCTAATGCTCGATCTATAGAGG
* *
16550944 CGTTTTTCAAAAAGCGCTGCTAATGCTCGATCTATAGTGG
1 CGTTTTTCAAAAAGCGCCGCTAATGCTCGATCTATAGAGG
*
16550984 CGTTTTTCAAAAAGCGCCGCTAATGCTCGATCTATAGGGG
1 CGTTTTTCAAAAAGCGCCGCTAATGCTCGATCTATAGAGG
* *
16551024 CGTCATTT-AAAAATCGCCGCTAATGC-C-A-CTA-A-A-G
1 CGT-TTTTCAAAAAGCGCCGCTAATGCTCGATCTATAGAGG
*** * ** ** * * * *
16551058 C--TCAACATAAAATGACGGCG-TTGTGCTTAATGTTTTTGCA-C
1 CGTTTTTCA-AAAA-G-CGCCGCTAATGCTCGAT-CTATAG-AGG
* * *
16551099 CATTTTCCAAAAAGTGCCGCTAATGCTCGATCTATAGCA-G
1 CGTTTTTCAAAAAGCGCCGCTAATGCTCGATCTATAG-AGG
* * * * *
16551139 CGTTGTTCAAAAAGCACCACTAATGCTCCATCTATAGCGG
1 CGTTTTTCAAAAAGCGCCGCTAATGCTCGATCTATAGAGG
* * *
16551179 AGTTTTTCAAAAAGCGCCGCTAATGCTCGATCAATAGCGG
1 CGTTTTTCAAAAAGCGCCGCTAATGCTCGATCTATAGAGG
* * * *
16551219 CGTTGTTCAAAAAGCGTCGCTAATGCTCAATCTATAGCGG
1 CGTTTTTCAAAAAGCGCCGCTAATGCTCGATCTATAGAGG
* *
16551259 CGTTTTTCAAAAAGTGTCGCTAATGCTCGATCTATA
1 CGTTTTTCAAAAAGCGCCGCTAATGCTCGATCTATA
16551295 ATGGCATTTT
Statistics
Matches: 309, Mismatches: 64, Indels: 36
0.76 0.16 0.09
Matches are distributed among these distances:
32 1 0.00
33 4 0.01
34 6 0.02
35 4 0.01
36 2 0.01
37 3 0.01
38 2 0.01
39 6 0.02
40 257 0.83
41 17 0.06
42 4 0.01
43 3 0.01
ACGTcount: A:0.28, C:0.22, G:0.21, T:0.29
Consensus pattern (40 bp):
CGTTTTTCAAAAAGCGCCGCTAATGCTCGATCTATAGAGG
Found at i:16550997 original size:80 final size:80
Alignment explanation
Indices: 16550864--16551294 Score: 376
Period size: 80 Copynumber: 5.5 Consensus size: 80
16550854 TTTTTTGCGA
* * * *
16550864 CGTTTTGCAAAAAGCGCCGCTAATGCTGGATCTATAGCGGCGATTTTT-GAAAAGTGCCGCTAAT
1 CGTTTTTCAAAAAGCGCCGCTAATGCTCGATCTATAGCGGCG-TTTTTCAAAAAGCGCCGCTAAT
* **
16550928 GCTCGATCTATAGAAG
65 GCTCAATCTATAGCGG
* *
16550944 CGTTTTTCAAAAAGCGCTGCTAATGCTCGATCTATAGTGGCGTTTTTCAAAAAGCGCCGCTAATG
1 CGTTTTTCAAAAAGCGCCGCTAATGCTCGATCTATAGCGGCGTTTTTCAAAAAGCGCCGCTAATG
* *
16551009 CTCGATCTATAGGGG
66 CTCAATCTATAGCGG
* * * * **** * * **
16551024 CGTCATTT-AAAAATCGCCGCTAATGC-C-A-CTAAAGC-TC-AACAT-AAAATGACGGCG-TTG
1 CGT-TTTTCAAAAAGCGCCGCTAATGCTCGATCTATAGCGGCGTTTTTCAAAAAG-CGCCGCTAA
* * * * **
16551081 TGCTTAATGTTTTTGCAC
64 TGCTCAAT-CTATAGCGG
* * * * * * *
16551099 CATTTTCCAAAAAGTGCCGCTAATGCTCGATCTATAGCAGCGTTGTTCAAAAAGCACCACTAATG
1 CGTTTTTCAAAAAGCGCCGCTAATGCTCGATCTATAGCGGCGTTTTTCAAAAAGCGCCGCTAATG
*
16551164 CTCCATCTATAGCGG
66 CTCAATCTATAGCGG
* * * *
16551179 AGTTTTTCAAAAAGCGCCGCTAATGCTCGATCAATAGCGGCGTTGTTCAAAAAGCGTCGCTAATG
1 CGTTTTTCAAAAAGCGCCGCTAATGCTCGATCTATAGCGGCGTTTTTCAAAAAGCGCCGCTAATG
16551244 CTCAATCTATAGCGG
66 CTCAATCTATAGCGG
* *
16551259 CGTTTTTCAAAAAGTGTCGCTAATGCTCGATCTATA
1 CGTTTTTCAAAAAGCGCCGCTAATGCTCGATCTATA
16551295 ATGGCATTTT
Statistics
Matches: 271, Mismatches: 68, Indels: 24
0.75 0.19 0.07
Matches are distributed among these distances:
74 14 0.05
75 26 0.10
76 2 0.01
77 6 0.02
78 7 0.03
79 7 0.03
80 194 0.72
81 15 0.06
ACGTcount: A:0.28, C:0.22, G:0.21, T:0.29
Consensus pattern (80 bp):
CGTTTTTCAAAAAGCGCCGCTAATGCTCGATCTATAGCGGCGTTTTTCAAAAAGCGCCGCTAATG
CTCAATCTATAGCGG
Found at i:16551206 original size:235 final size:236
Alignment explanation
Indices: 16550744--16551283 Score: 719
Period size: 235 Copynumber: 2.3 Consensus size: 236
16550734 ATGCTTTTTT
* * * * *
16550744 GTGGCGTTTTTGATAAAGCGCCACTAAAGCTCGATCTATAGCGGCGTTTTTCAAAAAGCGCCGCT
1 GTGGCGTTTTTCAAAAAGCGCCGCTAATGCTCGATCTATAGCGGCGTATTTCAAAAAGCGCCGCT
* * * *
16550809 AATGATACTAAAGCTCAACATAAAACGACGGCGTTGTGCTTAAATTTTTTTGCGACGTTTTGCAA
66 AATGACACTAAAGCTCAACATAAAACGACGGCGTTGTGCTTAAATGTTTTTGCGACATTTTCCAA
* * ** ** * *
16550874 AAAGCGCCGCTAATGCTGGATCTATAGCGGCGATTTTTGAAAAGTGCCGCTAATGCTCGATCTAT
131 AAAGCGCCGCTAATGCTCGATCTATAGCAGCGATTTTCAAAAAGCACCACTAATGCTCCATCTAT
* * *
16550939 AGAAGCGTTTTTCAAAAAGCGCTGCTAATGCTCGATCTATA
196 AGAAGAGTTTTTCAAAAAGCGCCGCTAATGCTCGATCAATA
* *
16550980 GTGGCGTTTTTCAAAAAGCGCCGCTAATGCTCGATCTATAGGGGCGTCATTT-AAAAATCGCCGC
1 GTGGCGTTTTTCAAAAAGCGCCGCTAATGCTCGATCTATAGCGGCGT-ATTTCAAAAAGCGCCGC
* *
16551044 TAATGCCACTAAAGCTCAACATAAAATGACGGCGTTGTGCTT-AATGTTTTTGC-ACCATTTTCC
65 TAATGACACTAAAGCTCAACATAAAACGACGGCGTTGTGCTTAAATGTTTTTGCGA-CATTTTCC
*
16551107 AAAAAGTGCCGCTAATGCTCGATCTATAGCAGCG-TTGTTCAAAAAGCACCACTAATGCTCCATC
129 AAAAAGCGCCGCTAATGCTCGATCTATAGCAGCGATT-TTCAAAAAGCACCACTAATGCTCCATC
**
16551171 TATAGCGGAGTTTTTCAAAAAGCGCCGCTAATGCTCGATCAATA
193 TATAGAAGAGTTTTTCAAAAAGCGCCGCTAATGCTCGATCAATA
* * * * * * *
16551215 GCGGCGTTGTTCAAAAAGCGTCGCTAATGCTCAATCTATAGCGGCGTTTTTCAAAAAGTGTCGCT
1 GTGGCGTTTTTCAAAAAGCGCCGCTAATGCTCGATCTATAGCGGCGTATTTCAAAAAGCGCCGCT
16551280 AATG
66 AATG
16551284 CTCGATCTAT
Statistics
Matches: 264, Mismatches: 36, Indels: 9
0.85 0.12 0.03
Matches are distributed among these distances:
234 6 0.02
235 163 0.62
236 92 0.35
237 3 0.01
ACGTcount: A:0.29, C:0.22, G:0.21, T:0.29
Consensus pattern (236 bp):
GTGGCGTTTTTCAAAAAGCGCCGCTAATGCTCGATCTATAGCGGCGTATTTCAAAAAGCGCCGCT
AATGACACTAAAGCTCAACATAAAACGACGGCGTTGTGCTTAAATGTTTTTGCGACATTTTCCAA
AAAGCGCCGCTAATGCTCGATCTATAGCAGCGATTTTCAAAAAGCACCACTAATGCTCCATCTAT
AGAAGAGTTTTTCAAAAAGCGCCGCTAATGCTCGATCAATA
Found at i:16562176 original size:60 final size:60
Alignment explanation
Indices: 16562111--16562235 Score: 178
Period size: 60 Copynumber: 2.1 Consensus size: 60
16562101 AGGGACATTG
* * * * * *
16562111 AAGTGTATACAGGGGCATTGGAGTGCGAACATGAGCATAGATGTGAAAATAGAGACACCA
1 AAGTGTATACAGGGGCATCGAAGTGCGAACAGGAGCACAAATGTGAAAATAAAGACACCA
* *
16562171 AAGTGTATACAGGGGCATCGAAGTGCGAACAGGAGCACAAATGTGCAAATAAAGACACGA
1 AAGTGTATACAGGGGCATCGAAGTGCGAACAGGAGCACAAATGTGAAAATAAAGACACCA
16562231 AAGTG
1 AAGTG
16562236 CAAACTGGGG
Statistics
Matches: 57, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
60 57 1.00
ACGTcount: A:0.40, C:0.14, G:0.30, T:0.16
Consensus pattern (60 bp):
AAGTGTATACAGGGGCATCGAAGTGCGAACAGGAGCACAAATGTGAAAATAAAGACACCA
Found at i:16564088 original size:5 final size:5
Alignment explanation
Indices: 16564051--16564300 Score: 340
Period size: 5 Copynumber: 50.0 Consensus size: 5
16564041 CAAATCAGAG
* * * * *
16564051 CATAT CTTAT CATTT CATAA CGTAT CAGAT CATAT CATA- CTATAT CATAT
1 CATAT CATAT CATAT CATAT CATAT CATAT CATAT CATAT C-ATAT CATAT
*** * * * *
16564101 CATAT TGGAT CATAT CAGAT CATAT CACAC CATAT CATAT CATAT CAGAT
1 CATAT CATAT CATAT CATAT CATAT CATAT CATAT CATAT CATAT CATAT
* *
16564151 CAGAT CATAT CATAT CATAT CATAT CATAT CATAC CATAT CATAT CATAT
1 CATAT CATAT CATAT CATAT CATAT CATAT CATAT CATAT CATAT CATAT
16564201 CATAT CATAT CATAT CATAT CATAT CATAT CATAT CATAT CATAT CATAT
1 CATAT CATAT CATAT CATAT CATAT CATAT CATAT CATAT CATAT CATAT
* *
16564251 CATAT CATAT CATAT CATAA CATAT CATAT TATAT CATAT CATAT CATAT
1 CATAT CATAT CATAT CATAT CATAT CATAT CATAT CATAT CATAT CATAT
16564301 AATGTCCTAC
Statistics
Matches: 213, Mismatches: 30, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
4 1 0.00
5 211 0.99
6 1 0.00
ACGTcount: A:0.39, C:0.20, G:0.03, T:0.38
Consensus pattern (5 bp):
CATAT
Found at i:16580147 original size:43 final size:43
Alignment explanation
Indices: 16580065--16580149 Score: 143
Period size: 43 Copynumber: 2.0 Consensus size: 43
16580055 TTATCCTAGA
* *
16580065 AAAAAATAATTTAAAAAGAGGAGAAGATAATCTTAGGTTGTTG
1 AAAAAATAATTTAAAAAGAGGAGAAGATAAACATAGGTTGTTG
*
16580108 AAAAAATAATTTAAAAAGAGGAGAAGATAAACATGGGTTGTT
1 AAAAAATAATTTAAAAAGAGGAGAAGATAAACATAGGTTGTT
16580150 CGATTTACCC
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
43 39 1.00
ACGTcount: A:0.51, C:0.02, G:0.21, T:0.26
Consensus pattern (43 bp):
AAAAAATAATTTAAAAAGAGGAGAAGATAAACATAGGTTGTTG
Found at i:16583754 original size:15 final size:15
Alignment explanation
Indices: 16583734--16583763 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
16583724 AACCATAATC
16583734 GGAAAAAATAAAAGA
1 GGAAAAAATAAAAGA
*
16583749 GGAAAAAGTAAAAGA
1 GGAAAAAATAAAAGA
16583764 AGAAGAGAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.70, C:0.00, G:0.23, T:0.07
Consensus pattern (15 bp):
GGAAAAAATAAAAGA
Found at i:16589625 original size:30 final size:29
Alignment explanation
Indices: 16589591--16589888 Score: 229
Period size: 30 Copynumber: 9.9 Consensus size: 29
16589581 GTGTGCTAAA
* *
16589591 CGATGGTCGAAGCCATCCTTTTTCATTAAC
1 CGATGGTCGAA-CCATCCCTTTTCATTAAT
* * *
16589621 CGATGGT-TATCACCATCACTTTTAATTAAT
1 CGATGGTCGA--ACCATCCCTTTTCATTAAT
* * * *
16589651 CGATGGTCGTCACTATCCCTTTTTCGTAAAAT
1 CGATGGTCG-AACCATCCC-TTTTCAT-TAAT
*
16589683 CGGTGGTCGAAACCATCCCTTTTCATTAAT
1 CGATGGTCG-AACCATCCCTTTTCATTAAT
* * *
16589713 CGATGGTCGTCACCATCCCTTTTAATAAAT
1 CGATGGTCG-AACCATCCCTTTTCATTAAT
* * *
16589743 CGATGGTCAAAATCATCCCTTTTCATTATT
1 CGATGGTC-GAACCATCCCTTTTCATTAAT
* * * *
16589773 TGATGATCGTCACCATCCCTTTTCATAAAT
1 CGATGGTCG-AACCATCCCTTTTCATTAAT
* *
16589803 CAATGGTCAAAACCATCCCTTTTCATTAAT
1 CGATGGTC-GAACCATCCCTTTTCATTAAT
* * * * *
16589833 TGATGGTTGTCACCATCCCTTTTCATAAAC
1 CGATGGTCG-AACCATCCCTTTTCATTAAT
16589863 CGATGGTCGAAGCCATCCCTTTTCAT
1 CGATGGTCGAA-CCATCCCTTTTCAT
16589889 ATTCAATAGT
Statistics
Matches: 205, Mismatches: 52, Indels: 22
0.73 0.19 0.08
Matches are distributed among these distances:
29 2 0.01
30 173 0.84
31 12 0.06
32 18 0.09
ACGTcount: A:0.26, C:0.26, G:0.13, T:0.36
Consensus pattern (29 bp):
CGATGGTCGAACCATCCCTTTTCATTAAT
Found at i:16589761 original size:92 final size:92
Alignment explanation
Indices: 16589594--16589765 Score: 238
Period size: 92 Copynumber: 1.9 Consensus size: 92
16589584 TGCTAAACGA
* * * *
16589594 TGGTCGAAGCCATCCTTTTTCATTAACCGATGGTTATCACCATCACTTTTAATTAATCGATGGTC
1 TGGTCGAAACCATCCCTTTTCATTAACCGATGGTCATCACCATCACTTTTAATAAATCGATGGTC
***
16589659 GTCACTATCCCTTTTTCGTAAAATCGG
66 AAAACTATCCCTTTTTCGTAAAATCGG
* * *
16589686 TGGTCGAAACCATCCCTTTTCATTAATCGATGGTCGTCACCATCCCTTTTAATAAATCGATGGTC
1 TGGTCGAAACCATCCCTTTTCATTAACCGATGGTCATCACCATCACTTTTAATAAATCGATGGTC
16589751 AAAA-TCATCCCTTTT
66 AAAACT-ATCCCTTTT
16589766 CATTATTTGA
Statistics
Matches: 69, Mismatches: 10, Indels: 2
0.85 0.12 0.02
Matches are distributed among these distances:
91 1 0.01
92 68 0.99
ACGTcount: A:0.25, C:0.25, G:0.14, T:0.36
Consensus pattern (92 bp):
TGGTCGAAACCATCCCTTTTCATTAACCGATGGTCATCACCATCACTTTTAATAAATCGATGGTC
AAAACTATCCCTTTTTCGTAAAATCGG
Found at i:16589783 original size:60 final size:60
Alignment explanation
Indices: 16589603--16589888 Score: 347
Period size: 60 Copynumber: 4.7 Consensus size: 60
16589593 ATGGTCGAAG
* * * * ** * *
16589603 CCATCCTTTTTCATTAACCGATGGTTATCACCATCACTTTTAATTAATCGATGGTCGTCA
1 CCATCCCTTTTCATAAATCGATGGTCAAAACCATCCCTTTTCATTAATCGATGGTCGTCA
* * * *
16589663 CTATCCCTTTTTCGTAAAATCGGTGGTCGAAACCATCCCTTTTCATTAATCGATGGTCGTCA
1 CCATCCC-TTTTCAT-AAATCGATGGTCAAAACCATCCCTTTTCATTAATCGATGGTCGTCA
* * * * *
16589725 CCATCCCTTTTAATAAATCGATGGTCAAAATCATCCCTTTTCATTATTTGATGATCGTCA
1 CCATCCCTTTTCATAAATCGATGGTCAAAACCATCCCTTTTCATTAATCGATGGTCGTCA
* * *
16589785 CCATCCCTTTTCATAAATCAATGGTCAAAACCATCCCTTTTCATTAATTGATGGTTGTCA
1 CCATCCCTTTTCATAAATCGATGGTCAAAACCATCCCTTTTCATTAATCGATGGTCGTCA
* * *
16589845 CCATCCCTTTTCATAAACCGATGGTCGAAGCCATCCCTTTTCAT
1 CCATCCCTTTTCATAAATCGATGGTCAAAACCATCCCTTTTCAT
16589889 ATTCAATAGT
Statistics
Matches: 193, Mismatches: 31, Indels: 4
0.85 0.14 0.02
Matches are distributed among these distances:
60 139 0.72
61 11 0.06
62 43 0.22
ACGTcount: A:0.26, C:0.26, G:0.12, T:0.36
Consensus pattern (60 bp):
CCATCCCTTTTCATAAATCGATGGTCAAAACCATCCCTTTTCATTAATCGATGGTCGTCA
Found at i:16589879 original size:90 final size:90
Alignment explanation
Indices: 16589587--16589889 Score: 313
Period size: 90 Copynumber: 3.4 Consensus size: 90
16589577 CAAAGTGTGC
* * * * *
16589587 TAAA-CGATGGTCGAAGCCATCCTTTTTCATTAACCGATGGTTATCACCATCACTTTTAATTAAT
1 TAAATCGATGGTCGAAGCCATCCCTTTTCATAAATCGATGGTCATCACCATCCCTTTTAATTAAT
* *
16589651 CGATGGTCGTCACTATCCCTTTTTCG
66 CGATGGTCGTCACCATCCC-TTTTCA
* * * * *
16589677 TAAAATCGGTGGTCGAAACCATCCCTTTTCATTAATCGATGGTCGTCACCATCCCTTTTAATAAA
1 T-AAATCGATGGTCGAAGCCATCCCTTTTCATAAATCGATGGTCATCACCATCCCTTTTAATTAA
*** *
16589742 TCGATGGTCAAAATCATCCCTTTTCA
65 TCGATGGTCGTCACCATCCCTTTTCA
* * * * * * ** *
16589768 TTATTTGATGATCGTCA-CCATCCCTTTTCATAAATCAATGGTCAAAACCATCCCTTTTCATTAA
1 TAAATCGATGGTCG-AAGCCATCCCTTTTCATAAATCGATGGTCATCACCATCCCTTTTAATTAA
* *
16589832 TTGATGGTTGTCACCATCCCTTTTCA
65 TCGATGGTCGTCACCATCCCTTTTCA
*
16589858 TAAACCGATGGTCGAAGCCATCCCTTTTCATA
1 TAAATCGATGGTCGAAGCCATCCCTTTTCATA
16589890 TTCAATAGTC
Statistics
Matches: 170, Mismatches: 39, Indels: 8
0.78 0.18 0.04
Matches are distributed among these distances:
89 1 0.01
90 93 0.55
91 10 0.06
92 66 0.39
ACGTcount: A:0.26, C:0.25, G:0.13, T:0.35
Consensus pattern (90 bp):
TAAATCGATGGTCGAAGCCATCCCTTTTCATAAATCGATGGTCATCACCATCCCTTTTAATTAAT
CGATGGTCGTCACCATCCCTTTTCA
Found at i:16599781 original size:17 final size:16
Alignment explanation
Indices: 16599761--16599792 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
16599751 TCAAAACTTT
16599761 CTCTTTCTTCTCTCATG
1 CTCTTTCTTC-CTCATG
16599778 CTCTTTCTTCCTCAT
1 CTCTTTCTTCCTCAT
16599793 TCTTTCCTCT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.06, C:0.38, G:0.03, T:0.53
Consensus pattern (16 bp):
CTCTTTCTTCCTCATG
Found at i:16600115 original size:10 final size:9
Alignment explanation
Indices: 16600101--16600283 Score: 77
Period size: 9 Copynumber: 19.2 Consensus size: 9
16600091 ATGAGAAAAA
16600101 ATAAAAATT
1 ATAAAAATT
**
16600110 AGTAAATGTT
1 A-TAAAAATT
16600120 ATAAAAATT
1 ATAAAAATT
**
16600129 ATTAAATTTT
1 A-TAAAAATT
*
16600139 AATAAAAACT
1 -ATAAAAATT
16600149 ATAAAAATAT
1 ATAAAAAT-T
* *
16600159 TTAAAATTT
1 ATAAAAATT
*
16600168 ATAAAAAAT
1 ATAAAAATT
16600177 AT-AAAATAT
1 ATAAAAAT-T
*
16600186 ATAGAAATTT
1 ATA-AAAATT
* *
16600196 AGAAAAAAAT
1 A-TAAAAATT
16600206 ATAAAAATT
1 ATAAAAATT
16600215 -TATAAAATCGT
1 ATA-AAAAT--T
16600226 A-AGAAAATT
1 ATA-AAAATT
*
16600235 ATAAAAAAT
1 ATAAAAATT
* *
16600244 GTAAAGAAAT
1 ATAAA-AATT
16600254 AT-AAAATT
1 ATAAAAATT
*
16600262 CATAAAAAAAT
1 -AT-AAAAATT
16600273 ATAAAAATT
1 ATAAAAATT
16600282 AT
1 AT
16600284 CATTTTAAAG
Statistics
Matches: 128, Mismatches: 29, Indels: 34
0.67 0.15 0.18
Matches are distributed among these distances:
8 9 0.07
9 61 0.48
10 40 0.31
11 18 0.14
ACGTcount: A:0.62, C:0.02, G:0.04, T:0.32
Consensus pattern (9 bp):
ATAAAAATT
Found at i:16600151 original size:29 final size:28
Alignment explanation
Indices: 16600119--16600222 Score: 106
Period size: 29 Copynumber: 3.6 Consensus size: 28
16600109 TAGTAAATGT
* *
16600119 TATAAAAAT-TATTAAATTTTAATAAAAAC
1 TATAAAAATAT-TTAAAATTT-ATAAAAAA
16600148 TATAAAAATATTTAAAATTTATAAAAAA
1 TATAAAAATATTTAAAATTTATAAAAAA
* *
16600176 TAT-AAAATATATAGAAATTTAGAAAAAAA
1 TATAAAAATATTTA-AAATTTA-TAAAAAA
16600205 TATAAAAAT-TTATAAAAT
1 TATAAAAATATT-TAAAAT
16600223 CGTAAGAAAA
Statistics
Matches: 65, Mismatches: 5, Indels: 10
0.81 0.06 0.12
Matches are distributed among these distances:
27 9 0.14
28 17 0.26
29 31 0.48
30 8 0.12
ACGTcount: A:0.62, C:0.01, G:0.02, T:0.35
Consensus pattern (28 bp):
TATAAAAATATTTAAAATTTATAAAAAA
Found at i:16600153 original size:19 final size:20
Alignment explanation
Indices: 16600100--16600146 Score: 69
Period size: 19 Copynumber: 2.4 Consensus size: 20
16600090 AATGAGAAAA
16600100 AATAAAAATTAGTAAATGTT
1 AATAAAAATTAGTAAATGTT
* *
16600120 -ATAAAAATTATTAAATTTT
1 AATAAAAATTAGTAAATGTT
16600139 AATAAAAA
1 AATAAAAA
16600147 CTATAAAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 17 0.71
20 7 0.29
ACGTcount: A:0.60, C:0.00, G:0.04, T:0.36
Consensus pattern (20 bp):
AATAAAAATTAGTAAATGTT
Found at i:16600207 original size:20 final size:20
Alignment explanation
Indices: 16600179--16600221 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
16600169 TAAAAAATAT
* *
16600179 AAAATATATAGAAATTTAGA
1 AAAAAATATAAAAATTTAGA
*
16600199 AAAAAATATAAAAATTTATA
1 AAAAAATATAAAAATTTAGA
16600219 AAA
1 AAA
16600222 TCGTAAGAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.67, C:0.00, G:0.05, T:0.28
Consensus pattern (20 bp):
AAAAAATATAAAAATTTAGA
Found at i:16600210 original size:38 final size:37
Alignment explanation
Indices: 16600167--16600279 Score: 111
Period size: 39 Copynumber: 2.9 Consensus size: 37
16600157 ATTTAAAATT
*
16600167 TATAAAAAATATAAAAT-ATATAGAAATTTAGAAAAAAA
1 TATAAAAAATATAAAATCATA-AGAAAATTA-AAAAAAA
* * *
16600205 TATAAAAATTTATAAAATCGTAAGAAAATTATAAAAAA
1 TATAAAAA-ATATAAAATCATAAGAAAATTAAAAAAAA
* *
16600243 TGTAAAGAAATATAAAATTCATAAAAAAATATAAAAA
1 TATAAA-AAATATAAAA-TCATAAGAAAAT-TAAAAA
16600280 TTATCATTTT
Statistics
Matches: 61, Mismatches: 9, Indels: 8
0.78 0.12 0.10
Matches are distributed among these distances:
38 26 0.43
39 28 0.46
40 7 0.11
ACGTcount: A:0.66, C:0.02, G:0.05, T:0.27
Consensus pattern (37 bp):
TATAAAAAATATAAAATCATAAGAAAATTAAAAAAAA
Found at i:16600231 original size:39 final size:38
Alignment explanation
Indices: 16600167--16600260 Score: 102
Period size: 38 Copynumber: 2.4 Consensus size: 38
16600157 ATTTAAAATT
*
16600167 TATAAAAAATATAAAATATATAGAAATTTAGAAAAAAA
1 TATAAAAAATATAAAATATATAGAAAATTAGAAAAAAA
* * *
16600205 TATAAAAATTTATAAAATCGTA-AGAAAATTA-TAAAAAA
1 TATAAAAA-ATATAAAAT-ATATAGAAAATTAGAAAAAAA
*
16600243 TGTAAAGAAATATAAAAT
1 TATAAA-AAATATAAAAT
16600261 TCATAAAAAA
Statistics
Matches: 47, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
38 27 0.57
39 18 0.38
40 2 0.04
ACGTcount: A:0.65, C:0.01, G:0.06, T:0.28
Consensus pattern (38 bp):
TATAAAAAATATAAAATATATAGAAAATTAGAAAAAAA
Found at i:16600241 original size:20 final size:19
Alignment explanation
Indices: 16600207--16600280 Score: 64
Period size: 19 Copynumber: 3.9 Consensus size: 19
16600197 GAAAAAAATA
*
16600207 TAAAAATTTAT-AAAATCG
1 TAAAAAATTATAAAAATCG
16600225 TAAGAAAATTATAAAAAAT-G
1 TAA-AAAATTAT-AAAAATCG
* *
16600245 TAAAGAAA-TATAAAATTCA
1 TAAA-AAATTATAAAAATCG
*
16600264 TAAAAAAATATAAAAAT
1 TAAAAAATTATAAAAAT
16600281 TATCATTTTA
Statistics
Matches: 46, Mismatches: 4, Indels: 11
0.75 0.07 0.18
Matches are distributed among these distances:
18 11 0.24
19 23 0.50
20 7 0.15
21 5 0.11
ACGTcount: A:0.65, C:0.03, G:0.05, T:0.27
Consensus pattern (19 bp):
TAAAAAATTATAAAAATCG
Found at i:16600242 original size:21 final size:19
Alignment explanation
Indices: 16600199--16600259 Score: 56
Period size: 20 Copynumber: 3.2 Consensus size: 19
16600189 GAAATTTAGA
*
16600199 AAAAAATAT-AAAAATT-T
1 AAAAAATGTAAAAAATTAT
*
16600216 ATAAAATCGTAAGAAAATTAT
1 AAAAAAT-GTAA-AAAATTAT
16600237 AAAAAATGTAAAGAAA-TAT
1 AAAAAATGTAAA-AAATTAT
16600256 AAAA
1 AAAA
16600260 TTCATAAAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
17 6 0.17
18 1 0.03
19 9 0.25
20 13 0.36
21 7 0.19
ACGTcount: A:0.67, C:0.02, G:0.07, T:0.25
Consensus pattern (19 bp):
AAAAAATGTAAAAAATTAT
Found at i:16600491 original size:19 final size:18
Alignment explanation
Indices: 16600463--16600522 Score: 70
Period size: 19 Copynumber: 3.3 Consensus size: 18
16600453 TTTCTATGCA
16600463 TTTTAT-ATTTTTTATGAT
1 TTTTATAATTTTTTAT-AT
*
16600481 TTTTATAATTTTTAATAAT
1 TTTTATAATTTTTTAT-AT
*
16600500 TTTTA-AAATTTTTATAT
1 TTTTATAATTTTTTATAT
16600517 TTTTAT
1 TTTTAT
16600523 TTATATTTAA
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
17 7 0.19
18 14 0.39
19 15 0.42
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (18 bp):
TTTTATAATTTTTTATAT
Found at i:16600512 original size:37 final size:37
Alignment explanation
Indices: 16600471--16600551 Score: 101
Period size: 37 Copynumber: 2.2 Consensus size: 37
16600461 CATTTTATAT
*
16600471 TTTTTATGATTTTTA-TAATTTTTAATAATTTTTAAAA
1 TTTTTAT-ATTTTTATTAATATTTAATAATTTTTAAAA
* * *
16600508 TTTTTATATTTTTATTTATATTTAATATTTTTTATAA
1 TTTTTATATTTTTATTAATATTTAATAATTTTTAAAA
*
16600545 CTTTTAT
1 TTTTTAT
16600552 CACATGTCAC
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
36 7 0.18
37 31 0.82
ACGTcount: A:0.31, C:0.01, G:0.01, T:0.67
Consensus pattern (37 bp):
TTTTTATATTTTTATTAATATTTAATAATTTTTAAAA
Found at i:16600541 original size:10 final size:9
Alignment explanation
Indices: 16600463--16600551 Score: 81
Period size: 9 Copynumber: 9.7 Consensus size: 9
16600453 TTTCTATGCA
*
16600463 TTTTATATT
1 TTTTATAAT
*
16600472 TTTTATGAT
1 TTTTATAAT
16600481 TTTTATAAT
1 TTTTATAAT
16600490 TTTTAATAAT
1 TTTT-ATAAT
*
16600500 TTTTAAAAT
1 TTTTATAAT
16600509 TTTTAT-AT
1 TTTTATAAT
*
16600517 TTTTATTTAT
1 TTTTA-TAAT
* *
16600527 ATTTAATATT
1 -TTTTATAAT
*
16600537 TTTTATAAC
1 TTTTATAAT
16600546 TTTTAT
1 TTTTAT
16600552 CACATGTCAC
Statistics
Matches: 65, Mismatches: 11, Indels: 8
0.77 0.13 0.10
Matches are distributed among these distances:
8 7 0.11
9 41 0.63
10 13 0.20
11 4 0.06
ACGTcount: A:0.30, C:0.01, G:0.01, T:0.67
Consensus pattern (9 bp):
TTTTATAAT
Found at i:16600550 original size:19 final size:17
Alignment explanation
Indices: 16600463--16600550 Score: 68
Period size: 19 Copynumber: 4.8 Consensus size: 17
16600453 TTTCTATGCA
* *
16600463 TTTTATATTTTTTATGAT
1 TTTTATAATTTTAAT-AT
16600481 TTTTATAATTTTTAATAAT
1 TTTTATAA-TTTTAAT-AT
* *
16600500 TTTTAAAATTTTTATAT
1 TTTTATAATTTTAATAT
*
16600517 TTTTATTTATATTTAATATT
1 TTTTA-TAAT-TTTAATA-T
16600537 TTTTATAACTTTTA
1 TTTTATAA-TTTTA
16600551 TCACATGTCA
Statistics
Matches: 56, Mismatches: 9, Indels: 9
0.76 0.12 0.12
Matches are distributed among these distances:
17 7 0.12
18 15 0.27
19 27 0.48
20 7 0.12
ACGTcount: A:0.31, C:0.01, G:0.01, T:0.67
Consensus pattern (17 bp):
TTTTATAATTTTAATAT
Found at i:16600828 original size:91 final size:90
Alignment explanation
Indices: 16600628--16600894 Score: 292
Period size: 91 Copynumber: 2.9 Consensus size: 90
16600618 TTAACGATCA
* * * *
16600628 AAGGGCCTTTTTGATACATTT-AATATTTCAAGTATCCAATTGAGTGCAAAAAAATAATAATTAA
1 AAGGG-CTTTTTGATGCATTTGAA-AGTTCAAGTACCCAATTGAGTG--AAAAAA-AA-AA-TAG
* * *
16600692 GGGCTTAATTGC-TTTTTCTGAAAAAAGTTTG
59 GGGCTTAATTGCATTTTTTTAAAAAAAATTTG
*
16600723 AAGGGCTTTTTGATGCATTTCGAAAGTTCAAGTACCCAATTGAGTGAAAAAAAAAGTAGGGGCTT
1 AAGGGCTTTTTGATGCATTT-GAAAGTTCAAGTACCCAATTGAGTGAAAAAAAAAATAGGGGCTT
16600788 AATTGCATTTTTTTAAAAAAAATTTG
65 AATTGCATTTTTTTAAAAAAAATTTG
* * * *
16600814 -AGGGTCTTTTTGATGTATTTTGAAAGTTCAAGTACCCAATTGAATGTAAAAGAAAATAGGGGCT
1 AAGGG-CTTTTTGATGCA-TTTGAAAGTTCAAGTACCCAATTGAGTGAAAAAAAAAATAGGGGCT
16600878 TAATT--ATTATTTTTAAA
64 TAATTGCATT-TTTTTAAA
16600895 TGTTTGAAGA
Statistics
Matches: 153, Mismatches: 13, Indels: 17
0.84 0.07 0.09
Matches are distributed among these distances:
89 3 0.02
90 26 0.17
91 72 0.47
92 5 0.03
93 6 0.04
94 14 0.09
95 25 0.16
96 2 0.01
ACGTcount: A:0.37, C:0.09, G:0.18, T:0.36
Consensus pattern (90 bp):
AAGGGCTTTTTGATGCATTTGAAAGTTCAAGTACCCAATTGAGTGAAAAAAAAAATAGGGGCTTA
ATTGCATTTTTTTAAAAAAAATTTG
Found at i:16603609 original size:76 final size:75
Alignment explanation
Indices: 16603524--16603687 Score: 190
Period size: 76 Copynumber: 2.1 Consensus size: 75
16603514 TAAAAGTATA
** *** *
16603524 AGGGAAAAATAAAAAGTTTTGGGGGTTTTTAGGGGAGTAAAATTTT-AGTAGGAAAGTGGAA-GA
1 AGGG-AAAATAAAAAGTTTTAAGGGTTTTTAACAGAGTAAAATTTTGAG--GGAAAGT-AAAGGA
16603587 GAGTAAAAGTTTTGG
62 GAGTAAAA-TTTTGG
16603602 -GGGAAAATAAAAAGTTTTAAGGGTTTTTAACAGAGTAAAATTTTGAGGGAAAGTAAATGGGAGA
1 AGGGAAAATAAAAAGTTTTAAGGGTTTTTAACAGAGTAAAATTTTGAGGGAAAGTAAA--GGAGA
16603666 GTAAAATTTTGG
64 GTAAAATTTTGG
16603678 AGGGAAAATA
1 AGGGAAAATA
16603688 TTCAAAAAAA
Statistics
Matches: 75, Mismatches: 6, Indels: 11
0.82 0.07 0.12
Matches are distributed among these distances:
74 2 0.03
75 7 0.09
76 42 0.56
77 24 0.32
ACGTcount: A:0.41, C:0.01, G:0.30, T:0.27
Consensus pattern (75 bp):
AGGGAAAATAAAAAGTTTTAAGGGTTTTTAACAGAGTAAAATTTTGAGGGAAAGTAAAGGAGAGT
AAAATTTTGG
Found at i:16604342 original size:17 final size:17
Alignment explanation
Indices: 16604303--16604362 Score: 52
Period size: 17 Copynumber: 3.4 Consensus size: 17
16604293 TTTACGTTTA
*
16604303 ATAACTAAAATTAAATT
1 ATAATTAAAATTAAATT
*
16604320 ATAATTAAATTTAAA-T
1 ATAATTAAAATTAAATT
16604336 ATCAATTAATAGATATAAATT
1 AT-AATTAA-A-AT-TAAATT
16604357 A-AATTA
1 ATAATTA
16604363 TGATAATACT
Statistics
Matches: 35, Mismatches: 3, Indels: 8
0.76 0.07 0.17
Matches are distributed among these distances:
16 3 0.09
17 19 0.54
18 1 0.03
19 6 0.17
20 4 0.11
21 2 0.06
ACGTcount: A:0.57, C:0.03, G:0.02, T:0.38
Consensus pattern (17 bp):
ATAATTAAAATTAAATT
Found at i:16613686 original size:27 final size:28
Alignment explanation
Indices: 16613649--16613871 Score: 259
Period size: 27 Copynumber: 8.3 Consensus size: 28
16613639 TGCGATTCTT
* *
16613649 GGGTAAAATGACT-AAAATACCCTCGAT
1 GGGTAAAATGACTCGAAATACCCTCGAA
* * *
16613676 GGGTAAAATGA-TGGAAATA-CCTTGAT
1 GGGTAAAATGACTCGAAATACCCTCGAA
*
16613702 GGGTAAAATGA-TCGAAATACCCTTGAA
1 GGGTAAAATGACTCGAAATACCCTCGAA
**
16613729 GGGTAAAATGA-TCGAAATACCCTTAAA
1 GGGTAAAATGACTCGAAATACCCTCGAA
* *
16613756 GGGTAAAATGAC-CAAAATACCCTCGAT
1 GGGTAAAATGACTCGAAATACCCTCGAA
*
16613783 GGGTAAAAT-AATCGAAATACCCTCGAA
1 GGGTAAAATGACTCGAAATACCCTCGAA
*
16613810 GGGTAAAATGACT-GAAATACCCCCGAA
1 GGGTAAAATGACTCGAAATACCCTCGAA
*
16613837 GGGTAAAATGACT-GAAATACCC-CAAA
1 GGGTAAAATGACTCGAAATACCCTCGAA
16613863 GGGTAAAAT
1 GGGTAAAAT
16613872 AACTTTTATA
Statistics
Matches: 176, Mismatches: 15, Indels: 11
0.87 0.07 0.05
Matches are distributed among these distances:
26 38 0.22
27 136 0.77
28 2 0.01
ACGTcount: A:0.42, C:0.17, G:0.21, T:0.20
Consensus pattern (28 bp):
GGGTAAAATGACTCGAAATACCCTCGAA
Found at i:16613819 original size:81 final size:81
Alignment explanation
Indices: 16613649--16613873 Score: 294
Period size: 81 Copynumber: 2.8 Consensus size: 81
16613639 TGCGATTCTT
* * ** * *
16613649 GGGTAAAATGACTAAAATACCCTCGATGGGTAAAATGATGGAAATA-CCTTGATGGGTAAAATGA
1 GGGTAAAATGACTGAAATACCCTCGAAGGGTAAAATGACCGAAATACCCTCGATGGGTAAAATAA
*
16613713 TCGAAATACCCTTGAA
66 TCGAAATACCCTCGAA
** *
16613729 GGGTAAAATGA-TCGAAATACCCTTAAAGGGTAAAATGACCAAAATACCCTCGATGGGTAAAATA
1 GGGTAAAATGACT-GAAATACCCTCGAAGGGTAAAATGACCGAAATACCCTCGATGGGTAAAATA
16613793 ATCGAAATACCCTCGAA
65 ATCGAAATACCCTCGAA
* * * *
16613810 GGGTAAAATGACTGAAATACCCCCGAAGGGTAAAATGACTGAAATACCC-CAAAGGGTAAAATAA
1 GGGTAAAATGACTGAAATACCCTCGAAGGGTAAAATGACCGAAATACCCTCGATGGGTAAAATAA
16613874 CTTTTATACC
Statistics
Matches: 125, Mismatches: 17, Indels: 6
0.84 0.11 0.04
Matches are distributed among these distances:
79 1 0.01
80 50 0.40
81 73 0.58
82 1 0.01
ACGTcount: A:0.43, C:0.16, G:0.21, T:0.20
Consensus pattern (81 bp):
GGGTAAAATGACTGAAATACCCTCGAAGGGTAAAATGACCGAAATACCCTCGATGGGTAAAATAA
TCGAAATACCCTCGAA
Found at i:16614137 original size:26 final size:26
Alignment explanation
Indices: 16614108--16614208 Score: 121
Period size: 26 Copynumber: 3.9 Consensus size: 26
16614098 TTGCCACATA
16614108 TACTGTTACTGGCAGCTTTGCTGTGT
1 TACTGTTACTGGCAGCTTTGCTGTGT
* * * * ***
16614134 TACTGATACTGGTAGCTCTGGTACAT
1 TACTGTTACTGGCAGCTTTGCTGTGT
*
16614160 TACTGTTACTGGTAGCTTTGCTGTGT
1 TACTGTTACTGGCAGCTTTGCTGTGT
*
16614186 TACTATTACTGGCAGCTTTGCTG
1 TACTGTTACTGGCAGCTTTGCTG
16614209 CGATATTGGT
Statistics
Matches: 60, Mismatches: 15, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
26 60 1.00
ACGTcount: A:0.16, C:0.19, G:0.25, T:0.41
Consensus pattern (26 bp):
TACTGTTACTGGCAGCTTTGCTGTGT
Found at i:16614170 original size:52 final size:53
Alignment explanation
Indices: 16614103--16614202 Score: 159
Period size: 52 Copynumber: 1.9 Consensus size: 53
16614093 TGGCTTTGCC
*
16614103 ACATATACTGTTACTGGCAGCTTTGCTGTGTTACTGA-TACTGGTAGCTCTGGT
1 ACATATACTGTTACTGGCAGCTTTGCTGTGTTACT-ATTACTGGCAGCTCTGGT
*
16614156 ACAT-TACTGTTACTGGTAGCTTTGCTGTGTTACTATTACTGGCAGCT
1 ACATATACTGTTACTGGCAGCTTTGCTGTGTTACTATTACTGGCAGCT
16614203 TTGCTGCGAT
Statistics
Matches: 44, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
51 1 0.02
52 39 0.89
53 4 0.09
ACGTcount: A:0.19, C:0.19, G:0.23, T:0.39
Consensus pattern (53 bp):
ACATATACTGTTACTGGCAGCTTTGCTGTGTTACTATTACTGGCAGCTCTGGT
Found at i:16614359 original size:29 final size:29
Alignment explanation
Indices: 16614318--16614431 Score: 111
Period size: 30 Copynumber: 3.9 Consensus size: 29
16614308 TGCATTTGCA
*
16614318 CTGTTACTGTATTGGGCTAAGGCCCCACT
1 CTGTTACTATATTGGGCTAAGGCCCCACT
* * *
16614347 CTATTACTATATTAGGCTAAGGGCCACACT
1 CTGTTACTATATTGGGCTAA-GGCCCCACT
* * * *
16614377 CTGTTATTGTATTGGGCTATGGCCCACACA
1 CTGTTACTATATTGGGCTAAGGCCC-CACT
* * *
16614407 CTGCTACTATATAGGGCTCAGGCCC
1 CTGTTACTATATTGGGCTAAGGCCC
16614432 AGACTGATTC
Statistics
Matches: 66, Mismatches: 17, Indels: 3
0.77 0.20 0.03
Matches are distributed among these distances:
29 21 0.32
30 45 0.68
ACGTcount: A:0.22, C:0.26, G:0.22, T:0.30
Consensus pattern (29 bp):
CTGTTACTATATTGGGCTAAGGCCCCACT
Found at i:16623792 original size:13 final size:13
Alignment explanation
Indices: 16623774--16623800 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
16623764 CATCGGTAAA
16623774 ATATAGATTTGGT
1 ATATAGATTTGGT
16623787 ATATAGATTTGGT
1 ATATAGATTTGGT
16623800 A
1 A
16623801 ATAAACTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (13 bp):
ATATAGATTTGGT
Found at i:16624081 original size:14 final size:15
Alignment explanation
Indices: 16624058--16624086 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
16624048 TATTTAGATG
16624058 TTTTGATTATTAAAT
1 TTTTGATTATTAAAT
16624073 TTTTG-TTATTAAAT
1 TTTTGATTATTAAAT
16624087 ATTCTTGAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.31, C:0.00, G:0.07, T:0.62
Consensus pattern (15 bp):
TTTTGATTATTAAAT
Found at i:16627068 original size:23 final size:22
Alignment explanation
Indices: 16627042--16627143 Score: 69
Period size: 19 Copynumber: 5.0 Consensus size: 22
16627032 CAATTAAATC
16627042 TCTAAGATTACAAAATCATATCT
1 TCTAAGATTAC-AAATCATATCT
* *
16627065 TCTAAGATTGCATATCATA---
1 TCTAAGATTACAAATCATATCT
* *
16627084 TCTAAGATTGCATATCATA---
1 TCTAAGATTACAAATCATATCT
* *
16627103 TCTAAGATTGCATATCATA---
1 TCTAAGATTACAAATCATATCT
*
16627122 TCTAAGATTACATATCATATCT
1 TCTAAGATTACAAATCATATCT
16627144 AAGATTGCAT
Statistics
Matches: 73, Mismatches: 3, Indels: 7
0.88 0.04 0.08
Matches are distributed among these distances:
19 56 0.77
22 7 0.10
23 10 0.14
ACGTcount: A:0.38, C:0.17, G:0.08, T:0.37
Consensus pattern (22 bp):
TCTAAGATTACAAATCATATCT
Found at i:16627089 original size:19 final size:19
Alignment explanation
Indices: 16627065--16627158 Score: 179
Period size: 19 Copynumber: 4.9 Consensus size: 19
16627055 AATCATATCT
16627065 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
16627084 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
16627103 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
*
16627122 TCTAAGATTACATATCATA
1 TCTAAGATTGCATATCATA
16627141 TCTAAGATTGCATATCAT
1 TCTAAGATTGCATATCAT
16627159 TGAAGATTAT
Statistics
Matches: 73, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 73 1.00
ACGTcount: A:0.37, C:0.16, G:0.10, T:0.37
Consensus pattern (19 bp):
TCTAAGATTGCATATCATA
Found at i:16627111 original size:38 final size:38
Alignment explanation
Indices: 16627042--16627158 Score: 180
Period size: 38 Copynumber: 3.0 Consensus size: 38
16627032 CAATTAAATC
*
16627042 TCTAAGATTACAAAATCATATCTTCTAAGATTGCATATCATA
1 TCTAAGATTAC-ATATCATA---TCTAAGATTGCATATCATA
*
16627084 TCTAAGATTGCATATCATATCTAAGATTGCATATCATA
1 TCTAAGATTACATATCATATCTAAGATTGCATATCATA
16627122 TCTAAGATTACATATCATATCTAAGATTGCATATCAT
1 TCTAAGATTACATATCATATCTAAGATTGCATATCAT
16627159 TGAAGATTAT
Statistics
Matches: 72, Mismatches: 3, Indels: 4
0.91 0.04 0.05
Matches are distributed among these distances:
38 55 0.76
41 7 0.10
42 10 0.14
ACGTcount: A:0.38, C:0.16, G:0.09, T:0.37
Consensus pattern (38 bp):
TCTAAGATTACATATCATATCTAAGATTGCATATCATA
Found at i:16634883 original size:55 final size:56
Alignment explanation
Indices: 16634799--16634909 Score: 161
Period size: 55 Copynumber: 2.0 Consensus size: 56
16634789 AAAGGGGTCT
* * *
16634799 TTTTTTTTTAGCTACGGTTTATAATTTGGGCAAACCAAAAT-ATTAAAATTTGAAA
1 TTTTTTTTTAACTACCGTTTATAATTTGGGCAAACCAAAATAATCAAAATTTGAAA
* * *
16634854 TTTTTTTTTAATTACCGTTTATAATTTGGGTAAACTAAAATAATCAAAATTTGAAA
1 TTTTTTTTTAACTACCGTTTATAATTTGGGCAAACCAAAATAATCAAAATTTGAAA
16634910 AGGAATTCTT
Statistics
Matches: 49, Mismatches: 6, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
55 36 0.73
56 13 0.27
ACGTcount: A:0.38, C:0.08, G:0.11, T:0.43
Consensus pattern (56 bp):
TTTTTTTTTAACTACCGTTTATAATTTGGGCAAACCAAAATAATCAAAATTTGAAA
Found at i:16634942 original size:62 final size:55
Alignment explanation
Indices: 16634799--16634945 Score: 159
Period size: 55 Copynumber: 2.5 Consensus size: 55
16634789 AAAGGGGTCT
* *
16634799 TTTTTTTTTAGCTACGGTTTATAATTTGGGCAAACCAAAATATTAAAATTTGAAA
1 TTTTTTTTTAACTACGGTTTATAATTTGGGCAAACCAAAATATCAAAATTTGAAA
* * * *
16634854 TTTTTTTTTAATTACCGTTTATAATTTGGGTAAACTAAAATAATCAAAATTTGAAAAGGAA
1 TTTTTTTTTAACTACGGTTTATAATTTGGGCAAACCAAAAT-ATCAAAATTTG---A--AA
* *
16634915 TTCTTTTTTAAACTACGGTTTAAAATTTGGG
1 TT-TTTTTTTAACTACGGTTTATAATTTGGG
16634946 AATAGAAATT
Statistics
Matches: 75, Mismatches: 10, Indels: 7
0.82 0.11 0.08
Matches are distributed among these distances:
55 36 0.48
56 10 0.13
59 1 0.01
61 4 0.05
62 24 0.32
ACGTcount: A:0.36, C:0.08, G:0.13, T:0.43
Consensus pattern (55 bp):
TTTTTTTTTAACTACGGTTTATAATTTGGGCAAACCAAAATATCAAAATTTGAAA
Found at i:16640693 original size:16 final size:16
Alignment explanation
Indices: 16640672--16640709 Score: 67
Period size: 16 Copynumber: 2.4 Consensus size: 16
16640662 TTTTGAATCG
*
16640672 ATTTAGATGGAACACT
1 ATTTAGATGGAACACA
16640688 ATTTAGATGGAACACA
1 ATTTAGATGGAACACA
16640704 ATTTAG
1 ATTTAG
16640710 TGTGAAAGTA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.39, C:0.11, G:0.18, T:0.32
Consensus pattern (16 bp):
ATTTAGATGGAACACA
Found at i:16651016 original size:45 final size:45
Alignment explanation
Indices: 16650952--16651046 Score: 147
Period size: 45 Copynumber: 2.1 Consensus size: 45
16650942 TAACATATAC
* *
16650952 TCGGTGGATTCAGCACATAGCAACCACCTTATTAATCAATGTTGT
1 TCGGTGGATTCAGCACATAGCAACCACCTTACTAATCAATGATGT
*
16650997 TCGGTGGAATT-AGCACATAGCAACCACCTTACTAATGAATGATGT
1 TCGGTGG-ATTCAGCACATAGCAACCACCTTACTAATCAATGATGT
16651042 TCGGT
1 TCGGT
16651047 TCCCATAGTA
Statistics
Matches: 46, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
45 43 0.93
46 3 0.07
ACGTcount: A:0.29, C:0.21, G:0.20, T:0.29
Consensus pattern (45 bp):
TCGGTGGATTCAGCACATAGCAACCACCTTACTAATCAATGATGT
Found at i:16659088 original size:21 final size:20
Alignment explanation
Indices: 16659041--16659093 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 20
16659031 CTAAATGAAC
*
16659041 AAATTCAATTCAATTCAATA
1 AAATTCTATTCAATTCAATA
*
16659061 ATTATTCTATTCAATTCAATCA
1 A-AATTCTATTCAATTCAAT-A
16659083 AAATTCATATT
1 AAATTC-TATT
16659094 TTATCAAAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
20 1 0.04
21 20 0.74
22 6 0.22
ACGTcount: A:0.43, C:0.15, G:0.00, T:0.42
Consensus pattern (20 bp):
AAATTCTATTCAATTCAATA
Found at i:16659800 original size:237 final size:239
Alignment explanation
Indices: 16659365--16660079 Score: 1172
Period size: 238 Copynumber: 3.0 Consensus size: 239
16659355 TGGCAAAACT
** *
16659365 CTAACCTT-TTAACAGGTTTGCAAATTAGTCTTCAGGCTAGCTAGATTAAGCTACAACGATTCTA
1 CTAA-CTTATTAACAGGTTTGCAAATTAGTCCCCGGGCTAGCTAGATTAAGCTACAACGATTCTA
16659429 AAAACATAGAAATCATT-AAAATCAGGACGAAAAATACTCACATGCAAGCAAAATAAGGATGGCC
65 AAAACATAGAAATCATTAAAAAT-AGGACGAAAAATACTCACATGCAAGCAAAATAAGGATGGCC
* *
16659493 GAATGTTCAAGCTTCT-TGGTTTCTTTTCCTTCAACTTTCGGTGGTGTTTAACAAATTAAAAAAG
129 GAATGTTCAAGCTTCTATGGTTTCTTTTCGTTCAATTTTCGGTGGTGTTTAACAAATTAAAAAAG
* *
16659557 ATGATACATTATTTATTTTATTTTAATTCACTTATTAACTAATTTA
194 ATGATACATTATTTCTTTTGTTTTAATTCACTTATTAACTAATTTA
* * * *
16659603 CTAACTTATTAATAGGTTAGCAAATTAGTCCCCGGGCTTGCTAGATTAAGCTACAATGATTCTAA
1 CTAACTTATTAACAGGTTTGCAAATTAGTCCCCGGGCTAGCTAGATTAAGCTACAACGATTCTAA
* * *
16659668 AAATATA-AAATTATTAAAAATAGGAC-AAAAATACTCACATGCAATCAAAATAAGGATGGCCGA
66 AAACATAGAAATCATTAAAAATAGGACGAAAAATACTCACATGCAAGCAAAATAAGGATGGCCGA
*
16659731 ATGTTCAAGCTTCTATGGTTTCTTTTCGTTCAATTTTCGGTGGTGTTTAACAAATTAAAGAAGAT
131 ATGTTCAAGCTTCTATGGTTTCTTTTCGTTCAATTTTCGGTGGTGTTTAACAAATTAAAAAAGAT
*
16659796 GATACATTATTTCTTTTGTTTTAATTCACTTATTAACTAAATTA
196 GATACATTATTTCTTTTGTTTTAATTCACTTATTAACTAATTTA
*
16659840 CTAACTTATTAACATGTTTGCAAATTAGT-CCCGGGCTAGCTAGATTAAGCTACAACGATTCTAA
1 CTAACTTATTAACAGGTTTGCAAATTAGTCCCCGGGCTAGCTAGATTAAGCTACAACGATTCTAA
* * * *
16659904 AAACATAGAAATCATTAATAACAAGACGAAAAATACTCACATGCAAGCAAAATAAGGATGGTCGA
66 AAACATAGAAATCATTAAAAATAGGACGAAAAATACTCACATGCAAGCAAAATAAGGATGGCCGA
*
16659969 ATGTTCAAGCTTCTATGGTTTCTTTTCGTTCAATTTTTGGTGGTGTTTAACAAATTAAAAAAGAT
131 ATGTTCAAGCTTCTATGGTTTCTTTTCGTTCAATTTTCGGTGGTGTTTAACAAATTAAAAAAGAT
16660034 GATACATTATTTCTTTTGTTTTAATTCACTTATTAACTAATTTA
196 GATACATTATTTCTTTTGTTTTAATTCACTTATTAACTAATTTA
16660078 CT
1 CT
16660080 GATTTAACCT
Statistics
Matches: 441, Mismatches: 31, Indels: 10
0.91 0.06 0.02
Matches are distributed among these distances:
236 89 0.20
237 144 0.33
238 208 0.47
ACGTcount: A:0.36, C:0.15, G:0.14, T:0.35
Consensus pattern (239 bp):
CTAACTTATTAACAGGTTTGCAAATTAGTCCCCGGGCTAGCTAGATTAAGCTACAACGATTCTAA
AAACATAGAAATCATTAAAAATAGGACGAAAAATACTCACATGCAAGCAAAATAAGGATGGCCGA
ATGTTCAAGCTTCTATGGTTTCTTTTCGTTCAATTTTCGGTGGTGTTTAACAAATTAAAAAAGAT
GATACATTATTTCTTTTGTTTTAATTCACTTATTAACTAATTTA
Found at i:16660494 original size:23 final size:24
Alignment explanation
Indices: 16660450--16660494 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
16660440 TTTCCTATTT
16660450 GGAGAAACAAGGAAGGTGAGAGAA
1 GGAGAAACAAGGAAGGTGAGAGAA
* *
16660474 GGAGAAATAAGG-TGGTGAGAG
1 GGAGAAACAAGGAAGGTGAGAG
16660495 GTTAAGGGTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 8 0.42
24 11 0.58
ACGTcount: A:0.44, C:0.02, G:0.44, T:0.09
Consensus pattern (24 bp):
GGAGAAACAAGGAAGGTGAGAGAA
Found at i:16668802 original size:56 final size:56
Alignment explanation
Indices: 16668736--16668847 Score: 215
Period size: 56 Copynumber: 2.0 Consensus size: 56
16668726 GACTCTTAAA
*
16668736 TAGACAGAAAATAAAGTGATCTAGTAATGGGAATGAACATGTCTAGGATTGGATTC
1 TAGACAGAAAATAAAGTGATCTAGTAATGGGAATGAAAATGTCTAGGATTGGATTC
16668792 TAGACAGAAAATAAAGTGATCTAGTAATGGGAATGAAAATGTCTAGGATTGGATTC
1 TAGACAGAAAATAAAGTGATCTAGTAATGGGAATGAAAATGTCTAGGATTGGATTC
16668848 CAGAGAAAGA
Statistics
Matches: 55, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
56 55 1.00
ACGTcount: A:0.40, C:0.08, G:0.25, T:0.27
Consensus pattern (56 bp):
TAGACAGAAAATAAAGTGATCTAGTAATGGGAATGAAAATGTCTAGGATTGGATTC
Found at i:16669005 original size:25 final size:24
Alignment explanation
Indices: 16668977--16669025 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 24
16668967 TAAAAAGGGG
*
16668977 TAAGGCATTTCGTATGAAATTTTAA
1 TAAGGCATTTCGCATG-AATTTTAA
16669002 TAAGGCATTTCGCATGAATTTTAA
1 TAAGGCATTTCGCATGAATTTTAA
16669026 AGTATGTTTC
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
24 8 0.35
25 15 0.65
ACGTcount: A:0.35, C:0.10, G:0.16, T:0.39
Consensus pattern (24 bp):
TAAGGCATTTCGCATGAATTTTAA
Found at i:16681234 original size:20 final size:21
Alignment explanation
Indices: 16681206--16681244 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
16681196 AAAAAATTAA
*
16681206 TTAATTAATTTAA-ATGATAT
1 TTAAATAATTTAATATGATAT
16681226 TTAAATAATTTAATATGAT
1 TTAAATAATTTAATATGAT
16681245 CATACATTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.49
Consensus pattern (21 bp):
TTAAATAATTTAATATGATAT
Found at i:16686752 original size:33 final size:33
Alignment explanation
Indices: 16686710--16686864 Score: 106
Period size: 33 Copynumber: 4.6 Consensus size: 33
16686700 AAAATACGGT
16686710 GGAATCAGCACTTAGCAACCACTAATGAATCGG
1 GGAATCAGCACTTAGCAACCACTAATGAATCGG
** *
16686743 GGAATCAGCACACAGCAACCCCT--TG----GG
1 GGAATCAGCACTTAGCAACCACTAATGAATCGG
* * *
16686770 GGAATCAACACTTAGCAACCCCCTTCACATTTCAGATGCGG
1 GGAATCAGCACTTAGCAA-CCAC-T-A-A--TGA-AT-CGG
*
16686811 TGGAATCAGCACTTAGCAACCACCAATGAATCGG
1 -GGAATCAGCACTTAGCAACCACTAATGAATCGG
**
16686845 GGAATCAGCACACAGCAACC
1 GGAATCAGCACTTAGCAACC
16686865 CCTTTATATG
Statistics
Matches: 94, Mismatches: 13, Indels: 30
0.69 0.09 0.22
Matches are distributed among these distances:
27 17 0.18
28 4 0.04
29 1 0.01
31 2 0.02
33 38 0.40
34 3 0.03
35 3 0.03
36 2 0.02
38 1 0.01
39 1 0.01
41 5 0.05
42 17 0.18
ACGTcount: A:0.34, C:0.30, G:0.21, T:0.16
Consensus pattern (33 bp):
GGAATCAGCACTTAGCAACCACTAATGAATCGG
Found at i:16686839 original size:102 final size:102
Alignment explanation
Indices: 16686500--16686868 Score: 558
Period size: 102 Copynumber: 3.6 Consensus size: 102
16686490 TAACCGTTAT
* *
16686500 CGGTGGATTCCGCACTTAGCAACCACCAATGAATCGGGGAATCAGCACACAGCAACCCCTTGGGG
1 CGGTGGAATCAGCACTTAGCAACCACCAATGAATCGGGGAATCAGCACACAGCAACCCCTTGGGG
* *
16686565 GAATTAGCACTTAGGAACCCCCTTCACATTTCAGATG
66 GAATCAGCACTTAGCAACCCCCTTCACATTTCAGATG
* * * * * * ** *
16686602 TGGTGGAATCAGCACTTAGCAACCACCAATTAATAGGGTAATTAGTACTTAGCAACCCCTCGGGG
1 CGGTGGAATCAGCACTTAGCAACCACCAATGAATCGGGGAATCAGCACACAGCAACCCCTTGGGG
* * *
16686667 GAAATCAGCACTTAGCAACCCCCTTTCACATTTAAAATA
66 G-AATCAGCACTTAGCAACCCCC-TTCACATTTCAGATG
*
16686706 CGGTGGAATCAGCACTTAGCAACCACTAATGAATCGGGGAATCAGCACACAGCAACCCCTTGGGG
1 CGGTGGAATCAGCACTTAGCAACCACCAATGAATCGGGGAATCAGCACACAGCAACCCCTTGGGG
*
16686771 GAATCAACACTTAGCAACCCCCTTCACATTTCAGATG
66 GAATCAGCACTTAGCAACCCCCTTCACATTTCAGATG
16686808 CGGTGGAATCAGCACTTAGCAACCACCAATGAATCGGGGAATCAGCACACAGCAACCCCTT
1 CGGTGGAATCAGCACTTAGCAACCACCAATGAATCGGGGAATCAGCACACAGCAACCCCTT
16686869 TATATGCAAT
Statistics
Matches: 234, Mismatches: 31, Indels: 4
0.87 0.12 0.01
Matches are distributed among these distances:
102 127 0.54
103 39 0.17
104 68 0.29
ACGTcount: A:0.31, C:0.28, G:0.20, T:0.20
Consensus pattern (102 bp):
CGGTGGAATCAGCACTTAGCAACCACCAATGAATCGGGGAATCAGCACACAGCAACCCCTTGGGG
GAATCAGCACTTAGCAACCCCCTTCACATTTCAGATG
Found at i:16694485 original size:30 final size:29
Alignment explanation
Indices: 16694449--16694513 Score: 105
Period size: 28 Copynumber: 2.2 Consensus size: 29
16694439 AATAGTAAAG
16694449 TAAGAGTTTTGATATATTTATTGGCGAATA
1 TAAGAG-TTTGATATATTTATTGGCGAATA
*
16694479 TAAGAG-TTGATATATTTATTGGCTAATA
1 TAAGAGTTTGATATATTTATTGGCGAATA
16694507 TAAGAGT
1 TAAGAGT
16694514 CCCTTTCAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
28 27 0.82
30 6 0.18
ACGTcount: A:0.35, C:0.03, G:0.20, T:0.42
Consensus pattern (29 bp):
TAAGAGTTTGATATATTTATTGGCGAATA
Found at i:16695458 original size:8 final size:8
Alignment explanation
Indices: 16695447--16695479 Score: 66
Period size: 8 Copynumber: 4.1 Consensus size: 8
16695437 TGTGTATAAA
16695447 TGTATGTT
1 TGTATGTT
16695455 TGTATGTT
1 TGTATGTT
16695463 TGTATGTT
1 TGTATGTT
16695471 TGTATGTT
1 TGTATGTT
16695479 T
1 T
16695480 ATACGTTAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 25 1.00
ACGTcount: A:0.12, C:0.00, G:0.24, T:0.64
Consensus pattern (8 bp):
TGTATGTT
Found at i:16697420 original size:27 final size:27
Alignment explanation
Indices: 16697382--16697765 Score: 379
Period size: 27 Copynumber: 14.3 Consensus size: 27
16697372 ATTTGTGGGC
* *
16697382 AAATGACTGAAATACCCTCGAAGGATA
1 AAATGACCGAAATACCCTCGAAGGGTA
* *
16697409 AAATGATCGAAATACCC-CTAAAGGGTA
1 AAATGACCGAAATACCCTC-GAAGGGTA
** * *
16697436 AAATGACTAAAACACCCTCGAGGGGTA
1 AAATGACCGAAATACCCTCGAAGGGTA
* * *
16697463 AAATCATCGAAATACCC-CTAAAGGGTA
1 AAATGACCGAAATACCCTC-GAAGGGTA
* *
16697490 AAATGACTGAAATACCCTCGAGGGGTA
1 AAATGACCGAAATACCCTCGAAGGGTA
16697517 AAATGACCGAAATACCCT-GAAGGGTA
1 AAATGACCGAAATACCCTCGAAGGGTA
*
16697543 AAATGACTGAAATACCCTCGAAGGGTA
1 AAATGACCGAAATACCCTCGAAGGGTA
* * *
16697570 AAATGATCGAAATACCCCCGAGGGGTA
1 AAATGACCGAAATACCCTCGAAGGGTA
*
16697597 AAATGACCGAAATACCC-CAGTAGGGTA
1 AAATGACCGAAATACCCTC-GAAGGGTA
*
16697624 AAATGACCGAAATACCCTCAAAGGGTA
1 AAATGACCGAAATACCCTCGAAGGGTA
* * *
16697651 AATTGACCG-AATACCC-CTTAGGGGTA
1 AAATGACCGAAATACCCTC-GAAGGGTA
* * *
16697677 AAATGATCGAAATACCC-CTAAAAGGTA
1 AAATGACCGAAATACCCTC-GAAGGGTA
* * *
16697704 AAATGATCAAAATACCCTCGAGGGGTA
1 AAATGACCGAAATACCCTCGAAGGGTA
* * *
16697731 ACATGACCGAAATACCC-CTGAAAGATA
1 AAATGACCGAAATACCCTC-GAAGGGTA
16697758 AAATGACC
1 AAATGACC
16697766 CCGTAGGGTA
Statistics
Matches: 293, Mismatches: 53, Indels: 22
0.80 0.14 0.06
Matches are distributed among these distances:
25 1 0.00
26 48 0.16
27 240 0.82
28 4 0.01
ACGTcount: A:0.42, C:0.21, G:0.20, T:0.17
Consensus pattern (27 bp):
AAATGACCGAAATACCCTCGAAGGGTA
Found at i:16697465 original size:54 final size:54
Alignment explanation
Indices: 16697382--16697764 Score: 467
Period size: 54 Copynumber: 7.1 Consensus size: 54
16697372 ATTTGTGGGC
* *
16697382 AAATGACTGAAATACCCTCGAAGGATAAAATGATCGAAATACCCCTAAAGGGTA
1 AAATGACTGAAATACCCTCGAGGGGTAAAATGATCGAAATACCCCTAAAGGGTA
* * *
16697436 AAATGACTAAAACACCCTCGAGGGGTAAAATCATCGAAATACCCCTAAAGGGTA
1 AAATGACTGAAATACCCTCGAGGGGTAAAATGATCGAAATACCCCTAAAGGGTA
* *
16697490 AAATGACTGAAATACCCTCGAGGGGTAAAATGACCGAAATA-CCCTGAAGGGTA
1 AAATGACTGAAATACCCTCGAGGGGTAAAATGATCGAAATACCCCTAAAGGGTA
* ** *
16697543 AAATGACTGAAATACCCTCGAAGGGTAAAATGATCGAAATACCCCCGAGGGGTA
1 AAATGACTGAAATACCCTCGAGGGGTAAAATGATCGAAATACCCCTAAAGGGTA
* *
16697597 AAATGACCGAAATACCC-C-AGTAGGGTAAAATGACCGAAATA-CCCTCAAAGGGTA
1 AAATGACTGAAATACCCTCGAG--GGGTAAAATGATCGAAATACCCCT-AAAGGGTA
* * * *
16697651 AATTGACCG-AATACCC-CTTAGGGGTAAAATGATCGAAATACCCCTAAAAGGTA
1 AAATGACTGAAATACCCTC-GAGGGGTAAAATGATCGAAATACCCCTAAAGGGTA
* * * *
16697704 AAATGA-TCAAAATACCCTCGAGGGGTAACATGACCGAAATACCCCTGAAA-GATA
1 AAATGACT-GAAATACCCTCGAGGGGTAAAATGATCGAAATACCCCT-AAAGGGTA
16697758 AAATGAC
1 AAATGAC
16697765 CCCGTAGGGT
Statistics
Matches: 287, Mismatches: 30, Indels: 23
0.84 0.09 0.07
Matches are distributed among these distances:
52 1 0.00
53 92 0.32
54 188 0.66
55 6 0.02
ACGTcount: A:0.42, C:0.21, G:0.20, T:0.17
Consensus pattern (54 bp):
AAATGACTGAAATACCCTCGAGGGGTAAAATGATCGAAATACCCCTAAAGGGTA
Found at i:16697806 original size:27 final size:26
Alignment explanation
Indices: 16697763--16697814 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 26
16697753 AGATAAAATG
*
16697763 ACCCCGTAGGGTAAAATGATTGTTAT
1 ACCCCGTAGGGTAAAATGACTGTTAT
16697789 ACCCC-TAGGAGTCAAAATGACTGTTA
1 ACCCCGTAGG-GT-AAAATGACTGTTA
16697815 CGACCTTATG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
25 4 0.17
26 7 0.30
27 12 0.52
ACGTcount: A:0.33, C:0.19, G:0.21, T:0.27
Consensus pattern (26 bp):
ACCCCGTAGGGTAAAATGACTGTTAT
Found at i:16697983 original size:26 final size:26
Alignment explanation
Indices: 16697945--16698025 Score: 119
Period size: 26 Copynumber: 3.1 Consensus size: 26
16697935 TGGAGGAAGT
*
16697945 ATACTGATTCTGGCAGCTTTGCTGCG
1 ATACTGATACTGGCAGCTTTGCTGCG
*
16697971 ATACTGATACTGGCAGCTCTGCTGCG
1 ATACTGATACTGGCAGCTTTGCTGCG
*
16697997 ATGCT-ACTACTGGCAGCTTTGCTGCG
1 ATACTGA-TACTGGCAGCTTTGCTGCG
16698023 ATA
1 ATA
16698026 TTGGTATGTT
Statistics
Matches: 49, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
25 1 0.02
26 48 0.98
ACGTcount: A:0.19, C:0.25, G:0.26, T:0.31
Consensus pattern (26 bp):
ATACTGATACTGGCAGCTTTGCTGCG
Found at i:16698855 original size:53 final size:53
Alignment explanation
Indices: 16698775--16698922 Score: 235
Period size: 53 Copynumber: 2.8 Consensus size: 53
16698765 TGGCCATGGC
*
16698775 AAGAAGATCATATAGTGTAAGACCTAGTCTAGGACTTAACATCATATGAAGAT
1 AAGAAGACCATATAGTGTAAGACCTAGTCTAGGACTTAACATCATATGAAGAT
* *
16698828 AAGAAGACCATATAGTGTAAAACCTAGTCTAGAAC-TAGACATCATATGAAGAT
1 AAGAAGACCATATAGTGTAAGACCTAGTCTAGGACTTA-ACATCATATGAAGAT
* *
16698881 AAGAAGACCATATAGTGTAAGACCTAGTCGAGGACTAAACAT
1 AAGAAGACCATATAGTGTAAGACCTAGTCTAGGACTTAACAT
16698923 AGGCGATTCG
Statistics
Matches: 86, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
52 2 0.02
53 83 0.97
54 1 0.01
ACGTcount: A:0.43, C:0.15, G:0.19, T:0.23
Consensus pattern (53 bp):
AAGAAGACCATATAGTGTAAGACCTAGTCTAGGACTTAACATCATATGAAGAT
Found at i:16699672 original size:54 final size:53
Alignment explanation
Indices: 16699466--16699663 Score: 270
Period size: 53 Copynumber: 3.7 Consensus size: 53
16699456 ATGGCCATGG
* *
16699466 TAAGAAGATCATATAGTGTAAGACCTAGTCTAGGACTAGACATCATATGAAGA
1 TAAGAAGACCATATAGTGTAAGACCTAATCTAGGACTAGACATCATATGAAGA
* * *
16699519 TAAGAAGACCATATAGTGTAAGACCTAGTCGAGGACTAAACATCATATGAAGA
1 TAAGAAGACCATATAGTGTAAGACCTAATCTAGGACTAGACATCATATGAAGA
* * * **
16699572 TAAGAAGACCATATAATGTAAGACCTAATCTAAGACTATGGCATCATATGGGGA
1 TAAGAAGACCATATAGTGTAAGACCTAATCTAGGACTA-GACATCATATGAAGA
* * *
16699626 TACGAAGACCACATAGTGTAAGACCTAATTTAGGACTA
1 TAAGAAGACCATATAGTGTAAGACCTAATCTAGGACTA
16699664 TGGTATCATG
Statistics
Matches: 128, Mismatches: 16, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
53 84 0.66
54 44 0.34
ACGTcount: A:0.41, C:0.15, G:0.20, T:0.23
Consensus pattern (53 bp):
TAAGAAGACCATATAGTGTAAGACCTAATCTAGGACTAGACATCATATGAAGA
Found at i:16699686 original size:107 final size:106
Alignment explanation
Indices: 16699466--16699663 Score: 279
Period size: 107 Copynumber: 1.9 Consensus size: 106
16699456 ATGGCCATGG
* * * * *
16699466 TAAGAAGATCATATAGTGTAAGACCTAGTCTAGGACTAGACATCATATGAAGATAAGAAGACCAT
1 TAAGAAGACCATATAATGTAAGACCTAATCTAAGACTAGACATCATATGAAGATAAGAAGACCAC
*
16699531 ATAGTGTAAGACCTAGTCGAGGACTAAACATCATATGAAGA
66 ATAGTGTAAGACCTAATCGAGGACTAAACATCATATGAAGA
* ** *
16699572 TAAGAAGACCATATAATGTAAGACCTAATCTAAGACTATGGCATCATATGGGGATACGAAGACCA
1 TAAGAAGACCATATAATGTAAGACCTAATCTAAGACTA-GACATCATATGAAGATAAGAAGACCA
**
16699637 CATAGTGTAAGACCTAATTTAGGACTA
65 CATAGTGTAAGACCTAATCGAGGACTA
16699664 TGGTATCATG
Statistics
Matches: 79, Mismatches: 12, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
106 34 0.43
107 45 0.57
ACGTcount: A:0.41, C:0.15, G:0.20, T:0.23
Consensus pattern (106 bp):
TAAGAAGACCATATAATGTAAGACCTAATCTAAGACTAGACATCATATGAAGATAAGAAGACCAC
ATAGTGTAAGACCTAATCGAGGACTAAACATCATATGAAGA
Found at i:16700123 original size:30 final size:30
Alignment explanation
Indices: 16700061--16700128 Score: 75
Period size: 30 Copynumber: 2.3 Consensus size: 30
16700051 CGTCTTTATT
* * *
16700061 GCTATTTAATGATTTGTGGACACCCTTCTG
1 GCTATCTAGTGATGTGTGGACACCCTTCTG
* *
16700091 GCTTTCTAGTGATGTGTGGACA-CCTCTGTG
1 GCTATCTAGTGATGTGTGGACACCCT-TCTG
16700121 GCTATCTA
1 GCTATCTA
16700129 ATTCAAGTGG
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
29 3 0.10
30 28 0.90
ACGTcount: A:0.18, C:0.21, G:0.24, T:0.38
Consensus pattern (30 bp):
GCTATCTAGTGATGTGTGGACACCCTTCTG
Found at i:16702599 original size:29 final size:28
Alignment explanation
Indices: 16702557--16702611 Score: 74
Period size: 29 Copynumber: 1.9 Consensus size: 28
16702547 AGGAGCCATA
* * *
16702557 CGGGTTGGGCACACGCCCATGTGACCACG
1 CGGGCTGGACACACACCCATGT-ACCACG
16702586 CGGGCTGGACACACACCCATGTACCA
1 CGGGCTGGACACACACCCATGTACCA
16702612 ACCCGTGTCG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
28 4 0.17
29 19 0.83
ACGTcount: A:0.22, C:0.36, G:0.29, T:0.13
Consensus pattern (28 bp):
CGGGCTGGACACACACCCATGTACCACG
Found at i:16708392 original size:42 final size:42
Alignment explanation
Indices: 16708334--16708417 Score: 159
Period size: 42 Copynumber: 2.0 Consensus size: 42
16708324 GATGATTTTT
*
16708334 TCATCATCTTTCCTCCATTTTATATTAATCATTTAATAATAA
1 TCATCATCTTTCCTCCATTTTAAATTAATCATTTAATAATAA
16708376 TCATCATCTTTCCTCCATTTTAAATTAATCATTTAATAATAA
1 TCATCATCTTTCCTCCATTTTAAATTAATCATTTAATAATAA
16708418 AATAATACTA
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.35, C:0.19, G:0.00, T:0.46
Consensus pattern (42 bp):
TCATCATCTTTCCTCCATTTTAAATTAATCATTTAATAATAA
Found at i:16716999 original size:22 final size:22
Alignment explanation
Indices: 16716968--16717010 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
16716958 ATTTTAGTTA
*
16716968 AATAATTATTATTTTAAATAAT
1 AATAACTATTATTTTAAATAAT
*
16716990 AATAACTATTATTTTTAATAA
1 AATAACTATTATTTTAAATAA
16717011 ATTGATTTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (22 bp):
AATAACTATTATTTTAAATAAT
Found at i:16717114 original size:103 final size:102
Alignment explanation
Indices: 16716976--16717187 Score: 372
Period size: 103 Copynumber: 2.1 Consensus size: 102
16716966 TAAATAATTA
16716976 TTATTTTAAATAATAATAACTATTATTTTTAATAAATTGATTTATAGAATTATTTGTAGATCGAT
1 TTATTTTAAATAATAATAACTATTATTTTTAATAAATTGATTTATAGAATTATTTGTAGATCGAT
*
16717041 TTAGTATTTGTATCCTATTATTTTAAAAAT-AAAAAG
66 TTAGTATTTGTATCCTATTATTTGAAAAATAAAAAAG
*
16717077 TTATTTTAAATAATAATAACTTTATTATTTTTAATAAATTGATTTATAGAATTATTTGTAGATTG
1 TTATTTTAAATAATAATAAC--TATTATTTTTAATAAATTGATTTATAGAATTATTTGTAGATCG
16717142 ATTTAGTATTTGTATCCTATTATTTGAAAAATAAAAAAG
64 ATTTAGTATTTGTATCCTATTATTTGAAAAATAAAAAAG
*
16717181 TTTTTTT
1 TTATTTT
16717188 TGTTATAAAA
Statistics
Matches: 105, Mismatches: 3, Indels: 3
0.95 0.03 0.03
Matches are distributed among these distances:
101 20 0.19
103 73 0.70
104 12 0.11
ACGTcount: A:0.39, C:0.03, G:0.08, T:0.50
Consensus pattern (102 bp):
TTATTTTAAATAATAATAACTATTATTTTTAATAAATTGATTTATAGAATTATTTGTAGATCGAT
TTAGTATTTGTATCCTATTATTTGAAAAATAAAAAAG
Found at i:16719871 original size:64 final size:64
Alignment explanation
Indices: 16719801--16719920 Score: 204
Period size: 64 Copynumber: 1.9 Consensus size: 64
16719791 TAACTGATTC
*
16719801 CAACTAAATAGTCACCTGCAAACATTTATTAACAAACACATTTAAACACACTAAACTTAATAAG
1 CAACTAAATAGTCACCTGCAAACATTTATTAACAAACACATTAAAACACACTAAACTTAATAAG
* * *
16719865 CAACTAAATAGTCACCTGCAAGCATTTATTAACAAACATATTAAAACACATTAAAC
1 CAACTAAATAGTCACCTGCAAACATTTATTAACAAACACATTAAAACACACTAAAC
16719921 ATATTAAACA
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
64 52 1.00
ACGTcount: A:0.48, C:0.22, G:0.05, T:0.25
Consensus pattern (64 bp):
CAACTAAATAGTCACCTGCAAACATTTATTAACAAACACATTAAAACACACTAAACTTAATAAG
Found at i:16719922 original size:19 final size:19
Alignment explanation
Indices: 16719898--16719940 Score: 70
Period size: 19 Copynumber: 2.3 Consensus size: 19
16719888 ATTTATTAAC
16719898 AAACATATTAAAACACA-TT
1 AAACATATT-AAACACATTT
16719917 AAACATATTAAACACATTT
1 AAACATATTAAACACATTT
16719936 AAACA
1 AAACA
16719941 CATATTAGAC
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
18 7 0.30
19 16 0.70
ACGTcount: A:0.58, C:0.16, G:0.00, T:0.26
Consensus pattern (19 bp):
AAACATATTAAACACATTT
Found at i:16719926 original size:9 final size:9
Alignment explanation
Indices: 16719898--16719943 Score: 56
Period size: 10 Copynumber: 4.9 Consensus size: 9
16719888 ATTTATTAAC
*
16719898 AAACATATT
1 AAACACATT
16719907 AAAACACATT
1 -AAACACATT
*
16719917 AAACATATT
1 AAACACATT
16719926 AAACACATTT
1 AAACACA-TT
16719936 AAACACAT
1 AAACACAT
16719944 ATTAGACTTA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
9 15 0.47
10 17 0.53
ACGTcount: A:0.57, C:0.17, G:0.00, T:0.26
Consensus pattern (9 bp):
AAACACATT
Found at i:16720073 original size:19 final size:19
Alignment explanation
Indices: 16720046--16720138 Score: 79
Period size: 19 Copynumber: 5.1 Consensus size: 19
16720036 TTATTCCAGC
*
16720046 AACTAAATTAACTAAGATG
1 AACTTAATTAACTAAGATG
*
16720065 AACTTAATTAACTAATATG
1 AACTTAATTAACTAAGATG
* * *
16720084 -A-GTAATTTATTCT-AG--C
1 AACTTAA-TTA-ACTAAGATG
16720100 AACTTAATTAACTAAGATG
1 AACTTAATTAACTAAGATG
*
16720119 AACTCAATTAACTAAGATG
1 AACTTAATTAACTAAGATG
16720138 A
1 A
16720139 GTAATTTATT
Statistics
Matches: 57, Mismatches: 10, Indels: 14
0.70 0.12 0.17
Matches are distributed among these distances:
16 2 0.04
17 9 0.16
18 8 0.14
19 38 0.67
ACGTcount: A:0.46, C:0.12, G:0.10, T:0.32
Consensus pattern (19 bp):
AACTTAATTAACTAAGATG
Found at i:16720101 original size:54 final size:54
Alignment explanation
Indices: 16720036--16720161 Score: 216
Period size: 54 Copynumber: 2.3 Consensus size: 54
16720026 CAATAATAAA
* *
16720036 TTATTCCAGCAACTAAATTAACTAAGATGAACTTAATTAACTAATATGAGTAAT
1 TTATTCCAGCAACTAAATTAACTAAGATGAACTCAATTAACTAAGATGAGTAAT
* *
16720090 TTATTCTAGCAACTTAATTAACTAAGATGAACTCAATTAACTAAGATGAGTAAT
1 TTATTCCAGCAACTAAATTAACTAAGATGAACTCAATTAACTAAGATGAGTAAT
16720144 TTATTCCAGCAACTAAAT
1 TTATTCCAGCAACTAAAT
16720162 ACTTATTCCA
Statistics
Matches: 66, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
54 66 1.00
ACGTcount: A:0.43, C:0.14, G:0.10, T:0.33
Consensus pattern (54 bp):
TTATTCCAGCAACTAAATTAACTAAGATGAACTCAATTAACTAAGATGAGTAAT
Found at i:16720915 original size:16 final size:16
Alignment explanation
Indices: 16720894--16720924 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
16720884 CTGGCCATCA
*
16720894 TCTTTTTTTTTTTTGC
1 TCTTTTTCTTTTTTGC
16720910 TCTTTTTCTTTTTTG
1 TCTTTTTCTTTTTTG
16720925 AATATTCTTG
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:0.00, C:0.13, G:0.06, T:0.81
Consensus pattern (16 bp):
TCTTTTTCTTTTTTGC
Found at i:16733433 original size:8 final size:8
Alignment explanation
Indices: 16733418--16733452 Score: 63
Period size: 8 Copynumber: 4.5 Consensus size: 8
16733408 AAATTTAAAA
16733418 TTTA-ATT
1 TTTATATT
16733425 TTTATATT
1 TTTATATT
16733433 TTTATATT
1 TTTATATT
16733441 TTTATATT
1 TTTATATT
16733449 TTTA
1 TTTA
16733453 CTTTTAGAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 4 0.15
8 23 0.85
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (8 bp):
TTTATATT
Found at i:16733443 original size:16 final size:15
Alignment explanation
Indices: 16733418--16733457 Score: 62
Period size: 16 Copynumber: 2.6 Consensus size: 15
16733408 AAATTTAAAA
16733418 TTTAATTTTTATATT
1 TTTAATTTTTATATT
16733433 TTTATATTTTTATATT
1 TTTA-ATTTTTATATT
*
16733449 TTTACTTTT
1 TTTAATTTT
16733458 AGAAATTTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 8 0.35
16 15 0.65
ACGTcount: A:0.23, C:0.03, G:0.00, T:0.75
Consensus pattern (15 bp):
TTTAATTTTTATATT
Found at i:16733723 original size:39 final size:37
Alignment explanation
Indices: 16733680--16733754 Score: 123
Period size: 37 Copynumber: 2.0 Consensus size: 37
16733670 TGACTAAATT
16733680 TCAAATTTTAAAAAAAAATAGAAAAACTTATAACATGTG
1 TCAAATTTT--AAAAAAATAGAAAAACTTATAACATGTG
*
16733719 TCAAATTTTTAAAAAATAGAAAAACTTATAACATGT
1 TCAAATTTTAAAAAAATAGAAAAACTTATAACATGT
16733755 TTTAGTTAAT
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
37 26 0.74
39 9 0.26
ACGTcount: A:0.55, C:0.08, G:0.07, T:0.31
Consensus pattern (37 bp):
TCAAATTTTAAAAAAATAGAAAAACTTATAACATGTG
Found at i:16742409 original size:18 final size:18
Alignment explanation
Indices: 16742386--16742424 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
16742376 CAACATCAAT
16742386 ATTATCATCAGTTTTT-AC
1 ATTATCATCA-TTTTTCAC
*
16742404 ATTATCTTCATTTTTCAC
1 ATTATCATCATTTTTCAC
16742422 ATT
1 ATT
16742425 TGGTGGTGAG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 5 0.26
18 14 0.74
ACGTcount: A:0.26, C:0.18, G:0.03, T:0.54
Consensus pattern (18 bp):
ATTATCATCATTTTTCAC
Found at i:16743983 original size:21 final size:23
Alignment explanation
Indices: 16743939--16743984 Score: 60
Period size: 21 Copynumber: 2.1 Consensus size: 23
16743929 AAGGATATGC
*
16743939 AATCTTAGAAGATATGATTTTGT
1 AATCTTAGAAGATATGAATTTGT
*
16743962 AATCTTAG-AGAT-TTAATTTGT
1 AATCTTAGAAGATATGAATTTGT
16743983 AA
1 AA
16743985 ATACCCTTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 9 0.43
22 4 0.19
23 8 0.38
ACGTcount: A:0.37, C:0.04, G:0.15, T:0.43
Consensus pattern (23 bp):
AATCTTAGAAGATATGAATTTGT
Found at i:16746650 original size:19 final size:19
Alignment explanation
Indices: 16746626--16746670 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
16746616 TCTTTCTTTT
*
16746626 TGCATT-CATTCCATGCATC
1 TGCATTACATTCCAT-CATA
*
16746645 TGCATTACATTGCATCATA
1 TGCATTACATTCCATCATA
16746664 TGCATTA
1 TGCATTA
16746671 GATTTTCACA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 16 0.70
20 7 0.30
ACGTcount: A:0.27, C:0.24, G:0.11, T:0.38
Consensus pattern (19 bp):
TGCATTACATTCCATCATA
Found at i:16750486 original size:24 final size:24
Alignment explanation
Indices: 16750454--16750534 Score: 119
Period size: 24 Copynumber: 3.4 Consensus size: 24
16750444 GTCCCAAAAG
*
16750454 TACATTGGATTGAACCTTGAAGAT
1 TACAGTGGATTGAACCTTGAAGAT
* *
16750478 TACATTGGATCGAA-CTTAGAAGAT
1 TACAGTGGATTGAACCTT-GAAGAT
16750502 TACAGTGGATTGAACCTTGAAGAT
1 TACAGTGGATTGAACCTTGAAGAT
16750526 TACAGTGGA
1 TACAGTGGA
16750535 GGCATCTGAT
Statistics
Matches: 52, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
23 3 0.06
24 46 0.88
25 3 0.06
ACGTcount: A:0.35, C:0.12, G:0.23, T:0.30
Consensus pattern (24 bp):
TACAGTGGATTGAACCTTGAAGAT
Found at i:16750920 original size:45 final size:45
Alignment explanation
Indices: 16750817--16751468 Score: 469
Period size: 45 Copynumber: 14.6 Consensus size: 45
16750807 GCACAAATCC
* * * * * **
16750817 TATCTCCATGAGGTTGCAGTGGAGCGGATTAAAGTTA-CAAGTCT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGAAAGCAAGTCT
* *
16750861 TATCTCCCTGAAGTTACAGTGGAACAGACTGAAGAAAGCAAGTCT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGAAAGCAAGTCT
* * *
16750906 TAT-TCCCCTAAAGTTGCAGTAGG-GCAGACTGAAG-ATGACAAATCT
1 TATCT-CCCTGAAGTTGCAGT-GGAGCAGACTGAAGAAAG-CAAGTCT
* * * * **
16750951 TATCTCCTTGAAGTTGCAGTGGAGCGGATTAAAGTTA-CAAGTCT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGAAAGCAAGTCT
* * * * *
16750995 TATCTCCCTGAAGTTACAGTGGAGCAGATTGAAGCCAA-TAA-TCC
1 TATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAG-AAAGCAAGTCT
* *
16751039 TATCTCCCTAAAAGTTGCAGTGGAGCGGACTGAAGAAAGCAAGTCT
1 TATCTCCCT-GAAGTTGCAGTGGAGCAGACTGAAGAAAGCAAGTCT
* **
16751085 TATC-CCCTTGAAGTTGCAGTGGGGCAGACTGAAGATGGCGAA-TCT
1 TATCTCCC-TGAAGTTGCAGTGGAGCAGACTGAAGAAAGC-AAGTCT
* * * * * *
16751130 CATCTCCCTGAAGTTGCAGTGAAGCAGA-TCAAAGCCAA-TAA-TCC
1 TATCTCCCTGAAGTTGCAGTGGAGCAGACT-GAAG-AAAGCAAGTCT
* * * * **
16751174 TATCTCCCTGAAGTTGCAGTGAAGCGGATTAAAGTTA-CAAGTCT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGAAAGCAAGTCT
*
16751218 TATCTCCCTGAAGTTGCAGTGGAACAGACTGAAGAAAGCAAGTCT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGAAAGCAAGTCT
* * * * ** *
16751263 TATCCCCCTGAAGTTGTAGTGGGGCAGACTAAAGATGGCAAATCT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGAAAGCAAGTCT
* * * * * *
16751308 TATCTTCCTGAAGTTGCAGTGGAGCAGATTAAAGCTAA-TAA-TCC
1 TATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAG-AAAGCAAGTCT
* * * * * *
16751352 TATCTCCCTGAGGTTGCAGTGGAGCAGATTAAAGCTAA-TAA-TCC
1 TATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAG-AAAGCAAGTCT
* *
16751396 TATCTCCCTGAGGTTGCAGTGGAGCAGACTGAAGATAGCGAA-TCT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGAAAGC-AAGTCT
* * *
16751441 TATTTCCCT-AGCGTTGCAATGGAGCAGA
1 TATCTCCCTGA-AGTTGCAGTGGAGCAGA
16751469 TTAAAGCTAC
Statistics
Matches: 492, Mismatches: 93, Indels: 45
0.78 0.15 0.07
Matches are distributed among these distances:
43 4 0.01
44 226 0.46
45 247 0.50
46 15 0.03
ACGTcount: A:0.30, C:0.20, G:0.24, T:0.26
Consensus pattern (45 bp):
TATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGAAAGCAAGTCT
Done.