Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr03 135709677
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 135709677
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 350 characters in sequence are not A, C, G, or T
File 21 of 438
Found at i:5598703 original size:44 final size:43
Alignment explanation
Indices: 5598567--5598699 Score: 110
Period size: 43 Copynumber: 3.1 Consensus size: 43
5598557 GATCTTGTAT
5598567 CCCTAAACAGTAGTGGAGCAGATCAAAGACGGCAAGCCTTAAC
1 CCCTAAACAGTAGTGGAGCAGATCAAAGACGGCAAGCCTTAAC
** * * * * ** * * *
5598610 CCCTAAGTAGTAAG-GTAACAG-GCTGAAGATTGC-AGATCTTGTAT
1 CCCTAAACAGT-AGTGGAGCAGATC-AAAGACGGCAAG-CCTT-AAC
5598654 CCCTAAACAGTAGTGGAGCAGATCAAAGACGGCAAGCCTTAAC
1 CCCTAAACAGTAGTGGAGCAGATCAAAGACGGCAAGCCTTAAC
5598697 CCC
1 CCC
5598700 CTAAGTAGTA
Statistics
Matches: 61, Mismatches: 22, Indels: 14
0.63 0.23 0.14
Matches are distributed among these distances:
42 3 0.05
43 29 0.48
44 26 0.43
45 3 0.05
ACGTcount: A:0.35, C:0.24, G:0.23, T:0.18
Consensus pattern (43 bp):
CCCTAAACAGTAGTGGAGCAGATCAAAGACGGCAAGCCTTAAC
Found at i:5598710 original size:44 final size:43
Alignment explanation
Indices: 5598575--5598710 Score: 107
Period size: 44 Copynumber: 3.1 Consensus size: 43
5598565 ATCCCTAAAC
5598575 AGTAGTGGAGCAGATCAAAGACGGCAAGCCTTAACCCCTAAGT
1 AGTAGTGGAGCAGATCAAAGACGGCAAGCCTTAACCCCTAAGT
* * * * ** * * * **
5598618 AGTAAG-GTAACAG-GCTGAAGATTGC-AGATCTTGTATCCCTAAAC
1 AGT-AGTGGAGCAGATC-AAAGACGGCAAG-CCTT-AACCCCTAAGT
5598662 AGTAGTGGAGCAGATCAAAGACGGCAAGCCTTAACCCCCTAAGT
1 AGTAGTGGAGCAGATCAAAGACGGCAAGCCTTAA-CCCCTAAGT
5598706 AGTAG
1 AGTAG
5598711 GGTAACAGGC
Statistics
Matches: 63, Mismatches: 22, Indels: 15
0.63 0.22 0.15
Matches are distributed among these distances:
42 3 0.05
43 20 0.32
44 37 0.59
45 3 0.05
ACGTcount: A:0.35, C:0.21, G:0.25, T:0.19
Consensus pattern (43 bp):
AGTAGTGGAGCAGATCAAAGACGGCAAGCCTTAACCCCTAAGT
Found at i:5599120 original size:44 final size:44
Alignment explanation
Indices: 5598984--5599120 Score: 111
Period size: 44 Copynumber: 3.1 Consensus size: 44
5598974 GTAACAGGCT
* *
5598984 GAAGATTGTAGATCTTGTCTCCCTAAACAGTAGTGGAGCAAATC
1 GAAGATTGCAGATCTTGTCTCCCTAAGCAGTAGTGGAGCAAATC
* * ** * * * **
5599028 GAAGA-AGCA-AGCCTTAACCCCCTAAGTAGTAGTGTA--ATAGGC
1 GAAGATTGCAGA-TCTTGTCTCCCTAAGCAGTAGTGGAGCA-AATC
*
5599070 TAAAGATTGCAGATCTTGTCTCCCTAAGCAGTAGTGGAGCAAATC
1 -GAAGATTGCAGATCTTGTCTCCCTAAGCAGTAGTGGAGCAAATC
5599115 GAAGAT
1 GAAGAT
5599121 AAGCAGTAGG
Statistics
Matches: 64, Mismatches: 22, Indels: 14
0.64 0.22 0.14
Matches are distributed among these distances:
41 1 0.02
42 3 0.05
43 24 0.38
44 32 0.50
45 3 0.05
46 1 0.02
ACGTcount: A:0.34, C:0.19, G:0.23, T:0.24
Consensus pattern (44 bp):
GAAGATTGCAGATCTTGTCTCCCTAAGCAGTAGTGGAGCAAATC
Found at i:5601348 original size:20 final size:21
Alignment explanation
Indices: 5601312--5601351 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
5601302 AGATTAAACT
5601312 GGTCAAAACATAAAAATTCTG
1 GGTCAAAACATAAAAATTCTG
*
5601333 GGTCAAAAC-TATAAATTCT
1 GGTCAAAACATAAAAATTCT
5601352 TAGTTCTAGG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 9 0.50
21 9 0.50
ACGTcount: A:0.45, C:0.15, G:0.12, T:0.28
Consensus pattern (21 bp):
GGTCAAAACATAAAAATTCTG
Found at i:5604999 original size:26 final size:26
Alignment explanation
Indices: 5604963--5605046 Score: 150
Period size: 26 Copynumber: 3.2 Consensus size: 26
5604953 CATGAAATTC
*
5604963 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCTA
5604989 TTATCATGAAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCTA
*
5605015 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCTA
5605041 TTATCA
1 TTATCA
5605047 ATTTGTATCA
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 56 1.00
ACGTcount: A:0.37, C:0.24, G:0.05, T:0.35
Consensus pattern (26 bp):
TTATCATGAAACATTTACCTAACCTA
Found at i:5613487 original size:29 final size:29
Alignment explanation
Indices: 5613438--5613493 Score: 85
Period size: 29 Copynumber: 1.9 Consensus size: 29
5613428 TGAGGGTTTG
5613438 GATCAAATTAGTCCCTCTATTATTAAATT
1 GATCAAATTAGTCCCTCTATTATTAAATT
* * *
5613467 GATCAATTTAGTCTCTTTATTATTAAA
1 GATCAAATTAGTCCCTCTATTATTAAA
5613494 AGGAATAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.34, C:0.14, G:0.07, T:0.45
Consensus pattern (29 bp):
GATCAAATTAGTCCCTCTATTATTAAATT
Found at i:5615149 original size:12 final size:12
Alignment explanation
Indices: 5615121--5615182 Score: 58
Period size: 12 Copynumber: 5.4 Consensus size: 12
5615111 ACTAGTGTAG
* *
5615121 TTGGAGGTGGTA
1 TTGGAGCTGGAA
5615133 TTGGAGCTGGAA
1 TTGGAGCTGGAA
* *
5615145 CTGGATCT--AA
1 TTGGAGCTGGAA
*
5615155 -TGGAGCTGGAG
1 TTGGAGCTGGAA
5615166 TTGGAGCTGGAA
1 TTGGAGCTGGAA
5615178 TTGGA
1 TTGGA
5615183 ATTGGTGGTG
Statistics
Matches: 40, Mismatches: 7, Indels: 6
0.75 0.13 0.11
Matches are distributed among these distances:
9 6 0.15
10 2 0.05
11 1 0.03
12 31 0.77
ACGTcount: A:0.23, C:0.08, G:0.42, T:0.27
Consensus pattern (12 bp):
TTGGAGCTGGAA
Found at i:5615237 original size:12 final size:12
Alignment explanation
Indices: 5615217--5615298 Score: 110
Period size: 12 Copynumber: 6.8 Consensus size: 12
5615207 GAAAACGGAG
* *
5615217 ATGGTGCTGTTT
1 ATGGAGCTGGTT
5615229 ATGGAGCTGGTT
1 ATGGAGCTGGTT
*
5615241 ATGGAGTTGGTT
1 ATGGAGCTGGTT
*
5615253 ATGGAGCTGGTA
1 ATGGAGCTGGTT
*
5615265 ATGGAGTTGGTT
1 ATGGAGCTGGTT
*
5615277 ATGGAGCTAGTT
1 ATGGAGCTGGTT
5615289 ATGGAGCTGG
1 ATGGAGCTGG
5615299 AGAAGCTGCT
Statistics
Matches: 60, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 60 1.00
ACGTcount: A:0.18, C:0.06, G:0.40, T:0.35
Consensus pattern (12 bp):
ATGGAGCTGGTT
Found at i:5615334 original size:15 final size:15
Alignment explanation
Indices: 5615314--5615355 Score: 66
Period size: 15 Copynumber: 2.8 Consensus size: 15
5615304 CTGCTGGTGG
*
5615314 TGGAACTCGTGGAAC
1 TGGAACTAGTGGAAC
5615329 TGGAACTAGTGGAAC
1 TGGAACTAGTGGAAC
*
5615344 TGGAACTGGTGG
1 TGGAACTAGTGG
5615356 TGGTGGAGCT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.26, C:0.14, G:0.38, T:0.21
Consensus pattern (15 bp):
TGGAACTAGTGGAAC
Found at i:5615347 original size:21 final size:21
Alignment explanation
Indices: 5615323--5615547 Score: 84
Period size: 21 Copynumber: 10.9 Consensus size: 21
5615313 GTGGAACTCG
*
5615323 TGGAACTGGAACTAGTGGAAC
1 TGGAACTGGAACTAGTGGAGC
*** *
5615344 TGGAACTGGTGGTGGTGGAGC
1 TGGAACTGGAACTAGTGGAGC
* * * *
5615365 TGGAGCTGGAGCTAGTGGTGG
1 TGGAACTGGAACTAGTGGAGC
* * * *
5615386 TGGAACTGGAACTGGAGGTGG
1 TGGAACTGGAACTAGTGGAGC
* ** * * *
5615407 TGGAGCTGGAGTTGGTGGTGG
1 TGGAACTGGAACTAGTGGAGC
* *
5615428 TGGAGCTGGAACTGGT-G-G-
1 TGGAACTGGAACTAGTGGAGC
* *
5615446 TCGAACTGGAACT-G-GTAG-
1 TGGAACTGGAACTAGTGGAGC
* * *
5615464 TGGAACTGGAACTGGTGGTGT
1 TGGAACTGGAACTAGTGGAGC
* * * *
5615485 TGGAATTGGAACTGGTGGTGG
1 TGGAACTGGAACTAGTGGAGC
* *
5615506 TGGAGCTGGAACTAGAATTGGAAC
1 TGGAACTGGAACTAG---TGGAGC
*
5615530 TGGAATTGGAACTAGTGG
1 TGGAACTGGAACTAGTGG
5615548 TGGTTTAGGA
Statistics
Matches: 159, Mismatches: 37, Indels: 16
0.75 0.17 0.08
Matches are distributed among these distances:
17 1 0.01
18 24 0.15
19 2 0.01
20 3 0.02
21 113 0.71
24 16 0.10
ACGTcount: A:0.22, C:0.10, G:0.44, T:0.24
Consensus pattern (21 bp):
TGGAACTGGAACTAGTGGAGC
Found at i:5615374 original size:42 final size:42
Alignment explanation
Indices: 5615323--5615518 Score: 134
Period size: 42 Copynumber: 4.7 Consensus size: 42
5615313 GTGGAACTCG
*
5615323 TGGAACTGGAACTAGTGGAACTGGAACTGGTGGTGGTGGAGC
1 TGGAACTGGAGCTAGTGGAACTGGAACTGGTGGTGGTGGAGC
* *
5615365 TGGAGCTGGAGCTAGTGGTGGTGGAACTGGAACTGGAGGTGGTGGAGC
1 TGGAACTGGAGCTA------GTGGAACTGGAACTGGTGGTGGTGGAGC
** * * * * * *
5615413 TGGAGTTGGTGGTGGTGGAGCTGGAAC---TGGTGGTCGAAC
1 TGGAACTGGAGCTAGTGGAACTGGAACTGGTGGTGGTGGAGC
* **
5615452 TGGAACT-G-G-TAGTGGAACTGGAACTGGTGGTGTTGGAAT
1 TGGAACTGGAGCTAGTGGAACTGGAACTGGTGGTGGTGGAGC
* * * *
5615491 TGGAACTGGTGGTGGTGGAGCTGGAACT
1 TGGAACTGGAGCTAGTGGAACTGGAACT
5615519 AGAATTGGAA
Statistics
Matches: 122, Mismatches: 20, Indels: 24
0.73 0.12 0.14
Matches are distributed among these distances:
36 13 0.11
37 1 0.01
38 1 0.01
39 30 0.25
40 1 0.01
41 1 0.01
42 38 0.31
48 37 0.30
ACGTcount: A:0.20, C:0.10, G:0.46, T:0.24
Consensus pattern (42 bp):
TGGAACTGGAGCTAGTGGAACTGGAACTGGTGGTGGTGGAGC
Found at i:5615409 original size:27 final size:27
Alignment explanation
Indices: 5615338--5615409 Score: 99
Period size: 27 Copynumber: 2.7 Consensus size: 27
5615328 CTGGAACTAG
* *
5615338 TGGAACTGGAACTGGTGGTGGTGGAGC
1 TGGAACTGGAGCTGGTGGTGGTGGAAC
* *
5615365 TGGAGCTGGAGCTAGTGGTGGTGGAAC
1 TGGAACTGGAGCTGGTGGTGGTGGAAC
*
5615392 TGGAACTGGAGGTGGTGG
1 TGGAACTGGAGCTGGTGG
5615410 AGCTGGAGTT
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 38 1.00
ACGTcount: A:0.18, C:0.10, G:0.50, T:0.22
Consensus pattern (27 bp):
TGGAACTGGAGCTGGTGGTGGTGGAAC
Found at i:5615438 original size:48 final size:48
Alignment explanation
Indices: 5615338--5615442 Score: 147
Period size: 48 Copynumber: 2.2 Consensus size: 48
5615328 CTGGAACTAG
* * *
5615338 TGGAACTGGAACTGGTGGTGGTGGAGCTGGAGCTGGAGCTAGTGGTGG
1 TGGAACTGGAACTGGAGGTGGTGGAGCTGGAGCTGGAGCTAGTGGAGC
* * * *
5615386 TGGAACTGGAACTGGAGGTGGTGGAGCTGGAGTTGGTGGTGGTGGAGC
1 TGGAACTGGAACTGGAGGTGGTGGAGCTGGAGCTGGAGCTAGTGGAGC
5615434 TGGAACTGG
1 TGGAACTGG
5615443 TGGTCGAACT
Statistics
Matches: 50, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
48 50 1.00
ACGTcount: A:0.17, C:0.10, G:0.50, T:0.23
Consensus pattern (48 bp):
TGGAACTGGAACTGGAGGTGGTGGAGCTGGAGCTGGAGCTAGTGGAGC
Found at i:5615443 original size:18 final size:18
Alignment explanation
Indices: 5615380--5615505 Score: 108
Period size: 21 Copynumber: 6.5 Consensus size: 18
5615370 CTGGAGCTAG
5615380 TGGTGGTGGAACTGGAAC
1 TGGTGGTGGAACTGGAAC
* **
5615398 TGGAGGTGGTGGAGCTGGAGTTGG
1 T---GGTGGTGGAACTGGA---AC
*
5615422 TGGTGGTGGAGCTGGAAC
1 TGGTGGTGGAACTGGAAC
*
5615440 TGGTGGTCGAACTGGAAC
1 TGGTGGTGGAACTGGAAC
*
5615458 TGGTAGTGGAACTGGAAC
1 TGGTGGTGGAACTGGAAC
*
5615476 TGGTGGTGTTGGAATTGGAAC
1 TGGT-G-G-TGGAACTGGAAC
5615497 TGGTGGTGG
1 TGGTGGTGG
5615506 TGGAGCTGGA
Statistics
Matches: 88, Mismatches: 11, Indels: 18
0.75 0.09 0.15
Matches are distributed among these distances:
18 40 0.45
19 1 0.01
20 2 0.02
21 44 0.50
24 1 0.01
ACGTcount: A:0.18, C:0.09, G:0.48, T:0.25
Consensus pattern (18 bp):
TGGTGGTGGAACTGGAAC
Found at i:5615529 original size:12 final size:12
Alignment explanation
Indices: 5615512--5615544 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
5615502 GTGGTGGAGC
5615512 TGGAACTAGAAT
1 TGGAACTAGAAT
*
5615524 TGGAACTGGAAT
1 TGGAACTAGAAT
5615536 TGGAACTAG
1 TGGAACTAG
5615545 TGGTGGTTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.36, C:0.09, G:0.30, T:0.24
Consensus pattern (12 bp):
TGGAACTAGAAT
Found at i:5615530 original size:78 final size:78
Alignment explanation
Indices: 5615380--5615534 Score: 202
Period size: 78 Copynumber: 2.0 Consensus size: 78
5615370 CTGGAGCTAG
* * ** * **
5615380 TGGTGGTGGAACTGGAACTGGAGGTGGTGGAGCTGGAGTTGGTGGTGGTGGAGCTGGAACTGGTG
1 TGGTAGTGGAACTGGAACTGGAGGTGGTGGAACTGGAACTGGTGGTGGTGGAGCTGGAACTAGAA
5615445 GTCGAACTGGAAC
66 GTCGAACTGGAAC
* * *
5615458 TGGTAGTGGAACTGGAACTGGTGGTGTTGGAATTGGAACTGGTGGTGGTGGAGCTGGAACTAGAA
1 TGGTAGTGGAACTGGAACTGGAGGTGGTGGAACTGGAACTGGTGGTGGTGGAGCTGGAACTAGAA
* *
5615523 TTGGAACTGGAA
66 GTCGAACTGGAA
5615535 TTGGAACTAG
Statistics
Matches: 65, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
78 65 1.00
ACGTcount: A:0.21, C:0.09, G:0.45, T:0.25
Consensus pattern (78 bp):
TGGTAGTGGAACTGGAACTGGAGGTGGTGGAACTGGAACTGGTGGTGGTGGAGCTGGAACTAGAA
GTCGAACTGGAAC
Found at i:5615668 original size:9 final size:9
Alignment explanation
Indices: 5615656--5615726 Score: 52
Period size: 9 Copynumber: 7.6 Consensus size: 9
5615646 GATCTGGAAG
*
5615656 TGGTGGAGT
1 TGGTGGAGC
*
5615665 TGGTGGAGT
1 TGGTGGAGC
*
5615674 TGGAGGAGC
1 TGGTGGAGC
* *
5615683 TGGTGGTGG
1 TGGTGGAGC
5615692 TGGAACTGGAGC
1 TGG---TGGAGC
*
5615704 TGGTGGAGT
1 TGGTGGAGC
*
5615713 TGGAGGAGC
1 TGGTGGAGC
5615722 TGGTG
1 TGGTG
5615727 ATGGTGGAAC
Statistics
Matches: 48, Mismatches: 11, Indels: 6
0.74 0.17 0.09
Matches are distributed among these distances:
9 41 0.85
12 7 0.15
ACGTcount: A:0.14, C:0.06, G:0.55, T:0.25
Consensus pattern (9 bp):
TGGTGGAGC
Found at i:5615681 original size:18 final size:18
Alignment explanation
Indices: 5615660--5615726 Score: 80
Period size: 18 Copynumber: 3.6 Consensus size: 18
5615650 TGGAAGTGGT
*
5615660 GGAGTTGGTGGAGTTGGA
1 GGAGCTGGTGGAGTTGGA
* *
5615678 GGAGCTGGTGGTGGTGGAA
1 GGAGCTGGTGGAGTTGG-A
5615697 CTGGAGCTGGTGGAGTTGGA
1 --GGAGCTGGTGGAGTTGGA
5615717 GGAGCTGGTG
1 GGAGCTGGTG
5615727 ATGGTGGAAC
Statistics
Matches: 41, Mismatches: 5, Indels: 6
0.79 0.10 0.12
Matches are distributed among these distances:
18 24 0.59
19 1 0.02
20 1 0.02
21 15 0.37
ACGTcount: A:0.15, C:0.06, G:0.55, T:0.24
Consensus pattern (18 bp):
GGAGCTGGTGGAGTTGGA
Found at i:5615682 original size:39 final size:37
Alignment explanation
Indices: 5615650--5615756 Score: 110
Period size: 39 Copynumber: 2.8 Consensus size: 37
5615640 GAGCTGGATC
*
5615650 TGGAAGTGG-TGGAGTTGGTGGAGTTGGAGGAGCTGG
1 TGGAAGTGGATGGAGCTGGTGGAGTTGGAGGAGCTGG
**
5615686 TGGTGGTGGAACTGGAGCTGGTGGAGTTGGAGGAGCTGG
1 TGGAAGTGG-A-TGGAGCTGGTGGAGTTGGAGGAGCTGG
* *
5615725 T-GATGGTGGAACTGGAACTGGTGGAGTTGGAG
1 TGGA-AGTGG-A-TGGAGCTGGTGGAGTTGGAG
5615757 CTAAAGGTGA
Statistics
Matches: 62, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
36 7 0.11
38 1 0.02
39 54 0.87
ACGTcount: A:0.18, C:0.06, G:0.52, T:0.24
Consensus pattern (37 bp):
TGGAAGTGGATGGAGCTGGTGGAGTTGGAGGAGCTGG
Found at i:5615734 original size:18 final size:18
Alignment explanation
Indices: 5615674--5615734 Score: 61
Period size: 18 Copynumber: 3.2 Consensus size: 18
5615664 TTGGTGGAGT
*
5615674 TGGAGGAGCTGGTGGTGG
1 TGGAGGAGCTGGTGATGG
*
5615692 TGGAACTGGAGCTGGTGGA-GT
1 TGG-A--GGAGCTGGT-GATGG
5615713 TGGAGGAGCTGGTGATGG
1 TGGAGGAGCTGGTGATGG
5615731 TGGA
1 TGGA
5615735 ACTGGAACTG
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
17 2 0.06
18 17 0.49
19 1 0.03
20 1 0.03
21 13 0.37
22 1 0.03
ACGTcount: A:0.16, C:0.07, G:0.54, T:0.23
Consensus pattern (18 bp):
TGGAGGAGCTGGTGATGG
Found at i:5615766 original size:39 final size:39
Alignment explanation
Indices: 5615665--5615756 Score: 130
Period size: 39 Copynumber: 2.4 Consensus size: 39
5615655 GTGGTGGAGT
** * *
5615665 TGGTGGAGTTGGAGGAGCTGGTGGTGGTGGAACTGGAGC
1 TGGTGGAGTTGGAGGAGAAGGTGATGGTGGAACTGGAAC
**
5615704 TGGTGGAGTTGGAGGAGCTGGTGATGGTGGAACTGGAAC
1 TGGTGGAGTTGGAGGAGAAGGTGATGGTGGAACTGGAAC
5615743 TGGTGGAGTTGGAG
1 TGGTGGAGTTGGAG
5615757 CTAAAGGTGA
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
39 51 1.00
ACGTcount: A:0.17, C:0.07, G:0.52, T:0.24
Consensus pattern (39 bp):
TGGTGGAGTTGGAGGAGAAGGTGATGGTGGAACTGGAAC
Found at i:5616354 original size:34 final size:35
Alignment explanation
Indices: 5616316--5616390 Score: 107
Period size: 36 Copynumber: 2.1 Consensus size: 35
5616306 AATTTTCTTC
* *
5616316 TAAAATTTTTCCA-TTTTTTTTCTCAATTCCCTTT
1 TAAAATTTATCCAGTTTTTTTTCTCAACTCCCTTT
*
5616350 TAAAATTTATCTAGTTTTTTTTTCTCAACTCCCTTT
1 TAAAATTTATCCAG-TTTTTTTTCTCAACTCCCTTT
5616386 TAAAA
1 TAAAA
5616391 ACCCCTTGGT
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
34 11 0.31
36 25 0.69
ACGTcount: A:0.25, C:0.19, G:0.01, T:0.55
Consensus pattern (35 bp):
TAAAATTTATCCAGTTTTTTTTCTCAACTCCCTTT
Found at i:5617064 original size:26 final size:26
Alignment explanation
Indices: 5617027--5617162 Score: 236
Period size: 26 Copynumber: 5.2 Consensus size: 26
5617017 TGATACAAAT
* *
5617027 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTTCA
5617053 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTTCA
* *
5617079 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTTCA
5617105 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTTCA
5617131 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTTCA
5617157 TGATAA
1 TGATAA
5617163 GAATATCATG
Statistics
Matches: 104, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
26 104 1.00
ACGTcount: A:0.33, C:0.05, G:0.25, T:0.37
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTTCA
Found at i:5619233 original size:136 final size:137
Alignment explanation
Indices: 5618948--5619222 Score: 489
Period size: 136 Copynumber: 2.0 Consensus size: 137
5618938 GAGTAGTCTC
5618948 CCCAAATGGGCTTGCATATGTTTACTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATAC
1 CCCAAATGGGCTTGCATATGTTTACTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATAC
* * * *
5619013 TGTTATCTGAATAAGGGGCTAAGGCCTAGTTTATTGTAATCTGAAAAGGGCTTTGGCCTAGTATC
66 TGTTATCTGAATAAGGGGCTAAGGCCCAGTTTATTGTAATCTGAAAAGGGCTGTGGCCCAGTACC
*
5619078 ACTGTTA
131 ACTATTA
*
5619085 CCCAAATGGGCTTGCATATG-TTATTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATAC
1 CCCAAATGGGCTTGCATATGTTTACTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATAC
5619149 TGTTATCTGAATAAGGGGCTAAGGCCCAGTTTATTGTAATCTGAAAAGGGCTGTGGCCCAGTACC
66 TGTTATCTGAATAAGGGGCTAAGGCCCAGTTTATTGTAATCTGAAAAGGGCTGTGGCCCAGTACC
5619214 ACTATTA
131 ACTATTA
5619221 CC
1 CC
5619223 TGGATGGGCT
Statistics
Matches: 132, Mismatches: 6, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
136 112 0.85
137 20 0.15
ACGTcount: A:0.25, C:0.17, G:0.25, T:0.33
Consensus pattern (137 bp):
CCCAAATGGGCTTGCATATGTTTACTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATAC
TGTTATCTGAATAAGGGGCTAAGGCCCAGTTTATTGTAATCTGAAAAGGGCTGTGGCCCAGTACC
ACTATTA
Found at i:5623885 original size:2 final size:2
Alignment explanation
Indices: 5623880--5623918 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
5623870 TATATAAAAG
5623880 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
5623919 GAATGTTAAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:5627781 original size:23 final size:22
Alignment explanation
Indices: 5627747--5627797 Score: 66
Period size: 23 Copynumber: 2.3 Consensus size: 22
5627737 ATGTGAAAAT
* *
5627747 AATAATAGTATGTTAATAACAAC
1 AATAATACTATGGTAA-AACAAC
*
5627770 AATAATACTATGGTAAAACAAT
1 AATAATACTATGGTAAAACAAC
5627792 AATAAT
1 AATAAT
5627798 GCATAAAATA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
22 11 0.44
23 14 0.56
ACGTcount: A:0.55, C:0.08, G:0.08, T:0.29
Consensus pattern (22 bp):
AATAATACTATGGTAAAACAAC
Found at i:5633725 original size:34 final size:34
Alignment explanation
Indices: 5633636--5633726 Score: 96
Period size: 34 Copynumber: 2.7 Consensus size: 34
5633626 TTGAAGGTAT
* *
5633636 TTTTAATAGGGAGTTGAGAAAAAAATTAGATAAA
1 TTTTAAAAGGGAATTGAGAAAAAAATTAGATAAA
* * *
5633670 TTTTAAAAGTGATTTGAGAAAAAAATTGGA-AACA
1 TTTTAAAAGGGAATTGAGAAAAAAATTAGATAA-A
*
5633704 TTTTAGAAGGGAATT-ATGAAAAA
1 TTTTAAAAGGGAATTGA-GAAAAA
5633727 CGAATATCGT
Statistics
Matches: 48, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
33 3 0.06
34 45 0.94
ACGTcount: A:0.49, C:0.01, G:0.20, T:0.30
Consensus pattern (34 bp):
TTTTAAAAGGGAATTGAGAAAAAAATTAGATAAA
Found at i:5634130 original size:26 final size:24
Alignment explanation
Indices: 5634090--5634149 Score: 75
Period size: 26 Copynumber: 2.4 Consensus size: 24
5634080 TTATTTCATT
* * *
5634090 AAATAAAAAAATTTAAAAATATAA
1 AAATAAATATATTTAAAAACATAA
5634114 TAAATCAAATATATTTAAAAACATAA
1 -AAAT-AAATATATTTAAAAACATAA
5634140 AAATAAATAT
1 AAATAAATAT
5634150 TAAAACAAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
24 6 0.19
25 8 0.26
26 17 0.55
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.28
Consensus pattern (24 bp):
AAATAAATATATTTAAAAACATAA
Found at i:5634154 original size:20 final size:20
Alignment explanation
Indices: 5634139--5634177 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
5634129 TAAAAACATA
*
5634139 AAAATAAATATTAAAACAAAT
1 AAAAT-AATACTAAAACAAAT
5634160 AAAATAATACTAAAACAA
1 AAAATAATACTAAAACAA
5634178 TTCTTAAAAC
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:0.72, C:0.08, G:0.00, T:0.21
Consensus pattern (20 bp):
AAAATAATACTAAAACAAAT
Found at i:5634164 original size:21 final size:19
Alignment explanation
Indices: 5634131--5634177 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
5634121 AATATATTTA
* *
5634131 AAAACATAAAAATAAATATT
1 AAAACAAAAAAAT-AATACT
5634151 AAAACAAATAAAATAATACT
1 AAAACAAA-AAAATAATACT
5634171 AAAACAA
1 AAAACAA
5634178 TTCTTAAAAC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 19 0.79
21 5 0.21
ACGTcount: A:0.72, C:0.09, G:0.00, T:0.19
Consensus pattern (19 bp):
AAAACAAAAAAATAATACT
Found at i:5634924 original size:3 final size:3
Alignment explanation
Indices: 5634877--5634908 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
5634867 TCTAGCTCCT
5634877 CCA CCA CCA CCA CCA CCA CCA CCA CCA CCA CC
1 CCA CCA CCA CCA CCA CCA CCA CCA CCA CCA CC
5634909 TCTAGCTCCA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.31, C:0.69, G:0.00, T:0.00
Consensus pattern (3 bp):
CCA
Found at i:5634938 original size:30 final size:30
Alignment explanation
Indices: 5634904--5635026 Score: 112
Period size: 30 Copynumber: 4.2 Consensus size: 30
5634894 ACCACCACCA
5634904 CCACCTCTAGCTCCACCACCATTGTTGTGC
1 CCACCTCTAGCTCCACCACCATTGTTGTGC
****
5634934 CCACCTTCCT--CTCCACCACCATTACCATGC
1 CCACC-T-CTAGCTCCACCACCATTGTTGTGC
*** *
5634964 CCACCTCTAGCTCCACCACCA-CCAT-T-A
1 CCACCTCTAGCTCCACCACCATTGTTGTGC
*
5634991 CCACCTCTAGCTCCATCACCATTGTTGTGC
1 CCACCTCTAGCTCCACCACCATTGTTGTGC
5635021 CCACCT
1 CCACCT
5635027 TCCTCTCCAC
Statistics
Matches: 72, Mismatches: 14, Indels: 14
0.72 0.14 0.14
Matches are distributed among these distances:
27 20 0.28
28 4 0.06
29 2 0.03
30 43 0.60
31 1 0.01
32 2 0.03
ACGTcount: A:0.20, C:0.48, G:0.08, T:0.24
Consensus pattern (30 bp):
CCACCTCTAGCTCCACCACCATTGTTGTGC
Found at i:5634987 original size:27 final size:27
Alignment explanation
Indices: 5634957--5635011 Score: 83
Period size: 27 Copynumber: 2.0 Consensus size: 27
5634947 CACCACCATT
*
5634957 ACCATGCCCACCTCTAGCTCCACCACC
1 ACCATGACCACCTCTAGCTCCACCACC
* *
5634984 ACCATTACCACCTCTAGCTCCATCACC
1 ACCATGACCACCTCTAGCTCCACCACC
5635011 A
1 A
5635012 TTGTTGTGCC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.25, C:0.51, G:0.05, T:0.18
Consensus pattern (27 bp):
ACCATGACCACCTCTAGCTCCACCACC
Found at i:5636840 original size:23 final size:22
Alignment explanation
Indices: 5636798--5636861 Score: 62
Period size: 22 Copynumber: 2.9 Consensus size: 22
5636788 TGTATTAGCG
*
5636798 TATGATATTTTATATATATGTA
1 TATGATATTTAATATATATGTA
5636820 TATG-TATTTAATATACTTATGTA
1 TATGATATTTAATATA--TATGTA
5636843 T-T-ATATTATATATATATAT
1 TATGATATT-TA-ATATATAT
5636862 ATTTTTTATA
Statistics
Matches: 36, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
21 10 0.28
22 12 0.33
23 9 0.25
24 5 0.14
ACGTcount: A:0.38, C:0.02, G:0.06, T:0.55
Consensus pattern (22 bp):
TATGATATTTAATATATATGTA
Found at i:5636872 original size:37 final size:37
Alignment explanation
Indices: 5636807--5636877 Score: 90
Period size: 37 Copynumber: 1.9 Consensus size: 37
5636797 GTATGATATT
* *
5636807 TTATATATATGTATATGTATTTAATATAC-TTATGTA
1 TTATATATATATATATATATTTAATATACGTTATGTA
**
5636843 TTATATTATATATATATATATTTTTTATACGTTAT
1 TTATA-TATATATATATATATTTAATATACGTTAT
5636878 ATGCGCTTTT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
36 5 0.17
37 20 0.69
38 4 0.14
ACGTcount: A:0.35, C:0.03, G:0.06, T:0.56
Consensus pattern (37 bp):
TTATATATATATATATATATTTAATATACGTTATGTA
Found at i:5637086 original size:26 final size:26
Alignment explanation
Indices: 5637039--5637095 Score: 80
Period size: 26 Copynumber: 2.2 Consensus size: 26
5637029 TAAACATACT
* *
5637039 TTTATTATTATTTTACCTTATTA-TA
1 TTTATTATTATTTTAACATATTATTA
5637064 TTTATTATTTATTTTAACATATTATTA
1 TTTATTA-TTATTTTAACATATTATTA
5637091 TTTAT
1 TTTAT
5637096 ATCATCATTT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
25 7 0.25
26 14 0.50
27 7 0.25
ACGTcount: A:0.30, C:0.05, G:0.00, T:0.65
Consensus pattern (26 bp):
TTTATTATTATTTTAACATATTATTA
Found at i:5638057 original size:25 final size:24
Alignment explanation
Indices: 5638016--5638078 Score: 72
Period size: 25 Copynumber: 2.5 Consensus size: 24
5638006 GATTATGTAG
5638016 AAAGAATAAAGAAATGAAAAAAAAA
1 AAAGAA-AAAGAAATGAAAAAAAAA
* * *
5638041 AAAGAAAGAGAATATGAAGAAAAAC
1 AAAGAAAAAGAA-ATGAAAAAAAAA
*
5638066 AAAGAAAAGGAAA
1 AAAGAAAAAGAAA
5638079 AAAAAAGTGT
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
24 6 0.19
25 26 0.81
ACGTcount: A:0.75, C:0.02, G:0.17, T:0.06
Consensus pattern (24 bp):
AAAGAAAAAGAAATGAAAAAAAAA
Found at i:5639276 original size:29 final size:29
Alignment explanation
Indices: 5639243--5639307 Score: 112
Period size: 29 Copynumber: 2.2 Consensus size: 29
5639233 GTGACGAGAT
*
5639243 TGGCACTAAGTGTGCATGCTGGAAATATA
1 TGGCACTAAGTGTGCATGCTGGAAAAATA
5639272 TGGCACTAAGTGTGCATGCTGGAAAAATA
1 TGGCACTAAGTGTGCATGCTGGAAAAATA
*
5639301 CGGCACT
1 TGGCACT
5639308 GGGTGTGCGA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 34 1.00
ACGTcount: A:0.31, C:0.17, G:0.28, T:0.25
Consensus pattern (29 bp):
TGGCACTAAGTGTGCATGCTGGAAAAATA
Found at i:5645956 original size:25 final size:24
Alignment explanation
Indices: 5645915--5645977 Score: 72
Period size: 25 Copynumber: 2.5 Consensus size: 24
5645905 GATTATGTAG
5645915 AAAGAATAAAGAAATGAAAAAAAAA
1 AAAGAA-AAAGAAATGAAAAAAAAA
* * *
5645940 AAAGAAAGAGAATATGAAGAAAAAC
1 AAAGAAAAAGAA-ATGAAAAAAAAA
*
5645965 AAAGAAAAGGAAA
1 AAAGAAAAAGAAA
5645978 AAAAAAGTGT
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
24 6 0.19
25 26 0.81
ACGTcount: A:0.75, C:0.02, G:0.17, T:0.06
Consensus pattern (24 bp):
AAAGAAAAAGAAATGAAAAAAAAA
Found at i:5647173 original size:29 final size:29
Alignment explanation
Indices: 5647140--5647204 Score: 112
Period size: 29 Copynumber: 2.2 Consensus size: 29
5647130 GTGACGAGAT
*
5647140 TGGCACTAAGTGTGCATGCTGGAAATATA
1 TGGCACTAAGTGTGCATGCTGGAAAAATA
5647169 TGGCACTAAGTGTGCATGCTGGAAAAATA
1 TGGCACTAAGTGTGCATGCTGGAAAAATA
*
5647198 CGGCACT
1 TGGCACT
5647205 GGGTGTGCGA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 34 1.00
ACGTcount: A:0.31, C:0.17, G:0.28, T:0.25
Consensus pattern (29 bp):
TGGCACTAAGTGTGCATGCTGGAAAAATA
Found at i:5648826 original size:11 final size:11
Alignment explanation
Indices: 5648802--5648832 Score: 53
Period size: 11 Copynumber: 2.7 Consensus size: 11
5648792 TTCATATATA
5648802 TATATATATATG
1 TATATAT-TATG
5648814 TATATATTATG
1 TATATATTATG
5648825 TATATATT
1 TATATATT
5648833 TTAACATTAC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 12 0.63
12 7 0.37
ACGTcount: A:0.39, C:0.00, G:0.06, T:0.55
Consensus pattern (11 bp):
TATATATTATG
Found at i:5651835 original size:3 final size:3
Alignment explanation
Indices: 5651829--5652287 Score: 93
Period size: 3 Copynumber: 154.3 Consensus size: 3
5651819 AAAAGAAAAT
* * * *
5651829 ATA ATA ATA ATA TATA GTA ATA AT- ACA ATA GTG ATA ATA ATA A-A
1 ATA ATA ATA ATA -ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* * *
5651873 A-A AGGT- ATA ATA AT- ATA TTA GATA GTGA AGA ATA ATA ATA ATA ATA
1 ATA A--TA ATA ATA ATA ATA ATA -ATA AT-A ATA ATA ATA ATA ATA ATA
* * * * * * * *
5651919 ACA GTA ATA A-A ATTG GTA ATA GTG ATA TTA GTA ATA ATA ATA ATA
1 ATA ATA ATA ATA A-TA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* * * *
5651964 GGA-A ATA ATA GTA CATTA ATA ATA ATA ATA ATA AT- ATG TTA ATA ACA
1 --ATA ATA ATA ATA -A-TA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* * * *
5652011 ATA ATA ACA TATA A-A AAA ATA GGA-A ATA ATA AT- ATG GTA A-A A-A
1 ATA ATA ATA -ATA ATA ATA ATA --ATA ATA ATA ATA ATA ATA ATA ATA
* * * * * * *
5652054 ATA ATA ATA ATA ACA A-A AAA AGA GTA ATA ATA GTA GTA A-A AAA AT-
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* * * * *
5652099 ATA AAA ATA ATA ATA ATA GTA CA-A A-A ATG ACA ATA A-A ATA A-G
1 ATA ATA ATA ATA ATA ATA ATA -ATA ATA ATA ATA ATA ATA ATA ATA
* * * * * **
5652141 ATG ATA ATA ATG ATA ATA A-A A-A ATA AAA ATA GTA ATA ATG GCA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* * * * *
5652187 ATA ATA ATA CCATA ATA A-A AGA AAA AGAA ATA ATA ACA TGTAA ATA
1 ATA ATA ATA --ATA ATA ATA ATA ATA A-TA ATA ATA ATA -AT-A ATA
* * * * *
5652233 ATA ATA ACA ATA ATA ACA ATA AT- ATA TTTA ATA ACA ATA ATA GTA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA -ATA ATA ATA ATA ATA ATA
*
5652278 AAA ATA ATA A
1 ATA ATA ATA A
5652288 AATTAACTAA
Statistics
Matches: 326, Mismatches: 90, Indels: 80
0.66 0.18 0.16
Matches are distributed among these distances:
2 42 0.13
3 258 0.79
4 18 0.06
5 8 0.02
ACGTcount: A:0.61, C:0.03, G:0.08, T:0.27
Consensus pattern (3 bp):
ATA
Found at i:5651996 original size:23 final size:23
Alignment explanation
Indices: 5651967--5652017 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
5651957 AATAATAGGA
* *
5651967 AATAATAGTACATTAATAATAAT
1 AATAATAATACATTAATAACAAT
**
5651990 AATAATAATATGTTAATAACAAT
1 AATAATAATACATTAATAACAAT
5652013 AATAA
1 AATAA
5652018 CATATAAAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.59, C:0.04, G:0.04, T:0.33
Consensus pattern (23 bp):
AATAATAATACATTAATAACAAT
Found at i:5652085 original size:23 final size:22
Alignment explanation
Indices: 5652049--5652111 Score: 65
Period size: 23 Copynumber: 2.9 Consensus size: 22
5652039 ATAATATGGT
5652049 AAAAA-ATAATAATAATAACAA
1 AAAAAGATAATAATAATAACAA
* **
5652070 AAAAAGAGTAATAATAGTAGTAA
1 AAAAAGA-TAATAATAATAACAA
* *
5652093 AAAAATATAAAAATAATAA
1 AAAAAGATAATAATAATAA
5652112 TAATAGTACA
Statistics
Matches: 33, Mismatches: 7, Indels: 3
0.77 0.16 0.07
Matches are distributed among these distances:
21 5 0.15
22 10 0.30
23 18 0.55
ACGTcount: A:0.71, C:0.02, G:0.06, T:0.21
Consensus pattern (22 bp):
AAAAAGATAATAATAATAACAA
Found at i:5652138 original size:28 final size:28
Alignment explanation
Indices: 5652049--5652139 Score: 73
Period size: 28 Copynumber: 3.4 Consensus size: 28
5652039 ATAATATGGT
* *
5652049 AAAA-AATAATAATAATAACAAAA-A-A
1 AAAATAATAATAATAGTAAAAAAATACA
* * * *
5652074 AGAGTAATAATAGTAGTAAAAAAATATA
1 AAAATAATAATAATAGTAAAAAAATACA
*
5652102 AAAATAATAATAATAGTACAAAAATGACA
1 AAAATAATAATAATAGTAAAAAAAT-ACA
*
5652131 ATAA-AATAA
1 AAAATAATAA
5652140 GATGATAATA
Statistics
Matches: 51, Mismatches: 11, Indels: 5
0.76 0.16 0.07
Matches are distributed among these distances:
25 2 0.04
26 16 0.31
27 1 0.02
28 27 0.53
29 5 0.10
ACGTcount: A:0.69, C:0.03, G:0.07, T:0.21
Consensus pattern (28 bp):
AAAATAATAATAATAGTAAAAAAATACA
Found at i:5653985 original size:19 final size:19
Alignment explanation
Indices: 5653944--5653991 Score: 53
Period size: 20 Copynumber: 2.5 Consensus size: 19
5653934 TATAATTTTA
* *
5653944 TAATTATTTTTGTTCTATG
1 TAATTATTTTTATTATATG
5653963 TAATTAGTTTTTATTATAT-
1 TAATTA-TTTTTATTATATG
5653982 TAATTTATTT
1 TAA-TTATTT
5653992 AATGTTCATA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
19 12 0.48
20 13 0.52
ACGTcount: A:0.27, C:0.02, G:0.06, T:0.65
Consensus pattern (19 bp):
TAATTATTTTTATTATATG
Found at i:5655047 original size:17 final size:17
Alignment explanation
Indices: 5655025--5655065 Score: 73
Period size: 17 Copynumber: 2.4 Consensus size: 17
5655015 CCGAAGAGTT
*
5655025 ATCGAGCTTGCCTCCAG
1 ATCGAGATTGCCTCCAG
5655042 ATCGAGATTGCCTCCAG
1 ATCGAGATTGCCTCCAG
5655059 ATCGAGA
1 ATCGAGA
5655066 CGTCAAGTTC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.24, C:0.29, G:0.24, T:0.22
Consensus pattern (17 bp):
ATCGAGATTGCCTCCAG
Found at i:5662815 original size:6 final size:6
Alignment explanation
Indices: 5662806--5662878 Score: 60
Period size: 6 Copynumber: 11.8 Consensus size: 6
5662796 TATTAGAACT
* *
5662806 AGAATC AGAATC AGAATC AG-GTGAC AGAATC AGAATC AGAATC AGTATC
1 AGAATC AGAATC AGAATC AGAAT--C AGAATC AGAATC AGAATC AGAATC
* *
5662855 AGGTAA-C AGAATC AAAATT AGAAT
1 A-G-AATC AGAATC AGAATC AGAAT
5662879 TAGTATTAGG
Statistics
Matches: 54, Mismatches: 7, Indels: 12
0.74 0.10 0.16
Matches are distributed among these distances:
5 3 0.06
6 43 0.80
7 6 0.11
8 2 0.04
ACGTcount: A:0.48, C:0.14, G:0.19, T:0.19
Consensus pattern (6 bp):
AGAATC
Found at i:5662842 original size:31 final size:31
Alignment explanation
Indices: 5662806--5662893 Score: 113
Period size: 31 Copynumber: 2.8 Consensus size: 31
5662796 TATTAGAACT
*
5662806 AGAATCAGAATCAGAATCAGGTGACAGAATC
1 AGAATCAGAATCAGAATCAGGTAACAGAATC
*
5662837 AGAATCAGAATCAGTATCAGGTAACAGAATC
1 AGAATCAGAATCAGAATCAGGTAACAGAATC
* * * * *
5662868 AAAATTAGAATTAGTATTAGGTAACA
1 AGAATCAGAATCAGAATCAGGTAACA
5662894 TAATTAAAAA
Statistics
Matches: 51, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 51 1.00
ACGTcount: A:0.47, C:0.12, G:0.19, T:0.22
Consensus pattern (31 bp):
AGAATCAGAATCAGAATCAGGTAACAGAATC
Found at i:5663100 original size:27 final size:26
Alignment explanation
Indices: 5663034--5663135 Score: 114
Period size: 27 Copynumber: 3.8 Consensus size: 26
5663024 GCTCAGTTAT
* *
5663034 CAGATATTGTGACAGAGTCACCAGATA
1 CAGATATTGTGGCAGAGCCACCAGA-A
*
5663061 CAGATATTATGGCAGAGCCACCAGAA
1 CAGATATTGTGGCAGAGCCACCAGAA
* *
5663087 CAGATATTTGTGGCATAGCCACAAGAAA
1 CAGATA-TTGTGGCAGAGCCACCAG-AA
* *
5663115 CAGATAATGTGGCAAAGCCAC
1 CAGATATTGTGGCAGAGCCAC
5663136 TTAACAGAAT
Statistics
Matches: 65, Mismatches: 8, Indels: 4
0.84 0.10 0.05
Matches are distributed among these distances:
26 7 0.11
27 50 0.77
28 8 0.12
ACGTcount: A:0.38, C:0.21, G:0.23, T:0.19
Consensus pattern (26 bp):
CAGATATTGTGGCAGAGCCACCAGAA
Found at i:5663328 original size:22 final size:22
Alignment explanation
Indices: 5663294--5663358 Score: 69
Period size: 22 Copynumber: 3.0 Consensus size: 22
5663284 GCAAATACGT
*
5663294 TTGGCACACAGCCATAATCAGG
1 TTGGCACAAAGCCATAATCAGG
* * *
5663316 TTGGCATAGAGCCAT-ATGTAGG
1 TTGGCACAAAGCCATAAT-CAGG
*
5663338 TTGACACAAAGCCATAATCAG
1 TTGGCACAAAGCCATAATCAG
5663359 AAGGCTTTAA
Statistics
Matches: 34, Mismatches: 7, Indels: 4
0.76 0.16 0.09
Matches are distributed among these distances:
21 2 0.06
22 30 0.88
23 2 0.06
ACGTcount: A:0.34, C:0.22, G:0.23, T:0.22
Consensus pattern (22 bp):
TTGGCACAAAGCCATAATCAGG
Found at i:5663635 original size:16 final size:16
Alignment explanation
Indices: 5663614--5663644 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
5663604 ATTCCAACCC
*
5663614 ATGCAACATGTCATGT
1 ATGCAAAATGTCATGT
5663630 ATGCAAAATGTCATG
1 ATGCAAAATGTCATG
5663645 CCCATATTTG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.16, G:0.19, T:0.29
Consensus pattern (16 bp):
ATGCAAAATGTCATGT
Found at i:5663841 original size:27 final size:27
Alignment explanation
Indices: 5663785--5663999 Score: 281
Period size: 27 Copynumber: 8.0 Consensus size: 27
5663775 GGGGCAAAAT
* * * *
5663785 GGTAATTTTACCCCACA-AGGTATCTC
1 GGTAATTCTACCCTACAGGGGTATTTC
* *
5663811 GGTAATTCCACCCTACAGGGGTATTTT
1 GGTAATTCTACCCTACAGGGGTATTTC
5663838 GGTAATTCTA-CCTACAGGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
*
5663864 GGTAATTCTACCCTACAGGGGTATTTT
1 GGTAATTCTACCCTACAGGGGTATTTC
*
5663891 GGTAATTCTACCTTACAGGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
* * * * *
5663918 AGTAATTCTACCTTATAAGGGTATTCC
1 GGTAATTCTACCCTACAGGGGTATTTC
*
5663945 GGTAATTCTGCCCTACAGGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
*
5663972 GGTGATTCTACCCTACAGGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
5663999 G
1 G
5664000 ATATTTTACA
Statistics
Matches: 164, Mismatches: 23, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
26 39 0.24
27 125 0.76
ACGTcount: A:0.23, C:0.21, G:0.22, T:0.34
Consensus pattern (27 bp):
GGTAATTCTACCCTACAGGGGTATTTC
Found at i:5664176 original size:21 final size:21
Alignment explanation
Indices: 5664150--5664189 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
5664140 TTATAAACAA
5664150 AGGGTATTTTAGTAATTTTAC
1 AGGGTATTTTAGTAATTTTAC
*
5664171 AGGGTATTTTGGTAATTTT
1 AGGGTATTTTAGTAATTTT
5664190 GTAAACCAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.25, C:0.03, G:0.23, T:0.50
Consensus pattern (21 bp):
AGGGTATTTTAGTAATTTTAC
Found at i:5664227 original size:156 final size:156
Alignment explanation
Indices: 5664043--5664327 Score: 471
Period size: 156 Copynumber: 1.8 Consensus size: 156
5664033 CACAAATCAG
* *
5664043 GGGTATTTTGGTAATTTCACAAATCAGGGGTATTTTGGTAATTTTACAAACTAGGGGTATTTTGA
1 GGGTATTTTGGTAATTTCACAAACCAGGGGTATTTTGGTAATTTTACAAACCAGGGGTATTTTGA
*
5664108 TAATTTTACAAACCAGGGGTATTTTGGTAATTTTATAAACAAAGGGTATTTTAGTAATTTTACAG
66 TAATTTTACAAACCAAGGGTATTTTGGTAATTTTATAAACAAAGGGTATTTTAGTAATTTTACAG
5664173 GGTATTTTGGTAATTTTGTAAACCAA
131 GGTATTTTGGTAATTTTGTAAACCAA
* *
5664199 GGGTATTTTGGTAATTTTACAAACCAGGGGTATTTTGGTAATTTTACAAACCAGGGGTATTTTGG
1 GGGTATTTTGGTAATTTCACAAACCAGGGGTATTTTGGTAATTTTACAAACCAGGGGTATTTTGA
** * * * *
5664264 TAATTTTGTAAACCAATGGTATTTTGGTAATTTTGTAAACCAAGGGTATTTTGGTAATTTTACA
66 TAATTTTACAAACCAAGGGTATTTTGGTAATTTTATAAACAAAGGGTATTTTAGTAATTTTACA
5664328 AACCAGGGGT
Statistics
Matches: 118, Mismatches: 11, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
156 118 1.00
ACGTcount: A:0.30, C:0.08, G:0.21, T:0.41
Consensus pattern (156 bp):
GGGTATTTTGGTAATTTCACAAACCAGGGGTATTTTGGTAATTTTACAAACCAGGGGTATTTTGA
TAATTTTACAAACCAAGGGTATTTTGGTAATTTTATAAACAAAGGGTATTTTAGTAATTTTACAG
GGTATTTTGGTAATTTTGTAAACCAA
Found at i:5664357 original size:27 final size:27
Alignment explanation
Indices: 5663987--5664350 Score: 438
Period size: 27 Copynumber: 13.7 Consensus size: 27
5663977 TTCTACCCTA
* * *
5663987 CAGGGGTATTTCGAT-ATTTTACAAAT
1 CAGGGGTATTTTGGTAATTTTACAAAC
* * * *
5664013 C-GAGAGTATTTTGATAATTTCACAAAT
1 CAG-GGGTATTTTGGTAATTTTACAAAC
* *
5664040 CAGGGGTATTTTGGTAATTTCACAAAT
1 CAGGGGTATTTTGGTAATTTTACAAAC
5664067 CAGGGGTATTTTGGTAATTTTACAAAC
1 CAGGGGTATTTTGGTAATTTTACAAAC
* *
5664094 TAGGGGTATTTTGATAATTTTACAAAC
1 CAGGGGTATTTTGGTAATTTTACAAAC
*
5664121 CAGGGGTATTTTGGTAATTTTATAAAC
1 CAGGGGTATTTTGGTAATTTTACAAAC
* * *
5664148 AAAGGGTATTTTAGTAATTTT----A-
1 CAGGGGTATTTTGGTAATTTTACAAAC
**
5664170 CA-GGGTATTTTGGTAATTTTGTAAAC
1 CAGGGGTATTTTGGTAATTTTACAAAC
*
5664196 CAAGGGTATTTTGGTAATTTTACAAAC
1 CAGGGGTATTTTGGTAATTTTACAAAC
5664223 CAGGGGTATTTTGGTAATTTTACAAAC
1 CAGGGGTATTTTGGTAATTTTACAAAC
**
5664250 CAGGGGTATTTTGGTAATTTTGTAAAC
1 CAGGGGTATTTTGGTAATTTTACAAAC
** **
5664277 CAATGGTATTTTGGTAATTTTGTAAAC
1 CAGGGGTATTTTGGTAATTTTACAAAC
*
5664304 CAAGGGTATTTTGGTAATTTTACAAAC
1 CAGGGGTATTTTGGTAATTTTACAAAC
5664331 CAGGGGTATTTTGGTAATTT
1 CAGGGGTATTTTGGTAATTT
5664351 GGTAAACTAA
Statistics
Matches: 301, Mismatches: 28, Indels: 17
0.87 0.08 0.05
Matches are distributed among these distances:
21 17 0.06
22 1 0.00
23 1 0.00
25 2 0.01
26 13 0.04
27 266 0.88
28 1 0.00
ACGTcount: A:0.30, C:0.09, G:0.21, T:0.40
Consensus pattern (27 bp):
CAGGGGTATTTTGGTAATTTTACAAAC
Found at i:5666410 original size:36 final size:35
Alignment explanation
Indices: 5666353--5666446 Score: 100
Period size: 36 Copynumber: 2.6 Consensus size: 35
5666343 TTATATTATA
* *
5666353 TTTAAAAGGGAGTTAGAAAAAAACAACTAGG-TAAAT
1 TTTAAAAGAGAATTAGAAAAAAA-AACTAGGAT-AAT
*
5666389 TTTAAAAGAGAATTGAGAAAAAAAAATTAGGATAAT
1 TTTAAAAGAGAATT-AGAAAAAAAAACTAGGATAAT
* *
5666425 TTTAGAAGAAAATTATGAAAAA
1 TTTAAAAGAGAATTA-GAAAAA
5666447 CAAGTATCGT
Statistics
Matches: 50, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
35 1 0.02
36 39 0.78
37 10 0.20
ACGTcount: A:0.56, C:0.02, G:0.17, T:0.24
Consensus pattern (35 bp):
TTTAAAAGAGAATTAGAAAAAAAAACTAGGATAAT
Found at i:5667159 original size:12 final size:12
Alignment explanation
Indices: 5667144--5667182 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
5667134 AGTTCCAGTT
*
5667144 CCACCTCCACTA
1 CCACCACCACTA
*
5667156 CCACCACTACTA
1 CCACCACCACTA
*
5667168 CCACCACCACCA
1 CCACCACCACTA
5667180 CCA
1 CCA
5667183 ATTCCAAAAC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.31, C:0.59, G:0.00, T:0.10
Consensus pattern (12 bp):
CCACCACCACTA
Found at i:5668670 original size:29 final size:29
Alignment explanation
Indices: 5668637--5668692 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
5668627 TTTTATTCCT
5668637 TTTAATAATAAAGAGACTAAATTGATCAA
1 TTTAATAATAAAGAGACTAAATTGATCAA
* * * *
5668666 TTTAATAGTAGAGGGACTAATTTGATC
1 TTTAATAATAAAGAGACTAAATTGATC
5668693 TAGTCCATAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.43, C:0.07, G:0.16, T:0.34
Consensus pattern (29 bp):
TTTAATAATAAAGAGACTAAATTGATCAA
Found at i:5674767 original size:23 final size:22
Alignment explanation
Indices: 5674737--5674779 Score: 68
Period size: 23 Copynumber: 1.9 Consensus size: 22
5674727 TATTGGATTT
5674737 ATATTAATAAAAATAAAAAATC
1 ATATTAATAAAAATAAAAAATC
*
5674759 ATATGTAATAAATATAAAAAA
1 ATAT-TAATAAAAATAAAAAA
5674780 GTTAGATTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 4 0.21
23 15 0.79
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.28
Consensus pattern (22 bp):
ATATTAATAAAAATAAAAAATC
Found at i:5677212 original size:20 final size:20
Alignment explanation
Indices: 5677177--5677226 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
5677167 TATCTTATTG
* *
5677177 TTTTATTTGT-TTTTATTAT
1 TTTTATTTTTATTTTATTAA
5677196 TTTTATTTTTATTTTATTAA
1 TTTTATTTTTATTTTATTAA
*
5677216 TTTTAATTTTA
1 TTTTATTTTTA
5677227 ATTCCTCCAA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
19 9 0.33
20 18 0.67
ACGTcount: A:0.22, C:0.00, G:0.02, T:0.76
Consensus pattern (20 bp):
TTTTATTTTTATTTTATTAA
Found at i:5678521 original size:25 final size:25
Alignment explanation
Indices: 5678493--5678553 Score: 68
Period size: 25 Copynumber: 2.4 Consensus size: 25
5678483 TAAAATATGC
* *
5678493 TATGTTATGATTCGATATAACATGA
1 TATGTTAAGATTCAATATAACATGA
* * *
5678518 TATGCTAAGATTCAATATGATATGA
1 TATGTTAAGATTCAATATAACATGA
*
5678543 TACGTTAAGAT
1 TATGTTAAGAT
5678554 ATTCGTATAA
Statistics
Matches: 29, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.38, C:0.08, G:0.16, T:0.38
Consensus pattern (25 bp):
TATGTTAAGATTCAATATAACATGA
Found at i:5680994 original size:23 final size:23
Alignment explanation
Indices: 5680968--5681012 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
5680958 TATATAATAA
* *
5680968 ATATATATTTTTTATTTTTAATC
1 ATATATATATTTTAATTTTAATC
*
5680991 ATATTTATATTTTAATTTTAAT
1 ATATATATATTTTAATTTTAAT
5681013 TTTAATATAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.64
Consensus pattern (23 bp):
ATATATATATTTTAATTTTAATC
Found at i:5681083 original size:40 final size:41
Alignment explanation
Indices: 5681028--5681114 Score: 122
Period size: 40 Copynumber: 2.1 Consensus size: 41
5681018 TATAATCAAT
*
5681028 TTTTATTATATTTTTTAATTTGTGTATTGTTTTAAGAATTG
1 TTTTAATATATTTTTTAATTTGTGTATTGTTTTAAGAATTG
* * * *
5681069 TTTTAATATATTTTTT-ATTTGTTTCTTGTTTTAATATTTG
1 TTTTAATATATTTTTTAATTTGTGTATTGTTTTAAGAATTG
5681109 TTTTAA
1 TTTTAA
5681115 ATGTATTTGA
Statistics
Matches: 41, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
40 26 0.63
41 15 0.37
ACGTcount: A:0.23, C:0.01, G:0.09, T:0.67
Consensus pattern (41 bp):
TTTTAATATATTTTTTAATTTGTGTATTGTTTTAAGAATTG
Found at i:5682893 original size:45 final size:44
Alignment explanation
Indices: 5682790--5682914 Score: 142
Period size: 45 Copynumber: 2.8 Consensus size: 44
5682780 GTCATTTTAC
* * * * * *
5682790 TCTGCTCCTTTGCAACTTCAGAGAAATAAGATTTGCTATCTTCAG
1 TCTGCT-CTCTGCAACTTTAGGGAGATAAGACTTGCTATCTTCAA
* * *
5682835 TCTACTTCGCTGCAACTTTAGGGAGATGAGACTTGCTATCTTCAA
1 TCTGC-TCTCTGCAACTTTAGGGAGATAAGACTTGCTATCTTCAA
5682880 TCTGCTCATCTGCAACTTTAGGGAGATAAGACTTG
1 TCTGCTC-TCTGCAACTTTAGGGAGATAAGACTTG
5682915 TGACTTCTAT
Statistics
Matches: 66, Mismatches: 12, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
44 2 0.03
45 63 0.95
46 1 0.02
ACGTcount: A:0.26, C:0.22, G:0.19, T:0.34
Consensus pattern (44 bp):
TCTGCTCTCTGCAACTTTAGGGAGATAAGACTTGCTATCTTCAA
Found at i:5683232 original size:86 final size:87
Alignment explanation
Indices: 5683026--5683380 Score: 421
Period size: 86 Copynumber: 4.1 Consensus size: 87
5683016 GACCTTATTA
** * * * *
5683026 CTTAGGGGTTTAAGGGCCATCA-CTTCTGCTATGTTTCCCTACTGCTTAGGGGGTTAAGATTTGT
1 CTTAGGGGTTTAAGACCCTTCATCTTC-GATCTGTTTCCCTACTGCTTAGGGGGTTAAGATCTGT
* *
5683090 CAATTTTCAGCCTGTTACCCTATTA
65 CAA-TTT-AGCCTGTTACCCTACTG
* * * * * * *
5683115 TTTAGGGGTTTAAG-GCTTGTCACCTTTGATCTGTTTCCCTACTGCTTAGGGAGATAAGATCTG-
1 CTTAGGGGTTTAAGACCCT-TCATCTTCGATCTGTTTCCCTACTGCTTAGGGGGTTAAGATCTGT
* *
5683178 CAATTTGGTCTGTTACCCTACTG
65 CAATTTAGCCTGTTACCCTACTG
* * *
5683201 CTTAGGGGTTTAAGACCCTTCGTCTTCGATCTGTTTCCTTACTACTTAGGGGGTTAAGATCTG-C
1 CTTAGGGGTTTAAGACCCTTCATCTTCGATCTGTTTCCCTACTGCTTAGGGGGTTAAGATCTGTC
* *
5683265 AATTTGGTCTGTTACCCTACTG
66 AATTTAGCCTGTTACCCTACTG
* *
5683287 CTTAGGGGTTTAAGACCCTTCATCTCCGATCTGTTTCCCTACTGCTTAGGGGGTTAAGATCTGTA
1 CTTAGGGGTTTAAGACCCTTCATCTTCGATCTGTTTCCCTACTGCTTAGGGGGTTAAGATCTGTC
*
5683352 AATTCAGCCTGTTACCCTACTG
66 AATTTAGCCTGTTACCCTACTG
5683374 CTTAGGG
1 CTTAGGG
5683381 AGATAATGCT
Statistics
Matches: 231, Mismatches: 31, Indels: 10
0.85 0.11 0.04
Matches are distributed among these distances:
86 145 0.63
87 31 0.13
88 5 0.02
89 47 0.20
90 3 0.01
ACGTcount: A:0.19, C:0.22, G:0.22, T:0.37
Consensus pattern (87 bp):
CTTAGGGGTTTAAGACCCTTCATCTTCGATCTGTTTCCCTACTGCTTAGGGGGTTAAGATCTGTC
AATTTAGCCTGTTACCCTACTG
Found at i:5683345 original size:44 final size:42
Alignment explanation
Indices: 5683057--5683380 Score: 204
Period size: 44 Copynumber: 7.5 Consensus size: 42
5683047 ACTTCTGCTA
** *
5683057 TGTTTCCCTACTGCTTAGGGGGTTAAGATTTGTCAATTTTC-AGCC
1 TGTTTCCCTACTGCTTAGGGGGTTAAGACCTG-CAA--TTCGA-TC
* * ** * * * * *
5683102 TGTTACCCTATTATTTAGGGGTTTAAGGCTTGTCACCTTTGATC
1 TGTTTCCCTACTGCTTAGGGGGTTAAGACCTG-CA-ATTCGATC
* * * * *
5683146 TGTTTCCCTACTGCTTAGGGAGATAAGATCTGCAATTTGGTC
1 TGTTTCCCTACTGCTTAGGGGGTTAAGACCTGCAATTCGATC
* * * **
5683188 TGTTACCCTACTGCTTAGGGGTTTAAGACCCTTCGTCTTCGATC
1 TGTTTCCCTACTGCTTAGGGGGTTAAGA-CCTGC-AATTCGATC
* * * * *
5683232 TGTTTCCTTACTACTTAGGGGGTTAAGATCTGCAATTTGGTC
1 TGTTTCCCTACTGCTTAGGGGGTTAAGACCTGCAATTCGATC
* * *
5683274 TGTTACCCTACTGCTTAGGGGTTTAAGACCCTTC-ATCTCCGATC
1 TGTTTCCCTACTGCTTAGGGGGTTAAGA-CCTGCAAT-T-CGATC
* * *
5683318 TGTTTCCCTACTGCTTAGGGGGTTAAGATCTGTAAATTC-AGCC
1 TGTTTCCCTACTGCTTAGGGGGTTAAGACCTG-CAATTCGA-TC
*
5683361 TGTTACCCTACTGCTTAGGG
1 TGTTTCCCTACTGCTTAGGG
5683381 AGATAATGCT
Statistics
Matches: 212, Mismatches: 57, Indels: 22
0.73 0.20 0.08
Matches are distributed among these distances:
42 62 0.29
43 35 0.17
44 84 0.40
45 31 0.15
ACGTcount: A:0.19, C:0.22, G:0.22, T:0.38
Consensus pattern (42 bp):
TGTTTCCCTACTGCTTAGGGGGTTAAGACCTGCAATTCGATC
Found at i:5685795 original size:18 final size:15
Alignment explanation
Indices: 5685766--5685819 Score: 54
Period size: 18 Copynumber: 3.2 Consensus size: 15
5685756 ATGGGGTTAA
5685766 GGGTTAGTTGGGTTTT
1 GGGTT-GTTGGGTTTT
5685782 GGGCTTCTGTTGGGTTTAGT
1 GGG--T-TGTTGGGTTT--T
5685802 GGGTTGTTGGGTTTT
1 GGGTTGTTGGGTTTT
5685817 GGG
1 GGG
5685820 GCTAGGGTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 11
0.75 0.00 0.25
Matches are distributed among these distances:
15 4 0.12
16 3 0.09
17 10 0.30
18 11 0.33
19 1 0.03
20 4 0.12
ACGTcount: A:0.04, C:0.04, G:0.46, T:0.46
Consensus pattern (15 bp):
GGGTTGTTGGGTTTT
Found at i:5685946 original size:24 final size:24
Alignment explanation
Indices: 5685914--5685976 Score: 81
Period size: 24 Copynumber: 2.6 Consensus size: 24
5685904 AGATGTTACA
* *
5685914 CCACCACCACCACTATGACCACCT
1 CCACCACCACCACCAAGACCACCT
** *
5685938 CCACCACCAAGACCAAGACCATCT
1 CCACCACCACCACCAAGACCACCT
5685962 CCACCACCACCACCA
1 CCACCACCACCACCA
5685977 CCTCCAAAAC
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.33, C:0.54, G:0.05, T:0.08
Consensus pattern (24 bp):
CCACCACCACCACCAAGACCACCT
Found at i:5685951 original size:18 final size:18
Alignment explanation
Indices: 5685913--5685952 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
5685903 GAGATGTTAC
* *
5685913 ACCACCACCACCACTATG
1 ACCACCACCACCACCAAG
*
5685931 ACCACCTCCACCACCAAG
1 ACCACCACCACCACCAAG
5685949 ACCA
1 ACCA
5685953 AGACCATCTC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.35, C:0.53, G:0.05, T:0.07
Consensus pattern (18 bp):
ACCACCACCACCACCAAG
Found at i:5685966 original size:30 final size:30
Alignment explanation
Indices: 5685932--5686037 Score: 95
Period size: 30 Copynumber: 3.5 Consensus size: 30
5685922 ACCACTATGA
* *
5685932 CCACCTCCACCACCAAGACCAAGACCATCT
1 CCACCTCCACCACCAAGACCAAAACCAGCT
* ***
5685962 CCACCACCACCACCACCTCCAAAACCAGCT
1 CCACCTCCACCACCAAGACCAAAACCAGCT
** **
5685992 CCAATTCCACCACCAAGACCAGCACCAGCT
1 CCACCTCCACCACCAAGACCAAAACCAGCT
* * *
5686022 CTAACTCCGCCACCAA
1 CCACCTCCACCACCAA
5686038 AATAACCCAT
Statistics
Matches: 59, Mismatches: 17, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
30 59 1.00
ACGTcount: A:0.33, C:0.51, G:0.07, T:0.09
Consensus pattern (30 bp):
CCACCTCCACCACCAAGACCAAAACCAGCT
Found at i:5691884 original size:41 final size:40
Alignment explanation
Indices: 5691810--5691951 Score: 131
Period size: 41 Copynumber: 3.5 Consensus size: 40
5691800 GCAAAAATTG
* *
5691810 TAAAACACAGAGCAATAGCGGCATTTTACCAAAAACACCAC
1 TAAAA-ACAGAGCAATAGCGGCGTTTTTCCAAAAACACCAC
* *
5691851 TAAAAACAGAGCAATAGCGGCGTTTTTCACAAAAACGCCGC
1 TAAAAACAGAGCAATAGCGGCGTTTTTC-CAAAAACACCAC
* * * * ** * *
5691892 TAAAGACAGAGCATTAGCAGCGCTTTTGGAAAAACGCCGC
1 TAAAAACAGAGCAATAGCGGCGTTTTTCCAAAAACACCAC
* *
5691932 TAAAGACCAGAGCATTAGCG
1 TAAA-AACAGAGCAATAGCG
5691952 CGCTTATGGA
Statistics
Matches: 86, Mismatches: 13, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
40 36 0.42
41 50 0.58
ACGTcount: A:0.40, C:0.24, G:0.20, T:0.16
Consensus pattern (40 bp):
TAAAAACAGAGCAATAGCGGCGTTTTTCCAAAAACACCAC
Found at i:5691983 original size:81 final size:81
Alignment explanation
Indices: 5691881--5692129 Score: 340
Period size: 81 Copynumber: 3.2 Consensus size: 81
5691871 CGTTTTTCAC
*
5691881 AAAAACGCCGCTAAAGA-CAGAGCATTAGCAGCGCTTTTGGAAAAACGCCGCTAAAGACCAGAGC
1 AAAAACGCCGCT-AAGACCAGAGCATTAGCGGCGCTTTTGGAAAAACGCCGCTAAAGACCAGAGC
5691945 ATTAGC-GCGCTTATGG
65 ATTAGCGGCGCTTATGG
*
5691961 AAAAACGCCGCTACAGACCAGAGCATTAGCGGCGCTTTTGGCAAAACGCCGCTAAAGACCAGAGC
1 AAAAACGCCGCTA-AGACCAGAGCATTAGCGGCGCTTTTGGAAAAACGCCGCTAAAGACCAGAGC
*
5692026 ATTAGCGGCTCTTATGG
65 ATTAGCGGCGCTTATGG
*
5692043 AAAAACGCCGCTAATGACCAGAGCATTAGCGGCGCTTTT--------G-TGCTAAAGACCAGAGC
1 AAAAACGCCGCTAA-GACCAGAGCATTAGCGGCGCTTTTGGAAAAACGCCGCTAAAGACCAGAGC
*
5692099 ATTAGCGGCGCTTTTGG
65 ATTAGCGGCGCTTATGG
*
5692116 AAAAAAGCCGCTAA
1 AAAAACGCCGCTAA
5692130 AAGTCACATA
Statistics
Matches: 158, Mismatches: 7, Indels: 15
0.88 0.04 0.08
Matches are distributed among these distances:
73 43 0.27
74 1 0.01
79 1 0.01
80 15 0.09
81 52 0.33
82 46 0.29
ACGTcount: A:0.33, C:0.24, G:0.25, T:0.18
Consensus pattern (81 bp):
AAAAACGCCGCTAAGACCAGAGCATTAGCGGCGCTTTTGGAAAAACGCCGCTAAAGACCAGAGCA
TTAGCGGCGCTTATGG
Found at i:5692008 original size:41 final size:41
Alignment explanation
Indices: 5691840--5692130 Score: 345
Period size: 41 Copynumber: 7.4 Consensus size: 41
5691830 GCATTTTACC
* * * * * **
5691840 AAAAACACCACTAAA-AACAGAGCAATAGCGGCGTTTTTCAC
1 AAAAACGCCGCTAAAGACCAGAGCATTAGCGGCGCTTTT-GG
*
5691881 AAAAACGCCGCTAAAGA-CAGAGCATTAGCAGCGCTTTTGG
1 AAAAACGCCGCTAAAGACCAGAGCATTAGCGGCGCTTTTGG
*
5691921 AAAAACGCCGCTAAAGACCAGAGCATTAGC-GCGCTTATGG
1 AAAAACGCCGCTAAAGACCAGAGCATTAGCGGCGCTTTTGG
*
5691961 AAAAACGCCGCTACAGACCAGAGCATTAGCGGCGCTTTTGG
1 AAAAACGCCGCTAAAGACCAGAGCATTAGCGGCGCTTTTGG
* * *
5692002 CAAAACGCCGCTAAAGACCAGAGCATTAGCGGCTCTTATGG
1 AAAAACGCCGCTAAAGACCAGAGCATTAGCGGCGCTTTTGG
*
5692043 AAAAACGCCGCTAATGACCAGAGCATTAGCGGCGCTTTT--
1 AAAAACGCCGCTAAAGACCAGAGCATTAGCGGCGCTTTTGG
*
5692082 ------G-TGCTAAAGACCAGAGCATTAGCGGCGCTTTTGG
1 AAAAACGCCGCTAAAGACCAGAGCATTAGCGGCGCTTTTGG
*
5692116 AAAAAAGCCGCTAAA
1 AAAAACGCCGCTAAA
5692131 AGTCACATAA
Statistics
Matches: 217, Mismatches: 21, Indels: 24
0.83 0.08 0.09
Matches are distributed among these distances:
32 29 0.13
33 1 0.00
40 56 0.26
41 130 0.60
42 1 0.00
ACGTcount: A:0.34, C:0.24, G:0.24, T:0.18
Consensus pattern (41 bp):
AAAAACGCCGCTAAAGACCAGAGCATTAGCGGCGCTTTTGG
Found at i:5692044 original size:122 final size:123
Alignment explanation
Indices: 5691857--5692079 Score: 351
Period size: 122 Copynumber: 1.8 Consensus size: 123
5691847 CCACTAAAAA
* *
5691857 CAGAGCAATAGCGGCGTTTTTCACAAAAACGCCGCTAAAGACAGAGCATTAGCAGCGCTTTTGGA
1 CAGAGCAATAGCGGCGCTTTTCACAAAAACGCCGCTAAAGACAGAGCATTAGCAGCGCTTATGGA
5691922 AAAACGCCGCTAAAGACCAGAGCATTAGC-GCGCTTATGGAAAAACGCCGCTACAGAC
66 AAAACGCCGCTAAAGACCAGAGCATTAGCGGCGCTTATGGAAAAACGCCGCTACAGAC
* ** * *
5691979 CAGAGCATTAGCGGCGCTTTTGGC-AAAACGCCGCTAAAGACCAGAGCATTAGCGGCTCTTATGG
1 CAGAGCAATAGCGGCGCTTTTCACAAAAACGCCGCTAAAGA-CAGAGCATTAGCAGCGCTTATGG
*
5692043 AAAAACGCCGCTAATGACCAGAGCATTAGCGGCGCTT
65 AAAAACGCCGCTAAAGACCAGAGCATTAGCGGCGCTT
5692080 TTGTGCTAAA
Statistics
Matches: 91, Mismatches: 8, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
121 16 0.18
122 69 0.76
123 6 0.07
ACGTcount: A:0.32, C:0.26, G:0.25, T:0.17
Consensus pattern (123 bp):
CAGAGCAATAGCGGCGCTTTTCACAAAAACGCCGCTAAAGACAGAGCATTAGCAGCGCTTATGGA
AAAACGCCGCTAAAGACCAGAGCATTAGCGGCGCTTATGGAAAAACGCCGCTACAGAC
Found at i:5692094 original size:32 final size:32
Alignment explanation
Indices: 5692052--5692114 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
5692042 GAAAAACGCC
*
5692052 GCTAATGACCAGAGCATTAGCGGCGCTTTTGT
1 GCTAAAGACCAGAGCATTAGCGGCGCTTTTGT
5692084 GCTAAAGACCAGAGCATTAGCGGCGCTTTTG
1 GCTAAAGACCAGAGCATTAGCGGCGCTTTTG
5692115 GAAAAAAGCC
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.24, C:0.22, G:0.29, T:0.25
Consensus pattern (32 bp):
GCTAAAGACCAGAGCATTAGCGGCGCTTTTGT
Found at i:5692321 original size:21 final size:21
Alignment explanation
Indices: 5692297--5692381 Score: 80
Period size: 21 Copynumber: 3.9 Consensus size: 21
5692287 CATTATAGTT
* *
5692297 TATGGTTTATGATTTAAGATA
1 TATGGTTTAGGGTTTAAGATA
* * *
5692318 TATGATTTAGGGTTTAAGGTT
1 TATGGTTTAGGGTTTAAGATA
*
5692339 TATGAGTTAACTATGGTTTAAGATA
1 TATG-GTT---TAGGGTTTAAGATA
5692364 TATGGTTTAGGGTTTAAG
1 TATGGTTTAGGGTTTAAG
5692382 GTTTAGGAGT
Statistics
Matches: 50, Mismatches: 10, Indels: 8
0.74 0.15 0.12
Matches are distributed among these distances:
21 30 0.60
22 2 0.04
24 3 0.06
25 15 0.30
ACGTcount: A:0.29, C:0.01, G:0.25, T:0.45
Consensus pattern (21 bp):
TATGGTTTAGGGTTTAAGATA
Found at i:5692361 original size:46 final size:46
Alignment explanation
Indices: 5692304--5692397 Score: 161
Period size: 46 Copynumber: 2.0 Consensus size: 46
5692294 GTTTATGGTT
*
5692304 TATGATTTAAGATATATGATTTAGGGTTTAAGGTTTATGAGTTAAC
1 TATGATTTAAGATATATGATTTAGGGTTTAAGGTTTAGGAGTTAAC
* *
5692350 TATGGTTTAAGATATATGGTTTAGGGTTTAAGGTTTAGGAGTTAAC
1 TATGATTTAAGATATATGATTTAGGGTTTAAGGTTTAGGAGTTAAC
5692396 TA
1 TA
5692398 GTATTTGAAG
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
46 45 1.00
ACGTcount: A:0.31, C:0.02, G:0.24, T:0.43
Consensus pattern (46 bp):
TATGATTTAAGATATATGATTTAGGGTTTAAGGTTTAGGAGTTAAC
Found at i:5692456 original size:6 final size:7
Alignment explanation
Indices: 5692424--5692494 Score: 65
Period size: 7 Copynumber: 10.1 Consensus size: 7
5692414 GATGAATTAT
5692424 GGGTTTA
1 GGGTTTA
5692431 GGGTTTA
1 GGGTTTA
5692438 GGGTTTAA
1 GGGTTT-A
5692446 GGG-TTA
1 GGGTTTA
5692452 GGG-TTA
1 GGGTTTA
*
5692458 GAGTTTA
1 GGGTTTA
* *
5692465 AGGTGTAA
1 GGGT-TTA
*
5692473 GGGTTTG
1 GGGTTTA
*
5692480 GGGTTAA
1 GGGTTTA
5692487 GGGTTTA
1 GGGTTTA
5692494 G
1 G
5692495 ACTTTAGTAT
Statistics
Matches: 51, Mismatches: 10, Indels: 6
0.76 0.15 0.09
Matches are distributed among these distances:
6 9 0.18
7 33 0.65
8 9 0.18
ACGTcount: A:0.20, C:0.00, G:0.44, T:0.37
Consensus pattern (7 bp):
GGGTTTA
Found at i:5693160 original size:17 final size:18
Alignment explanation
Indices: 5693128--5693162 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
5693118 CTTAATGAAT
*
5693128 TTAATAGCTACCATTTAA
1 TTAATAGCTACAATTTAA
5693146 TTAATA-CTACAATTTAA
1 TTAATAGCTACAATTTAA
5693163 AAATTTCAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.43, C:0.14, G:0.03, T:0.40
Consensus pattern (18 bp):
TTAATAGCTACAATTTAA
Found at i:5699253 original size:43 final size:43
Alignment explanation
Indices: 5699122--5699316 Score: 214
Period size: 43 Copynumber: 4.5 Consensus size: 43
5699112 AATTTTTTTA
* * *
5699122 AAAGGTCATGGTTTTTAACGGCGTTTATG-AAAAAGCGCCGCT
1 AAAGGTCATGGTCTTTAGCGGCGTTTGTGAAAAAAGCGCCGCT
* * * * * *
5699164 AAAGGTTATAGT-TTTCAGTGGCATTTTTTGAGAAAAGCGCCGCT
1 AAAGGTCATGGTCTTT-AGCGGC-GTTTGTGAAAAAAGCGCCGCT
* **
5699208 AAAGATCATGGTCTTTAGCGGCGTTTGTGGGAAAAGCGCCGCT
1 AAAGGTCATGGTCTTTAGCGGCGTTTGTGAAAAAAGCGCCGCT
* ** *
5699251 AAAGGTCATGGCCTTTAGCGGCGTTTGCAAAAAAAGAGCCGCT
1 AAAGGTCATGGTCTTTAGCGGCGTTTGTGAAAAAAGCGCCGCT
5699294 AAAGGTCATGGTCTTTAGCGGCG
1 AAAGGTCATGGTCTTTAGCGGCG
5699317 CCTGCTATAG
Statistics
Matches: 127, Mismatches: 22, Indels: 7
0.81 0.14 0.04
Matches are distributed among these distances:
41 3 0.02
42 14 0.11
43 81 0.64
44 26 0.20
45 3 0.02
ACGTcount: A:0.27, C:0.17, G:0.29, T:0.27
Consensus pattern (43 bp):
AAAGGTCATGGTCTTTAGCGGCGTTTGTGAAAAAAGCGCCGCT
Found at i:5700725 original size:23 final size:22
Alignment explanation
Indices: 5700678--5700731 Score: 72
Period size: 23 Copynumber: 2.4 Consensus size: 22
5700668 TATTTTATGC
* *
5700678 ATTATTATTGTTTTACCATAGT
1 ATTATTATTGTTTTAACATACT
*
5700700 ATTATTGTTGTTATTAACATACT
1 ATTATTATTGTT-TTAACATACT
5700723 ATTATTATT
1 ATTATTATT
5700732 ATCACATTTA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
22 11 0.41
23 16 0.59
ACGTcount: A:0.30, C:0.07, G:0.07, T:0.56
Consensus pattern (22 bp):
ATTATTATTGTTTTAACATACT
Found at i:5706615 original size:59 final size:59
Alignment explanation
Indices: 5706475--5706615 Score: 171
Period size: 60 Copynumber: 2.4 Consensus size: 59
5706465 TTTAGTGTTA
* *
5706475 ACTGGGCCTTAGCCCATATCAATATTAATCTGGGCCATAGCCCCTTACAGTAACAGAGTAT
1 ACTGGGCCTT-GCCCATATCAGTATCAATCTGGGCCATAGCCCCTTACAGT-ACAGAGTAT
* *
5706536 ACTGGGCCTAGCCCATATCAGTATCAATCTGGGCCGTAG-CCCTATACAAGT-C-GAGATAT
1 ACTGGGCCTTGCCCATATCAGTATCAATCTGGGCCATAGCCCCT-TAC-AGTACAGAG-TAT
*
5706595 ATTGGGCCTTGCCCATATCAG
1 ACTGGGCCTTGCCCATATCAG
5706616 CACAGTTGGG
Statistics
Matches: 71, Mismatches: 6, Indels: 8
0.84 0.07 0.09
Matches are distributed among these distances:
58 3 0.04
59 27 0.38
60 29 0.41
61 12 0.17
ACGTcount: A:0.27, C:0.27, G:0.21, T:0.26
Consensus pattern (59 bp):
ACTGGGCCTTGCCCATATCAGTATCAATCTGGGCCATAGCCCCTTACAGTACAGAGTAT
Found at i:5707257 original size:8 final size:8
Alignment explanation
Indices: 5707243--5707282 Score: 53
Period size: 8 Copynumber: 5.0 Consensus size: 8
5707233 TCACAAATGC
5707243 CGGCTTTT
1 CGGCTTTT
*
5707251 TGGCTTTT
1 CGGCTTTT
*
5707259 CGACTTTT
1 CGGCTTTT
*
5707267 TGGCTTTT
1 CGGCTTTT
5707275 CGGCTTTT
1 CGGCTTTT
5707283 ACCGATCTAG
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
8 26 1.00
ACGTcount: A:0.03, C:0.20, G:0.23, T:0.55
Consensus pattern (8 bp):
CGGCTTTT
Found at i:5707267 original size:16 final size:16
Alignment explanation
Indices: 5707246--5707282 Score: 65
Period size: 16 Copynumber: 2.3 Consensus size: 16
5707236 CAAATGCCGG
5707246 CTTTTTGGCTTTTCGA
1 CTTTTTGGCTTTTCGA
*
5707262 CTTTTTGGCTTTTCGG
1 CTTTTTGGCTTTTCGA
5707278 CTTTT
1 CTTTT
5707283 ACCGATCTAG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.03, C:0.19, G:0.19, T:0.59
Consensus pattern (16 bp):
CTTTTTGGCTTTTCGA
Found at i:5709190 original size:21 final size:23
Alignment explanation
Indices: 5709151--5709195 Score: 58
Period size: 21 Copynumber: 2.0 Consensus size: 23
5709141 TTCAAATACG
*
5709151 ATAATATATATATATTTTTAATA
1 ATAATATATATATAATTTTAATA
*
5709174 ATAATA-AT-TATAATTTTCATA
1 ATAATATATATATAATTTTAATA
5709195 A
1 A
5709196 ATCAATAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 12 0.60
22 2 0.10
23 6 0.30
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (23 bp):
ATAATATATATATAATTTTAATA
Found at i:5715580 original size:71 final size:71
Alignment explanation
Indices: 5715496--5715659 Score: 310
Period size: 71 Copynumber: 2.3 Consensus size: 71
5715486 CGATTTGTCT
5715496 CGTAGCTCTCTTGTCTACATGGTGTCCGTCACTTGGAATCACGCATGCGACCCAGCTACATTTAT
1 CGTAGCTCTCTTGTCTACATGGTGTCCGTCACTTGGAATCACGCATGCGACCCAGCTACATTTAT
5715561 CTTTCA
66 CTTTCA
* *
5715567 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
1 CGTAGCTCTCTTGTCTACATGGTGTCCGTCACTTGGAATCACGCATGCGACCCAGCTACATTTAT
5715632 CTTTCA
66 CTTTCA
5715638 CGTAGCTCTCTTGTCTACATGG
1 CGTAGCTCTCTTGTCTACATGG
5715660 GATACATCTC
Statistics
Matches: 91, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
71 91 1.00
ACGTcount: A:0.19, C:0.29, G:0.18, T:0.34
Consensus pattern (71 bp):
CGTAGCTCTCTTGTCTACATGGTGTCCGTCACTTGGAATCACGCATGCGACCCAGCTACATTTAT
CTTTCA
Found at i:5715697 original size:71 final size:70
Alignment explanation
Indices: 5715496--5715693 Score: 240
Period size: 71 Copynumber: 2.8 Consensus size: 70
5715486 CGATTTGTCT
* * * * *
5715496 CGTAGCTCTCTTGTCTACATGGTGTCCGTCACTTGGAATCACGCATGCGACCCAGCTACATTTAT
1 CGTAGCTCTCTTGTCTACATGGTGTACAT-ACTTCGAATCACACATGCGACCTAGCTACATTTAT
5715561 CTTTCA
65 CTTTCA
* * * *
5715567 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
1 CGTAGCTCTCTTGTCTACATGGTGTACAT-ACTTCGAATCACACATGCGACCTAGCTACATTTAT
5715632 CTTTCA
65 CTTTCA
* * *
5715638 CGTAGCTCTCTTGTCTACATGG-GATACAT-C-TCGTATCGCACATGTGACCTAGCTAC
1 CGTAGCTCTCTTGTCTACATGGTG-TACATACTTCGAATCACACATGCGACCTAGCTAC
5715694 TACAGGGTGT
Statistics
Matches: 117, Mismatches: 9, Indels: 5
0.89 0.07 0.04
Matches are distributed among these distances:
68 21 0.18
69 1 0.01
70 1 0.01
71 94 0.80
ACGTcount: A:0.20, C:0.29, G:0.18, T:0.33
Consensus pattern (70 bp):
CGTAGCTCTCTTGTCTACATGGTGTACATACTTCGAATCACACATGCGACCTAGCTACATTTATC
TTTCA
Found at i:5720035 original size:213 final size:213
Alignment explanation
Indices: 5719684--5720145 Score: 818
Period size: 213 Copynumber: 2.2 Consensus size: 213
5719674 CTGTTTTCAA
*
5719684 AAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTTTAATTTTTAAAATCAACTCTTATTGCGA
1 AAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTTTAATTTTTAAAATCAACTCATATTGCGA
* *
5719749 TAGGTGAGTTGAGCCTGGGTCATATGTCGAGGTATTTTCAAAATCTATTTTTAAGTTTCAAAAAG
66 GAGGTGAGTTGAGCCTGGGTCATATGTCGAGGTATTTTCAAAATCTACTTTTAAGTTTCAAAAAG
*
5719814 GCCAACTCATATGGCGAGAGGTGAGTTGAGCCTTGGCTCACATGCTGAGCTATTTTCAATTTCTG
131 GCCAACTCATATGGCGAGAGGTGAGTTGAGCCTTAGCTCACATGCTGAGCTATTTTCAATTTCTG
5719879 TTTTAATGTCTG-TTTTT
196 TTTTAATGTCTGTTTTTT
*
5719896 AAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTTTAATTTTTAAAATCATCTCATATTGCGA
1 AAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTTTAATTTTTAAAATCAACTCATATTGCGA
*
5719961 GAGGTGAGTTGAGCCTCGGGTCATATGTCGAGGTATTTTCAAAATCTGCTTTTAAGTTTCAAAAA
66 GAGGTGAGTTGAGCCT-GGGTCATATGTCGAGGTATTTTCAAAATCTACTTTTAAGTTTCAAAAA
* * *
5720026 GGCCAACTCATATGGCGAGAGGTGAGTTGAGCCTTAGTTCACGTGCTGAGCTATTTTCAATTTTT
130 GGCCAACTCATATGGCGAGAGGTGAGTTGAGCCTTAGCTCACATGCTGAGCTATTTTCAATTTCT
5720091 GTTTTAATGTCTGTTTTTTT
195 GTTTTAATGTCTG-TTTTTT
5720111 AAATCAACTCATATTGCGAGAGGTGAGTTGAGCCT
1 AAATCAACTCATATTGCGAGAGGTGAGTTGAGCCT
5720146 CAGGACACGC
Statistics
Matches: 238, Mismatches: 9, Indels: 3
0.95 0.04 0.01
Matches are distributed among these distances:
212 78 0.33
213 120 0.50
215 40 0.17
ACGTcount: A:0.26, C:0.15, G:0.22, T:0.37
Consensus pattern (213 bp):
AAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTTTAATTTTTAAAATCAACTCATATTGCGA
GAGGTGAGTTGAGCCTGGGTCATATGTCGAGGTATTTTCAAAATCTACTTTTAAGTTTCAAAAAG
GCCAACTCATATGGCGAGAGGTGAGTTGAGCCTTAGCTCACATGCTGAGCTATTTTCAATTTCTG
TTTTAATGTCTGTTTTTT
Found at i:5720142 original size:86 final size:85
Alignment explanation
Indices: 5720029--5720303 Score: 252
Period size: 73 Copynumber: 3.3 Consensus size: 85
5720019 TCAAAAAGGC
* * *
5720029 CAACTCATATGGCGAGAGGTGAGTTGAGCCTTAGTTCACGTGCTGAGCTATTTTCAATTTTTGTT
1 CAACTCATATTGCGAGAGGTGAGTTGAGCCTTAGCTCACGTGCTGAGCTATTTT-AATTTATGTT
***
5720094 TTAATGTCTGTTTTTTTAAAT
65 TTAATGTCTGTTTTCAAAAAT
* ** * *
5720115 CAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACAC--GCTGAGGTATTTTAA---AT-TTC
1 CAACTCATATTGCGAGAGGTGAGTTGAGCCTTAGCTCACGTGCTGAGCTATTTTAATTTATGTTT
5720174 T-AT-T-TG---TCAAAAAT
66 TAATGTCTGTTTTCAAAAAT
* * *
5720188 CAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGCTCACGTGTTGAGCTATTTTTAATTTCTGTT
1 CAACTCATATTGCGAGAGGTGAGTTGAGCCTTAGCTCACGTGCTGAGCTA-TTTTAATTTATGTT
*
5720253 TTAATGTCTGTTTT-AAAGAGT
65 TTAATGTCTGTTTTCAAA-AAT
* * **
5720274 CATATTCATATTACGAGAAATGAGTTGAGC
1 CA-ACTCATATTGCGAGAGGTGAGTTGAGC
5720304 TCAGGATCAC
Statistics
Matches: 151, Mismatches: 23, Indels: 29
0.74 0.11 0.14
Matches are distributed among these distances:
73 40 0.26
75 7 0.05
76 8 0.05
77 1 0.01
78 2 0.01
79 4 0.03
80 4 0.03
81 2 0.01
82 1 0.01
83 4 0.03
84 12 0.08
85 3 0.02
86 40 0.26
87 23 0.15
ACGTcount: A:0.26, C:0.15, G:0.22, T:0.38
Consensus pattern (85 bp):
CAACTCATATTGCGAGAGGTGAGTTGAGCCTTAGCTCACGTGCTGAGCTATTTTAATTTATGTTT
TAATGTCTGTTTTCAAAAAT
Found at i:5720256 original size:12 final size:12
Alignment explanation
Indices: 5720239--5720268 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
5720229 GTTGAGCTAT
*
5720239 TTTTAATTTCTG
1 TTTTAATGTCTG
5720251 TTTTAATGTCTG
1 TTTTAATGTCTG
5720263 TTTTAA
1 TTTTAA
5720269 AGAGTCATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.20, C:0.07, G:0.10, T:0.63
Consensus pattern (12 bp):
TTTTAATGTCTG
Found at i:5722280 original size:23 final size:22
Alignment explanation
Indices: 5722233--5722286 Score: 72
Period size: 23 Copynumber: 2.4 Consensus size: 22
5722223 TATTTTATGC
* *
5722233 ATTATTATTGTTTTACCATAGT
1 ATTATTATTGTTTTAACATACT
*
5722255 ATTATTGTTGTTATTAACATACT
1 ATTATTATTGTT-TTAACATACT
5722278 ATTATTATT
1 ATTATTATT
5722287 ATCACATTTA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
22 11 0.41
23 16 0.59
ACGTcount: A:0.30, C:0.07, G:0.07, T:0.56
Consensus pattern (22 bp):
ATTATTATTGTTTTAACATACT
Found at i:5726266 original size:23 final size:22
Alignment explanation
Indices: 5726219--5726272 Score: 72
Period size: 23 Copynumber: 2.4 Consensus size: 22
5726209 TATTTTATGC
* *
5726219 ATTATTATTGTTTTACCATAGT
1 ATTATTATTGTTTTAACATACT
*
5726241 ATTATTGTTGTTATTAACATACT
1 ATTATTATTGTT-TTAACATACT
5726264 ATTATTATT
1 ATTATTATT
5726273 ATCACATTTA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
22 11 0.41
23 16 0.59
ACGTcount: A:0.30, C:0.07, G:0.07, T:0.56
Consensus pattern (22 bp):
ATTATTATTGTTTTAACATACT
Found at i:5726586 original size:20 final size:22
Alignment explanation
Indices: 5726558--5726599 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
5726548 TTTACTATTG
5726558 AACATTATTA-TAATTTATTTT
1 AACATTATTATTAATTTATTTT
*
5726579 AACA-TATTATTATTTTATTTT
1 AACATTATTATTAATTTATTTT
5726600 CTTTATATCA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 5 0.26
21 14 0.74
ACGTcount: A:0.36, C:0.05, G:0.00, T:0.60
Consensus pattern (22 bp):
AACATTATTATTAATTTATTTT
Found at i:5733176 original size:59 final size:59
Alignment explanation
Indices: 5733036--5733176 Score: 180
Period size: 60 Copynumber: 2.4 Consensus size: 59
5733026 TTTAGTGTTA
* *
5733036 ACTGGGCCTTAGCCCATATCAATATTAATCTGGGCCATAGCCCCTTACAGTAACAGAGTAT
1 ACTGGGCCTT-GCCCATATCAGTATCAATCTGGGCCATAGCCCCTTACAGT-ACAGAGTAT
*
5733097 ACTGGGCCTAGCCCATATCAGTATCAATCTGGGCCATAG-CCCTATACAAGT-C-GAGATAT
1 ACTGGGCCTTGCCCATATCAGTATCAATCTGGGCCATAGCCCCT-TAC-AGTACAGAG-TAT
*
5733156 ATTGGGCCTTGCCCATATCAG
1 ACTGGGCCTTGCCCATATCAG
5733177 CACAGTTGGG
Statistics
Matches: 72, Mismatches: 5, Indels: 8
0.85 0.06 0.09
Matches are distributed among these distances:
58 3 0.04
59 27 0.38
60 30 0.42
61 12 0.17
ACGTcount: A:0.28, C:0.27, G:0.20, T:0.26
Consensus pattern (59 bp):
ACTGGGCCTTGCCCATATCAGTATCAATCTGGGCCATAGCCCCTTACAGTACAGAGTAT
Found at i:5733818 original size:8 final size:8
Alignment explanation
Indices: 5733804--5733843 Score: 53
Period size: 8 Copynumber: 5.0 Consensus size: 8
5733794 TCACAAATGC
5733804 CGGCTTTT
1 CGGCTTTT
*
5733812 TGGCTTTT
1 CGGCTTTT
*
5733820 CGACTTTT
1 CGGCTTTT
*
5733828 TGGCTTTT
1 CGGCTTTT
5733836 CGGCTTTT
1 CGGCTTTT
5733844 ACCGATCTAG
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
8 26 1.00
ACGTcount: A:0.03, C:0.20, G:0.23, T:0.55
Consensus pattern (8 bp):
CGGCTTTT
Found at i:5733828 original size:16 final size:16
Alignment explanation
Indices: 5733807--5733843 Score: 65
Period size: 16 Copynumber: 2.3 Consensus size: 16
5733797 CAAATGCCGG
5733807 CTTTTTGGCTTTTCGA
1 CTTTTTGGCTTTTCGA
*
5733823 CTTTTTGGCTTTTCGG
1 CTTTTTGGCTTTTCGA
5733839 CTTTT
1 CTTTT
5733844 ACCGATCTAG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.03, C:0.19, G:0.19, T:0.59
Consensus pattern (16 bp):
CTTTTTGGCTTTTCGA
Found at i:5734711 original size:39 final size:39
Alignment explanation
Indices: 5734630--5734703 Score: 102
Period size: 38 Copynumber: 2.0 Consensus size: 39
5734620 GGAAAAAAGA
*
5734630 AAAAGAAGAGGAGAAAGTAGATGGAGAGAAAAAGAAAAC
1 AAAAGAAGAAGAGAAAGTAGATGGAGAGAAAAAGAAAAC
5734669 AAAAGAAGAAG-GAAAG-AGAATGGA-AG-AAAAGAAAA
1 AAAAGAAGAAGAGAAAGTAG-ATGGAGAGAAAAAGAAAA
5734704 TATCAAAACC
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
36 9 0.27
37 4 0.12
38 10 0.30
39 10 0.30
ACGTcount: A:0.65, C:0.01, G:0.30, T:0.04
Consensus pattern (39 bp):
AAAAGAAGAAGAGAAAGTAGATGGAGAGAAAAAGAAAAC
Found at i:5735810 original size:21 final size:23
Alignment explanation
Indices: 5735771--5735815 Score: 58
Period size: 21 Copynumber: 2.0 Consensus size: 23
5735761 TTCAAATACG
*
5735771 ATAATATATATATATTTTTAATA
1 ATAATATATATATAATTTTAATA
*
5735794 ATAATA-AT-TATAATTTTCATA
1 ATAATATATATATAATTTTAATA
5735815 A
1 A
5735816 ATCAATAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 12 0.60
22 2 0.10
23 6 0.30
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (23 bp):
ATAATATATATATAATTTTAATA
Found at i:5743942 original size:85 final size:83
Alignment explanation
Indices: 5743661--5743952 Score: 260
Period size: 83 Copynumber: 3.5 Consensus size: 83
5743651 ACCTTTTAAT
* * * * * *
5743661 TTTTAAAATCAACTCATATTGCGATAGGTGAGTTGAGCCTCGGGTCATATGTC-GAGGTATTTTC
1 TTTTAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCT-AGG-CACACGGCTGAGCTATTTTC
**
5743725 AAAATCTGCTTTTAA-G--T-
64 AATTTCTG-TTTTAATGTCTA
** * * * * *
5743742 TTCAAAAAGGCCAACTCATATGGCGAGAGGTGAGTTGAGCCTTGGCTCACGTGTTGAGCTATTTT
1 TTTTAAAA--TCAACTCATATTGCGAGAGGTGAGTTGAGCCTAGGCACACG-GCTGAGCTATTTT
5743807 CAATTTCTGTTTTAATGTCTA
63 CAATTTCTGTTTTAATGTCTA
* *
5743828 TTTTTAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGG-ACAC-GCTGAGGTATTTTCA
1 TTTTAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCT-AGGCACACGGCTGAGCTATTTTCA
5743891 ATTTCTGTATTTTCAAT-T-TAA
65 ATTTCTG--TTTT-AATGTCT-A
5743912 TTTTCAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCT
1 TTTT-AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCT
5743953 TTTAATTTTT
Statistics
Matches: 173, Mismatches: 24, Indels: 24
0.78 0.11 0.11
Matches are distributed among these distances:
81 9 0.05
82 28 0.16
83 47 0.27
84 43 0.25
85 41 0.24
86 5 0.03
ACGTcount: A:0.27, C:0.16, G:0.21, T:0.36
Consensus pattern (83 bp):
TTTTAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTAGGCACACGGCTGAGCTATTTTCAA
TTTCTGTTTTAATGTCTA
Found at i:5743974 original size:46 final size:46
Alignment explanation
Indices: 5743907--5743998 Score: 166
Period size: 46 Copynumber: 2.0 Consensus size: 46
5743897 GTATTTTCAA
5743907 TTTAATTTTCAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCT
1 TTTAATTTTCAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCT
* *
5743953 TTTAATTTTTAAAATCAACTCATATTGTGAGAGGTGAGTTGAGCCT
1 TTTAATTTTCAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCT
5743999 CGGGTCATAT
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
46 44 1.00
ACGTcount: A:0.30, C:0.13, G:0.20, T:0.37
Consensus pattern (46 bp):
TTTAATTTTCAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCT
Found at i:5743996 original size:215 final size:213
Alignment explanation
Indices: 5743753--5744167 Score: 489
Period size: 215 Copynumber: 1.9 Consensus size: 213
5743743 TCAAAAAGGC
* * ** **
5743753 CAACTCATATGGCGAGAGGTGAGTTGAGCCTTGGCTCACGTGTTGAGCTATTTTCAATTTCTG-T
1 CAACTCATATGGCGAGAGGTGAGTTGAGCCTCGGCTCACATGTCAAGCTATTTTCAAAATCTGCT
*** * * *
5743817 TTTAATGTCTATTTTTAAA-TCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACAC-GCTG
66 TTTAA-G--T-TTCAAAAAGCCAACTCATATGGCGAGAGGTGAGTTGAGCCTCAGCACACGGCTG
*
5743880 AGGTATTTTCAATTTCTGTATTTTCAAT-T-TAATTTTCAAAATCAACTCATATTGCGAGAGGTG
127 AGCTATTTTCAATTTCTG--TTTT-AATGTCTAATTTTCAAAATCAACTCATATTGCGAGAGGTG
5743943 AGTTGAGCCTTTTAATTTTTAAAAT
189 AGTTGAGCCTTTTAATTTTTAAAAT
* * * * *
5743968 CAACTCATATTGTGAGAGGTGAGTTGAGCCTCGGGTCATATGTCAAGGTATTTTCAAAATCTGCT
1 CAACTCATATGGCGAGAGGTGAGTTGAGCCTCGGCTCACATGTCAAGCTATTTTCAAAATCTGCT
* * *
5744033 TTTAAGTTTCAAAAAGGCCAACTCATATGGCGAGAGGTGAGTTGAGTCTTAGCTCACGTGCTGAG
66 TTTAAGTTTCAAAAA-GCCAACTCATATGGCGAGAGGTGAGTTGAGCCTCAGCACACG-GCTGAG
** **
5744098 CTATTTTCAATTTCTGTTTTAATGTCTGTTTTTTTAAATCAACTCATATTGCGAGAGGTGAGTTG
129 CTATTTTCAATTTCTGTTTTAATGTCTAATTTTCAAAATCAACTCATATTGCGAGAGGTGAGTTG
5744163 AGCCT
194 AGCCT
5744168 CAGGACACGC
Statistics
Matches: 168, Mismatches: 25, Indels: 14
0.81 0.12 0.07
Matches are distributed among these distances:
212 5 0.03
213 4 0.02
214 39 0.23
215 93 0.55
216 27 0.16
ACGTcount: A:0.26, C:0.16, G:0.21, T:0.37
Consensus pattern (213 bp):
CAACTCATATGGCGAGAGGTGAGTTGAGCCTCGGCTCACATGTCAAGCTATTTTCAAAATCTGCT
TTTAAGTTTCAAAAAGCCAACTCATATGGCGAGAGGTGAGTTGAGCCTCAGCACACGGCTGAGCT
ATTTTCAATTTCTGTTTTAATGTCTAATTTTCAAAATCAACTCATATTGCGAGAGGTGAGTTGAG
CCTTTTAATTTTTAAAAT
Found at i:5744161 original size:86 final size:85
Alignment explanation
Indices: 5744051--5744291 Score: 281
Period size: 73 Copynumber: 3.0 Consensus size: 85
5744041 TCAAAAAGGC
* * *
5744051 CAACTCATATGGCGAGAGGTGAGTTGAGTCTTAGCTCACGTGCTGAGCTATTTTCAATTTCTGTT
1 CAACTCATATTGCGAGAGGTGAGTTGAGCCTTAGCTCACGTGCTGAGCTATTTTAAATTTCTGTT
**
5744116 TTAATGTCTGTTTTTTTAAAT
66 TTAATGTCTG-TTTTAAAAAT
* ** *
5744137 CAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACAC--GCTGAGGTATTTTAAATTTCTG--
1 CAACTCATATTGCGAGAGGTGAGTTGAGCCTTAGCTCACGTGCTGAGCTATTTTAAATTTCTGTT
5744198 TT--TGTC------AAAAAT
66 TTAATGTCTGTTTTAAAAAT
* * *
5744210 CAACTCATATTGCGAGAGGTGAGTTGAGCCTTAGCTCACGTGTTGAGCTATTTTTAATTTCTATT
1 CAACTCATATTGCGAGAGGTGAGTTGAGCCTTAGCTCACGTGCTGAGCTATTTTAAATTTCTGTT
5744275 TTAATGTCTGTTTTAAA
66 TTAATGTCTGTTTTAAA
5744292 GAGTTATATT
Statistics
Matches: 127, Mismatches: 16, Indels: 25
0.76 0.10 0.15
Matches are distributed among these distances:
73 40 0.31
75 18 0.14
77 2 0.02
79 4 0.03
80 4 0.03
82 2 0.02
84 20 0.16
85 3 0.02
86 34 0.27
ACGTcount: A:0.25, C:0.15, G:0.21, T:0.39
Consensus pattern (85 bp):
CAACTCATATTGCGAGAGGTGAGTTGAGCCTTAGCTCACGTGCTGAGCTATTTTAAATTTCTGTT
TTAATGTCTGTTTTAAAAAT
Found at i:5752914 original size:46 final size:44
Alignment explanation
Indices: 5752814--5752921 Score: 135
Period size: 44 Copynumber: 2.4 Consensus size: 44
5752804 TGTCTTTGAC
** * * *
5752814 ATGGACTTACATGAATTATTCCTGTCTCCAATGCCATATATAAT
1 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATATAAT
* *
5752858 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCTATATTTCTAAT
1 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATA--TATAAT
5752904 ATGGACTTACATGGCTCA
1 ATGGACTTACATGGCTCA
5752922 TTTCTGTTCT
Statistics
Matches: 55, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
44 32 0.58
46 23 0.42
ACGTcount: A:0.30, C:0.22, G:0.14, T:0.34
Consensus pattern (44 bp):
ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATATAAT
Found at i:5759272 original size:28 final size:28
Alignment explanation
Indices: 5759175--5759275 Score: 103
Period size: 29 Copynumber: 3.5 Consensus size: 28
5759165 ATTTAAGCCC
* *** *
5759175 GCACACATAGTGCCATACCCTTCGAGCT
1 GCACACTTAGTGCCATATATTTCCAGCT
** * *
5759203 CGCACACCCAGTGCCGTATTTTTCCAGCAT
1 -GCACACTTAGTGCCATATATTTCCAGC-T
5759233 GCACACTTAGTGCCATATATTTCCAGCT
1 GCACACTTAGTGCCATATATTTCCAGCT
5759261 GCACACTTAGTGCCA
1 GCACACTTAGTGCCA
5759276 ATCTCGTCAC
Statistics
Matches: 60, Mismatches: 11, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
28 16 0.27
29 43 0.72
30 1 0.02
ACGTcount: A:0.24, C:0.34, G:0.17, T:0.26
Consensus pattern (28 bp):
GCACACTTAGTGCCATATATTTCCAGCT
Found at i:5760483 original size:25 final size:23
Alignment explanation
Indices: 5760447--5760493 Score: 67
Period size: 25 Copynumber: 2.0 Consensus size: 23
5760437 TTTTTTTCCT
5760447 TTTCTTTGTTTTTCTTCATATTCTC
1 TTTCTTTGTTTTT-TTCAT-TTCTC
*
5760472 TTTCTTTTTTTTTTTCATTTCT
1 TTTCTTTGTTTTTTTCATTTCT
5760494 TTATTCTTCT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 4 0.19
24 5 0.24
25 12 0.57
ACGTcount: A:0.06, C:0.17, G:0.02, T:0.74
Consensus pattern (23 bp):
TTTCTTTGTTTTTTTCATTTCTC
Found at i:5760501 original size:24 final size:25
Alignment explanation
Indices: 5760447--5760493 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 25
5760437 TTTTTTTCCT
5760447 TTTCTTTGTTTTTCTTCATATTCTC
1 TTTCTTTGTTTTTCTTCATATTCTC
*
5760472 TTTCTTT-TTTTTTTTCAT-TTCT
1 TTTCTTTGTTTTTCTTCATATTCT
5760494 TTATTCTTCT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 4 0.19
24 10 0.48
25 7 0.33
ACGTcount: A:0.06, C:0.17, G:0.02, T:0.74
Consensus pattern (25 bp):
TTTCTTTGTTTTTCTTCATATTCTC
Found at i:5761466 original size:26 final size:26
Alignment explanation
Indices: 5761387--5761477 Score: 80
Period size: 26 Copynumber: 3.4 Consensus size: 26
5761377 AAAAAGAAAT
*
5761387 ATAATATATAAACAA-AATTAA-GTAAA
1 ATAATA-ATAAATAATAA-TAAGGTAAA
* * *
5761413 ATGATGATATAAATAATAATATGTTAAA
1 ATAAT-A-ATAAATAATAATAAGGTAAA
5761441 ATAAATAATAAAT-ATAATAAGGTAAA
1 AT-AATAATAAATAATAATAAGGTAAA
5761467 ATAATAATAAA
1 ATAATAATAAA
5761478 AGTATGTTTA
Statistics
Matches: 54, Mismatches: 7, Indels: 9
0.77 0.10 0.13
Matches are distributed among these distances:
25 9 0.17
26 17 0.31
27 17 0.31
28 9 0.17
29 2 0.04
ACGTcount: A:0.63, C:0.01, G:0.07, T:0.30
Consensus pattern (26 bp):
ATAATAATAAATAATAATAAGGTAAA
Found at i:5763522 original size:30 final size:30
Alignment explanation
Indices: 5763488--5763610 Score: 112
Period size: 30 Copynumber: 4.2 Consensus size: 30
5763478 GTGGAGAGGA
*
5763488 AGGTGGGCACAACAATGGTGATGGAGCTAG
1 AGGTGGGCACAACAATGGTGGTGGAGCTAG
* ***
5763518 AGGT-GG--TAATGGTGGTGGTGGAGCTAG
1 AGGTGGGCACAACAATGGTGGTGGAGCTAG
****
5763545 AGGTGGGCATGGTAATGGTGGTGGAG--AGG
1 AGGTGGGCACAACAATGGTGGTGGAGCTA-G
5763574 AAGGTGGGCACAACAATGGTGGTGGAGCTAG
1 -AGGTGGGCACAACAATGGTGGTGGAGCTAG
5763605 AGGTGG
1 AGGTGG
5763611 TGGTGGTGGT
Statistics
Matches: 73, Mismatches: 13, Indels: 14
0.73 0.13 0.14
Matches are distributed among these distances:
27 20 0.27
28 3 0.04
29 3 0.04
30 45 0.62
31 1 0.01
32 1 0.01
ACGTcount: A:0.24, C:0.08, G:0.48, T:0.20
Consensus pattern (30 bp):
AGGTGGGCACAACAATGGTGGTGGAGCTAG
Found at i:5763556 original size:27 final size:27
Alignment explanation
Indices: 5763503--5763557 Score: 83
Period size: 27 Copynumber: 2.0 Consensus size: 27
5763493 GGCACAACAA
*
5763503 TGGTGATGGAGCTAGAGGTGGTAATGG
1 TGGTGATGGAGCTAGAGGTGGGAATGG
* *
5763530 TGGTGGTGGAGCTAGAGGTGGGCATGG
1 TGGTGATGGAGCTAGAGGTGGGAATGG
5763557 T
1 T
5763558 AATGGTGGTG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.18, C:0.05, G:0.51, T:0.25
Consensus pattern (27 bp):
TGGTGATGGAGCTAGAGGTGGGAATGG
Found at i:5763563 original size:27 final size:27
Alignment explanation
Indices: 5763509--5763565 Score: 78
Period size: 27 Copynumber: 2.1 Consensus size: 27
5763499 ACAATGGTGA
* **
5763509 TGGAGCTAGAGGTGGTAATGGTGGTGG
1 TGGAGCTAGAGGTGGGAATGGTAATGG
*
5763536 TGGAGCTAGAGGTGGGCATGGTAATGG
1 TGGAGCTAGAGGTGGGAATGGTAATGG
5763563 TGG
1 TGG
5763566 TGGAGAGGAA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.19, C:0.05, G:0.51, T:0.25
Consensus pattern (27 bp):
TGGAGCTAGAGGTGGGAATGGTAATGG
Found at i:5763612 original size:3 final size:3
Alignment explanation
Indices: 5763606--5763640 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
5763596 TGGAGCTAGA
5763606 GGT GGT GGT GGT GGT GGT GGT GGT GGT GGT GGT GG
1 GGT GGT GGT GGT GGT GGT GGT GGT GGT GGT GGT GG
5763641 AGGAGCTAGA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.00, C:0.00, G:0.69, T:0.31
Consensus pattern (3 bp):
GGT
Found at i:5764384 original size:22 final size:22
Alignment explanation
Indices: 5764345--5764403 Score: 70
Period size: 21 Copynumber: 2.8 Consensus size: 22
5764335 GTTTTAAGAA
*
5764345 TTGTTTTAGTA-TTATTTTTAT
1 TTGTTTTAATATTTATTTTTAT
5764366 TTGTTTTAATATTTATTTTTAT
1 TTGTTTTAATATTTATTTTTAT
* *
5764388 GT-TTTTAA-ATATATTT
1 TTGTTTTAATATTTATTT
5764404 GATTTATTAT
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
20 7 0.21
21 16 0.47
22 11 0.32
ACGTcount: A:0.24, C:0.00, G:0.07, T:0.69
Consensus pattern (22 bp):
TTGTTTTAATATTTATTTTTAT
Found at i:5764420 original size:26 final size:24
Alignment explanation
Indices: 5764374--5764433 Score: 75
Period size: 26 Copynumber: 2.4 Consensus size: 24
5764364 ATTTGTTTTA
*
5764374 ATATTTATTTTTATGTTTTTAAAT
1 ATATTTATTTTTATATTTTTAAAT
5764398 ATATTTGATTTATTATATTTTTAAAT
1 ATATTT-ATTT-TTATATTTTTAAAT
* *
5764424 TTTTTTATTT
1 ATATTTATTT
5764434 AATGAAATAA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
24 6 0.19
25 8 0.26
26 17 0.55
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.68
Consensus pattern (24 bp):
ATATTTATTTTTATATTTTTAAAT
Found at i:5766679 original size:35 final size:35
Alignment explanation
Indices: 5766637--5766704 Score: 111
Period size: 35 Copynumber: 1.9 Consensus size: 35
5766627 GATACACAAA
*
5766637 TCGGGCCTGTGCCCATGTT-AGATACAGATACAGAT
1 TCGGGCCTGAGCCCAT-TTCAGATACAGATACAGAT
5766672 TCGGGCCTGAGCCCATTTCAGATACAGATACAG
1 TCGGGCCTGAGCCCATTTCAGATACAGATACAG
5766705 TTACAGATAT
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
34 2 0.06
35 29 0.94
ACGTcount: A:0.26, C:0.25, G:0.25, T:0.24
Consensus pattern (35 bp):
TCGGGCCTGAGCCCATTTCAGATACAGATACAGAT
Found at i:5769221 original size:2 final size:2
Alignment explanation
Indices: 5769214--5769247 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
5769204 GTCATATACC
5769214 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5769248 GTATGTATCT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5772014 original size:46 final size:46
Alignment explanation
Indices: 5771962--5772179 Score: 253
Period size: 46 Copynumber: 4.7 Consensus size: 46
5771952 TGGGCATTCG
5771962 AACTCGTTGAGTTGAGTTCGAGTTCACTTATGGATGCGAACGTCCA
1 AACTCGTTGAGTTGAGTTCGAGTTCACTTATGGATGCGAACGTCCA
* * *
5772008 AACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCG
1 AACTCGTTGAGTTGAGTTCGAGTTCACTTATGGATGCGAACGTCCA
* * * * * * *
5772054 AACTCGTCGAGTTGAGTTCGAGTTCA-TGAAATGTA-ACTAGGCATCCA
1 AACTCGTTGAGTTGAGTTCGAGTTCACT--TATGGATGCGA-ACGTCCA
* *
5772101 AACTCGTTGAGTTGAG-TCTGAGTTCACTTATGGATGCGAACGCCCG
1 AACTCGTTGAGTTGAGTTC-GAGTTCACTTATGGATGCGAACGTCCA
* *
5772147 AGCTCGTTGAGTTGAGTTCGAGTTCGCTTATGG
1 AACTCGTTGAGTTGAGTTCGAGTTCACTTATGG
5772180 GCGGGTTACA
Statistics
Matches: 141, Mismatches: 24, Indels: 14
0.79 0.13 0.08
Matches are distributed among these distances:
45 1 0.01
46 106 0.75
47 33 0.23
48 1 0.01
ACGTcount: A:0.23, C:0.19, G:0.28, T:0.30
Consensus pattern (46 bp):
AACTCGTTGAGTTGAGTTCGAGTTCACTTATGGATGCGAACGTCCA
Found at i:5775580 original size:51 final size:51
Alignment explanation
Indices: 5775500--5775607 Score: 171
Period size: 51 Copynumber: 2.1 Consensus size: 51
5775490 CAATGGCAAT
* *
5775500 TGATAAGTGGTAGCTTTAACTACATTTATCTGATCAGTAACAATTGACAAG
1 TGATAAGTGGTAGCTTTAACTACACTTATCTGATCAGTAACAAGTGACAAG
* * *
5775551 TGATAAGTGGTAGCTTTAGCTACACTTATCTTATCAGTGACAAGTGACAAG
1 TGATAAGTGGTAGCTTTAACTACACTTATCTGATCAGTAACAAGTGACAAG
5775602 TGATAA
1 TGATAA
5775608 ATGCGATCCG
Statistics
Matches: 52, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
51 52 1.00
ACGTcount: A:0.34, C:0.14, G:0.19, T:0.32
Consensus pattern (51 bp):
TGATAAGTGGTAGCTTTAACTACACTTATCTGATCAGTAACAAGTGACAAG
Found at i:5779318 original size:33 final size:32
Alignment explanation
Indices: 5779274--5779341 Score: 109
Period size: 33 Copynumber: 2.1 Consensus size: 32
5779264 ACCAACATAC
* *
5779274 AAAGTATAATTAAATAATGCATGATATACAAA
1 AAAGTATAATTAAATAATGCATAACATACAAA
5779306 AAAGTGATAATTAAATAATGCATAACATACAAA
1 AAAGT-ATAATTAAATAATGCATAACATACAAA
5779339 AAA
1 AAA
5779342 AAAAAAGTAA
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
32 5 0.15
33 28 0.85
ACGTcount: A:0.59, C:0.07, G:0.09, T:0.25
Consensus pattern (32 bp):
AAAGTATAATTAAATAATGCATAACATACAAA
Found at i:5779918 original size:11 final size:10
Alignment explanation
Indices: 5779889--5780020 Score: 56
Period size: 11 Copynumber: 12.6 Consensus size: 10
5779879 ATATATGTAA
*
5779889 AATAATATAT
1 AATAATAAAT
5779899 AATATATAAAT
1 AATA-ATAAAT
5779910 AATTAATAAAT
1 AA-TAATAAAT
*
5779921 ACATAATACA-
1 A-ATAATAAAT
* *
5779931 AGTAAAAAAT
1 AATAATAAAT
**
5779941 AATAA-CGAT
1 AATAATAAAT
*
5779950 GAAAAAT-AAT
1 -AATAATAAAT
**
5779960 AATAATTTAT
1 AATAATAAAT
*
5779970 GAAAAATAAA-
1 -AATAATAAAT
5779980 ATATAATAAAT
1 A-ATAATAAAT
5779991 AATAATATAAAT
1 AAT-A-ATAAAT
5780003 AATATATAAAT
1 AATA-ATAAAT
5780014 AGATAAT
1 A-ATAAT
5780021 TATATAATAT
Statistics
Matches: 93, Mismatches: 16, Indels: 25
0.69 0.12 0.19
Matches are distributed among these distances:
9 13 0.14
10 26 0.28
11 39 0.42
12 15 0.16
ACGTcount: A:0.64, C:0.02, G:0.04, T:0.30
Consensus pattern (10 bp):
AATAATAAAT
Done.