Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032244.1 Gossypioides kirkii chromosome KI_01
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: 38174113
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 1000 characters in sequence are not A, C, G, or T
File 83 of 126
Found at i:25235772 original size:41 final size:40
Alignment explanation
Indices: 25235665--25235836 Score: 233
Period size: 41 Copynumber: 4.2 Consensus size: 40
25235655 AGGTTCATGT
25235665 GTCTTCCTTTTTAACAATCTTATGCTCTACCGAGT-ATAA
1 GTCTTCCTTTTTAACAATCTTATGCTCTACCGAGTCATAA
25235704 GTCTTCC-TTTTAACAATCTTATGCTCTACCGAGTCATAA
1 GTCTTCCTTTTTAACAATCTTATGCTCTACCGAGTCATAA
*
25235743 GTCTTCGTTTTTAAACAATCTTATGCTCTACCGAGTCATAA
1 GTCTTCCTTTTT-AACAATCTTATGCTCTACCGAGTCATAA
* ** *
25235784 GTCTTCC-TTTTAACAATATTCTAATGCTCCTTTCGAGTCATGA
1 GTCTTCCTTTTTAAC-A-A-TCTTATGCT-CTACCGAGTCATAA
25235827 GTCTTCCTTT
1 GTCTTCCTTT
25235837 ATCACATTCT
Statistics
Matches: 119, Mismatches: 6, Indels: 11
0.88 0.04 0.08
Matches are distributed among these distances:
38 27 0.23
39 20 0.17
40 9 0.08
41 35 0.29
42 8 0.07
43 18 0.15
44 2 0.02
ACGTcount: A:0.24, C:0.24, G:0.11, T:0.41
Consensus pattern (40 bp):
GTCTTCCTTTTTAACAATCTTATGCTCTACCGAGTCATAA
Found at i:25248212 original size:6 final size:6
Alignment explanation
Indices: 25248201--25248225 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
25248191 AATCATTCAC
25248201 AAATAT AAATAT AAATAT AAATAT A
1 AAATAT AAATAT AAATAT AAATAT A
25248226 TTATTTAAGG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (6 bp):
AAATAT
Found at i:25267526 original size:13 final size:13
Alignment explanation
Indices: 25267508--25267547 Score: 53
Period size: 13 Copynumber: 2.9 Consensus size: 13
25267498 ATTGTGAAGG
25267508 ATATTAATCTAAA
1 ATATTAATCTAAA
25267521 ATATTAATCTAAA
1 ATATTAATCTAAA
*
25267534 CTAATTTAATCTAA
1 AT-A-TTAATCTAA
25267548 GTTAAAGCTA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
13 14 0.58
14 1 0.04
15 9 0.38
ACGTcount: A:0.50, C:0.10, G:0.00, T:0.40
Consensus pattern (13 bp):
ATATTAATCTAAA
Found at i:25269203 original size:40 final size:40
Alignment explanation
Indices: 25269155--25269426 Score: 332
Period size: 40 Copynumber: 6.8 Consensus size: 40
25269145 CACTAAGCCA
* **
25269155 TAGCTTGAATCACATCATCGACTCAAAGCCTATTAAG-CTG
1 TAGCTTGAATCACATCACCGACTCAAAGCCTGCTAAGTC-G
* *
25269195 TAGCTTGAATCAAATCACCTG-CTCAAAGCTTGCTAAGTCG
1 TAGCTTGAATCACATCACC-GACTCAAAGCCTGCTAAGTCG
** *
25269235 TAGCTTGAATCACATCATTGGCTCAAAGCCTGCTAAGTCG
1 TAGCTTGAATCACATCACCGACTCAAAGCCTGCTAAGTCG
* * * * *
25269275 TAGGTTGAATCACATCACTGACTCAAAACATGCTAAGTCA
1 TAGCTTGAATCACATCACCGACTCAAAGCCTGCTAAGTCG
*
25269315 TAGCTTGAATCACATCACCGACTCAAAGCCTGCTAAGCCG
1 TAGCTTGAATCACATCACCGACTCAAAGCCTGCTAAGTCG
* * * *
25269355 TAGCTTGAATTACATCACCAACTCAAAGCCCGCTAAGCCG
1 TAGCTTGAATCACATCACCGACTCAAAGCCTGCTAAGTCG
* *
25269395 TAGCGTGAATTACATCACCGACTCAAAGCCTG
1 TAGCTTGAATCACATCACCGACTCAAAGCCTG
25269427 TTAATCTCTA
Statistics
Matches: 202, Mismatches: 27, Indels: 6
0.86 0.11 0.03
Matches are distributed among these distances:
39 1 0.00
40 199 0.99
41 2 0.01
ACGTcount: A:0.32, C:0.27, G:0.17, T:0.24
Consensus pattern (40 bp):
TAGCTTGAATCACATCACCGACTCAAAGCCTGCTAAGTCG
Found at i:25271641 original size:30 final size:29
Alignment explanation
Indices: 25271592--25271655 Score: 76
Period size: 30 Copynumber: 2.2 Consensus size: 29
25271582 TTTTTTGATC
* *
25271592 TTTTAATTGAATCCTTTTTATTTTTAATTT
1 TTTTAATTGAATCCATTTTACTTTT-ATTT
*
25271622 ATTTTAATTGCA-CCATTTTACTTTTATTT
1 -TTTTAATTGAATCCATTTTACTTTTATTT
25271651 TTTTA
1 TTTTA
25271656 GCAATTTAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
28 5 0.17
29 4 0.13
30 11 0.37
31 10 0.33
ACGTcount: A:0.23, C:0.09, G:0.03, T:0.64
Consensus pattern (29 bp):
TTTTAATTGAATCCATTTTACTTTTATTT
Found at i:25271749 original size:6 final size:6
Alignment explanation
Indices: 25271738--25271783 Score: 60
Period size: 6 Copynumber: 8.0 Consensus size: 6
25271728 TTTAGTCCCC
* *
25271738 TTATTT TTATTT TTATTT TTA-TT TTA-TT TTAATT TTATTT TAATTT
1 TTATTT TTATTT TTATTT TTATTT TTATTT TTATTT TTATTT TTATTT
25271784 AATCTTTTCT
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
5 10 0.27
6 27 0.73
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (6 bp):
TTATTT
Found at i:25271756 original size:5 final size:5
Alignment explanation
Indices: 25271742--25271784 Score: 50
Period size: 5 Copynumber: 8.0 Consensus size: 5
25271732 GTCCCCTTAT
*
25271742 TTTTA TTTTTA TTTTTA TTTTA TTTTAA TTTTA TTTTA ATTTA
1 TTTTA -TTTTA -TTTTA TTTTA TTTT-A TTTTA TTTTA TTTTA
25271785 ATCTTTTCTT
Statistics
Matches: 35, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
5 19 0.54
6 16 0.46
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (5 bp):
TTTTA
Found at i:25271762 original size:11 final size:11
Alignment explanation
Indices: 25271742--25271783 Score: 66
Period size: 11 Copynumber: 3.8 Consensus size: 11
25271732 GTCCCCTTAT
*
25271742 TTTTATTTTTA
1 TTTTAATTTTA
*
25271753 TTTTTATTTTA
1 TTTTAATTTTA
25271764 TTTTAATTTTA
1 TTTTAATTTTA
25271775 TTTTAATTT
1 TTTTAATTT
25271784 AATCTTTTCT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 28 1.00
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (11 bp):
TTTTAATTTTA
Found at i:25288931 original size:6 final size:6
Alignment explanation
Indices: 25288922--25288952 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
25288912 ACTGGTCGCT
*
25288922 GTCGAG GTCGAG GTTGAG GTCGAG GTCGAG G
1 GTCGAG GTCGAG GTCGAG GTCGAG GTCGAG G
25288953 CCGTATTGCT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.16, C:0.13, G:0.52, T:0.19
Consensus pattern (6 bp):
GTCGAG
Found at i:25291339 original size:27 final size:27
Alignment explanation
Indices: 25291293--25291359 Score: 91
Period size: 27 Copynumber: 2.5 Consensus size: 27
25291283 TTAACCTGCC
25291293 CATTGAC-TTGACCCGCTGACCCGACT
1 CATTGACTTTGACCCGCTGACCCGACT
* *
25291319 CATTGACTTTGACCCGTTGACCCGATT
1 CATTGACTTTGACCCGCTGACCCGACT
* *
25291346 TATTAACTTTGACC
1 CATTGACTTTGACC
25291360 TTTTGACTTT
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
26 7 0.19
27 29 0.81
ACGTcount: A:0.21, C:0.31, G:0.16, T:0.31
Consensus pattern (27 bp):
CATTGACTTTGACCCGCTGACCCGACT
Found at i:25293402 original size:36 final size:36
Alignment explanation
Indices: 25293361--25293429 Score: 138
Period size: 36 Copynumber: 1.9 Consensus size: 36
25293351 TGGAGAAATA
25293361 AGAGTTGCAAAAGAGGCAAGATTAAGTAGGGAGAAG
1 AGAGTTGCAAAAGAGGCAAGATTAAGTAGGGAGAAG
25293397 AGAGTTGCAAAAGAGGCAAGATTAAGTAGGGAG
1 AGAGTTGCAAAAGAGGCAAGATTAAGTAGGGAG
25293430 GAGATCAAGT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.43, C:0.06, G:0.36, T:0.14
Consensus pattern (36 bp):
AGAGTTGCAAAAGAGGCAAGATTAAGTAGGGAGAAG
Found at i:25296008 original size:51 final size:50
Alignment explanation
Indices: 25295918--25296115 Score: 140
Period size: 50 Copynumber: 4.0 Consensus size: 50
25295908 CCTATACTCA
*
25295918 TGAAGTTGCAGTGGGTCAGATTAAAGCTACAGAAACAAATCTTGATCTC-C
1 TGAAGTTGCAGTGGATCAGATTAAAGCTACAGAAACAAATCTT-ATCTCTC
** * * *
25295968 TTGAAGTTGCAGTGGATTGGATTGAAGTTA-AGACAGCAAATCTTATCTCTC
1 -TGAAGTTGCAGTGGATCAGATTAAAGCTACAGA-AACAAATCTTATCTCTC
* ** * * * *
25296019 TGAAGTTGCACTAAAGCTAGA-TGAGGCTACA-ACACTAAAT-TCTATAC-CTC
1 TGAAGTTGCAGTGGATC-AGATTAAAGCTACAGAAAC-AAATCT-TAT-CTCTC
* * *
25296069 TGAACTTGCAGTGGGTCGGATTAAAGCTA-AGAAACAAATCTTATCTC
1 TGAAGTTGCAGTGGATCAGATTAAAGCTACAGAAACAAATCTTATCTC
25296116 CCTAAAAATA
Statistics
Matches: 110, Mismatches: 26, Indels: 24
0.69 0.16 0.15
Matches are distributed among these distances:
48 1 0.01
49 13 0.12
50 58 0.53
51 38 0.35
ACGTcount: A:0.33, C:0.18, G:0.21, T:0.28
Consensus pattern (50 bp):
TGAAGTTGCAGTGGATCAGATTAAAGCTACAGAAACAAATCTTATCTCTC
Found at i:25301915 original size:18 final size:18
Alignment explanation
Indices: 25301879--25301918 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
25301869 ACCAAATAAT
**
25301879 ATGCGATCACATGACCAA
1 ATGCGATCACAAAACCAA
*
25301897 ATGCGATCACAAAATCAA
1 ATGCGATCACAAAACCAA
25301915 ATGC
1 ATGC
25301919 ATTCATACAA
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:0.42, C:0.25, G:0.15, T:0.17
Consensus pattern (18 bp):
ATGCGATCACAAAACCAA
Found at i:25306596 original size:51 final size:50
Alignment explanation
Indices: 25306478--25306657 Score: 209
Period size: 52 Copynumber: 3.5 Consensus size: 50
25306468 ATGGTATGTT
* * *
25306478 GATGACTAAGTGTCATCGTGAGTAAGTGAATCCTTTACGGATTTAAAGGTCT
1 GATGACTAAGTGTCATCGTGAGTAAATGAATCC-ATACGGA-TTAAAGGTCC
*
25306530 GATGACTAAGTGTCATCGTGAGTAAATGAATCCATGATGGATTAAAGGTCC
1 GATGACTAAGTGTCATCGTGAGTAAATGAATCCAT-ACGGATTAAAGGTCC
* * * * *
25306581 GATGACTCAGTGTCATTGTGAGTATATCAATTCCTATACGGAATAAGAGGTCC
1 GATGACTAAGTGTCATCGTGAGTAAATGAA-TCC-ATACGGATTAA-AGGTCC
25306634 GATGACTATA-TGTCATCGTGAGTA
1 GATGACTA-AGTGTCATCGTGAGTA
25306658 TTAAATGAAA
Statistics
Matches: 111, Mismatches: 12, Indels: 9
0.84 0.09 0.07
Matches are distributed among these distances:
51 36 0.32
52 46 0.41
53 28 0.25
54 1 0.01
ACGTcount: A:0.31, C:0.14, G:0.24, T:0.31
Consensus pattern (50 bp):
GATGACTAAGTGTCATCGTGAGTAAATGAATCCATACGGATTAAAGGTCC
Found at i:25313971 original size:18 final size:18
Alignment explanation
Indices: 25313945--25313984 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
25313935 ACTTTGCAAA
*
25313945 CACACTTTATCTTCTTAT
1 CACACTTTATCTTCTTAG
* *
25313963 CACATTTTATTTTCTTAG
1 CACACTTTATCTTCTTAG
25313981 CACA
1 CACA
25313985 AATTTTTTGT
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:0.25, C:0.25, G:0.03, T:0.47
Consensus pattern (18 bp):
CACACTTTATCTTCTTAG
Found at i:25315285 original size:81 final size:83
Alignment explanation
Indices: 25315127--25315286 Score: 279
Period size: 81 Copynumber: 2.0 Consensus size: 83
25315117 CTCTCTGTGG
*
25315127 GTACGATACTTTACTTATCACTTTATTACTTGAACGTTGTGTACACTTGCACATGCTATAGCAAT
1 GTACGATACTGTACTTATCACTTTATTACTTGAACGTTGTGTACACTTGCACATGCTATAGCAAT
*
25315192 ATTATTTTACACGTGATA
66 ATTAATTTACACGTGATA
*
25315210 GTACGATACTGTACTTATCACTTTATTACTTGAATG-T-TGTACACTTGCACATGCTATAGCAAT
1 GTACGATACTGTACTTATCACTTTATTACTTGAACGTTGTGTACACTTGCACATGCTATAGCAAT
25315273 ATTAATTTACACGT
66 ATTAATTTACACGT
25315287 CACAGTTTCA
Statistics
Matches: 74, Mismatches: 3, Indels: 2
0.94 0.04 0.03
Matches are distributed among these distances:
81 39 0.53
82 1 0.01
83 34 0.46
ACGTcount: A:0.29, C:0.18, G:0.13, T:0.39
Consensus pattern (83 bp):
GTACGATACTGTACTTATCACTTTATTACTTGAACGTTGTGTACACTTGCACATGCTATAGCAAT
ATTAATTTACACGTGATA
Found at i:25316252 original size:50 final size:49
Alignment explanation
Indices: 25316119--25316303 Score: 223
Period size: 50 Copynumber: 3.8 Consensus size: 49
25316109 GATGAATCAT
* * *
25316119 ATACCCCTAAAGCTGTAGAGGAACAAATTGAAGCCGCAATGG-AAATCTC
1 ATACACCTAAAGCTGTAGAGGGA-AGATTGAAGCCGCAATGGCAAATCTC
* **
25316168 --ACACCTAAAGTTGTAGAGGCCAGATTGAAGCCGCAATGGCAAATCTC
1 ATACACCTAAAGCTGTAGAGGGAAGATTGAAGCCGCAATGGCAAATCTC
* * * *
25316215 ATACATCTAACGCTATAGAGCGGTAGATTGAAGCCGCAATGGCAAATCTC
1 ATACACCTAAAGCTGTAGAG-GGAAGATTGAAGCCGCAATGGCAAATCTC
*
25316265 ATTCACCTAAAGCTGTAGAGGGGAAGATTGAAGCCGCAA
1 ATACACCTAAAGCTGTAGA-GGGAAGATTGAAGCCGCAA
25316304 GGGTGAATCT
Statistics
Matches: 115, Mismatches: 16, Indels: 9
0.82 0.11 0.06
Matches are distributed among these distances:
46 17 0.15
47 24 0.21
49 14 0.12
50 59 0.51
51 1 0.01
ACGTcount: A:0.36, C:0.22, G:0.23, T:0.19
Consensus pattern (49 bp):
ATACACCTAAAGCTGTAGAGGGAAGATTGAAGCCGCAATGGCAAATCTC
Found at i:25316557 original size:42 final size:42
Alignment explanation
Indices: 25316498--25316579 Score: 121
Period size: 42 Copynumber: 2.0 Consensus size: 42
25316488 CGAAGTTACA
* *
25316498 ACCATCCAATCTTTTACCCTAATCA-GAGGGCAGATTGAAAAC
1 ACCATCCAATCTCTTACCCTAACCATG-GGGCAGATTGAAAAC
*
25316540 ACCATTCAATCTCTTACCCTAACCATGGGGCAGATTGAAA
1 ACCATCCAATCTCTTACCCTAACCATGGGGCAGATTGAAA
25316580 CAATCTAATC
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
42 35 0.97
43 1 0.03
ACGTcount: A:0.34, C:0.27, G:0.15, T:0.24
Consensus pattern (42 bp):
ACCATCCAATCTCTTACCCTAACCATGGGGCAGATTGAAAAC
Found at i:25318250 original size:17 final size:17
Alignment explanation
Indices: 25318228--25318265 Score: 76
Period size: 17 Copynumber: 2.2 Consensus size: 17
25318218 TTGACCTTCG
25318228 AATTTTCCAAAAATCCA
1 AATTTTCCAAAAATCCA
25318245 AATTTTCCAAAAATCCA
1 AATTTTCCAAAAATCCA
25318262 AATT
1 AATT
25318266 ATACCATCGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.47, C:0.21, G:0.00, T:0.32
Consensus pattern (17 bp):
AATTTTCCAAAAATCCA
Found at i:25318306 original size:30 final size:30
Alignment explanation
Indices: 25318248--25318483 Score: 264
Period size: 30 Copynumber: 7.8 Consensus size: 30
25318238 AAATCCAAAT
* *
25318248 TTTCCAAAAATCCAAATTAT-ACCATCGAA-
1 TTTCCAAAAATTCAAATT-TGACCCTCGAAC
25318277 TTTCCAAAAATTCAAATTTGACCCCTCGAAC
1 TTTCCAAAAATTCAAATTTGA-CCCTCGAAC
*
25318308 TTTCCAAAAATTCAAATTTGACCCTCAAAC
1 TTTCCAAAAATTCAAATTTGACCCTCGAAC
* *
25318338 TTTCCAAGAATTCAAATTTAACCC-CTGAAC
1 TTTCCAAAAATTCAAATTTGACCCTC-GAAC
* * * *
25318368 TTTCCAAAAAATT-GAATTTAACCATCAAAC
1 TTTCC-AAAAATTCAAATTTGACCCTCGAAC
* * *
25318398 TTTCCAAAAAATTCCAATTTAACCCTTGAAC
1 TTTCC-AAAAATTCAAATTTGACCCTCGAAC
* * *
25318429 TTTCTAAACATTCAAATTTGACCCTTGAAC
1 TTTCCAAAAATTCAAATTTGACCCTCGAAC
25318459 TTTCCAAAAATTCAAATTTGACCCT
1 TTTCCAAAAATTCAAATTTGACCCT
25318484 ATTTTAATGT
Statistics
Matches: 180, Mismatches: 20, Indels: 13
0.85 0.09 0.06
Matches are distributed among these distances:
28 1 0.01
29 19 0.11
30 115 0.64
31 45 0.25
ACGTcount: A:0.39, C:0.25, G:0.05, T:0.31
Consensus pattern (30 bp):
TTTCCAAAAATTCAAATTTGACCCTCGAAC
Found at i:25318386 original size:91 final size:92
Alignment explanation
Indices: 25318277--25318482 Score: 267
Period size: 91 Copynumber: 2.3 Consensus size: 92
25318267 TACCATCGAA
* * *
25318277 TTTCCAAAAATTCAAATTTGACCCCTCGAACTTTCC-AAAAATTCAAATTTGACCCTCAAACTTT
1 TTTCCAAAAATTCAAATTTGACCCATCAAACTTTCCAAAAAATTCAAATTTAACCCTCAAACTTT
25318341 CCAAGA-ATTCAAATTTAACCCCTGAAC
66 CCAA-ACATTCAAATTTAACCCCTGAAC
* * * **
25318368 TTTCCAAAAAATT-GAATTT-AACCATCAAACTTTCCAAAAAATTCCAATTTAACCCTTGAACTT
1 TTTCC-AAAAATTCAAATTTGACCCATCAAACTTTCCAAAAAATTCAAATTTAACCCTCAAACTT
* * *
25318431 TCTAAACATTCAAATTTGACCCTTGAAC
65 TCCAAACATTCAAATTTAACCCCTGAAC
25318459 TTTCCAAAAATTCAAATTTGACCC
1 TTTCCAAAAATTCAAATTTGACCC
25318483 TATTTTAATG
Statistics
Matches: 97, Mismatches: 13, Indels: 9
0.82 0.11 0.08
Matches are distributed among these distances:
90 21 0.22
91 66 0.68
92 10 0.10
ACGTcount: A:0.38, C:0.25, G:0.05, T:0.32
Consensus pattern (92 bp):
TTTCCAAAAATTCAAATTTGACCCATCAAACTTTCCAAAAAATTCAAATTTAACCCTCAAACTTT
CCAAACATTCAAATTTAACCCCTGAAC
Found at i:25326152 original size:30 final size:30
Alignment explanation
Indices: 25326116--25326182 Score: 107
Period size: 30 Copynumber: 2.2 Consensus size: 30
25326106 AAAATTCTAT
* *
25326116 TTTTTTAATATTTAAAATTTTCTGTAAAAC
1 TTTTTTAATATTTAAAAATTTCTATAAAAC
*
25326146 TTTTTTAATATTTAAAAATTTCTATAAAAT
1 TTTTTTAATATTTAAAAATTTCTATAAAAC
25326176 TTTTTTA
1 TTTTTTA
25326183 TGATTTTTTT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
30 34 1.00
ACGTcount: A:0.37, C:0.04, G:0.01, T:0.57
Consensus pattern (30 bp):
TTTTTTAATATTTAAAAATTTCTATAAAAC
Found at i:25330061 original size:41 final size:41
Alignment explanation
Indices: 25330004--25330099 Score: 165
Period size: 41 Copynumber: 2.3 Consensus size: 41
25329994 GAATTTTATT
* *
25330004 TTAACAAGAATTCTAGTCACCCAATTCTAATAATCTCCACC
1 TTAACAAGAATTCTAGTAACCCAATTCTAACAATCTCCACC
25330045 TTAACAAGAATTCTAGTAACCCAATTCTAACAATCTCCACC
1 TTAACAAGAATTCTAGTAACCCAATTCTAACAATCTCCACC
*
25330086 TTGACAAGAATTCT
1 TTAACAAGAATTCT
25330100 CTACGAACAA
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.38, C:0.27, G:0.06, T:0.29
Consensus pattern (41 bp):
TTAACAAGAATTCTAGTAACCCAATTCTAACAATCTCCACC
Found at i:25333142 original size:31 final size:31
Alignment explanation
Indices: 25333104--25333166 Score: 126
Period size: 31 Copynumber: 2.0 Consensus size: 31
25333094 AATAAAATAA
25333104 AAGAAGTCTAATTTATTTGGACTTTTCTTTT
1 AAGAAGTCTAATTTATTTGGACTTTTCTTTT
25333135 AAGAAGTCTAATTTATTTGGACTTTTCTTTT
1 AAGAAGTCTAATTTATTTGGACTTTTCTTTT
25333166 A
1 A
25333167 TTTTATTTTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.27, C:0.10, G:0.13, T:0.51
Consensus pattern (31 bp):
AAGAAGTCTAATTTATTTGGACTTTTCTTTT
Found at i:25333596 original size:30 final size:31
Alignment explanation
Indices: 25333532--25333601 Score: 90
Period size: 30 Copynumber: 2.3 Consensus size: 31
25333522 ACAACAAGAA
*
25333532 GACTATTTTGTCACTTTTCGATAACTTTAGT
1 GACTATTTTGTCACTTTTCGATAACTTGAGT
*
25333563 GACTATTTTGTCACATTTTC-A-AAGTTGAGT
1 GACTATTTTGTCAC-TTTTCGATAACTTGAGT
*
25333593 GACTGTTTT
1 GACTATTTT
25333602 ATTAAATGTG
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
30 15 0.43
31 15 0.43
32 5 0.14
ACGTcount: A:0.23, C:0.14, G:0.16, T:0.47
Consensus pattern (31 bp):
GACTATTTTGTCACTTTTCGATAACTTGAGT
Found at i:25334170 original size:192 final size:194
Alignment explanation
Indices: 25333843--25334231 Score: 674
Period size: 192 Copynumber: 2.0 Consensus size: 194
25333833 TATCACTTGA
*
25333843 GTGTGAATATTGTTACTAAAAATATGAAATTGAGGTAGTGTCCGCAAATATACGGGTCAAATTAT
1 GTGTGAATATTGTTACTAAAAATACGAAATTGAGGTAGTGTCCGCAAATATACGGGTCAAATTAT
* * *
25333908 AATATAGTACGGAGTCGATAAGTACTCCGAGGATTGTACCCAAAGAAATGAATACTAAATTAATA
66 AATACACTACGGAGTCGATAAGTACTCCGAGGATCGTACCCAAAGAAATGAATACTAAATTAATA
25333973 TTAACCT-AC-ACATAAATAATCTAATTAGTAGTTTAAATAAATTATAGTACGACGAACATAAT
131 TTAACCTAACGACATAAATAATCTAATTAGTAGTTTAAATAAATTATAGTACGACGAACATAAT
* *
25334035 GTGTGAATATTGTTACTAAAAATACGGAATTGAGGTAGTGTCCGCAAATATACGGGTCAAATTGT
1 GTGTGAATATTGTTACTAAAAATACGAAATTGAGGTAGTGTCCGCAAATATACGGGTCAAATTAT
25334100 AATACACTACGGAGTCGATAAGTACTCCGAGGATCGTACCCAAAGAAATGAATACTAAATTAATA
66 AATACACTACGGAGTCGATAAGTACTCCGAGGATCGTACCCAAAGAAATGAATACTAAATTAATA
* *
25334165 TTAACCTACACGTACATAAATAATCTAATTAGTAGTTTAAATAAATTATAGTAGGAGGAACATAA
131 TTAACCTA-ACG-ACATAAATAATCTAATTAGTAGTTTAAATAAATTATAGTACGACGAACATAA
25334230 T
194 T
25334231 G
1 G
25334232 CAAAATAAAC
Statistics
Matches: 185, Mismatches: 8, Indels: 4
0.94 0.04 0.02
Matches are distributed among these distances:
192 131 0.71
194 2 0.01
196 52 0.28
ACGTcount: A:0.41, C:0.13, G:0.17, T:0.29
Consensus pattern (194 bp):
GTGTGAATATTGTTACTAAAAATACGAAATTGAGGTAGTGTCCGCAAATATACGGGTCAAATTAT
AATACACTACGGAGTCGATAAGTACTCCGAGGATCGTACCCAAAGAAATGAATACTAAATTAATA
TTAACCTAACGACATAAATAATCTAATTAGTAGTTTAAATAAATTATAGTACGACGAACATAAT
Found at i:25341595 original size:20 final size:20
Alignment explanation
Indices: 25341572--25341612 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
25341562 GCTAAATAAG
*
25341572 TAACTTTTGAAGAAA-ATTTT
1 TAACTTTTCAA-AAATATTTT
25341592 TAACTTTTCAAAAATATTTT
1 TAACTTTTCAAAAATATTTT
25341612 T
1 T
25341613 TTTCAATGGA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 3 0.16
20 16 0.84
ACGTcount: A:0.39, C:0.07, G:0.05, T:0.49
Consensus pattern (20 bp):
TAACTTTTCAAAAATATTTT
Found at i:25343461 original size:18 final size:18
Alignment explanation
Indices: 25343440--25343475 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
25343430 GGCGAACAAC
25343440 CCAAATATGGCGGATAGT
1 CCAAATATGGCGGATAGT
* *
25343458 CCAAATGTGGTGGATAGT
1 CCAAATATGGCGGATAGT
25343476 TCGAGTGTGT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.31, C:0.14, G:0.31, T:0.25
Consensus pattern (18 bp):
CCAAATATGGCGGATAGT
Found at i:25345256 original size:30 final size:30
Alignment explanation
Indices: 25345222--25345283 Score: 115
Period size: 30 Copynumber: 2.1 Consensus size: 30
25345212 TAATGTACTG
*
25345222 TCAGTCCAATCAGTCACATCTATGTCTTTA
1 TCAGTCCAATCAGTCACATCTATGTCTCTA
25345252 TCAGTCCAATCAGTCACATCTATGTCTCTA
1 TCAGTCCAATCAGTCACATCTATGTCTCTA
25345282 TC
1 TC
25345284 TTCTTGGAGT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.26, C:0.29, G:0.10, T:0.35
Consensus pattern (30 bp):
TCAGTCCAATCAGTCACATCTATGTCTCTA
Found at i:25348354 original size:7 final size:7
Alignment explanation
Indices: 25348344--25348427 Score: 89
Period size: 7 Copynumber: 12.1 Consensus size: 7
25348334 AACCCAAAAA
*
25348344 GTCAATG
1 GTCAACG
*
25348351 GTCAAGG
1 GTCAACG
25348358 GTC-ACG
1 GTCAACG
*
25348364 GTCCACG
1 GTCAACG
*
25348371 GTCAACT
1 GTCAACG
*
25348378 GTCAATG
1 GTCAACG
*
25348385 GTCAATG
1 GTCAACG
25348392 GTCAACG
1 GTCAACG
25348399 GTCAACG
1 GTCAACG
*
25348406 GTCAACT
1 GTCAACG
*
25348413 ATCAACG
1 GTCAACG
25348420 GTCAACG
1 GTCAACG
25348427 G
1 G
25348428 GTTTGGTTCA
Statistics
Matches: 65, Mismatches: 11, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
6 5 0.08
7 60 0.92
ACGTcount: A:0.27, C:0.25, G:0.27, T:0.20
Consensus pattern (7 bp):
GTCAACG
Found at i:25355436 original size:20 final size:20
Alignment explanation
Indices: 25355411--25355469 Score: 82
Period size: 20 Copynumber: 2.9 Consensus size: 20
25355401 CTTAGAAAAA
25355411 GTCAACTGTCAATGGTCACG
1 GTCAACTGTCAATGGTCACG
25355431 GTCAACTGTCAATGGTCAACG
1 GTCAACTGTCAATGGTC-ACG
* * *
25355452 ATTAACTGTCAACGGTCA
1 GTCAACTGTCAATGGTCA
25355470 ACGATCAACG
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
20 18 0.51
21 17 0.49
ACGTcount: A:0.29, C:0.24, G:0.22, T:0.25
Consensus pattern (20 bp):
GTCAACTGTCAATGGTCACG
Found at i:25355460 original size:21 final size:21
Alignment explanation
Indices: 25355412--25355478 Score: 100
Period size: 21 Copynumber: 3.2 Consensus size: 21
25355402 TTAGAAAAAG
*
25355412 TCAACTGTCAATGGTC-ACGG
1 TCAACTGTCAATGGTCAACGA
25355432 TCAACTGTCAATGGTCAACGA
1 TCAACTGTCAATGGTCAACGA
* *
25355453 TTAACTGTCAACGGTCAACGA
1 TCAACTGTCAATGGTCAACGA
25355474 TCAAC
1 TCAAC
25355479 GATTGGGTCG
Statistics
Matches: 42, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
20 16 0.38
21 26 0.62
ACGTcount: A:0.31, C:0.25, G:0.19, T:0.24
Consensus pattern (21 bp):
TCAACTGTCAATGGTCAACGA
Found at i:25355471 original size:7 final size:7
Alignment explanation
Indices: 25355411--25355479 Score: 59
Period size: 7 Copynumber: 10.0 Consensus size: 7
25355401 CTTAGAAAAA
*
25355411 GTCAACT
1 GTCAACG
*
25355418 GTCAATG
1 GTCAACG
25355425 GTC-ACG
1 GTCAACG
*
25355431 GTCAACT
1 GTCAACG
*
25355438 GTCAATG
1 GTCAACG
25355445 GTCAACG
1 GTCAACG
* * *
25355452 ATTAACT
1 GTCAACG
25355459 GTCAACG
1 GTCAACG
25355466 GTCAACG
1 GTCAACG
*
25355473 ATCAACG
1 GTCAACG
25355480 ATTGGGTCGG
Statistics
Matches: 47, Mismatches: 14, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
6 5 0.11
7 42 0.89
ACGTcount: A:0.30, C:0.25, G:0.22, T:0.23
Consensus pattern (7 bp):
GTCAACG
Found at i:25359563 original size:18 final size:18
Alignment explanation
Indices: 25359515--25359598 Score: 96
Period size: 18 Copynumber: 4.6 Consensus size: 18
25359505 TCTTTGCGAT
*
25359515 CCAGTAATGCTCTTACGAG
1 CCAGT-ATGCTCTAACGAG
*
25359534 CCAGTAATGCTCTTACGAG
1 CCAGT-ATGCTCTAACGAG
* **
25359553 CCAGTATGCTCAAATAAG
1 CCAGTATGCTCTAACGAG
25359571 CCAGTATGCTCTAACGAG
1 CCAGTATGCTCTAACGAG
*
25359589 CCAATATGCT
1 CCAGTATGCT
25359599 ATTCCTTCCG
Statistics
Matches: 57, Mismatches: 8, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
18 33 0.58
19 24 0.42
ACGTcount: A:0.30, C:0.26, G:0.19, T:0.25
Consensus pattern (18 bp):
CCAGTATGCTCTAACGAG
Found at i:25362116 original size:20 final size:21
Alignment explanation
Indices: 25362081--25362119 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
25362071 TGTTTCTTTT
25362081 AAAACATTTAATTTAAAGAAA
1 AAAACATTTAATTTAAAGAAA
*
25362102 AAAACGTTTAA-TTAAAGA
1 AAAACATTTAATTTAAAGA
25362120 GATTTTGCAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.59, C:0.05, G:0.08, T:0.28
Consensus pattern (21 bp):
AAAACATTTAATTTAAAGAAA
Found at i:25362678 original size:19 final size:19
Alignment explanation
Indices: 25362656--25362717 Score: 52
Period size: 26 Copynumber: 2.9 Consensus size: 19
25362646 TTATATGTGG
25362656 TAAAAAAAATTATAAAAAA
1 TAAAAAAAATTATAAAAAA
25362675 TAAAAATTATTAAATTTAATAAAAAA
1 T-AAAA--A--AAA-TT-ATAAAAAA
*
25362701 TATAAAAAATTATAAAA
1 TAAAAAAAATTATAAAA
25362718 TGCTTCAAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 14
0.70 0.02 0.28
Matches are distributed among these distances:
19 7 0.20
20 6 0.17
21 3 0.09
22 1 0.03
23 1 0.03
24 3 0.09
25 5 0.14
26 9 0.26
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (19 bp):
TAAAAAAAATTATAAAAAA
Found at i:25366788 original size:49 final size:49
Alignment explanation
Indices: 25366668--25366791 Score: 126
Period size: 49 Copynumber: 2.5 Consensus size: 49
25366658 CTAATTCATG
* * * * * **
25366668 GTGGTTATACGATCACGTGTTCAAGTATAATTAGGGCTCCCGATTGATG
1 GTGGTTATGCGATCACGAGTTCAAGTATAACTAGAGCTCCCAATTGACA
* * *
25366717 GTGGTTATGCAACCAC-AGGTTCAAGTATAACTCGAGC-CCTCAATTGACA
1 GTGGTTATGCGATCACGA-GTTCAAGTATAACTAGAGCTCC-CAATTGACA
25366766 GTGGTTATGCGATCACGAGTTCAAGT
1 GTGGTTATGCGATCACGAGTTCAAGT
25366792 TTCATGTCAC
Statistics
Matches: 60, Mismatches: 12, Indels: 6
0.77 0.15 0.08
Matches are distributed among these distances:
48 2 0.03
49 57 0.95
50 1 0.02
ACGTcount: A:0.27, C:0.19, G:0.25, T:0.29
Consensus pattern (49 bp):
GTGGTTATGCGATCACGAGTTCAAGTATAACTAGAGCTCCCAATTGACA
Found at i:25368161 original size:12 final size:12
Alignment explanation
Indices: 25368144--25368174 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
25368134 GAGTTTAGAA
25368144 AGATTTTGAAAT
1 AGATTTTGAAAT
25368156 AGATTTTGAAAT
1 AGATTTTGAAAT
25368168 AGATTTT
1 AGATTTT
25368175 TACTTTGAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.39, C:0.00, G:0.16, T:0.45
Consensus pattern (12 bp):
AGATTTTGAAAT
Found at i:25370318 original size:28 final size:26
Alignment explanation
Indices: 25370275--25370326 Score: 68
Period size: 28 Copynumber: 1.9 Consensus size: 26
25370265 TATTCAGAAA
*
25370275 TTTTTTTATACAACATTCAAAGAATT
1 TTTTTTTAGACAACATTCAAAGAATT
*
25370301 TTTTTTTGAGACATACATTTAAAGAA
1 TTTTTTT-AGACA-ACATTCAAAGAA
25370327 AACTCAAAGC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 7 0.32
27 4 0.18
28 11 0.50
ACGTcount: A:0.38, C:0.10, G:0.08, T:0.44
Consensus pattern (26 bp):
TTTTTTTAGACAACATTCAAAGAATT
Found at i:25370543 original size:20 final size:22
Alignment explanation
Indices: 25370506--25370579 Score: 75
Period size: 20 Copynumber: 3.4 Consensus size: 22
25370496 CGTCTTTTAT
25370506 TATTATTATTAT-TATTTAGTTG
1 TATTATT-TTATGTATTTAGTTG
25370528 T-TTATTTT-TGTATTTAGTT-
1 TATTATTTTATGTATTTAGTTG
* *
25370547 TATTATTTTATTTATTTATTTG
1 TATTATTTTATGTATTTAGTTG
25370569 TCATTTATTTT
1 T-A-TTATTTT
25370580 CATGCTTAAT
Statistics
Matches: 44, Mismatches: 2, Indels: 10
0.79 0.04 0.18
Matches are distributed among these distances:
19 2 0.05
20 18 0.41
21 14 0.32
22 2 0.05
23 1 0.02
24 7 0.16
ACGTcount: A:0.22, C:0.01, G:0.07, T:0.70
Consensus pattern (22 bp):
TATTATTTTATGTATTTAGTTG
Found at i:25370549 original size:17 final size:16
Alignment explanation
Indices: 25370514--25370567 Score: 58
Period size: 17 Copynumber: 3.4 Consensus size: 16
25370504 ATTATTATTA
* *
25370514 TTATTATTTAGTT-GT
1 TTATTTTTTATTTAGT
25370529 TTATTTTTGTATTTAGT
1 TTATTTTT-TATTTAGT
25370546 TTATTATTTTATTTA-T
1 TTATT-TTTTATTTAGT
25370562 TTATTT
1 TTATTT
25370568 GTCATTTATT
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
15 8 0.24
16 10 0.29
17 13 0.38
18 3 0.09
ACGTcount: A:0.20, C:0.00, G:0.07, T:0.72
Consensus pattern (16 bp):
TTATTTTTTATTTAGT
Found at i:25385774 original size:38 final size:36
Alignment explanation
Indices: 25385674--25385780 Score: 142
Period size: 36 Copynumber: 2.9 Consensus size: 36
25385664 TGGTAACAAG
* * *
25385674 CATGACCTTTGGGTCAACAGGGAGAAAAATGAGCAT
1 CATGACCTTTGGGTCAACAGGGAGTAAAACGAACAT
* *
25385710 AATGACCTTTGGGTCAAGAGGGAGTAAAACGAACAT
1 CATGACCTTTGGGTCAACAGGGAGTAAAACGAACAT
*
25385746 CATGACCTTTTAGGATCAACAGGGAGTAAAACGAA
1 CATGACC-TTT-GGGTCAACAGGGAGTAAAACGAA
25385781 TAACAATCAC
Statistics
Matches: 61, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
36 37 0.61
37 3 0.05
38 21 0.34
ACGTcount: A:0.38, C:0.16, G:0.26, T:0.20
Consensus pattern (36 bp):
CATGACCTTTGGGTCAACAGGGAGTAAAACGAACAT
Found at i:25391769 original size:51 final size:51
Alignment explanation
Indices: 25391688--25391922 Score: 281
Period size: 51 Copynumber: 4.6 Consensus size: 51
25391678 TAAACGAAAC
*
25391688 GGTCCGATGACTAAGTTTCATCGTGAGTAAATGAATCCTTTACGGATTAAA
1 GGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATTAAA
* * *
25391739 GGTCTGATGACTAAGTGTCATCGTCAGTAAATGAATCCTTTACAGATTAAA
1 GGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATTAAA
* * * * * *
25391790 GGTTCGATGACTAAGTGTCATCGTGAGTAACTGAATCCATGATGGATTAAG
1 GGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATTAAA
** * * * **
25391841 GGTCCGATGACTTTGTGTCATCGTGAGTATATGAATTCCTATATGGAACAAGA
1 GGTCCGATGACTAAGTGTCATCGTGAGTAAATGAA-TCCTTTACGGATTAA-A
**
25391894 GGTCCGATGACTATCTGTCATCGTGAGTA
1 GGTCCGATGACTAAGTGTCATCGTGAGTA
25391923 TTAAATGAAA
Statistics
Matches: 156, Mismatches: 26, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
51 119 0.76
52 10 0.06
53 27 0.17
ACGTcount: A:0.29, C:0.16, G:0.24, T:0.31
Consensus pattern (51 bp):
GGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATTAAA
Found at i:25398998 original size:51 final size:51
Alignment explanation
Indices: 25398917--25399056 Score: 158
Period size: 51 Copynumber: 2.8 Consensus size: 51
25398907 TATAAATGAA
* * *
25398917 AAGGG-CCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGAATT
1 AAGGGCCCGATGACTAATTGTCATCGTGAGTAAATGAATCCATGACGAATT
* * * * *
25398967 AATGGCCCGATGACTAATTGTCATCATGAGTAACTGAATCCATGATGGATT
1 AAGGGCCCGATGACTAATTGTCATCGTGAGTAAATGAATCCATGACGAATT
* * *
25399018 AAGGGTCCGATGACT-TTGTGTCATCGTGAGTATATGAAT
1 AAGGGCCCGATGACTAAT-TGTCATCGTGAGTAAATGAAT
25399057 TCTTATATGG
Statistics
Matches: 74, Mismatches: 14, Indels: 3
0.81 0.15 0.03
Matches are distributed among these distances:
50 5 0.07
51 69 0.93
ACGTcount: A:0.30, C:0.16, G:0.24, T:0.30
Consensus pattern (51 bp):
AAGGGCCCGATGACTAATTGTCATCGTGAGTAAATGAATCCATGACGAATT
Found at i:25400169 original size:24 final size:24
Alignment explanation
Indices: 25400141--25400188 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 24
25400131 TACTGGTTAT
25400141 CCATTCTGGGCTCGTAAGAGCTAA
1 CCATTCTGGGCTCGTAAGAGCTAA
* *
25400165 CCATTCTGGGCTTGTGAGAGCTAA
1 CCATTCTGGGCTCGTAAGAGCTAA
25400189 TATTATCTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.23, C:0.23, G:0.27, T:0.27
Consensus pattern (24 bp):
CCATTCTGGGCTCGTAAGAGCTAA
Found at i:25403303 original size:52 final size:52
Alignment explanation
Indices: 25403222--25403563 Score: 524
Period size: 52 Copynumber: 6.6 Consensus size: 52
25403212 AATGATATAA
25403222 GTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATGAG
1 GTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATGAG
* * *
25403274 GTTCGATGACTATGTGTCATCATGAGTATATGAATCCTTTATGGATTATGAG
1 GTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATGAG
* *
25403326 GTCCGTTGACTATGTGTCATCGTGAGTATATGAATCTTTTACGGATTATGAG
1 GTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATGAG
*
25403378 GTTCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATGAG
1 GTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATGAG
* *
25403430 GTCCAATGACTATGTGTCATCGTGAGTATACGAATCCTTTACGGATTATGAG
1 GTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATGAG
** * * *
25403482 GTTTGATGACTATGTGTCATCGTGAGTATATGATTCCTAATACGGATTA-AAG
1 GTCCGATGACTATGTGTCATCGTGAGTATATGAATCCT-TTACGGATTATGAG
* * *
25403534 GTCCGATGACTTTATGTCATCGTGATTATA
1 GTCCGATGACTATGTGTCATCGTGAGTATA
25403564 AAAAATGCAT
Statistics
Matches: 263, Mismatches: 26, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
52 254 0.97
53 9 0.03
ACGTcount: A:0.26, C:0.14, G:0.24, T:0.37
Consensus pattern (52 bp):
GTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATGAG
Found at i:25410273 original size:52 final size:52
Alignment explanation
Indices: 25410195--25410486 Score: 417
Period size: 52 Copynumber: 5.6 Consensus size: 52
25410185 TGAATGAAAT
* * *
25410195 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCATTTATGGATTATG
1 AGGTCTGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATG
*
25410247 AGGTCTGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACAGATTATG
1 AGGTCTGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATG
* * *
25410299 AGGT-TCAATGATTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTTTG
1 AGGTCT-GATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATG
*
25410351 AGGTCTGATGACTATGTGTCATCGTGAGTATATGAATCCTTTATGGATTATG
1 AGGTCTGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATG
* * ** *
25410403 AGGTCTGAAGACTATGTGTCATCGTGAGTATATGATTCCCAATACGGATTA-A
1 AGGTCTGATGACTATGTGTCATCGTGAGTATATGAAT-CCTTTACGGATTATG
* *
25410455 AGGTCCGATGACTCTGTGTCATCGTGAGTATA
1 AGGTCTGATGACTATGTGTCATCGTGAGTATA
25410487 AAAAATTCAT
Statistics
Matches: 216, Mismatches: 21, Indels: 6
0.89 0.09 0.02
Matches are distributed among these distances:
51 1 0.00
52 204 0.94
53 11 0.05
ACGTcount: A:0.26, C:0.13, G:0.24, T:0.36
Consensus pattern (52 bp):
AGGTCTGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATG
Found at i:25410479 original size:156 final size:156
Alignment explanation
Indices: 25410195--25410486 Score: 460
Period size: 156 Copynumber: 1.9 Consensus size: 156
25410185 TGAATGAAAT
*
25410195 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCATTTATGGATTATGAGGTCTGATGACT
1 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCATTTATGGATTATGAGGTCTGAAGACT
** * * *
25410260 ATGTGTCATCGTGAGTATATGAATCCTTTACAGATTATGAGGTTCAATGATTATGTGTCATCGTG
66 ATGTGTCATCGTGAGTATATGAATCCAATACAGATTATAAGGTCCAATGACTATGTGTCATCGTG
25410325 AGTATATGAATCCTTTACGGATTTTG
131 AGTATATGAATCCTTTACGGATTTTG
* *
25410351 AGGTCTGATGACTATGTGTCATCGTGAGTATATGAATCCTTTATGGATTATGAGGTCTGAAGACT
1 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCATTTATGGATTATGAGGTCTGAAGACT
* * * *
25410416 ATGTGTCATCGTGAGTATATGATTCCCAATACGGATTA-AAGGTCCGATGACTCTGTGTCATCGT
66 ATGTGTCATCGTGAGTATATGAAT-CCAATACAGATTATAAGGTCCAATGACTATGTGTCATCGT
25410480 GAGTATA
130 GAGTATA
25410487 AAAAATTCAT
Statistics
Matches: 123, Mismatches: 12, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
156 113 0.92
157 10 0.08
ACGTcount: A:0.26, C:0.13, G:0.24, T:0.36
Consensus pattern (156 bp):
AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCATTTATGGATTATGAGGTCTGAAGACT
ATGTGTCATCGTGAGTATATGAATCCAATACAGATTATAAGGTCCAATGACTATGTGTCATCGTG
AGTATATGAATCCTTTACGGATTTTG
Found at i:25411281 original size:21 final size:21
Alignment explanation
Indices: 25411240--25411314 Score: 73
Period size: 21 Copynumber: 3.6 Consensus size: 21
25411230 ACAGTTTTTA
* *
25411240 GTATCGGTAGAGGTGA-AACTT
1 GTATCGGTAGA-ATGATCACTT
25411261 GTATCGGTAGAA-GAGTCACTT
1 GTATCGGTAGAATGA-TCACTT
* * *
25411282 GTATCAGTAGAATTATCACCT
1 GTATCGGTAGAATGATCACTT
25411303 GTATCGGTAGAA
1 GTATCGGTAGAA
25411315 ATTTGTACTA
Statistics
Matches: 45, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
19 2 0.04
21 42 0.93
22 1 0.02
ACGTcount: A:0.31, C:0.13, G:0.27, T:0.29
Consensus pattern (21 bp):
GTATCGGTAGAATGATCACTT
Found at i:25414402 original size:24 final size:23
Alignment explanation
Indices: 25414357--25414406 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 23
25414347 GTATACTGGT
*
25414357 TAACCATTTGGGCTCGTAAGAGC
1 TAACCATTTGGGCTCGCAAGAGC
* *
25414380 TAACCATTTTGGGCTTGCGAGAGC
1 TAACCA-TTTGGGCTCGCAAGAGC
25414404 TAA
1 TAA
25414407 TATTATCTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
23 6 0.26
24 17 0.74
ACGTcount: A:0.26, C:0.20, G:0.26, T:0.28
Consensus pattern (23 bp):
TAACCATTTGGGCTCGCAAGAGC
Found at i:25415459 original size:21 final size:22
Alignment explanation
Indices: 25415435--25415488 Score: 60
Period size: 21 Copynumber: 2.5 Consensus size: 22
25415425 CCTGTGCTAG
25415435 TTCTACCAATACAAGT-ATG-A
1 TTCTACCAATACAAGTCATGCA
**
25415455 TTTCTACCGGTACAAGTCATGCA
1 -TTCTACCAATACAAGTCATGCA
25415478 -TCTACCAATAC
1 TTCTACCAATAC
25415489 CAAAAACTCC
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
21 23 0.85
22 3 0.11
23 1 0.04
ACGTcount: A:0.33, C:0.26, G:0.11, T:0.30
Consensus pattern (22 bp):
TTCTACCAATACAAGTCATGCA
Found at i:25417908 original size:14 final size:14
Alignment explanation
Indices: 25417889--25417933 Score: 90
Period size: 14 Copynumber: 3.2 Consensus size: 14
25417879 TAACCCAGAT
25417889 GGCACCTGGTGTTC
1 GGCACCTGGTGTTC
25417903 GGCACCTGGTGTTC
1 GGCACCTGGTGTTC
25417917 GGCACCTGGTGTTC
1 GGCACCTGGTGTTC
25417931 GGC
1 GGC
25417934 TTTCACTTGC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 31 1.00
ACGTcount: A:0.07, C:0.29, G:0.38, T:0.27
Consensus pattern (14 bp):
GGCACCTGGTGTTC
Found at i:25427745 original size:37 final size:36
Alignment explanation
Indices: 25427653--25427756 Score: 154
Period size: 36 Copynumber: 2.9 Consensus size: 36
25427643 GGTGACAGGC
* * * *
25427653 ATGATCTTTGGGTCAATAGGGAGAAAAATGAGCATA
1 ATGACCTTTGGGTCAACAGGGAGTAAAACGAGCATA
*
25427689 ATGACCTTTGGGTCAACAGGGAGTAAAACGAGCATC
1 ATGACCTTTGGGTCAACAGGGAGTAAAACGAGCATA
25427725 ATGACCTTTTGGGTCAACAGGGAGTAAAACGA
1 ATGACC-TTTGGGTCAACAGGGAGTAAAACGA
25427757 ATAACGATCA
Statistics
Matches: 62, Mismatches: 5, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
36 37 0.60
37 25 0.40
ACGTcount: A:0.36, C:0.14, G:0.28, T:0.22
Consensus pattern (36 bp):
ATGACCTTTGGGTCAACAGGGAGTAAAACGAGCATA
Found at i:25428944 original size:21 final size:21
Alignment explanation
Indices: 25428920--25428967 Score: 51
Period size: 21 Copynumber: 2.3 Consensus size: 21
25428910 CTTTACCCAG
* *
25428920 ACAAGTGAAAGTTCTACTGAT
1 ACAAGTGAAACTTCTACTGAA
* **
25428941 ACAAATGACTCTTCTACTGAA
1 ACAAGTGAAACTTCTACTGAA
25428962 ACAAGT
1 ACAAGT
25428968 TTTACTTCTA
Statistics
Matches: 21, Mismatches: 6, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.40, C:0.19, G:0.15, T:0.27
Consensus pattern (21 bp):
ACAAGTGAAACTTCTACTGAA
Found at i:25431226 original size:49 final size:49
Alignment explanation
Indices: 25431142--25431745 Score: 320
Period size: 49 Copynumber: 12.4 Consensus size: 49
25431132 CTAGAGTTTT
* * * * *
25431142 AGAGGGATAGATTAAAG-CTGCAACGGTGGACCTAACACCTTAAAATCGA
1 AGAGGGATAGATTGAAGTC-GCAATGATGAATCTAACACCTTAAAATCGA
* ** * * *
25431191 AGAGGGATAGATTGAAGTCGTAATGGCGAATCTAACATCATAAAA-CTAA
1 AGAGGGATAGATTGAAGTCGCAATGATGAATCTAACACCTTAAAATC-GA
* * * * *
25431240 AGAGGGAAAGATTAAAG-CTGCAATGATAAATCTTACACCTTAAAA-CTAA
1 AGAGGGATAGATTGAAGTC-GCAATGATGAATCTAACACCTTAAAATC-GA
* * * * * * * * *
25431289 AGAGGTATCG-TTAAAG-CTGTAATGGTGGACCTAACACCCTAAAACCGA
1 AGAGGGATAGATTGAAGTC-GCAATGATGAATCTAACACCTTAAAATCGA
* * * ** * * * * *
25431337 AGAAGGAAAGATTAAAGTTACAATAATAAATCTTATACCTTAAAA-CTAA
1 AGAGGGATAGATTGAAGTCGCAATGATGAATCTAACACCTTAAAATC-GA
* * * ** *
25431386 AGAGGGATAGGTTGAAGTCGTAACGGCGAACCTAACA-CTCTAAAATCGA
1 AGAGGGATAGATTGAAGTCGCAATGATGAATCTAACACCT-TAAAATCGA
* * *
25431435 AGAGGGA-AGGATTAAAGTCGCAATGATGAATCTTACACCTTAAAATTGA
1 AGAGGGATA-GATTGAAGTCGCAATGATGAATCTAACACCTTAAAATCGA
* * * * *
25431484 AGAGGGATAGGTTGAAGTCGCAACGACGGACCTAACACCTTAAAATCGA
1 AGAGGGATAGATTGAAGTCGCAATGATGAATCTAACACCTTAAAATCGA
* * *
25431533 AGAGGG-TAGATTGAAG-CAGCAACGGA-GGATCTAACACCCTAAAATCGA
1 AGAGGGATAGATTGAAGTC-GCAA-TGATGAATCTAACACCTTAAAATCGA
* * ** * * *
25431581 AGAGGGGA-AGATTGAAGCCTCAACAATGGATCTTACACCTTAAAATTGA
1 AGA-GGGATAGATTGAAGTCGCAATGATGAATCTAACACCTTAAAATCGA
* * ** * * **
25431630 AGAGGGATAGGTTTAAGTCAAAATGATGGACCTAACAGCC-TAAAATTAA
1 AGAGGGATAGATTGAAGTCGCAATGATGAATCTAACA-CCTTAAAATCGA
* * * * * *
25431679 AGAGGGAAATATTGAAGTCGCAATAAT-AGATCTTATACCTTAAAACCGA
1 AGAGGGATAGATTGAAGTCGCAATGATGA-ATCTAACACCTTAAAATCGA
*
25431728 AGAGGGATAGGTTGAAGT
1 AGAGGGATAGATTGAAGT
25431746 TGTAAGGGCG
Statistics
Matches: 418, Mismatches: 115, Indels: 44
0.72 0.20 0.08
Matches are distributed among these distances:
47 1 0.00
48 83 0.20
49 326 0.78
50 8 0.02
ACGTcount: A:0.41, C:0.15, G:0.23, T:0.21
Consensus pattern (49 bp):
AGAGGGATAGATTGAAGTCGCAATGATGAATCTAACACCTTAAAATCGA
Found at i:25431450 original size:98 final size:99
Alignment explanation
Indices: 25431176--25431538 Score: 400
Period size: 98 Copynumber: 3.7 Consensus size: 99
25431166 GGTGGACCTA
* * * *
25431176 ACACCTTAAAA-TCGAAGAGGGATAGATTGAAGTCGTAATGGCGAATCTAACA-TCATAAAA-CT
1 ACACCTTAAAACT-AAAGAGGGATAGGTTGAAGTCGTAACGGCGAACCTAACACTCATAAAATC-
* *
25431238 AAAGAGGGAAAGATTAAAGCTGCAATGATAAATCTT
64 GAAGAGGGAAAGATTAAAGTTGCAATGATAAATCTT
* * * * * * * *
25431274 ACACCTTAAAACTAAAGAGGTAT-CGTTAAAG-CTGTAATGGTGGACCTAACAC-CCTAAAACCG
1 ACACCTTAAAACTAAAGAGGGATAGGTTGAAGTC-GTAACGGCGAACCTAACACTCATAAAATCG
* * *
25431336 AAGAAGGAAAGATTAAAGTTACAATAATAAATCTT
65 AAGAGGGAAAGATTAAAGTTGCAATGATAAATCTT
*
25431371 ATACCTTAAAACTAAAGAGGGATAGGTTGAAGTCGTAACGGCGAACCTAACACTC-TAAAATCGA
1 ACACCTTAAAACTAAAGAGGGATAGGTTGAAGTCGTAACGGCGAACCTAACACTCATAAAATCGA
* * *
25431435 AGAGGGAAGGATTAAAGTCGCAATGATGAATCTT
66 AGAGGGAAAGATTAAAGTTGCAATGATAAATCTT
* * * * * *
25431469 ACACCTTAAAATTGAAGAGGGATAGGTTGAAGTCGCAACGACGGACCTAACAC-CTTAAAATCGA
1 ACACCTTAAAACTAAAGAGGGATAGGTTGAAGTCGTAACGGCGAACCTAACACTCATAAAATCGA
25431533 AGAGGG
66 AGAGGG
25431539 TAGATTGAAG
Statistics
Matches: 223, Mismatches: 34, Indels: 16
0.82 0.12 0.06
Matches are distributed among these distances:
96 1 0.00
97 79 0.35
98 140 0.63
99 3 0.01
ACGTcount: A:0.42, C:0.16, G:0.21, T:0.21
Consensus pattern (99 bp):
ACACCTTAAAACTAAAGAGGGATAGGTTGAAGTCGTAACGGCGAACCTAACACTCATAAAATCGA
AGAGGGAAAGATTAAAGTTGCAATGATAAATCTT
Found at i:25431583 original size:146 final size:146
Alignment explanation
Indices: 25431417--25431684 Score: 378
Period size: 146 Copynumber: 1.8 Consensus size: 146
25431407 AACGGCGAAC
* * **
25431417 CTAACACTCTAAAATCGAAGA-GGGAAGGATTAAAGTCGCAATGATGAATCTTACACCTTAAAAT
1 CTAACACCCTAAAATCGAAGAGGGGAA-GATTAAAGCCGCAACAATGAATCTTACACCTTAAAAT
** *
25431481 TGAAGAGGGATAGGTTGAAGTCGCAACGACGGACCTAACA-CCTTAAAATCGAAGAGGGTAGATT
65 TGAAGAGGGATAGGTTGAAGTCAAAACGACGGACCTAACAGCC-TAAAATCAAAGAGGGTAGATT
25431545 GAAGCAGCAACGGAGGAT
129 GAAGCAGCAACGGAGGAT
* * *
25431563 CTAACACCCTAAAATCGAAGAGGGGAAGATTGAAGCCTCAACAATGGATCTTACACCTTAAAATT
1 CTAACACCCTAAAATCGAAGAGGGGAAGATTAAAGCCGCAACAATGAATCTTACACCTTAAAATT
* * * *
25431628 GAAGAGGGATAGGTTTAAGTCAAAATGATGGACCTAACAGCCTAAAATTAAAGAGGG
66 GAAGAGGGATAGGTTGAAGTCAAAACGACGGACCTAACAGCCTAAAATCAAAGAGGG
25431685 AAATATTGAA
Statistics
Matches: 106, Mismatches: 14, Indels: 4
0.85 0.11 0.03
Matches are distributed among these distances:
146 99 0.93
147 7 0.07
ACGTcount: A:0.40, C:0.16, G:0.24, T:0.20
Consensus pattern (146 bp):
CTAACACCCTAAAATCGAAGAGGGGAAGATTAAAGCCGCAACAATGAATCTTACACCTTAAAATT
GAAGAGGGATAGGTTGAAGTCAAAACGACGGACCTAACAGCCTAAAATCAAAGAGGGTAGATTGA
AGCAGCAACGGAGGAT
Found at i:25431586 original size:195 final size:194
Alignment explanation
Indices: 25431142--25431597 Score: 469
Period size: 195 Copynumber: 2.3 Consensus size: 194
25431132 CTAGAGTTTT
* * *
25431142 AGAGGGATAGATTAAAGCTGCAACGGTGGACCTAACACCTTAAAATCGAAGAGGGATAGATTGAA
1 AGAGGG-TAGATTAAAGCAGCAACGGAGGATCTAACACCTTAAAATCGAAGAGGGATAGATTGAA
* *
25431207 GTCGTAATGGCGAATCTAACATCATAAAACTAAAGAGGGAAAGATTAAAGCTGCAATGATAAATC
65 GTCGTAACGGCGAACCTAACATCATAAAACTAAAGAGGGAAAGATTAAAGCTGCAATGATAAATC
* * * **
25431272 TTACACCTTAAAACTAAAGAGGTATCGTTAAAGCTGTAATGGTGGACCTAACACCCTAAAACCGA
130 TTACACCTTAAAACTAAAGAGGGATCGTTAAAGCTGCAACGACGGACCTAACACCCTAAAACCGA
** * ** ** * * * *
25431337 AGAAGGAAAGATTAAAGTTA-CAA-TAATAAATCTTATACCTTAAAA-CTAAAGAGGGATAGGTT
1 AG-AGGGTAGATTAAAG-CAGCAACGGA-GGATCTAACACCTTAAAATC-GAAGAGGGATAGATT
* *
25431399 GAAGTCGTAACGGCGAACCTAACACTC-TAAAA-TCGAAGAGGGAAGGATTAAAG-TCGCAATGA
62 GAAGTCGTAACGGCGAACCTAACA-TCATAAAACT-AAAGAGGGAAAGATTAAAGCT-GCAATGA
* * * * * *
25431461 TGAATCTTACACCTTAAAATTGAAGAGGGATAGGTTGAAG-TCGCAACGACGGACCTAACACCTT
124 TAAATCTTACACCTTAAAACTAAAGAGGGAT-CGTTAAAGCT-GCAACGACGGACCTAACACCCT
*
25431525 AAAATCGA
187 AAAACCGA
* *
25431533 AGAGGGTAGATTGAAGCAGCAACGGAGGATCTAACACCCTAAAATCGAAGAGGGGA-AGATTGAA
1 AGAGGGTAGATTAAAGCAGCAACGGAGGATCTAACACCTTAAAATCGAAGA-GGGATAGATTGAA
25431597 G
65 G
25431598 CCTCAACAAT
Statistics
Matches: 205, Mismatches: 43, Indels: 26
0.75 0.16 0.09
Matches are distributed among these distances:
194 4 0.02
195 158 0.77
196 43 0.21
ACGTcount: A:0.41, C:0.16, G:0.23, T:0.20
Consensus pattern (194 bp):
AGAGGGTAGATTAAAGCAGCAACGGAGGATCTAACACCTTAAAATCGAAGAGGGATAGATTGAAG
TCGTAACGGCGAACCTAACATCATAAAACTAAAGAGGGAAAGATTAAAGCTGCAATGATAAATCT
TACACCTTAAAACTAAAGAGGGATCGTTAAAGCTGCAACGACGGACCTAACACCCTAAAACCGA
Found at i:25431764 original size:98 final size:98
Alignment explanation
Indices: 25431518--25431794 Score: 247
Period size: 98 Copynumber: 2.8 Consensus size: 98
25431508 GACGGACCTA
* * * * * *
25431518 ACACCTTAAAATCGAAGAGGG-TAGATTGAAG-CAGCAACGGA-GGATCTAACACCCTAAAATCG
1 ACACCTTAAAACCGAAGAGGGATAGGTTGAAGTCA--AAAGGACGAACCTAACACCCTAAAATCA
* * *
25431580 AAGAGGGGAAGATTGAAGCCTCAACAATGGATCTT
64 AAGAGGGAAAGATTGAAGCCGCAACAATAGATCTT
** * * * * * *
25431615 ACACCTTAAAATTGAAGAGGGATAGGTTTAAGTCAAAATGATGGACCTAACAGCCTAAAATTAAA
1 ACACCTTAAAACCGAAGAGGGATAGGTTGAAGTCAAAAGGACGAACCTAACACCCTAAAATCAAA
* * *
25431680 GAGGGAAATATTGAAGTCGCAATAATAGATCTT
66 GAGGGAAAGATTGAAGCCGCAACAATAGATCTT
* *** * *
25431713 ATACCTTAAAACCGAAGAGGGATAGGTTGAAGTTGTAAGGGCGAACTTAACACCCTAAAA-CAAA
1 ACACCTTAAAACCGAAGAGGGATAGGTTGAAGTCAAAAGGACGAACCTAACACCCTAAAATCAAA
* * *
25431777 GAGAGATAGATTAAAGCC
66 GAGGGAAAGATTGAAGCC
25431795 ATGACGTTGA
Statistics
Matches: 143, Mismatches: 34, Indels: 6
0.78 0.19 0.03
Matches are distributed among these distances:
97 40 0.28
98 101 0.71
99 2 0.01
ACGTcount: A:0.42, C:0.16, G:0.23, T:0.20
Consensus pattern (98 bp):
ACACCTTAAAACCGAAGAGGGATAGGTTGAAGTCAAAAGGACGAACCTAACACCCTAAAATCAAA
GAGGGAAAGATTGAAGCCGCAACAATAGATCTT
Found at i:25431860 original size:244 final size:243
Alignment explanation
Indices: 25431319--25431865 Score: 559
Period size: 244 Copynumber: 2.2 Consensus size: 243
25431309 AATGGTGGAC
* * * * * * *
25431319 CTAACACCCTAAAACCGAAGAAGGAAAGATTAAAG-TTACAATAATAAATCTTATACCTTAAAAC
1 CTAACACCCTAAAACCAAAGAGGGAAAGATTGAAGCAT-CAACAATGAATCTTACACCTTAAAAC
** * * *
25431383 TAAAGAGGGATAGGTTGAAGTCGTAACGGCGAACCTAACACTCTAAAATCGAAGAGGGAAGGATT
65 TAAAGAGGGATAGGTTGAAGTCAAAACGACGAACCTAACACTCTAAAATCAAAGAGGGAAAGATT
* ** *
25431448 AAAGTCGCAATGATGAATCTTACACCTTAAAATTGAAGAGGGATAGGTTGAAGTCGCAACGACGG
130 AAAGTCGCAATAATGAATCTTACACCTTAAAACCGAAGAGGGATAGGTTGAAGTCGCAACGACGA
* * * *
25431513 ACCTAACACCTTAAAATCGAAGAGGGTAGATTGAAGCAGCAACGGAGGAT
195 ACCTAACACCCTAAAATCAAAGAGGATAGATTAAAGCAG-AACGGAGGAT
* * * * * *
25431563 CTAACACCCTAAAATCGAAGAGGGGAAGATTGAAGCCTCAACAATGGATCTTACACCTTAAAATT
1 CTAACACCCTAAAACCAAAGAGGGAAAGATTGAAGCATCAACAATGAATCTTACACCTTAAAACT
* * * * * * *
25431628 GAAGAGGGATAGGTTTAAGTCAAAATGATGGACCTAACAGC-CTAAAATTAAAGAGGGAAATATT
66 AAAGAGGGATAGGTTGAAGTCAAAACGACGAACCTAACA-CTCTAAAATCAAAGAGGGAAAGATT
* * * * * *
25431692 GAAGTCGCAATAAT-AGATCTTATACCTTAAAACCGAAGAGGGATAGGTTGAAGTTGTAAGGGCG
130 AAAGTCGCAATAATGA-ATCTTACACCTTAAAACCGAAGAGGGATAGGTTGAAGTCGCAACGACG
* **
25431756 AACTTAACACCCTAAAA-CAAAGAGAGATAGATTAAAGCCATG-AC-GTTGAT
194 AACCTAACACCCTAAAATCAAAGAG-GATAGATTAAAG-CA-GAACGGAGGAT
* * *
25431806 CTAACACTCTAAAACCAAAGAGGGAATAGATTGAA-TATGCAACAGTGAATCTTACACCTT
1 CTAACACCCTAAAACCAAAGAGGGAA-AGATTGAAGCAT-CAACAATGAATCTTACACCTT
25431866 TTGAAAAAAA
Statistics
Matches: 248, Mismatches: 47, Indels: 16
0.80 0.15 0.05
Matches are distributed among these distances:
243 34 0.14
244 209 0.84
245 4 0.02
246 1 0.00
ACGTcount: A:0.41, C:0.16, G:0.21, T:0.21
Consensus pattern (243 bp):
CTAACACCCTAAAACCAAAGAGGGAAAGATTGAAGCATCAACAATGAATCTTACACCTTAAAACT
AAAGAGGGATAGGTTGAAGTCAAAACGACGAACCTAACACTCTAAAATCAAAGAGGGAAAGATTA
AAGTCGCAATAATGAATCTTACACCTTAAAACCGAAGAGGGATAGGTTGAAGTCGCAACGACGAA
CCTAACACCCTAAAATCAAAGAGGATAGATTAAAGCAGAACGGAGGAT
Found at i:25431925 original size:52 final size:52
Alignment explanation
Indices: 25431822--25431925 Score: 129
Period size: 52 Copynumber: 2.0 Consensus size: 52
25431812 CTCTAAAACC
* * * * **
25431822 AAAGAGGGAATAGATTGAATATGCAACAGTGAATCTTACACCTTTTGAAAAA
1 AAAGAGGGAAAAGATTGAATACGCAACAGTAAATCTTACACCCTTAAAAAAA
*
25431874 AAAGAGGGAAAAGATTGAACT-CGCAACGGTAAATCTTACACCCTTAAAAAAA
1 AAAGAGGGAAAAGATTGAA-TACGCAACAGTAAATCTTACACCCTTAAAAAAA
25431926 CTGTAGAGGG
Statistics
Matches: 44, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
52 43 0.98
53 1 0.02
ACGTcount: A:0.46, C:0.14, G:0.18, T:0.21
Consensus pattern (52 bp):
AAAGAGGGAAAAGATTGAATACGCAACAGTAAATCTTACACCCTTAAAAAAA
Found at i:25432481 original size:20 final size:19
Alignment explanation
Indices: 25432456--25432522 Score: 57
Period size: 20 Copynumber: 3.5 Consensus size: 19
25432446 GGGAGGATTT
25432456 TTTTTTTTGTTCAGAGAGAA
1 TTTTTTTTGTTCAGA-AGAA
* **
25432476 TTTTTTTT-TAT-GGAAGGT
1 TTTTTTTTGT-TCAGAAGAA
25432494 TTTTTTTTGTTCAGAAAGAA
1 TTTTTTTTGTTCAG-AAGAA
*
25432514 ATTTTTTTG
1 TTTTTTTTG
25432523 AAATAAGATT
Statistics
Matches: 36, Mismatches: 7, Indels: 8
0.71 0.14 0.16
Matches are distributed among these distances:
18 11 0.31
19 5 0.14
20 20 0.56
ACGTcount: A:0.22, C:0.03, G:0.18, T:0.57
Consensus pattern (19 bp):
TTTTTTTTGTTCAGAAGAA
Found at i:25432543 original size:25 final size:24
Alignment explanation
Indices: 25432515--25432584 Score: 77
Period size: 25 Copynumber: 2.8 Consensus size: 24
25432505 CAGAAAGAAA
* *
25432515 TTTTTTTGAAATAAGATTCAAAGAT
1 TTTTTTTGAAACAACATTCAAA-AT
* *
25432540 TTTTTTTTATACAACATTCAAAAT
1 TTTTTTTGAAACAACATTCAAAAT
*
25432564 TTTTTTTGAGACATACATTCA
1 TTTTTTTGAAACA-ACATTCA
25432585 CAGAAAATTC
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
24 13 0.34
25 25 0.66
ACGTcount: A:0.36, C:0.10, G:0.07, T:0.47
Consensus pattern (24 bp):
TTTTTTTGAAACAACATTCAAAAT
Found at i:25432565 original size:24 final size:26
Alignment explanation
Indices: 25432530--25432584 Score: 78
Period size: 25 Copynumber: 2.2 Consensus size: 26
25432520 TTGAAATAAG
* *
25432530 ATTCAAAGATTTTTTTTTATACA-AC
1 ATTCAAAGATTTTTTTTGAGACATAC
25432555 ATTCAAA-ATTTTTTTTGAGACATAC
1 ATTCAAAGATTTTTTTTGAGACATAC
25432580 ATTCA
1 ATTCA
25432585 CAGAAAATTC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
24 13 0.48
25 14 0.52
ACGTcount: A:0.36, C:0.13, G:0.05, T:0.45
Consensus pattern (26 bp):
ATTCAAAGATTTTTTTTGAGACATAC
Found at i:25432843 original size:15 final size:15
Alignment explanation
Indices: 25432821--25432860 Score: 62
Period size: 15 Copynumber: 2.7 Consensus size: 15
25432811 GTTTATTTTC
25432821 TCATTTATTTATTTA
1 TCATTTATTTATTTA
* *
25432836 TTATTTATTTATTTG
1 TCATTTATTTATTTA
25432851 TCATTTATTT
1 TCATTTATTT
25432861 TCATGCCTAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.23, C:0.05, G:0.03, T:0.70
Consensus pattern (15 bp):
TCATTTATTTATTTA
Found at i:25433006 original size:41 final size:40
Alignment explanation
Indices: 25432960--25433064 Score: 103
Period size: 41 Copynumber: 2.6 Consensus size: 40
25432950 TATTTTCATG
*
25432960 TCATTTTATTGTTATCTCTTTTATTTTTTTTTATTTAATTTA
1 TCATTTTATTGTTAT-TCTTTTATTTTTGTTTATTT-ATTTA
*
25433002 -CA-TTTATTGTTATTATCTTGTT-TGTTTGTTTATTTATTTA
1 TCATTTTATTGTTA-T-TCTT-TTATTTTTGTTTATTTATTTA
*
25433042 TCATTATATT-TTATT-TTTTATTT
1 TCATTTTATTGTTATTCTTTTATTT
25433065 AATTACATGT
Statistics
Matches: 53, Mismatches: 5, Indels: 14
0.74 0.07 0.19
Matches are distributed among these distances:
37 2 0.04
38 4 0.08
39 1 0.02
40 16 0.30
41 23 0.43
42 7 0.13
ACGTcount: A:0.19, C:0.06, G:0.05, T:0.70
Consensus pattern (40 bp):
TCATTTTATTGTTATTCTTTTATTTTTGTTTATTTATTTA
Found at i:25433041 original size:40 final size:42
Alignment explanation
Indices: 25432964--25433056 Score: 106
Period size: 41 Copynumber: 2.3 Consensus size: 42
25432954 TTCATGTCAT
* * *
25432964 TTTATTGTTA-TCTCTTTTATTTTTTTTTATTTAATTTA-CA
1 TTTATTGTTATTATCTTTTATGTTTGTTTATTTAATTTATCA
25433004 TTTATTGTTATTATCTTGTT-TGTTTGTTTATTT-ATTTATCA
1 TTTATTGTTATTATCTT-TTATGTTTGTTTATTTAATTTATCA
25433045 TTATATT-TTATT
1 TT-TATTGTTATT
25433057 TTTTATTTAA
Statistics
Matches: 46, Mismatches: 3, Indels: 7
0.82 0.05 0.12
Matches are distributed among these distances:
40 15 0.33
41 25 0.54
42 6 0.13
ACGTcount: A:0.19, C:0.05, G:0.05, T:0.70
Consensus pattern (42 bp):
TTTATTGTTATTATCTTTTATGTTTGTTTATTTAATTTATCA
Found at i:25433127 original size:21 final size:21
Alignment explanation
Indices: 25433103--25433143 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
25433093 ATTAGGTTAG
*
25433103 ATATTTTTA-TAATTGCATTTT
1 ATATATTTATTAATTG-ATTTT
25433124 ATATATTTATTAATTGATTT
1 ATATATTTATTAATTGATTT
25433144 GTTATTTATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 12 0.67
22 6 0.33
ACGTcount: A:0.32, C:0.02, G:0.05, T:0.61
Consensus pattern (21 bp):
ATATATTTATTAATTGATTTT
Found at i:25438887 original size:14 final size:14
Alignment explanation
Indices: 25438868--25438895 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
25438858 TCTAACAATT
25438868 TTCAGAATTTCTCC
1 TTCAGAATTTCTCC
25438882 TTCAGAATTTCTCC
1 TTCAGAATTTCTCC
25438896 ATGAGTGAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.21, C:0.29, G:0.07, T:0.43
Consensus pattern (14 bp):
TTCAGAATTTCTCC
Found at i:25449687 original size:12 final size:12
Alignment explanation
Indices: 25449670--25449699 Score: 51
Period size: 12 Copynumber: 2.4 Consensus size: 12
25449660 TAATTTTTAG
25449670 CTTGTTAGTAAA
1 CTTGTTAGTAAA
25449682 CTTGTTAGTAAA
1 CTTGTTAGTAAA
25449694 CATTGT
1 C-TTGT
25449700 CATTGCATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 13 0.76
13 4 0.24
ACGTcount: A:0.30, C:0.10, G:0.17, T:0.43
Consensus pattern (12 bp):
CTTGTTAGTAAA
Found at i:25451527 original size:7 final size:7
Alignment explanation
Indices: 25451515--25451540 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
25451505 GACAAGGAGT
25451515 CCTAAAC
1 CCTAAAC
25451522 CCTAAAC
1 CCTAAAC
25451529 CCTAAAC
1 CCTAAAC
25451536 CCTAA
1 CCTAA
25451541 GTACGACACA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.42, C:0.42, G:0.00, T:0.15
Consensus pattern (7 bp):
CCTAAAC
Found at i:25454539 original size:21 final size:21
Alignment explanation
Indices: 25454515--25454554 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
25454505 GAATCAAATG
25454515 AATATACATTTGAAGAATTAC
1 AATATACATTTGAAGAATTAC
* * *
25454536 AATATGCCTTTGATGAATT
1 AATATACATTTGAAGAATT
25454555 GGCTATAGAT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.40, C:0.10, G:0.12, T:0.38
Consensus pattern (21 bp):
AATATACATTTGAAGAATTAC
Found at i:25460153 original size:3 final size:3
Alignment explanation
Indices: 25460145--25460174 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
25460135 ATATGCAAGG
25460145 ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA
1 ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA
25460175 GTGTTCCCAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.33, G:0.00, T:0.00
Consensus pattern (3 bp):
ACA
Found at i:25484931 original size:21 final size:21
Alignment explanation
Indices: 25484906--25484956 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
25484896 GTGAAAAACG
*
25484906 TGATATGTGTTATGTGATCTA
1 TGATATGTGTTATGTAATCTA
* *
25484927 TGATAAGTGTTATGTAATGTA
1 TGATATGTGTTATGTAATCTA
*
25484948 TGATGTGTG
1 TGATATGTG
25484957 AATTCATTTC
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.25, C:0.02, G:0.27, T:0.45
Consensus pattern (21 bp):
TGATATGTGTTATGTAATCTA
Found at i:25485150 original size:46 final size:46
Alignment explanation
Indices: 25485088--25485197 Score: 202
Period size: 46 Copynumber: 2.4 Consensus size: 46
25485078 AAGTGAAATT
* *
25485088 ATGTGATATGTGAGCATGATACATGCTAAAATGTGGAAATCGTGAA
1 ATGTGATATGTGAGCATGATACATGCTAAAATGCGAAAATCGTGAA
25485134 ATGTGATATGTGAGCATGATACATGCTAAAATGCGAAAATCGTGAA
1 ATGTGATATGTGAGCATGATACATGCTAAAATGCGAAAATCGTGAA
25485180 ATGTGATATGTGAGCATG
1 ATGTGATATGTGAGCATG
25485198 CATGGGGTGT
Statistics
Matches: 62, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
46 62 1.00
ACGTcount: A:0.36, C:0.09, G:0.26, T:0.28
Consensus pattern (46 bp):
ATGTGATATGTGAGCATGATACATGCTAAAATGCGAAAATCGTGAA
Found at i:25485990 original size:21 final size:22
Alignment explanation
Indices: 25485966--25486013 Score: 62
Period size: 23 Copynumber: 2.2 Consensus size: 22
25485956 TTTGCATGCA
*
25485966 TTTTTATTGTC-ATTGCATTTT
1 TTTTTATTGTCTATTGCATTTC
*
25485987 TTTTTATTTTCTTATTGCATTTC
1 TTTTTATTGTC-TATTGCATTTC
25486010 TTTT
1 TTTT
25486014 GTTAATTTAG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 10 0.43
23 13 0.57
ACGTcount: A:0.12, C:0.10, G:0.06, T:0.71
Consensus pattern (22 bp):
TTTTTATTGTCTATTGCATTTC
Found at i:25486619 original size:17 final size:17
Alignment explanation
Indices: 25486593--25486649 Score: 62
Period size: 17 Copynumber: 3.3 Consensus size: 17
25486583 TCAGCCACTT
25486593 GAAAAAAGAAAATGAAAA
1 GAAAAAAGAAAA-GAAAA
* *
25486611 -AAGAAAGAAAAAGGAAA
1 GAAAAAAG-AAAAGAAAA
*
25486628 GAGAAAAGAAAAGAAAA
1 GAAAAAAGAAAAGAAAA
25486645 GAAAA
1 GAAAA
25486650 TGTTTGCTAT
Statistics
Matches: 31, Mismatches: 6, Indels: 5
0.74 0.14 0.12
Matches are distributed among these distances:
17 22 0.71
18 9 0.29
ACGTcount: A:0.77, C:0.00, G:0.21, T:0.02
Consensus pattern (17 bp):
GAAAAAAGAAAAGAAAA
Found at i:25486620 original size:11 final size:11
Alignment explanation
Indices: 25486593--25486648 Score: 60
Period size: 11 Copynumber: 5.0 Consensus size: 11
25486583 TCAGCCACTT
25486593 GAAAAAAGAAAA
1 GAAAAAAG-AAA
25486605 TGAAAAAAGAAA
1 -GAAAAAAGAAA
*
25486617 GAAAAAGGAAA
1 GAAAAAAGAAA
*
25486628 GAGAAAAGAAA
1 GAAAAAAGAAA
*
25486639 -AGAAAAGAAA
1 GAAAAAAGAAA
25486649 ATGTTTGCTA
Statistics
Matches: 40, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
10 10 0.25
11 19 0.47
12 3 0.08
13 8 0.20
ACGTcount: A:0.77, C:0.00, G:0.21, T:0.02
Consensus pattern (11 bp):
GAAAAAAGAAA
Found at i:25486637 original size:5 final size:5
Alignment explanation
Indices: 25486596--25486649 Score: 54
Period size: 5 Copynumber: 9.8 Consensus size: 5
25486586 GCCACTTGAA
*
25486596 AAAAG AAAATG AAAAA AGAAAG AAAAAGG AAAGAG AAAAG AAAAG AAAAG
1 AAAAG AAAA-G AAAAG A-AAAG -AAAA-G AAA-AG AAAAG AAAAG AAAAG
25486646 AAAA
1 AAAA
25486650 TGTTTGCTAT
Statistics
Matches: 42, Mismatches: 2, Indels: 10
0.78 0.04 0.19
Matches are distributed among these distances:
5 21 0.50
6 18 0.43
7 3 0.07
ACGTcount: A:0.78, C:0.00, G:0.20, T:0.02
Consensus pattern (5 bp):
AAAAG
Found at i:25494103 original size:15 final size:15
Alignment explanation
Indices: 25494083--25494117 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
25494073 TTTATATTTT
*
25494083 CTTTTATTTGTTTCA
1 CTTTTACTTGTTTCA
25494098 CTTTTACTTGTTTCA
1 CTTTTACTTGTTTCA
25494113 -TTTTA
1 CTTTTA
25494118 AATTTTACGC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 5 0.26
15 14 0.74
ACGTcount: A:0.14, C:0.14, G:0.06, T:0.66
Consensus pattern (15 bp):
CTTTTACTTGTTTCA
Found at i:25497116 original size:11 final size:11
Alignment explanation
Indices: 25497095--25497134 Score: 55
Period size: 11 Copynumber: 3.6 Consensus size: 11
25497085 AGGAAAAATG
25497095 AGAAAAA-GAA
1 AGAAAAAGGAA
25497105 AGAAAAAGGAA
1 AGAAAAAGGAA
*
25497116 AGAGAAAAGTAA
1 AGA-AAAAGGAA
25497128 AGAAAAA
1 AGAAAAA
25497135 AAATGTTTGC
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
10 7 0.26
11 10 0.37
12 10 0.37
ACGTcount: A:0.75, C:0.00, G:0.23, T:0.03
Consensus pattern (11 bp):
AGAAAAAGGAA
Found at i:25497129 original size:23 final size:25
Alignment explanation
Indices: 25497080--25497134 Score: 71
Period size: 23 Copynumber: 2.2 Consensus size: 25
25497070 TCAATCACTT
25497080 GAAAAAGGAAAAATGAGAAAAAGAAA
1 GAAAAAGG-AAAATGAGAAAAAGAAA
25497106 GAAAAAGG-AAA-GAG-AAAAGTAAA
1 GAAAAAGGAAAATGAGAAAAAG-AAA
25497129 GAAAAA
1 GAAAAA
25497135 AAATGTTTGC
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
22 5 0.18
23 12 0.43
24 3 0.11
26 8 0.29
ACGTcount: A:0.73, C:0.00, G:0.24, T:0.04
Consensus pattern (25 bp):
GAAAAAGGAAAATGAGAAAAAGAAA
Found at i:25510021 original size:69 final size:70
Alignment explanation
Indices: 25509910--25510045 Score: 229
Period size: 69 Copynumber: 2.0 Consensus size: 70
25509900 ACGTACATAT
**
25509910 CAACCATTGTTCCCTTTTGAAATTATCAGTAAGTTAACAATTAACTTGGATAT-TAAAACCCCAC
1 CAACCATTGTTCCCTTTCAAAATTATCAGTAAGTTAACAATTAACTTGGATATATAAAACCCCAC
25509974 TAGAA
66 TAGAA
* *
25509979 CAACCATTGTTCCCTTTCAAAATTATCAGTAAGTTAACAATTAACTTTGATATATAAAACCTCAC
1 CAACCATTGTTCCCTTTCAAAATTATCAGTAAGTTAACAATTAACTTGGATATATAAAACCCCAC
25510044 TA
66 TA
25510046 CTTCTAAACA
Statistics
Matches: 62, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
69 50 0.81
70 12 0.19
ACGTcount: A:0.38, C:0.21, G:0.08, T:0.33
Consensus pattern (70 bp):
CAACCATTGTTCCCTTTCAAAATTATCAGTAAGTTAACAATTAACTTGGATATATAAAACCCCAC
TAGAA
Found at i:25514218 original size:20 final size:20
Alignment explanation
Indices: 25514181--25514218 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
25514171 ATTTTGATCA
*
25514181 TGAAAAATAATGATGAAGGT
1 TGAAAAATAATGAAGAAGGT
25514201 TGAAAAATGAA-GAAGAAG
1 TGAAAAAT-AATGAAGAAG
25514219 AGAGGGGAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 14 0.88
21 2 0.12
ACGTcount: A:0.55, C:0.00, G:0.26, T:0.18
Consensus pattern (20 bp):
TGAAAAATAATGAAGAAGGT
Found at i:25517691 original size:50 final size:50
Alignment explanation
Indices: 25517623--25517758 Score: 166
Period size: 50 Copynumber: 2.7 Consensus size: 50
25517613 AGAGTTTAGA
* * * * *
25517623 TCTTACGAGGCCAGACAGAATTAT-GCTCTTGCGAGCTAGATAGAATTTTGT
1 TCTTACGA-GCCAAACAGAA-TATCGCTCTTACGAGCTAGATAGAATATCGC
* *
25517674 TCTTATGAGCCAAACAGAATATCGCTCTTACGATCTAGATAGAATATCGC
1 TCTTACGAGCCAAACAGAATATCGCTCTTACGAGCTAGATAGAATATCGC
* *
25517724 TCTTACAAGCCAAATAGAATATCGCTCTTACGAGC
1 TCTTACGAGCCAAACAGAATATCGCTCTTACGAGC
25517759 CAAACTTCAA
Statistics
Matches: 73, Mismatches: 11, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
49 3 0.04
50 63 0.86
51 7 0.10
ACGTcount: A:0.32, C:0.21, G:0.18, T:0.29
Consensus pattern (50 bp):
TCTTACGAGCCAAACAGAATATCGCTCTTACGAGCTAGATAGAATATCGC
Found at i:25517702 original size:25 final size:25
Alignment explanation
Indices: 25517623--25517763 Score: 122
Period size: 25 Copynumber: 5.6 Consensus size: 25
25517613 AGAGTTTAGA
*
25517623 TCTTACGAGGCCAGACAGAATTAT-GC
1 TCTTACGA-GCCAAACAGAA-TATCGC
* * * * * * *
25517649 TCTTGCGAGCTAGATAGAATTTTGT
1 TCTTACGAGCCAAACAGAATATCGC
*
25517674 TCTTATGAGCCAAACAGAATATCGC
1 TCTTACGAGCCAAACAGAATATCGC
* * * *
25517699 TCTTACGATCTAGATAGAATATCGC
1 TCTTACGAGCCAAACAGAATATCGC
* *
25517724 TCTTACAAGCCAAATAGAATATCGC
1 TCTTACGAGCCAAACAGAATATCGC
25517749 TCTTACGAGCCAAAC
1 TCTTACGAGCCAAAC
25517764 TTCAAAAATT
Statistics
Matches: 90, Mismatches: 24, Indels: 3
0.77 0.21 0.03
Matches are distributed among these distances:
24 2 0.02
25 81 0.90
26 7 0.08
ACGTcount: A:0.33, C:0.22, G:0.18, T:0.28
Consensus pattern (25 bp):
TCTTACGAGCCAAACAGAATATCGC
Found at i:25519028 original size:3 final size:3
Alignment explanation
Indices: 25519020--25519085 Score: 68
Period size: 3 Copynumber: 23.0 Consensus size: 3
25519010 TAGGGCAACC
* **
25519020 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCCT TC- TCT TCT TTT TAA
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT T-CT TCT TCT TCT TCT TCT
25519065 TCT TCT T-T TCT T-T TC- TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT
25519086 CTTGCTTCAA
Statistics
Matches: 53, Mismatches: 5, Indels: 10
0.78 0.07 0.15
Matches are distributed among these distances:
2 8 0.15
3 42 0.79
4 3 0.06
ACGTcount: A:0.03, C:0.30, G:0.00, T:0.67
Consensus pattern (3 bp):
TCT
Found at i:25520896 original size:24 final size:24
Alignment explanation
Indices: 25520851--25520896 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
25520841 TGCAAAAACT
*
25520851 AAAGAAACAAATTAAAATAAAATA
1 AAAGAAACAAATTAAAAGAAAATA
*
25520875 AAAGACAA-AAATTAATAGAAAA
1 AAAGA-AACAAATTAAAAGAAAA
25520897 ATTACAATGA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
24 17 0.89
25 2 0.11
ACGTcount: A:0.74, C:0.04, G:0.07, T:0.15
Consensus pattern (24 bp):
AAAGAAACAAATTAAAAGAAAATA
Found at i:25525176 original size:18 final size:18
Alignment explanation
Indices: 25525134--25525179 Score: 83
Period size: 18 Copynumber: 2.6 Consensus size: 18
25525124 TTATATGACT
*
25525134 GCATCTAGTTCTGTGATC
1 GCATCTGGTTCTGTGATC
25525152 GCATCTGGTTCTGTGATC
1 GCATCTGGTTCTGTGATC
25525170 GCATCTGGTT
1 GCATCTGGTT
25525180 AGGCTGCGCA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.13, C:0.22, G:0.26, T:0.39
Consensus pattern (18 bp):
GCATCTGGTTCTGTGATC
Found at i:25526481 original size:18 final size:17
Alignment explanation
Indices: 25526458--25526491 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
25526448 TTTAAAAGAA
25526458 AATCAACAAAAGATTAGT
1 AATCAACAAAAG-TTAGT
*
25526476 AATCAATAAAAGTTAG
1 AATCAACAAAAGTTAG
25526492 AAAAAACATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.56, C:0.09, G:0.12, T:0.24
Consensus pattern (17 bp):
AATCAACAAAAGTTAGT
Found at i:25532501 original size:17 final size:17
Alignment explanation
Indices: 25532479--25532526 Score: 60
Period size: 17 Copynumber: 2.8 Consensus size: 17
25532469 CGACAAATAG
* *
25532479 AAATGCAATGATAATGC
1 AAATGCAATGACAATGA
* *
25532496 AAATGCAGTGACAATTA
1 AAATGCAATGACAATGA
25532513 AAATGCAATGACAA
1 AAATGCAATGACAA
25532527 AGGGGATGTG
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
17 26 1.00
ACGTcount: A:0.50, C:0.12, G:0.17, T:0.21
Consensus pattern (17 bp):
AAATGCAATGACAATGA
Found at i:25541837 original size:25 final size:25
Alignment explanation
Indices: 25541758--25541874 Score: 92
Period size: 25 Copynumber: 4.6 Consensus size: 25
25541748 TAGAGTTTAG
*
25541758 CTCTTACGAGCCCAAACAAAAT-TACA
1 CTCTTACGAG-CCAGACAAAATAT-CA
** * * **
25541784 CTCTTGTGAGCCAGATAAAATTTTG
1 CTCTTACGAGCCAGACAAAATATCA
*
25541809 CTCTTACGAGCCAGACAGAATATCA
1 CTCTTACGAGCCAGACAAAATATCA
* * *
25541834 CTCTCACAAGCCAGACAAAATATCG
1 CTCTTACGAGCCAGACAAAATATCA
* *
25541859 CTCCTATGAGCCAGAC
1 CTCTTACGAGCCAGAC
25541875 TTTAGAAATT
Statistics
Matches: 69, Mismatches: 21, Indels: 3
0.74 0.23 0.03
Matches are distributed among these distances:
25 60 0.87
26 9 0.13
ACGTcount: A:0.35, C:0.28, G:0.15, T:0.22
Consensus pattern (25 bp):
CTCTTACGAGCCAGACAAAATATCA
Found at i:25542625 original size:25 final size:25
Alignment explanation
Indices: 25542591--25542639 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
25542581 GAGTCCAGAC
*
25542591 AGAATATCGCTCACACGAGCTAGAT
1 AGAACATCGCTCACACGAGCTAGAT
**
25542616 AGAACATCGCTCTTACGAGCTAGA
1 AGAACATCGCTCACACGAGCTAGA
25542640 ATCAGAATTA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.35, C:0.24, G:0.20, T:0.20
Consensus pattern (25 bp):
AGAACATCGCTCACACGAGCTAGAT
Found at i:25548752 original size:16 final size:16
Alignment explanation
Indices: 25548731--25548761 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
25548721 ATAATGTGAA
25548731 AATAAAGATAAAATGT
1 AATAAAGATAAAATGT
*
25548747 AATAAAGGTAAAATG
1 AATAAAGATAAAATG
25548762 GGATCCACAA
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:0.61, C:0.00, G:0.16, T:0.23
Consensus pattern (16 bp):
AATAAAGATAAAATGT
Found at i:25549594 original size:26 final size:26
Alignment explanation
Indices: 25549551--25549609 Score: 66
Period size: 26 Copynumber: 2.3 Consensus size: 26
25549541 AATTCTGGGC
* * *
25549551 ACAATTCTATACATGTTCATGCAGCG
1 ACAATTCTAGACACGTTCATACAGCG
* *
25549577 ACAATTCTGGACACGTTCATACAGTG
1 ACAATTCTAGACACGTTCATACAGCG
25549603 AC-ATTCT
1 ACAATTCT
25549610 TGGGTGCAAT
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
25 5 0.18
26 23 0.82
ACGTcount: A:0.31, C:0.24, G:0.15, T:0.31
Consensus pattern (26 bp):
ACAATTCTAGACACGTTCATACAGCG
Found at i:25550365 original size:21 final size:21
Alignment explanation
Indices: 25550339--25550392 Score: 63
Period size: 21 Copynumber: 2.6 Consensus size: 21
25550329 ATAGTGCAAT
* **
25550339 CTTCTACCGAAACTTGTGTCA
1 CTTCTACAGAAACAAGTGTCA
*
25550360 CTTCTACAGAAACAAGTGTGA
1 CTTCTACAGAAACAAGTGTCA
*
25550381 CTTCTACTGAAA
1 CTTCTACAGAAA
25550393 TAACTCATAC
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.31, C:0.24, G:0.15, T:0.30
Consensus pattern (21 bp):
CTTCTACAGAAACAAGTGTCA
Found at i:25551108 original size:25 final size:25
Alignment explanation
Indices: 25551068--25551151 Score: 87
Period size: 25 Copynumber: 3.2 Consensus size: 25
25551058 TAGCTCTGAT
*
25551068 GAGCCTAGACAAAATAACACTCTTAC
1 GAGCC-AGACAAAATAACGCTCTTAC
* *
25551094 GAGCCAGACAGAATATCGCTCTTAC
1 GAGCCAGACAAAATAACGCTCTTAC
* * *
25551119 AAGCTAGAATCAAAATTACGCTCTTAC
1 GAGCCAG-A-CAAAATAACGCTCTTAC
25551146 GAGCCA
1 GAGCCA
25551152 AAATCAGAAT
Statistics
Matches: 46, Mismatches: 10, Indels: 3
0.78 0.17 0.05
Matches are distributed among these distances:
25 22 0.48
26 6 0.13
27 18 0.39
ACGTcount: A:0.38, C:0.26, G:0.15, T:0.20
Consensus pattern (25 bp):
GAGCCAGACAAAATAACGCTCTTAC
Found at i:25551156 original size:27 final size:27
Alignment explanation
Indices: 25551077--25551162 Score: 70
Period size: 27 Copynumber: 3.3 Consensus size: 27
25551067 TGAGCCTAGA
* * *
25551077 CAAAATAACACTCTTACGAGCC-AGA-
1 CAAAATTACGCTCTTACGAGCCAAAAT
* * * *
25551102 CAGAA-TATCGCTCTTACAAGCTAGAAT
1 CAAAATTA-CGCTCTTACGAGCCAAAAT
25551129 CAAAATTACGCTCTTACGAGCCAAAAT
1 CAAAATTACGCTCTTACGAGCCAAAAT
*
25551156 CAGAATT
1 CAAAATT
25551163 TGCCTTCGTC
Statistics
Matches: 45, Mismatches: 12, Indels: 6
0.71 0.19 0.10
Matches are distributed among these distances:
24 1 0.02
25 15 0.33
26 1 0.02
27 26 0.58
28 2 0.04
ACGTcount: A:0.41, C:0.24, G:0.13, T:0.22
Consensus pattern (27 bp):
CAAAATTACGCTCTTACGAGCCAAAAT
Found at i:25555080 original size:19 final size:19
Alignment explanation
Indices: 25555056--25555095 Score: 71
Period size: 19 Copynumber: 2.1 Consensus size: 19
25555046 TTATACACAA
25555056 AGTCTTCAAGAGAGATAAC
1 AGTCTTCAAGAGAGATAAC
*
25555075 AGTCTTCAAGAGAGGTAAC
1 AGTCTTCAAGAGAGATAAC
25555094 AG
1 AG
25555096 AATAACAAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.40, C:0.15, G:0.25, T:0.20
Consensus pattern (19 bp):
AGTCTTCAAGAGAGATAAC
Found at i:25556630 original size:16 final size:15
Alignment explanation
Indices: 25556605--25556635 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
25556595 TAATATTATT
25556605 TTAATAAATTTAATA
1 TTAATAAATTTAATA
25556620 TTAATTAAATTTAATA
1 TTAA-TAAATTTAATA
25556636 CTTATTTTGA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 4 0.27
16 11 0.73
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
TTAATAAATTTAATA
Found at i:25558073 original size:47 final size:46
Alignment explanation
Indices: 25557967--25558110 Score: 148
Period size: 47 Copynumber: 3.0 Consensus size: 46
25557957 CAAAGAAAAA
* *
25557967 TGGGAGGATTTTGATTTTTGGGGTAAAGGGGGGAAATACAAAATTTT
1 TGGGA-GATTTTGATTTTTGGGGTAAAGGGGGGAAATAAAAAATTTG
* *
25558014 TAGGG-GACTTTGATTTTGGGGGTAAAAGGGGTGG-AATAAAAAATTTG
1 T-GGGAGATTTTGATTTTTGGGGT-AAAGGGG-GGAAATAAAAAATTTG
*
25558061 TGGGAGATTTTGATTTTTGGGGTGAATGAGGGAGGGAAAGTAAACAATTT
1 TGGGAGATTTTGATTTTTGGGGT-AA--AGGG-GGGAAA-TAAAAAATTT
25558111 TGAAGAGAAG
Statistics
Matches: 80, Mismatches: 8, Indels: 14
0.78 0.08 0.14
Matches are distributed among these distances:
46 19 0.24
47 38 0.47
48 5 0.06
49 6 0.08
50 3 0.04
51 9 0.11
ACGTcount: A:0.31, C:0.02, G:0.35, T:0.32
Consensus pattern (46 bp):
TGGGAGATTTTGATTTTTGGGGTAAAGGGGGGAAATAAAAAATTTG
Found at i:25562655 original size:13 final size:13
Alignment explanation
Indices: 25562637--25562672 Score: 54
Period size: 15 Copynumber: 2.6 Consensus size: 13
25562627 TAGCTGATTT
25562637 TTAGAGATTCTAA
1 TTAGAGATTCTAA
25562650 TTAGAGATATTCTAA
1 TTAGAG--ATTCTAA
25562665 TTAGAGAT
1 TTAGAGAT
25562673 ATCTCATAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
13 8 0.38
15 13 0.62
ACGTcount: A:0.39, C:0.06, G:0.17, T:0.39
Consensus pattern (13 bp):
TTAGAGATTCTAA
Found at i:25562663 original size:15 final size:15
Alignment explanation
Indices: 25562643--25562674 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
25562633 ATTTTTAGAG
25562643 ATTCTAATTAGAGAT
1 ATTCTAATTAGAGAT
25562658 ATTCTAATTAGAGAT
1 ATTCTAATTAGAGAT
25562673 AT
1 AT
25562675 CTCATAATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.41, C:0.06, G:0.12, T:0.41
Consensus pattern (15 bp):
ATTCTAATTAGAGAT
Found at i:25565639 original size:24 final size:24
Alignment explanation
Indices: 25565612--25565665 Score: 108
Period size: 24 Copynumber: 2.2 Consensus size: 24
25565602 TCTTTGCCCC
25565612 CTTGGGTTCGCTCAAACCAAGCTT
1 CTTGGGTTCGCTCAAACCAAGCTT
25565636 CTTGGGTTCGCTCAAACCAAGCTT
1 CTTGGGTTCGCTCAAACCAAGCTT
25565660 CTTGGG
1 CTTGGG
25565666 CACCTTGTCT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.19, C:0.28, G:0.24, T:0.30
Consensus pattern (24 bp):
CTTGGGTTCGCTCAAACCAAGCTT
Found at i:25567971 original size:14 final size:14
Alignment explanation
Indices: 25567952--25567988 Score: 74
Period size: 14 Copynumber: 2.6 Consensus size: 14
25567942 TGATAGTAAA
25567952 CAACCATTTGCAGC
1 CAACCATTTGCAGC
25567966 CAACCATTTGCAGC
1 CAACCATTTGCAGC
25567980 CAACCATTT
1 CAACCATTT
25567989 TTTGCCCCAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.30, C:0.35, G:0.11, T:0.24
Consensus pattern (14 bp):
CAACCATTTGCAGC
Found at i:25574003 original size:19 final size:18
Alignment explanation
Indices: 25573979--25574077 Score: 74
Period size: 19 Copynumber: 5.3 Consensus size: 18
25573969 AATATATATA
25573979 TTTTTAGAATTTTTTAAATT
1 TTTTTA-AATTTTTTAAA-T
25573999 TTTTATAAATTTTTTAAA-
1 TTTT-TAAATTTTTTAAAT
** * *
25574017 AATATAAATTTTTGAAAT
1 TTTTTAAATTTTTTAAAT
*
25574035 TTTTATAAATATTTTAAAT
1 TTTT-TAAATTTTTTAAAT
** *
25574054 TTTAAAAATTATTTTGAAT
1 TTTTTAAATT-TTTTAAAT
25574073 TTTTT
1 TTTTT
25574078 GTAATTTTTA
Statistics
Matches: 60, Mismatches: 15, Indels: 9
0.71 0.18 0.11
Matches are distributed among these distances:
17 12 0.20
18 6 0.10
19 25 0.42
20 15 0.25
21 2 0.03
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (18 bp):
TTTTTAAATTTTTTAAAT
Found at i:25576248 original size:51 final size:49
Alignment explanation
Indices: 25576162--25576276 Score: 126
Period size: 51 Copynumber: 2.3 Consensus size: 49
25576152 AAACACCATT
* * *
25576162 TGTGGACACGCCA-CACTAATTTGCAGATAAACTGCCACTAA-TAACATTGA
1 TGTGGACAAGCCACCACTAATGTGCAAATAAACTGCCACTAATTAA-A-T-A
** * *
25576212 TGTGGACAAGCCACCACTAATGTGCAAATTTACTGCCATTAATTTAATA
1 TGTGGACAAGCCACCACTAATGTGCAAATAAACTGCCACTAATTAAATA
25576261 TGTGGACAAGCCACCA
1 TGTGGACAAGCCACCA
25576277 TTGATTTGTA
Statistics
Matches: 56, Mismatches: 7, Indels: 5
0.82 0.10 0.07
Matches are distributed among these distances:
49 17 0.30
50 13 0.23
51 24 0.43
52 2 0.04
ACGTcount: A:0.35, C:0.23, G:0.17, T:0.25
Consensus pattern (49 bp):
TGTGGACAAGCCACCACTAATGTGCAAATAAACTGCCACTAATTAAATA
Found at i:25576296 original size:49 final size:51
Alignment explanation
Indices: 25576162--25576296 Score: 143
Period size: 49 Copynumber: 2.7 Consensus size: 51
25576152 AAACACCATT
*
25576162 TGTGGACACGCCA-CACTAATTTGCAGATAAACTGCCACTAATAACATTGA
1 TGTGGACAAGCCACCACTAATTTGCAGATAAACTGCCACTAATAACATTGA
* * ** * *
25576212 TGTGGACAAGCCACCACTAATGTGCAAATTTACTGCCATTAATTTA-A-T-A
1 TGTGGACAAGCCACCACTAATTTGCAGATAAACTGCCACTAA-TAACATTGA
* * *
25576261 TGTGGACAAGCCACCATTGATTTGTAGATAAACTGC
1 TGTGGACAAGCCACCACTAATTTGCAGATAAACTGC
25576297 TACTGCTTCC
Statistics
Matches: 69, Mismatches: 14, Indels: 5
0.78 0.16 0.06
Matches are distributed among these distances:
49 30 0.43
50 13 0.19
51 24 0.35
52 2 0.03
ACGTcount: A:0.34, C:0.21, G:0.17, T:0.27
Consensus pattern (51 bp):
TGTGGACAAGCCACCACTAATTTGCAGATAAACTGCCACTAATAACATTGA
Found at i:25577958 original size:20 final size:22
Alignment explanation
Indices: 25577922--25577970 Score: 59
Period size: 20 Copynumber: 2.3 Consensus size: 22
25577912 TTAATATATA
*
25577922 TTTTTA-TTTTGTTTTATTT-C
1 TTTTTATTTTTGTCTTATTTAC
25577942 TTTTTATTTTTG-CTTATTTAAC
1 TTTTTATTTTTGTCTTATTT-AC
25577964 TTTTTAT
1 TTTTTAT
25577971 GCTTATTTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
20 12 0.48
21 5 0.20
22 8 0.32
ACGTcount: A:0.14, C:0.06, G:0.04, T:0.76
Consensus pattern (22 bp):
TTTTTATTTTTGTCTTATTTAC
Found at i:25590078 original size:17 final size:17
Alignment explanation
Indices: 25590056--25590088 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
25590046 TGTTAGTAAA
*
25590056 CATTGTTATTGCATTTC
1 CATTGTCATTGCATTTC
25590073 CATTGTCATTGCATTT
1 CATTGTCATTGCATTT
25590089 TAGTGTTAGT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.18, C:0.18, G:0.12, T:0.52
Consensus pattern (17 bp):
CATTGTCATTGCATTTC
Found at i:25604472 original size:11 final size:11
Alignment explanation
Indices: 25604456--25604499 Score: 70
Period size: 11 Copynumber: 4.0 Consensus size: 11
25604446 CTCCTAAAGC
*
25604456 CTTTCTCATTT
1 CTTTCTCTTTT
25604467 CTTTCTCTTTT
1 CTTTCTCTTTT
*
25604478 CTTTCCCTTTT
1 CTTTCTCTTTT
25604489 CTTTCTCTTTT
1 CTTTCTCTTTT
25604500 TCGACGTATC
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
11 30 1.00
ACGTcount: A:0.02, C:0.30, G:0.00, T:0.68
Consensus pattern (11 bp):
CTTTCTCTTTT
Found at i:25605060 original size:7 final size:7
Alignment explanation
Indices: 25605036--25605083 Score: 57
Period size: 7 Copynumber: 7.3 Consensus size: 7
25605026 ACCAAGTCAA
25605036 ACCGTTG
1 ACCGTTG
25605043 A-C-TTG
1 ACCGTTG
25605048 -CCGTTG
1 ACCGTTG
25605054 ACCGTTG
1 ACCGTTG
25605061 ACCGTTG
1 ACCGTTG
*
25605068 ATCGTTG
1 ACCGTTG
*
25605075 ATCGTTG
1 ACCGTTG
25605082 AC
1 AC
25605084 TTTTTTCGAA
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
5 4 0.11
6 4 0.11
7 28 0.78
ACGTcount: A:0.15, C:0.25, G:0.27, T:0.33
Consensus pattern (7 bp):
ACCGTTG
Found at i:25606147 original size:19 final size:20
Alignment explanation
Indices: 25606115--25606172 Score: 57
Period size: 19 Copynumber: 2.9 Consensus size: 20
25606105 TTAGTTACAA
25606115 ATTTATATTA-TATTATATT-
1 ATTT-TATTATTATTATATTG
*
25606134 ATTTTATTATTATTATTTTG
1 ATTTTATTATTATTATATTG
*
25606154 ATTTTGGATTATTAATATA
1 ATTTT--ATTATTATTATA
25606173 CTTTGTTAGT
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
18 5 0.16
19 12 0.38
20 5 0.16
22 10 0.31
ACGTcount: A:0.33, C:0.00, G:0.05, T:0.62
Consensus pattern (20 bp):
ATTTTATTATTATTATATTG
Found at i:25611786 original size:36 final size:36
Alignment explanation
Indices: 25611739--25611836 Score: 169
Period size: 36 Copynumber: 2.7 Consensus size: 36
25611729 GGAACGGCCT
*
25611739 TGACCGTTGGGTCAACAGGGAGTAAAATGAGCATCA
1 TGACCATTGGGTCAACAGGGAGTAAAATGAGCATCA
*
25611775 TGACCATTGGGTTAACAGGGAGTAAAATGAGCATCA
1 TGACCATTGGGTCAACAGGGAGTAAAATGAGCATCA
*
25611811 TGACCATTGGGTCAACAAGGAGTAAA
1 TGACCATTGGGTCAACAGGGAGTAAA
25611837 TCAGATATCG
Statistics
Matches: 58, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 58 1.00
ACGTcount: A:0.36, C:0.15, G:0.29, T:0.20
Consensus pattern (36 bp):
TGACCATTGGGTCAACAGGGAGTAAAATGAGCATCA
Found at i:25614194 original size:2 final size:2
Alignment explanation
Indices: 25614187--25614221 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
25614177 AGTCCTCTTT
25614187 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 T
25614222 TATTTTGTAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:25614281 original size:18 final size:17
Alignment explanation
Indices: 25614238--25614281 Score: 54
Period size: 18 Copynumber: 2.6 Consensus size: 17
25614228 GTATTATTTC
25614238 TTTTTA-TTTTTGCTTA
1 TTTTTATTTTTTGCTTA
* *
25614254 TTTATCTTTTTATGCTTA
1 TTTTTATTTTT-TGCTTA
25614272 TTTTTATTTT
1 TTTTTATTTT
25614282 ATTTTCTAGT
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
16 4 0.18
17 4 0.18
18 14 0.64
ACGTcount: A:0.14, C:0.07, G:0.05, T:0.75
Consensus pattern (17 bp):
TTTTTATTTTTTGCTTA
Found at i:25624725 original size:17 final size:17
Alignment explanation
Indices: 25624686--25624725 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
25624676 ATGTAGTATA
*
25624686 ATTGTCCCTGCATTATT
1 ATTGTCACTGCATTATT
* *
25624703 AATGTCACTGCATTTTT
1 ATTGTCACTGCATTATT
25624720 ATTGTC
1 ATTGTC
25624726 GTTGCATCTA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.20, C:0.20, G:0.12, T:0.47
Consensus pattern (17 bp):
ATTGTCACTGCATTATT
Found at i:25627215 original size:15 final size:16
Alignment explanation
Indices: 25627195--25627224 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
25627185 CTTCCTTATT
25627195 TTCTA-TTTCTTTTAA
1 TTCTATTTTCTTTTAA
25627210 TTCTATTTTCTTTTA
1 TTCTATTTTCTTTTA
25627225 TCTTTAATTC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.17, C:0.13, G:0.00, T:0.70
Consensus pattern (16 bp):
TTCTATTTTCTTTTAA
Found at i:25627242 original size:21 final size:22
Alignment explanation
Indices: 25627191--25627246 Score: 80
Period size: 22 Copynumber: 2.6 Consensus size: 22
25627181 TCGACTTCCT
*
25627191 TATTTTCTATTTCT-TTTAATTC
1 TATTTTCT-TTTATCTTTAATTC
25627213 TATTTTCTTTTATCTTTAATTC
1 TATTTTCTTTTATCTTTAATTC
25627235 TA-TTTCTTTTAT
1 TATTTTCTTTTAT
25627247 TTTTCCTTAG
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
21 14 0.44
22 18 0.56
ACGTcount: A:0.18, C:0.12, G:0.00, T:0.70
Consensus pattern (22 bp):
TATTTTCTTTTATCTTTAATTC
Found at i:25638030 original size:14 final size:14
Alignment explanation
Indices: 25637994--25638058 Score: 62
Period size: 16 Copynumber: 4.6 Consensus size: 14
25637984 AACAAAGCAC
*
25637994 AAATAATTATACGA
1 AAATAAATATACGA
25638008 ATGAATAAATATACGA
1 A--AATAAATATACGA
**
25638024 AAATAAATATCAAAA
1 AAATAAATAT-ACGA
25638039 AAATAAA-ATACG-
1 AAATAAATATACGA
25638051 AAATAAAT
1 AAATAAAT
25638059 GAGAAAATAC
Statistics
Matches: 42, Mismatches: 5, Indels: 9
0.75 0.09 0.16
Matches are distributed among these distances:
12 7 0.17
13 1 0.02
14 12 0.29
15 9 0.21
16 13 0.31
ACGTcount: A:0.65, C:0.06, G:0.06, T:0.23
Consensus pattern (14 bp):
AAATAAATATACGA
Done.