Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr10
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: 95480121
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.31
Warning! 2980117 characters in sequence are not A, C, G, or T
File 91 of 284
Found at i:30055560 original size:39 final size:39
Alignment explanation
Indices: 30055514--30055598 Score: 152
Period size: 39 Copynumber: 2.2 Consensus size: 39
30055504 GCTCTGATGA
30055514 GCTTCAGTTAGCCTTCGGGCTTCCGTTTAGCACTTATGT
1 GCTTCAGTTAGCCTTCGGGCTTCCGTTTAGCACTTATGT
* *
30055553 GCTTCAGTTAGCGTTCGGGCTTCCGTTTAGCACTTATTT
1 GCTTCAGTTAGCCTTCGGGCTTCCGTTTAGCACTTATGT
30055592 GCTTCAG
1 GCTTCAG
30055599 CTAGACTTTG
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
39 44 1.00
ACGTcount: A:0.13, C:0.25, G:0.24, T:0.39
Consensus pattern (39 bp):
GCTTCAGTTAGCCTTCGGGCTTCCGTTTAGCACTTATGT
Found at i:30056080 original size:12 final size:12
Alignment explanation
Indices: 30056065--30056090 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
30056055 TATATTAGTG
30056065 AATACTACTTGA
1 AATACTACTTGA
30056077 AATACTACTTGA
1 AATACTACTTGA
30056089 AA
1 AA
30056091 GTATGAATGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.46, C:0.15, G:0.08, T:0.31
Consensus pattern (12 bp):
AATACTACTTGA
Found at i:30060570 original size:46 final size:45
Alignment explanation
Indices: 30060517--30060778 Score: 251
Period size: 46 Copynumber: 5.7 Consensus size: 45
30060507 AGATTTGTGT
30060517 GCCAGTGTAAGACATGTCTGGGACATGCATCGGCCACATTATGATA
1 GCCAGTGTAAGACATGTCTGGGACATGCATCGGCCACA-TATGATA
* * * **
30060563 GCCAGTGTAAGACCATGTCTGGGACATGGCATCGG-CATTGAGACGAGG
1 GCCAGTGTAAGA-CATGTCTGGGACAT-GCATCGGCCA--CATATGATA
* * *
30060611 GCTAGTGTAAGACATGTCTGGGACATGCATCAGCCACAGTATGAGA
1 GCCAGTGTAAGACATGTCTGGGACATGCATCGGCCACA-TATGATA
* * * * * *
30060657 GCCAATATAAGACATGTCTAGGACATGCATCGGCCTCGAGATGTTA
1 GCCAGTGTAAGACATGTCTGGGACATGCATCGGCCAC-ATATGATA
* * * * *
30060703 GCCAGTGTCAGACATGTCTGGGACATGCGTCAGCTACGAGATG-T-
1 GCCAGTGTAAGACATGTCTGGGACATGCATCGGCCAC-ATATGATA
*
30060747 GCTAGTGTAAGACATGTCTGGGACATGCATCG
1 GCCAGTGTAAGACATGTCTGGGACATGCATCG
30060779 ACACGGTTAC
Statistics
Matches: 177, Mismatches: 32, Indels: 16
0.79 0.14 0.07
Matches are distributed among these distances:
44 28 0.16
45 2 0.01
46 92 0.52
47 33 0.19
48 21 0.12
49 1 0.01
ACGTcount: A:0.27, C:0.21, G:0.29, T:0.23
Consensus pattern (45 bp):
GCCAGTGTAAGACATGTCTGGGACATGCATCGGCCACATATGATA
Found at i:30060638 original size:94 final size:91
Alignment explanation
Indices: 30060517--30060778 Score: 312
Period size: 94 Copynumber: 2.8 Consensus size: 91
30060507 AGATTTGTGT
*
30060517 GCCAGTGTAAGACATGTCTGGGACATGCATCGGCCACATTATGATAGCCAGTGTAAGACCATGTC
1 GCCAGTGTAAGACATGTCTGGGACATGCATCAGCCACA-TATGATAGCCAGTGTAAGA-CATGTC
* *
30060582 TGGGACATGGCATCGGCATTGAGACGAGG
64 TGGGACAT-GCATCGGCATCGAGACGAGA
* * * *
30060611 GCTAGTGTAAGACATGTCTGGGACATGCATCAGCCACAGTATGAGAGCCAATATAAGACATGTCT
1 GCCAGTGTAAGACATGTCTGGGACATGCATCAGCCACA-TATGATAGCCAGTGTAAGACATGTCT
* * * **
30060676 AGGACATGCATCGGCCTCGAGATGTTA
65 GGGACATGCATCGGCATCGAGACGAGA
* * * * *
30060703 GCCAGTGTCAGACATGTCTGGGACATGCGTCAGCTACGAGATG-T-GCTAGTGTAAGACATGTCT
1 GCCAGTGTAAGACATGTCTGGGACATGCATCAGCCAC-ATATGATAGCCAGTGTAAGACATGTCT
30060766 GGGACATGCATCG
65 GGGACATGCATCG
30060779 ACACGGTTAC
Statistics
Matches: 144, Mismatches: 23, Indels: 6
0.83 0.13 0.03
Matches are distributed among these distances:
90 28 0.19
92 50 0.35
93 14 0.10
94 52 0.36
ACGTcount: A:0.27, C:0.21, G:0.29, T:0.23
Consensus pattern (91 bp):
GCCAGTGTAAGACATGTCTGGGACATGCATCAGCCACATATGATAGCCAGTGTAAGACATGTCTG
GGACATGCATCGGCATCGAGACGAGA
Found at i:30062376 original size:20 final size:20
Alignment explanation
Indices: 30062351--30062390 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
30062341 TATTTCAGAG
30062351 TAAGATTTGAGTACTGAGGA
1 TAAGATTTGAGTACTGAGGA
30062371 TAAGATTTGAGTACTGAGGA
1 TAAGATTTGAGTACTGAGGA
30062391 ACTCTAGGCT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.35, C:0.05, G:0.30, T:0.30
Consensus pattern (20 bp):
TAAGATTTGAGTACTGAGGA
Found at i:30073447 original size:41 final size:42
Alignment explanation
Indices: 30073399--30073481 Score: 141
Period size: 43 Copynumber: 2.0 Consensus size: 42
30073389 ATATATGTGC
*
30073399 CATCCGAGCTCGTT-GTGGTCCGAGTTCATTATGGATGCGAG
1 CATCCGAGCTCGTTAGTGGTCCGAGTTCATAATGGATGCGAG
30073440 CATCCGAGCTCGTTGAGTGGTCCGAGTTCATAATGGATGCGA
1 CATCCGAGCTCGTT-AGTGGTCCGAGTTCATAATGGATGCGA
30073482 TATATGTGAT
Statistics
Matches: 39, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
41 14 0.36
43 25 0.64
ACGTcount: A:0.19, C:0.22, G:0.31, T:0.28
Consensus pattern (42 bp):
CATCCGAGCTCGTTAGTGGTCCGAGTTCATAATGGATGCGAG
Found at i:30076887 original size:18 final size:17
Alignment explanation
Indices: 30076866--30076935 Score: 61
Period size: 18 Copynumber: 3.9 Consensus size: 17
30076856 ATAATACAAT
*
30076866 AAAACAAATAAATAAAAG
1 AAAACAAA-AAAGAAAAG
*
30076884 AAAA-AAAAAAGACAAG
1 AAAACAAAAAAGAAAAG
*
30076900 CAAAACAAAATAGAAAAG
1 -AAAACAAAAAAGAAAAG
*
30076918 AAAAGAAAGAAAAGAAAA
1 AAAA-CAA-AAAAGAAAA
30076936 AGGGAAAGAA
Statistics
Matches: 42, Mismatches: 6, Indels: 7
0.76 0.11 0.13
Matches are distributed among these distances:
16 7 0.17
17 11 0.26
18 16 0.38
19 8 0.19
ACGTcount: A:0.79, C:0.06, G:0.11, T:0.04
Consensus pattern (17 bp):
AAAACAAAAAAGAAAAG
Found at i:30076943 original size:21 final size:20
Alignment explanation
Indices: 30076919--30076957 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
30076909 ATAGAAAAGA
30076919 AAAGAAAGAAAAGAAAAAGGG
1 AAAGAAAG-AAAGAAAAAGGG
*
30076940 AAAGAAAGAACGAAAAAG
1 AAAGAAAGAAAGAAAAAG
30076958 AAGGAGACGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.72, C:0.03, G:0.26, T:0.00
Consensus pattern (20 bp):
AAAGAAAGAAAGAAAAAGGG
Found at i:30076995 original size:8 final size:8
Alignment explanation
Indices: 30076982--30077006 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
30076972 CCTTAAGGGC
30076982 TTCAAAGT
1 TTCAAAGT
30076990 TTCAAAGT
1 TTCAAAGT
30076998 TTCAAAGT
1 TTCAAAGT
30077006 T
1 T
30077007 CAATTGGTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.36, C:0.12, G:0.12, T:0.40
Consensus pattern (8 bp):
TTCAAAGT
Found at i:30077933 original size:37 final size:38
Alignment explanation
Indices: 30077858--30077936 Score: 97
Period size: 37 Copynumber: 2.1 Consensus size: 38
30077848 GTCAATTTAC
** *
30077858 TACTTCGGATTTATTCGATGAGGCACTGGGTGTCAATT
1 TACTTCGGATTTAACCGATGAGACACTGGGTGTCAATT
* * *
30077896 TACTTCGG-TTTAACCGATTAGACACTGTGTGTTAATT
1 TACTTCGGATTTAACCGATGAGACACTGGGTGTCAATT
30077933 TACT
1 TACT
30077937 ACTTCGAATT
Statistics
Matches: 35, Mismatches: 6, Indels: 1
0.83 0.14 0.02
Matches are distributed among these distances:
37 27 0.77
38 8 0.23
ACGTcount: A:0.23, C:0.16, G:0.22, T:0.39
Consensus pattern (38 bp):
TACTTCGGATTTAACCGATGAGACACTGGGTGTCAATT
Found at i:30077953 original size:40 final size:40
Alignment explanation
Indices: 30077847--30077966 Score: 138
Period size: 40 Copynumber: 3.0 Consensus size: 40
30077837 AGACATTGGA
*
30077847 TGTCAATTTACTACTTCGGATTTATTCGATGAGGCACTGGG
1 TGTCAATTTACTACTTC-GATTTATCCGATGAGGCACTGGG
* * * * *
30077888 TGTCAA-TT--TACTTCGGTTTAACCGATTAGACACTGTG
1 TGTCAATTTACTACTTCGATTTATCCGATGAGGCACTGGG
* *
30077925 TGTTAATTTACTACTTCGAATTATCCGATGAGGCACTGGG
1 TGTCAATTTACTACTTCGATTTATCCGATGAGGCACTGGG
30077965 TG
1 TG
30077967 CCAAACTGGT
Statistics
Matches: 63, Mismatches: 13, Indels: 7
0.76 0.16 0.08
Matches are distributed among these distances:
37 22 0.35
38 8 0.13
40 27 0.43
41 6 0.10
ACGTcount: A:0.23, C:0.17, G:0.23, T:0.37
Consensus pattern (40 bp):
TGTCAATTTACTACTTCGATTTATCCGATGAGGCACTGGG
Found at i:30081225 original size:18 final size:19
Alignment explanation
Indices: 30081185--30081228 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 19
30081175 ATACATTATT
*
30081185 TTTTTAATAGTTTTACAAC
1 TTTTTAATAGTTTTACAAA
30081204 TTTTTAATA-TTTTA-ATAA
1 TTTTTAATAGTTTTACA-AA
30081222 TTTTTAA
1 TTTTTAA
30081229 ACTTTTTAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
17 1 0.04
18 13 0.57
19 9 0.39
ACGTcount: A:0.34, C:0.05, G:0.02, T:0.59
Consensus pattern (19 bp):
TTTTTAATAGTTTTACAAA
Found at i:30081225 original size:27 final size:28
Alignment explanation
Indices: 30081186--30081254 Score: 90
Period size: 27 Copynumber: 2.5 Consensus size: 28
30081176 TACATTATTT
*
30081186 TTTTAAT-AGTTTTACAACTTTTT-AATA
1 TTTTAATAATTTTTA-AACTTTTTAAATA
30081213 TTTTAATAATTTTTAAACTTTTTAAATA
1 TTTTAATAATTTTTAAACTTTTTAAATA
*
30081241 TTTT-ACAATTTTTA
1 TTTTAATAATTTTTA
30081255 TAATTTTATA
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
27 24 0.63
28 14 0.37
ACGTcount: A:0.35, C:0.06, G:0.01, T:0.58
Consensus pattern (28 bp):
TTTTAATAATTTTTAAACTTTTTAAATA
Found at i:30081235 original size:19 final size:18
Alignment explanation
Indices: 30081212--30081261 Score: 59
Period size: 18 Copynumber: 2.8 Consensus size: 18
30081202 ACTTTTTAAT
*
30081212 ATTTTAATAATTTTTA-A
1 ATTTTTATAATTTTTACA
30081229 ACTTTTTA-AATATTTTACA
1 A-TTTTTATAAT-TTTTACA
30081248 ATTTTTATAATTTT
1 ATTTTTATAATTTT
30081262 ATAAGTTTTG
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
17 4 0.14
18 19 0.68
19 5 0.18
ACGTcount: A:0.36, C:0.04, G:0.00, T:0.60
Consensus pattern (18 bp):
ATTTTTATAATTTTTACA
Found at i:30081259 original size:9 final size:9
Alignment explanation
Indices: 30081212--30081270 Score: 52
Period size: 9 Copynumber: 6.6 Consensus size: 9
30081202 ACTTTTTAAT
*
30081212 ATTTTAATA
1 ATTTTTATA
30081221 ATTTTTA-A
1 ATTTTTATA
30081229 ACTTTTTA-A
1 A-TTTTTATA
*
30081238 ATATTTTACA
1 AT-TTTTATA
30081248 ATTTTTATA
1 ATTTTTATA
30081257 A-TTTTATA
1 ATTTTTATA
30081265 AGTTTT
1 A-TTTT
30081271 GTTTTACATT
Statistics
Matches: 43, Mismatches: 2, Indels: 9
0.80 0.04 0.17
Matches are distributed among these distances:
8 11 0.26
9 26 0.60
10 6 0.14
ACGTcount: A:0.36, C:0.03, G:0.02, T:0.59
Consensus pattern (9 bp):
ATTTTTATA
Found at i:30081341 original size:15 final size:16
Alignment explanation
Indices: 30081313--30081355 Score: 70
Period size: 15 Copynumber: 2.8 Consensus size: 16
30081303 CAATTGTTTC
30081313 TTTTTATTTATTGTAA
1 TTTTTATTTATTGTAA
30081329 TTTTTATTT-TTGTAA
1 TTTTTATTTATTGTAA
*
30081344 TTTTTATGTATT
1 TTTTTATTTATT
30081356 TTTTAAATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
15 14 0.56
16 11 0.44
ACGTcount: A:0.21, C:0.00, G:0.07, T:0.72
Consensus pattern (16 bp):
TTTTTATTTATTGTAA
Found at i:30081393 original size:21 final size:20
Alignment explanation
Indices: 30081344--30081395 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 20
30081334 ATTTTTGTAA
*
30081344 TTTTTATGTATTTTTTAAAT
1 TTTTTATATATTTTTTAAAT
** *
30081364 TTTAGATATATTTTTCTTAAT
1 TTTTTATATATTTTT-TAAAT
30081385 TTTTTATATAT
1 TTTTTATATAT
30081396 CTGTTTATTT
Statistics
Matches: 25, Mismatches: 6, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
20 12 0.48
21 13 0.52
ACGTcount: A:0.27, C:0.02, G:0.04, T:0.67
Consensus pattern (20 bp):
TTTTTATATATTTTTTAAAT
Found at i:30082525 original size:20 final size:19
Alignment explanation
Indices: 30082502--30082542 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
30082492 AATACAACAC
30082502 TATTGCAATCAATTCTCTTT
1 TATT-CAATCAATTCTCTTT
**
30082522 TATTCTTTCAATTCTCTTT
1 TATTCAATCAATTCTCTTT
30082541 TA
1 TA
30082543 GTTTGTTTTC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 15 0.79
20 4 0.21
ACGTcount: A:0.22, C:0.20, G:0.02, T:0.56
Consensus pattern (19 bp):
TATTCAATCAATTCTCTTT
Found at i:30085850 original size:42 final size:42
Alignment explanation
Indices: 30085743--30085893 Score: 131
Period size: 42 Copynumber: 3.6 Consensus size: 42
30085733 ATACCAATGC
* * * * * * *
30085743 CATATCCTAGATATGGTCTTACATGCAATCTCGTATCGATGC
1 CATATCCCAAATATGGTCTTACACGAAATCTCATATTGATGT
* *** * *
30085785 CAATAGCCCGGCTATGGTTTTACACGAAATCTCTTATTGATGT
1 C-ATATCCCAAATATGGTCTTACACGAAATCTCATATTGATGT
* * * *
30085828 TATATCCTAAATATGGTCTTACATGAAGTCTCATATTGATGT
1 CATATCCCAAATATGGTCTTACACGAAATCTCATATTGATGT
*
30085870 CATATCCCAGATATGGTCTTACAC
1 CATATCCCAAATATGGTCTTACAC
30085894 ATAGACTTAG
Statistics
Matches: 84, Mismatches: 24, Indels: 2
0.76 0.22 0.02
Matches are distributed among these distances:
42 53 0.63
43 31 0.37
ACGTcount: A:0.28, C:0.21, G:0.16, T:0.35
Consensus pattern (42 bp):
CATATCCCAAATATGGTCTTACACGAAATCTCATATTGATGT
Found at i:30087388 original size:24 final size:24
Alignment explanation
Indices: 30087337--30087389 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
30087327 GGTAGATTCT
* **
30087337 TGGGTAGTCTGTTGGGTCAAATGC
1 TGGGCAGTCTGTTGGGTCAAATAA
30087361 TGGGCAGTCTGTTGGG-CAGAATAA
1 TGGGCAGTCTGTTGGGTCA-AATAA
30087385 TGGGC
1 TGGGC
30087390 CGCATAGTGA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 2 0.08
24 23 0.92
ACGTcount: A:0.19, C:0.13, G:0.40, T:0.28
Consensus pattern (24 bp):
TGGGCAGTCTGTTGGGTCAAATAA
Found at i:30088592 original size:39 final size:39
Alignment explanation
Indices: 30088539--30088664 Score: 180
Period size: 39 Copynumber: 3.2 Consensus size: 39
30088529 GGACTTTAGC
* * ** * *
30088539 CCGGACATATTTCCAGCATGTAGCCTGTGGACCTTAAGT
1 CCGGATATAATTCCAGCACATAGCCTGCGGACCCTAAGT
* *
30088578 CCAGATATAATTCCAGTACATAGCCTGCGGACCCTAAGT
1 CCGGATATAATTCCAGCACATAGCCTGCGGACCCTAAGT
30088617 CCGGATATAATTCCAGCACATAGCCTGCGGACCCTAAGT
1 CCGGATATAATTCCAGCACATAGCCTGCGGACCCTAAGT
30088656 CCGGATATA
1 CCGGATATA
30088665 CATCACTGAA
Statistics
Matches: 77, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
39 77 1.00
ACGTcount: A:0.28, C:0.28, G:0.21, T:0.24
Consensus pattern (39 bp):
CCGGATATAATTCCAGCACATAGCCTGCGGACCCTAAGT
Found at i:30093384 original size:47 final size:44
Alignment explanation
Indices: 30093225--30093447 Score: 148
Period size: 47 Copynumber: 4.8 Consensus size: 44
30093215 GGATATATTA
* *
30093225 CCGATGCCATGTTCCAGACATGGTCTTACACTGGCTC-TCATATGTACGTG
1 CCGATG-CATGTCCCAGACA-CGTCTTACACTGGCTCATC-T-T-T--GTG
* * * * *
30093275 CTGATGCATGTCCCAGACATGTCTTACACTAGCACAACTCTTAGT-
1 CCGATGCATGTCCCAGACACGTCTTACACTGGCTC-A-TCTTTGTG
* * *
30093320 -CAATGCGTGTCCTAGACACGTCTTACACTGGCT-ATCTTTGTCGAGG
1 CCGATGCATGTCCCAGACACGTCTTACACTGGCTCATCTTTGT----G
* *
30093366 CCGATGCATGTCCCAGACATGTCTTACTCTGGCACTCATCTTTGTG
1 CCGATGCATGTCCCAGACACGTCTTACACTGG--CTCATCTTTGTG
*
30093412 CCGATGCCATGTCCCAGACATGGTCTTACACTGGCT
1 CCGATG-CATGTCCCAGACA-CGTCTTACACTGGCT
30093448 TTCAAGTCAC
Statistics
Matches: 138, Mismatches: 21, Indels: 32
0.72 0.11 0.17
Matches are distributed among these distances:
41 6 0.04
42 1 0.01
44 26 0.19
46 11 0.08
47 39 0.28
48 24 0.17
49 15 0.11
50 14 0.10
51 2 0.01
ACGTcount: A:0.21, C:0.29, G:0.21, T:0.30
Consensus pattern (44 bp):
CCGATGCATGTCCCAGACACGTCTTACACTGGCTCATCTTTGTG
Found at i:30098657 original size:50 final size:50
Alignment explanation
Indices: 30098599--30098699 Score: 193
Period size: 50 Copynumber: 2.0 Consensus size: 50
30098589 GTGCATTGAA
*
30098599 TTATCATACATAAATGTGATTTCTATGATTATGGATTTTATGGGAAATTG
1 TTATCATACATAAATGTGATTTCTATGATTATGGATATTATGGGAAATTG
30098649 TTATCATACATAAATGTGATTTCTATGATTATGGATATTATGGGAAATTG
1 TTATCATACATAAATGTGATTTCTATGATTATGGATATTATGGGAAATTG
30098699 T
1 T
30098700 AAGTTCATAT
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
50 50 1.00
ACGTcount: A:0.33, C:0.06, G:0.18, T:0.44
Consensus pattern (50 bp):
TTATCATACATAAATGTGATTTCTATGATTATGGATATTATGGGAAATTG
Found at i:30099639 original size:51 final size:51
Alignment explanation
Indices: 30099563--30099664 Score: 204
Period size: 51 Copynumber: 2.0 Consensus size: 51
30099553 TCTCAGTGAG
30099563 TCTATTTTCATATAAAAGAAACAGATCAAGAAAAGGAGTTCTATATTTTGA
1 TCTATTTTCATATAAAAGAAACAGATCAAGAAAAGGAGTTCTATATTTTGA
30099614 TCTATTTTCATATAAAAGAAACAGATCAAGAAAAGGAGTTCTATATTTTGA
1 TCTATTTTCATATAAAAGAAACAGATCAAGAAAAGGAGTTCTATATTTTGA
30099665 GATATTTATG
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
51 51 1.00
ACGTcount: A:0.43, C:0.10, G:0.14, T:0.33
Consensus pattern (51 bp):
TCTATTTTCATATAAAAGAAACAGATCAAGAAAAGGAGTTCTATATTTTGA
Found at i:30104940 original size:49 final size:49
Alignment explanation
Indices: 30104868--30105011 Score: 200
Period size: 49 Copynumber: 2.9 Consensus size: 49
30104858 GCCGAAGCTA
30104868 TCTGGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCAACAG-
1 TCTGGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACC-ACAGT
* * * * *
30104917 TCTGGTACACGTAGTAGCCTGCACTTAGTACTACACACGTGATCACAGTTT
1 TCTGGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCACAG--T
*
30104968 TCGGGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACC
1 TCTGGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACC
30105012 TCACAATAGA
Statistics
Matches: 81, Mismatches: 11, Indels: 4
0.84 0.11 0.04
Matches are distributed among these distances:
48 4 0.05
49 39 0.48
51 38 0.47
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.25
Consensus pattern (49 bp):
TCTGGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCACAGT
Found at i:30104996 original size:51 final size:49
Alignment explanation
Indices: 30104871--30105011 Score: 185
Period size: 51 Copynumber: 2.8 Consensus size: 49
30104861 GAAGCTATCT
* *
30104871 GGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCAACAGTCT
1 GGTACGCATAGTAGCCTGCACTTAGTACTACACACGCGACCAACAGTCG
* * * *
30104920 GGTACACGTAGTAGCCTGCACTTAGTACTACACACGTGATC-ACAGTTTTCG
1 GGTACGCATAGTAGCCTGCACTTAGTACTACACACGCGACCAACAG---TCG
*
30104971 GGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACC
1 GGTACGCATAGTAGCCTGCACTTAGTACTACACACGCGACC
30105012 TCACAATAGA
Statistics
Matches: 78, Mismatches: 11, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
48 4 0.05
49 36 0.46
51 38 0.49
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (49 bp):
GGTACGCATAGTAGCCTGCACTTAGTACTACACACGCGACCAACAGTCG
Found at i:30115576 original size:11 final size:11
Alignment explanation
Indices: 30115534--30115570 Score: 56
Period size: 11 Copynumber: 3.4 Consensus size: 11
30115524 CCACCCCAAA
30115534 CATATACATAT
1 CATATACATAT
*
30115545 CATATGCATAT
1 CATATACATAT
*
30115556 CTTATACATAT
1 CATATACATAT
30115567 CATA
1 CATA
30115571 ATCATAAACG
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.41, C:0.19, G:0.03, T:0.38
Consensus pattern (11 bp):
CATATACATAT
Found at i:30119048 original size:38 final size:37
Alignment explanation
Indices: 30118982--30119096 Score: 124
Period size: 38 Copynumber: 3.0 Consensus size: 37
30118972 AAAAACGCCT
* *
30118982 CTATAGATCGAACATTAGTGGTGTTTTTTAAAAAAGTCG
1 CTATAGATCGAGCATTAGTGGCGTTTTTTAAAAAA--CG
** *
30119021 CTATAGAT-TTGCATTAGTGGCGCTTTTTGAAAACAACG
1 CTATAGATCGAGCATTAGTGGCG-TTTTTTAAAA-AACG
* *
30119059 CTATAGGTCGAGCATTAGTGGCATTTTTTAAAAAACG
1 CTATAGATCGAGCATTAGTGGCGTTTTTTAAAAAACG
30119096 C
1 C
30119097 CGCAAAATAA
Statistics
Matches: 63, Mismatches: 10, Indels: 8
0.78 0.12 0.10
Matches are distributed among these distances:
37 5 0.08
38 28 0.44
39 28 0.44
40 2 0.03
ACGTcount: A:0.31, C:0.14, G:0.21, T:0.34
Consensus pattern (37 bp):
CTATAGATCGAGCATTAGTGGCGTTTTTTAAAAAACG
Found at i:30119200 original size:40 final size:39
Alignment explanation
Indices: 30119139--30119268 Score: 136
Period size: 40 Copynumber: 3.2 Consensus size: 39
30119129 TTTTGAGCCT
* * *
30119139 TCGAGGCATTAGCGGCACTTTTCAAGAAATGGCGCTATAGA
1 TCGA-GCATTAGCGGCGCTTTTCAA-AAACGCCGCTATAGA
* *
30119180 TCGAG-ATTTAGCGGCGCTTTTTTAAAAACGCCGCTATATA
1 TCGAGCA-TTAGCGGCGC-TTTTCAAAAACGCCGCTATAGA
* *
30119220 TCGAGCATTAGCGGCGCTTTTTGAAAAACGCCGCTATAGG
1 TCGAGCATTAGCGGCGC-TTTTCAAAAACGCCGCTATAGA
*
30119260 TCTAGCATT
1 TCGAGCATT
30119269 TTGGCATTTT
Statistics
Matches: 77, Mismatches: 9, Indels: 7
0.83 0.10 0.08
Matches are distributed among these distances:
39 1 0.01
40 65 0.84
41 11 0.14
ACGTcount: A:0.27, C:0.21, G:0.24, T:0.28
Consensus pattern (39 bp):
TCGAGCATTAGCGGCGCTTTTCAAAAACGCCGCTATAGA
Found at i:30119700 original size:15 final size:15
Alignment explanation
Indices: 30119680--30119732 Score: 72
Period size: 15 Copynumber: 3.6 Consensus size: 15
30119670 AATATTTTAA
*
30119680 GGTTTATGGATTATG
1 GGTTTAGGGATTATG
30119695 GGTTTAGGGATTATG
1 GGTTTAGGGATTATG
* *
30119710 GGTTTAGGGTTTA-A
1 GGTTTAGGGATTATG
30119724 GGTTTAGGG
1 GGTTTAGGG
30119733 GTTTATATTT
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
14 9 0.26
15 26 0.74
ACGTcount: A:0.19, C:0.00, G:0.40, T:0.42
Consensus pattern (15 bp):
GGTTTAGGGATTATG
Found at i:30119719 original size:22 final size:22
Alignment explanation
Indices: 30119694--30119737 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
30119684 TATGGATTAT
* *
30119694 GGGTTTAGGGATTATGGGTTTA
1 GGGTTTAAGGATTAGGGGTTTA
*
30119716 GGGTTTAAGGTTTAGGGGTTTA
1 GGGTTTAAGGATTAGGGGTTTA
30119738 TATTTTATGA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.18, C:0.00, G:0.41, T:0.41
Consensus pattern (22 bp):
GGGTTTAAGGATTAGGGGTTTA
Found at i:30119781 original size:22 final size:22
Alignment explanation
Indices: 30119756--30119798 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
30119746 GAGTTAATAT
*
30119756 TTTAAGGTTTATGGATTATGGA
1 TTTAAGGATTATGGATTATGGA
* *
30119778 TTTAGGGATTATGGTTTATGG
1 TTTAAGGATTATGGATTATGG
30119799 TTCAAGGGTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.23, C:0.00, G:0.30, T:0.47
Consensus pattern (22 bp):
TTTAAGGATTATGGATTATGGA
Found at i:30119786 original size:15 final size:14
Alignment explanation
Indices: 30119761--30119795 Score: 52
Period size: 15 Copynumber: 2.4 Consensus size: 14
30119751 AATATTTTAA
*
30119761 GGTTTATGGATTAT
1 GGTTTAGGGATTAT
30119775 GGATTTAGGGATTAT
1 GG-TTTAGGGATTAT
30119790 GGTTTA
1 GGTTTA
30119796 TGGTTCAAGG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
14 6 0.32
15 13 0.68
ACGTcount: A:0.23, C:0.00, G:0.31, T:0.46
Consensus pattern (14 bp):
GGTTTAGGGATTAT
Found at i:30119799 original size:7 final size:7
Alignment explanation
Indices: 30119609--30119800 Score: 69
Period size: 7 Copynumber: 26.1 Consensus size: 7
30119599 TTAATTATCA
*
30119609 TTATAGT
1 TTATGGT
*
30119616 TTAAGGT
1 TTATGGT
*
30119623 TTATGAT
1 TTATGGT
*
30119630 TTAGGGT
1 TTATGGT
*
30119637 ATATGGT
1 TTATGGT
*
30119644 TTAGGGT
1 TTATGGT
*
30119651 TTATAGTT
1 TTAT-GGT
30119659 TATGATGAGT
1 T-T-ATG-GT
* **
30119669 TAATATT
1 TTATGGT
*
30119676 TTAAGGT
1 TTATGGT
*
30119683 TTATGGA
1 TTATGGT
30119690 TTATGGGT
1 TTAT-GGT
* *
30119698 TTAGGGA
1 TTATGGT
30119705 TTATGGGT
1 TTAT-GGT
*
30119713 TTAGGGT
1 TTATGGT
*
30119720 TTAAGGT
1 TTATGGT
*
30119727 TTAGGGGT
1 TTA-TGGT
**
30119735 TTATATT
1 TTATGGT
30119742 TTATGAGT
1 TTATG-GT
* **
30119750 TAATATT
1 TTATGGT
*
30119757 TTAAGGT
1 TTATGGT
*
30119764 TTATGGA
1 TTATGGT
30119771 TTATGGAT
1 TTATGG-T
* *
30119779 TTAGGGA
1 TTATGGT
30119786 TTATGGT
1 TTATGGT
30119793 TTATGGT
1 TTATGGT
30119800 T
1 T
30119801 CAAGGGTTGA
Statistics
Matches: 127, Mismatches: 49, Indels: 18
0.65 0.25 0.09
Matches are distributed among these distances:
7 91 0.72
8 30 0.24
9 2 0.02
10 4 0.03
ACGTcount: A:0.24, C:0.00, G:0.28, T:0.48
Consensus pattern (7 bp):
TTATGGT
Found at i:30119822 original size:22 final size:22
Alignment explanation
Indices: 30119797--30119893 Score: 85
Period size: 22 Copynumber: 4.4 Consensus size: 22
30119787 TATGGTTTAT
30119797 GGTTCAAGGGTTGA-GGTTTAGG
1 GGTT-AAGGGTTGAGGGTTTAGG
* *
30119819 GGTTAAGAGTTAAGGGTTTAGG
1 GGTTAAGGGTTGAGGGTTTAGG
*
30119841 GGTTAGGGGTT-AGGGGTTTAAGG
1 GGTTAAGGGTTGA-GGGTTT-AGG
* *
30119864 GG-CATGGGTT-AGGAGTTTAGG
1 GGTTAAGGGTTGAGG-GTTTAGG
30119885 GGTTAAGGG
1 GGTTAAGGG
30119894 GGCATGGGTT
Statistics
Matches: 62, Mismatches: 8, Indels: 10
0.77 0.10 0.12
Matches are distributed among these distances:
21 15 0.24
22 42 0.68
23 5 0.08
ACGTcount: A:0.21, C:0.02, G:0.47, T:0.30
Consensus pattern (22 bp):
GGTTAAGGGTTGAGGGTTTAGG
Found at i:30119872 original size:29 final size:29
Alignment explanation
Indices: 30119840--30119923 Score: 127
Period size: 30 Copynumber: 2.9 Consensus size: 29
30119830 AAGGGTTTAG
30119840 GGGTTAGGGGTTAGGGGTTTAAGGGGCAT
1 GGGTTAGGGGTTAGGGGTTTAAGGGGCAT
*
30119869 GGGTTAGGAGTTTAGGGG-TTAAGGGGGCAT
1 GGGTTAGG-GGTTAGGGGTTTAA-GGGGCAT
30119899 GGGTTAGGGGTTAGGGGTTT-AGGGG
1 GGGTTAGGGGTTAGGGGTTTAAGGGG
30119924 TTAAGGCATT
Statistics
Matches: 50, Mismatches: 2, Indels: 7
0.85 0.03 0.12
Matches are distributed among these distances:
28 4 0.08
29 21 0.42
30 25 0.50
ACGTcount: A:0.17, C:0.02, G:0.54, T:0.27
Consensus pattern (29 bp):
GGGTTAGGGGTTAGGGGTTTAAGGGGCAT
Found at i:30119873 original size:37 final size:35
Alignment explanation
Indices: 30119836--30119929 Score: 110
Period size: 30 Copynumber: 2.8 Consensus size: 35
30119826 AGTTAAGGGT
30119836 TTAGGGGTTAGGGGTTAGGGGTTTAAGGGGCATGGG
1 TTAGGGGTTAGGGGTTAGGGG-TTAAGGGGCATGGG
*
30119872 TTA--GG--A--GTTTAGGGGTTAAGGGGGCATGGG
1 TTAGGGGTTAGGGGTTAGGGGTTAA-GGGGCATGGG
30119902 TTAGGGGTTAGGGGTTTAGGGGTTAAGG
1 TTAGGGGTTAGGGG-TTAGGGGTTAAGG
30119930 CATTAAGGGG
Statistics
Matches: 48, Mismatches: 2, Indels: 16
0.73 0.03 0.24
Matches are distributed among these distances:
29 4 0.08
30 21 0.44
32 3 0.06
34 3 0.06
36 6 0.12
37 11 0.23
ACGTcount: A:0.18, C:0.02, G:0.51, T:0.29
Consensus pattern (35 bp):
TTAGGGGTTAGGGGTTAGGGGTTAAGGGGCATGGG
Found at i:30119911 original size:7 final size:7
Alignment explanation
Indices: 30119814--30119926 Score: 84
Period size: 7 Copynumber: 15.4 Consensus size: 7
30119804 GGGTTGAGGT
30119814 TTAGGGG
1 TTAGGGG
* *
30119821 TTAAGAG
1 TTAGGGG
*
30119828 TTAAGGGT
1 TT-AGGGG
30119836 TTAGGGG
1 TTAGGGG
30119843 TTAGGGG
1 TTAGGGG
30119850 TTAGGGG
1 TTAGGGG
30119857 TTTAAGGGG
1 -TT-AGGGG
* *
30119866 -CATGGG
1 TTAGGGG
*
30119872 TTAGGAGT
1 TTAGG-GG
30119880 TTAGGGG
1 TTAGGGG
30119887 TTAAGGGG
1 TT-AGGGG
** *
30119895 GCATGGG
1 TTAGGGG
30119902 TTAGGGG
1 TTAGGGG
30119909 TTAGGGG
1 TTAGGGG
30119916 TTTAGGGG
1 -TTAGGGG
30119924 TTA
1 TTA
30119927 AGGCATTAAG
Statistics
Matches: 81, Mismatches: 18, Indels: 14
0.72 0.16 0.12
Matches are distributed among these distances:
6 4 0.05
7 48 0.59
8 24 0.30
9 5 0.06
ACGTcount: A:0.19, C:0.02, G:0.49, T:0.30
Consensus pattern (7 bp):
TTAGGGG
Found at i:30119926 original size:22 final size:22
Alignment explanation
Indices: 30119815--30119925 Score: 100
Period size: 22 Copynumber: 5.0 Consensus size: 22
30119805 GGTTGAGGTT
* * *
30119815 TAGGGGTTAAGAGTTAAGGGTT
1 TAGGGGTTAGGGGTTAGGGGTT
30119837 TAGGGGTTAGGGGTTAGGGGTT
1 TAGGGGTTAGGGGTTAGGGGTT
* * *
30119859 TAAGGGG-CATGGGTTAGGAGTT
1 T-AGGGGTTAGGGGTTAGGGGTT
** *
30119881 TAGGGGTTAAGGGGGCATGGG-T
1 TAGGGGTT-AGGGGTTAGGGGTT
30119903 TAGGGGTTAGGGGTTTAGGGGTT
1 TAGGGGTTAGGGG-TTAGGGGTT
30119926 AAGGCATTAA
Statistics
Matches: 69, Mismatches: 15, Indels: 9
0.74 0.16 0.10
Matches are distributed among these distances:
21 10 0.14
22 46 0.67
23 13 0.19
ACGTcount: A:0.19, C:0.02, G:0.50, T:0.30
Consensus pattern (22 bp):
TAGGGGTTAGGGGTTAGGGGTT
Found at i:30120066 original size:17 final size:17
Alignment explanation
Indices: 30120046--30120090 Score: 56
Period size: 16 Copynumber: 2.7 Consensus size: 17
30120036 AATTTATATA
30120046 TTAAATAATTTTAAATT
1 TTAAATAATTTTAAATT
* *
30120063 TTAAGT-ATTTCAAATT
1 TTAAATAATTTTAAATT
*
30120079 TTCAATAATTTT
1 TTAAATAATTTT
30120091 CAAGATTTCA
Statistics
Matches: 22, Mismatches: 5, Indels: 2
0.76 0.17 0.07
Matches are distributed among these distances:
16 13 0.59
17 9 0.41
ACGTcount: A:0.40, C:0.04, G:0.02, T:0.53
Consensus pattern (17 bp):
TTAAATAATTTTAAATT
Found at i:30122935 original size:24 final size:24
Alignment explanation
Indices: 30122886--30122938 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
30122876 CTATGTCATA
*
30122886 ATATTTGTAACTAAAATTAATATT
1 ATATTTGTAACTAAAATTAACATT
* * *
30122910 ATATTTGTATCTAAAATTACCGTT
1 ATATTTGTAACTAAAATTAACATT
30122934 ATATT
1 ATATT
30122939 ATAAAACACT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.40, C:0.08, G:0.06, T:0.47
Consensus pattern (24 bp):
ATATTTGTAACTAAAATTAACATT
Found at i:30123208 original size:76 final size:76
Alignment explanation
Indices: 30123082--30124536 Score: 2847
Period size: 76 Copynumber: 19.1 Consensus size: 76
30123072 CCTCCTCCTG
30123082 AAGCCCTTTTCAATAACTGGGGCATAAGCCTTTTTCGGTAAACTGGGGCAAAAGCCCTTTCGGTA
1 AAGCCCTTTTCAATAACTGGGGCATAAGCCTTTTTCGGTAAACTGGGGCAAAAGCCCTTTCGGTA
30123147 ATCTGGGGCGT
66 ATCTGGGGCGT
30123158 AAGCCCTTTTCAATAACTGGGGCATAAGCCTTTTTCGGTAAACTGGGGCAAAAGCCCTTTCGGTA
1 AAGCCCTTTTCAATAACTGGGGCATAAGCCTTTTTCGGTAAACTGGGGCAAAAGCCCTTTCGGTA
30123223 ATCTGGGGCGT
66 ATCTGGGGCGT
30123234 AAGCCCTTTTCAATAACTGGGGCATAAGCCTTTTTCGGTAAACTGGGGCAAAAGCCCTTTCGGTA
1 AAGCCCTTTTCAATAACTGGGGCATAAGCCTTTTTCGGTAAACTGGGGCAAAAGCCCTTTCGGTA
30123299 ATCTGGGGCGT
66 ATCTGGGGCGT
30123310 AAGCCCTTTTCAATAACTGGGGCATAAGCCTTTTTCGGTAAACTGGGGCAAAAGCCCTTTCGGTA
1 AAGCCCTTTTCAATAACTGGGGCATAAGCCTTTTTCGGTAAACTGGGGCAAAAGCCCTTTCGGTA
30123375 ATCTGGGGCGT
66 ATCTGGGGCGT
30123386 AAGCCCTTTTCAATAACTGGGGCATAAGCCTTTTTCGGTAAACTGGGGCAAAAGCCCTTTCGGTA
1 AAGCCCTTTTCAATAACTGGGGCATAAGCCTTTTTCGGTAAACTGGGGCAAAAGCCCTTTCGGTA
30123451 ATCTGGGGCGT
66 ATCTGGGGCGT
30123462 AAGCCCTTTTCAATAACTGGGGCATAAGCCTTTTTCGGTAAACTGGGGCAAAAGCCCTTTCGGTA
1 AAGCCCTTTTCAATAACTGGGGCATAAGCCTTTTTCGGTAAACTGGGGCAAAAGCCCTTTCGGTA
30123527 ATCTGGGGCGT
66 ATCTGGGGCGT
30123538 AAGCCCTTTTCAATAACTGGGGCATAAGCCTTTTTCGGTAAACTGGGGCAAAAGCCCTTTCGGTA
1 AAGCCCTTTTCAATAACTGGGGCATAAGCCTTTTTCGGTAAACTGGGGCAAAAGCCCTTTCGGTA
30123603 ATCTGGGGCGT
66 ATCTGGGGCGT
30123614 AAGCCCTTTTCAATAACTGGGGCATAAGCCTTTTTCGGTAAACTGGGGCAAAAGCCCTTTCGGTA
1 AAGCCCTTTTCAATAACTGGGGCATAAGCCTTTTTCGGTAAACTGGGGCAAAAGCCCTTTCGGTA
30123679 ATCTGGGGCGT
66 ATCTGGGGCGT
30123690 AAGCCCTTTTCAATAACTGGGGCATAAGCCTTTTTCGGTAAACTGGGGCAAAAGCCCTTTCGGTA
1 AAGCCCTTTTCAATAACTGGGGCATAAGCCTTTTTCGGTAAACTGGGGCAAAAGCCCTTTCGGTA
30123755 ATCTGGGGCGT
66 ATCTGGGGCGT
30123766 AAGCCCTTTTCAATAACTGGGGCATAAGCCTTTTTCGGTAAACTGGGGCAAAAGCCCTTTCGGTA
1 AAGCCCTTTTCAATAACTGGGGCATAAGCCTTTTTCGGTAAACTGGGGCAAAAGCCCTTTCGGTA
30123831 ATCTGGGGCGT
66 ATCTGGGGCGT
30123842 AAGCCCTTTTCAATAACTGGGGCATAAGCCTTTTTCGGTAAACTGGGGCAAAAGCCCTTTCGGTA
1 AAGCCCTTTTCAATAACTGGGGCATAAGCCTTTTTCGGTAAACTGGGGCAAAAGCCCTTTCGGTA
30123907 ATCTGGGGCGT
66 ATCTGGGGCGT
30123918 AAGCCCTTTTCAATAACTGGGGCATAAGCCTTTTTCGGTAAACTGGGGCAAAAGCCCTTTCGGTA
1 AAGCCCTTTTCAATAACTGGGGCATAAGCCTTTTTCGGTAAACTGGGGCAAAAGCCCTTTCGGTA
30123983 ATCTGGGGCGT
66 ATCTGGGGCGT
30123994 AAGCCCTTTTCAATAACTGGGGCATAAGCCTTTTTCGGTAAACTGGGGCAAAAGCCCTTTCGGTA
1 AAGCCCTTTTCAATAACTGGGGCATAAGCCTTTTTCGGTAAACTGGGGCAAAAGCCCTTTCGGTA
30124059 ATCTGGGGCGT
66 ATCTGGGGCGT
30124070 AAGCCCTTTTCAATAACTGGGGCATAAGCCTTTTTCGGTAAACTGGGGCAAAAGCCCTTTCGGTA
1 AAGCCCTTTTCAATAACTGGGGCATAAGCCTTTTTCGGTAAACTGGGGCAAAAGCCCTTTCGGTA
30124135 ATCTGGGGCGT
66 ATCTGGGGCGT
30124146 AAGCCCTTTTCAATAACTGGGGCATAAGCCTTTTTCGGTAAACTGGGGCAAAAGCCCTTTCGGTA
1 AAGCCCTTTTCAATAACTGGGGCATAAGCCTTTTTCGGTAAACTGGGGCAAAAGCCCTTTCGGTA
30124211 ATCTGGGGCGT
66 ATCTGGGGCGT
30124222 AAGCCCTTTTCAATAACTGGGGCATAAGCCTTTTTCGGTAAACTGGGGCAAAAGCCCTTTCGGTA
1 AAGCCCTTTTCAATAACTGGGGCATAAGCCTTTTTCGGTAAACTGGGGCAAAAGCCCTTTCGGTA
30124287 ATCTGGGGCGT
66 ATCTGGGGCGT
30124298 AAGCCCTTTTCAATAACTGGGGCATAAGCCTTTTTCGGTAAACTGGGGCAAAAGCCCTTTCGGTA
1 AAGCCCTTTTCAATAACTGGGGCATAAGCCTTTTTCGGTAAACTGGGGCAAAAGCCCTTTCGGTA
30124363 ATCTGGGGCGT
66 ATCTGGGGCGT
30124374 AAGCCCTTTTCAATAACTGGGGCATAAGCCTTTTTCGGTAAACTGGGGCAAAAGCCCTTTCGGTA
1 AAGCCCTTTTCAATAACTGGGGCATAAGCCTTTTTCGGTAAACTGGGGCAAAAGCCCTTTCGGTA
30124439 ATCTGGGGCGT
66 ATCTGGGGCGT
* **
30124450 AAGCCCTTTTCAATAACTGGGGCATAAGCCTTTTTCGGTAAACTGGGGCATAAGCCCTTTTCAAT
1 AAGCCCTTTTCAATAACTGGGGCATAAGCCTTTTTCGGTAAACTGGGGCAAAAGCCC-TTTCGGT
* * *
30124515 AAACTAGGGCCT
65 AATCTGGGGCGT
30124527 AAGCCCTTTT
1 AAGCCCTTTT
30124537 GCACTTCCTC
Statistics
Matches: 1372, Mismatches: 6, Indels: 1
0.99 0.00 0.00
Matches are distributed among these distances:
76 1348 0.98
77 24 0.02
ACGTcount: A:0.24, C:0.22, G:0.26, T:0.28
Consensus pattern (76 bp):
AAGCCCTTTTCAATAACTGGGGCATAAGCCTTTTTCGGTAAACTGGGGCAAAAGCCCTTTCGGTA
ATCTGGGGCGT
Found at i:30124611 original size:20 final size:20
Alignment explanation
Indices: 30124586--30124660 Score: 111
Period size: 20 Copynumber: 3.9 Consensus size: 20
30124576 TTATGAATAC
*
30124586 ATCATGTGCATTTCATACAT
1 ATCATGTGCATATCATACAT
30124606 ATCATGTGCATATCATACAT
1 ATCATGTGCATATCATACAT
30124626 ATCATGTGCATATCATATCA-
1 ATCATGTGCATATCATA-CAT
30124646 ATCATGT--ATATCATA
1 ATCATGTGCATATCATA
30124661 TCCCACGTAT
Statistics
Matches: 53, Mismatches: 1, Indels: 4
0.91 0.02 0.07
Matches are distributed among these distances:
18 8 0.15
20 43 0.81
21 2 0.04
ACGTcount: A:0.35, C:0.19, G:0.09, T:0.37
Consensus pattern (20 bp):
ATCATGTGCATATCATACAT
Found at i:30124617 original size:11 final size:11
Alignment explanation
Indices: 30124586--30124641 Score: 57
Period size: 11 Copynumber: 5.5 Consensus size: 11
30124576 TTATGAATAC
30124586 ATCATGTGCAT
1 ATCATGTGCAT
* *
30124597 TTCA--TACAT
1 ATCATGTGCAT
30124606 ATCATGTGCAT
1 ATCATGTGCAT
*
30124617 ATCA--TACAT
1 ATCATGTGCAT
30124626 ATCATGTGCAT
1 ATCATGTGCAT
30124637 ATCAT
1 ATCAT
30124642 ATCAATCATG
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
9 15 0.43
11 20 0.57
ACGTcount: A:0.32, C:0.20, G:0.11, T:0.38
Consensus pattern (11 bp):
ATCATGTGCAT
Found at i:30124658 original size:9 final size:10
Alignment explanation
Indices: 30124603--30124659 Score: 57
Period size: 9 Copynumber: 5.8 Consensus size: 10
30124593 GCATTTCATA
30124603 CATATCATGT
1 CATATCATGT
*
30124613 GCATATCAT-A
1 -CATATCATGT
30124623 CATATCATGT
1 CATATCATGT
*
30124633 GCATATCATAT
1 -CATATCATGT
30124644 CA-ATCATGT
1 CATATCATGT
30124653 -ATATCAT
1 CATATCAT
30124660 ATCCCACGTA
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
8 1 0.03
9 19 0.49
10 2 0.05
11 17 0.44
ACGTcount: A:0.35, C:0.19, G:0.09, T:0.37
Consensus pattern (10 bp):
CATATCATGT
Found at i:30126370 original size:57 final size:57
Alignment explanation
Indices: 30126278--30126392 Score: 212
Period size: 57 Copynumber: 2.0 Consensus size: 57
30126268 AAGTCCAAAA
* *
30126278 TTCAAAAATTCTACCGGGTTTTGGCCAACACATGGGCCTTCCATAAGCCCATTTACC
1 TTCAAAAATTCCACCGGGTTTTGGCCAACAAATGGGCCTTCCATAAGCCCATTTACC
30126335 TTCAAAAATTCCACCGGGTTTTGGCCAACAAATGGGCCTTCCATAAGCCCATTTACC
1 TTCAAAAATTCCACCGGGTTTTGGCCAACAAATGGGCCTTCCATAAGCCCATTTACC
30126392 T
1 T
30126393 ACCCAAATTA
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
57 56 1.00
ACGTcount: A:0.27, C:0.30, G:0.16, T:0.28
Consensus pattern (57 bp):
TTCAAAAATTCCACCGGGTTTTGGCCAACAAATGGGCCTTCCATAAGCCCATTTACC
Found at i:30126512 original size:8 final size:9
Alignment explanation
Indices: 30126487--30126611 Score: 119
Period size: 9 Copynumber: 13.7 Consensus size: 9
30126477 GGATGTTACA
*
30126487 TACACAACT
1 TACATAACT
30126496 TACATAACT
1 TACATAACT
30126505 TA-ATAACT
1 TACATAACT
*
30126513 TATATATA-T
1 TACATA-ACT
30126522 AATATCATAACT
1 --TA-CATAACT
30126534 TACATAACT
1 TACATAACT
* *
30126543 CACATCACT
1 TACATAACT
30126552 TACATAACT
1 TACATAACT
* *
30126561 CACATAGCT
1 TACATAACT
* *
30126570 CACATAAGT
1 TACATAACT
30126579 TACATAACT
1 TACATAACT
*
30126588 CACATAACT
1 TACATAACT
30126597 TACATAACT
1 TACATAACT
30126606 TACATA
1 TACATA
30126612 TATAATACAT
Statistics
Matches: 96, Mismatches: 14, Indels: 12
0.79 0.11 0.10
Matches are distributed among these distances:
8 8 0.08
9 78 0.81
10 3 0.03
11 3 0.03
12 4 0.04
ACGTcount: A:0.44, C:0.23, G:0.02, T:0.31
Consensus pattern (9 bp):
TACATAACT
Found at i:30129503 original size:39 final size:39
Alignment explanation
Indices: 30129449--30129526 Score: 138
Period size: 39 Copynumber: 2.0 Consensus size: 39
30129439 TCGATATGTT
30129449 CTTTTTAACCACGATTCAATTGAACCATTACGCAAGTAA
1 CTTTTTAACCACGATTCAATTGAACCATTACGCAAGTAA
* *
30129488 CTTTTTCACCACGATTCAATTGAACCATTACGTAAGTAA
1 CTTTTTAACCACGATTCAATTGAACCATTACGCAAGTAA
30129527 GTTCTAAAAT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 37 1.00
ACGTcount: A:0.35, C:0.23, G:0.10, T:0.32
Consensus pattern (39 bp):
CTTTTTAACCACGATTCAATTGAACCATTACGCAAGTAA
Found at i:30131769 original size:13 final size:14
Alignment explanation
Indices: 30131753--30131781 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
30131743 TTTTAAATAT
30131753 TTATAAT-GTTTAA
1 TTATAATGGTTTAA
30131766 TTATAATGGTTTAA
1 TTATAATGGTTTAA
30131780 TT
1 TT
30131782 TGTCATTAGT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.47
14 8 0.53
ACGTcount: A:0.34, C:0.00, G:0.10, T:0.55
Consensus pattern (14 bp):
TTATAATGGTTTAA
Found at i:30132174 original size:21 final size:21
Alignment explanation
Indices: 30132148--30132187 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
30132138 AAATTGCTCA
*
30132148 ACTTAAAGCGGAGGCAGCATC
1 ACTTAAAGAGGAGGCAGCATC
30132169 ACTTAAAGAGGAGGCAGCA
1 ACTTAAAGAGGAGGCAGCA
30132188 ATGAGGGAAG
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:0.38, C:0.20, G:0.30, T:0.12
Consensus pattern (21 bp):
ACTTAAAGAGGAGGCAGCATC
Found at i:30132459 original size:47 final size:47
Alignment explanation
Indices: 30132390--30132483 Score: 170
Period size: 47 Copynumber: 2.0 Consensus size: 47
30132380 CGTTGAATTT
*
30132390 TTGAAGTATCATTTAGATTTGCTGTTATTGGTTGGATTTGATGTTGC
1 TTGAAGTATCATTTAGATTTGCTATTATTGGTTGGATTTGATGTTGC
*
30132437 TTGAAGTATCATTTAGATTTGCTATTATTGGTTGGATTTGATTTTGC
1 TTGAAGTATCATTTAGATTTGCTATTATTGGTTGGATTTGATGTTGC
30132484 AGGAAGGATT
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
47 45 1.00
ACGTcount: A:0.20, C:0.06, G:0.23, T:0.50
Consensus pattern (47 bp):
TTGAAGTATCATTTAGATTTGCTATTATTGGTTGGATTTGATGTTGC
Found at i:30137214 original size:16 final size:16
Alignment explanation
Indices: 30137193--30137226 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
30137183 AAAGTGTGGT
30137193 GTTTGCAAGTGTACAG
1 GTTTGCAAGTGTACAG
*
30137209 GTTTGCAAGTGTATAG
1 GTTTGCAAGTGTACAG
30137225 GT
1 GT
30137227 CAAATTGTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.24, C:0.09, G:0.32, T:0.35
Consensus pattern (16 bp):
GTTTGCAAGTGTACAG
Found at i:30143145 original size:44 final size:42
Alignment explanation
Indices: 30143014--30143160 Score: 154
Period size: 44 Copynumber: 3.4 Consensus size: 42
30143004 CCAATGTCTT
* * * **
30143014 AGACGTGGTCTTACATGTAATCAAATATTAATGCC-ACTGTCCC
1 AGACATGGTCTTACACGAAATCAAATA-CGATGCCAAC-GTCCC
* * *
30143057 AGACAGGGTCTTACCCGAAATCAAATACGATGCCAACATCCC
1 AGACATGGTCTTACACGAAATCAAATACGATGCCAACGTCCC
30143099 AGACATGGTCTTACACGTAAATCATAAGT-CGATGCCAACGTCCC
1 AGACATGGTCTTACACG-AAATCA-AA-TACGATGCCAACGTCCC
*
30143143 AGACGTGGTCTTACACGA
1 AGACATGGTCTTACACGA
30143161 TAACACATAT
Statistics
Matches: 88, Mismatches: 12, Indels: 8
0.81 0.11 0.07
Matches are distributed among these distances:
42 24 0.27
43 31 0.35
44 32 0.36
45 1 0.01
ACGTcount: A:0.32, C:0.27, G:0.18, T:0.23
Consensus pattern (42 bp):
AGACATGGTCTTACACGAAATCAAATACGATGCCAACGTCCC
Found at i:30149445 original size:18 final size:19
Alignment explanation
Indices: 30149399--30149445 Score: 53
Period size: 18 Copynumber: 2.6 Consensus size: 19
30149389 CTTAAAGAAG
* *
30149399 ATAAATAAAGATAAAAGTG
1 ATAAATAAAAATAAAAGTA
*
30149418 A-AAATGAAAATAAAA-TA
1 ATAAATAAAAATAAAAGTA
30149435 ATAAATAAAAA
1 ATAAATAAAAA
30149446 GTTTTTAAAC
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
17 2 0.09
18 20 0.87
19 1 0.04
ACGTcount: A:0.72, C:0.00, G:0.09, T:0.19
Consensus pattern (19 bp):
ATAAATAAAAATAAAAGTA
Found at i:30158488 original size:64 final size:63
Alignment explanation
Indices: 30158407--30158590 Score: 199
Period size: 67 Copynumber: 2.9 Consensus size: 63
30158397 AGACATTATG
*
30158407 ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGGGATA
1 ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATA
* * * * * *
30158470 TATGTAGCTAGGTCGCATGCGTGGTTCCAAGTGAAGGACACCATGTAGACAAGAGAGCTACGAGA
1 -ATGTAGCTAGGTCGCATGGGT-GATACTA-TG-TGTACACCATGTAGACAAGAGAGCTACGAGA
30158535 TA
62 TA
* * * * * *
30158537 ATCTGGCTAGGTCACATGGGTGGTACTAAGTGTTCACCATGT-GTACAAGAGAGC
1 ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAG-ACAAGAGAGC
30158591 CGAACTATAT
Statistics
Matches: 98, Mismatches: 18, Indels: 9
0.78 0.14 0.07
Matches are distributed among these distances:
62 1 0.01
63 19 0.19
64 21 0.21
65 8 0.08
66 19 0.19
67 30 0.31
ACGTcount: A:0.29, C:0.17, G:0.30, T:0.23
Consensus pattern (63 bp):
ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATA
Found at i:30166208 original size:46 final size:46
Alignment explanation
Indices: 30166028--30166209 Score: 249
Period size: 46 Copynumber: 4.0 Consensus size: 46
30166018 TTATCTTCGA
* * * * *
30166028 CATGATGCCATAGTGTCTTTCAACTATGGTCTTACTCATTTTC-TGT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACA-TTTCATGT
* **
30166074 CATGTTGCCATGGTATCTGTCAACCATGGTCTTATTCATTTCATGT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATGT
* * *
30166120 CATGTTGCCATGGTATCATTCAACCATGGTCTTACACTTTTCATAT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATGT
30166166 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCAT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCAT
30166210 TTCAGGAAGC
Statistics
Matches: 121, Mismatches: 14, Indels: 2
0.88 0.10 0.01
Matches are distributed among these distances:
45 4 0.03
46 117 0.97
ACGTcount: A:0.21, C:0.23, G:0.15, T:0.41
Consensus pattern (46 bp):
CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATGT
Found at i:30167079 original size:51 final size:51
Alignment explanation
Indices: 30167006--30167105 Score: 157
Period size: 51 Copynumber: 2.0 Consensus size: 51
30166996 CTTCATTCGA
*
30167006 AATTATTATTTTGTTGCCCTAGCTTCAACAAGAGCTTCATAATTT-ATCCAG
1 AATTATTACTTTGTTGCCCTAGCTTCAACAAGAGCTTCAT-ATTTCATCCAG
* *
30167057 AATTGTTACTTTGTTGCTCTAGCTTCAACAAGAGCTTCATATTTCATCC
1 AATTATTACTTTGTTGCCCTAGCTTCAACAAGAGCTTCATATTTCATCC
30167106 GGATAACTTA
Statistics
Matches: 45, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
50 4 0.09
51 41 0.91
ACGTcount: A:0.27, C:0.21, G:0.12, T:0.40
Consensus pattern (51 bp):
AATTATTACTTTGTTGCCCTAGCTTCAACAAGAGCTTCATATTTCATCCAG
Found at i:30168329 original size:3 final size:3
Alignment explanation
Indices: 30168315--30168360 Score: 55
Period size: 3 Copynumber: 16.3 Consensus size: 3
30168305 TTTTCTACTA
30168315 AAT AATT AAT AAT AA- AAT AAT AAT AA- AAT AAT AA- AAT AAT AA-
1 AAT AA-T AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
30168357 AAT A
1 AAT A
30168361 TCTCATTAAA
Statistics
Matches: 38, Mismatches: 0, Indels: 10
0.79 0.00 0.21
Matches are distributed among these distances:
2 8 0.21
3 27 0.71
4 3 0.08
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (3 bp):
AAT
Found at i:30168335 original size:8 final size:8
Alignment explanation
Indices: 30168314--30168360 Score: 60
Period size: 8 Copynumber: 5.6 Consensus size: 8
30168304 CTTTTCTACT
30168314 AAATAATTA
1 AAATAA-TA
30168323 ATAATAA-A
1 A-AATAATA
30168331 ATAATAATA
1 A-AATAATA
30168340 AAATAATA
1 AAATAATA
30168348 AAATAATA
1 AAATAATA
30168356 AAATA
1 AAATA
30168361 TCTCATTAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
8 28 0.78
9 3 0.08
10 5 0.14
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (8 bp):
AAATAATA
Found at i:30168337 original size:11 final size:11
Alignment explanation
Indices: 30168321--30168360 Score: 57
Period size: 11 Copynumber: 3.7 Consensus size: 11
30168311 ACTAAATAAT
30168321 TAATAATAAAA
1 TAATAATAAAA
30168332 TAATAATAAAA
1 TAATAATAAAA
30168343 TAATAA-AATAA
1 TAATAATAA-AA
30168354 TAA-AATA
1 TAATAATA
30168361 TCTCATTAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
10 4 0.15
11 23 0.85
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (11 bp):
TAATAATAAAA
Found at i:30173023 original size:28 final size:27
Alignment explanation
Indices: 30172959--30173055 Score: 149
Period size: 27 Copynumber: 3.6 Consensus size: 27
30172949 ATATTAAGTC
* *
30172959 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAATCAACT
30172986 CGCACACTTAGTGCTACATAATCATACT
1 CGCACACTTAGTGCTACATAATCA-ACT
* *
30173014 CGCACACTTAGTGCTACATAGTCAATT
1 CGCACACTTAGTGCTACATAATCAACT
30173041 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
30173056 GCACAATTTA
Statistics
Matches: 65, Mismatches: 4, Indels: 2
0.92 0.06 0.03
Matches are distributed among these distances:
27 39 0.60
28 26 0.40
ACGTcount: A:0.30, C:0.29, G:0.13, T:0.28
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAATCAACT
Found at i:30180607 original size:28 final size:27
Alignment explanation
Indices: 30180543--30180667 Score: 187
Period size: 28 Copynumber: 4.6 Consensus size: 27
30180533 TTATTAAGTC
* *
30180543 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAATCAACT
30180570 CGCACACTTAGTGCTACATAATCATACT
1 CGCACACTTAGTGCTACATAATCA-ACT
*
30180598 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAATC-AACT
* *
30180626 CGCACACTTAGTGCTACATATTCAATT
1 CGCACACTTAGTGCTACATAATCAACT
30180653 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
30180668 GCACAATTTA
Statistics
Matches: 91, Mismatches: 5, Indels: 4
0.91 0.05 0.04
Matches are distributed among these distances:
27 40 0.44
28 50 0.55
29 1 0.01
ACGTcount: A:0.30, C:0.29, G:0.13, T:0.28
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAATCAACT
Found at i:30180656 original size:55 final size:55
Alignment explanation
Indices: 30180543--30180667 Score: 189
Period size: 55 Copynumber: 2.3 Consensus size: 55
30180533 TTATTAAGTC
* *
30180543 CGCACACTCAGTGCTATATAATCAACTCGCACACTTAGTGCTACATAATCATACT
1 CGCACACTTAGTGCTACATAATCAACTCGCACACTTAGTGCTACATAATCATACT
* * *
30180598 CGCACACTTAGTGCTACATAGTCAAACTCGCACACTTAGTGCTACATATTCA-ATT
1 CGCACACTTAGTGCTACATAATC-AACTCGCACACTTAGTGCTACATAATCATACT
30180653 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
30180668 GCACAATTTA
Statistics
Matches: 64, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
55 37 0.58
56 27 0.42
ACGTcount: A:0.30, C:0.29, G:0.13, T:0.28
Consensus pattern (55 bp):
CGCACACTTAGTGCTACATAATCAACTCGCACACTTAGTGCTACATAATCATACT
Found at i:30180686 original size:56 final size:56
Alignment explanation
Indices: 30180543--30180692 Score: 180
Period size: 56 Copynumber: 2.7 Consensus size: 56
30180533 TTATTAAGTC
* * * *
30180543 CGCACACTCAGTGCTATATAATC-AACTCGCACACTTAGTGCTACATAATCATACT
1 CGCACACTTAGTGCTACATAGTCAAACCCGCACACTTAGTGCTACATAATCATACT
* * *
30180598 CGCACACTTAGTGCTACATAGTCAAACTCGCACACTTAGTGCTACATATTCA-ATT
1 CGCACACTTAGTGCTACATAGTCAAACCCGCACACTTAGTGCTACATAATCATACT
* *
30180653 CGCACACTTAGTGCTGCACA-ATTTAAACCCGCACACTTAG
1 CGCACACTTAGTGCT--ACATAGTCAAACCCGCACACTTAG
30180693 CGCCAATCTC
Statistics
Matches: 84, Mismatches: 8, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
55 37 0.44
56 44 0.52
57 3 0.04
ACGTcount: A:0.31, C:0.29, G:0.13, T:0.27
Consensus pattern (56 bp):
CGCACACTTAGTGCTACATAGTCAAACCCGCACACTTAGTGCTACATAATCATACT
Found at i:30186933 original size:13 final size:13
Alignment explanation
Indices: 30186915--30186941 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
30186905 GCCTTTGTCA
30186915 TATTTATTGTTAG
1 TATTTATTGTTAG
30186928 TATTTATTGTTAG
1 TATTTATTGTTAG
30186941 T
1 T
30186942 TTAGTGACCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.22, C:0.00, G:0.15, T:0.63
Consensus pattern (13 bp):
TATTTATTGTTAG
Found at i:30188416 original size:54 final size:54
Alignment explanation
Indices: 30188340--30188457 Score: 175
Period size: 54 Copynumber: 2.2 Consensus size: 54
30188330 AGTCCTAATG
* * * *
30188340 GACTTTCCAATTACGACAGTCCTGGCAAACTTCTACATTAAGACTGTCTTGACG
1 GACTTCCCAATTACGACAGTCCTGACAAACTTCAACATTAAGACTGTCTTGACA
*
30188394 GGCTTCCCAATTACGATC-GTCCTGACAAACTTCAACATTAAGACTGTCTTGACA
1 GACTTCCCAATTACGA-CAGTCCTGACAAACTTCAACATTAAGACTGTCTTGACA
30188448 GACTTCCCAA
1 GACTTCCCAA
30188458 ATAGATAGTC
Statistics
Matches: 57, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
54 56 0.98
55 1 0.02
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.28
Consensus pattern (54 bp):
GACTTCCCAATTACGACAGTCCTGACAAACTTCAACATTAAGACTGTCTTGACA
Found at i:30188446 original size:27 final size:26
Alignment explanation
Indices: 30188365--30188453 Score: 72
Period size: 27 Copynumber: 3.3 Consensus size: 26
30188355 ACAGTCCTGG
30188365 CAAACTTCTACATTAAGACTGTCTTGA
1 CAAACTTC-ACATTAAGACTGTCTTGA
*** * * *
30188392 CGGGCTTCCCAATTACGA-TCGTCCTGA
1 CAAACTTCAC-ATTAAGACT-GTCTTGA
30188419 CAAACTTCAACATTAAGACTGTCTTGA
1 CAAACTTC-ACATTAAGACTGTCTTGA
*
30188446 CAGACTTC
1 CAAACTTC
30188454 CCAAATAGAT
Statistics
Matches: 45, Mismatches: 13, Indels: 8
0.68 0.20 0.12
Matches are distributed among these distances:
26 2 0.04
27 41 0.91
28 2 0.04
ACGTcount: A:0.29, C:0.27, G:0.15, T:0.29
Consensus pattern (26 bp):
CAAACTTCACATTAAGACTGTCTTGA
Found at i:30188583 original size:23 final size:22
Alignment explanation
Indices: 30188529--30188584 Score: 67
Period size: 22 Copynumber: 2.5 Consensus size: 22
30188519 TCGCCCCACT
* *
30188529 AAAGGCTCTCATACGTCCCCTA
1 AAAGGCTCTCAAACGTCCCATA
* *
30188551 ATAGGCTCTCAAATGTCCCATA
1 AAAGGCTCTCAAACGTCCCATA
30188573 AAAGGGCTCTCA
1 AAA-GGCTCTCA
30188585 TAAATGAGTG
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
22 20 0.71
23 8 0.29
ACGTcount: A:0.30, C:0.30, G:0.16, T:0.23
Consensus pattern (22 bp):
AAAGGCTCTCAAACGTCCCATA
Found at i:30188971 original size:16 final size:16
Alignment explanation
Indices: 30188950--30188983 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
30188940 ACATAACCAT
30188950 TATTTGTACTTTATCA
1 TATTTGTACTTTATCA
30188966 TATTTGTACTTTATCA
1 TATTTGTACTTTATCA
30188982 TA
1 TA
30188984 CTTACAGTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.26, C:0.12, G:0.06, T:0.56
Consensus pattern (16 bp):
TATTTGTACTTTATCA
Found at i:30190520 original size:23 final size:21
Alignment explanation
Indices: 30190479--30190601 Score: 86
Period size: 22 Copynumber: 5.4 Consensus size: 21
30190469 CAGCTCGTAA
30190479 GAGCTTACTATTTTCAGCTCATT
1 GAGCTTACT-TTTT-AGCTCATT
*
30190502 GCAGCTTACCTTTTTAGCTCGTAT
1 G-AGCTTA-CTTTTTAGCTCAT-T
* *
30190526 GAGCTTA-TTGTTCAGCTCAATA
1 GAGCTTACTT-TTTAGCTC-ATT
* *
30190548 GAGCTTACTGTTTAGCTCGATA
1 GAGCTTACTTTTTAGCTC-ATT
* *
30190570 GAGCTTACCGTTTCAGCTCATT
1 GAGCTTA-CTTTTTAGCTCATT
30190592 AGAGCTTACT
1 -GAGCTTACT
30190602 GTTCATCAGC
Statistics
Matches: 80, Mismatches: 12, Indels: 17
0.73 0.11 0.16
Matches are distributed among these distances:
21 2 0.03
22 34 0.43
23 30 0.38
24 12 0.15
25 2 0.03
ACGTcount: A:0.22, C:0.22, G:0.18, T:0.38
Consensus pattern (21 bp):
GAGCTTACTTTTTAGCTCATT
Found at i:30190551 original size:22 final size:22
Alignment explanation
Indices: 30190526--30190606 Score: 108
Period size: 22 Copynumber: 3.6 Consensus size: 22
30190516 TAGCTCGTAT
*
30190526 GAGCTTATTGTTCAGCTCAATA
1 GAGCTTACTGTTCAGCTCAATA
* *
30190548 GAGCTTACTGTTTAGCTCGATA
1 GAGCTTACTGTTCAGCTCAATA
* *
30190570 GAGCTTACCGTTTCAGCTCATTA
1 GAGCTTACTG-TTCAGCTCAATA
30190593 GAGCTTACTGTTCA
1 GAGCTTACTGTTCA
30190607 TCAGCTTAGG
Statistics
Matches: 50, Mismatches: 8, Indels: 2
0.83 0.13 0.03
Matches are distributed among these distances:
22 32 0.64
23 18 0.36
ACGTcount: A:0.23, C:0.21, G:0.20, T:0.36
Consensus pattern (22 bp):
GAGCTTACTGTTCAGCTCAATA
Found at i:30190554 original size:45 final size:45
Alignment explanation
Indices: 30190470--30190604 Score: 134
Period size: 45 Copynumber: 3.0 Consensus size: 45
30190460 CCGATATATC
* * * *
30190470 AGCTCGTAAGAGCTTACTATTTTCAGCTC-ATTGCAGCTTACCTTTTT
1 AGCTCGTATGAGCTTA-T-TGTTCAGCTCAATAG-AGCTTACCTGTTT
30190517 AGCTCGTATGAGCTTATTGTTCAGCTCAATAGAGCTTA-CTGTTT
1 AGCTCGTATGAGCTTATTGTTCAGCTCAATAGAGCTTACCTGTTT
** *
30190561 AGCTCG-ATAGAGCTTACCGTTTCAGCTCATTAGAGCTTA-CTGTT
1 AGCTCGTAT-GAGCTTATTG-TTCAGCTCAATAGAGCTTACCTGTT
30190605 CATCAGCTTA
Statistics
Matches: 78, Mismatches: 7, Indels: 8
0.84 0.08 0.09
Matches are distributed among these distances:
43 2 0.03
44 19 0.24
45 38 0.49
46 4 0.05
47 15 0.19
ACGTcount: A:0.22, C:0.21, G:0.19, T:0.38
Consensus pattern (45 bp):
AGCTCGTATGAGCTTATTGTTCAGCTCAATAGAGCTTACCTGTTT
Found at i:30190588 original size:67 final size:69
Alignment explanation
Indices: 30190478--30190606 Score: 158
Period size: 67 Copynumber: 1.9 Consensus size: 69
30190468 TCAGCTCGTA
* * * * * *
30190478 AGAGCTTACTATTTTCAGCTCATTGCAGCTTACCTTTTTAGCTC-GTATGAGCTTATTGTTCAGC
1 AGAGCTTACTAGTTTCAGCTCATAGCAGCTTACCGTTTCAGCTCATTA-GAGCTTACTGTTCAGC
30190542 TCAAT
65 TCAAT
30190547 AGAGCTTACT-GTTT-AGCTCGATAG-AGCTTACCGTTTCAGCTCATTAGAGCTTACTGTTCA
1 AGAGCTTACTAGTTTCAGCTC-ATAGCAGCTTACCGTTTCAGCTCATTAGAGCTTACTGTTCA
30190607 TCAGCTTAGG
Statistics
Matches: 52, Mismatches: 6, Indels: 6
0.81 0.09 0.09
Matches are distributed among these distances:
67 34 0.65
68 8 0.15
69 10 0.19
ACGTcount: A:0.22, C:0.22, G:0.18, T:0.38
Consensus pattern (69 bp):
AGAGCTTACTAGTTTCAGCTCATAGCAGCTTACCGTTTCAGCTCATTAGAGCTTACTGTTCAGCT
CAAT
Found at i:30194047 original size:6 final size:6
Alignment explanation
Indices: 30194015--30194055 Score: 55
Period size: 6 Copynumber: 6.7 Consensus size: 6
30194005 ACAGTACCTA
* *
30194015 AACAGT AATCAGT AACGGT AGCAGT AACAGT AACAGT AACA
1 AACAGT AA-CAGT AACAGT AACAGT AACAGT AACAGT AACA
30194056 ACATTCAACA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
6 24 0.80
7 6 0.20
ACGTcount: A:0.46, C:0.17, G:0.20, T:0.17
Consensus pattern (6 bp):
AACAGT
Found at i:30194143 original size:12 final size:12
Alignment explanation
Indices: 30194126--30194150 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
30194116 AGTGTCGAAT
30194126 CGGTAACAGTAA
1 CGGTAACAGTAA
30194138 CGGTAACAGTAA
1 CGGTAACAGTAA
30194150 C
1 C
30194151 AATTTATAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.20, G:0.24, T:0.16
Consensus pattern (12 bp):
CGGTAACAGTAA
Found at i:30194146 original size:45 final size:45
Alignment explanation
Indices: 30194038--30194148 Score: 125
Period size: 45 Copynumber: 2.5 Consensus size: 45
30194028 AACGGTAGCA
* ** **
30194038 GTAACAGTAACAGTAACAACATTCAACACACAAAGTGCTAAATTT
1 GTAACAGTAACGGTAACAGTATTCAACACACAAAGTGCTAAATCG
* ** *
30194083 GTAACAGTAATGGTAACAGTATTTGACACACAAAGTG-TCGAATCG
1 GTAACAGTAACGGTAACAGTATTCAACACACAAAGTGCT-AAATCG
30194128 GTAACAGTAACGGTAACAGTA
1 GTAACAGTAACGGTAACAGTA
30194149 ACAATTTATA
Statistics
Matches: 55, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
44 1 0.02
45 54 0.98
ACGTcount: A:0.42, C:0.17, G:0.18, T:0.23
Consensus pattern (45 bp):
GTAACAGTAACGGTAACAGTATTCAACACACAAAGTGCTAAATCG
Found at i:30202840 original size:15 final size:16
Alignment explanation
Indices: 30202814--30202843 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
30202804 CTTAATTTTC
30202814 CCTTTCTTCTTTCTTT
1 CCTTTCTTCTTTCTTT
30202830 CCTTT-TTCTTTCTT
1 CCTTTCTTCTTTCTT
30202844 GCTCTGTTTC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (16 bp):
CCTTTCTTCTTTCTTT
Found at i:30202911 original size:14 final size:13
Alignment explanation
Indices: 30202878--30202961 Score: 58
Period size: 13 Copynumber: 6.9 Consensus size: 13
30202868 TTCTTCTTTA
* *
30202878 CTTTGTTTTGTTT
1 CTTTATTTTATTT
30202891 CTTTATTTTATTT
1 CTTTATTTTATTT
30202904 CATTTATTTTA-TT
1 C-TTTATTTTATTT
30202917 C----TTTTA-TT
1 CTTTATTTTATTT
*
30202925 CTTTTATTTTATTA
1 C-TTTATTTTATTT
*
30202939 ATTTATTTTA-TT
1 CTTTATTTTATTT
30202951 CTTT-TTTTATT
1 CTTTATTTTATT
30202962 AACTTAATAA
Statistics
Matches: 57, Mismatches: 6, Indels: 17
0.71 0.08 0.21
Matches are distributed among these distances:
8 8 0.14
11 5 0.09
12 5 0.09
13 29 0.51
14 10 0.18
ACGTcount: A:0.15, C:0.07, G:0.02, T:0.75
Consensus pattern (13 bp):
CTTTATTTTATTT
Found at i:30202932 original size:21 final size:22
Alignment explanation
Indices: 30202896--30202946 Score: 68
Period size: 21 Copynumber: 2.4 Consensus size: 22
30202886 TGTTTCTTTA
30202896 TTTTATTTCATTTATTTTATTC
1 TTTTATTTCATTTATTTTATTC
* *
30202918 TTTTA-TTCTTTTATTTTATTA
1 TTTTATTTCATTTATTTTATTC
*
30202939 ATTTATTT
1 TTTTATTT
30202947 TATTCTTTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 18 0.72
22 7 0.28
ACGTcount: A:0.20, C:0.06, G:0.00, T:0.75
Consensus pattern (22 bp):
TTTTATTTCATTTATTTTATTC
Found at i:30203246 original size:3 final size:3
Alignment explanation
Indices: 30203238--30203335 Score: 53
Period size: 3 Copynumber: 33.7 Consensus size: 3
30203228 AATTTATTTT
* * * * *
30203238 TAA TAA TAA TAA TCA TAA TCA TAA T-T TAA TAT TAA TAC TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
** * * *
30203285 T-A TAA -AA CCA TAA CAA TTAA TAA TTA TAA TAA TCAA TTA T-A TAA
1 TAA TAA TAA TAA TAA TAA -TAA TAA TAA TAA TAA T-AA TAA TAA TAA
30203329 T-A TAA TA
1 TAA TAA TA
30203336 TATATAATCT
Statistics
Matches: 70, Mismatches: 18, Indels: 14
0.69 0.18 0.14
Matches are distributed among these distances:
2 9 0.13
3 56 0.80
4 5 0.07
ACGTcount: A:0.56, C:0.07, G:0.00, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:30203321 original size:20 final size:19
Alignment explanation
Indices: 30203294--30203335 Score: 59
Period size: 20 Copynumber: 2.2 Consensus size: 19
30203284 ATATAAAACC
30203294 ATAACAATTA-ATAATTATA
1 ATAACAATTATATAA-TATA
30203313 ATAATCAATTATATAATATA
1 ATAA-CAATTATATAATATA
30203333 ATA
1 ATA
30203336 TATATAATCT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 4 0.19
20 13 0.62
21 4 0.19
ACGTcount: A:0.57, C:0.05, G:0.00, T:0.38
Consensus pattern (19 bp):
ATAACAATTATATAATATA
Found at i:30208494 original size:11 final size:11
Alignment explanation
Indices: 30208467--30208517 Score: 54
Period size: 11 Copynumber: 4.9 Consensus size: 11
30208457 GATTTTGACA
*
30208467 TACATGATTTG
1 TACATGATATG
30208478 -ACATGATATG
1 TACATGATATG
30208488 TACATGATATG
1 TACATGATATG
*
30208499 T--ATGAAATG
1 TACATGATATG
*
30208508 CACATGATAT
1 TACATGATAT
30208518 AGTCATATAT
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
9 7 0.21
10 9 0.27
11 17 0.52
ACGTcount: A:0.37, C:0.10, G:0.18, T:0.35
Consensus pattern (11 bp):
TACATGATATG
Found at i:30208595 original size:25 final size:25
Alignment explanation
Indices: 30208562--30208628 Score: 98
Period size: 25 Copynumber: 2.7 Consensus size: 25
30208552 GAGGAAGTGA
*
30208562 AAAAAGGCTTTGCCCCAATTTACCG
1 AAAAGGGCTTTGCCCCAATTTACCG
**
30208587 AAAAGGGCTTTGCCCCTGTTTACCG
1 AAAAGGGCTTTGCCCCAATTTACCG
*
30208612 AAGAGGGCTTTGCCCCA
1 AAAAGGGCTTTGCCCCA
30208629 GTTATTAAAA
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 37 1.00
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.24
Consensus pattern (25 bp):
AAAAGGGCTTTGCCCCAATTTACCG
Found at i:30210039 original size:33 final size:33
Alignment explanation
Indices: 30210002--30210067 Score: 114
Period size: 33 Copynumber: 2.0 Consensus size: 33
30209992 GATGTGGCAG
* *
30210002 GTGTACTACTTTGAGTTCTCGGACAATCTTTAA
1 GTGTACTACTCTGAGTTCGCGGACAATCTTTAA
30210035 GTGTACTACTCTGAGTTCGCGGACAATCTTTAA
1 GTGTACTACTCTGAGTTCGCGGACAATCTTTAA
30210068 CAAAGTGTTC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.24, C:0.20, G:0.20, T:0.36
Consensus pattern (33 bp):
GTGTACTACTCTGAGTTCGCGGACAATCTTTAA
Found at i:30212209 original size:6 final size:6
Alignment explanation
Indices: 30212185--30212228 Score: 52
Period size: 6 Copynumber: 7.2 Consensus size: 6
30212175 GTAGTACCTA
* * *
30212185 AACAGT AATCAGT AACAGT AGCAGT AACTGT AACAAT AACAGT A
1 AACAGT AA-CAGT AACAGT AACAGT AACAGT AACAGT AACAGT A
30212229 TTCAGCACAC
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
6 25 0.81
7 6 0.19
ACGTcount: A:0.48, C:0.16, G:0.16, T:0.20
Consensus pattern (6 bp):
AACAGT
Found at i:30212227 original size:18 final size:19
Alignment explanation
Indices: 30212185--30212233 Score: 55
Period size: 18 Copynumber: 2.6 Consensus size: 19
30212175 GTAGTACCTA
*
30212185 AACAGTAATCAGTAACAGT
1 AACAGTAATCAGTAACAAT
* *
30212204 AGCAGTAA-CTGTAACAAT
1 AACAGTAATCAGTAACAAT
*
30212222 AACAGTATTCAG
1 AACAGTAATCAG
30212234 CACACAAAAT
Statistics
Matches: 23, Mismatches: 6, Indels: 2
0.74 0.19 0.06
Matches are distributed among these distances:
18 14 0.61
19 9 0.39
ACGTcount: A:0.45, C:0.16, G:0.16, T:0.22
Consensus pattern (19 bp):
AACAGTAATCAGTAACAAT
Found at i:30212296 original size:45 final size:45
Alignment explanation
Indices: 30212208--30212307 Score: 114
Period size: 45 Copynumber: 2.2 Consensus size: 45
30212198 AACAGTAGCA
* *
30212208 GTAACTGTAACAATAACAGTATTCAGCACACAAAATGCTGAATCT
1 GTAACAGTAACAATAACAGTATTCAGCACACAAAATGCTGAATCG
* * * *
30212253 GTAATAGTAACGATAATAGTATTC-GACACACAAAGTG-TCGAATCG
1 GTAACAGTAACAATAACAGTATTCAG-CACACAAAATGCT-GAATCG
30212298 GTAACAGTAA
1 GTAACAGTAA
30212308 AGGTAACAAT
Statistics
Matches: 46, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
44 2 0.04
45 44 0.96
ACGTcount: A:0.42, C:0.17, G:0.17, T:0.24
Consensus pattern (45 bp):
GTAACAGTAACAATAACAGTATTCAGCACACAAAATGCTGAATCG
Found at i:30212604 original size:40 final size:40
Alignment explanation
Indices: 30212533--30212608 Score: 98
Period size: 40 Copynumber: 1.9 Consensus size: 40
30212523 TTTCATCAGA
**
30212533 AATTTTACAGTTCAATGCAGTATACGTAACAATATTCGGT
1 AATTTTACAGTTCAATGCAGTATACAAAACAATATTCGGT
* * * *
30212573 AATTTTAGAGTTCAATTCGGTATTCAAAACAATATT
1 AATTTTACAGTTCAATGCAGTATACAAAACAATATT
30212609 TAATAATCCA
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
40 30 1.00
ACGTcount: A:0.37, C:0.13, G:0.13, T:0.37
Consensus pattern (40 bp):
AATTTTACAGTTCAATGCAGTATACAAAACAATATTCGGT
Found at i:30218559 original size:139 final size:138
Alignment explanation
Indices: 30218328--30218604 Score: 518
Period size: 139 Copynumber: 2.0 Consensus size: 138
30218318 ATGCATGCAA
30218328 ATGTTCATCTTTTCCCCCGAAATGAAAGCTTGAGAAAGCTATAAAACAAGTTTGAACATTCGGCT
1 ATGTTCATCTTTTCCCCCGAAATGAAAGCTTGAGAAAGCTATAAAACAAGTTTGAACATTCGGCT
*
30218393 ACTTTGAGGGCTAGATTAAGGTATGTTTTTGGATCGATTTTTAATGATATTTACGTTTTTGAGAT
66 ACTTTGAGGGCTAGATTAAGGTATGTTTTTGGATCGATTTTTAATGATATTTACATTTTTGAGAT
30218458 CATTGCTT
131 CATTGCTT
30218466 ATGTTCATCTTTTCCCCCGAAATGAAAGCTTGAGAAAGCTATAAGAACAAGTTTGAACATTCGGC
1 ATGTTCATCTTTTCCCCCGAAATGAAAGCTTGAGAAAGCTATAA-AACAAGTTTGAACATTCGGC
*
30218531 TACTTTGAGGGCTAGATTAAGGTATGTTTTTGGATCGGTTTTTAATGATATTTACATTTTTGAGA
65 TACTTTGAGGGCTAGATTAAGGTATGTTTTTGGATCGATTTTTAATGATATTTACATTTTTGAGA
*
30218596 TCGTTGCTT
130 TCATTGCTT
30218605 TGTACTCTAG
Statistics
Matches: 135, Mismatches: 3, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
138 44 0.33
139 91 0.67
ACGTcount: A:0.28, C:0.14, G:0.20, T:0.38
Consensus pattern (138 bp):
ATGTTCATCTTTTCCCCCGAAATGAAAGCTTGAGAAAGCTATAAAACAAGTTTGAACATTCGGCT
ACTTTGAGGGCTAGATTAAGGTATGTTTTTGGATCGATTTTTAATGATATTTACATTTTTGAGAT
CATTGCTT
Found at i:30219414 original size:22 final size:22
Alignment explanation
Indices: 30219354--30219466 Score: 93
Period size: 22 Copynumber: 5.0 Consensus size: 22
30219344 TACTATTTTT
* * *
30219354 AGCTCATTGGAGCTTATTGTTTC
1 AGCTCAATAGAGCTTACTG-TTC
* *
30219377 AGCTC-ATATGATCTTATTGTTC
1 AGCTCAATA-GAGCTTACTGTTC
*
30219399 AGCTCAATAGAGCTTACTGTTT
1 AGCTCAATAGAGCTTACTGTTC
* * * *
30219421 AACTCGATCGAGCTTACCGTTTC
1 AGCTCAATAGAGCTTACTG-TTC
*
30219444 AGCTCATTAGAGCTTACTGTTC
1 AGCTCAATAGAGCTTACTGTTC
30219466 A
1 A
30219467 TCAGCTCAGG
Statistics
Matches: 71, Mismatches: 16, Indels: 7
0.76 0.17 0.07
Matches are distributed among these distances:
22 38 0.54
23 33 0.46
ACGTcount: A:0.23, C:0.21, G:0.18, T:0.38
Consensus pattern (22 bp):
AGCTCAATAGAGCTTACTGTTC
Found at i:30227950 original size:28 final size:28
Alignment explanation
Indices: 30227910--30227967 Score: 98
Period size: 28 Copynumber: 2.1 Consensus size: 28
30227900 CCGGATGGTA
* *
30227910 AGATTCTACGGGTCGAATCAAGAGAATT
1 AGATGCTACGGGTCAAATCAAGAGAATT
30227938 AGATGCTACGGGTCAAATCAAGAGAATT
1 AGATGCTACGGGTCAAATCAAGAGAATT
30227966 AG
1 AG
30227968 GTTCATCGCT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.38, C:0.14, G:0.26, T:0.22
Consensus pattern (28 bp):
AGATGCTACGGGTCAAATCAAGAGAATT
Found at i:30235845 original size:38 final size:38
Alignment explanation
Indices: 30235794--30235870 Score: 145
Period size: 38 Copynumber: 2.0 Consensus size: 38
30235784 CTGAACCAGG
30235794 TATGTTTCGAGCCTTTAAAGATTGACATGTTGGCAAAA
1 TATGTTTCGAGCCTTTAAAGATTGACATGTTGGCAAAA
*
30235832 TATGTTTCGAGCCTTTAAAGATTGTCATGTTGGCAAAA
1 TATGTTTCGAGCCTTTAAAGATTGACATGTTGGCAAAA
30235870 T
1 T
30235871 TTCTAGTTTG
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.30, C:0.13, G:0.21, T:0.36
Consensus pattern (38 bp):
TATGTTTCGAGCCTTTAAAGATTGACATGTTGGCAAAA
Found at i:30239612 original size:29 final size:30
Alignment explanation
Indices: 30239580--30239639 Score: 68
Period size: 29 Copynumber: 2.0 Consensus size: 30
30239570 ACTTAGCCTG
*
30239580 TGTGGTCCACACAGCCTACCACAC-GGCTA
1 TGTGGTCCACACAACCTACCACACTGGCTA
* * * *
30239609 TGTGTTCCGCACAATCTACTACACTGGCTA
1 TGTGGTCCACACAACCTACCACACTGGCTA
30239639 T
1 T
30239640 TTAATTACAC
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
29 19 0.76
30 6 0.24
ACGTcount: A:0.23, C:0.33, G:0.18, T:0.25
Consensus pattern (30 bp):
TGTGGTCCACACAACCTACCACACTGGCTA
Found at i:30240226 original size:20 final size:20
Alignment explanation
Indices: 30240201--30240260 Score: 59
Period size: 20 Copynumber: 3.0 Consensus size: 20
30240191 AAGAATCAAC
30240201 AAAGAAAGAAAGAAAAGAAA
1 AAAGAAAGAAAGAAAAGAAA
* * **
30240221 AAAGAAACAATGTGAAGAAA
1 AAAGAAAGAAAGAAAAGAAA
* *
30240241 AAA-AAAGGAAGAAAACAAA
1 AAAGAAAGAAAGAAAAGAAA
30240260 A
1 A
30240261 TGTGAGGAAA
Statistics
Matches: 30, Mismatches: 10, Indels: 1
0.73 0.24 0.02
Matches are distributed among these distances:
19 11 0.37
20 19 0.63
ACGTcount: A:0.75, C:0.03, G:0.18, T:0.03
Consensus pattern (20 bp):
AAAGAAAGAAAGAAAAGAAA
Found at i:30240270 original size:16 final size:15
Alignment explanation
Indices: 30240229--30240270 Score: 50
Period size: 14 Copynumber: 2.8 Consensus size: 15
30240219 AAAAAGAAAC
30240229 AATGTGAAGAAAAAA
1 AATGTGAAGAAAAAA
*
30240244 AAAG-GAAGAAAACAA
1 AATGTGAAGAAAA-AA
*
30240259 AATGTGAGGAAA
1 AATGTGAAGAAA
30240271 GTGATGGAGG
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
14 8 0.36
15 8 0.36
16 6 0.27
ACGTcount: A:0.64, C:0.02, G:0.24, T:0.10
Consensus pattern (15 bp):
AATGTGAAGAAAAAA
Found at i:30241087 original size:19 final size:18
Alignment explanation
Indices: 30241060--30241127 Score: 75
Period size: 19 Copynumber: 3.7 Consensus size: 18
30241050 ATTAATGCTA
*
30241060 TTTTCTTATTTTTTGAACT
1 TTTTATTATTTTTTGAA-T
30241079 TTTTATTATTTTTTGAAT
1 TTTTATTATTTTTTGAAT
* *
30241097 TTTAAAT-TTTTTTGAAT
1 TTTTATTATTTTTTGAAT
*
30241114 ATTTTATAATTTTT
1 -TTTTATTATTTTT
30241128 AAATTATTTT
Statistics
Matches: 41, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
17 10 0.24
18 10 0.24
19 21 0.51
ACGTcount: A:0.24, C:0.03, G:0.04, T:0.69
Consensus pattern (18 bp):
TTTTATTATTTTTTGAAT
Found at i:30241109 original size:28 final size:29
Alignment explanation
Indices: 30241078--30241141 Score: 78
Period size: 28 Copynumber: 2.2 Consensus size: 29
30241068 TTTTTTGAAC
* *
30241078 TTTTTATTATTTTTTGAA-TTTTAAATT-T
1 TTTTTAATATTTTAT-AATTTTTAAATTAT
*
30241106 TTTTGAATATTTTATAATTTTTAAATTAT
1 TTTTTAATATTTTATAATTTTTAAATTAT
30241135 TTTTTAA
1 TTTTTAA
30241142 CATGACATAT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
27 2 0.07
28 21 0.70
29 7 0.23
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.67
Consensus pattern (29 bp):
TTTTTAATATTTTATAATTTTTAAATTAT
Found at i:30241255 original size:18 final size:18
Alignment explanation
Indices: 30241234--30241270 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
30241224 ATGACCAAAC
30241234 ATTGAAAAGAAAATTAAG
1 ATTGAAAAGAAAATTAAG
30241252 ATTGAAAAGAAAATTAAG
1 ATTGAAAAGAAAATTAAG
30241270 A
1 A
30241271 GTGTGTTTGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.62, C:0.00, G:0.16, T:0.22
Consensus pattern (18 bp):
ATTGAAAAGAAAATTAAG
Found at i:30241531 original size:27 final size:28
Alignment explanation
Indices: 30241494--30241548 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 28
30241484 TTTGTAAGAT
* *
30241494 TTTATAAATAT-TTTTAATAAAATAAAA
1 TTTAAAAATATATTATAATAAAATAAAA
*
30241521 TTTAAAAATATATTATAATTAAATAAAA
1 TTTAAAAATATATTATAATAAAATAAAA
30241549 ATTATTTTTA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
27 10 0.42
28 14 0.58
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (28 bp):
TTTAAAAATATATTATAATAAAATAAAA
Found at i:30242276 original size:35 final size:35
Alignment explanation
Indices: 30242236--30242306 Score: 142
Period size: 35 Copynumber: 2.0 Consensus size: 35
30242226 CTAGGTCCTC
30242236 AATCATTTTCTAAATTAAAACTCAATAGCGATTGA
1 AATCATTTTCTAAATTAAAACTCAATAGCGATTGA
30242271 AATCATTTTCTAAATTAAAACTCAATAGCGATTGA
1 AATCATTTTCTAAATTAAAACTCAATAGCGATTGA
30242306 A
1 A
30242307 CTTTTACAAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.44, C:0.14, G:0.08, T:0.34
Consensus pattern (35 bp):
AATCATTTTCTAAATTAAAACTCAATAGCGATTGA
Found at i:30245990 original size:15 final size:15
Alignment explanation
Indices: 30245970--30246000 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
30245960 ACTATGAAAG
30245970 ATATGTTTTGGATTA
1 ATATGTTTTGGATTA
*
30245985 ATATGTTTTGTATTA
1 ATATGTTTTGGATTA
30246000 A
1 A
30246001 AGTTTTTGAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.29, C:0.00, G:0.16, T:0.55
Consensus pattern (15 bp):
ATATGTTTTGGATTA
Found at i:30246059 original size:30 final size:30
Alignment explanation
Indices: 30246025--30246081 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
30246015 TTGAATTATT
*
30246025 AGGACTAAATTGAAAAATATAAT-AAATTGA
1 AGGACTAAAATGAAAAATA-AATGAAATTGA
*
30246055 AGGACTAAAATGCAAAATAAATGAAAT
1 AGGACTAAAATGAAAAATAAATGAAAT
30246082 ATATGGATTA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 3 0.12
30 21 0.88
ACGTcount: A:0.58, C:0.05, G:0.14, T:0.23
Consensus pattern (30 bp):
AGGACTAAAATGAAAAATAAATGAAATTGA
Found at i:30247035 original size:35 final size:35
Alignment explanation
Indices: 30246859--30247037 Score: 198
Period size: 35 Copynumber: 5.1 Consensus size: 35
30246849 TAGGTATGTA
30246859 CATATGTGATGATATATTGAACTTGTATATTTGGC
1 CATATGTGATGATATATTGAACTTGTATATTTGGC
* * * * *
30246894 CACATGTGATGTTATATTAAACTTGAATATTTGAC
1 CATATGTGATGATATATTGAACTTGTATATTTGGC
* * * * * *
30246929 TACATGTGATGTTTTATTGAGCTTGTATATTTGGT
1 CATATGTGATGATATATTGAACTTGTATATTTGGC
* * *
30246964 CATATATGATGATTTATTGTACTTGTATATTTGGC
1 CATATGTGATGATATATTGAACTTGTATATTTGGC
* *
30246999 CATATGTGATGATATAATGAACTTG-AGTATTCGGC
1 CATATGTGATGATATATTGAACTTGTA-TATTTGGC
30247034 CATA
1 CATA
30247038 CAAGTAAGTA
Statistics
Matches: 119, Mismatches: 24, Indels: 2
0.82 0.17 0.01
Matches are distributed among these distances:
34 1 0.01
35 118 0.99
ACGTcount: A:0.28, C:0.09, G:0.19, T:0.43
Consensus pattern (35 bp):
CATATGTGATGATATATTGAACTTGTATATTTGGC
Found at i:30261537 original size:16 final size:16
Alignment explanation
Indices: 30261516--30261547 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
30261506 AGAAAGATCT
30261516 GAATTTGAGACAGCGC
1 GAATTTGAGACAGCGC
30261532 GAATTTGAGACAGCGC
1 GAATTTGAGACAGCGC
30261548 CGATGGTTAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.31, C:0.19, G:0.31, T:0.19
Consensus pattern (16 bp):
GAATTTGAGACAGCGC
Found at i:30264468 original size:25 final size:25
Alignment explanation
Indices: 30264440--30264491 Score: 68
Period size: 25 Copynumber: 2.1 Consensus size: 25
30264430 TTTGGTTTGA
* *
30264440 CATTTACTAAGCAATATCGAATATT
1 CATTTACTAAGCAATACCAAATATT
* *
30264465 CATTTATTAGGCAATACCAAATATT
1 CATTTACTAAGCAATACCAAATATT
30264490 CA
1 CA
30264492 AATTATTCTT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.40, C:0.17, G:0.08, T:0.35
Consensus pattern (25 bp):
CATTTACTAAGCAATACCAAATATT
Found at i:30266777 original size:21 final size:22
Alignment explanation
Indices: 30266753--30266802 Score: 57
Period size: 23 Copynumber: 2.3 Consensus size: 22
30266743 ATTGTATAAA
*
30266753 AAATGAATAT-TCATAACCCCT
1 AAATCAATATCTCATAACCCCT
* *
30266774 AAATTCATTATCTTATAACCCCT
1 AAA-TCAATATCTCATAACCCCT
30266797 AAATCA
1 AAATCA
30266803 TGTATAAACT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
21 3 0.12
22 8 0.33
23 13 0.54
ACGTcount: A:0.42, C:0.24, G:0.02, T:0.32
Consensus pattern (22 bp):
AAATCAATATCTCATAACCCCT
Found at i:30283189 original size:33 final size:34
Alignment explanation
Indices: 30283149--30283225 Score: 84
Period size: 35 Copynumber: 2.2 Consensus size: 34
30283139 AATTATGAAC
*
30283149 ACTTCATT-AAGAGTTCACTGATTTACGATCACA
1 ACTTCATTAAAGAGCTCACTGATTTACGATCACA
* * * *
30283182 ACTTCATTTAAATAGCTCATTGATTTATGATCATA
1 ACTTCA-TTAAAGAGCTCACTGATTTACGATCACA
30283217 ACTTTCATT
1 AC-TTCATT
30283226 TTTTAAAACT
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
33 6 0.17
34 2 0.06
35 24 0.67
36 4 0.11
ACGTcount: A:0.32, C:0.18, G:0.09, T:0.40
Consensus pattern (34 bp):
ACTTCATTAAAGAGCTCACTGATTTACGATCACA
Found at i:30283353 original size:108 final size:108
Alignment explanation
Indices: 30283129--30283357 Score: 323
Period size: 108 Copynumber: 2.1 Consensus size: 108
30283119 GCTTCACTTT
*
30283129 ATTGATTTACAATTATGAACACTTCATTAAGAGTTCACTGATTTACGATCACAACTTCATTTAAA
1 ATTGATTTACAATTATGAACACTTCATTAAGAATTCACTGATTTACGATCACAACTTCATTTAAA
* * *
30283194 TAGCTCATTGATTTATGATCATAACTTTCATTTTTTAAAACTC
66 CAGCTCATTGATTTATGATCACAACTTTCATTTTTCAAAACTC
* * * ** ** *
30283237 ACTAATTTACGATTATGAACACTTCATTAAGAATTCGTTGATTTACGATTGCAGCTTCATTTAAA
1 ATTGATTTACAATTATGAACACTTCATTAAGAATTCACTGATTTACGATCACAACTTCATTTAAA
* *
30283302 CAGTTCATTGATTTATGATCACAACTTTCATTTTTCAAAGCTC
66 CAGCTCATTGATTTATGATCACAACTTTCATTTTTCAAAACTC
*
30283345 GTTGATTTACAAT
1 ATTGATTTACAAT
30283358 CACAGCTACA
Statistics
Matches: 103, Mismatches: 18, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
108 103 1.00
ACGTcount: A:0.33, C:0.17, G:0.10, T:0.41
Consensus pattern (108 bp):
ATTGATTTACAATTATGAACACTTCATTAAGAATTCACTGATTTACGATCACAACTTCATTTAAA
CAGCTCATTGATTTATGATCACAACTTTCATTTTTCAAAACTC
Found at i:30283537 original size:136 final size:136
Alignment explanation
Indices: 30283294--30283543 Score: 329
Period size: 136 Copynumber: 1.8 Consensus size: 136
30283284 ATTGCAGCTT
* ** * *
30283294 CATTTAAACAGTTCATTGATTTATGATCACAACTTTCATTTTTCAAAGCTCGTTGATTTACAATC
1 CATTTAAACAGTTCACTGATTTACAATCACAACTGTAATTTTTCAAAGCTCGTTGATTTACAATC
* * * * *
30283359 ACAGCTACAGTTCATTGATTTACAATCATGACCATTTTATTAAGAGTTTCACCGATTTACAATCG
66 ACAACTACAGTTCATTGATTTACAATCATAAACAATTCATTAAGAGTTTCACCGATTTACAATCG
30283424 CAACAC
131 CAACAC
* * **
30283430 CATTTAAATAGTTCACTGATTTACAATCACAACTGTAATTTTTTAAAGCTCGTTGATTTATGATC
1 CATTTAAACAGTTCACTGATTTACAATCACAACTGTAATTTTTCAAAGCTCGTTGATTTACAATC
** * * *
30283495 ACAACTTTAGTTTATTGATTTATAATCATAAATAATTCATTAAGAGTTT
66 ACAACTACAGTTCATTGATTTACAATCATAAACAATTCATTAAGAGTTT
30283544 GTTTATTTAC
Statistics
Matches: 95, Mismatches: 19, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
136 95 1.00
ACGTcount: A:0.34, C:0.17, G:0.10, T:0.40
Consensus pattern (136 bp):
CATTTAAACAGTTCACTGATTTACAATCACAACTGTAATTTTTCAAAGCTCGTTGATTTACAATC
ACAACTACAGTTCATTGATTTACAATCATAAACAATTCATTAAGAGTTTCACCGATTTACAATCG
CAACAC
Found at i:30283552 original size:36 final size:36
Alignment explanation
Indices: 30283503--30283589 Score: 120
Period size: 36 Copynumber: 2.4 Consensus size: 36
30283493 TCACAACTTT
* * *
30283503 AGTTTATTGATTTATAATCATAAATAATTCATTAAG
1 AGTTTGTTGATTTACAATCATAAACAATTCATTAAG
* *
30283539 AGTTTGTTTATTTACAATCATGAACAATTCATTAAG
1 AGTTTGTTGATTTACAATCATAAACAATTCATTAAG
*
30283575 AGTTCGTTGATTTAC
1 AGTTTGTTGATTTAC
30283590 GATCGTAACT
Statistics
Matches: 44, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
36 44 1.00
ACGTcount: A:0.36, C:0.09, G:0.11, T:0.44
Consensus pattern (36 bp):
AGTTTGTTGATTTACAATCATAAACAATTCATTAAG
Found at i:30285068 original size:5 final size:5
Alignment explanation
Indices: 30285058--30285124 Score: 68
Period size: 5 Copynumber: 13.0 Consensus size: 5
30285048 TAAGAATATA
30285058 TTATT TTATT TT-TAT TTACTT TTATT TT-TAT TTATTT TTATT TT-TAT
1 TTATT TTATT TTAT-T TTA-TT TTATT TTAT-T TTA-TT TTATT TTAT-T
30285105 TTATT TTATT TTATT TTATT
1 TTATT TTATT TTATT TTATT
30285125 AAATTAGTTA
Statistics
Matches: 54, Mismatches: 0, Indels: 16
0.77 0.00 0.23
Matches are distributed among these distances:
4 3 0.06
5 40 0.74
6 9 0.17
7 2 0.04
ACGTcount: A:0.19, C:0.01, G:0.00, T:0.79
Consensus pattern (5 bp):
TTATT
Found at i:30285070 original size:6 final size:6
Alignment explanation
Indices: 30285061--30285121 Score: 58
Period size: 6 Copynumber: 10.5 Consensus size: 6
30285051 GAATATATTA
*
30285061 TTTTAT TTTTA- -TTTAC TTTTAT TTTTA- -TTTAT TTTTAT TTTTAT
1 TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT
*
30285105 TTATTTT ATTTTAT TTT
1 TT-TTAT -TTTTAT TTT
30285122 ATTAAATTAG
Statistics
Matches: 46, Mismatches: 3, Indels: 12
0.75 0.05 0.20
Matches are distributed among these distances:
4 8 0.17
6 30 0.65
7 6 0.13
8 2 0.04
ACGTcount: A:0.18, C:0.02, G:0.00, T:0.80
Consensus pattern (6 bp):
TTTTAT
Found at i:30285082 original size:16 final size:15
Alignment explanation
Indices: 30285058--30285120 Score: 101
Period size: 16 Copynumber: 4.1 Consensus size: 15
30285048 TAAGAATATA
30285058 TTATTTTATTTTTAT
1 TTATTTTATTTTTAT
30285073 TTACTTTTATTTTTAT
1 TTA-TTTTATTTTTAT
30285089 TTATTTTTATTTTTAT
1 TTA-TTTTATTTTTAT
30285105 TTATTTTA-TTTTAT
1 TTATTTTATTTTTAT
30285119 TT
1 TT
30285121 TATTAAATTA
Statistics
Matches: 46, Mismatches: 1, Indels: 3
0.92 0.02 0.06
Matches are distributed among these distances:
14 8 0.17
15 8 0.17
16 30 0.65
ACGTcount: A:0.19, C:0.02, G:0.00, T:0.79
Consensus pattern (15 bp):
TTATTTTATTTTTAT
Found at i:30285093 original size:26 final size:26
Alignment explanation
Indices: 30285058--30285121 Score: 87
Period size: 26 Copynumber: 2.5 Consensus size: 26
30285048 TAAGAATATA
30285058 TTATTTTATTTTTATTTACT-TTTATT
1 TTATTTTATTTTTATTT-CTATTTATT
*
30285084 TT-TATTTATTTTTATTTTTATTTATT
1 TTAT-TTTATTTTTATTTCTATTTATT
30285110 TTATTTTATTTT
1 TTATTTTATTTT
30285122 ATTAAATTAG
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
25 2 0.06
26 31 0.91
27 1 0.03
ACGTcount: A:0.19, C:0.02, G:0.00, T:0.80
Consensus pattern (26 bp):
TTATTTTATTTTTATTTCTATTTATT
Found at i:30292115 original size:166 final size:166
Alignment explanation
Indices: 30291905--30292239 Score: 591
Period size: 166 Copynumber: 2.0 Consensus size: 166
30291895 TTTCATGAAT
* *
30291905 TTGTGATTTGATGAAATAGGACTAAATTGTAAAAGTTGTGAAATTCTATGGGCAAATGTGTAAAA
1 TTGTGATTTGATGAAATAGGACTAAATTGTAAAAATTATGAAATTCTATGGGCAAATGTGTAAAA
*
30291970 ATGCCTTCAAGTGAATTTTTGGATTAAATTGAATAGAGAGATAATTGAATAAGTTGAATTTGATA
66 ATGCCTTCAAGTGAATTTTTGGATTAAATTGAATAGAGAGATAATTGAATAAGCTGAATTTGATA
** *
30292035 TTATATAGATCAAGAAAAGTGAAATACGGAC-TAAA
131 TTATATAGATCAAGAAAAGCAAAATACAGACTTAAA
*
30292070 TTGTGATTTGATGAAATAAGGACTAAATTGTAAAAATTATGAAATTTTATGGGCAAATGTGTAAA
1 TTGTGATTTGATGAAAT-AGGACTAAATTGTAAAAATTATGAAATTCTATGGGCAAATGTGTAAA
30292135 AATGCCTTCAAGTGAATTTTTGGATTAAATTGAATAGAGAGATAATTGAATAAGCTGAATTTGAT
65 AATGCCTTCAAGTGAATTTTTGGATTAAATTGAATAGAGAGATAATTGAATAAGCTGAATTTGAT
30292200 ATTATATAGATCAAGAAAAGCAAAATACAGACTTAAA
130 ATTATATAGATCAAGAAAAGCAAAATACAGACTTAAA
30292237 TTG
1 TTG
30292240 GGGAAAGAAC
Statistics
Matches: 161, Mismatches: 7, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
165 17 0.11
166 137 0.85
167 7 0.04
ACGTcount: A:0.42, C:0.06, G:0.19, T:0.33
Consensus pattern (166 bp):
TTGTGATTTGATGAAATAGGACTAAATTGTAAAAATTATGAAATTCTATGGGCAAATGTGTAAAA
ATGCCTTCAAGTGAATTTTTGGATTAAATTGAATAGAGAGATAATTGAATAAGCTGAATTTGATA
TTATATAGATCAAGAAAAGCAAAATACAGACTTAAA
Found at i:30294127 original size:83 final size:83
Alignment explanation
Indices: 30293986--30294151 Score: 224
Period size: 83 Copynumber: 2.0 Consensus size: 83
30293976 ACTGTATGTG
* * ** * * * *
30293986 AAATGTATGTTTGAATGTGTTATAAGTCTGGTAATGCTCCGTAACCCCATTTCGGCATTGAATAT
1 AAATGTATGTTTAAATGTGTTATAAGTATAATAATACTCCGTAACCCCATTCCAGCATTGAATAC
30294051 GGGTAAAGGGTGTTACAT
66 GGGTAAAGGGTGTTACAT
* *
30294069 AAATGTATGTTTAAATGTGTTATAAGTATAATAATACTTCGTAACCCTATTCCAGCATTGAATAC
1 AAATGTATGTTTAAATGTGTTATAAGTATAATAATACTCCGTAACCCCATTCCAGCATTGAATAC
* *
30294134 GGGTGAGGGGTGTTACAT
66 GGGTAAAGGGTGTTACAT
30294152 TCTTACTCAG
Statistics
Matches: 71, Mismatches: 12, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
83 71 1.00
ACGTcount: A:0.30, C:0.13, G:0.22, T:0.35
Consensus pattern (83 bp):
AAATGTATGTTTAAATGTGTTATAAGTATAATAATACTCCGTAACCCCATTCCAGCATTGAATAC
GGGTAAAGGGTGTTACAT
Found at i:30296780 original size:47 final size:47
Alignment explanation
Indices: 30296671--30297125 Score: 155
Period size: 47 Copynumber: 9.7 Consensus size: 47
30296661 GATTTGTGCG
** * *
30296671 CCAGTGTAAGACATGTCTGGGACAT-GCTTCGGCCACATTATGAGAG
1 CCAGTGTAAGACATGTCTGGGACATGGAATCGGCCACAATATGAGAC
* *
30296717 CCAGTGTAAGACCATGTTTGGGACATGGAATCGG-CACAGATATGAGTC
1 CCAGTGTAAGA-CATGTCTGGGACATGGAATCGGCCACA-ATATGAGAC
* * * * * * * *
30296765 CCAGAGTAAGACATGTCTGGTACAT-GCATCAGCCTCGACAGA-GATAG
1 CCAGTGTAAGACATGTCTGGGACATGGAATCGGCCAC-A-ATATGAGAC
* * ** *
30296812 CCAGTGTAAGACGTGTCTGGGACAT-GTATCGGGTA-AGAGT-TGTG--
1 CCAGTGTAAGACATGTCTGGGACATGGAATCGGCCACA-A-TATGAGAC
* * * *
30296856 CTAGTGTAAGACATGTCTGGGACAT-GCATCAG-CATGCATATATGAGAG
1 CCAGTGTAAGACATGTCTGGGACATGGAATCGGCCA--CA-ATATGAGAC
* * * * **
30296904 CCAGTGTAAGACCATGTCTAGGACATGGCATCAG-CACAGAGATGAGTG
1 CCAGTGTAAGA-CATGTCTGGGACATGGAATCGGCCACA-ATATGAGAC
* * * * *
30296952 CCAGAGTGAGACATGTCTGGGATAT--ACATTGGCTTCGACAGAGAT-AG--
1 CCAGTGTAAGACATGTCTGGGACATGGA-ATCGGC--C-ACA-ATATGAGAC
* * ** *
30296999 CCAGTGTAAGACGTGTCTGGGACAT-GTATCGGGTA-AGAGT-TGTG--
1 CCAGTGTAAGACATGTCTGGGACATGGAATCGGCCACA-A-TATGAGAC
* * * *
30297043 CTAGTGTAAGACATGTCTGGGACAT-GCATCAGCACACATATATGAGAG
1 CCAGTGTAAGACATGTCTGGGACATGGAATCGGC-CACA-ATATGAGAC
* *
30297091 CTAGTGTAAGACCATGTCTGGGACATGGCATCGGC
1 CCAGTGTAAGA-CATGTCTGGGACATGGAATCGGC
30297126 AATTTATCCC
Statistics
Matches: 312, Mismatches: 67, Indels: 56
0.72 0.15 0.13
Matches are distributed among these distances:
43 5 0.02
44 58 0.19
45 5 0.02
46 30 0.10
47 97 0.31
48 63 0.20
49 30 0.10
50 24 0.08
ACGTcount: A:0.28, C:0.19, G:0.30, T:0.23
Consensus pattern (47 bp):
CCAGTGTAAGACATGTCTGGGACATGGAATCGGCCACAATATGAGAC
Found at i:30296873 original size:44 final size:45
Alignment explanation
Indices: 30296670--30297072 Score: 203
Period size: 47 Copynumber: 8.7 Consensus size: 45
30296660 TGATTTGTGC
* ** * * *
30296670 GCCAGTGTAAGACATGTCTGGGACATGCTTCGGCCACATTA-TGAGA
1 GCCAGTGTAAGACATGTCTGGGACATGCATCGGGTACA-GAGT-TGT
* * *
30296716 GCCAGTGTAAGACCATGTTTGGGACATGGAATC-GGCACAGA-TATGAGT
1 GCCAGTGTAAGA-CATGTCTGGGACAT-GCATCGGGTACAGAGT-T--GT
* * * ** * *
30296764 CCCAGAGTAAGACATGTCTGGTACATGCATCAGCCTCGACAGAGAT-A
1 GCCAGTGTAAGACATGTCTGGGACATGCATC-GGGT--ACAGAGTTGT
* *
30296811 GCCAGTGTAAGACGTGTCTGGGACATGTATCGGGTA-AGAGTTGT
1 GCCAGTGTAAGACATGTCTGGGACATGCATCGGGTACAGAGTTGT
* ** * * *
30296855 GCTAGTGTAAGACATGTCTGGGACATGCATCAGCATGCATA-TATGAGA
1 GCCAGTGTAAGACATGTCTGGGACATGCATC-GGGTACAGAGT-T--GT
* * * *
30296903 GCCAGTGTAAGACCATGTCTAGGACATGGCATC-AGCACAGAGATGAGT
1 GCCAGTGTAAGA-CATGTCTGGGACAT-GCATCGGGTACAGAG-T-TGT
* * * * * * * *
30296951 GCCAGAGTGAGACATGTCTGGGATATACATTGGCTTCGACAGAGAT-A
1 GCCAGTGTAAGACATGTCTGGGACATGCATCGG-GT--ACAGAGTTGT
* *
30296998 GCCAGTGTAAGACGTGTCTGGGACATGTATCGGGTA-AGAGTTGT
1 GCCAGTGTAAGACATGTCTGGGACATGCATCGGGTACAGAGTTGT
*
30297042 GCTAGTGTAAGACATGTCTGGGACATGCATC
1 GCCAGTGTAAGACATGTCTGGGACATGCATC
30297073 AGCACACATA
Statistics
Matches: 263, Mismatches: 70, Indels: 50
0.69 0.18 0.13
Matches are distributed among these distances:
43 10 0.04
44 58 0.22
45 3 0.01
46 27 0.10
47 94 0.36
48 40 0.15
49 13 0.05
50 18 0.07
ACGTcount: A:0.28, C:0.18, G:0.30, T:0.24
Consensus pattern (45 bp):
GCCAGTGTAAGACATGTCTGGGACATGCATCGGGTACAGAGTTGT
Found at i:30296881 original size:91 final size:91
Alignment explanation
Indices: 30296770--30297076 Score: 366
Period size: 91 Copynumber: 3.3 Consensus size: 91
30296760 GAGTCCCAGA
* *
30296770 GTAAGACATGTCTGGTACATGCATCAGCCTCGACAGAGATAGCCAGTGTAAGACGTGTCTGGGAC
1 GTAAGACATGTCTGGGACATGCATCAGCATCGACAGAGATAGCCAGTGTAAGACGTGTCTGGGAC
30296835 ATGTATCGGGTAAGAGTTGTGCTAGT
66 ATGTATCGGGTAAGAGTTGTGCTAGT
* * * * *
30296861 GTAAGACATGTCTGGGACATGCATCAGCAT-GCATATATGAGAGCCAGTGTAAGACCATGTCTAG
1 GTAAGACATGTCTGGGACATGCATCAGCATCG-ACAGA-GATAGCCAGTGTAAGA-CGTGTCTGG
* * * * * *
30296925 GACATGGCATC-AGCACAGAGATGAGTGCCAGA
63 GACAT-GTATCGGGTA-AGAG-T-TGTGCTAGT
* * * ** *
30296957 GTGAGACATGTCTGGGATATACATTGGCTTCGACAGAGATAGCCAGTGTAAGACGTGTCTGGGAC
1 GTAAGACATGTCTGGGACATGCATCAGCATCGACAGAGATAGCCAGTGTAAGACGTGTCTGGGAC
30297022 ATGTATCGGGTAAGAGTTGTGCTAGT
66 ATGTATCGGGTAAGAGTTGTGCTAGT
30297048 GTAAGACATGTCTGGGACATGCATCAGCA
1 GTAAGACATGTCTGGGACATGCATCAGCA
30297077 CACATATATG
Statistics
Matches: 171, Mismatches: 36, Indels: 18
0.76 0.16 0.08
Matches are distributed among these distances:
90 1 0.01
91 60 0.35
92 16 0.09
93 22 0.13
94 22 0.13
95 16 0.09
96 33 0.19
97 1 0.01
ACGTcount: A:0.28, C:0.18, G:0.30, T:0.24
Consensus pattern (91 bp):
GTAAGACATGTCTGGGACATGCATCAGCATCGACAGAGATAGCCAGTGTAAGACGTGTCTGGGAC
ATGTATCGGGTAAGAGTTGTGCTAGT
Found at i:30296992 original size:187 final size:185
Alignment explanation
Indices: 30296673--30297122 Score: 704
Period size: 187 Copynumber: 2.4 Consensus size: 185
30296663 TTTGTGCGCC
* * *
30296673 AGTGTAAGACATGTCTGGGACATGCTTCGGCCACAT-TATGAGAGCCAGTGTAAGACCATGTTTG
1 AGTGTAAGACATGTCTGGGACATGCATCAG-CACATATATGAGAGCCAGTGTAAGACCATGTCTG
* * * * *
30296737 GGACATGGAATCGGCACAGATATGAGTCCCAGAGTAAGACATGTCTGGTACATGCATCAGCCTCG
65 GGACATGGCATCAGCACAGAGATGAGTCCCAGAGTAAGACATGTCTGGGACATACATCAGCCTCG
30296802 ACAGAGATAGCCAGTGTAAGACGTGTCTGGGACATGTATCGGGTAAGAGTTGTGCT
130 ACAGAGATAGCCAGTGTAAGACGTGTCTGGGACATGTATCGGGTAAGAGTTGTGCT
30296858 AGTGTAAGACATGTCTGGGACATGCATCAGCATGCATATATGAGAGCCAGTGTAAGACCATGTCT
1 AGTGTAAGACATGTCTGGGACATGCATCAGCA--CATATATGAGAGCCAGTGTAAGACCATGTCT
* * * * ** *
30296923 AGGACATGGCATCAGCACAGAGATGAGTGCCAGAGTGAGACATGTCTGGGATATACATTGGCTTC
64 GGGACATGGCATCAGCACAGAGATGAGTCCCAGAGTAAGACATGTCTGGGACATACATCAGCCTC
30296988 GACAGAGATAGCCAGTGTAAGACGTGTCTGGGACATGTATCGGGTAAGAGTTGTGCT
129 GACAGAGATAGCCAGTGTAAGACGTGTCTGGGACATGTATCGGGTAAGAGTTGTGCT
*
30297045 AGTGTAAGACATGTCTGGGACATGCATCAGCACACATATATGAGAGCTAGTGTAAGACCATGTCT
1 AGTGTAAGACATGTCTGGGACATGCATCAG--CACATATATGAGAGCCAGTGTAAGACCATGTCT
30297110 GGGACATGGCATC
64 GGGACATGGCATC
30297123 GGCAATTTAT
Statistics
Matches: 243, Mismatches: 17, Indels: 8
0.91 0.06 0.03
Matches are distributed among these distances:
184 2 0.01
185 28 0.12
186 3 0.01
187 208 0.86
189 2 0.01
ACGTcount: A:0.29, C:0.18, G:0.30, T:0.24
Consensus pattern (185 bp):
AGTGTAAGACATGTCTGGGACATGCATCAGCACATATATGAGAGCCAGTGTAAGACCATGTCTGG
GACATGGCATCAGCACAGAGATGAGTCCCAGAGTAAGACATGTCTGGGACATACATCAGCCTCGA
CAGAGATAGCCAGTGTAAGACGTGTCTGGGACATGTATCGGGTAAGAGTTGTGCT
Done.