Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr7
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: 55462051
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2780933 characters in sequence are not A, C, G, or T
File 147 of 163
Found at i:48436796 original size:18 final size:18
Alignment explanation
Indices: 48436770--48436806 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
48436760 AACCAGAAAT
*
48436770 TAAAATTAACTTGAAAAC
1 TAAAATTAAATTGAAAAC
*
48436788 TAAATTTAAATTGAAAAC
1 TAAAATTAAATTGAAAAC
48436806 T
1 T
48436807 TATAACGAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.54, C:0.08, G:0.05, T:0.32
Consensus pattern (18 bp):
TAAAATTAAATTGAAAAC
Found at i:48441747 original size:19 final size:18
Alignment explanation
Indices: 48441687--48441749 Score: 51
Period size: 18 Copynumber: 3.6 Consensus size: 18
48441677 ATCTTTTAAA
48441687 TATAAAAAATT-TGAAAA-
1 TATAAAAAATTAT-AAAAC
* *
48441704 AAT-AAAAAGTATAAAAC
1 TATAAAAAATTATAAAAC
* *
48441721 TATTAAAAATTATAAAGAT
1 TATAAAAAATTATAAA-AC
48441740 TATAAAAAAT
1 TATAAAAAAT
48441750 ATTTTAAAAA
Statistics
Matches: 36, Mismatches: 6, Indels: 6
0.75 0.12 0.12
Matches are distributed among these distances:
16 10 0.28
17 5 0.14
18 11 0.31
19 10 0.28
ACGTcount: A:0.65, C:0.02, G:0.05, T:0.29
Consensus pattern (18 bp):
TATAAAAAATTATAAAAC
Found at i:48441766 original size:21 final size:20
Alignment explanation
Indices: 48441725--48441768 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 20
48441715 TAAAACTATT
*
48441725 AAAAATTATAAAGATTATAA
1 AAAAATTATAAAAATTATAA
* *
48441745 AAAATATTTTAAAAATTTTAA
1 AAAA-ATTATAAAAATTATAA
48441766 AAA
1 AAA
48441769 TTAAATTTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 4 0.20
21 16 0.80
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (20 bp):
AAAAATTATAAAAATTATAA
Found at i:48443796 original size:3 final size:3
Alignment explanation
Indices: 48443788--48443830 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
48443778 TTATACCATC
48443788 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
48443831 ACCTTTAATT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:48445007 original size:2 final size:2
Alignment explanation
Indices: 48444994--48445030 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
48444984 ATATGTTGTC
*
48444994 TG TG TT TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
48445031 AAATATGCAT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.00, C:0.00, G:0.46, T:0.54
Consensus pattern (2 bp):
TG
Found at i:48451843 original size:3 final size:3
Alignment explanation
Indices: 48451831--48451882 Score: 97
Period size: 3 Copynumber: 17.7 Consensus size: 3
48451821 ATTTAAAGGT
48451831 ATA A-A ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
48451878 ATA AT
1 ATA AT
48451883 TTCAACCAGC
Statistics
Matches: 48, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 2 0.04
3 46 0.96
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:48452201 original size:80 final size:80
Alignment explanation
Indices: 48452068--48452309 Score: 484
Period size: 80 Copynumber: 3.0 Consensus size: 80
48452058 TAAATCAAAT
48452068 TGCAAGTACAATGTAGTTATTGCATAGACGGTTTAATCGCTCTTTGTTGCCTTTTTTGGGGTGAA
1 TGCAAGTACAATGTAGTTATTGCATAGACGGTTTAATCGCTCTTTGTTGCCTTTTTTGGGGTGAA
48452133 AAAAAGAAAAGAAAA
66 AAAAAGAAAAGAAAA
48452148 TGCAAGTACAATGTAGTTATTGCATAGACGGTTTAATCGCTCTTTGTTGCCTTTTTTGGGGTGAA
1 TGCAAGTACAATGTAGTTATTGCATAGACGGTTTAATCGCTCTTTGTTGCCTTTTTTGGGGTGAA
48452213 AAAAAGAAAAGAAAA
66 AAAAAGAAAAGAAAA
48452228 TGCAAGTACAATGTAGTTATTGCATAGACGGTTTAATCGCTCTTTGTTGCCTTTTTTGGGGTGAA
1 TGCAAGTACAATGTAGTTATTGCATAGACGGTTTAATCGCTCTTTGTTGCCTTTTTTGGGGTGAA
48452293 AAAAAGAAAAGAAAA
66 AAAAAGAAAAGAAAA
48452308 TG
1 TG
48452310 AAAATGAAAA
Statistics
Matches: 162, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
80 162 1.00
ACGTcount: A:0.33, C:0.11, G:0.23, T:0.33
Consensus pattern (80 bp):
TGCAAGTACAATGTAGTTATTGCATAGACGGTTTAATCGCTCTTTGTTGCCTTTTTTGGGGTGAA
AAAAAGAAAAGAAAA
Found at i:48459332 original size:15 final size:16
Alignment explanation
Indices: 48459303--48459335 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
48459293 TTCGTCTCTT
48459303 TTTTCTTTTAGTTTTA
1 TTTTCTTTTAGTTTTA
*
48459319 TTTT-TTTTATTTTTA
1 TTTTCTTTTAGTTTTA
48459334 TT
1 TT
48459336 GAAAAAACTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.12, C:0.03, G:0.03, T:0.82
Consensus pattern (16 bp):
TTTTCTTTTAGTTTTA
Found at i:48461668 original size:68 final size:67
Alignment explanation
Indices: 48461536--48461668 Score: 160
Period size: 68 Copynumber: 2.0 Consensus size: 67
48461526 TTACAATACT
* * * **
48461536 AATAGCTTATAAATTACCACAAATGTCCTAAAGGCTAAAGCAAAATAGTAATACTAACTTACAAG
1 AATACCTTATAAATTACCAAAAATGTCCTAAAGGCTAAAGCAAAAGAGTAATACT-ACCAACAAG
48461601 ACC
65 ACC
* * *
48461604 AATACCTTATAAGTTACCAAAAATGTCGTAAAGGCTAAAGCAAAAGGATTAATTACT-CCAACAA
1 AATACCTTATAAATTACCAAAAATGTCCTAAAGGCTAAAGCAAAA-GAGTAA-TACTACCAACAA
48461668 G
64 G
48461669 TGAGATGATT
Statistics
Matches: 55, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
68 47 0.85
69 4 0.07
70 4 0.07
ACGTcount: A:0.47, C:0.18, G:0.12, T:0.23
Consensus pattern (67 bp):
AATACCTTATAAATTACCAAAAATGTCCTAAAGGCTAAAGCAAAAGAGTAATACTACCAACAAGA
CC
Found at i:48462762 original size:46 final size:46
Alignment explanation
Indices: 48462642--48462765 Score: 185
Period size: 46 Copynumber: 2.7 Consensus size: 46
48462632 TTTATTTTAG
* *
48462642 TTATTTTTATAATTTTGAAATTATAAGTCAATACGATGATAAAATT
1 TTATTTTTATAATTTTAAAATTATAAGTTAATACGATGATAAAATT
* * * * *
48462688 ATATTTTTGTAATTTTCAATTTATAAGTTAGTACGATGATAAAATT
1 TTATTTTTATAATTTTAAAATTATAAGTTAATACGATGATAAAATT
48462734 TTATTTTTATAATTTTAAAATTATAAGTTAAT
1 TTATTTTTATAATTTTAAAATTATAAGTTAAT
48462766 CTTTTTATAC
Statistics
Matches: 67, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
46 67 1.00
ACGTcount: A:0.40, C:0.03, G:0.08, T:0.49
Consensus pattern (46 bp):
TTATTTTTATAATTTTAAAATTATAAGTTAATACGATGATAAAATT
Found at i:48463339 original size:6 final size:6
Alignment explanation
Indices: 48463328--48463356 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
48463318 TTTCATTGGG
48463328 ATTATA ATTATA ATTATA ATTATA ATTAT
1 ATTATA ATTATA ATTATA ATTATA ATTAT
48463357 TGCTTCCCAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (6 bp):
ATTATA
Found at i:48464409 original size:24 final size:22
Alignment explanation
Indices: 48464351--48464405 Score: 56
Period size: 24 Copynumber: 2.3 Consensus size: 22
48464341 ATAGCCTCTT
*
48464351 TTTTATATATATATTTAAAATAA
1 TTTTATAT-TATATATAAAATAA
*
48464374 TTTTCATTATTATATATAATATAA
1 TTTT-A-TATTATATATAAAATAA
48464398 TATTTATA
1 T-TTTATA
48464406 ATTAATAAAC
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
23 6 0.22
24 15 0.56
25 6 0.22
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.55
Consensus pattern (22 bp):
TTTTATATTATATATAAAATAA
Found at i:48467600 original size:12 final size:12
Alignment explanation
Indices: 48467583--48467612 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
48467573 TTTTAGACAT
48467583 TATATAAAAATA
1 TATATAAAAATA
*
48467595 TATATAAATATA
1 TATATAAAAATA
48467607 TATATA
1 TATATA
48467613 TATATATAGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (12 bp):
TATATAAAAATA
Found at i:48469742 original size:19 final size:19
Alignment explanation
Indices: 48469707--48469745 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
48469697 TCTTGTGTCA
*
48469707 TTTTTCTATTTTTGTTGCT
1 TTTTTCTATTTTAGTTGCT
48469726 TTTTTC-ATTTTAAGTTGCT
1 TTTTTCTATTTT-AGTTGCT
48469745 T
1 T
48469746 CCACTTTATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 5 0.28
19 13 0.72
ACGTcount: A:0.10, C:0.10, G:0.10, T:0.69
Consensus pattern (19 bp):
TTTTTCTATTTTAGTTGCT
Found at i:48471046 original size:23 final size:23
Alignment explanation
Indices: 48471019--48471077 Score: 118
Period size: 23 Copynumber: 2.6 Consensus size: 23
48471009 CAGTGCTCTT
48471019 CTTGTTTTTTTAATTATTCAATA
1 CTTGTTTTTTTAATTATTCAATA
48471042 CTTGTTTTTTTAATTATTCAATA
1 CTTGTTTTTTTAATTATTCAATA
48471065 CTTGTTTTTTTAA
1 CTTGTTTTTTTAA
48471078 CACAATTACA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.24, C:0.08, G:0.05, T:0.63
Consensus pattern (23 bp):
CTTGTTTTTTTAATTATTCAATA
Found at i:48478332 original size:12 final size:12
Alignment explanation
Indices: 48478317--48478341 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
48478307 TATTACTATT
48478317 TTAATTTAATTA
1 TTAATTTAATTA
48478329 TTAATTTAATTA
1 TTAATTTAATTA
48478341 T
1 T
48478342 GTTTTATTTG
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:0.00, G:0.00, T:0.60
Consensus pattern (12 bp):
TTAATTTAATTA
Found at i:48496849 original size:29 final size:29
Alignment explanation
Indices: 48496798--48496853 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
48496788 ATAGTAACCT
**
48496798 GATCAAACTAGTCCTTTTACTATTAAATG
1 GATCAAACTAGTCCTCGTACTATTAAATG
* *
48496827 GATCAATCTAGTCCTCGTGCTATTAAA
1 GATCAAACTAGTCCTCGTACTATTAAA
48496854 AAGAATCTAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.32, C:0.20, G:0.12, T:0.36
Consensus pattern (29 bp):
GATCAAACTAGTCCTCGTACTATTAAATG
Found at i:48497117 original size:29 final size:31
Alignment explanation
Indices: 48497085--48497147 Score: 76
Period size: 31 Copynumber: 2.1 Consensus size: 31
48497075 ACAGTATAAT
48497085 GACTAAATTAATC-AA-TTTAATAATAAAGG
1 GACTAAATTAATCTAATTTTAATAATAAAGG
* * * *
48497114 GACTAATTTGATCTAATTTTTATAATATAGG
1 GACTAAATTAATCTAATTTTAATAATAAAGG
48497145 GAC
1 GAC
48497148 CTCCTAGGTA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
29 11 0.39
30 2 0.07
31 15 0.54
ACGTcount: A:0.43, C:0.08, G:0.13, T:0.37
Consensus pattern (31 bp):
GACTAAATTAATCTAATTTTAATAATAAAGG
Found at i:48499280 original size:99 final size:100
Alignment explanation
Indices: 48499154--48499354 Score: 395
Period size: 99 Copynumber: 2.0 Consensus size: 100
48499144 AGGAATAATT
48499154 TATTTTAAATTTTTAATAAAATAAAATCAGGTTAATATTAATAAAGATTGTAGGTTTGATTGATG
1 TATTTTAAATTTTTAATAAAATAAAATCAGGTTAATATTAATAAAGATTGTAGGTTTGATTGATG
48499219 TTATAAAGATATTAGATTTGATTTAAATTTTTATA
66 TTATAAAGATATTAGATTTGATTTAAATTTTTATA
48499254 TATTTTAAA-TTTTAATAAAATAAAATCAGGTTAATATTAATAAAGATTGTAGGTTTGATTGATG
1 TATTTTAAATTTTTAATAAAATAAAATCAGGTTAATATTAATAAAGATTGTAGGTTTGATTGATG
48499318 TTATAAAGATATTAGATTTGATTTAAATTTTTATA
66 TTATAAAGATATTAGATTTGATTTAAATTTTTATA
48499353 TA
1 TA
48499355 CATGATAAGT
Statistics
Matches: 101, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
99 92 0.91
100 9 0.09
ACGTcount: A:0.41, C:0.01, G:0.12, T:0.46
Consensus pattern (100 bp):
TATTTTAAATTTTTAATAAAATAAAATCAGGTTAATATTAATAAAGATTGTAGGTTTGATTGATG
TTATAAAGATATTAGATTTGATTTAAATTTTTATA
Found at i:48501616 original size:13 final size:13
Alignment explanation
Indices: 48501598--48501625 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
48501588 ACATGTGCTC
48501598 TTCTTTTTCTTTT
1 TTCTTTTTCTTTT
48501611 TTCTTTTTCTTTT
1 TTCTTTTTCTTTT
48501624 TT
1 TT
48501626 TAAAGAAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (13 bp):
TTCTTTTTCTTTT
Found at i:48502774 original size:20 final size:20
Alignment explanation
Indices: 48502736--48502774 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
48502726 TCCGTCTATA
* *
48502736 CCCAAGGTGCTCTCTGAAGG
1 CCCAAGGTGCTCACAGAAGG
48502756 CCCAAGGTGCTCACAGAAG
1 CCCAAGGTGCTCACAGAAG
48502775 TGAGATCAAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.26, C:0.31, G:0.28, T:0.15
Consensus pattern (20 bp):
CCCAAGGTGCTCACAGAAGG
Found at i:48504650 original size:10 final size:10
Alignment explanation
Indices: 48504637--48504683 Score: 51
Period size: 10 Copynumber: 4.8 Consensus size: 10
48504627 ATCATAAAAT
*
48504637 ATAAAAATCA
1 ATAAAAATTA
*
48504647 ATAAAAGTT-
1 ATAAAAATTA
48504656 ATAAAAATTA
1 ATAAAAATTA
* *
48504666 TTAAAATTTA
1 ATAAAAATTA
48504676 ATAAAAAT
1 ATAAAAAT
48504684 ATAANNNNNN
Statistics
Matches: 29, Mismatches: 7, Indels: 2
0.76 0.18 0.05
Matches are distributed among these distances:
9 8 0.28
10 21 0.72
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.32
Consensus pattern (10 bp):
ATAAAAATTA
Found at i:48504658 original size:19 final size:18
Alignment explanation
Indices: 48504623--48504683 Score: 63
Period size: 19 Copynumber: 3.3 Consensus size: 18
48504613 ATTTGACAAA
48504623 AAAAATC-ATAAAA-TAT
1 AAAAATCAATAAAATTAT
48504639 AAAAATCAATAAAAGTTAT
1 AAAAATCAATAAAA-TTAT
* *
48504658 AAAAATTATTAAAATTTAAT
1 AAAAATCAATAAAA-TT-AT
48504678 AAAAAT
1 AAAAAT
48504684 ATAANNNNNN
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
16 7 0.18
17 6 0.16
19 17 0.45
20 8 0.21
ACGTcount: A:0.66, C:0.03, G:0.02, T:0.30
Consensus pattern (18 bp):
AAAAATCAATAAAATTAT
Found at i:48511850 original size:9 final size:8
Alignment explanation
Indices: 48511814--48511849 Score: 54
Period size: 8 Copynumber: 4.5 Consensus size: 8
48511804 TTCGGTCACC
48511814 AAAAGAAA
1 AAAAGAAA
* *
48511822 AACAGAAG
1 AAAAGAAA
48511830 AAAAGAAA
1 AAAAGAAA
48511838 AAAAGAAA
1 AAAAGAAA
48511846 AAAA
1 AAAA
48511850 ACTTTGCCTC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
8 24 1.00
ACGTcount: A:0.83, C:0.03, G:0.14, T:0.00
Consensus pattern (8 bp):
AAAAGAAA
Found at i:48515375 original size:30 final size:30
Alignment explanation
Indices: 48515339--48515397 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 30
48515329 AGTTAATATA
* * *
48515339 ATGATAAAATTATATTTTGGTCCTTACAAG
1 ATGATAAAATTATAGTTTAGTCCCTACAAG
*
48515369 ATGATAAAATTCTAGTTTAGTCCCTACAA
1 ATGATAAAATTATAGTTTAGTCCCTACAA
48515398 AAAATCCAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.37, C:0.14, G:0.12, T:0.37
Consensus pattern (30 bp):
ATGATAAAATTATAGTTTAGTCCCTACAAG
Found at i:48521301 original size:2 final size:2
Alignment explanation
Indices: 48521294--48521327 Score: 59
Period size: 2 Copynumber: 16.5 Consensus size: 2
48521284 ATAGAGGGAA
48521294 AT AT AT AT AT AT AT AT AT AT AT AT AT AT GAT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT A
48521328 GGAAAATATT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 29 0.94
3 2 0.06
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:48526024 original size:41 final size:41
Alignment explanation
Indices: 48525978--48526095 Score: 114
Period size: 41 Copynumber: 3.1 Consensus size: 41
48525968 ATTTTTAAGC
48525978 TTGTTCGTTTTCAGTTTGTATTTGTTAAGAATTTCAAATTT
1 TTGTTCGTTTTCAGTTTGTATTTGTTAAGAATTTCAAATTT
* * * **
48526019 TTGTTCATGTTC-GTTTG--TTTATT-----TTT--AA-GC
1 TTGTTCGTTTTCAGTTTGTATTTGTTAAGAATTTCAAATTT
48526049 TTGTTCGTTTTCAGTTTGTATTTGTTAAGAATTTCAAATTT
1 TTGTTCGTTTTCAGTTTGTATTTGTTAAGAATTTCAAATTT
48526090 TTGTTC
1 TTGTTC
48526096 ATGTTCGTTT
Statistics
Matches: 56, Mismatches: 10, Indels: 22
0.64 0.11 0.25
Matches are distributed among these distances:
30 10 0.18
31 7 0.12
33 8 0.14
38 8 0.14
40 7 0.12
41 16 0.29
ACGTcount: A:0.19, C:0.08, G:0.15, T:0.58
Consensus pattern (41 bp):
TTGTTCGTTTTCAGTTTGTATTTGTTAAGAATTTCAAATTT
Found at i:48526063 original size:71 final size:71
Alignment explanation
Indices: 48525947--48526110 Score: 319
Period size: 71 Copynumber: 2.3 Consensus size: 71
48525937 TGAACAAACC
48525947 TTTGTTCATGTTCGTTTGTTTATTTTTAAGCTTGTTCGTTTTCAGTTTGTATTTGTTAAGAATTT
1 TTTGTTCATGTTCGTTTGTTTATTTTTAAGCTTGTTCGTTTTCAGTTTGTATTTGTTAAGAATTT
48526012 CAAATT
66 CAAATT
48526018 TTTGTTCATGTTCGTTTGTTTATTTTTAAGCTTGTTCGTTTTCAGTTTGTATTTGTTAAGAATTT
1 TTTGTTCATGTTCGTTTGTTTATTTTTAAGCTTGTTCGTTTTCAGTTTGTATTTGTTAAGAATTT
48526083 CAAATT
66 CAAATT
*
48526089 TTTGTTCATGTTCGTTTATTTA
1 TTTGTTCATGTTCGTTTGTTTA
48526111 AAATTATGGG
Statistics
Matches: 92, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
71 92 1.00
ACGTcount: A:0.18, C:0.09, G:0.15, T:0.59
Consensus pattern (71 bp):
TTTGTTCATGTTCGTTTGTTTATTTTTAAGCTTGTTCGTTTTCAGTTTGTATTTGTTAAGAATTT
CAAATT
Found at i:48526164 original size:12 final size:12
Alignment explanation
Indices: 48526144--48526194 Score: 50
Period size: 12 Copynumber: 4.2 Consensus size: 12
48526134 TTGTTTAATA
*
48526144 TTCACGAACATG
1 TTCATGAACATG
48526156 TTCATGAACAT-
1 TTCATGAACATG
* *
48526167 ATAATTGAACATG
1 TTCA-TGAACATG
48526180 TTCATGAACAATG
1 TTCATGAAC-ATG
48526193 TT
1 TT
48526195 AATAAATAAT
Statistics
Matches: 31, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
11 2 0.06
12 22 0.71
13 7 0.23
ACGTcount: A:0.37, C:0.16, G:0.14, T:0.33
Consensus pattern (12 bp):
TTCATGAACATG
Found at i:48527743 original size:5 final size:5
Alignment explanation
Indices: 48527735--48527768 Score: 50
Period size: 5 Copynumber: 6.4 Consensus size: 5
48527725 ATTATATTAC
48527735 AAATT AAATT AAAATT AAATT AAAATT AAATT AA
1 AAATT AAATT -AAATT AAATT -AAATT AAATT AA
48527769 TTCAAGATAA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
5 17 0.63
6 10 0.37
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (5 bp):
AAATT
Found at i:48527751 original size:11 final size:11
Alignment explanation
Indices: 48527724--48527768 Score: 72
Period size: 11 Copynumber: 4.0 Consensus size: 11
48527714 AAAATTTCGT
*
48527724 AATTATATTACA
1 AATTAAATTA-A
48527736 AATTAAATTAA
1 AATTAAATTAA
48527747 AATTAAATTAA
1 AATTAAATTAA
48527758 AATTAAATTAA
1 AATTAAATTAA
48527769 TTCAAGATAA
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
11 23 0.72
12 9 0.28
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (11 bp):
AATTAAATTAA
Found at i:48527781 original size:16 final size:16
Alignment explanation
Indices: 48527735--48527782 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 16
48527725 ATTATATTAC
*
48527735 AAATTAAATTAAAATT
1 AAATTAAAATAAAATT
*
48527751 AAATTAAAATTAAATT
1 AAATTAAAATAAAATT
*
48527767 -AATTCAAGATAAAATT
1 AAATT-AAAATAAAATT
48527783 TCTAATGTTG
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
15 4 0.15
16 23 0.85
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.35
Consensus pattern (16 bp):
AAATTAAAATAAAATT
Found at i:48531018 original size:15 final size:16
Alignment explanation
Indices: 48530998--48531034 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
48530988 TAATCTCCTG
48530998 TTGAAACACATA-A-AT
1 TTGAAAC-CATATATAT
48531013 TTGAAACCATATATAT
1 TTGAAACCATATATAT
48531029 TTGAAA
1 TTGAAA
48531035 AATTTTTCAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
14 4 0.20
15 8 0.40
16 8 0.40
ACGTcount: A:0.49, C:0.11, G:0.08, T:0.32
Consensus pattern (16 bp):
TTGAAACCATATATAT
Found at i:48531220 original size:18 final size:19
Alignment explanation
Indices: 48531197--48531234 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
48531187 ATTTTTTAAA
48531197 TTATAAA-ATT-TGAAATTT
1 TTATAAATATTCTG-AATTT
48531215 TTATAAATATTCTGAATTT
1 TTATAAATATTCTGAATTT
48531234 T
1 T
48531235 AAAATCTATT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 7 0.39
19 9 0.50
20 2 0.11
ACGTcount: A:0.39, C:0.03, G:0.05, T:0.53
Consensus pattern (19 bp):
TTATAAATATTCTGAATTT
Found at i:48532448 original size:2 final size:2
Alignment explanation
Indices: 48532443--48532468 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
48532433 AAAAAAATTA
48532443 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
48532469 TTGTTTGTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:48534344 original size:31 final size:32
Alignment explanation
Indices: 48534309--48534372 Score: 85
Period size: 33 Copynumber: 2.0 Consensus size: 32
48534299 GTTTCACGTG
* *
48534309 TATAATT-ACATCAAATTAAAATTTATATATA
1 TATAATTAACATCAAATCAAAATTCATATATA
*
48534340 TATAATTACACATTAAATCAAAATTCATATATA
1 TATAATTA-ACATCAAATCAAAATTCATATATA
48534373 ATTTCGAGAT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
31 7 0.25
33 21 0.75
ACGTcount: A:0.52, C:0.09, G:0.00, T:0.39
Consensus pattern (32 bp):
TATAATTAACATCAAATCAAAATTCATATATA
Found at i:48542871 original size:25 final size:25
Alignment explanation
Indices: 48542811--48542871 Score: 59
Period size: 25 Copynumber: 2.4 Consensus size: 25
48542801 GCAAACGAAC
** * *
48542811 GACGGTGGTCACTTGGTGGATGCCA
1 GACGGTGGTGGCTTAGTGGATACCA
* * *
48542836 AATGGTAGTGGCTTAGTGGATACCA
1 GACGGTGGTGGCTTAGTGGATACCA
48542861 GACGGTGGTGG
1 GACGGTGGTGG
48542872 GTGTGTTGAG
Statistics
Matches: 26, Mismatches: 10, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.20, C:0.15, G:0.41, T:0.25
Consensus pattern (25 bp):
GACGGTGGTGGCTTAGTGGATACCA
Found at i:48543178 original size:14 final size:15
Alignment explanation
Indices: 48543159--48543191 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
48543149 CACCACATAA
48543159 TTTAAA-AACATTTT
1 TTTAAATAACATTTT
*
48543173 TTTAAATAACCTTTT
1 TTTAAATAACATTTT
48543188 TTTA
1 TTTA
48543192 TATTTTTAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 6 0.35
15 11 0.65
ACGTcount: A:0.36, C:0.09, G:0.00, T:0.55
Consensus pattern (15 bp):
TTTAAATAACATTTT
Found at i:48547286 original size:31 final size:31
Alignment explanation
Indices: 48547251--48547326 Score: 125
Period size: 31 Copynumber: 2.5 Consensus size: 31
48547241 AAAAAAACTT
*
48547251 AATAGTCCAATGACTTAAATAAAAACTTTCA
1 AATAGTTCAATGACTTAAATAAAAACTTTCA
*
48547282 AATAGTTCAATGACTTAAATGAAAACTTTCA
1 AATAGTTCAATGACTTAAATAAAAACTTTCA
*
48547313 AATAATTCAATGAC
1 AATAGTTCAATGAC
48547327 CATTTTGCAA
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 42 1.00
ACGTcount: A:0.47, C:0.14, G:0.08, T:0.30
Consensus pattern (31 bp):
AATAGTTCAATGACTTAAATAAAAACTTTCA
Found at i:48559418 original size:22 final size:22
Alignment explanation
Indices: 48559393--48559435 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
48559383 AAATTTAGTC
*
48559393 TTTA-TCCTTTTATTTCTAAAAA
1 TTTAGTCCTTCTATTT-TAAAAA
48559415 TTTAGTCCTTCTATTTTAAAA
1 TTTAGTCCTTCTATTTTAAAA
48559436 TTCAAGTACA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 9 0.47
23 10 0.53
ACGTcount: A:0.30, C:0.14, G:0.02, T:0.53
Consensus pattern (22 bp):
TTTAGTCCTTCTATTTTAAAAA
Found at i:48560031 original size:9 final size:10
Alignment explanation
Indices: 48560008--48560032 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
48559998 AAGGGTCAAA
48560008 TTTTTCCTTC
1 TTTTTCCTTC
48560018 TTTTTCCTTC
1 TTTTTCCTTC
48560028 TTTTT
1 TTTTT
48560033 ATAAGGTGCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (10 bp):
TTTTTCCTTC
Found at i:48564623 original size:16 final size:16
Alignment explanation
Indices: 48564577--48564623 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
48564567 GAAAAATATT
48564577 TATATTGTTTTATTTTA
1 TATATT-TTTTATTTTA
* *
48564594 -ATATTTAATAATTTTA
1 TATATTT-TTTATTTTA
48564610 TATATTTTTTATTT
1 TATATTTTTTATTT
48564624 ATTGAAAATT
Statistics
Matches: 24, Mismatches: 4, Indels: 5
0.73 0.12 0.15
Matches are distributed among these distances:
15 1 0.04
16 17 0.71
17 6 0.25
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (16 bp):
TATATTTTTTATTTTA
Found at i:48565639 original size:30 final size:30
Alignment explanation
Indices: 48565604--48565667 Score: 92
Period size: 30 Copynumber: 2.1 Consensus size: 30
48565594 GAATTTGATT
* * *
48565604 AAAATTTGAAGGTTAGGAGTTAAAATGACA
1 AAAATTTAAAAGTTAGGAGCTAAAATGACA
*
48565634 AAAATTTAAAAGTTAGGAGCTAAAGTGACA
1 AAAATTTAAAAGTTAGGAGCTAAAATGACA
48565664 AAAA
1 AAAA
48565668 GAAGTAAATA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.52, C:0.05, G:0.20, T:0.23
Consensus pattern (30 bp):
AAAATTTAAAAGTTAGGAGCTAAAATGACA
Found at i:48567591 original size:93 final size:93
Alignment explanation
Indices: 48567427--48567614 Score: 351
Period size: 93 Copynumber: 2.0 Consensus size: 93
48567417 GAATTAATAG
*
48567427 GAAAACTAATACAGCTATATTTCATTTCAAGGGTTGTTAGATATTTTATCATAAATTTGGATGTT
1 GAAAACTAATACAGCTATATTTCATTTCAAGGGTTGTTAGAAATTTTATCATAAATTTGGATGTT
48567492 TTTTTTTTTCATTAATTGATTTATGCTT
66 TTTTTTTTTCATTAATTGATTTATGCTT
48567520 GAAAACTAATACAGCTATATTTCATTTTCAAGGGTTGTTAGAAATTTTATCATAAATTTGGATG-
1 GAAAACTAATACAGCTATATTTCA-TTTCAAGGGTTGTTAGAAATTTTATCATAAATTTGGATGT
48567584 TTTTTTTTTTCATTAATTGATTTATGCTT
65 TTTTTTTTTTCATTAATTGATTTATGCTT
48567613 GA
1 GA
48567615 TGGATCTACT
Statistics
Matches: 93, Mismatches: 1, Indels: 2
0.97 0.01 0.02
Matches are distributed among these distances:
93 55 0.59
94 38 0.41
ACGTcount: A:0.30, C:0.09, G:0.13, T:0.48
Consensus pattern (93 bp):
GAAAACTAATACAGCTATATTTCATTTCAAGGGTTGTTAGAAATTTTATCATAAATTTGGATGTT
TTTTTTTTTCATTAATTGATTTATGCTT
Found at i:48568879 original size:14 final size:15
Alignment explanation
Indices: 48568860--48568888 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
48568850 CAATTGACCC
48568860 TGAAATTT-AAAATT
1 TGAAATTTGAAAATT
48568874 TGAAATTTGAAAATT
1 TGAAATTTGAAAATT
48568889 AAAAAGTAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.48, C:0.00, G:0.10, T:0.41
Consensus pattern (15 bp):
TGAAATTTGAAAATT
Found at i:48568939 original size:30 final size:31
Alignment explanation
Indices: 48568882--48568939 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 31
48568872 TTTGAAATTT
* *
48568882 GAAAATTAAAAAGTAAAGAGGCTAAATTCTA
1 GAAAAATAAAAAGTAAAGAGACTAAATTCTA
*
48568913 GAAAAATAAAAA-TATAGAGACTAAATT
1 GAAAAATAAAAAGTAAAGAGACTAAATT
48568940 ATAAATTTAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
30 13 0.54
31 11 0.46
ACGTcount: A:0.59, C:0.05, G:0.14, T:0.22
Consensus pattern (31 bp):
GAAAAATAAAAAGTAAAGAGACTAAATTCTA
Found at i:48570460 original size:25 final size:24
Alignment explanation
Indices: 48570423--48570473 Score: 66
Period size: 25 Copynumber: 2.1 Consensus size: 24
48570413 TTTTGAACAA
48570423 TTTAAATTTTTTCTTTTATATTCT
1 TTTAAATTTTTTCTTTTATATTCT
* * *
48570447 TTTAACTTTCTTTCTTTTTTCTTCT
1 TTTAAATTT-TTTCTTTTATATTCT
48570472 TT
1 TT
48570474 ATTTTCCATT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
24 8 0.35
25 15 0.65
ACGTcount: A:0.14, C:0.14, G:0.00, T:0.73
Consensus pattern (24 bp):
TTTAAATTTTTTCTTTTATATTCT
Found at i:48571993 original size:21 final size:20
Alignment explanation
Indices: 48571967--48572008 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
48571957 TTATGAAAAA
48571967 TGGGTTTTTCATCTTCTTTTT
1 TGGG-TTTTCATCTTCTTTTT
* *
48571988 TGGGTTTTCTTTTTCTTTTT
1 TGGGTTTTCATCTTCTTTTT
48572008 T
1 T
48572009 CTTTAGGTGG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 15 0.79
21 4 0.21
ACGTcount: A:0.02, C:0.12, G:0.14, T:0.71
Consensus pattern (20 bp):
TGGGTTTTCATCTTCTTTTT
Found at i:48575295 original size:2 final size:2
Alignment explanation
Indices: 48575288--48575315 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
48575278 TTAATATGTG
48575288 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
48575316 GCTATATTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:48578126 original size:25 final size:25
Alignment explanation
Indices: 48578088--48578137 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
48578078 TGAATGTTGG
*
48578088 TACTTAAACCAACATTAAATTTAAA
1 TACTTAAACCAACATTAAAATTAAA
**
48578113 TACTTAAATTAACATTAAAATTAAA
1 TACTTAAACCAACATTAAAATTAAA
48578138 CTCAAGGACC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.54, C:0.12, G:0.00, T:0.34
Consensus pattern (25 bp):
TACTTAAACCAACATTAAAATTAAA
Found at i:48583017 original size:14 final size:16
Alignment explanation
Indices: 48582993--48583026 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
48582983 TTGAAACAAA
48582993 AAAAAAGTT-AAAAAG
1 AAAAAAGTTAAAAAAG
48583008 AAAAAA-TTAAAAAAG
1 AAAAAAGTTAAAAAAG
48583023 AAAA
1 AAAA
48583027 CCCTATAAGT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 2 0.11
15 16 0.89
ACGTcount: A:0.79, C:0.00, G:0.09, T:0.12
Consensus pattern (16 bp):
AAAAAAGTTAAAAAAG
Found at i:48590745 original size:31 final size:31
Alignment explanation
Indices: 48590704--48590835 Score: 81
Period size: 31 Copynumber: 4.3 Consensus size: 31
48590694 AAAAAAGATT
*
48590704 AGGTATCAAATTAGGAAAAAGAGTCAAGTTC
1 AGGTACCAAATTAGGAAAAAGAGTCAAGTTC
**** **
48590735 AGGTACCAAATT-GGATCCCGA-AAAAGATT-
1 AGGTACCAAATTAGGAAAAAGAGTCAAG-TTC
* * * * *
48590764 AAGTACCAACTTAAGAAGAAAAATGTCAAGTTT
1 AGGTACCAAATTAGGAA-AAAGA-GTCAAGTTC
* * *
48590797 AAGTATCAAATTAGGAAAAAGTGTCAAGTTC
1 AGGTACCAAATTAGGAAAAAGAGTCAAGTTC
48590828 AGGTACCA
1 AGGTACCA
48590836 GATTGGATCC
Statistics
Matches: 70, Mismatches: 25, Indels: 12
0.65 0.23 0.11
Matches are distributed among these distances:
29 13 0.19
30 9 0.13
31 26 0.37
32 5 0.07
33 17 0.24
ACGTcount: A:0.45, C:0.13, G:0.20, T:0.23
Consensus pattern (31 bp):
AGGTACCAAATTAGGAAAAAGAGTCAAGTTC
Found at i:48590813 original size:93 final size:93
Alignment explanation
Indices: 48590706--48590935 Score: 415
Period size: 93 Copynumber: 2.5 Consensus size: 93
48590696 AAAAGATTAG
*
48590706 GTATCAAATTAGGAAAAAGAGTCAAGTTCAGGTACCAAATTGGATCCCGAAAAAGATTAAGTACC
1 GTATCAAATTAGGAAAAAGTGTCAAGTTCAGGTACCAAATTGGATCCCGAAAAAGATTAAGTACC
48590771 AACTTAAGAAGAAAAATGTCAAGTTTAA
66 AACTTAAGAAGAAAAATGTCAAGTTTAA
*
48590799 GTATCAAATTAGGAAAAAGTGTCAAGTTCAGGTACCAGATTGGATCCCGAAAAAGATTAAGTACC
1 GTATCAAATTAGGAAAAAGTGTCAAGTTCAGGTACCAAATTGGATCCCGAAAAAGATTAAGTACC
48590864 AACTTAAGAAGAAAAATGTCAAGTTTAA
66 AACTTAAGAAGAAAAATGTCAAGTTTAA
** *
48590892 GTATCAAATTAGGAAAAAGTGTCAAGTTTGGGTATCAAATTGGA
1 GTATCAAATTAGGAAAAAGTGTCAAGTTCAGGTACCAAATTGGA
48590936 CCAAAAAATG
Statistics
Matches: 131, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 131 1.00
ACGTcount: A:0.44, C:0.12, G:0.20, T:0.24
Consensus pattern (93 bp):
GTATCAAATTAGGAAAAAGTGTCAAGTTCAGGTACCAAATTGGATCCCGAAAAAGATTAAGTACC
AACTTAAGAAGAAAAATGTCAAGTTTAA
Found at i:48590917 original size:31 final size:31
Alignment explanation
Indices: 48590781--48590932 Score: 105
Period size: 31 Copynumber: 4.9 Consensus size: 31
48590771 AACTTAAGAA
48590781 GAAAAA-TGTCAAGTTTAAGTATCAAATTAG
1 GAAAAAGTGTCAAGTTTAAGTATCAAATTAG
* * * *
48590811 GAAAAAGTGTCAAGTTCAGGTACCAGATT-G
1 GAAAAAGTGTCAAGTTTAAGTATCAAATTAG
**** *** * * *
48590841 GATCCCG-AAAAAGATTAAGTACCAACTTAAG
1 GAAAAAGTGTCAAGTTTAAGTATCAAATT-AG
48590872 AAGAAAAA-TGTCAAGTTTAAGTATCAAATTAG
1 --GAAAAAGTGTCAAGTTTAAGTATCAAATTAG
**
48590904 GAAAAAGTGTCAAGTTTGGGTATCAAATT
1 GAAAAAGTGTCAAGTTTAAGTATCAAATT
48590933 GGACCAAAAA
Statistics
Matches: 87, Mismatches: 28, Indels: 13
0.68 0.22 0.10
Matches are distributed among these distances:
29 13 0.15
30 16 0.18
31 39 0.45
32 2 0.02
33 17 0.20
ACGTcount: A:0.43, C:0.11, G:0.20, T:0.26
Consensus pattern (31 bp):
GAAAAAGTGTCAAGTTTAAGTATCAAATTAG
Found at i:48590991 original size:31 final size:30
Alignment explanation
Indices: 48590875--48590991 Score: 82
Period size: 31 Copynumber: 3.9 Consensus size: 30
48590865 ACTTAAGAAG
*
48590875 AAAAATGTCAAGTTTAAGTATCAAATTAGGA
1 AAAAATGTCAAGTTTAGGTATCAAATTA-GA
* * *
48590906 AAAAGTGTCAAGTTTGGGTATCAAATTGGA
1 AAAAATGTCAAGTTTAGGTATCAAATTAGA
* * *
48590936 CCAAAAA----ATGTTGATGTA-CTAAATTAGA
1 --AAAAATGTCAAGTTTAGGTATC-AAATTAGA
*
48590964 AAAAAGTGTCAAGTTCAGGTATCAAATT
1 AAAAA-TGTCAAGTTTAGGTATCAAATT
48590992 GTTATATGTG
Statistics
Matches: 64, Mismatches: 13, Indels: 18
0.67 0.14 0.19
Matches are distributed among these distances:
26 5 0.08
27 1 0.02
28 14 0.22
30 2 0.03
31 37 0.58
32 5 0.08
ACGTcount: A:0.44, C:0.09, G:0.19, T:0.29
Consensus pattern (30 bp):
AAAAATGTCAAGTTTAGGTATCAAATTAGA
Found at i:48591685 original size:17 final size:17
Alignment explanation
Indices: 48591655--48591689 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
48591645 CATTTAACTT
48591655 TTGTAAAAAATATTTAA
1 TTGTAAAAAATATTTAA
* *
48591672 TTGTATAAATTATTTAA
1 TTGTAAAAAATATTTAA
48591689 T
1 T
48591690 ATGCCGGGAC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.46, C:0.00, G:0.06, T:0.49
Consensus pattern (17 bp):
TTGTAAAAAATATTTAA
Found at i:48596633 original size:11 final size:10
Alignment explanation
Indices: 48596619--48596645 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
48596609 AAAAGTTCAG
48596619 AAAAAATAAA
1 AAAAAATAAA
48596629 AAAAAATAAA
1 AAAAAATAAA
48596639 AAAAAAT
1 AAAAAAT
48596646 CAGTTCGACC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.89, C:0.00, G:0.00, T:0.11
Consensus pattern (10 bp):
AAAAAATAAA
Found at i:48597299 original size:31 final size:32
Alignment explanation
Indices: 48597245--48597308 Score: 80
Period size: 31 Copynumber: 2.0 Consensus size: 32
48597235 TAAAGTTTCA
48597245 TGTATATATTTGAACCATAATCAAAATTTGATG
1 TGTATATATTTGAACCATAATCAAAATTT-ATG
*
48597278 TGTATA-ATTT-ACACCA-AATCAATATTTATG
1 TGTATATATTTGA-ACCATAATCAAAATTTATG
48597308 T
1 T
48597309 ATCAAATTGT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
30 4 0.14
31 11 0.38
32 8 0.28
33 6 0.21
ACGTcount: A:0.39, C:0.11, G:0.09, T:0.41
Consensus pattern (32 bp):
TGTATATATTTGAACCATAATCAAAATTTATG
Found at i:48601245 original size:90 final size:89
Alignment explanation
Indices: 48601124--48601339 Score: 213
Period size: 90 Copynumber: 2.4 Consensus size: 89
48601114 TAAATTTTTA
* * * * **
48601124 TTTTTTT-ACTTAATTGGATATTTAAATTTTCAAAATACATTAAAAAGGCCCTTAAA-TTTTTTT
1 TTTTTTTCACTTAATTGGATACTTGAACTTTCAAAATACATCAAAAAGGCCCACAAATTTTTTTT
* * *
48601187 AAGAAA-AGTAATTAAACCATTGCTT
66 AA-AAAGAGCAATTAAACCACTG-AT
* * *
48601212 TTTTTTTCCACTTAATTGGGTACTTGAACTTTCAAAATATATCAAAAAGGCTCACAAACTTTTTT
1 TTTTTTT-CACTTAATTGGATACTTGAACTTTCAAAATACATCAAAAAGGCCCACAAA--TTTTT
*
48601277 TTTAAAAAGAGCAATTAAATCACTGAT
63 TTTAAAAAGAGCAATTAAACCACTGAT
* * *
48601304 TTTTTTTGCACTCAATTGGTTACTTGAACTATCAAA
1 TTTTTTT-CACTTAATTGGATACTTGAACTTTCAAA
48601340 TGCTTCAAAA
Statistics
Matches: 105, Mismatches: 17, Indels: 8
0.81 0.13 0.06
Matches are distributed among these distances:
88 7 0.07
90 40 0.38
92 36 0.34
93 22 0.21
ACGTcount: A:0.36, C:0.13, G:0.09, T:0.41
Consensus pattern (89 bp):
TTTTTTTCACTTAATTGGATACTTGAACTTTCAAAATACATCAAAAAGGCCCACAAATTTTTTTT
AAAAAGAGCAATTAAACCACTGAT
Found at i:48601534 original size:9 final size:9
Alignment explanation
Indices: 48601457--48601552 Score: 70
Period size: 9 Copynumber: 10.4 Consensus size: 9
48601447 CATGTGGCAA
48601457 AAAAATTAT
1 AAAAATTAT
48601466 AAAAA--AT
1 AAAAATTAT
*
48601473 AAAAATCAAT
1 AAAAAT-TAT
*
48601483 AAAAGTTAT
1 AAAAATTAT
*
48601492 AACAATTAT
1 AAAAATTAT
* *
48601501 TAAATTATATT
1 AAAAAT-TA-T
* *
48601512 AAAAAATAG
1 AAAAATTAT
48601521 AAAAATTTAT
1 AAAAA-TTAT
*
48601531 AAAAATCAT
1 AAAAATTAT
48601540 AAAAATTAT
1 AAAAATTAT
48601549 AAAA
1 AAAA
48601553 TGCATAAAAA
Statistics
Matches: 66, Mismatches: 15, Indels: 12
0.71 0.16 0.13
Matches are distributed among these distances:
7 7 0.11
9 37 0.56
10 18 0.27
11 4 0.06
ACGTcount: A:0.66, C:0.03, G:0.02, T:0.29
Consensus pattern (9 bp):
AAAAATTAT
Found at i:48601535 original size:19 final size:19
Alignment explanation
Indices: 48601511--48601552 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
48601501 TAAATTATAT
48601511 TAAAAAAT-AGAAAAATT-
1 TAAAAAATCAGAAAAATTA
*
48601528 TATAAAAATCATAAAAATTA
1 TA-AAAAATCAGAAAAATTA
48601548 TAAAA
1 TAAAA
48601553 TGCATAAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
17 2 0.10
18 6 0.29
19 11 0.52
20 2 0.10
ACGTcount: A:0.69, C:0.02, G:0.02, T:0.26
Consensus pattern (19 bp):
TAAAAAATCAGAAAAATTA
Found at i:48601558 original size:18 final size:19
Alignment explanation
Indices: 48601521--48601562 Score: 61
Period size: 18 Copynumber: 2.3 Consensus size: 19
48601511 TAAAAAATAG
48601521 AAAAATTTATAAAAATCAT
1 AAAAATTTATAAAAATCAT
48601540 AAAAA-TTAT-AAAATGCAT
1 AAAAATTTATAAAAAT-CAT
48601558 AAAAA
1 AAAAA
48601563 ATGTCATTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 5 0.23
18 12 0.55
19 5 0.23
ACGTcount: A:0.67, C:0.05, G:0.02, T:0.26
Consensus pattern (19 bp):
AAAAATTTATAAAAATCAT
Found at i:48601562 original size:19 final size:19
Alignment explanation
Indices: 48601509--48601564 Score: 57
Period size: 18 Copynumber: 3.1 Consensus size: 19
48601499 ATTAAATTAT
*
48601509 ATTA-AAAAAT-AGAAAAA
1 ATTATAAAAATCATAAAAA
*
48601526 TTTATAAAAATCAT-AAAA
1 ATTATAAAAATCATAAAAA
48601544 ATTAT-AAAATGCATAAAAA
1 ATTATAAAAAT-CATAAAAA
48601563 AT
1 AT
48601565 GTCATTTAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
17 8 0.25
18 17 0.53
19 7 0.22
ACGTcount: A:0.66, C:0.04, G:0.04, T:0.27
Consensus pattern (19 bp):
ATTATAAAAATCATAAAAA
Found at i:48601773 original size:19 final size:20
Alignment explanation
Indices: 48601751--48601794 Score: 54
Period size: 19 Copynumber: 2.2 Consensus size: 20
48601741 TAAATATATT
48601751 TTTACAAATTTTAT-ATTTC
1 TTTACAAATTTTATAATTTC
** *
48601770 TTTACATTTTTTATAATTTT
1 TTTACAAATTTTATAATTTC
48601790 TTTAC
1 TTTAC
48601795 GACTTTATAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 12 0.57
20 9 0.43
ACGTcount: A:0.27, C:0.09, G:0.00, T:0.64
Consensus pattern (20 bp):
TTTACAAATTTTATAATTTC
Found at i:48601811 original size:29 final size:29
Alignment explanation
Indices: 48601778--48601839 Score: 90
Period size: 29 Copynumber: 2.1 Consensus size: 29
48601768 TCTTTACATT
48601778 TTTTATAATTTTTTTACGA-CTTTATAAAA
1 TTTTATAA-TTTTTTACGATCTTTATAAAA
* *
48601807 TTTTATAATTTTTTATGATTTTTATAAAA
1 TTTTATAATTTTTTACGATCTTTATAAAA
48601836 TTTT
1 TTTT
48601840 TACGATATTT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
28 9 0.30
29 21 0.70
ACGTcount: A:0.32, C:0.03, G:0.03, T:0.61
Consensus pattern (29 bp):
TTTTATAATTTTTTACGATCTTTATAAAA
Found at i:48601839 original size:20 final size:20
Alignment explanation
Indices: 48601807--48601925 Score: 70
Period size: 20 Copynumber: 6.2 Consensus size: 20
48601797 CTTTATAAAA
*
48601807 TTTTAT-AATTTTTTATGAT
1 TTTTATAAAATTTTTATGAT
*
48601826 TTTTATAAAATTTTTACGAT
1 TTTTATAAAATTTTTATGAT
* * ** * *
48601846 ATTTGTAATTTTTTTCTAAT
1 TTTTATAAAATTTTTATGAT
* **
48601866 TTTAATAAAATTTAAAT-AT
1 TTTTATAAAATTTTTATGAT
*
48601885 TTTTATTAAAA-TTTAAT-AT
1 TTTTA-TAAAATTTTTATGAT
48601904 TTTT-TATAAATTTTTATG-T
1 TTTTATA-AAATTTTTATGAT
48601923 TTT
1 TTT
48601926 ATTATTTTTT
Statistics
Matches: 75, Mismatches: 20, Indels: 10
0.71 0.19 0.10
Matches are distributed among these distances:
17 2 0.03
18 3 0.04
19 32 0.43
20 38 0.51
ACGTcount: A:0.34, C:0.02, G:0.03, T:0.61
Consensus pattern (20 bp):
TTTTATAAAATTTTTATGAT
Found at i:48601902 original size:19 final size:20
Alignment explanation
Indices: 48601865--48601913 Score: 73
Period size: 19 Copynumber: 2.5 Consensus size: 20
48601855 TTTTTTCTAA
48601865 TTTTAATAAAATTTAAATAT
1 TTTTAATAAAATTTAAATAT
*
48601885 TTTTATTAAAATTT-AATAT
1 TTTTAATAAAATTTAAATAT
*
48601904 TTTTTATAAA
1 TTTTAATAAA
48601914 TTTTTATGTT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
19 13 0.50
20 13 0.50
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (20 bp):
TTTTAATAAAATTTAAATAT
Found at i:48602177 original size:92 final size:90
Alignment explanation
Indices: 48601996--48602208 Score: 268
Period size: 92 Copynumber: 2.3 Consensus size: 90
48601986 ATTAAGGGCG
* * ** * **
48601996 GTTCAAGTACCCAATTAAGTGCAAAAAAAGGCAGGGCTTAATTGTTTTTTTTTTTGAAAAATTTT
1 GTTCAAGTGCCCAATTGAGTGCAAAAAAAAACAGGGCTTAATTGTATTTTTTTTTGAAAAAAATT
*
48602061 GAGGGCCTTTTTATGCATTTTGAAA
66 GAGGGCCTTTTTATGCATTGTGAAA
*
48602086 GTTCAAGTGCCCAATTGAGTGCAAAAAAGAAACAATGGCTTAATTG-ATTTTTTTTTGAAAAAAA
1 GTTCAAGTGCCCAATTGAGTGCAAAAAA-AAAC-AGGGCTTAATTGTATTTTTTTTTGAAAAAAA
*
48602150 TTGAGGG-TTATTTTGATGCATTGTGAAA
64 TTGAGGGCCT-TTTT-ATGCATTGTGAAA
* *
48602178 GCTCAAGTGCCCAAGTGAGTGCAAAAAAAAA
1 GTTCAAGTGCCCAATTGAGTGCAAAAAAAAA
48602209 ACGCAGGGGC
Statistics
Matches: 107, Mismatches: 12, Indels: 7
0.85 0.10 0.06
Matches are distributed among these distances:
90 27 0.25
91 31 0.29
92 49 0.46
ACGTcount: A:0.35, C:0.11, G:0.20, T:0.33
Consensus pattern (90 bp):
GTTCAAGTGCCCAATTGAGTGCAAAAAAAAACAGGGCTTAATTGTATTTTTTTTTGAAAAAAATT
GAGGGCCTTTTTATGCATTGTGAAA
Found at i:48602231 original size:92 final size:91
Alignment explanation
Indices: 48601998--48602239 Score: 251
Period size: 92 Copynumber: 2.7 Consensus size: 91
48601988 TAAGGGCGGT
* * * ** * * **
48601998 TCAAGTACCCAATTAAGTGC-AAAAAAAGGC-AGGGCTTAATTGTTTTTTTTTTTGAAAAATTTT
1 TCAAGTGCCCAAGTGAGTGCAAAAAAAAAACAAGGGCTTAATTG-ATCTTTTTTTGAAAAAAATT
* *
48602061 GAGGGCCTTTTTATGCATTTTGAAAGT
65 GAGGGCCTTTTTATGCATTGTGAAAGC
* * * *
48602088 TCAAGTGCCCAATTGAGTGCAAAAAAGAAACAATGGCTTAATTGATTTTTTTTTGAAAAAAATTG
1 TCAAGTGCCCAAGTGAGTGCAAAAAAAAAACAAGGGCTTAATTGATCTTTTTTTGAAAAAAATTG
*
48602153 AGGG-TTATTTTGATGCATTGTGAAAGC
66 AGGGCCT-TTTT-ATGCATTGTGAAAGC
*
48602180 TCAAGTGCCCAAGTGAGTGCAAAAAAAAAACGCAGGGGCTTAATT-A-CTTTTTTTGAAAAA
1 TCAAGTGCCCAAGTGAGTGCAAAAAAAAAA--CAAGGGCTTAATTGATCTTTTTTTGAAAAA
48602240 GTTTGAAGGC
Statistics
Matches: 129, Mismatches: 17, Indels: 10
0.83 0.11 0.06
Matches are distributed among these distances:
90 19 0.15
91 33 0.26
92 65 0.50
93 1 0.01
94 11 0.09
ACGTcount: A:0.35, C:0.12, G:0.20, T:0.33
Consensus pattern (91 bp):
TCAAGTGCCCAAGTGAGTGCAAAAAAAAAACAAGGGCTTAATTGATCTTTTTTTGAAAAAAATTG
AGGGCCTTTTTATGCATTGTGAAAGC
Found at i:48603174 original size:30 final size:32
Alignment explanation
Indices: 48603139--48603222 Score: 102
Period size: 30 Copynumber: 2.7 Consensus size: 32
48603129 TAGGCTCCCA
*
48603139 AATTTTTTAAAATTCTCATTATA-CTTT-TTA-
1 AATTTTTGAAAATTCTCATTA-AGCTTTCTTAC
* * *
48603169 TATTTTTGAAAATTTTGATTAAGCTTTCTTAC
1 AATTTTTGAAAATTCTCATTAAGCTTTCTTAC
48603201 AATTTTTGAAAATTCTCATTAA
1 AATTTTTGAAAATTCTCATTAA
48603223 TCTCACACAA
Statistics
Matches: 44, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
29 1 0.02
30 21 0.48
31 3 0.07
32 19 0.43
ACGTcount: A:0.33, C:0.10, G:0.05, T:0.52
Consensus pattern (32 bp):
AATTTTTGAAAATTCTCATTAAGCTTTCTTAC
Found at i:48604018 original size:21 final size:21
Alignment explanation
Indices: 48603992--48604033 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
48603982 TATATTATAT
* *
48603992 AATAAAACAAAATAAATAAAG
1 AATAAAACAAAAGAAAGAAAG
*
48604013 AATAAATCAAAAGAAAGAAAG
1 AATAAAACAAAAGAAAGAAAG
48604034 GTAGAAACGA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.74, C:0.05, G:0.10, T:0.12
Consensus pattern (21 bp):
AATAAAACAAAAGAAAGAAAG
Found at i:48604993 original size:41 final size:40
Alignment explanation
Indices: 48604948--48605073 Score: 125
Period size: 41 Copynumber: 3.2 Consensus size: 40
48604938 CGACTTCGAG
48604948 TCGATGAGACATTGGGTGTCAATTTACTACTTCGGATTAAT
1 TCGATGAGACATTGGGTGTCAATTTA-TACTTCGGATTAAT
* * * * *
48604989 TCGATGAGGCATTGGATGCCAA-TT-TACTTCTGTTTAA-
1 TCGATGAGACATTGGGTGTCAATTTATACTTCGGATTAAT
* * * *
48605026 CCGATGAGACACTGGGTGTCAATTTATTATTTCGAATT-AT
1 TCGATGAGACATTGGGTGTCAATTTA-TACTTCGGATTAAT
48605066 TCGATGAG
1 TCGATGAG
48605074 GCACTGGGAG
Statistics
Matches: 66, Mismatches: 15, Indels: 9
0.73 0.17 0.10
Matches are distributed among these distances:
37 17 0.26
38 13 0.20
39 1 0.02
40 16 0.24
41 19 0.29
ACGTcount: A:0.26, C:0.15, G:0.22, T:0.37
Consensus pattern (40 bp):
TCGATGAGACATTGGGTGTCAATTTATACTTCGGATTAAT
Found at i:48605049 original size:37 final size:38
Alignment explanation
Indices: 48604949--48605051 Score: 109
Period size: 37 Copynumber: 2.7 Consensus size: 38
48604939 GACTTCGAGT
*
48604949 CGATGAGACATTGGGTGTCAATTTACTACTTCGGATTAATT
1 CGATGAGACATTGGGTGTCAA-TT--TACTTCGGATTAATC
* * * * *
48604990 CGATGAGGCATTGGATGCCAATTTACTTCTGTTTAA-C
1 CGATGAGACATTGGGTGTCAATTTACTTCGGATTAATC
*
48605027 CGATGAGACACTGGGTGTCAATTTA
1 CGATGAGACATTGGGTGTCAATTTA
48605052 TTATTTCGAA
Statistics
Matches: 52, Mismatches: 10, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
37 21 0.40
38 11 0.21
40 2 0.04
41 18 0.35
ACGTcount: A:0.26, C:0.17, G:0.23, T:0.34
Consensus pattern (38 bp):
CGATGAGACATTGGGTGTCAATTTACTTCGGATTAATC
Found at i:48619130 original size:73 final size:73
Alignment explanation
Indices: 48619022--48619175 Score: 231
Period size: 73 Copynumber: 2.1 Consensus size: 73
48619012 TGGGTTTAGA
* * *
48619022 GGAAGGAAAAGAAAGGTTTGAAAGGAAACTAGTTTCATTTTTGCTTTTTTTTTTGGTAGAAGGAA
1 GGAAGGAAAAGAAAGATTTGAAAGGAAACTAGTTTCATTTTTGCCTTTTTCTTTGGTAGAA-GAA
48619087 A-AT-GAGAG
65 AGATAG-GAG
* *
48619095 GGAAGGAAAAGAAAGATTTGAAAGGAAACTAGTTTCCTTTTTTCCTTTTTCTTTGGTAGAAGAAA
1 GGAAGGAAAAGAAAGATTTGAAAGGAAACTAGTTTCATTTTTGCCTTTTTCTTTGGTAGAAGAAA
48619160 GATAGGAG
66 GATAGGAG
48619168 GGAAGGAA
1 GGAAGGAA
48619176 GGAAAATGGG
Statistics
Matches: 74, Mismatches: 5, Indels: 4
0.89 0.06 0.05
Matches are distributed among these distances:
72 4 0.05
73 69 0.93
74 1 0.01
ACGTcount: A:0.36, C:0.06, G:0.27, T:0.31
Consensus pattern (73 bp):
GGAAGGAAAAGAAAGATTTGAAAGGAAACTAGTTTCATTTTTGCCTTTTTCTTTGGTAGAAGAAA
GATAGGAG
Found at i:48620064 original size:17 final size:18
Alignment explanation
Indices: 48620039--48620114 Score: 63
Period size: 18 Copynumber: 4.3 Consensus size: 18
48620029 TAAGAGAGAA
*
48620039 AGAAAGAAC-TGAAAAGG
1 AGAAGGAACGTGAAAAGG
48620056 AGAAGGAACGTGAAAAGG
1 AGAAGGAACGTGAAAAGG
* *
48620074 A-AAGGGAGAAG-G-AACGCG
1 AGAA-GGA-ACGTGAAAAG-G
48620092 AGAAGGAACGTGAAAAGG
1 AGAAGGAACGTGAAAAGG
48620110 A-AAGG
1 AGAAGG
48620115 GAGAAGGCTG
Statistics
Matches: 47, Mismatches: 5, Indels: 14
0.71 0.08 0.21
Matches are distributed among these distances:
17 19 0.40
18 21 0.45
19 7 0.15
ACGTcount: A:0.51, C:0.07, G:0.38, T:0.04
Consensus pattern (18 bp):
AGAAGGAACGTGAAAAGG
Found at i:48620081 original size:24 final size:24
Alignment explanation
Indices: 48620049--48620099 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
48620039 AGAAAGAACT
*
48620049 GAAAAGGAGAAGGAACGTGAAAAG
1 GAAAAGGAGAAGGAACGCGAAAAG
* *
48620073 GAAAGGGAGAAGGAACGCGAGAAG
1 GAAAAGGAGAAGGAACGCGAAAAG
48620097 GAA
1 GAA
48620100 CGTGAAAAGG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.51, C:0.06, G:0.41, T:0.02
Consensus pattern (24 bp):
GAAAAGGAGAAGGAACGCGAAAAG
Found at i:48620121 original size:12 final size:12
Alignment explanation
Indices: 48620049--48620121 Score: 65
Period size: 12 Copynumber: 6.1 Consensus size: 12
48620039 AGAAAGAACT
*
48620049 GAAAAGGAGAAG
1 GAAAGGGAGAAG
* * *
48620061 GAACGTGAAAAG
1 GAAAGGGAGAAG
48620073 GAAAGGGAGAAG
1 GAAAGGGAGAAG
* *
48620085 GAACGCGAGAAG
1 GAAAGGGAGAAG
* * *
48620097 GAACGTGAAAAG
1 GAAAGGGAGAAG
48620109 GAAAGGGAGAAG
1 GAAAGGGAGAAG
48620121 G
1 G
48620122 CTGAAAGCAA
Statistics
Matches: 47, Mismatches: 14, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
12 47 1.00
ACGTcount: A:0.49, C:0.05, G:0.42, T:0.03
Consensus pattern (12 bp):
GAAAGGGAGAAG
Found at i:48621886 original size:25 final size:25
Alignment explanation
Indices: 48621852--48621902 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
48621842 TTTTCTTGAG
48621852 ATCATATAATGAACCTGATTAGTTT
1 ATCATATAATGAACCTGATTAGTTT
48621877 ATCATATAATGAACCTGATTAGTTT
1 ATCATATAATGAACCTGATTAGTTT
48621902 A
1 A
48621903 GTTGTTATGG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.37, C:0.12, G:0.12, T:0.39
Consensus pattern (25 bp):
ATCATATAATGAACCTGATTAGTTT
Found at i:48627660 original size:10 final size:11
Alignment explanation
Indices: 48627629--48627654 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
48627619 TTTTAAAAAA
48627629 TAATAACTTTT
1 TAATAACTTTT
48627640 TAATAACTTTT
1 TAATAACTTTT
48627651 TAAT
1 TAAT
48627655 TATTTTCACT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.38, C:0.08, G:0.00, T:0.54
Consensus pattern (11 bp):
TAATAACTTTT
Found at i:48629108 original size:16 final size:16
Alignment explanation
Indices: 48629089--48629127 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
48629079 TGCATGCATC
48629089 TATGTTTGTATATATG
1 TATGTTTGTATATATG
* *
48629105 TATGTCTGTATGTATG
1 TATGTTTGTATATATG
48629121 TATGTTT
1 TATGTTT
48629128 TGCAGGATTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.21, C:0.03, G:0.21, T:0.56
Consensus pattern (16 bp):
TATGTTTGTATATATG
Found at i:48630350 original size:23 final size:23
Alignment explanation
Indices: 48630296--48630352 Score: 71
Period size: 23 Copynumber: 2.5 Consensus size: 23
48630286 ATATTTTTAA
*
48630296 ATTTTATATTTAATTATAAAAAT
1 ATTTTAAATTTAATTATAAAAAT
* *
48630319 ATATAAAATGTTAA-TATAAAAAT
1 ATTTTAAAT-TTAATTATAAAAAT
48630342 ATTTTAAATTT
1 ATTTTAAATTT
48630353 TTAATAATTT
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
22 2 0.07
23 22 0.79
24 4 0.14
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (23 bp):
ATTTTAAATTTAATTATAAAAAT
Found at i:48630356 original size:24 final size:23
Alignment explanation
Indices: 48630304--48630358 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 23
48630294 AAATTTTATA
48630304 TTTAATTATAAAAATATATAAAAT
1 TTTAA-TATAAAAATATATAAAAT
* * *
48630328 GTTAATATAAAAATATTTTAAATT
1 TTTAATATAAAAATA-TATAAAAT
48630352 TTTAATA
1 TTTAATA
48630359 ATTTTAAATA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
23 10 0.38
24 16 0.62
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (23 bp):
TTTAATATAAAAATATATAAAAT
Found at i:48632940 original size:5 final size:6
Alignment explanation
Indices: 48632915--48632943 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
48632905 TATTTGTATA
48632915 AATTTT AATTTT AATTTT AA-TTT AATTTT
1 AATTTT AATTTT AATTTT AATTTT AATTTT
48632944 CCCATTTTAC
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
5 5 0.23
6 17 0.77
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (6 bp):
AATTTT
Found at i:48632940 original size:11 final size:12
Alignment explanation
Indices: 48632915--48632943 Score: 51
Period size: 11 Copynumber: 2.5 Consensus size: 12
48632905 TATTTGTATA
48632915 AATTTTAATTTT
1 AATTTTAATTTT
48632927 AATTTTAA-TTT
1 AATTTTAATTTT
48632938 AATTTT
1 AATTTT
48632944 CCCATTTTAC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 9 0.53
12 8 0.47
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (12 bp):
AATTTTAATTTT
Found at i:48636267 original size:168 final size:169
Alignment explanation
Indices: 48635978--48636314 Score: 667
Period size: 168 Copynumber: 2.0 Consensus size: 169
48635968 AAATTGAATA
48635978 TTTATATATATATATATATATTTTATGATGGCATGAATGTTTAAATTGAACAATATTTGACAAAA
1 TTTATATATATATATATATATTTTATGATGGCATGAATGTTTAAATTGAACAATATTTGACAAAA
48636043 TTGAATAAGAATTTGGAGTAATACAAATAAAAAGCAGTGTTCCATGATATTTTATTAGAATATAA
66 TTGAATAAGAATTTGGAGTAATACAAATAAAAAGCAGTGTTCCATGATATTTTATTAGAATATAA
48636108 TAGTCATATAGATAGTCTATCATATCATTATCTAGTTGT
131 TAGTCATATAGATAGTCTATCATATCATTATCTAGTTGT
48636147 TTTATATATA-ATATATATATTTTATGATGGCATGAATGTTTAAATTGAACAATATTTGACAAAA
1 TTTATATATATATATATATATTTTATGATGGCATGAATGTTTAAATTGAACAATATTTGACAAAA
48636211 TTGAATAAGAATTTGGAGTAATACAAATAAAAAGCAGTGTTCCATGATATTTTATTAGAATATAA
66 TTGAATAAGAATTTGGAGTAATACAAATAAAAAGCAGTGTTCCATGATATTTTATTAGAATATAA
48636276 TAGTCATATAGATAGTCTATCATATCATTATCTAGTTGT
131 TAGTCATATAGATAGTCTATCATATCATTATCTAGTTGT
48636315 ATTTGTTCAT
Statistics
Matches: 168, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
168 158 0.94
169 10 0.06
ACGTcount: A:0.40, C:0.07, G:0.13, T:0.39
Consensus pattern (169 bp):
TTTATATATATATATATATATTTTATGATGGCATGAATGTTTAAATTGAACAATATTTGACAAAA
TTGAATAAGAATTTGGAGTAATACAAATAAAAAGCAGTGTTCCATGATATTTTATTAGAATATAA
TAGTCATATAGATAGTCTATCATATCATTATCTAGTTGT
Found at i:48636863 original size:3 final size:3
Alignment explanation
Indices: 48636855--48636922 Score: 136
Period size: 3 Copynumber: 22.7 Consensus size: 3
48636845 GAAGTTCTGG
48636855 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
48636903 ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT AT
48636923 ATGCCATCAC
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 65 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:48643402 original size:27 final size:27
Alignment explanation
Indices: 48643372--48643438 Score: 89
Period size: 27 Copynumber: 2.5 Consensus size: 27
48643362 TAAGTTTCGT
*
48643372 GGGACAGTCCACCATATAGGTGTTTGC
1 GGGACAGTCCACCAAATAGGTGTTTGC
* ** *
48643399 GGGACATTCCATAAAATAGGTGTTTGT
1 GGGACAGTCCACCAAATAGGTGTTTGC
48643426 GGGACAGTCCACC
1 GGGACAGTCCACC
48643439 GTTTAGCCTA
Statistics
Matches: 32, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.25
Consensus pattern (27 bp):
GGGACAGTCCACCAAATAGGTGTTTGC
Found at i:48646254 original size:27 final size:27
Alignment explanation
Indices: 48646203--48646277 Score: 80
Period size: 27 Copynumber: 2.7 Consensus size: 27
48646193 CTTTCTTTAG
* *
48646203 AATATGCCACGAAGGCGTTTCTTTTCATA
1 AATAT-CCACAAAGGC-TTCCTTTTCATA
*
48646232 AATCAT-TACAAAGGCTTCCTTTTCATA
1 AAT-ATCCACAAAGGCTTCCTTTTCATA
*
48646259 GATATCCACAAAGGCTTCC
1 AATATCCACAAAGGCTTCC
48646278 CTTCTTTAGA
Statistics
Matches: 39, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
26 2 0.05
27 25 0.64
28 7 0.18
29 3 0.08
30 2 0.05
ACGTcount: A:0.31, C:0.24, G:0.13, T:0.32
Consensus pattern (27 bp):
AATATCCACAAAGGCTTCCTTTTCATA
Found at i:48646287 original size:27 final size:26
Alignment explanation
Indices: 48646239--48646302 Score: 78
Period size: 27 Copynumber: 2.4 Consensus size: 26
48646229 ATAAATCATT
48646239 ACAAAGGCTTCCTTTTCATAGATAT-CC
1 ACAAAGGCTTCCTTTT-ATAGAT-TGCC
48646266 ACAAAGGCTTCCCTTCTT-TAGATTGCC
1 ACAAAGGCTT-CCTT-TTATAGATTGCC
48646293 ACAAAGGCTT
1 ACAAAGGCTT
48646303 TTATCTTTAG
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
26 1 0.03
27 27 0.79
28 4 0.12
29 2 0.06
ACGTcount: A:0.28, C:0.27, G:0.14, T:0.31
Consensus pattern (26 bp):
ACAAAGGCTTCCTTTTATAGATTGCC
Found at i:48646513 original size:50 final size:50
Alignment explanation
Indices: 48646418--48646516 Score: 117
Period size: 50 Copynumber: 2.0 Consensus size: 50
48646408 CTTTTAGTCA
* * * * * *
48646418 TTTCTATATTATGTCATAACCCACCAGTTATGGTATTATATAATATGGTC
1 TTTCCATATGATGCCATAACCCACCAGCTATGGTATTACACAATATGGTC
* * *
48646468 TTTCCATATGATGCCATAGCCCACTAGCTATGGTCTTACACAATATGGT
1 TTTCCATATGATGCCATAACCCACCAGCTATGGTATTACACAATATGGT
48646517 GCCATGGTCA
Statistics
Matches: 40, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
50 40 1.00
ACGTcount: A:0.28, C:0.20, G:0.14, T:0.37
Consensus pattern (50 bp):
TTTCCATATGATGCCATAACCCACCAGCTATGGTATTACACAATATGGTC
Found at i:48657271 original size:105 final size:105
Alignment explanation
Indices: 48657089--48657302 Score: 410
Period size: 105 Copynumber: 2.0 Consensus size: 105
48657079 CTGGTGCGAG
*
48657089 TCAAACAATGTGAAGTTGCCTGATCTCGTGGAGTCCACTTTAAATCAGGTCTATCCGCCTTGTGC
1 TCAAACAATGTGAAGTTGCCTGATCTCGTGGAGTCCACTTTAAATCAGGTCTATCCGCCTCGTGC
48657154 AACTAAGGTTAAGAAGTTGGTTGAGGACTTGAAGAGTACA
66 AACTAAGGTTAAGAAGTTGGTTGAGGACTTGAAGAGTACA
*
48657194 TCAAACAATGTGAAGTTGCCTGATCTTGTGGAGTCCACTTTAAATCAGGTCTATCCGCCTCGTGC
1 TCAAACAATGTGAAGTTGCCTGATCTCGTGGAGTCCACTTTAAATCAGGTCTATCCGCCTCGTGC
48657259 AACTAAGGTTAAGAAGTTGGTTGAGGACTTGAAGAGTACA
66 AACTAAGGTTAAGAAGTTGGTTGAGGACTTGAAGAGTACA
48657299 TCAA
1 TCAA
48657303 CTTATACTCA
Statistics
Matches: 107, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
105 107 1.00
ACGTcount: A:0.29, C:0.18, G:0.24, T:0.29
Consensus pattern (105 bp):
TCAAACAATGTGAAGTTGCCTGATCTCGTGGAGTCCACTTTAAATCAGGTCTATCCGCCTCGTGC
AACTAAGGTTAAGAAGTTGGTTGAGGACTTGAAGAGTACA
Found at i:48667838 original size:107 final size:101
Alignment explanation
Indices: 48667694--48667928 Score: 280
Period size: 107 Copynumber: 2.3 Consensus size: 101
48667684 AAAAAATATA
*
48667694 TATTTTTTTTTACTTTTGGTT--TGTCAATGTCCAGCACCAGTATACGAAAAAAGTAAAAAAAAA
1 TATTTTTTTTTACTTTT--TTCGTGTCAATGTCCAGCACCAGTATACAAAAAAAGT--AAAAAAA
* * * **
48667757 AAATTTTGTGGTGGCCTGCCAATTGCCGGCACCACCTTTAT
62 AAATTTGGTGGTGGCCTACCAATGGCCGGCACCA-CTAAAT
*
48667798 TGGAATTTTTTTTTACTTTTTTCGTGTCAATG-GCAGGCACCAGTATACAAAAAAAGTAAAAAAA
1 T---ATTTTTTTTTACTTTTTTCGTGTCAATGTCCA-GCACCAGTATACAAAAAAAGTAAAAAAA
* *
48667862 AAATTTGGTGGTGGCCTACCAATGGTCGGCACCAGTAAAT
62 AAATTTGGTGGTGGCCTACCAATGGCCGGCACCACTAAAT
48667902 T-TTTTTTTTTACTTTTTTCGTGTCAAT
1 TATTTTTTTTTACTTTTTTCGTGTCAAT
48667929 AGCCGGCCCA
Statistics
Matches: 116, Mismatches: 9, Indels: 16
0.82 0.06 0.11
Matches are distributed among these distances:
100 26 0.22
104 5 0.04
105 39 0.34
106 2 0.02
107 44 0.38
ACGTcount: A:0.30, C:0.16, G:0.17, T:0.37
Consensus pattern (101 bp):
TATTTTTTTTTACTTTTTTCGTGTCAATGTCCAGCACCAGTATACAAAAAAAGTAAAAAAAAAAT
TTGGTGGTGGCCTACCAATGGCCGGCACCACTAAAT
Found at i:48668348 original size:13 final size:13
Alignment explanation
Indices: 48668330--48668354 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
48668320 CGCGACAATT
48668330 TTAATTTTTTCTG
1 TTAATTTTTTCTG
48668343 TTAATTTTTTCT
1 TTAATTTTTTCT
48668355 TTTTTTAAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.16, C:0.08, G:0.04, T:0.72
Consensus pattern (13 bp):
TTAATTTTTTCTG
Found at i:48669696 original size:115 final size:113
Alignment explanation
Indices: 48669462--48669702 Score: 300
Period size: 115 Copynumber: 2.2 Consensus size: 113
48669452 CAGACCATTT
* *
48669462 TTTTTACTTTTTTCGTATACTGGTGCCTTCCATTGACACGAAAAATGTAAAAAAAATTATTATTT
1 TTTTTACTTTTTTCGTATACTAGTGCCGTCCATTGACACGAAAAATGTAAAAAAAA-TA-TATTT
* * *
48669527 TCCAATAAAGGTGGTGCTGGCCATTGGCAGGCCACCACCAAAATTATTAT
64 TCCAAAAAAGGTGGTGCCGGCCATTGGCAGGCCACCACCAAAATTATTAC
48669577 TTTTTACTTTTTTCGTATACTAGTGCCGTCCATTGACA-GACCAAAA-GTAAAAAAAA-A-AGTT
1 TTTTTACTTTTTTCGTATACTAGTGCCGTCCATTGACACGA--AAAATGTAAAAAAAATATA-TT
* * **
48669638 TT-GAAAAAAGGTGGTGCCGGCCATTGGCAGGCCACCA-C-TAATT-TTTT
63 TTCCAAAAAAGGTGGTGCCGGCCATTGGCAGGCCACCACCAAAATTATTAC
48669685 TTTTTACTTTTTTCGTAT
1 TTTTTACTTTTTTCGTAT
48669703 TCTGGTATCG
Statistics
Matches: 116, Mismatches: 7, Indels: 13
0.85 0.05 0.10
Matches are distributed among these distances:
108 21 0.18
109 4 0.03
110 1 0.01
111 33 0.28
112 4 0.03
113 1 0.01
114 2 0.02
115 46 0.40
116 4 0.03
ACGTcount: A:0.30, C:0.18, G:0.16, T:0.36
Consensus pattern (113 bp):
TTTTTACTTTTTTCGTATACTAGTGCCGTCCATTGACACGAAAAATGTAAAAAAAATATATTTTC
CAAAAAAGGTGGTGCCGGCCATTGGCAGGCCACCACCAAAATTATTAC
Found at i:48669738 original size:108 final size:111
Alignment explanation
Indices: 48669533--48669740 Score: 271
Period size: 108 Copynumber: 1.9 Consensus size: 111
48669523 ATTTTCCAAT
*
48669533 AAAGGTGGTGCTGGCCATTGGCAGGCCACCACCAAAATTATTATTTTTTACTTTTTTCGTATACT
1 AAAGGTGGTGCCGGCCATTGGCAGGCCACCACCAAAATTATTATTTTTTACTTTTTTCGTATACT
* * *
48669598 AGTGCCGTCCATTGACAGACCAAAAGTAAAAAAAAAAGTTTTGAAA
66 AGTACCGTCCATTGACAAACCAAAACTAAAAAAAAAAGTTTTGAAA
* * *
48669644 AAAGGTGGTGCCGGCCATTGGCAGGCCACCA-C-TAATT-TTTTTTTTTACTTTTTTCGTATTCT
1 AAAGGTGGTGCCGGCCATTGGCAGGCCACCACCAAAATTATTATTTTTTACTTTTTTCGTATACT
* * * * *
48669706 GGTATCGAT-TATTGACAAACCAATACTCAAAAAAA
66 AGTACCG-TCCATTGACAAACCAAAACTAAAAAAAA
48669741 TATTTTTTTT
Statistics
Matches: 84, Mismatches: 12, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
108 48 0.57
109 5 0.06
110 1 0.01
111 30 0.36
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32
Consensus pattern (111 bp):
AAAGGTGGTGCCGGCCATTGGCAGGCCACCACCAAAATTATTATTTTTTACTTTTTTCGTATACT
AGTACCGTCCATTGACAAACCAAAACTAAAAAAAAAAGTTTTGAAA
Found at i:48671551 original size:2 final size:2
Alignment explanation
Indices: 48671546--48671573 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
48671536 TTTAGAAAAC
48671546 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
48671574 AAAGATAAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:48672386 original size:17 final size:17
Alignment explanation
Indices: 48672366--48672416 Score: 59
Period size: 17 Copynumber: 2.9 Consensus size: 17
48672356 CTTTTTTATA
48672366 TAATATATTTGTTTAAT
1 TAATATATTTGTTTAAT
*
48672383 TAATACTAGTTT-TTTTAT
1 TAATA-TA-TTTGTTTAAT
*
48672401 AAATATATTTGTTTAA
1 TAATATATTTGTTTAA
48672417 GTTACTTATC
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
16 3 0.11
17 11 0.39
18 11 0.39
19 3 0.11
ACGTcount: A:0.35, C:0.02, G:0.06, T:0.57
Consensus pattern (17 bp):
TAATATATTTGTTTAAT
Found at i:48674157 original size:2 final size:2
Alignment explanation
Indices: 48674152--48674180 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
48674142 ATTGAACTTT
48674152 TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
48674181 ACATTTTTCT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:48679032 original size:36 final size:36
Alignment explanation
Indices: 48678992--48679067 Score: 152
Period size: 36 Copynumber: 2.1 Consensus size: 36
48678982 TTTGCCTTTA
48678992 CTTAGGAATTCGGTTTACCTCCAAAAATAATTGCTG
1 CTTAGGAATTCGGTTTACCTCCAAAAATAATTGCTG
48679028 CTTAGGAATTCGGTTTACCTCCAAAAATAATTGCTG
1 CTTAGGAATTCGGTTTACCTCCAAAAATAATTGCTG
48679064 CTTA
1 CTTA
48679068 ATATGATTAC
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 40 1.00
ACGTcount: A:0.30, C:0.20, G:0.16, T:0.34
Consensus pattern (36 bp):
CTTAGGAATTCGGTTTACCTCCAAAAATAATTGCTG
Found at i:48687432 original size:16 final size:16
Alignment explanation
Indices: 48687411--48687447 Score: 74
Period size: 16 Copynumber: 2.3 Consensus size: 16
48687401 TTGGTTCGCT
48687411 GTAATGGAATAGAGGC
1 GTAATGGAATAGAGGC
48687427 GTAATGGAATAGAGGC
1 GTAATGGAATAGAGGC
48687443 GTAAT
1 GTAAT
48687448 AGGTAATTCT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.38, C:0.05, G:0.35, T:0.22
Consensus pattern (16 bp):
GTAATGGAATAGAGGC
Found at i:48687516 original size:44 final size:46
Alignment explanation
Indices: 48687427--48687517 Score: 159
Period size: 46 Copynumber: 2.0 Consensus size: 46
48687417 GAATAGAGGC
*
48687427 GTAATGGAATAGAGGCGTAATAGGTAATTCTTTTGTTTGGTTGAAT
1 GTAATGGAATAGAGGCGTAATAGGTAATTCTTGTGTTTGGTTGAAT
48687473 GTAATGGAATAGAGGCGTAAT-GGT-ATTCTTGTGTTTGGTTGAAT
1 GTAATGGAATAGAGGCGTAATAGGTAATTCTTGTGTTTGGTTGAAT
48687517 G
1 G
48687518 GAATAGAGGT
Statistics
Matches: 44, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
44 20 0.45
45 3 0.07
46 21 0.48
ACGTcount: A:0.26, C:0.04, G:0.31, T:0.38
Consensus pattern (46 bp):
GTAATGGAATAGAGGCGTAATAGGTAATTCTTGTGTTTGGTTGAAT
Found at i:48687518 original size:39 final size:44
Alignment explanation
Indices: 48687427--48687534 Score: 145
Period size: 46 Copynumber: 2.5 Consensus size: 44
48687417 GAATAGAGGC
*
48687427 GTAATGGAATAGAGGCGTAATAGGTAATTCTTTTGTTTGGTTGAAT
1 GTAATGGAATAGAGGCGTAATAGGTAATTCTTGTGTTTGGTT--AT
48687473 GTAATGGAATAGAGGCGTAAT-GGT-ATTCTTGTGTTTGG-T-T
1 GTAATGGAATAGAGGCGTAATAGGTAATTCTTGTGTTTGGTTAT
*
48687513 G-AATGGAATAGAGGTGTAATAG
1 GTAATGGAATAGAGGCGTAATAG
48687535 CATAAGGAAA
Statistics
Matches: 59, Mismatches: 2, Indels: 8
0.86 0.03 0.12
Matches are distributed among these distances:
39 18 0.31
40 3 0.05
43 1 0.02
44 13 0.22
45 3 0.05
46 21 0.36
ACGTcount: A:0.29, C:0.04, G:0.31, T:0.36
Consensus pattern (44 bp):
GTAATGGAATAGAGGCGTAATAGGTAATTCTTGTGTTTGGTTAT
Found at i:48695099 original size:13 final size:13
Alignment explanation
Indices: 48695081--48695105 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
48695071 AACATTCGGC
48695081 CGGTGGGAATAAT
1 CGGTGGGAATAAT
48695094 CGGTGGGAATAA
1 CGGTGGGAATAA
48695106 ACAAATAAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.08, G:0.40, T:0.20
Consensus pattern (13 bp):
CGGTGGGAATAAT
Found at i:48704146 original size:61 final size:61
Alignment explanation
Indices: 48704051--48704231 Score: 299
Period size: 61 Copynumber: 3.0 Consensus size: 61
48704041 CTTTGTCTAC
* **
48704051 CCCTTGGCTAGGCTATATTCTATCCACGTGTTTCTGAGCGAATCTAATTCGATTTTTTTGT
1 CCCTTGGCTAGGCTATAATCTATCCACGTGTTTCTGATTGAATCTAATTCGATTTTTTTGT
* *
48704112 CCCTTAGCTAGGCTATAATCTATCCATGTGTTTCTGATTGAATCTAATTCGATTTTTTTGT
1 CCCTTGGCTAGGCTATAATCTATCCACGTGTTTCTGATTGAATCTAATTCGATTTTTTTGT
* *
48704173 CCCTTGGCTGGGCTATAATCTATCCACGTGTTTCTGATTTAATCTAATTCGATTTTTTT
1 CCCTTGGCTAGGCTATAATCTATCCACGTGTTTCTGATTGAATCTAATTCGATTTTTTT
48704232 TGTTTGTATA
Statistics
Matches: 111, Mismatches: 9, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
61 111 1.00
ACGTcount: A:0.19, C:0.20, G:0.16, T:0.45
Consensus pattern (61 bp):
CCCTTGGCTAGGCTATAATCTATCCACGTGTTTCTGATTGAATCTAATTCGATTTTTTTGT
Found at i:48708604 original size:44 final size:44
Alignment explanation
Indices: 48708539--48708624 Score: 136
Period size: 44 Copynumber: 2.0 Consensus size: 44
48708529 GTCTTTTTAA
* *
48708539 AATTTGTTGGTAAACATTTGTTTCAATGTTTTTAATGTATTTTC
1 AATTTGTTGGGAAACACTTGTTTCAATGTTTTTAATGTATTTTC
* *
48708583 AATTTGTTGGGAAACACTTGTTTTAATGTTTTTAGTGTATTT
1 AATTTGTTGGGAAACACTTGTTTCAATGTTTTTAATGTATTT
48708625 GATATATTAT
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
44 38 1.00
ACGTcount: A:0.24, C:0.06, G:0.16, T:0.53
Consensus pattern (44 bp):
AATTTGTTGGGAAACACTTGTTTCAATGTTTTTAATGTATTTTC
Found at i:48710497 original size:29 final size:31
Alignment explanation
Indices: 48710455--48710531 Score: 104
Period size: 29 Copynumber: 2.5 Consensus size: 31
48710445 TTTACCTCAG
*
48710455 GTTACATTTTAGTCACTTATGTT-TA-AAAT
1 GTTACATTTTAGTCACTTACGTTATAGAAAT
* *
48710484 GTTACATTTTAGTCACTTACGTTATAGTATT
1 GTTACATTTTAGTCACTTACGTTATAGAAAT
*
48710515 GTAACATTTTAGTCACT
1 GTTACATTTTAGTCACT
48710532 GAGTCGTTAG
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
29 22 0.52
30 2 0.05
31 18 0.43
ACGTcount: A:0.29, C:0.13, G:0.12, T:0.47
Consensus pattern (31 bp):
GTTACATTTTAGTCACTTACGTTATAGAAAT
Found at i:48710742 original size:27 final size:26
Alignment explanation
Indices: 48710685--48710744 Score: 68
Period size: 27 Copynumber: 2.2 Consensus size: 26
48710675 TTTTAACTTT
* *
48710685 CTTTTTTTCTTCCTTATTTTCCATTCT
1 CTTTTTTTCTCCCTTATTTTCCA-TCC
48710712 CTTTTGTTTCTCCCTCTATTTTCC-TCC
1 CTTTT-TTTCTCCCT-TATTTTCCATCC
48710739 CTTTTT
1 CTTTTT
48710745 CATTTTTTAA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
26 1 0.03
27 12 0.41
28 8 0.28
29 8 0.28
ACGTcount: A:0.05, C:0.30, G:0.02, T:0.63
Consensus pattern (26 bp):
CTTTTTTTCTCCCTTATTTTCCATCC
Found at i:48710960 original size:10 final size:11
Alignment explanation
Indices: 48710935--48710959 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
48710925 AATTTTTAAC
48710935 TTTTCTTTTTT
1 TTTTCTTTTTT
48710946 TTTTCTTTTTT
1 TTTTCTTTTTT
48710957 TTT
1 TTT
48710960 CCATTCTCTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.00, C:0.08, G:0.00, T:0.92
Consensus pattern (11 bp):
TTTTCTTTTTT
Found at i:48715121 original size:17 final size:16
Alignment explanation
Indices: 48715099--48715132 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
48715089 AAATCCAGGG
48715099 ATTAAAGTGAAAAGAAT
1 ATTAAA-TGAAAAGAAT
*
48715116 ATTAAATTAAAAGAAT
1 ATTAAATGAAAAGAAT
48715132 A
1 A
48715133 AATGTTATAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.62, C:0.00, G:0.12, T:0.26
Consensus pattern (16 bp):
ATTAAATGAAAAGAAT
Found at i:48722862 original size:19 final size:20
Alignment explanation
Indices: 48722829--48722876 Score: 53
Period size: 22 Copynumber: 2.4 Consensus size: 20
48722819 AAAATTAGTA
* *
48722829 TTTATTTGTG-TTTTTATTT
1 TTTATTTCTGATTTTCATTT
48722848 TTTATTTCTGATTTTCCAATTT
1 TTTATTTCTGATTTT-C-ATTT
48722870 TTTATTT
1 TTTATTT
48722877 TTACTTTTCT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 9 0.38
20 4 0.17
22 11 0.46
ACGTcount: A:0.15, C:0.06, G:0.06, T:0.73
Consensus pattern (20 bp):
TTTATTTCTGATTTTCATTT
Found at i:48726061 original size:2 final size:2
Alignment explanation
Indices: 48726054--48726084 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
48726044 NNNNNCTAGA
48726054 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
48726085 AATTGTTAGC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:48732673 original size:57 final size:57
Alignment explanation
Indices: 48732585--48732701 Score: 216
Period size: 57 Copynumber: 2.1 Consensus size: 57
48732575 GAGAAAAAAA
48732585 AAAAAAAAAAAAAAACTCCATCACCCATTTTTGCCCCAAAAAAAAAACTCTGAACCT
1 AAAAAAAAAAAAAAACTCCATCACCCATTTTTGCCCCAAAAAAAAAACTCTGAACCT
* *
48732642 AAAAAAAAAAAGAAACTCCATCACCCATTTTTGCCCCAAAAAAGAAACTCTGAACCT
1 AAAAAAAAAAAAAAACTCCATCACCCATTTTTGCCCCAAAAAAAAAACTCTGAACCT
48732699 AAA
1 AAA
48732702 CTTCCTCACA
Statistics
Matches: 58, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
57 58 1.00
ACGTcount: A:0.52, C:0.26, G:0.05, T:0.17
Consensus pattern (57 bp):
AAAAAAAAAAAAAAACTCCATCACCCATTTTTGCCCCAAAAAAAAAACTCTGAACCT
Found at i:48733142 original size:6 final size:6
Alignment explanation
Indices: 48733130--48733167 Score: 58
Period size: 6 Copynumber: 6.3 Consensus size: 6
48733120 TATAAACTCT
* *
48733130 GCATCA TCATCA TCATCA GCATCA GCATCA GCATCA GC
1 GCATCA GCATCA GCATCA GCATCA GCATCA GCATCA GC
48733168 TGGATGTTCT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.32, C:0.34, G:0.13, T:0.21
Consensus pattern (6 bp):
GCATCA
Found at i:48734955 original size:14 final size:15
Alignment explanation
Indices: 48734930--48734958 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
48734920 TAACTTTCTG
48734930 AATATATATTTATTT
1 AATATATATTTATTT
48734945 AATAT-TATTTATTT
1 AATATATATTTATTT
48734959 TTTATAGGTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (15 bp):
AATATATATTTATTT
Found at i:48737926 original size:97 final size:98
Alignment explanation
Indices: 48737797--48737992 Score: 369
Period size: 97 Copynumber: 2.0 Consensus size: 98
48737787 TAATATTTTT
48737797 GTCTAAGCCCTTCAAAAATTTTTTTTTTTGACTTGAGCCCTTT-ATATTTTAAATATCAAGCAAA
1 GTCTAAGCCCTTCAAAAATTTTTTTTTTTGACTTGAGCCCTTTAAT-TTTTAAATATCAAGCAAA
48737861 ACAGTCCAATCTTTAAATAAGTCTAATTCAAAAG
65 ACAGTCCAATCTTTAAATAAGTCTAATTCAAAAG
48737895 GTCTAAGCCC-TCAAAAATTTTTTTTTTTGACTTGAGCCCTTTAATTTTTAAATATCAAGCAAAA
1 GTCTAAGCCCTTCAAAAATTTTTTTTTTTGACTTGAGCCCTTTAATTTTTAAATATCAAGCAAAA
48737959 CAGTCCAATCTTTAAATAAGTCTAATTCAAAAG
66 CAGTCCAATCTTTAAATAAGTCTAATTCAAAAG
48737992 G
1 G
48737993 AAGAATATAT
Statistics
Matches: 97, Mismatches: 0, Indels: 3
0.97 0.00 0.03
Matches are distributed among these distances:
97 85 0.88
98 12 0.12
ACGTcount: A:0.36, C:0.17, G:0.10, T:0.37
Consensus pattern (98 bp):
GTCTAAGCCCTTCAAAAATTTTTTTTTTTGACTTGAGCCCTTTAATTTTTAAATATCAAGCAAAA
CAGTCCAATCTTTAAATAAGTCTAATTCAAAAG
Found at i:48743639 original size:27 final size:27
Alignment explanation
Indices: 48743578--48743666 Score: 114
Period size: 27 Copynumber: 3.4 Consensus size: 27
48743568 TTTATTTTTG
48743578 TTAAAA-TAATGTCCAAAAACTAAAATT
1 TTAAAATTAAT-TCCAAAAACTAAAATT
48743605 TTAAAATTAATTCCAAAAACTAAAATT
1 TTAAAATTAATTCCAAAAACTAAAATT
* *
48743632 TTAAAATTAA-TACAAAAA--AAAAGT
1 TTAAAATTAATTCCAAAAACTAAAATT
*
48743656 TAAAAATTAAT
1 TTAAAATTAAT
48743667 CTGAATTATT
Statistics
Matches: 57, Mismatches: 3, Indels: 6
0.86 0.05 0.09
Matches are distributed among these distances:
24 14 0.25
26 7 0.12
27 32 0.56
28 4 0.07
ACGTcount: A:0.60, C:0.08, G:0.02, T:0.30
Consensus pattern (27 bp):
TTAAAATTAATTCCAAAAACTAAAATT
Found at i:48748264 original size:20 final size:21
Alignment explanation
Indices: 48748227--48748265 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
48748217 GGATAGTGGG
48748227 GTCAAATCCATAAACAGTAGA
1 GTCAAATCCATAAACAGTAGA
*
48748248 GTCAAAT-CATGAACAGTA
1 GTCAAATCCATAAACAGTA
48748266 ATAATATATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.46, C:0.18, G:0.15, T:0.21
Consensus pattern (21 bp):
GTCAAATCCATAAACAGTAGA
Found at i:48755104 original size:109 final size:109
Alignment explanation
Indices: 48754948--48755148 Score: 316
Period size: 109 Copynumber: 1.8 Consensus size: 109
48754938 TATTTAGTTG
48754948 TTTGGTTAAACGAGAAATCGAAACCCAGCACCTTAGGGCATGTTTTCTCGAATTTCCAAAC-GCA
1 TTTGGTTAAACGAGAAATCGAAACCCAGCACCTTAGGGCATGTTTTCTCGAATTTCCAAACGGCA
* *
48755012 AAACAATGCCTTATTTT-AAAATTTTTAAAAGGATATTAAGCCA
66 AAACAATACCTTATTTTGAAAAATTTTAAAAGGATATTAAGCCA
* * *
48755055 TTTGGTTGAACGAGAAAAATCGACACCTAGCACCTTAGGGCATGTTTTCTCGAATTTCCAAACGG
1 TTTGGTTAAACGAG--AAATCGAAACCCAGCACCTTAGGGCATGTTTTCTCGAATTTCCAAACGG
*
48755120 CAAAACATTACCTTATTTTGAAAAATTTT
64 CAAAACAATACCTTATTTTGAAAAATTTT
48755149 CCTTTTTGAA
Statistics
Matches: 84, Mismatches: 6, Indels: 4
0.89 0.06 0.04
Matches are distributed among these distances:
107 13 0.15
109 45 0.54
110 18 0.21
111 8 0.10
ACGTcount: A:0.35, C:0.19, G:0.15, T:0.31
Consensus pattern (109 bp):
TTTGGTTAAACGAGAAATCGAAACCCAGCACCTTAGGGCATGTTTTCTCGAATTTCCAAACGGCA
AAACAATACCTTATTTTGAAAAATTTTAAAAGGATATTAAGCCA
Found at i:48755484 original size:3 final size:3
Alignment explanation
Indices: 48755476--48755534 Score: 118
Period size: 3 Copynumber: 19.7 Consensus size: 3
48755466 NNNNNNNNNN
48755476 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
48755524 ATA ATA ATA AT
1 ATA ATA ATA AT
48755535 GCTAAAAAGG
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 56 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:48756156 original size:18 final size:18
Alignment explanation
Indices: 48756133--48756171 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
48756123 TGAAAGGAAG
48756133 AAAAATCAA-AAGAAAAAT
1 AAAAAT-AAGAAGAAAAAT
48756151 AAAAATAAGAAGAAAAAT
1 AAAAATAAGAAGAAAAAT
48756169 AAA
1 AAA
48756172 GCTTATACCA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 2 0.10
18 18 0.90
ACGTcount: A:0.79, C:0.03, G:0.08, T:0.10
Consensus pattern (18 bp):
AAAAATAAGAAGAAAAAT
Done.