Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr12 103066607
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: 103066607
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Warning! 238 characters in sequence are not A, C, G, or T
File 16 of 345
Found at i:5446518 original size:21 final size:21
Alignment explanation
Indices: 5446479--5446531 Score: 58
Period size: 19 Copynumber: 2.6 Consensus size: 21
5446469 ATAATTTTCA
*
5446479 AAATATT-TTTTTATATAA-T
1 AAATATTATTTATATATAATT
5446498 AAATATTATTTATATTATAATTT
1 AAATATTATTTATA-TATAA-TT
5446521 AAAT-TTATTTA
1 AAATATTATTTA
5446532 ATTTTTTGAT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
19 7 0.24
20 5 0.17
21 5 0.17
22 7 0.24
23 5 0.17
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (21 bp):
AAATATTATTTATATATAATT
Found at i:5454386 original size:6 final size:6
Alignment explanation
Indices: 5454366--5454399 Score: 50
Period size: 6 Copynumber: 5.5 Consensus size: 6
5454356 ATGTGCCGAA
*
5454366 TACTGT TACTGGT TACTGT TACCGT TACTGT TAC
1 TACTGT TACT-GT TACTGT TACTGT TACTGT TAC
5454400 CGATTCGACA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
6 19 0.76
7 6 0.24
ACGTcount: A:0.18, C:0.21, G:0.18, T:0.44
Consensus pattern (6 bp):
TACTGT
Found at i:5454501 original size:53 final size:53
Alignment explanation
Indices: 5454440--5454560 Score: 179
Period size: 53 Copynumber: 2.3 Consensus size: 53
5454430 TACTATTACC
*
5454440 GTTACTGTTACTGTTTCAGATTTGTTCCGATGAGGTACTCTGTGTACCGTAAT
1 GTTACTGTTACTGTTTCAGATTTATTCCGATGAGGTACTCTGTGTACCGTAAT
* * * *
5454493 GTTACTGTTACTATTTCGGATTTATTCCGATGAGGTGCTCTGTGTACCGTACT
1 GTTACTGTTACTGTTTCAGATTTATTCCGATGAGGTACTCTGTGTACCGTAAT
* *
5454546 GCTATTGTTACTGTT
1 GTTACTGTTACTGTT
5454561 ACTGTTCCGG
Statistics
Matches: 60, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
53 60 1.00
ACGTcount: A:0.17, C:0.17, G:0.22, T:0.43
Consensus pattern (53 bp):
GTTACTGTTACTGTTTCAGATTTATTCCGATGAGGTACTCTGTGTACCGTAAT
Found at i:5454817 original size:18 final size:18
Alignment explanation
Indices: 5454766--5454821 Score: 53
Period size: 18 Copynumber: 3.2 Consensus size: 18
5454756 TGGTTATTAT
* *
5454766 TGAATAATTTATTGTTAC
1 TGAATAACTAATTGTTAC
* *
5454784 CGAATAACTAACTGTTAC
1 TGAATAACTAATTGTTAC
5454802 TGAATAGA-TAATTGTT-C
1 TGAATA-ACTAATTGTTAC
5454819 TGA
1 TGA
5454822 GTGTTAATGG
Statistics
Matches: 31, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
17 4 0.13
18 26 0.84
19 1 0.03
ACGTcount: A:0.36, C:0.11, G:0.14, T:0.39
Consensus pattern (18 bp):
TGAATAACTAATTGTTAC
Found at i:5458993 original size:15 final size:15
Alignment explanation
Indices: 5458973--5459005 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
5458963 GCACTGCCAG
5458973 AGGAATATAATATTA
1 AGGAATATAATATTA
5458988 AGGAATATAATATTA
1 AGGAATATAATATTA
5459003 AGG
1 AGG
5459006 GTAGTAAGAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.52, C:0.00, G:0.18, T:0.30
Consensus pattern (15 bp):
AGGAATATAATATTA
Found at i:5463128 original size:2 final size:2
Alignment explanation
Indices: 5463115--5463149 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
5463105 ACAATTACAA
* *
5463115 AG AG AA AG AG AG AG AG AG AG AG AG AA AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
5463150 CGGTAACCTT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.57, C:0.00, G:0.43, T:0.00
Consensus pattern (2 bp):
AG
Found at i:5463134 original size:10 final size:10
Alignment explanation
Indices: 5463115--5463149 Score: 61
Period size: 10 Copynumber: 3.5 Consensus size: 10
5463105 ACAATTACAA
5463115 AGAGAAAGAG
1 AGAGAAAGAG
*
5463125 AGAGAGAGAG
1 AGAGAAAGAG
5463135 AGAGAAAGAG
1 AGAGAAAGAG
5463145 AGAGA
1 AGAGA
5463150 CGGTAACCTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
10 23 1.00
ACGTcount: A:0.57, C:0.00, G:0.43, T:0.00
Consensus pattern (10 bp):
AGAGAAAGAG
Found at i:5467546 original size:18 final size:18
Alignment explanation
Indices: 5467523--5467567 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 18
5467513 ATGATAATTA
*
5467523 TATTTTAATTTTGTCTTC
1 TATTTTAATTTTGTATTC
* *
5467541 TATTTTTATTTTTTATTC
1 TATTTTAATTTTGTATTC
*
5467559 TTTTTTAAT
1 TATTTTAAT
5467568 AATTTTTATA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.18, C:0.07, G:0.02, T:0.73
Consensus pattern (18 bp):
TATTTTAATTTTGTATTC
Found at i:5473925 original size:11 final size:11
Alignment explanation
Indices: 5473909--5473933 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
5473899 TTAATAAATA
5473909 TATTAATACTT
1 TATTAATACTT
5473920 TATTAATACTT
1 TATTAATACTT
5473931 TAT
1 TAT
5473934 ATTTTTAAAT
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:0.36, C:0.08, G:0.00, T:0.56
Consensus pattern (11 bp):
TATTAATACTT
Found at i:5481848 original size:15 final size:15
Alignment explanation
Indices: 5481828--5481857 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
5481818 GCTACCCCAT
5481828 CACTCGCCGCACCAA
1 CACTCGCCGCACCAA
5481843 CACTCGCCGCACCAA
1 CACTCGCCGCACCAA
5481858 TCTTGGATGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.27, C:0.53, G:0.13, T:0.07
Consensus pattern (15 bp):
CACTCGCCGCACCAA
Found at i:5483540 original size:15 final size:15
Alignment explanation
Indices: 5483520--5483570 Score: 50
Period size: 15 Copynumber: 3.5 Consensus size: 15
5483510 ACAAAACAAT
5483520 AATATAAATAACTAA
1 AATATAAATAACTAA
** *
5483535 AATAT-AATATTTCA
1 AATATAAATAACTAA
* *
5483549 AACATAAATTACTAA
1 AATATAAATAACTAA
5483564 AATATAA
1 AATATAA
5483571 TCTGACTATT
Statistics
Matches: 26, Mismatches: 9, Indels: 2
0.70 0.24 0.05
Matches are distributed among these distances:
14 10 0.38
15 16 0.62
ACGTcount: A:0.61, C:0.08, G:0.00, T:0.31
Consensus pattern (15 bp):
AATATAAATAACTAA
Found at i:5486597 original size:30 final size:30
Alignment explanation
Indices: 5486537--5486597 Score: 88
Period size: 30 Copynumber: 2.0 Consensus size: 30
5486527 CTAAAAATCC
* *
5486537 ATACGTATCTTACTATTTTATTTTATCAAA
1 ATACGTATCTTACTAATTTATTTCATCAAA
5486567 ATACGTATCTTACTAATTTA-TTCATGCAAA
1 ATACGTATCTTACTAATTTATTTCAT-CAAA
5486597 A
1 A
5486598 AAAAAAAAAC
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 4 0.14
30 24 0.86
ACGTcount: A:0.36, C:0.15, G:0.05, T:0.44
Consensus pattern (30 bp):
ATACGTATCTTACTAATTTATTTCATCAAA
Found at i:5494976 original size:25 final size:25
Alignment explanation
Indices: 5494927--5494976 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
5494917 ATTTTATAAA
**
5494927 TTAAAATAATAATTATGACTTTCAT
1 TTAAAATAATAATTATGACAATCAT
*
5494952 TTAAAATTATAATTATGACAATCAT
1 TTAAAATAATAATTATGACAATCAT
5494977 ACTTCTATTA
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:0.46, C:0.08, G:0.04, T:0.42
Consensus pattern (25 bp):
TTAAAATAATAATTATGACAATCAT
Found at i:5505100 original size:31 final size:31
Alignment explanation
Indices: 5505063--5505131 Score: 95
Period size: 30 Copynumber: 2.3 Consensus size: 31
5505053 ATTATAAAAT
*
5505063 AATTATTAAATTATTTAAAAATTTTCATTTA
1 AATTATTAAACTATTTAAAAATTTTCATTTA
* * *
5505094 AGTTATT-AACTATTTAAAAGTTTTTATTTA
1 AATTATTAAACTATTTAAAAATTTTCATTTA
5505124 AATTATTA
1 AATTATTA
5505132 GATTTAAGGT
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
30 26 0.81
31 6 0.19
ACGTcount: A:0.42, C:0.03, G:0.03, T:0.52
Consensus pattern (31 bp):
AATTATTAAACTATTTAAAAATTTTCATTTA
Found at i:5506667 original size:25 final size:25
Alignment explanation
Indices: 5506633--5506698 Score: 80
Period size: 25 Copynumber: 2.6 Consensus size: 25
5506623 TTTTCTCATG
*
5506633 TATTATTTATTTTAAATTGTTTTAT-
1 TATTATTTATTTTAAATT-TTATATA
* *
5506658 TATTGTTTATTTTAAGTTTTATATA
1 TATTATTTATTTTAAATTTTATATA
*
5506683 TATTATGTATTTTAAA
1 TATTATTTATTTTAAA
5506699 CTAATTCAAA
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
24 5 0.15
25 29 0.85
ACGTcount: A:0.30, C:0.00, G:0.06, T:0.64
Consensus pattern (25 bp):
TATTATTTATTTTAAATTTTATATA
Found at i:5506856 original size:28 final size:28
Alignment explanation
Indices: 5506824--5506885 Score: 72
Period size: 28 Copynumber: 2.2 Consensus size: 28
5506814 GTTTTTTGTT
*
5506824 TTATTTAGTTTCAAC-TTCTTTCTACATA
1 TTATTTAGTTTAAACGTTCTTTC-ACATA
* * *
5506852 TTATTTATTTTAAACGTTTTTTCATATA
1 TTATTTAGTTTAAACGTTCTTTCACATA
5506880 TTATTT
1 TTATTT
5506886 TAAGTTGTCT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
28 23 0.79
29 6 0.21
ACGTcount: A:0.26, C:0.11, G:0.03, T:0.60
Consensus pattern (28 bp):
TTATTTAGTTTAAACGTTCTTTCACATA
Found at i:5506912 original size:25 final size:25
Alignment explanation
Indices: 5506878--5506985 Score: 71
Period size: 25 Copynumber: 4.2 Consensus size: 25
5506868 TTTTTTCATA
* *
5506878 TATTATTTTAAGTTGTC-TTATGTAT
1 TATTTTTTTAA-TTGTCTTTATATAT
*
5506903 TATTTTTTTAAACTG-CTTTATATAT
1 TATTTTTTT-AATTGTCTTTATATAT
* *
5506928 TATTCTTTTTAATTGT-TTTACATAC
1 TATT-TTTTTAATTGTCTTTATATAT
*
5506953 TATTTATCTTAAATTGT-TTTATACTATT
1 TATTT-T-TTTAATTGTCTTTATA-TA-T
5506981 TATTT
1 TATTT
5506986 CAAACTGCTT
Statistics
Matches: 66, Mismatches: 9, Indels: 13
0.75 0.10 0.15
Matches are distributed among these distances:
24 2 0.03
25 37 0.56
26 20 0.30
27 2 0.03
28 5 0.08
ACGTcount: A:0.26, C:0.07, G:0.06, T:0.61
Consensus pattern (25 bp):
TATTTTTTTAATTGTCTTTATATAT
Found at i:5506938 original size:75 final size:75
Alignment explanation
Indices: 5506849--5507005 Score: 178
Period size: 75 Copynumber: 2.1 Consensus size: 75
5506839 TTCTTTCTAC
* * * * *
5506849 ATATTATTTATTTTAAACGTTTTTTCATA-TA-TTATTTTAAGTTGTCTTATGTATTATTT-TTT
1 ATATTATTTATTTTAAACG-TTTTACATACTATTTATCTTAAATTGT-TT-TATACTATTTATTT
*
5506911 TAAACTGCTTTAT
63 CAAACTGCTTTAT
**
5506924 ATATTATTCT-TTTTAATTGTTTTACATACTATTTATCTTAAATTGTTTTATACTATTTATTTCA
1 ATATTATT-TATTTTAAACGTTTTACATACTATTTATCTTAAATTGTTTTATACTATTTATTTCA
5506988 AACTGCTTTAT
65 AACTGCTTTAT
5506999 ATATTAT
1 ATATTAT
5507006 GTCGTTTCAC
Statistics
Matches: 70, Mismatches: 8, Indels: 8
0.81 0.09 0.09
Matches are distributed among these distances:
74 16 0.23
75 41 0.59
76 13 0.19
ACGTcount: A:0.28, C:0.08, G:0.05, T:0.59
Consensus pattern (75 bp):
ATATTATTTATTTTAAACGTTTTACATACTATTTATCTTAAATTGTTTTATACTATTTATTTCAA
ACTGCTTTAT
Found at i:5506997 original size:24 final size:24
Alignment explanation
Indices: 5506949--5507003 Score: 69
Period size: 24 Copynumber: 2.3 Consensus size: 24
5506939 ATTGTTTTAC
* *
5506949 ATACTATTTATCTTAAATTGTTTT
1 ATACTATTTATCTTAAACTGCTTT
5506973 ATACTATTTAT-TTCAAACTGCTTT
1 ATACTATTTATCTT-AAACTGCTTT
5506997 ATA-TATT
1 ATACTATT
5507004 ATGTCGTTTC
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
23 6 0.21
24 22 0.79
ACGTcount: A:0.31, C:0.11, G:0.04, T:0.55
Consensus pattern (24 bp):
ATACTATTTATCTTAAACTGCTTT
Found at i:5507890 original size:222 final size:221
Alignment explanation
Indices: 5507505--5507949 Score: 854
Period size: 222 Copynumber: 2.0 Consensus size: 221
5507495 ATTTTATTAC
5507505 TTCGGGACAAAAAGGTCTTTAGCATCCGCTTTGATTTATTCAAACATTTTTTTTGTAAAATTAAC
1 TTCGGGACAAAAAGGTCTTTAGCATCCGCTTTGATTTATTCAAACATTTTTTTTGTAAAATTAAC
*
5507570 ATTAATAAAAAAGGAGGATCATATTTTTAAATTCTTTATGGCTTTCCAACTTCCAACATTAAGAC
66 ATTAATAAAAAAGGAGGATCATATTTTTAAATTCTTTACGGCTTTCCAACTTCCAACATTAAGAC
*
5507635 ATTAATTAATCAATTAGGTACCAATTTTGGGCGTTACGAGGGTGTTAATCCTTCCTCGTATGTAA
131 ATTAATTAATCAATTAGGTACCAATTTTGGGCGTTACGAGGGTGTTAATCCTTCCTCGTACGTAA
5507700 CTGACTCCCGAACCCGTTTTCTTGAA
196 CTGACTCCCGAACCCGTTTTCTTGAA
5507726 TTCGGGACAAAAAGGTCTTTAGCATCCGCTTTGATTTATTCAAACATTTTTTTTTGTAAAATTAA
1 TTCGGGACAAAAAGGTCTTTAGCATCCGCTTTGATTTATTCAAACA-TTTTTTTTGTAAAATTAA
5507791 CATTAATAAAAAAGGAGGATCATATTTTTAAATTCTTTACGGCTTTCCAACTTCCAACATTAAGA
65 CATTAATAAAAAAGGAGGATCATATTTTTAAATTCTTTACGGCTTTCCAACTTCCAACATTAAGA
5507856 CATTAATTAATCAATTAGGTACCAATTTTGGGCGTTACGAGGGTGTTAATCCTTCCTCGTACGTA
130 CATTAATTAATCAATTAGGTACCAATTTTGGGCGTTACGAGGGTGTTAATCCTTCCTCGTACGTA
*
5507921 ACTGACTCTCGAACCCGTTTTCTTGAA
195 ACTGACTCCCGAACCCGTTTTCTTGAA
5507948 TT
1 TT
5507950 TTGTAGACCA
Statistics
Matches: 220, Mismatches: 3, Indels: 1
0.98 0.01 0.00
Matches are distributed among these distances:
221 46 0.21
222 174 0.79
ACGTcount: A:0.31, C:0.18, G:0.15, T:0.37
Consensus pattern (221 bp):
TTCGGGACAAAAAGGTCTTTAGCATCCGCTTTGATTTATTCAAACATTTTTTTTGTAAAATTAAC
ATTAATAAAAAAGGAGGATCATATTTTTAAATTCTTTACGGCTTTCCAACTTCCAACATTAAGAC
ATTAATTAATCAATTAGGTACCAATTTTGGGCGTTACGAGGGTGTTAATCCTTCCTCGTACGTAA
CTGACTCCCGAACCCGTTTTCTTGAA
Found at i:5509842 original size:2 final size:2
Alignment explanation
Indices: 5509835--5509859 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
5509825 TTTGAGAAGG
5509835 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 A
5509860 GACTTCAATG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5515914 original size:51 final size:51
Alignment explanation
Indices: 5515843--5516054 Score: 334
Period size: 51 Copynumber: 4.2 Consensus size: 51
5515833 CCGATCACAT
*
5515843 TTATCACTTGTCACTGATCAGATAAGTGTAGTTAAAACTACCACTTATCAC
1 TTATCACTTGTCACTGATCAGATAAGTGTAGCTAAAACTACCACTTATCAC
* * * *
5515894 TTATCACTTGTCATTGATCAGATAAGTGTAGCTAGAGCTACCACTTATCAT
1 TTATCACTTGTCACTGATCAGATAAGTGTAGCTAAAACTACCACTTATCAC
*
5515945 TTATCACTTGTCACTGATCAGATAAGTATAGCTAAAACTACCACTTATCAC
1 TTATCACTTGTCACTGATCAGATAAGTGTAGCTAAAACTACCACTTATCAC
* * *
5515996 TTATCACCTGTCATTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCAC
1 TTATCACTTGTCACTGATCAGATAAGTGTAGCTAAAACTACCACTTATCAC
*
5516047 TTGTCACT
1 TTATCACT
5516055 GATCAGGAGT
Statistics
Matches: 145, Mismatches: 16, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
51 145 1.00
ACGTcount: A:0.32, C:0.22, G:0.13, T:0.33
Consensus pattern (51 bp):
TTATCACTTGTCACTGATCAGATAAGTGTAGCTAAAACTACCACTTATCAC
Found at i:5515958 original size:102 final size:102
Alignment explanation
Indices: 5515840--5516054 Score: 376
Period size: 102 Copynumber: 2.1 Consensus size: 102
5515830 ACACCGATCA
* * *
5515840 CATTTATCACTTGTCACTGATCAGATAAGTGTAGTTAAAACTACCACTTATCACTTATCACTTGT
1 CATTTATCACTTGTCACTGATCAGATAAGTATAGCTAAAACTACCACTTATCACTTATCACCTGT
*
5515905 CATTGATCAGATAAGTGTAGCTAGAGCTACCACTTAT
66 CATTGATCAGATAAGTGTAGCTAAAGCTACCACTTAT
5515942 CATTTATCACTTGTCACTGATCAGATAAGTATAGCTAAAACTACCACTTATCACTTATCACCTGT
1 CATTTATCACTTGTCACTGATCAGATAAGTATAGCTAAAACTACCACTTATCACTTATCACCTGT
5516007 CATTGATCAGATAAGTGTAGCTAAAGCTACCACTTAT
66 CATTGATCAGATAAGTGTAGCTAAAGCTACCACTTAT
* *
5516044 CACTTGTCACT
1 CATTTATCACT
5516055 GATCAGGAGT
Statistics
Matches: 107, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
102 107 1.00
ACGTcount: A:0.32, C:0.22, G:0.13, T:0.33
Consensus pattern (102 bp):
CATTTATCACTTGTCACTGATCAGATAAGTATAGCTAAAACTACCACTTATCACTTATCACCTGT
CATTGATCAGATAAGTGTAGCTAAAGCTACCACTTAT
Found at i:5518768 original size:19 final size:20
Alignment explanation
Indices: 5518740--5518778 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
5518730 TCCCATTATT
5518740 TATTTATTTTT-TGTTTTAA
1 TATTTATTTTTATGTTTTAA
*
5518759 TATTTGTTTTTATGTTTTAA
1 TATTTATTTTTATGTTTTAA
5518779 ATGTATTTGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 10 0.56
20 8 0.44
ACGTcount: A:0.21, C:0.00, G:0.08, T:0.72
Consensus pattern (20 bp):
TATTTATTTTTATGTTTTAA
Found at i:5518796 original size:25 final size:23
Alignment explanation
Indices: 5518759--5518804 Score: 65
Period size: 25 Copynumber: 1.9 Consensus size: 23
5518749 TTTGTTTTAA
*
5518759 TATTTGTTTTTATGTTTTAAATG
1 TATTTGTTTTTATATTTTAAATG
5518782 TATTTGATTTATTATATTTTAAA
1 TATTTG-TTT-TTATATTTTAAA
5518805 GTTTTTTATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 3 0.15
25 11 0.55
ACGTcount: A:0.28, C:0.00, G:0.09, T:0.63
Consensus pattern (23 bp):
TATTTGTTTTTATATTTTAAATG
Found at i:5521520 original size:786 final size:786
Alignment explanation
Indices: 5520008--5522367 Score: 4515
Period size: 786 Copynumber: 3.0 Consensus size: 786
5519998 TTAGGGTAAT
5520008 ACTCAGTGTTATCGATTCAGTTTTTATTTTATCCACAAAACTCTTCATTTTCAGCATACATCTTA
1 ACTCAGTGTTATCGATTCAGTTTTTATTTTATCCACAAAACTCTTCATTTTCAGCATACATCTTA
5520073 TAATCAATTCTATCAACATATTCTTCTAATATTTACACTATAAAACAAAAGCAAACAATTATATC
66 TAATCAATTCTATCAACATATTCTTCTAATATTTACACTATAAAACAAAAGCAAACAATTATATC
5520138 AGCATCCGATCCCGATTCAATTTCAACTTAACTTTTGGCATGTACCTCTAGACTCAATTTCGAGC
131 AGCATCCGATCCCGATTCAATTTCAACTTAACTTTTGGCATGTACCTCTAGACTCAATTTCGAGC
*
5520203 TCAATTTAGTCCGAGAATCGGCTAAACCTGATAGCTTTGATACCAAAAATTGTAACACCCCTTAA
196 TCAATTTAGTCCGAGAATCGGCTAAACCTGATAGCTCTGATACCAAAAATTGTAACACCCCTTAA
5520268 CCCCAAA-TCGTCACCAGAAGAGGGTTATGGAGCATTACCGGAGTTTACAGAATAATTACACACA
261 CCCCAAACT-GTCACCAGAAGAGGGTTATGGAGCATTACCGGAGTTTACAGAATAATTACACACA
*
5520332 ATTCTATTATTTTCTTATGTTTATGTCAAAGTTGTCTTCTTGAGCAGCAGTCACTAAAATATTTA
325 ATTCCATTATTTTCTTATGTTTATGTCAAAGTTGTCTTCTTGAGCAGCAGTCACTAAAATATTTA
5520397 TAACTGGAGCTACGAAACTTCAAATTAAGTTCTGTTAATTTTCCTTAAAACTAGACTCATATACC
390 TAACTGGAGCTACGAAACTTCAAATTAAGTTCTGTTAATTTTCCTTAAAACTAGACTCATATACC
5520462 TTTCTACCATAAAATTTTCAGAATTTTTAATATTGCCAATTAGTACAGTTTATTCCTCAAAGTTA
455 TTTCTACCATAAAATTTTCAGAATTTTTAATATTGCCAATTAGTACAGTTTATTCCTCAAAGTTA
*
5520527 CCCTTGGTCTGCTATTTGACAACTTCGACCCTTTTTTACTAAAATTTAATTATCTCATAACATAG
520 CCCTTGGTCTGCTATTTGACAACTTCGACCCTTTTTTACTAAAATTTAATTATCTCATAGCATAG
*
5520592 GACTTGGATGATGTTCCCATTTATTTCTCTTAAAAATAGACTCATTAAAGATTCTAAGCATATAA
585 GACTTGGATGATGTTCCCGTTTATTTCTCTTAAAAATAGACTCATTAAAGATTCTAAGCATATAA
* *
5520657 ATTATAGCTCATAATTATTTTTATACAACTTTTAATGATTTTCTCAATTCAAAATAGGGAATTCC
650 ATTATAGCTCATAATTATTTTTATACAACTTTTAATGATTTTCCCAATTCAGAATAGGGAATTCC
5520722 AAAATCAATCTGACATTGTCCCACAAAAATTCAAATTCATACCAAATTAGTCAAATCCTATTTTA
715 AAAATCAATCTGACATTGTCCCACAAAAATTCAAATTCATACCAAATTAGTCAAATCCTATTTTA
5520787 TACCATA
780 TACCATA
5520794 ACTCAGTGTTATCGATTCAGTTTTTATTTTATCCACAAAACTCTTCATTTTCAGCATACATCTTA
1 ACTCAGTGTTATCGATTCAGTTTTTATTTTATCCACAAAACTCTTCATTTTCAGCATACATCTTA
5520859 TAATCAATTCTATCAACATATTCTTCTAATATTTACACTATAAAACAAAAGCAAACAATTATATC
66 TAATCAATTCTATCAACATATTCTTCTAATATTTACACTATAAAACAAAAGCAAACAATTATATC
*
5520924 AGCATCCGATCCCGATTCAATTTCAACTTAACTTTTGGAATGTACCTCTAGACTCAATTTCGAGC
131 AGCATCCGATCCCGATTCAATTTCAACTTAACTTTTGGCATGTACCTCTAGACTCAATTTCGAGC
*
5520989 TCAATTTAGTCCGAGAATCGGCTAAACCTGACAGCTCTGATACCAAAAATTGTAACACCCCTTAA
196 TCAATTTAGTCCGAGAATCGGCTAAACCTGATAGCTCTGATACCAAAAATTGTAACACCCCTTAA
* * *
5521054 CCCTAAACTGTCACCAGGAGAGGGTTATGGAGCATTACCAGAGTTTACAGAATAATTACACACAA
261 CCCCAAACTGTCACCAGAAGAGGGTTATGGAGCATTACCGGAGTTTACAGAATAATTACACACAA
*
5521119 TTCCATTATTTTCTTATGTTTATGTCAAAGTTGTCTTCTTGAGCAGAAGTCACTAAAATATTTAT
326 TTCCATTATTTTCTTATGTTTATGTCAAAGTTGTCTTCTTGAGCAGCAGTCACTAAAATATTTAT
*
5521184 AACTGGAGCTACGAAACTTCAAATTAAGTTCCGTTAATTTTCCTTAAAACTAGACTCATATACCT
391 AACTGGAGCTACGAAACTTCAAATTAAGTTCTGTTAATTTTCCTTAAAACTAGACTCATATACCT
5521249 TTCTACCATAAAATTTTCAGAATTTTTAATATTGCCAATTAGTACAGTTTATTCCTCAAAGTTAC
456 TTCTACCATAAAATTTTCAGAATTTTTAATATTGCCAATTAGTACAGTTTATTCCTCAAAGTTAC
* *
5521314 CCTTGGTCTGCTATTTGACAACTTTGACCCTTTTTTACTAAAATTTAATTATCTCATAGCATAGA
521 CCTTGGTCTGCTATTTGACAACTTCGACCCTTTTTTACTAAAATTTAATTATCTCATAGCATAGG
5521379 ACTTGGATGATGTTCCCGTTTATTTCTCTTAAAAATAGACTCATTAAAGATTCTAAGCATATAAA
586 ACTTGGATGATGTTCCCGTTTATTTCTCTTAAAAATAGACTCATTAAAGATTCTAAGCATATAAA
5521444 TTATAGCTCATAATTATTTTTATACAACTTTTAATGATTTTCCCAATTCAGAATAGGGAATTCCA
651 TTATAGCTCATAATTATTTTTATACAACTTTTAATGATTTTCCCAATTCAGAATAGGGAATTCCA
5521509 AAATCAATCTGACATTGTCCCACAAAAATTCAAATTCATACCAAATTAGTCAAATCCTATTTTAT
716 AAATCAATCTGACATTGTCCCACAAAAATTCAAATTCATACCAAATTAGTCAAATCCTATTTTAT
5521574 ACCATA
781 ACCATA
*
5521580 ACTCAATGTTATCGATTCAGTTTTTATTTTATCCACAAAACTCTTCATTTTCAGCATACATCTTA
1 ACTCAGTGTTATCGATTCAGTTTTTATTTTATCCACAAAACTCTTCATTTTCAGCATACATCTTA
*
5521645 TAATCAATTCTATTAACATATTCTTCTAATATTTACACTATAAAACAAAAGCAAACAATTATATC
66 TAATCAATTCTATCAACATATTCTTCTAATATTTACACTATAAAACAAAAGCAAACAATTATATC
5521710 AGCATCCGATCCCGATTCAATTTCAACTTAACTTTTGGCATGTACCTCTAGACTCAATTTCGAGC
131 AGCATCCGATCCCGATTCAATTTCAACTTAACTTTTGGCATGTACCTCTAGACTCAATTTCGAGC
5521775 TCAATTTAGTCCGAGAATCGGCTAAACCTGATAGCTCTGATACCAAAAATTGTAACACCCCTTAA
196 TCAATTTAGTCCGAGAATCGGCTAAACCTGATAGCTCTGATACCAAAAATTGTAACACCCCTTAA
*
5521840 CCCCAAACCGTCACCAGAAGAGGGTTATGGAGCATTACCGGAGTTTACAGAATAATTACACACAA
261 CCCCAAACTGTCACCAGAAGAGGGTTATGGAGCATTACCGGAGTTTACAGAATAATTACACACAA
5521905 TTCCATTATTTTCTTATGTTTATGTCAAAGTTGTCTTCTTGAGCAGCAGTCACTAAAATATTTAT
326 TTCCATTATTTTCTTATGTTTATGTCAAAGTTGTCTTCTTGAGCAGCAGTCACTAAAATATTTAT
* *
5521970 AACTGGAGCTATGAAACTTCAAATTAAGTTCTGTTAATTTTCCTTAAAACTAGACTCATATATCT
391 AACTGGAGCTACGAAACTTCAAATTAAGTTCTGTTAATTTTCCTTAAAACTAGACTCATATACCT
5522035 TTCTACCATAAAATTTTCAGAATTTTTAATATTGCCAATTAGTACAGTTTATTCCTCAAAGTTAC
456 TTCTACCATAAAATTTTCAGAATTTTTAATATTGCCAATTAGTACAGTTTATTCCTCAAAGTTAC
5522100 CCTTGGTCTGCTATTTGACAACTTCGACCCTTTTTTACTAAAATTTAATTATCTCATAGCATAGG
521 CCTTGGTCTGCTATTTGACAACTTCGACCCTTTTTTACTAAAATTTAATTATCTCATAGCATAGG
*
5522165 ACTTGGATGATGTTCCCGTTTATCTCTCTTAAAAATAGACTCATTAAAGATTCTAAGCATATAAA
586 ACTTGGATGATGTTCCCGTTTATTTCTCTTAAAAATAGACTCATTAAAGATTCTAAGCATATAAA
5522230 TTATAGCTCATAATTATTTTTATACAACTTTTAATGATTTTCCCAATTCAGAATAGGGAATTCCA
651 TTATAGCTCATAATTATTTTTATACAACTTTTAATGATTTTCCCAATTCAGAATAGGGAATTCCA
5522295 AAATCAATCTGACATTGTCCCACAAAAATTCAAATTCATACCAAATTAGTCAAATCCTATTTTAT
716 AAATCAATCTGACATTGTCCCACAAAAATTCAAATTCATACCAAATTAGTCAAATCCTATTTTAT
5522360 ACCATA
781 ACCATA
5522366 AC
1 AC
5522368 CAGACCTAAA
Statistics
Matches: 1543, Mismatches: 30, Indels: 2
0.98 0.02 0.00
Matches are distributed among these distances:
786 1542 1.00
787 1 0.00
ACGTcount: A:0.34, C:0.20, G:0.10, T:0.36
Consensus pattern (786 bp):
ACTCAGTGTTATCGATTCAGTTTTTATTTTATCCACAAAACTCTTCATTTTCAGCATACATCTTA
TAATCAATTCTATCAACATATTCTTCTAATATTTACACTATAAAACAAAAGCAAACAATTATATC
AGCATCCGATCCCGATTCAATTTCAACTTAACTTTTGGCATGTACCTCTAGACTCAATTTCGAGC
TCAATTTAGTCCGAGAATCGGCTAAACCTGATAGCTCTGATACCAAAAATTGTAACACCCCTTAA
CCCCAAACTGTCACCAGAAGAGGGTTATGGAGCATTACCGGAGTTTACAGAATAATTACACACAA
TTCCATTATTTTCTTATGTTTATGTCAAAGTTGTCTTCTTGAGCAGCAGTCACTAAAATATTTAT
AACTGGAGCTACGAAACTTCAAATTAAGTTCTGTTAATTTTCCTTAAAACTAGACTCATATACCT
TTCTACCATAAAATTTTCAGAATTTTTAATATTGCCAATTAGTACAGTTTATTCCTCAAAGTTAC
CCTTGGTCTGCTATTTGACAACTTCGACCCTTTTTTACTAAAATTTAATTATCTCATAGCATAGG
ACTTGGATGATGTTCCCGTTTATTTCTCTTAAAAATAGACTCATTAAAGATTCTAAGCATATAAA
TTATAGCTCATAATTATTTTTATACAACTTTTAATGATTTTCCCAATTCAGAATAGGGAATTCCA
AAATCAATCTGACATTGTCCCACAAAAATTCAAATTCATACCAAATTAGTCAAATCCTATTTTAT
ACCATA
Found at i:5522920 original size:13 final size:14
Alignment explanation
Indices: 5522904--5522939 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 14
5522894 CAATCTCATA
5522904 TCTCAATTTCAA-T
1 TCTCAATTTCAATT
5522917 TCTCAA-TTCAATT
1 TCTCAATTTCAATT
5522930 TCTC-ATTTCA
1 TCTCAATTTCA
5522940 TTCCAATAGC
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
12 6 0.29
13 15 0.71
ACGTcount: A:0.28, C:0.25, G:0.00, T:0.47
Consensus pattern (14 bp):
TCTCAATTTCAATT
Found at i:5522929 original size:18 final size:19
Alignment explanation
Indices: 5522891--5522931 Score: 59
Period size: 18 Copynumber: 2.2 Consensus size: 19
5522881 TGGTTCATGT
5522891 TTTCAATCTCATATCTCAA
1 TTTCAATCTCATATCTCAA
5522910 TTTCAATTCTCA-AT-TCAA
1 TTTCAA-TCTCATATCTCAA
5522928 TTTC
1 TTTC
5522932 TCATTTCATT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 8 0.38
19 8 0.38
20 5 0.24
ACGTcount: A:0.29, C:0.24, G:0.00, T:0.46
Consensus pattern (19 bp):
TTTCAATCTCATATCTCAA
Found at i:5523088 original size:23 final size:23
Alignment explanation
Indices: 5523036--5523093 Score: 71
Period size: 23 Copynumber: 2.5 Consensus size: 23
5523026 GCAGATTCCT
*
5523036 CCCAAACACACTAGAATATCCAA
1 CCCAAACACACCAGAATATCCAA
* * * *
5523059 TCAAAACACACCAGAATTTTCAA
1 CCCAAACACACCAGAATATCCAA
5523082 CCCAAACACACC
1 CCCAAACACACC
5523094 TGGAATATTA
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.47, C:0.36, G:0.03, T:0.14
Consensus pattern (23 bp):
CCCAAACACACCAGAATATCCAA
Found at i:5523489 original size:15 final size:15
Alignment explanation
Indices: 5523471--5523517 Score: 67
Period size: 15 Copynumber: 3.1 Consensus size: 15
5523461 TATATTATAT
5523471 TTCAATCAATATAAA
1 TTCAATCAATATAAA
* * *
5523486 TTCAATCAAAATGAT
1 TTCAATCAATATAAA
5523501 TTCAATCAATATAAA
1 TTCAATCAATATAAA
5523516 TT
1 TT
5523518 TGATAAATTC
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
15 26 1.00
ACGTcount: A:0.49, C:0.13, G:0.02, T:0.36
Consensus pattern (15 bp):
TTCAATCAATATAAA
Found at i:5524500 original size:31 final size:32
Alignment explanation
Indices: 5524442--5524505 Score: 87
Period size: 32 Copynumber: 2.0 Consensus size: 32
5524432 CATACATTTG
*
5524442 TCATAATTTAATATATTTATTACATAAAAATC
1 TCATAATATAATATATTTATTACATAAAAATC
*
5524474 TCATAATATAAT-TATTTAATTA-ATAAATATC
1 TCATAATATAATATATTT-ATTACATAAAAATC
5524505 T
1 T
5524506 TATTTAATAT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
31 14 0.48
32 15 0.52
ACGTcount: A:0.47, C:0.08, G:0.00, T:0.45
Consensus pattern (32 bp):
TCATAATATAATATATTTATTACATAAAAATC
Found at i:5524642 original size:30 final size:30
Alignment explanation
Indices: 5524585--5524642 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 30
5524575 TACAATTGTC
* **
5524585 ATTATTTAATTTATTTAATCTTATTATTTA
1 ATTATTTAATTAATAAAATCTTATTATTTA
5524615 ATTATTTAATTAATAAATATCTT-TTATT
1 ATTATTTAATTAATAAA-ATCTTATTATT
5524643 CTAAAATTAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 19 0.79
31 5 0.21
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.60
Consensus pattern (30 bp):
ATTATTTAATTAATAAAATCTTATTATTTA
Found at i:5525027 original size:13 final size:14
Alignment explanation
Indices: 5525009--5525037 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
5524999 CATTAACTTC
5525009 ATAAATATTTT-TA
1 ATAAATATTTTCTA
5525022 ATAAATATTTTCTA
1 ATAAATATTTTCTA
5525036 AT
1 AT
5525038 CCATTTTTCA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.73
14 4 0.27
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (14 bp):
ATAAATATTTTCTA
Found at i:5527266 original size:18 final size:19
Alignment explanation
Indices: 5527239--5527276 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
5527229 ATATTAAAAT
* *
5527239 AATTTGCAAGTATT-TATA
1 AATTTACAAGAATTATATA
5527257 AATTTACAAGAATTATATA
1 AATTTACAAGAATTATATA
5527276 A
1 A
5527277 TAACATAATT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 12 0.71
19 5 0.29
ACGTcount: A:0.47, C:0.05, G:0.08, T:0.39
Consensus pattern (19 bp):
AATTTACAAGAATTATATA
Found at i:5527901 original size:13 final size:13
Alignment explanation
Indices: 5527840--5527908 Score: 68
Period size: 13 Copynumber: 5.2 Consensus size: 13
5527830 TTAGTTTGAT
5527840 AATATTTTTGAAA
1 AATATTTTTGAAA
* *
5527853 AGTAATTTTTTAAA
1 AAT-ATTTTTGAAA
*
5527867 AATA-TTGTGAAAA
1 AATATTTTTG-AAA
*
5527880 AATAATTTTGAAA
1 AATATTTTTGAAA
*
5527893 AGTATTTTTGAAA
1 AATATTTTTGAAA
5527906 AAT
1 AAT
5527909 TTAATTTAAA
Statistics
Matches: 44, Mismatches: 9, Indels: 6
0.75 0.15 0.10
Matches are distributed among these distances:
12 3 0.07
13 26 0.59
14 15 0.34
ACGTcount: A:0.48, C:0.00, G:0.10, T:0.42
Consensus pattern (13 bp):
AATATTTTTGAAA
Found at i:5528978 original size:19 final size:19
Alignment explanation
Indices: 5528956--5528995 Score: 71
Period size: 19 Copynumber: 2.1 Consensus size: 19
5528946 AGTAAAAAGT
*
5528956 AAAAGATGAAATGAAAATA
1 AAAAGATGAAATAAAAATA
5528975 AAAAGATGAAATAAAAATA
1 AAAAGATGAAATAAAAATA
5528994 AA
1 AA
5528996 TAACAAAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.72, C:0.00, G:0.12, T:0.15
Consensus pattern (19 bp):
AAAAGATGAAATAAAAATA
Found at i:5529912 original size:16 final size:16
Alignment explanation
Indices: 5529882--5529929 Score: 57
Period size: 15 Copynumber: 3.1 Consensus size: 16
5529872 GAAAATTAAT
5529882 ATAAAATCT-AAAAT-A
1 ATAAAAT-TAAAAATAA
5529897 ATAATAATTAAAAATAA
1 ATAA-AATTAAAAATAA
5529914 ATAAAATT-AAAATAA
1 ATAAAATTAAAAATAA
5529929 A
1 A
5529930 CTTAAAATAG
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
15 13 0.43
16 12 0.40
17 5 0.17
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.27
Consensus pattern (16 bp):
ATAAAATTAAAAATAA
Found at i:5529928 original size:11 final size:11
Alignment explanation
Indices: 5529873--5529943 Score: 58
Period size: 11 Copynumber: 6.5 Consensus size: 11
5529863 ATAGCTTAAG
*
5529873 AAAATTAATAT
1 AAAATTAAAAT
5529884 AAAATCTAAAAT
1 AAAAT-TAAAAT
*
5529896 AATAA-T-AATT
1 AA-AATTAAAAT
*
5529906 AAAAAT-AAAT
1 AAAATTAAAAT
5529916 AAAATTAAAAT
1 AAAATTAAAAT
*
5529927 AAACTTAAAAT
1 AAAATTAAAAT
*
5529938 AGAATT
1 AAAATT
5529944 TCCTATTTTT
Statistics
Matches: 49, Mismatches: 7, Indels: 8
0.77 0.11 0.12
Matches are distributed among these distances:
9 2 0.04
10 14 0.29
11 24 0.49
12 7 0.14
13 2 0.04
ACGTcount: A:0.66, C:0.03, G:0.01, T:0.30
Consensus pattern (11 bp):
AAAATTAAAAT
Found at i:5536145 original size:14 final size:12
Alignment explanation
Indices: 5536104--5536149 Score: 56
Period size: 12 Copynumber: 3.8 Consensus size: 12
5536094 TATTAGCTTT
* *
5536104 TTTTAATATTAA
1 TTTTATTATAAA
5536116 TTTTATTATAAA
1 TTTTATTATAAA
*
5536128 TTTTATTATATA
1 TTTTATTATAAA
*
5536140 TTTTTTTATA
1 TTTTATTATA
5536150 TATAATCTCC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 30 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (12 bp):
TTTTATTATAAA
Found at i:5536150 original size:12 final size:12
Alignment explanation
Indices: 5536115--5536152 Score: 58
Period size: 12 Copynumber: 3.2 Consensus size: 12
5536105 TTTAATATTA
*
5536115 ATTTTATTATAA
1 ATTTTATTATAT
5536127 ATTTTATTATAT
1 ATTTTATTATAT
*
5536139 ATTTTTTTATAT
1 ATTTTATTATAT
5536151 AT
1 AT
5536153 AATCTCCCCT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (12 bp):
ATTTTATTATAT
Found at i:5536270 original size:34 final size:35
Alignment explanation
Indices: 5536224--5536294 Score: 108
Period size: 34 Copynumber: 2.1 Consensus size: 35
5536214 TCGATACAAA
*
5536224 TTAAGTTAAGAATAATCCCTCAATAATATTGTATT
1 TTAAGTTAAGAATAATCCCTCAATAATATTATATT
**
5536259 TTAA-TTAAGAATAATCGGTCAATAATATTATATT
1 TTAAGTTAAGAATAATCCCTCAATAATATTATATT
5536293 TT
1 TT
5536295 GGGGTTGGCA
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
34 29 0.88
35 4 0.12
ACGTcount: A:0.41, C:0.08, G:0.08, T:0.42
Consensus pattern (35 bp):
TTAAGTTAAGAATAATCCCTCAATAATATTATATT
Found at i:5552642 original size:21 final size:21
Alignment explanation
Indices: 5552616--5552665 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
5552606 TTCGATATTC
5552616 AAGATTTAAAATTTGAGATTT
1 AAGATTTAAAATTTGAGATTT
***
5552637 AAGATTTATGGTTTGAGATTT
1 AAGATTTAAAATTTGAGATTT
*
5552658 AAGGTTTA
1 AAGATTTA
5552666 TAGATAAAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.36, C:0.00, G:0.20, T:0.44
Consensus pattern (21 bp):
AAGATTTAAAATTTGAGATTT
Found at i:5552666 original size:21 final size:21
Alignment explanation
Indices: 5552627--5552666 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
5552617 AGATTTAAAA
5552627 TTTGAGATTTAAGATTTATGG
1 TTTGAGATTTAAGATTTATGG
*
5552648 TTTGAGATTTAAGGTTTAT
1 TTTGAGATTTAAGATTTAT
5552667 AGATAAAAAA
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:0.28, C:0.00, G:0.23, T:0.50
Consensus pattern (21 bp):
TTTGAGATTTAAGATTTATGG
Found at i:5554715 original size:11 final size:11
Alignment explanation
Indices: 5554699--5554724 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
5554689 AATTATATTA
5554699 GTATATAGATT
1 GTATATAGATT
5554710 GTATATAGATT
1 GTATATAGATT
5554721 GTAT
1 GTAT
5554725 TTTATTTTAA
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:0.35, C:0.00, G:0.19, T:0.46
Consensus pattern (11 bp):
GTATATAGATT
Found at i:5554793 original size:25 final size:26
Alignment explanation
Indices: 5554760--5554808 Score: 66
Period size: 25 Copynumber: 1.9 Consensus size: 26
5554750 TTAAAGAGTA
5554760 ATTTGATTTATT-CTAGTAAAAATTTT
1 ATTTGATTT-TTACTAGTAAAAATTTT
*
5554786 ATTT-ATTTTTACTATTAAAAATT
1 ATTTGATTTTTACTAGTAAAAATT
5554809 GGTGTTACTA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 2 0.10
25 15 0.71
26 4 0.19
ACGTcount: A:0.37, C:0.04, G:0.04, T:0.55
Consensus pattern (26 bp):
ATTTGATTTTTACTAGTAAAAATTTT
Found at i:5554951 original size:2 final size:2
Alignment explanation
Indices: 5554944--5554978 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
5554934 CTTTGATAAA
5554944 AT AT 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 AT AT A
5554979 CTAATTTACC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:5555791 original size:2 final size:2
Alignment explanation
Indices: 5555784--5555822 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
5555774 GGGGTAAAAT
5555784 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
5555823 TTATTAATTA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:5560044 original size:20 final size:19
Alignment explanation
Indices: 5560019--5560079 Score: 59
Period size: 19 Copynumber: 3.1 Consensus size: 19
5560009 TAACTACTTT
5560019 AAAAATAATTATTTATATTA
1 AAAAATAATTATTTA-ATTA
* *
5560039 AAAAATTTATTTTTTAATTA
1 AAAAA-TAATTATTTAATTA
** *
5560059 AATTATAATTATTTAAGTA
1 AAAAATAATTATTTAATTA
5560078 AA
1 AA
5560080 CTGGATGAGT
Statistics
Matches: 33, Mismatches: 7, Indels: 3
0.77 0.16 0.07
Matches are distributed among these distances:
19 13 0.39
20 12 0.36
21 8 0.24
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.48
Consensus pattern (19 bp):
AAAAATAATTATTTAATTA
Found at i:5565817 original size:23 final size:24
Alignment explanation
Indices: 5565776--5565825 Score: 84
Period size: 23 Copynumber: 2.1 Consensus size: 24
5565766 TTATGAATGG
5565776 AAATAGTATAAAAAAAAAACGAGTT
1 AAATAGTAT-AAAAAAAAACGAGTT
5565801 AAATAGTAT-AAAAAAAACGAGTT
1 AAATAGTATAAAAAAAAACGAGTT
5565824 AA
1 AA
5565826 CGTACACACA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
23 16 0.64
25 9 0.36
ACGTcount: A:0.64, C:0.04, G:0.12, T:0.20
Consensus pattern (24 bp):
AAATAGTATAAAAAAAAACGAGTT
Found at i:5566163 original size:24 final size:23
Alignment explanation
Indices: 5566073--5566178 Score: 83
Period size: 23 Copynumber: 4.5 Consensus size: 23
5566063 TAATCAAAGA
*
5566073 AAAATAAATAATATA-ACAAGGTTT
1 AAAATAAATAATATATA-AAAG-TT
* * * *
5566097 AAAATAAATGATAGATGAAACCAATC
1 AAAATAAATAATATAT-AAA--AGTT
*
5566123 AAAATAAA-GATATA-AAAAGTT
1 AAAATAAATAATATATAAAAGTT
*
5566144 AAAATAAATAATATATAAAATTT
1 AAAATAAATAATATATAAAAGTT
5566167 AAAATAAATAAT
1 AAAATAAATAAT
5566179 GTAGGAAATG
Statistics
Matches: 66, Mismatches: 10, Indels: 13
0.74 0.11 0.15
Matches are distributed among these distances:
21 10 0.15
22 5 0.08
23 21 0.32
24 13 0.20
25 7 0.11
26 10 0.15
ACGTcount: A:0.63, C:0.04, G:0.07, T:0.26
Consensus pattern (23 bp):
AAAATAAATAATATATAAAAGTT
Found at i:5566688 original size:17 final size:18
Alignment explanation
Indices: 5566666--5566699 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
5566656 ATATGTAAAT
5566666 TTTAAA-ATGAATAATAG
1 TTTAAATATGAATAATAG
*
5566683 TTTAAATATGTATAATA
1 TTTAAATATGAATAATA
5566700 TGTGAAAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.50, C:0.00, G:0.09, T:0.41
Consensus pattern (18 bp):
TTTAAATATGAATAATAG
Found at i:5567670 original size:15 final size:16
Alignment explanation
Indices: 5567622--5567668 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
5567612 TATAAAATAA
5567622 ATAAAACAAA-AACAAAT
1 ATAAAA-AAAGAA-AAAT
* *
5567639 ATCAAAAACGAAAAAT
1 ATAAAAAAAGAAAAAT
5567655 ATAAAAAAAGAAAA
1 ATAAAAAAAGAAAA
5567669 TAAGAAAATA
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
16 18 0.72
17 7 0.28
ACGTcount: A:0.77, C:0.09, G:0.04, T:0.11
Consensus pattern (16 bp):
ATAAAAAAAGAAAAAT
Found at i:5571596 original size:11 final size:11
Alignment explanation
Indices: 5571580--5571604 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
5571570 CGTTTGGAAC
5571580 ACCTACAATCT
1 ACCTACAATCT
5571591 ACCTACAATCT
1 ACCTACAATCT
5571602 ACC
1 ACC
5571605 GCCTAACGGA
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:0.36, C:0.40, G:0.00, T:0.24
Consensus pattern (11 bp):
ACCTACAATCT
Found at i:5578119 original size:17 final size:17
Alignment explanation
Indices: 5578099--5578132 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
5578089 TAAGAGATTA
5578099 TAAATAAAAATAAACAT
1 TAAATAAAAATAAACAT
* *
5578116 TAAATCAAAATATACAT
1 TAAATAAAAATAAACAT
5578133 ACATATTAAG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.65, C:0.09, G:0.00, T:0.26
Consensus pattern (17 bp):
TAAATAAAAATAAACAT
Found at i:5585831 original size:22 final size:22
Alignment explanation
Indices: 5585801--5585875 Score: 62
Period size: 22 Copynumber: 3.4 Consensus size: 22
5585791 TGGTTTGGAC
*
5585801 TATATTTAGTTCTTTTTCTTTT
1 TATAATTAGTTCTTTTTCTTTT
* * * ***
5585823 TATAATTAG-ACAGTATTCGAAT
1 TATAATTAGTTC-TTTTTCTTTT
*
5585845 TATATTTAGTTCTTTTTCTTTT
1 TATAATTAGTTCTTTTTCTTTT
5585867 TATAATTAG
1 TATAATTAG
5585876 ACGGTATTCA
Statistics
Matches: 36, Mismatches: 15, Indels: 4
0.65 0.27 0.07
Matches are distributed among these distances:
21 1 0.03
22 34 0.94
23 1 0.03
ACGTcount: A:0.25, C:0.08, G:0.08, T:0.59
Consensus pattern (22 bp):
TATAATTAGTTCTTTTTCTTTT
Found at i:5585864 original size:44 final size:44
Alignment explanation
Indices: 5585801--5585884 Score: 159
Period size: 44 Copynumber: 1.9 Consensus size: 44
5585791 TGGTTTGGAC
5585801 TATATTTAGTTCTTTTTCTTTTTATAATTAGACAGTATTCGAAT
1 TATATTTAGTTCTTTTTCTTTTTATAATTAGACAGTATTCGAAT
*
5585845 TATATTTAGTTCTTTTTCTTTTTATAATTAGACGGTATTC
1 TATATTTAGTTCTTTTTCTTTTTATAATTAGACAGTATTC
5585885 AAATCAAGCG
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
44 39 1.00
ACGTcount: A:0.25, C:0.10, G:0.10, T:0.56
Consensus pattern (44 bp):
TATATTTAGTTCTTTTTCTTTTTATAATTAGACAGTATTCGAAT
Found at i:5590935 original size:24 final size:24
Alignment explanation
Indices: 5590903--5590954 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
5590893 GAAACATTGG
*
5590903 CAGCCGCAGCCGCAGCCT-TTGCAA
1 CAGCAGCAGCCGCAG-CTATTGCAA
* *
5590927 CAGCAGCAGCTGCTGCTATTGCAA
1 CAGCAGCAGCCGCAGCTATTGCAA
5590951 CAGC
1 CAGC
5590955 TGCGGAAGTC
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 2 0.08
24 22 0.92
ACGTcount: A:0.23, C:0.37, G:0.25, T:0.15
Consensus pattern (24 bp):
CAGCAGCAGCCGCAGCTATTGCAA
Found at i:5598345 original size:7 final size:7
Alignment explanation
Indices: 5598321--5598361 Score: 59
Period size: 7 Copynumber: 6.1 Consensus size: 7
5598311 GATTTAAGAA
5598321 TAAATAT
1 TAAATAT
*
5598328 T-TATA-
1 TAAATAT
5598333 TAAATAT
1 TAAATAT
5598340 TAAATAT
1 TAAATAT
5598347 TAAATAT
1 TAAATAT
5598354 TAAATAT
1 TAAATAT
5598361 T
1 T
5598362 TATTTTTCAA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
5 1 0.03
6 6 0.20
7 23 0.77
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (7 bp):
TAAATAT
Found at i:5599924 original size:18 final size:17
Alignment explanation
Indices: 5599895--5599933 Score: 53
Period size: 16 Copynumber: 2.2 Consensus size: 17
5599885 ATAATTCATG
5599895 AAAAAATTTAAAAT-TT
1 AAAAAATTTAAAATATT
5599911 AAAAAATATATAAAATATT
1 AAAAAAT-T-TAAAATATT
5599930 AAAA
1 AAAA
5599934 TATTATCCAC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
16 7 0.35
17 1 0.05
18 6 0.30
19 6 0.30
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (17 bp):
AAAAAATTTAAAATATT
Found at i:5608668 original size:21 final size:21
Alignment explanation
Indices: 5608627--5608668 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
5608617 TAATAAATAT
**
5608627 TAATATAAAAATTTTAACTAA
1 TAATATAAAAATTCGAACTAA
5608648 TAATAT-AAAATTCGAATCTAA
1 TAATATAAAAATTCGAA-CTAA
5608669 CCCGAACAAG
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
20 8 0.44
21 10 0.56
ACGTcount: A:0.55, C:0.07, G:0.02, T:0.36
Consensus pattern (21 bp):
TAATATAAAAATTCGAACTAA
Found at i:5611021 original size:17 final size:17
Alignment explanation
Indices: 5611001--5611034 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
5610991 AGGTTTAGGT
5611001 TTAAAAATTTTAATTAA
1 TTAAAAATTTTAATTAA
**
5611018 TTAAATTTTTTAATTAA
1 TTAAAAATTTTAATTAA
5611035 AAATCTATTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
TTAAAAATTTTAATTAA
Found at i:5611201 original size:29 final size:29
Alignment explanation
Indices: 5611162--5611242 Score: 153
Period size: 29 Copynumber: 2.8 Consensus size: 29
5611152 ACAAAATCAT
*
5611162 AACATAAGTGACTAAAACGTAACATTTCA
1 AACATAAGTGACTAAAATGTAACATTTCA
5611191 AACATAAGTGACTAAAATGTAACATTTCA
1 AACATAAGTGACTAAAATGTAACATTTCA
5611220 AACATAAGTGACTAAAATGTAAC
1 AACATAAGTGACTAAAATGTAAC
5611243 CTGGGACAAA
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
29 51 1.00
ACGTcount: A:0.49, C:0.15, G:0.11, T:0.25
Consensus pattern (29 bp):
AACATAAGTGACTAAAATGTAACATTTCA
Found at i:5611260 original size:31 final size:29
Alignment explanation
Indices: 5611162--5611264 Score: 125
Period size: 29 Copynumber: 3.5 Consensus size: 29
5611152 ACAAAATCAT
* **
5611162 AACATAAGTGACTAAAACGTAACATTTCA
1 AACATAAGTGACTAAAATGTAACATGACA
**
5611191 AACATAAGTGACTAAAATGTAACATTTCA
1 AACATAAGTGACTAAAATGTAACATGACA
*
5611220 AACATAAGTGACTAAAATGTAACCTGGGACA
1 AACATAAGTGACTAAAATGTAACAT--GACA
*
5611251 AACAAAAGTGACTA
1 AACATAAGTGACTA
5611265 TTTTTATATA
Statistics
Matches: 67, Mismatches: 5, Indels: 2
0.91 0.07 0.03
Matches are distributed among these distances:
29 52 0.78
31 15 0.22
ACGTcount: A:0.49, C:0.16, G:0.14, T:0.22
Consensus pattern (29 bp):
AACATAAGTGACTAAAATGTAACATGACA
Found at i:5612197 original size:31 final size:30
Alignment explanation
Indices: 5612160--5612229 Score: 79
Period size: 31 Copynumber: 2.3 Consensus size: 30
5612150 CATAATTGTG
5612160 AAATAGTAGCAAAATAATGAAAACAACAAG-A
1 AAATAGTAGCAAAATAAT-AAAA-AACAAGAA
* * **
5612191 AAATAGTAACGAAATAATAAAAAAGTAGAA
1 AAATAGTAGCAAAATAATAAAAAACAAGAA
5612221 AAATAGTAG
1 AAATAGTAG
5612230 TTTTTTTTGC
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
29 4 0.12
30 13 0.39
31 16 0.48
ACGTcount: A:0.64, C:0.06, G:0.14, T:0.16
Consensus pattern (30 bp):
AAATAGTAGCAAAATAATAAAAAACAAGAA
Found at i:5612605 original size:17 final size:17
Alignment explanation
Indices: 5612583--5612618 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
5612573 ATAGTGATCT
5612583 CAAGTCTAAACATTATA
1 CAAGTCTAAACATTATA
*
5612600 CAAGTCTAAAGATTATA
1 CAAGTCTAAACATTATA
5612617 CA
1 CA
5612619 TACCTTTATC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.47, C:0.17, G:0.08, T:0.28
Consensus pattern (17 bp):
CAAGTCTAAACATTATA
Found at i:5614137 original size:29 final size:28
Alignment explanation
Indices: 5614053--5614141 Score: 79
Period size: 29 Copynumber: 3.0 Consensus size: 28
5614043 AATTGAATTA
* *
5614053 AAATCAAAGTTTCATGTATACATATGAACC
1 AAATCAAAG-TTCATGTATAAAT-TGCACC
* * *
5614083 ACAATTTAAATTTCATGTGTATAATTGCACC
1 A-AA-TCAAAGTTCATGTATA-AATTGCACC
5614114 AAATCAAAGTTCATGTATCAAATTGCAC
1 AAATCAAAGTTCATGTAT-AAATTGCAC
5614142 ATTAGACTAA
Statistics
Matches: 47, Mismatches: 8, Indels: 9
0.73 0.12 0.14
Matches are distributed among these distances:
29 20 0.43
30 4 0.09
31 17 0.36
32 6 0.13
ACGTcount: A:0.40, C:0.17, G:0.10, T:0.33
Consensus pattern (28 bp):
AAATCAAAGTTCATGTATAAATTGCACC
Found at i:5618404 original size:34 final size:34
Alignment explanation
Indices: 5618358--5618426 Score: 111
Period size: 34 Copynumber: 2.0 Consensus size: 34
5618348 TTTAACCTTA
*
5618358 AAAAAAACTTTTAGAACACCCAAAAATTTAAAGC
1 AAAAAAACTTTTAAAACACCCAAAAATTTAAAGC
* *
5618392 AAAAAAAGTTTTAAAACACTCAAAAATTTAAAGC
1 AAAAAAACTTTTAAAACACCCAAAAATTTAAAGC
5618426 A
1 A
5618427 TCACCCTCCT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
34 32 1.00
ACGTcount: A:0.58, C:0.14, G:0.06, T:0.22
Consensus pattern (34 bp):
AAAAAAACTTTTAAAACACCCAAAAATTTAAAGC
Found at i:5621150 original size:15 final size:15
Alignment explanation
Indices: 5621130--5621160 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
5621120 AATAATGTAC
5621130 TTTGGCACCACCCAT
1 TTTGGCACCACCCAT
5621145 TTTGGCACCACCCAT
1 TTTGGCACCACCCAT
5621160 T
1 T
5621161 AGCTAAGACC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.19, C:0.39, G:0.13, T:0.29
Consensus pattern (15 bp):
TTTGGCACCACCCAT
Found at i:5623173 original size:8 final size:8
Alignment explanation
Indices: 5623160--5623186 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
5623150 AAGGATATGG
5623160 ATATGGAA
1 ATATGGAA
5623168 ATATGGAA
1 ATATGGAA
5623176 ATATGGAA
1 ATATGGAA
5623184 ATA
1 ATA
5623187 AAGGAAGCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.52, C:0.00, G:0.22, T:0.26
Consensus pattern (8 bp):
ATATGGAA
Found at i:5652328 original size:19 final size:19
Alignment explanation
Indices: 5652304--5652350 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
5652294 CCTCAACCGT
5652304 AAAAAAAATTGAAAA-AGAA
1 AAAAAAAATTGAAAACA-AA
* *
5652323 AAAAAACACTGAAAACAAA
1 AAAAAAAATTGAAAACAAA
5652342 AAAAAAAAT
1 AAAAAAAAT
5652351 GGGTCATGTT
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
19 22 0.96
20 1 0.04
ACGTcount: A:0.79, C:0.06, G:0.06, T:0.09
Consensus pattern (19 bp):
AAAAAAAATTGAAAACAAA
Found at i:5652527 original size:19 final size:18
Alignment explanation
Indices: 5652505--5652572 Score: 68
Period size: 19 Copynumber: 3.7 Consensus size: 18
5652495 TTCATTTTCG
5652505 AGAACAAAGAAGGAGAAAA
1 AGAA-AAAGAAGGAGAAAA
5652524 AG-AAAAGAAGGAGAAGGAA
1 AGAAAAAGAAGGAGAA--AA
* *
5652543 AG-AAGAGAAGAAGAAGAA
1 AGAAAAAGAAGGAGAA-AA
5652561 AGAAAAAGAAGG
1 AGAAAAAGAAGG
5652573 GGAGGAGGAG
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
17 12 0.29
18 6 0.14
19 24 0.57
ACGTcount: A:0.66, C:0.01, G:0.32, T:0.00
Consensus pattern (18 bp):
AGAAAAAGAAGGAGAAAA
Found at i:5653689 original size:299 final size:297
Alignment explanation
Indices: 5653132--5654338 Score: 1651
Period size: 299 Copynumber: 4.1 Consensus size: 297
5653122 ATTTTTTTGT
* * * * *
5653132 TAAAATAATATAAA-AAATAAAATATGAAAATAGTATATTTTAAAAAATAAAATCCGAAAATTAA
1 TAAAATAATATAAAGAAATAAAATACGAAAATAATATATTTTAAAAAATAAGATACGAAAATAAA
* * * *
5653196 AAAATACGAACAAGGTGCCAAAGTCAGGGTTATTTATTAAATTAATATAAAAAAA-ACTTAAATA
66 AAAATACGAAGAAAGTGTCAAAATCAGGGTTATTTATTAAATTAATATAAAAAAACACTT-AATA
* * * *
5653260 ATACATTTGAAAGATTTTATGC----------T--AAAACAAAATACGAAAATAATATATTTTAA
130 ATACATTTGAAACATTTTTTGCTAAAATAATATAAAAAATAAAATACAAAAATAATATATTTTAA
* * * *
5653313 TAAATAATATACG--AAAAATATGAATAAAGTGCTAAAATTAGGGTTACTTATTAAAAAAATAT-
195 AAAATAATATACGAAAAAAATACGAATAAAGTGCTAAAATCAGGGTTATTTATTAAAAAAATATA
* *
5653375 AAAAAACATTTAAATAATACATTTGAAACATTAAGTAC
260 AAAAAACACTTAAATAATACATTTGAAACATTATGTAC
5653413 TAAAATAATATAAAGAAATAAAATACGAAAATAATATATTTTAAAAAATAAGATACGAAAATAAA
1 TAAAATAATATAAAGAAATAAAATACGAAAATAATATATTTTAAAAAATAAGATACGAAAATAAA
* *
5653478 AAAATTACGAAGAAAGTGTCAAAATCAGGGTTATTTATTACATTAATATAAAGAAACACTTAAGT
66 AAAA-TACGAAGAAAGTGTCAAAATCAGGGTTATTTATTAAATTAATATAAAAAAACACTTAA-T
* *
5653543 AGTACATTTGAAACATTTTTTGCTAAAATAATATAAAAACATAAAATACGAAAATAATATATTTT
129 AATACATTTGAAACATTTTTTGCTAAAATAATATAAAAA-ATAAAATACAAAAATAATATATTTT
* * * *
5653608 AAAAAATAATATACGAAAAAAGTAAGAATAAAGTGCTAAAATCAGGGTTATTTATTGAAAAAGTA
193 AAAAAATAATATACGAAAAAAATACGAATAAAGTGCTAAAATCAGGGTTATTTATTAAAAAAATA
*
5653673 T-AAAAAATACTTAAATAATACATTTGAAACATTATGTAC
258 TAAAAAAACACTTAAATAATACATTTGAAACATTATGTAC
*
5653712 TAAAATAATATGAAGAAATAAAATACGAAAATAATATATTTTAAAAAATAAGATACGAAAAT--A
1 TAAAATAATATAAAGAAATAAAATACGAAAATAATATATTTTAAAAAATAAGATACGAAAATAAA
5653775 AAAATACGAAGAAAGTGTCAAAATCAGGGTTATTTATTAAATTAATATAAAAAAACACTTACATA
66 AAAATACGAAGAAAGTGTCAAAATCAGGGTTATTTATTAAATTAATATAAAAAAACACTTA-ATA
5653840 ATACATTTGAAACATTTTTTGCTAAAATAATATAAAAAAATAAAATACAAAAATAATATATTTT-
130 ATACATTTGAAACATTTTTTGCTAAAATAATAT-AAAAAATAAAATACAAAAATAATATATTTTA
*
5653904 AAAAATAATATATGAAAAAAATACGAATAAAGTGCTAAAATCAGGGTTATTTATTAAAAAAATAT
194 AAAAATAATATACGAAAAAAATACGAATAAAGTGCTAAAATCAGGGTTATTTATTAAAAAAATAT
* *
5653969 AAAAAAATACTTAAATAATACATTTGAAATATTATGTAC
259 AAAAAAACACTTAAATAATACATTTGAAACATTATGTAC
*
5654008 TAAAATAATATAAAGAAATAAAATACGAAAATAATATATTTTAAAAAATAAGATATG-----AAA
1 TAAAATAATATAAAGAAATAAAATACGAAAATAATATATTTTAAAAAATAAGATACGAAAATAAA
* **
5654068 AAAATACGAATAAAGTG-CTAAAATCAGGGTTATTTATTAAAAAAATATAAAAAAACACTTAAAT
66 AAAATACGAAGAAAGTGTC-AAAATCAGGGTTATTTATTAAATTAATATAAAAAAACACTT-AAT
* * *
5654132 AATACAATTGAAACATTATTTACTAAAATAATATAAAGAAATAAAATACAAAAATAATATATTTT
129 AATACATTTGAAACATTTTTTGCTAAAATAATATAAA-AAATAAAATACAAAAATAATATATTTT
* * * *
5654197 AAAAAATAAGATACGAAAATAAAAAAATACGAAAAAAGTGCCAAAATCAGGGTTATTTATTAAAT
193 AAAAAATAATATACG-----AAAAAAATACGAATAAAGTGCTAAAATCAGGGTTATTTATTAAAA
* * * * *
5654262 TAATATAAAAAAACACTTACATAATACATTTGAAACATTTTTTGC
253 AAATATAAAAAAACACTTAAATAATACATTTGAAACATTATGTAC
*
5654307 TAAAATAATATAAA-AAATAATATACGAAAATA
1 TAAAATAATATAAAGAAATAAAATACGAAAATA
5654339 TTTTACTTAT
Statistics
Matches: 836, Mismatches: 57, Indels: 49
0.89 0.06 0.05
Matches are distributed among these distances:
281 14 0.02
282 49 0.06
283 47 0.06
284 25 0.03
292 4 0.00
293 116 0.14
294 14 0.02
295 60 0.07
296 208 0.25
297 49 0.06
298 17 0.02
299 233 0.28
ACGTcount: A:0.56, C:0.07, G:0.08, T:0.29
Consensus pattern (297 bp):
TAAAATAATATAAAGAAATAAAATACGAAAATAATATATTTTAAAAAATAAGATACGAAAATAAA
AAAATACGAAGAAAGTGTCAAAATCAGGGTTATTTATTAAATTAATATAAAAAAACACTTAATAA
TACATTTGAAACATTTTTTGCTAAAATAATATAAAAAATAAAATACAAAAATAATATATTTTAAA
AAATAATATACGAAAAAAATACGAATAAAGTGCTAAAATCAGGGTTATTTATTAAAAAAATATAA
AAAAACACTTAAATAATACATTTGAAACATTATGTAC
Found at i:5653733 original size:146 final size:145
Alignment explanation
Indices: 5653288--5654338 Score: 1398
Period size: 146 Copynumber: 7.1 Consensus size: 145
5653278 ATGCTAAAAC
* * *
5653288 AAAATACGAAAATAATATATTTTAATAAATAATATACG--AAAAATATGAATAAAGTGCTAAAAT
1 AAAATACGAAAATAATATATTTTAAAAAATAAGATACGAAAAAAATACGAATAAAGTGCTAAAAT
* * * * **
5653351 TAGGGTTACTTATTAAAAAAATATAAAAAACATTTAAATAATACATTTGAAACATTAAGTACTAA
66 CAGGGTTATTTATTAAAAATATA-AAAAAACACTTAAATAATACATTTGAAACATTATTTACTAA
5653416 AATAATATAAAGAAAT
130 AATAATATAAAGAAAT
*
5653432 AAAATACGAAAATAATATATTTTAAAAAATAAGATACGAAAATAAAAAAATTACGAAGAAAGTG-
1 AAAATACGAAAATAATATATTTTAAAAAATAAGATACG-----AAAAAAA-TACGAATAAAGTGC
* * * * *
5653496 TCAAAATCAGGGTTATTTATTACATTAATATAAAGAAACACTTAAGTAGTACATTTGAAACATTT
60 T-AAAATCAGGGTTATTTATTA-A-AAATATAAAAAAACACTTAAATAATACATTTGAAACATTA
*
5653561 TTTGCTAAAATAATATAAA-AACAT
122 TTTACTAAAATAATATAAAGAA-AT
* * *
5653585 AAAATACGAAAATAATATATTTTAAAAAATAATATACGAAAAAAGTAAGAATAAAGTGCTAAAAT
1 AAAATACGAAAATAATATATTTTAAAAAATAAGATACGAAAAAAATACGAATAAAGTGCTAAAAT
* *
5653650 CAGGGTTATTTATTGAAAAAGTAT-AAAAAATACTTAAATAATACATTTGAAACATTATGTACTA
66 CAGGGTTATTTATT-AAAAA-TATAAAAAAACACTTAAATAATACATTTGAAACATTATTTACTA
*
5653714 AAATAATATGAAGAAAT
129 AAATAATATAAAGAAAT
*
5653731 AAAATACGAAAATAATATATTTTAAAAAATAAGATACGAAAATAAAAATACGAAGAAAGTG-TCA
1 AAAATACGAAAATAATATATTTTAAAAAATAAGATACG--AA-AAAAATACGAATAAAGTGCT-A
* *
5653795 AAATCAGGGTTATTTATTAAATTAATATAAAAAAACACTTACATAATACATTTGAAACATTTTTT
62 AAATCAGGGTTATTTATTAAA--AATATAAAAAAACACTTAAATAATACATTTGAAACATTATTT
* *
5653860 GCTAAAATAATATAAAAAAAT
125 ACTAAAATAATATAAAGAAAT
* * *
5653881 AAAATACAAAAATAATATATTTT-AAAAATAATATATGAAAAAAATACGAATAAAGTGCTAAAAT
1 AAAATACGAAAATAATATATTTTAAAAAATAAGATACGAAAAAAATACGAATAAAGTGCTAAAAT
* * *
5653945 CAGGGTTATTTATTAAAAAAATATAAAAAAATACTTAAATAATACATTTGAAATATTATGTACTA
66 CAGGGTTATTTATT--AAAAATATAAAAAAACACTTAAATAATACATTTGAAACATTATTTACTA
5654010 AAATAATATAAAGAAAT
129 AAATAATATAAAGAAAT
*
5654027 AAAATACGAAAATAATATATTTTAAAAAATAAGATATGAAAAAAATACGAATAAAGTGCTAAAAT
1 AAAATACGAAAATAATATATTTTAAAAAATAAGATACGAAAAAAATACGAATAAAGTGCTAAAAT
*
5654092 CAGGGTTATTTATTAAAAAAATATAAAAAAACACTTAAATAATACAATTGAAACATTATTTACTA
66 CAGGGTTATTTATT--AAAAATATAAAAAAACACTTAAATAATACATTTGAAACATTATTTACTA
5654157 AAATAATATAAAGAAAT
129 AAATAATATAAAGAAAT
* * *
5654174 AAAATACAAAAATAATATATTTTAAAAAATAAGATACGAAAATAAAAAAATACGAAAAAAGTGCC
1 AAAATACGAAAATAATATATTTTAAAAAATAAGATACG-----AAAAAAATACGAATAAAGTGCT
* *
5654239 AAAATCAGGGTTATTTATTAAATTAATATAAAAAAACACTTACATAATACATTTGAAACATTTTT
61 AAAATCAGGGTTATTTATTAAA--AATATAAAAAAACACTTAAATAATACATTTGAAACATTATT
*
5654304 TGCTAAAATAATATAAA-AAAT
124 TACTAAAATAATATAAAGAAAT
*
5654325 AATATACGAAAATA
1 AAAATACGAAAATA
5654339 TTTTACTTAT
Statistics
Matches: 806, Mismatches: 67, Indels: 61
0.86 0.07 0.07
Matches are distributed among these distances:
144 36 0.04
146 199 0.25
147 193 0.24
148 17 0.02
149 49 0.06
150 77 0.10
151 22 0.03
152 124 0.15
153 84 0.10
154 5 0.01
ACGTcount: A:0.56, C:0.06, G:0.08, T:0.29
Consensus pattern (145 bp):
AAAATACGAAAATAATATATTTTAAAAAATAAGATACGAAAAAAATACGAATAAAGTGCTAAAAT
CAGGGTTATTTATTAAAAATATAAAAAAACACTTAAATAATACATTTGAAACATTATTTACTAAA
ATAATATAAAGAAAT
Found at i:5653921 original size:13 final size:13
Alignment explanation
Indices: 5653863--5653926 Score: 58
Period size: 13 Copynumber: 4.7 Consensus size: 13
5653853 ATTTTTTGCT
*
5653863 AAAATAATATAAA
1 AAAATAATATATA
* *
5653876 AAAATAAAATACA
1 AAAATAATATATA
5653889 AAAATAATATATTTTA
1 AAAATAATATA---TA
5653905 AAAATAATATATGA
1 AAAATAATATAT-A
5653919 AAAA-AATA
1 AAAATAATA
5653927 CGAATAAAGT
Statistics
Matches: 43, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
13 26 0.60
14 5 0.12
16 12 0.28
ACGTcount: A:0.70, C:0.02, G:0.02, T:0.27
Consensus pattern (13 bp):
AAAATAATATATA
Found at i:5653923 original size:16 final size:15
Alignment explanation
Indices: 5653869--5653926 Score: 57
Period size: 16 Copynumber: 3.9 Consensus size: 15
5653859 TGCTAAAATA
5653869 ATATAAAAAAATAA-
1 ATATAAAAAAATAAT
*
5653883 A-ATACAAAAATAAT
1 ATATAAAAAAATAAT
**
5653897 ATATTTTAAAAATAAT
1 ATA-TAAAAAAATAAT
5653913 ATATGAAAAAAATA
1 ATAT-AAAAAAATA
5653927 CGAATAAAGT
Statistics
Matches: 35, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
13 11 0.31
14 2 0.06
15 2 0.06
16 20 0.57
ACGTcount: A:0.69, C:0.02, G:0.02, T:0.28
Consensus pattern (15 bp):
ATATAAAAAAATAAT
Found at i:5656303 original size:72 final size:72
Alignment explanation
Indices: 5656210--5656347 Score: 240
Period size: 72 Copynumber: 1.9 Consensus size: 72
5656200 AGTCCGAGCG
* *
5656210 ATCGCATTCACATTTGACTGATACTTCTTATCATCCGGATTTGGCAGGCAATGACTATTTCCCGG
1 ATCGCATTCACATTCGACTGATACTTCTTATCATCCGGATTTGGCAGGCAATGACAATTTCCCGG
5656275 GCTCGTC
66 GCTCGTC
* *
5656282 ATCGCATTCACATTCGGCTGATACTTCTTATCATCCGGATTTGGCGGGCAATGACAATTTCCCGG
1 ATCGCATTCACATTCGACTGATACTTCTTATCATCCGGATTTGGCAGGCAATGACAATTTCCCGG
5656347 G
66 G
5656348 ATCATCGGGG
Statistics
Matches: 62, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
72 62 1.00
ACGTcount: A:0.21, C:0.26, G:0.21, T:0.32
Consensus pattern (72 bp):
ATCGCATTCACATTCGACTGATACTTCTTATCATCCGGATTTGGCAGGCAATGACAATTTCCCGG
GCTCGTC
Found at i:5656921 original size:17 final size:17
Alignment explanation
Indices: 5656885--5656928 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
5656875 CTTTAAATAC
*
5656885 ATTACAACATTAATCTA
1 ATTAGAACATTAATCTA
5656902 ATTAGAACATTAAT-TAA
1 ATTAGAACATTAATCT-A
*
5656919 ATTGGAACAT
1 ATTAGAACAT
5656929 ACTATTACCG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
16 1 0.04
17 23 0.96
ACGTcount: A:0.48, C:0.11, G:0.07, T:0.34
Consensus pattern (17 bp):
ATTAGAACATTAATCTA
Found at i:5659876 original size:47 final size:47
Alignment explanation
Indices: 5659812--5659922 Score: 154
Period size: 47 Copynumber: 2.4 Consensus size: 47
5659802 GACATTGAGT
*
5659812 CGATG-AGACACTATGTGT-CGACTACTGTTAAAGTTCCGGATTTGTTC
1 CGATGAAG-CACTATGTGTACGA-TAATGTTAAAGTTCCGGATTTGTTC
* * *
5659859 CGATGAAGTACTTTGTGTACTATAATGTTAAAGTTCCGGATTTGTTC
1 CGATGAAGCACTATGTGTACGATAATGTTAAAGTTCCGGATTTGTTC
5659906 CGATGAAGCACTATGTG
1 CGATGAAGCACTATGTG
5659923 CTTATCCCGG
Statistics
Matches: 56, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
47 52 0.93
48 4 0.07
ACGTcount: A:0.25, C:0.16, G:0.23, T:0.35
Consensus pattern (47 bp):
CGATGAAGCACTATGTGTACGATAATGTTAAAGTTCCGGATTTGTTC
Found at i:5667102 original size:47 final size:47
Alignment explanation
Indices: 5667038--5667148 Score: 154
Period size: 47 Copynumber: 2.4 Consensus size: 47
5667028 GACATTGAGT
*
5667038 CGATG-AGACACTATGTGT-CGACTACTGTTAAAGTTCCGGATTTGTTC
1 CGATGAAG-CACTATGTGTACGA-TAATGTTAAAGTTCCGGATTTGTTC
* * *
5667085 CGATGAAGTACTTTGTGTACTATAATGTTAAAGTTCCGGATTTGTTC
1 CGATGAAGCACTATGTGTACGATAATGTTAAAGTTCCGGATTTGTTC
5667132 CGATGAAGCACTATGTG
1 CGATGAAGCACTATGTG
5667149 CTTATCCCGG
Statistics
Matches: 56, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
47 52 0.93
48 4 0.07
ACGTcount: A:0.25, C:0.16, G:0.23, T:0.35
Consensus pattern (47 bp):
CGATGAAGCACTATGTGTACGATAATGTTAAAGTTCCGGATTTGTTC
Found at i:5671321 original size:23 final size:25
Alignment explanation
Indices: 5671291--5671349 Score: 77
Period size: 26 Copynumber: 2.4 Consensus size: 25
5671281 AATAATAATA
* *
5671291 ACTAACAATAAT-TATGG-TTTTTT
1 ACTAACAATAATACAAGGATTTTTT
5671314 ACTAACAATAATAACAAGGATTTTTT
1 ACTAACAATAAT-ACAAGGATTTTTT
5671340 ACTAACAATA
1 ACTAACAATA
5671350 TTAATAACTA
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
23 12 0.39
25 3 0.10
26 16 0.52
ACGTcount: A:0.44, C:0.12, G:0.07, T:0.37
Consensus pattern (25 bp):
ACTAACAATAATACAAGGATTTTTT
Found at i:5671686 original size:20 final size:19
Alignment explanation
Indices: 5671656--5671705 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 19
5671646 CCCATTTTTT
5671656 ATTTTTATTTTTCGTTTTCA
1 ATTTTT-TTTTTCGTTTTCA
* *
5671676 GTGTTTTTTTTTCTTTTTCA
1 AT-TTTTTTTTTCGTTTTCA
5671696 ATTTTTTTTT
1 ATTTTTTTTT
5671706 ACTGTTGAGG
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
19 8 0.31
20 14 0.54
21 4 0.15
ACGTcount: A:0.10, C:0.08, G:0.06, T:0.76
Consensus pattern (19 bp):
ATTTTTTTTTTCGTTTTCA
Found at i:5677843 original size:17 final size:18
Alignment explanation
Indices: 5677821--5677865 Score: 56
Period size: 20 Copynumber: 2.4 Consensus size: 18
5677811 AATAACTAAG
5677821 ATAAATAAA-ATAGAACA
1 ATAAATAAATATAGAACA
*
5677838 ATAAATTAAATTTTAGAACA
1 ATAAA-TAAA-TATAGAACA
5677858 ATAAATAA
1 ATAAATAA
5677866 TAAAATAAAG
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
17 5 0.21
18 4 0.17
19 3 0.12
20 12 0.50
ACGTcount: A:0.64, C:0.04, G:0.04, T:0.27
Consensus pattern (18 bp):
ATAAATAAATATAGAACA
Found at i:5686238 original size:14 final size:15
Alignment explanation
Indices: 5686219--5686247 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
5686209 TTTTAAAATT
5686219 ATATAAAAA-TAATA
1 ATATAAAAATTAATA
5686233 ATATAAAAATTAATA
1 ATATAAAAATTAATA
5686248 CGGGCAGGCC
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:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (15 bp):
ATATAAAAATTAATA
Found at i:5688952 original size:13 final size:12
Alignment explanation
Indices: 5688938--5688972 Score: 54
Period size: 11 Copynumber: 2.9 Consensus size: 12
5688928 ATTTATAGTA
5688938 AAATTATATATT
1 AAATTATATATT
5688950 AAATT-TATATT
1 AAATTATATATT
5688961 AAATTCATATAT
1 AAATT-ATATAT
5688973 ATATATTAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
11 11 0.52
12 5 0.24
13 5 0.24
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (12 bp):
AAATTATATATT
Found at i:5688958 original size:11 final size:11
Alignment explanation
Indices: 5688928--5688970 Score: 50
Period size: 11 Copynumber: 3.7 Consensus size: 11
5688918 TACCAAGTTT
*
5688928 ATTTATAGTAAA
1 ATTTATA-TTAA
5688940 ATTATATATTAA
1 ATT-TATATTAA
5688952 ATTTATATTAA
1 ATTTATATTAA
*
5688963 ATTCATAT
1 ATTTATAT
5688971 ATATATATTA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
11 15 0.54
12 9 0.32
13 4 0.14
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (11 bp):
ATTTATATTAA
Found at i:5691689 original size:23 final size:24
Alignment explanation
Indices: 5691655--5691709 Score: 69
Period size: 23 Copynumber: 2.3 Consensus size: 24
5691645 ATCTCAATGC
* *
5691655 TTAAAGTAAAATT-TGTA-ATATT
1 TTAAATTAAAATTATGTATAAATT
5691677 TTAACATTAAAATTATGTATAAATT
1 TTAA-ATTAAAATTATGTATAAATT
5691702 TTAAATTA
1 TTAAATTA
5691710 TACAATTAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
22 4 0.14
23 8 0.29
24 8 0.29
25 8 0.29
ACGTcount: A:0.47, C:0.02, G:0.05, T:0.45
Consensus pattern (24 bp):
TTAAATTAAAATTATGTATAAATT
Found at i:5709925 original size:19 final size:19
Alignment explanation
Indices: 5709901--5709937 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
5709891 GAAGGTATAT
5709901 TATCATATATGGCCAAACC
1 TATCATATATGGCCAAACC
5709920 TATCATATATGGCCAAAC
1 TATCATATATGGCCAAAC
5709938 AATGGTTGGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.38, C:0.24, G:0.11, T:0.27
Consensus pattern (19 bp):
TATCATATATGGCCAAACC
Found at i:5711078 original size:26 final size:27
Alignment explanation
Indices: 5711028--5711081 Score: 76
Period size: 27 Copynumber: 2.0 Consensus size: 27
5711018 TCACACAATG
5711028 TAATATTAAAATATTTATATTTTAAAA
1 TAATATTAAAATATTTATATTTTAAAA
*
5711055 TAATTTTAAAATA-TTAT-TTATTAAAA
1 TAATATTAAAATATTTATATT-TTAAAA
5711081 T
1 T
5711082 TCAATCTCGT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
25 2 0.08
26 11 0.44
27 12 0.48
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (27 bp):
TAATATTAAAATATTTATATTTTAAAA
Found at i:5712977 original size:277 final size:276
Alignment explanation
Indices: 5712483--5713029 Score: 995
Period size: 277 Copynumber: 2.0 Consensus size: 276
5712473 TCATCAATTT
5712483 TTTTTACTAAGAGATAGTTAATTTTTAGCAAAGAAAGGTTGAAGCTGTCAGACAGCAGAATAGGG
1 TTTTTACTAAGAGATAGTTAATTTTTAGCAAAGAAAGGTTGAAGCTGTCAGACAGCAGAATAGGG
* *
5712548 GTAAGTTTGAAGATTTTACTGTACTTATTGGCTGAACCAAAATTTCTGAAAATTTTATGGTAGAA
66 GTAAGTTTGAAGATTTTACTGTACTTATTGGCTGAACCAAAAATTCTAAAAATTTTATGGTAGAA
* *
5712613 AGGTATTTGAGTATAGTTTCAGAAACATCAAGCTTTTTTTAATTTGGAATTCTGTATCTTGATAT
131 AGGTATTTGAGTATAGTTTCAGAAACATCAAGCTTTTTTTAATTTGGAATCCTGTATCTTGAGAT
5712678 ATAAATAATTTAGTGACTACGACTCAAGTAGATAGTTTTGAATGAACTATAAAATAATAGTGGAA
196 ATAAATAATTTAGTGACTACGACTCAAGTAGATAGTTTTGAATGAACTAT-AAATAATAGTGGAA
5712743 TTATATAGAATCCAAAG
260 TTATATAGAATCCAAAG
* * *
5712760 TTTTTACTAATAGATTGTTAATTTTTAGCAAAGAAAGGTTGAAGCTGTCAGACAGCATAATAGGG
1 TTTTTACTAAGAGATAGTTAATTTTTAGCAAAGAAAGGTTGAAGCTGTCAGACAGCAGAATAGGG
5712825 GTAAGTTTGAAGATTTTACTGTACTTATTGGCTGAACCAAAAATTCTAAAAATTTTATGGTAGAA
66 GTAAGTTTGAAGATTTTACTGTACTTATTGGCTGAACCAAAAATTCTAAAAATTTTATGGTAGAA
*
5712890 AGGTATTTGAGTCTAGTTTCAGAAACATCAAGCTTTTTTTAATTTGGAATCCTGTATCTTGAGAT
131 AGGTATTTGAGTATAGTTTCAGAAACATCAAGCTTTTTTTAATTTGGAATCCTGTATCTTGAGAT
*
5712955 ATAAATAATTTAGTGACTACGACTCAAGTAGATAGTTTTGAATGAATTATAAATAATAGTGGAAT
196 ATAAATAATTTAGTGACTACGACTCAAGTAGATAGTTTTGAATGAACTATAAATAATAGTGGAAT
*
5713020 TGTATAGAAT
261 TATATAGAAT
5713030 GTTACATATG
Statistics
Matches: 260, Mismatches: 10, Indels: 1
0.96 0.04 0.00
Matches are distributed among these distances:
276 24 0.09
277 236 0.91
ACGTcount: A:0.36, C:0.09, G:0.19, T:0.36
Consensus pattern (276 bp):
TTTTTACTAAGAGATAGTTAATTTTTAGCAAAGAAAGGTTGAAGCTGTCAGACAGCAGAATAGGG
GTAAGTTTGAAGATTTTACTGTACTTATTGGCTGAACCAAAAATTCTAAAAATTTTATGGTAGAA
AGGTATTTGAGTATAGTTTCAGAAACATCAAGCTTTTTTTAATTTGGAATCCTGTATCTTGAGAT
ATAAATAATTTAGTGACTACGACTCAAGTAGATAGTTTTGAATGAACTATAAATAATAGTGGAAT
TATATAGAATCCAAAG
Found at i:5715016 original size:35 final size:35
Alignment explanation
Indices: 5714917--5715074 Score: 129
Period size: 35 Copynumber: 4.5 Consensus size: 35
5714907 CATGGAAAAG
*
5714917 TGTGAAACGTAAGGTAT-AGTATTAACCATACCGAGT
1 TGTGAAACAT-AGGTATGA-TATTAACCATACCGAGT
* * * *
5714953 CGTGAAACATAGGTATGGTATCAACCATACTGAGT
1 TGTGAAACATAGGTATGATATTAACCATACCGAGT
* * **
5714988 TGTGAAACACAGGTATGATATTATCCATACTTAGT
1 TGTGAAACATAGGTATGATATTAACCATACCGAGT
** * * * **
5715023 TAAGAACCGTAGGTATGACATTTCCCATACCGAGT
1 TGTGAAACATAGGTATGATATTAACCATACCGAGT
**
5715058 TGTGAAATGTAGGTATG
1 TGTGAAACATAGGTATG
5715075 GCATTTCGAT
Statistics
Matches: 96, Mismatches: 25, Indels: 3
0.77 0.20 0.02
Matches are distributed among these distances:
35 88 0.92
36 8 0.08
ACGTcount: A:0.34, C:0.15, G:0.22, T:0.29
Consensus pattern (35 bp):
TGTGAAACATAGGTATGATATTAACCATACCGAGT
Found at i:5716207 original size:24 final size:24
Alignment explanation
Indices: 5716168--5716213 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
5716158 CTTGTAACCC
*
5716168 TGTTACGATGATGGATGTGGGTCA
1 TGTTACGATGACGGATGTGGGTCA
*
5716192 TGTTACGGTGACGGATGTGGGT
1 TGTTACGATGACGGATGTGGGT
5716214 TAAGGGTGTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.17, C:0.09, G:0.41, T:0.33
Consensus pattern (24 bp):
TGTTACGATGACGGATGTGGGTCA
Found at i:5717189 original size:35 final size:35
Alignment explanation
Indices: 5717149--5717273 Score: 126
Period size: 35 Copynumber: 3.5 Consensus size: 35
5717139 GATCCGATTA
*
5717149 ACCATACCTACGTTTCGCAACTCAATAT-GATTAAT
1 ACCATACCTACGTTTCACAACTCAATATGGA-TAAT
** *
5717184 ACCATACCTACGTTTCACAACTCGGTATGGATGAT
1 ACCATACCTACGTTTCACAACTCAATATGGATAAT
* * * *
5717219 ACCATACCTACGTTTTATAACTCAGTATGGTTAAT
1 ACCATACCTACGTTTCACAACTCAATATGGATAAT
** *
5717254 ATTATACCTTATGTTTCACA
1 ACCATACC-TACGTTTCACA
5717274 CTTTGCCATG
Statistics
Matches: 74, Mismatches: 14, Indels: 3
0.81 0.15 0.03
Matches are distributed among these distances:
35 64 0.86
36 10 0.14
ACGTcount: A:0.31, C:0.23, G:0.11, T:0.34
Consensus pattern (35 bp):
ACCATACCTACGTTTCACAACTCAATATGGATAAT
Found at i:5717293 original size:70 final size:69
Alignment explanation
Indices: 5717148--5717293 Score: 150
Period size: 70 Copynumber: 2.1 Consensus size: 69
5717138 TGATCCGATT
* **
5717148 AACCATACCTACGTTTCGCAACTCAATATGATTAATACCATACCTACGTTTCACAACTCGGTATG
1 AACCATACCTACGTTTCACAACTCAATATGATTAATACCATACCTACGTTTCACAACTCGCCATG
*
5717213 GATG
66 GATC
* * * * ** * *
5717217 ATACCATACCTACGTTTTATAACTCAGTATGGTTAATATTATACCTTATGTTTCAC-ACTTTGCC
1 A-ACCATACCTACGTTTCACAACTCAATATGATTAATACCATACC-TACGTTTCACAAC-TCGCC
5717281 ATGGATC
63 ATGGATC
5717288 AACCAT
1 AACCAT
5717294 GGTCTTATCC
Statistics
Matches: 62, Mismatches: 12, Indels: 5
0.78 0.15 0.06
Matches are distributed among these distances:
69 1 0.02
70 43 0.69
71 18 0.29
ACGTcount: A:0.31, C:0.24, G:0.12, T:0.34
Consensus pattern (69 bp):
AACCATACCTACGTTTCACAACTCAATATGATTAATACCATACCTACGTTTCACAACTCGCCATG
GATC
Found at i:5719441 original size:5 final size:5
Alignment explanation
Indices: 5719415--5719472 Score: 62
Period size: 5 Copynumber: 10.8 Consensus size: 5
5719405 ATGTGTTAAA
* *
5719415 ATATAT ATATT AAATT ATTATT ATATT ATAGT ATATT ATATTAT ATATT
1 ATAT-T ATATT ATATT A-TATT ATATT ATATT ATATT ATA-T-T ATATT
5719464 ATATT ATAT
1 ATATT ATAT
5719473 AAATAAGCAA
Statistics
Matches: 45, Mismatches: 4, Indels: 7
0.80 0.07 0.12
Matches are distributed among these distances:
5 31 0.69
6 10 0.22
7 4 0.09
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (5 bp):
ATATT
Found at i:5719451 original size:10 final size:9
Alignment explanation
Indices: 5719416--5719473 Score: 61
Period size: 8 Copynumber: 6.7 Consensus size: 9
5719406 TGTGTTAAAA
5719416 TATATATAT
1 TATATATAT
*
5719425 TAAAT-TAT
1 TATATATAT
5719433 TAT-TATAT
1 TATATATAT
5719441 TATAGTATAT
1 TATA-TATAT
5719451 TATAT-TA-
1 TATATATAT
5719458 TATATTATAT
1 TATA-TATAT
5719468 TATATA
1 TATATA
5719474 AATAAGCAAA
Statistics
Matches: 41, Mismatches: 2, Indels: 12
0.75 0.04 0.22
Matches are distributed among these distances:
7 5 0.12
8 14 0.34
9 9 0.22
10 13 0.32
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (9 bp):
TATATATAT
Found at i:5719463 original size:12 final size:12
Alignment explanation
Indices: 5719418--5719473 Score: 69
Period size: 12 Copynumber: 4.5 Consensus size: 12
5719408 TGTTAAAATA
*
5719418 TATATATTAAAT
1 TATATATTATAT
5719430 TAT-TATTATATT
1 TATATATTATA-T
5719442 ATAGTATATTATAT
1 -TA-TATATTATAT
5719456 TATATATTATAT
1 TATATATTATAT
5719468 TATATA
1 TATATA
5719474 AATAAGCAAA
Statistics
Matches: 39, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
11 6 0.15
12 20 0.51
13 4 0.10
14 2 0.05
15 7 0.18
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (12 bp):
TATATATTATAT
Found at i:5720813 original size:18 final size:19
Alignment explanation
Indices: 5720792--5720830 Score: 62
Period size: 18 Copynumber: 2.1 Consensus size: 19
5720782 ATATAGATAT
5720792 ATATATATTGAATA-TTGA
1 ATATATATTGAATATTTGA
*
5720810 ATATATATTGATTATTTGA
1 ATATATATTGAATATTTGA
5720829 AT
1 AT
5720831 TGAATTGAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 13 0.68
19 6 0.32
ACGTcount: A:0.41, C:0.00, G:0.10, T:0.49
Consensus pattern (19 bp):
ATATATATTGAATATTTGA
Found at i:5721180 original size:39 final size:39
Alignment explanation
Indices: 5721070--5721204 Score: 112
Period size: 39 Copynumber: 3.4 Consensus size: 39
5721060 GACCTCGAGT
* * * *
5721070 CGATGAGACACTGGGTGTCACTATATTTCTTCGGATAGATT
1 CGATGAGACACTGGGTGTCA-AATATTACTTCGGCTAG-TC
** ** * *
5721111 CGATGAGGTACTGGGTACCAACT-TTACTTCGGCTAGGC
1 CGATGAGACACTGGGTGTCAAATATTACTTCGGCTAGTC
* *
5721149 CGATGAGACACTGGGTGTCAAATATTGCTTCGAACTA-TC
1 CGATGAGACACTGGGTGTCAAATATTACTTCG-GCTAGTC
*
5721188 CGATGAGGCACTGGGTG
1 CGATGAGACACTGGGTG
5721205 CCATATTGGT
Statistics
Matches: 73, Mismatches: 19, Indels: 6
0.74 0.19 0.06
Matches are distributed among these distances:
38 18 0.25
39 35 0.48
40 4 0.05
41 16 0.22
ACGTcount: A:0.24, C:0.20, G:0.28, T:0.28
Consensus pattern (39 bp):
CGATGAGACACTGGGTGTCAAATATTACTTCGGCTAGTC
Found at i:5721348 original size:18 final size:19
Alignment explanation
Indices: 5721327--5721367 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
5721317 AATGAAATGA
5721327 GAAATTGA-AT-TGAGAATT
1 GAAATTGAGATATGAG-ATT
5721345 GAAATTGAGATATGAGATT
1 GAAATTGAGATATGAGATT
5721364 GAAA
1 GAAA
5721368 ACATGAACCA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 8 0.38
19 9 0.43
20 4 0.19
ACGTcount: A:0.46, C:0.00, G:0.24, T:0.29
Consensus pattern (19 bp):
GAAATTGAGATATGAGATT
Found at i:5725501 original size:14 final size:14
Alignment explanation
Indices: 5725482--5725511 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
5725472 TTAAACCTAG
5725482 ACCAATCCAAATCA
1 ACCAATCCAAATCA
*
5725496 ACCAATCCAATTCA
1 ACCAATCCAAATCA
5725510 AC
1 AC
5725512 ATATGTTAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.47, C:0.37, G:0.00, T:0.17
Consensus pattern (14 bp):
ACCAATCCAAATCA
Found at i:5728013 original size:22 final size:24
Alignment explanation
Indices: 5727988--5728035 Score: 57
Period size: 23 Copynumber: 2.1 Consensus size: 24
5727978 ATATTTATGA
5727988 AAAAATT-AAGAAATA-ATTAAAT
1 AAAAATTCAAGAAATAGATTAAAT
**
5728010 -AAAATTCAATTAATAGATTAAAT
1 AAAAATTCAAGAAATAGATTAAAT
5728033 AAA
1 AAA
5728036 CTAAATACAT
Statistics
Matches: 21, Mismatches: 2, Indels: 4
0.78 0.07 0.15
Matches are distributed among these distances:
21 6 0.29
22 6 0.29
23 7 0.33
24 2 0.10
ACGTcount: A:0.65, C:0.02, G:0.04, T:0.29
Consensus pattern (24 bp):
AAAAATTCAAGAAATAGATTAAAT
Found at i:5729534 original size:23 final size:23
Alignment explanation
Indices: 5729499--5729560 Score: 67
Period size: 23 Copynumber: 2.8 Consensus size: 23
5729489 TATTCATTTA
* *
5729499 ATTAAAAAT-TTTATAATTTAATT
1 ATTAAAATTATTTAAAATTT-ATT
*
5729522 ATT-AAATTATTTAAAATTTTTT
1 ATTAAAATTATTTAAAATTTATT
5729544 ATTAAAATTA-TTAAAAT
1 ATTAAAATTATTTAAAAT
5729561 ATTAGAGTTG
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
22 16 0.47
23 18 0.53
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (23 bp):
ATTAAAATTATTTAAAATTTATT
Found at i:5729539 original size:31 final size:31
Alignment explanation
Indices: 5729503--5729563 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 31
5729493 CATTTAATTA
* *
5729503 AAAATTTTATAATT-TAATTATTAAATTATTT
1 AAAATTTT-TAATTAAAATTATTAAAATATTT
*
5729534 AAAATTTTTTATTAAAATTATTAAAATATT
1 AAAATTTTTAATTAAAATTATTAAAATATT
5729564 AGAGTTGATA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
30 4 0.15
31 22 0.85
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (31 bp):
AAAATTTTTAATTAAAATTATTAAAATATTT
Found at i:5731429 original size:20 final size:21
Alignment explanation
Indices: 5731394--5731432 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
5731384 AAATAATCAC
*
5731394 TTTTATTTATTTTATATTATA
1 TTTTAGTTATTTTATATTATA
5731415 TTTTAGTTA-TTTATATTA
1 TTTTAGTTATTTTATATTA
5731433 ATGTATTGTA
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:0.28, C:0.00, G:0.03, T:0.69
Consensus pattern (21 bp):
TTTTAGTTATTTTATATTATA
Found at i:5733430 original size:16 final size:16
Alignment explanation
Indices: 5733406--5733436 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
5733396 TTATTTTAAG
5733406 TTTAAATTTTGATTTA
1 TTTAAATTTTGATTTA
*
5733422 TTTATATTTTGATTT
1 TTTAAATTTTGATTT
5733437 TTAATATGTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.26, C:0.00, G:0.06, T:0.68
Consensus pattern (16 bp):
TTTAAATTTTGATTTA
Found at i:5745967 original size:25 final size:25
Alignment explanation
Indices: 5745933--5746090 Score: 225
Period size: 25 Copynumber: 6.4 Consensus size: 25
5745923 GACTTCAGCA
5745933 TGCTCTCTGATATTTAGCACGCCAG
1 TGCTCTCTGATATTTAGCACGCCAG
****
5745958 TGCTCTCTG--A-TTAGCACATTTG
1 TGCTCTCTGATATTTAGCACGCCAG
5745980 TGCTCTCTGATATTTAGCACGCCAG
1 TGCTCTCTGATATTTAGCACGCCAG
5746005 TGCTCTCTGATATTTAGCACGCCAG
1 TGCTCTCTGATATTTAGCACGCCAG
*
5746030 TGCTCTCTGAT-TACTAGCACGCCAG
1 TGCTCTCTGATAT-TTAGCACGCCAG
*
5746055 TGCTCTCTGATATTTAGCACGTCAG
1 TGCTCTCTGATATTTAGCACGCCAG
5746080 TGCTCTCTGAT
1 TGCTCTCTGAT
5746091 TAGCACATTT
Statistics
Matches: 117, Mismatches: 11, Indels: 10
0.85 0.08 0.07
Matches are distributed among these distances:
22 17 0.15
23 1 0.01
24 2 0.02
25 96 0.82
26 1 0.01
ACGTcount: A:0.19, C:0.27, G:0.20, T:0.34
Consensus pattern (25 bp):
TGCTCTCTGATATTTAGCACGCCAG
Found at i:5745974 original size:22 final size:23
Alignment explanation
Indices: 5745933--5746132 Score: 181
Period size: 25 Copynumber: 8.4 Consensus size: 23
5745923 GACTTCAGCA
5745933 TGCTCTCTGATATTTAGCACGCCAG
1 TGCTCTCTG--ATTTAGCACGCCAG
****
5745958 TGCTCTCTGA-TTAGCACATTTG
1 TGCTCTCTGATTTAGCACGCCAG
5745980 TGCTCTCTGATATTTAGCACGCCAG
1 TGCTCTCTG--ATTTAGCACGCCAG
5746005 TGCTCTCTGATATTTAGCACGCCAG
1 TGCTCTCTG--ATTTAGCACGCCAG
5746030 TGCTCTCTGATTACTAGCACGCCAG
1 TGCTCTCTGATT--TAGCACGCCAG
*
5746055 TGCTCTCTGATATTTAGCACGTCAG
1 TGCTCTCTG--ATTTAGCACGCCAG
****
5746080 TGCTCTCTGA-TTAGCACATTTG
1 TGCTCTCTGATTTAGCACGCCAG
* **
5746102 TGCTCTCTG-TATAGCACTTCAG
1 TGCTCTCTGATTTAGCACGCCAG
5746124 TGCTCTCTG
1 TGCTCTCTG
5746133 TTCATTAGTG
Statistics
Matches: 151, Mismatches: 16, Indels: 19
0.81 0.09 0.10
Matches are distributed among these distances:
22 52 0.34
23 5 0.03
24 1 0.01
25 90 0.60
27 3 0.02
ACGTcount: A:0.18, C:0.27, G:0.20, T:0.35
Consensus pattern (23 bp):
TGCTCTCTGATTTAGCACGCCAG
Found at i:5748180 original size:5 final size:5
Alignment explanation
Indices: 5748170--5748198 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
5748160 TAGTCTGAAA
5748170 AAAAT AAAAT AAAAT AAAAT AAAA- AAAAT
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT
5748199 TGCTACATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
4 4 0.17
5 19 0.83
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (5 bp):
AAAAT
Found at i:5759045 original size:2 final size:2
Alignment explanation
Indices: 5759038--5759130 Score: 179
Period size: 2 Copynumber: 47.0 Consensus size: 2
5759028 TTAATAACAC
5759038 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
5759080 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
5759122 GA GA G- GA GA
1 GA GA GA GA GA
5759131 CTTACCAGGG
Statistics
Matches: 90, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
1 1 0.01
2 89 0.99
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:5759705 original size:13 final size:14
Alignment explanation
Indices: 5759687--5759715 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
5759677 ATGGTTAATC
5759687 TTTTA-TTTTATTT
1 TTTTATTTTTATTT
5759700 TTTTATTTTTATTT
1 TTTTATTTTTATTT
5759714 TT
1 TT
5759716 AAAATTTACT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 5 0.33
14 10 0.67
ACGTcount: A:0.14, C:0.00, G:0.00, T:0.86
Consensus pattern (14 bp):
TTTTATTTTTATTT
Found at i:5760937 original size:127 final size:125
Alignment explanation
Indices: 5760570--5761135 Score: 650
Period size: 127 Copynumber: 4.5 Consensus size: 125
5760560 GACATAAGGA
* * * * * * *
5760570 AATATTTCGTGTTTGGGAGTTCGAGG-GGTCGTGCCCAATCGTGCTGGGTTTCGATTTTTCGTTC
1 AATATTTCGTATTTGGAAGTTTG-GGAAGTCGTGCCCAATCGTGCTGGGTTTCAATTTTCCATTC
* * * * * *
5760634 AGCTAAAATACGGAATATCCTTTGGAAATTTCGTCCATGTTTTTTTTAAAATTAAAATGAGGC
65 AACTAAAATACGAAATATCCTTTTGAAATTTCATCCAT-ATTTTCTTAAAA-TAAAATGAGGC
* * * * *
5760697 AATATTTTGTATTTGGGGAGTTTGAG-AGATCGTGCCCAATCGTGCTGGGTTTCATTTTTTTCAT
1 AATATTTCGTATTT-GGAAGTTTGGGAAG-TCGTGCCCAATCGTGCTGGGTTTCA-ATTTTCCAT
* * * * * *
5760761 TCGACTAAGATATGGAATATCCTTTTTTTGAAATTTCATCCACATTTTCTTAAAATAAAACGAGG
63 TCAACTAAAATACGAAATATCC---TTTTGAAATTTCATCCATATTTTCTTAAAATAAAATGAGG
5760826 C
125 C
* * *
5760827 AATATTTCGTGTTTGGAAGTTTGGGAAGTCGTGCCCAATCGTGCTGGGCTTCAATTTTCCATTCG
1 AATATTTCGTATTTGGAAGTTTGGGAAGTCGTGCCCAATCGTGCTGGGTTTCAATTTTCCATTCA
* *
5760892 GCTAAAATATGAAATATCCTTTTTTGAAATTTCATCCATATTTTCTTAAAATAAAATGAGGC
66 ACTAAAATACGAAATATCC--TTTTGAAATTTCATCCATATTTTCTTAAAATAAAATGAGGC
*
5760954 AATATTTCGTATTTGGAAGTTTGGGAAGTCGTGCCCAATCGTGCTGGGCTTCAATTTTCCATTCA
1 AATATTTCGTATTTGGAAGTTTGGGAAGTCGTGCCCAATCGTGCTGGGTTTCAATTTTCCATTCA
* * * *
5761019 ACTAAAATACAAAATATCCTTTTGAAATTTCATCCATGTTTTCTCAAATTAAAATGAGGC
66 ACTAAAATACGAAATATCCTTTTGAAATTTCATCCATATTTTCTTAAAATAAAATGAGGC
* * * ** * *
5761079 AATGTTTCGTATTTGGAAATTCGATAAATCGTGCCCAATCGTGCTGGGTTTCGATTT
1 AATATTTCGTATTTGGAAGTTTGGGAAGTCGTGCCCAATCGTGCTGGGTTTCAATTT
5761136 ATCGTTTGGG
Statistics
Matches: 386, Mismatches: 46, Indels: 16
0.86 0.10 0.04
Matches are distributed among these distances:
125 87 0.23
127 134 0.35
128 58 0.15
129 58 0.15
130 24 0.06
131 10 0.03
132 15 0.04
ACGTcount: A:0.27, C:0.16, G:0.19, T:0.38
Consensus pattern (125 bp):
AATATTTCGTATTTGGAAGTTTGGGAAGTCGTGCCCAATCGTGCTGGGTTTCAATTTTCCATTCA
ACTAAAATACGAAATATCCTTTTGAAATTTCATCCATATTTTCTTAAAATAAAATGAGGC
Found at i:5761073 original size:257 final size:250
Alignment explanation
Indices: 5760570--5761135 Score: 642
Period size: 257 Copynumber: 2.2 Consensus size: 250
5760560 GACATAAGGA
* * * *
5760570 AATATTTCGTGTTTGGGAGTTCGAGG-GGTCGTGCCCAATCGTGCTGGGTTTCGATTTTTCGTTC
1 AATATTTCGTGTTTGGAAGTTCG-GGAAGTCGTGCCCAATCGTGCTGGGTTTCGATTTTCCATTC
* * * *
5760634 AGCTAAAATACGGAATATCCTTTGGAAATTTCGTCCATGTTTTTTTTAAAATTAAAATGAGGCAA
65 AGCTAAAATACGAAATATCCTTTGGAAATTTCATCCATGATTTTCTTAAAATTAAAATGAGGCAA
* * * * * *
5760699 TATTTTGTATTTGGGGAGTTTGAGAGATCGTGCCCAATCGTGCTGGGTTTCATTTTTTTCATTCG
130 TATTTCGTATTTGGGAAGTTTGAGAGATCGTGCCCAATCGTGCTGGGCTTCATATTTTCCATTCA
* ***
5760764 ACTAAGATATGGAATATCCTTTTTTTGAAATTTCATCCACATTTTCTTAAAATAAAACGAGGC
195 ACTAAAATACAAAATATCC--TTTTTGAAATTTCATCCACATTTTCTTAAAAT-----GAGGC
* * * *
5760827 AATATTTCGTGTTTGGAAGTTTGGGAAGTCGTGCCCAATCGTGCTGGGCTTCAATTTTCCATTCG
1 AATATTTCGTGTTTGGAAGTTCGGGAAGTCGTGCCCAATCGTGCTGGGTTTCGATTTTCCATTCA
* *
5760892 GCTAAAATATGAAATATCCTTTTTTGAAATTTCATCCAT-ATTTTCTTAAAA-TAAAATGAGGCA
66 GCTAAAATACGAAATATCC--TTTGGAAATTTCATCCATGATTTTCTTAAAATTAAAATGAGGCA
*
5760955 ATATTTCGTATTT-GGAAGTTTGGGA-AGTCGTGCCCAATCGTGCTGGGCTTCA-ATTTTCCATT
129 ATATTTCGTATTTGGGAAGTTTGAGAGA-TCGTGCCCAATCGTGCTGGGCTTCATATTTTCCATT
**
5761017 CAACTAAAATACAAAATATCC-TTTTGAAATTTCATCCATGTTTTCTCAAATTAAAATGAGGC
193 CAACTAAAATACAAAATATCCTTTTTGAAATTTCATCCA-CATTT-TC---TTAAAATGAGGC
* * * ** *
5761079 AATGTTTCGTATTTGGAAATTCGATAAATCGTGCCCAATCGTGCTGGGTTTCGATTT
1 AATATTTCGTGTTTGGAAGTTCGGGAAGTCGTGCCCAATCGTGCTGGGTTTCGATTT
5761136 ATCGTTTGGG
Statistics
Matches: 264, Mismatches: 36, Indels: 23
0.82 0.11 0.07
Matches are distributed among these distances:
252 70 0.27
253 3 0.01
254 2 0.01
255 25 0.09
256 36 0.14
257 102 0.39
258 10 0.04
259 16 0.06
ACGTcount: A:0.27, C:0.16, G:0.19, T:0.38
Consensus pattern (250 bp):
AATATTTCGTGTTTGGAAGTTCGGGAAGTCGTGCCCAATCGTGCTGGGTTTCGATTTTCCATTCA
GCTAAAATACGAAATATCCTTTGGAAATTTCATCCATGATTTTCTTAAAATTAAAATGAGGCAAT
ATTTCGTATTTGGGAAGTTTGAGAGATCGTGCCCAATCGTGCTGGGCTTCATATTTTCCATTCAA
CTAAAATACAAAATATCCTTTTTGAAATTTCATCCACATTTTCTTAAAATGAGGC
Found at i:5761168 original size:252 final size:255
Alignment explanation
Indices: 5760570--5761168 Score: 651
Period size: 252 Copynumber: 2.3 Consensus size: 255
5760560 GACATAAGGA
* * * *** *
5760570 AATATTTCGTGTTTGGGAGTTCGAGGGGTCGTGCCCAATCGTGCTGGGTTTCGATTTTTCGTTCA
1 AATATTTCGTATTTGGAAATTCGAGAAATCGTGCCCAATCGTGCTGGGTTTCGA-TTTTCGTTCG
* * * * * *
5760635 GCTAAAATA-CGGAATATC-CTTTGGAAATTTCGTCCATGTTTTTTTTAAAATTAAAATGAGGCA
65 GCTAAAATAGC-AAATATCTTTTTTGAAATTTCATCCATGATTTTCTTAAAATTAAAATGAGGCA
* * * * *
5760698 ATATTTTGTATTTGGGGAGTTTGAGAGATCGTGCCCAATCGTGCTGGGTTTCATTTTTTTCATTC
129 ATATTTCGTATTTGGGAAGTTTGAGAGATCGTGCCCAATCGTGCTGGGCTTCATATTTTCCATTC
* * *** *
5760763 GACTAAGATATGGAATATCCTTTTTTTGAAATTTCATCCACATTTTCTTAAAATAAAACGAGGC
194 AACTAAAATACAAAATATCC--TTTTTGAAATTTCATCCACATTTTCTCAAAATAAAACGAGGC
* * * * * * * *
5760827 AATATTTCGTGTTTGGAAGTTTGGGAAGTCGTGCCCAATCGTGCTGGGCTTCAATTTTCCATTCG
1 AATATTTCGTATTTGGAAATTCGAGAAATCGTGCCCAATCGTGCTGGGTTTCGATTTT-CGTTCG
5760892 GCTAAAATATG-AAATATCCTTTTTTGAAATTTCATCCAT-ATTTTCTTAAAA-TAAAATGAGGC
65 GCTAAAATA-GCAAATAT-CTTTTTTGAAATTTCATCCATGATTTTCTTAAAATTAAAATGAGGC
*
5760954 AATATTTCGTATTT-GGAAGTTTGGGA-AGTCGTGCCCAATCGTGCTGGGCTTCA-ATTTTCCAT
128 AATATTTCGTATTTGGGAAGTTTGAGAGA-TCGTGCCCAATCGTGCTGGGCTTCATATTTTCCAT
** * *
5761016 TCAACTAAAATACAAAATATCC-TTTTGAAATTTCATCCATGTTTTCTCAAATTAAAATGAGGC
192 TCAACTAAAATACAAAATATCCTTTTTGAAATTTCATCCACATTTTCTCAAAATAAAACGAGGC
* * *
5761079 AATGTTTCGTATTTGGAAATTCGATAAATCGTGCCCAATCGTGCTGGGTTTCGATTTATCGTTTG
1 AATATTTCGTATTTGGAAATTCGAGAAATCGTGCCCAATCGTGCTGGGTTTCGATTT-TCG-TTC
**
5761144 GGC-CGAATAGCCAAATATCTTTTTT
64 GGCTAAAATAG-CAAATATCTTTTTT
5761169 AAAAGTTTTA
Statistics
Matches: 288, Mismatches: 44, Indels: 25
0.81 0.12 0.07
Matches are distributed among these distances:
251 1 0.00
252 96 0.33
253 12 0.04
255 25 0.09
256 38 0.13
257 89 0.31
258 11 0.04
259 16 0.06
ACGTcount: A:0.27, C:0.16, G:0.19, T:0.38
Consensus pattern (255 bp):
AATATTTCGTATTTGGAAATTCGAGAAATCGTGCCCAATCGTGCTGGGTTTCGATTTTCGTTCGG
CTAAAATAGCAAATATCTTTTTTGAAATTTCATCCATGATTTTCTTAAAATTAAAATGAGGCAAT
ATTTCGTATTTGGGAAGTTTGAGAGATCGTGCCCAATCGTGCTGGGCTTCATATTTTCCATTCAA
CTAAAATACAAAATATCCTTTTTGAAATTTCATCCACATTTTCTCAAAATAAAACGAGGC
Found at i:5763622 original size:21 final size:21
Alignment explanation
Indices: 5763588--5763628 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
5763578 ATAATATATA
*
5763588 TAATATAAATATT-ATTATTT
1 TAATATAAACATTAATTATTT
5763608 TAATAATAAACATTAATTATT
1 TAAT-ATAAACATTAATTATT
5763629 AACATAACTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 4 0.22
21 8 0.44
22 6 0.33
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (21 bp):
TAATATAAACATTAATTATTT
Found at i:5776902 original size:39 final size:39
Alignment explanation
Indices: 5776848--5776926 Score: 140
Period size: 39 Copynumber: 2.0 Consensus size: 39
5776838 TTGGACATAC
*
5776848 AACAGAGTAGTGACTTAAATAAATTTTTTTAAATAGTTT
1 AACAGAATAGTGACTTAAATAAATTTTTTTAAATAGTTT
*
5776887 AACAGAATAGTGACTTAAATGAATTTTTTTAAATAGTTT
1 AACAGAATAGTGACTTAAATAAATTTTTTTAAATAGTTT
5776926 A
1 A
5776927 GTGACTTTTT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 38 1.00
ACGTcount: A:0.42, C:0.05, G:0.13, T:0.41
Consensus pattern (39 bp):
AACAGAATAGTGACTTAAATAAATTTTTTTAAATAGTTT
Found at i:5783106 original size:16 final size:15
Alignment explanation
Indices: 5783067--5783117 Score: 54
Period size: 16 Copynumber: 3.5 Consensus size: 15
5783057 TCTACAGATG
*
5783067 TTTTTAACAT-AATT
1 TTTTTTACATAAATT
5783081 TTTTTT--ATAAATT
1 TTTTTTACATAAATT
5783094 TATTTTTACATAAACTT
1 T-TTTTTACATAAA-TT
5783111 TTTTTTA
1 TTTTTTA
5783118 TTGGCATCGA
Statistics
Matches: 31, Mismatches: 1, Indels: 8
0.77 0.03 0.20
Matches are distributed among these distances:
12 2 0.06
13 5 0.16
14 10 0.32
16 11 0.35
17 3 0.10
ACGTcount: A:0.31, C:0.06, G:0.00, T:0.63
Consensus pattern (15 bp):
TTTTTTACATAAATT
Found at i:5785417 original size:19 final size:20
Alignment explanation
Indices: 5785383--5785421 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
5785373 ACATAATTAC
5785383 AATTATAAATAATATATTTT
1 AATTATAAATAATATATTTT
*
5785403 AATTATTAA-AATATATTTT
1 AATTATAAATAATATATTTT
5785422 CAGCACGATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 10 0.56
20 8 0.44
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (20 bp):
AATTATAAATAATATATTTT
Found at i:5788479 original size:16 final size:15
Alignment explanation
Indices: 5788437--5788494 Score: 53
Period size: 16 Copynumber: 3.5 Consensus size: 15
5788427 ATAAATTGTC
5788437 TTTTTATTTTTTTTACCT
1 TTTTTA-TTTTTTT--CT
*
5788455 TTTTGATTTTTTTCT
1 TTTTTATTTTTTTCT
*
5788470 TATTTTATTTTGTTTAT
1 T-TTTTATTTT-TTTCT
5788487 TTTTTATT
1 TTTTTATT
5788495 ATTAACTTTA
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
15 3 0.09
16 15 0.43
17 12 0.34
18 5 0.14
ACGTcount: A:0.12, C:0.05, G:0.03, T:0.79
Consensus pattern (15 bp):
TTTTTATTTTTTTCT
Found at i:5788545 original size:21 final size:22
Alignment explanation
Indices: 5788506--5788552 Score: 71
Period size: 21 Copynumber: 2.2 Consensus size: 22
5788496 TTAACTTTAA
5788506 AAAATTTGTAATGTATATTTTT
1 AAAATTTGTAATGTATATTTTT
5788528 AAAATTT-TAAT-TATTATTTTT
1 AAAATTTGTAATGTA-TATTTTT
5788549 AAAA
1 AAAA
5788553 ATATTTTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
20 2 0.08
21 15 0.62
22 7 0.29
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.53
Consensus pattern (22 bp):
AAAATTTGTAATGTATATTTTT
Found at i:5788604 original size:21 final size:20
Alignment explanation
Indices: 5788521--5788608 Score: 75
Period size: 21 Copynumber: 4.6 Consensus size: 20
5788511 TTGTAATGTA
*
5788521 TATTTTTAAAATTTTAATTAT
1 TATTTTT-AAATTTTAAATAT
5788542 TATTTTT-AA----AAATAT
1 TATTTTTAAATTTTAAATAT
5788557 T-TTTTT-AATTTTATAATA-
1 TATTTTTAAATTTTA-AATAT
5788575 TATTTTTTACAATTTTAAATAT
1 TA-TTTTTA-AATTTTAAATAT
5788597 TATTTTTAAATT
1 TATTTTTAAATT
5788609 CTTTTTTTAA
Statistics
Matches: 56, Mismatches: 1, Indels: 21
0.72 0.01 0.27
Matches are distributed among these distances:
14 7 0.12
15 6 0.11
18 2 0.04
19 6 0.11
20 9 0.16
21 17 0.30
22 9 0.16
ACGTcount: A:0.38, C:0.01, G:0.00, T:0.61
Consensus pattern (20 bp):
TATTTTTAAATTTTAAATAT
Done.