Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001840.1 Hibiscus syriacus cultivar Beakdansim tig00003725_pilon, whole genome shotgun sequence
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: 2412736
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 12
Found at i:433301 original size:39 final size:39
Alignment explanation
Indices: 433223--433301 Score: 95
Period size: 39 Copynumber: 2.0 Consensus size: 39
433213 TTCTTTTTAA
* * * *
433223 AGAATATTTTATCTCACTTGAGATGGTTTCTCTCGAAAC
1 AGAAGATTTTATCTCACTTGAGATAGTTTCACTCAAAAC
** *
433262 AGAAGATTTTATCTTGCTTGAGATAGTTTCACTTAAAAC
1 AGAAGATTTTATCTCACTTGAGATAGTTTCACTCAAAAC
433301 A
1 A
433302 AGAGTTGTTT
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
39 33 1.00
ACGTcount: A:0.32, C:0.15, G:0.15, T:0.38
Consensus pattern (39 bp):
AGAAGATTTTATCTCACTTGAGATAGTTTCACTCAAAAC
Found at i:433374 original size:39 final size:39
Alignment explanation
Indices: 433314--433389 Score: 109
Period size: 39 Copynumber: 1.9 Consensus size: 39
433304 AGTTGTTTTA
* *
433314 CTTGAAACAGAAAATTTTGTCTCG-TTAGAGATAGTTTCC
1 CTTGAAACAGAAAATTCTGTCTCGCTT-GAGACAGTTTCC
*
433353 CTTGAAACAGAAGATTCTGTCTCGCTTGAGACAGTTT
1 CTTGAAACAGAAAATTCTGTCTCGCTTGAGACAGTTT
433390 TTACTCGAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
39 31 0.94
40 2 0.06
ACGTcount: A:0.29, C:0.17, G:0.20, T:0.34
Consensus pattern (39 bp):
CTTGAAACAGAAAATTCTGTCTCGCTTGAGACAGTTTCC
Found at i:433467 original size:76 final size:72
Alignment explanation
Indices: 433363--433557 Score: 216
Period size: 76 Copynumber: 2.6 Consensus size: 72
433353 CTTGAAACAG
433363 AAGATTCTGTCTCGCTTGAGACAGTTTTTACTCGAAACAAGAAGATTT-ATTTCACTCAAGATTG
1 AAGATT-TGTCTCGCTTGAGACA-TTTTTACTCGAAACAAGAAGATTTCATTTCACTCAAGATT-
433427 GTTTTCTTAAAAC
63 G-TTT-TT-AAAC
* * * *
433440 AAGATTTGTCTCGTTTGAGACGATTTTTACTCGAAAGAA-AACATTTCATTTCACTCAATATTGT
1 AAGATTTGTCTCGCTTGAGAC-ATTTTTACTCGAAACAAGAAGATTTCATTTCACTCAAGATTGT
*
433504 TTTTAAAG
65 TTTTAAAC
* * * *
433512 AAGATTTTATCTCGCTTGAGATAGTTTCACTCGAAAC-AGAAGATTT
1 AAGA-TTTGTCTCGCTTGAGACATTTTTACTCGAAACAAGAAGATTT
433558 TATCTCGTTT
Statistics
Matches: 102, Mismatches: 12, Indels: 13
0.80 0.09 0.10
Matches are distributed among these distances:
71 1 0.01
72 25 0.25
73 16 0.16
74 3 0.03
75 7 0.07
76 43 0.42
77 7 0.07
ACGTcount: A:0.32, C:0.15, G:0.15, T:0.37
Consensus pattern (72 bp):
AAGATTTGTCTCGCTTGAGACATTTTTACTCGAAACAAGAAGATTTCATTTCACTCAAGATTGTT
TTTAAAC
Found at i:433564 original size:39 final size:39
Alignment explanation
Indices: 433510--433811 Score: 291
Period size: 39 Copynumber: 8.0 Consensus size: 39
433500 TTGTTTTTAA
*
433510 AGAAGATTTTATCTCGCTTGAGATAGTTTCACTCGAAAC
1 AGAAGATTTTATCTCGCTTGAGATAGTTTCACTTGAAAC
* *
433549 AGAAGATTTTATCTCGTTTCAGATAGTTTCACTTGAAAC
1 AGAAGATTTTATCTCGCTTGAGATAGTTTCACTTGAAAC
* *
433588 AGAAGATTTTATCTCGCTTGAGGTAGTTTCCCTTGAAAC
1 AGAAGATTTTATCTCGCTTGAGATAGTTTCACTTGAAAC
* * *
433627 ATAAGATTTTATCTCGCTTGAGGTAGTTTCCCTTGAAAC
1 AGAAGATTTTATCTCGCTTGAGATAGTTTCACTTGAAAC
* * * * *
433666 AAAAGATTTTATCTCTCTTGTGATAATTTCCCTT-AAA-
1 AGAAGATTTTATCTCGCTTGAGATAGTTTCACTTGAAAC
* * * *
433703 ACAA-ATTTTGTCTCTCTTGAGACAGTTTC-CGTTGAAAC
1 AGAAGATTTTATCTCGCTTGAGATAGTTTCAC-TTGAAAC
* * * *
433741 --AA-ATTTTGTCTCTCTTGAGAGAGTTTCCCTT-AAA-
1 AGAAGATTTTATCTCGCTTGAGATAGTTTCACTTGAAAC
* * * * *
433775 ACAA-ATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAA
1 AGAAGATTTTATCTCGCTTGAGATAGTTTCACTTGAAA
433812 AAAAATCTTT
Statistics
Matches: 236, Mismatches: 20, Indels: 16
0.87 0.07 0.06
Matches are distributed among these distances:
35 4 0.02
36 81 0.34
37 10 0.04
38 3 0.01
39 138 0.58
ACGTcount: A:0.28, C:0.18, G:0.16, T:0.38
Consensus pattern (39 bp):
AGAAGATTTTATCTCGCTTGAGATAGTTTCACTTGAAAC
Found at i:433718 original size:36 final size:36
Alignment explanation
Indices: 433593--433982 Score: 249
Period size: 36 Copynumber: 11.0 Consensus size: 36
433583 GAAACAGAAG
* * ** *
433593 ATTTTATCTCGCTTGAGGTAGTTTCCCTTGAAACATAA
1 ATTTTGTCTCTCTTGAGACAGTTTCCCTT-AAA-ACAA
* * ** *
433631 GATTTTATCTCGCTTGAGGTAGTTTCCCTTGAAACAAAA
1 -ATTTTGTCTCTCTTGAGACAGTTTCCCTT-AAA-ACAA
* * * *
433670 GATTTTATCTCTCTTGTGATAATTTCCCTTAAAACAA
1 -ATTTTGTCTCTCTTGAGACAGTTTCCCTTAAAACAA
* *
433707 ATTTTGTCTCTCTTGAGACAGTTTCCGTTGAAACAA
1 ATTTTGTCTCTCTTGAGACAGTTTCCCTTAAAACAA
*
433743 ATTTTGTCTCTCTTGAGAGAGTTTCCCTTAAAACAA
1 ATTTTGTCTCTCTTGAGACAGTTTCCCTTAAAACAA
433779 ATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAAA-AA
1 ATTTTGTCTCTCTTGAGACAGTTTCCCTT-AAAACAA
* * **
433815 A------ATCT-TTGA-ATCTGTTTCCCTGGAAACAA
1 ATTTTGTCTCTCTTGAGA-CAGTTTCCCTTAAAACAA
* * * *
433844 ATTTTATCTCTCTTGAGACAGTTTTCCTTGAAATAA
1 ATTTTGTCTCTCTTGAGACAGTTTCCCTTAAAACAA
* * * * *
433880 GTTTTATCTCCCTTTAGACAGTTTCTCTTGAAACACAA
1 ATTTTGTCTCTCTTGAGACAGTTTCCCTT-AAA-ACAA
*
433918 A------C-CT-TTGAGATC-GTTTCCCTTGAAACAA
1 ATTTTGTCTCTCTTGAGA-CAGTTTCCCTTAAAACAA
* * *
433946 ATTTTTTCTCTCTTGAGACAGTTACCCTTGAAACAA
1 ATTTTGTCTCTCTTGAGACAGTTTCCCTTAAAACAA
433982 A
1 A
433983 ATCTATCTCA
Statistics
Matches: 290, Mismatches: 38, Indels: 49
0.77 0.10 0.13
Matches are distributed among these distances:
28 9 0.03
29 18 0.06
30 16 0.06
31 2 0.01
32 1 0.00
34 1 0.00
35 6 0.02
36 158 0.54
37 10 0.03
38 6 0.02
39 63 0.22
ACGTcount: A:0.28, C:0.20, G:0.13, T:0.39
Consensus pattern (36 bp):
ATTTTGTCTCTCTTGAGACAGTTTCCCTTAAAACAA
Found at i:433777 original size:72 final size:74
Alignment explanation
Indices: 433512--433982 Score: 312
Period size: 78 Copynumber: 6.5 Consensus size: 74
433502 GTTTTTAAAG
* * * * * * * *
433512 AAGATTTTATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGATTTTATCTCGT-TTCAGATAGT
1 AAGATTTTATCTCTCTTGAGAGAGTTTCCCT-TAAA-ACAA-ATTTTGTCTC-TCTTGAGACAGT
*
433576 TTCACTTGAAACA
62 TTCCCTTGAAACA
* * * * **
433589 GAAGATTTTATCTCGCTTGAG-GTAGTTTCCCTTGAAACATAAGATTTTATCTCGCTTGAGGTAG
1 -AAGATTTTATCTCTCTTGAGAG-AGTTTCCCTT-AAA-ACAA-ATTTTGTCTCTCTTGAGACAG
433653 TTTCCCTTGAAACAA
61 TTTCCCTTGAAAC-A
* * *
433668 AAGATTTTATCTCTCTTGTGATAATTTCCCTTAAAACAAATTTTGTCTCTCTTGAGACAGTTTCC
1 AAGATTTTATCTCTCTTGAGAGAGTTTCCCTTAAAACAAATTTTGTCTCTCTTGAGACAGTTTCC
*
433733 GTTGAAAC-
66 CTTGAAACA
*
433741 AA-ATTTTGTCTCTCTTGAGAGAGTTTCCCTTAAAACAAATTTTGTCTCTCTTGAGACAGTTTCC
1 AAGATTTTATCTCTCTTGAGAGAGTTTCCCTTAAAACAAATTTTGTCTCTCTTGAGACAGTTTCC
433805 CTTGAAA-A
66 CTTGAAACA
** ** * *
433813 AA-A----A--TCT-TTGA-ATCTGTTTCCCTGGAAACAAATTTTATCTCTCTTGAGACAGTTTT
1 AAGATTTTATCTCTCTTGAGA-GAGTTTCCCTTAAAACAAATTTTGTCTCTCTTGAGACAGTTTC
*
433869 CCTTGAAA-T
65 CCTTGAAACA
* * * *
433878 AAG-TTTTATCTCCCTTTAGACAGTTTCTCTTGAAACACAAA------C-CT-TTGAGATC-GTT
1 AAGATTTTATCTCTCTTGAGAGAGTTTCCCTT-AAA-ACAAATTTTGTCTCTCTTGAGA-CAGTT
433933 TCCCTTGAAAC-
63 TCCCTTGAAACA
* * * *
433944 AA-ATTTTTTCTCTCTTGAGACAGTTACCCTTGAAACAAA
1 AAGATTTTATCTCTCTTGAGAGAGTTTCCCTTAAAACAAA
433983 ATCTATCTCA
Statistics
Matches: 328, Mismatches: 44, Indels: 56
0.77 0.10 0.13
Matches are distributed among these distances:
64 6 0.02
65 53 0.16
66 46 0.14
67 3 0.01
68 1 0.00
69 1 0.00
71 2 0.01
72 78 0.24
73 5 0.02
74 5 0.02
75 29 0.09
76 3 0.01
77 3 0.01
78 92 0.28
79 1 0.00
ACGTcount: A:0.29, C:0.19, G:0.14, T:0.38
Consensus pattern (74 bp):
AAGATTTTATCTCTCTTGAGAGAGTTTCCCTTAAAACAAATTTTGTCTCTCTTGAGACAGTTTCC
CTTGAAACA
Found at i:433854 original size:101 final size:102
Alignment explanation
Indices: 433613--433999 Score: 366
Period size: 101 Copynumber: 3.7 Consensus size: 102
433603 GCTTGAGGTA
* **
433613 GTTTCCCTTGAAACATAAGATTTTATCTCGCTTGAGGTAGTTTCCCTTGAAACAAAAGATTTTAT
1 GTTTCCCTTGAAAC--AA-ATTTTATCTCTCTTGAGACAGTTTCCCTTGAAAC--AA-ATTTTAT
* * * * * **
433678 CTCTCTTGTGATAATTTCCCTTAAAACAAATTTTGTCTCTCTTGAGA-C
60 CTCCCTTGAGACAGTTTCCCTTGAAACAAA----AAC-CT-TTGAGATC
* * * * * *
433726 AGTTTCCGTTGAAACAAATTTTGTCTCTCTTGAGAGAGTTTCCCTTAAAACAAATTTTGTCTCTC
1 -GTTTCCCTTGAAACAAATTTTATCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTTATCTCCC
*
433791 TTGAGACAGTTTCCCTTGAAA-AAAAATCTTTGA-ATC
65 TTGAGACAGTTTCCCTTGAAACAAAAACCTTTGAGATC
* * * *
433827 TGTTTCCCTGGAAACAAATTTTATCTCTCTTGAGACAGTTTTCCTTGAAATAAGTTTTATCTCCC
1 -GTTTCCCTTGAAACAAATTTTATCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTTATCTCCC
* * *
433892 TTTAGACAGTTTCTCTTGAAACACAAACCTTTGAGATC
65 TTGAGACAGTTTCCCTTGAAACAAAAACCTTTGAGATC
* * * * *
433930 GTTTCCCTTGAAACAAATTTTTTCTCTCTTGAGACAGTTACCCTTGAAACAAAATCTATCTCACT
1 GTTTCCCTTGAAACAAATTTTATCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTTATCTCCCT
433995 TGAGA
66 TGAGA
434000 TGGTTTTTTT
Statistics
Matches: 231, Mismatches: 39, Indels: 18
0.80 0.14 0.06
Matches are distributed among these distances:
100 1 0.00
101 78 0.34
102 72 0.31
103 3 0.01
107 3 0.01
108 28 0.12
109 2 0.01
111 29 0.13
112 2 0.01
114 13 0.06
ACGTcount: A:0.28, C:0.20, G:0.13, T:0.38
Consensus pattern (102 bp):
GTTTCCCTTGAAACAAATTTTATCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTTATCTCCCT
TGAGACAGTTTCCCTTGAAACAAAAACCTTTGAGATC
Found at i:433965 original size:66 final size:66
Alignment explanation
Indices: 433856--433980 Score: 162
Period size: 66 Copynumber: 1.9 Consensus size: 66
433846 TTTATCTCTC
* * * * * *
433856 TTGAGACAGTTTTCCTTGAAATAAGTTTTATCTCCCTTTAGACAGTTTCTCTTGAAACACAAACC
1 TTGAGACAGTTTCCCTTGAAACAAATTTTATCTCCCTTGAGACAGTTACCCTTGAAACACAAACC
433921 T
66 T
* *
433922 TTGAGATC-GTTTCCCTTGAAACAAATTTTTTCTCTCTTGAGACAGTTACCCTTGAAACA
1 TTGAGA-CAGTTTCCCTTGAAACAAATTTTATCTCCCTTGAGACAGTTACCCTTGAAACA
433981 AAATCTATCT
Statistics
Matches: 50, Mismatches: 8, Indels: 2
0.83 0.13 0.03
Matches are distributed among these distances:
66 49 0.98
67 1 0.02
ACGTcount: A:0.28, C:0.22, G:0.13, T:0.38
Consensus pattern (66 bp):
TTGAGACAGTTTCCCTTGAAACAAATTTTATCTCCCTTGAGACAGTTACCCTTGAAACACAAACC
T
Found at i:434608 original size:91 final size:91
Alignment explanation
Indices: 434501--434764 Score: 377
Period size: 91 Copynumber: 2.9 Consensus size: 91
434491 ACATTTCAAA
*
434501 TGGAGAGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAAGAAGTTCATAAAGAGAAGAACTT
1 TGGAGAGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAAGAAGTTCATAATGAGAAGAACTT
** *
434566 GTTCAACCTTGGTTCAAGATTTCCAG
66 GTTCAACCTTGCATCAAGATTTACAG
* *
434592 TGGAAAGTTCATAATGAGAAGAACTTATCCAACGAGGGAGAAGAAGTTCATAATGAGAAGAACTT
1 TGGAGAGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAAGAAGTTCATAATGAGAAGAACTT
* *
434657 GTTCAATCTTGCATCAATATTTACAG
66 GTTCAACCTTGCATCAAGATTTACAG
* * *
434683 CGGAGAGTTCATAATGAGAAGAACTCATCCGATA-GAGGCAGAAGAAGTTCATAATCAGAAGAAC
1 TGGAGAGTTCATAATGAGAAGAACTCATCC-A-ACGAGGGAGAAGAAGTTCATAATGAGAAGAAC
* **
434747 TTATTCAACAATGCATCA
64 TTGTTCAACCTTGCATCA
434765 CATATGGAGT
Statistics
Matches: 154, Mismatches: 17, Indels: 3
0.89 0.10 0.02
Matches are distributed among these distances:
91 110 0.71
92 43 0.28
93 1 0.01
ACGTcount: A:0.39, C:0.15, G:0.22, T:0.23
Consensus pattern (91 bp):
TGGAGAGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAAGAAGTTCATAATGAGAAGAACTT
GTTCAACCTTGCATCAAGATTTACAG
Found at i:434998 original size:30 final size:30
Alignment explanation
Indices: 434958--435052 Score: 145
Period size: 30 Copynumber: 3.2 Consensus size: 30
434948 TTTTTATTCC
* *
434958 ACCATATTTTATTCAACATCCCATTCCACT
1 ACCATTTTTTATTCAACATCCCATGCCACT
434988 ACCATTTTTTATTCAACATCCCATGCCACT
1 ACCATTTTTTATTCAACATCCCATGCCACT
* * *
435018 ACCATTTTATATTCAATATCCCATGCCACC
1 ACCATTTTTTATTCAACATCCCATGCCACT
435048 ACCAT
1 ACCAT
435053 GCCCCCACGT
Statistics
Matches: 60, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
30 60 1.00
ACGTcount: A:0.29, C:0.34, G:0.02, T:0.35
Consensus pattern (30 bp):
ACCATTTTTTATTCAACATCCCATGCCACT
Found at i:441643 original size:39 final size:39
Alignment explanation
Indices: 441565--441643 Score: 95
Period size: 39 Copynumber: 2.0 Consensus size: 39
441555 TTCTTTTTAA
* * * *
441565 AGAATATTTTATCTCACATGAGATGGTTTCTCTCGAAAC
1 AGAAGATTTTATCTCACATGAGATAGTTTCACTCAAAAC
* * *
441604 AGAAGATTTTATCTCGCTTGAGATAGTTTCACTTAAAAC
1 AGAAGATTTTATCTCACATGAGATAGTTTCACTCAAAAC
441643 A
1 A
441644 AGAGTTGTTT
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
39 33 1.00
ACGTcount: A:0.33, C:0.16, G:0.15, T:0.35
Consensus pattern (39 bp):
AGAAGATTTTATCTCACATGAGATAGTTTCACTCAAAAC
Found at i:441687 original size:60 final size:60
Alignment explanation
Indices: 441590--441703 Score: 167
Period size: 60 Copynumber: 1.9 Consensus size: 60
441580 ACATGAGATG
* *
441590 GTTTCTCTCGAAACAGAAGATTTTATCTCGCTTGAGATAGTTTCACTTAAAACAAGAGTT
1 GTTTCGCTCGAAACAGAAAATTTTATCTCGCTTGAGATAGTTTCACTTAAAACAAGAGTT
* * *
441650 GTTTCGCTTGAAACAGAAAATTTTGTCTCG-TTGGAGATAGTTTCCCTTAAAACA
1 GTTTCGCTCGAAACAGAAAATTTTATCTCGCTT-GAGATAGTTTCACTTAAAACA
441704 GAAGATTCTG
Statistics
Matches: 48, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
59 2 0.04
60 46 0.96
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.35
Consensus pattern (60 bp):
GTTTCGCTCGAAACAGAAAATTTTATCTCGCTTGAGATAGTTTCACTTAAAACAAGAGTT
Found at i:441704 original size:39 final size:39
Alignment explanation
Indices: 441650--441731 Score: 103
Period size: 39 Copynumber: 2.1 Consensus size: 39
441640 AACAAGAGTT
* * * *
441650 GTTTCGCTTGAAACAGAAAATTTTGTCTCG-TTGGAGATA
1 GTTTCCCTTAAAACAGAAAATTCTGTCTCGCTT-GAGACA
*
441689 GTTTCCCTTAAAACAGAAGATTCTGTCTCGCTTGAGACA
1 GTTTCCCTTAAAACAGAAAATTCTGTCTCGCTTGAGACA
441728 GTTT
1 GTTT
441732 TTACTCGAAA
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
39 35 0.95
40 2 0.05
ACGTcount: A:0.27, C:0.17, G:0.21, T:0.35
Consensus pattern (39 bp):
GTTTCCCTTAAAACAGAAAATTCTGTCTCGCTTGAGACA
Found at i:441802 original size:76 final size:75
Alignment explanation
Indices: 441695--441908 Score: 260
Period size: 76 Copynumber: 2.9 Consensus size: 75
441685 GATAGTTTCC
441695 CTTAAAACAGAAGATTCTGTCTCGCTTGAGACAGTTTTTACTCGAAACAAGAAGA-TTTATTTCA
1 CTTAAAAC--AAGATT-TGTCTCGCTTGAGACAGTTTTTACTCGAAACAAGAAGATTTTATTTCA
441759 CTCAAGATTATTTTT
63 CTCAAGATTA--TTT
* * *
441774 CTTAAAACAAGATTTGTCTCGCTTGAGACGGTTTTTACTCGAAAGAA-AACATTTTATTTCACTC
1 CTTAAAACAAGATTTGTCTCGCTTGAGACAGTTTTTACTCGAAACAAGAAGATTTTATTTCACTC
441838 AAGATTATTT
66 AAGATTATTT
* * * * *
441848 -TT-AAAGAAGATTTTATCTCGCTTGAGATAG-TTTCACTCGAAAC-AGAAGATTTTATCTCACT
1 CTTAAAACAAGA-TTTGTCTCGCTTGAGACAGTTTTTACTCGAAACAAGAAGATTTTATTTCACT
441909 TGAGATAGTT
Statistics
Matches: 121, Mismatches: 11, Indels: 13
0.83 0.08 0.09
Matches are distributed among these distances:
71 1 0.01
72 32 0.26
73 18 0.15
74 3 0.02
75 3 0.02
76 50 0.41
77 6 0.05
79 8 0.07
ACGTcount: A:0.33, C:0.16, G:0.14, T:0.37
Consensus pattern (75 bp):
CTTAAAACAAGATTTGTCTCGCTTGAGACAGTTTTTACTCGAAACAAGAAGATTTTATTTCACTC
AAGATTATTT
Found at i:441911 original size:39 final size:37
Alignment explanation
Indices: 441857--442273 Score: 434
Period size: 36 Copynumber: 11.1 Consensus size: 37
441847 TTTAAAGAAG
* * *
441857 ATTTTATCTCGCTTGAGATAGTTTCACTCGAAACAGAA
1 ATTTTATCTCTCTTGAGATAGTTTCCCTTGAAACA-AA
* *
441895 GATTTTATCTCACTTGAGATAGTTTCACTCT-AAACAGAA
1 -ATTTTATCTCTCTTGAGATAGTTTCCCT-TGAAACA-AA
* * *
441934 GATTTTATCTCGCTTGAGATAGTTTCACTTCAAACAGAA
1 -ATTTTATCTCTCTTGAGATAGTTTCCCTTGAAACA-AA
* * *
441973 GATTTTATCTCGCTTGAGGTAGTTTCCCTTGAAACAGACG
1 -ATTTTATCTCTCTTGAGATAGTTTCCCTTGAAACA-A-A
*
442013 ATTTTATCTCGT-TTGAGGTAGTTTCCCTTGAAACAAAA
1 ATTTTATCTC-TCTTGAGATAGTTTCCCTTGAAAC-AAA
* *
442051 GATTTTATCTCTCTCGAGATAATTTCCCTTGAAAC-AA
1 -ATTTTATCTCTCTTGAGATAGTTTCCCTTGAAACAAA
* * *
442088 ATTTTGTCTCTCTTGAGACAGTTTCCGTTGAAAC-AA
1 ATTTTATCTCTCTTGAGATAGTTTCCCTTGAAACAAA
* * *
442124 ATTTTGTCTCTCTTGAGACAGTTTCCTTTGAAAC-AA
1 ATTTTATCTCTCTTGAGATAGTTTCCCTTGAAACAAA
* **
442160 ATTTTGTCTCTCTTGAGACCGTTTCCCTTGAAAC-AA
1 ATTTTATCTCTCTTGAGATAGTTTCCCTTGAAACAAA
* *
442196 ATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAAC-AA
1 ATTTTATCTCTCTTGAGATAGTTTCCCTTGAAACAAA
* *
442232 ATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
1 ATTTTATCTCTCTTGAGATAGTTTCCCTTGAAACAAA
442269 ATTTT
1 ATTTT
442274 TGAATCTGTT
Statistics
Matches: 349, Mismatches: 21, Indels: 18
0.90 0.05 0.05
Matches are distributed among these distances:
36 169 0.48
37 9 0.03
38 2 0.01
39 168 0.48
40 1 0.00
ACGTcount: A:0.27, C:0.20, G:0.15, T:0.38
Consensus pattern (37 bp):
ATTTTATCTCTCTTGAGATAGTTTCCCTTGAAACAAA
Found at i:441949 original size:78 final size:77
Alignment explanation
Indices: 441650--442273 Score: 370
Period size: 72 Copynumber: 8.3 Consensus size: 77
441640 AACAAGAGTT
* * * * ** * * *
441650 GTTTCGCTTGAAACAGAAAATTTTGTCTCGTTGGAGATAGTTTCCCTTAAAACAGAAGATTCTGT
1 GTTTCACTCGAAACAGAAGATTTTATCTCACTCGAGATAGTTTCCCTT-AAACAGAAGATTTTAT
*
441715 CTCGCTTGAGACA
65 CTCGCTTGAGATA
* * * ** *
441728 GTTTTTACTCGAAACAAGAAGA-TTTATTTCACTCAAGATTA-TTTTTCTTAAA-ACAAGA-TTT
1 G-TTTCACTCGAAAC-AGAAGATTTTATCTCACTCGAGA-TAGTTTCCCTTAAACAGAAGATTTT
* **
441789 GTCTCGCTTGAGACG
63 ATCTCGCTTGAGATA
* * * * * *
441804 GTTTTTACTCGAAAGAAAACATTTTATTTCACTCAAGATTA-TTT---TT-AA-AGAAGATTTTA
1 G-TTTCACTCGAAACAGAAGATTTTATCTCACTCGAGA-TAGTTTCCCTTAAACAGAAGATTTTA
441863 TCTCGCTTGAGATA
64 TCTCGCTTGAGATA
* *
441877 GTTTCACTCGAAACAGAAGATTTTATCTCACTTGAGATAGTTTCACTCTAAACAGAAGATTTTAT
1 GTTTCACTCGAAACAGAAGATTTTATCTCACTCGAGATAGTTTCCCT-TAAACAGAAGATTTTAT
441942 CTCGCTTGAGATA
65 CTCGCTTGAGATA
* * * *
441955 GTTTCACTTC-AAACAGAAGATTTTATCTCGCTTGAGGTAGTTTCCCTTGAAACAGACGATTTTA
1 GTTTCAC-TCGAAACAGAAGATTTTATCTCACTCGAGATAGTTTCCCTT-AAACAGAAGATTTTA
* *
442019 TCTCGTTTGAGGTA
64 TCTCGCTTGAGATA
* * * * * *
442033 GTTTCCCTTGAAACAAAAGATTTTATCTCTCTCGAGATAATTTCCCTTGAAAC--AA-ATTTTGT
1 GTTTCACTCGAAACAGAAGATTTTATCTCACTCGAGATAGTTTCCCTT-AAACAGAAGATTTTAT
* *
442095 CTCTCTTGAGACA
65 CTCGCTTGAGATA
* * * * * * *
442108 GTTTC-CGTTGAAAC--AA-ATTTTGTCTCTCTTGAGACAGTTTCCTTTGAAAC--AA-ATTTTG
1 GTTTCAC-TCGAAACAGAAGATTTTATCTCACTCGAGATAGTTTCCCTT-AAACAGAAGATTTTA
* **
442166 TCTCTCTTGAGACC
64 TCTCGCTTGAGATA
* * * * * * *
442180 GTTTCCCTTGAAAC--AA-ATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAAC--AA-ATTTTGT
1 GTTTCACTCGAAACAGAAGATTTTATCTCACTCGAGATAGTTTCCCTT-AAACAGAAGATTTTAT
* *
442239 CTCTCTTGAGACA
65 CTCGCTTGAGATA
* *
442252 GTTTCCCTTGAAACA-AA-ATTTT
1 GTTTCACTCGAAACAGAAGATTTT
442274 TGAATCTGTT
Statistics
Matches: 472, Mismatches: 56, Indels: 41
0.83 0.10 0.07
Matches are distributed among these distances:
71 2 0.00
72 171 0.36
73 28 0.06
74 1 0.00
75 32 0.07
76 54 0.11
77 9 0.02
78 140 0.30
79 28 0.06
80 7 0.01
ACGTcount: A:0.29, C:0.18, G:0.15, T:0.38
Consensus pattern (77 bp):
GTTTCACTCGAAACAGAAGATTTTATCTCACTCGAGATAGTTTCCCTTAAACAGAAGATTTTATC
TCGCTTGAGATA
Found at i:441996 original size:117 final size:117
Alignment explanation
Indices: 441852--442269 Score: 341
Period size: 117 Copynumber: 3.7 Consensus size: 117
441842 TTATTTTTAA
441852 AGAAGATTTTATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGATTTTATCTCACTTGAGATAG
1 AGAAGATTTTATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGATTTTATCTCACTTGAGATAG
* * *
441917 TTTCACTCT-AAACAGAAGATTTTATCTCGCTTGAGATAGTTTCACTTCAAAC
66 TTTCACT-TGAAACAAAAGATTTTATCTCGCTCGAGATAATTTCACTTCAAAC
* * * * ** *
441969 AGAAGATTTTATCTCGCTTGAGGTAGTTTCCCTTGAAACAGACGATTTTATCTCGTTTGAGGTAG
1 AGAAGATTTTATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGATTTTATCTCACTTGAGATAG
* * * *
442034 TTTCCCTTGAAACAAAAGATTTTATCTCTCTCGAGATAATTTCCCTTGAAAC
66 TTTCACTTGAAACAAAAGATTTTATCTCGCTCGAGATAATTTCACTTCAAAC
* * * * * * *
442086 --AA-ATTTTGTCTCTCTTGAGACAGTTTC-CGTTGAAAC--AA-ATTTTGTCTCTCTTGAGACA
1 AGAAGATTTTATCTCGCTTGAGATAGTTTCAC-TCGAAACAGAAGATTTTATCTCACTTGAGATA
* * * *** * *
442144 GTTTC-CTTTGAAAC--AA-ATTTTGTCTCTCTTGAGACCGTTTCCCTTGAAAC
65 GTTTCAC-TTGAAACAAAAGATTTTATCTCGCTCGAGATAATTTCACTTCAAAC
* * * * * * * *
442194 --AA-ATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAAC--AA-ATTTTGTCTCTCTTGAGACAG
1 AGAAGATTTTATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGATTTTATCTCACTTGAGATAG
*
442253 TTTCCCTTGAAACAAAA
66 TTTCACTTGAAACAAAA
442270 TTTTTGAATC
Statistics
Matches: 265, Mismatches: 29, Indels: 21
0.84 0.09 0.07
Matches are distributed among these distances:
108 97 0.37
109 4 0.02
110 3 0.01
111 27 0.10
112 1 0.00
113 1 0.00
114 28 0.11
115 2 0.01
116 1 0.00
117 101 0.38
ACGTcount: A:0.28, C:0.20, G:0.15, T:0.37
Consensus pattern (117 bp):
AGAAGATTTTATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGATTTTATCTCACTTGAGATAG
TTTCACTTGAAACAAAAGATTTTATCTCGCTCGAGATAATTTCACTTCAAAC
Found at i:442286 original size:29 final size:29
Alignment explanation
Indices: 442252--442330 Score: 142
Period size: 29 Copynumber: 2.8 Consensus size: 29
442242 TCTTGAGACA
442252 GTTTCCCTTGAAACAAAATTTTTGAATCT
1 GTTTCCCTTGAAACAAAATTTTTGAATCT
*
442281 GTTTCCCTTGAAACAAAATCTTTGAATCT
1 GTTTCCCTTGAAACAAAATTTTTGAATCT
442310 GTTTCCCTTGAAAC-AAATTTT
1 GTTTCCCTTGAAACAAAATTTT
442331 ATCTCTCTTG
Statistics
Matches: 48, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
28 6 0.12
29 42 0.88
ACGTcount: A:0.30, C:0.19, G:0.10, T:0.41
Consensus pattern (29 bp):
GTTTCCCTTGAAACAAAATTTTTGAATCT
Found at i:442418 original size:66 final size:66
Alignment explanation
Indices: 442338--442462 Score: 180
Period size: 66 Copynumber: 1.9 Consensus size: 66
442328 TTTATCTCTC
* * * *
442338 TTGAGACAGTTTCCCTTGAAATAAGTTTTGTCTCCCTTTAGACAGTTTCTCTTGAAACACAAACC
1 TTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCCCTTGAAACACAAACC
442403 T
66 T
* *
442404 TTGAGATC-GTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACA
1 TTGAGA-CAGTTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCCCTTGAAACA
442463 AAATCTATCT
Statistics
Matches: 52, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
66 51 0.98
67 1 0.02
ACGTcount: A:0.26, C:0.22, G:0.14, T:0.38
Consensus pattern (66 bp):
TTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCCCTTGAAACACAAACC
T
Found at i:442482 original size:36 final size:36
Alignment explanation
Indices: 442310--442487 Score: 172
Period size: 36 Copynumber: 5.1 Consensus size: 36
442300 CTTTGAATCT
*
442310 GTTTCCCTTGAAACAAATTTTATCTCTCTTGAGACA
1 GTTTCCCTTGAAACAAATTTTATCTCTCTTGAGATA
* * * * * *
442346 GTTTCCCTTGAAATAAGTTTTGTCTCCCTTTAGACA
1 GTTTCCCTTGAAACAAATTTTATCTCTCTTGAGATA
* *
442382 GTTTCTCTTGAAACACAA----A-C-CT-TTGAGATC
1 GTTTCCCTTGAAACA-AATTTTATCTCTCTTGAGATA
*
442412 GTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGATA
1 GTTTCCCTTGAAACAAATTTTATCTCTCTTGAGATA
* * * *
442448 GTTTCCCTTGAAACAAAATCTATCTCACTTGAGATG
1 GTTTCCCTTGAAACAAATTTTATCTCTCTTGAGATA
442484 GTTT
1 GTTT
442488 TTTTAAAAAA
Statistics
Matches: 113, Mismatches: 21, Indels: 16
0.75 0.14 0.11
Matches are distributed among these distances:
29 2 0.02
30 19 0.17
31 1 0.01
32 1 0.01
34 1 0.01
35 2 0.02
36 86 0.76
37 1 0.01
ACGTcount: A:0.26, C:0.21, G:0.13, T:0.39
Consensus pattern (36 bp):
GTTTCCCTTGAAACAAATTTTATCTCTCTTGAGATA
Found at i:443085 original size:91 final size:91
Alignment explanation
Indices: 442983--443246 Score: 377
Period size: 91 Copynumber: 2.9 Consensus size: 91
442973 ACATTTCAAA
*
442983 TGGAGAGTTCATAATGAGAAGAACTCATACAACGAGGGAGAAGAAGTTCATAATGAGAAGAACTT
1 TGGAGAGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAAGAAGTTCATAATGAGAAGAACTT
** * *
443048 GTTCAACCTTGGTTCAAGATTTCCAG
66 GTTCAACCTTGCATCAACATTTACAG
*
443074 TGGAGAGTTCATAATGAGAAGAACTTATCCAACGAGGGAGAAGAAGTTCATAATGAGAAGAACTT
1 TGGAGAGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAAGAAGTTCATAATGAGAAGAACTT
*
443139 GTTCAATCTTGCATCAACATTTACAG
66 GTTCAACCTTGCATCAACATTTACAG
** * * * *
443165 CAGAGAGTTCATAATGATAAGAGCTCATCCGATA-GAGGCAGAAGAAGTTCATAATCAGAAGAAC
1 TGGAGAGTTCATAATGAGAAGAACTCATCC-A-ACGAGGGAGAAGAAGTTCATAATGAGAAGAAC
*
443229 TTATTCAACCTTGCATCA
64 TTGTTCAACCTTGCATCA
443247 CATATGAAGT
Statistics
Matches: 155, Mismatches: 16, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
91 109 0.70
92 45 0.29
93 1 0.01
ACGTcount: A:0.38, C:0.16, G:0.22, T:0.24
Consensus pattern (91 bp):
TGGAGAGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAAGAAGTTCATAATGAGAAGAACTT
GTTCAACCTTGCATCAACATTTACAG
Found at i:443479 original size:29 final size:29
Alignment explanation
Indices: 443440--443522 Score: 130
Period size: 29 Copynumber: 2.8 Consensus size: 29
443430 TTTTTATTCC
*
443440 ACCATATTTTATTAAACATCCCATGCCACT
1 ACCAT-TTTTATTCAACATCCCATGCCACT
443470 ACCATTTTTATTCAACATCCCATGCCACT
1 ACCATTTTTATTCAACATCCCATGCCACT
*
443499 ACCATTTTATATTCAATATCCCAT
1 ACCATTTT-TATTCAACATCCCAT
443523 ACCCCCACGT
Statistics
Matches: 50, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
29 31 0.62
30 19 0.38
ACGTcount: A:0.31, C:0.30, G:0.02, T:0.36
Consensus pattern (29 bp):
ACCATTTTTATTCAACATCCCATGCCACT
Found at i:446208 original size:29 final size:31
Alignment explanation
Indices: 446176--446233 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
446166 GGACTAATCT
446176 TTTCAACTAAC-TTGA-TTCTTGTTGTCTTG
1 TTTCAACTAACATTGATTTCTTGTTGTCTTG
* *
446205 TTTCTACTAACATTGATTTCTTTTTGTCT
1 TTTCAACTAACATTGATTTCTTGTTGTCT
446234 GCTTTTATTG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 10 0.40
30 4 0.16
31 11 0.44
ACGTcount: A:0.17, C:0.17, G:0.10, T:0.55
Consensus pattern (31 bp):
TTTCAACTAACATTGATTTCTTGTTGTCTTG
Found at i:446700 original size:15 final size:16
Alignment explanation
Indices: 446680--446709 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
446670 AGATCAATGT
446680 ATTTTGCAT-ACATTC
1 ATTTTGCATGACATTC
446695 ATTTTGCATGACATT
1 ATTTTGCATGACATT
446710 TGCATTCATC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.27, C:0.17, G:0.10, T:0.47
Consensus pattern (16 bp):
ATTTTGCATGACATTC
Found at i:449962 original size:39 final size:39
Alignment explanation
Indices: 449903--450472 Score: 383
Period size: 39 Copynumber: 15.0 Consensus size: 39
449893 TCTTTTTTAA
* * * **
449903 AGAATATTTTATCTCACTTGAGATGGTTTCTCTCAAAAC
1 AGAAGATTTTATCTCGCTTGAGATAGTTTCTCTTGAAAC
*
449942 AGAAGATTTTATCTCGCTTGAGATAGTTTCCCTTGAAAC
1 AGAAGATTTTATCTCGCTTGAGATAGTTTCTCTTGAAAC
* * ** * *
449981 AGAAGATTCTGTCTCGCTTGAGACGGTTTTTACTCGAAAC
1 AGAAGATTTTATCTCGCTTGAGATAGTTTCT-CTTGAAAC
* * ** ** *
450021 AAGAAGA-TTTATTTCACTCAAGATTTTTTTTCTT-AAA-
1 -AGAAGATTTTATCTCGCTTGAGATAGTTTCTCTTGAAAC
* * * * * *
450058 ACAAGA-TTTGTCTTGCTTGAGAT-GATTTTTACTCGAAAG
1 AGAAGATTTTATCTCGCTTGAGATAG-TTTCT-CTTGAAAC
* * * * * ** *
450097 AAAACATTTCATTTCACTCAAGATTG-TT-T-TT--AA-
1 AGAAGATTTTATCTCGCTTGAGATAGTTTCTCTTGAAAC
* * *
450130 AGAAGATTTTATCTCGCTTGAGATAGTTTCACTCGAAAT
1 AGAAGATTTTATCTCGCTTGAGATAGTTTCTCTTGAAAC
* * *
450169 AGATGATTTTATCTCGCTTCAGATAGTTTCACTAT-AAAC
1 AGAAGATTTTATCTCGCTTGAGATAGTTTCTCT-TGAAAC
*
450208 AGAAGATTTTATCTCGCTTGAGATAGTTTCACTTGAAAC
1 AGAAGATTTTATCTCGCTTGAGATAGTTTCTCTTGAAAC
* * *
450247 AGAAGATTTTATCTCGCTTGAGGTAGTTTCCCTTGATAC
1 AGAAGATTTTATCTCGCTTGAGATAGTTTCTCTTGAAAC
* *
450286 AGAAGATTTTATCTCGCTTGAGGTAGTTTCCCTTGAAAC
1 AGAAGATTTTATCTCGCTTGAGATAGTTTCTCTTGAAAC
* * * *
450325 AAAAGATTTTATCTCTCTTGAGATAATTTCCCTTGAAAC
1 AGAAGATTTTATCTCGCTTGAGATAGTTTCTCTTGAAAC
* * *
450364 --AA-ATTTTGTCTCTCTTGAGACT-GTTTCCCTTGAAA-
1 AGAAGATTTTATCTCGCTTGAGA-TAGTTTCTCTTGAAAC
* * * *
450399 A-CA-ATTTTGTCTCTCTTGAGATAGTTTCCCTTG-AA-
1 AGAAGATTTTATCTCGCTTGAGATAGTTTCTCTTGAAAC
* * * * *
450434 ATAAG-TTTTGTCTCCCTTTAGACAGTTTCTCTTGAAAC
1 AGAAGATTTTATCTCGCTTGAGATAGTTTCTCTTGAAAC
450472 A
1 A
450473 CAAACCTTTG
Statistics
Matches: 434, Mismatches: 74, Indels: 47
0.78 0.13 0.08
Matches are distributed among these distances:
33 18 0.04
34 4 0.01
35 4 0.01
36 107 0.25
37 7 0.02
38 11 0.03
39 244 0.56
40 32 0.07
41 7 0.02
ACGTcount: A:0.29, C:0.17, G:0.15, T:0.39
Consensus pattern (39 bp):
AGAAGATTTTATCTCGCTTGAGATAGTTTCTCTTGAAAC
Found at i:450087 original size:76 final size:77
Alignment explanation
Indices: 449983--450127 Score: 213
Period size: 76 Copynumber: 1.9 Consensus size: 77
449973 CTTGAAACAG
* * *
449983 AAGATTCTGTCTCGCTTGAGACGGTTTTTACTCGAAACAAGAAGATTT-ATTTCACTCAAGATTT
1 AAGATTCTGTCTCGCTTGAGACGATTTTTACTCGAAACAA-AACATTTCATTTCACTCAAGATTG
450047 TTTTTCTTAAAAC
65 TTTTTCTTAAAAC
* * *
450060 AAGATT-TGTCTTGCTTGAGATGATTTTTACTCGAAAGAAAACATTTCATTTCACTCAAGATTGT
1 AAGATTCTGTCTCGCTTGAGACGATTTTTACTCGAAACAAAACATTTCATTTCACTCAAGATTGT
450124 TTTT
66 TTTT
450128 AAAGAAGATT
Statistics
Matches: 61, Mismatches: 6, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
75 6 0.10
76 49 0.80
77 6 0.10
ACGTcount: A:0.30, C:0.15, G:0.14, T:0.41
Consensus pattern (77 bp):
AAGATTCTGTCTCGCTTGAGACGATTTTTACTCGAAACAAAACATTTCATTTCACTCAAGATTGT
TTTTCTTAAAAC
Found at i:450377 original size:36 final size:36
Alignment explanation
Indices: 450135--450563 Score: 311
Period size: 39 Copynumber: 11.7 Consensus size: 36
450125 TTTAAAGAAG
* * * *
450135 ATTTTATCTCGCTTGAGATAGTTTCACTCGAAATAGA
1 ATTTTATCTCTCTTGAGATAGTTTCCCTTGAAACA-A
* * *
450172 TGATTTTATCTCGCTTCAGATAGTTTCACTAT-AAACAGAA
1 --ATTTTATCTCTCTTGAGATAGTTTCCCT-TGAAAC--AA
* *
450212 GATTTTATCTCGCTTGAGATAGTTTCACTTGAAACAGAA
1 -ATTTTATCTCTCTTGAGATAGTTTCCCTTGAAAC--AA
* * *
450251 GATTTTATCTCGCTTGAGGTAGTTTCCCTTGATACAGAA
1 -ATTTTATCTCTCTTGAGATAGTTTCCCTTGA-A-ACAA
* *
450290 GATTTTATCTCGCTTGAGGTAGTTTCCCTTGAAACAAAA
1 -ATTTTATCTCTCTTGAGATAGTTTCCCTTGAAAC--AA
*
450329 GATTTTATCTCTCTTGAGATAATTTCCCTTGAAACAA
1 -ATTTTATCTCTCTTGAGATAGTTTCCCTTGAAACAA
*
450366 ATTTTGTCTCTCTTGAGACT-GTTTCCCTTGAAA-ACA
1 ATTTTATCTCTCTTGAGA-TAGTTTCCCTTGAAACA-A
* *
450402 ATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAATAA
1 ATTTTATCTCTCTTGAGATAGTTTCCCTTGAAACAA
* * * * * *
450438 GTTTTGTCTCCCTTTAGACAGTTTCTCTTGAAACACA
1 ATTTTATCTCTCTTGAGATAGTTTCCCTTGAAACA-A
* *
450475 A----A-C-CT-TTGAGATGGTTTCCCTTGAAACGA
1 ATTTTATCTCTCTTGAGATAGTTTCCCTTGAAACAA
* * * *
450504 ATTTTGTCTCTCTTTAGACAGTTTCCCTAGAAACAA
1 ATTTTATCTCTCTTGAGATAGTTTCCCTTGAAACAA
* * * *
450540 AATCTATCTCACTTGAGATGGTTT
1 ATTTTATCTCTCTTGAGATAGTTT
450564 TTTTTAAAAA
Statistics
Matches: 330, Mismatches: 40, Indels: 43
0.80 0.10 0.10
Matches are distributed among these distances:
29 2 0.01
30 18 0.05
31 1 0.00
32 1 0.00
34 1 0.00
35 4 0.01
36 127 0.38
37 6 0.02
38 2 0.01
39 164 0.50
40 2 0.01
41 2 0.01
ACGTcount: A:0.27, C:0.19, G:0.15, T:0.39
Consensus pattern (36 bp):
ATTTTATCTCTCTTGAGATAGTTTCCCTTGAAACAA
Found at i:451162 original size:91 final size:90
Alignment explanation
Indices: 451052--451325 Score: 359
Period size: 91 Copynumber: 3.0 Consensus size: 90
451042 TAAGGGATTG
*
451052 ACATTTCAAATGGAGAGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAAGAAGTTCATAATG
1 ACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCAA-GAGGGAGAAGAAGTTCATAATG
** *
451117 AGAAGAACTTGTTCAACCTGGGTTTA
65 AGAAGAACTTGTTCAACCTGGCATCA
* * *
451143 AGATTTCCAATGGAGAGTTCATAATGAGAAGAACTTATCCAAAAAGGGAGAAGAAGTTCATAATG
1 ACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCC-AAGAGGGAGAAGAAGTTCATAATG
* *
451208 AGAAGAACTTGTTCAATCTTGCATCA
65 AGAAGAACTTGTTCAACCTGGCATCA
* * * *
451234 ACATTTACAGTGGAGAGTACATAATGAGAAGAACTCATCCGATAGAGGCAGAAGAAGTTCATAAT
1 ACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCC-A-AGAGGGAGAAGAAGTTCATAAT
* * * *
451299 CAGAAGAACTTATTCAACATTGCATCA
64 GAGAAGAACTTGTTCAACCTGGCATCA
451326 CATATGGAGT
Statistics
Matches: 160, Mismatches: 21, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
91 115 0.72
92 45 0.28
ACGTcount: A:0.40, C:0.15, G:0.21, T:0.24
Consensus pattern (90 bp):
ACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCAAGAGGGAGAAGAAGTTCATAATGA
GAAGAACTTGTTCAACCTGGCATCA
Found at i:451221 original size:20 final size:20
Alignment explanation
Indices: 451159--451222 Score: 53
Period size: 17 Copynumber: 3.2 Consensus size: 20
451149 CCAATGGAGA
451159 GTTCATAATGAGAAGAACTT
1 GTTCATAATGAGAAGAACTT
* * * *
451179 ATCCAAAAAGGGAGAAGAA---
1 GTTC-ATAA-TGAGAAGAACTT
451198 GTTCATAATGAGAAGAACTT
1 GTTCATAATGAGAAGAACTT
451218 GTTCA
1 GTTCA
451223 ATCTTGCATC
Statistics
Matches: 31, Mismatches: 8, Indels: 10
0.63 0.16 0.20
Matches are distributed among these distances:
17 8 0.26
18 3 0.10
19 2 0.06
20 7 0.23
21 3 0.10
22 8 0.26
ACGTcount: A:0.44, C:0.11, G:0.22, T:0.23
Consensus pattern (20 bp):
GTTCATAATGAGAAGAACTT
Found at i:451508 original size:30 final size:30
Alignment explanation
Indices: 451474--451557 Score: 116
Period size: 30 Copynumber: 2.8 Consensus size: 30
451464 CCATAGTTTC
*
451474 TTCAACATCCCATTCCACTACCATTTTTTA
1 TTCAACATCCCATTCCACTACCATTTTATA
451504 TTCAACATCCCATGT-CACTACCATTTTATA
1 TTCAACATCCCAT-TCCACTACCATTTTATA
* * *
451534 TTCAATATCCCATGCCACCACCAT
1 TTCAACATCCCATTCCACTACCAT
451558 GCCCACATGT
Statistics
Matches: 48, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
30 47 0.98
31 1 0.02
ACGTcount: A:0.29, C:0.35, G:0.02, T:0.35
Consensus pattern (30 bp):
TTCAACATCCCATTCCACTACCATTTTATA
Found at i:458336 original size:39 final size:39
Alignment explanation
Indices: 458270--458351 Score: 103
Period size: 39 Copynumber: 2.1 Consensus size: 39
458260 AACAAGAGTT
* * * *
458270 GTTTCGCTTGAAACAAAATATTTTGTCTCG-TTAGAGATA
1 GTTTCCCTTGAAACAAAAGATTCTGTCTCGCTT-GAGACA
*
458309 GTTTCCCTTGAAACAGAAGATTCTGTCTCGCTTGAGACA
1 GTTTCCCTTGAAACAAAAGATTCTGTCTCGCTTGAGACA
458348 GTTT
1 GTTT
458352 TTACTCGAAA
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
39 35 0.95
40 2 0.05
ACGTcount: A:0.27, C:0.17, G:0.20, T:0.37
Consensus pattern (39 bp):
GTTTCCCTTGAAACAAAAGATTCTGTCTCGCTTGAGACA
Found at i:458419 original size:76 final size:73
Alignment explanation
Indices: 458325--458519 Score: 220
Period size: 76 Copynumber: 2.6 Consensus size: 73
458315 CTTGAAACAG
458325 AAGATTCTGTCTCGCTTGAGACAGTTTTTACTCGAAACAAGAAGATTT-ATTTCACTCAAGATTG
1 AAGATT-TGTCTCGCTTGAGACAGTTTTTACTCGAAACAAGAAGATTTCATTTCACTCAAGATTG
458389 TTTTTCTTAAAAC
65 --TTT-TT-AAAC
* * *
458402 AAGATTTGTCTCGCTTGAGAC-GATTTTTACTCGAAAGAA-AACATTTCATTTCACTCAATATTG
1 AAGATTTGTCTCGCTTGAGACAG-TTTTTACTCGAAACAAGAAGATTTCATTTCACTCAAGATTG
*
458465 TTTTTAAAG
65 TTTTTAAAC
* * * *
458474 AAGATTTTATCTCTCTTGAGATAG-TTTCACTCGAAAC-AGAAGATTT
1 AAGA-TTTGTCTCGCTTGAGACAGTTTTTACTCGAAACAAGAAGATTT
458520 TATCTCGCTT
Statistics
Matches: 103, Mismatches: 10, Indels: 15
0.80 0.08 0.12
Matches are distributed among these distances:
71 1 0.01
72 24 0.23
73 16 0.16
74 4 0.04
75 7 0.07
76 45 0.44
77 6 0.06
ACGTcount: A:0.32, C:0.16, G:0.14, T:0.38
Consensus pattern (73 bp):
AAGATTTGTCTCGCTTGAGACAGTTTTTACTCGAAACAAGAAGATTTCATTTCACTCAAGATTGT
TTTTAAAC
Found at i:458533 original size:20 final size:20
Alignment explanation
Indices: 458510--458568 Score: 59
Period size: 19 Copynumber: 3.0 Consensus size: 20
458500 TCACTCGAAA
458510 CAGAAGATTTTATCTCGCTT
1 CAGAAGATTTTATCTCGCTT
* ***
458530 CAGATAG-TTTTA-CTTGAAA
1 CAGA-AGATTTTATCTCGCTT
458549 CAGAAGATTTTATCTCGCTT
1 CAGAAGATTTTATCTCGCTT
458569 GAGGTAGTTT
Statistics
Matches: 28, Mismatches: 8, Indels: 6
0.67 0.19 0.14
Matches are distributed among these distances:
18 2 0.07
19 12 0.43
20 12 0.43
21 2 0.07
ACGTcount: A:0.29, C:0.17, G:0.15, T:0.39
Consensus pattern (20 bp):
CAGAAGATTTTATCTCGCTT
Found at i:458535 original size:39 final size:39
Alignment explanation
Indices: 458472--458809 Score: 349
Period size: 39 Copynumber: 9.0 Consensus size: 39
458462 TTGTTTTTAA
* * *
458472 AGAAGATTTTATCTCTCTTGAGATAGTTTCACTCGAAAC
1 AGAAGATTTTATCTCGCTTGAGATAGTTTCCCTTGAAAC
* **
458511 AGAAGATTTTATCTCGCTTCAGATAGTTTTACTTGAAAC
1 AGAAGATTTTATCTCGCTTGAGATAGTTTCCCTTGAAAC
*
458550 AGAAGATTTTATCTCGCTTGAGGTAGTTTCCCTTGAAAC
1 AGAAGATTTTATCTCGCTTGAGATAGTTTCCCTTGAAAC
* *
458589 ATAAGATTTTATCTCGCTTGAGGTAGTTTCCCTTGAAAC
1 AGAAGATTTTATCTCGCTTGAGATAGTTTCCCTTGAAAC
* * *
458628 AAAAGATTTTATCTCTCTTGAGATAATTTCCCTTGAAAC
1 AGAAGATTTTATCTCGCTTGAGATAGTTTCCCTTGAAAC
* * * **
458667 --AA-ATTTTGTCTCTCTTGAGACAGTTTCTGTTGAAAC
1 AGAAGATTTTATCTCGCTTGAGATAGTTTCCCTTGAAAC
* * *
458703 --AA-ATTTTGTCTCTCTTGAGAGAGTTTCCCTT-AAA-
1 AGAAGATTTTATCTCGCTTGAGATAGTTTCCCTTGAAAC
* * * *
458737 ACAA-ATTTTATATCTCTTGAGACAGTTTCCCTTGAAAC
1 AGAAGATTTTATCTCGCTTGAGATAGTTTCCCTTGAAAC
* * *
458775 --AA-ATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAA
1 AGAAGATTTTATCTCGCTTGAGATAGTTTCCCTTGAAA
458810 AAAAATCTTT
Statistics
Matches: 269, Mismatches: 26, Indels: 11
0.88 0.08 0.04
Matches are distributed among these distances:
35 3 0.01
36 118 0.44
37 5 0.02
39 143 0.53
ACGTcount: A:0.28, C:0.18, G:0.15, T:0.38
Consensus pattern (39 bp):
AGAAGATTTTATCTCGCTTGAGATAGTTTCCCTTGAAAC
Found at i:458559 original size:19 final size:20
Alignment explanation
Indices: 458503--458565 Score: 67
Period size: 20 Copynumber: 3.2 Consensus size: 20
458493 GATAGTTTCA
458503 CTCGAAACAGAAGATTTTAT
1 CTCGAAACAGAAGATTTTAT
***
458523 CTCGCTTCAGATAG-TTTTA-
1 CTCGAAACAGA-AGATTTTAT
*
458542 CTTGAAACAGAAGATTTTAT
1 CTCGAAACAGAAGATTTTAT
458562 CTCG
1 CTCG
458566 CTTGAGGTAG
Statistics
Matches: 32, Mismatches: 8, Indels: 6
0.70 0.17 0.13
Matches are distributed among these distances:
18 2 0.06
19 12 0.38
20 16 0.50
21 2 0.06
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.35
Consensus pattern (20 bp):
CTCGAAACAGAAGATTTTAT
Found at i:458680 original size:36 final size:38
Alignment explanation
Indices: 458474--458998 Score: 389
Period size: 36 Copynumber: 14.6 Consensus size: 38
458464 GTTTTTAAAG
* *
458474 AAGATTTTATCTCTCTTGAGATAGTTTCACTCGAAACA
1 AAGATTTTATCTCTCTTGAGATAGTTTCCCTTGAAACA
* * **
458512 GAAGATTTTATCTCGCTTCAGATAGTTTTACTTGAAACA
1 -AAGATTTTATCTCTCTTGAGATAGTTTCCCTTGAAACA
* *
458551 GAAGATTTTATCTCGCTTGAGGTAGTTTCCCTTGAAACA
1 -AAGATTTTATCTCTCTTGAGATAGTTTCCCTTGAAACA
* *
458590 TAAGATTTTATCTCGCTTGAGGTAGTTTCCCTTGAAACAA
1 -AAGATTTTATCTCTCTTGAGATAGTTTCCCTTGAAAC-A
*
458630 AAGATTTTATCTCTCTTGAGATAATTTCCCTTGAAAC-
1 AAGATTTTATCTCTCTTGAGATAGTTTCCCTTGAAACA
* * **
458667 AA-ATTTTGTCTCTCTTGAGACAGTTTCTGTTGAAAC-
1 AAGATTTTATCTCTCTTGAGATAGTTTCCCTTGAAACA
* * *
458703 AA-ATTTTGTCTCTCTTGAGAGAGTTTCCCTTAAAAC-
1 AAGATTTTATCTCTCTTGAGATAGTTTCCCTTGAAACA
* *
458739 AA-ATTTTATATCTCTTGAGACAGTTTCCCTTGAAAC-
1 AAGATTTTATCTCTCTTGAGATAGTTTCCCTTGAAACA
* *
458775 AA-ATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAA-A
1 AAGATTTTATCTCTCTTGAGATAGTTTCCCTTGAAACA
* * *
458811 AA-A----A--TCT-TT-AAATCTGTTTCCCTGGAAACA
1 AAGATTTTATCTCTCTTGAGAT-AGTTTCCCTTGAAACA
* * * * *
458841 AA-T-TTTATCTCTCTTAAGACAGTTTTCCTTGAAA-T
1 AAGATTTTATCTCTCTTGAGATAGTTTCCCTTGAAACA
* * * * *
458876 AAG-TTTTGTCTCCCTTTAGACAGTTTCTCTTGAAACA
1 AAGATTTTATCTCTCTTGAGATAGTTTCCCTTGAAACA
* *
458913 CA-A----A-C-CT-TTGAGATCGTTTCCCTTGAAAC-
1 AAGATTTTATCTCTCTTGAGATAGTTTCCCTTGAAACA
* * *
458942 AA-ATTTTTTCTCTCTTGAGACAGTTACCCTTGAAACA
1 AAGATTTTATCTCTCTTGAGATAGTTTCCCTTGAAACA
* *
458979 AA-A-TCTATCTCACTTGAGAT
1 AAGATTTTATCTCTCTTGAGAT
458999 GGATTTTTAA
Statistics
Matches: 402, Mismatches: 61, Indels: 49
0.79 0.12 0.10
Matches are distributed among these distances:
28 2 0.00
29 16 0.04
30 24 0.06
31 1 0.00
32 1 0.00
33 1 0.00
34 1 0.00
35 7 0.02
36 200 0.50
37 8 0.02
39 140 0.35
40 1 0.00
ACGTcount: A:0.29, C:0.19, G:0.14, T:0.38
Consensus pattern (38 bp):
AAGATTTTATCTCTCTTGAGATAGTTTCCCTTGAAACA
Found at i:458883 original size:101 final size:102
Alignment explanation
Indices: 458614--458980 Score: 405
Period size: 101 Copynumber: 3.5 Consensus size: 102
458604 GCTTGAGGTA
* *
458614 GTTTCCCTTGAAACAAAAGATTTTATCTCTCTTGAGATAATTTCCCTTGAAACAAATTTTGTCTC
1 GTTTCCCTTGAAAC--AA-ATTTTATCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTC
* ** ** * **
458679 TCTTGAGACAGTTTCTGTTGAAACAAATTTTGTCTCTCTTGAGAGA
63 CCTTGAGACAGTTTCCCTTGAAACAAA----AAC-CT-TTGAAATC
* * *
458725 GTTTCCCTTAAAACAAATTTTATATCTCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCTCT
1 GTTTCCCTTGAAACAAATTTTATCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCCCT
*
458790 TGAGACAGTTTCCCTTGAAA-AAAAATCTTT-AAATC
66 TGAGACAGTTTCCCTTGAAACAAAAACCTTTGAAATC
* * * * *
458825 TGTTTCCCTGGAAACAAATTTTATCTCTCTTAAGACAGTTTTCCTTGAAATAAGTTTTGTCTCCC
1 -GTTTCCCTTGAAACAAATTTTATCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCCC
* * * *
458890 TTTAGACAGTTTCTCTTGAAACACAAACCTTTGAGATC
65 TTGAGACAGTTTCCCTTGAAACAAAAACCTTTGAAATC
* *
458928 GTTTCCCTTGAAACAAATTTTTTCTCTCTTGAGACAGTTACCCTTGAAACAAA
1 GTTTCCCTTGAAACAAATTTTATCTCTCTTGAGACAGTTTCCCTTGAAACAAA
458981 ATCTATCTCA
Statistics
Matches: 221, Mismatches: 32, Indels: 15
0.82 0.12 0.06
Matches are distributed among these distances:
100 2 0.01
101 77 0.35
102 56 0.25
103 4 0.02
107 3 0.01
108 64 0.29
109 2 0.01
111 13 0.06
ACGTcount: A:0.29, C:0.20, G:0.12, T:0.38
Consensus pattern (102 bp):
GTTTCCCTTGAAACAAATTTTATCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCCCT
TGAGACAGTTTCCCTTGAAACAAAAACCTTTGAAATC
Found at i:459424 original size:30 final size:29
Alignment explanation
Indices: 459390--459476 Score: 120
Period size: 30 Copynumber: 2.9 Consensus size: 29
459380 TTTTTATTCC
459390 ACCATATTTTATTCAAAATCCCATGCCACT
1 ACCAT-TTTTATTCAAAATCCCATGCCACT
*
459420 ACCATTTTTTATTCAACATCCCATGCCACT
1 ACCA-TTTTTATTCAAAATCCCATGCCACT
* *
459450 GCCATTTTATATTCAATATCCCATGCC
1 ACCATTTT-TATTCAAAATCCCATGCC
459477 CCCACGTGAA
Statistics
Matches: 52, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
29 4 0.08
30 47 0.90
31 1 0.02
ACGTcount: A:0.29, C:0.31, G:0.05, T:0.36
Consensus pattern (29 bp):
ACCATTTTTATTCAAAATCCCATGCCACT
Found at i:461679 original size:23 final size:23
Alignment explanation
Indices: 461645--461688 Score: 56
Period size: 21 Copynumber: 1.9 Consensus size: 23
461635 AAATATTGCT
461645 TAATAATTATTT-AC-TATAAGA
1 TAATAATTATTTCACTTATAAGA
461666 TAATATATCTATTTCACTTATAA
1 TAATA-AT-TATTTCACTTATAA
461689 TATTGTTGAT
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
21 5 0.26
22 2 0.11
23 5 0.26
24 2 0.11
25 5 0.26
ACGTcount: A:0.43, C:0.09, G:0.02, T:0.45
Consensus pattern (23 bp):
TAATAATTATTTCACTTATAAGA
Found at i:462491 original size:22 final size:24
Alignment explanation
Indices: 462461--462509 Score: 66
Period size: 22 Copynumber: 2.1 Consensus size: 24
462451 AAACGGCCGA
*
462461 AAAAAGTGCCA-AAAGATATA-AG
1 AAAAAGTGCCATAAAGACATAGAG
*
462483 AAAATGTGCCATAAAGACATAGAG
1 AAAAAGTGCCATAAAGACATAGAG
462507 AAA
1 AAA
462510 CGTGATATAC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 10 0.43
23 8 0.35
24 5 0.22
ACGTcount: A:0.57, C:0.10, G:0.18, T:0.14
Consensus pattern (24 bp):
AAAAAGTGCCATAAAGACATAGAG
Found at i:463012 original size:91 final size:91
Alignment explanation
Indices: 462905--463168 Score: 370
Period size: 91 Copynumber: 2.9 Consensus size: 91
462895 ACATTTCAAA
*
462905 TGGAGAGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAAGAAGTTCATAAAGAGAAGAACTT
1 TGGAGAGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAAGAAGTTCATAATGAGAAGAACTT
**
462970 GTTCAACCTTGGTTCAAGATTT-CTAG
66 GTTCAACCTTGCATCAAGATTTAC-AG
* *
462996 TGGAAAGTTCATAATGAGAAGAACTTATCCAACGAGGGAGAAGAAGTTCATAATGAGAAGAACTT
1 TGGAGAGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAAGAAGTTCATAATGAGAAGAACTT
* *
463061 GTTCAATCTTGCATCAATATTTACAG
66 GTTCAACCTTGCATCAAGATTTACAG
* * * *
463087 CGGAGAGTTCATAATGAGAATAACTCATCCGATA-GAGGCAGAAGAAGTTCATAATCAGAAGAAC
1 TGGAGAGTTCATAATGAGAAGAACTCATCC-A-ACGAGGGAGAAGAAGTTCATAATGAGAAGAAC
* *
463151 TTATTCAACATTGCATCA
64 TTGTTCAACCTTGCATCA
463169 CATATGGAGT
Statistics
Matches: 154, Mismatches: 16, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
91 108 0.70
92 45 0.29
93 1 0.01
ACGTcount: A:0.39, C:0.15, G:0.22, T:0.25
Consensus pattern (91 bp):
TGGAGAGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAAGAAGTTCATAATGAGAAGAACTT
GTTCAACCTTGCATCAAGATTTACAG
Found at i:463396 original size:30 final size:30
Alignment explanation
Indices: 463360--463426 Score: 116
Period size: 30 Copynumber: 2.2 Consensus size: 30
463350 ATTTTTTATT
463360 CCACCATATTTTATTCAACATCCCATGCCA
1 CCACCATATTTTATTCAACATCCCATGCCA
* *
463390 CTACCATTTTTTATTCAACATCCCATGCCA
1 CCACCATATTTTATTCAACATCCCATGCCA
463420 CCACCAT
1 CCACCAT
463427 GCCCCCACGT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
30 34 1.00
ACGTcount: A:0.28, C:0.37, G:0.03, T:0.31
Consensus pattern (30 bp):
CCACCATATTTTATTCAACATCCCATGCCA
Found at i:465623 original size:23 final size:23
Alignment explanation
Indices: 465589--465632 Score: 56
Period size: 21 Copynumber: 1.9 Consensus size: 23
465579 AAATATTGCT
465589 TAATAATTATTT-AC-TATAAGA
1 TAATAATTATTTCACTTATAAGA
465610 TAATATATCTATTTCACTTATAA
1 TAATA-AT-TATTTCACTTATAA
465633 TATTGTTGAT
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
21 5 0.26
22 2 0.11
23 5 0.26
24 2 0.11
25 5 0.26
ACGTcount: A:0.43, C:0.09, G:0.02, T:0.45
Consensus pattern (23 bp):
TAATAATTATTTCACTTATAAGA
Found at i:466434 original size:22 final size:24
Alignment explanation
Indices: 466404--466452 Score: 66
Period size: 22 Copynumber: 2.1 Consensus size: 24
466394 AAACAGCCGA
*
466404 AAAAAGTGCCA-AAAGATATA-AG
1 AAAAAGTGCCATAAAGACATAGAG
*
466426 AAAATGTGCCATAAAGACATAGAG
1 AAAAAGTGCCATAAAGACATAGAG
466450 AAA
1 AAA
466453 CGTAATATAC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 10 0.43
23 8 0.35
24 5 0.22
ACGTcount: A:0.57, C:0.10, G:0.18, T:0.14
Consensus pattern (24 bp):
AAAAAGTGCCATAAAGACATAGAG
Found at i:466697 original size:2 final size:2
Alignment explanation
Indices: 466690--466723 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
466680 ATTTAGGTCA
466690 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
466724 CTGATTTATT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:471519 original size:13 final size:14
Alignment explanation
Indices: 471501--471539 Score: 62
Period size: 13 Copynumber: 2.9 Consensus size: 14
471491 TCATAAATGG
471501 CTGCTGTGAAGGT-
1 CTGCTGTGAAGGTC
471514 CTGCTGTGAAGGTC
1 CTGCTGTGAAGGTC
*
471528 CTGCTGAGAAGG
1 CTGCTGTGAAGG
471540 ATGAGCACCT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
13 13 0.54
14 11 0.46
ACGTcount: A:0.18, C:0.18, G:0.38, T:0.26
Consensus pattern (14 bp):
CTGCTGTGAAGGTC
Found at i:473142 original size:111 final size:111
Alignment explanation
Indices: 473005--473332 Score: 558
Period size: 111 Copynumber: 3.0 Consensus size: 111
472995 ATTACAAAAA
*
473005 TTAATTCTTAATCTAATAATCATGCATTATATAAATCAACTAATTATTACTAATAATTTAAATTA
1 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAATTA
* *
473070 AATTAAAACGTTAAAATGTTACCGTATCAACAAAGTGTCGATATAT
66 AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTCGAGATAT
473116 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAATTA
1 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAATTA
*
473181 AATTAAAACGTTAAAATATTACCGTATCAGCAAAGTGTCGAGATAT
66 AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTCGAGATAT
*
473227 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAAATATTACTAATAA--T---TTA
1 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAATTA
* *
473287 AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTATAGAGATAT
66 AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTCGAGATAT
473333 ATGATTTCCG
Statistics
Matches: 209, Mismatches: 8, Indels: 5
0.94 0.04 0.02
Matches are distributed among these distances:
106 46 0.22
109 1 0.00
111 162 0.78
ACGTcount: A:0.45, C:0.12, G:0.07, T:0.36
Consensus pattern (111 bp):
TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAATTA
AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTCGAGATAT
Found at i:473436 original size:17 final size:18
Alignment explanation
Indices: 473393--473433 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
473383 GAATTATATT
473393 AGTAAAATA-TTAAATAA
1 AGTAAAATACTTAAATAA
473410 AGTAAAATACTTAAATAA
1 AGTAAAATACTTAAATAA
*
473428 ATTAAA
1 AGTAAA
473434 TACATAATAG
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 9 0.41
18 13 0.59
ACGTcount: A:0.63, C:0.02, G:0.05, T:0.29
Consensus pattern (18 bp):
AGTAAAATACTTAAATAA
Found at i:473690 original size:50 final size:50
Alignment explanation
Indices: 473636--473766 Score: 147
Period size: 50 Copynumber: 2.6 Consensus size: 50
473626 AGATAACTAG
*
473636 GTATAGCGCGGATCAGGGGGCGCGCTATA-TCCACGTGGCGCCAGATCACC
1 GTATAGCGCGGATCAGGGGGCGCGCTATACT-CACGTGGCGCCAAATCACC
* ** * * *
473686 GTATATCGCGGGGCAGAGGGCGCGCTATACTCATGTGGCGCCAAATCAGC
1 GTATAGCGCGGATCAGGGGGCGCGCTATACTCACGTGGCGCCAAATCACC
* * * *
473736 GTATAGCACGGTTCAGGGGGCACGCTTTACT
1 GTATAGCGCGGATCAGGGGGCGCGCTATACT
473767 GTTACGAGTG
Statistics
Matches: 66, Mismatches: 14, Indels: 2
0.80 0.17 0.02
Matches are distributed among these distances:
50 65 0.98
51 1 0.02
ACGTcount: A:0.21, C:0.27, G:0.34, T:0.19
Consensus pattern (50 bp):
GTATAGCGCGGATCAGGGGGCGCGCTATACTCACGTGGCGCCAAATCACC
Found at i:479112 original size:31 final size:31
Alignment explanation
Indices: 479077--479135 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 31
479067 CTTGATAATT
*
479077 TTAAACTATAAAGCTTTT-AAGTCAAATTAAA
1 TTAAACTATAAA-CTTTTCAAATCAAATTAAA
* *
479108 TTAAATTTTAAACTTTTCAAATCAAATT
1 TTAAACTATAAACTTTTCAAATCAAATT
479136 TAATAATATT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 5 0.21
31 19 0.79
ACGTcount: A:0.46, C:0.10, G:0.03, T:0.41
Consensus pattern (31 bp):
TTAAACTATAAACTTTTCAAATCAAATTAAA
Found at i:490199 original size:19 final size:21
Alignment explanation
Indices: 490154--490199 Score: 57
Period size: 19 Copynumber: 2.4 Consensus size: 21
490144 TATTAGAGAT
490154 AAATCTTA-TAGAATCAAATA
1 AAATCTTATTAGAATCAAATA
490174 AAA--TTATTAGAA-C-AATA
1 AAATCTTATTAGAATCAAATA
490191 AAATCTTAT
1 AAATCTTAT
490200 CATTAAACTG
Statistics
Matches: 23, Mismatches: 0, Indels: 7
0.77 0.00 0.23
Matches are distributed among these distances:
17 7 0.30
18 4 0.17
19 9 0.39
20 3 0.13
ACGTcount: A:0.54, C:0.09, G:0.04, T:0.33
Consensus pattern (21 bp):
AAATCTTATTAGAATCAAATA
Found at i:498953 original size:43 final size:45
Alignment explanation
Indices: 498888--499040 Score: 142
Period size: 43 Copynumber: 3.5 Consensus size: 45
498878 TTTTAGATAA
* * *
498888 TTTGCGGCGTTT-TTTCCGAAAAA-GCTGTTATATATCTCGACCT
1 TTTGCGGCGTTTGTATCCAAAAAACGCTGTTATAGATCTCGACCT
* * *
498931 TTTACGGCGTTTGTATCCAAAAAACGCCGCTATAGATCTCGA-CT
1 TTTGCGGCGTTTGTATCCAAAAAACGCTGTTATAGATCTCGACCT
* ** *
498975 GTTTGCGGTGTTTG-AT-CAAAAAATACT-TATATAGAT-TTGACCT
1 -TTTGCGGCGTTTGTATCCAAAAAACGCTGT-TATAGATCTCGACCT
499018 TTTGCGGCGTTTGT-TCCAAAAAA
1 TTTGCGGCGTTTGTATCCAAAAAA
499041 ATATCGTCCT
Statistics
Matches: 89, Mismatches: 14, Indels: 14
0.76 0.12 0.12
Matches are distributed among these distances:
42 16 0.18
43 35 0.39
44 13 0.15
45 25 0.28
ACGTcount: A:0.26, C:0.19, G:0.19, T:0.36
Consensus pattern (45 bp):
TTTGCGGCGTTTGTATCCAAAAAACGCTGTTATAGATCTCGACCT
Found at i:501859 original size:16 final size:16
Alignment explanation
Indices: 501838--501871 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
501828 TACATAGTTA
501838 CATGTGATATTATAAT
1 CATGTGATATTATAAT
501854 CATGTGATATTATAAT
1 CATGTGATATTATAAT
501870 CA
1 CA
501872 AGGGTTGAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.38, C:0.09, G:0.12, T:0.41
Consensus pattern (16 bp):
CATGTGATATTATAAT
Found at i:505185 original size:113 final size:112
Alignment explanation
Indices: 505043--505374 Score: 477
Period size: 113 Copynumber: 2.9 Consensus size: 112
505033 ATAGAGTCAT
* * *
505043 GCAAAAGGTTGAACAAGCTCTTCTTATTATGAACTTCTTCTTCCTCTTCAGATAAGTTCTTCTCA
1 GCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCA
*
505108 TTATGAACTTTCTCTGGAAAAGTTGATCCATCGAGTTATGAATTCAA
66 TTATGAACTTTCTCTGGAAAAGTTGATCCATCGAGTGATGAATTCAA
* *
505155 GCAAAAGGTTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCT
1 GCAAAAGG-TTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCC-TCTTCAGATGAGTTCTTCT
* * * **
505220 CATTATGAACTCTAC-CTGGAAATGTTGATCCATCAAGTGATGAATTTGA
64 CATTATGAACT-TTCTCTGGAAAAGTTGATCCATCGAGTGATGAATTCAA
* * *
505269 GCAAAAGGTTAAACAAGTCCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTATTCTC
1 GCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCC-TCTTCAGATGAGTTCTTCTC
* *
505334 ATTATGAACTTTCTCTGGAAATGTTAATCCATCGAGTGATG
65 ATTATGAACTTTCTCTGGAAAAGTTGATCCATCGAGTGATG
505375 GATTTAAATC
Statistics
Matches: 197, Mismatches: 19, Indels: 7
0.88 0.09 0.03
Matches are distributed among these distances:
112 10 0.05
113 119 0.60
114 66 0.34
115 2 0.01
ACGTcount: A:0.28, C:0.19, G:0.15, T:0.38
Consensus pattern (112 bp):
GCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCA
TTATGAACTTTCTCTGGAAAAGTTGATCCATCGAGTGATGAATTCAA
Found at i:516837 original size:28 final size:26
Alignment explanation
Indices: 516779--516837 Score: 64
Period size: 28 Copynumber: 2.2 Consensus size: 26
516769 AACAATATTA
*
516779 AAAAATAATATACATATAAATATTGT
1 AAAAATAATATACATATAAAAATTGT
* * *
516805 GAAAATAATAAGTATATATAAAAATTTT
1 AAAAATAAT-A-TACATATAAAAATTGT
516833 AAAAA
1 AAAAA
516838 CATAATTATA
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
26 8 0.31
27 1 0.04
28 17 0.65
ACGTcount: A:0.61, C:0.02, G:0.05, T:0.32
Consensus pattern (26 bp):
AAAAATAATATACATATAAAAATTGT
Found at i:527972 original size:42 final size:42
Alignment explanation
Indices: 527910--528029 Score: 222
Period size: 42 Copynumber: 2.9 Consensus size: 42
527900 TTTCCCCGAA
* *
527910 TTCCCGTGTTTGTTTTACGTAATTCGTTTTCCGGAAAATGTT
1 TTCCCGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAACGTT
527952 TTCCCGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAACGTT
1 TTCCCGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAACGTT
527994 TTCCCGTGTTTGTTTCACGTAATTCGTTTTCCGGAA
1 TTCCCGTGTTTGTTTCACGTAATTCGTTTTCCGGAA
528030 TGTAATTCAT
Statistics
Matches: 76, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
42 76 1.00
ACGTcount: A:0.16, C:0.20, G:0.19, T:0.45
Consensus pattern (42 bp):
TTCCCGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAACGTT
Found at i:528251 original size:21 final size:22
Alignment explanation
Indices: 528218--528276 Score: 79
Period size: 21 Copynumber: 2.8 Consensus size: 22
528208 TAATTATTAA
*
528218 AATATTTAAAATATAT-TTATT
1 AATATTTATAATATATATTATT
528239 AATATTTATAATA-ATATTATT
1 AATATTTATAATATATATTATT
*
528260 -ATATTTTTAATATATAT
1 AATATTTATAATATATAT
528277 AAAATAATCA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
20 13 0.38
21 21 0.62
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (22 bp):
AATATTTATAATATATATTATT
Found at i:528305 original size:56 final size:59
Alignment explanation
Indices: 528229--528389 Score: 138
Period size: 56 Copynumber: 2.7 Consensus size: 59
528219 ATATTTAAAA
* * *
528229 TATATTTATTAATATTTATAATAATATTATTATATTTTTAATATATATAAA-ATAATCAAT
1 TATATATA-TAATATATA-AATAATATTATTATATTTTTAATATATATAAATAAAATCAAT
***
528289 TATAT-TATAATATATAAGATATATATT-TT-TA-TTTTAATA-ATATAAATAAAATTTTT
1 TATATATATAATATATAA-ATA-ATATTATTATATTTTTAATATATATAAATAAAATCAAT
* * *
528345 TATATATTTAATA-ATGAATAATATTATTTATATATTTCAATATAT
1 TATATATATAATATATAAATAATATTA-TTATAT-TTTTAATATAT
528390 TTAGTAAAGA
Statistics
Matches: 83, Mismatches: 8, Indels: 20
0.75 0.07 0.18
Matches are distributed among these distances:
54 5 0.06
55 10 0.12
56 23 0.28
57 11 0.13
58 13 0.16
59 14 0.17
60 7 0.08
ACGTcount: A:0.46, C:0.01, G:0.01, T:0.52
Consensus pattern (59 bp):
TATATATATAATATATAAATAATATTATTATATTTTTAATATATATAAATAAAATCAAT
Found at i:528321 original size:27 final size:27
Alignment explanation
Indices: 528211--528334 Score: 73
Period size: 27 Copynumber: 4.6 Consensus size: 27
528201 AAAATATTAA
* *
528211 TTATTAAAATATTTAAAATATAT-TTAT
1 TTATTATAATATATAAAATATATATT-T
**
528238 TAATATTTATAATA-ATATTAT-TATATTT
1 T--TA-TTATAATATATAAAATATATATTT
*
528266 TTA--AT-ATATATAAAATA-ATCAATT
1 TTATTATAATATATAAAATATAT-ATTT
* *
528290 ATATTATAATATATAAGATATATATTT
1 TTATTATAATATATAAAATATATATTT
*
528317 TTATTTTAATAATATAAA
1 TTATTATAAT-ATATAAA
528335 TAAAATTTTT
Statistics
Matches: 72, Mismatches: 13, Indels: 23
0.67 0.12 0.21
Matches are distributed among these distances:
22 3 0.04
23 9 0.12
24 5 0.07
26 4 0.06
27 23 0.32
28 13 0.18
29 8 0.11
30 7 0.10
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.50
Consensus pattern (27 bp):
TTATTATAATATATAAAATATATATTT
Found at i:528381 original size:59 final size:60
Alignment explanation
Indices: 528248--528389 Score: 144
Period size: 56 Copynumber: 2.5 Consensus size: 60
528238 TAATATTTAT
528248 AATAATATTA-TTATAT-TTTTAATATATATAAAATAATCAATTATATTATAATATATAAG
1 AATAATATTATTTATATATTTTAATATATATAAAATAA-CAATTATATTATAATATATAAG
* *
528307 -AT-ATA-TATTT-T-TATTTTAATA-ATAT-AAATAA-AATT-TTTTATATATTTAATAATG
1 AATAATATTATTTATATATTTTAATATATATAAAATAACAATTATATTATA-ATAT-ATAA-G
*
528361 AATAATATTATTTATATATTTCAATATAT
1 AATAATATTATTTATATATTTTAATATAT
528390 TTAGTAAAGA
Statistics
Matches: 69, Mismatches: 3, Indels: 21
0.74 0.03 0.23
Matches are distributed among these distances:
51 6 0.09
52 7 0.10
53 4 0.06
54 7 0.10
55 7 0.10
56 14 0.20
57 10 0.14
58 3 0.04
59 9 0.13
60 2 0.03
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.50
Consensus pattern (60 bp):
AATAATATTATTTATATATTTTAATATATATAAAATAACAATTATATTATAATATATAAG
Found at i:528628 original size:20 final size:20
Alignment explanation
Indices: 528550--528619 Score: 122
Period size: 20 Copynumber: 3.5 Consensus size: 20
528540 TTTCCAGATG
528550 TTTTCCAGAAATGTAATTCA
1 TTTTCCAGAAATGTAATTCA
*
528570 TTTTCTAGAAATGTAATTCA
1 TTTTCCAGAAATGTAATTCA
*
528590 TTTTACAGAAATGTAATTCA
1 TTTTCCAGAAATGTAATTCA
528610 TTTTCCAGAA
1 TTTTCCAGAA
528620 TTCAAATTCC
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 46 1.00
ACGTcount: A:0.36, C:0.13, G:0.10, T:0.41
Consensus pattern (20 bp):
TTTTCCAGAAATGTAATTCA
Found at i:528628 original size:40 final size:40
Alignment explanation
Indices: 528550--528628 Score: 113
Period size: 40 Copynumber: 2.0 Consensus size: 40
528540 TTTCCAGATG
* * **
528550 TTTTCCAGAAATGTAATTCATTTTCTAGAAATGTAATTCA
1 TTTTACAGAAATGTAATTCATTTTCCAGAAATCAAATTCA
*
528590 TTTTACAGAAATGTAATTCATTTTCCAGAATTCAAATTC
1 TTTTACAGAAATGTAATTCATTTTCCAGAAATCAAATTC
528629 CAGTAATTCA
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
40 34 1.00
ACGTcount: A:0.35, C:0.14, G:0.09, T:0.42
Consensus pattern (40 bp):
TTTTACAGAAATGTAATTCATTTTCCAGAAATCAAATTCA
Found at i:528638 original size:15 final size:15
Alignment explanation
Indices: 528602--528683 Score: 112
Period size: 15 Copynumber: 5.5 Consensus size: 15
528592 TTACAGAAAT
**
528602 GTAATTCATTTTCCA
1 GTAATTCAAATTCCA
528617 G-AATTCAAATTCCA
1 GTAATTCAAATTCCA
**
528631 GTAATTCATTTTCCA
1 GTAATTCAAATTCCA
*
528646 GTAATTCAAATTTCA
1 GTAATTCAAATTCCA
528661 GTAATTCAAATTCCA
1 GTAATTCAAATTCCA
528676 GTAATTCA
1 GTAATTCA
528684 TTTTCTGGAA
Statistics
Matches: 58, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
14 12 0.21
15 46 0.79
ACGTcount: A:0.35, C:0.18, G:0.07, T:0.39
Consensus pattern (15 bp):
GTAATTCAAATTCCA
Found at i:528654 original size:30 final size:30
Alignment explanation
Indices: 528602--528683 Score: 130
Period size: 30 Copynumber: 2.8 Consensus size: 30
528592 TTACAGAAAT
528602 GTAATTCATTTTCCAG-AATTCAAATTCCA
1 GTAATTCATTTTCCAGTAATTCAAATTCCA
*
528631 GTAATTCATTTTCCAGTAATTCAAATTTCA
1 GTAATTCATTTTCCAGTAATTCAAATTCCA
**
528661 GTAATTCAAATTCCAGTAATTCA
1 GTAATTCATTTTCCAGTAATTCA
528684 TTTTCTGGAA
Statistics
Matches: 49, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
29 16 0.33
30 33 0.67
ACGTcount: A:0.35, C:0.18, G:0.07, T:0.39
Consensus pattern (30 bp):
GTAATTCATTTTCCAGTAATTCAAATTCCA
Found at i:528674 original size:45 final size:44
Alignment explanation
Indices: 528602--528688 Score: 140
Period size: 45 Copynumber: 2.0 Consensus size: 44
528592 TTACAGAAAT
*
528602 GTAATTCATTTTCCAGAATTCAAATTCCAGTAATTCATTTTCCA
1 GTAATTCAATTTCCAGAATTCAAATTCCAGTAATTCATTTTCCA
528646 GTAATTCAAATTT-CAGTAATTCAAATTCCAGTAATTCATTTTC
1 GTAATTC-AATTTCCAG-AATTCAAATTCCAGTAATTCATTTTC
528689 TGGAAAACCA
Statistics
Matches: 40, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
44 10 0.25
45 30 0.75
ACGTcount: A:0.33, C:0.18, G:0.07, T:0.41
Consensus pattern (44 bp):
GTAATTCAATTTCCAGAATTCAAATTCCAGTAATTCATTTTCCA
Found at i:531654 original size:29 final size:27
Alignment explanation
Indices: 531618--531676 Score: 100
Period size: 29 Copynumber: 2.1 Consensus size: 27
531608 TGAAAAAATG
531618 AAAACCACATACACGTGGTTAACAAAAGC
1 AAAACCACATACACGTGGTT-AC-AAAGC
531647 AAAACCACATACACGTGGTTACAAAGC
1 AAAACCACATACACGTGGTTACAAAGC
531674 AAA
1 AAA
531677 TGAATATGGG
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
27 8 0.27
28 2 0.07
29 20 0.67
ACGTcount: A:0.49, C:0.24, G:0.14, T:0.14
Consensus pattern (27 bp):
AAAACCACATACACGTGGTTACAAAGC
Found at i:533475 original size:106 final size:106
Alignment explanation
Indices: 533167--534313 Score: 1594
Period size: 106 Copynumber: 10.9 Consensus size: 106
533157 GCATTGTTCC
* * * ** * *
533167 GAGTCCAATATCCTCCG-TCGTGAAGTTAAAATTGGCTCTGGAACCGGGAAATTGTTTATTGACA
1 GAGTCCAATATCCTTCGCT-GTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACA
* * * * * *
533231 ACCAACCGTCCTTTCGTTGTGAAGTTGAACTTGTGTTGTCTC
65 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
533273 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTG-AA-T--GAA-AT-TTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
* * * * * *
533332 TCAGCCGCCCCTTCATCGTGAAGTTGAGCTTGTGTTGTCTTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTC-TG
* * * * * * *
533374 GA-TCCAAGATCCTTCGTTGAGAACTTGAAATTGGCTTTGAAATTGGGAAGTTGTTTATTGACTA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
* *
533438 CCAGCGGTCCCTTCGCCGTGAAGTTGAACTTGCGTTGTCTT
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
533479 GAGTCCAATATCCTAT-GCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACA
1 GAGTCCAATATCCT-TCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACA
533543 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
65 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
533585 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTAAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
* * *
533650 CTAACGGTCCATTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
533691 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
* * * *
533756 CCAGTGGTCCCTTCATCGTGAAGTTGAACTTGCATTGTCTT
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
533797 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTAGCTCTGAAATTGGGAAATTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
** * * *
533862 CCAGCCATCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTT
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
** *
533903 GAGTCCAATATCCTTCATTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
* *
533968 CCAGTGGTCCCTTCGTCATGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
534009 GAGTCCAATATCCTTCGATGTGAAGTTGAAATTGGCTCCGAAATTGGGAAATTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
534074 CCAGCGG-CCCTTCGTCGTGAAGTTGAACTTGCGATTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCG-TTGTCTG
*
534115 GAGTCCAATATCTTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
* *
534180 CCAGCGGTCCCTTCGTCATGAAGTTGAACTTGCGTTGTCTC
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
534221 GAGTCCAATATCCTTCGCTGTGAAGTTAAAATTGGCTCTAAAATTGGGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
*
534286 CCAAACGGTCCCTTCGTCGTGAAGTTGA
66 CC-AGCGGTCCCTTCGTCGTGAAGTTGA
534314 GCCTTGACTT
Statistics
Matches: 928, Mismatches: 99, Indels: 27
0.88 0.09 0.03
Matches are distributed among these distances:
100 73 0.08
101 6 0.01
102 4 0.00
104 3 0.00
105 32 0.03
106 760 0.82
107 50 0.05
ACGTcount: A:0.24, C:0.18, G:0.24, T:0.34
Consensus pattern (106 bp):
GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
Found at i:534585 original size:37 final size:37
Alignment explanation
Indices: 534490--534695 Score: 168
Period size: 36 Copynumber: 5.8 Consensus size: 37
534480 GAAAATTGTG
* * *
534490 TTGTTTCGAGAGAAACTATCTCAAGGGAGACAACA-T
1 TTGTTTCAAGGGAAACTATCTCAAGGGAGACAAAATT
* *
534526 TTGTTTCAAGAGG-AACTGTCTCAAGTGAGACAAAATT
1 TTGTTTCAAG-GGAAACTATCTCAAGGGAGACAAAATT
534563 TTGTTTCAAGGGAAACTATCTCAAGGGAGACAAAA-T
1 TTGTTTCAAGGGAAACTATCTCAAGGGAGACAAAATT
** * * *
534599 TCATTTCAAGGGAAA-TGTTTTCAA---TG------TT
1 TTGTTTCAAGGGAAACT-ATCTCAAGGGAGACAAAATT
* *
534627 TATGTTTCAAGAGAACACTGTCTCAAGGGAGACAAAATT
1 T-TGTTTCAAGGGAA-ACTATCTCAAGGGAGACAAAATT
*
534666 TTGTTTCAAGGGAAACTATCTCAAGCGAGA
1 TTGTTTCAAGGGAAACTATCTCAAGGGAGA
534696 TAAGATCTTG
Statistics
Matches: 132, Mismatches: 21, Indels: 33
0.71 0.11 0.18
Matches are distributed among these distances:
28 2 0.02
29 10 0.08
30 6 0.05
31 1 0.01
33 2 0.02
35 1 0.01
36 49 0.37
37 46 0.35
38 12 0.09
39 3 0.02
ACGTcount: A:0.35, C:0.15, G:0.21, T:0.29
Consensus pattern (37 bp):
TTGTTTCAAGGGAAACTATCTCAAGGGAGACAAAATT
Found at i:534707 original size:37 final size:38
Alignment explanation
Indices: 534629--534713 Score: 100
Period size: 37 Copynumber: 2.3 Consensus size: 38
534619 TCAATGTTTA
* * *
534629 TGTTTCAAGAGAACACTGTCTCAAGGGAGACAAAATTT
1 TGTTTCAAGAGAACACTATCTCAAGCGAGACAAAATCT
* * *
534667 TGTTTCAAGGGAA-ACTATCTCAAGCGAGATAAGATCT
1 TGTTTCAAGAGAACACTATCTCAAGCGAGACAAAATCT
*
534704 TGTTTTAAGA
1 TGTTTCAAGA
534714 AAAACAATCT
Statistics
Matches: 39, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
37 27 0.69
38 12 0.31
ACGTcount: A:0.35, C:0.14, G:0.21, T:0.29
Consensus pattern (38 bp):
TGTTTCAAGAGAACACTATCTCAAGCGAGACAAAATCT
Found at i:534793 original size:72 final size:72
Alignment explanation
Indices: 534684--534867 Score: 244
Period size: 72 Copynumber: 2.5 Consensus size: 72
534674 AGGGAAACTA
* * **
534684 TCTCAAGCGAGATAAGATCTTGTTTTAAGAAAAACAATCTTGAGGGAAATAAATC-TCTTTTCGA
1 TCTCAAGCGAGACAAGGTC-TGTTTTAAGAAAAACAATCTCAAGGGAAATAAATCTTC-TTTCGA
*
534748 GTAAAGCAG
64 GTAAAACAG
* **
534757 TCTCAAGCGAGACAAGGTCTATTTTAAGAATGACAATCTCAAGGGAAATAAATCTTCTTTCGAGT
1 TCTCAAGCGAGACAAGGTCTGTTTTAAGAAAAACAATCTCAAGGGAAATAAATCTTCTTTCGAGT
534822 AAAACAG
66 AAAACAG
* * *
534829 TCTCAAGTGAGACAAAGTCTGTTTTAAGAAAAATAATCT
1 TCTCAAGCGAGACAAGGTCTGTTTTAAGAAAAACAATCT
534868 TGAGTGAGAT
Statistics
Matches: 96, Mismatches: 14, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
72 77 0.80
73 19 0.20
ACGTcount: A:0.39, C:0.15, G:0.18, T:0.28
Consensus pattern (72 bp):
TCTCAAGCGAGACAAGGTCTGTTTTAAGAAAAACAATCTCAAGGGAAATAAATCTTCTTTCGAGT
AAAACAG
Found at i:535718 original size:22 final size:22
Alignment explanation
Indices: 535693--535735 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
535683 ATTTTTGTTT
*
535693 ATTTGATGCTCAATGGTTTGAC
1 ATTTGATGCTCAAAGGTTTGAC
535715 ATTTGATGCTCAAAGGTTTGA
1 ATTTGATGCTCAAAGGTTTGA
535736 TGGGGTAGCT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.26, C:0.12, G:0.23, T:0.40
Consensus pattern (22 bp):
ATTTGATGCTCAAAGGTTTGAC
Found at i:536328 original size:9 final size:8
Alignment explanation
Indices: 536314--536386 Score: 53
Period size: 9 Copynumber: 9.0 Consensus size: 8
536304 TTTGCATGTG
536314 CTTTTTGT
1 CTTTTTGT
536322 CCTTTTT-T
1 -CTTTTTGT
536330 CTTTTTGTT
1 CTTTTTG-T
*
536339 CTTTTTTT
1 CTTTTTGT
536347 GC-TTTTGT
1 -CTTTTTGT
536355 -TTTTTGT
1 CTTTTTGT
* *
536362 TTTTTTTT
1 CTTTTTGT
*
536370 CTTTTTGCC
1 CTTTTTG-T
536379 CTTTTTGT
1 CTTTTTGT
536387 TCTGATTGAA
Statistics
Matches: 51, Mismatches: 7, Indels: 13
0.72 0.10 0.18
Matches are distributed among these distances:
7 12 0.24
8 18 0.35
9 21 0.41
ACGTcount: A:0.00, C:0.14, G:0.10, T:0.77
Consensus pattern (8 bp):
CTTTTTGT
Found at i:536335 original size:16 final size:16
Alignment explanation
Indices: 536314--536345 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
536304 TTTGCATGTG
536314 CTTTTTGTCCTTTTTT
1 CTTTTTGTCCTTTTTT
*
536330 CTTTTTGTTCTTTTTT
1 CTTTTTGTCCTTTTTT
536346 TGCTTTTGTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.00, C:0.16, G:0.06, T:0.78
Consensus pattern (16 bp):
CTTTTTGTCCTTTTTT
Found at i:536359 original size:13 final size:11
Alignment explanation
Indices: 536325--536369 Score: 54
Period size: 11 Copynumber: 3.8 Consensus size: 11
536315 TTTTTGTCCT
536325 TTTTTCTTTTTG
1 TTTTT-TTTTTG
*
536337 TTCTTTTTTTG
1 TTTTTTTTTTG
536348 CTTTTGTTTTTTG
1 -TTTT-TTTTTTG
536361 TTTTTTTTT
1 TTTTTTTTT
536370 CTTTTTGCCC
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
11 11 0.38
12 11 0.38
13 7 0.24
ACGTcount: A:0.00, C:0.07, G:0.09, T:0.84
Consensus pattern (11 bp):
TTTTTTTTTTG
Found at i:536376 original size:16 final size:16
Alignment explanation
Indices: 536314--536375 Score: 54
Period size: 17 Copynumber: 3.8 Consensus size: 16
536304 TTTGCATGTG
**
536314 CTTTTTGTCCTTTTTT
1 CTTTTTGTTTTTTTTT
536330 CTTTTTGTTCTTTTTTT
1 CTTTTTGTT-TTTTTTT
536347 GC-TTTTGTTTTTTGTTT
1 -CTTTTTGTTTTTT-TTT
* *
536364 TTTTTTCTTTTT
1 CTTTTTGTTTTT
536376 GCCCTTTTTG
Statistics
Matches: 38, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
16 12 0.32
17 25 0.66
18 1 0.03
ACGTcount: A:0.00, C:0.11, G:0.08, T:0.81
Consensus pattern (16 bp):
CTTTTTGTTTTTTTTT
Found at i:539566 original size:28 final size:29
Alignment explanation
Indices: 539509--539572 Score: 107
Period size: 29 Copynumber: 2.3 Consensus size: 29
539499 AAAAATGAAA
539509 AAAAG-AAAACCACATACACGTGGTTAAC
1 AAAAGCAAAACCACATACACGTGGTTAAC
539537 AAAAGCAAAACCACATACACGTGGTT-AC
1 AAAAGCAAAACCACATACACGTGGTTAAC
539565 -AAAGCAAA
1 AAAAGCAAA
539573 TGAATATGGG
Statistics
Matches: 35, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
27 8 0.23
28 7 0.20
29 20 0.57
ACGTcount: A:0.52, C:0.22, G:0.14, T:0.12
Consensus pattern (29 bp):
AAAAGCAAAACCACATACACGTGGTTAAC
Found at i:540549 original size:9 final size:9
Alignment explanation
Indices: 540535--540564 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
540525 AACGAAATTA
540535 ATAATATGT
1 ATAATATGT
*
540544 ATAATATAT
1 ATAATATGT
540553 ATAATATGT
1 ATAATATGT
540562 ATA
1 ATA
540565 TACGTATGTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.50, C:0.00, G:0.07, T:0.43
Consensus pattern (9 bp):
ATAATATGT
Found at i:541109 original size:31 final size:31
Alignment explanation
Indices: 541068--541175 Score: 108
Period size: 31 Copynumber: 3.5 Consensus size: 31
541058 TTACCTGAAT
* * * *
541068 CGAAGTCAACCAATCCAATATTGACCCAATC
1 CGAAGCCAACCGATCCGATATTGACCAAATC
** **
541099 CGAAGCCAACCGATCCGATATCAACCTGATC
1 CGAAGCCAACCGATCCGATATTGACCAAATC
* *
541130 CGAAAACTAACCGATCCGATATTGACCAAATC
1 CG-AAGCCAACCGATCCGATATTGACCAAATC
*
541162 CGAAGCCAATCGAT
1 CGAAGCCAACCGAT
541176 TTGATATCAA
Statistics
Matches: 60, Mismatches: 16, Indels: 2
0.77 0.21 0.03
Matches are distributed among these distances:
31 35 0.58
32 25 0.42
ACGTcount: A:0.37, C:0.31, G:0.14, T:0.18
Consensus pattern (31 bp):
CGAAGCCAACCGATCCGATATTGACCAAATC
Found at i:541131 original size:16 final size:15
Alignment explanation
Indices: 541105--541151 Score: 58
Period size: 16 Copynumber: 3.0 Consensus size: 15
541095 AATCCGAAGC
541105 CAACCGATCCGATAT
1 CAACCGATCCGATAT
* *
541120 CAACCTGATCCGAAAA
1 CAACC-GATCCGATAT
541136 CTAACCGATCCGATAT
1 C-AACCGATCCGATAT
541152 TGACCAAATC
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
15 5 0.19
16 17 0.65
17 4 0.15
ACGTcount: A:0.36, C:0.32, G:0.13, T:0.19
Consensus pattern (15 bp):
CAACCGATCCGATAT
Found at i:541144 original size:32 final size:32
Alignment explanation
Indices: 541106--541202 Score: 97
Period size: 32 Copynumber: 3.1 Consensus size: 32
541096 ATCCGAAGCC
541106 AACCGATCCGATATCAACCTGATCCGAAAACT
1 AACCGATCCGATATCAACCTGATCCGAAAACT
** ** * *
541138 AACCGATCCGATATTGACCAAATCCG-AAGCC
1 AACCGATCCGATATCAACCTGATCCGAAAACT
* ** *
541169 AATCGATTTGATATCAACCTGATCCAAAAACT
1 AACCGATCCGATATCAACCTGATCCGAAAACT
541201 AA
1 AA
541203 TCAATCTGAA
Statistics
Matches: 48, Mismatches: 16, Indels: 2
0.73 0.24 0.03
Matches are distributed among these distances:
31 21 0.44
32 27 0.56
ACGTcount: A:0.39, C:0.28, G:0.12, T:0.21
Consensus pattern (32 bp):
AACCGATCCGATATCAACCTGATCCGAAAACT
Found at i:541163 original size:63 final size:63
Alignment explanation
Indices: 541075--541208 Score: 196
Period size: 63 Copynumber: 2.1 Consensus size: 63
541065 AATCGAAGTC
* *
541075 AACCAATCCAATATTGACCCAATCCGAAGCCAACCGATCCGATATCAACCTGATCCGAAAACT
1 AACCAATCCAATATTGACCAAATCCGAAGCCAACCGATCCGATATCAACCTGATCCAAAAACT
* * * **
541138 AACCGATCCGATATTGACCAAATCCGAAGCCAATCGATTTGATATCAACCTGATCCAAAAACT
1 AACCAATCCAATATTGACCAAATCCGAAGCCAACCGATCCGATATCAACCTGATCCAAAAACT
*
541201 AATCAATC
1 AACCAATC
541209 TGAACTGAAT
Statistics
Matches: 62, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
63 62 1.00
ACGTcount: A:0.39, C:0.30, G:0.11, T:0.20
Consensus pattern (63 bp):
AACCAATCCAATATTGACCAAATCCGAAGCCAACCGATCCGATATCAACCTGATCCAAAAACT
Found at i:546853 original size:124 final size:124
Alignment explanation
Indices: 546633--546880 Score: 451
Period size: 124 Copynumber: 2.0 Consensus size: 124
546623 TTATTCACGT
* *
546633 CCATATGTCGACCAATTCATAATCCAACCAACTGTTTATTATTTTAATTTTTAATGATGTAATTG
1 CCATATGCCGACCAATTCATAATCCAACCAACCGTTTATTATTTTAATTTTTAATGATGTAATTG
*
546698 AAGATTGAATTATTGAATGGTTATTTTATTTTTAAATAATGCAATTAAAGTGTAAGTTA
66 AAGATTGAATTATTGAATGGTTATTTTATTTTTAAATAATGCAATTAAAGAGTAAGTTA
*
546757 CCATATGCCGACCAATTCATAATCCAACCAACCGTTTATTATTTTAGTTTTTAATGATGTAATTG
1 CCATATGCCGACCAATTCATAATCCAACCAACCGTTTATTATTTTAATTTTTAATGATGTAATTG
*
546822 AAGATTGAATTATTGAATGTTTATTTTATTTTTAAATAATGCAATTAAAGAGTAAGTTA
66 AAGATTGAATTATTGAATGGTTATTTTATTTTTAAATAATGCAATTAAAGAGTAAGTTA
546881 TTCAACTAAT
Statistics
Matches: 119, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
124 119 1.00
ACGTcount: A:0.35, C:0.10, G:0.12, T:0.42
Consensus pattern (124 bp):
CCATATGCCGACCAATTCATAATCCAACCAACCGTTTATTATTTTAATTTTTAATGATGTAATTG
AAGATTGAATTATTGAATGGTTATTTTATTTTTAAATAATGCAATTAAAGAGTAAGTTA
Found at i:549766 original size:23 final size:24
Alignment explanation
Indices: 549729--549793 Score: 96
Period size: 23 Copynumber: 2.8 Consensus size: 24
549719 AAATATGAAG
*
549729 ATTAGTATATTTTATTAAAATAAT
1 ATTATTATATTTTATTAAAATAAT
549753 ATTATTAT-TTTTATTAAAATAAT
1 ATTATTATATTTTATTAAAATAAT
* *
549776 ATTATTATCTTATATTAA
1 ATTATTATATTTTATTAA
549794 TAAAATTCAT
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
23 23 0.61
24 15 0.39
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.54
Consensus pattern (24 bp):
ATTATTATATTTTATTAAAATAAT
Found at i:550741 original size:10 final size:10
Alignment explanation
Indices: 550726--550750 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
550716 GAACACATTA
550726 TTAAAGATAT
1 TTAAAGATAT
550736 TTAAAGATAT
1 TTAAAGATAT
550746 TTAAA
1 TTAAA
550751 ACGATGGAGT
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:0.52, C:0.00, G:0.08, T:0.40
Consensus pattern (10 bp):
TTAAAGATAT
Found at i:555430 original size:24 final size:23
Alignment explanation
Indices: 555400--555445 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 23
555390 TAATTAAAAC
555400 AAAATAATAA-AAACATTAAAATAT
1 AAAATAA-AATAAACA-TAAAATAT
555424 AAAATAAAATAAACATAAAATA
1 AAAATAAAATAAACATAAAATA
555446 AATGCCTAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 9 0.43
24 12 0.57
ACGTcount: A:0.74, C:0.04, G:0.00, T:0.22
Consensus pattern (23 bp):
AAAATAAAATAAACATAAAATAT
Found at i:557310 original size:587 final size:587
Alignment explanation
Indices: 556198--557372 Score: 2350
Period size: 587 Copynumber: 2.0 Consensus size: 587
556188 GAATCTAAGC
556198 AGAGAAAAATACGAAAAAACCTTCGAAATTAAAGAGAAAAAAAACCTTCAAATATTGCTCTGTTA
1 AGAGAAAAATACGAAAAAACCTTCGAAATTAAAGAGAAAAAAAACCTTCAAATATTGCTCTGTTA
556263 TTACTTTCGAAAATGGAGTATTACAGCTTTTTTTAAGGATCTCAAATTCCCCCCTTTTCCTCCTC
66 TTACTTTCGAAAATGGAGTATTACAGCTTTTTTTAAGGATCTCAAATTCCCCCCTTTTCCTCCTC
556328 TCTTTTACACTGTTTTTGGGTGGGTTAAATACCCATTACAAAGGAAATAAAGACAAACGTAATGG
131 TCTTTTACACTGTTTTTGGGTGGGTTAAATACCCATTACAAAGGAAATAAAGACAAACGTAATGG
556393 AGCATGGACGAGGCGTATGTTTCTGCATGAATCAAGGGGTGATGGGAGTAGGTGTGGTGAGTGAA
196 AGCATGGACGAGGCGTATGTTTCTGCATGAATCAAGGGGTGATGGGAGTAGGTGTGGTGAGTGAA
556458 CTGCCTTTGACTTCTGATGCTGAAAAATGATGATTACAATGATGATACTTCAAGTAGGAGTTATG
261 CTGCCTTTGACTTCTGATGCTGAAAAATGATGATTACAATGATGATACTTCAAGTAGGAGTTATG
556523 GAGAAATTCAAGGGAATACCCATTGTTAGTAGCTTGGATCTTACCTGCTTCGCTGCTTCTGTATT
326 GAGAAATTCAAGGGAATACCCATTGTTAGTAGCTTGGATCTTACCTGCTTCGCTGCTTCTGTATT
556588 TCTTTCCTCAGCTTCTATATTCCTTCTCTCCAGGCTCTCAGTTGGCACCAGCACGGGAGATAATT
391 TCTTTCCTCAGCTTCTATATTCCTTCTCTCCAGGCTCTCAGTTGGCACCAGCACGGGAGATAATT
556653 AGGCACCCACATATATTTATATTAAGAAAGAGATTGCTAAGAAGATGTATATCTTTTATTCTTGT
456 AGGCACCCACATATATTTATATTAAGAAAGAGATTGCTAAGAAGATGTATATCTTTTATTCTTGT
556718 GGTTGATAATTCATTTTGTAGGCACTGATATATACATACACAGGAATAAGCTTGGATAAGAAATT
521 GGTTGATAATTCATTTTGTAGGCACTGATATATACATACACAGGAATAAGCTTGGATAAGAAATT
556783 AA
586 AA
556785 AGAGAAAAATACGAAAAAACCTTCGAAATTAAAGAGAAAAAAAACCTTCAAATATTGCTCTGTTA
1 AGAGAAAAATACGAAAAAACCTTCGAAATTAAAGAGAAAAAAAACCTTCAAATATTGCTCTGTTA
556850 TTACTTTCGAAAATGGAGTATTACAGCTTTTTTTAAGGATCTCAAATTCCCCCCTTTTCCTCCTC
66 TTACTTTCGAAAATGGAGTATTACAGCTTTTTTTAAGGATCTCAAATTCCCCCCTTTTCCTCCTC
556915 TCTTTTACACTGTTTTTGGGTGGGTTAAATACCCATTACAAAGGAAATAAAGACAAACGTAATGG
131 TCTTTTACACTGTTTTTGGGTGGGTTAAATACCCATTACAAAGGAAATAAAGACAAACGTAATGG
556980 AGCATGGACGAGGCGTATGTTTCTGCATGAATCAAGGGGTGATGGGAGTAGGTGTGGTGAGTGAA
196 AGCATGGACGAGGCGTATGTTTCTGCATGAATCAAGGGGTGATGGGAGTAGGTGTGGTGAGTGAA
557045 CTGCCTTTGACTTCTGATGCTGAAAAATGATGATTACAATGATGATACTTCAAGTAGGAGTTATG
261 CTGCCTTTGACTTCTGATGCTGAAAAATGATGATTACAATGATGATACTTCAAGTAGGAGTTATG
557110 GAGAAATTCAAGGGAATACCCATTGTTAGTAGCTTGGATCTTACCTGCTTCGCTGCTTCTGTATT
326 GAGAAATTCAAGGGAATACCCATTGTTAGTAGCTTGGATCTTACCTGCTTCGCTGCTTCTGTATT
557175 TCTTTCCTCAGCTTCTATATTCCTTCTCTCCAGGCTCTCAGTTGGCACCAGCACGGGAGATAATT
391 TCTTTCCTCAGCTTCTATATTCCTTCTCTCCAGGCTCTCAGTTGGCACCAGCACGGGAGATAATT
557240 AGGCACCCACATATATTTATATTAAGAAAGAGATTGCTAAGAAGATGTATATCTTTTATTCTTGT
456 AGGCACCCACATATATTTATATTAAGAAAGAGATTGCTAAGAAGATGTATATCTTTTATTCTTGT
557305 GGTTGATAATTCATTTTGTAGGCACTGATATATACATACACAGGAATAAGCTTGGATAAGAAATT
521 GGTTGATAATTCATTTTGTAGGCACTGATATATACATACACAGGAATAAGCTTGGATAAGAAATT
557370 AA
586 AA
557372 A
1 A
557373 AAGTCTTAAA
Statistics
Matches: 588, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
587 588 1.00
ACGTcount: A:0.31, C:0.17, G:0.20, T:0.32
Consensus pattern (587 bp):
AGAGAAAAATACGAAAAAACCTTCGAAATTAAAGAGAAAAAAAACCTTCAAATATTGCTCTGTTA
TTACTTTCGAAAATGGAGTATTACAGCTTTTTTTAAGGATCTCAAATTCCCCCCTTTTCCTCCTC
TCTTTTACACTGTTTTTGGGTGGGTTAAATACCCATTACAAAGGAAATAAAGACAAACGTAATGG
AGCATGGACGAGGCGTATGTTTCTGCATGAATCAAGGGGTGATGGGAGTAGGTGTGGTGAGTGAA
CTGCCTTTGACTTCTGATGCTGAAAAATGATGATTACAATGATGATACTTCAAGTAGGAGTTATG
GAGAAATTCAAGGGAATACCCATTGTTAGTAGCTTGGATCTTACCTGCTTCGCTGCTTCTGTATT
TCTTTCCTCAGCTTCTATATTCCTTCTCTCCAGGCTCTCAGTTGGCACCAGCACGGGAGATAATT
AGGCACCCACATATATTTATATTAAGAAAGAGATTGCTAAGAAGATGTATATCTTTTATTCTTGT
GGTTGATAATTCATTTTGTAGGCACTGATATATACATACACAGGAATAAGCTTGGATAAGAAATT
AA
Found at i:557640 original size:18 final size:17
Alignment explanation
Indices: 557603--557641 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
557593 TCCTAATTTT
*
557603 TTTTAATTTTTTTTAAA
1 TTTTAATTTTTTGTAAA
*
557620 TTTTATATTTTTTGTATA
1 TTTTA-ATTTTTTGTAAA
557638 TTTT
1 TTTT
557642 CTTTGGTAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 5 0.26
18 14 0.74
ACGTcount: A:0.23, C:0.00, G:0.03, T:0.74
Consensus pattern (17 bp):
TTTTAATTTTTTGTAAA
Found at i:558287 original size:24 final size:24
Alignment explanation
Indices: 558252--558299 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
558242 TTATTTTAAT
*
558252 AAAATATTAATTATTAA-AATACTA
1 AAAATATAAATT-TTAATAATACTA
558276 AAAATATAAATTTTAATAATACTA
1 AAAATATAAATTTTAATAATACTA
558300 TATCTTTTGA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 4 0.18
24 18 0.82
ACGTcount: A:0.58, C:0.04, G:0.00, T:0.38
Consensus pattern (24 bp):
AAAATATAAATTTTAATAATACTA
Found at i:558568 original size:24 final size:21
Alignment explanation
Indices: 558545--558582 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
558535 AAATATAATA
558545 TAATA-TA-ATATTTTAATTC
1 TAATATTATATATTTTAATTC
558564 TAATATTATATATTTTAAT
1 TAATATTATATATTTTAAT
558583 ATATTGAGTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 5 0.29
20 2 0.12
21 10 0.59
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (21 bp):
TAATATTATATATTTTAATTC
Found at i:559745 original size:32 final size:33
Alignment explanation
Indices: 559708--559773 Score: 98
Period size: 35 Copynumber: 2.0 Consensus size: 33
559698 TGACACCTAA
*
559708 CCCCGTTAACCCC-CTTTTCTTCTTCTTCTTCC
1 CCCCGTTAACCCCTCTTCTCTTCTTCTTCTTCC
559740 CCCCGTTAACCCCTATCTTCTCTTCTTCTTCTTC
1 CCCCGTTAACCCC--TCTTCTCTTCTTCTTCTTC
559774 TTCTTCTCTC
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
32 13 0.43
35 17 0.57
ACGTcount: A:0.08, C:0.45, G:0.03, T:0.44
Consensus pattern (33 bp):
CCCCGTTAACCCCTCTTCTCTTCTTCTTCTTCC
Found at i:560349 original size:12 final size:12
Alignment explanation
Indices: 560334--560365 Score: 64
Period size: 12 Copynumber: 2.7 Consensus size: 12
560324 GGGGTGTGAG
560334 AGAAGAAAAAGA
1 AGAAGAAAAAGA
560346 AGAAGAAAAAGA
1 AGAAGAAAAAGA
560358 AGAAGAAA
1 AGAAGAAA
560366 TGAAGATGGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (12 bp):
AGAAGAAAAAGA
Found at i:565168 original size:22 final size:22
Alignment explanation
Indices: 565142--565187 Score: 83
Period size: 22 Copynumber: 2.1 Consensus size: 22
565132 TGGCATGTGA
*
565142 AATATGTCTCGAAGGACCTATG
1 AATATGTCCCGAAGGACCTATG
565164 AATATGTCCCGAAGGACCTATG
1 AATATGTCCCGAAGGACCTATG
565186 AA
1 AA
565188 ACCCTCGACT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.35, C:0.20, G:0.22, T:0.24
Consensus pattern (22 bp):
AATATGTCCCGAAGGACCTATG
Found at i:566400 original size:7 final size:7
Alignment explanation
Indices: 566388--566421 Score: 61
Period size: 7 Copynumber: 5.0 Consensus size: 7
566378 GTTCACGACT
566388 GGAAGAA
1 GGAAGAA
566395 GGAAGAA
1 GGAAGAA
566402 GGAAGAA
1 GGAAGAA
566409 GGAAGAA
1 GGAAGAA
566416 -GAAGAA
1 GGAAGAA
566422 AGCTCTGGAG
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 6 0.22
7 21 0.78
ACGTcount: A:0.59, C:0.00, G:0.41, T:0.00
Consensus pattern (7 bp):
GGAAGAA
Found at i:569954 original size:22 final size:22
Alignment explanation
Indices: 569929--569974 Score: 83
Period size: 22 Copynumber: 2.1 Consensus size: 22
569919 TGACATGTGA
569929 AATATGTCCCGAAGGACCTATG
1 AATATGTCCCGAAGGACCTATG
*
569951 AATATGTCCCGAAGGACTTATG
1 AATATGTCCCGAAGGACCTATG
569973 AA
1 AA
569975 ACCCTCGACT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.35, C:0.20, G:0.22, T:0.24
Consensus pattern (22 bp):
AATATGTCCCGAAGGACCTATG
Found at i:572348 original size:3 final size:3
Alignment explanation
Indices: 572340--572369 Score: 51
Period size: 3 Copynumber: 9.7 Consensus size: 3
572330 TCTAGAGTTC
572340 TCT TCT TCT TCT TCT TCT TCT TCTT TCT TC
1 TCT TCT TCT TCT TCT TCT TCT TC-T TCT TC
572370 ATGCGTGAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 23 0.88
4 3 0.12
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TCT
Found at i:572725 original size:64 final size:63
Alignment explanation
Indices: 572583--572705 Score: 237
Period size: 64 Copynumber: 1.9 Consensus size: 63
572573 TCCATGCTTT
572583 AATAAAATATGTGTGAATGAATGCCATGATAAGAGAATCAATCCAGATACGTGAAGTAAAAGG
1 AATAAAATATGTGTGAATGAATGCCATGATAAGAGAATCAATCCAGATACGTGAAGTAAAAGG
572646 AATAAAATATTGTGTGAATGAATGCCATGATAAGAGAATCAATCCAGATACGTGAAGTAA
1 AATAAAATA-TGTGTGAATGAATGCCATGATAAGAGAATCAATCCAGATACGTGAAGTAA
572706 TGGAAGTAAT
Statistics
Matches: 59, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
63 9 0.15
64 50 0.85
ACGTcount: A:0.46, C:0.10, G:0.21, T:0.24
Consensus pattern (63 bp):
AATAAAATATGTGTGAATGAATGCCATGATAAGAGAATCAATCCAGATACGTGAAGTAAAAGG
Found at i:579705 original size:17 final size:17
Alignment explanation
Indices: 579683--579735 Score: 70
Period size: 17 Copynumber: 3.1 Consensus size: 17
579673 GGATTATCAG
*
579683 TGGTCCTTTGGGACAAA
1 TGGTCCTTCGGGACAAA
*
579700 TGGTCCTTCGGGACATAG
1 TGGTCCTTCGGGACA-AA
*
579718 TGGTCATTCGGGACAAA
1 TGGTCCTTCGGGACAAA
579735 T
1 T
579736 ATTCTGTGCC
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
17 16 0.52
18 15 0.48
ACGTcount: A:0.23, C:0.19, G:0.30, T:0.28
Consensus pattern (17 bp):
TGGTCCTTCGGGACAAA
Found at i:581804 original size:53 final size:51
Alignment explanation
Indices: 581744--581846 Score: 118
Period size: 51 Copynumber: 2.0 Consensus size: 51
581734 GCTCATAAGC
*
581744 TTATTTTTACCAAAATAC-TACCATTTAAATTCCATAAGCTCATAAGCTTATTA
1 TTATTTTTACCAAAATACTTACCA-TT--ATTCCATAAGATCATAAGCTTATTA
** * * *
581797 TTATTTTTTTCAATATACTTGCCATTATTCCGTAAGATCATAAGCTTATT
1 TTATTTTTACCAAAATACTTACCATTATTCCATAAGATCATAAGCTTATT
581847 TGCATGGTTA
Statistics
Matches: 43, Mismatches: 6, Indels: 4
0.81 0.11 0.08
Matches are distributed among these distances:
51 22 0.51
53 17 0.40
54 4 0.09
ACGTcount: A:0.33, C:0.17, G:0.06, T:0.44
Consensus pattern (51 bp):
TTATTTTTACCAAAATACTTACCATTATTCCATAAGATCATAAGCTTATTA
Found at i:586430 original size:92 final size:93
Alignment explanation
Indices: 586285--586470 Score: 329
Period size: 92 Copynumber: 2.0 Consensus size: 93
586275 ACACTAGTGG
*
586285 AAATGCAGACAAACTGAATCAATGATAGAGTGAAGACTGCTCTCGCAACCATTCTCCTAACAGAT
1 AAATGCAGACAAACTGAATCAATGATAGAGTGAAGACTGCTCTCACAACCATTCTCCTAACAGAT
586350 TAAGAAAAA-AAAAACACACACACACAC
66 TAAGAAAAACAAAAACACACACACACAC
*
586377 AAATGTAGACAAACTGAATCAATGATAGAGTGAAGACTGCTCTCACAACCATTCTCCTAACAGAT
1 AAATGCAGACAAACTGAATCAATGATAGAGTGAAGACTGCTCTCACAACCATTCTCCTAACAGAT
* *
586442 TAAGAAAAACACACACACACACACACAC
66 TAAGAAAAACAAAAACACACACACACAC
586470 A
1 A
586471 CACACACACA
Statistics
Matches: 89, Mismatches: 4, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
92 72 0.81
93 17 0.19
ACGTcount: A:0.46, C:0.25, G:0.12, T:0.17
Consensus pattern (93 bp):
AAATGCAGACAAACTGAATCAATGATAGAGTGAAGACTGCTCTCACAACCATTCTCCTAACAGAT
TAAGAAAAACAAAAACACACACACACAC
Found at i:586457 original size:2 final size:2
Alignment explanation
Indices: 586450--586494 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
586440 ATTAAGAAAA
586450 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
586492 AC A
1 AC A
586495 TACGTGATAC
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.49, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:586850 original size:31 final size:31
Alignment explanation
Indices: 586814--586872 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
586804 TTCTTGAAAC
* *
586814 AAAATTCTGTCTCTCTTGAGACATTTTTCCA
1 AAAATTCTGTCTCGCTTAAGACATTTTTCCA
*
586845 AAAATTTTGTCTCGCTTAAGACATTTTT
1 AAAATTCTGTCTCGCTTAAGACATTTTT
586873 TCCTCTGAGA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.27, C:0.19, G:0.10, T:0.44
Consensus pattern (31 bp):
AAAATTCTGTCTCGCTTAAGACATTTTTCCA
Found at i:587285 original size:65 final size:64
Alignment explanation
Indices: 587139--587264 Score: 184
Period size: 65 Copynumber: 2.0 Consensus size: 64
587129 GACACAACCC
*
587139 ATCTTTGAGTTTGTTT-ATTTGGAAACAAAAATTTGTCTCTTGAGACAGTTTCTTTTCAGAAAAA
1 ATCTTTGAGTTTGTTTCATTT-GAAACAAAAATTTGTCTCTCGAGACAGTTTCTTTT-AGAAAAA
587203 A
64 A
* **
587204 ATCTTTGAGTTTGTTTCATTTGAAACAAAATTTTGTCTCTCGAGATGGTTTCTTTT-GAAAA
1 ATCTTTGAGTTTGTTTCATTTGAAACAAAAATTTGTCTCTCGAGACAGTTTCTTTTAGAAAA
587265 CACTTATTTT
Statistics
Matches: 56, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
63 5 0.09
65 47 0.84
66 4 0.07
ACGTcount: A:0.29, C:0.11, G:0.16, T:0.44
Consensus pattern (64 bp):
ATCTTTGAGTTTGTTTCATTTGAAACAAAAATTTGTCTCTCGAGACAGTTTCTTTTAGAAAAAA
Found at i:587292 original size:65 final size:64
Alignment explanation
Indices: 587139--587296 Score: 160
Period size: 65 Copynumber: 2.4 Consensus size: 64
587129 GACACAACCC
* * *
587139 ATCTTTGAGTTTGTTT-ATTTGGAAACAAAAATTTGTCTCTTGAGACAGTTTCTTTTCAGAAAAA
1 ATCTTTGAGTCTGTTTCACTT-GAAACAAAAATTTGTCTCTCGAGACAGTTTCTTTT-AGAAAAA
587203 A
64 A
* * * **
587204 ATCTTTGAGTTTGTTTCATTTGAAACAAAATTTTGTCTCTCGAGATGGTTTCTTTT-GAAAACAC
1 ATCTTTGAGTCTGTTTCACTTGAAACAAAAATTTGTCTCTCGAGACAGTTTCTTTTAGAAAA-A-
*
587268 TT
64 -A
*
587270 AT-TTTGAGTCTGTTTCCCTTGAAACAA
1 ATCTTTGAGTCTGTTTCACTTGAAACAA
587297 GTAAAGAAAT
Statistics
Matches: 81, Mismatches: 8, Indels: 8
0.84 0.08 0.08
Matches are distributed among these distances:
63 5 0.06
64 1 0.01
65 69 0.85
66 6 0.07
ACGTcount: A:0.28, C:0.13, G:0.15, T:0.43
Consensus pattern (64 bp):
ATCTTTGAGTCTGTTTCACTTGAAACAAAAATTTGTCTCTCGAGACAGTTTCTTTTAGAAAAAA
Found at i:587320 original size:36 final size:34
Alignment explanation
Indices: 587272--587399 Score: 141
Period size: 38 Copynumber: 3.5 Consensus size: 34
587262 AAACACTTAT
*
587272 TTTGAGTCTGTTTCCCTTGAAACAAGTAA-AGAAATA
1 TTTGAGT-TGTTTCCCTTGAAACAA--AACAAAAATA
*
587308 TTTGAGTATGTTTCACTTGAAACAAAACAAAAATCA
1 TTTGAGT-TGTTTCCCTTGAAACAAAACAAAAAT-A
*
587344 TCTTTGAGTTTGTTTCCCTTGAAACAAAACAAAAATC
1 --TTTGAG-TTGTTTCCCTTGAAACAAAACAAAAATA
587381 TTTGAGTTCGTTTCCCTTG
1 TTTGAGTT-GTTTCCCTTG
587400 GAACTAATTT
Statistics
Matches: 81, Mismatches: 5, Indels: 13
0.82 0.05 0.13
Matches are distributed among these distances:
34 4 0.05
35 21 0.26
36 24 0.30
38 31 0.38
39 1 0.01
ACGTcount: A:0.34, C:0.16, G:0.14, T:0.36
Consensus pattern (34 bp):
TTTGAGTTGTTTCCCTTGAAACAAAACAAAAATA
Found at i:587739 original size:133 final size:131
Alignment explanation
Indices: 587492--587729 Score: 302
Period size: 133 Copynumber: 1.8 Consensus size: 131
587482 TGATCAGTCG
* * *
587492 TCCTCATCACATAGGAACCGAGTTATCATTCCTAAAGATGGTCTGCCATCATCATCAAGTAGAAA
1 TCCTCATCACATAGGAACCGAGTTATCATTCCTAAAGATGGCCAGACATCATCATCAAGTAGAAA
* *
587557 CCGTGTCATCCATCGACCAAACCTCCTCATCACGTAGGAGCCGCGTCACCCCTAGATAACCAGCC
66 CCGTGTCATCCACCGACCAAACCTCCTCATCAAGTAGGAGCCGCGTCACCCCTAGATAACCAGCC
587622 A
131 A
* * * *
587623 TCCTCATCACGTAGGAACCGAGTTATCACCCTTCCTGAAGATGGCCAGA-ACTCTTCATCATGTA
1 TCCTCATCACATAGGAACCGAGTTATCA---TTCCTAAAGATGGCCAGACA-TCATCATCAAGTA
* * *
587687 TG-AGCCGTG-CATCCACCGACCAGATCTCCTCATCAAGTAGGAG
62 -GAAACCGTGTCATCCACCGACCAAACCTCCTCATCAAGTAGGAG
587730 TCTTGTCACC
Statistics
Matches: 90, Mismatches: 12, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
131 27 0.30
133 31 0.34
134 31 0.34
135 1 0.01
ACGTcount: A:0.28, C:0.32, G:0.18, T:0.22
Consensus pattern (131 bp):
TCCTCATCACATAGGAACCGAGTTATCATTCCTAAAGATGGCCAGACATCATCATCAAGTAGAAA
CCGTGTCATCCACCGACCAAACCTCCTCATCAAGTAGGAGCCGCGTCACCCCTAGATAACCAGCC
A
Found at i:587945 original size:3 final size:3
Alignment explanation
Indices: 587937--587971 Score: 52
Period size: 3 Copynumber: 11.7 Consensus size: 3
587927 GGTTATCATT
* *
587937 TTA TTA TTA TTA TCA TTA TTA TTA TTG TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
587972 TAATACATAT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.29, C:0.03, G:0.03, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:593776 original size:31 final size:31
Alignment explanation
Indices: 593738--593827 Score: 137
Period size: 31 Copynumber: 2.9 Consensus size: 31
593728 TCGAGGGTTA
*
593738 ACCTATGTTCTTCGGGACATATGGACTGTTT
1 ACCTATGTTCTTCGGGACATATGGACTGATT
593769 ACCTATGTTCTTCGGGACATATGGACTGATT
1 ACCTATGTTCTTCGGGACATATGGACTGATT
* *
593800 ACCTAGGTTCTTCGGAATC-TATGGACTG
1 ACCTATGTTCTTCGGGA-CATATGGACTG
593828 GTCCTTCGGG
Statistics
Matches: 55, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
31 54 0.98
32 1 0.02
ACGTcount: A:0.21, C:0.20, G:0.23, T:0.36
Consensus pattern (31 bp):
ACCTATGTTCTTCGGGACATATGGACTGATT
Found at i:598230 original size:31 final size:31
Alignment explanation
Indices: 598192--598347 Score: 251
Period size: 31 Copynumber: 5.0 Consensus size: 31
598182 AGGGTCAAGG
*
598192 GTTTACCTATGTTCTTCGGGACATATAGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
598223 GTTTACCTATGTTCTTCGGGACATATGGATT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
598254 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
598285 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* * *
598316 GATTACCTAGGTTCTTCGGAATC-TATGGACT
1 GTTTACCTATGTTCTTCGGGA-CATATGGACT
598347 G
1 G
598348 GTCCTTCGGG
Statistics
Matches: 118, Mismatches: 6, Indels: 2
0.94 0.05 0.02
Matches are distributed among these distances:
31 117 0.99
32 1 0.01
ACGTcount: A:0.21, C:0.19, G:0.22, T:0.38
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:602753 original size:31 final size:31
Alignment explanation
Indices: 602715--602870 Score: 251
Period size: 31 Copynumber: 5.0 Consensus size: 31
602705 AGGGTCGAGG
602715 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
602746 GTTTACCTATGTTCTTCGGGACATATGGATT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
602777 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
602808 GTTTACCTATTTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* * *
602839 GATTACCTAGGTTCTTCGGAATC-TATGGACT
1 GTTTACCTATGTTCTTCGGGA-CATATGGACT
602870 G
1 G
602871 GTCCTTCGGG
Statistics
Matches: 117, Mismatches: 7, Indels: 2
0.93 0.06 0.02
Matches are distributed among these distances:
31 116 0.99
32 1 0.01
ACGTcount: A:0.20, C:0.19, G:0.22, T:0.39
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:607275 original size:31 final size:31
Alignment explanation
Indices: 607237--607392 Score: 260
Period size: 31 Copynumber: 5.0 Consensus size: 31
607227 AGGGTCGAGG
607237 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
607268 GTTTACCTATGTTCTTCGGGACATATGGATT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
607299 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
607330 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* * *
607361 GATTACCTAGGTTCTTCGGAATC-TATGGACT
1 GTTTACCTATGTTCTTCGGGA-CATATGGACT
607392 G
1 G
607393 GTCCTTCGGG
Statistics
Matches: 119, Mismatches: 5, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
31 118 0.99
32 1 0.01
ACGTcount: A:0.20, C:0.19, G:0.23, T:0.38
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:616942 original size:55 final size:54
Alignment explanation
Indices: 616826--616994 Score: 227
Period size: 55 Copynumber: 3.1 Consensus size: 54
616816 TTAGATCAAT
* *
616826 TTTGGAAGACGGGTTTGCTCCACTCTT-TTTTAGGGATATAAGACTCGAGAAAA-C
1 TTTGGAAGACGGGTATGCTCCACTCTTCTTTCAGGGA-ATAAGACTCGA-AAAATC
* * *
616880 TTTGGAAGACGAGTATGCTCCACTATTCTTTCATGGAGATAAGACTCGAAAAATC
1 TTTGGAAGACGGGTATGCTCCACTCTTCTTTCAGGGA-ATAAGACTCGAAAAATC
*
616935 TTTGGAAGACGGGTCTGCTCCACTCTTCTTTCAGGGAATTAAGACTCG-AAAATC
1 TTTGGAAGACGGGTATGCTCCACTCTTCTTTCAGGGAA-TAAGACTCGAAAAATC
616989 TTTGGA
1 TTTGGA
616995 TCCACTTTGC
Statistics
Matches: 102, Mismatches: 10, Indels: 6
0.86 0.08 0.05
Matches are distributed among these distances:
54 41 0.40
55 61 0.60
ACGTcount: A:0.28, C:0.18, G:0.22, T:0.31
Consensus pattern (54 bp):
TTTGGAAGACGGGTATGCTCCACTCTTCTTTCAGGGAATAAGACTCGAAAAATC
Found at i:617239 original size:13 final size:13
Alignment explanation
Indices: 617223--617256 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
617213 TTTTATTTTC
617223 ATTTTTTATTACT
1 ATTTTTTATTACT
* *
617236 ATTTATTATTATT
1 ATTTTTTATTACT
617249 ATTTTTTA
1 ATTTTTTA
617257 ATATTTTAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.26, C:0.03, G:0.00, T:0.71
Consensus pattern (13 bp):
ATTTTTTATTACT
Found at i:617261 original size:23 final size:23
Alignment explanation
Indices: 617214--617262 Score: 57
Period size: 23 Copynumber: 2.1 Consensus size: 23
617204 ATTTCATTTT
*
617214 TTTATTTTCATTTTTTATTACTA
1 TTTATTTTCATTTTTTATTAATA
617237 TTTATTATT-ATTATTTT-TTAATA
1 TTTATT-TTCATT-TTTTATTAATA
617260 TTT
1 TTT
617263 TAAATGAGAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
23 17 0.74
24 6 0.26
ACGTcount: A:0.24, C:0.04, G:0.00, T:0.71
Consensus pattern (23 bp):
TTTATTTTCATTTTTTATTAATA
Found at i:617675 original size:212 final size:212
Alignment explanation
Indices: 617400--617842 Score: 617
Period size: 212 Copynumber: 2.1 Consensus size: 212
617390 AAAGGATTTA
* * * *
617400 ATCATCATACTCGAAAGACTTACTGATGGCCCGAATGACTTACCAATTTTGGAAATAGTTTACTG
1 ATCATCTTGCTCGAAAGACTTACTGATGGCCCGAATGA--GACCAATTTTGAAAATAGTTTACTG
* **
617465 GGTAAGAAACTTTGAAAATCGCTTTCTTAATTTTCAAAATTTTCATTTCT-T-AAATACTAAATG
64 GGTAAGAAACTTTGAAAATCGATTTCTTAATTTTCAAAAAATTCATTT-TATAAAATACTAAATG
* *
617528 AGAAACTTTGGAAACCACTTTCTCATTTTTTTTGAAAATCACGTGAAAACATCTTGCCCTAAGGT
128 AGAAACTTTGGAAACCACTTTCTCA---TTTTTGAAAATCACGTGAAAACATCCTGCCCGAAGGT
* *
617593 CTTATAGATGGCTCGAATGACTT
190 CTTATAGATGGCCCGAATGAATT
*
617616 ATCATCTTGCTCGAAAGACTTACTGATGGCCTGAA-G-GACCAATTTTGAAAATAGTTTACTGGG
1 ATCATCTTGCTCGAAAGACTTACTGATGGCCCGAATGAGACCAATTTTGAAAATAGTTTACTGGG
* *
617679 TAAGAAACTTTGGAAATCGATTTCTTACTTTTCAAAAAATTCATTTTATGAAAATACTAAATGAG
66 TAAGAAACTTTGAAAATCGATTTCTTAATTTTCAAAAAATTCATTTTAT-AAAATACTAAATGAG
* * * * *
617744 AAACTTTGGAAATCACTTTCTCATTTTTGAAAATCATGTGGAAACATCCTGTCCGAAGGTGTTAT
130 AAACTTTGGAAACCACTTTCTCATTTTTGAAAATCACGTGAAAACATCCTGCCCGAAGGTCTTAT
617809 AGATGGCCCGAATGAATT
195 AGATGGCCCGAATGAATT
617827 ATCATCTTGCT-GAAAG
1 ATCATCTTGCTCGAAAG
617843 CCTGACATAT
Statistics
Matches: 205, Mismatches: 19, Indels: 12
0.87 0.08 0.05
Matches are distributed among these distances:
210 5 0.02
211 64 0.31
212 67 0.33
214 36 0.18
215 1 0.00
216 32 0.16
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.34
Consensus pattern (212 bp):
ATCATCTTGCTCGAAAGACTTACTGATGGCCCGAATGAGACCAATTTTGAAAATAGTTTACTGGG
TAAGAAACTTTGAAAATCGATTTCTTAATTTTCAAAAAATTCATTTTATAAAATACTAAATGAGA
AACTTTGGAAACCACTTTCTCATTTTTGAAAATCACGTGAAAACATCCTGCCCGAAGGTCTTATA
GATGGCCCGAATGAATT
Found at i:618120 original size:256 final size:255
Alignment explanation
Indices: 617616--618163 Score: 807
Period size: 256 Copynumber: 2.2 Consensus size: 255
617606 CGAATGACTT
* **
617616 ATCATCTTGCTCGAAAGACTTACTGATGGCCTGAAGG---ACCAATTTTGAAAATAGTTTACTGG
1 ATCATCATGCTCGAAAGACTTACTGATGGCCCAAAGGATTACCAATTTTGAAAATAGTTTACTGG
*
617678 GTAAGAAACTTTGGAAATCGATTTCTTACTTTTCAAAAAATTCATTTTATGAAAATACTAAATGA
66 GTAAGAAACTTTGGAAATAGATTTCTTACTTTTCAAAAAATTCATTTTATGAAAATACTAAATGA
* * *
617743 GAAACTTTGGAAATCACTTTCTCATTTTTGAAAATCATGTGGAAACATCCTGTCCGAAGGTGTTA
131 GAAACTTTGGAAATCACTTTCTCATTTTTGAAAATCATGTGGAAACATCCTGCCCAAAGGTCTTA
* * * *
617808 TAGATGGCCCGAATGAATTATCATCTTGCTGAAAGCCTGACATATGATCTGAAGGATTTA
196 TAGATAGCCCGAATGAATTATCATCTTGCTGAAAGCCTGACAGATGACCCGAAGGATTTA
* *
617868 ATCATCATGCTCGAAAGACTTACTAATGGCCCAAAGGACTTACCAATTTTGGAAATAGTTTACTG
1 ATCATCATGCTCGAAAGACTTACTGATGGCCCAAAGGA-TTACCAATTTTGAAAATAGTTTACTG
** ** * *
617933 GGTAAGAAACTTTGGAAATATCTTTCTTACTTTTCAAAAGTTTTATTTTTTGAAAATACTAAATG
65 GGTAAGAAACTTTGGAAATAGATTTCTTACTTTTCAAAAAATTCATTTTATGAAAATACTAAATG
* *
617998 AGAAACTTTGGAAATCGCTTTCTCATTTTTGAAAATCATGTGGAAACATCTTGCCCAAAGGTCTT
130 AGAAACTTTGGAAATCACTTTCTCATTTTTGAAAATCATGTGGAAACATCCTGCCCAAAGGTCTT
* * * *
618063 ATATATAG-CCGAATGACTTATCATCTTGCTCGAAATCCTGACAGGTGACCCGAAGGATTTA
195 ATAGATAGCCCGAATGAATTATCATCTTGCT-GAAAGCCTGACAGATGACCCGAAGGATTTA
* *
618124 ATCATCATGCTCGAAAGACTTACTGTTTGCCCAAAGGATT
1 ATCATCATGCTCGAAAGACTTACTGATGGCCCAAAGGATT
618164 TACTAAGTAA
Statistics
Matches: 263, Mismatches: 28, Indels: 7
0.88 0.09 0.02
Matches are distributed among these distances:
252 33 0.13
255 23 0.09
256 207 0.79
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Consensus pattern (255 bp):
ATCATCATGCTCGAAAGACTTACTGATGGCCCAAAGGATTACCAATTTTGAAAATAGTTTACTGG
GTAAGAAACTTTGGAAATAGATTTCTTACTTTTCAAAAAATTCATTTTATGAAAATACTAAATGA
GAAACTTTGGAAATCACTTTCTCATTTTTGAAAATCATGTGGAAACATCCTGCCCAAAGGTCTTA
TAGATAGCCCGAATGAATTATCATCTTGCTGAAAGCCTGACAGATGACCCGAAGGATTTA
Found at i:618618 original size:42 final size:41
Alignment explanation
Indices: 618536--618642 Score: 151
Period size: 42 Copynumber: 2.6 Consensus size: 41
618526 ACCCGAAGGT
* * *
618536 CTTATAGATGACCCGAAGGACTTATCATCTTGCTCGAAAGA
1 CTTACAGATGACCCGAAGGACTTATCATCATGCTCAAAAGA
*
618577 CTTACAGATGACCCGAAGGATTTAATCATCATGCTCAAAAGA
1 CTTACAGATGACCCGAAGGACTT-ATCATCATGCTCAAAAGA
* *
618619 CTTACTGATGGCCCGAAGGACTTA
1 CTTACAGATGACCCGAAGGACTTA
618643 CTAAGTAAGA
Statistics
Matches: 58, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
41 22 0.38
42 36 0.62
ACGTcount: A:0.33, C:0.22, G:0.20, T:0.25
Consensus pattern (41 bp):
CTTACAGATGACCCGAAGGACTTATCATCATGCTCAAAAGA
Found at i:618620 original size:240 final size:238
Alignment explanation
Indices: 617934--618719 Score: 1051
Period size: 240 Copynumber: 3.3 Consensus size: 238
617924 AGTTTACTGG
* * * ** * *
617934 GTAAGAAACTTTGGAAA-TATCTTTCTTAC-TTTTCAAAAGTTTTATTTTTTGAAAATACTAAAT
1 GTAAGAAACTTTGGAAATTAT-TTTCTTACTTTTTGAAAA-TCTCATTTTCAGAAAACATTAAAT
* * * *
617997 GAGAAACTTTGGAAATCGCTTTCTCATTTTT-GAAAATCATGTGGAAACATCTTGCCCAAAGGTC
64 GAGAAACTTTGGAAATCGCTTTCTCATTTTTCGAAAATCATGTGAAAACATCCTACCCGAAGGTC
* * ** * *
618061 TTATATAT-AGCCGAATGACTTATCATCTTGCTCGAAATCCTGACAGGTGACCCGAAGGATTTAA
129 TTATAGATGACCCGAATGACTTATCATCTTGCTCGAAAGACTTACAGATGACCCGAAGGATTTAA
* * *
618125 TCATCATGCTCGAAAGACTTACTGTTTGCCCAAAGGATTTACTAA
194 TCATCATGCTCGAAAGACTTACTGATGGCCCAAAGGACTTACTAA
*
618170 GTAAGAAACTTTGGAAATTGTTTTCTTACTTTTTGAAAATCTCATTTTCAGAAAACATTAAATGA
1 GTAAGAAACTTTGGAAATTATTTTCTTACTTTTTGAAAATCTCATTTTCAGAAAACATTAAATGA
* * * * * * * * *
618235 GAAACTGTGAAAATTGTTTTCTCATTTTTC-AAATTCATGTGACAACATCCCACTCGAAGGTATT
66 GAAACTTTGGAAATCGCTTTCTCATTTTTCGAAAATCATGTGAAAACATCCTACCCGAAGGTCTT
* * * * * * * *
618299 ATGGACGATCCAAATGACTTATCGTTTTGCTCAAAAGACTTACAGATGACCCGAAGAATTTAATC
131 ATAGATGACCCGAATGACTTATCATCTTGCTCGAAAGACTTACAGATGACCCGAAGGATTTAATC
* * *
618364 ATCATGCTCGAAAGACTTATTGATGGCCTAAATGACTTACTAA
196 ATCATGCTCGAAAGACTTACTGATGGCCCAAAGGACTTACTAA
** *
618407 GTAAGAAACTTAAGAAATTATTTTCTTACTTTTTGAAAATCTCATTTTCAGAAAATGATTAAAAT
1 GTAAGAAACTTTGGAAATTATTTTCTTACTTTTTGAAAATCTCATTTTCAGAAAA-CATT-AAAT
* *
618472 GAGAAACTTTGGAAATCACTTTCTCATTTTTCGAAAATCACGTGAAAACATCCTACCCGAAGGTC
64 GAGAAACTTTGGAAATCGCTTTCTCATTTTTCGAAAATCATGTGAAAACATCCTACCCGAAGGTC
*
618537 TTATAGATGACCCGAAGGACTTATCATCTTGCTCGAAAGACTTACAGATGACCCGAAGGATTTAA
129 TTATAGATGACCCGAATGACTTATCATCTTGCTCGAAAGACTTACAGATGACCCGAAGGATTTAA
* *
618602 TCATCATGCTCAAAAGACTTACTGATGGCCCGAAGGACTTACTAA
194 TCATCATGCTCGAAAGACTTACTGATGGCCCAAAGGACTTACTAA
*
618647 GTAAGAAACTTTGGAAATCATTTTCTTACTTTTTGAAAATCTCATTTTCAGAAAACATTAAATGA
1 GTAAGAAACTTTGGAAATTATTTTCTTACTTTTTGAAAATCTCATTTTCAGAAAACATTAAATGA
618712 GAAACTTT
66 GAAACTTT
618720 TCAAAAAATT
Statistics
Matches: 470, Mismatches: 73, Indels: 12
0.85 0.13 0.02
Matches are distributed among these distances:
236 98 0.21
237 147 0.31
238 17 0.04
239 34 0.07
240 174 0.37
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.33
Consensus pattern (238 bp):
GTAAGAAACTTTGGAAATTATTTTCTTACTTTTTGAAAATCTCATTTTCAGAAAACATTAAATGA
GAAACTTTGGAAATCGCTTTCTCATTTTTCGAAAATCATGTGAAAACATCCTACCCGAAGGTCTT
ATAGATGACCCGAATGACTTATCATCTTGCTCGAAAGACTTACAGATGACCCGAAGGATTTAATC
ATCATGCTCGAAAGACTTACTGATGGCCCAAAGGACTTACTAA
Found at i:620235 original size:18 final size:20
Alignment explanation
Indices: 620187--620243 Score: 82
Period size: 20 Copynumber: 3.0 Consensus size: 20
620177 CACTGAATAT
620187 TTGTCCCGAAGGACCACTGA
1 TTGTCCCGAAGGACCACTGA
* *
620207 TTGTTCCGAAGAACCACT-A
1 TTGTCCCGAAGGACCACTGA
620226 -TGTCCCGAAGGACCACTG
1 TTGTCCCGAAGGACCACTG
620244 TTAATCCATC
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
18 15 0.47
19 1 0.03
20 16 0.50
ACGTcount: A:0.26, C:0.30, G:0.23, T:0.21
Consensus pattern (20 bp):
TTGTCCCGAAGGACCACTGA
Found at i:623075 original size:17 final size:18
Alignment explanation
Indices: 623053--623124 Score: 55
Period size: 17 Copynumber: 4.1 Consensus size: 18
623043 ACTTGATTTA
*
623053 TTTTCTCTCTTTTT-CTT
1 TTTTCTATCTTTTTCCTT
*
623070 TTTTCTATTTTTTTCCTT
1 TTTTCTATCTTTTTCCTT
*
623088 TTTT-T-T-TTTCCTT-TTT
1 TTTTCTATCTTT--TTCCTT
623104 TTTTCTATCTTTTCTCCTT
1 TTTTCTATCTTTT-TCCTT
623123 TT
1 TT
623125 CCCTTTTTTT
Statistics
Matches: 43, Mismatches: 4, Indels: 14
0.70 0.07 0.23
Matches are distributed among these distances:
15 3 0.07
16 7 0.16
17 17 0.40
18 9 0.21
19 7 0.16
ACGTcount: A:0.03, C:0.19, G:0.00, T:0.78
Consensus pattern (18 bp):
TTTTCTATCTTTTTCCTT
Found at i:623095 original size:13 final size:13
Alignment explanation
Indices: 623077--623107 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
623067 CTTTTTTCTA
623077 TTTTTTTCCTTTT
1 TTTTTTTCCTTTT
623090 TTTTTTTCCTTTT
1 TTTTTTTCCTTTT
623103 TTTTT
1 TTTTT
623108 CTATCTTTTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (13 bp):
TTTTTTTCCTTTT
Done.