Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr02 ID=Chr02-JGI_221_v2.0
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: 62769430
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1067035 characters in sequence are not A, C, G, or T
File 13 of 206
Found at i:3859040 original size:110 final size:110
Alignment explanation
Indices: 3858525--3859121 Score: 630
Period size: 113 Copynumber: 5.4 Consensus size: 110
3858515 TAAAGTTTAA
* ** * *
3858525 TGCCGGCCATTGACAGGCCAGCACCCGAAATTTTTTTTTTTAAATTTTTTCGTATACTGGTGCCT
1 TGCCGGCCATTGACAGGCCACCACCAAAAATTTTTTTTTTTGAATTTTTTCGTATACTGGTGCCG
* *
3858590 GCCAATGATAGCCCAAAATGT-AA-TTTTTTTTACATAAAGGTGA
66 GCCAATGACAGCCCAAAATGTAAATTTTTTTTTACATAAAGGTGG
* * * ** * ** *
3858633 TGCAGGCCATTGCCAGGCCACCACCTAAAAAAAATTTTTTTTTAAAATTTTTTTCATATGTTAGT
1 TGCCGGCCATTGACAGGCCACCACC---AAAAATTTTTTTTTTTGAA-TTTTTTCGTATACTGGT
* * * *
3858698 GCCGGCCAATGATAG-CTAAAATGT-AATTTTTTTTTACATAAAGCTAG
62 GCCGGCCAATGACAGCCCAAAATGTAAATTTTTTTTTACATAAAGGTGG
* ** *
3858745 TGCCGACCATT-ACTAGGCCACCACCAAAAAATAAATTTTTTTTGAATTTTTTCGTATACTGATG
1 TGCCGGCCATTGAC-AGGCCACCACC-AAAAAT-TTTTTTTTTTGAATTTTTTCGTATACTGGTG
* *
3858809 CCGGCCAATAACAGCCCAAAATGTAAATTTTTTTTTACATCAAGGTGG
63 CCGGCCAATGACAGCCCAAAATGTAAATTTTTTTTTACATAAAGGTGG
* * * *** *
3858857 TGCCGGTCATTGTCAGGCCACCACAAAAAAAAAGCATTTTTTTTGAATTTTTTCGTATAGTGGTG
1 TGCCGGCCATTGACAGGCCACCAC---CAAAAATTTTTTTTTTTGAATTTTTTCGTATACTGGTG
** *
3858922 CCTTCCAATGACAGCCCAAAATGTAAAATTTTTTTTACATAAAGGTGG
63 CCGGCCAATGACAGCCCAAAATGTAAATTTTTTTTTACATAAAGGTGG
* *
3858970 TGCCGGCCATTGTCAGGCCACCACCAAAAATTTTTTTTTTTGAATTTTTTCGTATATTGGTGCCG
1 TGCCGGCCATTGACAGGCCACCACCAAAAATTTTTTTTTTTGAATTTTTTCGTATACTGGTGCCG
* * *
3859035 ACCAATGACAGCCCAAAATGTAATTTTTTTTTTTTTACATAAAAGTGG
66 GCCAATGACAGCCCAAAATGTAA---ATTTTTTTTTACATAAAGGTGG
* * *
3859083 TGCCAGCCATTGACAGACCAGCATCC-AAAATTTTTTTTT
1 TGCCGGCCATTGACAGGCCACCA-CCAAAAATTTTTTTTT
3859122 CCTTTTTTTC
Statistics
Matches: 409, Mismatches: 63, Indels: 29
0.82 0.13 0.06
Matches are distributed among these distances:
108 22 0.05
110 88 0.22
111 43 0.11
112 103 0.25
113 146 0.36
114 7 0.02
ACGTcount: A:0.30, C:0.19, G:0.16, T:0.36
Consensus pattern (110 bp):
TGCCGGCCATTGACAGGCCACCACCAAAAATTTTTTTTTTTGAATTTTTTCGTATACTGGTGCCG
GCCAATGACAGCCCAAAATGTAAATTTTTTTTTACATAAAGGTGG
Found at i:3860946 original size:12 final size:12
Alignment explanation
Indices: 3860929--3860953 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
3860919 TTATTAGACC
3860929 GATCAGCTAGGA
1 GATCAGCTAGGA
3860941 GATCAGCTAGGA
1 GATCAGCTAGGA
3860953 G
1 G
3860954 CAACCATCAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.32, C:0.16, G:0.36, T:0.16
Consensus pattern (12 bp):
GATCAGCTAGGA
Found at i:3882310 original size:19 final size:19
Alignment explanation
Indices: 3882260--3882311 Score: 61
Period size: 19 Copynumber: 2.7 Consensus size: 19
3882250 ATGTTTATGT
*
3882260 ATTTTCACATATTATAATA
1 ATTTTAACATATTATAATA
*
3882279 ATATTTAAAATATTAT-ATAA
1 AT-TTTAACATATTATAAT-A
3882299 ATTTTAACATATT
1 ATTTTAACATATT
3882312 TAAATTTCAT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
19 14 0.50
20 14 0.50
ACGTcount: A:0.46, C:0.06, G:0.00, T:0.48
Consensus pattern (19 bp):
ATTTTAACATATTATAATA
Found at i:3883719 original size:2 final size:2
Alignment explanation
Indices: 3883712--3883742 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
3883702 TGATTAGGAA
3883712 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3883743 AGTAAATATG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3886098 original size:31 final size:31
Alignment explanation
Indices: 3886044--3886108 Score: 85
Period size: 31 Copynumber: 2.1 Consensus size: 31
3886034 TACAAATTAA
* *
3886044 TCATTAGAGTATTTGAAAATTTTTATATAAG
1 TCATTAAAGTATTCGAAAATTTTTATATAAG
* * *
3886075 TCATTAAATTATTCGAAAGTTTTTATTTAAG
1 TCATTAAAGTATTCGAAAATTTTTATATAAG
3886106 TCA
1 TCA
3886109 CTAGGTTGTT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.37, C:0.06, G:0.11, T:0.46
Consensus pattern (31 bp):
TCATTAAAGTATTCGAAAATTTTTATATAAG
Found at i:3889349 original size:29 final size:29
Alignment explanation
Indices: 3889317--3889382 Score: 71
Period size: 29 Copynumber: 2.3 Consensus size: 29
3889307 ACTAATAAAA
*
3889317 GCCGTTTTTTTCAAAATTTACCGAAATGG
1 GCCGATTTTTTCAAAATTTACCGAAATGG
* ** *
3889346 GCCGATTTTTTGATTATTTACCGGAATGG
1 GCCGATTTTTTCAAAATTTACCGAAATGG
*
3889375 ACC-ATTTT
1 GCCGATTTT
3889383 CCGCGAAATC
Statistics
Matches: 31, Mismatches: 6, Indels: 1
0.82 0.16 0.03
Matches are distributed among these distances:
28 5 0.16
29 26 0.84
ACGTcount: A:0.24, C:0.17, G:0.18, T:0.41
Consensus pattern (29 bp):
GCCGATTTTTTCAAAATTTACCGAAATGG
Found at i:3898156 original size:37 final size:37
Alignment explanation
Indices: 3898101--3898181 Score: 144
Period size: 37 Copynumber: 2.2 Consensus size: 37
3898091 TCGCTCCACG
3898101 TTTGTCTGCGATCATTCAGTAAATTTTAGATAAGTGA
1 TTTGTCTGCGATCATTCAGTAAATTTTAGATAAGTGA
* *
3898138 TTTGTCTGCGATCGTTCAGTAAGTTTTAGATAAGTGA
1 TTTGTCTGCGATCATTCAGTAAATTTTAGATAAGTGA
3898175 TTTGTCT
1 TTTGTCT
3898182 TTGTTTGTTA
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 42 1.00
ACGTcount: A:0.25, C:0.11, G:0.21, T:0.43
Consensus pattern (37 bp):
TTTGTCTGCGATCATTCAGTAAATTTTAGATAAGTGA
Found at i:3901032 original size:6 final size:6
Alignment explanation
Indices: 3901021--3901051 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
3901011 TGTTAAATTA
3901021 TATTTT TATTTT TATTTT TATTTT TATTTT T
1 TATTTT TATTTT TATTTT TATTTT TATTTT T
3901052 GGTTTCTCTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (6 bp):
TATTTT
Found at i:3907760 original size:20 final size:21
Alignment explanation
Indices: 3907737--3907800 Score: 67
Period size: 23 Copynumber: 2.9 Consensus size: 21
3907727 CAATTTTTAT
3907737 TTTATTTATTATTATTT-TTC
1 TTTATTTATTATTATTTATTC
*
3907757 TTTACTTTATTTATTACTTTATTT
1 TTTA-TTTA-TTATTA-TTTATTC
3907781 TATTATTTATTACTTATTTA
1 T-TTATTTATTA-TTATTTA
3907801 GATATTAATC
Statistics
Matches: 37, Mismatches: 1, Indels: 9
0.79 0.02 0.19
Matches are distributed among these distances:
20 4 0.11
21 4 0.11
22 6 0.16
23 10 0.27
24 10 0.27
25 3 0.08
ACGTcount: A:0.23, C:0.06, G:0.00, T:0.70
Consensus pattern (21 bp):
TTTATTTATTATTATTTATTC
Found at i:3907765 original size:25 final size:26
Alignment explanation
Indices: 3907732--3907781 Score: 75
Period size: 25 Copynumber: 1.9 Consensus size: 26
3907722 CAACCCAATT
*
3907732 TTTATTTTATTTATTA-TTATTTTTC
1 TTTACTTTATTTATTACTTATTTTTC
3907757 TTTACTTTATTTATTACTTTATTTT
1 TTTACTTTATTTATTAC-TTATTTT
3907782 ATTATTTATT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 15 0.68
27 7 0.32
ACGTcount: A:0.20, C:0.06, G:0.00, T:0.74
Consensus pattern (26 bp):
TTTACTTTATTTATTACTTATTTTTC
Found at i:3907775 original size:12 final size:12
Alignment explanation
Indices: 3907758--3907791 Score: 52
Period size: 12 Copynumber: 2.8 Consensus size: 12
3907748 TTATTTTTCT
3907758 TTACTTTATTTA
1 TTACTTTATTTA
3907770 TTACTTTATTTTA
1 TTACTTTA-TTTA
3907783 TTA-TTTATT
1 TTACTTTATT
3907792 ACTTATTTAG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
11 2 0.10
12 12 0.57
13 7 0.33
ACGTcount: A:0.24, C:0.06, G:0.00, T:0.71
Consensus pattern (12 bp):
TTACTTTATTTA
Found at i:3907782 original size:17 final size:15
Alignment explanation
Indices: 3907731--3907784 Score: 56
Period size: 16 Copynumber: 3.5 Consensus size: 15
3907721 GCAACCCAAT
*
3907731 TTTTA-TTTTATTTA
1 TTTTATTTTTCTTTA
3907745 TTATTATTTTTCTTTA
1 TT-TTATTTTTCTTTA
*
3907761 CTTTATTTATTACTTTA
1 TTTTATTT-TT-CTTTA
3907778 TTTTATT
1 TTTTATT
3907785 ATTTATTACT
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
14 2 0.06
15 9 0.27
16 11 0.33
17 11 0.33
ACGTcount: A:0.20, C:0.06, G:0.00, T:0.74
Consensus pattern (15 bp):
TTTTATTTTTCTTTA
Found at i:3911571 original size:14 final size:14
Alignment explanation
Indices: 3911530--3911560 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
3911520 TTAATTCTGA
3911530 ATGGATGATGGACT
1 ATGGATGATGGACT
3911544 ATGGATGATGGACT
1 ATGGATGATGGACT
3911558 ATG
1 ATG
3911561 TATGCATGAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.29, C:0.06, G:0.35, T:0.29
Consensus pattern (14 bp):
ATGGATGATGGACT
Found at i:3921456 original size:273 final size:273
Alignment explanation
Indices: 3920969--3921513 Score: 729
Period size: 273 Copynumber: 2.0 Consensus size: 273
3920959 CATCGACGTT
* *
3920969 GGAAAAATATACTCCAAACCATAACAATTTGATATGCTGACGTCTCCTAACTCTGGGAAGCACAA
1 GGAAAAATATACTCCAAACCATAACAAGTAGATATGCTGACGTCTCCTAACTCTGGGAAGCACAA
* * *
3921034 AGAATTATGAGAATTGATGGTTGGTGATATTTCTCCCTCGTCGCCTTCCAATTCTGTCACTATTT
66 AGAAGTATGAGAATTGATAGTTGGTGATATTTCTCCCTCGTCACCTTCCAATTCTGTCACTATTT
** * * * * ** *
3921099 GCTTCATTTCATCACAGTAGCTTATGTCAAGACGTTTCAATTGTACTAGACTTTGAGCAAGAGAA
131 GCTTCAACTCAGCACAATAGATTATCTCAAGACGTTTCAAGAGTACGAGACTTTGAGCAAGAGAA
* **
3921164 AGTGAAAAGAGTGATTTCAAACGTGGGAACTTTTTTATAGTCAAAACAACTAAGCTTTCAAGTCT
196 AGTGAAAAGAGTGATTTCAAACGTGGGAACTGTAGTATAGTCAAAACAACTAAGCTTTCAAGTCT
3921229 TACATGTTGGGTC
261 TACATGTTGGGTC
* * ** * *
3921242 GGAAAAATATACTCCAAACCATCACAAGTAGATATG-TAGA-GTTTTGTTAACTTTGGGAAGGAC
1 GGAAAAATATACTCCAAACCATAACAAGTAGATATGCT-GACG-TCTCCTAACTCTGGGAAGCAC
* * *
3921305 AAAGAAGTATGAGAATTGATAGTAT-GTGATATTTCTCCCTTGTCACCTTCTAATTCTGTCACTG
64 AAAGAAGTATGAGAATTGATAGT-TGGTGATATTTCTCCCTCGTCACCTTCCAATTCTGTCACTA
* **
3921369 TTTGCTTCAACTCAGGACAATAGATTATCTCAAG-TTTTTCCAAGAGTACGAGACTTTGAGCAAG
128 TTTGCTTCAACTCAGCACAATAGATTATCTCAAGACGTTT-CAAGAGTACGAGACTTTGAGCAAG
* * **
3921433 AGAAAGTGAAAAGAGTGATTTCAAACGTGGGCAGTGTAGTATAGTCAATTCAACTAAGCTTTCAA
192 AGAAAGTGAAAAGAGTGATTTCAAACGTGGGAACTGTAGTATAGTCAAAACAACTAAGCTTTCAA
3921498 GTCTTACATGTTGGGT
257 GTCTTACATGTTGGGT
3921514 TGGCAATTCC
Statistics
Matches: 235, Mismatches: 33, Indels: 8
0.85 0.12 0.03
Matches are distributed among these distances:
272 5 0.02
273 229 0.97
274 1 0.00
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Consensus pattern (273 bp):
GGAAAAATATACTCCAAACCATAACAAGTAGATATGCTGACGTCTCCTAACTCTGGGAAGCACAA
AGAAGTATGAGAATTGATAGTTGGTGATATTTCTCCCTCGTCACCTTCCAATTCTGTCACTATTT
GCTTCAACTCAGCACAATAGATTATCTCAAGACGTTTCAAGAGTACGAGACTTTGAGCAAGAGAA
AGTGAAAAGAGTGATTTCAAACGTGGGAACTGTAGTATAGTCAAAACAACTAAGCTTTCAAGTCT
TACATGTTGGGTC
Found at i:3923551 original size:17 final size:17
Alignment explanation
Indices: 3923529--3923576 Score: 62
Period size: 17 Copynumber: 2.8 Consensus size: 17
3923519 AATCAAAAAT
3923529 TATTTTTAATAAGATAA
1 TATTTTTAATAAGATAA
3923546 TATTTTGTAATAA-ATAA
1 TATTTT-TAATAAGATAA
*
3923563 TATATTATAATAAG
1 TAT-TTTTAATAAG
3923577 CATTTTACTA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
17 19 0.70
18 8 0.30
ACGTcount: A:0.48, C:0.00, G:0.06, T:0.46
Consensus pattern (17 bp):
TATTTTTAATAAGATAA
Found at i:3924568 original size:14 final size:14
Alignment explanation
Indices: 3924549--3924575 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
3924539 TATTTTTAAT
3924549 ATTTTTATAAAAAC
1 ATTTTTATAAAAAC
3924563 ATTTTTATAAAAA
1 ATTTTTATAAAAA
3924576 TAATCTTACT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.44
Consensus pattern (14 bp):
ATTTTTATAAAAAC
Found at i:3928416 original size:30 final size:31
Alignment explanation
Indices: 3928382--3928440 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
3928372 TTAAATTGCT
*
3928382 TTTATTTATTTT-AATTACTATGATTAATTA
1 TTTATTTATTTTAAATTACTATAATTAATTA
*
3928412 TTTATTTATTTTAAATTACTTTAATTAAT
1 TTTATTTATTTTAAATTACTATAATTAAT
3928441 GATATGGGTT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 12 0.46
31 14 0.54
ACGTcount: A:0.34, C:0.03, G:0.02, T:0.61
Consensus pattern (31 bp):
TTTATTTATTTTAAATTACTATAATTAATTA
Found at i:3928901 original size:15 final size:16
Alignment explanation
Indices: 3928881--3928910 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
3928871 ACATTATGTG
3928881 ACAAAAA-TAAATAAA
1 ACAAAAAGTAAATAAA
3928896 ACAAAAAGTAAATAA
1 ACAAAAAGTAAATAA
3928911 CTAAACCTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.77, C:0.07, G:0.03, T:0.13
Consensus pattern (16 bp):
ACAAAAAGTAAATAAA
Found at i:3929422 original size:11 final size:11
Alignment explanation
Indices: 3929408--3929432 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
3929398 ATACTAATTC
3929408 TTATTTTGAAT
1 TTATTTTGAAT
3929419 TTATTTTGAAT
1 TTATTTTGAAT
3929430 TTA
1 TTA
3929433 ATAAATTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.28, C:0.00, G:0.08, T:0.64
Consensus pattern (11 bp):
TTATTTTGAAT
Found at i:3942133 original size:2 final size:2
Alignment explanation
Indices: 3942126--3942158 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
3942116 TAGATTGTTG
*
3942126 TA TA TA TA TT TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3942159 TATTTTGTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (2 bp):
TA
Found at i:3944626 original size:5 final size:5
Alignment explanation
Indices: 3944609--3944638 Score: 51
Period size: 5 Copynumber: 5.8 Consensus size: 5
3944599 TATATTTGGG
3944609 TAATT TAAATT TAATT TAATT TAATT TAAT
1 TAATT T-AATT TAATT TAATT TAATT TAAT
3944639 ATGTAAAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
5 19 0.79
6 5 0.21
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (5 bp):
TAATT
Found at i:3972853 original size:3 final size:3
Alignment explanation
Indices: 3972845--3972877 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
3972835 GCTGCTCCTA
3972845 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
3972878 TTCCCTTTAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
CTT
Found at i:4007945 original size:30 final size:31
Alignment explanation
Indices: 4007909--4007974 Score: 80
Period size: 30 Copynumber: 2.2 Consensus size: 31
4007899 AATAGTTTAT
* *
4007909 ATTTTTATAATTTTTAAAAGATTAAATTA-A
1 ATTTTTATAATTTCTAAAAGATTAAAGTATA
* * *
4007939 ATTTTTATTATTTCTAGAAGGTTAAAGTATA
1 ATTTTTATAATTTCTAAAAGATTAAAGTATA
4007970 ATTTT
1 ATTTT
4007975 ACCATTACTA
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
30 24 0.80
31 6 0.20
ACGTcount: A:0.39, C:0.02, G:0.08, T:0.52
Consensus pattern (31 bp):
ATTTTTATAATTTCTAAAAGATTAAAGTATA
Found at i:4011282 original size:30 final size:30
Alignment explanation
Indices: 4011242--4011298 Score: 87
Period size: 30 Copynumber: 1.9 Consensus size: 30
4011232 ACCAAAATGC
4011242 AACGACTATCATTTTCCTCACAATTTTGTA
1 AACGACTATCATTTTCCTCACAATTTTGTA
* * *
4011272 AACGATTATCATTTTTCTTACAATTTT
1 AACGACTATCATTTTCCTCACAATTTT
4011299 ATTTACATTT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.30, C:0.19, G:0.05, T:0.46
Consensus pattern (30 bp):
AACGACTATCATTTTCCTCACAATTTTGTA
Found at i:4016487 original size:11 final size:12
Alignment explanation
Indices: 4016457--4016491 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
4016447 ATATTATTTT
4016457 TATATAAAAATA
1 TATATAAAAATA
*
4016469 TATTTAAAAATA
1 TATATAAAAATA
4016481 TA-ATAAAAATA
1 TATATAAAAATA
4016492 ACTACACTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
11 8 0.38
12 13 0.62
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (12 bp):
TATATAAAAATA
Found at i:4016907 original size:32 final size:32
Alignment explanation
Indices: 4016866--4016926 Score: 88
Period size: 32 Copynumber: 1.9 Consensus size: 32
4016856 AAACAGCAAA
* *
4016866 AACAGCAGCATTTTTTC-TTCTGCAAATTTAGG
1 AACAGCAGCAATTTATCTTTC-GCAAATTTAGG
4016898 AACAGCAGCAATTTATCTTTCGCAAATTT
1 AACAGCAGCAATTTATCTTTCGCAAATTT
4016927 GGGTTGAGCC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
32 23 0.88
33 3 0.12
ACGTcount: A:0.31, C:0.20, G:0.13, T:0.36
Consensus pattern (32 bp):
AACAGCAGCAATTTATCTTTCGCAAATTTAGG
Found at i:4021417 original size:43 final size:42
Alignment explanation
Indices: 4021354--4021450 Score: 151
Period size: 43 Copynumber: 2.3 Consensus size: 42
4021344 TGCGTTTTTC
*
4021354 TAGACCTTTAGCGGCACTTTTATCACAAACACCGCTATAG-A
1 TAGACCTTTAGCGGCACTTTTATAACAAACACCGCTATAGAA
*
4021395 TCATGACCTTTAGCGGCACTTTTATAACAAACGCCGCTATAGAA
1 T-A-GACCTTTAGCGGCACTTTTATAACAAACACCGCTATAGAA
4021439 TAGACCTTTAGC
1 TAGACCTTTAGC
4021451 AGCGCTTCTC
Statistics
Matches: 51, Mismatches: 2, Indels: 5
0.88 0.03 0.09
Matches are distributed among these distances:
41 1 0.02
42 11 0.22
43 37 0.73
44 2 0.04
ACGTcount: A:0.31, C:0.26, G:0.15, T:0.28
Consensus pattern (42 bp):
TAGACCTTTAGCGGCACTTTTATAACAAACACCGCTATAGAA
Found at i:4022164 original size:5 final size:5
Alignment explanation
Indices: 4022154--4022180 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
4022144 CTTTCTTGCC
4022154 AATAA AATAA AATAA AATAA AATAA AA
1 AATAA AATAA AATAA AATAA AATAA AA
4022181 AACAAGAATC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
AATAA
Found at i:4024569 original size:14 final size:14
Alignment explanation
Indices: 4024532--4024569 Score: 60
Period size: 13 Copynumber: 2.8 Consensus size: 14
4024522 AGTTATATGA
*
4024532 TTTTATAAAATATT
1 TTTTATAAACTATT
4024546 TTTTAT-AACTATT
1 TTTTATAAACTATT
4024559 TTTTATAAACT
1 TTTTATAAACT
4024570 GGATTTTTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 12 0.55
14 10 0.45
ACGTcount: A:0.37, C:0.05, G:0.00, T:0.58
Consensus pattern (14 bp):
TTTTATAAACTATT
Found at i:4025187 original size:8 final size:8
Alignment explanation
Indices: 4025174--4025202 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
4025164 CTGACTCGAC
4025174 CCCTAAAT
1 CCCTAAAT
4025182 CCCTAAAT
1 CCCTAAAT
4025190 -CCTAAAT
1 CCCTAAAT
4025197 CCCTAA
1 CCCTAA
4025203 CTCTTAACCC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
7 7 0.35
8 13 0.65
ACGTcount: A:0.38, C:0.38, G:0.00, T:0.24
Consensus pattern (8 bp):
CCCTAAAT
Found at i:4025268 original size:21 final size:21
Alignment explanation
Indices: 4025237--4025316 Score: 58
Period size: 21 Copynumber: 3.8 Consensus size: 21
4025227 GTAACTCCTA
4025237 AACCC-TAAACCTTAAATCCC
1 AACCCTTAAACCTTAAATCCC
* *
4025257 AACCCTTAAACCAT-AATCTCA
1 AACCCTTAAACCTTAAATC-CC
* * * *
4025278 AATCCATAATCCTTAAAT-TC
1 AACCCTTAAACCTTAAATCCC
4025298 ATACCCCTTAAACCTTAAA
1 A-A-CCCTTAAACCTTAAA
4025317 ATAGTAACTC
Statistics
Matches: 44, Mismatches: 11, Indels: 8
0.70 0.17 0.13
Matches are distributed among these distances:
20 10 0.23
21 19 0.43
22 15 0.34
ACGTcount: A:0.41, C:0.33, G:0.00, T:0.26
Consensus pattern (21 bp):
AACCCTTAAACCTTAAATCCC
Found at i:4026341 original size:41 final size:40
Alignment explanation
Indices: 4025940--4026340 Score: 451
Period size: 41 Copynumber: 9.8 Consensus size: 40
4025930 AATATTTTTT
* * * *
4025940 GCGGCGCTTTTACAAAAACGACGCTAAATCCCAGAGAATTA
1 GCGGCGCTTTT-CAAAAACGCCGCTAAAGCCCCGAGCATTA
*
4025981 GCGGCGCTTTTCTAAAAACGCCGCTAAAGCCCAGAGCATTA
1 GCGGCGCTTTTC-AAAAACGCCGCTAAAGCCCCGAGCATTA
* *
4026022 GCGGCACTTTTCCAAAAACGCCTCTAAAGCCCCGAGCATTA
1 GCGGCGCTTTT-CAAAAACGCCGCTAAAGCCCCGAGCATTA
* * *
4026063 GCGGCGCTTTTCCAAAAACGCCGCTGAATCCTCGAGCATTA
1 GCGGCGCTTTT-CAAAAACGCCGCTAAAGCCCCGAGCATTA
* * * *
4026104 GTGGCGCTTTTCCAAAAACGCCGCTGAATCCTCGAGCATTA
1 GCGGCGCTTTT-CAAAAACGCCGCTAAAGCCCCGAGCATTA
* * * *
4026145 GCGGCGCTTTTCTAAAAATGCCACTAAATCCCCAAGCATTA
1 GCGGCGCTTTTC-AAAAACGCCGCTAAAGCCCCGAGCATTA
* * *
4026186 GCAGTGCTTTTCAAAAAACGCCGCTAAATCCCCGAGCATTA
1 GCGGCGCTTTTC-AAAAACGCCGCTAAAGCCCCGAGCATTA
* *
4026227 GCGGCGCTTTTACAAAAATGCTGCTAAAGCCCCGAGCATTA
1 GCGGCGCTTTT-CAAAAACGCCGCTAAAGCCCCGAGCATTA
* * * *
4026268 GCAGCGCCTTTCCAAAAACGCCGTTAAAGCCCTGAGCATTA
1 GCGGCG-CTTTTCAAAAACGCCGCTAAAGCCCCGAGCATTA
* *
4026309 GCGGCGCTTTCTCAGAAATGCCGCTAAAGCCC
1 GCGGCGCTTT-TCAAAAACGCCGCTAAAGCCC
4026341 TAAAAGGTCA
Statistics
Matches: 314, Mismatches: 40, Indels: 12
0.86 0.11 0.03
Matches are distributed among these distances:
40 6 0.02
41 302 0.96
42 6 0.02
ACGTcount: A:0.29, C:0.30, G:0.20, T:0.21
Consensus pattern (40 bp):
GCGGCGCTTTTCAAAAACGCCGCTAAAGCCCCGAGCATTA
Found at i:4031337 original size:16 final size:16
Alignment explanation
Indices: 4031316--4031348 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
4031306 TCTAATTGAT
4031316 GAATCATGTTTGTGGC
1 GAATCATGTTTGTGGC
4031332 GAATCATGTTTGTGGC
1 GAATCATGTTTGTGGC
4031348 G
1 G
4031349 TAAGAGGCTG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.18, C:0.12, G:0.33, T:0.36
Consensus pattern (16 bp):
GAATCATGTTTGTGGC
Found at i:4035211 original size:30 final size:33
Alignment explanation
Indices: 4035154--4035214 Score: 83
Period size: 34 Copynumber: 1.9 Consensus size: 33
4035144 TTCATCTAAC
*
4035154 AGTTATGTTTATCTTTCACCCTTGTGCCAATGAA
1 AGTTATGTTTATCTTTCA-CCTGGTGCCAATGAA
4035188 AGTTATGTTTATCTTT-A-C-GGTGCCAAT
1 AGTTATGTTTATCTTTCACCTGGTGCCAAT
4035215 CAATCTGTGG
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
30 8 0.31
31 1 0.04
33 1 0.04
34 16 0.62
ACGTcount: A:0.23, C:0.18, G:0.16, T:0.43
Consensus pattern (33 bp):
AGTTATGTTTATCTTTCACCTGGTGCCAATGAA
Found at i:4036724 original size:11 final size:11
Alignment explanation
Indices: 4036708--4036732 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
4036698 ATTTTTTAAC
4036708 TTTAAAATACT
1 TTTAAAATACT
4036719 TTTAAAATACT
1 TTTAAAATACT
4036730 TTT
1 TTT
4036733 TTAAATTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.40, C:0.08, G:0.00, T:0.52
Consensus pattern (11 bp):
TTTAAAATACT
Found at i:4036794 original size:23 final size:22
Alignment explanation
Indices: 4036747--4036833 Score: 71
Period size: 22 Copynumber: 4.1 Consensus size: 22
4036737 ATTTTTTTAA
4036747 TTTTAAAATTTTTTTTAAATAT
1 TTTTAAAATTTTTTTTAAATAT
4036769 TTTTAAAATACTTTTTTT-AAT-T
1 TTTTAAAAT--TTTTTTTAAATAT
* *
4036791 TTTT-TAA---TTTTAAAATAT
1 TTTTAAAATTTTTTTTAAATAT
*
4036809 TTTTAAAATACTTTTTTAAAT-T
1 TTTTAAAAT-TTTTTTTAAATAT
4036831 TTT
1 TTT
4036834 ATTTTAATTT
Statistics
Matches: 52, Mismatches: 4, Indels: 18
0.70 0.05 0.24
Matches are distributed among these distances:
16 4 0.08
17 3 0.06
18 5 0.10
19 2 0.04
21 2 0.04
22 18 0.35
23 11 0.21
24 7 0.13
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.63
Consensus pattern (22 bp):
TTTTAAAATTTTTTTTAAATAT
Found at i:4036845 original size:51 final size:52
Alignment explanation
Indices: 4036708--4036845 Score: 201
Period size: 51 Copynumber: 2.7 Consensus size: 52
4036698 ATTTTTTAAC
* *
4036708 TTTAAAATAC-TTTTAAAATACTTTTTTAAATTTTTTTAATTTTAAAATTTT
1 TTTAAAATACTTTTTAAAATACTTTTTTTAATTTTTTTAATTTTAAAATATT
*
4036759 TTTTAAATA-TTTTTAAAATACTTTTTTTAATTTTTTTAATTTTAAAATATT
1 TTTAAAATACTTTTTAAAATACTTTTTTTAATTTTTTTAATTTTAAAATATT
* *
4036810 TTTAAAATACTTTTTTAAAT-TTTTATTTTAATTTTT
1 TTTAAAATACTTTTTAAAATACTTT-TTTTAATTTTT
4036846 AAAATAAATT
Statistics
Matches: 78, Mismatches: 6, Indels: 5
0.88 0.07 0.06
Matches are distributed among these distances:
51 58 0.74
52 20 0.26
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (52 bp):
TTTAAAATACTTTTTAAAATACTTTTTTTAATTTTTTTAATTTTAAAATATT
Found at i:4046682 original size:15 final size:16
Alignment explanation
Indices: 4046662--4046692 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
4046652 TTCTTTTGTC
4046662 TTTTTC-TTTCTGTTT
1 TTTTTCTTTTCTGTTT
4046677 TTTTTCTTTTCTGTTT
1 TTTTTCTTTTCTGTTT
4046693 GCTGCTTTCT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.40
16 9 0.60
ACGTcount: A:0.00, C:0.13, G:0.06, T:0.81
Consensus pattern (16 bp):
TTTTTCTTTTCTGTTT
Found at i:4053645 original size:38 final size:38
Alignment explanation
Indices: 4053596--4053668 Score: 128
Period size: 38 Copynumber: 1.9 Consensus size: 38
4053586 GATAATTCAC
*
4053596 TATGTGAAATTCGAATGATTACAAGAGAAGTAGACTAT
1 TATGTGAAATTCGAATGATTACAAGAAAAGTAGACTAT
*
4053634 TATGTGGAATTCGAATGATTACAAGAAAAGTAGAC
1 TATGTGAAATTCGAATGATTACAAGAAAAGTAGAC
4053669 CATGTCTATT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
38 33 1.00
ACGTcount: A:0.42, C:0.08, G:0.22, T:0.27
Consensus pattern (38 bp):
TATGTGAAATTCGAATGATTACAAGAAAAGTAGACTAT
Found at i:4054100 original size:17 final size:17
Alignment explanation
Indices: 4054065--4054096 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
4054055 TAATACATAA
4054065 AATATTATATTTAAAAT
1 AATATTATATTTAAAAT
4054082 AATA-TATATTTAAAA
1 AATATTATATTTAAAA
4054097 ATAAACATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
AATATTATATTTAAAAT
Found at i:4061569 original size:30 final size:30
Alignment explanation
Indices: 4061512--4061570 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
4061502 CATTTATGGG
* **
4061512 TATTAATTAATTAAAATTTATTTATATTAT
1 TATTAATTAATTAAAATATATAAATATTAT
4061542 TATTAAATT-ATTAAAATATATAAATATTA
1 TATT-AATTAATTAAAATATATAAATATTA
4061571 ATAGAAAATA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 21 0.84
31 4 0.16
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (30 bp):
TATTAATTAATTAAAATATATAAATATTAT
Found at i:4072991 original size:41 final size:41
Alignment explanation
Indices: 4072934--4073068 Score: 225
Period size: 41 Copynumber: 3.3 Consensus size: 41
4072924 AATTTAACAT
*
4072934 ATTCAGATCACCGGCACTTAGCCTGCTAGGTTTATAACCTG
1 ATTCAGATCACCGGCACTTAGCCTACTAGGTTTATAACCTG
* * *
4072975 ATTCATATCACCGGCACTTAGCCTACTAGGCTTATAGCCTG
1 ATTCAGATCACCGGCACTTAGCCTACTAGGTTTATAACCTG
4073016 ATTCAGATCACCGGCACTTAGCCTACTAGGTTTATAACCTG
1 ATTCAGATCACCGGCACTTAGCCTACTAGGTTTATAACCTG
*
4073057 ATTCAAATCACC
1 ATTCAGATCACC
4073069 AATTCCAAAC
Statistics
Matches: 86, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
41 86 1.00
ACGTcount: A:0.27, C:0.28, G:0.16, T:0.29
Consensus pattern (41 bp):
ATTCAGATCACCGGCACTTAGCCTACTAGGTTTATAACCTG
Found at i:4073298 original size:41 final size:41
Alignment explanation
Indices: 4073238--4073334 Score: 158
Period size: 41 Copynumber: 2.4 Consensus size: 41
4073228 TTTGTTCCTT
*
4073238 TGATTCAGATCACCAGCACTTAGCCTGCTAGGCTTATAGCC
1 TGATTCAGATCACCAGCACTTAGCCTGCTAGGCTTATAACC
* *
4073279 TGATTCAGATCACCGGCACTTAGCCTGCTAGGTTTATAACC
1 TGATTCAGATCACCAGCACTTAGCCTGCTAGGCTTATAACC
*
4073320 TGATTCAAATCACCA
1 TGATTCAGATCACCA
4073335 ATTTCAAACT
Statistics
Matches: 51, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
41 51 1.00
ACGTcount: A:0.27, C:0.28, G:0.18, T:0.28
Consensus pattern (41 bp):
TGATTCAGATCACCAGCACTTAGCCTGCTAGGCTTATAACC
Found at i:4073563 original size:2 final size:2
Alignment explanation
Indices: 4073558--4073599 Score: 68
Period size: 2 Copynumber: 21.5 Consensus size: 2
4073548 ACACACACAC
*
4073558 AT AT AT AT AT AT AT AT AT AT AA AT AT -T 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 AT AT AT AT
4073599 A
1 A
4073600 CCTTTGATTA
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 36 0.97
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:4076889 original size:50 final size:50
Alignment explanation
Indices: 4076772--4076916 Score: 191
Period size: 50 Copynumber: 2.9 Consensus size: 50
4076762 TGATAATAAC
** * *
4076772 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCATGTTG
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGA-CCTCTCATCTCG
* * * * *
4076823 GTGCCCATGCCATGTCCCAGACATGGTCTTATAGGGGACCTCTCATCTCG
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCG
*
4076873 ATGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTC
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTC
4076917 GTCTTGGTGC
Statistics
Matches: 80, Mismatches: 14, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
50 47 0.59
51 33 0.41
ACGTcount: A:0.21, C:0.30, G:0.23, T:0.26
Consensus pattern (50 bp):
ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCG
Found at i:4077294 original size:29 final size:30
Alignment explanation
Indices: 4077260--4077316 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
4077250 CCTCGACTCT
4077260 AACTTTT-CAAAATTACAATTTTGCCCCTA
1 AACTTTTACAAAATTACAATTTTGCCCCTA
* *
4077289 AACTTTTACATAATTACATTTTTGCCCC
1 AACTTTTACAAAATTACAATTTTGCCCC
4077317 AAGGCTCGGA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
29 7 0.28
30 18 0.72
ACGTcount: A:0.32, C:0.25, G:0.04, T:0.40
Consensus pattern (30 bp):
AACTTTTACAAAATTACAATTTTGCCCCTA
Found at i:4080576 original size:16 final size:16
Alignment explanation
Indices: 4080551--4080586 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
4080541 CGACTTGCAG
*
4080551 TTTGATAGGCTCACAC
1 TTTGACAGGCTCACAC
4080567 TTTGACAGGCTCACAC
1 TTTGACAGGCTCACAC
4080583 TTTG
1 TTTG
4080587 CTTGCTGTCT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.22, C:0.25, G:0.19, T:0.33
Consensus pattern (16 bp):
TTTGACAGGCTCACAC
Found at i:4086767 original size:23 final size:23
Alignment explanation
Indices: 4086717--4086767 Score: 93
Period size: 23 Copynumber: 2.2 Consensus size: 23
4086707 ATAAAGAATG
*
4086717 ATTAATCTAAATTTAAACTTGAA
1 ATTAGTCTAAATTTAAACTTGAA
4086740 ATTAGTCTAAATTTAAACTTGAA
1 ATTAGTCTAAATTTAAACTTGAA
4086763 ATTAG
1 ATTAG
4086768 AAAGATGAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.45, C:0.08, G:0.08, T:0.39
Consensus pattern (23 bp):
ATTAGTCTAAATTTAAACTTGAA
Found at i:4087067 original size:2 final size:2
Alignment explanation
Indices: 4087048--4087099 Score: 86
Period size: 2 Copynumber: 26.0 Consensus size: 2
4087038 CTGATATGTC
* *
4087048 AT AT AT AC AT AT AC 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 AT AT AT AT
4087090 AT AT AT AT AT
1 AT AT AT AT AT
4087100 TCCTCTATCT
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:4088481 original size:22 final size:19
Alignment explanation
Indices: 4088456--4088514 Score: 55
Period size: 22 Copynumber: 2.8 Consensus size: 19
4088446 ATAAAATATT
4088456 ATTAAGATAAGTATTAAATTAA
1 ATTAA-ATAA-TATTAAATT-A
*
4088478 ATTAAATTAAATATTAAATTT
1 ATTAAA-T-AATATTAAATTA
4088499 ATTAAAATAATATTAA
1 ATT-AAATAATATTAA
4088515 TTTTGAAATA
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
20 8 0.24
21 5 0.15
22 18 0.55
23 2 0.06
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (19 bp):
ATTAAATAATATTAAATTA
Found at i:4096880 original size:16 final size:16
Alignment explanation
Indices: 4096859--4096907 Score: 50
Period size: 17 Copynumber: 3.1 Consensus size: 16
4096849 TCTGATAGCT
4096859 TTAGGTTATTGGGCCA
1 TTAGGTTATTGGGCCA
*
4096875 TTAGGTTTTTTGGGCCAA
1 TTAGG-TTATTGGGCC-A
4096893 TT--G-TATTGGGCCA
1 TTAGGTTATTGGGCCA
4096906 TT
1 TT
4096908 TGGGTTAGTT
Statistics
Matches: 29, Mismatches: 2, Indels: 7
0.76 0.05 0.18
Matches are distributed among these distances:
13 3 0.10
14 8 0.28
16 6 0.21
17 9 0.31
18 3 0.10
ACGTcount: A:0.16, C:0.12, G:0.29, T:0.43
Consensus pattern (16 bp):
TTAGGTTATTGGGCCA
Found at i:4097565 original size:131 final size:130
Alignment explanation
Indices: 4097258--4097808 Score: 587
Period size: 131 Copynumber: 4.2 Consensus size: 130
4097248 AGACTTGATG
* * * * * * *
4097258 CGATCTGCTCTACTATTGCTTAGAGAGATAAGATCTACAATCTTCAACCTACTCCACTGCTGCTA
1 CGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATCTTCGACCTGCTCCACTACTGCTT
* * * * ** *
4097323 AGGGAGATAGGAT-TGGTTTCTTTTG-TCTACTCCGCTACTGCTTAGGGAGATAAGA-CTTGATG
66 AGGGAGATAGGATCTAGTATC-TTTGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTCCATT
4097385 T
130 T
4097386 -GATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATCTTCGACCTGCTCCACTACTGCTT
1 CGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATCTTCGACCTGCTCCACTACTGCTT
* ** ** * *
4097450 AGGGAGATAGGA-CTGGTGGCTTAAATCTGCTTCACTACTGCTTAGGAAGATAAGATTCTCCATC
66 AGGGAGATAGGATCTAGTATCTTTGATCTGCTCCACTACTGCTTAGGGAGATAAGA-TCTCCAT-
4097514 TT
129 TT
* *
4097516 CGATCTGCTCCACTACTGCTTAGGGAGATAGGATCTA-ACATCTTTGACCTGCTCCACTACTGCT
1 CGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACA-ATCTTCGACCTGCTCCACTACTGCT
* * **
4097580 TAGGGAGATAGGATCTACTATCTTCGA-CTTGCTCCACTACTGCTTAGGGAGATAAGA-CTAGTG
65 TAGGGAGATAGGATCTAGTATCTTTGATC-TGCTCCACTACTGCTTAGGGAGATAAGATCT--CC
*
4097643 GTTT
127 ATTT
** * * * * ** *
4097647 AAATCTGCTTCACTACTGCTTAGGAAGATAAGATTTGCCGTCTTCGATCTGCTCCACTACTGCTT
1 CGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATCTTCGACCTGCTCCACTACTGCTT
** * *
4097712 AGGGAGATAGGATCTAACATCTTTGACCTGCTCCACTACTGCTTAGGGAGATAGGATCTACCATC
66 AGGGAGATAGGATCTAGTATCTTTGATCTGCTCCACTACTGCTTAGGGAGATAAGATCT-CCAT-
4097777 TT
129 TT
*
4097779 CGACCTGCTCCACTACTGCTTAGGGAGATA
1 CGATCTGCTCCACTACTGCTTAGGGAGATA
4097809 GGACTAGTGG
Statistics
Matches: 353, Mismatches: 55, Indels: 26
0.81 0.13 0.06
Matches are distributed among these distances:
126 2 0.01
127 100 0.28
129 4 0.01
130 4 0.01
131 179 0.51
132 64 0.18
ACGTcount: A:0.25, C:0.24, G:0.21, T:0.31
Consensus pattern (130 bp):
CGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATCTTCGACCTGCTCCACTACTGCTT
AGGGAGATAGGATCTAGTATCTTTGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTCCATTT
Found at i:4097588 original size:175 final size:175
Alignment explanation
Indices: 4097389--4097876 Score: 879
Period size: 175 Copynumber: 2.8 Consensus size: 175
4097379 TTGATGTGAT
*
4097389 CTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATCTTCGACCTGCTCCACTACTGCTTAGGG
1 CTGCTCCACTACTGCTTAGGGAGATAGGATCTACAATCTTCGACCTGCTCCACTACTGCTTAGGG
* * *
4097454 AGATAGGACTGGTGGCTTAAATCTGCTTCACTACTGCTTAGGAAGATAAGATTCTCCATCTTCGA
66 AGATAGGACTAGTGGTTTAAATCTGCTTCACTACTGCTTAGGAAGATAAGATTCTCCGTCTTCGA
4097519 TCTGCTCCACTACTGCTTAGGGAGATAGGATCTAACATCTTTGAC
131 TCTGCTCCACTACTGCTTAGGGAGATAGGATCTAACATCTTTGAC
* *
4097564 CTGCTCCACTACTGCTTAGGGAGATAGGATCTACTATCTTCGACTTGCTCCACTACTGCTTAGGG
1 CTGCTCCACTACTGCTTAGGGAGATAGGATCTACAATCTTCGACCTGCTCCACTACTGCTTAGGG
*
4097629 AGATAAGACTAGTGGTTTAAATCTGCTTCACTACTGCTTAGGAAGATAAGATT-TGCCGTCTTCG
66 AGATAGGACTAGTGGTTTAAATCTGCTTCACTACTGCTTAGGAAGATAAGATTCT-CCGTCTTCG
4097693 ATCTGCTCCACTACTGCTTAGGGAGATAGGATCTAACATCTTTGAC
130 ATCTGCTCCACTACTGCTTAGGGAGATAGGATCTAACATCTTTGAC
*
4097739 CTGCTCCACTACTGCTTAGGGAGATAGGATCTACCATCTTCGACCTGCTCCACTACTGCTTAGGG
1 CTGCTCCACTACTGCTTAGGGAGATAGGATCTACAATCTTCGACCTGCTCCACTACTGCTTAGGG
*
4097804 AGATAGGACTAGTGGTTTAAATCTGCTTCACTACTGCTTAGGAAGATAAGATTCGCCGTCTTCGA
66 AGATAGGACTAGTGGTTTAAATCTGCTTCACTACTGCTTAGGAAGATAAGATTCTCCGTCTTCGA
4097869 TCTGCTCC
131 TCTGCTCC
4097877 GCTAGTACTT
Statistics
Matches: 300, Mismatches: 11, Indels: 4
0.95 0.03 0.01
Matches are distributed among these distances:
174 1 0.00
175 299 1.00
ACGTcount: A:0.24, C:0.24, G:0.21, T:0.30
Consensus pattern (175 bp):
CTGCTCCACTACTGCTTAGGGAGATAGGATCTACAATCTTCGACCTGCTCCACTACTGCTTAGGG
AGATAGGACTAGTGGTTTAAATCTGCTTCACTACTGCTTAGGAAGATAAGATTCTCCGTCTTCGA
TCTGCTCCACTACTGCTTAGGGAGATAGGATCTAACATCTTTGAC
Found at i:4097809 original size:44 final size:44
Alignment explanation
Indices: 4097262--4097811 Score: 499
Period size: 44 Copynumber: 12.7 Consensus size: 44
4097252 TTGATGCGAT
* * * * * *
4097262 CTGCTCTACTATTGCTTAGAGAGATAAGATCTACAATCTTCAAC
1 CTGCTCCACTACTGCTTAGGGAGATAGGATCTACCATCTTCGAC
* * * **** * *
4097306 CTACTCCACTGCTGCTAAGGGAGATAGGAT-TGGTTTCTTTTG-T
1 CTGCTCCACTACTGCTTAGGGAGATAGGATCTACCATC-TTCGAC
* * * ** * *
4097349 CTACTCCGCTACTGCTTAGGGAGATAAGA-CT-TGAT-GT-GAT
1 CTGCTCCACTACTGCTTAGGGAGATAGGATCTACCATCTTCGAC
* *
4097389 CTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATCTTCGAC
1 CTGCTCCACTACTGCTTAGGGAGATAGGATCTACCATCTTCGAC
***** ** *
4097433 CTGCTCCACTACTGCTTAGGGAGATAGGA-CTGGTGGCTTAAAT
1 CTGCTCCACTACTGCTTAGGGAGATAGGATCTACCATCTTCGAC
* * * *
4097476 CTGCTTCACTACTGCTTAGGAAGATAAGATTCT-CCATCTTCGAT
1 CTGCTCCACTACTGCTTAGGGAGATAGGA-TCTACCATCTTCGAC
* *
4097520 CTGCTCCACTACTGCTTAGGGAGATAGGATCTAACATCTTTGAC
1 CTGCTCCACTACTGCTTAGGGAGATAGGATCTACCATCTTCGAC
*
4097564 CTGCTCCACTACTGCTTAGGGAGATAGGATCTACTATCTTCGAC
1 CTGCTCCACTACTGCTTAGGGAGATAGGATCTACCATCTTCGAC
* * *** ** *
4097608 TTGCTCCACTACTGCTTAGGGAGATAAGA-CTAGTGGT-TTAAAT
1 CTGCTCCACTACTGCTTAGGGAGATAGGATCTA-CCATCTTCGAC
* * * * * * *
4097651 CTGCTTCACTACTGCTTAGGAAGATAAGATTTGCCGTCTTCGAT
1 CTGCTCCACTACTGCTTAGGGAGATAGGATCTACCATCTTCGAC
* *
4097695 CTGCTCCACTACTGCTTAGGGAGATAGGATCTAACATCTTTGAC
1 CTGCTCCACTACTGCTTAGGGAGATAGGATCTACCATCTTCGAC
4097739 CTGCTCCACTACTGCTTAGGGAGATAGGATCTACCATCTTCGAC
1 CTGCTCCACTACTGCTTAGGGAGATAGGATCTACCATCTTCGAC
4097783 CTGCTCCACTACTGCTTAGGGAGATAGGA
1 CTGCTCCACTACTGCTTAGGGAGATAGGA
4097812 CTAGTGGTTT
Statistics
Matches: 410, Mismatches: 83, Indels: 26
0.79 0.16 0.05
Matches are distributed among these distances:
39 1 0.00
40 29 0.07
41 2 0.00
42 3 0.01
43 99 0.24
44 274 0.67
45 2 0.00
ACGTcount: A:0.25, C:0.23, G:0.21, T:0.31
Consensus pattern (44 bp):
CTGCTCCACTACTGCTTAGGGAGATAGGATCTACCATCTTCGAC
Found at i:4097874 original size:131 final size:129
Alignment explanation
Indices: 4097352--4097876 Score: 449
Period size: 131 Copynumber: 4.0 Consensus size: 129
4097342 CTTTTGTCTA
* ** *
4097352 CTCCGCTACTGCTTAGGGAGATAAGA-CT-TGAT-GT-GATCTGCTCCACTACTGCTTAGGGAGA
1 CTCCACTACTGCTTAGGGAGATAAGATCTACCATCTTCGATCTGCTCCACTACTGCTTAGGGAGA
* * * * * ***** **
4097413 TAAGATCTACAATCTTCGACCTGCTCCACTACTGCTTAGGGAGATAGGA-CTGGTGGCTTAAATC
66 TAGGA-CT--AGTGTTTGATCTGCTCCACTACTGCTTAGGGAGATAGGATCTACCATCTTCGATC
4097477 TG
128 TG
* *
4097479 CTTCACTACTGCTTAGGAAGATAAGATTCT-CCATCTTCGATCTGCTCCACTACTGCTTAGGGAG
1 CTCCACTACTGCTTAGGGAGATAAGA-TCTACCATCTTCGATCTGCTCCACTACTGCTTAGGGAG
* * * *
4097543 ATAGGATCTAACATCTTTGACCTGCTCCACTACTGCTTAGGGAGATAGGATCTACTATCTTCGA-
65 ATAGGA-CT-A-GTGTTTGATCTGCTCCACTACTGCTTAGGGAGATAGGATCTACCATCTTCGAT
4097607 CTTG
127 C-TG
*** ** * *
4097611 CTCCACTACTGCTTAGGGAGATAAGA-CTAGTGGT-TTAAATCTGCTTCACTACTGCTTAGGAAG
1 CTCCACTACTGCTTAGGGAGATAAGATCTA-CCATCTTCGATCTGCTCCACTACTGCTTAGGGAG
* * * * * * *
4097674 ATAAGATTTGCCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAGGATCTAACATCTTTGAC
65 ATAGGACTAG-TGT-TT-GATCTGCTCCACTACTGCTTAGGGAGATAGGATCTACCATCTTCGAT
4097739 CTG
127 CTG
* *
4097742 CTCCACTACTGCTTAGGGAGATAGGATCTACCATCTTCGACCTGCTCCACTACTGCTTAGGGAGA
1 CTCCACTACTGCTTAGGGAGATAAGATCTACCATCTTCGATCTGCTCCACTACTGCTTAGGGAGA
* * * * * *
4097807 TAGGACTAGTGGTTTAAATCTGCTTCACTACTGCTTAGGAAGATAAGAT-TCGCCGTCTTCGATC
66 TAGGACTAGT-GTTT-GATCTGCTCCACTACTGCTTAGGGAGATAGGATCT-ACCATCTTCGATC
4097871 TG
128 TG
4097873 CTCC
1 CTCC
4097877 GCTAGTACTT
Statistics
Matches: 324, Mismatches: 57, Indels: 30
0.79 0.14 0.07
Matches are distributed among these distances:
127 23 0.07
129 5 0.02
130 8 0.02
131 217 0.67
132 71 0.22
ACGTcount: A:0.24, C:0.24, G:0.22, T:0.30
Consensus pattern (129 bp):
CTCCACTACTGCTTAGGGAGATAAGATCTACCATCTTCGATCTGCTCCACTACTGCTTAGGGAGA
TAGGACTAGTGTTTGATCTGCTCCACTACTGCTTAGGGAGATAGGATCTACCATCTTCGATCTG
Found at i:4097992 original size:87 final size:87
Alignment explanation
Indices: 4097889--4098351 Score: 656
Period size: 87 Copynumber: 5.2 Consensus size: 87
4097879 TAGTACTTAA
* * *
4097889 GAAGGCAAGATTTGCTATCTTTAACCAGCTCTACTGCAACCGATGAAGGCAAGGCTTTGTTTTCG
1 GAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAACCGATGGAGGCAAGGCTTTGTTTTCG
*
4097954 GTCTGCTTCGCTGTTAACGCAG
66 GTCTGCTTCGCTGTTAACGTAG
* * *
4097976 GAAGGCAAGGTCTGCTATCTTTAACCAGCTCCACTGCAACTGGTGGAGGCAAGGCTTTGTTTTCG
1 GAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAACCGATGGAGGCAAGGCTTTGTTTTCG
*
4098041 ATCTGCTTCGCTGTTAACGTAG
66 GTCTGCTTCGCTGTTAACGTAG
* *
4098063 GAAGGCAAGATCTGCTATCTTGAACCAGCTCCACTGCAATCGATGGAGGCAAGGCTTTGTTTTCG
1 GAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAACCGATGGAGGCAAGGCTTTGTTTTCG
4098128 ATCTGCTTCGCTGGGCTTCGCTGTTAACGTAG
66 ----G--T--CT--GCTTCGCTGTTAACGTAG
* *
4098160 GAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAACCGATGGAGGTAAGGCTTTGTTTTTG
1 GAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAACCGATGGAGGCAAGGCTTTGTTTTCG
*
4098225 CGACTGCTTCGCTGTTAACGTAG
66 -GTCTGCTTCGCTGTTAACGTAG
* * *
4098248 GAAGGCAAGATCTGTTATCTTTAACCAGCTCCACTGCAACCGATGGAGGCAAGACTTTGTTTTTG
1 GAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAACCGATGGAGGCAAGGCTTTGTTTTCG
* * *
4098313 ATCTGCTTCGCTATTAATGTAG
66 GTCTGCTTCGCTGTTAACGTAG
4098335 GAAGGCAAGATCTGCTA
1 GAAGGCAAGATCTGCTA
4098352 CTTCATTGAT
Statistics
Matches: 338, Mismatches: 28, Indels: 20
0.88 0.07 0.05
Matches are distributed among these distances:
87 173 0.51
88 80 0.24
90 2 0.01
93 1 0.00
94 1 0.00
95 2 0.01
97 79 0.23
ACGTcount: A:0.23, C:0.22, G:0.25, T:0.30
Consensus pattern (87 bp):
GAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAACCGATGGAGGCAAGGCTTTGTTTTCG
GTCTGCTTCGCTGTTAACGTAG
Found at i:4098214 original size:97 final size:94
Alignment explanation
Indices: 4097956--4098324 Score: 505
Period size: 88 Copynumber: 4.0 Consensus size: 94
4097946 TGTTTTCGGT
* * * *
4097956 CTGCTTCGCTGTTAACGCAGGAAGGCAAGGTCTGCTATCTTTAACCAGCTCCACTGCAACTGGTG
1 CTGCTTCGCTGTTAACGTAGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAACCGATG
*
4098021 GAGGCAAGGCTTTG-TTT--TC-G-AT--
66 GAGGCAAGGCTTTGTTTTGATCTGCTTCG
* *
4098043 CTGCTTCGCTGTTAACGTAGGAAGGCAAGATCTGCTATCTTGAACCAGCTCCACTGCAATCGATG
1 CTGCTTCGCTGTTAACGTAGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAACCGATG
4098108 GAGGCAAGGCTTTGTTTTCGATCTGCTTCG
66 GAGGCAAGGCTTTGTTTT-GATCTGCTTCG
4098138 CTGGGCTTCGCTGTTAACGTAGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAACCGA
1 CT--GCTTCGCTGTTAACGTAGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAACCGA
*
4098203 TGGAGGTAAGGCTTTG-TTT--T-TG---CG
64 TGGAGGCAAGGCTTTGTTTTGATCTGCTTCG
*
4098227 ACTGCTTCGCTGTTAACGTAGGAAGGCAAGATCTGTTATCTTTAACCAGCTCCACTGCAACCGAT
1 -CTGCTTCGCTGTTAACGTAGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAACCGAT
*
4098292 GGAGGCAAGACTTTGTTTTTGATCTGCTTCG
65 GGAGGCAAGGCTTTG-TTTTGATCTGCTTCG
4098323 CT
1 CT
4098325 ATTAATGTAG
Statistics
Matches: 250, Mismatches: 13, Indels: 30
0.85 0.04 0.10
Matches are distributed among these distances:
87 73 0.29
88 77 0.31
89 2 0.01
90 5 0.02
91 2 0.01
92 4 0.02
93 4 0.02
95 4 0.02
96 5 0.02
97 74 0.30
ACGTcount: A:0.21, C:0.24, G:0.25, T:0.30
Consensus pattern (94 bp):
CTGCTTCGCTGTTAACGTAGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAACCGATG
GAGGCAAGGCTTTGTTTTGATCTGCTTCG
Found at i:4098308 original size:185 final size:184
Alignment explanation
Indices: 4097958--4098324 Score: 619
Period size: 185 Copynumber: 2.0 Consensus size: 184
4097948 TTTTCGGTCT
* * *
4097958 GCTTCGCTGTTAACGCAGGAAGGCAAGGTCTGCTATCTTTAACCAGCTCCACTGCAACTGGTGGA
1 GCTTCGCTGTTAACGCAGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAACCGATGGA
4098023 GGCAAGGCTTTGTTTTCGATCTGCTTCGCTGTTAACGTAGGAAGGCAAGATCTGCTATCTTGAAC
66 GGCAAGGCTTTGTTTTCGATCTGCTTCGCTGTTAACGTAGGAAGGCAAGATCTGCTATCTTGAAC
* *
4098088 CAGCTCCACTGCAATCGATGGAGGCAAGGCTTTGTTTTCGATCTGCTTCGCTGG
131 CAGCTCCACTGCAACCGATGGAGGCAAGACTTTGTTTTCGATCTGCTTCGCTGG
*
4098142 GCTTCGCTGTTAACGTAGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAACCGATGGA
1 GCTTCGCTGTTAACGCAGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAACCGATGGA
* * *
4098207 GGTAAGGCTTTGTTTTTGCGA-CTGCTTCGCTGTTAACGTAGGAAGGCAAGATCTGTTATCTTTA
66 GGCAAGGCTTTG-TTTT-CGATCTGCTTCGCTGTTAACGTAGGAAGGCAAGATCTGCTATCTTGA
*
4098271 ACCAGCTCCACTGCAACCGATGGAGGCAAGACTTTGTTTTTGATCTGCTTCGCT
129 ACCAGCTCCACTGCAACCGATGGAGGCAAGACTTTGTTTTCGATCTGCTTCGCT
4098325 ATTAATGTAG
Statistics
Matches: 171, Mismatches: 10, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
184 72 0.42
185 96 0.56
186 3 0.02
ACGTcount: A:0.22, C:0.23, G:0.25, T:0.30
Consensus pattern (184 bp):
GCTTCGCTGTTAACGCAGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAACCGATGGA
GGCAAGGCTTTGTTTTCGATCTGCTTCGCTGTTAACGTAGGAAGGCAAGATCTGCTATCTTGAAC
CAGCTCCACTGCAACCGATGGAGGCAAGACTTTGTTTTCGATCTGCTTCGCTGG
Found at i:4099586 original size:7 final size:7
Alignment explanation
Indices: 4099574--4099624 Score: 52
Period size: 7 Copynumber: 7.0 Consensus size: 7
4099564 TTAGCCTCTC
4099574 CATTTTT
1 CATTTTT
4099581 CA-TTTT
1 CATTTTT
4099587 C-TATTTT
1 CAT-TTTT
4099594 CATTTTT
1 CATTTTT
4099601 CATTTTTCAT
1 CA-TTTT--T
4099611 CATTTTT
1 CATTTTT
4099618 CATTTTT
1 CATTTTT
4099625 TTTGAAATCC
Statistics
Matches: 38, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
6 5 0.13
7 21 0.55
8 5 0.13
9 4 0.11
10 3 0.08
ACGTcount: A:0.16, C:0.16, G:0.00, T:0.69
Consensus pattern (7 bp):
CATTTTT
Found at i:4104510 original size:12 final size:13
Alignment explanation
Indices: 4104495--4104523 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
4104485 AATAGACATG
4104495 TAAATAAAT-AAA
1 TAAATAAATAAAA
4104507 TAAATAAATAAAA
1 TAAATAAATAAAA
4104520 TAAA
1 TAAA
4104524 AAAGAATATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 9 0.56
13 7 0.44
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (13 bp):
TAAATAAATAAAA
Found at i:4104582 original size:2 final size:2
Alignment explanation
Indices: 4104577--4104610 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
4104567 ATGTATATGG
4104577 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
4104611 GAAAAATATG
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:4104782 original size:3 final size:3
Alignment explanation
Indices: 4104774--4104869 Score: 97
Period size: 3 Copynumber: 31.0 Consensus size: 3
4104764 AAAATAAAAC
* *
4104774 TAA TAA TAA TTAA TAA TGA TAA TAA TAG TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA -TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* *
4104820 TAA TAA TAA TAA TAAA TGA TAA TACA TTAA -AA TAA TTAA CAA -AA TAA
1 TAA TAA TAA TAA T-AA TAA TAA TA-A -TAA TAA TAA -TAA TAA TAA TAA
4104867 TAA
1 TAA
4104870 GATTGCTAAA
Statistics
Matches: 79, Mismatches: 7, Indels: 14
0.79 0.07 0.14
Matches are distributed among these distances:
2 4 0.05
3 62 0.78
4 11 0.14
5 2 0.03
ACGTcount: A:0.62, C:0.02, G:0.03, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:4114429 original size:31 final size:29
Alignment explanation
Indices: 4114365--4114433 Score: 84
Period size: 29 Copynumber: 2.3 Consensus size: 29
4114355 ACGATAACGT
** *
4114365 AAGTGACTAAAATGTAATATTTCAAACAT
1 AAGTGACTAAAATGTAATATGACAAACAA
*
4114394 AAGTGACTAAAATGTAATCTGAGACAAACAA
1 AAGTGACTAAAATGTAATAT--GACAAACAA
4114425 AAGTGACTA
1 AAGTGACTA
4114434 TTTTTGTAGT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
29 19 0.56
31 15 0.44
ACGTcount: A:0.49, C:0.12, G:0.14, T:0.25
Consensus pattern (29 bp):
AAGTGACTAAAATGTAATATGACAAACAA
Found at i:4118036 original size:20 final size:20
Alignment explanation
Indices: 4118013--4118051 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
4118003 ATTTTTACAT
4118013 ATATTAATAAATTTATATAC
1 ATATTAATAAATTTATATAC
*
4118033 ATATTAATAAATTTTTATA
1 ATATTAATAAATTTATATA
4118052 TTTTAAATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (20 bp):
ATATTAATAAATTTATATAC
Found at i:4121310 original size:21 final size:21
Alignment explanation
Indices: 4121284--4121325 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
4121274 GGAAGAAAAT
4121284 TTGCTTAGAAGAGAAAAGAGA
1 TTGCTTAGAAGAGAAAAGAGA
*
4121305 TTGCTTAGAAGAGAAAGGAGA
1 TTGCTTAGAAGAGAAAAGAGA
4121326 AAGGGAAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.45, C:0.05, G:0.31, T:0.19
Consensus pattern (21 bp):
TTGCTTAGAAGAGAAAAGAGA
Found at i:4136544 original size:16 final size:17
Alignment explanation
Indices: 4136514--4136561 Score: 55
Period size: 16 Copynumber: 2.9 Consensus size: 17
4136504 TATATAATAT
* *
4136514 ATAAATAATTTTAAAAA
1 ATAAAAAATTCTAAAAA
*
4136531 AT-TAAAATTCT-AAAA
1 ATAAAAAATTCTAAAAA
4136546 ATAAAAAATTCTAAAA
1 ATAAAAAATTCTAAAA
4136562 CATATAAATA
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
15 6 0.24
16 14 0.56
17 5 0.20
ACGTcount: A:0.65, C:0.04, G:0.00, T:0.31
Consensus pattern (17 bp):
ATAAAAAATTCTAAAAA
Found at i:4136736 original size:29 final size:29
Alignment explanation
Indices: 4136704--4136759 Score: 69
Period size: 29 Copynumber: 1.9 Consensus size: 29
4136694 ATTTCTTCCA
*
4136704 AAAATTATAAAT-TTTAAAAATTAAAAAAG
1 AAAA-TATAAATCTCTAAAAATTAAAAAAG
* *
4136733 AAAATCTAAATCTCTAAAAATTTAAAA
1 AAAATATAAATCTCTAAAAATTAAAAA
4136760 CTTTATTACA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
28 6 0.26
29 17 0.74
ACGTcount: A:0.62, C:0.05, G:0.02, T:0.30
Consensus pattern (29 bp):
AAAATATAAATCTCTAAAAATTAAAAAAG
Found at i:4136967 original size:29 final size:30
Alignment explanation
Indices: 4136935--4136999 Score: 82
Period size: 28 Copynumber: 2.2 Consensus size: 30
4136925 TTCTTATAAT
*
4136935 TTTTTTTCAATTTTTA-TATAATATTTT-T-A
1 TTTTTTT-AATTTATATTAT-ATATTTTATCA
4136964 TTTTTTTAATTTATATTATATATTTTATCA
1 TTTTTTTAATTTATATTATATATTTTATCA
4136994 TTTTTT
1 TTTTTT
4137000 AAAACTTTTA
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
28 14 0.44
29 11 0.34
30 7 0.22
ACGTcount: A:0.26, C:0.03, G:0.00, T:0.71
Consensus pattern (30 bp):
TTTTTTTAATTTATATTATATATTTTATCA
Found at i:4136976 original size:26 final size:28
Alignment explanation
Indices: 4136947--4137001 Score: 78
Period size: 26 Copynumber: 2.0 Consensus size: 28
4136937 TTTTTCAATT
4136947 TTTATATAATAT-TTTTAT-TTTTTTAA
1 TTTATATAATATATTTTATATTTTTTAA
*
4136973 TTTATATTATATATTTTATCATTTTTTAA
1 TTTATATAATATATTTTAT-ATTTTTTAA
4137002 AACTTTTAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
26 11 0.44
27 6 0.24
29 8 0.32
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (28 bp):
TTTATATAATATATTTTATATTTTTTAA
Found at i:4140578 original size:22 final size:23
Alignment explanation
Indices: 4140552--4140598 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
4140542 ATATTTGGAA
* *
4140552 TTTAGT-TTTTTTTTTTTTACAT
1 TTTAGTCTTTTTGTTTTTTAAAT
4140574 TTTAGTCTTTTTGTTTTTTAAAT
1 TTTAGTCTTTTTGTTTTTTAAAT
4140597 TT
1 TT
4140599 CAAAATTTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 6 0.27
23 16 0.73
ACGTcount: A:0.15, C:0.04, G:0.06, T:0.74
Consensus pattern (23 bp):
TTTAGTCTTTTTGTTTTTTAAAT
Found at i:4147573 original size:34 final size:34
Alignment explanation
Indices: 4147530--4147595 Score: 132
Period size: 34 Copynumber: 1.9 Consensus size: 34
4147520 TGAAGAAAAC
4147530 TATATAGAAGTTTGCAAGCAAAGATGGCATAAAT
1 TATATAGAAGTTTGCAAGCAAAGATGGCATAAAT
4147564 TATATAGAAGTTTGCAAGCAAAGATGGCATAA
1 TATATAGAAGTTTGCAAGCAAAGATGGCATAA
4147596 GTATAGTAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 32 1.00
ACGTcount: A:0.44, C:0.09, G:0.21, T:0.26
Consensus pattern (34 bp):
TATATAGAAGTTTGCAAGCAAAGATGGCATAAAT
Found at i:4171522 original size:18 final size:19
Alignment explanation
Indices: 4171485--4171523 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
4171475 ATTACAAAAT
*
4171485 AATTCAAAATAATTTTTAA
1 AATTCAAAATAATTTATAA
*
4171504 AATTTAAAAT-ATTTATAA
1 AATTCAAAATAATTTATAA
4171522 AA
1 AA
4171524 ATTCTAAATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 9 0.50
19 9 0.50
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (19 bp):
AATTCAAAATAATTTATAA
Found at i:4171591 original size:22 final size:22
Alignment explanation
Indices: 4171544--4171591 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 22
4171534 TTGATATTTT
* *
4171544 ATATTTTAAAAAACATATATAT
1 ATATTTTAAAAAACATATAGAA
*
4171566 ATATTTTAAAAGA-ATATAGAGA
1 ATATTTTAAAAAACATATAGA-A
4171588 ATAT
1 ATAT
4171592 ATAAAGATAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
21 6 0.27
22 16 0.73
ACGTcount: A:0.54, C:0.02, G:0.06, T:0.38
Consensus pattern (22 bp):
ATATTTTAAAAAACATATAGAA
Found at i:4173146 original size:38 final size:39
Alignment explanation
Indices: 4173096--4173196 Score: 132
Period size: 38 Copynumber: 2.6 Consensus size: 39
4173086 TCATTTCTTT
*
4173096 TCATTTTAATAATTTTTTACAATATTTTACAATTTCTAA
1 TCATTTTTATAATTTTTTACAATATTTTACAATTTCTAA
* *
4173135 -CATTTTTATAATTTTTTACAATATTTTATAGTTTCTAA
1 TCATTTTTATAATTTTTTACAATATTTTACAATTTCTAA
* * *
4173173 TTACTTTTATATTTTTATTACAAT
1 TCATTTTTATAATTTT-TTACAAT
4173197 TTTAAAAAAA
Statistics
Matches: 54, Mismatches: 6, Indels: 3
0.86 0.10 0.05
Matches are distributed among these distances:
38 35 0.65
39 12 0.22
40 7 0.13
ACGTcount: A:0.33, C:0.09, G:0.01, T:0.57
Consensus pattern (39 bp):
TCATTTTTATAATTTTTTACAATATTTTACAATTTCTAA
Found at i:4173199 original size:19 final size:19
Alignment explanation
Indices: 4173138--4173200 Score: 51
Period size: 19 Copynumber: 3.3 Consensus size: 19
4173128 TTTCTAACAT
*
4173138 TTTTATAATTTT-TTACAATA
1 TTTTATATTTTTATTAC-A-A
*
4173158 TTTTATAGTTTCTAATTAC--
1 TTTTATA-TTT-TTATTACAA
4173177 TTTTATATTTTTATTACAA
1 TTTTATATTTTTATTACAA
4173196 TTTTA
1 TTTTA
4173201 AAAAAATCTA
Statistics
Matches: 35, Mismatches: 3, Indels: 11
0.71 0.06 0.22
Matches are distributed among these distances:
17 6 0.17
18 3 0.09
19 12 0.34
20 7 0.20
21 2 0.06
22 1 0.03
23 4 0.11
ACGTcount: A:0.30, C:0.06, G:0.02, T:0.62
Consensus pattern (19 bp):
TTTTATATTTTTATTACAA
Found at i:4176139 original size:2 final size:2
Alignment explanation
Indices: 4176132--4176158 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
4176122 TTTAAAGGAT
4176132 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
4176159 TAACATTAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:4179090 original size:14 final size:14
Alignment explanation
Indices: 4179071--4179100 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
4179061 TAAAATTGAG
*
4179071 AAAAATAACAATAA
1 AAAAATAACAACAA
4179085 AAAAATAACAACAA
1 AAAAATAACAACAA
4179099 AA
1 AA
4179101 CCAAATATCC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.80, C:0.10, G:0.00, T:0.10
Consensus pattern (14 bp):
AAAAATAACAACAA
Found at i:4193114 original size:15 final size:16
Alignment explanation
Indices: 4193094--4193123 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
4193084 CAATATAATA
4193094 AAATA-TTAAAAAAAT
1 AAATATTTAAAAAAAT
4193109 AAATATTTAAAAAAA
1 AAATATTTAAAAAAA
4193124 GGGACGCATG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (16 bp):
AAATATTTAAAAAAAT
Found at i:4195257 original size:42 final size:41
Alignment explanation
Indices: 4195168--4195259 Score: 114
Period size: 41 Copynumber: 2.2 Consensus size: 41
4195158 TTCGGATAGT
* *
4195168 TCGAAGCAATATAATTGACACCCAATGTCTCATCGAATCTA
1 TCGAAGAAATATAATTGACACCCAATGTCTCATCGAATCGA
* *
4195209 TCCGAAGAAATATAA-TGACACCCAGTGTCTCATCGACTCGA
1 T-CGAAGAAATATAATTGACACCCAATGTCTCATCGAATCGA
4195250 GGTCGAAGAA
1 --TCGAAGAA
4195260 TCCTTGAACT
Statistics
Matches: 44, Mismatches: 4, Indels: 5
0.83 0.08 0.09
Matches are distributed among these distances:
41 24 0.55
42 19 0.43
43 1 0.02
ACGTcount: A:0.36, C:0.24, G:0.17, T:0.23
Consensus pattern (41 bp):
TCGAAGAAATATAATTGACACCCAATGTCTCATCGAATCGA
Found at i:4196192 original size:2 final size:2
Alignment explanation
Indices: 4196185--4196228 Score: 60
Period size: 2 Copynumber: 24.0 Consensus size: 2
4196175 TTCTTTAGTT
4196185 TA TA TA TA TA TA TA TA TA TA T- TA TA TA TA -A TA TA -A TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
4196224 -A TA TA
1 TA TA TA
4196229 ATTAAAACAT
Statistics
Matches: 38, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
1 4 0.11
2 34 0.89
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:4196200 original size:10 final size:10
Alignment explanation
Indices: 4196185--4196228 Score: 60
Period size: 9 Copynumber: 4.8 Consensus size: 10
4196175 TTCTTTAGTT
4196185 TATATATATA
1 TATATATATA
4196195 TATATATATA
1 TATATATATA
4196205 T-TATATATA
1 TATATATATA
4196214 -ATATA-ATA
1 TATATATATA
4196222 TA-ATATA
1 TATATATA
4196229 ATTAAAACAT
Statistics
Matches: 31, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
8 6 0.19
9 14 0.45
10 11 0.35
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (10 bp):
TATATATATA
Found at i:4196211 original size:19 final size:17
Alignment explanation
Indices: 4196187--4196228 Score: 57
Period size: 17 Copynumber: 2.4 Consensus size: 17
4196177 CTTTAGTTTA
4196187 TATATATATATATATATAT
1 TATATATA-ATATA-ATAT
4196206 TATATATAATATAATAT
1 TATATATAATATAATAT
*
4196223 AATATA
1 TATATA
4196229 ATTAAAACAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 9 0.41
18 5 0.23
19 8 0.36
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (17 bp):
TATATATAATATAATAT
Found at i:4196217 original size:5 final size:5
Alignment explanation
Indices: 4196188--4196230 Score: 52
Period size: 5 Copynumber: 8.4 Consensus size: 5
4196178 TTTAGTTTAT
*
4196188 ATATA TATATA TATATA TTAT- ATATA ATATA ATATA ATATA AT
1 ATATA -ATATA -ATATA ATATA ATATA ATATA ATATA ATATA AT
4196231 TAAAACATAA
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
4 3 0.09
5 20 0.59
6 11 0.32
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (5 bp):
ATATA
Found at i:4196265 original size:21 final size:23
Alignment explanation
Indices: 4196184--4196273 Score: 73
Period size: 23 Copynumber: 4.0 Consensus size: 23
4196174 TTTCTTTAGT
*
4196184 TTATATATATATATATATATATTA
1 TTATATACATATA-ATATATATTA
*
4196208 -TATATA-ATATAATATAATATAA
1 TTATATACATATAATAT-ATATTA
* * *
4196230 TTA-AAACATAAAATATCT-TTA
1 TTATATACATATAATATATATTA
4196251 TTATATA-ATATAATAATATATTA
1 TTATATACATATAAT-ATATATTA
4196274 AACATAAAAA
Statistics
Matches: 52, Mismatches: 8, Indels: 13
0.71 0.11 0.18
Matches are distributed among these distances:
21 15 0.29
22 18 0.35
23 19 0.37
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (23 bp):
TTATATACATATAATATATATTA
Found at i:4197801 original size:13 final size:13
Alignment explanation
Indices: 4197783--4197876 Score: 97
Period size: 13 Copynumber: 7.2 Consensus size: 13
4197773 ATAAAGTAAT
**
4197783 AAATAATAGGATA
1 AAATAATAAAATA
*
4197796 AAATAAAATAAAACA
1 AAAT--AATAAAATA
4197811 AAATAATAAAATA
1 AAATAATAAAATA
4197824 AAATAATAAAATA
1 AAATAATAAAATA
4197837 AAATAA-AAAATTA
1 AAATAATAAAA-TA
4197850 GAAA-AATAAAAT-
1 -AAATAATAAAATA
4197862 AAATAA-AAAATA
1 AAATAATAAAATA
4197874 AAA
1 AAA
4197877 ATAAAAATTG
Statistics
Matches: 70, Mismatches: 4, Indels: 15
0.79 0.04 0.17
Matches are distributed among these distances:
11 8 0.11
12 9 0.13
13 36 0.51
14 7 0.10
15 10 0.14
ACGTcount: A:0.77, C:0.01, G:0.03, T:0.19
Consensus pattern (13 bp):
AAATAATAAAATA
Found at i:4197803 original size:5 final size:5
Alignment explanation
Indices: 4197793--4197882 Score: 75
Period size: 5 Copynumber: 18.2 Consensus size: 5
4197783 AAATAATAGG
*
4197793 ATAAA ATAAA ATAAA ACAAA AT--A ATAAA ATAAA AT--A ATAAA ATAAA
1 ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA
*
4197839 ATAAA A-AATTA GA-AAA ATAAA ATAAA TAAAAA ATAAAA ATAAA A
1 ATAAA ATAA--A -ATAAA ATAAA ATAAA -ATAAA AT-AAA ATAAA A
4197883 ATTGGATTAC
Statistics
Matches: 71, Mismatches: 4, Indels: 20
0.75 0.04 0.21
Matches are distributed among these distances:
3 6 0.08
4 3 0.04
5 49 0.69
6 10 0.14
7 3 0.04
ACGTcount: A:0.79, C:0.01, G:0.01, T:0.19
Consensus pattern (5 bp):
ATAAA
Found at i:4197806 original size:18 final size:17
Alignment explanation
Indices: 4197795--4197882 Score: 97
Period size: 18 Copynumber: 4.8 Consensus size: 17
4197785 ATAATAGGAT
*
4197795 AAAATAAAATAAAACAA
1 AAAATAAAATAAAATAA
4197812 AATAATAAAATAAAATAA
1 AA-AATAAAATAAAATAA
4197830 TAAAATAAAATAAAAAATTAGA
1 -AAAATAAAAT--AAAA-TA-A
4197852 AAAATAAAAT-AAATAA
1 AAAATAAAATAAAATAA
4197868 AAAATAAAAATAAAA
1 AAAAT-AAAATAAAA
4197883 ATTGGATTAC
Statistics
Matches: 62, Mismatches: 1, Indels: 15
0.79 0.01 0.19
Matches are distributed among these distances:
16 6 0.10
17 9 0.15
18 28 0.45
19 2 0.03
20 4 0.06
21 12 0.19
22 1 0.02
ACGTcount: A:0.80, C:0.01, G:0.01, T:0.18
Consensus pattern (17 bp):
AAAATAAAATAAAATAA
Found at i:4197857 original size:16 final size:15
Alignment explanation
Indices: 4197795--4197877 Score: 69
Period size: 16 Copynumber: 5.1 Consensus size: 15
4197785 ATAATAGGAT
*
4197795 AAAATAAAATAA-AAC
1 AAAATAAAA-AATAAA
4197810 AAAATAATAAAATAAA
1 AAAATAA-AAAATAAA
*
4197826 ATAATAAAATAAAATAAA
1 A-AA-ATAA-AAAATAAA
*
4197844 AAATTAGAAAAATAAA
1 AAAATA-AAAAATAAA
4197860 ATAAATAAAAAATAAA
1 A-AAATAAAAAATAAA
4197876 AA
1 AA
4197878 TAAAAATTGG
Statistics
Matches: 57, Mismatches: 5, Indels: 12
0.77 0.07 0.16
Matches are distributed among these distances:
15 10 0.18
16 25 0.44
17 9 0.16
18 13 0.23
ACGTcount: A:0.80, C:0.01, G:0.01, T:0.18
Consensus pattern (15 bp):
AAAATAAAAAATAAA
Found at i:4204222 original size:10 final size:10
Alignment explanation
Indices: 4204207--4204243 Score: 65
Period size: 10 Copynumber: 3.7 Consensus size: 10
4204197 AACTCTAAAA
4204207 GATAAATAAT
1 GATAAATAAT
4204217 GATAAATAAT
1 GATAAATAAT
*
4204227 GATAAATAAA
1 GATAAATAAT
4204237 GATAAAT
1 GATAAAT
4204244 GCTAAAATTA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
10 26 1.00
ACGTcount: A:0.62, C:0.00, G:0.11, T:0.27
Consensus pattern (10 bp):
GATAAATAAT
Found at i:4206334 original size:30 final size:31
Alignment explanation
Indices: 4206298--4206361 Score: 103
Period size: 31 Copynumber: 2.1 Consensus size: 31
4206288 ATATATTTTA
4206298 TTGTTAAA-TTTTTTATTATTTTAAAGACAT
1 TTGTTAAATTTTTTTATTATTTTAAAGACAT
* *
4206328 TTGTTAAATTTTTTTATTATTTTAGAGATAT
1 TTGTTAAATTTTTTTATTATTTTAAAGACAT
4206359 TTG
1 TTG
4206362 CTTGTTAAGT
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
30 8 0.26
31 23 0.74
ACGTcount: A:0.30, C:0.02, G:0.09, T:0.59
Consensus pattern (31 bp):
TTGTTAAATTTTTTTATTATTTTAAAGACAT
Found at i:4206515 original size:12 final size:12
Alignment explanation
Indices: 4206485--4206517 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
4206475 TATATTTTTT
4206485 AAAATT-ATATA
1 AAAATTAATATA
4206496 AAAA-TAATATA
1 AAAATTAATATA
4206507 AAAATTAATAT
1 AAAATTAATAT
4206518 GGGCGGGATG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
10 1 0.05
11 13 0.65
12 6 0.30
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (12 bp):
AAAATTAATATA
Found at i:4215015 original size:63 final size:63
Alignment explanation
Indices: 4214911--4215031 Score: 188
Period size: 63 Copynumber: 1.9 Consensus size: 63
4214901 ATCAAAATGC
* * *
4214911 AGAGGCACGGGCGTGCGTCTAGGCCGTGTGACTCACTGTTTACGATTTAGGACCACACGGACT
1 AGAGACACGGGCGTGCGTCTAGGCCGTGTGACTCACTGTTTACAAATTAGGACCACACGGACT
* * *
4214974 AGAGACACGGGCGTGTGTCTAGGTCGTGTGACTCACTGTTTACAAATTAGGATCACAC
1 AGAGACACGGGCGTGCGTCTAGGCCGTGTGACTCACTGTTTACAAATTAGGACCACAC
4215032 AAGCAGACGA
Statistics
Matches: 52, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
63 52 1.00
ACGTcount: A:0.23, C:0.23, G:0.30, T:0.24
Consensus pattern (63 bp):
AGAGACACGGGCGTGCGTCTAGGCCGTGTGACTCACTGTTTACAAATTAGGACCACACGGACT
Found at i:4226838 original size:7 final size:7
Alignment explanation
Indices: 4226826--4226850 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
4226816 AGTCGATTGA
4226826 TATTTAG
1 TATTTAG
4226833 TATTTAG
1 TATTTAG
4226840 TATTTAG
1 TATTTAG
4226847 TATT
1 TATT
4226851 ATGTATATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.28, C:0.00, G:0.12, T:0.60
Consensus pattern (7 bp):
TATTTAG
Found at i:4227974 original size:25 final size:25
Alignment explanation
Indices: 4227940--4228062 Score: 141
Period size: 25 Copynumber: 5.1 Consensus size: 25
4227930 TGAGTATTTT
4227940 GAAGTTTATTTGATGTAATAAAATA
1 GAAGTTTATTTGATGTAATAAAATA
4227965 GAAGTTTATTTGATGTAATAAAAATA
1 GAAGTTTATTTGATGTAAT-AAAATA
* * ***
4227991 GAAATTT-TTTGA-GTTAT-TTTTA
1 GAAGTTTATTTGATGTAATAAAATA
*
4228013 -TA--TTATTTGATGTAATAAAATA
1 GAAGTTTATTTGATGTAATAAAATA
4228035 GAAGTTTATTTGATGTAATAAAATA
1 GAAGTTTATTTGATGTAATAAAATA
4228060 GAA
1 GAA
4228063 ATTTTTGAAT
Statistics
Matches: 80, Mismatches: 11, Indels: 14
0.76 0.10 0.13
Matches are distributed among these distances:
19 2 0.03
20 5 0.06
21 5 0.06
22 4 0.05
23 1 0.01
24 4 0.05
25 47 0.59
26 12 0.15
ACGTcount: A:0.42, C:0.00, G:0.15, T:0.43
Consensus pattern (25 bp):
GAAGTTTATTTGATGTAATAAAATA
Found at i:4228079 original size:9 final size:9
Alignment explanation
Indices: 4228065--4228101 Score: 67
Period size: 9 Copynumber: 4.2 Consensus size: 9
4228055 AAATAGAAAT
4228065 TTTTGAATA
1 TTTTGAATA
4228074 TTTTGAATA
1 TTTTGAATA
4228083 TTTTGAATA
1 TTTTGAATA
4228092 TTTTG-ATA
1 TTTTGAATA
4228100 TT
1 TT
4228102 ATTTGAGAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
8 5 0.18
9 23 0.82
ACGTcount: A:0.30, C:0.00, G:0.11, T:0.59
Consensus pattern (9 bp):
TTTTGAATA
Found at i:4228387 original size:120 final size:120
Alignment explanation
Indices: 4228116--4228376 Score: 434
Period size: 120 Copynumber: 2.2 Consensus size: 120
4228106 GAGAATTCTA
*
4228116 CTAACCTAATTAAATTGAAAAGAAAACCCTAACCTAATTAAATTGAAAACCCTAACCTAATTAAA
1 CTAACCTAATTAAATTGAAAAGAAAACCCTAACCTAAGTAAATTGAAAACCCTAACCTAATTAAA
* * *
4228181 TTAAAAACCCTAACCTAATTAAATTAAAAACCCTAACCTAATTAAAAAGAAAACC
66 TTAAAAACCATAACCTAATTAAATAAAAAACCCTAACCTAATTAAAAACAAAACC
4228236 CTAACCTAATTAAATTGAAAAGAAAACCCTAACCTAAGTAAATTGAAAACCCTAACCTAATTAAA
1 CTAACCTAATTAAATTGAAAAGAAAACCCTAACCTAAGTAAATTGAAAACCCTAACCTAATTAAA
* ** *
4228301 TTAAAAACCATAACCTAATTAAA-AAGAAAACCTTAACCTAATTAAACCCTAAACC
66 TTAAAAACCATAACCTAATTAAATAA-AAAACCCTAACCTAATTAAAAACAAAACC
4228356 CTAACCTAATTAAATTGAAAA
1 CTAACCTAATTAAATTGAAAA
4228377 TCCTAACCTA
Statistics
Matches: 132, Mismatches: 8, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
119 1 0.01
120 131 0.99
ACGTcount: A:0.52, C:0.21, G:0.04, T:0.23
Consensus pattern (120 bp):
CTAACCTAATTAAATTGAAAAGAAAACCCTAACCTAAGTAAATTGAAAACCCTAACCTAATTAAA
TTAAAAACCATAACCTAATTAAATAAAAAACCCTAACCTAATTAAAAACAAAACC
Found at i:4228408 original size:23 final size:23
Alignment explanation
Indices: 4228137--4228392 Score: 332
Period size: 23 Copynumber: 10.9 Consensus size: 23
4228127 AAATTGAAAA
4228137 GAAAACCCTAACCTAATTAAATT
1 GAAAACCCTAACCTAATTAAATT
4228160 GAAAACCCTAACCTAATTAAATT
1 GAAAACCCTAACCTAATTAAATT
*
4228183 AAAAACCCTAACCTAATTAAATT
1 GAAAACCCTAACCTAATTAAATT
* **
4228206 AAAAACCCTAACCTAATTAAAAA
1 GAAAACCCTAACCTAATTAAATT
4228229 GAAAACCCTAACCTAATTAAATT
1 GAAAACCCTAACCTAATTAAATT
*
4228252 GAAAAGAAAACCCTAACCTAAGTAAATT
1 -----GAAAACCCTAACCTAATTAAATT
4228280 GAAAACCCTAACCTAATTAAATT
1 GAAAACCCTAACCTAATTAAATT
* * **
4228303 AAAAACCATAACCTAATTAAAAA
1 GAAAACCCTAACCTAATTAAATT
* **
4228326 GAAAACCTTAACCTAATTAAACC
1 GAAAACCCTAACCTAATTAAATT
**
4228349 CTAAACCCTAACCTAATTAAATT
1 GAAAACCCTAACCTAATTAAATT
*
4228372 GAAAATCCTAACCTAATTAAA
1 GAAAACCCTAACCTAATTAAA
4228393 CCCTAAACCC
Statistics
Matches: 204, Mismatches: 24, Indels: 10
0.86 0.10 0.04
Matches are distributed among these distances:
23 182 0.89
28 22 0.11
ACGTcount: A:0.52, C:0.21, G:0.04, T:0.23
Consensus pattern (23 bp):
GAAAACCCTAACCTAATTAAATT
Found at i:4229873 original size:124 final size:124
Alignment explanation
Indices: 4229649--4229988 Score: 538
Period size: 124 Copynumber: 2.7 Consensus size: 124
4229639 AACATGCTAC
* *
4229649 TGTAGCAAAAGCGCGTCTACGAGGGCGAGATTTTCACAAATTCTTCTCAAATAGCATCCTGCTAG
1 TGTAGCAAAAGCGCGTCCACGAGGGCGCGA-TTTCACAAATTCTTCTCAAATAGCATCCTGCTAG
4229714 AAGCGATTTTATACTATTTGCTCAGAAACGCCAAAAAAAATTATTTCATCCATGACCTAA
65 AAGCGATTTTATACTATTTGCTCAGAAACGCCAAAAAAAATTATTTCATCCATGACCTAA
*
4229774 TGTAGCAAAAGCGCGTCCACGAGGGCGCGATTGT-ACAAATTATTCTCAAATAGCATCCTGCTAG
1 TGTAGCAAAAGCGCGTCCACGAGGGCGCGATT-TCACAAATTCTTCTCAAATAGCATCCTGCTAG
* * * * *
4229838 AAGTGATTTTATACTATTTGCTCAGAAAGGTCAAAAAAATTTATTTCATCCATGACCTAC
65 AAGCGATTTTATACTATTTGCTCAGAAACGCCAAAAAAAATTATTTCATCCATGACCTAA
* * * *
4229898 TGTTGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTTAAATAGTATCTTGCTAGA
1 TGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCAAATAGCATCCTGCTAGA
*
4229963 AGCGATTTTATACTATTTGATCAGAA
66 AGCGATTTTATACTATTTGCTCAGAA
4229989 GCATCAACTC
Statistics
Matches: 198, Mismatches: 15, Indels: 5
0.91 0.07 0.02
Matches are distributed among these distances:
123 1 0.01
124 168 0.85
125 29 0.15
ACGTcount: A:0.33, C:0.20, G:0.18, T:0.29
Consensus pattern (124 bp):
TGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCAAATAGCATCCTGCTAGA
AGCGATTTTATACTATTTGCTCAGAAACGCCAAAAAAAATTATTTCATCCATGACCTAA
Found at i:4233513 original size:31 final size:29
Alignment explanation
Indices: 4233442--4233513 Score: 71
Period size: 28 Copynumber: 2.5 Consensus size: 29
4233432 TTTGTTTATA
*
4233442 CTTAT-TATGTAAATTTTATATATATATG
1 CTTATATATGTATATTTTATATATATATG
*
4233470 CTT-CATAT-TATATTATTAT-TATATAATTG
1 CTTATATATGTATATT-TTATATATAT-A-TG
4233499 CTTATATATGTATAT
1 CTTATATATGTATAT
4233514 AGGTATATGT
Statistics
Matches: 35, Mismatches: 3, Indels: 9
0.74 0.06 0.19
Matches are distributed among these distances:
27 10 0.29
28 11 0.31
29 5 0.14
30 4 0.11
31 5 0.14
ACGTcount: A:0.35, C:0.06, G:0.06, T:0.54
Consensus pattern (29 bp):
CTTATATATGTATATTTTATATATATATG
Found at i:4242626 original size:17 final size:18
Alignment explanation
Indices: 4242599--4242632 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
4242589 TAGTGAAACA
*
4242599 ATAACTTTTTATGATTTC
1 ATAACTTTTTATCATTTC
4242617 ATAA-TTTTTATCATTT
1 ATAACTTTTTATCATTT
4242633 TAATAATTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.29, C:0.09, G:0.03, T:0.59
Consensus pattern (18 bp):
ATAACTTTTTATCATTTC
Found at i:4242638 original size:18 final size:18
Alignment explanation
Indices: 4242598--4242664 Score: 55
Period size: 18 Copynumber: 3.6 Consensus size: 18
4242588 ATAGTGAAAC
*
4242598 AATAACTTTTTATGA-TTT
1 AATAA-TTTTTATCATTTT
*
4242616 CATAATTTTTATCATTTT
1 AATAATTTTTATCATTTT
*
4242634 AATAATTATTAATACATTTT
1 AATAATT-TTTAT-CATTTT
* *
4242654 TATAAATTTTA
1 AATAATTTTTA
4242665 ATAATTTATT
Statistics
Matches: 39, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
17 8 0.21
18 13 0.33
19 7 0.18
20 11 0.28
ACGTcount: A:0.37, C:0.06, G:0.01, T:0.55
Consensus pattern (18 bp):
AATAATTTTTATCATTTT
Found at i:4242647 original size:10 final size:9
Alignment explanation
Indices: 4242617--4242671 Score: 56
Period size: 9 Copynumber: 5.8 Consensus size: 9
4242607 TTATGATTTC
*
4242617 ATAATTTTT
1 ATAATTTTA
*
4242626 ATCATTTTA
1 ATAATTTTA
4242635 ATAATTATTA
1 ATAATT-TTA
*
4242645 ATACATTTTT
1 ATA-ATTTTA
4242655 ATAAATTTTA
1 AT-AATTTTA
4242665 ATAATTT
1 ATAATTT
4242672 ATTATTATTA
Statistics
Matches: 38, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
9 17 0.45
10 17 0.45
11 4 0.11
ACGTcount: A:0.40, C:0.04, G:0.00, T:0.56
Consensus pattern (9 bp):
ATAATTTTA
Found at i:4242653 original size:20 final size:20
Alignment explanation
Indices: 4242619--4242671 Score: 58
Period size: 20 Copynumber: 2.8 Consensus size: 20
4242609 ATGATTTCAT
*
4242619 AATTTTTAT-CATTTTAAT-
1 AATTTTAATACATTTTAATA
*
4242637 AATTATTAATACATTTTTATA
1 AATT-TTAATACATTTTAATA
4242658 AATTTTAATA-ATTT
1 AATTTTAATACATTT
4242672 ATTATTATTA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
18 4 0.13
19 8 0.27
20 14 0.47
21 4 0.13
ACGTcount: A:0.40, C:0.04, G:0.00, T:0.57
Consensus pattern (20 bp):
AATTTTAATACATTTTAATA
Found at i:4242676 original size:20 final size:21
Alignment explanation
Indices: 4242628--4242676 Score: 59
Period size: 20 Copynumber: 2.4 Consensus size: 21
4242618 TAATTTTTAT
*
4242628 CATTTTAAT-AATTATTAATA
1 CATTTTTATAAATTATTAATA
4242648 CATTTTTATAAATT-TTAATA
1 CATTTTTATAAATTATTAATA
4242668 -ATTTATTAT
1 CATTT-TTAT
4242677 TATTACAATT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
19 4 0.15
20 18 0.69
21 4 0.15
ACGTcount: A:0.41, C:0.04, G:0.00, T:0.55
Consensus pattern (21 bp):
CATTTTTATAAATTATTAATA
Found at i:4242888 original size:10 final size:9
Alignment explanation
Indices: 4242827--4242908 Score: 60
Period size: 9 Copynumber: 8.8 Consensus size: 9
4242817 CTTTTTAGTT
4242827 ATTTTTATTA
1 ATTTTTA-TA
**
4242837 ATTTTTAGG
1 ATTTTTATA
*
4242846 ATTTTTAAA
1 ATTTTTATA
4242855 ATTTTTATA
1 ATTTTTATA
4242864 TAGTTTTT-TA
1 -A-TTTTTATA
4242874 TATTTTTATA
1 -ATTTTTATA
*
4242884 GA-TTTGATA
1 -ATTTTTATA
*
4242893 ATTTCTATA
1 ATTTTTATA
4242902 ATTTTTA
1 ATTTTTA
4242909 AAATATTCTA
Statistics
Matches: 58, Mismatches: 10, Indels: 9
0.75 0.13 0.12
Matches are distributed among these distances:
8 1 0.02
9 37 0.64
10 15 0.26
11 5 0.09
ACGTcount: A:0.30, C:0.01, G:0.06, T:0.62
Consensus pattern (9 bp):
ATTTTTATA
Found at i:4246832 original size:26 final size:25
Alignment explanation
Indices: 4246784--4246833 Score: 64
Period size: 26 Copynumber: 2.0 Consensus size: 25
4246774 AAAGCGGATA
** *
4246784 ATTTTTTAAGTTTTTATATATTTTT
1 ATTTTTTAAGTTTGAATAAATTTTT
4246809 ATTTTTCTAAGTTTGAATAAATTTT
1 ATTTTT-TAAGTTTGAATAAATTTT
4246834 ATCTAAATTT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
25 6 0.29
26 15 0.71
ACGTcount: A:0.28, C:0.02, G:0.06, T:0.64
Consensus pattern (25 bp):
ATTTTTTAAGTTTGAATAAATTTTT
Found at i:4246903 original size:21 final size:22
Alignment explanation
Indices: 4246878--4246930 Score: 65
Period size: 20 Copynumber: 2.5 Consensus size: 22
4246868 TTATTTTTTA
4246878 TTTTTATAAAATTTCAAATA-G
1 TTTTTATAAAATTTCAAATATG
* * *
4246899 TTTTT-CAAAATTTTAAATATT
1 TTTTTATAAAATTTCAAATATG
4246920 TTTTTATAAAA
1 TTTTTATAAAA
4246931 ATTTTATTTT
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
20 12 0.46
21 10 0.38
22 4 0.15
ACGTcount: A:0.42, C:0.04, G:0.02, T:0.53
Consensus pattern (22 bp):
TTTTTATAAAATTTCAAATATG
Found at i:4250609 original size:40 final size:40
Alignment explanation
Indices: 4250558--4250674 Score: 182
Period size: 39 Copynumber: 3.0 Consensus size: 40
4250548 TTTATTTTTT
*
4250558 ATTTTTTTAATTTTAAAATACTTTTAAAATACTTTTTTAA
1 ATTTTTTTAATTTTAAAATATTTTTAAAATACTTTTTTAA
*
4250598 ATTTTTTTAATTTTAAAATATTTTTAAAATAC-TTTGTAA
1 ATTTTTTTAATTTTAAAATATTTTTAAAATACTTTTTTAA
* * *
4250637 AATTTTTTAATTTAAAAATATTTTTAAAATAATTTTTT
1 ATTTTTTTAATTTTAAAATATTTTTAAAATACTTTTTT
4250675 GGTATTTATT
Statistics
Matches: 70, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
39 35 0.50
40 35 0.50
ACGTcount: A:0.39, C:0.03, G:0.01, T:0.57
Consensus pattern (40 bp):
ATTTTTTTAATTTTAAAATATTTTTAAAATACTTTTTTAA
Found at i:4250616 original size:17 final size:17
Alignment explanation
Indices: 4250591--4250663 Score: 58
Period size: 17 Copynumber: 4.0 Consensus size: 17
4250581 TTAAAATACT
* *
4250591 TTTTTAAATTTTTTTAA
1 TTTTAAAATATTTTTAA
4250608 TTTTAAAATATTTTTAAAATA
1 TTTTAAAATATTTTT---A-A
4250629 CTTTGTAAAAT-TTTTTAA
1 -TTT-TAAAATATTTTTAA
*
4250647 TTTAAAAATATTTTTAA
1 TTTTAAAATATTTTTAA
4250664 AATAATTTTT
Statistics
Matches: 46, Mismatches: 3, Indels: 14
0.73 0.05 0.22
Matches are distributed among these distances:
16 5 0.11
17 23 0.50
18 1 0.02
19 1 0.02
20 1 0.02
21 1 0.02
22 8 0.17
23 6 0.13
ACGTcount: A:0.40, C:0.01, G:0.01, T:0.58
Consensus pattern (17 bp):
TTTTAAAATATTTTTAA
Found at i:4250667 original size:11 final size:11
Alignment explanation
Indices: 4250568--4250673 Score: 63
Period size: 11 Copynumber: 10.4 Consensus size: 11
4250558 ATTTTTTTAA
*
4250568 TTTTAAAATAC
1 TTTTAAAATAT
4250579 TTTTAAAATACT
1 TTTTAAAATA-T
*
4250591 TTTTTAAAT-T
1 TTTTAAAATAT
*
4250601 TTTT----TAA
1 TTTTAAAATAT
4250608 TTTTAAAATAT
1 TTTTAAAATAT
4250619 TTTTAAAATACT
1 TTTTAAAATA-T
*
4250631 TTGTAAAAT-T
1 TTTTAAAATAT
4250641 TTTT---A-A-
1 TTTTAAAATAT
*
4250647 TTTAAAAATAT
1 TTTTAAAATAT
4250658 TTTTAAAATAAT
1 TTTTAAAAT-AT
4250670 TTTT
1 TTTT
4250674 TGGTATTTAT
Statistics
Matches: 73, Mismatches: 8, Indels: 27
0.68 0.07 0.25
Matches are distributed among these distances:
6 4 0.05
7 5 0.07
9 1 0.01
10 10 0.14
11 30 0.41
12 23 0.32
ACGTcount: A:0.41, C:0.03, G:0.01, T:0.56
Consensus pattern (11 bp):
TTTTAAAATAT
Found at i:4250704 original size:5 final size:5
Alignment explanation
Indices: 4250694--4250718 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
4250684 TTAAAAAAAG
4250694 GGGCC GGGCC GGGCC GGGCC GGGCC
1 GGGCC GGGCC GGGCC GGGCC GGGCC
4250719 CGAGCTTATG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.00, C:0.40, G:0.60, T:0.00
Consensus pattern (5 bp):
GGGCC
Found at i:4254890 original size:18 final size:19
Alignment explanation
Indices: 4254854--4254891 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
4254844 TTGTAATGTA
4254854 TAATTTTTCTTTCATTTTT
1 TAATTTTTCTTTCATTTTT
4254873 TAATTTATT-TTT-ATTTTT
1 TAATTT-TTCTTTCATTTTT
4254891 T
1 T
4254892 CCAGAATTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 7 0.39
19 9 0.50
20 2 0.11
ACGTcount: A:0.18, C:0.05, G:0.00, T:0.76
Consensus pattern (19 bp):
TAATTTTTCTTTCATTTTT
Found at i:4258159 original size:24 final size:23
Alignment explanation
Indices: 4258106--4258161 Score: 60
Period size: 24 Copynumber: 2.4 Consensus size: 23
4258096 AAAAATTCGA
*
4258106 TAAATAAA-AATATAAAATTATT
1 TAAAAAAATAATATAAAATTATT
* *
4258128 AAATAAAAATAATATAAACATTTTT
1 TAA-AAAAATAATATAAA-ATTATT
4258153 TAAAAAAAT
1 TAAAAAAAT
4258162 TTAAAATAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
22 2 0.07
23 4 0.15
24 14 0.52
25 7 0.26
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (23 bp):
TAAAAAAATAATATAAAATTATT
Found at i:4268517 original size:22 final size:23
Alignment explanation
Indices: 4268471--4268517 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
4268461 TAAAATAGTG
* * *
4268471 AAATTATATTTTTATTGTTATAA
1 AAATTATAATTTAATTGTTAAAA
4268494 AAATTATAATTTAATT-TTAAAA
1 AAATTATAATTTAATTGTTAAAA
4268516 AA
1 AA
4268518 GTTTGATGCT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
22 7 0.33
23 14 0.67
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (23 bp):
AAATTATAATTTAATTGTTAAAA
Found at i:4271898 original size:10 final size:10
Alignment explanation
Indices: 4271883--4271911 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
4271873 AATTTCAGCT
4271883 TTTATCTTTA
1 TTTATCTTTA
4271893 TTTATCTTTA
1 TTTATCTTTA
4271903 TTTATCTTT
1 TTTATCTTT
4271912 TAGAATTTAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.17, C:0.10, G:0.00, T:0.72
Consensus pattern (10 bp):
TTTATCTTTA
Found at i:4275141 original size:87 final size:86
Alignment explanation
Indices: 4275008--4275171 Score: 258
Period size: 87 Copynumber: 1.9 Consensus size: 86
4274998 TTATTTTTGT
* *
4275008 ACTCAATTTGGTACTTGAACCGTCAAAATGCATCAAAAAGACCCTCAAACTTTTTCAAAAAAAAC
1 ACTCAATTTGGTACTTGAACCGTCAAAATGCATAAAAAAGACCCTCAAAATTTTTCAAAAAAAAC
4275073 AATTAAGCCCCTTTTTTTTAC
66 AATTAAGCCCCTTTTTTTTAC
* *
4275094 ACTCAATTTGGATACTT-AACTTGTCAAAATGCATAAAAAAGATCCTCAAAATTTTTCAAAAAAA
1 ACTCAATTTGG-TACTTGAAC-CGTCAAAATGCATAAAAAAGACCCTCAAAATTTTTCAAAAAAA
*
4275158 TCAATTAAGCCCCT
64 ACAATTAAGCCCCT
4275172 GCTGTTTCTT
Statistics
Matches: 71, Mismatches: 5, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
86 14 0.20
87 57 0.80
ACGTcount: A:0.41, C:0.21, G:0.08, T:0.30
Consensus pattern (86 bp):
ACTCAATTTGGTACTTGAACCGTCAAAATGCATAAAAAAGACCCTCAAAATTTTTCAAAAAAAAC
AATTAAGCCCCTTTTTTTTAC
Found at i:4275280 original size:8 final size:8
Alignment explanation
Indices: 4275267--4275297 Score: 62
Period size: 8 Copynumber: 3.9 Consensus size: 8
4275257 AAGTGACAAA
4275267 AAAATTTT
1 AAAATTTT
4275275 AAAATTTT
1 AAAATTTT
4275283 AAAATTTT
1 AAAATTTT
4275291 AAAATTT
1 AAAATTT
4275298 ACGAAAAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (8 bp):
AAAATTTT
Found at i:4275334 original size:18 final size:18
Alignment explanation
Indices: 4275311--4275370 Score: 66
Period size: 18 Copynumber: 3.2 Consensus size: 18
4275301 AAAAATTAGA
4275311 AAAAAAATATAAAAATAT
1 AAAAAAATATAAAAATAT
* * *
4275329 AAAAAAATGTAAAATTTT
1 AAAAAAATATAAAAATAT
*
4275347 ATAAAAATCATAAAAATTAT
1 AAAAAAAT-ATAAAAA-TAT
4275367 AAAA
1 AAAA
4275371 TGCATCAAAT
Statistics
Matches: 32, Mismatches: 8, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
18 22 0.69
19 5 0.16
20 5 0.16
ACGTcount: A:0.70, C:0.02, G:0.02, T:0.27
Consensus pattern (18 bp):
AAAAAAATATAAAAATAT
Found at i:4275369 original size:28 final size:28
Alignment explanation
Indices: 4275318--4275371 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 28
4275308 AGAAAAAAAA
*
4275318 TATAAAAATATAAAAAAATGTAAAATTT
1 TATAAAAATATAAAAAAATATAAAATTT
*
4275346 TATAAAAATCAT-AAAAATTATAAAAT
1 TATAAAAAT-ATAAAAAAATATAAAAT
4275372 GCATCAAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
28 21 0.91
29 2 0.09
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.31
Consensus pattern (28 bp):
TATAAAAATATAAAAAAATATAAAATTT
Found at i:4275509 original size:17 final size:16
Alignment explanation
Indices: 4275487--4275546 Score: 59
Period size: 17 Copynumber: 3.5 Consensus size: 16
4275477 ACATATGGTG
4275487 AAAAATGATAAAAAAAT
1 AAAAAT-ATAAAAAAAT
4275504 AAAAATA-AAAATAAAT
1 AAAAATATAAAA-AAAT
*
4275520 AAAAGTTATAAAAAAATT
1 AAAA-ATATAAAAAAA-T
4275538 ATAAAATAT
1 A-AAAATAT
4275547 TTTTTTTGGT
Statistics
Matches: 36, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
15 4 0.11
16 9 0.25
17 11 0.31
18 9 0.25
19 3 0.08
ACGTcount: A:0.73, C:0.00, G:0.03, T:0.23
Consensus pattern (16 bp):
AAAAATATAAAAAAAT
Done.